def configuration_upload(request): if request.method == 'POST': # script= request.POST.get('script') # print type(script) print request myFile = request.FILES.get('script', None) name = request.POST.get('name') describe = request.POST.get('describe') print name, describe if name: save_name = name else: save_name = myFile # print(myFile._size) # 文件大小字节数 if Configuration.objects.filter(configuration_name=myFile).exists(): return render_to_response('400.html', {'info': '脚本已经存在'}) data = myFile.read() job_obj = Configuration() job_obj.configuration_name = save_name job_obj.info = data job_obj.describe = describe job_obj.save() return render_to_response('configuration_upload.html', {'username': request.user.username}) else: return render_to_response('configuration_upload.html', {'username': request.user.username})
async def get_result(index: Index = Path(..., title="The name of the Index")): config = Configuration(index=index) try: result = await workflow_runner.run(config) return JSONResponse(status_code=200, content=result) except Exception as e: raise MyException(e)
def sendInitialEmail(order): status_base_url = Configuration().getValue('espa.status.url') status_url = ('%s/%s') % (status_base_url, order.email) header = ( """Thank you for your order ( %s ). Your order has been received and is currently being processed. You will receive an email notification when all units on this order have been completed. You can check the status of your order and download already completed scenes directly from %s Requested scenes:\n""") % (order.orderid, status_url) scenes = Scene.objects.filter(order__id=order.id) ordered = header if scenes: for s in scenes: ordered = ordered + s.name + '\n' #configure all these values msg = MIMEText(ordered) msg['Subject'] = 'Processing order received.' msg['To'] = order.email msg['From'] = '*****@*****.**' s = SMTP(host='gssdsflh01.cr.usgs.gov') s.sendmail('*****@*****.**', order.email, msg.as_string()) s.quit()
def test_set_kmer_freq_promoter(self): k = 7 exp_setting = Configuration() exp_setting.set_kmer_size(kmer_size=k) conn = Pgsql.Common.connect(settings.conn_string_test) #gnid = 58737 gnid = 76 seq_type = 'm1' gs_pep = GeneSequence(gnid=gnid, seq_type=seq_type, is_max_seq_len=True, conn=conn, k=k) print(gs_pep.get_seq_str()) kf = gs_pep.get_kmer_freq(k=k) kf.print(sort_type=4, limit=10)
class TestPredictionResults(unittest.TestCase): gnids = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] assigned_gnids = [1, 2, 3, 4, 5] corresp_tissue = 1 genes = Genes(gnids) class_size = 2 fold_size = 2 kmer_size = 3 target_features = '1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23' exp_setting = Configuration() exp_setting.set_target_features(target_features=target_features) #exp_setting.set_neg_class_mode(settings.NEG_CLASS_MODE_RND_S) exp_setting.set_neg_class_mode(settings.NEG_CLASS_MODE_NOT_P) def test_prediction_results(self): all_prediction_results = list() for corresp_tissue in range(1, 24): cv = CrossValidation(genes=self.genes, all_gnids=self.gnids, class_size=self.class_size, fold_size=self.fold_size, kmer_size=self.kmer_size, exp_setting=self.exp_setting) cv.build_datasets(assigned_genes=self.assigned_gnids, neg_class_mode=self.exp_setting.get_neg_class_mode(), corresp_tissue=corresp_tissue) prediction_results = cv.validation() all_prediction_results.append(prediction_results) feature_vector = dict() for gnid in self.gnids: gnid_vector = list() for prediction_results in all_prediction_results: if prediction_results: gnid_pr = prediction_results.get(gnid) if gnid_pr is None: gnid_vector.append('?') else: gnid_vector.append(gnid_pr.get_predicted_class()) feature_vector[gnid] = gnid_vector # show feature_vector for tissue in range(1, 24): print('Tissue#:', tissue) for gnid, vector in feature_vector.items(): line = ",".join(str(value) for value in vector) p_results = all_prediction_results[tissue - 1].get(gnid) if p_results is None: data_label = '?' else: data_label = 'data_label:{}'.format(p_results.get_assigned_class()) print("%s,%s,%s\n" % (gnid, line, data_label))
