From 97ccc478543a7bb08fe0cf178e320dd5811d8bfa Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 10 Feb 2018 07:53:53 +0000 Subject: Check for bimbam path and bail out if it is missing --- wqflask/base/webqtlConfig.py | 1 + wqflask/utility/tools.py | 4 ---- 2 files changed, 1 insertion(+), 4 deletions(-) (limited to 'wqflask') diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 1ef2bc26..1e66e957 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -82,6 +82,7 @@ assert_writable_dir(GENERATED_TEXT_DIR) # Flat file directories GENODIR = flat_files('genotype')+'/' assert_dir(GENODIR) +assert_dir(GENODIR+'bimbam') # for gemma # JSON genotypes are OBSOLETE JSON_GENODIR = flat_files('genotype/json')+'/' diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 57f97a81..e3fcd7c7 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -278,8 +278,4 @@ if os.environ.get('WQFLASK_OVERRIDES'): logger.debug(OVERRIDES) # assert_file(PHEWAS_FILES+"/auwerx/PheWAS_pval_EMMA_norm.RData") -# assert_dir(get_setting("JS_BIODALLIANCE")) -# assert_file(get_setting("JS_BIODALLIANCE")+"/build/dalliance-all.js") -# assert_file(get_setting("JS_BIODALLIANCE")+"/build/worker-all.js") -# assert_dir(get_setting("JS_TWITTER_POST_FETCHER")) assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js") -- cgit v1.2.3 From b3d9c748008d401ca5b5fa5d60a6a1eff505ee3e Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 10 Feb 2018 08:22:41 +0000 Subject: Fixed finding PATHs - one return statement! --- wqflask/utility/tools.py | 9 +++++---- wqflask/wqflask/marker_regression/gemma_mapping.py | 7 ++++--- 2 files changed, 9 insertions(+), 7 deletions(-) (limited to 'wqflask') diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index e3fcd7c7..d3113302 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -16,7 +16,7 @@ OVERRIDES = {} def app_set(command_id, value): """Set application wide value""" app.config.setdefault(command_id,value) - value + return value def get_setting(command_id,guess=None): """Resolve a setting from the environment or the global settings in @@ -51,7 +51,7 @@ def get_setting(command_id,guess=None): return None # ---- Check whether environment exists - logger.debug("Looking for "+command_id+"\n") + # print("Looking for "+command_id+"\n") command = value(os.environ.get(command_id)) if command is None or command == "": command = OVERRIDES.get(command_id) @@ -63,7 +63,7 @@ def get_setting(command_id,guess=None): if command is None or command == "": # print command raise Exception(command_id+' setting unknown or faulty (update default_settings.py?).') - logger.debug("Set "+command_id+"="+str(command)) + # print("Set "+command_id+"="+str(command)) return command def get_setting_bool(id): @@ -253,6 +253,7 @@ JS_GN_PATH = get_setting('JS_GN_PATH') PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command()) GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command()) +assert(GEMMA_COMMAND is not None) PLINK_COMMAND = app_set("PLINK_COMMAND",plink_command()) GEMMA_WRAPPER_COMMAND = gemma_wrapper_command() TEMPDIR = tempdir() # defaults to UNIX TMPDIR @@ -266,7 +267,7 @@ from six import string_types if os.environ.get('WQFLASK_OVERRIDES'): jsonfn = get_setting('WQFLASK_OVERRIDES') - logger.error("WQFLASK_OVERRIDES: %s" % jsonfn) + logger.info("WQFLASK_OVERRIDES: %s" % jsonfn) with open(jsonfn) as data_file: overrides = json.load(data_file) for k in overrides: diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index a24e43d4..c004983e 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -3,7 +3,7 @@ import os, math, string, random, json from base import webqtlConfig from base.trait import GeneralTrait from base.data_set import create_dataset -from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR +from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -11,6 +11,7 @@ logger = utility.logger.getLogger(__name__ ) def run_gemma(this_dataset, samples, vals, covariates, method, use_loco): """Generates p-values for