From 236278e864c2a4f532cad4436897fb1743d9a4ee Mon Sep 17 00:00:00 2001
From: David Glymph <Woozl@users.noreply.github.com>
Date: Sun, 16 Feb 2025 13:42:33 -0500
Subject: [PATCH 1/2] add curies back to csv + header

---
 src/components/DownloadDialog.jsx | 28 ++++++++++++++++++++++------
 1 file changed, 22 insertions(+), 6 deletions(-)

diff --git a/src/components/DownloadDialog.jsx b/src/components/DownloadDialog.jsx
index 171bfdf0..a78578b2 100644
--- a/src/components/DownloadDialog.jsx
+++ b/src/components/DownloadDialog.jsx
@@ -19,6 +19,27 @@ const jsonToCsvString = (json) => new Promise((res, rej) => {
   });
 });
 
+const constructCsvObj = (message) => {
+  const nodeLabelHeaders = Object.keys(
+    message.results[0].node_bindings,
+  ).flatMap((node_label) => [`${node_label} (Name)`, `${node_label} (CURIE)`]);
+  const header = [...nodeLabelHeaders, 'Score'];
+
+  const body = message.results.map((result) => {
+    const row = [];
+    Object.values(result.node_bindings).forEach((nb) => {
+      const curie = nb[0].id;
+      const node = message.knowledge_graph.nodes[curie];
+      row.push(node.name || node.categories[0]);
+      row.push(curie);
+    });
+    row.push(result.score);
+    return row;
+  });
+
+  return [header, ...body];
+};
+
 export default function DownloadDialog({
   open, setOpen, message,
 }) {
@@ -35,12 +56,7 @@ export default function DownloadDialog({
       blob = new Blob([JSON.stringify({ message }, null, 2)], { type: 'application/json' });
     }
     if (type === 'csv') {
-      const subsetMessage = message.results.map((r) => [
-        ...Object.values(r.node_bindings).map((nb) => {
-          const node = message.knowledge_graph.nodes[nb[0].id];
-          return node.name || node.categories[0];
-        }), r.score]);
-      const csvString = await jsonToCsvString(subsetMessage);
+      const csvString = await jsonToCsvString(constructCsvObj(message));
       blob = new Blob([csvString], { type: 'text/csv' });
     }
 

From b3c81afcb0e0a8d7828c7c94ed6f621735401285 Mon Sep 17 00:00:00 2001
From: David Glymph <Woozl@users.noreply.github.com>
Date: Sun, 16 Feb 2025 14:08:04 -0500
Subject: [PATCH 2/2] add publications to csv

---
 src/components/DownloadDialog.jsx | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/src/components/DownloadDialog.jsx b/src/components/DownloadDialog.jsx
index a78578b2..637383d9 100644
--- a/src/components/DownloadDialog.jsx
+++ b/src/components/DownloadDialog.jsx
@@ -19,11 +19,32 @@ const jsonToCsvString = (json) => new Promise((res, rej) => {
   });
 });
 
+const constructPmidOrPmcLink = (id) => {
+  if (id.startsWith('PMID')) {
+    return `https://pubmed.ncbi.nlm.nih.gov/${id.split(':')[1]}`;
+  }
+  if (id.startsWith('PMC')) {
+    return `https://pmc.ncbi.nlm.nih.gov/articles/${id.split(':')[1]}`;
+  }
+  return '';
+};
+
+const getConcatPublicationsForResult = (result, message) => {
+  const edgeIds = Object.values(result.analyses[0].edge_bindings)
+    .flat()
+    .map((e) => e.id);
+  const publications = edgeIds.flatMap((edgeId) => message.knowledge_graph.edges[edgeId].attributes.filter(
+    (attr) => attr.attribute_type_id === 'biolink:publications',
+  ).flatMap((attr) => attr.value)).map(constructPmidOrPmcLink);
+
+  return publications;
+};
+
 const constructCsvObj = (message) => {
   const nodeLabelHeaders = Object.keys(
     message.results[0].node_bindings,
   ).flatMap((node_label) => [`${node_label} (Name)`, `${node_label} (CURIE)`]);
-  const header = [...nodeLabelHeaders, 'Score'];
+  const header = [...nodeLabelHeaders, 'Score', 'Publications'];
 
   const body = message.results.map((result) => {
     const row = [];
@@ -34,6 +55,8 @@ const constructCsvObj = (message) => {
       row.push(curie);
     });
     row.push(result.score);
+    row.push(getConcatPublicationsForResult(result, message).join('\n'));
+
     return row;
   });