def cli(ctx, basepath, workflow_name, step, save, use_input):
ctx.obj["structure"] = Structure(basepath=basepath,
name=workflow_name,
step=step)
ctx.obj["json"] = False
ctx.obj["save"] = save
ctx.obj["use_input"] = use_input
def cli(ctx, basepath, workflow_name, step, save, use_input,
prototype_cache_preloaded_only):
ctx.obj["structure"] = Structure(basepath=basepath,
name=workflow_name,
step=step)
ctx.obj["json"] = True
ctx.obj["save"] = save
ctx.obj["use_input"] = use_input
ctx.obj["prototype_cache_preloaded_only"] = prototype_cache_preloaded_only
def cli(ctx, basepath, workflow_name, step, save, use_input, configuration):
ctx.obj["structure"] = Structure(basepath=basepath,
name=workflow_name,
step=step)
ctx.obj["save"] = save
ctx.obj["use_input"] = use_input
config_module = ctx.obj["structure"].configuration_module()
importlib.import_module(config_module)
configdict = sys.modules[config_module]
ctx.obj["configurations"] = configdict.configurations
def cli(ctx, basepath, workflow_name, step, configuration, save, use_input):
ctx.obj["structure"] = Structure(basepath=basepath,
name=workflow_name,
step=step)
ctx.obj["json"] = True
ctx.obj["save"] = save
ctx.obj["use_input"] = use_input
configdict = {}
execfile(configuration or ctx.obj["structure"].configuration_file_path(),
configdict)
ctx.obj["configurations"] = configdict["configurations"][:]
def cli(ctx, basepath, workflow_name, step, configuration, start, maximum,
json, hdf, save, use_input):
if not hdf and json:
ctx.obj["json"] = True
else:
ctx.obj["hdf"] = hdf
ctx.obj["json"] = json
if ctx.obj.get("json", False):
ctx.obj["file_type"] = "json"
elif ctx.obj.get("hdf", False):
ctx.obj["file_type"] = "h5"
ctx.obj["save"] = save
ctx.obj["use_input"] = use_input
ctx.obj["start"] = start
ctx.obj["maximum"] = maximum
ctx.obj["structure"] = Structure(basepath=basepath,
name=workflow_name,
step=step)
config_module = ctx.obj["structure"].configuration_module()
importlib.import_module(config_module)
configdict = sys.modules[config_module]
ctx.obj["configurations"] = configdict.configurations
def cli(ctx, basepath, workflow_name, step, use_input):
ctx.obj["structure"] = Structure(basepath=basepath,
name=workflow_name,
step=step)
ctx.obj["use_input"] = use_input
def start(start, end):
env_vars = json.load(
open(
os.path.join(os.path.dirname(__file__), os.pardir,
"base_configuration.json"), "r"))
env_vars.update(
json.load(
open(
os.path.join(os.path.dirname(__file__),
"workflow_configuration.json"), "r")))
if env_vars["DISS_BASEPATH"].startswith(
"./") or env_vars["DISS_BASEPATH"] == ".":
env_vars["DISS_BASEPATH"] = os.path.abspath(
os.path.join(os.path.dirname(__file__), os.pardir,
env_vars["DISS_BASEPATH"][1:]))
if env_vars["DISS_BASEPATH"] == "..":
env_vars["DISS_BASEPATH"] = os.path.abspath(
os.path.join(os.path.dirname(__file__), os.pardir, os.pardir,
env_vars["DISS_BASEPATH"][2:]))
if env_vars["DISS_WORKFLOWFOLDER_NAME"] == ".":
env_vars["DISS_WORKFLOWFOLDER_NAME"] = os.path.basename(
os.path.abspath(os.path.join(os.path.dirname(__file__),
os.pardir)))
workflow = Workflow()
workflow.add_task(
cli_path=Structure.data_selection_cli(),
cmd="index-valid-hdf-trees",
save=True,
pcount=1,
trees=[
os.path.join(
os.path.dirname(__file__), os.pardir,
"data/trees/Bd_Kpi_mdst_000001_prod00006875_task00000001.h5"),
os.path.join(
os.path.dirname(__file__), os.pardir,
"data/trees/Bd_Kspi0_mdst_000001_prod00006201_task00000001.h5")
],
name="Index valid HDF trees")
workflow.prepare_intermediate_as_input(reference="Index valid HDF trees")
workflow.add_task(cli_path=Structure.workflow_cli(),
cmd="process-as-matrix",
save=True,
hdf=True,
use_input=True,
name="Generate Distance Matrix",
pcount=16)
workflow.add_task(
cli_path=Structure.data_selection_cli(),
cmd="index-valid-hdf-trees",
save=True,
pcount=1,
representatives=[
os.path.join(
os.path.dirname(__file__), os.pardir,
"data/trees/Bd_Kpi_mdst_000001_prod00006875_task00000001.h5"),
os.path.join(
os.path.dirname(__file__), os.pardir,
"data/trees/Bd_Kspi0_mdst_000001_prod00006201_task00000001.h5")
],
trees=[
os.path.join(os.path.dirname(__file__), os.pardir,
"data/trees/toy_B-Kpi/1110020000_Kpi_Dplus.h5"),
os.path.join(os.path.dirname(__file__), os.pardir,
"data/trees/toy_B-Kpi/1110020000_Kpi_Dstar.h5"),
os.path.join(os.path.dirname(__file__), os.pardir,
"data/trees/toy_B-Kpi/1110026100_Kspi0_Dplus.h5"),
os.path.join(os.path.dirname(__file__), os.pardir,
"data/trees/toy_B-Kpi/1110026100_Kspi0_Dstar.h5")
],
name="Index trees and representatives")
workflow.prepare_intermediate_as_input(
reference="Index trees and representatives")
workflow.add_task(cli_path=Structure.workflow_cli(),
cmd="batch-process-as-vector",
save=True,
hdf=True,
use_input=True,
name="Generate Distance Vectors",
pcount=16)
# finalise results
workflow.finalise(file_type="h5", reference="Generate Distance Matrix")
workflow.finalise(file_type="h5", reference="Generate Distance Vectors")
workflow.execute(env_vars, start=start, end=end)
def cli(ctx, basepath, workflow_name, step):
ctx.obj["structure"] = Structure(basepath=basepath,
name=workflow_name,
step=step)