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Fix cmdname qp target gene #3364

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Merged
merged 12 commits into from
Feb 26, 2024
Merged

Fix cmdname qp target gene #3364

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57d1b14
Update CHANGELOG.md
antgonza Jan 29, 2024
67f2011
Merge branch 'dev' of github.com:qiita-spots/qiita into dev
sjanssen2 Feb 18, 2024
eb594e2
update QIIME name to QIIMEq2
sjanssen2 Feb 18, 2024
9908ce2
update plugin name
sjanssen2 Feb 19, 2024
ac99460
rename QIIME to QIIMEq2
sjanssen2 Feb 19, 2024
5c019f5
rename QIIME
sjanssen2 Feb 19, 2024
6a9c2f9
more renaming of QIIME to QIIMEq2 for qiita_db tests
sjanssen2 Feb 19, 2024
293ab38
arg, forgot to save changes in other files
sjanssen2 Feb 19, 2024
b085f94
another renaming of QIIME to QIIMEq2
sjanssen2 Feb 19, 2024
83030b1
codestyle
sjanssen2 Feb 19, 2024
1070359
adding q2
sjanssen2 Feb 19, 2024
f3825fc
another instance of renaming
sjanssen2 Feb 19, 2024
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30 changes: 15 additions & 15 deletions qiita_db/handlers/tests/test_plugin.py
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Expand Up @@ -18,7 +18,7 @@

class UtilTests(TestCase):
def test_get_plugin(self):
obs = _get_plugin("QIIME", "1.9.1")
obs = _get_plugin("QIIMEq2", "1.9.1")
exp = qdb.software.Software(1)
self.assertEqual(obs, exp)

Expand All @@ -27,7 +27,7 @@ def test_get_plugin(self):
_get_plugin("QiIME", "1.9.1")

def test_get_command(self):
obs = _get_command('QIIME', '1.9.1', 'Split libraries FASTQ')
obs = _get_command('QIIMEq2', '1.9.1', 'Split libraries FASTQ')
exp = qdb.software.Command(1)
self.assertEqual(obs, exp)

Expand All @@ -38,18 +38,18 @@ def test_get_command(self):

class PluginHandlerTests(OauthTestingBase):
def test_get_plugin_does_not_exist(self):
obs = self.get('/qiita_db/plugins/QIIME/1.9.0/', headers=self.header)
obs = self.get('/qiita_db/plugins/QIIMEq2/1.9.0/', headers=self.header)
self.assertEqual(obs.code, 404)

def test_get_no_header(self):
obs = self.get('/qiita_db/plugins/QIIME/1.9.0/')
obs = self.get('/qiita_db/plugins/QIIMEq2/1.9.0/')
self.assertEqual(obs.code, 400)

def test_get(self):
obs = self.get('/qiita_db/plugins/QIIME/1.9.1/', headers=self.header)
obs = self.get('/qiita_db/plugins/QIIMEq2/1.9.1/', headers=self.header)
self.assertEqual(obs.code, 200)
exp = {
'name': 'QIIME',
'name': 'QIIMEq2',
'version': '1.9.1',
'description': 'Quantitative Insights Into Microbial Ecology '
'(QIIME) is an open-source bioinformatics pipeline '
Expand Down Expand Up @@ -85,10 +85,10 @@ def test_post(self):
'param2': '2.4',
'param3': 'False'}})
}
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/', data=data,
obs = self.post('/qiita_db/plugins/QIIMEq2/1.9.1/commands/', data=data,
headers=self.header)
self.assertEqual(obs.code, 200)
obs = _get_command('QIIME', '1.9.1', 'New Command')
obs = _get_command('QIIMEq2', '1.9.1', 'New Command')
self.assertEqual(obs.name, 'New Command')
self.assertFalse(obs.analysis_only)

