Index

A

add_annotated_features() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) add_annotation() (phenomedb.compounds.ImportBrukerBiLISACompounds method) add_annotation_compounds() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) add_cas_from_hmdb() (phenomedb.compounds.CompoundTask method) add_compound_and_mappings() (phenomedb.compounds.ImportBrukerBiQuantCompounds method) add_feature_metadata() (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) add_filter() (phenomedb.query_factory.QueryFactory method) add_match() (phenomedb.query_factory.QueryFilter method) (phenomedb.query_factory.QuerySubFilter method) add_metadata() (phenomedb.imports.ImportSampleManifest method) add_metadata_field() (phenomedb.imports.ImportTask method) add_metadata_field_and_value() (phenomedb.imports.ImportTask method) add_metadata_from_sample_worksheet() (phenomedb.imports.ImportSampleManifest method) add_metadata_from_subject_worksheet() (phenomedb.imports.ImportSampleManifest method) add_metadata_value() (phenomedb.imports.ImportTask method) add_or_update_annotated_feature_not_unified() (phenomedb.imports.ImportPeakPantherAnnotations method) add_or_update_annotated_feature_unified() (phenomedb.imports.AnnotationImportTask method) add_or_update_chebi() (phenomedb.compounds.CompoundTask method) add_or_update_chembl() (phenomedb.compounds.CompoundTask method) add_or_update_classyfire() (phenomedb.compounds.CompoundTask method) add_or_update_compound() (phenomedb.compounds.ImportROICompounds method) add_or_update_compound_from_subrow() (phenomedb.compounds.ImportROICompounds method) add_or_update_feature_metadata() (phenomedb.imports.ImportBrukerIVDRAnnotations method) (phenomedb.imports.ImportPeakPantherAnnotations method) (phenomedb.imports.ImportTargetLynxAnnotations method)

add_or_update_hmdb() (phenomedb.compounds.CompoundTask method) add_or_update_kegg() (phenomedb.compounds.CompoundTask method) add_or_update_lipid_maps() (phenomedb.compounds.CompoundTask method) add_or_update_ontology_ref() (phenomedb.compounds.CompoundTask method) add_or_update_pubchem_from_api() (phenomedb.compounds.CompoundTask method) add_or_update_sample_assay() (phenomedb.imports.AnnotationImportTask method) add_stereo_group() (phenomedb.compounds.CompoundTask method) add_sub_filter() (phenomedb.query_factory.QueryFilter method) add_task() (phenomedb.pipeline_factory.BasePipelineManager method) (phenomedb.pipeline_factory.PipelineFactory method) AddMissingClassyFireClasses (class in phenomedb.compounds) AnalysisTask (class in phenomedb.analysis) AnnotatedFeature (class in phenomedb.models) Annotation (class in phenomedb.models) Annotation.MultiCompoundOperator (class in phenomedb.models) AnnotationCompound (class in phenomedb.models) AnnotationEvidence (class in phenomedb.models) AnnotationEvidenceFileUpload (class in phenomedb.models) AnnotationImportTask (class in phenomedb.imports) AnnotationMethod (class in phenomedb.models) Assay (class in phenomedb.models) Assay.QuantificationType (class in phenomedb.models) attribute_dict() (phenomedb.base_view.PhenomeDBBaseView method)

B

BasePipelineManager (class in phenomedb.pipeline_factory) BasicSetup (class in phenomedb.pipelines) BatchCorrectionAssessmentPipelineGenerator (class in phenomedb.pipelines) breakdown_annotation_id() (in module phenomedb.utilities) breakdown_compound_class_id() (in module phenomedb.utilities) build_comparison_operation() (phenomedb.query_factory.QueryFactory method) build_dataset() (phenomedb.compounds.ExportCompoundsToCSV method) build_feature_dict() (phenomedb.imports.ImportXCMSFeatures method) build_filter_string() (phenomedb.query_factory.QueryFactory method)

build_function_operation() (phenomedb.query_factory.QueryFactory method) build_intensity_data_sample_metadata_and_feature_metadata() (phenomedb.query_factory.QueryFactory method) build_logical_operator() (phenomedb.query_factory.QueryFactory method) build_match_string() (phenomedb.query_factory.QueryFactory method) build_match_value() (phenomedb.query_factory.QueryFactory method) build_model_property_name() (phenomedb.query_factory.QueryFactory method) build_query_string() (phenomedb.query_factory.QueryFactory method) build_row() (phenomedb.compounds.ExportCompoundsToCSV method) build_sub_filter_string() (phenomedb.query_factory.QueryFactory method) build_subrows() (phenomedb.compounds.CompoundTask method)

