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Extending post test call to accept analysis #2144

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Merged
merged 1 commit into from
Jun 13, 2017
Merged

Extending post test call to accept analysis #2144

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12 changes: 9 additions & 3 deletions qiita_db/handlers/artifact.py
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Original file line number Diff line number Diff line change
Expand Up @@ -169,15 +169,21 @@ def post(self):
"""
filepaths = loads(self.get_argument('filepaths'))
artifact_type = self.get_argument('type')
prep_template = self.get_argument('prep')
prep_template = self.get_argument('prep', None)
analysis = self.get_argument('analysis', None)
name = self.get_argument('name', None)
dtype = self.get_argument('data_type', None)

if prep_template:
if prep_template is not None:
prep_template = qdb.metadata_template.prep_template.PrepTemplate(
prep_template)
dtype = None
if analysis is not None:
analysis = qdb.analysis.Analysis(analysis)

a = qdb.artifact.Artifact.create(
filepaths, artifact_type, name=name, prep_template=prep_template)
filepaths, artifact_type, name=name, prep_template=prep_template,
analysis=analysis, data_type=dtype)

self.write({'artifact': a.id})

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23 changes: 23 additions & 0 deletions qiita_db/handlers/tests/test_artifact.py
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Expand Up @@ -16,6 +16,8 @@

from tornado.web import HTTPError
import pandas as pd
from biom import example_table as et
from biom.util import biom_open

from qiita_db.handlers.tests.oauthbase import OauthTestingBase
import qiita_db as qdb
Expand Down Expand Up @@ -206,6 +208,27 @@ def test_post(self):
self._clean_up_files.extend([fp for _, fp, _ in a.filepaths])
self.assertEqual(a.name, "New test artifact")

def test_post_analysis(self):
fd, fp = mkstemp(suffix='_table.biom')
close(fd)
with biom_open(fp, 'w') as f:
et.to_hdf5(f, "test")
self._clean_up_files.append(fp)

data = {'filepaths': dumps([(fp, 'biom')]),
'type': "BIOM",
'name': "New biom artifact",
'analysis': 1,
'data_type': '16S'}
obs = self.post('/apitest/artifact/', headers=self.header, data=data)
self.assertEqual(obs.code, 200)
obs = loads(obs.body)
self.assertEqual(obs.keys(), ['artifact'])

a = qdb.artifact.Artifact(obs['artifact'])
self._clean_up_files.extend([afp for _, afp, _ in a.filepaths])
self.assertEqual(a.name, "New biom artifact")

def test_post_error(self):
data = {'filepaths': dumps([('Do not exist', 'raw_forward_seqs')]),
'type': "FASTQ",
Expand Down