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MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM\n// === MAIN GALAXY LIBRARY MODULE ====\n// MMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMMM\n\nimport mod_utils from \"utils/utils\";\nimport mod_toastr from \"libs/toastr\";\nimport mod_baseMVC from \"mvc/base-mvc\";\nimport mod_library_model from \"mvc/library/library-model\";\nimport mod_folderlist_view from \"mvc/library/library-folderlist-view\";\nimport mod_librarylist_view from \"mvc/library/library-librarylist-view\";\nimport mod_librarytoolbar_view from \"mvc/library/library-librarytoolbar-view\";\nimport mod_foldertoolbar_view from \"mvc/library/library-foldertoolbar-view\";\nimport mod_library_dataset_view from \"mvc/library/library-dataset-view\";\nimport mod_library_library_view from \"mvc/library/library-library-view\";\nimport mod_library_folder_view from \"mvc/library/library-folder-view\";\n// ============================================================================\n/**\n * The Data Libraries router. Takes care about triggering routes\n * and sends users to proper pieces of the application.\n */\nvar LibraryRouter = Backbone.Router.extend({\n initialize: function() {\n this.routesHit = 0;\n // keep count of number of routes handled by the application\n Backbone.history.on(\n \"route\",\n function() {\n this.routesHit++;\n },\n this\n );\n\n this.bind(\"route\", this.trackPageview);\n },\n\n routes: {\n \"\": \"libraries\",\n \"page/:show_page\": \"libraries_page\",\n \"library/:library_id/permissions\": \"library_permissions\",\n \"folders/:folder_id/permissions\": \"folder_permissions\",\n \"folders/:id\": \"folder_content\",\n \"folders/:id/page/:show_page\": \"folder_page\",\n \"folders/:folder_id/datasets/:dataset_id\": \"dataset_detail\",\n \"folders/:folder_id/datasets/:dataset_id/permissions\": \"dataset_permissions\",\n \"folders/:folder_id/datasets/:dataset_id/versions/:ldda_id\": \"dataset_version\",\n \"folders/:folder_id/download/:format\": \"download\",\n \"folders/:folder_id/import/:source\": \"import_datasets\"\n },\n\n /**\n * If more than one route has been hit the user did not land on current\n * page directly so we can go back safely. Otherwise go to the home page.\n * Use replaceState if available so the navigation doesn't create an\n * extra history entry\n */\n back: function() {\n if (this.routesHit > 1) {\n window.history.back();\n } else {\n this.navigate(\"#\", { trigger: true, replace: true });\n }\n },\n\n /**\n * Track every route change as a page view in Google Analytics.\n */\n trackPageview: function() {\n var url = Backbone.history.getFragment();\n //prepend slash\n if (!/^\\//.test(url) && url != \"\") {\n url = `/${url}`;\n }\n if (typeof ga !== \"undefined\") {\n ga(\"send\", \"pageview\", `${Galaxy.root}library/list${url}`);\n }\n }\n});\n\n// ============================================================================\n/** session storage for library preferences */\nvar LibraryPrefs = mod_baseMVC.SessionStorageModel.extend({\n defaults: {\n with_deleted: false,\n without_restricted: false,\n sort_order: \"asc\",\n sort_by: \"name\",\n library_page_size: 20,\n folder_page_size: 15\n }\n});\n\n// ============================================================================\n/**\n * Main view of the Galaxy Data Libraries. Stores pointers to other subviews\n * and defines what router should do on the route triggers.