Do not try to implement a full UNIX daemon suitable for init.d with the
batch daemon, but rather keep it simple and depend on something like
supervisord to implement process control.

We now also correctly handle SIGINT (Ctrl+C) and SIGTERM signals.

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