From ccc31b7b99939fe6dd8bcb4c0c78692b25723e99 Mon Sep 17 00:00:00 2001
From: Ivkovic <sinisa.ivkovic@gmail.com>
Date: Mon, 1 Apr 2019 17:05:46 -0400
Subject: [PATCH 1/3] ability to configure and mount working dir as volume

---
 .../aws/batch/AwsBatchTaskHandler.groovy      | 29 +++++++++++++++++--
 .../cloud/aws/batch/AwsOptions.groovy         | 11 +++++++
 .../aws/batch/AwsBatchTaskHandlerTest.groovy  | 26 ++++++++++++-----
 3 files changed, 56 insertions(+), 10 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
index 9aa2c50fb0..ecb546381d 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
@@ -128,6 +128,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
                 cliPath: executor.getSession().getExecConfigProp(name,'awscli',null) as String,
                 storageClass: executor.getSession().config.navigate('aws.client.uploadStorageClass') as String,
                 storageEncryption: executor.getSession().config.navigate('aws.client.storageEncryption') as String,
+                mountPoint: executor.getSession().config.navigate('aws.mountPoint', '/tmp') as String,
                 remoteBinDir: executor.remoteBinDir as String,
                 region: executor.getSession().config.navigate('aws.region') as String
         )
@@ -376,6 +377,11 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         result.setJobDefinitionName(name)
         result.setType(JobDefinitionType.Container)
 
+        def mountPointPath = getAwsOptions().mountPoint
+        def tmpdir = new KeyValuePair()
+        tmpdir.setName("TMPDIR")
+        tmpdir.setValue(mountPointPath)
+
         // container definition
         def container = new ContainerProperties()
                 .withImage(image)
@@ -383,7 +389,23 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
                 .withCommand('true')
                 .withMemory(1024)
                 .withVcpus(1)
+                .withEnvironment([tmpdir])
+
         def awscli = getAwsOptions().cliPath
+        def mounts = new LinkedList<MountPoint>()
+        def volumes = new LinkedList<Volume>()
+        def mountPointName = 'mount'
+        def mountWorkDir = new MountPoint()
+                    .withSourceVolume(mountPointName)
+                    .withContainerPath(mountPointPath)
+                    .withReadOnly(false)
+        mounts.add(mountWorkDir)
+        def volumeWorkDir = new Volume()
+                .withName(mountPointName)
+                .withHost(new Host()
+                .withSourcePath(mountPointPath))
+        volumes.add(volumeWorkDir)
+
         if( awscli ) {
             def mountName = 'aws-cli'
             def path = Paths.get(awscli).parent.parent.toString()
@@ -391,14 +413,17 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
                     .withSourceVolume(mountName)
                     .withContainerPath(path)
                     .withReadOnly(true)
-            container.setMountPoints([mount])
+            mounts.add(mount)
 
             def vol = new Volume()
                     .withName(mountName)
                     .withHost(new Host()
                     .withSourcePath(path))
-            container.setVolumes([vol])
+            volumes.add(vol)
         }
+        container.setMountPoints(mounts)
+        container.setVolumes(volumes)
+
         result.setContainerProperties(container)
 
         // create a job marker uuid
diff --git a/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsOptions.groovy b/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsOptions.groovy
index 4c41b4868c..1de0188826 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsOptions.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsOptions.groovy
@@ -42,6 +42,8 @@ class AwsOptions {
 
     String region
 
+    String mountPoint
+
     AwsOptions() { }
 
     AwsOptions(Session session) {
@@ -78,6 +80,15 @@ class AwsOptions {
         }
     }
 
+    void setMountPath(String value) {
+        if( !value )
+            this.mountPoint = '/tmp'
+        else {
+            if (!value.startsWith('/')) throw new ProcessUnrecoverableException("Not a valid mount path: $value -- it must be an absolute path")
+            this.mountPoint = value
+        }
+    }
+
     String getAwsCli() {
         def result = getCliPath()
         if( !result ) result = 'aws'
diff --git a/modules/nextflow/src/test/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
index 3a590066ef..cccca96645 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandlerTest.groovy
@@ -457,25 +457,35 @@ class AwsBatchTaskHandlerTest extends Specification {
         def result = handler.makeJobDefRequest(IMAGE)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
-        1 * handler.getAwsOptions() >> new AwsOptions()
+        2 * handler.getAwsOptions() >> new AwsOptions()
         result.jobDefinitionName == JOB_NAME
         result.type == 'container'
         result.parameters.'nf-token' == 'fdb5ef295f566138a43252b2ea272282'
-        !result.containerProperties.mountPoints
+        result.containerProperties.mountPoints[0].sourceVolume == 'mount'
+        !result.containerProperties.mountPoints[0].readOnly
 
