diff --git a/.github/ISSUE_TEMPLATE/build-kg2.md b/.github/ISSUE_TEMPLATE/build-kg2.md index c692631f..d1ecc767 100644 --- a/.github/ISSUE_TEMPLATE/build-kg2.md +++ b/.github/ISSUE_TEMPLATE/build-kg2.md @@ -9,30 +9,30 @@ assignees: '' ##### 1. Build and load KG2: - [ ] (if necessary) Clear the instance using `bash -x instance_management/clear-instance.sh` +- [ ] (preferred option) Launch a new AWS EC2 `r5a.4xlarge` instance called `kg2XYbuild.rtx.ai` - [ ] Clone the RTX repo from Github `git clone https://github.com/RTXteam/RTX-KG2.git` - [ ] Checkout the branch that will be used for the build - [ ] Setup the KG2 build system `bash -x RTX-KG2/setup/setup-kg2-build.sh` - [ ] Check `~/kg2-build/setup-kg2-build.log` to ensure setup completed successfully - [ ] Run a dry build using `bash -x ~/kg2-code/build/build-kg2-snakemake.sh all -F -n` -- [ ] Check `~/kg2-build/build-kg2-snakemake-n.log` to ensure all rules are included +- [ ] Check `~/kg2-build/build-kg2-snakemake-KG2.X.Y-n.log` to ensure all rules are included - [ ] Run `touch ~/kg2-build/minor-release` for a minor release or `touch ~/kg2-build/major-release` for a major release. If you don't want to change the version number, ignore this step. - [ ] Initiate a screen session `screen -S buildkg2` - [ ] Start the build `bash -x ~/kg2-code/build/build-kg2-snakemake.sh all -F` -- [ ] Verify build completed by checking `~/kg2-build/build-kg2-snakemake.log` +- [ ] Verify build completed by checking `~/kg2-build/build-kg2-snakemake-KG2.X.Y.log` - [ ] Check the build version number in `~/kg2-build/kg2-version.txt` -- [ ] Check report file `kg2-simplified-report.json`; compare against previous `kg2-simplified-report.json` to identify any major changes +- [ ] Check report file `kg2-simplified-report-KG2.X.Y.json`; compare against previous `kg2-simplified-report.json` to identify any major changes - [ ] Find an available kg2endpoint by checking `rtx.ai` under `Networking` on Lightsail -- [ ] install the new KG2 TSV files into Neo4j on the kg2endpoint - [ ] Update code on kg2endpoint, then run setup-kg2-neo4j.sh if necessary -- [ ] Load KG2 into Neo4J `RTX-KG2/tsv-to-neo4j.sh > ~/kg2-build/tsv-to-neo4j.log 2>&1` -- [ ] Update kg2-versions.md +- [ ] Load KG2 into Neo4J `bash -x ~/neo4j/RTX-KG2/tsv-to-neo4j.sh > ~/kg2-build/tsv-to-neo4j.log 2>&1` +- [ ] Update `kg2-versions.md` - [ ] create a new DNS CNAME record with CNAME `kg2endpoint-kg2-X-Y.rtx.ai` pointing to the hostname for the Neo4j endpoint (which might be something like `kg2endpoint3.rtx.ai`). - [ ] Update version numbers of upstream knowledge sources, for the new version of KG2 in `kg2-versions.md` (see Cypher command below). - [ ] (if necessary) Merge working branch into `master` -- [ ] Create a new release for the build on GitHub +- [ ] Create a new release for the build on GitHub, including the content from `kg2-versions.md` in the description. Example Cypher to get versions of many of the knowledge sources in a specific build of KG2pre: ``` -match (n:`biolink:InformationResource`) where not n.id =~ 'umls_.*' and not n.id =~ 'OBO:.*' return n.id, n.name order by n.id; +match (n:`biolink:RetrievalSource`) where not n.id =~ 'umls_.*' and not n.id =~ 'OBO:.*' return n.id, n.name order by n.id; ```