From 57d1b146729223da9daa286a1cc75db6f2923746 Mon Sep 17 00:00:00 2001 From: Antonio Gonzalez Date: Mon, 29 Jan 2024 12:35:46 -0700 Subject: [PATCH 01/11] Update CHANGELOG.md --- CHANGELOG.md | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 1756c7238..24ad9a78a 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -13,7 +13,7 @@ Deployed on January 8th, 2024 * Workflow definitions can now use sample or preparation information columns/values to differentiate between them. * Updated the Adapter and host filtering plugin (qp-fastp-minimap2) to v2023.12 addressing a bug in adapter filtering; [more information](https://qiita.ucsd.edu/static/doc/html/processingdata/qp-fastp-minimap2.html). * Other fixes: [3334](https://github.com/qiita-spots/qiita/pull/3334), [3338](https://github.com/qiita-spots/qiita/pull/3338). Thank you @sjanssen2. -* The internal Sequence Processing Pipeline is now using the human pan-genome reference, together with the GRCh38 genome + PhiX and CHM13 genome for human host filtering. +* The internal Sequence Processing Pipeline is now using the human pan-genome reference, together with the GRCh38 genome + PhiX and T2T-CHM13v2.0 genome for human host filtering. Version 2023.10 From eb594e28148989e22152113368bc21e32af45a13 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Sun, 18 Feb 2024 23:18:23 +0100 Subject: [PATCH 02/11] update QIIME name to QIIMEq2 --- qiita_db/support_files/patches/91.sql | 15 +++++++++++++++ 1 file changed, 15 insertions(+) create mode 100644 qiita_db/support_files/patches/91.sql diff --git a/qiita_db/support_files/patches/91.sql b/qiita_db/support_files/patches/91.sql new file mode 100644 index 000000000..eb05c079c --- /dev/null +++ b/qiita_db/support_files/patches/91.sql @@ -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'; From 9908ce2d64ddf46227562b444b47ff05cd467cd0 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 19 Feb 2024 11:03:58 +0100 Subject: [PATCH 03/11] update plugin name --- .../handlers/artifact_handlers/tests/test_base_handlers.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py b/qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py index f386b3c24..b1f283700 100644 --- a/qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py +++ b/qiita_pet/handlers/artifact_handlers/tests/test_base_handlers.py @@ -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, From ac99460fe85d7786244ab6a77ca3616df234b490 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 19 Feb 2024 11:25:08 +0100 Subject: [PATCH 04/11] rename QIIME to QIIMEq2 --- .../handlers/analysis_handlers/tests/test_base_handlers.py | 6 +++--- qiita_pet/handlers/api_proxy/tests/test_processing.py | 2 +- qiita_pet/handlers/study_handlers/tests/test_processing.py | 2 +- 3 files changed, 5 insertions(+), 5 deletions(-) diff --git a/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py b/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py index 735c6db1d..2d7a1c2dd 100644 --- a/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py +++ b/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py @@ -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': '', diff --git a/qiita_pet/handlers/api_proxy/tests/test_processing.py b/qiita_pet/handlers/api_proxy/tests/test_processing.py index 63b52d1b8..cd8079b7e 100644 --- a/qiita_pet/handlers/api_proxy/tests/test_processing.py +++ b/qiita_pet/handlers/api_proxy/tests/test_processing.py @@ -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) diff --git a/qiita_pet/handlers/study_handlers/tests/test_processing.py b/qiita_pet/handlers/study_handlers/tests/test_processing.py index 0a7f616a6..53e607dcf 100644 --- a/qiita_pet/handlers/study_handlers/tests/test_processing.py +++ b/qiita_pet/handlers/study_handlers/tests/test_processing.py @@ -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) From 5c019f5b9a99fdabcc9d2a1bcd6772f45aa616ce Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 19 Feb 2024 11:39:33 +0100 Subject: [PATCH 05/11] rename QIIME --- .../analysis_handlers/tests/test_base_handlers.py | 12 ++++++------ 1 file changed, 6 insertions(+), 6 deletions(-) diff --git a/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py b/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py index 2d7a1c2dd..dec54fb9c 100644 --- a/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py +++ b/qiita_pet/handlers/analysis_handlers/tests/test_base_handlers.py @@ -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', @@ -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', From 6a9c2f9d7ee1c850abd36bdbb0a93a16453cbf14 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 19 Feb 2024 12:03:10 +0100 Subject: [PATCH 06/11] more renaming of QIIME to QIIMEq2 for qiita_db tests --- qiita_db/test/test_artifact.py | 2 +- qiita_db/test/test_meta_util.py | 6 +++--- qiita_db/test/test_software.py | 14 +++++++------- 3 files changed, 11 insertions(+), 11 deletions(-) diff --git a/qiita_db/test/test_artifact.py b/qiita_db/test/test_artifact.py index 5cd425e23..ff0b06375 100644 --- a/qiita_db/test/test_artifact.py +++ b/qiita_db/test/test_artifact.py @@ -469,7 +469,7 @@ 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')) diff --git a/qiita_db/test/test_meta_util.py b/qiita_db/test/test_meta_util.py index 93e96f10b..55ee763c9 100644 --- a/qiita_db/test/test_meta_util.py +++ b/qiita_db/test/test_meta_util.py @@ -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 diff --git a/qiita_db/test/test_software.py