refactor the package organization to create a separate package for mo…

…dels

plugins/nf-nomad/src/main/nextflow/nomad/config/NomadJobOpts.groovy

@@ -19,6 +19,10 @@ package nextflow.nomad.config
 
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
+import nextflow.nomad.models.JobAffinity
+import nextflow.nomad.models.JobConstraint
+import nextflow.nomad.models.JobConstraints
+import nextflow.nomad.models.JobVolume
 
 
 /**
@@ -37,11 +41,11 @@ class NomadJobOpts{
     String region
     String namespace
     String dockerVolume
-    VolumeSpec[] volumeSpec
-    AffinitySpec affinitySpec
-    ConstraintSpec constraintSpec
+    JobVolume[] volumeSpec
+    JobAffinity affinitySpec
+    JobConstraint constraintSpec
 
-    ConstraintsSpec constraintsSpec
+    JobConstraints constraintsSpec
 
     NomadJobOpts(Map nomadJobOpts, Map<String,String> env=null){
         assert nomadJobOpts!=null
@@ -74,10 +78,10 @@ class NomadJobOpts{
         this.constraintsSpec = parseConstraints(nomadJobOpts)
     }
 
-    VolumeSpec[] parseVolumes(Map nomadJobOpts){
-        List<VolumeSpec> ret = []
+    JobVolume[] parseVolumes(Map nomadJobOpts){
+        List<JobVolume> ret = []
         if( nomadJobOpts.volume && nomadJobOpts.volume instanceof Closure){
-            def volumeSpec = new VolumeSpec()
+            def volumeSpec = new JobVolume()
             def closure = (nomadJobOpts.volume as Closure)
             def clone = closure.rehydrate(volumeSpec, closure.owner, closure.thisObject)
             clone.resolveStrategy = Closure.DELEGATE_FIRST
@@ -89,7 +93,7 @@ class NomadJobOpts{
         if( nomadJobOpts.volumes && nomadJobOpts.volumes instanceof List){
             nomadJobOpts.volumes.each{ closure ->
                 if( closure instanceof Closure){
-                    def volumeSpec = new VolumeSpec()
+                    def volumeSpec = new JobVolume()
                     def clone = closure.rehydrate(volumeSpec, closure.owner, closure.thisObject)
                     clone.resolveStrategy = Closure.DELEGATE_FIRST
                     clone()
@@ -108,13 +112,13 @@ class NomadJobOpts{
             throw new IllegalArgumentException("No more than a workdir volume allowed")
         }
 
-        return ret as VolumeSpec[]
+        return ret as JobVolume[]
     }
 
-    AffinitySpec parseAffinity(Map nomadJobOpts) {
+    JobAffinity parseAffinity(Map nomadJobOpts) {
         if (nomadJobOpts.affinity && nomadJobOpts.affinity instanceof Closure) {
             log.info "affinity config will be deprecated, use affinities closure instead"
-            def affinitySpec = new AffinitySpec()
+            def affinitySpec = new JobAffinity()
             def closure = (nomadJobOpts.affinity as Closure)
             def clone = closure.rehydrate(affinitySpec, closure.owner, closure.thisObject)
             clone.resolveStrategy = Closure.DELEGATE_FIRST
@@ -126,10 +130,10 @@ class NomadJobOpts{
         }
     }
 
-    ConstraintSpec parseConstraint(Map nomadJobOpts){
+    JobConstraint parseConstraint(Map nomadJobOpts){
         if (nomadJobOpts.constraint && nomadJobOpts.constraint instanceof Closure) {
             log.info "constraint config will be deprecated, use constraints closure instead"
-            def constraintSpec = new ConstraintSpec()
+            def constraintSpec = new JobConstraint()
             def closure = (nomadJobOpts.constraint as Closure)
             def clone = closure.rehydrate(constraintSpec, closure.owner, closure.thisObject)
             clone.resolveStrategy = Closure.DELEGATE_FIRST
@@ -141,9 +145,9 @@ class NomadJobOpts{
         }
     }
 
