@abi-software/map-utilities 1.8.1 → 1.8.2

package/dist/map-utilities.js

@@ -36981,11 +36981,11 @@ async function eW(t, e, r, n) {
               });
             }
         } else if (v === "alert") {
-          g.label = "Alert";
+          g.label = "Notes";
           for (const m of ["with", "without"])
             y.push({
               key: `${g.key}.${m}`,
-              label: `${m} alerts`
+              label: `${m} notes`
             });
         }
         g.children = y.sort((m, b) => m.label.localeCompare(b.label)), g.label && g.children.length && a.push(g);

package/dist/map-utilities.umd.cjs

@@ -471,4 +471,4 @@ Licensed under The MIT License (http://opensource.org/licenses/MIT)
 `)}</ul>`,i="<div><strong>References</strong></div>";this.referecesListContent=i+`
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Tg(t,e,c)),[...new Set([...c,...d])]}async function YG(t,e,r){var a;const n=await Rr({flatmapAPI:t,knowledgeSource:e,queryId:1,parameters:[{column:"feature_id",value:r}]});if((a=n==null?void 0:n.results)!=null&&a.values){const i=n.results.values.map(o=>o[1]);return[...new Set(i)]}return[]}async function ZG(t,e,r){var a;const n=await Rr({flatmapAPI:t,knowledgeSource:e,queryId:1,parameters:[{column:"feature_id",value:r}]});if((a=n==null?void 0:n.results)!=null&&a.values){const i=n.results.values.map(o=>o[1]);return[...new Set(i)]}return[]}async function XG(t,e,r){var a;const n=await Rr({flatmapAPI:t,knowledgeSource:e,queryId:2,parameters:[{column:"feature_id",value:r}]});if((a=n==null?void 0:n.results)!=null&&a.values){const i=n.results.values.map(o=>o[1]);return[...new Set(i)]}return[]}function _g(t){const e=[];for(const r of t){const n=JSON.parse(r);Array.isArray(n)&&n.length>=2&&Array.isArray(n[1])&&n[1].length===0&&e.push(n[0])}return e}async function Tg(t,e,r){var a;const n=await Rr({flatmapAPI:t,knowledgeSource:e,queryId:26,parameters:[{column:"path_id",value:r}]});if((a=n==null?void 0:n.results)!=null&&a.values){const i=n.results.values.map(o=>o[2]);return[...new Set(i)]}return[]}async function JG({flatmapAPI:t,knowledgeSource:e,origins:r,destinations:n,vias:a}){var w,C,x,k;const i=_g(r),o=_g(n),l=_g(a),u=[{column:"source_feature_id",value:i},{column:"via_feature_id",value:l},{column:"dest_feature_id",value:o}],c=[{column:"source_node_id",value:r},{column:"via_node_id",value:a},{column:"dest_node_id",value:n}],d=u.some(E=>Array.isArray(E.value)&&E.value.length>0),f=[Rr({flatmapAPI:t,knowledgeSource:e,queryId:24,parameters:c})];d&&f.push(Rr({flatmapAPI:t,knowledgeSource:e,queryId:25,parameters:u}));const h=await Promise.all(f);let v=[],p;if(d){const E=h[0];p=h[1],v=((C=(w=E==null?void 0:E.results)==null?void 0:w.values)==null?void 0:C.map(_=>_[1]))||[]}else p=h[0];const g=((k=(x=p==null?void 0:p.results)==null?void 0:x.values)==null?void 0:k.map(E=>E[1]))||[],m=[...new Set([...v,...g])];let y=[];return m.length&&(y=await Tg(t,e,m)),[...new Set([...m,...y])]}const Ng=[];async function QG(t,e){const r=e.filter(i=>Ng.some(o=>o.taxon===i)),n=Ng.filter(i=>r.includes(i.taxon)),a=e.filter(i=>!r.includes(i));if(a.length){const i=await t.queryLabels(a);if(i.length)return i.forEach(o=>{let{entity:l,label:u}=o;u==="Mammalia"&&(u="Mammalia not otherwise specified");const c={taxon:l,label:u};n.push(c),Ng.push(c)}),n}else return n}async function e7(t,e,r){const n=`${t}knowledge/query/`,a={sql:e,params:r};try{const i=await fetch(n,{method:"POST",headers:{Accept:"application/json; charset=utf-8","Content-Type":"application/json"},body:JSON.stringify(a)});if(!i.ok)throw new Error(`Cannot access ${n}`);return await i.json()}catch{return{values:[]}}}async function G_(t,e){return e.length?await(await e7(t,`select entity, knowledge from knowledge
