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112019 (#2960)

* 112019

* fix redbiom

* rm unnecessary rsplit

* addressing @ElDeveloper comments
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antgonza authored and ElDeveloper committed Nov 14, 2019
1 parent 78d74ce commit 9c2e0476641befcac6a8a00d1f3d975dd482e2b4
Showing with 15 additions and 6 deletions.
  1. +10 −0 CHANGELOG.md
  2. +5 −6 qiita_pet/handlers/qiita_redbiom.py
@@ -1,5 +1,15 @@
# Qiita changelog

Version 112019
--------------

* Added PacBio_SMRT to the list of platform and PacBio RS, PacBio RS II, Sequel, Sequel II as valid instrument models
* Improved downloads for public data (BIOM, raw data, etc.; see https://qiita.ucsd.edu/static/doc/html/downloading.html)
* Added the possibility of just downloading sample or preparation information files
* During a meta-analysis if `sample_name` and `sample_id`/`sample-id` are present, Qiita will drop the columns `sample_id`/`sample-id` to avoid issues with QIIME2
* The redbiom webpage only accepts ' or " for escaping strings
* Added qiime2.2019.10 to the system; which updated these plugins: qp-qiime2, qtp-biom, qtp-diversity, qtp-visualization

Version 092019
--------------

@@ -49,13 +49,12 @@ def _redbiom_metadata_search(self, query, contexts):
study_artifacts = defaultdict(lambda: defaultdict(list))
for ctx in contexts:
# redbiom.fetch.data_from_samples returns a biom, which we
# will ignore, and a dict
# will ignore, and a dict: {sample_id_in_table: original_id}
_, data = redbiom.fetch.data_from_samples(ctx, redbiom_samples)
for vals in data.values():
for idx in vals:
aid, sample_id = idx.split('_', 1)
sid = sample_id.split('.', 1)[0]
study_artifacts[sid][aid].append(sample_id)
for idx in data.keys():
sample_id, aid = idx.rsplit('.', 1)
sid = sample_id.split('.', 1)[0]
study_artifacts[sid][aid].append(sample_id)

return message, study_artifacts

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