Merge branch 'main' of github.com:itcr-uni-luebeck/termite

Resolve conflicts after merge

Dockerfile

@@ -1,13 +1,13 @@
 # Build jar using Gradle
 FROM gradle:7.2.0-jdk17-alpine AS gradle_build
-COPY . /home/abide_validation/termite
-WORKDIR /home/abide_validation/termite
+COPY . /termite
+WORKDIR /termite
 # Create jar
-RUN gradle clean build bootJar --no-daemon
+RUN gradle clean build bootJar
 
 # Copy jar to new image for running terminology service
 FROM openjdk:17
-COPY --from=gradle_build /home/abide_validation/termite/build/libs/termite.jar /app/termite.jar
+COPY --from=gradle_build /termite/build/libs/termite.jar /app/termite.jar
 COPY /config/application.properties /app/config/application.properties
 COPY /config/log4j2.xml /app/config/log4j2.xml
 COPY upload.sh /app/upload.sh

build.gradle

@@ -8,7 +8,7 @@ plugins {
     id "org.jetbrains.kotlin.plugin.spring" version "2.0.0"
 }
 
-group 'org.example'
+group 'de.itcr'
 version '1.0-SNAPSHOT'
 
 repositories {
@@ -25,9 +25,17 @@ compileJava {
     targetCompatibility = "17"
 }
 
+sourceSets {
+    main {
+        java {
+            srcDir "src"
+        }
+    }
+}
+
 dependencies {
     //Kotlin
-    implementation "org.jetbrains.kotlin:kotlin-stdlib"
+    implementation "org.jetbrains.kotlin:kotlin-stdlib:2.0.0"
     implementation "org.jetbrains.kotlin:kotlin-reflect:2.0.0"
 
     //Spring Boot

docker/docker-compose.yaml

@@ -1,7 +1,6 @@
 services:
   termite:
-#    image: ghcr.io/itcr-uni-luebeck/termite:latest
-    image: termite
+    image: ghcr.io/itcr-uni-luebeck/termite:latest
     ports:
       - 9083:9083
     environment:
@@ -20,13 +19,14 @@ services:
     expose:
       - 5432
     environment:
+      - PGUSER=termite
       - POSTGRES_USER=termite
       - POSTGRES_PASSWORD=termite
       - POSTGRES_DB=termite
     volumes:
       - postgres-data:/var/lib/postgresql/data
     healthcheck:
-      test: [ "CMD-SHELL", "pg_isready", "-d", "termite" ]
+      test: [ "CMD-SHELL", "pg_isready", "-d", "termite", "-U", "${PGUSER}", "-q" ]
       interval: 10s
       timeout: 10s
       retries: 5

src/main/kotlin/de/itcr/termite/api/CodeSystemController.kt

@@ -1,6 +1,7 @@
 package de.itcr.termite.api
 
 import ca.uhn.fhir.context.FhirContext
+import de.itcr.termite.api.ValueSetController.Companion
 import de.itcr.termite.database.TerminologyStorage
 import de.itcr.termite.exception.NotFoundException
 import de.itcr.termite.metadata.annotation.*
@@ -18,15 +19,7 @@ import org.springframework.http.MediaType
 import org.springframework.http.RequestEntity
 import org.springframework.http.ResponseEntity
 import org.springframework.stereotype.Controller
-import org.springframework.web.bind.annotation.GetMapping
-import org.springframework.web.bind.annotation.PathVariable
-import org.springframework.web.bind.annotation.PostMapping
-import org.springframework.web.bind.annotation.PutMapping
-import org.springframework.web.bind.annotation.RequestBody
-import org.springframework.web.bind.annotation.RequestHeader
-import org.springframework.web.bind.annotation.RequestMapping
-import org.springframework.web.bind.annotation.RequestParam
-import org.springframework.web.bind.annotation.ResponseBody
+import org.springframework.web.bind.annotation.*
 import org.springframework.web.server.ResponseStatusException
 import java.net.URI
 import java.util.*
@@ -35,7 +28,7 @@ import java.util.*
     type = "CodeSystem",
     versioning = "no-version",
     readHistory = false,
-    updateCreate = false,
+    updateCreate = true,
     conditionalCreate = false,
     conditionalRead = "not-supported",
     conditionalUpdate = false,
@@ -48,10 +41,15 @@ import java.util.*
             name = "url",
             type = "uri",
             documentation = "URL of the resource to locate"
+        ),
+        SearchParameter(
+            name = "version",
+            type = "string",
+            documentation = "Version of the resource to locate"
         )
     ]
 )
-@SupportsInteraction(["create", "search-type"])
+@SupportsInteraction(["create", "search-type", "delete"])
 @SupportsOperation(
     name = "CodeSystem-lookup",
     title = "CodeSystem-lookup",
@@ -180,7 +178,7 @@ class CodeSystemController(
 
