def test_retrieve_results_folder(self):
job = Job(2)
self.assertEqual(job.results, ['2_test_folder/testres.htm',
'2_test_folder/subdir/subres.html'])
def setUp(self):
self.job = Job(1)
self.options = {"option1": False, "option2": 25, "option3": "NEW"}
self._delete_path = []
self._delete_dir = []
_, self._job_folder = get_mountpoint("job")[0]
def _construct_job_graph(self,
user,
analysis,
commands,
comm_opts=None,
rarefaction_depth=None):
"""Builds the job graph for running an analysis
Parameters
----------
user : str
user running this analysis.
analysis: Analysis object
Analysis to finalize.
commands : list of tuples
Commands to add as jobs in the analysis.
Format [(data_type, command name), ...]
comm_opts : dict of dicts, optional
Options for commands. Format {command name: {opt1: value,...},...}
Default None (use default options).
rarefaction_depth : int, optional
Rarefaction depth for analysis' biom tables. Default None.
"""
self._logger = stderr
# Add jobs to analysis
if comm_opts is None:
comm_opts = {}
for data_type, command in commands:
# get opts set by user, else make it empty dict
opts = comm_opts.get(command, {})
# Add commands to analysis as jobs
# HARD CODED HACKY THING FOR DEMO, FIX Issue #164
if (command == "Beta Diversity" or command == "Alpha Rarefaction"):
if data_type in {'16S', '18S'}:
opts["--tree_fp"] = join(get_db_files_base_dir(),
"reference",
"gg_97_otus_4feb2011.tre")
else:
opts["--parameter_fp"] = join(get_db_files_base_dir(),
"reference",
"params_qiime.txt")
if command == "Alpha Rarefaction":
opts["-n"] = 4
Job.create(data_type,
command,
opts,
analysis,
return_existing=True)
# Create the files for the jobs
files_node_name = "%d_ANALYSISFILES" % analysis.id
self._job_graph.add_node(files_node_name,
job=(_build_analysis_files, analysis,
rarefaction_depth),
requires_deps=False)
# Add the jobs
job_nodes = []
for job_id in analysis.jobs:
job = Job(job_id)
node_name = "%d_JOB_%d" % (analysis.id, job.id)
job_nodes.append(node_name)
self._job_graph.add_node(node_name,
job=(_job_comm_wrapper, user, analysis.id,
job),
requires_deps=False)
# Adding the dependency edges to the graph
self._job_graph.add_edge(files_node_name, node_name)
# Finalize the analysis
node_name = "FINISH_ANALYSIS_%d" % analysis.id
self._job_graph.add_node(node_name,
job=(_finish_analysis, user, analysis),
requires_deps=False)
# Adding the dependency edges to the graph
for job_node_name in job_nodes:
self._job_graph.add_edge(job_node_name, node_name)
def test_remove_highlight(self):
self.collection.remove_highlight(Job(1))
obs = self.collection.highlights
exp = []
self.assertEqual(obs, exp)
def test_highlight_job(self):
self.collection.highlight_job(Job(2))
obs = self.collection.highlights
exp = [1, 2]
self.assertEqual(obs, exp)
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 setUp(self):
self.job = Job(1)
self.options = {"option1": False, "option2": 25, "option3": "NEW"}
self._delete_path = []
self._delete_dir = []
