Merge pull request #3131 from antgonza/add-base-for-new-admin-plugin

add base for new admin plugin

Author: wasade

qiita_db/artifact.py

@@ -337,7 +337,7 @@ def create(cls, filepaths, artifact_type, name=None, prep_template=None,
             raise qdb.exceptions.QiitaDBArtifactCreationError(
                 "When provided, both parents and processing parameters should "
                 "be provided")
-        elif bool(analysis) != bool(data_type):
+        elif bool(analysis) and not bool(data_type):
             # When provided, analysis and data_type both should be
             # provided (this is effectively doing an XOR)
             raise qdb.exceptions.QiitaDBArtifactCreationError(
@@ -476,7 +476,8 @@ def _associate_with_analysis(instance, analysis_id):
                 instance = _common_creation_steps(
                     artifact_type, None, data_type, None)
                 # Associate the artifact with the analysis
-                analysis.add_artifact(instance)
+                if bool(analysis):
+                    analysis.add_artifact(instance)
 
             # Associate the artifact with its filepaths
             fp_ids = qdb.util.insert_filepaths(

qiita_db/handlers/processing_job.py

@@ -71,9 +71,11 @@ def get(self, job_id):
             cmd = job.command.name
             params = job.parameters.values
             status = job.status
+            msg = '' if status != 'error' else job.log.msg
 
         response = {'command': cmd, 'parameters': params,
-                    'status': status}
+                    'status': status, 'msg': msg}
+
         self.write(response)
 
 

qiita_db/handlers/tests/test_processing_job.py

@@ -51,7 +51,8 @@ def test_get(self):
                   "phred_quality_threshold": 3, "barcode_type": "golay_12",
                   "max_barcode_errors": 1.5, "input_data": 1,
                   'phred_offset': 'auto'}
-        exp = {'command': cmd, 'parameters': params, 'status': 'success'}
+        exp = {'command': cmd, 'parameters': params, 'status': 'success',
+               'msg': ''}
         self.assertEqual(loads(obs.body), exp)
 
     def test_get_no_header(self):

qiita_db/processing_job.py

@@ -1197,11 +1197,15 @@ def _complete_artifact_definition(self, artifact_data):
                                 AND processing_job_id = %s"""
                     qdb.sql_connection.TRN.add(sql, [an.id, self.id])
                     data_type = qdb.sql_connection.TRN.execute_fetchlast()
-                else:
+                elif job_params['template'] is not None:
                     pt = qdb.metadata_template.prep_template.PrepTemplate(
                         job_params['template'])
                     an = None
                     data_type = None
+                else:
+                    pt = None
+                    an = None
+                    data_type = 'Job Output Folder'
 
                 qdb.artifact.Artifact.create(
                     filepaths, atype, prep_template=pt, analysis=an,

qiita_db/support_files/patches/83.sql

@@ -0,0 +1,3 @@
+-- August 16, 2021
+-- adding new artifact_type for raw_job_folder
+INSERT INTO qiita.data_type (data_type) VALUES ('Job Output Folder');

qiita_db/test/test_util.py

@@ -156,7 +156,8 @@ def test_get_data_types(self):
         obs = qdb.util.get_data_types()
         exp = {'16S': 1, '18S': 2, 'ITS': 3, 'Proteomic': 4, 'Metabolomic': 5,
                'Metagenomic': 6, 'Multiomic': 7, 'Metatranscriptomics': 8,
-               'Viromics': 9, 'Genomics': 10, 'Transcriptomics': 11}
+               'Viromics': 9, 'Genomics': 10, 'Transcriptomics': 11,
+               'Job Output Folder': 12}
         self.assertEqual(obs, exp)
 
         obs = qdb.util.get_data_types(key='data_type_id')

qiita_pet/handlers/api_proxy/tests/test_prep_template.py

@@ -52,9 +52,11 @@ def test_new_prep_template_get_req(self):
         exp = {
             'status': 'success',
             'prep_files': ['uploaded_file.txt'],
-            'data_types': ['16S', '18S', 'Genomics', 'ITS', 'Metabolomic',
-                           'Metagenomic', 'Metatranscriptomics', 'Multiomic',
-                           'Proteomic', 'Transcriptomics', 'Viromics'],
+            'data_types': ['16S', '18S', 'Genomics', 'ITS',
+                           'Job Output Folder', 'Metabolomic',
+                           'Metagenomic', 'Metatranscriptomics',
+                           'Multiomic', 'Proteomic', 'Transcriptomics',
+                           'Viromics'],
             'ontology': {
                 'ENA': ['Cancer Genomics', 'Epigenetics', 'Exome Sequencing',
                         'Forensic or Paleo-genomics', 'Gene Regulation Study',

qiita_pet/handlers/study_handlers/tests/test_sample_template.py

@@ -305,10 +305,11 @@ def test_sample_template_overview_handler_get_request(self):
         obs = sample_template_overview_handler_get_request(new_study.id, user)
         exp = {'exists': False,
                'uploaded_files': [],
-               'data_types': ['16S', '18S', 'Genomics', 'ITS', 'Metabolomic',
-                              'Metagenomic', 'Metatranscriptomics',
-                              'Multiomic', 'Proteomic', 'Transcriptomics',
-                              'Viromics'],
+               'data_types':  ['16S', '18S', 'Genomics', 'ITS',
+                               'Job Output Folder', 'Metabolomic',
+                               'Metagenomic', 'Metatranscriptomics',
+                               'Multiomic', 'Proteomic', 'Transcriptomics',
+                               'Viromics'],
                'user_can_edit': True,
                'job': None,
                'download_id': None,

qiita_pet/test/test_download.py

@@ -425,7 +425,8 @@ def test_download(self):
         self.assertEqual(response.reason, 'Not a valid data_type. Valid types '
                          'are: 16S, 18S, ITS, Proteomic, Metabolomic, '
                          'Metagenomic, Multiomic, Metatranscriptomics, '
-                         'Viromics, Genomics, Transcriptomics')
+                         'Viromics, Genomics, Transcriptomics, '
+                         'Job Output Folder')
 
         response = self.get(
             '/public_download/?data=raw&study_id=1&data_type=Genomics')