fix qiita-spots#3300 (qiita-spots#3309)

* fix qiita-spots#3300 * update populate_test_db.sql * fix errors * fix test_prep_template.py * fix test_setup.py * addressing @charles-cowart and @wasade comments
AmandaBirmingham · Aug 7, 2023 · 45fa66a · 45fa66a
1 parent a412b45
commit 45fa66a
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Showing 8 changed files with 36 additions and 68 deletions.
diff --git a/qiita_db/metadata_template/prep_template.py b/qiita_db/metadata_template/prep_template.py
@@ -122,11 +122,6 @@ def create(cls, md_template, study, data_type, investigation_type=None,
             If a required column is missing in md_template
         """
         with qdb.sql_connection.TRN:
-            # If the investigation_type is supplied, make sure it is one of
-            # the recognized investigation types
-            if investigation_type is not None:
-                cls.validate_investigation_type(investigation_type)
-
             # Check if the data_type is the id or the string
             if isinstance(data_type, int):
                 data_type_id = data_type
@@ -136,6 +131,18 @@ def create(cls, md_template, study, data_type, investigation_type=None,
                 data_type_id = qdb.util.convert_to_id(data_type, "data_type")
                 data_type_str = data_type
 
+            # If the investigation_type is None let's add it based on the
+            # data_type being created - if possible
+            if investigation_type is None:
+                if data_type_str in TARGET_GENE_DATA_TYPES:
+                    investigation_type = 'Amplicon'
+                elif data_type_str == 'Metagenomic':
+                    investigation_type = 'WGS'
+                elif data_type_str == 'Metatranscriptomic':
+                    investigation_type = 'RNA-Seq'
+            if investigation_type is not None:
+                cls.validate_investigation_type(investigation_type)
+
             pt_cols = PREP_TEMPLATE_COLUMNS
             if data_type_str in TARGET_GENE_DATA_TYPES:
                 pt_cols = deepcopy(PREP_TEMPLATE_COLUMNS)

diff --git a/qiita_db/metadata_template/test/test_prep_template.py b/qiita_db/metadata_template/test/test_prep_template.py
@@ -911,7 +911,7 @@ def _common_creation_checks(self, pt, fp_count, name):
         self.assertEqual(pt.data_type(), self.data_type)
         self.assertEqual(pt.data_type(ret_id=True), self.data_type_id)
         self.assertEqual(pt.artifact, None)
-        self.assertEqual(pt.investigation_type, None)
+        self.assertEqual(pt.investigation_type, 'Amplicon')
         self.assertEqual(pt.study_id, self.test_study.id)
         self.assertEqual(pt.status, "sandbox")
         exp_sample_ids = {'%s.SKB8.640193' % self.test_study.id,
@@ -1076,7 +1076,7 @@ def test_create_warning(self):
         self.assertEqual(pt.data_type(), self.data_type)
         self.assertEqual(pt.data_type(ret_id=True), self.data_type_id)
         self.assertEqual(pt.artifact, None)
-        self.assertEqual(pt.investigation_type, None)
+        self.assertEqual(pt.investigation_type, 'Amplicon')
         self.assertEqual(pt.study_id, self.test_study.id)
         self.assertEqual(pt.status, 'sandbox')
         exp_sample_ids = {'%s.SKB8.640193' % self.test_study.id,
@@ -1247,7 +1247,7 @@ def test_investigation_type_setter(self):
         """Able to update the investigation type"""
         pt = qdb.metadata_template.prep_template.PrepTemplate.create(
             self.metadata, self.test_study, self.data_type_id)
-        self.assertEqual(pt.investigation_type, None)
+        self.assertEqual(pt.investigation_type, 'Amplicon')
         pt.investigation_type = "Other"
         self.assertEqual(pt.investigation_type, 'Other')
         with self.assertRaises(qdb.exceptions.QiitaDBColumnError):
@@ -1258,8 +1258,8 @@ def test_investigation_type_setter(self):
 
     def test_investigation_type_instance_setter(self):
         pt = qdb.metadata_template.prep_template.PrepTemplate(1)
-        pt.investigation_type = 'RNASeq'
-        self.assertEqual(pt.investigation_type, 'RNASeq')
+        pt.investigation_type = 'RNA-Seq'
+        self.assertEqual(pt.investigation_type, 'RNA-Seq')
 
     def test_deprecated_setter(self):
         pt = qdb.metadata_template.prep_template.PrepTemplate(1)

diff --git a/qiita_db/support_files/populate_test_db.sql b/qiita_db/support_files/populate_test_db.sql
@@ -480,19 +480,10 @@ INSERT INTO qiita.analysis_users (analysis_id, email) VALUES (1, '[email protected]
 INSERT INTO qiita.ontology (ontology_id, ontology, fully_loaded, fullname, query_url, source_url, definition, load_date) VALUES (999999999, E'ENA', E'1', E'European Nucleotide Archive Submission Ontology', NULL, E'http://www.ebi.ac.uk/embl/Documentation/ENA-Reads.html', E'The ENA CV is to be used to annotate XML submissions to the ENA.', '2009-02-23 00:00:00');
 
