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fix EBI-ENA submission with already submitted samples #2992

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Merged
merged 10 commits into from
Apr 27, 2020
Merged

fix EBI-ENA submission with already submitted samples #2992

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474790c
fix EBI-ENA submission with already submitted samples
antgonza Apr 13, 2020
723692c
fixing errors
antgonza Apr 13, 2020
03152a6
fixing errors
antgonza Apr 13, 2020
7dec875
fixing errors
antgonza Apr 13, 2020
6d2c5d0
readd tests
antgonza Apr 14, 2020
416246a
addressing @ElDeveloper comment
antgonza Apr 14, 2020
5a23e49
Updating metatranscriptome documentation (#2991)
smruthi98 Apr 21, 2020
900715c
fix #2773 (#2993)
antgonza Apr 27, 2020
a5d2299
Merge branch 'updates-EBI-ENA-submission' of github.com:antgonza/qiit…
antgonza Apr 27, 2020
b314c2b
addressing @ElDeveloper comment
antgonza Apr 27, 2020
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addressing @ElDeveloper comment
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@antgonza
antgonza committed Apr 27, 2020
commit b314c2b06020a4e2b67d06ade73bc4e7bf7024b7
3 changes: 1 addition & 2 deletions qiita_ware/commands.py
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Expand Up @@ -228,8 +228,7 @@ def submit_EBI(artifact_id, action, send, test=False, test_size=False):
cols_to_drop = cols_to_drop - {'taxon_id', 'scientific_name',
'description'}
all_samples = ebi_submission.sample_template.ebi_sample_accessions
samples = {k: all_samples[k] for k in ebi_submission.samples
if all_samples[k] is None}
samples = [k for k in ebi_submission.samples if all_samples[k] is None]
if samples:
ebi_submission.write_xml_file(
ebi_submission.generate_sample_xml(samples, cols_to_drop),
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