def blacklist_ms_run_post(request):
try:
blacklist = ast.literal_eval(request.params["ms_runs"])
for row in blacklist:
if row['filename'] != " ":
log_writer("blacklist",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
row['filename'] + "\t" +
row['person'] + "\t" +
row['trash_reason']
)
DBSession.query(MsRun).filter(MsRun.filename == row['filename']).update(
{"flag_trash": 1,
'trash_reason': row['trash_reason'],
'ms_run_date': None,
'used_share': None,
'comment': None,
'sample_mass': None,
'antibody_set': '',
'antibody_mass': None,
'sample_volume': None
})
transaction.commit()
except:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
return dict()
def unblacklist_ms_run_post(request):
try:
unblacklist = ast.literal_eval(request.params["ms_runs"])
for row in unblacklist:
if row['filename'] != " ":
log_writer("unblacklist", strftime("%Y.%m.%d %H:%M:%S", gmtime())+"\t"+row['filename']+"\t"+row['person'])
DBSession.query(MsRun).filter(MsRun.filename == row['filename']).update({"flag_trash": 0, 'trash_reason' : None})
transaction.commit()
except:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
return dict()
def blacklist_ms_run_post(request):
try:
blacklist = ast.literal_eval(request.params["ms_runs"])
for row in blacklist:
if row['filename'] != " ":
log_writer(
"blacklist",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
row['filename'] + "\t" + row['person'] + "\t" +
row['trash_reason'])
DBSession.query(MsRun).filter(
MsRun.filename == row['filename']).update({
"flag_trash":
1,
'trash_reason':
row['trash_reason'],
'ms_run_date':
None,
'used_share':
None,
'comment':
None,
'sample_mass':
None,
'antibody_set':
'',
'antibody_mass':
None,
'sample_volume':
None
})
transaction.commit()
except:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
return dict()
def unblacklist_ms_run_post(request):
try:
unblacklist = ast.literal_eval(request.params["ms_runs"])
for row in unblacklist:
if row['filename'] != " ":
log_writer(
"unblacklist",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
row['filename'] + "\t" + row['person'])
DBSession.query(MsRun).filter(
MsRun.filename == row['filename']).update({
"flag_trash":
0,
'trash_reason':
None
})
transaction.commit()
except:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
return dict()
def update_metadata_msrun_post(request):
ms_run = ast.literal_eval(request.params["ms_runs"])
# update if already in DB (without metadata included)
try:
log_writer("ms_run_update_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +ms_run)
ms_run_update = DBSession.query(MsRun).filter(MsRun.filename == ms_run["filename"]).all()
except:
log_writer("ms_run_update_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +"MS Run update failed!")
return Response(conn_err_msg + " \n MsRun insert failed", content_type='text/plain', status_int=500)
if len(ms_run_update)>0:
if ms_run['ms_run_date'] != "":
ms_run_update[0].ms_run_date = ms_run['ms_run_date']
if ms_run['used_share'] != "":
ms_run_update[0].used_share = ms_run['used_share']
if ms_run['comment'] != "":
ms_run_update[0].comment = ms_run['comment']
if ms_run['sample_mass'] != "":
ms_run_update[0].sample_mass = ms_run['sample_mass']
if ms_run['antibody_set'] != "":
ms_run_update[0].antibody_set = ms_run['antibody_set']
if ms_run['antibody_mass'] != "":
ms_run_update[0].antibody_mass = ms_run['antibody_mass']
if ms_run['sample_volume'] != "":
ms_run_update[0].sample_volume = ms_run['sample_volume']
if ms_run['source_source_id'] != "":
# TODO: update peptide_run and spectrum_hit if source changed
try:
spectrum_hits = DBSession.query(SpectrumHit)\
.filter(SpectrumHit.source_source_id == ms_run_update[0].source_source_id).update({'source_source_id': ms_run['source_source_id']})
except:
log_writer("ms_run_update_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +"SpectrumHit update failed!")