C

Cache (class in phenomedb.cache) calculate_joins() (phenomedb.query_factory.QueryFactory method) calculate_log_p() (phenomedb.compounds.CompoundTask method) calculate_summary_statistics() (phenomedb.query_factory.QueryFactory method) call_inbuilt_transform() (phenomedb.metadata.HarmoniseMetadataField method) call_lambda() (phenomedb.metadata.HarmoniseMetadataField method) categorise_bmi() (in module phenomedb.metadata) check_cas() (phenomedb.compounds.CleanROIFile method) check_chebi() (phenomedb.compounds.CleanROIFile method) check_chembl() (phenomedb.compounds.CleanROIFile method) check_chemspider() (phenomedb.compounds.CleanROIFile method) check_classyfire() (phenomedb.compounds.CleanROIFile method) check_field() (phenomedb.compounds.CleanROIFile method) check_fields() (phenomedb.compounds.CleanROIFile method) check_functions() (phenomedb.metadata.HarmoniseMetadataField method) check_hmdb() (phenomedb.compounds.CleanROIFile method) check_kegg() (phenomedb.compounds.CleanROIFile method) check_lipidmaps() (phenomedb.compounds.CleanROIFile method) check_logP_RDKit() (phenomedb.compounds.CleanROIFile method) check_merged_file() (phenomedb.compounds.CleanROIFile method) check_pubchem() (phenomedb.compounds.CleanROIFile method) check_refmet() (phenomedb.compounds.CleanROIFile method) check_sample_columns() (phenomedb.imports.AnnotationImportTask method) ChemicalStandardDataset (class in phenomedb.models)

ChemicalStandardPeakList (class in phenomedb.models) clean_project_name() (phenomedb.task.Task method) CleanROIFile (class in phenomedb.compounds) commit_definition() (phenomedb.pipeline_factory.BasePipelineManager method) (phenomedb.pipeline_factory.PipelineFactory method) Compound (class in phenomedb.models) CompoundClass (class in phenomedb.models) CompoundClass.CompoundClassType (class in phenomedb.models) CompoundClassCompound (class in phenomedb.models) CompoundExternalDB (class in phenomedb.models) CompoundTask (class in phenomedb.compounds) configure_logging() (in module phenomedb.utilities) (phenomedb.base_view.PhenomeDBBaseView method) create_saved_query() (phenomedb.imports.AnnotationImportTask method) CreateAnnotationMethod (class in phenomedb.task) CreateAssay (class in phenomedb.task) CreateHarmonisedMetadataField (class in phenomedb.task) CreateLab (class in phenomedb.task) CreateProject (class in phenomedb.task) CreateSavedQueryDataframeCache (class in phenomedb.cache) CreateSavedQuerySummaryStatsCache (class in phenomedb.cache) CreateTaskViewCache (class in phenomedb.cache) CreateUnit (class in phenomedb.task) CustomEncoder (class in phenomedb.utilities)

D

DataRepository (class in phenomedb.models) default() (phenomedb.utilities.CustomEncoder method) delete() (phenomedb.cache.Cache method) delete_cache() (phenomedb.query_factory.QueryFactory method) delete_entity() (phenomedb.base_view.PhenomeDBBaseView method) delete_keys_by_regex() (phenomedb.cache.Cache method) delete_pipeline() (phenomedb.pipeline_factory.PipelineFactory method)

delete_rows_by_id() (phenomedb.base_view.PhenomeDBBaseView method) delete_test_keys() (phenomedb.cache.Cache method) download_file() (phenomedb.compounds.ParseHMDBXMLtoCSV method) download_files_from_metabolights() (phenomedb.task.Task method) download_from_metabolights_api() (phenomedb.task.Task method) DownloadMetabolightsStudy (class in phenomedb.imports) DynamicPipelineTask (class in phenomedb.pipelines)

