@abi-software/map-utilities 1.3.3-beta.4 → 1.4.0-beta.0

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-utilities",
-  "version": "1.3.3-beta.4",
+  "version": "1.4.0-beta.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

@@ -42,6 +42,7 @@ const showConnectivityGraph = ref(false);
 const connectivityGraphEntry = "ilxtr:neuron-type-aacar-13";
 // const connectivityGraphEntry = "ilxtr:sparc-nlp/kidney/134";
 const mapServer = "https://mapcore-demo.org/curation/flatmap/";
+const sckanVersion = "sckan-2024-09-21-npo";
 
 onMounted(() => {
   console.log("🚀 ~ onMounted ~ appRef:", appRef.value);
@@ -548,6 +549,7 @@ function confirmCreate(value) {
       v-if="showConnectivityGraph"
       :entry="connectivityGraphEntry"
       :map-server="mapServer"
+      :sckanVersion="sckanVersion"
     />
   </div>
 </template>

package/src/components/ConnectivityGraph/graph.js

@@ -252,8 +252,6 @@ const GRAPH_STYLE = [
         'style': {
             'width': 1,
             'line-color': 'dimgray',
-            'target-arrow-color': 'dimgray',
-            'target-arrow-shape': 'triangle',
             'curve-style': 'bezier'
         }
     },

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',
+            };
+          });
         }
       }
     },

package/src/components/utilities.js

@@ -1,9 +1,3 @@
-import { Cite, plugins } from '@citation-js/core';
-import '@citation-js/plugin-doi';
-import '@citation-js/plugin-csl';
-import '@citation-js/plugin-bibtex';
-import '@citation-js/plugin-pubmed';
-
 const capitalise = term => {
   if (term)
     return term.charAt(0).toUpperCase() + term.slice(1);
@@ -54,42 +48,8 @@ const delay = (ms) => {
   return new Promise(resolve => setTimeout(resolve, ms));
 };
 
-/**
- * @param {id} id - DOI or PMID
- * @param {options:type} type - type of the ID, e.g., 'pmid'
- * @param {options:format} format - 'apa' (default), 'chicago', 'ieee', 'bibtex', etc.
- * @returns {citation} formatted citation text
- */
-const getCitationById = async (id, { type, format }) => {
-  // because 'chicago' and 'ieee' are not in citation.js default styles
-  if ((format !== 'bibtex') && (format !== 'apa')) {
-    const xml = `https://raw.githubusercontent.com/citation-style-language/styles/refs/heads/master/${format}.csl`;
-    const response = await fetch(xml);
-    const template = await response.text();
-    let config = plugins.config.get('@csl');
-    config.templates.add(format, template);
-  }
-
-  const option = {};
-
-  if (type === 'pmid') {
-    option['forceType'] = '@pubmed/id';
-  }
-
-  const cite = await Cite.async(id, option);
-  const citation = (format === 'bibtex') ?
-    cite.format(format) :
-    cite.format('bibliography', {
-      format: 'html',
-      template: format || 'apa', // default as 'apa' style
-      lang: 'en-US'
-    })
-  return citation;
-};
-
 export {
   capitalise,
   xmlToJSON,
   delay,
-  getCitationById,
 };