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Code Issues Packages Projects Releases Wiki Activity

Merge remote-tracking branch 'upstream/dev' into es6imports

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This commit is contained in:
Dannon Baker
2017-10-31 10:44:21 -04:00
parent 83f118e640 aacdf8d939
commit d85abaad31
418 changed files with 4542 additions and 20443 deletions
Download Patch File Download Diff File Expand all files Collapse all files
.ci/flake8_lint_include_list.txt
+24 -15
View File
@@ -1,4 +1,5 @@
client/galaxy/style/source_material/circle.py
config/
contrib/
cron/
doc/parse_gx_xsd.py
@@ -21,22 +22,13 @@ lib/galaxy/jobs/command_factory.py
lib/galaxy/jobs/datasets.py
lib/galaxy/jobs/deferred/
lib/galaxy/jobs/error_level.py
lib/galaxy/jobs/handler.py
lib/galaxy/jobs/__init__.py
lib/galaxy/jobs/manager.py
lib/galaxy/jobs/metrics/
lib/galaxy/jobs/output_checker.py
lib/galaxy/jobs/rules/
lib/galaxy/jobs/runners/cli.py
lib/galaxy/jobs/runners/condor.py
lib/galaxy/jobs/runners/drmaa.py
lib/galaxy/jobs/runners/godocker.py
lib/galaxy/jobs/runners/kubernetes.py
lib/galaxy/jobs/runners/local.py
lib/galaxy/jobs/runners/pbs.py
lib/galaxy/jobs/runners/pulsar.py
lib/galaxy/jobs/runners/slurm.py
lib/galaxy/jobs/runners/state_handlers/
lib/galaxy/jobs/runners/tasks.py
lib/galaxy/jobs/runners/util/
lib/galaxy/jobs/runners/
lib/galaxy/jobs/splitters/basic.py
lib/galaxy/jobs/splitters/__init__.py
lib/galaxy/jobs/stock_rules.py
@@ -61,9 +53,7 @@ lib/galaxy/objectstore/s3_multipart_upload.py
lib/galaxy/objectstore/s3.py
lib/galaxy/openid/__init__.py
lib/galaxy/quota/
lib/galaxy/sample_tracking/data_transfer.py
lib/galaxy/sample_tracking/__init__.py
lib/galaxy/sample_tracking/sample.py
lib/galaxy/sample_tracking/
lib/galaxy/security/
lib/galaxy/tags/
lib/galaxy/tools/
@@ -71,6 +61,7 @@ lib/galaxy/util/
lib/galaxy/version.py
lib/galaxy/visualization/data_providers/basic.py
lib/galaxy/visualization/data_providers/cigar.py
lib/galaxy/visualization/data_providers/genome.py
lib/galaxy/visualization/data_providers/__init__.py
lib/galaxy/visualization/data_providers/phyloviz/baseparser.py
lib/galaxy/visualization/genome/
@@ -99,14 +90,23 @@ lib/galaxy/web/framework/middleware/xforwardedhost.py
lib/galaxy/web/framework/webapp.py
lib/galaxy/web/__init__.py
lib/galaxy/web/params.py
lib/galaxy/web/stack/
lib/galaxy/webapps/galaxy/api/authenticate.py
lib/galaxy/webapps/galaxy/api/forms.py
lib/galaxy/webapps/galaxy/api/genomes.py
lib/galaxy/webapps/galaxy/api/group_roles.py
lib/galaxy/webapps/galaxy/api/group_users.py
lib/galaxy/webapps/galaxy/api/groups.py
lib/galaxy/webapps/galaxy/api/histories.py
lib/galaxy/webapps/galaxy/api/__init__.py
lib/galaxy/webapps/galaxy/api/jobs.py
lib/galaxy/webapps/galaxy/api/library_contents.py
lib/galaxy/webapps/galaxy/api/library_datasets.py
lib/galaxy/webapps/galaxy/api/requests.py
lib/galaxy/webapps/galaxy/api/request_types.py
lib/galaxy/webapps/galaxy/api/roles.py
lib/galaxy/webapps/galaxy/api/samples.py
lib/galaxy/webapps/galaxy/api/tool_data.py
lib/galaxy/webapps/galaxy/api/tools.py
lib/galaxy/webapps/galaxy/api/tours.py
lib/galaxy/webapps/galaxy/api/users.py
@@ -116,6 +116,7 @@ lib/galaxy/webapps/galaxy/config_watchers.py
lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
lib/galaxy/webapps/galaxy/controllers/async.py
lib/galaxy/webapps/galaxy/controllers/data_manager.py
lib/galaxy/webapps/galaxy/controllers/dataset.py
lib/galaxy/webapps/galaxy/controllers/error.py
lib/galaxy/webapps/galaxy/controllers/external_services.py
lib/galaxy/webapps/galaxy/controllers/forms.py
@@ -124,21 +125,29 @@ lib/galaxy/webapps/galaxy/controllers/__init__.py
lib/galaxy/webapps/galaxy/controllers/library_common.py
lib/galaxy/webapps/galaxy/controllers/mobile.py
lib/galaxy/webapps/galaxy/controllers/page.py
lib/galaxy/webapps/galaxy/controllers/requests_admin.py
lib/galaxy/webapps/galaxy/controllers/requests_common.py
lib/galaxy/webapps/galaxy/controllers/requests.py
lib/galaxy/webapps/galaxy/controllers/request_type.py
lib/galaxy/webapps/galaxy/controllers/root.py
lib/galaxy/webapps/galaxy/controllers/search.py
lib/galaxy/webapps/galaxy/controllers/tool_runner.py
lib/galaxy/webapps/galaxy/controllers/userskeys.py
lib/galaxy/webapps/galaxy/__init__.py
lib/galaxy/webapps/__init__.py
lib/galaxy/webapps/reports/buildapp.py
lib/galaxy/webapps/reports/config.py
lib/galaxy/webapps/reports/controllers/__init__.py
lib/galaxy/webapps/reports/controllers/query.py
lib/galaxy/webapps/reports/controllers/system.py
lib/galaxy/webapps/reports/controllers/tools.py
lib/galaxy/webapps/reports/__init__.py
lib/galaxy/webapps/tool_shed/api/__init__.py
lib/galaxy/webapps/tool_shed/buildapp.py
lib/galaxy/webapps/tool_shed/config.py
lib/galaxy/webapps/tool_shed/controllers/groups.py
lib/galaxy/webapps/tool_shed/controllers/__init__.py
lib/galaxy/webapps/tool_shed/controllers/repository.py
lib/galaxy/webapps/tool_shed/controllers/user.py
lib/galaxy/webapps/tool_shed/framework/__init__.py
lib/galaxy/webapps/tool_shed/framework/middleware/__init__.py
.travis.yml
+2
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@@ -13,10 +13,12 @@ env:
- TOX_ENV=py27-lint-imports-include-list
- TOX_ENV=validate-test-tools
- TOX_ENV=py27-lint-docstring-include-list
- TOX_ENV=check-python-dependencies
matrix:
allow_failures:
- env: TOX_ENV=py27-lint-imports
- env: TOX_ENV=check-python-dependencies
addons:
apt:
Makefile
+6
View File
@@ -30,6 +30,12 @@ docs: ## Generate HTML documentation.
$(IN_VENV) $(MAKE) -C doc clean
$(IN_VENV) $(MAKE) -C doc html
setup-venv:
if [ ! -f $(VENV)/bin/activate ]; then bash scripts/common_startup.sh --dev-wheels; fi
list-dependency-updates: setup-venv
$(IN_VENV) pip list --outdated --format=columns
docs-slides-ready:
test -f plantuml.jar || wget http://jaist.dl.sourceforge.net/project/plantuml/plantuml.jar
java -jar plantuml.jar -c $(DOC_SOURCE_DIR)/slideshow/architecture/images/plantuml_options.txt -tsvg $(SLIDESHOW_DIR)/architecture/images/ *.plantuml.txt
client/galaxy/scripts/apps/admin.js
+12
View File
@@ -22,6 +22,7 @@ window.app = function app(options, bootstrapped) {
"(/)admin(/)groups": "show_groups",
"(/)admin(/)tool_versions": "show_tool_versions",
"(/)admin(/)quotas": "show_quotas",
"(/)admin(/)repositories": "show_repositories",
"(/)admin(/)forms": "show_forms",
"(/)admin(/)form(/)(:form_id)": "show_form"
},
@@ -60,6 +61,17 @@ window.app = function app(options, bootstrapped) {
);
},
show_repositories: function() {
this.page.display(
new GridView({
url_base:
Galaxy.root + "admin_toolshed/browse_repositories",
url_data: Galaxy.params,
dict_format: true
})
);
},
show_tool_versions: function() {
this.page.display(
new GridView({
client/galaxy/scripts/apps/panels/admin-panel.js
+52 -90
View File
@@ -24,6 +24,10 @@ var AdminPanel = Backbone.View.extend({
title: "Data tables registry",
url: "admin/view_tool_data_tables"
},
{
title: "Data libraries",
url: "library_admin/browse_libraries"
},
{
title: "Display applications",
url: "admin/display_applications"
@@ -31,6 +35,50 @@ var AdminPanel = Backbone.View.extend({
{
title: "Manage jobs",
url: "admin/jobs"
},
{
title: "Local data",
url: "data_manager"
}
]
},
{
title: "User Management",
items: [
{
title: "Users",
url: "admin/users",
target: "__use_router__"
},
{
title: "Quotas",
url: "admin/quotas",
target: "__use_router__",
enabled: self.config.enable_quotas
},
{
title: "Groups",
url: "admin/groups",
target: "__use_router__"
},
{
title: "Roles",
url: "admin/roles",
target: "__use_router__"
},
{
title: "Forms",
url: "admin/forms",
target: "__use_router__"
},
{
title: "API keys",
url: "userskeys/all_users"
},
{
title: "Impersonate a user",
url: "admin/impersonate",
enabled: self.config.allow_user_impersonation
}
]
},
@@ -51,15 +99,14 @@ var AdminPanel = Backbone.View.extend({
},
{
title: "Monitor installing repositories",
url:
"admin_toolshed/monitor_repository_installation?installing_repository_ids=" +
self.settings.installing_repository_ids,
url: "admin_toolshed/monitor_repository_installation",
enabled: self.settings.installing_repository_ids
},
{
title: "Manage installed tools",
url: "admin_toolshed/browse_repositories",
enabled: self.settings.is_repo_installed
url: "admin/repositories",
enabled: self.settings.is_repo_installed,
target: "__use_router__"
},
{
title: "Reset metadata",
@@ -97,91 +144,6 @@ var AdminPanel = Backbone.View.extend({
url: "admin/manage_tool_dependencies"
}
]
},
{
title: "User Management",
items: [
{
title: "Users",
url: "admin/users",
target: "__use_router__"
},
{
title: "Groups",
url: "admin/groups",
target: "__use_router__"
},
{
title: "Roles",
url: "admin/roles",
target: "__use_router__"
},
{
title: "API keys",
url: "userskeys/all_users"
},
{
title: "Impersonate a user",
url: "admin/impersonate",
enabled: self.config.allow_user_impersonation
}
]
},
{
title: "Data",
items: [
{
title: "Quotas",
url: "admin/quotas",
target: "__use_router__",
enabled: self.config.enable_quotas
},
{
title: "Data libraries",
url: "library_admin/browse_libraries"
},
{
title: "Roles",
url: "admin/roles",
target: "__use_router__"
},
{
title: "Local data",
url: "data_manager"
}
]
},
{
title: "Form Definitions",
items: [
{
title: "Form definitions",
url: "admin/forms",
target: "__use_router__"
}
]
},
{
title: "Sample Tracking",
items: [
{
title: "Sequencers and external services",
url: "external_service/browse_external_services"
},
{
title: "Request types",
url: "request_type/browse_request_types"
},
{
title: "Sequencing requests",
url: "requests_admin/browse_requests"
},
{
title: "Find samples",
url:
"requests_common/find_samples?cntrller=requests_admin"
}
]
}
]);
this.setElement(this._template());
client/galaxy/scripts/galaxy.interactive_environments.js
+3 -1
View File
@@ -111,8 +111,10 @@ function spin(
type: "GET",
timeout: spin_state.ajax_timeout,
success: function(data, status, jqxhr) {
if (!success_callback(data, status, jqxhr))
if (!success_callback(data, status, jqxhr)) {
spin_state.count++;
spin_again(spin_state);
}
},
error: function(jqxhr, status, error) {
if (status == "timeout") {
client/galaxy/scripts/layout/menu.js
-23
View File
@@ -74,29 +74,6 @@ var Collection = Backbone.Collection.extend({
]
});
//
// Lab menu.
//
options.user_requests &&
this.add({
id: "lab",
title: "Lab",
menu: [
{
title: "Sequencing Requests",
url: "requests/index"
},
{
title: "Find Samples",
url: "requests/find_samples_index"
},
{
title: "Help",
url: options.lims_doc_url
}
]
});
//
// Visualization tab.
//
client/galaxy/scripts/layout/page.js
+1 -1
View File
@@ -143,7 +143,7 @@ var View = Backbone.View.extend({
'<div id="messagebox"/>',
'<div id="inactivebox" class="panel-warning-message" />',
'<div id="left" />',
'<div id="center" class="inbound" />',
'<div id="center" />',
'<div id="right" />',
"</div>",
'<div id="dd-helper" />'
client/galaxy/scripts/mvc/library/library-dataset-view.js
+31 -4
View File
@@ -512,7 +512,8 @@ var LibraryDatasetView = Backbone.View.extend({
}
},
copyToClipboard: function() {
copyToClipboard: function(e) {
e.preventDefault();
var href = Backbone.history.location.href;
if (href.lastIndexOf("/permissions") !== -1) {
href = href.substr(0, href.lastIndexOf("/permissions"));
@@ -732,7 +733,7 @@ var LibraryDatasetView = Backbone.View.extend({
'<% if (item.get("is_unrestricted")) { %>',
"<div>",
'This dataset is unrestricted so everybody with the link can access it. Just share <span class="copy-link-to-clipboard"><a>this page</a></span>.',
'This dataset is unrestricted so everybody with the link can access it. Just share <span class="copy-link-to-clipboard"><a href=""a>this page</a></span>.',
"</div>",
"<% } %>",
@@ -821,8 +822,34 @@ var LibraryDatasetView = Backbone.View.extend({
'<td scope="row"><%= _.escape(item.get("tags")) %></td>',
"</tr>",
"<% } %>",
'<% if ( item.get("uuid") !== "ok" ) { %>',
"<tr>",
'<th scope="row">UUID</th>',
'<td scope="row"><%= _.escape(item.get("uuid")) %></td>',
"</tr>",
"<% } %>",
'<% if ( item.get("state") !== "ok" ) { %>',
"<tr>",
'<th scope="row">State</th>',
'<td scope="row"><%= _.escape(item.get("state")) %></td>',
"</tr>",
"<% } %>",
"</table>",
'<% if (item.get("job_stderr")) { %>',
"<h4>Job Standard Error</h4>",
'<pre class="code">',
'<%= _.escape(item.get("job_stderr")) %>',
"</pre>",
"<% } %>",
'<% if (item.get("job_stdout")) { %>',
"<h4>Job Standard Output</h4>",
'<pre class="code">',
'<%= _.escape(item.get("job_stdout")) %>',
"</pre>",
"<% } %>",
"<div>",
'<pre class="peek">',
"</pre>",
@@ -1122,9 +1149,9 @@ var LibraryDatasetView = Backbone.View.extend({
"<h2>Dataset-related permissions</h2>",
'<div class="alert alert-warning">Changes made below will affect <strong>every</strong> library item that was created from this dataset and also every history this dataset is part of.</div>',
'<% if (!item.get("is_unrestricted")) { %>',
'<p>You can <span class="remove-restrictions"><a>remove all access restrictions</a></span> on this dataset.</p>',
'<p>You can <span class="remove-restrictions"><a href="">remove all access restrictions</a></span> on this dataset.</p>',
"<% } else { %>",
'<p>You can <span class="make-private"><a>make this dataset private</a></span> to you.</p>',
'<p>You can <span class="make-private"><a href="">make this dataset private</a></span> to you.</p>',
"<% } %>",
"<h4>Roles that can access the dataset</h4>",
'<div id="access_perm" class="access_perm roles-selection"></div>',
client/galaxy/scripts/mvc/library/library-folderlist-view.js
+34 -40
View File
@@ -13,13 +13,18 @@ var FolderListView = Backbone.View.extend({
folderContainer: null,
sort: "asc",
current_sort_order: "asc",
current_sort_key: "name",
events: {
"click #select-all-checkboxes": "selectAll",
"click .dataset_row": "selectClickedRow",
"click .folder_row": "selectClickedRow",
"click .sort-folder-link": "sortColumnClicked"
"click .sort-folder-name": "sortColumnClicked",
"click .sort-folder-file_ext": "sortColumnClicked",
"click .sort-folder-description": "sortColumnClicked",
"click .sort-folder-state": "sortColumnClicked"
},
collection: null,
@@ -123,7 +128,7 @@ var FolderListView = Backbone.View.extend({
.parent_library_id,
id: this.options.id,
upper_folder_id: upper_folder_id,
order: this.sort
order: this.current_sort_order
})
);
@@ -202,7 +207,7 @@ var FolderListView = Backbone.View.extend({
addAll: function(models) {
_.each(models, function(model) {
Galaxy.libraries.folderListView.collection.add(model, {
sort: false
current_sort_order: false
});
});
$("#center [data-toggle]").tooltip();
@@ -289,37 +294,21 @@ var FolderListView = Backbone.View.extend({
}
},
/** User clicked the table heading = he wants to sort stuff */
sortColumnClicked: function(event) {
event.preventDefault();
if (this.sort === "asc") {
this.sortFolder("name", "desc");
this.sort = "desc";
} else {
this.sortFolder("name", "asc");
this.sort = "asc";
}
this.current_sort_order =
this.current_sort_order === "asc" ? "desc" : "asc";
this.current_sort_key = event.currentTarget.className.replace(
"sort-folder-",
""
);
this.collection.sortFolder(
this.current_sort_key,
this.current_sort_order
);
this.renderSortIcon();
},
/**
* Sorts the underlying collection according to the parameters received.