-    ConstraintsSpec parseConstraints(Map nomadJobOpts){
+    JobConstraints parseConstraints(Map nomadJobOpts){
         if (nomadJobOpts.constraints && nomadJobOpts.constraints instanceof Closure) {
-            def constraintsSpec = new ConstraintsSpec()
+            def constraintsSpec = new JobConstraints()
             def closure = (nomadJobOpts.constraints as Closure)
             def clone = closure.rehydrate(constraintsSpec, closure.owner, closure.thisObject)
             clone.resolveStrategy = Closure.DELEGATE_FIRST

plugins/nf-nomad/src/main/nextflow/nomad/executor/ConstraintsBuilder.groovy

@@ -1,13 +1,13 @@
 package nextflow.nomad.executor
 
 import io.nomadproject.client.model.Constraint
-import nextflow.nomad.config.ConstraintAttrSpec
-import nextflow.nomad.config.ConstraintNodeSpec
-import nextflow.nomad.config.ConstraintsSpec
+import nextflow.nomad.models.JobConstraintsAttr
+import nextflow.nomad.models.JobConstraintsNode
+import nextflow.nomad.models.JobConstraints
 
 class ConstraintsBuilder {
 
-    protected static List<Constraint> constraintsSpecToList(ConstraintsSpec spec){
+    protected static List<Constraint> constraintsSpecToList(JobConstraints spec){
         def constraints = [] as List<Constraint>
         if( spec?.nodeSpecs ){
             def nodes = spec.nodeSpecs
@@ -24,7 +24,7 @@ class ConstraintsBuilder {
         return constraints
     }
 
-    protected static List<Constraint> nodeConstraints(ConstraintNodeSpec nodeSpec){
+    protected static List<Constraint> nodeConstraints(JobConstraintsNode nodeSpec){
         def ret = [] as List<Constraint>
         if( nodeSpec.id ){
             ret.add new Constraint()
@@ -65,7 +65,7 @@ class ConstraintsBuilder {
         ret
     }
 
-    protected static List<Constraint> attrConstraints(ConstraintAttrSpec nodeSpec) {
+    protected static List<Constraint> attrConstraints(JobConstraintsAttr nodeSpec) {
         def ret = [] as List<Constraint>
         if (nodeSpec.arch) {
             ret.add new Constraint()

plugins/nf-nomad/src/main/nextflow/nomad/executor/NomadService.groovy

@@ -22,9 +22,9 @@ import groovy.util.logging.Slf4j
 import io.nomadproject.client.ApiClient
 import io.nomadproject.client.api.JobsApi
 import io.nomadproject.client.model.*
-import nextflow.nomad.config.ConstraintsSpec
+import nextflow.nomad.models.JobConstraints
 import nextflow.nomad.config.NomadConfig
-import nextflow.nomad.config.VolumeSpec
+import nextflow.nomad.models.JobVolume
 import nextflow.processor.TaskRun
 import nextflow.util.MemoryUnit
 import nextflow.exception.ProcessSubmitException
@@ -136,7 +136,7 @@ class NomadService implements Closeable{
         if( config.jobOpts().volumeSpec ) {
             taskGroup.volumes = [:]
             config.jobOpts().volumeSpec.eachWithIndex { volumeSpec , idx->
-                if (volumeSpec && volumeSpec.type == VolumeSpec.VOLUME_CSI_TYPE) {
+                if (volumeSpec && volumeSpec.type == JobVolume.VOLUME_CSI_TYPE) {
                     taskGroup.volumes["vol_${idx}".toString()] = new VolumeRequest(
                             type: volumeSpec.type,
                             source: volumeSpec.name,
@@ -146,7 +146,7 @@ class NomadService implements Closeable{
                     )
                 }
 
-                if (volumeSpec && volumeSpec.type == VolumeSpec.VOLUME_HOST_TYPE) {
+                if (volumeSpec && volumeSpec.type == JobVolume.VOLUME_HOST_TYPE) {
                     taskGroup.volumes["vol_${idx}".toString()] = new VolumeRequest(
                             type: volumeSpec.type,
                             source: volumeSpec.name,
@@ -183,7 +183,7 @@ class NomadService implements Closeable{
 
         volumes(task, taskDef, workingDir)
         affinity(task, taskDef)
-        constrain(task, taskDef)
+        constraint(task, taskDef)
         constraints(task, taskDef)
 
         return taskDef
@@ -235,7 +235,7 @@ class NomadService implements Closeable{
         taskDef
     }
 