def new_configuration(): """ Add a new album """ form = ConfigurationForm(request.form) if request.method == 'POST': # save the album configuration = Configuration() save_changes_configuration(configuration, form, new=True) return redirect('/configurations') return render_template('new_configuration.html', form=form)
def get_activities_per_city(city: City = Path( ..., title="The name of the Ccity you want to scrap the activities")): url_scraping = 'http://www.tripadvisor.com' config = Configuration( city=city #I'm passing this argument from the path that the user use ) try: result = workflow_runner.run(config, url_scraping) return JSONResponse(status_code=200, content=result) except Exception as e: raise MyException(e)
def get_result(country: Country = Path( ..., title="The name of the country you want to scrap the best cities to explore" )): url_scraping = 'http://www.tripadvisor.com' config = Configuration( country= country #I'm passing this argument from the path that the user use ) try: result = workflow_runner.get_cities(config, url_scraping) return JSONResponse(status_code=200, content=result) except Exception as e: raise MyException(e)
def markSceneComplete(name, orderid, processing_loc, completed_file_location, destination_cksum_file=None, log_file_contents=""): print("Marking scene:%s complete for order:%s" % (name, orderid)) o = Order.objects.get(orderid=orderid) s = Scene.objects.get(name=name, order__id=o.id) if s: s.status = 'complete' s.processing_location = processing_loc s.product_distro_location = completed_file_location s.completion_date = datetime.datetime.now() s.cksum_distro_location = destination_cksum_file #if source_l1t_location is not None: #s.source_distro_location = source_l1t_location s.log_file_contents = log_file_contents #Need to modify this as soon as we're going to start #providing more than 1 product base_url = Configuration().getValue('distribution.cache.home.url') product_file_parts = completed_file_location.split('/') product_file = product_file_parts[len(product_file_parts) - 1] cksum_file_parts = destination_cksum_file.split('/') cksum_file = cksum_file_parts[len(cksum_file_parts) - 1] s.product_dload_url = ('%s/orders/%s/%s') % (base_url, orderid, product_file) s.cksum_download_url = ('%s/orders/%s/%s') % (base_url, orderid, cksum_file) s.save() if o.order_source == 'ee': #update ee lta_service = lta.LtaServices() lta_service.update_order(o.ee_order_id, s.ee_unit_id, 'C') update_order_if_complete(o.orderid, s) return True else: print("MarkSceneComplete:No scene was found with the name:%s" % name) return False
def create_conf(): form = ConfigurationForm(request.form) if request.method == 'POST' and form.validate(): try: configuration = Configuration() form.populate_obj(configuration) db.session.add(configuration) db.session.commit() return redirect(url_for('conf', id=configuration.id)) except Exception as error: flash("Error creating configuration.", category="danger") app.logger.error("Error creating configuration {}\n{}".format( error, traceback.format_exc())) return render_template('forms/model.jinja', form=form, action=url_for('create_conf'), section='other')
