Sake.re: Experiment sharing and publishing

See the prerequisite and be sure to be familiar with Sake.re.

Experiments may be published at any point of their lifecyle. They may first be registered in the cakes repository serving as a way to record experiments and the changes made to them. They may later be posted and synchronised with the sake.re web site, but not necessarily made accessible through a published link. Then they may be made visible on the sake.re web site and the results (in fact the full repository content) may be published in a bona fide research data repository: we provide the example for doing this on zenodo.

Sharing experiments in the cakes repository

$ git remote add origin cakes@felapton.inrialpes.fr:${LABEL}.git
$ git push -u --all
$ git push --tags

This can, and preferably should, be done early (as early as the design stage). This could play the role of preregistration. In this case, it is useful to push and tag the changes at all steps during design.

Publishing experiments on the sake.re web site

The generated html file can be made available online. The experiment should be found under https://sake.re/${LABEL} as soon as you registered it in the cakes repository.

For that reason, it is good that the notebook provides direct access to the various resources: params.sh and script.sh, input, result and the zip files containing all this.

To have it indexed on the sake.re index, ask for it as the same address as above.

The page can still be updated from the git repository, for instance, for adding within the notebook image a link to the results when published on files.inria.fr or Zenodo.

Creating a clean zip archive

It may be useful, for archiving on various places to create a minimal zip archive, containing all results, but only files of interest. This can be obtained in the following way:

$ git submodule deinit --all              # beware that there is no stuff there (compile results)
$ git reflog expire --all --expire=now    # next instructions to reduce the size of the zip
$ git gc --prune=now --aggressive
$ cd ..
$ zip -r -q ${LABEL}.zip ${LABEL}/        # Takes the .git as well

Instructions to publish results on Zenodo

In order to record an experiment under Zenodo, you first need to create a zenodo account. All the process can be achieved through the website, we describe the command line approach.

Generate the metadata needed by zenodo:

$ bash lazylav/scripts/genMetadata.sh

Create the zip file as above will generate a ${LABEL}.zip (and move you to the parent directory).

Get a zenodo token from this link https://zenodo.org/account/settings/applications/tokens/new/ and assign it to a variable (also set a variable for the zenodo server; sandbox.zenodo.org may be used for testing):

$ TOKEN=<paste_your_token_here>
$ ZENSERV=zenodo.org

Declare a new deposition:

$ DEP=$(curl -H "Content-Type: application/json" -X POST --data @${LABEL}/metadata.json "https://${ZENSERV}/api/deposit/depositions?access_token=${TOKEN}")

Extract ID and BUCKET link from the returned JSon (uses jq; can also be done manually):

$ ID=$(echo "${DEP}" | jq --raw-output .id)
$ BUCKET=$(echo "${DEP}" | jq --raw-output .links.bucket)

Upload the zip file:

$ curl --upload-file ${LABEL}.zip -X PUT "${BUCKET}/${LABEL}.zip?access_token=${TOKEN}"

Publish the deposition:

$ curl -i -X POST "https://${ZENSERV}/api/deposit/depositions/${ID}/actions/publish?access_token=${TOKEN}"

It is possible to modify the experiment description just after creating the deposit to include the DOI in them. This is achieved in markdown by (replace ${ID} by its value):

[![DOI:10.5281/zenodo.${ID}](https://zenodo.org/badge/DOI/10.5281/zenodo.${ID}.svg)](https://doi.org/10.5281/zenodo.${ID})

It is also possible to upload new versions of depositions.