@abi-software/map-utilities 1.2.2-beta.4 → 1.2.2-beta.5

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-utilities",
-  "version": "1.2.2-beta.4",
+  "version": "1.2.2-beta.5",
   "files": [
     "dist/*",
     "src/*",

package/src/components/ConnectivityGraph/graph.js

@@ -337,7 +337,7 @@ class CytoscapeGraph extends EventTarget
             },
             directed: true,
             style: GRAPH_STYLE,
-            minZoom: 0.5,
+            minZoom: 0.1,
             maxZoom: 10,
             wheelSensitivity: 0.4,
         }).on('mouseover', 'node', this.overNode.bind(this))

package/src/components/Tooltip/ExternalResourceCard.vue

@@ -3,7 +3,7 @@
     <div class="attribute-title-container">
       <div class="attribute-title">References</div>
     </div>
-    <div class="citation-tabs">
+    <div class="citation-tabs" v-if="referencesWithDOI">
       <el-button
         link
         v-for="citationOption of citationOptions"
@@ -16,7 +16,7 @@
     </div>
     <ul class="citation-list">
       <li
-        v-for="reference of references"
+        v-for="reference of pubMedReferences"
         :key="reference.id"
         :class="{'loading': reference.citation && reference.citation[citationType] === ''}"
       >
@@ -32,7 +32,7 @@
       </li>
 
       <li v-for="reference of isbnDBReferences">
-        <a :href="reference.url">{{ reference.url }}</a>
+        <a :href="reference.url" target="_blank">{{ reference.url }}</a>
         <CopyToClipboard :content="reference.url" />
       </li>
     </ul>
@@ -73,7 +73,6 @@ export default {
   },
   data: function () {
     return {
-      references: [],
       pubMedReferences: [],
       openLibReferences: [],
       isbnDBReferences: [],
@@ -84,7 +83,13 @@ export default {
   watch: {
     resources: function (_resources) {
       this.formatReferences([..._resources]);
-    }
+    },
+  },
+  computed: {
+    referencesWithDOI: function () {
+      const withDOI = this.pubMedReferences.filter((reference) => reference.type === 'doi' || reference.doi);
+      return withDOI.length;
+    },
   },
   mounted: function () {
     this.formatReferences([...this.resources]);
@@ -101,16 +106,26 @@ export default {
         this.extractPublicationIdFromURLString(reference)
       );
 
+      // pmc to pmid
+      this.pubMedReferences.forEach((reference) => {
+        if (reference.type === 'pmc') {
+          const pmcId = reference.id;
+          this.searchPMID(pmcId).then((data) => {
+            if (data && data.esearchresult) {
+              const idList = data.esearchresult.idlist || [];
+              reference.id = idList[0];
+              reference.type = 'pmid';
+            }
+          });
+        }
+      });
+
       this.formatNonPubMedReferences(nonPubMedReferences).then((responses) => {
         this.openLibReferences = responses.filter((response) => response.type === 'openlib');
         this.isbnDBReferences = responses.filter((response) => response.type === 'isbndb');
 
         this.formatOpenLibReferences();
       });
-
-      this.references = [
-        ...this.pubMedReferences,
-      ];
     },
     extractNonPubMedReferences: function (references) {
       const extractedReferences = [];
@@ -141,8 +156,7 @@ export default {
       const failedIDs = isbnIDs.slice();
 
       const openlibAPI = `https://openlibrary.org/api/books?bibkeys=${isbnIDsKey}&format=json`;
-      const response = await fetch(openlibAPI);
-      const data = await response.json();
+      const data = await this.fetchData(openlibAPI);
 
       for (const key in data) {
         const successKeyIndex = failedIDs.indexOf(key);
@@ -175,29 +189,6 @@ export default {
 
       return transformedReferences;
     },
-    getURLsForPubMed: function (data) {
-      return new Promise((resolve) => {
-        const ids = data.map((id) =>
-          (typeof id === 'object') ?
-          this.extractPublicationIdFromURLString(id[0]) :
-          this.extractPublicationIdFromURLString(id)
-        )
-        this.convertPublicationIds(ids).then((pmids) => {
-          if (pmids.length > 0) {
-            const transformedIDs = [];
-            pmids.forEach(pmid => {
-              transformedIDs.push({
-                id: pmid,
-                link: this.pubmedSearchUrl(pmid),
-              })
-            })
-            resolve(transformedIDs)
-          } else {
-            resolve([])
-          }
-        })
-      })
-    },
     extractPublicationIdFromURLString: function (urlStr) {
       if (!urlStr) return
 