def load_configuration() -> None: global configuration global mock_configuration global mock_configuration_file_observer print('Loading configuration...') path = f'{dirname(realpath(__file__))}/..' raw_config = yaml.safe_load(open(f'{path}/{CONFIG_FILE_NAME}', 'r')) configuration = Configuration( path=path, active_mock=raw_config.get('active_mock', None), record_session=bool(raw_config.get('record', False))) if configuration.active_mock: load_mock_configuration() if mock_configuration is not None: print(f'Active mock configuration: {configuration.active_mock}') mock_configuration_file_observer = observe_file_modifications( path=mock_configuration.path, update=load_mock_configuration) else: print('Failed to load mock configuration...') else: if mock_configuration is not None: mock_configuration = None print('Mock configuration disabled') else: pass if mock_configuration_file_observer is not None: mock_configuration_file_observer.stop() mock_configuration_file_observer.join() mock_configuration_file_observer = None else: pass return None
class TestCrossValidation(unittest.TestCase): gnids = [1, 2, 3, 4, 5, 6, 7, 8, 9, 10] assigned_gnids = [1, 2, 3, 4, 5] corresp_tissue = 1 genes = Genes(gnids) class_size = 2 fold_size = 2 kmer_size = 3 target_features = '1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23' exp_setting = Configuration() exp_setting.set_target_features(target_features=target_features) #exp_setting.set_neg_class_mode(settings.NEG_CLASS_MODE_RND_S) exp_setting.set_neg_class_mode(settings.NEG_CLASS_MODE_NOT_P) def test_cross_validation(self): all_prediction_results = list() for corresp_tissue in range(1, 24): cv = CrossValidation(genes=self.genes, all_gnids=self.gnids, class_size=self.class_size, fold_size=self.fold_size, kmer_size=self.kmer_size, exp_setting=self.exp_setting) cv.build_datasets(assigned_genes=self.assigned_gnids, neg_class_mode=self.exp_setting.get_neg_class_mode(), corresp_tissue=corresp_tissue) prediction_results = cv.validation() all_prediction_results.append(prediction_results) feature_vector = dict() for gnid in self.gnids: gnid_vector = list() for prediction_results in all_prediction_results: if prediction_results: gnid_pr = prediction_results.get(gnid) if gnid_pr is None: gnid_vector.append('?') else: gnid_vector.append(gnid_pr.get_predicted_class()) feature_vector[gnid] = gnid_vector
def sendCompletionEmail(email, ordernum, readyscenes=[]): status_base_url = Configuration().getValue('espa.status.url') status_url = ('%s/%s') % (status_base_url, email) msg = ("""Your order is now complete and can be downloaded from %s This order will remain available for 14 days. Any data not downloaded will need to be reordered after this time. Please contact Customer Services at 1-800-252-4547 or email [email protected] with any questions. Your scenes -------------------------------------------\n""") % (status_url) for r in readyscenes: msg = msg + r + '\n' #configure these values msg = MIMEText(msg) msg['Subject'] = 'Processing for %s complete.' % (ordernum) msg['To'] = email msg['From'] = '*****@*****.**' s = SMTP(host='gssdsflh01.cr.usgs.gov') s.sendmail('*****@*****.**', email, msg.as_string()) s.quit()
def upload_configuration(self, request): if request.GET.get('source') == 'master': data = request.DATA myFile = request.FILES.get('script', None) name = data.get('name') describe = data.get('describe') if name: save_name = name else: save_name = myFile.name # print(myFile._size) # 文件大小字节数 if Configuration.objects.filter( configuration_name=save_name).exists(): return Response('脚本已经存在', status=status.HTTP_400_BAD_REQUEST) data = myFile.read() job_obj = Configuration() job_obj.configuration_name = save_name job_obj.info = data job_obj.describe = describe job_obj.save() return Response("success", status=status.HTTP_200_OK)
