feat(model-ad): migrate model-ad comparison tools endpoints to java springboot server (MG-496) (Sage-Bionetworks#3667)

Co-authored-by: tschaffter <[email protected]>

Author: hallieswan

.devcontainer/devcontainer.json

@@ -16,10 +16,10 @@
   },
   "features": {},
   "forwardPorts": [
-    2000, 2432, 3333, 4200, 4211, 5200, 5601, 8010, 8071, 8000, 8080, 8082, 8084, 8085, 8086, 8087,
-    8091, 8100, 8111, 8112, 8113, 8114, 8115, 8116, 8400, 8401, 8402, 8403, 8404, 8405, 8406, 8200,
-    8500, 8501, 8502, 8503, 8504, 8505, 8506, 8507, 8508, 8509, 8510, 8511, 8887, 8888, 8889, 9200,
-    21000, 27017
+    2000, 2432, 3333, 3334, 4200, 4211, 5200, 5601, 8010, 8071, 8000, 8080, 8082, 8084, 8085, 8086,
+    8087, 8091, 8100, 8111, 8112, 8113, 8114, 8115, 8116, 8400, 8401, 8402, 8403, 8404, 8405, 8406,
+    8200, 8500, 8501, 8502, 8503, 8504, 8505, 8506, 8507, 8508, 8509, 8510, 8511, 8887, 8888, 8889,
+    9200, 21000, 27017
   ],
   "portsAttributes": {
     "2000": {
@@ -34,6 +34,10 @@
       "label": "agora-api",
       "onAutoForward": "silent"
     },
+    "3334": {
+      "label": "model-ad-api-next",
+      "onAutoForward": "silent"
+    },
     "4200": {
       "label": "openchallenges-app",
       "onAutoForward": "silent"

apps/model-ad/apex/.env.example

@@ -3,4 +3,6 @@ API_DOCS_PORT=8010
 API_HOST=model-ad-api
 API_PORT=3333
 APP_HOST=model-ad-app
-APP_PORT=4200
+APP_PORT=4200
+API_NEXT_HOST=model-ad-api-next
+API_NEXT_PORT=3334

apps/model-ad/apex/Caddyfile

@@ -3,7 +3,13 @@
     reverse_proxy {env.API_DOCS_HOST}:{env.API_DOCS_PORT}
   }
 
-  # Serve the API, stripping the /api prefix
+  # Route /api/v1/comparison-tools to the next api, stripping /api
+  handle /api/v1/comparison-tools/* {
+    uri strip_prefix /api
+    reverse_proxy {env.API_NEXT_HOST}:{env.API_NEXT_PORT}
+  }
+
+	# Route all other /api/* requests to the default API service, stripping /api
   handle_path /api/* {
     reverse_proxy {env.API_HOST}:{env.API_PORT}
   }

apps/model-ad/api-next/.env.example

@@ -0,0 +1,7 @@
+SERVER_PORT="3334"
+MODEL_AD_MONGO_HOST="model-ad-mongo"
+MODEL_AD_MONGO_PORT="27017"
+MODEL_AD_MONGO_DATABASE="model-ad"
+MODEL_AD_MONGO_USERNAME="root"
+MODEL_AD_MONGO_PASSWORD="changeme"
+MODEL_AD_MONGO_AUTH_DB="admin"

apps/model-ad/api-next/.gitignore

@@ -0,0 +1,39 @@
+.gradle
+bin/
+lib/*.jar
+maven-legacy/
+tmp/
+log/
+
+HELP.md
+target/
+!**/src/main/**/target/
+!**/src/test/**/target/
+
+### STS ###
+.apt_generated
+.classpath
+.factorypath
+.project
+.settings
+.springBeans
+.sts4-cache
+
+### IntelliJ IDEA ###
+.idea
+*.iws
+*.iml
+*.ipr
+
+### NetBeans ###
+/nbproject/private/
+/nbbuild/
+/dist/
+/nbdist/
+/.nb-gradle/
+build/
+!**/src/main/**/build/
+!**/src/test/**/build/
+
+### VS Code ###
+.vscode/

