Put recurseSubmodules option in the manifest scope

Signed-off-by: Akira Sekiguchi <akira.sekiguchi@dnaform.jp>
nextflow-io · Aug 1, 2020 · 4d888b1 · 4d888b1
1 parent 82c6fea
commit 4d888b1
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Showing 6 changed files with 22 additions and 21 deletions.
diff --git a/docs/config.rst b/docs/config.rst
@@ -414,6 +414,7 @@ Name                Description
 ================== ================
 author              Project author name (use a comma to separate multiple names).
 defaultBranch       Git repository default branch (default: ``master``).
+recurseSubmodules   Turn this flag to ``true`` to pull submodules recursively from the Git repository
 description         Free text describing the workflow project.
 homePage            Project home page URL.
 mainScript          Project main script (default: ``main.nf``).

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdClone.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdClone.groovy
@@ -39,9 +39,6 @@ class CmdClone extends CmdBase implements HubOptions {
     @Parameter(names='-r', description = 'Revision to clone - It can be a git branch, tag or revision number')
     String revision
 
-    @Parameter(names=['-recursive','-recurse-submodules'], description = 'initialize submodules in the clone', arity = 0)
-    boolean recurse_submodules
-
     @Override
     final String getName() { NAME }
 
@@ -66,7 +63,7 @@ class CmdClone extends CmdBase implements HubOptions {
 
         manager.checkValidRemoteRepo()
         print "Cloning ${manager.project}${revision ? ':'+revision:''} ..."
-        manager.clone(target, revision, recurse_submodules)
+        manager.clone(target, revision)
         print "\r"
         println "${manager.project} cloned to: $target"
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdPull.groovy
@@ -42,8 +42,6 @@ class CmdPull extends CmdBase implements HubOptions {
     @Parameter(names=['-r','-revision'], description = 'Revision of the project to run (either a git branch, tag or commit SHA number)')
     String revision
 
-    @Parameter(names='-recursive', description = 'control recursive fetching of submodules', arity = 0)
-    boolean recurse_submodules
 
 
     @Override
@@ -73,8 +71,8 @@ class CmdPull extends CmdBase implements HubOptions {
             log.info "Checking $it ..."
             def manager = new AssetManager(it, this)
 
-            def result = manager.download(recurse_submodules, revision)
-            manager.updateModules(recurse_submodules)
+            def result = manager.download(revision)
+            manager.updateModules()
 
             def scriptFile = manager.getScriptFile()
             String message = !result ? " done" : " $result"

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -101,9 +101,6 @@ class CmdRun extends CmdBase implements HubOptions {
     @Parameter(names=['-bucket-dir'], description = 'Remote bucket where intermediate result files are stored')
     String bucketDir
 
-    @Parameter(names=['-recursive','-recurse-submodules'], description = 'Try to download submodules recursively if those do not exist', arity = 0)
-    boolean recurse_submodules
-
     /**
      * Defines the parameters to be passed to the pipeline script
      */
@@ -339,15 +336,15 @@ class CmdRun extends CmdBase implements HubOptions {
             if( offline )
                 throw new AbortOperationException("Unknown project `$repo` -- NOTE: automatic download from remote repositories is disabled")
             log.info "Pulling $repo ..."
-            def result = manager.download(recurse_submodules)
+            def result = manager.download()
             if( result )
                 log.info " $result"
             checkForUpdate = false
         }
         // checkout requested revision
         try {
             manager.checkout(revision)
-            manager.updateModules(recurse_submodules)
+            manager.updateModules()
             def scriptFile = manager.getScriptFile()
             log.info "Launching `$repo` [$runName] - revision: ${scriptFile.revisionInfo}"
             if( checkForUpdate && !offline )

diff --git a/modules/nextflow/src/main/groovy/nextflow/config/Manifest.groovy b/modules/nextflow/src/main/groovy/nextflow/config/Manifest.groovy
@@ -78,6 +78,10 @@ class Manifest {
         target.gitmodules
     }
 
+    boolean getRecurseSubmodules() {
+        target.recurseSubmodules
+    }
+
     String getNextflowVersion() {
         target.nextflowVersion
     }

diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
@@ -567,7 +567,7 @@ class AssetManager {
      * @param revision The revision to download
      * @result A message representing the operation result
      */
-    def download(boolean recurse_submodules = false, String revision=null) {
+    def download(String revision=null) {
         assert project
 
         /*
@@ -593,7 +593,7 @@ class AssetManager {
             clone
                 .setURI(cloneURL)
                 .setDirectory(localPath)
-                .setCloneSubmodules(recurse_submodules)
+                .setCloneSubmodules(manifest.recurseSubmodules)
                 .call()
 
             // return status message
@@ -639,7 +639,9 @@ class AssetManager {
         if( provider.hasCredentials() )
             pull.setCredentialsProvider( new UsernamePasswordCredentialsProvider(provider.user, provider.password))
 
-        pull.setRecurseSubmodules(FetchRecurseSubmodulesMode.YES)
+        if( manifest.recurseSubmodules ) {
+            pull.setRecurseSubmodules(FetchRecurseSubmodulesMode.YES)
+        }
         def result = pull.call()
         if(!result.isSuccessful())
             throw new AbortOperationException("Cannot pull project `$project` -- ${result.toString()}")
@@ -654,7 +656,7 @@ class AssetManager {
      * @param directory The folder when the pipeline will be cloned
      * @param revision The revision to be cloned. It can be a branch, tag, or git revision number
      */
-    void clone(File directory, String revision = null, boolean recurse_submodules) {
+    void clone(File directory, String revision = null) {
 
         def clone = Git.cloneRepository()
         def uri = getGitRepositoryUrl()
@@ -665,7 +667,7 @@ class AssetManager {
 
         clone.setURI(uri)
         clone.setDirectory(directory)
-        clone.setCloneSubmodules(recurse_submodules)
+        clone.setCloneSubmodules(manifest.recurseSubmodules)
         if( provider.hasCredentials() )
             clone.setCredentialsProvider(new UsernamePasswordCredentialsProvider(provider.user, provider.password))
 
@@ -926,7 +928,9 @@ class AssetManager {
             if(provider.hasCredentials()) {
                 fetch.setCredentialsProvider( new UsernamePasswordCredentialsProvider(provider.user, provider.password) )
             }
-            fetch.setRecurseSubmodules(FetchRecurseSubmodulesMode.YES)
+            if( manifest.recurseSubmodules ) {
+                fetch.setRecurseSubmodules(FetchRecurseSubmodulesMode.YES)
+            }
             fetch.call()
             git.checkout()
                     .setCreateBranch(true)
@@ -941,7 +945,7 @@ class AssetManager {
 
     }
 
-    void updateModules(boolean recurse_submodules = false) {
+    void updateModules() {
 
         if( !localPath )
             return // nothing to do
@@ -966,7 +970,7 @@ class AssetManager {
         final init = git.submoduleInit()
         final update = git.submoduleUpdate()
 
-        if (recurse_submodules) {
+        if( manifest.recurseSubmodules ) {
             update.setStrategy(MergeStrategy.RECURSIVE)
         }