def test_jsonpointer():
tl = TypedLeafs(nested_data, datamodel)
for p, v in tl.leafs():
try:
assert tl.jsonpointer(p.path).json() == v.json()
except AttributeError:
assert tl.jsonpointer(p.path) == v
def __init__(self, name, spec, state, parameters=None, inputs=None):
self.metadata = {'name': name}
self.inputs = inputs or []
self.parameters = TypedLeafs(parameters or {},
state.datamodel if state else None)
self.spec = spec
self.state = state
def test_jsonpointer():
tl = TypedLeafs(nested_data,datamodel)
for p, v in tl.leafs():
try:
assert tl.jsonpointer(p.path).json() == v.json()
except AttributeError:
assert tl.jsonpointer(p.path) == v
def test_jsonpath():
tl = TypedLeafs(nested_data, datamodel)
assert tl.jsonpath('single_thing').json() == tl['single_thing'].json()
assert tl.jsonpath(
'list_of_things[*]',
multiple_output=True)[0].json() == tl['list_of_things'][0].json()
def test_modify():
import jq
tl = TypedLeafs(nested_data,datamodel)
tlnew = TypedLeafs({'$type': 'MyClass', 'second_attr':'newsecond', 'first_attr': 'newfirst'}, datamodel)
tl['single_thing'] = tlnew.typed()
assert type(tlnew.typed()) == MyClass
assert tl['single_thing'].json() == tlnew.typed().json()
def pub(publisher, parameters, state):
topublish = TypedLeafs(publisher['outputmap'], parameters.leafmodel)
for p, v in topublish.leafs():
value = parameters[v]
if type(value) == known_types.SimpleFile:
if not value.path:
ensure_publicity(value, state)
p.set(topublish, value)
return topublish
def test_init():
tl = TypedLeafs(simple_data,datamodel)
assert type(tl['hello']) == MyClass
assert tl['hello'].first_attr == 'hello'
assert tl['hello'].second_attr == 'world'
assert tl.json() == simple_data
tl = TypedLeafs.fromJSON(simple_data, deserialization_opts = {'leafmodel': datamodel})
assert tl.json() == simple_data
def test_jq():
tl = TypedLeafs(nested_data, datamodel)
assert tl.jq(
'.list_of_things[]',
multiple_output=True)[0].json() == tl['list_of_things'][0].json()
assert tl.jq(
'.list_of_things[]',
multiple_output=True)[1].json() == tl['list_of_things'][1].json()
assert tl.jq('[.list_of_things[]]').json() == nested_data['list_of_things']
def test_refs():
import jq
refs = TypedLeafs(nested_data,datamodel).asrefs()
assert refs['list_of_things'][0].path == '/list_of_things/0'
import jsonpointer
jp = jsonpointer.JsonPointer('/list_of_things/0')
tl = TypedLeafs(nested_data,datamodel)
assert tl.resolve_ref(jp).json() == tl['list_of_things'][0].json()
def test_init():
tl = TypedLeafs(simple_data, datamodel)
assert type(tl['hello']) == MyClass
assert tl['hello'].first_attr == 'hello'
assert tl['hello'].second_attr == 'world'
assert tl.json() == simple_data
tl = TypedLeafs.fromJSON(simple_data,
deserialization_opts={'leafmodel': datamodel})
assert tl.json() == simple_data
def test_refs():
import jq
refs = TypedLeafs(nested_data, datamodel).asrefs()
assert refs['list_of_things'][0].path == '/list_of_things/0'
import jsonpointer
jp = jsonpointer.JsonPointer('/list_of_things/0')
tl = TypedLeafs(nested_data, datamodel)
assert tl.resolve_ref(jp).json() == tl['list_of_things'][0].json()
def jq_stage(stage, spec):
'''
:param stage: common stage parent object
:param spec: stage JSON-like spec
:return: None
'''
binds = spec['bindings']
binds = process_jsonlike(binds, 'has("$wflowref")',
lambda x: process_wflowref(x, stage.view))
log.info('transforming binds: %s', binds)
stagescript = spec['stepscript']
singlesteps = jq.jq(stagescript).transform(binds, multiple_output=False)
singlesteppars = map(
lambda x: process_jsonlike(x, 'has("$wflowpointer")',
process_wflowpointer), singlesteps)
postscript = spec['postscript']
for i, pars in enumerate(singlesteppars):
singlename = '{}_{}'.format(stage.name, i)
finalized, inputs = finalize_input(pars, stage.view)
log.info('postscripting: %s', finalized)
after_post = jq.jq(postscript).transform(finalized,
multiple_output=False)
after_post = TypedLeafs(after_post)
log.info('finalized to: %s', after_post)
addStepOrWorkflow(singlename, stage, after_post, inputs, spec)
registerExpressions(stage, spec.get('register_values'))
def multistep_stage(stage, spec):
'''
a stage that attaches an array of nodes to the DAG. The number of nodes
is determined by a scattering recipe. Currently two algs are supported
- ``zip``: one or more arrays of length n are iterated through in lock-step.
n nodes are added to the DAG where the parameters values are set to
the values in the iteration
- ``cartesian``: a cartesian product of a number of arrays (possibly different sizes)
adds n1 x n2 x ... nj nodes.