E

EvidenceType (class in phenomedb.models) execute_and_build_dataframe() (phenomedb.query_factory.QueryFactory method) execute_query() (phenomedb.query_factory.QueryFactory method) execute_sql() (phenomedb.base_view.PhenomeDBBaseView method)

exists() (phenomedb.cache.Cache method) ExportCompoundsToCSV (class in phenomedb.compounds) ExternalDB (class in phenomedb.models) extract_and_set_compound_id() (phenomedb.compounds.ParseKEGGtoPubchemCIDTask method) extract_kegg_ids() (phenomedb.compounds.ParseKEGGtoPubchemCIDTask method)

F

FeatureDataset (class in phenomedb.models) FeatureDataset.CorrectionType (class in phenomedb.models) FeatureDataset.Type (class in phenomedb.models) FeatureMetadata (class in phenomedb.models)

find_chebi() (phenomedb.compounds.CompoundTask method) flask_form_to_ORM_dict() (phenomedb.base_view.PhenomeDBBaseView method) flatten_model_for_search() (in module phenomedb.utilities) flushall() (phenomedb.cache.Cache method) foreign_keys() (phenomedb.base_view.PhenomeDBBaseView method)

G

generate_and_execute_query() (phenomedb.query_factory.QueryFactory method) generate_feature_jsonb() (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) generate_file_cache_list() (phenomedb.cache.Cache method) generate_inchi_key() (phenomedb.compounds.CompoundTask method) generate_query() (phenomedb.query_factory.QueryFactory method) GenerateSingleTaskPipelines (class in phenomedb.pipelines) get() (phenomedb.cache.Cache method) get_all_by_model() (phenomedb.base_view.PhenomeDBBaseView method) get_annotated_feature() (phenomedb.imports.ImportTask method) get_annotation_by_cpd_name_and_annotation_method() (phenomedb.imports.ImportTask method) get_assay() (phenomedb.compounds.CleanROIFile method) get_beta_database_session() (in module phenomedb.database) get_cache_keys_dataframe() (phenomedb.cache.Cache method) get_cas_from_pubchem() (phenomedb.compounds.CompoundTask method) get_class_by_tablename() (phenomedb.base_view.PhenomeDBBaseView method) get_class_name() (phenomedb.task.Task method) get_classyfire_reference() (phenomedb.compounds.CompoundTask method) get_code_string() (phenomedb.query_factory.QueryFactory method) get_database_session() (in module phenomedb.database) get_dataframe_key() (phenomedb.query_factory.QueryFactory method) get_date() (in module phenomedb.utilities) get_db_session() (in module phenomedb.database) get_entities_as_dicts() (phenomedb.base_view.PhenomeDBBaseView method) get_entity_as_df() (phenomedb.base_view.PhenomeDBBaseView method) get_entity_as_dict() (phenomedb.base_view.PhenomeDBBaseView method) get_filter_dict() (phenomedb.query_factory.QueryFilter method) get_from_chebi() (phenomedb.compounds.CompoundTask method) get_from_chembl() (phenomedb.compounds.CompoundTask method) get_from_classyfire() (phenomedb.compounds.CompoundTask method) get_from_hmdb() (phenomedb.compounds.CompoundTask method) get_from_kegg() (phenomedb.compounds.CompoundTask method) get_from_lipidmaps() (phenomedb.compounds.CompoundTask method) get_from_pubchem() (phenomedb.compounds.CompoundTask method) get_from_pubchem_api() (phenomedb.compounds.CompoundTask method) get_from_refmet() (phenomedb.compounds.CompoundTask method) get_inchi_key_from_pubchem_or_hmdb() (phenomedb.compounds.CompoundTask method) get_json_task_spec() (phenomedb.pipeline_factory.PipelineFactory static method) get_keys_dict() (phenomedb.cache.Cache method) get_lipid_maps_reference() (phenomedb.compounds.CompoundTask method) get_match_dict() (phenomedb.query_factory.QueryMatch method) get_module_and_class_name() (in module phenomedb.utilities) get_npyc_enum_from_value() (in module phenomedb.utilities) get_or_add_annotated_features() (phenomedb.imports.ImportNPYC method) get_or_add_annotation() (phenomedb.imports.AnnotationImportTask method) get_or_add_annotation_method() (phenomedb.task.Task method) get_or_add_annotation_not_unified() (phenomedb.imports.AnnotationImportTask method) get_or_add_annotation_unified() (phenomedb.imports.AnnotationImportTask method) get_or_add_assay() (phenomedb.imports.ImportXCMSFeatures method) (phenomedb.task.Task method) get_or_add_compound_external_db() (phenomedb.compounds.CompoundTask method) get_or_add_data_repository() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method)

