From 04a63e47199babb155070559105731d9aefffcae Mon Sep 17 00:00:00 2001
From: Hendrik Cannoodt <hendrik.cannoodt@gmail.com>
Date: Wed, 3 Apr 2024 10:00:53 +0200
Subject: [PATCH] Fix an issue where if the first resource is not a script, the
 resource is silently dropped (#670)

* Fix an issue where if the first resource is not a script, the resource is silently dropped

* Fill in PR #

* Update src/main/scala/io/viash/functionality/Functionality.scala

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>

* Add other edge case in test

---------

Co-authored-by: Robrecht Cannoodt <rcannood@gmail.com>
---
 CHANGELOG.md                                  |   2 +
 .../viash/functionality/Functionality.scala   |   5 +-
 .../viash/functionality/MainScriptTest.scala  | 108 ++++++++++++++++++
 3 files changed, 113 insertions(+), 2 deletions(-)
 create mode 100644 src/test/scala/io/viash/functionality/MainScriptTest.scala

diff --git a/CHANGELOG.md b/CHANGELOG.md
index f4bc9e316..4fd27ac06 100644
--- a/CHANGELOG.md
+++ b/CHANGELOG.md
@@ -10,6 +10,8 @@
 
 * `Executable`: Check whether a multiple output file argument contains a wildcard (PR #639).
 
+* `Resources`: Fix an issue where if the first resource is not a script, the resource is silently dropped (PR #670).
+
 # Viash 0.8.5 (2024-02-21): Bug fixes and documentation improvements
 
 Fix a bug when building a test docker container which requires a test resource. Additional improvements for the website documentation and support for the latest version of Nextflow are added.
diff --git a/src/main/scala/io/viash/functionality/Functionality.scala b/src/main/scala/io/viash/functionality/Functionality.scala
index eaf657381..790af8b53 100644
--- a/src/main/scala/io/viash/functionality/Functionality.scala
+++ b/src/main/scala/io/viash/functionality/Functionality.scala
@@ -372,9 +372,10 @@ case class Functionality(
     }
   def mainCode: Option[String] = mainScript.flatMap(_.read)
   // provide function to use resources.tail but that allows resources to be an empty list
+  // If mainScript ends up being None because the first resource isn't a script, return the whole list
   def additionalResources = resources match {
-    case _ :: tail => tail
-    case _ => List.empty[Resource]
+    case head :: tail if head.isInstanceOf[Script] => tail
+    case list => list
   }
 
   def isEnabled: Boolean = status != Status.Disabled
diff --git a/src/test/scala/io/viash/functionality/MainScriptTest.scala b/src/test/scala/io/viash/functionality/MainScriptTest.scala
new file mode 100644
index 000000000..ab485abcc
--- /dev/null
+++ b/src/test/scala/io/viash/functionality/MainScriptTest.scala
@@ -0,0 +1,108 @@
+package io.viash.functionality
+
+import org.scalatest.funsuite.AnyFunSuite
+import io.viash.helpers.Logger
+import io.viash.functionality.resources.{BashScript, PlainFile}
+
+class MainScriptTest extends AnyFunSuite {
+  Logger.UseColorOverride.value = Some(false)
+
+  test("Single script") {
+    val resources = List(BashScript(path = Some("foo.sh")))
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isDefined)
+    assert(mainScript.get.path == Some("foo.sh"))
+    assert(additionalResources.isEmpty)
+  }
+
+  test("Multiple scripts") {
+    val resources = List(
+      BashScript(path = Some("foo.sh")),
+      BashScript(path = Some("bar.sh")),
+      BashScript(path = Some("baz.sh")),
+    )
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isDefined)
+    assert(mainScript.get.path == Some("foo.sh"))
+    assert(additionalResources.length == 2)
+  }
+
+  test("Single text file") {
+    val resources = List(PlainFile(path = Some("foo.txt")))
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isEmpty)
+    assert(additionalResources.length == 1)
+    assert(additionalResources.head.path == Some("foo.txt"))
+  }
+
+  test("Multiple text files") {
+    val resources = List(
+      PlainFile(path = Some("foo.txt")),
+      PlainFile(path = Some("bar.txt")),
+      PlainFile(path = Some("baz.txt")),
+    )
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isEmpty)
+    assert(additionalResources.length == 3)
+  }
+
+  test("Mixed Script and text files, first is script") {
+    val resources = List(
+      BashScript(path = Some("foo.sh")),
+      PlainFile(path = Some("bar.txt")),
+      BashScript(path = Some("baz.sh")),
+    )
+
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isDefined)
+    assert(mainScript.get.path == Some("foo.sh"))
+    assert(additionalResources.length == 2)
+  }
+
+  test("Mixed Script and text files, first is text file") {
+    val resources = List(
+      PlainFile(path = Some("foo.txt")),
+      BashScript(path = Some("bar.sh")),
+      PlainFile(path = Some("baz.txt")),
+    )
+
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isEmpty)
+    assert(additionalResources.length == 3)
+  }
+
+  test("No resources") {
+    val resources = List.empty
+    val fun = Functionality("fun", resources = resources)
+
+    val mainScript = fun.mainScript
+    val additionalResources = fun.additionalResources
+
+    assert(mainScript.isEmpty)
+    assert(additionalResources.isEmpty)
+  }
+}
\ No newline at end of file