def get_unbound_inputs(cls, cfg):
"""
Get the unbound inputs
"""
cfg = cls.load_cfg(cfg)
dag = cls.create_dag(cfg)
# Step parameters
uinputs = defaultdict(dict)
for stepname, classname in cfg['dag']['nodes'].iteritems():
step = Step.create(classname)
input_keys = step.keys('inputs', req_only=True)
if input_keys:
for pred in dag.predecessors(stepname):
# Remove any key that is already bound
for binding in dag[pred][stepname].get('bindings', []):
key = binding.split('.')[1]
#maybe it has been already removed
if key in input_keys:
input_keys.remove(key)
if input_keys:
uinputs[stepname] = input_keys
return uinputs
def get_unbound_inputs(cls, cfg):
"""
Get the unbound inputs
"""
cfg = cls.load_cfg(cfg)
dag = cls.create_dag(cfg)
# Step parameters
uinputs = defaultdict(dict)
for stepname, classname in cfg['dag']['nodes'].iteritems():
step = Step.create(classname)
input_keys = step.keys('inputs', req_only=True)
if input_keys:
for pred in dag.predecessors(stepname):
# Remove any key that is already bound
for binding in dag[pred][stepname].get('bindings', []):
key = binding.split('.')[1]
#maybe it has been already removed
if key in input_keys:
input_keys.remove(key)
if input_keys:
uinputs[stepname] = input_keys
return uinputs
def create_steps(cfg):
stepobjs = {}
if 'sys_path' in cfg:
sys.path.insert(0, cfg['sys_path'])
for stepname, classname in cfg['dag']['nodes'].iteritems():
stepobjs[stepname] = Step.create(classname)
if 'sys_path' in cfg:
del sys.path[0]
return stepobjs
def create_steps(cfg):
stepobjs = {}
if 'sys_path' in cfg:
sys.path.insert(0, cfg['sys_path'])
for stepname, classname in cfg['dag']['nodes'].iteritems():
stepobjs[stepname] = Step.create(classname)
if 'sys_path' in cfg:
del sys.path[0]
return stepobjs
def get_metainfo(self, step_name):
"""
Return a dictionary with generic information about pipeline and step
"""
info = {}
info['pipeline'] = { 'name': self.name,
'version': self.__version__ }
info['user'] = { 'login': self.user,
'fullname': pwd.getpwnam(self.user).pw_gecos }
step_class = self.dag.node[step_name]['class_name']
stepobj = Step.create(step_class)
info['step'] = { 'name': step_name,
'class': step_class,
'version': stepobj.__version__ }
return info
def get_refgenomes(cls, cfg, unbound=None):
"""
Return a 2 level dictionary containing the path of the reference
genome grouped by labels.
A label is a combination of species, version and variation
{
"label1": {
"stepname1" : { "input_key1" : "/path1"},
"stepname2" : { "input_key1" : "/path2"}
}
"label2": {
"stepname1" : { "input_key1 : "/path3"},
"stepname2" : { "input_key1" : "/path4"}
}
}
The "unbound" dictionary contains the steps that have unbound inputs:
if set, only those steps will be considered
"""
refs = defaultdict(dict)
tools = set()
# Collect all tools that require a ref. genome
for stepname, classname in cfg['dag']['nodes'].iteritems():
if unbound == None or stepname in unbound:
step = Step.create(classname)
for ref in step.get_refgenome_tools():
tools.add(ref['tool'])
refs[stepname][ref['name']] = ref['tool']
# Get corresponding ref genomes
refs_by_label = {}
for ref in mongo.get_refgenomes(tools):
label = "%s %s" % (ref['_id']['species'], ref['_id']['version'])
if 'variation' in ref['_id']:
label += " (%s)" % ref['_id']['variation']
for stepname in refs:
if not label in refs_by_label:
refs_by_label[label] = {}
refs_by_label[label][stepname] = {}
for param_key in refs[stepname]:
tool = refs[stepname][param_key]
if tool in ref['paths']:
refs_by_label[label][stepname][param_key] = ref[
'paths'][tool]
return refs_by_label
def get(self, run_id):
"""
Return the dag of the given run
"""
pipeline = db.pipelines.find_one({'run_id': run_id}, {'config': 1, 'file_registry':1})
