Re: [galaxy-dev] DB access and password field in galaxy
Hello all, Maybe I posted it wrong. But below my original message again. Any ideas? Thanks Alex -----Oorspronkelijk bericht----- Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: zaterdag 19 maart 2011 10:23 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] DB access and passowrd field Hi All, I have some tools that generate mostly tabular output. The next step is to aggregate the data for complex filtering and analysis. In my view the best way to do by using a DB (MySQL in my case). Also in light of some data curation tools we use externally of galaxy. Tools and cmd line wrappers can easily connect to a DB (another database than galaxy is using of course) when providing the details for access like address:port, username and password. Is there any way to embed a text field for a galaxy tool that is of type password or blinded? Don't want to share user specific login details when sharing histories or galaxy pages. Or is this a bad thing to pursue anyway? Thanks for any directions. Alex
Hello Alex, We have a similar setup, and this is how we implemented it: 1. all users must be logged in, so $userEmail is set to the correct user name and can't be changed by the user. 2. Created an admin Mysql user that can load data into the DB (and create tables, etc.) - with access to all users' tables. 3. the command line tool in galaxy uses this MySQL admin user to load the data, so password from the galaxy user is not an issue. 4. The command line galaxy tool takes $userEmail as parameter so the tool knows which user's tables need to be updated. -gordon On Mar 30, 2011, at 9:52, "Bossers, Alex" <Alex.Bossers@wur.nl> wrote:
Hello all, Maybe I posted it wrong. But below my original message again. Any ideas? Thanks Alex
-----Oorspronkelijk bericht----- Van: galaxy-dev-bounces@lists.bx.psu.edu [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: zaterdag 19 maart 2011 10:23 Aan: galaxy-dev@lists.bx.psu.edu Onderwerp: [galaxy-dev] DB access and passowrd field
Hi All,
I have some tools that generate mostly tabular output. The next step is to aggregate the data for complex filtering and analysis. In my view the best way to do by using a DB (MySQL in my case). Also in light of some data curation tools we use externally of galaxy.
Tools and cmd line wrappers can easily connect to a DB (another database than galaxy is using of course) when providing the details for access like address:port, username and password.
Is there any way to embed a text field for a galaxy tool that is of type password or blinded? Don't want to share user specific login details when sharing histories or galaxy pages. Or is this a bad thing to pursue anyway?
Thanks for any directions.
Alex
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Gordon, thanks for the directions! Indeed this can be a good solution for our local DBs ad other DBs that we maintain. External Dbs will be difficult but if we want to do that anyway is a different discussion. Thanks Alex ________________________________ Van: Gordon, Assaf [gordon@cshl.edu] Verzonden: woensdag 30 maart 2011 17:11 Aan: Bossers, Alex CC: galaxy-dev@lists.bx.psu.edu Onderwerp: Re: [galaxy-dev] DB access and password field in galaxy Hello Alex, We have a similar setup, and this is how we implemented it: 1. all users must be logged in, so $userEmail is set to the correct user name and can't be changed by the user. 2. Created an admin Mysql user that can load data into the DB (and create tables, etc.) - with access to all users' tables. 3. the command line tool in galaxy uses this MySQL admin user to load the data, so password from the galaxy user is not an issue. 4. The command line galaxy tool takes $userEmail as parameter so the tool knows which user's tables need to be updated. -gordon On Mar 30, 2011, at 9:52, "Bossers, Alex" <<mailto:Alex.Bossers@wur.nl>Alex.Bossers@wur.nl<mailto:Alex.Bossers@wur.nl>> wrote: Hello all, Maybe I posted it wrong. But below my original message again. Any ideas? Thanks Alex -----Oorspronkelijk bericht----- Van: <mailto:galaxy-dev-bounces@lists.bx.psu.edu> galaxy-dev-bounces@lists.bx.psu.edu<mailto:galaxy-dev-bounces@lists.bx.psu.edu> [mailto:galaxy-dev-bounces@lists.bx.psu.edu] Namens Bossers, Alex Verzonden: zaterdag 19 maart 2011 10:23 Aan: <mailto:galaxy-dev@lists.bx.psu.edu> <mailto:galaxy-dev@lists.bx.psu.edu> galaxy-dev@lists.bx.psu.edu<mailto:galaxy-dev@lists.bx.psu.edu> Onderwerp: [galaxy-dev] DB access and passowrd field Hi All, I have some tools that generate mostly tabular output. The next step is to aggregate the data for complex filtering and analysis. In my view the best way to do by using a DB (MySQL in my case). Also in light of some data curation tools we use externally of galaxy. Tools and cmd line wrappers can easily connect to a DB (another database than galaxy is using of course) when providing the details for access like address:port, username and password. Is there any way to embed a text field for a galaxy tool that is of type password or blinded? Don't want to share user specific login details when sharing histories or galaxy pages. Or is this a bad thing to pursue anyway? Thanks for any directions. Alex ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: <http://lists.bx.psu.edu/> <http://lists.bx.psu.edu/> http://lists.bx.psu.edu/
participants (2)
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Bossers, Alex -
Gordon, Assaf