def retrieve_diagnostics_by_kit_id(self, supplied_kit_id):
kit_repo = KitRepo(self._transaction)
kit = kit_repo.get_kit_all_samples(supplied_kit_id)
if kit is None:
return None
sample_assoc = []
for sample in kit.samples:
sample_assoc.append(
self.retrieve_diagnostics_by_barcode(sample.barcode,
grab_kit=False))
with self._transaction.dict_cursor() as cur:
cur.execute(
"SELECT "
"ag_login_id as account_id "
"FROM "
"ag_kit "
"WHERE "
"supplied_kit_id = %s",
(supplied_kit_id,))
row = cur.fetchone()
pre_microsetta_acct = None
if row['account_id'] is not None:
acct_repo = AccountRepo(self._transaction)
# This kit predated the microsetta migration, let's pull in the
# account info associated with it
pre_microsetta_acct = acct_repo.get_account(row['account_id'])
# obtain information on any accounts created using the kit ID
with self._transaction.dict_cursor() as cur:
cur.execute(
"SELECT id as account_id "
"FROM "
"account "
"WHERE "
"created_with_kit_id = %s",
(supplied_kit_id, ))
rows = cur.fetchall()
accounts_created = None
if len(rows) > 0:
acct_repo = AccountRepo(self._transaction)
accounts_created = [acct_repo.get_account(row['account_id'])
for row in rows]
diagnostic = {
'accounts_created': accounts_created,
'kit_id': kit.id,
'supplied_kit_id': supplied_kit_id,
'kit': kit,
'pre_microsetta_acct': pre_microsetta_acct,
'sample_diagnostic_info': sample_assoc
}
return diagnostic
def read_kit(kit_name):
# NOTE: Nothing in this route requires a particular user to be logged in,
# so long as the user has -an- account.
with Transaction() as t:
kit_repo = KitRepo(t)
kit = kit_repo.get_kit_unused_samples(kit_name)
if kit is None:
return jsonify(code=404, message="No such kit"), 404
return jsonify(kit.to_api()), 200
def register_account(body, token_info):
# First register with AuthRocket, then come here to make the account
new_acct_id = str(uuid.uuid4())
body["id"] = new_acct_id
# Account.from_dict requires a kit_name, even if blank
kit_name = body.get("kit_name", "")
body["kit_name"] = kit_name
code = body.get("code", "")
body["code"] = code
account_obj = Account.from_dict(body, token_info[JWT_ISS_CLAIM_KEY],
token_info[JWT_SUB_CLAIM_KEY])
if kit_name == "" and code == "":
return jsonify(code=400,
message="Account registration requires "
"valid kit ID or activation code"), 400
with Transaction() as t:
activation_repo = ActivationRepo(t)
if code != "":
can_activate, cause = activation_repo.can_activate_with_cause(
body["email"], code)
if not can_activate:
return jsonify(code=404, message=cause), 404
else:
activation_repo.use_activation_code(body["email"], code)
if kit_name != "":
kit_repo = KitRepo(t)
kit = kit_repo.get_kit_all_samples(kit_name)
if kit is None:
return jsonify(code=404, message="Kit name not found"), 404
acct_repo = AccountRepo(t)
acct_repo.create_account(account_obj)
new_acct = acct_repo.get_account(new_acct_id)
t.commit()
response = jsonify(new_acct.to_api())
response.status_code = 201
response.headers['Location'] = '/api/accounts/%s' % new_acct_id
return response
def register_account(body, token_info):
# First register with AuthRocket, then come here to make the account
new_acct_id = str(uuid.uuid4())
body["id"] = new_acct_id
account_obj = Account.from_dict(body, token_info[JWT_ISS_CLAIM_KEY],
token_info[JWT_SUB_CLAIM_KEY])
with Transaction() as t:
kit_repo = KitRepo(t)
kit = kit_repo.get_kit_all_samples(body['kit_name'])
if kit is None:
return jsonify(code=404, message="Kit name not found"), 404
acct_repo = AccountRepo(t)
acct_repo.create_account(account_obj)
new_acct = acct_repo.get_account(new_acct_id)
t.commit()
response = jsonify(new_acct.to_api())
response.status_code = 201
response.headers['Location'] = '/api/accounts/%s' % new_acct_id
return response
def retrieve_diagnostics_by_barcode(self, sample_barcode, grab_kit=True):
def _rows_to_dicts_list(rows):
return [dict(x) for x in rows]
with self._transaction.dict_cursor() as cur:
ids = self._get_ids_relevant_to_barcode(sample_barcode)
if ids is None:
ids = {}
# default for not found is None
sample_id = ids.get("sample_id")
source_id = ids.get("source_id")
account_id = ids.get("account_id")
# NB: this is the true UUID kit id (the primary key of
# ag.ag_kit), NOT the kit's participant-facing string "id"
kit_id = ids.get("kit_id")
account = None
source = None
sample = None
kit = None
# get sample object for this barcode, if any
if sample_id is not None:
sample_repo = SampleRepo(self._transaction)
sample = sample_repo._get_sample_by_id(sample_id)
# get account object for this barcode, if any
if account_id is not None:
account_repo = AccountRepo(self._transaction)
account = account_repo.get_account(account_id)
# and source object for this barcode, if any
if source_id is not None:
source_repo = SourceRepo(self._transaction)
source = source_repo.get_source(account_id, source_id)
# get (partial) projects_info list for this barcode
query = f"""
SELECT {p.DB_PROJ_NAME_KEY}, {p.IS_MICROSETTA_KEY},
{p.BANK_SAMPLES_KEY}, {p.PLATING_START_DATE_KEY}
FROM barcodes.project
INNER JOIN barcodes.project_barcode
USING (project_id)
WHERE barcode=%s;"""
cur.execute(query, (sample_barcode, ))
# this can't be None; worst-case is an empty list
projects_info = _rows_to_dicts_list(cur.fetchall())
