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Merge pull request #14466 from nsoranzo/release_22.01_fix_docs

Browse Source 
[22.01] Fix doc versioning banner and other doc fixes
This commit is contained in:
Dannon
2022-08-16 16:26:41 -04:00
committed by GitHub
parent 6c43d6664f 11c0c7bfdb
commit 6db32243a9
96 changed files with 1466 additions and 549 deletions
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Makefile
+2 -3
View File
@@ -4,7 +4,6 @@ VENV?=.venv
IN_VENV=if [ -f "$(VENV)/bin/activate" ]; then . "$(VENV)/bin/activate"; fi;
RELEASE_CURR:=22.01
RELEASE_UPSTREAM:=upstream
TARGET_BRANCH=$(RELEASE_UPSTREAM)/dev
CONFIG_MANAGE=$(IN_VENV) python lib/galaxy/config/config_manage.py
PROJECT_URL?=https://github.com/galaxyproject/galaxy
DOCS_DIR=doc
@@ -38,8 +37,8 @@ docs-develop: ## Fast doc generation and more warnings (for development)
setup-venv:
if [ ! -f $(VENV)/bin/activate ]; then bash scripts/common_startup.sh --dev-wheels; fi
diff-format:
$(IN_VENV) darker -r $(TARGET_BRANCH)
diff-format: ## Format Python code changes since last commit
$(IN_VENV) darker .
list-dependency-updates: setup-venv
$(IN_VENV) pip list --outdated --format=columns
doc/Makefile
+1 -2
View File
@@ -54,8 +54,6 @@ source/admin/config_logging_default_yaml.rst: ../lib/galaxy/config/__init__.py
printf ' logging:\n ' >> $@
PYTHONPATH=../lib python -c 'from __future__ import print_function; import yaml, galaxy.config; print("\n ".join(yaml.dump(galaxy.config.LOGGING_CONFIG_DEFAULT, indent=2, default_flow_style=False).splitlines()))' >> $@
# might also want to do
# cd source/lib; hg revert; rm *.rst.orig; or not.
clean:
-rm -rf $(BUILDDIR)/* $(GENERATED_RST)
@@ -172,4 +170,5 @@ doctest: $(GENERATED_RST)
# Update Sphinx RST files for lib/ to reflect code structure changes
updaterst:
-rm -rf source/lib/
$(SPHINXAPIDOC) -M --force -o source/lib/ ../lib/
doc/source/admin/nginx.md
+1 -1
View File
@@ -325,7 +325,7 @@ If you serve Galaxy at a prefix exchange `/api/upload/resumable_upload` with `/p
After reloading the nginx configuration you can verify that this configuration works correctly by uploading a file to Galaxy. Make sure the tusd server logs the request. It should look similar to the following
```log
```
[tusd] 2021/10/12 13:30:14 Using '/Users/mvandenb/src/galaxy/database/tmp' as directory storage.
[tusd] 2021/10/12 13:30:14 Using 0.00MB as maximum size.
[tusd] 2021/10/12 13:30:14 Using 'http://localhost:8000/api/upload/hooks' as the endpoint for hooks
doc/source/admin/special_topics/performance_tracking.rst
+4 -5
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@@ -2,22 +2,21 @@ Galaxy Performance Tracking
===========================
Tracking performance over time and identifying slow queries in your Galaxy can be an extremely important thing to do, especially for larger Galaxies.
[A more in-depth tutorial is available at the Galaxy Training Network](https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html).
A more `in-depth tutorial <https://training.galaxyproject.org/training-material/topics/admin/tutorials/monitoring/tutorial.html>`__ is available at the Galaxy Training Network.
Most performance tracking requires sending metrics to a metrics collection server such as `StatsD <https://github.com/etsy/statsd/>`__. This document assumes you have already deployed StatsD.
Gunicorn
-----
--------
There is some built-in `Gunicorn <https://docs.gunicorn.org/en/stable/instrumentation.html>`__ support for performance logging. You can send Gunicorn's internal metrics to a StatsD server by setting the `--statsd-host` and `--statsd-prefix` command line options for Gunicorn in the `gravity` section of `galaxy.yml`:
.. code-block:: yaml
gravity:
...
