Add tests for agent output mode (NXF_AGENT)

Tests for AI agent-friendly output mode via env vars.
All tests marked @PendingFeature until implementation.

Signed-off-by: Edmund Miller <edmund.miller@seqera.io>

Author: edmundmiller

modules/nextflow/src/test/groovy/nextflow/trace/AgentLogObserverTest.groovy

@@ -0,0 +1,233 @@
+/*
+ * Copyright 2013-2024, Seqera Labs
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package nextflow.trace
+
+import java.nio.file.Paths
+
+import nextflow.Session
+import nextflow.processor.TaskHandler
+import nextflow.processor.TaskRun
+import nextflow.trace.event.TaskEvent
+import spock.lang.PendingFeature
+import spock.lang.Specification
+
+/**
+ * Tests for AgentLogObserver
+ *
+ * @author Edmund Miller <edmund.miller@utdallas.edu>
+ */
+class AgentLogObserverTest extends Specification {
+
+    @PendingFeature
+    def 'should output pipeline info on flow begin'() {
+        given:
+        def output = []
+        def observer = new TestAgentLogObserver(output)
+        def session = Stub(Session) {
+            getManifest() >> [name: 'nf-core/rnaseq', version: '3.14.0']
+            getScriptName() >> 'main.nf'
+            getProfile() >> 'test,docker'
+            getWorkDir() >> Paths.get('/tmp/work')
+        }
+
+        when:
+        observer.onFlowCreate(session)
+        observer.onFlowBegin()
+
+        then:
+        output[0] == '[PIPELINE] nf-core/rnaseq 3.14.0 | profile=test,docker'
+        output[1].startsWith('[WORKDIR]')
+        output[1].contains('/tmp/work')
+    }
+
+    @PendingFeature
+    def 'should deduplicate warnings'() {
+        given:
+        def output = []
+        def observer = new TestAgentLogObserver(output)
+
+        when:
+        observer.appendWarning('Task runtime metrics are not reported when using macOS')
+        observer.appendWarning('Task runtime metrics are not reported when using macOS')
+        observer.appendWarning('Different warning message')
+
+        then:
+        output.size() == 2
+        output[0] == '[WARN] Task runtime metrics are not reported when using macOS'
+        output[1] == '[WARN] Different warning message'
+    }
+
+    @PendingFeature
+    def 'should output error with context'() {
+        given:
+        def output = []
+        def observer = new TestAgentLogObserver(output)
+        def task = Stub(TaskRun) {
+            getName() >> 'FASTQC (sample_1)'
+            getExitStatus() >> 127
+            getScript() >> 'fastqc --version'
+            getStderr() >> 'bash: fastqc: command not found'
+            getStdout() >> null
+            getWorkDir() >> Paths.get('/tmp/work/ab/123456')
+        }
+
+        when:
+        observer.printTaskError(task)
+
+        then:
+        output[0] == '[ERROR] FASTQC (sample_1)'
+        output[1] == 'exit: 127'
+        output[2] == 'cmd: fastqc --version'
+        output[3] == 'stderr: bash: fastqc: command not found'
+        output[4].startsWith('workdir:')
+        output[4].contains('/tmp/work/ab/123456')
+    }
+
+    @PendingFeature
+    def 'should output summary on flow complete'() {
+        given:
+        def output = []
+        def stats = new WorkflowStats()
+        stats.succeededCount = 10
+        stats.failedCount = 0
+        stats.cachedCount = 5
+        def statsObserver = Stub(WorkflowStatsObserver) {
+            getStats() >> stats
+        }
+        def observer = new TestAgentLogObserver(output)
+        observer.setStatsObserver(statsObserver)
+
+        when:
+        observer.onFlowComplete()
+
+        then:
+        output[0] == '\n[SUCCESS] completed=10 failed=0 cached=5'
+    }
+
+    @PendingFeature
+    def 'should output failed summary when tasks fail'() {
+        given:
+        def output = []
+        def stats = new WorkflowStats()
+        stats.succeededCount = 5