each marker using GEMMA""" + assert_bin(GEMMA_COMMAND); if this_dataset.group.genofile != None: genofile_name = this_dataset.group.genofile[:-5] else: @@ -27,7 +28,7 @@ def run_gemma(this_dataset, samples, vals, covariates, method, use_loco): if i < (len(this_chromosomes) - 1): chr_list_string += this_chromosomes[i+1].name + "," else: - chr_list_string += this_chromosomes[i+1].name + chr_list_string += this_chromosomes[i+1].name if covariates != "": gen_covariates_file(this_dataset, covariates) @@ -247,4 +248,4 @@ def parse_loco_output(this_dataset, gwa_output_filename): included_markers.append(line.split("\t")[1]) p_values.append(float(line.split("\t")[10])) - return marker_obs \ No newline at end of file + return marker_obs -- cgit v1.2.3 From 91365baf9ba657f56c19201874cdf60aede75dd1 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Sat, 10 Feb 2018 08:53:27 +0000 Subject: Fixing GEMMA LOCO --- bin/genenetwork2 | 4 +++- wqflask/wqflask/marker_regression/gemma_mapping.py | 11 ++++++++--- 2 files changed, 11 insertions(+), 4 deletions(-) (limited to 'wqflask') diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 7148c022..52144f4d 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -121,7 +121,9 @@ else export PLINK_COMMAND="$GN2_PROFILE/bin/plink2" export PYLMM_COMMAND="$GN2_PROFILE/bin/pylmm_redis" export GEMMA_COMMAND="$GN2_PROFILE/bin/gemma" - export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" + if [ -z GEMMA_WRAPPER_COMMAND ]; then + export GEMMA_WRAPPER_COMMAND="$GN2_PROFILE/bin/gemma-wrapper" + fi if [ ! -d $PYTHONPATH ] ; then echo "PYTHONPATH not valid "$PYTHONPATH ; exit 1 ; fi if [ ! -d $R_LIBS_SITE ] ; then echo "R_LIBS_SITE not valid "$R_LIBS_SITE ; exit 1 ; fi if [ ! -d $GEM_PATH ] ; then echo "GEM_PATH not valid "$GEM_PATH ; exit 1 ; fi diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py index c004983e..68920130 100644 --- a/wqflask/wqflask/marker_regression/gemma_mapping.py +++ b/wqflask/wqflask/marker_regression/gemma_mapping.py @@ -3,7 +3,7 @@ import os, math, string, random, json from base import webqtlConfig from base.trait import GeneralTrait from base.data_set import create_dataset -from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin +from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file import utility.logger logger = utility.logger.getLogger(__name__ ) @@ -210,8 +210,13 @@ def parse_gemma_output(genofile_name): def parse_loco_output(this_dataset, gwa_output_filename): output_filelist = [] - with open("{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json") as data_file: - data = json.load(data_file) + jsonfn = "{}/gn2/".format(TEMPDIR) + gwa_output_filename + ".json" + assert_file(jsonfn) + try: + with open(jsonfn) as data_file: + data = json.load(data_file) + except: + logger.error("Can not parse "+jsonfn) files = data['files'] for file in files: -- cgit v1.2.3 From 2602be69f2869de376d1b9ced6131d880e9476c2 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Tue, 13 Feb 2018 08:54:46 +0000 Subject: @zsloan: we should introduce full parameter checking and sensible defaults for every page we work on. It will help bug tracking. Probably fixes #279 --- wqflask/wqflask/correlation/show_corr_results.py | 100 ++++++++++++++++------- 1 file changed, 70 insertions(+), 30 deletions(-) (limited to 'wqflask') diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py index 24432ad0..3d1c0d17 100644 --- a/wqflask/wqflask/correlation/show_corr_results.py +++ b/wqflask/wqflask/correlation/show_corr_results.py @@ -75,6 +75,46 @@ def print_mem(stage=""): mem = resource.getrusage(resource.RUSAGE_SELF).ru_maxrss #print("{}: {}".format(stage, mem/1024)) +def is_float(value): + try: + float(value) + return True + except: + return False + +def is_int(value): + try: + int(value) + return True + except: + return False + +def is_str(value): + if value is None: + return False + try: + str(value) + return True + except: + return False + +def