Commits · 1caa029bf254c2119a308f06e40cb79ef6aae5f5 · Mirrors / mutalyzer

Sep 13, 2011

Use test mail address in batch unit tests · 1caa029b

Vermaat authored 13 years ago

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

1caa029b

By default, don't run mapping updates from cron in new installations. · 65b150f8

Vermaat authored 13 years ago

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

65b150f8

Sep 09, 2011

Merge r354 from trunk · e80a8d00

Vermaat authored 13 years ago

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

e80a8d00

Sep 08, 2011
- Added an optional versions parameter to the getTranscripts function. · d6caf734
  Laros authored 13 years ago
  
  git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@354 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  d6caf734
Sep 07, 2011

Do not crash on multiple reference definitions (bug #49). · 300fd6fe

Vermaat authored 13 years ago

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

300fd6fe

More cleanup in SOAP tools. · 3b169364

Vermaat authored 13 years ago

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

3b169364

Some cleanup in SOAP tools. · c1464089

Vermaat authored 13 years ago

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

c1464089

Sep 06, 2011

Fix bug in cache directory cleaning if it would have subdirectories. · c70bc59e

Vermaat authored 13 years ago

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

c70bc59e

Few fixes: · 2db1eb7e

Vermaat authored 13 years ago

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

2db1eb7e

Sep 05, 2011

Better color codes. · 62e7610b

Vermaat authored 13 years ago

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

62e7610b

Install/upgrade scripts output colorized messages. · a74b3515

Vermaat authored 13 years ago

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

a74b3515

Add SOAP method getdbSNPDescriptions. · 939603f5

Vermaat authored 13 years ago

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

939603f5

Fix in soaptools example client code. · ebeeace5

Vermaat authored 13 years ago

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

ebeeace5

Various small code and style fixes (some picked up by pychecker). · 0bc33a9b

Vermaat authored 13 years ago

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

0bc33a9b

Typo in previous commit. · 37ce9432

Vermaat authored 13 years ago

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

37ce9432

Sep 02, 2011

Convert 'map' table to 'Mapping' and use NCBI for updates. · 13737ad9

Vermaat authored 13 years ago

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

13737ad9

Aug 24, 2011

Tables mm1 and mm2 are not used. · 2e71548c

Vermaat authored 13 years ago

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

2e71548c

Oops, this is the proper fix for r338 and r339. · 670677bb

Vermaat authored 13 years ago

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

670677bb

Fix for typo in commit r338. · 0b110ba4

Vermaat authored 13 years ago

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

0b110ba4

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