Close #438 by searching for default pipelines by name.

micall/monitor/kive_watcher.py

@@ -172,6 +172,7 @@ def __init__(self,
         self.folder_watchers = {}  # {base_calls_folder: FolderWatcher}
         self.pipelines = {}  # {pipeline_id: pipeline}
         self.external_directory_path = self.external_directory_name = None
+        self.find_default_pipelines()
         self.input_pipeline_ids = config and dict(
             quality_csv=config.micall_filter_quality_pipeline_id,
             bad_cycles_csv=config.micall_main_pipeline_id,
@@ -181,6 +182,34 @@ def __init__(self,
         # Active runs started by other users.
         self.other_runs = None  # {(pipeline_id, dataset_id, dataset_id, ...): run}
 
+    def find_default_pipelines(self):
+        default_family_names = ['filter quality',
+                                'main',
+                                'resistance']
+        family_data = None
+        for family_name in default_family_names:
+            attribute_name = (
+                    'micall_' + family_name.replace(' ', '_') + '_pipeline_id')
+            if getattr(self.config, attribute_name) is not None:
+                continue
+            if family_data is None:
+                self.check_session()
+                filter_text = 'filters[0][key]=smart&filters[0][val]=micall'
+                family_data = self.session.get(
+                    '@api_pipeline_families',
+                    context={'filters': filter_text}).json()
+
+            search_text = 'micall ' + family_name
+            for family in family_data:
+                if search_text in family['name'].lower():
+                    for member in family['members']:
+                        setattr(self.config, attribute_name, member['id'])
+                        break
+                    break
+            else:
+                raise RuntimeError(f'Argument {attribute_name} not set, and '
+                                   f'no pipeline found named {search_text!r}.')
+
     def is_full(self):
         active_count = sum(len(folder_watcher.active_samples)
                            for folder_watcher in self.folder_watchers.values())

micall/tests/test_kive_watcher.py

@@ -150,6 +150,66 @@ def create_raw_data_with_two_runs(tmpdir):
     return raw_data
 
 
+def test_find_default_pipelines(mock_open_kive):
+    mock_session = mock_open_kive.return_value
+    mock_session.get.side_effect = [
+        Mock(name='get external file directories',
+             **{'json.return_value': []}),
+        Mock(name='get pipeline families',
+             **{'json.return_value': [
+                 dict(id=42,
+                      name='Other MiCall',
+                      members=[dict(id=420)]),
+                 dict(id=43,
+                      name='MiCall Filter Quality',
+                      members=[dict(id=435),
+                               dict(id=432)]),
+                 dict(id=44,
+                      name='MiCall Main',
+                      members=[dict(id=440)]),
+                 dict(id=45,
+                      name='MiCall Resistance',
+                      members=[dict(id=450)])]})]
+    expected_filter_quality_pipeline_id = 435
+    expected_main_pipeline_id = 440
+    expected_resistance_pipeline_id = 450
+    args = parse_args([])  # No parameters: all defaults.
+
+    kive_watcher = KiveWatcher(args)
+
+    assert expected_filter_quality_pipeline_id == \
+        kive_watcher.config.micall_filter_quality_pipeline_id
+    assert expected_main_pipeline_id == \
+        kive_watcher.config.micall_main_pipeline_id
+    assert expected_resistance_pipeline_id == \
+        kive_watcher.config.micall_resistance_pipeline_id
+
+
+def test_default_pipeline_not_found(mock_open_kive):
+    mock_session = mock_open_kive.return_value
+    mock_session.get.side_effect = [
+        Mock(name='get external file directories',
+             **{'json.return_value': []}),
+        Mock(name='get pipeline families',
+             **{'json.return_value': [
+                 dict(id=43,
+                      name='MiCall Filter Quality',
+                      members=[dict(id=435)]),
+                 dict(id=44,
+                      name='MiCrawl Main',  # <== Typo
+                      members=[dict(id=440)]),
+                 dict(id=45,
+                      name='MiCall Resistance',
+                      members=[dict(id=450)])]})]
+    args = parse_args([])  # No parameters: all defaults.
+
+    with pytest.raises(
+            RuntimeError,
+            match=r"Argument micall_main_pipeline_id not set, and no "
+                  r"pipeline found named 'micall main'\."):
+        KiveWatcher(args)
+
+
 def test_hcv_pair(raw_data_with_hcv_pair):
     sample_queue = DummyQueueSink()
     sample_queue.expect_put(

micall_watcher.py

@@ -91,9 +91,6 @@ def parse_args(argv=None):
         args.kive_password = os.environ.get('MICALL_KIVE_PASSWORD', 'kive')
     if not hasattr(args, 'qai_password'):
         args.qai_password = os.environ.get('MICALL_QAI_PASSWORD', 'testing')
-    if args.micall_filter_quality_pipeline_id is None:
-        parser.error('Missing micall_filter_quality_pipeline_id. Set the '
-                     'argument or environment variable.')
     return args