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Merged
merged 6 commits into from
Jun 14, 2022
Merged

archive biom: back changes #3202

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1762459
archive biom: back changes
antgonza Jun 8, 2022
ed44fb3
biom -> log
antgonza Jun 8, 2022
a90530b
fix transaction error
antgonza Jun 8, 2022
03cce99
fix test_get_visibilities
antgonza Jun 9, 2022
acfa033
doc fix [skip ci]
antgonza Jun 9, 2022
6959ceb
address @charles-cowart comments
antgonza Jun 14, 2022
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fix transaction error
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@antgonza
antgonza committed Jun 8, 2022
commit a90530bc60bdbb0ef0ab48ebfc4bf1da3300329f
6 changes: 2 additions & 4 deletions qiita_db/artifact.py
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Original file line number Diff line number Diff line change
Expand Up @@ -23,9 +23,6 @@
TypeNode = namedtuple('TypeNode', ['id', 'job_id', 'name', 'type'])


IgnoreVisibilities = tuple([qdb.util.convert_to_id('archived', "visibility")])


class Artifact(qdb.base.QiitaObject):
r"""Any kind of file (or group of files) stored in the system and its
attributes
Expand Down Expand Up @@ -1393,7 +1390,8 @@ def youngest_artifact(self):
WHERE visibility_id NOT IN %s
ORDER BY generated_timestamp DESC
LIMIT 1"""
qdb.sql_connection.TRN.add(sql, [self.id, IgnoreVisibilities])
qdb.sql_connection.TRN.add(
sql, [self.id, qdb.util.artifact_visibilities_to_skip()])
a_id = qdb.sql_connection.TRN.execute_fetchindex()
# If the current artifact has no children, the previous call will
# return an empty list, so the youngest artifact in the lineage is
Expand Down
2 changes: 1 addition & 1 deletion qiita_db/metadata_template/prep_template.py
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Expand Up @@ -550,7 +550,7 @@ def status(self):
JOIN qiita.visibility USING (visibility_id)
WHERE prep_template_id = %s and visibility_id NOT IN %s"""
qdb.sql_connection.TRN.add(
sql, [self._id, qdb.artifact.IgnoreVisibilities])
sql, [self._id, qdb.util.artifact_visibilities_to_skip()])

return qdb.util.infer_status(
qdb.sql_connection.TRN.execute_fetchindex())
Expand Down
4 changes: 2 additions & 2 deletions qiita_db/study.py
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Original file line number Diff line number Diff line change
Expand Up @@ -150,7 +150,7 @@ def status(self):
JOIN qiita.study_artifact USING (artifact_id)
WHERE study_id = %s and visibility_id NOT IN %s"""
qdb.sql_connection.TRN.add(
sql, [self._id, qdb.artifact.IgnoreVisibilities])
sql, [self._id, qdb.util.artifact_visibilities_to_skip()])
return qdb.util.infer_status(
qdb.sql_connection.TRN.execute_fetchindex())

Expand Down Expand Up @@ -1101,7 +1101,7 @@ def artifacts(self, dtype=None, artifact_type=None):
JOIN qiita.artifact_type USING (artifact_type_id)
WHERE study_id = %s{0} AND visibility_id NOT IN %s
ORDER BY artifact_id""".format(sql_where)
sql_args.append(qdb.artifact.IgnoreVisibilities)
sql_args.append(qdb.util.artifact_visibilities_to_skip())

qdb.sql_connection.TRN.add(sql, sql_args)
return [qdb.artifact.Artifact(aid)
Expand Down
8 changes: 6 additions & 2 deletions qiita_db/util.py
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Expand Up @@ -1775,8 +1775,8 @@ def get_artifacts_information(artifact_ids, only_biom=True):
ps = {}
algorithm_az = {'': ''}
PT = qdb.metadata_template.prep_template.PrepTemplate
qdb.sql_connection.TRN.add(
sql, [tuple(artifact_ids), qdb.artifact.IgnoreVisibilities])
qdb.sql_connection.TRN.add(sql, [
tuple(artifact_ids), qdb.util.artifact_visibilities_to_skip()])
for row in qdb.sql_connection.TRN.execute_fetchindex():
aid, name, cid, cname, gt, aparams, dt, pid, pcid, pname, \
pparams, filepaths, _, prep_template_id = row
Expand Down Expand Up @@ -1952,6 +1952,10 @@ def open_file(filepath_or, *args, **kwargs):
fh.close()


def artifact_visibilities_to_skip():
return tuple([qdb.util.convert_to_id('archived', "visibility")])
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A new function for one line of code seems a little excessive. However I appreciate the readability. Not sure I would suggest unfolding it.

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I tried adding as a global variable in the artifact.py and as a member of the Artifact object but turns out that this is not possible because the code will try to initialize those variables when the code is initiated (and there is no database) so it fails, for example.



def generate_analysis_list(analysis_ids, public_only=False):
"""Get general analysis information

Expand Down