def generate_output(project_id, dest_plate_list, best_sample_struct,total_lanes, req_lanes, lane_maps, rounded_ratios,
target_clusters, clusters_per_lane, extra_lanes, lane_volume, pool_excess, final_pool_sizes, volume_ratios, desired_ratios):
""""Gathers the container id and well name for all samples in project"""
timestamp = datetime.fromtimestamp(time()).strftime('%Y-%m-%d_%H:%M')
#Cred to Denis for providing a base epp
location = dict()
lims = Lims(BASEURI, USERNAME, PASSWORD)
allProjects = lims.get_projects()
for proj in allProjects:
if proj.id == project_id:
projName = proj.name
break
#Sets up source id
#All normalization processes for project
norms=['Library Normalization (MiSeq) 4.0', 'Library Normalization (Illumina SBS) 4.0','Library Normalization (HiSeq X) 1.0']
pros=lims.get_processes(type=norms, projectname=projName)
#For all processes
for p in pros:
#For all artifacts in process
for o in p.all_outputs():
#If artifact is analyte type and has project name in sample
if o.type=="Analyte" and project_id in o.name:
location[o.name.split()[0]] = list()
location[o.name.split()[0]].append(o.location[0].id)
location[o.name.split()[0]].append(o.location[1])
#Continue coding from here
generate_summary(projName, best_sample_struct, timestamp, project_id, dest_plate_list, total_lanes, req_lanes,
lane_maps, rounded_ratios, target_clusters, clusters_per_lane, extra_lanes, volume_ratios, desired_ratios, lane_volume, pool_excess)
generate_csv(projName, timestamp, location, dest_plate_list, total_lanes, best_sample_struct, rounded_ratios, lane_volume, pool_excess, final_pool_sizes)
generate_dumpfile(projName, timestamp, location, dest_plate_list, total_lanes, best_sample_struct, rounded_ratios, lane_volume, pool_excess, final_pool_sizes)
def main(args):
log = []
lims = Lims(BASEURI, USERNAME, PASSWORD)
process = Process(lims, id=args.pid)
for swp_iomap in process.input_output_maps:
if swp_iomap[1]['output-generation-type'] != 'PerInput':
continue
inp_artifact = swp_iomap[0]['uri']
amount_check_pros = lims.get_processes(
type='Amount confirmation QC', inputartifactlimsid=inp_artifact.id)
amount_check_pros.sort(reverse=True, key=lambda x: x.date_run)
try:
correct_amount_check_pro = amount_check_pros[0]
except KeyError:
sys.exit(
"Cannot find an Amount Confirmation QC step for artifact {}".
format(inp_artifact.id))
else:
for iomap in correct_amount_check_pro.input_output_maps:
if iomap[1]['output-generation-type'] != 'PerInput':
continue
if iomap[0]['limsid'] == inp_artifact.id:
for udf_name in [
'Concentration', 'Conc. Units', 'Total Volume (uL)'
]:
try:
swp_iomap[1]['uri'].udf[udf_name] = iomap[1][
'uri'].udf[udf_name]
except:
import pdb
pdb.set_trace()
swp_iomap[1]['uri'].udf['Amount taken (ng)'] = iomap[1][
'uri'].udf['Amount to take (ng)']
swp_iomap[1]['uri'].put()
def main(args):
log = []
lims = Lims(BASEURI,USERNAME,PASSWORD)
process = Process(lims, id=args.pid)
for swp_iomap in process.input_output_maps:
if swp_iomap[1]['output-generation-type'] != 'PerInput':
continue
inp_artifact = swp_iomap[0]['uri']
amount_check_pros = lims.get_processes(type='Amount confirmation QC', inputartifactlimsid=inp_artifact.id)
amount_check_pros.sort(reverse=True, key=lambda x:x.date_run)
try:
correct_amount_check_pro = amount_check_pros[0]
except KeyError:
sys.exit("Cannot find an Amount Confirmation QC step for artifact {}".format(inp_artifact.id))
else:
for iomap in correct_amount_check_pro.input_output_maps:
if iomap[1]['output-generation-type'] != 'PerInput':
continue
if iomap[0]['limsid'] == inp_artifact.id:
for udf_name in ['Concentration', 'Conc. Units', 'Total Volume (uL)']:
try:
swp_iomap[1]['uri'].udf[udf_name] = iomap[1]['uri'].udf[udf_name]
except:
import pdb;pdb.set_trace()
swp_iomap[1]['uri'].udf['Amount taken (ng)'] = iomap[1]['uri'].udf['Amount to take (ng)']
swp_iomap[1]['uri'].put()
def main(args):
log = []
lims = Lims(BASEURI, USERNAME, PASSWORD)
process = Process(lims, id=args.pid)
for io in process.input_output_maps:
if io[1]['output-generation-type'] != 'PerInput':
continue
try:
starting_amount = obtain_amount(io[0]['uri'])
except Exception as e:
log.append(str(e))
starting_amount = 0
log.append("Starting amount of {} : {} ng".format(
io[0]['uri'].samples[0].name, starting_amount))
current_amount = starting_amount
#preps
preps = lims.get_processes(
inputartifactlimsid=io[0]['uri'].id,
type=["Setup Workset/Plate", "Amount confirmation QC"])
for pro in preps:
if pro.id == args.pid:
continue # skip the current step
for prepio in pro.input_output_maps:
if prepio[1]['output-generation-type'] == 'PerInput' and prepio[
0]['uri'].id == io[0]['uri'].id:
if "Amount taken (ng)" in prepio[1][
'uri'].udf: #should always be true
prep_amount = prepio[1]['uri'].udf["Amount taken (ng)"]
log.append(
"Removing {} ng for prep {} for sample {}".format(
prep_amount, pro.id,
io[0]['uri'].samples[0].name))
current_amount = current_amount - prep_amount
else:
log.append(
"No Amount Taken found for prep {} of sample {}".
