Add env() function (#5506)

Signed-off-by: Ben Sherman <[email protected]> Signed-off-by: Paolo Di Tommaso <[email protected]> Co-authored-by: Paolo Di Tommaso <[email protected]>
nextflow-io · Nov 18, 2024 · fa0e8e0 · fa0e8e0
1 parent d1bbd3d
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diff --git a/docs/config.md b/docs/config.md
@@ -113,6 +113,15 @@ The following constants are globally available in a Nextflow configuration file:
 `projectDir`
 : The directory where the main script is located.
 
+## Functions
+
+The following functions are globally available in a Nextflow configuration file:
+
+`env( name )`
+: :::{versionadded} 24.11.0-edge
+  :::
+: Get the value of the environment variable with the specified name in the Nextflow launch environment.
+
 (config-params)=
 
 ## Parameters

diff --git a/docs/reference/stdlib.md b/docs/reference/stdlib.md
@@ -197,6 +197,11 @@ The following functions are available in Nextflow scripts:
 `branchCriteria( closure )`
 : Create a branch criteria to use with the {ref}`operator-branch` operator.
 
+`env( name )`
+: :::{versionadded} 24.11.0-edge
+  :::
+: Get the value of the environment variable with the specified name in the Nextflow launch environment.
+
 `error( message = null )`
 : Throw a script runtime error with an optional error message.
 

diff --git a/docs/vscode.md b/docs/vscode.md
@@ -275,6 +275,14 @@ The Nextflow language specification does not support implicit environment variab
 println "PWD = ${System.getenv('PWD')}"
 ```
 
+:::{versionadded} 24.11.0-edge
+The `env()` function can be used instead of `System.getenv()`:
+
+```nextflow
+println "PWD = ${env('PWD')}"
+```
+:::
+
 ### Restricted syntax
 
 The following patterns are still supported but have been restricted, i.e. some syntax variants have been removed.

diff --git a/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy b/modules/nextflow/src/main/groovy/nextflow/Nextflow.groovy
@@ -57,6 +57,17 @@ class Nextflow {
 
     private static final Random random = new Random()
 
+    /**
+     * Get the value of an environment variable from the launch environment.
+     *
+     * @param name
+     *      The environment variable name to be referenced
+     * @return
+     *      The value associate with the specified variable name or {@code null} if the variable does not exist.
+     */
+    static String env(String name) {
+        return SysEnv.get(name)
+    }
 
     static private fileNamePattern( FilePatternSplitter splitter, Map opts ) {
 

diff --git a/modules/nextflow/src/main/groovy/nextflow/config/ConfigBase.groovy b/modules/nextflow/src/main/groovy/nextflow/config/ConfigBase.groovy
@@ -16,12 +16,12 @@
 
 package nextflow.config
 
-import ch.artecat.grengine.Grengine
-import groovy.transform.Memoized
-
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
 
+import ch.artecat.grengine.Grengine
+import groovy.transform.Memoized
+import nextflow.SysEnv
 import nextflow.exception.IllegalConfigException
 import nextflow.file.FileHelper
 import org.codehaus.groovy.control.CompilerConfiguration
@@ -74,6 +74,18 @@ abstract class ConfigBase extends Script {
         this.configStack = stack
     }
 
+    /**
+     * Get the value of an environment variable from the launch environment.
+     *
+     * @param name
+     *      The environment variable name to be referenced
+     * @return
+     *      The value associate with the specified variable name or {@code null} if the variable does not exist.
+     */
+    String env(String name) {
+        return SysEnv.get(name)
+    }
+
     /**
      * Implements the config file include
      */

diff --git a/modules/nextflow/src/test/groovy/nextflow/NextflowTest.groovy b/modules/nextflow/src/test/groovy/nextflow/NextflowTest.groovy
@@ -35,6 +35,17 @@ class NextflowTest extends Specification {
         System.getenv('CI_GROOVY_VERSION') == GroovySystem.getVersion()
     }
 
+    def 'should get an environment variable' () {
+        given:
+        SysEnv.push(FOO: 'FOO_VALUE')
+
+        expect:
+        Nextflow.env('FOO') == 'FOO_VALUE'
+
+        cleanup:
+        SysEnv.pop()
+    }
+
     def testFile() {
         expect:
         Nextflow.file('file.log').toFile() == new File('file.log').canonicalFile

diff --git a/modules/nextflow/src/test/groovy/nextflow/config/ConfigParserTest.groovy b/modules/nextflow/src/test/groovy/nextflow/config/ConfigParserTest.groovy
@@ -16,8 +16,6 @@
 
 package nextflow.config
 
-import spock.lang.Ignore
-
 import java.nio.file.Files
 import java.nio.file.NoSuchFileException
 import java.nio.file.Path
@@ -26,18 +24,36 @@ import com.sun.net.httpserver.Headers
 import com.sun.net.httpserver.HttpExchange
 import com.sun.net.httpserver.HttpHandler
 import com.sun.net.httpserver.HttpServer
+import nextflow.SysEnv
 import nextflow.exception.ConfigParseException
-import spock.lang.Specification
-
 import nextflow.util.Duration
 import nextflow.util.MemoryUnit
+import spock.lang.Ignore
+import spock.lang.Specification
 
 /**
  *
  * @author Paolo Di Tommaso <[email protected]>
  */
 class ConfigParserTest extends Specification {
 
+    def 'should get an environment variable' () {
+        given:
+        SysEnv.push(MAX_CPUS: '1')
+
+        when:
+        def CONFIG = '''
+        process.cpus = env('MAX_CPUS')
+        '''
+        def config = new ConfigParser().parse(CONFIG)
+
+        then:
+        config.process.cpus == '1'
+
+        cleanup:
+        SysEnv.pop()
+    }
+
     def 'should parse plugins id' () {
         given:
         def CONFIG = '''