Hi John, Thanks. To elaborate a little more: we have a LabKey Server (web front end for a database) that manages raw files and metadata. The idea is to make a galaxy tool where a user could do thing like query for all genomes from males patients, age x-y, etc. I can use LabKey's APIs to return a list of those files. However, the information at this point is text (basically a list of filepaths).
It would be nice to automatically create datasets for those files. Some of the time there's a simple 1:1 between file and the user-facing dataset (like images); however, for genomes we really want to make a paired collection. BioBlend makes it relatively easy to go from filepaths to datasets; however, the authentication issue is what wasnt clear. If there's a more standard path to go from list of files -> galaxy dataset I'm all ears. -Ben On Wed, Apr 29, 2015 at 12:13 PM, John Chilton <jmchil...@gmail.com> wrote: > Unofficial way of doing this and the workaround of using configfiles > can be found in this thread: > > http://dev.list.galaxyproject.org/Simple-standard-for-API-use-of-a-global-user-key-that-all-loaded-tools-can-draw-upon-td4665659.html > . > There is a Trello card outlining platform work that should be done to > support this better but we have not made progress on that. > > I would be interested in your use case. One can dynamically discover > datasets with various db keys and build collections composted of > dynamically discovered datasets and keys - but there is no way to use > the tool xml to dynamically discover a variable number of collections > - but it should be supported - as should building a list of paired or > lists of lists where the outer list describes the key and the inner > the sample. > > -John > > > > On Wed, Apr 29, 2015 at 2:58 PM, Ben Bimber <bbim...@gmail.com> wrote: > > Hello, > > > > I am new to galaxy. I"m trying to write a data input tool wrapper. It > will > > call a script that does a query, produces a list of files, and then the > plan > > is to use the BioBlend API to create datasets/data collections in galaxy. > > In other words I am making the dataset(s) based on the contents of this > > file, rather than making a dataset from that file. In my case this file > has > > a pair of columns representing FASTQ files, and I want to create one > paired > > dataset collection in galaxy for each genome. > > > > In theory using bioblend to create datasets is easy. However, when I > call > > this as a galaxy tool, I have not found a clean way to pass the > credentials > > to bioblend. BioBlend needs to know the serverURL and either the user's > API > > key or username/password. I think if I poke around $__app__ or $__user__ > > there's a good change I will find a property with the information I need; > > however, this has the obvious problem of writing the API key to the log. > > > > Is there another way to approach this problem? > > > > Thanks in advance for any help, > > Ben > > > > > > ___________________________________________________________ > > 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: > > https://lists.galaxyproject.org/ > > > > To search Galaxy mailing lists use the unified search at: > > http://galaxyproject.org/search/mailinglists/ >
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