def registry_runner(registry_, rtasks, output_dir, emit_xml=False):
# this will emit the PTs to an output dir
from pbsmrtpipe.pb_io import pipeline_to_xml, write_pipeline_templates_to_json
d = os.path.abspath(os.path.expanduser(output_dir))
r = registry_
log.info("Writing Pipeline Templates to {o}".format(o=output_dir))
print "Emitting pipelines to output dir {d}".format(d=d)
# write_pipeline_templates_to_avro(r.pipelines.values(), rtasks, d)
write_pipeline_templates_to_json(r.pipelines.values(), rtasks, d)
for p in r.pipelines.values():
if emit_xml:
file_name = p.idx + "_pipeline.xml"
path = os.path.join(output_dir, file_name)
xml = pipeline_to_xml(p)
with open(path, 'w') as f:
f.write(str(xml))
log.info("writing pipeline {x}".format(x=path))
log.info("Successfully wrote {n} pipelines to {d}".format(n=len(r.pipelines), d=d))
return 0
def main(argv):
base_path = op.dirname(__file__)
dest_path = op.join(base_path, "resolved-pipeline-templates")
os.environ["PB_TOOL_CONTRACT_DIR"] = op.join(base_path, "registered-tool-contracts")
rtasks_d = load_all_tool_contracts()
pts = load_all_installed_pipelines()
write_pipeline_templates_to_json(pts.values(), rtasks_d, dest_path)
return 0
def main(argv):
base_path = op.dirname(__file__)
dest_path = op.join(base_path, "resolved-pipeline-templates")
os.environ["PB_TOOL_CONTRACT_DIR"] = op.join(base_path,
"registered-tool-contracts")
rtasks_d = load_all_tool_contracts()
pts = load_all_installed_pipelines()
write_pipeline_templates_to_json(pts.values(), rtasks_d, dest_path)
return 0
def registry_runner(registry_, rtasks, output_dir, emit_xml=False):
"""
:type registry_: PipelineRegistry
:param rtasks:
:type output_dir: str
:type emit_xml: bool
:rtype: int
"""
# this will emit the PTs to an output dir
import pbsmrtpipe.pb_io as IO
# get around circular imports
import pbsmrtpipe.graph.bgraph as B
r = registry_
log.info("Validating pipelines")
# Validating pipeline integrity
for i, p in r.pipelines.iteritems():
log.debug("Validating pipeline {}".format(i))
bg = B.binding_strs_to_binding_graph(rtasks, list(p.all_bindings))
# or this will raise
is_valid = B.validate_binding_graph_integrity(bg)
log.info("Pipeline {} is valid? {}".format(i, is_valid))
# Make the dir if it' doesn't exist
output_pipeline_dir = os.path.abspath(os.path.expanduser(output_dir))
log.info("Writing {x} Pipeline Templates to {o}".format(o=output_dir,
x=len(
r.pipelines)))
print "Emitting pipelines to output dir {d}".format(d=output_pipeline_dir)
IO.write_pipeline_templates_to_json(r.pipelines.values(), rtasks,
output_pipeline_dir)
for p in r.pipelines.values():
if emit_xml:
file_name = p.idx + "_pipeline.xml"
path = os.path.join(output_dir, file_name)
xml = IO.pipeline_to_xml(p)
with open(path, 'w') as f:
f.write(str(xml))
log.info("writing pipeline {x}".format(x=path))
_d = dict(n=len(r.pipelines),
d=output_pipeline_dir,
x=len(r.original_pipeline_ids),
a=len(r.all_pipelines))
log.info(
"Successfully wrote {n} new pipelines (previously loaded {x} all pipelines {a} to {d}"
.format(**_d))
return 0
def registry_runner(registry_, rtasks, output_dir, emit_xml=False):
"""
:type registry_: PipelineRegistry
:param rtasks:
:type output_dir: str
:type emit_xml: bool
:rtype: int
"""
# this will emit the PTs to an output dir
import pbsmrtpipe.pb_io as IO
# get around circular imports
import pbsmrtpipe.graph.bgraph as B
r = registry_
log.info("Validating pipelines")
# Validating pipeline integrity
for i, p in r.pipelines.iteritems():
log.debug("Validating pipeline {}".format(i))
bg = B.binding_strs_to_binding_graph(rtasks, list(p.all_bindings))
# or this will raise
is_valid = B.validate_binding_graph_integrity(bg)
log.info("Pipeline {} is valid? {}".format(i, is_valid))
# Make the dir if it' doesn't exist
output_pipeline_dir = os.path.abspath(os.path.expanduser(output_dir))
log.info("Writing {x} Pipeline Templates to {o}".format(o=output_dir, x=len(r.pipelines)))
print "Emitting pipelines to output dir {d}".format(d=output_pipeline_dir)
IO.write_pipeline_templates_to_json(r.pipelines.values(), rtasks, output_pipeline_dir)
for p in r.pipelines.values():
if emit_xml:
file_name = p.idx + "_pipeline.xml"
path = os.path.join(output_dir, file_name)
xml = IO.pipeline_to_xml(p)
with open(path, 'w') as f:
f.write(str(xml))
log.info("writing pipeline {x}".format(x=path))
_d = dict(n=len(r.pipelines),
d=output_pipeline_dir,
x=len(r.original_pipeline_ids),
a=len(r.all_pipelines))
log.info("Successfully wrote {n} new pipelines (previously loaded {x} all pipelines {a} to {d}".format(**_d))
return 0
def run_show_templates(avro_output_dir=None, json_output_dir=None):
import pbsmrtpipe.loader as L
from pbsmrtpipe.pb_io import (write_pipeline_templates_to_avro,
write_pipeline_templates_to_json)
rtasks_d, _, _, pts = L.load_all()
print pretty_registered_pipelines(pts)
if avro_output_dir is not None:
write_pipeline_templates_to_avro(pts.values(), rtasks_d, avro_output_dir)
if json_output_dir is not None:
write_pipeline_templates_to_json(pts.values(), rtasks_d, json_output_dir)
return 0
def run_show_templates(avro_output_dir=None, json_output_dir=None):
import pbsmrtpipe.loader as L
from pbsmrtpipe.pb_io import (write_pipeline_templates_to_avro,
write_pipeline_templates_to_json)
rtasks_d, _, _, pts = L.load_all()
print pretty_registered_pipelines(pts)
if avro_output_dir is not None:
write_pipeline_templates_to_avro(pts.values(), rtasks_d, avro_output_dir)
if json_output_dir is not None:
write_pipeline_templates_to_json(pts.values(), rtasks_d, json_output_dir)
return 0
def run_show_templates(avro_output_dir=None,
json_output_dir=None,
show_all=False):
import pbsmrtpipe.loader as L
from pbsmrtpipe.pb_io import (write_pipeline_templates_to_avro,
write_pipeline_templates_to_json)
rtasks_d, _, _, pts = L.load_all()
print pretty_registered_pipelines(pts, show_all=show_all)
if not show_all:
print "Run with --show-all to display (unsupported) developer/internal pipelines"
if avro_output_dir is not None:
write_pipeline_templates_to_avro(pts.values(), rtasks_d,
avro_output_dir)
if json_output_dir is not None:
write_pipeline_templates_to_json(pts.values(), rtasks_d,
json_output_dir)
return 0
