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Sample generate files improvements #2749

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Merged
merged 7 commits into from
Dec 12, 2018
Merged

Sample generate files improvements #2749

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8d8f674
sample info file generate_files is now "smart"
antgonza Dec 6, 2018
9401943
upstream dev
antgonza Dec 11, 2018
26dca2e
fix test
antgonza Dec 11, 2018
b0dc603
Merge branch 'dev' of https://github.com/biocore/qiita into sample-ge…
antgonza Dec 11, 2018
a93ca98
addressing @charles-cowart comments
antgonza Dec 12, 2018
9e5c964
fix error
antgonza Dec 12, 2018
1005f85
fix error
antgonza Dec 12, 2018
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fix test
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@antgonza
antgonza committed Dec 11, 2018
commit 26dca2e00b623963c927828fda9594b550bd58a3
4 changes: 3 additions & 1 deletion qiita_db/metadata_template/base_metadata_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -1360,7 +1360,9 @@ def _update(self, md_template):
# 4 XX.Sample3 physical_specimen_location new location
to_update.reset_index(inplace=True)
new_columns = []
samples_updated = []
for sid, df in to_update.groupby('sample_name'):
samples_updated.append(sid)
# getting just columns: column and to, and then using column
# as index will generate this for XX.Sample2:
# to
Expand All @@ -1381,7 +1383,7 @@ def _update(self, md_template):

nc = list(set(new_columns).union(set(self.categories())))
table_name = self._table_name(self.id)
values = dumps({"columns": new_columns})
values = dumps({"columns": nc})
sql = """UPDATE qiita.{0}
SET sample_values = %s
WHERE sample_id = '{1}'""".format(
Expand Down