Autocreate Zenodo DOIs and create shared access links (#5879)

https://ucsc-cgl.atlassian.net/browse/SEAB-5929 https://ucsc-cgl.atlassian.net/browse/SEAB-6371 * Adds DOI autocreation for published, valid, unhidden tags on publish, refresh and GitHub app release * Creates hoverfly-tests profile for tests that use Hoverfly * Adds DOI entity to allow for multiple DOIs * Adds endpoints for creating and deleting shared access links
dockstore · Jun 3, 2024 · e6eea04 · e6eea04
1 parent 2f81db3
commit e6eea04
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Showing 45 changed files with 2,403 additions and 658 deletions.
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -78,6 +78,10 @@ workflows:
           <<: *common_filters
           requires:
             - full_build_check
+      - hoverfly-tests:
+          <<: *common_filters
+          requires:
+            - full_build_check
       - tool-integration-tests:
           <<: *common_filters
           requires:
@@ -102,6 +106,7 @@ workflows:
             - bitbucket-tests
             - language-parsing-tests
             - localstack-tests
+            - hoverfly-tests
             - tool-integration-tests
             - integration-tests
             - regression-integration-tests
@@ -238,6 +243,18 @@ jobs:
       - setup_postgres_docker
       - setup_integration_test
       - save_test_results
+  hoverfly-tests:
+    executor: integration_test_exec
+    environment:
+      TESTING_PROFILE: hoverfly-tests
+      DOCKSTORE_DOCKER_DB: true
+    steps:
+      - setup_test
+      - install-postgres
+      - setup_postgres
+      - setup_integration_test:
+          use_hoverfly_cert: true
+      - save_test_results
   build:
     docker: # run the steps with Docker
       - image: cimg/openjdk:<< pipeline.parameters.java-tag >>
@@ -388,14 +405,11 @@ jobs:
               touch /tmp/non-confidential-tests-to-run.txt
               cat temp/test-lists/IT/all.txt | circleci tests run --command="> /tmp/non-confidential-tests-to-run.txt xargs echo" --verbose --split-by=timings --time-default=0.1s
             
