Galaxy Api run tool

Question: Galaxy Api run tool

5 months ago by

chavaldranis • 0

chavaldranis • 0 wrote:

Hello,

I have some issue to use the galaxy api to start a job.

From : https://docs.galaxyproject.org/en/master/_modules/galaxy/webapps/galaxy/api/tools.html#ToolsController.create

I'm using this command

curl -X POST -H "Content-Type: application/json" -d '{"key":"my_key","tool_id":"Show beginning1","tool_version":"1.0.0","inputs":{"lineNum":10,"input":{"values":[{"src":"hda","name":"Select first on data 18","tags":[],"keep":false,"hid":19,"id":"bbd44e69cb8906b5fc5c181d22be27d6"}],"batch":false}}}' https://usegalaxy.org/api/tools

And I got this error msg {"err_msg": "API authentication required for this request", "err_code": 403001}

Anyone have an idea or have an example of this kind of command working ?

tool api • 527 views

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modified 4 months ago • written 5 months ago by chavaldranis • 0

4 months ago by

chavaldranis • 0

chavaldranis • 0 wrote:

I'hv finally found a way to make it work

curl -v -X POST -H "X-Api-Key: 011d381c1e07fa288b0........ -H "Content-Type: application/json" -d '{"history_id":"3efc1e4fbcc09bd8","tool_id":"Show beginning1","tool_version":"1.0.0","inputs":{"lineNum":10,"input":{"values":[{"src":"hda","name":"Select first on data 18","tags":[],"keep":false,"hid":19,"id":"bbd44e69cb8906b5fc5c181d22be27d6"}],"batch":false}}}' https://usegalaxy.org/api/tools

The API key has to be sent with the header 'X-Api-Key". And I had forgotten to add the 'history_id' in the payload otherwise I got

{"err_msg": "Error executing tool: 'NoneType' object has no attribute 'user'", "err_code": 0}

ADD COMMENT • link modified 4 months ago • written 4 months ago by chavaldranis • 0

5 months ago by

Martin Čech ♦♦ 4.9k

United States

Martin Čech ♦♦ 4.9k wrote:

I assume in the actual call you replace my_key with your actual API key. Is that correct?

edit: check out the Galaxy API library for Python: http://bioblend.readthedocs.io/en/latest/api_docs/galaxy/all.html#bioblend.galaxy.tools.ToolClient.run_tool

ADD COMMENT • link modified 5 months ago • written 5 months ago by Martin Čech ♦♦ 4.9k

Yes I replace my_key with my actual API key.

Actually, I would like to make it work without using python :/

ADD REPLY • link modified 5 months ago • written 5 months ago by chavaldranis • 0

I tried with the Galaxy API library for Python, to check if I can make it work

from bioblend import galaxy

gi = galaxy.GalaxyInstance(url='https://usegalaxy.org/', key='011d381c1...')
inputs = {"lineNum":10,"input":{"values":[{"src":"hda","name":"Select first on data 18","tags":[],"keep":False,"hid":19,"id":"bbd44e69cb8906b5fc5c181d22be27d6"}],"batch":False}}
gi.tools.run_tool(history_id='3efc1e4fbcc09bd8',tool_id='Show beginning1',tool_inputs=inputs)

And it works. I'm wondering what's wrong in the first command

ADD REPLY • link written 5 months ago by chavaldranis • 0

I am no curl guru so I would probably catch/log the requests and compare them.

ADD REPLY • link written 5 months ago by Martin Čech ♦♦ 4.9k

Hello Martin, have you catch up the logs?

ADD REPLY • link written 4 months ago by chavaldranis • 0

That is for you to do, I cannot see your logs.

ADD REPLY • link written 4 months ago by Martin Čech ♦♦ 4.9k

Sorry I misunderstood the answer

ADD REPLY • link written 4 months ago by chavaldranis • 0

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