Package index • codecheck

All functions

add_abstract(): Inserts the abstract text and source link into the Markdown content if an abstract is found for the given repository. If no abstract is found, an empty string is inserted in place of the abstract content.
add_all_codecheckers_hyperlink(): Add Hyperlinks to Codecheckers Table
add_all_venues_hyperlinks_non_reg(): Add Hyperlinks to All Venues Table
add_cert_links(): Function for adding certificate identifier and link as extra columns
add_cert_pdf_links(): Add certificate PDF download URLs to the register table
add_check_time(): Function for adding check time to each report in the register table.
add_codecheck_details_md(): Populates an existing markdown content template with details about the CODECHECK details.
add_codechecker(): Function for adding codechecker to each report in the register table.
add_column_priority_classes(): Marks the lower-priority columns of the register tables so the stylesheet can hide them on a phone (see codecheck-register.css).
add_issue_number_links(): Function for adding clickable links to the issue number of each report in the register table.
add_markdown_title(): Function to add the markdown title based on the specific register table name.
add_openalex_ids(): Add OpenAlex work IDs to the register table (addresses register#185)
add_openalex_work_fields(): Add the publication facts behind each OpenAlex ID (register#50)
add_paper_details_md(): Populates an existing markdown content template with details about the codechecked paper.
add_paper_links(): Function for adding clickable links to the paper for each entry in the register table.
add_report_hyperlinks_reg(): Format Report column for display by creating markdown links with shortened text
add_report_links(): Function for adding report URLs for each entry in the register table.
add_repository_hyperlink(): Replaces a placeholder in Markdown content with a hyperlink to the repository, based on the repository type (e.g., GitHub, OSF, GitLab).
add_repository_links_csv(): Function for adding repository links in the register table for CSV files.
add_repository_links_json(): Function for adding repository links in the register table for the creation of the json file.
add_sortable_th_attributes(): Adds data-sort hints to <th> cells so stupidtable.js (see table-sort-init.js) knows which columns are sortable and how to compare their values.
add_venue_hyperlinks_reg(): Function for adding clickable links to the codecheck venue pages for each entry in the register table. Uses relative paths for HTML display (absolute URLs used in JSON/CSV).
add_venue_type_hyperlinks_non_reg(): Add Hyperlinks to Venue Type-Specific Table
add_venue_type_hyperlinks_reg(): Function for adding clickable links to the codecheck venue type pages for each entry in the register table. Uses relative paths for HTML display (absolute URLs used in JSON/CSV).
add_venues_hyperlinks_non_reg(): Add Hyperlinks to Venues Table
adjust_cert_links_relative(): Turn the plain Certificate column into a relative markdown link
as_latex_url(): Wrap URL for LaTeX
bootstrap_wikibase(): Build the CODECHECK Wikibase from the model
cached_lookup(): Cache the result of a metadata lookup on disk, but only when conclusive
cached_lookup_result(): Same as cached_lookup, but returns the full result
calculate_breadcrumb_base_path(): Calculate base path for breadcrumb links
cert_link_cache: In-session cache of resolved certificate download links, see get_cert_link()
check_certificate_id(): Function for checking ceritificate id if there is a codecheck_yaml. If there is a mismatch a stop is sent. Else a warning is thrown.
check_issue_status(): Function issue status. If the issue is not closed a warning is thrown stating that the issue is still open.
check_register_researchequals_policy(): Check a register's ResearchEquals certificates against the CODECHECK curation policy
check_register_zenodo_policy(): Check a register's Zenodo records against the CODECHECK curation policy
check_repository_archived(): Check that a repository is archived
check_repository_badge(): Check that a repository advertises the CODECHECK badge
check_repository_license(): Check that a repository has a license
check_repository_org(): Check that a repository is in an allowed organisation/group
check_repository_topic(): Check that a repository advertises the "codecheck" topic tag
check_researchequals_record(): Audit a ResearchEquals certificate against the CODECHECK curation policy
check_zenodo_record(): Audit a Zenodo record against the CODECHECK curation policy
cite_certificate(): Print a citation for the codecheck certificate.