-    protected Task constrain(TaskRun task, Task taskDef){
+    protected Task constraint(TaskRun task, Task taskDef){
         if( config.jobOpts().constraintSpec ){
             def constraint = new Constraint()
             if(config.jobOpts().constraintSpec.attribute){
@@ -264,7 +264,7 @@ class NomadService implements Closeable{
         if( task.processor?.config?.get(TaskDirectives.CONSTRAINTS) &&
                 task.processor?.config?.get(TaskDirectives.CONSTRAINTS) instanceof Closure) {
             Closure closure = task.processor?.config?.get(TaskDirectives.CONSTRAINTS) as Closure
-            ConstraintsSpec constraintsSpec = ConstraintsSpec.parse(closure)
+            JobConstraints constraintsSpec = JobConstraints.parse(closure)
             def list = ConstraintsBuilder.constraintsSpecToList(constraintsSpec)
             constraints.addAll(list)
         }

plugins/nf-nomad/src/main/nextflow/nomad/config/AffinitySpec.groovy → plugins/nf-nomad/src/main/nextflow/nomad/models/JobAffinity.groovy

@@ -15,13 +15,13 @@
  * limitations under the License.
  */
 
-package nextflow.nomad.config
+package nextflow.nomad.models
 /**
  * Nomad Job Affinity Spec
  *
  * @author Jorge Aguilera <[email protected]>
  */
-class AffinitySpec{
+class JobAffinity {
 
     private String attribute
     private String operator
@@ -44,22 +44,22 @@ class AffinitySpec{
         return weight
     }
 
-    AffinitySpec attribute(String attribute){
+    JobAffinity attribute(String attribute){
         this.attribute=attribute
         this
     }
 
-    AffinitySpec operator(String operator){
+    JobAffinity operator(String operator){
         this.operator = operator
         this
     }
 
-    AffinitySpec value(String value){
+    JobAffinity value(String value){
         this.value = value
         this
     }
 
-    AffinitySpec weight(int weight){
+    JobAffinity weight(int weight){
         this.weight = weight
         this
     }

plugins/nf-nomad/src/main/nextflow/nomad/config/ConstraintSpec.groovy → plugins/nf-nomad/src/main/nextflow/nomad/models/JobConstraint.groovy

@@ -15,14 +15,14 @@
  * limitations under the License.
  */
 
-package nextflow.nomad.config
+package nextflow.nomad.models
 /**
  * Nomad Job Constraint Spec
  *
  * @author Jorge Aguilera <[email protected]>
  */
 
-class ConstraintSpec {
+class JobConstraint {
 
     private String attribute
     private String operator
@@ -40,17 +40,17 @@ class ConstraintSpec {
         return value
     }
 
-    ConstraintSpec attribute(String attribute){
+    JobConstraint attribute(String attribute){
         this.attribute=attribute
         this
     }
 
-    ConstraintSpec operator(String operator){
+    JobConstraint operator(String operator){
         this.operator = operator
         this
     }
 
-    ConstraintSpec value(String value){
+    JobConstraint value(String value){
         this.value = value
         this
     }

plugins/nf-nomad/src/main/nextflow/nomad/config/ConstraintsSpec.groovy → plugins/nf-nomad/src/main/nextflow/nomad/models/JobConstraints.groovy

@@ -1,21 +1,21 @@
-package nextflow.nomad.config
+package nextflow.nomad.models
 
-class ConstraintsSpec {
+class JobConstraints {
 
-    List<ConstraintNodeSpec> nodeSpecs = []
-    List<ConstraintAttrSpec> attrSpecs = []
+    List<JobConstraintsNode> nodeSpecs = []
+    List<JobConstraintsAttr> attrSpecs = []
 
-    ConstraintsSpec node( @DelegatesTo(ConstraintNodeSpec)Closure closure){
-        ConstraintNodeSpec constraintSpec = new ConstraintNodeSpec()
+    JobConstraints node(@DelegatesTo(JobConstraintsNode)Closure closure){
+        JobConstraintsNode constraintSpec = new JobConstraintsNode()
         def clone = closure.rehydrate(constraintSpec, closure.owner, closure.thisObject)
         clone.resolveStrategy = Closure.DELEGATE_FIRST
         clone()
         nodeSpecs << constraintSpec
         this
     }
 
