Release/v6.0.0 alpha.3 (#383)

* No issue - bump version * Bump sq2cql and ontology version * #288 - Load availability files from file(s) (#364) #288 - Load availability files from file(s) * Add Update availability script and example file * #367 - Sort unavailable criteria to the bottom - add a function score query that boosts all queries with availability > 0 by 100 in score. It does not make a difference if the availability is 10 or 10000, all are boosted by the same fixed value * #366 - Builtin swagger doc is broken - move files back to /v3/api-docs since swagger ui wants to load a config file from there anyways. Supplying a custom config file under another folder did not work - update springdoc-openapi-starter-webmvc-ui to 2.6.0 so it can handle openapi 3.1.0 * #370 - Update fhir-resources dependency - update to 6.3.26 * #371 - Update spring boot to 3.3.4 - self-explanatory * #363 - Add "results" to GET query/{queryId} response - Add the totalNumberOfPatients from the saved query object back to the response when reading a query - the demanded queryId from the issue is already present as "id" - so nothing to do here imho * #376 - Allow Empty Search with filters (#377) #376 - Allow Empty Search with filters - Change score modification to add an offset instead of multiplying when availability > 0 - remove the inner "must" part of the bool query when searchterm is empty * bump ontology version * No issue - update undertow to 2.3.17.Final to fix CVE-2024-7885 * #380 - Change structure of dse profile_tree and profile details for translations (#381) * #380 - Change structure of dse profile_tree and profile details for translations - update ontology to v3.0.0-test.11 - modify DseProfile and Field according to changes in dse profile database entry - modify DseProfileTreeNode according to changes in profile_tree.json * Bump ontology version to v3.0.0-alpha and add ne aliases to sq2cql config * Release v6.0.0-alpha.3 --------- Co-authored-by: Michael Folz <folz@med.uni-frankfurt.de>
medizininformatik-initiative · Oct 20, 2024 · fbc5333 · fbc5333
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diff --git a/.github/integration-test/ontology/dse/profile_tree.json b/.github/integration-test/ontology/dse/profile_tree.json
@@ -1,63 +1,135 @@
 {
-    "name": "Root",
-    "module": "no-module",
-    "url": "no-url",
-    "children": [
+  "name": "Root",
+  "module": "no-module",
+  "url": "no-url",
+  "children": [
+    {
+      "id": "e5dbef02-a690-4f5a-b1b9-081302aff04d",
+      "name": "modul-medikation",
+      "display": {
+        "original": "Medikation",
+        "translations": [
+          {
+            "language": "de-DE",
+            "value": "Medikation"
+          },
+          {
+            "language": "en-US",
+            "value": "Medication"
+          }
+        ]
+      },
+      "url": "modul-medikation",
+      "module": "modul-medikation",
+      "selectable": false,
+      "leaf": false,
+      "children": [
         {
-            "id": "de5c2903-00aa-4d64-92e5-2161d56e3daf",
-            "children": [
-                {
-                    "id": "69f4718f-1767-4517-90f8-6c079f627eed",
-                    "name": "MII_PR_Medikation_MedicationStatement",
-                    "display": "MII PR Medikation MedicationStatement",
-                    "module": "modul-medikation",
-                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement",
-                    "leaf": true,
-                    "selectable": true
-                },
-                {
-                    "id": "83b4d6be-b3e1-451a-adf2-c307477e7b97",
-                    "name": "MII_PR_Medikation_Medikationsliste",
-                    "display": "MII PR Medikation Medikationsliste",
-                    "module": "modul-medikation",
-                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/medikationsliste",
-                    "leaf": true,
-                    "selectable": true
-                },
-                {
-                    "id": "fd375ed9-b3cd-414f-8a56-c70e10bb9609",
-                    "name": "MII_PR_Medikation_MedicationRequest",
-                    "display": "MII PR Medikation MedicationRequest",
-                    "module": "modul-medikation",
-                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationRequest",
-                    "leaf": true,
-                    "selectable": true
-                },
-                {
-                    "id": "323a3ad1-1c10-45f5-848a-2dc5fb100c47",
-                    "name": "MII_PR_Medikation_Medication",
-                    "display": "MII PR Medikation Medication",
-                    "module": "modul-medikation",
-                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/Medication",