# get scans_info list for this barcode
# NB: ORDER MATTERS here. Do not change the order unless you
# are positive you know what already depends on it.
cur.execute(
"SELECT barcode_scan_id, barcode, "
"scan_timestamp, sample_status, "
"technician_notes "
"FROM barcodes.barcode_scans "
"WHERE barcode=%s "
"ORDER BY scan_timestamp asc", (sample_barcode, ))
# this can't be None; worst-case is an empty list
scans_info = _rows_to_dicts_list(cur.fetchall())
latest_scan = None
if len(scans_info) > 0:
# NB: the correctness of this depends on the scans (queried
# right above) being in ascending order by timestamp
latest_scan = scans_info[len(scans_info) - 1]
# get details about this barcode itself; CAN be None if the
# barcode doesn't exist in db
barcode_info = None
cur.execute(
"SELECT barcode, assigned_on, status, "
"sample_postmark_date, biomass_remaining, "
"sequencing_status, obsolete, "
"create_date_time, kit_id "
"FROM barcodes.barcode "
"WHERE barcode = %s", (sample_barcode, ))
barcode_row = cur.fetchone()
if barcode_row is not None:
barcode_info = dict(barcode_row)
if account is None and source is None and sample is None and \
len(projects_info) == 0 and len(scans_info) == 0 \
and barcode_info is None:
return None
diagnostic = {
"account": account,
"source": source,
"sample": sample,
"latest_scan": latest_scan,
"scans_info": scans_info,
"barcode_info": barcode_info,
"projects_info": projects_info
}
if grab_kit:
# get kit object
if kit_id is not None:
kit_repo = KitRepo(self._transaction)
kit = kit_repo.get_kit_all_samples_by_kit_id(kit_id)
diagnostic["kit"] = kit
return diagnostic
def retrieve_diagnostics_by_barcode(self, sample_barcode, grab_kit=True):
def _rows_to_dicts_list(rows):
return [dict(x) for x in rows]
with self._transaction.dict_cursor() as cur:
ids = self._get_ids_relevant_to_barcode(sample_barcode)
if ids is None:
sample_id = None
source_id = None
account_id = None
kit_id = None
else:
sample_id = ids["sample_id"]
source_id = ids["source_id"]
account_id = ids["account_id"]
kit_id = ids["kit_id"]
account = None
source = None
sample = None
kit = None
# get sample object for this barcode
if sample_id is not None:
sample_repo = SampleRepo(self._transaction)
sample = sample_repo._get_sample_by_id(sample_id)
# get account and source objects for this barcode
if source_id is not None and account_id is not None:
account_repo = AccountRepo(self._transaction)
source_repo = SourceRepo(self._transaction)
account = account_repo.get_account(account_id)
source = source_repo.get_source(account_id, source_id)
# get projects_info list for this barcode
cur.execute("SELECT project, is_microsetta, "
"bank_samples, plating_start_date "
"FROM barcodes.project "
"INNER JOIN barcodes.project_barcode "
"USING (project_id) "
"WHERE barcode=%s",
(sample_barcode,))
# this can't be None; worst-case is an empty list
projects_info = _rows_to_dicts_list(cur.fetchall())
