class LimsService(object):
name = "lims_service"
def __init__(self):
super(LimsService, self).__init__()
self.lims = Lims(BASEURI, USERNAME, PASSWORD)
self.lims.check_version()
@rpc
def sample(self, lims_id):
"""Get a sample from LIMS."""
sample_obj = LimsSample(self.lims, id=lims_id)
sample_dict = transform_entry(sample_obj)
return sample_dict
@rpc
def validate_sample(self, lims_id):
"""Validate information in the LIMS on sample level."""
logger.debug("fetch sample from LIMS")
sample_obj = LimsSample(self.lims, id=lims_id)
try:
case_id = sample_obj.udf["familyID"]
cust_id = sample_obj.udf["customer"]
except KeyError as error:
raise MissingLimsDataException(error.message)
except HTTPError as error:
raise LimsSampleNotFoundError(error.message)
@rpc
def ls_case(self, cust_id, case_id):
"""Fetch all samples for a case from the LIMS."""
sample_objs = self.lims.get_samples(udf={"customer": cust_id, "familyID": case_id})
sample_dicts = [transform_entry(sample) for sample in sample_objs]
analysis_types = set(sample["analysis_type"] for sample in sample_dicts)
case_data = {"analysis_types": list(analysis_types), "samples": sample_dicts}
return case_data
@rpc
def ls_project(self, project_id):
"""List all samples in a project."""
samples = self.lims.get_samples(projectname=project_id)
lims_ids = [sample.id for sample in samples]
return lims_ids
@rpc
def pedigree(self, cust_id, case_id):
"""Generate pedigree content for a case."""
ped_content = serialize_pedigree(self.lims, cust_id, case_id)
return ped_content
@rpc
def target_reads(self, lims_id):
"""Determine the amount of reads to be sequenced."""
sample_obj = LimsSample(self.lims, id=lims_id)
app_tag = analysis_info(sample_obj)
# millions of reads
target_reads = app_tag["reads"] * 1000000
return target_reads
def __init__(self, current_step, logger=None, cache=False):
"""
Initializes the context.
:param current_step: The step from which the extension is running
:param logger: A logger instance
:param cache: Set to True to use the cache folder (.cache) for downloaded files
"""
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()
self.advanced = Advanced(lims)
self.current_step = Process(lims, id=current_step)
self.logger = logger or logging.getLogger(__name__)
self._local_shared_files = []
self.cache = cache
def __init__(self, current_step, logger=None, cache=False):
"""
Initializes the context.
:param current_step: The step from which the extension is running
:param logger: A logger instance
:param cache: Set to True to use the cache folder (.cache) for downloaded files
"""
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()
self.advanced = Advanced(lims)
self.current_step = Process(lims, id=current_step)
self.logger = logger or logging.getLogger(__name__)
self._local_shared_files = []
self.cache = cache
x for x in io if x[1]['output-generation-type'] == 'PerInput'
]
# Fetch the first input-output artifact pair
(input, output) = io_filtered[0]
# Instantiate the output artifact
output_artifact = Artifact(output['limsid'])
# Attach the file
attach_file(args.file, output_artifact)
if __name__ == "__main__":
parser = ArgumentParser()
# Arguments that are useful in all EPP scripts
parser.add_argument("--log", default=sys.stdout, help="Log file")
# Arguments specific for this scripts task
parser.add_argument("--pid", help="Process id")
parser.add_argument("--file", help="File to upload")
args = parser.parse_args()
# Log everything to log argument
with EppLogger(args.log):
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()
main(lims, args.pid, args.file)
elif lines: # Avoid printing empty files
lp_args = ["lp"]
if args.hostname:
#remove that when all the calls to this script have been updated
if args.hostname == 'homer.scilifelab.se:631':
args.hostname='homer2.scilifelab.se:631'
lp_args += ["-h",args.hostname]
if args.destination:
lp_args += ["-d",args.destination]
lp_args.append("-") # lp accepts stdin if '-' is given as filename
logging.info('Ready to call lp for printing.')
sp = subprocess.Popen(lp_args,
stdin=subprocess.PIPE,
stdout=subprocess.PIPE,
stderr=subprocess.PIPE)
sp.stdin.write(str('\n'.join(lines)))
logging.info('lp command is called for printing.')