-                    "leaf": true,
-                    "selectable": true
-                },
-                {
-                    "id": "81ed0f03-1d77-49c9-8391-d4c25702652c",
-                    "name": "MII_PR_Medikation_MedicationAdministration",
-                    "display": "MII PR Medikation MedicationAdministration",
-                    "module": "modul-medikation",
-                    "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationAdministration",
-                    "leaf": true,
-                    "selectable": true
-                }
-            ],
-            "name": "modul-medikation",
-            "display": "Medikation",
-            "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement",
-            "module": "modul-medikation",
-            "selectable": true,
-            "leaf": false
+          "id": "5486577b-430b-4a42-a3c8-28c6d6eaf4e8",
+          "name": "MII_PR_Medikation_MedicationStatement",
+          "display": {
+            "original": "MII PR Medikation MedicationStatement",
+            "translations": [
+              {
+                "language": "de-DE",
+                "value": ""
+              },
+              {
+                "language": "en-US",
+                "value": "MII PR Medikation MedicationStatement"
+              }
+            ]
+          },
+          "module": "modul-medikation",
+          "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationStatement",
+          "leaf": true,
+          "selectable": true
+        },
+        {
+          "id": "491759f1-8afc-4a35-9a35-34642211f02a",
+          "name": "MII_PR_Medikation_Medikationsliste",
+          "display": {
+            "original": "MII PR Medikation Medikationsliste",
+            "translations": [
+              {
+                "language": "de-DE",
+                "value": ""
+              },
+              {
+                "language": "en-US",
+                "value": "MII PR Medikation Medicationlist"
+              }
+            ]
+          },
+          "module": "modul-medikation",
+          "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/medikationsliste",
+          "leaf": true,
+          "selectable": true
+        },
+        {
+          "id": "9d1fe081-3964-4951-b743-716d1b60d779",
+          "name": "MII_PR_Medikation_MedicationRequest",
+          "display": {
+            "original": "MII PR Medikation MedicationRequest",
+            "translations": [
+              {
+                "language": "de-DE",
+                "value": ""
+              },
+              {
+                "language": "en-US",
+                "value": "MII PR Medikation MedicationRequest"
+              }
+            ]
+          },
+          "module": "modul-medikation",
+          "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationRequest",
+          "leaf": true,
+          "selectable": true
+        },
+        {
+          "id": "1026f31f-78ec-4e20-9b40-c5b02b857bc3",
+          "name": "MII_PR_Medikation_Medication",
+          "display": {
+            "original": "MII PR Medikation Medication",
+            "translations": [
+              {
+                "language": "de-DE",
+                "value": ""
+              },
+              {
+                "language": "en-US",
+                "value": "MII PR Medikation Medication"
+              }
+            ]
+          },
+          "module": "modul-medikation",
+          "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/Medication",
+          "leaf": true,
+          "selectable": true
+        },
+        {
+          "id": "d8affe77-892f-45b5-8747-b5ca5400d1be",
+          "name": "MII_PR_Medikation_MedicationAdministration",
+          "display": {
+            "original": "MII PR Medikation MedicationAdministration",
+            "translations": [
+              {
+                "language": "de-DE",
+                "value": ""
+              },
+              {
+                "language": "en-US",
+                "value": "MII PR Medikation MedicationAdministration"
+              }
+            ]
+          },
+          "module": "modul-medikation",
+          "url": "https://www.medizininformatik-initiative.de/fhir/core/modul-medikation/StructureDefinition/MedicationAdministration",
+          "leaf": true,
+          "selectable": true
         }
-    ]
+      ]
+    }
+  ]
 }
diff --git a/.gitignore b/.gitignore
@@ -56,4 +56,6 @@ googleCodeStyle.xml
 
 result.log
 ontology
+update-availability/*
+!update-availability/README.md
 
diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -4,6 +4,21 @@ All notable changes to this project will be documented in this file.
 
