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Dmitry
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New index for inherited rules was created. Behaviour of creating gutter icons in case of overridden rules was changed. Corresponding tests were extended.
Resolves: #462, #463, #429
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11 files changed

+208
-31
lines changed

11 files changed

+208
-31
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‎CHANGELOG.md

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Original file line numberDiff line numberDiff line change
@@ -10,6 +10,7 @@ Released on ...
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- TODO (see [#NNN](https://github.com/JetBrains-Research/snakecharm/issues/NNN))
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### Fixed
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- Complex cases in creation of gutter icons for rule inheritance (see [#462](https://github.com/JetBrains-Research/snakecharm/issues/462), [#463](https://github.com/JetBrains-Research/snakecharm/issues/463))
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- Resolve for rule names in `use rule` section (see [#455](https://github.com/JetBrains-Research/snakecharm/issues/455))
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- Multiple args inspection in `workdir` case (see [#140](https://github.com/JetBrains-Research/snakecharm/issues/140))
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- `localrules` and `ruleorder` now take into account `use rule` (see [#448](https://github.com/JetBrains-Research/snakecharm/issues/448))

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

Lines changed: 22 additions & 21 deletions
Original file line numberDiff line numberDiff line change
@@ -9,7 +9,8 @@ import com.intellij.psi.PsiElement
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import com.intellij.psi.search.GlobalSearchScope
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import com.intellij.psi.stubs.StubIndex
1111
import com.jetbrains.snakecharm.lang.psi.*
12-
import com.jetbrains.snakecharm.lang.psi.stubs.SmkModuleNameIndex.Companion.KEY
12+
import com.jetbrains.snakecharm.lang.psi.stubs.SmkUseInheritedRulesIndex
13+
import com.jetbrains.snakecharm.lang.psi.stubs.SmkUseInheritedRulesIndex.Companion.INHERITED_RULES_DECLARATION_VIA_WILDCARD
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1415
class SnakemakeRuleInheritanceMarkerProvider : RelatedItemLineMarkerProvider() {
1516

@@ -51,32 +52,32 @@ class SnakemakeRuleInheritanceMarkerProvider : RelatedItemLineMarkerProvider() {
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element: SmkRuleOrCheckpoint,
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result: MutableCollection<in RelatedItemLineMarkerInfo<*>>
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) {
54-
val currentFile = element.containingFile
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val identifier = when (val identifier = element.nameIdentifier) {
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is SmkUseNameIdentifier -> identifier.getNameBeforeWildcard()
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else -> identifier
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} ?: return
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val modulesFromStub = StubIndex.getInstance().getAllKeys(KEY, element.project)
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val module = element.let { ModuleUtilCore.findModuleForPsiElement(it.originalElement) } ?: return
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val files = mutableSetOf<SmkFile>()
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for (smkModule in modulesFromStub) {
63-
files.addAll(StubIndex.getElements(
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KEY,
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smkModule,
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module.project,
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GlobalSearchScope.moduleWithDependentsScope(module),
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SmkModule::class.java
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).mapNotNull { it.containingFile as? SmkFile })
70-
}
71-
if (currentFile is SmkFile) {
72-
files.add(currentFile)
73-
}
60+
val descendantsDefinedExplicitly = StubIndex.getElements(
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SmkUseInheritedRulesIndex.KEY,
62+
identifier.text,
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module.project,
64+
GlobalSearchScope.moduleWithDependentsScope(module),
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SmkUse::class.java
66+
)
67+
val potentialDescendants = StubIndex.getElements(
68+
SmkUseInheritedRulesIndex.KEY,
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INHERITED_RULES_DECLARATION_VIA_WILDCARD,
70+
module.project,
71+
GlobalSearchScope.moduleWithDependentsScope(module),
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SmkUse::class.java
73+
)
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val overrides = mutableListOf<SmkRuleOrCheckpoint>()
75-
files.forEach { file ->
76-
file.collectUses().forEach { (_, psi) ->
77-
if (psi.getImportedRules()?.firstOrNull { it == element } != null) {
78-
overrides.add(psi)
79-
}
75+
(descendantsDefinedExplicitly + potentialDescendants).forEach { descendant ->
76+
// We don't save it in stub because it requires 'resolve'
77+
// We compare resolve results even for descendantsDefinedExplicitly
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// Because there may be rules with the same names
79+
if (descendant.getImportedRules()?.contains(element) == true) {
80+
overrides.add(descendant)
8081
}
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}
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if (overrides.isEmpty()) {

‎src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/refs/SmkRuleOrCheckpointNameReference.kt

