From 38fe8d1b8d005e6e28abf1856c6f4f888c851852 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 18 May 2021 11:24:49 +0200 Subject: [PATCH 01/20] Fix FTP upload if remote file sources are not set up This broke in https://github.com/galaxyproject/galaxy/pull/11276. --- client/src/components/Upload/Collection.vue | 1 + client/src/components/Upload/Default.vue | 1 + client/src/components/Upload/UploadBoxMixin.js | 1 + client/src/components/Upload/UploadModalContent.vue | 2 +- client/src/mvc/upload/upload-model.js | 1 + 5 files changed, 5 insertions(+), 1 deletion(-) 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..9b63418134b 100644 --- a/client/src/components/Upload/UploadModalContent.vue +++ b/client/src/components/Upload/UploadModalContent.vue @@ -297,7 +297,7 @@ export default { const item = items[0]; let urls; if (item.get("file_mode") == "ftp") { - urls = [item.get("file_path")]; + urls = [item.get("file_uri") || item.get("file_path")]; } else { urls = item.get("url_paste").split("\n"); } 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, From 4e060878720b8436f4d5a81085b9b7b91b83ceec Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Tue, 18 May 2021 11:48:51 +0200 Subject: [PATCH 02/20] Wait for upload and verify history is OK --- test/integration_selenium/test_upload_ftp.py | 2 ++ 1 file changed, 2 insertions(+) diff --git a/test/integration_selenium/test_upload_ftp.py b/test/integration_selenium/test_upload_ftp.py index 13f62a51aee..38c0e7df93d 100644 --- a/test/integration_selenium/test_upload_ftp.py +++ b/test/integration_selenium/test_upload_ftp.py @@ -37,3 +37,5 @@ class UploadFtpSeleniumIntegrationTestCase(SeleniumIntegrationTestCase): 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() From 24610be13fe4f2b373d166214613b1554cc7c5a6 Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Tue, 18 May 2021 20:26:59 +0200 Subject: [PATCH 03/20] fix dataset BREADCRUMBS --- client/src/mvc/library/library-dataset-view.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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. From b68c5db71bab27da4e74cf5f86d2e5ee47cbdb82 Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Tue, 18 May 2021 20:03:44 +0200 Subject: [PATCH 04/20] restrict negative balues --- client/src/components/Libraries/LibrariesList.vue | 1 + 1 file changed, 1 insertion(+) diff --git a/client/src/components/Libraries/LibrariesList.vue b/client/src/components/Libraries/LibrariesList.vue index dc9db927fe7..3fd61dad3fb 100644 --- a/client/src/components/Libraries/LibrariesList.vue +++ b/client/src/components/Libraries/LibrariesList.vue @@ -158,6 +158,7 @@ id="paginationPerPage" autocomplete="off" type="number" + onkeyup="if(this.value<0)this.value=1" v-model="perPage" /> From ac865b76fcf6a0d0867e85c11e145f255b02847d Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Wed, 19 May 2021 15:42:23 +0200 Subject: [PATCH 05/20] hide 'include deleted' for non-admins --- client/src/components/Libraries/LibrariesList.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/src/components/Libraries/LibrariesList.vue b/client/src/components/Libraries/LibrariesList.vue index dc9db927fe7..603b58dcf8b 100644 --- a/client/src/components/Libraries/LibrariesList.vue +++ b/client/src/components/Libraries/LibrariesList.vue @@ -9,7 +9,7 @@ Library - include deleted + include deleted exclude restricted From b61ee98f795c20b40884588ba3ace89c7c983b0e Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Wed, 19 May 2021 15:58:16 +0200 Subject: [PATCH 06/20] return emty array if user queries for deleted libs --- lib/galaxy/managers/libraries.py | 55 +++++++++++++++++--------------- 1 file changed, 29 insertions(+), 26 deletions(-) diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py index 49bbd341d18..4c9f2a313e2 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: + query = [] + 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): From 7d3176016330e7fd122a9b933c38dcc20935bbc7 Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Wed, 19 May 2021 16:33:26 +0200 Subject: [PATCH 07/20] Update client/src/components/Libraries/LibrariesList.vue Co-authored-by: Marius van den Beek --- client/src/components/Libraries/LibrariesList.