[Papyrus-L] Cleaning up Papyrus files!

[Dave Goldman, Research Software Design]

Rene Hessling wrote:
>It seems that my database contains a lot of junk. I (probably wrongly)
>started the database a long time ago by using a database of a colleague,
>then deleting all his entries and entering my papers. I think we did this so
>I would already have his journals and abbreviations in my database.
>
>Now having a look at the Ref.bib in a normal text editor it seems that there
>is still a lot of old junk in this file. Is there any way to remove this? ...
>...
>Is there a way to simply clean up my original database? I tried creating
>back-up files and restoring from them as well as 'index file generation'
>with no luck.

In general, when you enter data into Papyrus and then delete it (e.g., when
you delete a duplicate journal entry or reference) the space that data
occupied in the *.BIB files is marked as available for re-use. Eventually
the space will be overwritten by new data, but in the interim it will
remain unerased (though Papyrus will never access that unerased data).

However, under some circumstances the old data will hang around for a long
time, or even forever. The files INDX.BIB and REFKEY.BIB, in particular, do
not always overwrite deleted records.

Here is a procedure that will allow you to rebuild your *.BIB files from
scratch, without losing any formats or preferences settings:

(1) Make a back-up copy of all of your *.BIB files, just to be safe. (You
can simply copy all of your *.BIB files to another folder, for example.)

(2) Launch Papyrus. Go to Utilities. Run "Create Back-up Files". This will
create a set of smaller *.BB files that contain all the data from your
*.BIB files. Then quit from Papyrus.

(3) Delete all of your *.BIB files except for PRINT.BIB.

(4) Launch Papyrus. It will ask if you wish to create a fresh, empty
database. Answer "Y". Papyrus will create a new set of small *.BIB files.

(5) Go to Utilities. Run "Restore From Back-up Files". This will read in
the data from the *.BB files and rebuild the *.BIB files accordingly.

The result will be a somewhat smaller set of *.BIB files than you started
with. Any formerly-deleted data should now be entirely absent from your
files.

Caveat: Actually, when Papyrus creates or enlarges a *.BIB file, it does
not take the time to zero out the section of hard disk newly owned by that
*.BIB file, but rather overwrites that data gradually as you enter new data
into Papyrus. So if you look into a *.BIB file using a text editor you will
discover that the most recent part of that file still contains data from
some previous use -- perhaps a snippet of text from a deleted word
processor document, perhaps some numbers from a deleted spreadsheet, or
even (if you just followed the above procedure) a section of random data
from a previously-deleted Papyrus *.BIB file.


-- Dave Goldman (dave at rsd.com)              Research Software Design
   503/796-1368, fax 503-452-8920           617 SW Hume Street
   The PAPYRUS Bibliography System          Portland OR 97219-4458 (U.S.A.)

   Technical Support: support at rsd.com       Other Questions: info at rsd.com
                       WWW Site: http://www.rsd.com/