Skip to content

Commit

Permalink
aligned uri-authority with human-readable authority
Browse files Browse the repository at this point in the history
  • Loading branch information
@nleanba
nleanba committed Sep 26, 2024
1 parent 83e7882 commit 84a98fd
Showing 1 changed file with 117 additions and 125 deletions.
242 changes: 117 additions & 125 deletions src/gg2rdf.ts
View file
Original file line number Diff line number Diff line change
Expand Up @@ -451,22 +451,30 @@ export function gg2rdf(
`taxonomicName ~ taxonomicNameLabel[rank="${rank}"]`,
)?.innerText ?? "ABSENT";

const cTaxonAuthority = getAuthority({
taxonName: cTaxon,
taxonStatus: cTaxonStatus,
});
const { authority, warnings, fallback_doc_info } = getFullAuthority(
taxon,
cTaxon,
!(cTaxonStatus.includes("comb") || cTaxonStatus.includes("stat") ||
cTaxonStatus.includes("ABSENT")),
);

const taxonRelation = getTaxonRelation({ taxon, cTaxon });
const cTaxonRankGroup = getTaxonRankGroup(cTaxon);

const tnuri = taxonNameURI(cTaxon);
makeTaxonName(cTaxon);

if (cTaxonAuthority === "INVALID") {
if (authority === "INVALID") {
log(`Warning: Invalid Authority for ${tnuri}`);
status = Math.max(status, Status.has_warnings);
return { ok: false, tnuri };
}

const year = authority.match(/[0-9]+/)?.[0] || "";
const cTaxonAuthority = `_${authorityNameForURI(authority)}_${
partialURI(year)
}`;

const uri = taxonConceptURI({
taxonName: cTaxon,
taxonAuthority: cTaxonAuthority,
Expand Down Expand Up @@ -529,6 +537,66 @@ export function gg2rdf(
// for debugging only
// s.addProperty("trt:verbatim", STR(cTaxon.innerText));

warnings.forEach((w) => s.addProperty("# Warning:", w));
s.addProperty("dwc:scientificNameAuthorship", STR(authority));

if (fallback_doc_info) {
// if taxon is the treated taxon and no explicit authority info is given on the element, fall back to document info
// unclear why dwc:authority* are only set in this one case
// also unlcear why they are simplified like in the uri
// TODO: change this if appropriate
let docAuthor = normalizeSpace(doc.getAttribute("docAuthor"))
.replaceAll(
/([^,@&]+),\s+[^,@&]+/g,
"$1@",
).replaceAll(
"@&",
" &",
).replaceAll(
"@",
"",
);
if (docAuthor.length >= 2) {
docAuthor = docAuthor.replaceAll(
/\w[A-Z]+\b[^.]|\w[A-Z]+$/g,
(s) => s[0] + s.slice(1).toLowerCase(),
);
}
s.addProperty(
`dwc:authority`,
STR(
normalizeAuthority(
`${docAuthor}, ${doc.getAttribute("docDate")}`,
),
),
);
s.addProperty(
"dwc:authorityName",
STR(docAuthor),
);
s.addProperty(
"dwc:authorityYear",
STR(doc.getAttribute("docDate")),
);
s.addProperty(
"# Info:",
"authority attributes generated from docAuthor",
);
}

s.addProperty("a", "dwcFP:TaxonConcept");
return { ok: true, uri, tnuri };
}

/** gets the human-readable authroty string for the cTaxon */
function getFullAuthority(
taxon: Element,
cTaxon: Element,
allow_fallback = true,
): { authority: string; warnings: string[]; fallback_doc_info?: boolean } {
let fullAuthority = "INVALID";
const warnings: string[] = [];

