feat(lapis): remove protected OpennessLevel

.github/workflows/lapis.yml

@@ -141,7 +141,6 @@ jobs:
           docker compose logs siloMultisegmented > e2e-logs/siloMultisegmented.log
           docker compose logs siloPreprocessingMultisegmented > e2e-logs/siloPreprocessingMultisegmented.log
           docker compose logs lapisOpen > e2e-logs/lapisOpen.log
-          docker compose logs lapisProtected > e2e-logs/lapisProtected.log
           docker compose logs lapisMultiSegmented > e2e-logs/lapisMultiSegmented.log
         env:
           SILO_TAG: 0.8.5

lapis-docs/src/components/ConfigGenerator/configContext.tsx

@@ -4,9 +4,8 @@ import { z } from 'zod';
 export type ConfigType = 'SILO' | 'Pathoplexus';
 
 export const LAPIS_OPENNESS_OPEN = 'OPEN';
-export const LAPIS_OPENNESS_PROTECTED = 'PROTECTED';
 
-export const opennessLevelSchema = z.enum([LAPIS_OPENNESS_OPEN, LAPIS_OPENNESS_PROTECTED]);
+export const opennessLevelSchema = z.enum([LAPIS_OPENNESS_OPEN]);
 export type OpennessLevel = z.infer<typeof opennessLevelSchema>;
 
 export const metadataTypeSchema = z.enum([

lapis-e2e/.prettierignore

@@ -1,3 +1,2 @@
 /test/lapisClient
-/test/lapisClientProtected
 /test/lapisClientMultiSegmented

lapis-e2e/generateOpenApiClients.sh

@@ -4,10 +4,8 @@ set -euo pipefail
 
 cd "../lapis"
 ./gradlew generateOpenApiDocs
-./gradlew generateOpenApiDocs -PopennessLevel=protected
 ./gradlew generateOpenApiDocs -Psegmented=true
 
 cd -
 npm run generateLapisClient
-npm run generateLapisClientProtected
 npm run generateLapisClientMultiSegmented

lapis-e2e/package.json

@@ -7,14 +7,10 @@
     "generateLapisClient": "npm run runOpenApiGenerator && npm run copyGeneratedFiles && npm run cleanUpGeneratedFiles",
     "runOpenApiGenerator": "openapi-generator-cli generate -i ../lapis/lapis-openapi-single-segmented.json -g typescript-fetch -o generated-sources",
     "copyGeneratedFiles": "mkdir -p test/lapisClient && cp generated-sources/index.ts generated-sources/runtime.ts test/lapisClient && cp -r generated-sources/apis generated-sources/models test/lapisClient",
-    "generateLapisClientProtected": "npm run runOpenApiGeneratorProtected && npm run copyGeneratedFilesProtected && npm run cleanUpGeneratedFilesProtected",
-    "runOpenApiGeneratorProtected": "openapi-generator-cli generate -i ../lapis/lapis-openapi-single-segmented-protected.json -g typescript-fetch -o generated-sources-protected",
-    "copyGeneratedFilesProtected": "mkdir -p test/lapisClientProtected && cp generated-sources-protected/index.ts generated-sources-protected/runtime.ts test/lapisClientProtected && cp -r generated-sources-protected/apis generated-sources-protected/models test/lapisClientProtected",
     "generateLapisClientMultiSegmented": "npm run runOpenApiGeneratorMultiSegmented && npm run copyGeneratedFilesMultiSegmented && npm run cleanUpGeneratedFilesMultiSegmented",
     "runOpenApiGeneratorMultiSegmented": "openapi-generator-cli generate -i ../lapis/lapis-openapi-multi-segmented.json -g typescript-fetch -o generated-sources-multi-segmented",
     "copyGeneratedFilesMultiSegmented": "mkdir -p test/lapisClientMultiSegmented && cp generated-sources-multi-segmented/index.ts generated-sources-multi-segmented/runtime.ts test/lapisClientMultiSegmented && cp -r generated-sources-multi-segmented/apis generated-sources-multi-segmented/models test/lapisClientMultiSegmented",
     "cleanUpGeneratedFiles": "rm -rf generated-sources",
-    "cleanUpGeneratedFilesProtected": "rm -rf generated-sources-protected",
     "cleanUpGeneratedFilesMultiSegmented": "rm -rf generated-sources-multi-segmented",
     "check-format": "prettier --check .",
     "format": "prettier --write ."

