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Decouple nf-tower plugin from cli module
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
1 parent a27ea08 commit 5117eca

12 files changed

Lines changed: 176 additions & 121 deletions

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‎modules/nextflow/src/main/groovy/nextflow/cli/AuthCommand.groovy‎

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/*
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* Copyright 2013-2026, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.cli
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import org.pf4j.ExtensionPoint
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/**
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* Extension point interface for the `auth` command.
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*
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* @see io.seqera.tower.plugin.auth.AuthCommandImpl
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*
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* @author Phil Ewels <phil.ewels@seqera.io>
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*/
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interface AuthCommand extends ExtensionPoint {
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/**
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* Authenticates with Seqera Platform and saves credentials to config.
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*
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* @param url the Seqera Platform API endpoint URL (null for default)
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*/
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void login(String url)
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/**
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* Revokes access token and removes authentication from local config.
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*/
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void logout()
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/**
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* Configures Seqera Platform settings (workspace, monitoring, compute environment).
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*/
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void config()
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/**
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* Displays current authentication status and configuration sources.
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*/
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void status()
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}

‎modules/nextflow/src/main/groovy/nextflow/cli/LaunchCommand.groovy‎

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/*
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* Copyright 2013-2026, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.cli
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import org.pf4j.ExtensionPoint
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/**
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* Extension point interface for the `launch` command.
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*
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* @see io.seqera.tower.plugin.launch.LaunchCommandImpl
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*
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* @author Phil Ewels <phil.ewels@seqera.io>
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*/
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interface LaunchCommand extends ExtensionPoint {
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void launch(LaunchOptions options)
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}

‎modules/nextflow/src/main/groovy/nextflow/cli/LaunchOptions.groovy‎

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/*
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* Copyright 2013-2026, Seqera Labs
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*
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* Licensed under the Apache License, Version 2.0 (the "License");
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* you may not use this file except in compliance with the License.
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* You may obtain a copy of the License at
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*
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* http://www.apache.org/licenses/LICENSE-2.0
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*
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* Unless required by applicable law or agreed to in writing, software
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* distributed under the License is distributed on an "AS IS" BASIS,
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* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
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* See the License for the specific language governing permissions and
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* limitations under the License.
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*/
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package nextflow.cli
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import groovy.transform.CompileStatic
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/**
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* Data class to hold launch options
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*
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* @author Phil Ewels <phil.ewels@seqera.io>
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*/
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@CompileStatic
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class LaunchOptions {
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String pipeline
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String workspace
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String computeEnv
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String runName
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String workDir
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String revision
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String profile
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List<String> configFiles
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String paramsFile
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String entryName
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String resume
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boolean latest
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boolean stubRun
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String mainScript
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Map<String, String> params
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List<String> userSecrets
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List<String> workspaceSecrets
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}

‎modules/nf-cli-v1/src/main/groovy/nextflow/cli/CmdAuth.groovy‎

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@@ -26,7 +26,6 @@ import nextflow.config.ConfigCmdAdapter
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import nextflow.exception.AbortOperationException
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import nextflow.platform.PlatformHelper
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import nextflow.plugin.Plugins
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import org.pf4j.ExtensionPoint
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/**
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* Command-line interface for managing Seqera Platform authentication and configuration.
@@ -107,47 +106,6 @@ class CmdAuth extends CmdBase implements UsageAware {
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void usage(List<String> result)
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}
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/**
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* Extension point interface for authentication command implementations.
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*
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* <p>This interface is implemented by the {@code nf-tower} plugin to provide the actual
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* authentication logic while keeping the CLI interface in the core Nextflow codebase.
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* The plugin system uses PF4J to discover and load implementations at runtime.
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*
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* <p>The implementation handles:
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* <ul>
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* <li>OAuth2 device flow for Seqera Platform Cloud
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* <li>PAT (Personal Access Token) authentication for Enterprise
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* <li>Token storage and management in config files
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* <li>Workspace and compute environment configuration
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* </ul>
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*
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* @see io.seqera.tower.plugin.auth.AuthCommandImpl
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*/
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interface AuthCommand extends ExtensionPoint {
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/**
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* Authenticates with Seqera Platform and saves credentials to config.
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*
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* @param url the Seqera Platform API endpoint URL (null for default)
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*/
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void login(String url)
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/**
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* Revokes access token and removes authentication from local config.
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*/
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void logout()
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/**
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* Configures Seqera Platform settings (workspace, monitoring, compute environment).
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*/
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void config()
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/**
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* Displays current authentication status and configuration sources.
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*/
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void status()
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}
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static public final String NAME = 'auth'
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private List<SubCmd> commands = []