let baseAuthority: string = cTaxon.getAttribute("baseAuthorityName") ?? "";
if (baseAuthority) {
baseAuthority = substringBefore(baseAuthority, " in ");
Expand All @@ -545,10 +613,7 @@ export function gg2rdf(
baseAuthority.match(/\(.*$/)?.[0] ??
baseAuthority.match(/^.*\)/)?.[0] ?? "";
if (/[a-zA-Z]/.test(inside) && inside != baseAuthority) {
s.addProperty(
"# Warning:",
`Removing "${inside}" from baseAuthority`,
);
warnings.push(`Removing "${inside}" from baseAuthority`);
status = Math.max(status, Status.has_warnings);
baseAuthority = baseAuthority.replace(inside, "").trim();
}
Expand Down Expand Up @@ -576,10 +641,7 @@ export function gg2rdf(
authority.match(/\(.*$/)?.[0] ??
authority.match(/^.*\)/)?.[0] ?? "";
if (/[a-zA-Z]/.test(inside) && inside != authority) {
s.addProperty(
"# Warning:",
`Removing "${inside}" from authority`,
);
warnings.push(`Removing "${inside}" from authority`);
status = Math.max(status, Status.has_warnings);
authority = authority.replace(inside, "").trim();
}
Expand All @@ -601,32 +663,17 @@ export function gg2rdf(
if (baseAuthority && authority) {
// Animalia has baseAuthority only in this case, all other Kingdoms get both.
if (getKingdom(cTaxon) === "Animalia") {
s.addProperty(
"dwc:scientificNameAuthorship",
STR(baseAuthority),
);
fullAuthority = baseAuthority;
} else {
s.addProperty(
"dwc:scientificNameAuthorship",
STR(baseAuthority + " " + authority),
);
fullAuthority = baseAuthority + " " + authority;
}
} else if (baseAuthority) {
s.addProperty(
"dwc:scientificNameAuthorship",
STR(baseAuthority),
);
fullAuthority = baseAuthority;
} else if (authority) {
s.addProperty(
"dwc:scientificNameAuthorship",
STR(authority),
);
fullAuthority = authority;
} else if (cTaxon.getAttribute("authority")) {
s.addProperty(
"dwc:scientificNameAuthorship",
STR(normalizeAuthority(cTaxon.getAttribute("authority"))),
);
} else if (taxon === cTaxon) {
fullAuthority = normalizeAuthority(cTaxon.getAttribute("authority"));
} else if (taxon === cTaxon || allow_fallback) {
// if taxon is the treated taxon and no explicit authority info is given on the element, fall back to document info
let docAuthor = normalizeSpace(doc.getAttribute("docAuthor"))
.replaceAll(
Expand All @@ -645,44 +692,12 @@ export function gg2rdf(
(s) => s[0] + s.slice(1).toLowerCase(),
);
}
s.addProperty(
"dwc:scientificNameAuthorship",
STR(
normalizeAuthority(
`${docAuthor}, ${doc.getAttribute("docDate")}`,
),
),
fullAuthority = normalizeAuthority(
`${docAuthor}, ${doc.getAttribute("docDate")}`,
);
if (!taxon.hasAttribute("authority")) {
// if taxon is the treated taxon and no explicit authority info is given on the element, fall back to document info
// unclear why dwc:authority* are only set in this one case
// also unlcear why they are simplified like in the uri
// TODO: change this if appropriate
s.addProperty(
`dwc:authority`,
STR(
normalizeAuthority(
`${docAuthor}, ${doc.getAttribute("docDate")}`,
),
),
);
s.addProperty(
"dwc:authorityName",
STR(docAuthor),
);
s.addProperty(
"dwc:authorityYear",
STR(doc.getAttribute("docDate")),
);
s.addProperty(
"# Info:",
"authority attributes generated from docAuthor",
);
}
return { authority: fullAuthority, warnings, fallback_doc_info: true };
}

s.addProperty("a", "dwcFP:TaxonConcept");
return { ok: true, uri, tnuri };
return { authority: fullAuthority, warnings };
}

/** for dwc:scientificNameAuthorship and dwc:authority */
Expand All @@ -694,13 +709,15 @@ export function gg2rdf(
", $1$2",
)
.replaceAll('"', "")
.replaceAll("'", "")
.replaceAll(/(?:\b\p{Uppercase_Letter}\.\s+)+(\w+)/ug, "$1")
.replaceAll(/\s+and\s+/g, " & ")
.replaceAll(/\s+et\s+([^a])/g, " & $1")
.replace(/\)\)$/, ")")
.replace(/^\(\(/, "(")
.replace(/^\s*[,:;]+\s*/, "")
.replace(/\s*[,:;]+\s*$/, "");
.replace(/\s*[,:;]+\s*$/, "")
.trim();
if (result.indexOf("&") != result.lastIndexOf("&")) {
const split = result.split("&").map((s) => s.trim());
result = split.slice(0, -1).join(", ") + " & " + split.at(-1);
Expand Down Expand Up @@ -961,10 +978,17 @@ export function gg2rdf(
taxon: Element,
cTaxon: Element,
): void {
const cTaxonAuthority = getAuthority({
taxonName: cTaxon,
taxonStatus: "ABSENT",
});
const { authority } = getFullAuthority(taxon, cTaxon, false);

