Index

A

accessibility (bridge.core.biotools.ToolModel attribute) Accessibility (class in bridge.core.biotools) added() (bridge.logging.BridgeLogger method) admin (bridge.core.github_repo.Permissions attribute) (bridge.core.github_repo.Permissions1 attribute) advanced_security (bridge.core.github_repo.SecurityAndAnalysis attribute) AdvancedSecurity (class in bridge.core.github_repo) allow_auto_merge (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) allow_forking (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) allow_issues (bridge.adapters.api.routers.biotools_to_github.BioToolsToGitHubPayload attribute) allow_merge_commit (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) allow_rebase_merge (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) allow_squash_merge (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) allow_update_branch (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) alt_text (bridge.pipelines.utils.Badge attribute) (bridge.pipelines.utils.badges.Badge attribute) anonymous_access_enabled (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

any_bt_newer_than_gh() (in module bridge.pipelines.shared.version) apply_changes_and_push() (bridge.services.github.github_repo_provider.GitHubRepoProvider method) (bridge.services.github.GitHubRepoProvider method) (bridge.services.GitHubRepoProvider method) (bridge.services.protocols.repo_provider.RepoProvider method) (bridge.services.protocols.RepoProvider method) archive_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) archived (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) as_markdown() (bridge.pipelines.utils.Badge method) (bridge.pipelines.utils.badges.Badge method) Asset (class in bridge.core.github_latest_release) assets (bridge.core.github_latest_release.Release attribute) assets_url (bridge.core.github_latest_release.Release attribute) assignees_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) author (bridge.core.github_latest_release.Release attribute) Author (class in bridge.core.github_latest_release) (class in bridge.core.publication) authors (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute) avatar_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute)

B

Badge (class in bridge.pipelines.utils) (class in bridge.pipelines.utils.badges) biotools_api_base (bridge.config.Settings property) biotools_api_url (bridge.config.Settings attribute) biotools_id (bridge.adapters.api.routers.biotools_to_github.BioToolsToGitHubPayload attribute) (bridge.adapters.api.routers.github_to_biotools.GitHubToBioToolsPayload attribute) biotools_to_github_pr_issues() (in module bridge.adapters.api.routers.biotools_to_github) biotools_url (bridge.config.Settings attribute) biotoolsCURIE (bridge.core.biotools.ToolModel attribute) biotoolsID (bridge.core.biotools.RelationItem attribute) (bridge.core.biotools.ToolModel attribute) BiotoolsIdType (class in bridge.core.biotools) BiotoolsIngestor (class in bridge.services) (class in bridge.services.biotools) (class in bridge.services.biotools.biotools_ingestor) BiotoolsToGitHubForPRPipelineArgs (class in bridge.pipelines) (class in bridge.pipelines.bt2gh_for_pr_issues) (class in bridge.pipelines.bt2gh_for_pr_issues.main) BioToolsToGitHubPayload (class in bridge.adapters.api.routers.biotools_to_github) BiotoolsToolModel (in module bridge.core) BiotoolsToolTransformer (class in bridge.builders.biotools.biotools_transformer) blobs_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) body (bridge.core.github_latest_release.Release attribute) body_html (bridge.core.github_latest_release.Release attribute) body_text (bridge.core.github_latest_release.Release attribute) branch (bridge.core.github_pages.Source attribute) branches_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) bridge module bridge.adapters module bridge.adapters.api module bridge.adapters.api.main module bridge.adapters.api.routers module bridge.adapters.api.routers.biotools_to_github module bridge.adapters.api.routers.github_to_biotools module bridge.adapters.cli module bridge.adapters.cli.commands module bridge.adapters.cli.commands.biotools_to_github module bridge.adapters.cli.commands.github_to_biotools module bridge.adapters.cli.main module bridge.bootstrap module bridge.bootstrap.base module bridge.bootstrap.register_handler module bridge.bootstrap.state module bridge.bootstrap.wiring module bridge.builders module bridge.builders.biotools module bridge.builders.biotools.biotools_composer module bridge.builders.biotools.biotools_transformer module bridge.builders.europe_pmc module bridge.builders.europe_pmc.europe_pmc_composer module bridge.builders.europe_pmc.europe_pmc_transformer module bridge.builders.github module bridge.builders.github.github_composer module bridge.builders.github.github_transformer module bridge.builders.protocols module bridge.builders.protocols.transformer module bridge.builders.spdx module bridge.builders.spdx.spdx_composer module bridge.builders.spdx.spdx_transormer module bridge.config module bridge.core module bridge.core.biotools module bridge.core.github module bridge.core.github_languages module bridge.core.github_latest_release module bridge.core.github_pages module bridge.core.github_repo module bridge.core.license module bridge.core.publication module bridge.handlers module bridge.handlers.create_pr_issues_from_meta module bridge.handlers.extract_meta_from_repo module bridge.logging module bridge.pipelines module bridge.pipelines.bt2gh_for_pr_issues module bridge.pipelines.bt2gh_for_pr_issues.main module bridge.pipelines.bt2gh_for_pr_issues.map module bridge.pipelines.bt2gh_for_pr_issues.map_funcs module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.citation module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.description module

