To get a hang on the basics of sharing a dataset,
you shared your
DataLad-101 dataset with your
room mate on a common, local file system. Your lucky
room mate now has your notes and can thus try to catch
up to still pass the course.
Moreover, though, he can also integrate all other notes
or changes you make to your dataset, and stay up to date.
This is because a DataLad dataset makes updating shared
data a matter of a single datalad update --how merge command.
But why does this need to be a one-way line? “I want to provide helpful information for you as well!”, says your room mate. “How could you get any insightful notes that I make in my dataset, or maybe the results of our upcoming mid-term project? Its a bit unfair that I can get your work, but you can not get mine.”
Consider, for example, that your room mate might have googled about DataLad
a bit. In the depths of the web, he might have found useful additional information, such
a script on dataset nesting.
Because he found this very helpful in understanding dataset
nesting concepts, he decided to download it from GitHub, and saved it in the
He does it using the datalad command datalad download-url
that you experienced in section Create a dataset already: This command will
download a file just as
wget, but it can also take a commit message
and will save the download right to the history of the dataset that you specify,
while recording its origin as provenance information.
Navigate into your dataset copy in
and run the following command
# navigate into the installed copy $ cd ../mock_user/DataLad-101 # download the shell script and save it in your code/ directory $ datalad download-url \ -d . \ -m "Include nesting demo from datalad website" \ -O code/nested_repos.sh \ https://raw.githubusercontent.com/datalad/datalad.org/7e8e39b1f08d0a54ab521586f27ee918b4441d69/content/asciicast/seamless_nested_repos.sh [INFO] Downloading 'https://raw.githubusercontent.com/datalad/datalad.org/7e8e39b1f08d0a54ab521586f27ee918b4441d69/content/asciicast/seamless_nested_repos.sh' into '/home/me/dl-101/mock_user/DataLad-101/code/nested_repos.sh' download_url(ok): /home/me/dl-101/mock_user/DataLad-101/code/nested_repos.sh (file) add(ok): code/nested_repos.sh (file) save(ok): . (dataset) action summary: add (ok: 1) download_url (ok: 1) save (ok: 1)
Run a quick datalad status:
$ datalad status nothing to save, working tree clean
Nice, the datalad download-url command saved this download right into the history, and datalad status does not report unsaved modifications! We’ll show an excerpt of the last commit here:
$ git log -n 1 -p commit 2c4f079eed776f7d3465fa38d9619771aae6ff60 Author: Elena Piscopia <email@example.com> Date: Tue Jun 18 16:13:00 2019 +0000 Include nesting demo from datalad website diff --git a/code/nested_repos.sh b/code/nested_repos.sh new file mode 100644 index 0000000..f84c817 --- /dev/null +++ b/code/nested_repos.sh @@ -0,0 +1,59 @@
Suddenly, your room mate has a file change that you do not have. His dataset evolved.
So how do we link back from the copy of the dataset to its origin, such that your room mate’s changes can be included in your dataset? How do we let the original dataset “know” about this copy your room mate has? Do we need to install the installed dataset of our room mate as a copy again?
No, luckily, it’s simpler and less convoluted. What we have to do is to register a datalad sibling: A reference to our room mate’s dataset in our own, original dataset.
Git repositories can configure clones of a dataset as remotes in order to fetch, pull, or push from and to them. A datalad sibling is the equivalent of a git clone that is configured as a remote.
Let’s see how this is done.
First of all, navigate back into the original dataset.
In the original dataset, “add” a “sibling” by using
the datalad siblings command (datalad-siblings manual).
The command takes the base command,
datalad siblings, an action, in this case
add, a path to the
root of the dataset
-d ., a name for the sibling,
and a URL or path to the sibling,
This registers your room mate’s
DataLad-101 as a “sibling” (we will call it
“roommate”) to your own
$ cd ../../DataLad-101 # add a sibling $ datalad siblings add -d . \ --name roommate --url ../mock_user/DataLad-101 .: roommate(+) [../mock_user/DataLad-101 (git)]
There are a few confusing parts about this command: For one, do not be surprised
--url argument – it’s called “URL” but it can be a path as well.
Also, do not forget to give a name to your dataset’s sibling. Without the
--name argument the command will fail. The reason behind this is that the default
name of a sibling if no name is given will be the host name of the specified URL,
but as you provide a path and not a URL, there is no host name to take as a default.
As you can see in the command output, the addition of a sibling succeeded:
roommate(+)[../mock_user/DataLad-101] means that your room mate’s dataset
is now known to your own dataset as “roommate”
$ datalad siblings .: here(+) [git] .: roommate(+) [../mock_user/DataLad-101 (git)]
This command will list all known siblings of the dataset. You can see it in the resulting list with the name “roommate” you have given to it.
What if I mistyped the name or want to remove the sibling?
You can remove a sibling using datalad siblings remove -s roommate
The fact that the
DataLad-101 dataset now has a sibling means that we
can also datalad update this repository. Awesome!
Your room mate previously ran a datalad update --how merge in the section Stay up to date. This got him changes he knew you made into a dataset that he so far did not change. This meant that nothing unexpected would happen with the datalad update --how merge.
But consider the current case: Your room mate made changes to his dataset, but you do not necessarily know which. You also made changes to your dataset in the meantime, and added a note on datalad update. How would you know that his changes and your changes are not in conflict with each other?
This scenario is where a plain datalad update becomes useful.
If you run a plain datalad update (which uses the default option
--how fetch), DataLad will query the sibling
for changes, and store those changes in a safe place in your own
dataset, but it will not yet integrate them into your dataset.
This gives you a chance to see whether you actually want to have the
changes your room mate made.
