def blacklist_ms_run(request):
result_dict = dict()
if "run" in request.params:
result_dict["run"] = request.params["run"]
else:
result_dict["run"] = ""
try:
# Query Data for autocomplete
# Person
query = DBSession.query(Source.person.distinct())
person = js_list_creator(query.all())
result_dict["person"] = person
# MS Runs
query = DBSession.query(MsRun.filename.distinct())
query = query.filter(MsRun.flag_trash == 0)
filename = js_list_creator(query.all())
result_dict["filename"] = filename
# Reason
query = DBSession.query(MsRun.trash_reason.distinct())
trash_reason = js_list_creator(query.all())
result_dict["trash_reason"] = trash_reason
except:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
return result_dict
def upload_metadata_ms_run(request):
result_dict = dict()
# fill out the "filename" if forwarded for orphan run table on home
if "run" in request.params:
result_dict["run"] = request.params["run"]
else:
result_dict["run"] = ""
try:
# query data for autocomplete
allowed_elements = {"used_share": MsRun.used_share, "source_id": Source.source_id,
"sample_mass": MsRun.sample_mass, "sample_volume": MsRun.sample_volume,
"antibody_set": MsRun.antibody_set, "antibody_mass": MsRun.antibody_mass}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
allowed_elements = {"filename": MsRun.filename}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.filter(MsRun.source_source_id == None)
query = query.filter(MsRun.flag_trash == 0)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
except:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
return result_dict
def unblacklist_ms_run(request):
result_dict = dict()
if "run" in request.params:
result_dict["run"] = request.params["run"]
else:
result_dict["run"] = ""
try:
# Query Data for autocomplete
# Person
query = DBSession.query(Source.person.distinct())
person = js_list_creator(query.all())
result_dict["person"] = person
# MS Runs
query = DBSession.query(MsRun.filename.distinct())
query = query.filter(MsRun.flag_trash == 1)
filename = js_list_creator(query.all())
result_dict["filename"] = filename
except:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
return result_dict
def update_metadata_source(request):
if "id" in request.params:
result_dict = dict()
result_dict["id"] = request.params['id']
query = DBSession.query(Source.patient_id, Source.organ,
Source.organism, Source.histology,
Source.dignity,Source.celltype,
Source.location, Source.metastatis,
Source.treatment,Source.person,
func.cast(Source.prep_date, String).label("prep_date")
).filter(Source.source_id==request.params["id"])
source = json.dumps(query.all())
result_dict['source'] = source
query = DBSession.query(Source.source_id, HlaType.hla_string).join(t_hla_map).join(HlaType).filter(Source.source_id==request.params["id"])
hla = json.dumps(query.all())
result_dict['hla'] = hla
# getting autocomplete items
allowed_elements = {"patient_id": Source.patient_id, "organ": Source.organ,
"organism": Source.organism, "histology": Source.histology,
"dignity": Source.dignity, "celltype": Source.celltype,
"location": Source.location, "metastatis": Source.metastatis,
"treatment": Source.treatment, "person": Source.person,
"comment" : Source.comment, "typing": HlaType.hla_string}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
#result_dict['original'] = source
return result_dict
else:
try:
# query data for autocomplete
result_dict = dict()
allowed_elements = {"source_id": Source.source_id}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
# setting a different renderer
result = render('../templates/upload_templates/update_metadata_source.pt',
result_dict,
request=request)
response = Response(result)
return response
except:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
def update_metadata_msrun(request):
if "filename" in request.params:
result_dict = dict()
result_dict["filename"] = request.params['filename']
query = DBSession.query(
MsRun.filename, MsRun.used_share, MsRun.comment,
MsRun.source_source_id, MsRun.sample_mass, MsRun.sample_volume,
MsRun.antibody_set, MsRun.antibody_mass,
func.cast(MsRun.ms_run_date, String).label("ms_run_date")).filter(
MsRun.filename == request.params["filename"])
ms_run = json.dumps(query.all())
result_dict['ms_run'] = ms_run
# getting autocomplete items
allowed_elements = {
"used_share": MsRun.used_share,
"comment": MsRun.comment,
"sample_mass": MsRun.sample_mass,
"antibody_set": MsRun.antibody_set,
"antibody_mass": MsRun.antibody_mass,
"sample_volume": MsRun.sample_volume,
'source_source_id': Source.source_id
}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
#result_dict['original'] = source
return result_dict
else:
try:
# query data for autocomplete
result_dict = dict()
result_dict["filename"] = js_list_creator(
