How does jBASE figure out where a file is located?

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I am working with customer using jBASE and I checked the MD item to determine where the file existed and there was no MD item for the file. How does jBASE determine where the file is?

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jBASE uses the locations as defined in the JEDIFILEPATH environment variable to find your files:

https://docs.zumasys.com/jbase/environment-variables/jedifilepath/

But anything defined in the MD/VOC takes precedence.

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It looks for the item (I suppose you mean a jBASE hashed file) either in VOC/MD (defined in JEDIFILENAME_MD environment variable) or HOME path or current working directory path. Perhaps your MD or VOC (Vocabulary) is pointing somewhere else than where you expect it to be - check the JEDIFILENAME_MD variable.