From ba768ca65c36520041cf41e2d7b9b2072834faee Mon Sep 17 00:00:00 2001
From: nleanba <25827850+nleanba@users.noreply.github.com>
Date: Fri, 8 Nov 2024 13:35:10 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20plazi/sy?=
=?UTF-8?q?nolib@57a06848d467f9ab065c7568acde4ec1fb99d463=20=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit
---
index.css | 19 +--
index.html | 6 +-
index.js | 374 ++++++++++++++++++++++++++-------------------------
index.js.map | 6 +-
index.ts | 5 +-
5 files changed, 204 insertions(+), 206 deletions(-)
diff --git a/index.css b/index.css
index 81e8e5b..6fedae9 100644
--- a/index.css
+++ b/index.css
@@ -96,13 +96,13 @@ syno-treatment,
transition: all 200ms;
clear: both;
- &>svg {
+ & > svg {
height: 1rem;
vertical-align: sub;
margin: 0 0.2rem 0 -1.2rem;
}
- >.icon.button {
+ > .icon.button {
float: right;
}
@@ -114,10 +114,6 @@ syno-treatment,
max-height: 0;
overflow: hidden;
transition: all 200ms;
-
- & img {
- display: none;
- }
}
&.expanded {
@@ -131,17 +127,13 @@ syno-treatment,
.hidden {
max-height: 200rem;
overflow: auto;
-
- & img {
- display: unset;
- }
}
}
}
.figures {
display: grid;
- grid-template-columns: repeat( auto-fill, minmax(12rem, 1fr) );
+ grid-template-columns: repeat(auto-fill, minmax(12rem, 1fr));
grid-template-rows: masonry;
margin: 0.2rem 0 0.2rem 2.2rem;
gap: 1rem;
@@ -155,7 +147,6 @@ syno-treatment,
}
}
-
.icon.button {
border-radius: 1rem;
border: none;
@@ -166,7 +157,7 @@ syno-treatment,
padding: 0;
position: relative;
- &>svg {
+ & > svg {
height: 1rem;
margin: 0;
}
@@ -204,4 +195,4 @@ syno-treatment,
.gray {
color: #666666;
-}
\ No newline at end of file
+}
diff --git a/index.html b/index.html
index c65e1c5..0643f32 100644
--- a/index.html
+++ b/index.html
@@ -29,9 +29,9 @@
SynoLib
- Expand a treatment with the button on the right to show all cited taxa, figures and materials. Click on a taxon identifier
- beneath a treatment to scroll to that name — if it is (already) in the
- list.
+ Expand a treatment with the button on the right to show all cited taxa,
+ figures and materials. Click on a taxon identifier beneath a treatment to
+ scroll to that name — if it is (already) in the list.
diff --git a/index.js b/index.js
index 1e44063..f641a17 100644
--- a/index.js
+++ b/index.js
@@ -1,28 +1,31 @@
-async function U(h){return await new Promise(i=>{setTimeout(i,h)})}var A=class{constructor(t){this.sparqlEnpointUri=t}async getSparqlResultSet(t,i={},s=""){
-i.headers=i.headers||{},i.headers.Accept="application/sparql-results+json";let l=0,c=async()=>{try{let d=await fetch(this.
-sparqlEnpointUri+"?query="+encodeURIComponent(t),i);if(!d.ok)throw new Error("Response not ok. Status "+d.status);return await d.
-json()}catch(d){if(i.signal?.aborted)throw d;if(l<10){let u=50*(1<{setTimeout(r,T)})}var O=class{constructor(t){this.sparqlEnpointUri=t}async getSparqlResultSet(t,r={},s=""){
+r.headers=r.headers||{},r.headers.Accept="application/sparql-results+json";let u=0,o=async()=>{try{let l=await fetch(this.
+sparqlEnpointUri+"?query="+encodeURIComponent(t),r);if(!l.ok)throw new Error("Response not ok. Status "+l.status);return await l.
+json()}catch(l){if(r.signal?.aborted)throw l;if(u<10){let m=50*(1<
+`,l),l}};return await o()}};var x=`PREFIX dc:
PREFIX dwc:
PREFIX dwcFP:
PREFIX cito:
PREFIX trt:
-SELECT DISTINCT ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority
+SELECT DISTINCT ?kingdom ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority
(group_concat(DISTINCT ?tcauth;separator=" / ") AS ?tcAuth)
(group_concat(DISTINCT ?aug;separator="|") as ?augs)
(group_concat(DISTINCT ?def;separator="|") as ?defs)
(group_concat(DISTINCT ?dpr;separator="|") as ?dprs)
(group_concat(DISTINCT ?cite;separator="|") as ?cites)
(group_concat(DISTINCT ?trtn;separator="|") as ?tntreats)
- (group_concat(DISTINCT ?citetn;separator="|") as ?tncites)`,P="GROUP BY ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?\
-infrasp ?name ?authority",q=h=>`${x} WHERE {
-BIND(<${h}> as ?col)
+ (group_concat(DISTINCT ?citetn;separator="|") as ?tncites)`,P="GROUP BY ?kingdom ?tn ?tc ?col ?rank ?genus ?subgenus ?\
+species ?infrasp ?name ?authority",k=T=>`${x} WHERE {
+BIND(<${T}> as ?col)
?col dwc:taxonRank ?rank .
?col dwc:scientificName ?name .
?col dwc:genericName ?genus .
- # TODO # ?col dwc:parent* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?kingdom .
+ OPTIONAL { ?col (dwc:parent|dwc:acceptedName)* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?colkingdom . }
+ BIND(COALESCE(?colkingdom, "") AS ?kingdom)
+ OPTIONAL { ?col dwc:infragenericEpithet ?colsubgenus . }
+ BIND(COALESCE(?colsubgenus, "") AS ?subgenus)
OPTIONAL {
?col dwc:specificEpithet ?species .
OPTIONAL { ?col dwc:infraspecificEpithet ?infrasp . }
@@ -33,22 +36,15 @@ BIND(<${h}> as ?col)
?tn dwc:rank ?trank ;
a dwcFP:TaxonName .
FILTER(LCASE(?rank) = LCASE(?trank))
- ?tn dwc:genus ?genus .
?tn dwc:kingdom ?kingdom .
- {
- ?col dwc:specificEpithet ?species .
- ?tn dwc:species ?species .
- {
- ?col dwc:infraspecificEpithet ?infrasp .
- ?tn dwc:subSpecies|dwc:variety|dwc:form ?infrasp .
- } UNION {
- FILTER NOT EXISTS { ?col dwc:infraspecificEpithet ?infrasp . }
- FILTER NOT EXISTS { ?tn dwc:subSpecies|dwc:variety|dwc:form ?infrasp . }
- }
- } UNION {
- FILTER NOT EXISTS { ?col dwc:specificEpithet ?species . }
- FILTER NOT EXISTS { ?tn dwc:species ?species . }
- }
+ ?tn dwc:genus ?genus .
+
+ OPTIONAL { ?tn dwc:subGenus ?tnsubgenus . }
+ FILTER(?subgenus = COALESCE(?tnsubgenus, ""))
+ OPTIONAL { ?tn dwc:species ?tnspecies . }
+ FILTER(?species = COALESCE(?tnspecies, ""))
+ OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }
+ FILTER(?infrasp = COALESCE(?tninfrasp, ""))
OPTIONAL {
?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .
@@ -82,8 +78,8 @@ BIND(<${h}> as ?col)
}
}
${P}
-LIMIT 500`,k=h=>`${x} WHERE {
- <${h}> trt:hasTaxonName ?tn .
+LIMIT 500`,_=T=>`${x} WHERE {
+ <${T}> trt:hasTaxonName ?tn .
?tc trt:hasTaxonName ?tn ;
dwc:scientificNameAuthorship ?tcauth ;
a dwcFP:TaxonConcept .
@@ -92,13 +88,14 @@ LIMIT 500`,k=h=>`${x} WHERE {
?tn dwc:rank ?tnrank .
?tn dwc:kingdom ?kingdom .
?tn dwc:genus ?genus .
- OPTIONAL { ?tn dwc:subGenus ?subgenus . }
+ OPTIONAL { ?tn dwc:subGenus ?tnsubgenus . }
OPTIONAL {
?tn dwc:species ?tnspecies .
OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }
}
BIND(LCASE(?tnrank) AS ?rank)
+ BIND(COALESCE(?tnsubgenus, "") AS ?subgenus)
BIND(COALESCE(?tnspecies, "") AS ?species)
BIND(COALESCE(?tninfrasp, "") AS ?infrasp)
@@ -106,8 +103,11 @@ LIMIT 500`,k=h=>`${x} WHERE {
?col dwc:taxonRank ?rank .
?col dwc:scientificName ?name . # Note: contains authority
?col dwc:genericName ?genus .
- # TODO # ?col dwc:parent* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?kingdom .
+ OPTIONAL { ?col (dwc:parent|dwc:acceptedName)* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?colkingdom . }
+ FILTER(?kingdom = COALESCE(?colkingdom, ""))
+ OPTIONAL { ?col dwc:infragenericEpithet ?colsubgenus . }
+ FILTER(?subgenus = COALESCE(?colsubgenus, ""))
OPTIONAL { ?col dwc:specificEpithet ?colspecies . }
FILTER(?species = COALESCE(?colspecies, ""))
OPTIONAL { ?col dwc:infraspecificEpithet ?colinfrasp . }
@@ -142,19 +142,20 @@ LIMIT 500`,k=h=>`${x} WHERE {
}
}
${P}
-LIMIT 500`,_=h=>`${x} WHERE {
- BIND(<${h}> as ?tn)
+LIMIT 500`,F=T=>`${x} WHERE {
+ BIND(<${T}> as ?tn)
?tn a dwcFP:TaxonName .
?tn dwc:rank ?tnrank .
?tn dwc:genus ?genus .
?tn dwc:kingdom ?kingdom .
- OPTIONAL { ?tn dwc:subGenus ?subgenus . }
+ OPTIONAL { ?tn dwc:subGenus ?tnsubgenus . }
OPTIONAL {
?tn dwc:species ?tnspecies .
OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }
}
BIND(LCASE(?tnrank) AS ?rank)
+ BIND(COALESCE(?tnsubgenus, "") AS ?subgenus)
BIND(COALESCE(?tnspecies, "") AS ?species)
BIND(COALESCE(?tninfrasp, "") AS ?infrasp)
@@ -162,8 +163,11 @@ LIMIT 500`,_=h=>`${x} WHERE {
?col dwc:taxonRank ?rank .
?col dwc:scientificName ?name . # Note: contains authority
?col dwc:genericName ?genus .
- # TODO # ?col dwc:parent* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?kingdom .
+ OPTIONAL { ?col (dwc:parent|dwc:acceptedName)* ?p . ?p dwc:rank "kingdom" ; dwc:taxonName ?colkingdom . }
+ FILTER(?kingdom = COALESCE(?colkingdom, ""))
+ OPTIONAL { ?col dwc:infragenericEpithet ?colsubgenus . }
+ FILTER(?subgenus = COALESCE(?colsubgenus, ""))
OPTIONAL { ?col dwc:specificEpithet ?colspecies . }
FILTER(?species = COALESCE(?colspecies, ""))
OPTIONAL { ?col dwc:infraspecificEpithet ?colinfrasp . }
@@ -202,23 +206,23 @@ LIMIT 500`,_=h=>`${x} WHERE {
}
}
${P}
-LIMIT 500`;var O=class{isFinished=!1;monitor=new EventTarget;controller=new AbortController;sparqlEndpoint;names=[];pushName(t){this.
+LIMIT 500`;var b=class{isFinished=!1;monitor=new EventTarget;controller=new AbortController;sparqlEndpoint;names=[];pushName(t){this.
names.push(t),this.monitor.dispatchEvent(new CustomEvent("updated"))}finish(){this.isFinished=!0,this.monitor.dispatchEvent(
-new CustomEvent("updated"))}expanded=new Set;acceptedCol=new Map;treatments=new Map;ignoreDeprecatedCoL;startWithSubTaxa;constructor(t,i,s=!0,l=!1){
-if(this.sparqlEndpoint=t,this.ignoreDeprecatedCoL=s,this.startWithSubTaxa=l,i.startsWith("http"))this.getName(i,{searchTerm:!0,
-subTaxon:!1}).catch(c=>{console.log("SynoGroup Failure: ",c),this.controller.abort("SynoGroup Failed")}).finally(()=>this.
-finish());else{let c=[...i.split(" ").filter(d=>!!d),void 0,void 0];this.getNameFromLatin(c,{searchTerm:!0,subTaxon:!1}).
-finally(()=>this.finish())}}findName(t){let i;for(let s of this.names){if(s.taxonNameURI===t||s.colURI===t){i=s;break}let l=s.
-authorizedNames.find(c=>c.taxonConceptURI===t||c.colURI===t);if(l){i=l;break}}return i?Promise.resolve(i):new Promise((s,l)=>{
-this.monitor.addEventListener("updated",()=>{(this.names.length===0||this.isFinished)&&l();let c=this.names.at(-1);if(c.
-taxonNameURI===t||c.colURI===t){s(c);return}let d=c.authorizedNames.find(u=>u.taxonConceptURI===t||u.colURI===t);if(d){s(
-d);return}})})}async getName(t,i){if(this.expanded.has(t)){console.log("Skipping known",t);return}if(this.controller.signal?.
+new CustomEvent("updated"))}expanded=new Set;acceptedCol=new Map;treatments=new Map;ignoreDeprecatedCoL;startWithSubTaxa;constructor(t,r,s=!0,u=!1){
+if(this.sparqlEndpoint=t,this.ignoreDeprecatedCoL=s,this.startWithSubTaxa=u,r.startsWith("http"))this.getName(r,{searchTerm:!0,
+subTaxon:!1}).catch(o=>{console.log("SynoGroup Failure: ",o),this.controller.abort("SynoGroup Failed")}).finally(()=>this.
+finish());else{let o=[...r.split(" ").filter(l=>!!l),void 0,void 0];this.getNameFromLatin(o,{searchTerm:!0,subTaxon:!1}).
+finally(()=>this.finish())}}findName(t){let r;for(let s of this.names){if(s.taxonNameURI===t||s.colURI===t){r=s;break}let u=s.
+authorizedNames.find(o=>o.taxonConceptURI===t||o.colURI===t);if(u){r=u;break}}return r?Promise.resolve(r):new Promise((s,u)=>{
+this.monitor.addEventListener("updated",()=>{(this.names.length===0||this.isFinished)&&u();let o=this.names.at(-1);if(o.
+taxonNameURI===t||o.colURI===t){s(o);return}let l=o.authorizedNames.find(m=>m.taxonConceptURI===t||m.colURI===t);if(l){s(
+l);return}})})}async getName(t,r){if(this.expanded.has(t)){console.log("Skipping known",t);return}if(this.controller.signal?.
aborted)return Promise.reject();let s;if(t.startsWith("https://www.catalogueoflife.org"))s=await this.sparqlEndpoint.getSparqlResultSet(
-q(t),{signal:this.controller.signal},`NameFromCol ${t}`);else if(t.startsWith("http://taxon-concept.plazi.org"))s=await this.
-sparqlEndpoint.getSparqlResultSet(k(t),{signal:this.controller.signal},`NameFromTC ${t}`);else if(t.startsWith("http://t\
-axon-name.plazi.org"))s=await this.sparqlEndpoint.getSparqlResultSet(_(t),{signal:this.controller.signal},`NameFromTN ${t}`);else
-throw`Cannot handle name-uri <${t}> !`;await this.handleName(s,i),this.startWithSubTaxa&&i.searchTerm&&!i.subTaxon&&await this.
-getSubtaxa(t)}async getSubtaxa(t){let i=t.startsWith("http://taxon-concept.plazi.org")?`
+k(t),{signal:this.controller.signal},`NameFromCol ${t}`);else if(t.startsWith("http://taxon-concept.plazi.org"))s=await this.
+sparqlEndpoint.getSparqlResultSet(_(t),{signal:this.controller.signal},`NameFromTC ${t}`);else if(t.startsWith("http://t\
+axon-name.plazi.org"))s=await this.sparqlEndpoint.getSparqlResultSet(F(t),{signal:this.controller.signal},`NameFromTN ${t}`);else
+throw`Cannot handle name-uri <${t}> !`;await this.handleName(s,r),this.startWithSubTaxa&&r.searchTerm&&!r.subTaxon&&await this.
+getSubtaxa(t)}async getSubtaxa(t){let r=t.startsWith("http://taxon-concept.plazi.org")?`
PREFIX trt:
SELECT DISTINCT ?sub WHERE {
BIND(<${t}> as ?url)
@@ -231,46 +235,46 @@ SELECT DISTINCT ?sub WHERE {
BIND(<${t}> as ?url)
?sub (dwc:parent|trt:hasParentName)* ?url .
}
-LIMIT 5000`;if(this.controller.signal?.aborted)return Promise.reject();let l=(await this.sparqlEndpoint.getSparqlResultSet(
-i,{signal:this.controller.signal},`Subtaxa ${t}`)).results.bindings.map(c=>c.sub?.value).filter(c=>c&&!this.expanded.has(
-c));await Promise.allSettled(l.map(c=>this.getName(c,{searchTerm:!0,subTaxon:!0})))}async getNameFromLatin([t,i,s],l){let c=`\
+LIMIT 5000`;if(this.controller.signal?.aborted)return Promise.reject();let u=(await this.sparqlEndpoint.getSparqlResultSet(
+r,{signal:this.controller.signal},`Subtaxa ${t}`)).results.bindings.map(o=>o.sub?.value).filter(o=>o&&!this.expanded.has(
+o));await Promise.allSettled(u.map(o=>this.getName(o,{searchTerm:!0,subTaxon:!0})))}async getNameFromLatin([t,r,s],u){let o=`\
PREFIX dwc:
SELECT DISTINCT ?uri WHERE {
?uri dwc:genus|dwc:genericName "${t}" .
- ${i?`?uri dwc:species|dwc:specificEpithet "${i}" .`:"FILTER NOT EXISTS { ?uri dwc:species|dwc:specificEpithet ?species\
+ ${r?`?uri dwc:species|dwc:specificEpithet "${r}" .`:"FILTER NOT EXISTS { ?uri dwc:species|dwc:specificEpithet ?species\
. }"}
${s?`?uri dwc:subSpecies|dwc:variety|dwc:form|dwc:infraspecificEpithet "${s}" .`:"FILTER NOT EXISTS { ?uri dwc:subSpec\
ies|dwc:variety|dwc:form|dwc:infraspecificEpithet ?infrasp . }"}
}
-LIMIT 500`;if(this.controller.signal?.aborted)return Promise.reject();let u=(await this.sparqlEndpoint.getSparqlResultSet(
-c,{signal:this.controller.signal},`NameFromLatin ${t} ${i} ${s}`)).results.bindings.map(a=>a.uri?.value).filter(a=>a&&!this.
-expanded.has(a));await Promise.allSettled(u.map(a=>this.getName(a,l)))}async handleName(t,i){let s=[],l=n=>{switch(n){case"\
-variety":return"var.";case"subspecies":return"subsp.";case"form":return"f.";default:return n}},c=(t.results.bindings[0].
+LIMIT 500`;if(this.controller.signal?.aborted)return Promise.reject();let m=(await this.sparqlEndpoint.getSparqlResultSet(
+o,{signal:this.controller.signal},`NameFromLatin ${t} ${r} ${s}`)).results.bindings.map(i=>i.uri?.value).filter(i=>i&&!this.
+expanded.has(i));await Promise.allSettled(m.map(i=>this.getName(i,u)))}async handleName(t,r){let s=[],u=e=>{switch(e){case"\
+variety":return"var.";case"subspecies":return"subsp.";case"form":return"f.";default:return e}},o=(t.results.bindings[0].
name?t.results.bindings[0].authority?t.results.bindings[0].name.value.replace(t.results.bindings[0].authority.value,""):
t.results.bindings[0].name.value:t.results.bindings[0].genus.value+(t.results.bindings[0].subgenus?.value?` (${t.results.
bindings[0].subgenus.value})`:"")+(t.results.bindings[0].species?.value?` ${t.results.bindings[0].species.value}`:"")+(t.
-results.bindings[0].infrasp?.value?` ${l(t.results.bindings[0].rank.value)} ${t.results.bindings[0].infrasp.value}`:"")).
-trim(),d,u=[],a=[],m=t.results.bindings[0].tn?.value;if(m){if(this.expanded.has(m))return;this.expanded.add(m)}for(let n of t.
-results.bindings){if(n.col){let r=n.col.value;if(n.authority?.value){if(!u.find(f=>f.colURI===r)){if(this.expanded.has(r)){
-console.log("Skipping known",r);return}u.push({displayName:c,authority:n.authority.value,colURI:n.col.value,treatments:{
-def:new Set,aug:new Set,dpr:new Set,cite:new Set}})}}else{if(this.expanded.has(r)){console.log("Skipping known",r);return}
-d&&d!==r&&console.log("Duplicate unathorized COL:",d,r),d=r}}if(n.tc&&n.tcAuth&&n.tcAuth.value){let r=this.makeTreatmentSet(
-n.defs?.value.split("|")),f=this.makeTreatmentSet(n.augs?.value.split("|")),S=this.makeTreatmentSet(n.dprs?.value.split(
-"|")),w=this.makeTreatmentSet(n.cites?.value.split("|")),N=u.find(v=>n.tcAuth.value.split(" / ").includes(v.authority));
-if(N)N.authority=n.tcAuth?.value,N.taxonConceptURI=n.tc.value,N.treatments={def:r,aug:f,dpr:S,cite:w};else{if(this.expanded.
-has(n.tc.value))return;a.push({displayName:c,authority:n.tcAuth.value,taxonConceptURI:n.tc.value,treatments:{def:r,aug:f,
-dpr:S,cite:w}})}r.forEach(v=>s.push(v)),f.forEach(v=>s.push(v)),S.forEach(v=>s.push(v))}}let T=this.makeTreatmentSet(t.results.
