Add Fusion logs and tags config

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
nextflow-io · Feb 26, 2023 · 0919207 · 0919207
1 parent 828583d
commit 0919207
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Showing 5 changed files with 88 additions and 2 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionConfig.groovy
@@ -18,7 +18,6 @@
 package nextflow.fusion
 
 import groovy.transform.CompileStatic
-
 /**
  * Model Fusion config options
  *
@@ -29,17 +28,30 @@ class FusionConfig {
 
     final static public String DEFAULT_FUSION_AMD64_URL = 'https://fusionfs.seqera.io/releases/v2.1-amd64.json'
     final static public String DEFAULT_FUSION_ARM64_URL = 'https://fusionfs.seqera.io/releases/v2.1-arm64.json'
+    final static public String DEFAULT_TAGS = "[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)"
 
     final static public String FUSION_PATH = '/usr/bin/fusion'
 
     final private Boolean enabled
     final private String containerConfigUrl
     final private Boolean exportAwsAccessKeys
+    final private String logOutput
+    final private String logLevel
+    final private boolean tagsEnabled
+    final private String tagsPattern
 
     boolean enabled() { enabled }
 
     boolean exportAwsAccessKeys() { exportAwsAccessKeys }
 
+    String logLevel() { logLevel }
+
+    String logOutput() { logOutput }
+
+    boolean tagsEnabled() { tagsEnabled }
+
+    String tagsPattern() { tagsPattern }
+
     URL containerConfigUrl() {
         this.containerConfigUrl ? new URL(this.containerConfigUrl) : null
     }
@@ -48,6 +60,10 @@ class FusionConfig {
         this.enabled = opts.enabled
         this.exportAwsAccessKeys = opts.exportAwsAccessKeys
         this.containerConfigUrl = opts.containerConfigUrl?.toString() ?: env.get('FUSION_CONTAINER_CONFIG_URL')
+        this.logLevel = opts.logLevel
+        this.logOutput = opts.logOutput
+        this.tagsEnabled = opts.tags==null || opts.tags.toString()!='false'
+        this.tagsPattern = (opts.tags==null || (opts.tags instanceof Boolean && opts.tags)) ? DEFAULT_TAGS : ( opts.tags !instanceof Boolean ? opts.tags as String : null )
         if( containerConfigUrl && !validProtocol(containerConfigUrl))
             throw new IllegalArgumentException("Fusion container config URL should start with 'http:' or 'https:' protocol prefix - offending value: $containerConfigUrl")
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionEnvProvider.groovy
@@ -17,6 +17,7 @@
 
 package nextflow.fusion
 
+
 import nextflow.Global
 import nextflow.SysEnv
 import nextflow.plugin.Plugins
@@ -35,6 +36,14 @@ class FusionEnvProvider {
             final env = it.getEnvironment(scheme,config)
             if( env ) result.putAll(env)
         }
+        // tags setting
+        if( config.tagsEnabled() )
+            result.FUSION_TAGS = config.tagsPattern()
+        // logs setting
+        if( config.logOutput() )
+            result.FUSION_LOG_OUTPUT = config.logOutput()
+        if( config.logLevel() )
+            result.FUSION_LOG_LEVEL = config.logLevel()
         return result
     }
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy b/modules/nextflow/src/main/groovy/nextflow/fusion/FusionScriptLauncher.groovy
@@ -88,7 +88,6 @@ class FusionScriptLauncher extends BashWrapperBuilder {
             final work = toContainerMount(remoteWorkDir).toString()
             final result = new LinkedHashMap(10)
             result.FUSION_WORK = work
-            result.FUSION_TAGS="[.command.*|.exitcode|.fusion.*](nextflow.io/metadata=true),[*](nextflow.io/temporary=true)"
             // foreign env
             final provider = new FusionEnvProvider()
             result.putAll(provider.getEnvironment(scheme))

diff --git a/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionScriptLauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/executor/fusion/FusionScriptLauncherTest.groovy
@@ -69,6 +69,37 @@ class FusionScriptLauncherTest extends Specification {
         ]
     }
 
+    def 'should get fusion logs env' () {
+        given:
+        Global.config = [fusion: [logLevel:'debug', logOutput:'stdout', tags: false]]
+        and:
+        def fusion = new FusionScriptLauncher(
+                scheme: 'http',
+                remoteWorkDir: XPath.get('http://foo/work'))
+
+        expect:
+        fusion.fusionEnv() == [
+                FUSION_WORK: '/fusion/http/foo/work',
+                FUSION_LOG_LEVEL: 'debug',
+                FUSION_LOG_OUTPUT: 'stdout'
+        ]
+    }
+
+    def 'should get fusion with custom tags' () {
+        given:
+        Global.config = [fusion: [tags: 'custom-tags-pattern-here']]
+        and:
+        def fusion = new FusionScriptLauncher(
+                scheme: 'http',
+                remoteWorkDir: XPath.get('http://foo/work'))
+
+        expect:
+        fusion.fusionEnv() == [
+                FUSION_WORK: '/fusion/http/foo/work',
+                FUSION_TAGS: 'custom-tags-pattern-here'
+        ]
+    }
+
     def 'should get header script' () {
         given:
         def fusion = new FusionScriptLauncher(scheme: 's3')

diff --git a/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy b/modules/nextflow/src/test/groovy/nextflow/fusion/FusionConfigTest.groovy
@@ -70,4 +70,35 @@ class FusionConfigTest extends Specification {
         [exportAwsAccessKeys: true]     | true
     }
 
+    @Unroll
+    def 'should configure log level and output' () {
+        given:
+        def opts = new FusionConfig(OPTS)
+        expect:
+        opts.logLevel() == LEVEL
+        opts.logOutput() == OUTPUT
+
+        where:
+        OPTS                            | LEVEL     | OUTPUT
+        [:]                             | null      | null
+        [logLevel: 'trace']             | 'trace'   | null
+        [logOutput: 'stdout']           | null      | 'stdout'
+    }
+
+    @Unroll
+    def 'should configure tags' () {
+        given:
+        def opts = new FusionConfig(OPTS)
+        expect:
+        opts.tagsEnabled() == ENABLED
+        opts.tagsPattern() == PATTERN
+
+        where:
+        OPTS                    | ENABLED   | PATTERN
+        [:]                     | true      | FusionConfig.DEFAULT_TAGS
+        [tags:true]             | true      | FusionConfig.DEFAULT_TAGS
+        [tags:false]            | false     | null
+        [tags:'[*.txt](x=1)']   | true      | '[*.txt](x=1)'
+
+    }
 }