def prepooling(currentStep, lims):
log = []
# First thing to do is to grab the volumes of the input artifacts. The method is ... rather unique.
data = compute_transfer_volume(currentStep, lims, log)
with open("bravo.csv", "w") as csvContext:
for s in data:
if s['vol_to_take'] > MAX_WARNING_VOLUME:
log.append("Volume for sample {} is above {}, redo the calculations manually".format(MAX_WARNING_VOLUME, s['name']))
if s['vol_to_take'] < MIN_WARNING_VOLUME:
log.append("Volume for sample {} is below {}, redo the calculations manually".format(MIN_WARNING_VOLUME, s['name']))
csvContext.write("{0},{1},{2},{3},{4}\n".format(s['src_fc_id'], s['src_well'], s['vol_to_take'], s['dst_fc'], s['dst_well']))
if log:
with open("bravo.log", "w") as logContext:
logContext.write("\n".join(log))
for out in currentStep.all_outputs():
# attach the csv file and the log file
if out.name == "Bravo CSV File":
attach_file(os.path.join(os.getcwd(), "bravo.csv"), out)
if log and out.name == "Bravo Log":
attach_file(os.path.join(os.getcwd(), "bravo.log"), out)
if log:
# to get an eror display in the lims, you need a non-zero exit code AND a message in STDERR
sys.stderr.write("Errors were met, please check the Log file\n")
sys.exit(2)
else:
logging.info("Work done")
def prepooling(currentStep, lims):
log = []
# First thing to do is to grab the volumes of the input artifacts. The method is ... rather unique.
data = compute_transfer_volume(currentStep, lims, log)
with open("bravo.csv", "w") as csvContext:
for s in data:
if s['vol_to_take'] > MAX_WARNING_VOLUME:
log.append("Volume for sample {} is above {}, redo the calculations manually".format(MAX_WARNING_VOLUME, s['name']))
if s['vol_to_take'] < MIN_WARNING_VOLUME:
log.append("Volume for sample {} is below {}, redo the calculations manually".format(MIN_WARNING_VOLUME, s['name']))
csvContext.write("{0},{1},{2},{3},{4}\n".format(s['src_fc_id'], s['src_well'], s['vol_to_take'], s['dst_fc'], s['dst_well']))
if log:
with open("bravo.log", "w") as logContext:
logContext.write("\n".join(log))
for out in currentStep.all_outputs():
# attach the csv file and the log file
if out.name == "Bravo CSV File":
attach_file(os.path.join(os.getcwd(), "bravo.csv"), out)
if log and out.name == "Bravo Log":
attach_file(os.path.join(os.getcwd(), "bravo.log"), out)
if log:
# to get an eror display in the lims, you need a non-zero exit code AND a message in STDERR
sys.stderr.write("Errors were met, please check the Log file\n")
sys.exit(2)
else:
logging.info("Work done")
def main(lims, args, logger):
"""This should be run at project summary level"""
p = Process(lims,id = args.pid)
samplenb=0
errnb=0
summary={}
logart=None
for output_artifact in p.all_outputs():
#filter to only keep solo sample demultiplexing output artifacts
if output_artifact.type=='Analyte' and len(output_artifact.samples)==1:
sample=output_artifact.samples[0]
samplenb+=1
#update the total number of reads
total_reads=sumreads(sample, summary)
sample.udf['Total Reads (M)']=total_reads
output_artifact.udf['Set Total Reads']=total_reads
logging.info("Total reads is {0} for sample {1}".format(sample.udf['Total Reads (M)'],sample.name))
try:
logging.info(" ###### updating {} with {}".format(sample.name, sample.project.udf.get('Reads Min',0)))
sample.udf['Reads Min'] = sample.project.udf.get('Reads Min',0) / 1000000
sample.put()
if sample.udf['Reads Min'] >= sample.udf['Total Reads (M)']:
sample.udf['Status (auto)']="In Progress"
sample.udf['Passed Sequencing QC']="False"
elif sample.udf['Reads Min'] < sample.udf['Total Reads (M)'] :
sample.udf['Passed Sequencing QC']="True"
sample.udf['Status (auto)']="Finished"
except KeyError as e:
print e
logging.warning("No reads minimum found, cannot set the status auto flag for sample {0}".format(sample.name))
errnb+=1
#commit the changes
sample.put()
output_artifact.put()
elif(output_artifact.type=='Analyte') and len(output_artifact.samples)!=1:
logging.error("Found {0} samples for the ouput analyte {1}, that should not happen".format(len(output_artifact.samples()),output_artifact.id))
elif(output_artifact.type=="ResultFile" and output_artifact.name=="AggregationLog"):
logart=output_artifact
#write the csv file, separated by pipes, no cell delimiter
with open("AggregationLog.csv", "w") as f:
f.write("sep=,\n")
f.write('sample name,number of flowcells,number of lanes,flowcell1:lane1|lane2;flowcell2:lane1|lane2|lane3 ...\n')
for sample in summary:
view=[]
totfc=len(summary[sample])
totlanes=0
