Commit 256dd034 authored by mvdbeek's avatar mvdbeek Committed by Sergey Golitsynskiy
Browse files

Simplify and fix JobExportHistoryArchive / GenomeIndexToolData handling 

Output parameters must behave somewhat like a HDA, in that they need to
have a dataset attribute that points to a Dataset instance.
`GenomeIndexToolData` fits that requirement, `JobExportHistoryArchive`
provides the fda property that behaves like a HDA.
parent 5aa8ee84

lib/galaxy/jobs/__init__.py

+4 −4
Original line number Diff line number Diff line
@@ -1093,10 +1093,10 @@ class JobWrapper(HasResourceParameters): 
        job = self._load_job()



        def get_special():

            special = self.sa_session.query(model.JobExportHistoryArchive).filter_by(job=job).first()

            if not special:

                special = self.sa_session.query(model.GenomeIndexToolData).filter_by(job=job).first()

            return special

            jeha = self.sa_session.query(model.JobExportHistoryArchive).filter_by(job=job).first()

            if jeha:

                return jeha.fda

            return self.sa_session.query(model.GenomeIndexToolData).filter_by(job=job).first()



        tool_evaluator = self._get_tool_evaluator(job)

        compute_environment = compute_environment or self.default_compute_environment(job)

lib/galaxy/tools/evaluation.py

+1 −1
Original line number Diff line number Diff line
@@ -86,7 +86,7 @@ class ToolEvaluator: 
        if get_special:

            special = get_special()

            if special:

                out_data["output_file"] = getattr(special, 'fda', None)

                out_data["output_file"] = special



        # These can be passed on the command line if wanted as $__user_*__

        incoming.update(model.User.user_template_environment(job.history and job.history.user))