Fix in extension behaviour.

Resolved: #277

src/main/kotlin/com/jetbrains/snakecharm/inspections/SmkUnresolvedReferenceInspectionExtension.kt

@@ -18,7 +18,7 @@ class SmkUnresolvedReferenceInspectionExtension : PyUnresolvedReferenceQuickFixP
                 return
             }
             val name = fileReference.path
-            existing.add(CreateMissedFile(section, name, sectionName))
+            existing.add(CreateMissedFile(section, name, sectionName, fileReference.searchRelativelyToCurrentFolder))
         }
     }
 }

src/main/kotlin/com/jetbrains/snakecharm/inspections/quickfix/CreateMissedFile.kt

@@ -6,6 +6,7 @@ import com.intellij.openapi.application.ModalityState
 import com.intellij.openapi.command.undo.*
 import com.intellij.openapi.editor.Editor
 import com.intellij.openapi.project.Project
+import com.intellij.openapi.roots.ProjectRootManager
 import com.intellij.openapi.vfs.LocalFileSystem
 import com.intellij.openapi.vfs.VfsUtil
 import com.intellij.openapi.vfs.VirtualFileManager
@@ -26,6 +27,7 @@ class CreateMissedFile(
     element: PsiElement,
     private val fileName: String,
     private val sectionName: String,
+    private val searchRelativelyToCurrentFolder: Boolean
 ) : LocalQuickFixAndIntentionActionOnPsiElement(element) {
     companion object {
         private val condaDefaultContext = """
@@ -57,7 +59,11 @@ class CreateMissedFile(
         startElement: PsiElement,
         endElement: PsiElement
     ) {
-        val targetFilePath = Paths.get(file.virtualFile.parent.path, fileName)
+        val dir =
+            if (searchRelativelyToCurrentFolder) file.virtualFile.parent else ProjectRootManager.getInstance(project).fileIndex.getContentRootForFile(
+                file.virtualFile
+            ) ?: return
+        val targetFilePath = Paths.get(dir.path, fileName)
         var firstAffectedFile = targetFilePath
         while (firstAffectedFile.parent.notExists()) {
             firstAffectedFile = firstAffectedFile.parent ?: break
@@ -70,7 +76,7 @@ class CreateMissedFile(
             } else {
                 Files.delete(firstAffectedFile)
             }
-            VirtualFileManager.getInstance().syncRefresh()
+            VirtualFileManager.getInstance().asyncRefresh { }
         }
         val redo = Runnable {
             if (!supportedSections.containsKey(sectionName)) {
@@ -80,7 +86,7 @@ class CreateMissedFile(
                 val directoryPath = Files.createDirectories(targetFilePath.parent)
                 val directoryVirtualFile = VfsUtil.findFile(directoryPath, true) ?: return@Runnable
                 LocalFileSystem.getInstance().createChildFile(this, directoryVirtualFile, targetFilePath.name)
-                VirtualFileManager.getInstance().syncRefresh()
+                VirtualFileManager.getInstance().asyncRefresh { }
                 val context = supportedSections[sectionName]
                 if (context != null) {
                     // We don't use the result of 'createChildFile()' because it has inappropriate type (and throw UnsupportedOperationException)

src/main/kotlin/com/jetbrains/snakecharm/lang/psi/SmkFileReference.kt

@@ -25,7 +25,7 @@ open class SmkFileReference(
     private val textRange: TextRange,
     private val stringLiteralExpression: PyStringLiteralExpression,
     val path: String,
-    private val searchRelativelyToCurrentFolder: Boolean = true,
+    val searchRelativelyToCurrentFolder: Boolean = true,
 ) : PsiReferenceBase<SmkArgsSection>(element, textRange), PsiReferenceEx {
     // Reference caching can be implemented with the 'ResolveCache' class if needed
 
@@ -159,7 +159,7 @@ open class SmkFileReference(
 
     override fun getUnresolvedDescription(): String? = null
 
-    open fun hasAppropriateSuffix():Boolean = false
+    open fun hasAppropriateSuffix(): Boolean = false
 }
 