b/qiita_db/test/test_software.py index a9e3dc5c3..059e0c15c 100644 --- a/qiita_db/test/test_software.py +++ b/qiita_db/test/test_software.py @@ -342,7 +342,7 @@ def test_create_error(self): self.outputs) # the output type doesn't exist - with self.assertRaisesRegex(ValueError, "Error creating QIIME, Split " + with self.assertRaisesRegex(ValueError, "Error creating QIIMEq2, Split " "libraries - wrong output, This is a " "command for testing - Unknown " "artifact_type: BLA!"): @@ -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) @@ -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") @@ -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 ' @@ -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")) From 293ab38e7068fd94bb0e83aa04ed0fb0c690dc3d Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 19 Feb 2024 13:52:16 +0100 Subject: [PATCH 07/11] arg, forgot to save changes in other files --- qiita_db/handlers/tests/test_plugin.py | 22 +++++++++---------- .../handlers/tests/test_processing_job.py | 6 +++-- qiita_db/test/test_artifact.py | 2 +- qiita_db/test/test_meta_util.py | 6 ++--- qiita_db/test/test_software.py | 10 ++++----- 5 files changed, 24 insertions(+), 22 deletions(-) diff --git a/qiita_db/handlers/tests/test_plugin.py b/qiita_db/handlers/tests/test_plugin.py index 0194ea608..db485dcad 100644 --- a/qiita_db/handlers/tests/test_plugin.py +++ b/qiita_db/handlers/tests/test_plugin.py @@ -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) @@ -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) @@ -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 ' @@ -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', @@ -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) diff --git a/qiita_db/handlers/tests/test_processing_job.py b/qiita_db/handlers/tests/test_processing_job.py index 09e4d39ce..5ef82669a 100644 --- a/qiita_db/handlers/tests/test_processing_job.py +++ b/qiita_db/handlers/tests/test_processing_job.py @@ -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, @@ -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, diff --git a/qiita_db/test/test_artifact.py b/qiita_db/test/test_artifact.py index ff0b06375..dd44739b4 100644 --- a/qiita_db/test/test_artifact.py +++ b/qiita_db/test/test_artifact.py @@ -472,7 +472,7 @@ def test_merging_scheme(self): '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 diff --git a/qiita_db/test/test_meta_util.py b/qiita_db/test/test_meta_util.py index 55ee763c9..1f8a30a23 100644 --- a/qiita_db/test/test_meta_util.py +++ b/qiita_db/test/test_meta_util.py @@ -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 diff --git a/qiita_db/test/test_software.py b/qiita_db/test/test_software.py index 059e0c15c..a778c7d14 100644 --- a/qiita_db/test/test_software.py +++ b/qiita_db/test/test_software.py @@ -711,7 +711,7 @@ 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', 'Different description', + ('QIIMEq2', '1.9.1', 'Different description', 'source activate qiime', 'start_qiime', 'artifact transformation', '[["10.1038/nmeth.f.303", "20383131"]]', client_id, @@ -719,10 +719,10 @@ def test_from_file(self): 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) From b085f942c6fa373f21ac6a35a82cff96c7596cb2 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 19 Feb 2024 14:36:13 +0100 Subject: [PATCH 08/11] another renaming of QIIME to QIIMEq2 --- qiita_db/handlers/tests/test_plugin.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qiita_db/handlers/tests/test_plugin.py b/qiita_db/handlers/tests/test_plugin.py index db485dcad..ee80bf345 100644 --- a/qiita_db/handlers/tests/test_plugin.py +++ b/qiita_db/handlers/tests/test_plugin.py @@ -85,7 +85,7 @@ 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') From 83030b1257051d96a9925ba836028a554bf03d82 Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 19 Feb 2024 14:52:26 +0100 Subject: [PATCH 09/11] codestyle --- qiita_db/test/test_software.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/qiita_db/test/test_software.py b/qiita_db/test/test_software.py index a778c7d14..0b5094f27 100644 --- a/qiita_db/test/test_software.py +++ b/qiita_db/test/test_software.py @@ -342,8 +342,8 @@ def test_create_error(self): self.outputs) # the output type doesn't exist - with self.assertRaisesRegex(ValueError, "Error creating QIIMEq2, 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( From 107035934b9168da53ad3a291a22dd26edf6ba5b Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 19 Feb 2024 15:29:12 +0100 Subject: [PATCH 10/11] adding q2 --- qiita_db/handlers/tests/test_plugin.py | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/qiita_db/handlers/tests/test_plugin.py b/qiita_db/handlers/tests/test_plugin.py index ee80bf345..fd8d10732 100644 --- a/qiita_db/handlers/tests/test_plugin.py +++ b/qiita_db/handlers/tests/test_plugin.py @@ -88,7 +88,7 @@ def test_post(self): 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) From f3825fc8c29b7f30a70684a6fc5af9c687c5575b Mon Sep 17 00:00:00 2001 From: Stefan Janssen Date: Mon, 19 Feb 2024 16:03:36 +0100 Subject: [PATCH 11/11] another instance of renaming --- qiita_db/handlers/tests/test_plugin.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/qiita_db/handlers/tests/test_plugin.py b/qiita_db/handlers/tests/test_plugin.py index fd8d10732..f5291c277 100644 --- a/qiita_db/handlers/tests/test_plugin.py +++ b/qiita_db/handlers/tests/test_plugin.py @@ -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,