* Currently supports only sorting by name.
*/
sortFolder: function(sort_by, order) {
// default to asc sort by name
if (sort_by === "undefined" && order === "undefined") {
return this.collection.sortByNameAsc();
}
if (sort_by === "name") {
if (order === "asc") {
return this.collection.sortByNameAsc();
} else if (order === "desc") {
return this.collection.sortByNameDesc();
}
}
},
/**
* User clicked the checkbox in the table heading
* @param {context} event
@@ -406,14 +395,17 @@ var FolderListView = Backbone.View.extend({
},
renderSortIcon: function() {
if (this.sort === "asc") {
$(".sort-icon")
if (this.current_sort_order === "asc") {
$('[class*="sort-icon"]')
.removeClass("fa-sort-alpha-desc")
.addClass("fa-sort-alpha-asc");
.removeClass("fa-sort-alpha-asc");
$(".sort-icon" + "-" + this.current_sort_key).addClass(
"fa-sort-alpha-asc"
);
} else {
$(".sort-icon")
.removeClass("fa-sort-alpha-asc")
.addClass("fa-sort-alpha-desc");
$(".sort-icon" + "-" + this.current_sort_key).addClass(
"fa-sort-alpha-desc"
);
}
},
@@ -437,12 +429,13 @@ var FolderListView = Backbone.View.extend({
"<thead>",
'<th class="button_heading"></th>',
'<th style="text-align: center; width: 20px; " title="Check to select all datasets"><input id="select-all-checkboxes" style="margin: 0;" type="checkbox"></th>',
'<th><a class="sort-folder-link" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="sort-icon fa fa-sort-alpha-<%- order %>"></span></th>',
'<th style="width:25%;">description</th>',
'<th style="width:5%;">data type</th>',
'<th><a class="sort-folder-name" title="Click to reverse order" href="#">name</a> <span title="Sorted alphabetically" class="sort-icon-name fa fa-sort-alpha-<%- order %>"></span></th>',
'<th style="width:20%;"><a class="sort-folder-description" title="Click to reverse order" href="#">description</a> <span title="Sorted alphabetically" class="sort-icon-description fa"></span></th>',
'<th style="width:5%;"><a class="sort-folder-file_ext" title="Click to reverse order" href="#">data type</a> <span title="Sorted alphabetically" class="sort-icon-file_ext fa"></span></th>',
'<th style="width:10%;">size</th>',
'<th style="width:160px;">time updated (UTC)</th>',
'<th style="width:10%;"></th> ',
'<th style="width:5%;"><a class="sort-folder-state" title="Click to reverse order" href="#">state</a> <span title="Sorted alphabetically" class="sort-icon-state fa"></span></th>',
'<th style="width:150px;"></th> ',
"</thead>",
'<tbody id="folder_list_body">',
'<tr id="first_folder_item">',
@@ -456,6 +449,7 @@ var FolderListView = Backbone.View.extend({
"<td></td>",
"<td></td>",
"<td></td>",
"<td></td>",
"</tr>",
"</tbody>",
"</table>",
client/galaxy/scripts/mvc/library/library-folderrow-view.js
+33 -19
View File
@@ -13,10 +13,10 @@ var FolderRowView = Backbone.View.extend({
defaults: {
type: null,
visibility_config: {
edit_folder_btn: true,
edit_folder_btn: false,
save_folder_btn: false,
cancel_folder_btn: false,
permission_folder_btn: true
permission_folder_btn: false
},
edit_mode: false
},
@@ -125,7 +125,10 @@ var FolderRowView = Backbone.View.extend({
Galaxy.libraries.folderListView.collection.remove(dataset_id);
var updated_dataset = new mod_library_model.Item(response);
Galaxy.libraries.folderListView.collection.add(updated_dataset);
Galaxy.libraries.folderListView.collection.sortByNameAsc();
Galaxy.libraries.folderListView.collection.sortFolder(
"name",
"asc"
);
mod_toastr.success(
"Dataset undeleted. Click this to see it.",
"",
@@ -173,7 +176,10 @@ var FolderRowView = Backbone.View.extend({
response
);
Galaxy.libraries.folderListView.collection.add(updated_folder);
Galaxy.libraries.folderListView.collection.sortByNameAsc();
Galaxy.libraries.folderListView.collection.sortFolder(
"name",
"asc"
);
mod_toastr.success("Folder undeleted.");
},
error: function(model, response) {
@@ -296,23 +302,22 @@ var FolderRowView = Backbone.View.extend({
"<td>",
'<%= _.escape(content_item.get("update_time")) %>',
"</td>",
"<td></td>",
"<td>",
"<% if(edit_mode) { %>", // start edit mode
'<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_folder_btn" type="button" style="<% if(button_config.save_folder_btn === false) { print("display:none;") } %>">',
'<span class="fa fa-floppy-o"/>',
"&nbsp;Save",
'<span class="fa fa-floppy-o"/> Save',
"</button>",
'<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_folder_btn" type="button" style="<% if(button_config.cancel_folder_btn === false) { print("display:none;") } %>">',
'<span class="fa fa-times"/>',
"&nbsp;Cancel",
'<span class="fa fa-times"/> Cancel',
"</button>",
"<% } else if (!edit_mode){%>", // start no edit mode
'<button data-toggle="tooltip" data-placement="top" title="Modify \'<%- content_item.get("name") %>\'" class="primary-button btn-xs edit_folder_btn" type="button" style="<% if(button_config.edit_folder_btn === false) { print("display:none;") } %>">',
'<span class="fa fa-pencil"/>',
'<span class="fa fa-pencil"/> Edit',
"</button>",
'<a href="#/folders/<%- content_item.id %>/permissions">',
'<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permission_folder_btn" title="Manage \'<%- content_item.get("name") %>\'" style="<% if(button_config.permission_folder_btn === false) { print("display:none;") } %>">',
'<span class="fa fa-group"/>',
'<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permission_folder_btn" title="Permissions of \'<%- content_item.get("name") %>\'" style="<% if(button_config.permission_folder_btn === false) { print("display:none;") } %>">',
'<span class="fa fa-group"/> Manage',
"</button>",
"</a>",
"<% } %>", //end no edit mode
@@ -342,6 +347,11 @@ var FolderRowView = Backbone.View.extend({
'<td><%= _.escape(content_item.get("file_size")) %></td>',
'<td><%= _.escape(content_item.get("update_time")) %></td>',
"<td>",
'<% if ( content_item.get("state") !== "ok" ) { %>',
'<%= _.escape(content_item.get("state")) %>',
"<% } %>",
"</td>",
"<td>",
'<% if (content_item.get("is_unrestricted")) { %>',
'<span data-toggle="tooltip" data-placement="top" title="Unrestricted dataset" style="color:grey;" class="fa fa-globe fa-lg"/>',
"<% } %>",
@@ -353,8 +363,8 @@ var FolderRowView = Backbone.View.extend({
"<% } %>",
'<% if (content_item.get("can_manage")) { %>',
'<a href="#folders/<%- content_item.get("folder_id") %>/datasets/<%- content_item.id %>/permissions">',
'<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn" title="Manage permissions">',
'<span class="fa fa-group"/>',
'<button data-toggle="tooltip" data-placement="top" class="primary-button btn-xs permissions-dataset-btn" title="Permissions of \'<%- content_item.get("name") %>\'">',
'<span class="fa fa-group"/> Manage',
"</button>",
"</a>",
"<% } %>",
@@ -388,10 +398,14 @@ var FolderRowView = Backbone.View.extend({
'<%= _.escape(content_item.get("update_time")) %>',
"</td>",
"<td>",
'<% if ( content_item.get("state") !== "ok" ) { %>',
'<%= _.escape(content_item.get("state")) %>',
"<% } %>",
"</td>",
"<td>",
'<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"/>',
'<button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_dataset_btn" type="button" style="margin-left:1em;">',
'<span class="fa fa-unlock"/>',
"&nbsp;Undelete",
'<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- content_item.get("name") %>\'" class="primary-button btn-xs undelete_dataset_btn" type="button" style="margin-left:1em;">',
'<span class="fa fa-unlock"/> Undelete',
"</button>",
"</td>",
"</tr>"
@@ -420,11 +434,11 @@ var FolderRowView = Backbone.View.extend({
"<td>",
'<%= _.escape(content_item.get("update_time")) %>',
"</td>",
"<td></td>",
"<td>",
'<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg"/>',
'<button data-toggle="tooltip" data-placement="top" title="Undelete <%- content_item.get("name") %>" class="primary-button btn-xs undelete_folder_btn" type="button" style="margin-left:1em;">',
'<span class="fa fa-unlock"/>',
"&nbsp;Undelete",
'<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- content_item.get("name") %>\'" class="primary-button btn-xs undelete_folder_btn" type="button" style="margin-left:1em;">',
'<span class="fa fa-unlock"/> Undelete',
"</button>",
"</td>",
"</tr>"
client/galaxy/scripts/mvc/library/library-foldertoolbar-view.js
+11 -10
View File
@@ -3,7 +3,7 @@ import mod_utils from "utils/utils";
import mod_toastr from "libs/toastr";
import mod_library_model from "mvc/library/library-model";
import mod_select from "mvc/ui/ui-select";
import jstree from "libs/jquery/jstree";
import "libs/jquery/jstree";
var FolderToolbarView = Backbone.View.extend({
el: "#center",
@@ -103,7 +103,10 @@ var FolderToolbarView = Backbone.View.extend({
show_page: parseInt(this.options.show_page),
page_count: parseInt(this.options.page_count),
total_items_count: this.options.total_items_count,
items_shown: this.options.items_shown
items_shown: this.options.items_shown,
folder_page_size: Galaxy.libraries.preferences.get(
"folder_page_size"
)
})
);
},
@@ -620,8 +623,6 @@ var FolderToolbarView = Backbone.View.extend({
disabled_jstree_element;
this.jstree.fetch({
success: function(model, response) {
// This is to prevent double jquery load. I think. Carl is magician.
// Now we need jstree, time to lazy load it.
$("#jstree_browser").jstree("destroy");
$("#jstree_browser").jstree({
core: {
@@ -1377,7 +1378,8 @@ var FolderToolbarView = Backbone.View.extend({
/**
* Show user the prompt to change the number of items shown on page.
*/
showPageSizePrompt: function() {
showPageSizePrompt: function(e) {
e.preventDefault();
var folder_page_size = prompt(
"How many items per page do you want to see?",
Galaxy.libraries.preferences.get("folder_page_size")
@@ -1831,11 +1833,10 @@ var FolderToolbarView = Backbone.View.extend({
"<% } %>",
"</ul>",
"<span>",
"&nbsp;showing&nbsp;",
'<a data-toggle="tooltip" data-placement="top" title="Click to change the number of items on page" class="page_size_prompt">',
"<%- items_shown %>",
"</a>",
"&nbsp;of <%- total_items_count %> items",
' <%- items_shown %> items shown <a href="" data-toggle="tooltip" data-placement="top" title="currently <%- folder_page_size %> per page" class="page_size_prompt">(change)</a>',
"</span>",
"<span>",
" <%- total_items_count %> total",
"</span>"
].join("")
);
client/galaxy/scripts/mvc/library/library-librarylist-view.js
+2 -2
View File
@@ -208,11 +208,11 @@ var LibraryListView = Backbone.View.extend({
sortLibraries: function() {
if (Galaxy.libraries.preferences.get("sort_by") === "name") {
if (Galaxy.libraries.preferences.get("sort_order") === "asc") {
this.collection.sortByNameAsc();
this.collection.sortLibraries("name", "asc");
} else if (
Galaxy.libraries.preferences.get("sort_order") === "desc"
) {
this.collection.sortByNameDesc();
this.collection.sortLibraries("name", "desc");
}
}
},
client/galaxy/scripts/mvc/library/library-libraryrow-view.js
+10 -8
View File
@@ -258,7 +258,7 @@ var LibraryRowView = Backbone.View.extend({
'<tr class="<% if(library.get("deleted") === true) { print("active") } %>" style="display:none;" data-id="<%- library.get("id") %>">',
"<% if(!edit_mode) { %>",
'<% if(library.get("deleted")) { %>',
'<td style="color:grey;"><span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey;" class="fa fa-ban fa-lg deleted_lib_ico"> </span> <%- library.get("name") %></td>',
'<td style="color:grey;"><%- library.get("name") %></td>',
"<% } else { %>",
'<td><a href="#folders/<%- library.get("root_folder_id") %>"><%- library.get("name") %></a></td>',
"<% } %>",
@@ -287,14 +287,16 @@ var LibraryRowView = Backbone.View.extend({
"<% } %>",
'<td class="right-center">',
'<% if( (library.get("public")) && (library.get("deleted") === false) ) { %>',
'<span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg public_lib_ico"> </span>',
'<span data-toggle="tooltip" data-placement="top" title="Unrestricted library" style="color:grey;" class="fa fa-globe fa-lg"> </span>',
"<% }%>",
'<button data-toggle="tooltip" data-placement="top" title="Modify \'<%- library.get("name") %>\'" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span></button>',
'<a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Manage \'<%- library.get("name") %>\'" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span></button></a>',
'<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"> Save</span></button>',
'<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"> Cancel</span></button>',
'<button data-toggle="tooltip" data-placement="top" title="Delete <%- library.get("name") %>" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"> Delete</span></button>',
'<button data-toggle="tooltip" data-placement="top" title="Undelete <%- library.get("name") %> " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"> Undelete</span></button>',
'<button data-toggle="tooltip" data-placement="top" title="Modify \'<%- library.get("name") %>\'" class="primary-button btn-xs edit_library_btn" type="button" style="<% if(button_config.edit_library_btn === false) { print("display:none;") } %>"><span class="fa fa-pencil"></span> Edit</button>',
'<a href="#library/<%- library.get("id") %>/permissions"><button data-toggle="tooltip" data-placement="top" title="Permissions of \'<%- library.get("name") %>\'" class="primary-button btn-xs permission_library_btn" type="button" style="<% if(button_config.permission_library_btn === false) { print("display:none;") } %>"><span class="fa fa-group"></span> Manage</button></a>',
'<button data-toggle="tooltip" data-placement="top" title="Save changes" class="primary-button btn-xs save_library_btn" type="button" style="<% if(button_config.save_library_btn === false) { print("display:none;") } %>"><span class="fa fa-floppy-o"></span> Save</button>',
'<button data-toggle="tooltip" data-placement="top" title="Discard changes" class="primary-button btn-xs cancel_library_btn" type="button" style="<% if(button_config.cancel_library_btn === false) { print("display:none;") } %>"><span class="fa fa-times"></span> Cancel</button>',
'<button data-toggle="tooltip" data-placement="top" title="Delete \'<%- library.get("name") %>\'" class="primary-button btn-xs delete_library_btn" type="button" style="<% if(button_config.delete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-trash-o"></span> Delete</button>',
// For deleted libraries
'<span data-toggle="tooltip" data-placement="top" title="Marked deleted" style="color:grey; <% if(button_config.undelete_library_btn === false) { print("display:none;") } %>" class="fa fa-ban fa-lg"></span>',
'<button data-toggle="tooltip" data-placement="top" title="Undelete \'<%- library.get("name") %>\' " class="primary-button btn-xs undelete_library_btn" type="button" style="<% if(button_config.undelete_library_btn === false) { print("display:none;") } %>"><span class="fa fa-unlock"></span> Undelete</button>',
"</td>",
"</tr>"
].join("")
client/galaxy/scripts/mvc/library/library-librarytoolbar-view.js
+12 -5
View File
@@ -15,7 +15,7 @@ var LibraryToolbarView = Backbone.View.extend({
"click #create_new_library_btn": "createLibraryFromModal",
"click #include_deleted_chk": "includeDeletedChecked",
"click #exclude_restricted_chk": "excludeRestrictedChecked",
"click #lib_page_size_prompt": "showPageSizePrompt",
"click .page_size_prompt": "showPageSizePrompt",
"keyup .library-search-input": "searchLibraries"
},
@@ -58,7 +58,10 @@ var LibraryToolbarView = Backbone.View.extend({
show_page: parseInt(this.options.show_page),
page_count: parseInt(this.options.page_count),
total_libraries_count: this.options.total_libraries_count,
libraries_shown: this.options.libraries_shown
libraries_shown: this.options.libraries_shown,
library_page_size: Galaxy.libraries.preferences.get(
"library_page_size"
)
})
);
},
@@ -120,7 +123,8 @@ var LibraryToolbarView = Backbone.View.extend({
/**
* Show user the propmpt to change the number of libs shown on page.
