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.
Eh, yeah, kind of -- that's taken directly from the old code, so those
terms were copy-and-pasted because that's what we had in the old database
(so it was designed to work with that and those special cases), but really
it should be redesigned slightly to work with the new ontology values.  So
yes, I think that should be "Metagenomics" instead, but I don't know what
the other should be, in all honesty...

On Tue, Oct 14, 2014 at 3:05 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)
>
> Okay, thanks. Is there a type [here](
> https://github.com/biocore/qiita/blob/master/scripts/qiita#L208) then?
> … <#14910b236ffc70e3_>
> 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> <
> 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 <
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>
> —
> Reply to this email directly or view it on GitHub
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>