diff --git a/.gitignore b/.gitignore index 9fbaa7c97f3..e52c67610a4 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,7 @@ database/files database/jobs_directory database/job_working_directory database/pbs +database/shed_tools database/test_errors database/tmp database/*.sqlite diff --git a/CONTRIBUTING.md b/CONTRIBUTING.md index 84fe45dc6e3..4c9fb28c3a2 100644 --- a/CONTRIBUTING.md +++ b/CONTRIBUTING.md @@ -112,5 +112,5 @@ If no existing Galaxy issue seems appropriate, a new issue can be opened using this repository - please checkout the [tools-iuc](https://github.com/galaxyproject/tools-iuc) repository on GitHub. - More information about tool development can be found [on the comunity + More information about tool development can be found [on the community hub](https://galaxyproject.org/develop). diff --git a/client/galaxy/docs/bootstrap.md b/client/galaxy/docs/bootstrap.md index d62f23def6f..3c8a48e9bb3 100644 --- a/client/galaxy/docs/bootstrap.md +++ b/client/galaxy/docs/bootstrap.md @@ -89,7 +89,6 @@ Disabled - ``` ```vue diff --git a/client/galaxy/scripts/components/PluginList.vue b/client/galaxy/scripts/components/PluginList.vue index e6ba960e8e8..2f70becf0c7 100644 --- a/client/galaxy/scripts/components/PluginList.vue +++ b/client/galaxy/scripts/components/PluginList.vue @@ -16,7 +16,7 @@ - + <% } %> diff --git a/client/galaxy/scripts/mvc/library/library-folderlist-view.js b/client/galaxy/scripts/mvc/library/library-folderlist-view.js index 55d210fb633..1b6c271f99c 100644 --- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js +++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js @@ -25,7 +25,9 @@ var FolderListView = Backbone.View.extend({ "click .folder_row": "selectClickedRow", "click .sort-folder-name": "sortColumnClicked", "click .sort-folder-file_ext": "sortColumnClicked", - "click .sort-folder-description": "sortColumnClicked", + "click .sort-folder-message": "sortColumnClicked", + "click .sort-folder-update_time": "sortColumnClicked", + "click .sort-folder-raw_size": "sortColumnClicked", "click .sort-folder-state": "sortColumnClicked" }, @@ -275,6 +277,21 @@ var FolderListView = Backbone.View.extend({ this.renderSortIcon(); }, + /** + * In case the search_term is not empty perform the search and render + * the result. Render all visible folder items otherwise. + * @param {string} search_term string to search for + */ + searchFolder: function(search_term) { + const trimmed_term = $.trim(search_term); + if (trimmed_term !== "") { + const result_collection = this.folder_container.search(search_term); + this.collection.reset(result_collection); + } else { + this.paginate(); + } + }, + /** * User clicked the checkbox in the table heading * @param {context} event @@ -337,10 +354,11 @@ var FolderListView = Backbone.View.extend({ }, renderSortIcon: function() { + $('[class*="sort-icon"]') + .removeClass("fa-sort-alpha-desc") + .removeClass("fa-sort-alpha-asc"); + if (this.current_sort_order === "asc") { - $('[class*="sort-icon"]') - .removeClass("fa-sort-alpha-desc") - .removeClass("fa-sort-alpha-asc"); $(`.sort-icon-${this.current_sort_key}`).addClass("fa-sort-alpha-asc"); } else { $(`.sort-icon-${this.current_sort_key}`).addClass("fa-sort-alpha-desc"); @@ -463,7 +481,7 @@ var FolderListView = Backbone.View.extend({ <%- path_item[1] %> - + <% } else { %>
  • @@ -484,24 +502,29 @@ var FolderListView = Backbone.View.extend({
    • + + - - - + diff --git a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js index b3d5ec39d6d..9be70b78858 100644 --- a/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js +++ b/client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js @@ -25,7 +25,8 @@ var FolderToolbarView = Backbone.View.extend({ "click .toolbtn-show-locinfo": "showLocInfo", "keydown .page_size": "changePageSize", "blur .page_size": "changePageSize", - "click .toolbtn-collection-import": "showCollectionSelect" + "click .toolbtn-collection-import": "showCollectionSelect", + "keyup .folder-search-input": "searchFolder" }, defaults: { @@ -210,10 +211,12 @@ var FolderToolbarView = Backbone.View.extend({ } }, + /** + * This function returns a promise + */ fetchUserHistories: function() { this.histories = new mod_library_model.GalaxyHistories(); - var promise = this.histories.fetch(); - return promise; + return this.histories.fetch(); }, importAllIntoHistory: function() { @@ -238,9 +241,11 @@ var FolderToolbarView = Backbone.View.extend({ } }, + /** + * This function returns a promise + */ createNewHistory: function(new_history_name) { - var promise = $.post(`${getAppRoot()}api/histories`, { name: new_history_name }); - return promise; + return $.post(`${getAppRoot()}api/histories`, { name: new_history_name }); }, processImportToHistory: function(history_id, history_name) { @@ -1416,6 +1421,17 @@ var FolderToolbarView = Backbone.View.extend({ return hdca.save(options); }, + /** + * Take the contents of the search field and send it to the list view + * to query the collection of folder items. + */ + searchFolder: function(event) { + const Galaxy = getGalaxyInstance(); + const search_term = $(".folder-search-input").val(); + this.options.search_term = search_term; + Galaxy.libraries.folderListView.searchFolder(search_term); + }, + templateToolBar: function() { return _.template( `
    @@ -1425,6 +1441,7 @@ var FolderToolbarView = Backbone.View.extend({
    +
    - + ui thumbnails
    		diff --git a/client/galaxy/scripts/components/Tags/model.js b/client/galaxy/scripts/components/Tags/model.js index a9dd7c68eae..821c1c0c009 100644 --- a/client/galaxy/scripts/components/Tags/model.js +++ b/client/galaxy/scripts/components/Tags/model.js @@ -50,8 +50,8 @@ function TagModel(props = {}) { enumerable: false, get: function() { if (!this.text.length) return false; - if (this.text == "name:") return false; - return true; + return this.text != "name:"; + } }); } diff --git a/client/galaxy/scripts/components/xrefs.vue b/client/galaxy/scripts/components/xrefs.vue new file mode 100644 index 00000000000..13c005243ba --- /dev/null +++ b/client/galaxy/scripts/components/xrefs.vue @@ -0,0 +1,53 @@ + + diff --git a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js index ddc58f00e5a..570bd3dc0c4 100644 --- a/client/galaxy/scripts/entry/analysis/AnalysisRouter.js +++ b/client/galaxy/scripts/entry/analysis/AnalysisRouter.js @@ -88,8 +88,7 @@ export const getAnalysisRouter = Galaxy => const instance = Vue.extend(component); const container = document.createElement("div"); this.page.display(container); - const vm = new instance(props).$mount(container); - return vm; + return new instance(props).$mount(container); }, show_tours: function(tour_id) { diff --git a/client/galaxy/scripts/layout/communication-server-view.js b/client/galaxy/scripts/layout/communication-server-view.js index 1bd1f682300..d71930ebb79 100644 --- a/client/galaxy/scripts/layout/communication-server-view.js +++ b/client/galaxy/scripts/layout/communication-server-view.js @@ -92,13 +92,12 @@ export const CommunicationServerView = Backbone.View.extend({ /**renders the chat icon as a nav item*/ render: function() { - const navItem = { + return { id: "show-chat-online", icon: "fa-comment-o", tooltip: _l("Chat online"), visible: false, onclick: this.makeModalIframe }; - return navItem; } }); diff --git a/client/galaxy/scripts/layout/masthead.js b/client/galaxy/scripts/layout/masthead.js index 17413de98b4..dc41a0b738d 100644 --- a/client/galaxy/scripts/layout/masthead.js +++ b/client/galaxy/scripts/layout/masthead.js @@ -99,7 +99,7 @@ const View = Backbone.View.extend({ return `
    MessageDescription <%= _.escape(item.get("message")) %>
    Name - + - Description - + Description + Data Type - + + + Size + + + Time Updated (UTC) + SizeTime Updated (UTC) State - +
    - + charts description
    diff --git a/client/galaxy/scripts/mvc/workflow/workflow-node.js b/client/galaxy/scripts/mvc/workflow/workflow-node.js index 4ac55fb2815..a93b421df47 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-node.js @@ -317,8 +317,7 @@ var Node = Backbone.Model.extend({ var new_body = nodeView.newInputsDiv(); var newTerminalViews = {}; _.each(data.inputs, input => { - var terminalView = node.nodeView.addDataInput(input, new_body); - newTerminalViews[input.name] = terminalView; + newTerminalViews[input.name] = node.nodeView.addDataInput(input, new_body); }); // Cleanup any leftover terminals _.each(_.difference(_.values(nodeView.terminalViews), _.values(newTerminalViews)), unusedView => { diff --git a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js index 3c89c1aa6d1..fd82f330151 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-terminals.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-terminals.js @@ -292,13 +292,9 @@ var BaseInputTerminal = Terminal.extend({ inputFilled = false; } else { if (this.multiple) { - if (this._collectionAttached()) { - // Can only attach one collection to multiple input - // data parameter. - inputFilled = true; - } else { - inputFilled = false; - } + // Can only attach one collection to multiple input + // data parameter. + inputFilled = !!this._collectionAttached(); } else { inputFilled = true; } diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js index 1eaa4d3d4f0..21fe17a89e1 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-view-node.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-view-node.js @@ -91,21 +91,19 @@ export default Backbone.View.extend({ } else if (output.parameter) { terminalViewClass = TerminalViews.OutputParameterTerminalView; } - const terminalView = new terminalViewClass({ + return new terminalViewClass({ node: this.node, output: output }); - return terminalView; }, outputViewforOutput: function(output, terminalView) { const outputViewClass = output.parameter ? DataViews.ParameterOutputView : DataViews.DataOutputView; - const outputView = new outputViewClass({ + return new outputViewClass({ output: output, terminalElement: terminalView.el, nodeView: this }); - return outputView; }, addDataOutput: function(output) { diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js index 00be7196c0c..adf822fe38f 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-view-terminals.js @@ -289,12 +289,11 @@ var OutputTerminalView = BaseOutputTerminalView.extend({ terminalMappingViewClass: TerminalMappingView, terminalForOutput: function(output) { var type = output.extensions; - var terminal = new Terminals.OutputTerminal({ + return new Terminals.OutputTerminal({ element: this.el, datatypes: type, force_datatype: output.force_datatype }); - return terminal; } }); @@ -304,14 +303,13 @@ var OutputCollectionTerminalView = BaseOutputTerminalView.extend({ terminalForOutput: function(output) { var collection_type = output.collection_type; var collection_type_source = output.collection_type_source; - var terminal = new Terminals.OutputCollectionTerminal({ + return new Terminals.OutputCollectionTerminal({ element: this.el, collection_type: collection_type, collection_type_source: collection_type_source, datatypes: output.extensions, force_datatype: output.force_datatype }); - return terminal; } }); @@ -319,11 +317,10 @@ var OutputParameterTerminalView = BaseOutputTerminalView.extend({ terminalMappingClass: Terminals.TerminalMapping, terminalMappingViewClass: TerminalMappingView, terminalForOutput: function(output) { - var terminal = new Terminals.OutputCollectionTerminal({ + return new Terminals.OutputCollectionTerminal({ element: this.el, type: output.type }); - return terminal; } }); diff --git a/client/galaxy/scripts/mvc/workflow/workflow-view.js b/client/galaxy/scripts/mvc/workflow/workflow-view.js index b6bde09ec82..eb5449e4268 100644 --- a/client/galaxy/scripts/mvc/workflow/workflow-view.js +++ b/client/galaxy/scripts/mvc/workflow/workflow-view.js @@ -771,7 +771,7 @@ export default Backbone.View.extend({ var node = new Node(this, { element: $f }); node.type = type; node.content_id = content_id; - var tmp = `
    loading tool info...
    `; + var tmp = `
    loading loading tool info...
    `; $f.find(".toolFormBody").append(tmp); // Fix width to computed width // Now add floats diff --git a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js index 2ecfabd1c3d..77d2812c8a4 100644 --- a/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js +++ b/client/galaxy/scripts/qunit/tests/workflow_editor_tests.js @@ -54,8 +54,7 @@ QUnit.module("Input terminal model test", { test_connector: function() { var outputTerminal = new Terminals.OutputTerminal({ datatypes: ["input"] }); var inputTerminal = this.input_terminal; - var connector = new Connector(outputTerminal, inputTerminal); - return connector; + return new Connector(outputTerminal, inputTerminal); }, with_test_connector: function(f) { this.test_connector(); @@ -557,9 +556,7 @@ QUnit.module("Node view ", { disableMapOver: function() {}, mapOver: Terminals.NULL_COLLECTION_TYPE_DESCRIPTION }; - var c = new Connector(outputTerminal, terminal); - - return c; + return new Connector(outputTerminal, terminal); }, connectAttachedMultiInputTerminal: function(inputType, outputType) { this.view.addDataInput({ name: "TestName", extensions: [inputType], multiple: true }); @@ -580,9 +577,7 @@ QUnit.module("Node view ", { disableMapOver: function() {}, mapOver: new Terminals.CollectionTypeDescription("list") }; - var c = new Connector(outputTerminal, terminal); - - return c; + return new Connector(outputTerminal, terminal); }, connectAttachedMappedOutput: function() { this.view.addDataInput({ name: "TestName", extensions: ["txt"], input_type: "dataset_collection" }); @@ -603,9 +598,7 @@ QUnit.module("Node view ", { disableMapOver: function() {}, mapOver: new Terminals.CollectionTypeDescription("list") }; - var c = new Connector(outputTerminal, terminal); - - return c; + return new Connector(outputTerminal, terminal); } }); @@ -917,8 +910,7 @@ QUnit.module("terminal mapping logic", { }, newNode: function() { var nodeEl = $("
    ")[0]; - var node = new Node(create_app(), { element: nodeEl }); - return node; + return new Node(create_app(), { element: nodeEl }); }, _addExistingOutput: function(terminal, output, connected) { var self = this; diff --git a/client/galaxy/scripts/reports/run_stats.js b/client/galaxy/scripts/reports/run_stats.js index 0c30bae7971..1a2ea951e13 100644 --- a/client/galaxy/scripts/reports/run_stats.js +++ b/client/galaxy/scripts/reports/run_stats.js @@ -178,9 +178,7 @@ export function create_chart(inp_data, name, time, title) { var m_x = margin.left; var m_y = margin.top + height; var l_x = m_x + width; - var l_y = m_y; - - return `M${m_x} ${m_y} L ${l_x} ${l_y}`; + return `M${m_x} ${m_y} L ${l_x} ${m_y}`; }); // Declare how high the y axis goes @@ -212,9 +210,7 @@ export function create_chart(inp_data, name, time, title) { var axis = d3.select(`#y_${name}`).node(); var left_pad = margin.left - axis.getBoundingClientRect().width - 5; var top_pad = margin.top + axis.getBoundingClientRect().height / 2 - 30; - var trans = `translate(${left_pad},${top_pad})rotate(-90)`; - - return trans; + return `translate(${left_pad},${top_pad})rotate(-90)`; }) .text("Number of Jobs"); @@ -625,9 +621,7 @@ export function create_histogram(inp_data, name, title) { var axis = d3.select(`#x_${name}`).node(); var left_pad = margin.left + axis.getBoundingClientRect().width / 2 + 30; var top_pad = margin.top + height + axis.getBoundingClientRect().height + 10; - var trans = `translate(${left_pad},${top_pad})`; - - return trans; + return `translate(${left_pad},${top_pad})`; }) .text("ETA - hrs:mins"); @@ -654,9 +648,7 @@ export function create_histogram(inp_data, name, title) { var axis = d3.select(`#y_${name}`).node(); var left_pad = margin.left - axis.getBoundingClientRect().width - 5; var top_pad = margin.top + axis.getBoundingClientRect().height / 2 - 30; - var trans = `translate(${left_pad},${top_pad})rotate(-90)`; - - return trans; + return `translate(${left_pad},${top_pad})rotate(-90)`; }) .text("Number of Jobs"); diff --git a/client/galaxy/scripts/ui/peek-column-selector.js b/client/galaxy/scripts/ui/peek-column-selector.js index 0a8ce1838fa..ff65acd58b0 100644 --- a/client/galaxy/scripts/ui/peek-column-selector.js +++ b/client/galaxy/scripts/ui/peek-column-selector.js @@ -175,8 +175,7 @@ function buildSingleSelectCell(control, columnIndex) { var eventData = {}; var key = $cell.parent().attr("id"); - var val = $cell.data(COLUMN_INDEX_DATA_KEY); - eventData[key] = val; + eventData[key] = $cell.data(COLUMN_INDEX_DATA_KEY); $cell.parents(".peek").trigger(CHANGE_EVENT, eventData); } }); @@ -209,8 +208,7 @@ function buildMultiSelectCell(control, columnIndex) { var eventData = {}; var key = $cell.parent().attr("id"); - var val = $.makeArray(selectedColumnIndeces); - eventData[key] = val; + eventData[key] = $.makeArray(selectedColumnIndeces); $cell.parents(".peek").trigger(CHANGE_EVENT, eventData); }); } diff --git a/client/galaxy/scripts/ui/popupmenu.js b/client/galaxy/scripts/ui/popupmenu.js index 4b00f445105..53d9ea8b168 100644 --- a/client/galaxy/scripts/ui/popupmenu.js +++ b/client/galaxy/scripts/ui/popupmenu.js @@ -54,7 +54,7 @@ export function make_popupmenu(button_element, initial_options) { ); } }); - var wrapper = $("
    ") + var wrapper = $("
    ") .append(menu_element) .appendTo("body"); diff --git a/client/galaxy/scripts/utils/installMonitor.js b/client/galaxy/scripts/utils/installMonitor.js index 146fda09384..68479548ba9 100644 --- a/client/galaxy/scripts/utils/installMonitor.js +++ b/client/galaxy/scripts/utils/installMonitor.js @@ -102,8 +102,7 @@ export function showMonitorToggles() { // retrieve toggle list from the session storage function getToggles() { const json = sessionStorage.getItem("global_monitors"); - const existinglist = json ? JSON.parse(json) : {}; - return existinglist; + return json ? JSON.parse(json) : {}; } // put the toggle list back in session storage diff --git a/client/galaxy/scripts/viz/trackster/filters.js b/client/galaxy/scripts/viz/trackster/filters.js index 34309eeda8e..cb458fe3371 100644 --- a/client/galaxy/scripts/viz/trackster/filters.js +++ b/client/galaxy/scripts/viz/trackster/filters.js @@ -322,10 +322,8 @@ _.extend(NumberFilter.prototype, { * Returns true if filter can be applied to element. */ applies_to: function(element) { - if (element.length > this.index) { - return true; - } - return false; + return element.length > this.index; + }, /** * Helper function: returns true if value in in filter's [low, high] range. diff --git a/client/galaxy/style/scss/autocomplete_tagging.scss b/client/galaxy/style/scss/autocomplete_tagging.scss index 8bae0fd2ccc..db169ee0b75 100644 --- a/client/galaxy/style/scss/autocomplete_tagging.scss +++ b/client/galaxy/style/scss/autocomplete_tagging.scss @@ -85,7 +85,6 @@ .toggle-link { font-weight: normal; - padding: 0.3em; margin-bottom: 1em; width: 100%; padding: 0.2em 0em 0.2em 0em; diff --git a/client/galaxy/style/scss/base.scss b/client/galaxy/style/scss/base.scss index b61022c664e..b39062180cb 100644 --- a/client/galaxy/style/scss/base.scss +++ b/client/galaxy/style/scss/base.scss @@ -1299,8 +1299,6 @@ div.permissionContainer { .text-content { hr { display: block; - background: black; - color: black; width: 100%; height: 1px; border: none; diff --git a/client/galaxy/style/scss/frame.scss b/client/galaxy/style/scss/frame.scss index 382e8c9492a..ef956308d4a 100644 --- a/client/galaxy/style/scss/frame.scss +++ b/client/galaxy/style/scss/frame.scss @@ -147,8 +147,6 @@ $frame-default-border: $border-default-color; width: 16px; height: 16px; color: $brand-dark; - right: 0px; - bottom: 0px; text-align: center; line-height: 16px; border: 0px; diff --git a/client/galaxy/style/scss/history.scss b/client/galaxy/style/scss/history.scss index 74132b79b41..4e4686de8d8 100644 --- a/client/galaxy/style/scss/history.scss +++ b/client/galaxy/style/scss/history.scss @@ -499,7 +499,6 @@ overflow: hidden; text-overflow: ellipsis; white-space: nowrap; - max-height: 22px; } &.control-column-right { text-align: right; diff --git a/client/galaxy/style/scss/overrides.scss b/client/galaxy/style/scss/overrides.scss index 456f65fc816..481e1143590 100644 --- a/client/galaxy/style/scss/overrides.scss +++ b/client/galaxy/style/scss/overrides.scss @@ -33,7 +33,6 @@ pre { } .dropdown-menu { - max-width: auto; .dropdown-item { text-decoration: none; } diff --git a/client/galaxy/style/scss/trackster.scss b/client/galaxy/style/scss/trackster.scss index ac15bd0b53c..5f06b7d1961 100644 --- a/client/galaxy/style/scss/trackster.scss +++ b/client/galaxy/style/scss/trackster.scss @@ -26,7 +26,6 @@ $separator-color: #888; padding: 0 0; color: #333; font-weight: bold; - background: #cccccc; display: inline-block; top: -2em; background: transparent; diff --git a/client/galaxy/style/scss/ui.scss b/client/galaxy/style/scss/ui.scss index e0fc091a557..8688b25bd28 100644 --- a/client/galaxy/style/scss/ui.scss +++ b/client/galaxy/style/scss/ui.scss @@ -154,7 +154,6 @@ $ui-margin-horizontal-large: $margin-v * 2; font-style: italic; } .ui-form-backdrop { - display: none; z-index: 10; position: absolute; top: 0px; diff --git a/doc/schema_template.md b/doc/schema_template.md index a08c3fc12ec..681ca56a5fe 100644 --- a/doc/schema_template.md +++ b/doc/schema_template.md @@ -18,6 +18,8 @@ $tag:tool|description://element[@name='tool']//element[@name='description'] $tag:tool|macros://complexType[@name='Macros'] $tag:tool|edam_topics://complexType[@name='EdamTopics'] $tag:tool|edam_operations://complexType[@name='EdamOperations'] +$tag:tool|xrefs://complexType[@name='xrefs'] +$tag:tool|xrefs|xref://complexType[@name='xref'] $tag:tool|requirements://complexType[@name='Requirements'] $tag:tool|requirements|requirement://complexType[@name='Requirement'] $tag:tool|requirements|container://complexType[@name='Container'] diff --git a/doc/source/lib/galaxy.actions.rst b/doc/source/lib/galaxy.actions.rst index dc400ceef5f..6bef88c7bc6 100644 --- a/doc/source/lib/galaxy.actions.rst +++ b/doc/source/lib/galaxy.actions.rst @@ -1,5 +1,5 @@ -galaxy\.actions package -======================= +galaxy.actions package +====================== .. automodule:: galaxy.actions :members: @@ -9,16 +9,16 @@ galaxy\.actions package Submodules ---------- -galaxy\.actions\.admin module ------------------------------ +galaxy.actions.admin module +--------------------------- .. automodule:: galaxy.actions.admin :members: :undoc-members: :show-inheritance: -galaxy\.actions\.library module -------------------------------- +galaxy.actions.library module +----------------------------- .. automodule:: galaxy.actions.library :members: diff --git a/doc/source/lib/galaxy.auth.providers.rst b/doc/source/lib/galaxy.auth.providers.rst index 7ead6289940..2a5a44ea5bf 100644 --- a/doc/source/lib/galaxy.auth.providers.rst +++ b/doc/source/lib/galaxy.auth.providers.rst @@ -1,5 +1,5 @@ -galaxy\.auth\.providers package -=============================== +galaxy.auth.providers package +============================= .. automodule:: galaxy.auth.providers :members: @@ -9,32 +9,32 @@ galaxy\.auth\.providers package Submodules ---------- -galaxy\.auth\.providers\.alwaysreject module --------------------------------------------- +galaxy.auth.providers.alwaysreject module +----------------------------------------- .. automodule:: galaxy.auth.providers.alwaysreject :members: :undoc-members: :show-inheritance: -galaxy\.auth\.providers\.ldap\_ad module ----------------------------------------- +galaxy.auth.providers.ldap\_ad module +------------------------------------- .. automodule:: galaxy.auth.providers.ldap_ad :members: :undoc-members: :show-inheritance: -galaxy\.auth\.providers\.localdb module ---------------------------------------- +galaxy.auth.providers.localdb module +------------------------------------ .. automodule:: galaxy.auth.providers.localdb :members: :undoc-members: :show-inheritance: -galaxy\.auth\.providers\.pam\_auth module ------------------------------------------ +galaxy.auth.providers.pam\_auth module +-------------------------------------- .. automodule:: galaxy.auth.providers.pam_auth :members: diff --git a/doc/source/lib/galaxy.auth.rst b/doc/source/lib/galaxy.auth.rst index 9ccf366fb84..ac0af26959e 100644 --- a/doc/source/lib/galaxy.auth.rst +++ b/doc/source/lib/galaxy.auth.rst @@ -1,5 +1,5 @@ -galaxy\.auth package -==================== +galaxy.auth package +=================== .. automodule:: galaxy.auth :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -galaxy\.auth\.util module -------------------------- +galaxy.auth.util module +----------------------- .. automodule:: galaxy.auth.util :members: diff --git a/doc/source/lib/galaxy.authnz.rst b/doc/source/lib/galaxy.authnz.rst index 0cf9364b89b..156c62d7961 100644 --- a/doc/source/lib/galaxy.authnz.rst +++ b/doc/source/lib/galaxy.authnz.rst @@ -1,5 +1,5 @@ -galaxy\.authnz package -====================== +galaxy.authnz package +===================== .. automodule:: galaxy.authnz :members: @@ -9,16 +9,24 @@ galaxy\.authnz package Submodules ---------- -galaxy\.authnz\.managers module -------------------------------- +galaxy.authnz.custos\_authnz module +----------------------------------- + +.. automodule:: galaxy.authnz.custos_authnz + :members: + :undoc-members: + :show-inheritance: + +galaxy.authnz.managers module +----------------------------- .. automodule:: galaxy.authnz.managers :members: :undoc-members: :show-inheritance: -galaxy\.authnz\.psa\_authnz module ----------------------------------- +galaxy.authnz.psa\_authnz module +-------------------------------- .. automodule:: galaxy.authnz.psa_authnz :members: diff --git a/doc/source/lib/galaxy.containers.rst b/doc/source/lib/galaxy.containers.rst index 79af3f5e408..8d61cd41340 100644 --- a/doc/source/lib/galaxy.containers.rst +++ b/doc/source/lib/galaxy.containers.rst @@ -1,5 +1,5 @@ -galaxy\.containers package -========================== +galaxy.containers package +========================= .. automodule:: galaxy.containers :members: @@ -9,32 +9,32 @@ galaxy\.containers package Submodules ---------- -galaxy\.containers\.docker module ---------------------------------- +galaxy.containers.docker module +------------------------------- .. automodule:: galaxy.containers.docker :members: :undoc-members: :show-inheritance: -galaxy\.containers\.docker\_decorators module ---------------------------------------------- +galaxy.containers.docker\_decorators module +------------------------------------------- .. automodule:: galaxy.containers.docker_decorators :members: :undoc-members: :show-inheritance: -galaxy\.containers\.docker\_model module ----------------------------------------- +galaxy.containers.docker\_model module +-------------------------------------- .. automodule:: galaxy.containers.docker_model :members: :undoc-members: :show-inheritance: -galaxy\.containers\.docker\_swarm module ----------------------------------------- +galaxy.containers.docker\_swarm module +-------------------------------------- .. automodule:: galaxy.containers.docker_swarm :members: diff --git a/doc/source/lib/galaxy.dataset_collections.rst b/doc/source/lib/galaxy.dataset_collections.rst deleted file mode 100644 index 45e1ae92fbb..00000000000 --- a/doc/source/lib/galaxy.dataset_collections.rst +++ /dev/null @@ -1,67 +0,0 @@ -galaxy\.dataset\_collections package -==================================== - -.. automodule:: galaxy.dataset_collections - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.dataset_collections.types - -Submodules ----------- - -galaxy\.dataset\_collections\.builder module --------------------------------------------- - -.. automodule:: galaxy.dataset_collections.builder - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.matching module ---------------------------------------------- - -.. automodule:: galaxy.dataset_collections.matching - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.registry module ---------------------------------------------- - -.. automodule:: galaxy.dataset_collections.registry - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.structure module ----------------------------------------------- - -.. automodule:: galaxy.dataset_collections.structure - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.subcollections module ---------------------------------------------------- - -.. automodule:: galaxy.dataset_collections.subcollections - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.type\_description module ------------------------------------------------------- - -.. automodule:: galaxy.dataset_collections.type_description - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.dataset_collections.types.rst b/doc/source/lib/galaxy.dataset_collections.types.rst deleted file mode 100644 index 64fe380d319..00000000000 --- a/doc/source/lib/galaxy.dataset_collections.types.rst +++ /dev/null @@ -1,28 +0,0 @@ -galaxy\.dataset\_collections\.types package -=========================================== - -.. automodule:: galaxy.dataset_collections.types - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.dataset\_collections\.types\.list module ------------------------------------------------- - -.. automodule:: galaxy.dataset_collections.types.list - :members: - :undoc-members: - :show-inheritance: - -galaxy\.dataset\_collections\.types\.paired module --------------------------------------------------- - -.. automodule:: galaxy.dataset_collections.types.paired - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.datatypes.converters.rst b/doc/source/lib/galaxy.datatypes.converters.rst index 6fd2583c819..17b7134c037 100644 --- a/doc/source/lib/galaxy.datatypes.converters.rst +++ b/doc/source/lib/galaxy.datatypes.converters.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes\.converters package -===================================== +galaxy.datatypes.converters package +=================================== .. automodule:: galaxy.datatypes.converters :members: @@ -9,256 +9,264 @@ galaxy\.datatypes\.converters package Submodules ---------- -galaxy\.datatypes\.converters\.bed\_to\_gff\_converter module -------------------------------------------------------------- +galaxy.datatypes.converters.bed\_to\_gff\_converter module +---------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.bed_to_gff_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.bedgraph\_to\_array\_tree\_converter module --------------------------------------------------------------------------- +galaxy.datatypes.converters.bedgraph\_to\_array\_tree\_converter module +----------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.bedgraph_to_array_tree_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.bgzip module -------------------------------------------- +galaxy.datatypes.converters.bgzip module +---------------------------------------- .. automodule:: galaxy.datatypes.converters.bgzip :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.cram\_to\_bam module ---------------------------------------------------- +galaxy.datatypes.converters.cram\_to\_bam module +------------------------------------------------ .. automodule:: galaxy.datatypes.converters.cram_to_bam :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fasta\_to\_len module ----------------------------------------------------- +galaxy.datatypes.converters.fasta\_to\_len module +------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fasta_to_len :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fasta\_to\_tabular\_converter module -------------------------------------------------------------------- +galaxy.datatypes.converters.fasta\_to\_tabular\_converter module +---------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fasta_to_tabular_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fastq\_to\_fqtoc module ------------------------------------------------------- +galaxy.datatypes.converters.fastq\_to\_fqtoc module +--------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastq_to_fqtoc :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fastqsolexa\_to\_fasta\_converter module ------------------------------------------------------------------------ +galaxy.datatypes.converters.fastqsolexa\_to\_fasta\_converter module +-------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastqsolexa_to_fasta_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.fastqsolexa\_to\_qual\_converter module ----------------------------------------------------------------------- +galaxy.datatypes.converters.fastqsolexa\_to\_qual\_converter module +------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.fastqsolexa_to_qual_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.gff\_to\_bed\_converter module -------------------------------------------------------------- +galaxy.datatypes.converters.gff\_to\_bed\_converter module +---------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.gff_to_bed_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.gff\_to\_interval\_index\_converter module -------------------------------------------------------------------------- +galaxy.datatypes.converters.gff\_to\_interval\_index\_converter module +---------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.gff_to_interval_index_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_bed\_converter module ------------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_bed\_converter module +--------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_bed_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_bedstrict\_converter module ------------------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_bedstrict\_converter module +--------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_bedstrict_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_coverage module ------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_coverage module +--------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_coverage :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_fli module -------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_fli module +---------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_fli :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_interval\_index\_converter module ------------------------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_interval\_index\_converter module +--------------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_interval_index_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.interval\_to\_tabix\_converter module --------------------------------------------------------------------- +galaxy.datatypes.converters.interval\_to\_tabix\_converter module +----------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.interval_to_tabix_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.lped\_to\_fped\_converter module ---------------------------------------------------------------- +galaxy.datatypes.converters.lped\_to\_fped\_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.lped_to_fped_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.lped\_to\_pbed\_converter module ---------------------------------------------------------------- +galaxy.datatypes.converters.lped\_to\_pbed\_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.lped_to_pbed_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.maf\_to\_fasta\_converter module ---------------------------------------------------------------- +galaxy.datatypes.converters.maf\_to\_fasta\_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.maf_to_fasta_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.maf\_to\_interval\_converter module ------------------------------------------------------------------- +galaxy.datatypes.converters.maf\_to\_interval\_converter module +--------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.maf_to_interval_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.pbed\_ldreduced\_converter module ----------------------------------------------------------------- +galaxy.datatypes.converters.pbed\_ldreduced\_converter module +------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pbed_ldreduced_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.pbed\_to\_lped\_converter module ---------------------------------------------------------------- +galaxy.datatypes.converters.pbed\_to\_lped\_converter module +------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.pbed_to_lped_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.picard\_interval\_list\_to\_bed6\_converter module ---------------------------------------------------------------------------------- +galaxy.datatypes.converters.picard\_interval\_list\_to\_bed6\_converter module +------------------------------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.picard_interval_list_to_bed6_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.pileup\_to\_interval\_index\_converter module ----------------------------------------------------------------------------- +galaxy.datatypes.converters.pileup\_to\_interval\_index\_converter module +------------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.pileup_to_interval_index_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.ref\_to\_seq\_taxonomy\_converter module ------------------------------------------------------------------------ +galaxy.datatypes.converters.ref\_to\_seq\_taxonomy\_converter module +-------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.ref_to_seq_taxonomy_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.sam\_to\_bam module --------------------------------------------------- +galaxy.datatypes.converters.sam\_to\_bam module +----------------------------------------------- .. automodule:: galaxy.datatypes.converters.sam_to_bam :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.tabular\_to\_dbnsfp module ---------------------------------------------------------- +galaxy.datatypes.converters.tabular\_csv module +----------------------------------------------- + +.. automodule:: galaxy.datatypes.converters.tabular_csv + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.converters.tabular\_to\_dbnsfp module +------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.tabular_to_dbnsfp :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.vcf\_to\_interval\_index\_converter module -------------------------------------------------------------------------- +galaxy.datatypes.converters.vcf\_to\_interval\_index\_converter module +---------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.vcf_to_interval_index_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.vcf\_to\_vcf\_bgzip module ---------------------------------------------------------- +galaxy.datatypes.converters.vcf\_to\_vcf\_bgzip module +------------------------------------------------------ .. automodule:: galaxy.datatypes.converters.vcf_to_vcf_bgzip :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.wiggle\_to\_array\_tree\_converter module ------------------------------------------------------------------------- +galaxy.datatypes.converters.wiggle\_to\_array\_tree\_converter module +--------------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.wiggle_to_array_tree_converter :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.converters\.wiggle\_to\_simple\_converter module -------------------------------------------------------------------- +galaxy.datatypes.converters.wiggle\_to\_simple\_converter module +---------------------------------------------------------------- .. automodule:: galaxy.datatypes.converters.wiggle_to_simple_converter :members: diff --git a/doc/source/lib/galaxy.datatypes.dataproviders.rst b/doc/source/lib/galaxy.datatypes.dataproviders.rst index 960b5c0c304..cd85ef190df 100644 --- a/doc/source/lib/galaxy.datatypes.dataproviders.rst +++ b/doc/source/lib/galaxy.datatypes.dataproviders.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes\.dataproviders package -======================================== +galaxy.datatypes.dataproviders package +====================================== .. automodule:: galaxy.datatypes.dataproviders :members: @@ -9,72 +9,72 @@ galaxy\.datatypes\.dataproviders package Submodules ---------- -galaxy\.datatypes\.dataproviders\.base module ---------------------------------------------- +galaxy.datatypes.dataproviders.base module +------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.base :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.chunk module ----------------------------------------------- +galaxy.datatypes.dataproviders.chunk module +------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.chunk :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.column module ------------------------------------------------ +galaxy.datatypes.dataproviders.column module +-------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.column :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.dataset module ------------------------------------------------- +galaxy.datatypes.dataproviders.dataset module +--------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.dataset :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.decorators module ---------------------------------------------------- +galaxy.datatypes.dataproviders.decorators module +------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.decorators :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.exceptions module ---------------------------------------------------- +galaxy.datatypes.dataproviders.exceptions module +------------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.exceptions :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.external module -------------------------------------------------- +galaxy.datatypes.dataproviders.external module +---------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.external :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.hierarchy module --------------------------------------------------- +galaxy.datatypes.dataproviders.hierarchy module +----------------------------------------------- .. automodule:: galaxy.datatypes.dataproviders.hierarchy :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.dataproviders\.line module ---------------------------------------------- +galaxy.datatypes.dataproviders.line module +------------------------------------------ .. automodule:: galaxy.datatypes.dataproviders.line :members: diff --git a/doc/source/lib/galaxy.datatypes.display_applications.rst b/doc/source/lib/galaxy.datatypes.display_applications.rst index e536e1ec0b6..acbf8fd2f9c 100644 --- a/doc/source/lib/galaxy.datatypes.display_applications.rst +++ b/doc/source/lib/galaxy.datatypes.display_applications.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes\.display\_applications package -================================================ +galaxy.datatypes.display\_applications package +============================================== .. automodule:: galaxy.datatypes.display_applications :members: @@ -9,24 +9,24 @@ galaxy\.datatypes\.display\_applications package Submodules ---------- -galaxy\.datatypes\.display\_applications\.application module ------------------------------------------------------------- +galaxy.datatypes.display\_applications.application module +--------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.application :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.display\_applications\.parameters module ------------------------------------------------------------ +galaxy.datatypes.display\_applications.parameters module +-------------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.parameters :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.display\_applications\.util module ------------------------------------------------------ +galaxy.datatypes.display\_applications.util module +-------------------------------------------------- .. automodule:: galaxy.datatypes.display_applications.util :members: diff --git a/doc/source/lib/galaxy.datatypes.rst b/doc/source/lib/galaxy.datatypes.rst index 94d35a51e72..b34c4e24783 100644 --- a/doc/source/lib/galaxy.datatypes.rst +++ b/doc/source/lib/galaxy.datatypes.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes package -========================= +galaxy.datatypes package +======================== .. automodule:: galaxy.datatypes :members: @@ -19,272 +19,296 @@ Subpackages Submodules ---------- -galaxy\.datatypes\.annotation module ------------------------------------- +galaxy.datatypes.annotation module +---------------------------------- .. automodule:: galaxy.datatypes.annotation :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.anvio module -------------------------------- +galaxy.datatypes.anvio module +----------------------------- .. automodule:: galaxy.datatypes.anvio :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.assembly module ----------------------------------- +galaxy.datatypes.assembly module +-------------------------------- .. automodule:: galaxy.datatypes.assembly :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.binary module --------------------------------- +galaxy.datatypes.binary module +------------------------------ .. automodule:: galaxy.datatypes.binary :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.blast module -------------------------------- +galaxy.datatypes.blast module +----------------------------- .. automodule:: galaxy.datatypes.blast :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.checkers module ----------------------------------- +galaxy.datatypes.checkers module +-------------------------------- .. automodule:: galaxy.datatypes.checkers :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.chrominfo module ------------------------------------ +galaxy.datatypes.chrominfo module +--------------------------------- .. automodule:: galaxy.datatypes.chrominfo :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.constructive\_solid\_geometry module -------------------------------------------------------- +galaxy.datatypes.constructive\_solid\_geometry module +----------------------------------------------------- .. automodule:: galaxy.datatypes.constructive_solid_geometry :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.coverage module ----------------------------------- +galaxy.datatypes.coverage module +-------------------------------- .. automodule:: galaxy.datatypes.coverage :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.data module ------------------------------- +galaxy.datatypes.data module +---------------------------- .. automodule:: galaxy.datatypes.data :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.genetics module ----------------------------------- +galaxy.datatypes.genetics module +-------------------------------- .. automodule:: galaxy.datatypes.genetics :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.graph module -------------------------------- +galaxy.datatypes.gis module +--------------------------- + +.. automodule:: galaxy.datatypes.gis + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.graph module +----------------------------- .. automodule:: galaxy.datatypes.graph :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.images module --------------------------------- +galaxy.datatypes.images module +------------------------------ .. automodule:: galaxy.datatypes.images :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.interval module ----------------------------------- +galaxy.datatypes.interval module +-------------------------------- .. automodule:: galaxy.datatypes.interval :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.isa module ------------------------------ +galaxy.datatypes.isa module +--------------------------- .. automodule:: galaxy.datatypes.isa :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.metadata module ----------------------------------- +galaxy.datatypes.metadata module +-------------------------------- .. automodule:: galaxy.datatypes.metadata :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.molecules module +galaxy.datatypes.microarrays module ----------------------------------- +.. automodule:: galaxy.datatypes.microarrays + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.molecules module +--------------------------------- + .. automodule:: galaxy.datatypes.molecules :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.mothur module --------------------------------- +galaxy.datatypes.mothur module +------------------------------ .. automodule:: galaxy.datatypes.mothur :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.msa module ------------------------------ +galaxy.datatypes.msa module +--------------------------- .. automodule:: galaxy.datatypes.msa :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.neo4j module -------------------------------- +galaxy.datatypes.neo4j module +----------------------------- .. automodule:: galaxy.datatypes.neo4j :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.ngsindex module ----------------------------------- +galaxy.datatypes.ngsindex module +-------------------------------- .. automodule:: galaxy.datatypes.ngsindex :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.phylip module --------------------------------- +galaxy.datatypes.phylip module +------------------------------ .. automodule:: galaxy.datatypes.phylip :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.plant\_tribes module ---------------------------------------- +galaxy.datatypes.plant\_tribes module +------------------------------------- .. automodule:: galaxy.datatypes.plant_tribes :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.proteomics module ------------------------------------- +galaxy.datatypes.proteomics module +---------------------------------- .. automodule:: galaxy.datatypes.proteomics :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.qualityscore module --------------------------------------- +galaxy.datatypes.qualityscore module +------------------------------------ .. automodule:: galaxy.datatypes.qualityscore :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.registry module ----------------------------------- +galaxy.datatypes.registry module +-------------------------------- .. automodule:: galaxy.datatypes.registry :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.sequence module ----------------------------------- +galaxy.datatypes.sequence module +-------------------------------- .. automodule:: galaxy.datatypes.sequence :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.sniff module -------------------------------- +galaxy.datatypes.sniff module +----------------------------- .. automodule:: galaxy.datatypes.sniff :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.tabular module ---------------------------------- +galaxy.datatypes.spaln module +----------------------------- + +.. automodule:: galaxy.datatypes.spaln + :members: + :undoc-members: + :show-inheritance: + +galaxy.datatypes.tabular module +------------------------------- .. automodule:: galaxy.datatypes.tabular :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.text module ------------------------------- +galaxy.datatypes.text module +---------------------------- .. automodule:: galaxy.datatypes.text :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.tracks module --------------------------------- +galaxy.datatypes.tracks module +------------------------------ .. automodule:: galaxy.datatypes.tracks :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.triples module ---------------------------------- +galaxy.datatypes.triples module +------------------------------- .. automodule:: galaxy.datatypes.triples :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.upload\_util module --------------------------------------- +galaxy.datatypes.upload\_util module +------------------------------------ .. automodule:: galaxy.datatypes.upload_util :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.xml module ------------------------------ +galaxy.datatypes.xml module +--------------------------- .. automodule:: galaxy.datatypes.xml :members: diff --git a/doc/source/lib/galaxy.datatypes.util.rst b/doc/source/lib/galaxy.datatypes.util.rst index 12c35b4fa78..8ac6f2c599d 100644 --- a/doc/source/lib/galaxy.datatypes.util.rst +++ b/doc/source/lib/galaxy.datatypes.util.rst @@ -1,5 +1,5 @@ -galaxy\.datatypes\.util package -=============================== +galaxy.datatypes.util package +============================= .. automodule:: galaxy.datatypes.util :members: @@ -9,16 +9,16 @@ galaxy\.datatypes\.util package Submodules ---------- -galaxy\.datatypes\.util\.generic\_util module ---------------------------------------------- +galaxy.datatypes.util.generic\_util module +------------------------------------------ .. automodule:: galaxy.datatypes.util.generic_util :members: :undoc-members: :show-inheritance: -galaxy\.datatypes\.util\.gff\_util module ------------------------------------------ +galaxy.datatypes.util.gff\_util module +-------------------------------------- .. automodule:: galaxy.datatypes.util.gff_util :members: diff --git a/doc/source/lib/galaxy.dependencies.rst b/doc/source/lib/galaxy.dependencies.rst index 4d1dd03016a..16ce685cbc1 100644 --- a/doc/source/lib/galaxy.dependencies.rst +++ b/doc/source/lib/galaxy.dependencies.rst @@ -1,5 +1,5 @@ -galaxy\.dependencies package -============================ +galaxy.dependencies package +=========================== .. automodule:: galaxy.dependencies :members: diff --git a/doc/source/lib/galaxy.eggs.rst b/doc/source/lib/galaxy.eggs.rst index f5f8f207e3a..6331aa38fdd 100644 --- a/doc/source/lib/galaxy.eggs.rst +++ b/doc/source/lib/galaxy.eggs.rst @@ -1,5 +1,5 @@ -galaxy\.eggs package -==================== +galaxy.eggs package +=================== .. automodule:: galaxy.eggs :members: diff --git a/doc/source/lib/galaxy.exceptions.rst b/doc/source/lib/galaxy.exceptions.rst index 2e52a13009d..8f118c6aa45 100644 --- a/doc/source/lib/galaxy.exceptions.rst +++ b/doc/source/lib/galaxy.exceptions.rst @@ -1,5 +1,5 @@ -galaxy\.exceptions package -========================== +galaxy.exceptions package +========================= .. automodule:: galaxy.exceptions :members: @@ -9,8 +9,8 @@ galaxy\.exceptions package Submodules ---------- -galaxy\.exceptions\.error\_codes module ---------------------------------------- +galaxy.exceptions.error\_codes module +------------------------------------- .. automodule:: galaxy.exceptions.error_codes :members: diff --git a/doc/source/lib/galaxy.forms.rst b/doc/source/lib/galaxy.forms.rst index ef27c97400e..088d52bcb9c 100644 --- a/doc/source/lib/galaxy.forms.rst +++ b/doc/source/lib/galaxy.forms.rst @@ -1,5 +1,5 @@ -galaxy\.forms package -===================== +galaxy.forms package +==================== .. automodule:: galaxy.forms :members: @@ -9,8 +9,8 @@ galaxy\.forms package Submodules ---------- -galaxy\.forms\.forms module ---------------------------- +galaxy.forms.forms module +------------------------- .. automodule:: galaxy.forms.forms :members: diff --git a/doc/source/lib/galaxy.job_execution.rst b/doc/source/lib/galaxy.job_execution.rst new file mode 100644 index 00000000000..58ab804eaf1 --- /dev/null +++ b/doc/source/lib/galaxy.job_execution.rst @@ -0,0 +1,28 @@ +galaxy.job\_execution package +============================= + +.. automodule:: galaxy.job_execution + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.job\_execution.datasets module +------------------------------------- + +.. automodule:: galaxy.job_execution.datasets + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_execution.output\_collect module +-------------------------------------------- + +.. automodule:: galaxy.job_execution.output_collect + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.job_metrics.collectl.rst b/doc/source/lib/galaxy.job_metrics.collectl.rst new file mode 100644 index 00000000000..74c5ee89df1 --- /dev/null +++ b/doc/source/lib/galaxy.job_metrics.collectl.rst @@ -0,0 +1,44 @@ +galaxy.job\_metrics.collectl package +==================================== + +.. automodule:: galaxy.job_metrics.collectl + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.job\_metrics.collectl.cli module +--------------------------------------- + +.. automodule:: galaxy.job_metrics.collectl.cli + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.collectl.processes module +--------------------------------------------- + +.. automodule:: galaxy.job_metrics.collectl.processes + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.collectl.stats module +----------------------------------------- + +.. automodule:: galaxy.job_metrics.collectl.stats + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.collectl.subsystems module +---------------------------------------------- + +.. automodule:: galaxy.job_metrics.collectl.subsystems + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.job_metrics.instrumenters.rst b/doc/source/lib/galaxy.job_metrics.instrumenters.rst new file mode 100644 index 00000000000..232ba437a5a --- /dev/null +++ b/doc/source/lib/galaxy.job_metrics.instrumenters.rst @@ -0,0 +1,76 @@ +galaxy.job\_metrics.instrumenters package +========================================= + +.. automodule:: galaxy.job_metrics.instrumenters + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.job\_metrics.instrumenters.cgroup module +----------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.cgroup + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.collectl module +------------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.collectl + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.core module +--------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.core + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.cpuinfo module +------------------------------------------------ + +.. automodule:: galaxy.job_metrics.instrumenters.cpuinfo + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.env module +-------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.env + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.hostname module +------------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.hostname + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.meminfo module +------------------------------------------------ + +.. automodule:: galaxy.job_metrics.instrumenters.meminfo + :members: + :undoc-members: + :show-inheritance: + +galaxy.job\_metrics.instrumenters.uname module +---------------------------------------------- + +.. automodule:: galaxy.job_metrics.instrumenters.uname + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.job_metrics.rst b/doc/source/lib/galaxy.job_metrics.rst new file mode 100644 index 00000000000..9419d2aebd1 --- /dev/null +++ b/doc/source/lib/galaxy.job_metrics.rst @@ -0,0 +1,28 @@ +galaxy.job\_metrics package +=========================== + +.. automodule:: galaxy.job_metrics + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.job_metrics.collectl + galaxy.job_metrics.instrumenters + +Submodules +---------- + +galaxy.job\_metrics.formatting module +------------------------------------- + +.. automodule:: galaxy.job_metrics.formatting + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.jobs.actions.rst b/doc/source/lib/galaxy.jobs.actions.rst index f0c64ad3699..7ec9a937d81 100644 --- a/doc/source/lib/galaxy.jobs.actions.rst +++ b/doc/source/lib/galaxy.jobs.actions.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.actions package -============================= +galaxy.jobs.actions package +=========================== .. automodule:: galaxy.jobs.actions :members: @@ -9,8 +9,8 @@ galaxy\.jobs\.actions package Submodules ---------- -galaxy\.jobs\.actions\.post module ----------------------------------- +galaxy.jobs.actions.post module +------------------------------- .. automodule:: galaxy.jobs.actions.post :members: diff --git a/doc/source/lib/galaxy.jobs.metrics.collectl.rst b/doc/source/lib/galaxy.jobs.metrics.collectl.rst deleted file mode 100644 index 8999b1f717f..00000000000 --- a/doc/source/lib/galaxy.jobs.metrics.collectl.rst +++ /dev/null @@ -1,44 +0,0 @@ -galaxy\.jobs\.metrics\.collectl package -======================================= - -.. automodule:: galaxy.jobs.metrics.collectl - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.jobs\.metrics\.collectl\.cli module -------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.collectl.cli - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.collectl\.processes module -------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.collectl.processes - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.collectl\.stats module ---------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.collectl.stats - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.collectl\.subsystems module --------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.collectl.subsystems - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst b/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst deleted file mode 100644 index 21123c4ca4c..00000000000 --- a/doc/source/lib/galaxy.jobs.metrics.instrumenters.rst +++ /dev/null @@ -1,76 +0,0 @@ -galaxy\.jobs\.metrics\.instrumenters package -============================================ - -.. automodule:: galaxy.jobs.metrics.instrumenters - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.jobs\.metrics\.instrumenters\.cgroup module ---------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.cgroup - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.collectl module ------------------------------------------------------ - -.. automodule:: galaxy.jobs.metrics.instrumenters.collectl - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.core module -------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.core - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.cpuinfo module ----------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.cpuinfo - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.env module ------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.env - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.hostname module ------------------------------------------------------ - -.. automodule:: galaxy.jobs.metrics.instrumenters.hostname - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.meminfo module ----------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.meminfo - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.metrics\.instrumenters\.uname module --------------------------------------------------- - -.. automodule:: galaxy.jobs.metrics.instrumenters.uname - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.jobs.metrics.rst b/doc/source/lib/galaxy.jobs.metrics.rst deleted file mode 100644 index 9e651976e30..00000000000 --- a/doc/source/lib/galaxy.jobs.metrics.rst +++ /dev/null @@ -1,28 +0,0 @@ -galaxy\.jobs\.metrics package -============================= - -.. automodule:: galaxy.jobs.metrics - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.jobs.metrics.collectl - galaxy.jobs.metrics.instrumenters - -Submodules ----------- - -galaxy\.jobs\.metrics\.formatting module ----------------------------------------- - -.. automodule:: galaxy.jobs.metrics.formatting - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.jobs.rst b/doc/source/lib/galaxy.jobs.rst index b70b8f2df86..900a19d1680 100644 --- a/doc/source/lib/galaxy.jobs.rst +++ b/doc/source/lib/galaxy.jobs.rst @@ -1,5 +1,5 @@ -galaxy\.jobs package -==================== +galaxy.jobs package +=================== .. automodule:: galaxy.jobs :members: @@ -12,87 +12,71 @@ Subpackages .. toctree:: galaxy.jobs.actions - galaxy.jobs.metrics + galaxy.jobs.rules galaxy.jobs.runners galaxy.jobs.splitters Submodules ---------- -galaxy\.jobs\.command\_factory module -------------------------------------- +galaxy.jobs.command\_factory module +----------------------------------- .. automodule:: galaxy.jobs.command_factory :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.datasets module ------------------------------ - -.. automodule:: galaxy.jobs.datasets - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.dynamic\_tool\_destination module ------------------------------------------------ +galaxy.jobs.dynamic\_tool\_destination module +--------------------------------------------- .. automodule:: galaxy.jobs.dynamic_tool_destination :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.handler module ----------------------------- +galaxy.jobs.handler module +-------------------------- .. automodule:: galaxy.jobs.handler :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.manager module ----------------------------- +galaxy.jobs.manager module +-------------------------- .. automodule:: galaxy.jobs.manager :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.mapper module ---------------------------- +galaxy.jobs.mapper module +------------------------- .. automodule:: galaxy.jobs.mapper :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.output\_checker module ------------------------------------- - -.. automodule:: galaxy.jobs.output_checker - :members: - :undoc-members: - :show-inheritance: - -galaxy\.jobs\.rule\_helper module ---------------------------------- +galaxy.jobs.rule\_helper module +------------------------------- .. automodule:: galaxy.jobs.rule_helper :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.stock\_rules module ---------------------------------- +galaxy.jobs.stock\_rules module +------------------------------- .. automodule:: galaxy.jobs.stock_rules :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.transfer\_manager module --------------------------------------- +galaxy.jobs.transfer\_manager module +------------------------------------ .. automodule:: galaxy.jobs.transfer_manager :members: diff --git a/doc/source/lib/galaxy.jobs.rules.rst b/doc/source/lib/galaxy.jobs.rules.rst new file mode 100644 index 00000000000..29f0510c5a9 --- /dev/null +++ b/doc/source/lib/galaxy.jobs.rules.rst @@ -0,0 +1,8 @@ +galaxy.jobs.rules package +========================= + +.. automodule:: galaxy.jobs.rules + :members: + :undoc-members: + :show-inheritance: + diff --git a/doc/source/lib/galaxy.jobs.runners.rst b/doc/source/lib/galaxy.jobs.runners.rst index cc47f56014c..937787d586c 100644 --- a/doc/source/lib/galaxy.jobs.runners.rst +++ b/doc/source/lib/galaxy.jobs.runners.