def findprojs(key):
projects=set()
if key == 'all':
udf={'Bioinformatic QC':'WG re-seq (IGN)'}
projects.update(lims.get_projects(udf=udf))
udf={'Sequencing platform':'HiSeq X'}
projects.update(lims.get_projects(udf=udf))
return [(p.name, p.id) for p in projects]
elif key == 'new':
ret=set()
udf={'Bioinformatic QC':'WG re-seq (IGN)'}
projects.update(lims.get_projects(udf=udf))
udf={'Sequencing platform':'HiSeq X'}
projects.update(lims.get_projects(udf=udf))
try:
from genologics_sql.queries import get_last_modified_projectids
from genologics_sql.utils import get_session
session=get_session()
valid_pids=get_last_modified_projectids(session)
ret=[x for x in projects if x.id in valid_pids]
except ImportError:
logging.info("direct sql query did not work")
valid_pids=[]
delta=datetime.timedelta(hours=240)
time_string_pc=(datetime.datetime.now()-delta).strftime('%Y-%m-%dT%H:%M:%SZ')
for p in projects:
if (not p.close_date) and lims.get_processes(projectname=p.name, last_modified=time_string_pc):
ret.add(p)
return [(p.name, p.id) for p in ret]
else:
projects=lims.get_projects(name=key)
return [(p.name, p.id) for p in projects]
def main(args):
lims_db = get_session()
lims = Lims(BASEURI, USERNAME, PASSWORD)
with open(args.conf) as cf:
db_conf = yaml.load(cf)
couch = setupServer(db_conf)
db = couch["expected_yields"]
postgres_string = "{} hours".format(args.hours)
project_ids = get_last_modified_projectids(lims_db, postgres_string)
for project in [Project(lims, id=x) for x in project_ids]:
samples_count = 0
samples = lims.get_samples(projectname=project.name)
for sample in samples:
if not ("Status (manual)" in sample.udf
and sample.udf["Status (manual)"] == "Aborted"):
samples_count += 1
try:
lanes_ordered = project.udf['Sequence units ordered (lanes)']
key = parse_sequencing_platform(project.udf['Sequencing platform'])
except:
continue
for row in db.view("yields/min_yield"):
db_key = [x.lower() if x else None for x in row.key]
if db_key == key:
try:
project.udf['Reads Min'] = float(
row.value) * lanes_ordered / samples_count
project.put()
except ZeroDivisionError:
pass
def findprojs(key):
projects = set()
if key == 'all':
udf = {'Bioinformatic QC': 'WG re-seq (IGN)'}
projects.update(lims.get_projects(udf=udf))
udf = {'Sequencing platform': 'HiSeq X'}
projects.update(lims.get_projects(udf=udf))
return [(p.name, p.id) for p in projects]
elif key == 'new':
ret = set()
udf = {'Bioinformatic QC': 'WG re-seq (IGN)'}
projects.update(lims.get_projects(udf=udf))
udf = {'Sequencing platform': 'HiSeq X'}
projects.update(lims.get_projects(udf=udf))
try:
from genologics_sql.queries import get_last_modified_projectids
from genologics_sql.utils import get_session
session = get_session()
valid_pids = get_last_modified_projectids(session)
ret = [x for x in projects if x.id in valid_pids]
except ImportError:
logging.info("direct sql query did not work")
valid_pids = []
delta = datetime.timedelta(hours=240)
time_string_pc = (datetime.datetime.now() -
delta).strftime('%Y-%m-%dT%H:%M:%SZ')
for p in projects:
if (not p.close_date) and lims.get_processes(
projectname=p.name, last_modified=time_string_pc):
ret.add(p)
return [(p.name, p.id) for p in ret]
else:
projects = lims.get_projects(name=key)
return [(p.name, p.id) for p in projects]
def create_projects_list(options, db_session, lims, log):
projects = []
if options.all_projects:
if options.hours:
postgres_string = "{} hours".format(options.hours)
project_ids = get_last_modified_projectids(db_session,
postgres_string)
valid_projects = db_session.query(DBProject).filter(
DBProject.luid.in_(project_ids)).all()
log.info("project list : {0}".format(" ".join(
[p.luid for p in valid_projects])))
