1.2. Populate a dataset¶
The first lecture in DataLad-101 referenced some useful literature. Even if we end up not reading those books at all, let’s download them nevertheless and put them into our dataset. You never know, right? Let’s first create a directory to save books for additional reading in.
$ mkdir books
Let’s take a look at the current directory structure with the tree command[1]:
$ tree
.
└── books
1 directory, 0 files
Arguably, not the most exciting thing to see. So let’s put some PDFs inside.
Below is a short list of optional readings. We decide to download them (they
are all free, in total about 15 MB), and save them in DataLad-101/books
.
Additional reading about the command line: The Linux Command Line
An intro to Python: A byte of Python
You can either visit the links and save them in books/
,
or run the following commands[2] to download the books right from the terminal.
Note that we line break the command with \
line continuation characters. In your own work you can write
commands like this into a single line. If you copy them into your terminal as they
are presented here, make sure to check the Windows-wit on peculiarities of its terminals.
Terminals other than Git Bash can’t handle multi-line commands
In Unix shells, \
can be used to split a command into several lines, for example to aid readability.
Standard Windows terminals (including the Anaconda prompt) do not support this.
They instead use the ^
character:
$ wget -q https://sourceforge.net/projects/linuxcommand/files/TLCL/19.01/TLCL-19.01.pdf/download ^
-O TLCL.pdf
If you are not using the Git Bash, you either need to copy multi-line commands into a single line, or use ^
(make sure that there is no space afterwards) instead of \
.
$ cd books
$ wget -q https://sourceforge.net/projects/linuxcommand/files/TLCL/19.01/TLCL-19.01.pdf/download \
-O TLCL.pdf
$ wget -q https://homepages.uc.edu/~becktl/byte_of_python.pdf \
-O byte-of-python.pdf
$ # get back into the root of the dataset
$ cd ../
Some machines will not have wget
available by default, but any command that can
download a file can work as an alternative. See the Windows-wit for the popular alternative
curl.
You can use curl instead of wget
Many versions of Windows do not ship with the tool wget
.
You can install it, but it may be easier to use the pre-installed curl
command:
$ cd books
$ curl -L https://sourceforge.net/projects/linuxcommand/files/TLCL/19.01/TLCL-19.01.pdf/download \
-o TLCL.pdf
$ curl -L https://github.com/swaroopch/byte-of-python/releases/download/vadb91fc6fce27c58e3f931f5861806d3ccd1054c/byte-of-python.pdf \
-o byte-of-python.pdf
$ cd ../
Let’s see what happened. First of all, in the root of DataLad-101
, show the directory
structure with tree:
$ tree
.
└── books
├── byte-of-python.pdf
└── TLCL.pdf
1 directory, 2 files
Now what does DataLad do with this new content? One command you will use very
often is datalad status
(manual).
It reports on the state of dataset content, and
regular status reports should become a habit in the wake of DataLad-101
.
$ datalad status
untracked: books (directory)
Interesting; the books/
directory is “untracked”. Remember how content
can be tracked if a user wants to?
Untracked means that DataLad does not know about this directory or its content,
because we have not instructed DataLad to actually track it. This means that DataLad
does not store the downloaded books in its history yet. Let’s change this by
saving the files to the dataset’s history with the datalad save
(manual) command.
This time, it is your turn to specify a helpful commit message
with the -m
option (although the DataLad command is datalad save
, we talk
about commit messages because datalad save
ultimately uses the command
git commit
(manual) to do its work):
$ datalad save -m "add books on Python and Unix to read later"
add(ok): books/TLCL.pdf (file)
add(ok): books/byte-of-python.pdf (file)
save(ok): . (dataset)
If you ever forget to specify a message, or made a typo, not all is lost. A Find-out-more explains how to amend a saved state.
“Oh no! I forgot the -m option for ‘datalad save’!”
If you forget to specify a commit message with the -m
option, DataLad will write
[DATALAD] Recorded changes
as a commit message into your history.
This is not particularly informative.
