Initial Commit

.github/workflows/build.yml

@@ -1,4 +1,4 @@
-name: nf-hello CI
+name: nf-polly CI
 on:
   push:
     branches:
@@ -10,7 +10,7 @@ on:
       - '*'
 jobs:
   build:
-    name: Build nf-hello
+    name: Build nf-polly
     if: "!contains(github.event.head_commit.message, '[ci skip]')"
     runs-on: ubuntu-latest
     timeout-minutes: 10

nextflow.config

@@ -1,3 +1,3 @@
 plugins {
-  id 'nf-hello'
+  id 'nf-polly'
 }

plugins/nf-hello/build.gradle → plugins/nf-polly/build.gradle

@@ -54,6 +54,16 @@ ext{
 }
 
 dependencies {
+    implementation platform('software.amazon.awssdk:bom:2.21.1')
+    implementation 'software.amazon.awssdk:s3'
+    implementation 'software.amazon.awssdk:kinesis'
+    implementation 'software.amazon.awssdk:sso'
+    implementation 'software.amazon.awssdk:ssooidc'
+    implementation platform('org.apache.logging.log4j:log4j-bom:2.20.0')
+    implementation 'org.apache.logging.log4j:log4j-slf4j2-impl'
+    implementation 'org.apache.logging.log4j:log4j-1.2-api'
+    implementation 'com.fasterxml.jackson.dataformat:jackson-dataformat-xml:2.13.0'
+
     // This dependency is exported to consumers, that is to say found on their compile classpath.
     compileOnly "io.nextflow:nextflow:$nextflowVersion"
     compileOnly 'org.slf4j:slf4j-api:1.7.10'

plugins/nf-hello/src/main/nextflow/hello/HelloConfig.groovy → plugins/nf-polly/src/main/nextflow/hello/PollyConfig.groovy

@@ -22,11 +22,11 @@ import groovy.transform.PackageScope
  *
  */
 @PackageScope
-class HelloConfig {
+class PollyConfig {
 
     final private String prefix
 
-    HelloConfig(Map map){
+    PollyConfig(Map map){
         def config = map ?: Collections.emptyMap()
         prefix = config.prefix ?: 'Mr.'
     }

plugins/nf-hello/src/main/nextflow/hello/HelloExtension.groovy → plugins/nf-polly/src/main/nextflow/hello/PollyExtension.groovy

@@ -1,5 +1,16 @@
 package nextflow.hello
 
+import com.fasterxml.jackson.databind.ObjectMapper;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.slf4j.MDC;
+import software.amazon.awssdk.core.SdkBytes;
+import software.amazon.awssdk.services.kinesis.KinesisClient;
+import software.amazon.awssdk.services.kinesis.model.KinesisException;
+import software.amazon.awssdk.services.kinesis.model.PutRecordRequest;
+import software.amazon.awssdk.services.kinesis.model.PutRecordResponse;
+import java.util.Map;
+import java.util.*;
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
@@ -23,7 +34,9 @@ import nextflow.plugin.extension.PluginExtensionPoint
  */
 @Slf4j
 @CompileStatic
-class HelloExtension extends PluginExtensionPoint {
+class PollyExtension extends PluginExtensionPoint {
+    // static final Logger logger = LogManager.getLogger(KinesisWriteApp.class);
+    static final ObjectMapper objMapper = new ObjectMapper();
 
     /*
      * A session hold information about current execution of the script
@@ -42,7 +55,7 @@ class HelloExtension extends PluginExtensionPoint {
      *    prefix = 'Mrs'
      * }
      */
-     private HelloConfig config
+     private PollyConfig config
 
     /*
      * nf-core initializes the plugin once loaded and session is ready
@@ -51,7 +64,7 @@ class HelloExtension extends PluginExtensionPoint {
     @Override
     protected void init(Session session) {
         this.session = session
-        this.config = new HelloConfig(session.config.navigate('hello') as Map)
+        this.config = new PollyConfig(session.config.navigate('hello') as Map)
     }
 