Nodes are attached to the DAG based on used upstream inputs
:param stage: common stage parent object
:param spec: stage JSON-like spec
:return: None
'''
log.debug('scheduling multistep stage with spec:\n%s', spec)
parameters = {
k: select_parameter(stage.view, v)
for k, v in get_parameters(spec['parameters']).items()
}
singlesteppars = scatter(parameters, spec['scatter'],
spec.get('batchsize'), spec.get('partitionsize'))
for i, pars in enumerate(singlesteppars):
singlename = '{}_{}'.format(stage.name, i)
finalized, inputs = finalize_input(pars, stage.view)
finalized = TypedLeafs(
finalized, getattr(stage.state_provider, 'datamodel', None))
addStepOrWorkflow(singlename, stage, finalized, inputs, spec)
registerExpressions(stage, spec.get('register_values'))
def main():
submissionspec = sys.argv[1]
log.info('staging out data according to specfile %s', submissionspec)
subdata = json.load(open(submissionspec))
pubspec = subdata['publisher_spec']
parameters = subdata['parameters']
state = subdata['state']
resultfile = subdata['resultfile']
log.info('pub: \n' + json.dumps(pubspec, indent=4))
log.info('pars: \n' + json.dumps(parameters, indent=4))
log.info('stat: \n' + json.dumps(state, indent=4))
ydgconfig = json.load(open(os.environ.get('YDGCONFIG', 'ydgconfig.json')))
state = LocalFSGlobalObjectsState.fromJSON(state)
parameters = TypedLeafs(parameters, state.datamodel)
teardown_spec, pubdata = publish(pubspec, parameters, state)
for upload in teardown_spec['uploads']:
state.put_file(upload['source'], upload['target'])
with open('result.json', 'wb') as fl:
fl.write(json.dumps(pubdata).encode('utf-8'))
client = Minio(ydgconfig['resultstorage']['host'],
access_key=ydgconfig['resultstorage']['access_key'],
secret_key=ydgconfig['resultstorage']['secret_key'],
secure=True)
client.fput_object(ydgconfig['resultstorage']['bucket'], resultfile,
'result.json')
log.info('writing result data to: %s', resultfile)
def create(data, model=None):
dmimpl = os.environ.get("PACKTIVITY_DATAMODEL_IMPL", "typedleafs")
if dmimpl == "typedleafs":
return TypedLeafs(data, model)
elif dmimpl == "purejson":
return PureJsonModel(data, model)
else:
raise RuntimeError("unknown implementation")
def fromparpub_handler(spec, parameters, state):
topublish = {}
for targetname, sourcename in spec['outputmap'].items():
value = parameters[sourcename]
if type(value) == yadageobjstore.known_types.SimpleFile:
value.local_path = value.local_path.format(
workdir=state.local_workdir)
topublish[targetname] = value
return TypedLeafs(topublish, state.datamodel)
def teardown_spec(topublish, state):
teardown_spec = {'uploads': []}
for p, value in topublish.leafs():
if type(value) == yadageobjstore.known_types.SimpleFile:
if not value.path:
log.info('this has no public path, so we need to upload it %s',
value.json())
teardown_spec['uploads'].append(upload_spec(value, state))
topublish.replace(p, TypedLeafs(value, state.datamodel).json())
log.info('topublish:\n%s', topublish.json())
return teardown_spec
def cachedresult(self, cacheid, state, silent=True):
'''
returns the cached result. when silent = True the mthod exits gracefully
and returns None
'''
if silent:
if not self.cacheexists(cacheid): return None
return {
'result':
TypedLeafs(self.cache[cacheid]['result']['result'],
state.datamodel),
'status':
self.cache[cacheid]['result']['status']
}
def fromJSON(cls, data, deserialization_opts=None):
if data['task']['type'] == 'packtivity_task':
task = packtivity_task.fromJSON(data['task'], deserialization_opts)
result = TypedLeafs(data['result'],
getattr(task.state, 'datamodel',
{})) if data['result'] else None
instance = cls(data['name'], task, data['id'], result)
adage.serialize.set_generic_data(instance, data)
instance.resultproxy = load_proxy(
data['proxy'], deserialization_opts,
best_effort_backend=False) if data['proxy'] else None
return instance
else:
raise RuntimeError('unknown task type', data['task']['type'])
def test_modify():
import jq
tl = TypedLeafs(nested_data, datamodel)
tlnew = TypedLeafs(
{
'$type': 'MyClass',
