Skip to content

rm ebi full submissions #2576

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Merged
merged 1 commit into from
May 2, 2018
Merged

rm ebi full submissions #2576

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
18 changes: 15 additions & 3 deletions qiita_ware/test/test_commands.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -13,12 +13,14 @@
from tempfile import mkdtemp
import pandas as pd
from datetime import datetime
from shutil import rmtree

from h5py import File
from qiita_files.demux import to_hdf5

from qiita_ware.exceptions import ComputeError
from qiita_ware.commands import submit_EBI
from qiita_db.util import get_mountpoint
from qiita_db.study import Study, StudyPerson
from qiita_db.software import DefaultParameters, Parameters
from qiita_db.artifact import Artifact
Expand All @@ -34,6 +36,7 @@ def setUp(self):
self.files_to_remove = []
self.temp_dir = mkdtemp()
self.files_to_remove.append(self.temp_dir)
_, self.base_fp = get_mountpoint("preprocessed_data")[0]

def write_demux_files(self, prep_template, generate_hdf5=True):
"""Writes a demux test file to avoid duplication of code"""
Expand Down Expand Up @@ -136,30 +139,39 @@ def generate_new_study_with_preprocessed_data(self):

def test_submit_EBI_step_2_failure(self):
ppd = self.write_demux_files(PrepTemplate(1), True)
pid = ppd.id

with self.assertRaises(ComputeError):
submit_EBI(ppd.id, 'VALIDATE', True)
submit_EBI(pid, 'VALIDATE', True)

rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)

@skipIf(
environ.get('ASPERA_SCP_PASS', '') == '', 'skip: ascp not configured')
def test_submit_EBI_parse_EBI_reply_failure(self):
ppd = self.write_demux_files(PrepTemplate(1))
pid = ppd.id

with self.assertRaises(ComputeError) as error:
submit_EBI(ppd.id, 'VALIDATE', True)
submit_EBI(pid, 'VALIDATE', True)
error = str(error.exception)
self.assertIn('EBI Submission failed! Log id:', error)
self.assertIn('The EBI submission failed:', error)

rmtree(join(self.base_fp, '%d_ebi_submission' % pid), True)

@skipIf(
environ.get('ASPERA_SCP_PASS', '') == '', 'skip: ascp not configured')
def test_full_submission(self):
artifact = self.generate_new_study_with_preprocessed_data()
self.assertEqual(
artifact.study.ebi_submission_status, 'not submitted')
submit_EBI(artifact.id, 'VALIDATE', True, test=True)
aid = artifact.id
submit_EBI(aid, 'VALIDATE', True, test=True)
self.assertEqual(artifact.study.ebi_submission_status, 'submitted')

rmtree(join(self.base_fp, '%d_ebi_submission' % aid), True)


FASTA_EXAMPLE = """>1.SKB2.640194_1 X orig_bc=X new_bc=X bc_diffs=0
CCACCCAGTAAC
Expand Down