Remove dockstore-webservice dependency (#470)

dockstore/dockstore#5528
https://ucsc-cgl.atlassian.net/browse/DOCK-2404
* Use dockstore-common instead of dockstore-webservice
* Remove javax
* Add back a depencency that's needed to run the metrics-aggregator and tooltester
* Use 1.15.0-alpha.4 dockstore tag & PR feedback
* Use cwlavro from bom

metricsaggregator/pom.xml

@@ -89,35 +89,20 @@
 
     <dependencies>
         <dependency>
-            <groupId>org.glassfish.jersey.inject</groupId>
-            <artifactId>jersey-hk2</artifactId>
-            <version>2.39</version>
+            <groupId>io.dockstore</groupId>
+            <artifactId>openapi-java-client</artifactId>
+            <version>${dockstore-core.version}</version>
         </dependency>
         <dependency>
             <groupId>io.dockstore</groupId>
-            <artifactId>openapi-java-client</artifactId>
+            <artifactId>dockstore-common</artifactId>
             <version>${dockstore-core.version}</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>org.glassfish.jersey.media</groupId>
-                    <artifactId>jersey-media-json-jackson</artifactId>
-                </exclusion>
-            </exclusions>
         </dependency>
         <dependency>
             <groupId>io.dockstore</groupId>
             <artifactId>dockstore-webservice</artifactId>
             <version>${dockstore-core.version}</version>
-            <exclusions>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.core</groupId>
-                    <artifactId>jackson-databind</artifactId>
-                </exclusion>
-                <exclusion>
-                    <groupId>com.fasterxml.jackson.module</groupId>
-                    <artifactId>jackson-module-jaxb-annotations</artifactId>
-                </exclusion>
-            </exclusions>
+            <scope>test</scope>
         </dependency>
         <dependency>
             <groupId>io.dockstore</groupId>
@@ -126,10 +111,26 @@
             <classifier>tests</classifier>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.glassfish.jersey.inject</groupId>
+            <artifactId>jersey-hk2</artifactId>
+        </dependency>
         <dependency>
             <groupId>com.beust</groupId>
             <artifactId>jcommander</artifactId>
         </dependency>
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-configuration2</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>org.slf4j</groupId>
+            <artifactId>slf4j-api</artifactId>
+        </dependency>
+        <dependency>
+            <groupId>software.amazon.awssdk</groupId>
+            <artifactId>s3</artifactId>
+        </dependency>
         <dependency>
             <groupId>org.junit.jupiter</groupId>
             <artifactId>junit-jupiter-api</artifactId>
@@ -144,7 +145,6 @@
         <dependency>
             <groupId>cloud.localstack</groupId>
             <artifactId>localstack-utils</artifactId>
-            <version>0.2.22</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -157,11 +157,6 @@
             <artifactId>system-stubs-core</artifactId>
             <scope>test</scope>
         </dependency>
-        <!-- https://mvnrepository.com/artifact/org.glassfish.hk2/hk2-api -->
-        <dependency>
-            <groupId>org.glassfish.hk2</groupId>
-            <artifactId>hk2-api</artifactId>
-        </dependency>
     </dependencies>
 
     <build>
@@ -264,8 +259,10 @@
                             <outputXML>true</outputXML>
                             <ignoreNonCompile>true</ignoreNonCompile>
                             <usedDependencies>
+                                <usedDependency>org.apache.commons:commons-configuration2</usedDependency>
+                                <usedDependency>org.slf4j:slf4j-api</usedDependency>
+                                <usedDependency>software.amazon.awssdk:s3</usedDependency>
                                 <usedDependency>org.glassfish.jersey.inject:jersey-hk2</usedDependency>
-                                <usedDependency>org.glassfish.hk2:hk2-api</usedDependency>
                             </usedDependencies>
                         </configuration>
                     </execution>

metricsaggregator/src/main/java/io/dockstore/metricsaggregator/MetricsAggregatorS3Client.java

