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2 changes: 1 addition & 1 deletion
2
centaur/src/main/resources/standardTestCases/reference_disk/reference_disk_test.inputs
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,3 +1,3 @@ | ||
| { | ||
| "wf_reference_disk_test.check_if_localized_as_symlink.reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/README" | ||
| "wf_reference_disk_test.check_if_localized_as_symlink.reference_file_input": "gs://gcp-public-data--broad-references/hg19/v0/Homo_sapiens_assembly19.tile_db_header.vcf" | ||
| } |
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77 changes: 77 additions & 0 deletions
77
cromwell-drs-localizer/src/main/scala/drs/localizer/CommandLineParser.scala
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,77 @@ | ||
| package drs.localizer | ||
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| import common.util.VersionUtil | ||
| import drs.localizer.CommandLineParser.AccessTokenStrategy._ | ||
| import drs.localizer.CommandLineParser.Usage | ||
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| class CommandLineParser extends scopt.OptionParser[CommandLineArguments](Usage) { | ||
| lazy val localizerVersion: String = VersionUtil.getVersion("cromwell-drs-localizer") | ||
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| version("version") | ||
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| help("help").text("Cromwell DRS Localizer") | ||
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| head("cromwell-drs-localizer", localizerVersion) | ||
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| arg[String]("drs-object-id").text("DRS object ID").required(). | ||
| action((s, c) => | ||
| c.copy(drsObject = Option(s))) | ||
| arg[String]("container-path").text("Container path").required(). | ||
| action((s, c) => | ||
| c.copy(containerPath = Option(s))) | ||
| arg[String]("requester-pays-project").text("Requester pays project").optional(). | ||
| action((s, c) => | ||
| c.copy(googleRequesterPaysProject = Option(s))) | ||
| opt[String]('t', "access-token-strategy").text(s"Access token strategy, must be one of '$Azure' or '$Google' (default '$Google')"). | ||
| action((s, c) => | ||
| c.copy(accessTokenStrategy = Option(s.toLowerCase()))) | ||
| opt[String]('v', "vault-name").text("Azure vault name"). | ||
| action((s, c) => | ||
| c.copy(azureVaultName = Option(s))) | ||
| opt[String]('s', "secret-name").text("Azure secret name"). | ||
| action((s, c) => | ||
| c.copy(azureSecretName = Option(s))) | ||
| opt[String]('i', "identity-client-id").text("Azure identity client id"). | ||
| action((s, c) => | ||
| c.copy(azureIdentityClientId = Option(s))) | ||
| checkConfig(c => | ||
| c.accessTokenStrategy match { | ||
| case Some(Azure) if c.googleRequesterPaysProject.isEmpty => Right(()) | ||
| case Some(Google) if List(c.azureSecretName, c.azureVaultName, c.azureIdentityClientId).forall(_.isEmpty) => Right(()) | ||
| case Some(Azure) => Left(s"Requester pays project is only valid with access token strategy '$Google'") | ||
| case Some(Google) => Left(s"One or more specified options are only valid with access token strategy '$Azure'") | ||
| case Some(huh) => Left(s"Unrecognized access token strategy '$huh'") | ||
| case None => Left("Unspecified access token strategy") | ||
| } | ||
| ) | ||
| } | ||
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| object CommandLineParser { | ||
| /** | ||
| * These access token strategies are named simplistically as there is currently only one access token strategy being | ||
| * used for each of these cloud vendors. But it is certainly possible that multiple strategies could come into use | ||
| * for a particular vendor, in which case the names may need to become more specific for disambiguation. | ||
| */ | ||
| object AccessTokenStrategy { | ||
| val Azure = "azure" | ||
| val Google = "google" | ||
| } | ||
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| val Usage = | ||
| s""" | ||
| Usage: | ||
| java -jar /path/to/localizer.jar [options] drs://provider/object /local/path/to/file.txt [requester pays project] | ||
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| Note that the <requester pays project> optional argument is only valid with access token strategy 'Google'. | ||
| """ | ||
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| } | ||
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| case class CommandLineArguments(accessTokenStrategy: Option[String] = Option(Google), | ||
| drsObject: Option[String] = None, | ||
| containerPath: Option[String] = None, | ||
| googleRequesterPaysProject: Option[String] = None, | ||
| azureVaultName: Option[String] = None, | ||
| azureSecretName: Option[String] = None, | ||
| azureIdentityClientId: Option[String] = None) |
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