classify_poppler_log(): Poppler (via pdftools) reports PDF parsing problems by printing "PDF error: ..." lines directly to R's message connection rather than raising a condition on them, so they bypass ordinary error handling and, uncaptured, flood the console - one line per malformed glyph or object, sometimes hundreds per certificate. This splits captured poppler output into messages that mean the PDF is genuinely broken (unparsable, not really a PDF) versus cosmetic rendering quirks that poppler recovers from on its own (e.g. malformed embedded fonts) and that don't affect the resulting page images.
clear_cert_link_cache(): Clear the in-session cache of resolved certificate download links
clear_researchequals_policy_cache(): Drop the cached policy metadata of one ResearchEquals module
clear_zenodo_policy_cache(): Drop the cached policy metadata of one Zenodo record
codecheck_GET(): Custom HTTP GET with proper User-Agent header and a bounded timeout
codecheck_GET_openalex(): GET an OpenAlex API URL with the configured API key and retries
codecheck_GET_retry(): Custom HTTP GET that retries transient failures
codecheck_metadata(): Return the metadata for the codecheck project in root folder of project
complete_codecheck_yml(): Analyze and complete codecheck.yml with missing fields
compute_annual_stats(): Compute annual statistics from the register table
convert_cert_pdf_to_png(): Converts each page of a certificate PDF to PNG images, saving them in the specified certificate directory.
copy_manifest_files(): Copy files from manifest into the codecheck folder and summarise.
copy_package_javascript(): Copy Package JavaScript Files to Output Directory
create_all_codecheckers_table(): Create Codecheckers Table
create_all_venues_table(): Create All Venues Table
create_cert_md(): Generates a Markdown file for a certificate based on a specified template, filling in details about the paper, authors, codecheck information, and the certificate images if available. The resulting Markdown file is later rendered to HTML.
create_cert_page_section_files(): Generates section files for a certificate HTML page, including prefix, postfix, and header HTML components.
create_codecheck_files(): Create template files for the codecheck process.
create_filtered_reg_csvs(): Creates filtered CSV files from a register based on specified filters.
create_index_header_html(): Dynamically generates the index_header.html from a template file
create_index_postfix_html(): Dynamically generates the index_postfix.html from a template file
create_index_prefix_html(): Dynamically generates the index_prefix.html with navigation header and breadcrumbs
create_index_section_files(): Creates index postfix, prefix and the header
create_md_table(): Creates a markdown table from a register template Adds title to the markdown and adjusts the column widths of the table before returning it.
create_non_register_files(): Create Non-Register Files
create_original_register_files(): Generates original register files in various output formats.
create_register_files(): Create Register Files
create_tables_non_register(): Create Non-Register Tables
create_temp_register_with_codechecker(): Creates a temporary CSV register with a "Codechecker" column.
create_venue_type_tables(): Create Venue Type-Specific Tables
create_venues_tables(): Create Venues Tables
curate_register_zenodo_records(): Curate all Zenodo records of a register
curate_zenodo_record(): Curate a published Zenodo record per the CODECHECK curation policy
detect_report_platform(): Detect the publication platform from a report URL
download_cert_pdf(): Downloads a certificate PDF from a report link and saves it locally. If the download link is a ZIP file, it extracts the PDF from the archive. Returns status based on success.
edit_html_lib_paths(): Loads a html file and replaces the libs path in the html file to the libs folder in "docs/libs" This is done so all html files can share one libs folder.
extract_cert_pdf_from_zip(): Downloads a ZIP file from the given URL, searches for "codecheck.pdf" within its contents, renames it to "cert.pdf," and saves it in the specified directory.