       where entity in (?${", ?".repeat(e.length-1)})
-      order by source desc`,[...e])).values:[]}function t7(t){var r;const e=(r=t["node-phenotypes"])==null?void 0:r["ilxtr:hasSomaLocatedIn"];return Array.isArray(t.connectivity)&&t.connectivity.length>0&&Array.isArray(e)&&e.length>0}function r7(t){var a,i;const e=(a=t["node-phenotypes"])==null?void 0:a["ilxtr:hasAxonPresynapticElementIn"],r=(i=t["node-phenotypes"])==null?void 0:i["ilxtr:hasAxonSensorySubcellularElementIn"],n=Array.isArray(e)&&e.length>0||Array.isArray(r)&&r.length>0;return Array.isArray(t.connectivity)&&t.connectivity.length>0&&n}function n7(t){var n,a,i;if(!Array.isArray(t.connectivity)||t.connectivity.length===0)return!1;const e=new Set((((n=t["node-phenotypes"])==null?void 0:n["ilxtr:hasSomaLocatedIn"])||[]).map(o=>o[0])),r=new Set([...(((a=t["node-phenotypes"])==null?void 0:a["ilxtr:hasAxonPresynapticElementIn"])||[]).map(o=>o[0]),...(((i=t["node-phenotypes"])==null?void 0:i["ilxtr:hasAxonSensorySubcellularElementIn"])||[]).map(o=>o[0])]);return t.connectivity.some(o=>{const[l,u]=o,c=l[0],d=u[0];return!e.has(c)&&!r.has(d)})}function Ig(t){if(!Array.isArray(t.connectivity))return[];const e=new Set;return t.connectivity.forEach(r=>{Array.isArray(r)&&r.length&&r.forEach(n=>{if(Array.isArray(n)&&typeof n[0]=="string"){const a=JSON.stringify(n);e.add(a)}})}),Array.from(e)}function Mr(t,e){var n;const r=(n=t["node-phenotypes"])==null?void 0:n[e];return Array.isArray(r)?r:[]}async function Bg(t,e,r){const n=Array.from(new Map(r.map(f=>[JSON.stringify(f),f])).values()),a=n.flat(1/0),i=[...new Set(a)],l=(await G_(t,i)).reduce((f,h)=>{const v=h[0],p=JSON.parse(h[1]);return f.push({id:v,label:p.label,source:p.source}),f},[]);l.sort((f,h)=>f.id===h.id?f.source===e&&h.source!==e?-1:f.source!==e&&h.source===e?1:0:f.id.localeCompare(h.id));const u=[];return[...n.map(f=>{const h=f.flat(),v=[];for(let p=0;p<h.length;p++){const g=l.find(m=>m.id===h[p]);g&&(v.push(g.label),p>0&&u.push({key:[h[p],[]],label:g.label}))}return{key:f,label:v.join(", ")}}),...u].filter((f,h,v)=>h===v.findIndex(p=>p.label===f.label))}async function U_(t,e,r){const n=[];return r.forEach(a=>{if(!Array.isArray(a.connectivity)||a.connectivity.length===0)return;const i=new Set(Ig(a));Mr(a,"ilxtr:hasSomaLocatedIn").forEach(o=>{const l=JSON.stringify(o);i.has(l)&&n.push(o)})}),await Bg(t,e,n)}async function W_(t,e,r){const n=[];return r.forEach(a=>{if(!Array.isArray(a.connectivity)||a.connectivity.length===0)return;const i=new Set(Ig(a));[...Mr(a,"ilxtr:hasAxonPresynapticElementIn"),...Mr(a,"ilxtr:hasAxonSensorySubcellularElementIn")].forEach(o=>{const l=JSON.stringify(o);i.has(l)&&n.push(o)})}),await Bg(t,e,n)}async function j_(t,e,r){const n=[];return r.forEach(a=>{if(!Array.isArray(a.connectivity)||a.connectivity.length===0)return;const i=new Set(Ig(a));[...Mr(a,"ilxtr:hasAxonLeadingToSensorySubcellularElementIn"),...Mr(a,"ilxtr:hasAxonLocatedIn")].forEach(o=>{const l=JSON.stringify(o);i.has(l)&&n.push(o)})}),await Bg(t,e,n)}function Y_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:Mr(r,"ilxtr:hasSomaLocatedIn").some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}function