Merge pull request galaxyproject#10241 from guerler/markdown_editor_001

Create Page from Invocation Report

client/src/bundleEntries.js

@@ -96,7 +96,6 @@ export { mountWorkflowEditor } from "components/Workflow/Editor/mount";
 export { mountPageEditor } from "components/PageEditor/mount";
 export { mountPageDisplay } from "components/PageDisplay";
 export { mountDestinationParams } from "components/JobDestinationParams";
-export { mountInvocationReport } from "components/Workflow/mount";
 
 // Used in common.mako
 export { default as store } from "storemodern";

client/src/components/Workflow/InvocationReport.vue

@@ -1,11 +1,5 @@
 <template>
-    <div id="columns">
-        <div id="center">
-            <div class="h-100 overflow-auto p-3">
-                <markdown :markdown-config="markdownConfig" :read-only="true" />
-            </div>
-        </div>
-    </div>
+    <markdown class="p-3" :markdown-config="markdownConfig" @onEdit="onEdit" />
 </template>
 
 <script>
@@ -46,9 +40,12 @@ export default {
             });
     },
     methods: {
+        onEdit() {
+            window.location = `${getAppRoot()}pages/create?invocation_id=${this.invocationId}`;
+        },
         /** Markdown data request helper **/
         async getMarkdown(id) {
-            const url = getAppRoot() + `api/invocations/${id}/report`;
+            const url = `${getAppRoot()}api/invocations/${id}/report`;
             try {
                 const { data } = await axios.get(url);
                 return data;

client/src/components/WorkflowInvocationState/WorkflowInvocationState.vue

@@ -125,7 +125,7 @@ export default {
             return this.invocationSchedulingTerminal && this.jobStatesTerminal;
         },
         invocationLink: function () {
-            return getUrl(`page/edit_report?id=${this.invocationId}`);
+            return getUrl(`workflows/invocations/report?id=${this.invocationId}`);
         },
         bcoJSON: function () {
             return getUrl(`api/invocations/${this.invocationId}/biocompute/download`);

client/src/entry/analysis/AnalysisRouter.js

@@ -32,6 +32,7 @@ import InteractiveTools from "components/InteractiveTools/InteractiveTools.vue";
 import WorkflowList from "components/Workflow/WorkflowList.vue";
 import HistoryImport from "components/HistoryImport.vue";
 import HistoryView from "components/HistoryView.vue";
+import WorkflowInvocationReport from "components/Workflow/InvocationReport.vue";
 import WorkflowRun from "components/Workflow/Run/WorkflowRun.vue";
 import RecentInvocations from "components/User/RecentInvocations.vue";
 import ToolsView from "components/ToolsView/ToolsView.vue";
@@ -75,6 +76,7 @@ export const getAnalysisRouter = (Galaxy) =>
             "(/)workflows/run(/)": "show_workflows_run",
             "(/)workflows(/)list": "show_workflows",
             "(/)workflows/invocations": "show_workflow_invocations",
+            "(/)workflows/invocations/report": "show_workflow_invocation_report",
             // "(/)workflows/invocations/view_bco": "show_invocation_bco",
             "(/)workflows/list_published(/)": "show_workflows_published",
             "(/)workflows/create(/)": "show_workflows_create",
@@ -192,6 +194,11 @@ export const getAnalysisRouter = (Galaxy) =>
             this._display_vue_helper(HistoryView, { id: QueryStringParsing.get("id") });
         },
 
+        show_workflow_invocation_report: function () {
+            const invocationId = QueryStringParsing.get("id");
+            this._display_vue_helper(WorkflowInvocationReport, { invocationId: invocationId }, null, true);
+        },
+
         show_workflow_invocations: function () {
             this._display_vue_helper(RecentInvocations, {});
         },
@@ -266,9 +273,14 @@ export const getAnalysisRouter = (Galaxy) =>
         },
 
         show_pages_create: function () {
+            let url = "page/create";
+            const invocation_id = QueryStringParsing.get("invocation_id");
+            if (invocation_id) {
+                url += `?invocation_id=${invocation_id}`;
+            }
             this.page.display(
                 new FormWrapper.View({
-                    url: "page/create",
+                    url: url,
                     redirect: "pages/list",
                     active_tab: "user",
                 })