‎modules/nf-cli-v1/src/main/groovy/nextflow/cli/CmdLaunch.groovy‎

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@@ -23,7 +23,6 @@ import groovy.transform.CompileStatic
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import groovy.util.logging.Slf4j
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import nextflow.exception.AbortOperationException
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import nextflow.plugin.Plugins
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import org.pf4j.ExtensionPoint
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/**
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* Implements the 'nextflow launch' command
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@Parameters(commandDescription = "Launch a workflow in Seqera Platform")
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class CmdLaunch extends CmdBase implements UsageAware {
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38-
interface LaunchCommand extends ExtensionPoint {
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void launch(LaunchOptions options)
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}
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static final public String NAME = 'launch'
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@Override
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stubRun: stubRun,
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mainScript: mainScript,
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params: params,
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launcher: launcher,
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userSecrets: userSecrets,
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workspaceSecrets: workspaceSecrets
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)
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// Get Launch command operations implementation from plugins
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return Plugins.getExtension(LaunchCommand)
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}
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/**
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* Data class to hold launch options
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*/
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@CompileStatic
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static class LaunchOptions {
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String pipeline
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String workspace
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String computeEnv
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String runName
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String workDir
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String revision
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String profile
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List<String> configFiles
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String paramsFile
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String entryName
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String resume
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boolean latest
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boolean stubRun
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String mainScript
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Map<String, String> params
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Launcher launcher
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List<String> userSecrets
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List<String> workspaceSecrets
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}
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}

‎modules/nf-cli-v1/src/test/groovy/nextflow/cli/CmdAuthTest.groovy‎

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given:
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def cmd = Spy(CmdAuth)
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cmd.args = ['unknown']
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def operation = Mock(CmdAuth.AuthCommand)
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def operation = Mock(AuthCommand)
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8888
when:
8989
cmd.run()
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def 'login command should validate too many arguments'() {
112112
given:
113113
def cmd = Spy(CmdAuth)
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def operation = Mock(CmdAuth.AuthCommand)
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def operation = Mock(AuthCommand)
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cmd.args = ['login', 'extra']
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117117
when:
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126126
def 'logout command should validate too many arguments'() {
127127
given:
128128
def cmd = Spy(CmdAuth)
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def operation = Mock(CmdAuth.AuthCommand)
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def operation = Mock(AuthCommand)
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cmd.args = ['logout', 'extra']
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when:
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141141
def 'config command should validate too many arguments'() {
142142
given:
143143
def cmd = Spy(CmdAuth)
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def operation = Mock(CmdAuth.AuthCommand)
144+
def operation = Mock(AuthCommand)
145145
cmd.args = ['config', 'extra']
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147147
when:
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156156
def 'status command should validate too many arguments'() {
157157
given:
158158
def cmd = Spy(CmdAuth)
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def operation = Mock(CmdAuth.AuthCommand)
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def operation = Mock(AuthCommand)
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cmd.args = ['status', 'extra']
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162162
when:
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171171
def 'login command should use provided API URL'() {
172172
given:
173173
def cmd = Spy(CmdAuth)
174-
def operation = Mock(CmdAuth.AuthCommand)
174+
def operation = Mock(AuthCommand)
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cmd.args = ['login']
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cmd.apiUrl = 'https://api.example.com'
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‎plugins/nf-seqera/build.gradle‎

