dcronkite
dcronkite
When processing files without extensions, `getBasename` will split on a directory name if it contains periods in it: https://github.com/lhncbc/metamaplite/blob/a7d10264a023afda497356f50faa4385ab7e3908/src/main/java/gov/nih/nlm/nls/ner/MetaMapLite.java#L1003-L1011 E.g., if I supply the path `/mapr/r.ds/mml/file_0`, it will attempt to...
How can I alter the logging level when running Metamaplite? I'd like to set it to at least WARN in order to reduce the amount of console output when running...
The default `bin/create_indexes.bat` runs into a FileNotFoundException when running GenerateVariants (see https://github.com/lhncbc/metamaplite/blob/827a5c1f7a0174247ea499117d82745af827c628/bin/create_indexes.bat#L58-L60) as the default value for `wordsFilename` is `/tmp/words.txt.tmp`: https://github.com/lhncbc/metamaplite/blob/8aae39319a4a4b40a013180bf6cde09b172c78a8/src/main/java/gov/nih/nlm/nls/metamap/dfbuilder/GenerateVariants.java#L226-L227. It appears Java on Windows is unable to resolve...
I built a custom UMLS and then attempted to index the output using `bin/create_indexes.bat`, but ran into an issue: ``` Exception in thread "main" java.io.FileNotFoundException: C:\path\to\indices\meshtcrelaxed\postings (The system cannot find...
I've been using the `DefaultFastPipeline.piper` configuration on version 4.0.0.1 and wanted to include the published [Smoking Status](https://cwiki.apache.org/confluence/display/CTAKES/cTAKES%204.0%20-%20Smoking%20status) pipeline to this (or as a separate pipeline if that makes more sense)...
On, e.g., ch3-ex2 and ch4-ex1, a string formatter is used to 'format' years on the x-axis which would otherwise appear as decimals (2015.0 -> 2015, 2017.5 -> 2018). This, however,...