bridge.pipelines.bt2gh_for_pr_issues.map_funcs.functions module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.homepage module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.license module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.name module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.readme module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.topics module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.version module bridge.pipelines.gh2bt_for_meta module bridge.pipelines.gh2bt_for_meta.main module bridge.pipelines.gh2bt_for_meta.map module bridge.pipelines.gh2bt_for_meta.map_funcs module bridge.pipelines.gh2bt_for_meta.map_funcs.biotools_id module bridge.pipelines.gh2bt_for_meta.map_funcs.description module bridge.pipelines.gh2bt_for_meta.map_funcs.documentation module bridge.pipelines.gh2bt_for_meta.map_funcs.functions module bridge.pipelines.gh2bt_for_meta.map_funcs.homepage module bridge.pipelines.gh2bt_for_meta.map_funcs.language module bridge.pipelines.gh2bt_for_meta.map_funcs.license module bridge.pipelines.gh2bt_for_meta.map_funcs.maturity module bridge.pipelines.gh2bt_for_meta.map_funcs.name module bridge.pipelines.gh2bt_for_meta.map_funcs.publication module bridge.pipelines.gh2bt_for_meta.map_funcs.version module bridge.pipelines.goals module bridge.pipelines.policies module bridge.pipelines.policies.bt2gh module bridge.pipelines.policies.bt2gh.reconcile_bt_ontop_gh module bridge.pipelines.policies.bt2gh.reconcile_bt_over_gh module bridge.pipelines.policies.gh2bt module bridge.pipelines.policies.gh2bt.reconcile_gh_ontop_bt module bridge.pipelines.policies.gh2bt.reconcile_gh_over_bt module bridge.pipelines.protocols module bridge.pipelines.protocols.map module bridge.pipelines.protocols.none_propagation module bridge.pipelines.protocols.pipeline_args module bridge.pipelines.shared module bridge.pipelines.shared.functions module bridge.pipelines.shared.publications module bridge.pipelines.shared.version module bridge.pipelines.utils module bridge.pipelines.utils.badges module bridge.pipelines.utils.cleaning module bridge.pipelines.utils.comparisons module bridge.pipelines.utils.conversions module bridge.pipelines.utils.files module bridge.pipelines.utils.templating module bridge.services module bridge.services.biotools module bridge.services.biotools.biotools_ingestor module bridge.services.europe_pmc module bridge.services.europe_pmc.europe_pmc_auth module bridge.services.europe_pmc.europe_pmc_ingestor module bridge.services.github module bridge.services.github.github_auth module bridge.services.github.github_ingestor module bridge.services.github.github_repo_provider module bridge.services.huggingface module bridge.services.huggingface.huggingface_provider module bridge.services.protocols module bridge.services.protocols.ingestor module bridge.services.protocols.llm_provider module bridge.services.protocols.repo_provider module bridge.services.spdx module bridge.services.spdx.spdx_ingestor module bridge.utils module BridgeLogger (class in bridge.logging) BridgeRegistration (class in bridge.bootstrap.base) browser_download_url (bridge.core.github_latest_release.Asset attribute) build_type (bridge.core.github_pages.GitHubPages attribute) BuildType (class in bridge.core.github_pages)

C

canonicalize_shields_url() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.cleaning) canonicalize_url() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.cleaning) ChatMessage (class in bridge.services) (class in bridge.services.protocols) (class in bridge.services.protocols.llm_provider) check_file_with_extension_exists() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.files) clone_context() (bridge.services.github.github_repo_provider.GitHubRepoProvider method) (bridge.services.github.GitHubRepoProvider method) (bridge.services.GitHubRepoProvider method) (bridge.services.protocols.repo_provider.RepoProvider method) (bridge.services.protocols.RepoProvider method) clone_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) cmd (bridge.core.biotools.FunctionItem attribute) cname (bridge.core.github_pages.GitHubPages attribute) code_of_conduct (bridge.core.github_repo.FullRepository attribute) code_search_index_status (bridge.core.github_repo.TemplateRepository attribute) code_security (bridge.core.github_repo.SecurityAndAnalysis attribute) CodeOfConduct (class in bridge.core.github_repo) CodeSearchIndexStatus (class in bridge.core.github_repo) CodeSecurity (in module bridge.core.github_repo) collaborators_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) collectionID (bridge.core.biotools.ToolModel attribute) comments_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) commits_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) compare_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) compose_badge() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.badges) compose_biotools_metadata() (in module bridge.builders) (in module bridge.builders.biotools) compose_europe_pmc_metadata() (in module bridge.builders) (in module bridge.builders.europe_pmc) (in module bridge.builders.europe_pmc.europe_pmc_composer)

compose_github_repo() (in module bridge.builders) (in module bridge.builders.github) compose_spdx_license_metadata() (in module bridge.builders) (in module bridge.builders.spdx) (in module bridge.builders.spdx.spdx_composer) conflict() (bridge.logging.BridgeLogger method) confused (bridge.core.github_latest_release.Reactions attribute) content (bridge.services.ChatMessage attribute), [1] (bridge.services.protocols.ChatMessage attribute), [1] (bridge.services.protocols.llm_provider.ChatMessage attribute), [1] content_type (bridge.core.github_latest_release.Asset attribute) contents_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) contributors_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) cost (bridge.core.biotools.ToolModel attribute) Cost (class in bridge.core.biotools) create_issue() (bridge.services.github.github_repo_provider.GitHubRepoProvider method) (bridge.services.github.GitHubRepoProvider method) (bridge.services.GitHubRepoProvider method) (bridge.services.protocols.repo_provider.RepoProvider method) (bridge.services.protocols.RepoProvider method) CREATE_PR_ISSUES (bridge.pipelines.goals.PipelineGoal attribute) (bridge.pipelines.PipelineGoal attribute) create_pr_issues_from_meta() (in module bridge), [1] (in module bridge.handlers) create_pull_request() (bridge.services.github.github_repo_provider.GitHubRepoProvider method) (bridge.services.github.GitHubRepoProvider method) (bridge.services.GitHubRepoProvider method) (bridge.services.protocols.repo_provider.RepoProvider method) (bridge.services.protocols.RepoProvider method) created_at (bridge.core.github_latest_release.Asset attribute) (bridge.core.github_latest_release.Release attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) credit (bridge.core.biotools.ToolModel attribute) CreditItem (class in bridge.core.biotools) crossRef (bridge.core.license.SPDXLicense attribute) (bridge.core.SPDXLicense attribute) custom_404 (bridge.core.github_pages.GitHubPages attribute) custom_properties (bridge.core.github_repo.FullRepository attribute)

D

data (bridge.core.biotools.DataType attribute) (bridge.core.biotools.InputItem attribute) (bridge.core.biotools.OutputItem attribute) DataType (class in bridge.core.biotools) deduplicate_references() (in module bridge.pipelines.shared.publications) deep_unwrap() (in module bridge.pipelines.protocols.none_propagation) default_branch (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) delete_branch_on_merge (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) dependabot_security_updates (bridge.core.github_repo.SecurityAndAnalysis attribute) DependabotSecurityUpdates (class in bridge.core.github_repo) deployments_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) description (bridge.core.biotools.ToolModel attribute) (bridge.core.github_pages.HttpsCertificate attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

digest (bridge.core.github_latest_release.Asset attribute) disabled (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) discussion_url (bridge.core.github_latest_release.Release attribute) documentation (bridge.core.biotools.ToolModel attribute) DocumentationItem (class in bridge.core.biotools) doi (bridge.core.biotools.PublicationItem attribute) (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute) domains (bridge.core.github_pages.HttpsCertificate attribute) download (bridge.core.biotools.ToolModel attribute) download_count (bridge.core.github_latest_release.Asset attribute) DownloadItem (class in bridge.core.biotools) downloads_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) draft (bridge.core.github_latest_release.Release attribute)