Z_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:[...Mr(r,"ilxtr:hasAxonPresynapticElementIn"),...Mr(r,"ilxtr:hasAxonSensorySubcellularElementIn")].some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}function X_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:[...Mr(r,"ilxtr:hasAxonLeadingToSensorySubcellularElementIn"),...Mr(r,"ilxtr:hasAxonLocatedIn")].some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}async function a7({knowledge:t,origins:e,destinations:r,vias:n}){let a=t;return e.length&&(a=Y_(a,e)),r.length&&(a=Z_(a,r)),n.length&&(a=X_(a,n)),a}async function i7(t,e,r,n){let a=[];const i=[];if(e){if(e&&typeof e.featureFilterRanges=="function"){const v=e.featureFilterRanges();for(const[p,g]of Object.entries(v)){let m={key:`flatmap.connectivity.${p}`,label:"",children:[]},y=[];if(p==="kind"){m.label="Pathways";for(const b of g){const w=n.find(C=>C.type===b);w&&y.push({key:`${m.key}.${b}`,label:w.label,colour:w.colour,colourStyle:"line",dashed:w.dashed})}}else if(p==="taxons"){m.label="Studied in";const b=await QG(e,e.taxonIdentifiers);if(b.length)for(const w of g){const C=b.find(x=>x.taxon===w);C&&y.push({key:`${m.key}.${w}`,label:`${C.label} `})}}else if(p==="alert"){m.label="Alert";for(const b of["with","without"])y.push({key:`${m.key}.${b}`,label:`${b} alerts`})}m.children=y.sort((b,w)=>b.label.localeCompare(w.label)),m.label&&m.children.length&&a.push(m)}}const o=e.pathways.paths,l=[];for(const v of r){const p=v.id;if(p){const g=o[p];if(g&&g.connectivity&&g["node-phenotypes"]){const m=g.connectivity,y=g["node-phenotypes"],b={};for(let w in v["node-phenotypes"])y[w]&&(b[w]=[...y[w]]);l.push({...v,connectivity:[...m],"node-phenotypes":b})}}}const u=e.knowledgeSource,c=await U_(t,u,l),d=await j_(t,u,l),f=await W_(t,u,l),h=(v,p)=>{const g=JSON.stringify(p.key);return{key:`flatmap.connectivity.source.${v}.${g}`,label:p.label||g}};for(const v of["origin","via","destination","all"]){let p=[];if(v==="origin")p=c.map(g=>h(v,g));else if(v==="via")p=d.map(g=>h(v,g));else if(v==="destination")p=f.map(g=>h(v,g));else{const g=[...c.map(y=>h(v,y)),...d.map(y=>h(v,y)),...f.map(y=>h(v,y))],m=new Set;p=g.filter(y=>m.has(y.key)?!1:(m.add(y.key),!0))}p=p.sort((g,m)=>{const y=C=>/^[a-zA-Z]/.test(C),b=y(g.label),w=y(m.label);return b&&!w?-1:!b&&w?1:g.label.localeCompare(m.label)}),p.length&&i.push({key:`flatmap.connectivity.source.${v}`,label:v,children:p})}i.length&&a.push(...i)}return a}_e.AnnotationPopup=T0,_e.ConnectivityGraph=uH,_e.ConnectivityList=wg,_e.ConnectivityReconciliationList=dK,_e.CopyToClipboard=fs,_e.CreateTooltipContent=VM,_e.DrawToolbar=MK,_e.ExternalResourceCard=Sg,_e.HelpModeDialog=HK,_e.Tooltip=PG,_e.TreeControls=GG,_e.competencyQuery=Rr,_e.extractDestinationItems=W_,_e.extractOriginItems=U_,_e.extractViaItems=j_,_e.fetchLabels=G_,_e.filterDestinations=r7,_e.filterOrigins=t7,_e.filterViaLocations=n7,_e.findPathsByDestinationItem=Z_,_e.findPathsByOriginItem=Y_,_e.findPathsByViaItem=X_,_e.getFlatmapFilterOptions=i7,_e.queryAllConnectedPaths=jG,_e.queryForwardBackwardConnections=Tg,_e.queryPathsByDestination=XG,_e.queryPathsByOrigin=YG,_e.queryPathsByRoute=JG,_e.queryPathsByRouteFromKnowledge=a7,_e.queryPathsByViaLocation=ZG,_e.querySingleConnectivityList=WG,Object.defineProperty(_e,Symbol.toStringTag,{value:"Module"})});
