def test_get_command(self):
obs = _get_command('QIIME', '1.9.1', 'Split libraries FASTQ')
exp = qdb.software.Command(1)
self.assertEqual(obs, exp)
# It does not exist
with self.assertRaises(HTTPError):
_get_command('QIIME', '1.9.1', 'UNKNOWN')
def test_get_command(self):
obs = _get_command('QIIME', '1.9.1', 'Split libraries FASTQ')
exp = qdb.software.Command(1)
self.assertEqual(obs, exp)
# It does not exist
with self.assertRaises(HTTPError):
_get_command('QIIME', '1.9.1', 'UNKNOWN')
def test_post(self):
data = {
'name': 'New Command',
'description': 'Command added for testing',
'required_parameters': dumps(
{'in_data': ['artifact:["FASTA"]', None]}),
'optional_parameters': dumps(
{'param1': ['string', ''],
'param2': ['float', '1.5'],
'param3': ['boolean', 'True'],
'param4': ['mchoice:["opt1", "opt2", "opt3"]',
dumps(['opt1', 'opt2'])]}),
'outputs': dumps({'out1': 'BIOM'}),
'default_parameter_sets': dumps(
{'dflt1': {'param1': 'test',
'param2': '2.4',
'param3': 'False'}})
}
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/', data=data,
headers=self.header)
self.assertEqual(obs.code, 200)
obs = _get_command('QIIME', '1.9.1', 'New Command')
self.assertEqual(obs.name, 'New Command')
self.assertFalse(obs.analysis_only)
# Create a new command that is analysis only
data = {
'name': 'New analysis command',
'description': 'Analysis command added for testing',
'required_parameters': dumps(
{'in_data': ['artifact:["BIOM"]', None]}),
'optional_parameters': dumps(
{'param1': ['string', 'default'],
'param4': ['mchoice:["opt1", "opt2", "opt3"]',
dumps(['opt1', 'opt2']), None, True]}),
'outputs': dumps({'outtable': 'BIOM'}),
'default_parameter_sets': dumps({'dflt1': {'param1': 'test'}}),
'analysis_only': True
}
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/', data=data,
headers=self.header)
self.assertEqual(obs.code, 200)
obs = _get_command('QIIME', '1.9.1', 'New analysis command')
self.assertEqual(obs.name, 'New analysis command')
self.assertTrue(obs.analysis_only)
self.assertEqual(obs.merging_scheme,
{'parameters': ['param4'], 'outputs': [],
'ignore_parent_command': False})
def test_post(self):
data = {
'name':
'New Command',
'description':
'Command added for testing',
'required_parameters':
dumps({'in_data': ['artifact:["FASTA"]', None]}),
'optional_parameters':
dumps({
'param1': ['string', ''],
'param2': ['float', '1.5'],
'param3': ['boolean', 'True']
}),
'outputs':
dumps({'out1': 'BIOM'}),
'default_parameter_sets':
dumps({
'dflt1': {
'param1': 'test',
'param2': '2.4',
'param3': 'False'
}
})
}
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/',
data=data,
headers=self.header)
self.assertEqual(obs.code, 200)
obs = _get_command('QIIME', '1.9.1', 'New Command')
self.assertEqual(obs.name, 'New Command')
def test_post(self):
data = {
'name': 'New Command',
'description': 'Command added for testing',
'required_parameters': dumps(
{'in_data': ['artifact:["FASTA"]', None]}),
'optional_parameters': dumps(
{'param1': ['string', ''],
'param2': ['float', '1.5'],
'param3': ['boolean', 'True'],
'param4': ['mchoice:["opt1", "opt2", "opt3"]',
dumps(['opt1', 'opt2'])]}),
'outputs': dumps({'out1': 'BIOM'}),
'default_parameter_sets': dumps(
{'dflt1': {'param1': 'test',
'param2': '2.4',
'param3': 'False'}})
}
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/', data=data,
headers=self.header)
self.assertEqual(obs.code, 200)
obs = _get_command('QIIME', '1.9.1', 'New Command')
self.assertEqual(obs.name, 'New Command')
self.assertFalse(obs.analysis_only)
# Create a new command that is analysis only
data = {
'name': 'New analysis command',
'description': 'Analysis command added for testing',
'required_parameters': dumps(
{'in_data': ['artifact:["BIOM"]', None]}),
'optional_parameters': dumps(
{'param1': ['string', 'default'],
'param4': ['mchoice:["opt1", "opt2", "opt3"]',
dumps(['opt1', 'opt2']), None, True]}),
'outputs': dumps({'outtable': 'BIOM'}),
'default_parameter_sets': dumps({'dflt1': {'param1': 'test'}}),
'analysis_only': True
}
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/', data=data,
headers=self.header)
self.assertEqual(obs.code, 200)
obs = _get_command('QIIME', '1.9.1', 'New analysis command')
self.assertEqual(obs.name, 'New analysis command')
self.assertTrue(obs.analysis_only)
self.assertEqual(obs.merging_scheme,
{'parameters': ['param4'], 'outputs': []})
def test_post(self):
data = {
'name': 'New Command',
'description': 'Command added for testing',
'required_parameters': dumps(
{'in_data': ['artifact:["FASTA"]', None]}),
'optional_parameters': dumps({'param1': ['string', ''],
'param2': ['float', '1.5'],
'param3': ['boolean', 'True']}),
'outputs': dumps({'out1': 'BIOM'}),
'default_parameter_sets': dumps(
{'dflt1': {'param1': 'test',
'param2': '2.4',
'param3': 'False'}})
}
obs = self.post('/qiita_db/plugins/QIIME/1.9.1/commands/', data=data,
headers=self.header)
self.assertEqual(obs.code, 200)
obs = _get_command('QIIME', '1.9.1', 'New Command')
self.assertEqual(obs.name, 'New Command')