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text-machine-lab / CliNER

Clinical Named Entity Recognition system (CliNER) is an open-source natural language processing system for named entity recognition in clinical text of electronic health records.

Home Page:http://text-machine.cs.uml.edu/cliner/

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evaluate not working

SimonSuster opened this issue · comments

commented

When running evaluate.py (official i2b2 evaluation script), I get the following error:

The Paramaters You Gave Were Invalid.
Valid Paramaters Are As Follows:
Default -> If only given -rcp and -scp everything else will be set to all and batch.
-rcp Classpath of the reference directory (String) *REQUIRED*
-scp Classpath of the system directory (String) *REQUIRED*
-ft all (for ratio tests on .ast,.rel and .con files)
-ft ast (for ratio tests on .ast files only)
-ft rel (for ratio tests on .rel files only)
-ft con (for ratio tests on .con files only)
-ex all (for both exact an inexact ratio tests)
-ex exact (for exact ratio tests only)
-ex inexact (for inexact ratio tests only)
-ag all (for both aggregated and seperate ratio tests)
-ag seperate (for seperate ratio tests only)
-ag aggregated (for aggregated ratio tests only)
-ba batch (testing in a batch format)
-ba perfile (testing for each file)
Your Given System Filepath is Invalid.
The Paramaters You Gave Were Invalid.
Valid Paramaters Are As Follows:
Default -> If only given -rcp and -scp everything else will be set to all and batch.
-rcp Classpath of the reference directory (String) *REQUIRED*
-scp Classpath of the system directory (String) *REQUIRED*
-ft all (for ratio tests on .ast,.rel and .con files)
-ft ast (for ratio tests on .ast files only)
-ft rel (for ratio tests on .rel files only)
-ft con (for ratio tests on .con files only)
-ex all (for both exact an inexact ratio tests)
-ex exact (for exact ratio tests only)
-ex inexact (for inexact ratio tests only)
-ag all (for both aggregated and seperate ratio tests)
-ag seperate (for seperate ratio tests only)
-ag aggregated (for aggregated ratio tests only)
-ba batch (testing in a batch format)
-ba perfile (testing for each file)
commented

Same issue, is there any solution? @SimonSuster

commented

I'm unsure of the issue here, but a few questions in trying to help others with this issue:

  1. Is data/tmp/ created successfully? If so, what's the path?
  2. Are pred/ and gold/ created successfully in data/tmp/?
  3. Does running java -jar i2b2-eval.jar -rcp <PATH_TO_GOLD> -scp <PATH_TO_PRED> -ft con -ex all succeed?