\n */\nvar GalaxyLibrary = Backbone.View.extend({\n libraryToolbarView: null,\n libraryListView: null,\n library_router: null,\n libraryView: null,\n folderToolbarView: null,\n folderListView: null,\n datasetView: null,\n\n initialize: function() {\n // This should go upstream in the js app once available\n if (window.Galaxy.config.ga_code) {\n ((i, s, o, g, r, a, m) => {\n i[\"GoogleAnalyticsObject\"] = r;\n (i[r] =\n i[r] ||\n function() {\n (i[r].q = i[r].q || []).push(arguments);\n }),\n (i[r].l = 1 * new Date());\n (a = s.createElement(o)), (m = s.getElementsByTagName(o)[0]);\n a.async = 1;\n a.src = g;\n m.parentNode.insertBefore(a, m);\n })(window, document, \"script\", \"//www.google-analytics.com/analytics.js\", \"ga\");\n ga(\"create\", window.Galaxy.config.ga_code, \"auto\");\n ga(\"send\", \"pageview\");\n }\n\n Galaxy.libraries = this;\n\n this.preferences = new LibraryPrefs({ id: \"global-lib-prefs\" });\n\n this.library_router = new LibraryRouter();\n\n this.library_router.on(\"route:libraries\", () => {\n if (Galaxy.libraries.libraryToolbarView) {\n Galaxy.libraries.libraryToolbarView.$el.unbind(\"click\");\n }\n Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();\n Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView();\n });\n\n this.library_router.on(\"route:libraries_page\", show_page => {\n if (Galaxy.libraries.libraryToolbarView === null) {\n Galaxy.libraries.libraryToolbarView = new mod_librarytoolbar_view.LibraryToolbarView();\n Galaxy.libraries.libraryListView = new mod_librarylist_view.LibraryListView({ show_page: show_page });\n } else {\n Galaxy.libraries.libraryListView.render({\n show_page: show_page\n });\n }\n });\n\n this.library_router.on(\"route:folder_content\", id => {\n if (Galaxy.libraries.folderToolbarView) {\n Galaxy.libraries.folderToolbarView.$el.unbind(\"click\");\n }\n Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({ id: id });\n Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({ id: id });\n });\n\n this.library_router.on(\"route:folder_page\", (id, show_page) => {\n if (Galaxy.libraries.folderToolbarView === null) {\n Galaxy.libraries.folderToolbarView = new mod_foldertoolbar_view.FolderToolbarView({ id: id });\n Galaxy.libraries.folderListView = new mod_folderlist_view.FolderListView({\n id: id,\n show_page: show_page\n });\n } else {\n Galaxy.libraries.folderListView.render({\n id: id,\n show_page: parseInt(show_page)\n });\n }\n });\n\n this.library_router.on(\"route:download\", (folder_id, format) => {\n if ($(\"#folder_list_body\").find(\":checked\").length === 0) {\n mod_toastr.info(\"You must select at least one dataset to download\");\n Galaxy.libraries.library_router.navigate(`folders/${folder_id}`, { trigger: true, replace: true });\n } else {\n Galaxy.libraries.folderToolbarView.download(folder_id, format);\n Galaxy.libraries.library_router.navigate(`folders/${folder_id}`, { trigger: false, replace: true });\n }\n });\n\n this.library_router.on(\"route:dataset_detail\", (folder_id, dataset_id) => {\n if (Galaxy.libraries.datasetView) {\n Galaxy.libraries.datasetView.$el.unbind(\"click\");\n }\n Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({\n id: dataset_id,\n show_version: false,\n show_permissions: false\n });\n });\n\n this.library_router.on(\"route:dataset_version\", (folder_id, dataset_id, ldda_id) => {\n if (Galaxy.libraries.datasetView) {\n Galaxy.libraries.datasetView.$el.unbind(\"click\");\n }\n Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({\n id: dataset_id,\n ldda_id: ldda_id,\n show_version: true\n });\n });\n\n this.library_router.on(\"route:dataset_permissions\", (folder_id, dataset_id) => {\n if (Galaxy.libraries.datasetView) {\n Galaxy.libraries.datasetView.$el.unbind(\"click\");\n }\n Galaxy.libraries.datasetView = new mod_library_dataset_view.LibraryDatasetView({\n id: dataset_id,\n show_permissions: true\n });\n });\n\n this.library_router.on(\"route:library_permissions\", library_id => {\n if (Galaxy.libraries.libraryView) {\n Galaxy.libraries.libraryView.$el.unbind(\"click\");\n }\n Galaxy.libraries.libraryView = new mod_library_library_view.LibraryView({\n id: library_id,\n show_permissions: true\n });\n });\n\n this.library_router.on(\"route:folder_permissions\", folder_id => {\n if (Galaxy.libraries.folderView) {\n Galaxy.libraries.folderView.