#...
gunicorn:
extra_args: `--statsd-host 127.0.0.1:8125 --statsd-prefix=gunicorn`
...
extra_args: '--statsd-host 127.0.0.1:8125 --statsd-prefix=gunicorn'
API / Route Timing Statistics
-----------------------------
doc/source/dev/debugging_galaxy_slurm.md
+10 -10
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@@ -2,15 +2,15 @@
# Debugging Galaxy: Slurm Compute Cluster
This document explains how to debug a Galaxy instance that uses a Slurm compute cluster (not the
default LocalRunner). If you have a MacOS machine, you need to create a Linux VM using Oracle's
VirtualBoxVM and run the instructions in the VM. For reference, I created a 64-bit Linux VM with
4096 MB of RAM and 32 GB of disk space (all other parameters were left as default) and managed to
successfully run the instructions. If using a Linux VM, you may need to install Git, Python, VSCode,
and Docker (if using Irods storage). Finally, These instructions are intended for developers who
want to debug their Galaxy instance and are not meant for deployment purposes (We have nice Ansible
default LocalRunner). If you have a MacOS machine, you need to create a Linux VM using Oracle's
VirtualBoxVM and run the instructions in the VM. For reference, I created a 64-bit Linux VM with
4096 MB of RAM and 32 GB of disk space (all other parameters were left as default) and managed to
successfully run the instructions. If using a Linux VM, you may need to install Git, Python, VSCode,
and Docker (if using Irods storage). Finally, These instructions are intended for developers who
want to debug their Galaxy instance and are not meant for deployment purposes (We have nice Ansible
playbooks for that).
## Debugging Galaxy in VS Code
## Debugging Galaxy in VS Code
1. Install libslurm-dev
* `sudo apt install libslurm-dev`
@@ -19,7 +19,7 @@ playbooks for that).
2. Install slurm-drmaa
* Download slurm-drmaa tar file from https://github.com/natefoo/slurm-drmaa/releases/download/1.1.2/slurm-drmaa-1.1.2.tar.gz
* Extract the downloaded tar file into home directory: `tar -xzvf slurm-drmaa-1.1.2.tar.gz -C ~`
* Extract the downloaded tar file into home directory: `tar -xzvf slurm-drmaa-1.1.2.tar.gz -C ~`
* To compile and install slurm-drmaa
* `cd ~/slurm-drmaa-1.1.2`
* `./configure --with-slurm-inc=/usr/include --with-slurm-lib=/usr/lib/x86_64-linux-gpu`
@@ -71,6 +71,6 @@ playbooks for that).
* `sudo service slurmd start`
* `sudo service slurmctld start`
6. Follow the instructions [here](./debuging_galaxy.md) to setup VSCode for debugging.
6. Follow the instructions [here](debugging_galaxy) to setup VSCode for debugging.
Enjoy debugging session your Galaxy instance backed by a Slurm cluster!
Enjoy debugging session your Galaxy instance backed by a Slurm cluster!
doc/source/dev/interactive_environments.rst
+1 -1
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@@ -1,5 +1,5 @@
Interactive Environments
=========================
Galaxy Interactive Environments are deprecated and were the precursors to the current :doc:`Galaxy Interactive Tools <../admin/special_topics/interactivetools>`.
Galaxy Interactive Environments are deprecated and were the precursors to the current :ref:`Galaxy Interactive Tools <interactivetools>`.
You can find information about Galaxy Interactive Environments in `older versions <https://docs.galaxyproject.org/en/release_21.09/admin/special_topics/interactive_environments.html>`__ of this document.
doc/source/dev/translating.rst
+4 -4
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@@ -45,19 +45,19 @@ There are a number of ways text gets used in the codebase, especially the new Vu
1. Text within an element:
.. code-block:: js
.. code-block:: html
<b>Some Text</b>
2. Text within a more complex element:
.. code-block:: javascript
.. code-block:: html
<b><icon library>Some Text</b>
3. Attribute or placeholder text
.. code-block:: javascript
.. code-block:: html
<b-form-input v-model="newLibraryForm.synopsis" placeholder="Synopsis of the library" />
@@ -88,7 +88,7 @@ The first one is the easiest, we can just add the ``v-localize`` tag and we're d
For those you'll need to have a quick overview of the structure of a Vue component to localize the correct place to set the variable. The exact structure will not always be identical but it should be similar. At the top is a ``<template>`` section which contains what will be rendered, and at the bottom is a ``<script>`` section which contains some code that's run as part of rendering that UI component.
