def test_write_chunks(self):
def f(i):
return {
"{c}movie_fofn_id".format(c=PipelineChunk.CHUNK_KEY_PREFIX):
"/path/to_movie-{i}.fofn".format(i=i),
"{c}region_fofn_id".format(c=PipelineChunk.CHUNK_KEY_PREFIX):
"/path/rgn_{i}.fofn".format(i=i)
}
def to_i(i):
return "chunk-id-{i}".format(i=i)
def to_p(i):
return PipelineChunk(to_i(i), **f(i))
nchunks = 5
pipeline_chunks = [to_p(i) for i in range(nchunks)]
log.debug(pipeline_chunks)
tmp_dir = get_temp_dir("pipeline-chunks")
tmp_name = get_temp_file("_chunk.json", tmp_dir)
write_pipeline_chunks(pipeline_chunks, tmp_name, "Example chunk file")
pchunks = load_pipeline_chunks_from_json(tmp_name)
assert len(pchunks) == nchunks
def test_01(self):
file_name = "resolved_tool_contract_dev_app.json"
rtc = load_resolved_tool_contract_from(get_data_file(file_name))
self.assertIsInstance(rtc, ResolvedToolContract)
d = get_temp_dir("rtc-app")
f = get_temp_file("-resolved-tool-contract.avro", d)
write_resolved_tool_contract_avro(rtc, f)
def test_01(self):
file_name = "resolved_tool_contract_dev_app.json"
rtc = load_resolved_tool_contract_from(get_resolved_tool_contract(file_name))
self.assertIsInstance(rtc, ResolvedToolContract)
d = get_temp_dir("rtc-app")
f = get_temp_file("-resolved-tool-contract.avro", d)
write_resolved_tool_contract_avro(rtc, f)
def test_simple_run_cmd(self):
d = get_temp_dir("simple-cmd")
txt_in = get_temp_file(".txt", d)
txt_out = get_temp_file("*.txt", d)
exe = "cat {i} > {o}".format(i=txt_in, o=txt_out)
# this could all be bundled into a context manager
# with RunCommand('/path/stdout', '/path/to/stderr') as r:
# r.exe("echo 'exe1')
# r.exe("echo 'exe2')
# result = r.get_result() # close the file handles
stdout = get_temp_file("-stdout", d)
stderr = get_temp_file("-stderr", d)
with open(stdout, 'w') as fo:
with open(stderr, 'w') as fe:
result = run_cmd(exe, fo, fe)
emgs = "Command {e} failed".format(e=exe)
if result.exit_code != 0:
print(emgs)
assert result.exit_code == 0
def test_write_chunks(self):
def f(i):
return {"{c}movie_fofn_id".format(c=PipelineChunk.CHUNK_KEY_PREFIX): "/path/to_movie-{i}.fofn".format(i=i),
"{c}region_fofn_id".format(c=PipelineChunk.CHUNK_KEY_PREFIX): "/path/rgn_{i}.fofn".format(i=i)}
to_i = lambda i: "chunk-id-{i}".format(i=i)
to_p = lambda i: PipelineChunk(to_i(i), **f(i))
nchunks = 5
pipeline_chunks = [to_p(i) for i in xrange(nchunks)]
log.debug(pipeline_chunks)
tmp_dir = get_temp_dir("pipeline-chunks")
tmp_name = get_temp_file("_chunk.json", tmp_dir)
write_pipeline_chunks(pipeline_chunks, tmp_name, "Example chunk file")
pchunks = load_pipeline_chunks_from_json(tmp_name)
self.assertEquals(len(pchunks), nchunks)