     /*
@@ -107,8 +120,21 @@ class HelloExtension extends PluginExtensionPoint {
      * Using @Function annotation we allow this function can be imported from the pipeline script
      */
     @Function
-    String randomString(int length=9){
-        new Random().with {(1..length).collect {(('a'..'z')).join(null)[ nextInt((('a'..'z')).join(null).length())]}.join(null)}
+    void reportMetric(var key,var val){
+        String streamName ="pravaah-dev-user-defined-metrics-events-v1";
+        String partitionKey="1234";
+        var keyValuePairs = Map.of(key, val);
+        var data = objMapper.writeValueAsBytes(Map.of("metric", keyValuePairs));
+        // Instantiate the client
+        var client = KinesisClient.builder().build();
+        try {
+            // construct single PutRecord request
+            var putRequest = PutRecordRequest.builder().partitionKey(partitionKey).streamName(streamName).data(SdkBytes.fromByteArray(data)).build();
+            // execute single PutRecord request
+            PutRecordResponse response = client.putRecord(putRequest);
+            System.out.println("Produced Record " + response.sequenceNumber() + " to Shard " + response.shardId() + " (line 145)");
+        }catch (KinesisException e) {
+            System.out.println("Failed to produce "  + ": " + e.getMessage());
+        }
     }
-
 }

plugins/nf-hello/src/main/nextflow/hello/HelloFactory.groovy → plugins/nf-polly/src/main/nextflow/hello/PollyFactory.groovy

@@ -26,12 +26,12 @@ import nextflow.trace.TraceObserverFactory
  * @author Paolo Di Tommaso <[email protected]>
  */
 @CompileStatic
-class HelloFactory implements TraceObserverFactory {
+class PollyFactory implements TraceObserverFactory {
 
     @Override
     Collection<TraceObserver> create(Session session) {
         final result = new ArrayList()
-        result.add( new HelloObserver() )
+        result.add( new PollyObserver() )
         return result
     }
 }

plugins/nf-hello/src/main/nextflow/hello/HelloObserver.groovy → plugins/nf-polly/src/main/nextflow/hello/PollyObserver.groovy

@@ -28,7 +28,7 @@ import nextflow.trace.TraceObserver
  */
 @Slf4j
 @CompileStatic
-class HelloObserver implements TraceObserver {
+class PollyObserver implements TraceObserver {
 
     @Override
     void onFlowCreate(Session session) {

plugins/nf-hello/src/main/nextflow/hello/HelloPlugin.groovy → plugins/nf-polly/src/main/nextflow/hello/PollyPlugin.groovy

@@ -27,9 +27,9 @@ import org.pf4j.PluginWrapper
  * @author Paolo Di Tommaso <[email protected]>
  */
 @CompileStatic
-class HelloPlugin extends BasePlugin {
+class PollyPlugin extends BasePlugin {
 
-    HelloPlugin(PluginWrapper wrapper) {
+    PollyPlugin(PluginWrapper wrapper) {
         super(wrapper)
     }
 }

plugins/nf-hello/src/resources/META-INF/MANIFEST.MF → plugins/nf-polly/src/resources/META-INF/MANIFEST.MF

@@ -1,6 +1,6 @@
 Manifest-Version: 1.0
-Plugin-Id: nf-hello
+Plugin-Id: nf-polly
 Plugin-Version: 0.5.0
-Plugin-Class: nextflow.hello.HelloPlugin
+Plugin-Class: nextflow.hello.PollyPlugin
 Plugin-Provider: nextflow
 Plugin-Requires: >=24.01.0-edge

plugins/nf-polly/src/resources/META-INF/extensions.idx

@@ -0,0 +1,2 @@
+nextflow.hello.PollyFactory
+nextflow.hello.PollyExtension

plugins/nf-hello/src/test/nextflow/hello/HelloDslTest.groovy → plugins/nf-polly/src/test/nextflow/hello/PollyDslTest.groovy