.. code-block:: javascript
.. code-block:: html
<template>
<span class="position-relative">
doc/source/lib/galaxy.actions.rst
-8
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@@ -9,14 +9,6 @@ galaxy.actions package
Submodules
----------
galaxy.actions.admin module
---------------------------
.. automodule:: galaxy.actions.admin
:members:
:undoc-members:
:show-inheritance:
galaxy.actions.library module
-----------------------------
doc/source/lib/galaxy.app_unittest_utils.rst
+34
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@@ -0,0 +1,34 @@
galaxy.app\_unittest\_utils package
===================================
.. automodule:: galaxy.app_unittest_utils
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.app\_unittest\_utils.celery\_helper module
-------------------------------------------------
.. automodule:: galaxy.app_unittest_utils.celery_helper
:members:
:undoc-members:
:show-inheritance:
galaxy.app\_unittest\_utils.galaxy\_mock module
-----------------------------------------------
.. automodule:: galaxy.app_unittest_utils.galaxy_mock
:members:
:undoc-members:
:show-inheritance:
galaxy.app\_unittest\_utils.tools\_support module
-------------------------------------------------
.. automodule:: galaxy.app_unittest_utils.tools_support
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.celery.rst
+18
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@@ -0,0 +1,18 @@
galaxy.celery package
=====================
.. automodule:: galaxy.celery
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.celery.tasks module
--------------------------
.. automodule:: galaxy.celery.tasks
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.datatypes.converters.rst
+8
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@@ -161,6 +161,14 @@ galaxy.datatypes.converters.maf\_to\_interval\_converter module
:undoc-members:
:show-inheritance:
galaxy.datatypes.converters.parquet\_to\_csv\_converter module
--------------------------------------------------------------
.. automodule:: galaxy.datatypes.converters.parquet_to_csv_converter
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.converters.pbed\_ldreduced\_converter module
-------------------------------------------------------------
doc/source/lib/galaxy.datatypes.rst
+32
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@@ -100,6 +100,14 @@ galaxy.datatypes.data module
:undoc-members:
:show-inheritance:
galaxy.datatypes.flow module
----------------------------
.. automodule:: galaxy.datatypes.flow
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.genetics module
--------------------------------
@@ -116,6 +124,14 @@ galaxy.datatypes.gis module
:undoc-members:
:show-inheritance:
galaxy.datatypes.goldenpath module
----------------------------------
.. automodule:: galaxy.datatypes.goldenpath
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.graph module
-----------------------------
@@ -124,6 +140,14 @@ galaxy.datatypes.graph module
:undoc-members:
:show-inheritance:
galaxy.datatypes.hdf5 module
----------------------------
.. automodule:: galaxy.datatypes.hdf5
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.images module
------------------------------
@@ -156,6 +180,14 @@ galaxy.datatypes.media module
:undoc-members:
:show-inheritance:
galaxy.datatypes.metacyto module
--------------------------------
.. automodule:: galaxy.datatypes.metacyto
:members:
:undoc-members:
:show-inheritance:
galaxy.datatypes.metadata module
--------------------------------
doc/source/lib/galaxy.eggs.rst
-7
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@@ -1,7 +0,0 @@
galaxy.eggs package
===================
.. automodule:: galaxy.eggs
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.files.rst
+1
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@@ -13,3 +13,4 @@ Subpackages
:maxdepth: 4
galaxy.files.sources
galaxy.files.unittest_utils
doc/source/lib/galaxy.files.sources.rst
+64
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@@ -9,6 +9,22 @@ galaxy.files.sources package
Submodules
----------
galaxy.files.sources.anvil module
---------------------------------
.. automodule:: galaxy.files.sources.anvil
:members:
:undoc-members:
:show-inheritance:
galaxy.files.sources.basespace module
-------------------------------------
.. automodule:: galaxy.files.sources.basespace
:members:
:undoc-members:
:show-inheritance:
galaxy.files.sources.dropbox module
-----------------------------------
@@ -17,6 +33,14 @@ galaxy.files.sources.dropbox module
:undoc-members:
:show-inheritance:
galaxy.files.sources.ftp module
-------------------------------
.. automodule:: galaxy.files.sources.ftp
:members:
:undoc-members:
:show-inheritance:
galaxy.files.sources.galaxy module
----------------------------------
@@ -25,6 +49,30 @@ galaxy.files.sources.galaxy module
:undoc-members:
:show-inheritance:
galaxy.files.sources.googlecloudstorage module
----------------------------------------------
.. automodule:: galaxy.files.sources.googlecloudstorage
:members:
:undoc-members:
:show-inheritance:
galaxy.files.sources.googledrive module
---------------------------------------
.. automodule:: galaxy.files.sources.googledrive
:members:
:undoc-members:
:show-inheritance:
galaxy.files.sources.onedata module
-----------------------------------
.. automodule:: galaxy.files.sources.onedata
:members:
:undoc-members:
:show-inheritance:
galaxy.files.sources.posix module
---------------------------------
@@ -41,6 +89,22 @@ galaxy.files.sources.s3 module
:undoc-members:
:show-inheritance:
galaxy.files.sources.s3fs module
--------------------------------
.. automodule:: galaxy.files.sources.s3fs
:members:
:undoc-members:
:show-inheritance:
galaxy.files.sources.ssh module
-------------------------------
.. automodule:: galaxy.files.sources.ssh
:members:
:undoc-members:
:show-inheritance:
galaxy.files.sources.webdav module
----------------------------------
doc/source/lib/galaxy.tools.toolbox.filters.rst → doc/source/lib/galaxy.files.unittest_utils.rst
+2 -2
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@@ -1,7 +1,7 @@
galaxy.tools.toolbox.filters package
galaxy.files.unittest\_utils package
====================================
