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validate-references Check BibTeX entries for completeness, DOI resolution, and broken links. Verify required fields per entry type (article, book, inproceedings), resolve and validate DOIs via the CrossRef API, check URL accessibility, and flag duplicate entries, missing abstracts, and inconsistent formatting. Use when preparing a manuscript bibliography for journal submission, auditing a shared .bib file before a project milestone, after merging bibliographies from multiple sources, when citations render incorrectly, or as a CI check on version-controlled .bib files.
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عرض تفاصيل Prompt يتجاوز الأمر المباشر Prompt المخصّص للمراجعة. افحص المصدر قبل تشغيله.
npx skills add https://github.com/pjt222/agent-almanac --skill validate-referencesيبقى الأمر في سطر واحد. مرّر أفقيًا لمراجعته كاملًا قبل النسخ.
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تحميل Zip جاري التحميل... المزيد من هذا المستودع Create production-ready Helm charts for Kubernetes application deployment with templating, values management, chart dependencies, hooks, and testing. Covers chart structure, Go template syntax, values.yaml design, chart repositories, versioning, and best practices for maintainable and reusable charts. Use when packaging a Kubernetes application for repeatable deployments, parameterizing manifests for multiple environments, managing complex multi-component applications with dependencies, or standardizing deployment practices with versioned rollback capability across teams.
Create production-ready Helm charts for Kubernetes application deployment with templating, values management, chart dependencies, hooks, and testing. Covers chart structure, Go template syntax, values.yaml design, chart repositories, versioning, and best practices for maintainable and reusable charts. Use when packaging a Kubernetes application for repeatable deployments, parameterizing manifests for multiple environments, managing complex multi-component applications with dependencies, or standardizing deployment practices with versioned rollback capability across teams.
Create production-ready Helm charts for Kubernetes application deployment with templating, values management, chart dependencies, hooks, and testing. Covers chart structure, Go template syntax, values.yaml design, chart repositories, versioning, and best practices for maintainable and reusable charts. Use when packaging a Kubernetes application for repeatable deployments, parameterizing manifests for multiple environments, managing complex multi-component applications with dependencies, or standardizing deployment practices with versioned rollback capability across teams.
name validate-references locale caveman-ultra source_locale en source_commit 82c77053 translator Julius Brussee homage — caveman translation_date 2026-05-03 description Check BibTeX entries for completeness, DOI resolution, and broken links. Verify required fields per entry type (article, book, inproceedings), resolve and validate DOIs via the CrossRef API, check URL accessibility, and flag duplicate entries, missing abstracts, and inconsistent formatting. Use when preparing a manuscript bibliography for journal submission, auditing a shared .bib file before a project milestone, after merging bibliographies from multiple sources, when citations render incorrectly, or as a CI check on version-controlled .bib files.
license MIT allowed-tools Read Write Edit Bash Grep Glob metadata {"author":"Philipp Thoss","version":"1.0","domain":"citations","complexity":"intermediate","language":"R","tags":"citations, validation, doi, bibtex, quality"}
Validate References
Check BibTeX entries for completeness, accuracy, consistency. Covers required fields per entry type, DOI resolution via CrossRef, URL access, dup detection, structured report by severity. Ensures .bib publication-ready before render.
Use When
Manuscript bib for journal submission
Audit shared .bib before project milestone
After merging bibs from multi sources
Citations render incorrectly → diagnose .bib issues
CI check on .bib in version-controlled
In
Required : Path to .bibOptional : Validation level (basic, standard, strict; default: standard)Optional : DOI resolution online check (default: TRUE)Optional : URL access check (default: TRUE)Optional : Out report path (default: console)Optional : CrossRef email for polite pool (recommended for large)
Do
Step 1: Install + Load Pkgs
required_packages <- c ( "RefManageR" , "httr2" , "curl" )
missing <- required_packages[ ! vapply( required_packages, requireNamespace,
logical( 1 ) , quietly = TRUE ) ]
if ( length ( missing
)
>
0
)
(
missing
)
(
)
Got: All pkgs load no errs.
If err: httr2 unavail → install.packages("httr2"). No curl headers → sudo apt install libcurl4-openssl-dev.
Step 2: Parse + Inventory bib <- RefManageR:: ReadBib( "references.bib" , check = FALSE )
message( sprintf( "Loaded %d entries from references.bib" , length ( bib) ) )
entry_types <- vapply( bib, function ( x) tolower( attr ( x, "bibtype" ) ) , character( 1 ) )
type_counts <- sort( table( entry_types) , decreasing = TRUE )
message( "Entry types:" )
for ( type in names ( type_counts) ) {
message( sprintf( " %s: %d" , type, type_counts[[ type] ] ) )
}
Got: Summary entry types (article, book, inproceedings, etc.) + total count matching @type{ blocks.