get_or_add_feature_dataset() (phenomedb.imports.ImportPeakPantherAnnotations method) get_or_add_feature_dataset_unified() (phenomedb.imports.AnnotationImportTask method) get_or_add_feature_metadata() (phenomedb.imports.ImportPeakPantherAnnotations method) get_or_add_feature_metadata_unified() (phenomedb.imports.AnnotationImportTask method) get_or_add_harmonised_field() (phenomedb.task.Task method) get_or_add_laboratory() (phenomedb.task.Task method) get_or_add_metabolights_compound() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) get_or_add_metadata() (phenomedb.imports.ImportBrukerIVDRAnnotations method) (phenomedb.imports.ImportNPYC method) get_or_add_metadata_field() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) get_or_add_project() (phenomedb.task.Task method) get_or_add_protocol() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) get_or_add_publication() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) get_or_add_sample() (phenomedb.imports.ImportDataLocations method) (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) (phenomedb.imports.ImportNPYC method) (phenomedb.imports.ImportSampleManifest method) (phenomedb.imports.ImportTask method) get_or_add_sample_assay() (phenomedb.imports.ImportDataLocations method) (phenomedb.imports.ImportNPYC method) get_or_add_subject() (phenomedb.imports.ImportDataLocations method) (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) (phenomedb.imports.ImportNPYC method) (phenomedb.imports.ImportSampleManifest method) (phenomedb.imports.ImportTask method) get_or_add_unit() (phenomedb.imports.ImportBrukerIVDRAnnotations method) (phenomedb.imports.ImportPeakPantherAnnotations method) (phenomedb.task.Task method) get_or_build_sample_name() (phenomedb.imports.ImportTask method) get_or_build_subject_name() (phenomedb.imports.ImportTask method) get_project() (phenomedb.imports.ImportTask method) get_project_metadata_fields() (phenomedb.base_view.PhenomeDBBaseView method) get_pubchem_cid() (phenomedb.compounds.ParseKEGGtoPubchemCIDTask method) get_pubchem_prop() (phenomedb.compounds.CompoundTask method) get_pubchem_sid() (phenomedb.compounds.ParseKEGGtoPubchemCIDTask method) get_pubchem_view_from_api() (phenomedb.compounds.CompoundTask method) get_query_rows() (phenomedb.query_factory.QueryFactory method) get_relations_by_fk() (phenomedb.base_view.PhenomeDBBaseView method) get_sample_assay() (phenomedb.imports.ImportTask method) get_sub_filter_dict() (phenomedb.query_factory.QuerySubFilter method) get_table_columns() (phenomedb.base_view.PhenomeDBBaseView method) get_table_names() (phenomedb.base_view.PhenomeDBBaseView method) get_tasks_from_json() (phenomedb.pipeline_factory.PipelineFactory static method) get_test_database_session() (in module phenomedb.database) get_unique_match_models() (phenomedb.query_factory.QueryFactory method) getrandbits() (in module phenomedb.imports) (in module phenomedb.metadata)

H

handle_json_error() (phenomedb.base_view.PhenomeDBBaseView method) HarmonisedAnnotatedFeature (class in phenomedb.models) HarmonisedAnnotation (class in phenomedb.models) HarmonisedAnnotation.MultiCompoundOperator (class in phenomedb.models)

HarmonisedDataset (class in phenomedb.models) HarmonisedDataset.Type (class in phenomedb.models) HarmonisedMetadataField (class in phenomedb.models) HarmonisedMetadataField.HarmonisedMetadataFieldDatatype (class in phenomedb.models) HarmoniseMetadataField (class in phenomedb.metadata)

