Re: [galaxy-dev] Customizing/reusing the workflows/run.mako template
Duddy, John wrote: > Interesting - this was a workflow with exactly 1 step - the "add a column" > tool. I looked in my database/files/000 directory, and there was no dataset > id 53 - would that be an id in the history_dataset_association table? Yeah, that's the hda id. The files are named with the dataset id. > In any case, I would like to be able to start a workflow for the user without > interfering with any notion of the "current" workflow they may have open in > their browser. Is that possible now, or do I need to: If you did this with an existing history with a running workflow, you'd have a bunch of interlaced datasets, which is probably not what you want. There's not a simple way of knowing whether there is currently a workflow running in a history, though, since once it's at that stage it's just a series of jobs. (recent enhancements aside, so someone correct me if I'm wrong). > - Create a history and set it be the "current" history (how is that > done?) It depends on the session - you probably want to get the most recent galaxy_session for the user and set its current_history to the new history. Histories are created with trans.new_history(), but note that your session in the API is not your session in your web browser. > - Import my datasets into it > > - Fetch the form (which will autopopulate the file inputs from the > "current" history > > - Let them launch it by submitting the form? The rest should work. --nate > > John Duddy > Sr. Staff Software Engineer > Illumina, Inc. > 9885 Towne Centre Drive > San Diego, CA 92121 > Tel: 858-736-3584 > E-mail: jdu...@illumina.com<mailto:jdu...@illumina.com> > > From: James Taylor [mailto:ja...@jamestaylor.org] > Sent: Tuesday, August 09, 2011 5:41 PM > To: Duddy, John > Cc: galaxy-dev > Subject: Re: [galaxy-dev] Customizing/reusing the workflows/run.mako template > > John, the prefixes like "22|" are added to the inputs associated with each > step, so that they can be separated back out. In this case, the chunk of HTML > you have pasted likely corresponds to the 22nd step of the workflow. > > 53 on the other hand should be a dataset id from the current history > (unencoded in this case). > > On Aug 9, 2011, at 8:24 PM, Duddy, John wrote: > > > I'd like to integrate with Galaxy and launch workflows, and I am hoping to > reuse Galaxy's support for prompting the user for items that are tagged as > being set at runtime. It looks to me that I could load the workflows/run page > in a frame on my app (on the same server) and reuse it. > > The problem I'm having is that I don't understand how the parameters for the > input files are encoded. For example, here is one for adding a column to a > dataset: > > > > > > > > > 1: Add column on data 6 > > > > > > > > > > > > > > > > > What are 22 and 53? They don't seem to correspond to dataset IDs. > > Is there a way that I can encode data library IDs such that I can submit this > form and have Galaxy run the workflow with the right files in a new history? > > Thanks! > > John Duddy > Sr. Staff Software Engineer > Illumina, Inc. > 9885 Towne Centre Drive > San Diego, CA 92121 > Tel: 858-736-3584 > E-mail: jdu...@illumina.com<mailto:jdu...@illumina.com> > > ___ > 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/ > > ___ > 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/ ___ 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/
Re: [galaxy-dev] Customizing/reusing the workflows/run.mako template
Interesting - this was a workflow with exactly 1 step - the "add a column" tool. I looked in my database/files/000 directory, and there was no dataset id 53 - would that be an id in the history_dataset_association table? In any case, I would like to be able to start a workflow for the user without interfering with any notion of the "current" workflow they may have open in their browser. Is that possible now, or do I need to: - Create a history and set it be the "current" history (how is that done?) - Import my datasets into it - Fetch the form (which will autopopulate the file inputs from the "current" history - Let them launch it by submitting the form? John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.com<mailto:jdu...@illumina.com> From: James Taylor [mailto:ja...@jamestaylor.org] Sent: Tuesday, August 09, 2011 5:41 PM To: Duddy, John Cc: galaxy-dev Subject: Re: [galaxy-dev] Customizing/reusing the workflows/run.mako template John, the prefixes like "22|" are added to the inputs associated with each step, so that they can be separated back out. In this case, the chunk of HTML you have pasted likely corresponds to the 22nd step of the workflow. 53 on the other hand should be a dataset id from the current history (unencoded in this case). On Aug 9, 2011, at 8:24 PM, Duddy, John wrote: I'd like to integrate with Galaxy and launch workflows, and I am hoping to reuse Galaxy's support for prompting the user for items that are tagged as being set at runtime. It looks to me that I could load the workflows/run page in a frame on my app (on the same server) and reuse it. The problem I'm having is that I don't understand how the parameters for the input files are encoded. For example, here is one for adding a column to a dataset: 1: Add column on data 6 What are 22 and 53? They don't seem to correspond to dataset IDs. Is there a way that I can encode data library IDs such that I can submit this form and have Galaxy run the workflow with the right files in a new history? Thanks! John Duddy Sr. Staff Software Engineer Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-736-3584 E-mail: jdu...@illumina.com<mailto:jdu...@illumina.com> ___ 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/ ___ 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/
Re: [galaxy-dev] Customizing/reusing the workflows/run.mako template
John, the prefixes like "22|" are added to the inputs associated with each step, so that they can be separated back out. In this case, the chunk of HTML you have pasted likely corresponds to the 22nd step of the workflow. 53 on the other hand should be a dataset id from the current history (unencoded in this case). On Aug 9, 2011, at 8:24 PM, Duddy, John wrote: > I’d like to integrate with Galaxy and launch workflows, and I am hoping to > reuse Galaxy’s support for prompting the user for items that are tagged as > being set at runtime. It looks to me that I could load the workflows/run page > in a frame on my app (on the same server) and reuse it. > > The problem I’m having is that I don’t understand how the parameters for the > input files are encoded. For example, here is one for adding a column to a > dataset: > > 1: Add column on data 6 > > > > > > What are 22 and 53? They don’t seem to correspond to dataset IDs. > > Is there a way that I can encode data library IDs such that I can submit this > form and have Galaxy run the workflow with the right files in a new history? > > Thanks! > > John Duddy > Sr. Staff Software Engineer > Illumina, Inc. > 9885 Towne Centre Drive > San Diego, CA 92121 > Tel: 858-736-3584 > E-mail: jdu...@illumina.com > > ___ > 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/ ___ 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/
