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Unify update category #1050

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Merged
merged 3 commits into from
Apr 9, 2015
Merged

Unify update category #1050

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319af8f
Moving update category to the base class
josenavas Apr 8, 2015
57ab913
Making my friend flake8 happy
josenavas Apr 8, 2015
bb63094
Merge branch 'master' of https://github.com/biocore/qiita into unify-…
josenavas Apr 9, 2015
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27 changes: 27 additions & 0 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 @@ -1083,3 +1083,30 @@ def categories(self):
cols[idx] = self.translate_cols_dict[c]

return cols

def update_category(self, category, samples_and_values):
"""Update an existing column

Parameters
----------
category : str
The category to update
samples_and_values : dict
A mapping of {sample_id: value}

Raises
------
QiitaDBUnknownIDError
If a sample_id is included in values that is not in the template
QiitaDBColumnError
If the column does not exist in the table. This is implicit, and
can be thrown by the contained Samples.
"""
if not set(self.keys()).issuperset(samples_and_values):
missing = set(self.keys()) - set(samples_and_values)
table_name = self._table_name(self.study_id)
raise QiitaDBUnknownIDError(missing, table_name)

for k, v in viewitems(samples_and_values):
sample = self[k]
sample[category] = v
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why not do self[k][category] = v and not need to instantiate sample.

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You're not saving the instantiation, it is happening at the moment that you do self[k]. Anyways, this is left like this because I modify this in my other PR #1054....

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ok

29 changes: 0 additions & 29 deletions qiita_db/metadata_template/sample_template.py
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Original file line number Diff line number Diff line change
Expand Up @@ -8,7 +8,6 @@

from __future__ import division
from future.builtins import zip
from future.utils import viewitems
from copy import deepcopy
from os.path import join
from time import strftime
Expand All @@ -20,7 +19,6 @@

from qiita_core.exceptions import IncompetentQiitaDeveloperError
from qiita_db.exceptions import (QiitaDBDuplicateError, QiitaDBColumnError,
QiitaDBUnknownIDError,
QiitaDBDuplicateHeaderError, QiitaDBError,
QiitaDBWarning)
from qiita_db.sql_connection import SQLConnectionHandler
Expand Down Expand Up @@ -407,33 +405,6 @@ def update(self, md_template):
if '_qiime_' not in basename(fp):
pt.create_qiime_mapping_file(fp)

def update_category(self, category, samples_and_values):
"""Update an existing column

Parameters
----------
category : str
The category to update
samples_and_values : dict
A mapping of {sample_id: value}

Raises
------
QiitaDBUnknownIDError
If a sample_id is included in values that is not in the template
QiitaDBColumnError
If the column does not exist in the table. This is implicit, and
can be thrown by the contained Samples.
"""
if not set(self.keys()).issuperset(samples_and_values):
missing = set(self.keys()) - set(samples_and_values)
table_name = self._table_name(self.study_id)
raise QiitaDBUnknownIDError(missing, table_name)

for k, v in viewitems(samples_and_values):
sample = self[k]
sample[category] = v

def add_category(self, category, samples_and_values, dtype, default):
"""Add a metadata category

Expand Down
31 changes: 31 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 @@ -1167,6 +1167,37 @@ def test_status(self):
self.test_study, self.data_type_id)
self.assertEqual(pt.status, 'sandbox')

def test_update_category(self):
with self.assertRaises(QiitaDBUnknownIDError):
self.tester.update_category('barcodesequence', {"foo": "bar"})

with self.assertRaises(QiitaDBColumnError):
self.tester.update_category('missing column',
{'1.SKB7.640196': 'bar'})

neg_test = self.tester['1.SKB7.640196']['barcodesequence']
mapping = {'1.SKB8.640193': 'AAAAAAAAAAAA',
'1.SKD8.640184': 'CCCCCCCCCCCC'}

self.tester.update_category('barcodesequence', mapping)

self.assertEqual(self.tester['1.SKB7.640196']['barcodesequence'],
neg_test)
self.assertEqual(self.tester['1.SKB8.640193']['barcodesequence'],
'AAAAAAAAAAAA')
self.assertEqual(self.tester['1.SKD8.640184']['barcodesequence'],
'CCCCCCCCCCCC')

neg_test = self.tester['1.SKB7.640196']['center_name']
mapping = {'1.SKB8.640193': 'FOO',
'1.SKD8.640184': 'BAR'}

self.tester.update_category('center_name', mapping)

self.assertEqual(self.tester['1.SKB7.640196']['center_name'], neg_test)
self.assertEqual(self.tester['1.SKB8.640193']['center_name'], 'FOO')
self.assertEqual(self.tester['1.SKD8.640184']['center_name'], 'BAR')


EXP_PREP_TEMPLATE = (
'sample_name\tbarcodesequence\tcenter_name\tcenter_project_name\t'
Expand Down