21.04.1 List of changes done by Lifebit #19
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* fix: Lustre recursive copy support * chore: add missing changes for batch with lustre * fix: Error of SSL certificate when running Jobs with Lustre | CI-213 * fix: update copy command evaluation Co-authored-by: rubengomex <ruben@lifebit.ai> Co-authored-by: RaduP <radu@lifebit.ai>
…1-gitlab-fixes # Conflicts: # modules/nf-commons/src/main/nextflow/Const.groovy
fix: Authorization header to enable oauth token for gitlab
* feat: 21.04.1-update-to-use-imdsv2 * feat: return IAM role not ARN
mageshwaran-lifebit
changed the title
mageshwaran-lifebit
requested review from
a team and
tiagofilipe12
and removed request for
a team
| @@ -262,6 +256,13 @@ class BashWrapperBuilder { | |||
| binding.launch_cmd = getLaunchCommand(interpreter,env) | |||
| binding.stage_cmd = getStageCommand() | |||
| binding.unstage_cmd = getUnstageCommand() | |||
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I dont think this change make sense. so dropping it
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What change did you drop? then, I'm siging the stagingScript prop being populated as well. This is needed because .getStageInputFilesScript can actually be fetching the files from s3 or directly from lustre mounted file system.
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@rubengomex I think only but line 263-23 is moved from 254-255, but this line (281) is newly added. that is considered for development
| @@ -58,12 +58,12 @@ class Const { | |||
| /** | |||
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not sure whether this is needed
| @@ -39,11 +39,12 @@ dependencies { | |||
| compileOnly 'org.pf4j:pf4j:3.4.1' | |||
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| compile ('io.nextflow:nxf-s3fs:1.1.0') { transitive = false } | |||
| compile ('com.amazonaws:aws-java-sdk-s3:1.11.542') | |||
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already packages are using 1.12.129
feat: fix .command.run upload issue for LP-5254
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This changes done by @mageshwaran-lifebit to make pipeline test rans
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This changes done by @mageshwaran-lifebit
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This changes done by @mageshwaran-lifebit to make pipeline test rans
| @@ -251,6 +253,20 @@ class AwsBatchExecutor extends Executor implements ExtensionPoint { | |||
| @PackageScope | |||
| ThrottlingExecutor getReaper() { reaper } | |||
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| String getInstanceIdByQueueAndTaskArn(String queue, String taskArn) { | |||
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this getInstanceIdByQueueAndTaskArn function is not required, as we are moving towards nf-monitor plugin
| @@ -132,37 +136,21 @@ class AmazonClientFactory { | |||
| * The IAM role name associated to this instance or {@code null} if no role is defined or | |||
| * it's not a EC2 instance | |||
| */ | |||
| protected String fetchIamRole() { | |||
| private String fetchIamRole() { | |||
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nf-amazon-1.12.0 already have this
| @@ -171,12 +159,11 @@ class AmazonClientFactory { | |||
| * The AWS region of the current EC2 instance eg. {@code eu-west-1} or | |||
| * {@code null} if it's not an EC2 instance. | |||
| */ | |||
| protected String fetchRegion() { | |||
| private String fetchRegion() { | |||
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nf-amazon-1.12.0 already this
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we dont need this file in newer version
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we dont need this change, as this is been deprecated and not used anymore in code
V19.10.0:
*v21.04.1
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