8.6. Walk-through: Dataset hosting on GIN

GIN (G-Node infrastructure) is a free data management system designed for comprehensive and reproducible management of scientific data. It is a web-based repository store and provides fine-grained access control to share data. GIN builds up on Git and git-annex, and is an easy alternative to other third-party services to host and share your DataLad datasets[1]. It allows to share datasets and their contents with selected collaborators or making them publicly and anonymously available. And even if you prefer to expose and share your datasets via GitHub, you can still use GIN to host your data.

Fig. 8.22 Some repository hosting services such as GIN have annex support, and can thus hold the complete dataset. This makes publishing datasets very easy.

8.6.1. Prerequisites

In order to use GIN for hosting and sharing your datasets, you need to

• register

• upload your public SSH key for SSH access

Once you have registered an account on the GIN server by providing your e-mail address, affiliation, and name, and selecting a user name and password, you should upload your SSH key to allow SSH access (you can find an explanation of what SSH keys are and how you can create one in this Findoutmore in the general section Publishing datasets to Git repository hosting). To do this, visit the settings of your user account. On the left hand side, select the tab “SSH Keys”, and click the button “Add Key”:

Fig. 8.23 Upload your SSH key to GIN

You should copy the contents of your public key file into the field labeled content, and enter an arbitrary but informative Key Name, such as “My private work station”. Afterwards, you are done!

8.6.2. Publishing your dataset to GIN

As outlined in the section Publishing datasets to Git repository hosting, there are two ways in which you can publish your dataset to GIN. Either by 1) creating a new, empty repository on GIN via the web interface, or 2) via the datalad create-sibling-gin (manual) command.

1) via webinterface: If you choose to create a new repository via GIN’s web interface, make sure to not initialize it with a README:

Fig. 8.24 Create a new repository on GIN using the web interface.

Afterwards, add this repository as a sibling of your dataset. To do this, use the datalad siblings add (manual) command and the SSH URL of the repository as shown below. Note that since this is the first time you will be connecting to the GIN server via SSH, you will likely be asked to confirm to connect. This is a safety measure, and you can type “yes” to continue:

$ datalad siblings add -d . \
  --name gin \
  --url git@gin.g-node.org:/adswa/DataLad-101.git

The authenticity of host 'gin.g-node.org (141.84.41.219)' can't be established.
ECDSA key fingerprint is SHA256:E35RRG3bhoAm/WD+0dqKpFnxJ9+yi0uUiFLi+H/lkdU.
Are you sure you want to continue connecting (yes/no)? yes
[INFO   ] Failed to enable annex remote gin, could be a pure git or not accessible
[WARNING] Failed to determine if gin carries annex.
.: gin(-) [git@gin.g-node.org:/adswa/DataLad-101.git (git)]

2) via command-line: If you choose to use the datalad create-sibling-gin command, supply the command with a name for the repository, and optionally add a -s/--siblingname [NAME] parameter (if unconfigured it will be gin), and --access-protocol [https|ssh|https-ssh] (ideally ssh). The command has a number of additional useful parameters, so make sure to take a look at its --help.

Afterwards, you can publish your dataset with datalad push (manual). As the repository on GIN supports a dataset annex, there is no publication dependency to an external data hosting service necessary, and the dataset contents stored in Git and in git-annex are published to the same place:

$ datalad push --to gin
copy(ok): books/TLCL.pdf (file) [to gin...]
copy(ok): books/bash_guide.pdf (file) [to gin...]
copy(ok): books/byte-of-python.pdf (file) [to gin...]
copy(ok): books/progit.pdf (file) [to gin...]
publish(ok): . (dataset) [refs/heads/git-annex->gin:refs/heads/git-annex ✂FROM✂..✂TO✂]
publish(ok): . (dataset) [refs/heads/main->gin:refs/heads/main [new branch]]

On the GIN web interface you will find all of your dataset – including annexed contents! What is especially cool is that the GIN web interface (unlike GitHub) can even preview your annexed contents.

Fig. 8.25 A published dataset in a GIN repository at gin.g-node.org.

8.6.3. Sharing and accessing the dataset

Once your dataset is published, you can point collaborators and friends to it.

If it is a public repository, retrieving the dataset and getting access to all published data contents (in a read-only fashion) is done by cloning the repository’s https url. This does not require a user account on GIN.

Take the URL in the browser, not the copy-paste URL

Please note that you need to use the browser URL of the repository, not the copy-paste URL on the upper right hand side of the repository if you want to get anonymous HTTPS access! The two URLs differ only by a .git extension:

• Browser bar: https://gin.g-node.org/<user>/<repo>

• Copy-paste “HTTPS clone”: https://gin.g-node.org/<user>/<repo>.git

A dataset cloned from https://gin.g-node.org/<user>/<repo>.git, however, cannot retrieve annexed files!

$ datalad clone https://gin.g-node.org/adswa/DataLad-101
install(ok): /home/me/dl-101/clone_of_dl-101/DataLad-101 (dataset)

Subsequently, datalad get (manual) calls will be able to retrieve all annexed file contents that have been published to the repository.

If it is a private dataset, cloning the dataset from GIN requires a user name and password for anyone you want to share your dataset with. The “Collaboration” tab under Settings lets you set fine-grained access rights, and it is possible to share datasets with collaborators that are not registered on GIN with provided Guest accounts. If you are unsure if your dataset is private, this find-out-more shows you how to find out. In order to get access to annexed contents, cloning requires setting up an SSH key as detailed above, and cloning via the SSH url:

$ datalad clone git@gin.g-node.org:/adswa/DataLad-101.git

Likewise, in order to publish changes back to a GIN repository, the repository needs to be cloned via its SSH url.

