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Feb 2, 2025
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v1.28 #6

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8 changes: 8 additions & 0 deletions CHANGELOG
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Original file line number Diff line number Diff line change
@@ -1,3 +1,11 @@
02.02.2025 v1.28
* Some adaptations for better integration with the awesome Zotero Cita plugin: https://github.com/diegodlh/zotero-cita.
* Slightly changed linkToShareAppendix() logic.
* Added downloadFile function.
! Fixed physics of Co-authorship network by reverting to default barnesHut configuration.
! Fix title of edges in Co-authorship network (only considers seed articles as of 1.21).
! Fixed some old terminology in comments.

11.11.2024 v1.27
+ Export options modal for CSV / RIS download.
* De-duplication of All Cited and All Citing is off again by default but can be turned on.
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45 changes: 24 additions & 21 deletions index.html
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Expand Up @@ -157,7 +157,7 @@ <h1 class="title">{{ (currentGraph?.API === 'Co*Citation Network via OpenAlex' |
<ul class="buttons">
<b-navbar-item tag="li" v-for="item, index in graphs" :key="index" class="navbar-item">
<b-button :type="(index==currentTabIndex) ? 'is-primary' : ''" :title="item.tabTitle" @click="setCurrentTabIndex(index)" rounded>
{{ item.tabLabel }} ({{ abbreviateAPI(item.API) }})
{{ item.tabLabel + ((abbreviateAPI(item.API)) ? ' (' + abbreviateAPI(item.API) + ')' : '') }}
<a title="Close tab" class="delete" @click.stop="clickCloseTab(index)"></a> <!-- .stop prevents event propagation to parent @click event -->
</b-button>
</b-navbar-item>
Expand Down Expand Up @@ -190,10 +190,10 @@ <h2 class="title is-4">Seed Articles ({{ seedArticles.length }})</h2>
</template>
<div class="content">
<p>
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a> /
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a>
<!-- Make sure network is fully loaded (otherwise citedArticles / citingArticles tabs would show eternal spinning wheels when JSON is reloaded) -->
<template v-if="citedArticles && citingArticles">
<a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
/ <a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
<b-tooltip dashed multilined position="is-bottom" type="is-dark"
label="Can be shared and reloaded through the 'File' button at the top right!">
<a @click="downloadJSON">download full network as JSON</a>
Expand Down Expand Up @@ -227,7 +227,7 @@ <h2 class="title is-4">Seed Articles ({{ seedArticles.length }})</h2>
<a @click="selected = seedArticles.filter(x => x.isSource)[0]">(select)</a>
</p>
<p>
Data retrieved through <a @click="indexFAQ = 'switch-api'; showFAQ = true;" href="#switch-api">{{ currentGraph.API + ' (' + abbreviateAPI(currentGraph.API) + ')' }}</a> API on {{ new Date(currentGraph.timestamp).toLocaleString(undefined, {"day": "numeric", "month": "long", "year": "numeric"}) }}
Data retrieved through <a @click="indexFAQ = 'switch-api'; showFAQ = true;" href="#switch-api">{{ currentGraph.API + ((abbreviateAPI(currentGraph.API)) ? ' (' + abbreviateAPI(currentGraph.API) + ')' : '') }}</a> on {{ new Date(currentGraph.timestamp).toLocaleString(undefined, {"day": "numeric", "month": "long", "year": "numeric"}) }}
<b-tooltip dashed multilined type="is-dark" position="is-bottom" :label="completenessLabel" v-if="currentGraph.API !== 'Co*Citation Network via OpenAlex'">
<a @click="indexFAQ = 'completeness'; showFAQ = true;" href="#completeness"
:style="'color: ' + ((completenessPercent > 40) ? '' : '#ff3860')">
Expand Down Expand Up @@ -365,7 +365,7 @@ <h4 class="title is-6">Reference contexts in source article, {{ currentGraph.sou
</b-tooltip>
</template>
</b-table-column>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" sortable>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" :visible="currentGraph.API !== 'Zotero Cita'" sortable>
<template v-slot:header="{ column }">
<b-tooltip :label="column.meta" dashed position="is-left" type="is-dark">
{{ column.label }}
Expand Down Expand Up @@ -471,17 +471,18 @@ <h4 class="title is-6">Reference contexts in source article, {{ currentGraph.sou
<!-- Have to use currentGraph.citedArticles === undefined to show progress indicator because the computed always returns [] if undefined -->