def main(argv): # global exp_setting exp_setting = Configuration() debug_mode = list() reduced_mode = False test_mode = False seq_type = None gene_prot = None feature_set = list() percentile_range = list() args = parser.parse_args(argv[1:]) if len(argv) <= 1: parser.parse_args(['--help']) return # set version exp_setting.set_version(settings.DEV_VERSION) # Show Version version = exp_setting.get_version() print('Version:', version.get_version()) # Get Cutoffs cutoffs = Cutoffs() cutoffs.query_cutoffs('95, 0, -5') exp_setting.set_cutoffs(cutoffs) print('Cutoffs data Initialized.') # enable debugging mode if args.enable_debug: if set(args.enable_debug) & enable_debug: #debug_mode = [1, 100000] debug_mode = [1, 1000] reduced_mode = True if args.use_real_db: if set(args.use_real_db) & choice_yes: print('USING TEST DB: NO (USEING REAL/PRODUCTION DB)') else: settings.conn_string = settings.conn_string_test print('USING TEST DB: YES') if set(args.test_mode) & choice_yes: exp_setting.set_test_mode(True) print('TEST MODE: YES') else: exp_setting.set_test_mode(False) print('TEST MODE: NO') # ignore zero values if set(args.ignore_zero) & choice_yes: exp_setting.set_ignore_null(True) print('Ignore zero values: YES') else: exp_setting.set_ignore_null(False) print('Ignore zero values: NO') # Gene info loading mode if args.gene_load_mode: if set(args.gene_load_mode) & gene_load_mode_pl: exp_setting.set_gene_load_mode(settings.GN_LD_MODE_PL) print('Gene loading mode: pre-load') elif set(args.gene_load_mode) & gene_load_mode_dl: exp_setting.set_gene_load_mode(settings.GN_LD_MODE_DL) print('Gene loading mode: dynamic load') # sequence type if args.seq_type: if set(args.seq_type) & seq_type_pep: seq_type = 'p' print('sequence type: amino acid (peptide)') elif set(args.seq_type) & seq_type_dna: seq_type = 'd' print('sequence type: DNA') elif set(args.seq_type) & seq_type_pmt: seq_type = 'm1' print('sequence type: Promoter data') # set missing gnids in promoter data exp_setting.set_missing_gnids_in_promoter() elif set(args.seq_type) & seq_type_rda: seq_type = 'p' print('sequence type: Reduced Alphabet') settings.RA_MODE = True else: # default seq_type = 'p' print('sequence type: amino acid (peptide) - Default') exp_setting.set_seq_type(seq_type) # gp_type gp_type = 'g' if args.gp_type: if set(args.gp_type) & gp_type_g: gp_type = 'g' print('gp type: g') elif set(args.gp_type) & gp_type_p: gp_type = 'p' print('gp type: p') elif set(args.gp_type) & gp_type_b: gp_type = 'b' print('gp type: b') else: gp_type = 'g' print('gp type: g (default)') exp_setting.set_gp_type(gp_type) # assign feature groups if args.feature_group: if set(args.feature_group) & feature_group_gl: print('new feature group: gene low expressed') Features.gene_low_exp() if set(args.feature_group) & feature_group_gh: print('new feature group: gene high expressed, top 5%') Features.gene_high_exp() if set(args.feature_group) & feature_group_gh10: print('new feature group: gene high expressed, top 10%') Features.gene_high_exp_t10() if set(args.feature_group) & feature_group_gt: print('new feature group: gene for each tissue, top 10%') Features.gene_tissues() # feature set if args.feature_set: feature_set = args.feature_set print('feature set: {}'.format(feature_set)) # set negative class mode if args.neg_class_mode: neg_class_mode = args.neg_class_mode print('NEG_CLASS_MODE:', neg_class_mode) if neg_class_mode in (settings.NEG_CLASS_MODE_NOT_P, settings.NEG_CLASS_MODE_RND_S, settings.NEG_CLASS_MODE_RND_M): exp_setting.set_neg_class_mode(neg_class_mode) else: error_mesg = 'NEG_CLASS_MODE:', neg_class_mode, 'is UNKNOWN.' raise ValueError(error_mesg) # set percentile for new feature set if args.percentile: percentile_range = args.percentile.split(',') percentile_range = [int(x) for x in percentile_range] # str -> int type print('Set percnetile range:', args.percentile) # set gp combo configurations feature_set_gp_comb = list() if args.multi_gp: multi_gp_conf = args.multi_gp for conf in multi_gp_conf: print(conf) conf_list = conf.split(':') feature_set_gp_comb.append(conf_list) print(feature_set_gp_comb) # class assignment for features if args.features: if set(args.features) & (settings.FN_GE_N | settings.FN_GE_B | settings.FN_PA_N | settings.FN_PA_B): if len(percentile_range) <= 0: raise ValueError( 'percentile range is empty. Please set percentile