*/
showPageSizePrompt: function() {
showPageSizePrompt: function(e) {
e.preventDefault();
var library_page_size = prompt(
"How many libraries per page do you want to see?",
Galaxy.libraries.preferences.get("library_page_size")
@@ -273,8 +277,11 @@ var LibraryToolbarView = Backbone.View.extend({
'<li class="disabled"><a href="#page/<% print( page_count ) %>"><span class="fa fa-angle-double-right"></span></a></li>',
"<% } %>",
"</ul>",
'<span id="lib_page_size_prompt">',
' showing <a data-toggle="tooltip" data-placement="top" title="Click to change the number of libraries on page"><%- libraries_shown %></a> of <%- total_libraries_count %> libraries',
"<span>",
' <%- libraries_shown %> libraries shown <a href="" data-toggle="tooltip" data-placement="top" title="currently <%- library_page_size %> per page" class="page_size_prompt">(change)</a>',
"</span>",
"<span>",
" <%- total_libraries_count %> total",
"</span>"
].join("")
);
client/galaxy/scripts/mvc/library/library-model.js
+11 -106
View File
@@ -1,3 +1,4 @@
import mod_util from "mvc/library/library-util";
// ============================================================================
// LIBRARY RELATED MODELS
@@ -21,10 +22,6 @@ var Libraries = Backbone.Collection.extend({
model: Library,
sort_key: "name", // default
sort_order: null, // default
initialize: function(options) {
options = options || {};
},
@@ -59,50 +56,12 @@ var Libraries = Backbone.Collection.extend({
return filteredLibraries;
},
/** Sort collection by library name (ascending) and return the sorted
* collection
*/
sortByNameAsc: function() {
this.comparator = function(libraryA, libraryB) {
if (
libraryA.get("name").toLowerCase() >
libraryB.get("name").toLowerCase()
) {
return 1; // after
}
if (
libraryB.get("name").toLowerCase() >
libraryA.get("name").toLowerCase()
) {
return -1; // before
}
return 0; // equal
};
sortLibraries: function(sort_key, sort_order) {
this.comparator = mod_util.generateLibraryComparator(
sort_key,
sort_order
);
this.sort();
return this;
},
/** Sort collection by library name (descending) and return the sorted
* collection
*/
sortByNameDesc: function() {
this.comparator = function(libraryA, libraryB) {
if (
libraryA.get("name").toLowerCase() >
libraryB.get("name").toLowerCase()
) {
return -1; // before
}
if (
libraryB.get("name").toLowerCase() >
libraryA.get("name").toLowerCase()
) {
return 1; // after
}
return 0; // equal
};
this.sort();
return this;
}
});
@@ -122,66 +81,12 @@ var FolderAsModel = LibraryItem.extend({
var Folder = Backbone.Collection.extend({
model: LibraryItem,
/** Sort collection by item name (ascending) and return the sorted
* collection. Folders go before datasets.
*/
sortByNameAsc: function() {
this.comparator = function(itemA, itemB) {
if (itemA.get("type") === itemB.get("type")) {
if (
itemA.get("name").toLowerCase() >
itemB.get("name").toLowerCase()
) {
return 1; // after
}
if (
itemB.get("name").toLowerCase() >
itemA.get("name").toLowerCase()
) {
return -1; // before
}
return 0; // equal
} else {
if (itemA.get("type") === "folder") {
return -1; // folder is always before dataset
} else {
return 1;
}
}
};
sortFolder: function(sort_key, sort_order) {
this.comparator = mod_util.generateFolderComparator(
sort_key,
sort_order
);
this.sort();
return this;
},
/** Sort collection by item name (descending) and return the sorted
* collection. Folders go before datasets.
*/
sortByNameDesc: function() {
this.comparator = function(itemA, itemB) {
if (itemA.get("type") === itemB.get("type")) {
if (
itemA.get("name").toLowerCase() >
itemB.get("name").toLowerCase()
) {
return -1; // after
}
if (
itemB.get("name").toLowerCase() >
itemA.get("name").toLowerCase()
) {
return 1; // before
}
return 0; // equal
} else {
if (itemA.get("type") === "folder") {
return -1; // folder is always before dataset
} else {
return 1;
}
}
};
this.sort();
return this;
}
});
client/galaxy/scripts/mvc/library/library-util.js
+66
View File
@@ -0,0 +1,66 @@
/**
* Create alphabetical based two-argument comparator
* that takes into account that Folder comes before Dataset.
* 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 generateFolderComparator = function(sort_key, sort_order) {
return function(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;
}
if (
itemA.get(sort_key).toLowerCase() >
itemB.get(sort_key).toLowerCase()
) {
return sort_order === "asc" ? 1 : -1;
}
if (
itemB.get(sort_key).toLowerCase() >
itemA.get(sort_key).toLowerCase()
) {
return sort_order === "asc" ? -1 : 1;
}
return 0; // equal
} else {
if (itemA.get("type") === "folder") {
return -1; // folder is always before dataset
}
return 1;
}
};
};
/**
* Create alphabetical based two-argument comparator
* @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 generateLibraryComparator = function(sort_key, sort_order) {
return function(libraryA, libraryB) {
if (
libraryA.get(sort_key).toLowerCase() >
libraryB.get(sort_key).toLowerCase()
) {
return sort_order === "asc" ? 1 : -1;
}
if (
libraryB.get(sort_key).toLowerCase() >
libraryA.get(sort_key).toLowerCase()
) {
return sort_order === "asc" ? -1 : 1;
}
return 0; // equal
};
};
export default {
generateFolderComparator: generateFolderComparator,
generateLibraryComparator: generateLibraryComparator
};
client/galaxy/scripts/mvc/toolshed/repository-queue-view.js
+1 -1
View File
@@ -100,7 +100,7 @@ var View = Backbone.View.extend({
var repositories = iri_params.repositories;
var new_route = "status/r/" + repositories.join("|");
$.post(
Galaxy.root + "admin_toolshed/manage_repositories",
Galaxy.root + "admin_toolshed/install_repositories",
iri_params,
function(data) {
console.log(
client/galaxy/scripts/mvc/toolshed/repository-view.js
+2 -1
View File
@@ -351,7 +351,8 @@ var ToolShedRepositoryView = Backbone.View.extend({
},
doInstall: function(params) {
var controller_url = Galaxy.root + "admin_toolshed/manage_repositories";
var controller_url =
Galaxy.root + "admin_toolshed/install_repositories";
var repositories = params.repositories;
var new_route = "status/r/" + repositories.join("|");
$.post(controller_url, params, function(data) {
client/galaxy/scripts/mvc/tours.js
+73 -11
View File
@@ -9,16 +9,38 @@ var gxy_root = typeof Galaxy === "undefined" ? "/" : Galaxy.root;
var tourpage_template = `<h2>Galaxy Tours</h2>
<p>This page presents a list of interactive tours available on this Galaxy server.
Select any tour to get started (and remember, you can click 'End Tour' at any time).</p>
<ul>
<% _.each(tours, function(tour) { %>
<li>
<a href="/tours/<%- tour.id %>" class="tourItem" data-tour.id=<%- tour.id %>>
<%- tour.attributes.name || tour.id %>
</a>
- <%- tour.attributes.description || "No description given." %>
</li>
<% }); %>
</ul>`;
<div class="col-12 btn-group" role="group" aria-label="Tag selector">
<% _.each(tourtagorder, function(tag) { %>
<button class="btn btn-primary tag-selector-button" tag-selector-button="<%- tag %>">
<%- tag %>
</button>
<% }); %>
</div>
<% _.each(tourtagorder, function(tourtagkey) { %>
<div tag="<%- tourtagkey %>" style="display: block;">
<% var tourtag = tourtags[tourtagkey]; %>
<h4>
<%- tourtag.name %>
</h4>
<ul class="list-group">
<% _.each(tourtag.tours, function(tour) { %>
<li class="list-group-item">
<a href="/tours/<%- tour.id %>" class="tourItem" data-tour.id=<%- tour.id %>>
<%- tour.name || tour.id %>
</a>
- <%- tour.attributes.description || \"No description given.\" %>
<% _.each(tour.attributes.tags, function(tag) { %>
<span class="label label-primary sm-label-pad">
<%- tag.charAt(0).toUpperCase() + tag.slice(1) %>
</span>
<% }); %>
</li>
<% }); %>
</ul>
</div>
<% }); %>`;
var tour_opts = {
storage: window.sessionStorage,
@@ -91,6 +113,7 @@ var giveTour = function(tour_id) {
tour.restart();
});
};
var ToursView = Backbone.View.extend({
title: "Tours",
// initialize
@@ -111,11 +134,50 @@ var ToursView = Backbone.View.extend({
render: function() {
var tpl = _.template(tourpage_template);
var tourtags = {};
_.each(this.model.models, function(tour) {
if (tour.attributes.tags === null) {
if (tourtags.Untagged === undefined) {
tourtags.Untagged = { name: "Untagged", tours: [] };
}
tourtags.Untagged.tours.push(tour);
} else {
_.each(tour.attributes.tags, function(tag) {
tag = tag.charAt(0).toUpperCase() + tag.slice(1);
if (tourtags[tag] === undefined) {
tourtags[tag] = { name: tag, tours: [] };
}
tourtags[tag].tours.push(tour);
});
}
});
var tourtagorder = Object.keys(tourtags).sort();
this.$el
.html(tpl({ tours: this.model.models }))
.html(
tpl({
tours: this.model.models,
tourtags: tourtags,
tourtagorder: tourtagorder
})
)
.on("click", ".tourItem", function(e) {
e.preventDefault();
giveTour($(this).data("tour.id"));
})
.on("click", ".tag-selector-button", function(e) {
var elem = $(e.target);
var display = "block";
var tag = elem.attr("tag-selector-button");
elem.toggleClass("btn-primary");
elem.toggleClass("btn-secondary");
if (elem.hasClass("btn-secondary")) {
display = "none";
}
$("div[tag='" + tag + "']").css({ display: display });
});
}
});
client/galaxy/scripts/utils/utils.js
+3 -2
View File
@@ -310,7 +310,7 @@ function time() {
var d = new Date();
var hours = (d.getHours() < 10 ? "0" : "") + d.getHours();
var minutes = (d.getMinutes() < 10 ? "0" : "") + d.getMinutes();
return (datetime =
return (
d.getDate() +
"/" +
(d.getMonth() + 1) +
@@ -319,7 +319,8 @@ function time() {
", " +
hours +
":" +
minutes);
minutes
);
}
/** Append script and style tags to Galaxy main application */
client/galaxy/style/less/base.less
+4
View File
@@ -1086,6 +1086,10 @@ div.odd_row {
.label-info();
}
.sm-label-pad {
margin-right: 2px;
}
span.toolParameterExpandableCollapsable {
font-weight: bold;
cursor: pointer;
client/galaxy/style/less/library.less
+1 -1
View File
@@ -11,7 +11,7 @@ overflow: auto !important;
.fa{
font-size: 12px;
}
.fa-globe{
.fa-globe, .fa-shield, .fa-key, .fa-ban{
font-size: initial;
margin-left: 0.6em;
}
client/galaxy/style/less/ui.less
+1
View File
@@ -212,6 +212,7 @@
color: @base-text-color;
background: @side-panel-bg;
padding: 10px;
min-height:100%;
.ui-side-section-title {
font-weight: bold;
}
client/galaxy/style/less/upload.less
+1 -1
View File
@@ -126,7 +126,7 @@
resize: none;
background: inherit;
color: @black;
white-space: nowrap;
white-space: pre;
overflow: scroll;
}
.upload-text-info {
client/gulpfile.js
+2
View File
@@ -8,6 +8,7 @@ var babel = require('gulp-babel');
var sourcemaps = require('gulp-sourcemaps');
var uglify = require('gulp-uglify');
var cached = require('gulp-cached');
var plumber = require('gulp-plumber');
var paths = {
node_modules: './node_modules',
@@ -37,6 +38,7 @@ var paths = {
gulp.task('scripts', function() {
return gulp.src(paths.scripts)
.pipe(plumber())
.pipe(cached('scripts'))
.pipe(sourcemaps.init())
.pipe(babel({
client/package.json
+1
View File
@@ -59,6 +59,7 @@
"gulp": "^3.9.1",
"gulp-babel": "^7.0.0",
"gulp-cached": "^1.1.1",
"gulp-plumber": "^1.1.0",
"gulp-sourcemaps": "^2.5.1",
"gulp-uglify": "^3.0.0",
"gulp-watch": "^4.3.11",
client/yarn.lock
+9 -2
View File
@@ -2218,6 +2218,13 @@ gulp-cached@^1.1.1:
lodash.defaults "^4.2.0"
through2 "^2.0.1"
gulp-plumber@^1.1.0:
version "1.1.0"
resolved "https://registry.yarnpkg.com/gulp-plumber/-/gulp-plumber-1.1.0.tgz#f12176c2d0422f60306c242fff6a01a394faba09"
dependencies:
gulp-util "^3"
through2 "^2"
gulp-sourcemaps@^2.5.1:
version "2.6.1"
resolved "https://registry.yarnpkg.com/gulp-sourcemaps/-/gulp-sourcemaps-2.6.1.tgz#833a4e28f0b8f4661075032cd782417f7cd8fb0b"
@@ -2247,7 +2254,7 @@ gulp-uglify@^3.0.0:
uglify-js "^3.0.5"
vinyl-sourcemaps-apply "^0.2.0"
gulp-util@^3.0.0, gulp-util@^3.0.7:
gulp-util@^3, gulp-util@^3.0.0, gulp-util@^3.0.7:
version "3.0.8"
resolved "https://registry.yarnpkg.com/gulp-util/-/gulp-util-3.0.8.tgz#0054e1e744502e27c04c187c3ecc505dd54bbb4f"
dependencies:
@@ -4630,7 +4637,7 @@ tar@^2.2.1:
fstream "^1.0.2"
inherits "2"
through2@2.X, through2@^2.0.0, through2@^2.0.1, through2@^2.0.3:
through2@2.X, through2@^2, through2@^2.0.0, through2@^2.0.1, through2@^2.0.3:
version "2.0.3"
resolved "https://registry.yarnpkg.com/through2/-/through2-2.0.3.tgz#0004569b37c7c74ba39c43f3ced78d1ad94140be"
dependencies:
config/datatypes_conf.xml.sample
+1
View File
@@ -245,6 +245,7 @@
<datatype extension="hardklor" type="galaxy.datatypes.tabular:Tabular" subclass="true" />
<datatype extension="kronik" type="galaxy.datatypes.tabular:Tabular" subclass="true" />
<datatype extension="imzml" type="galaxy.datatypes.proteomics:ImzML" mimetype="application/xml" display_in_upload="true"/>
<datatype extension="analyze75" type="galaxy.datatypes.proteomics:Analyze75" mimetype="application/xml" display_in_upload="true"/>
<!-- End Proteomics Datatypes -->
<datatype extension="deeptools_compute_matrix_archive" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
<datatype extension="deeptools_coverage_matrix" type="galaxy.datatypes.binary:CompressedArchive" subclass="true" display_in_upload="true"/>
