Basic NLM-Scrubber Configuration File

Instructions on this page consist of the most basic configuration file specifications.

Here is a typical configuration file content:

  1. ROOT1 = D:\ClinicalData\PHI
  2. ClinicalReports_dir = ROOT1/TEXT
  3. ClinicalReports_files = ^ds.*\.txt
  4. nPHI_outdir = ROOT1/TEXT/NPHI

The first line is not essential, but it would be useful if all the files in the following lines share some common path. In the above case, ROOT1 is the alias for D:\ClinicalData\PHI

The words to the left of the equal signs are preserved, case-sensitive terms. Please, make sure that there are no trailing whitespaces at the end of each line.

ClinicalReports_dir specifies the location path of the input reports. In this case, they are under D:\ClinicalData\PHI\TEXT\.

ClinicalReports_files specifies the input files in simple regular expression terms. In this example all (presumably discharge summary) files of interest start with a prefix"ds",followed by a string of unknown length (".*"), and finalized with a common suffix extension".txt".

nPHI_outdir specifies the output directory for the de-identified reports. This directory will be generated by the program as long as all its parent directory exists, the user who runs NLM-Scrubber can access the parent directory and has the write permission. For this example, we have to make sure that the path D:\ClinicalData\PHI\TEXT\ exists. In this example, we know that it exists, since all input files are supposed to be there.

If there is already a directory D:\ClinicalData\PHI\TEXT\NPHI, NLM-Scrubber will attempt to rename the existing directory, by prepending a dot . prefix and appending a timestamp suffix.

At the beginning of each run, an error file, "err.scrubber.&lttimestamp&gt", will be generated, and runtime errors would be written into this file. If the file is empty at the end of the run, it would be deleted automactially. In the case that NLM-Scrubber generates any error that you cannot resolve, please send us this error file along with a detailed description of the problem.