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners package -============================= +galaxy.jobs.runners package +=========================== .. automodule:: galaxy.jobs.runners :members: @@ -17,104 +17,104 @@ Subpackages Submodules ---------- -galaxy\.jobs\.runners\.chronos module -------------------------------------- +galaxy.jobs.runners.chronos module +---------------------------------- .. automodule:: galaxy.jobs.runners.chronos :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.cli module ---------------------------------- +galaxy.jobs.runners.cli module +------------------------------ .. automodule:: galaxy.jobs.runners.cli :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.condor module ------------------------------------- +galaxy.jobs.runners.condor module +--------------------------------- .. automodule:: galaxy.jobs.runners.condor :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.drmaa module ------------------------------------ +galaxy.jobs.runners.drmaa module +-------------------------------- .. automodule:: galaxy.jobs.runners.drmaa :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.godocker module --------------------------------------- +galaxy.jobs.runners.godocker module +----------------------------------- .. automodule:: galaxy.jobs.runners.godocker :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.kubernetes module ----------------------------------------- +galaxy.jobs.runners.kubernetes module +------------------------------------- .. automodule:: galaxy.jobs.runners.kubernetes :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.local module ------------------------------------ +galaxy.jobs.runners.local module +-------------------------------- .. automodule:: galaxy.jobs.runners.local :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.pbs module ---------------------------------- +galaxy.jobs.runners.pbs module +------------------------------ .. automodule:: galaxy.jobs.runners.pbs :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.pulsar module ------------------------------------- +galaxy.jobs.runners.pulsar module +--------------------------------- .. automodule:: galaxy.jobs.runners.pulsar :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.slurm module ------------------------------------ +galaxy.jobs.runners.slurm module +-------------------------------- .. automodule:: galaxy.jobs.runners.slurm :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.state\_handler\_factory module ------------------------------------------------------ +galaxy.jobs.runners.state\_handler\_factory module +-------------------------------------------------- .. automodule:: galaxy.jobs.runners.state_handler_factory :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.tasks module ------------------------------------ +galaxy.jobs.runners.tasks module +-------------------------------- .. automodule:: galaxy.jobs.runners.tasks :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.univa module ------------------------------------ +galaxy.jobs.runners.univa module +-------------------------------- .. automodule:: galaxy.jobs.runners.univa :members: diff --git a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst index be55fd3c029..1e71d735662 100644 --- a/doc/source/lib/galaxy.jobs.runners.state_handlers.rst +++ b/doc/source/lib/galaxy.jobs.runners.state_handlers.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.state\_handlers package -============================================== +galaxy.jobs.runners.state\_handlers package +=========================================== .. automodule:: galaxy.jobs.runners.state_handlers :members: @@ -9,8 +9,8 @@ galaxy\.jobs\.runners\.state\_handlers package Submodules ---------- -galaxy\.jobs\.runners\.state\_handlers\.resubmit module -------------------------------------------------------- +galaxy.jobs.runners.state\_handlers.resubmit module +--------------------------------------------------- .. automodule:: galaxy.jobs.runners.state_handlers.resubmit :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst index cb401ca9704..11813c7a0d1 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.job.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.cli\.job package -============================================= +galaxy.jobs.runners.util.cli.job package +======================================== .. automodule:: galaxy.jobs.runners.util.cli.job :members: @@ -9,32 +9,32 @@ galaxy\.jobs\.runners\.util\.cli\.job package Submodules ---------- -galaxy\.jobs\.runners\.util\.cli\.job\.lsf module -------------------------------------------------- +galaxy.jobs.runners.util.cli.job.lsf module +------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.lsf :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.cli\.job\.slurm module ---------------------------------------------------- +galaxy.jobs.runners.util.cli.job.slurm module +--------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.slurm :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.cli\.job\.slurm\_torque module ------------------------------------------------------------ +galaxy.jobs.runners.util.cli.job.slurm\_torque module +----------------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.slurm_torque :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.cli\.job\.torque module ----------------------------------------------------- +galaxy.jobs.runners.util.cli.job.torque module +---------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.job.torque :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.rst index 16294903ae9..dadd626718b 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.cli package -======================================== +galaxy.jobs.runners.util.cli package +==================================== .. automodule:: galaxy.jobs.runners.util.cli :members: @@ -17,8 +17,8 @@ Subpackages Submodules ---------- -galaxy\.jobs\.runners\.util\.cli\.factory module ------------------------------------------------- +galaxy.jobs.runners.util.cli.factory module +------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.factory :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst index db42713ebd0..42e5c7ffe73 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.cli.shell.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.cli\.shell package -=============================================== +galaxy.jobs.runners.util.cli.shell package +========================================== .. automodule:: galaxy.jobs.runners.util.cli.shell :members: @@ -9,16 +9,16 @@ galaxy\.jobs\.runners\.util\.cli\.shell package Submodules ---------- -galaxy\.jobs\.runners\.util\.cli\.shell\.local module ------------------------------------------------------ +galaxy.jobs.runners.util.cli.shell.local module +----------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.local :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.cli\.shell\.rsh module ---------------------------------------------------- +galaxy.jobs.runners.util.cli.shell.rsh module +--------------------------------------------- .. automodule:: galaxy.jobs.runners.util.cli.shell.rsh :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.condor.rst b/doc/source/lib/galaxy.jobs.runners.util.condor.rst index b1b5fa9f1d4..823ea51ac3e 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.condor.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.condor.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.condor package -=========================================== +galaxy.jobs.runners.util.condor package +======================================= .. automodule:: galaxy.jobs.runners.util.condor :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst index 562df4ae6b8..28119d40f7d 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.job_script.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.job_script.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util\.job\_script package -================================================ +galaxy.jobs.runners.util.job\_script package +============================================ .. automodule:: galaxy.jobs.runners.util.job_script :members: diff --git a/doc/source/lib/galaxy.jobs.runners.util.rst b/doc/source/lib/galaxy.jobs.runners.util.rst index 85487d46d30..ad9a2d1c85d 100644 --- a/doc/source/lib/galaxy.jobs.runners.util.rst +++ b/doc/source/lib/galaxy.jobs.runners.util.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.runners\.util package -=================================== +galaxy.jobs.runners.util package +================================ .. automodule:: galaxy.jobs.runners.util :members: @@ -18,32 +18,40 @@ Subpackages Submodules ---------- -galaxy\.jobs\.runners\.util\.env module ---------------------------------------- +galaxy.jobs.runners.util.env module +----------------------------------- .. automodule:: galaxy.jobs.runners.util.env :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.external module --------------------------------------------- +galaxy.jobs.runners.util.external module +---------------------------------------- .. automodule:: galaxy.jobs.runners.util.external :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.kill module ----------------------------------------- +galaxy.jobs.runners.util.kill module +------------------------------------ .. automodule:: galaxy.jobs.runners.util.kill :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.runners\.util\.sudo module ----------------------------------------- +galaxy.jobs.runners.util.pykube\_util module +-------------------------------------------- + +.. automodule:: galaxy.jobs.runners.util.pykube_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.jobs.runners.util.sudo module +------------------------------------ .. automodule:: galaxy.jobs.runners.util.sudo :members: diff --git a/doc/source/lib/galaxy.jobs.splitters.rst b/doc/source/lib/galaxy.jobs.splitters.rst index 545d1e121fe..d8af934e1be 100644 --- a/doc/source/lib/galaxy.jobs.splitters.rst +++ b/doc/source/lib/galaxy.jobs.splitters.rst @@ -1,5 +1,5 @@ -galaxy\.jobs\.splitters package -=============================== +galaxy.jobs.splitters package +============================= .. automodule:: galaxy.jobs.splitters :members: @@ -9,16 +9,16 @@ galaxy\.jobs\.splitters package Submodules ---------- -galaxy\.jobs\.splitters\.basic module -------------------------------------- +galaxy.jobs.splitters.basic module +---------------------------------- .. automodule:: galaxy.jobs.splitters.basic :members: :undoc-members: :show-inheritance: -galaxy\.jobs\.splitters\.multi module -------------------------------------- +galaxy.jobs.splitters.multi module +---------------------------------- .. automodule:: galaxy.jobs.splitters.multi :members: diff --git a/doc/source/lib/galaxy.managers.rst b/doc/source/lib/galaxy.managers.rst index a68ec4f53df..829568b9685 100644 --- a/doc/source/lib/galaxy.managers.rst +++ b/doc/source/lib/galaxy.managers.rst @@ -1,5 +1,5 @@ -galaxy\.managers package -======================== +galaxy.managers package +======================= .. automodule:: galaxy.managers :members: @@ -9,264 +9,264 @@ galaxy\.managers package Submodules ---------- -galaxy\.managers\.annotatable module ------------------------------------- +galaxy.managers.annotatable module +---------------------------------- .. automodule:: galaxy.managers.annotatable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.api\_keys module ----------------------------------- +galaxy.managers.api\_keys module +-------------------------------- .. automodule:: galaxy.managers.api_keys :members: :undoc-members: :show-inheritance: -galaxy\.managers\.base module ------------------------------ +galaxy.managers.base module +--------------------------- .. automodule:: galaxy.managers.base :members: :undoc-members: :show-inheritance: -galaxy\.managers\.citations module ----------------------------------- +galaxy.managers.citations module +-------------------------------- .. automodule:: galaxy.managers.citations :members: :undoc-members: :show-inheritance: -galaxy\.managers\.cloud module ------------------------------- +galaxy.managers.cloud module +---------------------------- .. automodule:: galaxy.managers.cloud :members: :undoc-members: :show-inheritance: -galaxy\.managers\.cloudauthzs module ------------------------------------- +galaxy.managers.cloudauthzs module +---------------------------------- .. automodule:: galaxy.managers.cloudauthzs :members: :undoc-members: :show-inheritance: -galaxy\.managers\.collections module ------------------------------------- +galaxy.managers.collections module +---------------------------------- .. automodule:: galaxy.managers.collections :members: :undoc-members: :show-inheritance: -galaxy\.managers\.collections\_util module ------------------------------------------- +galaxy.managers.collections\_util module +---------------------------------------- .. automodule:: galaxy.managers.collections_util :members: :undoc-members: :show-inheritance: -galaxy\.managers\.configuration module --------------------------------------- +galaxy.managers.configuration module +------------------------------------ .. automodule:: galaxy.managers.configuration :members: :undoc-members: :show-inheritance: -galaxy\.managers\.containers module ------------------------------------ +galaxy.managers.containers module +--------------------------------- .. automodule:: galaxy.managers.containers :members: :undoc-members: :show-inheritance: -galaxy\.managers\.context module --------------------------------- +galaxy.managers.context module +------------------------------ .. automodule:: galaxy.managers.context :members: :undoc-members: :show-inheritance: -galaxy\.managers\.datasets module ---------------------------------- +galaxy.managers.datasets module +------------------------------- .. automodule:: galaxy.managers.datasets :members: :undoc-members: :show-inheritance: -galaxy\.managers\.deletable module ----------------------------------- +galaxy.managers.deletable module +-------------------------------- .. automodule:: galaxy.managers.deletable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.folders module --------------------------------- +galaxy.managers.folders module +------------------------------ .. automodule:: galaxy.managers.folders :members: :undoc-members: :show-inheritance: -galaxy\.managers\.hdas module ------------------------------ +galaxy.managers.hdas module +--------------------------- .. automodule:: galaxy.managers.hdas :members: :undoc-members: :show-inheritance: -galaxy\.managers\.hdcas module ------------------------------- +galaxy.managers.hdcas module +---------------------------- .. automodule:: galaxy.managers.hdcas :members: :undoc-members: :show-inheritance: -galaxy\.managers\.histories module ----------------------------------- +galaxy.managers.histories module +-------------------------------- .. automodule:: galaxy.managers.histories :members: :undoc-members: :show-inheritance: -galaxy\.managers\.history\_contents module ------------------------------------------- +galaxy.managers.history\_contents module +---------------------------------------- .. automodule:: galaxy.managers.history_contents :members: :undoc-members: :show-inheritance: -galaxy\.managers\.jobs module ------------------------------ +galaxy.managers.jobs module +--------------------------- .. automodule:: galaxy.managers.jobs :members: :undoc-members: :show-inheritance: -galaxy\.managers\.lddas module ------------------------------- +galaxy.managers.lddas module +---------------------------- .. automodule:: galaxy.managers.lddas :members: :undoc-members: :show-inheritance: -galaxy\.managers\.libraries module ----------------------------------- +galaxy.managers.libraries module +-------------------------------- .. automodule:: galaxy.managers.libraries :members: :undoc-members: :show-inheritance: -galaxy\.managers\.library\_datasets module ------------------------------------------- +galaxy.managers.library\_datasets module +---------------------------------------- .. automodule:: galaxy.managers.library_datasets :members: :undoc-members: :show-inheritance: -galaxy\.managers\.pages module ------------------------------- +galaxy.managers.pages module +---------------------------- .. automodule:: galaxy.managers.pages :members: :undoc-members: :show-inheritance: -galaxy\.managers\.ratable module --------------------------------- +galaxy.managers.ratable module +------------------------------ .. automodule:: galaxy.managers.ratable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.rbac\_secured module --------------------------------------- +galaxy.managers.rbac\_secured module +------------------------------------ .. automodule:: galaxy.managers.rbac_secured :members: :undoc-members: :show-inheritance: -galaxy\.managers\.roles module ------------------------------- +galaxy.managers.roles module +---------------------------- .. automodule:: galaxy.managers.roles :members: :undoc-members: :show-inheritance: -galaxy\.managers\.secured module --------------------------------- +galaxy.managers.secured module +------------------------------ .. automodule:: galaxy.managers.secured :members: :undoc-members: :show-inheritance: -galaxy\.managers\.sharable module ---------------------------------- +galaxy.managers.sharable module +------------------------------- .. automodule:: galaxy.managers.sharable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.taggable module ---------------------------------- +galaxy.managers.taggable module +------------------------------- .. automodule:: galaxy.managers.taggable :members: :undoc-members: :show-inheritance: -galaxy\.managers\.tags module ------------------------------ +galaxy.managers.tools module +---------------------------- -.. automodule:: galaxy.managers.tags +.. automodule:: galaxy.managers.tools :members: :undoc-members: :show-inheritance: -galaxy\.managers\.users module ------------------------------- +galaxy.managers.users module +---------------------------- .. automodule:: galaxy.managers.users :members: :undoc-members: :show-inheritance: -galaxy\.managers\.visualizations module ---------------------------------------- +galaxy.managers.visualizations module +------------------------------------- .. automodule:: galaxy.managers.visualizations :members: :undoc-members: :show-inheritance: -galaxy\.managers\.workflows module ----------------------------------- +galaxy.managers.workflows module +-------------------------------- .. automodule:: galaxy.managers.workflows :members: diff --git a/doc/source/lib/galaxy.metadata.rst b/doc/source/lib/galaxy.metadata.rst index a6943075f44..43f1a71c0e2 100644 --- a/doc/source/lib/galaxy.metadata.rst +++ b/doc/source/lib/galaxy.metadata.rst @@ -1,8 +1,20 @@ -galaxy\.metadata package -======================== +galaxy.metadata package +======================= .. automodule:: galaxy.metadata :members: :undoc-members: :show-inheritance: +Submodules +---------- + +galaxy.metadata.set\_metadata module +------------------------------------ + +.. automodule:: galaxy.metadata.set_metadata + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.model.dataset_collections.rst b/doc/source/lib/galaxy.model.dataset_collections.rst new file mode 100644 index 00000000000..688cd5e87e7 --- /dev/null +++ b/doc/source/lib/galaxy.model.dataset_collections.rst @@ -0,0 +1,67 @@ +galaxy.model.dataset\_collections package +========================================= + +.. automodule:: galaxy.model.dataset_collections + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.model.dataset_collections.types + +Submodules +---------- + +galaxy.model.dataset\_collections.builder module +------------------------------------------------ + +.. automodule:: galaxy.model.dataset_collections.builder + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.matching module +------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.matching + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.registry module +------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.registry + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.structure module +-------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.structure + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.subcollections module +------------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.subcollections + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.type\_description module +---------------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.type_description + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.model.dataset_collections.types.rst b/doc/source/lib/galaxy.model.dataset_collections.types.rst new file mode 100644 index 00000000000..e13a8a83e88 --- /dev/null +++ b/doc/source/lib/galaxy.model.dataset_collections.types.rst @@ -0,0 +1,28 @@ +galaxy.model.dataset\_collections.types package +=============================================== + +.. automodule:: galaxy.model.dataset_collections.types + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.dataset\_collections.types.list module +--------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.types.list + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.dataset\_collections.types.paired module +----------------------------------------------------- + +.. automodule:: galaxy.model.dataset_collections.types.paired + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.model.migrate.rst b/doc/source/lib/galaxy.model.migrate.rst index 030077897a5..2d56bcc2878 100644 --- a/doc/source/lib/galaxy.model.migrate.rst +++ b/doc/source/lib/galaxy.model.migrate.rst @@ -1,16 +1,23 @@ -galaxy\.model\.migrate package -============================== +galaxy.model.migrate package +============================ .. automodule:: galaxy.model.migrate :members: :undoc-members: :show-inheritance: +Subpackages +----------- + +.. toctree:: + + galaxy.model.migrate.versions + Submodules ---------- -galaxy\.model\.migrate\.check module ------------------------------------- +galaxy.model.migrate.check module +--------------------------------- .. automodule:: galaxy.model.migrate.check :members: diff --git a/doc/source/lib/galaxy.model.migrate.versions.rst b/doc/source/lib/galaxy.model.migrate.versions.rst new file mode 100644 index 00000000000..e920777b10f --- /dev/null +++ b/doc/source/lib/galaxy.model.migrate.versions.rst @@ -0,0 +1,1252 @@ +galaxy.model.migrate.versions package +===================================== + +.. automodule:: galaxy.model.migrate.versions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.migrate.versions.0001\_initial\_tables module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0001_initial_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0002\_metadata\_file\_table module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0002_metadata_file_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0003\_security\_and\_libraries module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0003_security_and_libraries + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0004\_indexes\_and\_defaults module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0004_indexes_and_defaults + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0005\_cleanup\_datasets\_fix module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0005_cleanup_datasets_fix + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0006\_change\_qual\_datatype module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0006_change_qual_datatype + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0007\_sharing\_histories module +------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0007_sharing_histories + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0008\_galaxy\_forms module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0008_galaxy_forms + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0009\_request\_table module +--------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0009_request_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0010\_hda\_display\_at\_authz\_table module +------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0010_hda_display_at_authz_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0011\_v0010\_mysql\_index\_fix module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0011_v0010_mysql_index_fix + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0012\_user\_address module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0012_user_address + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0013\_change\_lib\_item\_templates\_to\_forms module +---------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0013_change_lib_item_templates_to_forms + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0014\_pages module +------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0014_pages + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0015\_tagging module +-------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0015_tagging + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0016\_v0015\_mysql\_index\_fix module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0016_v0015_mysql_index_fix + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0017\_library\_item\_indexes module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0017_library_item_indexes + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0018\_ordered\_tags\_and\_page\_tags module +------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0018_ordered_tags_and_page_tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0019\_request\_library\_folder module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0019_request_library_folder + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0020\_library\_upload\_job module +--------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0020_library_upload_job + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0021\_user\_prefs module +------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0021_user_prefs + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0022\_visualization\_tables module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0022_visualization_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0023\_page\_published\_and\_deleted\_columns module +--------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0023_page_published_and_deleted_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0024\_page\_slug\_unique\_constraint module +------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0024_page_slug_unique_constraint + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0025\_user\_info module +----------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0025_user_info + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0026\_cloud\_tables module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0026_cloud_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0027\_request\_events module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0027_request_events + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0028\_external\_metadata\_file\_override module +----------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0028_external_metadata_file_override + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0029\_user\_actions module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0029_user_actions + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0030\_history\_slug\_column module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0030_history_slug_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0031\_community\_and\_workflow\_tags module +------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0031_community_and_workflow_tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0032\_stored\_workflow\_slug\_column module +------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0032_stored_workflow_slug_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0033\_published\_cols\_for\_histories\_and\_workflows module +------------------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0033_published_cols_for_histories_and_workflows + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0034\_page\_user\_share\_association module +------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0034_page_user_share_association + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0035\_item\_annotations\_and\_workflow\_step\_tags module +--------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0035_item_annotations_and_workflow_step_tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0036\_add\_deleted\_column\_to\_library\_template\_assoc\_tables module +----------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0036_add_deleted_column_to_library_template_assoc_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0037\_samples\_library module +----------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0037_samples_library + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0038\_add\_inheritable\_column\_to\_library\_template\_assoc\_tables module +--------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0038_add_inheritable_column_to_library_template_assoc_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0039\_add\_synopsis\_column\_to\_library\_table module +------------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0039_add_synopsis_column_to_library_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0040\_page\_annotations module +------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0040_page_annotations + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0041\_workflow\_invocation module +--------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0041_workflow_invocation + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0042\_workflow\_invocation\_fix module +-------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0042_workflow_invocation_fix + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0043\_visualization\_sharing\_tagging\_annotating module +-------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0043_visualization_sharing_tagging_annotating + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0044\_add\_notify\_column\_to\_request\_table module +---------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0044_add_notify_column_to_request_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0045\_request\_type\_permissions\_table module +---------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0045_request_type_permissions_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0046\_post\_job\_actions module +------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0046_post_job_actions + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0047\_job\_table\_user\_id\_column module +----------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0047_job_table_user_id_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0048\_dataset\_instance\_state\_column module +--------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0048_dataset_instance_state_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0049\_api\_keys\_table module +----------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0049_api_keys_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0050\_drop\_cloud\_tables module +-------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0050_drop_cloud_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0051\_imported\_col\_for\_jobs\_table module +-------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0051_imported_col_for_jobs_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0052\_sample\_dataset\_table module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0052_sample_dataset_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0053\_item\_ratings module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0053_item_ratings + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0054\_visualization\_dbkey module +--------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0054_visualization_dbkey + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0055\_add\_pja\_assoc\_for\_jobs module +--------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0055_add_pja_assoc_for_jobs + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0056\_workflow\_outputs module +------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0056_workflow_outputs + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0057\_request\_notify module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0057_request_notify + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0058\_history\_import\_export module +------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0058_history_import_export + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0059\_sample\_dataset\_file\_path module +---------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0059_sample_dataset_file_path + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0060\_history\_archive\_import module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0060_history_archive_import + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0061\_tasks module +------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0061_tasks + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0062\_user\_openid\_table module +-------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0062_user_openid_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0063\_sequencer\_table module +----------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0063_sequencer_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0064\_add\_run\_and\_sample\_run\_association\_tables module +------------------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0064_add_run_and_sample_run_association_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0065\_add\_name\_to\_form\_fields\_and\_values module +----------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0065_add_name_to_form_fields_and_values + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0066\_deferred\_job\_and\_transfer\_job\_tables module +------------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0066_deferred_job_and_transfer_job_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0067\_populate\_sequencer\_table module +--------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0067_populate_sequencer_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0068\_rename\_sequencer\_to\_external\_services module +------------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0068_rename_sequencer_to_external_services + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0069\_rename\_sequencer\_form\_type module +------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0069_rename_sequencer_form_type + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0070\_add\_info\_column\_to\_deferred\_job\_table module +-------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0070_add_info_column_to_deferred_job_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0071\_add\_history\_and\_workflow\_to\_sample module +---------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0071_add_history_and_workflow_to_sample + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0072\_add\_pid\_and\_socket\_columns\_to\_transfer\_job\_table module +--------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0072_add_pid_and_socket_columns_to_transfer_job_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0073\_add\_ldda\_to\_implicit\_conversion\_table module +------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0073_add_ldda_to_implicit_conversion_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0074\_add\_purged\_column\_to\_library\_dataset\_table module +------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0074_add_purged_column_to_library_dataset_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0075\_add\_subindex\_column\_to\_run\_table module +-------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0075_add_subindex_column_to_run_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0076\_fix\_form\_values\_data\_corruption module +------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0076_fix_form_values_data_corruption + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0077\_create\_tool\_tag\_association\_table module +-------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0077_create_tool_tag_association_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0078\_add\_columns\_for\_disk\_usage\_accounting module +------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0078_add_columns_for_disk_usage_accounting + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0079\_input\_library\_to\_job\_table module +------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0079_input_library_to_job_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0080\_quota\_tables module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0080_quota_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0081\_add\_tool\_version\_to\_hda\_ldda module +---------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0081_add_tool_version_to_hda_ldda + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0082\_add\_tool\_shed\_repository\_table module +----------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0082_add_tool_shed_repository_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0083\_add\_prepare\_files\_to\_task module +------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0083_add_prepare_files_to_task + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0084\_add\_ldda\_id\_to\_implicit\_conversion\_table module +----------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0084_add_ldda_id_to_implicit_conversion_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0085\_add\_task\_info module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0085_add_task_info + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0086\_add\_tool\_shed\_repository\_table\_columns module +-------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0086_add_tool_shed_repository_table_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0087\_tool\_id\_guid\_map\_table module +--------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0087_tool_id_guid_map_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0088\_add\_installed\_changeset\_revison\_column module +------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0088_add_installed_changeset_revison_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0089\_add\_object\_store\_id\_columns module +-------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0089_add_object_store_id_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0090\_add\_tool\_shed\_repository\_table\_columns module +-------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0090_add_tool_shed_repository_table_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0091\_add\_tool\_version\_tables module +--------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0091_add_tool_version_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0092\_add\_migrate\_tools\_table module +--------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0092_add_migrate_tools_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0093\_add\_job\_params\_col module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0093_add_job_params_col + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0094\_add\_job\_handler\_col module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0094_add_job_handler_col + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0095\_hda\_subsets module +------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0095_hda_subsets + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0096\_openid\_provider module +----------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0096_openid_provider + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0097\_add\_ctx\_rev\_column module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0097_add_ctx_rev_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0098\_genome\_index\_tool\_data\_table module +--------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0098_genome_index_tool_data_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0099\_add\_tool\_dependency\_table module +----------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0099_add_tool_dependency_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0100\_alter\_tool\_dependency\_table\_version\_column module +------------------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0100_alter_tool_dependency_table_version_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0101\_drop\_installed\_changeset\_revision\_column module +--------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0101_drop_installed_changeset_revision_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0102\_add\_tool\_dependency\_status\_columns module +--------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0102_add_tool_dependency_status_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0103\_add\_tool\_shed\_repository\_status\_columns module +--------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0103_add_tool_shed_repository_status_columns + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0104\_update\_genome\_downloader\_job\_parameters module +-------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0104_update_genome_downloader_job_parameters + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0105\_add\_cleanup\_event\_table module +--------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0105_add_cleanup_event_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0106\_add\_missing\_indexes module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0106_add_missing_indexes + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0107\_add\_exit\_code\_to\_job\_and\_task module +------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0107_add_exit_code_to_job_and_task + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0108\_add\_extended\_metadata module +------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0108_add_extended_metadata + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0109\_add\_repository\_dependency\_tables module +------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0109_add_repository_dependency_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0110\_add\_dataset\_uuid module +------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0110_add_dataset_uuid + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0111\_add\_job\_destinations module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0111_add_job_destinations + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0112\_add\_data\_manager\_history\_association\_and\_data\_manager\_job\_association\_tables module +--------------------------------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0112_add_data_manager_history_association_and_data_manager_job_association_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0113\_update\_migrate\_tools\_table module +------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0113_update_migrate_tools_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0114\_update\_migrate\_tools\_table\_again module +------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0114_update_migrate_tools_table_again + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0115\_longer\_user\_password\_field module +------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0115_longer_user_password_field + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0116\_drop\_update\_available\_col\_add\_tool\_shed\_status\_col module +----------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0116_drop_update_available_col_add_tool_shed_status_col + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0117\_add\_user\_activation module +---------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0117_add_user_activation + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0118\_add\_hda\_extended\_metadata module +----------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0118_add_hda_extended_metadata + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0119\_job\_metrics module +------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0119_job_metrics + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0120\_dataset\_collections module +--------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0120_dataset_collections + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0121\_workflow\_uuids module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0121_workflow_uuids + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0122\_grow\_mysql\_blobs module +------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0122_grow_mysql_blobs + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0123\_add\_workflow\_request\_tables module +------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0123_add_workflow_request_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0124\_job\_state\_history module +-------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0124_job_state_history + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0125\_workflow\_step\_tracking module +------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0125_workflow_step_tracking + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0126\_password\_reset module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0126_password_reset + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0127\_output\_collection\_adjustments module +-------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0127_output_collection_adjustments + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0128\_session\_timeout module +----------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0128_session_timeout + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0129\_job\_external\_output\_metadata\_validity module +------------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0129_job_external_output_metadata_validity + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0130\_change\_pref\_datatype module +----------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0130_change_pref_datatype + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0131\_subworkflow\_and\_input\_parameter\_modules module +-------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0131_subworkflow_and_input_parameter_modules + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0132\_add\_lastpasswordchange\_to\_user module +---------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0132_add_lastpasswordchange_to_user + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0133\_add\_dependency\_column\_to\_job module +--------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0133_add_dependency_column_to_job + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0134\_hda\_set\_deleted\_if\_purged module +------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0134_hda_set_deleted_if_purged + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0135\_add\_library\_tags module +------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0135_add_library_tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0136\_collection\_and\_workflow\_state module +--------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0136_collection_and_workflow_state + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0137\_add\_copied\_from\_job\_id\_column module +----------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0137_add_copied_from_job_id_column + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0138\_add\_hda\_version module +------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0138_add_hda_version + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0139\_add\_history\_dataset\_association\_history\_table module +--------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0139_add_history_dataset_association_history_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0140\_add\_dataset\_version\_to\_job\_to\_input\_dataset\_association\_table module +----------------------------------------------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0140_add_dataset_version_to_job_to_input_dataset_association_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0141\_add\_oidc\_tables module +------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0141_add_oidc_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0142\_change\_numeric\_metric\_precision module +----------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0142_change_numeric_metric_precision + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0143\_add\_cloudauthz\_tables module +------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0143_add_cloudauthz_tables + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0144\_add\_cleanup\_event\_user\_table module +--------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0144_add_cleanup_event_user_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0145\_add\_workflow\_step\_input module +--------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0145_add_workflow_step_input + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0146\_workflow\_paths module +---------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0146_workflow_paths + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0147\_job\_messages module +-------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0147_job_messages + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0148\_add\_checksum\_table module +--------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0148_add_checksum_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0149\_dynamic\_tools module +--------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0149_dynamic_tools + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0150\_add\_create\_time\_field\_for\_cloudauthz module +------------------------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0150_add_create_time_field_for_cloudauthz + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0151\_add\_worker\_process module +--------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0151_add_worker_process + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0152\_add\_metadata\_file\_uuid module +-------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0152_add_metadata_file_uuid + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0153\_add\_custos\_authnz\_token\_table module +---------------------------------------------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.0153_add_custos_authnz_token_table + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.0154\_created\_from\_basename module +------------------------------------------------------------------ + +.. automodule:: galaxy.model.migrate.versions.0154_created_from_basename + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.migrate.versions.util module +----------------------------------------- + +.. automodule:: galaxy.model.migrate.versions.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.model.orm.rst b/doc/source/lib/galaxy.model.orm.rst index 14a7389711f..c42fe0be8a6 100644 --- a/doc/source/lib/galaxy.model.orm.rst +++ b/doc/source/lib/galaxy.model.orm.rst @@ -1,5 +1,5 @@ -galaxy\.model\.orm package -========================== +galaxy.model.orm package +======================== .. automodule:: galaxy.model.orm :members: @@ -9,32 +9,32 @@ galaxy\.model\.orm package Submodules ---------- -galaxy\.model\.orm\.engine\_factory module ------------------------------------------- +galaxy.model.orm.engine\_factory module +--------------------------------------- .. automodule:: galaxy.model.orm.engine_factory :members: :undoc-members: :show-inheritance: -galaxy\.model\.orm\.logging\_connection\_proxy module ------------------------------------------------------ +galaxy.model.orm.logging\_connection\_proxy module +-------------------------------------------------- .. automodule:: galaxy.model.orm.logging_connection_proxy :members: :undoc-members: :show-inheritance: -galaxy\.model\.orm\.now module ------------------------------- +galaxy.model.orm.now module +--------------------------- .. automodule:: galaxy.model.orm.now :members: :undoc-members: :show-inheritance: -galaxy\.model\.orm\.scripts module ----------------------------------- +galaxy.model.orm.scripts module +------------------------------- .. automodule:: galaxy.model.orm.scripts :members: diff --git a/doc/source/lib/galaxy.model.rst b/doc/source/lib/galaxy.model.rst index 7345edf3cfb..828f4226020 100644 --- a/doc/source/lib/galaxy.model.rst +++ b/doc/source/lib/galaxy.model.rst @@ -1,5 +1,5 @@ -galaxy\.model package -===================== +galaxy.model package +==================== .. automodule:: galaxy.model :members: @@ -11,63 +11,97 @@ Subpackages .. toctree:: + galaxy.model.dataset_collections galaxy.model.migrate galaxy.model.orm + galaxy.model.store galaxy.model.tool_shed_install Submodules ---------- -galaxy\.model\.base module --------------------------- +galaxy.model.base module +------------------------ .. automodule:: galaxy.model.base :members: :undoc-members: :show-inheritance: -galaxy\.model\.custom\_types module ------------------------------------ +galaxy.model.custom\_types module +--------------------------------- .. automodule:: galaxy.model.custom_types :members: :undoc-members: :show-inheritance: -galaxy\.model\.item\_attrs module ---------------------------------- +galaxy.model.database\_heartbeat module +--------------------------------------- + +.. automodule:: galaxy.model.database_heartbeat + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.item\_attrs module +------------------------------- .. automodule:: galaxy.model.item_attrs :members: :undoc-members: :show-inheritance: -galaxy\.model\.mapping module ------------------------------ +galaxy.model.mapping module +--------------------------- .. automodule:: galaxy.model.mapping :members: :undoc-members: :show-inheritance: -galaxy\.model\.metadata module ------------------------------- +galaxy.model.metadata module +---------------------------- .. automodule:: galaxy.model.metadata :members: :undoc-members: :show-inheritance: -galaxy\.model\.search module ----------------------------- +galaxy.model.none\_like module +------------------------------ + +.. automodule:: galaxy.model.none_like + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.search module +-------------------------- .. automodule:: galaxy.model.search :members: :undoc-members: :show-inheritance: -galaxy\.model\.util module --------------------------- +galaxy.model.security module +---------------------------- + +.. automodule:: galaxy.model.security + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.tags module +------------------------ + +.. automodule:: galaxy.model.tags + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.util module +------------------------ .. automodule:: galaxy.model.util :members: diff --git a/doc/source/lib/galaxy.model.store.rst b/doc/source/lib/galaxy.model.store.rst new file mode 100644 index 00000000000..1ab8db02595 --- /dev/null +++ b/doc/source/lib/galaxy.model.store.rst @@ -0,0 +1,28 @@ +galaxy.model.store package +========================== + +.. automodule:: galaxy.model.store + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.model.store.build\_objects module +---------------------------------------- + +.. automodule:: galaxy.model.store.build_objects + :members: + :undoc-members: + :show-inheritance: + +galaxy.model.store.discover module +---------------------------------- + +.. automodule:: galaxy.model.store.discover + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst index b437c0167ff..fdd56b65033 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.migrate.rst @@ -1,5 +1,5 @@ -galaxy\.model\.tool\_shed\_install\.migrate package -=================================================== +galaxy.model.tool\_shed\_install.migrate package +================================================ .. automodule:: galaxy.model.tool_shed_install.migrate :members: @@ -9,8 +9,8 @@ galaxy\.model\.tool\_shed\_install\.migrate package Submodules ---------- -galaxy\.model\.tool\_shed\_install\.migrate\.check module ---------------------------------------------------------- +galaxy.model.tool\_shed\_install.migrate.check module +----------------------------------------------------- .. automodule:: galaxy.model.tool_shed_install.migrate.check :members: diff --git a/doc/source/lib/galaxy.model.tool_shed_install.rst b/doc/source/lib/galaxy.model.tool_shed_install.rst index 5346e7b2db8..d074ead1e89 100644 --- a/doc/source/lib/galaxy.model.tool_shed_install.rst +++ b/doc/source/lib/galaxy.model.tool_shed_install.rst @@ -1,5 +1,5 @@ -galaxy\.model\.tool\_shed\_install package -========================================== +galaxy.model.tool\_shed\_install package +======================================== .. automodule:: galaxy.model.tool_shed_install :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -galaxy\.model\.tool\_shed\_install\.mapping module --------------------------------------------------- +galaxy.model.tool\_shed\_install.mapping module +----------------------------------------------- .. automodule:: galaxy.model.tool_shed_install.mapping :members: diff --git a/doc/source/lib/galaxy.objectstore.rst b/doc/source/lib/galaxy.objectstore.rst index 7367d42410c..62acaf29546 100644 --- a/doc/source/lib/galaxy.objectstore.rst +++ b/doc/source/lib/galaxy.objectstore.rst @@ -1,5 +1,5 @@ -galaxy\.objectstore package -=========================== +galaxy.objectstore package +========================== .. automodule:: galaxy.objectstore :members: @@ -9,56 +9,56 @@ galaxy\.objectstore package Submodules ---------- -galaxy\.objectstore\.azure\_blob module ---------------------------------------- +galaxy.objectstore.azure\_blob module +------------------------------------- .. automodule:: galaxy.objectstore.azure_blob :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.cloud module ---------------------------------- +galaxy.objectstore.cloud module +------------------------------- .. automodule:: galaxy.objectstore.cloud :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.pithos module ----------------------------------- +galaxy.objectstore.pithos module +-------------------------------- .. automodule:: galaxy.objectstore.pithos :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.pulsar module ----------------------------------- +galaxy.objectstore.pulsar module +-------------------------------- .. automodule:: galaxy.objectstore.pulsar :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.rods module --------------------------------- +galaxy.objectstore.rods module +------------------------------ .. automodule:: galaxy.objectstore.rods :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.s3 module ------------------------------- +galaxy.objectstore.s3 module +---------------------------- .. automodule:: galaxy.objectstore.s3 :members: :undoc-members: :show-inheritance: -galaxy\.objectstore\.s3\_multipart\_upload module -------------------------------------------------- +galaxy.objectstore.s3\_multipart\_upload module +----------------------------------------------- .. automodule:: galaxy.objectstore.s3_multipart_upload :members: diff --git a/doc/source/lib/galaxy.openid.rst b/doc/source/lib/galaxy.openid.rst new file mode 100644 index 00000000000..90031e56aad --- /dev/null +++ b/doc/source/lib/galaxy.openid.rst @@ -0,0 +1,28 @@ +galaxy.openid package +===================== + +.. automodule:: galaxy.openid + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.openid.openid\_manager module +------------------------------------ + +.. automodule:: galaxy.openid.openid_manager + :members: + :undoc-members: + :show-inheritance: + +galaxy.openid.providers module +------------------------------ + +.. automodule:: galaxy.openid.providers + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.quota.rst b/doc/source/lib/galaxy.quota.rst index f04cf0b2872..36802033ce1 100644 --- a/doc/source/lib/galaxy.quota.rst +++ b/doc/source/lib/galaxy.quota.rst @@ -1,5 +1,5 @@ -galaxy\.quota package -===================== +galaxy.quota package +==================== .. automodule:: galaxy.quota :members: diff --git a/doc/source/lib/galaxy.rst b/doc/source/lib/galaxy.rst index b1160511c4b..321bfcfcd7c 100644 --- a/doc/source/lib/galaxy.rst +++ b/doc/source/lib/galaxy.rst @@ -15,24 +15,28 @@ Subpackages galaxy.auth galaxy.authnz galaxy.containers - galaxy.dataset_collections galaxy.datatypes galaxy.dependencies galaxy.eggs galaxy.exceptions galaxy.forms + galaxy.job_execution + galaxy.job_metrics galaxy.jobs galaxy.managers galaxy.metadata galaxy.model galaxy.objectstore + galaxy.openid galaxy.quota galaxy.security + galaxy.tool_util galaxy.tools galaxy.tours galaxy.util galaxy.visualization galaxy.web + galaxy.web_stack galaxy.webapps galaxy.webhooks galaxy.work @@ -41,48 +45,48 @@ Subpackages Submodules ---------- -galaxy\.app module ------------------- +galaxy.app module +----------------- .. automodule:: galaxy.app :members: :undoc-members: :show-inheritance: -galaxy\.config module ---------------------- +galaxy.config module +-------------------- .. automodule:: galaxy.config :members: :undoc-members: :show-inheritance: -galaxy\.main module -------------------- +galaxy.main module +------------------ .. automodule:: galaxy.main :members: :undoc-members: :show-inheritance: -galaxy\.queue\_worker module ----------------------------- +galaxy.queue\_worker module +--------------------------- .. automodule:: galaxy.queue_worker :members: :undoc-members: :show-inheritance: -galaxy\.queues module ---------------------- +galaxy.queues module +-------------------- .. automodule:: galaxy.queues :members: :undoc-members: :show-inheritance: -galaxy\.version module ----------------------- +galaxy.version module +--------------------- .. automodule:: galaxy.version :members: diff --git a/doc/source/lib/galaxy.security.rst b/doc/source/lib/galaxy.security.rst index b5c5757506f..351ecf61547 100644 --- a/doc/source/lib/galaxy.security.rst +++ b/doc/source/lib/galaxy.security.rst @@ -1,5 +1,5 @@ -galaxy\.security package -======================== +galaxy.security package +======================= .. automodule:: galaxy.security :members: @@ -9,16 +9,24 @@ galaxy\.security package Submodules ---------- -galaxy\.security\.passwords module ----------------------------------- +galaxy.security.idencoding module +--------------------------------- + +.. automodule:: galaxy.security.idencoding + :members: + :undoc-members: + :show-inheritance: + +galaxy.security.passwords module +-------------------------------- .. automodule:: galaxy.security.passwords :members: :undoc-members: :show-inheritance: -galaxy\.security\.validate\_user\_input module ----------------------------------------------- +galaxy.security.validate\_user\_input module +-------------------------------------------- .. automodule:: galaxy.security.validate_user_input :members: diff --git a/doc/source/lib/galaxy.tool_util.cwl.rst b/doc/source/lib/galaxy.tool_util.cwl.rst new file mode 100644 index 00000000000..5049af0a7af --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.cwl.rst @@ -0,0 +1,60 @@ +galaxy.tool\_util.cwl package +============================= + +.. automodule:: galaxy.tool_util.cwl + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.cwl.cwltool\_deps module +------------------------------------------ + +.. automodule:: galaxy.tool_util.cwl.cwltool_deps + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.parser module +----------------------------------- + +.. automodule:: galaxy.tool_util.cwl.parser + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.representation module +------------------------------------------- + +.. automodule:: galaxy.tool_util.cwl.representation + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.runtime\_actions module +--------------------------------------------- + +.. automodule:: galaxy.tool_util.cwl.runtime_actions + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.schema module +----------------------------------- + +.. automodule:: galaxy.tool_util.cwl.schema + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.cwl.util module +--------------------------------- + +.. automodule:: galaxy.tool_util.cwl.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.deps.container_resolvers.rst b/doc/source/lib/galaxy.tool_util.deps.container_resolvers.rst new file mode 100644 index 00000000000..3866cb37a3b --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.deps.container_resolvers.rst @@ -0,0 +1,28 @@ +galaxy.tool\_util.deps.container\_resolvers package +=================================================== + +.. automodule:: galaxy.tool_util.deps.container_resolvers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.deps.container\_resolvers.explicit module +----------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.container_resolvers.explicit + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.container\_resolvers.mulled module +--------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.container_resolvers.mulled + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.deps.mulled.rst b/doc/source/lib/galaxy.tool_util.deps.mulled.rst new file mode 100644 index 00000000000..2b1aff39940 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.deps.mulled.rst @@ -0,0 +1,60 @@ +galaxy.tool\_util.deps.mulled package +===================================== + +.. automodule:: galaxy.tool_util.deps.mulled + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.deps.mulled.mulled\_build module +-------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.mulled_build + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.mulled.mulled\_build\_channel module +----------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.mulled_build_channel + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.mulled.mulled\_build\_files module +--------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.mulled_build_files + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.mulled.mulled\_build\_tool module +-------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.mulled_build_tool + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.mulled.mulled\_search module +--------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.mulled_search + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.mulled.util module +----------------------------------------- + +.. automodule:: galaxy.tool_util.deps.mulled.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.deps.resolvers.rst b/doc/source/lib/galaxy.tool_util.deps.resolvers.rst new file mode 100644 index 00000000000..06be31af971 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.deps.resolvers.rst @@ -0,0 +1,84 @@ +galaxy.tool\_util.deps.resolvers package +======================================== + +.. automodule:: galaxy.tool_util.deps.resolvers + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.deps.resolvers.brewed\_tool\_shed\_packages module +-------------------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.brewed_tool_shed_packages + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.conda module +--------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.conda + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.galaxy\_packages module +-------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.galaxy_packages + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.homebrew module +------------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.resolvers.homebrew + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.lmod module +-------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.lmod + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.modules module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.modules + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.resolver\_mixins module +-------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.resolver_mixins + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.tool\_shed\_packages module +------------------------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.resolvers.tool_shed_packages + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.resolvers.unlinked\_tool\_shed\_packages module +---------------------------------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.resolvers.unlinked_tool_shed_packages + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.deps.rst b/doc/source/lib/galaxy.tool_util.deps.rst new file mode 100644 index 00000000000..9a1aaf79da2 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.deps.rst @@ -0,0 +1,133 @@ +galaxy.tool\_util.deps package +============================== + +.. automodule:: galaxy.tool_util.deps + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tool_util.deps.container_resolvers + galaxy.tool_util.deps.mulled + galaxy.tool_util.deps.resolvers + +Submodules +---------- + +galaxy.tool\_util.deps.brew\_exts module +---------------------------------------- + +.. automodule:: galaxy.tool_util.deps.brew_exts + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.brew\_util module +---------------------------------------- + +.. automodule:: galaxy.tool_util.deps.brew_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.commands module +-------------------------------------- + +.. automodule:: galaxy.tool_util.deps.commands + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.conda\_compat module +------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.conda_compat + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.conda\_util module +----------------------------------------- + +.. automodule:: galaxy.tool_util.deps.conda_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.container\_classes module +------------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.container_classes + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.containers module +---------------------------------------- + +.. automodule:: galaxy.tool_util.deps.containers + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.dependencies module +------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.dependencies + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.docker\_util module +------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.docker_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.dockerfiles module +----------------------------------------- + +.. automodule:: galaxy.tool_util.deps.dockerfiles + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.installable module +----------------------------------------- + +.. automodule:: galaxy.tool_util.deps.installable + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.requirements module +------------------------------------------ + +.. automodule:: galaxy.tool_util.deps.requirements + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.singularity\_util module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.deps.singularity_util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.deps.views module +----------------------------------- + +.. automodule:: galaxy.tool_util.deps.views + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.locations.rst b/doc/source/lib/galaxy.tool_util.locations.rst new file mode 100644 index 00000000000..12de3f42acf --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.locations.rst @@ -0,0 +1,36 @@ +galaxy.tool\_util.locations package +=================================== + +.. automodule:: galaxy.tool_util.locations + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.locations.dockstore module +-------------------------------------------- + +.. automodule:: galaxy.tool_util.locations.dockstore + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.locations.file module +--------------------------------------- + +.. automodule:: galaxy.tool_util.locations.file + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.locations.http module +--------------------------------------- + +.. automodule:: galaxy.tool_util.locations.http + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.parser.rst b/doc/source/lib/galaxy.tool_util.parser.rst new file mode 100644 index 00000000000..66a201433be --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.parser.rst @@ -0,0 +1,92 @@ +galaxy.tool\_util.parser package +================================ + +.. automodule:: galaxy.tool_util.parser + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tool\_util.parser.cwl module +----------------------------------- + +.. automodule:: galaxy.tool_util.parser.cwl + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.error\_level module +-------------------------------------------- + +.. automodule:: galaxy.tool_util.parser.error_level + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.factory module +--------------------------------------- + +.. automodule:: galaxy.tool_util.parser.factory + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.interface module +----------------------------------------- + +.. automodule:: galaxy.tool_util.parser.interface + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.output\_actions module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.parser.output_actions + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.output\_collection\_def module +------------------------------------------------------- + +.. automodule:: galaxy.tool_util.parser.output_collection_def + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.output\_objects module +----------------------------------------------- + +.. automodule:: galaxy.tool_util.parser.output_objects + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.util module +------------------------------------ + +.. automodule:: galaxy.tool_util.parser.util + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.xml module +----------------------------------- + +.. automodule:: galaxy.tool_util.parser.xml + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.parser.yaml module +------------------------------------ + +.. automodule:: galaxy.tool_util.parser.yaml + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tool_util.rst b/doc/source/lib/galaxy.tool_util.rst new file mode 100644 index 00000000000..02818574534 --- /dev/null +++ b/doc/source/lib/galaxy.tool_util.rst @@ -0,0 +1,62 @@ +galaxy.tool\_util package +========================= + +.. automodule:: galaxy.tool_util + :members: + :undoc-members: + :show-inheritance: + +Subpackages +----------- + +.. toctree:: + + galaxy.tool_util.cwl + galaxy.tool_util.deps + galaxy.tool_util.locations + galaxy.tool_util.parser + +Submodules +---------- + +galaxy.tool\_util.fetcher module +-------------------------------- + +.. automodule:: galaxy.tool_util.fetcher + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.loader module +------------------------------- + +.. automodule:: galaxy.tool_util.loader + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.loader\_directory module +------------------------------------------ + +.. automodule:: galaxy.tool_util.loader_directory + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.output\_checker module +---------------------------------------- + +.. automodule:: galaxy.tool_util.output_checker + :members: + :undoc-members: + :show-inheritance: + +galaxy.tool\_util.provided\_metadata module +------------------------------------------- + +.. automodule:: galaxy.tool_util.provided_metadata + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.actions.rst b/doc/source/lib/galaxy.tools.actions.rst index 4a706194a7e..1ef158180cd 100644 --- a/doc/source/lib/galaxy.tools.actions.rst +++ b/doc/source/lib/galaxy.tools.actions.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.actions package -============================== +galaxy.tools.actions package +============================ .. automodule:: galaxy.tools.actions :members: @@ -9,56 +9,56 @@ galaxy\.tools\.actions package Submodules ---------- -galaxy\.tools\.actions\.data\_manager module --------------------------------------------- +galaxy.tools.actions.data\_manager module +----------------------------------------- .. automodule:: galaxy.tools.actions.data_manager :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.data\_source module -------------------------------------------- +galaxy.tools.actions.data\_source module +---------------------------------------- .. automodule:: galaxy.tools.actions.data_source :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.history\_imp\_exp module ------------------------------------------------- +galaxy.tools.actions.history\_imp\_exp module +--------------------------------------------- .. automodule:: galaxy.tools.actions.history_imp_exp :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.metadata module ---------------------------------------- +galaxy.tools.actions.metadata module +------------------------------------ .. automodule:: galaxy.tools.actions.metadata :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.model\_operations module ------------------------------------------------- +galaxy.tools.actions.model\_operations module +--------------------------------------------- .. automodule:: galaxy.tools.actions.model_operations :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.upload module -------------------------------------- +galaxy.tools.actions.upload module +---------------------------------- .. automodule:: galaxy.tools.actions.upload :members: :undoc-members: :show-inheritance: -galaxy\.tools\.actions\.upload\_common module ---------------------------------------------- +galaxy.tools.actions.upload\_common module +------------------------------------------ .. automodule:: galaxy.tools.actions.upload_common :members: diff --git a/doc/source/lib/galaxy.tools.cwl.rst b/doc/source/lib/galaxy.tools.cwl.rst deleted file mode 100644 index 9b0875eb8fd..00000000000 --- a/doc/source/lib/galaxy.tools.cwl.rst +++ /dev/null @@ -1,60 +0,0 @@ -galaxy\.tools\.cwl package -========================== - -.. automodule:: galaxy.tools.cwl - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.cwl\.cwltool\_deps module ----------------------------------------- - -.. automodule:: galaxy.tools.cwl.cwltool_deps - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.parser module ---------------------------------- - -.. automodule:: galaxy.tools.cwl.parser - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.representation module ------------------------------------------ - -.. automodule:: galaxy.tools.cwl.representation - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.runtime\_actions module -------------------------------------------- - -.. automodule:: galaxy.tools.cwl.runtime_actions - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.schema module ---------------------------------- - -.. automodule:: galaxy.tools.cwl.schema - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.cwl\.util module -------------------------------- - -.. automodule:: galaxy.tools.cwl.util - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.data.rst b/doc/source/lib/galaxy.tools.data.rst index 6c2c91c2e65..4435ba549f8 100644 --- a/doc/source/lib/galaxy.tools.data.rst +++ b/doc/source/lib/galaxy.tools.data.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.data package -=========================== +galaxy.tools.data package +========================= .. automodule:: galaxy.tools.data :members: diff --git a/doc/source/lib/galaxy.tools.data_manager.rst b/doc/source/lib/galaxy.tools.data_manager.rst index c80f07b3db3..53e9b630fb9 100644 --- a/doc/source/lib/galaxy.tools.data_manager.rst +++ b/doc/source/lib/galaxy.tools.data_manager.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.data\_manager package -==================================== +galaxy.tools.data\_manager package +================================== .. automodule:: galaxy.tools.data_manager :members: @@ -9,8 +9,8 @@ galaxy\.tools\.data\_manager package Submodules ---------- -galaxy\.tools\.data\_manager\.manager module --------------------------------------------- +galaxy.tools.data\_manager.manager module +----------------------------------------- .. automodule:: galaxy.tools.data_manager.manager :members: diff --git a/doc/source/lib/galaxy.tools.deps.container_resolvers.rst b/doc/source/lib/galaxy.tools.deps.container_resolvers.rst deleted file mode 100644 index 1c36a12f77e..00000000000 --- a/doc/source/lib/galaxy.tools.deps.container_resolvers.rst +++ /dev/null @@ -1,28 +0,0 @@ -galaxy\.tools\.deps\.container\_resolvers package -================================================= - -.. automodule:: galaxy.tools.deps.container_resolvers - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.deps\.container\_resolvers\.explicit module ----------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.container_resolvers.explicit - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.container\_resolvers\.mulled module --------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.container_resolvers.mulled - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.deps.mulled.rst b/doc/source/lib/galaxy.tools.deps.mulled.rst deleted file mode 100644 index 9fc6df39628..00000000000 --- a/doc/source/lib/galaxy.tools.deps.mulled.rst +++ /dev/null @@ -1,60 +0,0 @@ -galaxy\.tools\.deps\.mulled package -=================================== - -.. automodule:: galaxy.tools.deps.mulled - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.deps\.mulled\.mulled\_build module -------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_build - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.mulled\_build\_channel module ----------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_build_channel - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.mulled\_build\_files module --------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_build_files - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.mulled\_build\_tool module -------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_build_tool - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.mulled\_search module --------------------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.mulled_search - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.mulled\.util module ----------------------------------------- - -.. automodule:: galaxy.tools.deps.mulled.util - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.deps.resolvers.rst b/doc/source/lib/galaxy.tools.deps.resolvers.rst deleted file mode 100644 index 2c64033be73..00000000000 --- a/doc/source/lib/galaxy.tools.deps.resolvers.rst +++ /dev/null @@ -1,84 +0,0 @@ -galaxy\.tools\.deps\.resolvers package -====================================== - -.. automodule:: galaxy.tools.deps.resolvers - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.deps\.resolvers\.brewed\_tool\_shed\_packages module -------------------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.brewed_tool_shed_packages - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.conda module --------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.conda - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.galaxy\_packages module -------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.galaxy_packages - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.homebrew module ------------------------------------------------ - -.. automodule:: galaxy.tools.deps.resolvers.homebrew - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.lmod module -------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.lmod - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.modules module ----------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.modules - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.resolver\_mixins module -------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.resolver_mixins - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.tool\_shed\_packages module ------------------------------------------------------------ - -.. automodule:: galaxy.tools.deps.resolvers.tool_shed_packages - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.resolvers\.unlinked\_tool\_shed\_packages module ---------------------------------------------------------------------- - -.. automodule:: galaxy.tools.deps.resolvers.unlinked_tool_shed_packages - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.deps.rst b/doc/source/lib/galaxy.tools.deps.rst deleted file mode 100644 index f9539e01adc..00000000000 --- a/doc/source/lib/galaxy.tools.deps.rst +++ /dev/null @@ -1,133 +0,0 @@ -galaxy\.tools\.deps package -=========================== - -.. automodule:: galaxy.tools.deps - :members: - :undoc-members: - :show-inheritance: - -Subpackages ------------ - -.. toctree:: - - galaxy.tools.deps.container_resolvers - galaxy.tools.deps.mulled - galaxy.tools.deps.resolvers - -Submodules ----------- - -galaxy\.tools\.deps\.brew\_exts module --------------------------------------- - -.. automodule:: galaxy.tools.deps.brew_exts - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.brew\_util module --------------------------------------- - -.. automodule:: galaxy.tools.deps.brew_util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.commands module ------------------------------------- - -.. automodule:: galaxy.tools.deps.commands - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.conda\_compat module ------------------------------------------ - -.. automodule:: galaxy.tools.deps.conda_compat - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.conda\_util module ---------------------------------------- - -.. automodule:: galaxy.tools.deps.conda_util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.container\_classes module ----------------------------------------------- - -.. automodule:: galaxy.tools.deps.container_classes - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.containers module --------------------------------------- - -.. automodule:: galaxy.tools.deps.containers - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.dependencies module ----------------------------------------- - -.. automodule:: galaxy.tools.deps.dependencies - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.docker\_util module ----------------------------------------- - -.. automodule:: galaxy.tools.deps.docker_util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.dockerfiles module ---------------------------------------- - -.. automodule:: galaxy.tools.deps.dockerfiles - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.installable module ---------------------------------------- - -.. automodule:: galaxy.tools.deps.installable - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.requirements module ----------------------------------------- - -.. automodule:: galaxy.tools.deps.requirements - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.singularity\_util module ---------------------------------------------- - -.. automodule:: galaxy.tools.deps.singularity_util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.deps\.views module ---------------------------------- - -.. automodule:: galaxy.tools.deps.views - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.error_reports.plugins.rst b/doc/source/lib/galaxy.tools.error_reports.plugins.rst index 5f6c51b9612..3491c92977c 100644 --- a/doc/source/lib/galaxy.tools.error_reports.plugins.rst +++ b/doc/source/lib/galaxy.tools.error_reports.plugins.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.error\_reports\.plugins package -============================================== +galaxy.tools.error\_reports.plugins package +=========================================== .. automodule:: galaxy.tools.error_reports.plugins :members: @@ -9,48 +9,56 @@ galaxy\.tools\.error\_reports\.plugins package Submodules ---------- -galaxy\.tools\.error\_reports\.plugins\.biostars module -------------------------------------------------------- +galaxy.tools.error\_reports.plugins.base\_git module +---------------------------------------------------- -.. automodule:: galaxy.tools.error_reports.plugins.biostars +.. automodule:: galaxy.tools.error_reports.plugins.base_git :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.email module ----------------------------------------------------- +galaxy.tools.error\_reports.plugins.email module +------------------------------------------------ .. automodule:: galaxy.tools.error_reports.plugins.email :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.github module ------------------------------------------------------ +galaxy.tools.error\_reports.plugins.github module +------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.github :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.influxdb module -------------------------------------------------------- +galaxy.tools.error\_reports.plugins.gitlab module +------------------------------------------------- + +.. automodule:: galaxy.tools.error_reports.plugins.gitlab + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.error\_reports.plugins.influxdb module +--------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.influxdb :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.json module ---------------------------------------------------- +galaxy.tools.error\_reports.plugins.json module +----------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.json :members: :undoc-members: :show-inheritance: -galaxy\.tools\.error\_reports\.plugins\.sentry module ------------------------------------------------------ +galaxy.tools.error\_reports.plugins.sentry module +------------------------------------------------- .. automodule:: galaxy.tools.error_reports.plugins.sentry :members: diff --git a/doc/source/lib/galaxy.tools.error_reports.rst b/doc/source/lib/galaxy.tools.error_reports.rst index 8e4012b832a..7cf8be64e4c 100644 --- a/doc/source/lib/galaxy.tools.error_reports.rst +++ b/doc/source/lib/galaxy.tools.error_reports.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.error\_reports package -===================================== +galaxy.tools.error\_reports package +=================================== .. automodule:: galaxy.tools.error_reports :members: diff --git a/doc/source/lib/galaxy.tools.expressions.rst b/doc/source/lib/galaxy.tools.expressions.rst new file mode 100644 index 00000000000..6c952368f2e --- /dev/null +++ b/doc/source/lib/galaxy.tools.expressions.rst @@ -0,0 +1,36 @@ +galaxy.tools.expressions package +================================ + +.. automodule:: galaxy.tools.expressions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.tools.expressions.evaluation module +------------------------------------------ + +.. automodule:: galaxy.tools.expressions.evaluation + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.expressions.script module +-------------------------------------- + +.. automodule:: galaxy.tools.expressions.script + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.expressions.util module +------------------------------------ + +.. automodule:: galaxy.tools.expressions.util + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.tools.filters.rst b/doc/source/lib/galaxy.tools.filters.rst index aa10e47d4fe..bbea7ec45e4 100644 --- a/doc/source/lib/galaxy.tools.filters.rst +++ b/doc/source/lib/galaxy.tools.filters.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.filters package -============================== +galaxy.tools.filters package +============================ .. automodule:: galaxy.tools.filters :members: diff --git a/doc/source/lib/galaxy.tools.imp_exp.rst b/doc/source/lib/galaxy.tools.imp_exp.rst index c0dc717f6cf..6cefd450f76 100644 --- a/doc/source/lib/galaxy.tools.imp_exp.rst +++ b/doc/source/lib/galaxy.tools.imp_exp.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.imp\_exp package -=============================== +galaxy.tools.imp\_exp package +============================= .. automodule:: galaxy.tools.imp_exp :members: @@ -9,16 +9,16 @@ galaxy\.tools\.imp\_exp package Submodules ---------- -galaxy\.tools\.imp\_exp\.export\_history module ------------------------------------------------ +galaxy.tools.imp\_exp.export\_history module +-------------------------------------------- .. automodule:: galaxy.tools.imp_exp.export_history :members: :undoc-members: :show-inheritance: -galaxy\.tools\.imp\_exp\.unpack\_tar\_gz\_archive module --------------------------------------------------------- +galaxy.tools.imp\_exp.unpack\_tar\_gz\_archive module +----------------------------------------------------- .. automodule:: galaxy.tools.imp_exp.unpack_tar_gz_archive :members: diff --git a/doc/source/lib/galaxy.tools.linters.rst b/doc/source/lib/galaxy.tools.linters.rst index 2012642a7cb..f79ce27f18b 100644 --- a/doc/source/lib/galaxy.tools.linters.rst +++ b/doc/source/lib/galaxy.tools.linters.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.linters package -============================== +galaxy.tools.linters package +============================ .. automodule:: galaxy.tools.linters :members: @@ -9,72 +9,80 @@ galaxy\.tools\.linters package Submodules ---------- -galaxy\.tools\.linters\.citations module ----------------------------------------- +galaxy.tools.linters.citations module +------------------------------------- .. automodule:: galaxy.tools.linters.citations :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.command module --------------------------------------- +galaxy.tools.linters.command module +----------------------------------- .. automodule:: galaxy.tools.linters.command :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.general module --------------------------------------- +galaxy.tools.linters.cwl module +------------------------------- + +.. automodule:: galaxy.tools.linters.cwl + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.linters.general module +----------------------------------- .. automodule:: galaxy.tools.linters.general :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.help module ------------------------------------ +galaxy.tools.linters.help module +-------------------------------- .. automodule:: galaxy.tools.linters.help :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.inputs module -------------------------------------- +galaxy.tools.linters.inputs module +---------------------------------- .. automodule:: galaxy.tools.linters.inputs :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.outputs module --------------------------------------- +galaxy.tools.linters.outputs module +----------------------------------- .. automodule:: galaxy.tools.linters.outputs :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.stdio module ------------------------------------- +galaxy.tools.linters.stdio module +--------------------------------- .. automodule:: galaxy.tools.linters.stdio :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.tests module ------------------------------------- +galaxy.tools.linters.tests module +--------------------------------- .. automodule:: galaxy.tools.linters.tests :members: :undoc-members: :show-inheritance: -galaxy\.tools\.linters\.xml\_order module ------------------------------------------ +galaxy.tools.linters.xml\_order module +-------------------------------------- .. automodule:: galaxy.tools.linters.xml_order :members: diff --git a/doc/source/lib/galaxy.tools.locations.rst b/doc/source/lib/galaxy.tools.locations.rst deleted file mode 100644 index 719eed3e90d..00000000000 --- a/doc/source/lib/galaxy.tools.locations.rst +++ /dev/null @@ -1,36 +0,0 @@ -galaxy\.tools\.locations package -================================ - -.. automodule:: galaxy.tools.locations - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.locations\.dockstore module ------------------------------------------- - -.. automodule:: galaxy.tools.locations.dockstore - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.locations\.file module -------------------------------------- - -.. automodule:: galaxy.tools.locations.file - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.locations\.http module -------------------------------------- - -.. automodule:: galaxy.tools.locations.http - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.parameters.rst b/doc/source/lib/galaxy.tools.parameters.rst index 6a8136986d8..568fb0c2c5f 100644 --- a/doc/source/lib/galaxy.tools.parameters.rst +++ b/doc/source/lib/galaxy.tools.parameters.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.parameters package -================================= +galaxy.tools.parameters package +=============================== .. automodule:: galaxy.tools.parameters :members: @@ -9,96 +9,88 @@ galaxy\.tools\.parameters package Submodules ---------- -galaxy\.tools\.parameters\.basic module ---------------------------------------- +galaxy.tools.parameters.basic module +------------------------------------ .. automodule:: galaxy.tools.parameters.basic :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.dataset\_matcher module --------------------------------------------------- +galaxy.tools.parameters.dataset\_matcher module +----------------------------------------------- .. automodule:: galaxy.tools.parameters.dataset_matcher :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.dynamic\_options module --------------------------------------------------- +galaxy.tools.parameters.dynamic\_options module +----------------------------------------------- .. automodule:: galaxy.tools.parameters.dynamic_options :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.grouping module ------------------------------------------- +galaxy.tools.parameters.grouping module +--------------------------------------- .. automodule:: galaxy.tools.parameters.grouping :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.history\_query module ------------------------------------------------- +galaxy.tools.parameters.history\_query module +--------------------------------------------- .. automodule:: galaxy.tools.parameters.history_query :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.input\_translation module ----------------------------------------------------- +galaxy.tools.parameters.input\_translation module +------------------------------------------------- .. automodule:: galaxy.tools.parameters.input_translation :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.meta module --------------------------------------- +galaxy.tools.parameters.meta module +----------------------------------- .. automodule:: galaxy.tools.parameters.meta :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.output\_collect module -------------------------------------------------- - -.. automodule:: galaxy.tools.parameters.output_collect - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parameters\.sanitize module ------------------------------------------- +galaxy.tools.parameters.sanitize module +--------------------------------------- .. automodule:: galaxy.tools.parameters.sanitize :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.validation module --------------------------------------------- +galaxy.tools.parameters.validation module +----------------------------------------- .. automodule:: galaxy.tools.parameters.validation :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.wrapped module ------------------------------------------ +galaxy.tools.parameters.wrapped module +-------------------------------------- .. automodule:: galaxy.tools.parameters.wrapped :members: :undoc-members: :show-inheritance: -galaxy\.tools\.parameters\.wrapped\_json module ------------------------------------------------ +galaxy.tools.parameters.wrapped\_json module +-------------------------------------------- .. automodule:: galaxy.tools.parameters.wrapped_json :members: diff --git a/doc/source/lib/galaxy.tools.parser.rst b/doc/source/lib/galaxy.tools.parser.rst deleted file mode 100644 index 474be80027c..00000000000 --- a/doc/source/lib/galaxy.tools.parser.rst +++ /dev/null @@ -1,92 +0,0 @@ -galaxy\.tools\.parser package -============================= - -.. automodule:: galaxy.tools.parser - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.tools\.parser\.cwl module ---------------------------------- - -.. automodule:: galaxy.tools.parser.cwl - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.error\_level module ------------------------------------------- - -.. automodule:: galaxy.tools.parser.error_level - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.factory module -------------------------------------- - -.. automodule:: galaxy.tools.parser.factory - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.interface module ---------------------------------------- - -.. automodule:: galaxy.tools.parser.interface - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.output\_actions module ---------------------------------------------- - -.. automodule:: galaxy.tools.parser.output_actions - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.output\_collection\_def module ------------------------------------------------------ - -.. automodule:: galaxy.tools.parser.output_collection_def - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.output\_objects module ---------------------------------------------- - -.. automodule:: galaxy.tools.parser.output_objects - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.util module ----------------------------------- - -.. automodule:: galaxy.tools.parser.util - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.xml module ---------------------------------- - -.. automodule:: galaxy.tools.parser.xml - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.parser\.yaml module ----------------------------------- - -.. automodule:: galaxy.tools.parser.yaml - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.tools.rst b/doc/source/lib/galaxy.tools.rst index 1c6441f5780..e544594648a 100644 --- a/doc/source/lib/galaxy.tools.rst +++ b/doc/source/lib/galaxy.tools.rst @@ -1,5 +1,5 @@ -galaxy\.tools package -===================== +galaxy.tools package +==================== .. automodule:: galaxy.tools :members: @@ -12,17 +12,14 @@ Subpackages .. toctree:: galaxy.tools.actions - galaxy.tools.cwl galaxy.tools.data galaxy.tools.data_manager - galaxy.tools.deps galaxy.tools.error_reports + galaxy.tools.expressions galaxy.tools.filters galaxy.tools.imp_exp galaxy.tools.linters - galaxy.tools.locations galaxy.tools.parameters - galaxy.tools.parser galaxy.tools.search galaxy.tools.toolbox galaxy.tools.util @@ -31,128 +28,96 @@ Subpackages Submodules ---------- -galaxy\.tools\.cache module ---------------------------- +galaxy.tools.cache module +------------------------- .. automodule:: galaxy.tools.cache :members: :undoc-members: :show-inheritance: -galaxy\.tools\.data\_fetch module ---------------------------------- +galaxy.tools.data\_fetch module +------------------------------- .. automodule:: galaxy.tools.data_fetch :members: :undoc-members: :show-inheritance: -galaxy\.tools\.errors module ----------------------------- +galaxy.tools.errors module +-------------------------- .. automodule:: galaxy.tools.errors :members: :undoc-members: :show-inheritance: -galaxy\.tools\.evaluation module --------------------------------- +galaxy.tools.evaluation module +------------------------------ .. automodule:: galaxy.tools.evaluation :members: :undoc-members: :show-inheritance: -galaxy\.tools\.exception\_handling module ------------------------------------------ +galaxy.tools.exception\_handling module +--------------------------------------- .. automodule:: galaxy.tools.exception_handling :members: :undoc-members: :show-inheritance: -galaxy\.tools\.execute module ------------------------------ +galaxy.tools.execute module +--------------------------- .. automodule:: galaxy.tools.execute :members: :undoc-members: :show-inheritance: -galaxy\.tools\.fetcher module ------------------------------ - -.. automodule:: galaxy.tools.fetcher - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.lint module --------------------------- +galaxy.tools.lint module +------------------------ .. automodule:: galaxy.tools.lint :members: :undoc-members: :show-inheritance: -galaxy\.tools\.lint\_util module --------------------------------- +galaxy.tools.lint\_util module +------------------------------ .. automodule:: galaxy.tools.lint_util :members: :undoc-members: :show-inheritance: -galaxy\.tools\.loader module ----------------------------- - -.. automodule:: galaxy.tools.loader - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.loader\_directory module ---------------------------------------- - -.. automodule:: galaxy.tools.loader_directory - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.provided\_metadata module ----------------------------------------- - -.. automodule:: galaxy.tools.provided_metadata - :members: - :undoc-members: - :show-inheritance: - -galaxy\.tools\.repositories module ----------------------------------- +galaxy.tools.repositories module +-------------------------------- .. automodule:: galaxy.tools.repositories :members: :undoc-members: :show-inheritance: -galaxy\.tools\.special\_tools module ------------------------------------- +galaxy.tools.special\_tools module +---------------------------------- .. automodule:: galaxy.tools.special_tools :members: :undoc-members: :show-inheritance: -galaxy\.tools\.test module --------------------------- +galaxy.tools.test module +------------------------ .. automodule:: galaxy.tools.test :members: :undoc-members: :show-inheritance: -galaxy\.tools\.wrappers module ------------------------------- +galaxy.tools.wrappers module +---------------------------- .. automodule:: galaxy.tools.wrappers :members: diff --git a/doc/source/lib/galaxy.tools.search.rst b/doc/source/lib/galaxy.tools.search.rst index 8f67c61620f..edbb5bf3c79 100644 --- a/doc/source/lib/galaxy.tools.search.rst +++ b/doc/source/lib/galaxy.tools.search.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.search package -============================= +galaxy.tools.search package +=========================== .. automodule:: galaxy.tools.search :members: diff --git a/doc/source/lib/galaxy.tools.toolbox.filters.rst b/doc/source/lib/galaxy.tools.toolbox.filters.rst index a04372a8eb1..a5a81d279fb 100644 --- a/doc/source/lib/galaxy.tools.toolbox.filters.rst +++ b/doc/source/lib/galaxy.tools.toolbox.filters.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.toolbox\.filters package -======================================= +galaxy.tools.toolbox.filters package +==================================== .. automodule:: galaxy.tools.toolbox.filters :members: diff --git a/doc/source/lib/galaxy.tools.toolbox.lineages.rst b/doc/source/lib/galaxy.tools.toolbox.lineages.rst index 1f7794bff3d..e2628fd8bc4 100644 --- a/doc/source/lib/galaxy.tools.toolbox.lineages.rst +++ b/doc/source/lib/galaxy.tools.toolbox.lineages.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.toolbox\.lineages package -======================================== +galaxy.tools.toolbox.lineages package +===================================== .. automodule:: galaxy.tools.toolbox.lineages :members: @@ -9,16 +9,16 @@ galaxy\.tools\.toolbox\.lineages package Submodules ---------- -galaxy\.tools\.toolbox\.lineages\.factory module ------------------------------------------------- +galaxy.tools.toolbox.lineages.factory module +-------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.factory :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.lineages\.interface module --------------------------------------------------- +galaxy.tools.toolbox.lineages.interface module +---------------------------------------------- .. automodule:: galaxy.tools.toolbox.lineages.interface :members: diff --git a/doc/source/lib/galaxy.tools.toolbox.rst b/doc/source/lib/galaxy.tools.toolbox.rst index 6ff0362872e..9631687f40f 100644 --- a/doc/source/lib/galaxy.tools.toolbox.rst +++ b/doc/source/lib/galaxy.tools.toolbox.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.toolbox package -============================== +galaxy.tools.toolbox package +============================ .. automodule:: galaxy.tools.toolbox :members: @@ -17,48 +17,48 @@ Subpackages Submodules ---------- -galaxy\.tools\.toolbox\.base module ------------------------------------ +galaxy.tools.toolbox.base module +-------------------------------- .. automodule:: galaxy.tools.toolbox.base :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.integrated\_panel module ------------------------------------------------- +galaxy.tools.toolbox.integrated\_panel module +--------------------------------------------- .. automodule:: galaxy.tools.toolbox.integrated_panel :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.panel module ------------------------------------- +galaxy.tools.toolbox.panel module +--------------------------------- .. automodule:: galaxy.tools.toolbox.panel :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.parser module -------------------------------------- +galaxy.tools.toolbox.parser module +---------------------------------- .. automodule:: galaxy.tools.toolbox.parser :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.tags module ------------------------------------ +galaxy.tools.toolbox.tags module +-------------------------------- .. automodule:: galaxy.tools.toolbox.tags :members: :undoc-members: :show-inheritance: -galaxy\.tools\.toolbox\.watcher module --------------------------------------- +galaxy.tools.toolbox.watcher module +----------------------------------- .. automodule:: galaxy.tools.toolbox.watcher :members: diff --git a/doc/source/lib/galaxy.tools.util.galaxyops.rst b/doc/source/lib/galaxy.tools.util.galaxyops.rst index c4f03d0cc4c..4ea949a2fac 100644 --- a/doc/source/lib/galaxy.tools.util.galaxyops.rst +++ b/doc/source/lib/galaxy.tools.util.galaxyops.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.util\.galaxyops package -====================================== +galaxy.tools.util.galaxyops package +=================================== .. automodule:: galaxy.tools.util.galaxyops :members: diff --git a/doc/source/lib/galaxy.tools.util.rst b/doc/source/lib/galaxy.tools.util.rst index d0e040291c7..588817928fa 100644 --- a/doc/source/lib/galaxy.tools.util.rst +++ b/doc/source/lib/galaxy.tools.util.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.util package -=========================== +galaxy.tools.util package +========================= .. automodule:: galaxy.tools.util :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -galaxy\.tools\.util\.maf\_utilities module ------------------------------------------- +galaxy.tools.util.maf\_utilities module +--------------------------------------- .. automodule:: galaxy.tools.util.maf_utilities :members: diff --git a/doc/source/lib/galaxy.tools.verify.asserts.rst b/doc/source/lib/galaxy.tools.verify.asserts.rst index 97d35d8da2e..66b69426efb 100644 --- a/doc/source/lib/galaxy.tools.verify.asserts.rst +++ b/doc/source/lib/galaxy.tools.verify.asserts.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.verify\.asserts package -====================================== +galaxy.tools.verify.asserts package +=================================== .. automodule:: galaxy.tools.verify.asserts :members: @@ -9,32 +9,40 @@ galaxy\.tools\.verify\.asserts package Submodules ---------- -galaxy\.tools\.verify\.asserts\.hdf5 module -------------------------------------------- +galaxy.tools.verify.asserts.archive module +------------------------------------------ + +.. automodule:: galaxy.tools.verify.asserts.archive + :members: + :undoc-members: + :show-inheritance: + +galaxy.tools.verify.asserts.hdf5 module +--------------------------------------- .. automodule:: galaxy.tools.verify.asserts.hdf5 :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.asserts\.tabular module ----------------------------------------------- +galaxy.tools.verify.asserts.tabular module +------------------------------------------ .. automodule:: galaxy.tools.verify.asserts.tabular :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.asserts\.text module -------------------------------------------- +galaxy.tools.verify.asserts.text module +--------------------------------------- .. automodule:: galaxy.tools.verify.asserts.text :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.asserts\.xml module ------------------------------------------- +galaxy.tools.verify.asserts.xml module +-------------------------------------- .. automodule:: galaxy.tools.verify.asserts.xml :members: diff --git a/doc/source/lib/galaxy.tools.verify.rst b/doc/source/lib/galaxy.tools.verify.rst index 11325b39a71..4daf18a03de 100644 --- a/doc/source/lib/galaxy.tools.verify.rst +++ b/doc/source/lib/galaxy.tools.verify.rst @@ -1,5 +1,5 @@ -galaxy\.tools\.verify package -============================= +galaxy.tools.verify package +=========================== .. automodule:: galaxy.tools.verify :members: @@ -16,24 +16,24 @@ Subpackages Submodules ---------- -galaxy\.tools\.verify\.interactor module ----------------------------------------- +galaxy.tools.verify.interactor module +------------------------------------- .. automodule:: galaxy.tools.verify.interactor :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.script module ------------------------------------- +galaxy.tools.verify.script module +--------------------------------- .. automodule:: galaxy.tools.verify.script :members: :undoc-members: :show-inheritance: -galaxy\.tools\.verify\.test\_data module ----------------------------------------- +galaxy.tools.verify.test\_data module +------------------------------------- .. automodule:: galaxy.tools.verify.test_data :members: diff --git a/doc/source/lib/galaxy.tours.rst b/doc/source/lib/galaxy.tours.rst index f83cb65d652..9729a10a6fe 100644 --- a/doc/source/lib/galaxy.tours.rst +++ b/doc/source/lib/galaxy.tours.rst @@ -1,5 +1,5 @@ -galaxy\.tours package -===================== +galaxy.tours package +==================== .. automodule:: galaxy.tours :members: diff --git a/doc/source/lib/galaxy.util.logging.rst b/doc/source/lib/galaxy.util.logging.rst index 1bc9f1ab01f..84e18059461 100644 --- a/doc/source/lib/galaxy.util.logging.rst +++ b/doc/source/lib/galaxy.util.logging.rst @@ -1,5 +1,5 @@ -galaxy\.util\.logging package -============================= +galaxy.util.logging package +=========================== .. automodule:: galaxy.util.logging :members: @@ -9,8 +9,8 @@ galaxy\.util\.logging package Submodules ---------- -galaxy\.util\.logging\.fluent\_log module ------------------------------------------ +galaxy.util.logging.fluent\_log module +-------------------------------------- .. automodule:: galaxy.util.logging.fluent_log :members: diff --git a/doc/source/lib/galaxy.util.pastescript.rst b/doc/source/lib/galaxy.util.pastescript.rst index 92f5eb055b5..0a861eb5a4f 100644 --- a/doc/source/lib/galaxy.util.pastescript.rst +++ b/doc/source/lib/galaxy.util.pastescript.rst @@ -1,5 +1,5 @@ -galaxy\.util\.pastescript package -================================= +galaxy.util.pastescript package +=============================== .. automodule:: galaxy.util.pastescript :members: @@ -9,16 +9,16 @@ galaxy\.util\.pastescript package Submodules ---------- -galaxy\.util\.pastescript\.loadwsgi module ------------------------------------------- +galaxy.util.pastescript.loadwsgi module +--------------------------------------- .. automodule:: galaxy.util.pastescript.loadwsgi :members: :undoc-members: :show-inheritance: -galaxy\.util\.pastescript\.serve module ---------------------------------------- +galaxy.util.pastescript.serve module +------------------------------------ .. automodule:: galaxy.util.pastescript.serve :members: diff --git a/doc/source/lib/galaxy.util.path.rst b/doc/source/lib/galaxy.util.path.rst index 2476ed017ef..c74056d2d89 100644 --- a/doc/source/lib/galaxy.util.path.rst +++ b/doc/source/lib/galaxy.util.path.rst @@ -1,5 +1,5 @@ -galaxy\.util\.path package -========================== +galaxy.util.path package +======================== .. automodule:: galaxy.util.path :members: @@ -9,16 +9,16 @@ galaxy\.util\.path package Submodules ---------- -galaxy\.util\.path\.ntpath module ---------------------------------- +galaxy.util.path.ntpath module +------------------------------ .. automodule:: galaxy.util.path.ntpath :members: :undoc-members: :show-inheritance: -galaxy\.util\.path\.posixpath module ------------------------------------- +galaxy.util.path.posixpath module +--------------------------------- .. automodule:: galaxy.util.path.posixpath :members: diff --git a/doc/source/lib/galaxy.util.rst b/doc/source/lib/galaxy.util.rst index 9da8e2db529..792c0dfabb9 100644 --- a/doc/source/lib/galaxy.util.rst +++ b/doc/source/lib/galaxy.util.rst @@ -1,5 +1,5 @@ -galaxy\.util package -==================== +galaxy.util package +=================== .. automodule:: galaxy.util :members: @@ -18,352 +18,360 @@ Subpackages Submodules ---------- -galaxy\.util\.aliaspickler module ---------------------------------- +galaxy.util.aliaspickler module +------------------------------- .. automodule:: galaxy.util.aliaspickler :members: :undoc-members: :show-inheritance: -galaxy\.util\.biostar module ----------------------------- - -.. automodule:: galaxy.util.biostar - :members: - :undoc-members: - :show-inheritance: - -galaxy\.util\.bunch module --------------------------- +galaxy.util.bunch module +------------------------ .. automodule:: galaxy.util.bunch :members: :undoc-members: :show-inheritance: -galaxy\.util\.checkers module ------------------------------ +galaxy.util.bytesize module +--------------------------- + +.. automodule:: galaxy.util.bytesize + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.checkers module +--------------------------- .. automodule:: galaxy.util.checkers :members: :undoc-members: :show-inheritance: -galaxy\.util\.compression\_utils module ---------------------------------------- +galaxy.util.compression\_utils module +------------------------------------- .. automodule:: galaxy.util.compression_utils :members: :undoc-members: :show-inheritance: -galaxy\.util\.create\_history\_template module ----------------------------------------------- - -.. automodule:: galaxy.util.create_history_template - :members: - :undoc-members: - :show-inheritance: - -galaxy\.util\.dbkeys module ---------------------------- +galaxy.util.dbkeys module +------------------------- .. automodule:: galaxy.util.dbkeys :members: :undoc-members: :show-inheritance: -galaxy\.util\.dictifiable module --------------------------------- +galaxy.util.dictifiable module +------------------------------ .. automodule:: galaxy.util.dictifiable :members: :undoc-members: :show-inheritance: -galaxy\.util\.expressions module --------------------------------- +galaxy.util.expressions module +------------------------------ .. automodule:: galaxy.util.expressions :members: :undoc-members: :show-inheritance: -galaxy\.util\.facts module --------------------------- +galaxy.util.facts module +------------------------ .. automodule:: galaxy.util.facts :members: :undoc-members: :show-inheritance: -galaxy\.util\.filelock module ------------------------------ +galaxy.util.filelock module +--------------------------- .. automodule:: galaxy.util.filelock :members: :undoc-members: :show-inheritance: -galaxy\.util\.hash\_util module -------------------------------- +galaxy.util.form\_builder module +-------------------------------- + +.. automodule:: galaxy.util.form_builder + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.getargspec module +----------------------------- + +.. automodule:: galaxy.util.getargspec + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.hash\_util module +----------------------------- .. automodule:: galaxy.util.hash_util :members: :undoc-members: :show-inheritance: -galaxy\.util\.heartbeat module ------------------------------- +galaxy.util.heartbeat module +---------------------------- .. automodule:: galaxy.util.heartbeat :members: :undoc-members: :show-inheritance: -galaxy\.util\.image\_util module --------------------------------- +galaxy.util.image\_util module +------------------------------ .. automodule:: galaxy.util.image_util :members: :undoc-members: :show-inheritance: -galaxy\.util\.inflection module -------------------------------- +galaxy.util.inflection module +----------------------------- .. automodule:: galaxy.util.inflection :members: :undoc-members: :show-inheritance: -galaxy\.util\.json module -------------------------- +galaxy.util.json module +----------------------- .. automodule:: galaxy.util.json :members: :undoc-members: :show-inheritance: -galaxy\.util\.jstree module ---------------------------- +galaxy.util.jstree module +------------------------- .. automodule:: galaxy.util.jstree :members: :undoc-members: :show-inheritance: -galaxy\.util\.lazy\_process module ----------------------------------- +galaxy.util.lazy\_process module +-------------------------------- .. automodule:: galaxy.util.lazy_process :members: :undoc-members: :show-inheritance: -galaxy\.util\.monitors module ------------------------------ +galaxy.util.monitors module +--------------------------- .. automodule:: galaxy.util.monitors :members: :undoc-members: :show-inheritance: -galaxy\.util\.none\_like module -------------------------------- - -.. automodule:: galaxy.util.none_like - :members: - :undoc-members: - :show-inheritance: - -galaxy\.util\.object\_wrapper module ------------------------------------- +galaxy.util.object\_wrapper module +---------------------------------- .. automodule:: galaxy.util.object_wrapper :members: :undoc-members: :show-inheritance: -galaxy\.util\.odict module --------------------------- +galaxy.util.odict module +------------------------ .. automodule:: galaxy.util.odict :members: :undoc-members: :show-inheritance: -galaxy\.util\.oset module -------------------------- +galaxy.util.oset module +----------------------- .. automodule:: galaxy.util.oset :members: :undoc-members: :show-inheritance: -galaxy\.util\.permutations module ---------------------------------- +galaxy.util.permutations module +------------------------------- .. automodule:: galaxy.util.permutations :members: :undoc-members: :show-inheritance: -galaxy\.util\.plugin\_config module ------------------------------------ +galaxy.util.plugin\_config module +--------------------------------- .. automodule:: galaxy.util.plugin_config :members: :undoc-members: :show-inheritance: -galaxy\.util\.properties module -------------------------------- +galaxy.util.properties module +----------------------------- .. automodule:: galaxy.util.properties :members: :undoc-members: :show-inheritance: -galaxy\.util\.renamed\_temporary\_file module ---------------------------------------------- +galaxy.util.renamed\_temporary\_file module +------------------------------------------- .. automodule:: galaxy.util.renamed_temporary_file :members: :undoc-members: :show-inheritance: -galaxy\.util\.rules\_dsl module -------------------------------- +galaxy.util.rules\_dsl module +----------------------------- .. automodule:: galaxy.util.rules_dsl :members: :undoc-members: :show-inheritance: -galaxy\.util\.sanitize\_html module ------------------------------------ +galaxy.util.sanitize\_html module +--------------------------------- .. automodule:: galaxy.util.sanitize_html :members: :undoc-members: :show-inheritance: -galaxy\.util\.script module ---------------------------- +galaxy.util.script module +------------------------- .. automodule:: galaxy.util.script :members: :undoc-members: :show-inheritance: -galaxy\.util\.simplegraph module --------------------------------- +galaxy.util.simplegraph module +------------------------------ .. automodule:: galaxy.util.simplegraph :members: :undoc-members: :show-inheritance: -galaxy\.util\.sleeper module ----------------------------- +galaxy.util.sleeper module +-------------------------- .. automodule:: galaxy.util.sleeper :members: :undoc-members: :show-inheritance: -galaxy\.util\.sockets module ----------------------------- +galaxy.util.sockets module +-------------------------- .. automodule:: galaxy.util.sockets :members: :undoc-members: :show-inheritance: -galaxy\.util\.specs module --------------------------- +galaxy.util.specs module +------------------------ .. automodule:: galaxy.util.specs :members: :undoc-members: :show-inheritance: -galaxy\.util\.sqlite module ---------------------------- +galaxy.util.sqlite module +------------------------- .. automodule:: galaxy.util.sqlite :members: :undoc-members: :show-inheritance: -galaxy\.util\.streamball module -------------------------------- +galaxy.util.streamball module +----------------------------- .. automodule:: galaxy.util.streamball :members: :undoc-members: :show-inheritance: -galaxy\.util\.submodules module -------------------------------- +galaxy.util.submodules module +----------------------------- .. automodule:: galaxy.util.submodules :members: :undoc-members: :show-inheritance: -galaxy\.util\.template module ------------------------------ +galaxy.util.template module +--------------------------- .. automodule:: galaxy.util.template :members: :undoc-members: :show-inheritance: -galaxy\.util\.tool\_version module ----------------------------------- +galaxy.util.tool\_version module +-------------------------------- .. automodule:: galaxy.util.tool_version :members: :undoc-members: :show-inheritance: -galaxy\.util\.topsort module ----------------------------- +galaxy.util.topsort module +-------------------------- .. automodule:: galaxy.util.topsort :members: :undoc-members: :show-inheritance: -galaxy\.util\.ucsc module -------------------------- +galaxy.util.ucsc module +----------------------- .. automodule:: galaxy.util.ucsc :members: :undoc-members: :show-inheritance: -galaxy\.util\.validation module -------------------------------- +galaxy.util.validation module +----------------------------- .. automodule:: galaxy.util.validation :members: :undoc-members: :show-inheritance: -galaxy\.util\.watcher module ----------------------------- +galaxy.util.watcher module +-------------------------- .. automodule:: galaxy.util.watcher :members: :undoc-members: :show-inheritance: -galaxy\.util\.xml\_macros module --------------------------------- +galaxy.util.web\_compat module +------------------------------ + +.. automodule:: galaxy.util.web_compat + :members: + :undoc-members: + :show-inheritance: + +galaxy.util.xml\_macros module +------------------------------ .. automodule:: galaxy.util.xml_macros :members: diff --git a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst index ee55c5577f0..1866488ed19 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.phyloviz.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.data\_providers\.phyloviz package -======================================================== +galaxy.visualization.data\_providers.phyloviz package +===================================================== .. automodule:: galaxy.visualization.data_providers.phyloviz :members: @@ -9,32 +9,32 @@ galaxy\.visualization\.data\_providers\.phyloviz package Submodules ---------- -galaxy\.visualization\.data\_providers\.phyloviz\.baseparser module -------------------------------------------------------------------- +galaxy.visualization.data\_providers.phyloviz.baseparser module +--------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.baseparser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.phyloviz\.newickparser module ---------------------------------------------------------------------- +galaxy.visualization.data\_providers.phyloviz.newickparser module +----------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.newickparser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.phyloviz\.nexusparser module --------------------------------------------------------------------- +galaxy.visualization.data\_providers.phyloviz.nexusparser module +---------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.nexusparser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.phyloviz\.phyloxmlparser module ------------------------------------------------------------------------ +galaxy.visualization.data\_providers.phyloviz.phyloxmlparser module +------------------------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.phyloviz.phyloxmlparser :members: diff --git a/doc/source/lib/galaxy.visualization.data_providers.rst b/doc/source/lib/galaxy.visualization.data_providers.rst index 7502835ba31..326f6c75321 100644 --- a/doc/source/lib/galaxy.visualization.data_providers.rst +++ b/doc/source/lib/galaxy.visualization.data_providers.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.data\_providers package -============================================== +galaxy.visualization.data\_providers package +============================================ .. automodule:: galaxy.visualization.data_providers :members: @@ -16,32 +16,32 @@ Subpackages Submodules ---------- -galaxy\.visualization\.data\_providers\.basic module ----------------------------------------------------- +galaxy.visualization.data\_providers.basic module +------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.basic :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.cigar module ----------------------------------------------------- +galaxy.visualization.data\_providers.cigar module +------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.cigar :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.genome module ------------------------------------------------------ +galaxy.visualization.data\_providers.genome module +-------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.genome :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.data\_providers\.registry module -------------------------------------------------------- +galaxy.visualization.data\_providers.registry module +---------------------------------------------------- .. automodule:: galaxy.visualization.data_providers.registry :members: diff --git a/doc/source/lib/galaxy.visualization.genome.rst b/doc/source/lib/galaxy.visualization.genome.rst index f32e8d9c115..9097529321c 100644 --- a/doc/source/lib/galaxy.visualization.genome.rst +++ b/doc/source/lib/galaxy.visualization.genome.