Check Nextflow version before loading plugins (#6591)

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/Session.groovy

@@ -88,7 +88,6 @@ import nextflow.util.NameGenerator
 import nextflow.util.SysHelper
 import nextflow.util.ThreadPoolManager
 import nextflow.util.Threads
-import nextflow.util.VersionNumber
 import org.apache.commons.lang3.exception.ExceptionUtils
 import sun.misc.Signal
 import sun.misc.SignalHandler
@@ -686,7 +685,6 @@ class Session implements ISession {
         throw new IllegalStateException("Not a valid config env object: $config.env")
     }
 
-    @Memoized
     Manifest getManifest() {
         if( !config.manifest )
             return new Manifest()
@@ -890,13 +888,6 @@ class Session implements ISession {
 
     ExecutorService getExecService() { execService }
 
-    /**
-     * Check preconditions before run the main script
-     */
-    protected void validate() {
-        checkVersion()
-    }
-
     @PackageScope void checkConfig() {
         final enabled = config.navigate('nextflow.enable.configProcessNamesValidation', true) as boolean
         if( enabled ) {
@@ -918,36 +909,6 @@ class Session implements ISession {
         config.navigate('workflow.failOnIgnore', false) as boolean
     }
 
-    @PackageScope VersionNumber getCurrentVersion() {
-        new VersionNumber(BuildInfo.version)
-    }
-
-    @PackageScope void checkVersion() {
-        def version = manifest.getNextflowVersion()?.trim()
-        if( !version )
-            return
-
-        // when the version string is prefix with a `!`
-        // an exception is thrown is the version does not match
-        boolean important = false
-        if( version.startsWith('!') ) {
-            important = true
-            version = version.substring(1).trim()
-        }
-
-        if( !getCurrentVersion().matches(version) ) {
-            important ? showVersionError(version) : showVersionWarning(version)
-        }
-    }
-
-    @PackageScope void showVersionError(String ver) {
-        throw new AbortOperationException("Nextflow version $BuildInfo.version does not match workflow required version: $ver")
-    }
-
-    @PackageScope void showVersionWarning(String ver) {
-        log.warn "Nextflow version $BuildInfo.version does not match workflow required version: $ver -- Execution will continue, but things may break!"
-    }
-
     /**
      * Validate the config file
      *
@@ -1090,7 +1051,6 @@ class Session implements ISession {
     }
 
     void notifyBeforeWorkflowExecution() {
-        validate()
     }
 
     void notifyAfterWorkflowExecution() {

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

@@ -38,6 +38,7 @@ import nextflow.SysEnv
 import nextflow.config.ConfigBuilder
 import nextflow.config.ConfigMap
 import nextflow.config.ConfigValidator
+import nextflow.config.Manifest
 import nextflow.exception.AbortOperationException
 import nextflow.file.FileHelper
 import nextflow.plugin.Plugins
@@ -49,6 +50,7 @@ import nextflow.secret.SecretsLoader
 import nextflow.util.CustomPoolFactory
 import nextflow.util.Duration
 import nextflow.util.HistoryFile
+import nextflow.util.VersionNumber
 import org.apache.commons.lang3.StringUtils
 import org.fusesource.jansi.AnsiConsole
 import org.yaml.snakeyaml.Yaml
@@ -360,6 +362,9 @@ class CmdRun extends CmdBase implements HubOptions {
         ConfigMap config = builder.build()
         Map configParams = builder.getConfigParams()
 
+        // -- Check Nextflow version
+        checkVersion(config)
+
         // -- Load plugins (may register secret providers)
         Plugins.load(config)
 
@@ -677,6 +682,45 @@ class CmdRun extends CmdBase implements HubOptions {
         return result
     }
 