+      order by source desc`,[...e])).values:[]}function t7(t){var r;const e=(r=t["node-phenotypes"])==null?void 0:r["ilxtr:hasSomaLocatedIn"];return Array.isArray(t.connectivity)&&t.connectivity.length>0&&Array.isArray(e)&&e.length>0}function r7(t){var a,i;const e=(a=t["node-phenotypes"])==null?void 0:a["ilxtr:hasAxonPresynapticElementIn"],r=(i=t["node-phenotypes"])==null?void 0:i["ilxtr:hasAxonSensorySubcellularElementIn"],n=Array.isArray(e)&&e.length>0||Array.isArray(r)&&r.length>0;return Array.isArray(t.connectivity)&&t.connectivity.length>0&&n}function n7(t){var n,a,i;if(!Array.isArray(t.connectivity)||t.connectivity.length===0)return!1;const e=new Set((((n=t["node-phenotypes"])==null?void 0:n["ilxtr:hasSomaLocatedIn"])||[]).map(o=>o[0])),r=new Set([...(((a=t["node-phenotypes"])==null?void 0:a["ilxtr:hasAxonPresynapticElementIn"])||[]).map(o=>o[0]),...(((i=t["node-phenotypes"])==null?void 0:i["ilxtr:hasAxonSensorySubcellularElementIn"])||[]).map(o=>o[0])]);return t.connectivity.some(o=>{const[l,u]=o,c=l[0],d=u[0];return!e.has(c)&&!r.has(d)})}function Ig(t){if(!Array.isArray(t.connectivity))return[];const e=new Set;return t.connectivity.forEach(r=>{Array.isArray(r)&&r.length&&r.forEach(n=>{if(Array.isArray(n)&&typeof n[0]=="string"){const a=JSON.stringify(n);e.add(a)}})}),Array.from(e)}function Mr(t,e){var n;const r=(n=t["node-phenotypes"])==null?void 0:n[e];return Array.isArray(r)?r:[]}async function Bg(t,e,r){const n=Array.from(new Map(r.map(f=>[JSON.stringify(f),f])).values()),a=n.flat(1/0),i=[...new Set(a)],l=(await G_(t,i)).reduce((f,h)=>{const v=h[0],p=JSON.parse(h[1]);return f.push({id:v,label:p.label,source:p.source}),f},[]);l.sort((f,h)=>f.id===h.id?f.source===e&&h.source!==e?-1:f.source!==e&&h.source===e?1:0:f.id.localeCompare(h.id));const u=[];return[...n.map(f=>{const h=f.flat(),v=[];for(let p=0;p<h.length;p++){const g=l.find(m=>m.id===h[p]);g&&(v.push(g.label),p>0&&u.push({key:[h[p],[]],label:g.label}))}return{key:f,label:v.join(", ")}}),...u].filter((f,h,v)=>h===v.findIndex(p=>p.label===f.label))}async function U_(t,e,r){const n=[];return r.forEach(a=>{if(!Array.isArray(a.connectivity)||a.connectivity.length===0)return;const i=new Set(Ig(a));Mr(a,"ilxtr:hasSomaLocatedIn").forEach(o=>{const l=JSON.stringify(o);i.has(l)&&n.push(o)})}),await Bg(t,e,n)}async function W_(t,e,r){const n=[];return r.forEach(a=>{if(!Array.isArray(a.connectivity)||a.connectivity.length===0)return;const i=new Set(Ig(a));[...Mr(a,"ilxtr:hasAxonPresynapticElementIn"),...Mr(a,"ilxtr:hasAxonSensorySubcellularElementIn")].forEach(o=>{const l=JSON.stringify(o);i.has(l)&&n.push(o)})}),await Bg(t,e,n)}async function j_(t,e,r){const n=[];return r.forEach(a=>{if(!Array.isArray(a.connectivity)||a.connectivity.length===0)return;const i=new Set(Ig(a));[...Mr(a,"ilxtr:hasAxonLeadingToSensorySubcellularElementIn"),...Mr(a,"ilxtr:hasAxonLocatedIn")].forEach(o=>{const l=JSON.stringify(o);i.has(l)&&n.push(o)})}),await Bg(t,e,n)}function Y_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:Mr(r,"ilxtr:hasSomaLocatedIn").some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}function Z_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:[...Mr(r,"ilxtr:hasAxonPresynapticElementIn"),...Mr(r,"ilxtr:hasAxonSensorySubcellularElementIn")].some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}function X_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:[...Mr(r,"ilxtr:hasAxonLeadingToSensorySubcellularElementIn"),...Mr(r,"ilxtr:hasAxonLocatedIn")].some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}async function a7({knowledge:t,origins:e,destinations:r,vias:n}){let a=t;return e.length&&(a=Y_(a,e)),r.length&&(a=Z_(a,r)),n.length&&(a=X_(a,n)),a}async function i7(t,e,r,n){let a=[];const i=[];if(e){if(e&&typeof e.featureFilterRanges=="function"){const v=e.featureFilterRanges();for(const[p,g]of Object.entries(v)){let m={key:`flatmap.connectivity.