cleaning up development stuff

mmeds/config.py

@@ -268,7 +268,7 @@
 
 
 WORKFLOWS = {
-    "standard_pipeline": {
+    "core_pipeline_taxonomic": {
         "parameters": [
             'sampling_depth',
             'metadata',
@@ -350,7 +350,7 @@
 
 CURRENT_PROCESSES = DATABASE_DIR / 'current_processes.yaml'
 CONFIG_PARAMETERS = {
-    'standard_pipeline': [
+    'core_pipeline_taxonomic': [
         'sampling_depth',
         'metadata',
         'alpha_metrics',

mmeds/database/database.py

@@ -1042,7 +1042,6 @@ def get_sequencing_run_locations(self, metadata, user, column=("RawDataProtocol"
             doc = MMEDSDoc.objects(doc_type='sequencing_run', study_name=run, owner=user).first()
             run_paths[run] = {}
             # Get individual files within sequencing run directories
-            print(Path(doc.path) / fig.SEQUENCING_DIRECTORY_FILE)
             with open(Path(doc.path) / fig.SEQUENCING_DIRECTORY_FILE, "rt") as f:
                 content = f.read().split('\n')
                 # Read the key value pair of datafile type and file location

mmeds/database/documents.py

@@ -121,7 +121,6 @@ def generate_MMEDSDoc(self, name, workflow_type, analysis_type, config, access_c
         files['metadata'] = new_dir / 'metadata.tsv'
         string_files = {str(key): str(value) for key, value in files.items()}
 
-        print(config)
         doc = MMEDSDoc(created=datetime.now(),
                        last_accessed=datetime.now(),
                        sub_analysis=False,

mmeds/tests/unit/test_analysis.py

@@ -22,7 +22,7 @@ def setUpClass(self):
         self.watcher = Watcher()
         self.watcher.connect()
         self.queue = self.watcher.get_queue()
-        self.config = load_config(fig.DEFAULT_CONFIG, fig.TEST_MIXED_METADATA, 'standard_pipeline')
+        self.config = load_config(fig.DEFAULT_CONFIG, fig.TEST_MIXED_METADATA, 'core_pipeline_taxonomic')
         self.config_lefse = load_config(fig.DEFAULT_CONFIG_LEFSE, fig.TEST_MIXED_METADATA, 'lefse')
         self.analysis = []
         with Database(owner=fig.TEST_USER_0, testing=True) as db:
@@ -43,15 +43,15 @@ def test_b_analysis_init(self):
         with Database(owner=fig.TEST_USER_0, testing=True) as db:
             self.runs = db.get_sequencing_run_locations(fig.TEST_MIXED_METADATA, fig.TEST_USER_0)
         self.analysis += [Analysis(self.queue, fig.TEST_USER_0, self.analysis_code_0, fig.TEST_CODE_MIXED,
-                                'standard_pipeline', 'default', 'test_init', self.config, True, self.runs, False, threads=2)]
+                                'core_pipeline_taxonomic', 'default', 'test_init', self.config, True, self.runs, False, threads=2)]
         self.analysis += [Analysis(self.queue, fig.TEST_USER_0, self.analysis_code_1, fig.TEST_CODE_MIXED,
                                 'lefse', 'default', 'test_lefse', self.config_lefse, True, {}, False, threads=2)]
 
 
-    def test_c_standard_pipeline(self):
+    def test_c_core_pipeline_taxonomic(self):
         """ Test running a standard analysis """
         # run_analysis() executes analyses synchronously rather than submitting as a job
-        run_analysis(self.test_study, 'standard_pipeline', testing=True)
+        run_analysis(self.test_study, 'core_pipeline_taxonomic', testing=True)
 
     def test_d_analysis_class(self):
         """ Test the analysis objects """

mmeds/tests/unit/test_documents.py

@@ -30,7 +30,7 @@ def test_creation(self):
 
     def create_from_study(self):
         """ Test creating a document """
-        config = util.load_config(None, fig.TEST_METADATA, 'standard_pipeline')
+        config = util.load_config(None, fig.TEST_METADATA, 'core_pipeline_taxonomic')
         sd = docs.MMEDSDoc.objects(access_code=self.test_code).first()
         ad = sd.generate_MMEDSDoc('testDocument', 'qiime2', 'DADA2', config, 'test_documents')
         self.assertEqual(Path(sd.path), Path(ad.path).parent)

mmeds/tests/unit/test_snakemake.py

@@ -37,9 +37,9 @@ def run_snakemake(self, path):
         return 0
 
 
-    def test_a_standard_pipeline(self):
+    def test_a_core_pipeline_taxonomic(self):
         """ Test snakemake standard pipeline analysis """
-        result = self.run_snakemake(Path(fig.TEST_SNAKEMAKE_DIR) / "standard_pipeline")
+        result = self.run_snakemake(Path(fig.TEST_SNAKEMAKE_DIR) / "core_pipeline_taxonomic")
         self.assertEquals(result, 0)
 