-bindings[0].tntreats?.value.split("|"));T.forEach(n=>s.push(n));let o={displayName:c,rank:t.results.bindings[0].rank.value,
-taxonNameURI:m,authorizedNames:[...u,...a],colURI:d,justification:i,treatments:{treats:T,cite:this.makeTreatmentSet(t.results.
-bindings[0].tncites?.value.split("|"))},vernacularNames:m?this.getVernacular(m):Promise.resolve(new Map)};for(let n of o.
-authorizedNames)n.colURI&&this.expanded.add(n.colURI),n.taxonConceptURI&&this.expanded.add(n.taxonConceptURI);let p=[];if(d){
-let[n,r]=await this.getAcceptedCol(d,o);o.acceptedColURI=n,p.push(...r)}await Promise.all(u.map(async n=>{let[r,f]=await this.
-getAcceptedCol(n.colURI,o);n.acceptedColURI=r,p.push(...f)})),this.pushName(o);let e=new Map;(await Promise.all(s.map(n=>n.
-details.then(r=>[n,r])))).map(([n,r])=>{r.treats.aug.difference(this.expanded).forEach(f=>e.set(f,n)),r.treats.def.difference(
-this.expanded).forEach(f=>e.set(f,n)),r.treats.dpr.difference(this.expanded).forEach(f=>e.set(f,n)),r.treats.treattn.difference(
-this.expanded).forEach(f=>e.set(f,n))}),await Promise.allSettled([...p,...[...e].map(([n,r])=>this.getName(n,{searchTerm:!1,
-parent:o,treatment:r}))])}async getAcceptedCol(t,i){let s=`
+results.bindings[0].infrasp?.value?` ${u(t.results.bindings[0].rank.value)} ${t.results.bindings[0].infrasp.value}`:"")).
+trim(),l,m=[],i=[],c=t.results.bindings[0].tn?.value;if(c){if(this.expanded.has(c))return;this.expanded.add(c)}for(let e of t.
+results.bindings){if(e.col){let n=e.col.value;if(e.authority?.value){if(!m.find(h=>h.colURI===n)){if(this.expanded.has(n)){
+console.log("Skipping known",n);return}m.push({displayName:o,authority:e.authority.value,colURI:e.col.value,treatments:{
+def:new Set,aug:new Set,dpr:new Set,cite:new Set}})}}else{if(this.expanded.has(n)){console.log("Skipping known",n);return}
+l&&l!==n&&console.log("Duplicate unathorized COL:",l,n),l=n}}if(e.tc&&e.tcAuth&&e.tcAuth.value){let n=this.makeTreatmentSet(
+e.defs?.value.split("|")),h=this.makeTreatmentSet(e.augs?.value.split("|")),v=this.makeTreatmentSet(e.dprs?.value.split(
+"|")),w=this.makeTreatmentSet(e.cites?.value.split("|")),S=m.find(N=>e.tcAuth.value.split(" / ").includes(N.authority));
+if(S)S.authority=e.tcAuth?.value,S.taxonConceptURI=e.tc.value,S.treatments={def:n,aug:h,dpr:v,cite:w};else{if(this.expanded.
+has(e.tc.value))return;i.push({displayName:o,authority:e.tcAuth.value,taxonConceptURI:e.tc.value,treatments:{def:n,aug:h,
+dpr:v,cite:w}})}n.forEach(N=>s.push(N)),h.forEach(N=>s.push(N)),v.forEach(N=>s.push(N))}}let f=this.makeTreatmentSet(t.results.
+bindings[0].tntreats?.value.split("|"));f.forEach(e=>s.push(e));let d={kingdom:t.results.bindings[0].kingdom.value,displayName:o,
+rank:t.results.bindings[0].rank.value,taxonNameURI:c,authorizedNames:[...m,...i],colURI:l,justification:r,treatments:{treats:f,
+cite:this.makeTreatmentSet(t.results.bindings[0].tncites?.value.split("|"))},vernacularNames:c?this.getVernacular(c):Promise.
+resolve(new Map)};for(let e of d.authorizedNames)e.colURI&&this.expanded.add(e.colURI),e.taxonConceptURI&&this.expanded.
+add(e.taxonConceptURI);let p=[];if(l){let[e,n]=await this.getAcceptedCol(l,d);d.acceptedColURI=e,p.push(...n)}await Promise.
+all(m.map(async e=>{let[n,h]=await this.getAcceptedCol(e.colURI,d);e.acceptedColURI=n,p.push(...h)})),this.pushName(d);let a=new Map;
+(await Promise.all(s.map(e=>e.details.then(n=>[e,n])))).map(([e,n])=>{n.treats.aug.difference(this.expanded).forEach(h=>a.
+set(h,e)),n.treats.def.difference(this.expanded).forEach(h=>a.set(h,e)),n.treats.dpr.difference(this.expanded).forEach(h=>a.
+set(h,e)),n.treats.treattn.difference(this.expanded).forEach(h=>a.set(h,e))}),await Promise.allSettled([...p,...[...a].map(
+([e,n])=>this.getName(e,{searchTerm:!1,parent:d,treatment:n}))])}async getAcceptedCol(t,r){let s=`
PREFIX dwc:
SELECT DISTINCT ?current ?current_status (GROUP_CONCAT(DISTINCT ?dpr; separator="|") AS ?dprs) WHERE {
BIND(<${t}> AS ?col)
@@ -285,19 +289,19 @@ SELECT DISTINCT ?current ?current_status (GROUP_CONCAT(DISTINCT ?dpr; separator=
BIND(?col AS ?current)
}
}
-GROUP BY ?current ?current_status`;if(this.acceptedCol.has(t))return[this.acceptedCol.get(t),[]];let l=await this.sparqlEndpoint.
-getSparqlResultSet(s,{signal:this.controller.signal},`AcceptedCol ${t}`),c=[];for(let d of l.results.bindings)for(let u of d.
-dprs.value.split("|"))u&&(this.acceptedCol.has(d.current.value)||(this.acceptedCol.set(d.current.value,d.current.value),
-c.push(this.getName(d.current.value,{searchTerm:!1,parent:i}))),this.acceptedCol.set(u,d.current.value),this.ignoreDeprecatedCoL||
-c.push(this.getName(u,{searchTerm:!1,parent:i})));return l.results.bindings.length===0?(this.acceptedCol.has(t)||this.acceptedCol.
-set(t,"INVALID COL"),[this.acceptedCol.get(t),c]):(this.acceptedCol.has(t)||this.acceptedCol.set(t,t),[this.acceptedCol.
-get(t),c])}async getVernacular(t){let i=new Map,s=`SELECT DISTINCT ?n WHERE { <${t}> ?n . }`,l=(await this.sparqlEndpoint.getSparqlResultSet(s,{signal:this.controller.signal},`Vernacular ${t}`)).
-results.bindings;for(let c of l)c.n?.value&&(c.n["xml:lang"]?i.has(c.n["xml:lang"])?i.get(c.n["xml:lang"]).push(c.n.value):
-i.set(c.n["xml:lang"],[c.n.value]):i.has("??")?i.get("??").push(c.n.value):i.set("??",[c.n.value]));return i}makeTreatmentSet(t){
-return t?new Set(t.filter(i=>!!i).map(i=>{let[s,l]=i.split(">");if(!this.treatments.has(s)){let c=this.getTreatmentDetails(
-s);this.treatments.set(s,{url:s,date:l?parseInt(l,10):void 0,details:c})}return this.treatments.get(s)})):new Set}async getTreatmentDetails(t){
-let i=`
+GROUP BY ?current ?current_status`;if(this.acceptedCol.has(t))return[this.acceptedCol.get(t),[]];let u=await this.sparqlEndpoint.
+getSparqlResultSet(s,{signal:this.controller.signal},`AcceptedCol ${t}`),o=[];for(let l of u.results.bindings)for(let m of l.
+dprs.value.split("|"))m&&(this.acceptedCol.has(l.current.value)||(this.acceptedCol.set(l.current.value,l.current.value),
+o.push(this.getName(l.current.value,{searchTerm:!1,parent:r}))),this.acceptedCol.set(m,l.current.value),this.ignoreDeprecatedCoL||
+o.push(this.getName(m,{searchTerm:!1,parent:r})));return u.results.bindings.length===0?(this.acceptedCol.has(t)||this.acceptedCol.
+set(t,"INVALID COL"),[this.acceptedCol.get(t),o]):(this.acceptedCol.has(t)||this.acceptedCol.set(t,t),[this.acceptedCol.
+get(t),o])}async getVernacular(t){let r=new Map,s=`SELECT DISTINCT ?n WHERE { <${t}> ?n . }`,u=(await this.sparqlEndpoint.getSparqlResultSet(s,{signal:this.controller.signal},`Vernacular ${t}`)).
+results.bindings;for(let o of u)o.n?.value&&(o.n["xml:lang"]?r.has(o.n["xml:lang"])?r.get(o.n["xml:lang"]).push(o.n.value):
+r.set(o.n["xml:lang"],[o.n.value]):r.has("??")?r.get("??").push(o.n.value):r.set("??",[o.n.value]));return r}makeTreatmentSet(t){
+return t?new Set(t.filter(r=>!!r).map(r=>{let[s,u]=r.split(">");if(!this.treatments.has(s)){let o=this.getTreatmentDetails(
+s);this.treatments.set(s,{url:s,date:u?parseInt(u,10):void 0,details:o})}return this.treatments.get(s)})):new Set}async getTreatmentDetails(t){
+let r=`
PREFIX dc:
PREFIX dwc:
PREFIX dwcFP:
@@ -364,14 +368,14 @@ WHERE {
}
GROUP BY ?date ?title ?mc`;if(this.controller.signal.aborted)return{materialCitations:[],figureCitations:[],treats:{def:new Set,
aug:new Set,dpr:new Set,citetc:new Set,treattn:new Set,citetn:new Set}};try{let s=await this.sparqlEndpoint.getSparqlResultSet(
-i,{signal:this.controller.signal},`TreatmentDetails ${t}`),l=s.results.bindings.filter(a=>a.mc&&a.catalogNumbers?.value).
-map(a=>{let m=a.httpUris?.value?.split("|");return{catalogNumber:a.catalogNumbers.value,collectionCode:a.collectionCodes?.
-value||void 0,typeStatus:a.typeStatuss?.value||void 0,countryCode:a.countryCodes?.value||void 0,stateProvince:a.stateProvinces?.
-value||void 0,municipality:a.municipalitys?.value||void 0,county:a.countys?.value||void 0,locality:a.localitys?.value||void 0,
-verbatimLocality:a.verbatimLocalitys?.value||void 0,recordedBy:a.recordedBys?.value||void 0,eventDate:a.eventDates?.value||
-void 0,samplingProtocol:a.samplingProtocols?.value||void 0,decimalLatitude:a.decimalLatitudes?.value||void 0,decimalLongitude:a.
-decimalLongitudes?.value||void 0,verbatimElevation:a.verbatimElevations?.value||void 0,gbifOccurrenceId:a.gbifOccurrenceIds?.
-value||void 0,gbifSpecimenId:a.gbifSpecimenIds?.value||void 0,httpUri:m?.length?m:void 0}}),c=`
+r,{signal:this.controller.signal},`TreatmentDetails ${t}`),u=s.results.bindings.filter(i=>i.mc&&i.catalogNumbers?.value).
+map(i=>{let c=i.httpUris?.value?.split("|");return{catalogNumber:i.catalogNumbers.value,collectionCode:i.collectionCodes?.
+value||void 0,typeStatus:i.typeStatuss?.value||void 0,countryCode:i.countryCodes?.value||void 0,stateProvince:i.stateProvinces?.
+value||void 0,municipality:i.municipalitys?.value||void 0,county:i.countys?.value||void 0,locality:i.localitys?.value||void 0,
+verbatimLocality:i.verbatimLocalitys?.value||void 0,recordedBy:i.recordedBys?.value||void 0,eventDate:i.eventDates?.value||
+void 0,samplingProtocol:i.samplingProtocols?.value||void 0,decimalLatitude:i.decimalLatitudes?.value||void 0,decimalLongitude:i.
+decimalLongitudes?.value||void 0,verbatimElevation:i.verbatimElevations?.value||void 0,gbifOccurrenceId:i.gbifOccurrenceIds?.
+value||void 0,gbifSpecimenId:i.gbifSpecimenIds?.value||void 0,httpUri:c?.length?c:void 0}}),o=`
PREFIX cito:
PREFIX fabio:
PREFIX dc:
@@ -380,20 +384,20 @@ SELECT DISTINCT ?url ?description WHERE {
?cites a fabio:Figure ;
fabio:hasRepresentation ?url .
OPTIONAL { ?cites dc:description ?description . }
-} `,u=(await this.sparqlEndpoint.getSparqlResultSet(c,{signal:this.controller.signal},`TreatmentDetails/Figures ${t}`)).
-results.bindings.filter(a=>a.url?.value).map(a=>({url:a.url.value,description:a.description?.value}));return{creators:s.
-results.bindings[0]?.creators?.value,title:s.results.bindings[0]?.title?.value,materialCitations:l,figureCitations:u,treats:{
+} `,m=(await this.sparqlEndpoint.getSparqlResultSet(o,{signal:this.controller.signal},`TreatmentDetails/Figures ${t}`)).
+results.bindings.filter(i=>i.url?.value).map(i=>({url:i.url.value,description:i.description?.value}));return{creators:s.
+results.bindings[0]?.creators?.value,title:s.results.bindings[0]?.title?.value,materialCitations:u,figureCitations:m,treats:{
def:new Set(s.results.bindings[0]?.defs?.value?s.results.bindings[0].defs.value.split("|"):void 0),aug:new Set(s.results.
bindings[0]?.augs?.value?s.results.bindings[0].augs.value.split("|"):void 0),dpr:new Set(s.results.bindings[0]?.dprs?.value?
s.results.bindings[0].dprs.value.split("|"):void 0),citetc:new Set(s.results.bindings[0]?.cites?.value?s.results.bindings[0].
cites.value.split("|"):void 0),treattn:new Set(s.results.bindings[0]?.trttns?.value?s.results.bindings[0].trttns.value.split(
"|"):void 0),citetn:new Set(s.results.bindings[0]?.citetns?.value?s.results.bindings[0].citetns.value.split("|"):void 0)}}}catch(s){
return console.warn("SPARQL Error: "+s),{materialCitations:[],figureCitations:[],treats:{def:new Set,aug:new Set,dpr:new Set,
-citetc:new Set,treattn:new Set,citetn:new Set}}}}[Symbol.asyncIterator](){let t=0;return{next:()=>new Promise((i,s)=>{let l=()=>{
-if(this.controller.signal.aborted)s(new Error("SynyonymGroup has been aborted"));else if(t{this.monitor.removeEventListener("updated",c),
-l()};this.monitor.addEventListener("updated",c)}};l()})}}};function F(h){let t=new Set(h);return Array.from(t)}var E=new URLSearchParams(document.location.search),M=!E.has("show_col"),$=E.has("subtaxa"),H=E.has("sort_treatments_by_\
-type"),Q=E.get("server")||"https://treatment.ld.plazi.org/sparql",z=E.get("q")||"https://www.catalogueoflife.org/data/ta\
+citetc:new Set,treattn:new Set,citetn:new Set}}}}[Symbol.asyncIterator](){let t=0;return{next:()=>new Promise((r,s)=>{let u=()=>{
+if(this.controller.signal.aborted)s(new Error("SynyonymGroup has been aborted"));else if(t{this.monitor.removeEventListener("updated",o),
+u()};this.monitor.addEventListener("updated",o)}};u()})}}};function z(T){let t=new Set(T);return Array.from(t)}var E=new URLSearchParams(document.location.search),$=!E.has("show_col"),H=E.has("subtaxa"),Q=E.has("sort_treatments_by_\
+type"),Z=E.get("server")||"https://treatment.ld.plazi.org/sparql",B=E.get("q")||"https://www.catalogueoflife.org/data/ta\
xon/3WD9M",D=document.getElementById("root");var g={def:'',collapse:'',west:'',empty:''},L=document.createElement("div");D.insertAdjacentElement(
-"beforebegin",L);L.append(`Finding Synonyms for ${z} `);var X=document.createElement("progress");L.append(X);var Z=performance.
-now(),W=new A(Q),I=new O(W,z,M,$),C=class extends HTMLElement{constructor(t,i){super(),this.innerHTML=g[i]??g.unknown;let s=document.
+"beforebegin",L);L.append(`Finding Synonyms for ${B} `);var X=document.createElement("progress");L.append(X);var W=performance.
+now(),J=new O(Z),I=new b(J,B,$,H),C=class extends HTMLElement{constructor(t,r){super(),this.innerHTML=g[r]??g.unknown;let s=document.
createElement("button");s.classList.add("icon","button"),s.innerHTML=g.expand,s.addEventListener("click",()=>{this.classList.
-toggle("expanded")?s.innerHTML=g.collapse:s.innerHTML=g.expand});let l=document.createElement("span");t.date?l.innerText=
-""+t.date:(l.classList.add("missing"),l.innerText="No Date"),this.append(l);let c=document.createElement("progress");this.
-append(": ",c);let d=document.createElement("a");d.classList.add("treatment","uri"),d.href=t.url,d.target="_blank",d.innerText=
-t.url.replace("http://treatment.plazi.org/id/",""),d.innerHTML+=g.link,this.append(" ",d),this.append(s);let u=document.
-createElement("div");u.classList.add("indent","details"),this.append(u),t.details.then(a=>{let m=document.createElement(
-"span"),T=document.createElement("i");if(c.replaceWith(m," ",T),a.creators?m.innerText=a.creators:(m.classList.add("miss\
-ing"),m.innerText="No Authors"),a.title?T.innerText="\u201C"+a.title+"\u201D":(T.classList.add("missing"),T.innerText="N\
-o Title"),a.treats.def.size>0){let o=document.createElement("div");o.innerHTML=g.east,o.innerHTML+=g.def,(i==="def"||i===
-"cite")&&o.classList.add("hidden"),u.append(o),a.treats.def.forEach(p=>{let e=document.createElement("a");e.classList.add(
-"taxon","uri");let n=p.replace("http://taxon-concept.plazi.org/id/","");e.innerText=n,e.href="#"+n,e.title="show name",o.
-append(" ",e),I.findName(p).then(r=>{e.classList.remove("uri"),r.authority?e.innerText=r.displayName+" "+r.authority:e.innerText=
-r.displayName},()=>{e.removeAttribute("href")})})}if(a.treats.aug.size>0||a.treats.treattn.size>0){let o=document.createElement(
-"div");o.innerHTML=g.east,o.innerHTML+=g.aug,(i==="aug"||i==="cite")&&o.classList.add("hidden"),u.append(o),a.treats.aug.
-forEach(p=>{let e=document.createElement("a");e.classList.add("taxon","uri");let n=p.replace("http://taxon-concept.plazi\
-.org/id/","");e.innerText=n,e.href="#"+n,e.title="show name",o.append(" ",e),I.findName(p).then(r=>{e.classList.remove("\
-uri"),r.authority?e.innerText=r.displayName+" "+r.authority:e.innerText=r.displayName},()=>{e.removeAttribute("href")})}),
-a.treats.treattn.forEach(p=>{let e=document.createElement("a");e.classList.add("taxon","uri");let n=p.replace("http://ta\
-xon-name.plazi.org/id/","");e.innerText=n,e.href="#"+n,e.title="show name",o.append(" ",e),I.findName(p).then(r=>{e.classList.
-remove("uri"),r.authority?e.innerText=r.displayName+" "+r.authority:e.innerText=r.displayName},()=>{e.removeAttribute("h\
-ref")})})}if(a.treats.dpr.size>0){let o=document.createElement("div");o.innerHTML=g.west,o.innerHTML+=g.dpr,(i==="dpr"||
-i==="cite")&&o.classList.add("hidden"),u.append(o),a.treats.dpr.forEach(p=>{let e=document.createElement("a");e.classList.
-add("taxon","uri");let n=p.replace("http://taxon-concept.plazi.org/id/","");e.innerText=n,e.href="#"+n,e.title="show nam\
-e",o.append(" ",e),I.findName(p).then(r=>{e.classList.remove("uri"),r.authority?e.innerText=r.displayName+" "+r.authority:
-e.innerText=r.displayName},()=>{e.removeAttribute("href")})})}if(a.treats.citetc.size>0||a.treats.citetn.size>0){let o=document.
-createElement("div");o.innerHTML=g.empty+g.cite,o.classList.add("hidden"),u.append(o),a.treats.citetc.forEach(p=>{let e=document.
-createElement("a");e.classList.add("taxon","uri");let n=p.replace("http://taxon-concept.plazi.org/id/","");e.innerText=n,
-e.href="#"+n,e.title="show name",o.append(" ",e),I.findName(p).then(r=>{e.classList.remove("uri"),r.authority?e.innerText=
-r.displayName+" "+r.authority:e.innerText=r.displayName},()=>{e.removeAttribute("href")})}),a.treats.citetn.forEach(p=>{
-let e=document.createElement("a");e.classList.add("taxon","uri");let n=p.replace("http://taxon-name.plazi.org/id/","");e.
-innerText=n,e.href="#"+n,e.title="show name",o.append(" ",e),I.findName(p).then(r=>{e.classList.remove("uri"),r.authority?
-e.innerText=r.displayName+" "+r.authority:e.innerText=r.displayName},()=>{e.removeAttribute("href")})})}if(a.figureCitations.
-length>0){let o=document.createElement("div");o.classList.add("figures","hidden"),u.append(o);for(let p of a.figureCitations){
-let e=document.createElement("figure");o.append(e);let n=document.createElement("img");n.src=p.url,n.loading="lazy",n.alt=
-p.description??"Cited Figure without caption",e.append(n);let r=document.createElement("figcaption");r.innerText=p.description??