apps/model-ad/api-next/.openapi-generator-ignore

@@ -0,0 +1,28 @@
+# OpenAPI Generator Ignore
+# Generated by openapi-generator https://github.com/openapitools/openapi-generator
+
+# Use this file to prevent files from being overwritten by the generator.
+# The patterns follow closely to .gitignore or .dockerignore.
+
+# As an example, the C# client generator defines ApiClient.cs.
+# You can make changes and tell OpenAPI Generator to ignore just this file by uncommenting the following line:
+#ApiClient.cs
+
+# You can match any string of characters against a directory, file or extension with a single asterisk (*):
+#foo/*/qux
+# The above matches foo/bar/qux and foo/baz/qux, but not foo/bar/baz/qux
+
+# You can recursively match patterns against a directory, file or extension with a double asterisk (**):
+#foo/**/qux
+# This matches foo/bar/qux, foo/baz/qux, and foo/bar/baz/qux
+
+# You can also negate patterns with an exclamation (!).
+# For example, you can ignore all files in a docs folder with the file extension .md:
+#docs/*.md
+# Then explicitly reverse the ignore rule for a single file:
+#!docs/README.md
+pom.xml
+# README.md
+**/application.properties
+**/OpenApiGeneratorApplication.java
+**/OpenApiGeneratorApplicationTests.java

apps/model-ad/api-next/.openapi-generator/FILES

@@ -0,0 +1,39 @@
+README.md
+src/main/java/org/sagebionetworks/model/ad/api/next/RFC3339DateFormat.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ApiUtil.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ComparisonToolConfigApi.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ComparisonToolConfigApiController.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ComparisonToolConfigApiDelegate.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/DataVersionApi.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/DataVersionApiController.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/DataVersionApiDelegate.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/DiseaseCorrelationApi.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/DiseaseCorrelationApiController.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/DiseaseCorrelationApiDelegate.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ModelApi.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ModelApiController.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ModelApiDelegate.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ModelOverviewApi.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ModelOverviewApiController.java
+src/main/java/org/sagebionetworks/model/ad/api/next/api/ModelOverviewApiDelegate.java
+src/main/java/org/sagebionetworks/model/ad/api/next/configuration/EnumConverterConfiguration.java
+src/main/java/org/sagebionetworks/model/ad/api/next/configuration/HomeController.java
+src/main/java/org/sagebionetworks/model/ad/api/next/configuration/SpringDocConfiguration.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/BasicErrorDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/ComparisonToolConfigColumnDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/ComparisonToolConfigDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/ComparisonToolConfigFilterDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/ComparisonToolPageDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/CorrelationResultDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/DataVersionDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/DiseaseCorrelationDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/GeneticInfoDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/IndividualDataDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/ItemFilterTypeQueryDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/ModelDataDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/ModelDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/ModelOverviewDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/ModelOverviewLinkDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/SearchResultDto.java
+src/main/java/org/sagebionetworks/model/ad/api/next/model/dto/SexDto.java
+src/main/resources/openapi.yaml

apps/model-ad/api-next/.openapi-generator/VERSION

@@ -0,0 +1 @@
+7.14.0

apps/model-ad/api-next/Dockerfile

@@ -0,0 +1 @@
+FROM ghcr.io/sage-bionetworks/model-ad-api-next-base:local

apps/model-ad/api-next/README.md

@@ -0,0 +1,21 @@
+# OpenAPI generated server
+
+Spring Boot Server
+
+## Overview
+
+This server was generated by the [OpenAPI Generator](https://openapi-generator.tech) project.
+By using the [OpenAPI-Spec](https://openapis.org), you can easily generate a server stub.
+This is an example of building a OpenAPI-enabled server in Java using the SpringBoot framework.
+
+The underlying library integrating OpenAPI to Spring Boot is [springdoc](https://springdoc.org).
+Springdoc will generate an OpenAPI v3 specification based on the generated Controller and Model classes.
+The specification is available to download using the following url:
+http://localhost:8080/v3/api-docs/
+
+Start your server as a simple java application
+
+You can view the api documentation in swagger-ui by pointing to
+http://localhost:8080/swagger-ui.html
+
+Change default port value in application.properties