config/galaxy.ini.sample
+22 -12
View File
@@ -447,10 +447,9 @@ paste.app_factory = galaxy.web.buildapp:app_factory
# -- Mail and notification
# Galaxy sends mail for various things: subscribing users to the mailing list
# if they request it, password resets, notifications from the Galaxy Sample
# Tracking system, reporting dataset errors, and sending activation emails.
# To do this, it needs to send mail through an SMTP server, which you may
# define here (host:port).
# if they request it, password resets, reporting dataset errors, and sending
# activation emails. To do this, it needs to send mail through an SMTP server,
# which you may define here (host:port).
# Galaxy will automatically try STARTTLS but will continue upon failure.
#smtp_server = None
@@ -912,6 +911,14 @@ use_interactive = True
# sub-directories of files contained in their directory.
#user_library_import_dir = None
# For security reasons, users may not import any files that actually lie
# outside of their `user_library_import_dir` (e.g. using symbolic links). A
# list of directories can be allowed by setting the following option (the list
# is comma-separated). Be aware that *any* user with library import permissions
# can import from anywhere in these directories (assuming they are able to
# create symlinks to them).
#user_library_import_symlink_whitelist = None
# Allow admins to paste filesystem paths during upload. For libraries this
# adds an option to the admin library upload tool allowing admins to paste
# filesystem paths to files and directories in a box, and these paths will be
@@ -1224,6 +1231,9 @@ use_interactive = True
# Directory to store Data Manager based tool-data; defaults to tool_data_path.
#galaxy_data_manager_data_path = tool-data
# Enable the API for sample tracking
#enable_legacy_sample_tracking_api = False
# -- Job Execution
# To increase performance of job execution and the web interface, you can
@@ -1325,16 +1335,16 @@ use_interactive = True
#drmaa_external_killjob_script = sudo -E scripts/drmaa_external_killer.py
#external_chown_script = sudo -E scripts/external_chown_script.py
# For the job submission as the actual system user, Galaxy can extract
# the user name from the email address (actually the local-part before the @)
# or the username which are both stored in the Galaxy data base.
# The latter option is particularly useful for installations that get the
# For the job submission as the actual system user, Galaxy can extract
# the user name from the email address (actually the local-part before the @)
# or the username which are both stored in the Galaxy data base.
# The latter option is particularly useful for installations that get the
# authentication from LDAP.
# Also, Galaxy can accept the name of a common system user (eg. galaxy_worker)
# who can run every job being submitted. This user should not be the same user
# running the galaxy system.
# Also, Galaxy can accept the name of a common system user (eg. galaxy_worker)
# who can run every job being submitted. This user should not be the same user
# running the galaxy system.
# Possible values are user_email (default), username or <common_system_user>
#real_system_username = user_email
#real_system_username = user_email
# File to source to set up the environment when running jobs. By default, the
# environment in which the Galaxy server starts is used when running jobs
config/local_conda_mapping.yml.sample
+1 -1
View File
@@ -1,2 +1,2 @@
# See $GALAXY_ROOT/lib/galaxy/tools/deps/default_conda_mapping.yml for example mapping -
# See $GALAXY_ROOT/lib/galaxy/tools/deps/resolvers/default_conda_mapping.yml for example mapping -
# additional site-specific mappings can be added to config/conda_mapping.yml.
config/plugins/interactive_environments/jupyter/static/js/jupyter.js
+2 -2
View File
@@ -53,7 +53,7 @@ function keep_alive(){
var count_max = 60;
// we sleep 15 seconds between requests and the default timeout for the Jupyter container is 120 seconds, so start
// with a pretty high ajax timeout. sleep starts low because we want to get the warning up pretty quickly
var spin_state = make_spin_state("IE keep alive", 8000, 16000, 2000, 5000, 15000, 5000, false);
var spin_state = make_spin_state("IE keepalive", 8000, 16000, 2000, 5000, 15000, 5000, false);
var success = function(){
console.log("IE keepalive request succeeded");
toastr.clear()
@@ -85,7 +85,7 @@ function keep_alive(){
return true; // stop spinning
}
}
console.log("IE keep alive worker starting");
console.log("IE keepalive worker starting");
spin(notebook_access_url, false, success, timeout_error, timeout_error, spin_state);
}
config/plugins/tours/core.galaxy_ui.yaml
+3
View File
@@ -2,6 +2,9 @@ id: galaxy_ui
name: Galaxy UI
description: A gentle introduction to the Galaxy User Interface
title_default: "Welcome to Galaxy"
tags:
- "core"
- "UI"
# A tour is made of several steps, each of them beginning with a dash '-'
steps:
config/plugins/tours/core.history.yaml
+4
View File
@@ -1,6 +1,10 @@
name: History Introduction
description: A detailed introduction to the Galaxy History
title_default: "Galaxy History Introduction"
tags:
- "core"
- "history"
steps:
- content: "This short tour will guide you through <b>Galaxy's History</b> and datasets."
config/plugins/tours/core.scratchbook.yaml
+5
View File
@@ -1,6 +1,11 @@
name: Scratchbook - Introduction
title_default: "Scratchbook Introduction"
description: "An introduction on how to display multiple datasets and visualizations next to each other."
tags:
- "core"
- "UI"
- "visualization"
steps:
- content: "This short tour will walk you through <b>Galaxy's Scratchbook</b> feature"
config/plugins/webhooks/demo/tour_generator/helper/__init__.py
+1 -1
View File
@@ -1,5 +1,5 @@
import os
import logging
import os
from cgi import FieldStorage
from galaxy.util import Params
cron/add_manual_builds.py
+3 -3
View File
@@ -19,7 +19,7 @@ def add_manual_builds(input_file, build_file, chr_dir):
if line.startswith("#"):
continue
existing_builds.append(line.replace("\n", "").replace("\r", "").split("\t")[0])
except:
except Exception:
continue
build_file_out = open(build_file, 'a')
for line in open(input_file):
@@ -31,7 +31,7 @@ def add_manual_builds(input_file, build_file, chr_dir):
name = fields.pop(0)
try: # get chrom lens if included in file, otherwise still add build
chrs = fields.pop(0).split(",")
except:
except Exception:
chrs = []
print>>build_file_out, build + "\t" + name + " (" + build + ")"
if chrs: # create len file if provided chrom lens
@@ -39,7 +39,7 @@ def add_manual_builds(input_file, build_file, chr_dir):
for chr in chrs:
print>>chr_len_out, chr.replace("=", "\t")
chr_len_out.close()
except:
except Exception:
continue
build_file_out.close()
cron/build_chrom_db.py
+2 -2
View File
@@ -60,13 +60,13 @@ if __name__ == "__main__":
if line.startswith("#"):
continue
builds.append(line.split("\t")[0])
except:
except Exception:
sys.exit("Bad input file.")
else:
try:
for build in parse_builds.getbuilds("http://genome.cse.ucsc.edu/cgi-bin/das/dsn"):
builds.append(build[0])
except:
except Exception:
sys.exit("Unable to retrieve builds.")
for build in builds:
if build == "?":
cron/parse_builds.py
+2 -2
View File
@@ -15,14 +15,14 @@ import requests
def getbuilds(url):
try:
text = requests.get(url).text
except:
except Exception:
print("#Unable to open " + url)
print("?\tunspecified (?)")
sys.exit(1)
try:
tree = ElementTree.fromstring(text)
except:
except Exception:
print("#Invalid xml passed back from " + url)
print("?\tunspecified (?)")
sys.exit(1)
cron/parse_builds_3_sites.py
+2 -2
View File
@@ -21,13 +21,13 @@ def main():
builds = []
try:
text = requests.get(site).text
except:
except Exception:
print("#Unable to connect to " + site)
continue
try:
tree = ElementTree.fromstring(text)
except:
except Exception:
print("#Invalid xml passed back from " + site)
continue
print("#Harvested from", site)
doc/schema_template.md
+21 -12
View File
@@ -15,8 +15,23 @@ number of tutorials on building Galaxy tools that would better serve that purpos
$tag:tool://element[@name='tool']
$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|requirements://complexType[@name='Requirements']
$tag:tool|requirements|requirement://complexType[@name='Requirement']
$tag:tool|requirements|container://complexType[@name='Container']
$tag:tool|code://complexType[@name='Code']
$tag:tool|stdio://complexType[@name='Stdio']
$tag:tool|stdio|exit_code://complexType[@name='ExitCode'] hide_attributes
$tag:tool|stdio|regex://complexType[@name='Regex'] hide_attributes
$tag:tool|version_command://complexType[@name='VersionCommand']
$tag:tool|command://element[@name='tool']//element[@name='command'] hide_attributes
$tag:tool|environment_variables://complexType[@name='EnvironmentVariables']
$tag:tool|environment_variables|environment_variable://complexType[@name='EnvironmentVariable']
$tag:tool|configfiles://complexType[@name='ConfigFiles']
$tag:tool|configfiles|configfile://complexType[@name='ConfigFile']
$tag:tool|configfiles|inputs://complexType[@name='ConfigInputs']
$tag:tool|inputs://complexType[@name='Inputs']
$tag:tool|inputs|section://complexType[@name='Section']
$tag:tool|inputs|repeat://complexType[@name='Repeat']
@@ -36,11 +51,12 @@ $tag:tool|inputs|param|sanitizer|valid|remove://complexType[@name='SanitizerVali
$tag:tool|inputs|param|sanitizer|mapping://complexType[@name='SanitizerMapping']
$tag:tool|inputs|param|sanitizer|mapping|add://complexType[@name='SanitizerMappingAdd']
$tag:tool|inputs|param|sanitizer|mapping|remove://complexType[@name='SanitizerMappingRemove']
$tag:tool|configfiles://complexType[@name='ConfigFiles']
$tag:tool|configfiles|configfile://complexType[@name='ConfigFile']
$tag:tool|configfiles|inputs://complexType[@name='ConfigInputs']
$tag:tool|environment_variables://complexType[@name='EnvironmentVariables']
$tag:tool|environment_variables|environment_variable://complexType[@name='EnvironmentVariable']
$tag:tool|request_param_translation://complexType[@name='RequestParameterTranslation']
$tag:tool|request_param_translation|request_param://complexType[@name='RequestParameter']
$tag:tool|request_param_translation|request_param|append_param://complexType[@name='RequestParameterAppend']
$tag:tool|request_param_translation|request_param|append_param|value://complexType[@name='RequestParameterAppendValue']
$tag:tool|request_param_translation|request_param|value_translation://complexType[@name='RequestParameterValueTranslation']
$tag:tool|request_param_translation|request_param|value_translation|value://complexType[@name='RequestParameterValueTranslationValue']
$tag:tool|outputs://complexType[@name='Outputs']
$tag:tool|outputs|data://complexType[@name='Data']
$tag:tool|outputs|data|filter://complexType[@name='OutputFilter']
@@ -68,13 +84,6 @@ $tag:tool|tests|test|output_collection://complexType[@name='TestOutputCollection
$tag:tool|tests|test|assert_command://group[@name='TestParamElement']//element[@name='assert_command']
$tag:tool|tests|test|assert_stdout://group[@name='TestParamElement']//element[@name='assert_stdout']
$tag:tool|tests|test|assert_stderr://group[@name='TestParamElement']//element[@name='assert_stderr']
$tag:tool|code://complexType[@name='Code']
$tag:tool|requirements://complexType[@name='Requirements']
$tag:tool|requirements|requirement://complexType[@name='Requirement']
$tag:tool|requirements|container://complexType[@name='Container']
$tag:tool|stdio://complexType[@name='Stdio']
$tag:tool|stdio|exit_code://complexType[@name='ExitCode'] hide_attributes
$tag:tool|stdio|regex://complexType[@name='Regex'] hide_attributes
$tag:tool|help://element[@name='tool']//element[@name='help']
$tag:tool|citations://complexType[@name='Citations']
$tag:tool|citations|citation://complexType[@name='Citation']
doc/source/releases/17.09.rst
+1019
View File
File diff suppressed because it is too large Load Diff
doc/source/releases/17.09_announce.rst
+144 -3
View File
@@ -3,8 +3,149 @@
September 2017 Galaxy Release (v 17.09)
===========================================================
.. include:: _header.rst
Schedule
Highlights
===========================================================
* Planned Freeze Date: 2017-09-04
* Planned Release Date: 2017-09-25
**Singularity**
Tool execution using the HPC-friendly container technology `Singularity <http://singularity.lbl.gov/>`__
is now supported. Custom containers can be specified by the Galaxy admin on a per job destination basis
or standardized containers corresponding to Conda requirements can be built or downloaded automatically
using the mulled toolkit built into Galaxy (just like is possible for Docker). For more information
checkout `this presentation <http://bit.ly/gcc-biocontainers>`__ from the 2017 Galaxy Community Conference.
`Pull Request 4175`_
**Download entire collection**
Downloading whole colections is now possible from the history interface. `Pull Request 4098`_
Thanks to `@mvdbeek <https://github.com/mvdbeek>`__.
**Switch tool versions in workflows**
You can now select exactly what version of tool you want to use when building workflows. `Pull Request 4373`_
Thanks to `@mvdbeek <https://github.com/mvdbeek>`__.
Get Galaxy
==========
The code lives at `Github <https://github.com/galaxyproject/galaxy>`__ and you should have `Git <https://git-scm.com/>`__ to obtain it.
To get a new Galaxy repository run:
.. code-block:: shell
$ git clone -b release_17.09 https://github.com/galaxyproject/galaxy.git
To update an existing Galaxy repository run:
.. code-block:: shell
$ git checkout release_17.09 && git pull --ff-only origin release_17.09
See `the community hub <https://galaxyproject.org/develop/source-code/>`__ for additional details regarding the source code locations.
Security
========
The 17.09 Galaxy version includes many security patches. Per our new `Security Policy
<https://github.com/galaxyproject/galaxy/blob/dev/SECURITY_POLICY.md>`__ some of these have been
applied to Galaxy releases going back 12 months.
Details of the vulnerabilities that have been backported can be found in the `Security patch details`_
section of these release notes. Some issues have only been addressed in 17.09, for this reason
if security is important to your Galaxy instance we strongly recommend upgrading to this latest release
as soon as possible.
If you maintain a publicly accessible Galaxy please consider signing up for this `mailing list <https://lists.galaxyproject.org/listinfo/galaxy-public-servers>`__ to receive the future security patches in advance of the public disclosure.
Deprecation Notices
===================
* The Galaxy Sample Tracking and External Services functionality is now considered deprecated. In future releases we will strip down the related
user interface and introduce configuration option to keep relevant API controllers active if desired. `Related PR <https://github.com/galaxyproject/galaxy/pull/4526>`__.
* The deprecated admin-only interface for Galaxy Data Libraries is staged to be removed in the next release.
* Workflows API: When exposing WorkflowInvocationSteps ``state`` will no longer be available.
* The ``refresh_on_change`` attribute of a ``<param>`` tag in the tool syntax can no longer be set to a value of another parameter. Use boolean instead (e.g.``refresh_on_change="True"``). `Details <https://github.com/galaxyproject/galaxy/issues/4810>`__
Release Notes
===========================================================
.. include:: 17.09.rst
:start-after: announce_start
Security patch details
======================
Limited Galaxy Data Library unauthorized filesystem access
----------------------------------------------------------
Tracked as `GX-2017-0001 <https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-October/026058.html>`__
A medium severity security vulnerability in Galaxy Data Libraries was
recently discovered by `Jelle Scholtalbers <https://github.com/scholtalbers>`__.
This vulnerability allows the following unauthorized actions:
1. Any user that has been granted the permission to add datasets to a
library, library folder, or to modify an existing library dataset (an
"authorized user"), is able to import any file on the system that is
readable by the user running the Galaxy server.
2. Anyone can create libraries and library folders (but not add datasets to them)
The fix for this issue has been applied to Galaxy releases back to 16.07 and can be found in this `commit <https://github.com/galaxyproject/galaxy/commit/93a8bfc7cb5e9c3395c5057910ec39d68ad787b4>`__
Arbitrary code execution for Galaxy servers with Galaxy Interactive Environments enabled
----------------------------------------------------------------------------------------
Tracked as `GX-2017-0002 <https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-October/026059.html>`__
A high severity security vulnerability was recently discovered in Galaxy
Interactive Environments (GIEs) by the Galaxy Committers Team. Anyone with
a Galaxy account can exploit this vulnerability to execute arbitrary code
on the Galaxy server as the user running the Galaxy server process.
The vulnerability only affects Galaxy servers on which Galaxy Interactive
Environments are enabled (by setting the
`interactive_environment_plugins_directory`
option in `galaxy.ini`). Because the vulnerability can be exploited to
execute arbitrary code, the impact for affected servers is severe.
Administrators of Galaxy servers where GIEs *are* enabled should update
immediately.
The fix for this issue has been applied to Galaxy releases back to 17.05 and can be found in this `commit <https://github.com/galaxyproject/galaxy/commit/9f8d3ee444ad10038add204ed1c1dc11e636dd9d>`__
Unauthorized filesystem access via data source tools
----------------------------------------------------
Tracked as `GX-2017-0003 <https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-October/026060.html>`__
A medium severity security vulnerability in tools utilizing the Galaxy data
source protocol was recently discovered by the Galaxy Committers Team.