file_registry = pipeline.get('file_registry', [])
if file_registry:
file_registry = json.loads(file_registry)
conf_str = json.loads(pipeline['config'])
config = Pipeline.load_cfg(conf_str);
result_steps = config.get('config', {}).get('pipeline', {}).get('results', [])
delete_steps = config.get('config', {}).get('pipeline', {}).get('delete', [])
delete_steps.append('finalize')
delete_steps.append('inputs')
steps = list(db.steps.find(
{"run_id":run_id, "name": {"$nin": delete_steps}, "jobs": {"$elemMatch": {"outputs": {"$exists": True}}}},
{"name":1, "jobs":1, "outputs.output_dir": 1, "step_config": 1}))
outputs = {}
for step in steps:
if step.get('step_config', {}):
s = Step.load_step(step['step_config'])
output_files = []
for job_id, job in enumerate(step['jobs']):
for key in job['outputs']:
if key in s.keys(key_groups='outputs', key_filter={'type':'file'}):
for i, filename in enumerate(job['outputs'][key]):
output = { 'path': filename }
if not isinstance(filename, list):
output['archived'] = (filename in file_registry)
else:
output['archived'] = False
output_files.append(output)
if output_files:
outputs[step['name']] = defaultdict(list)
outputs[step['name']]['archive'] = step['name'] in result_steps
outputs[step['name']]['dir'] = step.get('outputs', {}).get('output_dir')
outputs[step['name']]['files'] = copy.deepcopy(output_files)
return outputs
def get_refgenomes(cls, cfg, unbound=None):
"""
Return a 2 level dictionary containing the path of the reference
genome grouped by labels.
A label is a combination of species, version and variation
{
"label1": {
"stepname1" : { "input_key1" : "/path1"},
"stepname2" : { "input_key1" : "/path2"}
}
"label2": {
"stepname1" : { "input_key1 : "/path3"},
"stepname2" : { "input_key1" : "/path4"}
}
}
The "unbound" dictionary contains the steps that have unbound inputs:
if set, only those steps will be considered
"""
refs = defaultdict(dict)
tools = set()
# Collect all tools that require a ref. genome
for stepname, classname in cfg['dag']['nodes'].iteritems():
if unbound==None or stepname in unbound:
step = Step.create(classname)
for ref in step.get_refgenome_tools():
tools.add(ref['tool'])
refs[stepname][ref['name']] = ref['tool']
# Get corresponding ref genomes
refs_by_label = {}
for ref in mongo.get_refgenomes(tools):
label = "%s %s" % (ref['_id']['species'], ref['_id']['version'])
if 'variation' in ref['_id']:
label += " (%s)" % ref['_id']['variation']
for stepname in refs:
if not label in refs_by_label:
refs_by_label[label] = {}
refs_by_label[label][stepname] = {}
for param_key in refs[stepname]:
tool = refs[stepname][param_key]
if tool in ref['paths']:
refs_by_label[label][stepname][param_key] = ref['paths'][tool]
return refs_by_label
def get_metainfo(self, step_name):
"""
Return a dictionary with generic information about pipeline and step
"""
info = {}
info['pipeline'] = {'name': self.name, 'version': self.__version__}
info['user'] = {
'login': self.user,
'fullname': pwd.getpwnam(self.user).pw_gecos
}
step_class = self.dag.node[step_name]['class_name']
stepobj = Step.create(step_class)
info['step'] = {
'name': step_name,
'class': step_class,
'version': stepobj.__version__
}
return info
def run_step(self, step_name):
"""
Configure and run a job for the given step
"""
#skip the input step
if step_name == 'inputs':
self.completed.append(step_name)
self.outputs[step_name] = self.cfg['config']['steps'].get(step_name, {})
self.outputs[step_name]['output_dir'] = ''
self.db.update_step_status(step_name, JOB_STATUS.RUNNING)
self.db.update_step_status(step_name, JOB_STATUS.SUCCEEDED)
self.db.set_step_outputs(step_name, self.outputs[step_name])
else:
if self.one_step:
step_config = self.cfg
step_config['sys_path'] = self.sys_path
step_config['output_dir'] = self.output_dir