Expand All @@ -106,10 +106,10 @@ def test_post(self):
'default_parameter_sets': dumps({'dflt1': {'param1': 'test'}}),
'analysis_only': True
}
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/', data=data,
obs = self.post('/qiita_db/plugins/QIIMEq2/1.9.1/commands/', data=data,
headers=self.header)
self.assertEqual(obs.code, 200)
obs = _get_command('QIIME', '1.9.1', 'New analysis command')
obs = _get_command('QIIMEq2', '1.9.1', 'New analysis command')
self.assertEqual(obs.name, 'New analysis command')
self.assertTrue(obs.analysis_only)
self.assertEqual(obs.merging_scheme,
Expand All @@ -125,12 +125,12 @@ def test_get_command_does_not_exist(self):

def test_get_no_header(self):
obs = self.get(
'/qiita_db/plugins/QIIME/1.9.1/commands/Split%20libraries/')
'/qiita_db/plugins/QIIMEq2/1.9.1/commands/Split%20libraries/')
self.assertEqual(obs.code, 400)

def test_get(self):
obs = self.get(
'/qiita_db/plugins/QIIME/1.9.1/commands/Split%20libraries/',
'/qiita_db/plugins/QIIMEq2/1.9.1/commands/Split%20libraries/',
headers=self.header)
self.assertEqual(obs.code, 200)
exp = {'name': 'Split libraries',
Expand Down Expand Up @@ -195,20 +195,20 @@ def test_get(self):

class CommandActivateHandlerTests(OauthTestingBase):
def test_post_command_does_not_exist(self):
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/'
obs = self.post('/qiita_db/plugins/QIIMEq2/1.9.1/commands/'
'UNKNOWN/activate/',
headers=self.header, data={})
self.assertEqual(obs.code, 404)

def test_post_no_header(self):
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/'
obs = self.post('/qiita_db/plugins/QIIMEq2/1.9.1/commands/'
'Split%20libraries/activate/', data={})
self.assertEqual(obs.code, 400)

def test_post(self):
qdb.software.Software.deactivate_all()
self.assertFalse(qdb.software.Command(2).active)
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/'
obs = self.post('/qiita_db/plugins/QIIMEq2/1.9.1/commands/'
'Split%20libraries/activate/', headers=self.header,
data={})
self.assertEqual(obs.code, 200)
Expand Down
6 changes: 4 additions & 2 deletions qiita_db/handlers/tests/test_processing_job.py
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Expand Up @@ -277,7 +277,8 @@ class ProcessingJobAPItestHandlerTests(OauthTestingBase):
def test_post_processing_job(self):
data = {
'user': 'demo@microbio.me',
'command': dumps(['QIIME', '1.9.1', 'Pick closed-reference OTUs']),
'command': dumps(['QIIMEq2', '1.9.1',
'Pick closed-reference OTUs']),
'parameters': dumps({"reference": 1,
"sortmerna_e_value": 1,
"sortmerna_max_pos": 10000,
Expand All @@ -298,7 +299,8 @@ def test_post_processing_job(self):
def test_post_processing_job_status(self):
data = {
'user': 'demo@microbio.me',
'command': dumps(['QIIME', '1.9.1', 'Pick closed-reference OTUs']),
'command': dumps(['QIIMEq2', '1.9.1',
'Pick closed-reference OTUs']),
'status': 'running',
'parameters': dumps({"reference": 1,
"sortmerna_e_value": 1,
Expand Down
15 changes: 15 additions & 0 deletions qiita_db/support_files/patches/91.sql
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Original file line number Diff line number Diff line change
@@ -0,0 +1,15 @@
-- Feb 19, 2024
-- update qp-target-gene command name to "QIIMEq2" to be in sync with plugin repo
-- When setting up a new instance of Qiita, we end up using qiita-env make
-- which creates entries in the postgress database, also for qiita.software.
-- One of these entries belongs to the qp-target-gene plugin with name "QIIME"
-- and version "1.9.1". However, with
-- qp_target_gene/support_files/patches/171029_QIIME_v191_to_QIIMEq2_v191.sql
-- the plugin was renamed into QIIMEq2, but this change was not relected in
-- the qiita.software table. Thus, updating plugin information finds a mismatch
-- between old (QIIME) and new (QIIMEq2) names and therefor creates a new
-- command. However, the also provided default workflows hold command_ids to
-- the old version and subsequently the commands for artifact processing
-- will result in an empty list, even though the plugin is available.
-- Therefore, this patch updates the name of QIIME.
UPDATE qiita.software SET name = 'QIIMEq2' WHERE name = 'QIIME';
4 changes: 2 additions & 2 deletions qiita_db/test/test_artifact.py
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Expand Up @@ -469,10 +469,10 @@ def test_merging_scheme(self):
('Split libraries FASTQ | N/A', 'N/A'))
self.assertEqual(qdb.artifact.Artifact(4).merging_scheme,
('Pick closed-reference OTUs | Split libraries FASTQ',
'QIIME v1.9.1'))
'QIIMEq2 v1.9.1'))
self.assertEqual(qdb.artifact.Artifact(5).merging_scheme,
('Pick closed-reference OTUs | Split libraries FASTQ',
'QIIME v1.9.1'))
'QIIMEq2 v1.9.1'))

