* Template Name

Optional text description

** Metadata

#+NAME: datalad-meta
#+BEGIN_SRC python :results output verbatim drawer :exports results
import json

with open("meta.json") as file:
    data = json.load(file)

for item in data:
    if item[0] == '@': continue
    print('|', item, '|', data[item], '|')
#+END_SRC

#+RESULTS: datalad-meta
:results:
| name              | Template data  |
| science reference | Paper citation |
| science DOI       | doi:           |
| data DOI          | doi:           |
| data URL          | https://       |
| keywords          | foo, bar       |
:end:


** Create dataset
:PROPERTIES:
:CUSTOM_ID: ceate-data
:END:

+ Remove the following text, or replace with explanation of how datalad dataset is created
+ Replace the =bash= block with =python= or other preferred language
+ Keep the =#+NAME: datalad-create= name so that these blocks can be called via script

#+NAME: datalad-create
#+BEGIN_SRC bash
# datalad create -f -d . -c text2git -D "Template"
datalad create -f -d . -D "Cryo data template"

git remote add origin git@github.com:cryo-data/template.git

git add meta.json README.org
git commit -m "README & metadata"
git branch -M main
git push -u origin main
#+END_SRC

** How to use this template
:PROPERTIES:
:CUSTOM_ID: how-to-use-this-template
:END:

+ Pick a name for the new dataset
  + Folder name should be "Author_YYYY" if possible, or some other common name for the dataset (e.g. =ArcticDEM= or =MEaSUREs.0471=)
  + In this example, we'll use =Mankoff_2020=, and convert https://dataverse01.geus.dk/dataset.xhtml?persistentId=doi:10.22008/promice/data/ice_discharge/d/v02 to a datalad dataset.

+ Copy template to clean directory using the new dataset name

#+BEGIN_SRC bash
dest="Mankoff_2020"
git clone https://github.com/cryo-data/template.git ${dest}
cd ${dest}
#+END_SRC

+ Set up a new repository, ideally under the [[https://github.com/cryo-data][cryo-data portal on GitHub]], but can be hosted anywhere.
  + Set up by visiting https://github.com/organizations/cryo-data/repositories/new and do **not** initialize with any files, then:

#+BEGIN_SRC bash
git remote rm origin
git remote add origin git@github.com:cryo-data/${dest}.git
git branch -M main
git push -u origin main
#+END_SRC

+ If the dataset already contains its own =README.org=, then keep that and rename this one to =datalad.org=

#+BEGIN_SRC bash
git mv README.org datalad.org
git commit datalad.org -m 'Rename README.org to datalad.org because dataset has README.org'
#+END_SRC

+ Populate the datalad dataset 
  + NOTE :: The code below should go into the [[#create-data][create data]] section above.

The code below downloads each file using ~datalad download-url~. This is one of many ways to populate a dalatad dataset.

+ TODO: Show examples for adding data that is accessible via an archive (Zenodo?) or data already in git.
+ TODO: Provide small shell or Python script in template folder for traversing and downloading remote directory structure (e.g. =wget -r ...=).

#+BEGIN_SRC bash
export SERVER=https://dataverse01.geus.dk
export DOI=10.22008/promice/data/ice_discharge/d/v02

curl ${SERVER}/api/datasets/:persistentId?persistentId=doi:${DOI} > dv.json
cat dv.json | tr ',' '\n' | grep -E '"persistentId"' | cut -d'"' -f4 > urls.txt
while read -r PID; do
  datalad download-url $SERVER/api/access/datafile/:persistentId?persistentId=${PID}
done < urls.txt
rm dv.json urls.txt # cleanup
#+END_SRC

+ Push changes

#+BEGIN_SRC bash
git push
#+END_SRC

+ Remove [[#how-to-use-this-template][this section]] from the [[./README.org]] file.