#!/usr/bin/env python
-import copy
-import os
from pprint import pprint
import shutil
-import tempfile
-from unittest2 import TestCase, defaultTestLoader
+from unittest import TestCase, defaultTestLoader
from htsworkflow.submission.results import ResultMap
-
-S1_NAME = '1000-sample'
-S2_NAME = '2000-sample'
-
-S1_FILES = [
- os.path.join(S1_NAME, 'file1_l8_r1.fastq'),
- os.path.join(S1_NAME, 'file1_l8_r2.fastq'),
-]
-
-S2_FILES = [
- os.path.join(S2_NAME, 'file1.bam'),
- os.path.join(S2_NAME, 'file1_l5.fastq'),
-]
-
-def generate_sample_results_tree(obj):
- obj.tempdir = tempfile.mkdtemp(prefix="results_test")
- obj.sourcedir = os.path.join(obj.tempdir, 'source')
- obj.resultdir = os.path.join(obj.tempdir, 'results')
-
- for d in [obj.sourcedir,
- os.path.join(obj.sourcedir, S1_NAME),
- os.path.join(obj.sourcedir, S2_NAME),
- obj.resultdir]:
- os.mkdir(os.path.join(obj.tempdir, d))
-
- tomake = []
- tomake.extend(S1_FILES)
- tomake.extend(S2_FILES)
- for f in tomake:
- stream = open(os.path.join(obj.sourcedir, f), 'w')
- stream.write(f)
- stream.close()
+from submission_test_common import *
class TestResultMap(TestCase):
def setUp(self):
- generate_sample_results_tree(self)
+ generate_sample_results_tree(self, 'results_test')
def tearDown(self):
shutil.rmtree(self.tempdir)
os.path.islink(
os.path.join(self.resultdir, f)))
+ def test_make_from_shared_directory(self):
+ """Split multiple datasets stored in a single directory
+ """
+ self.skipTest("not implemented yet")
+ results = ResultMap()
+ results['S1'] = os.path.join(SCOMBINED_NAME, 's1*')
+ results['S2'] = os.path.join(SCOMBINED_NAME, 's2*')
def suite():
suite = defaultTestLoader.loadTestsFromTestCase(TestResultMap)
if __name__ == "__main__":
import logging
logging.basicConfig(level=logging.DEBUG)
- from unittest2 import main
+ from unittest import main
main(defaultTest='suite')