+    /**
+     * Check the Nextflow version against the version required by
+     * the pipeline via `manifest.nextflowVersion`.
+     *
+     * When the version spec is prefixed with '!', the run will fail
+     * if the Nextflow version does not match.
+     *
+     * @param config
+     */
+    protected void checkVersion(Map config) {
+        final manifest = new Manifest(config.manifest as Map ?: Collections.emptyMap())
+        String version = manifest.nextflowVersion?.trim()
+        if( !version )
+            return
+
+        final important = version.startsWith('!')
+        if( important )
+            version = version.substring(1).trim()
+
+        if( !getCurrentVersion().matches(version) ) {
+            if( important )
+                showVersionError(version)
+            else
+                showVersionWarning(version)
+        }
+    }
+
+    protected VersionNumber getCurrentVersion() {
+        return new VersionNumber(BuildInfo.version)
+    }
+
+    protected void showVersionError(String ver) {
+        throw new AbortOperationException("Nextflow version ${BuildInfo.version} does not match version required by pipeline: ${ver}")
+    }
+
+    protected void showVersionWarning(String ver) {
+        log.warn "Nextflow version ${BuildInfo.version} does not match version required by pipeline: ${ver} -- execution will continue, but things might break!"
+    }
+
     @Memoized  // <-- avoid parse multiple times the same file and params
     Map parsedParams(Map configVars) {
 

modules/nextflow/src/test/groovy/nextflow/SessionTest.groovy

@@ -317,7 +317,7 @@ class SessionTest extends Specification {
         when:
         def session = new Session([manifest: MAN])
         then:
-        session.manifest.with {
+        session.getManifest().with {
             author == 'pablo'
             nextflowVersion == '1.2.3'
             name == 'foo'
@@ -401,49 +401,6 @@ class SessionTest extends Specification {
         session.fetchContainers() == 'ngi/rnaseq:1.2'
     }
 
-
-    def 'should validate version'() {
-
-        given:
-        def manifest = Mock(Manifest)
-        def session = Spy(Session)
-
-        when:
-        session.checkVersion()
-        then:
-        session.getManifest() >> manifest
-        1 * session.getCurrentVersion() >> new VersionNumber('1.1')
-        1 * manifest.getNextflowVersion() >> '>= 1.0'
-        0 * session.showVersionWarning(_)
-
-        when:
-        session.checkVersion()
-        then:
-        session.getManifest() >> manifest
-        1 * session.getCurrentVersion() >> new VersionNumber('1.1')
-        1 * manifest.getNextflowVersion() >> '>= 1.2'
-        1 * session.showVersionWarning('>= 1.2')
-
-        when:
-        session.checkVersion()
-        then:
-        session.getManifest() >> manifest
-        1 * session.getCurrentVersion() >> new VersionNumber('1.1')
-        1 * manifest.getNextflowVersion() >> '! >= 1.2'
-        1 * session.showVersionError('>= 1.2')
-        thrown(AbortOperationException)
-
-        when:
-        session.checkVersion()
-        then:
-        session.getManifest() >> manifest
-        1 * manifest.getNextflowVersion() >> null
-        0 * session.getCurrentVersion() >> null
-        0 * session.showVersionWarning(_)
-        0 * session.showVersionError(_)
-
-    }
-
     @Unroll
     def 'should get module binaries status'() {
         given:

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

@@ -23,6 +23,7 @@ import nextflow.NextflowMeta
 import nextflow.SysEnv
 import nextflow.config.ConfigMap
 import nextflow.exception.AbortOperationException
+import nextflow.util.VersionNumber
 import spock.lang.Specification
 import spock.lang.Unroll
 
@@ -438,4 +439,37 @@ class CmdRunTest extends Specification {
         true    | [:]                                     | [NXF_ENABLE_STRICT: true ] | true
 
     }
+
+    def 'should validate Nextflow version against version required by pipeline'() {
+
+        given:
+        def cmd = Spy(new CmdRun())
+
+        when:
+        cmd.checkVersion([manifest: [nextflowVersion: '>= 1.0']])
+        then:
+        1 * cmd.getCurrentVersion() >> new VersionNumber('1.1')
+        0 * cmd.showVersionWarning(_)
+
+        when:
+        cmd.checkVersion([manifest: [nextflowVersion: '>= 1.2']])
+        then:
+        1 * cmd.getCurrentVersion() >> new VersionNumber('1.1')
+        1 * cmd.showVersionWarning('>= 1.2')
+
+        when:
+        cmd.checkVersion([manifest: [nextflowVersion: '! >= 1.2']])
+        then:
+        1 * cmd.getCurrentVersion() >> new VersionNumber('1.1')
+        1 * cmd.showVersionError('>= 1.2')
+        thrown(AbortOperationException)
+
+        when:
+        cmd.checkVersion([:])
+        then:
+        0 * cmd.getCurrentVersion()
+        0 * cmd.showVersionWarning(_)
+        0 * cmd.showVersionError(_)
+    }
+
 }