format(pro.id, io[0]['uri'].samples[0].name))
if current_amount < 0:
log.append(
"Estimated amount for sample {} is {}, correcting to zero".
format(io[0]['uri'].samples[0].name, current_amount))
current_amount = 0
update_output_values(io[0]['uri'], io[1]['uri'], current_amount)
with open("amount_check_log.txt", "w") as f:
f.write("\n".join(log))
for out in process.all_outputs():
if out.name == "QC Assignment Log File":
for f in out.files:
lims.request_session.delete(f.uri)
lims.upload_new_file(out, "amount_check_log.txt")
def test_C(server_test1):
# GIVEN: A lims with a process with:
# process type: 'CG002 - qPCR QC (Library Validation) (Dev)'
# input artifact: '2-1155237'
# Udf 'Instrument Used': 'Cava'
# WHEN creating a genologics Lims object and filtering on the fields.
lims = Lims("http://127.0.0.1:8000", 'dummy', 'dummy')
processes = lims.get_processes(type=['CG002 - qPCR QC (Library Validation) (Dev)'], inputartifactlimsid=['2-1155237'], udf={'Instrument Used': 'Cava'})
# Then the process should be found
assert processes == [Process(lims, id='24-168017')]
def main(args):
log = []
lims = Lims(BASEURI,USERNAME,PASSWORD)
process = Process(lims, id=args.pid)
for io in process.input_output_maps:
if io[1]['output-generation-type'] != 'PerInput':
continue
try:
starting_amount = obtain_amount(io[0]['uri'])
except Exception as e:
log.append(str(e))
starting_amount = 0
log.append("Starting amount of {} : {} ng".format(io[0]['uri'].samples[0].name, starting_amount))
current_amount = starting_amount
#preps
preps = lims.get_processes(inputartifactlimsid=io[0]['uri'].id, type=["Setup Workset/Plate", "Amount confirmation QC"])
for pro in preps:
if pro.id == args.pid:
continue # skip the current step
for prepio in pro.input_output_maps:
if prepio[1]['output-generation-type'] == 'PerInput' and prepio[0]['uri'].id == io[0]['uri'].id:
if "Amount taken (ng)" in prepio[1]['uri'].udf: #should always be true
prep_amount = prepio[1]['uri'].udf["Amount taken (ng)"]
log.append("Removing {} ng for prep {} for sample {}".format(prep_amount, pro.id, io[0]['uri'].samples[0].name))
current_amount = current_amount - prep_amount
else:
log.append("No Amount Taken found for prep {} of sample {}".format(pro.id, io[0]['uri'].samples[0].name))
if current_amount < 0:
log.append("Estimated amount for sample {} is {}, correcting to zero".format(io[0]['uri'].samples[0].name, current_amount))
current_amount = 0
update_output_values(io[0]['uri'], io[1]['uri'], current_amount)
with open("amount_check_log.txt", "w") as f:
f.write("\n".join(log))
for out in process.all_outputs():
if out.name == "QC Assignment Log File" :
for f in out.files:
lims.request_session.delete(f.uri)
lims.upload_new_file(out, "amount_check_log.txt")
NOTE: You need to set the BASEURI, USERNAME AND PASSWORD.
Per Kraulis, Science for Life Laboratory, Stockholm, Sweden.
