Merge pull request #1074 from nci-hcmi-catalog/develop

🔖 Release 1.24.0
nci-hcmi-catalog · Jul 10, 2024 · cd00c27 · cd00c27
2 parents 11b67a2 + 51a9982
commit cd00c27
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Showing 2 changed files with 48 additions and 3 deletions.
diff --git a/cms/src/helpers/genomicVariants.js b/cms/src/helpers/genomicVariants.js
@@ -67,9 +67,7 @@ const buildVariantId = ({
 
 const buildModelUrl = caseId => `${BASE_GDC_URL}/cases/${caseId}`;
 const buildMafUrl = fileId => `${BASE_GDC_URL}/files/${fileId}`;
-// URL encoded: /v1/repository?facetTab=files&filters={"op":"and","content":[{"op":"in","content":{"field":"cases.case_id","value":["caseId"]}}]}&searchTableTab=files
-const buildSequenceUrl = caseId =>
-  `${BASE_GDC_URL}/v1/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.case_id%22%2C%22value%22%3A%5B%22${caseId}%22%5D%7D%7D%5D%7D&searchTableTab=files`;
+const buildSequenceUrl = caseId => `${BASE_GDC_URL}/cases/${caseId}#files`;
 
 export const addGenomicVariantsFromMaf = async (name, mafData, { filename, fileId }, caseId) => {
   const model = await Model.findOne({ name });

diff --git a/cms/variant-migrations/migrations/20240708184150-update-models-gdc-v2-sequence-urls.js b/cms/variant-migrations/migrations/20240708184150-update-models-gdc-v2-sequence-urls.js
@@ -0,0 +1,47 @@
+const OLD_URL_PATTERN = /https:\/\/portal\.gdc\.cancer\.gov\/v1\/repository\?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases\.case_id%22%2C%22value%22%3A%5B%22(.*?)%22%5D%7D%7D%5D%7D&searchTableTab=files/;
+const NEW_URL_PATTERN = /https:\/\/portal\.gdc\.cancer\.gov\/cases\/(.*?)#files/;
+
+module.exports = {
+  async up(db) {
+    const collection = db.collection('models');
+
+    const cursor = collection.find({
+      source_sequence_url: {
+        $regex: OLD_URL_PATTERN,
+      },
+    });
+
+    while (await cursor.hasNext()) {
+      const doc = await cursor.next();
+      const match = doc.source_sequence_url.match(OLD_URL_PATTERN);
+
+      if (match) {
+        const caseId = match[1];
+        const newUrl = `https://portal.gdc.cancer.gov/cases/${caseId}#files`;
+
+        await collection.updateOne({ _id: doc._id }, { $set: { source_sequence_url: newUrl } });
+      }
+    }
+  },
+  async down(db) {
+    const collection = db.collection('models');
+
+    const cursor = collection.find({
+      source_sequence_url: {
+        $regex: NEW_URL_PATTERN,
+      },
+    });
+
+    while (await cursor.hasNext()) {
+      const doc = await cursor.next();
+      const match = doc.source_sequence_url.match(NEW_URL_PATTERN);
+
+      if (match) {
+        const caseId = match[1];
+        const newUrl = `https://portal.gdc.cancer.gov/v1/repository?facetTab=files&filters=%7B%22op%22%3A%22and%22%2C%22content%22%3A%5B%7B%22op%22%3A%22in%22%2C%22content%22%3A%7B%22field%22%3A%22cases.case_id%22%2C%22value%22%3A%5B%22${caseId}%22%5D%7D%7D%5D%7D&searchTableTab=files`;
+
+        await collection.updateOne({ _id: doc._id }, { $set: { source_sequence_url: newUrl } });
+      }
+    }
+  },
+};