Changes between Initial Version and Version 1 of Configuration


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Timestamp:
Jun 29, 2011, 11:12:06 AM (8 years ago)
Author:
robert@…
Comment:

Initial setup of configuration documentation

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  • Configuration

    v1 v1  
     1= Configuration =
     2You can configure the sequencing module by editing the file
     3{{{
     4  ~/grails-config/[environment]-massSequencing.properties
     5}}}
     6where [environment] will be the environment the war has been created for. Normally this will be 'prod'. If you have created your own package, the environment name might be different.
     7
     8== File contents ==
     9The file might look like the following
     10{{{
     11# server URL
     12grails.serverURL=http://massSequencing.dbnp.org
     13
     14# DATABASE
     15dataSource.driverClassName=org.postgresql.Driver
     16dataSource.dialect=org.hibernate.dialect.PostgreSQLDialect
     17dataSource.url=jdbc:postgresql://localhost:5432/metagenomics-test
     18dataSource.dbCreate=update
     19dataSource.username=metagenomics
     20dataSource.password=dbnp
     21#dataSource.logSql=true
     22
     23# GSCF configuration - in order to synchronize correctly
     24gscf.baseURL=http://studies.dbnp.org
     25massSequencing.consumerID=http://metagenomics.dbnp.org
     26massSequencing.synchronization = true
     27
     28# File uploads
     29massSequencing.fileUploadDir=/tmp/metagenomics/temp
     30massSequencing.fileDir=/tmp/metagenomics/permanent
     31
     32# Filename of the (.fna, .qual and .oligos) files that are exported
     33massSequencing.exportFilename=1.TCA.454Reads
     34}}}
     35
     36== Parameters ==
     37The different options you can set are:
     38
     39'''grails.serverURL'''::
     40  The url where this module is placed on. Don't add a trailing /
     41'''database.*'''::
     42  Datasource configuration. See http://grails.org/doc/latest/guide/3.%20Configuration.html#3.3%20The%20DataSource
     43'''gscf.baseURL''':
     44  Base URL of GSCF instance. Don't add a trailing /
     45'''massSequencing.consumerID'''::
     46  Consumer ID describing this module. This is used for synchronization with GSCF. Set to the same value as '''grails.serverURL''', unless you know what you're doing.
     47'''massSequencing.synchronization'''::
     48  If set to true, the module will synchronize its studies with GSCF. If set to false, this module won't communicate with GSCF for synchronization (only for authorization). However, if set to false, you won't be able to add any data to the system. So use it only if you know what you're doing.
     49'''massSequencing.fileUploadDir'''::
     50  Directory where uploaded files will be permanently stored. This is used for sequence files, quality files etc. that have been associated with a sample. If the directory is given relative (e.g. 'fileuploads/temp'), it is taken relative to the web-app directory. Otherwise, it should be given as an absolute path (e.g. '/home/user/sequences'). The directory should be writable by the webserver user
     51'''massSequencing.fileDir'''::
     52  Directory where uploaded files will be temporarily stored. This directory is used to store files when they are just uploaded. Files in this directory will be deleted when they are older than ''massSequencing.fileUploadMaxAge''. If the directory is given relative (e.g. 'fileuploads/temp'), it is taken relative to the web-app directory. Otherwise, it should be given as an absolute path (e.g. '/home/user/sequences'). The directory should be writable by the webserver user
     53'''massSequencing.fileUploadMaxAge'''::
     54  Maximum age that uploaded files should be kept on the server before deleting them. When a user uploads a file, but doesn't process the file (e.g. because he leaves the page beforehand or his computer crashes), the files remain in the upload directory. This mechanism ensures that the upload directory is cleaned after some time. The time is given in seconds.