Changes to cv.ra

Background

cv.ra stands for controlled vocabulary, it was a way to be sure everyone was talking about the same cell or antibody or lab when discussing metada (data that describes data).

History

The controlled vocabulary file, cv.ra, exists at the trackDb level, in a directory called cv, with three sub directories, alpha, beta, and public.

/kent/src/hg/makeDb/trackDb/cv 
                           |_/alpha
                           |_/beta
                           |_/public

Each of the directories were a convenient way to keep cv.ra changes staged. One person would edit the cv.ra in the alpha directory and see changes with a "make alpha DBS", the QA person would periodically copy the alpha/cv.ra to beta/cv.ra, creating a snap shot to QA. When ready for release, they QA person would copy the final beta/cv.ra version to public/cv.ra, thus again creating a third public snapshot.

Previously the process of "make public DBS=hg##" would use the copy of cv.ra in the public directory to populate beta-public. Then a request to push trackDb and friends took beta-public cv.ra and brought it to the RR. That changed in 2013 when we moved machines to San Diego. While the request to push trackDb and friends to the RR in 2013 would still take the cv.ra from beta-public, getting that cv.ra to beta-public is was different in 2013.

It all changed once again in 2014 when it cv.ra was axed completely from the trackDb make and push process.

Current Release Process

Now, one must request a push of the copy of cv.ra in beta to the beta-public machine (and for housekeeping purposes, also copy the beta/cv.ra version to public/cv.ra).

Please push cv.ra form beta machine to public machine: 
/usr/local/apache/cgi-bin/encode/cv.ra    
      hgwbeta --> hgwbeta-public
/usr/local/apache/cgi-bin-public/encode/cv.ra
Reason: cv.ra changes ready for public release.

Overview:

• 1) Original edits start at /kent/src/hg/makeDb/trackDb/cv/alpha/cv.ra, do "make alpha DBS=hg##" to see changes.
• 2) FInal version of alpha copied from alpha/cv.ra to beta/cv.ra and public/cv.ra
• 3) Do "make beta DBS=hg##" to double check changes on beta. (If changes needed, start edits on alpha and copy to beta &public when done).
• 4) Request a push /usr/local/apache/cgi-bin/encode/cv.ra from hgwbeta --> hgwbeta-public /usr/local/apache/cgi-bin-public/encode/cv.ra
• 5) Do "make public DBS=hg##" and check that cv.ra changes are on beta-public
• 6) Request a push of trackDb and friends for the related $db.
• 7) Check RR to see that cv.ra change is now public.
• 8) Housecleaning: do a diff alpha/cv.ra beta/cv.ra public/cv.ra (in the least beta and public should be the same, alpha only different if you have more changes coming). Also you may want to navigate and download and check to see that your cv.ra changes ended up here: http://hgdownload.soe.ucsc.edu/goldenPath/encodeDCC/cv.ra, that is part of the regular push of beta-public to RR for cv.ra process.