validate-references

pjt222

Aktualisiert 6 days ago

16 Ansichten

Designapidesign

Über

Diese Fähigkeit validiert BibTeX-Bibliografiedateien, indem sie erforderliche Felder prüft, DOIs über die CrossRef-API auflöst und verifiziert sowie die Erreichbarkeit von URLs testet. Sie markiert Duplikate, fehlende Abstracts und Formatierungsprobleme, was sie ideal für die Vorbereitung von Manuskripten oder die Überprüfung gemeinsamer .bib-Dateien macht. Entwickler können sie in CI-Pipelines integrieren oder beim Zusammenführen von Bibliografien verwenden, um die Qualität der Zitate sicherzustellen.

Schnellinstallation

Claude Code

Dokumentation

驗參

察 BibTeX 目以盡、準、一。涵驗每型必欄、解 DOI、察 URL 通、標重項、生分嚴之結構驗報。確 .bib 呈版前備。

用

備稿目以投刊→用
案里程前審共 .bib 質→用
合多源目後→用
引示誤須診 .bib 疾→用
控版案 .bib 之 CI 察→用

入

必：.bib 路
可：驗級（basic、standard、strict；默 standard）
可：在線察 DOI 否（默 TRUE）
可：察 URL 通否（默 TRUE）
可：報路（默：印於台）
可：CrossRef API 信箱以入禮池（大檔薦）

行

一：裝載必包

required_packages <- c("RefManageR", "httr2", "curl")
missing <- required_packages[!vapply(required_packages, requireNamespace,
                                     logical(1), quietly = TRUE)]
if (length(missing) > 0) install.packages(missing)

library(RefManageR)

得：諸包載無誤。

敗：httr2 缺→install.packages("httr2")。系無 curl 頭→sudo apt install libcurl4-openssl-dev。

二：析計目

bib <- RefManageR::ReadBib("references.bib", check = FALSE)
message(sprintf("Loaded %d entries from references.bib", length(bib)))

# Inventory entry types
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]]))
}

得：目型摘（article、book、inproceedings 等）、總計合檔中 @type{ 塊數。

敗：析誤示 BibTeX 壞。察不配括、欄間缺逗、非 UTF-8 字。

三：驗每型必欄

# BibTeX required fields by entry type
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  unpublished   = c("author", "title", "note")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)))

得：缺必欄之疾列。良養目零疾。

敗：此步本地行不應敗。若敗，察步二析正。

四：解驗 DOI

validate_dois <- function(bib, email = NULL) {
  issues <- list()

  # Set polite API headers
  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
    }

    # Normalize DOI
    doi <- gsub("^https?://doi\\.org/", "", doi)
    doi <- gsub("^doi:", "", doi, ignore.case = TRUE)
    doi <- trimws(doi)

    # Resolve via CrossRef
    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)  # Rate limiting
  }
  issues
}

# Only run online checks if requested
doi_issues <- validate_dois(bib, email = "[email protected]")
message(sprintf("DOI validation: %d issues found", length(doi_issues)))

得：每 DOI 解成（CrossRef HTTP 200）。無 DOI 之目標為信息。

敗：網誤或率限生警，非硬敗。設 email 參以入 CrossRef 禮池得高率限。

五：察 URL 通

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)))

得：諸 URL 返 HTTP 200（或 301/302 重導）。壞鏈標。

敗：某器拒 HEAD。HEAD 敗以 GET 重試。慢學術器超時常見。

六：偵重項

detect_duplicates <- function(bib) {
  issues <- list()

  # Check for duplicate DOIs
  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 = ", "))
    )
  }

  # Check for duplicate titles (fuzzy)
  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)))

得：清目零重。覓重者標附特目鍵。

七：生驗報

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")

得：結構 markdown 報，諸疾按嚴分組。

驗

忌

DOI 式不一：DOI 或現為 10.1234/...、https://doi.org/10.1234/...、doi:10.1234/...。較前規範
CrossRef 率限：未認請限 ~50/秒。必用 email 參入禮池得高限
URL 過敗：學術器偶超時。敗 URL 標壞前再試一
目型變：BibLaTeX 用 @online、BibTeX 用 @misc。驗器應應二者
假重：「Introduction」「Methods」標致模糊配。手察標重
舊作無 DOI：2000 年前出版常無 DOI。標為信息、非誤

參

manage-bibliography - 修此驗器覓之疾（去重、加欄）
format-citations - 將驗目格式化為樣式引文
../reporting/format-apa-report - APA 報須完驗之參
../r-packages/write-vignette - 含引之示例須效 .bib 目

GitHub Repository

pjt222/agent-almanac

Pfad: i18n/wenyan-ultra/skills/validate-references

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