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2 changes: 1 addition & 1 deletion submodules/score
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Submodule score updated 14 files
+1 −1 Jenkinsfile
+4 −1 README.md
+1 −1 docs/setup.md
+15 −14 docs/usage/01-upload.md
+20 −19 docs/usage/02-download.md
+0 −4 score-client/src/main/java/bio/overture/score/client/config/ProfileConfig.java
+4 −8 score-client/src/main/java/bio/overture/score/client/exception/ConnectivityResponseHandler.java
+1 −0 score-client/src/main/java/bio/overture/score/client/manifest/DownloadManifest.java
+0 −3 score-core/src/main/java/bio/overture/score/core/security/ssl/SSLCertificateValidation.java
+10 −5 score-server/src/main/java/bio/overture/score/server/config/SecurityConfig.java
+23 −2 score-server/src/main/java/bio/overture/score/server/config/SwaggerConfig.java
+0 −8 score-server/src/main/java/bio/overture/score/server/controller/BenchmarkUploadController.java
+6 −12 score-server/src/main/java/bio/overture/score/server/controller/DownloadController.java
+16 −31 score-server/src/main/java/bio/overture/score/server/controller/UploadController.java
2 changes: 1 addition & 1 deletion submodules/song
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Submodule song updated 56 files
+3 −0 README.md
+10 −0 data-migration/.env.schema
+9 −0 data-migration/.gitignore
+5 −0 data-migration/.prettierignore
+8 −0 data-migration/.prettierrc
+67 −0 data-migration/README.md
+53 −0 data-migration/eslint.config.js
+32 −0 data-migration/package.json
+1,414 −0 data-migration/pnpm-lock.yaml
+34 −0 data-migration/src/config/db.ts
+16 −0 data-migration/src/config/env.ts
+3 −0 data-migration/src/index.ts
+106 −0 data-migration/src/migration/migrate.ts
+138 −0 data-migration/src/migration/samplesStructureForAnalyses.ts
+32 −0 data-migration/src/migration/updateAnalyses.ts
+41 −0 data-migration/src/types/index.ts
+113 −0 data-migration/tsconfig.json
+1 −1 dev/Makefile
+5 −5 docker-compose.yml
+1 −1 docs/01-setup.md
+60 −53 docs/02-Usage/00-submitting-metadata.md
+5 −0 docs/02-Usage/10-client-reference.md
+6 −1 song-client/src/main/java/bio/overture/song/client/command/SubmitCommand.java
+2 −1 song-client/src/test/java/bio/overture/song/client/HappyPathClientMainTest.java
+1 −1 song-docker-demo/storage-client/Dockerfile
+3 −2 song-java-sdk/src/main/java/bio/overture/song/sdk/SongApi.java
+2 −2 song-java-sdk/src/main/java/bio/overture/song/sdk/web/Endpoint.java
+79 −0 song-server/src/main/java/bio/overture/song/server/config/JwtDecoderConfig.java
+3 −4 song-server/src/main/java/bio/overture/song/server/config/KeycloakConfig.java
+113 −111 song-server/src/main/java/bio/overture/song/server/config/SecurityConfig.java
+25 −2 song-server/src/main/java/bio/overture/song/server/config/SwaggerConfig.java
+5 −15 song-server/src/main/java/bio/overture/song/server/controller/AnalysisController.java
+1 −13 song-server/src/main/java/bio/overture/song/server/controller/FileController.java
+1 −4 song-server/src/main/java/bio/overture/song/server/controller/StudyController.java
+0 −2 song-server/src/main/java/bio/overture/song/server/controller/SubmitController.java
+1 −4 song-server/src/main/java/bio/overture/song/server/controller/analysisType/AnalysisTypeController.java
+1 −1 song-server/src/main/java/bio/overture/song/server/kafka/Sender.java
+5 −6 song-server/src/main/java/bio/overture/song/server/kafka/impl/KafkaSender.java
+3 −3 song-server/src/main/java/bio/overture/song/server/kafka/impl/NoopSender.java
+10 −11 song-server/src/main/java/bio/overture/song/server/oauth/AccessTokenConverterWithExpiry.java
+11 −11 song-server/src/main/java/bio/overture/song/server/oauth/ExpiringOauth2Authentication.java
+2 −6 song-server/src/main/java/bio/overture/song/server/repository/search/IdSearchRequest.java
+93 −101 song-server/src/main/java/bio/overture/song/server/security/ApiKeyIntrospector.java
+1 −2 song-server/src/main/java/bio/overture/song/server/security/KeycloakPermission.java
+6 −7 song-server/src/main/java/bio/overture/song/server/security/StudySecurity.java
+7 −10 song-server/src/main/java/bio/overture/song/server/security/SystemSecurity.java
+9 −1 song-server/src/main/java/bio/overture/song/server/service/SubmitService.java
+2 −2 song-server/src/main/java/bio/overture/song/server/service/analysis/AnalysisService.java
+10 −9 song-server/src/main/java/bio/overture/song/server/service/analysis/AnalysisServiceSender.java
+14 −22 song-server/src/main/java/bio/overture/song/server/service/auth/KeycloakAuthorizationService.java
+10 −10 song-server/src/main/java/bio/overture/song/server/utils/Scopes.java
+3 −1 song-server/src/main/resources/application.yml
+0 −4 song-server/src/main/resources/schemas/analysis/analysisTypeRegistration.json
+1 −7 song-server/src/test/java/bio/overture/song/server/service/AnalysisServiceSenderTest.java
+1 −2 song-server/src/test/java/bio/overture/song/server/service/AnalysisServiceTest.java
+7 −5 song-server/src/test/java/bio/overture/song/server/service/MockedSubmitTest.java
2 changes: 1 addition & 1 deletion website/guides/03-user-guides/01-cli-submissions.md
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Original file line number Diff line number Diff line change
Expand Up @@ -90,7 +90,7 @@ API Keys are brokered by Keycloak and accessible when logged in to the Stage UI.
--network="host" \
--platform="linux/amd64" \
--mount type=bind,source=./guideMaterials/dataSubmission,target=/output \
ghcr.io/overture-stack/score:latest
ghcr.io/overture-stack/score-client:latest
```

<details>
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2 changes: 1 addition & 1 deletion website/guides/03-user-guides/02-cli-downloads.md
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Original file line number Diff line number Diff line change
Expand Up @@ -64,7 +64,7 @@ docker run -d -it --name score-client \
--network="host" \
--platform="linux/amd64" \
--mount type=bind,source=./guideMaterials/dataDownload/,target=/output \
ghcr.io/overture-stack/score:latest
ghcr.io/overture-stack/score-client:latest
```

:::caution
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