return valid_projects
else:
projects = db_session.query(DBProject).all()
log.info("project list : {0}".format(" ".join(
[p.luid for p in projects])))
return projects
elif options.input:
with open(options.input, "r") as input_file:
for pname in input_file:
try:
projects.append(lims.get_projects(name=pname.rstrip())[0])
except IndexError:
pass
return projects
def main(args):
lims_db = get_session()
lims = Lims(BASEURI,USERNAME,PASSWORD)
with open(args.conf) as cf:
db_conf = yaml.load(cf)
couch = setupServer(db_conf)
db = couch["expected_yields"]
postgres_string="{} hours".format(args.hours)
project_ids=get_last_modified_projectids(lims_db, postgres_string)
for project in [Project(lims, id=x) for x in project_ids]:
samples_count = 0
samples = lims.get_samples(projectname=project.name)
for sample in samples:
if not("Status (manual)" in sample.udf and sample.udf["Status (manual)"] == "Aborted"):
samples_count +=1
try:
lanes_ordered = project.udf['Sequence units ordered (lanes)']
key = parse_sequencing_platform(project.udf['Sequencing platform'])
except:
continue
for row in db.view("yields/min_yield"):
db_key = [x.lower() if x else None for x in row.key]
if db_key==key:
try:
project.udf['Reads Min'] = float(row.value) * lanes_ordered / samples_count
project.put()
except ZeroDivisionError:
pass
def update_order_status(self, to_date, dry_run):
lims_db = genologics_sql.utils.get_session()
pjs = queries.get_last_modified_projectids(lims_db, '24 hours')
yesterday = (to_date - timedelta(days=1)).strftime('%Y-%m-%d')
today = to_date.strftime('%Y-%m-%d')
for p in pjs:
project = Project(self.lims, id=p)
try:
ORDER_ID = project.udf['Portal ID']
except KeyError:
continue
if not ORDER_ID.startswith('NGI'):
continue
url = '{base}/api/v1/order/{id}'.format(base=self.base_url,
id=ORDER_ID)
response = requests.get(url, headers=self.headers)
data = ''
try:
data = response.json()
except ValueError: #In case a portal id does not exit on lims, skip the proj
continue
url = ''
status = ''
if (data['status'] == 'accepted' and project.udf.get('Queued')
and not project.close_date):
url = data['links']['processing']['href']
status_set = 'processing'
if data['status'] == 'processing':
if project.udf.get('Aborted') and (
project.udf.get('Aborted') == today
or project.udf.get('Aborted') == yesterday):
url = data['links']['aborted']['href']
status_set = 'aborted'
elif project.close_date and (project.close_date == today or
project.close_date == yesterday):
url = data['links']['closed']['href']
status_set = 'closed'
if url:
if not dry_run:
#Order portal sends a mail to user on status change
response = requests.post(url, headers=self.headers)
assert response.status_code == 200, (response.status_code,
response.reason)
self.log.info(
'Updated status for order {} from {} to {}'.format(
ORDER_ID, data['status'], status_set))
else:
print(
'Dry run: {} Updated status for order {} from {} to {}'
.format(date.today(), ORDER_ID, data['status'],
status_set))
def create_projects_list(options, lims, log):
projects=[]
if options.all_projects:
projects = lims.get_projects()
if options.hours:
postgres_string="{} hours".format(options.hours)
db_session=get_session()
project_ids=get_last_modified_projectids(db_session, postgres_string)
valid_projects=[Project(lims, id=x) for x in project_ids]
log.info("project list : {0}".format(" ".join([p.id for p in valid_projects])))
return valid_projects
else:
log.info("project list : {0}".format(" ".join([p.id for p in projects])))
return projects
elif options.input:
with open(options.input, "r") as input_file:
for pname in input_file:
try:
projects.append(lims.get_projects(name=pname.rstrip())[0] )
except IndexError:
pass
return projects