@@ -21,15 +21,15 @@
 
 import com.google.gson.Gson;
 import com.google.gson.JsonSyntaxException;
+import io.dockstore.common.Partner;
+import io.dockstore.common.S3ClientHelper;
+import io.dockstore.common.metrics.MetricsData;
+import io.dockstore.common.metrics.MetricsDataS3Client;
 import io.dockstore.openapi.client.api.ExtendedGa4GhApi;
 import io.dockstore.openapi.client.model.ExecutionsRequestBody;
 import io.dockstore.openapi.client.model.Metrics;
 import io.dockstore.openapi.client.model.RunExecution;
 import io.dockstore.openapi.client.model.ValidationExecution;
-import io.dockstore.webservice.core.Partner;
-import io.dockstore.webservice.core.metrics.MetricsData;
-import io.dockstore.webservice.core.metrics.MetricsDataS3Client;
-import io.dockstore.webservice.helpers.S3ClientHelper;
 import java.io.IOException;
 import java.net.URISyntaxException;
 import java.util.ArrayDeque;

metricsaggregator/src/main/java/io/dockstore/metricsaggregator/client/cli/CommandLineArgs.java

@@ -19,8 +19,8 @@
 
 import com.beust.jcommander.Parameter;
 import com.beust.jcommander.Parameters;
+import io.dockstore.common.Partner;
 import io.dockstore.openapi.client.model.ValidationExecution.ValidatorToolEnum;
-import io.dockstore.webservice.core.Partner;
 import java.io.File;
 
 public class CommandLineArgs {

metricsaggregator/src/main/java/io/dockstore/metricsaggregator/client/cli/MetricsAggregatorClient.java

@@ -20,6 +20,7 @@
 import com.beust.jcommander.JCommander;
 import com.beust.jcommander.MissingCommandException;
 import com.beust.jcommander.ParameterException;
+import io.dockstore.common.Partner;
 import io.dockstore.metricsaggregator.MetricsAggregatorConfig;
 import io.dockstore.metricsaggregator.MetricsAggregatorS3Client;
 import io.dockstore.metricsaggregator.client.cli.CommandLineArgs.AggregateMetricsCommand;
@@ -30,7 +31,6 @@
 import io.dockstore.openapi.client.model.ExecutionsRequestBody;
 import io.dockstore.openapi.client.model.ValidationExecution;
 import io.dockstore.openapi.client.model.ValidationExecution.ValidatorToolEnum;
-import io.dockstore.webservice.core.Partner;
 import java.io.File;
 import java.io.IOException;
 import java.net.URISyntaxException;

metricsaggregator/src/main/java/io/dockstore/metricsaggregator/helper/AggregationHelper.java

@@ -1,7 +1,7 @@
 package io.dockstore.metricsaggregator.helper;
 
-import static io.dockstore.webservice.core.metrics.RunExecution.checkExecutionTimeISO8601Format;
-import static io.dockstore.webservice.core.metrics.ValidationExecution.checkExecutionDateISO8601Format;
+import static io.dockstore.common.metrics.FormatCheckHelper.checkExecutionDateISO8601Format;
+import static io.dockstore.common.metrics.FormatCheckHelper.checkExecutionTimeISO8601Format;
 import static java.util.stream.Collectors.groupingBy;
 
 import io.dockstore.metricsaggregator.Statistics;

metricsaggregator/src/test/java/io/dockstore/metricsaggregator/MetricsAggregatorS3ClientIT.java

@@ -32,6 +32,8 @@
 import cloud.localstack.docker.annotation.LocalstackDockerProperties;
 import io.dockstore.common.CommonTestUtilities;
 import io.dockstore.common.LocalStackTestUtilities;
+import io.dockstore.common.Partner;
+import io.dockstore.common.S3ClientHelper;
 import io.dockstore.common.TestingPostgres;
 import io.dockstore.openapi.client.ApiClient;
 import io.dockstore.openapi.client.api.ContainersApi;
@@ -46,8 +48,6 @@
 import io.dockstore.openapi.client.model.WorkflowVersion;
 import io.dockstore.webservice.DockstoreWebserviceApplication;
 import io.dockstore.webservice.DockstoreWebserviceConfiguration;
-import io.dockstore.webservice.core.Partner;
-import io.dockstore.webservice.helpers.S3ClientHelper;
 import io.dropwizard.testing.DropwizardTestSupport;
 import java.util.List;
 import java.util.Objects;

metricsaggregator/src/test/java/io/dockstore/metricsaggregator/client/cli/MetricsAggregatorClientIT.java