@@ -17,12 +17,12 @@ import java.nio.file.Path
 
 
 /**
- * Unit test for Hello DSL
+ * Unit test for Polly DSL
  *
  * @author : jorge <[email protected]>
  */
 @Timeout(10)
-class HelloDslTest extends Dsl2Spec{
+class PollyDslTest extends Dsl2Spec{
 
     @Shared String pluginsMode
 
@@ -66,11 +66,11 @@ class HelloDslTest extends Dsl2Spec{
     def 'should perform a hi and create a channel' () {
         when:
         def SCRIPT = '''
-            include {reverse} from 'plugin/nf-hello'
+            include {reverse} from 'plugin/nf-polly'
             channel.reverse('hi!') 
             '''
         and:
-        def result = new MockScriptRunner([hello:[prefix:'>>']]).setScript(SCRIPT).execute()
+        def result = new MockScriptRunner([Polly:[prefix:'>>']]).setScript(SCRIPT).execute()
         then:
         result.val == 'hi!'.reverse()
         result.val == Channel.STOP
@@ -79,7 +79,7 @@ class HelloDslTest extends Dsl2Spec{
     def 'should store a goodbye' () {
         when:
         def SCRIPT = '''
-            include {goodbye} from 'plugin/nf-hello'
+            include {goodbye} from 'plugin/nf-polly'
             channel
                 .of('folks')
                 .goodbye() 
@@ -95,9 +95,9 @@ class HelloDslTest extends Dsl2Spec{
     def 'can use an imported function' () {
         when:
         def SCRIPT = '''
-            include {randomString} from 'plugin/nf-hello'
+            include {reportMetric} from 'plugin/nf-polly'
             channel
-                .of( randomString(20) )                
+                .of( reportMetric("key","value") )                
             '''
         and:
         def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()

plugins/nf-hello/src/test/nextflow/hello/HelloFactoryTest.groovy → plugins/nf-polly/src/test/nextflow/hello/PollyFactoryTest.groovy

@@ -23,14 +23,14 @@ import spock.lang.Specification
  *
  * @author Paolo Di Tommaso <[email protected]>
  */
-class HelloFactoryTest extends Specification {
+class PollyFactoryTest extends Specification {
 
     def 'should return observer' () {
         when:
-        def result = new HelloFactory().create(Mock(Session))
+        def result = new PollyFactory().create(Mock(Session))
         then:
         result.size()==1
-        result[0] instanceof HelloObserver
+        result[0] instanceof PollyObserver
     }
 
 }

plugins/nf-hello/src/test/nextflow/hello/TestHelper.groovy → plugins/nf-polly/src/test/nextflow/hello/PollyHelper.groovy

@@ -29,7 +29,7 @@ import java.util.zip.GZIPInputStream
  *
  * @author Paolo Di Tommaso <[email protected]>
  */
-class TestHelper {
+class PollyHelper {
 
     static private fs = Jimfs.newFileSystem(Configuration.unix());
 

plugins/nf-hello/src/test/nextflow/hello/MockHelpers.groovy → plugins/nf-polly/src/test/nextflow/hello/PollyHelpers.groovy

@@ -27,7 +27,7 @@ class MockScriptRunner extends ScriptRunner {
     }
 
     MockScriptRunner setScript(String str) {
-        def script = TestHelper.createInMemTempFile('main.nf', str)
+        def script = PollyHelper.createInMemTempFile('main.nf', str)
         setScript(script)
         return this
     }

settings.gradle

@@ -21,6 +21,6 @@ plugins {
     id("org.gradle.toolchains.foojay-resolver-convention") version "0.7.0"
 }
 
-rootProject.name = 'nf-hello'
+rootProject.name = 'nf-polly'
 include('plugins')
-include('plugins:nf-hello')
+include('plugins:nf-polly')