mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #7215 from nsoranzo/recommonmark_0.5.0
Dependency update and doc fixes
This commit is contained in:
Marius van den Beek
@@ -54,7 +54,7 @@ time it starts up and be configured to use it by default.
|
||||
|
||||
The long answer is that Galaxy's tool dependency resolution is managed via
|
||||
``dependency_resolvers_conf.xml`` configuration file. This configuration
|
||||
file is discussed in detail in the :ref:`Dependency Resolvers <dependency_resolvers>`
|
||||
file is discussed in detail in the :doc:`Dependency Resolvers <dependency_resolvers>`
|
||||
documentation. Most Galaxy administrators will be using Galaxy's default dependency
|
||||
resolvers configuration file (``config/dependency_resolvers_conf.xml.sample``). With
|
||||
release 16.04, Galaxy has enabled Conda dependency resolution by default when
|
||||
@@ -68,7 +68,7 @@ entry should remain first. This means that tools that have specified Tool Shed p
|
||||
as their dependencies will work without a change.
|
||||
|
||||
The most common configuration settings related to Conda are listed in Table 1.
|
||||
See `galaxy.yml.sample`_ for the complete list.
|
||||
See :doc:`Configuration Options <options>` for the complete list.
|
||||
|
||||
+-------------------------+------------------------------------+---------------------------+
|
||||
| Setting | Default setting | Meaning |
|
||||
@@ -105,7 +105,7 @@ handle these dependencies for you, but admins are not required to use Galaxy for
|
||||
dependency management.
|
||||
|
||||
There are a few config options in the ``galaxy.yml`` file (see Table 1 or
|
||||
`galaxy.yml.sample`_ for more information), but by default Galaxy will install
|
||||
:doc:`Configuration Options <options>` for more information), but by default Galaxy will install
|
||||
Conda (the package manager) and the required packages in the
|
||||
``<tool_dependency_dir>/_conda/`` directory. In this directory, Galaxy will
|
||||
create an ``envs`` folder with all of the environments managed by Galaxy. Each
|
||||
@@ -203,7 +203,7 @@ The order in which resolvers are tried is listed in the
|
||||
- Conda packages
|
||||
|
||||
The first system that satisfies a requirement will be used. See
|
||||
`resolver docs`_ for detailed documentation.
|
||||
:doc:`Dependency Resolvers <dependency_resolvers>` for detailed documentation.
|
||||
|
||||
This however is not recommended, ideally tools will target and test
|
||||
against Conda for all dependencies. Also resolving all requirements
|
||||
@@ -408,13 +408,11 @@ The command can obviously be adapted to install any version of Conda.
|
||||
.. _Conda quick-start: https://conda.io/docs/user-guide/getting-started.html
|
||||
.. _ansible role: https://github.com/galaxyproject/ansible-galaxy-tools
|
||||
.. _BioBlend: https://github.com/galaxyproject/bioblend
|
||||
.. _resolver docs: https://docs.galaxyproject.org/en/master/admin/dependency_resolvers.html
|
||||
.. _Conda channels: https://conda.io/docs/user-guide/tasks/manage-channels.html
|
||||
.. _create a Conda package: https://conda.io/docs/user-guide/tasks/build-packages/recipe.html
|
||||
.. _submit: https://bioconda.github.io/#step-4-join-the-team
|
||||
.. _BioConda: https://bioconda.github.io
|
||||
.. _contact with the IUC: https://gitter.im/galaxy-iuc/iuc
|
||||
.. _galaxy.yml.sample: https://docs.galaxyproject.org/en/master/admin/options.html
|
||||
.. _Pull Request #3106: https://github.com/galaxyproject/galaxy/pull/3106
|
||||
.. _Pull Request #3348: https://github.com/galaxyproject/galaxy/pull/3348
|
||||
.. _Pull Request #3391: https://github.com/galaxyproject/galaxy/pull/3391
|
||||
|
||||
@@ -10,7 +10,7 @@ single configuration file, ``config/error_report.yml.sample``.