         when:
         result = handler.makeJobDefRequest(IMAGE)
         then:
         1 * handler.normalizeJobDefinitionName(IMAGE) >> JOB_NAME
-        1 * handler.getAwsOptions() >> new AwsOptions(cliPath: '/home/conda/bin/aws')
+        2 * handler.getAwsOptions() >> new AwsOptions(cliPath: '/home/conda/bin/aws', mountPoint: '/tmp')
         result.jobDefinitionName == JOB_NAME
         result.type == 'container'
         result.parameters.'nf-token' == '9c56fd073d32e0c29f51f12afdfe4750'
-        result.containerProperties.mountPoints[0].sourceVolume == 'aws-cli'
-        result.containerProperties.mountPoints[0].containerPath == '/home/conda'
-        result.containerProperties.mountPoints[0].readOnly
-        result.containerProperties.volumes[0].host.sourcePath == '/home/conda'
-        result.containerProperties.volumes[0].name == 'aws-cli'
+        result.containerProperties.mountPoints[0].sourceVolume == 'mount'
+        result.containerProperties.mountPoints[0].containerPath == '/tmp'
+        !result.containerProperties.mountPoints[0].readOnly
+        result.containerProperties.volumes[0].host.sourcePath == '/tmp'
+        result.containerProperties.volumes[0].name == 'mount'
+
+        result.containerProperties.mountPoints[1].sourceVolume == 'aws-cli'
+        result.containerProperties.mountPoints[1].containerPath == '/home/conda'
+        result.containerProperties.mountPoints[1].readOnly
+        result.containerProperties.volumes[1].host.sourcePath == '/home/conda'
+        result.containerProperties.volumes[1].name == 'aws-cli'
+
+        result.containerProperties.environment[0].name == "TMPDIR"
+        result.containerProperties.environment[0].value == "/tmp"
 
     }
 

From cf3b8d61ce3d3e9045dbe5cd71353db22ff6dccd Mon Sep 17 00:00:00 2001
From: Ivkovic <sinisa.ivkovic@gmail.com>
Date: Mon, 1 Apr 2019 17:15:29 -0400
Subject: [PATCH 2/3] fix generating uuid

---
 .../groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy  | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
index ecb546381d..3893071249 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
@@ -427,7 +427,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         result.setContainerProperties(container)
 
         // create a job marker uuid
-        def uuid = CacheHelper.hasher([name, image, awscli]).hash().toString()
+        def uuid = CacheHelper.hasher([name, image, awscli, tmpdir]).hash().toString()
         result.setParameters(['nf-token':uuid])
 
         return result

From 7a893b28801c87444c64a5acbfef046c0bbaac9b Mon Sep 17 00:00:00 2001
From: Ivkovic <sinisa.ivkovic@gmail.com>
Date: Fri, 5 Apr 2019 15:30:40 -0400
Subject: [PATCH 3/3] remove export of TMPDIR. should use scratch in process to
 change workdir

---
 .../nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy     | 6 +-----
 1 file changed, 1 insertion(+), 5 deletions(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
index 3893071249..f387c605d1 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy
@@ -378,9 +378,6 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         result.setType(JobDefinitionType.Container)
 
         def mountPointPath = getAwsOptions().mountPoint
-        def tmpdir = new KeyValuePair()
-        tmpdir.setName("TMPDIR")
-        tmpdir.setValue(mountPointPath)
 
         // container definition
         def container = new ContainerProperties()
@@ -389,7 +386,6 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
                 .withCommand('true')
                 .withMemory(1024)
                 .withVcpus(1)
-                .withEnvironment([tmpdir])
 
         def awscli = getAwsOptions().cliPath
         def mounts = new LinkedList<MountPoint>()
@@ -427,7 +423,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         result.setContainerProperties(container)
 
         // create a job marker uuid
-        def uuid = CacheHelper.hasher([name, image, awscli, tmpdir]).hash().toString()
+        def uuid = CacheHelper.hasher([name, image, awscli]).hash().toString()
         result.setParameters(['nf-token':uuid])
 
         return result