def changed_dict(properties, block, key, input): if get_dict_value(properties, block, key) != input: print "%s.%s = %s != %s" % ( block, key, get_dict_value(properties, block, key), input) return True else: return False
def changed_dict(properties, block, key, input): if get_dict_value(properties, block, key) != input: print "%s.%s = %s != %s" % (block, key, get_dict_value(properties, block, key), input) return True else: return False
def verify_ope_account_in_smc(student_user, smc_url, smc_admin_user, smc_admin_pw): # Bounce off the SMC server to see if the student account exists in SMC # NOTE - this one does NOT check canvas for the user laptop_admin_user = "" laptop_admin_password = "" student_full_name = "" smc_version = "" p("\n}}gnChecking user status in SMC tool...}}xx") json_response = RestClient.send_rest_call(server=smc_url, api_endpoint="lms/verify_ope_account_in_smc.json/" + student_user, auth_user=smc_admin_user, auth_password=smc_admin_pw) if json_response is None: # If None - fatal error! return None # Interpret response from SMC try: msg = util.get_dict_value(json_response, "msg") if msg == "": p("}}rbUnable to interpret response from SMC - no msg parameter returned}}xx") p(json_response) return None if msg.startswith("Invalid User!"): p("\n}}rbInvalid User!}}xx") p("}}ynUser doesn't exit in system, please import this student in the SMC first!}}xx") return None if msg == "No username specified!": p("\n}}rbInvalid User!}}xx") p("}}mnNo user with this name exists, please import this student in the SMC first!}}xx") return None student_full_name = util.get_dict_value(json_response, "student_full_name") laptop_admin_user = util.get_dict_value(json_response, "laptop_admin_user") smc_version = util.get_dict_value(json_response, "smc_version") # Password moved to credential step #laptop_admin_password = util.get_dict_value(json_response, "laptop_admin_password") except Exception as ex: p("}}rbUnable to interpret response from SMC - no msg parameter returned}}xx") p("}}mn" + str(ex) + "}}xx") # p(str(smc_response)) return None if laptop_admin_user == "": # or laptop_admin_password == "": p("}}rbERR - Please set the laptop admin credentials in the SMC before continuing (Admin -> Configure App -> Laptop Admin Credentials) }}xx") return None # sys.exit(-1) if student_full_name == "": p("}}rbERR - Unable to find student user in the SMC? Make sure it is imported.}}xx") return None # sys.exit(-1) #return (laptop_admin_user, laptop_admin_password, student_full_name) return (laptop_admin_user, student_full_name, smc_version)
def ping_smc(smc_url): json_response = RestClient.send_rest_call(server=smc_url, api_endpoint="lms/ping.json", ) if json_response is None: # If None - unable to communicate - likely offline p("}}ynNo response from smc server}}xx", log_level=4) return False server_time = util.get_dict_value(json_response, "server_time") p("}}mnPING - Got SMC Server time: " + str(server_time) + "}}xx") return True
def credential_student_in_smc(student_user, smc_url, smc_admin_user, smc_admin_pw, ex_info): # Send the info to the SMC server to json_response = RestClient.send_rest_call(server=smc_url, api_endpoint="lms/credential_student.json/" + student_user, method="POST", json_params=ex_info, auth_user=smc_admin_user, auth_password=smc_admin_pw) if json_response is None: # If None - fatal error! return None # Interpret response from SMC try: #p("RESP: " + str(smc_response)) msg = util.get_dict_value(json_response, "msg", default="missing") if msg == "missing": p("}}rbUnable to interpret response from SMC - no msg parameter returned}}xx") return None if msg == "Invalid User!": p("\n}}rbInvalid User!}}xx") p("}}mnUser doesn't exit in system, please import this student in the SMC first!}}xx") return None if msg == "No username specified!": p("\n}}rbInvalid User!}}xx") p("}}mnNo user with this name exists, please import this student in the SMC first!