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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
f6c4d34
Merge branch 'master' into 6158_azcopy_hides_error_message
pditommaso Aug 14, 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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