From 10012d5f39add9a9143bb2595f4fb315a98fae6c Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Wed, 21 Aug 2024 16:10:25 +0200 Subject: [PATCH 01/11] added --launch-container --- src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java | 6 +++++- 1 file changed, 5 insertions(+), 1 deletion(-) diff --git a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java index 93c27179..1cdc6b57 100644 --- a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java +++ b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java @@ -104,6 +104,9 @@ public class LaunchCmd extends AbstractRootCmd { @Option(names = {"-l", "--labels"}, split = ",", description = "Comma-separated list of labels for the pipeline.") List labels; + @Option(names = {"--launch-container"}, split = ",", description = "Container to be used to run the nextflow head job.") + List launchContainer; + @ArgGroup(heading = "%nAdvanced options:%n", validate = false) AdvancedOptions adv; @@ -165,7 +168,8 @@ private WorkflowLaunchRequest updateLaunchRequest(WorkflowLaunchRequest base) th .optimizationTargets(coalesce(adv().disableOptimization, false) ? null : base.getOptimizationTargets()) .labelIds(base.getLabelIds()) .headJobCpus(base.getHeadJobCpus()) - .headJobMemoryMb(base.getHeadJobMemoryMb()); + .headJobMemoryMb(base.getHeadJobMemoryMb() + .launchContainer(coalesce(launchContainer, base.getLaunchContainer()))); } protected Response runTowerPipeline(Long wspId) throws ApiException, IOException { From dafe28cf29831c0a51bb67dfc9551501e1c3d3b0 Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Wed, 21 Aug 2024 16:16:40 +0200 Subject: [PATCH 02/11] minor change --- src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java index 1cdc6b57..651a89e7 100644 --- a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java +++ b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java @@ -104,7 +104,7 @@ public class LaunchCmd extends AbstractRootCmd { @Option(names = {"-l", "--labels"}, split = ",", description = "Comma-separated list of labels for the pipeline.") List labels; - @Option(names = {"--launch-container"}, split = ",", description = "Container to be used to run the nextflow head job.") + @Option(names = {"--launch-container"}, description = "Container to be used to run the nextflow head job.") List launchContainer; @ArgGroup(heading = "%nAdvanced options:%n", validate = false) From bd591cf96f5f9ae6911fef7c272db69ddfe3ab2b Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Wed, 21 Aug 2024 16:33:20 +0200 Subject: [PATCH 03/11] remove default value --- src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java index 651a89e7..81ab238d 100644 --- a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java +++ b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java @@ -169,7 +169,7 @@ private WorkflowLaunchRequest updateLaunchRequest(WorkflowLaunchRequest base) th .labelIds(base.getLabelIds()) .headJobCpus(base.getHeadJobCpus()) .headJobMemoryMb(base.getHeadJobMemoryMb() - .launchContainer(coalesce(launchContainer, base.getLaunchContainer()))); + .launchContainer(coalesce(launchContainer, null))); } protected Response runTowerPipeline(Long wspId) throws ApiException, IOException { From d6f97393ff3d60c11a9cbc4f33577393cc911678 Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Wed, 21 Aug 2024 16:42:27 +0200 Subject: [PATCH 04/11] removed coalesce --- src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java index 81ab238d..c097b2ff 100644 --- a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java +++ b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java @@ -169,7 +169,7 @@ private WorkflowLaunchRequest updateLaunchRequest(WorkflowLaunchRequest base) th .labelIds(base.getLabelIds()) .headJobCpus(base.getHeadJobCpus()) .headJobMemoryMb(base.getHeadJobMemoryMb() - .launchContainer(coalesce(launchContainer, null))); + .launchContainer(launchContainer)); } protected Response runTowerPipeline(Long wspId) throws ApiException, IOException { From b627b7b90832cb486466d4f6d637a694f1290efd Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Wed, 21 Aug 2024 17:36:28 +0200 Subject: [PATCH 05/11] bump tower-java-sdk:1.9.7 --- build.gradle | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/build.gradle b/build.gradle index 28ab0d24..e8b6b357 100644 --- a/build.gradle +++ b/build.gradle @@ -23,7 +23,7 @@ dependencies { implementation 'org.slf4j:slf4j-api:1.7.36' implementation 'ch.qos.logback:logback-core:1.2.11' implementation 'ch.qos.logback:logback-classic:1.2.11' - implementation 'io.seqera.tower:tower-java-sdk:1.9.6' + implementation 'io.seqera.tower:tower-java-sdk:1.9.7' implementation 'info.picocli:picocli:4.6.3' implementation 'org.apache.commons:commons-compress:1.22' implementation 'org.tukaani:xz:1.9' From d5edf732fd279ba7b1bfb24142283e875444c108 Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Wed, 21 Aug 2024 17:43:28 +0200 Subject: [PATCH 06/11] fixed launchContainer datatype --- src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java index c097b2ff..28f3a97f 100644 --- a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java +++ b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java @@ -105,7 +105,7 @@ public class LaunchCmd extends AbstractRootCmd { List labels; @Option(names = {"--launch-container"}, description = "Container to be used to run the nextflow head job.") - List launchContainer; + String launchContainer; @ArgGroup(heading = "%nAdvanced options:%n", validate = false) AdvancedOptions adv; From 32acc8757628f3476969b46f0f7232cf6f634537 Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Wed, 21 Aug 2024 17:52:39 +0200 Subject: [PATCH 07/11] fixed error --- src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java index 28f3a97f..34c32bdf 100644 --- a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java +++ b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java @@ -168,8 +168,8 @@ private WorkflowLaunchRequest updateLaunchRequest(WorkflowLaunchRequest base) th .optimizationTargets(coalesce(adv().disableOptimization, false) ? null : base.getOptimizationTargets()) .labelIds(base.getLabelIds()) .headJobCpus(base.getHeadJobCpus()) - .headJobMemoryMb(base.getHeadJobMemoryMb() - .launchContainer(launchContainer)); + .headJobMemoryMb(base.getHeadJobMemoryMb()) + .launchContainer(launchContainer); } protected Response runTowerPipeline(Long wspId) throws ApiException, IOException { From 22137b9fb44b1fcd70baaa898ec9dd05df79c582 Mon Sep 17 00:00:00 2001 From: munish chouhan Date: Thu, 22 Aug 2024 12:47:12 +0200 Subject: [PATCH 08/11] added getNextflowConfig in reflect-config.json --- conf/reflect-config.json | 6 ++++++ 1 file changed, 6 insertions(+) diff --git a/conf/reflect-config.json b/conf/reflect-config.json index 0ea74561..e208d25f 100644 --- a/conf/reflect-config.json +++ b/conf/reflect-config.json @@ -3271,6 +3271,12 @@ "allDeclaredMethods":true, "methods":[{"name":"fromValue","parameterTypes":["java.lang.String"] }] }, +{ + "name":"io.seqera.tower.model.GoogleBatchConfig", + "allDeclaredFields":true, + "allDeclaredMethods":true, + "methods":[{"name":"getNextflowConfig","parameterTypes":[] }] +}, { "name":"java.io.Console", "methods":[{"name":"readPassword","parameterTypes":["java.lang.String","java.lang.Object[]"] }] From 8a86f23988485afca08c8b53d32ac0e505f1457c Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Thu, 22 Aug 2024 16:04:53 +0200 Subject: [PATCH 09/11] refactored --- conf/reflect-config.json | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/conf/reflect-config.json b/conf/reflect-config.json index e208d25f..1a1f0fdc 100644 --- a/conf/reflect-config.json +++ b/conf/reflect-config.json @@ -2710,7 +2710,7 @@ "allDeclaredFields":true, "queryAllDeclaredMethods":true, "queryAllDeclaredConstructors":true, - "methods":[{"name":"","parameterTypes":[] }, {"name":"getBootDiskSizeGb","parameterTypes":[] }, {"name":"getComputeJobsInstanceTemplate","parameterTypes":[] }, {"name":"getCopyImage","parameterTypes":[] }, {"name":"getCpuPlatform","parameterTypes":[] }, {"name":"getDebugMode","parameterTypes":[] }, {"name":"getDiscriminator","parameterTypes":[] }, {"name":"getEnvironment","parameterTypes":[] }, {"name":"getFusion2Enabled","parameterTypes":[] }, {"name":"getHeadJobCpus","parameterTypes":[] }, {"name":"getHeadJobInstanceTemplate","parameterTypes":[] }, {"name":"getHeadJobMemoryMb","parameterTypes":[] }, {"name":"getHeadJobOptions","parameterTypes":[] }, {"name":"getHostName","parameterTypes":[] }, {"name":"getLabels","parameterTypes":[] }, {"name":"getLaunchDir","parameterTypes":[] }, {"name":"getLocation","parameterTypes":[] }, {"name":"getMachineType","parameterTypes":[] }, {"name":"getMaxQueueSize","parameterTypes":[] }, {"name":"getNetwork","parameterTypes":[] }, {"name":"getNfsMount","parameterTypes":[] }, {"name":"getNfsTarget","parameterTypes":[] }, {"name":"getPort","parameterTypes":[] }, {"name":"getPostRunScript","parameterTypes":[] }, {"name":"getPreRunScript","parameterTypes":[] }, {"name":"getProjectId","parameterTypes":[] }, {"name":"getPropagateHeadJobOptions","parameterTypes":[] }, {"name":"getServiceAccount","parameterTypes":[] }, {"name":"getSpot","parameterTypes":[] }, {"name":"getSshDaemon","parameterTypes":[] }, {"name":"getSshImage","parameterTypes":[] }, {"name":"getSubnetwork","parameterTypes":[] }, {"name":"getUsePrivateAddress","parameterTypes":[] }, {"name":"getUserName","parameterTypes":[] }, {"name":"getWaveEnabled","parameterTypes":[] }, {"name":"getWorkDir","parameterTypes":[] }, {"name":"setBootDiskSizeGb","parameterTypes":["java.lang.Integer"] }, {"name":"setCopyImage","parameterTypes":["java.lang.String"] }, {"name":"setCpuPlatform","parameterTypes":["java.lang.String"] }, {"name":"setDebugMode","parameterTypes":["java.lang.Integer"] }, {"name":"setEnvironment","parameterTypes":["java.util.List"] }, {"name":"setFusion2Enabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setHeadJobCpus","parameterTypes":["java.lang.Integer"] }, {"name":"setHeadJobMemoryMb","parameterTypes":["java.lang.Integer"] }, {"name":"setLabels","parameterTypes":["java.util.Map"] }, {"name":"setLocation","parameterTypes":["java.lang.String"] }, {"name":"setMachineType","parameterTypes":["java.lang.String"] }, {"name":"setNetwork","parameterTypes":["java.lang.String"] }, {"name":"setNfsMount","parameterTypes":["java.lang.String"] }, {"name":"setNfsTarget","parameterTypes":["java.lang.String"] }, {"name":"setPostRunScript","parameterTypes":["java.lang.String"] }, {"name":"setPreRunScript","parameterTypes":["java.lang.String"] }, {"name":"setProjectId","parameterTypes":["java.lang.String"] }, {"name":"setServiceAccount","parameterTypes":["java.lang.String"] }, {"name":"setSpot","parameterTypes":["java.lang.Boolean"] }, {"name":"setSshDaemon","parameterTypes":["java.lang.Boolean"] }, {"name":"setSshImage","parameterTypes":["java.lang.String"] }, {"name":"setSubnetwork","parameterTypes":["java.lang.String"] }, {"name":"setUsePrivateAddress","parameterTypes":["java.lang.Boolean"] }, {"name":"setWaveEnabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setWorkDir","parameterTypes":["java.lang.String"] }] + "methods":[{"name":"","parameterTypes":[] }, {"name":"getBootDiskSizeGb","parameterTypes":[] }, {"name":"getComputeJobsInstanceTemplate","parameterTypes":[] }, {"name":"getCopyImage","parameterTypes":[] }, {"name":"getCpuPlatform","parameterTypes":[] }, {"name":"getDebugMode","parameterTypes":[] }, {"name":"getDiscriminator","parameterTypes":[] }, {"name":"getEnvironment","parameterTypes":[] }, {"name":"getFusion2Enabled","parameterTypes":[] }, {"name":"getHeadJobCpus","parameterTypes":[] }, {"name":"getHeadJobInstanceTemplate","parameterTypes":[] }, {"name":"getHeadJobMemoryMb","parameterTypes":[] }, {"name":"getHeadJobOptions","parameterTypes":[] }, {"name":"getHostName","parameterTypes":[] }, {"name":"getLabels","parameterTypes":[] }, {"name":"getLaunchDir","parameterTypes":[] }, {"name":"getLocation","parameterTypes":[] }, {"name":"getMachineType","parameterTypes":[] }, {"name":"getMaxQueueSize","parameterTypes":[] }, {"name":"getNetwork","parameterTypes":[] }, {"name":"getNfsMount","parameterTypes":[] }, {"name":"getNfsTarget","parameterTypes":[] }, {"name":"getPort","parameterTypes":[] }, {"name":"getPostRunScript","parameterTypes":[] }, {"name":"getPreRunScript