|
||||
|
||||
Let's look at that briefly:
|
||||
|
||||
.. code-block:: yml
|
||||
.. code-block:: yaml
|
||||
|
||||
- type: email
|
||||
verbose: true
|
||||
|
||||
@@ -45,23 +45,26 @@ For each type there is an example provided:
|
||||
- Additional functionality can be added to the top menu. Two dummy buttons are implemented to show the idea:
|
||||
|
||||
- A button that links to biostars
|
||||
.. image:: images_webhooks/masthead.png
|
||||
:scale: 50 %
|
||||
|
||||
.. image:: images_webhooks/masthead.png
|
||||
:scale: 50 %
|
||||
|
||||
- A button that shows a pop-up with information about an user.
|
||||
.. image:: images_webhooks/masthead_trans_object.png
|
||||
:scale: 50 %
|
||||
|
||||
.. image:: images_webhooks/masthead_trans_object.png
|
||||
:scale: 50 %
|
||||
|
||||
- The history menu can be extended. In this case we use two dummy entries 'History Menu Webhook Item 1' and 'History Menu Webhook Item 2'.
|
||||
.. image:: images_webhooks/history-menu.png
|
||||
:scale: 25 %
|
||||
|
||||
.. image:: images_webhooks/history-menu.png
|
||||
:scale: 25 %
|
||||
|
||||
Plugin structure
|
||||
----------------
|
||||
|
||||
Each plugin has the following folder structure:
|
||||
|
||||
.. code-block::
|
||||
.. code-block:: yaml
|
||||
|
||||
- plugin_name
|
||||
- config.yml (mandatory)
|
||||
|
||||
+4
-10
@@ -17,14 +17,9 @@ import sys
|
||||
|
||||
import sphinx_rtd_theme
|
||||
# Library to make .md to slideshow
|
||||
from recommonmark.parser import CommonMarkParser
|
||||
from recommonmark.transform import AutoStructify
|
||||
|
||||
source_parsers = {
|
||||
'.md': CommonMarkParser,
|
||||
}
|
||||
|
||||
# Set GALAXY_DOCS_SKIP_SOURCE=1 to skip building source and release information and
|
||||
# Set GALAXY_DOCS_SKIP_SOURCE=1 to skip building source information and
|
||||
# just build primary documentation. (Quicker to debug issues in most frequently updated
|
||||
# docs).
|
||||
SKIP_SOURCE = os.environ.get("GALAXY_DOCS_SKIP_SOURCE", False) == "1"
|
||||
@@ -45,7 +40,7 @@ sys.path.insert(1, os.path.abspath(os.path.join(os.path.dirname(__file__), os.pa
|
||||
|
||||
# Add any Sphinx extension module names here, as strings. They can be extensions
|
||||
# coming with Sphinx (named 'sphinx.ext.*') or your custom ones.
|
||||
extensions = ['sphinx.ext.autodoc', 'sphinx.ext.intersphinx']
|
||||
extensions = ['recommonmark', 'sphinx.ext.autodoc', 'sphinx.ext.intersphinx']
|
||||
if not SKIP_SOURCE:
|
||||
extensions += ['sphinx.ext.doctest', 'sphinx.ext.todo', 'sphinx.ext.coverage', 'sphinx.ext.viewcode']
|
||||
|
||||
@@ -108,10 +103,9 @@ release = VERSION
|
||||
|
||||
# List of patterns, relative to source directory, that match files and
|
||||
# directories to ignore when looking for source files.
|
||||
exclude_patterns = ['**/_*.rst']
|
||||
if SKIP_SOURCE:
|
||||
exclude_patterns = ['lib', 'releases']
|
||||
else:
|
||||
exclude_patterns = []
|
||||
exclude_patterns.extend(['lib'])
|
||||
|
||||
# The reST default role (used for this markup: `text`) to use for all documents.
|
||||
#default_role = None
|
||||
|
||||
@@ -1,5 +1,5 @@
|
||||
Development Documentation
|
||||
=======================
|
||||
=========================
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 1
|
||||
|
||||
@@ -12,7 +12,7 @@ Highlights
|
||||
Galaxy admins obtained the ability to install Galaxy tool's
|
||||
dependencies using the Conda package manager. This is a Beta feature
|
||||
and we encourage interested deployers to opt-in by modifying configuration.
|
||||
Documentation that explains this switch and answers FAQ is `available <https://docs.galaxyproject.org/en/master/admin/conda_faq.html>`__.