step_config['meta'] = { 'meta' : { 'pipeline':{}, 'step':{}, 'job':{} }}
ut.dict_update(step_config['meta']['pipeline'], self.meta['pipeline'])
elif step_name == FINAL_STEP:
step_config = { 'meta' : { 'pipeline':{}, 'step':{}, 'job':{} } }
ut.dict_update(step_config['meta']['pipeline'], self.meta['pipeline'])
step_config['name'] = FINAL_STEP
step_config['step_class'] = self.dag.node[step_name]['class_name']
step_config['target_dir'] = self.output_dir
step_config['source_dir'] = self.work_dir
step_config['output_dir'] = os.path.join(self.work_dir, step_name)
self.configure_finalstep(step_config)
else:
step_config = { 'meta' : { 'pipeline':{}, 'step':{}, 'job':{} } }
ut.dict_update(step_config['meta']['pipeline'], self.meta['pipeline'])
step_class = self.dag.node[step_name]['class_name']
step_config['name'] = step_name
step_config['sys_path'] = self.sys_path
step_config['step_class'] = step_class
step_config['output_dir'] = os.path.join(self.work_dir, step_name)
# 1. Form input keys
# Remember: edges are labelled by 'from' keys
for pred in self.dag.predecessors(step_name):
edge = self.dag[pred][step_name]
# Not an actual loop: just get key/value
for bind_to, bind_from in edge.get('bindings', {}).iteritems():
to_key = bind_to.split('.')[1]
if hasattr(bind_from, '__iter__'):
for from_key in bind_from:
key = from_key.split('.')[1]
out = self.outputs[pred][key]
if to_key in step_config:
if isinstance(step_config[to_key], basestring):
step_config[to_key] = [step_config[to_key]]
step_config[to_key].extend(out)
else:
step_config[to_key] = out
else:
from_key = bind_from.split('.')[1]
out = self.outputs[pred][from_key]
if to_key in step_config:
if isinstance(step_config[to_key], basestring):
step_config[to_key] = [step_config[to_key]]
step_config[to_key].extend(out)
else:
step_config[to_key] = out
# Transfer metadata of previous step to next step
for key in self.meta['steps'].get(pred, {}):
step_config['meta'][key] = self.meta['steps'][pred][key]
# 2. Form step config.
if not self.one_step:
ut.dict_update(step_config, self.cfg['config']['steps'].get(step_name, {}), replace=False)
if step_name == FINAL_STEP:
# final step: pass full pipeline metadata
step_config['meta'].update(self.meta)
else:
self.update_metadata(step_name, step_config[KEY_META])
# 3. Submit step
self.log.info('Executing step %s' % str(step_name))
self.log.debug(' step configuration:\n %s' % ut.format_dict(step_config, indent=4))
self.log.info(' step %s queued ' % str(step_name))
self.running[step_name] = Step.load_step(step_config)
job_counter = self.running[step_name].distribute()
self.db.start_step(step_name, step_config, job_counter)
def validate_config(cls, cfg, user):
"""
Check if all the config params are ok
"""
retval = defaultdict(dict)
s_errors = defaultdict(dict)
#try:
cfg = cls.load_cfg(cfg)
params = cls.get_params(cfg)
unb_inputs = cls.get_unbound_inputs(cfg)
#validate step section
for stepname in params['steps']:
if stepname is not 'inputs':
classname = cfg['dag']['nodes'][stepname]
stepobj = Step.create(classname)
if stepname in cfg['config']['steps']:
required_keys = []
required_keys.extend(unb_inputs.get(stepname, []))
required_keys.extend(stepobj.keys(['params'], req_only=True))
stepcfg = cfg['config']['steps'][stepname]
for key in required_keys:
if key in stepcfg:
param_spec = stepobj.key_spec(key)
error_msg = stepobj.validate_value(stepcfg[key], param_spec['type'], param_spec['name'])
if error_msg:
s_errors[stepname][key] = error_msg
else:
s_errors[stepname][key] = 'missing value'
else:
for key in stepobj.keys(['params'], req_only=True):
s_errors[stepname][key] = 'missing value'
if stepname in unb_inputs:
for key in unb_inputs[stepname]:
s_errors[stepname][key] = 'missing value'