 The format is based on [Keep a Changelog](https://keepachangelog.com/en/1.0.0/),
 
+## [UNRELEASED] - yyyy-mm-dd
+
+### Added
+### Changed
+### Deprecated
+### Removed
+### Fixed
+### Security
+
+## [6.0.0-alpha.3] - 2024-10-21
+
+### Changed
+- Allow empty search
+- Change structure of dse profile and details for new translation structure
+
 ## [6.0.0-alpha.2] - 2024-09-04
 
 ### Added

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -139,7 +139,7 @@ services:
         condition: service_healthy
     environment:
       ELASTIC_HOST: http://dataportal-elastic:9200
-      ELASTIC_GIT_TAG: v3.0.0-test.2
+      ELASTIC_GIT_TAG: v3.0.0-alpha
       ELASTIC_FILEPATH: https://github.com/medizininformatik-initiative/fhir-ontology-generator/raw/TAGPLACEHOLDER/example/fdpg-ontology/
       ELASTIC_FILENAME: elastic.zip
       # if set to false, existing indices are not overridden.

diff --git a/elastic-update-availability.sh b/elastic-update-availability.sh
@@ -0,0 +1,17 @@
+#!/usr/bin/env bash
+set -e
+
+BASE_DIR="$( cd -- "$(dirname "$0")" >/dev/null 2>&1 || exit 1 ; pwd -P )"
+ES_BASE_URL=${ES_BASE_URL:-http://localhost:9200}
+ES_INDEX=${ES_INDEX:-ontology}
+
+FILES=("$BASE_DIR"/update-availability/*)
+for availUpdateBundle in "${FILES[@]}"; do
+  if [[ $(basename "$availUpdateBundle") == *.json ]]; then
+    echo "Sending Availability Update bundle $availUpdateBundle ..."
+    response=$(curl --write-out "%{http_code}" -s --output /dev/null -XPOST -H 'Content-Type: application/json' --data-binary @"$availUpdateBundle" "$ES_BASE_URL/$ES_INDEX/_bulk")
+    echo "$response"
+  else
+    echo "Skipping $availUpdateBundle (not a .json file)"
+  fi
+done
diff --git a/pom.xml b/pom.xml
@@ -6,13 +6,13 @@
   <parent>
     <groupId>org.springframework.boot</groupId>
     <artifactId>spring-boot-starter-parent</artifactId>
-    <version>3.3.3</version>
+    <version>3.3.4</version>
     <relativePath /> <!-- lookup parent from repository -->
   </parent>
 
   <groupId>de.medizininformatik-initiative</groupId>
   <artifactId>DataportalBackend</artifactId>
-  <version>6.0.0-alpha.2</version>
+  <version>6.0.0-alpha.3</version>
 
   <name>Dataportal Backend</name>
   <description>Backend of the Dataportal</description>
@@ -27,7 +27,7 @@
     <java.version>17</java.version>
     <mockwebserver.version>4.10.0</mockwebserver.version>
     <okhttp3.version>4.10.0</okhttp3.version>
-    <ontology-tag>v3.0.0-test.2</ontology-tag>
+    <ontology-tag>v3.0.0-alpha</ontology-tag>
   </properties>
 
   <dependencies>
@@ -49,17 +49,17 @@
     <dependency>
       <groupId>io.undertow</groupId>
       <artifactId>undertow-core</artifactId>
-      <version>2.3.16.Final</version>
+      <version>2.3.17.Final</version>
     </dependency>
     <dependency>
       <groupId>io.undertow</groupId>
       <artifactId>undertow-servlet</artifactId>
-      <version>2.3.16.Final</version>
+      <version>2.3.17.Final</version>
     </dependency>
     <dependency>
       <groupId>io.undertow</groupId>
       <artifactId>undertow-websockets-jsr</artifactId>
-      <version>2.3.16.Final</version>
+      <version>2.3.17.Final</version>
     </dependency>
 