Anyone who is able to run an external data source tool can access
any file that is readable by the user running Galaxy jobs
on the host where the job runs.
Many such "external data source" tools are provided with the Galaxy
distribution and are enabled by default (most tools under the "Get Data"
section of the tool panel), meaning that its exploitability is fairly high,
as only one such tool needs to be enabled to be vulnerable, including any
custom data source tools (any tool that uses
`tools/data_source/data_source.py`).
What files are readable depends entirely upon what the job's user has
access to read on the host(s) where jobs run.
The fix for this issue has been applied to Galaxy releases back to 16.07 and can be found in this `commit <https://github.com/galaxyproject/galaxy/commit/0e698813a96f1ad61d797255686f69cf5e6b1280>`__
Cross site scripting and session fixation
-----------------------------------------
Disclosed on the `mailing list <https://lists.galaxyproject.org/pipermail/galaxy-dev/2017-August/025938.html>`__ in August 2017.
Vulnerabilities were found by Eric Rasche and Manabu Ishii respectively. Detailed descriptions of these categories of vulnerabilities can be found at:
- https://www.owasp.org/index.php/Cross-site_Scripting_(XSS)
- https://www.owasp.org/index.php/Session_fixation
The fix for these issues has been applied to Galaxy releases back to 16.10 and can be found in this `diff <https://gist.githubusercontent.com/jmchilton/760bf8ba6055b9a47a48529fcc49a493/raw/01bc98e5a8067a435f38d7cf4fda4e304c4425a2/2017augsecurity_1610.patch>`__
.. include:: _thanks.rst
doc/source/releases/18.01_announce.rst
+10
View File
@@ -0,0 +1,10 @@
===========================================================
January 2018 Galaxy Release (v 18.01)
===========================================================
Schedule
===========================================================
* Planned Freeze Date: 2018-01-08
* Planned Release Date: 2018-01-29
doc/source/releases/index.rst
+1
View File
@@ -4,6 +4,7 @@ Releases
.. toctree::
:maxdepth: 1
17.09_announce
17.05_announce
17.01_announce
16.10_announce
lib/galaxy/auth/providers/ldap_ad.py
+1 -1
View File
@@ -95,7 +95,7 @@ class LDAP(AuthProvider):
try:
import ldap
except:
except ImportError:
log.debug('LDAP authenticate: could not load ldap module')
return (failure_mode, '', '')
lib/galaxy/config.py
+6 -2
View File
@@ -212,7 +212,7 @@ class Configuration(object):
self.hours_between_check = 12.0
else:
self.hours_between_check = 12
except:
except Exception:
self.hours_between_check = 12
self.update_integrated_tool_panel = kwargs.get("update_integrated_tool_panel", True)
self.enable_data_manager_user_view = string_as_bool(kwargs.get("enable_data_manager_user_view", "False"))
@@ -338,6 +338,9 @@ class Configuration(object):
# Beta containers interface used by GIEs
self.enable_beta_containers_interface = string_as_bool(kwargs.get('enable_beta_containers_interface', 'False'))
# Deprecated API for sample tracking
self.enable_legacy_sample_tracking_api = string_as_bool(kwargs.get('enable_legacy_sample_tracking_api', 'False'))
# Certain modules such as the pause module will automatically cause
# workflows to be scheduled in job handlers the way all workflows will
# be someday - the following two properties can also be used to force this
@@ -395,6 +398,7 @@ class Configuration(object):
self.genomespace_ui_url = kwargs.get('genomespace_ui_url', 'https://gsui.genomespace.org/jsui/')
self.library_import_dir = kwargs.get('library_import_dir', None)
self.user_library_import_dir = kwargs.get('user_library_import_dir', None)
self.user_library_import_symlink_whitelist = listify(kwargs.get('user_library_import_symlink_whitelist', []), do_strip=True)
# Searching data libraries
self.enable_lucene_library_search = string_as_bool(kwargs.get('enable_lucene_library_search', False))
self.enable_whoosh_library_search = string_as_bool(kwargs.get('enable_whoosh_library_search', False))
@@ -793,7 +797,7 @@ class Configuration(object):
try:
port = config.getint('server:%s' % self.server_name, 'port')
except:
except Exception:
# uWSGI galaxy installations don't use paster and only speak uWSGI not http
port = None
return port
lib/galaxy/containers/docker_model.py
+1 -1
View File
@@ -374,7 +374,7 @@ class DockerNode(object):
@property
def labels(self):
labels = self.inspect[0]['Spec'].get('Labels', {})
labels = self.inspect[0]['Spec'].get('Labels', {}) or {}
return DockerNodeLabels.from_label_dictionary(labels)
def label_add(self, label, value):
lib/galaxy/datatypes/annotation.py
+2 -2
View File
@@ -23,7 +23,7 @@ class SnapHmm(Text):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "SNAP HMM model (%s)" % (nice_size(dataset.get_size()))
def sniff(self, filename):
@@ -54,7 +54,7 @@ class Augustus(CompressedArchive):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Augustus model (%s)" % (nice_size(dataset.get_size()))
def sniff(self, filename):
lib/galaxy/datatypes/assembly.py
+4 -4
View File
@@ -63,7 +63,7 @@ class Amos(data.Text):
if re.match(r'{(RED|CTG|TLE)$', line):
isAmos = True
fh.close()
except:
except Exception:
pass
return isAmos
@@ -102,7 +102,7 @@ class Sequences(sequence.Fasta):
else:
break # we found a non-empty line, but it's not a fasta header
fh.close()
except:
except Exception:
pass
return False
@@ -138,7 +138,7 @@ class Roadmaps(data.Text):
else:
break # we found a non-empty line, but it's not a fasta header
fh.close()
except:
except Exception:
pass
return False
@@ -202,7 +202,7 @@ class Velvet(Html):
gen_msg = gen_msg + ' Long Reads'
if len(gen_msg) > 0:
gen_msg = 'Uses: ' + gen_msg
except:
except Exception:
log.debug("Velveth could not read Log file in %s" % efp)
log.debug("Velveth log info %s" % gen_msg)
rval = ['<html><head><title>Velvet Galaxy Composite Dataset </title></head><p/>']
lib/galaxy/datatypes/binary.py
+36 -36
View File
@@ -106,7 +106,7 @@ class Ab1(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Binary ab1 sequence file (%s)" % (nice_size(dataset.get_size()))
@@ -125,7 +125,7 @@ class Idat(Binary):
if header == b'IDAT':
return True
return False
except:
except Exception:
return False
@@ -157,7 +157,7 @@ class Cel(Binary):
if header == b';\x01\x00\x00':
return True
return False
except:
except Exception:
return False
@@ -183,7 +183,7 @@ class CompressedArchive(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Compressed binary file (%s)" % (nice_size(dataset.get_size()))
@@ -208,7 +208,7 @@ class CompressedZipArchive(CompressedArchive):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Compressed zip file (%s)" % (nice_size(dataset.get_size()))
@@ -425,7 +425,7 @@ class Bam(Binary):
dataset.metadata.read_groups = [read_group['ID'] for read_group in dataset.metadata.bam_header.get('RG', []) if 'ID' in read_group]
dataset.metadata.sort_order = dataset.metadata.bam_header.get('HD', {}).get('SO', None)
dataset.metadata.bam_version = dataset.metadata.bam_header.get('HD', {}).get('VN', None)
except:
except Exception:
# Per Dan, don't log here because doing so will cause datasets that
# fail metadata to end in the error state
pass
@@ -438,7 +438,7 @@ class Bam(Binary):
if header == b'BAM\1':
return True
return False
except:
except Exception:
return False
def set_peek(self, dataset, is_multi_byte=False):
@@ -452,7 +452,7 @@ class Bam(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Binary bam alignments file (%s)" % (nice_size(dataset.get_size()))
def to_archive(self, trans, dataset, name=""):
@@ -664,7 +664,7 @@ class CRAM(Binary):
if header == b"CRAM":
return True
return False
except:
except Exception:
return False
@@ -700,7 +700,7 @@ class Bcf(BaseBcf):
if header == b'BCF':
return True
return False
except:
except Exception:
return False
def set_meta(self, dataset, overwrite=True, **kwd):
@@ -756,7 +756,7 @@ class BcfUncompressed(Bcf):
if header == b'BCF':
return True
return False
except:
except Exception:
return False
@@ -789,7 +789,7 @@ class H5(Binary):
if header == self._magic:
return True
return False
except:
except Exception:
return False
def set_peek(self, dataset, is_multi_byte=False):
@@ -803,7 +803,7 @@ class H5(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Binary HDF5 file (%s)" % (nice_size(dataset.get_size()))
@@ -886,7 +886,7 @@ class Biom2(H5):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Biom2 (HDF5) file (%s)" % (nice_size(dataset.get_size()))
@@ -911,7 +911,7 @@ class Scf(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Binary scf sequence file (%s)" % (nice_size(dataset.get_size()))
@@ -932,7 +932,7 @@ class Sff(Binary):
if header == b'.sff':
return True
return False
except:
except Exception:
return False
def set_peek(self, dataset, is_multi_byte=False):
@@ -946,7 +946,7 @@ class Sff(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Binary sff file (%s)" % (nice_size(dataset.get_size()))
@@ -976,7 +976,7 @@ class BigWig(Binary):
try:
magic = self._unpack("I", open(filename, 'rb'))
return magic[0] == self._magic
except:
except Exception:
return False
def set_peek(self, dataset, is_multi_byte=False):
@@ -990,7 +990,7 @@ class BigWig(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Binary UCSC %s file (%s)" % (self._name, nice_size(dataset.get_size()))
@@ -1040,7 +1040,7 @@ class TwoBit(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Binary TwoBit format nucleotide file (%s)" % (nice_size(dataset.get_size()))
@@ -1097,7 +1097,7 @@ class SQlite(Binary):
if header == b'SQLite format 3\0':
return True
return False
except:
except Exception:
return False
def set_peek(self, dataset, is_multi_byte=False):
@@ -1108,7 +1108,7 @@ class SQlite(Binary):
for table in dataset.metadata.tables:
try:
lines.append('%s [%s]' % (table, dataset.metadata.table_row_count[table]))
except:
except Exception:
continue
dataset.peek = '\n'.join(lines)
dataset.blurb = nice_size(dataset.get_size())
@@ -1119,7 +1119,7 @@ class SQlite(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "SQLite Database (%s)" % (nice_size(dataset.get_size()))
@dataproviders.decorators.dataprovider_factory('sqlite', dataproviders.dataset.SQliteDataProvider.settings)
@@ -1191,7 +1191,7 @@ class GeminiSQLite(SQlite):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Gemini SQLite Database, version %s" % (dataset.metadata.gemini_version or 'unknown')
@@ -1265,7 +1265,7 @@ class IdpDB(SQlite):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "IDPickerDB SQLite file (%s)" % (nice_size(dataset.get_size()))
@@ -1289,7 +1289,7 @@ class Xlsx(Binary):
if "[Content_Types].xml" in tempzip.namelist() and tempzip.read("[Content_Types].xml").find(b'application/vnd.openxmlformats-officedocument.spreadsheetml.sheet.main+xml') != -1:
return True
return False
except:
except Exception:
return False
@@ -1320,7 +1320,7 @@ class ExcelXls(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Microsoft Excel XLS file (%s)" % (data.nice_size(dataset.get_size()))
@@ -1341,7 +1341,7 @@ class Sra(Binary):
return True
else:
return False
except:
except Exception:
return False
def set_peek(self, dataset, is_multi_byte=False):
@@ -1355,7 +1355,7 @@ class Sra(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return 'Binary sra file (%s)' % (nice_size(dataset.get_size()))
@@ -1376,7 +1376,7 @@ class RData(Binary):
header = gzip.open(filename).read(7)
if header == rdata_header:
return True
except:
except Exception:
return False
@@ -1612,7 +1612,7 @@ class PostgresqlArchive(CompressedArchive):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "PostgreSQL Archive (%s)" % (nice_size(dataset.get_size()))
@@ -1669,7 +1669,7 @@ class Fast5Archive(CompressedArchive):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "FAST5 Archive (%s)" % (nice_size(dataset.get_size()))
@@ -1771,7 +1771,7 @@ class SearchGuiArchive(CompressedArchive):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "SearchGUI Archive, version %s" % (dataset.metadata.searchgui_version or 'unknown')
@@ -1795,7 +1795,7 @@ class NetCDF(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Binary netCDF file (%s)" % (nice_size(dataset.get_size()))
def sniff(self, filename):
@@ -1805,7 +1805,7 @@ class NetCDF(Binary):
if header == b'CDF':
return True
return False
except:
except Exception:
return False
@@ -1838,7 +1838,7 @@ class DMND(Binary):
if header == self._magic:
return True
return False
except:
except Exception:
return False
lib/galaxy/datatypes/constructive_solid_geometry.py
+4 -4
View File
@@ -111,7 +111,7 @@ class Ply(object):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Ply file (%s)" % (nice_size(dataset.get_size()))
@@ -301,7 +301,7 @@ class Vtk(object):
dataset.metadata.field_names.append(field_name)
try:
num_components = int(items[-1])
except:
except Exception:
num_components = 1
field_component_indexes = [str(i) for i in range(num_components)]
field_components[field_name] = field_component_indexes
@@ -319,7 +319,7 @@ class Vtk(object):
float(items[0])
# Don't process the cell data.
# 0.0123457 0.197531
except:
except Exception:
# Line consists of arrayName numComponents numTuples dataType.
# Example: surface_field1 1 12 double
field_name = items[0]
@@ -438,7 +438,7 @@ class Vtk(object):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Vtk file (%s)" % (nice_size(dataset.get_size()))
lib/galaxy/datatypes/converters/bed_to_gff_converter.py
+5 -5
View File
@@ -30,21 +30,21 @@ def __main__():
else:
try:
feature = elems[3]
except:
except Exception:
feature = 'feature%d' % (i + 1)
start = int(elems[1]) + 1
end = int(elems[2])
try:
score = elems[4]
except:
except Exception:
score = '0'
try:
strand = elems[5]
except:
except Exception:
strand = '+'
try:
group = elems[3]
except:
except Exception:
group = 'group%d' % (i + 1)
if complete_bed:
out.write('%s\tbed2gff\t%s\t%d\t%d\t%s\t%s\t.\t%s %s;\n' % (chrom, feature, start, end, score, strand, feature, group))
@@ -59,7 +59,7 @@ def __main__():
exon_start = int(start) + int(block_starts[j])
exon_end = exon_start + int(block_sizes[j]) - 1
out.write('%s\tbed2gff\texon\t%d\t%d\t%s\t%s\t.\texon %s;\n' % (chrom, exon_start, exon_end, score, strand, group))
except:
except Exception:
skipped_lines += 1
if not first_skipped_line:
first_skipped_line = i + 1
lib/galaxy/datatypes/converters/fastqsolexa_to_qual_converter.py
+2 -2
View File
@@ -68,10 +68,10 @@ def __main__():
