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error message of azcopy is no longer hidden #6187

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8ffe60b
Prevents azcopy hiding error messages by redirection
adamrtalbot Jun 6, 2025
0053f94
Handle azcopy failure better
adamrtalbot Jun 12, 2025
6cc9020
Remove --output-level quiet from azcopy calls
adamrtalbot Jun 16, 2025
5a0ebdb
fix test indentation
adamrtalbot Jun 16, 2025
14a2491
Merge branch 'master' into 6158_azcopy_hides_error_message
adamrtalbot Jun 16, 2025
cfdf0cb
Replace azcopy cp with azcopy sync in bash lib
adamrtalbot Jun 16, 2025
be4eca9
Merge branch 'master' into 6158_azcopy_hides_error_message
adamrtalbot Jun 20, 2025
5a514d7
fix tests
adamrtalbot Jun 20, 2025
6231d76
Revert "Replace azcopy cp with azcopy sync in bash lib"
adamrtalbot Jun 20, 2025
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23 changes: 12 additions & 11 deletions plugins/nf-azure/src/main/nextflow/cloud/azure/file/AzBashLib.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -73,25 +73,26 @@ class AzBashLib extends BashFunLib<AzBashLib> {
azcopy cp "$name" "$target/$name?$AZ_SAS" --block-blob-tier $AZCOPY_BLOCK_BLOB_TIER --block-size-mb $AZCOPY_BLOCK_SIZE_MB
fi
}

nxf_az_download() {
local source=$1
local target=$2
local basedir=$(dirname $2)
local ret
mkdir -p "$basedir"

ret=$(azcopy cp "$source?$AZ_SAS" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir -p $target
azcopy cp "$source/*?$AZ_SAS" "$target" --recursive >/dev/null || {
rm -rf $target

# Try to download as file first, let azcopy handle the detection
if ! azcopy cp "$source?$AZ_SAS" "$target"; then
# If failed, remove any partial target and try as directory
rm -rf "$target"
mkdir -p "$target"
if ! azcopy cp "$source/*?$AZ_SAS" "$target" --recursive; then
rm -rf "$target"
>&2 echo "Unable to download path: $source"
exit 1
}
}
fi
fi
}
'''.stripIndent(true)
'''.stripIndent()
}

String render() {
Expand Down
51 changes: 27 additions & 24 deletions plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzFileCopyStrategyTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -179,18 +179,19 @@ class AzFileCopyStrategyTest extends Specification {
local source=$1
local target=$2
local basedir=$(dirname $2)
local ret
mkdir -p "$basedir"

ret=$(azcopy cp "$source?$AZ_SAS" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir -p $target
azcopy cp "$source/*?$AZ_SAS" "$target" --recursive >/dev/null || {
rm -rf $target
# Try to download as file first, let azcopy handle the detection
if ! azcopy cp "$source?$AZ_SAS" "$target"; then
# If failed, remove any partial target and try as directory
rm -rf "$target"
mkdir -p "$target"
if ! azcopy cp "$source/*?$AZ_SAS" "$target" --recursive; then
rm -rf "$target"
>&2 echo "Unable to download path: $source"
exit 1
}
}
fi
fi
}

'''.stripIndent(true)
Expand Down Expand Up @@ -316,18 +317,19 @@ class AzFileCopyStrategyTest extends Specification {
local source=$1
local target=$2
local basedir=$(dirname $2)
local ret
mkdir -p "$basedir"

ret=$(azcopy cp "$source?$AZ_SAS" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir -p $target
azcopy cp "$source/*?$AZ_SAS" "$target" --recursive >/dev/null || {
rm -rf $target
# Try to download as file first, let azcopy handle the detection
if ! azcopy cp "$source?$AZ_SAS" "$target"; then
# If failed, remove any partial target and try as directory
rm -rf "$target"
mkdir -p "$target"
if ! azcopy cp "$source/*?$AZ_SAS" "$target" --recursive; then
rm -rf "$target"
>&2 echo "Unable to download path: $source"
exit 1
}
}
fi
fi
}

'''.stripIndent(true)
Expand Down Expand Up @@ -477,18 +479,19 @@ class AzFileCopyStrategyTest extends Specification {
local source=$1
local target=$2
local basedir=$(dirname $2)
local ret
mkdir -p "$basedir"

ret=$(azcopy cp "$source?$AZ_SAS" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir -p $target
azcopy cp "$source/*?$AZ_SAS" "$target" --recursive >/dev/null || {
rm -rf $target
# Try to download as file first, let azcopy handle the detection
if ! azcopy cp "$source?$AZ_SAS" "$target"; then
# If failed, remove any partial target and try as directory
rm -rf "$target"
mkdir -p "$target"
if ! azcopy cp "$source/*?$AZ_SAS" "$target" --recursive; then
rm -rf "$target"
>&2 echo "Unable to download path: $source"
exit 1
}
}
fi
fi
}

