Bug fixes, new tests

Resolves: #433

src/main/java/com/jetbrains/snakecharm/framework/SmkConfigurationFilesConfigurable.java

@@ -65,7 +65,7 @@ private void initJPanel() {
         filesChooserDescriptor.setTitle(SnakemakeBundle.message("smk.framework.configurable.panel.configuration.files.file.chooser"));
         filesChooserDescriptor.withFileFilter(file -> {
             String path = file.getCanonicalPath();
-            return path != null && path.endsWith(".yaml");
+            return path != null && (path.endsWith(".yaml") || path.endsWith(".yml"));
         });
 
         var yamlFilesPanel = ToolbarDecorator.createDecorator(yamlFilesTable)
@@ -141,7 +141,7 @@ public boolean isModified() {
     @NotNull
     private SmkSupportProjectSettings.State getUIState() {
         SmkSupportProjectSettings.State state = SmkSupportProjectSettings.Companion.getInstance(project).stateSnapshot();
-        state.setConfigurationFiles(yamlFilesPaths.stream().distinct().collect(Collectors.toList()));
+        state.setConfigurationFiles(yamlFilesPaths);
         state.setExplicitlyDefinedKeyValuePairs(keyValuePairs.stream().distinct().collect(Collectors.toList()));
         return state;
     }
@@ -154,12 +154,17 @@ public void apply() throws ConfigurationException {
     @Override
     public void reset() {
         final SmkSupportProjectSettings conf = SmkSupportProjectSettings.Companion.getInstance(project);
-
+        // Here we create a new instances for FilePathState and KeyValuePairState
+        // Because we want to know, when settings state was changed
+        // Otherwise, if we use provided objects
+        // Old settings state and the new one will be the same
         yamlFilesPaths.clear();
-        yamlFilesPaths.addAll(conf.getConfigurationFiles());
+        yamlFilesPaths.addAll(conf.getConfigurationFiles().stream()
+                .map(it -> new SmkSupportProjectSettings.FilePathState(Objects.requireNonNull(it.getPath()), it.getEnabled())).collect(Collectors.toList()));
         ((AbstractTableModel) yamlFilesTable.getModel()).fireTableRowsInserted(0, yamlFilesPaths.size() - 1);
         keyValuePairs.clear();
-        keyValuePairs.addAll(conf.getExplicitlyDefinedKeyValuePairs());
+        keyValuePairs.addAll(conf.getExplicitlyDefinedKeyValuePairs().stream()
+                .map(it -> new SmkSupportProjectSettings.KeyValuePairState(Objects.requireNonNull(it.getKey()), Objects.requireNonNull(it.getValue()))).collect(Collectors.toList()));
         ((AbstractTableModel) keyValuePairsTable.getModel()).fireTableRowsInserted(0, keyValuePairs.size() - 1);
     }
 }

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/completion/yamlKeys/SmkYAMLKeysStorage.kt

@@ -24,10 +24,9 @@ import org.jetbrains.yaml.psi.*
 import java.io.File
 
 // TODO: Support JSON
-// TODO: disable unresolved reference inspection for predefined key-value pairs
 class SmkYAMLKeysStorage(val project: Project) : Disposable {
 
-    private var reversedYAMLFiles = mutableListOf<SmartPsiElementPointer<YAMLFile>>()
+    private var reversedYAMLFiles = mutableListOf<Pair<SmartPsiElementPointer<YAMLFile>, Boolean>>()
     private var definedPairs = mutableMapOf<String, String>()
 
     fun initOnStartup() {
@@ -56,6 +55,8 @@ class SmkYAMLKeysStorage(val project: Project) : Disposable {
         })
     }
 
+    fun keyWasDefinedInYAMLKeyValuePairs(key: String) = definedPairs.containsKey(key)
+
     /**
      * Returns top-level [YAMLKeyValue] by its name or null
      */
@@ -68,10 +69,10 @@ class SmkYAMLKeysStorage(val project: Project) : Disposable {
      */
     fun getTopLevelKeysVariants(file: SmkFile): List<String> {
         val result = mutableListOf<String>()
-        val allYamlFiles = reversedYAMLFiles.mapNotNull { it.element } + file.advancedCollectConfigFiles()
-            .mapNotNull { (it.reference?.resolve() as? YAMLFile) }
         result.addAll(definedPairs.keys)
-        result.addAll(allYamlFiles.map { YAMLUtil.getTopLevelKeys(it).map { yamlKeyValue -> yamlKeyValue.keyText } }
+        result.addAll(getYamlFilesForSmkFile(file).map {
+            YAMLUtil.getTopLevelKeys(it).map { yamlKeyValue -> yamlKeyValue.keyText }
+        }
             .flatten())
         return result
     }
@@ -85,7 +86,7 @@ class SmkYAMLKeysStorage(val project: Project) : Disposable {
         val targetPsi = resolveToOperandOrItsChild(file, path) ?: return emptyArray()
         // We don't provide completion for YAMLSequence
         // Because it receives indexes, not keys
-        return when (val variantsProvider = (targetPsi as? YAMLKeyValue)?.value ?: targetPsi) {
+        return when (val variantsProvider = SmkYAMLUtil.getValueOrParam(targetPsi)) {
             is YAMLMapping -> variantsProvider.keyValues.mapNotNull { it.keyText }.toTypedArray()
             else -> return emptyArray()
         }
@@ -179,7 +180,7 @@ class SmkYAMLKeysStorage(val project: Project) : Disposable {
                 if (file.enabled && path != null) {
                     val yamlFile = fileSystem.findFileByIoFile(File(path))?.toPsi(project) as? YAMLFile
                     if (yamlFile != null) {
-                        reversedYAMLFiles.add(pointerManager.createSmartPsiElementPointer(yamlFile))
+                        reversedYAMLFiles.add(pointerManager.createSmartPsiElementPointer(yamlFile) to file.enabled)
                     }
                 }
             }
@@ -206,7 +207,13 @@ class SmkYAMLKeysStorage(val project: Project) : Disposable {
      * Collects '.yaml' files that produce keys for specific [file]
      */
     private fun getYamlFilesForSmkFile(file: SmkFile) =
-        reversedYAMLFiles.mapNotNull { it.element } + file.advancedCollectConfigFiles()
+        reversedYAMLFiles.mapNotNull {
+            if (it.second) {
+                it.first.element
+            } else {
+                null
+            }
+        } + file.advancedCollectConfigFiles()
             .mapNotNull { it.reference?.resolve() as? YAMLFile }
 
     private fun subscribeOnEvents() {
@@ -237,6 +244,19 @@ class SmkYAMLKeysStorage(val project: Project) : Disposable {
         })
     }
 
+    /**
+     * Adds YAML file into storage if project runs in unit test mode
+     */
+    fun addFilesInTestMode(file: YAMLFile, enabled: Boolean) {
+        if (!ApplicationManager.getApplication().isUnitTestMode) {
+            throw IllegalStateException("Method 'addFilesInTestMode' is available only in unit test mode")
+        }
+
+        val pointerManager = SmartPointerManager.getInstance(project)
+
+        reversedYAMLFiles.add(pointerManager.createSmartPsiElementPointer(file) to enabled)
+    }
+
     override fun dispose() {
         // Same as in SmkWrapperStorage
     }

src/main/kotlin/com/jetbrains/snakecharm/codeInsight/completion/yamlKeys/SmkYAMLUtil.kt

