From 671ca0a7fefe612381733bcd228a4355a951cbd3 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 2 Feb 2022 13:47:51 -0500
Subject: [PATCH] Implement bioconductor xref on the frontend.

Cleanup xref rendering a bit.
---
 client/src/components/Tool/ToolFooter.vue     | 15 +++---
 client/src/components/xrefs.vue               | 53 -------------------
 .../tools/mulled_example_explicit.xml         |  3 ++
 3 files changed, 12 insertions(+), 59 deletions(-)
 delete mode 100644 client/src/components/xrefs.vue

diff --git a/client/src/components/Tool/ToolFooter.vue b/client/src/components/Tool/ToolFooter.vue
index a57514711c8..f15b83248c7 100644
--- a/client/src/components/Tool/ToolFooter.vue
+++ b/client/src/components/Tool/ToolFooter.vue
@@ -35,11 +35,10 @@
         <div v-if="hasReferences" class="mb-1">
             <span class="font-weight-bold">References:</span>
             <div v-for="(xref, index) in xrefs" :key="index">
-                - {{ xref.reftype }}:
+                -
                 <template v-if="xref.reftype == 'bio.tools'">
-                    {{ xref.value }}
-                    (<a :href="`https://bio.tools/${xref.value}`" target="_blank">
-                        bio.tools
+                    bio.tools: {{ xref.value }} (<a :href="`https://bio.tools/${xref.value}`" target="_blank"
+                        >bio.tools
                         <font-awesome-icon
                             v-b-tooltip.hover
                             title="Visit bio.tools reference"
@@ -52,9 +51,13 @@
                             icon="external-link-alt" /> </a
                     >)
                 </template>
-                <template v-else>
-                    {{ xref.value }}
+                <template v-else-if="xref.reftype == 'bioconductor'">
+                    Bioconductor Package:
+                    <a :href="`https://bioconductor.org/packages/${xref.value}/`" target="_blank"
+                        >{{ xref.value }} (doi:10.18129/B9.bioc.{{ xref.value }})</a
+                    >
                 </template>
+                <template v-else> {{ xref.reftype }}: {{ xref.value }} </template>
             </div>
         </div>
         <div v-if="hasCreators" class="mb-1">
diff --git a/client/src/components/xrefs.vue b/client/src/components/xrefs.vue
deleted file mode 100644
index 0cdf65c2a7e..00000000000
--- a/client/src/components/xrefs.vue
+++ /dev/null
@@ -1,53 +0,0 @@
-<template>
-    <b-card>
-        <template v-slot:header>
-            <h4 class="mb-0">References</h4>
-        </template>
-        <table>
-            <tr v-for="(xref, index) in xrefs" :key="index">
-                <th>- {{ xref.reftype }}:</th>
-                <td>
-                    <template v-if="xref.reftype == 'bio.tools'">
-                        <a :href="`https://bio.tools/${xref.value}`" target="_blank">{{ xref.value }}</a>
-                    </template>
-                    <template v-else>
-                        {{ xref.value }}
-                    </template>
-                </td>
-            </tr>
-        </table>
-    </b-card>
-</template>
-<script>
-import { getAppRoot } from "onload/loadConfig";
-import axios from "axios";
-
-export default {
-    props: {
-        source: {
-            type: String,
-            required: true,
-        },
-        id: {
-            type: String,
-            required: true,
-        },
-    },
-    data() {
-        return {
-            xrefs: [],
-            errors: [],
-        };
-    },
-    created: function () {
-        axios
-            .get(`${getAppRoot()}api/${this.source}/${this.id}/xrefs`)
-            .then((response) => {
-                this.xrefs = response.data;
-            })
-            .catch((e) => {
-                console.error(e);
-            });
-    },
-};
-</script>
diff --git a/test/functional/tools/mulled_example_explicit.xml b/test/functional/tools/mulled_example_explicit.xml
index 03db8e436e5..edbf26117d1 100644
--- a/test/functional/tools/mulled_example_explicit.xml
+++ b/test/functional/tools/mulled_example_explicit.xml
@@ -16,6 +16,9 @@ bwa > $output_1 2>&1
     </outputs>
     <tests>
     </tests>
+    <xrefs>
+        <xref type="bioconductor">dada2</xref>
+    </xrefs>
     <help><![CDATA[
 TODO: Fill in help.
     ]]></help>