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Running complex pipelines #963

Open FelixNeutatz opened 5 years ago

FelixNeutatz commented 5 years ago

Dear all,

I am a great fan of OpenML! It's great :) Currently, I am looking into more complex custom generated Pipelines and unfortunately, I run into exceptions, e.g.:

  File "/home/felix/FastFeatures/new_project/fastsklearnfeature/feature_selection/ComplexityDrivenFeatureConstruction.py", line 497, in run
    my_run = openml.runs.run_model_on_task(my_pipeline, self.reader.task)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/runs/functions.py", line 44, in run_model_on_task
    flow = sklearn_to_flow(model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 43, in sklearn_to_flow
    rval = _serialize_model(o)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 393, in _serialize_model
    _extract_information_from_model(model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 501, in _extract_information_from_model
    rval = sklearn_to_flow(v, model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 43, in sklearn_to_flow
    rval = _serialize_model(o)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 393, in _serialize_model
    _extract_information_from_model(model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 501, in _extract_information_from_model
    rval = sklearn_to_flow(v, model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 43, in sklearn_to_flow
    rval = _serialize_model(o)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 393, in _serialize_model
    _extract_information_from_model(model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 501, in _extract_information_from_model
    rval = sklearn_to_flow(v, model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 43, in sklearn_to_flow
    rval = _serialize_model(o)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 397, in _serialize_model
    _check_multiple_occurence_of_component_in_flow(model, sub_components)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 479, in _check_multiple_occurence_of_component_in_flow
    'trying to serialize %s.' % (visitee.name, model))
ValueError: Found a second occurence of component sklearn.compose._column_transformer.ColumnTransformer(identity=sklearn.preprocessing._function_transformer.FunctionTransformer) when trying to serialize FeatureUnion(n_jobs=None,
       transformer_list=[('deficit1557515560.9003851', Pipeline(memory=None,
     steps=[('deficit', ColumnTransformer(n_jobs=None, remainder='drop', sparse_threshold=0.3,
         transformer_weights=None,
         transformers=[('identity', FunctionTransformer(accept_sparse=False, check_inverse=True,
   ...        inverse_func=None, kw_args=None, pass_y='deprecated',
          validate=False), [0])]))]))],
       transformer_weights=None).

Is this a bug or a missing feature?

Best regards, Felix

mfeurer commented 5 years ago

It's the latter: https://github.com/openml/OpenML/issues/340

One way to work around this is to write wrapper subclasses and use them instead.

FelixNeutatz commented 5 years ago

I see. Is there any example of how to write such as wrapper subclass?

Thank you for your help, Felix

mfeurer commented 5 years ago

No, sorry. But it's basically as simple as:

class wrapper(sklearn.ensemble.RandomForestClassifier):
    pass
FelixNeutatz commented 5 years ago

Ah, ok. Thank you for your quick help :)

FelixNeutatz commented 5 years ago

Dear Matthias,

I implemented a simple wrapper class:

from sklearn.base import BaseEstimator
from sklearn.pipeline import Pipeline

class ComplexPipelineWrapper(BaseEstimator):

    def __init__(self, my_pipeline: Pipeline):
        self.my_pipeline = my_pipeline

    def fit(self, X, y=None, **fit_params):
        self.my_pipeline.fit(X, y, **fit_params)
        self.classes_ = self.my_pipeline.named_steps['classifier'].classes_
        return self

    def predict(self, X, **predict_params):
        return self.my_pipeline.predict(X, **predict_params)

and I call it like this

from fastsklearnfeature.feature_selection.openml_wrapper.ComplexPipelineWrapper import ComplexPipelineWrapper

my_pipeline = Pipeline([('features', max_feature.pipeline),
                                    ('classifier', my_globale_module.classifier_global(**max_feature.runtime_properties['hyperparameters']))
                                    ])

my_wrapper = ComplexPipelineWrapper(my_pipeline)
my_run = openml.runs.run_model_on_task(my_wrapper, self.reader.task, avoid_duplicate_runs=False)

Unfortunately, I still get an exception:

  File "/home/felix/FastFeatures/new_project/fastsklearnfeature/feature_selection/ComplexityDrivenFeatureConstruction.py", line 553, in run
    my_run = openml.runs.run_model_on_task(my_wrapper, self.reader.task, avoid_duplicate_runs=False)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/runs/functions.py", line 44, in run_model_on_task
    flow = sklearn_to_flow(model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 43, in sklearn_to_flow
    rval = _serialize_model(o)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 393, in _serialize_model
    _extract_information_from_model(model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 501, in _extract_information_from_model
    rval = sklearn_to_flow(v, model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 43, in sklearn_to_flow
    rval = _serialize_model(o)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 393, in _serialize_model
    _extract_information_from_model(model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 501, in _extract_information_from_model
    rval = sklearn_to_flow(v, model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 43, in sklearn_to_flow
    rval = _serialize_model(o)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 393, in _serialize_model
    _extract_information_from_model(model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 501, in _extract_information_from_model
    rval = sklearn_to_flow(v, model)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in sklearn_to_flow
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 46, in <listcomp>
    rval = [sklearn_to_flow(element, parent_model) for element in o]
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 43, in sklearn_to_flow
    rval = _serialize_model(o)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 397, in _serialize_model
    _check_multiple_occurence_of_component_in_flow(model, sub_components)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/sklearn_converter.py", line 479, in _check_multiple_occurence_of_component_in_flow
    'trying to serialize %s.' % (visitee.name, model))
ValueError: Found a second occurence of component sklearn.pipeline.Pipeline(Temperature=sklearn.compose._column_transformer.ColumnTransformer(identity=sklearn.preprocessing._function_transformer.FunctionTransformer)) when trying to serialize FeatureUnion(n_jobs=None,
       transformer_list=[('Temperature1557772718.8705542', Pipeline(memory=None,
     steps=[('Temperature', ColumnTransformer(n_jobs=None, remainder='drop', sparse_threshold=0.3,
         transformer_weights=None,
         transformers=[('identity', FunctionTransformer(accept_sparse=False, check_inverse=T...        inverse_func=None, kw_args=None, pass_y='deprecated',
          validate=False), [0])]))]))],
       transformer_weights=None).

Did I implement the wrapper incorrectly?

Best regards, Felix

mfeurer commented 5 years ago

Sorry for not being clear enough. You need to write a wrapper class for every occurence of a method beyond the first and need to make sure that every wrapper class is used only once.

FelixNeutatz commented 5 years ago

Thank you for the hint. I implemented as you suggested:

def replaceColumnTransformer(value: ColumnTransformer):
    NewClass = type(value.__class__.__name__ + str(time.time()).replace('.', ''), value.__class__.__bases__, dict(value.__class__.__dict__))
    return NewClass(value.transformers, value.remainder, value.sparse_threshold, value.n_jobs, value.transformer_weights)

def replaceFeatureUnion(value: FeatureUnion):
    NewClass = type(value.__class__.__name__ + str(time.time()).replace('.', ''), value.__class__.__bases__, dict(value.__class__.__dict__))
    return NewClass(value.transformer_list, value.n_jobs, value.transformer_weights)

def replacePipeline(value: Pipeline):
    NewClass = type(value.__class__.__name__ + str(time.time()).replace('.', ''), value.__class__.__bases__, dict(value.__class__.__dict__))
    return NewClass(value.steps, value.memory)

def replaceFunctionTransformer(value: FunctionTransformer):
    NewClass = type(value.__class__.__name__ + str(time.time()).replace('.', ''), value.__class__.__bases__, dict(value.__class__.__dict__))
    return NewClass(value.func, value.inverse_func, value.validate, value.accept_sparse, value.pass_y, value.check_inverse, value.kw_args, value.inv_kw_args)

def replaceIdentityTransformation(value: IdentityTransformation):
    NewClass = type(value.__class__.__name__ + str(time.time()).replace('.', ''), value.__class__.__bases__, dict(value.__class__.__dict__))
    return NewClass(value.number_parent_features)

def replace_with_new_wrapper(pip):
    my_class = pip
    if isinstance(pip, Pipeline):
        for step_counter in range(len(pip.steps)):
            pip.steps[step_counter] = (pip.steps[step_counter][0], replace_with_new_wrapper(pip.steps[step_counter][1]))
        my_class = replacePipeline(pip)
    elif isinstance(pip, FeatureUnion):
        for step_counter in range(len(pip.transformer_list)):
            pip.transformer_list[step_counter] = (pip.transformer_list[step_counter][0], replace_with_new_wrapper(pip.transformer_list[step_counter][1]))
        my_class = replaceFeatureUnion(pip)
    elif isinstance(pip, ColumnTransformer):
        for step_counter in range(len(pip.transformers)):
            pip.transformers[step_counter] = (pip.transformers[step_counter][0], replace_with_new_wrapper(pip.transformers[step_counter][1]), pip.transformers[step_counter][2])
        my_class = replaceColumnTransformer(pip)
    elif isinstance(pip, FunctionTransformer):
        my_class = replaceFunctionTransformer(pip)
    elif isinstance(pip, IdentityTransformation):
        my_class = replaceIdentityTransformation(pip)

    return my_class

...

TASK_ID = 10101
task = openml.tasks.get_task(TASK_ID)
my_run = openml.runs.run_model_on_task(my_wrapped_pipeline, task, avoid_duplicate_runs=False)
my_run.publish()

However, now I get the following exception:

Traceback (most recent call last):
  File "/home/felix/FastFeatures/new_project/fastsklearnfeature/test/openml/generate_openml_pipeline.py", line 140, in <module>
    my_run = openml.runs.run_model_on_task(my_pipeline, task, avoid_duplicate_runs=False)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/runs/functions.py", line 49, in run_model_on_task
    add_local_measures=add_local_measures)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/runs/functions.py", line 131, in run_flow_on_task
    _publish_flow_if_necessary(flow)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/runs/functions.py", line 199, in _publish_flow_if_necessary
    raise e
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/runs/functions.py", line 186, in _publish_flow_if_necessary
    flow.publish()
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/flows/flow.py", line 334, in publish
    file_elements=file_elements,
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/_api_calls.py", line 41, in _perform_api_call
    return _read_url_files(url, data=data, file_elements=file_elements)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/_api_calls.py", line 74, in _read_url_files
    raise _parse_server_exception(response, url=url)
openml.exceptions.OpenMLServerException: https://www.openml.org/api/v1/xml/flow/ returned code 163: Problem validating uploaded description file
<oml:error xmlns:oml="http://openml.org/openml">
    <oml:code>163</oml:code>
    <oml:message>Problem validating uploaded description file</oml:message>
        <oml:additional_information>XML does not correspond to XSD schema. </oml:additional_information>
    </oml:error>
mfeurer commented 5 years ago

Could you please add a print statement to File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/_api_calls.py", line 41, in _perform_api_call and print the url, data and file_elements, and then post the xml which it tries to upload?

FelixNeutatz commented 5 years ago

Sure:

url: https://www.openml.org/api/v1/xml/flow/
data: None
file elements: {'description': '<oml:flow xmlns:oml="http://openml.org/openml">\n\t<oml:name>sklearn.pipeline.Pipeline(features=sklearn.pipeline.Pipeline15591400193736384(parents=sklearn.pipeline.FeatureUnion15591400193734686({V1, V4}1559109118.490439=sklearn.pipeline.Pipeline1559140019373153(parents=sklearn.pipeline.FeatureUnion15591400193729897(V11559109116.7628496=sklearn.pipeline.Pipeline1559140019372707(V1=sklearn.compose._column_transformer.ColumnTransformer15591400193726637(identity=sklearn.preprocessing._function_transformer.FunctionTransformer15591400193726282)),V41559109116.7630394=sklearn.pipeline.Pipeline1559140019372885(V4=sklearn.compose._column_transformer.ColumnTransformer155914001937284(identity=sklearn.preprocessing._function_transformer.FunctionTransformer15591400193728094))),identity=fastsklearnfeature.transformations.IdentityTransformation.IdentityTransformation15591400193731127),V21559109118.4906723=sklearn.pipeline.Pipeline15591400193733547(V2=sklearn.compose._column_transformer.ColumnTransformer1559140019373304(identity=sklearn.preprocessing._function_transformer.FunctionTransformer15591400193732696))),identity=fastsklearnfeature.transformations.IdentityTransformation.IdentityTransformation1559140019373596),classifier=sklearn.linear_model.logistic.LogisticRegression)</oml:name>\n\t<oml:class_name>sklearn.pipeline.Pipeline</oml:class_name>\n\t<oml:external_version>fastsklearnfeature==0.20.3,openml==0.8.0,sklearn==0.20.3</oml:external_version>\n\t<oml:description>Automatically created scikit-learn flow.</oml:description>\n\t<oml:language>English</oml:language>\n\t<oml:dependencies>sklearn==0.20.3\nnumpy&gt;=1.6.1\nscipy&gt;=0.9</oml:dependencies>\n\t<oml:parameter>\n\t\t<oml:name>memory</oml:name>\n\t\t<oml:default_value>null</oml:default_value>\n\t</oml:parameter>\n\t<oml:parameter>\n\t\t<oml:name>steps</oml:name>\n\t\t<oml:default_value>[{"oml-python:serialized_object": "component_reference", "value": {"key": "features", "step_name": "features"}}, {"oml-python:serialized_object": "component_reference", "value": {"key": "classifier", "step_name": "classifier"}}]</oml:default_value>\n\t</oml:parameter>\n\t<oml:component>\n\t\t<oml:identifier>features</oml:identifier>\n\t\t<oml:flow xmlns:oml="http://openml.org/openml">\n\t\t\t<oml:name>sklearn.pipeline.Pipeline15591400193736384(parents=sklearn.pipeline.FeatureUnion15591400193734686({V1, V4}1559109118.490439=sklearn.pipeline.Pipeline1559140019373153(parents=sklearn.pipeline.FeatureUnion15591400193729897(V11559109116.7628496=sklearn.pipeline.Pipeline1559140019372707(V1=sklearn.compose._column_transformer.ColumnTransformer15591400193726637(identity=sklearn.preprocessing._function_transformer.FunctionTransformer15591400193726282)),V41559109116.7630394=sklearn.pipeline.Pipeline1559140019372885(V4=sklearn.compose._column_transformer.ColumnTransformer155914001937284(identity=sklearn.preprocessing._function_transformer.FunctionTransformer15591400193728094))),identity=fastsklearnfeature.transformations.IdentityTransformation.IdentityTransformation15591400193731127),V21559109118.4906723=sklearn.pipeline.Pipeline15591400193733547(V2=sklearn.compose._column_transformer.ColumnTransformer1559140019373304(identity=sklearn.preprocessing._function_transformer.FunctionTransformer15591400193732696))),identity=fastsklearnfeature.transformations.IdentityTransformation.IdentityTransformation1559140019373596)</oml:name>\n\t\t\t<oml:class_name>sklearn.pipeline.Pipeline15591400193736384</oml:class_name>\n\t\t\t<oml:external_version>fastsklearnfeature==0.20.3,openml==0.8.0,sklearn==0.20.3</oml:external_version>\n\t\t\t<oml:description>Automatically created scikit-learn flow.</oml:description>\n\t\t\t<oml:language>English</oml:language>\n\t\t\t<oml:dependencies>sklearn==0.20.3\nnumpy&gt;=1.6.1\nscipy&gt;=0.9</oml:dependencies>\n\t\t\t<oml:parameter>\n\t\t\t\t<oml:name>memory</oml:name>\n\t\t\t\t<oml:default_value>null</oml:default_value>\n\t\t\t</oml:parameter>\n\t\t\t<oml:parameter>\n\t\t\t\t<oml:name>steps</oml:name>\n\t\t\t\t<oml:default_value>[{"oml-python:serialized_object": "component_reference", "value": {"key": "parents", "step_name": "parents"}}, {"oml-python:serialized_object": "component_reference", "value": {"key": "identity", "step_name": "identity"}}]</oml:default_value>\n\t\t\t</oml:parameter>\n\t\t\t<oml:component>\n\t\t\t\t<oml:identifier>parents</oml:identifier>\n\t\t\t\t<oml:flow xmlns:oml="http://openml.org/openml">\n\t\t\t\t\t<oml:name>sklearn.pipeline.FeatureUnion15591400193734686({V1, 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Do you need something else?