#validate pipeline section
p_errors = {}
if not cfg['config']['pipeline']['project_name']:
p_errors['project_name'] = 'missing value'
if not cfg['config']['pipeline']['description']:
p_errors['description'] = 'missing value'
if not cfg['config']['pipeline']['output_dir']:
p_errors['output_dir'] = 'missing value'
else:
output_dir = cfg['config']['pipeline']['output_dir']
if not output_dir.startswith('/'):
p_errors['output_dir'] = '%s : not an absolute path' % output_dir
if not isinstance(output_dir, basestring):
p_errors['output_dir'] = '%s : invalid type, found %s, expected %s' % (output_dir, type(output_dir), 'str')
#elif not ut.has_write_access(output_dir):
# p_errors['output_dir'] = '%s : not writable by user' % (output_dir)
if s_errors:
retval['steps'] = s_errors
if p_errors:
retval['pipeline'] = p_errors
return retval
def post(self, run_id):
"""
Pushes files into iRODS
"""
data = request.get_json(force=True)
runmeta = data.get('meta')
selection = data.get('selection')
user = auth_get_username(request.authorization, data.get('user'))
npdis = dbmodel.get_npdi_projects()
npdi = runmeta.get('Project NPDI ID', '')
study_nickname = runmeta.get('Study nickname',
'Required field missing')
if (npdi + study_nickname) not in npdis:
return {
'pipeline': {
'Project': '%s (%s)' % (npdi, study_nickname)
}
}, 400
run = db.pipelines.find_one({'run_id': run_id}, {
'meta': 1,
'run_id': 1
})
steps_names = selection.keys()
steps = list(
db.steps.find(
{
"run_id": run_id,
"name": {
'$in': steps_names
},
"jobs": {
"$elemMatch": {
"outputs": {
"$exists": True
}
}
}
}, {
"name": 1,
"jobs": 1,
"outputs.output_dir": 1,
"step_config": 1
}))
outputs = {}
for step in steps:
if step.get('step_config', {}):
s = Step.load_step(step['step_config'])
output_files = {}
for job_id, job in enumerate(step['jobs']):
for key in job['outputs']:
if key in s.keys(key_groups='outputs',
key_filter={'type': 'file'}):
for i, filename in enumerate(
job['outputs'][key]):
filemeta = {
'step': step['name'],
'job_id': job_id
}
ext = os.path.splitext(
filename)[1][1:].upper()
for key in job.get('meta', {}):
meta = job['meta'][key]
if key == 'sample_id':
okey = 'Operational sample accession'
else:
okey = key
if isinstance(meta, list):
filemeta[okey] = meta[i]
else:
filemeta[okey] = meta
filemeta[
'File type'] = 'Processed data file'
filemeta['File format'] = ext
output_files[filename] = filemeta
if output_files:
outputs[step['name']] = output_files
input_files = []
meta_data = []
for step_name, step_selection in selection.iteritems():
for filepath in step_selection:
input_files.append(filepath)
filemeta = outputs[step_name][filepath]
filemeta.update(runmeta)
meta_data.append(filemeta)
cfg = Pipeline.load_cfg(pipeline_specs['irods_lz'])
cfg['config']['steps']['irods_mvtolz'] = {
'input_files': input_files,
'meta_data': meta_data
}
cfg['config']['steps']['irods_monitorlz'] = {
'prun_id': run['run_id']
}
cfg['config']['pipeline']['project_name'] = run['meta'][
'project_name']
cfg['config']['pipeline'][
'description'] = 'Archive data for run %s' % run['run_id']
cfg['config']['pipeline']['output_dir'] = '/scratch/cgi/irods'
# Get id from DB
db_info = dbmodel.PipelineDb(cfg['name'], cfg,
Pipeline.ordered_steps(cfg), user)
cfg['run_id'] = db_info.run_id
ut.pretty_print("Submitting pipeline %s (ID %d) for user %s" %
(cfg['label'], cfg['run_id'], user))
return pm.add_pipeline(cfg, user)
def run_step(self, step_name):
"""
Configure and run a job for the given step
"""
#skip the input step
if step_name == 'inputs':
self.completed.append(step_name)
self.outputs[step_name] = self.cfg['config']['steps'].get(
step_name, {})
self.outputs[step_name]['output_dir'] = ''
self.db.update_step_status(step_name, JOB_STATUS.RUNNING)