 -- Add some ontology values
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508974, 999999999, E'Whole Genome Sequencing', E'ENA:0000059', NULL, NULL, NULL, NULL, NULL);
+INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508974, 999999999, E'WGS', E'ENA:0000059', NULL, NULL, NULL, NULL, NULL);
 INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508975, 999999999, E'Metagenomics', E'ENA:0000060', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508976, 999999999, E'Transcriptome Analysis', E'ENA:0000061', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508977, 999999999, E'Resequencing', E'ENA:0000062', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508978, 999999999, E'Epigenetics', E'ENA:0000066', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508979, 999999999, E'Synthetic Genomics', E'ENA:0000067', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508980, 999999999, E'Forensic or Paleo-genomics', E'ENA:0000065', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508981, 999999999, E'Gene Regulation Study', E'ENA:0000068', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508982, 999999999, E'Cancer Genomics', E'ENA:0000063', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508983, 999999999, E'Population Genomics', E'ENA:0000064', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508984, 999999999, E'RNASeq', E'ENA:0000070', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508985, 999999999, E'Exome Sequencing', E'ENA:0000071', NULL, NULL, NULL, NULL, NULL);
-INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508986, 999999999, E'Pooled Clone Sequencing', E'ENA:0000072', NULL, NULL, NULL, NULL, NULL);
+INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508976, 999999999, E'Amplicon', E'ENA:0000061', NULL, NULL, NULL, NULL, NULL);
+INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508984, 999999999, E'RNA-Seq', E'ENA:0000070', NULL, NULL, NULL, NULL, NULL);
 INSERT INTO qiita.term (term_id, ontology_id, term, identifier, definition, namespace, is_obsolete, is_root_term, is_leaf) VALUES (2052508987, 999999999, E'Other', E'ENA:0000069', NULL, NULL, NULL, NULL, NULL);
 
 -- Create the new sample_template_filepath

diff --git a/qiita_db/test/test_ontology.py b/qiita_db/test/test_ontology.py
@@ -34,28 +34,15 @@ def testShortNameProperty(self):
 
     def testTerms(self):
         obs = self.ontology.terms
-        self.assertEqual(obs, [
-            'Whole Genome Sequencing',
-            'Metagenomics',
-            'Transcriptome Analysis',
-            'Resequencing',
-            'Epigenetics',
-            'Synthetic Genomics',
-            'Forensic or Paleo-genomics',
-            'Gene Regulation Study',
-            'Cancer Genomics',
-            'Population Genomics',
-            'RNASeq',
-            'Exome Sequencing',
-            'Pooled Clone Sequencing',
-            'Other'])
+        self.assertEqual(
+            obs, ['WGS', 'Metagenomics', 'Amplicon', 'RNA-Seq', 'Other'])
 
     def test_user_defined_terms(self):
         obs = self.ontology.user_defined_terms
         self.assertEqual(obs, [])
 
     def test_term_type(self):
-        obs = self.ontology.term_type('RNASeq')
+        obs = self.ontology.term_type('RNA-Seq')
         self.assertEqual('ontology', obs)
 
         obs = self.ontology.term_type('Sasquatch')

diff --git a/qiita_db/test/test_setup.py b/qiita_db/test/test_setup.py
@@ -75,7 +75,7 @@ def test_ontology(self):
         self.assertTrue(check_count('qiita.ontology', 1))
 
     def test_ontology_terms(self):
-        self.assertTrue(check_count('qiita.term', 14))
+        self.assertTrue(check_count('qiita.term', 5))
 
 
 if __name__ == '__main__':

diff --git a/qiita_pet/handlers/api_proxy/tests/test_prep_template.py b/qiita_pet/handlers/api_proxy/tests/test_prep_template.py
@@ -38,12 +38,7 @@ class TestPrepAPIReadOnly(TestCase):
     def test_get_ENA_ontology(self):
         obs = _get_ENA_ontology()
         exp = {
-            'ENA': ['Cancer Genomics', 'Epigenetics', 'Exome Sequencing',
-                    'Forensic or Paleo-genomics', 'Gene Regulation Study',
-                    'Metagenomics', 'Pooled Clone Sequencing',
-                    'Population Genomics', 'RNASeq', 'Resequencing',
-                    'Synthetic Genomics', 'Transcriptome Analysis',
-                    'Whole Genome Sequencing', 'Other'],
+            'ENA': ['Amplicon', 'Metagenomics', 'RNA-Seq', 'WGS', 'Other'],
             'User': []}
         self.assertEqual(obs, exp)
 
