From b87672a1566537402f96888e83b73e311405e3d8 Mon Sep 17 00:00:00 2001
From: suman <suman@ebi.ac.uk>
Date: Mon, 22 Jan 2024 11:18:56 +0000
Subject: [PATCH 1/2] DCP-3954 : Uniprot support: Seq snapshot change tracking
 using livelist endpoint

---
 build.gradle                                        |  2 +-
 .../uk/ac/ebi/ena/dcap/scl/service/MainService.java |  4 ++--
 .../{PortalApiClient.java => SnapshotClient.java}   | 13 ++++++++++---
 3 files changed, 13 insertions(+), 6 deletions(-)
 rename src/main/java/uk/ac/ebi/ena/dcap/scl/service/{PortalApiClient.java => SnapshotClient.java} (83%)

diff --git a/build.gradle b/build.gradle
index f32dfc5..3fa067d 100644
--- a/build.gradle
+++ b/build.gradle
@@ -20,7 +20,7 @@ plugins {
 }
 
 group = 'uk.ac.ebi.ena.dcap'
-version = '1.2.0'
+version = '1.2.1'
 sourceCompatibility = '1.8'
 
 configurations {
diff --git a/src/main/java/uk/ac/ebi/ena/dcap/scl/service/MainService.java b/src/main/java/uk/ac/ebi/ena/dcap/scl/service/MainService.java
index b30b024..d18587d 100644
--- a/src/main/java/uk/ac/ebi/ena/dcap/scl/service/MainService.java
+++ b/src/main/java/uk/ac/ebi/ena/dcap/scl/service/MainService.java
@@ -46,7 +46,7 @@ public class MainService {
     final ExecutorService executorService = Executors.newFixedThreadPool(2);
 
     @Autowired
-    PortalApiClient portalApiClient;
+    SnapshotClient snapshotClient;
 
 
     public File writeLatestSnapshot(DataType dataType, File outputLocation, String fileName, String query) {
@@ -55,7 +55,7 @@ public File writeLatestSnapshot(DataType dataType, File outputLocation, String f
         if (outFile.exists()) {
             outFile.delete();
         }
-        return portalApiClient.getLatestSnapshot(dataType, outFile, query);
+        return snapshotClient.getLatestSnapshot(dataType, outFile, query);
     }
 
     @SneakyThrows
diff --git a/src/main/java/uk/ac/ebi/ena/dcap/scl/service/PortalApiClient.java b/src/main/java/uk/ac/ebi/ena/dcap/scl/service/SnapshotClient.java
similarity index 83%
rename from src/main/java/uk/ac/ebi/ena/dcap/scl/service/PortalApiClient.java
rename to src/main/java/uk/ac/ebi/ena/dcap/scl/service/SnapshotClient.java
index 86bb0c7..11ab38b 100644
--- a/src/main/java/uk/ac/ebi/ena/dcap/scl/service/PortalApiClient.java
+++ b/src/main/java/uk/ac/ebi/ena/dcap/scl/service/SnapshotClient.java
@@ -35,16 +35,23 @@
 
 @Component
 @Slf4j
-public class PortalApiClient {
+public class SnapshotClient {
 
-    static final String URL = "https://www.ebi.ac.uk/ena/portal/api/search?result=%s&fields=accession," +
+    static final String PORTAL_API_URL = "https://www.ebi.ac.uk/ena/portal/api/search?result=%s&fields=accession," +
+            "last_updated";
+
+    static final String LIVELST_URL = "https://www.ebi.ac.uk/ena/browser/api/livelist/%s?fields=accession," +
             "last_updated";
 
     @SneakyThrows
     public File getLatestSnapshot(DataType dataType, File outputFile, String query) {
-        String req = String.format(URL, dataType.name().toLowerCase());
+        String req;
         if (StringUtils.isNotBlank(query)) {
+            req = String.format(PORTAL_API_URL, dataType.name().toLowerCase());
             req += "&query=" + query;
+
+        } else {
+            req = String.format(LIVELST_URL, dataType.name().toLowerCase());
         }
         URL url = new URL(req);
 

From a434eb6b7d9d35e5e748b7a67b981b825e4a0230 Mon Sep 17 00:00:00 2001
From: suman <suman@ebi.ac.uk>
Date: Mon, 22 Jan 2024 12:04:29 +0000
Subject: [PATCH 2/2] DCP-3954 : Uniprot support: Seq snapshot change tracking
 using livelist endpoint

---
 .github/workflows/gradle.yml | 22 ++++++++++++----------
 1 file changed, 12 insertions(+), 10 deletions(-)

diff --git a/.github/workflows/gradle.yml b/.github/workflows/gradle.yml
index 393133a..86a6ea6 100644
--- a/.github/workflows/gradle.yml
+++ b/.github/workflows/gradle.yml
@@ -22,13 +22,15 @@ jobs:
     runs-on: ubuntu-latest
 
     steps:
-    - uses: actions/checkout@v3
-    - name: Set up JDK 11
-      uses: actions/setup-java@v3
-      with:
-        java-version: '11'
-        distribution: 'temurin'
-    - name: Build with Gradle
-      uses: gradle/gradle-build-action@bd5760595778326ba7f1441bcf7e88b49de61a25 # v2.6.0
-      with:
-        arguments: build
+      - uses: actions/checkout@v3
+      - name: Set up JDK 11
+        uses: actions/setup-java@v3
+        with:
+          java-version: '11'
+          distribution: 'temurin'
+      - name: Make Gradlew Executable
+        run: chmod u+x gradlew
+      - name: Build with Gradle
+        uses: gradle/gradle-build-action@bd5760595778326ba7f1441bcf7e88b49de61a25 # v2.6.0
+        with:
+          arguments: build