@abi-software/map-utilities 1.7.3 → 1.7.4

package/dist/map-utilities.js

@@ -35712,20 +35712,21 @@ async function J7(t, e, r, n) {
         g.children = y.sort((m, b) => m.label.localeCompare(b.label)), g.label && g.children.length && a.push(g);
       }
     }
-    const o = e.pathways.paths, s = r.reduce((h, v) => {
-      const p = v.id;
-      if (p) {
-        const g = o[p];
-        if (g && g.connectivity && g["node-phenotypes"]) {
-          const y = g.connectivity, m = g["node-phenotypes"];
-          v.connectivity = [...y];
-          for (let b in v["node-phenotypes"])
-            m[b] && (v["node-phenotypes"][b] = [...m[b]]);
-          h.push(JSON.parse(JSON.stringify(v)));
+    const o = e.pathways.paths, s = [];
+    for (const h of s) {
+      const v = h.id;
+      if (v) {
+        const p = o[v];
+        if (p && p.connectivity && p["node-phenotypes"]) {
+          const g = p.connectivity, y = p["node-phenotypes"];
+          h.connectivity = [...g];
+          for (let m in h["node-phenotypes"])
+            y[m] && (h["node-phenotypes"][m] = [...y[m]]);
+          s.push(JSON.parse(JSON.stringify(h)));
         }
       }
-      return h;
-    }, []), u = e.knowledgeSource, l = await T7(t, u, s), c = await O7(t, u, s), d = await I7(t, u, s), f = (h, v) => {
+    }
+    const u = e.knowledgeSource, l = await T7(t, u, s), c = await O7(t, u, s), d = await I7(t, u, s), f = (h, v) => {
       const p = JSON.stringify(v.key);
       return {
         key: `flatmap.connectivity.source.${h}.${p}`,