# peek: ascii or digits?
val = line.split()[0]
fastq_integer = True
try:
int(val)
fastq_integer = True
except:
except ValueError:
fastq_integer = False
if fastq_integer: # digits
lib/galaxy/datatypes/converters/gff_to_bed_converter.py
+1 -1
View File
@@ -28,7 +28,7 @@ def __main__():
# Replace any spaces in the name with underscores so UCSC will not complain
name = elems[2].replace(" ", "_")
out.write("%s\t%s\t%s\t%s\t0\t%s\n" % (elems[0], start, elems[4], name, strand))
except:
except Exception:
skipped_lines += 1
if not first_skipped_line:
first_skipped_line = i + 1
lib/galaxy/datatypes/converters/interval_to_bed_converter.py
+7 -7
View File
@@ -19,23 +19,23 @@ def __main__():
input_name = sys.argv[2]
try:
chromCol = int(sys.argv[3]) - 1
except:
except Exception:
stop_err("'%s' is an invalid chrom column, correct the column settings before attempting to convert the data format." % str(sys.argv[3]))
try:
startCol = int(sys.argv[4]) - 1
except:
except Exception:
stop_err("'%s' is an invalid start column, correct the column settings before attempting to convert the data format." % str(sys.argv[4]))
try:
endCol = int(sys.argv[5]) - 1
except:
except Exception:
stop_err("'%s' is an invalid end column, correct the column settings before attempting to convert the data format." % str(sys.argv[5]))
try:
strandCol = int(sys.argv[6]) - 1
except:
except Exception:
strandCol = -1
try:
nameCol = int(sys.argv[7]) - 1
except:
except Exception:
nameCol = -1
skipped_lines = 0
first_skipped_line = 0
@@ -47,12 +47,12 @@ def __main__():
name = region.fields[nameCol]
else:
raise IndexError
except:
except Exception:
name = "region_%i" % count
try:
out.write("%s\t%i\t%i\t%s\t%i\t%s\n" % (region.chrom, region.start, region.end, name, 0, region.strand))
except:
except Exception:
skipped_lines += 1
if not first_skipped_line:
first_skipped_line = count + 1
lib/galaxy/datatypes/converters/interval_to_bedstrict_converter.py
+10 -10
View File
@@ -41,31 +41,31 @@ def __main__():
input_name = sys.argv[2]
try:
chromCol = int(sys.argv[3]) - 1
except:
except Exception:
stop_err("'%s' is an invalid chrom column, correct the column settings before attempting to convert the data format." % str(sys.argv[3]))
try:
startCol = int(sys.argv[4]) - 1
except:
except Exception:
stop_err("'%s' is an invalid start column, correct the column settings before attempting to convert the data format." % str(sys.argv[4]))
try:
endCol = int(sys.argv[5]) - 1
except:
except Exception:
stop_err("'%s' is an invalid end column, correct the column settings before attempting to convert the data format." % str(sys.argv[5]))
try:
strandCol = int(sys.argv[6]) - 1
except:
except Exception:
strandCol = -1
try:
nameCol = int(sys.argv[7]) - 1
except:
except Exception:
nameCol = -1
try:
extension = sys.argv[8]
except:
except IndexError:
extension = 'interval' # default extension
try:
force_num_columns = int(sys.argv[9])
except:
except Exception:
force_num_columns = None
skipped_lines = 0
@@ -116,7 +116,7 @@ def __main__():
fields2 = fields[11].rstrip(",").split(",") # remove trailing comma and split on comma
for field in fields2:
int(field)
except:
except Exception:
strict_bed = False
break
if force_num_columns is not None and len(fields) != force_num_columns:
@@ -137,14 +137,14 @@ def __main__():
name = region.fields[nameCol]
else:
raise IndexError
except:
except Exception:
name = "region_%i" % count
try:
fields = [str(item) for item in (region.chrom, region.start, region.end, name, 0, region.strand)]
if force_num_columns is not None and len(fields) != force_num_columns:
fields = force_bed_field_count(fields, count, force_num_columns)
out.write("%s\n" % '\t'.join(fields))
except:
except Exception:
skipped_lines += 1
if first_skipped_line is None:
first_skipped_line = count + 1
lib/galaxy/datatypes/converters/interval_to_coverage.py
+1 -1
View File
@@ -127,7 +127,7 @@ if __name__ == "__main__":
chr_col_1, start_col_1, end_col_1, strand_col_1 = [int(x) - 1 for x in options.cols1.split(',')]
chr_col_2, position_col_2, forward_col_2, reverse_col_2 = [int(x) - 1 for x in options.cols2.split(',')]
in_fname, out_fname = args
except:
except Exception:
doc_optparse.exception()
# Sort through a tempfile first
lib/galaxy/datatypes/converters/interval_to_fli.py
+1 -1
View File
@@ -48,7 +48,7 @@ def main():
try:
float(val)
continue
except:
except ValueError:
convert_gff_coords_to_bed(feature)
# Value is not a number, so it can be indexed.
if val not in name_loc_dict:
lib/galaxy/datatypes/converters/lped_to_fped_converter.py
+5 -5
View File
@@ -41,17 +41,17 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath):
outfpath = os.path.join(outfilepath, outf) # where to write the fbat format file to
try:
mf = open(inmap, 'r')
except:
except Exception:
sys.stderr.write('%s cannot open inmap file %s - do you have permission?\n' % (prog, inmap))
sys.exit(1)
try:
rsl = [x.split()[1] for x in mf]
except:
except Exception:
sys.stderr.write('## cannot parse %s' % inmap)
sys.exit(1)
try:
os.makedirs(outfilepath)
except:
except Exception:
pass # already exists
head = ' '.join(rsl) # list of rs numbers
# TODO add anno to rs but fbat will prolly barf?
@@ -64,7 +64,7 @@ def rgConv(inpedfilepath, outhtmlname, outfilepath):
lrow = row.split()
try:
[int(x) for x in lrow[10:50]] # look for non numeric codes
except:
except Exception:
dorecode = 1
if dorecode:
lrow = row.strip().split()
@@ -94,7 +94,7 @@ def main():
outfilepath = sys.argv[3]
try:
os.makedirs(outfilepath)
except:
except Exception:
pass
rgConv(inpedfilepath, outhtmlname, outfilepath)
flist = os.listdir(outfilepath)
lib/galaxy/datatypes/converters/lped_to_pbed_converter.py
+3 -3
View File
@@ -42,13 +42,13 @@ def getMissval(inped=''):
commonmissvals = {'N': 'N', '0': '0', 'n': 'n', '9': '9', '-': '-', '.': '.'}
try:
f = open(inped, 'r')
except:
except Exception:
return None # signal no in file
missval = None
while missval is None: # doggedly continue until we solve the mystery
try:
l = f.readline()
except:
except Exception:
break
ll = l.split()[6:] # ignore pedigree stuff
for c in ll:
@@ -94,7 +94,7 @@ def main():
outfilepath = sys.argv[3]
try:
os.makedirs(outfilepath)
except:
except Exception:
pass
plink = sys.argv[4]
rgConv(inpedfilepath, outhtmlname, outfilepath, plink)
lib/galaxy/datatypes/converters/pbed_ldreduced_converter.py
+2 -2
View File
@@ -48,7 +48,7 @@ def pruneLD(plinktasks=[], cd='./', vclbase=[]):
alog += lplog
alog.append('\n')
os.unlink(plog) # no longer needed
except:
except Exception:
alog.append('### %s Strange - no std out from plink when running command line\n%s\n' % (timenow(), ' '.join(vcl)))
return alog
@@ -92,7 +92,7 @@ def main():
outfilepath = sys.argv[6]
try:
os.makedirs(outfilepath)
except:
except Exception:
pass
plink = sys.argv[7]
makeLDreduced(base_name, infpath=inpedfilepath, outfpath=outfilepath, plinke=plink, forcerebuild=False, returnFname=False,
lib/galaxy/datatypes/converters/pbed_to_lped_converter.py
+1 -1
View File
@@ -60,7 +60,7 @@ def main():
outfilepath = sys.argv[3]
try:
os.makedirs(outfilepath)
except:
except Exception:
pass
plink = sys.argv[4]
rgConv(inpedfilepath, outhtmlname, outfilepath, plink)
lib/galaxy/datatypes/data.py
+7 -7
View File
@@ -179,7 +179,7 @@ class Data(object):
def set_max_optional_metadata_filesize(self, max_value):
try:
max_value = int(max_value)
except:
except (TypeError, ValueError):
return
self.__class__._max_optional_metadata_filesize = max_value
@@ -394,7 +394,7 @@ class Data(object):
if not mime:
try:
mime = trans.app.datatypes_registry.get_mimetype_by_extension(".".split(file_path)[-1])
except:
except Exception:
mime = "text/plain"
self._clean_and_set_mime_type(trans, mime)
return self._yield_user_file_content(trans, data, file_path)
@@ -490,7 +490,7 @@ class Data(object):
info = unicodify(info, 'utf-8')
return info
except:
except Exception:
return "info unavailable"
def validate(self, dataset):
@@ -521,7 +521,7 @@ class Data(object):
self.supported_display_apps = self.supported_display_apps.copy()
try:
del self.supported_display_apps[app_id]
except:
except Exception:
log.exception('Tried to remove display app %s from datatype %s, but this display app is not declared.', type, self.__class__.__name__)
def clear_display_apps(self):
@@ -551,7 +551,7 @@ class Data(object):
"""Returns primary label for display app"""
try:
return self.supported_display_apps[type]['label']
except:
except Exception:
return 'unknown'
def as_display_type(self, dataset, type, **kwd):
@@ -559,7 +559,7 @@ class Data(object):
try:
if type in self.get_display_types():
return getattr(self, self.supported_display_apps[type]['file_function'])(dataset, **kwd)
except:
except Exception:
log.exception('Function %s is referred to in datatype %s for displaying as type %s, but is not accessible', self.supported_display_apps[type]['file_function'], self.__class__.__name__, type)
return "This display type (%s) is not implemented for this datatype (%s)." % (type, dataset.ext)
@@ -573,7 +573,7 @@ class Data(object):
try:
if app.config.enable_old_display_applications and type in self.get_display_types():
return target_frame, getattr(self, self.supported_display_apps[type]['links_function'])(dataset, type, app, base_url, **kwd)
except:
except Exception:
log.exception('Function %s is referred to in datatype %s for generating links for type %s, but is not accessible',
self.supported_display_apps[type]['links_function'], self.__class__.__name__, type)
return target_frame, []
lib/galaxy/datatypes/dataproviders/external.py
+4 -1
View File
@@ -7,7 +7,7 @@ import logging
import subprocess
import tempfile
from six.moves.urllib.parse import urlencode
from six.moves.urllib.parse import urlencode, urlparse
from six.moves.urllib.request import urlopen
from . import (
@@ -112,6 +112,9 @@ class URLDataProvider(base.DataProvider):
self.data = data or {}
encoded_data = urlencode(self.data)
scheme = urlparse(url).scheme
assert scheme in ('http', 'https', 'ftp'), 'Invalid URL scheme: %s' % scheme
if method == 'GET':
self.url += '?%s' % (encoded_data)
opened = urlopen(url)
lib/galaxy/datatypes/display_applications/application.py
+3 -3
View File
@@ -122,7 +122,7 @@ class DynamicDisplayApplicationBuilder(object):
id_col = elem.get('id', None)
try:
id_col = int(id_col)
except:
except (TypeError, ValueError):
if data_table:
if id_col is None:
id_col = data_table.columns.get('id', None)
@@ -130,14 +130,14 @@ class DynamicDisplayApplicationBuilder(object):
id_col = data_table.columns.get('value', None)
try:
id_col = int(id_col)
except:
except (TypeError, ValueError):
# id is set to a string or None, use column by that name if available
id_col = data_table.columns.get(id_col, None)
id_col = int(id_col)
name_col = elem.get('name', None)
try:
name_col = int(name_col)
except:
except (TypeError, ValueError):
if data_table:
if name_col is None:
name_col = data_table.columns.get('name', None)
lib/galaxy/datatypes/genetics.py
+9 -9
View File
@@ -126,7 +126,7 @@ class GenomeGraphs(Tabular):
hasheader = 0
try:
['%f' % x for x in d[0][1:]] # first is name - see if starts all numerics
except:
except Exception:
hasheader = 1
# Generate column header
out.append('<tr>')
@@ -158,7 +158,7 @@ class GenomeGraphs(Tabular):
for j, x in enumerate(ll):
try:
x = float(x)
except:
except Exception:
badvals.append('col%d:%s' % (j + 1, x))
if len(badvals) > 0:
errors.append('row %d, %s' % (' '.join(badvals)))
@@ -331,13 +331,13 @@ class Rgenetics(Html):
return True
try:
efp = dataset.extra_files_path
except:
except Exception:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
return False
try:
flist = os.listdir(efp)
except:
except Exception:
if verbose:
gal_Log.debug('@@@rgenetics set_meta failed %s - dataset %s has no efp ?' % (sys.exc_info()[0], dataset.name))
return False
@@ -655,7 +655,7 @@ class RexpBase(Html):
pp = os.path.join(dataset.extra_files_path, '%s.pheno' % dataset.metadata.base_name)
try:
p = open(pp, 'r').readlines()
except:
except Exception:
p = ['##failed to find %s' % pp, ]
dataset.peek = ''.join(p[:5])
dataset.blurb = 'Galaxy Rexpression composite file'
@@ -670,7 +670,7 @@ class RexpBase(Html):
pp = os.path.join(dataset.extra_files_path, '%s.pheno' % dataset.metadata.base_name)
try:
p = open(pp, 'r').readlines()
except:
except Exception:
p = ['##failed to find %s' % pp]
return ''.join(p[:5])
@@ -681,7 +681,7 @@ class RexpBase(Html):
h = '## rexpression get_file_peek: no file found'
try:
h = open(filename, 'r').readlines()
except:
except Exception:
pass
return ''.join(h[:5])
@@ -713,7 +713,7 @@ class RexpBase(Html):
Html.set_meta(self, dataset, **kwd)
try:
flist = os.listdir(dataset.extra_files_path)
except:
except Exception:
if verbose:
gal_Log.debug('@@@rexpression set_meta failed - no dataset?')
return False
@@ -731,7 +731,7 @@ class RexpBase(Html):
dataset.metadata.pheno_path = pp
try:
pf = open(pp, 'r').readlines() # read the basename.phenodata in the extra_files_path
except:
except Exception:
pf = None
if pf:
h = pf[0].strip()
lib/galaxy/datatypes/images.py
+2 -2
View File
@@ -225,7 +225,7 @@ class Gmaj(data.Data):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "peek unavailable"
def get_mime(self):
@@ -285,5 +285,5 @@ class Laj(data.Text):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "peek unavailable"
lib/galaxy/datatypes/interval.py
+42 -42
View File
@@ -111,20 +111,20 @@ class Interval(Tabular):
int(elems[1])
if overwrite or not dataset.metadata.element_is_set('startCol'):
dataset.metadata.startCol = 2
except:
except Exception:
pass # Metadata default will be used
try:
int(elems[2])
if overwrite or not dataset.metadata.element_is_set('endCol'):
dataset.metadata.endCol = 3
except:
except Exception:
pass # Metadata default will be used
# we no longer want to guess that this column is the 'name', name must now be set manually for interval files
# we will still guess at the strand, as we can make a more educated guess
# if len( elems ) > 3:
# try:
# int( elems[3] )
# except:
# except Exception:
# if overwrite or not dataset.metadata.element_is_set( 'nameCol' ):
# dataset.metadata.nameCol = 4
if len(elems) < 6 or elems[5] not in data.valid_strand:
@@ -149,7 +149,7 @@ class Interval(Tabular):
and dataset.metadata.chromCol \
and dataset.metadata.startCol \
and dataset.metadata.endCol
except:
except Exception:
return False
def get_estimated_display_viewport(self, dataset, chrom_col=None, start_col=None, end_col=None):
@@ -331,10 +331,10 @@ class Interval(Tabular):
# respectively ( for 0 based columns )
int(hdr[1])
int(hdr[2])
except:
except Exception:
return False
return True
except:
except Exception:
return False
def get_track_resolution(self, dataset, start, end):
@@ -458,14 +458,14 @@ class Bed(Interval):
fields2 = fields[11].rstrip(",").split(",") # remove trailing comma and split on comma
for field in fields2:
int(field)
except:
except Exception:
return Interval.as_ucsc_display_file(self, dataset)
# only check first line for proper form
break
try:
return open(dataset.file_name)
except:
except Exception:
return "This item contains no content"
def sniff(self, filename):
@@ -510,7 +510,7 @@ class Bed(Interval):
try:
int(hdr[1])
int(hdr[2])
except:
except Exception:
return False
if len(hdr) > 4:
# hdr[3] is a string, 'name', which defines the name of the BED line - difficult to test for this.
@@ -518,7 +518,7 @@ class Bed(Interval):
try:
if int(hdr[4]) < 0 or int(hdr[4]) > 1000:
return False
except:
except Exception:
return False
if len(hdr) > 5:
# hdr[5] is strand
@@ -528,48 +528,48 @@ class Bed(Interval):
# hdr[6] is thickStart, the starting position at which the feature is drawn thickly.
try:
int(hdr[6])
except:
except Exception:
return False
if len(hdr) > 7:
# hdr[7] is thickEnd, the ending position at which the feature is drawn thickly
try:
int(hdr[7])
except:
except Exception:
return False
if len(hdr) > 8:
# hdr[8] is itemRgb, an RGB value of the form R,G,B (e.g. 255,0,0). However, this could also be an int (e.g., 0)
try:
int(hdr[8])
except:
except Exception:
try:
hdr[8].split(',')
except:
except Exception:
return False
if len(hdr) > 9:
# hdr[9] is blockCount, the number of blocks (exons) in the BED line.
try:
block_count = int(hdr[9])
except:
except Exception:
return False
if len(hdr) > 10:
# hdr[10] is blockSizes - A comma-separated list of the block sizes.
# Sometimes the blosck_sizes and block_starts lists end in extra commas
try:
block_sizes = hdr[10].rstrip(',').split(',')
except:
except Exception:
return False
if len(hdr) > 11:
# hdr[11] is blockStarts - A comma-separated list of block starts.
try:
block_starts = hdr[11].rstrip(',').split(',')
except:
except Exception:
return False
if len(block_sizes) != block_count or len(block_starts) != block_count:
return False
else:
return False
return True
except:
except Exception:
return False
@@ -678,15 +678,15 @@ class Gff(Tabular, _RemoteCallMixin):
# Try int.
int(value)
value_type = "int"
except:
except ValueError:
try:
# Try float.
float(value)
value_type = "float"
except:
except ValueError:
pass
attribute_types[name] = value_type
except:
except Exception:
pass
if i + 1 == num_lines:
break
@@ -708,7 +708,7 @@ class Gff(Tabular, _RemoteCallMixin):
int(elems[3])
int(elems[4])
break
except:
except Exception:
pass
Tabular.set_meta(self, dataset, overwrite=overwrite, skip=i)
@@ -771,7 +771,7 @@ class Gff(Tabular, _RemoteCallMixin):
# Make sure we have not spanned chromosomes
start = min(start, int(elems[3]))
stop = max(stop, int(elems[4]))
except:
except Exception:
# most likely start/stop is not an int or not enough fields
pass
# make sure we are at the next new line
@@ -848,19 +848,19 @@ class Gff(Tabular, _RemoteCallMixin):
try:
int(hdr[3])
int(hdr[4])
except:
except Exception:
return False
if hdr[5] != '.':
try:
float(hdr[5])
except:
except Exception:
return False
if hdr[6] not in data.valid_strand:
return False
if hdr[7] not in self.valid_gff_frame:
return False
return True
except:
except Exception:
return False
# ------------- Dataproviders
@@ -919,13 +919,13 @@ class Gff3(Gff):
try:
start = int(elems[3])
valid_start = True
except:
except Exception:
if elems[3] == '.':
valid_start = True
try:
end = int(elems[4])
valid_end = True
except:
except Exception:
if elems[4] == '.':
valid_end = True
strand = elems[6]
@@ -982,18 +982,18 @@ class Gff3(Gff):
return False
try:
int(hdr[3])
except:
except Exception:
if hdr[3] != '.':
return False
try:
int(hdr[4])
except:
except Exception:
if hdr[4] != '.':
return False
if hdr[5] != '.':
try:
float(hdr[5])
except:
except Exception:
return False
if hdr[6] not in self.valid_gff3_strand:
return False
@@ -1001,7 +1001,7 @@ class Gff3(Gff):
return False
parse_gff3_attributes(hdr[8])
return True
except:
except Exception:
return False
@@ -1055,12 +1055,12 @@ class Gtf(Gff):
try:
int(hdr[3])
int(hdr[4])
except:
except Exception:
return False
if hdr[5] != '.':
try:
float(hdr[5])
except:
except Exception:
return False
if hdr[6] not in data.valid_strand:
return False
@@ -1077,7 +1077,7 @@ class Gtf(Gff):
else:
return False
return True
except:
except Exception:
return False
@@ -1140,7 +1140,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
start = min(int(fields[0]), start)
end = max(end, int(fields[0]) + span)
viewport_feature_count -= 1
except:
except Exception:
pass
# make sure we are at the next new line
readline_count = VIEWPORT_MAX_READS_PER_LINE
@@ -1199,7 +1199,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
try:
float(elems[0]) # "Wiggle track data values can be integer or real, positive or negative values"
break
except:
except Exception:
do_break = False
for col_startswith in data.col1_startswith:
if elems[0].lower().startswith(col_startswith):
@@ -1244,7 +1244,7 @@ class Wiggle(Tabular, _RemoteCallMixin):
if len(hdr) > 1 and hdr[0] == 'track' and hdr[1].startswith('type=wiggle'):
return True
return False
except:
except Exception:
return False
def get_track_resolution(self, dataset, start, end):
@@ -1394,7 +1394,7 @@ class CustomTrack (Tabular):
return False
else:
return False
except:
except Exception:
return False
else:
try:
@@ -1404,9 +1404,9 @@ class CustomTrack (Tabular):
try:
int(hdr[1])
int(hdr[2])
except:
except Exception:
return False
except:
except Exception:
return False
return True
@@ -1539,7 +1539,7 @@ class ScIdx(Tabular):
count += 1
if count < 100 and count > 0:
return True
except:
except Exception:
return False
finally:
fh.close()
lib/galaxy/datatypes/molecules.py
+4 -4
View File
@@ -33,7 +33,7 @@ def count_special_lines(word, filename, invert=False):
cmd.extend([word, filename])
out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
return int(out.communicate()[0].split()[0])
except:
except Exception:
pass
return 0
@@ -48,7 +48,7 @@ def count_lines(filename, non_empty=False):
else:
out = subprocess.Popen(['wc', '-l', filename], stdout=subprocess.PIPE)
return int(out.communicate()[0].split()[0])
except:
except Exception:
pass
return 0
@@ -427,7 +427,7 @@ class OBFS(Binary):
"""Create HTML content, used for displaying peek."""
try:
return dataset.peek
except:
except Exception:
return "OpenBabel Fastsearch Index"
def display_data(self, trans, data, preview=False, filename=None,
@@ -702,7 +702,7 @@ class SMILES(Tabular):
# if we have atoms, we have a molecule
if not len(pybel.readstring('smi', smiles).atoms) > 0:
return False
except:
except Exception:
# if convert fails its not a smiles string
return False
return True
lib/galaxy/datatypes/msa.py
+2 -2
View File
@@ -26,7 +26,7 @@ class Hmmer(Text):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "HMMER database (%s)" % (nice_size(dataset.get_size()))
@abc.abstractmethod
@@ -77,7 +77,7 @@ class HmmerPress(Binary):
"""Create HTML content, used for displaying peek."""
try:
return dataset.peek
except:
except Exception:
return "HMMER3 database (multiple files)"
def __init__(self, **kwd):
lib/galaxy/datatypes/ngsindex.py
+1 -1
View File
@@ -55,7 +55,7 @@ class BowtieIndex(Html):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Bowtie index file"
lib/galaxy/datatypes/plant_tribes.py
+2 -2
View File
@@ -18,7 +18,7 @@ class Smat(Text):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "ESTScan scores matrices (%s)" % (nice_size(dataset.get_size()))
def set_peek(self, dataset, is_multi_byte=False):
@@ -98,7 +98,7 @@ class PlantTribesKsComponents(Tabular):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Significant components in the Ks distribution (%s)" % (nice_size(dataset.get_size()))
def set_meta(self, dataset, **kwd):
lib/galaxy/datatypes/proteomics.py
+48 -2
View File
@@ -285,7 +285,7 @@ class ThermoRAW(Binary):
if header.find(finnigan) != -1:
return True
return False
except:
except Exception:
return False
def set_peek(self, dataset, is_multi_byte=False):
@@ -299,7 +299,7 @@ class ThermoRAW(Binary):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Thermo Finnigan RAW file (%s)" % (nice_size(dataset.get_size()))
@@ -464,3 +464,49 @@ class ImzML(Binary):
rval.append('<li><a href="%s" type="text/plain">%s</a>%s</li>' % (fn, fn, opt_text))
rval.append('</ul></div></html>')
return "\n".join(rval)
class Analyze75(Binary):
"""
Mayo Analyze 7.5 files
http://www.imzml.org
"""
file_ext = 'analyze75'
allow_datatype_change = False
composite_type = 'auto_primary_file'
def __init__(self, **kwd):
Binary.__init__(self, **kwd)
"""The header file. Provides information about dimensions, identification, and processing history."""
self.add_composite_file(
'hdr',
description='The Analyze75 header file.',
is_binary=False)
"""The image file. Image data, whose data type and ordering are described by the header file."""
self.add_composite_file(
'img',
description='The Analyze75 image file.',
is_binary=True)
"""The optional t2m file."""
self.add_composite_file(
't2m',
description='The Analyze75 t2m file.',
optional='True', is_binary=True)
def generate_primary_file(self, dataset=None):
rval = ['<html><head><title>Analyze75 Composite Dataset.</title></head><p/>']
rval.append('<div>This composite dataset is composed of the following files:<p/><ul>')
for composite_name, composite_file in self.get_composite_files(dataset=dataset).iteritems():
fn = composite_name
opt_text = ''
if composite_file.optional:
opt_text = ' (optional)'
if composite_file.get('description'):
rval.append('<li><a href="%s" type="text/plain">%s (%s)</a>%s</li>' % (fn, fn, composite_file.get('description'), opt_text))
else:
rval.append('<li><a href="%s" type="text/plain">%s</a>%s</li>' % (fn, fn, opt_text))
rval.append('</ul></div></html>')
return "\n".join(rval)
lib/galaxy/datatypes/qualityscore.py
+4 -4
View File
@@ -56,7 +56,7 @@ class QualityScoreSOLiD (QualityScore):
if not(readlen):
readlen = len(line.split())
assert len(line.split()) == readlen # SOLiD reads should be of the same length
except:
except Exception:
break
goodblock += 1
if goodblock > 10:
@@ -64,7 +64,7 @@ class QualityScoreSOLiD (QualityScore):
else:
break # we found a non-empty line, but it's not a header
fh.close()
except:
except Exception:
pass
return False
@@ -106,13 +106,13 @@ class QualityScore454 (QualityScore):
break
try:
[int(x) for x in line.split()]
except:
except Exception:
break
return True
else:
break # we found a non-empty line, but it's not a header
fh.close()
except:
except Exception:
pass
return False
lib/galaxy/datatypes/sequence.py
+11 -11
View File
@@ -81,7 +81,7 @@ class SequenceSplitLocations(data.Text):
if 'start' not in section or 'end' not in section or 'sequences' not in section:
return False
return True
except:
except Exception:
pass
return False
@@ -376,7 +376,7 @@ class Fasta(Sequence):
else:
break # we found a non-empty line, but it's not a fasta header
fh.close()
except:
except Exception:
pass
return False
@@ -543,7 +543,7 @@ class csFasta(Sequence):
else:
break # we found a non-empty line, but it's not a header
fh.close()
except:
except Exception:
pass
return False
@@ -634,7 +634,7 @@ class BaseFastq (Sequence):
return False
return True
return False
except:
except Exception:
return False
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
@@ -930,7 +930,7 @@ class Maf(Alignment):
return True
else:
return False
except:
except Exception:
return False
@@ -968,7 +968,7 @@ class MafCustomTrack(data.Text):
dataset.metadata.vp_chromosome = chrom
dataset.metadata.vp_start = forward_strand_start
dataset.metadata.vp_end = forward_strand_end
except:
except Exception:
pass
@@ -1019,7 +1019,7 @@ class Axt(data.Text):
return False
try:
map(int, [hdr[0], hdr[2], hdr[3], hdr[5], hdr[6], hdr[8]])
except:
except Exception:
return False
if hdr[7] not in data.valid_strand:
return False
@@ -1060,7 +1060,7 @@ class Lav(data.Text):
return True
else:
return False
except:
except Exception:
return False
@@ -1205,7 +1205,7 @@ class Genbank(data.Text):
try:
with open(filename, 'r') as handle:
return 'LOCUS ' == handle.read(6)
except:
except Exception:
pass
return False
@@ -1236,7 +1236,7 @@ class MemePsp(Sequence):
for item in l.split():
try:
float(item)
except:
except ValueError:
return False
return True
try:
@@ -1269,7 +1269,7 @@ class MemePsp(Sequence):
# We found a non-empty line,
# but it's not a psp id width.
return False
except:
except Exception:
return False
# We've reached EOF in less than 100 lines.
return True
lib/galaxy/datatypes/sniff.py
+3 -3
View File
@@ -54,7 +54,7 @@ def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source
is_multi_byte = False
try:
codecs.lookup(target_encoding)
except:
except Exception:
target_encoding = util.DEFAULT_ENCODING # utf-8
if not source_encoding:
source_encoding = util.DEFAULT_ENCODING # sys.getdefaultencoding() would mimic old behavior (defaults to ascii)
@@ -70,7 +70,7 @@ def stream_to_open_named_file(stream, fd, filename, source_encoding=None, source
try:
if text_type(chunk[:2]) == text_type(util.gzip_magic):
is_compressed = True
except:
except Exception:
pass
if not is_compressed:
# See if we have a multi-byte character file
@@ -408,7 +408,7 @@ def guess_ext(fname, sniff_order, is_multi_byte=False):
if datatype.sniff(fname):
file_ext = datatype.file_ext
break
except:
except Exception:
pass
# Ugly hack for tsv vs tabular sniffing, we want to prefer tabular
# to tsv but it doesn't have a sniffer - is TSV was sniffed just check
lib/galaxy/datatypes/tabular.py
+11 -11
View File
@@ -62,7 +62,7 @@ class TabularData(data.Text):
and dataset.state == dataset.states.OK \
and dataset.metadata.columns > 0 \
and dataset.metadata.data_lines != 0
except:
except Exception:
return False
def get_chunk(self, trans, dataset, offset=0, ck_size=None):
@@ -156,7 +156,7 @@ class TabularData(data.Text):
if isinstance(spec.param, metadata.ColumnParameter):
try:
i = int(getattr(dataset.metadata, name)) - 1
except:
except Exception:
i = -1
if 0 <= i < columns and column_headers[i] is None:
column_headers[i] = column_parameter_alias.get(name, name)
@@ -294,14 +294,14 @@ class Tabular(TabularData):
try:
int(column_text)
return True
except:
except ValueError:
return False
def is_float(column_text):
try:
float(column_text)
return True
except:
except ValueError:
if column_text.strip().lower() == 'na':
return True # na is special cased to be a float
return False
@@ -488,7 +488,7 @@ class Sam(Tabular):
fh.close()
if count < 5 and count > 0:
return True
except:
except Exception:
pass
return False
@@ -650,10 +650,10 @@ class Pileup(Tabular):
chrom = int(hdr[1])
assert chrom >= 0
assert hdr[2] in ['A', 'C', 'G', 'T', 'N', 'a', 'c', 'g', 't', 'n']
except:
except Exception:
return False
return True
except:
except Exception:
return False
# Dataproviders
@@ -919,14 +919,14 @@ class BaseCSV(TabularData):
try:
int(column_text)
return True
except:
except ValueError:
return False
def is_float(self, column_text):
try:
float(column_text)
return True
except:
except ValueError:
if column_text.strip().lower() == 'na':
return True # na is special cased to be a float
return False
@@ -990,7 +990,7 @@ class BaseCSV(TabularData):
if not csv.Sniffer().has_header(open(filename, 'r').read(self.big_peek_size)):
return False
return True
except:
except Exception:
# Not readable by Python's csv using this dialect
return False
@@ -1137,7 +1137,7 @@ class ConnectivityTable(Tabular):
j += 1
i += 1
return False
except:
except Exception:
return False
def get_chunk(self, trans, dataset, chunk):
lib/galaxy/datatypes/text.py
+5 -5
View File
@@ -55,7 +55,7 @@ class Html(Text):
if hdr and hdr[0].lower().find('<html>') >= 0:
return True
return False
except:
except Exception:
return True
@@ -104,7 +104,7 @@ class Json(Text):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "JSON file (%s)" % (nice_size(dataset.get_size()))
@@ -130,7 +130,7 @@ class Ipynb(Json):
return True
else:
return False
except:
except Exception:
return False
def display_data(self, trans, dataset, preview=False, filename=None, to_ext=None, **kwd):
@@ -420,7 +420,7 @@ class SnpEffDb(Text):
if m:
snpeff_version = m.groups()[0] + m.groups()[1]
fh.close()
except:
except Exception:
pass
return snpeff_version
@@ -465,7 +465,7 @@ class SnpEffDb(Text):
fh.write("annotations: %s\n" % ','.join(annotations))
if regulations:
fh.write("regulations: %s\n" % ','.join(regulations))
except:
except Exception:
pass
lib/galaxy/datatypes/tracks.py
+1 -1
View File
@@ -78,7 +78,7 @@ class UCSCTrackHub(Html):
def display_peek(self, dataset):
try:
return dataset.peek
except:
except Exception:
return "Track Hub structure: Visualization in UCSC Track Hub"
def sniff(self, filename):
lib/galaxy/datatypes/util/generic_util.py
+1 -1
View File
@@ -14,6 +14,6 @@ def count_special_lines(word, filename, invert=False):
cmd.extend([word, filename])
out = subprocess.Popen(cmd, stdout=subprocess.PIPE)
return int(out.communicate()[0].split()[0])
except:
except Exception:
pass
return 0
lib/galaxy/dependencies/__init__.py
+1 -1
View File
@@ -63,7 +63,7 @@ class ConditionalDependencies(object):
try:
name = name.replace('-', '_').replace('.', '_')
return getattr(self, 'check_' + name)()
except:
except Exception:
return False
def check_psycopg2(self):
lib/galaxy/dependencies/dev-requirements.txt
+1
View File
@@ -2,6 +2,7 @@
nose
NoseHTML
twill==0.9.1
testfixtures
mock
selenium
watchdog
lib/galaxy/dependencies/pinned-requirements.txt
+11 -5
View File
@@ -25,19 +25,18 @@ WebOb==1.4.1
WebHelpers==1.3
Mako==1.0.2
pytz==2015.4
Babel==2.4.0
Babel==2.5.1
Beaker==1.7.0
dictobj==0.3.1
nose==1.3.7
Parsley==1.3
six==1.10.0
Whoosh==2.7.4
testfixtures==4.10.0
galaxy_sequence_utils==1.0.2
h5py==2.7.1
# pykwalify and dependencies
pykwalify==1.5.1
pykwalify==1.6.0
python-dateutil==2.5.3
docopt==0.6.2
@@ -45,11 +44,18 @@ docopt==0.6.2
Cheetah==2.4.4
Markdown==2.6.3
# Requests and dependencies
requests==2.18.4
certifi==2017.7.27.1
urllib3==1.22
chardet==3.0.4
idna==2.6
# BioBlend and dependencies
bioblend==0.7.0
boto==2.38.0
requests==2.10.0
requests-toolbelt==0.4.0
requests-toolbelt==0.8.0
# kombu and dependencies
kombu==3.0.30
lib/galaxy/jobs/__init__.py
+4 -4
View File
@@ -1166,7 +1166,7 @@ class JobWrapper(object, HasResourceParameters):