-    ConstraintsSpec attr( @DelegatesTo(ConstraintAttrSpec)Closure closure){
-        ConstraintAttrSpec constraintSpec = new ConstraintAttrSpec()
+    JobConstraints attr(@DelegatesTo(JobConstraintsAttr)Closure closure){
+        JobConstraintsAttr constraintSpec = new JobConstraintsAttr()
         def clone = closure.rehydrate(constraintSpec, closure.owner, closure.thisObject)
         clone.resolveStrategy = Closure.DELEGATE_FIRST
         clone()
@@ -27,8 +27,8 @@ class ConstraintsSpec {
 
     }
 
-    static ConstraintsSpec parse(@DelegatesTo(ConstraintsSpec)Closure closure){
-        ConstraintsSpec constraintsSpec = new ConstraintsSpec()
+    static JobConstraints parse(@DelegatesTo(JobConstraints)Closure closure){
+        JobConstraints constraintsSpec = new JobConstraints()
         def clone = closure.rehydrate(constraintsSpec, closure.owner, closure.thisObject)
         clone.resolveStrategy = Closure.DELEGATE_FIRST
         clone()

plugins/nf-nomad/src/main/nextflow/nomad/config/ConstraintAttrSpec.groovy → plugins/nf-nomad/src/main/nextflow/nomad/models/JobConstraintsAttr.groovy

@@ -1,6 +1,6 @@
-package nextflow.nomad.config
+package nextflow.nomad.models
 
-class ConstraintAttrSpec {
+class JobConstraintsAttr {
 
     private String arch = null
     private Integer numcores= null
@@ -23,11 +23,11 @@ class ConstraintAttrSpec {
         return totalcompute
     }
 
-    ConstraintAttrSpec setCpu(Map map){
+    JobConstraintsAttr setCpu(Map map){
         cpu(map)
     }
 
-    ConstraintAttrSpec cpu(Map map){
+    JobConstraintsAttr cpu(Map map){
         this.arch = map.containsKey("arch") ? map["arch"].toString() : null
         this.numcores = map.containsKey("numcores") ? map["numcores"] as int : null
         this.reservablecores = map.containsKey("reservablecores") ? map["reservablecores"] as int : null

plugins/nf-nomad/src/main/nextflow/nomad/config/ConstraintNodeSpec.groovy → plugins/nf-nomad/src/main/nextflow/nomad/models/JobConstraintsNode.groovy

@@ -1,6 +1,6 @@
-package nextflow.nomad.config
+package nextflow.nomad.models
 
-class ConstraintNodeSpec {
+class JobConstraintsNode {
 
     private String id = null
     private String name = null
@@ -33,48 +33,48 @@ class ConstraintNodeSpec {
         return region
     }
 
-    ConstraintNodeSpec setUnique(Map map){
+    JobConstraintsNode setUnique(Map map){
         unique(map)
     }
 
-    ConstraintNodeSpec unique(Map map){
+    JobConstraintsNode unique(Map map){
         this.id = map.containsKey("id") ? map["id"].toString() : null
         this.name = map.containsKey("name") ? map["name"].toString() : null
         this
     }
 
-    ConstraintNodeSpec setClientClass(Object map){
+    JobConstraintsNode setClientClass(Object map){
         clientClass(map)
     }
 
-    ConstraintNodeSpec clientClass(Object clientClass){
+    JobConstraintsNode clientClass(Object clientClass){
         this.clientClass = clientClass.toString()
         this
     }
 
-    ConstraintNodeSpec setPool(Object map){
+    JobConstraintsNode setPool(Object map){
         pool(map)
     }
 
-    ConstraintNodeSpec pool(Object pool){
+    JobConstraintsNode pool(Object pool){
         this.pool = pool.toString()
         this
     }
 
-    ConstraintNodeSpec setDataCenter(Object map){
+    JobConstraintsNode setDataCenter(Object map){
         dataCenter(map)
     }
 
-    ConstraintNodeSpec dataCenter(Object dataCenter){
+    JobConstraintsNode dataCenter(Object dataCenter){
         this.dataCenter = dataCenter.toString()
         this
     }
 
-    ConstraintNodeSpec setRegion(Object map){
+    JobConstraintsNode setRegion(Object map){
         region(map)
     }
 
-    ConstraintNodeSpec region(Object region){
+    JobConstraintsNode region(Object region){
         this.region = region.toString()
         this
     }