get_float(vars,name,default=None): + if name in vars: + if is_float(vars[name]): + return float(vars[name]) + return None + +def get_int(vars,name,default=None): + if name in vars: + if is_int(vars[name]): + return float(vars[name]) + return default + +def get_string(vars,name,default=None): + if name in vars: + if not vars[name] is None: + return str(vars[name]) + return default class AuthException(Exception): pass @@ -96,7 +136,19 @@ class CorrelationResults(object): # get trait list from db (database name) # calculate correlation with Base vector and targets - print("TESTING...") + # Check parameters + assert('corr_type' in start_vars) + assert(is_str(start_vars['corr_type'])) + assert('dataset' in start_vars) + # assert('group' in start_vars) permitted to be empty? + assert('corr_sample_method' in start_vars) + assert('corr_samples_group' in start_vars) + assert('corr_dataset' in start_vars) + assert('min_expr' in start_vars) + assert('corr_return_results' in start_vars) + if 'loc_chr' in start_vars: + assert('min_loc_mb' in start_vars) + assert('max_loc_mb' in start_vars) with Bench("Doing correlations"): if start_vars['dataset'] == "Temp": @@ -115,27 +167,17 @@ class CorrelationResults(object): self.sample_data = {} self.corr_type = start_vars['corr_type'] self.corr_method = start_vars['corr_sample_method'] - if 'min_expr' in start_vars: - if start_vars['min_expr'] != "": - self.min_expr = float(start_vars['min_expr']) - else: - self.min_expr = None - self.p_range_lower = float(start_vars['p_range_lower']) - self.p_range_upper = float(start_vars['p_range_upper']) + self.min_expr = get_float(start_vars,'min_expr') + self.p_range_lower = get_float(start_vars,'p_range_lower',-1.0) + self.p_range_upper = get_float(start_vars,'p_range_upper',1.0) if ('loc_chr' in start_vars and 'min_loc_mb' in start_vars and 'max_loc_mb' in start_vars): - self.location_chr = start_vars['loc_chr'] - if start_vars['min_loc_mb'].isdigit(): - self.min_location_mb = start_vars['min_loc_mb'] - else: - self.min_location_mb = None - if start_vars['max_loc_mb'].isdigit(): - self.max_location_mb = start_vars['max_loc_mb'] - else: - self.max_location_mb = None + self.location_chr = get_string(start_vars,'loc_chr') + self.min_location_mb = get_int(start_vars,'min_loc_mb') + self.max_location_mb = get_int(start_vars,'max_loc_mb') self.get_formatted_corr_type() self.return_number = int(start_vars['corr_return_results']) @@ -183,7 +225,7 @@ class CorrelationResults(object): else: for trait, values in self.target_dataset.trait_data.iteritems(): self.get_sample_r_and_p_values(trait, values) - + elif self.corr_type == "lit": self.trait_geneid_dict = self.dataset.retrieve_genes("GeneId") lit_corr_data = self.do_lit_correlation_for_all_traits() @@ -564,7 +606,7 @@ class CorrelationResults(object): self.this_trait_vals.append(sample_value) target_vals.append(target_sample_value) - self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) + self.this_trait_vals, target_vals, num_overlap = corr_result_helpers.normalize_values(self.this_trait_vals, target_vals) #ZS: 2015 could add biweight correlation, see http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3465711/ if self.corr_method == 'pearson': @@ -574,8 +616,8 @@ class CorrelationResults(object): if num_overlap > 5: self.correlation_data[trait] = [sample_r, sample_p, num_overlap] - - + + """ correlations = [] @@ -673,8 +715,8 @@ class CorrelationResults(object): method=self.method) return trait_list - """ - + """ + def do_tissue_corr_for_all_traits_2(self): """Comments Possibly Out of Date!!!!! @@ -1089,7 +1131,7 @@ class CorrelationResults(object): totalTraits = len(traits) #XZ, 09/18/2008: total trait number return traits - + def calculate_corr_for_all_tissues(self, tissue_dataset_id=None): symbol_corr_dict = {} @@ -1129,7 +1171,7 @@ class CorrelationResults(object): values_2.append(target_value) correlation = calCorrelation(values_1, values_2) self.correlation_data[trait] = correlation - + def getFileName(self, target_db_name): ### dcrowell August 2008 """Returns the name of the reference database file with which correlations are calculated. Takes argument cursor which is a cursor object of any instance of a subclass of templatePage @@ -1144,7 +1186,7 @@ class CorrelationResults(object): return FileName def do_parallel_correlation(self, db_filename, num_overlap): - + #XZ, 01/14/2009: This method is for parallel computing only. #XZ: It is supposed to be called when "Genetic Correlation, Pearson's r" (method 1) #XZ: or "Genetic Correlation, Spearman's rho" (method 2) is selected @@ -1313,7 +1355,7 @@ class CorrelationResults(object): z_value = z_value*math.sqrt(nOverlap-3) sample_p = 2.0*(1.0 - reaper.normp(abs(z_value))) - correlation_data[traitdataName] = [sample_r, sample_p, nOverlap] + correlation_data[traitdataName] = [sample_r, sample_p, nOverlap] # traitinfo = [traitdataName, sample_r, nOverlap] # allcorrelations.append(traitinfo) @@ -1321,7 +1363,7 @@ class CorrelationResults(object): return correlation_data # return allcorrelations - + datasetFile = open(webqtlConfig.GENERATED_TEXT_DIR+db_filename,'r') print("Invoking parallel computing") @@ -1378,5 +1420,3 @@ class CorrelationResults(object): # for one_result in results: # for one_traitinfo in one_result: # allcorrelations.append( one_traitinfo ) - - -- cgit v1.2.3 From 9d47ad572f46397bdd778d8f6e1c37d40e12aa2a Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 15 Feb 2018 10:30:52 +0000 Subject: Fixing authentication stuff so it uses parameters properly. Also no PYTHONPATH needed as it is now in the Guix build. --- bin/genenetwork2 | 12 +++++++----- etc/default_settings.py | 18 ++++++++++++++++++ wqflask/run_gunicorn.py | 3 +++ wqflask/utility/elasticsearch_tools.py | 16 ++++++++++++---- wqflask/utility/tools.py | 29 +++++++++++------------------ wqflask/wqflask/user_manager.py | 7 +++++-- 6 files changed, 56 insertions(+), 29 deletions(-) (limited to 'wqflask') diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 5438c1c0..42f79650 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -95,11 +95,13 @@ export WQFLASK_OVERRIDES=$overrides # JSON echo WQFLASK_SETTINGS=$settings echo WQFLASK_OVERRIDES=$overrides -if [ -z $ELASTICSEARCH_PROFILE ]; then - echo -e "\033[1;33mWARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE\033[0m"; -else - PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages" -fi +# This is a temporary hack to inject ES - should have added python2-elasticsearch package to guix instead +# if [ -z $ELASTICSEARCH_PROFILE ]; then +# echo -e "WARNING: Elastic Search profile has not been set - use ELASTICSEARCH_PROFILE"; +# else +# PYTHONPATH="$PYTHONPATH${PYTHONPATH:+:}$ELASTICSEARCH_PROFILE/lib/python2.7/site-packages" +# fi + if [ -z $GN2_PROFILE ] ; then echo "WARNING: GN2_PROFILE has not been set - you need the environment, so I hope you know what you are doing!" export GN2_PROFILE=$(dirname $(dirname $(which genenetwork2))) diff --git a/etc/default_settings.py b/etc/default_settings.py index 699d21f1..a70d8aec 100644 --- a/etc/default_settings.py +++ b/etc/default_settings.py @@ -41,6 +41,24 @@ SECURITY_POST_LOGIN_VIEW = "/thank_you" SERVER_PORT = 5003 # running on localhost SECRET_HMAC_CODE = '\x08\xdf\xfa\x93N\x80\xd9\\H@\\\x9f`\x98d^\xb4a;\xc6OM\x946a\xbc\xfc\x80:*\xebc' +GITHUB_CLIENT_ID = "UNKNOWN" +GITHUB_CLIENT_SECRET = "UNKNOWN" +GITHUB_AUTH_URL = "UNKNOWN" +GITHUB_API_URL = "UNKNOWN" + +ORCID_CLIENT_ID = "UNKNOWN" +ORCID_CLIENT_SECRET = "UNKNOWN" +ORCID_AUTH_URL = "UNKNOWN" +ORCID_TOKEN_URL = "UNKNOWN" + +ELASTICSEARCH_HOST = "localhost" +ELASTICSEARCH_PORT = '9200' + +SMTP_CONNECT = "UNKNOWN" +SMTP_USERNAME = "UNKNOWN" +SMTP_PASSWORD = "UNKNOWN" + + # ---- Behavioural settings (defaults) note that logger and log levels can # be overridden at the module level and with enviroment settings WEBSERVER_MODE = 'DEV' # Python webserver mode (DEBUG|DEV|PROD) diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py index 14a2d689..ebe3add5 100644 --- a/wqflask/run_gunicorn.py +++ b/wqflask/run_gunicorn.py @@ -11,6 +11,9 @@ print "Starting up Gunicorn process" from wqflask import app +app.config['SESSION_TYPE'] = 'filesystem' +app.config['SECRET_KEY'] = 'super secret key' + @app.route("/gunicorn") def hello(): return "

