On Mon, Apr 8, 2013 at 7:58 AM, Marc Logghe Marc.Logghe@ablynx.com wrote:
YES!!! I really could not have found that by myself. Thank you very much.
Great, I am re-responding to galaxy-dev just in case someone else has this problem.
BTW: I have made some additions to blend4j in order to make it compatible to Richard Park's REST API changes regarding the passing of tool parameters.
Are these the changes that have made it into Galaxy? If so, if you send me a patch or pull request I would be happy to review it for inclusion into blend4j.
Thanks for using blend4j!
-John
It allows to pass parameters like this: WorkflowInputs inputs = new WorkflowInputs(); inputs.setDestination(new WorkflowInputs.ExistingHistory(history.getId())); inputs.setWorkflowId(projectWorkflow.getId()); // Set parameters for params2yaml tool inputs.setParameters("params2yaml", new ToolParameters("project", "APR000200"));
Not entirely satisfied with it; might need some api changes but was kind of POC. I also would need some more info from Richard because it is not clear to me if his REST API adjustments allow for multiple parameters.
Cheers, Marc
-----Original Message----- From: jmchilton@gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton Sent: Monday, April 08, 2013 2:50 PM To: Marc Logghe Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ?
Can you retry that with "?" as the db key, admittedly that could use some more documentation :). The db key is the short identifier associated with the genome corresponding to the data, "?" indicates none is specified.
-John
On Sun, Apr 7, 2013 at 2:06 PM, Marc Logghe Marc.Logghe@ablynx.com wrote:
Thanks John. Not sure what I am doing wrong, but in my hands it does not work. No errors but there is no file upload either.
ToolsClient toolsClient = galaxyInstance.getToolsClient(); ClientResponse result = toolsClient.fileUploadRequest(history.getId(), "txt", "whatIsAdbKey?", new File("C:\Users\mlogghe\Documents\bb3d562ec52a9fc5.yml")); System.out.println(result.getClientResponseStatus());
In paster.log I also do not see any evidence that upload_handler is called.
Regards, Marc
-----Original Message----- From: jmchilton@gmail.com [mailto:jmchilton@gmail.com] On Behalf Of John Chilton Sent: Thursday, April 04, 2013 3:40 PM To: Marc Logghe Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] REST API: upload of dataset to history possible ?
On Tue, Apr 2, 2013 at 5:23 AM, Marc Logghe Marc.Logghe@ablynx.com wrote:
Hi,
Is it currently possible to upload an input dataset to a history via the REST API ?
This has been possible since pull request 94: https://bitbucket.org/galaxy/galaxy-central/pull-request/94/enable-upload-of.... The idea is to use the tools API and to invoke the upload1 tool. I imagine this is a little tricky to do with the bioblend Python library right now, but the blend4j Java library has a high-level helper function (ToolsClient.fileUploadRequest) to make this pretty simple:
https://github.com/jmchilton/blend4j/blob/master/src/main/java/com/github/jm...
-John
Or should one use a library dataset instead ?
But in the latter case, only an admin can upload data, right ?
Thanks,
Marc
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