Features/#277 create missing env file

CHANGELOG.md

@@ -24,6 +24,7 @@ Released on ...
 - TODO  (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN))
 
 ### Added
+- Quick fix for unresolved '.yaml' / '.yml' files (see [#277](https://github.com/JetBrains-Research/snakecharm/issues/277))
 - Color Settings Page (see [#431](https://github.com/JetBrains-Research/snakecharm/issues/431))
 - Inspection: highlights 'use rule' section which overrides several rules as one (see [#411](https://github.com/JetBrains-Research/snakecharm/issues/411))
 - Weak warnings for unused 'log' sections in 'use rule' (see [#414](https://github.com/JetBrains-Research/snakecharm/issues/414))

src/main/kotlin/com/jetbrains/snakecharm/SmkNotifier.kt

@@ -30,6 +30,22 @@ object SmkNotifier {
         }).notify(module.project)
     }
 
+    fun notifyImpossibleToCreateFileOrDirectory(name: String, project: Project){
+        NotificationGroupManager.getInstance().getNotificationGroup(NOTIFICATION_GROUP_ID).createNotification(
+            title = SnakemakeBundle.message("notifier.msg.create.env.file.title"),
+            content = SnakemakeBundle.message("notifier.msg.create.env.file.io.exception", name),
+            type = NotificationType.ERROR
+        ).notify(project)
+    }
+
+    fun notifyTargetFileIsInvalid(name: String, project: Project) {
+        NotificationGroupManager.getInstance().getNotificationGroup(NOTIFICATION_GROUP_ID).createNotification(
+            title = SnakemakeBundle.message("notifier.msg.create.env.file.title"),
+            content = SnakemakeBundle.message("notifier.msg.create.env.file.invalid.file.exception", name),
+            type = NotificationType.ERROR
+        ).notify(project)
+    }
+
     fun notify(content: String, type: NotificationType = NotificationType.INFORMATION, project: Project? = null) =
         NotificationGroupManager.getInstance().getNotificationGroup(NOTIFICATION_GROUP_ID)
             .createNotification(content, type).also {

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

@@ -0,0 +1,19 @@
+package com.jetbrains.snakecharm.inspections
+
+import com.intellij.codeInspection.LocalQuickFix
+import com.intellij.psi.*
+import com.jetbrains.python.inspections.PyUnresolvedReferenceQuickFixProvider
+import com.jetbrains.snakecharm.inspections.quickfix.CreateEnvFile
+import com.jetbrains.snakecharm.lang.SnakemakeNames
+import com.jetbrains.snakecharm.lang.psi.SmkFileReference
+import com.jetbrains.snakecharm.lang.psi.SmkRuleOrCheckpointArgsSection
+
+class SmkUnresolvedReferenceInspectionExtension : PyUnresolvedReferenceQuickFixProvider {
+    override fun registerQuickFixes(reference: PsiReference, existing: MutableList<LocalQuickFix>) {
+        val sec = reference.element as? SmkRuleOrCheckpointArgsSection ?: return
+        if (sec.sectionKeyword == SnakemakeNames.SECTION_CONDA) {
+            val name = (sec.reference as? SmkFileReference)?.getReferencePath() ?: return
+            existing.add(CreateEnvFile(sec, name))
+        }
+    }
+}

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

@@ -0,0 +1,50 @@
+package com.jetbrains.snakecharm.inspections.quickfix
+
+import com.intellij.codeInspection.LocalQuickFixOnPsiElement
+import com.intellij.openapi.project.Project
+import com.intellij.openapi.vfs.InvalidVirtualFileAccessException
+import com.intellij.psi.PsiDocumentManager
+import com.intellij.psi.PsiElement
+import com.intellij.psi.PsiFile
+import com.intellij.psi.PsiManager
+import com.jetbrains.snakecharm.SmkNotifier
+import com.jetbrains.snakecharm.SnakemakeBundle
+import java.io.IOException
+
+class CreateEnvFile(expr: PsiElement, private val fileName: String) : LocalQuickFixOnPsiElement(expr) {
+    private val defaultContext = """
+        channels:
+        dependencies:
+    """.trimIndent()
+
+    override fun getFamilyName() = SnakemakeBundle.message("INSP.NAME.conda.env.missing.fix", fileName)
+
+    override fun getText() = familyName
+
+    override fun invoke(project: Project, file: PsiFile, startElement: PsiElement, endElement: PsiElement) {
+        val tokens = fileName.split('/')
+        val targetName = tokens.lastOrNull() ?: return
+        var currentFile = file.virtualFile.parent
+        try {
+            tokens.forEach {
+                if (it == targetName) {
+                    val resultVirtualFile = currentFile.createChildData(this, targetName)
+                    val resultPsiFile = PsiManager.getInstance(project).findFile(resultVirtualFile) ?: return
+                    val doc = PsiDocumentManager.getInstance(project).getDocument(resultPsiFile) ?: return
+                    doc.insertString(0, defaultContext)
+                    return
+                }
+                currentFile = if (it == "..") {
+                    currentFile.parent ?: return
+                } else {
+                    currentFile.findChild(it) ?: currentFile.createChildDirectory(this, it)
+                }
+            }
+        } catch (e: InvalidVirtualFileAccessException) {
+            SmkNotifier.notifyTargetFileIsInvalid(currentFile.name, project)
+        } catch (e: IOException) {
+            SmkNotifier.notifyImpossibleToCreateFileOrDirectory(currentFile.name, project)
+        }
+    }
+
+}

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

@@ -158,6 +158,8 @@ open class SmkFileReference(
         }
 
     override fun getUnresolvedDescription(): String? = null
+
+    fun getReferencePath() = path
 }
 
 /**

src/main/resources/META-INF/plugin.xml

@@ -633,5 +633,7 @@
     />
     <inspectionExtension
             implementation="com.jetbrains.snakecharm.inspections.SmkIgnorePyInspectionExtension"/>
+    <unresolvedReferenceQuickFixProvider
+            implementation="com.jetbrains.snakecharm.inspections.SmkUnresolvedReferenceInspectionExtension"/>
   </extensions>
 </idea-plugin>

src/main/resources/SnakemakeBundle.properties

@@ -89,6 +89,9 @@ INSP.NAME.wrapper.args.missed.message=Argument ''{0}'' missed in ''{1}''
 INSP.NAME.wrapper.args.section.missed.message=Section ''{0}'' is missed
 INSP.NAME.wrapper.args.section.with.args.missed.message=Section ''{0}'' with args ''{1}'' is missed
 
+# SmkUnresolvedReferenceInspectionExtension
+INSP.NAME.conda.env.missing.fix=Create ''{0}''
+
 # SmkSubworkflowRedeclarationInspection
 INSP.NAME.subworkflow.redeclaration=Only last subworkflow with the same name will be executed
 
@@ -253,6 +256,9 @@ notifier.group.title=SnakeCharm plugin notifications
 notifier.msg.framework.by.snakefile.title=Snakemake framework detected
 notifier.msg.framework.by.snakefile.action.configure=Configure Framework...
 notifier.msg.framework.by.snakefile=Snakefile was found in ''{0}''.
+notifier.msg.create.env.file.title=Impossible to create .yaml/.yml file
+notifier.msg.create.env.file.io.exception=Impossible to create ''{0}''. Check permissions and the target path correctness.
+notifier.msg.create.env.file.invalid.file.exception=One of path parts with name ''{0}'' was changed during its handling. Please try again later.
 
 #######################
 # Facet

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

@@ -0,0 +1,33 @@
+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 |