Update ctakes-ytex to support MySQLversion 8.0.x database #10
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… the concept graphs to reference SNOMEDCT as SNOMEDCT_US which is the current name in UMLS. Update the create_tables.sql to support MySQL 8.0.x SQL commands. Update the ytex.properties examples to reflect that we need an xmldb.url to specify when JDBC URLs contain an ampersand and must be escaped in the generation of the conn.xml scripts in the ant build process.
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This pull requests makes the following changes:
Further notes for testing:
Once this patch is applied, you can generate new concept graphs using a locally installed version of the UMLS database following the previous directions from the ctakes website. Running the command "ant -f build-setup.xml all" will create the ytex database using a new version of the UMLS, but you should update the scripts/data/umls/MRCONSO.RRF and MRSTY.RRF with your current extract. These files are too large now to commit to github. If you are going to build multiple sources into a single concept graph, insure that all sources are represented in the MRCONSO.RRF file for the umls_aui_fword generation steps which setup the ytex database prior to creating concept graphs.
The concept graph sct-rxnorm database by default as specified in the buildnon-asf.xml file. If you want to generate an alternate concept network, update the cg.name to match one of the templates provided (e.g. sct-umls will build ONLY the Snomed concept graph - you can specify any number of sources as long as they exist in your local UMLS database). See the main method in o.a.ctakes.ytex.kernal.dao.ConceptDaoImpl.java for examples on how to generate a new concept graph from code.