-"",e.append(r)}}if(a.materialCitations.length>0){let o=document.createElement("div");o.innerHTML=g.empty+g.cite+" Materi\
-al Citations:
-",o.classList.add("hidden"),u.append(o),o.innerText+=a.materialCitations.map(p=>JSON.stringify(p).replaceAll(
+toggle("expanded")?s.innerHTML=g.collapse:s.innerHTML=g.expand});let u=document.createElement("span");t.date?u.innerText=
+""+t.date:(u.classList.add("missing"),u.innerText="No Date"),this.append(u);let o=document.createElement("progress");this.
+append(": ",o);let l=document.createElement("a");l.classList.add("treatment","uri"),l.href=t.url,l.target="_blank",l.innerText=
+t.url.replace("http://treatment.plazi.org/id/",""),l.innerHTML+=g.link,this.append(" ",l),this.append(s);let m=document.
+createElement("div");m.classList.add("indent","details"),this.append(m),t.details.then(i=>{let c=document.createElement(
+"span"),f=document.createElement("i");if(o.replaceWith(c," ",f),i.creators?c.innerText=i.creators:(c.classList.add("miss\
+ing"),c.innerText="No Authors"),i.title?f.innerText="\u201C"+i.title+"\u201D":(f.classList.add("missing"),f.innerText="N\
+o Title"),i.treats.def.size>0){let d=document.createElement("div");d.innerHTML=g.east,d.innerHTML+=g.def,(r==="def"||r===
+"cite")&&d.classList.add("hidden"),m.append(d),i.treats.def.forEach(p=>{let a=document.createElement("a");a.classList.add(
+"taxon","uri");let e=p.replace("http://taxon-concept.plazi.org/id/","");a.innerText=e,a.href="#"+e,a.title="show name",d.
+append(" ",a),I.findName(p).then(n=>{a.classList.remove("uri"),n.authority?a.innerText=n.displayName+" "+n.authority:a.innerText=
+n.displayName},()=>{a.removeAttribute("href")})})}if(i.treats.aug.size>0||i.treats.treattn.size>0){let d=document.createElement(
+"div");d.innerHTML=g.east,d.innerHTML+=g.aug,(r==="aug"||r==="cite")&&d.classList.add("hidden"),m.append(d),i.treats.aug.
+forEach(p=>{let a=document.createElement("a");a.classList.add("taxon","uri");let e=p.replace("http://taxon-concept.plazi\
+.org/id/","");a.innerText=e,a.href="#"+e,a.title="show name",d.append(" ",a),I.findName(p).then(n=>{a.classList.remove("\
+uri"),n.authority?a.innerText=n.displayName+" "+n.authority:a.innerText=n.displayName},()=>{a.removeAttribute("href")})}),
+i.treats.treattn.forEach(p=>{let a=document.createElement("a");a.classList.add("taxon","uri");let e=p.replace("http://ta\
+xon-name.plazi.org/id/","");a.innerText=e,a.href="#"+e,a.title="show name",d.append(" ",a),I.findName(p).then(n=>{a.classList.
+remove("uri"),n.authority?a.innerText=n.displayName+" "+n.authority:a.innerText=n.displayName},()=>{a.removeAttribute("h\
+ref")})})}if(i.treats.dpr.size>0){let d=document.createElement("div");d.innerHTML=g.west,d.innerHTML+=g.dpr,(r==="dpr"||
+r==="cite")&&d.classList.add("hidden"),m.append(d),i.treats.dpr.forEach(p=>{let a=document.createElement("a");a.classList.
+add("taxon","uri");let e=p.replace("http://taxon-concept.plazi.org/id/","");a.innerText=e,a.href="#"+e,a.title="show nam\
+e",d.append(" ",a),I.findName(p).then(n=>{a.classList.remove("uri"),n.authority?a.innerText=n.displayName+" "+n.authority:
+a.innerText=n.displayName},()=>{a.removeAttribute("href")})})}if(i.treats.citetc.size>0||i.treats.citetn.size>0){let d=document.
+createElement("div");d.innerHTML=g.empty+g.cite,d.classList.add("hidden"),m.append(d),i.treats.citetc.forEach(p=>{let a=document.
+createElement("a");a.classList.add("taxon","uri");let e=p.replace("http://taxon-concept.plazi.org/id/","");a.innerText=e,
+a.href="#"+e,a.title="show name",d.append(" ",a),I.findName(p).then(n=>{a.classList.remove("uri"),n.authority?a.innerText=
+n.displayName+" "+n.authority:a.innerText=n.displayName},()=>{a.removeAttribute("href")})}),i.treats.citetn.forEach(p=>{
+let a=document.createElement("a");a.classList.add("taxon","uri");let e=p.replace("http://taxon-name.plazi.org/id/","");a.
+innerText=e,a.href="#"+e,a.title="show name",d.append(" ",a),I.findName(p).then(n=>{a.classList.remove("uri"),n.authority?
+a.innerText=n.displayName+" "+n.authority:a.innerText=n.displayName},()=>{a.removeAttribute("href")})})}if(i.figureCitations.
+length>0){let d=document.createElement("div");d.classList.add("figures","hidden"),m.append(d);for(let p of i.figureCitations){
+let a=document.createElement("figure");d.append(a);let e=document.createElement("img");e.src=p.url,e.loading="lazy",e.alt=
+p.description??"Cited Figure without caption",a.append(e);let n=document.createElement("figcaption");n.innerText=p.description??
+"",a.append(n)}}if(i.materialCitations.length>0){let d=document.createElement("div");d.innerHTML=g.empty+g.cite+" Materi\
+al Citations:
-",d.classList.add("hidden"),m.append(d),d.innerText+=i.materialCitations.map(p=>JSON.stringify(p).replaceAll(
"{","").replaceAll("}","").replaceAll('":',": ").replaceAll(",",", ").replaceAll('"',"")).join(`
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-cite){let m=new C(a,"cite");d.append(m)}}let u=document.createElement("abbr");u.classList.add("justification"),u.innerText=
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-this.append(m);let o=document.createElement("ul");if(this.append(o),a.taxonConceptURI){let e=document.createElement("a");
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-S),a.acceptedColURI!==a.colURI){let w=document.createElement("div");w.innerHTML=g.east+g.col_aug,S.append(w);let N=document.
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-ref")})}}let p=[];for(let e of a.treatments.def)p.push({trt:e,status:"def"});for(let e of a.treatments.aug)p.push({trt:e,
-status:"aug"});for(let e of a.treatments.dpr)p.push({trt:e,status:"dpr"});for(let e of a.treatments.cite)p.push({trt:e,status:"\
-cite"});H||p.sort((e,n)=>e.trt.date&&n.trt.date?e.trt.date-n.trt.date:e.trt.date?1:n.trt.date?-1:0);for(let{trt:e,status:n}of p){
-let r=new C(e,n);o.append(r)}}}};customElements.define("syno-name",b);async function R(h){if(h.justification.searchTerm)
-return h.justification.subTaxon?"is a sub-taxon of the search term.":"is the search term.";if(h.justification.treatment){
-let t=await h.justification.treatment.details,i=await R(h.justification.parent);return`is, according to ${t.creators} ${h.
-justification.treatment.date},
- a synonym of ${h.justification.parent.displayName} which ${i}`}else{let t=await R(h.justification.parent);return`is\
+ -`)}})}};customElements.define("syno-treatment",C);var y=class extends HTMLElement{constructor(t){super();let r=document.
+createElement("h2"),s=document.createElement("i");s.innerText=t.displayName,r.append(s),this.append(r);let u=document.createElement(
+"span");u.classList.add("rank"),u.innerText=t.rank;let o=document.createElement("span");if(o.classList.add("rank"),o.innerText=
+t.kingdom||"Missing Kingdom",r.append(" ",o," ",u),t.taxonNameURI){let c=document.createElement("a");c.classList.add("ta\
+xon","uri");let f=t.taxonNameURI.replace("http://taxon-name.plazi.org/id/","");c.innerText=f,c.id=f,c.href=t.taxonNameURI,
+c.target="_blank",c.innerHTML+=g.link,r.append(" ",c)}let l=document.createElement("div");l.classList.add("vernacular"),
+t.vernacularNames.then(c=>{c.size>0&&(l.innerText="\u201C"+z([...c.values()].flat()).join("\u201D, \u201C")+"\u201D")}),
+this.append(l);let m=document.createElement("ul");if(this.append(m),t.colURI){let c=document.createElement("a");c.classList.
+add("col","uri");let f=t.colURI.replace("https://www.catalogueoflife.org/data/taxon/","");c.innerText=f,c.id=f,c.href=t.
+colURI,c.target="_blank",c.innerHTML+=g.link,r.append(" ",c);let d=document.createElement("div");d.classList.add("treatm\
+entline"),d.innerHTML=t.acceptedColURI!==t.colURI?g.col_dpr:g.col_aug,m.append(d);let p=document.createElement("span");p.
+innerText="Catalogue of Life",d.append(p);let a=document.createElement("div");if(a.classList.add("indent"),d.append(a),t.
+acceptedColURI!==t.colURI){let e=document.createElement("div");e.innerHTML=g.east+g.col_aug,a.append(e);let n=document.createElement(
+"a");n.classList.add("col","uri");let h=t.acceptedColURI.replace("https://www.catalogueoflife.org/data/taxon/","");n.innerText=
+h,n.href=`#${h}`,n.title="show name",e.append(n),I.findName(t.acceptedColURI).then(v=>{v.authority?n.innerText=v.displayName+
+" "+v.authority:n.innerText=v.displayName},()=>{n.removeAttribute("href")})}}if(t.treatments.treats.size>0||t.treatments.
+cite.size>0){for(let c of t.treatments.treats){let f=new C(c,"aug");m.append(f)}for(let c of t.treatments.cite){let f=new C(
+c,"cite");m.append(f)}}let i=document.createElement("abbr");i.classList.add("justification"),i.innerText="...?",R(t).then(
+c=>i.title=`This ${c}`),r.append(" ",i);for(let c of t.authorizedNames){let f=document.createElement("h3"),d=document.createElement(
+"i");d.innerText=c.displayName,d.classList.add("gray"),f.append(d),f.append(" ",c.authority),this.append(f);let p=document.
+createElement("ul");if(this.append(p),c.taxonConceptURI){let e=document.createElement("a");e.classList.add("taxon","uri");
+let n=c.taxonConceptURI.replace("http://taxon-concept.plazi.org/id/","");e.innerText=n,e.id=n,e.href=c.taxonConceptURI,e.
+target="_blank",e.innerHTML+=g.link,f.append(" ",e)}if(c.colURI){let e=document.createElement("a");e.classList.add("col",
+"uri");let n=c.colURI.replace("https://www.catalogueoflife.org/data/taxon/","");e.innerText=n,e.id=n,e.href=c.colURI,e.target=
+"_blank",e.innerHTML+=g.link,f.append(" ",e);let h=document.createElement("div");h.classList.add("treatmentline"),h.innerHTML=
+c.acceptedColURI!==c.colURI?g.col_dpr:g.col_aug,p.append(h);let v=document.createElement("span");v.innerText="Catalogue \
+of Life",h.append(v);let w=document.createElement("div");if(w.classList.add("indent"),h.append(w),c.acceptedColURI!==c.colURI){
+let S=document.createElement("div");S.innerHTML=g.east+g.col_aug,w.append(S);let N=document.createElement("a");N.classList.
+add("col","uri");let q=c.acceptedColURI.replace("https://www.catalogueoflife.org/data/taxon/","");N.innerText=q,N.href=`\
+#${q}`,N.title="show name",S.append(" ",N),I.findName(c.acceptedColURI).then(A=>{N.classList.remove("uri"),A.authority?N.
+innerText=A.displayName+" "+A.authority:N.innerText=A.displayName},()=>{N.removeAttribute("href")})}}let a=[];for(let e of c.
+treatments.def)a.push({trt:e,status:"def"});for(let e of c.treatments.aug)a.push({trt:e,status:"aug"});for(let e of c.treatments.
+dpr)a.push({trt:e,status:"dpr"});for(let e of c.treatments.cite)a.push({trt:e,status:"cite"});Q||a.sort((e,n)=>e.trt.date&&
+n.trt.date?e.trt.date-n.trt.date:e.trt.date?1:n.trt.date?-1:0);for(let{trt:e,status:n}of a){let h=new C(e,n);p.append(h)}}}};
+customElements.define("syno-name",y);async function R(T){if(T.justification.searchTerm)return T.justification.subTaxon?"\
+is a sub-taxon of the search term.":"is the search term.";if(T.justification.treatment){let t=await T.justification.treatment.
+details,r=await R(T.justification.parent);return`is, according to ${t.creators} ${T.justification.treatment.date},
+ a synonym of ${T.justification.parent.displayName} which ${r}`}else{let t=await R(T.justification.parent);return`is\
, according to the Catalogue of Life,
- a synonym of ${h.justification.parent.displayName} which ${t}`}}for await(let h of I){let t=new b(h);D.append(t)}var J=performance.
-now();L.innerHTML="";L.innerText=`Found ${I.names.length} names with ${I.treatments.size} treatments. This took ${(J-Z)/
+ a synonym of ${T.justification.parent.displayName} which ${t}`}}for await(let T of I){let t=new y(T);D.append(t)}var G=performance.
+now();L.innerHTML="";L.innerText=`Found ${I.names.length} names with ${I.treatments.size} treatments. This took ${(G-W)/
1e3} seconds.`;I.names.length===0&&D.append(":[");
//# sourceMappingURL=index.js.map
diff --git a/index.js.map b/index.js.map
index da8fa8a..6273e29 100644
--- a/index.js.map
+++ b/index.js.map
@@ -1,7 +1,7 @@
{
"version": 3,
"sources": ["../SparqlEndpoint.ts", "../Queries.ts", "../SynonymGroup.ts", "https://jsr.io/@std/collections/1.0.9/distinct.ts", "index.ts"],
- "sourcesContent": ["// deno-lint-ignore-file no-unused-labels\nasync function sleep(ms: number): Promise {\n const p = new Promise((resolve) => {\n setTimeout(resolve, ms);\n });\n return await p;\n}\n\n/** Describes the format of the JSON return by SPARQL endpoints */\nexport type SparqlJson = {\n head: {\n vars: string[];\n };\n results: {\n bindings: {\n [key: string]:\n | { type: string; value: string; \"xml:lang\"?: string }\n | undefined;\n }[];\n };\n};\n\n/**\n * Represents a remote sparql endpoint and provides a uniform way to run queries.\n */\nexport class SparqlEndpoint {\n /** Create a new SparqlEndpoint with the given URI */\n constructor(private sparqlEnpointUri: string) {}\n\n /** @ignore */\n // reasons: string[] = [];\n\n /**\n * Run a query against the sparql endpoint\n *\n * It automatically retries up to 10 times on fetch errors, waiting 50ms on the first retry and doupling the wait each time.\n * Retries are logged to the console (`console.warn`)\n *\n * @throws In case of non-ok response status codes or if fetch failed 10 times.\n * @param query The sparql query to run against the endpoint\n * @param fetchOptions Additional options for the `fetch` request\n * @param _reason (Currently ignored, used internally for debugging purposes)\n * @returns Results of the query\n */\n async getSparqlResultSet(\n query: string,\n fetchOptions: RequestInit = {},\n _reason = \"\",\n ): Promise {\n // this.reasons.push(_reason);\n // DEBUG: console.info(`SPARQL ${_reason}:\\n${query}`);\n\n fetchOptions.headers = fetchOptions.headers || {};\n (fetchOptions.headers as Record)[\"Accept\"] =\n \"application/sparql-results+json\";\n let retryCount = 0;\n const sendRequest = async (): Promise => {\n try {\n // DEBUG: console.info(`SPARQL ${_reason} (${retryCount + 1})`);\n const response = await fetch(\n this.sparqlEnpointUri + \"?query=\" + encodeURIComponent(query),\n fetchOptions,\n );\n if (!response.ok) {\n throw new Error(\"Response not ok. Status \" + response.status);\n }\n return await response.json();\n } catch (error) {\n if (fetchOptions.signal?.aborted) {\n throw error;\n } else if (retryCount < 10) {\n const wait = 50 * (1 << retryCount++);\n console.warn(`!! Fetch Error. Retrying in ${wait}ms (${retryCount})`);\n await sleep(wait);\n return await sendRequest();\n }\n console.warn(\"!! Fetch Error:\", query, \"\\n---\\n\", error);\n throw error;\n }\n };\n return await sendRequest();\n }\n}\n", "/**\n * Common to all of the `getNameFrom_`-queries.\n *\n * As its own variable to ensure consistency in the resturned bindings.\n */\nconst preamble = `PREFIX dc: \nPREFIX dwc: \nPREFIX dwcFP: \nPREFIX cito: \nPREFIX trt: \nSELECT DISTINCT ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority\n (group_concat(DISTINCT ?tcauth;separator=\" / \") AS ?tcAuth)\n (group_concat(DISTINCT ?aug;separator=\"|\") as ?augs)\n (group_concat(DISTINCT ?def;separator=\"|\") as ?defs)\n (group_concat(DISTINCT ?dpr;separator=\"|\") as ?dprs)\n (group_concat(DISTINCT ?cite;separator=\"|\") as ?cites)\n (group_concat(DISTINCT ?trtn;separator=\"|\") as ?tntreats)\n (group_concat(DISTINCT ?citetn;separator=\"|\") as ?tncites)`;\n\n/**\n * Common to all of the `getNameFrom_`-queries.\n *\n * As its own variable to ensure consistency in the resturned bindings.\n */\nconst postamble =\n `GROUP BY ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority`;\n\n// For unclear reasons, the queries breaks if the limit is removed.\n\n/**\n * Note: this query assumes that there is no sub-species taxa with missing dwc:species\n *\n * Note: the handling assumes that at most one taxon-name matches this colTaxon\n */\nexport const getNameFromCol = (colUri: string) =>\n `${preamble} WHERE {\nBIND(<${colUri}> as ?col)\n ?col dwc:taxonRank ?rank .\n ?col dwc:scientificName ?name .\n ?col dwc:genericName ?genus .\n # TODO # ?col dwc:parent* ?p . ?p dwc:rank \"kingdom\" ; dwc:taxonName ?kingdom .\n OPTIONAL {\n ?col dwc:specificEpithet ?species .\n OPTIONAL { ?col dwc:infraspecificEpithet ?infrasp . }\n }\n OPTIONAL { ?col dwc:scientificNameAuthorship ?authority . }\n\n OPTIONAL {\n ?tn dwc:rank ?trank ;\n a dwcFP:TaxonName .\n FILTER(LCASE(?rank) = LCASE(?trank))\n ?tn dwc:genus ?genus .\n ?tn dwc:kingdom ?kingdom .\n {\n ?col dwc:specificEpithet ?species .\n ?tn dwc:species ?species .\n {\n ?col dwc:infraspecificEpithet ?infrasp .\n ?tn dwc:subSpecies|dwc:variety|dwc:form ?infrasp .\n } UNION {\n FILTER NOT EXISTS { ?col dwc:infraspecificEpithet ?infrasp . }\n FILTER NOT EXISTS { ?tn dwc:subSpecies|dwc:variety|dwc:form ?infrasp . }\n }\n } UNION {\n FILTER NOT EXISTS { ?col dwc:specificEpithet ?species . }\n FILTER NOT EXISTS { ?tn dwc:species ?species . }\n }\n\n OPTIONAL {\n ?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .\n BIND(CONCAT(STR(?trtnt), \">\", ?trtndate) AS ?trtn)\n }\n OPTIONAL {\n ?citetnt trt:citesTaxonName ?tn ; trt:publishedIn/dc:date ?citetndate .\n BIND(CONCAT(STR(?citetnt), \">\", ?citetndate) AS ?citetn)\n }\n\n OPTIONAL {\n ?tc trt:hasTaxonName ?tn ; dwc:scientificNameAuthorship ?tcauth ; a dwcFP:TaxonConcept .\n\n OPTIONAL {\n ?augt trt:augmentsTaxonConcept ?tc ; trt:publishedIn/dc:date ?augdate .\n BIND(CONCAT(STR(?augt), \">\", ?augdate) AS ?aug)\n }\n OPTIONAL {\n ?deft trt:definesTaxonConcept ?tc ; trt:publishedIn/dc:date ?defdate .\n BIND(CONCAT(STR(?deft), \">\", ?defdate) AS ?def)\n }\n OPTIONAL {\n ?dprt trt:deprecates ?tc ; trt:publishedIn/dc:date ?dprdate .\n BIND(CONCAT(STR(?dprt), \">\", ?dprdate) AS ?dpr)\n }\n OPTIONAL {\n ?citet cito:cites ?tc ; trt:publishedIn/dc:date ?citedate .\n BIND(CONCAT(STR(?citet), \">\", ?citedate) AS ?cite)\n }\n }\n }\n}\n${postamble}\nLIMIT 500`;\n\n/**\n * Note: this query assumes that there is no sub-species taxa with missing dwc:species\n *\n * Note: the handling assumes that at most one taxon-name matches this colTaxon\n */\nexport const getNameFromTC = (tcUri: string) =>\n `${preamble} WHERE {\n <${tcUri}> trt:hasTaxonName ?tn .\n ?tc trt:hasTaxonName ?tn ;\n dwc:scientificNameAuthorship ?tcauth ;\n a dwcFP:TaxonConcept .\n\n ?tn a dwcFP:TaxonName .\n ?tn dwc:rank ?tnrank .\n ?tn dwc:kingdom ?kingdom .\n ?tn dwc:genus ?genus .\n OPTIONAL { ?tn dwc:subGenus ?subgenus . }\n OPTIONAL {\n ?tn dwc:species ?tnspecies .\n OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }\n }\n \n BIND(LCASE(?tnrank) AS ?rank)\n BIND(COALESCE(?tnspecies, \"\") AS ?species)\n BIND(COALESCE(?tninfrasp, \"\") AS ?infrasp)\n \n OPTIONAL {\n ?col dwc:taxonRank ?rank .\n ?col dwc:scientificName ?name . # Note: contains authority\n ?col dwc:genericName ?genus .