@@ -248,79 +239,15 @@ export default {
 
       return names;
     },
-    convertPublicationIds: function (ids) {
-      return new Promise((resolve) => {
-        const pmids = []
-        const toBeConverted = []
-        ids.forEach((id) => {
-          if (id.type === "pmid") {
-            pmids.push(id.id)
-          } else if (id.type === "doi" || id.type === "pmc") {
-            toBeConverted.push(id.id)
-          }
-        })
-        this.getPMID(toBeConverted).then((idList) => {
-          pmids.push(...idList)
-          resolve(pmids)
-        })
-        .catch(() => {
-          resolve(pmids)
-        })
-      })
-    },
-    pubmedSearchUrl: function (ids) {
-      let url = 'https://pubmed.ncbi.nlm.nih.gov/?'
-      let params = new URLSearchParams()
-      params.append('term', ids)
-      return url + params.toString()
-    },
     stripPMIDPrefix: function (pubmedId) {
       return pubmedId.split(':')[1]
     },
-    getPMID: function(idsList) {
-      return new Promise((resolve) => {
-        if (idsList.length > 0) {
-          //Muliple term search does not work well,
-          //DOIs term get splitted unexpectedly
-          //
-          const promises = []
-          const results = []
-          let wrapped = ''
-          idsList.forEach((id, i) => {
-            wrapped += i > 0 ? 'OR"' + id + '"' : '"' + id + '"'
-          })
-
-          const params = new URLSearchParams({
-            db: 'pubmed',
-            term: wrapped,
-            format: 'json'
-          })
-          const promise = fetch(`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?${params}`, {
-            method: 'GET',
-          })
-          .then((response) => response.json())
-          .then((data) => {
-            const newIds = data.esearchresult ? data.esearchresult.idlist : []
-            results.push(...newIds)
-          })
-          promises.push(promise)
-
-          Promise.all(promises).then(() => {
-            resolve(results)
-          }).catch(() => {
-            resolve(results)
-          })
-        } else {
-          resolve([])
-        }
-      })
-    },
     onCitationFormatChange: function(citationType) {
       this.citationType = citationType;
       this.getCitationText(citationType);
     },
     getCitationText: function(citationType) {
-      this.references.forEach((reference) => {
+      this.pubMedReferences.forEach((reference) => {
         const { id, type, doi } = reference;
 
         if (
@@ -331,31 +258,71 @@ export default {
 
           if (type === 'doi' || doi) {
             const doiID = type === 'doi' ? id : doi;
-
-            this.getCitationTextByDOI(doiID)
-              .then((text) => {
-                reference.citation[citationType] = this.replaceLinkInText(text);
-              });
+            this.getCitationTextByDOI(doiID).then((text) => {
+              const formattedText = this.replaceLinkInText(text);
+              reference.citation[citationType] = formattedText;
+              this.updateCopyContents();
+            });
           } else if (type === 'pmid') {
-            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;
+            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) => {
-                      reference.citation[citationType] = this.replaceLinkInText(text);
-                    });
+                  this.getCitationTextByDOI(doiID).then((text) => {
+                    const formattedText = this.replaceLinkInText(text);
+                    reference.citation[citationType] = formattedText;
+                    this.updateCopyContents();
+                  });
+                } 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/${id}`,
+                  });
+                  reference.citation[citationType] = formattedText;
+                  this.updateCopyContents();
                 }
-              });
+              }
+            });
           }
         }
       });
     },
+    updateCopyContents: function () {
+      const citationTypeObj = this.citationOptions.find((item) => item.value === this.citationType);
+      let citationFormatStyle = '';
+      const values = [];
+
+      if (this.referencesWithDOI) {
+        citationFormatStyle = citationTypeObj?.label;
+      }
+
+      this.pubMedReferences.forEach((reference) => {
+        values.push(reference.citation[this.citationType]);
+      });
+
+      this.openLibReferences.forEach((reference) => {
+        values.push(this.formatCopyReference(reference));
+      });
+
+      this.isbnDBReferences.forEach((reference) => {
+        values.push(reference.url);
+      });
+
+      this.$emit('references-loaded', {
+        style: citationFormatStyle,
+        list: values
+      });
+    },
     replaceLinkInText: function (text) {
       const protocol = 'https://';
       let linkBody = text.split(protocol)[1];
@@ -376,87 +343,55 @@ export default {
 
