fix nomad config issues using environment variables

Signed-off-by: Jorge Aguilera <[email protected]>
nextflow-io · Jul 2, 2024 · 656eb28 · 656eb28
1 parent 5fb5039
commit 656eb28
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Showing 4 changed files with 9 additions and 7 deletions.
diff --git a/plugins/nf-nomad/build.gradle b/plugins/nf-nomad/build.gradle
@@ -96,6 +96,7 @@ dependencies {
 test {
     useJUnitPlatform()
     jvmArgs '--add-opens=java.base/java.lang=ALL-UNNAMED'
+    environment 'NOMAD_ADDR', 'http://test-nf-nomad'
 }
 
 jar {

diff --git a/plugins/nf-nomad/src/main/nextflow/nomad/config/NomadClientOpts.groovy b/plugins/nf-nomad/src/main/nextflow/nomad/config/NomadClientOpts.groovy
@@ -43,11 +43,12 @@ class NomadClientOpts{
 
         sysEnv = env==null ? new HashMap<String,String>(System.getenv()) : env
 
-        def tmp = (nomadClientOpts.address?.toString() ?: sysEnv.get('NOMAD_ADDR'))
+        def address = (nomadClientOpts.address?.toString() ?: sysEnv.get('NOMAD_ADDR'))
+        assert address != null, "Nomad Address is required"
 
-        if( !tmp.endsWith("/"))
-            tmp +="/"
-        this.address = tmp + API_VERSION
+        if( !address.endsWith("/"))
+            address +="/"
+        this.address = address + API_VERSION
         this.token = nomadClientOpts.token ?: sysEnv.get('NOMAD_TOKEN')
 
         //TODO: Add mTLS properties and env vars

diff --git a/plugins/nf-nomad/src/main/nextflow/nomad/config/NomadJobOpts.groovy b/plugins/nf-nomad/src/main/nextflow/nomad/config/NomadJobOpts.groovy
@@ -44,7 +44,7 @@ class NomadJobOpts{
     NomadJobOpts(Map nomadJobOpts, Map<String,String> env=null){
         assert nomadJobOpts!=null
 
-        sysEnv = env==null ? new HashMap<String,String>(System.getenv()) : env
+        sysEnv = env ?: new HashMap<String,String>(System.getenv())
 
         deleteOnCompletion = nomadJobOpts.containsKey("deleteOnCompletion") ?
                 nomadJobOpts.deleteOnCompletion : false
@@ -53,7 +53,7 @@ class NomadJobOpts{
                     nomadJobOpts.datacenters : nomadJobOpts.datacenters.toString().split(","))
                     as List<String>).findAll{it.size()}.unique()
         }else{
-            datacenters = List.of(sysEnv.get('NOMAD_DC'))
+            datacenters = (sysEnv.get('NOMAD_DC')?:"").split(",") as List<String>
         }
 
         region = nomadJobOpts.region ?: sysEnv.get('NOMAD_REGION')

diff --git a/plugins/nf-nomad/src/test/nextflow/nomad/NomadConfigSpec.groovy b/plugins/nf-nomad/src/test/nextflow/nomad/NomadConfigSpec.groovy
@@ -49,7 +49,7 @@ class NomadConfigSpec extends Specification {
 
         where:
         ADDRESS                                  |  EXPECTED
-        null                                     | "${System.getenv('NOMAD_ADDR')}/v1"
+        null                                     | "http://test-nf-nomad/v1" // see build.gradle
         "http://nomad"                           | "http://nomad/v1"
     }
-Original file line number
+Diff line change
@@ Expand Up / @@ -96,6 +96,7 @@ dependencies { @@
     test {
         useJUnitPlatform()
         jvmArgs '--add-opens=java.base/java.lang=ALL-UNNAMED'
+        environment 'NOMAD_ADDR', 'http://test-nf-nomad'
     }
     jar {
@@ Expand Down @@