range.') ''' It supports adding multiple features at the same time, so it needs to do independently as belows. ''' if set(args.features) & settings.FN_GE_N: print('GE_N') is_top = True gp_type = 'g' feature_set_name = next(iter(settings.FN_GE_N)) for percentile in range(percentile_range[0], percentile_range[1], percentile_range[2]): add_feature_by_percentile( gp_type=gp_type, feature_set_name=feature_set_name, percentile=percentile, is_top=is_top) if set(args.features) & settings.FN_GE_B: print('GE_B') is_top = False gp_type = 'g' feature_set_name = next(iter(settings.FN_GE_B)) for percentile in range(percentile_range[0], percentile_range[1], percentile_range[2]): add_feature_by_percentile( gp_type=gp_type, feature_set_name=feature_set_name, percentile=percentile, is_top=is_top) if set(args.features) & settings.FN_PA_N: print('PA_N') is_top = True gp_type = 'p' feature_set_name = next(iter(settings.FN_PA_N)) for percentile in range(percentile_range[0], percentile_range[1], percentile_range[2]): add_feature_by_percentile( gp_type=gp_type, feature_set_name=feature_set_name, percentile=percentile, is_top=is_top) if set(args.features) & settings.FN_PA_B: print('PA_B') is_top = False gp_type = 'p' feature_set_name = next(iter(settings.FN_PA_B)) for percentile in range(percentile_range[0], percentile_range[1], percentile_range[2]): add_feature_by_percentile( gp_type=gp_type, feature_set_name=feature_set_name, percentile=percentile, is_top=is_top) if set(args.features) & settings.FN_GPCB: print('GE&PA Combination data') for conf in feature_set_gp_comb: add_feature_gp_comb(conf, exp_setting) # build feature vector if args.feature_vector: intervals = [1000] if set(args.feature_vector) & feature_vector: print('build feature vector') fs_set_idx = 0 #build_feature_vector() if reduced_mode: #for i in range(1,58938, interval): for interval in intervals: for i in range(1, 39324, interval): #for i in range(16001,39324, interval): debug_mode = [i, interval] exp_setting.set_debug_mode(debug_mode) build_feature_vector(exp_setting) else: for k in range(3, 8): exp_setting.set_kmer_size(kmer_size=k) exp_setting.set_genes_info(genes_info=None) for fsid in feature_set: # Version Info print('Version:', settings.DEV_VERSION) if fsid == 0: # set feature info with dummy data for small assigned gene at random fs_info = FeatureInfo(fsid=0, fs_name='SM_RND', gp_type='g', class_size=2) # Set assigned genes limit assigned_genes_limit = [ int((x + 23 * fs_set_idx) * 10) for x in range(1, 24) ] exp_setting.set_assigned_genes_limit( assigned_genes_limit) fs_set_idx += 1 else: # get feature set info from DB res_fs_info = Pgsql.Common.select_data( sqls.get_feature_set, (fsid)) fs_info = FeatureInfo( fsid=fsid, fs_name=res_fs_info[0][0].strip(), gp_type=res_fs_info[0][1].strip(), class_size=int(res_fs_info[0][2])) exp_setting.set_fs_info(fs_info) # for test print( '### MESSAGE ### fsid: {}, fs_name: {}, gp_type: {}, class_size: {}' .format(exp_setting.get_fsid(), exp_setting.get_fs_name(), exp_setting.get_gp_type(), exp_setting.get_class_size())) debug_mode = [1, 0] exp_setting.set_debug_mode(debug_mode) build_feature_vector(exp_setting) # single step classification if args.validation_mode: if set(args.validation_mode) & validation_mode_rg: # reduced gene model intervals = [1000, 2000, 3000, 4000, 5000] print('validation - reduced genes model mode') for interval in intervals: for i in range(1, 39324, interval): #for i in range(16001,39324, interval): debug_mode = [i, interval] exp_setting.set_debug_mode(debug_mode) build_feature_vector(debug_mode=debug_mode, gene_prot=gene_prot, seq_type=seq_type)