 

mmeds/tests/unit/test_spawn.py

@@ -69,7 +69,7 @@ def test_a_upload_data(self):
     def test_b_start_analysis(self):
         """ Test starting analysis through the queue """
         for proc in self.infos:
-            self.q.put(('analysis', proc['owner'], proc['access_code'], 'standard_pipeline',
+            self.q.put(('analysis', proc['owner'], proc['access_code'], 'core_pipeline_taxonomic',
                         'default', 'test_analysis', None, {}, -1, False))
 
         Logger.info('Waiting on analysis')
@@ -114,7 +114,7 @@ def test_c_restart_analysis(self):
     def test_d_node_analysis(self):
         Logger.info("node analysis")
         for i in range(5):
-            self.q.put(('analysis', self.infos[0]['owner'], self.infos[0]['access_code'], 'standard_pipeline',
+            self.q.put(('analysis', self.infos[0]['owner'], self.infos[0]['access_code'], 'core_pipeline_taxonomic',
                         'default', 'test_analysis_node', None, {}, -1, True))
 
         pipe_results = self.receive_all_pipe_output(8)

mmeds/tests/unit/test_tools.py

@@ -18,7 +18,7 @@ class ToolsTests(TestCase):
 
     @classmethod
     def setUpClass(self):
-        self.config = load_config(None, fig.TEST_METADATA_SHORT, 'standard_pipeline')
+        self.config = load_config(None, fig.TEST_METADATA_SHORT, 'core_pipeline_taxonomic')
         self.q = Queue()
         self.testing = True
 

mmeds/tests/unit/test_util.py

@@ -122,28 +122,28 @@ def test_f_get_valid_columns(self):
 
     def test_g_load_config_file(self):
         # Test when no config is given
-        config = util.load_config(None, fig.TEST_METADATA, 'standard_pipeline')
-        for param in fig.WORKFLOWS['standard_pipeline']['parameters']:
+        config = util.load_config(None, fig.TEST_METADATA, 'core_pipeline_taxonomic')
+        for param in fig.WORKFLOWS['core_pipeline_taxonomic']['parameters']:
             assert config.get(param) is not None
 
-        config = util.load_config(Path(fig.TEST_CONFIG_ALL), fig.TEST_METADATA, 'standard_pipeline')
+        config = util.load_config(Path(fig.TEST_CONFIG_ALL), fig.TEST_METADATA, 'core_pipeline_taxonomic')
         assert len(config['taxa_levels']) == 7
 
         # Check the config file fail states
         with raises(InvalidConfigError) as e_info:
-            config = util.load_config(Path(fig.TEST_CONFIG_1), fig.TEST_METADATA, 'standard_pipeline')
+            config = util.load_config(Path(fig.TEST_CONFIG_1), fig.TEST_METADATA, 'core_pipeline_taxonomic')
         assert 'Missing parameter' in e_info.value.message
 
         with raises(InvalidConfigError) as e_info:
-            config = util.load_config(Path(fig.TEST_CONFIG_2), fig.TEST_METADATA, 'standard_pipeline')
+            config = util.load_config(Path(fig.TEST_CONFIG_2), fig.TEST_METADATA, 'core_pipeline_taxonomic')
         assert 'Invalid metadata column' in e_info.value.message
 
         with raises(InvalidConfigError) as e_info:
-            config = util.load_config(Path(fig.TEST_CONFIG_3), fig.TEST_METADATA, 'standard_pipeline')
+            config = util.load_config(Path(fig.TEST_CONFIG_3), fig.TEST_METADATA, 'core_pipeline_taxonomic')
         assert 'Invalid parameter' in e_info.value.message
 
         with raises(InvalidConfigError) as e_info:
-            config = util.load_config(Path(fig.TEST_METADATA), fig.TEST_METADATA, 'standard_pipeline')
+            config = util.load_config(Path(fig.TEST_METADATA), fig.TEST_METADATA, 'core_pipeline_taxonomic')
         assert 'YAML format' in e_info.value.message
 
     def test_h_mmeds_to_MIxS(self):