Merge pull request #52 from sanctuuary/dev

Release 1.5.0

CHANGELOG.md

@@ -6,6 +6,24 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## [Unreleased]
 
+## [1.5.0] - 2021-12-20
+
+### Added
+
+- Clear buttons to clear all input data, output data, constraints on the explore page.
+- Domains can now be permanently deleted in the domain edit page.
+
+### Changed
+
+- Update back-end Kotlin version from 1.3.72 -> 1.6.0.
+- Update APE dependency version 1.1.9 -> 1.1.12 (includes log4j vulnerability fix).
+
+### Fixed
+
+- Remove "tab" as suggestion for separating data taxonomy roots as this also moves the user to the next input field. 
+- Some dependencies were updated to fix vulnerability issues.
+- When there are many inputs, outputs, or constraints on the explore page; a scrollbar will now appear inside the workflow input box to prevent the workflow result from appearing far below.
+
 ## [1.4.0] - 2021-11-06
 
 ### Added
@@ -157,6 +175,7 @@ This release is paired with the APE Web [DOI release](https://zenodo.org/badge/l
   * Approve user accounts.
 
 [Unreleased]: https://github.com/sanctuuary/APE-Web/compare/master...dev
+[1.5.0]: https://github.com/sanctuuary/APE-Web/compare/v1.4.0...v1.5.0
 [1.4.0]: https://github.com/sanctuuary/APE-Web/compare/v1.3.3...v1.4.0
 [1.3.3]: https://github.com/sanctuuary/APE-Web/compare/v1.3.2...v1.3.3
 [1.3.2]: https://github.com/sanctuuary/APE-Web/compare/v1.3.1...v1.3.2

back-end/Dockerfile

@@ -6,4 +6,4 @@ COPY pom.xml /app
 RUN mvn compile
 COPY . /app
 RUN mvn package -DskipTests=true -P docker
-ENTRYPOINT ["java", "-jar", "target/backend-1.4.0.jar"]
+ENTRYPOINT ["java", "-jar", "target/backend-1.5.0.jar"]

back-end/pom.xml

@@ -10,13 +10,13 @@
     </parent>
     <groupId>com.apexdevs</groupId>
     <artifactId>backend</artifactId>
-    <version>1.4.0</version>
+    <version>1.5.0</version>
     <name>backend</name>
     <description>APE Web back-end</description>
 
     <properties>
         <java.version>11</java.version>
-        <kotlin.version>1.3.72</kotlin.version>
+        <kotlin.version>1.6.0</kotlin.version>
         <orchid.version>0.21.0</orchid.version>
     </properties>
 
@@ -46,7 +46,7 @@
 		<dependency>
 			<groupId>io.github.sanctuuary</groupId>
 			<artifactId>APE</artifactId>
-			<version>1.1.9</version>
+			<version>1.1.12</version>
 			<exclusions>
 				<exclusion>
 					<groupId>ch.qos.logback</groupId>

back-end/src/main/kotlin/com/apexdevs/backend/ape/ApeRequest.kt

@@ -25,6 +25,7 @@ import nl.uu.cs.ape.sat.models.enums.SynthesisFlag
 import nl.uu.cs.ape.sat.models.logic.constructs.TaxonomyPredicate
 import java.io.ByteArrayOutputStream
 import java.nio.file.Path
+import java.util.Locale
 import javax.imageio.ImageIO
 
 /**
@@ -141,7 +142,11 @@ class ApeRequest(val domain: Domain, private val rootLocation: Path, val ape: AP
     /**
      * String extension to format taxonomy labels into a pretty printed label
      */
-    private fun String.formatLabel(): String = replace("_", " ").split(" ").joinToString(" ") { it.capitalize() }
+    private fun String.formatLabel(): String = replace("_", " ").split(" ").joinToString(" ") { it ->
+        it.replaceFirstChar {
+            if (it.isLowerCase()) it.titlecase(Locale.getDefault()) else it.toString()
+        }
+    }
 
     private fun String.removePrefixIRI(): String = replace(domain.ontologyPrefixIRI, "").replace("\"", "")
 

back-end/src/main/kotlin/com/apexdevs/backend/web/controller/api/ApiDomainController.kt

@@ -134,6 +134,54 @@ class ApiDomainController(
         }
     }
 
+    /**
+     * Allows the owner of a domain to permanently delete a domain.
+     * @param user authenticated user, automatically retrieved from session
+     * @param domainId The ID of the domain that should be deleted.
+     */
+    @ResponseStatus(HttpStatus.OK)
+    @PostMapping("/delete/{domainId}")
+    fun deleteDomain(@AuthenticationPrincipal user: User, @PathVariable domainId: ObjectId) {
+        try {
+            // find the current user in the database
+            val userResult = userOperation.getByEmail(user.username)
+
+            // check if the domain exists
+            val domain = domainOperation.getDomain(domainId)
+
+            // check if the user is the owner of the domain
+            val owner = domainOperation.getOwner(domainId)
+            if (owner.id != userResult.id)
+                throw AccessDeniedException("User is not the owner of this domain")
+
+            // delete the domain and related database entries
+            // delete access to the domain
+            val accessList = domainOperation.userDomainAccessRepository.findByDomainId(domainId)
+            for (access in accessList) {
+                domainOperation.userDomainAccessRepository.deleteById(access.id)
+            }
+            // delete the connections to topics
+            val domainTopics = domainOperation.domainTopicRepository.findByDomainId(domainId)
+            for (topic in domainTopics) {
+                domainOperation.domainTopicRepository.deleteById(topic.id)
+            }
+            // delete the domain itself
+            domainOperation.domainRepository.deleteById(domainId)
+            storageService.deleteDomainDirectories(domainId)
+        } catch (exc: Exception) {
+            when (exc) {
+                is UserNotFoundException ->
+                    throw ResponseStatusException(HttpStatus.UNAUTHORIZED, "Authorized user not found", exc)
+                is DomainNotFoundException ->
+                    throw ResponseStatusException(HttpStatus.BAD_REQUEST, exc.message, exc)
+                is AccessDeniedException ->
+                    throw ResponseStatusException(HttpStatus.UNAUTHORIZED, exc.message, exc)
+                else ->
+                    throw ResponseStatusException(HttpStatus.INTERNAL_SERVER_ERROR, exc.message, exc)
+            }
+        }
+    }
+
     /**
      * Downloads the toolsAnnotations file for the specified domain
      * @param user if the user needs to be authenticated for the domain

front-end/jest.config.js

@@ -30,11 +30,11 @@ module.exports = {
     "../styles/globals.less": "<rootDir>/config/jest/cssTransform.js",
     "package.json": "<rootDir>/config/jest/packageTransform.js",
     // Path aliases, same as in tsconfig.json
-    "@components(.*)$": "<rootDir>/src/components$1",
-    "@pages(.*)$": "<rootDir>/src/pages$1",
-    "@models(.*)$": "<rootDir>/src/models$1",
-    "@helpers(.*)$": "<rootDir>/src/helpers$1",
-    "@tests(.*)$": "<rootDir>/tests$1",
+    "@components/(.*)$": "<rootDir>/src/components/$1",
+    "@pages/(.*)$": "<rootDir>/src/pages/$1",
+    "@models/(.*)$": "<rootDir>/src/models/$1",
+    "@helpers/(.*)$": "<rootDir>/src/helpers/$1",
+    "@tests/(.*)$": "<rootDir>/tests/$1",
   },
   setupFiles: [
     "<rootDir>/node_modules/jest-fetch-mock/setupJest.js"