From 78cf9be78829520f98921f3bcec9f2708cbc3d7a Mon Sep 17 00:00:00 2001
From: Liam Appelbe <liamappelbe@gmail.com>
Date: Sat, 20 Jul 2024 19:02:29 +1000
Subject: [PATCH] web: pubmedtool now checks if IDs are being reused

---
 vetupdates/pubmedtool.html      | 39 +++++++++++++++++++++++++++------
 vetupdates/vetupdates_search.js | 13 +++++++++++
 2 files changed, 45 insertions(+), 7 deletions(-)

diff --git a/vetupdates/pubmedtool.html b/vetupdates/pubmedtool.html
index 75ecd85..84c7407 100644
--- a/vetupdates/pubmedtool.html
+++ b/vetupdates/pubmedtool.html
@@ -22,7 +22,7 @@
 </script>
 <script src="vetupdates_search.js"></script>
 <script>
-const {metadataRequest, kMajorTags} = module.exports;
+const {metadataRequest, kMajorTags, getIdsRequest} = module.exports;
 
 let domWrap = null;
 let domLoad = null;
@@ -138,10 +138,12 @@
 }
 
 class ArticleResult {
-  constructor(id, article, err) {
+  constructor(id, aid, article, err) {
     this.id = id;
+    this.aid = aid;
     this.article = article;
     this.err = err;
+    this.seen = false;
   }
 }
 
@@ -156,12 +158,34 @@
     try {
       const aid = await asyncPubMedConvertId(id);
       const art = await getArticleImpl(aid);
-      return new ArticleResult(id, new ArticleInfo(
+      return new ArticleResult(id, aid, new ArticleInfo(
           aid, art.title, art.authors, art.getDateText(), art.doi,
           art.journalName, art.journalAbbr, art.getLink()), null);
     } catch (err) {
-      return new ArticleResult(id, null, err);
+      return new ArticleResult(id, null, null, err);
+    }
+  }
+
+  async function checkUsed(results) {
+    const pmids = [];
+    const pmcids = [];
+    for (const ar of results) {
+      if (ar.aid == null) continue;
+      if (ar.aid.pmid != null) {
+        pmids.push(ar.aid.pmid);
+      } else if (ar.aid.pmcid != null) {
+        pmcids.push(ar.aid.pmcid);
+      }
+    }
+    const known = new Set(await getIdsRequest(pmids, pmcids));
+    for (const ar of results) {
+      if (ar.aid == null) continue;
+      if (known.has(parseInt(ar.aid.pmid)) ||
+          known.has(-parseInt(ar.aid.pmcid))) {
+        ar.seen = true;
+      }
     }
+    return results;
   }
 
   domWrap.classList.add('loading');
@@ -173,7 +197,7 @@
   state.errorText = '';
   saveState();
 
-  const results = await Promise.all(state.ids.map(getArticle));
+  const results = await checkUsed(await Promise.all(state.ids.map(getArticle)));
   domWrap.classList.remove('loading');
   domLoad.classList.remove('loading');
 
@@ -181,7 +205,8 @@
     if (ar.err != null) {
       addError(`Invalid ID: ${ar.id}`);
       console.error(ar.id, ar.err);
-      continue;
+    } else if (ar.seen) {
+      addError(`Reused ID: ${ar.id}`);
     }
   }
 
@@ -519,7 +544,7 @@ <h1>PubMed Formatter</h1>
       <br/>
       Errors:
       <br/>
-      <textarea id="errors" rows="6" cols="40"></textarea>
+      <textarea id="errors" rows="8" cols="40"></textarea>
     </div>
     <div class="middle">
       <span>Elements: <a onclick="selectTextArea('tags')">[SELECT]</a></span>
diff --git a/vetupdates/vetupdates_search.js b/vetupdates/vetupdates_search.js
index cffc447..97a9597 100644
--- a/vetupdates/vetupdates_search.js
+++ b/vetupdates/vetupdates_search.js
@@ -4,6 +4,7 @@ const kApiEndpoint =
     kLocalDev ? 'http://localhost:8080' : 'https://squeakysqueenoctopus.com';
 const kAdvancedSearchApi = kApiEndpoint + '/zpqk';
 const kSearchApi = kApiEndpoint + '/gqmo';
+const kGetIdsApi = kApiEndpoint + '/rmdl';
 const kMetadataApi = kApiEndpoint + '/meta';
 const kRetries = 10;
 const kMajorTagText = 'Topics';
@@ -104,6 +105,12 @@ async function searchRequest(q) {
   return JSON.parse(await asyncRequest(kSearchApi + '?' + q));
 }
 
+async function getIdsRequest(pmids, pmcids) {
+  const q = [encodeIdQuery('p', pmids), encodeIdQuery('c', pmcids)];
+  return JSON.parse(await asyncRequest(
+      kGetIdsApi + '?' + q.filter(w => w.length > 0).join('&')));
+}
+
 function getUniqueElementId() {
   while (true) {
     const newId = `id_${Math.floor(1e9 * Math.random())}`;
@@ -240,6 +247,11 @@ function cleanMetadata(a) {
   return b;
 }
 
+function encodeIdQuery(q, v) {
+  if (v.length == 0) return '';
+  return q + '=' + encodeURIComponent(v.join(','));
+}
+
 function encodeTextQuery(q, t) {
   if (t.value.length == 0) return '';
   return q + '=' +
@@ -396,6 +408,7 @@ if (typeof (module) != 'undefined') {
     metadataRequest,
     advancedSearchRequest,
     searchRequest,
+    getIdsRequest,
     kMajorTags,
   };
 }