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fixed mismatched CoL-IDs
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also add some minimal info for treatments without taxon
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@nleanba
nleanba committed Sep 29, 2024
1 parent 1ff1b3c commit e40c36f
Showing 1 changed file with 93 additions and 92 deletions.
185 changes: 93 additions & 92 deletions src/gg2rdf.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -87,12 +87,12 @@ export function gg2rdf(
const taxonNames: Subject[] = [];
const figures: Subject[] = [];
const citedMaterials: Subject[] = [];
let treatmentTaxonUri = "";

let status: Status = Status.successful;

const treatmentTaxon = getTreatmentTaxon();

try {
checkForErrors();
makeTreatment();
makePublication();

Expand Down Expand Up @@ -131,13 +131,15 @@ export function gg2rdf(
// end of top-level code

/** replaces <xsl:template match="/"> (root template) */
function checkForErrors() {
const errors: string[] = [];
function getTreatmentTaxon(): { uri: string | null; el: Element } | null {
const taxon: Element | undefined = document.querySelector(
'document treatment subSubSection[type="nomenclature"] taxonomicName',
);

if (!taxon) {
errors.push("the treatment is lacking the taxon");
log("Error: the treatment is lacking the taxon");
output("# Error: the treatment is lacking the taxon");
status = Math.max(status, Status.has_errors);
} else if (!taxon.getAttribute("kingdom")) {
log(
"Warning: treatment taxon is missing ancestor kingdom, defaulting to 'Animalia'",
Expand All @@ -147,12 +149,8 @@ export function gg2rdf(
);
status = Math.max(status, Status.has_warnings);
}
if (errors.length) {
throw new Error(
"Cannot produce RDF due to data errors:\n - " +
errors.join("\n - "),
);
}

return taxon ? { el: taxon, uri: null } : null;
}

function checkForEpithetErrors(taxon: Element): string[] {
Expand Down Expand Up @@ -236,79 +234,80 @@ export function gg2rdf(
function makeTreatment() {
const t = new Subject(URI(`http://treatment.plazi.org/id/${id}`));

const taxon: Element = document.querySelector(
'document treatment subSubSection[type="nomenclature"] taxonomicName',
); // existence asserted by checkForErrors

const epithetErrors = checkForEpithetErrors(taxon);
if (epithetErrors.length) {
epithetErrors.forEach((e) => {
t.addProperty("# Warning: Could not add treatment taxon because", e);
log(`Warning: Could not add treatment taxon because ${e}`);
status = Math.max(status, Status.has_warnings);
});
} else {
const rank: string = taxon.getAttribute("rank");
const taxonStatus: string = taxon.getAttribute("status") ??
taxon.parentNode.querySelector(
`taxonomicName ~ taxonomicNameLabel[rank="${rank}"]`,
)?.innerText ?? "ABSENT";

const is_defining = taxonStatus !== "nomen dubium" &&
(taxonStatus !== "ABSENT" ||
taxon.parentNode.querySelector(`taxonomicName ~ taxonomicNameLabel`));

const taxonConcept = makeTaxonConcept(taxon, taxon, is_defining);

// 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", taxonConcept.tnuri);
if (treatmentTaxon) {
const taxon = treatmentTaxon.el;
const epithetErrors = checkForEpithetErrors(taxon);
if (epithetErrors.length) {
epithetErrors.forEach((e) => {
t.addProperty("# Warning: Could not add treatment taxon because", e);
log(`Warning: Could not add treatment taxon because ${e}`);
status = Math.max(status, Status.has_warnings);
});
} else {
// we have a valid authority, go for the taxon stringconcept
if (taxonStatus === "nomen dubium") {
t.addProperty(`trt:deprecates`, taxonConcept.uri);
} else if (is_defining) {
t.addProperty(`trt:definesTaxonConcept`, taxonConcept.uri);
const rank: string = taxon.getAttribute("rank");
const taxonStatus: string = taxon.getAttribute("status") ??
taxon.parentNode.querySelector(
`taxonomicName ~ taxonomicNameLabel[rank="${rank}"]`,
)?.innerText ?? "ABSENT";

const is_defining = taxonStatus !== "nomen dubium" &&
(taxonStatus !== "ABSENT" ||
taxon.parentNode.querySelector(
`taxonomicName ~ taxonomicNameLabel`,
));

const taxonConcept = makeTaxonConcept(taxon, is_defining);