<b-tab-item value="citedArticlesTab" :disabled="currentGraph.citedArticles === undefined" v-if="currentGraph.citedArticles === undefined || citedArticles.length || currentGraph.API === 'Co*Citation Network via OpenAlex'">
<template slot="header">
<h2 class="title is-4">{{ (currentGraph.allCited) ? 'All ' : ((currentGraph.ricsRankCutoff) ? '' : 'Top ') }}Cited
<h2 class="title is-4">
{{ (currentGraph.allCited) ? 'All ' : ((currentGraph.ricsRankCutoff) ? '' : 'Top ') }}Cited
(<template v-if="citedArticles.length">{{ citedArticles.length }}</template>
<b-progress v-else :value="(isLoadingTotal > 1) ? isLoadingIndex/isLoadingTotal*100 : undefined" size="is-medium" show-value format="percent" :precision="0" style="width: 50px; display: inline-block"></b-progress>)
</h2>
</template>
<div class="content" v-if="citedArticles.length">
<p>
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a> /
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a>
<!-- Make sure network is fully loaded (otherwise citedArticles / citingArticles tabs would show eternal spinning wheels when JSON is reloaded) -->
<template v-if="citedArticles && citingArticles">
<a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
/ <a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
<b-tooltip dashed multilined position="is-bottom" type="is-dark"
label="Can be shared and reloaded through the 'File' button at the top right!">
<a @click="downloadJSON">download full network as JSON</a>
Expand Down Expand Up @@ -600,7 +601,7 @@ <h4 class="title is-6">Abstract</h4>
</b-tooltip>
</template>
</b-table-column>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" sortable>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" :visible="currentGraph.API !== 'Zotero Cita'" sortable>
<template v-slot:header="{ column }">
<b-tooltip :label="column.meta" dashed position="is-left" type="is-dark">
{{ column.label }}
Expand Down Expand Up @@ -706,16 +707,18 @@ <h4 class="title is-6">Abstract</h4>
<!-- Have to use currentGraph.citingArticles === undefined to show progress indicator because the computed always returns [] if undefined -->
<b-tab-item value="citingArticlesTab" :disabled="currentGraph.citingArticles === undefined" v-if="currentGraph.citingArticles === undefined || citingArticles.length || currentGraph.API === 'Co*Citation Network via OpenAlex'">
<template slot="header">
<h2 class="title is-4">{{ (currentGraph.allCiting) ? 'All ' : ((currentGraph.ricsRankCutoff) ? '' : 'Top ') }}Citing
<h2 class="title is-4">
{{ (currentGraph.allCiting) ? 'All ' : ((currentGraph.ricsRankCutoff) ? '' : 'Top ') }}Citing
(<template v-if="citingArticles.length">{{ citingArticles.length }}</template>
<b-progress v-else :value="(currentGraph.citedArticles === undefined) ? undefined : (isLoadingTotal > 1) ? isLoadingIndex/isLoadingTotal*100 : undefined" size="is-medium" show-value format="percent" :precision="0" style="width: 50px; display: inline-block"></b-progress>)
</h2>
</template>
<div class="content" v-if="citingArticles.length">
<p>
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a> /
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a>
<!-- Make sure network is fully loaded (otherwise citedArticles / citingArticles tabs would show eternal spinning wheels when JSON is reloaded) -->
<template v-if="citedArticles && citingArticles">
<a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
/ <a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
<b-tooltip dashed multilined position="is-bottom" type="is-dark"
label="Can be shared and reloaded through the 'File' button at the top right!">
<a @click="downloadJSON">download full network as JSON</a>
Expand Down Expand Up @@ -834,7 +837,7 @@ <h4 class="title is-6">Abstract</h4>
</b-tooltip>
</template>
</b-table-column>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" sortable>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" :visible="currentGraph.API !== 'Zotero Cita'" sortable>
<template v-slot:header="{ column }">
<b-tooltip :label="column.meta" dashed position="is-left" type="is-dark">
{{ column.label }}
Expand Down Expand Up @@ -943,10 +946,10 @@ <h2 class="title is-4">Co-Cited ({{ coCitedArticles.length }})</h2>
</template>
<div class="content">
<p>
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a> /
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a>