","parameterTypes":[] }, {"name":"getProjectId","parameterTypes":[] }, {"name":"getPropagateHeadJobOptions","parameterTypes":[] }, {"name":"getServiceAccount","parameterTypes":[] }, {"name":"getSpot","parameterTypes":[] }, {"name":"getSshDaemon","parameterTypes":[] }, {"name":"getSshImage","parameterTypes":[] }, {"name":"getSubnetwork","parameterTypes":[] }, {"name":"getUsePrivateAddress","parameterTypes":[] }, {"name":"getUserName","parameterTypes":[] }, {"name":"getWaveEnabled","parameterTypes":[] }, {"name":"getWorkDir","parameterTypes":[] }, {"name":"setBootDiskSizeGb","parameterTypes":["java.lang.Integer"] }, {"name":"setCopyImage","parameterTypes":["java.lang.String"] }, {"name":"setCpuPlatform","parameterTypes":["java.lang.String"] }, {"name":"setDebugMode","parameterTypes":["java.lang.Integer"] }, {"name":"setEnvironment","parameterTypes":["java.util.List"] }, {"name":"setFusion2Enabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setHeadJobCpus","parameterTypes":["java.lang.Integer"] }, {"name":"setHeadJobMemoryMb","parameterTypes":["java.lang.Integer"] }, {"name":"setLabels","parameterTypes":["java.util.Map"] }, {"name":"setLocation","parameterTypes":["java.lang.String"] }, {"name":"setMachineType","parameterTypes":["java.lang.String"] }, {"name":"setNetwork","parameterTypes":["java.lang.String"] }, {"name":"setNfsMount","parameterTypes":["java.lang.String"] }, {"name":"setNfsTarget","parameterTypes":["java.lang.String"] }, {"name":"setPostRunScript","parameterTypes":["java.lang.String"] }, {"name":"setPreRunScript","parameterTypes":["java.lang.String"] }, {"name":"setProjectId","parameterTypes":["java.lang.String"] }, {"name":"setServiceAccount","parameterTypes":["java.lang.String"] }, {"name":"setSpot","parameterTypes":["java.lang.Boolean"] }, {"name":"setSshDaemon","parameterTypes":["java.lang.Boolean"] }, {"name":"setSshImage","parameterTypes":["java.lang.String"] }, {"name":"setSubnetwork","parameterTypes":["java.lang.String"] }, {"name":"setUsePrivateAddress","parameterTypes":["java.lang.Boolean"] }, {"name":"setWaveEnabled","parameterTypes":["java.lang.Boolean"] }, {"name":"setWorkDir","parameterTypes":["java.lang.String"] }, {"name":"getNextflowConfig","parameterTypes":[] }] }, { "name":"io.seqera.tower.model.GoogleLifeSciencesConfig", From 36f89effbc735e224bceb10060b3bb11c5b55cc2 Mon Sep 17 00:00:00 2001 From: munishchouhan Date: Thu, 22 Aug 2024 16:05:57 +0200 Subject: [PATCH 10/11] refactored --- conf/reflect-config.json | 6 ------ 1 file changed, 6 deletions(-) diff --git a/conf/reflect-config.json b/conf/reflect-config.json index 1a1f0fdc..55cd6b9a 100644 --- a/conf/reflect-config.json +++ b/conf/reflect-config.json @@ -3271,12 +3271,6 @@ "allDeclaredMethods":true, "methods":[{"name":"fromValue","parameterTypes":["java.lang.String"] }] }, -{ - "name":"io.seqera.tower.model.GoogleBatchConfig", - "allDeclaredFields":true, - "allDeclaredMethods":true, - "methods":[{"name":"getNextflowConfig","parameterTypes":[] }] -}, { "name":"java.io.Console", "methods":[{"name":"readPassword","parameterTypes":["java.lang.String","java.lang.Object[]"] }] From 522a32f68718f8697221ac61510cbcb4ade9e755 Mon Sep 17 00:00:00 2001 From: Munish Chouhan Date: Thu, 22 Aug 2024 18:40:12 +0200 Subject: [PATCH 11/11] Update src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java Co-authored-by: Paolo Di Tommaso --- src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java index 34c32bdf..7053b71d 100644 --- a/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java +++ b/src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java @@ -104,7 +104,7 @@ public class LaunchCmd extends AbstractRootCmd { @Option(names = {"-l", "--labels"}, split = ",", description = "Comma-separated list of labels for the pipeline.") List labels; - @Option(names = {"--launch-container"}, description = "Container to be used to run the nextflow head job.") + @Option(names = {"--launch-container"}, description = "Container to be used to run the nextflow head job (BETA).") String launchContainer; @ArgGroup(heading = "%nAdvanced options:%n", validate = false)