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addressing @josenavas comments
1 parent 6baaf66 commit bcb3c2f

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3 files changed

+10
-8
lines changed

3 files changed

+10
-8
lines changed

qiita_db/metadata_template/base_metadata_template.py

Lines changed: 2 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -1063,6 +1063,8 @@ def to_dataframe(self):
10631063
df.where((pd.notnull(df)), None)
10641064
df.set_index('sample_id', inplace=True, drop=True)
10651065
id_column_name = 'qiita_%sid' % (self._table_prefix)
1066+
if id_column_name == 'qiita_sample_id':
1067+
id_column_name = 'qiita_study_id'
10661068
df[id_column_name] = str(self.id)
10671069

10681070
return df

qiita_db/metadata_template/test/test_sample_template.py

Lines changed: 6 additions & 6 deletions
Original file line numberDiff line numberDiff line change
@@ -1820,7 +1820,7 @@ def test_to_dataframe(self):
18201820
'latitude': '42.42',
18211821
'longitude': '41.41',
18221822
'taxon_id': '9606',
1823-
'qiita_sample_id': str(new_id),
1823+
'qiita_study_id': str(new_id),
18241824
'scientific_name': 'homo sapiens'},
18251825
'%s.Sample2' % new_id: {
18261826
'physical_specimen_location': 'location1',
@@ -1834,7 +1834,7 @@ def test_to_dataframe(self):
18341834
'latitude': '4.2',
18351835
'longitude': '1.1',
18361836
'taxon_id': '9606',
1837-
'qiita_sample_id': str(new_id),
1837+
'qiita_study_id': str(new_id),
18381838
'scientific_name': 'homo sapiens'},
18391839
'%s.Sample3' % new_id: {
18401840
'physical_specimen_location': 'location1',
@@ -1848,7 +1848,7 @@ def test_to_dataframe(self):
18481848
'latitude': '4.8',
18491849
'longitude': '4.41',
18501850
'taxon_id': '9606',
1851-
'qiita_sample_id': str(new_id),
1851+
'qiita_study_id': str(new_id),
18521852
'scientific_name': 'homo sapiens'},
18531853
}
18541854
exp = pd.DataFrame.from_dict(exp_dict, orient='index', dtype=str)
@@ -1885,7 +1885,7 @@ def test_to_dataframe(self):
18851885
'water_content_soil', 'elevation', 'temp', 'tot_nitro',
18861886
'samp_salinity', 'altitude', 'env_biome', 'country', 'ph',
18871887
'anonymized_name', 'tot_org_carb', 'description_duplicate',
1888-
'env_feature', 'scientific_name', 'qiita_sample_id'})
1888+
'env_feature', 'scientific_name', 'qiita_study_id'})
18891889

18901890
def test_check_restrictions(self):
18911891
obs = self.tester.check_restrictions(
@@ -2170,7 +2170,7 @@ def test_delete_sample(self):
21702170
EXP_SAMPLE_TEMPLATE = (
21712171
"sample_name\tcollection_timestamp\tdescription\tdna_extracted\t"
21722172
"host_subject_id\tlatitude\tlongitude\tphysical_specimen_location\t"
2173-
"physical_specimen_remaining\tqiita_sample_id\tsample_type\t"
2173+
"physical_specimen_remaining\tqiita_study_id\tsample_type\t"
21742174
"scientific_name\ttaxon_id\n"
21752175
"{0}.Sample1\t05/29/2014 12:24:15\tTest Sample 1\ttrue\tNotIdentified\t"
21762176
"42.42\t41.41\tlocation1\ttrue\t{0}\ttype1\thomo sapiens\t9606\n"
@@ -2182,7 +2182,7 @@ def test_delete_sample(self):
21822182
EXP_SAMPLE_TEMPLATE_FEWER_SAMPLES = (
21832183
"sample_name\tcollection_timestamp\tdescription\tdna_extracted\t"
21842184
"host_subject_id\tlatitude\tlongitude\tphysical_specimen_location\t"
2185-
"physical_specimen_remaining\tqiita_sample_id\tsample_type\t"
2185+
"physical_specimen_remaining\tqiita_study_id\tsample_type\t"
21862186
"scientific_name\ttaxon_id\n"
21872187
"{0}.Sample1\t05/29/2014 12:24:15\tTest Sample 1\ttrue\tNotIdentified\t"
21882188
"42.42\t41.41\tlocation1\ttrue\t{0}\ttype1\thomo sapiens\t9606\n"

qiita_pet/handlers/api_proxy/tests/test_sample_template.py

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -115,7 +115,7 @@ def test_sample_template_get_req(self):
115115
'host_subject_id': '1001:B4',
116116
'season_environment': 'winter',
117117
'temp': '15',
118-
'qiita_sample_id': '1',
118+
'qiita_study_id': '1',
119119
'country': 'GAZ:United States of America',
120120
'longitude': '68.5041623253',
121121
'tot_nitro': '1.41',
@@ -271,7 +271,7 @@ def test_sample_template_summary_get_req(self):
271271
('Not applicable', 1)],
272272
'tot_nitro': [('1.3', 9), ('1.41', 9), ('1.51', 9)],
273273
'depth': [('0.15', 27)],
274-
'qiita_sample_id': [('1', 27)],
274+
'qiita_study_id': [('1', 27)],
275275
'anonymized_name': [
276276
('SKB1', 1), ('SKB2', 1), ('SKB3', 1), ('SKB4', 1),
277277
('SKB5', 1), ('SKB6', 1), ('SKB7', 1), ('SKB8', 1),

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