stdout,stderr = sp.communicate() # Will wait for sp to finish
logging.info('lp stdout: {0}'.format(stdout))
logging.info('lp stderr: {0}'.format(stderr))
logging.info('lp command finished')
sp.stdin.close()
if __name__ == '__main__':
arguments = getArgs()
lims = Lims(BASEURI,USERNAME,PASSWORD)
lims.check_version()
prepend = not arguments.no_prepend
with EppLogger(arguments.log,lims=lims,prepend=prepend) as epp_logger:
main(arguments,lims,epp_logger)
def namesetter(PID):
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()
#Find LIMS entry with same PID
allProjects = lims.get_projects()
for proj in allProjects:
if proj.id == PID:
limsproject = proj.name
break
#Error handling
if not 'limsproject' in locals():
print("{} not available in LIMS.".format(PID))
return None
#Enter project summary process
stepname=['Project Summary 1.3']
process=lims.get_processes(type=stepname, projectname=limsproject)
#Error handling
if process == []:
print("{} for {} is not available in LIMS.".format(stepname, limsproject))
return None
loop = True
while loop:
if "Bioinfo responsible" in process[0].udf:
response = process[0].udf["Bioinfo responsible"]
else:
response = "Unassigned"
print("Existing Bioinfo responsible for project {} aka {} is: {}".format(limsproject, PID, response.encode('utf-8')))
#Checks for valid name
in_responsibles = False
config_responsibles =Udfconfig(lims, id="1128")
while not in_responsibles:
if sys.version_info[0] == 3:
newname = input("Enter name of new Bioinfo responsible: ")
elif sys.version_info[0] == 2:
newname = raw_input("Enter name of new Bioinfo responsible: ")
for names in config_responsibles.presets:
if newname in names:
in_responsibles = True
newname = names
if not in_responsibles:
print("Subset {} not found in accepted Bioinfo responsible list.".format(newname))
else:
print("Suggested name is {}".format(newname))
if sys.version_info[0] == 3:
confirmation = input("Project {} aka {} will have {} as new Bioinfo responsible, is this correct (Y/N)? ".format(limsproject, PID, newname))
elif sys.version_info[0] == 2:
confirmation = raw_input("Project {} aka {} will have {} as new Bioinfo responsible, is this correct (Y/N)? ".format(limsproject, PID, newname))
if confirmation == 'Y' or confirmation == 'y':
try:
newname.encode('ascii')
process[0].udf["Bioinfo responsible"] = str(newname)
process[0].put()
print("Project {} aka {} assigned to {}".format(limsproject, PID, newname))
return None
except (UnicodeDecodeError, UnicodeEncodeError):
#Weird solution due to put function
process[0].udf["Bioinfo responsible"] = response
print("ERROR: You tried to use a special character, didn't you? Don't do that. New standards and stuff...")
elif confirmation == 'N' or confirmation == 'n':
loop = False
else:
print("Invalid answer.")
def namesetter(PID):
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()
#Find LIMS entry with same PID
allProjects = lims.get_projects()
for proj in allProjects:
if proj.id == PID:
limsproject = proj.name
break
#Error handling
if not 'limsproject' in locals():
print "{} not available in LIMS.".format(PID)
return None
#Enter project summary process
stepname=['Project Summary 1.3']
process=lims.get_processes(type=stepname, projectname=limsproject)
#Error handling
if process == []:
print "{} for {} is not available in LIMS.".format(stepname, limsproject)
return None
loop = True
while loop:
if "Bioinfo responsible" in process[0].udf:
response = process[0].udf["Bioinfo responsible"]
else:
response = "Unassigned"
print "Existing Bioinfo responsible for project {} aka {} is: {}".format(limsproject, PID, response.encode('utf-8'))
#Checks for valid name
in_responsibles = False
config_responsibles =Udfconfig(lims, id="1128")
while not in_responsibles:
newname = raw_input("Enter name of new Bioinfo responsible: ")
for names in config_responsibles.presets:
if newname in names:
in_responsibles = True
newname = names
if not in_responsibles:
print "Subset {} not found in accepted Bioinfo responsible list.".format(newname)
else:
print "Suggested name is {}".format(newname)
confirmation = raw_input("Project {} aka {} will have {} as new Bioinfo responsible, is this correct (Y/N)? ".format(limsproject, PID, newname))
if confirmation == 'Y' or confirmation == 'y':
try:
newname.decode('ascii')
process[0].udf["Bioinfo responsible"] = unicode(newname)
process[0].put()
print "Project {} aka {} assigned to {}".format(limsproject, PID, newname)
return None
except UnicodeDecodeError:
#Weird solution due to put function
process[0].udf["Bioinfo responsible"] = response
print "ERROR: You tried to use a special character, didn't you? Don't do that. New standards and stuff..."
elif confirmation == 'N' or confirmation == 'n':
loop = False
else:
print "Invalid answer."