def test_translate_ids_with_sample_id(self):
# Tests sample_id_to_specimen_id and specimen_id_to_sample_id when
# there is no specimen identifier set for the study
s = Study(1)
obs = s.sample_id_to_specimen_id('1.SKM4.640180')
self.assertEqual(obs, '1.SKM4.640180')
# doesn't even need to be a valid sample id
obs = s.sample_id_to_specimen_id('SKM3')
self.assertEqual(obs, 'SKM3')
with self.assertRaisesRegex(ValueError, 'Could not find "SKM4"'):
s.specimen_id_to_sample_id('SKM4')
with self.assertRaisesRegex(ValueError, 'Could not find "SSSS"'):
s.specimen_id_to_sample_id('SSSS')
def test_translate_ids_with_specimen_id(self):
s = Study(1)
# HACK: the Study object in labman can't modify specimen_id_column
# hence we do this directly in SQL, if a test fails the transaction
# will rollback, otherwise we reset the column to NULL.
sql = """UPDATE qiita.study
SET specimen_id_column = %s
WHERE study_id = 1"""
with sql_connection.TRN as TRN:
TRN.add(sql, ['anonymized_name'])
obs = s.sample_id_to_specimen_id('1.SKM4.640180')
self.assertEqual(obs, 'SKM4')
obs = s.specimen_id_to_sample_id('SKM4')
self.assertEqual(obs, '1.SKM4.640180')
# should be an exact match
with self.assertRaisesRegex(ValueError,
'Could not find \"1\.skm4\.640180\"'):
s.sample_id_to_specimen_id('1.skm4.640180')
with self.assertRaisesRegex(ValueError, 'Could not find \"skm4\"'):
s.specimen_id_to_sample_id('skm4')
# raise an error in the rare case that the specimen_id_column was
# set to something that's not unique (this could only accidentally
# happen)
TRN.add(sql, ['taxon_id'])
with self.assertRaisesRegex(
RuntimeError, 'There are several '
'matches found for "1118232"; there is'
' a problem with the specimen id '
'column'):
s.specimen_id_to_sample_id('1118232')
TRN.add(sql, [None])
def sample_plating_process_handler_patch_request(
user, process_id, req_op, req_path, req_value, req_from):
"""Performs the patch operation on the sample plating process
Parameters
----------
user: labman.db.user.User
User performing the request
process_id: int
The SamplePlatingProcess to apply the patch operation
req_op: string
JSON PATCH op parameter
req_path: string
JSON PATCH path parameter
req_value: string
JSON PATCH value parameter
req_from: string
JSON PATCH from parameter
Returns
-------
dict
The results of the patch operation
Raises
------
HTTPError
400: If req_op is not a supported operation
400: If req_path is incorrect
"""
if req_op == 'replace':
req_path = [v for v in req_path.split('/') if v]
if len(req_path) != 5:
raise HTTPError(400, 'Incorrect path parameter')
attribute = req_path[0]
if attribute == 'well':
row = req_path[1]
col = req_path[2]
study_id = int(req_path[3])
well_attribute = req_path[4]
# The default values of the variables sample_id and
# blank_or_unknown are set before the try, and these are the values
# that are used if either (a) study_id is not 0 OR (b) the try
# fails with a ValueError (see comment in try below). If the try
# fails with anything other than a ValueError then the entire
# function bails, so it doesn't matter what these variables are set
# to. If and only if the try succeeds are these variables set to
# the values within the try.
sample_id = req_value
blank_or_unknown = True
# It actually IS possible to plate a plate without specifying
# separate study id(s); can plate just all blanks, or can provide
# the fully qualified sample id(s)--i.e., <studyid>.<sampleid>.
if study_id != 0:
try:
# Note that the try fails iff the
# Study(study_id).specimen_id_to_sample_id() call fails,
# as the blank_or_unknown = False can't really fail ...
# this assures that we can't realistically end up in an
# inconsistent situation where sample_id has been set
# during the try but blank_or_unknown has not.
#
# Thus, the ordering of these two statements within the try
# is really important: do not change it unless you
# understand all of the above!
the_study = Study(study_id)
sample_id = the_study.specimen_id_to_sample_id(
req_value)
blank_or_unknown = False
except ValueError:
pass
# end try/except
# end if
if well_attribute == 'sample':
if req_value is None or not req_value.strip():
raise HTTPError(
400, 'A new value for the well should be provided')
plates = Plate.search(samples=[sample_id])
process = SamplePlatingProcess(process_id)
plates = set(plates) - {process.plate}
prev_plates = [{'plate_id': p.id, 'plate_name': p.external_id}
for p in plates]
content, sample_ok = process.update_well(row, col, sample_id)
if blank_or_unknown:
req_value = content
return {'sample_id': req_value, 'previous_plates': prev_plates,
'sample_ok': sample_ok}
elif well_attribute == 'notes':
if req_value is not None:
# If the user provides an empty string, just store None
# in the database
req_value = (req_value.strip()
if req_value.strip() else None)
SamplePlatingProcess(process_id).comment_well(
row, col, req_value)
return {'comment': req_value}
else:
raise HTTPError(
404, 'Well attribute %s not found' % well_attribute)
else:
raise HTTPError(404, 'Attribute %s not found' % attribute)
else:
raise HTTPError(400, 'Operation %s not supported. Current supported '
'operations: replace' % req_op)