Main Page

Welcome to the Wiki of the GGBN Portal Software

Further information about the software will follow soon.

Presentation

TBD

Workflow

TBD

Installation

You will need

• Apache (tested with Apache/2.4.7 (Ubuntu), Apache/2.2.22 (Debian), Apache/2.4.10 (Win64)) with libapache2-mod-php5
• PHP5 (tested with 5.5.9, 5.5.30 and 5.5.15). You also might need to install php5-xsl, php5-gd and php5-mysql.
• a SOLR instance (tested with Apache SOLR 4.9.0). Contact us for getting the appropriate SOLR configuration files.
• a MySQL database (tested with MySQL 5.5.46). It will contain data harvested thanks to B-HIT

Yii (version 2) will be fully contained in the subversion code of the portal software.

Copy a working version from the svn

Create a destination folder, for the rest of this documentation we will choose "my_portal" in your web-folder (ie. /var/www/, or *WINPATH*).
Get http://ww2.biocase.org/svn/dnabank/Dnabank_Portal/ggbn_portal/trunk/ into "my_portal".

Configuration

TBD yii, Apache, rights, SOLR (SOLR config files also & Java)
First, let say we want to access the portal under the URL http://localhost/ggbn_portal.

• Check that the Apache User has writing/editing rights in the whole "my_portal" folder.
• Edit the file "my_portal/frontend/config/main.php".
  • Configure the portal URL: $baseUrl = str_replace ( '/SUBDIR_AFTER_YOUR_WEB_FOLDER/my_portal/frontend/web', '/ggbn_portal', (new Request ())->getBaseUrl () );
  • Configure the MySQL database credentials

                                               'db' => [
                                               'class' => '\yii\db\Connection',
                                               'dsn' => 'mysql:host=IP;dbname=DBNAME',
                                               'username' => 'USER',
                                               'password' => 'PASS',
                                               'charset' => 'utf8' 
                               ],

• Edit the file "my_portal/frontend/config/params.php".
  • e-mails
    • Configure the admin e-mail 'adminEmail' => 'ADMIN@DOMAIN',. The admin will get error/bug messages.
    • Configure the support e-mail(s) 'supportEmail' => ['MAIL1','MAIL2'..],.
    • Configure the feedback e-mail(s) 'feedbackMail' => ['MAIL1','MAIL2'..],. They will get the messages sent with the feedback function.
    • Configure the no-reply-mail (who is supposed to sent e-mail(s) to the users) 'noreplyMail'=>'MAIL'
  • Configure the location of the DarwinCore Archives (harvested with B-HIT) <code>'dwcArchivesPath' => 'PATH_TO_THE_PARENT_FOLDER' ,. Check the access rights! (read is enough)
  • Configure the location(root) of your SOLR instance 'solrhost'=> 'SOLR_HOST' and the SOLR core names

                                               $searchname="SEARCH_CORE";
                                               $previewname="PREVIEW_CORE";
                                               $detailsname="DETAILS_CORE";

• • Set the temporary folder 'tmpFolder'=>'TEMP_FOLDER'. Check the access rights! (write is needed)
  • Configure the options
    • 'useLogin'=>true_OR_false: is the login enabled or disabled
    • 'noBack'=>true_OR_false: a special backbone is used
    • 'shopping'=>true_OR_false: the shopping system is enabled or disabled
    • 'useLogin'=>true_OR_false: is the login enabled or disabled
    • 'newsService'=>true_OR_false: uses the GGBN news services - if it has to be used with a different wiki news, edit the SiteController.py
    • 'displayMore'=>true_OR_false: displays the categories with internal links on the details page
    • 'displayExternals'=>true_OR_false: displays the categories with external links (GBIF, BOLD, NCBI...) on the details page
    • 'ABCDdownloable'=>true_OR_false: ABCD files are downloadable or not
    • 'useAnnosys'=>true_OR_false: link to annosys (annotation system) on the details page
    • 'annosysAP'=>'https://annosys.bgbm.fu-berlin.de/AnnoSys/AnnoSys?providerURL=': root URL for Annosys
    • 'siteName'=>'my_portal',: the portal name (used in the URL)
    • 'siteTitle'=>'GGBN Portal',: the default site name/title

Personalisation

If you want to change the icon (favicon), it is located in frontend/web.
If you want to change the slider images on the home page, they are located in frontend/web/images/slider. Then you will have to modify the view in frontend/view/site/index.php to load the pictures you chose.
If you want to change the menu icons, they are located in frontend/web/images/icons.

The CSS and JS files are also in the frontend/web folder.