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Merged
merged 2 commits into from
Jan 12, 2023
Merged

adding support for new /qiita_db/artifacts #45

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620869b
adding support for new /qiita_db/artifacts
antgonza Jan 12, 2023
5a802dd
filepaths is a dict
antgonza Jan 12, 2023
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10 changes: 9 additions & 1 deletion qtp_sequencing/summary.py
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Original file line number Diff line number Diff line change
Expand Up @@ -88,11 +88,19 @@ def generate_html_summary(qclient, job_id, parameters, out_dir):
"""
# Step 1: gather file information from qiita using REST api
artifact_id = parameters['input_data']
# we are going to use the "raw" code for retrieving artifact_info vs. the
# qiita_client.artifact_and_preparation_files method because fqtools
# returns 0 (vs. failing, which is nice) on an empty file
# $ touch x.fastq
# $ gzip x.fastq
# $ fqtools count x.fastq.gz
# 0
qclient_url = "/qiita_db/artifacts/%s/" % artifact_id
artifact_info = qclient.get(qclient_url)

# 1a. getting the file paths
filepaths = artifact_info['files']
filepaths = {k: [vv['filepath'] for vv in v]
for k, v in artifact_info['files'].items()}
# 1.b get the artifact type_info
artifact_type = artifact_info['type']

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4 changes: 2 additions & 2 deletions qtp_sequencing/tests/test_plugin.py
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Expand Up @@ -54,11 +54,11 @@ def test_plugin_summary(self):
files = self.qclient.get(
'/qiita_db/artifacts/%s/' % artifact_id)['files']

bcds_fp = files['raw_barcodes'][0]
bcds_fp = files['raw_barcodes'][0]['filepath']
self._clean_up_files.append(bcds_fp)
with GzipFile(bcds_fp, mode='w', mtime=1) as fh:
fh.write(BARCODES.encode())
fwd_fp = files['raw_forward_seqs'][0]
fwd_fp = files['raw_forward_seqs'][0]['filepath']
self._clean_up_files.append(fwd_fp)
with GzipFile(fwd_fp, mode='w', mtime=1) as fh:
fh.write(READS.encode())
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10 changes: 5 additions & 5 deletions qtp_sequencing/tests/test_summary.py
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Expand Up @@ -51,11 +51,11 @@ def test_generate_html_summary_no_demux(self):
files = self.qclient.get(
'/qiita_db/artifacts/%s/' % artifact_id)['files']

bcds_fp = files['raw_barcodes'][0]
bcds_fp = files['raw_barcodes'][0]['filepath']
self._clean_up_files.append(bcds_fp)
with GzipFile(bcds_fp, mode='w', mtime=1) as fh:
fh.write(BARCODES.encode())
fwd_fp = files['raw_forward_seqs'][0]
fwd_fp = files['raw_forward_seqs'][0]['filepath']
self._clean_up_files.append(fwd_fp)
with GzipFile(fwd_fp, mode='w', mtime=1) as fh:
fh.write(READS.encode())
Expand All @@ -71,7 +71,7 @@ def test_generate_html_summary_no_demux(self):

# asserting content of html
res = self.qclient.get("/qiita_db/artifacts/%s/" % artifact_id)
html_fp = res['files']['html_summary'][0]
html_fp = res['files']['html_summary'][0]['filepath']
self._clean_up_files.append(html_fp)
with open(html_fp) as html_f:
html = html_f.read()
Expand All @@ -92,7 +92,7 @@ def test_generate_html_summary_demux(self):
# files fo not exist create them
files = self.qclient.get(
'/qiita_db/artifacts/%s/' % artifact_id)['files']
demux_fp = files['preprocessed_demux'][0]
demux_fp = files['preprocessed_demux'][0]['filepath']
copyfile(join(dirname(__file__), 'test_data', '101_seqs.demux'),
demux_fp)
self._clean_up_files.append(demux_fp)
Expand All @@ -107,7 +107,7 @@ def test_generate_html_summary_demux(self):

# asserting content of html
res = self.qclient.get("/qiita_db/artifacts/%s/" % artifact_id)
html_fp = res['files']['html_summary'][0]
html_fp = res['files']['html_summary'][0]['filepath']
self._clean_up_files.append(html_fp)

with open(html_fp) as html_f:
Expand Down