dockstore · denis-yuen · Jun 27, 2023 · Jun 22, 2023 · Jun 22, 2023 · Jun 22, 2023
diff --git a/THIRD-PARTY-LICENSES.txt b/THIRD-PARTY-LICENSES.txt
@@ -1,5 +1,5 @@
 
-Lists of 388 third-party dependencies.
+Lists of 392 third-party dependencies.
      (Apache License, Version 2.0) akka-actor (com.typesafe.akka:akka-actor_2.13:2.5.32 - https://akka.io/)
      (Apache License, Version 2.0) akka-protobuf (com.typesafe.akka:akka-protobuf_2.13:2.5.32 - https://akka.io/)
      (Apache License, Version 2.0) akka-slf4j (com.typesafe.akka:akka-slf4j_2.13:2.5.32 - https://akka.io/)
@@ -13,6 +13,7 @@ Lists of 388 third-party dependencies.
      (Apache License, Version 2.0) Apache Commons BeanUtils (commons-beanutils:commons-beanutils:1.9.4 - https://commons.apache.org/proper/commons-beanutils/)
      (Apache License, Version 2.0) Apache Commons Codec (commons-codec:commons-codec:1.15 - https://commons.apache.org/proper/commons-codec/)
      (Apache License, Version 2.0) Apache Commons Collections (commons-collections:commons-collections:3.2.2 - http://commons.apache.org/collections/)
+     (Apache License, Version 2.0) Apache Commons Collections (org.apache.commons:commons-collections4:4.4 - https://commons.apache.org/proper/commons-collections/)
      (Apache License, Version 2.0) Apache Commons Compress (org.apache.commons:commons-compress:1.21 - https://commons.apache.org/proper/commons-compress/)
      (Apache License, Version 2.0) Apache Commons Configuration (org.apache.commons:commons-configuration2:2.8.0 - https://commons.apache.org/proper/commons-configuration/)
      (Apache License, Version 2.0) Apache Commons CSV (org.apache.commons:commons-csv:1.5 - http://commons.apache.org/proper/commons-csv/)
@@ -28,6 +29,7 @@ Lists of 388 third-party dependencies.
      (The Apache Software License, Version 2.0) Apache HTTP transport v2 for the Google HTTP Client Library for Java. (com.google.http-client:google-http-client-apache-v2:1.41.8 - https://github.com/googleapis/google-http-java-client/google-http-client-apache-v2)
      (Apache License, Version 2.0) Apache HttpAsyncClient (org.apache.httpcomponents:httpasyncclient:4.1.4 - http://hc.apache.org/httpcomponents-asyncclient)
      (Apache License, Version 2.0) Apache HttpClient (org.apache.httpcomponents:httpclient:4.5.14 - http://hc.apache.org/httpcomponents-client-ga)
+     (Apache License, Version 2.0) Apache HttpClient (org.apache.httpcomponents.client5:httpclient5:5.2.1 - https://hc.apache.org/httpcomponents-client-5.0.x/5.2.1/httpclient5/)
      (Apache License, Version 2.0) Apache HttpClient Cache (org.apache.httpcomponents:httpclient-cache:4.5.2 - http://hc.apache.org/httpcomponents-client)
      (Apache License, Version 2.0) Apache HttpClient Fluent API (org.apache.httpcomponents:fluent-hc:4.5.2 - http://hc.apache.org/httpcomponents-client)
      (Apache License, Version 2.0) Apache HttpClient Mime (org.apache.httpcomponents:httpmime:4.5.2 - http://hc.apache.org/httpcomponents-client)
@@ -102,7 +104,10 @@ Lists of 388 third-party dependencies.
      (BSD-3-Clause) commons-compiler (org.codehaus.janino:commons-compiler:3.1.6 - http://janino-compiler.github.io/commons-compiler/)
      (Apache License 2.0) compiler (com.github.spullara.mustache.java:compiler:0.9.10 - http://github.com/spullara/mustache.java)
      (Apache-2.0) config (com.typesafe:config:1.4.1 - https://github.com/lightbend/config)
-     (Apache 2) (Apache 2.0) (Three-clause BSD-style) core (com.chuusai:shapeless_2.13:2.3.7 - https://github.com/milessabin/shapeless)
+     (Apache 2) core (com.chuusai:shapeless_2.13:2.3.7 - https://github.com/milessabin/shapeless)
+     (Apache 2.0) core (com.softwaremill.sttp:core_2.13:1.7.2 - http://softwaremill.com/open-source)
+     (Apache 2) core (org.typelevel:kittens_2.13:2.3.2 - https://github.com/typelevel/kittens)
+     (Three-clause BSD-style) core (org.typelevel:simulacrum_2.13:1.0.1 - http://github.com/mpilquist/simulacrum)
      (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-common (org.broadinstitute:cromwell-common_2.13:84 - no url defined)