def test_jobs(self):
# Returning all jobs
Expand Down
12 changes: 6 additions & 6 deletions qiita_db/test/test_meta_util.py
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Expand Up @@ -381,15 +381,15 @@ def test_generate_biom_and_metadata_release(self):
'processed_data/1_study_1001_closed_reference_otu_table.biom\t'
'%s\t%s\t4\tIllumina\t16S rRNA\t'
'Pick closed-reference OTUs | Split libraries FASTQ\t'
'QIIME v1.9.1\tQIIME v1.9.1\n' % (fn_sample, fn_prep),
'QIIMEq2 v1.9.1\tQIIMEq2 v1.9.1\n' % (fn_sample, fn_prep),
'processed_data/1_study_1001_closed_reference_otu_table.biom\t'
'%s\t%s\t5\tIllumina\t16S rRNA\t'
'Pick closed-reference OTUs | Split libraries FASTQ\t'
'QIIME v1.9.1\tQIIME v1.9.1\n' % (fn_sample, fn_prep),
'QIIMEq2 v1.9.1\tQIIMEq2 v1.9.1\n' % (fn_sample, fn_prep),
'processed_data/1_study_1001_closed_reference_otu_table_Silva.bio'
'm\t%s\t%s\t6\tIllumina\t16S rRNA\t'
'Pick closed-reference OTUs | Split libraries FASTQ\t'
'QIIME v1.9.1\tQIIME v1.9.1' % (fn_sample, fn_prep)]
'QIIMEq2 v1.9.1\tQIIMEq2 v1.9.1' % (fn_sample, fn_prep)]
self.assertEqual(txt_obs, txt_exp)

# whatever the configuration was, we will change to settings so we can
Expand Down Expand Up @@ -465,15 +465,15 @@ def test_generate_biom_and_metadata_release(self):
'processed_data/1_study_1001_closed_reference_otu_table.biom\t'
'%s\t%s\t4\tIllumina\t16S rRNA\t'
'Pick closed-reference OTUs | Split libraries FASTQ\t'
'QIIME v1.9.1\tQIIME v1.9.1\n' % (fn_sample, fn_prep),
'QIIMEq2 v1.9.1\tQIIMEq2 v1.9.1\n' % (fn_sample, fn_prep),
'processed_data/1_study_1001_closed_reference_otu_table.biom\t'
'%s\t%s\t5\tIllumina\t16S rRNA\t'
'Pick closed-reference OTUs | Split libraries FASTQ\t'
'QIIME v1.9.1\tQIIME v1.9.1\n' % (fn_sample, fn_prep),
'QIIMEq2 v1.9.1\tQIIMEq2 v1.9.1\n' % (fn_sample, fn_prep),
'processed_data/1_study_1001_closed_reference_otu_table_Silva.bio'
'm\t%s\t%s\t6\tIllumina\t16S rRNA\t'
'Pick closed-reference OTUs | Split libraries FASTQ'
'\tQIIME v1.9.1\tQIIME v1.9.1' % (fn_sample, fn_prep)]
'\tQIIMEq2 v1.9.1\tQIIMEq2 v1.9.1' % (fn_sample, fn_prep)]
self.assertEqual(txt_obs, txt_exp)

# returning configuration
Expand Down
26 changes: 13 additions & 13 deletions qiita_db/test/test_software.py
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Expand Up @@ -342,8 +342,8 @@ def test_create_error(self):
self.outputs)