     @PutMapping(path = ["{id}"], consumes = ["application/json", "application/fhir+json", "application/xml", "application/fhir+xml", "application/fhir+ndjson", "application/ndjson"])
     @ResponseBody
-    fun conditionalCreate(requestEntity: RequestEntity<String>, @RequestHeader("Content-Type") contentType: String, @PathVariable(name = "id") id: String): ResponseEntity<String> {
+    fun updateCreate(requestEntity: RequestEntity<String>, @RequestHeader("Content-Type") contentType: String, @PathVariable(name = "id") id: String): ResponseEntity<String> {
         logger.info("Creating CodeSystem instance if not present")
         try {
             val cs = parseBodyAsResource(requestEntity, contentType)
@@ -353,19 +351,22 @@ class CodeSystemController(
         }
     }
 
-    @GetMapping(params = ["url"])
+    @GetMapping
     @ResponseBody
-    fun search(@RequestParam url: String): ResponseEntity<String>{
+    fun search(
+        @RequestParam url: String,
+        @RequestParam(required = false) version: String?
+    ): ResponseEntity<String>{
         logger.info("Searching for code system [url = $url]")
         try{
-            val csList = database.searchCodeSystem(url)
+            val csList = database.searchCodeSystem(url, version)
             val bundle = Bundle()
             bundle.id = UUID.randomUUID().toString()
             bundle.type = Bundle.BundleType.SEARCHSET
             bundle.total = csList.size
             //Should be faster since otherwise an internal array list would have to resized all the time
             bundle.entry = csList.map { cs -> Bundle.BundleEntryComponent().setResource(cs) }
-            logger.debug("Found ${csList.size} code systems for URL $url")
+            logger.debug("Found ${csList.size} CodeSystem instances for URL $url" + if (version != null) " and version $version" else "")
             return ResponseEntity.ok().contentType(MediaType.APPLICATION_JSON).body(jsonParser.encodeResourceToString(bundle))
         }
         catch (e: Exception){
@@ -384,4 +385,40 @@ class CodeSystemController(
         }
     }
 
+    @DeleteMapping("{id}")
+    @ResponseBody
+    fun delete(@PathVariable id: String): ResponseEntity<String> {
+        logger.info("Deleting CodeSystem instance [id = $id]")
+        try {
+            var opOutcome: String
+            try {
+                database.deleteCodeSystem(id)
+                opOutcome = generateOperationOutcomeString(
+                    OperationOutcome.IssueSeverity.INFORMATION,
+                    OperationOutcome.IssueType.INFORMATIONAL,
+                    "Successfully deleted CodeSystem instance [ID = $id]",
+                    jsonParser
+                )
+            }
+            catch (e: NotFoundException) {
+                opOutcome = generateOperationOutcomeString(
+                    OperationOutcome.IssueSeverity.INFORMATION,
+                    OperationOutcome.IssueType.INFORMATIONAL,
+                    "No CodeSystem instance with such an ID [ID = $id]",
+                    jsonParser
+                )
+            }
+            return ResponseEntity.ok().eTag("W/\"0\"").contentType(MediaType.APPLICATION_JSON).body(opOutcome)
+        }
+        catch (e: Exception) {
+            val opOutcome = generateOperationOutcomeString(
+                OperationOutcome.IssueSeverity.ERROR,
+                OperationOutcome.IssueType.PROCESSING,
+                e.message,
+                jsonParser
+            )
+            return ResponseEntity.internalServerError().contentType(MediaType.APPLICATION_JSON).body(opOutcome)
+        }
+    }
+
 }

src/main/kotlin/de/itcr/termite/api/ResourceController.kt

@@ -20,12 +20,17 @@ abstract class ResourceController(protected val database: TerminologyStorage, pr
         val ndjson = fhirContext.newNDJsonParser() to "ndjson"
         this.parsers = mapOf(
             "application/json" to json,
+            "application/json;charset=utf-8" to json,
             "application/fhir+json" to json,
-            "application/fhir+json; charset=UTF-8" to json,
+            "application/fhir+json;charset=utf-8" to json,
             "application/xml" to xml,
+            "application/xml;charset=utf-8" to xml,
             "application/fhir+xml" to xml,
+            "application/fhir+xml;charset=utf-8" to xml,
             "application/ndjson" to ndjson,
-            "application/fhir+ndjson" to ndjson
+            "application/ndjson;charset=utf-8" to ndjson,
+            "application/fhir+ndjson" to ndjson,
+            "application/fhir+ndjson;charset=utf-8" to ndjson
         )
     }
 