# TODO: After failing here, consider returning from the function.
try:
self.reclaim_ownership()
except:
except Exception:
log.exception('(%s) Failed to change ownership of %s, failing' % (job.id, self.working_directory))
return self.fail(job.info, stdout=stdout, stderr=stderr, exit_code=tool_exit_code)
@@ -1316,7 +1316,7 @@ class JobWrapper(object, HasResourceParameters):
dataset.set_peek(line_count=context['line_count'], is_multi_byte=True)
else:
dataset.set_peek(line_count=context['line_count'])
except:
except Exception:
if (not dataset.datatype.composite_type and dataset.dataset.is_multi_byte()) or self.tool.is_multi_byte:
dataset.set_peek(is_multi_byte=True)
else:
@@ -1467,7 +1467,7 @@ class JobWrapper(object, HasResourceParameters):
galaxy.tools.imp_exp.JobImportHistoryArchiveWrapper(self.app, self.job_id).cleanup_after_job()
if delete_files:
self.app.object_store.delete(self.get_job(), base_dir='job_work', entire_dir=True, dir_only=True, obj_dir=True)
except:
except Exception:
log.exception("Unable to cleanup job %d", self.job_id)
def _collect_extra_files(self, dataset, job_working_directory):
@@ -1765,7 +1765,7 @@ class JobWrapper(object, HasResourceParameters):
if external_chown_script and job.user is not None:
try:
self._change_ownership(self.user_system_pwent[0], str(self.user_system_pwent[3]))
except:
except Exception:
log.exception('(%s) Failed to change ownership of %s, making world-writable instead' % (job.id, self.working_directory))
os.chmod(self.working_directory, 0o777)
lib/galaxy/jobs/deferred/__init__.py
+3 -3
View File
@@ -39,7 +39,7 @@ class DeferredJobQueue(object):
module_name = 'galaxy.jobs.deferred.' + name
try:
module = __import__(module_name)
except:
except ImportError:
log.exception('Deferred job plugin appears to exist but is not loadable: %s', module_name)
continue
for comp in module_name.split(".")[1:]:
@@ -76,7 +76,7 @@ class DeferredJobQueue(object):
while self.running:
try:
self.__monitor_step()
except:
except Exception:
log.exception('Exception in monitor_step')
self.sleeper.sleep(1)
log.info('job queue stopped')
@@ -100,7 +100,7 @@ class DeferredJobQueue(object):
# Recovered jobs are passed in by ID
assert type(job) is int
job = self.sa_session.query(model.DeferredJob).get(job)
except:
except Exception:
pass
if job.is_check_time:
try:
lib/galaxy/jobs/handler.py
+22 -9
View File
@@ -1,20 +1,33 @@
"""
Galaxy job handler, prepares, runs, tracks, and finishes Galaxy jobs
"""
import datetime
import os
import time
import logging
import os
import threading
from Queue import Queue, Empty
import time
from Queue import (
Empty,
Queue
)
from sqlalchemy.sql.expression import and_, or_, select, func, true, null
from sqlalchemy.sql.expression import (
and_,
func,
null,
or_,
select,
true
)
from galaxy import model
from galaxy.util.sleeper import Sleeper
from galaxy.jobs import JobWrapper, TaskWrapper, JobDestination
from galaxy.jobs import (
JobDestination,
JobWrapper,
TaskWrapper
)
from galaxy.jobs.mapper import JobNotReadyException
from galaxy.util.sleeper import Sleeper
log = logging.getLogger(__name__)
@@ -196,7 +209,7 @@ class JobHandlerQueue(object):
# to the sleep.
if not self.app.job_manager.job_lock:
self.__monitor_step()
except:
except Exception:
log.exception("Exception in monitor_step")
# Sleep
self.sleeper.sleep(1)
@@ -703,7 +716,7 @@ class JobHandlerStopQueue(object):
while self.running:
try:
self.monitor_step()
except:
except Exception:
log.exception("Exception in monitor_step")
# Sleep
self.sleeper.sleep(1)
lib/galaxy/jobs/output_checker.py
+3 -3
View File
@@ -1,9 +1,9 @@
import re
from .error_level import StdioErrorLevel
import traceback
from logging import getLogger
from .error_level import StdioErrorLevel
log = getLogger(__name__)
@@ -126,7 +126,7 @@ def check_output(tool, stdout, stderr, tool_exit_code, job):
success = True
# On any exception, return True.
except:
except Exception:
tb = traceback.format_exc()
log.warning("Tool check encountered unexpected exception; " +
"assuming tool was successful: " + tb)
lib/galaxy/jobs/runners/__init__.py
+29 -23
View File
@@ -1,28 +1,34 @@
"""
Base classes for job runner plugins.
"""
import os
import time
import string
import logging
import datetime
import threading
import logging
import os
import string
import subprocess
from Queue import Queue, Empty
import threading
import time
from Queue import (
Empty,
Queue
)
import galaxy.jobs
from galaxy.jobs.command_factory import build_command
from galaxy import model
from galaxy.util import DATABASE_MAX_STRING_SIZE, shrink_stream_by_size
from galaxy.util import in_directory
from galaxy.util import ParamsWithSpecs
from galaxy.util import ExecutionTimer
from galaxy.util.bunch import Bunch
from galaxy.jobs.runners.util.job_script import write_script
from galaxy.jobs.runners.util.job_script import job_script
from galaxy.jobs.command_factory import build_command
from galaxy.jobs.runners.util.env import env_to_statement
from galaxy.jobs.runners.util.job_script import (
job_script,
write_script
)
from galaxy.util import (
DATABASE_MAX_STRING_SIZE,
ExecutionTimer,
in_directory,
ParamsWithSpecs,
shrink_stream_by_size
)
from galaxy.util.bunch import Bunch
from .state_handler_factory import build_state_handlers
@@ -94,15 +100,15 @@ class BaseJobRunner(object):
else:
# arg should be a JobWrapper/TaskWrapper
job_id = arg.get_id_tag()
except:
except Exception:
job_id = 'unknown'
try:
name = method.__name__
except:
except Exception:
name = 'unknown'
try:
method(arg)
except:
except Exception:
log.exception("(%s) Unhandled exception calling %s" % (job_id, name))
# Causes a runner's `queue_job` method to be called from a worker thread
@@ -366,7 +372,7 @@ class BaseJobRunner(object):
handler(self.app, self, job_state)
if job_state.runner_state_handled:
break
except:
except Exception:
log.exception('Caught exception in runner state handler')
def fail_job(self, job_state, exception=False):
@@ -610,14 +616,14 @@ class AsynchronousJobRunner(BaseJobRunner):
try:
# This should be an 8-bit exit code, but read ahead anyway:
exit_code_str = open(job_state.exit_code_file, "r").read(32)
except:
except Exception:
# By default, the exit code is 0, which typically indicates success.
exit_code_str = "0"
try:
# Decode the exit code. If it's bogus, then just use 0.
exit_code = int(exit_code_str)
except:
except ValueError:
log.warning("(%s/%s) Exit code '%s' invalid. Using 0." % (galaxy_id_tag, external_job_id, exit_code_str))
exit_code = 0
@@ -628,7 +634,7 @@ class AsynchronousJobRunner(BaseJobRunner):
try:
job_state.job_wrapper.finish(stdout, stderr, exit_code)
except:
except Exception:
log.exception("(%s/%s) Job wrapper finish method failed" % (galaxy_id_tag, external_job_id))
job_state.job_wrapper.fail("Unable to finish job", exception=True)
lib/galaxy/jobs/runners/cli.py
+1 -1
View File
@@ -82,7 +82,7 @@ class ShellJobRunner(AsynchronousJobRunner):
try:
self.write_executable_script(ajs.job_file, script)
except:
except Exception:
log.exception("(%s) failure writing job script" % galaxy_id_tag)
job_wrapper.fail("failure preparing job script", exception=True)
return
lib/galaxy/jobs/runners/condor.py
+1 -1
View File
@@ -105,7 +105,7 @@ class CondorJobRunner(AsynchronousJobRunner):
)
try:
self.write_executable_script(executable, script)
except:
except Exception:
job_wrapper.fail("failure preparing job script", exception=True)
log.exception("(%s) failure preparing job script" % galaxy_id_tag)
return
lib/galaxy/jobs/runners/drmaa.py
+3 -3
View File
@@ -110,7 +110,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
"""Get any native DRM arguments specified by the site configuration"""
try:
return url.split('/')[2] or None
except:
except Exception:
return None
def queue_job(self, job_wrapper):
@@ -151,7 +151,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
script = self.get_job_file(job_wrapper, exit_code_path=ajs.exit_code_file)
try:
self.write_executable_script(ajs.job_file, script)
except:
except Exception:
job_wrapper.fail("failure preparing job script", exception=True)
log.exception("(%s) failure writing job script" % galaxy_id_tag)
return
@@ -183,7 +183,7 @@ class DRMAAJobRunner(AsynchronousJobRunner):
log.warning('(%s) drmaa.Session.runJob() failed, will retry: %s', galaxy_id_tag, e)
fail_msg = "Unable to run this job due to a cluster error, please retry it later"
time.sleep(5)
except:
except Exception:
log.exception('(%s) drmaa.Session.runJob() failed unconditionally', galaxy_id_tag)
trynum = 5
else:
lib/galaxy/jobs/runners/godocker.py
+5 -5
View File
@@ -336,16 +336,16 @@ class GodockerJobRunner(AsynchronousJobRunner):
job_destination = job_wrapper.job_destination
try:
docker_cpu = int(job_destination.params["docker_cpu"])
except:
except Exception:
docker_cpu = 1
try:
docker_ram = int(job_destination.params["docker_memory"])
except:
except Exception:
docker_ram = 1
try:
docker_image = self._find_container(job_wrapper).container_id
log.debug("GoDocker runner using container %s.", docker_image)
except:
except Exception:
log.error("Unable to find docker_image for job %s, failing." % job_wrapper.job_id)
return False
@@ -367,7 +367,7 @@ class GodockerJobRunner(AsynchronousJobRunner):
for i in volume:
temp = dict({"name": i})
volumes.append(temp)
except:
except Exception:
log.debug("godocker_volume not set, using default.")
dt = datetime.now()
@@ -379,7 +379,7 @@ class GodockerJobRunner(AsynchronousJobRunner):
command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + venv + "\n" + job_wrapper.runner_command_line
else:
command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + job_wrapper.runner_command_line
except:
except Exception:
command = "#!/bin/bash\n" + "cd " + job_wrapper.working_directory + "\n" + job_wrapper.runner_command_line
# GoDocker Job model schema
lib/galaxy/jobs/runners/kubernetes.py
+2 -2
View File
@@ -131,7 +131,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
if "k8s_supplemental_group_id" in self.runner_params:
try:
return int(self.runner_params["k8s_supplemental_group_id"])
except:
except Exception:
log.warning("Supplemental group passed for Kubernetes runner needs to be an integer, value "
+ self.runner_params["k8s_supplemental_group_id"] + " passed is invalid")
return None
@@ -141,7 +141,7 @@ class KubernetesJobRunner(AsynchronousJobRunner):
if "k8s_fs_group_id" in self.runner_params:
try:
return int(self.runner_params["k8s_fs_group_id"])
except:
except Exception:
log.warning("FS group passed for Kubernetes runner needs to be an integer, value "
+ self.runner_params["k8s_fs_group_id"] + " passed is invalid")
return None
lib/galaxy/jobs/runners/local.py
+1 -1
View File
@@ -128,7 +128,7 @@ class LocalJobRunner(BaseJobRunner):
# Finish the job!
try:
job_wrapper.finish(stdout, stderr, exit_code)
except:
except Exception:
log.exception("Job wrapper finish method failed")
self._fail_job_local(job_wrapper, "Unable to finish job")
lib/galaxy/jobs/runners/pbs.py
+4 -4
View File
@@ -143,7 +143,7 @@ class PBSJobRunner(AsynchronousJobRunner):
# stripping the - comes later (in parse_destination_params)
for i, opt in enumerate(opts):
opts[i] = '-' + opt
except:
except Exception:
opts = []
for opt in opts:
param, value = opt.split(None, 1)
@@ -168,7 +168,7 @@ class PBSJobRunner(AsynchronousJobRunner):
arg = PBS_ARGMAP[arg]
arg = arg.lstrip('-')
args[arg] = value
except:
except Exception:
log.warning('Unrecognized long argument in destination params: %s' % arg)
return self.__args_to_attrs(args)
@@ -371,7 +371,7 @@ class PBSJobRunner(AsynchronousJobRunner):
self.check_single_job(pbs_server_name, job_id)
log.warning("(%s/%s) PBS job was not in state check list, but was found with individual state check" % (galaxy_job_id, job_id))
new_watched.append(pbs_job_state)
except:
except Exception:
errno, text = pbs.error()
if errno == 15001:
# 15001 == job not in queue
@@ -525,7 +525,7 @@ class PBSJobRunner(AsynchronousJobRunner):
pbs.pbs_deljob(c, job_id, '')
log.debug("%s Removed from PBS queue before job completion"
% job_tag)
except:
except Exception:
e = traceback.format_exc()
log.debug("%s Unable to stop job: %s" % (job_tag, e))
finally:
lib/galaxy/jobs/runners/slurm.py
+2 -2
View File
@@ -104,7 +104,7 @@ class SlurmJobRunner(DRMAAJobRunner):
try:
self.queue_job(ajs.job_wrapper)
return
except:
except Exception:
ajs.fail_message = "This job failed due to a cluster node failure, and an attempt to resubmit the job failed."
elif slurm_state == 'CANCELLED':
# Check to see if the job was killed for exceeding memory consumption
@@ -164,7 +164,7 @@ class SlurmJobRunner(DRMAAJobRunner):
return 'This job was terminated because it used more memory than it was allocated.'
elif any(_ in stripped_line for _ in SLURM_MEMORY_LIMIT_EXCEEDED_PARTIAL_WARNINGS):
return 'This job was cancelled probably because it used more memory than it was allocated.'
except:
except Exception:
log.exception('Error reading end of %s:', efile_path)
return False
lib/galaxy/jobs/runners/state_handler_factory.py
+1 -3
View File
@@ -1,9 +1,7 @@
import logging
from galaxy.util.submodules import submodules
import galaxy.jobs.runners.state_handlers
from galaxy.util.submodules import submodules
log = logging.getLogger(__name__)
lib/galaxy/jobs/runners/tasks.py
+2 -2
View File
@@ -52,7 +52,7 @@ class TaskedJobRunner(BaseJobRunner):
parallelism = job_wrapper.get_parallelism()
try:
splitter = getattr(__import__('galaxy.jobs.splitters', globals(), locals(), [parallelism.method]), parallelism.method)
except:
except Exception:
job_wrapper.change_state(model.Job.states.ERROR)
job_wrapper.fail("Job Splitting Failed, no match for '%s'" % parallelism)
return
@@ -125,7 +125,7 @@ class TaskedJobRunner(BaseJobRunner):
# Finish the job
try:
job_wrapper.finish(stdout, stderr, job_exit_code)
except:
except Exception:
log.exception("Job wrapper finish method failed")
job_wrapper.fail("Unable to finish job", exception=True)
lib/galaxy/jobs/runners/util/cli/job/slurm.py
+1 -1
View File
@@ -41,7 +41,7 @@ class Slurm(BaseJobExec):
if not k.startswith('-'):
k = argmap[k]
scriptargs[k] = v
except:
except Exception:
log.warning('Unrecognized long argument passed to Slurm CLI plugin: %s' % k)
# Generated template.

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