diff options
| -rwxr-xr-x | bin/genenetwork2 | 18 | ||||
| -rw-r--r-- | doc/elasticsearch.org | 41 | ||||
| -rw-r--r-- | wqflask/utility/elasticsearch_tools.py | 9 | ||||
| -rw-r--r-- | wqflask/wqflask/user_manager.py | 30 |
4 files changed, 67 insertions, 31 deletions
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..5f6c818e 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): @@ -437,6 +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 @@ -467,6 +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 = [] @@ -663,8 +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") @@ -742,12 +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: |