Merge pull request #19525 from mvdbeek/fix_extracting_workflow_from_p…

…urged_histories

[24.1] Fix extracting workflows from purged and deleted histories

lib/galaxy/model/__init__.py

@@ -3645,6 +3645,10 @@ def active_contents(self):
         """Return all active contents ordered by hid."""
         return self.contents_iter(types=["dataset", "dataset_collection"], deleted=False, visible=True)
 
+    @property
+    def visible_contents(self):
+        return self.contents_iter(types=["dataset", "dataset_collection"], visible=True)
+
     def contents_iter(self, **kwds):
         """
         Fetch filtered list of contents of history.

lib/galaxy/workflow/extract.py

@@ -283,7 +283,7 @@ def __summarize(self):
         # just grab the implicitly mapped jobs and handle in second pass. Second pass is
         # needed because cannot allow selection of individual datasets from an implicit
         # mapping during extraction - you get the collection or nothing.
-        for content in self.history.active_contents:
+        for content in self.history.visible_contents:
             self.__summarize_content(content)
 
     def __summarize_content(self, content):

templates/webapps/galaxy/workflow/build_from_current_history.mako

@@ -88,7 +88,7 @@ into a workflow will be shown in gray.</p>
     <div class="warningmark">${warning}</div>
 %endfor
 
-<form method="post" action="${h.url_for(controller='workflow', action='build_from_current_history')}">
+<form method="post" action="${h.url_for(controller='workflow', action='build_from_current_history', history_id=trans.security.encode_id(history.id))}">
 <div class='form-row'>
     <label>Workflow name</label>
     <input name="workflow_name" type="text" value="Workflow constructed from history '${ util.unicodify( history.name )}'" size="60"/>
@@ -112,6 +112,7 @@ into a workflow will be shown in gray.</p>
     <%
     cls = "toolForm"
     tool_name = "Unknown"
+    checked_job = "checked" if any(True for d in datasets if not d[1].deleted) else ""
     if hasattr( job, 'is_fake' ) and job.is_fake:
         cls += " toolFormDisabled"
         disabled = True
@@ -142,7 +143,10 @@ into a workflow will be shown in gray.</p>
                     %if disabled:
                         <div style="font-style: italic; color: gray">${disabled_why}</div>
                     %else:
-                        <div><input type="checkbox" name="job_ids" value="${job.id}" checked="true" />Include "${tool_name}" in workflow</div>
+                        <div><input type="checkbox" name="job_ids" value="${job.id}" ${checked_job} />Include "${tool_name}" in workflow</div>
+                        %if not checked_job:
+                            ${ render_msg( "All job outputs have been deleted", status="info" ) }
+                        %endif
                         %if tool_version_warning:
                             ${ render_msg( tool_version_warning, status="warning" ) }
                         %endif

test/unit/workflows/test_extract_summary.py

@@ -121,6 +121,10 @@ def __init__(self):
     def active_contents(self):
         return self.active_datasets
 
+    @property
+    def visible_contents(self):
+        return self.active_contents
+
 
 class MockTrans:
     def __init__(self, history):