upload-to-zenodo

A simple, stupid, quick and dirty script to batch upload papers to Zenodo.

What is Zenodo?

Zenodo is a free, open-source research repository, containing papers, but also data sets and software.

Quick start for CCG

You don't want to accidentally flood your real Zenodo account with dummy submissions. We don't want that either. That's why by default the script upload_to_zenodo.py uses the sandbox of Zenodo. When you are done with experimenting, just replace sandbox.zenodo.org with zenodo.org in that script.

1. Get a Personal access token at https://zenodo.org/account/settings/applications/. The deposit:write is enough: to be on the safe side, the script does not publish the uploaded papers, the Publish button has to be pushed manually. (Once a document is published on Zenodo, the attached files cannot be modified.)
2. Paste your personal token into a file called .token and place in your working directory (or paste into run.bat file)
3. Place Starter Kit - List of Countries.xlsx in the root folder
4. Place authors.xlsx in the root folder
5. Place subfolders of csv files in the data folder. Subfolder names should match country names in Starter Kit - List of Countries.xlsx
6. You may wish to update certain fields in data/template.txt such as publication date. This is used as a template for each of the metadata files generated in the next step.
7. Run run.sh (Linux or OSX) or run.bat (Windows). This scripts should first create a file data/data.csv which contains all of the countries info. Then, individual <country>.json Zenodo metadata files are created. Finally, the folders are uploaded to Zenodo.

Customising the uploads

1. Create a template JSON describing your submissions. Check the documentation (Representations > Deposition metadata) for details about it.

   • Use {key-name} for parts that are different for each submission.
   • An example template and some example deposition metadata files can be found in the example folder.
   • The JSON description of any submitted document can be checked by clicking on the JSON link in the Export panel (or by checking the https://zenodo.org/record/{ID}/export/json URL.)

2. Create a CSV file that describes the parts that are different for each submission.

   • The {key-name} strings of the template will be replaced by the values from the colmn having key-name as header in the CSV file.
   • The CSV file should contain a FILENAME column, describing the name of the file created by substituting the values from the given row to the template.

3. Place the CSV datafile and template into the data folder.

4. Execute the script fill_template.py to generate the descriptors (deposition metadata) for each submission.

   • Usage: fill_template.py <template_filename> <data_filename>, where <template_filename> is the name (path) of the template file, and <data_filename> is the name (path) of the CSV data file.

5. Place subfolders of CSV files into the data folder

6. Execute the script upload_to_zenodo.py to upload your submissions.

   • Usage: upload_to_zenodo.py <token> <directory>, where <token> is your personal access token, and <directory> is the directory that contains the JSON and PDF files to be uploaded.

7. Go to the Upload page, check and publish your submissions.