     <dependency>
@@ -141,7 +141,7 @@
     <dependency>
       <groupId>org.springdoc</groupId>
       <artifactId>springdoc-openapi-starter-webmvc-ui</artifactId>
-      <version>2.0.4</version>
+      <version>2.6.0</version>
     </dependency>
 
     <dependency>
@@ -198,6 +198,12 @@
       <version>6.6.2</version>
     </dependency>
 
+    <dependency>
+      <groupId>ca.uhn.hapi.fhir</groupId>
+      <artifactId>org.hl7.fhir.utilities</artifactId>
+      <version>6.3.26</version>
+    </dependency>
+
     <dependency>
       <groupId>com.bucket4j</groupId>
       <artifactId>bucket4j-core</artifactId>
@@ -237,7 +243,7 @@
     <dependency>
       <groupId>de.medizininformatik-initiative</groupId>
       <artifactId>sq2cql</artifactId>
-      <version>0.3.0</version>
+      <version>v0.5.0-alpha.1</version>
     </dependency>
 
     <dependency>

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/config/WebSecurityConfig.java b/src/main/java/de/numcodex/feasibility_gui_backend/config/WebSecurityConfig.java
@@ -51,7 +51,7 @@ public class WebSecurityConfig {
   public static final String PATH_DSE = "/dse";
   public static final String PATH_CODEABLE_CONCEPT = "/codeable-concept";
   public static final String PATH_SWAGGER_UI = "/swagger-ui/**";
-  public static final String PATH_SWAGGER_CONFIG = "/v4/api-docs/**";
+  public static final String PATH_SWAGGER_CONFIG = "/v3/api-docs/**";
   @Value("${app.keycloakAllowedRole}")
   private String keycloakAllowedRole;
 

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/DisplayEntry.java b/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/DisplayEntry.java
@@ -0,0 +1,15 @@
+package de.numcodex.feasibility_gui_backend.dse.api;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.Builder;
+
+import java.util.List;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@Builder
+public record DisplayEntry(
+    @JsonProperty String original,
+    @JsonProperty List<LocalizedValue> translations
+    ) {
+}
diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/DseProfile.java b/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/DseProfile.java
@@ -10,7 +10,7 @@
 @Builder
 public record DseProfile(
     @JsonProperty String url,
-    @JsonProperty String display,
+    @JsonProperty DisplayEntry display,
     @JsonProperty List<Field> fields,
     @JsonProperty List<Filter> filters,
     @JsonProperty String errorCode,

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/DseProfileTreeNode.java b/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/DseProfileTreeNode.java
@@ -12,7 +12,7 @@ public record DseProfileTreeNode(
     @JsonProperty String id,
     @JsonProperty List<DseProfileTreeNode> children,
     @JsonProperty String name,
-    @JsonProperty String display,
+    @JsonProperty DisplayEntry display,
     @JsonProperty String module,
     @JsonProperty String url,
     @JsonProperty boolean leaf,

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/Field.java b/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/Field.java
@@ -10,8 +10,8 @@
 @Builder
 public record Field(
     @JsonProperty String id,
-    @JsonProperty String display,
-    @JsonProperty String name,
+    @JsonProperty DisplayEntry display,
+    @JsonProperty DisplayEntry description,
     @JsonProperty String type,
     @JsonProperty List<Field> children
 ) {

diff --git a/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/LocalizedValue.java b/src/main/java/de/numcodex/feasibility_gui_backend/dse/api/LocalizedValue.java
@@ -0,0 +1,13 @@
+package de.numcodex.feasibility_gui_backend.dse.api;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+import com.fasterxml.jackson.annotation.JsonProperty;
+import lombok.Builder;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+@Builder
+public record LocalizedValue(
+    @JsonProperty String language,
+    @JsonProperty String value
+) {
+}