@abi-software/map-utilities 1.3.2-beta.0 → 1.3.2

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@abi-software/map-utilities",
-  "version": "1.3.2-beta.0",
+  "version": "1.3.2",
   "files": [
     "dist/*",
     "src/*",

package/src/components.d.ts

@@ -42,7 +42,6 @@ declare module 'vue' {
     ElTooltip: typeof import('element-plus/es')['ElTooltip']
     ElTree: typeof import('element-plus/es')['ElTree']
     ExternalResourceCard: typeof import('./components/Tooltip/ExternalResourceCard.vue')['default']
-    ExternalResourceCard1: typeof import('./components/Tooltip/ExternalResourceCard-1.vue')['default']
     HelpModeDialog: typeof import('./components/HelpModeDialog/HelpModeDialog.vue')['default']
     ProvenancePopup: typeof import('./components/Tooltip/ProvenancePopup.vue')['default']
     Tooltip: typeof import('./components/Tooltip/Tooltip.vue')['default']

package/src/components/Tooltip/ExternalResourceCard-1.vue

@@ -1,614 +0,0 @@
-<template>
-  <div class="resource-container">
-    <div class="attribute-title-container">
-      <div class="attribute-title">References</div>
-      <div class="copy-button">
-        <CopyToClipboard label="Copy list to clipboard" :content="referecesListContent" />
-      </div>
-    </div>
-    <div class="citation-tabs" v-if="pubMedReferences.length">
-      <el-button
-        link
-        v-for="citationOption of citationOptions"
-        :key="citationOption.value"
-        :type="citationType === citationOption.value ? 'primary' : ''"
-        @click="onCitationFormatChange(citationOption.value)"
-      >
-        {{ citationOption.label }}
-      </el-button>
-    </div>
-    <ul class="citation-list">
-      <li
-        v-for="reference of pubMedReferences"
-        :key="reference.id"
-        :class="{'loading': reference.citation && reference.citation[citationType] === ''}"
-      >
-        <template v-if="reference.citation && reference.citation[citationType]">
-          <span v-html="reference.citation[citationType]"></span>
-          <CopyToClipboard :content="reference.citation[citationType]" />
-        </template>
-      </li>
-
-      <li v-for="reference of openLibReferences">
-        <div v-html="formatCopyReference(reference)"></div>
-        <CopyToClipboard :content="formatCopyReference(reference)" />
-      </li>
-
-      <li v-for="reference of isbnDBReferences">
-        <a :href="reference.url" target="_blank">{{ reference.url }}</a>
-        <CopyToClipboard :content="reference.url" />
-      </li>
-    </ul>
-  </div>
-</template>
-
-<script>
-import CopyToClipboard from '../CopyToClipboard/CopyToClipboard.vue';
-import { Cite } 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 CROSSCITE_API_HOST = 'https://citation.doi.org';
-const CITATION_OPTIONS = [
-  {
-    label: 'APA',
-    value: 'apa',
-  },
-  {
-    label: 'Chicago',
-    value: 'chicago-note-bibliography',
-  },
-  {
-    label: 'IEEE',
-    value: 'ieee',
-  },
-  {
-    label: 'Bibtex',
-    value: 'bibtex',
-  },
-];
-const CITATION_DEFAULT = 'apa';
-
-export default {
-  name: "ExternalResourceCard",
-  props: {
-    resources: {
-      type: Array,
-      default: () => [],
-    },
-  },
-  data: function () {
-    return {
-      pubMedReferences: [],
-      openLibReferences: [],
-      isbnDBReferences: [],
-      referecesListContent: '',
-      citationOptions: CITATION_OPTIONS,
-      citationType: CITATION_DEFAULT,
-    }
-  },
-  watch: {
-    resources: function (_resources) {
-      this.formatReferences([..._resources]);
-      this.getCitationText(CITATION_DEFAULT);
-    },
-  },
-  computed: {
-    referencesWithDOI: function () {
-      const withDOI = this.pubMedReferences.filter((reference) => reference.type === 'doi' || reference.doi);
-      return withDOI.length;
-    },
-  },
-  mounted: function () {
-    this.formatReferences([...this.resources]);
-    this.getCitationText(CITATION_DEFAULT);
-  },
-  methods: {
-    formatReferences: function (references) {
-      const nonPubMedReferences = this.extractNonPubMedReferences(references);
-      const pubMedReferences = references.filter((reference) => !nonPubMedReferences.includes(reference));
-
-      this.pubMedReferences = pubMedReferences.map((reference) =>
-        (typeof reference === 'object') ?
