Passing quoted argument in json payload to shell script

Question

I am working on a python script that passes arguments to a shell script that lives in a Docker container. I'm achieving this using this Go webhook tool (https://github.com/adnanh/webhook). So far I've had success passing simple arguments to my shell script via the requests module. However, I've hit a roadblock.

The purpose of my tool is to trigger a dna assembly program that has a number of optional parameters that can be tuned by users. Currently, I have been triggering the webhook like so:

def trigger_assembler(out, assem_opts):
    id = "assemble"
    payload = {"FWD": f"-f data/{out}/R1.fq", "REV": f"-r data/{out}/R2.fq", "OUT": f"-o {out}",
                "OPT": f'-p \" {assem_opts} \"'}

    try:
        r = requests.post(f"http://0.0.0.0:9000/hooks/{id}", json=payload)
        r.raise_for_status()
    except requests.exceptions.RequestException as e:  # This is the correct syntax
        raise SystemExit(e)

In the shell script I am parsing the arguments and then trying to execute the following command:

   nohup Trinity --left "${FWD}" --right "${REV}" "${ASSEM_ARGS}" \
    --output data/"${OUT}"/trinity &

I have tried escaping the double quotes as you see in the example code. I have tried various numbers of backslashes after reading other stack overflow answers. I have tried simply using single quotes for the f-string and using double quotes within the string. None of these approaches has worked. No matter what I do there is a backslash present in the arguments delivered to my shell script, which obviously is problematic.

Also, I have tested the shell script in isolation with arguments of the form that I am hoping to pass and it works fine, so the problem seems to not be on that end.

Thanks for your help.

Answer 1

If anyone comes here looking for an answer, I never found one! I decided to store information in a yaml file that was accessible to all containers in my system. I would still very much like to know how to work around this problem in the future.

Answer 2

try this, pass-arguments-to-command pass argument as array start from 1

source: https://github.com/adnanh/webhook/issues/357

another reference https://gitlab.com/-/snippets/1972594

//payload json
{
    "data": {
        "id": "1651565",
        "username": "change me"
    }
}

---

//hook.json
[
  {
    "id": "payload",
    "execute-command": "/path/to/command.sh",
    "response-message": "Executing simple webhook...",
    "pass-arguments-to-command":
    [
      {
        "source": "payload",
        "name": "data.id"
      },
      {
        "source": "payload",
        "name": "data.username"
      }
   ]
  }
]

---

//command.sh
#!/bin/sh
ID=$1
USERNAME=$2

echo $ID //1651565
echo $USERNAME //change me