Display bedhost API schemas

Display bedhost API schemas

# S4 method for class 'BEDbase'
schemas(x)

Arguments

x

BEDbase() object

Value

list() API endpoints

Examples

bedbase <- BEDbase()
#> 125977 BED files available.
schemas(bedbase)
#> $AccessMethod
#>   AccessMethod(access_id, access_url, region, type)
#> 
#> $AccessURL
#>   AccessURL(headers, url)
#> 
#> $BaseListResponse
#>   BaseListResponse(count, limit, offset, results)
#> 
#> $BedClassification
#>   BedClassification(bed_compliance, compliant_columns, data_format,
#>     genome_alias, genome_digest, header, name, non_compliant_columns)
#> 
#> $BedEmbeddingResult
#>   BedEmbeddingResult(embedding, identifier, payload)
#> 
#> $BedFiles
#>   BedFiles(bed_file, bigbed_file)
#> 
#> $BedListResult
#>   BedListResult(count, limit, offset, results)
#> 
#> $BedListSearchResult
#>   BedListSearchResult(count, limit, offset, results)
#> 
#> $BedMetadataAll
#>   BedMetadataAll(annotation, bed_compliance, bedsets,
#>     compliant_columns, data_format, description, files, genome_alias,
#>     genome_digest, header, id, is_universe, last_update_date,
#>     license_id, name, non_compliant_columns, plots, processed,
#>     raw_metadata, stats, submission_date, universe_metadata)
#> 
#> $BedMetadataBasic
#>   BedMetadataBasic(annotation, bed_compliance, compliant_columns,
#>     data_format, description, genome_alias, genome_digest, header, id,
#>     is_universe, last_update_date, license_id, name,
#>     non_compliant_columns, processed, submission_date)
#> 
#> $BedPEPHub
#>   BedPEPHub(antibody, cell_line, cell_type, description, exp_protocol,
#>     genome, genotype, global_experiment_id, global_sample_id,
#>     library_source, organism, sample_name, species_id, target, tissue,
#>     treatment)
#> 
#> $BedPEPHubRestrict
#>   BedPEPHubRestrict(antibody, cell_line, cell_type, description,
#>     exp_protocol, genome, genotype, global_experiment_id,
#>     global_sample_id, library_source, organism, sample_name,
#>     species_id, target, tissue, treatment)
#> 
#> $BedPlots
#>   BedPlots(chrombins, cumulative_partitions, expected_partitions,
#>     gccontent, neighbor_distances, open_chromatin, partitions,
#>     tss_distance, widths_histogram)
#> 
#> $BedSetBedFiles
#>   BedSetBedFiles(count, results)
#> 
#> $BedSetListResult
#>   BedSetListResult(count, limit, offset, results)
#> 
#> $BedSetMetadata
#>   BedSetMetadata(author, bed_ids, description, id, last_update_date,
#>     md5sum, name, plots, source, statistics, submission_date, summary)
#> 
#> $BedSetMinimal
#>   BedSetMinimal(description, id, name)
#> 
#> $BedSetPlots
#>   BedSetPlots(region_commonality)
#> 
#> $BedSetStats
#>   BedSetStats(mean, sd)
#> 
#> $BedStatsModel
#>   BedStatsModel(exon_frequency, exon_percentage, fiveutr_frequency,
#>     fiveutr_percentage, gc_content, intergenic_frequency,
#>     intergenic_percentage, intron_frequency, intron_percentage,
#>     mean_region_width, median_tss_dist, number_of_regions,
#>     promotercore_frequency, promotercore_percentage,
#>     promoterprox_frequency, promoterprox_percentage,
#>     threeutr_frequency, threeutr_percentage)
#> 
#> $Body_bed_to_bed_search_v1_bed_search_bed_post
#>   Body_bed_to_bed_search_v1_bed_search_bed_post(file)
#> 
#> $Body_embed_bed_file_v1_bed_embed_post
#>   Body_embed_bed_file_v1_bed_embed_post(file)
#> 
#> $ComponentVersions
#>   ComponentVersions(bbconf_version, bedhost_version, geniml_version,
#>     openapi_version, python_version)
#> 
#> $CreateBEDsetRequest
#>   CreateBEDsetRequest(registry_path)
#> 
#> $DRSModel
#>   DRSModel(access_methods, checksums, created_time, description, id,
#>     name, self_uri, size, updated_time)
#> 
#> $EmbeddingModels
#>   EmbeddingModels(region2vec, text2vec)
#> 
#> $FileModel
#>   FileModel(access_methods, description, file_digest, name, object_id,
#>     path, size, thumbnail_path, title)
#> 
#> $FileStats
#>   FileStats(bed_compliance, data_format, file_genome, file_organism)
#> 
#> $HTTPValidationError
#>   HTTPValidationError(detail)
#> 
#> $Organization
#>   Organization(name, url)
#> 
#> $QdrantSearchResult
#>   QdrantSearchResult(id, metadata, payload, score)
#> 
#> $RefGenValidModel
#>   RefGenValidModel(assigned_points, compared_genome, oobr,
#>     provided_genome, sequence_fit, tier_ranking, xs)
#> 
#> $RefGenValidReturnModel
#>   RefGenValidReturnModel(compared_genome, id, provided_genome)
#> 
#> $ServiceInfoResponse
#>   ServiceInfoResponse(component_versions, contactUrl, description,
#>     documentationUrl, embedding_models, environment, id, name,
#>     organization, type, updatedAt, version)
#> 
#> $StandardMeta
#>   StandardMeta(antibody, cell_line, cell_type, description,
#>     exp_protocol, genotype, global_experiment_id, global_sample_id,
#>     library_source, organism, original_file_name, phenotype,
#>     species_id, target, tissue, treatment)
#> 
#> $StatsReturn
#>   StatsReturn(bedfiles_number, bedsets_number, genomes_number)
#> 
#> $TokenizedBedResponse
#>   TokenizedBedResponse(bed_id, tokenized_bed, universe_id)
#> 
#> $TokenizedPathResponse
#>   TokenizedPathResponse(bed_id, endpoint_url, file_path, universe_id)
#> 
#> $Type
#>   Type(artifact, group, version)
#> 
#> $UniverseMetadata
#>   UniverseMetadata(bedset_id, construct_method)
#> 
#> $UsageStats
#>   UsageStats(bed_metadata, bed_search_terms, bedset_metadata,
#>     bedset_search_terms)
#> 
#> $ValidationError
#>   ValidationError(loc, msg, type)
#>