From e410be47c775c28f604107ebd0a0aac64bc7167b Mon Sep 17 00:00:00 2001 From: Paolo Di Tommaso Date: Sat, 15 Jun 2024 15:55:14 +0200 Subject: [PATCH] Fix support for s5cmd 2.2.2 Signed-off-by: Paolo Di Tommaso --- .../src/main/nextflow/cloud/aws/util/S3BashLib.groovy | 2 +- .../test/nextflow/cloud/aws/util/S3BashLibTest.groovy | 4 ++-- .../src/main/io/seqera/wave/plugin/WaveClient.groovy | 4 ++-- .../test/io/seqera/wave/plugin/WaveClientTest.groovy | 10 +++++----- 4 files changed, 10 insertions(+), 10 deletions(-) diff --git a/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy index 1e300dd71b..3d2aa346fd 100644 --- a/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy +++ b/plugins/nf-amazon/src/main/nextflow/cloud/aws/util/S3BashLib.groovy @@ -162,7 +162,7 @@ class S3BashLib extends BashFunLib { local source=\$1 local target=\$2 local file_name=\$(basename \$1) - local is_dir=\$($cli ls \$source | grep -F "DIR \${file_name}/" -c) + local is_dir=\$($cli ls \$source | grep -F "DIR \${file_name}/" -c) if [[ \$is_dir == 1 ]]; then $cli cp "\$source/*" "\$target" else diff --git a/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy b/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy index 524dda71ee..d05d4df994 100644 --- a/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy +++ b/plugins/nf-amazon/src/test/nextflow/cloud/aws/util/S3BashLibTest.groovy @@ -770,7 +770,7 @@ class S3BashLibTest extends Specification { local source=$1 local target=$2 local file_name=$(basename $1) - local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c) + local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c) if [[ $is_dir == 1 ]]; then s5cmd cp "$source/*" "$target" else @@ -807,7 +807,7 @@ class S3BashLibTest extends Specification { local source=$1 local target=$2 local file_name=$(basename $1) - local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c) + local is_dir=$(s5cmd ls $source | grep -F "DIR ${file_name}/" -c) if [[ $is_dir == 1 ]]; then s5cmd cp "$source/*" "$target" else diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy index 315216edf7..aa4df3c88b 100644 --- a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy +++ b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy @@ -73,8 +73,8 @@ import org.slf4j.LoggerFactory @CompileStatic class WaveClient { - final static public String DEFAULT_S5CMD_AMD64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.0.0.json' - final static public String DEFAULT_S5CMD_ARM64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json' + final static public String DEFAULT_S5CMD_AMD64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.2.2.json' + final static public String DEFAULT_S5CMD_ARM64_URL = 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.2.2.json' private static Logger log = LoggerFactory.getLogger(WaveClient) diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy index 64e9cd4e40..1e72d46124 100644 --- a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy +++ b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy @@ -1092,11 +1092,11 @@ class WaveClientTest extends Specification { where: ARCH | EXPECTED - 'linux/amd64' | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.0.0.json' - 'linux/x86_64' | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.0.0.json' - 'arm64' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json' - 'linux/arm64' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json' - 'linux/arm64/v8' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.0.0.json' + 'linux/amd64' | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.2.2.json' + 'linux/x86_64' | 'https://nf-xpack.seqera.io/s5cmd/linux_amd64_2.2.2.json' + 'arm64' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.2.2.json' + 'linux/arm64' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.2.2.json' + 'linux/arm64/v8' | 'https://nf-xpack.seqera.io/s5cmd/linux_arm64_2.2.2.json' } def 'should configure custom s5cmd' () {