E

EDAMdata (class in bridge.core.biotools) EDAMformat (class in bridge.core.biotools) elixirCommunity (bridge.core.biotools.ToolModel attribute) ElixirCommunityEnum (class in bridge.core.biotools) elixirNode (bridge.core.biotools.ToolModel attribute) ElixirNodeEnum (class in bridge.core.biotools) elixirPlatform (bridge.core.biotools.ToolModel attribute) ElixirPlatformEnum (class in bridge.core.biotools) email (bridge.core.biotools.CreditItem attribute) (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) ensure_callable_or_none() (bridge.pipelines.protocols.map.MapItem class method) (bridge.pipelines.protocols.MapItem class method) escape_shields_part() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.cleaning) europe_pmc_api_url (bridge.config.Settings attribute) europepmc_api_base (bridge.config.Settings property) EuropePMCIngestor (class in bridge.services) (class in bridge.services.europe_pmc) (class in bridge.services.europe_pmc.europe_pmc_ingestor)

EuropePMCNotFoundError EuropePMCTransformer (class in bridge.builders.europe_pmc.europe_pmc_transformer) events_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.Owner attribute) (bridge.core.github_repo.TemplateRepository attribute) exact() (bridge.logging.BridgeLogger method) existing_metadata (bridge.pipelines.gh2bt_for_meta.GitHubToBiotoolsForMetaPipelineArgs attribute) (bridge.pipelines.gh2bt_for_meta.main.GitHubToBiotoolsForMetaPipelineArgs attribute) (bridge.pipelines.GitHubToBiotoolsForMetaPipelineArgs attribute) existing_repo_model (bridge.pipelines.BiotoolsToGitHubForPRPipelineArgs attribute) (bridge.pipelines.bt2gh_for_pr_issues.BiotoolsToGitHubForPRPipelineArgs attribute) (bridge.pipelines.bt2gh_for_pr_issues.main.BiotoolsToGitHubForPRPipelineArgs attribute) expires_at (bridge.core.github_pages.HttpsCertificate attribute) extract() (in module bridge.adapters.cli.commands.github_to_biotools) extract_cff_references() (in module bridge.pipelines.shared.publications) extract_meta_from_repo() (in module bridge), [1] (in module bridge.handlers) EXTRACT_METADATA (bridge.pipelines.goals.PipelineGoal attribute) (bridge.pipelines.PipelineGoal attribute) eyes (bridge.core.github_latest_release.Reactions attribute)

F

fetch() (bridge.services.biotools.biotools_ingestor.BiotoolsIngestor method) (bridge.services.biotools.BiotoolsIngestor method) (bridge.services.BiotoolsIngestor method) (bridge.services.europe_pmc.europe_pmc_ingestor.EuropePMCIngestor method) (bridge.services.europe_pmc.EuropePMCIngestor method) (bridge.services.EuropePMCIngestor method) (bridge.services.github.github_ingestor.GitHubIngestor method) (bridge.services.github.GitHubIngestor method) (bridge.services.GitHubIngestor method) (bridge.services.protocols.Ingestor method) (bridge.services.protocols.ingestor.Ingestor method) (bridge.services.spdx.spdx_ingestor.SPDXLicenseIngestor method) (bridge.services.spdx.SPDXLicenseIngestor method) (bridge.services.SPDXLicenseIngestor method) fetch_github_pages() (bridge.services.github.github_ingestor.GitHubIngestor method) (bridge.services.github.GitHubIngestor method) (bridge.services.GitHubIngestor method) fetch_languages() (bridge.services.github.github_ingestor.GitHubIngestor method) (bridge.services.github.GitHubIngestor method) (bridge.services.GitHubIngestor method) fetch_latest_release() (bridge.services.github.github_ingestor.GitHubIngestor method) (bridge.services.github.GitHubIngestor method) (bridge.services.GitHubIngestor method) fetch_readme() (bridge.services.github.github_ingestor.GitHubIngestor method) (bridge.services.github.GitHubIngestor method) (bridge.services.GitHubIngestor method) fetch_repo() (bridge.services.github.github_ingestor.GitHubIngestor method) (bridge.services.github.GitHubIngestor method) (bridge.services.GitHubIngestor method) field_1 (bridge.core.github_latest_release.Reactions attribute) field_1_1 (bridge.core.github_latest_release.Reactions attribute) fill_template() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.templating) find_latest_bt_version() (in module bridge.pipelines.shared.version) find_match_yamls() (in module bridge.pipelines.shared.functions) find_matches() (in module bridge.pipelines.shared.functions)

find_matching_enum_member() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.conversions) first_name (bridge.core.publication.Author attribute) fn (bridge.pipelines.protocols.map.MapItem attribute) (bridge.pipelines.protocols.MapItem attribute) followers_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) following_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) fork (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) fork() (bridge.services.github.github_repo_provider.GitHubRepoProvider method) (bridge.services.github.GitHubRepoProvider method) (bridge.services.GitHubRepoProvider method) (bridge.services.protocols.repo_provider.RepoProvider method) (bridge.services.protocols.RepoProvider method) ForkInfo (class in bridge.services.protocols) (class in bridge.services.protocols.repo_provider) forks (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) forks_count (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) forks_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) format (bridge.core.biotools.DataType attribute) (bridge.core.biotools.InputItem attribute) (bridge.core.biotools.OutputItem attribute) full_match (bridge.pipelines.utils.Badge attribute) (bridge.pipelines.utils.badges.Badge attribute) full_name (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) (bridge.services.protocols.ForkInfo attribute) (bridge.services.protocols.repo_provider.ForkInfo attribute) FullRepository (class in bridge.core.github_repo) function (bridge.core.biotools.ToolModel attribute) FunctionItem (class in bridge.core.biotools) fundrefid (bridge.core.biotools.CreditItem attribute)