@@ -11,7 +11,7 @@ class SmkYAMLUtil {
             for (node in path) {
                 // We're getting value here instead of getting it in 'is YAMLMapping'
                 // In order to return YAMLKeyValue and produce correct resolve
-                yamlPsiElement = (yamlPsiElement as? YAMLKeyValue)?.value ?: yamlPsiElement
+                yamlPsiElement = getValueOrParam(yamlPsiElement)
                 yamlPsiElement = when (yamlPsiElement) {
                     is YAMLMapping -> yamlPsiElement.keyValues.firstOrNull { it.key?.text == node }
                     is YAMLSequence -> {
@@ -24,5 +24,10 @@ class SmkYAMLUtil {
             }
             return yamlPsiElement
         }
+
+        fun getValueOrParam(yamlPsiElement: YAMLPsiElement?): YAMLPsiElement? {
+            val result = (yamlPsiElement as? YAMLKeyValue)?.value ?: yamlPsiElement
+            return (result as? YAMLAlias)?.reference?.resolve()?.markedValue ?: result
+        }
     }
 }

src/main/kotlin/com/jetbrains/snakecharm/framework/SmkFrameworkProjectSettings.kt

@@ -163,17 +163,6 @@ class SmkSupportProjectSettings(val project: Project) : PersistentStateComponent
             this.path = path
             this.enabled = enabled
         }
-
-        override fun equals(other: Any?): Boolean {
-            if (this === other) return true
-            if (javaClass != other?.javaClass) return false
-
-            other as FilePathState
-
-            return path == other.path
-        }
-
-        override fun hashCode() = path?.hashCode() ?: 0
     }
 
     class KeyValuePairState() : BaseState() {

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

@@ -1,5 +1,6 @@
 package com.jetbrains.snakecharm.inspections
 
+import com.intellij.openapi.components.service
 import com.intellij.openapi.vfs.impl.http.HttpVirtualFile
 import com.intellij.psi.PsiElement
 import com.intellij.psi.PsiReference
@@ -10,11 +11,15 @@ import com.jetbrains.python.psi.PyQualifiedExpression
 import com.jetbrains.python.psi.types.PyType
 import com.jetbrains.python.psi.types.TypeEvalContext
 import com.jetbrains.snakecharm.codeInsight.SnakemakeAPI
+import com.jetbrains.snakecharm.codeInsight.completion.yamlKeys.SmkYAMLKeysStorage
 import com.jetbrains.snakecharm.lang.psi.SmkModule
 import com.jetbrains.snakecharm.lang.psi.SmkRuleOrCheckpointArgsSection
 import com.jetbrains.snakecharm.lang.psi.SmkUse
 import com.jetbrains.snakecharm.lang.psi.impl.SmkPsiUtil
+import com.jetbrains.snakecharm.lang.psi.references.SmkSectionNameArgInPySubscriptionLikeReference
 import com.jetbrains.snakecharm.lang.psi.types.SmkAvailableForSubscriptionType
+import com.jetbrains.snakecharm.lang.psi.types.SmkConfigType
+import com.jetbrains.snakecharm.stringLanguage.lang.psi.references.SmkSLSubscriptionKeyReference
 
 /**
  * See also: [com.jetbrains.snakecharm.lang.highlighter.SnakemakeVisitorFilter]
@@ -38,6 +43,10 @@ class SmkIgnorePyInspectionExtension : PyInspectionExtension() {
             return false
         }
 
+        if(isDefinedYAMLKeyValuePair(reference)) {
+            return true
+        }
+
         val refElement = reference.element
 
         val use = node.parentOfType<SmkUse>()
@@ -62,6 +71,15 @@ class SmkIgnorePyInspectionExtension : PyInspectionExtension() {
         return false
     }
 
+    private fun isDefinedYAMLKeyValuePair(reference: PsiReference) : Boolean{
+        val type = (reference as? SmkSectionNameArgInPySubscriptionLikeReference)?.type ?: (reference as? SmkSLSubscriptionKeyReference)?.type
+        if (type !is SmkConfigType){
+            return false
+        }
+        val storage = reference.element.project.service<SmkYAMLKeysStorage>()
+        return storage.keyWasDefinedInYAMLKeyValuePairs(reference.canonicalText)
+    }
+
     // ignoreMissingDocstring
     // ignoreMethodParameters
     // getFunctionParametersFromUsage

src/main/kotlin/com/jetbrains/snakecharm/stringLanguage/lang/psi/SmkSLSubscriptionIndexKeyExpressionImpl.kt

