def run_show_template_details(template_id, output_preset_xml, output_preset_json):
rtasks, rfiles, operators, pipelines_d = __dynamically_load_all()
from pbsmrtpipe.pb_io import binding_str_to_task_id_and_instance_id
task_options = {}
if template_id in pipelines_d:
pipeline = pipelines_d[template_id]
print "**** Pipeline Summary ****"
print "id : {i}".format(i=pipeline.idx)
print "version : {i}".format(i=pipeline.version)
print "name : {x}".format(x=pipeline.display_name)
if pipeline.tags:
print "Tags : {t} ".format(t=",".join(pipeline.tags))
print "Description: \n {x}".format(x=pipeline.description.strip())
print
print pretty_bindings(pipeline.all_bindings)
for b_out, b_in, in pipeline.all_bindings:
for x in (b_out, b_in):
if not binding_str_is_entry_id(x):
task_id, _, _ = binding_str_to_task_id_and_instance_id(x)
task = rtasks.get(task_id, None)
if task is None:
log.warn("Unable to load task {x}".format(x=task_id))
else:
for k, vx in task.option_schemas.iteritems():
if k in pipeline.task_options:
# this is kinda not awesome. there's the double API here
# pbcommand and pbsmrtpipe need to be converted to
# use a non-jsonschema model
v = copy.deepcopy(vx)
v['properties'][k]['default'] = pipeline.task_options[k]
v['pb_option']['default'] = pipeline.task_options[k]
task_options[k] = v
else:
task_options[k] = copy.deepcopy(vx)
warn_msg = "Pipeline {i} has no options.".format(i=pipeline.idx)
if isinstance(output_preset_xml, str):
write_task_options_to_preset_xml_and_print(task_options, output_preset_xml, warn_msg)
if isinstance(output_preset_json, str):
write_presets_json_and_print(pipeline, task_options, output_preset_json, warn_msg)
if task_options:
_print_option_schemas(task_options)
else:
print "No default task options"
else:
msg = "Unable to find template id '{t}' in registered pipelines. Use the show-templates option to get a list of workflow options.".format(t=template_id)
log.error(msg)
print msg
return 0
def run_show_template_details(template_id, output_preset_xml):
rtasks, rfiles, operators, pipelines_d = __dynamically_load_all()
from pbsmrtpipe.pb_io import binding_str_to_task_id_and_instance_id
if template_id in pipelines_d:
pipeline = pipelines_d[template_id]
print "Pipeline id : {i}".format(i=pipeline.idx)
print "Pipeline name : {x}".format(x=pipeline.display_name)
print "Description : {x}".format(x=pipeline.description)
if pipeline.tags:
print "Tags : {t} ".format(t=",".join(pipeline.tags))
print pretty_bindings(pipeline.all_bindings)
if isinstance(output_preset_xml, str):
rtasks, rfiles, operators, pipelines = __dynamically_load_all()
task_options = {}
for b_out, b_in, in pipeline.bindings:
for x in (b_out, b_in):
task_id, _, _ = binding_str_to_task_id_and_instance_id(x)
task = rtasks.get(task_id, None)
if task is None:
log.warn("Unable to load task {x}".format(x=task_id))
else:
for k, v in task.option_schemas.iteritems():
task_options[k] = v
warn_msg = "Pipeline {i} has no options.".format(i=pipeline.idx)
write_task_options_to_preset_xml_and_print(task_options, output_preset_xml, warn_msg)
else:
msg = "Unable to find template id '{t}' in registered pipelines. Use the show-templates option to get a list of workflow options.".format(t=template_id)
log.error(msg)
print msg
return 0
def test_binding_str_format(self):
for b, r in zip(self.bs, self.results):
r2 = IO.binding_str_to_task_id_and_instance_id(b)
self.assertEquals(r, r2)
def run_show_template_details(template_id, output_preset_xml,
output_preset_json):
rtasks, rfiles, operators, pipelines_d = __dynamically_load_all()
from pbsmrtpipe.pb_io import binding_str_to_task_id_and_instance_id
pb_options = {}
if template_id in pipelines_d:
pipeline = pipelines_d[template_id]
print "**** Pipeline Summary ****"
print "id : {i}".format(i=pipeline.idx)
print "version : {i}".format(i=pipeline.version)
print "name : {x}".format(x=pipeline.display_name)
# print "Schema version: {}".format(pipeline.schema_version)
if pipeline.tags:
print "Tags : {t} ".format(t=",".join(pipeline.tags))
print "Description: \n {x}".format(x=pipeline.description.strip())
print
print pretty_bindings(pipeline.all_bindings)
for b_out, b_in, in pipeline.all_bindings:
for x in (b_out, b_in):
if not binding_str_is_entry_id(x):
task_id, _, _ = binding_str_to_task_id_and_instance_id(x)
task = rtasks.get(task_id, None)
if task is None:
log.warn("Unable to load task {x}".format(x=task_id))
else:
for pb_opt in task.option_schemas:
if pb_opt.option_id in pb_options:
continue
elif pb_opt.option_id in pipeline.task_options:
x = copy.deepcopy(pb_opt)
value = pipeline.task_options[pb_opt.option_id]
x._default = value # XXX hacky
pb_options[pb_opt.option_id] = x
else:
pb_options[pb_opt.option_id] = pb_opt
warn_msg = "Pipeline {i} has no options.".format(i=pipeline.idx)
task_options_d = OrderedDict([(k, pb_options[k].default)
for k in sorted(pb_options.keys())])
if isinstance(output_preset_xml, str):
write_task_options_to_preset_xml_and_print(task_options_d,
output_preset_xml,
warn_msg)
if isinstance(output_preset_json, str):
write_presets_json_and_print(pipeline, task_options_d,
output_preset_json, warn_msg)
if pb_options:
_print_pacbio_options(
[pb_options[k] for k in sorted(pb_options.keys())])
else:
print "No default task options"
else:
msg = "Unable to find template id '{t}' in registered pipelines. Use the show-templates option to get a list of workflow options.".format(
t=template_id)
log.error(msg)
print msg
return 0
def test_binding_str_format(self):
for b, r in zip(self.bs, self.results):
r2 = IO.binding_str_to_task_id_and_instance_id(b)
self.assertEquals(r, r2)