Hello There!

" diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py index a964b025..2d3d5add 100644 --- a/wqflask/utility/elasticsearch_tools.py +++ b/wqflask/utility/elasticsearch_tools.py @@ -1,10 +1,18 @@ from elasticsearch import Elasticsearch, TransportError import logging +from utility.logger import getLogger +logger = getLogger(__name__) + +from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT + def get_elasticsearch_connection(): + logger.info("get_elasticsearch_connection") es = None try: - from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT + assert(ELASTICSEARCH_HOST) + assert(ELASTICSEARCH_PORT) + logger.info("ES HOST",ELASTICSEARCH_HOST) es = Elasticsearch([{ "host": ELASTICSEARCH_HOST @@ -31,12 +39,12 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type): response = es.search( index = index , doc_type = doc_type - , body = { - "query": { "match": { column_name: column_value } } + , body = { + "query": { "match": { column_name: column_value } } }) if len(response["hits"]["hits"]) > 0: item_details = response["hits"]["hits"][0]["_source"] - except TransportError as te: + except TransportError as te: pass return item_details diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py index 005f9b0f..8c9fed96 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -251,32 +251,25 @@ assert_dir(JS_GUIX_PATH) JS_GN_PATH = get_setting('JS_GN_PATH') # assert_dir(JS_GN_PATH) -def get_setting_safe(setting): - try: - return get_setting(setting) - except: - print("Could not find the setting '", setting, "'. Continuing with value unset") - return None - -GITHUB_CLIENT_ID = get_setting_safe('GITHUB_CLIENT_ID') -GITHUB_CLIENT_SECRET = get_setting_safe('GITHUB_CLIENT_SECRET') +GITHUB_CLIENT_ID = get_setting('GITHUB_CLIENT_ID') +GITHUB_CLIENT_SECRET = get_setting('GITHUB_CLIENT_SECRET') GITHUB_AUTH_URL = None if GITHUB_CLIENT_ID and GITHUB_CLIENT_SECRET: GITHUB_AUTH_URL = "https://github.com/login/oauth/authorize?client_id="+GITHUB_CLIENT_ID+"&client_secret="+GITHUB_CLIENT_SECRET -GITHUB_API_URL = get_setting_safe('GITHUB_API_URL') -ORCID_CLIENT_ID = get_setting_safe('ORCID_CLIENT_ID') -ORCID_CLIENT_SECRET = get_setting_safe('ORCID_CLIENT_SECRET') +GITHUB_API_URL = get_setting('GITHUB_API_URL') +ORCID_CLIENT_ID = get_setting('ORCID_CLIENT_ID') +ORCID_CLIENT_SECRET = get_setting('ORCID_CLIENT_SECRET') ORCID_AUTH_URL = None if ORCID_CLIENT_ID and ORCID_CLIENT_SECRET: ORCID_AUTH_URL = "https://sandbox.orcid.org/oauth/authorize?response_type=code&scope=/authenticate&show_login=true&client_id="+ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET -ORCID_TOKEN_URL = get_setting_safe('ORCID_TOKEN_URL') +ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL') -ELASTICSEARCH_HOST = get_setting_safe('ELASTICSEARCH_HOST') -ELASTICSEARCH_PORT = get_setting_safe('ELASTICSEARCH_PORT') +ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST') +ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT') -SMTP_CONNECT = get_setting_safe('SMTP_CONNECT') -SMTP_USERNAME = get_setting_safe('SMTP_USERNAME') -SMTP_PASSWORD = get_setting_safe('SMTP_PASSWORD') +SMTP_CONNECT = get_setting('SMTP_CONNECT') +SMTP_USERNAME = get_setting('SMTP_USERNAME') +SMTP_PASSWORD = get_setting('SMTP_PASSWORD') PYLMM_COMMAND = app_set("PYLMM_COMMAND",pylmm_command()) GEMMA_COMMAND = app_set("GEMMA_COMMAND",gemma_command()) diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py index 6b667615..c8471cb1 100644 --- a/wqflask/wqflask/user_manager.py +++ b/wqflask/wqflask/user_manager.py @@ -55,9 +55,8 @@ logger = getLogger(__name__) from base.data_set import create_datasets_list import requests -from