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minor fixes from latests ENA and SPP changes #3472

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Merged
merged 2 commits into from
May 27, 2025
Merged

minor fixes from latests ENA and SPP changes #3472

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833a954
minor fixes from latests ENA and SPP changes
antgonza May 15, 2025
d652026
Merge branch 'dev' of github.com:biocore/qiita into minor-fixes-2025.05
antgonza May 23, 2025
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3 changes: 3 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -75,3 +75,6 @@ notebooks/*/*.tsv.gz

# jupyter notebooks input data
notebooks/resource-allocation/data

# ignore plugin SQL injection file
qiita_db/support_files/patches/test_db_sql/91.sql
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Why shouldn't the patch file go into git? Does it have sensitive info in it or something?

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Good question! Patch 91.sql doesn't actually exist, see https://github.com/qiita-spots/qiita/blob/master/CONTRIBUTING.md#patch-91sql. However, this can be used to "inject" SQL for extra plugin testing, like https://github.com/qiita-spots/qp-knight-lab-processing/blob/main/tests/qiita-sql/91.sql. Note that raw/non-testing deployment will never hit this as the patching starts in 92.

24 changes: 14 additions & 10 deletions qiita_pet/handlers/study_handlers/prep_template.py
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Expand Up @@ -77,18 +77,22 @@ def get(self):
res['alert_message'] = url_escape(res['alert_message'])
res['user_level'] = current_user.level
if res['creation_job'] is not None:
fp = res['creation_job'].parameters.values['sample_sheet']
res['creation_job_filename'] = fp['filename']
res['creation_job_filename_body'] = fp['body']
params = res['creation_job'].parameters.values
summary = None
if res['creation_job'].status == 'success':
if res['creation_job'].outputs:
# [0] is the id, [1] is the filepath
_file = res['creation_job'].outputs[
'output'].html_summary_fp[1]
summary = relpath(_file, qiita_config.base_data_dir)
if 'sample_sheet' in params:
fp = params['sample_sheet']
res['creation_job_filename'] = fp['filename']
res['creation_job_filename_body'] = fp['body']
if res['creation_job'].status == 'success':
if res['creation_job'].outputs:
# [0] is the id, [1] is the filepath
_file = res['creation_job'].outputs[
'output'].html_summary_fp[1]
summary = relpath(_file, qiita_config.base_data_dir)
else:
res['creation_job_filename'] = None
res['creation_job_filename_body'] = None
res['creation_job_artifact_summary'] = summary
# res['']
res['human_reads_filter_method'] = None
a = PrepTemplate(prep_id).artifact
if a is not None:
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12 changes: 9 additions & 3 deletions qiita_ware/ebi.py
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Expand Up @@ -33,6 +33,12 @@
from qiita_db.processing_job import _system_call as system_call


ENA_COLS_TO_FIX = {
'country': 'geographic location (country and/or sea)',
'collection_date': 'collection date'
}


def clean_whitespace(text):
"""Standardizes whitespaces so there is only one space separating tokens

Expand Down Expand Up @@ -406,9 +412,9 @@ def generate_sample_xml(self, samples=None, ignore_columns=None):

for sample_name in sorted(samples):
sample_info = dict(self.samples[sample_name])
if 'country' in sample_info.keys():
nname = 'geographic location (country and/or sea)'
sample_info[nname] = sample_info['country']
for qname, ename in ENA_COLS_TO_FIX.items():
if qname in sample_info.keys():
sample_info[ename] = sample_info[qname]

sample_accession = self._ebi_sample_accessions[sample_name]
if self.action in ('ADD', 'VALIDATE'):
Expand Down