Fix Inspect command fails with Singularity

Signed-off-by: Paolo Di Tommaso <[email protected]>

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

@@ -23,8 +23,8 @@ import com.beust.jcommander.Parameters
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
+import nextflow.container.inspect.ContainerInspectMode
 import nextflow.container.inspect.ContainersInspector
-import nextflow.exception.AbortOperationException
 import nextflow.util.LoggerHelper
 /**
  * Implement `inspect` command
@@ -70,6 +70,7 @@ class CmdInspect extends CmdBase {
 
     @Override
     void run() {
+        ContainerInspectMode.activate(true)
         // configure quiet mode
         LoggerHelper.setQuiet(true)
         // setup the target run command
@@ -89,8 +90,6 @@ class CmdInspect extends CmdBase {
     }
 
     protected void applyInspect(Session session) {
-        // disallow singularity w/o wave and freeze
-        checkSingularityConfig(session.config)
         // disable wave await mode when running
         if( session.config.wave instanceof Map )
             checkWaveConfig(session.config.wave as Map)
@@ -106,11 +105,4 @@ class CmdInspect extends CmdBase {
             wave.dryRun = !concretize
     }
 
-    protected void checkSingularityConfig(Map config) {
-        final sing = config.navigate('singularity.enabled',false)
-        final wave = config.navigate('wave.enabled',false)
-        final freeze = config.navigate('wave.freeze',false)
-        if( sing && (!wave || !freeze) )
-            throw new AbortOperationException("Inspect command with Singularity requires enabling 'wave' and 'freeze' settings")
-    }
 }

modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy

@@ -23,6 +23,7 @@ import java.util.regex.Pattern
 import groovy.transform.CompileStatic
 import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
+import nextflow.container.inspect.ContainerInspectMode
 import nextflow.util.Escape
 /**
  * Helper class to normalise a container image name depending
@@ -67,7 +68,8 @@ class ContainerHandler {
             if( !config.isEnabled() || !normalizedImageName )
                 return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
-
+            if( ContainerInspectMode.active() && requiresCaching )
+                return imageName
             final result = requiresCaching ? createSingularityCache(this.config, normalizedImageName) : normalizedImageName
             return Escape.path(result)
         }
@@ -76,14 +78,17 @@ class ContainerHandler {
             if( !config.isEnabled() || !normalizedImageName )
                 return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
-
+            if( ContainerInspectMode.active() && requiresCaching )
+                return imageName
             final result = requiresCaching ? createApptainerCache(this.config, normalizedImageName) : normalizedImageName
             return Escape.path(result)
         }
         if( engine == 'charliecloud' ) {
             // if the imagename starts with '/' it's an absolute path
             // otherwise we assume it's in a remote registry and pull it from there
             final requiresCaching = !imageName.startsWith('/')
+            if( ContainerInspectMode.active() && requiresCaching )
+                return imageName
             final result = requiresCaching ? createCharliecloudCache(this.config, imageName) : imageName
             return Escape.path(result)
         }

modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy

@@ -0,0 +1,35 @@
+/*
+ * Copyright 2013-2023, 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.container.inspect
+
+import groovy.transform.CompileStatic
+/**
+ * Activate the container inspect mode
+ *
+ * @author Paolo Di Tommaso <[email protected]>
+ */
+@CompileStatic
+class ContainerInspectMode {
+
+    private static boolean active
+
+    static boolean active() { return active }
+
+    static void activate(boolean value) { active=value }
+
+}

modules/nextflow/src/test/groovy/nextflow/cli/CmdInspectTest.groovy

@@ -17,7 +17,7 @@
 
 package nextflow.cli
 
-import nextflow.exception.AbortOperationException
+
 import spock.lang.Specification
 import spock.lang.Unroll
 /**
@@ -51,41 +51,4 @@ class CmdInspectTest extends Specification {
 