self.db.update_step_status(step_name, JOB_STATUS.SUCCEEDED)
self.db.set_step_outputs(step_name, self.outputs[step_name])
else:
if self.one_step:
step_config = self.cfg
step_config['sys_path'] = self.sys_path
step_config['output_dir'] = self.output_dir
step_config['meta'] = {
'meta': {
'pipeline': {},
'step': {},
'job': {}
}
}
ut.dict_update(step_config['meta']['pipeline'],
self.meta['pipeline'])
elif step_name == FINAL_STEP:
step_config = {'meta': {'pipeline': {}, 'step': {}, 'job': {}}}
ut.dict_update(step_config['meta']['pipeline'],
self.meta['pipeline'])
step_config['name'] = FINAL_STEP
step_config['step_class'] = self.dag.node[step_name][
'class_name']
step_config['target_dir'] = self.output_dir
step_config['source_dir'] = self.work_dir
step_config['output_dir'] = os.path.join(
self.work_dir, step_name)
self.configure_finalstep(step_config)
else:
step_config = {'meta': {'pipeline': {}, 'step': {}, 'job': {}}}
ut.dict_update(step_config['meta']['pipeline'],
self.meta['pipeline'])
step_class = self.dag.node[step_name]['class_name']
step_config['name'] = step_name
step_config['sys_path'] = self.sys_path
step_config['step_class'] = step_class
step_config['output_dir'] = os.path.join(
self.work_dir, step_name)
# 1. Form input keys
# Remember: edges are labelled by 'from' keys
for pred in self.dag.predecessors(step_name):
edge = self.dag[pred][step_name]
# Not an actual loop: just get key/value
for bind_to, bind_from in edge.get('bindings',
{}).iteritems():
to_key = bind_to.split('.')[1]
if hasattr(bind_from, '__iter__'):
for from_key in bind_from:
key = from_key.split('.')[1]
out = self.outputs[pred][key]
if to_key in step_config:
if isinstance(step_config[to_key],
basestring):
step_config[to_key] = [
step_config[to_key]
]
step_config[to_key].extend(out)
else:
step_config[to_key] = out
else:
from_key = bind_from.split('.')[1]
out = self.outputs[pred][from_key]
if to_key in step_config:
if isinstance(step_config[to_key], basestring):
step_config[to_key] = [step_config[to_key]]
step_config[to_key].extend(out)
else:
step_config[to_key] = out
# Transfer metadata of previous step to next step
for key in self.meta['steps'].get(pred, {}):
step_config['meta'][key] = self.meta['steps'][pred][
key]
# 2. Form step config.
if not self.one_step:
ut.dict_update(step_config,
self.cfg['config']['steps'].get(step_name, {}),
replace=False)
if step_name == FINAL_STEP:
# final step: pass full pipeline metadata
step_config['meta'].update(self.meta)
else:
self.update_metadata(step_name, step_config[KEY_META])
# 3. Submit step
self.log.info('Executing step %s' % str(step_name))
self.log.debug(' step configuration:\n %s' %
ut.format_dict(step_config, indent=4))
self.log.info(' step %s queued ' % str(step_name))
self.running[step_name] = Step.load_step(step_config)
job_counter = self.running[step_name].distribute()
self.db.start_step(step_name, step_config, job_counter)
def validate_config(cls, cfg, user):
"""
Check if all the config params are ok
"""
retval = defaultdict(dict)
s_errors = defaultdict(dict)
#try:
cfg = cls.load_cfg(cfg)
params = cls.get_params(cfg)
unb_inputs = cls.get_unbound_inputs(cfg)
#validate step section
for stepname in params['steps']:
if stepname is not 'inputs':
classname = cfg['dag']['nodes'][stepname]
stepobj = Step.create(classname)
if stepname in cfg['config']['steps']:
required_keys = []
required_keys.extend(unb_inputs.get(stepname, []))
required_keys.extend(
stepobj.keys(['params'], req_only=True))
stepcfg = cfg['config']['steps'][stepname]
for key in required_keys:
if key in stepcfg:
param_spec = stepobj.key_spec(key)
error_msg = stepobj.validate_value(
stepcfg[key], param_spec['type'],
param_spec['name'])
if error_msg:
s_errors[stepname][key] = error_msg
else:
