biocore/qiita — pull request #338 by adamrp (2014-09-30 08:05:40+00:00)
Title: Issue 333 EBI XML Generation and Submission Commands

There are some outstanding issues, but this works pretty well.

The major changes:
- Removed one of the convenience classmethods (and associated tests). Rather than calling the QIIME library function `split_sequence_file_on_sample_ids_to_files `, the QIIME script should be called beforehand, and the files it outputs have to be gzipped separately. So now, instead of having both `from_templates_and_demux_fastq` and `from_templates_and_per_samlple_fastqs`, we have only the latter
- Added new click command `qiita ebi from_files ...`. It's a little funky because it gets passed a study_id (which references the qiita database),one filepath for a sample template, and one file path for a prep template. Eventually, we will want to pull *all* of this information from the database, but for now (while we are trying to relieve the backlog of EBI submissions where we know the metadata is sound), this will work. Reasoning is that I needed a way to get the required information (e.g., study title, abstract, etc) that I could think of.
- Added a few more instance methods `generate_curl_command`, `send_sequences`, and `send_xml` that are used by the new commands
- Added EBI configuration parameters to the qiita_config