On 07/04/2016 02:40 AM, Aaron Taudt wrote:
Dear all,
I am trying to update my experiment data package. I read the instructions
at
http://bioconductor.org/developers/how-to/source-control#experiment-data-packages
but it's not clear to me at all how to do it the right way. The package
infrastructure and data folders are stored in different repositories. When
updating a package, do I make the changes in both repositories separately?
What is the role of the python script to fold in the data? What does the
external_data_store.txt file need to contain? The files that are stored in
the "data_store" repository?
Changes to the large data need to be commited to
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/data_store/<PKG>
Changes to the package itself (e.g., version bump, documentation) need
to be commited to
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/<PKG>
external_data_store.txt is a list of svn endpoints in the
data_store/<PKG> that are to be folded into the checked-out pkgs/<PKG>
hierarchy. Typically the end points in external_data_store.txt are
folders, changes to the data replace files within folders that are
already specified in external_data_store.txt, and there is no need to
change external_data_store.txt.
From SVN it looks like you want to change
data_store/chromstaRData/data/experiment_table.RData
and friends. It looks like external_data_store.txt already contained the
path 'data', so that no change was necessary to this file. Having
changed the content of the package, you would add a version bump to
DESCRIPTION and commit pkgs/chromstaRData/DESCRIPTION. I think you've
arrived at this state. I would have done something like
svn co -N https://hedgehog.fhcrc.org/bioc-data/trunk/experiment
cd experiment
svn up pkgs/chromstaRData data_store/chromstaRData pkgs/add_data.py
make changes, and commit
svn ci pkgs/chromstaRData data_store/chromstaRData
If things are successful, then in some temporary location checking out
pkgs/chromstaRData and running the add_data.py script should result in a
valid R package:
cd /tmp
svn export
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/add_data.py
svn co
https://hedgehog.fhcrc.org/bioc-data/trunk/experiment/pkgs/chromstaRData
./add_data.py chromstaRData
It would be nice if there was a more detailed description on how to update
experiment data packages. I'm not an expert in using svn and figuring this
out by trial and error takes a lot of time because of the biweekly build
cycles.
Thanks,
Aaron
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