$el.unbind(\"click\");\n }\n Galaxy.libraries.folderView = new mod_library_folder_view.FolderView({\n id: folder_id,\n show_permissions: true\n });\n });\n\n this.library_router.on(\"route:import_datasets\", (folder_id, source) => {\n if (Galaxy.libraries.folderToolbarView && Galaxy.libraries.folderListView) {\n 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$ from \"jquery\";\nimport * as _ from \"libs/underscore\";\nimport * as Backbone from \"libs/backbone\";\n\nvar MIN_PANEL_WIDTH = 160;\nvar MAX_PANEL_WIDTH = 800;\n\n/** View for left/right panels used by Page view */\nvar SidePanel = Backbone.View.extend({\n initialize: function(options) {\n this.view = options.view;\n this.hidden = false;\n this.saved_size = null;\n this.hiddenByTool = false;\n },\n\n $center: function() {\n return this.$el.siblings(\"#center\");\n },\n\n $toggleButton: function() {\n return this.$(\".unified-panel-footer > .panel-collapse\");\n },\n\n render: function() {\n var self = this;\n var panel = this.view;\n var components = this.view.model.attributes || {};\n this.$el.html(this._templatePanel(this.id));\n _.each(components.buttons, button => {\n self.$(\".panel-header-buttons\").append(button.$el);\n });\n this.$el.addClass(components.cls);\n this.$(\".panel-header-text\").html(_.escape(components.title));\n this.$(\".unified-panel-body\").append(panel.$el);\n panel.render();\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templatePanel: function() {\n return [this._templateHeader(), this._templateBody(), this._templateFooter()].join(\"\");\n },\n\n /** panel dom template. id is 'right' or 'left' */\n _templateHeader: function(data) {\n return [\n '
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`);\n return this;\n },\n formattedReference: function() {\n var model = this.model;\n var entryType = model.entryType();\n var fields = model.fields();\n\n var ref = \"\";\n // Code inspired by...\n // https://github.com/vkaravir/bib-publication-list/blob/master/src/bib-publication-list.js\n var authorsAndYear = `${this._asSentence(\n (fields.author ? fields.author : \"\") + (fields.year ? ` (${fields.year})` : \"\")\n )} `;\n var title = fields.title || \"\";\n var pages = fields.pages ? `pp. ${fields.pages}` : \"\";\n var address = fields.address;\n if (entryType == \"article\") {\n var volume =\n (fields.volume ? fields.volume : \"\") +\n (fields.number ? ` (${fields.number})` : \"\") +\n (pages ? `, ${pages}` : \"\");\n ref = `${authorsAndYear +\n this._asSentence(title) +\n (fields.journal ? `In ${fields.journal}, ` : \"\") +\n this._asSentence(volume) +\n this._asSentence(fields.address)}`;\n } else if (entryType == \"inproceedings\" || entryType == \"proceedings\") {\n ref = `${authorsAndYear +\n this._asSentence(title) +\n (fields.booktitle ? `In ${fields.booktitle}, ` : \"\") +\n (pages ? pages : \"\") +\n (address ? `, ${address}` : \"\")}.`;\n } else if (entryType == \"mastersthesis\" || entryType == \"phdthesis\") {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n (fields.howpublished ? `${fields.howpublished}. ` : \"\") +\n (fields.note ? `${fields.note}.` : \"\");\n } else if (entryType == \"techreport\") {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n this._asSentence(fields.institution) +\n this._asSentence(fields.number) +\n this._asSentence(fields.type);\n } else if (entryType == \"book\" || entryType == \"inbook\" || entryType == \"incollection\") {\n ref = `${authorsAndYear} ${this._formatBookInfo(fields)}`;\n } else {\n ref = `${authorsAndYear} ${this._asSentence(title)}${this._asSentence(\n fields.howpublished\n )}${this._asSentence(fields.note)}`;\n }\n var doiUrl = \"\";\n if (fields.doi) {\n doiUrl = `http://dx.doi.org/${fields.doi}`;\n ref += `[doi:${fields.doi}]`;\n }\n var url = fields.url || doiUrl;\n if (url) {\n ref += `[Link]`;\n }\n return ref;\n },\n _formatBookInfo: function(fields) {\n var info = \"\";\n if (fields.chapter) {\n info += `${fields.chapter} in `;\n }\n if (fields.title) {\n info += `${fields.title}`;\n }\n if (fields.editor) {\n info += `, Edited by ${fields.editor}, `;\n }\n if (fields.publisher) {\n info += `, ${fields.publisher}`;\n }\n if (fields.pages) {\n info += `, pp. ${fields.pages}`;\n }\n if (fields.series) {\n info += `, ${fields.series}`;\n }\n if (fields.volume) {\n info += `, Vol.