From 9961d9af171ac61a72b69a845c8a8e438676b995 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Mon, 2 Apr 2018 08:51:04 +0000 Subject: Testing moved to Python --- bin/mechnical-rob | 111 ------------------------------------------------------ 1 file changed, 111 deletions(-) delete mode 100755 bin/mechnical-rob (limited to 'bin') diff --git a/bin/mechnical-rob b/bin/mechnical-rob deleted file mode 100755 index be223d94..00000000 --- a/bin/mechnical-rob +++ /dev/null @@ -1,111 +0,0 @@ -#!/usr/bin/env ruby - - -USAGE = <0 - ARGV.shift - else - "http://localhost:5003" - end - -$stderr.print "Testing <",$host,">\n" - -require 'mechanize' -require 'minitest/spec' -require 'minitest/autorun' - -# These are the actual testing modules - -libpath = File.dirname(File.dirname(__FILE__)) -$: << File.join(libpath,'test/lib') - -require 'main_web_functionality' - -if options[:all] or options[:mapping] - require 'mapping' -end - -if options[:all] or options[:link_checker] - require 'link_checker' -end - -if options[:all] or options[:navigation] - require 'navigation' -end -- cgit v1.2.3 From 8145507d6d617554cf996e6cebf286d30ae64df0 Mon Sep 17 00:00:00 2001 From: Pjotr Prins Date: Wed, 4 Apr 2018 16:58:21 +0000 Subject: ES: doc --- bin/genenetwork2 | 18 ++++++++++----- doc/elasticsearch.org | 41 ++++++++++++++++++++++++++++++++++ wqflask/utility/elasticsearch_tools.py | 9 ++++---- wqflask/wqflask/user_manager.py | 23 +++++-------------- 4 files changed, 62 insertions(+), 29 deletions(-) create mode 100644 doc/elasticsearch.org (limited to 'bin') diff --git a/bin/genenetwork2 b/bin/genenetwork2 index 3f06e7f9..18e02388 100755 --- a/bin/genenetwork2 +++ b/bin/genenetwork2 @@ -21,10 +21,18 @@ # # env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_settings.py # -# To run a maintenance script with settings (instead of the webserver) add that with -# a -c switch, e.g. +# To run a maintenance python script with settings (instead of the +# webserver) add that with a -c switch, e.g. # -# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ~/my_overrides.json -c ./wqflask/maintenance/gen_select_dataset.py +# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 -c ./wqflask/maintenance/gen_select_dataset.py +# +# To run any script in the environment +# +# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli echo "HELLO WORLD" +# +# To get a python REPL(!) +# +# env GN2_PROFILE=~/opt/gn-latest-guix ./bin/genenetwork2 ./etc/default_settings.py -cli python # # For development you may want to run # @@ -114,7 +122,6 @@ else export PATH=$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