Split libraries fastq

Adds the StudyPreprocesser class, which allows to preprocess the raw data of a study. Currently, it only supports Illumina data, but the code should be easy to expand to support other types.

I've also modified the `insert_filepaths` function, so it now supports to pass the filepath type either by id or by the string (name).

I've modified the initialize.sql file, to support the correct filetypes for the Illumina data and its preprocessed data. I had to modify multiple files due to this change.
Both working_dir and upload_dir are defined to /tmp/ on this PR

2014-10-13 10:52 GMT-06:00 adamrp <notifications@github.com>:

> In qiita_core/configuration_manager.py:
>
> > @@ -124,6 +126,11 @@ def _get_main(self, config):
> >              raise ValueError("The UPLOAD_DATA_DIR (%s) folder doesn't exist" %
> >                               self.upload_data_dir)
> >
> > +        self.working_dir = config.get('main', 'WORKING_DIR')
> > +        if not isdir(self.upload_data_dir):
> > +            raise ValueError("The WORKING_DIR (%s) folder doesn't exist" %
> > +                             self.upload_data_dir)
> > +
>
> The config file used by travis is qiita_core/support_files/config_test.txt
> … <#1490a6ccda99db59_>
> On Mon, Oct 13, 2014 at 9:51 AM, Adam robbins-pianka <adamrp@gmail.com>
> wrote: > Actually, it is defined in both files as empty string > <
> https://github.com/biocore/qiita/blob/master/qiita_core/support_files/config_test.txt#L25>,
> > which is then caught in the configuration manager and set > <
> https://github.com/biocore/qiita/blob/master/qiita_core/configuration_manager.py#L112-L116>
> > to the default directory. The default directory for the working directory
> > should be > > join(abspath(__file__), '..', 'qiita_db', 'support_files',
> 'work_data'). > > On Mon, Oct 13, 2014 at 9:35 AM, josenavas <
> notifications@github.com> > wrote: > In
> qiita_core/configuration_manager.py: > > > @@ -124,6 +126,11 @@ def
> _get_main(self, config): > > raise ValueError("The UPLOAD_DATA_DIR (%s)
> folder doesn't exist" % > > self.upload_data_dir) > > > > +
> self.working_dir = config.get('main', 'WORKING_DIR') > > + if not
> isdir(self.upload_data_dir): > > + raise ValueError("The WORKING_DIR (%s)
> folder doesn't exist" % > > + self.upload_data_dir) > > + > > We don't have
> a default config file for Qiita? i.e. how Travis is > handling all the
> other directories? I just did the same that is done for > all the other
> ones. on the config_test.txt and the config_demo.txt config > files it is
> defined to /tmp/ > > — > Reply to this email directly or view it on GitHub
> > <https://github.com/biocore/qiita/pull/353/files#r18779576>. >
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/biocore/qiita/pull/353/files#r18780407>.
>



-- 
Jose Navas