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.genome package -===================================== +galaxy.visualization.genome package +=================================== .. automodule:: galaxy.visualization.genome :members: diff --git a/doc/source/lib/galaxy.visualization.plugins.rst b/doc/source/lib/galaxy.visualization.plugins.rst index 78ddcd27c36..019f744d8b4 100644 --- a/doc/source/lib/galaxy.visualization.plugins.rst +++ b/doc/source/lib/galaxy.visualization.plugins.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.plugins package -====================================== +galaxy.visualization.plugins package +==================================== .. automodule:: galaxy.visualization.plugins :members: @@ -9,48 +9,48 @@ galaxy\.visualization\.plugins package Submodules ---------- -galaxy\.visualization\.plugins\.config\_parser module ------------------------------------------------------ +galaxy.visualization.plugins.config\_parser module +-------------------------------------------------- .. automodule:: galaxy.visualization.plugins.config_parser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.interactive\_environments module ----------------------------------------------------------------- +galaxy.visualization.plugins.interactive\_environments module +------------------------------------------------------------- .. automodule:: galaxy.visualization.plugins.interactive_environments :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.plugin module ---------------------------------------------- +galaxy.visualization.plugins.plugin module +------------------------------------------ .. automodule:: galaxy.visualization.plugins.plugin :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.registry module ------------------------------------------------ +galaxy.visualization.plugins.registry module +-------------------------------------------- .. automodule:: galaxy.visualization.plugins.registry :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.resource\_parser module -------------------------------------------------------- +galaxy.visualization.plugins.resource\_parser module +---------------------------------------------------- .. automodule:: galaxy.visualization.plugins.resource_parser :members: :undoc-members: :show-inheritance: -galaxy\.visualization\.plugins\.utils module --------------------------------------------- +galaxy.visualization.plugins.utils module +----------------------------------------- .. automodule:: galaxy.visualization.plugins.utils :members: diff --git a/doc/source/lib/galaxy.visualization.rst b/doc/source/lib/galaxy.visualization.rst index 862305917c7..1f334499e29 100644 --- a/doc/source/lib/galaxy.visualization.rst +++ b/doc/source/lib/galaxy.visualization.rst @@ -1,5 +1,5 @@ -galaxy\.visualization package -============================= +galaxy.visualization package +============================ .. automodule:: galaxy.visualization :members: @@ -19,8 +19,8 @@ Subpackages Submodules ---------- -galaxy\.visualization\.genomes module -------------------------------------- +galaxy.visualization.genomes module +----------------------------------- .. automodule:: galaxy.visualization.genomes :members: diff --git a/doc/source/lib/galaxy.visualization.tracks.rst b/doc/source/lib/galaxy.visualization.tracks.rst index 370ed638ff0..2d279399ef6 100644 --- a/doc/source/lib/galaxy.visualization.tracks.rst +++ b/doc/source/lib/galaxy.visualization.tracks.rst @@ -1,5 +1,5 @@ -galaxy\.visualization\.tracks package -===================================== +galaxy.visualization.tracks package +=================================== .. automodule:: galaxy.visualization.tracks :members: diff --git a/doc/source/lib/galaxy.web.base.rst b/doc/source/lib/galaxy.web.base.rst index f1a799c04a7..f81bd29947a 100644 --- a/doc/source/lib/galaxy.web.base.rst +++ b/doc/source/lib/galaxy.web.base.rst @@ -1,5 +1,5 @@ -galaxy\.web\.base package -========================= +galaxy.web.base package +======================= .. automodule:: galaxy.web.base :members: @@ -9,8 +9,8 @@ galaxy\.web\.base package Submodules ---------- -galaxy\.web\.base\.controller module ------------------------------------- +galaxy.web.base.controller module +--------------------------------- .. automodule:: galaxy.web.base.controller :members: diff --git a/doc/source/lib/galaxy.web.framework.helpers.rst b/doc/source/lib/galaxy.web.framework.helpers.rst index 420afef6be1..e0024343c0c 100644 --- a/doc/source/lib/galaxy.web.framework.helpers.rst +++ b/doc/source/lib/galaxy.web.framework.helpers.rst @@ -1,5 +1,5 @@ -galaxy\.web\.framework\.helpers package -======================================= +galaxy.web.framework.helpers package +==================================== .. automodule:: galaxy.web.framework.helpers :members: @@ -9,16 +9,16 @@ galaxy\.web\.framework\.helpers package Submodules ---------- -galaxy\.web\.framework\.helpers\.grids module ---------------------------------------------- +galaxy.web.framework.helpers.grids module +----------------------------------------- .. automodule:: galaxy.web.framework.helpers.grids :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.helpers\.tags module --------------------------------------------- +galaxy.web.framework.helpers.tags module +---------------------------------------- .. automodule:: galaxy.web.framework.helpers.tags :members: diff --git a/doc/source/lib/galaxy.web.framework.middleware.rst b/doc/source/lib/galaxy.web.framework.middleware.rst index f320560dbae..675615531da 100644 --- a/doc/source/lib/galaxy.web.framework.middleware.rst +++ b/doc/source/lib/galaxy.web.framework.middleware.rst @@ -1,5 +1,5 @@ -galaxy\.web\.framework\.middleware package -========================================== +galaxy.web.framework.middleware package +======================================= .. automodule:: galaxy.web.framework.middleware :members: @@ -9,88 +9,88 @@ galaxy\.web\.framework\.middleware package Submodules ---------- -galaxy\.web\.framework\.middleware\.batch module ------------------------------------------------- +galaxy.web.framework.middleware.batch module +-------------------------------------------- .. automodule:: galaxy.web.framework.middleware.batch :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.error module ------------------------------------------------- +galaxy.web.framework.middleware.error module +-------------------------------------------- .. automodule:: galaxy.web.framework.middleware.error :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.profile module --------------------------------------------------- +galaxy.web.framework.middleware.profile module +---------------------------------------------- .. automodule:: galaxy.web.framework.middleware.profile :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.remoteuser module ------------------------------------------------------ +galaxy.web.framework.middleware.remoteuser module +------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.remoteuser :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.request\_id module ------------------------------------------------------- +galaxy.web.framework.middleware.request\_id module +-------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.request_id :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.sentry module -------------------------------------------------- +galaxy.web.framework.middleware.sentry module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.sentry :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.sqldebug module ---------------------------------------------------- +galaxy.web.framework.middleware.sqldebug module +----------------------------------------------- .. automodule:: galaxy.web.framework.middleware.sqldebug :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.static module -------------------------------------------------- +galaxy.web.framework.middleware.static module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.static :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.statsd module -------------------------------------------------- +galaxy.web.framework.middleware.statsd module +--------------------------------------------- .. automodule:: galaxy.web.framework.middleware.statsd :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.translogger module ------------------------------------------------------- +galaxy.web.framework.middleware.translogger module +-------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.translogger :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.middleware\.xforwardedhost module ---------------------------------------------------------- +galaxy.web.framework.middleware.xforwardedhost module +----------------------------------------------------- .. automodule:: galaxy.web.framework.middleware.xforwardedhost :members: diff --git a/doc/source/lib/galaxy.web.framework.rst b/doc/source/lib/galaxy.web.framework.rst index 6aba7ac3035..a7dc4812d56 100644 --- a/doc/source/lib/galaxy.web.framework.rst +++ b/doc/source/lib/galaxy.web.framework.rst @@ -1,5 +1,5 @@ -galaxy\.web\.framework package -============================== +galaxy.web.framework package +============================ .. automodule:: galaxy.web.framework :members: @@ -17,24 +17,24 @@ Subpackages Submodules ---------- -galaxy\.web\.framework\.base module ------------------------------------ +galaxy.web.framework.base module +-------------------------------- .. automodule:: galaxy.web.framework.base :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.decorators module ------------------------------------------ +galaxy.web.framework.decorators module +-------------------------------------- .. automodule:: galaxy.web.framework.decorators :members: :undoc-members: :show-inheritance: -galaxy\.web\.framework\.webapp module -------------------------------------- +galaxy.web.framework.webapp module +---------------------------------- .. automodule:: galaxy.web.framework.webapp :members: diff --git a/doc/source/lib/galaxy.web.proxy.rst b/doc/source/lib/galaxy.web.proxy.rst index 04e2eb4b105..d69630ba177 100644 --- a/doc/source/lib/galaxy.web.proxy.rst +++ b/doc/source/lib/galaxy.web.proxy.rst @@ -1,5 +1,5 @@ -galaxy\.web\.proxy package -========================== +galaxy.web.proxy package +======================== .. automodule:: galaxy.web.proxy :members: diff --git a/doc/source/lib/galaxy.web.rst b/doc/source/lib/galaxy.web.rst index 846708b7f88..dc3fd75cfd6 100644 --- a/doc/source/lib/galaxy.web.rst +++ b/doc/source/lib/galaxy.web.rst @@ -1,5 +1,5 @@ -galaxy\.web package -=================== +galaxy.web package +================== .. automodule:: galaxy.web :members: @@ -14,38 +14,36 @@ Subpackages galaxy.web.base galaxy.web.framework galaxy.web.proxy - galaxy.web.security - galaxy.web.stack Submodules ---------- -galaxy\.web\.buildapp module ----------------------------- +galaxy.web.buildapp module +-------------------------- .. automodule:: galaxy.web.buildapp :members: :undoc-members: :show-inheritance: -galaxy\.web\.form\_builder module ---------------------------------- +galaxy.web.form\_builder module +------------------------------- .. automodule:: galaxy.web.form_builder :members: :undoc-members: :show-inheritance: -galaxy\.web\.formatting module ------------------------------- +galaxy.web.formatting module +---------------------------- .. automodule:: galaxy.web.formatting :members: :undoc-members: :show-inheritance: -galaxy\.web\.params module --------------------------- +galaxy.web.params module +------------------------ .. automodule:: galaxy.web.params :members: diff --git a/doc/source/lib/galaxy.web.security.rst b/doc/source/lib/galaxy.web.security.rst deleted file mode 100644 index c321bda248b..00000000000 --- a/doc/source/lib/galaxy.web.security.rst +++ /dev/null @@ -1,8 +0,0 @@ -galaxy\.web\.security package -============================= - -.. automodule:: galaxy.web.security - :members: - :undoc-members: - :show-inheritance: - diff --git a/doc/source/lib/galaxy.web.stack.rst b/doc/source/lib/galaxy.web.stack.rst deleted file mode 100644 index c2c5c305c2e..00000000000 --- a/doc/source/lib/galaxy.web.stack.rst +++ /dev/null @@ -1,36 +0,0 @@ -galaxy\.web\.stack package -========================== - -.. automodule:: galaxy.web.stack - :members: - :undoc-members: - :show-inheritance: - -Submodules ----------- - -galaxy\.web\.stack\.handlers module ------------------------------------ - -.. automodule:: galaxy.web.stack.handlers - :members: - :undoc-members: - :show-inheritance: - -galaxy\.web\.stack\.message module ----------------------------------- - -.. automodule:: galaxy.web.stack.message - :members: - :undoc-members: - :show-inheritance: - -galaxy\.web\.stack\.transport module ------------------------------------- - -.. automodule:: galaxy.web.stack.transport - :members: - :undoc-members: - :show-inheritance: - - diff --git a/doc/source/lib/galaxy.web_stack.rst b/doc/source/lib/galaxy.web_stack.rst new file mode 100644 index 00000000000..26d7b0e02d6 --- /dev/null +++ b/doc/source/lib/galaxy.web_stack.rst @@ -0,0 +1,36 @@ +galaxy.web\_stack package +========================= + +.. automodule:: galaxy.web_stack + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy.web\_stack.handlers module +--------------------------------- + +.. automodule:: galaxy.web_stack.handlers + :members: + :undoc-members: + :show-inheritance: + +galaxy.web\_stack.message module +-------------------------------- + +.. automodule:: galaxy.web_stack.message + :members: + :undoc-members: + :show-inheritance: + +galaxy.web\_stack.transport module +---------------------------------- + +.. automodule:: galaxy.web_stack.transport + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy.webapps.galaxy.api.rst b/doc/source/lib/galaxy.webapps.galaxy.api.rst index 2f91b43359a..fffbce8dbf1 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.api.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.api.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.galaxy\.api package -==================================== +galaxy.webapps.galaxy.api package +================================= .. automodule:: galaxy.webapps.galaxy.api :members: @@ -9,360 +9,368 @@ galaxy\.webapps\.galaxy\.api package Submodules ---------- -galaxy\.webapps\.galaxy\.api\.annotations module ------------------------------------------------- +galaxy.webapps.galaxy.api.annotations module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.annotations :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.authenticate module -------------------------------------------------- +galaxy.webapps.galaxy.api.authenticate module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.authenticate :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.cloud module ------------------------------------------- +galaxy.webapps.galaxy.api.cloud module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.cloud :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.cloudauthz module ------------------------------------------------ +galaxy.webapps.galaxy.api.cloudauthz module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.cloudauthz :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.configuration module --------------------------------------------------- +galaxy.webapps.galaxy.api.configuration module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.configuration :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.dataset\_collections module ---------------------------------------------------------- +galaxy.webapps.galaxy.api.dataset\_collections module +----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.dataset_collections :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.datasets module ---------------------------------------------- +galaxy.webapps.galaxy.api.datasets module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.datasets :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.datatypes module ----------------------------------------------- +galaxy.webapps.galaxy.api.datatypes module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.datatypes :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.display\_applications module ----------------------------------------------------------- +galaxy.webapps.galaxy.api.display\_applications module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.display_applications :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.extended\_metadata module -------------------------------------------------------- +galaxy.webapps.galaxy.api.dynamic\_tools module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.api.dynamic_tools + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.api.extended\_metadata module +--------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.extended_metadata :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.folder\_contents module ------------------------------------------------------ +galaxy.webapps.galaxy.api.folder\_contents module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.folder_contents :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.folders module --------------------------------------------- +galaxy.webapps.galaxy.api.folders module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.folders :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.forms module ------------------------------------------- +galaxy.webapps.galaxy.api.forms module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.forms :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.genomes module --------------------------------------------- +galaxy.webapps.galaxy.api.genomes module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.genomes :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.group\_roles module -------------------------------------------------- +galaxy.webapps.galaxy.api.group\_roles module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_roles :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.group\_users module -------------------------------------------------- +galaxy.webapps.galaxy.api.group\_users module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.group_users :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.groups module -------------------------------------------- +galaxy.webapps.galaxy.api.groups module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.groups :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.histories module ----------------------------------------------- +galaxy.webapps.galaxy.api.histories module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.histories :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.history\_contents module ------------------------------------------------------- +galaxy.webapps.galaxy.api.history\_contents module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.history_contents :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.item\_tags module ------------------------------------------------ +galaxy.webapps.galaxy.api.item\_tags module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.item_tags :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.job\_files module ------------------------------------------------ +galaxy.webapps.galaxy.api.job\_files module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.job_files :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.jobs module ------------------------------------------ +galaxy.webapps.galaxy.api.jobs module +------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.jobs :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.libraries module ----------------------------------------------- +galaxy.webapps.galaxy.api.libraries module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.libraries :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.library\_contents module ------------------------------------------------------- +galaxy.webapps.galaxy.api.library\_contents module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.library_contents :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.library\_datasets module ------------------------------------------------------- +galaxy.webapps.galaxy.api.library\_datasets module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.library_datasets :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.metrics module --------------------------------------------- +galaxy.webapps.galaxy.api.metrics module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.metrics :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.page\_revisions module ----------------------------------------------------- +galaxy.webapps.galaxy.api.page\_revisions module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.page_revisions :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.pages module ------------------------------------------- +galaxy.webapps.galaxy.api.pages module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.pages :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.plugins module --------------------------------------------- +galaxy.webapps.galaxy.api.plugins module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.plugins :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.provenance module ------------------------------------------------ +galaxy.webapps.galaxy.api.provenance module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.provenance :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.quotas module -------------------------------------------- +galaxy.webapps.galaxy.api.quotas module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.quotas :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.remote\_files module --------------------------------------------------- +galaxy.webapps.galaxy.api.remote\_files module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.remote_files :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.roles module ------------------------------------------- +galaxy.webapps.galaxy.api.roles module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.roles :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.search module -------------------------------------------- +galaxy.webapps.galaxy.api.search module +--------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.search :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tool\_data module ------------------------------------------------ +galaxy.webapps.galaxy.api.tool\_data module +------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_data :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tool\_dependencies module -------------------------------------------------------- +galaxy.webapps.galaxy.api.tool\_dependencies module +--------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_dependencies :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tool\_shed\_repositories module -------------------------------------------------------------- +galaxy.webapps.galaxy.api.tool\_shed\_repositories module +--------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tool_shed_repositories :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tools module ------------------------------------------- +galaxy.webapps.galaxy.api.tools module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tools :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.toolshed module ---------------------------------------------- +galaxy.webapps.galaxy.api.toolshed module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.toolshed :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.tours module ------------------------------------------- +galaxy.webapps.galaxy.api.tours module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.tours :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.uploads module --------------------------------------------- +galaxy.webapps.galaxy.api.uploads module +---------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.uploads :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.users module ------------------------------------------- +galaxy.webapps.galaxy.api.users module +-------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.users :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.visualizations module ---------------------------------------------------- +galaxy.webapps.galaxy.api.visualizations module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.visualizations :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.webhooks module ---------------------------------------------- +galaxy.webapps.galaxy.api.webhooks module +----------------------------------------- .. automodule:: galaxy.webapps.galaxy.api.webhooks :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.api\.workflows module ----------------------------------------------- +galaxy.webapps.galaxy.api.workflows module +------------------------------------------ .. automodule:: galaxy.webapps.galaxy.api.workflows :members: diff --git a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst index a30a246f2d9..880ae45d9ba 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.controllers.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.controllers.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.galaxy\.controllers package -============================================ +galaxy.webapps.galaxy.controllers package +========================================= .. automodule:: galaxy.webapps.galaxy.controllers :members: @@ -9,160 +9,168 @@ galaxy\.webapps\.galaxy\.controllers package Submodules ---------- -galaxy\.webapps\.galaxy\.controllers\.admin module --------------------------------------------------- +galaxy.webapps.galaxy.controllers.admin module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.admin\_toolshed module ------------------------------------------------------------- +galaxy.webapps.galaxy.controllers.admin\_toolshed module +-------------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.admin_toolshed :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.async module --------------------------------------------------- +galaxy.webapps.galaxy.controllers.async module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.async :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.authnz module ---------------------------------------------------- +galaxy.webapps.galaxy.controllers.authnz module +----------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.authnz :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.biostar module ----------------------------------------------------- - -.. automodule:: galaxy.webapps.galaxy.controllers.biostar - :members: - :undoc-members: - :show-inheritance: - -galaxy\.webapps\.galaxy\.controllers\.data\_manager module ----------------------------------------------------------- +galaxy.webapps.galaxy.controllers.data\_manager module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.data_manager :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.dataset module ----------------------------------------------------- +galaxy.webapps.galaxy.controllers.dataset module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.dataset :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.error module --------------------------------------------------- +galaxy.webapps.galaxy.controllers.error module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.error :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.forms module --------------------------------------------------- +galaxy.webapps.galaxy.controllers.forms module +---------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.forms :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.history module ----------------------------------------------------- +galaxy.webapps.galaxy.controllers.history module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.history :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.interactive\_environments module ----------------------------------------------------------------------- +galaxy.webapps.galaxy.controllers.interactive\_environments module +------------------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.interactive_environments :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.library module ----------------------------------------------------- +galaxy.webapps.galaxy.controllers.library module +------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.library :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.page module -------------------------------------------------- +galaxy.webapps.galaxy.controllers.openid module +----------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.openid + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.controllers.page module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.page :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.root module -------------------------------------------------- +galaxy.webapps.galaxy.controllers.root module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.root :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.tag module ------------------------------------------------- +galaxy.webapps.galaxy.controllers.shed\_tool\_static module +----------------------------------------------------------- + +.. automodule:: galaxy.webapps.galaxy.controllers.shed_tool_static + :members: + :undoc-members: + :show-inheritance: + +galaxy.webapps.galaxy.controllers.tag module +-------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tag :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.tool\_runner module ---------------------------------------------------------- +galaxy.webapps.galaxy.controllers.tool\_runner module +----------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.tool_runner :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.user module -------------------------------------------------- +galaxy.webapps.galaxy.controllers.user module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.user :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.userskeys module ------------------------------------------------------- +galaxy.webapps.galaxy.controllers.userskeys module +-------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.userskeys :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.visualization module ----------------------------------------------------------- +galaxy.webapps.galaxy.controllers.visualization module +------------------------------------------------------ .. automodule:: galaxy.webapps.galaxy.controllers.visualization :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.controllers\.workflow module ------------------------------------------------------ +galaxy.webapps.galaxy.controllers.workflow module +------------------------------------------------- .. automodule:: galaxy.webapps.galaxy.controllers.workflow :members: diff --git a/doc/source/lib/galaxy.webapps.galaxy.rst b/doc/source/lib/galaxy.webapps.galaxy.rst index e9a3b53c3b2..f5e0f2027ef 100644 --- a/doc/source/lib/galaxy.webapps.galaxy.rst +++ b/doc/source/lib/galaxy.webapps.galaxy.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.galaxy package -=============================== +galaxy.webapps.galaxy package +============================= .. automodule:: galaxy.webapps.galaxy :members: @@ -17,16 +17,16 @@ Subpackages Submodules ---------- -galaxy\.webapps\.galaxy\.buildapp module ----------------------------------------- +galaxy.webapps.galaxy.buildapp module +------------------------------------- .. automodule:: galaxy.webapps.galaxy.buildapp :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.galaxy\.config\_watchers module ------------------------------------------------- +galaxy.webapps.galaxy.config\_watchers module +--------------------------------------------- .. automodule:: galaxy.webapps.galaxy.config_watchers :members: diff --git a/doc/source/lib/galaxy.webapps.reports.controllers.rst b/doc/source/lib/galaxy.webapps.reports.controllers.rst index 8b969287dc6..b6039634602 100644 --- a/doc/source/lib/galaxy.webapps.reports.controllers.rst +++ b/doc/source/lib/galaxy.webapps.reports.controllers.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.reports\.controllers package -============================================= +galaxy.webapps.reports.controllers package +========================================== .. automodule:: galaxy.webapps.reports.controllers :members: @@ -9,72 +9,72 @@ galaxy\.webapps\.reports\.controllers package Submodules ---------- -galaxy\.webapps\.reports\.controllers\.history module ------------------------------------------------------ +galaxy.webapps.reports.controllers.history module +------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.history :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.home module --------------------------------------------------- +galaxy.webapps.reports.controllers.home module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.home :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.jobs module --------------------------------------------------- +galaxy.webapps.reports.controllers.jobs module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.jobs :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.query module ---------------------------------------------------- +galaxy.webapps.reports.controllers.query module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.query :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.root module --------------------------------------------------- +galaxy.webapps.reports.controllers.root module +---------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.root :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.system module ----------------------------------------------------- +galaxy.webapps.reports.controllers.system module +------------------------------------------------ .. automodule:: galaxy.webapps.reports.controllers.system :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.tools module ---------------------------------------------------- +galaxy.webapps.reports.controllers.tools module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.tools :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.users module ---------------------------------------------------- +galaxy.webapps.reports.controllers.users module +----------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.users :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.controllers\.workflows module -------------------------------------------------------- +galaxy.webapps.reports.controllers.workflows module +--------------------------------------------------- .. automodule:: galaxy.webapps.reports.controllers.workflows :members: diff --git a/doc/source/lib/galaxy.webapps.reports.framework.rst b/doc/source/lib/galaxy.webapps.reports.framework.rst index 0b5a37f2e89..0d4cec5661f 100644 --- a/doc/source/lib/galaxy.webapps.reports.framework.rst +++ b/doc/source/lib/galaxy.webapps.reports.framework.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.reports\.framework package -=========================================== +galaxy.webapps.reports.framework package +======================================== .. automodule:: galaxy.webapps.reports.framework :members: @@ -9,8 +9,8 @@ galaxy\.webapps\.reports\.framework package Submodules ---------- -galaxy\.webapps\.reports\.framework\.grids module -------------------------------------------------- +galaxy.webapps.reports.framework.grids module +--------------------------------------------- .. automodule:: galaxy.webapps.reports.framework.grids :members: diff --git a/doc/source/lib/galaxy.webapps.reports.rst b/doc/source/lib/galaxy.webapps.reports.rst index 4e74f62ff70..84dcee28911 100644 --- a/doc/source/lib/galaxy.webapps.reports.rst +++ b/doc/source/lib/galaxy.webapps.reports.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.reports package -================================ +galaxy.webapps.reports package +============================== .. automodule:: galaxy.webapps.reports :members: @@ -17,24 +17,24 @@ Subpackages Submodules ---------- -galaxy\.webapps\.reports\.app module ------------------------------------- +galaxy.webapps.reports.app module +--------------------------------- .. automodule:: galaxy.webapps.reports.app :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.buildapp module ------------------------------------------ +galaxy.webapps.reports.buildapp module +-------------------------------------- .. automodule:: galaxy.webapps.reports.buildapp :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.reports\.config module ---------------------------------------- +galaxy.webapps.reports.config module +------------------------------------ .. automodule:: galaxy.webapps.reports.config :members: diff --git a/doc/source/lib/galaxy.webapps.rst b/doc/source/lib/galaxy.webapps.rst index 59ecc84180d..0ca4f9f0d3a 100644 --- a/doc/source/lib/galaxy.webapps.rst +++ b/doc/source/lib/galaxy.webapps.rst @@ -1,5 +1,5 @@ -galaxy\.webapps package -======================= +galaxy.webapps package +====================== .. automodule:: galaxy.webapps :members: @@ -18,16 +18,16 @@ Subpackages Submodules ---------- -galaxy\.webapps\.config\_manage module --------------------------------------- +galaxy.webapps.config\_manage module +------------------------------------ .. automodule:: galaxy.webapps.config_manage :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.util module ----------------------------- +galaxy.webapps.util module +-------------------------- .. automodule:: galaxy.webapps.util :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.api.rst b/doc/source/lib/galaxy.webapps.tool_shed.api.rst index 528a3eacdc1..10918ec1adf 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.api.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.api.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.api package -======================================== +galaxy.webapps.tool\_shed.api package +===================================== .. automodule:: galaxy.webapps.tool_shed.api :members: @@ -9,64 +9,64 @@ galaxy\.webapps\.tool\_shed\.api package Submodules ---------- -galaxy\.webapps\.tool\_shed\.api\.authenticate module ------------------------------------------------------ +galaxy.webapps.tool\_shed.api.authenticate module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.authenticate :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.categories module ---------------------------------------------------- +galaxy.webapps.tool\_shed.api.categories module +----------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.categories :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.configuration module ------------------------------------------------------- +galaxy.webapps.tool\_shed.api.configuration module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.configuration :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.groups module ------------------------------------------------ +galaxy.webapps.tool\_shed.api.groups module +------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.groups :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.repositories module ------------------------------------------------------ +galaxy.webapps.tool\_shed.api.repositories module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.repositories :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.repository\_revisions module --------------------------------------------------------------- +galaxy.webapps.tool\_shed.api.repository\_revisions module +---------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.api.repository_revisions :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.tools module ----------------------------------------------- +galaxy.webapps.tool\_shed.api.tools module +------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.tools :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.api\.users module ----------------------------------------------- +galaxy.webapps.tool\_shed.api.users module +------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.api.users :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst index 877e0aff95c..04a6f48e325 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.controllers.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.controllers package -================================================ +galaxy.webapps.tool\_shed.controllers package +============================================= .. automodule:: galaxy.webapps.tool_shed.controllers :members: @@ -9,56 +9,56 @@ galaxy\.webapps\.tool\_shed\.controllers package Submodules ---------- -galaxy\.webapps\.tool\_shed\.controllers\.admin module ------------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.admin module +-------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.admin :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.groups module -------------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.groups module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.groups :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.hg module ---------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.hg module +----------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.hg :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.repository module ------------------------------------------------------------ +galaxy.webapps.tool\_shed.controllers.repository module +------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.repository :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.repository\_review module -------------------------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.repository\_review module +--------------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.repository_review :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.upload module -------------------------------------------------------- +galaxy.webapps.tool\_shed.controllers.upload module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.upload :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.controllers\.user module ------------------------------------------------------ +galaxy.webapps.tool\_shed.controllers.user module +------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.controllers.user :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst index 4073f7d8f48..0272f31b493 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.middleware.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.framework\.middleware package -========================================================== +galaxy.webapps.tool\_shed.framework.middleware package +====================================================== .. automodule:: galaxy.webapps.tool_shed.framework.middleware :members: @@ -9,8 +9,8 @@ galaxy\.webapps\.tool\_shed\.framework\.middleware package Submodules ---------- -galaxy\.webapps\.tool\_shed\.framework\.middleware\.remoteuser module ---------------------------------------------------------------------- +galaxy.webapps.tool\_shed.framework.middleware.remoteuser module +---------------------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.framework.middleware.remoteuser :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst index 94949aafb2a..316a36615a8 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.framework.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.framework.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.framework package -============================================== +galaxy.webapps.tool\_shed.framework package +=========================================== .. automodule:: galaxy.webapps.tool_shed.framework :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst index 425b4c1583a..3faeb2ab908 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.migrate.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.model\.migrate package -=================================================== +galaxy.webapps.tool\_shed.model.migrate package +=============================================== .. automodule:: galaxy.webapps.tool_shed.model.migrate :members: @@ -9,8 +9,8 @@ galaxy\.webapps\.tool\_shed\.model\.migrate package Submodules ---------- -galaxy\.webapps\.tool\_shed\.model\.migrate\.check module ---------------------------------------------------------- +galaxy.webapps.tool\_shed.model.migrate.check module +---------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.model.migrate.check :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.model.rst b/doc/source/lib/galaxy.webapps.tool_shed.model.rst index 9b15ee2704a..f530aa8d272 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.model.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.model.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.model package -========================================== +galaxy.webapps.tool\_shed.model package +======================================= .. automodule:: galaxy.webapps.tool_shed.model :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -galaxy\.webapps\.tool\_shed\.model\.mapping module --------------------------------------------------- +galaxy.webapps.tool\_shed.model.mapping module +---------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.model.mapping :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.rst b/doc/source/lib/galaxy.webapps.tool_shed.rst index 2b69f949ec6..75bae1a95a2 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed package -=================================== +galaxy.webapps.tool\_shed package +================================= .. automodule:: galaxy.webapps.tool_shed :members: @@ -22,24 +22,24 @@ Subpackages Submodules ---------- -galaxy\.webapps\.tool\_shed\.app module ---------------------------------------- +galaxy.webapps.tool\_shed.app module +------------------------------------ .. automodule:: galaxy.webapps.tool_shed.app :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.buildapp module --------------------------------------------- +galaxy.webapps.tool\_shed.buildapp module +----------------------------------------- .. automodule:: galaxy.webapps.tool_shed.buildapp :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.config module ------------------------------------------- +galaxy.webapps.tool\_shed.config module +--------------------------------------- .. automodule:: galaxy.webapps.tool_shed.config :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.search.rst b/doc/source/lib/galaxy.webapps.tool_shed.search.rst index e7a919f32be..0577e985c4a 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.search.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.search.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.search package -=========================================== +galaxy.webapps.tool\_shed.search package +======================================== .. automodule:: galaxy.webapps.tool_shed.search :members: @@ -9,16 +9,16 @@ galaxy\.webapps\.tool\_shed\.search package Submodules ---------- -galaxy\.webapps\.tool\_shed\.search\.repo\_search module --------------------------------------------------------- +galaxy.webapps.tool\_shed.search.repo\_search module +---------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.search.repo_search :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.search\.tool\_search module --------------------------------------------------------- +galaxy.webapps.tool\_shed.search.tool\_search module +---------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.search.tool_search :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.security.rst b/doc/source/lib/galaxy.webapps.tool_shed.security.rst index f12f0747fba..a8923945985 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.security.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.security.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.security package -============================================= +galaxy.webapps.tool\_shed.security package +========================================== .. automodule:: galaxy.webapps.tool_shed.security :members: diff --git a/doc/source/lib/galaxy.webapps.tool_shed.util.rst b/doc/source/lib/galaxy.webapps.tool_shed.util.rst index 8081fe26591..7400a9864c3 100644 --- a/doc/source/lib/galaxy.webapps.tool_shed.util.rst +++ b/doc/source/lib/galaxy.webapps.tool_shed.util.rst @@ -1,5 +1,5 @@ -galaxy\.webapps\.tool\_shed\.util package -========================================= +galaxy.webapps.tool\_shed.util package +====================================== .. automodule:: galaxy.webapps.tool_shed.util :members: @@ -9,24 +9,24 @@ galaxy\.webapps\.tool\_shed\.util package Submodules ---------- -galaxy\.webapps\.tool\_shed\.util\.hgweb\_config module -------------------------------------------------------- +galaxy.webapps.tool\_shed.util.hgweb\_config module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.hgweb_config :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.util\.ratings\_util module -------------------------------------------------------- +galaxy.webapps.tool\_shed.util.ratings\_util module +--------------------------------------------------- .. automodule:: galaxy.webapps.tool_shed.util.ratings_util :members: :undoc-members: :show-inheritance: -galaxy\.webapps\.tool\_shed\.util\.shed\_statistics module ----------------------------------------------------------- +galaxy.webapps.tool\_shed.util.shed\_statistics module +------------------------------------------------------ .. automodule:: galaxy.webapps.tool_shed.util.shed_statistics :members: diff --git a/doc/source/lib/galaxy.webhooks.rst b/doc/source/lib/galaxy.webhooks.rst index fb714f1d80a..866964ebc4c 100644 --- a/doc/source/lib/galaxy.webhooks.rst +++ b/doc/source/lib/galaxy.webhooks.rst @@ -1,5 +1,5 @@ -galaxy\.webhooks package -======================== +galaxy.webhooks package +======================= .. automodule:: galaxy.webhooks :members: diff --git a/doc/source/lib/galaxy.work.rst b/doc/source/lib/galaxy.work.rst index a10a6da6d9b..415a5b881c8 100644 --- a/doc/source/lib/galaxy.work.rst +++ b/doc/source/lib/galaxy.work.rst @@ -1,5 +1,5 @@ -galaxy\.work package -==================== +galaxy.work package +=================== .. automodule:: galaxy.work :members: @@ -9,8 +9,8 @@ galaxy\.work package Submodules ---------- -galaxy\.work\.context module ----------------------------- +galaxy.work.context module +-------------------------- .. automodule:: galaxy.work.context :members: diff --git a/doc/source/lib/galaxy.workflow.resources.rst b/doc/source/lib/galaxy.workflow.resources.rst index 4a5ab70fb6c..30773bc1ce9 100644 --- a/doc/source/lib/galaxy.workflow.resources.rst +++ b/doc/source/lib/galaxy.workflow.resources.rst @@ -1,5 +1,5 @@ -galaxy\.workflow\.resources package -=================================== +galaxy.workflow.resources package +================================= .. automodule:: galaxy.workflow.resources :members: diff --git a/doc/source/lib/galaxy.workflow.rst b/doc/source/lib/galaxy.workflow.rst index 31ba5fdf1be..b4c6c95299c 100644 --- a/doc/source/lib/galaxy.workflow.rst +++ b/doc/source/lib/galaxy.workflow.rst @@ -1,5 +1,5 @@ -galaxy\.workflow package -======================== +galaxy.workflow package +======================= .. automodule:: galaxy.workflow :members: @@ -17,56 +17,56 @@ Subpackages Submodules ---------- -galaxy\.workflow\.extract module --------------------------------- +galaxy.workflow.extract module +------------------------------ .. automodule:: galaxy.workflow.extract :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.modules module --------------------------------- +galaxy.workflow.modules module +------------------------------ .. automodule:: galaxy.workflow.modules :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.render module -------------------------------- +galaxy.workflow.render module +----------------------------- .. automodule:: galaxy.workflow.render :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.run module ----------------------------- +galaxy.workflow.run module +-------------------------- .. automodule:: galaxy.workflow.run :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.run\_request module -------------------------------------- +galaxy.workflow.run\_request module +----------------------------------- .. automodule:: galaxy.workflow.run_request :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.scheduling\_manager module --------------------------------------------- +galaxy.workflow.scheduling\_manager module +------------------------------------------ .. automodule:: galaxy.workflow.scheduling_manager :members: :undoc-members: :show-inheritance: -galaxy\.workflow\.steps module ------------------------------- +galaxy.workflow.steps module +---------------------------- .. automodule:: galaxy.workflow.steps :members: diff --git a/doc/source/lib/galaxy.workflow.schedulers.rst b/doc/source/lib/galaxy.workflow.schedulers.rst index 8232320f3a5..43801194aa8 100644 --- a/doc/source/lib/galaxy.workflow.schedulers.rst +++ b/doc/source/lib/galaxy.workflow.schedulers.rst @@ -1,5 +1,5 @@ -galaxy\.workflow\.schedulers package -==================================== +galaxy.workflow.schedulers package +================================== .. automodule:: galaxy.workflow.schedulers :members: @@ -9,8 +9,8 @@ galaxy\.workflow\.schedulers package Submodules ---------- -galaxy\.workflow\.schedulers\.core module ------------------------------------------ +galaxy.workflow.schedulers.core module +-------------------------------------- .. automodule:: galaxy.workflow.schedulers.core :members: diff --git a/doc/source/lib/galaxy_ext.expressions.rst b/doc/source/lib/galaxy_ext.expressions.rst new file mode 100644 index 00000000000..8ddd34f7020 --- /dev/null +++ b/doc/source/lib/galaxy_ext.expressions.rst @@ -0,0 +1,20 @@ +galaxy\_ext.expressions package +=============================== + +.. automodule:: galaxy_ext.expressions + :members: + :undoc-members: + :show-inheritance: + +Submodules +---------- + +galaxy\_ext.expressions.handle\_job module +------------------------------------------ + +.. automodule:: galaxy_ext.expressions.handle_job + :members: + :undoc-members: + :show-inheritance: + + diff --git a/doc/source/lib/galaxy_ext.metadata.rst b/doc/source/lib/galaxy_ext.metadata.rst index 0beb59a7750..f02145f9106 100644 --- a/doc/source/lib/galaxy_ext.metadata.rst +++ b/doc/source/lib/galaxy_ext.metadata.rst @@ -1,5 +1,5 @@ -galaxy\_ext\.metadata package -============================= +galaxy\_ext.metadata package +============================ .. automodule:: galaxy_ext.metadata :members: @@ -9,8 +9,8 @@ galaxy\_ext\.metadata package Submodules ---------- -galaxy\_ext\.metadata\.set\_metadata module -------------------------------------------- +galaxy\_ext.metadata.set\_metadata module +----------------------------------------- .. automodule:: galaxy_ext.metadata.set_metadata :members: diff --git a/doc/source/lib/galaxy_ext.rst b/doc/source/lib/galaxy_ext.rst index b6fc32b517d..824dc1eaf63 100644 --- a/doc/source/lib/galaxy_ext.rst +++ b/doc/source/lib/galaxy_ext.rst @@ -11,5 +11,6 @@ Subpackages .. toctree:: + galaxy_ext.expressions galaxy_ext.metadata diff --git a/doc/source/lib/tool_shed.capsule.rst b/doc/source/lib/tool_shed.capsule.rst index ef81ac2ad3a..620229be4ca 100644 --- a/doc/source/lib/tool_shed.capsule.rst +++ b/doc/source/lib/tool_shed.capsule.rst @@ -1,5 +1,5 @@ -tool\_shed\.capsule package -=========================== +tool\_shed.capsule package +========================== .. automodule:: tool_shed.capsule :members: @@ -9,8 +9,8 @@ tool\_shed\.capsule package Submodules ---------- -tool\_shed\.capsule\.capsule\_manager module --------------------------------------------- +tool\_shed.capsule.capsule\_manager module +------------------------------------------ .. automodule:: tool_shed.capsule.capsule_manager :members: diff --git a/doc/source/lib/tool_shed.dependencies.repository.rst b/doc/source/lib/tool_shed.dependencies.repository.rst index 723d86b61d6..a0fec837ad4 100644 --- a/doc/source/lib/tool_shed.dependencies.repository.rst +++ b/doc/source/lib/tool_shed.dependencies.repository.rst @@ -1,5 +1,5 @@ -tool\_shed\.dependencies\.repository package -============================================ +tool\_shed.dependencies.repository package +========================================== .. automodule:: tool_shed.dependencies.repository :members: @@ -9,8 +9,8 @@ tool\_shed\.dependencies\.repository package Submodules ---------- -tool\_shed\.dependencies\.repository\.relation\_builder module --------------------------------------------------------------- +tool\_shed.dependencies.repository.relation\_builder module +----------------------------------------------------------- .. automodule:: tool_shed.dependencies.repository.relation_builder :members: diff --git a/doc/source/lib/tool_shed.dependencies.rst b/doc/source/lib/tool_shed.dependencies.rst index c273abec922..d78fa5a2b7b 100644 --- a/doc/source/lib/tool_shed.dependencies.rst +++ b/doc/source/lib/tool_shed.dependencies.rst @@ -1,5 +1,5 @@ -tool\_shed\.dependencies package -================================ +tool\_shed.dependencies package +=============================== .. automodule:: tool_shed.dependencies :members: @@ -17,8 +17,8 @@ Subpackages Submodules ---------- -tool\_shed\.dependencies\.attribute\_handlers module ----------------------------------------------------- +tool\_shed.dependencies.attribute\_handlers module +-------------------------------------------------- .. automodule:: tool_shed.dependencies.attribute_handlers :members: diff --git a/doc/source/lib/tool_shed.dependencies.tool.rst b/doc/source/lib/tool_shed.dependencies.tool.rst index a86bbcf02f2..024726c14b2 100644 --- a/doc/source/lib/tool_shed.dependencies.tool.rst +++ b/doc/source/lib/tool_shed.dependencies.tool.rst @@ -1,5 +1,5 @@ -tool\_shed\.dependencies\.tool package -====================================== +tool\_shed.dependencies.tool package +==================================== .. automodule:: tool_shed.dependencies.tool :members: @@ -9,8 +9,8 @@ tool\_shed\.dependencies\.tool package Submodules ---------- -tool\_shed\.dependencies\.tool\.tag\_attribute\_handler module --------------------------------------------------------------- +tool\_shed.dependencies.tool.tag\_attribute\_handler module +----------------------------------------------------------- .. automodule:: tool_shed.dependencies.tool.tag_attribute_handler :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst index 55842225535..b5a24ff3508 100644 --- a/doc/source/lib/tool_shed.galaxy_install.datatypes.rst +++ b/doc/source/lib/tool_shed.galaxy_install.datatypes.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.datatypes package -============================================== +tool\_shed.galaxy\_install.datatypes package +============================================ .. automodule:: tool_shed.galaxy_install.datatypes :members: @@ -9,8 +9,8 @@ tool\_shed\.galaxy\_install\.datatypes package Submodules ---------- -tool\_shed\.galaxy\_install\.datatypes\.custom\_datatype\_manager module ------------------------------------------------------------------------- +tool\_shed.galaxy\_install.datatypes.custom\_datatype\_manager module +--------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.datatypes.custom_datatype_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.grids.rst b/doc/source/lib/tool_shed.galaxy_install.grids.rst index c1f626a6926..04e2fc38e54 100644 --- a/doc/source/lib/tool_shed.galaxy_install.grids.rst +++ b/doc/source/lib/tool_shed.galaxy_install.grids.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.grids package -========================================== +tool\_shed.galaxy\_install.grids package +======================================== .. automodule:: tool_shed.galaxy_install.grids :members: @@ -9,8 +9,8 @@ tool\_shed\.galaxy\_install\.grids package Submodules ---------- -tool\_shed\.galaxy\_install\.grids\.admin\_toolshed\_grids module ------------------------------------------------------------------ +tool\_shed.galaxy\_install.grids.admin\_toolshed\_grids module +-------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.grids.admin_toolshed_grids :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.metadata.rst b/doc/source/lib/tool_shed.galaxy_install.metadata.rst index 6e21b8d2d95..a32894a3a7c 100644 --- a/doc/source/lib/tool_shed.galaxy_install.metadata.rst +++ b/doc/source/lib/tool_shed.galaxy_install.metadata.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.metadata package -============================================= +tool\_shed.galaxy\_install.metadata package +=========================================== .. automodule:: tool_shed.galaxy_install.metadata :members: @@ -9,8 +9,8 @@ tool\_shed\.galaxy\_install\.metadata package Submodules ---------- -tool\_shed\.galaxy\_install\.metadata\.installed\_repository\_metadata\_manager module --------------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.metadata.installed\_repository\_metadata\_manager module +----------------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.metadata.installed_repository_metadata_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.migrate.rst b/doc/source/lib/tool_shed.galaxy_install.migrate.rst index 2a09d1b9d07..12d29998abc 100644 --- a/doc/source/lib/tool_shed.galaxy_install.migrate.rst +++ b/doc/source/lib/tool_shed.galaxy_install.migrate.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.migrate package -============================================ +tool\_shed.galaxy\_install.migrate package +========================================== .. automodule:: tool_shed.galaxy_install.migrate :members: @@ -9,16 +9,16 @@ tool\_shed\.galaxy\_install\.migrate package Submodules ---------- -tool\_shed\.galaxy\_install\.migrate\.check module --------------------------------------------------- +tool\_shed.galaxy\_install.migrate.check module +----------------------------------------------- .. automodule:: tool_shed.galaxy_install.migrate.check :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.migrate\.common module ---------------------------------------------------- +tool\_shed.galaxy\_install.migrate.common module +------------------------------------------------ .. automodule:: tool_shed.galaxy_install.migrate.common :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst index bfd9f0ad840..e2e52b611bc 100644 --- a/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst +++ b/doc/source/lib/tool_shed.galaxy_install.repository_dependencies.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.repository\_dependencies package -============================================================= +tool\_shed.galaxy\_install.repository\_dependencies package +=========================================================== .. automodule:: tool_shed.galaxy_install.repository_dependencies :members: @@ -9,8 +9,8 @@ tool\_shed\.galaxy\_install\.repository\_dependencies package Submodules ---------- -tool\_shed\.galaxy\_install\.repository\_dependencies\.repository\_dependency\_manager module ---------------------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.repository\_dependencies.repository\_dependency\_manager module +------------------------------------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.repository_dependencies.repository_dependency_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.rst b/doc/source/lib/tool_shed.galaxy_install.rst index 0ce8f3729e9..4813a78c80d 100644 --- a/doc/source/lib/tool_shed.galaxy_install.rst +++ b/doc/source/lib/tool_shed.galaxy_install.