@abi-software/map-utilities 1.4.3-beta.1 → 1.4.3-isan.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-utilities",
-  "version": "1.4.3-beta.1",
+  "version": "1.4.3-isan.0",
   "files": [
     "dist/*",
     "src/*",
@@ -30,11 +30,6 @@
   },
   "dependencies": {
     "@abi-software/svg-sprite": "^1.0.1",
-    "@citation-js/core": "^0.7.14",
-    "@citation-js/plugin-bibtex": "^0.7.17",
-    "@citation-js/plugin-csl": "^0.7.14",
-    "@citation-js/plugin-doi": "^0.7.16",
-    "@citation-js/plugin-pubmed": "^0.3.0",
     "@element-plus/icons-vue": "^2.3.1",
     "cytoscape": "^3.30.2",
     "element-plus": "2.8.4",

package/src/App.vue

@@ -130,7 +130,7 @@ function onActionClick(value) {
  * Tooltip
  */
 const tooltipDisplay = ref(false);
-const tooltipEntry = ref({});
+const tooltipEntry = ref([]);
 const featuresAlert = ref(undefined);
 const annotationDisplay = ref(false);
 const annotationEntry = ref({});
@@ -141,33 +141,90 @@ provide(/* key */ "userApiKey", /* value */ undefined);
 