# get scans_info list for this barcode
# NB: ORDER MATTERS here. Do not change the order unless you
# are positive you know what already depends on it.
cur.execute("SELECT barcode_scan_id, barcode, "
"scan_timestamp, sample_status, "
"technician_notes "
"FROM barcodes.barcode_scans "
"WHERE barcode=%s "
"ORDER BY scan_timestamp asc",
(sample_barcode,))
# this can't be None; worst-case is an empty list
scans_info = _rows_to_dicts_list(cur.fetchall())
latest_scan = None
if len(scans_info) > 0:
# NB: the correctness of this depends on the scans (queried
# right above) being in ascending order by timestamp
latest_scan = scans_info[len(scans_info)-1]
# get details about this barcode itself; CAN be None if the
# barcode doesn't exist in db
barcode_info = None
cur.execute("SELECT barcode, assigned_on, status, "
"sample_postmark_date, biomass_remaining, "
"sequencing_status, obsolete, "
"create_date_time, kit_id "
"FROM barcodes.barcode "
"WHERE barcode = %s",
(sample_barcode,))
barcode_row = cur.fetchone()
if barcode_row is not None:
barcode_info = dict(barcode_row)
if account is None and source is None and sample is None and \
len(projects_info) == 0 and len(scans_info) == 0 \
and barcode_info is None:
return None
diagnostic = {
"account": account,
"source": source,
"sample": sample,
"latest_scan": latest_scan,
"scans_info": scans_info,
"barcode_info": barcode_info,
"projects_info": projects_info
}
if grab_kit:
# get kit object
if kit_id is not None:
kit_repo = KitRepo(self._transaction)
kit = kit_repo.get_kit_all_samples_by_kit_id(kit_id)
diagnostic["kit"] = kit
return diagnostic
def retrieve_diagnostics_by_barcode(self, sample_barcode, grab_kit=True):
with self._transaction.dict_cursor() as cur:
ids = self._get_ids_relevant_to_barcode(sample_barcode)
if ids is None:
sample_id = None
source_id = None
account_id = None
kit_id = None
else:
sample_id = ids["sample_id"]
source_id = ids["source_id"]
account_id = ids["account_id"]
kit_id = ids["kit_id"]
account = None
source = None
sample = None
kit = None
if sample_id is not None:
sample_repo = SampleRepo(self._transaction)
sample = sample_repo._get_sample_by_id(sample_id)
if source_id is not None and account_id is not None:
account_repo = AccountRepo(self._transaction)
source_repo = SourceRepo(self._transaction)
account = account_repo.get_account(account_id)
source = source_repo.get_source(account_id, source_id)
if kit_id is not None and grab_kit:
kit_repo = KitRepo(self._transaction)
kit = kit_repo.get_kit_all_samples_by_kit_id(kit_id)
cur.execute("SELECT * from barcodes.barcode "
"LEFT OUTER JOIN barcodes.project_barcode "
"USING (barcode) "
"LEFT OUTER JOIN barcodes.project "
"USING (project_id) "
"where barcode=%s",
(sample_barcode,))
barcode_info = cur.fetchall()
# How to unwrap a psycopg2 DictRow. I feel dirty.
barcode_info = [{k: v for k, v in x.items()}
for x in barcode_info] # Get Inceptioned!!
# Collapse info from joined project_barcode and project tables
# into array within barcode_info
if barcode_info:
first = barcode_info[0]
first['projects'] = [
{
'project_id': r['project_id'],
'project': r['project']
}
for r in barcode_info]
del first['project_id']
del first['project']
barcode_info = first
else:
barcode_info = None
if account is None and \
source is None and \
sample is None and \
barcode_info is None:
return None
diagnostic = {
"barcode": sample_barcode,
"account": account,
"source": source,
"sample": sample,
"barcode_info": barcode_info
}
if grab_kit:
diagnostic["kit"] = kit
return diagnostic
def query_email_stats(body, token_info):
validate_admin_access(token_info)
email_list = body.get("emails", [])
project = body.get("project")
results = []
with Transaction() as t:
account_repo = AccountRepo(t)
kit_repo = KitRepo(t)
source_repo = SourceRepo(t)
sample_repo = SampleRepo(t)
for email in email_list:
result = {'email': email, 'project': project}
results.append(result)
# can use internal lookup by email, because we have admin access
account = account_repo._find_account_by_email(email) # noqa
if account is None:
result['summary'] = "No Account"
continue
else:
result['account_id'] = account.id
result['creation_time'] = account.creation_time
result['kit_name'] = account.created_with_kit_id
if account.created_with_kit_id is not None:
unused = kit_repo.get_kit_unused_samples(
account.created_with_kit_id
)
if unused is None:
result['unclaimed-samples-in-kit'] = 0
else:
result['unclaimed-samples-in-kit'] = len(unused.samples)
sample_statuses = defaultdict(int)
sources = source_repo.get_sources_in_account(account.id)
samples_in_project = 0
for source in sources:
samples = sample_repo.get_samples_by_source(account.id,
source.id)
for sample in samples:
if project is not None and \
project != "" and \
project not in sample.sample_projects:
continue
samples_in_project += 1
sample_status = sample_repo.get_sample_status(
sample.barcode,
sample._latest_scan_timestamp # noqa
)
if sample_status is None:
sample_status = "never-scanned"
sample_statuses[sample_status] += 1
result.update(sample_statuses)
if result.get('unclaimed-samples-in-kit', 0) > 0:
result['summary'] = 'Possible Unreturned Samples'
elif samples_in_project == 0:
result['summary'] = "No Samples In Specified Project"
elif result.get('sample-is-valid') == samples_in_project:
result['summary'] = 'All Samples Valid'
else:
result['summary'] = 'May Require User Interaction'
return jsonify(results), 200