for fc in summary[sample]:
view.append("{0}:{1}".format(fc, "|".join(summary[sample][fc])))
totlanes+=len(summary[sample][fc])
f.write('{0},{1},{2},{3}\n'.format(sample, totfc, totlanes, ";".join(view)))
try:
attach_file(os.path.join(os.getcwd(), "AggregationLog.csv"), logart)
logging.info("updated {0} samples with {1} errors".format(samplenb, errnb))
except AttributeError:
#happens if the log artifact does not exist, if the step has been started before the configuration changes
logging.info("Could not upload the log file")
def main(lims, args):
p = Process(lims, id=args.pid)
log = []
datamap = {}
wsname = None
username = "******".format(p.technician.first_name,
p.technician.last_name)
user_email = p.technician.email
for art in p.all_inputs():
if len(art.samples) != 1:
log.append(
"Warning : artifact {0} has more than one sample".format(
art.id))
for sample in art.samples:
#take care of lamda DNA
if sample.project:
if sample.project.id not in datamap:
datamap[sample.project.id] = [sample.name]
else:
datamap[sample.project.id].append(sample.name)
for art in p.all_outputs():
try:
wsname = art.location[0].name
break
except:
pass
now = datetime.now().strftime("%Y-%m-%d %H:%M:%S.%f")
for pid in datamap:
pj = Project(lims, id=pid)
if len(datamap[pid]) > 1:
rnt = "{0} samples planned for {1}".format(len(datamap[pid]),
wsname)
else:
rnt = "{0} sample planned for {1}".format(len(datamap[pid]),
wsname)
running_note = {
"note": rnt,
"user": username,
"email": user_email,
"category": "Workset"
}
write_note_to_couch(pid, now, running_note, lims.get_uri())
log.append(
"Updated project {0} : {1}, {2} samples in this workset".format(
pid, pj.name, len(datamap[pid])))
with open("EPP_Notes.log", "w") as flog:
flog.write("\n".join(log))
for out in p.all_outputs():
#attach the log file
if out.name == "RNotes Log":
attach_file(os.path.join(os.getcwd(), "EPP_Notes.log"), out)
sys.stderr.write("Updated {0} projects successfully".format(
len(list(datamap.keys()))))
def main(lims, args, logger):
"""This should be run at project summary level"""
p = Process(lims,id = args.pid)
samplenb=0
errnb=0
summary={}
logart=None
for output_artifact in p.all_outputs():
#filter to only keep solo sample demultiplexing output artifacts
if output_artifact.type=='Analyte' and len(output_artifact.samples)==1:
sample=output_artifact.samples[0]
samplenb+=1
#update the total number of reads
total_reads=sumreads(sample, summary)
sample.udf['Total Reads (M)']=total_reads
output_artifact.udf['Set Total Reads']=total_reads
logging.info("Total reads is {0} for sample {1}".format(sample.udf['Total Reads (M)'],sample.name))
try:
logging.info(" ###### updating {} with {}".format(sample.name, sample.project.udf.get('Reads Min',0)))
sample.udf['Reads Min'] = sample.project.udf.get('Reads Min',0) / 1000000
sample.put()
if sample.udf['Reads Min'] >= sample.udf['Total Reads (M)']:
sample.udf['Status (auto)']="In Progress"
sample.udf['Passed Sequencing QC']="False"
elif sample.udf['Reads Min'] < sample.udf['Total Reads (M)'] :
sample.udf['Passed Sequencing QC']="True"
sample.udf['Status (auto)']="Finished"
except KeyError as e:
print e
logging.warning("No reads minimum found, cannot set the status auto flag for sample {0}".format(sample.name))
errnb+=1
#commit the changes
sample.put()
output_artifact.put()
elif(output_artifact.type=='Analyte') and len(output_artifact.samples)!=1:
logging.error("Found {0} samples for the ouput analyte {1}, that should not happen".format(len(output_artifact.samples()),output_artifact.id))
elif(output_artifact.type=="ResultFile" and output_artifact.name=="AggregationLog"):
logart=output_artifact
#write the csv file, separated by pipes, no cell delimiter
with open("AggregationLog.csv", "w") as f:
f.write("sep=,\n")
f.write('sample name,number of flowcells,number of lanes,flowcell1:lane1|lane2;flowcell2:lane1|lane2|lane3 ...\n')
for sample in summary:
view=[]
totfc=len(summary[sample])
totlanes=0
for fc in summary[sample]:
view.append("{0}:{1}".format(fc, "|".join(summary[sample][fc])))
totlanes+=len(summary[sample][fc])
f.write('{0},{1},{2},{3}\n'.format(sample, totfc, totlanes, ";".join(view)))
try:
attach_file(os.path.join(os.getcwd(), "AggregationLog.csv"), logart)
logging.info("updated {0} samples with {1} errors".format(samplenb, errnb))
except AttributeError:
#happens if the log artifact does not exist, if the step has been started before the configuration changes
logging.info("Could not upload the log file")