 function addTooltipEntry() {
   tooltipDisplay.value = true;
-  tooltipEntry.value = {
-    destinations: [null],
-    origins: [null],
-    components: ["pudendal nerve"],
-    destinationsWithDatasets: [
-      { id: "UBERON:0004917", name: "urethral sphincter" },
-    ],
-    originsWithDatasets: [
-      { id: "UBERON:0022278", name: "nucleus of pudendal nerve" },
-    ],
-    componentsWithDatasets: [{ id: "UBERON:0011390", name: "pudendal nerve" }],
-    title:
-      "Nucleus of the pudendal nerve to urethral sphincter via pudendal nerve",
-    featureId: ["ilxtr:sparc-nlp/mmset1/1"],
-    hyperlinks: [
-      {
-        url: "https://pubmed.ncbi.nlm.nih.gov/?term=%2F%2Fdoi.org%2F10.1155%252F2012%252F816274",
-        id: "pubmed",
-      },
-    ],
-    provenanceTaxonomy: ["NCBITaxon:9606"],
-    provenanceTaxonomyLabel: ["Homo sapiens"],
-  };
+  tooltipEntry.value = [
+    {
+      destinations: ["eccrine sweat gland of the trunk"],
+      origins: [
+        "Sixth thoracic ganglion",
+        "Twelfth thoracic ganglion",
+        "Fifth thoracic ganglion",
+        "Ninth thoracic ganglion",
+        "Seventh thoracic ganglion",
+        "Eighth thoracic ganglion",
+        "Fourth thoracic ganglion",
+        "Tenth thoracic ganglion",
+        "Eleventh thoracic ganglion",
+      ],
+      components: ["nerve"],
+      destinationsWithDatasets: [
+        { id: "ILX:0795061", name: "eccrine sweat gland of the trunk" },
+      ],
+      originsWithDatasets: [
+        { id: "ILX:0784378", name: "Ninth thoracic ganglion" },
+        { id: "ILX:0784569", name: "Tenth thoracic ganglion" },
+        { id: "ILX:0784721", name: "Eighth thoracic ganglion" },
+        { id: "ILX:0786141", name: "Fifth thoracic ganglion" },
+        { id: "ILX:0786272", name: "Fourth thoracic ganglion" },
+        { id: "ILX:0787009", name: "Twelfth thoracic ganglion" },
+        { id: "ILX:0787015", name: "Eleventh thoracic ganglion" },
+        { id: "ILX:0789947", name: "Sixth thoracic ganglion" },
+        { id: "ILX:0790482", name: "Seventh thoracic ganglion" },
+      ],
+      componentsWithDatasets: [{ id: "UBERON:0001021", name: "nerve" }],
+      title: "neuron type swglnd 161",
+      featureId: ["ilxtr:sparc-nlp/swglnd/161"],
+      hyperlinks: [
+        "https://doi.org/10.1007/s10286-015-0282-1",
+        "https://doi.org/10.1111/bjd.15808",
+        "https://doi.org/10.1159/000060678",
+      ],
+      provenanceTaxonomy: ["NCBITaxon:9606"],
+      provenanceTaxonomyLabel: ["Homo sapiens"],
+      knowledgeSource: "sckan-2024-09-21-npo",
+      mapId: "rat-flatmap",
+      mapuuid: "b4ae1699-5690-5640-97b7-d711ae02dcb9",
+    },
+    {
+      destinations: ["intramural ganglion of the kidney"],
+      origins: ["dorsal motor nucleus of vagus nerve"],
+      components: [
+        "renal nerve plexus",
+        "aortic plexus",
+        "esophageal vagus trunk",
+        "vagus X nerve trunk",
+        "vagus nerve",
+      ],
+      destinationsWithDatasets: [
+        { id: "ILX:0795056", name: "intramural ganglion of the kidney" },
+      ],
+      originsWithDatasets: [
+        { id: "UBERON:0002870", name: "dorsal motor nucleus of vagus nerve" },
+      ],
+      componentsWithDatasets: [
+        { id: "ILX:0794853", name: "esophageal vagus trunk" },
+        { id: "UBERON:0001759", name: "vagus nerve" },
+        { id: "UBERON:0003535", name: "vagus X nerve trunk" },
+        { id: "UBERON:0018676", name: "renal nerve plexus" },
+        { id: "UBERON:0035772", name: "aortic plexus" },
+      ],
+      title:
+        "dorsal motor nucleus of vagus nerve to intramural ganglia of the kidney via vagus nerve via esophageal vagus trunk via vagal trunks via aortic plexus via renal plexus",
+      featureId: ["ilxtr:sparc-nlp/kidney/135"],
+      hyperlinks: [
+        "https://uilx.org/tgbugs/u/r/isbn-13/978-0323680424",
+        "https://doi.org/10.1016/j.aanat.2015.11.004",
+      ],
+      provenanceTaxonomy: ["NCBITaxon:9606"],
+      provenanceTaxonomyLabel: ["Homo sapiens"],
+      knowledgeSource: "sckan-2024-09-21-npo",
+      mapId: "rat-flatmap",
+      mapuuid: "b4ae1699-5690-5640-97b7-d711ae02dcb9",
+    },
+  ];
 }
 function removeTooltipEntry() {
   tooltipDisplay.value = false;
-  tooltipEntry.value = {};
+  tooltipEntry.value = [];
 }
 function addAnnotationEntry() {
   tooltipDisplay.value = true;
@@ -234,7 +291,7 @@ function setColourField(treeData, nodeData, activeColour) {
 function setColour(nodeData, value) {
   if (nodeData && nodeData.isPrimitives) {
     const activeColour = value ? value : nodeData.defaultColour;
-    setColourField(treeDataEntry.value, nodeData, activeColour)
+    setColourField(treeDataEntry.value, nodeData, activeColour);
   }
 }
 function checkAll(value) {
@@ -263,7 +320,7 @@ const createData = ref({
   editingIndex: -1,
   faceIndex: -1,
   toBeDeleted: false,
-})
+});
 function cancelCreate() {
   console.log("🚀 ~ CreateTooltipContent : cancelCreate");
 }
@@ -422,14 +479,14 @@ function confirmCreate(value) {
           Add Tooltip Entry
         </el-button>
         <el-button
-          v-show="Object.keys(tooltipEntry).length > 0"
+          v-show="tooltipEntry.length > 0"
           @click="removeTooltipEntry"
           size="small"
         >
           Remove Tooltip Entry
         </el-button>
         <el-button
-          v-show="!Object.keys(tooltipEntry).length > 0"
+          v-show="tooltipEntry.length === 0"
           @click="addAnnotationEntry"
           size="small"
         >
@@ -449,10 +506,18 @@ function confirmCreate(value) {
         <h3>TreeControls - {{ mapType }}</h3>
       </el-col>
       <el-col>
-        <el-button v-show="mapType==='scaffold'" @click="switchTreeEntry('flatmap')" size="small">
+        <el-button
+          v-show="mapType === 'scaffold'"
+          @click="switchTreeEntry('flatmap')"
+          size="small"
+        >
           Display Flatmap Tree
         </el-button>
-        <el-button v-show="mapType==='flatmap'" @click="switchTreeEntry('scaffold')" size="small">
+        <el-button
+          v-show="mapType === 'flatmap'"
+          @click="switchTreeEntry('scaffold')"
+          size="small"
+        >
           Display Scaffold Tree
         </el-button>
       </el-col>
@@ -462,16 +527,10 @@ function confirmCreate(value) {
         <h3>Connectivity Graph</h3>
       </el-col>
       <el-col>
-        <el-button
-          @click="showConnectivityGraph = true"
-          size="small"
-        >
+        <el-button @click="showConnectivityGraph = true" size="small">
           Show connectivity graph
         </el-button>
-        <el-button
-          @click="showConnectivityGraph = false"
-          size="small"
-        >
+        <el-button @click="showConnectivityGraph = false" size="small">
           Hide connectivity graph
         </el-button>
       </el-col>
@@ -568,9 +627,9 @@ function confirmCreate(value) {
   top: calc(50% - 100px);
   left: calc(50% - 200px);
 }
-.annotation-popup{
+.annotation-popup {
   margin-top: 8px;
-  width:400px;
+  width: 400px;
   border-style: solid;
   border-width: 1px;
   border-color: black;

package/src/components/ConnectivityList/ConnectivityList.vue

@@ -46,20 +46,6 @@
     >
       <div class="attribute-title-container">
         <span class="attribute-title">Components</span>
-        <el-popover
-          width="250"
-          trigger="hover"
-          :teleported="false"
-          popper-class="popover-origin-help"
-        >
-          <template #reference>
-            <el-icon class="info"><el-icon-warning /></el-icon>
-          </template>
-          <span style="word-break: keep-all">
-            The list is not in any specific order.<br>
-            Specific paths can be viewed using Graph View.
-          </span>
-        </el-popover>
       </div>
       <div
         v-for="(component, i) in components"

package/src/components/Tooltip/ExternalResourceCard.vue

@@ -6,7 +6,7 @@
         <CopyToClipboard label="Copy list to clipboard" :content="referecesListContent" />
       </div>
     </div>
-    <div class="citation-tabs" v-if="useDOIFormatter ? referencesWithDOI : pubMedReferences.length">
+    <div class="citation-tabs" v-if="referencesWithDOI">
       <el-button
         link
         v-for="citationOption of citationOptions"
@@ -102,7 +102,7 @@
 
