lmu-bioinformatics / xmlpipedb

XMLPipeDB is a suite of tools for building relational databases from XML sources with minimal manual processing of the data. While the applicability is general, our motivation was to facilitate the management of biological data from different sources.
http://xmlpipedb.cs.lmu.edu
GNU Lesser General Public License v3.0
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Write Documentation on Updating GMBuilder to work with new obo-xml files #42

Closed NAnguiano closed 7 years ago

NAnguiano commented 8 years ago

I wrote these steps in Issue #34, but I think it can use some more formal documentation on the wiki.

  1. Run xsd2db on the manually edited dtd file
  2. Run godbpostprocessor.
  3. Select .sql file and hbm file specified by the post processor.
  4. Build the .jar with the new sql and hbm files.
  5. Replace godb.sql with the edited sql file.
  6. replace godb.jar with the new jar file.
  7. Copy the contents of the new godb.sql file and replace the corresponding section in gmbuilder.sql with the new contents, excluding the sections at the beginning that alter the tables.
  8. Create a new database and run the new gmbuilder.sql.
  9. Run GMbuilder.
kdahlquist commented 8 years ago

Let's remember to note the expected error, as noted by @dondi on issue #41:

Yes, this error is actually normal. The geneontologystage table is an intermediate table that is created during GO processing. There is code that first tries to delete a pre-existing geneontologystage table before running the processing routine, and on a “fresh” database that has never been processed, that table does not exist. The error you are seeing is the failure of the deletion, and is totally expected for a freshly-initialized database.

kdahlquist commented 8 years ago

Add to this the schema spy documentation, both doing it for GODB and UniProtDB and also writing some instructions on how to do it for the future.

kdahlquist commented 7 years ago

This is now on the wiki; schema spy has been broken out into its own separate issue #46.