Merge branch 'truncate_labels_for_k8s' of https://github.com/ebi-gene…

…-expression-group/nextflow into ebi-gene-expression-group-truncate_labels_for_k8s
nextflow-io · May 10, 2020 · 6434b9d · 6434b9d
2 parents 2784cdb + a2cc3f8
commit 6434b9d
Show file tree

Hide file tree

Showing 2 changed files with 73 additions and 3 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/model/PodSpecBuilder.groovy
@@ -24,12 +24,15 @@ import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import nextflow.executor.res.AcceleratorResource
 import nextflow.util.MemoryUnit
+import groovy.util.logging.Slf4j
+
 /**
  * Object build for a K8s pod specification
  *
  * @author Paolo Di Tommaso <paolo.ditommaso@gmail.com>
  */
 @CompileStatic
+@Slf4j
 class PodSpecBuilder {
 
     static @PackageScope AtomicInteger VOLUMES = new AtomicInteger()
@@ -146,12 +149,12 @@ class PodSpecBuilder {
     }
 
     PodSpecBuilder withLabel( String name, String value ) {
-        this.labels.put(name, value)
+        this.labels.put(name, normalizeLabel(name, value))
         return this
     }
 
     PodSpecBuilder withLabels(Map labels) {
-        this.labels.putAll(labels)
+        this.labels.putAll(normalizeLabels(labels)) 
         return this
     }
 
@@ -216,6 +219,24 @@ class PodSpecBuilder {
         return this
     }
 
+    String normalizeLabel( String name, String value ) {
+        if( !name || !value ) {
+            log.debug "K8s invalid label name=$name value=$value"  
+        }
+        else if( value.size() > 63 ) {
+            log.debug "K8s label exceeds allowed size: 63 -- offending name=$name value=$value"  
+            value=value.substring(0,63)   
+        }
+        return value
+    }
+
+    Map<String, String> normalizeLabels(Map<String, String> labels) {
+        for( Map.Entry<String,String> entry : labels ) {
+            labels.put(entry.key, normalizeLabel(entry.key, entry.value))
+        }
+        return labels
+    }
+
     PodSpecBuilder withPodOptions(PodOptions opts) {
         // -- pull policy
         if( opts.imagePullPolicy )
@@ -239,7 +260,7 @@ class PodSpecBuilder {
             def keys = opts.labels.keySet()
             if( 'app' in keys ) throw new IllegalArgumentException("Invalid pod label -- `app` is a reserved label")
             if( 'runName' in keys ) throw new IllegalArgumentException("Invalid pod label -- `runName` is a reserved label")
-            labels.putAll( opts.labels )
+            labels.putAll(normalizeLabels(opts.labels)) 
         }
         // - annotations
         if( opts.annotations ) {

diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/model/PodSpecBuilderTest.groovy
@@ -103,6 +103,55 @@ class PodSpecBuilderTest extends Specification {
                    ]
         ]
     }
+
+    def 'should truncate labels longer than 63 chars' () {
+
+        when:
+        def spec = new PodSpecBuilder()
+                .withPodName('foo')
+                .withImageName('busybox')
+                .withWorkDir('/some/work/dir')
+                .withCommand(['sh', '-c', 'echo hello'])
+                .withNamespace('xyz')
+                .withLabel('app','myApp')
+                .withLabel('runName','something')
+                .withLabel('tag','somethingreallylonggggggggggggggggggggggggggggggggggggggggggendEXTRABIT')
+                .withLabels([tag2: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggendEXTRABIT', tag3: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggendEXTRABIT'])
+                .withAnnotation("anno1", "value1")
+                .withAnnotations([anno2: "value2", anno3: "value3"])
+                .build()
+
+        then:
+        spec ==  [ apiVersion: 'v1',
+                   kind: 'Pod',
+                   metadata: [
+                           name:'foo',
+                           namespace:'xyz',
+                           labels: [
+                                   app: 'myApp',
+                                   runName: 'something',
+                                   tag: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggend',
+                                   tag2: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggend',
+                                   tag3: 'somethingreallylonggggggggggggggggggggggggggggggggggggggggggend'
+                           ],
+                           annotations: [
+                                   anno1: "value1",
+                                   anno2: "value2",
+                                   anno3: "value3"
+                           ]
+                   ],
+                   spec: [
+                           restartPolicy:'Never',
+                           containers:[
+                                   [name:'foo',
+                                    image:'busybox',
+                                    command: ['sh', '-c', 'echo hello'],
+                                    workingDir:'/some/work/dir'
+                                   ]
+                           ]
+                   ]
+        ]
+    }
 
 
     def 'should set resources and env' () {