let cTaxonAuthority = authority;

if (authority !== "INVALID") {
const year = authority.match(/[0-9]+/)?.[0] || "";
cTaxonAuthority = `_${authorityNameForURI(authority)}_${
partialURI(year)
}`;
}

const taxonRelation = getTaxonRelation({ taxon, cTaxon });
const cTaxonRankGroup = getTaxonRankGroup(cTaxon);
// check required attributes
Expand Down Expand Up @@ -1105,61 +1129,29 @@ export function gg2rdf(
return RANKS.INVALID;
}

/** replaces <xsl:call-template name="authority"> */
function getAuthority(
{ taxonName, taxonStatus }: { taxonName: Element; taxonStatus: string },
) {
const baseAuthorityName: string = taxonName.getAttribute(
"baseAuthorityName",
);
const baseAuthorityYear: string = taxonName.getAttribute(
"baseAuthorityYear",
);
const authorityName: string = taxonName.getAttribute("authorityName");
const authorityYear: string = taxonName.getAttribute("authorityYear");
let docAuthor: string = doc.getAttribute("docAuthor");
let docDate: string = doc.getAttribute("docDate");

if (
taxonStatus.includes("ABSENT") || taxonStatus.includes("comb") ||
taxonStatus.includes("stat")
) {
// in this case, don't consider docAuthor & docDate
docAuthor = "";
docDate = "";
}

const name = baseAuthorityName || authorityName || docAuthor;
const year = baseAuthorityYear || authorityYear || docDate;
if (name && year) {
return `_${authorityNameForURI(name)}_${partialURI(year)}`;
}
return "INVALID";
}

/** replaces <xsl:call-template name="authorityNameForURI"> */
function authorityNameForURI(authorityName: string) {
authorityName = normalizeSpace(normalizeAuthority(authorityName));
authorityName = authorityName.replaceAll(/\([^\)]*\)/g, "");
authorityName = authorityName.replaceAll(/\[[^\]]*\]/g, "");
// authorityName = substringAfter(authorityName, ") ");
// authorityName = substringAfter(authorityName, ")");
// authorityName = substringAfter(authorityName, "] ");
// authorityName = substringAfter(authorityName, "]");
// authorityName = normalizeSpace(normalizeAuthority(authorityName));
// authorityName = authorityName.replaceAll(/\([^\)]*\)/g, "");
// authorityName = authorityName.replaceAll(/\[[^\]]*\]/g, "");
// // authorityName = substringAfter(authorityName, ") ");
// // authorityName = substringAfter(authorityName, ")");
// // authorityName = substringAfter(authorityName, "] ");
// // authorityName = substringAfter(authorityName, "]");
authorityName = substringBefore(authorityName, " &");
authorityName = substringBefore(authorityName, " and");
authorityName = substringBefore(authorityName, " et");
// authorityName = substringBefore(authorityName, " and");
// authorityName = substringBefore(authorityName, " et");
authorityName = substringBefore(authorityName, ",");
authorityName = substringAfter(authorityName, ". ");
// authorityName = substringAfter(authorityName, ". ");
authorityName = substringAfter(authorityName, " ");
if (authorityName.length >= 2) {
authorityName = authorityName.replaceAll(
/\w[A-Z]+\b[^.]|\w[A-Z]+$/g,
(s) => s[0] + s.slice(1).toLowerCase(),
);
}
if (authorityName === "L.") return partialURI("Linnaeus");
const match = authorityName.match(/^\S+/);
// if (authorityName.length >= 2) {
// authorityName = authorityName.replaceAll(
// /\w[A-Z]+\b[^.]|\w[A-Z]+$/g,
// (s) => s[0] + s.slice(1).toLowerCase(),
// );
// }
// if (authorityName === "L.") return partialURI("Linnaeus");
const match = authorityName.match(/\p{L}+/u);
if (match && match[0]) return partialURI(match[0]);
return partialURI(authorityName);
}
Expand Down

0 comments on commit 84a98fd

Please sign in to comment.