\n # TODO # ?col dwc:parent* ?p . ?p dwc:rank \"kingdom\" ; dwc:taxonName ?kingdom .\n\n OPTIONAL { ?col dwc:specificEpithet ?colspecies . }\n FILTER(?species = COALESCE(?colspecies, \"\"))\n OPTIONAL { ?col dwc:infraspecificEpithet ?colinfrasp . }\n FILTER(?infrasp = COALESCE(?colinfrasp, \"\"))\n OPTIONAL { ?col dwc:scientificNameAuthorship ?authority . }\n }\n\n OPTIONAL {\n ?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .\n BIND(CONCAT(STR(?trtnt), \">\", ?trtndate) AS ?trtn)\n }\n OPTIONAL {\n ?citetnt trt:citesTaxonName ?tn ; trt:publishedIn/dc:date ?citetndate .\n BIND(CONCAT(STR(?citetnt), \">\", ?citetndate) AS ?citetn)\n }\n\n OPTIONAL {\n ?augt trt:augmentsTaxonConcept ?tc ; trt:publishedIn/dc:date ?augdate .\n BIND(CONCAT(STR(?augt), \">\", ?augdate) AS ?aug)\n }\n OPTIONAL {\n ?deft trt:definesTaxonConcept ?tc ; trt:publishedIn/dc:date ?defdate .\n BIND(CONCAT(STR(?deft), \">\", ?defdate) AS ?def)\n }\n OPTIONAL {\n ?dprt trt:deprecates ?tc ; trt:publishedIn/dc:date ?dprdate .\n BIND(CONCAT(STR(?dprt), \">\", ?dprdate) AS ?dpr)\n }\n OPTIONAL {\n ?citet cito:cites ?tc ; trt:publishedIn/dc:date ?citedate .\n BIND(CONCAT(STR(?citet), \">\", ?citedate) AS ?cite)\n }\n}\n${postamble}\nLIMIT 500`;\n\n/**\n * Note: this query assumes that there is no sub-species taxa with missing dwc:species\n *\n * Note: the handling assumes that at most one taxon-name matches this colTaxon\n */\nexport const getNameFromTN = (tnUri: string) =>\n `${preamble} WHERE {\n BIND(<${tnUri}> as ?tn)\n ?tn a dwcFP:TaxonName .\n ?tn dwc:rank ?tnrank .\n ?tn dwc:genus ?genus .\n ?tn dwc:kingdom ?kingdom .\n OPTIONAL { ?tn dwc:subGenus ?subgenus . }\n OPTIONAL {\n ?tn dwc:species ?tnspecies .\n OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }\n }\n \n BIND(LCASE(?tnrank) AS ?rank)\n BIND(COALESCE(?tnspecies, \"\") AS ?species)\n BIND(COALESCE(?tninfrasp, \"\") AS ?infrasp)\n \n OPTIONAL {\n ?col dwc:taxonRank ?rank .\n ?col dwc:scientificName ?name . # Note: contains authority\n ?col dwc:genericName ?genus .\n # TODO # ?col dwc:parent* ?p . ?p dwc:rank \"kingdom\" ; dwc:taxonName ?kingdom .\n\n OPTIONAL { ?col dwc:specificEpithet ?colspecies . }\n FILTER(?species = COALESCE(?colspecies, \"\"))\n OPTIONAL { ?col dwc:infraspecificEpithet ?colinfrasp . }\n FILTER(?infrasp = COALESCE(?colinfrasp, \"\"))\n OPTIONAL { ?col dwc:scientificNameAuthorship ?authority . }\n }\n\n OPTIONAL {\n ?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .\n BIND(CONCAT(STR(?trtnt), \">\", ?trtndate) AS ?trtn)\n }\n OPTIONAL {\n ?citetnt trt:citesTaxonName ?tn ; trt:publishedIn/dc:date ?citetndate .\n BIND(CONCAT(STR(?citetnt), \">\", ?citetndate) AS ?citetn)\n }\n\n OPTIONAL {\n ?tc trt:hasTaxonName ?tn ; dwc:scientificNameAuthorship ?tcauth ; a dwcFP:TaxonConcept .\n\n OPTIONAL {\n ?augt trt:augmentsTaxonConcept ?tc ; trt:publishedIn/dc:date ?augdate .\n BIND(CONCAT(STR(?augt), \">\", ?augdate) AS ?aug)\n }\n OPTIONAL {\n ?deft trt:definesTaxonConcept ?tc ; trt:publishedIn/dc:date ?defdate .\n BIND(CONCAT(STR(?deft), \">\", ?defdate) AS ?def)\n }\n OPTIONAL {\n ?dprt trt:deprecates ?tc ; trt:publishedIn/dc:date ?dprdate .\n BIND(CONCAT(STR(?dprt), \">\", ?dprdate) AS ?dpr)\n }\n OPTIONAL {\n ?citet cito:cites ?tc ; trt:publishedIn/dc:date ?citedate .\n BIND(CONCAT(STR(?citet), \">\", ?citedate) AS ?cite)\n }\n }\n}\n${postamble}\nLIMIT 500`;\n", "import type { SparqlEndpoint, SparqlJson } from \"./mod.ts\";\nimport * as Queries from \"./Queries.ts\";\n\n/** Finds all synonyms of a taxon */\nexport class SynonymGroup implements AsyncIterable {\n /** Indicates whether the SynonymGroup has found all synonyms.\n *\n * @readonly\n */\n isFinished = false;\n /** Used internally to watch for new names found */\n private monitor: EventTarget = new EventTarget();\n\n /** Used internally to abort in-flight network requests when SynonymGroup is aborted */\n private controller = new AbortController();\n\n /** The SparqlEndpoint used */\n private sparqlEndpoint: SparqlEndpoint;\n\n /**\n * List of names found so-far.\n *\n * Contains full list of synonyms _if_ .isFinished and not .isAborted\n *\n * @readonly\n */\n names: Name[] = [];\n /**\n * Add a new Name to this.names.\n *\n * Note: does not deduplicate on its own\n *\n * @internal */\n private pushName(name: Name) {\n this.names.push(name);\n this.monitor.dispatchEvent(new CustomEvent(\"updated\"));\n }\n\n /**\n * Call when all synonyms are found\n *\n * @internal */\n private finish() {\n this.isFinished = true;\n this.monitor.dispatchEvent(new CustomEvent(\"updated\"));\n }\n\n /** contains TN, TC, CoL uris of synonyms which are in-flight somehow or are done already */\n private expanded = new Set(); // new Map();\n\n /** contains CoL uris where we don't need to check for Col \"acceptedName\" links\n *\n * col -> accepted col\n */\n private acceptedCol = new Map();\n\n /**\n * Used internally to deduplicate treatments, maps from URI to Object.\n *\n * Contains full list of treatments _if_ .isFinished and not .isAborted\n *\n * @readonly\n */\n treatments: Map = new Map();\n\n /**\n * Whether to show taxa deprecated by CoL that would not have been found otherwise.\n * This significantly increases the number of results in some cases.\n */\n ignoreDeprecatedCoL: boolean;\n\n /**\n * if set to true, subTaxa of the search term are also considered as starting points.\n *\n * Not that \"weird\" ranks like subGenus are always included when searching for a genus by latin name.\n */\n startWithSubTaxa: boolean;\n\n /**\n * Constructs a SynonymGroup\n *\n * @param sparqlEndpoint SPARQL-Endpoint to query\n * @param taxonName either a string of the form \"Genus species infraspecific\" (species & infraspecific names optional), or an URI of a http://filteredpush.org/ontologies/oa/dwcFP#TaxonConcept or ...#TaxonName or a CoL taxon URI\n * @param [ignoreDeprecatedCoL=true] Whether to show taxa deprecated by CoL that would not have been found otherwise\n * @param [startWithSubTaxa=false] if set to true, subTaxa of the search term are also considered as starting points.\n */\n constructor(\n sparqlEndpoint: SparqlEndpoint,\n taxonName: string,\n ignoreDeprecatedCoL = true,\n startWithSubTaxa = false,\n ) {\n this.sparqlEndpoint = sparqlEndpoint;\n this.ignoreDeprecatedCoL = ignoreDeprecatedCoL;\n this.startWithSubTaxa = startWithSubTaxa;\n\n if (taxonName.startsWith(\"http\")) {\n this.getName(taxonName, { searchTerm: true, subTaxon: false })\n .catch((e) => {\n console.log(\"SynoGroup Failure: \", e);\n this.controller.abort(\"SynoGroup Failed\");\n })\n .finally(() => this.finish());\n } else {\n const name = [\n ...taxonName.split(\" \").filter((n) => !!n),\n undefined,\n undefined,\n ] as [string, string | undefined, string | undefined];\n this.getNameFromLatin(name, { searchTerm: true, subTaxon: false })\n .finally(\n () => this.finish(),\n );\n }\n }\n\n /**\n * Finds the given name (identified by taxon-name, taxon-concept or CoL uri) among the list of synonyms.\n *\n * Will reject when the SynonymGroup finishes but the name was not found \u2014 this means that this was not a synonym.\n */\n findName(uri: string): Promise {\n let name: Name | AuthorizedName | undefined;\n for (const n of this.names) {\n if (n.taxonNameURI === uri || n.colURI === uri) {\n name = n;\n break;\n }\n const an = n.authorizedNames.find((an) =>\n an.taxonConceptURI === uri || an.colURI === uri\n );\n if (an) {\n name = an;\n break;\n }\n }\n if (name) return Promise.resolve(name);\n return new Promise((resolve, reject) => {\n this.monitor.addEventListener(\"updated\", () => {\n if (this.names.length === 0 || this.isFinished) reject();\n const n = this.names.at(-1)!;\n if (n.taxonNameURI === uri || n.colURI === uri) {\n resolve(n);\n return;\n }\n const an = n.authorizedNames.find((an) =>\n an.taxonConceptURI === uri || an.colURI === uri\n );\n if (an) {\n resolve(an);\n return;\n }\n });\n });\n }\n\n /** @internal */\n private async getName(\n taxonName: string,\n justification: Justification,\n ): Promise {\n if (this.expanded.has(taxonName)) {\n console.log(\"Skipping known\", taxonName);\n return;\n }\n\n if (this.controller.signal?.aborted) return Promise.reject();\n\n let json: SparqlJson | undefined;\n\n if (taxonName.startsWith(\"https://www.catalogueoflife.org\")) {\n json = await this.sparqlEndpoint.getSparqlResultSet(\n Queries.getNameFromCol(taxonName),\n { signal: this.controller.signal },\n `NameFromCol ${taxonName}`,\n );\n } else if (taxonName.startsWith(\"http://taxon-concept.plazi.org\")) {\n json = await this.sparqlEndpoint.getSparqlResultSet(\n Queries.getNameFromTC(taxonName),\n { signal: this.controller.signal },\n `NameFromTC ${taxonName}`,\n );\n } else if (taxonName.startsWith(\"http://taxon-name.plazi.org\")) {\n json = await this.sparqlEndpoint.getSparqlResultSet(\n Queries.getNameFromTN(taxonName),\n { signal: this.controller.signal },\n `NameFromTN ${taxonName}`,\n );\n } else {\n throw `Cannot handle name-uri <${taxonName}> !`;\n }\n\n await this.handleName(json!, justification);\n\n if (\n this.startWithSubTaxa && justification.searchTerm &&\n !justification.subTaxon\n ) {\n await this.getSubtaxa(taxonName);\n }\n }\n\n /** @internal */\n private async getSubtaxa(url: string): Promise {\n const query = url.startsWith(\"http://taxon-concept.plazi.org\")\n ? `\nPREFIX trt: \nSELECT DISTINCT ?sub WHERE {\n BIND(<${url}> as ?url)\n ?sub trt:hasParentName*/^trt:hasTaxonName ?url .\n}\nLIMIT 5000`\n : `\nPREFIX dwc: \nPREFIX trt: \nSELECT DISTINCT ?sub WHERE {\n BIND(<${url}> as ?url)\n ?sub (dwc:parent|trt:hasParentName)* ?url .\n}\nLIMIT 5000`;\n\n if (this.controller.signal?.aborted) return Promise.reject();\n const json = await this.sparqlEndpoint.getSparqlResultSet(\n query,\n { signal: this.controller.signal },\n `Subtaxa ${url}`,\n );\n\n const names = json.results.bindings\n .map((n) => n.sub?.value)\n .filter((n) => n && !this.expanded.has(n)) as string[];\n\n await Promise.allSettled(\n names.map((n) => this.getName(n, { searchTerm: true, subTaxon: true })),\n );\n }\n\n /** @internal */\n private async getNameFromLatin(\n [genus, species, infrasp]: [string, string | undefined, string | undefined],\n justification: Justification,\n ): Promise {\n const query = `\n PREFIX dwc: \nSELECT DISTINCT ?uri WHERE {\n ?uri dwc:genus|dwc:genericName \"${genus}\" .\n ${\n species\n ? `?uri dwc:species|dwc:specificEpithet \"${species}\" .`\n : \"FILTER NOT EXISTS { ?uri dwc:species|dwc:specificEpithet ?species . }\"\n }\n ${\n infrasp\n ? `?uri dwc:subSpecies|dwc:variety|dwc:form|dwc:infraspecificEpithet \"${infrasp}\" .`\n : \"FILTER NOT EXISTS { ?uri dwc:subSpecies|dwc:variety|dwc:form|dwc:infraspecificEpithet ?infrasp . }\"\n }\n}\nLIMIT 500`;\n\n if (this.controller.signal?.aborted) return Promise.reject();\n const json = await this.sparqlEndpoint.getSparqlResultSet(\n query,\n { signal: this.controller.signal },\n `NameFromLatin ${genus} ${species} ${infrasp}`,\n );\n\n const names = json.results.bindings\n .map((n) => n.uri?.value)\n .filter((n) => n && !this.expanded.has(n)) as string[];\n\n await Promise.allSettled(names.map((n) => this.getName(n, justification)));\n }\n\n /**\n * Note this makes some assumptions on which variables are present in the bindings\n *\n * @internal */\n private async handleName(\n json: SparqlJson,\n justification: Justification,\n ): Promise {\n const treatmentPromises: Treatment[] = [];\n\n const abbreviateRank = (rank: string) => {\n switch (rank) {\n case \"variety\":\n return \"var.\";\n case \"subspecies\":\n return \"subsp.\";\n case \"form\":\n return \"f.\";\n default:\n return rank;\n }\n };\n\n const displayName: string = (json.results.bindings[0].name\n ? (\n json.results.bindings[0].authority\n ? json.results.bindings[0].name.value\n .replace(\n json.results.bindings[0].authority.value,\n \"\",\n )\n : json.results.bindings[0].name.value\n )\n : json.results.bindings[0].genus!.value +\n (json.results.bindings[0].subgenus?.value\n ? ` (${json.results.bindings[0].subgenus.value})`\n : \"\") +\n (json.results.bindings[0].species?.value\n ? ` ${json.results.bindings[0].species.value}`\n : \"\") +\n (json.results.bindings[0].infrasp?.value\n ? ` ${abbreviateRank(json.results.bindings[0].rank!.value)} ${\n json.results.bindings[0].infrasp.value\n }`\n : \"\")).trim();\n\n // Case where the CoL-taxon has no authority. There should only be one of these.\n let unathorizedCol: string | undefined;\n\n // there can be multiple CoL-taxa with same latin name, e.g. Leontopodium alpinum has 3T6ZY and 3T6ZX.\n const authorizedCoLNames: AuthorizedName[] = [];\n const authorizedTCNames: AuthorizedName[] = [];\n\n const taxonNameURI = json.results.bindings[0].tn?.value;\n if (taxonNameURI) {\n if (this.expanded.has(taxonNameURI)) return;\n this.expanded.add(taxonNameURI); //, NameStatus.madeName);\n }\n\n for (const t of json.results.bindings) {\n if (t.col) {\n const colURI = t.col.value;\n if (!t.authority?.value) {\n if (this.expanded.has(colURI)) {\n console.log(\"Skipping known\", colURI);\n return;\n }\n if (unathorizedCol && unathorizedCol !== colURI) {\n console.log(\"Duplicate unathorized COL:\", unathorizedCol, colURI);\n }\n unathorizedCol = colURI;\n } else if (!authorizedCoLNames.find((e) => e.colURI === colURI)) {\n if (this.expanded.has(colURI)) {\n console.log(\"Skipping known\", colURI);\n return;\n }\n authorizedCoLNames.push({\n displayName,\n authority: t.authority!.value,\n colURI: t.col.value,\n treatments: {\n def: new Set(),\n aug: new Set(),\n dpr: new Set(),\n cite: new Set(),\n },\n });\n }\n }\n\n if (t.tc && t.tcAuth && t.tcAuth.value) {\n const def = this.makeTreatmentSet(t.defs?.value.split(\"|\"));\n const aug = this.makeTreatmentSet(t.augs?.value.split(\"|\"));\n const dpr = this.makeTreatmentSet(t.dprs?.value.split(\"|\"));\n const cite = this.makeTreatmentSet(t.cites?.value.split(\"|\"));\n\n const colName = authorizedCoLNames.find((e) =>\n t.tcAuth!.value.split(\" / \").includes(e.authority)\n );\n if (colName) {\n colName.authority = t.tcAuth?.value;\n colName.taxonConceptURI = t.tc.value;\n colName.treatments = {\n def,\n aug,\n dpr,\n cite,\n };\n } else if (this.expanded.has(t.tc.value)) {\n // console.log(\"Skipping known\", t.tc.value);\n return;\n } else {\n authorizedTCNames.push({\n displayName,\n authority: t.tcAuth.value,\n taxonConceptURI: t.tc.value,\n treatments: {\n def,\n aug,\n dpr,\n cite,\n },\n });\n }\n\n def.forEach((t) => treatmentPromises.push(t));\n aug.forEach((t) => treatmentPromises.push(t));\n dpr.forEach((t) => treatmentPromises.push(t));\n }\n }\n\n const treats = this.makeTreatmentSet(\n json.results.bindings[0].tntreats?.value.split(\"|\"),\n );\n treats.forEach((t) => treatmentPromises.push(t));\n\n const name: Name = {\n displayName,\n rank: json.results.bindings[0].rank!.value,\n taxonNameURI,\n authorizedNames: [...authorizedCoLNames, ...authorizedTCNames],\n colURI: unathorizedCol,\n justification,\n treatments: {\n treats,\n cite: this.makeTreatmentSet(\n json.results.bindings[0].tncites?.value.split(\"|\"),\n ),\n },\n vernacularNames: taxonNameURI\n ? this.getVernacular(taxonNameURI)\n : Promise.resolve(new Map()),\n };\n\n for (const authName of name.authorizedNames) {\n if (authName.colURI) this.expanded.add(authName.colURI);\n if (authName.taxonConceptURI) this.expanded.add(authName.taxonConceptURI);\n }\n\n const colPromises: Promise[] = [];\n\n if (unathorizedCol) {\n const [acceptedColURI, promises] = await this.getAcceptedCol(\n unathorizedCol,\n name,\n );\n name.acceptedColURI = acceptedColURI;\n colPromises.push(...promises);\n }\n\n await Promise.all(\n authorizedCoLNames.map(async (n) => {\n const [acceptedColURI, promises] = await this.getAcceptedCol(\n n.colURI!,\n name,\n );\n n.acceptedColURI = acceptedColURI;\n colPromises.push(...promises);\n }),\n );\n\n this.pushName(name);\n\n /** Map */\n const newSynonyms = new Map();\n (await Promise.all(\n treatmentPromises.map((treat) =>\n treat.details.then((d): [Treatment, TreatmentDetails] => {\n return [treat, d];\n })\n ),\n )).map(([treat, d]) => {\n d.treats.aug.difference(this.expanded).forEach((s) =>\n newSynonyms.set(s, treat)\n );\n d.treats.def.difference(this.expanded).forEach((s) =>\n newSynonyms.set(s, treat)\n );\n d.treats.dpr.difference(this.expanded).forEach((s) =>\n newSynonyms.set(s, treat)\n );\n d.treats.treattn.difference(this.expanded).forEach((s) =>\n newSynonyms.set(s, treat)\n );\n });\n\n await Promise.allSettled(\n [\n ...colPromises,\n ...[...newSynonyms].map(([n, treatment]) =>\n this.getName(n, { searchTerm: false, parent: name, treatment })\n ),\n ],\n );\n }\n\n /** @internal */\n private async getAcceptedCol(\n colUri: string,\n parent: Name,\n ): Promise<[string, Promise[]]> {\n const query = `\nPREFIX dwc: \nSELECT DISTINCT ?current ?current_status (GROUP_CONCAT(DISTINCT ?dpr; separator=\"|\") AS ?dprs) WHERE {\n BIND(<${colUri}> AS ?col)\n {\n ?col dwc:acceptedName ?current .\n ?dpr dwc:acceptedName ?current .\n OPTIONAL { ?current dwc:taxonomicStatus ?current_status . }\n } UNION {\n ?col dwc:taxonomicStatus ?current_status .\n OPTIONAL { ?dpr dwc:acceptedName ?col . }\n FILTER NOT EXISTS { ?col dwc:acceptedName ?_ . }\n BIND(?col AS ?current)\n }\n}\nGROUP BY ?current ?current_status`;\n\n if (this.acceptedCol.has(colUri)) {\n return [this.acceptedCol.get(colUri)!, []];\n }\n\n const json = await this.sparqlEndpoint.getSparqlResultSet(\n query,\n { signal: this.controller.signal },\n `AcceptedCol ${colUri}`,\n );\n\n const promises: Promise[] = [];\n\n for (const b of json.results.bindings) {\n for (const dpr of b.dprs!.value.split(\"|\")) {\n if (dpr) {\n if (!this.acceptedCol.has(b.current!.value)) {\n this.acceptedCol.set(b.current!.value, b.current!.value);\n promises.push(\n this.getName(b.current!.value, {\n searchTerm: false,\n parent,\n }),\n );\n }\n\n this.acceptedCol.set(dpr, b.current!.value);\n if (!this.ignoreDeprecatedCoL) {\n promises.push(\n this.getName(dpr, { searchTerm: false, parent }),\n );\n }\n }\n }\n }\n\n if (json.results.bindings.length === 0) {\n // the provided colUri is not in CoL\n // promises === []\n if (!this.acceptedCol.has(colUri)) {\n this.acceptedCol.set(colUri, \"INVALID COL\");\n }\n return [this.acceptedCol.get(colUri)!, promises];\n }\n\n if (!this.acceptedCol.has(colUri)) this.acceptedCol.set(colUri, colUri);\n return [this.acceptedCol.get(colUri)!, promises];\n }\n\n /** @internal */\n private async getVernacular(uri: string): Promise {\n const result: vernacularNames = new Map();\n const query =\n `SELECT DISTINCT ?n WHERE { <${uri}> ?n . }`;\n const bindings = (await this.sparqlEndpoint.getSparqlResultSet(query, {\n signal: this.controller.signal,\n }, `Vernacular ${uri}`)).results.bindings;\n for (const b of bindings) {\n if (b.n?.value) {\n if (b.n[\"xml:lang\"]) {\n if (result.has(b.n[\"xml:lang\"])) {\n result.get(b.n[\"xml:lang\"])!.push(b.n.value);\n } else result.set(b.n[\"xml:lang\"], [b.n.value]);\n } else {\n if (result.has(\"??