DBSession.rollback()
return Response("SpectrumHit update failed!",
content_type='text/plain', status_int=500)
try:
peptide_runs = DBSession.query(PeptideRun) \
.filter(PeptideRun.source_source_id == ms_run_update[0].source_source_id).update({'source_source_id': ms_run['source_source_id']})
except:
log_writer("ms_run_update_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +"Peptide Run update failed!")
DBSession.rollback()
return Response("Peptide Run update failed!",
content_type='text/plain', status_int=500)
ms_run_update[0].source_source_id = ms_run['source_source_id']
try:
transaction.commit()
DBSession.flush()
log_writer("ms_run_update", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +ms_run)
except:
log_writer("ms_run_update_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +"MS Run update failed!")
DBSession.rollback()
return Response("MS Run update failed!",
content_type='text/plain', status_int=500)
return HTTPFound(location="/update_metadata_ms_run?filename=%s" % ms_run["filename"])
def upload_metadata_source_post(request):
source_upload = ast.literal_eval(request.params["sources"])
# Check if source already in DB
for source in source_upload:
try:
query = DBSession.query(Source.source_id) \
.filter(Source.patient_id == source['patient_id']) \
.filter(Source.organ == source['organ']) \
.filter(Source.organism == source['organism']) \
.filter(Source.histology == source['histology']) \
.filter(Source.dignity == source['dignity']) \
.filter(Source.location == source['location']) \
.filter(Source.treatment == source['treatment']) \
.filter(Source.metastatis == source['metastatis']) \
.filter(Source.celltype == source['celltype']) \
.filter(Source.comment == source['comment']) \
.filter(Source.person == source['person']) \
.filter(Source.prep_date == source['prep_date'])
test_source = query.all()
except DBAPIError:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
# if in DB abort whole upload
if len(test_source) > 0:
log_writer("source_metadata_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +source)
log_writer("source_metadata_complete",strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +"The source is already in the Database. Aborted whole upload!")
return Response("The source is already in the Database. Aborted whole upload!",
content_type='text/plain', status_int=500)
# upload each source
for source in source_upload:
# ####################################################
# Source: #
# ####################################################
try:
sample_id = source["patient_id"]+"_"+ source["organ"]+"_"+source['dignity']+"_"+ source['histology']+"_"+\
source['celltype'] +"_"+ source['location'] +"_"+ source['treatment'] +"_"+ source['prep_date']
source_insert = Source(patient_id=source['patient_id'], organ=source['organ'], organism=source['organism'],
histology=source['histology'], dignity=source['dignity'],
location=source['location'], treatment=source['treatment'],
metastatis=source['metastatis'], celltype=source['celltype'],
comment=source['comment'], prep_date= source['prep_date'],
person=source['person'], sample_id=sample_id)
#DBSession.add(source_insert)
#DBSession.flush()
#source_id = source_insert.source_id
except DBAPIError:
return Response(conn_err_msg + "\n Insert into Source failed!",
content_type='text/plain', status_int=500)
if source['typing'] is not "":
# ###############
# hla_types #
# ###############
hla_alleles = source['typing'].split(";")
for hla_typing in hla_alleles:
hla_typing_split = hla_typing.strip().split(":")
for i in range(0, len(hla_typing_split)):
sub_type = ":".join(hla_typing_split[0:i + 1])
try:
query = DBSession.query(HlaType.hla_types_id).filter(HlaType.hla_string == sub_type)
hla_types_id = query.all()
except DBAPIError:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
# unknown hla_lookup
if len(hla_types_id) == 0:
try:
hla_type = HlaType(hla_string=sub_type, digits=hla_digits_extractor(sub_type))
DBSession.add(hla_type)
DBSession.flush()
hla_types_id = hla_type.hla_types_id
except DBAPIError:
return Response(conn_err_msg + "\n Insert into Hla-Types failed!",
content_type='text/plain', status_int=500)
else:
hla_types_id = hla_types_id[0]
hla_type = query = DBSession.query(HlaType).filter(HlaType.hla_string == sub_type).all()[0]
# ###############
# hla_map #
# ###############
try:
source_insert.append(hla_type)
except DBAPIError:
return Response(conn_err_msg + "\n Insert into Hla-Map failed!",
content_type='text/plain', status_int=500)
try:
log_writer("source_metadata", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +source)
log_writer("source_metadata_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +source)
DBSession.add(source_insert)
DBSession.flush()
except DBAPIError:
return Response(conn_err_msg + "\n Insert into Source failed!",
content_type='text/plain', status_int=500)
else:
log_writer("source_metadata", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +source)
log_writer("source_metadata_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +source)
DBSession.add(source_insert)
DBSession.flush()
hla_lookup_id = "NULL"
return dict()
def update_metadata_source_post(request):
source = ast.literal_eval(request.params["sources"])
try:
log_writer("source_update_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +source)
source_update = DBSession.query(Source).join(t_hla_map).join(HlaType).filter(Source.source_id == source["source_id"]).all()
except:
log_writer("source_update_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +" Source update failed!")