DBSession.query(MsRun.filename).filter(
MsRun.flag_trash == 0).group_by(MsRun.filename).all())
# setting a different renderer
result = render(
'../templates/upload_templates/update_metadata_msrun.pt',
result_dict,
request=request)
response = Response(result)
return response
except:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
def upload_metadata_source(request):
try:
# query data for autocomplete
result_dict = dict()
allowed_elements = {
"patient_id": Source.patient_id,
"organ": Source.organ,
"organism": Source.organism,
"histology": Source.histology,
"dignity": Source.dignity,
"celltype": Source.celltype,
"location": Source.location,
"metastatis": Source.metastatis,
"treatment": Source.treatment,
"person": Source.person,
"typing": HlaType.hla_string,
'comment': Source.comment
}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
except:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
return result_dict
def venn_analysis(request):
# try:
# getting source patient_id for autocomplete
query = DBSession.query(Source.patient_id.distinct())
patient_id = js_list_creator(query.all())
# getting source.source_id for auto complete
query = DBSession.query(Source.source_id.distinct())
source_id = js_list_creator(query.all())
# getting ms_runs for autocomplete
query = DBSession.query(MsRun.filename.distinct())
ms_runs = js_list_creator(query.all())
# Antibody for autocomplete
query = DBSession.query(MsRun.antibody_set.distinct()).order_by(MsRun.antibody_set)
antibody = js_list_creator(query.all())
# except:
# return Response(conn_err_msg, content_type='text/plain', status_int=500)
return {"patient_id": patient_id, "source_id": source_id, "ms_runs": ms_runs, "antibody": antibody}
def update_metadata_msrun(request):
if "filename" in request.params:
result_dict = dict()
result_dict["filename"] = request.params['filename']
query = DBSession.query(MsRun.filename, MsRun.used_share,
MsRun.comment, MsRun.source_source_id,
MsRun.sample_mass, MsRun.sample_volume,
MsRun.antibody_set, MsRun.antibody_mass,
func.cast(MsRun.ms_run_date, String).label("ms_run_date")
).filter(MsRun.filename==request.params["filename"])
ms_run = json.dumps(query.all())
result_dict['ms_run'] = ms_run
# getting autocomplete items
allowed_elements = {"used_share":MsRun.used_share, "comment":MsRun.comment,
"sample_mass":MsRun.sample_mass, "antibody_set":MsRun.antibody_set,
"antibody_mass":MsRun.antibody_mass,"sample_volume":MsRun.sample_volume, 'source_source_id': Source.source_id }
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
#result_dict['original'] = source
return result_dict
else:
try:
# query data for autocomplete
result_dict = dict()
result_dict["filename"] = js_list_creator(DBSession.query(MsRun.filename).filter(MsRun.flag_trash==0).group_by(MsRun.filename).all())
# setting a different renderer
result = render('../templates/upload_templates/update_metadata_msrun.pt',
result_dict,
request=request)
response = Response(result)
return response
except:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
def upload_metadata_ms_run(request):
result_dict = dict()
# fill out the "filename" if forwarded for orphan run table on home
if "run" in request.params:
result_dict["run"] = request.params["run"]
else:
result_dict["run"] = ""
try:
# query data for autocomplete
allowed_elements = {
"used_share": MsRun.used_share,
"source_id": Source.source_id,
"sample_mass": MsRun.sample_mass,
"sample_volume": MsRun.sample_volume,
"antibody_set": MsRun.antibody_set,
"antibody_mass": MsRun.antibody_mass
}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
allowed_elements = {"filename": MsRun.filename}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.filter(MsRun.source_source_id == None)
query = query.filter(MsRun.flag_trash == 0)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
except:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
return result_dict
def venn_analysis(request):
# try:
# getting source patient_id for autocomplete
query = DBSession.query(Source.patient_id.distinct())
patient_id = js_list_creator(query.all())
# getting source.source_id for auto complete
query = DBSession.query(Source.source_id.distinct())
source_id = js_list_creator(query.all())
# getting ms_runs for autocomplete
query = DBSession.query(MsRun.filename.distinct())
ms_runs = js_list_creator(query.all())
# Antibody for autocomplete
query = DBSession.query(MsRun.antibody_set.distinct()).order_by(
MsRun.antibody_set)
antibody = js_list_creator(query.all())
# except:
# return Response(conn_err_msg, content_type='text/plain', status_int=500)
return {
"patient_id": patient_id,
"source_id": source_id,
"ms_runs": ms_runs,
"antibody": antibody
}
def upload_metadata_source(request):
try:
# query data for autocomplete
result_dict = dict()
allowed_elements = {"patient_id": Source.patient_id, "organ": Source.organ,
"organism": Source.organism, "histology": Source.histology, "dignity": Source.dignity,
"celltype": Source.celltype, "location": Source.location, "metastatis": Source.metastatis,
"treatment": Source.treatment, "person": Source.person, "typing": HlaType.hla_string,
'comment' : Source.comment}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
except:
return Response(conn_err_msg, content_type='text/plain', status_int=500)
return result_dict
def peptide_query(request):
# patient_id
query = DBSession.query(Source.patient_id.distinct()).order_by(
Source.patient_id)
patient_id = js_list_creator(query.all())
# antibodys
query = DBSession.query(MsRun.antibody_set.distinct())
antibody = js_list_creator(query.all())
# dignity
query = DBSession.query(Source.dignity.distinct()).order_by(Source.dignity)
dignity = js_list_creator(query.all())
# organ
query = DBSession.query(Source.organ.distinct()).order_by(Source.organ)
organ = js_list_creator(query.all())
# histology
query = DBSession.query(Source.histology.distinct()).order_by(
Source.histology)
histology = js_list_creator(query.all())
# celltype
query = DBSession.query(Source.celltype.distinct()).order_by(
Source.celltype)
celltype = js_list_creator(query.all())
# celltype
query = DBSession.query(HlaType.hla_string.distinct()).order_by(
HlaType.hla_string)
hla = js_list_creator(query.all())
# treatment
query = DBSession.query(Source.treatment.distinct()).order_by(
Source.treatment)
treatment = js_list_creator(query.all())
return {
"antibody": antibody,
"dignity": dignity,
"organ": organ,
"histology": histology,
"celltype": celltype,
"hla": hla,
'patient_id': patient_id,
'treatment': treatment
}
def peptide_query(request):
# patient_id
query = DBSession.query(Source.patient_id.distinct()).order_by(Source.patient_id)
patient_id = js_list_creator(query.all())
# antibodys
query = DBSession.query(MsRun.antibody_set.distinct())
antibody = js_list_creator(query.all())
# dignity
query = DBSession.query(Source.dignity.distinct()).order_by(Source.dignity)
dignity = js_list_creator(query.all())
# organ
query = DBSession.query(Source.organ.distinct()).order_by(Source.organ)
organ = js_list_creator(query.all())
# histology
query = DBSession.query(Source.histology.distinct()).order_by(Source.histology)
histology = js_list_creator(query.all())
# celltype
query = DBSession.query(Source.celltype.distinct()).order_by(Source.celltype)
celltype = js_list_creator(query.all())
# celltype
query = DBSession.query(HlaType.hla_string.distinct()).order_by(HlaType.hla_string)
hla = js_list_creator(query.all())
# treatment
query = DBSession.query(Source.treatment.distinct()).order_by(Source.treatment)
treatment = js_list_creator(query.all())
return {
"antibody": antibody,
"dignity": dignity,
"organ": organ,
"histology": histology,
"celltype": celltype,
"hla": hla,
"patient_id": patient_id,
"treatment": treatment,
}
def update_metadata_source(request):
if "id" in request.params:
result_dict = dict()
result_dict["id"] = request.params['id']
query = DBSession.query(
Source.patient_id, Source.organ, Source.organism, Source.histology,
Source.dignity, Source.celltype, Source.location,
Source.metastatis, Source.treatment, Source.person,
func.cast(Source.prep_date, String).label("prep_date")).filter(
Source.source_id == request.params["id"])
source = json.dumps(query.all())
result_dict['source'] = source
query = DBSession.query(
Source.source_id,
HlaType.hla_string).join(t_hla_map).join(HlaType).filter(
Source.source_id == request.params["id"])
hla = json.dumps(query.all())
result_dict['hla'] = hla
# getting autocomplete items
allowed_elements = {
"patient_id": Source.patient_id,
"organ": Source.organ,
"organism": Source.organism,
"histology": Source.histology,
"dignity": Source.dignity,
"celltype": Source.celltype,
"location": Source.location,
"metastatis": Source.metastatis,
"treatment": Source.treatment,
"person": Source.person,
"comment": Source.comment,
"typing": HlaType.hla_string
}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
#result_dict['original'] = source
return result_dict
else:
try:
# query data for autocomplete
result_dict = dict()
allowed_elements = {"source_id": Source.source_id}
for k, v in allowed_elements.iteritems():
query = DBSession.query(v)
query = query.group_by(v)
query_result = js_list_creator(query.all())
result_dict[k] = query_result
# setting a different renderer
result = render(
'../templates/upload_templates/update_metadata_source.pt',
result_dict,
request=request)
response = Response(result)
return response
except:
return Response(conn_err_msg,
content_type='text/plain',
status_int=500)