-        this.extractPublicationIdFromURLString(reference[0]) :
-        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();
-      });
-    },
-    extractNonPubMedReferences: function (references) {
-      const extractedReferences = [];
-      const pubmedDomains = this.getPubMedDomains();
-
-      references.forEach((reference) => {
-        let count = 0;
-        pubmedDomains.forEach((name) => {
-          if (reference.includes(name)) {
-            count++;
-          }
-        });
-        if (!count) {
-          extractedReferences.push(reference);
-        }
-      });
-
-      return extractedReferences;
-    },
-    formatNonPubMedReferences: async function (references) {
-      const transformedReferences = [];
-      const filteredReferences = references.filter((referenceURL) => referenceURL.indexOf('isbn') !== -1);
-      const isbnIDs = filteredReferences.map((url) => {
-        const isbnId = url.split('/').pop();
-        return 'ISBN:' + isbnId;
-      });
-      const isbnIDsKey = isbnIDs.join(',');
-      const failedIDs = isbnIDs.slice();
-
-      const openlibAPI = `https://openlibrary.org/api/books?bibkeys=${isbnIDsKey}&format=json`;
-      const data = await this.fetchData(openlibAPI);
-
-      for (const key in data) {
-        const successKeyIndex = failedIDs.indexOf(key);
-        failedIDs.splice(successKeyIndex, 1);
-
-        const url = data[key].info_url;
-        const urlSegments = url.split('/');
-        const endpointIndex = urlSegments.indexOf('books');
-        const bookId = urlSegments[endpointIndex + 1];
-
-        transformedReferences.push({
-          id: key.split(':')[1], // Key => "ISBN:1234"
-          type: 'openlib',
-          url: url,
-          bookId: bookId,
-        });
-      }
-
-      failedIDs.forEach((failedID) => {
-        const id = failedID.split(':')[1];
-        // Data does not exist in OpenLibrary
-        // Provide ISBNDB link for reference
-        const url = `https://isbndb.com/book/${id}`;
-        transformedReferences.push({
-          id: id,
-          url: url,
-          type: 'isbndb'
-        });
-      });
-
-      return transformedReferences;
-    },
-    extractPublicationIdFromURLString: function (urlStr) {
-      if (!urlStr) return
-
-      const str = decodeURIComponent(urlStr)
-
-      let term = {id: '', type: '', citation: {}}
-
-      const names = this.getPubMedDomains()
-
-      names.forEach((name) => {
-        const lastIndex = str.lastIndexOf(name)
-        if (lastIndex !== -1) {
-          term.id = str.slice(lastIndex + name.length)
-          if (name === 'doi.org/') {
-            term.type = "doi"
-          } else if (name === 'pmc/articles/') {
-            term.type = "pmc"
-          } else {
-            term.type = "pmid"
-          }
-        }
-      })
-
-      //Backward compatability with doi: and PMID:
-      if (term.id === '') {
-        if (urlStr.includes("doi:")) {
-          term.id = this.stripPMIDPrefix(urlStr)
-          term.type = "doi"
-        } else if (urlStr.includes("PMID:")) {
-          term.id = this.stripPMIDPrefix(urlStr)
-          term.type = "pmid"
-        }
-      }
-
-      if (term.id.endsWith('/')) {
-        term.id = term.id.slice(0, -1)
-      }
-
-      return term
-    },
-    getPubMedDomains: function () {
-      const names = [
-        'doi.org/',
-        'nih.gov/pubmed/',
-        'pmc/articles/',
-        'pubmed.ncbi.nlm.nih.gov/',
-      ]
-
-      return names;
-    },
-    stripPMIDPrefix: function (pubmedId) {
-      return pubmedId.split(':')[1]
-    },
-    onCitationFormatChange: function(citationType) {
-      this.citationType = citationType;
-      this.getCitationText(citationType);
-    },
-    getCitationText: function(citationType) {
-      this.pubMedReferences.forEach((reference) => {