return Response(conn_err_msg + " \n Source update failed", content_type='text/plain', status_int=500)
if len(source_update)>0:
if source['patient_id'] != "":
source_update[0].patient_id = source['patient_id']
if source['organ'] != "":
source_update[0].organ = source['organ']
if source['organism'] != "":
source_update[0].orgnaism = source['organism']
if source['comment'] != "":
source_update[0].comment = source['comment']
if source['histology'] != "":
source_update[0].histology = source['histology']
if source['dignity'] != "":
source_update[0].dignity = source['dignity']
if source['celltype'] != "":
source_update[0].celltype = source['celltype']
if source['person'] != "":
source_update[0].person = source['person']
if source['location'] != "":
source_update[0].location = source['location']
if source['metastatis'] != "":
source_update[0].metastatis = source['metastatis']
if source['treatment'] != "":
source_update[0].treatment = source['treatment']
if source['prep_date'] != "":
source_update[0].prep_date = source['prep_date']
source_update[0].sample_id = source_update[0].patient_id + "_" + source_update[0].organ + "_" + source_update[0].dignity\
+ "_" + source_update[0].histology + "_" + \
source_update[0].celltype + "_" + source_update[0].location + "_" + source_update[0].treatment\
+ "_" + source_update[0].prep_date
if source['typing'] != "":
# remove all mappings
source_update[0].hlatypes[:] = []
# create all hla links
hla_split = source['typing'].split(";")
for hla_typing in hla_split:
hla_typing_split = hla_typing.strip().split(":")
for i in range(0, len(hla_typing_split)):
sub_type = ":".join(hla_typing_split[0:i + 1])
try:
query = DBSession.query(HlaType.hla_types_id).filter(HlaType.hla_string == sub_type)
hla_types_id = query.all()
except DBAPIError:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
# unknown hla_lookup
if len(hla_types_id) == 0:
try:
hla_type = HlaType(hla_string=sub_type, digits=hla_digits_extractor(sub_type))
DBSession.add(hla_type)
DBSession.flush()
hla_types_id = hla_type.hla_types_id
except DBAPIError:
return Response(conn_err_msg + "\n Insert into Hla-Types failed!",
content_type='text/plain', status_int=500)
else:
hla_types_id = hla_types_id[0]
hla_type = query = DBSession.query(HlaType).filter(HlaType.hla_string == sub_type).all()[0]
try:
# add the hla type
source_update[0].hlatypes.append(hla_type)
except DBAPIError:
return Response(conn_err_msg + "\n Insert into Hla-Map failed!",
content_type='text/plain', status_int=500)
try:
transaction.commit()
DBSession.flush()
log_writer("source_update", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +source)
except:
log_writer("source_update_complete",strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + "Source update failed!")
