Commits · 3a3ba6607b561d865b537f3aa32e47788289ff16 · Mirrors / mutalyzer

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

Fix unit tests to work with changes in r284. · 68f00f2f

Vermaat authored 13 years ago

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

68f00f2f

Jun 27, 2011

Opened development for release 2.0.beta-10. · 088eb4ba

Vermaat authored 13 years ago

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

088eb4ba

Release 2.0.beta-9 · c5b68769

Vermaat authored 13 years ago

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

c5b68769

Typography. · cf7ad1b2

Vermaat authored 13 years ago

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

cf7ad1b2

Fix: typo in variant checker. · 72ecf06d

Vermaat authored 13 years ago

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

72ecf06d

Some stylistic changes (valid Markdown text). · f8a134cb

Vermaat authored 13 years ago

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

f8a134cb

Jun 21, 2011

Refactoring of deployment, now using Fabric. · 4c913d58

Vermaat authored 13 years ago

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

4c913d58

Jun 20, 2011

Merged r282 from trunk (actually this fix was already in). · 028211e0

Vermaat authored 13 years ago

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

028211e0

Jun 19, 2011
- Fixed a bug that was triggered when an error occurred while parsing a batch · b888861b
  Laros authored 13 years ago
  
  file. git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@282 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  b888861b
May 23, 2011

mutalyzer/util.py: · 3b13484f

Vermaat authored 13 years ago

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

3b13484f

Merging r279 from trunk. · 24a495ab

Vermaat authored 13 years ago

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

24a495ab

May 20, 2011

Added a presentation, added acknowledgements. · 2a452208

Laros authored 13 years ago


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

2a452208

May 16, 2011

Merging r274 through r277 from trunk. · 08fab97d

Vermaat authored 13 years ago

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

08fab97d

May 13, 2011
- Extracted the BNF language definition for the lstlisting package. · e835c620
  Laros authored 13 years ago
  
  git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@277 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  e835c620
Apr 21, 2011

Fixed bug in previous commit: summary with number of warnings was incorrect. · 5b08e3e0

Vermaat authored 13 years ago

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

5b08e3e0

Fixes for roll on reverse strand. · 8c350459

Vermaat authored 13 years ago

- 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

8c350459

Apr 18, 2011

Merged r269 r270 r271 r273 from trunk. · 38bf9c11

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@274 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

38bf9c11

Swapped names (Jeroen <-> Martijn) in NBIC presentation. Fixed text... · 74c5623b

Vermaat authored 13 years ago

Swapped names (Jeroen <-> Martijn) in NBIC presentation. Fixed text positioning in transcript picture.

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@273 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

74c5623b

Several small fixes and comments. · e61ddd5e

Vermaat authored 13 years ago

Also updated the web interface name checker output:
- Visualised raw variants are now in a separate box with the input form.
- In the case of non-coding transcripts, exon information correctly uses
  n. positioning system.
- Updated message to be non-clickable and have extra info in tooltip.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@272 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e61ddd5e

Apr 13, 2011

Made some final alterations to the NBIC poster. · 2e48dcef

Laros authored 13 years ago


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@271 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2e48dcef

Apr 12, 2011

Added a picture in one of the presentations, added a poster presentation. · c37509b0
Laros authored 13 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@270 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
c37509b0
Added a presentation that Martijn will give on the NBIC conference. · 191632fd
Laros authored 13 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@269 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
191632fd

Small fixes. · abcc9460

Vermaat authored 13 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@268 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

abcc9460

Apr 11, 2011

Fixes for whole-exon deletions. · 38e90d0b

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@267 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

38e90d0b

Quick fix for navigation menu highlighting (Fixes Trac #47). · 95eaea9b

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@266 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

95eaea9b

Batch interface now accepts new-style input with multiple columns. · 4911ffb7

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@265 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4911ffb7

Apr 08, 2011

Moved GBparser and LRGparser to parsers/genbank and parsers/lrg. · 65f8f996

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@264 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

65f8f996

Fixed VarInfo. · 9bc19e07

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@263 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9bc19e07

Moved Serializers.py to models.py. · 23fca441

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@262 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

23fca441

Removed dead configuration options. · d9a5d0a8

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@261 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d9a5d0a8

Fixed UCSC update. · 2e68c7fa

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@260 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2e68c7fa

Apr 07, 2011

Updated README and INSTALL files. · aa863451

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@259 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

aa863451

Updated installation instructions. · 95d76894

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@258 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

95d76894

Fixed installation scripts. · 25f0d9c1

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@257 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

25f0d9c1

Revised installation instructions. Added pre-install script. · ddffc86a

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@256 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

ddffc86a

Fixed batch daemon init script. · 20196ccb

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@255 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

20196ccb

Use environment variable MUTALYZER_ENV=test to use testing settings. · d2c3743f

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@254 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

d2c3743f

Completed post-install script. Related fixes. · 9289bd3f

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@253 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

9289bd3f

Apr 06, 2011

Some reorganisation. Added post-install script. · 6c4f4bdd

Vermaat authored 14 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@252 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6c4f4bdd