package/dist/map-utilities.umd.cjs

@@ -467,4 +467,4 @@ Licensed under The MIT License (http://opensource.org/licenses/MIT)
 `)}</ul>`,i="<div><strong>References</strong></div>";this.referecesListContent=i+`
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       where entity in (?${", ?".repeat(e.length-1)})
-      order by source desc`,[...e])).values:[]}function XK(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 JK(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 QK(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,c]=o,u=l[0],d=c[0];return!e.has(u)&&!r.has(d)})}function xg(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 Lr(t,e){var n;const r=(n=t["node-phenotypes"])==null?void 0:n[e];return Array.isArray(r)?r:[]}async function kg(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 k_(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 c=[];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&&c.push({key:[h[p],[]],label:g.label}))}return{key:f,label:v.join(", 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t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:Lr(r,"ilxtr:hasSomaLocatedIn").some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}function I_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:[...Lr(r,"ilxtr:hasAxonPresynapticElementIn"),...Lr(r,"ilxtr:hasAxonSensorySubcellularElementIn")].some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}function B_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:[...Lr(r,"ilxtr:hasAxonLeadingToSensorySubcellularElementIn"),...Lr(r,"ilxtr:hasAxonLocatedIn")].some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}async function eG({knowledge:t,origins:e,destinations:r,vias:n}){let a=t;return e.length&&(a=N_(a,e)),r.length&&(a=I_(a,r)),n.length&&(a=B_(a,n)),a}async function tG(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 YK(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=r.reduce((v,p)=>{const g=p.id;if(g){const m=o[g];if(m&&m.connectivity&&m["node-phenotypes"]){const y=m.connectivity,b=m["node-phenotypes"];p.connectivity=[...y];for(let w in p["node-phenotypes"])b[w]&&(p["node-phenotypes"][w]=[...b[w]]);v.push(JSON.parse(JSON.stringify(p)))}}return v},[]),c=e.knowledgeSource,u=await S_(t,c,l),d=await T_(t,c,l),f=await __(t,c,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=u.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=[...u.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}Te.AnnotationPopup=g0,Te.ConnectivityGraph=$9,Te.ConnectivityList=hg,Te.CopyToClipboard=us,Te.CreateTooltipContent=gM,Te.DrawToolbar=AH,Te.ExternalResourceCard=bg,Te.HelpModeDialog=VH,Te.Tooltip=DK,Te.TreeControls=zK,Te.competencyQuery=On,Te.extractDestinationItems=__,Te.extractOriginItems=S_,Te.extractViaItems=T_,Te.fetchLabels=k_,Te.filterDestinations=JK,Te.filterOrigins=XK,Te.filterViaLocations=QK,Te.findPathsByDestinationItem=I_,Te.findPathsByOriginItem=N_,Te.findPathsByViaItem=B_,Te.getFlatmapFilterOptions=tG,Te.queryAllConnectedPaths=KK,Te.queryForwardBackwardConnections=Cg,Te.queryPathsByDestination=jK,Te.queryPathsByOrigin=GK,Te.queryPathsByRoute=WK,Te.queryPathsByRouteFromKnowledge=eG,Te.queryPathsByViaLocation=UK,Object.defineProperty(Te,Symbol.toStringTag,{value:"Module"})});
+      order by source desc`,[...e])).values:[]}function XK(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 JK(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 QK(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,c]=o,u=l[0],d=c[0];return!e.has(u)&&!r.has(d)})}function xg(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 Lr(t,e){var n;const r=(n=t["node-phenotypes"])==null?void 0:n[e];return Array.isArray(r)?r:[]}async function kg(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 k_(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 c=[];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&&c.push({key:[h[p],[]],label:g.label}))}return{key:f,label:v.join(", ")}}),...c].filter((f,h,v)=>h===v.findIndex(p=>p.label===f.label))}async function S_(t,e,r){const n=[];return r.forEach(a=>{if(!Array.isArray(a.connectivity)||a.connectivity.length===0)return;const i=new Set(xg(a));Lr(a,"ilxtr:hasSomaLocatedIn").forEach(o=>{const l=JSON.stringify(o);i.has(l)&&n.push(o)})}),await kg(t,e,n)}async function __(t,e,r){const n=[];return r.forEach(a=>{if(!Array.isArray(a.connectivity)||a.connectivity.length===0)return;const i=new Set(xg(a));[...Lr(a,"ilxtr:hasAxonPresynapticElementIn"),...Lr(a,"ilxtr:hasAxonSensorySubcellularElementIn")].forEach(o=>{const l=JSON.stringify(o);i.has(l)&&n.push(o)})}),await kg(t,e,n)}async function T_(t,e,r){const n=[];return r.forEach(a=>{if(!Array.isArray(a.connectivity)||a.connectivity.length===0)return;const i=new Set(xg(a));[...Lr(a,"ilxtr:hasAxonLeadingToSensorySubcellularElementIn"),...Lr(a,"ilxtr:hasAxonLocatedIn")].forEach(o=>{const l=JSON.stringify(o);i.has(l)&&n.push(o)})}),await kg(t,e,n)}function N_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:Lr(r,"ilxtr:hasSomaLocatedIn").some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}function I_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:[...Lr(r,"ilxtr:hasAxonPresynapticElementIn"),...Lr(r,"ilxtr:hasAxonSensorySubcellularElementIn")].some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}function B_(t,e){return t.filter(r=>!Array.isArray(r.connectivity)||r.connectivity.length===0?!1:[...Lr(r,"ilxtr:hasAxonLeadingToSensorySubcellularElementIn"),...Lr(r,"ilxtr:hasAxonLocatedIn")].some(a=>e.map(i=>JSON.stringify(i)).includes(JSON.stringify(a))))}async function eG({knowledge:t,origins:e,destinations:r,vias:n}){let a=t;return e.length&&(a=N_(a,e)),r.length&&(a=I_(a,r)),n.length&&(a=B_(a,n)),a}async function tG(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 YK(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 l){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"];v.connectivity=[...m];for(let b in v["node-phenotypes"])y[b]&&(v["node-phenotypes"][b]=[...y[b]]);l.push(JSON.parse(JSON.stringify(v)))}}}const c=e.knowledgeSource,u=await S_(t,c,l),d=await T_(t,c,l),f=await __(t,c,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=u.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=[...u.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}Te.AnnotationPopup=g0,Te.ConnectivityGraph=$9,Te.ConnectivityList=hg,Te.CopyToClipboard=us,Te.CreateTooltipContent=gM,Te.DrawToolbar=AH,Te.ExternalResourceCard=bg,Te.HelpModeDialog=VH,Te.Tooltip=DK,Te.TreeControls=zK,Te.competencyQuery=On,Te.extractDestinationItems=__,Te.extractOriginItems=S_,Te.extractViaItems=T_,Te.fetchLabels=k_,Te.filterDestinations=JK,Te.filterOrigins=XK,Te.filterViaLocations=QK,Te.findPathsByDestinationItem=I_,Te.findPathsByOriginItem=N_,Te.findPathsByViaItem=B_,Te.getFlatmapFilterOptions=tG,Te.queryAllConnectedPaths=KK,Te.queryForwardBackwardConnections=Cg,Te.queryPathsByDestination=jK,Te.queryPathsByOrigin=GK,Te.queryPathsByRoute=WK,Te.queryPathsByRouteFromKnowledge=eG,Te.queryPathsByViaLocation=UK,Object.defineProperty(Te,Symbol.toStringTag,{value:"Module"})});

package/package.json

@@ -1,6 +1,11 @@
 {
   "name": "@abi-software/map-utilities",
-  "version": "1.7.3",
+  "version": "1.7.4",
+  "license": "Apache-2.0",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/ABI-Software/map-utilities.git"
+  },
   "files": [
     "dist/*",
     "src/*",

package/src/components/CompetencyQueries/knowledgeQueries.js

@@ -315,7 +315,8 @@ async function getFlatmapFilterOptions (flatmapAPI, mapImp, providedKnowledge, p
     }
 
     const mapKnowledge = mapImp.pathways.paths;
-    const flatmapKnowledge = providedKnowledge.reduce((arr, knowledge) => {
+    const flatmapKnowledge = [];
+    for (const knowledge of flatmapKnowledge) {
       const id = knowledge.id;
       if (id) {
         const mapKnowledgeObj = mapKnowledge[id];
@@ -331,11 +332,11 @@ async function getFlatmapFilterOptions (flatmapAPI, mapImp, providedKnowledge, p
             }
           }
           // to avoid mutation
-          arr.push(JSON.parse(JSON.stringify(knowledge)));
+          flatmapKnowledge.push(JSON.parse(JSON.stringify(knowledge)));
         }
       }
-      return arr;
-    }, []);
+    }
+
     const knowledgeSource = mapImp.knowledgeSource;
     const originItems = await extractOriginItems(flatmapAPI, knowledgeSource, flatmapKnowledge);
     const viaItems = await extractViaItems(flatmapAPI, knowledgeSource, flatmapKnowledge);