G

generate() (bridge.services.huggingface.huggingface_provider.HuggingFaceProvider method) (bridge.services.huggingface.HuggingFaceProvider method) (bridge.services.HuggingFaceProvider method) (bridge.services.protocols.llm_provider.LLMProvider method) (bridge.services.protocols.LLMProvider method) get_europe_pmc_headers() (in module bridge.services.europe_pmc.europe_pmc_auth) get_file_content() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.files) get_github_headers() (in module bridge.services.github.github_auth) get_handler() (in module bridge.bootstrap) (in module bridge.bootstrap.base) get_pipeline() (in module bridge.bootstrap) (in module bridge.bootstrap.base) get_repo_components() (in module bridge.bootstrap) (in module bridge.bootstrap.base) get_schema_composer() (in module bridge.bootstrap) (in module bridge.bootstrap.base) get_user() (bridge.services.github.github_ingestor.GitHubIngestor method) (bridge.services.github.GitHubIngestor method) (bridge.services.GitHubIngestor method) get_user_logger() (in module bridge.logging) gists_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) git_commits_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) git_refs_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

git_tags_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) git_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) github_api_base (bridge.config.Settings property) github_api_url (bridge.config.Settings attribute) github_pages (bridge.core.github.GitHubRepoModel attribute) (bridge.core.GitHubRepoModel attribute) github_to_biotools() (in module bridge.adapters.api.routers.github_to_biotools) github_token (bridge.config.Settings attribute) GitHubIngestor (class in bridge.services) (class in bridge.services.github) (class in bridge.services.github.github_ingestor) GitHubPages (class in bridge.core.github_pages) GitHubRepoModel (class in bridge.core) (class in bridge.core.github) GitHubRepoProvider (class in bridge.services) (class in bridge.services.github) (class in bridge.services.github.github_repo_provider) GitHubRepoTransformer (class in bridge.builders.github.github_transformer) GitHubToBiotoolsForMetaPipelineArgs (class in bridge.pipelines) (class in bridge.pipelines.gh2bt_for_meta) (class in bridge.pipelines.gh2bt_for_meta.main) GitHubToBioToolsPayload (class in bridge.adapters.api.routers.github_to_biotools) gravatar_id (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) gridid (bridge.core.biotools.CreditItem attribute)

H

has_discussions (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) has_downloads (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) has_issues (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) has_pages (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) has_projects (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) has_wiki (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) heart (bridge.core.github_latest_release.Reactions attribute) homepage (bridge.core.biotools.ToolModel attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) hooks_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

hooray (bridge.core.github_latest_release.Reactions attribute) html_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_latest_release.Release attribute) (bridge.core.github_pages.GitHubPages attribute) (bridge.core.github_repo.CodeOfConduct attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.License attribute) (bridge.core.github_repo.Owner attribute) (bridge.core.github_repo.TemplateRepository attribute) https_certificate (bridge.core.github_pages.GitHubPages attribute) https_enforced (bridge.core.github_pages.GitHubPages attribute) HttpsCertificate (class in bridge.core.github_pages) huggingface_api_base (bridge.config.Settings property) huggingface_api_url (bridge.config.Settings attribute) huggingface_token (bridge.config.Settings attribute) HuggingFaceProvider (class in bridge.services) (class in bridge.services.huggingface) (class in bridge.services.huggingface.huggingface_provider)

I

id (bridge.core.github_latest_release.Asset attribute) (bridge.core.github_latest_release.Author attribute) (bridge.core.github_latest_release.Release attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.Owner attribute) (bridge.core.github_repo.TemplateRepository attribute) image_url (bridge.pipelines.utils.Badge attribute) (bridge.pipelines.utils.badges.Badge attribute) immutable (bridge.core.github_latest_release.Release attribute) ingestor (bridge.builders.biotools.biotools_transformer.BiotoolsToolTransformer attribute) (bridge.builders.europe_pmc.europe_pmc_transformer.EuropePMCTransformer attribute) (bridge.builders.spdx.spdx_transormer.SPDXLicenseTransformer attribute) Ingestor (class in bridge.services.protocols) (class in bridge.services.protocols.ingestor) input (bridge.core.biotools.FunctionItem attribute) InputItem (class in bridge.core.biotools) is_initialized() (in module bridge.bootstrap.state) is_template (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

isDeprecatedLicenseId (bridge.core.license.SPDXLicense attribute) (bridge.core.SPDXLicense attribute) isFsfLibre (bridge.core.license.SPDXLicense attribute) (bridge.core.SPDXLicense attribute) isLive (bridge.core.license.SPDXCrossRef attribute) isOsiApproved (bridge.core.license.SPDXLicense attribute) (bridge.core.SPDXLicense attribute) issue (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute) (bridge.pipelines.bt2gh_for_pr_issues.map.MapDestination attribute) issue_comment_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) issue_events_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) issues_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) isValid (bridge.core.license.SPDXCrossRef attribute) isWayBackLink (bridge.core.license.SPDXCrossRef attribute)

J

journal (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute)

K

key (bridge.core.github_repo.CodeOfConduct attribute) (bridge.core.github_repo.License attribute)

keys_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) kind (bridge.pipelines.shared.version.ParsedVersion attribute)

L

label (bridge.core.github_latest_release.Asset attribute) labels_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) language (bridge.core.biotools.ToolModel attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) Language (class in bridge.core.github_languages) LanguageEnum (class in bridge.core.biotools) languages (bridge.core.github.GitHubRepoModel attribute) (bridge.core.GitHubRepoModel attribute) languages_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) last_name (bridge.core.publication.Author attribute) latest_release (bridge.core.github.GitHubRepoModel attribute) (bridge.core.GitHubRepoModel attribute) laugh (bridge.core.github_latest_release.Reactions attribute) lexical_commit_sha (bridge.core.github_repo.CodeSearchIndexStatus attribute) lexical_search_ok (bridge.core.github_repo.CodeSearchIndexStatus attribute) license (bridge.core.biotools.ToolModel attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

License (class in bridge.core.biotools) (class in bridge.core.github_repo) licenseId (bridge.core.license.SPDXLicense attribute) (bridge.core.SPDXLicense attribute) licenseText (bridge.core.license.SPDXLicense attribute) (bridge.core.SPDXLicense attribute) licenseTextHtml (bridge.core.license.SPDXLicense attribute) (bridge.core.SPDXLicense attribute) lifespan() (in module bridge.adapters.api.main) link (bridge.core.biotools.ToolModel attribute) link_url (bridge.pipelines.utils.Badge attribute) (bridge.pipelines.utils.badges.Badge attribute) LinkItem (class in bridge.core.biotools) LLMProvider (class in bridge.services.protocols) (class in bridge.services.protocols.llm_provider) load_dict_from_yaml_file() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.files) log_level (bridge.config.Settings attribute) login (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute)

M

main() (in module bridge.adapters.cli.main) maintain (bridge.core.github_repo.Permissions attribute) (bridge.core.github_repo.Permissions1 attribute) map (bridge.pipelines.bt2gh_for_pr_issues.map.MapBioTools2GitHub property) (bridge.pipelines.gh2bt_for_meta.map.MapGitHub2BioTools property) (bridge.pipelines.protocols.map.ModelsMap property) (bridge.pipelines.protocols.ModelsMap property) map_biotools_id() (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.biotools_id) map_citation() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs) (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.citation) map_description() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs) (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.description) (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.description) map_documentation() (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.documentation) map_functions() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs) (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.functions) (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.functions) map_functions_to_readme() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.functions) map_homepage() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs) (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.homepage) (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.homepage) map_language() (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.language) map_license() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs) (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.license) (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.license) map_maturity() (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.maturity) map_name() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs) (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.name) (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.name) map_publication() (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.publication) map_readme() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs) (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.readme) map_topics() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs) (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.topics) map_version() (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs) (in module bridge.pipelines.bt2gh_for_pr_issues.map_funcs.version) (in module bridge.pipelines.gh2bt_for_meta.map_funcs) (in module bridge.pipelines.gh2bt_for_meta.map_funcs.version) MapBioTools2GitHub (class in bridge.pipelines.bt2gh_for_pr_issues.map) MapDestination (class in bridge.pipelines.bt2gh_for_pr_issues.map) MapGitHub2BioTools (class in bridge.pipelines.gh2bt_for_meta.map) MapItem (class in bridge.pipelines.protocols) (class in bridge.pipelines.protocols.map) mark_initialized() (in module bridge.bootstrap.state) master_branch (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) match_ (bridge.core.license.SPDXCrossRef attribute) maturity (bridge.core.biotools.ToolModel attribute) Maturity (class in bridge.core.biotools) maybe_await() (in module bridge.utils) mentions_count (bridge.core.github_latest_release.Release attribute) merge_commit_message (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) merge_commit_title (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) MergeCommitMessage (class in bridge.core.github_repo) MergeCommitTitle (class in bridge.core.github_repo) merges_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) metadata_model (bridge.pipelines.BiotoolsToGitHubForPRPipelineArgs attribute) (bridge.pipelines.bt2gh_for_pr_issues.BiotoolsToGitHubForPRPipelineArgs attribute) (bridge.pipelines.bt2gh_for_pr_issues.main.BiotoolsToGitHubForPRPipelineArgs attribute) method (bridge.pipelines.protocols.map.MapItem attribute) (bridge.pipelines.protocols.MapItem attribute) Method (class in bridge.pipelines.protocols) (class in bridge.pipelines.protocols.map) milestones_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) mirror_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) ModelsMap (class in bridge.pipelines.protocols) (class in bridge.pipelines.protocols.map) module bridge bridge.adapters bridge.adapters.api bridge.adapters.api.main bridge.adapters.api.routers bridge.adapters.api.routers.biotools_to_github bridge.adapters.api.routers.github_to_biotools bridge.adapters.cli bridge.adapters.cli.commands bridge.adapters.cli.commands.biotools_to_github bridge.adapters.cli.commands.github_to_biotools bridge.adapters.cli.main bridge.bootstrap bridge.bootstrap.base bridge.bootstrap.register_handler bridge.bootstrap.state bridge.bootstrap.wiring bridge.builders bridge.builders.biotools bridge.builders.biotools.biotools_composer bridge.builders.biotools.biotools_transformer bridge.builders.europe_pmc bridge.builders.europe_pmc.europe_pmc_composer bridge.builders.europe_pmc.europe_pmc_transformer bridge.builders.github bridge.builders.github.github_composer bridge.builders.github.github_transformer bridge.builders.protocols bridge.builders.protocols.transformer bridge.builders.spdx bridge.builders.spdx.spdx_composer bridge.builders.spdx.spdx_transormer bridge.config bridge.core bridge.core.biotools bridge.core.github bridge.core.github_languages bridge.core.github_latest_release bridge.core.github_pages bridge.core.github_repo bridge.core.license bridge.core.publication bridge.handlers bridge.handlers.create_pr_issues_from_meta bridge.handlers.extract_meta_from_repo bridge.logging bridge.pipelines bridge.pipelines.bt2gh_for_pr_issues bridge.pipelines.bt2gh_for_pr_issues.main bridge.pipelines.bt2gh_for_pr_issues.map bridge.pipelines.bt2gh_for_pr_issues.map_funcs bridge.pipelines.bt2gh_for_pr_issues.map_funcs.citation bridge.pipelines.bt2gh_for_pr_issues.map_funcs.description bridge.pipelines.bt2gh_for_pr_issues.map_funcs.functions bridge.pipelines.bt2gh_for_pr_issues.map_funcs.homepage bridge.pipelines.bt2gh_for_pr_issues.map_funcs.license bridge.pipelines.bt2gh_for_pr_issues.map_funcs.name bridge.pipelines.bt2gh_for_pr_issues.map_funcs.readme bridge.pipelines.bt2gh_for_pr_issues.map_funcs.topics bridge.pipelines.bt2gh_for_pr_issues.map_funcs.version bridge.pipelines.gh2bt_for_meta bridge.pipelines.gh2bt_for_meta.main bridge.pipelines.gh2bt_for_meta.map bridge.pipelines.gh2bt_for_meta.map_funcs bridge.pipelines.gh2bt_for_meta.map_funcs.biotools_id bridge.pipelines.gh2bt_for_meta.map_funcs.description bridge.pipelines.gh2bt_for_meta.map_funcs.documentation bridge.pipelines.gh2bt_for_meta.map_funcs.functions bridge.pipelines.gh2bt_for_meta.map_funcs.homepage bridge.pipelines.gh2bt_for_meta.map_funcs.language bridge.pipelines.gh2bt_for_meta.map_funcs.license bridge.pipelines.gh2bt_for_meta.map_funcs.maturity bridge.pipelines.gh2bt_for_meta.map_funcs.name bridge.pipelines.gh2bt_for_meta.map_funcs.publication bridge.pipelines.gh2bt_for_meta.map_funcs.version bridge.pipelines.goals bridge.pipelines.policies bridge.pipelines.policies.bt2gh bridge.pipelines.policies.bt2gh.reconcile_bt_ontop_gh bridge.pipelines.policies.bt2gh.reconcile_bt_over_gh bridge.pipelines.policies.gh2bt bridge.pipelines.policies.gh2bt.reconcile_gh_ontop_bt bridge.pipelines.policies.gh2bt.reconcile_gh_over_bt bridge.pipelines.protocols bridge.pipelines.protocols.map bridge.pipelines.protocols.none_propagation bridge.pipelines.protocols.pipeline_args bridge.pipelines.shared bridge.pipelines.shared.functions bridge.pipelines.shared.publications bridge.pipelines.shared.version bridge.pipelines.utils bridge.pipelines.utils.badges bridge.pipelines.utils.cleaning bridge.pipelines.utils.comparisons bridge.pipelines.utils.conversions bridge.pipelines.utils.files bridge.pipelines.utils.templating bridge.services bridge.services.biotools bridge.services.biotools.biotools_ingestor bridge.services.europe_pmc bridge.services.europe_pmc.europe_pmc_auth bridge.services.europe_pmc.europe_pmc_ingestor bridge.services.github bridge.services.github.github_auth bridge.services.github.github_ingestor bridge.services.github.github_repo_provider bridge.services.huggingface bridge.services.huggingface.huggingface_provider bridge.services.protocols bridge.services.protocols.ingestor bridge.services.protocols.llm_provider bridge.services.protocols.repo_provider bridge.services.spdx bridge.services.spdx.spdx_ingestor bridge.utils