${p}`,label:"",children:[]},y=[];if(p==="kind"){m.label="Pathways";for(const b of g){const w=n.find(C=>C.type===b);w&&y.push({key:`${m.key}.${b}`,label:w.label,colour:w.colour,colourStyle:"line",dashed:w.dashed})}}else if(p==="taxons"){m.label="Studied in";const b=await QG(e,e.taxonIdentifiers);if(b.length)for(const w of g){const C=b.find(x=>x.taxon===w);C&&y.push({key:`${m.key}.${w}`,label:`${C.label} `})}}else if(p==="alert"){m.label="Notes";for(const b of["with","without"])y.push({key:`${m.key}.${b}`,label:`${b} notes`})}m.children=y.sort((b,w)=>b.label.localeCompare(w.label)),m.label&&m.children.length&&a.push(m)}}const o=e.pathways.paths,l=[];for(const v of r){const p=v.id;if(p){const g=o[p];if(g&&g.connectivity&&g["node-phenotypes"]){const m=g.connectivity,y=g["node-phenotypes"],b={};for(let w in v["node-phenotypes"])y[w]&&(b[w]=[...y[w]]);l.push({...v,connectivity:[...m],"node-phenotypes":b})}}}const u=e.knowledgeSource,c=await U_(t,u,l),d=await j_(t,u,l),f=await W_(t,u,l),h=(v,p)=>{const g=JSON.stringify(p.key);return{key:`flatmap.connectivity.source.${v}.${g}`,label:p.label||g}};for(const v of["origin","via","destination","all"]){let p=[];if(v==="origin")p=c.map(g=>h(v,g));else if(v==="via")p=d.map(g=>h(v,g));else if(v==="destination")p=f.map(g=>h(v,g));else{const g=[...c.map(y=>h(v,y)),...d.map(y=>h(v,y)),...f.map(y=>h(v,y))],m=new Set;p=g.filter(y=>m.has(y.key)?!1:(m.add(y.key),!0))}p=p.sort((g,m)=>{const y=C=>/^[a-zA-Z]/.test(C),b=y(g.label),w=y(m.label);return b&&!w?-1:!b&&w?1:g.label.localeCompare(m.label)}),p.length&&i.push({key:`flatmap.connectivity.source.${v}`,label:v,children:p})}i.length&&a.push(...i)}return a}_e.AnnotationPopup=T0,_e.ConnectivityGraph=uH,_e.ConnectivityList=wg,_e.ConnectivityReconciliationList=dK,_e.CopyToClipboard=fs,_e.CreateTooltipContent=VM,_e.DrawToolbar=MK,_e.ExternalResourceCard=Sg,_e.HelpModeDialog=HK,_e.Tooltip=PG,_e.TreeControls=GG,_e.competencyQuery=Rr,_e.extractDestinationItems=W_,_e.extractOriginItems=U_,_e.extractViaItems=j_,_e.fetchLabels=G_,_e.filterDestinations=r7,_e.filterOrigins=t7,_e.filterViaLocations=n7,_e.findPathsByDestinationItem=Z_,_e.findPathsByOriginItem=Y_,_e.findPathsByViaItem=X_,_e.getFlatmapFilterOptions=i7,_e.queryAllConnectedPaths=jG,_e.queryForwardBackwardConnections=Tg,_e.queryPathsByDestination=XG,_e.queryPathsByOrigin=YG,_e.queryPathsByRoute=JG,_e.queryPathsByRouteFromKnowledge=a7,_e.queryPathsByViaLocation=ZG,_e.querySingleConnectivityList=WG,Object.defineProperty(_e,Symbol.toStringTag,{value:"Module"})});

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-utilities",
-  "version": "1.8.1",
+  "version": "1.8.2",
   "license": "Apache-2.0",
   "repository": {
     "type": "git",

package/src/components/CompetencyQueries/knowledgeQueries.js

@@ -299,11 +299,11 @@ async function getFlatmapFilterOptions (flatmapAPI, mapImp, providedKnowledge, p
             }
           }
         } else if (key === "alert") {
-          main.label = "Alert"
+          main.label = "Notes"
           for (const facet of ["with", "without"]) {
             children.push({
               key: `${main.key}.${facet}`,
-              label: `${facet} alerts`
+              label: `${facet} notes`
             })
           }
         }