def generate_csv(lims,step_id, logfile):
logger=setupLog(logfile)
pro=Process(lims, id=step_id)
data=generate_data(pro)
with open("neoprep_input.csv", 'wb') as f:
f.write(data)
for out in pro.all_outputs():
#attach the csv file
if out.name=="Input CSV File":
attach_file(os.path.join(os.getcwd(), "neoprep_input.csv"), out)
if out.name=="Log File":
attach_file(os.path.join(os.getcwd(), logfile), out)
def generate_csv(lims, step_id, logfile):
logger = setupLog(logfile)
pro = Process(lims, id=step_id)
data = generate_data(pro)
with open("neoprep_input.csv", 'wb') as f:
f.write(data)
for out in pro.all_outputs():
#attach the csv file
if out.name == "Input CSV File":
attach_file(os.path.join(os.getcwd(), "neoprep_input.csv"), out)
if out.name == "Log File":
attach_file(os.path.join(os.getcwd(), logfile), out)
def main(lims, args):
p=Process(lims, id=args.pid)
log=[]
datamap={}
wsname=None
username="******".format(p.technician.first_name, p.technician.last_name)
user_email=p.technician.email
for art in p.all_inputs():
if len(art.samples)!=1:
log.append("Warning : artifact {0} has more than one sample".format(art.id))
for sample in art.samples:
#take care of lamda DNA
if sample.project:
if sample.project.id not in datamap:
datamap[sample.project.id]=[sample.name]
else:
datamap[sample.project.id].append(sample.name)
for art in p.all_outputs():
try:
wsname=art.location[0].name
break
except:
pass
now=datetime.now().strftime("%Y-%m-%d %H:%M:%S.%f")
for pid in datamap:
pj=Project(lims, id=pid)
running_notes=json.loads(pj.udf['Running Notes'])
if len(datamap[pid]) > 1:
rnt="{0} samples planned for {1}".format(len(datamap[pid]), wsname)
else:
rnt="{0} sample planned for {1}".format(len(datamap[pid]), wsname)
running_notes[now]={"note": rnt, "user" : username, "email":user_email, "category":"Workset"}
pj.udf['Running Notes']=json.dumps(running_notes)
pj.put()
log.append("Updated project {0} : {1}, {2} samples in this workset".format(pid,pj.name, len(datamap[pid])))
with open("EPP_Notes.log", "w") as flog:
flog.write("\n".join(log))
for out in p.all_outputs():
#attach the log file
if out.name=="RNotes Log":
attach_file(os.path.join(os.getcwd(), "EPP_Notes.log"), out)
sys.stderr.write("Updated {0} projects successfully".format(len(datamap.keys())))
def default_bravo(currentStep, with_total_vol=True):
checkTheLog = [False]
with open("bravo.csv", "w") as csvContext:
with open("bravo.log", "w") as logContext:
# working directly with the map allows easier input/output handling
for art_tuple in currentStep.input_output_maps:
# filter out result files
if art_tuple[0]['uri'].type == 'Analyte' and art_tuple[1][
'uri'].type == 'Analyte':
source_fc = art_tuple[0]['uri'].location[0].name
source_well = art_tuple[0]['uri'].location[1]
dest_fc = art_tuple[1]['uri'].location[0].id
dest_well = art_tuple[1]['uri'].location[1]
if with_total_vol:
try:
# might not be filled in
final_volume = art_tuple[1]['uri'].udf[
"Total Volume (uL)"]
except KeyError:
logContext.write(
"No Total Volume found for sample {0}\n".
format(art_tuple[0]['uri'].samples[0].name))
checkTheLog[0] = True
else:
volume = calc_vol(art_tuple, logContext,
checkTheLog)
csvContext.write(
"{0},{1},{2},{3},{4},{5}\n".format(
source_fc, source_well, volume, dest_fc,
dest_well, final_volume))
else:
volume = calc_vol(art_tuple, logContext, checkTheLog)
csvContext.write("{0},{1},{2},{3},{4}\n".format(
source_fc, source_well, volume, dest_fc,
dest_well))
for out in currentStep.all_outputs():
# attach the csv file and the log file
if out.name == "Bravo CSV File":
attach_file(os.path.join(os.getcwd(), "bravo.csv"), out)
if out.name == "Bravo Log":
attach_file(os.path.join(os.getcwd(), "bravo.log"), out)
if checkTheLog[0]:
# to get an eror display in the lims, you need a non-zero exit code AND a message in STDERR
sys.stderr.write("Errors were met, please check the Log file\n")
sys.exit(2)
else:
logging.info("Work done")
def default_bravo(currentStep, with_total_vol=True):
checkTheLog = [False]
with open("bravo.csv", "w") as csvContext:
with open("bravo.log", "w") as logContext:
# working directly with the map allows easier input/output handling
for art_tuple in currentStep.input_output_maps:
# filter out result files
if art_tuple[0]['uri'].type == 'Analyte' and art_tuple[1]['uri'].type == 'Analyte':
source_fc = art_tuple[0]['uri'].location[0].name
source_well = art_tuple[0]['uri'].location[1]
dest_fc = art_tuple[1]['uri'].location[0].id
dest_well = art_tuple[1]['uri'].location[1]
