def test_generate_target_dirname(self):
lines = []
lines.append("#pspec\n")
lines.append("(permute):number=1-3\n")
lines.append("(permute):letter=AAA,BBB\n")
lines.append("(permute):singleton_val=300\n")
lines.append("(permute):animal=dog,cat\n")
lines.append("concise_print:animal,an\n")
lines.append("concise_print:letter,l\n")
lines.append("concise_print:singleton_val,s\n")
lines.append("concise_print:resolution,res\n")
lines.append("concise_print:AAA,aa\n")
lines.append("concise_print:BBB,bb\n")
lines.append("scores_permute:resolution=userDay,userMonth\n")
lines.append(
"scores_from:file=<permutation_output_dir>/(resolution).csv,column_name=auc,row_number=1\n"
)
lines.append("scores_to:./collected_results\n")
lines.append("scores_y_axis:letter\n")
lines.append("scores_x_axis:number,animal\n")
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", lines, stdout,
[], False, False)
dirname = pooled_results_file.generate_target_dirname(cspec)
#print "DIR IS : {0}".format(dirname)
self.assertTrue(dirname == './collected_results/baz')
def test_gen_cluster_job_perm_code_from_pieces(self):
lines = []
lines.append("#pspec\n")
lines.append("trials:2\n")
lines.append("(permute):number=1-3\n")
lines.append("(permute):letter=AAA,BBB\n")
lines.append("(permute):singleton_val=300\n")
lines.append("(permute):animal=dog,cat\n")
lines.append("concise_print:animal,an\n")
lines.append("concise_print:letter,l\n")
lines.append("concise_print:singleton_val,s\n")
lines.append("concise_print:resolution,res\n")
lines.append("concise_print:AAA,aa\n")
lines.append("concise_print:BBB,bb\n")
lines.append("scores_permute:resolution=userDay,userMonth\n")
lines.append(
"scores_from:file=<permutation_output_dir>/(resolution).csv,column_name=auc,row_number=1\n"
)
lines.append("scores_to:./collected_results\n")
lines.append("scores_y_axis:letter\n")
lines.append("scores_x_axis:number,animal\n")
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", lines, stdout,
[], False, False)
y_permutation = {'letter': 'AAA'}
x_permutation = {'number': '3', 'animal': 'dog'}
filename_perm_dict = {'singleton_val': '300', 'resolution': 'userDay'}
result = pooled_timings_file.gen_cluster_job_perm_code_from_pieces(
y_permutation, x_permutation, filename_perm_dict, cspec, '2')
print "RESULT : {0}".format(result)
self.assertTrue(result == 'an_dog_l_aa_number_3_s_300_trial_2')
def testCreateScript(self):
pcode = 'l_a_n_1_trial_1'
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", self.lines,
stdout, [], False, False)
cluster_runs = cluster_runs_info.ClusterRunsInfo(cspec, stdout)
cluster = mock_cluster.MockCluster(cluster_runs)
self.assertFalse(cluster.scripts)
cscript = cluster.create_script(pcode)
self.assertTrue(cluster.scripts[pcode] == cscript)
def testIsPermissionBlocked(self):
pcode = 'l_a_n_1_trial_1'
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", self.lines,
stdout, [], False, False)
cluster_runs = cluster_runs_info.ClusterRunsInfo(cspec, stdout)
cluster = mock_cluster.MockCluster(cluster_runs)
cluster.create_script(pcode)
cluster.launch(pcode)
cluster.test_helper_set_invoke_error(pcode)
self.assertTrue(cluster.get_invoke_error(pcode) != '')
def testStopWaitingRun(self):
pcode = 'l_a_n_1_trial_1'
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", self.lines,
stdout, [], False, False)
cluster_runs = cluster_runs_info.ClusterRunsInfo(cspec, stdout)
cluster = mock_cluster.MockCluster(cluster_runs)
cluster.create_script(pcode)
cluster.launch(pcode)
cluster.stop_run(pcode)
self.assertTrue(not (cluster.running_state.has_key(pcode)))
def testGetModTimeOutputFileRunIncomplete(self):
pcode = 'l_a_n_1_trial_1'
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", self.lines,
stdout, [], False, False)
cluster_runs = cluster_runs_info.ClusterRunsInfo(cspec, stdout)
cluster = mock_cluster.MockCluster(cluster_runs)