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/src/components/Libraries/LibrariesList.vue b/client/src/components/Libraries/LibrariesList.vue index 3fd61dad3fb..5d04adad527 100644 --- a/client/src/components/Libraries/LibrariesList.vue +++ b/client/src/components/Libraries/LibrariesList.vue @@ -158,7 +158,7 @@ id="paginationPerPage" autocomplete="off" type="number" - onkeyup="if(this.value<0)this.value=1" + onkeyup="if(this.value<1)this.value=1" v-model="perPage" /> From 932cc516bf806a4f522e50adbd531dbb32a76cab Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Wed, 19 May 2021 16:40:55 +0200 Subject: [PATCH 08/20] restrict to integers only --- client/src/components/Libraries/LibrariesList.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/client/src/components/Libraries/LibrariesList.vue b/client/src/components/Libraries/LibrariesList.vue index 5d04adad527..7b540aa764a 100644 --- a/client/src/components/Libraries/LibrariesList.vue +++ b/client/src/components/Libraries/LibrariesList.vue @@ -158,7 +158,7 @@ id="paginationPerPage" autocomplete="off" type="number" - onkeyup="if(this.value<1)this.value=1" + onkeyup="this.value|=0;if(this.value<1)this.value=1" v-model="perPage" /> From d10b4dab033c5a842caefbaac2b35b7e4181333d Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Wed, 19 May 2021 16:43:23 +0200 Subject: [PATCH 09/20] fix prettier --- client/src/components/Libraries/LibrariesList.vue | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/client/src/components/Libraries/LibrariesList.vue b/client/src/components/Libraries/LibrariesList.vue index 603b58dcf8b..ce3757dcf9d 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 From 7e73fe91e6df2cfe05bb8e9a6d84b94ca4b0c831 Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Wed, 19 May 2021 17:04:56 +0200 Subject: [PATCH 10/20] fix dataset permissions --- client/src/components/Libraries/library-utils.js | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) 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; } From 0ab3985288c889915230f5843a1e78290d09a6de Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Wed, 19 May 2021 17:35:39 +0200 Subject: [PATCH 11/20] disable import --- .../TopToolbar/import-to-history/import-dataset.js | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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"); } }, From c1382faf04b27710f6e9f9ca235cf79fb28439d4 Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Thu, 20 May 2021 11:52:08 +0200 Subject: [PATCH 12/20] throw AdminRequiredException --- lib/galaxy/managers/libraries.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/managers/libraries.py b/lib/galaxy/managers/libraries.py index 4c9f2a313e2..aa8b4f096d0 100644 --- a/lib/galaxy/managers/libraries.py +++ b/lib/galaxy/managers/libraries.py @@ -148,7 +148,7 @@ class LibraryManager: else: # Nonadmins can't see deleted libraries if deleted: - query = [] + 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()] From 41ab4d03c6b5cc462e67b84f49bba8793feb5d91 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 19 May 2021 22:04:20 +0200 Subject: [PATCH 13/20] Allow trs_version to refer to name or id field This has diverged between workflowhub.eu and dockstore implementations. --- client/src/components/Workflow/TrsImport.vue | 15 +++++++++++++-- client/src/components/Workflow/trsMixin.js | 2 +- 2 files changed, 14 insertions(+), 3 deletions(-) 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); }) From 804fc9f9db671340cb1bbb32658f80819f8c84d3 Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Thu, 20 May 2021 16:53:42 +0200 Subject: [PATCH 14/20] fix library download --- .../Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue | 8 ++++---- .../Libraries/LibraryFolder/TopToolbar/download.js | 2 ++ 2 files changed, 6 insertions(+), 4 deletions(-) diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue index f269faafa4b..97a2085fcef 100644 --- a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue +++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue @@ -287,7 +287,7 @@ export default { Toast.info("You must select at least one dataset to download"); return; } - + console.log(folders); download(format, datasets, folders); }); }, @@ -303,12 +303,12 @@ 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; + item.type === "file" ? datasets.push(idOnly ? item.id : item) : folders.push(idOnly ? item.id : 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/download.js b/client/src/components/Libraries/LibraryFolder/TopToolbar/download.js index 227e9d61777..d7b09a457f6 100644 --- a/client/src/components/Libraries/LibraryFolder/TopToolbar/download.js +++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/download.js @@ -32,5 +32,7 @@ export default function download(format, dataset_ids, folder_ids) { // function download(format) { var url = `${getAppRoot()}api/libraries/datasets/download/${format}`; var data = { ld_ids: dataset_ids, folder_ids: folder_ids }; + console.log("data", data); + console.log("data", data); processDownload(url, data, "get"); } From 7f7cc7d6a4b6a8a126b160e6494c366e2a989da0 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 20 May 2021 16:53:50 +0200 Subject: [PATCH 15/20] Fix subworkflow upgrade action Fixes https://github.com/galaxyproject/galaxy/issues/12024. --- client/src/components/Workflow/Editor/Index.vue | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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; From fc2de2c029a7129050143954ab857bcb3ff863d0 Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Thu, 20 May 2021 16:54:17 +0200 Subject: [PATCH 16/20] remove debug code --- .../Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue | 1 - .../components/Libraries/LibraryFolder/TopToolbar/download.js | 2 -- 2 files changed, 3 deletions(-) diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue index 97a2085fcef..a0035da71b7 100644 --- a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue +++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue @@ -287,7 +287,6 @@ export default { Toast.info("You must select at least one dataset to download"); return; } - console.log(folders); download(format, datasets, folders); }); }, diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/download.js b/client/src/components/Libraries/LibraryFolder/TopToolbar/download.js index d7b09a457f6..227e9d61777 100644 --- a/client/src/components/Libraries/LibraryFolder/TopToolbar/download.js +++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/download.js @@ -32,7 +32,5 @@ export default function download(format, dataset_ids, folder_ids) { // function download(format) { var url = `${getAppRoot()}api/libraries/datasets/download/${format}`; var data = { ld_ids: dataset_ids, folder_ids: folder_ids }; - console.log("data", data); - console.log("data", data); processDownload(url, data, "get"); } From a002b75291693de15309f189eede422051584d5a Mon Sep 17 00:00:00 2001 From: Oleg Zharkov Date: Thu, 20 May 2021 17:02:40 +0200 Subject: [PATCH 17/20] simplify if/else a bit --- .../Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue | 4 +++- 1 file changed, 3 insertions(+), 1 deletion(-) diff --git a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue index a0035da71b7..a9fddc56612 100644 --- a/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue +++ b/client/src/components/Libraries/LibraryFolder/TopToolbar/FolderTopBar.vue @@ -287,6 +287,7 @@ export default { Toast.info("You must select at least one dataset to download"); return; } + download(format, datasets, folders); }); }, @@ -305,7 +306,8 @@ export default { const folders = []; const selected = await this.getSelected(); selected.forEach((item) => { - item.type === "file" ? datasets.push(idOnly ? item.id : item) : folders.push(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: folders }; }, From aa45f1e13f9dc63e20dc028d53dd61f21ad79644 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 20 May 2021 17:45:15 +0200 Subject: [PATCH 18/20] Fix uploading multiple files from FTP --- .../components/Upload/UploadModalContent.vue | 33 +++++++++---------- 1 file changed, 16 insertions(+), 17 deletions(-) diff --git a/client/src/components/Upload/UploadModalContent.vue b/client/src/components/Upload/UploadModalContent.vue index 9b63418134b..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_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"), - }); + 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; }, From e5b4af2704f16d45fa704b0c62794c9aeffaff9c Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Thu, 20 May 2021 18:58:49 +0200 Subject: [PATCH 19/20] Add selenium test for uploading multiple files --- test/integration_selenium/test_upload_ftp.py | 38 ++++++++++++++------ 1 file changed, 28 insertions(+), 10 deletions(-) diff --git a/test/integration_selenium/test_upload_ftp.py b/test/integration_selenium/test_upload_ftp.py index 38c0e7df93d..ac7b2002382 100644 --- a/test/integration_selenium/test_upload_ftp.py +++ b/test/integration_selenium/test_upload_ftp.py @@ -20,22 +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() From 4023806080f84ce61a32aec965c4acc287814536 Mon Sep 17 00:00:00 2001 From: Dave B Date: Tue, 18 May 2021 15:42:22 -0400 Subject: [PATCH 20/20] Open input file in read mode --- tools/extract/liftOver_wrapper.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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