diff --git a/client/src/components/Libraries/LibrariesList.vue b/client/src/components/Libraries/LibrariesList.vue index dc9db927fe7..df1e5a6d85e 100644 --- a/client/src/components/Libraries/LibrariesList.vue +++ b/client/src/components/Libraries/LibrariesList.vue @@ -9,7 +9,9 @@ Library - include deleted + + include deleted + exclude restricted @@ -158,6 +160,7 @@ id="paginationPerPage" autocomplete="off" type="number" + onkeyup="this.value|=0;if(this.value<1)this.value=1" v-model="perPage" /> diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue index f269faafa4b..a9fddc56612 100644 --- a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue +++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue @@ -303,12 +303,13 @@ export default { // helper function to make legacy code compatible findCheckedItems: async function (idOnly = true) { const datasets = []; - const folder = []; + const folders = []; const selected = await this.getSelected(); selected.forEach((item) => { - item.type === "file" ? datasets.push(idOnly ? item.id : item) : idOnly ? item.id : item; + const selected_item = idOnly ? item.id : item; + item.type === "file" ? datasets.push(selected_item) : folders.push(selected_item); }); - return { datasets: datasets, folders: folder }; + return { datasets: datasets, folders: folders }; }, importToHistoryModal: function (isCollection) { this.findCheckedItems(!isCollection).then(({ datasets, folders }) => { diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js b/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js index d57051a0f37..f9d17e703e7 100644 --- a/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js +++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/import-to-history/import-dataset.js @@ -79,13 +79,13 @@ var ImportDatasetModal = Backbone.View.extend({ Toast.error("An error occurred."); }) .always(() => { - this.modal.enableButton("Import"); + this.modal.disableButton("Import"); }); } else { var history_id = $("select[name=import_to_history] option:selected").val(); var history_name = $("select[name=import_to_history] option:selected").text(); this.processImportToHistory(history_id, history_name); - this.modal.enableButton("Import"); + this.modal.disableButton("Import"); } }, diff --git a/client/src/components/Libraries/library-utils.js b/client/src/components/Libraries/library-utils.js index 11b4b1af569..ac4ba93c5e3 100644 --- a/client/src/components/Libraries/library-utils.js +++ b/client/src/components/Libraries/library-utils.js @@ -13,9 +13,12 @@ export function onError(error) { // legacy code export function extractRoles(role_list) { const selected_roles = []; - role_list.forEach((item) => { - selected_roles.push({ name: item[0], id: item[1] }); - }); + + if (role_list) { + role_list.forEach((item) => { + selected_roles.push({ name: item[0], id: item[1] }); + }); + } return selected_roles; } diff --git a/client/src/components/Upload/Collection.vue b/client/src/components/Upload/Collection.vue index 9dc2f04474b..22b872a63fe 100644 --- a/client/src/components/Upload/Collection.vue +++ b/client/src/components/Upload/Collection.vue @@ -242,6 +242,7 @@ export default { file_mode: file.mode || "local", file_path: file.path, file_data: file, + file_uri: file.uri, extension: this.extension, genome: this.genome, }; diff --git a/client/src/components/Upload/Default.vue b/client/src/components/Upload/Default.vue index b73cefdf61e..b8cdfb00eb0 100644 --- a/client/src/components/Upload/Default.vue +++ b/client/src/components/Upload/Default.vue @@ -249,6 +249,7 @@ export default { file_size: file.size, file_mode: file.mode || "local", file_path: file.path, + file_uri: file.uri, file_data: file, }; }, diff --git a/client/src/components/Upload/UploadBoxMixin.js b/client/src/components/Upload/UploadBoxMixin.js index 97a9dc485ac..6b4c7cfed39 100644 --- a/client/src/components/Upload/UploadBoxMixin.js +++ b/client/src/components/Upload/UploadBoxMixin.js @@ -242,6 +242,7 @@ export default { name: ftp_file.path, size: ftp_file.size, path: ftp_file.path, + uri: ftp_file.uri, }, ]); }, diff --git a/client/src/components/Upload/UploadModalContent.vue b/client/src/components/Upload/UploadModalContent.vue index dad838fe24a..adb7a993247 100644 --- a/client/src/components/Upload/UploadModalContent.vue +++ b/client/src/components/Upload/UploadModalContent.vue @@ -292,24 +292,23 @@ export default { auto_decompress: true, }; - // Composite does not use the fetch API, so we can just - // index into the first element of items - const item = items[0]; - let urls; - if (item.get("file_mode") == "ftp") { - urls = [item.get("file_path")]; - } else { - urls = item.get("url_paste").split("\n"); - } - urls.forEach((url) => { - if (url != "") { - data.targets[0].elements.push({ - url: url.trim(), - src: "url", - dbkey: item.get("genome", "?"), - ext: item.get("extension", "auto"), - }); + items.forEach((item) => { + let urls; + if (item.get("file_mode") == "ftp") { + urls = [item.get("file_uri") || item.get("file_path")]; + } else { + urls = item.get("url_paste").split("\n"); } + urls.forEach((url) => { + if (url != "") { + data.targets[0].elements.push({ + url: url.trim(), + src: "url", + dbkey: item.get("genome", "?"), + ext: item.get("extension", "auto"), + }); + } + }); }); return data; }, diff --git a/client/src/components/Workflow/Editor/Index.vue b/client/src/components/Workflow/Editor/Index.vue index 23b31e6ea4c..2789c869b7c 100644 --- a/client/src/components/Workflow/Editor/Index.vue +++ b/client/src/components/Workflow/Editor/Index.vue @@ -469,7 +469,7 @@ export default { } }, onUpgrade() { - this.attemptRefactor([{ action_type: "upgrade_all_steps" }]); + this.onAttemptRefactor([{ action_type: "upgrade_all_steps" }]); }, onEdit() { this.isCanvas = true; diff --git a/client/src/components/Workflow/TrsImport.vue b/client/src/components/Workflow/TrsImport.vue index 04a22a1ec57..3ec341dbdba 100644 --- a/client/src/components/Workflow/TrsImport.vue +++ b/client/src/components/Workflow/TrsImport.vue @@ -105,9 +105,20 @@ export default { this.trsTool = tool; this.errorMessage = null; if (this.isAutoImport) { - const version = this.trsTool.versions.find((version) => version.id === this.queryTrsVersionId); + /* Resolve discrepancy between workflowhub, which sends an id as query parameter, + and dockstore, which uses the version name as the query parameter. + Should just be one of them eventually. */ + let versionField = "name"; + const version = this.trsTool.versions.find((version) => { + if (version.name === this.queryTrsVersionId) { + return true; + } else if (version.id === this.queryTrsVersionId) { + versionField = "id"; + return true; + } + }); if (version) { - this.importVersion(this.trsTool.id, version, this.isRun); + this.importVersion(this.trsTool.id, version[versionField], this.isRun); } else { Toast.warning(`Specified version: ${this.queryTrsVersionId} doesn't exist`); this.isAutoImport = false; diff --git a/client/src/components/Workflow/trsMixin.js b/client/src/components/Workflow/trsMixin.js index dfd944df435..32a9ab780f0 100644 --- a/client/src/components/Workflow/trsMixin.js +++ b/client/src/components/Workflow/trsMixin.js @@ -11,7 +11,7 @@ export default { methods: { importVersion(toolId, version, isRunFormRedirect = false) { this.services - .importTrsTool(this.trsSelection.id, toolId, version.name) + .importTrsTool(this.trsSelection.id, toolId, version) .then((response_data) => { redirectOnImport(getAppRoot(), response_data, isRunFormRedirect); }) diff --git a/client/src/mvc/library/library-dataset-view.js b/client/src/mvc/library/library-dataset-view.js index 0f326e6a8e2..931f013dc7e 100644 --- a/client/src/mvc/library/library-dataset-view.js +++ b/client/src/mvc/library/library-dataset-view.js @@ -492,12 +492,12 @@ var LibraryDatasetView = Backbone.View.extend({
  1. - Libraries + Libraries
    2. <% _.each(item.get("full_path"), function(path_item) { %> <% if (path_item[0] != item.id) { %>
  2. - + <%- path_item[1] %>
    3. diff --git a/client/src/mvc/upload/upload-model.js b/client/src/mvc/upload/upload-model.js index 51876ccf91e..37ea008e2d5 100644 --- a/client/src/mvc/upload/upload-model.js +++ b/client/src/mvc/upload/upload-model.js @@ -12,6 +12,7 @@ var Model = Backbone.Model.extend({ file_size: 0, file_type: null, file_path: "", + file_uri: null, file_data: null, percentage: 0, space_to_tab: false, diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py index 639cac2f518..050c737e613 100644 --- a/lib/galaxy/managers/libraries.py +++ b/lib/galaxy/managers/libraries.py @@ -147,32 +147,35 @@ class LibraryManager: query = query.filter(trans.app.model.Library.table.c.deleted == false()) else: # Nonadmins can't see deleted libraries - query = query.filter(trans.app.model.Library.table.c.deleted == false()) - current_user_role_ids = [role.id for role in trans.get_current_user_roles()] - all_actions = trans.sa_session.query(trans.model.LibraryPermissions).filter(trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids)) - library_add_action = trans.app.security_agent.permitted_actions.LIBRARY_ADD.action - library_modify_action = trans.app.security_agent.permitted_actions.LIBRARY_MODIFY.action - library_manage_action = trans.app.security_agent.permitted_actions.LIBRARY_MANAGE.action - accessible_restricted_library_ids = set() - allowed_library_add_ids = set() - allowed_library_modify_ids = set() - allowed_library_manage_ids = set() - for action in all_actions: - if action.action == library_access_action: - accessible_restricted_library_ids.add(action.library_id) - if action.action == library_add_action: - allowed_library_add_ids.add(action.library_id) - if