How do I know if my repository is private?

Private repos are marked with a lock sign. To make it public, untick the “Private” box, found under “Settings”:

8.6.4. Subdataset publishing

Just as the input subdataset iris_data in your published midterm_project was referencing its source on GitHub, the longnow subdataset in your published DataLad-101 dataset directly references the original dataset on GitHub. If you click onto recordings and then longnow in GIN’s webinterface, you will be redirected to the podcast’s original dataset.

The subdataset midterm_project, however, is not successfully referenced. If you click on it, you would get to a 404 Error page. The crucial difference between this subdataset and the longnow dataset is its entry in the .gitmodules file of DataLad-101:

$ cat .gitmodules
[submodule "recordings/longnow"]
        path = recordings/longnow
        url = https://github.com/datalad-datasets/longnow-podcasts.git
        datalad-id = b3ca2718-8901-11e8-99aa-a0369f7c647e
[submodule "midterm_project"]
        path = midterm_project
        url = ./midterm_project
        datalad-id = e5a3d370-223d-11ea-af8b-e86a64c8054c

While the longnow subdataset is referenced with a valid URL to GitHub, the midterm project’s URL is a relative path from the root of the superdataset. This is because the longnow subdataset was installed with datalad clone -d . (manual) (that records the source of the subdataset), and the midterm_project dataset was created as a subdataset with datalad create -d . midterm_project (manual). Since there is no repository at https://gin.g-node.org/<USER>/DataLad-101/midterm_project (which this submodule entry would resolve to), accessing the subdataset fails.

However, since you have already published this dataset (to GitHub), you could update the submodule entry and provide the accessible GitHub URL instead. This can be done via the set-property <NAME> <VALUE> option of datalad subdatasets (manual)[2] (replace the URL shown here with the URL your dataset was published to – likely, you only need to change the user name):

$ datalad subdatasets --contains midterm_project \
  --set-property url https://github.com/adswa/midtermproject
add(ok): .gitmodules (file)
save(ok): . (dataset)
subdataset(ok): midterm_project (dataset)

$ cat .gitmodules
[submodule "recordings/longnow"]
	path = recordings/longnow
	url = https://github.com/datalad-datasets/longnow-podcasts.git
	datalad-id = b3ca2718-8901-11e8-99aa-a0369f7c647e
	datalad-url = https://github.com/datalad-datasets/longnow-podcasts.git
[submodule "midterm_project"]
	path = midterm_project
	url = https://github.com/adswa/midtermproject
	datalad-id = d95bafc8-f2a4-d27b-dcf4-bb99f4bea973

Handily, the datalad subdatasets command saved this change to the .gitmodules file automatically and the state of the dataset is clean:

$ datalad status
nothing to save, working tree clean

Afterwards, publish these changes to gin and see for yourself how this fixed the problem:

$ datalad push --to gin
publish(ok): . (dataset) [refs/heads/main->gin:refs/heads/main 6d3d93b..344b0ec]
action summary:
  publish (notneeded: 1, ok: 1)

If the subdataset was not published before, you could publish the subdataset to a location of your choice, and modify the .gitmodules entry accordingly.

8.6.5. Using GIN as a data source behind the scenes

Even if you do not want to point collaborators to yet another hosting site but want to be able to expose your datasets via services they use and know already (such as GitHub or GitLab), GIN can be very useful: You can let GIN perform data hosting in the background by using it as an “autoenabled data source” that a dataset sibling (even if it is published to GitHub or GitLab) can retrieve data from. You will need to have a GIN account and SSH key setup, so please take a look at the first part of this section if you do not yet know how to do this.

Then, follow these steps:

• First, create a new repository on GIN (see step by step instructions above).

• In your to-be-published dataset, add this repository as a sibling, this time setting –url and –pushurl arguments explicitly. Make sure to configure a SSH URL as a --pushurl but a HTTPS URL as a url. Please also note that the HTTPS URL written after --url DOES NOT have the .git suffix. Here is the command:

$ datalad siblings add \
 -d . \
 --name gin \
 --pushurl git@gin.g-node.org:/studyforrest/aggregate-fmri-timeseries.git \
 --url https://gin.g-node.org/studyforrest/aggregate-fmri-timeseries \

• Locally, run git config --unset-all remote.gin.annex-ignore to prevent git-annex from ignoring this new dataset

• Push your data to the repository on GIN (datalad push --to gin). This pushes the actual state of the repository, including content, but also adjusts the git-annex configuration.

• Configure this sibling as a “common data source”. Use the same name as previously in --name (to indicate which sibling you are configuring) and give a new, different, name after --as-common-datasrc:

$ datalad siblings configure \
   --name gin \
   --as-common-datasrc gin-src

• Push to the repository on GIN again (datalad push --to gin) to make the configuration change known to the Gin sibling.

• Publish your dataset to GitHub/GitLab/…, or update an existing published dataset (datalad push)

Afterwards, datalad get retrieves files from GIN, even if the dataset has been cloned from GitHub.

Siblings as a common data source

The argument as-common-datasrc <name> configures a sibling as a common data source – in technical terms, as an auto-enabled git-annex special remote.

Footnotes

[1]

GIN looks and feels similar to GitHub, and among a number advantages, it can assign a DOI to your dataset, making it cite-able. Moreover, its web interface and client are useful tools with a variety of features that are worthwhile to check out, as well.

[2]

Alternatively, you can configure the siblings URL with git config (manual):

$ git config -f .gitmodules --replace-all  submodule.midterm_project.url https://github.com/adswa/midtermproject

Remember, though, that this command modifies .gitmodules without an automatic, subsequent datalad save (manual), so that you will have to save this change manually.