Ebi submit page

_Mostly_ there. This is not linked up yet, so you have to go to the page manually (e.g., `localhost:8888/ebi_submission/1`. Second, `send` is forced to `False` right now so it is not sending. The actual submission is done on a worker, and allows for a somewhat general way to submit arbitrary compute with a waiting page.

It is awkward to push and publish messages, and I think there is a better way, but this works as far as I can tell.
Okay, thanks. Is there a type [here](
https://github.com/biocore/qiita/blob/master/scripts/qiita#L208) then?

On Tue, Oct 14, 2014 at 4:04 PM, adamrp <notifications@github.com> wrote:

> In qiita_ware/dispatchable.py:
>
> > +    output_dir = tmp_dir + '_submission'
> > +
> > +    samp_fp = join(tmp_dir, 'sample_metadata.txt')
> > +    prep_fp = join(tmp_dir, 'prep_metadata.txt')
> > +
> > +    st.to_file(samp_fp)
> > +    pt.to_file(prep_fp)
> > +
> > +    with open_file(demux) as demux_fh:
> > +        for samp, iterator in to_per_sample_ascii(demux_fh, list(st)):
> > +            with gzopen(join(tmp_dir, "%s.fastq.gz" % samp), 'w') as fh:
> > +                for record in iterator:
> > +                    fh.write(record)
> > +
> > +    submit_EBI_from_files(study_id, open(samp_fp), open(prep_fp), tmp_dir,
> > +                          output_dir, 'metagenomic', 'ADD', False)
>
> Sorry, yes, that is correct. "Metagenomics" For reference, you can find
> these terms in populate.sql (although I understand not wanting to trust
> that since it's test data), or from thebeast at
> /var/ftp/pub/qiita/qiitaontoandvocab.sql.gz
> … <#14910b10d2e3f145_>
> On Tue, Oct 14, 2014 at 3:01 PM, Daniel McDonald <notifications@github.com>
> wrote: > In qiita_ware/dispatchable.py: > > > + output_dir = tmp_dir +
> '_submission' > > + > > + samp_fp = join(tmp_dir, 'sample_metadata.txt') >
> > + prep_fp = join(tmp_dir, 'prep_metadata.txt') > > + > > +
> st.to_file(samp_fp) > > + pt.to_file(prep_fp) > > + > > + with
> open_file(demux) as demux_fh: > > + for samp, iterator in
> to_per_sample_ascii(demux_fh, list(st)): > > + with gzopen(join(tmp_dir,
> "%s.fastq.gz" % samp), 'w') as fh: > > + for record in iterator: > > +
> fh.write(record) > > + > > + submit_EBI_from_files(study_id, open(samp_fp),
> open(prep_fp), tmp_dir, > > + output_dir, 'metagenomic', 'ADD', False) > >
> What about "Metagenomics"? That is currently what I'm getting back from >
> `RawData` > … <#14910ae77783aa82_> > On Tue, Oct 14, 2014 at 3:55 PM,
> adamrp <notifications@github.com> wrote: In qiita_ware/dispatchable.py: >
> + output_dir = tmp_dir + '_submission' > + > + samp_fp = join(tmp_dir,
> 'sample_metadata.txt') > + prep_fp = join(tmp_dir, 'prep_metadata.txt') > +
> > + st.to_file(samp_fp) > + pt.to_file(prep_fp) > + > + with
> open_file(demux) as demux_fh: > + for samp, iterator in
> to_per_sample_ascii(demux_fh, list(st)): > + with gzopen(join(tmp_dir,
> "%s.fastq.gz" % samp), 'w') as fh: > + for record in iterator: > +
> fh.write(record) > + > + submit_EBI_from_files(study_id, open(samp_fp),
> open(prep_fp), tmp_dir, > + output_dir, 'metagenomic', 'ADD', False)
> Metagenomic is one of the supported types in the ENA ontology, yes; not
> sure about case sensitivity … <#14910a8fffcf9ea4_> On Tue, Oct 14, 2014 at
> 12:01 PM, josenavas <notifications@github.com> wrote: In
> qiita_ware/dispatchable.py: > + output_dir = tmp_dir + '_submission' > + >
> + samp_fp = join(tmp_dir, 'sample_metadata.txt') > + prep_fp =
> join(tmp_dir, 'prep_metadata.txt') > + > + st.to_file(samp_fp) > +
> pt.to_file(prep_fp) > + > + with open_file(demux) as demux_fh: > + for
> samp, iterator in to_per_sample_ascii(demux_fh, list(st)): > + with
> gzopen(join(tmp_dir, "%s.fastq.gz" % samp), 'w') as fh: > + for record in
> iterator: > + fh.write(record) > + > + submit_EBI_from_files(study_id,
> open(samp_fp), open(prep_fp), tmp_dir, > + output_dir, 'metagenomic',
> 'ADD', False) This investigation type was the one added by @adamrp
> <https://github.com/adamrp> <https://github.com/adamrp> <
> https://github.com/adamrp> < https://github.com/adamrp> right? If so, I
> think it is raw_data.investigation_type — Reply to this email directly or
> view it on GitHub <
> https://github.com/biocore/qiita/pull/387/files#r18850872>. — Reply to
> this email directly or view it on GitHub <
> https://github.com/biocore/qiita/pull/387/files#r18861769>. — Reply to
> this email directly or view it on GitHub <
> https://github.com/biocore/qiita/pull/387/files#r18862207>.
>
> —
> Reply to this email directly or view it on GitHub
> <https://github.com/biocore/qiita/pull/387/files#r18862360>.
>