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Fix 2920 #3042

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Merged
merged 4 commits into from
Nov 9, 2020
Merged

Fix 2920 #3042

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8e7abc5
Version 092020 (#3034)
antgonza Sep 16, 2020
f6d6094
Merge branch 'dev' of https://github.com/biocore/qiita into dev
antgonza Nov 5, 2020
eff15de
fix #2920
antgonza Nov 5, 2020
a8ff862
fix test
antgonza Nov 5, 2020
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6 changes: 3 additions & 3 deletions qiita_pet/handlers/download.py
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Original file line number Diff line number Diff line change
Expand Up @@ -113,10 +113,10 @@ def _list_artifact_files_nginx(self, artifact):
elif x['fp'].startswith(basedir):
spath = x['fp'][basedir_len:]
to_download.append(
(spath, spath, str(x['checksum']), str(x['fp_size'])))
(spath, spath, '-', str(x['fp_size'])))
else:
to_download.append(
(x['fp'], x['fp'], str(x['checksum']), str(x['fp_size'])))
(x['fp'], x['fp'], '-', str(x['fp_size'])))

for pt in artifact.prep_templates:
qmf = pt.qiime_map_fp
Expand Down Expand Up @@ -404,7 +404,7 @@ def get(self):

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

zip_fn = '%s_%s.zip' % (
Expand Down
26 changes: 13 additions & 13 deletions qiita_pet/test/test_download.py
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Original file line number Diff line number Diff line change
Expand Up @@ -146,26 +146,26 @@ def test_download_study(self):
response = self.get('/download_study_bioms/1')
self.assertEqual(response.code, 200)
exp = (
'1579715020 1256812 /protected/processed_data/1_study_1001_closed_'
'- 1256812 /protected/processed_data/1_study_1001_closed_'
'reference_otu_table.biom processed_data/1_study_1001_closed_'
'reference_otu_table.biom\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/4_mapping_file.txt\n'
'1579715020 1256812 /protected/processed_data/'
'- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table.biom processed_data/'
'1_study_1001_closed_reference_otu_table.biom\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/5_mapping_file.txt\n'
'1579715020 1256812 /protected/processed_data/'
'- 1256812 /protected/processed_data/'
'1_study_1001_closed_reference_otu_table_Silva.biom processed_data'
'/1_study_1001_closed_reference_otu_table_Silva.biom\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/6_mapping_file.txt\n'
'1756512010 1093210 /protected/BIOM/7/biom_table.biom '
'- 1093210 /protected/BIOM/7/biom_table.biom '
'BIOM/7/biom_table.biom\n'
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-'
'[0-9]*.txt mapping_files/7_mapping_file.txt\n'
'[0-9]* [0-9]* /protected/BIOM/{0}/otu_table.biom '
'- [0-9]* /protected/BIOM/{0}/otu_table.biom '
'BIOM/{0}/otu_table.biom\n'
'- 1 /protected/BIOM/{0}/sortmerna_picked_otus/seqs_otus.log '
'BIOM/{0}/sortmerna_picked_otus/seqs_otus.log\n'
Expand Down Expand Up @@ -237,14 +237,14 @@ def test_download_raw_data(self):
self.assertEqual(response.code, 200)

exp = (
'2125826711 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
'- 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
'raw_data/1_s_G1_L001_sequences.fastq.gz\n'
'2125826711 58 /protected/raw_data/'
'- 58 /protected/raw_data/'
'1_s_G1_L001_sequences_barcodes.fastq.gz '
'raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz\n'
'- [0-9]* /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.txt '
'mapping_files/1_mapping_file.txt\n'
'1756512010 1093210 /protected/BIOM/7/biom_table.biom '
'- 1093210 /protected/BIOM/7/biom_table.biom '
'BIOM/7/biom_table.biom\n'
'- [0-9]* /protected/templates/1_prep_2_qiime_[0-9]*-[0-9]*.txt '
'mapping_files/7_mapping_file.txt\n')
Expand Down Expand Up @@ -437,11 +437,11 @@ def test_download(self):
'/public_download/?data=biom&study_id=1&data_type=18S')
self.assertEqual(response.code, 200)
exp = (
'[0-9]* [0-9]* /protected/processed_data/1_study_1001_closed_'
'- [0-9]* /protected/processed_data/1_study_1001_closed_'
'reference_otu_table.biom processed_data/1_study_1001_closed_'
'reference_otu_table.biom\n- [0-9]* /protected/templates/1_prep_'
'1_qiime_[0-9]*-[0-9]*.txt mapping_files/4_mapping_file.txt\n'
'[0-9]* [0-9]* /protected/processed_data/1_study_1001_closed_'
'- [0-9]* /protected/processed_data/1_study_1001_closed_'
'reference_otu_table.biom processed_data/1_study_1001_closed_'
'reference_otu_table.biom\n- [0-9]* /protected/templates/1_prep_1'
'_qiime_[0-9]*-[0-9]*.txt mapping_files/5_mapping_file.txt\n')
Expand Down Expand Up @@ -515,7 +515,7 @@ def test_download(self):
response = self.get('/public_artifact_download/?artifact_id=5')
self.assertEqual(response.code, 200)
exp = (
'[0-9]* [0-9]* /protected/processed_data/'
'- [0-9]* /protected/processed_data/'
'1_study_1001_closed_reference_otu_table.biom '
'processed_data/1_study_1001_closed_reference_otu_table.biom\n'
'- 36762 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.txt '
Expand All @@ -541,9 +541,9 @@ def test_download(self):
self.assertEqual(response_file.code, 200)

exp = (
'2125826711 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
'- 58 /protected/raw_data/1_s_G1_L001_sequences.fastq.gz '
'raw_data/1_s_G1_L001_sequences.fastq.gz\n'
'2125826711 58 /protected/raw_data/1_s_G1_L001_sequences_barcodes.'
'- 58 /protected/raw_data/1_s_G1_L001_sequences_barcodes.'
'fastq.gz raw_data/1_s_G1_L001_sequences_barcodes.fastq.gz\n'
'- 36762 /protected/templates/1_prep_1_qiime_[0-9]*-[0-9]*.txt '
'mapping_files/1_mapping_file.txt\n'
Expand Down