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Iteration on Nomad/Variables <-> Nextflow/Secrets (#75)
* first iteration in secrets implementation Signed-off-by: Jorge Aguilera <[email protected]> * tweak the start-nomad script for different platforms [ci skip] * nomad secrets, add get set and list commands Signed-off-by: Jorge Aguilera <[email protected]> * delete nomad with stop command [ci skip] * tweak the sun-nomadlab config to accommodate variables [ci skip] * update the sun-nomadlab config for config level secret vars [ci skip] * enable nomad secrets via nextflow config if false use Local implementation Signed-off-by: Jorge Aguilera <[email protected]> * add test Signed-off-by: Jorge Aguilera <[email protected]> * fix small bug Signed-off-by: Jorge Aguilera <[email protected]> * improve local testing env [ci skip] * test with sun-nomadlab and localsecretstore [ci skip] * rename enable -> enabled to comply with standard * use the functional config for sun-nomadlab [ci skip] * update authors [ci skip] --------- Signed-off-by: Jorge Aguilera <[email protected]> Co-authored-by: Jorge Aguilera <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
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@@ -18,26 +18,50 @@ | |
| package nextflow.nomad | ||
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| import groovy.transform.CompileStatic | ||
| import groovy.util.logging.Slf4j | ||
| import nextflow.cli.PluginAbstractExec | ||
| import nextflow.nomad.secrets.NomadSecretCmd | ||
| import nextflow.nomad.executor.TaskDirectives | ||
| import nextflow.plugin.BasePlugin | ||
| import nextflow.script.ProcessConfig | ||
| import nextflow.secret.SecretsLoader | ||
| import org.pf4j.PluginWrapper | ||
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| /** | ||
| * Nextflow plugin for Nomad executor | ||
| * | ||
| * @author Abhinav Sharma <[email protected]> | ||
| * @author : matthdsm <[email protected]> | ||
| * @author Jorge Aguilera <[email protected]> | ||
| */ | ||
| @CompileStatic | ||
| class NomadPlugin extends BasePlugin { | ||
| @Slf4j | ||
| class NomadPlugin extends BasePlugin implements PluginAbstractExec{ | ||
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| NomadPlugin(PluginWrapper wrapper) { | ||
| super(wrapper) | ||
| addCustomDirectives() | ||
| SecretsLoader.instance.reset() | ||
| } | ||
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| private static void addCustomDirectives() { | ||
| ProcessConfig.DIRECTIVES.addAll(TaskDirectives.ALL) | ||
| } | ||
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| @Override | ||
| List<String> getCommands() { | ||
| return ['secrets'] | ||
| } | ||
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| @Override | ||
| int exec(String cmd, List<String> args) { | ||
| return switch (cmd){ | ||
| case 'secrets'-> secrets(args.first(), args.drop(1)) | ||
| default -> -1 | ||
| } | ||
| } | ||
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| int secrets(String action, List<String>args){ | ||
| NomadSecretCmd nomadSecretCmd = new NomadSecretCmd() | ||
| nomadSecretCmd.runCommand( session.config , action, args) | ||
| } | ||
| } | ||
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13 changes: 13 additions & 0 deletions
13
plugins/nf-nomad/src/main/nextflow/nomad/config/NomadSecretOpts.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,13 @@ | ||
| package nextflow.nomad.config | ||
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| class NomadSecretOpts { | ||
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| final Boolean enabled | ||
| final String path | ||
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| NomadSecretOpts(Map map){ | ||
| this.enabled = map.containsKey('enabled') ? map.get('enabled') as boolean : false | ||
| this.path = map.path ?: "secrets/nf-nomad" | ||
| } | ||
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| } |
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79 changes: 79 additions & 0 deletions
79
plugins/nf-nomad/src/main/nextflow/nomad/secrets/NomadSecretCmd.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,79 @@ | ||
| package nextflow.nomad.secrets | ||
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| import groovy.util.logging.Slf4j | ||
| import nextflow.exception.AbortOperationException | ||
| import nextflow.nomad.config.NomadConfig | ||
| import nextflow.nomad.executor.NomadService | ||
| import nextflow.plugin.Priority | ||
| import nextflow.secret.Secret | ||
| import nextflow.secret.SecretImpl | ||
| import nextflow.secret.SecretsProvider | ||
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| @Slf4j | ||
| class NomadSecretCmd { | ||
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| protected NomadService service | ||
| protected NomadConfig nomadConfig | ||
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| int runCommand(Map config, String action, List<String> args){ | ||
| nomadConfig = new NomadConfig((config.nomad ?: Collections.emptyMap()) as Map) | ||
| service = new NomadService(nomadConfig) | ||
| return switch (action){ | ||
| case 'get' ->execGetSecretNames(args.removeAt(0).toString()) | ||
| case 'set' ->execSetSecretNames(args.removeAt(0).toString(),args.removeAt(0).toString()) | ||
| case 'list'->execListSecretsNames() | ||
| case 'delete'->execDeleteSecretNames(args.removeAt(0).toString()) | ||
| default -> -1 | ||
| } | ||
| } | ||
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| int execListSecretsNames(){ | ||
| def list = listSecretsNames() | ||
| println list.join('\n') | ||
| return 0 | ||
| } | ||
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| int execGetSecretNames(String name){ | ||
| if(!name){ | ||
| throw new AbortOperationException("Wrong number of arguments") | ||
| } | ||
| def secret = getSecret(name) | ||
| println secret | ||
| return 0 | ||
| } | ||
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| int execSetSecretNames(String name, String value){ | ||
| if(!name){ | ||
| throw new AbortOperationException("Wrong number of arguments") | ||
| } | ||
| setSecret(name, value) | ||
| return 0 | ||
| } | ||
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| int execDeleteSecretNames(String name){ | ||
| if(!name){ | ||
| throw new AbortOperationException("Wrong number of arguments") | ||
| } | ||
| deleteSecret(name) | ||
| return 0 | ||
| } | ||
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| String getSecret(String name) { | ||
| String value = service.getVariableValue(name) | ||
| if( !value ) | ||
| throw new AbortOperationException("Missing secret name") | ||
| value | ||
| } | ||
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| Set<String> listSecretsNames() { | ||
| service.variablesList | ||
| } | ||
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| void setSecret(String name, String value) { | ||
| service.setVariableValue(name, value) | ||
| } | ||
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| void deleteSecret(String name){ | ||
| service.deleteVariable(name) | ||
| } | ||
| } |
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