import unittest
from htsworkflow.submission import condorfastq
+from htsworkflow.submission.results import ResultMap
FCDIRS = [
'C02F9ACXX',
self.subdir = os.path.join(self.tempdir, self.subname)
os.mkdir(self.subdir)
+ self.result_map = ResultMap()
+ self.result_map.add_result('11154', self.subname)
+
def tearDown(self):
shutil.rmtree(self.tempdir)
os.chdir(self.cwd)
self.tempdir,
self.logdir)
extract.api = FakeApi()
- result_map = [('11154', self.subname)]
- lib_db = extract.find_archive_sequence_files(result_map)
+
+ lib_db = extract.find_archive_sequence_files(self.result_map)
self.failUnlessEqual(len(lib_db['11154']['lanes']), 5)
lanes = [
self.tempdir,
self.logdir)
extract.api = FakeApi()
- result_map = [('11154', self.subname)]
- lib_db = extract.find_archive_sequence_files(result_map)
+ lib_db = extract.find_archive_sequence_files(self.result_map)
- needed_targets = extract.find_missing_targets(result_map,
+ needed_targets = extract.find_missing_targets(self.result_map,
lib_db)
self.failUnlessEqual(len(needed_targets), 7)
srf_30221 = needed_targets[
self.tempdir,
self.logdir)
extract.api = FakeApi()
- result_map = [('11154', self.subdir)]
- commands = extract.build_condor_arguments(result_map)
+ commands = extract.build_condor_arguments(self.result_map)
srf = commands['srf']
qseq = commands['qseq']
self.failUnlessEqual(len(split), 2)
srf_data = {
- os.path.join(self.subdir, '11154_30221AAXX_c33_l4.fastq'): {
+ os.path.join(self.subname, '11154_30221AAXX_c33_l4.fastq'): {
'mid': None,
'ispaired': False,
'sources': [u'woldlab_090425_HWI-EAS229_0110_30221AAXX_4.srf'],
'flowcell': u'30221AAXX',
- 'target': os.path.join(self.subdir,
+ 'target': os.path.join(self.subname,
u'11154_30221AAXX_c33_l4.fastq'),
},
- os.path.join(self.subdir, '11154_30DY0AAXX_c151_l8_r1.fastq'): {
+ os.path.join(self.subname, '11154_30DY0AAXX_c151_l8_r1.fastq'): {
'mid': None,
'ispaired': True,
'flowcell': u'30DY0AAXX',
'sources': [u'woldlab_090725_HWI-EAS229_0110_30DY0AAXX_8.srf'],
'mid': 76,
'target':
- os.path.join(self.subdir,
+ os.path.join(self.subname,
u'11154_30DY0AAXX_c151_l8_r1.fastq'),
'target_right':
- os.path.join(self.subdir,
+ os.path.join(self.subname,
u'11154_30DY0AAXX_c151_l8_r2.fastq'),
}
}
self.failUnlessEqual(args['mid'], expected['mid'])
qseq_data = {
- os.path.join(self.subdir, '11154_42JUYAAXX_c76_l5_r1.fastq'): {
+ os.path.join(self.subname, '11154_42JUYAAXX_c76_l5_r1.fastq'): {
'istar': True,
'ispaired': True,
'sources': [
u'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r1.tar.bz2']
},
- os.path.join(self.subdir, '11154_42JUYAAXX_c76_l5_r2.fastq'): {
+ os.path.join(self.subname, '11154_42JUYAAXX_c76_l5_r2.fastq'): {
'istar': True,
'ispaired': True,
'sources': [
u'woldlab_100826_HSI-123_0001_42JUYAAXX_l5_r2.tar.bz2']
},
- os.path.join(self.subdir, '11154_61MJTAAXX_c76_l6.fastq'): {
+ os.path.join(self.subname, '11154_61MJTAAXX_c76_l6.fastq'): {
'istar': True,
'ispaired': False,
'sources': [
self.tempdir,
self.logdir)
extract.api = FakeApi()
- result_map = [('11154', self.subname)]
- extract.create_scripts(result_map)
+ extract.create_scripts(self.result_map)
self.failUnless(os.path.exists('srf.condor'))
with open('srf.condor', 'r') as srf: