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GN1 annotation page broken


  • assigned: zsloan, pjotrp
  • priority: high
  • status: testing
  • type: bug
  • keywords: GN1, genenetwork1, annotation, from github


  • [ ] Fix PHP view
  • [ ] Fix CKEDITOR


Turns out that it is a PHP page that is not working. Also CKEDITOR is not visible.

is broken. An exception stack trace is displayed, instead of the annotations page content.


Lily runs a PHP from 2006(!)

PHP 5.1.6 (cli) (built: Mar 18 2014 20:48:55) Copyright (c) 1997-2006 The PHP Group Zend Engine v2.1.0, Copyright (c) 1998-2006 Zend Technologies

In guix-bioinformatics we have

php     5.6.40  out     /home/gn1/guix-bioinformatics/gn/packages/php.scm:14:2

Even if this page is for windows, it is the best description of using PHP:

On lily:

AddType application/x-httpd-php .htm .html

And Apache:

[root@lily conf]# /usr/sbin/httpd -V
Server version: Apache/2.2.3
Server built:   Sep 16 2014 11:05:09
Server's Module Magic Number: 20051115:3
Server loaded:  APR 1.2.7, APR-Util 1.2.7
Compiled using: APR 1.2.7, APR-Util 1.2.7
Architecture:   64-bit
Server MPM:     Prefork
  threaded:     no
    forked:     yes (variable process count)
Server compiled with....
 -D APACHE_MPM_DIR="server/mpm/prefork"
 -D APR_HAVE_IPV6 (IPv4-mapped addresses enabled)
 -D HTTPD_ROOT="/etc/httpd"
 -D SUEXEC_BIN="/usr/sbin/suexec"
 -D DEFAULT_PIDLOG="run/httpd.pid"
 -D DEFAULT_SCOREBOARD="logs/apache_runtime_status"
 -D DEFAULT_LOCKFILE="logs/accept.lock"
 -D DEFAULT_ERRORLOG="logs/error_log"
 -D AP_TYPES_CONFIG_FILE="conf/mime.types"
 -D SERVER_CONFIG_FILE="conf/httpd.conf"

This is similar what we have in Guix GN1. No mention of PHP in either.

For simplicity we may switch to php-cgi

Test instance of GN1

I started a test instance that listens on port 8044 and is hosted in this dir and started with:

. .guix-deploy
gn1@tux01 ~/production/gnshare/gn-pjotr-test [env]$ httpd -f `pwd`/etc/pjotr-test-httpd.conf

Restart with

pkill httpd ; sleep 1 ; httpd -f `pwd`/etc/pjotr-test-httpd.conf

Created a file in web/test/index.html and it displays as

Now a php version

works after setting

# CUSTOM: Add PHP 5 parsing (via CGI) handler and action
ScriptAlias /local-bin /gnu/store/213zqkj0r6q41cqarwkz5x568ybhd62b-profile/bin
AddHandler application/x-httpd-php5 php
Action application/x-httpd-php5 /local-bin/php-cgi
<Directory "/usr/local/bin">
    Order allow,deny
    Allow from all

<Directory /home/gn1/production/gnshare/gn-pjotr-test/web/test>
    AllowOverride None
    Order allow,deny
    Allow from all

Finding PHP files

All files that have ?php are in ./infoshare. Try

gn1@tux01:~/production/gnshare/gn-pjotr-test$ grep '?php' -r > phpfiles.txt

they end in .htm and .html so we need to wire that together.

So adding a test in

and updating Addhandler to parse .htm and .html works.

AddHandler application/x-httpd-php5 php htm html

MySQL connector

We need to tell GN1 to use a more recent mysql connector and drive it over sockets, rather than the web interface. This requires telling it where the INI file is.

This required adding a path for Apache:

SetEnv PHP_INI_SCAN_DIR /home/gn1/production/gnshare/gn-pjotr-test

and a php.ini file with

pdo_mysql.default_socket= /run/mysqld/mysqld.sock

mysqli.default_socket = /run/mysqld/mysqld.sock

Now it remains to replace the mysql connectors with mysqli - a newer driver for PHP. For this we use a translation script from

that gets included with


At the final step we have to fix CKEDITOR


FF console says:

Uncaught ReferenceError: CKEDITOR is not defined
    <anonymous> Ember

Turns out that lily URLs were hard-coded in the source. So, that was an easy fix. There are still some complaints about CSS links missing in the browser console, but until someone sees a difference I does not need fixing.

Changing the status to testing now.

Updating production

The source code is now in sync on 'master' branch. Now I need to update guix-bioinformatics package to set up the container correctly with Apache httpd.conf.

(made with skribilo)