This changes the output format of the JSON webservice. Results are no longer
wrapped (twice) in an object. For example, the request

    /checkSyntax?variant=AB026906.1:c.274del

used to return

    {"checkSyntaxResponse": {"checkSyntaxResult":
      {"valid": true, "messages": {"SoapMessage": []}}}}

and now returns

    {"valid": true, "messages": []}

We also use "soft" input validation.

See http://stackoverflow.com/a/12297929

This removes the need for the top-level package_root function. On the
way we also remove the top-level is_test function that was obsolete.

This is more in line with common practice. Furthermore, the web.py
built-in HTTP server only looks there (hard-coded unfortunately), so
this is the only way to easily run Mutalyzer without a separate
webserver.

The actual conversion of the repository was done using svn2git [1].

[1] https://github.com/nirvdrum/svn2git

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@753 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@752 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@751 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@749 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@748 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@747 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@744 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

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

This enables using POST requests for the JSON webservice.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@742 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@703 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@701 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@699 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

Rework the caching of transcript<->protein accession number links. If no
link is reported by the NCBI, this is now also cached. For these type of
negative links and the normal links, separate cache lifetimes can be
defined.


git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@698 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@697 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@694 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@693 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@692 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1

git-svn-id: https://humgenprojects.lumc.nl/svn/mutalyzer/trunk@690 eb6bd6ab-9ccd-42b9-aceb-e2899b4a52f1