Difference between revisions of "iRefIndex Release Process"
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* Validation | * Validation | ||
* Parsing the final output files - see [[iRefIndex MITAB Parser]] for details. | * Parsing the final output files - see [[iRefIndex MITAB Parser]] for details. | ||
| + | |||
| + | == Posting the Output Files == | ||
| + | |||
| + | The output files themselves are made available on the iRefIndex FTP site as described on the [[iRefIndex#Data_availability_via_download|iRefIndex information page]]. This involves making a directory in the following local location: | ||
| + | |||
| + | <pre>/biotek/proteas/ftp/irefindex/data/archive</pre> | ||
| + | |||
| + | For example, for the iRefIndex 3.0 release, the following directory hierarchy is created: | ||
| + | |||
| + | <pre>mkdir -p /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi_tab</pre> | ||
| + | |||
| + | The data files are then copied into this new directory. For example: | ||
| + | |||
| + | <pre>cp /home/irefindex/output/*.zip /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi_tab/</pre> | ||
| + | |||
| + | A <tt>README</tt> file should be placed in the directory containing a link to the format description. For example: | ||
| + | |||
| + | <pre> | ||
| + | Please see | ||
| + | |||
| + | http://irefindex.uio.no/wiki/README_iRefIndex_MITAB_3.0 | ||
| + | </pre> | ||
| + | |||
| + | The symbolic link indicating the location of the current release needs to be updated. For iRefIndex 3.0 this is done as follows: | ||
| + | |||
| + | <pre> | ||
| + | cd /biotek/proteas/ftp/irefindex/data | ||
| + | rm current | ||
| + | ln -s archive/release_3.0 current | ||
| + | </pre> | ||
| + | |||
| + | Finally, the <tt>release</tt> file must be updated to indicate the current release number. For iRefIndex 3.0 this contains the following text: | ||
| + | |||
| + | <pre> | ||
| + | release3.0 | ||
| + | </pre> | ||
| + | |||
| + | === Optional/Experimental Output Files === | ||
| + | |||
| + | Additional PSI-MI-XML files may be made available within the release directory within a subdirectory created as follows (for iRefIndex 3.0): | ||
| + | |||
| + | <pre>mkdir -p /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi25xml</pre> | ||
| + | |||
| + | (Instructions on copying these files will be added in future.) | ||
| + | |||
| + | A <tt>README</tt> file should be placed in the directory with the following form: | ||
| + | |||
| + | <pre> | ||
| + | Please see | ||
| + | |||
| + | http://irefindex.uio.no/wiki/README_iRefIndex_PSIMI25XML_3.0 | ||
| + | |||
| + | (This directory contains a sample of iRefIndex data in PSI-MI 2.5 XML format for testing purposes only) | ||
| + | </pre> | ||
[[Category:iRefIndex]] | [[Category:iRefIndex]] | ||
Revision as of 15:17, 6 March 2009
The release process consists of the following activities:
- Build the database - see iRefIndex Build Process for details.
- Generate output files and statistics - see iRefIndex Output and Statistics for details.
- Test the output.
- Post the output files, statistics and release information.
Testing the Output
- Checking for errors and log messages
- Web services
- Spot checks
- Counting XML tags
- Validation
- Parsing the final output files - see iRefIndex MITAB Parser for details.
Posting the Output Files
The output files themselves are made available on the iRefIndex FTP site as described on the iRefIndex information page. This involves making a directory in the following local location:
/biotek/proteas/ftp/irefindex/data/archive
For example, for the iRefIndex 3.0 release, the following directory hierarchy is created:
mkdir -p /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi_tab
The data files are then copied into this new directory. For example:
cp /home/irefindex/output/*.zip /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi_tab/
A README file should be placed in the directory containing a link to the format description. For example:
Please see http://irefindex.uio.no/wiki/README_iRefIndex_MITAB_3.0
The symbolic link indicating the location of the current release needs to be updated. For iRefIndex 3.0 this is done as follows:
cd /biotek/proteas/ftp/irefindex/data rm current ln -s archive/release_3.0 current
Finally, the release file must be updated to indicate the current release number. For iRefIndex 3.0 this contains the following text:
release3.0
Optional/Experimental Output Files
Additional PSI-MI-XML files may be made available within the release directory within a subdirectory created as follows (for iRefIndex 3.0):
mkdir -p /biotek/proteas/ftp/irefindex/data/archive/release_3.0/psimi25xml
(Instructions on copying these files will be added in future.)
A README file should be placed in the directory with the following form:
Please see http://irefindex.uio.no/wiki/README_iRefIndex_PSIMI25XML_3.0 (This directory contains a sample of iRefIndex data in PSI-MI 2.5 XML format for testing purposes only)