Lines changed: 7 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -61,12 +61,18 @@ class SmkRuleOrCheckpointNameReference(
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return results
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}
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val allImportedFiles = smkFile.collectIncludedFiles()
64+
val potentialModule = moduleRef?.reference?.resolve() as? SmkModule
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return results.filter { resolveResult ->
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// If we resolve module references, there must be only SmkModules
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(resolveResult.element is SmkModule && itIsModuleMameReference) ||
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// We don't want to suggest local resolve result for the reference of rule, which was imported
6869
(moduleRef != null // Module name reference is defined and resolve result is from another file
69-
&& element.containingFile.originalFile != resolveResult.element?.containingFile?.originalFile)
70+
&& element.containingFile.originalFile != resolveResult.element?.containingFile?.originalFile
71+
// Also, because of using indexes, we need to check if the resolve result file
72+
// Connected to the file, which was declared in moduleRef, via 'include' or 'module'
73+
// Later, allImportedFiles will be stored in cache
74+
&& resolveResult.element?.containingFile?.originalFile in ((potentialModule?.getPsiFile() as? SmkFile)?.collectIncludedFiles()
75+
?: listOf()))
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// OR There are no 'from *name*' combination, so it hasn't been imported
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|| (moduleRef == null && resolveResult.element?.containingFile?.originalFile in allImportedFiles)
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}.toMutableList()

‎src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/stubs/SmkRuleDescendantElementType.kt

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Original file line numberDiff line numberDiff line change
@@ -0,0 +1,48 @@
1+
package com.jetbrains.snakecharm.lang.psi.impl.stubs
2+
3+
import com.intellij.psi.stubs.*
4+
import com.jetbrains.python.psi.PyElement
5+
import com.jetbrains.python.psi.PyStubElementType
6+
import com.jetbrains.snakecharm.lang.psi.SmkRuleLike
7+
import com.jetbrains.snakecharm.lang.psi.stubs.RuleDescendantStub
8+
import com.jetbrains.snakecharm.lang.psi.stubs.SmkUseInheritedRulesIndex
9+
10+
abstract class SmkRuleDescendantElementType<StubT : RuleDescendantStub<*>, PsiT : PyElement>(
11+
debugName: String,
12+
private val nameIndexKey: StubIndexKey<String, out SmkRuleLike<*>>?
13+
) :
14+
PyStubElementType<StubT, PsiT>(debugName) {
15+
abstract fun createStub(name: String?, inheritedRules: List<String?>, parentStub: StubElement<*>?): StubT
16+
17+
override fun serialize(stub: StubT, dataStream: StubOutputStream) {
18+
dataStream.writeName(stub.name)
19+
dataStream.writeInt(stub.getInheritedRulesNames().size)
20+
stub.getInheritedRulesNames().forEach { name ->
21+
dataStream.writeName(name)
22+
}
23+
}
24+
25+
override fun deserialize(dataStream: StubInputStream, parentStub: StubElement<*>?): StubT {
26+
val name = dataStream.readNameString()
27+
val size = dataStream.readInt()
28+
val inheritedRules = mutableListOf<String?>()
29+
for (x in 0 until size) {
30+
inheritedRules.add(dataStream.readNameString())
31+
}
32+
return createStub(name, inheritedRules, parentStub)
33+
}
34+
35+
override fun indexStub(stub: StubT, sink: IndexSink) {
36+
if (nameIndexKey != null) {
37+
stub.name?.let { name ->
38+
sink.occurrence(nameIndexKey, name)
39+
}
40+
}
41+
stub.getInheritedRulesNames().forEach { inheritedName ->
42+
if (inheritedName != null) {
43+
sink.occurrence(SmkUseInheritedRulesIndex.KEY, inheritedName)
44+
}
45+
}
46+
super.indexStub(stub, sink)
47+
}
48+
}

‎src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/stubs/SmkRuleLikeStubImpl.kt

Lines changed: 13 additions & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -18,6 +18,16 @@ abstract class SmkRuleLikeStubImpl<StubT : NamedStub<PsiT>, PsiT>(
1818
override fun getName() = myName
1919
}
2020

21+
abstract class SmkRuleDescendantStubImpl<StubT : RuleDescendantStub<PsiT>, PsiT>(
22+
private val myName: String?,
23+
private val inheritedRulesNames: List<String?>,
24+
parent: StubElement<*>?,
25+
type: IStubElementType<StubT, PsiT>
26+
) : StubBase<PsiT>(parent, type), RuleDescendantStub<PsiT> where PsiT : PsiNamedElement, PsiT : PyElement {
27+
override fun getName() = myName
28+
override fun getInheritedRulesNames() = inheritedRulesNames
29+
}
30+
2131
class SmkCheckpointStubImpl(
2232
name: String?,
2333
parent: StubElement<*>?
@@ -42,5 +52,7 @@ class SmkModuleStubImpl(
4252

4353
class SmkUseStubImpl(
4454
name: String?,
55+
inheritedRulesNames: List<String?>,
4556
parent: StubElement<*>?
46-
) : SmkRuleLikeStubImpl<SmkUseStub, SmkUse>(name, parent, USE_DECLARATION_STATEMENT), SmkUseStub
57+
) : SmkRuleDescendantStubImpl<SmkUseStub, SmkUse>(name, inheritedRulesNames, parent, USE_DECLARATION_STATEMENT),
58+
SmkUseStub

‎src/main/kotlin/com/jetbrains/snakecharm/lang/psi/impl/stubs/SmkUseElementType.kt