|
||||
Documentation that explains this switch and answers FAQ is :doc:`available <../admin/conda_faq>`.
|
||||
|
||||
**Dynamic tool destinations**
|
||||
Our friends from Canada National Microbiology Laboratory enhanced
|
||||
@@ -24,7 +24,7 @@ Highlights
|
||||
**Galaxy chat**
|
||||
Admins can now plug in the included communication server to enable
|
||||
users of their instance to use real-time chat within the Galaxy interface.
|
||||
Please see the `documentation <https://docs.galaxyproject.org/en/master/admin/chat.html>`__
|
||||
Please see the :doc:`documentation <../admin/special_topics/chat>`
|
||||
to learn how to activate and use this feature.
|
||||
Implemented in `PR #2515 <https://github.com/galaxyproject/galaxy/pull/2515>`__
|
||||
|
||||
|
||||
@@ -18,7 +18,7 @@ Highlighted Enhancements
|
||||
* Implement a collection operation tool for merging collections
|
||||
(thanks to `@Takadonet <https://github.com/Takadonet>`__).
|
||||
`Pull Request 2771`_
|
||||
* Replace `reference documentation <https://docs.galaxyproject.org/en/master/dev/schema.html>`__
|
||||
* Replace :doc:`reference documentation <../dev/schema>`
|
||||
for tool XML files with automatically generated
|
||||
documentation from a now official Galaxy XSD documentation (with help from many).
|
||||
`Pull Request 2923`_, `Pull Request 2936`_, `Pull Request 3086`_,
|
||||
|
||||
@@ -9,7 +9,7 @@ Highlights
|
||||
==========
|
||||
|
||||
**Galaxu UI plugins - Webhooks**
|
||||
We introduce Galaxy Webhooks - optional plugins for the web UI that allow for better customization of your instance. See the `documentation <https://docs.galaxyproject.org/en/master/admin/webhooks.html>`__.
|
||||
We introduce Galaxy Webhooks - optional plugins for the web UI that allow for better customization of your instance. See the :doc:`documentation <../admin/special_topics/webhooks>`.
|
||||
Includes work from `@bgruening <https://github.com/bgruening>`__, `@anatskiy <https://github.com/anatskiy>`__, and Joachim Wolff `@joachimwolff <https://github.com/joachimwolff>`__.
|
||||
Implemented in `Pull Request 3040`_.
|
||||
|
||||
|
||||
@@ -14,7 +14,7 @@ Highlights
|
||||
such as `BioConda <https://bioconda.github.io/>`__. Such channels are already being used for new and updated tools by IUC
|
||||
and we suggest adopting this tool dependency resolution method to all tool developers instead of Tool Shed package
|
||||
recipes - which are now considered deprecated.
|
||||
Please see the details at the admin `documentation <https://docs.galaxyproject.org/en/master/admin/conda_faq.html>`__
|
||||
Please see the details at the admin :doc:`documentation <../admin/conda_faq>`.
|
||||
|
||||
**New interface for user preferences**
|
||||
User preferences menu has been reworked for clarity and consistency.
|
||||
@@ -27,7 +27,7 @@ Highlights
|
||||
or ``fastqsanger.bz2`` for compressed files).
|
||||
Existing tools will work as before and future tools will be able to consume archives and save space in your quota.
|
||||
Thanks to `@abretaud <https://github.com/abretaud>`__, `@ashvark <https://github.com/ashvark>`__, `@jvolkening <https://github.com/jvolkening>`__, and `@mvdbeek <https://github.com/mvdbeek>`__.
|
||||
Implemented in `Pull Request 3145`_, `PullRequest 3510`_ and `PullRequest 3514`_.
|
||||
Implemented in `Pull Request 3145`_, `Pull Request 3510`_ and `Pull Request 3514`_.
|
||||
|
||||
Get Galaxy
|
||||
==========
|
||||
|
||||
@@ -111,6 +111,7 @@ Enhancements
|
||||
* Add Phylip datatype
|
||||
(thanks to `@khillion <https://github.com/khillion>`__).