# the output type doesn't exist
with self.assertRaisesRegex(ValueError, "Error creating QIIME, Split "
"libraries - wrong output, This is a "
with self.assertRaisesRegex(ValueError, "Error creating QIIMEq2, Split"
" libraries - wrong output, This is a "
"command for testing - Unknown "
"artifact_type: BLA!"):
qdb.software.Command.create(
Expand Down Expand Up @@ -567,7 +567,7 @@ def tearDown(self):
remove(f)

def test_from_name_and_version(self):
obs = qdb.software.Software.from_name_and_version('QIIME', '1.9.1')
obs = qdb.software.Software.from_name_and_version('QIIMEq2', '1.9.1')
exp = qdb.software.Software(1)
self.assertEqual(obs, exp)

Expand All @@ -578,13 +578,13 @@ def test_from_name_and_version(self):

# Wrong name
with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError):
qdb.software.Software.from_name_and_version('QiIME', '1.9.1')
qdb.software.Software.from_name_and_version('QiIMEq2', '1.9.1')
# Wrong version
with self.assertRaises(qdb.exceptions.QiitaDBUnknownIDError):
qdb.software.Software.from_name_and_version('QIIME', '1.9.0')
qdb.software.Software.from_name_and_version('QIIMEq2', '1.9.0')

def test_name(self):
self.assertEqual(qdb.software.Software(1).name, "QIIME")
self.assertEqual(qdb.software.Software(1).name, "QIIMEq2")

def test_version(self):
self.assertEqual(qdb.software.Software(1).version, "1.9.1")
Expand Down Expand Up @@ -694,7 +694,7 @@ def test_from_file(self):
self._clean_up_files.append(fp)
with open(fp, 'w') as f:
f.write(CONF_TEMPLATE %
('QIIME', '1.9.1',
('QIIMEq2', '1.9.1',
'Quantitative Insights Into Microbial Ecology (QIIME) '
'is an open-source bioinformatics pipeline for '
'performing microbiome analysis from raw DNA '
Expand All @@ -711,18 +711,18 @@ def test_from_file(self):
self._clean_up_files.append(fp)
with open(fp, 'w') as f:
f.write(CONF_TEMPLATE %
('QIIME', '1.9.1', 'Different description',
('QIIMEq2', '1.9.1', 'Different description',
'source activate qiime', 'start_qiime',
'artifact transformation',
'[["10.1038/nmeth.f.303", "20383131"]]', client_id,
client_secret))
with warnings.catch_warnings(record=True) as warns:
obs = qdb.software.Software.from_file(fp)
obs_warns = [str(w.message) for w in warns]
exp_warns = ['Plugin "QIIME" version "1.9.1" config file does not '
'match with stored information. Check the config file'
' or run "qiita plugin update" to update the plugin '
'information. Offending values: description, '
exp_warns = ['Plugin "QIIMEq2" version "1.9.1" config file does '
'not match with stored information. Check the config '
'file or run "qiita plugin update" to update the '
'plugin information. Offending values: description, '
'environment_script, start_script']
self.assertCountEqual(obs_warns, exp_warns)

Expand Down Expand Up @@ -829,7 +829,7 @@ def test_from_file(self):
self.assertEqual(obs.client_secret, 'client_secret')

def test_exists(self):
self.assertTrue(qdb.software.Software.exists("QIIME", "1.9.1"))
self.assertTrue(qdb.software.Software.exists("QIIMEq2", "1.9.1"))
self.assertFalse(qdb.software.Software.exists("NewPlugin", "1.9.1"))
self.assertFalse(qdb.software.Software.exists("QIIME", "2.0.0"))