N

name (bridge.core.biotools.CreditItem attribute) (bridge.core.biotools.ToolModel attribute) (bridge.core.github_latest_release.Asset attribute) (bridge.core.github_latest_release.Author attribute) (bridge.core.github_latest_release.Release attribute) (bridge.core.github_repo.CodeOfConduct attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.License attribute) (bridge.core.github_repo.Owner attribute) (bridge.core.github_repo.TemplateRepository attribute) (bridge.core.license.SPDXLicense attribute) (bridge.core.publication.Author attribute) (bridge.core.SPDXLicense attribute) network_count (bridge.core.github_repo.FullRepository attribute) node_id (bridge.core.github_latest_release.Asset attribute) (bridge.core.github_latest_release.Author attribute) (bridge.core.github_latest_release.Release attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.License attribute) (bridge.core.github_repo.Owner attribute) (bridge.core.github_repo.TemplateRepository attribute)

normalize_color() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.cleaning) normalize_dict_strings() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.cleaning) normalize_pydantic_model_strings() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.cleaning) normalize_text() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.cleaning) note (bridge.core.biotools.CreditItem attribute) (bridge.core.biotools.DocumentationItem attribute) (bridge.core.biotools.DownloadItem attribute) (bridge.core.biotools.FunctionItem attribute) (bridge.core.biotools.LinkItem attribute) (bridge.core.biotools.PublicationItem attribute) note() (bridge.logging.BridgeLogger method) notifications_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

O

object_to_primitive() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.conversions) OntologyConcept (class in bridge.core.biotools) open_issues (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) open_issues_count (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) operatingSystem (bridge.core.biotools.ToolModel attribute) OperatingSystemEnum (class in bridge.core.biotools) operation (bridge.core.biotools.FunctionItem attribute) OperationItem (class in bridge.core.biotools) orcidid (bridge.core.biotools.CreditItem attribute) order (bridge.core.license.SPDXCrossRef attribute) organization (bridge.core.github_repo.FullRepository attribute)

Organization (in module bridge.core.github_repo) organizations_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) otherID (bridge.core.biotools.ToolModel attribute) OtherIDItem (class in bridge.core.biotools) output (bridge.core.biotools.FunctionItem attribute) OutputItem (class in bridge.core.biotools) owner (bridge.adapters.api.routers.biotools_to_github.BioToolsToGitHubPayload attribute) (bridge.adapters.api.routers.github_to_biotools.GitHubToBioToolsPayload attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) (bridge.services.protocols.ForkInfo attribute) (bridge.services.protocols.repo_provider.ForkInfo attribute) Owner (class in bridge.core.github_repo)

P

page_end (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute) page_start (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute) parent (bridge.core.github_repo.FullRepository attribute) Parent (in module bridge.core.github_repo) ParsedVersion (class in bridge.pipelines.shared.version) path (bridge.core.github_pages.Source attribute) pending_domain_unverified_at (bridge.core.github_pages.GitHubPages attribute) permissions (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) Permissions (class in bridge.core.github_repo) Permissions1 (class in bridge.core.github_repo) PipelineArgs (class in bridge.pipelines.protocols) (class in bridge.pipelines.protocols.pipeline_args) PipelineGoal (class in bridge.pipelines) (class in bridge.pipelines.goals) pmcid (bridge.core.biotools.PublicationItem attribute) pmid (bridge.core.biotools.PublicationItem attribute) pr (bridge.pipelines.bt2gh_for_pr_issues.map.MapDestination attribute)

prerelease (bridge.core.github_latest_release.Release attribute) private (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) protected_domain_state (bridge.core.github_pages.GitHubPages attribute) ProtectedDomainState (class in bridge.core.github_pages) pub_type (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute) public (bridge.core.github_pages.GitHubPages attribute) publication (bridge.core.biotools.ToolModel attribute) Publication (class in bridge.core) (class in bridge.core.publication) PublicationItem (class in bridge.core.biotools) published_at (bridge.core.github_latest_release.Release attribute) pull (bridge.core.github_repo.Permissions attribute) (bridge.core.github_repo.Permissions1 attribute) pulls_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) push (bridge.core.github_repo.Permissions attribute) (bridge.core.github_repo.Permissions1 attribute) pushed_at (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

