예제 #1
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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
예제 #2
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파일: tasks.py 프로젝트: vvolkl/yadage
 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
예제 #3
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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
예제 #4
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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()
예제 #5
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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()
예제 #6
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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
예제 #7
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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
예제 #8
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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']
예제 #9
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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()
예제 #10
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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
예제 #11
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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()
예제 #12
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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'))
예제 #13
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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'))
예제 #14
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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)
예제 #15
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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")
예제 #16
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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)
예제 #17
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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
예제 #18
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파일: caching.py 프로젝트: vvolkl/yadage
 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']
     }
예제 #19
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    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'])
예제 #20
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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()
예제 #21
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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'))
예제 #22
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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)
예제 #23
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파일: tasks.py 프로젝트: vvolkl/yadage
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,
        }
예제 #24
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 def result(self, resultproxy):
     return TypedLeafs(resultproxy.resultdata, resultproxy.datamodel)
예제 #25
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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'])
예제 #26
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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']
예제 #27
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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()
예제 #28
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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'])