filter_and_drop_register_columns(): Filter and Drop Columns from Register Table
generate_404_page(): Generate the register's 404 page
generate_breadcrumb(): Generate breadcrumb navigation HTML
generate_cert_citation_meta(): Generate Highwire citation meta tags for a certificate page
generate_cert_json(): Generates a JSON file with all certificate metadata
generate_cert_schema_org(): Generate Schema.org JSON-LD for Certificate Page
generate_cert_signposting(): Signposting links for a certificate page
generate_certs_redirect(): Generate redirect page for /certs/ directory
generate_codechecker_metadata_html(): Generate the codechecker metadata HTML panel (avatar + ORCID + GitHub + venues)
generate_codechecker_metadata_yaml(): Generate the codechecker metadata YAML frontmatter block for register.md
generate_codechecker_redirect(): Generate HTML redirect page for codechecker
generate_codechecker_redirects(): Generate redirect pages for all codecheckers with ORCID
generate_codechecker_schema_org(): Generate Schema.org JSON-LD for codechecker pages
generate_footer_build_info(): Generate Footer Build Information HTML
generate_href(): Generate full href for for different href types.
generate_html_document_yml(): Dynamically generates a html_document.yml with the full paths to the index header, prefix and postfix.html files.
generate_html_extra_text_non_register(): Generates the extra text of the HTML pages for non registers. This extra text is to be placed under the table. There is only extra text for the codecheckers HTML page to explain the reason for discrepancy between total_codechecks != SUM(no.of codechecks)
generate_html_postfix_hrefs_non_reg(): Generates postfix hrefs for the venues/ codecheckers list pages
generate_html_postfix_hrefs_reg(): Generates the hrefs to set in the postfix.html file for the rendering of register tables.
generate_html_subtext_non_register(): Generates the subtext of the HTML pages for non registers with a summary of the number of codechecks and number of codechecks/ venues etc.
generate_html_title_non_registers(): Generate HTML Title for Non-Register Pages
generate_list_signposting(): Signposting links for a listing or overview page
generate_meta_generator_content(): Generate Meta Generator Content
generate_navigation_header(): Generate navigation header with logo and menu
generate_output_dir(): Generate Output Directory Path
generate_page_signposting(): Signposting links for any non-certificate register page
generate_person_schema_org(): Generate Schema.org JSON-LD for a person page (codecheckers/register#123)
generate_person_signposting(): Signposting links for a person page
generate_robots_txt(): Generate robots.txt for the register
generate_sitemap(): Generate sitemap.xml for the register
generate_table_details(): Generate Table Details
generate_table_details_non_reg(): Generate Table Details for Non-Register Files
generate_venue_schema_org(): Generate Schema.org JSON-LD for venue pages
generate_venue_signposting(): Signposting links for a venue page
generate_work_schema_org(): Generate Schema.org JSON-LD for a work page (codecheckers/register#150)
generate_work_signposting(): Signposting links for a work page
get_abstract(): Retrieves the abstract of a research paper from CrossRef or OpenAlex.
get_abstract_result(): Retrieves the abstract and reports whether the answer is conclusive
get_abstract_text_crossref(): Extracts the paper DOI from the config_yml of the paper, constructs a CrossRef API request, and returns the abstract text if available.
get_abstract_text_crossref_result(): Retrieves the abstract from CrossRef and reports whether the API answered
get_abstract_text_openalex(): Retrieves the abstract of a research paper using the OpenAlex API.
get_abstract_text_openalex_result(): Retrieves the abstract from OpenAlex and reports whether the API answered
get_agile_codecheckers_data(): Fetch and cache agile-codecheckers.csv data from GitHub
get_build_metadata(): Get Build Metadata
get_cert_link(): Retrieves the download link for a certificate file from Zenodo, OSF, or ResearchEquals.
get_cert_link_uncached(): Resolves the download link for a certificate file without caching, see get_cert_link().