      (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-core (org.broadinstitute:cromwell-core_2.13:84 - no url defined)
      (Cromwell License https://github.com/broadinstitute/cromwell/blob/develop/LICENSE.txt) cromwell-wdl-model-biscayne (org.broadinstitute:cromwell-wdl-model-biscayne_2.13:84 - no url defined)
@@ -121,10 +126,6 @@ Lists of 388 third-party dependencies.
      (The Apache Software License, Version 2.0) docker-java-core (com.github.docker-java:docker-java-core:3.3.0 - https://github.com/docker-java/docker-java)
      (The Apache Software License, Version 2.0) docker-java-transport (com.github.docker-java:docker-java-transport:3.3.0 - https://github.com/docker-java/docker-java)
      (The Apache Software License, Version 2.0) docker-java-transport-httpclient5 (com.github.docker-java:docker-java-transport-httpclient5:3.3.0 - https://github.com/docker-java/docker-java)
-     (Apache Software License, Version 2.0) dockstore-common (io.dockstore:dockstore-common:1.15.0-alpha.1 - no url defined)
-     (Apache Software License, Version 2.0) dockstore-integration-testing (io.dockstore:dockstore-integration-testing:1.15.0-alpha.1 - no url defined)
-     (Apache Software License, Version 2.0) dockstore-language-plugin-parent (io.dockstore:dockstore-language-plugin-parent:1.15.0-alpha.1 - no url defined)
-     (Apache Software License, Version 2.0) dockstore-webservice (io.dockstore:dockstore-webservice:1.15.0-alpha.1 - no url defined)
      (Apache License 2.0) Dropwizard (io.dropwizard:dropwizard-core:4.0.0 - http://www.dropwizard.io/4.0.0/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-core)
      (Apache License 2.0) Dropwizard Asset Bundle (io.dropwizard:dropwizard-assets:4.0.0 - http://www.dropwizard.io/4.0.0/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-assets)
      (Apache License 2.0) Dropwizard Authentication (io.dropwizard:dropwizard-auth:4.0.0 - http://www.dropwizard.io/4.0.0/dropwizard-bom/dropwizard-dependencies/dropwizard-parent/dropwizard-auth)
@@ -328,16 +329,24 @@ Lists of 388 third-party dependencies.
      (Apache License, Version 2.0) Objenesis (org.objenesis:objenesis:3.2 - http://objenesis.org/objenesis)
      (The Apache Software License, Version 2.0) okhttp (com.squareup.okhttp3:okhttp:4.10.0 - https://square.github.io/okhttp/)
      (The Apache Software License, Version 2.0) okio (com.squareup.okio:okio-jvm:3.0.0 - https://github.com/square/okio/)
-     (Apache Software License, Version 2.0) openapi-java-client (io.dockstore:openapi-java-client:1.15.0-alpha.1 - no url defined)
      (The Apache License, Version 2.0) OpenCensus (io.opencensus:opencensus-api:0.31.0 - https://github.com/census-instrumentation/opencensus-java)
+     (The Apache License, Version 2.0) OpenCensus (io.opencensus:opencensus-contrib-http-util:0.31.0 - https://github.com/census-instrumentation/opencensus-java)
      (Apache 2) opencsv (com.opencsv:opencsv:5.7.1 - http://opencsv.sf.net)
      (MIT License) ORCID - Model (org.orcid:orcid-model-jakarta:3.3.0 - https://github.com/ORCID/orcid-model)
      (The Apache License, Version 2.0) org.apiguardian:apiguardian-api (org.apiguardian:apiguardian-api:1.1.2 - https://github.com/apiguardian-team/apiguardian)
      (The Apache License, Version 2.0) org.opentest4j:opentest4j (org.opentest4j:opentest4j:1.2.0 - https://github.com/ota4j-team/opentest4j)
      (EPL 2.0) (GPL2 w/ CPE) OSGi resource locator (org.glassfish.hk2:osgi-resource-locator:1.0.3 - https://projects.eclipse.org/projects/ee4j/osgi-resource-locator)
      (The Apache Software License, Version 2.0) PF4J (org.pf4j:pf4j:3.2.0 - http://nexus.sonatype.org/oss-repository-hosting.html/pf4j-parent/pf4j)
+     (The Apache Software License, Version 2.0) PF4J (ro.fortsoft.pf4j:pf4j:1.1.1 - http://nexus.sonatype.org/oss-repository-hosting.html/pf4j-parent/pf4j)
      (BSD-2-Clause) PostgreSQL JDBC Driver (org.postgresql:postgresql:42.4.3 - https://jdbc.postgresql.org)
      (The Apache Software License, Version 2.0) PowerMock (org.powermock:powermock-api-easymock:2.0.9 - http://www.powermock.org)