Lines changed: 12 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -5,17 +5,25 @@ import com.intellij.psi.PsiElement
55
import com.intellij.psi.stubs.StubElement
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import com.jetbrains.snakecharm.lang.psi.SmkUse
77
import com.jetbrains.snakecharm.lang.psi.impl.SmkUseImpl
8+
import com.jetbrains.snakecharm.lang.psi.stubs.SmkUseInheritedRulesIndex.Companion.INHERITED_RULES_DECLARATION_VIA_WILDCARD
89
import com.jetbrains.snakecharm.lang.psi.stubs.SmkUseNameIndex.Companion.KEY
910
import com.jetbrains.snakecharm.lang.psi.stubs.SmkUseStub
1011

1112
class SmkUseElementType
12-
: SmkRuleLikeElementType<SmkUseStub, SmkUse>("SMK_USE_DECLARATION_STATEMENT", KEY) {
13+
: SmkRuleDescendantElementType<SmkUseStub, SmkUse>("SMK_USE_DECLARATION_STATEMENT", KEY) {
1314

14-
override fun createStub(name: String?, parentStub: StubElement<*>?): SmkUseStub =
15-
SmkUseStubImpl(name, parentStub)
15+
lateinit var psi: SmkUse
16+
17+
override fun createStub(name: String?, inheritedRules: List<String?>, parentStub: StubElement<*>?) =
18+
SmkUseStubImpl(name, inheritedRules, parentStub)
1619

1720
override fun createStub(psi: SmkUse, parentStub: StubElement<out PsiElement>?): SmkUseStub =
18-
createStub(psi.name, parentStub)
21+
createStub(
22+
psi.name,
23+
psi.getDefinedReferencesOfImportedRuleNames()?.map { it.text } ?: listOf(
24+
INHERITED_RULES_DECLARATION_VIA_WILDCARD
25+
),
26+
parentStub).also { this.psi = psi }
1927

2028
override fun createPsi(stub: SmkUseStub): SmkUse = SmkUseImpl(stub)
2129

‎src/main/kotlin/com/jetbrains/snakecharm/lang/psi/stubs/RuleDescendantStub.kt

Lines changed: 11 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,11 @@
1+
package com.jetbrains.snakecharm.lang.psi.stubs
2+
3+
import com.intellij.psi.PsiNamedElement
4+
import com.intellij.psi.stubs.NamedStub
5+
6+
/**
7+
* Stub of rule like element which inherits at least one rule
8+
*/
9+
interface RuleDescendantStub<T : PsiNamedElement> : NamedStub<T> {
10+
fun getInheritedRulesNames(): List<String?>
11+
}

‎src/main/kotlin/com/jetbrains/snakecharm/lang/psi/stubs/SmkStubs.kt

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -7,4 +7,4 @@ interface SmkRuleStub : NamedStub<SmkRule>
77
interface SmkCheckpointStub : NamedStub<SmkCheckPoint>
88
interface SmkSubworkflowStub : NamedStub<SmkSubworkflow>
99
interface SmkModuleStub : NamedStub<SmkModule>
10-
interface SmkUseStub : NamedStub<SmkUse>
10+
interface SmkUseStub : RuleDescendantStub<SmkUse>

‎src/main/kotlin/com/jetbrains/snakecharm/lang/psi/stubs/SmkUseInheritedRulesIndex.kt

Lines changed: 16 additions & 0 deletions
Original file line numberDiff line numberDiff line change
@@ -0,0 +1,16 @@
1+
package com.jetbrains.snakecharm.lang.psi.stubs
2+
3+
import com.intellij.psi.stubs.StringStubIndexExtension
4+
import com.intellij.psi.stubs.StubIndexKey
5+
import com.jetbrains.snakecharm.lang.psi.SmkUse
6+
7+
class SmkUseInheritedRulesIndex :
8+
StringStubIndexExtension<SmkUse>() {
9+
override fun getKey() = KEY
10+
11+
companion object {
12+
const val INHERITED_RULES_DECLARATION_VIA_WILDCARD = "*"
13+
14+
val KEY = StubIndexKey.createIndexKey<String, SmkUse>("Smk.use.inheritedRules")
15+
}
16+
}

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

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Original file line numberDiff line numberDiff line change
@@ -94,6 +94,7 @@
9494
<lang.documentationProvider language="Snakemake" implementationClass="com.jetbrains.snakecharm.lang.documentation.SmkWrapperDocumentation"/>
9595
<lang.psiStructureViewFactory language="Snakemake" implementationClass="com.jetbrains.snakecharm.lang.structureView.SmkStructureViewFactory"/>
9696
<stubIndex implementation="com.jetbrains.snakecharm.lang.psi.stubs.SmkRuleNameIndex"/>
97+
<stubIndex implementation="com.jetbrains.snakecharm.lang.psi.stubs.SmkUseInheritedRulesIndex"/>
9798
<stubIndex implementation="com.jetbrains.snakecharm.lang.psi.stubs.SmkCheckpointNameIndex"/>
9899
<stubIndex implementation="com.jetbrains.snakecharm.lang.psi.stubs.SmkUseNameIndex"/>
99100
<stubIndex implementation="com.jetbrains.snakecharm.lang.psi.stubs.SmkModuleNameIndex"/>

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