def bake_pipe_with_matlab_user_path_extend():
return MockPipesModule('''
{
// Define iBRAIN pipe type
"type": "CellProfiler.Pipe",
// Define chain of processes
"chain": [
{
"type": "CustomCode.MatlabCall",
"submit_call": "disp(['Call result is: ' foo()])",
"default_parameters": {
"job_submission_queue": "8:00",
"job_resubmission_queue": "36:00"
}
}
]
}
\n''')
def bake_a_matlab_pipe():
return MockPipesModule('''
{
// Define iBRAIN pipe type
"type": "CellProfiler.Pipe",
// Define chain of processes
"chain": [
{
"type": "CustomCode.MatlabCall",
"submit_call": "disp('I am a mock custom matlab call')",
"default_parameters": {
"job_submission_queue": "8:00",
"job_resubmission_queue": "36:00"
}
}
]
}
\n''')
def bake_a_mock_pipe_with_no_param():
return MockPipesModule('''
{
// Define iBRAIN pipe type
"type": "CellProfiler.Pipe",
// Define chain of processes
"chain": [
{
"type": "CustomCode.PythonCall",
"default_parameters": {
"job_submission_queue": "8:00",
"job_resubmission_queue": "36:00",
"batch_path": "../../BATCH"
}
}
]
}
\n''')
def bake_a_bash_pipe():
return MockPipesModule('''
{
// Define iBRAIN pipe type
"type": "CellProfiler.Pipe",
// Define chain of processes
"chain": [
{
"type": "CustomCode.BashCall",
"submit_call": "echo 'I am a mock custom bash call'",
"default_parameters": {
"job_submission_queue": "8:00",
"job_resubmission_queue": "36:00",
"batch_path": "../../BATCH"
}
}
]
}
\n''')
def bake_a_pipe_for_folder_linking():
return MockPipesModule('''
{
// Define iBRAIN pipe type
"type": "CellProfiler.Pipe",
// Define chain of processes
"chain": [
{
"type": "Tools.LinkFiles",
"source_location": "{process_path}",
"target_location": "{plate_path}",
"file_patterns": {
"symlink": ["BATCH_*"]
},
"file_type": "d"
//"recursively": 0
}
]
}
\n''')
def bake_a_working_mock_pipe():
return MockPipesModule('''
{
// Define iBRAIN pipe type
"type": "CellProfiler.Pipe",
// Define chain of processes
"chain": [
{
"type": "Tools.LinkFiles",
"source_location": "{batch_path}_old",
"target_location": "{batch_path}",
"file_patterns": {
"symlink": ["test_sym_linking*"],
"hardlink": ["/^.*_hard_linking$/"]
},
"default_parameters": {
"job_submission_queue": "8:00",
"job_resubmission_queue": "36:00"
}
}
]
}
\n''')
def bake_an_empty_filepattern_list_pipe():
return MockPipesModule('''
{
// Define iBRAIN pipe type
"type": "CellProfiler.Pipe",
// Define chain of processes
"chain": [
{
"type": "Tools.LinkFiles",
"source_location": "''' + MOCK_LINKING_FILEPATH + '''",
"target_location": "{batch_path}",
"file_patterns": {
"hardlink": [],
"symlink": []
},
"default_parameters": {
"job_submission_queue": "8:00",
"job_resubmission_queue": "36:00"
}
}
]
}
\n''')