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-rw-r--r--wqflask/base/webqtlConfig.py1
-rw-r--r--wqflask/mock/__init__.py (renamed from wqflask/tests/__init__.py)0
-rw-r--r--wqflask/mock/es_double.py15
-rw-r--r--wqflask/run_gunicorn.py3
-rw-r--r--wqflask/tests/es_double.py30
-rw-r--r--wqflask/tests/test_registration.py113
-rw-r--r--wqflask/utility/elasticsearch_tools.py16
-rw-r--r--wqflask/utility/tools.py42
-rw-r--r--wqflask/wqflask/correlation/show_corr_results.py100
-rw-r--r--wqflask/wqflask/marker_regression/gemma_mapping.py16
-rw-r--r--wqflask/wqflask/user_manager.py7
11 files changed, 133 insertions, 210 deletions
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/tests/__init__.py b/wqflask/mock/__init__.py
index e69de29b..e69de29b 100644
--- a/wqflask/tests/__init__.py
+++ b/wqflask/mock/__init__.py
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/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 "<h1 style='color:blue'>Hello There!</h1>"
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()
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 ec673cf5..8c9fed96 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):
@@ -251,35 +251,29 @@ 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())
+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
@@ -293,7 +287,7 @@ 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:
@@ -305,8 +299,4 @@ 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")
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 )
-
-
diff --git a/wqflask/wqflask/marker_regression/gemma_mapping.py b/wqflask/wqflask/marker_regression/gemma_mapping.py
index a24e43d4..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
+from utility.tools import flat_files, GEMMA_COMMAND, GEMMA_WRAPPER_COMMAND, TEMPDIR, assert_bin, assert_file
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)
@@ -209,8 +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:
@@ -247,4 +253,4 @@ 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
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:
generated by cgit v1.2.3 (git 2.44.0) at 2024-10-20 05:37:54 +0000