You can change the last commit message with the Git command
git commit --amend
. This will open up your default editor
and you can edit
the commit message. Careful – the default editor might be vim!
The section Back and forth in time will show you many more ways in which you can
interact with a dataset’s history.
As already noted, any files you save
in this dataset, and all modifications
to these files that you save
, are tracked in this history.
Importantly, this file tracking works
regardless of the size of the files – a DataLad dataset could be
your private music or movie collection with single files being many GB in size.
This is one aspect that distinguishes DataLad from many other
version control tools, among them Git.
Large content is tracked in an annex that is automatically
created and handled by DataLad. Whether text files or larger files change,
all of these changes can be written to your DataLad dataset’s history.
Let’s see how the saved content shows up in the history of the dataset with git log
(manual).
The option -n 1
specifies that we want to take a look at the most recent commit.
In order to get a bit more details, we add the -p
flag. If you end up in a
pager, navigate with up and down arrow keys and leave the log by typing q
:
$ git log -p -n 1
commit b40316a6✂SHA1
Author: Elena Piscopia <elena@example.net>
Date: Tue Jun 18 16:13:00 2019 +0000
add books on Python and Unix to read later
diff --git a/books/TLCL.pdf b/books/TLCL.pdf
new file mode 120000
index 0000000..4c84b61
--- /dev/null
+++ b/books/TLCL.pdf
@@ -0,0 +1 @@
+../.git/annex/objects/jf/3M/✂/MD5E-s2120211--06d1efcb✂MD5.pdf
\ No newline at end of file
diff --git a/books/byte-of-python.pdf b/books/byte-of-python.pdf
new file mode 120000
index 0000000..7a6e51e
--- /dev/null
+++ b/books/byte-of-python.pdf
Now this might look a bit cryptic (and honestly, tig[3] makes it look prettier).
But this tells us the date and time in which a particular author added two PDFs to
the directory books/
, and thanks to that commit message we have a nice
human-readable summary of that action. A Find-out-more explains what makes
a good message.
DOs and DON’Ts for commit messages
DOs
Write a title line with 72 characters or less
Use imperative voice, e.g., “Add notes from lecture 2”
If a title line is not enough to express your changes and reasoning behind it, add a body to your commit message: hit enter twice (before closing the quotation marks), and continue writing a brief summary of the changes after a blank line. This summary should explain “what” has been done and “why”, but not “how”. Close the quotation marks, and hit enter to save the change with your message.
DON’Ts
Avoid passive voice
Extensive formatting (hashes, asterisks, quotes, …) will most likely make your shell complain
Do not say nasty things about other people
There is no staging area in DataLad
Just as in Git, new files are not tracked from their creation on, but only when
explicitly added to Git (in Git terms, with an initial git add
(manual)). But different
from the common Git workflow, DataLad skips the staging area. A datalad save
combines a git add
and a git commit
, and therefore, the commit message
is specified with datalad save
.
Cool, so now you have added some files to your dataset history. But what is a bit
inconvenient is that both books were saved together. You begin to wonder: “A Python
book and a Unix book do not have that much in common. I probably should not save them
in the same commit. And … what happens if I have files I do not want to track?
datalad save -m "some commit message"
would save all of what is currently
untracked or modified in the dataset into the history!”
Regarding your first remark, you are absolutely right! It is good practice to save only those changes together that belong together. We do not want to squish completely unrelated changes into the same spot of our history, because it would get very nasty should we want to revert some of the changes without affecting others in this commit.
Luckily, we can point datalad save
to exactly the changes we want it to record.
Let’s try this by adding yet another book, a good reference work about git,
Pro Git:
$ cd books
$ wget -q https://github.com/progit/progit2/releases/download/2.1.154/progit.pdf
$ cd ../
datalad status
shows that there is a new untracked file:
$ datalad status
untracked: books/progit.pdf (file)
Let’s give datalad save
precisely this file by specifying its path after the commit message:
$ datalad save -m "add reference book about git" books/progit.pdf
add(ok): books/progit.pdf (file)
save(ok): . (dataset)
Regarding your second remark, you are right that a datalad save
without a
path specification would write all of the currently untracked files or modifications
to the history. But check the Find-out-more on how to tell it otherwise.
