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antgonzawasademcmk3ElDeveloper
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Fix 2920 (#3042)
* Version 092020 (#3034) * inject study_type in EBI and improvements to current automatic processing pipeline (#3023) * inject study_type in ebi and improvements to current automatic proecssing pipeline * addressing @ElDeveloper comments * some general fixes/additions for next release (#3026) * some general fixes/additions for next release * adding test for not None job.release_validator_job * fix #2839 * fix #2868 (#3028) * fix #2868 * 2nd round * fix errors * more changes * fix errors * fix ProcessingJobTest * fix PY_PATCH * add missing TRN.add * encapsulated_query -> perform_as_transaction * fix #3022 (#3030) * fix #3022 * adding tests * fix #2320 (#3031) * fix #2320 * adding prints to debug * children -> 1 * APIArtifactHandlerTest -> APIArtifactHandlerTests * configure_biom * qdb.util.activate_or_update_plugins * improving code * almost there * add values.template * fix filepaths * filepaths -> files * fixing errors * add prep.artifact insertion * addressing @ElDeveloper comments * fix artifact_definition active command * != -> == * Added three tutorial sections to the Qiita documentation (#3032) * Added three tutorial sections to the Qiita documentation: 'Retrieving Public Data for Own Analysis' and 'Processing public data retrieved with redbiom' to the redbiom tab, and 'Statistical Analysis to Justify Clinical Trial Sample Size Tutorial' to the analyzing samples tab. * Update redbiom.rst * Update redbiom.rst * Update redbiom.rst * Further updates to redbiom.rst and the Stats tutorial. * update redbiom.rst * Finished proof-reading * Placed all three tutorials/sections together under Introduction to the download and analysis of public Qiita data * added a new introduction, with links to the three sections * Added figures to stats tutorial and contexts explanation * Added figures to stats tutorial and contexts explanation * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Antonio Gonzalez <antgonza@gmail.com> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * 092020 (#3033) * 092020 * connect artifact with job * rm INSERT qiita.artifact_processing_job * Apply suggestions from code review [skip ci] Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> Co-authored-by: Daniel McDonald <danielmcdonald@ucsd.edu> Co-authored-by: Mirte Kuijpers <67341505+mcmk3@users.noreply.github.com> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu> * fix #2920 * fix test Co-authored-by: Daniel McDonald <danielmcdonald@ucsd.edu> Co-authored-by: Mirte Kuijpers <67341505+mcmk3@users.noreply.github.com> Co-authored-by: Yoshiki Vázquez Baeza <yoshiki@ucsd.edu>
1 parent e4ad2d2 commit d1ddfbb

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+16
-16
lines changed

2 files changed

+16
-16
lines changed

‎qiita_pet/handlers/download.py

Lines changed: 3 additions & 3 deletions
Original file line numberDiff line numberDiff line change
@@ -113,10 +113,10 @@ def _list_artifact_files_nginx(self, artifact):
113113
elif x['fp'].startswith(basedir):
114114
spath = x['fp'][basedir_len:]
115115
to_download.append(
116-
(spath, spath, str(x['checksum']), str(x['fp_size'])))
116+
(spath, spath, '-', str(x['fp_size'])))
117117
else:
118118
to_download.append(
119-
(x['fp'], x['fp'], str(x['checksum']), str(x['fp_size'])))
119+
(x['fp'], x['fp'], '-', str(x['fp_size'])))
120120

121121
for pt in artifact.prep_templates:
122122
qmf = pt.qiime_map_fp
@@ -404,7 +404,7 @@ def get(self):
404404

405405
basedir_len = len(get_db_files_base_dir()) + 1
406406
fp = x['fp'][basedir_len:]
407-
to_download.append((fp, fp, str(x['checksum']), str(x['fp_size'])))
407+
to_download.append((fp, fp, '-', str(x['fp_size'])))
408408
self._write_nginx_file_list(to_download)
409409