     }
 
-    def 'should allow singularity only with wave and freeze' () {
-        given:
-        def cmd = Spy(new CmdInspect())
-
-        when:
-        cmd.checkSingularityConfig([:])
-        then:
-        noExceptionThrown()
-
-        when:
-        cmd.checkSingularityConfig([singularity:[enabled:false]])
-        then:
-        noExceptionThrown()
-
-        when:
-        cmd.checkSingularityConfig([wave:[enabled:true, freeze:true]])
-        then:
-        noExceptionThrown()
-
-        when:
-        cmd.checkSingularityConfig([singularity:[enabled:true], wave:[enabled:true, freeze:true]])
-        then:
-        noExceptionThrown()
-
-        // singularity w/o wave and freeze is not allowed
-        when:
-        cmd.checkSingularityConfig([singularity:[enabled:true]])
-        then:
-        thrown(AbortOperationException)
-
-        when:
-        cmd.checkSingularityConfig([singularity:[enabled:true], wave:[enabled:true]])
-        then:
-        thrown(AbortOperationException)
-
-    }
-
 }

plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveAssets.groovy

@@ -85,11 +85,11 @@ class WaveAssets {
     }
 
 
-    static void validateContainerRepo(String name) {
+    static void validateContainerName(String name) {
         if( !name )
             return
         final scheme = StringUtils.getUrlProtocol(name)
         if( scheme )
-            throw new IllegalArgumentException("Container repository should not start with URL like prefix - offending value: $name")
+            throw new IllegalArgumentException("Wave container request image cannot start with URL like prefix - offending value: $name")
     }
 }

plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy

@@ -51,6 +51,7 @@ import io.seqera.wave.plugin.exception.UnauthorizedException
 import io.seqera.wave.plugin.packer.Packer
 import nextflow.Session
 import nextflow.SysEnv
+import nextflow.container.inspect.ContainerInspectMode
 import nextflow.container.resolver.ContainerInfo
 import nextflow.fusion.FusionConfig
 import nextflow.processor.Architecture
@@ -184,7 +185,7 @@ class WaveClient {
                 fingerprint: assets.fingerprint(),
                 freeze: config.freezeMode(),
                 format: assets.singularity ? 'sif' : null,
-                dryRun: config.dryRun()
+                dryRun: ContainerInspectMode.active()
         )
     }
 
@@ -208,7 +209,7 @@ class WaveClient {
                 towerEndpoint: tower.endpoint,
                 workflowId: tower.workflowId,
                 freeze: config.freezeMode(),
-                dryRun: config.dryRun(),
+                dryRun: ContainerInspectMode.active(),
         )
         return sendRequest(request)
     }
@@ -489,7 +490,7 @@ class WaveClient {
         final platform = dockerArch
 
         // check is a valid container image
-        WaveAssets.validateContainerRepo(containerImage)
+        WaveAssets.validateContainerName(containerImage)
         // read the container config and go ahead
         final containerConfig = this.resolveContainerConfig(platform)
         return new WaveAssets(
@@ -521,7 +522,7 @@ class WaveClient {
             // get from cache or submit a new request
             final response = cache.get(key, { sendRequest(assets) } as Callable )
             if( config.freezeMode() )  {
-                if( response.buildId && !config.dryRun() ) {
+                if( response.buildId && !ContainerInspectMode.active() ) {
                     // await the image to be available when a new image is being built
                     awaitImage(response.targetImage)
                 }

plugins/nf-wave/src/main/io/seqera/wave/plugin/config/WaveConfig.groovy

@@ -49,13 +49,11 @@ class WaveConfig {
     final private RetryOpts retryOpts
     final private HttpOpts httpClientOpts
     final private Boolean freezeMode
-    final private Boolean dryRunMode
 