I

import_row() (phenomedb.compounds.ImportROICompounds method) ImportAllMetabolightsPipelineGenerator (class in phenomedb.pipelines) ImportBrukerBiLISACompounds (class in phenomedb.compounds) ImportBrukerBiQuantCompounds (class in phenomedb.compounds) ImportBrukerIVDRAnnotations (class in phenomedb.imports) ImportCompoundsFromCSV (class in phenomedb.compounds) ImportDataLocations (class in phenomedb.imports) ImportMetabolightsStudy (class in phenomedb.imports) ImportMetabolightsXCMSAnnotations (class in phenomedb.imports) ImportMetadata (class in phenomedb.imports) ImportNPYC (class in phenomedb.imports)

ImportPeakPantherAnnotations (class in phenomedb.imports) ImportROICompounds (class in phenomedb.compounds) ImportSampleManifest (class in phenomedb.imports) ImportStandardsV1 (class in phenomedb.compounds) ImportTargetLynxAnnotations (class in phenomedb.imports) ImportTask (class in phenomedb.imports) ImportXCMSFeatures (class in phenomedb.imports) insert_entity() (phenomedb.base_view.PhenomeDBBaseView method) is_number() (in module phenomedb.utilities) isfloat() (in module phenomedb.utilities) isint() (in module phenomedb.utilities)

K

key_filename() (phenomedb.cache.Cache method)

L

Laboratory (class in phenomedb.models) load_cache_from_file() (phenomedb.cache.Cache method) load_data() (phenomedb.analysis.AnalysisTask method) (phenomedb.analysis.RunNPYCReport method) (phenomedb.analysis.RunXCMS method) (phenomedb.batch_correction.RunNPYCBatchCorrection method) (phenomedb.batch_correction.RunNPYCBatchCorrectionReportsForExistingCorrectedFeatureDataset method) (phenomedb.compounds.AddMissingClassyFireClasses method) (phenomedb.compounds.CleanROIFile method) (phenomedb.compounds.CompoundTask method) (phenomedb.compounds.ImportBrukerBiLISACompounds method) (phenomedb.compounds.ImportBrukerBiQuantCompounds method) (phenomedb.compounds.ImportCompoundsFromCSV method) (phenomedb.compounds.ImportROICompounds method) (phenomedb.compounds.ImportStandardsV1 method) (phenomedb.compounds.UpdateCompoundRefs method) load_dataframe() (phenomedb.query_factory.QueryFactory method) load_dataset() (phenomedb.imports.ImportBrukerIVDRAnnotations method) (phenomedb.imports.ImportDataLocations method) (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) (phenomedb.imports.ImportMetadata method) (phenomedb.imports.ImportPeakPantherAnnotations method) (phenomedb.imports.ImportSampleManifest method) (phenomedb.imports.ImportTargetLynxAnnotations method) (phenomedb.imports.ImportTask method) (phenomedb.imports.ImportXCMSFeatures method) (phenomedb.metadata.HarmoniseMetadataField method)

load_file_cache_list() (phenomedb.cache.Cache method) load_study_description_file() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) load_tabular_file() (phenomedb.task.Task method) log_info() (phenomedb.task.Task method) loop_and_map_data() (phenomedb.compounds.AddMissingClassyFireClasses method) (phenomedb.compounds.CleanROIFile method) (phenomedb.compounds.CompoundTask method) (phenomedb.compounds.ImportBrukerBiLISACompounds method) (phenomedb.compounds.ImportBrukerBiQuantCompounds method) (phenomedb.compounds.ImportCompoundsFromCSV method) (phenomedb.compounds.ImportROICompounds method) (phenomedb.compounds.ImportStandardsV1 method) (phenomedb.compounds.UpdateCompoundRefs method) loop_into_brite_fields() (phenomedb.compounds.ParseKEGGtoPubchemCIDTask method)