utility.elasticsearch_tools import * +from utility.elasticsearch_tools import get_elasticsearch_connection, get_user_by_unique_column, save_user -es = get_elasticsearch_connection() THREE_DAYS = 60 * 60 * 24 * 3 #THREE_DAYS = 45 @@ -479,6 +478,7 @@ def password_reset_step2(): password = request.form['password'] set_password(password, user) + es = get_elasticsearch_connection() es.update( index = "users" , doc_type = "local" @@ -620,6 +620,7 @@ class LoginUser(object): """Login through the normal form""" params = request.form if request.form else request.args logger.debug("in login params are:", params) + es = get_elasticsearch_connection() if not params: from utility.tools import GITHUB_AUTH_URL, ORCID_AUTH_URL external_login = None @@ -628,6 +629,7 @@ class LoginUser(object): "github": GITHUB_AUTH_URL, "orcid": ORCID_AUTH_URL } + assert(es is not None) return render_template( "new_security/login_user.html" , external_login=external_login @@ -822,6 +824,7 @@ def register(): params = request.form if request.form else request.args params = params.to_dict(flat=True) + es = get_elasticsearch_connection() params["es_connection"] = es if params: -- cgit v1.2.3 From 4097723cfd6331f41d8b8e7abec322cb12f39f10 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Thu, 15 Feb 2018 14:03:38 +0000 Subject: Added unittest example --- test/unittest/test_registration.py | 27 +++++++++ wqflask/mock/__init__.py | 0 wqflask/mock/es_double.py | 15 +++++ wqflask/tests/__init__.py | 0 wqflask/tests/es_double.py | 30 ---------- wqflask/tests/test_registration.py | 113 ------------------------------------- 6 files changed, 42 insertions(+), 143 deletions(-) create mode 100644 test/unittest/test_registration.py create mode 100644 wqflask/mock/__init__.py create mode 100644 wqflask/mock/es_double.py delete mode 100644 wqflask/tests/__init__.py delete mode 100644 wqflask/tests/es_double.py delete mode 100644 wqflask/tests/test_registration.py (limited to 'wqflask') diff --git a/test/unittest/test_registration.py b/test/unittest/test_registration.py new file mode 100644 index 00000000..98d0cdff --- /dev/null +++ b/test/unittest/test_registration.py @@ -0,0 +1,27 @@ +# Run test with something like +# +# env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=$HOME/gn2_data ./bin/genenetwork2 ./etc/default_settings.py -c ../test/unittest/test_registration.py +# + +import unittest +import mock.es_double as es +from wqflask.user_manager import RegisterUser + +class TestRegisterUser(unittest.TestCase): + def setUp(self): + self.es = es.ESDouble() + + def testRegisterUserWithCorrectData(self): + data = { + "email_address": "user@example.com" + , "full_name": "A.N. Other" + , "organization": "Some Organisation" + , "password": "testing" + , "password_confirm": "testing" + , "es_connection": self.es + } + result = RegisterUser(data) + self.assertEqual(len(result.errors), 0, "Errors were not expected") + +if __name__ == "__main__": + unittest.main() diff --git a/wqflask/mock/__init__.py b/wqflask/mock/__init__.py new file mode 100644 index 00000000..e69de29b diff --git a/wqflask/mock/es_double.py b/wqflask/mock/es_double.py new file mode 100644 index 00000000..6ef8a1b9 --- /dev/null +++ b/wqflask/mock/es_double.py @@ -0,0 +1,15 @@ +class ESDouble(object): + def __init__(self): + self.items = {} + + def ping(self): + return true + + def create(self, index, doc_type, body, id): + self.items["index"] = {doc_type: {"id": id, "_source": data}} + + def search(self, index, doc_type, body): + return { + "hits": { + "hits": self.items[index][doc_type][body] + }} diff --git a/wqflask/tests/__init__.py b/wqflask/tests/__init__.py deleted file mode 100644 index e69de29b..00000000 diff --git a/wqflask/tests/es_double.py b/wqflask/tests/es_double.py deleted file mode 100644 index 00739016..00000000 --- a/wqflask/tests/es_double.py +++ /dev/null @@ -1,30 +0,0 @@ -class ESDouble(object): - def __init__(self): - self.items = { - "users": { - "local": [] - }} - - def