def post(self):
plate_comment_keywords = self.get_argument("plate_comment_keywords")
well_comment_keywords = self.get_argument("well_comment_keywords")
operation = self.get_argument("operation")
sample_names = json_decode(self.get_argument('sample_names'))
res = {
"data": [[p.id, p.external_id]
for p in Plate.search(samples=sample_names,
plate_notes=plate_comment_keywords,
well_notes=well_comment_keywords,
query_type=operation)]
}
self.write(res)
def test_search(self):
with self.assertRaises(ValueError):
Plate.search()
with self.assertRaises(ValueError):
Plate.search(samples=['1.SKB1.640202'], query_type='WRONG')
plate21 = Plate(21)
plate22 = Plate(22)
plate23 = Plate(23)
plate27 = Plate(27)
plate30 = Plate(30)
plate33 = Plate(33)
self.assertEqual(
Plate.search(samples=['1.SKB1.640202', '1.SKB2.640194']),
[plate21, plate27, plate30, plate33])
self.assertEqual(Plate.search(samples=['1.SKB1.640202']),
[plate21, plate27, plate30, plate33])
self.assertEqual(Plate.search(plate_notes='interesting'), [])
# Add comments to a plate so we can actually test the
# search functionality
plate22.notes = 'Some interesting notes'
plate23.notes = 'More boring notes'
self.assertEqual(Plate.search(plate_notes='interesting'), [plate22])
self.assertCountEqual(Plate.search(plate_notes='interesting boring'),
[])
self.assertEqual(
Plate.search(samples=['1.SKB1.640202'], plate_notes='interesting'),
[])
# sample '1.SKB1.640202' is on 4 sample plates, plus there is a
# gdna plate with a note containing the word 'interesting'
self.assertCountEqual(
Plate.search(samples=['1.SKB1.640202'],
plate_notes='interesting',
query_type='UNION'),
[plate21, plate22, plate27, plate30, plate33])
# The search engine ignores common english words
self.assertEqual(Plate.search(plate_notes='more'), [])
# Add comments to some wells
plate23.get_well(1, 1).composition.notes = 'What else should I write?'
self.assertEqual(Plate.search(well_notes='write'), [plate23])
self.assertEqual(
Plate.search(plate_notes='interesting', well_notes='write'), [])
self.assertCountEqual(
Plate.search(plate_notes='interesting',
well_notes='write',
query_type='UNION'), [plate22, plate23])
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: labcontrol.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)