lapis-e2e/test/common.ts

@@ -7,17 +7,13 @@ import {
   SingleSegmentedSequenceControllerApi,
 } from './lapisClient';
 import { MutationsOverTimeControllerApi } from './lapisClient/index';
-import { LapisControllerApi as LapisControllerApiMultiSegmented } from './lapisClientMultiSegmented';
-import { expect } from 'chai';
-
 import {
-  LapisControllerApi as LapisControllerApiProtected,
-  Configuration as ConfigurationProtected,
-} from './lapisClientProtected';
-import { MultiSegmentedSequenceControllerApi } from './lapisClientMultiSegmented';
+  LapisControllerApi as LapisControllerApiMultiSegmented,
+  MultiSegmentedSequenceControllerApi,
+} from './lapisClientMultiSegmented';
+import { expect } from 'chai';
 
 export const basePath = 'http://localhost:8090';
-export const basePathProtected = 'http://localhost:8092';
 export const basePathMultiSegmented = 'http://localhost:8094';
 
 const middleware: Middleware = {
@@ -51,9 +47,6 @@ export const actuatorClient = new ActuatorApi(new Configuration({ basePath })).w
 export const mutOverTimeClient = new MutationsOverTimeControllerApi(
   new Configuration({ basePath })
 ).withMiddleware(middleware);
-export const lapisClientProtected = new LapisControllerApiProtected(
-  new ConfigurationProtected({ basePath: basePathProtected })
-).withMiddleware(middleware);
 export const lapisClientMultiSegmented = new LapisControllerApiMultiSegmented(
   new Configuration({ basePath: basePathMultiSegmented })
 ).withMiddleware(middleware);

lapis/.gitignore

@@ -4,9 +4,7 @@ build/
 !**/src/main/**/build/
 !**/src/test/**/build/
 /lapis-openapi.json
-/lapis-openapi-protected.json
 log/
 logs/
 /lapis-openapi-multi-segmented.json
 /lapis-openapi-single-segmented.json
-/lapis-openapi-single-segmented-protected.json

lapis/README.md

@@ -135,9 +135,3 @@ To generate the OpenApi docs for an instance with multi-segmented reference geno
 ```bash
 ./gradlew generateOpenApiDocs -Psegmented=true
 ```
-
-To generate the OpenApi docs for a protected instance run
-```bash
-./gradlew generateOpenApiDocs -PopennessLevel=protected
-```
-

lapis/build.gradle

@@ -90,24 +90,21 @@ ktlint {
 openApi {
     outputDir.set(file("$rootDir"))
 
-    def opennessLevel = project.hasProperty("opennessLevel") ? project.opennessLevel : "open"
     def segmented = project.hasProperty("segmented") ? project.segmented : "false"
 
-    def getCustomOutputFileName = { opennessLevel_, segmented_ ->
+    def getCustomOutputFileName = { segmented_ ->
         if (segmented_ == "true") {
             return "lapis-openapi-multi-segmented.json"
         } else {
-            return opennessLevel_ == "open" ? "lapis-openapi-single-segmented.json" : "lapis-openapi-single-segmented-protected.json"
+            return "lapis-openapi-single-segmented.json"
         }
     }
 
-    def getCustomLapisConfig = { opennessLevel_, segmented_ ->
+    def getCustomLapisConfig = { segmented_ ->
         if (segmented_ == "true") {
             return "$rootDir/../lapis-e2e/testData/multiSegmented/testDatabaseConfig.yaml"
         } else {
-            return opennessLevel_ == "open"
-                    ? "$rootDir/../lapis-e2e/testData/singleSegmented/testDatabaseConfig.yaml"
-                    : "$rootDir/../lapis-e2e/testData/singleSegmented/protectedTestDatabaseConfig.yaml"
+            return "$rootDir/../lapis-e2e/testData/singleSegmented/testDatabaseConfig.yaml"
         }
     }
 
@@ -119,8 +116,8 @@ openApi {
         }
     }
 
-    def customOutputFileName = getCustomOutputFileName(opennessLevel, segmented)
-    def customLapisConfig = getCustomLapisConfig(opennessLevel, segmented)
+    def customOutputFileName = getCustomOutputFileName(segmented)
+    def customLapisConfig = getCustomLapisConfig(segmented)
     def referenceGenomeFilename = getReferenceGenomeFilename(segmented)
 
     outputFileName.set(customOutputFileName)
@@ -131,7 +128,6 @@ openApi {
                 "--silo.url=does.not.matter.here",
                 "--lapis.databaseConfig.path=$customLapisConfig",
                 "--referenceGenomeFilename=$referenceGenomeFilename",
-                "--lapis.accessKeys.path=$rootDir/src/test/resources/config/testAccessKeys.yaml"
         ])
     }
 }

lapis/docker-compose.yml

@@ -74,22 +74,3 @@ services:
         source: ../lapis-e2e/testData/multiSegmented/reference_genomes.json
         target: /workspace/reference_genomes.json
         read_only: true
-
-  lapisProtected:
-    image: ghcr.io/genspectrum/lapis:${LAPIS_TAG}
-    platform: linux/amd64
-    ports:
-      - "8092:8080"
-    command: --silo.url=http://silo:8081 --lapis.accessKeys.path=/workspace/access_keys.yaml
-    volumes:
-      - type: bind
-        source: ../lapis-e2e/testData/singleSegmented/protectedTestDatabaseConfig.yaml
-        target: /workspace/database_config.yaml
-        read_only: true
-      - type: bind
-        source: ../lapis-e2e/testData/singleSegmented/reference_genomes.json
-        target: /workspace/reference_genomes.json
-        read_only: true
-      - type: bind
-        source: ./src/test/resources/config/testAccessKeys.yaml
-        target: /workspace/access_keys.yaml