s_errors[stepname][key] = 'missing value'
else:
for key in stepobj.keys(['params'], req_only=True):
s_errors[stepname][key] = 'missing value'
if stepname in unb_inputs:
for key in unb_inputs[stepname]:
s_errors[stepname][key] = 'missing value'
#validate pipeline section
p_errors = {}
if not cfg['config']['pipeline']['project_name']:
p_errors['project_name'] = 'missing value'
if not cfg['config']['pipeline']['description']:
p_errors['description'] = 'missing value'
if not cfg['config']['pipeline']['output_dir']:
p_errors['output_dir'] = 'missing value'
else:
output_dir = cfg['config']['pipeline']['output_dir']
if not output_dir.startswith('/'):
p_errors[
'output_dir'] = '%s : not an absolute path' % output_dir
if not isinstance(output_dir, basestring):
p_errors[
'output_dir'] = '%s : invalid type, found %s, expected %s' % (
output_dir, type(output_dir), 'str')
#elif not ut.has_write_access(output_dir):
# p_errors['output_dir'] = '%s : not writable by user' % (output_dir)
if s_errors:
retval['steps'] = s_errors
if p_errors:
retval['pipeline'] = p_errors
return retval
def post(self, run_id):
"""
Pushes files into iRODS
"""
data = request.get_json(force=True)
runmeta = data.get('meta')
selection = data.get('selection')
user = auth_get_username(request.authorization, data.get('user'))
npdis = dbmodel.get_npdi_projects()
npdi = runmeta.get('Project NPDI ID', '')
study_nickname = runmeta.get('Study nickname', 'Required field missing')
if (npdi + study_nickname) not in npdis:
return {'pipeline': {
'Project': '%s (%s)' %(npdi, study_nickname)
}}, 400
run = db.pipelines.find_one({'run_id': run_id}, {'meta':1, 'run_id':1})
steps_names = selection.keys()
steps = list(db.steps.find(
{"run_id":run_id, "name": {'$in': steps_names}, "jobs": {"$elemMatch": {"outputs": {"$exists": True}}}},
{"name":1, "jobs":1, "outputs.output_dir": 1, "step_config": 1}))
outputs = {}
for step in steps:
if step.get('step_config', {}):
s = Step.load_step(step['step_config'])
output_files = {}
for job_id, job in enumerate(step['jobs']):
for key in job['outputs']:
if key in s.keys(key_groups='outputs', key_filter={'type':'file'}):
for i, filename in enumerate(job['outputs'][key]):
filemeta = {'step': step['name'], 'job_id': job_id}
ext = os.path.splitext(filename)[1][1:].upper()
for key in job.get('meta', {}):
meta = job['meta'][key]
if key == 'sample_id':
okey = 'Operational sample accession'
else:
okey = key
if isinstance(meta, list):
filemeta[okey] = meta[i]
else:
filemeta[okey] = meta
filemeta['File type'] = 'Processed data file'
filemeta['File format'] = ext
output_files[filename] = filemeta
if output_files:
outputs[step['name']] = output_files
input_files = []
meta_data = []
for step_name, step_selection in selection.iteritems():
for filepath in step_selection:
input_files.append(filepath)
filemeta = outputs[step_name][filepath]
filemeta.update(runmeta)
meta_data.append(filemeta)
cfg = Pipeline.load_cfg(pipeline_specs['irods_lz'])
cfg['config']['steps']['irods_mvtolz'] = {
'input_files' : input_files,
'meta_data' : meta_data
}
cfg['config']['steps']['irods_monitorlz'] = {
'prun_id' : run['run_id']
}
cfg['config']['pipeline']['project_name'] = run['meta']['project_name']
cfg['config']['pipeline']['description'] = 'Archive data for run %s' %run['run_id']
cfg['config']['pipeline']['output_dir'] = '/scratch/cgi/irods'
# Get id from DB
db_info = dbmodel.PipelineDb(cfg['name'], cfg, Pipeline.ordered_steps(cfg), user)
cfg['run_id'] = db_info.run_id
ut.pretty_print("Submitting pipeline %s (ID %d) for user %s" % (cfg['label'], cfg['run_id'], user))
return pm.add_pipeline(cfg, user)
def __init__(self, cfg, user='******', db=True, schedname="SCHED_CONDOR"):
"""
Read in the pipeline graph and load the configuration.
