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mvdbeek
60d8290842
Any request to GET /api/datasets/{id}/content/{content_type} could read
an entire HDF5 dataset into memory: h5grove's DatasetContent.data() with
no selection executes dataset[()], selections are unbounded, data_stats
reads everything, attributes() reads all attribute values and group
metadata grows with child count.
Cap in-memory reads at 1 MB:
- data (format=bin/npy/csv) and stats now stream/accumulate in <= 1 MB
slabs, so datasets of any size remain fully usable (h5web requests
numeric data as format=bin)
- data (format=json/tiff), attr and group meta reject oversized requests
with a 400 suggesting the selection parameter, computed pre-read from
shape, dtype itemsize and the parsed selection
- variable-length dtypes cannot be pre-sized (h5py exposes no
H5Dvlen_get_buf_size), so they are capped at ~1000 elements
- invalid selection strings now return 400 instead of 500
.. figure:: https://galaxyproject.org/images/galaxy-logos/galaxy_project_logo.jpg
:alt: Galaxy Logo
The latest information about Galaxy can be found on the `Galaxy Community Hub <https://galaxyproject.org/>`__.
Community support is available at `Galaxy Help <https://help.galaxyproject.org/>`__.
.. image:: https://img.shields.io/badge/chat-gitter-blue.svg
:target: https://gitter.im/galaxyproject/Lobby
:alt: Chat on gitter
.. image:: https://img.shields.io/badge/chat-irc.freenode.net%23galaxyproject-blue.svg
:target: https://webchat.freenode.net/?channels=galaxyproject
:alt: Chat on irc
.. image:: https://img.shields.io/badge/release-documentation-blue.svg
:target: https://docs.galaxyproject.org/en/master/
:alt: Release Documentation
.. image:: https://travis-ci.org/galaxyproject/galaxy.svg?branch=dev
:target: https://travis-ci.org/galaxyproject/galaxy
:alt: Inspect the test results
Galaxy Quickstart
=================
Galaxy requires Python 3.10 or higher. To check your Python version, run:
.. code:: console
$ python -V
Python 3.10.12
Start Galaxy:
.. code:: console
$ sh run.sh
Once Galaxy completes startup, you should be able to view Galaxy in your
browser at: http://localhost:8080
For more installation details please see: https://getgalaxy.org/
Documentation is available at: https://docs.galaxyproject.org/
Tutorials on how to use Galaxy, perform scientific analyses with it, develop Galaxy and its tools, and admin a Galaxy server are at: https://training.galaxyproject.org/
Tools
=====
Tools can be either installed from the Tool Shed or added manually.
For details please see the `tutorial <https://galaxyproject.org/admin/tools/add-tool-from-toolshed-tutorial/>`__.
Note that not all dependencies for the tools provided in the
``tool_conf.xml.sample`` are included. To install them please visit
"Manage dependencies" in the admin interface.
Issues and Galaxy Development
=============================
Please see `CONTRIBUTING.md <CONTRIBUTING.md>`_ .