From 8145507d6d617554cf996e6cebf286d30ae64df0 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 4 Apr 2018 16:58:21 +0000
Subject: ES: doc
---
bin/genenetwork2 | 18 ++++++++++-----
doc/elasticsearch.org | 41 ++++++++++++++++++++++++++++++++++
wqflask/utility/elasticsearch_tools.py | 9 ++++----
wqflask/wqflask/user_manager.py | 23 +++++--------------
4 files changed, 62 insertions(+), 29 deletions(-)
create mode 100644 doc/elasticsearch.org
diff --git a/bin/genenetwork2 b/bin/genenetwork2
index 3f06e7f9..18e02388 100755
--- a/bin/genenetwork2
+++ b/bin/genenetwork2
@@ -21,10 +21,18 @@
#
# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_settings.py
#
-# To run a maintenance script with settings (instead of the webserver) add that with
-# a -c switch, e.g.
+# To run a maintenance python script with settings (instead of the
+# webserver) add that with a -c switch, e.g.
#
-# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py
+# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 -c ./wqflask/maintenance/gen_select_dataset.py
+#
+# To run any script in the environment
+#
+# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD"
+#
+# To get a python REPL(!)
+#
+# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli python
#
# For development you may want to run
#
@@ -114,7 +122,6 @@ else
export PATH=$GN2_PROFILE/bin:$PATH
export PYTHONPATH="$GN2_PROFILE/lib/python2.7/site-packages" # never inject another PYTHONPATH!!
export R_LIBS_SITE=$GN2_PROFILE/site-library
- export GEM_PATH=$GN2_PROFILE/lib/ruby/gems/2.4.0
export JS_GUIX_PATH=$GN2_PROFILE/share/genenetwork2/javascript
export GUIX_GTK3_PATH="$GN2_PROFILE/lib/gtk-3.0"
export GI_TYPELIB_PATH="$GN2_PROFILE/lib/girepository-1.0"
@@ -134,7 +141,6 @@ else
done
done <<< "$PYTHONPATH"
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
fi
if [ -z $PYTHONPATH ] ; then
echo "ERROR PYTHONPATH has not been set - use GN2_PROFILE!"
@@ -170,9 +176,9 @@ if [ "$1" = '-c' ] ; then
python $cmd $*
exit $?
fi
+
# Now handle command parameter -cli which runs in bash
if [ "$1" = "-cli" ] ; then
- echo "HERE"
cd $GN2_BASE_DIR/wqflask
cmd=$2
echo PYTHONPATH=$PYTHONPATH
diff --git a/doc/elasticsearch.org b/doc/elasticsearch.org
new file mode 100644
index 00000000..18adfc8b
--- /dev/null
+++ b/doc/elasticsearch.org
@@ -0,0 +1,41 @@
+* Elasticsearch
+
+To get the right environment, first you can get a python REPL with something like
+
+: env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ../etc/default_settings.py -cli python
+
+(make sure to use the correct GN2_PROFILE!)
