What is that, "Thank me for making you aware of the MySQL licensing issue"? No no, it was my pleasure. If you ever get your legal problems worked out, you can feel free to go back and review my application materials.
Well, you can even do that right now if you feel it is necessary. -Robin Kramer The difference between a fiddle and a violin. No one cries when beer is spilled on a fiddle. The difference between a computational biologist and a bioinformatician. No one cries when ethanol is spilled on a computational biologist's computer. -----Original Message----- From: Jim Kent [mailto:[EMAIL PROTECTED] Sent: Tuesday, October 28, 2008 2:54 AM To: Kramer, Robin S. (MU-Student) Cc: [email protected] Subject: Re: [Genome] Genome Digest, Vol 69, Issue 23 Hmm. Mark and Mike looked into the licensing issues around MySQL some, and it turns out they are complex. The area that is less than straightforward hinges on the fact that we do link to the MySQL client libraries. MySQL has changed their license on these libraries from LGPL to GPL as of version 4.1. Since we are actually on version 4.0.27, this doesn't apply to us yet. We were planning on upgrading all the way to version 5 or 6 as we bring in new hardware for the web servers in the next few months though, so this is an issue we will have to think about. The LGPL is the license that the C libraries that ship with the GNU Compiler Collection use. The LGPL is such that just linking with these libraries does not force your program to itself be available with any particular license. Since the MySQL client libraries used to be the same, we were used to just not having to think about these issues. A lot of people got upset with MySQL when they did change the license. Personally I was living in happy ignorance of this change until today. It won't affect us as much as it did a lot of more commercial products or programming languages that have built-in database connectivity. Possibly it will be the wedge that drives us to release the browser under BSD, which wouldn't be an entirely bad thing from my personal point of view. We'd have to get UCSC's intellectual property office to sign off on that though. It'd be a modest loss of revenue in tough economic times. Possibly we could compensate by changing our licenses to support agreements. Possibly we can just dodge the issue by only licensing source, and insisting people do the compiling and linking themselves, which actually is the current practice anyway. (As it turns out most of our mirrors are on 4.1 and more recent libraries. I can't speak for our commercial licensees.) We are pretty dependent on MySQL, though not inextricably so. There just seem to be two mysql.h includes in the source for the browser itself - one in jksql.c and the other in hdb.c. The one in hdb.h was not needed so I took it out. We encapsulate all of the database i/o through jksql. Theoretically we'd just need to rewrite this one module, which amounts to about 1% of the code base, to switch to another database. Still, there's place where we've grown to depend on MySQL-specific queries, primarily to get metadata such as lists of all the fields in a table, that would be a pain to port. Even 1% of the code base is a lot of work to rewrite at this point for that matter too. Definitely we'd rather spend the time working on adding new data, improving ways to view existing data, and new analysis programs. There are no patents associated with the Genome Browser. There are copyrights though. On Oct 27, 2008, at 6:21 PM, Robin Kramer wrote: > Hi Jim, > > Maybe I can stake my claim on being the person to ensure that the > human > genome and its browser remain in public domain for the benefit of > everyone, > not just those in academics or CBSC, not much to it really. > > The language in the FOSS doesn't apply to modifications of code that > is > clearly covered under GPL. The language applies to derivative > works. Which > means the two sources have to clearly be delineated and marked, the > most > common criterion is linking and compiling and or running either with > necessary and dependent, without unnecessary and not dependent. The > law > also frowns upon reverse engineering of Copy righted material, which > would > fall under the heading of distributing modified versions and would > obviously > be covered under GPL. Greping through the code it seems "mysql.h" > is used > many places. > > I think one of the confusing areas, might be the browser its self > since it > contains much graphics that isn't as directly related to the database > connectivity, which quite frankly is the part which all the academic > students want to use when they go out into the workforce, and probably > depends on the mysql.h, in a way which is inseparable. > > The rest of the code isn't too different from the mysql program > anyway, and > no one could tell the difference if it wasn't the interface, do you > have a > patent on the interface? > > Regards, > > -Robin Kramer > > > -----Original Message----- > From: Jim Kent [mailto:[EMAIL PROTECTED] > Sent: Monday, October 27, 2008 5:42 PM > To: Kramer, Robin S. (MU-Student) > Cc: [email protected] > Subject: Re: [Genome] Genome Digest, Vol 69, Issue 23 > > Hi Robin - your notion of derivative work is different and broader > than what I'm used to and what I think the common legal meaning is. > Hgsql is just a thin wrapper for convenience around a command that > just calls mysql with your password and user name taken from a > configuration file (so you don't have to supply it at the command line > every time). There's certainly lots of helper applications out there > that are distributed independently of the main application, and who's > copyright and other intellectual property issues are considered > separate from the main application. The simple fact that they do not > run without the main application is enough to insure that users do > obtain the main application to run them. This ensures that the > developers of the main application are fairly compensated - by the > purchase of the main application if it's being sold, or by respecting > the GNU license for the main app if it's not being sold. > > In general for people to use the Genome Browser, they'll have to > install MySQL as well. They'll need to either get the GNU or the > commercial license to MySQL at that point. The main advantage of the > commercial license is support for most people. MySQL is not always > the easiest thing to install, so this can be a noticable advantage. > If you were a company that wanted to build your own database engine > that made use of the MySQL source code base, you would have to either > abide by the sticky terms of GNU, or license the source another way. > However for mere users of the database engine this is not much of an > issue, and the main reason to license is support. > > Take care, > Jim > > On Oct 27, 2008, at 1:46 PM, Kramer, Robin S. (MU-Student) wrote: > >> Parts of your distribution are still derivative works for example >> hgsql, >> in that they are not independent (ie hgsql doesn't compile or run >> without mysql.h). >> >> http://www.mysql.com/about/legal/licensing/foss-exception/ >> >> >> IE as a FOSS program developer you (CBSC) may develop a derivative >> program and distribute that program provided you and your program >> comply >> with GPL, and it doesn't matter whether you distribute mysql.h or >> not, >> your work is a derivative, and must comply with the GPL as well. >> >> -Robin Kramer >> >> Hello Robin, >> >> We do not have a license agreement with MySQL. We do not distribute >> MySQL, nor have we imported any of its code. Users who wish to >> compile >> our source code in kent/src/hg/* need to obtain their own copy of >> MySQL. >> >> The Genome Browser source is not derived from MySQL, but simply links >> with its client libraries. >> >> I hope this answers your question. Please feel free to email us >> again >> should you have further questions. >> >> -- >> Brooke Rhead >> UCSC Genome Bioinformatics Group >> >> >> Kramer, Robin S. (MU-Student) wrote: >>> I am just looking at the expense of marketing skills developed while >>> installing the UCSC browser and something that is not clear to me is >> the >>> relicensing of the MySQL header files or derived code. >>> >>> Does, UCSC have some sort of non GPL license agreement with MySQL. >>> >>> http://dev.mysql.com/doc/refman/5.0/es/gpl-license.html >>> >>> Under 3b "You must cause any work that you distribute or publish, >>> that >>> in whole or in part contains or is derived from the Program or any >> part >>> thereof, to be licensed as a whole at no charge to all third parties >>> under the terms of this License." >>> >>> -Robin Kramer >>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> http://www.soe.ucsc.edu/mailman/listinfo/genome >> >> >> >> _______________________________________________ >> Genome maillist - [email protected] >> http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