"""
self.all_ok = True
self.user = user
self.status = JOB_STATUS.QUEUED
self.lock = ''
self.completed = []
self.running = {}
self.outputs = {}
self.schedname = schedname
db_model_name = "MONGO_DB" if db else "STUB_DB"
# Load configuration
self.one_step = False
try:
self.cfg = Pipeline.load_cfg(cfg)
except Exception as e1:
print('Failed to load config as pipeline (error=%s). Trying as step' % e1)
try:
self.cfg = Step.load_cfg(cfg)
self.step = Step.load_step(self.cfg)
self.one_step = True
except Exception as e2:
Exception("Unable to load config file %s:\n" \
"pipeline load: %s\n" \
"step load: %s" % (cfg, e1, e2))
# Set all additional information
self.run_id = self.cfg.get('run_id')
if self.one_step:
self.name = self.step.name
self.label = self.step.name
self.project_name = self.cfg.get('project_name', '')
self.description = self.cfg.get('description', '')
self.output_dir = self.step.output_dir
self.ordered = [self.step.name]
else:
self.name = self.cfg['name']
self.label = self.cfg['label']
self.project_name = self.cfg['config']['pipeline'].get('project_name', '')
self.description = self.cfg['config']['pipeline'].get('description', '')
self.output_dir = self.cfg['config']['pipeline']['output_dir']
if not self.output_dir.startswith('/scratch'):
self.cfg['dag']['nodes'][FINAL_STEP] = 'utils.Finalize' #TODO: Make it work for one_step as well
self.ordered = Pipeline.ordered_steps(self.cfg)
self.sys_path = self.cfg.get('sys_path')
if self.sys_path:
sys.path.insert(0, self.sys_path)
self.dag = self.create_dag(self.cfg, one_step=self.one_step)
self.meta = {
'pipeline': {
'label': self.label,
'project_name': self.project_name,
'descr': self.description,
'run_id': self.run_id
},
'steps': {},
'job' : {}
}
self.db = db_models[db_model_name](self.name, self.cfg, self.ordered, self.user, output_dir=self.output_dir)
if hasattr(self.db, 'run_id'):
self.run_id = self.db.run_id
self.cfg['run_id'] = self.run_id
# Define the output directories
if not os.path.exists(self.output_dir):
os.makedirs(self.output_dir, 0775)
# Use default output dir under /scratch/cgi/nespipe (linked to user-defined dir.)
# if: a) this run is using the db (so we have a run ID); b) it is not a demux. run;
# and c) the user-defined directory is not already under /scratch
if self.run_id and not (self.name == 'demultiplexing'):
dirname = '%s_%d' % (self.name, self.db.run_id)
self.output_dir = os.path.join(self.output_dir, dirname)
if not os.path.exists(self.output_dir):
os.makedirs(self.output_dir, 0775)
# In case of /scratch, do not create an additional sub-directory
if self.output_dir.startswith('/scratch'):
self.work_dir = self.output_dir
else:
self.work_dir = os.path.join(WORK_DIR, self.user, dirname)
if not os.path.exists(self.work_dir):
os.makedirs(self.work_dir, 0775)
symlink = os.path.join(self.output_dir, 'work_area')
if not os.path.exists(symlink):
os.symlink(self.work_dir, symlink)
else:
self.work_dir = self.output_dir
ut.pretty_print('Output directories: output_dir=%s, work_dir=%s' % (self.output_dir, self.work_dir))
self.db.update_pipeline(self.run_id, {'output_dir': self.output_dir,
'work_dir': self.work_dir })
def __init__(self, cfg, user='******', db=True, schedname="SCHED_CONDOR"):
"""
Read in the pipeline graph and load the configuration.