action.action == library_modify_action: - allowed_library_modify_ids.add(action.library_id) - if action.action == library_manage_action: - allowed_library_manage_ids.add(action.library_id) - query = query.filter(or_( - not_(trans.model.Library.table.c.id.in_(restricted_library_ids)), - trans.model.Library.table.c.id.in_(accessible_restricted_library_ids) - )) - prefetched_ids['allowed_library_add_ids'] = allowed_library_add_ids - prefetched_ids['allowed_library_modify_ids'] = allowed_library_modify_ids - prefetched_ids['allowed_library_manage_ids'] = allowed_library_manage_ids + if deleted: + raise exceptions.AdminRequiredException() + else: + query = query.filter(trans.app.model.Library.table.c.deleted == false()) + current_user_role_ids = [role.id for role in trans.get_current_user_roles()] + all_actions = trans.sa_session.query(trans.model.LibraryPermissions).filter(trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids)) + library_add_action = trans.app.security_agent.permitted_actions.LIBRARY_ADD.action + library_modify_action = trans.app.security_agent.permitted_actions.LIBRARY_MODIFY.action + library_manage_action = trans.app.security_agent.permitted_actions.LIBRARY_MANAGE.action + accessible_restricted_library_ids = set() + allowed_library_add_ids = set() + allowed_library_modify_ids = set() + allowed_library_manage_ids = set() + for action in all_actions: + if action.action == library_access_action: + accessible_restricted_library_ids.add(action.library_id) + if action.action == library_add_action: + allowed_library_add_ids.add(action.library_id) + if action.action == library_modify_action: + allowed_library_modify_ids.add(action.library_id) + if action.action == library_manage_action: + allowed_library_manage_ids.add(action.library_id) + query = query.filter(or_( + not_(trans.model.Library.table.c.id.in_(restricted_library_ids)), + trans.model.Library.table.c.id.in_(accessible_restricted_library_ids) + )) + prefetched_ids['allowed_library_add_ids'] = allowed_library_add_ids + prefetched_ids['allowed_library_modify_ids'] = allowed_library_modify_ids + prefetched_ids['allowed_library_manage_ids'] = allowed_library_manage_ids return query, prefetched_ids def secure(self, trans, library, check_accessible=True): diff --git a/test/integration_selenium/test_upload_ftp.py b/test/integration_selenium/test_upload_ftp.py index 13f62a51aee..ac7b2002382 100644 --- a/test/integration_selenium/test_upload_ftp.py +++ b/test/integration_selenium/test_upload_ftp.py @@ -20,20 +20,40 @@ class UploadFtpSeleniumIntegrationTestCase(SeleniumIntegrationTestCase): def ftp_dir(cls): return cls.temp_config_dir("ftp") - @selenium_test - def test_upload_simplest(self): - email = self.get_logged_in_user()["email"] - user_ftp_dir = os.path.join(self.ftp_dir(), email) - os.makedirs(user_ftp_dir) - file_path = os.path.join(user_ftp_dir, "1.txt") - with open(file_path, "w")as f: - f.write("Hello World!") - + def _upload_all(self): self.home() self.components.upload.start.wait_for_and_click() self.components.upload.ftp_add.wait_for_and_click() self.components.upload.ftp_popup.wait_for_visible() - self.components.upload.ftp_items().all()[0].click() + for item in self.components.upload.ftp_items().all(): + item.click() self.components.upload.ftp_close.wait_for_and_click() self.components.upload.row(n=0).wait_for_visible() self.upload_start() + self.sleep_for(self.wait_types.UX_RENDER) + self.wait_for_history() + + def _create_ftp_dir(self): + email = self.get_logged_in_user()["email"] + user_ftp_dir = os.path.join(self.ftp_dir(), email) + os.makedirs(user_ftp_dir) + return user_ftp_dir + + @selenium_test + def test_upload_simplest(self): + user_ftp_dir = self._create_ftp_dir() + file_path = os.path.join(user_ftp_dir, "1.txt") + with open(file_path, "w") as f: + f.write("Hello World!") + self._upload_all() + + @selenium_test + def test_upload_multiple(self): + user_ftp_dir = self._create_ftp_dir() + file_path = os.path.join(user_ftp_dir, "1.txt") + with open(file_path, "w") as f: + f.write("Hello World!") + file_path = os.path.join(user_ftp_dir, "2.txt") + with open(file_path, "w") as f: + f.write("Hello Galaxy!") + self._upload_all() diff --git a/tools/extract/liftOver_wrapper.py b/tools/extract/liftOver_wrapper.py index 9cd077e3baf..90385814c8a 100644 --- a/tools/extract/liftOver_wrapper.py +++ b/tools/extract/liftOver_wrapper.py @@ -26,7 +26,7 @@ def safe_bed_file(infile): https://lists.soe.ucsc.edu/pipermail/genome/2007-May/013561.html """ fix_pat = re.compile("^(track|browser)") - with tempfile.NamedTemporaryFile(mode='w', delete=False) as out_handle, open(infile, 'w') as in_handle: + with tempfile.NamedTemporaryFile(mode='w', delete=False) as out_handle, open(infile, 'r') as in_handle: for line in in_handle: if fix_pat.match(line): line = "#" + line