.. automodule:: galaxy.tools.toolbox.filters
.. automodule:: galaxy.files.unittest_utils
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.actions.rst → doc/source/lib/galaxy.job_execution.actions.rst
+4 -4
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@@ -1,5 +1,5 @@
galaxy.job_execution.actions package
===========================
galaxy.job\_execution.actions package
=====================================
.. automodule:: galaxy.job_execution.actions
:members:
@@ -9,8 +9,8 @@ galaxy.job_execution.actions package
Submodules
----------
galaxy.job_execution.actions.post module
-------------------------------
galaxy.job\_execution.actions.post module
-----------------------------------------
.. automodule:: galaxy.job_execution.actions.post
:members:
doc/source/lib/galaxy.job_execution.rst
+9
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@@ -12,11 +12,20 @@ Subpackages
.. toctree::
:maxdepth: 4
galaxy.job_execution.actions
galaxy.job_execution.ports
Submodules
----------
galaxy.job\_execution.compute\_environment module
-------------------------------------------------
.. automodule:: galaxy.job_execution.compute_environment
:members:
:undoc-members:
:show-inheritance:
galaxy.job\_execution.datasets module
-------------------------------------
doc/source/lib/galaxy.jobs.rst
-9
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@@ -12,7 +12,6 @@ Subpackages
.. toctree::
:maxdepth: 4
galaxy.job_execution.actions
galaxy.jobs.rules
galaxy.jobs.runners
galaxy.jobs.splitters
@@ -75,11 +74,3 @@ galaxy.jobs.stock\_rules module
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.transfer\_manager module
------------------------------------
.. automodule:: galaxy.jobs.transfer_manager
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.jobs.runners.util.cli.job.rst
+8
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@@ -17,6 +17,14 @@ galaxy.jobs.runners.util.cli.job.lsf module
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.util.cli.job.pbs module
-------------------------------------------
.. automodule:: galaxy.jobs.runners.util.cli.job.pbs
:members:
:undoc-members:
:show-inheritance:
galaxy.jobs.runners.util.cli.job.slurm module
---------------------------------------------
doc/source/lib/galaxy.managers.rst
+88 -8
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@@ -81,14 +81,6 @@ galaxy.managers.configuration module
:undoc-members:
:show-inheritance:
galaxy.managers.containers module
---------------------------------
.. automodule:: galaxy.managers.containers
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.context module
------------------------------
@@ -105,6 +97,14 @@ galaxy.managers.datasets module
:undoc-members:
:show-inheritance:
galaxy.managers.datatypes module
--------------------------------
.. automodule:: galaxy.managers.datatypes
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.deletable module
--------------------------------
@@ -113,6 +113,14 @@ galaxy.managers.deletable module
:undoc-members:
:show-inheritance:
galaxy.managers.display\_applications module
--------------------------------------------
.. automodule:: galaxy.managers.display_applications
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.executables module
----------------------------------
@@ -129,6 +137,38 @@ galaxy.managers.folders module
:undoc-members:
:show-inheritance:
galaxy.managers.genomes module
------------------------------
.. automodule:: galaxy.managers.genomes
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.group\_roles module
-----------------------------------
.. automodule:: galaxy.managers.group_roles
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.group\_users module
-----------------------------------
.. automodule:: galaxy.managers.group_users
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.groups module
-----------------------------
.. automodule:: galaxy.managers.groups
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.hdas module
---------------------------
@@ -225,6 +265,14 @@ galaxy.managers.markdown\_util module
:undoc-members:
:show-inheritance:
galaxy.managers.metrics module
------------------------------
.. automodule:: galaxy.managers.metrics
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.pages module
----------------------------
@@ -233,6 +281,14 @@ galaxy.managers.pages module
:undoc-members:
:show-inheritance:
galaxy.managers.quotas module
-----------------------------
.. automodule:: galaxy.managers.quotas
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.ratable module
------------------------------
@@ -249,6 +305,14 @@ galaxy.managers.rbac\_secured module
:undoc-members:
:show-inheritance:
galaxy.managers.remote\_files module
------------------------------------
.. automodule:: galaxy.managers.remote_files
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.roles module
----------------------------
@@ -289,6 +353,22 @@ galaxy.managers.taggable module
:undoc-members:
:show-inheritance:
galaxy.managers.tags module
---------------------------
.. automodule:: galaxy.managers.tags
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.tool\_data module
---------------------------------
.. automodule:: galaxy.managers.tool_data
:members:
:undoc-members:
:show-inheritance:
galaxy.managers.tools module
----------------------------
doc/source/lib/galaxy.model.migrate.rst
+1
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@@ -12,6 +12,7 @@ Subpackages
.. toctree::
:maxdepth: 4
galaxy.model.migrate.triggers
galaxy.model.migrate.versions
Submodules
doc/source/lib/galaxy.model.migrate.triggers.rst
+26
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@@ -0,0 +1,26 @@
galaxy.model.migrate.triggers package
=====================================
.. automodule:: galaxy.model.migrate.triggers
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.model.migrate.triggers.history\_update\_time\_field module
-----------------------------------------------------------------
.. automodule:: galaxy.model.migrate.triggers.history_update_time_field
:members:
:undoc-members:
:show-inheritance:
galaxy.model.migrate.triggers.update\_audit\_table module
