Features/#277 create missing env file

CHANGELOG.md

@@ -13,6 +13,7 @@ Released on ...
 - TODO  (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN)) 
 
 ### Added
+- Quick fix for unresolved files (conda, configfile. etc.)(see [#277](https://github.com/JetBrains-Research/snakecharm/issues/277))
 - TODO  (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN)) 
 
 ## [2021.3.661]

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 +1,24 @@
+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.CreateMissedFile
+import com.jetbrains.snakecharm.lang.psi.SmkArgsSection
+import com.jetbrains.snakecharm.lang.psi.SmkFileReference
+
+class SmkUnresolvedReferenceInspectionExtension : PyUnresolvedReferenceQuickFixProvider {
+
+    override fun registerQuickFixes(reference: PsiReference, existing: MutableList<LocalQuickFix>) {
+        val section = reference.element as? SmkArgsSection ?: return
+        val sectionName = section.sectionKeyword ?: return
+        if (CreateMissedFile.supportedSections.containsKey(sectionName)) {
+            val fileReference = (section.reference as? SmkFileReference) ?: return
+            if (!fileReference.hasAppropriateSuffix()) {
+                return
+            }
+            val name = fileReference.path
+            existing.add(CreateMissedFile(section, name, sectionName, fileReference.searchRelativelyToCurrentFolder))
+        }
+    }
+}

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

@@ -0,0 +1,120 @@
+package com.jetbrains.snakecharm.inspections.quickfix
+
+import com.intellij.codeInspection.LocalQuickFixAndIntentionActionOnPsiElement
+import com.intellij.openapi.application.ApplicationManager
+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
+import com.intellij.psi.PsiElement
+import com.intellij.psi.PsiFile
+import com.jetbrains.snakecharm.SmkNotifier
+import com.jetbrains.snakecharm.SnakemakeBundle
+import com.jetbrains.snakecharm.lang.SnakemakeNames
+import org.apache.commons.io.FileUtils
+import java.io.IOException
+import java.nio.file.Files
+import java.nio.file.Paths
+import kotlin.io.path.isDirectory
+import kotlin.io.path.name
+import kotlin.io.path.notExists
+
+class CreateMissedFile(
+    element: PsiElement,
+    private val fileName: String,
+    private val sectionName: String,
+    private val searchRelativelyToCurrentFolder: Boolean
+) : LocalQuickFixAndIntentionActionOnPsiElement(element) {
+    companion object {
+        private val condaDefaultContext = """
+        channels:
+        dependencies:
+    """.trimIndent()
+
+        // Update it if wee need default text
+        val supportedSections = mapOf(
+            SnakemakeNames.SECTION_CONDA to condaDefaultContext,
+            SnakemakeNames.SECTION_NOTEBOOK to null,
+            SnakemakeNames.SECTION_SCRIPT to null,
+            SnakemakeNames.MODULE_SNAKEFILE_KEYWORD to null,
+
+            SnakemakeNames.WORKFLOW_CONFIGFILE_KEYWORD to null,
+            SnakemakeNames.WORKFLOW_PEPFILE_KEYWORD to null,
+            SnakemakeNames.WORKFLOW_PEPSCHEMA_KEYWORD to null
+        )
+    }
+
+    override fun getFamilyName() = SnakemakeBundle.message("INSP.NAME.conda.env.missing.fix", fileName)
+
+    override fun getText() = familyName
+
+    override fun invoke(
+        project: Project,
+        file: PsiFile,
+        editor: Editor?,
+        startElement: PsiElement,
+        endElement: PsiElement
+    ) {
+        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
+        }
+
+        val undo = Runnable {
+            firstAffectedFile ?: return@Runnable
+            if (firstAffectedFile.isDirectory()) {
+                FileUtils.deleteDirectory(firstAffectedFile.toFile())
+            } else {
+                Files.delete(firstAffectedFile)
+            }
+            VirtualFileManager.getInstance().asyncRefresh { }
+        }
+        val redo = Runnable {
+            if (!supportedSections.containsKey(sectionName)) {
+                return@Runnable
+            }
+            try {
+                val directoryPath = Files.createDirectories(targetFilePath.parent)
+                val directoryVirtualFile = VfsUtil.findFile(directoryPath, true) ?: return@Runnable
+                LocalFileSystem.getInstance().createChildFile(this, directoryVirtualFile, targetFilePath.name)
+                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)
+                    targetFilePath.toFile().appendText(context)
+                }
+            } catch (e: SecurityException) {
+                SmkNotifier.notifyTargetFileIsInvalid(fileName, project)
+            } catch (e: IOException) {
+                SmkNotifier.notifyImpossibleToCreateFileOrDirectory(fileName, project)
+            }
+        }
+        val action = object : UndoableAction {
+            override fun undo() {
+                // invoke later because changing document inside undo/redo is not allowed (see ChangeFileEncodingAction)
+                ApplicationManager.getApplication().invokeLater(undo, ModalityState.NON_MODAL, project.disposed)
+            }
+
+            override fun redo() {
+                // invoke later because changing document inside undo/redo is not allowed (see ChangeFileEncodingAction)
+                ApplicationManager.getApplication().invokeLater(redo, ModalityState.NON_MODAL, project.disposed)
+            }
+
+            override fun getAffectedDocuments(): Array<DocumentReference> =
+                arrayOf(DocumentReferenceManager.getInstance().create(file.virtualFile))
+
+            override fun isGlobal() = true
+        }
+        action.redo()
+        UndoManager.getInstance(project).undoableActionPerformed(action)
+    }
+}

