4.4. Stay up to date

All of what you have seen about sharing dataset was really cool, and for the most part also surprisingly intuitive. datalad run commands or file retrieval worked exactly as you imagined it to work, and you begin to think that slowly but steadily you’re getting a feel about how DataLad really works.

But to be honest, so far, sharing the dataset with DataLad was also remarkably unexciting given that you already knew most of the dataset magic that your room mate currently is still mesmerized about. To be honest, you’re not yet certain whether sharing data with DataLad really improves your life up until this point. After all, you could have just copied your directory into your mock_user directory and this would have resulted in about the same output, right?

What we will be looking into now is how shared DataLad datasets can be updated.

Remember that you added some notes on datalad clone, datalad get, and git annex whereis into the original DataLad-101?

This is a change that is not reflected in your “shared” installation in ../mock_user/DataLad-101:

# inside the installed copy, view the last 15 lines of notes.txt
$ tail notes.txt
it. If no changes happen with a rerun, the command will not be written
to history. Note: you can also rerun a datalad rerun command!

You should specify all files that a command takes as input with an
-i/--input flag. These files will be retrieved prior to the command
execution. Any content that is modified or produced by the command
should be specified with an -o/--output flag. Upon a run or rerun of
the command, the contents of these files will get unlocked so that
they can be modified.

Important! If the dataset is not "clean" (a datalad status output is
empty), datalad run will not work - you will have to save
modifications present in your dataset.
A suboptimal alternative is the --explicit flag, used to record only
those changes done to the files listed with --output flags.

But the original intention of sharing the dataset with your room mate was to give him access to your notes. How does he get the notes that you have added in the last two sections, for example?

This installed copy of DataLad-101 knows its origin, i.e., the place it was installed from. Using this information, it can query the original dataset whether any changes happened since the last time it checked, and if so, retrieve and integrate them.

This is done with the datalad update --merge command (datalad-update manual).

$ datalad update --merge
[INFO] Fetching updates for Dataset(/home/me/dl-101/mock_user/DataLad-101)
[INFO] Start enumerating objects
[INFO] Start counting objects
[INFO] Start compressing objects
merge(ok): . (dataset) [Merged origin/master]
update(ok): . (dataset)
action summary:
  merge (ok: 1)
  update (ok: 1)

Importantly, run this command either within the specific (sub)dataset you are interested in, or provide a path to the root of the dataset you are interested in with the -d/--dataset flag. If you would run the command within the longnow subdataset, you would query this subdatasets’ origin for updates, not the original DataLad-101 dataset.

Let’s check the contents in notes.txt to see whether the previously missing changes are now present:

# view the last 15 lines of notes.txt
$ tail notes.txt
Note that subdatasets will not be installed by default, but are only
registered in the superdataset -- you will have to do a
"datalad get -n PATH/TO/SUBDATASET" to install the subdataset for file
availability meta data. The -n/--no-data options prevents that file
contents are also downloaded.

Note that a recursive "datalad get" would install all further
registered subdatasets underneath a subdataset, so a safer way to
proceed is to set a decent --recursion-limit:
"datalad get -n -r --recursion-limit 2 <subds>"

The command "git annex whereis PATH" lists the repositories that have
the file content of an annexed file. When using "datalad get" to
retrieve file content, those repositories will be queried.

Wohoo, the contents are here!

Therefore, sharing DataLad datasets by installing them enables you to update the datasets content should the original datasets’ content change – in only a single command. How cool is that?!

Conclude this section by adding a note about updating a dataset to your own DataLad-101 dataset:

# navigate back:
$ cd ../../DataLad-101

# write the note
$ cat << EOT >> notes.txt
To update a shared dataset, run the command "datalad update --merge".
This command will query its origin for changes, and integrate the
changes into the dataset.

# save the changes

$ datalad save -m "add note about datalad update"
add(ok): notes.txt (file)
save(ok): . (dataset)
action summary:
  add (ok: 1)
  save (ok: 1)

PS: You might wonder whether there is also a sole datalad update command. Yes, there is – if you are a Git-user and know about branches and merging you can read the Note for Git-users below. However, a thorough explanation and demonstration will be in the next section.

Update internals

datalad update is the DataLad equivalent of a git fetch, datalad update --merge is the DataLad equivalent of a git pull. Upon a simple datalad update, the remote information is available on a branch separate from the master branch – in most cases this will be remotes/origin/master. You can git checkout this branch or run git diff to explore the changes and identify potential merge conflicts.