---------------------------------------------------------
.. automodule:: galaxy.model.migrate.triggers.update_audit_table
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.model.migrate.versions.rst
+64
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@@ -1385,6 +1385,70 @@ galaxy.model.migrate.versions.0172\_it\_entrypoint\_requires\_domain module
:undoc-members:
:show-inheritance:
galaxy.model.migrate.versions.0173\_add\_job\_id\_to\_dataset module
--------------------------------------------------------------------
.. automodule:: galaxy.model.migrate.versions.0173_add_job_id_to_dataset
:members:
:undoc-members:
:show-inheritance:
galaxy.model.migrate.versions.0174\_readd\_update\_time\_triggers module
------------------------------------------------------------------------
.. automodule:: galaxy.model.migrate.versions.0174_readd_update_time_triggers
:members:
:undoc-members:
:show-inheritance:
galaxy.model.migrate.versions.0175\_history\_audit module
---------------------------------------------------------
.. automodule:: galaxy.model.migrate.versions.0175_history_audit
:members:
:undoc-members:
:show-inheritance:
galaxy.model.migrate.versions.0176\_add\_indexes\_on\_update\_time module
-------------------------------------------------------------------------
.. automodule:: galaxy.model.migrate.versions.0176_add_indexes_on_update_time
:members:
:undoc-members:
:show-inheritance:
galaxy.model.migrate.versions.0177\_update\_job\_state\_summary module
----------------------------------------------------------------------
.. automodule:: galaxy.model.migrate.versions.0177_update_job_state_summary
:members:
:undoc-members:
:show-inheritance:
galaxy.model.migrate.versions.0178\_drop\_deferredjob\_table module
-------------------------------------------------------------------
.. automodule:: galaxy.model.migrate.versions.0178_drop_deferredjob_table
:members:
:undoc-members:
:show-inheritance:
galaxy.model.migrate.versions.0179\_drop\_transferjob\_table module
-------------------------------------------------------------------
.. automodule:: galaxy.model.migrate.versions.0179_drop_transferjob_table
:members:
:undoc-members:
:show-inheritance:
galaxy.model.migrate.versions.0180\_add\_vault\_table module
------------------------------------------------------------
.. automodule:: galaxy.model.migrate.versions.0180_add_vault_table
:members:
:undoc-members:
:show-inheritance:
galaxy.model.migrate.versions.util module
-----------------------------------------
doc/source/lib/galaxy.model.rst
+17 -8
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@@ -17,6 +17,7 @@ Subpackages
galaxy.model.orm
galaxy.model.store
galaxy.model.tool_shed_install
galaxy.model.unittest_utils
galaxy.model.view
Submodules
@@ -46,6 +47,14 @@ galaxy.model.database\_heartbeat module
:undoc-members:
:show-inheritance:
galaxy.model.database\_utils module
-----------------------------------
.. automodule:: galaxy.model.database_utils
:members:
:undoc-members:
:show-inheritance:
galaxy.model.item\_attrs module
-------------------------------
@@ -78,6 +87,14 @@ galaxy.model.none\_like module
:undoc-members:
:show-inheritance:
galaxy.model.scoped\_session module
-----------------------------------
.. automodule:: galaxy.model.scoped_session
:members:
:undoc-members:
:show-inheritance:
galaxy.model.search module
--------------------------
@@ -101,11 +118,3 @@ galaxy.model.tags module
:members:
:undoc-members:
:show-inheritance:
galaxy.model.triggers module
----------------------------
.. automodule:: galaxy.model.triggers
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.model.tool_shed_install.migrate.rst
+8
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@@ -6,6 +6,14 @@ galaxy.model.tool\_shed\_install.migrate package
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
:maxdepth: 4
galaxy.model.tool_shed_install.migrate.versions
Submodules
----------
doc/source/lib/galaxy.model.tool_shed_install.migrate.versions.rst
+146
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@@ -0,0 +1,146 @@
galaxy.model.tool\_shed\_install.migrate.versions package
=========================================================
.. automodule:: galaxy.model.tool_shed_install.migrate.versions
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.model.tool\_shed\_install.migrate.versions.0001\_add\_tool\_shed\_repository\_table module
-------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0001_add_tool_shed_repository_table
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0002\_add\_tool\_shed\_repository\_table\_columns module
----------------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0002_add_tool_shed_repository_table_columns
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0003\_tool\_id\_guid\_map\_table module
-----------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0003_tool_id_guid_map_table
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0004\_add\_installed\_changeset\_revison\_column module
---------------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0004_add_installed_changeset_revison_column
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0005\_add\_tool\_shed\_repository\_table\_columns module
----------------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0005_add_tool_shed_repository_table_columns
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0006\_add\_tool\_version\_tables module
-----------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0006_add_tool_version_tables
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0007\_add\_migrate\_tools\_table module
-----------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0007_add_migrate_tools_table
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0008\_add\_ctx\_rev\_column module
------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0008_add_ctx_rev_column
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0009\_add\_tool\_dependency\_table module
-------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0009_add_tool_dependency_table
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0010\_alter\_tool\_dependency\_table\_version\_column module