if with_total_vol:
try:
# might not be filled in
final_volume = art_tuple[1]['uri'].udf["Total Volume (uL)"]
except KeyError:
logContext.write("No Total Volume found for sample {0}\n".format(art_tuple[0]['uri'].samples[0].name))
checkTheLog[0] = True
else:
volume = calc_vol(art_tuple, logContext, checkTheLog)
csvContext.write("{0},{1},{2},{3},{4},{5}\n".format(source_fc, source_well, volume, dest_fc, dest_well, final_volume))
else:
volume = calc_vol(art_tuple, logContext, checkTheLog)
csvContext.write("{0},{1},{2},{3},{4}\n".format(source_fc, source_well, volume, dest_fc, dest_well))
for out in currentStep.all_outputs():
# attach the csv file and the log file
if out.name == "Bravo CSV File":
attach_file(os.path.join(os.getcwd(), "bravo.csv"), out)
if out.name == "Bravo Log":
attach_file(os.path.join(os.getcwd(), "bravo.log"), out)
if checkTheLog[0]:
# to get an eror display in the lims, you need a non-zero exit code AND a message in STDERR
sys.stderr.write("Errors were met, please check the Log file\n")
sys.exit(2)
else:
logging.info("Work done")
def main(lims, args, epp_logger):
p = Process(lims, id=args.pid)
if not args.path:
args.path = os.getcwd()
file_list = os.listdir(args.path)
# Find all per input result files
io = p.input_output_maps
io_filtered = filter(
lambda (x, y): y['output-generation-type'] == 'PerInput', io)
io_filtered = filter(lambda (x, y): y['output-type'] == 'ResultFile',
io_filtered)
artifact_missing_file = []
artifact_multiple_file = []
found_files = []
for input, output in io_filtered:
i_a = Artifact(lims, id=input['limsid'])
o_a = Artifact(lims, id=output['limsid'])
# Input Well, Input Container
i_w, i_c = i_a.location[1], i_a.location[0]
# Well is typed without colon in filename:
i_w = ''.join(i_w.split(':'))
# Use a reguluar expression to find the file name given
# the container and sample. This is all assuming the driver template name ends with:
# ${INPUT.CONTAINER.PLACEMENT}_${INPUT.NAME}_${INPUT.CONTAINER.LIMSID}_${INPUT.LIMSID}
# However, names are excluded to improve robustness.
if args.instrument == "fragment_analyzer":
info = {
'well': o_a.location[1].replace(":", ""),
'output_artifact_name': o_a.samples[0].name
}
re_str = '.*{well}.*{output_artifact_name}'\
.format(**info)
else:
info = {
'well': i_w,
'container_id': i_c.id,
'input_artifact_id': i_a.id
}
re_str = '.*{well}_.*_.*{container_id}_.*{input_artifact_id}'\
.format(**info)
logging.info(
("Looking for file for artifact id: {input_artifact_id} "
"from container with id: {container_id}.").format(**info))
im_file_r = re.compile(re_str)
fns = filter(im_file_r.match, file_list)
if len(fns) == 0:
logging.warning(
"No image file found for artifact with id {0}".format(i_a.id))
artifact_missing_file.append(i_a)
elif len(fns) > 1:
logging.warning(
("Multiple image files found for artifact with id {0}, "
"please attach files manually").format(i_a.id))
artifact_multiple_file.append(i_a)
else:
fn = fns[0]
found_files.append(fn)
logging.info(
"Found image file {0} for artifact with id {1}".format(
fn, i_a.id))
fp = os.path.join(args.path, fn)
# Attach file to the LIMS
location = attach_file(fp, o_a)
logging.debug("Moving {0} to {1}".format(fp, location))
warning = ""
if len(artifact_missing_file):
warning = "Did not find any file for {0} artifact(s). ".format(
len(artifact_missing_file))
if len(artifact_multiple_file):
warning += "Found multiple files for {0} artifact(s), none of these were uploaded.".format(
len(artifact_multiple_file))
if warning:
warning = "Warning: " + warning
abstract = "Uploaded {0} file(s). {1}".format(len(found_files), warning)
print >> sys.stderr, abstract # stderr will be logged and printed in GUI
def normalization(current_step):
log = []
with open("normalization.csv", "w") as csv:
for art in current_step.input_output_maps:
src = art[0]["uri"]
dest = art[1]["uri"]
if src.type == dest.type == "Analyte":
# Source sample:
src_plate = src.location[0].id
src_well = src.location[1]
try:
src_tot_volume = float(src.udf["Volume (ul)"])
except:
src_tot_volume = 999999
log.append("WARNING: No volume found for input sample {0}".format(src.samples[0].name))
try:
src_volume = float(dest.udf["Volume to take (uL)"])
except:
sys.stderr.write("Field 'Volume to take (uL)' is empty for artifact {0}\n".format(dest.name))
sys.exit(2)
if "Concentration" in src.udf:
src_conc = src.udf["Concentration"]
if src.udf["Conc. Units"] != "nM":
log.append("ERROR: No valid concentration found for sample {0}".format(src.samples[0].name))