mfeurer commented 5 years ago

No, that's sufficient. I checked the xml against the xsd definition and it turns out that it is illegal for the following reasons:

Ideally, we'd catch these in the Python API, but we currently don't use an XSD checker there. @janvanrijn would it be possible to return the error message from the XSD checker via the API so that the user knows why the upload is failing?

As the generated pipeline name is only a little bit too long you could get around this issue by using a shorter hexadecimal string instead of a long integer value. @joaquinvanschoren is there anything else which could be done here? I assume this would be resolved if we update the flow description at some point in the future?

FelixNeutatz commented 5 years ago

Thank you @mfeurer :)

Yes, the XSD format was the problem. It would be great if we could put the format checker, such as the following in the client:

import xmlschema
my_schema = xmlschema.XMLSchema('openml.implementation.upload.xsd')
print(my_schema.validate('my_config.xml'))

Best regards, Felix

FelixNeutatz commented 5 years ago

I encountered one more exception:

  File "/home/felix/FastFeatures/new_project/fastsklearnfeature/feature_selection/OpenMlFeatures.py", line 296, in <module>
    selector.run()
  File "/home/felix/FastFeatures/new_project/fastsklearnfeature/feature_selection/OpenMlFeatures.py", line 238, in run
    candidate2openmltest(results[0], self.classifier, self.reader.task, 'Test')
  File "/home/felix/FastFeatures/new_project/fastsklearnfeature/feature_selection/openml_wrapper/pipeline2openml.py", line 171, in candidate2openmltest
    my_run.publish()
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/runs/run.py", line 323, in publish
    return_value = openml._api_calls._perform_api_call("/run/", file_elements=file_elements)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/_api_calls.py", line 47, in _perform_api_call
    return _read_url_files(url, data=data, file_elements=file_elements)
  File "/home/felix/FastFeatures/new_project/venv/lib/python3.7/site-packages/openml/_api_calls.py", line 80, in _read_url_files
    raise _parse_server_exception(response, url=url)
openml.exceptions.OpenMLServerException: https://www.openml.org/api/v1/xml//run/ returned code 215: Database error. Setup search query failed

I guess it's another XSD error. Can you direct me to xsd file for https://www.openml.org/api/v1/xml//run/?

mfeurer commented 5 years ago

All XSDs are available here. However, it seems that the issue is that the function in question (https://www.openml.org/api/v1/xml//run/) is not valid. Therefore, it would be best to see what's happening if you can track down why the python connector tries to open a run without an ID.

