Change crypt4gh and clearinghouse settings to use fega-norway repo

neicnordic · Nov 11, 2024 · f881616 · f881616
1 parent 80b00cd
commit f881616
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Showing 8 changed files with 26 additions and 51 deletions.
diff --git a/.github/dependabot.yml b/.github/dependabot.yml
@@ -1,15 +1,11 @@
 version: 2
 registries:
-  maven-github-uio-bmi:
+  maven-github-elixir-no:
     type: maven-repository
-    url: 'https://maven.pkg.github.com/uio-bmi'
-    username: '${{secrets.MAVEN_USER}}'
-    password: '${{secrets.MAVEN_GITHUB}}'
-  maven-github-elixir-oslo:
-    type: maven-repository
-    url: 'https://maven.pkg.github.com/elixir-oslo'
+    url: 'https://maven.pkg.github.com/ELIXIR-NO'
     username: '${{secrets.MAVEN_USER}}'
     password: '${{secrets.MAVEN_GITHUB}}'
+
 updates:
 - package-ecosystem: maven
   directory: "/"

diff --git a/.github/workflows/build-and-scan-PR-container.yml b/.github/workflows/build-and-scan-PR-container.yml
@@ -17,12 +17,7 @@ jobs:
         with:
           servers: |
             [{
-              "id":"github-clearinghouse",
-              "username": "${{github.actor}}",
-              "password": "${{ secrets.GITHUB_TOKEN }}"
-            },
-            {
-              "id":"github-crypt4gh",
+              "id":"github-fega-norway",
               "username": "${{github.actor}}",
               "password": "${{ secrets.GITHUB_TOKEN }}"
             }]

diff --git a/.github/workflows/docker-build-test.yml b/.github/workflows/docker-build-test.yml
@@ -20,12 +20,7 @@ jobs:
         with:
           servers: |
             [{
-              "id":"github-clearinghouse",
-              "username": "${{ github.actor }}",
-              "password": "${{ secrets.GITHUB_TOKEN }}"
-            },
-            {
-              "id":"github-crypt4gh",
+              "id":"github-fega-norway",
               "username": "${{ github.actor }}",
               "password": "${{ secrets.GITHUB_TOKEN }}"
             }]

diff --git a/.github/workflows/publish.yml b/.github/workflows/publish.yml
@@ -59,12 +59,7 @@ jobs:
         with:
           servers: |
             [{
-              "id":"github-clearinghouse",
-              "username": "${{ github.actor }}",
-              "password": "${{ secrets.GITHUB_TOKEN }}"
-            },
-            {
-              "id":"github-crypt4gh",
+              "id":"github-fega-norway",
               "username": "${{ github.actor }}",
               "password": "${{ secrets.GITHUB_TOKEN }}"
             }]

diff --git a/.github/workflows/test.yml b/.github/workflows/test.yml
@@ -74,12 +74,7 @@ jobs:
         with:
           servers: |
             [{
-              "id":"github-clearinghouse",
-              "username": "${{github.actor}}",
-              "password": "${{ secrets.GITHUB_TOKEN }}"
-            },
-            {
-              "id":"github-crypt4gh",
+              "id":"github-fega-norway",
               "username": "${{github.actor}}",
               "password": "${{ secrets.GITHUB_TOKEN }}"
             }]

diff --git a/pom.xml b/pom.xml
@@ -19,6 +19,11 @@
     </properties>
 
     <dependencies>
+        <dependency>
+            <groupId>com.google.code.gson</groupId>
+            <artifactId>gson</artifactId>
+            <version>2.11.0</version>
+        </dependency>
         <dependency>
             <groupId>org.springframework.boot</groupId>
             <artifactId>spring-boot-starter-data-jpa</artifactId>
@@ -110,9 +115,9 @@
             <scope>test</scope>
         </dependency>
         <dependency>
-            <groupId>no.uio.ifi</groupId>
+            <groupId>no.elixir</groupId>
             <artifactId>crypt4gh</artifactId>
-            <version>2.5.0</version>
+            <version>3.0.1</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -123,7 +128,7 @@
         <dependency>
             <groupId>no.elixir</groupId>
             <artifactId>clearinghouse</artifactId>
-            <version>2.0.1</version>
+            <version>2.0.2</version>
             <exclusions>
                 <exclusion>
                     <groupId>org.slf4j</groupId>
@@ -140,14 +145,8 @@
 
     <repositories>
         <repository>
-            <id>github-clearinghouse</id>
-            <name>elixir-oslo-clearinghouse</name>
-            <url>https://maven.pkg.github.com/elixir-oslo/clearinghouse</url>
-        </repository>
-        <repository>
-            <id>github-crypt4gh</id>
-            <name>uio-bmi-Crypt4GH</name>
-            <url>https://maven.pkg.github.com/uio-bmi/crypt4gh</url>
+            <id>github-fega-norway</id>
+            <url>https://maven.pkg.github.com/ELIXIR-NO/FEGA-Norway</url>
         </repository>
     </repositories>
 

diff --git a/src/main/java/no/uio/ifi/localega/doa/services/StreamingService.java b/src/main/java/no/uio/ifi/localega/doa/services/StreamingService.java
@@ -4,13 +4,13 @@
 import io.minio.MinioClient;
 import io.minio.errors.*;
 import lombok.extern.slf4j.Slf4j;
-import no.uio.ifi.crypt4gh.pojo.header.DataEditList;
-import no.uio.ifi.crypt4gh.pojo.header.Header;
-import no.uio.ifi.crypt4gh.pojo.header.HeaderPacket;
-import no.uio.ifi.crypt4gh.pojo.header.X25519ChaCha20IETFPoly1305HeaderPacket;
-import no.uio.ifi.crypt4gh.stream.Crypt4GHInputStream;
-import no.uio.ifi.crypt4gh.util.Crypt4GHUtils;
-import no.uio.ifi.crypt4gh.util.KeyUtils;
+import no.elixir.crypt4gh.pojo.header.DataEditList;
+import no.elixir.crypt4gh.pojo.header.Header;
+import no.elixir.crypt4gh.pojo.header.HeaderPacket;
+import no.elixir.crypt4gh.pojo.header.X25519ChaCha20IETFPoly1305HeaderPacket;
+import no.elixir.crypt4gh.stream.Crypt4GHInputStream;
+import no.elixir.crypt4gh.util.Crypt4GHUtils;
+import no.elixir.crypt4gh.util.KeyUtils;
 import no.uio.ifi.localega.doa.dto.DestinationFormat;
 import no.uio.ifi.localega.doa.model.LEGADataset;
 import no.uio.ifi.localega.doa.model.LEGAFile;

diff --git a/src/test/java/no/uio/ifi/localega/doa/LocalEGADOAApplicationTests.java b/src/test/java/no/uio/ifi/localega/doa/LocalEGADOAApplicationTests.java
@@ -11,8 +11,8 @@
 import kong.unirest.json.JSONArray;
 import lombok.SneakyThrows;
 import lombok.extern.slf4j.Slf4j;
-import no.uio.ifi.crypt4gh.stream.Crypt4GHInputStream;
-import no.uio.ifi.crypt4gh.util.KeyUtils;
+import no.elixir.crypt4gh.stream.Crypt4GHInputStream;
+import no.elixir.crypt4gh.util.KeyUtils;
 import org.apache.commons.codec.digest.DigestUtils;
 import org.apache.commons.io.FileUtils;
 import org.apache.commons.io.IOUtils;