QuickNDirty Dates from DOIs

[korbinib]

#!/usr/bin/env bash
set -euo pipefail

echo "Starting add_dates.sh — $(date -u +"%Y-%m-%dT%H:%M:%SZ")"

err() { printf '%s\n' "$*" >&2; }

encode_uri() { printf '%s' "$1" | jq -sRr @uri; }

# ISO date from DataCite (Issued or Published)
get_datacite_date() {
  local enc url resp
  enc=$(encode_uri "$1")
  url="https://api.datacite.org/dois/${enc}"
  resp=$(curl -sfL --max-time 15 "$url") || return 1
  printf '%s' "$resp" | jq -r '
    .data.attributes.dates[]?
    | select(.dateType == "Issued" or .dateType == "Published")
    | .date' | head -n1 | grep -q . || return 1
  printf '%s' "$resp" | jq -r '
    .data.attributes.dates[]?
    | select(.dateType == "Issued" or .dateType == "Published")
    | .date' | head -n1
}

# ISO date from CrossRef (created → published fallback)
get_crossref_date() {
  local enc resp
  enc=$(encode_uri "$1")
  resp=$(curl -sfL --max-time 15 -H "Accept: application/json" \
    "https://api.crossref.org/works/${enc}") || return 1

  # Try date-time string first, then date-parts array
  printf '%s' "$resp" | jq -r '
    .message |
    ( .created["date-time"]
    // ( .created["date-parts"][0] | if . then
            (.[0] | tostring) + "-" +
            (if .[1] then (.[1] | tostring | if length==1 then "0"+. else . end) else "01" end) + "-" +
            (if .[2] then (.[2] | tostring | if length==1 then "0"+. else . end) else "01" end) + "T00:00:00Z"
          else empty end )
    // ( .published["date-parts"][0] | if . then
            (.[0] | tostring) + "-" +
            (if .[1] then (.[1] | tostring | if length==1 then "0"+. else . end) else "01" end) + "-" +
            (if .[2] then (.[2] | tostring | if length==1 then "0"+. else . end) else "01" end) + "T00:00:00Z"
          else empty end )
    ) // empty' | grep -q . || return 1

  printf '%s' "$resp" | jq -r '
    .message |
    ( .created["date-time"]
    // ( .created["date-parts"][0] | if . then
            (.[0] | tostring) + "-" +
            (if .[1] then (.[1] | tostring | if length==1 then "0"+. else . end) else "01" end) + "-" +
            (if .[2] then (.[2] | tostring | if length==1 then "0"+. else . end) else "01" end) + "T00:00:00Z"
          else empty end )
    // ( .published["date-parts"][0] | if . then
            (.[0] | tostring) + "-" +
            (if .[1] then (.[1] | tostring | if length==1 then "0"+. else . end) else "01" end) + "-" +
            (if .[2] then (.[2] | tostring | if length==1 then "0"+. else . end) else "01" end) + "T00:00:00Z"
          else empty end )
    ) // empty'
}

# Insert or overwrite the DATE line immediately after the DOI key line
insert_or_update_date() {
  local file="$1" key="$2" datev="$3"
  local tmp
  tmp="$(mktemp "$(dirname "$file")/tmp.XXXXXX")"

  awk -v key="$key" -v datev="$datev" '
    BEGIN { found = 0 }
    { lines[NR] = $0 }
    END {
      for (i = 1; i <= NR; i++) {
        if (lines[i] ~ "^[[:space:]]*" key "[[:space:]]*:") { found = i; break }
      }
      if (!found) { print "ERR: key not found" > "/dev/stderr"; exit 1 }
      match(lines[found], /^[[:space:]]*/)
      indent = substr(lines[found], RSTART, RLENGTH)
      next_is_date = (found+1 <= NR && lines[found+1] ~ "^[[:space:]]*DATE[[:space:]]*:")
      for (i = 1; i <= NR; i++) {
        if (i == found+1 && next_is_date)
          print indent "DATE: " datev
        else
          print lines[i]
        if (i == found && !next_is_date)
          print indent "DATE: " datev
      }
    }
  ' "$file" >"$tmp" || { err "awk failed for $file"; rm -f "$tmp"; return 1; }

  mv "$tmp" "$file"
}

ROOT_DIR="${1:-Simulations}"
found_any=0

while IFS= read -r -d '' file; do
  found_any=1
  echo "Processing: $file"

  doi_line=$(grep -m1 -E "^[[:space:]]*(ARTICLE_DOI|DATA_DOI|DOI)[[:space:]]*:" "$file" || true)
  [[ -z "$doi_line" ]] && { echo "  Skipping: no DOI key"; continue; }

  doi_key=$(printf '%s' "$doi_line" | sed 's/^[[:space:]]*\(ARTICLE_DOI\|DATA_DOI\|DOI\)[[:space:]]*:.*/\1/')
  doi_val=$(printf '%s' "$doi_line" | sed 's/^[^:]*:[[:space:]]*//' | tr -d "\"'[:space:]")

  [[ -z "$doi_val" ]] && { echo "  Skipping: empty DOI value"; continue; }
  echo "  ${doi_key} -> ${doi_val}"

  date_val=""
  if [[ "$doi_key" == "ARTICLE_DOI" ]]; then
    if date_val=$(get_crossref_date "$doi_val"); then
      echo "  CrossRef date: $date_val"
    else
      echo "  Warning: CrossRef failed, trying DataCite"
    fi
  fi

  if [[ -z "$date_val" ]]; then
    if date_val=$(get_datacite_date "$doi_val"); then
      echo "  DataCite date: $date_val"
    else
      echo "  Warning: no date found for $doi_val — skipping"
      continue
    fi
  fi

  if insert_or_update_date "$file" "$doi_key" "$date_val"; then
    echo "  Updated: $file"
  else
    echo "  Failed:  $file"
  fi

  sleep 10
done < <(find "$ROOT_DIR" -type f -name "README.yaml" -print0)

[[ "$found_any" -eq 0 ]] && echo "No README.yaml files found under ${ROOT_DIR}/**"
echo "Done."

[korbinib]

One could use a similar approach to add e.g. LICENSE and AUTHORS - in case one would want to implement e.g. bioschema.org dataset profiles