diff --git a/.ci/flake8_blacklist.txt b/.ci/flake8_blacklist.txt index 26ece30af32..f5276b3fc47 100644 --- a/.ci/flake8_blacklist.txt +++ b/.ci/flake8_blacklist.txt @@ -15,3 +15,5 @@ lib/galaxy/util/jstree.py lib/galaxy/web/proxy/js/node_modules static/maps static/scripts +build +dist diff --git a/.gitignore b/.gitignore index e52c67610a4..d17e2a9d68f 100644 --- a/.gitignore +++ b/.gitignore @@ -9,6 +9,17 @@ scripts/scramble/archives .venv .venv3 +# Python build artifacts +build +dist +lib/galaxy.egg-info +.eggs + +# Generated static content +lib/galaxy/web/framework/static/maps +lib/galaxy/web/framework/static/scripts +lib/galaxy/web/framework/static/style + # Database stuff database/beaker_sessions database/citations diff --git a/.travis.yml b/.travis.yml index 32b0bba580d..942e8625b46 100644 --- a/.travis.yml +++ b/.travis.yml @@ -14,7 +14,7 @@ install: sh scripts/common_startup.sh wget -q https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0127.sqlite mv db_gx_rev_0127.sqlite database/universe.sqlite - sh manage_db.sh -c ./config/galaxy.yml.sample upgrade + sh manage_db.sh upgrade elif [ "$TOX_ENV" == "py35-first_startup" ]; then MINICONDA_URL="https://repo.anaconda.com/miniconda" MINICONDA_FILE="Miniconda3-latest-MacOSX-x86_64.sh" diff --git a/client/galaxy/scripts/components/PluginList.vue b/client/galaxy/scripts/components/PluginList.vue index 2909e7e9439..2f70becf0c7 100644 --- a/client/galaxy/scripts/components/PluginList.vue +++ b/client/galaxy/scripts/components/PluginList.vue @@ -2,14 +2,16 @@
{{ error }}
- +
+ +
diff --git a/client/galaxy/scripts/entry/panels/admin-panel.js b/client/galaxy/scripts/entry/panels/admin-panel.js index e67252912a6..a91e6703a8e 100644 --- a/client/galaxy/scripts/entry/panels/admin-panel.js +++ b/client/galaxy/scripts/entry/panels/admin-panel.js @@ -93,16 +93,6 @@ const AdminPanel = Backbone.View.extend({ target: "__use_router__", enabled: this.settings.is_tool_shed_installed }, - { - title: _l("Install new tools (Legacy)"), - url: "admin_toolshed/browse_tool_sheds", - enabled: this.settings.is_tool_shed_installed - }, - { - title: "Install new tools (Beta)", - url: "admin_toolshed/browse_toolsheds", - enabled: this.settings.is_tool_shed_installed && this.config.enable_beta_ts_api_install - }, { title: _l("Monitor installation"), url: "admin_toolshed/monitor_repository_installation", diff --git a/client/galaxy/scripts/entry/panels/tool-panel.js b/client/galaxy/scripts/entry/panels/tool-panel.js index d3c134a77d0..47b1ab4cfbe 100644 --- a/client/galaxy/scripts/entry/panels/tool-panel.js +++ b/client/galaxy/scripts/entry/panels/tool-panel.js @@ -141,9 +141,9 @@ const ToolPanel = Backbone.View.extend({
diff --git a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js index 15ec4654c2b..52d84691d82 100644 --- a/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js +++ b/client/galaxy/scripts/mvc/collection/list-of-pairs-collection-creator.js @@ -1568,7 +1568,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin) "", '', "
", - '
', + '
', '', @@ -1596,7 +1596,7 @@ var PairedCollectionCreator = Backbone.View.extend(baseMVC.LoggableMixin) "", '', "
", - '
', + '
', '', diff --git a/client/galaxy/scripts/mvc/library/library-dataset-view.js b/client/galaxy/scripts/mvc/library/library-dataset-view.js index 53c6d30eb6f..8137376b77f 100644 --- a/client/galaxy/scripts/mvc/library/library-dataset-view.js +++ b/client/galaxy/scripts/mvc/library/library-dataset-view.js @@ -703,6 +703,12 @@ var LibraryDatasetView = Backbone.View.extend({
<% } %> + <% if (item.get("update_time")) { %> + + + + + <% } %> <% if (item.get("date_uploaded")) { %> @@ -880,6 +886,12 @@ var LibraryDatasetView = Backbone.View.extend({ <% } %> + <% if (ldda.get("update_time")) { %> + + + + + <% } %> <% if (ldda.get("date_uploaded")) { %> @@ -1006,6 +1018,10 @@ var LibraryDatasetView = Backbone.View.extend({ + + + + diff --git a/client/galaxy/scripts/mvc/library/library-folderlist-view.js b/client/galaxy/scripts/mvc/library/library-folderlist-view.js index 1b6c271f99c..cedc161f341 100644 --- a/client/galaxy/scripts/mvc/library/library-folderlist-view.js +++ b/client/galaxy/scripts/mvc/library/library-folderlist-view.js @@ -517,7 +517,7 @@ var FolderListView = Backbone.View.extend({