elif "Normalized conc. (nM)" in src.udf:
src_conc = src.udf["Normalized conc. (nM)"]
else:
sys.stderr.write("Non input concentration found for sample {0}\n".format(dest.name))
sys.exit(2)
# Diluted sample:
dest_plate = dest.location[0].id
dest_well = dest.location[1]
try:
dest_conc = dest.udf["Normalized conc. (nM)"]
except:
sys.stderr.write("Field 'Normalized conc. (nM)' is empty for artifact {0}\n".format(dest.name))
sys.exit(2)
if src_conc < dest_conc:
log.append("ERROR: Too low concentration for sample {0}".format(src.samples[0].name))
else:
# Warn if volume to take > volume available or max volume is
# exceeded but still do the calculation:
if src_volume > src_tot_volume:
log.append("WARNING: Not enough available volume of sample {0}".format(src.samples[0].name))
final_volume = src_conc * src_volume / dest_conc
if final_volume > MAX_WARNING_VOLUME:
log.append("WARNING: Maximum volume exceeded for sample {0}".format(src.samples[0].name))
csv.write("{0},{1},{2},{3},{4},{5}\n".format(src_plate, src_well, src_volume, dest_plate, dest_well, final_volume))
if log:
with open("normalization.log", "w") as log_context:
log_context.write("\n".join(log))
for out in current_step.all_outputs():
# attach the csv file and the log file
if out.name == "Normalization buffer volumes CSV":
attach_file(os.path.join(os.getcwd(), "normalization.csv"), out)
elif out.name == "Normalization Log" and log:
attach_file(os.path.join(os.getcwd(), "normalization.log"), out)
if log:
# to get an eror display in the lims, you need a non-zero exit code AND a message in STDERR
sys.stderr.write("Errors were met, please check the log file\n")
sys.exit(2)
else:
logging.info("Work done")
def dilution(currentStep):
checkTheLog = [False]
# Read in the presets of minimum required conc for setup workset, maximum conc for dilution and minimum volume for dilution
if "SMARTer Pico RNA" in currentStep.input_output_maps[0][0]['uri'].workflow_stages[0].workflow.name:
preset = Dilution_preset['Smarter pico']
with open("bravo.csv", "w") as csvContext:
with open("bravo.log", "w") as logContext:
# working directly with the map allows easier input/output handling
for art_tuple in currentStep.input_output_maps:
# filter out result files
if art_tuple[0]['uri'].type == 'Analyte' and art_tuple[1]['uri'].type == 'Analyte':
source_fc = art_tuple[0]['uri'].location[0].name
source_well = art_tuple[0]['uri'].location[1]
dest_fc = art_tuple[1]['uri'].location[0].id
dest_well = art_tuple[1]['uri'].location[1]
try:
# Only ng/ul or ng/uL are supported
assert art_tuple[0]['uri'].udf['Conc. Units'] in ["ng/ul", "ng/uL"]
# Fill in all necessary UDFs
art_tuple[1]['uri'].udf['Concentration'] = art_tuple[0]['uri'].udf['Concentration']
art_tuple[1]['uri'].udf['Conc. Units'] = art_tuple[0]['uri'].udf['Conc. Units']
# Case that sample concentration lower than the minimum required conc for setup workset
if art_tuple[1]['uri'].udf['Concentration'] < preset[0]:
if art_tuple[0]['uri'].udf['Volume (ul)'] >= preset[2]:
art_tuple[1]['uri'].udf['Volume to take (uL)'] = preset[2]
art_tuple[1]['uri'].udf['Final Concentration'] = art_tuple[1]['uri'].udf['Concentration']
art_tuple[1]['uri'].udf['Final Volume (uL)'] = preset[2]
logContext.write("WARN : Sample {0} located {1} {2} has a LOWER conc than {3}. Take {4} ul directly into the dilution plate.\n".format(art_tuple[1]['uri'].samples[0].name,art_tuple[0]['uri'].location[0].name, art_tuple[0]['uri'].location[1],preset[0],preset[2]))
else:
art_tuple[1]['uri'].udf['Volume to take (uL)'] = 0
art_tuple[1]['uri'].udf['Final Concentration'] = 0
art_tuple[1]['uri'].udf['Final Volume (uL)'] = 0
logContext.write("ERROR : Sample {0} located {1} {2} has a LOWER conc than {3} and total volume less than {4} ul. It is skipped in dilution.\n".format(art_tuple[1]['uri'].samples[0].name,art_tuple[0]['uri'].location[0].name, art_tuple[0]['uri'].location[1],preset[0],preset[2]))
# Case that sample concentration higher than the maximum conc for dilution
elif art_tuple[1]['uri'].udf['Concentration'] > preset[1]:
art_tuple[1]['uri'].udf['Volume to take (uL)'] = 0
art_tuple[1]['uri'].udf['Final Concentration'] = 0
art_tuple[1]['uri'].udf['Final Volume (uL)'] = 0
logContext.write("ERROR : Sample {0} located {1} {2} has a HIGHER conc than {3}. It is skipped in dilution.\n".format(art_tuple[1]['uri'].samples[0].name,art_tuple[0]['uri'].location[0].name, art_tuple[0]['uri'].location[1],preset[1]))
