Index

A

analyte_category (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1]

B

BioOntologyInfoRetriever (class in src.bio_ontology_api)

Biosample (src.data_classes.NmdcTypes attribute), [1] biosample_id (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1]

C

calibration_id (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] CalibrationInformation (src.data_classes.NmdcTypes attribute), [1] check_doj_urls() (src.metadata_generator.NMDCMetadataGenerator method) check_for_biosamples() (src.metadata_generator.NMDCMetadataGenerator method) chromat_config_name (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] clean_dict() (src.metadata_generator.NMDCMetadataGenerator method) ControlledIdentifiedTermValue (src.data_classes.NmdcTypes attribute), [1] create_controlled_identified_term_value() (src.metadata_parser.MetadataParser method)

create_geo_loc_value() (src.metadata_parser.MetadataParser method) create_quantity_value() (src.metadata_parser.MetadataParser method) create_text_value() (src.metadata_parser.MetadataParser method) create_timestamp_value() (src.metadata_parser.MetadataParser method) create_workflow_metadata() (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator method) (src.lcms_metadata_generator.LCMSMetadataGenerator method) csv_process_data_description (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1]

D

DataObject (src.data_classes.NmdcTypes attribute), [1]

dump_nmdc_database() (src.metadata_generator.NMDCMetadataGenerator method) dynam_parse_biosample_metadata() (src.metadata_parser.MetadataParser method)

E

execution_resource (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] (src.data_classes.LCMSLipidWorkflowMetadata attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1]

G

GCMSMetabolomicsMetadataGenerator (class in src.gcms_metab_metadata_generator) GCMSMetabWorkflowMetadata (class in src.data_classes) generate_biosample() (src.metadata_generator.NMDCMetadataGenerator method) generate_calibration() (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator method) generate_calibration_id() (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator method) generate_data_object() (src.metadata_generator.NMDCMetadataGenerator method) generate_example_biosample_csv() (src.metadata_parser.MetadataParser method) generate_mass_spectrometry() (src.metadata_generator.NMDCMetadataGenerator method)

generate_metab_identifications() (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator method) generate_metabolomics_analysis() (src.metadata_generator.NMDCMetadataGenerator method) generate_nom_analysis() (src.nom_metadata_generator.NOMMetadataGenerator method) GeolocationValue (src.data_classes.NmdcTypes attribute), [1] get_calibration_id() (src.nom_metadata_generator.NOMMetadataGenerator method) get_envo_terms() (src.bio_ontology_api.BioOntologyInfoRetriever method) get_value() (src.metadata_parser.MetadataParser method) get_workflow_version() (src.metadata_generator.NMDCMetadataGenerator method)

H

handle_biosample() (src.metadata_generator.NMDCMetadataGenerator method) hdf5_process_data_description (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1]

hdf5_process_data_obj_type (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1]

I

instrument_analysis_end_date (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] (src.data_classes.LCMSLipidWorkflowMetadata attribute), [1] instrument_analysis_start_date (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] (src.data_classes.LCMSLipidWorkflowMetadata attribute), [1]

instrument_used (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] (src.data_classes.LCMSLipidWorkflowMetadata attribute), [1] is_type() (src.metadata_parser.MetadataParser method)

L

lc_config_name (src.data_classes.LCMSLipidWorkflowMetadata attribute), [1] LCMSLipidomicsMetadataGenerator (class in src.lcms_lipid_metadata_generator) LCMSLipidWorkflowMetadata (class in src.data_classes) LCMSMetabolomicsMetadataGenerator (class in src.lcms_metab_metadata_generator)

LCMSMetadataGenerator (class in src.lcms_metadata_generator) load_bio_credentials() (src.metadata_generator.NMDCMetadataGenerator method) load_credentials() (src.metadata_generator.NMDCMetadataGenerator method) load_metadata() (src.metadata_generator.NMDCMetadataGenerator method)

M

mass_spec_config_name (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] (src.data_classes.LCMSLipidWorkflowMetadata attribute), [1] mass_spec_desc (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1] mass_spec_eluent_intro (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1]

MassSpectrometry (src.data_classes.NmdcTypes attribute), [1] MetaboliteIdentification (src.data_classes.NmdcTypes attribute), [1] MetabolomicsAnalysis (src.data_classes.NmdcTypes attribute), [1] MetadataParser (class in src.metadata_parser)

N

nmdc_study (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] NMDCMetadataGenerator (class in src.metadata_generator) NmdcTypes (class in src.data_classes) no_config_process_data_category (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1]

no_config_process_data_obj_type (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] NomAnalysis (src.data_classes.NmdcTypes attribute), [1] NOMMetadataGenerator (class in src.nom_metadata_generator)

O

OntologyClass (src.data_classes.NmdcTypes attribute), [1]

P

parse_biosample_metadata() (src.metadata_parser.MetadataParser method) processed_data_category (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1] processed_data_dir (src.data_classes.LCMSLipidWorkflowMetadata attribute), [1] processed_data_file (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1]

processed_data_object_description (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] processed_data_object_type (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1] processing_institution (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1]

Q

QuantityValue (src.data_classes.NmdcTypes attribute), [1]

R

raw_data_file (src.data_classes.GCMSMetabWorkflowMetadata attribute), [1] (src.data_classes.LCMSLipidWorkflowMetadata attribute), [1] raw_data_obj_desc (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] raw_data_obj_type (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] raw_data_object_type (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1]

rerun() (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator method) (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator method) (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator method) (src.lcms_metadata_generator.LCMSMetadataGenerator method) (src.nom_metadata_generator.NOMMetadataGenerator method) run() (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator method) (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator method) (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator method) (src.lcms_metadata_generator.LCMSMetadataGenerator method) (src.nom_metadata_generator.NOMMetadataGenerator method)

S

start_nmdc_database() (src.metadata_generator.NMDCMetadataGenerator method)

T

TextValue (src.data_classes.NmdcTypes attribute), [1]

TimeStampValue (src.data_classes.NmdcTypes attribute), [1]

U

unique_columns (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1]

update_outputs() (src.metadata_generator.NMDCMetadataGenerator method)

W

wf_config_process_data_category (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] wf_config_process_data_description (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] wf_config_process_data_obj_type (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] workflow_analysis_name (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1] workflow_category (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1]

workflow_description (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1] workflow_git_url (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1] workflow_param_data_category (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1] workflow_param_data_object_type (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1] workflow_version (src.gcms_metab_metadata_generator.GCMSMetabolomicsMetadataGenerator attribute), [1] (src.lcms_lipid_metadata_generator.LCMSLipidomicsMetadataGenerator attribute), [1] (src.lcms_metab_metadata_generator.LCMSMetabolomicsMetadataGenerator attribute), [1] (src.nom_metadata_generator.NOMMetadataGenerator attribute), [1]