Lucene indexes creation - Revision history

Lan@dote.ru: /* Indexes in BioUML server */

2014-12-11T09:47:33Z

‎Indexes in BioUML server

Lan@dote.ru: /* Indexes in BioUML server */

2014-11-18T05:59:10Z

‎Indexes in BioUML server

Lan@dote.ru: /* Indexes in BioUML server */

2014-11-18T05:58:22Z

‎Indexes in BioUML server

Lan@dote.ru: /* Indexes in BioUML server */

2014-11-18T05:58:00Z

‎Indexes in BioUML server

Lan@dote.ru: See also

2013-07-10T04:41:59Z

Lan@dote.ru: Cosmetic

2013-07-10T04:40:31Z

Cosmetic

Lan@dote.ru: Created page with "'''Lucene indexes''' are necessary for Lucene search to work. Indexes are created for each database separately in `databases` collection and stored inside
2013-07-10T04:36:52Z

Created page with "'''Lucene indexes''' are necessary for Lucene search to work. Indexes are created for each database separately in <code>databases</code> collection and stored inside <code..."

New page
'''Lucene indexes''' are necessary for [[Lucene search]] to work. Indexes are created for each database separately in <code>databases</code> collection and stored inside <code>luceneIndexes</code> subfolder of database folder on the disk.

TOC

=== Indexes in BioUML workbench ===
In [[BioUML workbench]] indexes are created automatically when you try to search the corresponding database:

[[File:Lucene_indexes_creation_workbench.png|400px]]

An indexes creation window will appear prompting you on which indexes you want to create. Upon pressing Ok button indexes recreation procedure will start. It may time a lot of time depending on the database:

[[File:Lucene_indexes_creation_workbench_process.png|300px]]

After it finishes you may use the search.

=== Indexes in BioUML server ===
To create indexes in [[BioUML server]] you have to use separate helper application which can be launched using <code>rebuild_indexes.sh</code> (on Unix) or <code>rebuild_indexes.bat</code> (on Windows) script. Place this script into <code>$SERVER_PATH</code> folder (see [[BioUML server installation]]).

This application reads the configuration from <code>rebuild_indexes.properties</code> file, so you have to create one. It contains several rows in <code>key=value</code> manner. The following keys are defined:

;user
:user name (e-mail of the user to log in to BioUML server during indexes creation). This user must be a [[server administrator]] for the current server.
;pass
:password for the specified user
;database
:semicolon-separated list of databases to reindex
;folder
:name of indexes folder. Must be <code>luceneIndex</code>

An example of <code>rebuild_indexes.properties</code> file is shown below.

user=administrator@myserver.example.com
pass=secretAdministratorPassword
database=Ensembl;GO;Reactome
folder=luceneIndex

After this file is created, launch rebuild_indexes script and it will try to create the missing indexes. It's desired to shutdown the BioUML server for the indexes creation procedure.

=== Recreating indexes after the database update ===
When you update the database indexes will become obsolete. The easiest way to update them is to terminate BioUML, remove <code>luceneIndexes</code> subfolder and recreate the indexes using the procedure above.

[[Category:Installation]]

@@ Line 25: / Line 25: @@
 :semicolon-separated list of repository root folders which are necessary for indexes recreation. Eg: ./repo;./resources
 ;modules
-:list of databases to reindex in [[WildcardPathSet]] format (just semicolon separated list of database names will usually work)
+:list of databases to reindex in [[WildcardPathSet]] format (just semicolon separated list of database names started from 'databases/' will usually work)
 An example of <code>rebuild_indexes.properties</code> file is shown below.
@@ Line 31: / Line 31: @@
   user=administrator@myserver.example.com
   pass=secretAdministratorPassword
-  modules=Ensembl;GO;Reactome
+  modules=databases/Ensembl;GO;Reactome
   repositories=repo

@@ Line 25: / Line 25: @@
 :semicolon-separated list of repository root folders which are necessary for indexes recreation. Eg: ./repo;./resources
 ;modules
-:list of databases to reindex in [[WildcardPathSet]] format (just semicolon separated list will work)
+:list of databases to reindex in [[WildcardPathSet]] format (just semicolon separated list of database names will usually work)
 An example of <code>rebuild_indexes.properties</code> file is shown below.

@@ Line 14: / Line 14: @@
 === Indexes in BioUML server ===
-To create indexes in [[BioUML server]] you have to use separate helper application which can be launched using <code>rebuild_indexes.sh</code> (on Unix) or <code>rebuild_indexes.bat</code> (on Windows) script. Place this script into <code>$SERVER_PATH</code> folder (see [[BioUML server installation]]).
+Indexes on BioUML server can be created using administrative analysis [[Rebuild search indexes (analysis)|Rebuild search indexes]].
-−
-This application reads the configuration from <code>rebuild_indexes.properties</code> file, so you have to create one. It contains several rows in <code>key=value</code> manner. The following keys are defined:
-−
-;user
-:user name (e-mail of the user to log in to BioUML server during indexes creation). This user must be a [[server administrator]] for the current server.
-;pass
-:password for the specified user
-;repositories
-:semicolon-separated list of repository root folders which are necessary for indexes recreation. Eg: ./repo;./resources
-;modules
-:list of databases to reindex in [[WildcardPathSet]] format (just semicolon separated list of database names started from 'databases/' will usually work)
-−
-An example of <code>rebuild_indexes.properties</code> file is shown below.
-−
- user=administrator@myserver.example.com
- pass=secretAdministratorPassword
- modules=databases/Ensembl;GO;Reactome
- repositories=repo
-−
-After this file is created, launch rebuild_indexes script and it will try to create the missing indexes. It's desired to shutdown the BioUML server for the indexes creation procedure.
 === Recreating indexes after the database update ===

@@ Line 1: / Line 1: @@
 '''Lucene indexes''' are necessary for [[Lucene search]] to work. Indexes are created for each database separately in <code>databases</code> collection and stored inside <code>luceneIndexes</code> subfolder of database folder on the disk.
 __TOC__
@@ Line 39: / Line 38: @@
 === Recreating indexes after the database update ===
 When you update the database indexes will become obsolete. The easiest way to update them is to terminate BioUML, remove <code>luceneIndexes</code> subfolder and recreate the indexes using the procedure above.
 [[Category:Installation]]