Before you use the reBiND archiving system the data must be transformed into a suitable XML format. We use ABCD format (ABCD_in_reBiND) and to create ABCD XML files we recommend using the Biocase Provider Software (BPS). To install this software please follow the installation instructions in the BPS wiki.
reBiND Data Portal Prerequisites
To be able to install the reBiND archiving system you first need to install the eXist database, version 2.0 or later. the eXist database requires 512 MB of RAM and about 200 MB of disk space. The critical requirement is that Java be installed. We have tested the reBiND Data Portal with eXist version 2.1 and Java version 1.7. All software components have been tested on Windows 7 and Debian GNU/Linux 6.
Installing the reBiND Data Portal
The following steps should be carried out to install the reBiND components. After each step we've provided the location of the diectory on Windows where the files should be added or modified assuming that eXist has been installed on the C drive at C:\eXist-db.
- The rebind_module.jar is available from our subversion repository at: subversion rebind module. Add the rebind_module.jar to the eXist/lib/user directory. (on Windows C:\eXist-db\lib\user).
- Copy the folder called rebind (available from our subersion repository) to eXist/webapp (on Windows C:\eXist-db\webapp).
Configuring the reBiND Data Portal
- Register the rebind-module by editing the eXist configuration file - eXist/conf.xml (on Windows C:\eXist-db\conf.xml). The following lines should be added within the <builtin-modules> element in the conf.xml:
- Add the settings.conf file to the eXist-root (available from our subversion repository at http://ww2.biocase.org/svn/rebind/trunk/configuration/settings.conf). On Windows C:\eXist-db\settings.conf)
- (Optional) In eXist-root/webapp/controller.xql replace lines 37-40 (within the <dispatch> element) with.:
- In eXist-root/webapp/WEB-INF/web.xml add the following at line 371:
<!-- modules for reBiND --> <?xml version='1.0' encoding='UTF-8'?> <module class="org.exist.xquery.modules.datetime.DateTimeModule" uri="http://exist-db.org/xquery/datetime"/> <module class="org.exist.backup.xquery.BackupModule" uri="http://exist-db.org/xquery/backups"/> <!-- Custom reBiND Module --> <module class="org.bgbm.rebind.exist.module.RebindModule" uri="http://rebind.bgbm.org/code/module"/>
Consult the eXist documentation for further details about the module system.
This ensures the host URL formards to the homepage with the login to the rebind portal.
<filter-mapping> <filter-name>XFormsFilter</filter-name> <url-pattern>/rebind/*</url-pattern> </filter-mapping>
Using the eXist Java admin client to prepare the database
- Open the Java webstart admin client. There are several ways of launching the client. These are documented in detail on the eXist web-site/.
- When prompted enter the password for the admin user. This should have already been set during eXist installation.
- Download the eXist db directory from our svn repository (this contains database files that must be stored directly in eXist).
- In the admin client navigate to db/apps and create a new collection called eXide2.
- In the Tools menu of the admin client click 'Restore'. Then use the file browser to select the file to restore - in this case db/apps/eXide2/_contents_.xml from svn (see step 3).
- Navigate back to the base collection in the admin client and create a collection called 'rebind'. Create the following child collections of 'rebind':
- Navigate to each child collection and restore the corresponding data files from svn as in step 5.
For example navigate to /db/correction and restore the data with data from http://ww2.biocase.org/svn/rebind/trunk/exist-db/db/rebind/correction
(Note the public and protected collections listed above remain empty until data is stored in eXist via the reBiND workflow.)