M

ManualSQL (class in phenomedb.task) map_and_add_dataset_data() (phenomedb.imports.ImportBrukerIVDRAnnotations method) (phenomedb.imports.ImportDataLocations method) (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) (phenomedb.imports.ImportMetadata method) (phenomedb.imports.ImportNPYC method) (phenomedb.imports.ImportPeakPantherAnnotations method) (phenomedb.imports.ImportSampleManifest method) (phenomedb.imports.ImportTargetLynxAnnotations method) (phenomedb.imports.ImportTask method) (phenomedb.imports.ImportXCMSFeatures method) (phenomedb.metadata.HarmoniseMetadataField method) MetadataField (class in phenomedb.models) MetadataFilter (class in phenomedb.query_factory) MetadataValue (class in phenomedb.models) MissingImportData (class in phenomedb.models)

module phenomedb.analysis phenomedb.base_view phenomedb.batch_correction phenomedb.cache phenomedb.compounds phenomedb.database phenomedb.imports phenomedb.metadata phenomedb.models phenomedb.pipeline_factory phenomedb.pipelines phenomedb.query_factory phenomedb.task phenomedb.utilities phenomedb.views MoveTaskOutputToCache (class in phenomedb.cache)

N

nmr_assay_regexes (phenomedb.imports.ImportDataLocations attribute)

NPYCTask (class in phenomedb.analysis)

O

OntologyRef (class in phenomedb.models)

OntologySource (class in phenomedb.models)

P

parse_assay_file() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) parse_assays() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) parse_kegg_compound_class() (phenomedb.compounds.ParseKEGGtoPubchemCIDTask method) parse_persons() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) parse_protocols() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) parse_pubchem_value() (phenomedb.compounds.CompoundTask method) parse_publications() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) parse_sample_information() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) parse_study_description() (phenomedb.imports.ImportMetabolightsStudy method) (phenomedb.imports.ImportMetabolightsXCMSAnnotations method) parse_value() (phenomedb.imports.ImportTask method) ParseHMDBXMLtoCSV (class in phenomedb.compounds) ParseKEGGtoPubchemCIDTask (class in phenomedb.compounds) pause_pipeline() (phenomedb.pipeline_factory.PipelineFactory method) phenomedb.analysis module phenomedb.base_view module phenomedb.batch_correction module phenomedb.cache module phenomedb.compounds module phenomedb.database module phenomedb.imports module phenomedb.metadata module phenomedb.models module

phenomedb.pipeline_factory module phenomedb.pipelines module phenomedb.query_factory module phenomedb.task module phenomedb.utilities module phenomedb.views module PhenomeDBBaseView (class in phenomedb.base_view) Pipeline (class in phenomedb.models) PipelineFactory (class in phenomedb.pipeline_factory) PipelineGeneratorTask (class in phenomedb.pipelines) post_commit_actions() (phenomedb.imports.ImportBrukerIVDRAnnotations method) (phenomedb.imports.ImportPeakPantherAnnotations method) process() (phenomedb.analysis.AnalysisTask method) (phenomedb.analysis.NPYCTask method) (phenomedb.cache.CreateSavedQueryDataframeCache method) (phenomedb.cache.CreateSavedQuerySummaryStatsCache method) (phenomedb.cache.CreateTaskViewCache method) (phenomedb.compounds.CleanROIFile method) (phenomedb.compounds.CompoundTask method) (phenomedb.compounds.ExportCompoundsToCSV method) (phenomedb.compounds.ImportROICompounds method) (phenomedb.compounds.ParseHMDBXMLtoCSV method) (phenomedb.compounds.ParseKEGGtoPubchemCIDTask method) (phenomedb.imports.AnnotationImportTask method) (phenomedb.imports.ImportTask method) (phenomedb.metadata.HarmoniseMetadataField method) Project (class in phenomedb.models) ProjectRoleFilter (class in phenomedb.query_factory) Protocol (class in phenomedb.models) ProtocolParameter (class in phenomedb.models) Publication (class in phenomedb.models)

Q

QueryFactory (class in phenomedb.query_factory) QueryFilter (class in phenomedb.query_factory)

QueryMatch (class in phenomedb.query_factory) QuerySubFilter (class in phenomedb.query_factory)

