def setUp(self):
com1 = Command(
'Summarize Taxa', 'summarize_taxa_through_plots.py',
'{"--otu_table_fp":null}', '{}',
'{"--mapping_category":null, "--mapping_fp":null,'
'"--sort":null}', '{"--output_dir":null}')
com2 = Command(
'Beta Diversity', 'beta_diversity_through_plots.py',
'{"--otu_table_fp":null,"--mapping_fp":null}', '{}',
'{"--tree_fp":null,"--color_by_all_fields":null,'
'"--seqs_per_sample":null}', '{"--output_dir":null}')
com3 = Command(
'Alpha Rarefaction', 'alpha_rarefaction.py',
'{"--otu_table_fp":null,"--mapping_fp":null}', '{}',
'{"--tree_fp":null,"--num_steps":null,'
'"--min_rare_depth"'
':null,"--max_rare_depth":null,'
'"--retain_intermediate_files":false}', '{"--output_dir":null}')
self.all_comms = {
"16S": [com1, com2, com3],
"18S": [com1, com2, com3],
"ITS": [com2, com3],
"Proteomic": [com2, com3],
"Metabolomic": [com2, com3],
"Metagenomic": [com2, com3],
}
def post(self):
analysis = Analysis(int(self.get_argument('analysis-id')))
# set to third step since this page is third step in workflow
analysis.step = SELECT_COMMANDS
data_types = analysis.data_types
commands = Command.get_commands_by_datatype()
self.render('select_commands.html',
commands=commands, data_types=data_types, aid=analysis.id)
def test_get_commands(self):
exp = [
Command('Summarize Taxa', 'summarize_taxa_through_plots.py',
'{"--otu_table_fp":null}', '{}',
'{"--mapping_category":null, "--mapping_fp":null,'
'"--sort":null}', '{"--output_dir":null}'),
Command('Beta Diversity', 'beta_diversity_through_plots.py',
'{"--otu_table_fp":null,"--mapping_fp":null}', '{}',
'{"--tree_fp":null,"--color_by_all_fields":null,'
'"--seqs_per_sample":null}', '{"--output_dir":null}'),
Command('Alpha Rarefaction', 'alpha_rarefaction.py',
'{"--otu_table_fp":null,"--mapping_fp":null}', '{}',
'{"--tree_fp":null,"--num_steps":null,''"--min_rare_depth"'
':null,"--max_rare_depth":null,'
'"--retain_intermediate_files":false}',
'{"--output_dir":null}')
]
self.assertEqual(Job.get_commands(), exp)
def get(self):
analysis_id = int(self.get_argument('aid'))
analysis = Analysis(analysis_id)
check_analysis_access(self.current_user, analysis)
data_types = analysis.data_types
commands = Command.get_commands_by_datatype()
self.render('select_commands.html',
commands=commands, data_types=data_types, aid=analysis.id)
def get(self):
analysis_id = int(self.get_argument('aid'))
analysis = Analysis(analysis_id)
check_analysis_access(self.current_user, analysis)
data_types = analysis.data_types
commands = Command.get_commands_by_datatype()
self.render('select_commands.html',
commands=commands, data_types=data_types, aid=analysis.id)
def post(self):
analysis = Analysis(int(self.get_argument('analysis-id')))
# set to third step since this page is third step in workflow
analysis.step = SELECT_COMMANDS
data_types = analysis.data_types
commands = Command.get_commands_by_datatype()
self.render('select_commands.html',
commands=commands,
data_types=data_types,
aid=analysis.id)
def post(self):
name = self.get_argument('name')
desc = self.get_argument('description')
analysis = Analysis.create(self.current_user, name, desc,
from_default=True)
# set to third step since this page is third step in workflow
analysis.step = SELECT_COMMANDS
data_types = analysis.data_types
commands = Command.get_commands_by_datatype()
self.render('select_commands.html',
commands=commands, data_types=data_types, aid=analysis.id)
def post(self):
name = self.get_argument('name')
desc = self.get_argument('description')
analysis = Analysis.create(self.current_user, name, desc,
from_default=True)
# set to third step since this page is third step in workflow
analysis.step = SELECT_COMMANDS
data_types = analysis.data_types
commands = Command.get_commands_by_datatype()
self.render('select_commands.html',
commands=commands, data_types=data_types, aid=analysis.id)
def test_not_equal(self):
commands = Command.create_list()
self.assertFalse(commands[1] != commands[1])
self.assertTrue(commands[1] != commands[2])
self.assertTrue(commands[1] != Job(1))
def test_get_commands_by_datatype(self):
obs = Command.get_commands_by_datatype()
self.assertEqual(obs, self.all_comms)
obs = Command.get_commands_by_datatype(["16S", "Metabolomic"])
exp = {k: self.all_comms[k] for k in ('16S', 'Metabolomic')}
self.assertEqual(obs, exp)
