<reponame>isb-cgc/ISB-CGC-Webapp
#
# Copyright 2015-2019, Institute for Systems Biology
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#    http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

from builtins import object
def enum(**enums):
    return type('Enum', (), enums)

# TODO decouple from protorpc.messages
class ValueType(object):
    STRING = 1
    INTEGER = 2
    FLOAT = 3
    BOOLEAN = 4
    UNKNOWN = 5 # We can get queries that return no data, which may be of an unknown type


def is_log_transformable(attr_type):
    return isinstance(attr_type, ValueType) and (attr_type == ValueType.FLOAT or attr_type == ValueType.INTEGER)

IdentifierTypes = enum(PATIENT=1, SAMPLE=2, ALIQUOT=3)
DataTypes = enum(CLIN=1, GEXP=2, METH=3, CNVR=4, RPPA=5, MIRN=6, GNAB=7, USER=8)

IDENTIER_FIELDS_FOR_DATA_TYPES = {
    #TODO: change clin to match new BQ clin table in tcga_data_open
    DataTypes.CLIN: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode'
    },
    #TODO: change gexp to match new BQ gexp table in tcga_data_open; not yet uploaded yet
    DataTypes.GEXP: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.METH: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.CNVR: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.RPPA: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.MIRN: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.GNAB: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'Tumor_SampleBarcode',
        IdentifierTypes.ALIQUOT: 'Tumor_AliquotBarcode'
    },
    DataTypes.USER: {
        IdentifierTypes.SAMPLE: 'sample_barcode'
    }
}

class DataPointIdentifierTools(object):
    @classmethod
    def get_id_field_name_for_data_type(cls, data_type, identifier_type):
        return IDENTIER_FIELDS_FOR_DATA_TYPES[data_type][identifier_type]

class BigQuerySchemaToValueTypeConverter(object):
    field_to_value_types = {
        'STRING': ValueType.STRING,
        'INTEGER': ValueType.INTEGER,
        'FLOAT': ValueType.FLOAT,
        'BOOLEAN': ValueType.BOOLEAN
    }

    @classmethod
    def get_value_type(cls, schema_field):
        return cls.field_to_value_types[schema_field]

class StringToDataTypeConverter(object):
    @classmethod
    def get_datatype(cls, x):
        pass
#
# Copyright 2015-2019, Institute for Systems Biology
#
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#    http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.
#

from builtins import object
def enum(**enums):
    return type('Enum', (), enums)

# TODO decouple from protorpc.messages
class ValueType(object):
    STRING = 1
    INTEGER = 2
    FLOAT = 3
    BOOLEAN = 4
    UNKNOWN = 5 # We can get queries that return no data, which may be of an unknown type


def is_log_transformable(attr_type):
    return isinstance(attr_type, ValueType) and (attr_type == ValueType.FLOAT or attr_type == ValueType.INTEGER)

IdentifierTypes = enum(PATIENT=1, SAMPLE=2, ALIQUOT=3)
DataTypes = enum(CLIN=1, GEXP=2, METH=3, CNVR=4, RPPA=5, MIRN=6, GNAB=7, USER=8)

IDENTIER_FIELDS_FOR_DATA_TYPES = {
    #TODO: change clin to match new BQ clin table in tcga_data_open
    DataTypes.CLIN: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode'
    },
    #TODO: change gexp to match new BQ gexp table in tcga_data_open; not yet uploaded yet
    DataTypes.GEXP: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.METH: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.CNVR: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.RPPA: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.MIRN: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'SampleBarcode',
        IdentifierTypes.ALIQUOT: 'AliquotBarcode'
    },
    DataTypes.GNAB: {
        IdentifierTypes.PATIENT: 'ParticipantBarcode',
        IdentifierTypes.SAMPLE: 'Tumor_SampleBarcode',
        IdentifierTypes.ALIQUOT: 'Tumor_AliquotBarcode'
    },
    DataTypes.USER: {
        IdentifierTypes.SAMPLE: 'sample_barcode'
    }
}

class DataPointIdentifierTools(object):
    @classmethod
    def get_id_field_name_for_data_type(cls, data_type, identifier_type):
        return IDENTIER_FIELDS_FOR_DATA_TYPES[data_type][identifier_type]

class BigQuerySchemaToValueTypeConverter(object):
    field_to_value_types = {
        'STRING': ValueType.STRING,
        'INTEGER': ValueType.INTEGER,
        'FLOAT': ValueType.FLOAT,
        'BOOLEAN': ValueType.BOOLEAN
    }

    @classmethod
    def get_value_type(cls, schema_field):
        return cls.field_to_value_types[schema_field]

class StringToDataTypeConverter(object):
    @classmethod
    def get_datatype(cls, x):
        pass
# # Copyright 2015-2019, Institute for Systems Biology # # Licensed under the Apache License, Version 2.0 (the "License"); # you may not use this file except in compliance with the License. # You may obtain a copy of the License at # #    http://www.apache.org/licenses/LICENSE-2.0 # # Unless required by applicable law or agreed to in writing, software # distributed under the License is distributed on an "AS IS" BASIS, # WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. # See the License for the specific language governing permissions and # limitations under the License. # # TODO decouple from protorpc.messages # We can get queries that return no data, which may be of an unknown type #TODO: change clin to match new BQ clin table in tcga_data_open #TODO: change gexp to match new BQ gexp table in tcga_data_open; not yet uploaded yet