def __init__(self, config):
self.trello = TrelloUtils(config)
self.config = config
class Monitor(object):
def __init__(self, config):
self.trello = TrelloUtils(config)
self.config = config
def list_trello_cards(self, lists):
# Loop over the lists and fetch the cards, returning a dictionary keyed with the card title
cards = {}
for tlist in lists:
list_obj = self.trello.get_list(self.trello_board,tlist,True)
if not list_obj:
continue
# Loop over the cards in the list
for card in list_obj.list_cards():
# Get the description and convert it to a dictionary
cards[card.name] = card
return cards
def list_runs(self):
"""Get a list of folders matching the run folder pattern"""
pattern = r'(\d{6})_([SNMD]+\d+)_\d+_([AB]?)([A-Z0-9\-]+)'
runs = []
for dump_folder in self.run_folders:
for fname in os.listdir(dump_folder):
if not os.path.isdir(os.path.join(dump_folder,fname)):
continue
m = re.match(pattern, fname)
if m is not None:
run = {'name': fname,
'path': os.path.join(dump_folder,fname),
'date': m.group(1),
'instrument': m.group(2),
'position': m.group(3),
'flowcell_id': m.group(4),
'short_name': "{}_{}{}".format(m.group(1),m.group(3),m.group(4))}
run['technology'] = 'MiSeq' if self.is_miseq_run(run) else 'HiSeq'
run['run_info'] = self.get_run_info(run)
run['run_parameters'] = self.get_run_parameters(run)
run['samplesheet'] = self.get_run_samplesheet(run)
run['projects'] = self.get_run_projects(run)
# Don't track MiSeq runs that are not production, qc or applications
if self.is_miseq_run(run) and len([d for d in self.get_samplesheet_descriptions(run) if d.lower() in ["qc","production","applications"]]) == 0:
continue
runs.append(run)
return runs
def is_miseq_run(self, run):
"""Determine whether this is a MiSeq run, from the flowcell-id format
"""
return not run['flowcell_id'].endswith("XX")
def get_samplesheet_descriptions(self, run):
"""Return the set of descriptions in the samplesheet"""
ss = run['samplesheet']
return list(set([s['Description'] for s in ss])) if ss else []
def get_run_info(self, run):
"""Parse the RunInfo.xml file into a dict"""
f = os.path.join(run['path'],'RunInfo.xml')
if not os.path.exists(f):
return {}
with open(f) as fh:
rip = RunInfoParser()
runinfo = rip.parse(fh)
return runinfo
def get_run_parameters(self, run):
"""Parse the runParameters.xml file into a dict"""
f = os.path.join(run['path'],'runParameters.xml')
if not os.path.exists(f):
return {}
with open(f) as fh:
rpp = RunParametersParser()
runparameters = rpp.parse(fh)
return runparameters
def get_run_samplesheet(self, run):
"""Locate and parse the samplesheet for a run"""
fname = "{}.csv".format(run.get("flowcell_id","SampleSheet"))
ssheet = None
for folder in self.samplesheet_folders + [run.get("path","")]:
f = os.path.join(folder,fname)
if os.path.exists(f):
ssheet = f
break
if ssheet is None:
return None
return HiSeqSampleSheet(ssheet)
def get_run_projects(self, run):
"""Locate and parse the samplesheet to extract projects in the run"""
ss = run['samplesheet']
projects = list(set([s['SampleProject'].replace("__",".") for s in ss])) if ss else []
return projects
def get_run_project_samples(self, run, project):
"""Locate and parse the samplesheet to extract samples for a project in the run"""
ss = run['samplesheet']
samples = list(set([s['SampleID'].replace("__",".") for s in ss if s['SampleProject'].replace("__",".") == project])) if ss else []
return samples
def send_notification(self, subject, msg, users=[]):
"""Send an email notification that a run has been moved to a list
"""
addresses = self.config.get("email",{})
recipients = []
for user in users:
try:
recipients.extend(addresses[user].split(","))
except:
pass
if len(recipients) == 0:
recipients = self.config.get("email",{}).get("default","").split(",")
if len(recipients) == 0 or all([len(r) == 0 for r in recipients]):
return
msg = MIMEText("{}\nSent from {}".format(msg,
socket.gethostname()))
msg['Subject'] = subject
msg['From'] = SENDER
msg['To'] = ",".join(recipients)
try:
s = smtplib.SMTP(self.config.get("email",{}).get("smtp_host","localhost"))
s.sendmail(SENDER, recipients, msg.as_string())
s.quit()
except Exception, e:
print("WARNING: Sending email to {} failed: {}".format(",".join(recipients),str(e)))