${fields.volume}`;\n }\n if (fields.issn) {\n info += `, ISBN: ${fields.issn}`;\n }\n return `${info}.`;\n },\n _asSentence: function(str) {\n return str && str.trim() ? `${str}. ` : \"\";\n }\n});\n\nvar CitationListView = Backbone.View.extend({\n /**\n * Set up view.\n */\n initialize: function() {\n this.setElement(\"\");\n this.listenTo(this.collection, \"add\", this.renderCitation);\n this.render();\n },\n\n events: {\n \"click .citations-to-bibtex\": \"showBibtex\",\n \"click .citations-to-formatted\": \"showFormatted\"\n },\n\n renderCitation: function(citation) {\n var citationView = new CitationView({ model: citation });\n this.$(\".citations-formatted\").append(citationView.render().el);\n var rawTextarea = this.$(\".citations-bibtex-text\");\n rawTextarea.val(`${rawTextarea.val()}\\n\\r${citation.attributes.content}`);\n },\n\n render: function() {\n this.$el.html(this.citationsElement());\n this.collection.each(function(item) {\n this.renderCitation(item);\n }, this);\n this.showFormatted();\n },\n\n showBibtex: function() {\n this.$(\".citations-to-formatted\").show();\n this.$(\".citations-to-bibtex\").hide();\n this.$(\".citations-bibtex\").show();\n this.$(\".citations-formatted\").hide();\n this.$(\".citations-bibtex-text\").select();\n },\n\n showFormatted: function() {\n this.$(\".citations-to-formatted\").hide();\n this.$(\".citations-to-bibtex\").show();\n this.$(\".citations-bibtex\").hide();\n this.$(\".citations-formatted\").show();\n },\n\n partialWarningElement: function() {\n if (this.collection.partial) {\n return [\n '${this.formattedReference()}
`);\n return this;\n },\n formattedReference: function() {\n var model = this.model;\n var entryType = model.entryType();\n var fields = model.fields();\n\n var ref = \"\";\n // Code inspired by...\n // https://github.com/vkaravir/bib-publication-list/blob/master/src/bib-publication-list.js\n var authorsAndYear = `${this._asSentence(\n (fields.author ? fields.author : \"\") + (fields.year ? ` (${fields.year})` : \"\")\n )} `;\n var title = fields.title || \"\";\n var pages = fields.pages ? `pp. ${fields.pages}` : \"\";\n var address = fields.address;\n if (entryType == \"article\") {\n var volume =\n (fields.volume ? fields.volume : \"\") +\n (fields.number ? ` (${fields.number})` : \"\") +\n (pages ? `, ${pages}` : \"\");\n ref = `${authorsAndYear +\n this._asSentence(title) +\n (fields.journal ? `In ${fields.journal}, ` : \"\") +\n this._asSentence(volume) +\n this._asSentence(fields.address)}`;\n } else if (entryType == \"inproceedings\" || entryType == \"proceedings\") {\n ref = `${authorsAndYear +\n this._asSentence(title) +\n (fields.booktitle ? `In ${fields.booktitle}, ` : \"\") +\n (pages ? pages : \"\") +\n (address ? `, ${address}` : \"\")}.`;\n } else if (entryType == \"mastersthesis\" || entryType == \"phdthesis\") {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n (fields.howpublished ? `${fields.howpublished}. ` : \"\") +\n (fields.note ? `${fields.note}.