# Case that dilution will be done with 2uL sample
elif art_tuple[1]['uri'].udf['Concentration'] <= preset[1] and art_tuple[1]['uri'].udf['Concentration'] > float(preset[0]*preset[2]/MIN_WARNING_VOLUME):
if art_tuple[0]['uri'].udf['Volume (ul)'] >= MIN_WARNING_VOLUME:
final_conc = preset[0]
step = 0.25
while final_conc <= 5.0:
if float(art_tuple[1]['uri'].udf['Concentration']*MIN_WARNING_VOLUME/final_conc) <= MAX_WARNING_VOLUME:
art_tuple[1]['uri'].udf['Volume to take (uL)'] = MIN_WARNING_VOLUME
art_tuple[1]['uri'].udf['Final Concentration'] = final_conc
art_tuple[1]['uri'].udf['Final Volume (uL)'] = float(art_tuple[1]['uri'].udf['Concentration']*MIN_WARNING_VOLUME/final_conc)
logContext.write("INFO : Sample {0} looks okay.\n".format(art_tuple[1]['uri'].samples[0].name))
break
else:
final_conc = final_conc+0.25
else:
art_tuple[1]['uri'].udf['Volume to take (uL)'] = 0
art_tuple[1]['uri'].udf['Final Concentration'] = 0
art_tuple[1]['uri'].udf['Final Volume (uL)'] = 0
logContext.write("ERROR : Sample {0} located {1} {2} has a LOWER volume than {3} ul. It is skipped in dilution.\n".format(art_tuple[1]['uri'].samples[0].name,art_tuple[0]['uri'].location[0].name, art_tuple[0]['uri'].location[1],MIN_WARNING_VOLUME))
# Case that more than 2uL sample is needed for dilution
elif art_tuple[1]['uri'].udf['Concentration'] <= float(preset[0]*preset[2]/MIN_WARNING_VOLUME) and art_tuple[1]['uri'].udf['Concentration'] >= preset[0]:
if art_tuple[0]['uri'].udf['Volume (ul)'] >= float(preset[0]*preset[2]/art_tuple[1]['uri'].udf['Concentration']):
art_tuple[1]['uri'].udf['Volume to take (uL)'] = float(preset[0]*preset[2]/art_tuple[1]['uri'].udf['Concentration'])
art_tuple[1]['uri'].udf['Final Concentration'] = preset[0]
art_tuple[1]['uri'].udf['Final Volume (uL)'] = preset[2]
logContext.write("INFO : Sample {0} looks okay.\n".format(art_tuple[1]['uri'].samples[0].name))
else:
art_tuple[1]['uri'].udf['Volume to take (uL)'] = 0
art_tuple[1]['uri'].udf['Final Concentration'] = 0
art_tuple[1]['uri'].udf['Final Volume (uL)'] = 0
logContext.write("ERROR : Sample {0} located {1} {2} has a LOWER volume than {3} ul. It is skipped in dilution.\n".format(art_tuple[1]['uri'].samples[0].name,art_tuple[0]['uri'].location[0].name, art_tuple[0]['uri'].location[1],float(preset[0]*preset[2]/art_tuple[1]['uri'].udf['Concentration'])))
except KeyError as e:
logContext.write("ERROR : The input artifact is lacking a field : {0}\n".format(e))
checkTheLog[0] = True
except AssertionError:
logContext.write("ERROR : This script expects the concentration to be in ng/ul or ng/uL, this does not seem to be the case.\n")
checkTheLog[0] = True
except ZeroDivisionError:
logContext.write("ERROR: Sample {0} has a concentration of 0\n".format(art_tuple[1]['uri'].samples[0].name))
checkTheLog[0] = True
art_tuple[1]['uri'].put()
csvContext.write("{0},{1},{2},{3},{4},{5}\n".format(source_fc, source_well, art_tuple[1]['uri'].udf['Volume to take (uL)'], dest_fc, dest_well, art_tuple[1]['uri'].udf['Final Volume (uL)']))
for out in currentStep.all_outputs():
# attach the csv file and the log file
if out.name == "Bravo CSV File":
attach_file(os.path.join(os.getcwd(), "bravo.csv"), out)
if out.name == "Bravo Log":
attach_file(os.path.join(os.getcwd(), "bravo.log"), out)
if checkTheLog[0]:
# to get an eror display in the lims, you need a non-zero exit code AND a message in STDERR
sys.stderr.write("Errors were met, please check the Log file\n")
sys.exit(2)
else:
logging.info("Work done")
def read_log(lims, pid, logfile):
logger=setupLog(logfile)
pro=Process(lims, id=pid)
f=None
for out in pro.all_outputs():
if out.type == "ResultFile" and out.name == "NeoPrep Output Log File":
try:
fid=out.files[0].id
except IndexError:
logger.error("Can't find the machine log file")
print("Cannot find the NeoPrep Output Log File", file=sys.stderr)
exit(2)
file_contents=lims.get_file_contents(id=fid)
logger.info("Found the machine log file")
if file_contents:
data={}
read=False
#default values
ist_size_idx=5
sample_idx=2
conc_idx=6
norm_idx=7
stat_idx=8
logger.info("Reading the file")
for line in file_contents.split('\n') :
#This does something that is close from csv.dictreader, but the file is FUBAR
if not line.rstrip():
read=False
if read:
if "Start Well" in line:
#Header row
#identify which column goes with which index
elements=line.split('\t')
for idx, el in enumerate(elements):
if el == "Name":
sample_idx=idx
elif el == "Quant":
conc_idx=idx
elif el == "Norm":
norm_idx=idx
