On Mon, Apr 8, 2013 at 7:58 AM, Marc Logghe <marc.log...@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: jmchil...@gmail.com [mailto:jmchil...@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.log...@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: jmchil...@gmail.com [mailto:jmchil...@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.log...@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-files-to-history-through/diff.
>> 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/jmchilton/blend4j/galaxy/ToolsClient.java
>>
>> -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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