Source code for nmdc_ms_metadata_gen.data_classes

# -*- coding: utf-8 -*-
from dataclasses import dataclass

"""
This module defines data classes for NMDC (National Microbiome Data Collaborative) type constants.
"""




@dataclass
class NmdcTypes:
    """
    Data class holding NMDC type constants.

    Attributes
    ----------
    Biosample : str
        NMDC type for Biosample.
    MassSpectrometry : str
        NMDC type for Mass Spectrometry.
    MetabolomicsAnalysis : str
        NMDC type for Metabolomics Analysis.
    DataObject : str
        NMDC type for Data Object.
    CalibrationInformation : str
        NMDC type for Calibration Information.
    MetaboliteIdentification : str
        NMDC type for Metabolite Identification.
    NomAnalysis : str
        NMDC type for NOM Analysis.
    OntologyClass : str
        NMDC type for Ontology Class.
    ControlledIdentifiedTermValue : str
        NMDC type for Controlled Identified Term Value.
    TextValue : str
        NMDC type for Text Value.
    GeolocationValue : str
        NMDC type for Geolocation Value.
    TimeStampValue : str
        NMDC type for Timestamp Value.
    QuantityValue : str
        NMDC type for Quantity Value.
    MassSpectrometryConfiguration : str
        NMDC type for Mass Spectrometry Configuration.
    PortionOfSubstance : str
        NMDC type for Portion of Substance.
    MobilePhaseSegment : str
        NMDC type for Mobile Phase Segment.
    ChromatographyConfiguration : str
        NMDC type for Chromatography Configuration.
    Instrument : str
        NMDC type for Instrument.
    Manifest : str
        NMDC type for Manifest.
    Protocol : str
        NMDC type for Protocol.
    """

    Biosample: str = "nmdc:Biosample"
    MassSpectrometry: str = "nmdc:MassSpectrometry"
    MetabolomicsAnalysis: str = "nmdc:MetabolomicsAnalysis"
    DataObject: str = "nmdc:DataObject"
    CalibrationInformation: str = "nmdc:CalibrationInformation"
    MetaboliteIdentification: str = "nmdc:MetaboliteIdentification"
    NomAnalysis: str = "nmdc:NomAnalysis"
    OntologyClass: str = "nmdc:OntologyClass"
    ControlledIdentifiedTermValue: str = "nmdc:ControlledIdentifiedTermValue"
    TextValue: str = "nmdc:TextValue"
    GeolocationValue: str = "nmdc:GeolocationValue"
    TimeStampValue: str = "nmdc:TimestampValue"
    QuantityValue: str = "nmdc:QuantityValue"
    MassSpectrometryConfiguration: str = "nmdc:MassSpectrometryConfiguration"
    PortionOfSubstance: str = "nmdc:PortionOfSubstance"
    MobilePhaseSegment: str = "nmdc:MobilePhaseSegment"
    ChromatographyConfiguration: str = "nmdc:ChromatographyConfiguration"
    Instrument: str = "nmdc:Instrument"
    Protocol: str = "nmdc:Protocol"
    Manifest: str = "nmdc:Manifest"





@dataclass
class GCMSMetabWorkflowMetadata:
    """
    Data class for holding GCMS metabolomic workflow metadata information.

    Attributes
    ----------
    biosample_id: str
        Identifier for the biosample.s
    nmdc_study : str
        Identifier for the NMDC study.
    processed_data_file : str
        Path or name of the processed data file.
    raw_data_file : str
        Path or name of the raw data file.
    mass_spec_configuration_id : str
        Identifier for the mass spectrometry configuration used.
    lc_config_id: str
        Identifier for the liquid chromatography configuration used.
    instrument_id: str
        Identifier for the instrument used for analysis.
    calibration_id : str
        Identifier for the calibration information used.
    instrument_analysis_start_date: str, optional
        Start date of the instrument analysis.
    instrument_analysis_end_date: str, optional
        End date of the instrument analysis.
    processing_institution : str
        Name of the processing institution. Must be a value from ProcessingInstitutionEnum. OPTIONAL IF processing_institution_generation AND processing_institution_workflow ARE PROVIDED
    processing_institution_generation : str
        Name of the processing institution where the data was generated. Must be a value from ProcessingInstitutionEnum. OPTIONAL IF processing_institution IS PROVIDED
    processing_institution_workflow : str
        Name of the processing institution where the workflow was executed. Must be a value from ProcessingInstitutionEnum. OPTIONAL IF processing_institution IS PROVIDED
    execution_resource : str, optional
        Name of the execution resource. Must be a value from ExecutionResourceEnum.
    raw_data_url : str, optional
        Complete URL for the raw data file. If provided, this takes precedence
        over constructing the URL from base_url + filename.
    manifest_id : str
        Identifier for the manifest associated with this workflow metadata.
    """

