I am running the below code in Google Colab and get The server encountered an internal error or misconfiguration and was unable to complete your request
. If I am running the command without passing in the variable $data
like below, it runs perfectly fine. Only when I'm looping through the file and passing variables it seems to be failing
import csv
import json
reader = csv.reader(open('/content/drive/MyDrive/file5.csv'))
for row in reader:
data = {"snps": row[0], "pop": "YRI", "r2_threshold": "0.9", "maf_threshold": "0.01"}
data = json.dumps(data)
data = "'{}'".format(data)
!curl -k -H "Content-Type: application/json" -X POST -d "$data" 'https://ldlink.nci.nih.gov/LDlinkRest/snpclip?token=e3e559472899'
This works:
!curl -k -H "Content-Type: application/json" -X POST -d '{"snps": "rs3\nrs4", "pop":"YRI", "r2_threshold": "0.1", "maf_threshold": "0.01"}' 'https://ldlink.nci.nih.gov/LDlinkRest/snpclip?token=e3e559472899'
CodePudding user response:
UPDATE: Actually, ipython
does allow you to run !
escapes in a loop; the actual error in your code is purely in the incorrect quoting (especially the addition of single quotes around the data
value, but there could be more).
Original (partially incorrect) answer below.
The !
escape tells your notebook (Google Colab, Jupyter, or what have you; basically whatever is running ipython
as a kernel or similar) to leave Python and run a shell command. Python itself has no support for this; the closest approximation would be something like
import subprocess
...
for row in reader:
data = {"snps": row[0], "pop": "YRI", "r2_threshold": "0.9", "maf_threshold": "0.01"}
data = json.dumps(data)
# This was wrong on so many levels
# data = "'{}'".format(data)
subprocess.run(['curl', '-k',
'-H', "Content-Type: application/json",
'-X', 'POST', '-d', data,
'https://ldlink.nci.nih.gov/LDlinkRest/snpclip?token=e3e559472899'],
text=True, check=True)
though avoiding subprocess
and running Python urllib
or requests
code to perform the POST
would be more efficient and elegant, and give you more control over what gets sent and how it gets handled.
How to properly quote strings when translating between shell commands and Python requires you to understand the shell's quoting behavior. I'll just briefly note that I left double quotes where they were not incorrect in your original command, but otherwise preferred single quotes, and of course, data
now refers to a proper Python variable with that name, not a shell variable with the same name.
To reiterate: ipython
(which is what your notebook is an interface to) knows how to run both Python code and shell scipt code via !
; but once you ask it to run Python code, ipython
hands it over to Python proper, and you are no longer in ipython
.