R

raw (bridge.pipelines.shared.version.ParsedVersion attribute) reactions (bridge.core.github_latest_release.Release attribute) Reactions (class in bridge.core.github_latest_release) readme (bridge.core.github.GitHubRepoModel attribute) (bridge.core.GitHubRepoModel attribute) received_events_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) reconcile_bt_ontop_gh() (in module bridge.pipelines.policies.bt2gh) (in module bridge.pipelines.policies.bt2gh.reconcile_bt_ontop_gh) reconcile_bt_over_gh() (in module bridge.pipelines.policies.bt2gh) (in module bridge.pipelines.policies.bt2gh.reconcile_bt_over_gh) reconcile_gh_ontop_bt() (in module bridge.pipelines.policies.gh2bt) (in module bridge.pipelines.policies.gh2bt.reconcile_gh_ontop_bt) reconcile_gh_over_bt() (in module bridge.pipelines.policies.gh2bt) (in module bridge.pipelines.policies.gh2bt.reconcile_gh_over_bt) ref_ids() (in module bridge.pipelines.shared.publications) register_bridge() (in module bridge.bootstrap.base) register_handler() (in module bridge.bootstrap) (in module bridge.bootstrap.register_handler) register_repo() (in module bridge.bootstrap.base) register_schema() (in module bridge.bootstrap.base) relation (bridge.core.biotools.ToolModel attribute) RelationItem (class in bridge.core.biotools) Release (class in bridge.core.github_latest_release) releases_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) remove_first_snippet_from_text() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.templating) repo (bridge.adapters.api.routers.biotools_to_github.BioToolsToGitHubPayload attribute) (bridge.adapters.api.routers.github_to_biotools.GitHubToBioToolsPayload attribute) (bridge.core.github.GitHubRepoModel attribute) (bridge.core.GitHubRepoModel attribute) (bridge.services.protocols.ForkInfo attribute) (bridge.services.protocols.repo_provider.ForkInfo attribute) repo_entry (bridge.pipelines.protocols.map.MapItem attribute) (bridge.pipelines.protocols.MapItem attribute)

repo_model (bridge.pipelines.gh2bt_for_meta.GitHubToBiotoolsForMetaPipelineArgs attribute) (bridge.pipelines.gh2bt_for_meta.main.GitHubToBiotoolsForMetaPipelineArgs attribute) (bridge.pipelines.GitHubToBiotoolsForMetaPipelineArgs attribute) repo_path (bridge.pipelines.BiotoolsToGitHubForPRPipelineArgs attribute) (bridge.pipelines.bt2gh_for_pr_issues.BiotoolsToGitHubForPRPipelineArgs attribute) (bridge.pipelines.bt2gh_for_pr_issues.main.BiotoolsToGitHubForPRPipelineArgs attribute) (bridge.pipelines.gh2bt_for_meta.GitHubToBiotoolsForMetaPipelineArgs attribute) (bridge.pipelines.gh2bt_for_meta.main.GitHubToBiotoolsForMetaPipelineArgs attribute) (bridge.pipelines.GitHubToBiotoolsForMetaPipelineArgs attribute) RepoProvider (class in bridge.services.protocols) (class in bridge.services.protocols.repo_provider) RepoRegistration (class in bridge.bootstrap.base) repos_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) require_args() (in module bridge.utils) require_github_token() (bridge.config.Settings method) require_huggingface_token() (bridge.config.Settings method) rocket (bridge.core.github_latest_release.Reactions attribute) role (bridge.services.ChatMessage attribute), [1] (bridge.services.protocols.ChatMessage attribute), [1] (bridge.services.protocols.llm_provider.ChatMessage attribute), [1] root (bridge.core.biotools.BiotoolsIdType attribute) (bridge.core.biotools.TextType attribute) (bridge.core.biotools.UrlftpType attribute) (bridge.core.biotools.VersionType attribute) (bridge.core.github_languages.Language attribute) rorid (bridge.core.biotools.CreditItem attribute) run() (bridge.pipelines.protocols.map.MapItem method) (bridge.pipelines.protocols.MapItem method) (in module bridge.pipelines.bt2gh_for_pr_issues) (in module bridge.pipelines.bt2gh_for_pr_issues.main) (in module bridge.pipelines.gh2bt_for_meta) (in module bridge.pipelines.gh2bt_for_meta.main) run_bt2gh_pipeline_for_pr_issues() (in module bridge.pipelines) run_gh2bt_pipeline_for_meta() (in module bridge.pipelines)

S

SafeAttr (class in bridge.pipelines.protocols.none_propagation) schema_entry (bridge.pipelines.protocols.map.MapItem attribute) (bridge.pipelines.protocols.MapItem attribute) SchemaRegistration (class in bridge.bootstrap.base) secret_scanning (bridge.core.github_repo.SecurityAndAnalysis attribute) secret_scanning_ai_detection (bridge.core.github_repo.SecurityAndAnalysis attribute) secret_scanning_non_provider_patterns (bridge.core.github_repo.SecurityAndAnalysis attribute) secret_scanning_push_protection (bridge.core.github_repo.SecurityAndAnalysis attribute) SecretScanning (in module bridge.core.github_repo) SecretScanningAiDetection (in module bridge.core.github_repo) SecretScanningNonProviderPatterns (in module bridge.core.github_repo) SecretScanningPushProtection (in module bridge.core.github_repo) security_and_analysis (bridge.core.github_repo.FullRepository attribute) SecurityAndAnalysis (class in bridge.core.github_repo) seeAlso (bridge.core.license.SPDXLicense attribute) (bridge.core.SPDXLicense attribute) separate_snippet_from_text() (in module bridge.pipelines.utils.templating) separate_snippets_from_text() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.templating) serialize_fn() (bridge.pipelines.protocols.map.MapItem method) (bridge.pipelines.protocols.MapItem method) Settings (class in bridge.config) setup_logging() (in module bridge.logging) site_admin (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) size (bridge.core.github_latest_release.Asset attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) source (bridge.core.github_pages.GitHubPages attribute) (bridge.core.github_repo.FullRepository attribute) Source (class in bridge.core.github_pages) (in module bridge.core.github_repo) spdx_id (bridge.core.github_repo.License attribute) spdx_license_base (bridge.config.Settings property) spdx_license_base_url (bridge.config.Settings attribute) SPDXCrossRef (class in bridge.core.license) SPDXLicense (class in bridge.core) (class in bridge.core.license) SPDXLicenseIngestor (class in bridge.services) (class in bridge.services.spdx) (class in bridge.services.spdx.spdx_ingestor) SPDXLicenseNotFoundError SPDXLicenseTransformer (class in bridge.builders.spdx.spdx_transormer)

