add default-workflow to future artifact - SPP

qiita_db/handlers/artifact.py

@@ -267,6 +267,7 @@ def post(self):
         atype = self.get_argument('artifact_type')
         aname = self.get_argument('command_artifact_name', 'Name')
         files = self.get_argument('files')
+        add_default_workflow = self.get_argument('add_default_workflow', False)
 
         if job_id is None and prep_id is None:
             raise HTTPError(
@@ -314,8 +315,18 @@ def post(self):
         values['template'] = prep_id
         cmd = qdb.software.Command.get_validator(atype)
         params = qdb.software.Parameters.load(cmd, values_dict=values)
-        new_job = PJ.create(user, params, True)
-        new_job.submit()
+        if add_default_workflow:
+            pwk = qdb.processing_job.ProcessingWorkflow.from_scratch(
+                user, params, name=f'ProcessingWorkflow for {job_id}')
+            # the new job is the first job in the workflow
+            new_job = list(pwk.graph.nodes())[0]
+            # adding default pipeline to the preparation
+            pt = qdb.metadata_template.prep_template.PrepTemplate(prep_id)
+            pt.add_default_workflow(user, pwk)
+            pwk.submit()
+        else:
+            new_job = PJ.create(user, params, True)
+            new_job.submit()
 
         r_client.set('prep_template_%d' % prep_id,
                      dumps({'job_id': new_job.id, 'is_qiita_job': True}))

qiita_db/handlers/tests/test_artifact.py

@@ -411,6 +411,58 @@ def test_post(self):
             sleep(0.5)
         self.assertIsNotNone(new_prep.artifact)
 
+    def test_post_insert_artifact_and_add_default_processing(self):
+        # now let's test adding an artifact + default processing to a new
+        # preparation
+        new_prep = qdb.metadata_template.prep_template.PrepTemplate.create(
+            pd.DataFrame({'new_col': {'1.SKB1.640202': 1,
+                                      '1.SKD3.640198': 2,
+                                      '1.SKM4.640180': 3}}),
+            qdb.study.Study(1), '16S')
+
+        # creating the fastq files to be added
+        fd, fp1 = mkstemp(suffix='_seqs.fastq')
+        close(fd)
+        self._clean_up_files.append(fp1)
+        with open(fp1, 'w') as f:
+            f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 1:N:0:\n"
+                    "NACGTAGGGTGCAAGCGTTGTCCGGAATNA\n"
+                    "+\n"
+                    "#1=DDFFFHHHHHJJJJJJJJJJJJGII#0\n")
+
+        fd, fp2 = mkstemp(suffix='_barcodes.fastq')
+        close(fd)
+        self._clean_up_files.append(fp2)
+        with open(fp2, 'w') as f:
+            f.write("@HWI-ST753:189:D1385ACXX:1:1101:1214:1906 2:N:0:\n"
+                    "NNNCNNNNNNNNN\n"
+                    "+\n"
+                    "#############\n")
+
+        data = {'user_email': 'demo@microbio.me',
+                'artifact_type': 'FASTQ',
+                'prep_id': new_prep.id,
+                'files': dumps([(fp1, 'raw_forward_seqs'),
+                                (fp2, 'raw_barcodes')]),
+                'add_default_workflow': False}
+        obs = self.post('/qiita_db/artifact/', headers=self.header, data=data)
+        self.assertEqual(obs.code, 200)
+        jid = loads(obs.body)['job_id']
+        # if we got to this point, then we should have a job and that job
+        # should have children jobs (generated by the default workflow)
+        job = qdb.processing_job.ProcessingJob(jid)
+        children = [c.command.name for c in job.children]
+        grandchildren = [gc.command.name for c in job.children
+                         for gc in c.children]
+        self.assertEqual('Validate', job.command.name)
+        self.assertEqual(['Split libraries FASTQ'], children)
+        self.assertEqual(['Pick closed-reference OTUs'], grandchildren)
+
+        # just to avoid any tentative issues, let's wait for the main job to
+        # finish
+        while job.status not in ('error', 'success'):
+            sleep(0.5)
+
 
 if __name__ == '__main__':
     main()

qiita_db/metadata_template/prep_template.py

@@ -726,13 +726,15 @@ def modification_timestamp(self):
     def max_samples():
         return qdb.util.max_preparation_samples()
 