Let’s see how it’s done. First, run a plain datalad update without
--how merge option.
$ datalad update -s roommate [INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) [INFO] Start enumerating objects [INFO] Start counting objects [INFO] Start compressing objects update(ok): . (dataset)
Note that we supplied the sibling’s name with the
This is good practice, and allows you to be precise in where you want to get
updates from. It would have worked without the specification (just as a bare
datalad update --how merge worked for your room mate), because there is only
one other known location, though.
This plain datalad update informs you that it “fetched” updates from
the dataset. The changes however, are not yet visible – the script that
he added is not yet in your
$ ls code/ list_titles.sh
So where is the file? It is in a different branch of your dataset.
If you do not use Git, the concept of a branch can be a big source of confusion. There will be sections later in this book that will elaborate a bit more what branches are, and how to work with them, but for now envision a branch just like a bunch of drawers on your desk. The paperwork that you have in front of you right on your desk is your dataset as you currently see it. These drawers instead hold documents that you are in principle working on, just not now – maybe different versions of paperwork you currently have in front of you, or maybe other files than the ones currently in front of you on your desk.
Imagine that a datalad update created a small drawer, placed all of the changed or added files from the sibling inside, and put it on your desk. You can now take a look into that drawer to see whether you want to have the changes right in front of you.
The drawer is a branch, and it is usually called
To look inside of it you can git checkout BRANCHNAME, or you can
diff between the branch (your drawer) and the dataset as it
is currently in front of you (your desk). We will do the latter, and leave
the former for a different lecture:
Please use datalad diff –from master –to remotes/roommate/master
Please use the following command instead:
datalad diff --from master --to remotes/roommate/master
This syntax specifies the master branch as a starting point for the comparison instead of the current
$ datalad diff --to remotes/roommate/master added: code/nested_repos.sh (file) modified: notes.txt (file)
This shows us that there is an additional file, and it also shows us
that there is a difference in
notes.txt! Let’s ask
git diff to show us what the differences in detail (note that it is a shortened excerpt, cut in the middle to reduce its length):
Please use git diff master..remotes/roommate/master
Please use the following command instead:
git diff master..remotes/roommate/master
This is Gits syntax for specifying a comparison between two branches.
$ git diff remotes/roommate/master diff --git a/code/nested_repos.sh b/code/nested_repos.sh deleted file mode 100644 index f84c817..0000000 --- a/code/nested_repos.sh +++ /dev/null @@ -1,59 +0,0 @@ -#!/bin/bash -# This script was converted using cast2script from: -# docs/casts/seamless_nested_repos.sh -set -e -u -export GIT_PAGER=cat - -# DataLad provides seamless management of nested Git repositories... - -# Let's create a dataset -datalad create demo -cd demo diff --git a/notes.txt b/notes.txt index 655be7d..3bf3281 100644 --- a/notes.txt +++ b/notes.txt @@ -59,3 +59,7 @@ 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. +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. +
Let’s digress into what is shown here.
We are comparing the current state of your dataset against
the current state of your room mate’s dataset. Everything marked with
- is a change that your room mate has, but not you: This is the
script that he downloaded!
Everything that is marked with a
+ is a change that you have,
but not your room mate: It is the additional note on datalad update
you made in your own dataset in the previous section.
Cool! So now that you know what the changes are that your room mate made, you can safely datalad update --how merge them to integrate them into your dataset. In technical terms you will “merge the branch remotes/roommate/master into master”. But the details of this will be stated in a standalone section later.
Note that the fact that your room mate does not have the note on datalad update does not influence your note. It will not get deleted by the merge. You do not set your dataset to the state of your room mate’s dataset, but you incorporate all changes he made – which is only the addition of the script.
$ datalad update --merge -s roommate [INFO] Fetching updates for Dataset(/home/me/dl-101/DataLad-101) merge(ok): . (dataset) [Merged roommate/master] update.annex_merge(ok): . (dataset) [Merged annex branch] update(ok): . (dataset) action summary: merge (ok: 1) update (ok: 1) update.annex_merge (ok: 1)
The exciting question is now whether your room mate’s change is now
also part of your own dataset. Let’s list the contents of the
directory and also peek into the history:
$ ls code/ list_titles.sh nested_repos.sh
$ git log --oneline 0c0c105 Merge remote-tracking branch 'roommate/master' f70d195 add note about datalad update 2c4f079 Include nesting demo from datalad website 11b542b add note on git annex whereis fd551f7 add note about cloning from paths and recursive datalad get
Wohoo! Here it is: The script now also exists in your own dataset.
You can see the commit that your room mate made when he saved the script,
and you can also see a commit that records how you
room mate’s dataset changes into your own dataset. The commit message of this
latter commit for now might contain many words yet unknown to you if you
do not use Git, but a later section will get into the details of what
the meaning of “merge”, “branch”, “refs”
or “master” is.
For now, you’re happy to have the changes your room mate made available. This is how it should be! You helped him, and he helps you. Awesome! There actually is a wonderful word for it: Collaboration. Thus, without noticing, you have successfully collaborated for the first time using DataLad datasets.
Create a note about this, and save it.
$ cat << EOT >> notes.txt To update from a dataset with a shared history, you need to add this dataset as a sibling to your dataset. "Adding a sibling" means providing DataLad with info about the location of a dataset, and a name for it. Afterwards, a "datalad update --merge -s name" will integrate the changes made to the sibling into the dataset. A safe step in between is to do a "datalad update -s name" and checkout the changes with "git/datalad diff" to remotes/origin/master EOT $ datalad save -m "Add note on adding siblings" add(ok): notes.txt (file) save(ok): . (dataset) action summary: add (ok: 1) save (ok: 1)