Close #706 by adding the cascade_csv argument to the proviral pipeline.

micall/monitor/kive_watcher.py

@@ -706,8 +706,7 @@ def run_pipeline(self,
             run = self.run_proviral_pipeline(
                 sample_watcher,
                 folder_watcher,
-                (PipelineType.DENOVO_MAIN,),
-                'MiCall proviral')
+                'Proviral HIVSeqinR')
             return run
         if pipeline_type == PipelineType.RESISTANCE:
             run = self.run_resistance_pipeline(
@@ -849,27 +848,26 @@ def run_resistance_pipeline(self, sample_watcher, folder_watcher, input_pipeline
             folder_watcher.batch)
         return run
 
-    def run_proviral_pipeline(self, sample_watcher, folder_watcher, input_pipeline_types, description):
+    def run_proviral_pipeline(self, sample_watcher, folder_watcher, description):
         pipeline_id = self.config.proviral_pipeline_id
         if pipeline_id is None:
             return None
-        main_runs = filter(None,
-                           (sample_watcher.runs.get(pipeline_type)
-                            for pipeline_type in input_pipeline_types))
-        input_dataset_urls = [run_dataset['dataset']
-                              for run in main_runs
-                              for run_dataset in run['datasets']
-                              if run_dataset['argument_name'] in ('conseq_csv', 'contigs_csv')]
-        input_datasets = [self.kive_retry(lambda: self.session.get(url).json())
-                          for url in input_dataset_urls]
-        if len(input_datasets) == 1:
-            input_datasets *= 2
-        input_datasets = sorted(input_datasets, key=lambda x: x['name'])
-        inputs_dict = dict(zip(('conseqs_csv', 'contigs_csv'),
-                               input_datasets))
+        main_run = sample_watcher.runs.get(PipelineType.DENOVO_MAIN)
+        if main_run is None:
+            return None
+        input_dataset_urls = {
+            run_dataset['argument_name']: run_dataset['dataset']
+            for run_dataset in main_run['datasets']
+            if run_dataset['argument_name'] in ('conseq_csv',
+                                                'contigs_csv',
+                                                'cascade_csv')}
+        input_datasets = {
+            argument_name: self.kive_retry(lambda: self.session.get(url).json())
+            for argument_name, url in input_dataset_urls.items()}
+        input_datasets['conseqs_csv'] = input_datasets.pop('conseq_csv')
         run = self.find_or_launch_run(
             pipeline_id,
-            inputs_dict,
+            input_datasets,
             description + ' on ' + sample_watcher.sample_group.enum,
             folder_watcher.batch)
         return run

micall/monitor/sample_watcher.py

@@ -140,7 +140,7 @@ def poll_runs(self):
                     name for name in sample_watcher.sample_group.names
                     if name is not None)
 
-    def poll_sample_runs(self, sample_watcher):
+    def poll_sample_runs(self, sample_watcher: 'SampleWatcher'):
         """ Poll all active runs for a sample.
 
         :param sample_watcher: details about the sample to poll
@@ -203,7 +203,7 @@ def poll_sample_runs(self, sample_watcher):
                         or self.fetch_run_status(denovo_resistance_run))
                 proviral_run = sample_watcher.runs.get(PipelineType.PROVIRAL)
                 if proviral_run is None:
-                    if 'NFL' not in sample_watcher.sample_group.names[0]:
+                    if 'NFL' not in sample_watcher.sample_group.project_codes[0]:
                         is_proviral_complete = True
                     else:
                         self.run_pipeline(PipelineType.PROVIRAL,

micall/tests/test_kive_watcher.py

@@ -1717,6 +1717,71 @@ def test_launch_resistance_run(raw_data_with_two_samples, mock_open_kive, pipeli
         groups_allowed=['Everyone']))
 
 
+def test_launch_proviral_run(raw_data_with_two_samples, mock_open_kive):
+    pipelines_config = parse_args(argv=['--micall_filter_quality_pipeline_id', '42',
+                                        '--denovo_main_pipeline_id', '43',
+                                        '--proviral_pipeline_id', '145'])
+
+    base_calls = (raw_data_with_two_samples /
+                  "MiSeq/runs/140101_M01234/Data/Intensities/BaseCalls")
+    kive_watcher = KiveWatcher(pipelines_config)
+    kive_watcher.app_urls = {
+        pipelines_config.proviral_pipeline_id: '/containerapps/103'}
+    kive_watcher.app_args = {
+        pipelines_config.proviral_pipeline_id: dict(
+            contigs_csv='/containerargs/104',
+            conseqs_csv='/containerargs/105',
+            cascade_csv='/containerargs/106')}
+
+    folder_watcher = kive_watcher.add_folder(base_calls)
+    folder_watcher.batch = dict(url='/batches/101')
+    folder_watcher.add_run(dict(id=106),
+                           PipelineType.FILTER_QUALITY,
+                           is_complete=True)
+    sample_watcher = kive_watcher.add_sample_group(
+        base_calls=base_calls,
+        sample_group=SampleGroup('2120A',
+                                 ('2120A-PR_S14_L001_R1_001.fastq.gz',
+                                  None),
+                                 ('HIVNFLDNA', None)))
+    folder_watcher.add_run(
+        dict(id=107),
+        PipelineType.DENOVO_MAIN,
+        sample_watcher)
+
+    kive_watcher.check_session()
+    mock_session = kive_watcher.session
+    mock_session.endpoints.containerruns.get.side_effect = [
+        dict(id=107, state='C'),  # refresh run state
+        [dict(dataset='/datasets/111/',
+              argument_type='O',
+              argument_name='contigs_csv'),
+         dict(dataset='/datasets/112/',
+              argument_type='O',
+              argument_name='conseq_csv'),
+         dict(dataset='/datasets/113/',
+              argument_type='O',
+              argument_name='cascade_csv')]]  # run datasets
+    mock_session.get.return_value.json.side_effect = [
+        dict(url='/datasets/111/', id=111),
+        dict(url='/datasets/112/', id=112),
+        dict(url='/datasets/113/', id=113)]
+
+    kive_watcher.poll_runs()
+
+    mock_session.endpoints.containerruns.post.assert_called_once_with(json=dict(
+        app='/containerapps/103',
+        datasets=[dict(argument='/containerargs/104',
+                       dataset='/datasets/111/'),
+                  dict(argument='/containerargs/105',
+                       dataset='/datasets/112/'),
+                  dict(argument='/containerargs/106',
+                       dataset='/datasets/113/')],
+        name='Proviral HIVSeqinR on 2120A',
+        batch='/batches/101',
+        groups_allowed=['Everyone']))
+
+
 def test_skip_resistance_run(raw_data_with_two_samples, mock_open_kive, pipelines_config):
     pipelines_config.micall_resistance_pipeline_id = None
     base_calls = (raw_data_with_two_samples /