}}xx") return None if "unable to connect to canvas db" in msg: p("\n}}rbSMC Unable to connect to Canvas DB - make sure canvas app is running and\n" + "the SMC tool is configured to talk to Canvas}}xx") p("}}yn" + str(msg) + "}}xx") return None if "Unable to find user in canvas:" in msg: p("\n}}rbInvalid User!}}xx") p("}}mnUser exists in SMC but not in Canvas, please rerun import this student in the SMC to correct the issue!}}xx") return None #full_name = util.get_dict_value(json_response, "full_name") canvas_access_token = util.get_dict_value(json_response, "key") student_hash = util.get_dict_value(json_response, "hash") admin_hash = util.get_dict_value(json_response, "admin_hash") student_full_name = util.get_dict_value(json_response, "full_name") canvas_url = util.get_dict_value(json_response, "canvas_url") except Exception as ex: p("}}rbUnable to interpret response from SMC - no msg parameter returned}}xx") p("}}mn" + str(ex) + "}}xx") return None # Decrypt scrambled parts student_password = Encryption.decrypt(student_hash, canvas_access_token) laptop_admin_password = Encryption.decrypt(admin_hash, canvas_access_token) # TODO - DEBUG - Disable this line! adm_pw_masked = (len(laptop_admin_password)-1) * "*" + laptop_admin_password[-1:] #p(student_password + "/" + adm_pw_masked, log_level=5) return (student_full_name, canvas_url, canvas_access_token, student_password, laptop_admin_password)
# Only show commands if UAC active if is_admin[1]: commands = sorted(valid_commands.keys()) p("}}yn Valid Commands: " + str(commands) + "}}xx") p("}}ybFor help - type mgmt.exe help (command)}}xx") sys.exit(1) # Run the function associated w the command cmd_parts = valid_commands[cmd] if cmd_parts is None: p("}}rnERROR - Command not avaialable " + cmd + " - coming soon...}}xx", log_level=1) sys.exit(1) cmd_requires_admin = util.get_dict_value(cmd_parts, "require_admin", True) if cmd_requires_admin is True and is_admin[1] is not True: # Command requires elevation and this user doesn't have it! if is_admin[0] is not True: # User is NOT in the administrators group p("}}rbINVALID USER - Must be in the administrators group to use this utility!\n" + "Attempt logged for user " + is_admin[2] + ".}}xx", log_level=1) sys.exit(2) if is_admin[1] is not True: # User is NOT running with UAC enabled p("}}rbINVALID USER - Must be in UAC prompt to use this utility!\n" + "Attempt logged for user " + is_admin[2] + ".}}xx",
def update_fields(service_id): properties = get_properties(service_id) if not properties.keys(): return if get_value(properties, "AutoConnect") == "true": autoconn = "Yes" else: autoconn = "No" form.get('autoconnect').value = autoconn form.get('nameservers').value = get_str_value(properties, "Nameservers.Configuration") form.get('timeservers').value = get_str_value(properties, "Timeservers.Configuration") form.get('domains').value = get_str_value(properties, "Domains.Configuration") value = get_dict_value(properties, "Proxy.Configuration", "Method") if value == "": value = "auto" form.get('proxymethod').value = value form.get('proxyurl').value = get_dict_value(properties, "Proxy.Configuration", "URL") form.get('proxyservers').value = get_dict_value(properties, "Proxy.Configuration", "Servers") form.get('proxyexcludes').value = get_dict_value(properties, "Proxy.Configuration", "Excludes") form.get('ipv4method').value = get_dict_value(properties, "IPv4.Configuration", "Method") form.get('ipv4address').value = get_dict_value(properties, "IPv4.Configuration", "Address") form.get('ipv4netmask').value = get_dict_value(properties, "IPv4.Configuration", "Netmask") form.get('ipv4gateway').value = get_dict_value(properties, "IPv4.Configuration", "Gateway") form.get('ipv6method').value = get_dict_value(properties, "IPv6.Configuration", "Method") form.get('ipv6address').value = get_dict_value(properties, "IPv6.Configuration", "Address") value = get_dict_value(properties, "IPv6.Configuration", "PrefixLength") if value != "": value = "%d" % value form.get('ipv6prefixlen').value = value form.get('ipv6gateway').value = get_dict_value(properties, "IPv6.Configuration", "Gateway") form.get('ipv6privacy').value = get_dict_value(properties, "IPv6.Configuration", "Privacy")