get_certificate_from_github_issue(): Get certificate identifier from GitHub issues by matching author names
get_codecheck_yml(): Get the CODECHECK configuration file from a repository
get_codecheck_yml_github(): Retrieve a codecheck.yml file from a GitHub repository
get_codecheck_yml_gitlab(): Retrieve a codecheck.yml file from an GitLab.com project
get_codecheck_yml_or_null(): Fetch a `codecheck.yml` without aborting the whole render
get_codecheck_yml_osf(): Retrieve a codecheck.yml file from an OSF project
get_codecheck_yml_uncached(): Retrieve a codecheck.yml file from a remote repository
get_codecheck_yml_zenodo(): Retrieve a codecheck.yml file from a Zenodo record
get_codechecker_profile(): Get codechecker profile information by ORCID
get_codechecker_profile_by_handle(): Get codechecker profile information by GitHub handle
get_codechecker_venues(): Compute a codechecker's contributed venues, with per-venue check counts
get_codecheckers_data(): Fetch and cache codecheckers.csv data from GitHub
get_git_info(): Get git repository information
get_github_handle_by_name(): Get GitHub handle for a codechecker by name
get_github_readme_raw(): Retrieve the rendered README of a GitHub repository, as raw text
get_github_repo_metadata(): Retrieve repository metadata from the GitHub API
get_gitlab_project_metadata(): Retrieve repository metadata from the GitLab.com API
get_gitlab_readme_raw(): Retrieve the README of a GitLab.com project, as raw text
get_institutional_codecheckers_data(): Fetch and cache institutional-codecheckers.csv data from GitHub
get_lifecycle_metadata(): Retrieve metadata from Lifecycle Journal
get_openalex_id(): Look up the OpenAlex work ID for a paper reference URL
get_openalex_id_result(): Look up the OpenAlex work ID and report whether the answer is conclusive
get_or_create_zenodo_record(): Create or retrieve Zenodo record, submit to CODECHECK community, and update codecheck.yml
get_osf_cert_link(): Retrieves the link to a certificate PDF file from an OSF project node. It retrieves its files, and searches for a single PDF certificate file within the node. If multiple or no PDF files are found, it returns NULL with a warning.
get_researchequals_cert_link(): Accesses a codecheck's ResearchEquals record via its report link and download the main file of the module
get_researchequals_collection(): Retrieve a collection on ResearchEquals
get_researchequals_collections(): Retrieve the collections a certificate must be part of
get_researchequals_version_metadata(): Retrieve a ResearchEquals version's metadata
get_zenodo_cert_link(): Accesses a codecheck's Zenodo record via its report link, retrieves the record ID, and searches for a certificate PDF or ZIP file within the record's files using the Zenodo API.
get_zenodo_id(): Extract the Zenodo record number from the report URL
get_zenodo_record(): Get the full zenodo record using the record number stored in the metadata.
get_zenodo_record_metadata(): Fetch metadata of a published Zenodo record
is_placeholder_certificate(): Check if certificate identifier or DOI is a placeholder
is_zenodo_concept_doi(): Check whether a report DOI is a Zenodo concept DOI
is_zenodo_latest_version(): Check whether a report DOI is the latest version of its Zenodo record
latex_codecheck_logo(): Print the latex code to include the CODECHECK logo
latex_summary_of_manifest(): Print a latex table to summarise CODECHECK metadata
latex_summary_of_metadata(): Print a latex table to summarise CODECHECK metadata
list_manifest_files(): Summarise manifest files.
load_venues_config(): Load venues configuration from CSV file
load_wikibase_register(): Load the register into the CODECHECK Wikibase
normalize_person_lists(): Normalize person fields of a codecheck.yml to lists of persons
openalex_api_key(): The configured OpenAlex API key
openalex_url_with_key(): Add the OpenAlex API key to a request URL
orcid_rors(): The RORs a person's ORCID profile asserts
parse_repository_spec(): Parse the repository specification in the column "Repo" in the register CSV file
prefetch_cert_links(): Resolves every certificate's PDF link up front, in parallel
preprocess_register(): Function for preprocessing the register to create and return the preprocessed register table.
