Merge pull request #1 from ElucidataInc/PRD-138/productionize_nf_polly

Productionize nf-polly plugin

.github/workflows/build.yml

@@ -17,7 +17,7 @@ jobs:
     strategy:
       fail-fast: false
       matrix:
-        java_version: [11, 21]
+        java_version: [8, 11]
 
     steps:
       - name: Environment

.gitignore

@@ -7,3 +7,5 @@
 build
 work
 out
+
+gradle.properties

README.md

@@ -1,114 +1,82 @@
-# nf-hello plugin 
-
-This project contains a simple Nextflow plugin called `nf-hello` which provides examples of different plugin extensions:
+# nf-polly plugin
 
-- A custom trace observer that prints a message when the workflow starts and when the workflow completes
-- A custom channel factory called `reverse`
-- A custom operator called `goodbye`
-- A custom function called `randomString`
-
-NOTE: If you want to use this project as a starting point for a custom plugin, you must rename the `plugins/nf-hello` folder and update `settings.gradle` with your plugin name.
-
-See the [Nextflow documentation](https://nextflow.io/docs/latest/plugins.html) for more information about developing plugins.
+This project contains a Nextflow plugin called `nf-polly` which provides utilities for using the
+Polly platform developed by [Elucidata](https://www.elucidata.io/).
 
 ## Plugin structure
-                    
-- `settings.gradle`
-
-    Gradle project settings. 
 
-- `plugins/nf-hello`
-
-    The plugin implementation base directory.
+- `settings.gradle` – Gradle project settings.
 
-- `plugins/nf-hello/build.gradle` 
-
-    Plugin Gradle build file. Project dependencies should be added here.
+- `plugins/nf-polly` – The plugin implementation base directory.
 
-- `plugins/nf-hello/src/resources/META-INF/MANIFEST.MF` 
-
-    Manifest file defining the plugin attributes e.g. name, version, etc. The attribute `Plugin-Class` declares the plugin main class. This class should extend the base class `nextflow.plugin.BasePlugin` e.g. `nextflow.hello.HelloPlugin`.
+- `plugins/nf-polly/build.gradle` – Plugin Gradle build file. Project dependencies should be added
+  here.
 
-- `plugins/nf-hello/src/resources/META-INF/extensions.idx`
-
-    This file declares one or more extension classes provided by the plugin. Each line should contain the fully qualified name of a Java class that implements the `org.pf4j.ExtensionPoint` interface (or a sub-interface).
+- `plugins/nf-polly/src/resources/META-INF/MANIFEST.MF` – Manifest file defining the plugin
+  attributes e.g. name, version, etc. The attribute `Plugin-Class` declares the plugin main class.
+  This class should extend the base class `nextflow.plugin.BasePlugin`
+  e.g. `nextflow.polly.PollyPlugin`.
 
-- `plugins/nf-hello/src/main` 
+- `plugins/nf-polly/src/resources/META-INF/extensions.idx` – This file declares one or more
+  extension classes provided by the plugin. Each line should contain
+  the fully qualified name of a Java class that implements the `org.pf4j.ExtensionPoint` interface (
+  or a sub-interface).
 
-    The plugin implementation sources.
+- `plugins/nf-polly/src/main` – The plugin implementation sources.
 
-- `plugins/nf-hello/src/test` 
-
-    The plugin unit tests. 
+- `plugins/nf-polly/src/test` – The plugin unit tests.
 
 ## Plugin classes
 
-- `HelloConfig`: shows how to handle options from the Nextflow configuration
-
-- `HelloExtension`: shows how to create custom channel factories, operators, and fuctions that can be included into pipeline scripts
+- `PollyConfig` – to handle options from the Nextflow configuration
 
-- `HelloFactory` and `HelloObserver`: shows how to react to workflow events with custom behavior
+- `PollyExtension` – contains custom utilities (operators, functions, etc.) for use in the Polly
+  pipelines environment.
 
-- `HelloPlugin`: the plugin entry point
+- `PollyPlugin` – the plugin entry point
 
-## Unit testing 
+## Unit testing
 
-To run your unit tests, run the following command in the project root directory (ie. where the file `settings.gradle` is located):
+To run your unit tests, run the following command in the project root directory (ie. where the file
+`settings.gradle` is located):
 
 ```bash
 ./gradlew check
 ```
 
 ## Testing and debugging
 
-To build and test the plugin during development, configure a local Nextflow build with the following steps:
+To build and test the plugin during development, configure a local Nextflow build with the following
+steps:
 
 1. Clone the Nextflow repository in your computer into a sibling directory:
     ```bash
     git clone --depth 1 https://github.com/nextflow-io/nextflow ../nextflow
     ```
-  
+
 2. Configure the plugin build to use the local Nextflow code:
     ```bash
     echo "includeBuild('../nextflow')" >> settings.gradle
     ```
-  
+
    (Make sure to not add it more than once!)
 