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install package -=================================== +tool\_shed.galaxy\_install package +================================== .. automodule:: tool_shed.galaxy_install :members: @@ -23,48 +23,48 @@ Subpackages Submodules ---------- -tool\_shed\.galaxy\_install\.dependency\_display module -------------------------------------------------------- +tool\_shed.galaxy\_install.dependency\_display module +----------------------------------------------------- .. automodule:: tool_shed.galaxy_install.dependency_display :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.install\_manager module ----------------------------------------------------- +tool\_shed.galaxy\_install.install\_manager module +-------------------------------------------------- .. automodule:: tool_shed.galaxy_install.install_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.installed\_repository\_manager module ------------------------------------------------------------------- +tool\_shed.galaxy\_install.installed\_repository\_manager module +---------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.installed_repository_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.repair\_repository\_manager module ---------------------------------------------------------------- +tool\_shed.galaxy\_install.repair\_repository\_manager module +------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.repair_repository_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_migration\_manager module ------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_migration\_manager module +---------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_migration_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.update\_repository\_manager module ---------------------------------------------------------------- +tool\_shed.galaxy\_install.update\_repository\_manager module +------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.update_repository_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst index 56869254e93..a91e9694191 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.recipe.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe package -=============================================================== +tool\_shed.galaxy\_install.tool\_dependencies.recipe package +============================================================ .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe :members: @@ -9,48 +9,48 @@ tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe package Submodules ---------- -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.asynchronous\_reader module ------------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.asynchronous\_reader module +-------------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.env\_file\_builder module ----------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.env\_file\_builder module +------------------------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.install\_environment module ------------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.install\_environment module +-------------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.install_environment :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.recipe\_manager module -------------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.recipe\_manager module +--------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.step\_handler module ------------------------------------------------------------------------------ +tool\_shed.galaxy\_install.tool\_dependencies.recipe.step\_handler module +------------------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.step_handler :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tool\_dependencies\.recipe\.tag\_handler module ----------------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.recipe.tag\_handler module +------------------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst index a5064984b24..63efd9498f4 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tool_dependencies.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.tool\_dependencies package -======================================================= +tool\_shed.galaxy\_install.tool\_dependencies package +===================================================== .. automodule:: tool_shed.galaxy_install.tool_dependencies :members: @@ -16,8 +16,8 @@ Subpackages Submodules ---------- -tool\_shed\.galaxy\_install\.tool\_dependencies\.env\_manager module --------------------------------------------------------------------- +tool\_shed.galaxy\_install.tool\_dependencies.env\_manager module +----------------------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tool_dependencies.env_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.tools.rst b/doc/source/lib/tool_shed.galaxy_install.tools.rst index f62f9de8286..811e11122be 100644 --- a/doc/source/lib/tool_shed.galaxy_install.tools.rst +++ b/doc/source/lib/tool_shed.galaxy_install.tools.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.tools package -========================================== +tool\_shed.galaxy\_install.tools package +======================================== .. automodule:: tool_shed.galaxy_install.tools :members: @@ -9,16 +9,16 @@ tool\_shed\.galaxy\_install\.tools package Submodules ---------- -tool\_shed\.galaxy\_install\.tools\.data\_manager module --------------------------------------------------------- +tool\_shed.galaxy\_install.tools.data\_manager module +----------------------------------------------------- .. automodule:: tool_shed.galaxy_install.tools.data_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.galaxy\_install\.tools\.tool\_panel\_manager module ---------------------------------------------------------------- +tool\_shed.galaxy\_install.tools.tool\_panel\_manager module +------------------------------------------------------------ .. automodule:: tool_shed.galaxy_install.tools.tool_panel_manager :members: diff --git a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst index 20c6f6a504f..768dac7ce96 100644 --- a/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst +++ b/doc/source/lib/tool_shed.galaxy_install.utility_containers.rst @@ -1,5 +1,5 @@ -tool\_shed\.galaxy\_install\.utility\_containers package -======================================================== +tool\_shed.galaxy\_install.utility\_containers package +====================================================== .. automodule:: tool_shed.galaxy_install.utility_containers :members: diff --git a/doc/source/lib/tool_shed.grids.rst b/doc/source/lib/tool_shed.grids.rst index 4654eb7e4cd..59ec7e90ad8 100644 --- a/doc/source/lib/tool_shed.grids.rst +++ b/doc/source/lib/tool_shed.grids.rst @@ -1,5 +1,5 @@ -tool\_shed\.grids package -========================= +tool\_shed.grids package +======================== .. automodule:: tool_shed.grids :members: @@ -9,40 +9,40 @@ tool\_shed\.grids package Submodules ---------- -tool\_shed\.grids\.admin\_grids module --------------------------------------- +tool\_shed.grids.admin\_grids module +------------------------------------ .. automodule:: tool_shed.grids.admin_grids :members: :undoc-members: :show-inheritance: -tool\_shed\.grids\.repository\_grid\_filter\_manager module ------------------------------------------------------------ +tool\_shed.grids.repository\_grid\_filter\_manager module +--------------------------------------------------------- .. automodule:: tool_shed.grids.repository_grid_filter_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.grids\.repository\_grids module -------------------------------------------- +tool\_shed.grids.repository\_grids module +----------------------------------------- .. automodule:: tool_shed.grids.repository_grids :members: :undoc-members: :show-inheritance: -tool\_shed\.grids\.repository\_review\_grids module ---------------------------------------------------- +tool\_shed.grids.repository\_review\_grids module +------------------------------------------------- .. automodule:: tool_shed.grids.repository_review_grids :members: :undoc-members: :show-inheritance: -tool\_shed\.grids\.util module ------------------------------- +tool\_shed.grids.util module +---------------------------- .. automodule:: tool_shed.grids.util :members: diff --git a/doc/source/lib/tool_shed.managers.rst b/doc/source/lib/tool_shed.managers.rst index dabbd71ea24..5c7928cf6e1 100644 --- a/doc/source/lib/tool_shed.managers.rst +++ b/doc/source/lib/tool_shed.managers.rst @@ -1,5 +1,5 @@ -tool\_shed\.managers package -============================ +tool\_shed.managers package +=========================== .. automodule:: tool_shed.managers :members: @@ -9,16 +9,16 @@ tool\_shed\.managers package Submodules ---------- -tool\_shed\.managers\.groups module ------------------------------------ +tool\_shed.managers.groups module +--------------------------------- .. automodule:: tool_shed.managers.groups :members: :undoc-members: :show-inheritance: -tool\_shed\.managers\.repositories module ------------------------------------------ +tool\_shed.managers.repositories module +--------------------------------------- .. automodule:: tool_shed.managers.repositories :members: diff --git a/doc/source/lib/tool_shed.metadata.rst b/doc/source/lib/tool_shed.metadata.rst index 26eda3d0718..8f0215125f6 100644 --- a/doc/source/lib/tool_shed.metadata.rst +++ b/doc/source/lib/tool_shed.metadata.rst @@ -1,5 +1,5 @@ -tool\_shed\.metadata package -============================ +tool\_shed.metadata package +=========================== .. automodule:: tool_shed.metadata :members: @@ -9,16 +9,16 @@ tool\_shed\.metadata package Submodules ---------- -tool\_shed\.metadata\.metadata\_generator module ------------------------------------------------- +tool\_shed.metadata.metadata\_generator module +---------------------------------------------- .. automodule:: tool_shed.metadata.metadata_generator :members: :undoc-members: :show-inheritance: -tool\_shed\.metadata\.repository\_metadata\_manager module ----------------------------------------------------------- +tool\_shed.metadata.repository\_metadata\_manager module +-------------------------------------------------------- .. automodule:: tool_shed.metadata.repository_metadata_manager :members: diff --git a/doc/source/lib/tool_shed.repository_types.rst b/doc/source/lib/tool_shed.repository_types.rst index 67a6ba69bf3..55d6b2743bc 100644 --- a/doc/source/lib/tool_shed.repository_types.rst +++ b/doc/source/lib/tool_shed.repository_types.rst @@ -1,5 +1,5 @@ -tool\_shed\.repository\_types package -===================================== +tool\_shed.repository\_types package +==================================== .. automodule:: tool_shed.repository_types :members: @@ -9,48 +9,48 @@ tool\_shed\.repository\_types package Submodules ---------- -tool\_shed\.repository\_types\.metadata module ----------------------------------------------- +tool\_shed.repository\_types.metadata module +-------------------------------------------- .. automodule:: tool_shed.repository_types.metadata :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.registry module ----------------------------------------------- +tool\_shed.repository\_types.registry module +-------------------------------------------- .. automodule:: tool_shed.repository_types.registry :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.repository\_suite\_definition module -------------------------------------------------------------------- +tool\_shed.repository\_types.repository\_suite\_definition module +----------------------------------------------------------------- .. automodule:: tool_shed.repository_types.repository_suite_definition :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.tool\_dependency\_definition module ------------------------------------------------------------------- +tool\_shed.repository\_types.tool\_dependency\_definition module +---------------------------------------------------------------- .. automodule:: tool_shed.repository_types.tool_dependency_definition :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.unrestricted module --------------------------------------------------- +tool\_shed.repository\_types.unrestricted module +------------------------------------------------ .. automodule:: tool_shed.repository_types.unrestricted :members: :undoc-members: :show-inheritance: -tool\_shed\.repository\_types\.util module ------------------------------------------- +tool\_shed.repository\_types.util module +---------------------------------------- .. automodule:: tool_shed.repository_types.util :members: diff --git a/doc/source/lib/tool_shed.rst b/doc/source/lib/tool_shed.rst index e357746748c..3a3a78ab5b0 100644 --- a/doc/source/lib/tool_shed.rst +++ b/doc/source/lib/tool_shed.rst @@ -25,16 +25,16 @@ Subpackages Submodules ---------- -tool\_shed\.repository\_registry module ---------------------------------------- +tool\_shed.repository\_registry module +-------------------------------------- .. automodule:: tool_shed.repository_registry :members: :undoc-members: :show-inheritance: -tool\_shed\.tool\_shed\_registry module ---------------------------------------- +tool\_shed.tool\_shed\_registry module +-------------------------------------- .. automodule:: tool_shed.tool_shed_registry :members: diff --git a/doc/source/lib/tool_shed.tools.rst b/doc/source/lib/tool_shed.tools.rst index 8d4b23e6172..79b0a68851f 100644 --- a/doc/source/lib/tool_shed.tools.rst +++ b/doc/source/lib/tool_shed.tools.rst @@ -1,5 +1,5 @@ -tool\_shed\.tools package -========================= +tool\_shed.tools package +======================== .. automodule:: tool_shed.tools :members: @@ -9,24 +9,24 @@ tool\_shed\.tools package Submodules ---------- -tool\_shed\.tools\.data\_table\_manager module ----------------------------------------------- +tool\_shed.tools.data\_table\_manager module +-------------------------------------------- .. automodule:: tool_shed.tools.data_table_manager :members: :undoc-members: :show-inheritance: -tool\_shed\.tools\.tool\_validator module ------------------------------------------ +tool\_shed.tools.tool\_validator module +--------------------------------------- .. automodule:: tool_shed.tools.tool_validator :members: :undoc-members: :show-inheritance: -tool\_shed\.tools\.tool\_version\_manager module ------------------------------------------------- +tool\_shed.tools.tool\_version\_manager module +---------------------------------------------- .. automodule:: tool_shed.tools.tool_version_manager :members: diff --git a/doc/source/lib/tool_shed.util.rst b/doc/source/lib/tool_shed.util.rst index 4e5e36e3bca..cda03e77ecc 100644 --- a/doc/source/lib/tool_shed.util.rst +++ b/doc/source/lib/tool_shed.util.rst @@ -1,5 +1,5 @@ -tool\_shed\.util package -======================== +tool\_shed.util package +======================= .. automodule:: tool_shed.util :members: @@ -9,152 +9,152 @@ tool\_shed\.util package Submodules ---------- -tool\_shed\.util\.admin\_util module ------------------------------------- +tool\_shed.util.admin\_util module +---------------------------------- .. automodule:: tool_shed.util.admin_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.basic\_util module ------------------------------------- +tool\_shed.util.basic\_util module +---------------------------------- .. automodule:: tool_shed.util.basic_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.commit\_util module -------------------------------------- +tool\_shed.util.commit\_util module +----------------------------------- .. automodule:: tool_shed.util.commit_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.common\_util module -------------------------------------- +tool\_shed.util.common\_util module +----------------------------------- .. automodule:: tool_shed.util.common_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.container\_util module ----------------------------------------- +tool\_shed.util.container\_util module +-------------------------------------- .. automodule:: tool_shed.util.container_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.encoding\_util module ---------------------------------------- +tool\_shed.util.encoding\_util module +------------------------------------- .. automodule:: tool_shed.util.encoding_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.hg\_util module ---------------------------------- +tool\_shed.util.hg\_util module +------------------------------- .. automodule:: tool_shed.util.hg_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.metadata\_util module ---------------------------------------- +tool\_shed.util.metadata\_util module +------------------------------------- .. automodule:: tool_shed.util.metadata_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.readme\_util module -------------------------------------- +tool\_shed.util.readme\_util module +----------------------------------- .. automodule:: tool_shed.util.readme_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.repository\_content\_util module --------------------------------------------------- +tool\_shed.util.repository\_content\_util module +------------------------------------------------ .. automodule:: tool_shed.util.repository_content_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.repository\_util module ------------------------------------------ +tool\_shed.util.repository\_util module +--------------------------------------- .. automodule:: tool_shed.util.repository_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.review\_util module -------------------------------------- +tool\_shed.util.review\_util module +----------------------------------- .. automodule:: tool_shed.util.review_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.search\_util module -------------------------------------- +tool\_shed.util.search\_util module +----------------------------------- .. automodule:: tool_shed.util.search_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.shed\_util\_common module -------------------------------------------- +tool\_shed.util.shed\_util\_common module +----------------------------------------- .. automodule:: tool_shed.util.shed_util_common :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.tool\_dependency\_util module ------------------------------------------------ +tool\_shed.util.tool\_dependency\_util module +--------------------------------------------- .. automodule:: tool_shed.util.tool_dependency_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.tool\_util module ------------------------------------ +tool\_shed.util.tool\_util module +--------------------------------- .. automodule:: tool_shed.util.tool_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.web\_util module ----------------------------------- +tool\_shed.util.web\_util module +-------------------------------- .. automodule:: tool_shed.util.web_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.workflow\_util module ---------------------------------------- +tool\_shed.util.workflow\_util module +------------------------------------- .. automodule:: tool_shed.util.workflow_util :members: :undoc-members: :show-inheritance: -tool\_shed\.util\.xml\_util module ----------------------------------- +tool\_shed.util.xml\_util module +-------------------------------- .. automodule:: tool_shed.util.xml_util :members: diff --git a/doc/source/lib/tool_shed.utility_containers.rst b/doc/source/lib/tool_shed.utility_containers.rst index 4dd4ca953b8..f34ec9cf8f5 100644 --- a/doc/source/lib/tool_shed.utility_containers.rst +++ b/doc/source/lib/tool_shed.utility_containers.rst @@ -1,5 +1,5 @@ -tool\_shed\.utility\_containers package -======================================= +tool\_shed.utility\_containers package +====================================== .. automodule:: tool_shed.utility_containers :members: @@ -9,8 +9,8 @@ tool\_shed\.utility\_containers package Submodules ---------- -tool\_shed\.utility\_containers\.utility\_container\_manager module -------------------------------------------------------------------- +tool\_shed.utility\_containers.utility\_container\_manager module +----------------------------------------------------------------- .. automodule:: tool_shed.utility_containers.utility_container_manager :members: diff --git a/lib/galaxy/app.py b/lib/galaxy/app.py index 03d56cac84b..f704bd72bb0 100644 --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -11,6 +11,7 @@ import galaxy.queues import galaxy.quota import galaxy.security from galaxy import config, job_metrics, jobs +from galaxy.config_watchers import ConfigWatchers from galaxy.containers import build_container_interfaces from galaxy.managers.collections import DatasetCollectionManager from galaxy.managers.folders import FolderManager @@ -40,7 +41,6 @@ from galaxy.visualization.plugins.registry import VisualizationsRegistry from galaxy.web import url_for from galaxy.web.proxy import ProxyManager from galaxy.web_stack import application_stack_instance -from galaxy.webapps.galaxy.config_watchers import ConfigWatchers from galaxy.webhooks import WebhooksRegistry from tool_shed.galaxy_install import ( installed_repository_manager, diff --git a/lib/galaxy/config.py b/lib/galaxy/config.py index b3e54bc52e2..dfcfd15de42 100644 --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -506,24 +506,16 @@ class Configuration(object): self.tool_ngram_maxsize = kwargs.get("tool_ngram_maxsize", 4) default_tool_test_data_directories = os.environ.get("GALAXY_TEST_FILE_DIR", resolve_path("test-data", self.root)) self.tool_test_data_directories = kwargs.get("tool_test_data_directories", default_tool_test_data_directories) - # Location for tool dependencies. - use_tool_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies = \ - parse_dependency_options(kwargs, self.root, self.dependency_resolvers_config_file) - self.use_tool_dependencies = use_tool_dependencies - self.tool_dependency_dir = tool_dependency_dir - self.use_cached_dependency_manager = use_cached_dependency_manager - self.tool_dependency_cache_dir = tool_dependency_cache_dir - self.precache_dependencies = precache_dependencies - self.dependency_resolvers = kwargs.get("dependency_resolvers") # Deployers may either specify a complete list of mapping files or get the default for free and just # specify a local mapping file to adapt and extend the default one. - if "conda_mapping_files" in kwargs: - self.conda_mapping_files = kwargs["conda_mapping_files"] - else: - self.conda_mapping_files = [ + if "conda_mapping_files" not in kwargs: + conda_mapping_files = [ self.local_conda_mapping_file, os.path.join(self.root, "lib", "galaxy", "tool_util", "deps", "resolvers", "default_conda_mapping.yml"), ] + # dependency resolution options are consumed via config_dict - so don't populate + # self, populate config_dict + self.config_dict["conda_mapping_files"] = conda_mapping_files self.enable_beta_mulled_containers = string_as_bool(kwargs.get('enable_beta_mulled_containers', 'False')) containers_resolvers_config_file = kwargs.get('containers_resolvers_config_file', None) @@ -533,7 +525,10 @@ class Configuration(object): involucro_path = kwargs.get('involucro_path', None) if involucro_path is None: - involucro_path = os.path.join(tool_dependency_dir or "database", "involucro") + target_dir = kwargs.get("tool_dependency_dir", "database/dependencies") + if target_dir == "none": + target_dir = "database" + involucro_path = os.path.join(target_dir, "involucro") self.involucro_path = resolve_path(involucro_path, self.root) self.involucro_auto_init = string_as_bool(kwargs.get('involucro_auto_init', True)) mulled_channels = kwargs.get('mulled_channels') @@ -926,34 +921,6 @@ class Configuration(object): return [parse(v) for v in allowed_origin_hostnames if v] -def parse_dependency_options(kwargs, root, dependency_resolvers_config_file): - # Location for tool dependencies. - tool_dependency_dir = kwargs.get("tool_dependency_dir", "database/dependencies") - if tool_dependency_dir.lower() == "none": - tool_dependency_dir = None - - if tool_dependency_dir is not None: - tool_dependency_dir = resolve_path(tool_dependency_dir, root) - # Setting the following flag to true will ultimately cause tool dependencies - # to be located in the shell environment and used by the job that is executing - # the tool. - use_tool_dependencies = True - tool_dependency_cache_dir = kwargs.get('tool_dependency_cache_dir', os.path.join(tool_dependency_dir, '_cache')) - use_cached_dependency_manager = string_as_bool(kwargs.get("use_cached_dependency_manager", 'False')) - precache_dependencies = string_as_bool(kwargs.get("precache_dependencies", 'True')) - else: - tool_dependency_dir = None - if dependency_resolvers_config_file is None: - use_tool_dependencies = bool(kwargs.get("dependency_resolvers", None)) - else: - use_tool_dependencies = os.path.exists(dependency_resolvers_config_file) - tool_dependency_cache_dir = None - precache_dependencies = False - use_cached_dependency_manager = False - - return use_tool_dependencies, tool_dependency_dir, use_cached_dependency_manager, tool_dependency_cache_dir, precache_dependencies - - def get_database_engine_options(kwargs, model_prefix=''): """ Allow options for the SQLAlchemy database engine to be passed by using @@ -1230,3 +1197,7 @@ class ConfiguresGalaxyMixin(object): except Exception: log.info("Waiting for database: attempt %d of %d" % (i, attempts)) time.sleep(pause) + + @property + def tool_dependency_dir(self): + return self.toolbox.dependency_manager.default_base_path diff --git a/lib/galaxy/webapps/galaxy/config_watchers.py b/lib/galaxy/config_watchers.py similarity index 100% rename from lib/galaxy/webapps/galaxy/config_watchers.py rename to lib/galaxy/config_watchers.py diff --git a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py index 98e6af16c01..1b893f1ab5d 100644 --- a/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py +++ b/lib/galaxy/datatypes/converters/maf_to_fasta_converter.py @@ -6,7 +6,7 @@ import sys import bx.align.maf -from galaxy.tools.util import maf_utilities +from galaxy.datatypes.util import maf_utilities assert sys.version_info[:2] >= (2, 6) diff --git a/lib/galaxy/datatypes/converters/maf_to_interval_converter.py b/lib/galaxy/datatypes/converters/maf_to_interval_converter.py index 51049ed54c6..a19ab25cabb 100644 --- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.py +++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.py @@ -6,7 +6,7 @@ import sys import bx.align.maf -from galaxy.tools.util import maf_utilities +from galaxy.datatypes.util import maf_utilities assert sys.version_info[:2] >= (2, 6) diff --git a/lib/galaxy/datatypes/test/temp2.txt b/lib/galaxy/datatypes/test/temp2.txt new file mode 100644 index 00000000000..2c3f803432c --- /dev/null +++ b/lib/galaxy/datatypes/test/temp2.txt @@ -0,0 +1,2 @@ +1 2 +3 4 diff --git a/lib/galaxy/datatypes/util/maf_utilities.py b/lib/galaxy/datatypes/util/maf_utilities.py new file mode 100644 index 00000000000..3a5aa531bb2 --- /dev/null +++ b/lib/galaxy/datatypes/util/maf_utilities.py @@ -0,0 +1,760 @@ +#!/usr/bin/env python +""" +Provides wrappers and utilities for working with MAF files and alignments. +""" +# Dan Blankenberg +from __future__ import print_function + +import functools +import logging +import os +import resource +import sys +import tempfile +from copy import deepcopy +from errno import EMFILE + +import bx.align.maf +import bx.interval_index_file +import bx.intervals +from six.moves import xrange + +try: + from string import maketrans +except ImportError: + maketrans = str.maketrans + +assert sys.version_info[:2] >= (2, 6) + +log = logging.getLogger(__name__) + +GAP_CHARS = ['-'] +SRC_SPLIT_CHAR = '.' + + +def src_split(src): + fields = src.split(SRC_SPLIT_CHAR, 1) + spec = fields.pop(0) + if fields: + chrom = fields.pop(0) + else: + chrom = spec + return spec, chrom + + +def src_merge(spec, chrom, contig=None): + if None in [spec, chrom]: + spec = chrom = spec or chrom + return bx.align.maf.src_merge(spec, chrom, contig) + + +def get_species_in_block(block): + species = [] + for c in block.components: + spec, chrom = src_split(c.src) + if spec not in species: + species.append(spec) + return species + + +def tool_fail(msg="Unknown Error"): + print("Fatal Error: %s" % msg, file=sys.stderr) + sys.exit() + + +class TempFileHandler(object): + ''' + Handles creating, opening, closing, and deleting of Temp files, with a + maximum number of files open at one time. + ''' + + DEFAULT_MAX_OPEN_FILES = max(resource.getrlimit(resource.RLIMIT_NOFILE)[0] / 2, 1) + + def __init__(self, max_open_files=None, **kwds): + if max_open_files is None: + max_open_files = self.DEFAULT_MAX_OPEN_FILES + self.max_open_files = max_open_files + self.files = [] + self.open_file_indexes = [] + self.kwds = kwds + + def get_open_tempfile(self, index=None, **kwds): + if index is not None and index in self.open_file_indexes: + self.open_file_indexes.remove(index) + else: + if self.max_open_files: + while len(self.open_file_indexes) >= self.max_open_files: + self.close(self.open_file_indexes[0]) + if index is None: + index = len(self.files) + temp_kwds = dict(self.kwds) + temp_kwds.update(kwds) + # Being able to use delete=True here, would simplify a bit, + # but we support python2.4 in these tools + while True: + try: + tmp_file = tempfile.NamedTemporaryFile(**temp_kwds) + filename = tmp_file.name + break + except OSError as e: + if self.open_file_indexes and e.errno == EMFILE: + self.max_open_files = len(self.open_file_indexes) + self.close(self.open_file_indexes[0]) + else: + raise e + tmp_file.close() + self.files.append(open(filename, 'w+b')) + else: + while True: + try: + self.files[index] = open(self.files[index].name, 'r+b') + break + except OSError as e: + if self.open_file_indexes and e.errno == EMFILE: + self.max_open_files = len(self.open_file_indexes) + self.close(self.open_file_indexes[0]) + else: + raise e + self.files[index].seek(0, 2) + self.open_file_indexes.append(index) + return index, self.files[index] + + def close(self, index, delete=False): + if index in self.open_file_indexes: + self.open_file_indexes.remove(index) + rval = self.files[index].close() + if delete: + try: + os.unlink(self.files[index].name) + except OSError: + pass + return rval + + def flush(self, index): + if index in self.open_file_indexes: + self.files[index].flush() + + def __del__(self): + for i in xrange(len(self.files)): + self.close(i, delete=True) + + +# an object corresponding to a reference layered alignment +class RegionAlignment(object): + + DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca") + MAX_SEQUENCE_SIZE = sys.maxsize # Maximum length of sequence allowed + + def __init__(self, size, species=[], temp_file_handler=None): + assert size <= self.MAX_SEQUENCE_SIZE, "Maximum length allowed for an individual sequence has been exceeded (%i > %i)." % (size, self.MAX_SEQUENCE_SIZE) + self.size = size + if not temp_file_handler: + temp_file_handler = TempFileHandler() + self.temp_file_handler = temp_file_handler + self.sequences = {} + if not isinstance(species, list): + species = [species] + for spec in species: + self.add_species(spec) + + # add a species to the alignment + def add_species(self, species): + # make temporary sequence files + file_index, fh = self.temp_file_handler.get_open_tempfile() + self.sequences[species] = file_index + fh.write("-" * self.size) + + # returns the names for species found in alignment, skipping names as requested + def get_species_names(self, skip=[]): + if not isinstance(skip, list): + skip = [skip] + names = list(self.sequences.keys()) + for name in skip: + try: + names.remove(name) + except ValueError: + pass + return names + + # returns the sequence for a species + def get_sequence(self, species): + file_index, fh = self.temp_file_handler.get_open_tempfile(self.sequences[species]) + fh.seek(0) + return fh.read() + + # returns the reverse complement of the sequence for a species + def get_sequence_reverse_complement(self, species): + complement = [base for base in self.get_sequence(species).translate(self.DNA_COMPLEMENT)] + complement.reverse() + return "".join(complement) + + # sets a position for a species + def set_position(self, index, species, base): + if len(base) != 1: + raise Exception("A genomic position can only have a length of 1.") + return self.set_range(index, species, base) + # sets a range for a species + + def set_range(self, index, species, bases): + if index >= self.size or index < 0: + raise Exception("Your index (%i) is out of range (0 - %i)." % (index, self.size - 1)) + if len(bases) == 0: + raise Exception("A set of genomic positions can only have a positive length.") + if species not in self.sequences.keys(): + self.add_species(species) + file_index, fh = self.temp_file_handler.get_open_tempfile(self.sequences[species]) + fh.seek(index) + fh.write(bases) + + # Flush temp file of specified species, or all species + def flush(self, species=None): + if species is None: + species = self.sequences.keys() + elif not isinstance(species, list): + species = [species] + for spec in species: + self.temp_file_handler.flush(self.sequences[spec]) + + +class GenomicRegionAlignment(RegionAlignment): + + def __init__(self, start, end, species=[], temp_file_handler=None): + RegionAlignment.__init__(self, end - start, species, temp_file_handler=temp_file_handler) + self.start = start + self.end = end + + +class SplicedAlignment(object): + + DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca") + + def __init__(self, exon_starts, exon_ends, species=[], temp_file_handler=None): + if not isinstance(exon_starts, list): + exon_starts = [exon_starts] + if not isinstance(exon_ends, list): + exon_ends = [exon_ends] + assert len(exon_starts) == len(exon_ends), "The number of starts does not match the number of sizes." + self.exons = [] + if not temp_file_handler: + temp_file_handler = TempFileHandler() + self.temp_file_handler = temp_file_handler + for i in range(len(exon_starts)): + self.exons.append(GenomicRegionAlignment(exon_starts[i], exon_ends[i], species, temp_file_handler=temp_file_handler)) + + # returns the names for species found in alignment, skipping names as requested + def get_species_names(self, skip=[]): + if not isinstance(skip, list): + skip = [skip] + names = [] + for exon in self.exons: + for name in exon.get_species_names(skip=skip): + if name not in names: + names.append(name) + return names + + # returns the sequence for a species + def get_sequence(self, species): + index, fh = self.temp_file_handler.get_open_tempfile() + for exon in self.exons: + if species in exon.get_species_names(): + seq = exon.get_sequence(species) + # we need to refetch fh here, since exon.get_sequence( species ) uses a tempfile + # and if max==1, it would close fh + index, fh = self.temp_file_handler.get_open_tempfile(index) + fh.write(seq) + else: + fh.write("-" * exon.size) + fh.seek(0) + rval = fh.read() + self.temp_file_handler.close(index, delete=True) + return rval + + # returns the reverse complement of the sequence for a species + def get_sequence_reverse_complement(self, species): + complement = [base for base in self.get_sequence(species).translate(self.DNA_COMPLEMENT)] + complement.reverse() + return "".join(complement) + + # Start and end of coding region + @property + def start(self): + return self.exons[0].start + + @property + def end(self): + return self.exons[-1].end + + +# Open a MAF index using a UID +def maf_index_by_uid(maf_uid, index_location_file): + for line in open(index_location_file): + try: + # read each line, if not enough fields, go to next line + if line[0:1] == "#": + continue + fields = line.split('\t') + if maf_uid == fields[1]: + try: + maf_files = fields[4].replace("\n", "").replace("\r", "").split(",") + return bx.align.maf.MultiIndexed(maf_files, keep_open=True, parse_e_rows=False) + except Exception as e: + raise Exception('MAF UID (%s) found, but configuration appears to be malformed: %s' % (maf_uid, e)) + except Exception: + pass + return None + + +# return ( index, temp_index_filename ) for user maf, if available, or build one and return it, return None when no tempfile is created +def open_or_build_maf_index(maf_file, index_filename, species=None): + try: + return (bx.align.maf.Indexed(maf_file, index_filename=index_filename, keep_open=True, parse_e_rows=False), None) + except Exception: + return build_maf_index(maf_file, species=species) + + +def build_maf_index_species_chromosomes(filename, index_species=None): + species = [] + species_chromosomes = {} + indexes = bx.interval_index_file.Indexes() + blocks = 0 + try: + maf_reader = bx.align.maf.Reader(open(filename)) + while True: + pos = maf_reader.file.tell() + block = next(maf_reader) + if block is None: + break + blocks += 1 + for c in block.components: + spec = c.src + chrom = None + if "." in spec: + spec, chrom = spec.split(".", 1) + if spec not in species: + species.append(spec) + species_chromosomes[spec] = [] + if chrom and chrom not in species_chromosomes[spec]: + species_chromosomes[spec].append(chrom) + if index_species is None or spec in index_species: + forward_strand_start = c.forward_strand_start + forward_strand_end = c.forward_strand_end + try: + forward_strand_start = int(forward_strand_start) + forward_strand_end = int(forward_strand_end) + except ValueError: + continue # start and end are not integers, can't add component to index, goto next component + # this likely only occurs when parse_e_rows is True? + # could a species exist as only e rows? should the + if forward_strand_end > forward_strand_start: + # require positive length; i.e. certain lines have start = end = 0 and cannot be indexed + indexes.add(c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size) + except Exception as e: + # most likely a bad MAF + log.debug('Building MAF index on %s failed: %s' % (filename, e)) + return (None, [], {}, 0) + return (indexes, species, species_chromosomes, blocks) + + +# builds and returns ( index, index_filename ) for specified maf_file +def build_maf_index(maf_file, species=None): + indexes, found_species, species_chromosomes, blocks = build_maf_index_species_chromosomes(maf_file, species) + if indexes is not None: + fd, index_filename = tempfile.mkstemp() + out = os.fdopen(fd, 'w') + indexes.write(out) + out.close() + return (bx.align.maf.Indexed(maf_file, index_filename=index_filename, keep_open=True, parse_e_rows=False), index_filename) + return (None, None) + + +def component_overlaps_region(c, region): + if c is None: + return False + start, end = c.get_forward_strand_start(), c.get_forward_strand_end() + if region.start >= end or region.end <= start: + return False + return True + + +def chop_block_by_region(block, src, region, species=None, mincols=0): + # This chopping method was designed to maintain consistency with how start/end padding gaps have been working in Galaxy thus far: + # behavior as seen when forcing blocks to be '+' relative to src sequence (ref) and using block.slice_by_component( ref, slice_start, slice_end ) + # whether-or-not this is the 'correct' behavior is questionable, but this will at least maintain consistency + # comments welcome + slice_start = block.text_size # max for the min() + slice_end = 0 # min for the max() + old_score = block.score # save old score for later use + # We no longer assume only one occurance of src per block, so we need to check them all + for c in iter_components_by_src(block, src): + if component_overlaps_region(c, region): + if c.text is not None: + rev_strand = False + if c.strand == "-": + # We want our coord_to_col coordinates to be returned from positive stranded component + rev_strand = True + c = c.reverse_complement() + start = max(region.start, c.start) + end = min(region.end, c.end) + start = c.coord_to_col(start) + end = c.coord_to_col(end) + if rev_strand: + # need to orient slice coordinates to the original block direction + slice_len = end - start + end = len(c.text) - start + start = end - slice_len + slice_start = min(start, slice_start) + slice_end = max(end, slice_end) + + if slice_start < slice_end: + block = block.slice(slice_start, slice_end) + if block.text_size > mincols: + # restore old score, may not be accurate, but it is better than 0 for everything? + block.score = old_score + if species is not None: + block = block.limit_to_species(species) + block.remove_all_gap_columns() + return block + return None + + +def orient_block_by_region(block, src, region, force_strand=None): + # loop through components matching src, + # make sure each of these components overlap region + # cache strand for each of overlaping regions + # if force_strand / region.strand not in strand cache, reverse complement + # we could have 2 sequences with same src, overlapping region, on different strands, this would cause no reverse_complementing + strands = [c.strand for c in iter_components_by_src(block, src) if component_overlaps_region(c, region)] + if strands and (force_strand is None and region.strand not in strands) or (force_strand is not None and force_strand not in strands): + block = block.reverse_complement() + return block + + +def get_oriented_chopped_blocks_for_region(index, src, region, species=None, mincols=0, force_strand=None): + for block, idx, offset in get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols, force_strand): + yield block + + +def get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0, force_strand=None): + for block, idx, offset in get_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols): + yield orient_block_by_region(block, src, region, force_strand), idx, offset + + +# split a block with multiple occurances of src into one block per src +def iter_blocks_split_by_src(block, src): + for src_c in iter_components_by_src(block, src): + new_block = bx.align.Alignment(score=block.score, attributes=deepcopy(block.attributes)) + new_block.text_size = block.text_size + for c in block.components: + if c == src_c or c.src != src: + new_block.add_component(deepcopy(c)) # components have reference to alignment, don't want to lose reference to original alignment block in original components + yield new_block + + +# split a block into multiple blocks with all combinations of a species appearing only once per block +def iter_blocks_split_by_species(block, species=None): + def __split_components_by_species(components_by_species, new_block): + if components_by_species: + # more species with components to add to this block + components_by_species = deepcopy(components_by_species) + spec_comps = components_by_species.pop(0) + for c in spec_comps: + newer_block = deepcopy(new_block) + newer_block.add_component(deepcopy(c)) + for value in __split_components_by_species(components_by_species, newer_block): + yield value + else: + # no more components to add, yield this block + yield new_block + + # divide components by species + spec_dict = {} + if not species: + species = [] + for c in block.components: + spec, chrom = src_split(c.src) + if spec not in spec_dict: + spec_dict[spec] = [] + species.append(spec) + spec_dict[spec].append(c) + else: + for spec in species: + spec_dict[spec] = [] + for c in iter_components_by_src_start(block, spec): + spec_dict[spec].append(c) + + empty_block = bx.align.Alignment(score=block.score, attributes=deepcopy(block.attributes)) # should we copy attributes? + empty_block.text_size = block.text_size + # call recursive function to split into each combo of spec/blocks + for value in __split_components_by_species(list(spec_dict.values()), empty_block): + sort_block_components_by_block(value, block) # restore original component order + yield value + + +# generator yielding only chopped and valid blocks for a specified region +def get_chopped_blocks_for_region(index, src, region, species=None, mincols=0): + for block, idx, offset in get_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols): + yield block + + +def get_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0): + for block, idx, offset in index.get_as_iterator_with_index_and_offset(src, region.start, region.end): + block = chop_block_by_region(block, src, region, species, mincols) + if block is not None: + yield block, idx, offset + + +# returns a filled region alignment for specified regions +def get_region_alignment(index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True, temp_file_handler=None): + if species is not None: + alignment = RegionAlignment(end - start, species, temp_file_handler=temp_file_handler) + else: + alignment = RegionAlignment(end - start, primary_species, temp_file_handler=temp_file_handler) + return fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand, species, mincols, overwrite_with_gaps) + + +# reduces a block to only positions exisiting in the src provided +def reduce_block_by_primary_genome(block, species, chromosome, region_start): + # returns ( startIndex, {species:texts} + # where texts' contents are reduced to only positions existing in the primary genome + src = "%s.%s" % (species, chromosome) + ref = block.get_component_by_src(src) + start_offset = ref.start - region_start + species_texts = {} + for c in block.components: + species_texts[c.src.split('.')[0]] = list(c.text) + # remove locations which are gaps in the primary species, starting from the downstream end + for i in range(len(species_texts[species]) - 1, -1, -1): + if species_texts[species][i] == '-': + for text in species_texts.values(): + text.pop(i) + for spec, text in species_texts.items(): + species_texts[spec] = ''.join(text) + return (start_offset, species_texts) + + +# fills a region alignment +def fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True): + region = bx.intervals.Interval(start, end) + region.chrom = chrom + region.strand = strand + primary_src = "%s.%s" % (primary_species, chrom) + + # Order blocks overlaping this position by score, lowest first + blocks = [] + for block, idx, offset in index.get_as_iterator_with_index_and_offset(primary_src, start, end): + score = float(block.score) + for i in range(0, len(blocks)): + if score < blocks[i][0]: + blocks.insert(i, (score, idx, offset)) + break + else: + blocks.append((score, idx, offset)) + + # gap_chars_tuple = tuple( GAP_CHARS ) + gap_chars_str = ''.join(GAP_CHARS) + # Loop through ordered blocks and layer by increasing score + for block_dict in blocks: + for block in iter_blocks_split_by_species(block_dict[1].get_at_offset(block_dict[2])): # need to handle each occurance of sequence in block seperately + if component_overlaps_region(block.get_component_by_src(primary_src), region): + block = chop_block_by_region(block, primary_src, region, species, mincols) # chop block + block = orient_block_by_region(block, primary_src, region) # orient block + start_offset, species_texts = reduce_block_by_primary_genome(block, primary_species, chrom, start) + for spec, text in species_texts.items(): + # we should trim gaps from both sides, since these are not positions in this species genome (sequence) + text = text.rstrip(gap_chars_str) + gap_offset = 0 + # while text.startswith( gap_chars_tuple ): + while True in [text.startswith(gap_char) for gap_char in GAP_CHARS]: # python2.4 doesn't accept a tuple for .startswith() + gap_offset += 1 + text = text[1:] + if not text: + break + if text: + if overwrite_with_gaps: + alignment.set_range(start_offset + gap_offset, spec, text) + else: + for i, char in enumerate(text): + if char not in GAP_CHARS: + alignment.set_position(start_offset + gap_offset + i, spec, char) + return alignment + + +# returns a filled spliced region alignment for specified region with start and end lists +def get_spliced_region_alignment(index, primary_species, chrom, starts, ends, strand='+', species=None, mincols=0, overwrite_with_gaps=True, temp_file_handler=None): + # create spliced alignment object + if species is not None: + alignment = SplicedAlignment(starts, ends, species, temp_file_handler=temp_file_handler) + else: + alignment = SplicedAlignment(starts, ends, [primary_species], temp_file_handler=temp_file_handler) + for exon in alignment.exons: + fill_region_alignment(exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols, overwrite_with_gaps) + return alignment + + +# loop through string array, only return non-commented lines +def line_enumerator(lines, comment_start='#'): + i = 0 + for line in lines: + if not line.startswith(comment_start): + i += 1 + yield (i, line) + + +# read a GeneBed file, return list of starts, ends, raw fields +def get_starts_ends_fields_from_gene_bed(line): + # Starts and ends for exons + starts = [] + ends = [] + + fields = line.split() + # Requires atleast 12 BED columns + if len(fields) < 12: + raise Exception("Not a proper 12 column BED line (%s)." % line) + tx_start = int(fields[1]) + strand = fields[5] + if strand != '-': + strand = '+' # Default strand is + + cds_start = int(fields[6]) + cds_end = int(fields[7]) + + # Calculate and store starts and ends of coding exons + region_start, region_end = cds_start, cds_end + exon_starts = list(map(int, fields[11].rstrip(',\n').split(','))) + exon_starts = [x + tx_start for x in exon_starts] + exon_ends = list(map(int, fields[10].rstrip(',').split(','))) + exon_ends = [x + y for x, y in zip(exon_starts, exon_ends)] + for start, end in zip(exon_starts, exon_ends): + start = max(start, region_start) + end = min(end, region_end) + if start < end: + starts.append(start) + ends.append(end) + return (starts, ends, fields) + + +def iter_components_by_src(block, src): + for c in block.components: + if c.src == src: + yield c + + +def get_components_by_src(block, src): + return [value for value in iter_components_by_src(block, src)] + + +def iter_components_by_src_start(block, src): + for c in block.components: + if c.src.startswith(src): + yield c + + +def get_components_by_src_start(block, src): + return [value for value in iter_components_by_src_start(block, src)] + + +def sort_block_components_by_block(block1, block2): + # orders the components in block1 by the index of the component in block2 + # block1 must be a subset of block2 + # occurs in-place + return block1.components.sort(key=functools.cmp_to_key(lambda x, y: block2.components.index(x) - block2.components.index(y))) + + +def get_species_in_maf(maf_filename): + species = [] + for block in bx.align.maf.Reader(open(maf_filename)): + for spec in get_species_in_block(block): + if spec not in species: + species.append(spec) + return species + + +def parse_species_option(species): + if species: + species = species.split(',') + if 'None' not in species: + return species + return None # provided species was '', None, or had 'None' in it + + +def remove_temp_index_file(index_filename): + try: + os.unlink(index_filename) + except Exception: + pass + +# Below are methods to deal with FASTA files + + +def get_fasta_header(component, attributes={}, suffix=None): + header = ">%s(%s):%i-%i|" % (component.src, component.strand, component.get_forward_strand_start(), component.get_forward_strand_end()) + for key, value in attributes.items(): + header = "%s%s=%s|" % (header, key, value) + if suffix: + header = "%s%s" % (header, suffix) + else: + header = "%s%s" % (header, src_split(component.src)[0]) + return header + + +def get_attributes_from_fasta_header(header): + if not header: + return {} + attributes = {} + header = header.lstrip('>') + header = header.strip() + fields = header.split('|') + try: + region = fields[0] + region = region.split('(', 1) + temp = region[0].split('.', 1) + attributes['species'] = temp[0] + if len(temp) == 2: + attributes['chrom'] = temp[1] + else: + attributes['chrom'] = temp[0] + region = region[1].split(')', 1) + attributes['strand'] = region[0] + region = region[1].lstrip(':').split('-') + attributes['start'] = int(region[0]) + attributes['end'] = int(region[1]) + except Exception: + # fields 0 is not a region coordinate + pass + if len(fields) > 2: + for i in range(1, len(fields) - 1): + prop = fields[i].split('=', 1) + if len(prop) == 2: + attributes[prop[0]] = prop[1] + if len(fields) > 1: + attributes['__suffix__'] = fields[-1] + return attributes + + +def iter_fasta_alignment(filename): + class fastaComponent(object): + def __init__(self, species, text=""): + self.species = species + self.text = text + + def extend(self, text): + self.text = self.text + text.replace('\n', '').replace('\r', '').strip() + # yields a list of fastaComponents for a FASTA file + f = open(filename, 'rb') + components = [] + # cur_component = None + while True: + line = f.readline() + if not line: + if components: + yield components + return + line = line.strip() + if not line: + if components: + yield components + components = [] + elif line.startswith('>'): + attributes = get_attributes_from_fasta_header(line) + components.append(fastaComponent(attributes['species'])) + elif components: + components[-1].extend(line) diff --git a/lib/galaxy/jobs/__init__.py b/lib/galaxy/jobs/__init__.py index 7ec38255bb9..4d1582a936c 100644 --- a/lib/galaxy/jobs/__init__.py +++ b/lib/galaxy/jobs/__init__.py @@ -2394,22 +2394,3 @@ class NoopQueue(object): def shutdown(self): return - - -class ParallelismInfo(object): - """ - Stores the information (if any) for running multiple instances of the tool in parallel - on the same set of inputs. - """ - - def __init__(self, tag): - self.method = tag.get('method') - if isinstance(tag, dict): - items = tag.items() - else: - items = tag.attrib.items() - self.attributes = dict([item for item in items if item[0] != 'method']) - if len(self.attributes) == 0: - # legacy basic mode - provide compatible defaults - self.attributes['split_size'] = 20 - self.attributes['split_mode'] = 'number_of_parts' diff --git a/lib/galaxy/model/store/build_objects.py b/lib/galaxy/model/store/build_objects.py index bc2c4fea4f6..8cedcaffafe 100644 --- a/lib/galaxy/model/store/build_objects.py +++ b/lib/galaxy/model/store/build_objects.py @@ -14,17 +14,17 @@ from galaxy.util.bunch import Bunch DESCRIPTION = """Build import ready model objects from YAML description of files. -The positional argument to this script should be a a YAML file containing a data -fetch API-like YAML file describing files. This script will then import this data -into a defined object store and populate metadata corresponding to these files as -datasets into a "model store". +The positional argument to this script should be a a YAML file containing a +data fetch API-like YAML file describing files. This script will then import +this data into a defined object store and populate metadata corresponding to +these files as datasets into a "model store". -The YAML file should contain a dictionary of destination+elements objects or a list -of such dictionaries. Each such destination+elements dictionary should contain at least -two keys - 'destination' and 'items'. +The YAML file should contain a dictionary of destination+elements objects or a +list of such dictionaries. Each such destination+elements dictionary should +contain at least two keys - 'destination' and 'items'. -Examples of destinations for creating libraries and just populating history datasets -are as follows: +Examples of destinations for creating libraries and just populating history +datasets are as follows: ``` destination: @@ -38,10 +38,10 @@ destination: type: hdas ```` -The 'items' definition should be a list of files or library folders. If library folders -need to be setup they should each be defined with a name and recursive set of items ( -again files or folders). The following code fragment describes both a library folder -definition and a file entry: +The 'items' definition should be a list of files or library folders. If library +folders need to be setup they should each be defined with a name and recursive +set of items (again files or folders). The following code fragment describes +both a library folder definition and a file entry: ``` items: @@ -56,14 +56,15 @@ items: md5: e5d21b1ea57fc9a31f8ea0110531bf3d ``` -Currently for each file a filename must be supplied, url information will be stored if -provided but not fetched on-demand like the upload 2.0/data fetch endpoint. +Currently for each file a filename must be supplied, url information will be +stored if provided but not fetched on-demand like the upload 2.0/data fetch +endpoint. -Differences with respect to the Upload 2.0 YAML/JSON format: currently various src tags -such as 'url' are not supported, data cleaning options such as to_posix_lines, and -space_to_tab are not supported, unpacking zip files and walking directoriesm etc.. are -not supported either. The format consumed by this script should continue to evolve to -converge with the upload 2.0 format. +Differences with respect to the Upload 2.0 YAML/JSON format: currently various +src tags such as 'url' are not supported, data cleaning options such as +to_posix_lines, and space_to_tab are not supported, unpacking zip files and +walking directories etc.. are not supported either. The format consumed by +this script should continue to evolve to converge with the upload 2.0 format. """ logging.basicConfig() @@ -118,7 +119,7 @@ def main(argv=None): def _arg_parser(): - parser = argparse.ArgumentParser(description=DESCRIPTION) + parser = argparse.ArgumentParser(description=DESCRIPTION, formatter_class=argparse.RawDescriptionHelpFormatter) parser.add_argument('objects', metavar='OBJECT_CONFIG', help='config file describing files to build objects for') parser.add_argument('--object-store-config', help="object store configuration file") parser.add_argument('-e', '--export', default="export", help='export path') diff --git a/lib/galaxy/model/tags.py b/lib/galaxy/model/tags.py index 14e73d67784..3b72f31a223 100644 --- a/lib/galaxy/model/tags.py +++ b/lib/galaxy/model/tags.py @@ -30,7 +30,7 @@ class TagHandler(object): def __init__(self, sa_session): self.sa_session = sa_session # Minimum tag length. - self.min_tag_len = 2 + self.min_tag_len = 1 # Maximum tag length. self.max_tag_len = 255 # Tag separator. diff --git a/lib/galaxy/model/tool_shed_install/__init__.py b/lib/galaxy/model/tool_shed_install/__init__.py index 4aef91b43b7..1a7d611967f 100644 --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -4,7 +4,7 @@ import os from galaxy.util import asbool from galaxy.util.bunch import Bunch from galaxy.util.dictifiable import Dictifiable -from tool_shed.util import common_util +from galaxy.util.tool_shed import common_util log = logging.getLogger(__name__) @@ -555,14 +555,14 @@ class ToolDependency(object): def installation_directory(self, app): if self.type == 'package': - return os.path.join(app.config.tool_dependency_dir, + return os.path.join(app.tool_dependency_dir, self.name, self.version, self.tool_shed_repository.owner, self.tool_shed_repository.name, self.tool_shed_repository.installed_changeset_revision) if self.type == 'set_environment': - return os.path.join(app.config.tool_dependency_dir, + return os.path.join(app.tool_dependency_dir, 'environment_settings', self.name, self.tool_shed_repository.owner, diff --git a/lib/galaxy/tool_util/deps/__init__.py b/lib/galaxy/tool_util/deps/__init__.py index 397a9a12faf..af255a818de 100644 --- a/lib/galaxy/tool_util/deps/__init__.py +++ b/lib/galaxy/tool_util/deps/__init__.py @@ -10,7 +10,8 @@ from collections import OrderedDict from galaxy.util import ( hash_util, - plugin_config + plugin_config, + string_as_bool, ) from galaxy.util.oset import OrderedSet from .container_resolvers import ContainerResolver @@ -31,27 +32,59 @@ log = logging.getLogger(__name__) CONFIG_VAL_NOT_FOUND = object() -def build_dependency_manager(config): - config_dict = { - "use_tool_dependencies": getattr(config, "use_tool_dependencies", False), - "default_base_path": getattr(config, "tool_dependency_dir", None), - "conf_file": getattr(config, "dependency_resolvers_config_file", None), - "cache": getattr(config, "use_cached_dependency_manager", False), - "app_config": config, - "dependency_resolvers": getattr(config, "dependency_resolvers", None), - } - return build_dependency_manager_from_dict(config_dict) +def build_dependency_manager(app_config_dict=None, resolution_config_dict=None, conf_file=None, default_tool_dependency_dir=None): + """Build a DependencyManager object from app and/or resolution config. + If app_config_dict is specified, it should be application configuration information + and configuration options are generally named to identify the context of dependency + management (e.g. conda_prefix not prefix or use_cached_dependency_manager not cache). + resolution_config_dict if specified is assumed to be the to_dict() version of a + DependencyManager and should only contain dependency configuration options. + """ -def build_dependency_manager_from_dict(config_dict): - if config_dict.get("use_tool_dependencies", False): - dependency_manager_kwds = { - 'default_base_path': config_dict.get("default_base_path"), - 'conf_file': config_dict.get("conf_file"), - 'app_config': config_dict.get("app_config"), - "dependency_resolver_dicts": config_dict.get("dependency_resolvers"), + if app_config_dict is None: + app_config_dict = {} + else: + app_config_dict = app_config_dict.copy() + + tool_dependency_dir = app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir) + if tool_dependency_dir and tool_dependency_dir.lower() == "none": + app_config_dict["tool_dependency_dir"] = None + + if resolution_config_dict is None and "dependency_resolution" in app_config_dict: + resolution_config_dict = app_config_dict["dependency_resolution"] + + if resolution_config_dict: + # Convert local to_dict options into global ones. + + # to_dict() has "cache", "cache_dir", "use", "default_base_path", "resolvers", "precache" + app_config_props_from_resolution_config = { + "use_tool_dependencies": resolution_config_dict.get("use", None), + "tool_dependency_dir": resolution_config_dict.get("default_base_path", None), + "dependency_resolvers": resolution_config_dict.get("resolvers", None), + "tool_dependency_cache_dir": resolution_config_dict.get("cache_dir", None), + "precache_dependencies": resolution_config_dict.get("precache", None), + "use_cached_dependency_manager": resolution_config_dict.get("cache", None), } - if config_dict.get("cache"): + + for key, value in app_config_props_from_resolution_config.items(): + if value is not None: + app_config_dict[key] = value + + use_tool_dependencies = app_config_dict.get("use_tool_dependencies", None) + # if we haven't set an explicit True or False, try to infer from config... + if use_tool_dependencies is None: + use_tool_dependencies = app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir) is not None or \ + app_config_dict.get("dependency_resolvers") or \ + (conf_file and os.path.exists(conf_file)) + + if use_tool_dependencies: + dependency_manager_kwds = { + "default_base_path": app_config_dict.get("tool_dependency_dir", default_tool_dependency_dir), + "conf_file": conf_file, + "app_config": app_config_dict, + } + if string_as_bool(app_config_dict.get("use_cached_dependency_manager")): dependency_manager = CachedDependencyManager(**dependency_manager_kwds) else: dependency_manager = DependencyManager(**dependency_manager_kwds) @@ -74,7 +107,7 @@ class DependencyManager(object): """ cached = False - def __init__(self, default_base_path, conf_file=None, app_config={}, dependency_resolver_dicts=None): + def __init__(self, default_base_path, conf_file=None, app_config={}): """ Create a new dependency manager looking for packages under the paths listed in `base_paths`. The default base path is app.config.tool_dependency_dir. @@ -88,6 +121,7 @@ class DependencyManager(object): self.resolver_classes = self.__resolvers_dict() plugin_source = None + dependency_resolver_dicts = app_config.get("dependency_resolvers") if dependency_resolver_dicts is not None: plugin_source = ('dict', dependency_resolver_dicts) else: @@ -139,6 +173,10 @@ class DependencyManager(object): value = default return value + @property + def precache(self): + return string_as_bool(self.get_app_option("precache_dependencies", True)) + def dependency_shell_commands(self, requirements, **kwds): requirements_to_dependencies = self.requirements_to_dependencies(requirements, **kwds) ordered_dependencies = OrderedSet(requirements_to_dependencies.values()) @@ -281,11 +319,12 @@ class DependencyManager(object): def to_dict(self): return { + "use": True, "cache": self.cached, - "use_tool_dependencies": True, + "precache": self.precache, + "cache_dir": getattr(self, "tool_dependency_cache_dir", None), "default_base_path": self.default_base_path, - "dependency_resolvers": [m.to_dict() for m in self.dependency_resolvers], - "tool_dependency_cache_dir": getattr(self, "tool_dependency_cache_dir", None), + "resolvers": [m.to_dict() for m in self.dependency_resolvers], } @@ -294,7 +333,7 @@ class CachedDependencyManager(DependencyManager): def __init__(self, default_base_path, **kwd): super(CachedDependencyManager, self).__init__(default_base_path=default_base_path, **kwd) - self.tool_dependency_cache_dir = self.get_app_option("tool_dependency_cache_dir") + self.tool_dependency_cache_dir = self.get_app_option("tool_dependency_cache_dir") or os.path.join(default_base_path, "_cache") def build_cache(self, requirements, **kwds): resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds) @@ -323,7 +362,7 @@ class CachedDependencyManager(DependencyManager): resolved_dependencies = self.requirements_to_dependencies(requirements, **kwds) cacheable_dependencies = [dep for dep in resolved_dependencies.values() if dep.cacheable] hashed_dependencies_dir = self.get_hashed_dependencies_path(cacheable_dependencies) - if not os.path.exists(hashed_dependencies_dir) and self.get_app_option("precache_dependencies", False): + if not os.path.exists(hashed_dependencies_dir) and self.precache: # Cache not present, try to create it self.build_cache(requirements, **kwds) if os.path.exists(hashed_dependencies_dir): @@ -352,6 +391,7 @@ class CachedDependencyManager(DependencyManager): class NullDependencyManager(DependencyManager): + cached = False def __init__(self, default_base_path=None, conf_file=None, app_config={}): self.