-              # Adding all "normal" certs into this local one that has the Hoverfly cert (instead of adding Hoverfly cert to the global one so it doesn't potentially affect other tests)
-              /usr/local/jdk-<< pipeline.parameters.java-tag >>/bin/keytool -importkeystore -srckeystore $JAVA_HOME/lib/security/cacerts -destkeystore LocalTrustStore -srcstorepass changeit -deststorepass changeit
-            
-              ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean install -Pnon-confidential-tests,coverage -Djavax.net.ssl.trustStore=../LocalTrustStore \
-              -Dtest=`cat /tmp/non-confidential-tests-to-run.txt | tr ' ' ','` -DfailIfNoTests=false -Djavax.net.ssl.trustStorePassword=changeit  -ntp | grep  -v "^Running Changeset:"         
+              ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean install -Pnon-confidential-tests,coverage \
+              -Dtest=`cat /tmp/non-confidential-tests-to-run.txt | tr ' ' ','` -DfailIfNoTests=false -ntp | grep  -v "^Running Changeset:"         
             else 
-              ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean install -Pnon-confidential-tests,coverage -Djavax.net.ssl.trustStore=../LocalTrustStore \
-              -Djavax.net.ssl.trustStorePassword=changeit  -ntp | grep  -v "^Running Changeset:"      
+              ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean install -Pnon-confidential-tests,coverage \
+              -ntp | grep  -v "^Running Changeset:"      
             fi
             # The piping grep command is a temporary fix to this issue https://github.com/liquibase/liquibase/issues/2396
       - setup_codecov_uploader
@@ -575,6 +589,10 @@ commands:
             - dockstore-web-cache-{{ .Environment.CIRCLE_JOB }}-
             - dockstore-web-cache-
   setup_integration_test:
+    parameters:
+      use_hoverfly_cert:
+        type: boolean
+        default: false
     steps:
       - run:
           name: decrypt and expand confidential test data
@@ -600,18 +618,41 @@ commands:
             java -version
             ./mvnw -v
             python3 -V
-      - run:
-          name: run integration test
-          command: |  # Runs normally if it is not being run in parallel
-            export DOCKSTORE_CACHE_MIGRATIONS=true
-            if [ $CIRCLE_NODE_TOTAL != 1 ] 
-            then
-              ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate -P$TESTING_PROFILE,coverage -ntp \
-              clean verify -Dit.test=`cat /tmp/tests-to-run.txt | tr ' ' ','` -DfailIfNoTests=false | grep  -v "^Running Changeset:"
-            else 
-              ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean install -P$TESTING_PROFILE,coverage -ntp | grep  -v "^Running Changeset:"
-            fi
-          # The piping grep command is a temporary fix to this issue https://github.com/liquibase/liquibase/issues/2396
+      - when:
+          condition: <<parameters.use_hoverfly_cert>>
+          steps:
+            - run:
+                name: run integration test with hoverfly cert
+                command: |                  
+                  # Adding all "normal" certs into this local one that has the Hoverfly cert (instead of adding Hoverfly cert to the global one so it doesn't potentially affect other tests)
+                  /usr/local/jdk-<< pipeline.parameters.java-tag >>/bin/keytool -importkeystore -srckeystore $JAVA_HOME/lib/security/cacerts -destkeystore LocalTrustStore -srcstorepass changeit -deststorepass changeit
+                  
+                  if [ $CIRCLE_NODE_TOTAL != 1 ] 
+                  then
+                    ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate -P$TESTING_PROFILE,coverage -ntp \
+                    clean verify -Dit.test=`cat /tmp/tests-to-run.txt | tr ' ' ','` -DfailIfNoTests=false -Djavax.net.ssl.trustStore=../LocalTrustStore \
+                    -Djavax.net.ssl.trustStorePassword=changeit | grep  -v "^Running Changeset:"
+                  else
+                    ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean install -P$TESTING_PROFILE,coverage -ntp -Djavax.net.ssl.trustStore=../LocalTrustStore \
+                    -Djavax.net.ssl.trustStorePassword=changeit | grep  -v "^Running Changeset:"
+                  fi
+      - when:
+          condition:
+            not: <<parameters.use_hoverfly_cert>>
+          steps:
+            - run:
+                name: run integration test
+                command: |  # Runs normally if it is not being run in parallel
+                  export DOCKSTORE_CACHE_MIGRATIONS=true
+                  
+                  if [ $CIRCLE_NODE_TOTAL != 1 ] 
+                  then
+                    ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate -P$TESTING_PROFILE,coverage -ntp \
+                    clean verify -Dit.test=`cat /tmp/tests-to-run.txt | tr ' ' ','` -DfailIfNoTests=false | grep  -v "^Running Changeset:"
+                  else 
+                    ./mvnw -B org.jacoco:jacoco-maven-plugin:report org.jacoco:jacoco-maven-plugin:report-aggregate clean install -P$TESTING_PROFILE,coverage -ntp | grep  -v "^Running Changeset:"
+                  fi
+                # The piping grep command is a temporary fix to this issue https://github.com/liquibase/liquibase/issues/2396
       - setup_codecov_uploader
       - run:
           name: send coverage

diff --git a/dockstore-common/src/main/java/io/dockstore/common/HoverflyTest.java b/dockstore-common/src/main/java/io/dockstore/common/HoverflyTest.java
@@ -0,0 +1,30 @@
+/*
+ * Copyright 2024 OICR and UCSC
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *           http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ *
+ */
+
+package io.dockstore.common;
+
+/**
+ * Setting aside tests that require Hoverfly to mock API responses.
+ */
+public interface HoverflyTest {
+    String NAME = "io.dockstore.common.HoverflyTest";
+
+    default String getName() {
+        // silly method to satisfy CheckStyle
+        return NAME;
+    }
+}
diff --git a/dockstore-integration-testing/src/test/java/io/dockstore/client/cli/BaseIT.java b/dockstore-integration-testing/src/test/java/io/dockstore/client/cli/BaseIT.java
@@ -341,7 +341,7 @@ protected static ApiClient getAnonymousWebClient() {
         return client;
     }
 
-    protected static io.dockstore.openapi.client.ApiClient getAnonymousOpenAPIWebClient() {
+    public static io.dockstore.openapi.client.ApiClient getAnonymousOpenAPIWebClient() {
         File configFile = FileUtils.getFile("src", "test", "resources", "config");
         INIConfiguration parseConfig = Utilities.parseConfig(configFile.getAbsolutePath());
         io.dockstore.openapi.client.ApiClient client = new io.dockstore.openapi.client.ApiClient();