Round out all features and ensure tests work too

plugins/nf-dotenv/src/main/nextflow/dotenv/DotenvExtension.groovy

@@ -3,42 +3,62 @@ package nextflow.dotenv
 import groovy.transform.CompileStatic
 import io.github.cdimascio.dotenv.Dotenv
 import io.github.cdimascio.dotenv.DotenvBuilder
+import io.github.cdimascio.dotenv.DotenvException
 import nextflow.Session
 import nextflow.plugin.extension.Function
 import nextflow.plugin.extension.PluginExtensionPoint
 
+import java.nio.file.Path
+
 /** An extension to make dotenv file variables available to Nextflow scripts through a function call. */
 @CompileStatic
 class DotenvExtension extends PluginExtensionPoint {
 
     /** The default filename for the dotenv file. */
-    static final String DEFAULT_FILENAME = ".env"
+    static final String DEFAULT_FILENAME = '.env'
 
     /** The configuration of this Nextflow session. */
     private Map config
 
-    /** The dotenv environment result for this Nextflow session. */
-    private Dotenv dotenv
+    /** The directory where the dotenv file is supposed to be located. */
+    private Path directory
 
-    /** The default value to return when none is found in the environmental configuration file. */
-    private String defaultValue
+    /** The filename of the dotenv file used in this session. */
+    private String filename
 
     /** Initializes the plugin once it is loaded and the session is ready. */
     @Override
     protected void init(Session session) {
         this.config = session.config.navigate('dotenv', [:]) as Map
-        this.defaultValue = config.get("default", "").toString()
-        this.dotenv = new DotenvBuilder()
-            // The filename of the dotenv file which is typically '.env' but could be '.envrc' or other
-            .filename(config.get("filename", DEFAULT_FILENAME).toString())
-            // The relative directory to the main Nextflow script.
-            .directory(config.get("relative", session.baseDir.toUriString()).toString())
-            .load()
+        this.directory = session.baseDir.resolve(this.config.get('relative', '.'))
+        this.filename = config.get('filename', DEFAULT_FILENAME).toString()
     }
 
-    /** Return a value in the dotenv environment, or an empty string if the key is missing. */
+    /** The dotenv environment for this Nextflow session. Marked as lazy to only raise exceptions at call time. */
+    @Lazy private Dotenv dotenv = {
+        try {
+            new DotenvBuilder()
+                .filename(this.filename)
+                .directory(this.directory.toString())
+                .load()
+        } catch (DotenvException) {
+            throw new DotenvException(
+                "Could not find dotenv file at path ${this.directory}/${this.filename}\n\n" +
+                "Consider modifying the following properties in your Nextflow config:\n\n" +
+                "\tdotenv.filename = '${DEFAULT_FILENAME}'\n" +
+                "\tdotenv.relative = '.'\n\n"
+            )
+        }
+    }()
+
+    /** Return a value in the dotenv environment, or raise an exception if the key is missing. */
     @Function
     String dotenv(String key) {
-        this.dotenv.get(key, this.defaultValue).toString()
+        def value = this.dotenv.get(key)
+        if (value == null) {
+            throw new DotenvException("Could not find key ${key} in dotenv ${this.directory}/${this.filename}")
+        } else {
+            return value
+        }
     }
 }

plugins/nf-dotenv/src/test/nextflow/dotenv/DotenvTest.groovy

@@ -57,19 +57,20 @@ class DotenvTest extends Dsl2Spec{
             result.val == Channel.STOP
     }
 
-    def 'should import the plugin and raise an exception if a dotenv is not found' () {
+    def 'should import the plugin and not raise an exception if a dotenv is not found but unused' () {
         when:
             String SCRIPT = '''
                 include { dotenv } from 'plugin/nf-dotenv'
                 channel.of('hi-mom')
             '''
         and:
-            new MockScriptRunner([:]).setScript(SCRIPT).execute()
+            def result = new MockScriptRunner([:]).setScript(SCRIPT).execute()
         then:
-            thrown DotenvException
+            result.val == 'hi-mom'
+            result.val == Channel.STOP
     }
 
-    def 'should import the plugin and raise no exceptions the dotenv is found' () {
+    def 'should import the plugin and raise no exceptions when the dotenv is found' () {
         when:
             String SCRIPT = '''
                 include { dotenv } from 'plugin/nf-dotenv'
@@ -85,7 +86,7 @@ class DotenvTest extends Dsl2Spec{
             result.val == Channel.STOP
     }
 
-    def 'should import the plugin and return an empty value for a key that does not exist' () {
+    def 'should import the plugin and by default throw an exception for a key that does not exist' () {
         when:
             String SCRIPT = '''
                 include { dotenv } from 'plugin/nf-dotenv'
@@ -95,14 +96,12 @@ class DotenvTest extends Dsl2Spec{
                 FOO=bar
             '''
         and:
-            def result = new MockScriptRunner([:]).setScript(SCRIPT).setDotenv(DOTENV).execute()
+            new MockScriptRunner([:]).setScript(SCRIPT).setDotenv(DOTENV).execute()
         then:
-            result.val == ''
-            result.val == Channel.STOP
+            thrown DotenvException
     }
 
-
-    def 'should import the plugin and return a the correct value for a key that does exist' () {
+    def 'should import the plugin and return the correct value for a key that does exist' () {
         when:
             String SCRIPT = '''
                 include { dotenv } from 'plugin/nf-dotenv'
@@ -119,7 +118,7 @@ class DotenvTest extends Dsl2Spec{
     }
 
