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Adding vernacular names
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closes #20
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@nleanba
nleanba committed Apr 8, 2024
1 parent a7ed7c4 commit 6c22085
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Showing 2 changed files with 66 additions and 30 deletions.
2 changes: 2 additions & 0 deletions src/deps.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -16,6 +16,8 @@ export { parseArgs } from "https://deno.land/std@0.215.0/cli/parse_args.ts";

export { DOMParser } from "https://esm.sh/linkedom@0.16.8/cached";

export { iso6393To1 } from "https://esm.sh/iso-639-3@3.0.1"

// broken somehow??
// export { Element } from "https://esm.sh/v135/linkedom@0.16.8/types/interface/element.d.ts";
// export type Element = globalThis.Element
94 changes: 64 additions & 30 deletions src/gg2rdf.ts
View file
Original file line number Diff line number Diff line change
@@ -1,4 +1,4 @@
import { DOMParser, parseArgs } from "./deps.ts";
import { DOMParser, iso6393To1, parseArgs } from "./deps.ts";
import type { Element } from "https://esm.sh/v135/linkedom@0.16.8/types/interface/element.d.ts"; // this does not work if imported via deps.ts for unclear reasons

class Subject {
Expand Down Expand Up @@ -94,7 +94,7 @@ export function gg2rdf(
output(
`# There was some Error in gg2rdf\n${error}\n${
error.stack ?? "[no stacktrace]"
}`.replace(/\n/g, "\n# "),
}`.replaceAll(/\n/g, "\n# "),
);
}

Expand Down Expand Up @@ -227,7 +227,7 @@ export function gg2rdf(
// add reference to subject taxon concept, using taxon name as a fallback if we're lacking a valid authority
if (!taxonConcept.ok) {
// no valid authority given, fall back to taxon name
t.addProperty("trt:treatsTaxonName", taxonNameURI(taxon));
t.addProperty("trt:treatsTaxonName", taxonConcept.tnuri);
} else {
// we have a valid authority, go for the taxon stringconcept
if (taxonStatus === "nomen dubium") {
Expand All @@ -243,7 +243,39 @@ export function gg2rdf(
treatmentTaxonUri = taxonConcept.uri;
}

makeTaxonName(taxon);
const treatmentTaxon = taxonNames.find((tn) =>
tn.uri === taxonConcept.tnuri
);
if (!treatmentTaxon) {
log("# Warning: Lost treatment-taxon, cannot add vernacular names");
} else {
doc.querySelectorAll("vernacularName").forEach((v: Element) => {
const language = v.getAttribute("language") || undefined;
const tag = language ? iso6393To1[language] : undefined;
if (tag) {
treatmentTaxon.addProperty(
"dwc:vernacularName",
`${STR(normalizeSpace(v.innerText))}@${tag}`,
);
} else {
treatmentTaxon.addProperty(
"dwc:vernacularName",
STR(normalizeSpace(v.innerText)),
);
treatmentTaxon.addProperty(
"# Info:",
`Couldn't generate language tag for ${
STR(normalizeSpace(v.innerText))
}@${language}`,
);
log(
`Info: Couldn't generate language tag for ${
STR(normalizeSpace(v.innerText))
}@${language}`,
);
}
});
}
}

if (doc.hasAttribute("docTitle")) {
Expand Down Expand Up @@ -277,7 +309,7 @@ export function gg2rdf(
t.addProperty(
"# Error:",
`Could not add TaxonConceptCitation\n${error}\n${error.stack ?? ""}`
.replace(/\n/g, "\n# "),
.replaceAll(/\n/g, "\n# "),
);
}
} else {
Expand Down Expand Up @@ -371,12 +403,14 @@ export function gg2rdf(
/** outputs turtle describing the cTaxon concept
* @returns object with
* - ok: could create taxon-concept
* - uri: uri of taxon-concept or taxon-name if invalid authority
* - uri?: uri of taxon-concept or `undefined` if invalid authority
* - tnuri: uri of taxon-name
* both returned uris are valid turtle uris
*/
function makeTaxonConcept(
taxon: Element,
cTaxon: Element,
): { ok: boolean; uri: string } {
): { ok: false; tnuri: string } | { ok: true; uri: string; tnuri: string } {
const rank: string = cTaxon.getAttribute("rank");
const cTaxonStatus: string = cTaxon.getAttribute("status") ??
taxon.parentNode.querySelector(
Expand All @@ -390,10 +424,12 @@ export function gg2rdf(
const taxonRelation = getTaxonRelation({ taxon, cTaxon });
const cTaxonRankGroup = getTaxonRankGroup(cTaxon);

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

if (cTaxonAuthority === "INVALID") {
const uri = taxonNameURI(cTaxon);
log(`Warning: Invalid Authority for ${uri}`);
return { ok: false, uri };
log(`Warning: Invalid Authority for ${tnuri}`);
return { ok: false, tnuri };
}

const uri = taxonConceptURI({
Expand All @@ -405,6 +441,8 @@ export function gg2rdf(
const s = prev || new Subject(uri);
if (!prev) taxonConcepts.push(s);

s.addProperty("trt:hasTaxonName", tnuri);

// check required attributes
if (
cTaxonRankGroup === RANKS.INVALID ||
Expand All @@ -417,8 +455,7 @@ export function gg2rdf(
s.addProperty("# Error:", "Invalid taxon relation");
}
s.addProperty("a", "dwcFP:TaxonConcept");
makeTaxonName(cTaxon);
return { ok: true, uri };
return { ok: true, uri, tnuri };
}

