def test_create_user_job_order_does_not_modify_original(self):
job_template = JobTemplate(tag='sometag', name='myjob', fund_code='001', job_order={
'myfile': {
'class': 'File',
'path': 'dds://project/somepath.txt'
}
})
job_template.create_user_job_order()
self.assertEqual(job_template.job_order, {
'myfile': {
'class': 'File',
'path': 'dds://project/somepath.txt',
}
})
def test_create_user_job_order_json(self):
job_template = JobTemplate(tag='sometag', name='myjob', fund_code='001', job_order={
'myfile': {
'class': 'File',
'path': 'dds://project/somepath.txt'
},
'my_path_file': {
'class': 'File',
'path': '/tmp/data.txt'
},
'my_url_file': {
'class': 'File',
'location': 'https://github.com/datafile1.dat'
},
'myint': 123,
'myfileary': [
{
'class': 'File',
'path': 'dds://project/somepath1.txt'
},
{
'class': 'File',
'path': 'dds://project/somepath2.txt'
},
],
'myfastq_pairs': [
{'file1':
{'class': 'File',
'path': 'dds://myproject/rawData/SAAAA_R1_001.fastq.gz'
},
'file2': {
'class': 'File',
'path': 'dds://myproject/rawData/SAAAA_R2_001.fastq.gz'
},
'name': 'Sample1'}]
})
user_job_order = job_template.create_user_job_order()
self.assertEqual(user_job_order['myint'], 123)
self.assertEqual(user_job_order['myfile'], {
'class': 'File',
'path': 'dds_project_somepath.txt'
})
self.assertEqual(user_job_order['myfileary'], [
{
'class': 'File',
'path': 'dds_project_somepath1.txt'
},
{
'class': 'File',
'path': 'dds_project_somepath2.txt'
},
])
self.assertEqual(user_job_order['myfastq_pairs'], [
{'file1':
{'class': 'File',
'path': 'dds_myproject_rawData_SAAAA_R1_001.fastq.gz'
},
'file2': {
'class': 'File',
'path': 'dds_myproject_rawData_SAAAA_R2_001.fastq.gz'
},
'name': 'Sample1'}])
self.assertEqual(user_job_order['my_path_file'], {
'class': 'File',
'path': '/tmp/data.txt'
}, "Plain file paths should not be modified.")
self.assertEqual(user_job_order['my_url_file'], {
'class': 'File',
'location': 'https://github.com/datafile1.dat'
}, "URL file paths should not be modified.")