lib/galaxy/managers/pages.py

@@ -18,6 +18,7 @@
     ready_galaxy_markdown_for_export,
     ready_galaxy_markdown_for_import,
 )
+from galaxy.managers.workflows import WorkflowsManager
 from galaxy.model.item_attrs import UsesAnnotations
 from galaxy.util import unicodify
 from galaxy.util.sanitize_html import sanitize_html
@@ -72,6 +73,7 @@ def __init__(self, app, *args, **kwargs):
         """
         """
         super().__init__(app, *args, **kwargs)
+        self.workflow_manager = WorkflowsManager(app)
 
     def copy(self, trans, page, user, **kwargs):
         """
@@ -80,17 +82,23 @@ def copy(self, trans, page, user, **kwargs):
     def create(self, trans, payload):
         user = trans.get_user()
 
-        if not payload.get("title", None):
+        if not payload.get("title"):
             raise exceptions.ObjectAttributeMissingException("Page name is required")
-        elif not payload.get("slug", None):
+        elif not payload.get("slug"):
             raise exceptions.ObjectAttributeMissingException("Page id is required")
         elif not base.is_valid_slug(payload["slug"]):
             raise exceptions.ObjectAttributeInvalidException("Page identifier must consist of only lowercase letters, numbers, and the '-' character")
         elif trans.sa_session.query(trans.app.model.Page).filter_by(user=user, slug=payload["slug"], deleted=False).first():
             raise exceptions.DuplicatedSlugException("Page identifier must be unique")
 
-        content = payload.get("content", "")
-        content_format = payload.get("content_format", "html")
+        if payload.get("invocation_id"):
+            invocation_id = payload.get("invocation_id")
+            invocation_report = self.workflow_manager.get_invocation_report(trans, invocation_id)
+            content = invocation_report.get("markdown")
+            content_format = "markdown"
+        else:
+            content = payload.get("content", "")
+            content_format = payload.get("content_format", "html")
         content = self.rewrite_content_for_import(trans, content, content_format)
 
         # Create the new stored page

lib/galaxy/managers/workflows.py

@@ -39,6 +39,7 @@
     ToolModule,
     WorkflowModuleInjector
 )
+from galaxy.workflow.reports import generate_report
 from galaxy.workflow.resources import get_resource_mapper_function
 from galaxy.workflow.steps import attach_ordered_steps
 from .base import decode_id
@@ -168,6 +169,22 @@ def get_invocation(self, trans, decoded_invocation_id):
         self.check_security(trans, workflow_invocation, check_ownership=True, check_accessible=False)
         return workflow_invocation
 
+    def get_invocation_report(self, trans, invocation_id, **kwd):
+        decoded_workflow_invocation_id = trans.security.decode_id(invocation_id)
+        workflow_invocation = self.get_invocation(trans, decoded_workflow_invocation_id)
+        generator_plugin_type = kwd.get("generator_plugin_type")
+        runtime_report_config_json = kwd.get("runtime_report_config_json")
+        invocation_markdown = kwd.get("invocation_markdown", None)
+        target_format = kwd.get("format", "json")
+        if invocation_markdown:
+            runtime_report_config_json = {"markdown": invocation_markdown}
+        return generate_report(
+            trans, workflow_invocation,
+            runtime_report_config_json=runtime_report_config_json,
+            plugin_type=generator_plugin_type,
+            target_format=target_format,
+        )
+
     def cancel_invocation(self, trans, decoded_invocation_id):
         workflow_invocation = self.get_invocation(trans, decoded_invocation_id)
         cancelled = workflow_invocation.cancel()

lib/galaxy/selenium/navigates_galaxy.py

@@ -1100,7 +1100,7 @@ def tool_parameter_edit_rules(self, expanded_parameter_id="rules"):
     def tool_set_value(self, expanded_parameter_id, value, expected_type=None, test_data_resolver=None):
         div_element = self.tool_parameter_div(expanded_parameter_id)
         assert div_element
-        if expected_type in ["data", "data_collection"]:
+        if expected_type in ["select", "data", "data_collection"]:
             div_selector = "div.ui-form-element[tour_id$='%s']" % expanded_parameter_id
             self.select2_set_value(div_selector, value)
         else:

lib/galaxy/webapps/galaxy/api/pages.py

@@ -95,10 +95,6 @@ def create(self, trans, payload, **kwd):
         self.manager.rewrite_content_for_export(trans, rval)
         return rval
 
-    @expose_api
-    def create_report(self, trans, payload, **kwd):
-        pass
-
     @expose_api
     def delete(self, trans, id, **kwd):
         """

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -44,7 +44,6 @@
 )
 from galaxy.workflow.extract import extract_workflow
 from galaxy.workflow.modules import module_factory
-from galaxy.workflow.reports import generate_report
 from galaxy.workflow.run import invoke, queue_invoke
 from galaxy.workflow.run_request import build_workflow_run_configs
 
@@ -964,7 +963,7 @@ def show_invocation_report(self, trans, invocation_id, **kwd):
         Get JSON summarizing invocation for reporting.
         """
         kwd["format"] = "json"
-        return self._generate_report(trans, invocation_id, **kwd)
+        return self.workflow_manager.get_invocation_report(trans, invocation_id, **kwd)
 
     @expose_api_raw
     def show_invocation_report_pdf(self, trans, invocation_id, **kwd):
@@ -976,23 +975,7 @@ def show_invocation_report_pdf(self, trans, invocation_id, **kwd):
         """
         kwd["format"] = "pdf"
         trans.response.set_content_type("application/pdf")
-        return self._generate_report(trans, invocation_id, **kwd)
-
-    def _generate_report(self, trans, invocation_id, **kwd):
-        decoded_workflow_invocation_id = self.decode_id(invocation_id)
-        workflow_invocation = self.workflow_manager.get_invocation(trans, decoded_workflow_invocation_id)
-        generator_plugin_type = kwd.get("generator_plugin_type")
-        runtime_report_config_json = kwd.get("runtime_report_config_json")
-        invocation_markdown = kwd.get("invocation_markdown", None)
-        target_format = kwd.get("format", "json")
-        if invocation_markdown:
-            runtime_report_config_json = {"markdown": invocation_markdown}
-        return generate_report(
-            trans, workflow_invocation,
-            runtime_report_config_json=runtime_report_config_json,
-            plugin_type=generator_plugin_type,
-            target_format=target_format,
-        )
+        return self.workflow_manager.get_invocation_report(trans, invocation_id, **kwd)
 
     def _generate_invocation_bco(self, trans, invocation_id, **kwd):
         decoded_workflow_invocation_id = self.decode_id(invocation_id)

lib/galaxy/webapps/galaxy/buildapp.py

@@ -161,6 +161,7 @@ def app_factory(global_conf, load_app_kwds={}, **kwargs):
     webapp.add_client_route('/workflows/trs_import')
     webapp.add_client_route('/workflows/trs_search')
     webapp.add_client_route('/workflows/invocations')
+    webapp.add_client_route('/workflows/invocations/report')
     # webapp.add_client_route('/workflows/invocations/view_bco')
     webapp.add_client_route('/custom_builds')
     webapp.add_client_route('/interactivetool_entry_points/list')

lib/galaxy/webapps/galaxy/controllers/page.py

@@ -23,6 +23,7 @@
     PageContentProcessor,
     PageManager,
 )
+from galaxy.managers.workflows import WorkflowsManager
 from galaxy.model.item_attrs import UsesItemRatings
 from galaxy.util import unicodify
 from galaxy.util.sanitize_html import sanitize_html
@@ -275,6 +276,7 @@ def __init__(self, app):
         self.history_manager = HistoryManager(app)
         self.history_serializer = HistorySerializer(self.app)
         self.hda_manager = HDAManager(app)
+        self.workflow_manager = WorkflowsManager(app)
 