__app_config = app_config @@ -359,6 +399,7 @@ class NullDependencyManager(DependencyManager): self.dependency_resolvers = [] self._enabled_container_types = [] self._destination_for_container_type = {} + self.default_base_path = None def uses_tool_shed_dependencies(self): return False @@ -370,4 +411,4 @@ class NullDependencyManager(DependencyManager): return NullDependency(version=version, name=name) def to_dict(self): - return {"use_tool_dependencies": False} + return {"use": False} diff --git a/lib/galaxy/tool_util/deps/dockerfiles.py b/lib/galaxy/tool_util/deps/dockerfiles.py index 67944dcbc04..72a44e9a2c7 100644 --- a/lib/galaxy/tool_util/deps/dockerfiles.py +++ b/lib/galaxy/tool_util/deps/dockerfiles.py @@ -1,11 +1,11 @@ import logging import os -from ..deps import commands -from ..deps import docker_util -from ..deps.container_classes import docker_cache_path -from ..deps.requirements import parse_requirements_from_xml -from ...tools import loader_directory +from galaxy.tool_util.deps import commands +from galaxy.tool_util.deps import docker_util +from galaxy.tool_util.deps.container_classes import docker_cache_path +from galaxy.tool_util.deps.requirements import parse_requirements_from_xml +from galaxy.tool_util.loader_directory import load_tool_elements_from_path log = logging.getLogger(__name__) @@ -22,7 +22,7 @@ def docker_host_args(**kwds): def dockerfile_build(path, dockerfile=None, error=log.error, **kwds): expected_container_names = set() tool_directories = set() - for (tool_path, tool_xml) in loader_directory.load_tool_elements_from_path(path): + for (tool_path, tool_xml) in load_tool_elements_from_path(path): requirements, containers = parse_requirements_from_xml(tool_xml) for container in containers: if container.type == "docker": diff --git a/lib/galaxy/tool_util/deps/resolvers/conda.py b/lib/galaxy/tool_util/deps/resolvers/conda.py index e7f4d3a25f0..745f843b723 100644 --- a/lib/galaxy/tool_util/deps/resolvers/conda.py +++ b/lib/galaxy/tool_util/deps/resolvers/conda.py @@ -65,7 +65,7 @@ log = logging.getLogger(__name__) class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, ListableDependencyResolver, InstallableDependencyResolver, SpecificationPatternDependencyResolver, MappableDependencyResolver): - dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['conda_prefix', 'versionless', 'ensure_channels', 'auto_install', 'auto_init'] + dict_collection_visible_keys = DependencyResolver.dict_collection_visible_keys + ['conda_prefix', 'versionless', 'ensure_channels', 'auto_install', 'auto_init', 'use_local'] resolver_type = "conda" config_options = { 'prefix': None, @@ -127,6 +127,7 @@ class CondaDependencyResolver(DependencyResolver, MultipleDependencyResolver, Li copy_dependencies=copy_dependencies, use_local=use_local, ) + self.use_local = use_local self.ensure_channels = ensure_channels # Conda operations options (these define how resolution will occur) diff --git a/lib/galaxy/tools/lint.py b/lib/galaxy/tool_util/lint.py similarity index 97% rename from lib/galaxy/tools/lint.py rename to lib/galaxy/tool_util/lint.py index 7a808dad744..fee04c77ea0 100644 --- a/lib/galaxy/tools/lint.py +++ b/lib/galaxy/tool_util/lint.py @@ -28,9 +28,9 @@ def lint_xml(tool_xml, level=LEVEL_ALL, fail_level=LEVEL_WARN, extra_modules=[], def lint_tool_source_with(lint_context, tool_source, extra_modules=[]): - import galaxy.tools.linters + import galaxy.tool_util.linters tool_xml = getattr(tool_source, "xml_tree", None) - linter_modules = submodules.import_submodules(galaxy.tools.linters, ordered=True) + linter_modules = submodules.import_submodules(galaxy.tool_util.linters, ordered=True) linter_modules.extend(extra_modules) for module in linter_modules: tool_type = tool_source.parse_tool_type() or "default" diff --git a/lib/galaxy/tools/linters/__init__.py b/lib/galaxy/tool_util/linters/__init__.py similarity index 100% rename from lib/galaxy/tools/linters/__init__.py rename to lib/galaxy/tool_util/linters/__init__.py diff --git a/lib/galaxy/tools/lint_util.py b/lib/galaxy/tool_util/linters/_util.py similarity index 100% rename from lib/galaxy/tools/lint_util.py rename to lib/galaxy/tool_util/linters/_util.py diff --git a/lib/galaxy/tools/linters/citations.py b/lib/galaxy/tool_util/linters/citations.py similarity index 100% rename from lib/galaxy/tools/linters/citations.py rename to lib/galaxy/tool_util/linters/citations.py diff --git a/lib/galaxy/tools/linters/command.py b/lib/galaxy/tool_util/linters/command.py similarity index 100% rename from lib/galaxy/tools/linters/command.py rename to lib/galaxy/tool_util/linters/command.py diff --git a/lib/galaxy/tools/linters/cwl.py b/lib/galaxy/tool_util/linters/cwl.py similarity index 100% rename from lib/galaxy/tools/linters/cwl.py rename to lib/galaxy/tool_util/linters/cwl.py diff --git a/lib/galaxy/tools/linters/general.py b/lib/galaxy/tool_util/linters/general.py similarity index 100% rename from lib/galaxy/tools/linters/general.py rename to lib/galaxy/tool_util/linters/general.py diff --git a/lib/galaxy/tools/linters/help.py b/lib/galaxy/tool_util/linters/help.py similarity index 100% rename from lib/galaxy/tools/linters/help.py rename to lib/galaxy/tool_util/linters/help.py diff --git a/lib/galaxy/tools/linters/inputs.py b/lib/galaxy/tool_util/linters/inputs.py similarity index 99% rename from lib/galaxy/tools/linters/inputs.py rename to lib/galaxy/tool_util/linters/inputs.py index ffcc5c974d5..542320ef9b1 100644 --- a/lib/galaxy/tools/linters/inputs.py +++ b/lib/galaxy/tool_util/linters/inputs.py @@ -1,6 +1,6 @@ """This module contains a linting functions for tool inputs.""" from galaxy.util import string_as_bool -from ..lint_util import is_datasource +from ._util import is_datasource def lint_inputs(tool_xml, lint_ctx): diff --git a/lib/galaxy/tools/linters/outputs.py b/lib/galaxy/tool_util/linters/outputs.py similarity index 100% rename from lib/galaxy/tools/linters/outputs.py rename to lib/galaxy/tool_util/linters/outputs.py diff --git a/lib/galaxy/tools/linters/stdio.py b/lib/galaxy/tool_util/linters/stdio.py similarity index 100% rename from lib/galaxy/tools/linters/stdio.py rename to lib/galaxy/tool_util/linters/stdio.py diff --git a/lib/galaxy/tools/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py similarity index 98% rename from lib/galaxy/tools/linters/tests.py rename to lib/galaxy/tool_util/linters/tests.py index aca2351e7a8..8fc60317419 100644 --- a/lib/galaxy/tools/linters/tests.py +++ b/lib/galaxy/tool_util/linters/tests.py @@ -1,5 +1,5 @@ """This module contains a linting functions for tool tests.""" -from ..lint_util import is_datasource +from ._util import is_datasource # Misspelled so as not be picked up by nosetests. diff --git a/lib/galaxy/tools/linters/xml_order.py b/lib/galaxy/tool_util/linters/xml_order.py similarity index 100% rename from lib/galaxy/tools/linters/xml_order.py rename to lib/galaxy/tool_util/linters/xml_order.py diff --git a/lib/galaxy/tools/loader_directory.py b/lib/galaxy/tool_util/loader_directory.py similarity index 100% rename from lib/galaxy/tools/loader_directory.py rename to lib/galaxy/tool_util/loader_directory.py diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py index 24eca5a78a4..1182fac116c 100644 --- a/lib/galaxy/tool_util/parser/xml.py +++ b/lib/galaxy/tool_util/parser/xml.py @@ -95,6 +95,12 @@ class XmlToolSource(ToolSource): return [] return [edam_topic.text for edam_topic in edam_topics.findall("edam_topic")] + def parse_xrefs(self): + xrefs = self.root.find("xrefs") + if xrefs is None: + return [] + return [dict(value=xref.text.strip(), reftype=xref.attrib['type']) for xref in xrefs.findall("xref") if xref.get("type")] + def parse_description(self): return xml_text(self.root, "description") @@ -191,7 +197,6 @@ class XmlToolSource(ToolSource): parallelism = self.root.find("parallelism") parallelism_info = None if parallelism is not None and parallelism.get("method"): - from galaxy.jobs import ParallelismInfo return ParallelismInfo(parallelism) return parallelism_info @@ -1092,3 +1097,22 @@ class XmlInputSource(InputSource): case_page_source = XmlPageSource(case_elem) sources.append((value, case_page_source)) return sources + + +class ParallelismInfo(object): + """ + Stores the information (if any) for running multiple instances of the tool in parallel + on the same set of inputs. + """ + + def __init__(self, tag): + self.method = tag.get('method') + if isinstance(tag, dict): + items = tag.items() + else: + items = tag.attrib.items() + self.attributes = dict([item for item in items if item[0] != 'method']) + if len(self.attributes) == 0: + # legacy basic mode - provide compatible defaults + self.attributes['split_size'] = 20 + self.attributes['split_mode'] = 'number_of_parts' diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py index d13331cd768..8790c0419ea 100644 --- a/lib/galaxy/tool_util/parser/yaml.py +++ b/lib/galaxy/tool_util/parser/yaml.py @@ -40,6 +40,10 @@ class YamlToolSource(ToolSource): def parse_edam_topics(self): return self.root_dict.get("edam_topics", []) + def parse_xrefs(self): + xrefs = self.root_dict.get("xrefs", []) + return [dict(value=xref["value"], reftype=xref["type"]) for xref in xrefs if xref["type"]] + def parse_is_multi_byte(self): return self.root_dict.get("is_multi_byte", self.default_is_multi_byte) diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd index a9c208e62ca..2f4e839d557 100644 --- a/lib/galaxy/tool_util/xsd/galaxy.xsd +++ b/lib/galaxy/tool_util/xsd/galaxy.xsd @@ -47,6 +47,7 @@ A ``data_source`` tool contains a few more relevant attributes. + @@ -5581,14 +5582,60 @@ A tool can have any number of EDAM operation references. ]]> - - - - - - - - - + + + + + + + + + + + + `` tags. +A tool can refer multiple reference IDs. + +```xml + + + seqtk + + +``` + +]]> + + + + + + + + + The ``xref`` element specifies reference +information according to a catalog. + + + + + + Type of reference - currently ``bio.tools`` +is the only supported options. + + + + + + + + Type of Reference. + + + + + + diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index a6c9581a3be..a5892132aee 100755 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -797,6 +797,7 @@ class Tool(Dictifiable): self.containers = containers self.citations = self._parse_citations(tool_source) + self.xrefs = tool_source.parse_xrefs() # Determine if this tool can be used in workflows self.is_workflow_compatible = self.check_workflow_compatible(tool_source) @@ -1865,6 +1866,7 @@ class Tool(Dictifiable): tool_dict["edam_operations"] = self.edam_operations tool_dict["edam_topics"] = self.edam_topics + tool_dict["xrefs"] = self.xrefs # Fill in ToolShedRepository info if hasattr(self, 'tool_shed') and self.tool_shed: diff --git a/lib/galaxy/tools/toolbox/base.py b/lib/galaxy/tools/toolbox/base.py index df38375939d..de8c4bc51a3 100644 --- a/lib/galaxy/tools/toolbox/base.py +++ b/lib/galaxy/tools/toolbox/base.py @@ -12,7 +12,7 @@ from six.moves.urllib.parse import urlparse from galaxy.exceptions import MessageException, ObjectNotFound from galaxy.tool_util.deps import build_dependency_manager -from galaxy.tools.loader_directory import looks_like_a_tool +from galaxy.tool_util.loader_directory import looks_like_a_tool from galaxy.util import ( ExecutionTimer, listify, @@ -1136,7 +1136,9 @@ class BaseGalaxyToolBox(AbstractToolBox): return looks_like_a_tool(path, enable_beta_formats=getattr(self.app.config, "enable_beta_tool_formats", False)) def _init_dependency_manager(self): - self.dependency_manager = build_dependency_manager(self.app.config) + app_config_dict = self.app.config.config_dict + conf_file = app_config_dict.get("dependency_resolvers_config_file") + self.dependency_manager = build_dependency_manager(app_config_dict=app_config_dict, conf_file=conf_file, default_tool_dependency_dir="database/dependencies") def reload_dependency_manager(self): self._init_dependency_manager() diff --git a/lib/galaxy/tools/util/maf_utilities.py b/lib/galaxy/tools/util/maf_utilities.py deleted file mode 100644 index 3a5aa531bb2..00000000000 --- a/lib/galaxy/tools/util/maf_utilities.py +++ /dev/null @@ -1,760 +0,0 @@ -#!/usr/bin/env python -""" -Provides wrappers and utilities for working with MAF files and alignments. -""" -# Dan Blankenberg -from __future__ import print_function - -import functools -import logging -import os -import resource -import sys -import tempfile -from copy import deepcopy -from errno import EMFILE - -import bx.align.maf -import bx.interval_index_file -import bx.intervals -from six.moves import xrange - -try: - from string import maketrans -except ImportError: - maketrans = str.maketrans - -assert sys.version_info[:2] >= (2, 6) - -log = logging.getLogger(__name__) - -GAP_CHARS = ['-'] -SRC_SPLIT_CHAR = '.' - - -def src_split(src): - fields = src.split(SRC_SPLIT_CHAR, 1) - spec = fields.pop(0) - if fields: - chrom = fields.pop(0) - else: - chrom = spec - return spec, chrom - - -def src_merge(spec, chrom, contig=None): - if None in [spec, chrom]: - spec = chrom = spec or chrom - return bx.align.maf.src_merge(spec, chrom, contig) - - -def get_species_in_block(block): - species = [] - for c in block.components: - spec, chrom = src_split(c.src) - if spec not in species: - species.append(spec) - return species - - -def tool_fail(msg="Unknown Error"): - print("Fatal Error: %s" % msg, file=sys.stderr) - sys.exit() - - -class TempFileHandler(object): - ''' - Handles creating, opening, closing, and deleting of Temp files, with a - maximum number of files open at one time. - ''' - - DEFAULT_MAX_OPEN_FILES = max(resource.getrlimit(resource.RLIMIT_NOFILE)[0] / 2, 1) - - def __init__(self, max_open_files=None, **kwds): - if max_open_files is None: - max_open_files = self.DEFAULT_MAX_OPEN_FILES - self.max_open_files = max_open_files - self.files = [] - self.open_file_indexes = [] - self.kwds = kwds - - def get_open_tempfile(self, index=None, **kwds): - if index is not None and index in self.open_file_indexes: - self.open_file_indexes.remove(index) - else: - if self.max_open_files: - while len(self.open_file_indexes) >= self.max_open_files: - self.close(self.open_file_indexes[0]) - if index is None: - index = len(self.files) - temp_kwds = dict(self.kwds) - temp_kwds.update(kwds) - # Being able to use delete=True here, would simplify a bit, - # but we support python2.4 in these tools - while True: - try: - tmp_file = tempfile.NamedTemporaryFile(**temp_kwds) - filename = tmp_file.name - break - except OSError as e: - if self.open_file_indexes and e.errno == EMFILE: - self.max_open_files = len(self.open_file_indexes) - self.close(self.open_file_indexes[0]) - else: - raise e - tmp_file.close() - self.files.append(open(filename, 'w+b')) - else: - while True: - try: - self.files[index] = open(self.files[index].name, 'r+b') - break - except OSError as e: - if self.open_file_indexes and e.errno == EMFILE: - self.max_open_files = len(self.open_file_indexes) - self.close(self.open_file_indexes[0]) - else: - raise e - self.files[index].seek(0, 2) - self.open_file_indexes.append(index) - return index, self.files[index] - - def close(self, index, delete=False): - if index in self.open_file_indexes: - self.open_file_indexes.remove(index) - rval = self.files[index].close() - if delete: - try: - os.unlink(self.files[index].name) - except OSError: - pass - return rval - - def flush(self, index): - if index in self.open_file_indexes: - self.files[index].flush() - - def __del__(self): - for i in xrange(len(self.files)): - self.close(i, delete=True) - - -# an object corresponding to a reference layered alignment -class RegionAlignment(object): - - DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca") - MAX_SEQUENCE_SIZE = sys.maxsize # Maximum length of sequence allowed - - def __init__(self, size, species=[], temp_file_handler=None): - assert size <= self.MAX_SEQUENCE_SIZE, "Maximum length allowed for an individual sequence has been exceeded (%i > %i)." % (size, self.MAX_SEQUENCE_SIZE) - self.size = size - if not temp_file_handler: - temp_file_handler = TempFileHandler() - self.temp_file_handler = temp_file_handler - self.sequences = {} - if not isinstance(species, list): - species = [species] - for spec in species: - self.add_species(spec) - - # add a species to the alignment - def add_species(self, species): - # make temporary sequence files - file_index, fh = self.temp_file_handler.get_open_tempfile() - self.sequences[species] = file_index - fh.write("-" * self.size) - - # returns the names for species found in alignment, skipping names as requested - def get_species_names(self, skip=[]): - if not isinstance(skip, list): - skip = [skip] - names = list(self.sequences.keys()) - for name in skip: - try: - names.remove(name) - except ValueError: - pass - return names - - # returns the sequence for a species - def get_sequence(self, species): - file_index, fh = self.temp_file_handler.get_open_tempfile(self.sequences[species]) - fh.seek(0) - return fh.read() - - # returns the reverse complement of the sequence for a species - def get_sequence_reverse_complement(self, species): - complement = [base for base in self.get_sequence(species).translate(self.DNA_COMPLEMENT)] - complement.reverse() - return "".join(complement) - - # sets a position for a species - def set_position(self, index, species, base): - if len(base) != 1: - raise Exception("A genomic position can only have a length of 1.") - return self.set_range(index, species, base) - # sets a range for a species - - def set_range(self, index, species, bases): - if index >= self.size or index < 0: - raise Exception("Your index (%i) is out of range (0 - %i)." % (index, self.size - 1)) - if len(bases) == 0: - raise Exception("A set of genomic positions can only have a positive length.") - if species not in self.sequences.keys(): - self.add_species(species) - file_index, fh = self.temp_file_handler.get_open_tempfile(self.sequences[species]) - fh.seek(index) - fh.write(bases) - - # Flush temp file of specified species, or all species - def flush(self, species=None): - if species is None: - species = self.sequences.keys() - elif not isinstance(species, list): - species = [species] - for spec in species: - self.temp_file_handler.flush(self.sequences[spec]) - - -class GenomicRegionAlignment(RegionAlignment): - - def __init__(self, start, end, species=[], temp_file_handler=None): - RegionAlignment.__init__(self, end - start, species, temp_file_handler=temp_file_handler) - self.start = start - self.end = end - - -class SplicedAlignment(object): - - DNA_COMPLEMENT = maketrans("ACGTacgt", "TGCAtgca") - - def __init__(self, exon_starts, exon_ends, species=[], temp_file_handler=None): - if not isinstance(exon_starts, list): - exon_starts = [exon_starts] - if not isinstance(exon_ends, list): - exon_ends = [exon_ends] - assert len(exon_starts) == len(exon_ends), "The number of starts does not match the number of sizes." - self.exons = [] - if not temp_file_handler: - temp_file_handler = TempFileHandler() - self.temp_file_handler = temp_file_handler - for i in range(len(exon_starts)): - self.exons.append(GenomicRegionAlignment(exon_starts[i], exon_ends[i], species, temp_file_handler=temp_file_handler)) - - # returns the names for species found in alignment, skipping names as requested - def get_species_names(self, skip=[]): - if not isinstance(skip, list): - skip = [skip] - names = [] - for exon in self.exons: - for name in exon.get_species_names(skip=skip): - if name not in names: - names.append(name) - return names - - # returns the sequence for a species - def get_sequence(self, species): - index, fh = self.temp_file_handler.get_open_tempfile() - for exon in self.exons: - if species in exon.get_species_names(): - seq = exon.get_sequence(species) - # we need to refetch fh here, since exon.get_sequence( species ) uses a tempfile - # and if max==1, it would close fh - index, fh = self.temp_file_handler.get_open_tempfile(index) - fh.write(seq) - else: - fh.write("-" * exon.size) - fh.seek(0) - rval = fh.read() - self.temp_file_handler.close(index, delete=True) - return rval - - # returns the reverse complement of the sequence for a species - def get_sequence_reverse_complement(self, species): - complement = [base for base in self.get_sequence(species).translate(self.DNA_COMPLEMENT)] - complement.reverse() - return "".join(complement) - - # Start and end of coding region - @property - def start(self): - return self.exons[0].start - - @property - def end(self): - return self.exons[-1].end - - -# Open a MAF index using a UID -def maf_index_by_uid(maf_uid, index_location_file): - for line in open(index_location_file): - try: - # read each line, if not enough fields, go to next line - if line[0:1] == "#": - continue - fields = line.split('\t') - if maf_uid == fields[1]: - try: - maf_files = fields[4].replace("\n", "").replace("\r", "").split(",") - return bx.align.maf.MultiIndexed(maf_files, keep_open=True, parse_e_rows=False) - except Exception as e: - raise Exception('MAF UID (%s) found, but configuration appears to be malformed: %s' % (maf_uid, e)) - except Exception: - pass - return None - - -# return ( index, temp_index_filename ) for user maf, if available, or build one and return it, return None when no tempfile is created -def open_or_build_maf_index(maf_file, index_filename, species=None): - try: - return (bx.align.maf.Indexed(maf_file, index_filename=index_filename, keep_open=True, parse_e_rows=False), None) - except Exception: - return build_maf_index(maf_file, species=species) - - -def build_maf_index_species_chromosomes(filename, index_species=None): - species = [] - species_chromosomes = {} - indexes = bx.interval_index_file.Indexes() - blocks = 0 - try: - maf_reader = bx.align.maf.Reader(open(filename)) - while True: - pos = maf_reader.file.tell() - block = next(maf_reader) - if block is None: - break - blocks += 1 - for c in block.components: - spec = c.src - chrom = None - if "." in spec: - spec, chrom = spec.split(".", 1) - if spec not in species: - species.append(spec) - species_chromosomes[spec] = [] - if chrom and chrom not in species_chromosomes[spec]: - species_chromosomes[spec].append(chrom) - if index_species is None or spec in index_species: - forward_strand_start = c.forward_strand_start - forward_strand_end = c.forward_strand_end - try: - forward_strand_start = int(forward_strand_start) - forward_strand_end = int(forward_strand_end) - except ValueError: - continue # start and end are not integers, can't add component to index, goto next component - # this likely only occurs when parse_e_rows is True? - # could a species exist as only e rows? should the - if forward_strand_end > forward_strand_start: - # require positive length; i.e. certain lines have start = end = 0 and cannot be indexed - indexes.add(c.src, forward_strand_start, forward_strand_end, pos, max=c.src_size) - except Exception as e: - # most likely a bad MAF - log.debug('Building MAF index on %s failed: %s' % (filename, e)) - return (None, [], {}, 0) - return (indexes, species, species_chromosomes, blocks) - - -# builds and returns ( index, index_filename ) for specified maf_file -def build_maf_index(maf_file, species=None): - indexes, found_species, species_chromosomes, blocks = build_maf_index_species_chromosomes(maf_file, species) - if indexes is not None: - fd, index_filename = tempfile.mkstemp() - out = os.fdopen(fd, 'w') - indexes.write(out) - out.close() - return (bx.align.maf.Indexed(maf_file, index_filename=index_filename, keep_open=True, parse_e_rows=False), index_filename) - return (None, None) - - -def component_overlaps_region(c, region): - if c is None: - return False - start, end = c.get_forward_strand_start(), c.get_forward_strand_end() - if region.start >= end or region.end <= start: - return False - return True - - -def chop_block_by_region(block, src, region, species=None, mincols=0): - # This chopping method was designed to maintain consistency with how start/end padding gaps have been working in Galaxy thus far: - # behavior as seen when forcing blocks to be '+' relative to src sequence (ref) and using block.slice_by_component( ref, slice_start, slice_end ) - # whether-or-not this is the 'correct' behavior is questionable, but this will at least maintain consistency - # comments welcome - slice_start = block.text_size # max for the min() - slice_end = 0 # min for the max() - old_score = block.score # save old score for later use - # We no longer assume only one occurance of src per block, so we need to check them all - for c in iter_components_by_src(block, src): - if component_overlaps_region(c, region): - if c.text is not None: - rev_strand = False - if c.strand == "-": - # We want our coord_to_col coordinates to be returned from positive stranded component - rev_strand = True - c = c.reverse_complement() - start = max(region.start, c.start) - end = min(region.end, c.end) - start = c.coord_to_col(start) - end = c.coord_to_col(end) - if rev_strand: - # need to orient slice coordinates to the original block direction - slice_len = end - start - end = len(c.text) - start - start = end - slice_len - slice_start = min(start, slice_start) - slice_end = max(end, slice_end) - - if slice_start < slice_end: - block = block.slice(slice_start, slice_end) - if block.text_size > mincols: - # restore old score, may not be accurate, but it is better than 0 for everything? - block.score = old_score - if species is not None: - block = block.limit_to_species(species) - block.remove_all_gap_columns() - return block - return None - - -def orient_block_by_region(block, src, region, force_strand=None): - # loop through components matching src, - # make sure each of these components overlap region - # cache strand for each of overlaping regions - # if force_strand / region.strand not in strand cache, reverse complement - # we could have 2 sequences with same src, overlapping region, on different strands, this would cause no reverse_complementing - strands = [c.strand for c in iter_components_by_src(block, src) if component_overlaps_region(c, region)] - if strands and (force_strand is None and region.strand not in strands) or (force_strand is not None and force_strand not in strands): - block = block.reverse_complement() - return block - - -def get_oriented_chopped_blocks_for_region(index, src, region, species=None, mincols=0, force_strand=None): - for block, idx, offset in get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols, force_strand): - yield block - - -def get_oriented_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0, force_strand=None): - for block, idx, offset in get_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols): - yield orient_block_by_region(block, src, region, force_strand), idx, offset - - -# split a block with multiple occurances of src into one block per src -def iter_blocks_split_by_src(block, src): - for src_c in iter_components_by_src(block, src): - new_block = bx.align.Alignment(score=block.score, attributes=deepcopy(block.attributes)) - new_block.text_size = block.text_size - for c in block.components: - if c == src_c or c.src != src: - new_block.add_component(deepcopy(c)) # components have reference to alignment, don't want to lose reference to original alignment block in original components - yield new_block - - -# split a block into multiple blocks with all combinations of a species appearing only once per block -def iter_blocks_split_by_species(block, species=None): - def __split_components_by_species(components_by_species, new_block): - if components_by_species: - # more species with components to add to this block - components_by_species = deepcopy(components_by_species) - spec_comps = components_by_species.pop(0) - for c in spec_comps: - newer_block = deepcopy(new_block) - newer_block.add_component(deepcopy(c)) - for value in __split_components_by_species(components_by_species, newer_block): - yield value - else: - # no more components to add, yield this block - yield new_block - - # divide components by species - spec_dict = {} - if not species: - species = [] - for c in block.components: - spec, chrom = src_split(c.src) - if spec not in spec_dict: - spec_dict[spec] = [] - species.append(spec) - spec_dict[spec].append(c) - else: - for spec in species: - spec_dict[spec] = [] - for c in iter_components_by_src_start(block, spec): - spec_dict[spec].append(c) - - empty_block = bx.align.Alignment(score=block.score, attributes=deepcopy(block.attributes)) # should we copy attributes? - empty_block.text_size = block.text_size - # call recursive function to split into each combo of spec/blocks - for value in __split_components_by_species(list(spec_dict.values()), empty_block): - sort_block_components_by_block(value, block) # restore original component order - yield value - - -# generator yielding only chopped and valid blocks for a specified region -def get_chopped_blocks_for_region(index, src, region, species=None, mincols=0): - for block, idx, offset in get_chopped_blocks_with_index_offset_for_region(index, src, region, species, mincols): - yield block - - -def get_chopped_blocks_with_index_offset_for_region(index, src, region, species=None, mincols=0): - for block, idx, offset in index.get_as_iterator_with_index_and_offset(src, region.start, region.end): - block = chop_block_by_region(block, src, region, species, mincols) - if block is not None: - yield block, idx, offset - - -# returns a filled region alignment for specified regions -def get_region_alignment(index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True, temp_file_handler=None): - if species is not None: - alignment = RegionAlignment(end - start, species, temp_file_handler=temp_file_handler) - else: - alignment = RegionAlignment(end - start, primary_species, temp_file_handler=temp_file_handler) - return fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand, species, mincols, overwrite_with_gaps) - - -# reduces a block to only positions exisiting in the src provided -def reduce_block_by_primary_genome(block, species, chromosome, region_start): - # returns ( startIndex, {species:texts} - # where texts' contents are reduced to only positions existing in the primary genome - src = "%s.%s" % (species, chromosome) - ref = block.get_component_by_src(src) - start_offset = ref.start - region_start - species_texts = {} - for c in block.components: - species_texts[c.src.split('.')[0]] = list(c.text) - # remove locations which are gaps in the primary species, starting from the downstream end - for i in range(len(species_texts[species]) - 1, -1, -1): - if species_texts[species][i] == '-': - for text in species_texts.values(): - text.pop(i) - for spec, text in species_texts.items(): - species_texts[spec] = ''.join(text) - return (start_offset, species_texts) - - -# fills a region alignment -def fill_region_alignment(alignment, index, primary_species, chrom, start, end, strand='+', species=None, mincols=0, overwrite_with_gaps=True): - region = bx.intervals.Interval(start, end) - region.chrom = chrom - region.strand = strand - primary_src = "%s.%s" % (primary_species, chrom) - - # Order blocks overlaping this position by score, lowest first - blocks = [] - for block, idx, offset in index.get_as_iterator_with_index_and_offset(primary_src, start, end): - score = float(block.score) - for i in range(0, len(blocks)): - if score < blocks[i][0]: - blocks.insert(i, (score, idx, offset)) - break - else: - blocks.append((score, idx, offset)) - - # gap_chars_tuple = tuple( GAP_CHARS ) - gap_chars_str = ''.join(GAP_CHARS) - # Loop through ordered blocks and layer by increasing score - for block_dict in blocks: - for block in iter_blocks_split_by_species(block_dict[1].get_at_offset(block_dict[2])): # need to handle each occurance of sequence in block seperately - if component_overlaps_region(block.get_component_by_src(primary_src), region): - block = chop_block_by_region(block, primary_src, region, species, mincols) # chop block - block = orient_block_by_region(block, primary_src, region) # orient block - start_offset, species_texts = reduce_block_by_primary_genome(block, primary_species, chrom, start) - for spec, text in species_texts.items(): - # we should trim gaps from both sides, since these are not positions in this species genome (sequence) - text = text.rstrip(gap_chars_str) - gap_offset = 0 - # while text.startswith( gap_chars_tuple ): - while True in [text.startswith(gap_char) for gap_char in GAP_CHARS]: # python2.4 doesn't accept a tuple for .startswith() - gap_offset += 1 - text = text[1:] - if not text: - break - if text: - if overwrite_with_gaps: - alignment.set_range(start_offset + gap_offset, spec, text) - else: - for i, char in enumerate(text): - if char not in GAP_CHARS: - alignment.set_position(start_offset + gap_offset + i, spec, char) - return alignment - - -# returns a filled spliced region alignment for specified region with start and end lists -def get_spliced_region_alignment(index, primary_species, chrom, starts, ends, strand='+', species=None, mincols=0, overwrite_with_gaps=True, temp_file_handler=None): - # create spliced alignment object - if species is not None: - alignment = SplicedAlignment(starts, ends, species, temp_file_handler=temp_file_handler) - else: - alignment = SplicedAlignment(starts, ends, [primary_species], temp_file_handler=temp_file_handler) - for exon in alignment.exons: - fill_region_alignment(exon, index, primary_species, chrom, exon.start, exon.end, strand, species, mincols, overwrite_with_gaps) - return alignment - - -# loop through string array, only return non-commented lines -def line_enumerator(lines, comment_start='#'): - i = 0 - for line in lines: - if not line.startswith(comment_start): - i += 1 - yield (i, line) - - -# read a GeneBed file, return list of starts, ends, raw fields -def get_starts_ends_fields_from_gene_bed(line): - # Starts and ends for exons - starts = [] - ends = [] - - fields = line.split() - # Requires atleast 12 BED columns - if len(fields) < 12: - raise Exception("Not a proper 12 column BED line (%s)." % line) - tx_start = int(fields[1]) - strand = fields[5] - if strand != '-': - strand = '+' # Default strand is + - cds_start = int(fields[6]) - cds_end = int(fields[7]) - - # Calculate and store starts and ends of coding exons - region_start, region_end = cds_start, cds_end - exon_starts = list(map(int, fields[11].rstrip(',\n').split(','))) - exon_starts = [x + tx_start for x in exon_starts] - exon_ends = list(map(int, fields[10].rstrip(',').split(','))) - exon_ends = [x + y for x, y in zip(exon_starts, exon_ends)] - for start, end in zip(exon_starts, exon_ends): - start = max(start, region_start) - end = min(end, region_end) - if start < end: - starts.append(start) - ends.append(end) - return (starts, ends, fields) - - -def iter_components_by_src(block, src): - for c in block.components: - if c.src == src: - yield c - - -def get_components_by_src(block, src): - return [value for value in iter_components_by_src(block, src)] - - -def iter_components_by_src_start(block, src): - for c in block.components: - if c.src.startswith(src): - yield c - - -def get_components_by_src_start(block, src): - return [value for value in iter_components_by_src_start(block, src)] - - -def sort_block_components_by_block(block1, block2): - # orders the components in block1 by the index of the component in block2 - # block1 must be a subset of block2 - # occurs in-place - return block1.components.sort(key=functools.cmp_to_key(lambda x, y: block2.components.index(x) - block2.components.index(y))) - - -def get_species_in_maf(maf_filename): - species = [] - for block in bx.align.maf.Reader(open(maf_filename)): - for spec in get_species_in_block(block): - if spec not in species: - species.append(spec) - return species - - -def parse_species_option(species): - if species: - species = species.split(',') - if 'None' not in species: - return species - return None # provided species was '', None, or had 'None' in it - - -def remove_temp_index_file(index_filename): - try: - os.unlink(index_filename) - except Exception: - pass - -# Below are methods to deal with FASTA files - - -def get_fasta_header(component, attributes={}, suffix=None): - header = ">%s(%s):%i-%i|" % (component.src, component.strand, component.get_forward_strand_start(), component.get_forward_strand_end()) - for key, value in attributes.items(): - header = "%s%s=%s|" % (header, key, value) - if suffix: - header = "%s%s" % (header, suffix) - else: - header = "%s%s" % (header, src_split(component.src)[0]) - return header - - -def get_attributes_from_fasta_header(header): - if not header: - return {} - attributes = {} - header = header.lstrip('>') - header = header.strip() - fields = header.split('|') - try: - region = fields[0] - region = region.split('(', 1) - temp = region[0].split('.', 1) - attributes['species'] = temp[0] - if len(temp) == 2: - attributes['chrom'] = temp[1] - else: - attributes['chrom'] = temp[0] - region = region[1].split(')', 1) - attributes['strand'] = region[0] - region = region[1].lstrip(':').split('-') - attributes['start'] = int(region[0]) - attributes['end'] = int(region[1]) - except Exception: - # fields 0 is not a region coordinate - pass - if len(fields) > 2: - for i in range(1, len(fields) - 1): - prop = fields[i].split('=', 1) - if len(prop) == 2: - attributes[prop[0]] = prop[1] - if len(fields) > 1: - attributes['__suffix__'] = fields[-1] - return attributes - - -def iter_fasta_alignment(filename): - class fastaComponent(object): - def __init__(self, species, text=""): - self.species = species - self.text = text - - def extend(self, text): - self.text = self.text + text.replace('\n', '').replace('\r', '').strip() - # yields a list of fastaComponents for a FASTA file - f = open(filename, 'rb') - components = [] - # cur_component = None - while True: - line = f.readline() - if not line: - if components: - yield components - return - line = line.strip() - if not line: - if components: - yield components - components = [] - elif line.startswith('>'): - attributes = get_attributes_from_fasta_header(line) - components.append(fastaComponent(attributes['species'])) - elif components: - components[-1].extend(line) diff --git a/lib/galaxy/tools/util/maf_utilities.py b/lib/galaxy/tools/util/maf_utilities.py new file mode 120000 index 00000000000..07bafe2d1a5 --- /dev/null +++ b/lib/galaxy/tools/util/maf_utilities.py @@ -0,0 +1 @@ +../../datatypes/util/maf_utilities.py \ No newline at end of file diff --git a/lib/galaxy/web/base/__init__.py b/lib/galaxy/util/tool_shed/__init__.py similarity index 100% rename from lib/galaxy/web/base/__init__.py rename to lib/galaxy/util/tool_shed/__init__.py diff --git a/lib/galaxy/util/tool_shed/common_util.py b/lib/galaxy/util/tool_shed/common_util.py new file mode 100644 index 00000000000..1faa08ac6b4 --- /dev/null +++ b/lib/galaxy/util/tool_shed/common_util.py @@ -0,0 +1,362 @@ +import json +import logging +import os + +from routes import url_for +from six.moves.urllib.parse import urljoin + +from galaxy import util +from galaxy.util.odict import odict +from galaxy.util.tool_shed import encoding_util, xml_util + +log = logging.getLogger(__name__) + +REPOSITORY_OWNER = 'devteam' + + +def accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies): + if tool_shed_accessible: + if tool_dependencies: + for tool_dependency in tool_dependencies: + if tool_dependency not in all_tool_dependencies: + all_tool_dependencies.append(tool_dependency) + return all_tool_dependencies + + +def check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number): + # Get the 000x_tools.xml file associated with the current migrate_tools version number. + tools_xml_file_path = os.path.abspath(os.path.join('scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number)) + # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. + migrated_tool_configs_dict = odict() + tree, error_message = xml_util.parse_xml(tools_xml_file_path) + if tree is None: + return False, odict() + root = tree.getroot() + tool_shed = root.get('name') + tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, tool_shed) + # The default behavior is that the tool shed is down. + tool_shed_accessible = False + missing_tool_configs_dict = odict() + if tool_shed_url: + for elem in root: + if elem.tag == 'repository': + repository_dependencies = [] + all_tool_dependencies = [] + repository_name = elem.get('name') + changeset_revision = elem.get('changeset_revision') + tool_shed_accessible, repository_dependencies_dict = get_repository_dependencies(app, + tool_shed_url, + repository_name, + REPOSITORY_OWNER, + changeset_revision) + if tool_shed_accessible: + # Accumulate all tool dependencies defined for repository dependencies for display to the user. + for rd_key, rd_tups in repository_dependencies_dict.items(): + if rd_key in ['root_key', 'description']: + continue + for rd_tup in rd_tups: + tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ + parse_repository_dependency_tuple(rd_tup) + tool_shed_accessible, tool_dependencies = get_tool_dependencies(app, + tool_shed_url, + name, + owner, + changeset_revision) + all_tool_dependencies = accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies) + tool_shed_accessible, tool_dependencies = get_tool_dependencies(app, + tool_shed_url, + repository_name, + REPOSITORY_OWNER, + changeset_revision) + all_tool_dependencies = accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies) + for tool_elem in elem.findall('tool'): + tool_config_file_name = tool_elem.get('file') + if tool_config_file_name: + # We currently do nothing with repository dependencies except install them (we do not display repositories that will be + # installed to the user). However, we'll store them in the following dictionary in case we choose to display them in the + # future. + dependencies_dict = dict(tool_dependencies=all_tool_dependencies, + repository_dependencies=repository_dependencies) + migrated_tool_configs_dict[tool_config_file_name] = dependencies_dict + else: + break + if tool_shed_accessible: + # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. + for tool_panel_config in tool_panel_configs: + tree, error_message = xml_util.parse_xml(tool_panel_config) + if tree: + root = tree.getroot() + for elem in root: + if elem.tag == 'tool': + missing_tool_configs_dict = check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict) + elif elem.tag == 'section': + for section_elem in elem: + if section_elem.tag == 'tool': + missing_tool_configs_dict = check_tool_tag_set(section_elem, migrated_tool_configs_dict, missing_tool_configs_dict) + else: + exception_msg = '\n\nThe entry for the main Galaxy tool shed at %s is missing from the %s file. ' % (tool_shed, app.config.tool_sheds_config) + exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n' + raise Exception(exception_msg) + return tool_shed_accessible, missing_tool_configs_dict + + +def check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict): + file_path = elem.get('file', None) + if file_path: + name = os.path.basename(file_path) + for migrated_tool_config in migrated_tool_configs_dict.keys(): + if migrated_tool_config in [file_path, name]: + missing_tool_configs_dict[name] = migrated_tool_configs_dict[migrated_tool_config] + return missing_tool_configs_dict + + +def generate_clone_url_for_installed_repository(app, repository): + """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" + tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, str(repository.tool_shed)) + return util.build_url(tool_shed_url, pathspec=['repos', str(repository.owner), str(repository.name)]) + + +def generate_clone_url_for_repository_in_tool_shed(user, repository): + """Generate the URL for cloning a repository that is in the tool shed.""" + base_url = url_for('/', qualified=True).rstrip('/') + if user: + protocol, base = base_url.split('://') + username = '%s@' % user.username + return '%s://%s%s/repos/%s/%s' % (protocol, username, base, repository.user.username, repository.name) + else: + return '%s/repos/%s/%s' % (base_url, repository.user.username, repository.name) + + +def generate_clone_url_from_repo_info_tup(app, repo_info_tup): + """Generate the URL for cloning a repository given a tuple of toolshed, name, owner, changeset_revision.""" + # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab', False] + toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ + parse_repository_dependency_tuple(repo_info_tup) + tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, toolshed) + # Don't include the changeset_revision in clone urls. + return util.build_url(tool_shed_url, pathspec=['repos', owner, name]) + + +def get_non_shed_tool_panel_configs(app): + """Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml.""" + config_filenames = [] + for config_filename in app.config.tool_configs: + # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. + # + tree, error_message = xml_util.parse_xml(config_filename) + if tree is None: + continue + root = tree.getroot() + tool_path = root.get('tool_path', None) + if tool_path is None: + config_filenames.append(config_filename) + return config_filenames + + +def get_repository_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision): + repository_dependencies_dict = {} + tool_shed_accessible = True + params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision) + pathspec = ['repository', 'get_repository_dependencies'] + try: + raw_text = util.url_get(tool_shed_url, password_mgr=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) + tool_shed_accessible = True + except Exception as e: + tool_shed_accessible = False + log.warning("The URL\n%s\nraised the exception:\n%s\n", util.build_url(tool_shed_url, pathspec=pathspec, params=params), e) + if tool_shed_accessible: + if len(raw_text) > 2: + encoded_text = json.loads(util.unicodify(raw_text)) + repository_dependencies_dict = encoding_util.tool_shed_decode(encoded_text) + return tool_shed_accessible, repository_dependencies_dict + + +def get_protocol_from_tool_shed_url(tool_shed_url): + """Return the protocol from the received tool_shed_url if it exists.""" + try: + if tool_shed_url.find('://') > 0: + return tool_shed_url.split('://')[0].lower() + except Exception: + # We receive a lot of calls here where the tool_shed_url is None. The container_util uses + # that value when creating a header row. If the tool_shed_url is not None, we have a problem. + if tool_shed_url is not None: + log.exception("Handled exception getting the protocol from Tool Shed URL %s", str(tool_shed_url)) + # Default to HTTP protocol. + return 'http' + + +def get_tool_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision): + tool_dependencies = [] + tool_shed_accessible = True + params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision) + pathspec = ['repository', 'get_tool_dependencies'] + try: + text = util.url_get(tool_shed_url, password_mgr=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) + tool_shed_accessible = True + except Exception as e: + tool_shed_accessible = False + log.warning("The URL\n%s\nraised the exception:\n%s\n", util.build_url(tool_shed_url, pathspec=pathspec, params=params), e) + if tool_shed_accessible: + if text: + tool_dependencies_dict = encoding_util.tool_shed_decode(text) + for requirements_dict in tool_dependencies_dict.values(): + tool_dependency_name = requirements_dict['name'] + tool_dependency_version = requirements_dict['version'] + tool_dependency_type = requirements_dict['type'] + tool_dependencies.append((tool_dependency_name, tool_dependency_version, tool_dependency_type)) + return tool_shed_accessible, tool_dependencies + + +def get_tool_shed_repository_ids(as_string=False, **kwd): + tsrid = kwd.get('tool_shed_repository_id', None) + tsridslist = util.listify(kwd.get('tool_shed_repository_ids', None)) + if not tsridslist: + tsridslist = util.listify(kwd.get('id', None)) + if tsridslist is not None: + if tsrid is not None and tsrid not in tsridslist: + tsridslist.append(tsrid) + if as_string: + return ','.join(tsridslist) + return tsridslist + else: + tsridslist = util.listify(kwd.get('ordered_tsr_ids', None)) + if tsridslist is not None: + if as_string: + return ','.join(tsridslist) + return tsridslist + if as_string: + return '' + return [] + + +def get_tool_shed_url_from_tool_shed_registry(app, tool_shed): + """ + The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is + something like: http://toolshed.g2.bx.psu.edu/ + """ + cleaned_tool_shed = remove_protocol_from_tool_shed_url(tool_shed) + for shed_url in app.tool_shed_registry.tool_sheds.values(): + if shed_url.find(cleaned_tool_shed) >= 0: + if shed_url.endswith('/'): + shed_url = shed_url.rstrip('/') + return shed_url + # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. + return None + + +def get_tool_shed_repository_url(app, tool_shed, owner, name): + tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, tool_shed) + if tool_shed_url: + # Append a slash to the tool shed URL, because urlparse.urljoin will eliminate + # the last part of a URL if it does not end with a forward slash. + tool_shed_url = '%s/' % tool_shed_url + return urljoin(tool_shed_url, 'view/%s/%s' % (owner, name)) + return tool_shed_url + + +def get_user_by_username(app, username): + """Get a user from the database by username.""" + sa_session = app.model.context.current + try: + user = sa_session.query(app.model.User) \ + .filter(app.model.User.table.c.username == username) \ + .one() + return user + except Exception: + return None + + +def handle_galaxy_url(trans, **kwd): + galaxy_url = kwd.get('galaxy_url', None) + if galaxy_url: + trans.set_cookie(galaxy_url, name='toolshedgalaxyurl') + else: + galaxy_url = trans.get_cookie(name='toolshedgalaxyurl') + return galaxy_url + + +def handle_tool_shed_url_protocol(app, shed_url): + """Handle secure and insecure HTTP protocol since they may change over time.""" + try: + if app.name == 'galaxy': + url = remove_protocol_from_tool_shed_url(shed_url) + tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, url) + else: + tool_shed_url = str(url_for('/', qualified=True)).rstrip('/') + return tool_shed_url + except Exception: + # We receive a lot of calls here where the tool_shed_url is None. The container_util uses + # that value when creating a header row. If the tool_shed_url is not None, we have a problem. + if shed_url is not None: + log.exception("Handled exception removing protocol from URL %s", str(shed_url)) + return shed_url + + +def parse_repository_dependency_tuple(repository_dependency_tuple, contains_error=False): + # Default both prior_installation_required and only_if_compiling_contained_td to False in cases where metadata should be reset on the + # repository containing the repository_dependency definition. + prior_installation_required = 'False' + only_if_compiling_contained_td = 'False' + if contains_error: + if len(repository_dependency_tuple) == 5: + tool_shed, name, owner, changeset_revision, error = repository_dependency_tuple + elif len(repository_dependency_tuple) == 6: + tool_shed, name, owner, changeset_revision, prior_installation_required, error = repository_dependency_tuple + elif len(repository_dependency_tuple) == 7: + tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \ + repository_dependency_tuple + return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error + else: + if len(repository_dependency_tuple) == 4: + tool_shed, name, owner, changeset_revision = repository_dependency_tuple + elif len(repository_dependency_tuple) == 5: + tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency_tuple + elif len(repository_dependency_tuple) == 6: + tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = repository_dependency_tuple + return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td + + +def remove_port_from_tool_shed_url(tool_shed_url): + """Return a partial Tool Shed URL, eliminating the port if it exists.""" + try: + if tool_shed_url.find(':') > 0: + # Eliminate the port, if any, since it will result in an invalid directory name. + new_tool_shed_url = tool_shed_url.split(':')[0] + else: + new_tool_shed_url = tool_shed_url + return new_tool_shed_url.rstrip('/') + except Exception: + # We receive a lot of calls here where the tool_shed_url is None. The container_util uses + # that value when creating a header row. If the tool_shed_url is not None, we have a problem. + if tool_shed_url is not None: + log.exception("Handled exception removing the port from Tool Shed URL %s", str(tool_shed_url)) + return tool_shed_url + + +def remove_protocol_and_port_from_tool_shed_url(tool_shed_url): + """Return a partial Tool Shed URL, eliminating the protocol and/or port if either exists.""" + tool_shed = remove_protocol_from_tool_shed_url(tool_shed_url) + tool_shed = remove_port_from_tool_shed_url(tool_shed) + return tool_shed + + +def remove_protocol_and_user_from_clone_url(repository_clone_url): + """Return a URL that can be used to clone a repository, eliminating the protocol and user if either exists.""" + if repository_clone_url.find('@') > 0: + # We have an url that includes an authenticated user, something like: + # http://test@bx.psu.edu:9009/repos/some_username/column + items = repository_clone_url.split('@') + tmp_url = items[1] + elif repository_clone_url.find('//') > 0: + # We have an url that includes only a protocol, something like: + # http://bx.psu.edu:9009/repos/some_username/column + items = repository_clone_url.split('//') + tmp_url = items[1] + else: + tmp_url = repository_clone_url + return tmp_url.rstrip('/') + + +def remove_protocol_from_tool_shed_url(tool_shed_url): + """Return a partial Tool Shed URL, eliminating the protocol if it exists.""" + return util.remove_protocol_from_url(tool_shed_url) diff --git a/lib/galaxy/util/tool_shed/encoding_util.py b/lib/galaxy/util/tool_shed/encoding_util.py new file mode 100644 index 00000000000..57c1a11c8a7 --- /dev/null +++ b/lib/galaxy/util/tool_shed/encoding_util.py @@ -0,0 +1,41 @@ +import binascii +import json + +from galaxy.util import ( + smart_str, + unicodify +) +from galaxy.util.hash_util import hmac_new + + +encoding_sep = '__esep__' +encoding_sep2 = '__esepii__' + + +def tool_shed_decode(value): + # Extract and verify hash + value = unicodify(value) + a, b = value.split(":") + value = binascii.unhexlify(b) + test = hmac_new(b'ToolShedAndGalaxyMustHaveThisSameKey', value) + assert a == test + # Restore from string + values = None + value = unicodify(value) + try: + values = json.loads(value) + except Exception: + pass + if values is None: + values = value + return values + + +def tool_shed_encode(val): + if isinstance(val, dict) or isinstance(val, list): + value = json.dumps(val) + else: + value = val + a = hmac_new(b'ToolShedAndGalaxyMustHaveThisSameKey', smart_str(value)) + b = unicodify(binascii.hexlify(smart_str(value))) + return "%s:%s" % (a, b) diff --git a/lib/galaxy/util/tool_shed/xml_util.py b/lib/galaxy/util/tool_shed/xml_util.py new file mode 100644 index 00000000000..5e7e9db05e4 --- /dev/null +++ b/lib/galaxy/util/tool_shed/xml_util.py @@ -0,0 +1,92 @@ +import io +import logging +import os +import tempfile +from xml.etree import ElementTree as XmlET + +from galaxy.util import ( + xml_to_string +) + +log = logging.getLogger(__name__) + + +class Py27CommentedTreeBuilder(XmlET.TreeBuilder): + + def doctype(*args): + # handle deprecation warning for XMLParsing a file with DOCTYPE + pass + + def comment(self, data): + self.start(XmlET.Comment, {}) + self.data(data) + self.end(XmlET.Comment) + + +def create_and_write_tmp_file(elem): + tmp_str = xml_to_string(elem, pretty=True) + with tempfile.NamedTemporaryFile(prefix="tmp-toolshed-cawrf", delete=False) as fh: + tmp_filename = fh.name + with io.open(tmp_filename, mode='w', encoding='utf-8') as fh: + fh.write(tmp_str) + return tmp_filename + + +def create_element(tag, attributes=None, sub_elements=None): + """ + Create a new element whose tag is the value of the received tag, and whose attributes are all + key / value pairs in the received attributes and sub_elements. + """ + if tag: + elem = XmlET.Element(tag) + if attributes: + # The received attributes is an odict to preserve ordering. + for k, v in attributes.items(): + elem.set(k, v) + if sub_elements: + # The received attributes is an odict. These handle information that tends to be + # long text including paragraphs (e.g., description and long_description. + for k, v in sub_elements.items(): + # Don't include fields that are blank. + if v: + if k == 'packages': + # The received sub_elements is an odict whose key is 'packages' and whose + # value is a list of ( name, version ) tuples. + for v_tuple in v: + sub_elem = XmlET.SubElement(elem, 'package') + sub_elem_name, sub_elem_version = v_tuple + sub_elem.set('name', sub_elem_name) + sub_elem.set('version', sub_elem_version) + elif isinstance(v, list): + sub_elem = XmlET.SubElement(elem, k) + # If v is a list, then it must be a list of tuples where the first + # item is the tag and the second item is the text value. + for v_tuple in v: + if len(v_tuple) == 2: + v_tag = v_tuple[0] + v_text = v_tuple[1] + # Don't include fields that are blank. + if v_text: + v_elem = XmlET.SubElement(sub_elem, v_tag) + v_elem.text = v_text + else: + sub_elem = XmlET.SubElement(elem, k) + sub_elem.text = v + return elem + return None + + +def parse_xml(file_name): + """Returns a parsed xml tree with comments intact.""" + error_message = '' + if not os.path.exists(file_name): + return None, "File does not exist %s" % str(file_name) + + with open(file_name, 'r') as fobj: + try: + tree = XmlET.parse(fobj, parser=XmlET.XMLParser(target=Py27CommentedTreeBuilder())) + except Exception as e: + error_message = "Exception attempting to parse %s: %s" % (str(file_name), str(e)) + log.exception(error_message) + return None, error_message + return tree, error_message diff --git a/lib/galaxy/web/buildapp.py b/lib/galaxy/web/buildapp.py index e6a04c8bfba..7f95507bdae 100644 --- a/lib/galaxy/web/buildapp.py +++ b/lib/galaxy/web/buildapp.py @@ -1,5 +1,10 @@ """For backward compatibility only, pulls app_factor from galaxy.webapps.main""" -from galaxy.webapps.galaxy.buildapp import app_factory +try: + from galaxy.webapps.galaxy.buildapp import app_factory +except ImportError: + # when installed as a library, galaxy-web-apps may not be available - this + # is fine - we shouldn't be using this entry point anyway. + app_factory = None __all__ = ('app_factory', ) diff --git a/lib/galaxy/web/framework/webapp.py b/lib/galaxy/web/framework/webapp.py index 284598d0260..f59ac0b8c6b 100644 --- a/lib/galaxy/web/framework/webapp.py +++ b/lib/galaxy/web/framework/webapp.py @@ -114,8 +114,8 @@ class WebApplication(base.WebApplication): Search for UI controllers in `package_name` and add them to the webapp. """ - from galaxy.web.base.controller import BaseUIController - from galaxy.web.base.controller import ControllerUnavailable + from galaxy.webapps.base.controller import BaseUIController + from galaxy.webapps.base.controller import ControllerUnavailable package = import_module(package_name) controller_dir = package.__path__[0] for fname in os.listdir(controller_dir): @@ -139,8 +139,8 @@ class WebApplication(base.WebApplication): Search for UI controllers in `package_name` and add them to the webapp. """ - from galaxy.web.base.controller import BaseAPIController - from galaxy.web.base.controller import ControllerUnavailable + from galaxy.webapps.base.controller import BaseAPIController + from galaxy.webapps.base.controller import ControllerUnavailable package = import_module(package_name) controller_dir = package.__path__[0] for fname in os.listdir(controller_dir): diff --git a/lib/galaxy/webapps/base/__init__.py b/lib/galaxy/webapps/base/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/lib/galaxy/web/base/controller.py b/lib/galaxy/webapps/base/controller.py similarity index 100% rename from lib/galaxy/web/base/controller.py rename to lib/galaxy/webapps/base/controller.py diff --git a/lib/galaxy/webapps/galaxy/api/annotations.py b/lib/galaxy/webapps/galaxy/api/annotations.py index a78c800ebb0..27e7c59619b 100644 --- a/lib/galaxy/webapps/galaxy/api/annotations.py +++ b/lib/galaxy/webapps/galaxy/api/annotations.py @@ -10,7 +10,7 @@ from galaxy import ( from galaxy.model.item_attrs import UsesAnnotations from galaxy.util.sanitize_html import sanitize_html from galaxy.web import expose_api -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, UsesStoredWorkflowMixin ) diff --git a/lib/galaxy/webapps/galaxy/api/authenticate.py b/lib/galaxy/webapps/galaxy/api/authenticate.py index 78074926dcf..2f9eb4d442e 100644 --- a/lib/galaxy/webapps/galaxy/api/authenticate.py +++ b/lib/galaxy/webapps/galaxy/api/authenticate.py @@ -22,7 +22,7 @@ from galaxy.util import ( unicodify ) from galaxy.web import expose_api_anonymous_and_sessionless -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/cloud.py b/lib/galaxy/webapps/galaxy/api/cloud.py index 697ea736c8e..66f795d5880 100644 --- a/lib/galaxy/webapps/galaxy/api/cloud.py +++ b/lib/galaxy/webapps/galaxy/api/cloud.py @@ -11,7 +11,7 @@ from galaxy.managers import ( datasets ) from galaxy.web import expose_api -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/cloudauthz.py b/lib/galaxy/webapps/galaxy/api/cloudauthz.py index 03cc7f17310..a0590eeffb7 100644 --- a/lib/galaxy/webapps/galaxy/api/cloudauthz.py +++ b/lib/galaxy/webapps/galaxy/api/cloudauthz.py @@ -22,7 +22,7 @@ from galaxy.util import unicodify from galaxy.web import ( expose_api ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/configuration.py b/lib/galaxy/webapps/galaxy/api/configuration.py index dd57130658f..92e447bc2e0 100644 --- a/lib/galaxy/webapps/galaxy/api/configuration.py +++ b/lib/galaxy/webapps/galaxy/api/configuration.py @@ -13,7 +13,7 @@ from galaxy.web import ( expose_api_anonymous_and_sessionless, require_admin ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/dataset_collections.py b/lib/galaxy/webapps/galaxy/api/dataset_collections.py index 7048fdd9d19..a66c58839c2 100644 --- a/lib/galaxy/webapps/galaxy/api/dataset_collections.py +++ b/lib/galaxy/webapps/galaxy/api/dataset_collections.py @@ -3,7 +3,7 @@ from logging import getLogger from galaxy import managers from galaxy.managers.collections_util import api_payload_to_create_params, dictify_dataset_collection_instance from galaxy.web import expose_api -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, UsesLibraryMixinItems ) diff --git a/lib/galaxy/webapps/galaxy/api/datasets.py b/lib/galaxy/webapps/galaxy/api/datasets.py index b729933f8cf..51bbf0495c7 100644 --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -22,11 +22,11 @@ from galaxy.visualization.data_providers.genome import ( FeatureLocationIndexDataProvider, SamDataProvider ) -from galaxy.web.base.controller import ( +from galaxy.web.framework.helpers import is_true +from galaxy.webapps.base.controller import ( BaseAPIController, UsesVisualizationMixin ) -from galaxy.web.framework.helpers import is_true log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/datatypes.py b/lib/galaxy/webapps/galaxy/api/datatypes.py index 782d6b31ba9..d4891d5e4f8 100644 --- a/lib/galaxy/webapps/galaxy/api/datatypes.py +++ b/lib/galaxy/webapps/galaxy/api/datatypes.py @@ -10,7 +10,7 @@ from galaxy.util import ( unicodify ) from galaxy.web import expose_api_anonymous_and_sessionless -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/display_applications.py b/lib/galaxy/webapps/galaxy/api/display_applications.py index bda880e35e0..325c040764a 100644 --- a/lib/galaxy/webapps/galaxy/api/display_applications.py +++ b/lib/galaxy/webapps/galaxy/api/display_applications.py @@ -5,7 +5,7 @@ import logging from galaxy import queue_worker from galaxy.web import legacy_expose_api, require_admin -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/dynamic_tools.py b/lib/galaxy/webapps/galaxy/api/dynamic_tools.py index 49f1b0942fb..a5c471a7c8f 100644 --- a/lib/galaxy/webapps/galaxy/api/dynamic_tools.py +++ b/lib/galaxy/webapps/galaxy/api/dynamic_tools.py @@ -4,7 +4,7 @@ from galaxy import util, web from galaxy.exceptions import ObjectNotFound from galaxy.web import expose_api from galaxy.web import expose_api_anonymous_and_sessionless -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/extended_metadata.py b/lib/galaxy/webapps/galaxy/api/extended_metadata.py index 9d7d5ed2f9f..a4a650774bb 100644 --- a/lib/galaxy/webapps/galaxy/api/extended_metadata.py +++ b/lib/galaxy/webapps/galaxy/api/extended_metadata.py @@ -7,7 +7,7 @@ from galaxy import ( managers, web ) -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, HTTPNotImplemented, UsesExtendedMetadataMixin, diff --git a/lib/galaxy/webapps/galaxy/api/folder_contents.py b/lib/galaxy/webapps/galaxy/api/folder_contents.py index 8ee9745f23c..a7ecc98481d 100644 --- a/lib/galaxy/webapps/galaxy/api/folder_contents.py +++ b/lib/galaxy/webapps/galaxy/api/folder_contents.py @@ -13,7 +13,7 @@ from galaxy.web import ( expose_api, expose_api_anonymous ) -from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems +from galaxy.webapps.