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Decouple nf-tower plugin from cli module
Signed-off-by: Ben Sherman <bentshermann@gmail.com>
1 parent 9e602ee commit a0bdfae

11 files changed

Lines changed: 158 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 2013-2025, 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 2013-2025, 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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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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}
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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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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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}
150-
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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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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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@@ -83,7 +83,7 @@ class CmdAuthTest extends Specification {
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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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when:
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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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when:
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def 'logout command should validate too many arguments'() {
127127
given:
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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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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:
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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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when:
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def 'login command should use provided API URL'() {
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given:
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def cmd = Spy(CmdAuth)
174-
def operation = Mock(CmdAuth.AuthCommand)
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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 {
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compileOnly project(':nf-cli-v1')
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compileOnly project(':nextflow')
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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', '')
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}
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protected Map readConfig() {
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protected ConfigObject readConfig() {
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// note: the Nextflow home config file is `$HOME/.nextflow/config` (not `nextflow.config`)
5455
final configFile = Const.APP_HOME_DIR.resolve('config')
55-
return new ConfigBuilder().build(configFile.exists() ? [ configFile ] : []).flatten()
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return new ConfigBuilder().build(configFile.exists() ? [ configFile ] : [])
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}
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59+
protected Map readConfigFlat() {
60+
return readConfig().flatten()
5661
}
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5863
protected List<Map> listUserWorkspaces(TowerClient client, String userId) {

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

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@@ -37,8 +37,8 @@ import groovy.transform.InheritConstructors
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import groovy.util.logging.Slf4j
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import nextflow.Const
3939
import nextflow.SysEnv
40-
import nextflow.cli.CmdAuth
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import nextflow.config.ConfigCmdAdapter
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import nextflow.cli.AuthCommand
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import nextflow.config.ConfigBuilder
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import nextflow.exception.AbortOperationException
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import nextflow.platform.PlatformHelper
4444

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6060
@Slf4j
6161
@InheritConstructors
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@CompileStatic
63-
class AuthCommandImpl extends BaseCommandImpl implements CmdAuth.AuthCommand {
63+
class AuthCommandImpl extends BaseCommandImpl implements AuthCommand {
6464
static final String OIDC_CLIENT_ID = 'nextflow_cli'
6565
static final int WORKSPACE_SELECTION_THRESHOLD = 8 // Max workspaces to show in single list; above this uses org-first selection
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236236
private String normalizeApiUrl(String url) {
237237
if( !url ) {
238238
// Read config to get the actual resolved endpoint value
239-
final builder = new ConfigCmdAdapter().setHomeDir(Const.APP_HOME_DIR).setCurrentDir(Const.APP_HOME_DIR)
240-
final configObject = builder.buildConfigObject()
241-
final towerConfig = configObject.navigate('tower') as Map ?: [:]
239+
final configObject = readConfig()
240+
final towerConfig = configObject.tower as Map ?: [:]
242241
return PlatformHelper.getEndpoint(towerConfig, SysEnv.get())
243242
}
244243
if( !url.startsWith('http://') && !url.startsWith('https://') ) {
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404403
@Override
405404
void config(Boolean showHeader = true) {
406405
// Read from both main config and seqera-auth.config file
407-
final builder = new ConfigCmdAdapter().setHomeDir(Const.APP_HOME_DIR).setCurrentDir(Const.APP_HOME_DIR)
408-
final configObject = builder.buildConfigObject()
406+
final configObject = readConfig()
409407
final config = configObject.flatten()
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411409
// Navigate to tower config section (returns map without 'tower.' prefix)
412-
final towerConfig = configObject.navigate('tower') as Map ?: [:]
410+
final towerConfig = configObject.tower as Map ?: [:]
413411
final existingToken = PlatformHelper.getAccessToken(towerConfig, SysEnv.get())
414412
final endpoint = PlatformHelper.getEndpoint(towerConfig, SysEnv.get())
415413

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792790
*/
793791
@Override
794792
void status() {
795-
final config = readConfig()
793+
final config = readConfigFlat()
796794
printStatus(collectStatus(config))
797795
}
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