@@ -18,6 +18,7 @@
 package io.dockstore.metricsaggregator.client.cli;
 
 import static io.dockstore.client.cli.BaseIT.ADMIN_USERNAME;
+import static io.dockstore.common.Partner.DNA_STACK;
 import static io.dockstore.metricsaggregator.common.TestUtilities.BUCKET_NAME;
 import static io.dockstore.metricsaggregator.common.TestUtilities.CONFIG_FILE_PATH;
 import static io.dockstore.metricsaggregator.common.TestUtilities.ENDPOINT_OVERRIDE;
@@ -27,7 +28,6 @@
 import static io.dockstore.openapi.client.model.RunExecution.ExecutionStatusEnum.SUCCESSFUL;
 import static io.dockstore.openapi.client.model.ValidationExecution.ValidatorToolEnum.MINIWDL;
 import static io.dockstore.openapi.client.model.ValidationExecution.ValidatorToolEnum.WOMTOOL;
-import static io.dockstore.webservice.core.Partner.DNA_STACK;
 import static org.junit.jupiter.api.Assertions.assertEquals;
 import static org.junit.jupiter.api.Assertions.assertFalse;
 import static org.junit.jupiter.api.Assertions.assertNotNull;
@@ -42,7 +42,10 @@
 import com.google.gson.Gson;
 import io.dockstore.common.CommonTestUtilities;
 import io.dockstore.common.LocalStackTestUtilities;
+import io.dockstore.common.Partner;
 import io.dockstore.common.TestingPostgres;
+import io.dockstore.common.metrics.MetricsData;
+import io.dockstore.common.metrics.MetricsDataS3Client;
 import io.dockstore.openapi.client.ApiClient;
 import io.dockstore.openapi.client.api.ExtendedGa4GhApi;
 import io.dockstore.openapi.client.api.WorkflowsApi;
@@ -56,11 +59,6 @@
 import io.dockstore.openapi.client.model.WorkflowVersion;
 import io.dockstore.webservice.DockstoreWebserviceApplication;
 import io.dockstore.webservice.DockstoreWebserviceConfiguration;
-import io.dockstore.webservice.core.Partner;
-import io.dockstore.webservice.core.metrics.ExecutionTimeStatisticMetric;
-import io.dockstore.webservice.core.metrics.MemoryStatisticMetric;
-import io.dockstore.webservice.core.metrics.MetricsData;
-import io.dockstore.webservice.core.metrics.MetricsDataS3Client;
 import io.dropwizard.testing.DropwizardTestSupport;
 import io.dropwizard.testing.ResourceHelpers;
 import java.io.IOException;
@@ -206,13 +204,13 @@ void testAggregateMetrics() {
         assertEquals(2, platform1Metrics.getMemory().getMinimum());
         assertEquals(4.5, platform1Metrics.getMemory().getMaximum());
         assertEquals(3.25, platform1Metrics.getMemory().getAverage());
-        assertEquals(MemoryStatisticMetric.UNIT, platform1Metrics.getMemory().getUnit());
+        assertNotNull(platform1Metrics.getMemory().getUnit());
 
         assertEquals(2, platform1Metrics.getExecutionTime().getNumberOfDataPointsForAverage());
         assertEquals(1, platform1Metrics.getExecutionTime().getMinimum());
         assertEquals(300, platform1Metrics.getExecutionTime().getMaximum());
         assertEquals(150.5, platform1Metrics.getExecutionTime().getAverage());
-        assertEquals(ExecutionTimeStatisticMetric.UNIT, platform1Metrics.getExecutionTime().getUnit());
+        assertNotNull(platform1Metrics.getExecutionTime().getUnit());
 
         assertEquals(1, platform1Metrics.getValidationStatus().getValidatorTools().size());
         validationInfo = platform1Metrics.getValidationStatus().getValidatorTools().get(MINIWDL.toString());
@@ -247,13 +245,13 @@ private static void compareAggregateMetricsWithPlatforms(String platform2, Workf
         assertEquals(2, platform1Metrics.getMemory().getMinimum());
         assertEquals(2, platform1Metrics.getMemory().getMaximum());
         assertEquals(2, platform1Metrics.getMemory().getAverage());
-        assertEquals(MemoryStatisticMetric.UNIT, platform1Metrics.getMemory().getUnit());
+        assertNotNull(platform1Metrics.getMemory().getUnit());
 