|
||||
`Pull Request 5301`_
|
||||
|
||||
.. enhancement
|
||||
|
||||
* Option to group Galaxy Tours for viewing clarity
|
||||
|
||||
@@ -36,7 +36,7 @@ Mercurial = {version = "<=3.7.3", markers = "python_version < '3'"}
|
||||
nodeenv = "*"
|
||||
pycryptodome = "*"
|
||||
uWSGI = "*"
|
||||
pysam = "==0.15.1"
|
||||
pysam = "==0.15.2"
|
||||
bdbag = "==1.4.1" # 1.5.0 requires Python >=2.7.9
|
||||
bleach = "*"
|
||||
"bz2file" = {version = "*", markers = "python_version < '3.3'"}
|
||||
|
||||
@@ -7,34 +7,35 @@ attrs==18.2.0
|
||||
babel==2.6.0
|
||||
certifi==2018.11.29
|
||||
chardet==3.0.4
|
||||
commonmark==0.5.4
|
||||
commonmark==0.8.1
|
||||
docutils==0.14
|
||||
funcsigs==1.0.2 ; python_version < '3.3'
|
||||
future==0.17.1
|
||||
gunicorn==19.9.0
|
||||
idna==2.7
|
||||
idna==2.8
|
||||
imagesize==1.1.0
|
||||
jinja2==2.10
|
||||
lxml==4.2.5
|
||||
lxml==4.3.0
|
||||
markupsafe==1.1.0
|
||||
mock==2.0.0
|
||||
more-itertools==4.3.0
|
||||
more-itertools==5.0.0
|
||||
nose==1.3.7
|
||||
nosehtml==0.4.5
|
||||
pathlib2==2.3.3 ; python_version < '3.6'
|
||||
pathtools==0.1.2
|
||||
pbr==5.1.1
|
||||
pluggy==0.8.0
|
||||
pluggy==0.8.1
|
||||
py==1.7.0
|
||||
pygithub3==0.5.1 ; python_version < '3'
|
||||
pygments==2.3.0
|
||||
pygments==2.3.1
|
||||
pytest-html==1.19.0
|
||||
pytest-metadata==1.7.0
|
||||
pytest-metadata==1.8.0
|
||||
pytest-pythonpath==0.7.3
|
||||
pytest==4.0.1
|
||||
pytz==2018.7
|
||||
pytest==4.1.0
|
||||
pytz==2018.9
|
||||
pyyaml==3.13
|
||||
recommonmark==0.4.0
|
||||
requests==2.20.1
|
||||
recommonmark==0.5.0
|
||||
requests==2.21.0
|
||||
scandir==1.9.0 ; python_version < '3.5'
|
||||
selenium==3.141.0
|
||||
six==1.11.0
|
||||
@@ -42,7 +43,7 @@ snowballstemmer==1.2.1
|
||||
sphinx-rtd-theme==0.4.2
|
||||
sphinx==1.6.7
|
||||
sphinxcontrib-websupport==1.1.0
|
||||
testfixtures==6.3.0
|
||||
testfixtures==6.4.3
|
||||
twill==0.9.1 ; python_version < '3'
|
||||
typing==3.6.6 ; python_version < '3.5'
|
||||
urllib3==1.24.1
|
||||
|
||||
@@ -19,11 +19,11 @@ azure-storage-common==1.4.0
|
||||
azure-storage-nspkg==3.1.0
|
||||
babel==2.6.0
|
||||
bagit==1.6.4
|
||||
bcrypt==3.1.4
|
||||
bcrypt==3.1.5
|
||||
bdbag==1.4.1
|
||||
beaker==1.10.0
|
||||
bioblend==0.11.0
|
||||
bleach==3.0.2
|
||||
bioblend==0.12.0
|
||||
bleach==3.1.0
|
||||
boltons==18.0.1
|
||||
boto3==1.7.84
|
||||
boto==2.49.0
|
||||
@@ -48,7 +48,7 @@ deprecation==2.0.6
|
||||
dictobj==0.4
|
||||
docopt==0.6.2
|
||||
docutils==0.14
|
||||
dogpile.cache==0.6.8
|
||||
dogpile.cache==0.7.1
|
||||
enum34==1.1.6 ; python_version < '3.4'
|
||||
fabric3==1.14.post1
|
||||
funcsigs==1.0.2 ; python_version < '3.3'
|
||||
@@ -57,8 +57,8 @@ future==0.17.1
|
||||
futures==3.2.0 ; python_version == '2.6' or python_version == '2.7'
|
||||
galaxy-sequence-utils==1.1.3
|
||||
gxformat2==0.8.0
|
||||
h5py==2.8.0
|
||||
idna==2.7
|
||||
h5py==2.9.0
|
||||
idna==2.8
|
||||
ipaddress==1.0.22 ; python_version < '3.3'
|
||||
isa-rwval==0.10.7
|
||||
iso8601==0.1.12
|
||||
@@ -67,8 +67,8 @@ jmespath==0.9.3
|
||||
jsonpatch==1.23
|
||||
jsonpointer==2.0
|
||||
jsonschema==2.6.0
|
||||
keystoneauth1==3.11.1
|
||||
kombu==4.2.1
|
||||
keystoneauth1==3.11.2
|
||||
kombu==4.2.2.post1
|
||||
mako==1.0.7
|
||||
markupsafe==1.1.0
|
||||
mercurial==3.7.3 ; python_version < '3'
|
||||
@@ -78,7 +78,7 @@ msrest==0.5.5
|
||||
msrestazure==0.5.0
|
||||
munch==2.3.2
|
||||
netaddr==0.7.19
|
||||
netifaces==0.10.7
|
||||
netifaces==0.10.9
|
||||
networkx==1.11
|
||||
nodeenv==1.3.3
|
||||
nose==1.3.7
|
||||
@@ -87,36 +87,36 @@ oauthlib==2.1.0
|
||||
openstacksdk==0.17.0
|
||||
os-client-config==1.31.2
|
||||
os-service-types==1.4.0
|
||||
osc-lib==1.11.1
|
||||
osc-lib==1.12.0
|
||||
oslo.config==6.7.0
|
||||
oslo.context==2.22.0
|
||||
oslo.i18n==3.23.0
|
||||
oslo.log==3.42.0
|
||||
oslo.log==3.42.2
|
||||
oslo.serialization==2.28.1
|
||||
oslo.utils==3.38.0
|
||||
oslo.utils==3.39.1
|
||||
packaging==18.0
|
||||
paramiko==2.4.2
|
||||
parsley==1.3
|
||||
paste==3.0.5
|
||||
paste==3.0.6
|
||||
pastedeploy==2.0.1
|
||||
pastescript==3.0.0
|
||||
pbr==5.1.1
|
||||
prettytable==0.7.2
|
||||
psutil==5.4.8
|
||||
pulsar-galaxy-lib==0.8.3
|
||||
pyasn1==0.4.4
|
||||
pyasn1==0.4.5
|
||||
pycparser==2.19
|
||||
pycryptodome==3.7.2
|
||||
pycryptodomex==3.7.2
|
||||
pyinotify==0.9.6 ; sys_platform != 'win32' and sys_platform != 'darwin' and sys_platform != 'sunos5'
|
||||
pyjwkest==1.4.0
|
||||
pyjwt==1.7.0
|
||||
pyjwt==1.7.1
|
||||
pykwalify==1.7.0
|
||||
pynacl==1.3.0
|
||||
pyopenssl==18.0.0
|
||||
pyparsing==2.3.0
|
||||
pyperclip==1.7.0
|
||||
pysam==0.15.1
|
||||
pysam==0.15.2
|
||||
pysftp==0.2.9
|
||||
python-cinderclient==4.0.0
|
||||
python-dateutil==2.7.5
|
||||
@@ -127,12 +127,12 @@ python-neutronclient==6.9.0
|
||||
python-novaclient==11.0.0
|
||||
python-openid==2.2.5
|
||||
python-swiftclient==3.6.0
|
||||
pytz==2018.7
|
||||
pytz==2018.9
|
||||
pyyaml==3.13
|
||||
repoze.lru==0.7
|
||||
requests-oauthlib==1.0.0
|
||||
requests-oauthlib==1.1.0
|
||||
requests-toolbelt==0.8.0
|
||||
requests==2.20.1
|
||||
requests==2.21.0
|
||||
requestsexceptions==1.4.0
|
||||
rfc3986==1.2.0
|
||||
routes==2.4.1
|
||||
@@ -141,8 +141,8 @@ simplejson==3.16.0
|
||||
six==1.11.0
|
||||
social-auth-core[openidconnect]==1.5.0
|
||||
sqlalchemy-migrate==0.11.0
|
||||
sqlalchemy-utils==0.33.9
|
||||
sqlalchemy==1.2.14
|
||||
sqlalchemy-utils==0.33.10
|
||||
sqlalchemy==1.2.16
|
||||
sqlparse==0.2.4
|
||||
stevedore==1.30.0
|
||||
subprocess32==3.5.3 ; python_version < '3.0'
|
||||
@@ -154,10 +154,10 @@ tzlocal==1.5.1
|
||||
unicodecsv==0.14.1 ; python_version < '3.0'
|
||||
urllib3==1.24.1
|
||||
uwsgi==2.0.17.1
|
||||
vine==1.1.4
|
||||
vine==1.2.0
|
||||
warlock==1.3.0
|
||||
wcwidth==0.1.7 ; sys_platform != 'win32'
|
||||
webencodings==0.5.1
|
||||
webob==1.8.4
|
||||
webob==1.8.5
|
||||
whoosh==2.7.4
|
||||
wrapt==1.10.11
|