/** replaces <xsl:template name="taxonNameDetails"> and <xsl:template match="taxonomicName/@*"> */
Expand Down Expand Up @@ -452,16 +489,14 @@ export function gg2rdf(
}
});

s.addProperty("trt:hasTaxonName", taxonNameURI(cTaxon));

// for debugging only
// s.addProperty("trt:verbatim", STR(cTaxon.innerText));

let baseAuthority: string = cTaxon.getAttribute("baseAuthorityName") ?? "";
if (baseAuthority) {
baseAuthority = substringBefore(baseAuthority, " in ");
if (baseAuthority.length >= 2) {
baseAuthority = baseAuthority.replace(
baseAuthority = baseAuthority.replaceAll(
/\w[A-Z]+\b[^.]|\w[A-Z]+$/g,
(s) => s[0] + s.slice(1).toLowerCase(),
);
Expand All @@ -477,7 +512,7 @@ export function gg2rdf(
authority = substringBefore(authority, " in ");
if (authority === "L.") authority = "Linnaeus";
if (authority.length >= 2) {
authority = authority.replace(
authority = authority.replaceAll(
/\w[A-Z]+\b[^.]|\w[A-Z]+$/g,
(s) => s[0] + s.slice(1).toLowerCase(),
);
Expand Down Expand Up @@ -517,7 +552,7 @@ export function gg2rdf(
} else if (taxon === cTaxon) {
// 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"))
.replace(
.replaceAll(
/([^,@&]+),\s+[^,@&]+/g,
"$1@",
).replaceAll(
Expand All @@ -528,7 +563,7 @@ export function gg2rdf(
"",
);
if (docAuthor.length >= 2) {
docAuthor = docAuthor.replace(
docAuthor = docAuthor.replaceAll(
/\w[A-Z]+\b[^.]|\w[A-Z]+$/g,
(s) => s[0] + s.slice(1).toLowerCase(),
);
Expand Down Expand Up @@ -570,8 +605,7 @@ export function gg2rdf(
}

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

/** for dwc:scientificNameAuthorship and dwc:authority */
Expand All @@ -580,10 +614,10 @@ export function gg2rdf(
let result = normalizeSpace(a).replace(
/\s*,?\s*(\(?[0-9]{4}\)?)\s*[a-z]*\s*:?(?:\s*[0-9]*\s*[a-z-]*\s*,?)*(\)?)\s*$/,
", $1$2",
).replace(
).replaceAll(
/\s+and\s+/g,
" & ",
).replace(
).replaceAll(
/\s+et\s+([^a])/g,
" & $1",
).replace(
Expand Down Expand Up @@ -890,7 +924,7 @@ export function gg2rdf(
if (taxonConcept.ok) {
t.addProperty(`cito:cites`, taxonConcept.uri);
} else {
t.addProperty(`trt:citesTaxonName`, taxonNameURI(cTaxon));
t.addProperty(`trt:citesTaxonName`, taxonConcept.tnuri);
}
return;
}
Expand All @@ -904,7 +938,7 @@ export function gg2rdf(
if (taxonConcept.uri === treatmentTaxonUri) return;
t.addProperty(`trt:deprecates`, taxonConcept.uri);
} else {
t.addProperty(`trt:citesTaxonName`, taxonNameURI(cTaxon));
t.addProperty(`trt:citesTaxonName`, taxonConcept.tnuri);
}
return;
}
Expand Down Expand Up @@ -1057,7 +1091,7 @@ export function gg2rdf(
authorityName = substringAfter(authorityName, ". ");
authorityName = substringAfter(authorityName, " ");
if (authorityName.length >= 2) {
authorityName = authorityName.replace(
authorityName = authorityName.replaceAll(
/\w[A-Z]+\b[^.]|\w[A-Z]+$/g,
(s) => s[0] + s.slice(1).toLowerCase(),
);
Expand Down Expand Up @@ -1259,9 +1293,9 @@ export function gg2rdf(

function removePunctuation(s: string) {
if (!s) return "";
const result = s.replace(/(?:\p{Z}|\p{S}|\p{P})(?<![-])/ug, "");
const result = s.replaceAll(/(?:\p{Z}|\p{S}|\p{P})(?<![-])/ug, "");
if (result !== s) {
console.log(`Warning: Normalizing "${s}" to "${result}".`);
log(`Warning: Normalizing "${s}" to "${result}".`);
}
return result;
}
Expand All @@ -1274,12 +1308,12 @@ export function gg2rdf(
/** removes reserved uri characters from `s`, to be later passed to URI */
function partialURI(s: string) {
if (!s) return "";
return normalizeSpace(s.replace(/[;\/\?:@&=\+\$,#]+/g, " "));
return normalizeSpace(s.replaceAll(/[;\/\?:@&=\+\$,#]+/g, " "));
}

function URI(uri: string, replaceSpace = "") {
if (!uri) return "[]"; // unique blank node
return `<${encodeURI(uri.trim().replace(/\s+/g, replaceSpace))}>`;
return `<${encodeURI(uri.trim().replaceAll(/\s+/g, replaceSpace))}>`;
}

/** returns the part of s before c, not including c
Expand All @@ -1299,7 +1333,7 @@ export function gg2rdf(

function normalizeSpace(s: string) {
if (!s) return "";
return s.replace(/\s+/, " ").trim();
return s.replaceAll(/\s+/g, " ").trim();
}

/** this function should only be called with valid turtle segments,
Expand Down

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