- Writes to log file.
- Can be run from bin/mutalyzer-cache-sync.
- Post-install script installs (by default disabled) cronjob.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@318 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@317 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@316 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@315 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@314 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@313 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@312 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

database table between different Mutalyzer instances.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@311 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

This makes that we can keep running 1.0.4 on the old server, after changing
the DNS to point mutalyzer.nl to the new server.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@310 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@309 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@307 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@306 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@305 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@304 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@303 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@300 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@299 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@298 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@297 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Getting the next batch queue entry to process was slow with a large database
due to the getFromQueue select query. This query is now replaced by one that
can make use of an index on the BatchQueue table.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@296 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@295 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@294 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@293 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Generating SOAP webservice API documentation on the fly fails mysteriously
if mutalyzer/webservice.py does not contain the WSGI application variable.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@292 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@291 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@290 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@288 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@287 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@286 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@285 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

fabfile.py:
- Automatic deployment to remote servers using Fabric.

extras/pre-install.sh:
extras/post-install.sh:
extras/post-upgrade.sh:
INSTALL:
- Refactoring of deployment.
- Better handling of installation vs upgrade.
- Install crontab.
- Install init script links.
- Restart Apache and Mutalyzer batch daemon.

bin/mutalyzer-webservice.wsgi:
bin/mutalyzer-website.wsgi:
- Moved WSGI interfaces from mutalyzer package to bin directory.
- Fixed use of built-in webserver.

extras/apache/mutalyzer.conf:
- Use /var/www/mutalyzer/base symlink for static files.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@284 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@283 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

file.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@282 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

tests/test_wsgi.py:
- Option to skip 'slow' unit tests (decorated by @slow).

tests/test_webservice.py:
- Monkey-patched suds to download xml.xsd from other URL.

mutalyzer/templates/check.html:
- Experimentally colored boxes in namechecker.

mutalyzer/Retriever.py:
- More robust dbSNP API error handling.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@281 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@280 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@279 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@278 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@277 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@276 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Warning can also be shown for a roll on the reverse strand.
- Only the roll warning about the selected strand is shown.
- Roll of insertion where the inserted sequence changes now has correct
  description on the reverse strand.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@275 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1