'second_attr': 'newsecond',
'first_attr': 'newfirst'
}, datamodel)
tl['single_thing'] = tlnew.typed()
assert type(tlnew.typed()) == MyClass
assert tl['single_thing'].json() == tlnew.typed().json()
def singlestep_stage(stage, spec):
'''
a simple state that adds a single step/workflow. The node is attached
to the DAG based on used upstream outputs
:param stage: common stage parent object
:param spec: stage JSON-like spec
:return: None
'''
log.debug('scheduling singlestep stage with spec:\n%s', spec)
parameters = {
k: select_parameter(stage.view, v)
for k, v in get_parameters(spec['parameters']).items()
}
finalized, inputs = finalize_input(parameters, stage.view)
finalized = TypedLeafs(finalized,
getattr(stage.state_provider, 'datamodel', None))
addStepOrWorkflow(stage.name, stage, finalized, inputs, spec)
registerExpressions(stage, spec.get('register_values'))
def interpolated_pub_handler(publisher, parameters, state):
workdir = state.local_workdir
forinterp = {}
for p, v in parameters.leafs():
if isinstance(v, yadageobjstore.known_types.SimpleFile):
continue
p.set(forinterp, v)
log.info('interpolation dict: %s', forinterp)
result = copy.deepcopy(publisher['publish'])
for path, value in leaf_iterator(publisher['publish']):
if not isinstance(value, string_types):
continue
resultval = value.format(**forinterp)
resultval = resultval.format(workdir=workdir)
globexpr = resultval
log.info('value: %s | expression %s', value, globexpr)
if publisher['relative_paths'] and os.path.commonprefix(
[workdir, globexpr]) == '':
globexpr = os.path.join(workdir, resultval)
if publisher['glob']:
globbed = glob2.glob(globexpr)
if globbed:
resultval = [
yadageobjstore.known_types.SimpleFile(local_path=p)
for p in globbed
]
else:
#if it's a string and the full path exists replace relative path
resultval = yadageobjstore.known_types.SimpleFile(
local_path=globexpr)
log.info('result value: %s', resultval)
path.set(result, resultval)
log.info('returning result: %s', result)
return TypedLeafs(result, state.datamodel)
class packtivity_task(object):
'''
packtivity task
'''
def __init__(self, name, spec, state, parameters=None, inputs=None):
self.metadata = {'name': name}
self.inputs = inputs or []
self.parameters = TypedLeafs(parameters or {},
state.datamodel if state else None)
self.spec = spec
self.state = state
def pubOnlyTask(self):
return (self.spec['environment'] is None) and (self.spec['process'] is
None)
#(de-)serialization
@classmethod
def fromJSON(cls, data, deserialization_opts=None):
instance = cls(data['metadata']['name'],
data['spec'],
load_state(data['state'], deserialization_opts)
if data['state'] else None,
data['parameters'],
inputs=map(outputReference.fromJSON, data['inputs']))
instance.metadata.update(**data['metadata'])
return instance
def json(self):
return {
'metadata': self.metadata,
'parameters': self.parameters.json(),
'inputs': [x.json() for x in self.inputs],
'type': 'packtivity_task',
'spec': self.spec,
'state': self.state.json() if self.state else None,
}
def result(self, resultproxy):
return TypedLeafs(resultproxy.resultdata, resultproxy.datamodel)
def test_deepnest():
tl = TypedLeafs(nested_data,datamodel)
paths = [p.path for p,v in tl.leafs()]
assert set(paths) == set(['/list_of_things/0','/list_of_things/1','/single_thing'])
def test_jq():
tl = TypedLeafs(nested_data,datamodel)
assert tl.jq('.list_of_things[]',multiple_output = True)[0].json() == tl['list_of_things'][0].json()
assert tl.jq('.list_of_things[]',multiple_output = True)[1].json() == tl['list_of_things'][1].json()
assert tl.jq('[.list_of_things[]]').json() == nested_data['list_of_things']
def test_jsonpath():
tl = TypedLeafs(nested_data,datamodel)
assert tl.jsonpath('single_thing').json() == tl['single_thing'].json()
assert tl.jsonpath('list_of_things[*]', multiple_output = True)[0].json() == tl['list_of_things'][0].json()
def test_deepnest():
tl = TypedLeafs(nested_data, datamodel)
paths = [p.path for p, v in tl.leafs()]
assert set(paths) == set(
['/list_of_things/0', '/list_of_things/1', '/single_thing'])