Expand Down
18 changes: 9 additions & 9 deletions qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py
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Expand Up @@ -43,17 +43,17 @@ def test_analysis_description_handler_get_request(self):
'artifacts': {
4: (1, 'Identification of the Microbiomes for Cannabis '
'Soils', ('Pick closed-reference OTUs | Split '
'libraries FASTQ', 'QIIME v1.9.1'), [
'libraries FASTQ', 'QIIMEq2 v1.9.1'), [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'], {'1'}),
5: (1, 'Identification of the Microbiomes for Cannabis '
'Soils', ('Pick closed-reference OTUs | Split '
'libraries FASTQ', 'QIIME v1.9.1'), [
'libraries FASTQ', 'QIIMEq2 v1.9.1'), [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'], {'1'}),
6: (1, 'Identification of the Microbiomes for Cannabis '
'Soils', ('Pick closed-reference OTUs | Split '
'libraries FASTQ', 'QIIME v1.9.1'), [
'libraries FASTQ', 'QIIMEq2 v1.9.1'), [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'], {'1'})},
'analysis_reservation': '',
Expand All @@ -72,17 +72,17 @@ def test_analysis_description_handler_get_request(self):
'artifacts': {
4: (1, 'Identification of the Microbiomes for Cannabis '
'Soils', ('Pick closed-reference OTUs | Split '
'libraries FASTQ', 'QIIME v1.9.1'), [
'libraries FASTQ', 'QIIMEq2 v1.9.1'), [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'], {'1'}),
5: (1, 'Identification of the Microbiomes for Cannabis '
'Soils', ('Pick closed-reference OTUs | Split '
'libraries FASTQ', 'QIIME v1.9.1'), [
'libraries FASTQ', 'QIIMEq2 v1.9.1'), [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'], {'1'}),
6: (1, 'Identification of the Microbiomes for Cannabis '
'Soils', ('Pick closed-reference OTUs | Split '
'libraries FASTQ', 'QIIME v1.9.1'), [
'libraries FASTQ', 'QIIMEq2 v1.9.1'), [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'], {'1'})},
'alert_msg': 'An artifact is being deleted from this analysis',
Expand All @@ -103,17 +103,17 @@ def test_analysis_description_handler_get_request(self):
'artifacts': {
4: (1, 'Identification of the Microbiomes for Cannabis '
'Soils', ('Pick closed-reference OTUs | Split '
'libraries FASTQ', 'QIIME v1.9.1'), [
'libraries FASTQ', 'QIIMEq2 v1.9.1'), [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'], {'1'}),
5: (1, 'Identification of the Microbiomes for Cannabis '
'Soils', ('Pick closed-reference OTUs | Split '
'libraries FASTQ', 'QIIME v1.9.1'), [
'libraries FASTQ', 'QIIMEq2 v1.9.1'), [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'], {'1'}),
6: (1, 'Identification of the Microbiomes for Cannabis '
'Soils', ('Pick closed-reference OTUs | Split '
'libraries FASTQ', 'QIIME v1.9.1'), [
'libraries FASTQ', 'QIIMEq2 v1.9.1'), [
'1.SKB7.640196', '1.SKB8.640193', '1.SKD8.640184',
'1.SKM4.640180', '1.SKM9.640192'], {'1'})},
'alert_msg': 'Error deleting artifact',
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/handlers/api_proxy/tests/test_processing.py
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Expand Up @@ -103,7 +103,7 @@ def test_job_ajax_get_req(self):
'command': 'Split libraries FASTQ',
'command_description': 'Demultiplexes and applies quality '
'control to FASTQ data',
'software': 'QIIME',
'software': 'QIIMEq2',
'software_version': '1.9.1'}
self.assertEqual(obs, exp)

Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py
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Expand Up @@ -258,7 +258,7 @@ def test_artifact_summary_get_request(self):
'rev_comp_mapping_barcodes': 'False',
'min_per_read_length_fraction': '0.75',
'barcode_type': 'golay_12'},
'software_version': '1.9.1', 'software': 'QIIME'},
'software_version': '1.9.1', 'software': 'QIIMEq2'},
'files': exp_files,
'is_from_analysis': False,
'summary': None,
Expand Down
2 changes: 1 addition & 1 deletion qiita_pet/handlers/study_handlers/tests/test_processing.py
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Expand Up @@ -99,7 +99,7 @@ def test_get(self):
'command': 'Split libraries FASTQ',
'command_description': 'Demultiplexes and applies quality '
'control to FASTQ data',
'software': 'QIIME',
'software': 'QIIMEq2',
'software_version': '1.9.1'}
self.assertEqual(loads(response.body), exp)

Expand Down