@@ -58,12 +53,7 @@ def test_new_prep_template_get_req(self):
                            'Multiomic', 'Proteomic', 'Transcriptomics',
                            'Viromics'],
             'ontology': {
-                'ENA': ['Cancer Genomics', 'Epigenetics', 'Exome Sequencing',
-                        'Forensic or Paleo-genomics', 'Gene Regulation Study',
-                        'Metagenomics', 'Pooled Clone Sequencing',
-                        'Population Genomics', 'RNASeq', 'Resequencing',
-                        'Synthetic Genomics', 'Transcriptome Analysis',
-                        'Whole Genome Sequencing', 'Other'],
+                'ENA': ['Amplicon', 'Metagenomics', 'RNA-Seq', 'WGS', 'Other'],
                 'User': []}}
 
         self.assertEqual(obs, exp)
@@ -83,12 +73,7 @@ def test_prep_template_ajax_get_req(self):
                'num_columns': 22,
                'investigation_type': 'Metagenomics',
                'ontology': {
-                   'ENA': ['Cancer Genomics', 'Epigenetics',
-                           'Exome Sequencing', 'Forensic or Paleo-genomics',
-                           'Gene Regulation Study', 'Metagenomics',
-                           'Pooled Clone Sequencing', 'Population Genomics',
-                           'RNASeq', 'Resequencing', 'Synthetic Genomics',
-                           'Transcriptome Analysis', 'Whole Genome Sequencing',
+                   'ENA': ['Amplicon', 'Metagenomics', 'RNA-Seq', 'WGS',
                            'Other'],
                    'User': []},
                'artifact_attached': True,
@@ -518,10 +503,10 @@ def test_prep_template_patch_req(self):
         # Update investigation type
         obs = prep_template_patch_req(
             '[email protected]', 'replace', '/%s/investigation_type' % pt.id,
-            'Cancer Genomics')
+            'RNA-Seq')
         exp = {'status': 'success', 'message': ''}
         self.assertEqual(obs, exp)
-        self.assertEqual(pt.investigation_type, 'Cancer Genomics')
+        self.assertEqual(pt.investigation_type, 'RNA-Seq')
         # Update prep template data
         obs = prep_template_patch_req(
             '[email protected]', 'replace', '/%s/data' % pt.id, 'update.txt')
@@ -551,7 +536,7 @@ def test_prep_template_patch_req(self):
         # Operation not supported
         obs = prep_template_patch_req(
             '[email protected]', 'add', '/1/investigation_type',
-            'Cancer Genomics')
+            'RNA-Seq')
         exp = {'status': 'error',
                'message': 'Operation "add" not supported. '
                           'Current supported operations: replace, remove',
@@ -560,22 +545,22 @@ def test_prep_template_patch_req(self):
         # Incorrect path parameter
         obs = prep_template_patch_req(
             '[email protected]', 'replace', '/investigation_type',
-            'Cancer Genomics')
+            'RNA-Seq')
         exp = {'status': 'error',
                'message': 'Incorrect path parameter'}
         self.assertEqual(obs, exp)
         # Incorrect attribute
         obs = prep_template_patch_req(
             '[email protected]', 'replace', '/1/other_attribute',
-            'Cancer Genomics')
+            'RNA-Seq')
         exp = {'status': 'error',
                'message': 'Attribute "other_attribute" not found. '
                           'Please, check the path parameter'}
         self.assertEqual(obs, exp)
         # User doesn't have access
         obs = prep_template_patch_req(
             '[email protected]', 'replace', '/%s/investigation_type' % pt.id,
-            'Cancer Genomics')
+            'RNA-Seq')
         exp = {'status': 'error',
                'message': 'User has insufficient permissions'}
         self.assertEqual(obs, exp)

diff --git a/qiita_pet/test/test_prep_template.py b/qiita_pet/test/test_prep_template.py
@@ -57,7 +57,7 @@ def test_post_broken_header(self):
     def test_patch(self):
         arguments = {'op': 'replace',
                      'path': '/1/investigation_type/',
-                     'value': 'Cancer Genomics'}
+                     'value': 'RNA-Seq'}
         response = self.patch('/prep_template/', data=arguments)
         self.assertEqual(response.code, 200)
         exp = {'status': 'success', 'message': ''}

diff --git a/qiita_ware/test/test_ebi.py b/qiita_ware/test/test_ebi.py
@@ -467,10 +467,8 @@ def test_init_exceptions(self):
         # raise error as we are missing columns
         # artifact.prep_templates[0] cause there should only be 1
         exp_text = ("Errors found during EBI submission for study #1, "
-                    "artifact #%d and prep template #%d:\nUnrecognized "
-                    "investigation type: 'None'. This term is neither one of "
-                    "the official terms nor one of the user-defined terms in "
-                    "the ENA ontology.\nThese samples do not have a valid "
+                    "artifact #%d and prep template #%d:\n"
+                    "These samples do not have a valid "
                     "platform (instrumet model wasn't checked): "
                     "1.SKD6.640190\nThese samples do not have a valid "
                     "instrument model: 1.SKM6.640187" % (