       return text;
     },
+    searchPMID: async function (term) {
+      const esearchAPI = `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=${term}&format=json`;
+      return await this.fetchData(esearchAPI);
+    },
     getCitationTextByDOI: async function (id) {
       const citationAPI = `${CROSSCITE_API_HOST}/format?doi=${id}&style=${this.citationType}&lang=en-US`;
-      try {
-        const response = await fetch(citationAPI);
-        if (!response.ok) {
-          throw new Error(`Response status: ${response.status}`);
-        }
-        const data = await response.text();
-        return data;
-      } catch (error) {
-        console.error(`Fetch citation text error: ${error}`);
-      }
+      return await this.fetchData(citationAPI, 'text');
     },
     getDOIFromPubMedID: async function (pubmedId) {
       const summaryAPI = `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi?db=pubmed&id=${pubmedId}&format=json`;
-      try {
-        const response = await fetch(summaryAPI);
-        if (!response.ok) {
-          throw new Error(`Response status: ${response.status}`);
-        }
-        const data = await response.json();
-        return data;
-      } catch (error) {
-        console.error(`Fetch article summary error: ${error}`);
-      }
+      return await this.fetchData(summaryAPI);
     },
     formatOpenLibReferences: function () {
       this.openLibReferences.forEach((reference) => {
         const { bookId } = reference;
-        this.getBookData(bookId)
-          .then((data) => {
-            const { title, authors, publish_date } = data;
-            if (title) {
-              reference['title'] = title;
-            }
+        this.getBookData(bookId).then((data) => {
+          const { title, authors, publish_date } = data;
+          if (title) {
+            reference['title'] = title;
+          }
 
-            if (publish_date) {
-              reference['date'] = publish_date;
-            }
+          if (publish_date) {
+            reference['date'] = publish_date;
+          }
 
-            if (authors) {
-              reference['authors'] = [];
+          if (authors) {
+            reference['authors'] = [];
 
-              authors.forEach((author) => {
-                this.getBookAuthor(author.key)
-                  .then((data) => {
-                    const { name } = data;
-                    if (name) {
-                      reference['authors'].push(name);
-                    }
-                  });
+            authors.forEach((author) => {
+              this.getBookAuthor(author.key).then((data) => {
+                const { name } = data;
+                if (name) {
+                  reference['authors'].push(name);
+                  this.updateCopyContents();
+                }
               });
-            }
-          });
+            });
+          }
+          this.updateCopyContents();
+        });
       });
     },
     getBookData: async function (bookId) {
       const apiURL = `https://openlibrary.org/books/${bookId}.json`;
-      try {
-        const response = await fetch(apiURL);
-        if (!response.ok) {
-          throw new Error(`Response status: ${response.status}`);
-        }
-        const data = await response.json();
-        return data;
-      } catch (error) {
-        console.error(`Fetch book data error: ${error}`);
-      }
+      return await this.fetchData(apiURL);
     },
     getBookAuthor: async function (key) {
       const apiURL = `https://openlibrary.org${key}.json`;
-      try {
-        const response = await fetch(apiURL);
-        if (!response.ok) {
-          throw new Error(`Response status: ${response.status}`);
-        }
-        const data = await response.json();
-        return data;
-      } catch (error) {
-        console.error(`Fetch book author error: ${error}`);
-      }
+      return await this.fetchData(apiURL);
     },
     formatCopyReference: function (reference) {
       const copyContents = [];
@@ -478,6 +413,22 @@ export default {
 
       return copyContents.join(' ');
     },
+    fetchData: async function (apiURL, format) {
+      try {
+        const response = await fetch(apiURL);
+        if (!response.ok) {
+          throw new Error(`Response status: ${response.status}`);
+        }
+
+        if (format === 'text') {
+          return await response.text();
+        } else {
+          return await response.json();
+        }
+      } catch (error) {
+        console.error(`Fetch data error: ${error}`);
+      }
+    },
   },
 }
 </script>