DBSession.rollback()
return Response("Source update failed!",
content_type='text/plain', status_int=500)
return HTTPFound(location="/update_metadata_source?id=%s" % source["source_id"])
def upload_metadata_ms_run_post(request):
ms_run_upload = ast.literal_eval(request.params["ms_runs"])
# Check if MS run is already in database with METADATA
for ms_run in ms_run_upload:
try:
ms_runs = DBSession.query(MsRun.ms_run_id).filter(MsRun.filename == ms_run['filename']).filter(
MsRun.source_source_id != None).all()
except DBAPIError:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
if len(ms_runs) > 0:
# if in MS run with Metadata in DB, abort whole Upload
return Response("The source " + ms_run['source'] + " is already in the Database. Aborted whole upload!",
content_type='text/plain', status_int=500)
# upload the each MS run
for ms_run in ms_run_upload:
source_id = ms_run["source_id"]
# update if already in DB (without metadata included)
try:
ms_run_update = DBSession.query(MsRun).filter(MsRun.filename == ms_run["filename"]).filter(
MsRun.source_source_id == None).all()
except:
return Response(conn_err_msg + " \n MsRun insert failed", content_type='text/plain', status_int=500)
if len(ms_run_update) > 0:
ms_run_update[0].source_source_id = source_id
if ms_run['date'] != "":
ms_run_update[0].ms_run_date = ms_run['date']
if ms_run['used_share'] != "" and ms_run['used_share'] != "None":
ms_run_update[0].used_share = ms_run['used_share']
if ms_run['comment'] != "":
ms_run_update[0].comment = ms_run['comment']
if ms_run['sample_mass'] != "" and ms_run['sample_mass'] != "None":
ms_run_update[0].sample_mass = ms_run['sample_mass']
if ms_run['sample_volume'] != "" and ms_run['sample_volume'] != "None":
ms_run_update[0].sample_volume = ms_run['sample_volume']
ms_run_update[0].antibody_set = ms_run['antibody_set'].replace(" ", "")
if ms_run['antibody_mass'] != "" and ms_run['antibody_mass'] != "None":
ms_run_update[0].antibody_mass = ms_run['antibody_mass']
# Updating all crossreferences for the source_id
try:
spectrum_hits = DBSession.query(SpectrumHit) \
.filter(SpectrumHit.ms_run_ms_run_id == ms_run_update[0].ms_run_id).update(
{'source_source_id': ms_run['source_source_id']})
except:
log_writer("ms_run_upload_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +"SpectrumHit update failed!")
DBSession.rollback()
return Response("SpectrumHit update failed!",
content_type='text/plain', status_int=500)
try:
peptide_runs = DBSession.query(PeptideRun) \
.filter(PeptideRun.ms_run_ms_run_id == ms_run_update[0].ms_run_id).update(
{'source_source_id': ms_run['source_source_id']})
except:
log_writer("ms_run_update_complete", "Peptide Run update failed!")
DBSession.rollback()
return Response("Peptide Run update failed!",
content_type='text/plain', status_int=500)
transaction.commit()
DBSession.flush()
log_writer("ms_run_metadata_complete", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +ms_run)
log_writer("ms_run_metadata", strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +ms_run)
else:
log_writer("ms_run_metadata_complete",strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +"MsRun insert failed! Only already registered MS Runs can be uploaded.")
DBSession.rollback()
return Response(conn_err_msg + " \n MsRun insert failed! Only already registered MS Runs can be uploaded.", content_type='text/plain', status_int=500)
return dict()
def update_metadata_msrun_post(request):
ms_run = ast.literal_eval(request.params["ms_runs"])
# update if already in DB (without metadata included)
try:
log_writer("ms_run_update_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + ms_run)
ms_run_update = DBSession.query(MsRun).filter(
MsRun.filename == ms_run["filename"]).all()
except:
log_writer(
"ms_run_update_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
"MS Run update failed!")
return Response(conn_err_msg + " \n MsRun insert failed",
content_type='text/plain',
status_int=500)
if len(ms_run_update) > 0:
if ms_run['ms_run_date'] != "":
ms_run_update[0].ms_run_date = ms_run['ms_run_date']
if ms_run['used_share'] != "":
ms_run_update[0].used_share = ms_run['used_share']
if ms_run['comment'] != "":
ms_run_update[0].comment = ms_run['comment']
if ms_run['sample_mass'] != "":
ms_run_update[0].sample_mass = ms_run['sample_mass']
if ms_run['antibody_set'] != "":
ms_run_update[0].antibody_set = ms_run['antibody_set']
if ms_run['antibody_mass'] != "":
ms_run_update[0].antibody_mass = ms_run['antibody_mass']
if ms_run['sample_volume'] != "":
ms_run_update[0].sample_volume = ms_run['sample_volume']
if ms_run['source_source_id'] != "":
# TODO: update peptide_run and spectrum_hit if source changed
try:
spectrum_hits = DBSession.query(SpectrumHit)\
.filter(SpectrumHit.source_source_id == ms_run_update[0].source_source_id).update({'source_source_id': ms_run['source_source_id']})
except:
log_writer(
"ms_run_update_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
"SpectrumHit update failed!")
