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Merged
merged 1 commit into from
Sep 4, 2020
Merged

fix #2839 #3029

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4 changes: 2 additions & 2 deletions qiita_db/metadata_template/base_metadata_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1158,8 +1158,8 @@ def to_file(self, fp, samples=None):
df.to_csv(fp, index_label='sample_name', na_rep="", sep='\t',
encoding='utf-8')

def to_dataframe(self):
"""Returns the metadata template as a dataframe
def _common_to_dataframe_steps(self):
"""Perform the common to_dataframe steps

Returns
-------
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17 changes: 17 additions & 0 deletions qiita_db/metadata_template/prep_template.py
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Expand Up @@ -767,3 +767,20 @@ def name(self, value):
WHERE prep_template_id = %s"""
qdb.sql_connection.TRN.add(sql, [value, self.id])
qdb.sql_connection.TRN.execute()

def to_dataframe(self, add_ebi_accessions=False):
"""Returns the metadata template as a dataframe

Parameters
----------
add_ebi_accessions : bool, optional
If this should add the ebi accessions
"""
df = self._common_to_dataframe_steps()

if add_ebi_accessions:
accessions = self.ebi_experiment_accessions
df['qiita_ebi_experiment_accessions'] = df.index.map(
lambda sid: accessions[sid])

return df
17 changes: 17 additions & 0 deletions qiita_db/metadata_template/sample_template.py
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Expand Up @@ -332,3 +332,20 @@ def biosample_accessions(self, value):
If a sample in `value` already has an accession number
"""
self._update_accession_numbers('biosample_accession', value)

def to_dataframe(self, add_ebi_accessions=False):
"""Returns the metadata template as a dataframe

Parameters
----------
add_ebi_accessions : bool, optional
If this should add the ebi accessions
"""
df = self._common_to_dataframe_steps()
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what about:

accessions = None
if add_ebi_accessions:
    accessions = self.ebi_sample_accessions

return self._common_to_dataframe_steps(accessions, 'ebi_sample_accessions')

...similar for the prep template to_dataframe, and then add into the common function:

if accessions is not None:
    df[f'qiita_{accession_type}'] = df.index.map(lambda sid: accessions[sid])

Would reduce a little of code duplication

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not strong feeling about leaving as is or changing ...

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cool cool, then :shipit: i think :)


if add_ebi_accessions:
accessions = self.ebi_sample_accessions
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Are all samples assured to be represented in this object? If not, would it be safer to have the lambda issue a accessions.get?

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yes, AFAIK all samples in the prep/sample are represented.

df['qiita_ebi_sample_accessions'] = df.index.map(
lambda sid: accessions[sid])

return df
6 changes: 6 additions & 0 deletions qiita_db/metadata_template/test/test_prep_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -685,6 +685,12 @@ def test_to_dataframe(self):
u'illumina_technology', u'sample_center', u'pcr_primers',
u'study_center', 'qiita_prep_id'})

# test with add_ebi_accessions as True
obs = self.tester.to_dataframe(True)
self.assertEqual(
self.tester.ebi_experiment_accessions,
obs.qiita_ebi_experiment_accessions.to_dict())

def test_clean_validate_template_error_bad_chars(self):
"""Raises an error if there are invalid characters in the sample names
"""
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6 changes: 6 additions & 0 deletions qiita_db/metadata_template/test/test_sample_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1975,6 +1975,12 @@ def test_to_dataframe(self):
'anonymized_name', 'tot_org_carb', 'description_duplicate',
'env_feature', 'scientific_name', 'qiita_study_id'})

# test with add_ebi_accessions as True
obs = self.tester.to_dataframe(True)
self.assertEqual(
self.tester.ebi_sample_accessions,
obs.qiita_ebi_sample_accessions.to_dict())

def test_check_restrictions(self):
obs = self.tester.check_restrictions(
[STC['EBI']])
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