 /**
@@ -176,7 +176,8 @@ class SmkIncludeReference(
         it is SmkFile && it.originalFile != element.containingFile.originalFile
     }
 
-    override fun hasAppropriateSuffix() = (path.endsWith(".smk") || path == "Snakemake") && element.containingFile.virtualFile.path != path
+    override fun hasAppropriateSuffix() =
+        (path.endsWith(".smk") || path == "Snakemake") && element.containingFile.virtualFile.path != path
 }
 
 /**
@@ -277,6 +278,8 @@ class SmkNotebookReference(
         val name = it.name.lowercase()
         name.endsWith(".ipynb")
     }
+
+    override fun hasAppropriateSuffix() = path.endsWith(".ipynb")
 }
 
 /**
@@ -291,10 +294,13 @@ class SmkScriptReference(
 ) : SmkFileReference(element, textRange, stringLiteralExpression, path) {
     override fun getVariants() = collectFileSystemItemLike {
         val name = it.name.lowercase()
-        name.endsWith(".py") or name.endsWith(".r") or name.endsWith(".rmd") or name.endsWith(".jl") or name.endsWith(".rs")
+        hasCorrectEnding(name)
     }
 
-    override fun hasAppropriateSuffix() = path.endsWith(".ipynb")
+    override fun hasAppropriateSuffix() = hasCorrectEnding(path.lowercase())
+
+    private fun hasCorrectEnding(name: String) =
+        name.endsWith(".py") or name.endsWith(".r") or name.endsWith(".rmd") or name.endsWith(".jl") or name.endsWith(".rs")
 }
 
 /**

src/test/resources/features/highlighting/inspections/unresolved_reference_extension.feature

@@ -1,38 +1,6 @@
 Feature: Inspection: SmkUnresolvedReferenceInspectionExtension
-  Checks, that extension + inspection work
 
-  Scenario Outline: Unresolved conda file
-    Given a snakemake project
-    Given I open a file "foo.smk" with text
-     """
-     rule NAME:
-         conda:
-             "<path>"
-     """
-    And PyUnresolvedReferencesInspection inspection is enabled
-    Then I expect inspection error on <<path>> with message
-     """
-     Unresolved reference '<path>'
-     """
-    When I check highlighting warnings
-    And I invoke quick fix Create '<path>' and see text:
-     """
-     rule NAME:
-         conda:
-             "<path>"
-     """
-    Then the file "<path>" should have text
-     """
-     channels:
-     dependencies:
-     """
-    Examples:
-      | path              |
-      | NAME.yaml         |
-      | envs/NAME.yaml    |
-      | ../envs/NAME.yaml |
-
-  Scenario Outline: other unresolved sections
+  Scenario Outline: Quick fix fot missed files
     Given a snakemake project
     Given I open a file "foo.smk" with text
      """
@@ -49,10 +17,18 @@ Feature: Inspection: SmkUnresolvedReferenceInspectionExtension
      <section>: "<path>"
      """
     Examples:
-      | path          | section                |
-      | NAME.py.ipynb | rule NAME: notebook    |
-      | NAME.py       | rule NAME: script      |
-      | boo.smk       | module NAME: snakefile |
-      | NAME.yaml     | configfile             |
-      | NAME.yaml     | pepfile                |
-      | NAME.yml      | pepschema              |
+      | path              | section                |
+      | NAME.yaml         | rule NAME: conda       |
+      | envs/NAME.yaml    | rule NAME: conda       |
+      | ../envs/NAME.yaml | rule NAME: conda       |
+      | NAME.py.ipynb     | rule NAME: notebook    |
+      | NAME.py           | rule NAME: script      |
+      | boo.smk           | module NAME: snakefile |
+      | NAME.yaml         | configfile             |
+      | NAME.yaml         | pepfile                |
+      | NAME.yml          | pepschema              |
+
+    # Impossible to check whether the file has been created because:
+    # 1) It is being creating asynchronously
+    # 2) So, we may need async refresh() (see LightTempDirTestFixtureImpl.java:137)
+    # It leads to Exception: "Do not perform a synchronous refresh under read lock ..."