Unverified Commit e7e348ab authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #19525 from mvdbeek/fix_extracting_workflow_from_purged_histories 

[24.1] Fix extracting workflows from purged and deleted histories
parents 94456cb7 bd42a470

lib/galaxy/model/__init__.py

+4 −0
Original line number Diff line number Diff line
@@ -3645,6 +3645,10 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable 
        """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

+1 −1
Original line number Diff line number Diff line
@@ -283,7 +283,7 @@ class WorkflowSummary: 
        # 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

+6 −2
Original line number Diff line number Diff line
@@ -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

+4 −0
Original line number Diff line number Diff line
@@ -121,6 +121,10 @@ class MockHistory: 
    def active_contents(self):

        return self.active_datasets



    @property

    def visible_contents(self):

        return self.active_contents





class MockTrans:

    def __init__(self, history):