` : \"\");\n } else if (entryType == \"techreport\") {\n ref =\n authorsAndYear +\n this._asSentence(title) +\n this._asSentence(fields.institution) +\n this._asSentence(fields.number) +\n this._asSentence(fields.type);\n } else if (entryType == \"book\" || entryType == \"inbook\" || entryType == \"incollection\") {\n ref = `${authorsAndYear} ${this._formatBookInfo(fields)}`;\n } else {\n ref = `${authorsAndYear} ${this._asSentence(title)}${this._asSentence(\n fields.howpublished\n )}${this._asSentence(fields.note)}`;\n }\n var doiUrl = \"\";\n if (fields.doi) {\n doiUrl = `http://dx.doi.org/${fields.doi}`;\n ref += `[doi:${fields.doi}]`;\n }\n var url = fields.url || doiUrl;\n if (url) {\n ref += `[Link]`;\n }\n return convertLaTeX({ onError: (error, latex) => `\\{${stringifyLaTeX(latex)}\\}` }, ref);\n },\n _formatBookInfo: function(fields) {\n var info = \"\";\n if (fields.chapter) {\n info += `${fields.chapter} in `;\n }\n if (fields.title) {\n info += `${fields.title}`;\n }\n if (fields.editor) {\n info += `, Edited by ${fields.editor}, `;\n }\n if (fields.publisher) {\n info += `, ${fields.publisher}`;\n }\n if (fields.pages) {\n info += `, pp. ${fields.pages}`;\n }\n if (fields.series) {\n info += `, ${fields.series}`;\n }\n if (fields.volume) {\n info += `, Vol.${fields.volume}`;\n }\n if (fields.issn) {\n info += `, ISBN: ${fields.issn}`;\n }\n return `${info}.`;\n },\n _asSentence: function(str) {\n return str && str.trim() ? `${str}. ` : \"\";\n }\n});\n\nvar CitationListView = Backbone.View.extend({\n /**\n * Set up view.\n */\n initialize: function() {\n this.setElement(\"\");\n this.listenTo(this.collection, \"add\", this.renderCitation);\n this.render();\n },\n\n events: {\n \"click .citations-to-bibtex\": \"showBibtex\",\n \"click .citations-to-formatted\": \"showFormatted\"\n },\n\n renderCitation: function(citation) {\n var citationView = new CitationView({ model: citation });\n this.$(\".citations-formatted\").append(citationView.render().el);\n var rawTextarea = this.$(\".citations-bibtex-text\");\n rawTextarea.val(`${rawTextarea.val()}\\n\\r${citation.attributes.content}`);\n },\n\n render: function() {\n this.$el.html(this.citationsElement());\n this.collection.each(function(item) {\n this.renderCitation(item);\n }, this);\n this.showFormatted();\n },\n\n showBibtex: function() {\n this.$(\".citations-to-formatted\").show();\n this.$(\".citations-to-bibtex\").hide();\n this.$(\".citations-bibtex\").show();\n this.$(\".citations-formatted\").hide();\n this.$(\".citations-bibtex-text\").select();\n },\n\n showFormatted: function() {\n this.$(\".citations-to-formatted\").hide();\n this.$(\".citations-to-bibtex\").show();\n this.$(\".citations-bibtex\").hide();\n this.$(\".citations-formatted\").show();\n },\n\n partialWarningElement: function() {\n if (this.collection.partial) {\n return [\n '| ',\n ' | ',\n ' | name \"> | ',\n 'description | ',\n 'data type | ',\n 'size | ',\n 'time updated (UTC) | ',\n 'state | ',\n '',\n \"\",\n '',\n ' |
|---|---|---|---|---|---|---|---|---|
| \",\n '\" title=\"Go to parent folder\" class=\"btn_open_folder btn btn-default btn-xs\">..',\n \" | \",\n \"\",\n \" | \",\n \" | \",\n \" | \",\n \" | \",\n \" | \",\n \" | \",\n \" | \",\n \" |
| library | ',\n \"\",\n \"\",\n \"\",\n \" |
|---|---|
| name | \",\n '<%- library.get(\"name\") %> | ',\n \"
| description | \",\n '<%- library.get(\"description\") %> | ',\n \"
| synopsis | \",\n '<%- library.get(\"synopsis\") %> | ',\n \"
| created | \",\n '\"><%- library.get(\"create_time_pretty\") %> | ',\n \"
| id | \",\n '<%- library.get(\"id\") %> | ',\n \"
| folder | ',\n \"\",\n \"\",\n \"\",\n \" |
|---|---|
| name | \",\n \"<%- options.folder_name %> | \",\n \"
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You can set extension type and genome for all imported datasets at once:
\",\n \"You can set extension type and genome for all imported datasets at once:
\",\n \"2. Choose the datasets to import:
\",\n \"| Encoded UID | API Key | Actions | \" +\n \"\" +\n '|
|---|---|---|---|
| \" +\n \"{{ user.uid }}\" +\n \" | \" +\n \"\" +\n \"{{ user.email }}\" +\n \" | \" +\n \"\" +\n \"{{ user.key }}\" +\n \" | \" +\n \"\" +\n '' +\n \" | \" +\n \"