R

RAnalysisTask (class in phenomedb.analysis) random() (in module phenomedb.imports) (in module phenomedb.metadata) RebuildPipelinesFromDB (class in phenomedb.pipelines) relationship_dict() (phenomedb.base_view.PhenomeDBBaseView method) remove_whitespace_and_weird_characters() (phenomedb.compounds.CleanROIFile method) RemoveUntransformedDataFromCache (class in phenomedb.cache) reset_found_fields() (phenomedb.compounds.ParseHMDBXMLtoCSV method) round_decimals_down() (in module phenomedb.utilities) round_decimals_up() (in module phenomedb.utilities) run() (phenomedb.task.Task method) run_analysis() (phenomedb.analysis.AnalysisTask method) (phenomedb.analysis.RAnalysisTask method) (phenomedb.analysis.RunNPYCReport method) (phenomedb.analysis.RunPCA method) (phenomedb.batch_correction.RunNPYCBatchCorrection method)

run_pipeline() (phenomedb.pipeline_factory.BasePipelineManager method) (phenomedb.pipeline_factory.PipelineFactory method) RunBatchCorrectionAssessmentPipeline (class in phenomedb.pipelines) RunCombatCorrection (class in phenomedb.batch_correction) RunDBnormCorrection (class in phenomedb.batch_correction) RunMWAS (class in phenomedb.analysis) RunMWASMulti (class in phenomedb.pipelines) RunNormResidualsMM (class in phenomedb.batch_correction) RunNPYCBatchCorrection (class in phenomedb.batch_correction) RunNPYCBatchCorrectionReportsForExistingCorrectedFeatureDataset (class in phenomedb.batch_correction) RunNPYCReport (class in phenomedb.analysis) RunPCA (class in phenomedb.analysis) RunPCPR2 (class in phenomedb.analysis) RunWilcoxonRankTest (class in phenomedb.analysis) RunXCMS (class in phenomedb.analysis)

S

Sample (class in phenomedb.models) SampleAssay (class in phenomedb.models) SampleAssayFeatures (class in phenomedb.models) SampleAssayProtocol (class in phenomedb.models) save_query() (phenomedb.query_factory.QueryFactory method) save_results() (phenomedb.analysis.AnalysisTask method) (phenomedb.analysis.RunMWAS method) (phenomedb.batch_correction.RunCombatCorrection method) (phenomedb.batch_correction.RunDBnormCorrection method) (phenomedb.batch_correction.RunNormResidualsMM method) (phenomedb.batch_correction.RunNPYCBatchCorrection method) (phenomedb.batch_correction.RunNPYCBatchCorrectionReportsForExistingCorrectedFeatureDataset method) SaveBatchCorrection (class in phenomedb.batch_correction)

SavedQuery (class in phenomedb.models) SavedQuery.Type (class in phenomedb.models) send_tls_email() (in module phenomedb.utilities) send_user_failure_email() (phenomedb.imports.ImportTask method) send_user_success_email() (phenomedb.imports.ImportTask method) serialise_unserialise() (in module phenomedb.utilities) set() (phenomedb.cache.Cache method) set_db() (phenomedb.base_view.PhenomeDBBaseView method) set_db_session() (phenomedb.base_view.PhenomeDBBaseView method) (phenomedb.query_factory.QueryFactory method) simple_assignment() (in module phenomedb.metadata) simple_report() (phenomedb.imports.ImportTask method) sql_to_dataframe() (phenomedb.base_view.PhenomeDBBaseView method) Subject (class in phenomedb.models)

T

Task (class in phenomedb.task) task_validation() (phenomedb.imports.ImportBrukerIVDRAnnotations method) (phenomedb.imports.ImportDataLocations method) (phenomedb.imports.ImportPeakPantherAnnotations method) (phenomedb.imports.ImportSampleManifest method) (phenomedb.imports.ImportTargetLynxAnnotations method) (phenomedb.imports.ImportTask method) (phenomedb.metadata.HarmoniseMetadataField method)

TaskRun (class in phenomedb.models) TaskRun.Status (class in phenomedb.models) total_size() (in module phenomedb.utilities) transform_dob_and_sampling_date_to_age() (in module phenomedb.metadata)

U

Unit (class in phenomedb.models) update_annotation() (phenomedb.compounds.CompoundTask method)

update_entity() (phenomedb.base_view.PhenomeDBBaseView method) update_name_to_refmet() (phenomedb.compounds.CompoundTask method) UpdateCompoundRefs (class in phenomedb.compounds)