     @web.expose
     @web.json
@@ -324,15 +326,32 @@ def create(self, trans, payload=None, **kwd):
         Create a new page.
         """
         if trans.request.method == 'GET':
+            form_title = "Create new Page"
+            title = ""
+            slug = ""
+            content = ""
+            content_format_hide = False
+            content_hide = True
+            if "invocation_id" in kwd:
+                invocation_id = kwd.get("invocation_id")
+                form_title = form_title + " from Invocation Report"
+                slug = "invocation-report-" + invocation_id
+                invocation_report = self.workflow_manager.get_invocation_report(trans, invocation_id)
+                title = invocation_report.get("title")
+                content = invocation_report.get("markdown")
+                content_format_hide = True
+                content_hide = False
             return {
-                'title'  : 'Create a new page',
+                'title'  : form_title,
                 'inputs' : [{
                     'name'      : 'title',
-                    'label'     : 'Name'
+                    'label'     : 'Name',
+                    'value'     : title,
                 }, {
                     'name'      : 'slug',
                     'label'     : 'Identifier',
-                    'help'      : 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).'
+                    'help'      : 'A unique identifier that will be used for public links to this page. This field can only contain lowercase letters, numbers, and dashes (-).',
+                    'value'     : slug,
                 }, {
                     'name'      : 'annotation',
                     'label'     : 'Annotation',
@@ -341,8 +360,15 @@ def create(self, trans, payload=None, **kwd):
                     'name'      : 'content_format',
                     'label'     : 'Content Format',
                     'type'      : 'select',
-                    'options'   : [('HTML', 'html'), ('Markdown', 'markdown')],
+                    'hidden'    : content_format_hide,
+                    'options'   : [('Markdown', 'markdown'), ('HTML', 'html')],
                     'help'      : 'Use the traditional rich HTML editor or the newer experimental Markdown editor to create the page content. The HTML editor has several known bugs, is unmaintained and pages created with it will be read-only in future releases of Galaxy.'
+                }, {
+                    'name'      : 'content',
+                    'label'     : 'Content',
+                    'area'      : True,
+                    'value'     : content,
+                    'hidden'    : content_hide,
                 }]
             }
         else:
@@ -415,14 +441,6 @@ def edit_content(self, trans, id):
         """
         return trans.fill_template("page/editor.mako", id=id)
 
-    @web.expose
-    @web.require_login("edit workflow invocation report")
-    def edit_report(self, trans, id):
-        """
-        Render the report page interface.
-        """
-        return trans.fill_template("page/report.mako", id=id)
-
     @web.expose
     @web.require_login("use Galaxy pages")
     def share(self, trans, id, email="", use_panels=False):

lib/galaxy_test/api/test_pages.py

@@ -1,7 +1,7 @@
 from requests import delete
 
 from galaxy.exceptions import error_codes
-from galaxy_test.base.populators import DatasetPopulator
+from galaxy_test.base.populators import DatasetPopulator, skip_without_tool, WorkflowPopulator
 from ._framework import ApiTestCase
 
 
@@ -43,6 +43,57 @@ def test_create(self):
         response_json = self._create_valid_page_with_slug("mypage")
         self._assert_has_keys(response_json, "slug", "title", "id")
 
+    @skip_without_tool("cat")
+    def test_create_from_report(self):
+        dataset_populator = DatasetPopulator(self.galaxy_interactor)
+        workflow_populator = WorkflowPopulator(self.galaxy_interactor)
+        test_data = """
+input_1:
+  value: 1.bed
+  type: File
+"""
+        with dataset_populator.test_history() as history_id:
+            summary = workflow_populator.run_workflow("""
+class: GalaxyWorkflow
+inputs:
+  input_1: data
+outputs:
+  output_1:
+    outputSource: first_cat/out_file1
+steps:
+  first_cat:
+    tool_id: cat
+    in:
+      input1: input_1
+""", test_data=test_data, history_id=history_id)
+
+            workflow_id = summary.workflow_id
+            invocation_id = summary.invocation_id
+            report_json = workflow_populator.workflow_report_json(workflow_id, invocation_id)
+            assert "markdown" in report_json
+            self._assert_has_keys(report_json , "markdown", "render_format")
+            assert report_json["render_format"] == "markdown"
+            markdown_content = report_json["markdown"]
+            page_request = dict(
+                slug="invocation-report",
+                title="Invocation Report",
+                invocation_id=invocation_id,
+            )
+            page_response = self._post("pages", page_request)
+            self._assert_status_code_is(page_response, 200)
+            page_response = page_response.json()
+            show_response = self._get("pages/%s" % page_response['id'])
+            self._assert_status_code_is(show_response, 200)
+            show_json = show_response.json()
+            self._assert_has_keys(show_json, "slug", "title", "id")
+            self.assertEqual(show_json["slug"], "invocation-report")
+            self.assertEqual(show_json["title"], "Invocation Report")
+            self.assertEqual(show_json["content_format"], "markdown")
+            markdown_content = show_json["content"]
+            assert "## Workflow Outputs" in markdown_content
+            assert "## Workflow Inputs" in markdown_content
+            assert "## About This Report" not in markdown_content
+
     def test_index(self):
         create_response_json = self._create_valid_page_with_slug("indexpage")
         assert self._users_index_has_page_with_id(create_response_json["id"])