How to save already tracked dataset components only?
A datalad save -m "concise message" --updated
(or the shorter
form of --updated
, -u
) will only write modifications to the
history, not untracked files. Later, we will also see .gitignore
files
that let you hide content from version control. However, it is good
practice to safely store away modifications or new content. This improves
your dataset and workflow, and will be a requirement for executing certain
commands.
A datalad status
should now be empty, and our dataset’s history should look like this:
$ # lets make the output a bit more concise with the --oneline option
$ git log --oneline
a875e49 add reference book about git
b40316a add books on Python and Unix to read later
e0ff3a7 Instruct annex to add text files to Git
4ce681d [DATALAD] new dataset
“Wonderful! I’m getting a hang on this quickly”, you think. “Version controlling files is not as hard as I thought!”
But downloading and adding content to your dataset “manually” has two disadvantages: For one, it requires you to download the content and save it. Compared to a workflow with no DataLad dataset, this is one additional command you have to perform (and that additional time adds up, after a while). But a more serious disadvantage is that you have no electronic record of the source of the contents you added. The amount of provenance, the time, date, and author of file, is already quite nice, but we don’t know anything about where you downloaded these files from. If you would want to find out, you would have to remember where you got the content from – and brains are not made for such tasks.
Luckily, DataLad has a command that will solve both of these problems:
The datalad download-url
(manual) command.
We will dive deeper into the provenance-related benefits of using it in later chapters, but for now,
we’ll start with best-practice-building. datalad download-url
can retrieve content
from a URL (following any URL-scheme from https, http, or ftp or s3) and save it
into the dataset together with a human-readable commit message and a hidden,
machine-readable record of the origin of the content. This saves you time,
and captures provenance information about the data you add to your dataset.
To experience this, let’s add a final book,
a beginner’s guide to bash,
to the dataset. We provide the command with a URL, a pointer to the dataset the
file should be saved in (.
denotes “current directory”), and a commit message.
$ datalad download-url \
https://www.tldp.org/LDP/Bash-Beginners-Guide/Bash-Beginners-Guide.pdf \
--dataset . \
-m "add beginners guide on bash" \
-O books/bash_guide.pdf
download_url(ok): /home/me/dl-101/DataLad-101/books/bash_guide.pdf (file)
add(ok): books/bash_guide.pdf (file)
save(ok): . (dataset)
Afterwards, a fourth book is inside your books/
directory:
$ ls books
bash_guide.pdf
byte-of-python.pdf
progit.pdf
TLCL.pdf
However, the datalad status
command does not return any output –
the dataset state is “clean”:
$ datalad status
nothing to save, working tree clean
This is because datalad download-url
took care of saving for you:
$ git log -p -n 1
commit 59ac8d32✂SHA1
Author: Elena Piscopia <elena@example.net>
Date: Tue Jun 18 16:13:00 2019 +0000
add beginners guide on bash
diff --git a/books/bash_guide.pdf b/books/bash_guide.pdf
new file mode 120000
index 0000000..00ca6bd
--- /dev/null
+++ b/books/bash_guide.pdf
@@ -0,0 +1 @@
+../.git/annex/objects/WF/Gq/✂/MD5E-s1198170--0ab2c121✂MD5.pdf
\ No newline at end of file
At this point in time, the biggest advantage may seem to be the time save. However, soon you will experience how useful it is to have DataLad keep track for you where file content came from.
To conclude this section, let’s take a final look at the history of your dataset at this point:
$ git log --oneline
59ac8d3 add beginners guide on bash
a875e49 add reference book about git
b40316a add books on Python and Unix to read later
e0ff3a7 Instruct annex to add text files to Git
4ce681d [DATALAD] new dataset
Well done! Your DataLad-101
dataset and its history are slowly growing.
Footnotes