squash_merge_commit_message (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) squash_merge_commit_title (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) SquashMergeCommitMessage (class in bridge.core.github_repo) SquashMergeCommitTitle (class in bridge.core.github_repo) ssh_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) standardLicenseTemplate (bridge.core.license.SPDXLicense attribute) (bridge.core.SPDXLicense attribute) stargazers_count (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) stargazers_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) starred_at (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) (bridge.core.github_repo.TemplateRepository attribute) starred_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) state (bridge.core.github_latest_release.Asset attribute) (bridge.core.github_pages.HttpsCertificate attribute) State (class in bridge.core.github_latest_release) (class in bridge.core.github_pages) status (bridge.core.github_pages.GitHubPages attribute) (bridge.core.github_repo.AdvancedSecurity attribute) (bridge.core.github_repo.DependabotSecurityUpdates attribute) Status (class in bridge.core.github_pages) (class in bridge.core.github_repo) statuses_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) str_contain_each_other() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.comparisons) subscribers_count (bridge.core.github_repo.FullRepository attribute) subscribers_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) subscription_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) subscriptions_url (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) svg_to_base64() (in module bridge.pipelines.utils) (in module bridge.pipelines.utils.conversions) svn_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

T

tag_name (bridge.core.github_latest_release.Release attribute) tags_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) tarball_url (bridge.core.github_latest_release.Release attribute) target_commitish (bridge.core.github_latest_release.Release attribute) teams_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) temp_clone_token (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) template_repository (bridge.core.github_repo.FullRepository attribute) TemplateRepository (class in bridge.core.github_repo) term (bridge.core.biotools.EDAMdata attribute) (bridge.core.biotools.EDAMformat attribute) (bridge.core.biotools.OntologyConcept attribute) (bridge.core.biotools.OperationItem attribute) (bridge.core.biotools.TopicItem attribute) TextType (class in bridge.core.biotools) timestamp (bridge.core.license.SPDXCrossRef attribute) title (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute) Tool (class in bridge.core.biotools) ToolModel (class in bridge.core.biotools) toolType (bridge.core.biotools.ToolModel attribute) ToolTypeEnum (class in bridge.core.biotools) topic (bridge.core.biotools.ToolModel attribute) TopicItem (class in bridge.core.biotools) topics (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) total_count (bridge.core.github_latest_release.Reactions attribute)

transform() (bridge.builders.biotools.biotools_transformer.BiotoolsToolTransformer method) (bridge.builders.europe_pmc.europe_pmc_transformer.EuropePMCTransformer method) (bridge.builders.github.github_transformer.GitHubRepoTransformer method) (bridge.builders.protocols.Transformer method) (bridge.builders.protocols.transformer.Transformer method) (bridge.builders.spdx.spdx_transormer.SPDXLicenseTransformer method) Transformer (class in bridge.builders.protocols) (class in bridge.builders.protocols.transformer) trees_url (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) triage (bridge.core.github_repo.Permissions attribute) (bridge.core.github_repo.Permissions1 attribute) type (bridge.core.biotools.DocumentationItem attribute) (bridge.core.biotools.DownloadItem attribute) (bridge.core.biotools.LinkItem attribute) (bridge.core.biotools.OtherIDItem attribute) (bridge.core.biotools.PublicationItem attribute) (bridge.core.biotools.RelationItem attribute) (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute) Type (class in bridge.core.biotools) Type1 (class in bridge.core.biotools) Type2 (class in bridge.core.biotools) typeEntity (bridge.core.biotools.CreditItem attribute) TypeEntity (class in bridge.core.biotools) TypeEnum (class in bridge.core.biotools) TypeEnum1 (class in bridge.core.biotools) TypeEnum2 (class in bridge.core.biotools) typeRole (bridge.core.biotools.CreditItem attribute) TypeRoleEnum (class in bridge.core.biotools)

U

unchanged() (bridge.logging.BridgeLogger method) unwrap() (bridge.pipelines.protocols.none_propagation.SafeAttr method) update() (in module bridge.adapters.cli.commands.biotools_to_github) updated_at (bridge.core.github_latest_release.Asset attribute) (bridge.core.github_latest_release.Release attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) upload_url (bridge.core.github_latest_release.Release attribute) uploader (bridge.core.github_latest_release.Asset attribute) Uploader (in module bridge.core.github_latest_release) uri (bridge.core.biotools.EDAMdata attribute) (bridge.core.biotools.EDAMformat attribute) (bridge.core.biotools.OntologyConcept attribute) (bridge.core.biotools.OperationItem attribute) (bridge.core.biotools.TopicItem attribute) url (bridge.core.biotools.CreditItem attribute) (bridge.core.biotools.DocumentationItem attribute) (bridge.core.biotools.DownloadItem attribute) (bridge.core.biotools.LinkItem attribute) (bridge.core.github_latest_release.Asset attribute) (bridge.core.github_latest_release.Author attribute) (bridge.core.github_latest_release.Reactions attribute) (bridge.core.github_latest_release.Release attribute) (bridge.core.github_pages.GitHubPages attribute) (bridge.core.github_repo.CodeOfConduct attribute) (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.License attribute) (bridge.core.github_repo.Owner attribute) (bridge.core.github_repo.TemplateRepository attribute) (bridge.core.license.SPDXCrossRef attribute)

UrlftpType (class in bridge.core.biotools) use_squash_pr_title_as_default (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) user_view_type (bridge.core.github_latest_release.Author attribute) (bridge.core.github_repo.Owner attribute)

V

value (bridge.core.biotools.OtherIDItem attribute) (bridge.pipelines.shared.version.ParsedVersion attribute) version (bridge.core.biotools.DownloadItem attribute) (bridge.core.biotools.OtherIDItem attribute) (bridge.core.biotools.PublicationItem attribute) (bridge.core.biotools.ToolModel attribute)

VersionKind (class in bridge.pipelines.shared.version) VersionType (class in bridge.core.biotools) visibility (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) volume (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute)

W

watchers (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) watchers_count (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute)

web_commit_signoff_required (bridge.core.github_repo.FullRepository attribute) (bridge.core.github_repo.TemplateRepository attribute) wiring() (in module bridge.bootstrap.wiring)

Y

year (bridge.core.Publication attribute) (bridge.core.publication.Publication attribute)

Z

zipball_url (bridge.core.github_latest_release.Release attribute)