Web server mode and MySQL PGDBs

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Hi Mathieu,

I do not think that using a MySQL database instead of files would decrease the memory requirements -- the pgdbs would still all end up being loaded into memory. Instead, I would recommend using the -auto-close command line argument that sets a maximum number of pgdbs that can be open at a time by closing the least-recently accessed ones. A reasonable number to set it to is 100, so you would specify the -auto-close 100 as part of your pathway-tools invocation. BTW, I'm not sure how compatible this setting is with MySQL PGDBs -- we use it with files, and I don't know if it has been sufficiently tested with MySQL PGDBs.

As to your second question, when running with MySQL PGDBs, Pathway Tools attempts to refresh each PGDB (i.e. load in the latest updates) once a night. So in that respect, your server would get the updates. However, image files are generated once and then cached, so unless you also added a script to delete them all each night, they might get out of sync with the contents of the PGDB.