If err: Parsing errs → malformed BibTeX. Check unmatched braces, missing commas between fields, invalid UTF-8.
Step 3: Validate Required Fields
required_fields <- list (
article = c ( "author" , "title" , "journal" , "year" ) ,
book = c ( "author" , "title" , "publisher" , "year" ) ,
inproceedings = c ( "author" , "title" , "booktitle" , "year" ) ,
incollection = c ( "author" , "title" , "booktitle" , "publisher" , "year" ) ,
phdthesis = c ( "author" , "title" , "school" , "year" ) ,
mastersthesis = c ( "author" , "title" , "school" , "year" ) ,
techreport = c ( "author" , "title" , "institution" , "year" ) ,
misc = c ( "author" , "title" , "year" ) ,
unpublished = c ( "author" , "title" , "note" )
)
validate_fields <- function ( bib) {
issues <- list ( )
for ( i in seq_along ( bib) ) {
key <- names ( bib) [ i]
entry_type <- tolower( attr ( bib[[ i] ] , "bibtype" ) )
req <- required_fields[[ entry_type] ]
if ( is.null ( req) ) {
issues[[ length ( issues) + 1 ] ] <- list (
key = key, severity = "warning" ,
message = sprintf( "Unknown entry type: %s" , entry_type)
)
next
}
for ( field in req) {
value <- bib[[ i] ] [[ field] ]
if ( is.null ( value) || ! nzchar ( trimws( as.character ( value) ) ) ) {
issues[[ length ( issues) + 1 ] ] <- list (
key = key, severity = "error" ,
message = sprintf( "Missing required field: %s (type: %s)" , field, entry_type)
)
}
}
}
issues
}
field_issues <- validate_fields( bib)
message( sprintf( "Field validation: %d issues found" , length ( field_issues) ) )
Got: List of issues where required missing. Zero for well-maintained.
If err: Runs locally, no fail expected. If fails → check .bib parsed in Step 2.
Step 4: Resolve + Validate DOIs validate_dois <- function ( bib, email = NULL ) {
issues <- list ( )
headers <- list ( `User-Agent` = "R-bibliography-validator/1.0" )
if ( ! is.null ( email) ) {
headers[[ "mailto" ] ] <- email
}
for ( i in seq_along ( bib) ) {
key <- names ( bib) [ i]
doi <- bib[[ i] ] $ doi
if ( is.null ( doi) || ! nzchar ( doi) ) {
issues[[ length ( issues) + 1 ] ] <- list (
key = key, severity = "info" ,
message = "No DOI present"
)
next
}
doi <- gsub( "^https?://doi\\.org/" , "" , doi)
doi <- gsub( "^doi:" , "" , doi, ignore.case = TRUE )
doi <- trimws( doi)
tryCatch( {
resp <- httr2:: request( sprintf( "https://api.crossref.org/works/%s" , doi) ) |>
httr2:: req_headers( ! ! ! headers) |>
httr2:: req_timeout( 10 ) |>
httr2:: req_perform( )
if ( httr2:: resp_status( resp) != 200 ) {
issues[[ length ( issues) + 1 ] ] <- list (
key = key, severity = "error" ,
message = sprintf( "DOI does not resolve: %s (HTTP %d)" , doi,
httr2:: resp_status( resp) )
)
}
} , error = function ( e) {
issues[[ length ( issues) + 1 ] ] <<- list (
key = key, severity = "warning" ,
message = sprintf( "DOI check failed for %s: %s" , doi, e$ message)
)
} )
Sys.sleep( 0.5 )
}
issues
}
doi_issues <- validate_dois( bib, email = "your.email@example.com" )
message( sprintf( "DOI validation: %d issues found" , length ( doi_issues) ) )
Got: Each DOI resolves (HTTP 200 from CrossRef). No-DOI entries flagged informational.
If err: Net errs|rate limiting → warnings not hard fails. Set email for higher rate limits via CrossRef polite pool.
Step 5: URL Access validate_urls <- function ( bib) {
issues <- list ( )
for ( i in seq_along ( bib) ) {
key <- names ( bib) [ i]
url <- bib[[ i] ] $ url
if ( is.null ( url) || ! nzchar ( url) ) next
tryCatch( {
resp <- httr2:: request( url) |>
httr2:: req_method( "HEAD" ) |>
httr2:: req_timeout( 10 ) |>
httr2:: req_error( is_error = function ( resp) FALSE ) |>
httr2:: req_perform( )
status <- httr2:: resp_status( resp)
if ( status >= 400 ) {
issues[[ length ( issues) + 1 ] ] <- list (
key = key, severity = "warning" ,
message = sprintf( "URL returned HTTP %d: %s" , status, url)
)
}
} , error = function ( e) {
issues[[ length ( issues) + 1 ] ] <<- list (
key = key, severity = "warning" ,
message = sprintf( "URL unreachable: %s (%s)" , url, e$ message)
)
} )
Sys.sleep( 0.3 )
}
issues
}
url_issues <- validate_urls( bib)
message( sprintf( "URL validation: %d issues found" , length ( url_issues) ) )
Got: All URLs HTTP 200 (or 301/302 redirects). Broken links flagged.