<%= _.escape(item.get("file_size")) %>
Date last updated (UTC)<%= _.escape(item.get("update_time")) %>
Date uploaded (UTC)<%= _.escape(ldda.get("file_size")) %>
Date last updated (UTC)<%= _.escape(ldda.get("update_time")) %>
Date uploaded (UTC)Size <%= _.escape(item.get("file_size")) %>
Date last updated (UTC)<%= _.escape(item.get("update_time")) %>
Date uploaded (UTC) <%= _.escape(item.get("date_uploaded")) %> - Time Updated (UTC) + Date Updated (UTC) diff --git a/client/galaxy/scripts/mvc/library/library-util.js b/client/galaxy/scripts/mvc/library/library-util.js index c4d546c4b25..bb174a7cb56 100644 --- a/client/galaxy/scripts/mvc/library/library-util.js +++ b/client/galaxy/scripts/mvc/library/library-util.js @@ -1,45 +1,38 @@ /** - * Create alphabetical based two-argument comparator - * that takes into account that Folder comes before Dataset. + * Create alphabetical based two-argument comparator to handle library items (including folders) * If sort_key is not present it is set to ''. * @param {str} sort_key key to sort by * @param {str} sort_order order to sort by (asc, desc) * @return {function} two-argument comparator function */ var generateComparator = (sort_key, sort_order) => (itemA, itemB) => { - if (itemA.get("type") === itemB.get("type")) { - if (!itemA.has(sort_key) && !itemB.has(sort_key)) { - return 0; - } else if (!itemA.has(sort_key)) { - return 1; - } else if (!itemB.has(sort_key)) { - return -1; - } - var comparable_itemA_key; - var comparable_itemB_key; - if (typeof itemA.get(sort_key) === "number") { - comparable_itemA_key = itemA.get(sort_key); - comparable_itemB_key = itemB.get(sort_key); - } - else - { - comparable_itemA_key = itemA.get(sort_key).toLowerCase(); - comparable_itemB_key = itemB.get(sort_key).toLowerCase(); - } - if ( comparable_itemA_key > comparable_itemB_key) { - return sort_order === "asc" ? 1 : -1; - } - if (comparable_itemB_key > comparable_itemA_key) { - return sort_order === "asc" ? -1 : 1; - } - - return 0; // equal - } else { - if (itemA.get("type") === "folder") { - return -1; // folder is always before dataset - } + if (!itemA.has(sort_key) && !itemB.has(sort_key)) { + return 0; + } else if (!itemA.has(sort_key)) { return 1; + } else if (!itemB.has(sort_key)) { + return -1; } + var comparable_itemA_key; + var comparable_itemB_key; + if (typeof itemA.get(sort_key) === "number") { + comparable_itemA_key = itemA.get(sort_key); + comparable_itemB_key = itemB.get(sort_key); + } + else + { + comparable_itemA_key = itemA.get(sort_key).toLowerCase(); + comparable_itemB_key = itemB.get(sort_key).toLowerCase(); + } + + if ( comparable_itemA_key > comparable_itemB_key) { + return sort_order === "asc" ? 1 : -1; + } + if (comparable_itemB_key > comparable_itemA_key) { + return sort_order === "asc" ? -1 : 1; + } + + return 0; // equal }; export default { generateComparator: generateComparator diff --git a/client/galaxy/scripts/mvc/rules/rule-definitions.js b/client/galaxy/scripts/mvc/rules/rule-definitions.js index 23ccb754b8f..29909912306 100644 --- a/client/galaxy/scripts/mvc/rules/rule-definitions.js +++ b/client/galaxy/scripts/mvc/rules/rule-definitions.js @@ -42,7 +42,7 @@ const applyRegex = function(regex, target, data, replacement, groupCount) { return null; } if (!replacement) { - groupCount = groupCount && parseInt(groupCount); + groupCount = groupCount && parseInt(groupCount, 10); if (groupCount) { if (match.length != groupCount + 1) { failedCount++; @@ -108,7 +108,7 @@ const RULES = { } }, save: (component, rule) => { - rule.start = parseInt(component.addColumnRownumStart); + rule.start = parseInt(component.addColumnRownumStart, 10); }, apply: (rule, data, sources, columns) => { let rownum = rule.start; @@ -169,7 +169,7 @@ const RULES = { const ruleValue = rule.value; let newRow; if (ruleValue.indexOf("identifier") == 0) { - const identifierIndex = parseInt(ruleValue.substring("identifier".length)); + const identifierIndex = parseInt(ruleValue.substring("identifier".length), 10); newRow = (row, index) => { const newRow = row.slice(); newRow.push(sources[index]["identifiers"][identifierIndex]); @@ -253,7 +253,7 @@ const RULES = { component.addColumnRegexTarget = rule.target_column; component.addColumnRegexExpression = rule.expression; component.addColumnRegexReplacement = rule.replacement; - component.addColumnRegexGroupCount = rule.group_count; + component.addColumnRegexGroupCount = parseInt(rule.group_count); } let addColumnRegexType = "global"; if (component.addColumnRegexGroupCount) { @@ -347,7 +347,7 @@ const RULES = { }, save: (component, rule) => { rule.target_column = component.addColumnSubstrTarget; - rule.length = parseInt(component.addColumnSubstrLength); + rule.length = parseInt(component.addColumnSubstrLength, 10); rule.substr_type = component.addColumnSubstrType; }, apply: (rule, data, sources, columns) => { @@ -403,7 +403,7 @@ const RULES = { function newRow(row) { const newRow = []; for (const index in row) { - if (targets.indexOf(parseInt(index)) == -1) { + if (targets.indexOf(parseInt(index, 10)) == -1) { newRow.push(row[index]); } } @@ -448,7 +448,7 @@ const RULES = { const target = rule.target_column; const invert = rule.invert; const filterFunction = function(el, index) { - const row = data[parseInt(index)]; + const row = data[parseInt(index, 10)]; return regExp.exec(row[target]) ? !invert : invert; }; sources = sources.filter(filterFunction); @@ -477,13 +477,13 @@ const RULES = { component.addFilterCountWhich = "first"; component.addFilterCountInvert = false; } else { - component.addFilterCountN = parseInt(rule.count); + component.addFilterCountN = parseInt(rule.count, 10); component.addFilterCountWhich = rule.which; component.addFilterCountInvert = rule.inverse; } }, save: (component, rule) => { - rule.count = parseInt(component.addFilterCountN); + rule.count = parseInt(component.addFilterCountN, 10); rule.which = component.addFilterCountWhich; rule.invert = component.addFilterCountInvert; }, @@ -528,7 +528,7 @@ const RULES = { const target = rule.target_column; const invert = rule.invert; const filterFunction = function(el, index) { - const row = data[parseInt(index)]; + const row = data[parseInt(index, 10)]; return row[target].length ? !invert : invert; }; sources = sources.filter(filterFunction); @@ -562,7 +562,7 @@ const RULES = { const invert = rule.invert; const value = rule.value; const filterFunction = function(el, index) { - const row = data[parseInt(index)]; + const row = data[parseInt(index, 10)]; return row[target] == value ? !invert : invert; }; sources = sources.filter(filterFunction); @@ -598,7 +598,7 @@ const RULES = { const compare_type = rule.compare_type; const value = rule.value; const filterFunction = function(el, index) { - const row = data[parseInt(index)]; + const row = data[parseInt(index, 10)]; const targetValue = parseFloat(row[target]); let matches; if (compare_type == "less_than") { @@ -730,7 +730,7 @@ const RULES = { const newRow0 = [], newRow1 = []; for (let index in row) { - index = parseInt(index); + index = parseInt(index, 10); if (targets0.indexOf(index) > -1) { newRow0.push(row[index]); } else if (targets1.indexOf(index) > -1) { diff --git a/client/galaxy/scripts/mvc/tool/tools.js b/client/galaxy/scripts/mvc/tool/tools.js index d1831083fb9..ddda58bc452 100644 --- a/client/galaxy/scripts/mvc/tool/tools.js +++ b/client/galaxy/scripts/mvc/tool/tools.js @@ -347,9 +347,7 @@ var ToolSearch = Backbone.Model.extend({ SEARCH_RESERVED_TERMS_FAVORITES: ["#favs", "#favorites", "#favourites"], defaults: { - search_hint_string: "search tools", min_chars_for_search: 3, - clear_btn_url: "", visible: true, query: "", results: null, @@ -635,7 +633,7 @@ var ToolSectionView = BaseView.extend({ var ToolSearchView = Backbone.View.extend({ tagName: "div", id: "tool-search", - className: "bar", + className: "search-input", events: { click: "focus_and_select", @@ -649,7 +647,6 @@ var ToolSearchView = Backbone.View.extend({ if (!this.model.is_visible()) { this.$el.hide(); } - this.$el.find("[title]").tooltip(); return this; }, @@ -774,10 +771,9 @@ var templates = { // the search bar at the top of the tool panel tool_search: _.template( ` - - - ` + placeholder="search tools" autocomplete="off" type="text" /> + +