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add --launch-container option in launch command #444

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merged 11 commits into from
Aug 23, 2024
Merged

add --launch-container option in launch command #444

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10012d5
added --launch-container
munishchouhan Aug 21, 2024
dafe28c
minor change
munishchouhan Aug 21, 2024
bd591cf
remove default value
munishchouhan Aug 21, 2024
d6f9739
removed coalesce
munishchouhan Aug 21, 2024
b627b7b
bump tower-java-sdk:1.9.7
munishchouhan Aug 21, 2024
d5edf73
fixed launchContainer datatype
munishchouhan Aug 21, 2024
32acc87
fixed error
munishchouhan Aug 21, 2024
22137b9
added getNextflowConfig in reflect-config.json
munishchouhan Aug 22, 2024
8a86f23
refactored
munishchouhan Aug 22, 2024
36f89ef
refactored
munishchouhan Aug 22, 2024
522a32f
Update src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java
munishchouhan Aug 22, 2024
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2 changes: 1 addition & 1 deletion build.gradle
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Original file line number Diff line number Diff line change
Expand Up @@ -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'
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2 changes: 1 addition & 1 deletion conf/reflect-config.json
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Expand Up @@ -2710,7 +2710,7 @@
"allDeclaredFields":true,
"queryAllDeclaredMethods":true,
"queryAllDeclaredConstructors":true,
"methods":[{"name":"<init>","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":"<init>","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",
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6 changes: 5 additions & 1 deletion src/main/java/io/seqera/tower/cli/commands/LaunchCmd.java
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Expand Up @@ -104,6 +104,9 @@ public class LaunchCmd extends AbstractRootCmd {
@Option(names = {"-l", "--labels"}, split = ",", description = "Comma-separated list of labels for the pipeline.")
List<String> labels;

@Option(names = {"--launch-container"}, description = "Container to be used to run the nextflow head job.")
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String launchContainer;

@ArgGroup(heading = "%nAdvanced options:%n", validate = false)
AdvancedOptions adv;

Expand Down Expand Up @@ -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(launchContainer);
}

protected Response runTowerPipeline(Long wspId) throws ApiException, IOException {
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