-        const { id, type, doi } = reference;
-
-        if (
-          !(reference.citation && reference.citation[citationType])
-          && id
-        ) {
-          reference.citation[citationType] = ''; // loading
-
-          if (type === 'doi' || doi) {
-            const doiID = type === 'doi' ? id : doi;
-            this.getCitationTextByDOI(doiID).then((text) => {
-              const formattedText = this.replaceLinkInText(text);
-              reference.citation[citationType] = formattedText;
-              this.updateCopyContents();
-            });
-          } else if (type === 'pmid') {
-            this.getCitationTextByPMID(id).then((text) => {
-              const formattedText = this.replaceLinkInText(text);
-              reference.citation[citationType] = formattedText;
-              this.updateCopyContents();
-            })
-            // 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();
-            //       });
-            //     } 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/${id}`,
-            //       });
-            //       reference.citation[citationType] = formattedText;
-            //       this.updateCopyContents();
-            //     }
-            //   }
-            // });
-          }
-        }
-      });
-    },
-    updateCopyContents: function () {
-      const citationTypeObj = this.citationOptions.find((item) => item.value === this.citationType);
-      let citationFormatStyle = '';
-      const values = [];
-
-      if (this.referencesWithDOI) {
-        citationFormatStyle = citationTypeObj?.label;
-      }
-
-      this.pubMedReferences.forEach((reference) => {
-        values.push(reference.citation[this.citationType]);
-      });
-
-      this.openLibReferences.forEach((reference) => {
-        values.push(this.formatCopyReference(reference));
-      });
-
-      this.isbnDBReferences.forEach((reference) => {
-        values.push(reference.url);
-      });
-
-      if (values.length) {
-        const list = values.map((item) => `<li>${item}</li>`).join('\n');
-        const listContent = `<ul>${list}</ul>`;
-        const listTitle = `<div><strong>References</strong></div>`;
-        this.referecesListContent = listTitle + `\n` + listContent;
-      }
-
-      this.$emit('references-loaded', {
-        style: citationFormatStyle,
-        list: values
-      });
-    },
-    replaceLinkInText: function (text) {
-      const protocol = 'https://';
-      let linkBody = text.split(protocol)[1];
-
-      if (linkBody) {
-        linkBody = linkBody.split(' ')[0];
-        linkBody = linkBody.trim();
-
-        if (linkBody.endsWith('.')) {
-          linkBody = linkBody.substring(0, linkBody.length - 1);
-        }
-
-        const fullLink = protocol + linkBody;
-        const htmlLink = `<a href="${fullLink}" target="_blank">${fullLink}</a>`;
-
-        return text.replace(fullLink, htmlLink);
-      }
-
-      return text;
-    },
-    searchPMID: async function (term) {
-      const esearchAPI = `https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esearch.fcgi?db=pubmed&term=${term}&format=json`;
-      return await this.fetchData(esearchAPI);
-    },
-    getCitationTextByPMID: async function (id) {
-      const cite = await Cite.async(id, {forceType: '@pubmed/id'});
-      const citation = (this.citationType === 'bibtex') ?
-        cite.format(this.citationType) :
-        cite.format('bibliography', {
-          format: 'html',
-          template: this.citationType,
-          lang: 'en-US'
-        })
-      return citation;
-    },
-    getCitationTextByDOI: async function (id) {
-      console.table({doi: id, type: this.citationType})
-      const cite = await Cite.async(id);
-      console.log('response data', cite)
-      const citation = (this.citationType === 'bibtex') ?
