From ae402778364ac423073cc4f90fabac9567590066 Mon Sep 17 00:00:00 2001 From: Simon Bray Date: Wed, 23 Mar 2022 15:39:14 +0100 Subject: [PATCH 1/3] expose trs id of imported workflows in the ui --- .../components/Workflow/WorkflowDropdown.vue | 20 +++++++++++++++++++ lib/galaxy/managers/workflows.py | 1 + lib/galaxy/webapps/galaxy/api/workflows.py | 6 +++++- .../selenium/test_workflow_management.py | 2 +- 4 files changed, 27 insertions(+), 2 deletions(-) diff --git a/client/src/components/Workflow/WorkflowDropdown.vue b/client/src/components/Workflow/WorkflowDropdown.vue index a02444793c2..48757074e22 100644 --- a/client/src/components/Workflow/WorkflowDropdown.vue +++ b/client/src/components/Workflow/WorkflowDropdown.vue @@ -9,6 +9,12 @@ {{ workflow.name }} +

{{ workflow.description }}

@@ -45,6 +51,13 @@ View + + + View on Dockstore + Delete @@ -85,6 +98,13 @@ export default { this.workflow.slug }`; }, + urlDockstore() { + if (this.workflow.source_metadata && this.workflow.source_metadata.trs_tool_id) { + return `https://dockstore.org/workflows${this.workflow.source_metadata.trs_tool_id.slice(9)}`; + } else { + return null; + } + }, }, created() { this.root = getAppRoot(); diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py index 945fc2d3235..da66b41341b 100644 --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -1295,6 +1295,7 @@ class WorkflowContentsManager(UsesAnnotations): item["annotation"] = self.get_item_annotation_str(sa_session, stored.user, stored) item["license"] = workflow.license item["creator"] = workflow.creator_metadata + item["source_metadata"] = workflow.source_metadata steps = {} steps_to_order_index = {} for step in workflow.steps: diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py index cbd5550348d..c295fafe6b6 100644 --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -180,6 +180,7 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U item["annotations"] = [x.annotation for x in wf.annotations] item["url"] = url_for("workflow", id=encoded_id) item["owner"] = wf.user.username + item["source_metadata"] = wf.latest_workflow.source_metadata item["number_of_steps"] = wf.latest_workflow.step_count item["show_in_tool_panel"] = False if user is not None: @@ -360,10 +361,12 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U trs_server = payload.get("trs_server") trs_tool_id = payload.get("trs_tool_id") trs_version_id = payload.get("trs_version_id") + import_source = None archive_data = self.app.trs_proxy.get_version_descriptor(trs_server, trs_tool_id, trs_version_id) else: try: archive_data = requests.get(archive_source, timeout=util.DEFAULT_SOCKET_TIMEOUT).text + import_source = "URL" except Exception: raise exceptions.MessageException(f"Failed to open URL '{escape(archive_source)}'.") elif hasattr(archive_file, "file"): @@ -371,11 +374,12 @@ class WorkflowsAPIController(BaseGalaxyAPIController, UsesStoredWorkflowMixin, U uploaded_file_name = uploaded_file.name if os.path.getsize(os.path.abspath(uploaded_file_name)) > 0: archive_data = util.unicodify(uploaded_file.read()) + import_source = "uploaded file" else: raise exceptions.MessageException("You attempted to upload an empty file.") else: raise exceptions.MessageException("Please provide a URL or file.") - return self.__api_import_from_archive(trans, archive_data, "uploaded file", payload=payload) + return self.__api_import_from_archive(trans, archive_data, import_source, payload=payload) if "from_history_id" in payload: from_history_id = payload.get("from_history_id") diff --git a/lib/galaxy_test/selenium/test_workflow_management.py b/lib/galaxy_test/selenium/test_workflow_management.py index b204ef1ed55..0269276ba8c 100644 --- a/lib/galaxy_test/selenium/test_workflow_management.py +++ b/lib/galaxy_test/selenium/test_workflow_management.py @@ -19,7 +19,7 @@ class WorkflowManagementTestCase(SeleniumTestCase): assert len(table_elements) == 1 new_workflow = table_elements[0].find_element_by_css_selector(".workflow-dropdown") - assert "TestWorkflow1 (imported from uploaded file)" in new_workflow.text, new_workflow.text + assert "TestWorkflow1 (imported from URL)" in new_workflow.text, new_workflow.text @selenium_test def test_view(self): From 61a43603acf899cf0a527309eb1d01ad074aca32 Mon Sep 17 00:00:00 2001 From: Simon Bray Date: Mon, 28 Mar 2022 17:46:06 +0200 Subject: [PATCH 2/3] add link for url-imported workflows --- .../components/Workflow/WorkflowDropdown.vue | 41 ++++++++++++++----- 1 file changed, 30 insertions(+), 11 deletions(-) diff --git a/client/src/components/Workflow/WorkflowDropdown.vue b/client/src/components/Workflow/WorkflowDropdown.vue index 48757074e22..99e65ad3195 100644 --- a/client/src/components/Workflow/WorkflowDropdown.vue +++ b/client/src/components/Workflow/WorkflowDropdown.vue @@ -10,11 +10,16 @@ {{ workflow.name }} +

{{ workflow.description }}

@@ -51,12 +56,9 @@ View - - - View on Dockstore + + + {{ sourceLabel }} @@ -98,13 +100,30 @@ export default { this.workflow.slug }`; }, - urlDockstore() { - if (this.workflow.source_metadata && this.workflow.source_metadata.trs_tool_id) { - return `https://dockstore.org/workflows${this.workflow.source_metadata.trs_tool_id.slice(9)}`; + sourceUrl() { + if (this.workflow.source_metadata?.url) { + return this.workflow.source_metadata.url; + } else if (this.workflow.source_metadata?.trs_server) { + if (this.workflow.source_metadata?.trs_server == "dockstore") { + return `https://dockstore.org/workflows${this.workflow.source_metadata.trs_tool_id.slice(9)}`; + } else { + // TODO: add WorkflowHub + return null; + } } else { return null; } }, + sourceLabel() { + if (this.workflow.source_metadata?.url) { + return "View external link"; + } else if (this.workflow.source_metadata?.trs_server == "dockstore") { + return "View on Dockstore"; + } else { + // TODO: add WorkflowHub + return null; + } + }, }, created() { this.root = getAppRoot(); From e449930d72b93c63df05e62122c716205ea78edb Mon Sep 17 00:00:00 2001 From: Simon Bray Date: Tue, 29 Mar 2022 11:01:02 +0200 Subject: [PATCH 3/3] do not use optional chaining in vue template --- client/src/components/Workflow/WorkflowDropdown.vue | 13 +++++++++++-- 1 file changed, 11 insertions(+), 2 deletions(-) diff --git a/client/src/components/Workflow/WorkflowDropdown.vue b/client/src/components/Workflow/WorkflowDropdown.vue index 99e65ad3195..6d5ecf5caa7 100644 --- a/client/src/components/Workflow/WorkflowDropdown.vue +++ b/client/src/components/Workflow/WorkflowDropdown.vue @@ -10,13 +10,13 @@ {{ workflow.name }} @@ -124,6 +124,15 @@ export default { return null; } }, + sourceType() { + if (this.workflow.source_metadata?.url) { + return "url"; + } else if (this.workflow.source_metadata?.trs_server) { + return `trs_${this.workflow.source_metadata?.trs_server}`; + } else { + return ""; + } + }, }, created() { this.root = getAppRoot();