Commits · 11eb9eece964f8030fff696f8aebfe26117923a9 · Mirrors / mutalyzer

Aug 24, 2011

Get only primary assembly mappings in position converter (naive fix for #58). · 11eb9eec

Vermaat authored 13 years ago

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

11eb9eec

Aug 23, 2011

Documentation update. · 57f3a404

Vermaat authored 13 years ago

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

57f3a404

Aug 22, 2011

Support merging user configuration and system configuration. · cdf893ac

Vermaat authored 13 years ago

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

cdf893ac

Aug 19, 2011

Add website debugging flag to config file. · 4a941a65

Vermaat authored 13 years ago

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

4a941a65

Decorator @skip for unit tests. · 72c07ff1

Vermaat authored 13 years ago

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

72c07ff1

SOAP tools now use SUDS monkey patch from Mutalyzer. · e724048d

Vermaat authored 13 years ago

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

e724048d

Merge gbinfo-sync-branch. · e25f36e4

Vermaat authored 13 years ago

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

e25f36e4

Aug 18, 2011

Fix a bug in commit r324, allowing ordinary delins again. · 7bc44ba1

Vermaat authored 13 years ago

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

7bc44ba1

Fix splicing bug, affecting variant protein descriptions. · fb2e95c4

Vermaat authored 13 years ago

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

fb2e95c4

Preliminary implementation of issue #38 (unknown exon offsets). · abe2a056

Vermaat authored 13 years ago

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

abe2a056

Aug 16, 2011

Merged r321 from trunk. · fbe87c23

Vermaat authored 13 years ago

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

fbe87c23

Fix: better check for non-genomic reference. · e85f708f

Vermaat authored 13 years ago

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

e85f708f

Fix: don't remove flanking splice sites on deletion of exons on a transcript · a6434a92

Vermaat authored 13 years ago

reference.



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

a6434a92

Aug 03, 2011

Added a check that prevents the insertion of a range. · ab5fac83

Laros authored 13 years ago


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

ab5fac83

Jul 27, 2011

Fix for getCache webservice. · 5a33e5ee

Vermaat authored 13 years ago

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

5a33e5ee

Small update to SOAP tool. · 0264f312

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/gbinfo-sync-branch@319 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0264f312

Fully functional remote cache sync. · c7e609b9

Vermaat authored 13 years ago

- 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

c7e609b9

Jul 26, 2011

Some refactoring and docstrings added. · e5a17cd8

Vermaat authored 13 years ago

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

e5a17cd8

Basic working cache sync. · dfa57a20

Vermaat authored 13 years ago

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

dfa57a20

Jul 25, 2011

Some fixes for cache sync. · a61b28b7

Vermaat authored 13 years ago

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

a61b28b7

Skeleton for cache sync. Suds monkey patch in mutalyzer.util. · 674d94c1

Vermaat authored 13 years ago

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

674d94c1

Jul 21, 2011

Creation timestamp for cache entries. · 57cda6ff

Vermaat authored 13 years ago

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

57cda6ff

Webservice for getting cache listing. · d5ebf0f8

Vermaat authored 13 years ago

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

d5ebf0f8

Branched from refactor-mutalyzer-branch r310 for synchronisation of the GBInfo · 5dec8b43

Vermaat authored 13 years ago

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

5dec8b43

Link to Mutalyzer 1.0.4 by IP address instead of hostname. · 1d2fb941

Vermaat authored 13 years ago

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

1d2fb941

Opened development for 2.0.beta-11. · dc601e72

Vermaat authored 13 years ago

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

dc601e72

Release 2.0.beta-10 · 3f5ab0be

Vermaat authored 13 years ago

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

3f5ab0be

Fixes for failing unit tests (disabled temporary config values). · fd469a10

Vermaat authored 13 years ago

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

fd469a10

Fake merge of r303 from trunk. · 560c99ba

Vermaat authored 13 years ago

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

560c99ba

New index on BatchQueue table. · 9b4f7e9d

Vermaat authored 13 years ago

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

9b4f7e9d

This is basically r296 and r297 applied to trunk by hand. · f9bc0235

Vermaat authored 13 years ago

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

f9bc0235

Jul 20, 2011

Merged r298 from trunk into refactor-mutalyzer-branch. · 74a888b4

Vermaat authored 13 years ago

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

74a888b4

Just a comment. · 870264bf

Vermaat authored 13 years ago

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

870264bf

Found a typo. · d014ab31

Laros authored 13 years ago


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

d014ab31

Jul 19, 2011

Fix for r296: don't forget to take the MIN() for QueueID! · defa8b3e

Vermaat authored 13 years ago

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

defa8b3e

Optimization for batch scheduler. · 52e43af4

Vermaat authored 13 years ago

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

52e43af4

Jul 12, 2011

New SOAP method: info(). · 362dc830

Vermaat authored 13 years ago

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

362dc830

Jul 11, 2011

Comment. · 211e0e6e

Vermaat authored 13 years ago

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

211e0e6e

Use temporary cache directory for unit tests. · b042d254

Vermaat authored 13 years ago

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

b042d254

Jun 28, 2011

Fix for regression introduced in r284. · 3a3ba660

Vermaat authored 13 years ago

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

3a3ba660