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems log = logging.getLogger(__name__) @@ -105,8 +105,8 @@ class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryM # Can user manage the permissions on the dataset? can_manage = is_admin or (trans.user and trans.app.security_agent.can_manage_dataset(current_user_roles, content_item.library_dataset_dataset_association.dataset)) - - nice_size = util.nice_size(int(content_item.library_dataset_dataset_association.get_size())) + raw_size = int(content_item.library_dataset_dataset_association.get_size()) + nice_size = util.nice_size(raw_size) library_dataset_dict = content_item.to_dict() encoded_ldda_id = trans.security.encode_id(content_item.library_dataset_dataset_association.id) @@ -117,6 +117,7 @@ class FolderContentsController(BaseAPIController, UsesLibraryMixin, UsesLibraryM can_manage=can_manage, state=library_dataset_dict['state'], file_size=nice_size, + raw_size=raw_size, ldda_id=encoded_ldda_id)) if content_item.library_dataset_dataset_association.message: return_item.update(dict(message=content_item.library_dataset_dataset_association.message)) diff --git a/lib/galaxy/webapps/galaxy/api/folders.py b/lib/galaxy/webapps/galaxy/api/folders.py index 4d62f2b9a19..e168f242771 100644 --- a/lib/galaxy/webapps/galaxy/api/folders.py +++ b/lib/galaxy/webapps/galaxy/api/folders.py @@ -9,7 +9,7 @@ from galaxy import ( ) from galaxy.managers import folders, roles from galaxy.web import expose_api -from galaxy.web.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems +from galaxy.webapps.base.controller import BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/forms.py b/lib/galaxy/webapps/galaxy/api/forms.py index caa3e518005..5eb17b53a2f 100644 --- a/lib/galaxy/webapps/galaxy/api/forms.py +++ b/lib/galaxy/webapps/galaxy/api/forms.py @@ -6,7 +6,7 @@ from xml.etree.ElementTree import XML from galaxy import web from galaxy.forms.forms import form_factory -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.webapps.base.controller import BaseAPIController, url_for log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/genomes.py b/lib/galaxy/webapps/galaxy/api/genomes.py index f760d6d11bb..683f9a5707a 100644 --- a/lib/galaxy/webapps/galaxy/api/genomes.py +++ b/lib/galaxy/webapps/galaxy/api/genomes.py @@ -1,6 +1,6 @@ from galaxy import web -from galaxy.web.base.controller import BaseAPIController from galaxy.web.framework.helpers import is_true +from galaxy.webapps.base.controller import BaseAPIController def get_id(base, format): diff --git a/lib/galaxy/webapps/galaxy/api/group_roles.py b/lib/galaxy/webapps/galaxy/api/group_roles.py index f7b68e00dad..dfd5b4972f1 100644 --- a/lib/galaxy/webapps/galaxy/api/group_roles.py +++ b/lib/galaxy/webapps/galaxy/api/group_roles.py @@ -5,7 +5,7 @@ import logging from galaxy import web from galaxy.util import unicodify -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.webapps.base.controller import BaseAPIController, url_for log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/group_users.py b/lib/galaxy/webapps/galaxy/api/group_users.py index 5d5190f83c8..baa48597991 100644 --- a/lib/galaxy/webapps/galaxy/api/group_users.py +++ b/lib/galaxy/webapps/galaxy/api/group_users.py @@ -5,7 +5,7 @@ import logging from galaxy import web from galaxy.util import unicodify -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.webapps.base.controller import BaseAPIController, url_for log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/groups.py b/lib/galaxy/webapps/galaxy/api/groups.py index 4b4abd4715e..b4ed1d411ef 100644 --- a/lib/galaxy/webapps/galaxy/api/groups.py +++ b/lib/galaxy/webapps/galaxy/api/groups.py @@ -6,7 +6,7 @@ import logging from sqlalchemy import false from galaxy import web -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.webapps.base.controller import BaseAPIController, url_for log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/histories.py b/lib/galaxy/webapps/galaxy/api/histories.py index 4ebb6e71b0f..72c17dbcab7 100644 --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -34,7 +34,7 @@ from galaxy.web import ( expose_api_raw, url_for ) -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, ExportsHistoryMixin, ImportsHistoryMixin, diff --git a/lib/galaxy/webapps/galaxy/api/history_contents.py b/lib/galaxy/webapps/galaxy/api/history_contents.py index 0d716cf0161..f7b021b5275 100644 --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -30,7 +30,7 @@ from galaxy.web import ( expose_api_raw, expose_api_raw_anonymous ) -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, UsesLibraryMixin, UsesLibraryMixinItems, diff --git a/lib/galaxy/webapps/galaxy/api/item_tags.py b/lib/galaxy/webapps/galaxy/api/item_tags.py index 130f0b33147..c10a5557c4a 100644 --- a/lib/galaxy/webapps/galaxy/api/item_tags.py +++ b/lib/galaxy/webapps/galaxy/api/item_tags.py @@ -5,7 +5,7 @@ import logging from galaxy import exceptions from galaxy.web import expose_api -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, UsesTagsMixin ) diff --git a/lib/galaxy/webapps/galaxy/api/job_files.py b/lib/galaxy/webapps/galaxy/api/job_files.py index 5f571b94049..d95a44e1381 100644 --- a/lib/galaxy/webapps/galaxy/api/job_files.py +++ b/lib/galaxy/webapps/galaxy/api/job_files.py @@ -14,7 +14,7 @@ from galaxy.web import ( expose_api_anonymous_and_sessionless, expose_api_raw_anonymous_and_sessionless, ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/jobs.py b/lib/galaxy/webapps/galaxy/api/jobs.py index 0c4c9985d27..bd6b948f73b 100644 --- a/lib/galaxy/webapps/galaxy/api/jobs.py +++ b/lib/galaxy/webapps/galaxy/api/jobs.py @@ -17,7 +17,7 @@ from galaxy.web import ( expose_api, expose_api_anonymous, ) -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, UsesVisualizationMixin ) diff --git a/lib/galaxy/webapps/galaxy/api/libraries.py b/lib/galaxy/webapps/galaxy/api/libraries.py index e6c49026000..e7e6ba0f6d8 100644 --- a/lib/galaxy/webapps/galaxy/api/libraries.py +++ b/lib/galaxy/webapps/galaxy/api/libraries.py @@ -16,7 +16,7 @@ from galaxy.web import ( expose_api, expose_api_anonymous, ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/library_contents.py b/lib/galaxy/webapps/galaxy/api/library_contents.py index 85d662b55a0..d030f9e92b0 100644 --- a/lib/galaxy/webapps/galaxy/api/library_contents.py +++ b/lib/galaxy/webapps/galaxy/api/library_contents.py @@ -23,7 +23,7 @@ from galaxy.model import ( ExtendedMetadataIndex ) from galaxy.web import expose_api -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, HTTPBadRequest, url_for, diff --git a/lib/galaxy/webapps/galaxy/api/library_datasets.py b/lib/galaxy/webapps/galaxy/api/library_datasets.py index 56d2a8fe61e..7812afb538d 100644 --- a/lib/galaxy/webapps/galaxy/api/library_datasets.py +++ b/lib/galaxy/webapps/galaxy/api/library_datasets.py @@ -32,7 +32,7 @@ from galaxy.web import ( expose_api, expose_api_anonymous, ) -from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin +from galaxy.webapps.base.controller import BaseAPIController, UsesVisualizationMixin log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/metrics.py b/lib/galaxy/webapps/galaxy/api/metrics.py index 28ba5bf9c49..9bdea2f7080 100644 --- a/lib/galaxy/webapps/galaxy/api/metrics.py +++ b/lib/galaxy/webapps/galaxy/api/metrics.py @@ -8,7 +8,7 @@ import datetime import logging from galaxy.web import expose_api_anonymous -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/page_revisions.py b/lib/galaxy/webapps/galaxy/api/page_revisions.py index f240f6e9155..51b26f9bb82 100644 --- a/lib/galaxy/webapps/galaxy/api/page_revisions.py +++ b/lib/galaxy/webapps/galaxy/api/page_revisions.py @@ -7,7 +7,7 @@ from galaxy.managers.base import get_object from galaxy.managers.pages import PageManager from galaxy.model.item_attrs import UsesAnnotations from galaxy.web import expose_api -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, SharableItemSecurityMixin, SharableMixin diff --git a/lib/galaxy/webapps/galaxy/api/pages.py b/lib/galaxy/webapps/galaxy/api/pages.py index c86090a29f0..52fb6e6ffa8 100644 --- a/lib/galaxy/webapps/galaxy/api/pages.py +++ b/lib/galaxy/webapps/galaxy/api/pages.py @@ -10,7 +10,7 @@ from galaxy.managers.pages import ( ) from galaxy.model.item_attrs import UsesAnnotations from galaxy.web import expose_api -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, SharableItemSecurityMixin, SharableMixin diff --git a/lib/galaxy/webapps/galaxy/api/plugins.py b/lib/galaxy/webapps/galaxy/api/plugins.py index ba71aa44c54..326fd9bb0e7 100644 --- a/lib/galaxy/webapps/galaxy/api/plugins.py +++ b/lib/galaxy/webapps/galaxy/api/plugins.py @@ -6,7 +6,7 @@ import logging from galaxy import exceptions from galaxy.managers import hdas, histories from galaxy.web import expose_api -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/provenance.py b/lib/galaxy/webapps/galaxy/api/provenance.py index 72361ee2857..2e1f3fab02d 100644 --- a/lib/galaxy/webapps/galaxy/api/provenance.py +++ b/lib/galaxy/webapps/galaxy/api/provenance.py @@ -12,7 +12,7 @@ from galaxy import ( managers, web ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/quotas.py b/lib/galaxy/webapps/galaxy/api/quotas.py index 075bc444b42..437b2f9dbaf 100644 --- a/lib/galaxy/webapps/galaxy/api/quotas.py +++ b/lib/galaxy/webapps/galaxy/api/quotas.py @@ -15,12 +15,12 @@ from galaxy import ( ) from galaxy.actions.admin import AdminActions from galaxy.exceptions import ActionInputError -from galaxy.web.base.controller import ( +from galaxy.web.params import QuotaParamParser +from galaxy.webapps.base.controller import ( BaseAPIController, url_for, UsesQuotaMixin ) -from galaxy.web.params import QuotaParamParser log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/remote_files.py b/lib/galaxy/webapps/galaxy/api/remote_files.py index 918b830d803..49b914fd821 100644 --- a/lib/galaxy/webapps/galaxy/api/remote_files.py +++ b/lib/galaxy/webapps/galaxy/api/remote_files.py @@ -18,7 +18,7 @@ from galaxy.util.path import ( safe_walk ) from galaxy.web import expose_api -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/roles.py b/lib/galaxy/webapps/galaxy/api/roles.py index e849f9ae225..ac2a06a6e66 100644 --- a/lib/galaxy/webapps/galaxy/api/roles.py +++ b/lib/galaxy/webapps/galaxy/api/roles.py @@ -6,7 +6,7 @@ import logging from sqlalchemy import false from galaxy import web -from galaxy.web.base.controller import BaseAPIController, url_for +from galaxy.webapps.base.controller import BaseAPIController, url_for log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/search.py b/lib/galaxy/webapps/galaxy/api/search.py index 8f11f776b9a..7c5f4bead44 100644 --- a/lib/galaxy/webapps/galaxy/api/search.py +++ b/lib/galaxy/webapps/galaxy/api/search.py @@ -7,7 +7,7 @@ from galaxy import web from galaxy.exceptions import ItemAccessibilityException from galaxy.model.search import GalaxySearchEngine from galaxy.util import unicodify -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, SharableItemSecurityMixin ) diff --git a/lib/galaxy/webapps/galaxy/api/tool_data.py b/lib/galaxy/webapps/galaxy/api/tool_data.py index b0fede8ba20..a398b7e26ac 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_data.py +++ b/lib/galaxy/webapps/galaxy/api/tool_data.py @@ -9,7 +9,7 @@ from galaxy.web import ( expose_api, expose_api_raw ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController class ToolData(BaseAPIController): diff --git a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py index 5fea48074d4..ca209a75575 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_dependencies.py +++ b/lib/galaxy/webapps/galaxy/api/tool_dependencies.py @@ -8,7 +8,7 @@ from galaxy.web import ( expose_api, require_admin ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py index cf6bfb1da34..0d09fb62f4a 100644 --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -16,7 +16,7 @@ from galaxy import ( web ) from galaxy.web import expose_api -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController from tool_shed.galaxy_install.install_manager import InstallRepositoryManager from tool_shed.galaxy_install.installed_repository_manager import InstalledRepositoryManager from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager diff --git a/lib/galaxy/webapps/galaxy/api/tools.py b/lib/galaxy/webapps/galaxy/api/tools.py index d86a11d5b9b..f920b44b3be 100644 --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -14,8 +14,8 @@ from galaxy.web import ( expose_api_anonymous_and_sessionless, expose_api_raw_anonymous_and_sessionless, ) -from galaxy.web.base.controller import BaseAPIController -from galaxy.web.base.controller import UsesVisualizationMixin +from galaxy.webapps.base.controller import BaseAPIController +from galaxy.webapps.base.controller import UsesVisualizationMixin from ._fetch_util import validate_and_normalize_targets log = logging.getLogger(__name__) @@ -403,6 +403,11 @@ class ToolsController(BaseAPIController, UsesVisualizationMixin): rval.append(citation.to_dict('bibtex')) return rval + @expose_api_anonymous_and_sessionless + def xrefs(self, trans, id, **kwds): + tool = self._get_tool(id, user=trans.user) + return tool.xrefs + @web.legacy_expose_api_raw @web.require_admin def download(self, trans, id, **kwds): diff --git a/lib/galaxy/webapps/galaxy/api/toolshed.py b/lib/galaxy/webapps/galaxy/api/toolshed.py index 1ab675c9175..f16c03862b4 100644 --- a/lib/galaxy/webapps/galaxy/api/toolshed.py +++ b/lib/galaxy/webapps/galaxy/api/toolshed.py @@ -14,7 +14,7 @@ from galaxy import ( ) from galaxy.exceptions import MessageException from galaxy.web import expose_api -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController from tool_shed.util import ( common_util, repository_util, diff --git a/lib/galaxy/webapps/galaxy/api/tours.py b/lib/galaxy/webapps/galaxy/api/tours.py index d0dec04edf2..12cdf3dca6c 100644 --- a/lib/galaxy/webapps/galaxy/api/tours.py +++ b/lib/galaxy/webapps/galaxy/api/tours.py @@ -8,7 +8,7 @@ from galaxy.web import ( legacy_expose_api, require_admin ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/uploads.py b/lib/galaxy/webapps/galaxy/api/uploads.py index 50fa372c478..1519fd8f33f 100644 --- a/lib/galaxy/webapps/galaxy/api/uploads.py +++ b/lib/galaxy/webapps/galaxy/api/uploads.py @@ -7,7 +7,7 @@ import re from galaxy import exceptions from galaxy.web import legacy_expose_api_anonymous -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/users.py b/lib/galaxy/webapps/galaxy/api/users.py index 8131568d265..8251004130d 100644 --- a/lib/galaxy/webapps/galaxy/api/users.py +++ b/lib/galaxy/webapps/galaxy/api/users.py @@ -35,14 +35,14 @@ from galaxy.web import ( expose_api, expose_api_anonymous ) -from galaxy.web.base.controller import ( +from galaxy.web.form_builder import AddressField +from galaxy.webapps.base.controller import ( BaseAPIController, BaseUIController, CreatesApiKeysMixin, UsesFormDefinitionsMixin, UsesTagsMixin ) -from galaxy.web.form_builder import AddressField log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/visualizations.py b/lib/galaxy/webapps/galaxy/api/visualizations.py index e8fde2ce325..1afdb3164fb 100644 --- a/lib/galaxy/webapps/galaxy/api/visualizations.py +++ b/lib/galaxy/webapps/galaxy/api/visualizations.py @@ -20,7 +20,7 @@ from galaxy.managers.visualizations import ( ) from galaxy.model.item_attrs import UsesAnnotations from galaxy.web import expose_api -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, SharableMixin, UsesVisualizationMixin diff --git a/lib/galaxy/webapps/galaxy/api/webhooks.py b/lib/galaxy/webapps/galaxy/api/webhooks.py index 3dc7e6bb4a7..27336080f43 100644 --- a/lib/galaxy/webapps/galaxy/api/webhooks.py +++ b/lib/galaxy/webapps/galaxy/api/webhooks.py @@ -5,7 +5,7 @@ import imp import logging from galaxy.web import expose_api_anonymous_and_sessionless -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index 51d21275bcc..74271a6f127 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -30,7 +30,7 @@ from galaxy.web import ( expose_api, expose_api_anonymous_and_sessionless, ) -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, SharableMixin, url_for, diff --git a/lib/galaxy/webapps/galaxy/buildapp.py b/lib/galaxy/webapps/galaxy/buildapp.py index d754e7c09bb..6daf8803c00 100644 --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -349,6 +349,7 @@ def populate_api_routes(webapp, app): webapp.mapper.connect('/api/tools/{id:.+?}/test_data', action='test_data', controller="tools") webapp.mapper.connect('/api/tools/{id:.+?}/diagnostics', action='diagnostics', controller="tools") webapp.mapper.connect('/api/tools/{id:.+?}/citations', action='citations', controller="tools") + webapp.mapper.connect('/api/tools/{id:.+?}/xrefs', action='xrefs', controller="tools") webapp.mapper.connect('/api/tools/{id:.+?}/download', action='download', controller="tools") webapp.mapper.connect('/api/tools/{id:.+?}/requirements', action='requirements', controller="tools") webapp.mapper.connect('/api/tools/{id:.+?}/install_dependencies', action='install_dependencies', controller="tools", conditions=dict(method=["POST"])) diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml index ff34272c4c2..0a586fd22be 100644 --- a/lib/galaxy/webapps/galaxy/config_schema.yml +++ b/lib/galaxy/webapps/galaxy/config_schema.yml @@ -220,13 +220,13 @@ mapping: default: database/dependencies required: false desc: | - Path to the directory in which tool dependencies are placed. This is used by - the Tool Shed to install dependencies and can also be used by administrators - to manually install or link to dependencies. For details, see: - https://galaxyproject.org/admin/config/tool-dependencies + Various dependency resolver configuration parameters will have defaults set relative + to this path, such as the default conda prefix, default Galaxy packages path, legacy + tool shed dependencies path, and the dependency cache directory. + Set the string to None to explicitly disable tool dependency handling. If this option is set to none or an invalid path, installing tools with dependencies - from the Tool Shed will fail. + from the Tool Shed or in Conda will fail. dependency_resolvers_config_file: type: str @@ -317,6 +317,10 @@ mapping: used if you experience long waiting times before a job is actually submitted to your cluster. + This only affects tools where some requirements can be resolved but not others, + most modern best practice tools can use prebuilt environments in the Conda + directory. + tool_dependency_cache_dir: type: str default: /_cache @@ -2372,6 +2376,32 @@ mapping: resolvers to enable can be embedded into Galaxy's config with this option. This has no effect if a dependency_resolvers_config_file is used. + dependency_resolution: + type: map + desc: | + Alternative representation of various dependency resolution parameters. Takes the + dictified version of a DependencyManager object - so this is ideal for automating the + configuration of dependency resolution from one application that uses a DependencyManager + to another. + mapping: + cache: + type: bool + default: false + desc: See description of 'use_cached_dependency_manager'. + precache: + type: bool + default: true + desc: See description of 'precache_dependencies'. + cache_dir: + type: str + default: '/_cache' + desc: See description of 'tool_dependency_cache_dir'. + default_base_path: + default: database/dependencies + desc: See description of 'tool_dependency_dir'. + resolvers: + desc: See description of 'dependency_resolvers'. + default_job_resubmission_condition: type: str required: false diff --git a/lib/galaxy/webapps/galaxy/controllers/admin.py b/lib/galaxy/webapps/galaxy/controllers/admin.py index c4c24ebed04..f023ad177bd 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin.py @@ -25,10 +25,10 @@ from galaxy.util import ( from galaxy.util.hash_util import new_secure_hash from galaxy.util.odict import odict from galaxy.web import url_for -from galaxy.web.base import controller -from galaxy.web.base.controller import UsesQuotaMixin from galaxy.web.framework.helpers import grids, time_ago from galaxy.web.params import QuotaParamParser +from galaxy.webapps.base import controller +from galaxy.webapps.base.controller import UsesQuotaMixin from tool_shed.util import ( common_util, encoding_util, @@ -889,7 +889,7 @@ class AdminGalaxy(controller.JSAppLauncher, AdminActions, UsesQuotaMixin, QuotaP modules.sort() modules.reverse() for item in modules: - if not item.endswith('.py') or item.startswith('0001_tools'): + if not item.endswith('_tools.py') or item.startswith('0001_tools'): continue module = item.replace('.py', '') migration_stage = int(module.replace('_tools', '')) diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index 7eaff6c3ed7..8991a39f155 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -524,11 +524,11 @@ class AdminToolshed(AdminGalaxy): (escape(str(repository.name)), updating_to_changeset_revision) self.initiate_tool_dependency_installation(trans, tool_dependencies, message=message, status=status) # Handle tool dependencies check box. - if trans.app.config.tool_dependency_dir is None: + if not trans.app.toolbox.dependency_manager.uses_tool_shed_dependencies: if tool_dependencies_dict: message = ("Tool dependencies defined in this repository can be automatically installed if you set " "the value of your tool_dependency_dir setting in your Galaxy config file " - "(galaxy.ini) and restart your Galaxy server.") + "(galaxy.yml) and restart your Galaxy server.") status = "warning" install_tool_dependencies_check_box_checked = False else: @@ -696,7 +696,7 @@ class AdminToolshed(AdminGalaxy): message = 'No selected tool dependencies can be uninstalled, you may need to use the Repair repository feature.' status = 'error' elif operation == "install": - if trans.app.config.tool_dependency_dir: + if trans.app.toolbox.dependency_manager.uses_tool_shed_dependencies: tool_dependencies_for_installation = [] for tool_dependency_id in tool_dependency_ids: tool_dependency = tool_dependency_util.get_tool_dependency(trans.app, tool_dependency_id) @@ -756,7 +756,7 @@ class AdminToolshed(AdminGalaxy): action='browse_tool_dependency', **kwd)) elif operation == "install": - if trans.app.config.tool_dependency_dir: + if trans.app.toolbox.dependency_manager.uses_tool_shed_dependencies: tool_dependencies_for_installation = [] for tool_dependency_id in tool_dependency_ids: tool_dependency = tool_dependency_util.get_tool_dependency(trans.app, tool_dependency_id) @@ -1048,11 +1048,11 @@ class AdminToolshed(AdminGalaxy): # Merge all containers into a single container. containers_dict = dd.merge_containers_dicts_for_new_install(containers_dicts) # Handle tool dependencies check box. - if trans.app.config.tool_dependency_dir is None: + if not trans.app.toolbox.dependency_manager.uses_tool_shed_dependencies: if includes_tool_dependencies: message = "Tool dependencies defined in this repository can be automatically installed if you set " message += "the value of your tool_dependency_dir setting in your Galaxy config file " - message += "(galaxy.ini) and restart your Galaxy server before installing the repository." + message += "(galaxy.yml) and restart your Galaxy server before installing the repository." status = "warning" install_tool_dependencies_check_box_checked = False else: @@ -1429,10 +1429,10 @@ class AdminToolshed(AdminGalaxy): # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField('install_repository_dependencies', value=True) # Handle tool dependencies check box. - if trans.app.config.tool_dependency_dir is None: + if not trans.app.toolbox.dependency_manager.uses_tool_shed_dependencies: if includes_tool_dependencies: message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your tool_dependency_dir " - message += "setting in your Galaxy config file (galaxy.ini) and restart your Galaxy server before installing the repository. " + message += "setting in your Galaxy config file (galaxy.yml) and restart your Galaxy server before installing the repository. " status = "warning" install_tool_dependencies_check_box_checked = False else: diff --git a/lib/galaxy/webapps/galaxy/controllers/async.py b/lib/galaxy/webapps/galaxy/controllers/async.py index 68feeb0788b..019b86dd749 100644 --- a/lib/galaxy/webapps/galaxy/controllers/async.py +++ b/lib/galaxy/webapps/galaxy/controllers/async.py @@ -15,7 +15,7 @@ from galaxy.util import ( unicodify, ) from galaxy.util.hash_util import hmac_new -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/authnz.py b/lib/galaxy/webapps/galaxy/controllers/authnz.py index 0a07dbbba3a..28c4ac8a38e 100644 --- a/lib/galaxy/webapps/galaxy/controllers/authnz.py +++ b/lib/galaxy/webapps/galaxy/controllers/authnz.py @@ -9,7 +9,7 @@ import logging from galaxy import exceptions from galaxy import web from galaxy.web import url_for -from galaxy.web.base.controller import JSAppLauncher +from galaxy.webapps.base.controller import JSAppLauncher log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/data_manager.py b/lib/galaxy/webapps/galaxy/controllers/data_manager.py index fb5c47ce231..e5fa4f69d05 100644 --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -7,7 +7,7 @@ from six import string_types import galaxy.queue_worker from galaxy import web from galaxy.util import nice_size, unicodify -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py index 40df1ea0913..c9f7afd31a1 100644 --- a/lib/galaxy/webapps/galaxy/controllers/dataset.py +++ b/lib/galaxy/webapps/galaxy/controllers/dataset.py @@ -29,8 +29,8 @@ from galaxy.util import ( from galaxy.util.checkers import check_binary from galaxy.util.sanitize_html import sanitize_html from galaxy.web import form_builder -from galaxy.web.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesExtendedMetadataMixin from galaxy.web.framework.helpers import grids, iff, time_ago +from galaxy.webapps.base.controller import BaseUIController, ERROR, SUCCESS, url_for, UsesExtendedMetadataMixin log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/error.py b/lib/galaxy/webapps/galaxy/controllers/error.py index 25dd69d1896..ea8190898bb 100644 --- a/lib/galaxy/webapps/galaxy/controllers/error.py +++ b/lib/galaxy/webapps/galaxy/controllers/error.py @@ -1,4 +1,4 @@ -from galaxy.web.base.controller import BaseUIController, web +from galaxy.webapps.base.controller import BaseUIController, web class Error(BaseUIController): diff --git a/lib/galaxy/webapps/galaxy/controllers/forms.py b/lib/galaxy/webapps/galaxy/controllers/forms.py index 57662f69c0b..3fa8a8fb6a7 100644 --- a/lib/galaxy/webapps/galaxy/controllers/forms.py +++ b/lib/galaxy/webapps/galaxy/controllers/forms.py @@ -6,8 +6,8 @@ import six from markupsafe import escape from galaxy import model, util -from galaxy.web.base.controller import BaseUIController, web from galaxy.web.framework.helpers import grids, iff, time_ago +from galaxy.webapps.base.controller import BaseUIController, web log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py index e4231ef32df..880354a92c2 100644 --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -17,7 +17,8 @@ from galaxy.model.item_attrs import ( from galaxy.util import listify, Params, parse_int, sanitize_text from galaxy.util.odict import odict from galaxy.web import url_for -from galaxy.web.base.controller import ( +from galaxy.web.framework.helpers import grids, iff, time_ago +from galaxy.webapps.base.controller import ( BaseUIController, ERROR, ExportsHistoryMixin, @@ -27,7 +28,6 @@ from galaxy.web.base.controller import ( SUCCESS, WARNING, ) -from galaxy.web.framework.helpers import grids, iff, time_ago from ._create_history_template import render_item diff --git a/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py b/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py index 653fb42c640..b0d29c9d50d 100644 --- a/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py +++ b/lib/galaxy/webapps/galaxy/controllers/interactive_environments.py @@ -4,7 +4,7 @@ API check for whether the current session's interactive environment launch is re import logging from galaxy.web import expose, json -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/library.py b/lib/galaxy/webapps/galaxy/controllers/library.py index c12fc458530..73c5106ba49 100644 --- a/lib/galaxy/webapps/galaxy/controllers/library.py +++ b/lib/galaxy/webapps/galaxy/controllers/library.py @@ -1,7 +1,7 @@ import logging from galaxy import web -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/openid.py b/lib/galaxy/webapps/galaxy/controllers/openid.py index f892d0d05f7..c50147f7b2f 100644 --- a/lib/galaxy/webapps/galaxy/controllers/openid.py +++ b/lib/galaxy/webapps/galaxy/controllers/openid.py @@ -9,7 +9,7 @@ from galaxy.openid.openid_manager import OpenIDManager from galaxy.openid.providers import OpenIDProviders from galaxy.util import unicodify from galaxy.web import url_for -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/page.py b/lib/galaxy/webapps/galaxy/controllers/page.py index 3981b90f860..e7501e4e2c0 100644 --- a/lib/galaxy/webapps/galaxy/controllers/page.py +++ b/lib/galaxy/webapps/galaxy/controllers/page.py @@ -31,16 +31,16 @@ from galaxy.web import ( error, url_for ) -from galaxy.web.base.controller import ( +from galaxy.web.framework.helpers import ( + grids, + time_ago +) +from galaxy.webapps.base.controller import ( BaseUIController, SharableMixin, UsesStoredWorkflowMixin, UsesVisualizationMixin ) -from galaxy.web.framework.helpers import ( - grids, - time_ago -) def format_bool(b): diff --git a/lib/galaxy/webapps/galaxy/controllers/root.py b/lib/galaxy/webapps/galaxy/controllers/root.py index 00e8e012b57..8a284eedd3a 100644 --- a/lib/galaxy/webapps/galaxy/controllers/root.py +++ b/lib/galaxy/webapps/galaxy/controllers/root.py @@ -24,7 +24,7 @@ from galaxy.util import ( string_as_bool, unicodify, ) -from galaxy.web.base import controller +from galaxy.webapps.base import controller log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py index 258eaed3a21..d938f86c958 100644 --- a/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py +++ b/lib/galaxy/webapps/galaxy/controllers/shed_tool_static.py @@ -4,7 +4,7 @@ import os from galaxy import web from galaxy.exceptions import RequestParameterInvalidException from galaxy.util.path import join, safe_contains -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/tag.py b/lib/galaxy/webapps/galaxy/controllers/tag.py index 0320f2be72e..0085522eb8c 100644 --- a/lib/galaxy/webapps/galaxy/controllers/tag.py +++ b/lib/galaxy/webapps/galaxy/controllers/tag.py @@ -9,7 +9,7 @@ from sqlalchemy.sql import select from sqlalchemy.sql.expression import and_, func from galaxy import web -from galaxy.web.base.controller import BaseUIController, UsesTagsMixin +from galaxy.webapps.base.controller import BaseUIController, UsesTagsMixin log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py index e3a6b805565..e6778b47b27 100644 --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -9,7 +9,7 @@ import galaxy.util from galaxy import web from galaxy.tools import DataSourceTool from galaxy.web import error, url_for -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/user.py b/lib/galaxy/webapps/galaxy/controllers/user.py index 513475172f1..4baf0e40a19 100644 --- a/lib/galaxy/webapps/galaxy/controllers/user.py +++ b/lib/galaxy/webapps/galaxy/controllers/user.py @@ -23,7 +23,7 @@ from galaxy.security.validate_user_input import ( ) from galaxy.web import expose_api_anonymous_and_sessionless from galaxy.web import url_for -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseUIController, CreatesApiKeysMixin, UsesFormDefinitionsMixin diff --git a/lib/galaxy/webapps/galaxy/controllers/userskeys.py b/lib/galaxy/webapps/galaxy/controllers/userskeys.py index 00fda7343ba..422c6f70734 100644 --- a/lib/galaxy/webapps/galaxy/controllers/userskeys.py +++ b/lib/galaxy/webapps/galaxy/controllers/userskeys.py @@ -8,7 +8,7 @@ from galaxy import ( util, web ) -from galaxy.web.base.controller import BaseUIController, UsesFormDefinitionsMixin +from galaxy.webapps.base.controller import BaseUIController, UsesFormDefinitionsMixin class User(BaseUIController, UsesFormDefinitionsMixin): diff --git a/lib/galaxy/webapps/galaxy/controllers/visualization.py b/lib/galaxy/webapps/galaxy/controllers/visualization.py index b56104af9c9..f586aa6b578 100644 --- a/lib/galaxy/webapps/galaxy/controllers/visualization.py +++ b/lib/galaxy/webapps/galaxy/controllers/visualization.py @@ -24,12 +24,12 @@ from galaxy.visualization.data_providers.phyloviz import PhylovizDataProvider from galaxy.visualization.genomes import decode_dbkey from galaxy.visualization.genomes import GenomeRegion from galaxy.visualization.plugins import registry -from galaxy.web.base.controller import ( +from galaxy.web.framework.helpers import grids, time_ago +from galaxy.webapps.base.controller import ( BaseUIController, SharableMixin, UsesVisualizationMixin ) -from galaxy.web.framework.helpers import grids, time_ago log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/galaxy/controllers/workflow.py b/lib/galaxy/webapps/galaxy/controllers/workflow.py index 65f5edb237a..1d84c309f28 100644 --- a/lib/galaxy/webapps/galaxy/controllers/workflow.py +++ b/lib/galaxy/webapps/galaxy/controllers/workflow.py @@ -27,15 +27,15 @@ from galaxy.util import ( ) from galaxy.util.sanitize_html import sanitize_html from galaxy.web import error, url_for -from galaxy.web.base.controller import ( - BaseUIController, - SharableMixin, - UsesStoredWorkflowMixin -) from galaxy.web.framework.helpers import ( grids, time_ago, ) +from galaxy.webapps.base.controller import ( + BaseUIController, + SharableMixin, + UsesStoredWorkflowMixin +) from galaxy.workflow.extract import ( extract_workflow, summarize diff --git a/lib/galaxy/webapps/reports/buildapp.py b/lib/galaxy/webapps/reports/buildapp.py index af42f0d657a..61ce047a643 100644 --- a/lib/galaxy/webapps/reports/buildapp.py +++ b/lib/galaxy/webapps/reports/buildapp.py @@ -35,7 +35,7 @@ def add_ui_controllers(webapp, app): Search for controllers in the 'galaxy.webapps.controllers' module and add them to the webapp. """ - from galaxy.web.base.controller import BaseUIController + from galaxy.webapps.base.controller import BaseUIController import galaxy.webapps.reports.controllers controller_dir = galaxy.webapps.reports.controllers.__path__[0] for fname in os.listdir(controller_dir): diff --git a/lib/galaxy/webapps/reports/controllers/history.py b/lib/galaxy/webapps/reports/controllers/history.py index f1f61be9f5a..bd3741de938 100644 --- a/lib/galaxy/webapps/reports/controllers/history.py +++ b/lib/galaxy/webapps/reports/controllers/history.py @@ -7,7 +7,7 @@ from sqlalchemy import and_ import galaxy.model from galaxy import util -from galaxy.web.base.controller import BaseUIController, web +from galaxy.webapps.base.controller import BaseUIController, web log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/home.py b/lib/galaxy/webapps/reports/controllers/home.py index bdba42cdcb4..6c59fd0294f 100644 --- a/lib/galaxy/webapps/reports/controllers/home.py +++ b/lib/galaxy/webapps/reports/controllers/home.py @@ -5,7 +5,7 @@ from datetime import datetime, timedelta import sqlalchemy as sa from galaxy import model -from galaxy.web.base.controller import BaseUIController, web +from galaxy.webapps.base.controller import BaseUIController, web from galaxy.webapps.reports.controllers.query import ReportQueryBuilder log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/jobs.py b/lib/galaxy/webapps/reports/controllers/jobs.py index 6ec5384568e..2c8c2a5a773 100644 --- a/lib/galaxy/webapps/reports/controllers/jobs.py +++ b/lib/galaxy/webapps/reports/controllers/jobs.py @@ -16,7 +16,7 @@ from markupsafe import escape from sqlalchemy import and_, not_, or_ from galaxy import model, util -from galaxy.web.base.controller import BaseUIController, web +from galaxy.webapps.base.controller import BaseUIController, web from galaxy.webapps.reports.controllers.query import ReportQueryBuilder from galaxy.webapps.reports.framework import grids diff --git a/lib/galaxy/webapps/reports/controllers/root.py b/lib/galaxy/webapps/reports/controllers/root.py index 26f87ddc792..896c61b0a2c 100644 --- a/lib/galaxy/webapps/reports/controllers/root.py +++ b/lib/galaxy/webapps/reports/controllers/root.py @@ -1,6 +1,6 @@ import logging -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseUIController, web ) diff --git a/lib/galaxy/webapps/reports/controllers/system.py b/lib/galaxy/webapps/reports/controllers/system.py index 246aac7d199..51ec6c9cd56 100644 --- a/lib/galaxy/webapps/reports/controllers/system.py +++ b/lib/galaxy/webapps/reports/controllers/system.py @@ -8,7 +8,7 @@ from sqlalchemy import and_, desc, false, null, true from sqlalchemy.orm import eagerload from galaxy import model, util -from galaxy.web.base.controller import BaseUIController, web +from galaxy.webapps.base.controller import BaseUIController, web log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/tools.py b/lib/galaxy/webapps/reports/controllers/tools.py index 7ac7e140a25..789685c0cf7 100644 --- a/lib/galaxy/webapps/reports/controllers/tools.py +++ b/lib/galaxy/webapps/reports/controllers/tools.py @@ -11,7 +11,7 @@ from galaxy.util import ( restore_text, unicodify ) -from galaxy.web.base.controller import BaseUIController, web +from galaxy.webapps.base.controller import BaseUIController, web log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/reports/controllers/users.py b/lib/galaxy/webapps/reports/controllers/users.py index 58ffd1dcafd..54cf6645b4c 100644 --- a/lib/galaxy/webapps/reports/controllers/users.py +++ b/lib/galaxy/webapps/reports/controllers/users.py @@ -13,7 +13,7 @@ from sqlalchemy import false import galaxy.model from galaxy import util -from galaxy.web.base.controller import BaseUIController, web +from galaxy.webapps.base.controller import BaseUIController, web from galaxy.webapps.reports.controllers.jobs import sorter from galaxy.webapps.reports.controllers.query import ReportQueryBuilder diff --git a/lib/galaxy/webapps/reports/controllers/workflows.py b/lib/galaxy/webapps/reports/controllers/workflows.py index ff17c2b00d4..a61992333f6 100644 --- a/lib/galaxy/webapps/reports/controllers/workflows.py +++ b/lib/galaxy/webapps/reports/controllers/workflows.py @@ -17,7 +17,7 @@ from markupsafe import escape from sqlalchemy import and_ from galaxy import model, util -from galaxy.web.base.controller import BaseUIController, web +from galaxy.webapps.base.controller import BaseUIController, web from galaxy.webapps.reports.controllers.jobs import ( get_spark_time, sorter diff --git a/lib/galaxy/webapps/tool_shed/api/categories.py b/lib/galaxy/webapps/tool_shed/api/categories.py index 550acf2a48d..414a679ed64 100644 --- a/lib/galaxy/webapps/tool_shed/api/categories.py +++ b/lib/galaxy/webapps/tool_shed/api/categories.py @@ -11,7 +11,7 @@ from galaxy.web import ( expose_api_anonymous_and_sessionless, require_admin as require_admin ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController from tool_shed.util import repository_util log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/api/configuration.py b/lib/galaxy/webapps/tool_shed/api/configuration.py index bca269b94ae..0ea0cc89915 100644 --- a/lib/galaxy/webapps/tool_shed/api/configuration.py +++ b/lib/galaxy/webapps/tool_shed/api/configuration.py @@ -5,7 +5,7 @@ capabilities and configuration settings. import logging from galaxy.web import expose_api_anonymous_and_sessionless -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/api/groups.py b/lib/galaxy/webapps/tool_shed/api/groups.py index ffaa025922e..09a261ca647 100644 --- a/lib/galaxy/webapps/tool_shed/api/groups.py +++ b/lib/galaxy/webapps/tool_shed/api/groups.py @@ -15,7 +15,7 @@ from galaxy.web import ( expose_api_anonymous_and_sessionless, require_admin as require_admin ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController from tool_shed.managers import groups log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/api/repositories.py b/lib/galaxy/webapps/tool_shed/api/repositories.py index 0d044512a9f..06bc9c1d2b4 100644 --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -28,7 +28,7 @@ from galaxy.web import ( expose_api_anonymous_and_sessionless, expose_api_raw_anonymous_and_sessionless ) -from galaxy.web.base.controller import ( +from galaxy.webapps.base.controller import ( BaseAPIController, HTTPBadRequest ) diff --git a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py index 081d14a86c3..af1cc9b186e 100644 --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -4,7 +4,7 @@ from sqlalchemy import and_ from galaxy import util from galaxy import web -from galaxy.web.base.controller import BaseAPIController, HTTPBadRequest +from galaxy.webapps.base.controller import BaseAPIController, HTTPBadRequest from tool_shed.capsule import capsule_manager from tool_shed.util import metadata_util from tool_shed.util import repository_util diff --git a/lib/galaxy/webapps/tool_shed/api/tools.py b/lib/galaxy/webapps/tool_shed/api/tools.py index fd3f08c0373..428d3c37e50 100644 --- a/lib/galaxy/webapps/tool_shed/api/tools.py +++ b/lib/galaxy/webapps/tool_shed/api/tools.py @@ -10,7 +10,7 @@ from galaxy import ( from galaxy.tools.parameters import params_to_strings from galaxy.tools.repositories import ValidationContext from galaxy.web import expose_api_raw_anonymous_and_sessionless -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController from galaxy.webapps.tool_shed.search.tool_search import ToolSearch from tool_shed.dependencies.repository import relation_builder from tool_shed.tools import tool_validator diff --git a/lib/galaxy/webapps/tool_shed/api/users.py b/lib/galaxy/webapps/tool_shed/api/users.py index 4bc1acbc960..ba68ab24991 100644 --- a/lib/galaxy/webapps/tool_shed/api/users.py +++ b/lib/galaxy/webapps/tool_shed/api/users.py @@ -10,7 +10,7 @@ from galaxy.security.validate_user_input import ( validate_password, validate_publicname ) -from galaxy.web.base.controller import BaseAPIController +from galaxy.webapps.base.controller import BaseAPIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/buildapp.py b/lib/galaxy/webapps/tool_shed/buildapp.py index 176a0ac750d..bcbcdab7e90 100644 --- a/lib/galaxy/webapps/tool_shed/buildapp.py +++ b/lib/galaxy/webapps/tool_shed/buildapp.py @@ -36,7 +36,7 @@ def add_ui_controllers(webapp, app): Search for controllers in the 'galaxy.webapps.controllers' module and add them to the webapp. """ - from galaxy.web.base.controller import BaseUIController + from galaxy.webapps.base.controller import BaseUIController import galaxy.webapps.tool_shed.controllers controller_dir = galaxy.webapps.tool_shed.controllers.__path__[0] for fname in os.listdir(controller_dir): diff --git a/lib/galaxy/webapps/tool_shed/controllers/admin.py b/lib/galaxy/webapps/tool_shed/controllers/admin.py index 76ff1b70008..a5e2834d092 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -6,8 +6,8 @@ from galaxy import ( web ) from galaxy.util import inflector -from galaxy.web.base.controller import BaseUIController from galaxy.web.framework.helpers import grids +from galaxy.webapps.base.controller import BaseUIController from tool_shed.metadata import repository_metadata_manager from tool_shed.util import ( metadata_util, diff --git a/lib/galaxy/webapps/tool_shed/controllers/groups.py b/lib/galaxy/webapps/tool_shed/controllers/groups.py index 78f9572c863..b41ad39e17f 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/groups.py +++ b/lib/galaxy/webapps/tool_shed/controllers/groups.py @@ -1,7 +1,7 @@ import logging from galaxy import web -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/controllers/hg.py b/lib/galaxy/webapps/tool_shed/controllers/hg.py index 027de2df7e8..1501550e138 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/hg.py +++ b/lib/galaxy/webapps/tool_shed/controllers/hg.py @@ -4,7 +4,7 @@ from mercurial.hgweb.hgwebdir_mod import hgwebdir from mercurial.hgweb.request import wsgiapplication from galaxy import web -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController from tool_shed.util.repository_util import get_repository_by_name_and_owner log = logging.getLogger(__name__) diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository.py b/lib/galaxy/webapps/tool_shed/controllers/repository.py index 6f94f913ad2..2a49dbc4778 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -21,8 +21,8 @@ from galaxy import ( web ) from galaxy.tools.repositories import ValidationContext -from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import CheckboxField, SelectField +from galaxy.webapps.base.controller import BaseUIController from galaxy.webapps.reports.framework import grids from galaxy.webapps.tool_shed.util import ratings_util from tool_shed.capsule import capsule_manager diff --git a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py index b015a7c6da6..760e065b1ee 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -13,8 +13,8 @@ from galaxy import ( web ) from galaxy.util.odict import odict -from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import CheckboxField +from galaxy.webapps.base.controller import BaseUIController from galaxy.webapps.tool_shed.util import ratings_util from tool_shed.util import ( hg_util, diff --git a/lib/galaxy/webapps/tool_shed/controllers/upload.py b/lib/galaxy/webapps/tool_shed/controllers/upload.py index 91bfadc6e68..8043b12a983 100644 --- a/lib/galaxy/webapps/tool_shed/controllers/upload.py +++ b/lib/galaxy/webapps/tool_shed/controllers/upload.py @@ -11,7 +11,7 @@ from galaxy import ( web ) from galaxy.util import checkers -from galaxy.web.base.controller import BaseUIController +from galaxy.webapps.base.controller import BaseUIController from tool_shed.dependencies import attribute_handlers from tool_shed.galaxy_install import dependency_display from tool_shed.metadata import repository_metadata_manager diff --git a/lib/galaxy/webapps/tool_shed/model/migrate/versions/__init__.py b/lib/galaxy/webapps/tool_shed/model/migrate/versions/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/lib/tool_shed/galaxy_install/dependency_display.py b/lib/tool_shed/galaxy_install/dependency_display.py index 2ab5f97b706..44779571903 100644 --- a/lib/tool_shed/galaxy_install/dependency_display.py +++ b/lib/tool_shed/galaxy_install/dependency_display.py @@ -37,8 +37,8 @@ class DependencyDisplayer(object): changeset_revision = requirements_dict.get('changeset_revision', 'unknown') dependency_name = requirements_dict['name'] version = requirements_dict['version'] - if self.app.config.tool_dependency_dir: - root_dir = self.app.config.tool_dependency_dir + if self.app.tool_dependency_dir: + root_dir = self.app.tool_dependency_dir else: root_dir = '' install_dir = os.path.join(root_dir, diff --git a/lib/tool_shed/galaxy_install/install_manager.py b/lib/tool_shed/galaxy_install/install_manager.py index e75d0e0930d..20605e8fce1 100644 --- a/lib/tool_shed/galaxy_install/install_manager.py +++ b/lib/tool_shed/galaxy_install/install_manager.py @@ -899,8 +899,9 @@ class InstallRepositoryManager(object): new_tools = [self.app.toolbox._tools_by_id.get(tool_d['guid'], None) for tool_d in metadata['tools']] new_requirements = set([tool.requirements.packages for tool in new_tools if tool]) [self._view.install_dependencies(r) for r in new_requirements] - if self.app.config.use_cached_dependency_manager: - [self.app.toolbox.dependency_manager.build_cache(r) for r in new_requirements] + dependency_manager = self.app.toolbox.dependency_manager + if dependency_manager.cached: + [dependency_manager.build_cache(r) for r in new_requirements] if install_tool_dependencies and tool_shed_repository.tool_dependencies and 'tool_dependencies' in metadata: work_dir = tempfile.mkdtemp(prefix="tmp-toolshed-itsr") @@ -992,7 +993,7 @@ class InstallRepositoryManager(object): self.install_model.context.flush() def __assert_can_install_dependencies(self): - if self.app.config.tool_dependency_dir is None: + if self.app.tool_dependency_dir is None: no_tool_dependency_dir_message = "Tool dependencies can be automatically installed only if you set " no_tool_dependency_dir_message += "the value of your 'tool_dependency_dir' setting in your Galaxy " no_tool_dependency_dir_message += "configuration file (galaxy.ini) and restart your Galaxy server. " diff --git a/lib/tool_shed/galaxy_install/migrate/versions/__init__.py b/lib/tool_shed/galaxy_install/migrate/versions/__init__.py new file mode 100644 index 00000000000..e69de29bb2d diff --git a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py index b83281196c9..6b7176dee3a 100644 --- a/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py +++ b/lib/tool_shed/galaxy_install/tool_dependencies/recipe/step_handler.py @@ -1576,7 +1576,7 @@ class SetupVirtualEnv(Download, RecipeStep): # This class is not currently used during stage 1 of the installation process, so filter_actions # are not affected, and dir is not set. Enhancements can easily be made to this function if this # class is needed in stage 1. - venv_src_directory = os.path.abspath(os.path.join(self.app.config.tool_dependency_dir, '__virtualenv_src')) + venv_src_directory = os.path.abspath(os.path.join(self.app.tool_dependency_dir, '__virtualenv_src')) if not self.install_virtualenv(install_environment, venv_src_directory): log.debug('Unable to install virtualenv') return tool_dependency, None, None diff --git a/lib/tool_shed/galaxy_install/tool_migration_manager.py b/lib/tool_shed/galaxy_install/tool_migration_manager.py index e8de5dd15cb..945b433f111 100644 --- a/lib/tool_shed/galaxy_install/tool_migration_manager.py +++ b/lib/tool_shed/galaxy_install/tool_migration_manager.py @@ -47,7 +47,7 @@ class ToolMigrationManager(object): self.tpm = tool_panel_manager.ToolPanelManager(self.app) # If install_dependencies is True but tool_dependency_dir is not set, do not attempt # to install but print informative error message. - if install_dependencies and app.config.tool_dependency_dir is None: + if install_dependencies and app.tool_dependency_dir is None: message = 'You are attempting to install tool dependencies but do not have a value ' message += 'for "tool_dependency_dir" set in your galaxy.ini file. Set this ' message += 'location value to the path where you want tool dependencies installed and ' diff --git a/lib/tool_shed/metadata/metadata_generator.py b/lib/tool_shed/metadata/metadata_generator.py index 7aa5b0007f6..a37ddac7b0c 100644 --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -6,9 +6,9 @@ import tempfile from sqlalchemy import and_ from galaxy import util +from galaxy.tool_util.loader_directory import looks_like_a_tool from galaxy.tool_util.parser.interface import TestCollectionDef from galaxy.tools.data_manager.manager import DataManager -from galaxy.tools.loader_directory import looks_like_a_tool from galaxy.tools.repositories import ValidationContext from galaxy.web import url_for from tool_shed.repository_types import util as rt_util diff --git a/lib/tool_shed/util/common_util.py b/lib/tool_shed/util/common_util.py deleted file mode 100644 index 8f5686197a2..00000000000 --- a/lib/tool_shed/util/common_util.py +++ /dev/null @@ -1,362 +0,0 @@ -import json -import logging -import os - -from six.moves.urllib.parse import urljoin - -from galaxy import util -from galaxy.util.odict import odict -from galaxy.web import url_for -from tool_shed.util import encoding_util, xml_util - -log = logging.getLogger(__name__) - -REPOSITORY_OWNER = 'devteam' - - -def accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies): - if tool_shed_accessible: - if tool_dependencies: - for tool_dependency in tool_dependencies: - if tool_dependency not in all_tool_dependencies: - all_tool_dependencies.append(tool_dependency) - return all_tool_dependencies - - -def check_for_missing_tools(app, tool_panel_configs, latest_tool_migration_script_number): - # Get the 000x_tools.xml file associated with the current migrate_tools version number. - tools_xml_file_path = os.path.abspath(os.path.join('scripts', 'migrate_tools', '%04d_tools.xml' % latest_tool_migration_script_number)) - # Parse the XML and load the file attributes for later checking against the proprietary tool_panel_config. - migrated_tool_configs_dict = odict() - tree, error_message = xml_util.parse_xml(tools_xml_file_path) - if tree is None: - return False, odict() - root = tree.getroot() - tool_shed = root.get('name') - tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, tool_shed) - # The default behavior is that the tool shed is down. - tool_shed_accessible = False - missing_tool_configs_dict = odict() - if tool_shed_url: - for elem in root: - if elem.tag == 'repository': - repository_dependencies = [] - all_tool_dependencies = [] - repository_name = elem.get('name') - changeset_revision = elem.get('changeset_revision') - tool_shed_accessible, repository_dependencies_dict = get_repository_dependencies(app, - tool_shed_url, - repository_name, - REPOSITORY_OWNER, - changeset_revision) - if tool_shed_accessible: - # Accumulate all tool dependencies defined for repository dependencies for display to the user. - for rd_key, rd_tups in repository_dependencies_dict.items(): - if rd_key in ['root_key', 'description']: - continue - for rd_tup in rd_tups: - tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ - parse_repository_dependency_tuple(rd_tup) - tool_shed_accessible, tool_dependencies = get_tool_dependencies(app, - tool_shed_url, - name, - owner, - changeset_revision) - all_tool_dependencies = accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies) - tool_shed_accessible, tool_dependencies = get_tool_dependencies(app, - tool_shed_url, - repository_name, - REPOSITORY_OWNER, - changeset_revision) - all_tool_dependencies = accumulate_tool_dependencies(tool_shed_accessible, tool_dependencies, all_tool_dependencies) - for tool_elem in elem.findall('tool'): - tool_config_file_name = tool_elem.get('file') - if tool_config_file_name: - # We currently do nothing with repository dependencies except install them (we do not display repositories that will be - # installed to the user). However, we'll store them in the following dictionary in case we choose to display them in the - # future. - dependencies_dict = dict(tool_dependencies=all_tool_dependencies, - repository_dependencies=repository_dependencies) - migrated_tool_configs_dict[tool_config_file_name] = dependencies_dict - else: - break - if tool_shed_accessible: - # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. - for tool_panel_config in tool_panel_configs: - tree, error_message = xml_util.parse_xml(tool_panel_config) - if tree: - root = tree.getroot() - for elem in root: - if elem.tag == 'tool': - missing_tool_configs_dict = check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict) - elif elem.tag == 'section': - for section_elem in elem: - if section_elem.tag == 'tool': - missing_tool_configs_dict = check_tool_tag_set(section_elem, migrated_tool_configs_dict, missing_tool_configs_dict) - else: - exception_msg = '\n\nThe entry for the main Galaxy tool shed at %s is missing from the %s file. ' % (tool_shed, app.config.tool_sheds_config) - exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n' - raise Exception(exception_msg) - return tool_shed_accessible, missing_tool_configs_dict - - -def check_tool_tag_set(elem, migrated_tool_configs_dict, missing_tool_configs_dict): - file_path = elem.get('file', None) - if file_path: - name = os.path.basename(file_path) - for migrated_tool_config in migrated_tool_configs_dict.keys(): - if migrated_tool_config in [file_path, name]: - missing_tool_configs_dict[name] = migrated_tool_configs_dict[migrated_tool_config] - return missing_tool_configs_dict - - -def generate_clone_url_for_installed_repository(app, repository): - """Generate the URL for cloning a repository that has been installed into a Galaxy instance.""" - tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, str(repository.tool_shed)) - return util.build_url(tool_shed_url, pathspec=['repos', str(repository.owner), str(repository.name)]) - - -def generate_clone_url_for_repository_in_tool_shed(user, repository): - """Generate the URL for cloning a repository that is in the tool shed.""" - base_url = url_for('/', qualified=True).rstrip('/') - if user: - protocol, base = base_url.split('://') - username = '%s@' % user.username - return '%s://%s%s/repos/%s/%s' % (protocol, username, base, repository.user.username, repository.name) - else: - return '%s/repos/%s/%s' % (base_url, repository.user.username, repository.name) - - -def generate_clone_url_from_repo_info_tup(app, repo_info_tup): - """Generate the URL for cloning a repository given a tuple of toolshed, name, owner, changeset_revision.""" - # Example tuple: ['http://localhost:9009', 'blast_datatypes', 'test', '461a4216e8ab', False] - toolshed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = \ - parse_repository_dependency_tuple(repo_info_tup) - tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, toolshed) - # Don't include the changeset_revision in clone urls. - return util.build_url(tool_shed_url, pathspec=['repos', owner, name]) - - -def get_non_shed_tool_panel_configs(app): - """Get the non-shed related tool panel configs - there can be more than one, and the default is tool_conf.xml.""" - config_filenames = [] - for config_filename in app.config.tool_configs: - # Any config file that includes a tool_path attribute in the root tag set like the following is shed-related. - # - tree, error_message = xml_util.parse_xml(config_filename) - if tree is None: - continue - root = tree.getroot() - tool_path = root.get('tool_path', None) - if tool_path is None: - config_filenames.append(config_filename) - return config_filenames - - -def get_repository_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision): - repository_dependencies_dict = {} - tool_shed_accessible = True - params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision) - pathspec = ['repository', 'get_repository_dependencies'] - try: - raw_text = util.url_get(tool_shed_url, password_mgr=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) - tool_shed_accessible = True - except Exception as e: - tool_shed_accessible = False - log.warning("The URL\n%s\nraised the exception:\n%s\n", util.build_url(tool_shed_url, pathspec=pathspec, params=params), e) - if tool_shed_accessible: - if len(raw_text) > 2: - encoded_text = json.loads(util.unicodify(raw_text)) - repository_dependencies_dict = encoding_util.tool_shed_decode(encoded_text) - return tool_shed_accessible, repository_dependencies_dict - - -def get_protocol_from_tool_shed_url(tool_shed_url): - """Return the protocol from the received tool_shed_url if it exists.""" - try: - if tool_shed_url.find('://') > 0: - return tool_shed_url.split('://')[0].lower() - except Exception: - # We receive a lot of calls here where the tool_shed_url is None. The container_util uses - # that value when creating a header row. If the tool_shed_url is not None, we have a problem. - if tool_shed_url is not None: - log.exception("Handled exception getting the protocol from Tool Shed URL %s", str(tool_shed_url)) - # Default to HTTP protocol. - return 'http' - - -def get_tool_dependencies(app, tool_shed_url, repository_name, repository_owner, changeset_revision): - tool_dependencies = [] - tool_shed_accessible = True - params = dict(name=repository_name, owner=repository_owner, changeset_revision=changeset_revision) - pathspec = ['repository', 'get_tool_dependencies'] - try: - text = util.url_get(tool_shed_url, password_mgr=app.tool_shed_registry.url_auth(tool_shed_url), pathspec=pathspec, params=params) - tool_shed_accessible = True - except Exception as e: - tool_shed_accessible = False - log.warning("The URL\n%s\nraised the exception:\n%s\n", util.build_url(tool_shed_url, pathspec=pathspec, params=params), e) - if tool_shed_accessible: - if text: - tool_dependencies_dict = encoding_util.tool_shed_decode(text) - for requirements_dict in tool_dependencies_dict.values(): - tool_dependency_name = requirements_dict['name'] - tool_dependency_version = requirements_dict['version'] - tool_dependency_type = requirements_dict['type'] - tool_dependencies.append((tool_dependency_name, tool_dependency_version, tool_dependency_type)) - return tool_shed_accessible, tool_dependencies - - -def get_tool_shed_repository_ids(as_string=False, **kwd): - tsrid = kwd.get('tool_shed_repository_id', None) - tsridslist = util.listify(kwd.get('tool_shed_repository_ids', None)) - if not tsridslist: - tsridslist = util.listify(kwd.get('id', None)) - if tsridslist is not None: - if tsrid is not None and tsrid not in tsridslist: - tsridslist.append(tsrid) - if as_string: - return ','.join(tsridslist) - return tsridslist - else: - tsridslist = util.listify(kwd.get('ordered_tsr_ids', None)) - if tsridslist is not None: - if as_string: - return ','.join(tsridslist) - return tsridslist - if as_string: - return '' - return [] - - -def get_tool_shed_url_from_tool_shed_registry(app, tool_shed): - """ - The value of tool_shed is something like: toolshed.g2.bx.psu.edu. We need the URL to this tool shed, which is - something like: http://toolshed.g2.bx.psu.edu/ - """ - cleaned_tool_shed = remove_protocol_from_tool_shed_url(tool_shed) - for shed_url in app.tool_shed_registry.tool_sheds.values(): - if shed_url.find(cleaned_tool_shed) >= 0: - if shed_url.endswith('/'): - shed_url = shed_url.rstrip('/') - return shed_url - # The tool shed from which the repository was originally installed must no longer be configured in tool_sheds_conf.xml. - return None - - -def get_tool_shed_repository_url(app, tool_shed, owner, name): - tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, tool_shed) - if tool_shed_url: - # Append a slash to the tool shed URL, because urlparse.urljoin will eliminate - # the last part of a URL if it does not end with a forward slash. - tool_shed_url = '%s/' % tool_shed_url - return urljoin(tool_shed_url, 'view/%s/%s' % (owner, name)) - return tool_shed_url - - -def get_user_by_username(app, username): - """Get a user from the database by username.""" - sa_session = app.model.context.current - try: - user = sa_session.query(app.model.User) \ - .filter(app.model.User.table.c.username == username) \ - .one() - return user - except Exception: - return None - - -def handle_galaxy_url(trans, **kwd): - galaxy_url = kwd.get('galaxy_url', None) - if galaxy_url: - trans.set_cookie(galaxy_url, name='toolshedgalaxyurl') - else: - galaxy_url = trans.get_cookie(name='toolshedgalaxyurl') - return galaxy_url - - -def handle_tool_shed_url_protocol(app, shed_url): - """Handle secure and insecure HTTP protocol since they may change over time.""" - try: - if app.name == 'galaxy': - url = remove_protocol_from_tool_shed_url(shed_url) - tool_shed_url = get_tool_shed_url_from_tool_shed_registry(app, url) - else: - tool_shed_url = str(url_for('/', qualified=True)).rstrip('/') - return tool_shed_url - except Exception: - # We receive a lot of calls here where the tool_shed_url is None. The container_util uses - # that value when creating a header row. If the tool_shed_url is not None, we have a problem. - if shed_url is not None: - log.exception("Handled exception removing protocol from URL %s", str(shed_url)) - return shed_url - - -def parse_repository_dependency_tuple(repository_dependency_tuple, contains_error=False): - # Default both prior_installation_required and only_if_compiling_contained_td to False in cases where metadata should be reset on the - # repository containing the repository_dependency definition. - prior_installation_required = 'False' - only_if_compiling_contained_td = 'False' - if contains_error: - if len(repository_dependency_tuple) == 5: - tool_shed, name, owner, changeset_revision, error = repository_dependency_tuple - elif len(repository_dependency_tuple) == 6: - tool_shed, name, owner, changeset_revision, prior_installation_required, error = repository_dependency_tuple - elif len(repository_dependency_tuple) == 7: - tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error = \ - repository_dependency_tuple - return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td, error - else: - if len(repository_dependency_tuple) == 4: - tool_shed, name, owner, changeset_revision = repository_dependency_tuple - elif len(repository_dependency_tuple) == 5: - tool_shed, name, owner, changeset_revision, prior_installation_required = repository_dependency_tuple - elif len(repository_dependency_tuple) == 6: - tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td = repository_dependency_tuple - return tool_shed, name, owner, changeset_revision, prior_installation_required, only_if_compiling_contained_td - - -def remove_port_from_tool_shed_url(tool_shed_url): - """Return a partial Tool Shed URL, eliminating the port if it exists.""" - try: - if tool_shed_url.find(':') > 0: - # Eliminate the port, if any, since it will result in an invalid directory name. - new_tool_shed_url = tool_shed_url.split(':')[0] - else: - new_tool_shed_url = tool_shed_url - return new_tool_shed_url.rstrip('/') - except Exception: - # We receive a lot of calls here where the tool_shed_url is None. The container_util uses - # that value when creating a header row. If the tool_shed_url is not None, we have a problem. - if tool_shed_url is not None: - log.exception("Handled exception removing the port from Tool Shed URL %s", str(tool_shed_url)) - return tool_shed_url - - -def remove_protocol_and_port_from_tool_shed_url(tool_shed_url): - """Return a partial Tool Shed URL, eliminating the protocol and/or port if either exists.""" - tool_shed = remove_protocol_from_tool_shed_url(tool_shed_url) - tool_shed = remove_port_from_tool_shed_url(tool_shed) - return tool_shed - - -def remove_protocol_and_user_from_clone_url(repository_clone_url): - """Return a URL that can be used to clone a repository, eliminating the protocol and user if either exists.""" - if repository_clone_url.find('@') > 0: - # We have an url that includes an authenticated user, something like: - # http://test@bx.psu.edu:9009/repos/some_username/column - items = repository_clone_url.split('@') - tmp_url = items[1] - elif repository_clone_url.find('//') > 0: - # We have an url that includes only a protocol, something like: - # http://bx.psu.edu:9009/repos/some_username/column - items = repository_clone_url.split('//') - tmp_url = items[1] - else: - tmp_url = repository_clone_url - return tmp_url.rstrip('/') - - -def remove_protocol_from_tool_shed_url(tool_shed_url): - """Return a partial Tool Shed URL, eliminating the protocol if it exists.""" - return util.remove_protocol_from_url(tool_shed_url) diff --git a/lib/tool_shed/util/common_util.py b/lib/tool_shed/util/common_util.py new file mode 120000 index 00000000000..71148b57d1c --- /dev/null +++ b/lib/tool_shed/util/common_util.py @@ -0,0 +1 @@ +../../galaxy/util/tool_shed/common_util.py \ No newline at end of file diff --git a/lib/tool_shed/util/encoding_util.py b/lib/tool_shed/util/encoding_util.py deleted file mode 100644 index f5bb2ff6441..00000000000 --- a/lib/tool_shed/util/encoding_util.py +++ /dev/null @@ -1,43 +0,0 @@ -import binascii -import json -import logging - -from galaxy.util import ( - smart_str, - unicodify -) -from galaxy.util.hash_util import hmac_new - -log = logging.getLogger(__name__) - -encoding_sep = '__esep__' -encoding_sep2 = '__esepii__' - - -def tool_shed_decode(value): - # Extract and verify hash - value = unicodify(value) - a, b = value.split(":") - value = binascii.unhexlify(b) - test = hmac_new(b'ToolShedAndGalaxyMustHaveThisSameKey', value) - assert a == test - # Restore from string - values = None - value = unicodify(value) - try: - values = json.loads(value) - except Exception: - pass - if values is None: - values = value - return values - - -def tool_shed_encode(val): - if isinstance(val, dict) or isinstance(val, list): - value = json.dumps(val) - else: - value = val - a = hmac_new(b'ToolShedAndGalaxyMustHaveThisSameKey', smart_str(value)) - b = unicodify(binascii.hexlify(smart_str(value))) - return "%s:%s" % (a, b) diff --git a/lib/tool_shed/util/encoding_util.py b/lib/tool_shed/util/encoding_util.py new file mode 120000 index 00000000000..5bb58723d83 --- /dev/null +++ b/lib/tool_shed/util/encoding_util.py @@ -0,0 +1 @@ +../../galaxy/util/tool_shed/encoding_util.py \ No newline at end of file diff --git a/lib/tool_shed/util/tool_dependency_util.py b/lib/tool_shed/util/tool_dependency_util.py index 3b83716a515..fcddf11f867 100644 --- a/lib/tool_shed/util/tool_dependency_util.py +++ b/lib/tool_shed/util/tool_dependency_util.py @@ -207,14 +207,14 @@ def get_tool_dependency_ids(as_string=False, **kwd): def get_tool_dependency_install_dir(app, repository_name, repository_owner, repository_changeset_revision, tool_dependency_type, tool_dependency_name, tool_dependency_version): if tool_dependency_type == 'package': - return os.path.abspath(os.path.join(app.config.tool_dependency_dir, + return os.path.abspath(os.path.join(app.tool_dependency_dir, tool_dependency_name, tool_dependency_version, repository_owner, repository_name, repository_changeset_revision)) if tool_dependency_type == 'set_environment': - return os.path.abspath(os.path.join(app.config.tool_dependency_dir, + return os.path.abspath(os.path.join(app.tool_dependency_dir, 'environment_settings', tool_dependency_name, repository_owner, diff --git a/lib/tool_shed/util/xml_util.py b/lib/tool_shed/util/xml_util.py deleted file mode 100644 index 5e7e9db05e4..00000000000 --- a/lib/tool_shed/util/xml_util.py +++ /dev/null @@ -1,92 +0,0 @@ -import io -import logging -import os -import tempfile -from xml.etree import ElementTree as XmlET - -from galaxy.util import ( - xml_to_string -) - -log = logging.getLogger(__name__) - - -class Py27CommentedTreeBuilder(XmlET.TreeBuilder): - - def doctype(*args): - # handle deprecation warning for XMLParsing a file with DOCTYPE - pass - - def comment(self, data): - self.start(XmlET.Comment, {}) - self.data(data) - self.end(XmlET.Comment) - - -def create_and_write_tmp_file(elem): - tmp_str = xml_to_string(elem, pretty=True) - with tempfile.NamedTemporaryFile(prefix="tmp-toolshed-cawrf", delete=False) as fh: - tmp_filename = fh.name - with io.open(tmp_filename, mode='w', encoding='utf-8') as fh: - fh.write(tmp_str) - return tmp_filename - - -def create_element(tag, attributes=None, sub_elements=None): - """ - Create a new element whose tag is the value of the received tag, and whose attributes are all - key / value pairs in the received attributes and sub_elements. - """ - if tag: - elem = XmlET.Element(tag) - if attributes: - # The received attributes is an odict to preserve ordering. - for k, v in attributes.items(): - elem.set(k, v) - if sub_elements: - # The received attributes is an odict. These handle information that tends to be - # long text including paragraphs (e.g., description and long_description. - for k, v in sub_elements.items(): - # Don't include fields that are blank. - if v: - if k == 'packages': - # The received sub_elements is an odict whose key is 'packages' and whose - # value is a list of ( name, version ) tuples. - for v_tuple in v: - sub_elem = XmlET.SubElement(elem, 'package') - sub_elem_name, sub_elem_version = v_tuple - sub_elem.set('name', sub_elem_name) - sub_elem.set('version', sub_elem_version) - elif isinstance(v, list): - sub_elem = XmlET.SubElement(elem, k) - # If v is a list, then it must be a list of tuples where the first - # item is the tag and the second item is the text value. - for v_tuple in v: - if len(v_tuple) == 2: - v_tag = v_tuple[0] - v_text = v_tuple[1] - # Don't include fields that are blank. - if v_text: - v_elem = XmlET.SubElement(sub_elem, v_tag) - v_elem.text = v_text - else: - sub_elem = XmlET.SubElement(elem, k) - sub_elem.text = v - return elem - return None - - -def parse_xml(file_name): - """Returns a parsed xml tree with comments intact.""" - error_message = '' - if not os.path.exists(file_name): - return None, "File does not exist %s" % str(file_name) - - with open(file_name, 'r') as fobj: - try: - tree = XmlET.parse(fobj, parser=XmlET.XMLParser(target=Py27CommentedTreeBuilder())) - except Exception as e: - error_message = "Exception attempting to parse %s: %s" % (str(file_name), str(e)) - log.exception(error_message) - return None, error_message - return tree, error_message diff --git a/lib/tool_shed/util/xml_util.py b/lib/tool_shed/util/xml_util.py new file mode 120000 index 00000000000..cb738288301 --- /dev/null +++ b/lib/tool_shed/util/xml_util.py @@ -0,0 +1 @@ +../../galaxy/util/tool_shed/xml_util.py \ No newline at end of file diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst new file mode 100644 index 00000000000..ec2f0e746e9 --- /dev/null +++ b/packages/app/HISTORY.rst @@ -0,0 +1,12 @@ +.. :changelog: + +History +------- + +.. to_doc + +--------------------- +19.9.0.dev0 +--------------------- + +* Initial import from dev branch of Galaxy during 19.09 development cycle. diff --git a/packages/app/LICENSE b/packages/app/LICENSE new file mode 120000 index 00000000000..1ef648f64b3 --- /dev/null +++ b/packages/app/LICENSE @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/app/MANIFEST.in b/packages/app/MANIFEST.in new file mode 100644 index 00000000000..c74cefe0942 --- /dev/null +++ b/packages/app/MANIFEST.in @@ -0,0 +1 @@ +include *.rst LICENSE diff --git a/packages/app/Makefile b/packages/app/Makefile new file mode 120000 index 00000000000..37af8bae5ba --- /dev/null +++ b/packages/app/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/app/README.rst b/packages/app/README.rst new file mode 100644 index 00000000000..898b0262617 --- /dev/null +++ b/packages/app/README.rst @@ -0,0 +1,14 @@ + +.. image:: https://badge.fury.io/py/galaxy-app.svg + :target: https://pypi.org/project/galaxy-app/ + + +Overview +-------- + +The Galaxy_ application logic (backend). + +* Free software: Academic Free License version 3.0 +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/app/dev-requirements.txt b/packages/app/dev-requirements.txt new file mode 120000 index 00000000000..467b90d7a23 --- /dev/null +++ b/packages/app/dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/app/galaxy/__init__.py b/packages/app/galaxy/__init__.py new file mode 100644 index 00000000000..69e3be50dac --- /dev/null +++ b/packages/app/galaxy/__init__.py @@ -0,0 +1 @@ +__path__ = __import__('pkgutil').extend_path(__path__, __name__) diff --git a/packages/app/galaxy/actions b/packages/app/galaxy/actions new file mode 120000 index 00000000000..0a3660ca78f --- /dev/null +++ b/packages/app/galaxy/actions @@ -0,0 +1 @@ +../../../lib/galaxy/actions \ No newline at end of file diff --git a/packages/app/galaxy/app.py b/packages/app/galaxy/app.py new file mode 120000 index 00000000000..61ec0a3dd4d --- /dev/null +++ b/packages/app/galaxy/app.py @@ -0,0 +1 @@ +../../../lib/galaxy/app.py \ No newline at end of file diff --git a/packages/app/galaxy/config.py b/packages/app/galaxy/config.py new file mode 120000 index 00000000000..7e61acb3d31 --- /dev/null +++ b/packages/app/galaxy/config.py @@ -0,0 +1 @@ +../../../lib/galaxy/config.py \ No newline at end of file diff --git a/packages/app/galaxy/config_watchers.py b/packages/app/galaxy/config_watchers.py new file mode 120000 index 00000000000..ffd3e6bd109 --- /dev/null +++ b/packages/app/galaxy/config_watchers.py @@ -0,0 +1 @@ +../../../lib/galaxy/config_watchers.py \ No newline at end of file diff --git a/packages/app/galaxy/forms b/packages/app/galaxy/forms new file mode 120000 index 00000000000..b15f3ec2fa6 --- /dev/null +++ b/packages/app/galaxy/forms @@ -0,0 +1 @@ +../../../lib/galaxy/forms \ No newline at end of file diff --git a/packages/app/galaxy/jobs b/packages/app/galaxy/jobs new file mode 120000 index 00000000000..62e90b08b98 --- /dev/null +++ b/packages/app/galaxy/jobs @@ -0,0 +1 @@ +../../../lib/galaxy/jobs \ No newline at end of file diff --git a/packages/app/galaxy/main.py b/packages/app/galaxy/main.py new file mode 120000 index 00000000000..6b458fd3ff8 --- /dev/null +++ b/packages/app/galaxy/main.py @@ -0,0 +1 @@ +../../../lib/galaxy/main.py \ No newline at end of file diff --git a/packages/app/galaxy/managers b/packages/app/galaxy/managers new file mode 120000 index 00000000000..14228c5c999 --- /dev/null +++ b/packages/app/galaxy/managers @@ -0,0 +1 @@ +../../../lib/galaxy/managers \ No newline at end of file diff --git a/packages/app/galaxy/openid b/packages/app/galaxy/openid new file mode 120000 index 00000000000..e0bf26b2d37 --- /dev/null +++ b/packages/app/galaxy/openid @@ -0,0 +1 @@ +../../../lib/galaxy/openid \ No newline at end of file diff --git a/packages/app/galaxy/project_galaxy_app.py b/packages/app/galaxy/project_galaxy_app.py new file mode 100644 index 00000000000..95cac65f339 --- /dev/null +++ b/packages/app/galaxy/project_galaxy_app.py @@ -0,0 +1,13 @@ +# -*- coding: utf-8 -*- + +__version__ = '19.9.0.dev0' + +PROJECT_NAME = "galaxy-app" +PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" +PROJECT_URL = "https://github.com/galaxyproject/galaxy" +PROJECT_AUTHOR = 'Galaxy Project and Community' +PROJECT_DESCRIPTION = 'Galaxy Application (backend)' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' +RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( + PROJECT_USERAME, PROJECT_NAME +) diff --git a/packages/app/galaxy/queue_worker.py b/packages/app/galaxy/queue_worker.py new file mode 120000 index 00000000000..7fcb68fbea9 --- /dev/null +++ b/packages/app/galaxy/queue_worker.py @@ -0,0 +1 @@ +../../../lib/galaxy/queue_worker.py \ No newline at end of file diff --git a/packages/app/galaxy/queues.py b/packages/app/galaxy/queues.py new file mode 120000 index 00000000000..a5afab45290 --- /dev/null +++ b/packages/app/galaxy/queues.py @@ -0,0 +1 @@ +../../../lib/galaxy/queues.py \ No newline at end of file diff --git a/packages/app/galaxy/tools b/packages/app/galaxy/tools new file mode 120000 index 00000000000..b77e9bb0152 --- /dev/null +++ b/packages/app/galaxy/tools @@ -0,0 +1 @@ +../../../lib/galaxy/tools \ No newline at end of file diff --git a/packages/app/galaxy/tours b/packages/app/galaxy/tours new file mode 120000 index 00000000000..4cb21b13e3a --- /dev/null +++ b/packages/app/galaxy/tours @@ -0,0 +1 @@ +../../../lib/galaxy/tours \ No newline at end of file diff --git a/packages/app/galaxy/version.py b/packages/app/galaxy/version.py new file mode 120000 index 00000000000..42d972d9994 --- /dev/null +++ b/packages/app/galaxy/version.py @@ -0,0 +1 @@ +../../../lib/galaxy/version.py \ No newline at end of file diff --git a/packages/app/galaxy/visualization b/packages/app/galaxy/visualization new file mode 120000 index 00000000000..3fe58fc6407 --- /dev/null +++ b/packages/app/galaxy/visualization @@ -0,0 +1 @@ +../../../lib/galaxy/visualization \ No newline at end of file diff --git a/packages/app/galaxy/webhooks b/packages/app/galaxy/webhooks new file mode 120000 index 00000000000..4f76d9fd9ea --- /dev/null +++ b/packages/app/galaxy/webhooks @@ -0,0 +1 @@ +../../../lib/galaxy/webhooks \ No newline at end of file diff --git a/packages/app/galaxy/work b/packages/app/galaxy/work new file mode 120000 index 00000000000..92a02a7cb53 --- /dev/null +++ b/packages/app/galaxy/work @@ -0,0 +1 @@ +../../../lib/galaxy/work \ No newline at end of file diff --git a/packages/app/galaxy/workflow b/packages/app/galaxy/workflow new file mode 120000 index 00000000000..59308093ad1 --- /dev/null +++ b/packages/app/galaxy/workflow @@ -0,0 +1 @@ +../../../lib/galaxy/workflow \ No newline at end of file diff --git a/packages/app/requirements.txt b/packages/app/requirements.txt new file mode 100644 index 00000000000..da8a0e43f0c --- /dev/null +++ b/packages/app/requirements.txt @@ -0,0 +1,4 @@ +galaxy-auth +galaxy-job-execution +galaxy-web-framework +galaxy-web-stack diff --git a/packages/app/scripts b/packages/app/scripts new file mode 120000 index 00000000000..9aec9dc5a06 --- /dev/null +++ b/packages/app/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg new file mode 120000 index 00000000000..eb7cf09393f --- /dev/null +++ b/packages/app/setup.cfg @@ -0,0 +1 @@ +../../setup.cfg \ No newline at end of file diff --git a/packages/app/setup.py b/packages/app/setup.py new file mode 100644 index 00000000000..1f1b2fa3b07 --- /dev/null +++ b/packages/app/setup.py @@ -0,0 +1,169 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import ast +import os +import re +try: + from setuptools import setup +except ImportError: + from distutils.core import setup + +SOURCE_DIR = "galaxy" + +_version_re = re.compile(r'__version__\s+=\s+(.*)') + +project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__))) +with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f: + init_contents = f.read().decode('utf-8') + + def get_var(var_name): + pattern = re.compile(r'%s\s+=\s+(.*)' % var_name) + match = pattern.search(init_contents).group(1) + return str(ast.literal_eval(match)) + + version = get_var("__version__") + PROJECT_NAME = get_var("PROJECT_NAME") + PROJECT_URL = get_var("PROJECT_URL") + PROJECT_AUTHOR = get_var("PROJECT_AUTHOR") + PROJECT_EMAIL = get_var("PROJECT_EMAIL") + PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION") + +TEST_DIR = 'tests' +PACKAGES = [ + 'galaxy', + 'galaxy.actions', + 'galaxy.forms', + 'galaxy.jobs', + 'galaxy.jobs.actions', + 'galaxy.jobs.rules', + 'galaxy.jobs.runners', + 'galaxy.jobs.runners.state_handlers', + 'galaxy.jobs.runners.util', + 'galaxy.jobs.runners.util.cli', + 'galaxy.jobs.runners.util.cli.job', + 'galaxy.jobs.runners.util.cli.shell', + 'galaxy.jobs.runners.util.condor', + 'galaxy.jobs.runners.util.job_script', + 'galaxy.jobs.splitters', + 'galaxy.managers', + 'galaxy.openid', + 'galaxy.tools', + 'galaxy.tools.actions', + 'galaxy.tools.data', + 'galaxy.tools.data_manager', + 'galaxy.tools.error_reports', + 'galaxy.tools.expressions', + 'galaxy.tools.filters', + 'galaxy.tools.imp_exp', + 'galaxy.tools.parameters', + 'galaxy.tools.search', + 'galaxy.tools.toolbox', + 'galaxy.tools.toolbox.filters', + 'galaxy.tools.toolbox.lineages', + 'galaxy.tools.util', + 'galaxy.tools.util.galaxyops', + 'galaxy.tools.verify', + 'galaxy.tools.verify.asserts', + 'galaxy.tours', + 'galaxy.visualization', + 'galaxy.visualization.data_providers', + 'galaxy.visualization.data_providers.phyloviz', + 'galaxy.visualization.genome', + 'galaxy.visualization.plugins', + 'galaxy.visualization.tracks', + 'galaxy.webhooks', + 'galaxy.work', + 'galaxy.workflow', + 'galaxy.workflow.resources', + 'galaxy.workflow.schedulers', + 'tool_shed', + 'tool_shed.capsule', + 'tool_shed.dependencies', + 'tool_shed.dependencies.repository', + 'tool_shed.dependencies.tool', + 'tool_shed.galaxy_install.datatypes', + 'tool_shed.galaxy_install.grids', + 'tool_shed.galaxy_install.metadata', + 'tool_shed.galaxy_install.migrate', + 'tool_shed.galaxy_install.migrate.versions', + 'tool_shed.galaxy_install.repository_dependencies', + 'tool_shed.galaxy_install.tool_dependencies', + 'tool_shed.galaxy_install.tool_dependencies.recipe', + 'tool_shed.galaxy_install.tools', + 'tool_shed.galaxy_install.utility_containers', + 'tool_shed.grids', + 'tool_shed.managers', + 'tool_shed.metadata', + 'tool_shed.repository_types', + 'tool_shed.tools', + 'tool_shed.util', + 'tool_shed.utility_containers', +] +ENTRY_POINTS = ''' + [console_scripts] +''' +PACKAGE_DATA = { + # Be sure to update MANIFEST.in for source dist. + 'galaxy': [ + ], + 'tool_shed': [ + 'scripts/bootstrap_tool_shed/user_info.xml', + ], +} +PACKAGE_DIR = { + SOURCE_DIR: SOURCE_DIR, +} + +readme = open('README.rst').read() +history = open('HISTORY.rst').read().replace('.. :changelog:', '') + +if os.path.exists("requirements.txt"): + requirements = open("requirements.txt").read().split("\n") +else: + # In tox, it will cover them anyway. + requirements = [] + + +test_requirements = [ + # TODO: put package test requirements here +] + + +setup( + name=PROJECT_NAME, + version=version, + description=PROJECT_DESCRIPTION, + long_description=readme + '\n\n' + history, + long_description_content_type='text/x-rst', + author=PROJECT_AUTHOR, + author_email=PROJECT_EMAIL, + url=PROJECT_URL, + packages=PACKAGES, + entry_points=ENTRY_POINTS, + package_data=PACKAGE_DATA, + package_dir=PACKAGE_DIR, + include_package_data=True, + install_requires=requirements, + license="AFL", + zip_safe=False, + keywords='galaxy', + classifiers=[ + 'Development Status :: 5 - Production/Stable', + 'Intended Audience :: Developers', + 'Environment :: Console', + 'License :: OSI Approved :: Academic Free License (AFL)', + 'Operating System :: POSIX', + 'Topic :: Software Development', + 'Topic :: Software Development :: Code Generators', + 'Topic :: Software Development :: Testing', + 'Natural Language :: English', + "Programming Language :: Python :: 2", + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + test_suite=TEST_DIR, + tests_require=test_requirements +) diff --git a/packages/app/tool_shed b/packages/app/tool_shed new file mode 120000 index 00000000000..a24c5c74750 --- /dev/null +++ b/packages/app/tool_shed @@ -0,0 +1 @@ +../../lib/tool_shed \ No newline at end of file diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst new file mode 100644 index 00000000000..ec2f0e746e9 --- /dev/null +++ b/packages/auth/HISTORY.rst @@ -0,0 +1,12 @@ +.. :changelog: + +History +------- + +.. to_doc + +--------------------- +19.9.0.dev0 +--------------------- + +* Initial import from dev branch of Galaxy during 19.09 development cycle. diff --git a/packages/auth/LICENSE b/packages/auth/LICENSE new file mode 120000 index 00000000000..1ef648f64b3 --- /dev/null +++ b/packages/auth/LICENSE @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/auth/MANIFEST.in b/packages/auth/MANIFEST.in new file mode 100644 index 00000000000..c74cefe0942 --- /dev/null +++ b/packages/auth/MANIFEST.in @@ -0,0 +1 @@ +include *.rst LICENSE diff --git a/packages/auth/Makefile b/packages/auth/Makefile new file mode 120000 index 00000000000..37af8bae5ba --- /dev/null +++ b/packages/auth/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/auth/README.rst b/packages/auth/README.rst new file mode 100644 index 00000000000..13915272fcb --- /dev/null +++ b/packages/auth/README.rst @@ -0,0 +1,15 @@ + +.. image:: https://badge.fury.io/py/galaxy-auth.svg + :target: https://pypi.org/project/galaxy-auth/ + + + +Overview +-------- + +The Galaxy_ auth framework and default plugins. + +* Free software: Academic Free License version 3.0 +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/auth/dev-requirements.txt b/packages/auth/dev-requirements.txt new file mode 120000 index 00000000000..467b90d7a23 --- /dev/null +++ b/packages/auth/dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/auth/galaxy/__init__.py b/packages/auth/galaxy/__init__.py new file mode 100644 index 00000000000..69e3be50dac --- /dev/null +++ b/packages/auth/galaxy/__init__.py @@ -0,0 +1 @@ +__path__ = __import__('pkgutil').extend_path(__path__, __name__) diff --git a/packages/auth/galaxy/auth b/packages/auth/galaxy/auth new file mode 120000 index 00000000000..9c9b6bf2e30 --- /dev/null +++ b/packages/auth/galaxy/auth @@ -0,0 +1 @@ +../../../lib/galaxy/auth \ No newline at end of file diff --git a/packages/auth/galaxy/project_galaxy_auth.py b/packages/auth/galaxy/project_galaxy_auth.py new file mode 100644 index 00000000000..dbd94f1ced5 --- /dev/null +++ b/packages/auth/galaxy/project_galaxy_auth.py @@ -0,0 +1,13 @@ +# -*- coding: utf-8 -*- + +__version__ = '19.9.0.dev0' + +PROJECT_NAME = "galaxy-auth" +PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" +PROJECT_URL = "https://github.com/galaxyproject/galaxy" +PROJECT_AUTHOR = 'Galaxy Project and Community' +PROJECT_DESCRIPTION = 'Galaxy Auth Framework and Implementations' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' +RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( + PROJECT_USERAME, PROJECT_NAME +) diff --git a/packages/auth/requirements.txt b/packages/auth/requirements.txt new file mode 100644 index 00000000000..7dcf8f4def7 --- /dev/null +++ b/packages/auth/requirements.txt @@ -0,0 +1 @@ +galaxy-data diff --git a/packages/auth/scripts b/packages/auth/scripts new file mode 120000 index 00000000000..9aec9dc5a06 --- /dev/null +++ b/packages/auth/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg new file mode 120000 index 00000000000..eb7cf09393f --- /dev/null +++ b/packages/auth/setup.cfg @@ -0,0 +1 @@ +../../setup.cfg \ No newline at end of file diff --git a/packages/auth/setup.py b/packages/auth/setup.py new file mode 100644 index 00000000000..63367f57581 --- /dev/null +++ b/packages/auth/setup.py @@ -0,0 +1,101 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import ast +import os +import re +try: + from setuptools import setup +except ImportError: + from distutils.core import setup + +SOURCE_DIR = "galaxy" + +_version_re = re.compile(r'__version__\s+=\s+(.*)') + +project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__))) +with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f: + init_contents = f.read().decode('utf-8') + + def get_var(var_name): + pattern = re.compile(r'%s\s+=\s+(.*)' % var_name) + match = pattern.search(init_contents).group(1) + return str(ast.literal_eval(match)) + + version = get_var("__version__") + PROJECT_NAME = get_var("PROJECT_NAME") + PROJECT_URL = get_var("PROJECT_URL") + PROJECT_AUTHOR = get_var("PROJECT_AUTHOR") + PROJECT_EMAIL = get_var("PROJECT_EMAIL") + PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION") + +TEST_DIR = 'tests' +PACKAGES = [ + 'galaxy', + 'galaxy.auth', + 'galaxy.auth.providers', +] +ENTRY_POINTS = ''' + [console_scripts] +''' +PACKAGE_DATA = { + # Be sure to update MANIFEST.in for source dist. + 'galaxy': [ + ], +} +PACKAGE_DIR = { + SOURCE_DIR: SOURCE_DIR, +} + +readme = open('README.rst').read() +history = open('HISTORY.rst').read().replace('.. :changelog:', '') + +if os.path.exists("requirements.txt"): + requirements = open("requirements.txt").read().split("\n") +else: + # In tox, it will cover them anyway. + requirements = [] + + +test_requirements = [ + # TODO: put package test requirements here +] + + +setup( + name=PROJECT_NAME, + version=version, + description=PROJECT_DESCRIPTION, + long_description=readme + '\n\n' + history, + long_description_content_type='text/x-rst', + author=PROJECT_AUTHOR, + author_email=PROJECT_EMAIL, + url=PROJECT_URL, + packages=PACKAGES, + entry_points=ENTRY_POINTS, + package_data=PACKAGE_DATA, + package_dir=PACKAGE_DIR, + include_package_data=True, + install_requires=requirements, + license="AFL", + zip_safe=False, + keywords='galaxy', + classifiers=[ + 'Development Status :: 5 - Production/Stable', + 'Intended Audience :: Developers', + 'Environment :: Console', + 'License :: OSI Approved :: Academic Free License (AFL)', + 'Operating System :: POSIX', + 'Topic :: Software Development', + 'Topic :: Software Development :: Code Generators', + 'Topic :: Software Development :: Testing', + 'Natural Language :: English', + "Programming Language :: Python :: 2", + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + test_suite=TEST_DIR, + tests_require=test_requirements +) diff --git a/packages/authnz/HISTORY.rst b/packages/authnz/HISTORY.rst new file mode 100644 index 00000000000..ec2f0e746e9 --- /dev/null +++ b/packages/authnz/HISTORY.rst @@ -0,0 +1,12 @@ +.. :changelog: + +History +------- + +.. to_doc + +--------------------- +19.9.0.dev0 +--------------------- + +* Initial import from dev branch of Galaxy during 19.09 development cycle. diff --git a/packages/authnz/LICENSE b/packages/authnz/LICENSE new file mode 120000 index 00000000000..1ef648f64b3 --- /dev/null +++ b/packages/authnz/LICENSE @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/authnz/MANIFEST.in b/packages/authnz/MANIFEST.in new file mode 100644 index 00000000000..c74cefe0942 --- /dev/null +++ b/packages/authnz/MANIFEST.in @@ -0,0 +1 @@ +include *.rst LICENSE diff --git a/packages/authnz/Makefile b/packages/authnz/Makefile new file mode 120000 index 00000000000..37af8bae5ba --- /dev/null +++ b/packages/authnz/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/authnz/README.rst b/packages/authnz/README.rst new file mode 100644 index 00000000000..5f94cd6f231 --- /dev/null +++ b/packages/authnz/README.rst @@ -0,0 +1,14 @@ + +.. image:: https://badge.fury.io/py/galaxy-authnz.svg + :target: https://pypi.org/project/galaxy-authnz/ + + +Overview +-------- + +The Galaxy_ authnz module. + +* Free software: Academic Free License version 3.0 +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/authnz/dev-requirements.txt b/packages/authnz/dev-requirements.txt new file mode 120000 index 00000000000..467b90d7a23 --- /dev/null +++ b/packages/authnz/dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/authnz/galaxy/__init__.py b/packages/authnz/galaxy/__init__.py new file mode 100644 index 00000000000..69e3be50dac --- /dev/null +++ b/packages/authnz/galaxy/__init__.py @@ -0,0 +1 @@ +__path__ = __import__('pkgutil').extend_path(__path__, __name__) diff --git a/packages/authnz/galaxy/authnz b/packages/authnz/galaxy/authnz new file mode 120000 index 00000000000..801410c14dc --- /dev/null +++ b/packages/authnz/galaxy/authnz @@ -0,0 +1 @@ +../../../lib/galaxy/authnz \ No newline at end of file diff --git a/packages/authnz/galaxy/project_galaxy_authnz.py b/packages/authnz/galaxy/project_galaxy_authnz.py new file mode 100644 index 00000000000..bf401824d4f --- /dev/null +++ b/packages/authnz/galaxy/project_galaxy_authnz.py @@ -0,0 +1,13 @@ +# -*- coding: utf-8 -*- + +__version__ = '19.9.0.dev0' + +PROJECT_NAME = "galaxy-authnz" +PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" +PROJECT_URL = "https://github.com/galaxyproject/galaxy" +PROJECT_AUTHOR = 'Galaxy Project and Community' +PROJECT_DESCRIPTION = 'Galaxy AuthNZ' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' +RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( + PROJECT_USERAME, PROJECT_NAME +) diff --git a/packages/authnz/requirements.txt b/packages/authnz/requirements.txt new file mode 100644 index 00000000000..353d6bbd324 --- /dev/null +++ b/packages/authnz/requirements.txt @@ -0,0 +1,7 @@ +galaxy-data +pyjwt +cloudauthz +# Following three shouldn't be needed, cloudauthz should be updated to require them +google-api-python-client +httplib2 +oauth2client diff --git a/packages/authnz/scripts b/packages/authnz/scripts new file mode 120000 index 00000000000..9aec9dc5a06 --- /dev/null +++ b/packages/authnz/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/authnz/setup.cfg b/packages/authnz/setup.cfg new file mode 120000 index 00000000000..eb7cf09393f --- /dev/null +++ b/packages/authnz/setup.cfg @@ -0,0 +1 @@ +../../setup.cfg \ No newline at end of file diff --git a/packages/authnz/setup.py b/packages/authnz/setup.py new file mode 100644 index 00000000000..8c8f3053e79 --- /dev/null +++ b/packages/authnz/setup.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import ast +import os +import re +try: + from setuptools import setup +except ImportError: + from distutils.core import setup + +SOURCE_DIR = "galaxy" + +_version_re = re.compile(r'__version__\s+=\s+(.*)') + +project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__))) +with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f: + init_contents = f.read().decode('utf-8') + + def get_var(var_name): + pattern = re.compile(r'%s\s+=\s+(.*)' % var_name) + match = pattern.search(init_contents).group(1) + return str(ast.literal_eval(match)) + + version = get_var("__version__") + PROJECT_NAME = get_var("PROJECT_NAME") + PROJECT_URL = get_var("PROJECT_URL") + PROJECT_AUTHOR = get_var("PROJECT_AUTHOR") + PROJECT_EMAIL = get_var("PROJECT_EMAIL") + PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION") + +TEST_DIR = 'tests' +PACKAGES = [ + 'galaxy', + 'galaxy.authnz', +] +ENTRY_POINTS = ''' + [console_scripts] +''' +PACKAGE_DATA = { + # Be sure to update MANIFEST.in for source dist. + 'galaxy': [ + ], +} +PACKAGE_DIR = { + SOURCE_DIR: SOURCE_DIR, +} + +readme = open('README.rst').read() +history = open('HISTORY.rst').read().replace('.. :changelog:', '') + +if os.path.exists("requirements.txt"): + requirements = open("requirements.txt").read().split("\n") +else: + # In tox, it will cover them anyway. + requirements = [] + + +test_requirements = [ + # TODO: put package test requirements here +] + + +setup( + name=PROJECT_NAME, + version=version, + description=PROJECT_DESCRIPTION, + long_description=readme + '\n\n' + history, + long_description_content_type='text/x-rst', + author=PROJECT_AUTHOR, + author_email=PROJECT_EMAIL, + url=PROJECT_URL, + packages=PACKAGES, + entry_points=ENTRY_POINTS, + package_data=PACKAGE_DATA, + package_dir=PACKAGE_DIR, + include_package_data=True, + install_requires=requirements, + license="AFL", + zip_safe=False, + keywords='galaxy', + classifiers=[ + 'Development Status :: 5 - Production/Stable', + 'Intended Audience :: Developers', + 'Environment :: Console', + 'License :: OSI Approved :: Academic Free License (AFL)', + 'Operating System :: POSIX', + 'Topic :: Software Development', + 'Topic :: Software Development :: Code Generators', + 'Topic :: Software Development :: Testing', + 'Natural Language :: English', + "Programming Language :: Python :: 2", + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + test_suite=TEST_DIR, + tests_require=test_requirements +) diff --git a/packages/authnz/tests/test_custos_authnz.py b/packages/authnz/tests/test_custos_authnz.py new file mode 120000 index 00000000000..d41840c35c6 --- /dev/null +++ b/packages/authnz/tests/test_custos_authnz.py @@ -0,0 +1 @@ +../../../test/unit/authnz/test_custos_authnz.py \ No newline at end of file diff --git a/packages/containers/README.rst b/packages/containers/README.rst index ed360aeef60..90be9b0a80a 100644 --- a/packages/containers/README.rst +++ b/packages/containers/README.rst @@ -1,6 +1,6 @@ .. image:: https://badge.fury.io/py/galaxy-containers.svg - :target: https://pypi.python.org/pypi/galaxy-containers/ + :target: https://pypi.org/project/galaxy-containers/ Overview diff --git a/packages/containers/galaxy/project_galaxy_containers.py b/packages/containers/galaxy/project_galaxy_containers.py index 6442c8261bb..aaa2331fcce 100644 --- a/packages/containers/galaxy/project_galaxy_containers.py +++ b/packages/containers/galaxy/project_galaxy_containers.py @@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" PROJECT_URL = "https://github.com/galaxyproject/galaxy" PROJECT_AUTHOR = 'Galaxy Project and Community' PROJECT_DESCRIPTION = 'Galaxy Container Modeling and Interaction Abstractions' -PROJECT_EMAIL = 'jmchilton@gmail.com' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( PROJECT_USERAME, PROJECT_NAME ) diff --git a/packages/data/README.rst b/packages/data/README.rst index 4deccf230e9..daf960bc982 100644 --- a/packages/data/README.rst +++ b/packages/data/README.rst @@ -1,6 +1,6 @@ .. image:: https://badge.fury.io/py/galaxy-data.svg - :target: https://pypi.python.org/pypi/galaxy-data/ + :target: https://pypi.org/project/galaxy-data/ Overview diff --git a/packages/data/galaxy/project_galaxy_data.py b/packages/data/galaxy/project_galaxy_data.py index b7c780d82ab..1a2efe784b6 100644 --- a/packages/data/galaxy/project_galaxy_data.py +++ b/packages/data/galaxy/project_galaxy_data.py @@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" PROJECT_URL = "https://github.com/galaxyproject/galaxy" PROJECT_AUTHOR = 'Galaxy Project and Community' PROJECT_DESCRIPTION = 'Galaxy Datatype Framework and Datatypes' -PROJECT_EMAIL = 'jmchilton@gmail.com' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( PROJECT_USERAME, PROJECT_NAME ) diff --git a/packages/data/galaxy/quota b/packages/data/galaxy/quota new file mode 120000 index 00000000000..a16f2ec8773 --- /dev/null +++ b/packages/data/galaxy/quota @@ -0,0 +1 @@ +../../../lib/galaxy/quota \ No newline at end of file diff --git a/packages/data/requirements.txt b/packages/data/requirements.txt index f2b5c80f06e..40d2a9baed0 100644 --- a/packages/data/requirements.txt +++ b/packages/data/requirements.txt @@ -1,13 +1,16 @@ galaxy-objectstore -galaxy-util +galaxy-sequence-utils==1.1.3 +galaxy-util[template] bdbag bx-python h5py isa-rwval -numpy +parsley +numpy<=1.16 pycryptodome pysam social_auth_core SQLAlchemy==1.2 sqlalchemy-migrate +sqlalchemy-utils WebOb diff --git a/packages/data/setup.py b/packages/data/setup.py index 38ec5a74e13..12556d60ed4 100644 --- a/packages/data/setup.py +++ b/packages/data/setup.py @@ -42,6 +42,7 @@ PACKAGES = [ 'galaxy.model.orm', 'galaxy.model.store', 'galaxy.model.tool_shed_install', + 'galaxy.quota', 'galaxy.security', ] ENTRY_POINTS = ''' diff --git a/packages/data/tests/unittest_utils/__init__.py b/packages/data/tests/unittest_utils/__init__.py index 2115ad35783..290bb9ee29b 120000 --- a/packages/data/tests/unittest_utils/__init__.py +++ b/packages/data/tests/unittest_utils/__init__.py @@ -1 +1 @@ -../../test/unit/unittest_utils/__init__.py \ No newline at end of file +../../../../test/unit/unittest_utils/__init__.py \ No newline at end of file diff --git a/packages/data/tests/unittest_utils/tempfilecache.py b/packages/data/tests/unittest_utils/tempfilecache.py index 93fb83f1df7..588f6eec7d8 120000 --- a/packages/data/tests/unittest_utils/tempfilecache.py +++ b/packages/data/tests/unittest_utils/tempfilecache.py @@ -1 +1 @@ -../../test/unit/unittest_utils/tempfilecache.py \ No newline at end of file +../../../../test/unit/unittest_utils/tempfilecache.py \ No newline at end of file diff --git a/packages/data/tests/unittest_utils/utility.py b/packages/data/tests/unittest_utils/utility.py index 54dd4ca7a3b..3c69a8fd67e 120000 --- a/packages/data/tests/unittest_utils/utility.py +++ b/packages/data/tests/unittest_utils/utility.py @@ -1 +1 @@ -../../test/unit/unittest_utils/utility.py \ No newline at end of file +../../../../test/unit/unittest_utils/utility.py \ No newline at end of file diff --git a/packages/job_execution/README.rst b/packages/job_execution/README.rst index 3a7574eab70..8ec9c6f91cf 100644 --- a/packages/job_execution/README.rst +++ b/packages/job_execution/README.rst @@ -1,6 +1,6 @@ .. image:: https://badge.fury.io/py/galaxy-job-execution.svg - :target: https://pypi.python.org/pypi/galaxy-job-execution/ + :target: https://pypi.org/project/galaxy-job-execution/ Overview diff --git a/packages/job_execution/galaxy/project_galaxy_job_execution.py b/packages/job_execution/galaxy/project_galaxy_job_execution.py index a30f915133d..f2c11c58e0e 100644 --- a/packages/job_execution/galaxy/project_galaxy_job_execution.py +++ b/packages/job_execution/galaxy/project_galaxy_job_execution.py @@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" PROJECT_URL = "https://github.com/galaxyproject/galaxy" PROJECT_AUTHOR = 'Galaxy Project and Community' PROJECT_DESCRIPTION = 'Galaxy Job Execution Runtime Utilities' -PROJECT_EMAIL = 'jmchilton@gmail.com' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( PROJECT_USERAME, PROJECT_NAME ) diff --git a/packages/job_execution/tests/test_metadata.py b/packages/job_execution/tests/test_metadata.py deleted file mode 120000 index 9aa7e9cb83b..00000000000 --- a/packages/job_execution/tests/test_metadata.py +++ /dev/null @@ -1 +0,0 @@ -../../../test/unit/tools/test_metadata.py \ No newline at end of file diff --git a/packages/job_metrics/README.rst b/packages/job_metrics/README.rst index 65a810c4c24..f584e6b993d 100644 --- a/packages/job_metrics/README.rst +++ b/packages/job_metrics/README.rst @@ -1,6 +1,6 @@ .. image:: https://badge.fury.io/py/galaxy-job-metrics.svg - :target: https://pypi.python.org/pypi/galaxy-job-metrics/ + :target: https://pypi.org/project/galaxy-job-metrics/ Overview diff --git a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py index 5c5c5411ab8..a14ffc17c67 100644 --- a/packages/job_metrics/galaxy/project_galaxy_job_metrics.py +++ b/packages/job_metrics/galaxy/project_galaxy_job_metrics.py @@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" PROJECT_URL = "https://github.com/galaxyproject/galaxy" PROJECT_AUTHOR = 'Galaxy Project and Community' PROJECT_DESCRIPTION = 'Galaxy Job Metrics' -PROJECT_EMAIL = 'jmchilton@gmail.com' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( PROJECT_USERAME, PROJECT_NAME ) diff --git a/packages/objectstore/README.rst b/packages/objectstore/README.rst index fa243ffe29b..ceaa2466eaf 100644 --- a/packages/objectstore/README.rst +++ b/packages/objectstore/README.rst @@ -1,6 +1,6 @@ .. image:: https://badge.fury.io/py/galaxy-objectstore.svg - :target: https://pypi.python.org/pypi/galaxy-objectstore/ + :target: https://pypi.org/project/galaxy-objectstore/ Overview diff --git a/packages/objectstore/galaxy/project_galaxy_objectstore.py b/packages/objectstore/galaxy/project_galaxy_objectstore.py index 825abc23062..be0292f59e7 100644 --- a/packages/objectstore/galaxy/project_galaxy_objectstore.py +++ b/packages/objectstore/galaxy/project_galaxy_objectstore.py @@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" PROJECT_URL = "https://github.com/galaxyproject/galaxy" PROJECT_AUTHOR = 'Galaxy Project and Community' PROJECT_DESCRIPTION = 'Galaxy Objectstore Framework and Plugins' -PROJECT_EMAIL = 'jmchilton@gmail.com' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( PROJECT_USERAME, PROJECT_NAME ) diff --git a/packages/test.sh b/packages/test.sh index aacfab67a3e..43c4f70550c 100755 --- a/packages/test.sh +++ b/packages/test.sh @@ -22,10 +22,16 @@ PACKAGE_DIRS=( tool_util data job_execution + auth + authnz + web_stack + web_framework + app + web_apps ) # containers has no tests, tool_util not yet working 100%, # data has many problems quota, tool shed install database, etc.. -RUN_TESTS=(1 1 1 0 0 0 0 1) +RUN_TESTS=(1 1 1 0 1 1 1 0 1 0 0 0 0) for ((i=0; i<${#PACKAGE_DIRS[@]}; i++)); do package_dir=${PACKAGE_DIRS[$i]} diff --git a/packages/tool_util/README.rst b/packages/tool_util/README.rst index 74c8c0f1f31..badd671d78a 100644 --- a/packages/tool_util/README.rst +++ b/packages/tool_util/README.rst @@ -1,6 +1,6 @@ .. image:: https://badge.fury.io/py/galaxy-tool-util.svg - :target: https://pypi.python.org/pypi/galaxy-tool-util/ + :target: https://pypi.org/project/galaxy-tool-util/ Overview diff --git a/packages/tool_util/galaxy/project_galaxy_tool_util.py b/packages/tool_util/galaxy/project_galaxy_tool_util.py index 4f526958884..f9518421336 100644 --- a/packages/tool_util/galaxy/project_galaxy_tool_util.py +++ b/packages/tool_util/galaxy/project_galaxy_tool_util.py @@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" PROJECT_URL = "https://github.com/galaxyproject/galaxy" PROJECT_AUTHOR = 'Galaxy Project and Community' PROJECT_DESCRIPTION = 'Galaxy Tool and Tool Dependency Utilities' -PROJECT_EMAIL = 'jmchilton@gmail.com' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( PROJECT_USERAME, PROJECT_NAME ) diff --git a/packages/tool_util/setup.py b/packages/tool_util/setup.py index 33bf10b7794..3a07bdc2b5c 100644 --- a/packages/tool_util/setup.py +++ b/packages/tool_util/setup.py @@ -37,6 +37,7 @@ PACKAGES = [ 'galaxy.tool_util.deps.container_resolvers', 'galaxy.tool_util.deps.mulled', 'galaxy.tool_util.deps.resolvers', + 'galaxy.tool_util.linters', 'galaxy.tool_util.locations', 'galaxy.tool_util.parser', ] diff --git a/packages/util/README.rst b/packages/util/README.rst index 778c380a853..378cb991e37 100644 --- a/packages/util/README.rst +++ b/packages/util/README.rst @@ -1,6 +1,6 @@ .. image:: https://badge.fury.io/py/galaxy-util.svg - :target: https://pypi.python.org/pypi/galaxy-util/ + :target: https://pypi.org/project/galaxy-util/ Overview diff --git a/packages/util/galaxy/project_galaxy_util.py b/packages/util/galaxy/project_galaxy_util.py index c5a4d0ce99a..f8d1291d92b 100644 --- a/packages/util/galaxy/project_galaxy_util.py +++ b/packages/util/galaxy/project_galaxy_util.py @@ -7,7 +7,7 @@ PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" PROJECT_URL = "https://github.com/galaxyproject/galaxy" PROJECT_AUTHOR = 'Galaxy Project and Community' PROJECT_DESCRIPTION = 'Galaxy Generic Utilities' -PROJECT_EMAIL = 'jmchilton@gmail.com' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( PROJECT_USERAME, PROJECT_NAME ) diff --git a/packages/util/requirements.txt b/packages/util/requirements.txt index e15e5db251e..aad3e2dc97a 100644 --- a/packages/util/requirements.txt +++ b/packages/util/requirements.txt @@ -5,4 +5,5 @@ docutils markupsafe packaging pyyaml +routes six>=1.9.0 diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst new file mode 100644 index 00000000000..ec2f0e746e9 --- /dev/null +++ b/packages/web_apps/HISTORY.rst @@ -0,0 +1,12 @@ +.. :changelog: + +History +------- + +.. to_doc + +--------------------- +19.9.0.dev0 +--------------------- + +* Initial import from dev branch of Galaxy during 19.09 development cycle. diff --git a/packages/web_apps/LICENSE b/packages/web_apps/LICENSE new file mode 120000 index 00000000000..1ef648f64b3 --- /dev/null +++ b/packages/web_apps/LICENSE @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/web_apps/MANIFEST.in b/packages/web_apps/MANIFEST.in new file mode 100644 index 00000000000..c74cefe0942 --- /dev/null +++ b/packages/web_apps/MANIFEST.in @@ -0,0 +1 @@ +include *.rst LICENSE diff --git a/packages/web_apps/Makefile b/packages/web_apps/Makefile new file mode 120000 index 00000000000..37af8bae5ba --- /dev/null +++ b/packages/web_apps/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/web_apps/README.rst b/packages/web_apps/README.rst new file mode 100644 index 00000000000..2f28a9fefb6 --- /dev/null +++ b/packages/web_apps/README.rst @@ -0,0 +1,14 @@ + +.. image:: https://badge.fury.io/py/galaxy-web-apps.svg + :target: https://pypi.python.org/pypi/galaxy-web-apps/ + + +Overview +-------- + +The Galaxy_ web apps (Galaxy, Reports, Tool Shed). + +* Free software: Academic Free License version 3.0 +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/web_apps/dev-requirements.txt b/packages/web_apps/dev-requirements.txt new file mode 120000 index 00000000000..467b90d7a23 --- /dev/null +++ b/packages/web_apps/dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/web_apps/galaxy/__init__.py b/packages/web_apps/galaxy/__init__.py new file mode 100644 index 00000000000..69e3be50dac --- /dev/null +++ b/packages/web_apps/galaxy/__init__.py @@ -0,0 +1 @@ +__path__ = __import__('pkgutil').extend_path(__path__, __name__) diff --git a/packages/web_apps/galaxy/project_galaxy_web_apps.py b/packages/web_apps/galaxy/project_galaxy_web_apps.py new file mode 100644 index 00000000000..3f416bde726 --- /dev/null +++ b/packages/web_apps/galaxy/project_galaxy_web_apps.py @@ -0,0 +1,13 @@ +# -*- coding: utf-8 -*- + +__version__ = '19.9.0.dev0' + +PROJECT_NAME = "galaxy-web-apps" +PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" +PROJECT_URL = "https://github.com/galaxyproject/galaxy" +PROJECT_AUTHOR = 'Galaxy Project and Community' +PROJECT_DESCRIPTION = 'Galaxy Web Apps' +PROJECT_EMAIL = 'jmchilton@gmail.com' +RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( + PROJECT_USERAME, PROJECT_NAME +) diff --git a/packages/web_apps/galaxy/webapps b/packages/web_apps/galaxy/webapps new file mode 120000 index 00000000000..7f4c3888cef --- /dev/null +++ b/packages/web_apps/galaxy/webapps @@ -0,0 +1 @@ +../../../lib/galaxy/webapps \ No newline at end of file diff --git a/packages/web_apps/requirements.txt b/packages/web_apps/requirements.txt new file mode 100644 index 00000000000..eaf79b2a242 --- /dev/null +++ b/packages/web_apps/requirements.txt @@ -0,0 +1,2 @@ +galaxy-app + diff --git a/packages/web_apps/scripts b/packages/web_apps/scripts new file mode 120000 index 00000000000..9aec9dc5a06 --- /dev/null +++ b/packages/web_apps/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg new file mode 120000 index 00000000000..eb7cf09393f --- /dev/null +++ b/packages/web_apps/setup.cfg @@ -0,0 +1 @@ +../../setup.cfg \ No newline at end of file diff --git a/packages/web_apps/setup.py b/packages/web_apps/setup.py new file mode 100644 index 00000000000..a55e4a3ad29 --- /dev/null +++ b/packages/web_apps/setup.py @@ -0,0 +1,118 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import ast +import os +import re +try: + from setuptools import setup +except ImportError: + from distutils.core import setup + +SOURCE_DIR = "galaxy" + +_version_re = re.compile(r'__version__\s+=\s+(.*)') + +project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__))) +with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f: + init_contents = f.read().decode('utf-8') + + def get_var(var_name): + pattern = re.compile(r'%s\s+=\s+(.*)' % var_name) + match = pattern.search(init_contents).group(1) + return str(ast.literal_eval(match)) + + version = get_var("__version__") + PROJECT_NAME = get_var("PROJECT_NAME") + PROJECT_URL = get_var("PROJECT_URL") + PROJECT_AUTHOR = get_var("PROJECT_AUTHOR") + PROJECT_EMAIL = get_var("PROJECT_EMAIL") + PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION") + +TEST_DIR = 'tests' +PACKAGES = [ + 'galaxy', + 'galaxy.webapps', + 'galaxy.webapps.base', + 'galaxy.webapps.galaxy', + 'galaxy.webapps.galaxy.api', + 'galaxy.webapps.galaxy.controllers', + 'galaxy.webapps.reports', + 'galaxy.webapps.reports.controllers', + 'galaxy.webapps.reports.framework', + 'galaxy.webapps.tool_shed', + 'galaxy.webapps.tool_shed.api', + 'galaxy.webapps.tool_shed.controllers', + 'galaxy.webapps.tool_shed.framework', + 'galaxy.webapps.tool_shed.framework.middleware', + 'galaxy.webapps.tool_shed.model', + 'galaxy.webapps.tool_shed.model.migrate', + 'galaxy.webapps.tool_shed.model.migrate.versions', + 'galaxy.webapps.tool_shed.search', + 'galaxy.webapps.tool_shed.security', + 'galaxy.webapps.tool_shed.util', +] +ENTRY_POINTS = ''' + [console_scripts] +''' +PACKAGE_DATA = { + # Be sure to update MANIFEST.in for source dist. + 'galaxy': [ + ], +} +PACKAGE_DIR = { + SOURCE_DIR: SOURCE_DIR, +} + +readme = open('README.rst').read() +history = open('HISTORY.rst').read().replace('.. :changelog:', '') + +if os.path.exists("requirements.txt"): + requirements = open("requirements.txt").read().split("\n") +else: + # In tox, it will cover them anyway. + requirements = [] + + +test_requirements = [ + # TODO: put package test requirements here +] + + +setup( + name=PROJECT_NAME, + version=version, + description=PROJECT_DESCRIPTION, + long_description=readme + '\n\n' + history, + long_description_content_type='text/x-rst', + author=PROJECT_AUTHOR, + author_email=PROJECT_EMAIL, + url=PROJECT_URL, + packages=PACKAGES, + entry_points=ENTRY_POINTS, + package_data=PACKAGE_DATA, + package_dir=PACKAGE_DIR, + include_package_data=True, + install_requires=requirements, + license="AFL", + zip_safe=False, + keywords='galaxy', + classifiers=[ + 'Development Status :: 5 - Production/Stable', + 'Intended Audience :: Developers', + 'Environment :: Console', + 'License :: OSI Approved :: Academic Free License (AFL)', + 'Operating System :: POSIX', + 'Topic :: Software Development', + 'Topic :: Software Development :: Code Generators', + 'Topic :: Software Development :: Testing', + 'Natural Language :: English', + "Programming Language :: Python :: 2", + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + test_suite=TEST_DIR, + tests_require=test_requirements +) diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst new file mode 100644 index 00000000000..ec2f0e746e9 --- /dev/null +++ b/packages/web_framework/HISTORY.rst @@ -0,0 +1,12 @@ +.. :changelog: + +History +------- + +.. to_doc + +--------------------- +19.9.0.dev0 +--------------------- + +* Initial import from dev branch of Galaxy during 19.09 development cycle. diff --git a/packages/web_framework/LICENSE b/packages/web_framework/LICENSE new file mode 120000 index 00000000000..1ef648f64b3 --- /dev/null +++ b/packages/web_framework/LICENSE @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/web_framework/MANIFEST.in b/packages/web_framework/MANIFEST.in new file mode 100644 index 00000000000..c74cefe0942 --- /dev/null +++ b/packages/web_framework/MANIFEST.in @@ -0,0 +1 @@ +include *.rst LICENSE diff --git a/packages/web_framework/Makefile b/packages/web_framework/Makefile new file mode 120000 index 00000000000..37af8bae5ba --- /dev/null +++ b/packages/web_framework/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/web_framework/README.rst b/packages/web_framework/README.rst new file mode 100644 index 00000000000..2f71d34d375 --- /dev/null +++ b/packages/web_framework/README.rst @@ -0,0 +1,14 @@ + +.. image:: https://badge.fury.io/py/galaxy-web-framework.svg + :target: https://pypi.org/project/galaxy-web-framework/ + + +Overview +-------- + +The Galaxy_ web framework. + +* Free software: Academic Free License version 3.0 +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/web_framework/dev-requirements.txt b/packages/web_framework/dev-requirements.txt new file mode 120000 index 00000000000..467b90d7a23 --- /dev/null +++ b/packages/web_framework/dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/web_framework/galaxy/__init__.py b/packages/web_framework/galaxy/__init__.py new file mode 100644 index 00000000000..69e3be50dac --- /dev/null +++ b/packages/web_framework/galaxy/__init__.py @@ -0,0 +1 @@ +__path__ = __import__('pkgutil').extend_path(__path__, __name__) diff --git a/packages/web_framework/galaxy/project_galaxy_web_framework.py b/packages/web_framework/galaxy/project_galaxy_web_framework.py new file mode 100644 index 00000000000..e6f46b22814 --- /dev/null +++ b/packages/web_framework/galaxy/project_galaxy_web_framework.py @@ -0,0 +1,13 @@ +# -*- coding: utf-8 -*- + +__version__ = '19.9.0.dev0' + +PROJECT_NAME = "galaxy-web-framework" +PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" +PROJECT_URL = "https://github.com/galaxyproject/galaxy" +PROJECT_AUTHOR = 'Galaxy Project and Community' +PROJECT_DESCRIPTION = 'Galaxy Web Framework' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' +RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( + PROJECT_USERAME, PROJECT_NAME +) diff --git a/packages/web_framework/galaxy/web b/packages/web_framework/galaxy/web new file mode 120000 index 00000000000..1f0b59dddb4 --- /dev/null +++ b/packages/web_framework/galaxy/web @@ -0,0 +1 @@ +../../../lib/galaxy/web \ No newline at end of file diff --git a/packages/web_framework/requirements.txt b/packages/web_framework/requirements.txt new file mode 100644 index 00000000000..7dcf8f4def7 --- /dev/null +++ b/packages/web_framework/requirements.txt @@ -0,0 +1 @@ +galaxy-data diff --git a/packages/web_framework/scripts b/packages/web_framework/scripts new file mode 120000 index 00000000000..9aec9dc5a06 --- /dev/null +++ b/packages/web_framework/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg new file mode 120000 index 00000000000..eb7cf09393f --- /dev/null +++ b/packages/web_framework/setup.cfg @@ -0,0 +1 @@ +../../setup.cfg \ No newline at end of file diff --git a/packages/web_framework/setup.py b/packages/web_framework/setup.py new file mode 100644 index 00000000000..8b894882f6b --- /dev/null +++ b/packages/web_framework/setup.py @@ -0,0 +1,104 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import ast +import os +import re +try: + from setuptools import setup +except ImportError: + from distutils.core import setup + +SOURCE_DIR = "galaxy" + +_version_re = re.compile(r'__version__\s+=\s+(.*)') + +project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__))) +with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f: + init_contents = f.read().decode('utf-8') + + def get_var(var_name): + pattern = re.compile(r'%s\s+=\s+(.*)' % var_name) + match = pattern.search(init_contents).group(1) + return str(ast.literal_eval(match)) + + version = get_var("__version__") + PROJECT_NAME = get_var("PROJECT_NAME") + PROJECT_URL = get_var("PROJECT_URL") + PROJECT_AUTHOR = get_var("PROJECT_AUTHOR") + PROJECT_EMAIL = get_var("PROJECT_EMAIL") + PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION") + +TEST_DIR = 'tests' +PACKAGES = [ + 'galaxy', + 'galaxy.web', + 'galaxy.web.framework', + 'galaxy.web.framework.helpers', + 'galaxy.web.framework.middleware', + 'galaxy.web.proxy', +] +ENTRY_POINTS = ''' + [console_scripts] +''' +PACKAGE_DATA = { + # Be sure to update MANIFEST.in for source dist. + 'galaxy': [ + ], +} +PACKAGE_DIR = { + SOURCE_DIR: SOURCE_DIR, +} + +readme = open('README.rst').read() +history = open('HISTORY.rst').read().replace('.. :changelog:', '') + +if os.path.exists("requirements.txt"): + requirements = open("requirements.txt").read().split("\n") +else: + # In tox, it will cover them anyway. + requirements = [] + + +test_requirements = [ + # TODO: put package test requirements here +] + + +setup( + name=PROJECT_NAME, + version=version, + description=PROJECT_DESCRIPTION, + long_description=readme + '\n\n' + history, + long_description_content_type='text/x-rst', + author=PROJECT_AUTHOR, + author_email=PROJECT_EMAIL, + url=PROJECT_URL, + packages=PACKAGES, + entry_points=ENTRY_POINTS, + package_data=PACKAGE_DATA, + package_dir=PACKAGE_DIR, + include_package_data=True, + install_requires=requirements, + license="AFL", + zip_safe=False, + keywords='galaxy', + classifiers=[ + 'Development Status :: 5 - Production/Stable', + 'Intended Audience :: Developers', + 'Environment :: Console', + 'License :: OSI Approved :: Academic Free License (AFL)', + 'Operating System :: POSIX', + 'Topic :: Software Development', + 'Topic :: Software Development :: Code Generators', + 'Topic :: Software Development :: Testing', + 'Natural Language :: English', + "Programming Language :: Python :: 2", + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + test_suite=TEST_DIR, + tests_require=test_requirements +) diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst new file mode 100644 index 00000000000..ec2f0e746e9 --- /dev/null +++ b/packages/web_stack/HISTORY.rst @@ -0,0 +1,12 @@ +.. :changelog: + +History +------- + +.. to_doc + +--------------------- +19.9.0.dev0 +--------------------- + +* Initial import from dev branch of Galaxy during 19.09 development cycle. diff --git a/packages/web_stack/LICENSE b/packages/web_stack/LICENSE new file mode 120000 index 00000000000..1ef648f64b3 --- /dev/null +++ b/packages/web_stack/LICENSE @@ -0,0 +1 @@ +../../LICENSE.txt \ No newline at end of file diff --git a/packages/web_stack/MANIFEST.in b/packages/web_stack/MANIFEST.in new file mode 100644 index 00000000000..c74cefe0942 --- /dev/null +++ b/packages/web_stack/MANIFEST.in @@ -0,0 +1 @@ +include *.rst LICENSE diff --git a/packages/web_stack/Makefile b/packages/web_stack/Makefile new file mode 120000 index 00000000000..37af8bae5ba --- /dev/null +++ b/packages/web_stack/Makefile @@ -0,0 +1 @@ +../package.Makefile \ No newline at end of file diff --git a/packages/web_stack/README.rst b/packages/web_stack/README.rst new file mode 100644 index 00000000000..a0a63b19d2d --- /dev/null +++ b/packages/web_stack/README.rst @@ -0,0 +1,14 @@ + +.. image:: https://badge.fury.io/py/galaxy-web-stack.svg + :target: https://pypi.python.org/pypi/galaxy-web-stack/ + + +Overview +-------- + +The Galaxy_ web strack abstraction. + +* Free software: Academic Free License version 3.0 +* Code: https://github.com/galaxyproject/galaxy + +.. _Galaxy: http://galaxyproject.org/ diff --git a/packages/web_stack/dev-requirements.txt b/packages/web_stack/dev-requirements.txt new file mode 120000 index 00000000000..467b90d7a23 --- /dev/null +++ b/packages/web_stack/dev-requirements.txt @@ -0,0 +1 @@ +../package-dev-requirements.txt \ No newline at end of file diff --git a/packages/web_stack/galaxy/__init__.py b/packages/web_stack/galaxy/__init__.py new file mode 100644 index 00000000000..69e3be50dac --- /dev/null +++ b/packages/web_stack/galaxy/__init__.py @@ -0,0 +1 @@ +__path__ = __import__('pkgutil').extend_path(__path__, __name__) diff --git a/packages/web_stack/galaxy/project_galaxy_web_stack.py b/packages/web_stack/galaxy/project_galaxy_web_stack.py new file mode 100644 index 00000000000..987fdbbd1fd --- /dev/null +++ b/packages/web_stack/galaxy/project_galaxy_web_stack.py @@ -0,0 +1,13 @@ +# -*- coding: utf-8 -*- + +__version__ = '19.9.0.dev0' + +PROJECT_NAME = "galaxy-web-stack" +PROJECT_OWNER = PROJECT_USERAME = "galaxyproject" +PROJECT_URL = "https://github.com/galaxyproject/galaxy" +PROJECT_AUTHOR = 'Galaxy Project and Community' +PROJECT_DESCRIPTION = 'Galaxy Web Strack Abstraction' +PROJECT_EMAIL = 'galaxy-committers@lists.galaxyproject.org' +RAW_CONTENT_URL = "https://raw.github.com/%s/%s/master/" % ( + PROJECT_USERAME, PROJECT_NAME +) diff --git a/packages/web_stack/galaxy/web_stack b/packages/web_stack/galaxy/web_stack new file mode 120000 index 00000000000..e94ddd99c8a --- /dev/null +++ b/packages/web_stack/galaxy/web_stack @@ -0,0 +1 @@ +../../../lib/galaxy/web_stack \ No newline at end of file diff --git a/packages/web_stack/requirements.txt b/packages/web_stack/requirements.txt new file mode 100644 index 00000000000..326493b152d --- /dev/null +++ b/packages/web_stack/requirements.txt @@ -0,0 +1,2 @@ +sqlalchemy +galaxy-util diff --git a/packages/web_stack/scripts b/packages/web_stack/scripts new file mode 120000 index 00000000000..9aec9dc5a06 --- /dev/null +++ b/packages/web_stack/scripts @@ -0,0 +1 @@ +../build_scripts \ No newline at end of file diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg new file mode 120000 index 00000000000..eb7cf09393f --- /dev/null +++ b/packages/web_stack/setup.cfg @@ -0,0 +1 @@ +../../setup.cfg \ No newline at end of file diff --git a/packages/web_stack/setup.py b/packages/web_stack/setup.py new file mode 100644 index 00000000000..e75068a7065 --- /dev/null +++ b/packages/web_stack/setup.py @@ -0,0 +1,100 @@ +#!/usr/bin/env python +# -*- coding: utf-8 -*- + +import ast +import os +import re +try: + from setuptools import setup +except ImportError: + from distutils.core import setup + +SOURCE_DIR = "galaxy" + +_version_re = re.compile(r'__version__\s+=\s+(.*)') + +project_short_name = os.path.basename(os.path.dirname(os.path.realpath(__file__))) +with open('%s/project_galaxy_%s.py' % (SOURCE_DIR, project_short_name), 'rb') as f: + init_contents = f.read().decode('utf-8') + + def get_var(var_name): + pattern = re.compile(r'%s\s+=\s+(.*)' % var_name) + match = pattern.search(init_contents).group(1) + return str(ast.literal_eval(match)) + + version = get_var("__version__") + PROJECT_NAME = get_var("PROJECT_NAME") + PROJECT_URL = get_var("PROJECT_URL") + PROJECT_AUTHOR = get_var("PROJECT_AUTHOR") + PROJECT_EMAIL = get_var("PROJECT_EMAIL") + PROJECT_DESCRIPTION = get_var("PROJECT_DESCRIPTION") + +TEST_DIR = 'tests' +PACKAGES = [ + 'galaxy', + 'galaxy.web_stack', +] +ENTRY_POINTS = ''' + [console_scripts] +''' +PACKAGE_DATA = { + # Be sure to update MANIFEST.in for source dist. + 'galaxy': [ + ], +} +PACKAGE_DIR = { + SOURCE_DIR: SOURCE_DIR, +} + +readme = open('README.rst').read() +history = open('HISTORY.rst').read().replace('.. :changelog:', '') + +if os.path.exists("requirements.txt"): + requirements = open("requirements.txt").read().split("\n") +else: + # In tox, it will cover them anyway. + requirements = [] + + +test_requirements = [ + # TODO: put package test requirements here +] + + +setup( + name=PROJECT_NAME, + version=version, + description=PROJECT_DESCRIPTION, + long_description=readme + '\n\n' + history, + long_description_content_type='text/x-rst', + author=PROJECT_AUTHOR, + author_email=PROJECT_EMAIL, + url=PROJECT_URL, + packages=PACKAGES, + entry_points=ENTRY_POINTS, + package_data=PACKAGE_DATA, + package_dir=PACKAGE_DIR, + include_package_data=True, + install_requires=requirements, + license="AFL", + zip_safe=False, + keywords='galaxy', + classifiers=[ + 'Development Status :: 5 - Production/Stable', + 'Intended Audience :: Developers', + 'Environment :: Console', + 'License :: OSI Approved :: Academic Free License (AFL)', + 'Operating System :: POSIX', + 'Topic :: Software Development', + 'Topic :: Software Development :: Code Generators', + 'Topic :: Software Development :: Testing', + 'Natural Language :: English', + "Programming Language :: Python :: 2", + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3.5', + 'Programming Language :: Python :: 3.6', + 'Programming Language :: Python :: 3.7', + ], + test_suite=TEST_DIR, + tests_require=test_requirements +) diff --git a/run_tests.sh b/run_tests.sh index 1236e8742cc..08322c750a5 100755 --- a/run_tests.sh +++ b/run_tests.sh @@ -11,7 +11,7 @@ cat < - <% disabled = trans.app.config.tool_dependency_dir is None %> + <% disabled = trans.app.tool_dependency_dir is None %> ${render_checkbox(install_tool_dependencies_check_box, disabled=disabled)}
    %if disabled: diff --git a/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako b/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako index 9b360d10758..366eeb3bd3c 100644 --- a/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako +++ b/templates/admin/tool_shed_repository/install_tool_dependencies_with_update.mako @@ -31,7 +31,7 @@ ${render_galaxy_repository_actions( repository )} %if install_tool_dependencies_check_box is not None:
    - <% disabled = trans.app.config.tool_dependency_dir is None %> + <% disabled = trans.app.tool_dependency_dir is None %> ${render_checkbox(install_tool_dependencies_check_box, disabled=disabled)}
    %if disabled: @@ -63,7 +63,7 @@ ${render_galaxy_repository_actions( repository )} key_name = key_items[ 0 ] key_version = key_items[ 1 ] readme_text = requirements_dict.get( 'readme', None ) - install_dir = os.path.join( trans.app.config.tool_dependency_dir, + install_dir = os.path.join( trans.app.tool_dependency_dir, key_name, key_version, repository.owner, diff --git a/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako b/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako index d85700fb28d..321d5f708d2 100644 --- a/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako +++ b/templates/admin/tool_shed_repository/uninstall_tool_dependencies.mako @@ -26,14 +26,14 @@ ${render_galaxy_repository_actions( repository )} <% if tool_dependency.type == 'package': - install_dir = os.path.join( trans.app.config.tool_dependency_dir, + install_dir = os.path.join( trans.app.tool_dependency_dir, tool_dependency.name, tool_dependency.version, tool_dependency.tool_shed_repository.owner, tool_dependency.tool_shed_repository.name, tool_dependency.tool_shed_repository.installed_changeset_revision ) elif tool_dependency.type == 'set_environment': - install_dir = os.path.join( trans.app.config.tool_dependency_dir, + install_dir = os.path.join( trans.app.tool_dependency_dir, 'environment_settings', tool_dependency.name, tool_dependency.tool_shed_repository.owner, diff --git a/test/unit/tools/test_parsing.py b/test/unit/tools/test_parsing.py index 168bd09f0fd..dcce2145c94 100644 --- a/test/unit/tools/test_parsing.py +++ b/test/unit/tools/test_parsing.py @@ -12,6 +12,9 @@ from galaxy.util import galaxy_directory TOOL_XML_1 = """