         assertEquals(1, platform1Metrics.getExecutionTime().getNumberOfDataPointsForAverage());
         assertEquals(300, platform1Metrics.getExecutionTime().getMinimum());
         assertEquals(300, platform1Metrics.getExecutionTime().getMaximum());
         assertEquals(300, platform1Metrics.getExecutionTime().getAverage());
-        assertEquals(ExecutionTimeStatisticMetric.UNIT, platform1Metrics.getExecutionTime().getUnit());
+        assertNotNull(platform1Metrics.getExecutionTime().getUnit());
 
         assertEquals(1, platform1Metrics.getValidationStatus().getValidatorTools().size());
         ValidatorInfo validationInfo = platform1Metrics.getValidationStatus().getValidatorTools().get(MINIWDL.toString());
@@ -287,13 +285,13 @@ private static void compareAggregateMetricsWithPlatforms(String platform2, Workf
         assertEquals(2, platform2Metrics.getMemory().getMinimum());
         assertEquals(2, platform2Metrics.getMemory().getMaximum());
         assertEquals(2, platform2Metrics.getMemory().getAverage());
-        assertEquals(MemoryStatisticMetric.UNIT, platform2Metrics.getMemory().getUnit());
+        assertNotNull(platform2Metrics.getMemory().getUnit());
 
         assertEquals(1, platform2Metrics.getExecutionTime().getNumberOfDataPointsForAverage());
         assertEquals(300, platform2Metrics.getExecutionTime().getMinimum());
         assertEquals(300, platform2Metrics.getExecutionTime().getMaximum());
         assertEquals(300, platform2Metrics.getExecutionTime().getAverage());
-        assertEquals(ExecutionTimeStatisticMetric.UNIT, platform2Metrics.getExecutionTime().getUnit());
+        assertNotNull(platform2Metrics.getExecutionTime().getUnit());
 
         assertEquals(1, platform2Metrics.getValidationStatus().getValidatorTools().size());
         validationInfo = platform2Metrics.getValidationStatus().getValidatorTools().get(WOMTOOL.toString());
@@ -330,13 +328,13 @@ private static void testAggregatedMetrics(WorkflowVersion version, String valida
         assertEquals(2, overallMetrics.getMemory().getMinimum());
         assertEquals(4.5, overallMetrics.getMemory().getMaximum());
         assertEquals(2.833333333333333, overallMetrics.getMemory().getAverage());
-        assertEquals(MemoryStatisticMetric.UNIT, overallMetrics.getMemory().getUnit());
+        assertNotNull(overallMetrics.getMemory().getUnit());
 
         assertEquals(3, overallMetrics.getExecutionTime().getNumberOfDataPointsForAverage());
         assertEquals(1, overallMetrics.getExecutionTime().getMinimum());
         assertEquals(300, overallMetrics.getExecutionTime().getMaximum());
         assertEquals(200.33333333333331, overallMetrics.getExecutionTime().getAverage());
-        assertEquals(ExecutionTimeStatisticMetric.UNIT, overallMetrics.getExecutionTime().getUnit());
+        assertNotNull(overallMetrics.getExecutionTime().getUnit());
 
         assertEquals(2, overallMetrics.getValidationStatus().getValidatorTools().size());
         validationInfo = overallMetrics.getValidationStatus().getValidatorTools().get(MINIWDL.toString());

metricsaggregator/src/test/resources/miniwdl-failed-validation-workflow-names.csv

@@ -1,2 +1,2 @@
 trsId,versionName,isValid,dateExecuted
-#workflow/github.com/garyluu/testWorkflow,master,false,2023-04-04T14:52:42Z
+#workflow/github.com/dockstore-testing/testWorkflow,master,false,2023-04-04T14:52:42Z

metricsaggregator/src/test/resources/miniwdl-successful-validation-workflow-names.csv

@@ -1,4 +1,4 @@
 trsId,versionName,isValid,dateExecuted
-#workflow/github.com/garyluu/testWorkflow,master,true,2023-04-04T14:52:42Z
-#workflow/github.com/garyluu/testWorkflow
-#workflow/github.com/garyluu/testWorkflow,master,THIS_IS_NOT_A_BOOLEAN,2023-04-04T14:52:42Z
+#workflow/github.com/dockstore-testing/testWorkflow,master,true,2023-04-04T14:52:42Z
+#workflow/github.com/dockstore-testing/testWorkflow
+#workflow/github.com/dockstore-testing/testWorkflow,master,THIS_IS_NOT_A_BOOLEAN,2023-04-04T14:52:42Z