@@ -36,7 +41,7 @@ abstract class ResourceController(protected val database: TerminologyStorage, pr
      */
     protected fun parseBodyAsResource(requestEntity: RequestEntity<String>, contentType: String): IBaseResource {
         try{
-            val (parser, parserFormat) = parsers[contentType] ?: throw Exception("Unsupported content type: $contentType")
+            val (parser, parserFormat) = parsers[contentType.trim().lowercase().replace(" ", "")] ?: throw Exception("Unsupported content type: $contentType")
             try {
                 return parser.parseResource(requestEntity.body)
             } catch (e: DataFormatException) {

src/main/kotlin/de/itcr/termite/api/ValueSetController.kt

@@ -35,7 +35,7 @@ import kotlin.math.min
     type = "ValueSet",
     versioning = "no-version",
     readHistory = false,
-    updateCreate = false,
+    updateCreate = true,
     conditionalCreate = false,
     conditionalRead = "not-supported",
     conditionalUpdate = false,
@@ -48,10 +48,15 @@ import kotlin.math.min
             name = "url",
             type = "uri",
             documentation = "URL of the resource to locate"
+        ),
+        SearchParameter(
+            name = "version",
+            type = "string",
+            documentation = "Version of the resource to locate"
         )
     ]
 )
-@SupportsInteraction(["create", "search-type"])
+@SupportsInteraction(["create", "search-type", "delete"])
 @SupportsOperation(
     name = "ValueSet-lookup",
     title = "ValueSet-lookup",
@@ -217,7 +222,7 @@ class ValueSetController(
 
     @PutMapping(path = ["{id}"], consumes = ["application/json", "application/fhir+json", "application/xml", "application/fhir+xml", "application/fhir+ndjson", "application/ndjson"])
     @ResponseBody
-    fun conditionalCreate(requestEntity: RequestEntity<String>, @RequestHeader("Content-Type") contentType: String, @PathVariable(name = "id") id: String): ResponseEntity<String> {
+    fun updateCreate(requestEntity: RequestEntity<String>, @RequestHeader("Content-Type") contentType: String, @PathVariable(name = "id") id: String): ResponseEntity<String> {
         logger.info("Creating ValueSet instance if not present")
         try {
             val vs = parseBodyAsResource(requestEntity, contentType)
@@ -353,6 +358,42 @@ class ValueSetController(
         }
     }
 
+    @DeleteMapping("{id}")
+    @ResponseBody
+    fun delete(@PathVariable id: String): ResponseEntity<String> {
+        logger.info("Deleting ValueSet instance [id = $id]")
+        try {
+            var opOutcome: String
+            try {
+                database.deleteValueSet(id)
+                opOutcome = generateOperationOutcomeString(
+                    OperationOutcome.IssueSeverity.INFORMATION,
+                    OperationOutcome.IssueType.INFORMATIONAL,
+                    "Successfully deleted ValueSet instance [ID = $id]",
+                    jsonParser
+                )
+            }
+            catch (e: NotFoundException) {
+                opOutcome = generateOperationOutcomeString(
+                    OperationOutcome.IssueSeverity.INFORMATION,
+                    OperationOutcome.IssueType.INFORMATIONAL,
+                    "No ValueSet instance with such an ID [ID = $id]",
+                    jsonParser
+                )
+            }
+            return ResponseEntity.ok().eTag("W/\"0\"").contentType(MediaType.APPLICATION_JSON).body(opOutcome)
+        }
+        catch (e: Exception) {
+            val opOutcome = generateOperationOutcomeString(
+                OperationOutcome.IssueSeverity.ERROR,
+                OperationOutcome.IssueType.PROCESSING,
+                e.message,
+                jsonParser
+            )
+            return ResponseEntity.internalServerError().contentType(MediaType.APPLICATION_JSON).body(opOutcome)
+        }
+    }
+
     /**
      * Validates a code with respect to the given value set
      * @see <a href="http://www.hl7.org/FHIR/valueset-operation-validate-code.html">validate-code operation</a>

src/main/kotlin/de/itcr/termite/database/TerminologyStorage.kt

@@ -30,6 +30,12 @@ interface TerminologyStorage {
 
     fun readConceptMap(id: String): ConceptMap
 
+    fun deleteValueSet(id: String)
+
+    fun deleteCodeSystem(id: String)
+
+    fun deleteConceptMap(id: String)
+
     /**
      * Validates if the given code is in the given value set
      *
@@ -55,9 +61,9 @@ interface TerminologyStorage {
      */
     fun searchValueSet(url: String, version: String?): List<ValueSet>
 
-    fun searchCodeSystem(url: String): List<CodeSystem>
+    fun searchCodeSystem(url: String, version: String?): List<CodeSystem>
 
-    fun searchConceptMap(url: String): List<ConceptMap>
+    fun searchConceptMap(url: String, version: String?): List<ConceptMap>
 
     fun validateCodeCS(code: String, display: String?, url: String): Boolean