cluster.create_script(pcode)
cluster.launch(pcode)
cluster.test_helper_set_ok_to_run(pcode)
cluster.test_helper_set_run_finished_incomplete(pcode)
self.assertTrue(cluster.get_output_file_mod_time(pcode) == 0)
def testLaunch(self):
pcode = 'l_a_n_1_trial_1'
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", self.lines,
stdout, [], False, False)
cluster_runs = cluster_runs_info.ClusterRunsInfo(cspec, stdout)
cluster = mock_cluster.MockCluster(cluster_runs)
cluster.create_script(pcode)
cluster.launch(pcode)
self.assertTrue(cluster.running_state[pcode] == 'waiting')
cluster.test_helper_set_ok_to_run(pcode)
self.assertTrue(cluster.running_state[pcode] == 'running')
def testDeleteQstatLog(self):
pcode = 'l_a_n_1_trial_1'
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", self.lines,
stdout, [], False, False)
cluster_runs = cluster_runs_info.ClusterRunsInfo(cspec, stdout)
cluster = mock_cluster.MockCluster(cluster_runs)
self.assertFalse(cluster.is_qstat_log_present())
cluster.test_helper_set_qstat_info('qstatInfo')
self.assertTrue(cluster.is_qstat_log_present())
cluster.delete_qstat_log()
self.assertFalse(cluster.is_qstat_log_present())
def testDeleteInvokeLog(self):
pcode = 'l_a_n_1_trial_1'
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", self.lines,
stdout, [], False, False)
cluster_runs = cluster_runs_info.ClusterRunsInfo(cspec, stdout)
cluster = mock_cluster.MockCluster(cluster_runs)
cluster.create_script(pcode)
self.assertFalse(cluster.is_invoke_log_present(pcode))
cluster.launch(pcode)
self.assertTrue(cluster.is_invoke_log_present(pcode))
cluster.delete_invoke_log(pcode)
self.assertFalse(cluster.is_invoke_log_present(pcode))
def testDeleteResults(self):
pcode = 'l_a_n_1_trial_1'
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", self.lines,
stdout, [], False, False)
cluster_runs = cluster_runs_info.ClusterRunsInfo(cspec, stdout)
cluster = mock_cluster.MockCluster(cluster_runs)
cluster.create_script(pcode)
cluster.launch(pcode)
cluster.test_helper_set_ok_to_run(pcode)
cluster.test_helper_set_run_finished_complete(pcode)
self.assertTrue(cluster.is_output_files_present(pcode))
cluster.delete_results(pcode)
self.assertFalse(cluster.is_output_files_present(pcode))
def testIsDoneMarkerPresentRunIncomplete(self):
pcode = 'l_a_n_1_trial_1'
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", self.lines,
stdout, [], False, False)
cluster_runs = cluster_runs_info.ClusterRunsInfo(cspec, stdout)
cluster = mock_cluster.MockCluster(cluster_runs)
self.assertFalse(cluster.is_done_marker_present(pcode))
cluster.create_script(pcode)
cluster.launch(pcode)
self.assertFalse(cluster.is_done_marker_present(pcode))
cluster.test_helper_set_ok_to_run(pcode)
self.assertFalse(cluster.is_done_marker_present(pcode))
cluster.test_helper_set_run_finished_incomplete(pcode)
self.assertTrue(cluster.is_done_marker_present(pcode))
def test_build_code_using_dictionary(self):
lines = []
lines.append("#pspec\n")
lines.append("concise_print:letter,l\n")
lines.append("concise_print:singleton_val,s\n")
lines.append("concise_print:resolution,res\n")
lines.append("concise_print:AAA,aa\n")
lines.append("concise_print:BBB,bb\n")
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", lines, stdout,
[], False, False)
perm_dict = {'singleton_val': '300', 'res': 'userDay'}
code = pooled_results_file.build_code_using_dictionary(
perm_dict, cspec)
self.assertTrue(code == 'res_userDay_s_300')
def test_validate_statement_present_in_lines(self):
stdout = mock_stdout.MockStdout()
lines = []
lines.append("root_dir\n")
self.assertFalse(
cluster_spec.validate_statement_present(lines, "root_dir:",
"some_dir", stdout))
lines.append("root_dir:\n")
self.assertFalse(
cluster_spec.validate_statement_present(lines, "root_dir:",
"some_dir", stdout))
lines.append("root_dir:/foo/bar\n")
self.assertTrue(