DBSession.rollback()
return Response("SpectrumHit update failed!",
content_type='text/plain',
status_int=500)
try:
peptide_runs = DBSession.query(PeptideRun) \
.filter(PeptideRun.source_source_id == ms_run_update[0].source_source_id).update({'source_source_id': ms_run['source_source_id']})
except:
log_writer(
"ms_run_update_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
"Peptide Run update failed!")
DBSession.rollback()
return Response("Peptide Run update failed!",
content_type='text/plain',
status_int=500)
ms_run_update[0].source_source_id = ms_run['source_source_id']
try:
transaction.commit()
DBSession.flush()
log_writer("ms_run_update",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + ms_run)
except:
log_writer(
"ms_run_update_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
"MS Run update failed!")
DBSession.rollback()
return Response("MS Run update failed!",
content_type='text/plain',
status_int=500)
return HTTPFound(location="/update_metadata_ms_run?filename=%s" %
ms_run["filename"])
def upload_metadata_source_post(request):
source_upload = ast.literal_eval(request.params["sources"])
# Check if source already in DB
for source in source_upload:
try:
query = DBSession.query(Source.source_id) \
.filter(Source.patient_id == source['patient_id']) \
.filter(Source.organ == source['organ']) \
.filter(Source.organism == source['organism']) \
.filter(Source.histology == source['histology']) \
.filter(Source.dignity == source['dignity']) \
.filter(Source.location == source['location']) \
.filter(Source.treatment == source['treatment']) \
.filter(Source.metastatis == source['metastatis']) \
.filter(Source.celltype == source['celltype']) \
.filter(Source.comment == source['comment']) \
.filter(Source.person == source['person']) \
.filter(Source.prep_date == source['prep_date'])
test_source = query.all()
except DBAPIError:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
# if in DB abort whole upload
if len(test_source) > 0:
log_writer("source_metadata_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + source)
log_writer(
"source_metadata_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
"The source is already in the Database. Aborted whole upload!")
return Response(
"The source is already in the Database. Aborted whole upload!",
content_type='text/plain',
status_int=500)
# upload each source
for source in source_upload:
# ####################################################
# Source: #
# ####################################################
try:
sample_id = source["patient_id"]+"_"+ source["organ"]+"_"+source['dignity']+"_"+ source['histology']+"_"+\
source['celltype'] +"_"+ source['location'] +"_"+ source['treatment'] +"_"+ source['prep_date']
source_insert = Source(patient_id=source['patient_id'],
organ=source['organ'],
organism=source['organism'],
histology=source['histology'],
dignity=source['dignity'],
location=source['location'],
treatment=source['treatment'],
metastatis=source['metastatis'],
celltype=source['celltype'],
comment=source['comment'],
prep_date=source['prep_date'],
person=source['person'],
sample_id=sample_id)
#DBSession.add(source_insert)
#DBSession.flush()
#source_id = source_insert.source_id
except DBAPIError:
return Response(conn_err_msg + "\n Insert into Source failed!",
content_type='text/plain',
status_int=500)
if source['typing'] is not "":
# ###############
# hla_types #
# ###############
hla_alleles = source['typing'].split(";")
for hla_typing in hla_alleles:
hla_typing_split = hla_typing.strip().split(":")
for i in range(0, len(hla_typing_split)):
sub_type = ":".join(hla_typing_split[0:i + 1])
try:
query = DBSession.query(HlaType.hla_types_id).filter(
HlaType.hla_string == sub_type)
hla_types_id = query.all()
except DBAPIError:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
# unknown hla_lookup
if len(hla_types_id) == 0:
try:
hla_type = HlaType(
hla_string=sub_type,
digits=hla_digits_extractor(sub_type))
DBSession.add(hla_type)
DBSession.flush()
hla_types_id = hla_type.hla_types_id
except DBAPIError:
return Response(conn_err_msg +
"\n Insert into Hla-Types failed!",
content_type='text/plain',
status_int=500)
else:
hla_types_id = hla_types_id[0]
hla_type = query = DBSession.query(HlaType).filter(
HlaType.hla_string == sub_type).all()[0]
# ###############
# hla_map #
# ###############
try:
source_insert.append(hla_type)
except DBAPIError:
return Response(conn_err_msg +
"\n Insert into Hla-Map failed!",
content_type='text/plain',
status_int=500)
try:
log_writer(
"source_metadata",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + source)
log_writer(
"source_metadata_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + source)
DBSession.add(source_insert)
DBSession.flush()
except DBAPIError:
return Response(conn_err_msg + "\n Insert into Source failed!",
content_type='text/plain',
status_int=500)
else:
log_writer("source_metadata",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + source)
log_writer("source_metadata_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + source)
DBSession.add(source_insert)
DBSession.flush()
hla_lookup_id = "NULL"
return dict()
def update_metadata_source_post(request):
source = ast.literal_eval(request.params["sources"])
try:
log_writer("source_update_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + source)
source_update = DBSession.query(Source).join(t_hla_map).join(
HlaType).filter(Source.source_id == source["source_id"]).all()
except:
log_writer(
"source_update_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
" Source update failed!")
return Response(conn_err_msg + " \n Source update failed",
content_type='text/plain',
status_int=500)
if len(source_update) > 0:
if source['patient_id'] != "":
source_update[0].patient_id = source['patient_id']
if source['organ'] != "":
source_update[0].organ = source['organ']
if source['organism'] != "":
source_update[0].orgnaism = source['organism']
if source['comment'] != "":
source_update[0].comment = source['comment']
if source['histology'] != "":
source_update[0].histology = source['histology']
if source['dignity'] != "":
source_update[0].dignity = source['dignity']
if source['celltype'] != "":
source_update[0].celltype = source['celltype']
if source['person'] != "":
source_update[0].person = source['person']
if source['location'] != "":
source_update[0].location = source['location']
if source['metastatis'] != "":
source_update[0].metastatis = source['metastatis']
if source['treatment'] != "":
source_update[0].treatment = source['treatment']
if source['prep_date'] != "":
source_update[0].prep_date = source['prep_date']
source_update[0].sample_id = source_update[0].patient_id + "_" + source_update[0].organ + "_" + source_update[0].dignity\
+ "_" + source_update[0].histology + "_" + \
source_update[0].celltype + "_" + source_update[0].location + "_" + source_update[0].treatment\
+ "_" + source_update[0].prep_date
if source['typing'] != "":
# remove all mappings
source_update[0].hlatypes[:] = []
# create all hla links
hla_split = source['typing'].split(";")
for hla_typing in hla_split:
hla_typing_split = hla_typing.strip().split(":")
for i in range(0, len(hla_typing_split)):
sub_type = ":".join(hla_typing_split[0:i + 1])
try:
query = DBSession.query(HlaType.hla_types_id).filter(
HlaType.hla_string == sub_type)
hla_types_id = query.all()
except DBAPIError:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
# unknown hla_lookup
if len(hla_types_id) == 0:
try:
hla_type = HlaType(
hla_string=sub_type,
digits=hla_digits_extractor(sub_type))
DBSession.add(hla_type)
DBSession.flush()
hla_types_id = hla_type.hla_types_id
except DBAPIError:
return Response(conn_err_msg +
"\n Insert into Hla-Types failed!",
content_type='text/plain',
status_int=500)
else:
hla_types_id = hla_types_id[0]
hla_type = query = DBSession.query(HlaType).filter(
HlaType.hla_string == sub_type).all()[0]
try:
# add the hla type
source_update[0].hlatypes.append(hla_type)
except DBAPIError:
return Response(conn_err_msg +
"\n Insert into Hla-Map failed!",
content_type='text/plain',
status_int=500)
try:
transaction.commit()
DBSession.flush()
log_writer("source_update",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + source)
except:
log_writer(
"source_update_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
"Source update failed!")