     WaveConfig(Map opts, Map<String,String> env=System.getenv()) {
         this.enabled = opts.enabled
         this.endpoint = (opts.endpoint?.toString() ?: env.get('WAVE_API_ENDPOINT') ?: DEF_ENDPOINT)?.stripEnd('/')
         this.freezeMode = opts.freeze as Boolean
-        this.dryRunMode = opts.navigate('dryRun', false)
         this.containerConfigUrl = parseConfig(opts, env)
         this.tokensCacheMaxDuration = opts.navigate('tokens.cache.maxDuration', '30m') as Duration
         this.condaOpts = opts.navigate('build.conda', Collections.emptyMap()) as CondaOpts
@@ -87,8 +85,6 @@ class WaveConfig {
 
     boolean freezeMode() { return this.freezeMode }
 
-    boolean dryRun() { return this.dryRunMode }
-
     boolean bundleProjectResources() { bundleProjectResources }
 
     String buildRepository() { buildRepository }

plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveAssetsTest.groovy

@@ -39,22 +39,22 @@ class WaveAssetsTest extends Specification {
 
     def 'should validate container name' () {
         when:
-        WaveAssets.validateContainerRepo('ubuntu')
+        WaveAssets.validateContainerName('ubuntu')
         then:
         noExceptionThrown()
 
         when:
-        WaveAssets.validateContainerRepo('ubuntu:latest')
+        WaveAssets.validateContainerName('ubuntu:latest')
         then:
         noExceptionThrown()
 
         when:
-        WaveAssets.validateContainerRepo('quay.io/wtsicgp/nanoseq:3.3.0')
+        WaveAssets.validateContainerName('quay.io/wtsicgp/nanoseq:3.3.0')
         then:
         noExceptionThrown()
 
         when:
-        WaveAssets.validateContainerRepo('docker://quay.io/wtsicgp/nanoseq:3.3.0')
+        WaveAssets.validateContainerName('docker://quay.io/wtsicgp/nanoseq:3.3.0')
         then:
         thrown(IllegalArgumentException)
     }

plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy

@@ -32,6 +32,8 @@ import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
 import nextflow.Session
 import nextflow.SysEnv
+import nextflow.container.inspect.ContainerInspectMode
+import nextflow.container.inspect.ContainersInspector
 import nextflow.extension.FilesEx
 import nextflow.file.FileHelper
 import nextflow.processor.TaskRun
@@ -197,7 +199,8 @@ class WaveClientTest extends Specification {
 
     def 'should create request object with dry-run mode' () {
         given:
-        def session = Mock(Session) { getConfig() >> [wave:[dryRun:true]]}
+        ContainerInspectMode.activate(true)
+        def session = Mock(Session) { getConfig() >> [:]}
         def IMAGE =  'foo:latest'
         def wave = new WaveClient(session)
 
@@ -215,6 +218,9 @@ class WaveClientTest extends Specification {
         and:
         req.fingerprint == 'bd2cb4b32df41f2d290ce2366609f2ad'
         req.timestamp instanceof String
+
+        cleanup:
+        ContainerInspectMode.activate(false)
     }
 
     def 'should create request object and platform' () {

plugins/nf-wave/src/test/io/seqera/wave/plugin/config/WaveConfigTest.groovy

@@ -199,7 +199,7 @@ class WaveConfigTest extends Specification {
         given:
         def config = new WaveConfig([enabled: true])
         expect:
-        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.1; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null, dryRunMode:false)'
+        config.toString() == 'WaveConfig(enabled:true, endpoint:https://wave.seqera.io, containerConfigUrl:[], tokensCacheMaxDuration:30m, condaOpts:CondaOpts(mambaImage=mambaorg/micromamba:1.5.1; basePackages=conda-forge::procps-ng, commands=null), spackOpts:SpackOpts(basePackages=null, commands=null), strategy:[container, dockerfile, conda, spack], bundleProjectResources:null, buildRepository:null, cacheRepository:null, retryOpts:RetryOpts(delay:450ms, maxDelay:1m 30s, maxAttempts:10, jitter:0.25), httpClientOpts:HttpOpts(), freezeMode:null)'
     }
 
     def 'should not allow invalid settinga' () {