"""
from genologics.lims import Lims
# Login parameters for connecting to a LIMS instance.
# NOTE: Modify according to your setup.
from genologics.site_cloud import BASEURI, USERNAME, PASSWORD
# Create the LIMS interface instance, and check the connection and version.
lims = Lims(BASEURI, USERNAME, PASSWORD)
lims.check_version()
# Get the list of all processes.
processes = lims.get_processes()
print len(processes), 'processes in total'
process = processes[0]
print process, process.type, process.type.name
for process in lims.get_processes(type=process.type.name):
print process
name = '1a. Fragment DNA (TruSeq DNA) 3.0'
print name
for process in lims.get_processes(type=name):
print process
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 generate_output(project, destid, total_lanes, req_lanes, lane_maps, acc_ratios):
#Gathers the container id and well name for all samples in project
#Cred to Denis for providing a base epp
location = dict()
lims = Lims(BASEURI, USERNAME, PASSWORD)
allProjects = lims.get_projects()
for proj in allProjects:
if proj.id == project:
projName = proj.name
break
#All normalization processes for project
norms=['Library Normalization (MiSeq) 4.0', 'Library Normalization (Illumina SBS) 4.0','Library Normalization (HiSeq X) 1.0']
pros=lims.get_processes(type=norms, projectname=projName)
#For all processes
for p in pros:
#For all artifacts in process
for o in p.all_outputs():
#If artifact is analyte type and has project name in sample
if o.type=="Analyte" and project in o.name:
location[o.name.split()[0]] = list()
location[o.name.split()[0]].append(o.location[0].id)
location[o.name.split()[0]].append(o.location[1])
#PRINT section
#Print stats including duplicates
timestamp = datetime.fromtimestamp(time()).strftime('%Y-%m-%d_%H:%M')
sumName = projName, "_summary_", timestamp,".txt"
sumName = ''.join(sumName)
with open(sumName, "w") as summary:
if sum(req_lanes.values()) != 0:
OPT = sum(total_lanes)/sum(req_lanes.values())
else:
OPT = 0
output = "Ideal lanes (same schema): ", str(sum(req_lanes.values())) , ", Total lanes: ", str(sum(total_lanes)), ", OPT: ", str(round(OPT,3)),'\n'
output = ''.join(output)
summary.write( output )
output = "Unique pools: ", str(len(total_lanes)), ", Average pool duplication: ", str(sum(total_lanes)/float(len(total_lanes))) ,'\n'
output = ''.join(output)
summary.write( output )
bin = 0
for index in xrange(1, len(lane_maps)+1):
bin += 1
summary.write('\n')
output = "Wells ", str(bin) , '-' , str(bin+int(total_lanes[index-1])-1),':','\n'
output = ''.join(output)
summary.write( output )
bin += int(total_lanes[index-1]-1)
for counter in xrange(1, len(lane_maps[index])):
output = str(lane_maps[index][counter]),' ', str(acc_ratios[index][counter]), "%",'\n'
output = ''.join(output)
summary.write( output )
#Creates csv
name = projName,"_repool_",timestamp,".csv"
name = ''.join(name)
wells = ['Empty','A','B','C','D','E','F','G','H']
#Index 0 is number, index 1 is Letter
wellIndex = [1, 1]
destNo = 0
with open(name, 'w') as csvfile:
writer = csv.writer(csvfile)
for index in xrange(1, len(lane_maps)+1):
for dupes in xrange(1, int(total_lanes[index-1])+1):
if lane_maps[index] == 0:
raise Exception('Error: Project not logged in x_flowcells database!')
for counter in xrange(1, len(lane_maps[index])):
#<source plate ID>,<source well>,<volume>,<destination plate ID>,<destination well>
#Destination well 200 microL, minimum pipette 2 microL; acc_ratios multiplied by 2.
sample = lane_maps[index][counter]
position = wells[wellIndex[1]],':',str(wellIndex[0])
position = ''.join(position)
try:
output = location[sample][0],location[sample][1],str(int(acc_ratios[index][counter]*2)),str(destid[destNo]),position
except KeyError:
print "Error: Samples incorrectly parsed into database, thus causing sample name conflicts!"
if not acc_ratios[index][counter] == 0:
writer.writerow(output)
#Increment wellsindex
if not acc_ratios[index][counter] == 0:
if not wellIndex[1] >= 8:
wellIndex[1] += 1
else:
wellIndex[1] = 1
if not wellIndex[0] >= 8:
wellIndex[0] += 1
else:
wellIndex[0] = 1
destNo += 1
try:
destid[destNo]
except IndexError:
print "Critical error; not enough destination plates provided"
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."