-    def add_default_workflow(self, user):
-        """The modification timestamp of the prep information
+    def add_default_workflow(self, user, workflow=None):
+        """Adds the commands of the default workflow to this preparation
 
         Parameters
         ----------
         user : qiita_db.user.User
             The user that requested to add the default workflows
+        workflow : qiita_db.processing_job.ProcessingWorkflow, optional
+            The workflow to add the default processing
 
         Returns
         -------
@@ -745,6 +747,13 @@ def add_default_workflow(self, user):
             a. If this preparation doesn't have valid workflows
             b. This preparation has been fully processed (no new steps needed)
             c. If there is no valid initial artifact to start the workflow
+
+        Notes
+        -----
+        This method adds the commands in a default workflow (definition) to
+        the preparation, if a workflow (object) is passed it will add the
+        commands to the last artifact in that workflow but if it's None it will
+        create a new workflow (default)
         """
         # helper functions to avoid duplication of code
 
@@ -806,9 +815,14 @@ def _get_predecessors(workflow, node):
         #    workflow
 
         # 1.
-        prep_jobs = [j for c in self.artifact.descendants.nodes()
-                     for j in c.jobs(show_hidden=True)
-                     if j.command.software.type == 'artifact transformation']
+        # let's assume that if there is a workflow, there are no jobs
+        if workflow is not None:
+            prep_jobs = []
+        else:
+            prep_jobs = [j for c in self.artifact.descendants.nodes()
+                         for j in c.jobs(show_hidden=True)
+                         if j.command.software.type ==
+                         'artifact transformation']
         merging_schemes = {
             qdb.archive.Archive.get_merging_scheme_from_job(j): {
                 x: y.id for x, y in j.outputs.items()}
@@ -821,7 +835,14 @@ def _get_predecessors(workflow, node):
 
         # 2.
         pt_dt = self.data_type()
-        pt_artifact = self.artifact.artifact_type
+        # if there is a workflow, we would need to get the artifact_type from
+        # the job
+        if workflow is not None:
+            starting_job = list(workflow.graph.nodes())[0]
+            pt_artifact = starting_job.parameters.values['artifact_type']
+        else:
+            starting_job = None
+            pt_artifact = self.artifact.artifact_type
         workflows = [wk for wk in qdb.software.DefaultWorkflow.iter()
                      if wk.artifact_type == pt_artifact and
                      pt_dt in wk.data_type]
@@ -846,7 +867,6 @@ def _get_predecessors(workflow, node):
             raise ValueError('This preparation is complete')
 
         # 3.
-        workflow = None
         for wk, wk_data in missing_artifacts.items():
             previous_jobs = dict()
             for ma, node in wk_data.items():
@@ -886,12 +906,20 @@ def _get_predecessors(workflow, node):
 
                     cmds_to_create.append([pdp_cmd, params, reqp])
 
-                    init_artifacts = {wkartifact_type: self.artifact.id}
+                    if starting_job is not None:
+                        init_artifacts = {
+                            wkartifact_type: f'{starting_job.id}:'}
+                    else:
+                        init_artifacts = {wkartifact_type: self.artifact.id}
 
                 cmds_to_create.reverse()
                 current_job = None
                 for i, (cmd, params, rp) in enumerate(cmds_to_create):
-                    previous_job = current_job
+                    if starting_job is not None:
+                        previous_job = starting_job
+                        starting_job = None
+                    else:
+                        previous_job = current_job
                     if previous_job is None:
                         req_params = dict()
                         for iname, dname in rp.items():