'''.stripIndent(true)
Expand Down
53 changes: 28 additions & 25 deletions plugins/nf-azure/src/test/nextflow/cloud/azure/file/AzBashLibTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -38,18 +38,19 @@ class AzBashLibTest extends Specification {
local source=$1
local target=$2
local basedir=$(dirname $2)
local ret
mkdir -p "$basedir"

ret=$(azcopy cp "$source?$AZ_SAS" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir -p $target
azcopy cp "$source/*?$AZ_SAS" "$target" --recursive >/dev/null || {
rm -rf $target
# Try to download as file first, let azcopy handle the detection
if ! azcopy cp "$source?$AZ_SAS" "$target"; then
# If failed, remove any partial target and try as directory
rm -rf "$target"
mkdir -p "$target"
if ! azcopy cp "$source/*?$AZ_SAS" "$target" --recursive; then
rm -rf "$target"
>&2 echo "Unable to download path: $source"
exit 1
}
}
fi
fi
}
'''.stripIndent()
}
Expand Down Expand Up @@ -140,18 +141,19 @@ class AzBashLibTest extends Specification {
local source=$1
local target=$2
local basedir=$(dirname $2)
local ret
mkdir -p "$basedir"

ret=$(azcopy cp "$source?$AZ_SAS" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir -p $target
azcopy cp "$source/*?$AZ_SAS" "$target" --recursive >/dev/null || {
rm -rf $target

# Try to download as file first, let azcopy handle the detection
if ! azcopy cp "$source?$AZ_SAS" "$target"; then
# If failed, remove any partial target and try as directory
rm -rf "$target"
mkdir -p "$target"
if ! azcopy cp "$source/*?$AZ_SAS" "$target" --recursive; then
rm -rf "$target"
>&2 echo "Unable to download path: $source"
exit 1
}
}
fi
fi
}
'''.stripIndent()
}
Expand Down Expand Up @@ -242,18 +244,19 @@ class AzBashLibTest extends Specification {
local source=$1
local target=$2
local basedir=$(dirname $2)
local ret
mkdir -p "$basedir"

ret=$(azcopy cp "$source?$AZ_SAS" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir -p $target
azcopy cp "$source/*?$AZ_SAS" "$target" --recursive >/dev/null || {
rm -rf $target
# Try to download as file first, let azcopy handle the detection
if ! azcopy cp "$source?$AZ_SAS" "$target"; then
# If failed, remove any partial target and try as directory
rm -rf "$target"
mkdir -p "$target"
if ! azcopy cp "$source/*?$AZ_SAS" "$target" --recursive; then
rm -rf "$target"
>&2 echo "Unable to download path: $source"
exit 1
}
}
fi
fi
}
'''.stripIndent()
}
Expand Down
26 changes: 12 additions & 14 deletions plugins/nf-azure/src/test/nextflow/executor/BashWrapperBuilderWithAzTest.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -77,15 +77,14 @@ class BashWrapperBuilderWithAzTest extends Specification {
nxf_az_download() {
local source=$1
local target=$2
local basedir=$(dirname $2)
local ret
local basedir=$(dirname "$target")
mkdir -p "$basedir"

ret=$(azcopy cp "$source?$AZ_SAS" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir -p $target
azcopy cp "$source/*?$AZ_SAS" "$target" --recursive >/dev/null || {
rm -rf $target
if ! azcopy cp "$source?$AZ_SAS" "$target"; then
# If failed, remove any partial target and try as directory
rm -rf "$target"; mkdir -p "$target"
if ! azcopy cp "$source/*?$AZ_SAS" "$target" --recursive; then
rm -rf "$target"
>&2 echo "Unable to download path: $source"
exit 1
}
Expand Down Expand Up @@ -216,15 +215,14 @@ class BashWrapperBuilderWithAzTest extends Specification {
nxf_az_download() {
local source=$1
local target=$2
local basedir=$(dirname $2)
local ret
local basedir=$(dirname "$target")
mkdir -p "$basedir"

ret=$(azcopy cp "$source?$AZ_SAS" "$target" 2>&1) || {
## if fails check if it was trying to download a directory
mkdir -p $target
azcopy cp "$source/*?$AZ_SAS" "$target" --recursive >/dev/null || {
rm -rf $target
if ! azcopy cp "$source?$AZ_SAS" "$target"; then
# If failed, remove any partial target and try as directory
rm -rf "$target"; mkdir -p "$target"
if ! azcopy cp "$source/*?$AZ_SAS" "$target" --recursive; then
rm -rf "$target"
>&2 echo "Unable to download path: $source"
exit 1
}
Expand Down
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