+
+Next try
+
+#+BEGIN_SRC python
+
+from elasticsearch import Elasticsearch, TransportError
+
+es = Elasticsearch([{ "host": 'localhost', "port": '9200' }])
+
+# Dump all data
+
+es.search("*")
+
+# To fetch an E-mail record from the users index
+
+record = es.search(
+ index = 'users', doc_type = 'local', body = {
+ "query": { "match": { "email_address": "myname@email.com" } }
+ })
+
+# It is also possible to do wild card matching
+
+q = { "query": { "wildcard" : { "full_name" : "pjot*" } }}
+es.search(index = 'users', doc_type = 'local', body = q)
+
+# To get elements from that record:
+
+record['hits']['hits'][0][u'_source']['full_name']
+u'Pjotr'
+
+record['hits']['hits'][0][u'_source']['email_address']
+u"myname@email.com"
+
+#+END_SRC
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 734379f7..1dba357d 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -12,6 +12,7 @@ def test_elasticsearch_connection():
logger.warning("Elasticsearch is DOWN")
def get_elasticsearch_connection():
+ """Return a connection to ES. Returns None on failure"""
logger.info("get_elasticsearch_connection")
es = None
try:
@@ -20,14 +21,14 @@ def get_elasticsearch_connection():
logger.info("ES HOST",ELASTICSEARCH_HOST)
es = Elasticsearch([{
- "host": ELASTICSEARCH_HOST
- , "port": ELASTICSEARCH_PORT
+ "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
}]) if (ELASTICSEARCH_HOST and ELASTICSEARCH_PORT) else None
es_logger = logging.getLogger("elasticsearch")
es_logger.setLevel(logging.INFO)
es_logger.addHandler(logging.NullHandler())
except:
+ logger.error("Failed to get elasticsearch connection")
es = None
return es
@@ -42,9 +43,7 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
item_details = None
try:
response = es.search(
- index = index
- , doc_type = doc_type
- , body = {
+ index = index, doc_type = doc_type, body = {
"query": { "match": { column_name: column_value } }
})
if len(response["hits"]["hits"]) > 0:
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index ac3824a7..ead919fc 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -1,45 +1,30 @@
from __future__ import print_function, division, absolute_import
-"""Used to Access things in template like this:
-(BUT NOW OUT OF DATE)
-
- x: {{ g.identity.name }}
- security: {{ security.__dict__ }}
-
-"""
-
import os
import hashlib
import datetime
import time
import logging
-
import uuid
import hashlib
import hmac
import base64
-
import urlparse
import simplejson as json
#from redis import StrictRedis
-import redis
+import redis # used for collections
Redis = redis.StrictRedis()
-
from flask import (Flask, g, render_template, url_for, request, make_response,
redirect, flash, abort)
from wqflask import app
-
-
from pprint import pformat as pf
-from wqflask import pbkdf2
-
+from wqflask import pbkdf2 # password hashing
from wqflask.database import db_session
-
from wqflask import model
from utility import Bunch, Struct, after
@@ -62,8 +47,8 @@ THREE_DAYS = 60 * 60 * 24 * 3
def timestamp():
return datetime.datetime.utcnow().isoformat()
-
class AnonUser(object):
+ """Anonymous user handling"""
cookie_name = 'anon_user_v8'
def __init__(self):
@@ -169,6 +154,8 @@ def create_signed_cookie():
return the_uuid, uuid_signed
class UserSession(object):
+ """Logged in user handling"""
+
cookie_name = 'session_id_v2'
def __init__(self):
--
cgit v1.2.3
From 273c72ef02f839b88b3d2ad504e9d84eab0f9ec5 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Wed, 4 Apr 2018 17:10:14 +0000
Subject: Authentication: comments added
---
wqflask/wqflask/user_manager.py | 7 +++++--
1 file changed, 5 insertions(+), 2 deletions(-)
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index ead919fc..5f6c818e 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -424,6 +424,7 @@ def verify_email():
@app.route("/n/password_reset", methods=['GET'])
def password_reset():
+ """Entry point after user clicks link in E-mail"""
logger.debug("in password_reset request.url is:", request.url)
# We do this mainly just to assert that it's in proper form for displaying next page
# Really not necessary but doesn't hurt
@@ -454,6 +455,7 @@ def password_reset():
@app.route("/n/password_reset_step2", methods=('POST',))
def password_reset_step2():
+ """Handle confirmation E-mail for password reset"""
logger.debug("in password_reset request.url is:", request.url)
errors = []
@@ -650,8 +652,6 @@ class LoginUser(object):
VerificationEmail(user)
return render_template("new_security/verification_still_needed.html",
subject=VerificationEmail.subject)
-
-
if valid:
if params.get('remember'):
logger.debug("I will remember you")
@@ -729,12 +729,15 @@ def logout():
@app.route("/n/forgot_password")
def forgot_password():
+ """Entry point for forgotten password"""
return render_template("new_security/forgot_password.html")
@app.route("/n/forgot_password_submit", methods=('POST',))
def forgot_password_submit():
+ """When a forgotten password form is submitted we get here"""
params = request.form
email_address = params['email_address']
+ logger.debug("Wants to send password E-mail to ",email_address)
es = get_elasticsearch_connection()
user_details = get_user_by_unique_column(es, "email_address", email_address)
if user_details:
--
cgit v1.2.3