class TestFeatureVector(unittest.TestCase): # set target features #target_features = '1' #target_features = '23' #target_features = '1,2,3,4' #target_features = '4,7,9,10' #target_features = '1,2,3,4,5,6,7,8,9,10' #target_features = '1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22' #target_features = '1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20' target_features = '1,2,3,4,5,6,7,8,9,10,11,12,13,14,15,16,17,18,19,20,21,22,23' # set assigned genes limit #assigned_genes_limit = [int(10) + x for x in range(1, 24)] #assigned_genes_limit = [int(50) for x in range(1, 24)] assigned_genes_limit = [int(10) for x in range(1, 24)] exp_setting = Configuration() def test_feature_vector_random(self): self.exp_setting.set_target_features( target_features=self.target_features) self.exp_setting.set_assigned_genes_limit(self.assigned_genes_limit) # set debug_mode debug_mode = [1, 0] self.exp_setting.set_debug_mode(debug_mode) # set test_mode # exp_setting.set_test_mode(test_mode=True) # exp_setting.set_test_mode(test_mode=settings.TEST_MODE_KMER_FREQ) self.exp_setting.set_test_mode(test_mode=settings.TEST_MODE_TRUE) # set NEG class mode self.exp_setting.set_neg_class_mode(settings.NEG_CLASS_MODE_RND_S) # set class size self.exp_setting.set_class_size(class_size=2) # set fold size for cross-validation self.exp_setting.set_fold_size(fold_size=10) # set kmer size self.exp_setting.set_kmer_size(kmer_size=3) # set seq_type self.exp_setting.set_seq_type(seq_type='p') # set fsid fs_info = FeatureInfo(fsid=0, fs_name='SM_RND', gp_type='g', class_size=2) self.exp_setting.set_fs_info(fs_info=fs_info) # Feature Vector fv = FeatureVector(self.exp_setting) # fv.test_features_dataset() fv.cross_validation() # write prediction results into a file (.csv) #fv.write_prediction_results() # Build feature vectors with prediction results #fv.build_feature_vector() print('Build Feature Vector') #gene_dataset = self.exp_setting.get_gene_dataset() all_gnids_list = self.exp_setting.get_gene_dataset_all_gnids_list() #for gnid in gene_dataset.get_all_gnids(): for gnid in all_gnids_list: #for gnid in self.wd_all_gnids: gnid_vector = list() for feature in fv.features: #if feature.prediction_results is not None: if feature.prediction_results: predicted_results = feature.prediction_results.get( gnid, None) if predicted_results is None: gnid_vector.append('?') else: #gnid_vector.append(feature.prediction_results[gnid].get_predicted_class()) gnid_vector.append( predicted_results.get_predicted_class()) #print(gnid_vector) fv.feature_vector[gnid] = gnid_vector # TEST write feature vector for feature in fv.features: print('Feature Name: {}, tissue#: {}'.format( feature.name, feature.corresp_tissue)) # gnids gnids = self.exp_setting.get_gene_dataset_gnids_list( feature_id=feature.corresp_tissue) #for gnid, vector in fv.feature_vector.items(): for gnid in gnids: vector = fv.feature_vector.get(gnid, None) if vector is not None: line = ",".join(str(value) for value in vector) predicted_results = feature.prediction_results.get( gnid, None) if predicted_results is None: data_label = '?' else: data_label = predicted_results.get_assigned_class() #f.write("%s,%s,%s\n" % (gnid, line, feature.prediction_results[gnid].get_assigned_class())) print("%s,%s,%s\n" % (gnid, line, data_label)) #print('gnid:', gnid) #print('line:', line) #print('data_label:', data_label) #fv.write_feature_vector() #fv.create_arff() #fv.write_prediction_summary() def test_feature_vector_by_fsid(self): self.exp_setting.set_target_features( target_features=self.target_features) self.exp_setting.set_assigned_genes_limit(self.assigned_genes_limit) # set debug_mode debug_mode = [1, 0] self.exp_setting.set_debug_mode(debug_mode) # set test_mode # exp_setting.set_test_mode(test_mode=True) # exp_setting.set_test_mode(test_mode=settings.TEST_MODE_KMER_FREQ) self.exp_setting.set_test_mode(test_mode=settings.TEST_MODE_TRUE) # set NEG class mode self.exp_setting.set_neg_class_mode(settings.NEG_CLASS_MODE_RND_S) # set class size self.exp_setting.set_class_size(class_size=2) # set fold size