git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@363 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@362 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

We previously used the NCBI mapping data for the current build, but now a new
build was just released, the mapping data is missing (they are waiting for the
data and it should be up soon).

For now, we just use the mapping data for the archived previous build (it is
the build we were using until now anyway).


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@361 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@360 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Added a ping() function to the webservice.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@359 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@358 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@357 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@356 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Added an optional versions parameter to the getTranscripts function.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@355 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@354 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@353 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@352 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@351 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@350 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Add user configuration files from post-install script.
Fix bug in post-install script (failed at importing mapping data).
Suppress console warnings from mapping update script.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@349 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@348 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@347 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@346 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@345 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@344 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@343 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Convert the 'hg18.map' and 'hg19.map' tables are to 'hg18.Mapping' and
'hg19.Mapping'. These tables are now updated with mapping info from the
NCBI instead of the UCSC.

Also added database and configuration file migration scripts.

extras/config.example:
- Remove configuration values for UCSC updates.

extras/post-install.sh:
mutalyzer/Mapper.py:
mutalyzer/Db.py:
- Use 'Mapping' table instead of 'map' table.

extras/cron.d/mutalyzer-mapping-update:
mutalyzer/Mapper.py:
mutalyzer/Db.py:
- Get mapping updates from the NCBI.

extras/migrations:
extras/post-upgrade.sh:
- Automated migration scripts.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@342 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@341 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@340 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@339 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@338 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@337 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

mutalyzer/config.py:
- Try to load system configuration and user configuration, in that order, and
  merge them if we find both.

tests/test_website.py:
- Use running webserver to retrieve batch results.

extras/config.user.example:
- Example user configuration, overwriting some values from system
  configuration.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@336 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@335 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@334 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@333 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Synchronize the GBInfo database table with other Mutalyzer installations
by querying them for recently added entries via a webservice method. For
entries without creation info (e.g. uploaded genbank files), the file itself
is also transferred.

Changes to the mutalyzer database:

    ALTER TABLE GBInfo
        ADD COLUMN created TIMESTAMP NOT NULL DEFAULT CURRENT_TIMESTAMP,
        ADD INDEX created (created);

To setup automatic synchronization, use the crontab example in
extras/cron.d/mutalyzer-cache-sync (replace the path to the binary by
`which mutalyzer-cache-sync`).



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@331 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@328 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@326 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

This is a rebase of commit r202 to the current branch. Please not that this
is not a very clean implementation and still contains several Todo's. But
they don't affect functionality outside issue #38.

Please see the issue for more information.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@325 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Added a check that prevents the insertion of a range.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@324 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@323 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

reference.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@322 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@321 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@320 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1