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Does not validate Azure or Google blob storage #171

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Aug 7, 2024
Merged

Does not validate Azure or Google blob storage #171

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e50417e
Does not validate Azure or Google blob storage
adamrtalbot Jul 5, 2024
f70cecc
Add tests ignoring for az/s3/gs paths
adamrtalbot Jul 5, 2024
38b48b7
Correct tests
adamrtalbot Jul 5, 2024
de1fcda
Correct tests AGAIN
adamrtalbot Jul 5, 2024
8ab7282
CHANGELOG
adamrtalbot Jul 5, 2024
7e47cf2
Actually add path
adamrtalbot Jul 5, 2024
a22b3f0
Update CHANGELOG.md
adamrtalbot Jul 5, 2024
9c9a1fe
Bump nf-validation version
adamrtalbot Jul 5, 2024
5ff250f
Merge branch 'master' into do_not_validate_az_and_gcp_paths
nvnieuwk Jul 5, 2024
85057af
Update plugins/nf-validation/src/main/nextflow/validation/FormatValid…
adamrtalbot Aug 1, 2024
5a99d96
Apply suggestions from code review
adamrtalbot Aug 1, 2024
1a93ea9
Update plugins/nf-validation/src/main/nextflow/validation/FormatValid…
adamrtalbot Aug 1, 2024
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2 changes: 1 addition & 1 deletion ...nf-validation/src/main/nextflow/validation/FormatValidators/DirectoryPathValidator.groovy
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Expand Up @@ -11,7 +11,7 @@ public class DirectoryPathValidator implements FormatValidator {

@Override
public Optional<String> validate(final String subject) {
if (subject.startsWith('s3://')) {
if (subject.matches("(s3://|az://|gs://).*")) {
log.debug("S3 paths are not supported by 'DirectoryPathValidator': '${subject}'")
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return Optional.empty()
}
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2 changes: 1 addition & 1 deletion ...-validation/src/main/nextflow/validation/FormatValidators/FilePathPatternValidator.groovy
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Expand Up @@ -11,7 +11,7 @@ public class FilePathPatternValidator implements FormatValidator {

@Override
public Optional<String> validate(final String subject) {
if (subject.startsWith('s3://')) {
if (subject.matches("(s3://|az://|gs://).*")) {
log.debug("S3 paths are not supported by 'FilePathPatternValidator': '${subject}'")
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return Optional.empty()
}
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2 changes: 1 addition & 1 deletion plugins/nf-validation/src/main/nextflow/validation/FormatValidators/FilePathValidator.groovy
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Expand Up @@ -11,7 +11,7 @@ public class FilePathValidator implements FormatValidator {

@Override
public Optional<String> validate(final String subject) {
if (subject.startsWith('s3://')) {
if (subject.matches("(s3://|az://|gs://).*")) {
log.debug("S3 paths are not supported by 'FilePathValidator': '${subject}'")
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return Optional.empty()
}
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2 changes: 1 addition & 1 deletion plugins/nf-validation/src/main/nextflow/validation/FormatValidators/PathValidator.groovy
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Expand Up @@ -11,7 +11,7 @@ public class PathValidator implements FormatValidator {

@Override
public Optional<String> validate(final String subject) {
if (subject.startsWith('s3://')) {
if (subject.matches("(s3://|az://|gs://).*")) {
log.debug("S3 paths are not supported by 'PathValidator': '${subject}'")
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return Optional.empty()
}
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2 changes: 1 addition & 1 deletion plugins/nf-validation/src/main/nextflow/validation/SchemaValidator.groovy
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Expand Up @@ -615,7 +615,7 @@ class SchemaValidator extends PluginExtensionPoint {
// Function to check if a file or directory exists
//
List pathExists(String path, String paramName, Boolean s3PathCheck) {
if (path.startsWith('s3://') && !s3PathCheck) {
if (path.matches("(s3://|az://|gs://).*") && !s3PathCheck) {
log.debug "Ignoring validation of S3 URL path '${path}'".toString()
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} else {
def Path file = Nextflow.file(path) as Path
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