UPDATER_README

Update InterMine userprofile.xml files to reflect changes in the data model

  Installation:

There are four prerequisite modules:

  Log::Handler
  XML::Rules
  XML::Writer
  JSON

These can be installed with the "cpan 'module'" command.


  Synopsis:
updater.pl -i [file],[file] (-o [file],[file]) -m [file] -c [file.json] (-s [dir]) (-l [file])

This updater will read through an input file, checking the validity of 
any InterMine paths (in queries, classes or items), writing out the new updated
version to a specified file. It requires an example of the new data 
model, as well as a list of the changes between the old model and the 
current one.

The updater will attempt to transform paths wherever possible. If this is
not possible, then classes or fields will be deleted. All changes and 
deletions will be logged. If a deletion makes an query or an item invalid,
then in the case of a query it will be declared "broken" and the original
version will be inserted into the new file: please see grep your log
for "broken" to find out which queries are broken so you can edit them by
hand, if you wish. Items will be logged as deleted, and removed from the 
output stream. These are very rare (about 3 per million) but again they can
be grepped for from the log output.

At the end of the run (which takes roughly 1min for every 1 million xml 
elements in the input stream) basic statistics will be logged, listing
the total number of items, templates and saved-queries processed, changed
and broken.

  Options:

--help|usage   | -h|u : This help text

--inputfile    | -i   : The file to be processed

--outputfile   | -o   : The file to write the new output to
   (optional)           if not supplied, the inputfile name 
                        will be used, suffixed with '.new'

--modelfile    | -m   : The new model to validate paths against

--changesfile  | -c   : The file specifying model changes (deletions
                        and name changes)
--svndirectory | -s   : The location of the InterMine svn directory,
    (optional)          by default this is assumed to be "~/svn/dev"

--logfile      | -l   : File to save the log to. If there is no file, 
    (optional)          all logging output will go to STDOUT

options that take multiple values (-i, -o) can either be called as:

  updater -i [file] -i [file]

or

  updater -i [file],[file]

if you do supply outputfiles, make sure you have the same number of them
as inputfiles, otherwise an exception will be thrown.

  Example:

perl svn/dev/intermine/scripts/updater.pl -i Projects/userprofile.xml,Projects/webconfig-model.xml -o Projects/userprofile.xml.new -o Projects/webconfig-model.xml -c Projects/model_changes.json -m svn/model_update/flymine/dbmodel/build/model/genomic_model.xml -l log/userprofiles.log -s svn/dev