From c3f213f509e77d57955969dce01d0b1126c34b28 Mon Sep 17 00:00:00 2001
From: "dependabot[bot]" <49699333+dependabot[bot]@users.noreply.github.com>
Date: Fri, 25 Aug 2023 08:41:19 +0000
Subject: [PATCH 1/4] Bump no.uio.ifi:clearinghouse from 1.1.0 to 1.2.1

Bumps [no.uio.ifi:clearinghouse](https://github.com/elixir-oslo/clearinghouse) from 1.1.0 to 1.2.1.
- [Release notes](https://github.com/elixir-oslo/clearinghouse/releases)
- [Commits](https://github.com/elixir-oslo/clearinghouse/compare/v1.1.0...v1.2.1)

---
updated-dependencies:
- dependency-name: no.uio.ifi:clearinghouse
  dependency-type: direct:production
  update-type: version-update:semver-minor
...

Signed-off-by: dependabot[bot] <support@github.com>
---
 pom.xml | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index e372bf0..a9c0677 100644
--- a/pom.xml
+++ b/pom.xml
@@ -106,7 +106,7 @@
         <dependency>
             <groupId>no.uio.ifi</groupId>
             <artifactId>clearinghouse</artifactId>
-            <version>1.1.0</version>
+            <version>1.2.1</version>
             <exclusions>
              <exclusion>
                 <groupId>org.slf4j</groupId>

From 841a9303a18a67323431b1770334fe443138cc8f Mon Sep 17 00:00:00 2001
From: Parisa Tejari <parisa.tejari@uib.no>
Date: Mon, 28 Aug 2023 09:13:29 +0200
Subject: [PATCH 2/4] -add unirest and junit dependencies -increase the key
 size from 1024 to 2048 in mock_auth

---
 pom.xml           | 17 +++++++++++++++++
 test/mock_auth.py |  2 +-
 2 files changed, 18 insertions(+), 1 deletion(-)

diff --git a/pom.xml b/pom.xml
index a9c0677..1a305af 100644
--- a/pom.xml
+++ b/pom.xml
@@ -92,6 +92,23 @@
             <artifactId>spring-boot-starter-test</artifactId>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>com.konghq</groupId>
+            <artifactId>unirest-java</artifactId>
+            <version>3.6.01</version>
+            <exclusions>
+                <exclusion>
+                    <groupId>com.google.code.gson</groupId>
+                    <artifactId>gson</artifactId>
+                </exclusion>
+            </exclusions>
+        </dependency>
+        <dependency>
+            <groupId>junit</groupId>
+            <artifactId>junit</artifactId>
+            <version>4.12</version>
+            <scope>test</scope>
+        </dependency>
         <dependency>
           <groupId>no.uio.ifi</groupId>
           <artifactId>crypt4gh</artifactId>
diff --git a/test/mock_auth.py b/test/mock_auth.py
index fb6bfe6..dfd80d7 100644
--- a/test/mock_auth.py
+++ b/test/mock_auth.py
@@ -9,7 +9,7 @@
 
 def generate_token():
     """Generate RSA Key pair to be used to sign token and the JWT Token itself."""
-    private_key = rsa.generate_private_key(public_exponent=65537, key_size=1024, backend=default_backend())
+    private_key = rsa.generate_private_key(public_exponent=65537, key_size=2048, backend=default_backend())
     public_key = private_key.public_key().public_bytes(encoding=serialization.Encoding.PEM,
                                                        format=serialization.PublicFormat.SubjectPublicKeyInfo)
     pem = private_key.private_bytes(encoding=serialization.Encoding.PEM,

From 526429433dfa0bee6e7c60e48b959f601c0d7aea Mon Sep 17 00:00:00 2001
From: Parisa Tejari <parisa.tejari@uib.no>
Date: Tue, 29 Aug 2023 09:11:56 +0200
Subject: [PATCH 3/4] -add crypt4gh server to settings.xml in
 build-and-scan-PR-container.yml

---
 .../workflows/build-and-scan-PR-container.yml    | 16 ++++++++++++++--
 1 file changed, 14 insertions(+), 2 deletions(-)

diff --git a/.github/workflows/build-and-scan-PR-container.yml b/.github/workflows/build-and-scan-PR-container.yml
index 591e7e7..b56c6ea 100644
--- a/.github/workflows/build-and-scan-PR-container.yml
+++ b/.github/workflows/build-and-scan-PR-container.yml
@@ -12,8 +12,20 @@ jobs:
       - name: Checkout code
         uses: actions/checkout@v3
 
-      - name: Add Maven Github authentication
-        run: echo "<settings xmlns='http://maven.apache.org/SETTINGS/1.0.0' xmlns:xsi='http://www.w3.org/2001/XMLSchema-instance' xsi:schemaLocation='http://maven.apache.org/SETTINGS/1.0.0 https://maven.apache.org/xsd/settings-1.0.0.xsd'> <servers> <server> <id>github-clearinghouse</id> <username>${{ github.actor }}</username> <password>${{ secrets.GITHUB_TOKEN }}</password> </server> <server> <id>github-tsd-file-api-client</id> <username>${{ github.actor }}</username> <password>${{ secrets.GITHUB_TOKEN }}</password> </server> </servers> </settings>" > settings.xml
+      - name: create maven settings.xml
+        uses: s4u/maven-settings-action@v2.8.0
+        with:
+          servers: |
+            [{
+              "id":"github-clearinghouse",
+              "username": "${{github.actor}}",
+              "password": "${{ secrets.GITHUB_TOKEN }}"
+            },
+            {
+              "id":"github-crypt4gh",
+              "username": "${{github.actor}}",
+              "password": "${{ secrets.GITHUB_TOKEN }}"
+            }]
 
       - name: Log in to the Github Container registry
         uses: docker/login-action@v2

From ced45ad236952d903ef3e4cd416fd32d0e669341 Mon Sep 17 00:00:00 2001
From: Parisa Tejari <parisa.tejari@uib.no>
Date: Tue, 29 Aug 2023 09:31:49 +0200
Subject: [PATCH 4/4] add copy step to build-and-scan-PR-container.yml

---
 .github/workflows/build-and-scan-PR-container.yml | 4 ++++
 1 file changed, 4 insertions(+)

diff --git a/.github/workflows/build-and-scan-PR-container.yml b/.github/workflows/build-and-scan-PR-container.yml
index b56c6ea..4b5bcab 100644
--- a/.github/workflows/build-and-scan-PR-container.yml
+++ b/.github/workflows/build-and-scan-PR-container.yml
@@ -27,6 +27,10 @@ jobs:
               "password": "${{ secrets.GITHUB_TOKEN }}"
             }]
 
+      - name: Copy settings.xml to project root
+        shell: bash
+        run: cp /home/runner/.m2/settings.xml ./settings.xml
+
       - name: Log in to the Github Container registry
         uses: docker/login-action@v2
         with: