The old way of using the configuration file was by instantiating a Config
object which read the file. This instance was passed to every function and
object that might need it.

The new way is by simply calling config.get('name') to get the configuration
value for 'name'. This lazily reads the configuration file and the contents
are cached for future calls.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@408 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/implicit-config-branch@406 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Add optional gene argument to the numberConvertion webservice method. If
present, it will convert genomic variants to any transcript of the given
gene, no matter how far away they are located (but on the same chromosome
of course). Fixes #70.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@402 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@391 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Until protein reference sequences are supported, give an error with a message
instead of crashing. Fixes #62.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@388 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

The fix is a hack, basically copying the same functionality from the
namechecker. I think this should eventually be merged somehow.

Fixes #63


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git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@366 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

- Issue a warning instead of an UD number when a user uploads something
  that is not a genbank file (fixes #59).
- Fix a Heisenbug in the batch job unit tests. Wait a little before
  downloading the batch job results.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@365 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@362 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

We previously used the NCBI mapping data for the current build, but now a new
build was just released, the mapping data is missing (they are waiting for the
data and it should be up soon).

For now, we just use the mapping data for the archived previous build (it is
the build we were using until now anyway).


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@361 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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Added a ping() function to the webservice.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/branches/refactor-mutalyzer-branch@359 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@356 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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

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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

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