cluster_spec.validate_statement_present(lines, "root_dir:",
"some_dir", stdout))
# with spaces
lines = []
lines.append("root_dir: /foo/bar \n")
self.assertTrue(
cluster_spec.validate_statement_present(lines, "root_dir:",
"some_dir", stdout))
def test_gather_file_permuters(self):
lines = []
lines.append("#pspec\n")
lines.append("(permute):number=1-3\n")
lines.append("(permute):letter=AAA,BBB\n")
lines.append("(permute):singleton_val=300\n")
lines.append("(permute):animal=dog,cat\n")
lines.append("scores_permute:resolution=userDay,userMonth\n")
lines.append(
"scores_from:file=<permutation_output_dir>/(resolution).csv,column_name=auc,row_number=1\n"
)
lines.append("scores_to:./collected_results\n")
lines.append("scores_y_axis:letter\n")
lines.append("scores_x_axis:number,animal\n")
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", lines, stdout,
[], False, False)
perm_dict = pooled_results_file.gather_file_permuters(cspec)
keys = perm_dict.keys()
self.assertTrue(len(keys) == 2)
self.assertTrue(perm_dict.has_key('singleton_val'))
self.assertTrue(perm_dict.has_key('resolution'))
def test_load_cspec(self):
lines = []
lines.append("#pspec\n")
lines.append("trials:2\n")
lines.append("tag=_myTag\n")
lines.append("(permute):number=range(1,4)\n") # new form
lines.append("(permute):letter=AAA,BBB\n")
lines.append("(permute):singleton_val=300\n")
lines.append("(permute):animal=dog,cat\n")
lines.append("concise_print:animal,an\n")
lines.append("encode:letter,l\n") # alternate form
lines.append("concise_print:singleton_val,s\n")
lines.append("concise_print:resolution,res\n")
lines.append("concise_print:AAA,aa\n")
lines.append("concise_print:BBB,bb\n")
#lines.append("scores_permute:resolution=userDay,userMonth\n")
#lines.append("scores_from:file=<permutation_output_dir>/(resolution).csv,column_name=auc,row_number=1\n")
#lines.append("scores_to:./collected_results\n")
#lines.append("scores_y_axis:letter\n")
#lines.append("scores_x_axis:number,animal\n")
lines.append("<replace>:config[AAA]=aaa\n")
lines.append("<replace>:config[BBB]=bbb\n")
lines.append("<replace>:pretty[1]=one\n")
lines.append("<replace>:pretty[2]=two\n")
lines.append("<replace>:pretty[3]=three\n")
lines.append("<replace>:root=/nfs/foo/bar\n")
lines.append(
"<replace>:x_dir=<root>/(letter)/<config[(letter)]>/(number)\n")
lines.append("<replace>:algs_dir=/nfs/algs\n")
lines.append("<replace>:tools_dir=<algs_dir>/tools\n")
lines.append("<replace>:outfile_root=<pretty[(number)]>__TEST\n")
lines.append("root_dir:/myRuns\n")
lines.append("qsub_command:-q eecs,eecs1,eecs,share\n")
lines.append("qsub_command:-M [email protected]\n")
lines.append("qsub_command:-m beas\n")
lines.append("first_job_number:100\n")
lines.append(
"command:echo (letter) (number) (singleton_val) > <permutation_output_dir>/(letter)_(number)_<pretty[(number)]>.txt\n"
)
stdout = mock_stdout.MockStdout()
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", lines, stdout,
[], False, False)
#print self.cspec.concise_print_map
# concise_name
self.assertTrue(cspec.get_concise_name('number') == 'number')
self.assertTrue(cspec.get_concise_name('letter') == 'l')
self.assertTrue(cspec.get_concise_name('singleton_val') == 's')
self.assertTrue(cspec.get_concise_name('resolution') == 'res')
#scores_info
#self.assertTrue(cspec.scores_permuters['resolution'][0] == 'userDay')
#self.assertTrue(cspec.scores_permuters['resolution'][1] == 'userMonth')
#self.assertTrue(cspec.scores_from_filepath=='<permutation_output_dir>/(resolution).csv')
#self.assertTrue(cspec.scores_from_colname=='auc')
#self.assertTrue(cspec.scores_from_rownum=='1')
#print 'self.cspec.scores_to : {0}'.format(self.cspec.scores_to)
#self.assertTrue(cspec.scores_to=='./collected_results')
#self.assertTrue(cspec.scores_x_axis==['number', 'animal'])
#self.assertTrue(cspec.scores_y_axis==['letter'])