410410
zip_fn = '%s_%s.zip' % (

‎qiita_pet/test/test_download.py

Lines changed: 13 additions & 13 deletions
Original file line numberDiff line numberDiff line change
@@ -146,26 +146,26 @@ def test_download_study(self):
146146
response = self.get('/download_study_bioms/1')
147147
self.assertEqual(response.code, 200)
148148
exp = (
149-
'1579715020 1256812 /protected/processed_data/1_study_1001_closed_'
149+
'- 1256812 /protected/processed_data/1_study_1001_closed_'
150150
'reference_otu_table.biom processed_data/1_study_1001_closed_'
151151
'reference_otu_table.biom\n'
152152
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
153153
'[0-9]*.txt mapping_files/4_mapping_file.txt\n'
154-
'1579715020 1256812 /protected/processed_data/'
154+
'- 1256812 /protected/processed_data/'
155155
'1_study_1001_closed_reference_otu_table.biom processed_data/'
156156
'1_study_1001_closed_reference_otu_table.biom\n'
157157
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
158158
'[0-9]*.txt mapping_files/5_mapping_file.txt\n'
159-
'1579715020 1256812 /protected/processed_data/'
159+
'- 1256812 /protected/processed_data/'
160160
'1_study_1001_closed_reference_otu_table_Silva.biom processed_data'
161161
'/1_study_1001_closed_reference_otu_table_Silva.biom\n'
162162
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
163163
'[0-9]*.txt mapping_files/6_mapping_file.txt\n'
164-
'1756512010 1093210 /protected/BIOM/7/biom_table.biom '
164+
'- 1093210 /protected/BIOM/7/biom_table.biom '
165165
'BIOM/7/biom_table.biom\n'
166166
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-'
167167
'[0-9]*.txt mapping_files/7_mapping_file.txt\n'
168-
'[0-9]* [0-9]* /protected/BIOM/{0}/otu_table.biom '
168+
'- [0-9]* /protected/BIOM/{0}/otu_table.biom '
169169
'BIOM/{0}/otu_table.biom\n'
170170
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
171171
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
@@ -237,14 +237,14 @@ def test_download_raw_data(self):
237237
self.assertEqual(response.code, 200)
238238

239239
exp = (
240-
'2125826711 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
240+
'- 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
241241
'raw_data/1_s_G1_L001_sequences.fastq.gz\n'
242-
'2125826711 58 /protected/raw_data/'
242+
'- 58 /protected/raw_data/'
243243
'1_s_G1_L001_sequences_barcodes.fastq.gz '
244244
'raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz\n'
245245
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.txt '
246246
'mapping_files/1_mapping_file.txt\n'
247-
'1756512010 1093210 /protected/BIOM/7/biom_table.biom '
247+
'- 1093210 /protected/BIOM/7/biom_table.biom '
248248
'BIOM/7/biom_table.biom\n'
249249
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-[0-9]*.txt '
250250
'mapping_files/7_mapping_file.txt\n')
@@ -437,11 +437,11 @@ def test_download(self):
437437
'/public_download/?data=biom&study_id=1&data_type=18S')
438438
self.assertEqual(response.code, 200)
439439
exp = (
440-
'[0-9]* [0-9]* /protected/processed_data/1_study_1001_closed_'
440+
'- [0-9]* /protected/processed_data/1_study_1001_closed_'
441441
'reference_otu_table.biom processed_data/1_study_1001_closed_'
442442
'reference_otu_table.biom\n- [0-9]* /protected/templates/1_prep_'
443443
'1_qiime_[0-9]*-[0-9]*.txt mapping_files/4_mapping_file.txt\n'
444-
'[0-9]* [0-9]* /protected/processed_data/1_study_1001_closed_'
444+
'- [0-9]* /protected/processed_data/1_study_1001_closed_'
445445
'reference_otu_table.biom processed_data/1_study_1001_closed_'
446446
'reference_otu_table.biom\n- [0-9]* /protected/templates/1_prep_1'
447447
'_qiime_[0-9]*-[0-9]*.txt mapping_files/5_mapping_file.txt\n')
@@ -515,7 +515,7 @@ def test_download(self):
515515
response = self.get('/public_artifact_download/?artifact_id=5')
516516
self.assertEqual(response.code, 200)
517517
exp = (
518-
'[0-9]* [0-9]* /protected/processed_data/'
518+
'- [0-9]* /protected/processed_data/'
519519
'1_study_1001_closed_reference_otu_table.biom '
520520
'processed_data/1_study_1001_closed_reference_otu_table.biom\n'
521521
'- 36762 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.txt '
@@ -541,9 +541,9 @@ def test_download(self):
541541
self.assertEqual(response_file.code, 200)
542542

543543
exp = (
544-
'2125826711 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
544+
'- 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
545545
'raw_data/1_s_G1_L001_sequences.fastq.gz\n'
546-
'2125826711 58 /protected/raw_data/1_s_G1_L001_sequences_barcodes.'
546+
'- 58 /protected/raw_data/1_s_G1_L001_sequences_barcodes.'
547547
'fastq.gz raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz\n'
548548
'- 36762 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.txt '
549549
'mapping_files/1_mapping_file.txt\n'

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