Commits · e9bf1bc9d9fb10c02c25fee37d7e8dc64812e949 · Mirrors / mutalyzer

Jan 10, 2014

Port Mapping database module to SQLAlchemy · e9bf1bc9

Vermaat authored 11 years ago

This introduces a proper notion of genome assemblies. Transcript
mappings for alle genome assemblies are in the same database, which
is better for maintenance. Updating transcript mappings is also
simplified a lot, especially from NCBI mapview files where we now
require a preprocessing sort on the input file.

Overall, this port touches a lot of Mutalyzer code, so beware.

e9bf1bc9

Jan 04, 2014
- Some fixes for running the unit tests · f2a6cc59
  Vermaat authored 11 years ago
  
  f2a6cc59
- Temporarily skip tests using AL449423.14 (no longer valid) · 323a8be1
  Vermaat authored 11 years ago
  
  323a8be1
- Port Cache database module to SQLAlchemy · 45e799aa
  Vermaat authored 11 years ago
  
  45e799aa
Dec 23, 2013

Fix unit tests with SQLAlchemy · 94df7c07

Vermaat authored 11 years ago

This involves making the SQLAlchemy session reconfigurable at run-time,
which is done automatically on updating the Mutalyzer configuration using
configuration update callbacks.

94df7c07

SQLAlchemy in batch jobs · bb82e22e

Vermaat authored 11 years ago

Port the entire batch job infrastructure, including scheduler, to use
the SQLAlchemy ORM instead of the old Db module.

bb82e22e

Dec 19, 2013
- Update unit tests for new style configuration · 135866c3
  Vermaat authored 11 years ago
  
  135866c3
Dec 13, 2013
- Update SOAP batch job unit tests · c03cbccf
  Vermaat authored 11 years ago
  
  c03cbccf
- Update unit tests for SOAP webservice · b1b0d55f
  Vermaat authored 11 years ago
  
  b1b0d55f
- Add comment on testing POST requests to JSON API · 51b5300f
  Vermaat authored 11 years ago
  
  51b5300f
- Update unit tests for JSON services · 0f6ae962
  Vermaat authored 11 years ago
  
  0f6ae962
- Fix unit tests in virtualenv · 37935324
  Vermaat authored 11 years ago
  
  37935324
Sep 19, 2013

Add tests for JSON webservice using POST requests · b91d657b

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@746 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

b91d657b

Sep 18, 2013

Update unit tests to pass with latest NCBI data · 4ddd28ad

Vermaat authored 11 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@743 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

4ddd28ad

Apr 09, 2013
- No weird instance attribute names starting with double underscore · 206c51d9
  Vermaat authored 11 years ago
  
  git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@694 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
  206c51d9
Mar 25, 2013

Complete previous commit · c427e6ec

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@677 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c427e6ec

Transcript version update in unit tests · c519105f

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@676 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c519105f

Feb 25, 2013

Warning on non-adjacent exons in transcript reference · bd3ce1d1

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@671 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

bd3ce1d1

Feb 12, 2013

Include exon table for selected transcript in webservice · 8590f9b9

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@668 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8590f9b9

Use WNOMRNA_OTHER when appropriate (fixes #132) · c2b54871

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@667 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

c2b54871

Jan 14, 2013

Allow selectors on transcript references in position converter · 48a0b151
Vermaat authored 12 years ago
```
git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@664 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1
```
48a0b151

Accept trailing tabs in batch input · 2195ace0

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@663 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

2195ace0

Dec 11, 2012

Update LRG parser for updated schema (incomplete) · e84bdeb8

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/lrg-schema-update@654 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e84bdeb8

Nov 15, 2012

Some unit tests for mtDNA position converter · 455ae1e2

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@639 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

455ae1e2

Nov 14, 2012

Genomic reference transcript mappings · f17e991f

Vermaat authored 12 years ago

Support genomic references in the mapping database. At the moment, this is
only tested with mtDNA genes, but should in clear the way for NG_ mappings
as well.
Mappings for mtDNA genes can be added to the database using the command line
tool mutalyzer-mapping-import.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@635 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

f17e991f

Oct 05, 2012

Webservice interface for submitting batch jobs · a7248a86

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@621 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

a7248a86

Fix unit test for restriction site analysis · 8f31e51d

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@620 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8f31e51d

Oct 04, 2012

Warn on missing positioning scheme (fixes #114) · 1ec48b68

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@617 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

1ec48b68

Aug 21, 2012

Rename 'webservice' to 'web service' (for Peter) · 028f66b7

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@601 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

028f66b7

Aug 20, 2012

Fix unit tests for description extractor update · 8464555b

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@598 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8464555b

Jul 26, 2012

Unit test for issue #108 · 7e6dd859

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@590 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7e6dd859

Jul 16, 2012

Update tests for wrapped json responses · 7f986b76

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/spyne@578 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

7f986b76

Jul 12, 2012

Support non-coding transcripts in position converter (#102) · 8300b90f

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@573 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

8300b90f

Support compound variants in position converter · 0875bfe0

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@572 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

0875bfe0

Jul 11, 2012

Fix position converter for delins with explicit sequences · 5366cb35

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@570 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

5366cb35

Update unit tests for r563 · 6445361f

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@567 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6445361f

Jun 21, 2012

Disable old mapping info in unit tests · e7af8a68

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@558 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

e7af8a68

Do not crash on inversions (introduced in r528) (fixes #99) · acfb2415

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@557 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

acfb2415

First download reference in GI unit tests · 061f3d34

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@556 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

061f3d34

Jun 07, 2012

Unit test for non-interactive links · 6a90c42e

Vermaat authored 12 years ago

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@548 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

6a90c42e