    biosample_id: str
    nmdc_study: str
    processed_data_file: str
    raw_data_file: str
    mass_spec_configuration_id: str
    lc_config_id: str
    instrument_id: str
    calibration_id: str
    instrument_analysis_start_date: str = None
    instrument_analysis_end_date: str = None
    processing_institution: str = None
    processing_institution_generation: str = None
    processing_institution_workflow: str = None
    execution_resource: str = None
    raw_data_url: str = None
    manifest_id: str = None





@dataclass
class LCMSLipidWorkflowMetadata:
    """
    Data class for holding LC-MS lipidomics workflow metadata information.
    Also used for LC-MS Metabolomics workflows.

    Attributes
    ----------
    processed_data_dir : str
        Directory containing processed data files.
    raw_data_file : str
        Path or name of the raw data file.
    mass_spec_config_id : str
        Identifier for the mass spectrometry configuration used.
    lc_config_id : str
        Identifier for the liquid chromatography configuration used.
    instrument_id : str
        Identifier for the instrument used for analysis.
    processing_institution : str
        Name of the processing institution. Must be a value from ProcessingInstitutionEnum. OPTIONAL IF processing_institution_generation AND processing_institution_workflow ARE PROVIDED
    processing_institution_generation : str
        Name of the processing institution where the data was generated. Must be a value from ProcessingInstitutionEnum. OPTIONAL IF processing_institution IS PROVIDED
    processing_institution_workflow : str
        Name of the processing institution where the workflow was executed. Must be a value from ProcessingInstitutionEnum. OPTIONAL IF processing_institution IS PROVIDED
    execution_resource : str, optional
        Name of the execution resource. Must be a value from ExecutionResourceEnum.
    instrument_analysis_start_date : str, optional
        Start date of the instrument analysis.
    instrument_analysis_end_date : str, optional
        End date of the instrument analysis.
    raw_data_url : str, optional
        Complete URL for the raw data file. If provided, this takes precedence
        over constructing the URL from base_url + filename.
    manifest_id : str, optional
        Identifier for the manifest associated with this workflow metadata.
    """

    processed_data_dir: str
    raw_data_file: str
    mass_spec_configuration_id: str
    lc_config_id: str
    instrument_id: str
    processing_institution: str = None
    processing_institution_generation: str = None
    processing_institution_workflow: str = None
    execution_resource: str = None
    instrument_analysis_start_date: str = None
    instrument_analysis_end_date: str = None
    raw_data_url: str = None
    manifest_id: str = None



@dataclass
class NOMMetadata:
    """
    Data class for holding NOM workflow metadata information.

    Attributes
    ----------
    raw_data_file : str
        Path or name of the raw data file.
    processed_data_directory : str
        Directory containing processed data files.
    associated_studies : list
        List of associated study identifiers.
    biosample_id : str
        Identifier for the biosample.
    instrument_id : str
        Identifier for the instrument used for analysis.
    mass_spec_configuration_id : str
        Identifier for the mass spectrometry configuration used.
    lc_config_id : str
        Identifier for the liquid chromatography configuration used.
    manifest_id : str
        Identifier for the manifest associated with this workflow metadata.
    processing_institution : str
        Name of the processing institution. Must be a value from ProcessingInstitutionEnum. OPTIONAL IF processing_institution_generation AND processing_institution_workflow ARE PROVIDED
    processing_institution_generation : str
        Name of the processing institution where the data was generated. Must be a value from ProcessingInstitutionEnum. OPTIONAL IF processing_institution IS PROVIDED
    processing_institution_workflow : str
        Name of the processing institution where the workflow was executed. Must be a value from ProcessingInstitutionEnum. OPTIONAL IF processing_institution IS PROVIDED
    execution_resource : str, optional
        Name of the execution resource. Must be a value from ExecutionResourceEnum.
    """

    raw_data_file: str
    processed_data_directory: str
    associated_studies: list
    biosample_id: str
    instrument_id: str
    mass_spec_configuration_id: str
    lc_config_id: str
    manifest_id: str
    processing_institution: str = None
    processing_institution_generation: str = None
    processing_institution_workflow: str = None
    execution_resource: str = None