Revision as of 16:44, 11 January 2016

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

Minor configurations
- - 'siteName'=>'my_portal',: the portal name (used in the URL)

***'siteTitle'=>'GGBN Portal',: the default site name/title

@@ Line 30: / Line 30: @@
 *Check that the Apache User has writing/editing rights in the whole "my_portal" folder.
-#Edit the file "my_portal/frontend/config/main.php".
+*Edit the file "my_portal/frontend/config/main.php".
-*Configure the portal URL: <code>$baseUrl = str_replace ( '/SUBDIR_AFTER_YOUR_WEB_FOLDER/my_portal/frontend/web', '/ggbn_portal', (new Request ())->getBaseUrl () );</code>
+**Configure the portal URL: <code>$baseUrl = str_replace ( '/SUBDIR_AFTER_YOUR_WEB_FOLDER/my_portal/frontend/web', '/ggbn_portal', (new Request ())->getBaseUrl () );</code>
-*Configure the MySQL database credentials <code>
+**Configure the MySQL database credentials <code>
                                                  'db' => [
                                                  'class' => '\yii\db\Connection',
@@ Line 40: / Line 40: @@
                                                  'charset' => 'utf8'
                                  ],</code>
-#Edit the file "my_portal/frontend/config/params.php".
+*Edit the file "my_portal/frontend/config/params.php".
-*e-mails
+**e-mails
-**Configure the admin e-mail <code>'adminEmail' => 'ADMIN@DOMAIN',</code>. The admin will get error/bug messages.
+***Configure the admin e-mail <code>'adminEmail' => 'ADMIN@DOMAIN',</code>. The admin will get error/bug messages.
-**Configure the support e-mail(s) <code>'supportEmail' => ['MAIL1','MAIL2'..],</code>.
+***Configure the support e-mail(s) <code>'supportEmail' => ['MAIL1','MAIL2'..],</code>.
-**Configure the feedback e-mail(s) <code>'feedbackMail' => ['MAIL1','MAIL2'..],</code>. They will get the messages sent with the feedback function.
+***Configure the feedback e-mail(s) <code>'feedbackMail' => ['MAIL1','MAIL2'..],</code>. 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) <code>'noreplyMail'=>'MAIL'
+***Configure the no-reply-mail (who is supposed to sent e-mail(s) to the users) <code>'noreplyMail'=>'MAIL'
-*Configure the location of the DarwinCore Archives (harvested with B-HIT) <code>'dwcArchivesPath' => 'PATH_TO_THE_PARENT_FOLDER' ,</code>. Check the access rights! (read is enough)
+**Configure the location of the DarwinCore Archives (harvested with B-HIT) <code>'dwcArchivesPath' => 'PATH_TO_THE_PARENT_FOLDER' ,</code>. Check the access rights! (read is enough)
-*Configure the location(root) of your SOLR instance <code>'solrhost'=> 'SOLR_HOST'</code> and the SOLR core names
+**Configure the location(root) of your SOLR instance <code>'solrhost'=> 'SOLR_HOST'</code> and the SOLR core names
 <code>
                                                  $searchname="SEARCH_CORE";
@@ Line 53: / Line 53: @@
                                                  $detailsname="DETAILS_CORE";
 </code>
-*Set the temporary folder <code>'tmpFolder'=>'TEMP_FOLDER'</code>. Check the access rights! (write is needed)
+**Set the temporary folder <code>'tmpFolder'=>'TEMP_FOLDER'</code>. Check the access rights! (write is needed)
+**Configure the options
+***<code>'useLogin'=>true_OR_false</code>: is the login enabled or disabled
+***<code>'noBack'=>true_OR_false</code>: a special backbone is used
+***<code>'shopping'=>true_OR_false</code>: the shopping system is enabled or disabled
+***<code>'useLogin'=>true_OR_false</code>: is the login enabled or disabled
+***<code>'newsService'=>true_OR_false</code>: uses the GGBN news services - if it has to be used with a different wiki news, edit the SiteController.py
+***<code>'displayMore'=>true_OR_false</code>: displays the categories with internal links on the details page
+***<code>'displayExternals'=>true_OR_false</code>: displays the categories with external links (GBIF, BOLD, NCBI...) on the details page
+***<code>'ABCDdownloable'=>true_OR_false</code>: ABCD files are downloadable or not
+***<code>'useAnnosys'=>true_OR_false</code>: link to annosys (annotation system) on the details page
+***<code>'annosysAP'=>'https://annosys.bgbm.fu-berlin.de/AnnoSys/AnnoSys?providerURL='</code>: root URL for Annosys
+*Minor configurations
+***<code>'siteName'=>'my_portal',</code>: the portal name (used in the URL)
+ ***<code>'siteTitle'=>'GGBN Portal',</code>: the default site name/title

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Revision as of 16:44, 11 January 2016

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Copy a working version from the svn

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