Difference between revisions of "Session files"

Revision as of 14:32, 25 October 2013

Present your data through a Java Web Start session (recommended)

Instead of putting all files in the URL as explained in the previous section, you can also point GenomeView to a so called session file which contains a list of files which need to be loaded.

An example session file: http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php

You can use 'View source', or something similar, in your browser to see the actual file structure. It is a plain text file with on each line a file that needs to be loaded.

Make sure it starts with the line ##GenomeView session -- DO NOT...., as in the example. This header is used to detect the file format by GenomeView.

You can add a C line at the top which would contain the link to the configuration file. It is important this line is the first one after the header.

The U lines are links to data files, you can include as many as you want.

The URL to start GenomeView with this sesssion would be: http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php

Important: You should use the JNLP file we provide as it will integrate the parameters into the start-up parameters of the webstart application.

Typically you don't even have to expose this URL and you can use an index.php that redirects to that location. header("Location: http://genomeview.org/start/launch.jnlp?--session http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/session.php"); Session file format specification

A session files consists out of 1 header line and 1 or more information lines.

The header line should start with ##GenomeView session. This should be included literally (case-sensitive). The first line is the information GenomeView will use to detect the file format, in this case a session.

The information lines consists of a letter key and the actual data. The different key letters are defined in the table below. The key and the data are separated with a single space, colon or tab.

Keyword*	Data
CONFIG	URL or local file path to the configuration file. This line should be the first in the session file, otherwise some data may not have the correct configuration file when initializing.
DATA**	URL or local file path for a data file. This file will be loaded. You do not need to specify the index, GenomeView will look for it in the same folder.
PREFIX	URL or local file path prefix. The value of this instructions will be prepended to any DATA or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value.
OPTION	Key=value definition of a single configuration option. This is suited to override a few config options as needed.
ALIAS [primary name]=[alternative name].	Add an additional synonym for an Entry (chromosome). This can be useful if your data has different identifiers for the same sequence in different files. The primary name will be used to connect the data types.
LOCATION	Set the visible location to the specified location. The location needs to be specified [entry]:[start position]-[end position].
PLUGIN	Allows you to request the user to automatically install a plugin. The plugin needs to be specified as a URL to the zip file. You can use relative names in conjunction with the PREFIX parameter

Must be upper-case
- The legacy keywords C, U and F will continue to work.

Example session file:

##GenomeView session -- DO NOT DELETE THIS LINE
CONFIG http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/tbconfig.txt
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/MT_H37RV_V2.fasta
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/annotation.gff
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/operon.gff
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/sRNA.gff
DATA http://www.broadinstitute.org/software/genomeview/genomes/mtb_h37rv_v2/rRNA.gff

@@ Line 28: / Line 28: @@
 The information lines consists of a letter key and the actual data. The different key letters are defined in the table below. The key and the data are separated with a single space, colon or tab.
-Keyword*	Data
-CONFIG	URL or local file path to the configuration file. This line should be the first in the session file, otherwise some data may not have the correct configuration file when initializing.
+{|
-DATA**	URL or local file path for a data file. This file will be loaded. You do not need to specify the index, GenomeView will look for it in the same folder.
+!Keyword*
-PREFIX	URL or local file path prefix. The value of this instructions will be prepended to any DATA or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value.
+!Data
-OPTION	Key=value definition of a single configuration option. This is suited to override a few config options as needed.
+|-
-ALIAS	[primary name]=[alternative name]. Add an additional synonym for an Entry (chromosome). This can be useful if your data has different identifiers for the same sequence in different files. The primary name will be used to connect the data types.
+|CONFIG
-LOCATION	Set the visible location to the specified location. The location needs to be specified [entry]:[start position]-[end position].
+|URL or local file path to the configuration file. This line should be the first in the session file, otherwise some data may not have the correct configuration file when initializing.
-PLUGIN	Allows you to request the user to automatically install a plugin. The plugin needs to be specified as a URL to the zip file. You can use relative names in conjunction with the PREFIX parameter
+|-
+|DATA**
+|URL or local file path for a data file. This file will be loaded. You do not need to specify the index, GenomeView will look for it in the same folder.
+|-
+|PREFIX
+|URL or local file path prefix. The value of this instructions will be prepended to any DATA or CONFIG pairs that follow this instruction. A PREFIX values is only valid for subsequent DATA and CONFIG pairs. This can to simplify loading many files from multiple locations. To reset the PREFIX, you can use an empty value.
+|-
+|OPTION
+|Key=value definition of a single configuration option. This is suited to override a few config options as needed.
+|-
+|ALIAS	[primary name]=[alternative name].
+|Add an additional synonym for an Entry (chromosome). This can be useful if your data has different identifiers for the same sequence in different files. The primary name will be used to connect the data types.
+|-
+|LOCATION
+|Set the visible location to the specified location. The location needs to be specified [entry]:[start position]-[end position].
+|-
+|PLUGIN
+|Allows you to request the user to automatically install a plugin. The plugin needs to be specified as a URL to the zip file. You can use relative names in conjunction with the PREFIX parameter
+|}
 * Must be upper-case
 ** The legacy keywords C, U and F will continue to work.

Difference between revisions of "Session files"

Revision as of 14:32, 25 October 2013

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