<!-- Make sure network is fully loaded (otherwise citedArticles / citingArticles tabs would show eternal spinning wheels when JSON is reloaded) -->
<template v-if="citedArticles && citingArticles">
<a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
/ <a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
<b-tooltip dashed multilined position="is-bottom" type="is-dark"
label="Can be shared and reloaded through the 'File' button at the top right!">
<a @click="downloadJSON">download full network as JSON</a>
Expand Down Expand Up @@ -1067,7 +1070,7 @@ <h4 class="title is-6">Abstract</h4>
</b-tooltip>
</template>
</b-table-column>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" sortable>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" :visible="currentGraph.API !== 'Zotero Cita'" sortable>
<template v-slot:header="{ column }">
<b-tooltip :label="column.meta" dashed position="is-left" type="is-dark">
{{ column.label }}
Expand Down Expand Up @@ -1176,10 +1179,10 @@ <h2 class="title is-4">Co-Citing ({{ coCitingArticles.length }})</h2>
</template>
<div class="content">
<p>
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a> /
<a @click="fullscreenTable = !fullscreenTable; if (fullscreenTable) resetBothNetworks(); else initCurrentNetwork();" title="Toggle table fullscreen">{{ (fullscreenTable) ? 'show networks' : 'fullscreen table' }}</a>
<!-- Make sure network is fully loaded (otherwise citedArticles / citingArticles tabs would show eternal spinning wheels when JSON is reloaded) -->
<template v-if="citedArticles && citingArticles">
<a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
/ <a @click="showOptionsExportArticles = true">export articles as CSV or RIS</a> /
<b-tooltip dashed multilined position="is-bottom" type="is-dark"
label="Can be shared and reloaded through the 'File' button at the top right!">
<a @click="downloadJSON">download full network as JSON</a>
Expand Down Expand Up @@ -1300,7 +1303,7 @@ <h4 class="title is-6">Abstract</h4>
</b-tooltip>
</template>
</b-table-column>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" sortable>
<b-table-column field="citationsCount" label="Cit." meta="Number of global citations (cited by how many articles in total)" :visible="currentGraph.API !== 'Zotero Cita'" sortable>
<template v-slot:header="{ column }">
<b-tooltip :label="column.meta" dashed position="is-left" type="is-dark">
{{ column.label }}
Expand Down Expand Up @@ -1554,7 +1557,7 @@ <h3 class="modal-card-title">Co-authorship network settings</h3>
<header class="modal-card-head">
<content>
<h3 class="modal-card-title">Import custom list of IDs</h3>
<p>One ID per row. Use OpenAlex / Semantic Scholar for PMIDs. Empty rows are placeholders in order to help preserve original numbering.</p>
<p>One ID per row, usually DOI. Use OpenAlex / Semantic Scholar for PMIDs. Empty rows are placeholders in order to help preserve original numbering.</p>
</content>
</header>
<section style="position: relative; height:300px">
Expand All @@ -1579,7 +1582,7 @@ <h3 class="modal-card-title">API options</h3>
</header>
<div class="card-content">
<p class="content">
Cited Articles (References) can be retrieved through all <a @click="indexFAQ = 'switch-api'; showFAQ = true;" href="#switch-api">APIs</a>. Citing Articles (Citations) can be retrieved through OpenAlex (OA), Semantic Scholar (S2) and OpenCitations (OC). <a @click="indexFAQ = 'top-cited'; showFAQ = true;" href="#top-cited">Top Cited</a> are the most cited references by the Seed Articles. <a @click="indexFAQ = 'top-citing'; showFAQ = true;" href="#top-citing">Top Citing</a> are citing the most Seed Articles. Retrieving All References / Citations works best with OpenAlex (OA) & Semantic Scholar (S2).
Cited Articles (References) can be retrieved through all <a @click="indexFAQ = 'switch-api'; showFAQ = true;" href="#switch-api">APIs</a>. Citing Articles (Citations) can be retrieved through OpenAlex (OA), Semantic Scholar (S2) and OpenCitations (OC). <a @click="indexFAQ = 'top-cited'; showFAQ = true;" href="#top-cited">Top Cited</a> are the most cited references by the Seed Articles. <a @click="indexFAQ = 'top-citing'; showFAQ = true;" href="#top-citing">Top Citing</a> are citing the most Seed Articles. Retrieving All Cited (i.e. references) / All Citing (i.e. citations) works best with OpenAlex (OA) & Semantic Scholar (S2).
</p>
<b-field grouped>
<b-field label="Select API">
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