\")) result.get(\"??\")!.push(b.n.value);\n else result.set(\"??\", [b.n.value]);\n }\n }\n }\n return result;\n }\n\n /** @internal\n *\n * the supplied \"urls\" must be of the form \"URL>DATE\"\n */\n private makeTreatmentSet(urls?: string[]): Set {\n if (!urls) return new Set();\n return new Set(\n urls.filter((url) => !!url).map((url_d) => {\n const [url, date] = url_d.split(\">\");\n if (!this.treatments.has(url)) {\n const details = this.getTreatmentDetails(url);\n this.treatments.set(url, {\n url,\n date: date ? parseInt(date, 10) : undefined,\n details,\n });\n }\n return this.treatments.get(url) as Treatment;\n }),\n );\n }\n\n /** @internal */\n private async getTreatmentDetails(\n treatmentUri: string,\n ): Promise {\n const query = `\nPREFIX dc: \nPREFIX dwc: \nPREFIX dwcFP: \nPREFIX cito: \nPREFIX trt: \nSELECT DISTINCT\n ?date ?title ?mc\n (group_concat(DISTINCT ?catalogNumber;separator=\" / \") as ?catalogNumbers)\n (group_concat(DISTINCT ?collectionCode;separator=\" / \") as ?collectionCodes)\n (group_concat(DISTINCT ?typeStatus;separator=\" / \") as ?typeStatuss)\n (group_concat(DISTINCT ?countryCode;separator=\" / \") as ?countryCodes)\n (group_concat(DISTINCT ?stateProvince;separator=\" / \") as ?stateProvinces)\n (group_concat(DISTINCT ?municipality;separator=\" / \") as ?municipalitys)\n (group_concat(DISTINCT ?county;separator=\" / \") as ?countys)\n (group_concat(DISTINCT ?locality;separator=\" / \") as ?localitys)\n (group_concat(DISTINCT ?verbatimLocality;separator=\" / \") as ?verbatimLocalitys)\n (group_concat(DISTINCT ?recordedBy;separator=\" / \") as ?recordedBys)\n (group_concat(DISTINCT ?eventDate;separator=\" / \") as ?eventDates)\n (group_concat(DISTINCT ?samplingProtocol;separator=\" / \") as ?samplingProtocols)\n (group_concat(DISTINCT ?decimalLatitude;separator=\" / \") as ?decimalLatitudes)\n (group_concat(DISTINCT ?decimalLongitude;separator=\" / \") as ?decimalLongitudes)\n (group_concat(DISTINCT ?verbatimElevation;separator=\" / \") as ?verbatimElevations)\n (group_concat(DISTINCT ?gbifOccurrenceId;separator=\" / \") as ?gbifOccurrenceIds)\n (group_concat(DISTINCT ?gbifSpecimenId;separator=\" / \") as ?gbifSpecimenIds)\n (group_concat(DISTINCT ?creator;separator=\"; \") as ?creators)\n (group_concat(DISTINCT ?httpUri;separator=\"|\") as ?httpUris)\n (group_concat(DISTINCT ?aug;separator=\"|\") as ?augs)\n (group_concat(DISTINCT ?def;separator=\"|\") as ?defs)\n (group_concat(DISTINCT ?dpr;separator=\"|\") as ?dprs)\n (group_concat(DISTINCT ?cite;separator=\"|\") as ?cites)\n (group_concat(DISTINCT ?trttn;separator=\"|\") as ?trttns)\n (group_concat(DISTINCT ?citetn;separator=\"|\") as ?citetns)\nWHERE {\n BIND (<${treatmentUri}> as ?treatment)\n ?treatment dc:creator ?creator .\n OPTIONAL { ?treatment dc:title ?title }\n OPTIONAL { ?treatment trt:augmentsTaxonConcept ?aug . }\n OPTIONAL { ?treatment trt:definesTaxonConcept ?def . }\n OPTIONAL { ?treatment trt:deprecates ?dpr . }\n OPTIONAL { ?treatment cito:cites ?cite . ?cite a dwcFP:TaxonConcept . }\n OPTIONAL { ?treatment trt:treatsTaxonName ?trttn . }\n OPTIONAL { ?treatment trt:citesTaxonName ?citetn . }\n OPTIONAL {\n ?treatment dwc:basisOfRecord ?mc .\n ?mc dwc:catalogNumber ?catalogNumber .\n OPTIONAL { ?mc dwc:collectionCode ?collectionCode . }\n OPTIONAL { ?mc dwc:typeStatus ?typeStatus . }\n OPTIONAL { ?mc dwc:countryCode ?countryCode . }\n OPTIONAL { ?mc dwc:stateProvince ?stateProvince . }\n OPTIONAL { ?mc dwc:municipality ?municipality . }\n OPTIONAL { ?mc dwc:county ?county . }\n OPTIONAL { ?mc dwc:locality ?locality . }\n OPTIONAL { ?mc dwc:verbatimLocality ?verbatimLocality . }\n OPTIONAL { ?mc dwc:recordedBy ?recordedBy . }\n OPTIONAL { ?mc dwc:eventDate ?eventDate . }\n OPTIONAL { ?mc dwc:samplingProtocol ?samplingProtocol . }\n OPTIONAL { ?mc dwc:decimalLatitude ?decimalLatitude . }\n OPTIONAL { ?mc dwc:decimalLongitude ?decimalLongitude . }\n OPTIONAL { ?mc dwc:verbatimElevation ?verbatimElevation . }\n OPTIONAL { ?mc trt:gbifOccurrenceId ?gbifOccurrenceId . }\n OPTIONAL { ?mc trt:gbifSpecimenId ?gbifSpecimenId . }\n OPTIONAL { ?mc trt:httpUri ?httpUri . }\n }\n}\nGROUP BY ?date ?title ?mc`;\n if (this.controller.signal.aborted) {\n return {\n materialCitations: [],\n figureCitations: [],\n treats: {\n def: new Set(),\n aug: new Set(),\n dpr: new Set(),\n citetc: new Set(),\n treattn: new Set(),\n citetn: new Set(),\n },\n };\n }\n try {\n const json = await this.sparqlEndpoint.getSparqlResultSet(\n query,\n { signal: this.controller.signal },\n `TreatmentDetails ${treatmentUri}`,\n );\n const materialCitations: MaterialCitation[] = json.results.bindings\n .filter((t) => t.mc && t.catalogNumbers?.value)\n .map((t) => {\n const httpUri = t.httpUris?.value?.split(\"|\");\n return {\n \"catalogNumber\": t.catalogNumbers!.value,\n \"collectionCode\": t.collectionCodes?.value || undefined,\n \"typeStatus\": t.typeStatuss?.value || undefined,\n \"countryCode\": t.countryCodes?.value || undefined,\n \"stateProvince\": t.stateProvinces?.value || undefined,\n \"municipality\": t.municipalitys?.value || undefined,\n \"county\": t.countys?.value || undefined,\n \"locality\": t.localitys?.value || undefined,\n \"verbatimLocality\": t.verbatimLocalitys?.value || undefined,\n \"recordedBy\": t.recordedBys?.value || undefined,\n \"eventDate\": t.eventDates?.value || undefined,\n \"samplingProtocol\": t.samplingProtocols?.value || undefined,\n \"decimalLatitude\": t.decimalLatitudes?.value || undefined,\n \"decimalLongitude\": t.decimalLongitudes?.value || undefined,\n \"verbatimElevation\": t.verbatimElevations?.value || undefined,\n \"gbifOccurrenceId\": t.gbifOccurrenceIds?.value || undefined,\n \"gbifSpecimenId\": t.gbifSpecimenIds?.value || undefined,\n httpUri: httpUri?.length ? httpUri : undefined,\n };\n });\n const figureQuery = `\nPREFIX cito: \nPREFIX fabio: \nPREFIX dc: \nSELECT DISTINCT ?url ?description WHERE {\n <${treatmentUri}> cito:cites ?cites .\n ?cites a fabio:Figure ;\n fabio:hasRepresentation ?url .\n OPTIONAL { ?cites dc:description ?description . }\n} `;\n const figures = (await this.sparqlEndpoint.getSparqlResultSet(\n figureQuery,\n { signal: this.controller.signal },\n `TreatmentDetails/Figures ${treatmentUri}`,\n )).results.bindings;\n const figureCitations = figures.filter((f) => f.url?.value).map(\n (f) => {\n return { url: f.url!.value, description: f.description?.value };\n },\n );\n return {\n creators: json.results.bindings[0]?.creators?.value,\n title: json.results.bindings[0]?.title?.value,\n materialCitations,\n figureCitations,\n treats: {\n def: new Set(\n json.results.bindings[0]?.defs?.value\n ? json.results.bindings[0].defs.value.split(\"|\")\n : undefined,\n ),\n aug: new Set(\n json.results.bindings[0]?.augs?.value\n ? json.results.bindings[0].augs.value.split(\"|\")\n : undefined,\n ),\n dpr: new Set(\n json.results.bindings[0]?.dprs?.value\n ? json.results.bindings[0].dprs.value.split(\"|\")\n : undefined,\n ),\n citetc: new Set(\n json.results.bindings[0]?.cites?.value\n ? json.results.bindings[0].cites.value.split(\"|\")\n : undefined,\n ),\n treattn: new Set(\n json.results.bindings[0]?.trttns?.value\n ? json.results.bindings[0].trttns.value.split(\"|\")\n : undefined,\n ),\n citetn: new Set(\n json.results.bindings[0]?.citetns?.value\n ? json.results.bindings[0].citetns.value.split(\"|\")\n : undefined,\n ),\n },\n };\n } catch (error) {\n console.warn(\"SPARQL Error: \" + error);\n return {\n materialCitations: [],\n figureCitations: [],\n treats: {\n def: new Set(),\n aug: new Set(),\n dpr: new Set(),\n citetc: new Set(),\n treattn: new Set(),\n citetn: new Set(),\n },\n };\n }\n }\n\n /** Allows iterating over the synonyms while they are found */\n [Symbol.asyncIterator](): AsyncIterator {\n let returnedSoFar = 0;\n return {\n next: () =>\n new Promise>(\n (resolve, reject) => {\n const callback = () => {\n if (this.controller.signal.aborted) {\n reject(new Error(\"SynyonymGroup has been aborted\"));\n } else if (returnedSoFar < this.names.length) {\n resolve({ value: this.names[returnedSoFar++] });\n } else if (this.isFinished) {\n resolve({ done: true, value: true });\n } else {\n const listener = () => {\n this.monitor.removeEventListener(\"updated\", listener);\n callback();\n };\n this.monitor.addEventListener(\"updated\", listener);\n }\n };\n callback();\n },\n ),\n };\n }\n}\n\n// TODO: CoL taxa without authority -- associate them with the Name directly\n// eg. 5KTTT is \"Quercus robur subsp. robur\" w/o authority\n\n/** The central object.\n *\n * Each `Name` exists because of a taxon-name, taxon-concept or col-taxon in the data.\n * Each `Name` is uniquely determined by its human-readable latin name (for taxa ranking below genus, this is a multi-part name \u2014 binomial or trinomial) and kingdom.\n */\nexport type Name = {\n /** taxonomic kingdom */\n // kingdom: string;\n /** Human-readable name */\n displayName: string;\n /** taxonomic rank */\n rank: string;\n\n /** vernacular names */\n vernacularNames: Promise;\n\n // /** Contains the family tree / upper taxons accorindg to CoL / treatmentbank.\n // * //TODO */\n // trees: Promise<{\n // col?: Tree;\n // tb?: Tree;\n // }>;\n\n /** The URI of the respective `dwcFP:TaxonName` if it exists */\n taxonNameURI?: string;\n\n /**\n * The URI of the respective CoL-taxon if it exists\n *\n * Not that this is only for CoL-taxa which do not have an authority.\n */\n colURI?: string;\n /** The URI of the corresponding accepted CoL-taxon if it exists.\n *\n * Always present if colURI is present, they are the same if it is the accepted CoL-Taxon.\n *\n * May be the string \"INVALID COL\" if the colURI is not valid.\n */\n acceptedColURI?: string;\n\n /** All `AuthorizedName`s with this name */\n authorizedNames: AuthorizedName[];\n\n /** How this name was found */\n justification: Justification;\n\n /** treatments directly associated with .taxonNameUri */\n treatments: {\n treats: Set;\n cite: Set;\n };\n};\n\n/**\n * A map from language tags (IETF) to an array of vernacular names.\n */\nexport type vernacularNames = Map;\n\n/** Why a given Name was found (ther migth be other possible justifications) */\nexport type Justification = {\n searchTerm: true;\n /** indicates that this is a subTaxon of the parent */\n subTaxon: boolean;\n} | {\n searchTerm: false;\n parent: Name;\n /** if missing, indicates synonymy according to CoL or subTaxon */\n treatment?: Treatment;\n};\n\n/**\n * Corresponds to a taxon-concept or a CoL-Taxon\n */\nexport type AuthorizedName = {\n // TODO: neccesary?\n /** this may not be neccesary, as `AuthorizedName`s should only appear within a `Name` */\n // name: Name;\n /** Human-readable name */\n displayName: string;\n /** Human-readable authority */\n authority: string;\n\n /** The URI of the respective `dwcFP:TaxonConcept` if it exists */\n taxonConceptURI?: string;\n\n /** The URI of the respective CoL-taxon if it exists */\n colURI?: string;\n /** The URI of the corresponding accepted CoL-taxon if it exists.\n *\n * Always present if colURI is present, they are the same if it is the accepted CoL-Taxon.\n *\n * May be the string \"INVALID COL\" if the colURI is not valid.\n */\n acceptedColURI?: string;\n\n // TODO: sensible?\n // /** these are CoL-taxa linked in the rdf, which differ lexically */\n // seeAlsoCol: string[];\n\n /** treatments directly associated with .taxonConceptURI */\n treatments: {\n def: Set;\n aug: Set;\n dpr: Set;\n cite: Set;\n };\n};\n\n/** A plazi-treatment */\nexport type Treatment = {\n url: string;\n date?: number;\n\n /** Details are behind a promise becuase they are loaded with a separate query. */\n details: Promise;\n};\n\n/** Details of a treatment */\nexport type TreatmentDetails = {\n materialCitations: MaterialCitation[];\n figureCitations: FigureCitation[];\n creators?: string;\n title?: string;\n treats: {\n def: Set;\n aug: Set;\n dpr: Set;\n citetc: Set;\n treattn: Set;\n citetn: Set;\n };\n};\n\n/** A cited material */\nexport type MaterialCitation = {\n \"catalogNumber\": string;\n \"collectionCode\"?: string;\n \"typeStatus\"?: string;\n \"countryCode\"?: string;\n \"stateProvince\"?: string;\n \"municipality\"?: string;\n \"county\"?: string;\n \"locality\"?: string;\n \"verbatimLocality\"?: string;\n \"recordedBy\"?: string;\n \"eventDate\"?: string;\n \"samplingProtocol\"?: string;\n \"decimalLatitude\"?: string;\n \"decimalLongitude\"?: string;\n \"verbatimElevation\"?: string;\n \"gbifOccurrenceId\"?: string;\n \"gbifSpecimenId\"?: string;\n \"httpUri\"?: string[];\n};\n\n/** A cited figure */\nexport type FigureCitation = {\n url: string;\n description?: string;\n};\n", "// Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.\n// This module is browser compatible.\n\n/**\n * Returns all distinct elements in the given array, preserving order by first\n * occurrence.\n *\n * @typeParam T The type of the elements in the input array.\n *\n * @param array The array to filter for distinct elements.\n *\n * @returns An array of distinct elements in the input array.\n *\n * @example Basic usage\n * ```ts\n * import { distinct } from \"@std/collections/distinct\";\n * import { assertEquals } from \"@std/assert\";\n *\n * const numbers = [3, 2, 5, 2, 5];\n * const distinctNumbers = distinct(numbers);\n *\n * assertEquals(distinctNumbers, [3, 2, 5]);\n * ```\n */\nexport function distinct(array: Iterable): T[] {\n const set = new Set(array);\n\n return Array.from(set);\n}\n", "/// \nimport {\n type AuthorizedName,\n type Name,\n SparqlEndpoint,\n SynonymGroup,\n type Treatment,\n} from \"../mod.ts\";\nimport { distinct } from \"jsr:@std/collections/distinct\";\n\nconst params = new URLSearchParams(document.location.search);\nconst HIDE_COL_ONLY_SYNONYMS = !params.has(\"show_col\");\nconst START_WITH_SUBTAXA = params.has(\"subtaxa\");\nconst SORT_TREATMENTS_BY_TYPE = params.has(\"sort_treatments_by_type\");\nconst ENDPOINT_URL = params.get(\"server\") ||\n \"https://treatment.ld.plazi.org/sparql\";\nconst NAME = params.get(\"q\") ||\n \"https://www.catalogueoflife.org/data/taxon/3WD9M\";\n\nconst root = document.getElementById(\"root\") as HTMLDivElement;\n\nenum SynoStatus {\n Def = \"def\",\n Aug = \"aug\",\n Dpr = \"dpr\",\n Cite = \"cite\",\n}\n\nconst icons = {\n def:\n ``,\n aug:\n ``,\n dpr:\n ``,\n cite:\n ``,\n unknown:\n ``,\n\n col_aug:\n ``,\n col_dpr:\n ``,\n\n link:\n ``,\n\n expand:\n ``,\n collapse:\n ``,\n\n east:\n ``,\n west:\n ``,\n empty: ``,\n};\n\nconst indicator = document.createElement(\"div\");\nroot.insertAdjacentElement(\"beforebegin\", indicator);\nindicator.append(`Finding Synonyms for ${NAME} `);\nconst progress = document.createElement(\"progress\");\nindicator.append(progress);\n\nconst timeStart = performance.now();\n\nconst sparqlEndpoint = new SparqlEndpoint(ENDPOINT_URL);\nconst synoGroup = new SynonymGroup(\n sparqlEndpoint,\n NAME,\n HIDE_COL_ONLY_SYNONYMS,\n START_WITH_SUBTAXA,\n);\n\nclass SynoTreatment extends HTMLElement {\n constructor(trt: Treatment, status: SynoStatus) {\n super();\n\n this.innerHTML = icons[status] ?? icons.unknown;\n\n const button = document.createElement(\"button\");\n button.classList.add(\"icon\", \"button\");\n button.innerHTML = icons.expand;\n button.addEventListener(\"click\", () => {\n if (this.classList.toggle(\"expanded\")) {\n button.innerHTML = icons.collapse;\n } else {\n button.innerHTML = icons.expand;\n }\n });\n\n const date = document.createElement(\"span\");\n if (trt.date) date.innerText = \"\" + trt.date;\n else {\n date.classList.add(\"missing\");\n date.innerText = \"No Date\";\n }\n this.append(date);\n\n const spinner = document.createElement(\"progress\");\n this.append(\": \", spinner);\n\n const url = document.createElement(\"a\");\n url.classList.add(\"treatment\", \"uri\");\n url.href = trt.url;\n url.target = \"_blank\";\n url.innerText = trt.url.replace(\"http://treatment.plazi.org/id/\", \"\");\n url.innerHTML += icons.link;\n this.append(\" \", url);\n\n this.append(button);\n\n const names = document.createElement(\"div\");\n names.classList.add(\"indent\", \"details\");\n this.append(names);\n\n trt.details.then((details) => {\n const creators = document.createElement(\"span\");\n const title = document.createElement(\"i\");\n spinner.replaceWith(creators, \" \", title);\n\n if (details.creators) creators.innerText = details.creators;\n else {\n creators.classList.add(\"missing\");\n creators.innerText = \"No Authors\";\n }\n\n if (details.title) title.innerText = \"\u201C\" + details.title + \"\u201D\";\n else {\n title.classList.add(\"missing\");\n title.innerText = \"No Title\";\n }\n\n if (details.treats.def.size > 0) {\n const line = document.createElement(\"div\");\n // line.innerHTML = status === SynoStatus.Cite ? icons.line : icons.east;\n line.innerHTML = icons.east;\n line.innerHTML += icons.def;\n if (status === SynoStatus.Def || status === SynoStatus.Cite) {\n line.classList.add(\"hidden\");\n }\n names.append(line);\n\n details.treats.def.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-concept.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n }\n if (details.treats.aug.size > 0 || details.treats.treattn.size > 0) {\n const line = document.createElement(\"div\");\n // line.innerHTML = status === SynoStatus.Cite ? icons.line : icons.east;\n line.innerHTML = icons.east;\n line.innerHTML += icons.aug;\n if (status === SynoStatus.Aug || status === SynoStatus.Cite) {\n line.classList.add(\"hidden\");\n }\n names.append(line);\n\n details.treats.aug.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-concept.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n details.treats.treattn.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-name.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n }\n if (details.treats.dpr.size > 0) {\n const line = document.createElement(\"div\");\n // line.innerHTML = status === SynoStatus.Cite ? icons.line : icons.west;\n line.innerHTML = icons.west;\n line.innerHTML += icons.dpr;\n if (status === SynoStatus.Dpr || status === SynoStatus.Cite) {\n line.classList.add(\"hidden\");\n }\n names.append(line);\n\n details.treats.dpr.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-concept.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n }\n if (details.treats.citetc.size > 0 || details.treats.citetn.size > 0) {\n const line = document.createElement(\"div\");\n line.innerHTML = icons.empty + icons.cite;\n // if (status === SynoStatus.Dpr || status === SynoStatus.Cite) {\n line.classList.add(\"hidden\");\n // }\n names.append(line);\n\n details.treats.citetc.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-concept.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n details.treats.citetn.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-name.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n }\n if (details.figureCitations.length > 0) {\n const line = document.createElement(\"div\");\n line.classList.add(\"figures\", \"hidden\");\n names.append(line);\n for (const figure of details.figureCitations) {\n const el = document.createElement(\"figure\");\n line.append(el);\n const img = document.createElement(\"img\");\n img.src = figure.url;\n img.loading = \"lazy\";\n img.alt = figure.description ?? \"Cited Figure without caption\";\n el.append(img);\n const caption = document.createElement(\"figcaption\");\n caption.innerText = figure.description ?? \"\";\n el.append(caption);\n }\n }\n if (details.materialCitations.length > 0) {\n const line = document.createElement(\"div\");\n line.innerHTML = icons.empty + icons.cite +\n \" Material Citations:
-\";\n line.classList.add(\"hidden\");\n names.append(line);\n line.innerText += details.materialCitations.map((c) =>\n JSON.stringify(c)\n .replaceAll(\"{\", \"\")\n .replaceAll(\"}\", \"\")\n .replaceAll('\":', \": \")\n .replaceAll(\",\", \", \")\n .replaceAll('\"', \"\")\n ).join(\"\\n -\");\n }\n });\n }\n}\ncustomElements.define(\"syno-treatment\", SynoTreatment);\n\nclass SynoName extends HTMLElement {\n constructor(name: Name) {\n super();\n\n const title = document.createElement(\"h2\");\n const name_title = document.createElement(\"i\");\n name_title.innerText = name.displayName;\n title.append(name_title);\n this.append(title);\n\n const rank_badge = document.createElement(\"span\");\n rank_badge.classList.add(\"rank\");\n rank_badge.innerText = name.rank;\n title.append(\" \", rank_badge);\n\n if (name.taxonNameURI) {\n const name_uri = document.createElement(\"a\");\n name_uri.classList.add(\"taxon\", \"uri\");\n const short = name.taxonNameURI.replace(\n \"http://taxon-name.plazi.org/id/\",\n \"\",\n );\n name_uri.innerText = short;\n name_uri.id = short;\n name_uri.href = name.taxonNameURI;\n name_uri.target = \"_blank\";\n name_uri.innerHTML += icons.link;\n title.append(\" \", name_uri);\n }\n\n const vernacular = document.createElement(\"div\");\n vernacular.classList.add(\"vernacular\");\n name.vernacularNames.then((names) => {\n if (names.size > 0) {\n vernacular.innerText = \"\u201C\" +\n distinct([...names.values()].flat()).join(\"\u201D, \u201C\") + \"\u201D\";\n }\n });\n this.append(vernacular);\n\n const treatments = document.createElement(\"ul\");\n this.append(treatments);\n\n if (name.colURI) {\n const col_uri = document.createElement(\"a\");\n col_uri.classList.add(\"col\", \"uri\");\n const id = name.colURI.replace(\n \"https://www.catalogueoflife.org/data/taxon/\",\n \"\",\n );\n col_uri.innerText = id;\n col_uri.id = id;\n col_uri.href = name.colURI;\n col_uri.target = \"_blank\";\n col_uri.innerHTML += icons.link;\n title.append(\" \", col_uri);\n\n const li = document.createElement(\"div\");\n li.classList.add(\"treatmentline\");\n li.innerHTML = name.acceptedColURI !== name.colURI\n ? 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+ "sourcesContent": ["async function sleep(ms: number): Promise {\n const p = new Promise((resolve) => {\n setTimeout(resolve, ms);\n });\n return await p;\n}\n\n/** Describes the format of the JSON return by SPARQL endpoints */\nexport type SparqlJson = {\n head: {\n vars: string[];\n };\n results: {\n bindings: {\n [key: string]:\n | { type: string; value: string; \"xml:lang\"?: string }\n | undefined;\n }[];\n };\n};\n\n/**\n * Represents a remote sparql endpoint and provides a uniform way to run queries.\n */\nexport class SparqlEndpoint {\n /** Create a new SparqlEndpoint with the given URI */\n constructor(private sparqlEnpointUri: string) {}\n\n /** @ignore */\n // reasons: string[] = [];\n\n /**\n * Run a query against the sparql endpoint\n *\n * It automatically retries up to 10 times on fetch errors, waiting 50ms on the first retry and doupling the wait each time.\n * Retries are logged to the console (`console.warn`)\n *\n * @throws In case of non-ok response status codes or if fetch failed 10 times.\n * @param query The sparql query to run against the endpoint\n * @param fetchOptions Additional options for the `fetch` request\n * @param _reason (Currently ignored, used internally for debugging purposes)\n * @returns Results of the query\n */\n async getSparqlResultSet(\n query: string,\n fetchOptions: RequestInit = {},\n _reason = \"\",\n ): Promise {\n // this.reasons.push(_reason);\n // DEBUG: console.info(`SPARQL ${_reason}:\\n${query}`);\n\n fetchOptions.headers = fetchOptions.headers || {};\n (fetchOptions.headers as Record)[\"Accept\"] =\n \"application/sparql-results+json\";\n let retryCount = 0;\n const sendRequest = async (): Promise => {\n try {\n // DEBUG: console.info(`SPARQL ${_reason} (${retryCount + 1})`);\n const response = await fetch(\n this.sparqlEnpointUri + \"?query=\" + encodeURIComponent(query),\n fetchOptions,\n );\n if (!response.ok) {\n throw new Error(\"Response not ok. Status \" + response.status);\n }\n return await response.json();\n } catch (error) {\n if (fetchOptions.signal?.aborted) {\n throw error;\n } else if (retryCount < 10) {\n const wait = 50 * (1 << retryCount++);\n console.warn(`!! Fetch Error. Retrying in ${wait}ms (${retryCount})`);\n await sleep(wait);\n return await sendRequest();\n }\n console.warn(\"!! Fetch Error:\", query, \"\\n---\\n\", error);\n throw error;\n }\n };\n return await sendRequest();\n }\n}\n", "/**\n * Common to all of the `getNameFrom_`-queries.\n *\n * As its own variable to ensure consistency in the resturned bindings.\n */\nconst preamble = `PREFIX dc: \nPREFIX dwc: \nPREFIX dwcFP: \nPREFIX cito: \nPREFIX trt: \nSELECT DISTINCT ?kingdom ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority\n (group_concat(DISTINCT ?tcauth;separator=\" / \") AS ?tcAuth)\n (group_concat(DISTINCT ?aug;separator=\"|\") as ?augs)\n (group_concat(DISTINCT ?def;separator=\"|\") as ?defs)\n (group_concat(DISTINCT ?dpr;separator=\"|\") as ?dprs)\n (group_concat(DISTINCT ?cite;separator=\"|\") as ?cites)\n (group_concat(DISTINCT ?trtn;separator=\"|\") as ?tntreats)\n (group_concat(DISTINCT ?citetn;separator=\"|\") as ?tncites)`;\n\n/**\n * Common to all of the `getNameFrom_`-queries.\n *\n * As its own variable to ensure consistency in the resturned bindings.\n */\nconst postamble =\n `GROUP BY ?kingdom ?tn ?tc ?col ?rank ?genus ?subgenus ?species ?infrasp ?name ?authority`;\n\n// For unclear reasons, the queries breaks if the limit is removed.\n\n/**\n * Note: this query assumes that there is no sub-species taxa with missing dwc:species\n *\n * Note: the handling assumes that at most one taxon-name matches this colTaxon\n */\nexport const getNameFromCol = (colUri: string) =>\n `${preamble} WHERE {\nBIND(<${colUri}> as ?col)\n ?col dwc:taxonRank ?rank .\n ?col dwc:scientificName ?name .\n ?col dwc:genericName ?genus .\n OPTIONAL { ?col (dwc:parent|dwc:acceptedName)* ?p . ?p dwc:rank \"kingdom\" ; dwc:taxonName ?colkingdom . }\n BIND(COALESCE(?colkingdom, \"\") AS ?kingdom)\n OPTIONAL { ?col dwc:infragenericEpithet ?colsubgenus . }\n BIND(COALESCE(?colsubgenus, \"\") AS ?subgenus)\n OPTIONAL {\n ?col dwc:specificEpithet ?species .\n OPTIONAL { ?col dwc:infraspecificEpithet ?infrasp . }\n }\n OPTIONAL { ?col dwc:scientificNameAuthorship ?authority . }\n\n OPTIONAL {\n ?tn dwc:rank ?trank ;\n a dwcFP:TaxonName .\n FILTER(LCASE(?rank) = LCASE(?trank))\n ?tn dwc:kingdom ?kingdom .\n ?tn dwc:genus ?genus .\n\n OPTIONAL { ?tn dwc:subGenus ?tnsubgenus . }\n FILTER(?subgenus = COALESCE(?tnsubgenus, \"\"))\n OPTIONAL { ?tn dwc:species ?tnspecies . }\n FILTER(?species = COALESCE(?tnspecies, \"\"))\n OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }\n FILTER(?infrasp = COALESCE(?tninfrasp, \"\"))\n\n OPTIONAL {\n ?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .\n BIND(CONCAT(STR(?trtnt), \">\", ?trtndate) AS ?trtn)\n }\n OPTIONAL {\n ?citetnt trt:citesTaxonName ?tn ; trt:publishedIn/dc:date ?citetndate .\n BIND(CONCAT(STR(?citetnt), \">\", ?citetndate) AS ?citetn)\n }\n\n OPTIONAL {\n ?tc trt:hasTaxonName ?tn ; dwc:scientificNameAuthorship ?tcauth ; a dwcFP:TaxonConcept .\n\n OPTIONAL {\n ?augt trt:augmentsTaxonConcept ?tc ; trt:publishedIn/dc:date ?augdate .\n BIND(CONCAT(STR(?augt), \">\", ?augdate) AS ?aug)\n }\n OPTIONAL {\n ?deft trt:definesTaxonConcept ?tc ; trt:publishedIn/dc:date ?defdate .\n BIND(CONCAT(STR(?deft), \">\", ?defdate) AS ?def)\n }\n OPTIONAL {\n ?dprt trt:deprecates ?tc ; trt:publishedIn/dc:date ?dprdate .\n BIND(CONCAT(STR(?dprt), \">\", ?dprdate) AS ?dpr)\n }\n OPTIONAL {\n ?citet cito:cites ?tc ; trt:publishedIn/dc:date ?citedate .\n BIND(CONCAT(STR(?citet), \">\", ?citedate) AS ?cite)\n }\n }\n }\n}\n${postamble}\nLIMIT 500`;\n\n/**\n * Note: this query assumes that there is no sub-species taxa with missing dwc:species\n *\n * Note: the handling assumes that at most one taxon-name matches this colTaxon\n */\nexport const getNameFromTC = (tcUri: string) =>\n `${preamble} WHERE {\n <${tcUri}> trt:hasTaxonName ?tn .\n ?tc trt:hasTaxonName ?tn ;\n dwc:scientificNameAuthorship ?tcauth ;\n a dwcFP:TaxonConcept .\n\n ?tn a dwcFP:TaxonName .\n ?tn dwc:rank ?tnrank .\n ?tn dwc:kingdom ?kingdom .\n ?tn dwc:genus ?genus .\n OPTIONAL { ?tn dwc:subGenus ?tnsubgenus . }\n OPTIONAL {\n ?tn dwc:species ?tnspecies .\n OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }\n }\n \n BIND(LCASE(?tnrank) AS ?rank)\n BIND(COALESCE(?tnsubgenus, \"\") AS ?subgenus)\n BIND(COALESCE(?tnspecies, \"\") AS ?species)\n BIND(COALESCE(?tninfrasp, \"\") AS ?infrasp)\n \n OPTIONAL {\n ?col dwc:taxonRank ?rank .\n ?col dwc:scientificName ?name . # Note: contains authority\n ?col dwc:genericName ?genus .\n OPTIONAL { ?col (dwc:parent|dwc:acceptedName)* ?p . ?p dwc:rank \"kingdom\" ; dwc:taxonName ?colkingdom . }\n FILTER(?kingdom = COALESCE(?colkingdom, \"\"))\n\n OPTIONAL { ?col dwc:infragenericEpithet ?colsubgenus . }\n FILTER(?subgenus = COALESCE(?colsubgenus, \"\"))\n OPTIONAL { ?col dwc:specificEpithet ?colspecies . }\n FILTER(?species = COALESCE(?colspecies, \"\"))\n OPTIONAL { ?col dwc:infraspecificEpithet ?colinfrasp . }\n FILTER(?infrasp = COALESCE(?colinfrasp, \"\"))\n OPTIONAL { ?col dwc:scientificNameAuthorship ?authority . }\n }\n\n OPTIONAL {\n ?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .\n BIND(CONCAT(STR(?trtnt), \">\", ?trtndate) AS ?trtn)\n }\n OPTIONAL {\n ?citetnt trt:citesTaxonName ?tn ; trt:publishedIn/dc:date ?citetndate .\n BIND(CONCAT(STR(?citetnt), \">\", ?citetndate) AS ?citetn)\n }\n\n OPTIONAL {\n ?augt trt:augmentsTaxonConcept ?tc ; trt:publishedIn/dc:date ?augdate .\n BIND(CONCAT(STR(?augt), \">\", ?augdate) AS ?aug)\n }\n OPTIONAL {\n ?deft trt:definesTaxonConcept ?tc ; trt:publishedIn/dc:date ?defdate .\n BIND(CONCAT(STR(?deft), \">\", ?defdate) AS ?def)\n }\n OPTIONAL {\n ?dprt trt:deprecates ?tc ; trt:publishedIn/dc:date ?dprdate .\n BIND(CONCAT(STR(?dprt), \">\", ?dprdate) AS ?dpr)\n }\n OPTIONAL {\n ?citet cito:cites ?tc ; trt:publishedIn/dc:date ?citedate .\n BIND(CONCAT(STR(?citet), \">\", ?citedate) AS ?cite)\n }\n}\n${postamble}\nLIMIT 500`;\n\n/**\n * Note: this query assumes that there is no sub-species taxa with missing dwc:species\n *\n * Note: the handling assumes that at most one taxon-name matches this colTaxon\n */\nexport const getNameFromTN = (tnUri: string) =>\n `${preamble} WHERE {\n BIND(<${tnUri}> as ?tn)\n ?tn a dwcFP:TaxonName .\n ?tn dwc:rank ?tnrank .\n ?tn dwc:genus ?genus .\n ?tn dwc:kingdom ?kingdom .\n OPTIONAL { ?tn dwc:subGenus ?tnsubgenus . }\n OPTIONAL {\n ?tn dwc:species ?tnspecies .\n OPTIONAL { ?tn dwc:subSpecies|dwc:variety|dwc:form ?tninfrasp . }\n }\n \n BIND(LCASE(?tnrank) AS ?rank)\n BIND(COALESCE(?tnsubgenus, \"\") AS ?subgenus)\n BIND(COALESCE(?tnspecies, \"\") AS ?species)\n BIND(COALESCE(?tninfrasp, \"\") AS ?infrasp)\n \n OPTIONAL {\n ?col dwc:taxonRank ?rank .\n ?col dwc:scientificName ?name . # Note: contains authority\n ?col dwc:genericName ?genus .\n OPTIONAL { ?col (dwc:parent|dwc:acceptedName)* ?p . ?p dwc:rank \"kingdom\" ; dwc:taxonName ?colkingdom . }\n FILTER(?kingdom = COALESCE(?colkingdom, \"\"))\n\n OPTIONAL { ?col dwc:infragenericEpithet ?colsubgenus . }\n FILTER(?subgenus = COALESCE(?colsubgenus, \"\"))\n OPTIONAL { ?col dwc:specificEpithet ?colspecies . }\n FILTER(?species = COALESCE(?colspecies, \"\"))\n OPTIONAL { ?col dwc:infraspecificEpithet ?colinfrasp . }\n FILTER(?infrasp = COALESCE(?colinfrasp, \"\"))\n OPTIONAL { ?col dwc:scientificNameAuthorship ?authority . }\n }\n\n OPTIONAL {\n ?trtnt trt:treatsTaxonName ?tn ; trt:publishedIn/dc:date ?trtndate .\n BIND(CONCAT(STR(?trtnt), \">\", ?trtndate) AS ?trtn)\n }\n OPTIONAL {\n ?citetnt trt:citesTaxonName ?tn ; trt:publishedIn/dc:date ?citetndate .\n BIND(CONCAT(STR(?citetnt), \">\", ?citetndate) AS ?citetn)\n }\n\n OPTIONAL {\n ?tc trt:hasTaxonName ?tn ; dwc:scientificNameAuthorship ?tcauth ; a dwcFP:TaxonConcept .\n\n OPTIONAL {\n ?augt trt:augmentsTaxonConcept ?tc ; trt:publishedIn/dc:date ?augdate .\n BIND(CONCAT(STR(?augt), \">\", ?augdate) AS ?aug)\n }\n OPTIONAL {\n ?deft trt:definesTaxonConcept ?tc ; trt:publishedIn/dc:date ?defdate .\n BIND(CONCAT(STR(?deft), \">\", ?defdate) AS ?def)\n }\n OPTIONAL {\n ?dprt trt:deprecates ?tc ; trt:publishedIn/dc:date ?dprdate .\n BIND(CONCAT(STR(?dprt), \">\", ?dprdate) AS ?dpr)\n }\n OPTIONAL {\n ?citet cito:cites ?tc ; trt:publishedIn/dc:date ?citedate .\n BIND(CONCAT(STR(?citet), \">\", ?citedate) AS ?cite)\n }\n }\n}\n${postamble}\nLIMIT 500`;\n", "import type { SparqlEndpoint, SparqlJson } from \"./mod.ts\";\nimport * as Queries from \"./Queries.ts\";\n\n/** Finds all synonyms of a taxon */\nexport class SynonymGroup implements AsyncIterable {\n /** Indicates whether the SynonymGroup has found all synonyms.\n *\n * @readonly\n */\n isFinished = false;\n /** Used internally to watch for new names found */\n private monitor: EventTarget = new EventTarget();\n\n /** Used internally to abort in-flight network requests when SynonymGroup is aborted */\n private controller = new AbortController();\n\n /** The SparqlEndpoint used */\n private sparqlEndpoint: SparqlEndpoint;\n\n /**\n * List of names found so-far.\n *\n * Contains full list of synonyms _if_ .isFinished and not .isAborted\n *\n * @readonly\n */\n names: Name[] = [];\n /**\n * Add a new Name to this.names.\n *\n * Note: does not deduplicate on its own\n *\n * @internal */\n private pushName(name: Name) {\n this.names.push(name);\n this.monitor.dispatchEvent(new CustomEvent(\"updated\"));\n }\n\n /**\n * Call when all synonyms are found\n *\n * @internal */\n private finish() {\n this.isFinished = true;\n this.monitor.dispatchEvent(new CustomEvent(\"updated\"));\n }\n\n /** contains TN, TC, CoL uris of synonyms which are in-flight somehow or are done already */\n private expanded = new Set(); // new Map();\n\n /** contains CoL uris where we don't need to check for Col \"acceptedName\" links\n *\n * col -> accepted col\n */\n private acceptedCol = new Map();\n\n /**\n * Used internally to deduplicate treatments, maps from URI to Object.\n *\n * Contains full list of treatments _if_ .isFinished and not .isAborted\n *\n * @readonly\n */\n treatments: Map = new Map();\n\n /**\n * Whether to show taxa deprecated by CoL that would not have been found otherwise.\n * This significantly increases the number of results in some cases.\n */\n ignoreDeprecatedCoL: boolean;\n\n /**\n * if set to true, subTaxa of the search term are also considered as starting points.\n *\n * Not that \"weird\" ranks like subGenus are always included when searching for a genus by latin name.\n */\n startWithSubTaxa: boolean;\n\n /**\n * Constructs a SynonymGroup\n *\n * @param sparqlEndpoint SPARQL-Endpoint to query\n * @param taxonName either a string of the form \"Genus species infraspecific\" (species & infraspecific names optional), or an URI of a http://filteredpush.org/ontologies/oa/dwcFP#TaxonConcept or ...#TaxonName or a CoL taxon URI\n * @param [ignoreDeprecatedCoL=true] Whether to show taxa deprecated by CoL that would not have been found otherwise\n * @param [startWithSubTaxa=false] if set to true, subTaxa of the search term are also considered as starting points.\n */\n constructor(\n sparqlEndpoint: SparqlEndpoint,\n taxonName: string,\n ignoreDeprecatedCoL = true,\n startWithSubTaxa = false,\n ) {\n this.sparqlEndpoint = sparqlEndpoint;\n this.ignoreDeprecatedCoL = ignoreDeprecatedCoL;\n this.startWithSubTaxa = startWithSubTaxa;\n\n if (taxonName.startsWith(\"http\")) {\n this.getName(taxonName, { searchTerm: true, subTaxon: false })\n .catch((e) => {\n console.log(\"SynoGroup Failure: \", e);\n this.controller.abort(\"SynoGroup Failed\");\n })\n .finally(() => this.finish());\n } else {\n const name = [\n ...taxonName.split(\" \").filter((n) => !!n),\n undefined,\n undefined,\n ] as [string, string | undefined, string | undefined];\n this.getNameFromLatin(name, { searchTerm: true, subTaxon: false })\n .finally(\n () => this.finish(),\n );\n }\n }\n\n /**\n * Finds the given name (identified by taxon-name, taxon-concept or CoL uri) among the list of synonyms.\n *\n * Will reject when the SynonymGroup finishes but the name was not found \u2014 this means that this was not a synonym.