+     (The Apache Software License, Version 2.0) PowerMock (org.powermock:powermock-api-mockito-common:1.7.4 - http://www.powermock.org)
+     (The Apache Software License, Version 2.0) PowerMock (org.powermock:powermock-api-mockito2:2.0.9 - http://www.powermock.org)
+     (The Apache Software License, Version 2.0) PowerMock (org.powermock:powermock-api-support:2.0.9 - http://www.powermock.org)
+     (The Apache Software License, Version 2.0) PowerMock (org.powermock:powermock-core:2.0.9 - http://www.powermock.org)
+     (The Apache Software License, Version 2.0) PowerMock (org.powermock:powermock-module-junit4:2.0.9 - http://www.powermock.org)
+     (The Apache Software License, Version 2.0) PowerMock (org.powermock:powermock-module-junit4-common:2.0.9 - http://www.powermock.org)
+     (The Apache Software License, Version 2.0) PowerMock (org.powermock:powermock-reflect:2.0.9 - http://www.powermock.org)
      (MIT) pprint_2.13 (com.lihaoyi:pprint_2.13:0.7.1 - https://github.com/lihaoyi/PPrint)
      (The Apache Software License, Version 2.0) rank-eval (org.elasticsearch.plugin:rank-eval-client:7.10.2 - https://github.com/elastic/elasticsearch)
      (CC0) reactive-streams (org.reactivestreams:reactive-streams:1.0.3 - http://www.reactive-streams.org/)
@@ -353,6 +362,7 @@ Lists of 388 third-party dependencies.
      (Apache-2.0) scala-xml (org.scala-lang.modules:scala-xml_2.13:1.3.0 - http://www.scala-lang.org/)
      (MIT) scopt (com.github.scopt:scopt_2.13:4.0.1 - https://github.com/scopt/scopt)
      (MIT) Sentry SDK (io.sentry:sentry:5.2.4 - https://github.com/getsentry/sentry-java)
+     (MIT) Sentry SDK (io.sentry:sentry-logback:5.2.4 - https://github.com/getsentry/sentry-java)
      (The Apache Software License, Version 2.0) server (org.elasticsearch:elasticsearch:7.10.2 - https://github.com/elastic/elasticsearch)
      (EPL 2.0) (GPL2 w/ CPE) ServiceLocator Default Implementation (org.glassfish.hk2:hk2-locator:3.0.3 - https://github.com/eclipse-ee4j/glassfish-hk2/hk2-locator)
      (MIT License) SLF4J API Module (org.slf4j:slf4j-api:2.0.7 - http://www.slf4j.org)
@@ -367,12 +377,6 @@ Lists of 388 third-party dependencies.
      (Apache License 2.0) swagger-core (io.swagger:swagger-core:1.6.8 - https://github.com/swagger-api/swagger-core/modules/swagger-core)
      (Apache License 2.0) swagger-core-jakarta (io.swagger.core.v3:swagger-core-jakarta:2.2.9 - https://github.com/swagger-api/swagger-core/modules/swagger-core-jakarta)
      (Apache License 2.0) swagger-integration-jakarta (io.swagger.core.v3:swagger-integration-jakarta:2.2.9 - https://github.com/swagger-api/swagger-core/modules/swagger-integration-jakarta)
-     (Apache Software License, Version 2.0) swagger-java-bitbucket-client (io.dockstore:swagger-java-bitbucket-client:2.0.3 - no url defined)
-     (Apache Software License, Version 2.0) swagger-java-client (io.dockstore:swagger-java-client:1.15.0-alpha.1 - no url defined)
-     (Apache Software License, Version 2.0) swagger-java-discourse-client (io.dockstore:swagger-java-discourse-client:2.0.1 - no url defined)
-     (Apache Software License, Version 2.0) swagger-java-quay-client (io.dockstore:swagger-java-quay-client:2.0.2 - no url defined)
-     (Apache Software License, Version 2.0) swagger-java-sam-client (io.dockstore:swagger-java-sam-client:2.0.2 - no url defined)
-     (Apache Software License, Version 2.0) swagger-java-zenodo-client (io.dockstore:swagger-java-zenodo-client:2.0.0 - no url defined)
      (Apache License 2.0) swagger-jaxrs2-jakarta (io.swagger.core.v3:swagger-jaxrs2-jakarta:2.2.9 - https://github.com/swagger-api/swagger-core/modules/swagger-jaxrs2-jakarta)
      (Apache License 2.0) swagger-jaxrs2-servlet-initializer-jakarta (io.swagger.core.v3:swagger-jaxrs2-servlet-initializer-jakarta:2.2.9 - https://github.com/swagger-api/swagger-core/modules/swagger-jaxrs2-servlet-initializer-jakarta)
      (Apache License 2.0) swagger-models (io.swagger:swagger-models:1.6.8 - https://github.com/swagger-api/swagger-core/modules/swagger-models)

