From 3a26e0fb7b88cd9c105a1f7e9ca9d5a8b2130d82 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 15 Feb 2018 15:00:47 +0000
Subject: Requests added

---
 bin/test-website | 114 +++----------------------------------------------------
 1 file changed, 5 insertions(+), 109 deletions(-)

(limited to 'bin/test-website')

diff --git a/bin/test-website b/bin/test-website
index be223d94..5935f016 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -1,111 +1,7 @@
-#!/usr/bin/env ruby
+#! /bin/bash
 
-
-USAGE = <<EOT
-This is Mechanical-Rob - an automated web server tester for
-                         Genenetwork.org that uses the brilliant
-                         mechanize gem with minitest.
-
-To use this software you need to install mechanize. Run it from
-the root of the genenetwork2 source tree as, for example,
-
-  ./bin/test-website http://localhost:5003/ (default)
-
-If you are using the small deployment database you can use
-
-  ./bin/test-website --skip -n
-
-To run all tests
-
-  ./bin/test-website --all
-
-To run individual tests on localhost you can do
-
-  ruby -Itest -Itest/lib test/lib/mapping.rb --name="/Mapping/"
-
-For more information see http://genenetwork.org/
-
-EOT
-$stderr.print USAGE
-
-require 'optparse'
-
-options = { database: :small, link_checker: false}
-opts = OptionParser.new do |o|
-  o.banner = "Usage: #{File.basename($0)} [options] URL"
-
-  o.on('-d','--database', String, 'Use database (default db_webqtl_s)') do |s|
-    options[:database] =
-      case s
-      when 'xx'
-        :unknown
-      else
-        :small
-      end
-  end
-
-  o.on('--all', 'Run all tests') do
-    options[:all] = true
-  end
-
-  o.on('-l','--link-checker', 'Check for dead links') do
-    options[:link_checker] = true
-  end
-
-  o.on('--navigation', 'Check for navigation') do
-    options[:navigation] = true
-  end
-
-  o.on('--mapping', 'Check for mapping') do
-    options[:mapping] = true
-  end
-
-  o.on('--skip-broken', 'Skip tests that are known to be broken') do
-    options[:skip_broken] = true
-  end
-
-  o.separator ""
-  o.on_tail('-h', '--help', 'display this help and exit') do
-    options[:show_help] = true
-  end
-end
-
-opts.parse!(ARGV)
-
-if options[:show_help]
-  print opts
+if [ -z $GN2_PROFILE ]; then
+  echo "Run request tests with something like"
+  echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003
   exit 1
-end
-
-$options = options  # we are using a global here
-$host =
-  if ARGV.size>0
-    ARGV.shift
-  else
-    "http://localhost:5003"
-  end
-
-$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
+fi
-- 
cgit v1.2.3


From dda4697505aea2cd950533dfb3a0dfb0e66ec018 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 16 Apr 2018 09:00:52 +0000
Subject: Docs on elasticsearch use

---
 README.md                              | 24 ++++++++++++++------
 bin/test-website                       |  2 +-
 wqflask/utility/elasticsearch_tools.py | 41 ++++++++++++++++++++++++++++++++++
 3 files changed, 59 insertions(+), 8 deletions(-)

(limited to 'bin/test-website')

diff --git a/README.md b/README.md
index 3e7e64d0..59645994 100644
--- a/README.md
+++ b/README.md
@@ -17,25 +17,35 @@ deploy GN2 and dependencies as a self contained unit on any machine.
 The database can be run separately as well as the source tree (for
 developers).  See the [installation docs](doc/README.org).
 
-## Test
+## Run
 
 Once installed GN2 can be run online through a browser interface
 
 ```sh
-./bin/genenetwork2
+genenetwork2
 ```
 
-(default is http://localhost:5003/). For more examples, including running scripts and a Python REPL
-see the startup script [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
+(default is http://localhost:5003/). For full examples (you'll need to
+set a number of environment variables), including running scripts and
+a Python REPL, see the startup script
+[./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
 
+## Testing
 
-We are building up automated
-testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with
+We are building 'Mechanical Rob' automated testing using Python
+[requests](https://github.com/genenetwork/genenetwork2/tree/master/test/lib)
+which can be run with something like
 
 ```sh
-./bin/test-website
+env GN2_PROFILE=~/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003
 ```
 
+The GN2_PROFILE is the Guix profile that contains all
+dependencies. The ./bin/genenetwork2 script sets up the environment
+and executes test-website.py in a Python interpreter. The -a switch
+says to run all tests and the URL points to the running GN2 http
+server.
+
 ## Documentation
 
 User documentation can be found
diff --git a/bin/test-website b/bin/test-website
index 5935f016..7fbcfd2f 100755
--- a/bin/test-website
+++ b/bin/test-website
@@ -2,6 +2,6 @@
 
 if [ -z $GN2_PROFILE ]; then
   echo "Run request tests with something like"
-  echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003
+  echo env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py -a http://localhost:5003
   exit 1
 fi
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 7d2ee8c9..4d4a9844 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -1,3 +1,44 @@
+# Elasticsearch support
+#
+# Some helpful commands to view the database:
+#
+# You can test the server being up with
+#
+#   curl -H 'Content-Type: application/json' http://localhost:9200
+#
+# List all indices
+#
+#   curl -H 'Content-Type: application/json' 'localhost:9200/_cat/indices?v'
+#
+# To see the users index 'table'
+#
+#   curl http://localhost:9200/users
+#
+# To list all user ids
+#
+# curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d '
+# {
+#     "query" : {
+#         "match_all" : {}
+#     },
+#     "stored_fields": []
+# }'
+#
+# To view a record
+#
+#   curl -H 'Content-Type: application/json' http://localhost:9200/users/local/_search?pretty=true -d '
+#   {
+#     "query" : {
+#       "match" : { "email_address": "pjotr2017@thebird.nl"}
+#     }
+#   }'
+#
+#
+# To delete the users index and data (dangerous!)
+#
+#   curl -XDELETE -H 'Content-Type: application/json' 'localhost:9200/users'
+
+
 from elasticsearch import Elasticsearch, TransportError
 import logging
 
-- 
cgit v1.2.3