elif el == "Status":
stat_idx=idx
elif el == "Insert Size":
ist_size_idx=idx
else:
elements=line.split('\t')
#data rows
data[elements[sample_idx]]={}
data[elements[sample_idx]]['conc']=elements[conc_idx]
data[elements[sample_idx]]['norm']=elements[norm_idx]
data[elements[sample_idx]]['stat']=elements[stat_idx]
data[elements[sample_idx]]['ist_size']=elements[ist_size_idx]
if "[Sample Information]" in line:
read=True
logger.info("obtained data for samples {0}".format(data.keys()))
for inp in pro.all_inputs():
#save the data from the logfile to the lims artifacts
if inp.name in data:
if data[inp.name]['stat'] == 'Pass':
inp.qc="PASSED"
elif data[inp.name]['stat'] == 'Fail':
inp.qc="FAILED"
try:
inp.udf['Molar Conc. (nM)']=float(data[inp.name]['conc'])
except ValueError:
inp.udf['Molar Conc. (nM)']=0
try:
inp.udf['Normalized conc. (nM)']=float(data[inp.name]['norm'])
except ValueError:
inp.udf['Normalized conc. (nM)']=0
try:
inp.udf['Size (bp)']=float(data[inp.name]['ist_size'])
except ValueError:
inp.udf['Size (bp)']=0
inp.udf['NeoPrep Machine QC']=data[inp.name]['stat']
inp.put()
logger.info("updated sample {0}".format(inp.name))
for out in pro.all_outputs():
#attach the epp log
if out.name=="EPP Log":
attach_file(os.path.join(os.getcwd(), logfile), out)
def normalization(current_step):
log = []
with open("normalization.csv", "w") as csv:
for art in current_step.input_output_maps:
src = art[0]["uri"]
dest = art[1]["uri"]
if src.type == dest.type == "Analyte":
# Source sample:
src_plate = src.location[0].id
src_well = src.location[1]
try:
src_tot_volume = float(src.udf["Volume (ul)"])
except:
src_tot_volume = 999999
log.append("WARNING: No volume found for input sample {0}".format(src.samples[0].name))
try:
src_volume = float(dest.udf["Volume to take (uL)"])
except:
sys.stderr.write("Field 'Volume to take (uL)' is empty for artifact {0}\n".format(dest.name))
sys.exit(2)
if "Concentration" in src.udf:
src_conc = src.udf["Concentration"]
if src.udf["Conc. Units"] != "nM":
log.append("ERROR: No valid concentration found for sample {0}".format(src.samples[0].name))
elif "Normalized conc. (nM)" in src.udf:
src_conc = src.udf["Normalized conc. (nM)"]
else:
sys.stderr.write("Non input concentration found for sample {0}\n".format(dest.name))
sys.exit(2)
# Diluted sample:
dest_plate = dest.location[0].id
dest_well = dest.location[1]
try:
dest_conc = dest.udf["Normalized conc. (nM)"]
except:
sys.stderr.write("Field 'Normalized conc. (nM)' is empty for artifact {0}\n".format(dest.name))
sys.exit(2)
if src_conc < dest_conc:
log.append("ERROR: Too low concentration for sample {0}".format(src.samples[0].name))
else:
# Warn if volume to take > volume available or max volume is
# exceeded but still do the calculation:
if src_volume > src_tot_volume:
log.append("WARNING: Not enough available volume of sample {0}".format(src.samples[0].name))
final_volume = src_conc * src_volume / dest_conc
if final_volume > MAX_WARNING_VOLUME:
log.append("WARNING: Maximum volume exceeded for sample {0}".format(src.samples[0].name))
csv.write("{0},{1},{2},{3},{4},{5}\n".format(src_plate, src_well, src_volume, dest_plate, dest_well, final_volume))
if log:
with open("normalization.log", "w") as log_context:
log_context.write("\n".join(log))
for out in current_step.all_outputs():
# attach the csv file and the log file
if out.name == "Normalization buffer volumes CSV":
attach_file(os.path.join(os.getcwd(), "normalization.csv"), out)
elif out.name == "Normalization Log" and log:
attach_file(os.path.join(os.getcwd(), "normalization.log"), out)
if log:
# to get an eror display in the lims, you need a non-zero exit code AND a message in STDERR
sys.stderr.write("Errors were met, please check the log file\n")
sys.exit(2)
else:
logging.info("Work done")
def main(lims, args, epp_logger):
p = Process(lims, id=args.pid)
if not args.path:
args.path = os.getcwd()
file_list = os.listdir(args.path)
# Find all per input result files
io = p.input_output_maps
io_filtered = filter(lambda (x,y): y['output-generation-type']=='PerInput', io)
io_filtered = filter(lambda (x,y): y['output-type']=='ResultFile', io_filtered)
artifact_missing_file = []
artifact_multiple_file = []
found_files = []
for input, output in io_filtered:
i_a = Artifact(lims,id=input['limsid'])
o_a = Artifact(lims,id=output['limsid'])
# Input Well, Input Container
i_w, i_c = i_a.location[1], i_a.location[0]
# Well is typed without colon in filename:
i_w = ''.join(i_w.split(':'))