||||
wrapt==1.11.0
|
||||
|
||||
@@ -499,12 +499,12 @@ def send_file(start_response, trans, body):
|
||||
return body
|
||||
|
||||
|
||||
def iterate_file(file):
|
||||
def iterate_file(fh):
|
||||
"""
|
||||
Progressively return chunks from `file`.
|
||||
"""
|
||||
while 1:
|
||||
chunk = file.read(CHUNK_SIZE)
|
||||
chunk = fh.read(CHUNK_SIZE)
|
||||
if not chunk:
|
||||
break
|
||||
yield chunk
|
||||
|
||||
@@ -351,23 +351,23 @@ class DatasetsController(BaseAPIController, UsesVisualizationMixin):
|
||||
else:
|
||||
file_path = hda.file_name
|
||||
rval = open(file_path, 'rb')
|
||||
|
||||
else:
|
||||
display_kwd = kwd.copy()
|
||||
if 'key' in display_kwd:
|
||||
del display_kwd["key"]
|
||||
rval = hda.datatype.display_data(trans, hda, preview, filename, to_ext, **display_kwd)
|
||||
|
||||
except Exception as exception:
|
||||
log.error("Error getting display data for dataset (%s) from history (%s): %s",
|
||||
history_content_id, history_id, str(exception), exc_info=True)
|
||||
except Exception as e:
|
||||
log.exception("Error getting display data for dataset (%s) from history (%s)",
|
||||
history_content_id, history_id)
|
||||
trans.response.status = 500
|
||||
rval = ("Could not get display data for dataset: " + str(exception))
|
||||
|
||||
rval = "Could not get display data for dataset: %s" % e
|
||||
return rval
|
||||
|
||||
@web.expose_api_raw_anonymous
|
||||
def get_metadata_file(self, trans, history_content_id, history_id, metadata_file=None, **kwd):
|
||||
"""
|
||||
GET /api/histories/{history_id}/contents/{history_content_id}/metadata_file
|
||||
"""
|
||||
decoded_content_id = self.decode_id(history_content_id)
|
||||
rval = ''
|
||||
try:
|
||||
@@ -376,12 +376,12 @@ class DatasetsController(BaseAPIController, UsesVisualizationMixin):
|
||||
fname = ''.join(c in util.FILENAME_VALID_CHARS and c or '_' for c in hda.name)[0:150]
|
||||
trans.response.headers["Content-Type"] = "application/octet-stream"
|
||||
trans.response.headers["Content-Disposition"] = 'attachment; filename="Galaxy%s-[%s].%s"' % (hda.hid, fname, file_ext)
|
||||
return open(hda.metadata.get(metadata_file).file_name)
|
||||
except Exception as exception:
|
||||
log.error("Error getting metadata_file (%s) for dataset (%s) from history (%s): %s",
|
||||
metadata_file, history_content_id, history_id, str(exception), exc_info=True)
|
||||
return open(hda.metadata.get(metadata_file).file_name, 'rb')
|
||||
except Exception as e:
|
||||
log.exception("Error getting metadata_file (%s) for dataset (%s) from history (%s)",
|
||||
metadata_file, history_content_id, history_id)
|
||||
trans.response.status = 500
|
||||
rval = ("Could not get display data for dataset: " + str(exception))
|
||||
rval = "Could not get metadata for dataset: %s" % e
|
||||
return rval
|
||||
|
||||
@web._future_expose_api_anonymous
|
||||
|
||||
@@ -1,6 +1,7 @@
|
||||
"""
|
||||
This module manages loading of Galaxy webhooks.
