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test_submitter.py
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test_submitter.py
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from egasub.submission.submitter import Submitter
import os
import pytest
from egasub.submission.submittable import Unaligned, Alignment
from egasub.ega.entities.sample import Sample
from egasub.ega.entities.attribute import Attribute
def test_submitter(ctx, mock_server):
initial_directory = os.getcwd()
os.chdir('tests/data/workspace/submittable/')
unaligned = Unaligned('test_u')
alignment = Alignment('test_a')
os.chdir(initial_directory)
os.chdir('tests/data/workspace/unaligned.20170110/')
ctx.obj['CURRENT_DIR_TYPE'] = 'unaligned'
unaligned2 = Unaligned('ssample_y')
os.chdir(initial_directory)
submitter = Submitter(ctx)
#with pytest.raises(ValueError):
#submitter.submit(unaligned, True)
ctx.obj['SUBMISSION']['sessionToken'] = 'X-Token'
ctx.obj['SETTINGS']['icgc_project_code'] = "abjdh"
#ctx.obj['SETTINGS']['ega_study_id'] = "abjdh"
ctx.obj['SUBMISSION']['id'] = "55"
#fix the put fixture
#with pytest.raises(Exception):
submitter.submit(unaligned2,True)
submitter.submit(unaligned, True)
ctx.obj['CURRENT_DIR_TYPE'] = 'alignment'
submitter.submit(alignment,True)
attributes = [Attribute('tag1', 'value1'), Attribute('tag2', 'value2')]
sample = Sample('an alias','the title','the description',123,2,'head','test line','test region','a phenotype',33,'anonymized name',22,10,'some details',attributes,33)
with pytest.raises(Exception):
submitter.set_icgc_ids(sample, True)
ctx.obj['SETTINGS']['_icgc_sample_id'] = "abjdhf"
with pytest.raises(Exception):
submitter.set_icgc_ids(sample, True)