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fix qiita-spots#3300 (qiita-spots#3309)
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* 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
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@antgonza
antgonza authored Aug 7, 2023
1 parent a412b45 commit 45fa66a
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Showing 8 changed files with 36 additions and 68 deletions.
17 changes: 12 additions & 5 deletions qiita_db/metadata_template/prep_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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)
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10 changes: 5 additions & 5 deletions qiita_db/metadata_template/test/test_prep_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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,
Expand Down Expand Up @@ -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,
Expand Down Expand Up @@ -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):
Expand All @@ -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)
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15 changes: 3 additions & 12 deletions qiita_db/support_files/populate_test_db.sql
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Original file line number Diff line number Diff line change
Expand Up @@ -480,19 +480,10 @@ INSERT INTO qiita.analysis_users (analysis_id, email) VALUES (1, 'shared@foo.bar
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
Expand Down
19 changes: 3 additions & 16 deletions qiita_db/test/test_ontology.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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')
Expand Down
2 changes: 1 addition & 1 deletion qiita_db/test/test_setup.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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__':
Expand Down
33 changes: 9 additions & 24 deletions qiita_pet/handlers/api_proxy/tests/test_prep_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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)

Expand All @@ -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)
Expand All @@ -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,
Expand Down Expand Up @@ -518,10 +503,10 @@ def test_prep_template_patch_req(self):
# Update investigation type
obs = prep_template_patch_req(
'test@foo.bar', '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(
'test@foo.bar', 'replace', '/%s/data' % pt.id, 'update.txt')
Expand Down Expand Up @@ -551,7 +536,7 @@ def test_prep_template_patch_req(self):
# Operation not supported
obs = prep_template_patch_req(
'test@foo.bar', 'add', '/1/investigation_type',
'Cancer Genomics')
'RNA-Seq')
exp = {'status': 'error',
'message': 'Operation "add" not supported. '
'Current supported operations: replace, remove',
Expand All @@ -560,22 +545,22 @@ def test_prep_template_patch_req(self):
# Incorrect path parameter
obs = prep_template_patch_req(
'test@foo.bar', '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(
'test@foo.bar', '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(
'demo@microbio.me', 'replace', '/%s/investigation_type' % pt.id,
'Cancer Genomics')
'RNA-Seq')
exp = {'status': 'error',
'message': 'User has insufficient permissions'}
self.assertEqual(obs, exp)
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/test/test_prep_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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': ''}
Expand Down
6 changes: 2 additions & 4 deletions qiita_ware/test/test_ebi.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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" % (
Expand Down

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