Caterva2 is a distributed system written in Python meant for sharing Blosc2 datasets (either native or converted on-the-fly from HDF5) among different hosts by using a publish–subscribe messaging pattern. Here, publishers categorize datasets into root groups that are announced to the broker and propagated to subscribers. Also, every subscriber exposes a REST interface that allows clients to access the datasets.
Caterva2 subscribers perform on demand data access with local caching (fit for re-publishing), which can be particularly useful for the efficient sharing of remote datasets locally, thus optimizing communication and storage resources within work groups.
A Caterva2 deployment includes:
- One broker service to enable the communication between publishers and subscribers.
- Several publishers, each one providing subscribers with access to one root and the datasets that it contains. The root may be a native Caterva2 directory with Blosc2 and plain files, or an HDF5 file (support for other formats may be added).
- Several subscribers, each one tracking changes in multiple roots and datasets from publishers, and caching them locally for efficient reuse.
- Several clients, each one asking a subscriber to track roots and datasets, and provide access to their data and metadata.
Publishers and subscribers may be apart, in different networks with limited or expensive connectivity between them, while subscribers and clients will usually be close enough to have fast and cheap connectivity (e.g. a local network).
The Caterva2 package includes all the aforementioned components, although its main role is to provide a very simple and lightweight library to build your own Caterva2 clients.
Although this project is in advanced beta stage, it is not meant for production use yet. In case you are interested in Caterva2, please contact us at contact@blosc.org.
You may install Caterva2 in several ways:.
-
Pre-built wheel from PyPI:
python -m pip install caterva2
-
Wheel built from source code:
git clone https://github.com/ironArray/Caterva2 cd Caterva2 python -m build python -m pip install dist/caterva2-*.whl
-
Developer setup:
git clone https://github.com/ironArray/Caterva2 cd Caterva2 python -m pip install -e .
In any case, if you intend to run Caterva2 services, client programs, or the test suite, you need to enable the proper extra features by appending [feature1,feature2...]
to the last argument of pip
commands above. The following extras are supported:
services
for running all Caterva2 services (broker, publisher, subscriber)base-services
for running the Caterva2 broker or publisher services (lighter, less dependencies)subscriber
for running the Caterva2 subscriber service specifically (heavier, more dependencies)clients
to use Caterva2 client programs (command-line or terminal)hdf5
to enable serving HDF5 files as Caterva2 roots at the publisherblosc2-plugins
to enable extra Blosc2 features like Btune or JPEG 2000 supportplugins
to enable Web client features like the tomography displaytools
for additional utilities likecat2import
andcat2export
(see below)tests
if you want to run the Caterva2 test suite
After installing with the [tests]
extra, you can quickly check that the package is sane by running the test suite (that comes with the package):
python -m caterva2.tests -v
You may also run tests from source code:
cd Caterva2
python -m pytest -v
Tests will use a copy of Caterva2's root-example
directory. After they finish, state files will be left under the _caterva2_tests
directory for inspection (it will be re-created when tests are run again).
In case you want to run the tests with your own running daemons, you can do:
env CATERVA2_USE_EXTERNAL=1 python -m caterva2.tests -v
Neither root-example
nor _caterva2_tests
will be used in this case.
(Find more detailed step-by-step tutorials in Caterva2 documentation.)
For the purpose of this quick start, let's use the datasets within the root-example
folder:
cd Caterva2
ls -F root-example/
README.md dir2/ ds-1d-fields.b2nd ds-2d-fields.b2nd ds-sc-attr.b2nd
dir1/ ds-1d-b.b2nd ds-1d.b2nd ds-hello.b2frame
Now:
- create a virtual environment and install Caterva2 with the
[services,clients]
extras (see above). - copy the configuration file
caterva2.sample.toml
tocaterva2.toml
and edit to your needs
Then fire up the broker, start publishing a root named foo
with root-example
datasets, and create a subscriber:
cat2bro & # broker
cat2pub foo root-example & # publisher
cat2sub & # subscriber
(To stop them later on, bring each one to the foreground with fg
and press Ctrl+C.)
It's also possible to run only the subscriber. For this copy
caterva2-standalone.sample.toml
to caterva2.toml
.
Then only run the subscriber:
cat2sub & # subscriber
If you want to try and publish your own HDF5 file as a root, you need to include the hdf5
extra in your Caterva2 installation. Then you may just run:
cat2pub foo /path/to/your-file.h5 &
You can also get an example HDF5 file with some datasets by running:
python -m caterva2.services.hdf5root root-example.h5
You may want to test compatibility with silx' HDF5 examples (epics.h5
and grove.h5
are quite illustrative).
Now that the services are running, we can use the cat2cli
client to talk
to the subscriber. In another shell, let's list all the available roots in the system:
cat2cli roots
foo
We only have the foo
root that we started publishing. If other publishers were running,
we would see them listed here too.
Let's ask our local subscriber to subscribe to the foo
root:
cat2cli subscribe foo # -> Ok
Now, one can list the datasets in the foo
root:
cat2cli list foo
foo/README.md
...
foo/ds-hello.b2frame
...
foo/dir2/ds-4d.b2nd
Let's ask the subscriber for more info about the foo/dir2/ds-4d.b2nd
dataset:
cat2cli info foo/dir2/ds-4d.b2nd
{
'shape': [2, 3, 4, 5],
'chunks': [1, 2, 3, 4],
'blocks': [1, 2, 2, 2],
'dtype': 'complex128',
'schunk': {
# ...
}
}
Let's print data from a specified dataset:
cat2cli show foo/ds-hello.b2frame[:12] # -> Hello world!
It allows printing slices instead of the whole dataset too:
cat2cli show foo/dir2/ds-4d.b2nd[1,2,3]
[115.+115.j 116.+116.j 117.+117.j 118.+118.j 119.+119.j]
Finally, we can tell the subscriber to download the dataset:
cat2cli download foo/dir2/ds-4d.b2nd
Dataset saved to foo/dir2/ds-4d.b2nd
All the services mentioned above (and clients, to some limited extent) may get their configuration from a caterva2.toml
file at the current directory (or an alternative file given with the --conf
option). Caterva2 source code includes a fully documented caterva2.sample.toml
file (see also caterva2.toml in Caterva2 tutorials).
The Caterva2 subscriber includes some initial and incomplete support for authenticating users. To enable it, run the subscriber with the environment variable CATERVA2_SECRET
set to some non-empty, secure string that will be used for various user management operations. After that, accessing the subscriber's Web client will only be possible after logging in with an email address and a password. New accounts may be registered, but their addresses are not verified. Password recovery does not work either.
To tell the command line client to authenticate against a subscriber, add the --username
and --password
options:
cat2cli --user "user@example.com" --pass "foobar" info foo/README.md
Although Caterva2 allows publishing an HDF5 file directly as a root (with datasets converted to Blosc2 arrays on-the-fly), it also includes a simple script that can import its full hierarchy to a new Caterva2 root directory. You may use it like:
cat2import existing-hdf5-file.h5 new-caterva2-root
The tool is still pretty limited in its supported input and generated output, please invoke it with --help
for more information (see also cat2import in Caterva2 utilities documentation).
Caterva2 also ships a complementary tool to export a Caterva root directory to an HDF5 file; see cat2export in Caterva2 utilities documentation. You may use it like:
cat2export existing-caterva2-root new-hdf5-file.h5
That's all folks!