 3. Compile the plugin alongside the Nextflow code:
     ```bash
     make assemble
     ```
 
-4. Run Nextflow with the plugin, using `./launch.sh` as a drop-in replacement for the `nextflow` command, and adding the option `-plugins nf-hello` to load the plugin:
+4. Run Nextflow with the plugin, using `./launch.sh` as a drop-in replacement for the `nextflow`
+   command, and adding the option `-plugins nf-polly` to load the plugin:
     ```bash
-    ./launch.sh run nextflow-io/hello -plugins nf-hello
+    ./launch.sh run my_org/my_pipeline -plugins nf-polly
     ```
 
-## Testing without Nextflow build
+## Publishing with a Nextflow installation
 
-The plugin can be tested without using a local Nextflow build using the following steps:
+This plugin can be made available to a local Nextflow installation using the following steps:
 
 1. Build the plugin: `make buildPlugins`
-2. Copy `build/plugins/<your-plugin>` to `$HOME/.nextflow/plugins`
-3. Create a pipeline that uses your plugin and run it: `nextflow run ./my-pipeline-script.nf`
-
-## Package, upload, and publish
-
-The project should be hosted in a GitHub repository whose name matches the name of the plugin, that is the name of the directory in the `plugins` folder (e.g. `nf-hello`).
-
-Follow these steps to package, upload and publish the plugin:
-
-1. Create a file named `gradle.properties` in the project root containing the following attributes (this file should not be committed to Git):
-
-   * `github_organization`: the GitHub organisation where the plugin repository is hosted.
-   * `github_username`: The GitHub username granting access to the plugin repository.
-   * `github_access_token`: The GitHub access token required to upload and commit changes to the plugin repository.
-   * `github_commit_email`: The email address associated with your GitHub account.
-
-2. Use the following command to package and create a release for your plugin on GitHub:
-    ```bash
-    ./gradlew :plugins:nf-hello:upload
-    ```
+2. Copy `build/plugins/nf-polly-1.2.3` to `$HOME/.nextflow/plugins`
 
-3. Create a pull request against [nextflow-io/plugins](https://github.com/nextflow-io/plugins/blob/main/plugins.json) to make the plugin accessible to Nextflow.
+To test, create a pipeline that uses the plugin and run it: `nextflow run ./my-pipeline-script.nf`

plugins/nf-polly/build.gradle

@@ -50,7 +50,7 @@ sourceSets {
 }
 
 ext{
-    nextflowVersion = '24.01.0-edge'
+    nextflowVersion = '23.10.1'
 }
 
 dependencies {
@@ -68,15 +68,16 @@ dependencies {
     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'
+
     // test configuration
-    testImplementation "org.apache.groovy:groovy:4.0.18"
-    testImplementation "org.apache.groovy:groovy-nio:4.0.18"
+    testImplementation "org.codehaus.groovy:groovy:3.0.17"
+    testImplementation "org.codehaus.groovy:groovy-nio:3.0.17"
     testImplementation "io.nextflow:nextflow:$nextflowVersion"
-    testImplementation ("org.apache.groovy:groovy-test:4.0.18") { exclude group: 'org.apache.groovy' }
+    testImplementation ("org.codehaus.groovy:groovy-test:3.0.17") { exclude group: 'org.codehaus.groovy' }
     testImplementation ("cglib:cglib-nodep:3.3.0")
     testImplementation ("org.objenesis:objenesis:3.1")
-    testImplementation ("org.spockframework:spock-core:2.3-groovy-4.0") { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
-    testImplementation ('org.spockframework:spock-junit4:2.3-groovy-4.0') { exclude group: 'org.apache.groovy'; exclude group: 'net.bytebuddy' }
+    testImplementation ("org.spockframework:spock-core:2.2-groovy-3.0") { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
+    testImplementation ('org.spockframework:spock-junit4:2.2-groovy-3.0') { exclude group: 'org.codehaus.groovy'; exclude group: 'net.bytebuddy' }
     testImplementation ('com.google.jimfs:jimfs:1.1')
 
     testImplementation(testFixtures("io.nextflow:nextflow:$nextflowVersion"))

plugins/nf-polly/src/main/nextflow/polly/PollyConfig.groovy

@@ -1,35 +1,23 @@
-package nextflow.hello
+package nextflow.polly
 
 import groovy.transform.PackageScope
 
 
 /**
  * This class allows model an specific configuration, extracting values from a map and converting
  *
- * In this plugin, the user can configure how the messages are prefixed with a String, i.e.
- * due a nextflow.config
- *
- * hello {
- *     prefix = '>>'
- * }
- *
- * when the plugin reverse a String it will append '>>' at the beginning instead the default 'Mr.'
- *
- * We anotate this class as @PackageScope to restrict the access of their methods only to class in the
- * same package
- *
- * @author : jorge <[email protected]>
- *
+ * We anotate this class as @PackageScope to restrict the access of their methods only to class in
+ * the same package
  */
 @PackageScope
 class PollyConfig {
 
-    final private String prefix
+    final private String metricsStreamName
 
-    PollyConfig(Map map){
+    PollyConfig(Map map) {
         def config = map ?: Collections.emptyMap()
-        prefix = config.prefix ?: 'Mr.'
+        metricsStreamName = config.metricsStreamName ?: 'pravaah-dev-user-defined-metrics-events-stream-v1'
     }
 
-    String getPrefix() { prefix }
+    String getMetricsStreamName() { metricsStreamName }
 }