REST API: upload of dataset to history possible ?
Hi, Is it currently possible to upload an input dataset to a history via the REST API ? Or should one use a library dataset instead ? But in the latter case, only an admin can upload data, right ? Thanks, Marc ________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
On 04/02/2013 12:23 PM, Marc Logghe wrote:
Hi,
Is it currently possible to upload an input dataset to a history via the REST API ? Or should one use a library dataset instead ?
But in the latter case, only an admin can upload data, right ?
"non-admin user" can upload files as well, see the 'user_library_import_dir' option in the 'universe_wsgi.ini' file Regards, Hans-Rudolf
Thanks,
Marc
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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
________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
___________________________________________________________ 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/
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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
________________________________________ THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
___________________________________________________________ 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/
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THIS E-MAIL MESSAGE IS INTENDED ONLY FOR THE USE OF THE INDIVIDUAL OR ENTITY TO WHICH IT IS ADDRESSED AND MAY CONTAIN INFORMATION THAT IS PRIVILEGED, CONFIDENTIAL AND EXEMPT FROM DISCLOSURE. If the reader of this E-mail message is not the intended recipient, you are hereby notified that any dissemination, distribution or copying of this communication is strictly prohibited. If you have received this communication in error, please notify us immediately at ablynx@ablynx.com. Thank you for your co-operation. "NANOBODY" and "NANOCLONE" are registered trademarks of Ablynx N.V. ________________________________________
participants (3)
-
Hans-Rudolf Hotz -
John Chilton -
Marc Logghe