diff --git a/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml b/dockstore-cli-integration-testing/generated/src/main/resources/pom.xml
@@ -23,7 +23,7 @@
   <licenses>
     <license>
       <name>Apache Software License, Version 2.0</name>
-      <url>http://www.apache.org/licenses/LICENSE-2.0</url>
+      <url>https://www.apache.org/licenses/LICENSE-2.0</url>
     </license>
   </licenses>
   <dependencies>
@@ -39,6 +39,12 @@
       <version>1.15.0-alpha.1</version>
       <classifier>tests</classifier>
       <scope>compile</scope>
+      <exclusions>
+        <exclusion>
+          <groupId>io.dockstore</groupId>
+          <artifactId>swagger-java-client</artifactId>
+        </exclusion>
+      </exclusions>
     </dependency>
     <dependency>
       <groupId>io.dockstore</groupId>

diff --git a/dockstore-cli-integration-testing/pom.xml b/dockstore-cli-integration-testing/pom.xml
@@ -60,6 +60,12 @@
             <artifactId>dockstore-integration-testing</artifactId>
             <version>${dockstore-core.version}</version>
             <classifier>tests</classifier>
+            <exclusions>
+                <exclusion>
+                    <groupId>io.dockstore</groupId>
+                    <artifactId>swagger-java-client</artifactId>
+                </exclusion>
+            </exclusions>
         </dependency>
         <dependency>
             <groupId>io.dockstore</groupId>

diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/BaseIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/BaseIT.java
@@ -28,13 +28,13 @@
 import io.dockstore.common.MuteForSuccessfulTests;
 import io.dockstore.common.SourceControl;
 import io.dockstore.common.TestingPostgres;
+import io.dockstore.openapi.client.ApiClient;
+import io.dockstore.openapi.client.api.UsersApi;
+import io.dockstore.openapi.client.api.WorkflowsApi;
+import io.dockstore.openapi.client.model.Repository;
 import io.dockstore.webservice.DockstoreWebserviceApplication;
 import io.dockstore.webservice.DockstoreWebserviceConfiguration;
 import io.dropwizard.testing.DropwizardTestSupport;
-import io.swagger.client.ApiClient;
-import io.swagger.client.api.UsersApi;
-import io.swagger.client.api.WorkflowsApi;
-import io.swagger.client.model.Repository;
 import org.jline.utils.Log;
 import org.junit.jupiter.api.AfterAll;
 import org.junit.jupiter.api.AfterEach;

diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/BasicIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/BasicIT.java
@@ -25,11 +25,11 @@
 import io.dockstore.common.Registry;
 import io.dockstore.common.SlowTest;
 import io.dockstore.common.ToolTest;
+import io.dockstore.openapi.client.ApiClient;
+import io.dockstore.openapi.client.api.ContainersApi;
+import io.dockstore.openapi.client.api.HostedApi;
+import io.dockstore.openapi.client.model.DockstoreTool;
 import io.dropwizard.testing.ResourceHelpers;
-import io.swagger.client.ApiClient;
-import io.swagger.client.api.ContainersApi;
-import io.swagger.client.api.HostedApi;
-import io.swagger.client.model.DockstoreTool;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;
 import org.junit.jupiter.api.Tag;
@@ -487,22 +487,22 @@ void testTestParameterOtherUsers() {
         assertEquals(0, count, "there should be no sourcefiles that are test parameter files, there are " + count);
 
         containersApi
-            .addTestParameterFiles(containerByToolPath.getId(), Collections.singletonList("/test.json"), CWL.toString(), "",
-                "master");
+            .addTestParameterFiles(containerByToolPath.getId(), "", Collections.singletonList("/test.json"),
+                "master", CWL.toString());
 