\n */\n findName(uri: string): Promise {\n let name: Name | AuthorizedName | undefined;\n for (const n of this.names) {\n if (n.taxonNameURI === uri || n.colURI === uri) {\n name = n;\n break;\n }\n const an = n.authorizedNames.find((an) =>\n an.taxonConceptURI === uri || an.colURI === uri\n );\n if (an) {\n name = an;\n break;\n }\n }\n if (name) return Promise.resolve(name);\n return new Promise((resolve, reject) => {\n this.monitor.addEventListener(\"updated\", () => {\n if (this.names.length === 0 || this.isFinished) reject();\n const n = this.names.at(-1)!;\n if (n.taxonNameURI === uri || n.colURI === uri) {\n resolve(n);\n return;\n }\n const an = n.authorizedNames.find((an) =>\n an.taxonConceptURI === uri || an.colURI === uri\n );\n if (an) {\n resolve(an);\n return;\n }\n });\n });\n }\n\n /** @internal */\n private async getName(\n taxonName: string,\n justification: Justification,\n ): Promise {\n if (this.expanded.has(taxonName)) {\n console.log(\"Skipping known\", taxonName);\n return;\n }\n\n if (this.controller.signal?.aborted) return Promise.reject();\n\n let json: SparqlJson | undefined;\n\n if (taxonName.startsWith(\"https://www.catalogueoflife.org\")) {\n json = await this.sparqlEndpoint.getSparqlResultSet(\n Queries.getNameFromCol(taxonName),\n { signal: this.controller.signal },\n `NameFromCol ${taxonName}`,\n );\n } else if (taxonName.startsWith(\"http://taxon-concept.plazi.org\")) {\n json = await this.sparqlEndpoint.getSparqlResultSet(\n Queries.getNameFromTC(taxonName),\n { signal: this.controller.signal },\n `NameFromTC ${taxonName}`,\n );\n } else if (taxonName.startsWith(\"http://taxon-name.plazi.org\")) {\n json = await this.sparqlEndpoint.getSparqlResultSet(\n Queries.getNameFromTN(taxonName),\n { signal: this.controller.signal },\n `NameFromTN ${taxonName}`,\n );\n } else {\n throw `Cannot handle name-uri <${taxonName}> !`;\n }\n\n await this.handleName(json!, justification);\n\n if (\n this.startWithSubTaxa && justification.searchTerm &&\n !justification.subTaxon\n ) {\n await this.getSubtaxa(taxonName);\n }\n }\n\n /** @internal */\n private async getSubtaxa(url: string): Promise {\n const query = url.startsWith(\"http://taxon-concept.plazi.org\")\n ? `\nPREFIX trt: \nSELECT DISTINCT ?sub WHERE {\n BIND(<${url}> as ?url)\n ?sub trt:hasParentName*/^trt:hasTaxonName ?url .\n}\nLIMIT 5000`\n : `\nPREFIX dwc: \nPREFIX trt: \nSELECT DISTINCT ?sub WHERE {\n BIND(<${url}> as ?url)\n ?sub (dwc:parent|trt:hasParentName)* ?url .\n}\nLIMIT 5000`;\n\n if (this.controller.signal?.aborted) return Promise.reject();\n const json = await this.sparqlEndpoint.getSparqlResultSet(\n query,\n { signal: this.controller.signal },\n `Subtaxa ${url}`,\n );\n\n const names = json.results.bindings\n .map((n) => n.sub?.value)\n .filter((n) => n && !this.expanded.has(n)) as string[];\n\n await Promise.allSettled(\n names.map((n) => this.getName(n, { searchTerm: true, subTaxon: true })),\n );\n }\n\n /** @internal */\n private async getNameFromLatin(\n [genus, species, infrasp]: [string, string | undefined, string | undefined],\n justification: Justification,\n ): Promise {\n const query = `\n PREFIX dwc: \nSELECT DISTINCT ?uri WHERE {\n ?uri dwc:genus|dwc:genericName \"${genus}\" .\n ${\n species\n ? `?uri dwc:species|dwc:specificEpithet \"${species}\" .`\n : \"FILTER NOT EXISTS { ?uri dwc:species|dwc:specificEpithet ?species . }\"\n }\n ${\n infrasp\n ? `?uri dwc:subSpecies|dwc:variety|dwc:form|dwc:infraspecificEpithet \"${infrasp}\" .`\n : \"FILTER NOT EXISTS { ?uri dwc:subSpecies|dwc:variety|dwc:form|dwc:infraspecificEpithet ?infrasp . }\"\n }\n}\nLIMIT 500`;\n\n if (this.controller.signal?.aborted) return Promise.reject();\n const json = await this.sparqlEndpoint.getSparqlResultSet(\n query,\n { signal: this.controller.signal },\n `NameFromLatin ${genus} ${species} ${infrasp}`,\n );\n\n const names = json.results.bindings\n .map((n) => n.uri?.value)\n .filter((n) => n && !this.expanded.has(n)) as string[];\n\n await Promise.allSettled(names.map((n) => this.getName(n, justification)));\n }\n\n /**\n * Note this makes some assumptions on which variables are present in the bindings\n *\n * @internal */\n private async handleName(\n json: SparqlJson,\n justification: Justification,\n ): Promise {\n const treatmentPromises: Treatment[] = [];\n\n const abbreviateRank = (rank: string) => {\n switch (rank) {\n case \"variety\":\n return \"var.\";\n case \"subspecies\":\n return \"subsp.\";\n case \"form\":\n return \"f.\";\n default:\n return rank;\n }\n };\n\n const displayName: string = (json.results.bindings[0].name\n ? (\n json.results.bindings[0].authority\n ? json.results.bindings[0].name.value\n .replace(\n json.results.bindings[0].authority.value,\n \"\",\n )\n : json.results.bindings[0].name.value\n )\n : json.results.bindings[0].genus!.value +\n (json.results.bindings[0].subgenus?.value\n ? ` (${json.results.bindings[0].subgenus.value})`\n : \"\") +\n (json.results.bindings[0].species?.value\n ? ` ${json.results.bindings[0].species.value}`\n : \"\") +\n (json.results.bindings[0].infrasp?.value\n ? ` ${abbreviateRank(json.results.bindings[0].rank!.value)} ${\n json.results.bindings[0].infrasp.value\n }`\n : \"\")).trim();\n\n // Case where the CoL-taxon has no authority. There should only be one of these.\n let unathorizedCol: string | undefined;\n\n // there can be multiple CoL-taxa with same latin name, e.g. Leontopodium alpinum has 3T6ZY and 3T6ZX.\n const authorizedCoLNames: AuthorizedName[] = [];\n const authorizedTCNames: AuthorizedName[] = [];\n\n const taxonNameURI = json.results.bindings[0].tn?.value;\n if (taxonNameURI) {\n if (this.expanded.has(taxonNameURI)) return;\n this.expanded.add(taxonNameURI); //, NameStatus.madeName);\n }\n\n for (const t of json.results.bindings) {\n if (t.col) {\n const colURI = t.col.value;\n if (!t.authority?.value) {\n if (this.expanded.has(colURI)) {\n console.log(\"Skipping known\", colURI);\n return;\n }\n if (unathorizedCol && unathorizedCol !== colURI) {\n console.log(\"Duplicate unathorized COL:\", unathorizedCol, colURI);\n }\n unathorizedCol = colURI;\n } else if (!authorizedCoLNames.find((e) => e.colURI === colURI)) {\n if (this.expanded.has(colURI)) {\n console.log(\"Skipping known\", colURI);\n return;\n }\n authorizedCoLNames.push({\n displayName,\n authority: t.authority!.value,\n colURI: t.col.value,\n treatments: {\n def: new Set(),\n aug: new Set(),\n dpr: new Set(),\n cite: new Set(),\n },\n });\n }\n }\n\n if (t.tc && t.tcAuth && t.tcAuth.value) {\n const def = this.makeTreatmentSet(t.defs?.value.split(\"|\"));\n const aug = this.makeTreatmentSet(t.augs?.value.split(\"|\"));\n const dpr = this.makeTreatmentSet(t.dprs?.value.split(\"|\"));\n const cite = this.makeTreatmentSet(t.cites?.value.split(\"|\"));\n\n const colName = authorizedCoLNames.find((e) =>\n t.tcAuth!.value.split(\" / \").includes(e.authority)\n );\n if (colName) {\n colName.authority = t.tcAuth?.value;\n colName.taxonConceptURI = t.tc.value;\n colName.treatments = {\n def,\n aug,\n dpr,\n cite,\n };\n } else if (this.expanded.has(t.tc.value)) {\n // console.log(\"Skipping known\", t.tc.value);\n return;\n } else {\n authorizedTCNames.push({\n displayName,\n authority: t.tcAuth.value,\n taxonConceptURI: t.tc.value,\n treatments: {\n def,\n aug,\n dpr,\n cite,\n },\n });\n }\n\n def.forEach((t) => treatmentPromises.push(t));\n aug.forEach((t) => treatmentPromises.push(t));\n dpr.forEach((t) => treatmentPromises.push(t));\n }\n }\n\n const treats = this.makeTreatmentSet(\n json.results.bindings[0].tntreats?.value.split(\"|\"),\n );\n treats.forEach((t) => treatmentPromises.push(t));\n\n const name: Name = {\n kingdom: json.results.bindings[0].kingdom!.value,\n displayName,\n rank: json.results.bindings[0].rank!.value,\n taxonNameURI,\n authorizedNames: [...authorizedCoLNames, ...authorizedTCNames],\n colURI: unathorizedCol,\n justification,\n treatments: {\n treats,\n cite: this.makeTreatmentSet(\n json.results.bindings[0].tncites?.value.split(\"|\"),\n ),\n },\n vernacularNames: taxonNameURI\n ? this.getVernacular(taxonNameURI)\n : Promise.resolve(new Map()),\n };\n\n for (const authName of name.authorizedNames) {\n if (authName.colURI) this.expanded.add(authName.colURI);\n if (authName.taxonConceptURI) this.expanded.add(authName.taxonConceptURI);\n }\n\n const colPromises: Promise[] = [];\n\n if (unathorizedCol) {\n const [acceptedColURI, promises] = await this.getAcceptedCol(\n unathorizedCol,\n name,\n );\n name.acceptedColURI = acceptedColURI;\n colPromises.push(...promises);\n }\n\n await Promise.all(\n authorizedCoLNames.map(async (n) => {\n const [acceptedColURI, promises] = await this.getAcceptedCol(\n n.colURI!,\n name,\n );\n n.acceptedColURI = acceptedColURI;\n colPromises.push(...promises);\n }),\n );\n\n this.pushName(name);\n\n /** Map */\n const newSynonyms = new Map();\n (await Promise.all(\n treatmentPromises.map((treat) =>\n treat.details.then((d): [Treatment, TreatmentDetails] => {\n return [treat, d];\n })\n ),\n )).map(([treat, d]) => {\n d.treats.aug.difference(this.expanded).forEach((s) =>\n newSynonyms.set(s, treat)\n );\n d.treats.def.difference(this.expanded).forEach((s) =>\n newSynonyms.set(s, treat)\n );\n d.treats.dpr.difference(this.expanded).forEach((s) =>\n newSynonyms.set(s, treat)\n );\n d.treats.treattn.difference(this.expanded).forEach((s) =>\n newSynonyms.set(s, treat)\n );\n });\n\n await Promise.allSettled(\n [\n ...colPromises,\n ...[...newSynonyms].map(([n, treatment]) =>\n this.getName(n, { searchTerm: false, parent: name, treatment })\n ),\n ],\n );\n }\n\n /** @internal */\n private async getAcceptedCol(\n colUri: string,\n parent: Name,\n ): Promise<[string, Promise[]]> {\n const query = `\nPREFIX dwc: \nSELECT DISTINCT ?current ?current_status (GROUP_CONCAT(DISTINCT ?dpr; separator=\"|\") AS ?dprs) WHERE {\n BIND(<${colUri}> AS ?col)\n {\n ?col dwc:acceptedName ?current .\n ?dpr dwc:acceptedName ?current .\n OPTIONAL { ?current dwc:taxonomicStatus ?current_status . }\n } UNION {\n ?col dwc:taxonomicStatus ?current_status .\n OPTIONAL { ?dpr dwc:acceptedName ?col . }\n FILTER NOT EXISTS { ?col dwc:acceptedName ?_ . }\n BIND(?col AS ?current)\n }\n}\nGROUP BY ?current ?current_status`;\n\n if (this.acceptedCol.has(colUri)) {\n return [this.acceptedCol.get(colUri)!, []];\n }\n\n const json = await this.sparqlEndpoint.getSparqlResultSet(\n query,\n { signal: this.controller.signal },\n `AcceptedCol ${colUri}`,\n );\n\n const promises: Promise[] = [];\n\n for (const b of json.results.bindings) {\n for (const dpr of b.dprs!.value.split(\"|\")) {\n if (dpr) {\n if (!this.acceptedCol.has(b.current!.value)) {\n this.acceptedCol.set(b.current!.value, b.current!.value);\n promises.push(\n this.getName(b.current!.value, {\n searchTerm: false,\n parent,\n }),\n );\n }\n\n this.acceptedCol.set(dpr, b.current!.value);\n if (!this.ignoreDeprecatedCoL) {\n promises.push(\n this.getName(dpr, { searchTerm: false, parent }),\n );\n }\n }\n }\n }\n\n if (json.results.bindings.length === 0) {\n // the provided colUri is not in CoL\n // promises === []\n if (!this.acceptedCol.has(colUri)) {\n this.acceptedCol.set(colUri, \"INVALID COL\");\n }\n return [this.acceptedCol.get(colUri)!, promises];\n }\n\n if (!this.acceptedCol.has(colUri)) this.acceptedCol.set(colUri, colUri);\n return [this.acceptedCol.get(colUri)!, promises];\n }\n\n /** @internal */\n private async getVernacular(uri: string): Promise {\n const result: vernacularNames = new Map();\n const query =\n `SELECT DISTINCT ?n WHERE { <${uri}> ?n . }`;\n const bindings = (await this.sparqlEndpoint.getSparqlResultSet(query, {\n signal: this.controller.signal,\n }, `Vernacular ${uri}`)).results.bindings;\n for (const b of bindings) {\n if (b.n?.value) {\n if (b.n[\"xml:lang\"]) {\n if (result.has(b.n[\"xml:lang\"])) {\n result.get(b.n[\"xml:lang\"])!.push(b.n.value);\n } else result.set(b.n[\"xml:lang\"], [b.n.value]);\n } else {\n if (result.has(\"??\")) result.get(\"??\")!.push(b.n.value);\n else result.set(\"??\", [b.n.value]);\n }\n }\n }\n return result;\n }\n\n /** @internal\n *\n * the supplied \"urls\" must be of the form \"URL>DATE\"\n */\n private makeTreatmentSet(urls?: string[]): Set {\n if (!urls) return new Set();\n return new Set(\n urls.filter((url) => !!url).map((url_d) => {\n const [url, date] = url_d.split(\">\");\n if (!this.treatments.has(url)) {\n const details = this.getTreatmentDetails(url);\n this.treatments.set(url, {\n url,\n date: date ? parseInt(date, 10) : undefined,\n details,\n });\n }\n return this.treatments.get(url) as Treatment;\n }),\n );\n }\n\n /** @internal */\n private async getTreatmentDetails(\n treatmentUri: string,\n ): Promise {\n const query = `\nPREFIX dc: \nPREFIX dwc: \nPREFIX dwcFP: \nPREFIX cito: \nPREFIX trt: \nSELECT DISTINCT\n ?date ?title ?mc\n (group_concat(DISTINCT ?catalogNumber;separator=\" / \") as ?catalogNumbers)\n (group_concat(DISTINCT ?collectionCode;separator=\" / \") as ?collectionCodes)\n (group_concat(DISTINCT ?typeStatus;separator=\" / \") as ?typeStatuss)\n (group_concat(DISTINCT ?countryCode;separator=\" / \") as ?countryCodes)\n (group_concat(DISTINCT ?stateProvince;separator=\" / \") as ?stateProvinces)\n (group_concat(DISTINCT ?municipality;separator=\" / \") as ?municipalitys)\n (group_concat(DISTINCT ?county;separator=\" / \") as ?countys)\n (group_concat(DISTINCT ?locality;separator=\" / \") as ?localitys)\n (group_concat(DISTINCT ?verbatimLocality;separator=\" / \") as ?verbatimLocalitys)\n (group_concat(DISTINCT ?recordedBy;separator=\" / \") as ?recordedBys)\n (group_concat(DISTINCT ?eventDate;separator=\" / \") as ?eventDates)\n (group_concat(DISTINCT ?samplingProtocol;separator=\" / \") as ?samplingProtocols)\n (group_concat(DISTINCT ?decimalLatitude;separator=\" / \") as ?decimalLatitudes)\n (group_concat(DISTINCT ?decimalLongitude;separator=\" / \") as ?decimalLongitudes)\n (group_concat(DISTINCT ?verbatimElevation;separator=\" / \") as ?verbatimElevations)\n (group_concat(DISTINCT ?gbifOccurrenceId;separator=\" / \") as ?gbifOccurrenceIds)\n (group_concat(DISTINCT ?gbifSpecimenId;separator=\" / \") as ?gbifSpecimenIds)\n (group_concat(DISTINCT ?creator;separator=\"; \") as ?creators)\n (group_concat(DISTINCT ?httpUri;separator=\"|\") as ?httpUris)\n (group_concat(DISTINCT ?aug;separator=\"|\") as ?augs)\n (group_concat(DISTINCT ?def;separator=\"|\") as ?defs)\n (group_concat(DISTINCT ?dpr;separator=\"|\") as ?dprs)\n (group_concat(DISTINCT ?cite;separator=\"|\") as ?cites)\n (group_concat(DISTINCT ?trttn;separator=\"|\") as ?trttns)\n (group_concat(DISTINCT ?citetn;separator=\"|\") as ?citetns)\nWHERE {\n BIND (<${treatmentUri}> as ?treatment)\n ?treatment dc:creator ?creator .\n OPTIONAL { ?treatment dc:title ?title }\n OPTIONAL { ?treatment trt:augmentsTaxonConcept ?aug . }\n OPTIONAL { ?treatment trt:definesTaxonConcept ?def . }\n OPTIONAL { ?treatment trt:deprecates ?dpr . }\n OPTIONAL { ?treatment cito:cites ?cite . ?cite a dwcFP:TaxonConcept . }\n OPTIONAL { ?treatment trt:treatsTaxonName ?trttn . }\n OPTIONAL { ?treatment trt:citesTaxonName ?citetn . }\n OPTIONAL {\n ?treatment dwc:basisOfRecord ?mc .\n ?mc dwc:catalogNumber ?catalogNumber .\n OPTIONAL { ?mc dwc:collectionCode ?collectionCode . }\n OPTIONAL { ?mc dwc:typeStatus ?typeStatus . }\n OPTIONAL { ?mc dwc:countryCode ?countryCode . }\n OPTIONAL { ?mc dwc:stateProvince ?stateProvince . }\n OPTIONAL { ?mc dwc:municipality ?municipality . }\n OPTIONAL { ?mc dwc:county ?county . }\n OPTIONAL { ?mc dwc:locality ?locality . }\n OPTIONAL { ?mc dwc:verbatimLocality ?verbatimLocality . }\n OPTIONAL { ?mc dwc:recordedBy ?recordedBy . }\n OPTIONAL { ?mc dwc:eventDate ?eventDate . }\n OPTIONAL { ?mc dwc:samplingProtocol ?samplingProtocol . }\n OPTIONAL { ?mc dwc:decimalLatitude ?decimalLatitude . }\n OPTIONAL { ?mc dwc:decimalLongitude ?decimalLongitude . }\n OPTIONAL { ?mc dwc:verbatimElevation ?verbatimElevation . }\n OPTIONAL { ?mc trt:gbifOccurrenceId ?gbifOccurrenceId . }\n OPTIONAL { ?mc trt:gbifSpecimenId ?gbifSpecimenId . }\n OPTIONAL { ?mc trt:httpUri ?httpUri . }\n }\n}\nGROUP BY ?date ?title ?mc`;\n if (this.controller.signal.aborted) {\n return {\n materialCitations: [],\n figureCitations: [],\n treats: {\n def: new Set(),\n aug: new Set(),\n dpr: new Set(),\n citetc: new Set(),\n treattn: new Set(),\n citetn: new Set(),\n },\n };\n }\n try {\n const json = await this.sparqlEndpoint.getSparqlResultSet(\n query,\n { signal: this.controller.signal },\n `TreatmentDetails ${treatmentUri}`,\n );\n const materialCitations: MaterialCitation[] = json.results.bindings\n .filter((t) => t.mc && t.catalogNumbers?.value)\n .map((t) => {\n const httpUri = t.httpUris?.value?.split(\"|\");\n return {\n \"catalogNumber\": t.catalogNumbers!.value,\n \"collectionCode\": t.collectionCodes?.value || undefined,\n \"typeStatus\": t.typeStatuss?.value || undefined,\n \"countryCode\": t.countryCodes?.value || undefined,\n \"stateProvince\": t.stateProvinces?.value || undefined,\n \"municipality\": t.municipalitys?.value || undefined,\n \"county\": t.countys?.value || undefined,\n \"locality\": t.localitys?.value || undefined,\n \"verbatimLocality\": t.verbatimLocalitys?.value || undefined,\n \"recordedBy\": t.recordedBys?.value || undefined,\n \"eventDate\": t.eventDates?.value || undefined,\n \"samplingProtocol\": t.samplingProtocols?.value || undefined,\n \"decimalLatitude\": t.decimalLatitudes?.value || undefined,\n \"decimalLongitude\": t.decimalLongitudes?.value || undefined,\n \"verbatimElevation\": t.verbatimElevations?.value || undefined,\n \"gbifOccurrenceId\": t.gbifOccurrenceIds?.value || undefined,\n \"gbifSpecimenId\": t.gbifSpecimenIds?.value || undefined,\n httpUri: httpUri?.length ? httpUri : undefined,\n };\n });\n const figureQuery = `\nPREFIX cito: \nPREFIX fabio: \nPREFIX dc: \nSELECT DISTINCT ?url ?description WHERE {\n <${treatmentUri}> cito:cites ?cites .\n ?cites a fabio:Figure ;\n fabio:hasRepresentation ?url .