FelixNeutatz commented 5 years ago

I think https://www.openml.org/api/v1/xml//run/ is fine because in other runs that are uploaded successfully, I do see the same url. Also, if we run https://www.openml.org/api/v1/xml/flow/, you get the same message even though it is the correct url: image

Furthermore, I checked the description against openml.run.upload.xsd and the validation does not cause any issues. Any other ideas?

url = https://www.openml.org/api/v1/xml//run/
data = None
file_elements = {'description': ('description.xml', '<?xml version="1.0" encoding="utf-8"?>\n<oml:run xmlns:oml="http://openml.org/openml">\n\t<oml:task_id>31</oml:task_id>\n\t<oml:flow_id>11594</oml:flow_id>\n\t<oml:parameter_setting>\n\t\t<oml:name>memory</oml:name>\n\t\t<oml:value>null</oml:value>\n\t\t<oml:component>11594</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>steps</oml:name>\n\t\t<oml:value>[{"oml-python:serialized_object": "component_reference", "value": {"key": "n1", "step_name": "n1"}}, {"oml-python:serialized_object": "component_reference", "value": {"key": "n11", "step_name": "n11"}}, {"oml-python:serialized_object": "component_reference", "value": {"key": "c", "step_name": "c"}}]</oml:value>\n\t\t<oml:component>11594</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>n_jobs</oml:name>\n\t\t<oml:value>null</oml:value>\n\t\t<oml:component>11595</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>transformer_list</oml:name>\n\t\t<oml:value>[{"oml-python:serialized_object": "component_reference", "value": {"key": "n2", "step_name": "n2"}}, {"oml-python:serialized_object": "component_reference", "value": {"key": "n5", "step_name": "n5"}}, {"oml-python:serialized_object": "component_reference", "value": {"key": "n8", "step_name": "n8"}}]</oml:value>\n\t\t<oml:component>11595</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>transformer_weights</oml:name>\n\t\t<oml:value>null</oml:value>\n\t\t<oml:component>11595</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>memory</oml:name>\n\t\t<oml:value>null</oml:value>\n\t\t<oml:component>11596</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>steps</oml:name>\n\t\t<oml:value>[{"oml-python:serialized_object": "component_reference", "value": {"key": "n3", "step_name": 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[0]}}]</oml:value>\n\t\t<oml:component>11597</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>accept_sparse</oml:name>\n\t\t<oml:value>false</oml:value>\n\t\t<oml:component>11598</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>check_inverse</oml:name>\n\t\t<oml:value>true</oml:value>\n\t\t<oml:component>11598</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>func</oml:name>\n\t\t<oml:value>{"oml-python:serialized_object": "function", "value": 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"step_name": "n7", "argument_1": [5]}}]</oml:value>\n\t\t<oml:component>11600</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>accept_sparse</oml:name>\n\t\t<oml:value>false</oml:value>\n\t\t<oml:component>11601</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>check_inverse</oml:name>\n\t\t<oml:value>true</oml:value>\n\t\t<oml:component>11601</oml:component>\n\t</oml:parameter_setting>\n\t<oml:parameter_setting>\n\t\t<oml:name>func</oml:name>\n\t\t<oml:value>{"oml-python:serialized_object": "function", "value": 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mfeurer commented 5 years ago

Okay, I now get the error calling https://www.openml.org/api/v1/xml//run/. I assume the browser issues a get request, but server expects a push request. Now, I'm afraid that we hit a server issue with which I cannot help you any more. @janvanrijn @joaquinvanschoren could you please have a look at this?

FelixNeutatz commented 5 years ago

I have one more additional question: It would be great if we could upload longer pipeline names because since the name always contains the entire path to the given class, e.g. "sklearn.linear_model.logistic.LogisticRegression" or "sklearn.pipeline.Pipeline", we quickly reach the limit of 1024 characters. Of course, one can start to hack names to be smaller but this does not really help readability for other people who are interested in the corresponding flows.

Therefore, I would be super happy if we could loosen the name length limit here: https://github.com/openml/OpenML/blob/7499851f73fc0433d21fd4e156f09dd9fa231921/openml_OS/views/pages/api_new/v1/xsd/openml.implementation.upload.xsd#L13 I guess that this change would also propagate to the underlying database schema. Should I start a new issue for this question or can we discuss it here as well?