slicing-tool

This is the project that is used to slice release content from the curation database (in MySQL or Neo4j). The original codebase is refactored from the CurationTool project.

Note

The slicing tool runs directly using the controller in the curator-tool-ws. To run it in the development mode inside IDE (e.g. IntelliJ or Eclipse), you need to set up the run configuration for the curator-tool-ws module, and add the following enviornment variables in the running configuration or set up the enviornment variables in the terminal before running the application (org.gk.slicing.SlicingEngine.main()). For more details see: https://github.com/reactome/curator-tool-ws/blob/master/docs/QUICK_START_SECRETS.md.

Neo4j Configuration - LOCAL DEVELOPMENT ONLY

NEO4J_URI=bolt://localhost:7687 NEO4J_USER={} NEO4J_PASSWORD={}

H2 Database Configuration - LOCAL DEVELOPMENT ONLY

DATASOURCE_URL=jdbc:h2:file:{};DB_CLOSE_DELAY=-1;FILE_LOCK=NO DATASOURCE_USER={} DATASOURCE_PASSWORD={}

Note: You may use .env file in IntelliJ. Also make sure the two h2 files in the data folder match with your local configuration.

**TODO**: 

- need to check replacementDB_IDs in _Deleted (Deleted) after converting. This needs to create a new graph database. 
- Need stableIds at the node level in case the node is shell in the context (e.g. replacementInstnstance in Deleted)