Until now, the name checker form used POST requests. As a special case for
linking from LOVD, GET requests were handled by showing results without the
full interface (header, menu, etc). Ordinary linking was done to a separate
checkForward location which then set a cookie with the variant name and a
redirect to the name checker results. This was all very hackish and somewhat
broken (see Track issue #94).

This commit refactors the name checker to use GET requests, so ordinary
bookmarking of result pages is possible. All old entrypoints are handled with
a redirect for backwards compatibility.

Worth mentioning is that variant descriptions in the name checker are now
limited in length by the maximum query string length. However, this maximum
is several thousand characters with Internet Explorer having the lowest
maximum of just over 2000. Longer descriptions are not practically checked
with the name checker web interface anyway, so this should not be a problem.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@521 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Starting from Debian Wheezy, MySQLdb does no longer accept the auto_reconnect
keyword argument. Therefore it must be possible to disable this in the
configuration file. See Trac ticket #91.


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Added affiliations to the list of authors in the ESHG abstract.


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This bug was noticed and reported by S Venkata Suresh Kumar.


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For UD slices we also generate g. descriptions on the chromosome reference. We
now also apply the roll rule there and use correct ranges and sequences on the
reverse strand. Fixes #75.


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During import of the NCBI transcript mappings, CDS start or stop positions
were not picked up for some transcripts (where these are on exon boundaries).

Bug reported by S Venkata Suresh Kumar.


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Fetching genbank files was broken due to new default parameter values in the
efetch service. See http://www.ncbi.nlm.nih.gov/mailman/pipermail/utilities-announce/2012-February/000085.html

Also fix dbSNP converter web interface by properly logging IP address.


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Added simple error handling for the description extractor.



git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@480 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

describe.py:
- Module that provides the Variant Description Extractor functions.

__init__.py:
- Added an automated copyright year update.

website.py:
- Added the Variant Description Extractor web interface.

templates/descriptionExtract.html:
-  Template page for the Variant Description Extractor.

templates/snp.html:
templates/menu.html:
templates/converter.html:
templates/index.html:
templates/parse.html:
- Cosmetic changes.

Added a presentation.



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