 
-    def 'should import the plugin and allow for an override of the dotenv filename relative to the main script' () {
+    def 'should import the plugin and allow for an override of the dotenv filename' () {
         when:
             String SCRIPT = '''
                 include { dotenv } from 'plugin/nf-dotenv'
@@ -128,14 +127,12 @@ class DotenvTest extends Dsl2Spec{
             String DOTENV = '''
                 FOO=bar
             '''
-        and:
-            def result = new MockScriptRunner(['dotenv.filename': '.envrc'])
+            new MockScriptRunner(['dotenv': ['filename': '.envrc']])
                 .setScript(SCRIPT)
-                .setDotenv(DOTENV, '.envrc')
+                .setDotenv(DOTENV,'.env')
                 .execute()
         then:
-            result.val == 'bar'
-            result.val == Channel.STOP
+            thrown DotenvException
     }
 
 
@@ -149,7 +146,7 @@ class DotenvTest extends Dsl2Spec{
                 FOO=bar
             '''
         and:
-            def result = new MockScriptRunner(['dotenv.relative': 'test'])
+            def result = new MockScriptRunner(['dotenv': ['relative': 'test']])
                 .setScript(SCRIPT)
                 .setDotenv(DOTENV, DotenvExtension.DEFAULT_FILENAME, 'test')
                 .execute()
@@ -158,7 +155,7 @@ class DotenvTest extends Dsl2Spec{
             result.val == Channel.STOP
     }
 
-    def 'should import the plugin and allow for an override of the dotenv directory as a parent directory to the main script' () {
+    def 'should import the plugin and allow for an override of the dotenv directory as the same as the env file' () {
         when:
             String SCRIPT = '''
                 include { dotenv } from 'plugin/nf-dotenv'
@@ -168,16 +165,16 @@ class DotenvTest extends Dsl2Spec{
                 FOO=bar
             '''
         and:
-            def result = new MockScriptRunner(['dotenv.relative': '../other'])
+            def result = new MockScriptRunner(['dotenv': ['relative': '.']])
                 .setScript(SCRIPT)
-                .setDotenv(DOTENV, DotenvExtension.DEFAULT_FILENAME, '../other')
+                .setDotenv(DOTENV, DotenvExtension.DEFAULT_FILENAME, '.')
                 .execute()
         then:
             result.val == 'bar'
             result.val == Channel.STOP
     }
 
-    def 'should import the plugin and allow for an override of the dotenv directory as the same as the env file' () {
+    def 'should import the plugin and raise an exception if the override dotenv directory is incorrect' () {
         when:
             String SCRIPT = '''
                 include { dotenv } from 'plugin/nf-dotenv'
@@ -187,15 +184,11 @@ class DotenvTest extends Dsl2Spec{
                 FOO=bar
             '''
         and:
-            def result = new MockScriptRunner(['dotenv.relative': '.'])
+            new MockScriptRunner(['dotenv': ['relative': 'other/']])
                 .setScript(SCRIPT)
-                .setDotenv(DOTENV, DotenvExtension.DEFAULT_FILENAME, '.')
+                .setDotenv(DOTENV, DotenvExtension.DEFAULT_FILENAME)
                 .execute()
         then:
-            result.val == 'bar'
-            result.val == Channel.STOP
+            thrown DotenvException
     }
-
-    // TODO: Need a test that tests for default value return from config
-    // TODO: Need a test for environment variable override
 }

plugins/nf-dotenv/src/test/nextflow/dotenv/MockHelpers.groovy

@@ -37,15 +37,15 @@ class MockScriptRunner extends ScriptRunner {
     // /** An in-memory filesystem for unit testing. */
     // static private FileSystem fs = Jimfs.newFileSystem(Configuration.unix())
     //
-    // static private Path tmpDir = {
+    // private Path tmpDir = {
     //     Path tmp = fs.getPath('/tmp')
     //     tmp.mkdir()
     //     Path test = Files.createTempDirectory(tmp, 'test')
     //     test
-    //  }()
+    // }
 
     /** Return a random temporary directory for testing. */
-    static private Path tmpDir = {
+    private Path tmpDir = {
         Path tmp = Path.of(System.getProperty('java.io.tmpdir'))
         tmp.mkdir()
         Path test = Files.createTempDirectory(tmp, 'test')
@@ -58,13 +58,13 @@ class MockScriptRunner extends ScriptRunner {
       * @param content The content of the temporary file, if any.
       * @param relative The relative modifier to the temporary file e.g. 'child-folder/'
       */
-    static private Path createInMemTempFile(String name, String content=null, String relative=null) {
+    private Path createInMemTempFile(String name, String content=null, String relative=null) {
         Path result
         if (relative) {
-            tmpDir.resolve(relative).mkdir()
-            result = tmpDir.resolve(relative).resolve(name)
+            this.tmpDir.resolve(relative).mkdir()
+            result = this.tmpDir.resolve(relative).resolve(name)
         } else {
-            result = tmpDir.resolve(name)
+            result = this.tmpDir.resolve(name)
         }
         if (content) {
             result.text = content
@@ -79,17 +79,16 @@ class MockScriptRunner extends ScriptRunner {
     }
 
     /** Set the script `main.nf` with specific contents. */
-    MockScriptRunner setScript(String str) {
-        Path script = createInMemTempFile('main.nf', str)
+    MockScriptRunner setScript(String content) {
+        Path script = createInMemTempFile('main.nf', content)
         setScript(script)
         return this
     }
 
     /** Set the configuration file `.env` with specific contents. */
-    MockScriptRunner setDotenv(String str, String filename=DotenvExtension.DEFAULT_FILENAME, String relative=null) {
-        createInMemTempFile(filename, str, relative)
+    MockScriptRunner setDotenv(String content, String filename=DotenvExtension.DEFAULT_FILENAME, String relative=null) {
+        createInMemTempFile(filename, content, relative)
         return this
-
     }
 
     /** Normalize the output of the script result so it is easier to compare. */