DBSession.rollback()
return Response("Source update failed!",
content_type='text/plain',
status_int=500)
return HTTPFound(location="/update_metadata_source?id=%s" %
source["source_id"])
def upload_metadata_ms_run_post(request):
ms_run_upload = ast.literal_eval(request.params["ms_runs"])
# Check if MS run is already in database with METADATA
for ms_run in ms_run_upload:
try:
ms_runs = DBSession.query(MsRun.ms_run_id).filter(
MsRun.filename == ms_run['filename']).filter(
MsRun.source_source_id != None).all()
except DBAPIError:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
if len(ms_runs) > 0:
# if in MS run with Metadata in DB, abort whole Upload
return Response(
"The source " + ms_run['source'] +
" is already in the Database. Aborted whole upload!",
content_type='text/plain',
status_int=500)
# upload the each MS run
for ms_run in ms_run_upload:
source_id = ms_run["source_id"]
# update if already in DB (without metadata included)
try:
ms_run_update = DBSession.query(MsRun).filter(
MsRun.filename == ms_run["filename"]).filter(
MsRun.source_source_id == None).all()
except:
return Response(conn_err_msg + " \n MsRun insert failed",
content_type='text/plain',
status_int=500)
if len(ms_run_update) > 0:
ms_run_update[0].source_source_id = source_id
if ms_run['date'] != "":
ms_run_update[0].ms_run_date = ms_run['date']
if ms_run['used_share'] != "" and ms_run['used_share'] != "None":
ms_run_update[0].used_share = ms_run['used_share']
if ms_run['comment'] != "":
ms_run_update[0].comment = ms_run['comment']
if ms_run['sample_mass'] != "" and ms_run['sample_mass'] != "None":
ms_run_update[0].sample_mass = ms_run['sample_mass']
if ms_run['sample_volume'] != "" and ms_run[
'sample_volume'] != "None":
ms_run_update[0].sample_volume = ms_run['sample_volume']
ms_run_update[0].antibody_set = ms_run['antibody_set'].replace(
" ", "")
if ms_run['antibody_mass'] != "" and ms_run[
'antibody_mass'] != "None":
ms_run_update[0].antibody_mass = ms_run['antibody_mass']
# Updating all crossreferences for the source_id
try:
spectrum_hits = DBSession.query(SpectrumHit) \
.filter(SpectrumHit.ms_run_ms_run_id == ms_run_update[0].ms_run_id).update(
{'source_source_id': ms_run['source_source_id']})
except:
log_writer(
"ms_run_upload_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
"SpectrumHit update failed!")
DBSession.rollback()
return Response("SpectrumHit update failed!",
content_type='text/plain',
status_int=500)
try:
peptide_runs = DBSession.query(PeptideRun) \
.filter(PeptideRun.ms_run_ms_run_id == ms_run_update[0].ms_run_id).update(
{'source_source_id': ms_run['source_source_id']})
except:
log_writer("ms_run_update_complete",
"Peptide Run update failed!")
DBSession.rollback()
return Response("Peptide Run update failed!",
content_type='text/plain',
status_int=500)
transaction.commit()
DBSession.flush()
log_writer("ms_run_metadata_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + ms_run)
log_writer("ms_run_metadata",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" + ms_run)
else:
log_writer(
"ms_run_metadata_complete",
strftime("%Y.%m.%d %H:%M:%S", gmtime()) + "\t" +
"MsRun insert failed! Only already registered MS Runs can be uploaded."
)
DBSession.rollback()
return Response(
conn_err_msg +
" \n MsRun insert failed! Only already registered MS Runs can be uploaded.",
content_type='text/plain',
status_int=500)
return dict()
