From e1a0b240a3c438c9f289491a522b9a58535e5d19 Mon Sep 17 00:00:00 2001
From: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Date: Wed, 22 Dec 2021 05:59:52 +0100
Subject: [PATCH] Fix error reporting on missing script file #1951

---
 .../main/groovy/nextflow/cli/CmdRun.groovy    | 27 +++++++++++++++++++
 .../groovy/nextflow/scm/AssetManager.groovy   | 11 +++++++-
 .../groovy/nextflow/cli/CmdRunTest.groovy     | 15 +++++++++++
 .../nextflow/scm/AssetManagerTest.groovy      | 10 +++++++
 4 files changed, 62 insertions(+), 1 deletion(-)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
index 9ff8d7a502..5a18d110bf 100644
--- a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -338,6 +338,33 @@ class CmdRun extends CmdBase implements HubOptions {
     }
 
     protected ScriptFile getScriptFile(String pipelineName) {
+        try {
+            getScriptFile0(pipelineName)
+        }
+        catch (IllegalArgumentException | AbortOperationException e) {
+            if( e.message.startsWith("Not a valid project name:") && !guessIsRepo(pipelineName)) {
+                throw new AbortOperationException("Cannot find script file: $pipelineName")
+            }
+            else
+                throw e
+        }
+    }
+
+    static protected boolean guessIsRepo(String name) {
+        if( FileHelper.getUrlProtocol(name) != null )
+            return true
+        if( name.startsWith('/') )
+            return false
+        if( name.startsWith('./') || name.startsWith('../') )
+            return false
+        if( name.endsWith('.nf') )
+            return false
+        if( name.count('/') != 1 )
+            return false
+        return true
+    }
+
+    protected ScriptFile getScriptFile0(String pipelineName) {
         assert pipelineName
 
         /*
diff --git a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
index 30e1033c78..ea40e03d09 100644
--- a/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
+++ b/modules/nextflow/src/main/groovy/nextflow/scm/AssetManager.groovy
@@ -250,10 +250,19 @@ class AssetManager {
     String resolveName( String name ) {
         assert name
 
+        //
+        // check if it's a repository fully qualified URL e.g. https://github.com/foo/bar
+        //
         def project = resolveNameFromGitUrl(name)
         if( project )
             return project
 
+        //
+        // otherwise it must be a canonical repository name e.g. user/project
+        //
+        if( ['./','../', '/' ].any(it->name.startsWith(it)) )
+            throw new AbortOperationException("Not a valid project name: $name")
+
         def parts = name.split('/') as List<String>
         def last = parts[-1]
         if( last.endsWith('.nf') || last.endsWith('.nxf') ) {
@@ -459,7 +468,7 @@ class AssetManager {
             result = (ConfigObject)config.manifest
         }
         catch( Exception e ) {
-            throw new Exception("Project config file is malformed -- Cause: ${e.message ?: e}", e)
+            throw new AbortOperationException("Project config file is malformed -- Cause: ${e.message ?: e}", e)
         }
 
         // by default return an empty object
diff --git a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
index 7c00a9df17..be400a90d5 100644
--- a/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/cli/CmdRunTest.groovy
@@ -252,4 +252,19 @@ class CmdRunTest extends Specification {
         then:
         cmd.getDisableJobsCancellation() == true
     }
+
+    @Unroll
+    def 'should guss is repo' () {
+        expect:
+        CmdRun.guessIsRepo(PATH) == EXPECTED
+        
+        where:
+        EXPECTED    | PATH
+        true        | 'http://github.com/foo'
+        true        | 'foo/bar'
+        and:
+        false       | 'script.nf'
+        false       | '/some/path'
+        false       | '../some/path'
+    }
 }
diff --git a/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy b/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy
index e418bda3ec..fd1ea6dce4 100644
--- a/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy
+++ b/modules/nextflow/src/test/groovy/nextflow/scm/AssetManagerTest.groovy
@@ -130,6 +130,16 @@ class AssetManagerTest extends Specification {
         then:
         thrown(AbortOperationException)
 
+        when:
+        result = manager.resolveName('../blast/script.nf')
+        then:
+        thrown(AbortOperationException)
+
+        when:
+        result = manager.resolveName('./blast/script.nf')
+        then:
+        thrown(AbortOperationException)
+
     }