--------------------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0010_alter_tool_dependency_table_version_column
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0011\_drop\_installed\_changeset\_revision\_column module
-----------------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0011_drop_installed_changeset_revision_column
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0012\_add\_tool\_dependency\_status\_columns module
-----------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0012_add_tool_dependency_status_columns
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0013\_add\_tool\_shed\_repository\_status\_columns module
-----------------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0013_add_tool_shed_repository_status_columns
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0014\_add\_repository\_dependency\_tables module
--------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0014_add_repository_dependency_tables
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0015\_update\_migrate\_tools\_table module
--------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0015_update_migrate_tools_table
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0016\_update\_migrate\_tools\_table\_again module
---------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0016_update_migrate_tools_table_again
:members:
:undoc-members:
:show-inheritance:
galaxy.model.tool\_shed\_install.migrate.versions.0017\_drop\_update\_available\_col\_add\_tool\_shed\_status\_col module
-------------------------------------------------------------------------------------------------------------------------
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0017_drop_update_available_col_add_tool_shed_status_col
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.model.unittest_utils.rst
+18
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@@ -0,0 +1,18 @@
galaxy.model.unittest\_utils package
====================================
.. automodule:: galaxy.model.unittest_utils
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.model.unittest\_utils.data\_app module
---------------------------------------------
.. automodule:: galaxy.model.unittest_utils.data_app
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.objectstore.rst
+8
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@@ -6,6 +6,14 @@ galaxy.objectstore package
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
:maxdepth: 4
galaxy.objectstore.unittest_utils
Submodules
----------
doc/source/lib/galaxy.objectstore.unittest_utils.rst
+7
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@@ -0,0 +1,7 @@
galaxy.objectstore.unittest\_utils package
==========================================
.. automodule:: galaxy.objectstore.unittest_utils
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.openid.rst
-26
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@@ -1,26 +0,0 @@
galaxy.openid package
=====================
.. automodule:: galaxy.openid
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.openid.openid\_manager module
------------------------------------
.. automodule:: galaxy.openid.openid_manager
:members:
:undoc-members:
:show-inheritance:
galaxy.openid.providers module
------------------------------
.. automodule:: galaxy.openid.providers
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.rst
+26 -2
View File
@@ -13,13 +13,14 @@ Subpackages
:maxdepth: 4
galaxy.actions
galaxy.app_unittest_utils
galaxy.auth
galaxy.authnz
galaxy.celery
galaxy.config
galaxy.containers
galaxy.datatypes
galaxy.dependencies
galaxy.eggs
galaxy.exceptions
galaxy.files
galaxy.forms
@@ -30,7 +31,6 @@ Subpackages
galaxy.metadata
galaxy.model
galaxy.objectstore
galaxy.openid
galaxy.quota
galaxy.schema
galaxy.security
@@ -67,6 +67,14 @@ galaxy.config\_watchers module
:undoc-members:
:show-inheritance:
galaxy.di module
----------------
.. automodule:: galaxy.di
:members:
:undoc-members:
:show-inheritance:
galaxy.main module
------------------
@@ -75,6 +83,14 @@ galaxy.main module
:undoc-members:
:show-inheritance:
galaxy.main\_config module
--------------------------
.. automodule:: galaxy.main_config
:members:
:undoc-members:
:show-inheritance:
galaxy.queue\_worker module
---------------------------
@@ -91,6 +107,14 @@ galaxy.queues module
:undoc-members:
:show-inheritance:
galaxy.structured\_app module
-----------------------------
.. automodule:: galaxy.structured_app
:members:
:undoc-members:
:show-inheritance:
galaxy.version module
---------------------
doc/source/lib/galaxy.schema.rst
+16
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@@ -17,6 +17,14 @@ galaxy.schema.fields module
:undoc-members:
:show-inheritance:
galaxy.schema.remote\_files module
----------------------------------
.. automodule:: galaxy.schema.remote_files
:members:
:undoc-members:
:show-inheritance:
galaxy.schema.schema module
---------------------------
@@ -24,3 +32,11 @@ galaxy.schema.schema module
:members:
:undoc-members:
:show-inheritance:
galaxy.schema.types module
--------------------------
.. automodule:: galaxy.schema.types
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.security.rst
+24
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@@ -17,6 +17,14 @@ galaxy.security.idencoding module
:undoc-members:
:show-inheritance:
galaxy.security.object\_wrapper module
--------------------------------------
.. automodule:: galaxy.security.object_wrapper
:members:
:undoc-members:
:show-inheritance:
galaxy.security.passwords module
--------------------------------
@@ -25,6 +33,14 @@ galaxy.security.passwords module
:undoc-members:
:show-inheritance:
galaxy.security.ssh\_util module
--------------------------------
.. automodule:: galaxy.security.ssh_util
:members:
:undoc-members:
:show-inheritance:
galaxy.security.validate\_user\_input module
--------------------------------------------
@@ -32,3 +48,11 @@ galaxy.security.validate\_user\_input module
:members:
:undoc-members:
:show-inheritance:
galaxy.security.vault module
----------------------------
.. automodule:: galaxy.security.vault
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.rst
-34
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@@ -1,34 +0,0 @@