preview_wikidata_export(): Preview the export to Wikidata
prune_libs(): Prune Unreferenced Library Directories
quickstatements_submitted(): Record that a QuickStatements batch was actually submitted
quickstatements_write(): Write a QuickStatements batch out for somebody to paste
register_check(): Function for checking all entries in the register
register_clear_cache(): Function for clearing the register cache
register_render(): Function for rendering the register into different view
register_render_cert(): Render a single certificate page by its ID
register_ror_coverage(): How many register persons have a ROR in their ORCID profile
register_update_stats(): Regenerate all statistics files from existing register.json files
render_cert_html(): Renders an HTML certificate file from a Markdown template for a specific certificate.
render_cert_htmls(): Generates HTML files for each certificate listed in the given register table. It checks for the existence of the certificate PDF, downloads it if necessary, and converts it to JPEG format for embedding.
render_html(): Renders html for a single table
render_manifest_files(): Render manifest files for certificate output
render_non_register_md(): Render Non-Register Markdown Table
render_register(): Render Register in Specified Output Format
render_register_full(): Build a full metadata register from the preprocessed register table
render_register_json(): Renders register json for a single register_table
render_register_md(): Renders register md for a single register_table
render_statistics_page(): Render the register-wide statistics dashboard page
report_researchequals_policy_findings(): Report ResearchEquals curation policy findings
report_zenodo_policy_findings(): Report curation policy findings
researchequals_policy_check(): Check a ResearchEquals module against the CODECHECK curation policy
resolve_researchequals_version_id(): Resolve a certificate ID or ResearchEquals reference to a version ID
resolve_zenodo_record_id(): Resolve a certificate ID or Zenodo reference to a Zenodo record ID
ror_coverage_summary(): Summarise ROR coverage over the register
set_paper_title_references(): Set "Title" and "Paper reference" columns and values to the register_table
set_paper_title_references_csv(): Set "Title" and "Paper reference" columns for CSV files
setup_external_libraries(): Download and Setup External Libraries Locally
split_github_repo_spec(): Split a GitHub repo spec into org, repo and an optional sub-path
split_person_name(): Split a person name into given and family name
update_certificate_from_github(): Update certificate ID from GitHub issue
update_codecheck_yml_from_lifecycle(): Update codecheck.yml with Lifecycle Journal metadata
upload_zenodo_certificate() set_zenodo_certificate(): Upload the CODECHECK certificate and additional files to Zenodo.
upload_zenodo_metadata(): Upload metadata to Zenodo
validate_certificate_for_rendering(): Validate certificate for rendering with visual warning
validate_certificate_github_issue(): Validate certificate identifier exists in GitHub register issues
validate_codecheck_yml(): Validate a CODECHECK configuration
validate_codecheck_yml_crossref(): Validate codecheck.yml metadata against CrossRef
validate_codecheck_yml_orcid(): Validate codecheck.yml metadata against ORCID
validate_contents_references(): Validate codecheck.yml metadata against external references
validate_wikidata_model(): Check the model's invariants
validate_yaml_syntax(): Validate YAML syntax of a codecheck.yml file
verify_wikidata_export(): Check what actually arrived on Wikidata
wikidata_creates(): Whether the export may create this kind of entity on a target
wikidata_endpoint(): The SPARQL endpoint serving a kind of entity
wikidata_entity_kinds(): The entity kinds of the model
wikidata_model(): The CODECHECK Wikidata model
wikidata_pending(): The statements waiting on an item that does not exist yet
wikidata_properties(): Every property the model uses, as a flat table
wikidata_statements(): The statement definitions of one entity kind
with_elapsed_log(): Prefix every log line with the time elapsed since the render started
write_meta_json(): Write Build Metadata to JSON File
zenodo_policy_check(): Check Zenodo record metadata against the CODECHECK curation policy