\n OPTIONAL { ?cites dc:description ?description . }\n} `;\n const figures = (await this.sparqlEndpoint.getSparqlResultSet(\n figureQuery,\n { signal: this.controller.signal },\n `TreatmentDetails/Figures ${treatmentUri}`,\n )).results.bindings;\n const figureCitations = figures.filter((f) => f.url?.value).map(\n (f) => {\n return { url: f.url!.value, description: f.description?.value };\n },\n );\n return {\n creators: json.results.bindings[0]?.creators?.value,\n title: json.results.bindings[0]?.title?.value,\n materialCitations,\n figureCitations,\n treats: {\n def: new Set(\n json.results.bindings[0]?.defs?.value\n ? json.results.bindings[0].defs.value.split(\"|\")\n : undefined,\n ),\n aug: new Set(\n json.results.bindings[0]?.augs?.value\n ? json.results.bindings[0].augs.value.split(\"|\")\n : undefined,\n ),\n dpr: new Set(\n json.results.bindings[0]?.dprs?.value\n ? json.results.bindings[0].dprs.value.split(\"|\")\n : undefined,\n ),\n citetc: new Set(\n json.results.bindings[0]?.cites?.value\n ? json.results.bindings[0].cites.value.split(\"|\")\n : undefined,\n ),\n treattn: new Set(\n json.results.bindings[0]?.trttns?.value\n ? json.results.bindings[0].trttns.value.split(\"|\")\n : undefined,\n ),\n citetn: new Set(\n json.results.bindings[0]?.citetns?.value\n ? json.results.bindings[0].citetns.value.split(\"|\")\n : undefined,\n ),\n },\n };\n } catch (error) {\n console.warn(\"SPARQL Error: \" + error);\n return {\n materialCitations: [],\n figureCitations: [],\n treats: {\n def: new Set(),\n aug: new Set(),\n dpr: new Set(),\n citetc: new Set(),\n treattn: new Set(),\n citetn: new Set(),\n },\n };\n }\n }\n\n /** Allows iterating over the synonyms while they are found */\n [Symbol.asyncIterator](): AsyncIterator {\n let returnedSoFar = 0;\n return {\n next: () =>\n new Promise>(\n (resolve, reject) => {\n const callback = () => {\n if (this.controller.signal.aborted) {\n reject(new Error(\"SynyonymGroup has been aborted\"));\n } else if (returnedSoFar < this.names.length) {\n resolve({ value: this.names[returnedSoFar++] });\n } else if (this.isFinished) {\n resolve({ done: true, value: true });\n } else {\n const listener = () => {\n this.monitor.removeEventListener(\"updated\", listener);\n callback();\n };\n this.monitor.addEventListener(\"updated\", listener);\n }\n };\n callback();\n },\n ),\n };\n }\n}\n\n// TODO: CoL taxa without authority -- associate them with the Name directly\n// eg. 5KTTT is \"Quercus robur subsp. robur\" w/o authority\n\n/** The central object.\n *\n * Each `Name` exists because of a taxon-name, taxon-concept or col-taxon in the data.\n * Each `Name` is uniquely determined by its human-readable latin name (for taxa ranking below genus, this is a multi-part name \u2014 binomial or trinomial) and kingdom.\n */\nexport type Name = {\n /** taxonomic kingdom\n *\n * may be empty for some CoL-taxa with missing ancestors */\n kingdom: string;\n /** Human-readable name */\n displayName: string;\n /** taxonomic rank */\n rank: string;\n\n /** vernacular names */\n vernacularNames: Promise;\n\n // /** Contains the family tree / upper taxons accorindg to CoL / treatmentbank.\n // * //TODO */\n // trees: Promise<{\n // col?: Tree;\n // tb?: Tree;\n // }>;\n\n /** The URI of the respective `dwcFP:TaxonName` if it exists */\n taxonNameURI?: string;\n\n /**\n * The URI of the respective CoL-taxon if it exists\n *\n * Not that this is only for CoL-taxa which do not have an authority.\n */\n colURI?: string;\n /** The URI of the corresponding accepted CoL-taxon if it exists.\n *\n * Always present if colURI is present, they are the same if it is the accepted CoL-Taxon.\n *\n * May be the string \"INVALID COL\" if the colURI is not valid.\n */\n acceptedColURI?: string;\n\n /** All `AuthorizedName`s with this name */\n authorizedNames: AuthorizedName[];\n\n /** How this name was found */\n justification: Justification;\n\n /** treatments directly associated with .taxonNameUri */\n treatments: {\n treats: Set;\n cite: Set;\n };\n};\n\n/**\n * A map from language tags (IETF) to an array of vernacular names.\n */\nexport type vernacularNames = Map;\n\n/** Why a given Name was found (ther migth be other possible justifications) */\nexport type Justification = {\n searchTerm: true;\n /** indicates that this is a subTaxon of the parent */\n subTaxon: boolean;\n} | {\n searchTerm: false;\n parent: Name;\n /** if missing, indicates synonymy according to CoL or subTaxon */\n treatment?: Treatment;\n};\n\n/**\n * Corresponds to a taxon-concept or a CoL-Taxon\n */\nexport type AuthorizedName = {\n // TODO: neccesary?\n /** this may not be neccesary, as `AuthorizedName`s should only appear within a `Name` */\n // name: Name;\n /** Human-readable name */\n displayName: string;\n /** Human-readable authority */\n authority: string;\n\n /** The URI of the respective `dwcFP:TaxonConcept` if it exists */\n taxonConceptURI?: string;\n\n /** The URI of the respective CoL-taxon if it exists */\n colURI?: string;\n /** The URI of the corresponding accepted CoL-taxon if it exists.\n *\n * Always present if colURI is present, they are the same if it is the accepted CoL-Taxon.\n *\n * May be the string \"INVALID COL\" if the colURI is not valid.\n */\n acceptedColURI?: string;\n\n // TODO: sensible?\n // /** these are CoL-taxa linked in the rdf, which differ lexically */\n // seeAlsoCol: string[];\n\n /** treatments directly associated with .taxonConceptURI */\n treatments: {\n def: Set;\n aug: Set;\n dpr: Set;\n cite: Set;\n };\n};\n\n/** A plazi-treatment */\nexport type Treatment = {\n url: string;\n date?: number;\n\n /** Details are behind a promise becuase they are loaded with a separate query. */\n details: Promise;\n};\n\n/** Details of a treatment */\nexport type TreatmentDetails = {\n materialCitations: MaterialCitation[];\n figureCitations: FigureCitation[];\n creators?: string;\n title?: string;\n treats: {\n def: Set;\n aug: Set;\n dpr: Set;\n citetc: Set;\n treattn: Set;\n citetn: Set;\n };\n};\n\n/** A cited material */\nexport type MaterialCitation = {\n \"catalogNumber\": string;\n \"collectionCode\"?: string;\n \"typeStatus\"?: string;\n \"countryCode\"?: string;\n \"stateProvince\"?: string;\n \"municipality\"?: string;\n \"county\"?: string;\n \"locality\"?: string;\n \"verbatimLocality\"?: string;\n \"recordedBy\"?: string;\n \"eventDate\"?: string;\n \"samplingProtocol\"?: string;\n \"decimalLatitude\"?: string;\n \"decimalLongitude\"?: string;\n \"verbatimElevation\"?: string;\n \"gbifOccurrenceId\"?: string;\n \"gbifSpecimenId\"?: string;\n \"httpUri\"?: string[];\n};\n\n/** A cited figure */\nexport type FigureCitation = {\n url: string;\n description?: string;\n};\n", "// Copyright 2018-2024 the Deno authors. All rights reserved. MIT license.\n// This module is browser compatible.\n\n/**\n * Returns all distinct elements in the given array, preserving order by first\n * occurrence.\n *\n * @typeParam T The type of the elements in the input array.\n *\n * @param array The array to filter for distinct elements.\n *\n * @returns An array of distinct elements in the input array.\n *\n * @example Basic usage\n * ```ts\n * import { distinct } from \"@std/collections/distinct\";\n * import { assertEquals } from \"@std/assert\";\n *\n * const numbers = [3, 2, 5, 2, 5];\n * const distinctNumbers = distinct(numbers);\n *\n * assertEquals(distinctNumbers, [3, 2, 5]);\n * ```\n */\nexport function distinct(array: Iterable): T[] {\n const set = new Set(array);\n\n return Array.from(set);\n}\n", "/// \nimport {\n type AuthorizedName,\n type Name,\n SparqlEndpoint,\n SynonymGroup,\n type Treatment,\n} from \"../mod.ts\";\nimport { distinct } from \"jsr:@std/collections/distinct\";\n\nconst params = new URLSearchParams(document.location.search);\nconst HIDE_COL_ONLY_SYNONYMS = !params.has(\"show_col\");\nconst START_WITH_SUBTAXA = params.has(\"subtaxa\");\nconst SORT_TREATMENTS_BY_TYPE = params.has(\"sort_treatments_by_type\");\nconst ENDPOINT_URL = params.get(\"server\") ||\n \"https://treatment.ld.plazi.org/sparql\";\nconst NAME = params.get(\"q\") ||\n \"https://www.catalogueoflife.org/data/taxon/3WD9M\";\n\nconst root = document.getElementById(\"root\") as HTMLDivElement;\n\nenum SynoStatus {\n Def = \"def\",\n Aug = \"aug\",\n Dpr = \"dpr\",\n Cite = \"cite\",\n}\n\nconst icons = {\n def:\n ``,\n aug:\n ``,\n dpr:\n ``,\n cite:\n ``,\n unknown:\n ``,\n\n col_aug:\n ``,\n col_dpr:\n ``,\n\n link:\n ``,\n\n expand:\n ``,\n collapse:\n ``,\n\n east:\n ``,\n west:\n ``,\n empty: ``,\n};\n\nconst indicator = document.createElement(\"div\");\nroot.insertAdjacentElement(\"beforebegin\", indicator);\nindicator.append(`Finding Synonyms for ${NAME} `);\nconst progress = document.createElement(\"progress\");\nindicator.append(progress);\n\nconst timeStart = performance.now();\n\nconst sparqlEndpoint = new SparqlEndpoint(ENDPOINT_URL);\nconst synoGroup = new SynonymGroup(\n sparqlEndpoint,\n NAME,\n HIDE_COL_ONLY_SYNONYMS,\n START_WITH_SUBTAXA,\n);\n\nclass SynoTreatment extends HTMLElement {\n constructor(trt: Treatment, status: SynoStatus) {\n super();\n\n this.innerHTML = icons[status] ?? icons.unknown;\n\n const button = document.createElement(\"button\");\n button.classList.add(\"icon\", \"button\");\n button.innerHTML = icons.expand;\n button.addEventListener(\"click\", () => {\n if (this.classList.toggle(\"expanded\")) {\n button.innerHTML = icons.collapse;\n } else {\n button.innerHTML = icons.expand;\n }\n });\n\n const date = document.createElement(\"span\");\n if (trt.date) date.innerText = \"\" + trt.date;\n else {\n date.classList.add(\"missing\");\n date.innerText = \"No Date\";\n }\n this.append(date);\n\n const spinner = document.createElement(\"progress\");\n this.append(\": \", spinner);\n\n const url = document.createElement(\"a\");\n url.classList.add(\"treatment\", \"uri\");\n url.href = trt.url;\n url.target = \"_blank\";\n url.innerText = trt.url.replace(\"http://treatment.plazi.org/id/\", \"\");\n url.innerHTML += icons.link;\n this.append(\" \", url);\n\n this.append(button);\n\n const names = document.createElement(\"div\");\n names.classList.add(\"indent\", \"details\");\n this.append(names);\n\n trt.details.then((details) => {\n const creators = document.createElement(\"span\");\n const title = document.createElement(\"i\");\n spinner.replaceWith(creators, \" \", title);\n\n if (details.creators) creators.innerText = details.creators;\n else {\n creators.classList.add(\"missing\");\n creators.innerText = \"No Authors\";\n }\n\n if (details.title) title.innerText = \"\u201C\" + details.title + \"\u201D\";\n else {\n title.classList.add(\"missing\");\n title.innerText = \"No Title\";\n }\n\n if (details.treats.def.size > 0) {\n const line = document.createElement(\"div\");\n // line.innerHTML = status === SynoStatus.Cite ? icons.line : icons.east;\n line.innerHTML = icons.east;\n line.innerHTML += icons.def;\n if (status === SynoStatus.Def || status === SynoStatus.Cite) {\n line.classList.add(\"hidden\");\n }\n names.append(line);\n\n details.treats.def.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-concept.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n }\n if (details.treats.aug.size > 0 || details.treats.treattn.size > 0) {\n const line = document.createElement(\"div\");\n // line.innerHTML = status === SynoStatus.Cite ? icons.line : icons.east;\n line.innerHTML = icons.east;\n line.innerHTML += icons.aug;\n if (status === SynoStatus.Aug || status === SynoStatus.Cite) {\n line.classList.add(\"hidden\");\n }\n names.append(line);\n\n details.treats.aug.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-concept.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n details.treats.treattn.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-name.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n }\n if (details.treats.dpr.size > 0) {\n const line = document.createElement(\"div\");\n // line.innerHTML = status === SynoStatus.Cite ? icons.line : icons.west;\n line.innerHTML = icons.west;\n line.innerHTML += icons.dpr;\n if (status === SynoStatus.Dpr || status === SynoStatus.Cite) {\n line.classList.add(\"hidden\");\n }\n names.append(line);\n\n details.treats.dpr.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-concept.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n }\n if (details.treats.citetc.size > 0 || details.treats.citetn.size > 0) {\n const line = document.createElement(\"div\");\n line.innerHTML = icons.empty + icons.cite;\n // if (status === SynoStatus.Dpr || status === SynoStatus.Cite) {\n line.classList.add(\"hidden\");\n // }\n names.append(line);\n\n details.treats.citetc.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-concept.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n details.treats.citetn.forEach((n) => {\n const url = document.createElement(\"a\");\n url.classList.add(\"taxon\", \"uri\");\n const short = n.replace(\"http://taxon-name.plazi.org/id/\", \"\");\n url.innerText = short;\n url.href = \"#\" + short;\n url.title = \"show name\";\n line.append(\" \", url);\n synoGroup.findName(n).then((nn) => {\n url.classList.remove(\"uri\");\n if ((nn as AuthorizedName).authority) {\n url.innerText = nn.displayName + \" \" +\n (nn as AuthorizedName).authority;\n } else url.innerText = nn.displayName;\n }, () => {\n url.removeAttribute(\"href\");\n });\n });\n }\n if (details.figureCitations.length > 0) {\n const line = document.createElement(\"div\");\n line.classList.add(\"figures\", \"hidden\");\n names.append(line);\n for (const figure of details.figureCitations) {\n const el = document.createElement(\"figure\");\n line.append(el);\n const img = document.createElement(\"img\");\n img.src = figure.url;\n img.loading = \"lazy\";\n img.alt = figure.description ?? \"Cited Figure without caption\";\n el.append(img);\n const caption = document.createElement(\"figcaption\");\n caption.innerText = figure.description ?? \"\";\n el.append(caption);\n }\n }\n if (details.materialCitations.length > 0) {\n const line = document.createElement(\"div\");\n line.innerHTML = icons.empty + icons.cite +\n \" Material Citations:
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icons.col_dpr\n : icons.col_aug;\n treatments.append(li);\n\n const creators = document.createElement(\"span\");\n creators.innerText = \"Catalogue of Life\";\n li.append(creators);\n\n const names = document.createElement(\"div\");\n names.classList.add(\"indent\");\n li.append(names);\n\n if (name.acceptedColURI !== name.colURI) {\n const line = document.createElement(\"div\");\n line.innerHTML = icons.east + icons.col_aug;\n names.append(line);\n\n const col_uri = document.createElement(\"a\");\n col_uri.classList.add(\"col\", \"uri\");\n const id = name.acceptedColURI!.replace(\n \"https://www.catalogueoflife.org/data/taxon/\",\n \"\",\n );\n col_uri.innerText = id;\n col_uri.href = `#${id}`;\n col_uri.title = \"show name\";\n line.append(col_uri);\n synoGroup.findName(name.acceptedColURI!).then((n) => {\n if ((n as AuthorizedName).authority) {\n col_uri.innerText = n.displayName + \" \" +\n (n as AuthorizedName).authority;\n } else col_uri.innerText = n.displayName;\n }, () => {\n col_uri.removeAttribute(\"href\");\n });\n }\n }\n if (name.treatments.treats.size > 0 || name.treatments.cite.size > 0) {\n for (const trt of name.treatments.treats) {\n const li = new SynoTreatment(trt, SynoStatus.Aug);\n treatments.append(li);\n }\n for (const trt of name.treatments.cite) {\n const li = new SynoTreatment(trt, SynoStatus.Cite);\n treatments.append(li);\n }\n }\n\n const justification = document.createElement(\"abbr\");\n justification.classList.add(\"justification\");\n justification.innerText = \"...?\";\n justify(name).then((just) => justification.title = `This ${just}`);\n title.append(\" \", justification);\n\n for (const authorizedName of name.authorizedNames) {\n const authName = document.createElement(\"h3\");\n const name_title = document.createElement(\"i\");\n name_title.innerText = authorizedName.displayName;\n name_title.classList.add(\"gray\");\n authName.append(name_title);\n authName.append(\" \", authorizedName.authority);\n this.append(authName);\n\n const treatments = document.createElement(\"ul\");\n this.append(treatments);\n\n if (authorizedName.taxonConceptURI) {\n const name_uri = document.createElement(\"a\");\n name_uri.classList.add(\"taxon\", \"uri\");\n const short = authorizedName.taxonConceptURI.replace(\n \"http://taxon-concept.plazi.org/id/\",\n \"\",\n );\n name_uri.innerText = short;\n name_uri.id = short;\n name_uri.href = authorizedName.taxonConceptURI;\n name_uri.target = \"_blank\";\n name_uri.innerHTML += icons.link;\n authName.append(\" \", name_uri);\n }\n if (authorizedName.colURI) {\n const col_uri = document.createElement(\"a\");\n col_uri.classList.add(\"col\", \"uri\");\n const id = authorizedName.colURI.replace(\n \"https://www.catalogueoflife.org/data/taxon/\",\n \"\",\n );\n col_uri.innerText = id;\n col_uri.id = id;\n col_uri.href = authorizedName.colURI;\n col_uri.target = \"_blank\";\n col_uri.innerHTML += icons.link;\n authName.append(\" \", col_uri);\n\n const li = document.createElement(\"div\");\n li.classList.add(\"treatmentline\");\n li.innerHTML = authorizedName.acceptedColURI !== authorizedName.colURI\n ? 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+ "names": ["sleep", "ms", "resolve", "SparqlEndpoint", "sparqlEnpointUri", "query", "fetchOptions", "_reason", "retryCount", "sendRequest", "response", "error", "wait", "preamble", "postamble", "getNameFromCol", "colUri", "getNameFromTC", "tcUri", "getNameFromTN", "tnUri", "SynonymGroup", "name", "sparqlEndpoint", "taxonName", "ignoreDeprecatedCoL", "startWithSubTaxa", "e", "n", "uri", "an", "resolve", "reject", "justification", "json", "getNameFromCol", "getNameFromTC", "getNameFromTN", "url", "query", "names", "genus", "species", "infrasp", "treatmentPromises", "abbreviateRank", "rank", "displayName", "unathorizedCol", "authorizedCoLNames", "authorizedTCNames", "taxonNameURI", "t", "colURI", "def", "aug", "dpr", "cite", "colName", "treats", "authName", "colPromises", "acceptedColURI", "promises", "newSynonyms", "treat", "d", "s", "treatment", "colUri", "parent", "b", "result", "bindings", "urls", "url_d", "date", "details", "treatmentUri", "materialCitations", "httpUri", "figureQuery", "figureCitations", "f", "error", "returnedSoFar", "callback", "listener", "distinct", "array", "set", "params", "HIDE_COL_ONLY_SYNONYMS", "START_WITH_SUBTAXA", "SORT_TREATMENTS_BY_TYPE", "ENDPOINT_URL", "NAME", "root", "icons", "indicator", "root", "NAME", "progress", "timeStart", "sparqlEndpoint", "SparqlEndpoint", "ENDPOINT_URL", "synoGroup", "SynonymGroup", "HIDE_COL_ONLY_SYNONYMS", "START_WITH_SUBTAXA", "SynoTreatment", "trt", "status", "button", "date", "spinner", "url", "names", "details", "creators", "title", "line", "n", "short", "nn", "figure", "el", "img", "caption", "c", "SynoName", "name", "name_title", "rank_badge", "kingdom_badge", "name_uri", "vernacular", "distinct", "treatments", "col_uri", "id", "li", "justification", "justify", "just", "authorizedName", "authName", "treatments_array", "SORT_TREATMENTS_BY_TYPE", "a", "b", "parent", "element", "timeEnd"]
}
diff --git a/index.ts b/index.ts
index ee1f6c3..4a5aee4 100644
--- a/index.ts
+++ b/index.ts
@@ -333,7 +333,10 @@ class SynoName extends HTMLElement {
const rank_badge = document.createElement("span");
rank_badge.classList.add("rank");
rank_badge.innerText = name.rank;
- title.append(" ", rank_badge);
+ const kingdom_badge = document.createElement("span");
+ kingdom_badge.classList.add("rank");
+ kingdom_badge.innerText = name.kingdom || "Missing Kingdom";
+ title.append(" ", kingdom_badge, " ", rank_badge);
if (name.taxonNameURI) {
const name_uri = document.createElement("a");