galaxy.tool\_shed.galaxy\_install.migrate package
=================================================
.. automodule:: galaxy.tool_shed.galaxy_install.migrate
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
:maxdepth: 4
galaxy.tool_shed.galaxy_install.migrate.versions
Submodules
----------
galaxy.tool\_shed.galaxy\_install.migrate.check module
------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.check
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.common module
-------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.common
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_shed.galaxy_install.migrate.versions.rst
-106
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@@ -1,106 +0,0 @@
galaxy.tool\_shed.galaxy\_install.migrate.versions package
==========================================================
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tool\_shed.galaxy\_install.migrate.versions.0001\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0001_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0002\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0002_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0003\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0003_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0004\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0004_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0005\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0005_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0006\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0006_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0007\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0007_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0008\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0008_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0009\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0009_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0010\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0010_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0011\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0011_tools
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.migrate.versions.0012\_tools module
---------------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.migrate.versions.0012_tools
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_shed.galaxy_install.rst
-9
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@@ -14,7 +14,6 @@ Subpackages
galaxy.tool_shed.galaxy_install.datatypes
galaxy.tool_shed.galaxy_install.metadata
galaxy.tool_shed.galaxy_install.migrate
galaxy.tool_shed.galaxy_install.repository_dependencies
galaxy.tool_shed.galaxy_install.tool_dependencies
galaxy.tool_shed.galaxy_install.tools
@@ -38,14 +37,6 @@ galaxy.tool\_shed.galaxy\_install.installed\_repository\_manager module
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.tool\_migration\_manager module
-----------------------------------------------------------------
.. automodule:: galaxy.tool_shed.galaxy_install.tool_migration_manager
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_shed.galaxy\_install.update\_repository\_manager module
--------------------------------------------------------------------
doc/source/lib/galaxy.tool_util.biotools.rst
+26
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@@ -0,0 +1,26 @@
galaxy.tool\_util.biotools package
==================================
.. automodule:: galaxy.tool_util.biotools
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tool\_util.biotools.interface module
-------------------------------------------
.. automodule:: galaxy.tool_util.biotools.interface
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.biotools.source module
----------------------------------------
.. automodule:: galaxy.tool_util.biotools.source
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_util.deps.mulled.rst
+8
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@@ -49,6 +49,14 @@ galaxy.tool\_util.deps.mulled.mulled\_build\_tool module
:undoc-members:
:show-inheritance:
galaxy.tool\_util.deps.mulled.mulled\_hash module
-------------------------------------------------
.. automodule:: galaxy.tool_util.deps.mulled.mulled_hash
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.deps.mulled.mulled\_list module
-------------------------------------------------
doc/source/lib/galaxy.tool_util.rst
+11
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@@ -12,17 +12,28 @@ Subpackages
.. toctree::
:maxdepth: 4
galaxy.tool_util.biotools
galaxy.tool_util.client
galaxy.tool_util.cwl
galaxy.tool_util.deps
galaxy.tool_util.linters
galaxy.tool_util.locations
galaxy.tool_util.parser
galaxy.tool_util.toolbox
galaxy.tool_util.unittest_utils
galaxy.tool_util.verify
Submodules
----------
galaxy.tool\_util.edam\_util module
-----------------------------------
.. automodule:: galaxy.tool_util.edam_util
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.fetcher module
--------------------------------
doc/source/lib/galaxy.tool_util.toolbox.filters.rst
+7
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@@ -0,0 +1,7 @@
galaxy.tool\_util.toolbox.filters package
=========================================
.. automodule:: galaxy.tool_util.toolbox.filters
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_util.toolbox.lineages.rst
+26
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@@ -0,0 +1,26 @@
galaxy.tool\_util.toolbox.lineages package
==========================================
.. automodule:: galaxy.tool_util.toolbox.lineages
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tool\_util.toolbox.lineages.factory module
-------------------------------------------------
.. automodule:: galaxy.tool_util.toolbox.lineages.factory
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.lineages.interface module
---------------------------------------------------
.. automodule:: galaxy.tool_util.toolbox.lineages.interface
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_util.toolbox.rst
+68
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@@ -0,0 +1,68 @@
galaxy.tool\_util.toolbox package