-        cite.format(this.citationType) :
-        cite.format('bibliography', {
-          format: 'html',
-          template: this.citationType,
-          lang: 'en-US'
-        })
-      console.log(citation)
-      // return citation;
-
-      const citationAPI = `${CROSSCITE_API_HOST}/format?doi=${id}&style=${this.citationType}&lang=en-US`;
-      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=${pubmedId}&format=json`;
-      return await this.fetchData(summaryAPI);
-    },
-    formatOpenLibReferences: function () {
-      this.openLibReferences.forEach((reference) => {
-        const { bookId } = reference;
-        this.getBookData(bookId).then((data) => {
-          const { title, authors, publish_date } = data;
-          if (title) {
-            reference['title'] = title;
-          }
-
-          if (publish_date) {
-            reference['date'] = publish_date;
-          }
-
-          if (authors) {
-            reference['authors'] = [];
-
-            authors.forEach((author) => {
-              this.getBookAuthor(author.key).then((data) => {
-                const { name } = data;
-                if (name) {
-                  reference['authors'].push(name);
-                  this.updateCopyContents();
-                }
-              });
-            });
-          }
-          this.updateCopyContents();
-        });
-      });
-    },
-    getBookData: async function (bookId) {
-      const apiURL = `https://openlibrary.org/books/${bookId}.json`;
-      return await this.fetchData(apiURL);
-    },
-    getBookAuthor: async function (key) {
-      const apiURL = `https://openlibrary.org${key}.json`;
-      return await this.fetchData(apiURL);
-    },
-    formatCopyReference: function (reference) {
-      const copyContents = [];
-      const { title, date, authors, url } = reference;
-
-      if (title) {
-        copyContents.push(title);
-      }
-
-      if (date) {
-        copyContents.push(`(${date})`);
-      }
-
-      if (authors) {
-        copyContents.push(`- ${authors.join(', ')}`);
-      }
-
-      copyContents.push(`<div><a href="${url}" target="_blank">${url}</a></div>`);
-
-      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>
-
-<style lang="scss" scoped>
-.resource-container {
-  margin-top: 1em;
-
-  &:hover {
-    .attribute-title-container :deep(.copy-clipboard-button) {
-      opacity: 1;
-      visibility: visible;
-    }
-  }
-}
-
-.attribute-title-container {
-  margin-bottom: 0.5rem;
-  display: flex;
-  align-items: center;
-  gap: 0.5rem;
-
-  :deep(.copy-clipboard-button) {
-    opacity: 0;
-    visibility: hidden;
-  }
-}
-
-.attribute-title {
-  font-size: 16px;
-  font-weight: 600;
-  /* font-weight: bold; */
-  text-transform: uppercase;
-}
-
-.citation-list {
-  margin: 0;
-  margin-top: 0.5rem;
-  padding: 0;
-  list-style: none;
-  line-height: 1.3;
-
-  li {
-    margin: 0;
-    padding: 0.5rem 1.5rem 0.5rem 0.75rem;
-    border-radius: var(--el-border-radius-base);
-    background-color: var(--el-bg-color-page);
-    position: relative;
-
-    :deep(a) {
-      word-wrap: break-word;
-      color: $app-primary-color;
-    }
-
-    + li {
-      margin-top: 0.5rem;
-    }
-
-    &.loading {
-      padding: 1rem;
-
-      &::before {
-        content: "";
-        display: block;
-        width: 100%;
-        height: 100%;
-        position: absolute;
-        top: 0;
-        left: 0;
-        animation-duration: 3s;
-        animation-fill-mode: forwards;
-        animation-iteration-count: infinite;
-        animation-name: loadingAnimation;
-        animation-timing-function: linear;
-        background: linear-gradient(to right,
-          var(--el-bg-color-page) 5%,
-          var(--el-color-info-light-8) 15%,
-          var(--el-bg-color-page) 30%
-        );
-      }
-    }
-
-    :deep(.copy-clipboard-button) {
-      position: absolute;
-      bottom: 0.25rem;
-      right: 0.25rem;
-      opacity: 0;
-      visibility: hidden;
-    }
-
-    &:hover {
-      :deep(.copy-clipboard-button) {
-        opacity: 1;
-        visibility: visible;
-      }
-    }
-  }
-}
-
-.citation-tabs {
-  .el-button {
-    &:hover,
-    &:focus,
-    &:active {
-      color: $app-primary-color;
-    }
-
-    &.is-link {
-      background: transparent !important;
-      border-color: transparent !important;
-      color: var(--el-button-text-color) !important;
-      height: auto !important;
-      padding: 2px !important;
-
-      &:hover,
-      &:focus,
-      &:active {
-        color: $app-primary-color !important;
-        box-shadow: none !important;
-      }
-    }
-  }
-
-  .el-button + .el-button {
-    margin-left: 0.25rem;
-  }
-}
-
-@keyframes loadingAnimation {
-  0% {
-    background-position: -30vw 0;
-  }
-  100% {
-    background-position: 70vw 0;
-  }
-}
-</style>