"""
self.all_ok = True
self.user = user
self.status = JOB_STATUS.QUEUED
self.lock = ''
self.completed = []
self.running = {}
self.outputs = {}
self.schedname = schedname
db_model_name = "MONGO_DB" if db else "STUB_DB"
# Load configuration
self.one_step = False
try:
self.cfg = Pipeline.load_cfg(cfg)
except Exception as e1:
print(
'Failed to load config as pipeline (error=%s). Trying as step'
% e1)
try:
self.cfg = Step.load_cfg(cfg)
self.step = Step.load_step(self.cfg)
self.one_step = True
except Exception as e2:
Exception("Unable to load config file %s:\n" \
"pipeline load: %s\n" \
"step load: %s" % (cfg, e1, e2))
# Set all additional information
self.run_id = self.cfg.get('run_id')
if self.one_step:
self.name = self.step.name
self.label = self.step.name
self.project_name = self.cfg.get('project_name', '')
self.description = self.cfg.get('description', '')
self.output_dir = self.step.output_dir
self.ordered = [self.step.name]
else:
self.name = self.cfg['name']
self.label = self.cfg['label']
self.project_name = self.cfg['config']['pipeline'].get(
'project_name', '')
self.description = self.cfg['config']['pipeline'].get(
'description', '')
self.output_dir = self.cfg['config']['pipeline']['output_dir']
if not self.output_dir.startswith('/scratch'):
self.cfg['dag']['nodes'][
FINAL_STEP] = 'utils.Finalize' #TODO: Make it work for one_step as well
self.ordered = Pipeline.ordered_steps(self.cfg)
self.sys_path = self.cfg.get('sys_path')
if self.sys_path:
sys.path.insert(0, self.sys_path)
self.dag = self.create_dag(self.cfg, one_step=self.one_step)
self.meta = {
'pipeline': {
'label': self.label,
'project_name': self.project_name,
'descr': self.description,
'run_id': self.run_id
},
'steps': {},
'job': {}
}
self.db = db_models[db_model_name](self.name,
self.cfg,
self.ordered,
self.user,
output_dir=self.output_dir)
if hasattr(self.db, 'run_id'):
self.run_id = self.db.run_id
self.cfg['run_id'] = self.run_id
# Define the output directories
if not os.path.exists(self.output_dir):
os.makedirs(self.output_dir, 0775)
# Use default output dir under /scratch/cgi/nespipe (linked to user-defined dir.)
# if: a) this run is using the db (so we have a run ID); b) it is not a demux. run;
# and c) the user-defined directory is not already under /scratch
if self.run_id and not (self.name == 'demultiplexing'):
dirname = '%s_%d' % (self.name, self.db.run_id)
self.output_dir = os.path.join(self.output_dir, dirname)
if not os.path.exists(self.output_dir):
os.makedirs(self.output_dir, 0775)
# In case of /scratch, do not create an additional sub-directory
if self.output_dir.startswith('/scratch'):
self.work_dir = self.output_dir
else:
self.work_dir = os.path.join(WORK_DIR, self.user, dirname)
if not os.path.exists(self.work_dir):
os.makedirs(self.work_dir, 0775)
symlink = os.path.join(self.output_dir, 'work_area')
if not os.path.exists(symlink):
os.symlink(self.work_dir, symlink)
else:
self.work_dir = self.output_dir
ut.pretty_print('Output directories: output_dir=%s, work_dir=%s' %
(self.output_dir, self.work_dir))
self.db.update_pipeline(self.run_id, {
'output_dir': self.output_dir,
'work_dir': self.work_dir
})
def get(self, run_id):
"""
Return the dag of the given run
"""
pipeline = db.pipelines.find_one({'run_id': run_id}, {
'config': 1,
'file_registry': 1
})
file_registry = pipeline.get('file_registry', [])
if file_registry:
file_registry = json.loads(file_registry)
conf_str = json.loads(pipeline['config'])
config = Pipeline.load_cfg(conf_str)
result_steps = config.get('config', {}).get('pipeline',
{}).get('results', [])
delete_steps = config.get('config', {}).get('pipeline',
{}).get('delete', [])
delete_steps.append('finalize')
delete_steps.append('inputs')
steps = list(
db.steps.find(
{
"run_id": run_id,
"name": {
"$nin": delete_steps
},
"jobs": {
"$elemMatch": {
"outputs": {
"$exists": True
}
}
}
}, {
"name": 1,
"jobs": 1,
"outputs.output_dir": 1,
"step_config": 1
}))
outputs = {}
for step in steps:
if step.get('step_config', {}):
s = Step.load_step(step['step_config'])
output_files = []
for job_id, job in enumerate(step['jobs']):
for key in job['outputs']:
if key in s.keys(key_groups='outputs',
key_filter={'type': 'file'}):
for i, filename in enumerate(
job['outputs'][key]):
output = {'path': filename}
if not isinstance(filename, list):
output['archived'] = (filename
in file_registry)
else:
output['archived'] = False
output_files.append(output)
if output_files:
outputs[step['name']] = defaultdict(list)
outputs[step['name']]['archive'] = step[
'name'] in result_steps
outputs[step['name']]['dir'] = step.get(
'outputs', {}).get('output_dir')
outputs[step['name']]['files'] = copy.deepcopy(
output_files)
return outputs