If err: Some servers block HEAD → retry GET for failed HEAD checks. Timeouts common for slow academic servers.
Step 6: Detect Dups detect_duplicates <- function ( bib) {
issues <- list ( )
dois <- vapply( bib, function ( x) {
d <- x$ doi
if ( is.null ( d) ) NA_character_ else tolower( trimws( d) )
} , character( 1 ) )
doi_table <- table( dois[ ! is.na ( dois) ] )
dup_dois <- names ( doi_table[ doi_table > 1 ] )
for ( d in dup_dois) {
keys <- names ( bib) [ which( dois == d) ]
issues[[ length ( issues) + 1 ] ] <- list (
key = paste( keys, collapse = ", " ) , severity = "error" ,
message = sprintf( "Duplicate DOI %s in entries: %s" , d,
paste( keys, collapse = ", " ) )
)
}
titles <- vapply( bib, function ( x) {
t <- x$ title
if ( is.null ( t) ) NA_character_ else tolower( gsub( "[^a-z0-9 ]" , "" , tolower( t) ) )
} , character( 1 ) )
seen <- character( 0 )
for ( i in seq_along ( titles) ) {
if ( is.na ( titles[ i] ) ) next
for ( j in seen) {
if ( identical( titles[ i] , titles[ as.integer ( j) ] ) ) {
issues[[ length ( issues) + 1 ] ] <- list (
key = sprintf( "%s, %s" , names ( bib) [ as.integer ( j) ] , names ( bib) [ i] ) ,
severity = "warning" ,
message = sprintf( "Possible duplicate titles: '%s'" ,
substr( bib[[ i] ] $ title, 1 , 60 ) )
)
}
}
seen <- c ( seen, as.character ( i) )
}
issues
}
dup_issues <- detect_duplicates( bib)
message( sprintf( "Duplicate detection: %d issues found" , length ( dup_issues) ) )
Got: Zero dups for clean. Detected dups flagged w/ specific keys.
Step 7: Generate Report generate_report <- function ( all_issues, bib, output_file = NULL ) {
errors <- Filter( function ( x) x$ severity == "error" , all_issues)
warnings <- Filter( function ( x) x$ severity == "warning" , all_issues)
infos <- Filter( function ( x) x$ severity == "info" , all_issues)
lines <- c (
"# Bibliography Validation Report" ,
"" ,
sprintf( "**File**: references.bib" ) ,
sprintf( "**Entries**: %d" , length ( bib) ) ,
sprintf( "**Date**: %s" , Sys.Date( ) ) ,
"" ,
sprintf( "## Summary: %d errors, %d warnings, %d info" ,
length ( errors) , length ( warnings) , length ( infos) ) ,
""
)
if ( length ( errors) > 0 ) {
lines <- c ( lines, "## Errors" , "" )
for ( issue in errors) {
lines <- c ( lines, sprintf( "- **[%s]** %s" , issue$ key, issue$ message) )
}
lines <- c ( lines, "" )
}
if ( length ( warnings) > 0 ) {
lines <- c ( lines, "## Warnings" , "" )
for ( issue in warnings) {
lines <- c ( lines, sprintf( "- **[%s]** %s" , issue$ key, issue$ message) )
}
lines <- c ( lines, "" )
}
report_text <- paste( lines, collapse = "\n" )
if ( ! is.null ( output_file) ) {
writeLines( report_text, output_file)
message( sprintf( "Report written to %s" , output_file) )
}
cat( report_text)
invisible ( all_issues)
}
all_issues <- c ( field_issues, doi_issues, url_issues, dup_issues)
generate_report( all_issues, bib, output_file = "validation-report.md" )
Got: Structured md report listing all issues grouped by severity.
Check
Traps
DOI format inconsistency : DOIs may appear as 10.1234/..., https://doi.org/10.1234/..., or doi:10.1234/.... Normalize before compareCrossRef rate limit : Unauth req limited to ~50/sec. Always use email to join polite pool for higherTransient URL fails : Academic servers occasionally timeout. Retry once before flaggingEntry type variations : BibLaTeX uses @online where BibTeX uses @misc. Validator should handle bothFalse positive dups : "Introduction"|"Methods" titles trigger fuzzy match. Review flagged manuallyMissing DOIs for older works : Pre-2000 often lack DOIs. Flag informational, not errs
→
manage-bibliography — fix issues found by validator (dedup, add fields)format-citations — format validated entries into styled citations../reporting/format-apa-report — APA needs complete validated refs../r-packages/write-vignette — vignettes w/ citations need valid .bib entries 