+        stats.failedCount = 2
+        stats.cachedCount = 0
+        def statsObserver = Stub(WorkflowStatsObserver) {
+            getStats() >> stats
+        }
+        def observer = new TestAgentLogObserver(output)
+        observer.setStatsObserver(statsObserver)
+
+        when:
+        observer.onFlowComplete()
+
+        then:
+        output[0] == '\n[FAILED] completed=7 failed=2 cached=0'
+    }
+
+    @PendingFeature
+    def 'should handle task complete for failed task'() {
+        given:
+        def output = []
+        def observer = new TestAgentLogObserver(output)
+        def task = Stub(TaskRun) {
+            getName() >> 'TEST_PROC'
+            getExitStatus() >> 1
+            getScript() >> 'exit 1'
+            getStderr() >> 'error'
+            getStdout() >> null
+            getWorkDir() >> Paths.get('/work/xx/yy')
+            isFailed() >> true
+        }
+        def handler = Stub(TaskHandler) {
+            getTask() >> task
+        }
+        def event = Stub(TaskEvent) {
+            getHandler() >> handler
+        }
+
+        when:
+        observer.onTaskComplete(event)
+
+        then:
+        output.size() > 0
+        output[0] == '[ERROR] TEST_PROC'
+    }
+
+    @PendingFeature
+    def 'should not output for successful task'() {
+        given:
+        def output = []
+        def observer = new TestAgentLogObserver(output)
+        def task = Stub(TaskRun) {
+            isFailed() >> false
+        }
+        def handler = Stub(TaskHandler) {
+            getTask() >> task
+        }
+        def event = Stub(TaskEvent) {
+            getHandler() >> handler
+        }
+
+        when:
+        observer.onTaskComplete(event)
+
+        then:
+        output.size() == 0
+    }
+
+    @PendingFeature
+    def 'should truncate long command'() {
+        given:
+        def output = []
+        def observer = new TestAgentLogObserver(output)
+        def longCommand = 'x' * 300
+        def task = Stub(TaskRun) {
+            getName() >> 'PROC'
+            getExitStatus() >> 1
+            getScript() >> longCommand
+            getStderr() >> null
+            getStdout() >> null
+            getWorkDir() >> Paths.get('/work')
+        }
+
+        when:
+        observer.printTaskError(task)
+
+        then:
+        def cmdLine = output.find { it.startsWith('cmd:') }
+        cmdLine != null
+        cmdLine.length() < 250
+        cmdLine.endsWith('...')
+    }
+
+    /**
+     * Test subclass that captures output
+     */
+    static class TestAgentLogObserver extends AgentLogObserver {
+        private List<String> output
+
+        TestAgentLogObserver(List<String> output) {
+            this.output = output
+        }
+
+        @Override
+        protected void println(String line) {
+            output << line
+        }
+    }
+}

modules/nf-commons/src/test/nextflow/SysEnvTest.groovy

@@ -17,6 +17,7 @@
 
 package nextflow
 
+import spock.lang.PendingFeature
 import spock.lang.Specification
 import spock.lang.Unroll
 
@@ -120,4 +121,27 @@ class SysEnvTest extends Specification {
         [FOO:'0']       | 1         | 0
         [FOO:'100']     | 1         | 100
     }
+
+    @PendingFeature
+    @Unroll
+    def 'should detect agent mode' () {
+        given:
+        SysEnv.push(STATE)
+
+        expect:
+        SysEnv.isAgentMode() == EXPECTED
+
+        cleanup:
+        SysEnv.pop()
+
+        where:
+        STATE                       | EXPECTED
+        [:]                         | false
+        [NXF_AGENT:'true']          | true
+        [NXF_AGENT:'false']         | false
+        [AGENT:'true']              | true
+        [CLAUDECODE:'true']         | true
+        // Multiple can be set, any true triggers agent mode
+        [NXF_AGENT:'true', AGENT:'false']  | true
+    }
 }