use enum

Author: adamcantor22

mmeds/database/database.py

@@ -1005,14 +1005,14 @@ def check_study_name(self, study_name):
         """ Verifies the provided study name is valid and not already in use. """
         if not study_name.replace('_', '').isalnum():
             raise StudyNameError("Only alpha numeric characters and '_' are allowed in the study name")
-        if MMEDSDoc.objects(study_name=study_name, doc_type='study'):
+        if MMEDSDoc.objects(study_name=study_name, doc_type=DocType.STUDY):
             raise StudyNameError(f"Study name {study_name} already in use")
 
     def check_sequencing_run_name(self, run_name):
         """ Verifies the provided sequencing run name is valid and not already in use. """
         if not run_name.replace('_', '').isalnum():
             raise StudyNameError("Only alpha-numeric characters and '_' are allowed in the sequencing run name")
-        if MMEDSDoc.objects(study_name=run_name, doc_type='sequencing_run'):
+        if MMEDSDoc.objects(data_name=run_name, doc_type=DocType.DATA):
             raise StudyNameError(f"Sequencing Run name {run_name} already in use")
 
     def get_sequencing_run_locations(self, metadata, user, column=("RawDataProtocol", "RawDataProtocolID")):
@@ -1042,27 +1042,27 @@ def get_sequencing_run_locations(self, metadata, user, column=("RawDataProtocol"
 
     def get_all_studies(self):
         """ Return all studies currently stored in the database. """
-        return MMEDSDoc.objects(doc_type='study')
+        return MMEDSDoc.objects(doc_type=DocType.STUDY)
 
     def get_all_analyses(self):
         """ Return all analyses currently stored in the database. """
-        return MMEDSDoc.objects(doc_type='analysis')
+        return MMEDSDoc.objects(doc_type=DocType.ANALYSIS)
 
     def get_all_sequencing_runs(self):
         """ Return all sequencing runs currently stored in the database. """
-        return MMEDSDoc.objects(doc_type='sequencing_run')
+        return MMEDSDoc.objects(doc_type=DocType.DATA)
 
     def get_all_user_sequencing_runs(self, user):
         """ Return all sequencing runs currently stored in the database owned by USER. """
-        return MMEDSDoc.objects(doc_type='sequencing_run', owner=user)
+        return MMEDSDoc.objects(doc_type=DocType.DATA, owner=user)
 
     def get_all_user_studies(self, user):
         """ Return all studies currently stored in the database owned by USER. """
-        return MMEDSDoc.objects(doc_type='study', owner=user)
+        return MMEDSDoc.objects(doc_type=DocType.STUDY, owner=user)
 
     def get_all_analyses_from_study(self, access_code):
         """ Return all studies currently stored in the database. """
-        return MMEDSDoc.objects(study_code=access_code, doc_type='analysis')
+        return MMEDSDoc.objects(study_code=access_code, doc_type=DocType.ANALYSIS)
 
     def check_files(self, access_code):
         """ Check that all files associated with the study actually exist. """
@@ -1076,7 +1076,7 @@ def check_files(self, access_code):
 
     def get_metadata_file_location(self, study_name):
         """ Return the metadata.tsv file location for a given study """
-        doc = MMEDSDoc.objects(doc_type='study', study_name=study_name).first()
+        doc = MMEDSDoc.objects(doc_type=DocType.STUDY, study_name=study_name).first()
         return doc['files']['metadata']
 
     def delete_mongo_documents(self):

mmeds/secrets.py

@@ -22,7 +22,7 @@
 EMAIL_PASS = ''
 TEST_PASS = 'testpassL33TG@m3r'
 TEST_USER_PASS = 'password'
-TEST_ROOT_PASS = 'root'
+TEST_ROOT_PASS = ''
 REUPLOAD_PASS = 'r3Up10@D'
 AUTH_KEY = b'F1ndTh3W@tch3r'
 WATCHER_PORT = 52953

mmeds/spawn.py

@@ -328,7 +328,6 @@ def handle_upload(self, process):
             if 'ids' in process[0]:
                 (ptype, owner, access_code, aliquot_table, id_type, generate_id) = process
                 p = MetaDataAdder(owner, access_code, aliquot_table, id_type, generate_id, self.testing)
-                self.db_lock.acquire()
 
             # Add new sequencing run
             elif 'run' in process[0]:
@@ -337,7 +336,6 @@ def handle_upload(self, process):
 
                 p = DataUploader(new_access_code, username, sequencing_run_name, reads_type,
                                  datafiles, public, self.testing)
-                self.db_lock.acquire()
             # Add new study
             else:
                 Logger.debug(f"length: {len(process)}")

mmeds/tests/unit/test_analysis.py

@@ -1,4 +1,4 @@
-from unittest import TestCase
+from unittest import TestCase, skip
 from pathlib import Path
 import mmeds.config as fig
 from time import sleep
@@ -47,7 +47,7 @@ def test_b_analysis_init(self):
         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)]
 
-
+    @skip
     def test_c_core_pipeline_taxonomic(self):
         """ Test running a standard analysis """
         # run_analysis() executes analyses synchronously rather than submitting as a job