How to use the sbol3.config.ConfigOptions.VERBOSE.value function in sbol3

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github SynBioDex / pySBOL / sbol3 / property.py View on Github external
def get_uri(self, id):
        if Config.getOption(ConfigOptions.VERBOSE.value) is True:
            print('SBOL compliant URIs are set to ' + Config.getOption(ConfigOptions.SBOL_COMPLIANT_URIS.value))
            print('SBOL typed URIs are set to ' + Config.getOption(ConfigOptions.SBOL_TYPED_URIS.value))
            print('Searching for ' + id)
        # Search this property's object store for the uri
        object_store = self._sbol_owner.owned_objects[self._rdf_type]
        for obj in object_store:
            if id == obj.identity:
                return obj
        # If searching by the full URI fails, assume the user is searching
        # for an SBOL-compliant URI using the displayId only
        # Form compliant URI for child object
        parent_obj = self._sbol_owner
        resource_namespaces = []
        resource_namespaces.append(getHomespace())
        if parent_obj.doc is not None:
            for ns in parent_obj.doc.resource_namespaces:
github SynBioDex / pySBOL / sbol3 / property.py View on Github external
persistent_id_matches.append(obj)
                # Sort objects with same persistentIdentity by version
                # TODO is this right?
                persistent_id_matches.sort(key=sort_version)
            # If objects matching the persistentIdentity were found, return the most recent version
            if len(persistent_id_matches) > 0:
                return persistent_id_matches[-1]
            # Assume the object is not TopLevel # TODO Not sure what this is for
            if SBOL_PERSISTENT_IDENTITY in parent_obj.properties:
                persistentIdentity = parent_obj.properties[SBOL_PERSISTENT_IDENTITY][0]
            if SBOL_VERSION in parent_obj.properties:
                version = parent_obj.properties[SBOL_VERSION][0]
                compliant_uri = URIRef(os.path.join(persistentIdentity, uri, version))
            else:
                compliant_uri = URIRef(os.path.join(persistentIdentity, uri))
            if Config.getOption(ConfigOptions.VERBOSE.value) is True:
                print('Searching for non-TopLevel: ' + compliant_uri)
            for obj in object_store:
                if obj.identity == compliant_uri:
                    return obj
github SynBioDex / pySBOL / sbol3 / config.py View on Github external
valid_options = {
    ConfigOptions.SBOL_COMPLIANT_URIS.value: {True, False},
    ConfigOptions.SBOL_TYPED_URIS.value: {True, False},
    ConfigOptions.SERIALIZATION_FORMAT.value: {'sbol', 'rdfxml', 'json', 'ntriples'},
    ConfigOptions.VALIDATE.value: {True, False},
    ConfigOptions.LANGUAGE.value: {'SBOL2', 'FASTA', 'GenBank'},
    ConfigOptions.TEST_EQUALITY.value: {True, False},
    ConfigOptions.CHECK_URI_COMPLIANCE.value: {True, False},
    ConfigOptions.CHECK_COMPLETENESS.value: {True, False},
    ConfigOptions.CHECK_BEST_PRACTICES.value: {True, False},
    ConfigOptions.FAIL_ON_FIRST_ERROR.value: {True, False},
    ConfigOptions.PROVIDE_DETAILED_STACK_TRACE.value: {True, False},
    ConfigOptions.INSERT_TYPE.value: {True, False},
    ConfigOptions.RETURN_FILE.value: {True, False},
    ConfigOptions.VERBOSE.value: {True, False}
}


extension_namespaces = {}
# The authoritative namespace for the Document. Setting the home namespace is like signing a piece of paper.
home = None
# Flag indicating whether an object's type is included in SBOL-compliant URIs.
SBOLCompliantTypes = 1
catch_exceptions = 0
file_format = 'rdfxml'


class Config:
    """A class which contains global configuration variables for the libSBOL environment.

    Configuration variables are accessed through the setOptions and getOptions methods.