ping(self): - return true - - def create(self, index, doc_type, body, id): - item = {"id": id, "_source": body} - if not self.items.get("index", None): - self.items[index] = {doc_type: [item]} - else: - self.items[index][doc_type].append(item) - - def search(self, index, doc_type, body): - d = body["query"]["match"] - column = [(key, d[key]) for key in d] - - items = [] - for thing in self.items[index][doc_type]: - if thing["_source"][column[0][0]] == column[0][1]: - items.append(thing) - break - return { - "hits": { - "hits": items - }} diff --git a/wqflask/tests/test_registration.py b/wqflask/tests/test_registration.py deleted file mode 100644 index 50a2a84c..00000000 --- a/wqflask/tests/test_registration.py +++ /dev/null @@ -1,113 +0,0 @@ -import unittest -import es_double -import wqflask.user_manager -from wqflask.user_manager import RegisterUser - -class TestRegisterUser(unittest.TestCase): - def setUp(self): - # Mock elasticsearch - self.es = es_double.ESDouble() - - # Patch method - wqflask.user_manager.basic_info = lambda : {"basic_info": "some info"} - - def tearDown(self): - self.es = None - - def testRegisterUserWithNoData(self): - data = {} - result = RegisterUser(data) - self.assertNotEqual(len(result.errors), 0, "Data was not provided. Error was expected") - - def testRegisterUserWithNoEmail(self): - data = { - "email_address": "" - , "full_name": "A.N. Other" - , "organization": "Some Organisation" - , "password": "testing" - , "password_confirm": "testing" - , "es_connection": self.es - } - - result = RegisterUser(data) - self.assertNotEqual(len(result.errors), 0, "Email not provided. Error was expected") - - def testRegisterUserWithNoName(self): - data = { - "email_address": "user@example.com" - , "full_name": "" - , "organization": "Some Organisation" - , "password": "testing" - , "password_confirm": "testing" - , "es_connection": self.es - } - - result = RegisterUser(data) - self.assertNotEqual(len(result.errors), 0, "Name not provided. Error was expected") - - def testRegisterUserWithNoOrganisation(self): - data = { - "email_address": "user@example.com" - , "full_name": "A.N. Other" - , "organization": "" - , "password": "testing" - , "password_confirm": "testing" - , "es_connection": self.es - } - - result = RegisterUser(data) - self.assertEqual(len(result.errors), 0, "Organisation not provided. Error not expected") - - def testRegisterUserWithShortOrganisation(self): - data = { - "email_address": "user@example.com" - , "full_name": "A.N. Other" - , "organization": "SO" - , "password": "testing" - , "password_confirm": "testing" - , "es_connection": self.es - } - - result = RegisterUser(data) - self.assertNotEqual(len(result.errors), 0, "Organisation name too short. Error expected") - - def testRegisterUserWithNoPassword(self): - data = { - "email_address": "user@example.com" - , "full_name": "A.N. Other" - , "organization": "Some Organisation" - , "password": None - , "password_confirm": None - , "es_connection": self.es - } - - result = RegisterUser(data) - self.assertNotEqual(len(result.errors), 0, "Password not provided. Error was expected") - - def testRegisterUserWithNonMatchingPasswords(self): - data = { - "email_address": "user@example.com" - , "full_name": "A.N. Other" - , "organization": "Some Organisation" - , "password": "testing" - , "password_confirm": "stilltesting" - , "es_connection": self.es - } - - result = RegisterUser(data) - self.assertNotEqual(len(result.errors), 0, "Password mismatch. Error was expected") - - def testRegisterUserWithCorrectData(self): - data = { - "email_address": "user@example.com" - , "full_name": "A.N. Other" - , "organization": "Some Organisation" - , "password": "testing" - , "password_confirm": "testing" - , "es_connection": self.es - } - result = RegisterUser(data) - self.assertEqual(len(result.errors), 0, "All data items provided. Errors were not expected") - -if __name__ == "__main__": - unittest.main() -- cgit v1.2.3