|
||||
"""
|
||||
import io
|
||||
import logging
|
||||
import os
|
||||
|
||||
@@ -64,8 +65,8 @@ class WebhooksRegistry(object):
|
||||
log.exception(e)
|
||||
|
||||
def load_webhook_from_config(self, webhook_dir, config_file_path):
|
||||
with open(config_file_path) as file:
|
||||
config = yaml.safe_load(file)
|
||||
with open(config_file_path) as fh:
|
||||
config = yaml.safe_load(fh)
|
||||
|
||||
weight = config.get('weight', 1)
|
||||
if weight < 1:
|
||||
@@ -83,8 +84,8 @@ class WebhooksRegistry(object):
|
||||
# single file
|
||||
try:
|
||||
styles_file = os.path.join(webhook_dir, 'styles.css')
|
||||
with open(styles_file, 'r') as file:
|
||||
webhook.styles = file.read().replace('\n', '')
|
||||
with open(styles_file, 'r') as fh:
|
||||
webhook.styles = fh.read().replace('\n', '')
|
||||
except IOError:
|
||||
pass
|
||||
|
||||
@@ -92,8 +93,8 @@ class WebhooksRegistry(object):
|
||||
# single file
|
||||
try:
|
||||
script_file = os.path.join(webhook_dir, 'script.js')
|
||||
with open(script_file, 'r') as file:
|
||||
webhook.script = file.read()
|
||||
with io.open(script_file, 'r', encoding='utf-8') as fh:
|
||||
webhook.script = fh.read()
|
||||
except IOError:
|
||||
pass
|
||||
|
||||
|
||||
@@ -10,4 +10,4 @@ class GalaxyInteractorBackwardCompatTestCase(api.ApiTestCase):
|
||||
def test_local_test_data_download(self):
|
||||
self.galaxy_interactor._target_galaxy_version = Version("18.09")
|
||||
assert self.galaxy_interactor.supports_test_data_download is False
|
||||
assert self.galaxy_interactor.test_data_download(tool_id='cat1', filename='1.bed').readline().startswith('chr1\t147962192\t147962580')
|
||||
assert self.galaxy_interactor.test_data_download(tool_id='cat1', filename='1.bed').readline().startswith(b'chr1\t147962192\t147962580')
|
||||
|
||||
@@ -192,7 +192,7 @@ class HistoriesApiTestCase(api.ApiTestCase):
|
||||
def test_import_metadata_regeneration(self):
|
||||
history_name = "for_import_metadata_regeneration"
|
||||
history_id = self.dataset_populator.new_history(name=history_name)
|
||||
self.dataset_populator.new_dataset(history_id, content=open(self.test_data_resolver.get_filename("1.bam")), file_type='bam')
|
||||
self.dataset_populator.new_dataset(history_id, content=open(self.test_data_resolver.get_filename("1.bam"), 'rb'), file_type='bam')
|
||||
imported_history_id = self._reimport_history(history_id, history_name)
|
||||
self._assert_history_length(imported_history_id, 1)
|
||||
import_bam_metadata = self.dataset_populator.get_history_dataset_details(
|
||||
@@ -203,7 +203,7 @@ class HistoriesApiTestCase(api.ApiTestCase):
|
||||
assert bai_metadata["file_type"] == "bam_index"
|
||||
api_url = bai_metadata["download_url"].split("api/", 1)[1]
|
||||
bai_response = self._get(api_url)
|
||||
assert bai_response.status_code == 200
|
||||
self._assert_status_code_is(bai_response, 200)
|
||||
assert len(bai_response.content) > 4
|
||||
|
||||
def test_import_export_collection(self):
|
||||
|
||||
Reference in New Issue
Block a user