for cross-validation self.exp_setting.set_fold_size(fold_size=10) # set kmer size self.exp_setting.set_kmer_size(kmer_size=3) # set seq_type self.exp_setting.set_seq_type(seq_type='p') # set fsid fsid = 44 res_fs_info = Pgsql.Common.select_data(sqls.get_feature_set, (fsid)) fs_info = FeatureInfo(fsid=fsid, fs_name=res_fs_info[0][0].strip(), gp_type=res_fs_info[0][1].strip(), class_size=int(res_fs_info[0][2])) self.exp_setting.set_fs_info(fs_info=fs_info) # Feature Vector fv = FeatureVector(self.exp_setting) # fv.test_features_dataset() fv.cross_validation() # write prediction results into a file (.csv) #fv.write_prediction_results() # Build feature vectors with prediction results #fv.build_feature_vector() print('Build Feature Vector') #gene_dataset = self.exp_setting.get_gene_dataset() all_gnids_list = self.exp_setting.get_gene_dataset_all_gnids_list() #for gnid in gene_dataset.get_all_gnids(): for gnid in all_gnids_list: #for gnid in self.wd_all_gnids: gnid_vector = list() for feature in fv.features: #if feature.prediction_results is not None: if feature.prediction_results: predicted_results = feature.prediction_results.get( gnid, None) if predicted_results is None: gnid_vector.append('?') else: #gnid_vector.append(feature.prediction_results[gnid].get_predicted_class()) gnid_vector.append( predicted_results.get_predicted_class()) #print(gnid_vector) fv.feature_vector[gnid] = gnid_vector # TEST write feature vector for feature in fv.features: print('Feature Name: {}, tissue#: {}'.format( feature.name, feature.corresp_tissue)) # gnids gnids = self.exp_setting.get_gene_dataset_gnids_list( feature_id=feature.corresp_tissue) #for gnid, vector in fv.feature_vector.items(): for gnid in gnids: vector = fv.feature_vector.get(gnid, None) if vector is not None: line = ",".join(str(value) for value in vector) predicted_results = feature.prediction_results.get( gnid, None) if predicted_results is None: data_label = '?' else: data_label = predicted_results.get_assigned_class() #f.write("%s,%s,%s\n" % (gnid, line, feature.prediction_results[gnid].get_assigned_class())) print("%s,%s,%s\n" % (gnid, line, data_label))
from email.mime.text import MIMEText from smtplib import * from models import Scene from models import Order from models import Configuration from espa.scene_cache import SceneCache import json import datetime import lta ######################################################################################################################## #load configuration values at the module level... ######################################################################################################################## try: smtp_url = Configuration().getValue('smtp.url') espa_email_address = Configuration().getValue('espa.email.address') order_status_base_url = Configuration().getValue('order.status.base.url') except Exception, err: print("Could not load configuration values:%s" % err) ######################################################################################################################## # Default product options ######################################################################################################################## def get_default_product_options(): '''returns default options for product selection''' options = {} #standard product selection options options[ 'include_sourcefile'] = False #delivers underlying raster product as part of order
def test_congistore_admin_handles_unknown_keys(self): Configuration(key='unknown-key', site=Site.objects.get_current()).save() self.login() self.client.get(urlresolvers.reverse('admin:configstore_configuration_changelist'))
def run(self): conf = Configuration() conf.name = 'Aðalstilling' db.session.add(conf) db.session.commit()
def create(key, value): config = Configuration(id=key, key=key, value=value) config.put() return config