# Use a reguluar expression to find the file name given
# the container and sample. This is all assuming the driver template name ends with:
# ${INPUT.CONTAINER.PLACEMENT}_${INPUT.NAME}_${INPUT.CONTAINER.LIMSID}_${INPUT.LIMSID}
# However, names are excluded to improve robustness.
if args.instrument == "fragment_analyzer":
info = {'well':o_a.location[1].replace(":", ""),
'output_artifact_name':o_a.samples[0].name}
re_str = '.*{well}.*{output_artifact_name}'\
.format(**info)
else:
info = {'well':i_w,
'container_id':i_c.id,
'input_artifact_id':i_a.id}
re_str = '.*{well}_.*_.*{container_id}_.*{input_artifact_id}'\
.format(**info)
logging.info(("Looking for file for artifact id: {input_artifact_id} "
"from container with id: {container_id}.").format(**info))
im_file_r = re.compile(re_str)
fns = filter(im_file_r.match, file_list)
if len(fns) == 0:
logging.warning("No image file found for artifact with id {0}".format(i_a.id))
artifact_missing_file.append(i_a)
elif len(fns) > 1:
logging.warning(("Multiple image files found for artifact with id {0}, "
"please attach files manually").format(i_a.id))
artifact_multiple_file.append(i_a)
else:
fn = fns[0]
found_files.append(fn)
logging.info("Found image file {0} for artifact with id {1}".format(fn, i_a.id))
fp = os.path.join(args.path, fn)
# Attach file to the LIMS
location = attach_file(fp, o_a)
logging.debug("Moving {0} to {1}".format(fp,location))
warning = ""
if len(artifact_missing_file):
warning = "Did not find any file for {0} artifact(s). ".format(len(artifact_missing_file))
if len(artifact_multiple_file):
warning += "Found multiple files for {0} artifact(s), none of these were uploaded.".format(len(artifact_multiple_file))
if warning:
warning = "Warning: " + warning
abstract = "Uploaded {0} file(s). {1}".format(len(found_files), warning)
print >> sys.stderr, abstract # stderr will be logged and printed in GUI
def read_log(lims, pid, logfile):
logger=setupLog(logfile)
pro=Process(lims, id=pid)
f=None
for out in pro.all_outputs():
if out.type == "ResultFile" and out.name == "NeoPrep Output Log File":
try:
fid=out.files[0].id
except IndexError:
logger.error("Can't find the machine log file")
print("Cannot find the NeoPrep Output Log File", file=sys.stderr)
exit(2)
file_contents=lims.get_file_contents(id=fid)
if isinstance(file_contents, bytes):
file_contents = file_contents.decode('utf-8')
logger.info("Found the machine log file")
if file_contents:
data={}
read=False
#default values
ist_size_idx=5
sample_idx=2
conc_idx=6
norm_idx=7
stat_idx=8
logger.info("Reading the file")
for line in file_contents.split('\n') :
#This does something that is close from csv.dictreader, but the file is FUBAR
if not line.rstrip():
read=False
if read:
if "Start Well" in line:
#Header row
#identify which column goes with which index
elements=line.split('\t')
for idx, el in enumerate(elements):
if el == "Name":
sample_idx=idx
elif el == "Quant":
conc_idx=idx
elif el == "Norm":
norm_idx=idx
elif el == "Status":
stat_idx=idx
elif el == "Insert Size":
ist_size_idx=idx
else:
elements=line.split('\t')
#data rows
data[elements[sample_idx]]={}
data[elements[sample_idx]]['conc']=elements[conc_idx]
data[elements[sample_idx]]['norm']=elements[norm_idx]
data[elements[sample_idx]]['stat']=elements[stat_idx]
data[elements[sample_idx]]['ist_size']=elements[ist_size_idx]
if "[Sample Information]" in line:
read=True
logger.info("obtained data for samples {0}".format(list(data.keys())))
for inp in pro.all_inputs():
#save the data from the logfile to the lims artifacts
if inp.name in data:
if data[inp.name]['stat'] == 'Pass':
inp.qc="PASSED"
elif data[inp.name]['stat'] == 'Fail':
inp.qc="FAILED"
try:
inp.udf['Molar Conc. (nM)']=float(data[inp.name]['conc'])
except ValueError:
inp.udf['Molar Conc. (nM)']=0
try:
inp.udf['Normalized conc. (nM)']=float(data[inp.name]['norm'])
except ValueError:
inp.udf['Normalized conc. (nM)']=0
try:
inp.udf['Size (bp)']=float(data[inp.name]['ist_size'])
except ValueError:
inp.udf['Size (bp)']=0
inp.udf['NeoPrep Machine QC']=data[inp.name]['stat']
inp.put()
logger.info("updated sample {0}".format(inp.name))
for out in pro.all_outputs():
#attach the epp log
if out.name=="EPP Log":
attach_file(os.path.join(os.getcwd(), logfile), out)
