curl: (3) URL using bad/illegal format or missing URL

[jolespin]

Here's my error:

+ ZENODO_TOKEN=[token]
+ DEPOSITION=10081343
+ FILEPATH=S4_scaffolds.fasta.gz
++ echo S4_scaffolds.fasta.gz
++ sed 's+.*/++g'
+ FILENAME=S4_scaffolds.fasta.gz
++ curl -H 'Accept: application/json' -H 'Authorization: Bearer [token]' https://www.zenodo.org/api/deposit/depositions/10081343
++ jq --raw-output .links.bucket
  % Total    % Received % Xferd  Average Speed   Time    Time     Time  Current
                                 Dload  Upload   Total   Spent    Left  Speed
  0     0    0     0    0     0      0      0 --:--:-- --:--:-- --:--:--     0
+ BUCKET=
+ curl --progress-bar -o /dev/null --upload-file S4_scaffolds.fasta.gz '/S4_scaffolds.fasta.gz?access_token[token]'
curl: (3) URL using bad/illegal format or missing URL

Here's my script:

set -xe
ZENODO_TOKEN=[token]
DEPOSITION=$1
FILEPATH=$2
FILENAME=$(echo $FILEPATH | sed 's+.*/++g')

BUCKET=$(curl -H "Accept: application/json" -H "Authorization: Bearer $ZENODO_TOKEN" "https://www.zenodo.org/api/deposit/depositions/$DEPOSITION" | jq --raw-output .links.bucket)


curl --progress-bar -o /dev/null --upload-file $FILEPATH $BUCKET/$FILENAME?access_token=$ZENODO_TOKEN

[simone-says]

I'm having the same issue, any update on this?

[jolespin]

It's a little more complicated now. You gotta follow these instructions: https://developers.zenodo.org/

I ended up running the following script:

BUCKET=https://zenodo.org/api/files/[your-bucket-id]
ACCES_TOKEN=[your-access-token]
FILE=path/to/file
curl --progress-bar --upload-file ${FILE} ${BUCKET}/${FILE}?access_token=$ACCES_TOKEN

I forgot how I got the bucket id but I also have a json file that I don't remember making. That may have been where I got my bucket? It's been a few months since I ran this but that link I posted should have all the info you need.

[jveitchmichaelis]

Here's a typical workflow you can use in Python, based on the developer docs above. I used this in Colab:

import requests
from google.colab import userdata

ACCESS_TOKEN = userdata.get('ZENODO_TOKEN')
DEPOSITION_ID = <your-id>
r = requests.get(f'https://zenodo.org/api/deposit/depositions/{DEPOSITION_ID}',
                  params={'access_token': ACCESS_TOKEN})
r.status_code
data = r.json()

def upload(filename, path, bucket):
  # This is verbatim from the docs, but they forgot the params section
  with open(path, "rb") as fp:
      r = requests.put(
          "%s/%s" % (bucket, filename),
          data=fp,
          params={'access_token': ACCESS_TOKEN},
      )
  return r.json()

Usage:

upload(file, path, data['links']['bucket'])

Seems to work fine for me.