// 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", taxonConcept.tnuri);
} else {
t.addProperty(`trt:augmentsTaxonConcept`, taxonConcept.uri);
}
treatmentTaxonUri = taxonConcept.uri;
}

const treatmentTaxon = taxonNames.find((tn) =>
tn.uri === taxonConcept.tnuri
);
if (!treatmentTaxon) {
log("# Warning: Lost treatment-taxon, cannot add vernacular names");
status = Math.max(status, Status.has_warnings);
} 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}`,
);
// we have a valid authority, go for the taxon stringconcept
if (taxonStatus === "nomen dubium") {
t.addProperty(`trt:deprecates`, taxonConcept.uri);
} else if (is_defining) {
t.addProperty(`trt:definesTaxonConcept`, taxonConcept.uri);
} 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}`,
);
t.addProperty(`trt:augmentsTaxonConcept`, taxonConcept.uri);
}
});
treatmentTaxon.uri = taxonConcept.uri;
}

const treatmentTaxonSubject = taxonNames.find((tn) =>
tn.uri === taxonConcept.tnuri
);
if (!treatmentTaxonSubject) {
log("# Warning: Lost treatment-taxon, cannot add vernacular names");
status = Math.max(status, Status.has_warnings);
} else {
doc.querySelectorAll("vernacularName").forEach((v: Element) => {
const language = v.getAttribute("language") || undefined;
const tag = language ? iso6393To1[language] : undefined;
if (tag) {
treatmentTaxonSubject.addProperty(
"dwc:vernacularName",
`${STR(normalizeSpace(v.innerText))}@${tag}`,
);
} else {
treatmentTaxonSubject.addProperty(
"dwc:vernacularName",
STR(normalizeSpace(v.innerText)),
);
treatmentTaxonSubject.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}`,
);
}
});
}
}
}

Expand Down Expand Up @@ -337,7 +336,7 @@ export function gg2rdf(
: e.querySelector("taxonomicName");
if (cTaxon) {
try {
addTaxonConceptCitation(t, taxon, cTaxon);
addTaxonConceptCitation(t, cTaxon);
} catch (error) {
log(error);
t.addProperty(
Expand Down Expand Up @@ -443,7 +442,6 @@ export function gg2rdf(
* both returned uris are valid turtle uris
*/
function makeTaxonConcept(
taxon: Element,
cTaxon: Element,
is_defining: boolean,
): { ok: false; tnuri: string } | { ok: true; uri: string; tnuri: string } {
Expand All @@ -452,7 +450,7 @@ export function gg2rdf(
is_defining,
);

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

const tnuri = taxonNameURI(cTaxon);
Expand Down Expand Up @@ -519,7 +517,7 @@ export function gg2rdf(
"rdfs:seeAlso",
URI(
`https://www.catalogueoflife.org/data/taxon/${
normalizeSpace(taxon.getAttribute(n))
normalizeSpace(cTaxon.getAttribute(n))
}`,
),
);
Expand Down Expand Up @@ -993,7 +991,6 @@ export function gg2rdf(
/** replaces <xsl:template name="taxonConceptCitation"> */
function addTaxonConceptCitation(
t: Subject,
taxon: Element,
cTaxon: Element,
): void {
const { authority } = getFullAuthority(cTaxon, false);
Expand All @@ -1007,7 +1004,7 @@ export function gg2rdf(
}`;
}

const taxonRelation = getTaxonRelation({ taxon, cTaxon });
const taxonRelation = getTaxonRelation(cTaxon);
const cTaxonRankGroup = getTaxonRankGroup(cTaxon);
// check required attributes
if (
Expand Down Expand Up @@ -1043,7 +1040,7 @@ export function gg2rdf(
}
if (taxonRelation === REL.CITES) {
// do not let a citing treatment deprecate a cited name
const taxonConcept = makeTaxonConcept(taxon, cTaxon, false);
const taxonConcept = makeTaxonConcept(cTaxon, false);
if (taxonConcept.ok) {
t.addProperty(`cito:cites`, taxonConcept.uri);
} else {
Expand All @@ -1055,10 +1052,10 @@ export function gg2rdf(
// skip taxon names with insufficient attributes
if (taxonRelation === REL.SAME || taxonRelation === REL.NONE) return;
// deprecate recombined, renamed, and synonymized names
const taxonConcept = makeTaxonConcept(taxon, cTaxon, false);
const taxonConcept = makeTaxonConcept(cTaxon, false);
if (taxonConcept.ok) {
// do not let a taxon deprecate itself
if (taxonConcept.uri === treatmentTaxonUri) return;
if (taxonConcept.uri === treatmentTaxon?.uri) return;
t.addProperty(`trt:deprecates`, taxonConcept.uri);
} else {
t.addProperty(`trt:citesTaxonName`, taxonConcept.tnuri);
Expand All @@ -1067,9 +1064,13 @@ export function gg2rdf(
}

/** replaces <xsl:template name="taxonRelation"> */
function getTaxonRelation(
{ taxon, cTaxon }: { taxon: Element; cTaxon: Element },
) {
function getTaxonRelation(cTaxon: Element) {
if (!treatmentTaxon) {
return REL.CITES;
}

const taxon = treatmentTaxon.el;

const authorityMatch = (cTaxon.hasAttribute("authorityYear") &&
cTaxon.getAttribute("authorityYear") ===
taxon.getAttribute("authorityYear") &&
Expand Down

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