         boolean shouldFail = false;
         try {
             final ContainersApi containersApi1 = new ContainersApi(otherWebClient);
-            containersApi1.addTestParameterFiles(containerByToolPath.getId(), Collections.singletonList("/test2.cwl.json"),
-                CWL.toString(), "", "master");
+            containersApi1.addTestParameterFiles(containerByToolPath.getId(), "", Collections.singletonList("/test2.cwl.json"),
+                CWL.toString(), "master");
         } catch (Exception e) {
             shouldFail = true;
         }
         assertTrue(shouldFail);
 
         containersApi
-            .addTestParameterFiles(containerByToolPath.getId(), Collections.singletonList("/test2.cwl.json"), CWL.toString(),
-                "", "master");
+            .addTestParameterFiles(containerByToolPath.getId(), "", Collections.singletonList("/test2.cwl.json"),
+                 "master",  CWL.toString());
 
         final long count3 = testingPostgres.runSelectStatement("select count(*) from sourcefile where type like '%_TEST_JSON'", long.class);
         assertEquals(2, count3, "there should be one sourcefile that is a test parameter file, there are " + count3);
@@ -518,10 +518,10 @@ void testTestParameterOtherUsers() {
         }
         assertTrue(shouldFail);
         containersApi
-            .deleteTestParameterFiles(containerByToolPath.getId(), Collections.singletonList("/test.json"), CWL.toString(),
-                "master");
+            .deleteTestParameterFiles(containerByToolPath.getId(), Collections.singletonList("/test.json"),
+                "master", CWL.toString());
         containersApi.deleteTestParameterFiles(containerByToolPath.getId(), Collections.singletonList("/test2.cwl.js
CEB7
on"),
-            CWL.toString(), "master");
+            "master", CWL.toString());
 
         final long count4 = testingPostgres.runSelectStatement("select count(*) from sourcefile where type like '%_TEST_JSON'", long.class);
         assertEquals(0, count4, "there should be one sourcefile that is a test parameter file, there are " + count4);
@@ -680,7 +680,7 @@ void testManualPublishGitlabDocker() throws Exception {
 
         // Manual publish
         catchSystemExit(() -> Client.main(new String[] { CONFIG, ResourceHelpers.resourceFilePath("config_file.txt"), TOOL, MANUAL_PUBLISH, "--registry",
-            Registry.GITLAB.name(), Registry.GITLAB.toString(), "--namespace", "dockstore.test.user", "--name", "dockstore-whalesay",
+            Registry.GITLAB.name(), "--namespace", "dockstore.test.user", "--name", "dockstore-whalesay",
             "--git-url", "git@gitlab.com:dockstore.test.user/dockstore-whalesay.git", "--git-reference", "master", "--toolname",
             "alternate", "--private", "true", "--tool-maintainer-email", "duncan.andrew.g@gmail.com", SCRIPT_FLAG }));
 
@@ -855,7 +855,7 @@ void testPublishUnpublishHostedTool() {
         // Create a hosted tool
         final ApiClient webClient = getWebClient(BaseIT.USER_1_USERNAME, testingPostgres);
         HostedApi hostedApi = new HostedApi(webClient);
-        hostedApi.createHostedTool("testHosted", Registry.QUAY_IO.getDockerPath().toLowerCase(),
+        hostedApi.createHostedTool(Registry.QUAY_IO.getDockerPath().toLowerCase(), "testHosted",
                 CWL.getShortName(), "hostedToolNamespace", null);
 
         // verify there is an unpublished hosted tool

diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/ClientIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/ClientIT.java
@@ -27,8 +27,8 @@
 import io.dockstore.common.TestUtility;
 import io.dockstore.common.ToilCompatibleTest;
 import io.dockstore.common.ToolTest;
+import io.dockstore.openapi.client.ApiException;
 import io.dropwizard.testing.ResourceHelpers;
-import io.swagger.client.ApiException;
 import org.junit.experimental.categories.Category;
 import org.junit.jupiter.api.BeforeEach;
 import org.junit.jupiter.api.Disabled;

diff --git a/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/CromwellIT.java b/dockstore-cli-integration-testing/src/test/java/io/dockstore/client/cli/CromwellIT.java
@@ -35,8 +35,8 @@
 import io.dockstore.common.ToolTest;
 import io.dockstore.common.WDLFileProvisioning;
 import io.dockstore.common.WdlBridge;
+import io.dockstore.openapi.client.ApiException;
 import io.dropwizard.testing.ResourceHelpers;
-import io.swagger.client.ApiException;
 import org.apache.commons.io.FileUtils;
 import org.junit.jupiter.api.Tag;
 import org.junit.jupiter.api.Test;