#script_dir
self.assertTrue(cspec.script_dir == '/myRuns/baz/scripts')
#trials:
self.assertTrue(cspec.trials == '2')
#master_job_name:
self.assertTrue(cspec.cspec_name == 'baz')
#first_job_number:
self.assertTrue(cspec.first_job_number == '100')
#root_dir:
self.assertTrue(cspec.root_dir == '/myRuns')
# permuters:
self.assertTrue(cspec.permuters['number'][0] == '1')
self.assertTrue(cspec.permuters['number'][1] == '2')
self.assertTrue(cspec.permuters['number'][2] == '3')
self.assertTrue(cspec.permuters['letter'][0] == 'AAA')
self.assertTrue(cspec.permuters['letter'][1] == 'BBB')
# generate_results_dir_for_permutation:
self.assertTrue(
cspec.generate_results_dir_for_permutation('xyz_trial3') ==
'/myRuns/baz/results/xyz_trial3')
#concise_print_map:
self.assertTrue(cspec.concise_print_map['letter'] == 'l')
self.assertTrue(cspec.concise_print_map['singleton_val'] == 's')
#key_val_map:
kvm = cspec.key_val_map
self.assertTrue(kvm['config[AAA]'] == 'aaa')
self.assertTrue(kvm['config[BBB]'] == 'bbb')
self.assertTrue(kvm['pretty[1]'] == 'one')
self.assertTrue(kvm['pretty[2]'] == 'two')
self.assertTrue(kvm['pretty[3]'] == 'three')
self.assertTrue(kvm['cspec_name'] == 'baz')
self.assertTrue(kvm['root'] == '/nfs/foo/bar')
self.assertTrue(kvm['x_dir'] ==
'/nfs/foo/bar/(letter)/<config[(letter)]>/(number)')
self.assertTrue(kvm['algs_dir'] == '/nfs/algs')
self.assertTrue(kvm['tools_dir'] == '/nfs/algs/tools')
self.assertTrue(kvm['outfile_root'] == '<pretty[(number)]>__TEST')
#commands:
commands_as_string = "{0}".format(cspec.commands)
self.assertTrue(
commands_as_string ==
"['echo (letter) (number) (singleton_val) > <permutation_output_dir>/(letter)_(number)_<pretty[(number)]>.txt']"
)
#qsub_commands:
qsub_commands_as_string = "{0}".format(cspec.qsub_commands)
self.assertTrue(
qsub_commands_as_string ==
"['-q eecs,eecs1,eecs,share', '-M [email protected]', '-m beas']")
def test_expand_permutations(self):
stdout = mock_stdout.MockStdout()
lines = []
lines.append("#pspec\n")
lines.append("(permute):number=range(1,4)\n")
lines.append("(permute):letter=AAA,BBB\n")
lines.append("(permute):singleton_val=300\n")
lines.append("(permute):animal=dog,cat\n")
cspec = cluster_spec.ClusterSpec("/foo/bar/baz.cspec", lines, stdout,
[], False, False)
permuters = cspec.permuters
dict_list = permutations.expand_permutations(permuters)
#print dict_list
self.assertTrue(len(dict_list) == 12)
dict1 = {
'animal': 'cat',
'number': '1',
'letter': 'AAA',
'singleton_val': '300'
}
dict2 = {
'animal': 'cat',
'number': '1',
'letter': 'BBB',
'singleton_val': '300'
}
dict3 = {
'animal': 'cat',
'number': '2',
'letter': 'AAA',
'singleton_val': '300'
}
dict4 = {
'animal': 'cat',
'number': '2',
'letter': 'BBB',
'singleton_val': '300'
}
dict5 = {
'animal': 'cat',
'number': '3',
'letter': 'AAA',
'singleton_val': '300'
}
dict6 = {
'animal': 'cat',
'number': '3',
'letter': 'BBB',
'singleton_val': '300'
}
dict7 = {
'animal': 'dog',
'number': '1',
'letter': 'AAA',
'singleton_val': '300'
}
dict8 = {
'animal': 'dog',
'number': '1',
'letter': 'BBB',
'singleton_val': '300'
}
dict9 = {
'animal': 'dog',
'number': '2',
'letter': 'AAA',
'singleton_val': '300'
}
dict10 = {
'animal': 'dog',
'number': '2',
'letter': 'BBB',
'singleton_val': '300'
}
dict11 = {
'animal': 'dog',
'number': '3',
'letter': 'AAA',
'singleton_val': '300'
}
dict12 = {
'animal': 'dog',
'number': '3',
'letter': 'BBB',
'singleton_val': '300'
}
self.assertTrue(dict1 in dict_list)
self.assertTrue(dict2 in dict_list)
self.assertTrue(dict3 in dict_list)
self.assertTrue(dict4 in dict_list)
self.assertTrue(dict5 in dict_list)
self.assertTrue(dict6 in dict_list)
self.assertTrue(dict7 in dict_list)
self.assertTrue(dict8 in dict_list)
self.assertTrue(dict9 in dict_list)
self.assertTrue(dict10 in dict_list)
self.assertTrue(dict11 in dict_list)
self.assertTrue(dict12 in dict_list)