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

@@ -24,8 +24,8 @@ open class SmkFileReference(
     element: SmkArgsSection,
     private val textRange: TextRange,
     private val stringLiteralExpression: PyStringLiteralExpression,
-    private val path: String,
-    private val searchRelativelyToCurrentFolder: Boolean = true,
+    val path: String,
+    val searchRelativelyToCurrentFolder: Boolean = true,
 ) : PsiReferenceBase<SmkArgsSection>(element, textRange), PsiReferenceEx {
     // Reference caching can be implemented with the 'ResolveCache' class if needed
 
@@ -158,6 +158,8 @@ open class SmkFileReference(
         }
 
     override fun getUnresolvedDescription(): String? = null
+
+    open fun hasAppropriateSuffix(): Boolean = false
 }
 
 /**
@@ -173,6 +175,9 @@ class SmkIncludeReference(
     override fun getVariants() = collectFileSystemItemLike {
         it is SmkFile && it.originalFile != element.containingFile.originalFile
     }
+
+    override fun hasAppropriateSuffix() =
+        (path.endsWith(".smk") || path == "Snakemake") && element.containingFile.virtualFile.path != path
 }
 
 /**
@@ -193,8 +198,10 @@ class SmkConfigfileReference(
     searchRelativelyToCurrentFolder = false
 ) {
     override fun getVariants() = collectFileSystemItemLike {
-        isYamlFile(it)
+        isYamlFile(it.name)
     }
+
+    override fun hasAppropriateSuffix() = isYamlFile(path)
 }
 
 /**
@@ -215,8 +222,10 @@ class SmkPepfileReference(
     searchRelativelyToCurrentFolder = false
 ) {
     override fun getVariants() = collectFileSystemItemLike {
-        isYamlFile(it)
+        isYamlFile(it.name)
     }
+
+    override fun hasAppropriateSuffix() = isYamlFile(path)
 }
 
 /**
@@ -230,8 +239,10 @@ class SmkPepschemaReference(
     path: String
 ) : SmkFileReference(element, textRange, stringLiteralExpression, path) {
     override fun getVariants() = collectFileSystemItemLike {
-        isYamlFile(it)
+        isYamlFile(it.name)
     }
+
+    override fun hasAppropriateSuffix() = isYamlFile(path)
 }
 
 /**
@@ -245,11 +256,13 @@ class SmkCondaEnvReference(
     path: String
 ) : SmkFileReference(element, textRange, stringLiteralExpression, path) {
     override fun getVariants() = collectFileSystemItemLike {
-        isYamlFile(it)
+        isYamlFile(it.name)
     }
+
+    override fun hasAppropriateSuffix() = isYamlFile(path.lowercase())
 }
 
-private fun isYamlFile(it: PsiFileSystemItem) = it.name.endsWith(".yaml") || it.name.endsWith(".yml")
+private fun isYamlFile(it: String) = it.endsWith(".yaml") || it.endsWith(".yml")
 
 /**
  * The path must built from directory with current snakefile
@@ -265,6 +278,8 @@ class SmkNotebookReference(
         val name = it.name.lowercase()
         name.endsWith(".ipynb")
     }
+
+    override fun hasAppropriateSuffix() = path.endsWith(".ipynb")
 }
 
 /**
@@ -279,8 +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() = 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")
 }
 
 /**
@@ -296,6 +316,8 @@ class SmkReportReference(
     override fun getVariants() = collectFileSystemItemLike {
         it.name.endsWith(".html")
     }
+
+    override fun hasAppropriateSuffix() = path.endsWith(".html")
 }
 
 /**

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

@@ -632,5 +632,7 @@
     />
     <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
 
@@ -259,6 +262,9 @@ 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=Failed to create file
+notifier.msg.create.env.file.io.exception=Failed to create ''{0}''. Check permissions and the target path correctness.
+notifier.msg.create.env.file.invalid.file.exception=One of the parts of ''{0}'' was changed during its handling. Please try again later.
 
 #######################
 # Facet

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

@@ -0,0 +1,34 @@
+Feature: Inspection: SmkUnresolvedReferenceInspectionExtension
+
+  Scenario Outline: Quick fix fot missed files
+    Given a snakemake project
+    Given I open a file "foo.smk" with text
+     """
+     <section>: "<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:
+     """
+     <section>: "<path>"
+     """
+    Examples:
+      | 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 ..."