From 518be96a310963a4127a0b569a73c91187c02b64 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Thu, 12 Apr 2018 08:20:30 +0000
Subject: README and docs

---
 README.md | 13 ++++++++-----
 1 file changed, 8 insertions(+), 5 deletions(-)

(limited to 'README.md')

diff --git a/README.md b/README.md
index 8221ad65..3e7e64d0 100644
--- a/README.md
+++ b/README.md
@@ -25,7 +25,11 @@ Once installed GN2 can be run online through a browser interface
 ./bin/genenetwork2
 ```
 
-(default is http://localhost:5003/). We are building up automated
+(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).
+
+
+We are building up automated
 testing using [mechanize](https://github.com/genenetwork/genenetwork2/tree/master/test/lib) which can be run with
 
 ```sh
@@ -70,16 +74,15 @@ For more information visit http://www.genenetwork.org/
 
 [![JOSS](http://joss.theoj.org/papers/10.21105/joss.00025/status.svg)](http://joss.theoj.org/papers/10.21105/joss.00025)
 
-GeneNetwork was published in the Journal of Open Source Software as 'GeneNetwork: framework for web-based genetics' by Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert W. WIlliams and Pjotr Prins 
+GeneNetwork was published in the Journal of Open Source Software as 'GeneNetwork: framework for web-based genetics' by Zachary Sloan, Danny Arends, Karl W. Broman, Arthur Centeno, Nicholas Furlotte, Harm Nijveen, Lei Yan, Xiang Zhou, Robert W. WIlliams and Pjotr Prins
 
 You may also cite the software using
 
-[![DOI](https://zenodo.org/badge/5591/genenetwork/genenetwork2.svg)](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2). 
+[![DOI](https://zenodo.org/badge/5591/genenetwork/genenetwork2.svg)](https://zenodo.org/badge/latestdoi/5591/genenetwork/genenetwork2).
 
 ## Contact
 
 IRC on #genenetwork on irc.freenode.net.
 
 Code and primary web service managed by Dr. Robert W. Williams and the
-University of Tennessee Health Science Center, Memphis TN, USA. 
-
+University of Tennessee Health Science Center, Memphis TN, USA.
-- 
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 'README.md')

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


From 96e4efe928773b292f3d3b9b7ef3c23e5ec003fc Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 18 Feb 2019 11:28:41 +0000
Subject: Note on running tests

---
 README.md | 11 ++++++++++-
 1 file changed, 10 insertions(+), 1 deletion(-)

(limited to 'README.md')

diff --git a/README.md b/README.md
index 59645994..c9582d0f 100644
--- a/README.md
+++ b/README.md
@@ -27,9 +27,18 @@ 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
+a Python REPL, for example
+
+```sh
+env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=~/data/gn2_data ./bin/genenetrk2
+```
+
+see the startup script
 [./bin/genenetwork2](https://github.com/genenetwork/genenetwork2/blob/testing/bin/genenetwork2).
 
+Also Mysql and Elasticsearch need to be running, see
+[INSTALL](./doc/README.org).
+
 ## Testing
 
 We are building 'Mechanical Rob' automated testing using Python
-- 
cgit v1.2.3


From 6167e78f7c37b26f5226936e8eff0fe31be8691e Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Mon, 18 Feb 2019 11:32:51 +0000
Subject: typo

---
 README.md | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'README.md')

diff --git a/README.md b/README.md
index c9582d0f..523eeb76 100644
--- a/README.md
+++ b/README.md
@@ -30,7 +30,7 @@ set a number of environment variables), including running scripts and
 a Python REPL, for example
 
 ```sh
-env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=~/data/gn2_data ./bin/genenetrk2
+env GN2_PROFILE=~/opt/gn-latest GENENETWORK_FILES=~/data/gn2_data ./bin/genenetwork2
 ```
 
 see the startup script
-- 
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