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)