@@ -47,5 +47,5 @@ class SmkSLSubscriptionIndexKeyExpressionImpl(node: ASTNode) : PyReferenceExpres
 
     override fun toString() = "SmkSLSubscriptionKeyExpression: [${this.referencedName}]"
 
-    override fun hasEmptyIndex() = text == "IntellijIdeaRulezzz "
+    override fun hasEmptyIndex() = text.endsWith("IntellijIdeaRulezzz ")
 }

src/test/kotlin/features/glue/StepDefs.kt

@@ -11,15 +11,18 @@ import com.intellij.testFramework.UsefulTestCase
 import com.intellij.testFramework.fixtures.IdeaTestFixtureFactory
 import com.intellij.testFramework.fixtures.InjectionTestFixture
 import com.intellij.testFramework.fixtures.impl.LightTempDirTestFixtureImpl
+import com.jetbrains.extensions.python.toPsi
 import com.jetbrains.python.PythonMockSdk
 import com.jetbrains.python.codeInsight.controlflow.ControlFlowCache
 import com.jetbrains.python.fixtures.PyLightProjectDescriptor
 import com.jetbrains.python.psi.PyFile
 import com.jetbrains.snakecharm.SnakemakeTestCase
 import com.jetbrains.snakecharm.SnakemakeTestUtil
+import com.jetbrains.snakecharm.codeInsight.completion.yamlKeys.SmkYAMLKeysStorage
 import com.jetbrains.snakecharm.framework.SmkSupportProjectSettings
-import com.jetbrains.snakecharm.inspections.SmkUnrecognizedSectionInspection
+import io.cucumber.datatable.DataTable
 import io.cucumber.java.en.Given
+import org.jetbrains.yaml.psi.YAMLFile
 import javax.swing.SwingUtilities
 import kotlin.test.fail
 
@@ -172,6 +175,42 @@ class StepDefs {
         waitEDTEventsDispatching()
     }
 
+    @Given("^add file \"(.+)\" as configuration file to settings panel and (enable|disable) file")
+    fun addConfigFile(file: String, mode: String) {
+        if (!file.endsWith(".yaml") && file.endsWith(".yml")) {
+            fail("File ends with '.yaml' or '.yml' was expected, but received: $file")
+        }
+
+        val enabled = when(mode) {
+            "enable" -> true
+            "disable" -> false
+            else -> fail("Unexpected configuration file mode: $mode")
+        }
+
+        ApplicationManager.getApplication().runReadAction {
+            val yamlFile = SnakemakeWorld.fixture().findFileInTempDir(file).toPsi(SnakemakeWorld.fixture().project) as YAMLFile
+            val storage = SnakemakeWorld.fixture().project.getService(SmkYAMLKeysStorage::class.java)
+            storage.addFilesInTestMode(yamlFile, enabled)
+        }
+    }
+
+    @Given("^add key-value pairs to settings panel")
+    fun addYAMLKeyValuePairs(table: DataTable) {
+        if (table.width() != 2) {
+            fail("Data table with two columns was expected, but received: ${table.width()}")
+        }
+        val project = SnakemakeWorld.fixture().project
+        val pairs = table.asLists().map { row -> SmkSupportProjectSettings.KeyValuePairState(row.component1(), row.component2()) }
+        val state = SmkSupportProjectSettings.getInstance(project).stateSnapshot()
+
+        state.explicitlyDefinedKeyValuePairs.addAll(pairs)
+        ApplicationManager.getApplication().invokeAndWait {
+            SmkSupportProjectSettings.updateStateAndFireEvent(project, state)
+        }
+
+        waitEDTEventsDispatching()
+    }
+
     @Given("^add snakemake framework support (with|without) wrappers loaded")
     fun withSnakemakeFacet(withWrappersStr: String) {
         val project = SnakemakeWorld.fixture().project