def changed_dict_byte(properties, block, key, input): value = "%d" % get_dict_value(properties, block, key) if value != input: return True else: return False
def build_donor(app_ctx): click.echo('in build_donor...') schema = app_ctx['input_schemas']['donor'] fname = os.path.join(schema['data_path'], schema['main_file_name']) annotations = {} util.read_annotations(annotations, 'pcawg_donorlist', schema['annotations_path']+'pc_annotation-pcawg_final_list.tsv') util.read_annotations(annotations, 'blacklist', schema['annotations_path']+'blacklist/pc_annotation-donor_blacklist.tsv') util.read_annotations(annotations, 'graylist', schema['annotations_path']+'graylist/pc_annotation-donor_graylist.tsv') util.read_annotations(annotations, 'uuid_to_barcode', schema['annotations_path']+'pc_annotation-tcga_uuid2barcode.tsv') util.read_annotations(annotations, 'icgc_donor_id', schema['annotations_path']+'icgc_bioentity_ids/pc_annotation-icgc_donor_ids.csv') util.read_annotations(annotations, 'icgc_specimen_id', schema['annotations_path']+'icgc_bioentity_ids/pc_annotation-icgc_specimen_ids.csv') util.read_annotations(annotations, 'icgc_sample_id', schema['annotations_path']+'icgc_bioentity_ids/pc_annotation-icgc_sample_ids.csv') util.read_annotations(annotations, 'specimen_type_to_cv', schema['annotations_path']+'pc_annotation-tcga_specimen_type2icgc_cv.tsv') util.read_annotations(annotations, 'specimen_uuid_to_type', schema['annotations_path']+'pc_annotation-tcga_specimen_uuid2type.tsv') donor = {} specimen = {} # build the donor and specimen objects with open(fname, 'r') as f: reader = csv.DictReader(f, delimiter='\t', quoting=csv.QUOTE_NONE) for r in reader: donor_unique_id = r.get('disease.x')+'-US::'+r.get('participant_id') if not donor.get(donor_unique_id): #new donor: initial the donor donor[donor_unique_id] = create_obj(donor_unique_id, schema, r, annotations, 'donor') if not specimen.get('mirna'): specimen['mirna'] = {} specimen_id = r.get('sample_id') if not specimen['mirna'].get(specimen_id): specimen['mirna'][specimen_id] = create_obj(donor_unique_id, schema, r, annotations, 'mirna') aliquot = create_obj(donor_unique_id, schema, r, annotations, 'aliquot') specimen['mirna'][specimen_id]['aliquots'].append(copy.deepcopy(aliquot)) specimen['mirna'][specimen_id]['donor_unique_id'] = donor_unique_id # build the specimen object from help file fname = os.path.join(schema['data_path'], schema['help_file_name']) with open(fname, 'r') as f: reader = csv.DictReader(f, delimiter='\t', quoting=csv.QUOTE_NONE) for r in reader: donor_unique_id = r.get('donor_unique_id') specimen_id = r.get('submitter_specimen_id') dtype = 'rna_seq' if r.get('library_strategy') == 'RNA-Seq' else 'wgs' if not specimen.get(dtype): specimen[dtype] = {} if not specimen[dtype].get(specimen_id): specimen[dtype][specimen_id] = create_obj(donor_unique_id, schema, r, annotations, dtype) specimen[dtype][specimen_id]['donor_unique_id'] = donor_unique_id if os.path.exists(app_ctx['output_dir']): shutil.rmtree(app_ctx['output_dir']) os.makedirs(app_ctx['output_dir']) # add specimen to donor crossref_specimen_ids = {} crossref_specimen_ids['rna_seq'] = specimen['rna_seq'].keys() crossref_specimen_ids['wgs'] = specimen['wgs'].keys() json2tsv_fields_map = schema['json2tsv_fields_map'] sample_sheet_fields_donor = schema['target_tsv_file']['mirna_sample_sheet']['donor'] sample_sheet_fields_specimen = schema['target_tsv_file']['mirna_sample_sheet']['specimen'] sample_sheet_fields_sample = schema['target_tsv_file']['mirna_sample_sheet']['sample'] with open(os.path.join(app_ctx['output_dir'], 'mirna_sample_sheet.tsv'), 'a') as f: f.write('\t'.join(sample_sheet_fields_donor+sample_sheet_fields_specimen+sample_sheet_fields_sample) + '\n') for dtype in ['mirna', 'rna_seq', 'wgs']: #loop on the specimen to add it to donor for k, v in specimen[dtype].iteritems(): donor_unique_id = v.get('donor_unique_id') if