 <script>
 import CopyToClipboard from '../CopyToClipboard/CopyToClipboard.vue';
-import { delay, getCitationById } from '../utilities';
+import { delay } from '../utilities';
 
 const CROSSCITE_API_HOST = 'https://citation.doi.org';
 const CITATION_OPTIONS = [
@@ -128,18 +128,11 @@ const LOADING_DELAY = 600;
 
 export default {
   name: "ExternalResourceCard",
-  components: {
-    CopyToClipboard,
-  },
   props: {
     resources: {
       type: Array,
       default: () => [],
     },
-    useDOIFormatter: {
-      type: Boolean,
-      default: true,
-    }
   },
   data: function () {
     return {
@@ -345,14 +338,7 @@ export default {
 
         if (type === 'doi' || doi) {
           const doiID = type === 'doi' ? id : doi;
-          const fetchCitationFromAPI = this.useDOIFormatter ?
-            this.getCitationTextByDOI(doiID) :
-            getCitationById(doiID, {
-              type: 'doi',
-              format: citationType
-            });
-
-          fetchCitationFromAPI.then((text) => {
+          this.getCitationTextByDOI(doiID).then((text) => {
             const formattedText = this.replaceLinkInText(text);
             reference.citation[citationType] = formattedText;
             this.updateCopyContents();
@@ -363,61 +349,45 @@ export default {
             };
           });
         } else if (type === 'pmid') {
-          if (this.useDOIFormatter) {
-            this.getDOIFromPubMedID(id).then((data) => {
-              if (data?.result) {
-                const resultObj = data.result[id];
-                const articleIDs = resultObj?.articleids || [];
-                const doiObj = articleIDs.find((item) => item.idtype === 'doi');
-                const doiID = doiObj?.value;
-
-                if (doiID) {
-                  reference['doi'] = doiID;
-                  this.getCitationTextByDOI(doiID).then((text) => {
-                    const formattedText = this.replaceLinkInText(text);
-                    reference.citation[citationType] = formattedText;
-                    this.updateCopyContents();
-                  }).catch((error) => {
-                    reference.citation['error'] = {
-                      type: citationType,
-                      ref: 'doi',
-                    };
-                  });
-                } else {
-                  // If there has no doi in PubMed
-                  const { title, pubdate, authors } = resultObj;
-                  const authorNames = authors ? authors.map((author) => author.name) : [];
-                  const formattedText = this.formatCopyReference({
-                    title: title || '',
-                    date: pubdate || '',
-                    authors: authorNames,
-                    url: `https://pubmed.ncbi.nlm.nih.gov/${id}`,
-                  });
+          this.getDOIFromPubMedID(id).then((data) => {
+            if (data?.result) {
+              const resultObj = data.result[id];
+              const articleIDs = resultObj?.articleids || [];
+              const doiObj = articleIDs.find((item) => item.idtype === 'doi');
+              const doiID = doiObj?.value;
+
+              if (doiID) {
+                reference['doi'] = doiID;
+                this.getCitationTextByDOI(doiID).then((text) => {
+                  const formattedText = this.replaceLinkInText(text);
                   reference.citation[citationType] = formattedText;
                   this.updateCopyContents();
-                }
+                }).catch((error) => {
+                  reference.citation['error'] = {
+                    type: citationType,
+                    ref: 'doi',
+                  };
+                });
+              } else {
+                // If there has no doi in PubMed
+                const { title, pubdate, authors } = resultObj;
+                const authorNames = authors ? authors.map((author) => author.name) : [];
+                const formattedText = this.formatCopyReference({
+                  title: title || '',
+                  date: pubdate || '',
+                  authors: authorNames,
+                  url: `https://pubmed.ncbi.nlm.nih.gov/${id}`,
+                });
+                reference.citation[citationType] = formattedText;
+                this.updateCopyContents();
               }
-            }).catch((error) => {
-              reference.citation['error'] = {
-                type: citationType,
-                ref: 'pubmed',
-              };
-            });
-          } else {
-            getCitationById(id, {
-              type: 'pmid',
-              format: citationType
-            }).then((text) => {
-              const formattedText = this.replaceLinkInText(text);
-              reference.citation[citationType] = formattedText;
-              this.updateCopyContents();
-            }).catch((error) => {
-              reference.citation['error'] = {
-                type: citationType,
-                ref: 'pubmed',
-              };
-            });
-          }
+            }
+          }).catch((error) => {
+            reference.citation['error'] = {
+              type: citationType,
+              ref: 'pubmed',
+            };
+          });
         }
       }
     },