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}
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dependencies {
51-
compileOnly project(':nf-cli-v1')
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compileOnly project(':nextflow')
5252
compileOnly 'org.slf4j:slf4j-api:2.0.17'
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compileOnly 'org.pf4j:pf4j:3.14.1'
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‎plugins/nf-tower/src/main/io/seqera/tower/plugin/BaseCommandImpl.groovy‎

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return apiEndpoint.replace('://api.', '://').replace('/api', '')
5151
}
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53-
protected Map readConfig() {
53+
protected ConfigObject readConfig() {
5454
final configFile = Const.APP_HOME_DIR.resolve('config')
55-
return new ConfigBuilder().build(configFile.exists() ? [ configFile ] : []).flatten()
55+
return new ConfigBuilder().build(configFile.exists() ? [ configFile ] : [])
56+
}
57+
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protected Map readConfigFlat() {
59+
return readConfig().flatten()
5660
}
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5862
protected List<Map> listUserWorkspaces(TowerClient client, String userId) {

‎plugins/nf-tower/src/main/io/seqera/tower/plugin/auth/AuthCommandImpl.groovy‎

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import groovy.util.logging.Slf4j
3838
import nextflow.Const
3939
import nextflow.SysEnv
40-
import nextflow.cli.CmdAuth
41-
import nextflow.config.ConfigCmdAdapter
40+
import nextflow.cli.AuthCommand
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import nextflow.config.ConfigBuilder
4242
import nextflow.exception.AbortOperationException
4343
import nextflow.platform.PlatformHelper
4444
import nextflow.util.ProxyConfig
@@ -61,7 +61,7 @@ import static nextflow.util.ColorUtil.colorize
6161
@Slf4j
6262
@InheritConstructors
6363
@CompileStatic
64-
class AuthCommandImpl extends BaseCommandImpl implements CmdAuth.AuthCommand {
64+
class AuthCommandImpl extends BaseCommandImpl implements AuthCommand {
6565
static final String OIDC_CLIENT_ID = 'nextflow_cli'
6666
static final int WORKSPACE_SELECTION_THRESHOLD = 8 // Max workspaces to show in single list; above this uses org-first selection
6767

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237237
private String normalizeApiUrl(String url) {
238238
if( !url ) {
239239
// Read config to get the actual resolved endpoint value
240-
final builder = new ConfigCmdAdapter().setHomeDir(Const.APP_HOME_DIR).setCurrentDir(Const.APP_HOME_DIR)
241-
final configObject = builder.buildConfigObject()
242-
final towerConfig = configObject.navigate('tower') as Map ?: [:]
240+
final configObject = readConfig()
241+
final towerConfig = configObject.tower as Map ?: [:]
243242
return PlatformHelper.getEndpoint(towerConfig, SysEnv.get())
244243
}
245244
if( !url.startsWith('http://') && !url.startsWith('https://') ) {
@@ -405,12 +404,11 @@ class AuthCommandImpl extends BaseCommandImpl implements CmdAuth.AuthCommand {
405404
@Override
406405
void config(Boolean showHeader = true) {
407406
// Read from both main config and seqera-auth.config file
408-
final builder = new ConfigCmdAdapter().setHomeDir(Const.APP_HOME_DIR).setCurrentDir(Const.APP_HOME_DIR)
409-
final configObject = builder.buildConfigObject()
407+
final configObject = readConfig()
410408
final config = configObject.flatten()
411409

412410
// Navigate to tower config section (returns map without 'tower.' prefix)
413-
final towerConfig = configObject.navigate('tower') as Map ?: [:]
411+
final towerConfig = configObject.tower as Map ?: [:]
414412
final existingToken = PlatformHelper.getAccessToken(towerConfig, SysEnv.get())
415413
final endpoint = PlatformHelper.getEndpoint(towerConfig, SysEnv.get())
416414

@@ -793,7 +791,7 @@ class AuthCommandImpl extends BaseCommandImpl implements CmdAuth.AuthCommand {
793791
*/
794792
@Override
795793
void status() {
796-
final config = readConfig()
794+
final config = readConfigFlat()
797795
printStatus(collectStatus(config))
798796
}
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