not donor.get(donor_unique_id): continue if (not donor[donor_unique_id]['pcawg_donor']) and (not 'normal' in v.get('dcc_specimen_type').lower()): continue sample_sheet = OrderedDict() sample_sheet.update(util.get_dict_value(sample_sheet_fields_donor, donor[donor_unique_id], json2tsv_fields_map)) # check whether wgs and rna_seq has the mirna specimen if dtype == 'mirna': v['has_matched_wgs_specimen'] = True if k in crossref_specimen_ids.get('wgs') else False v['has_matched_rna_seq_specimen'] = True if k in crossref_specimen_ids.get('rna_seq') else False sample_sheet.update(util.get_dict_value(sample_sheet_fields_specimen, v, json2tsv_fields_map)) for aliquot in v.get('aliquots'): sample_sheet.update(util.get_dict_value(sample_sheet_fields_sample, aliquot, json2tsv_fields_map)) line = util.get_line(sample_sheet) # # generate mirna_sample_sheet with open(os.path.join(app_ctx['output_dir'], 'mirna_sample_sheet.tsv'), 'a') as f: f.write('\t'.join(line) + '\n') v.pop('donor_unique_id') if 'normal' in v.get('dcc_specimen_type').lower(): donor[donor_unique_id]['normal'][dtype] = v else: donor[donor_unique_id]['tumor'][dtype].append(v) # get release_tsv fields release_fields = schema['target_tsv_file']['mirna_release_tsv'] with open(os.path.join(app_ctx['output_dir'], 'mirna_release.tsv'), 'a') as f: f.write('\t'.join(release_fields) + '\n') # remove the donors only have tumor mirna specimen for k, v in donor.iteritems(): if (not v['pcawg_donor']) and (not v.get('normal').get('mirna')): continue for dtype in ['mirna', 'rna_seq', 'wgs']: v['tumor_'+dtype+'_specimen_count'] = len(v['tumor'][dtype]) if v['tumor'].get(dtype) else 0 # generate the jsonl dump with open(os.path.join(app_ctx['output_dir'], 'mirna_release.jsonl'), 'a') as f: f.write(json.dumps(v) + '\n') # # generate mirna_release_tsv list tsv_obj = util.get_dict_value(release_fields, v, json2tsv_fields_map) line = util.get_line(tsv_obj) with open(os.path.join(app_ctx['output_dir'], 'mirna_release.tsv'), 'a') as f: f.write('\t'.join(line) + '\n') click.echo('complete in build_donor...')
def update_fields(service_id): properties = get_properties(service_id) if not properties.keys(): return if get_value(properties, "AutoConnect") == "true": autoconn = "Yes" else: autoconn = "No" form.get('autoconnect').value = autoconn form.get('nameservers').value = get_str_value(properties, "Nameservers.Configuration") form.get('timeservers').value = get_str_value(properties, "Timeservers.Configuration") form.get('domains').value = get_str_value(properties, "Domains.Configuration") value = get_dict_value(properties, "Proxy.Configuration", "Method") if value == "": value = "auto" form.get('proxymethod').value = value form.get('proxyurl').value = get_dict_value(properties, "Proxy.Configuration", "URL") form.get('proxyservers').value = get_dict_value(properties, "Proxy.Configuration", "Servers") form.get('proxyexcludes').value = get_dict_value(properties, "Proxy.Configuration", "Excludes") form.get('ipv4method').value = get_dict_value(properties, "IPv4.Configuration", "Method") form.get('ipv4address').value = get_dict_value(properties, "IPv4.Configuration", "Address") form.get('ipv4netmask').value = get_dict_value(properties, "IPv4.Configuration", "Netmask") form.get('ipv4gateway').value = get_dict_value(properties, "IPv4.Configuration", "Gateway") form.get('ipv6method').value = get_dict_value(properties, "IPv6.Configuration", "Method") form.get('ipv6address').value = get_dict_value(properties, "IPv6.Configuration", "Address") value = get_dict_value(properties, "IPv6.Configuration", "PrefixLength") if value != "": value = "%d" % value form.get('ipv6prefixlen').value = value form.get('ipv6gateway').value = get_dict_value(properties, "IPv6.Configuration", "Gateway") form.get('ipv6privacy').value = get_dict_value(properties, "IPv6.Configuration", "Privacy")
def changed_dict_byte(properties, block, key, input): value = "%d" % get_dict_value(properties, block, key) if value != input: return True else: return False