=================================
.. automodule:: galaxy.tool_util.toolbox
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
:maxdepth: 4
galaxy.tool_util.toolbox.filters
galaxy.tool_util.toolbox.lineages
galaxy.tool_util.toolbox.views
Submodules
----------
galaxy.tool\_util.toolbox.base module
-------------------------------------
.. automodule:: galaxy.tool_util.toolbox.base
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.integrated\_panel module
--------------------------------------------------
.. automodule:: galaxy.tool_util.toolbox.integrated_panel
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.panel module
--------------------------------------
.. automodule:: galaxy.tool_util.toolbox.panel
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.parser module
---------------------------------------
.. automodule:: galaxy.tool_util.toolbox.parser
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.tags module
-------------------------------------
.. automodule:: galaxy.tool_util.toolbox.tags
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.watcher module
----------------------------------------
.. automodule:: galaxy.tool_util.toolbox.watcher
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_util.toolbox.views.rst
+50
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@@ -0,0 +1,50 @@
galaxy.tool\_util.toolbox.views package
=======================================
.. automodule:: galaxy.tool_util.toolbox.views
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tool\_util.toolbox.views.definitions module
--------------------------------------------------
.. automodule:: galaxy.tool_util.toolbox.views.definitions
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.views.edam module
-------------------------------------------
.. automodule:: galaxy.tool_util.toolbox.views.edam
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.views.interface module
------------------------------------------------
.. automodule:: galaxy.tool_util.toolbox.views.interface
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.views.sources module
----------------------------------------------
.. automodule:: galaxy.tool_util.toolbox.views.sources
:members:
:undoc-members:
:show-inheritance:
galaxy.tool\_util.toolbox.views.static module
---------------------------------------------
.. automodule:: galaxy.tool_util.toolbox.views.static
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tool_util.unittest_utils.rst
+18
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@@ -0,0 +1,18 @@
galaxy.tool\_util.unittest\_utils package
=========================================
.. automodule:: galaxy.tool_util.unittest_utils
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tool\_util.unittest\_utils.sample\_data module
-----------------------------------------------------
.. automodule:: galaxy.tool_util.unittest_utils.sample_data
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.rst
+17 -1
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@@ -13,6 +13,7 @@ Subpackages
:maxdepth: 4
galaxy.tools.actions
galaxy.tools.bundled
galaxy.tools.data
galaxy.tools.data_manager
galaxy.tools.error_reports
@@ -21,12 +22,19 @@ Subpackages
galaxy.tools.imp_exp
galaxy.tools.parameters
galaxy.tools.search
galaxy.tools.toolbox
galaxy.tools.util
Submodules
----------
galaxy.tools.biotools module
----------------------------
.. automodule:: galaxy.tools.biotools
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.cache module
-------------------------
@@ -83,6 +91,14 @@ galaxy.tools.recommendations module
:undoc-members:
:show-inheritance:
galaxy.tools.remote\_tool\_eval module
--------------------------------------
.. automodule:: galaxy.tools.remote_tool_eval
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.repositories module
--------------------------------
doc/source/lib/galaxy.tools.toolbox.lineages.rst
-26
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@@ -1,26 +0,0 @@
galaxy.tools.toolbox.lineages package
=====================================
.. automodule:: galaxy.tools.toolbox.lineages
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.tools.toolbox.lineages.factory module
--------------------------------------------
.. automodule:: galaxy.tools.toolbox.lineages.factory
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.lineages.interface module
----------------------------------------------
.. automodule:: galaxy.tools.toolbox.lineages.interface
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.tools.toolbox.rst
-67
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@@ -1,67 +0,0 @@
galaxy.tools.toolbox package
============================
.. automodule:: galaxy.tools.toolbox
:members:
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
:maxdepth: 4
galaxy.tools.toolbox.filters
galaxy.tools.toolbox.lineages
Submodules
----------
galaxy.tools.toolbox.base module
--------------------------------
.. automodule:: galaxy.tools.toolbox.base
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.integrated\_panel module
---------------------------------------------
.. automodule:: galaxy.tools.toolbox.integrated_panel
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.panel module
---------------------------------
.. automodule:: galaxy.tools.toolbox.panel
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.parser module
----------------------------------
.. automodule:: galaxy.tools.toolbox.parser
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.tags module
--------------------------------
.. automodule:: galaxy.tools.toolbox.tags
:members:
:undoc-members:
:show-inheritance:
galaxy.tools.toolbox.watcher module
-----------------------------------
.. automodule:: galaxy.tools.toolbox.watcher
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.util.rst
+32 -16
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@@ -28,6 +28,14 @@ galaxy.util.aliaspickler module
:undoc-members:
:show-inheritance:
galaxy.util.bool\_expressions module
------------------------------------
.. automodule:: galaxy.util.bool_expressions
:members:
:undoc-members:
:show-inheritance:
galaxy.util.bunch module
------------------------
@@ -84,6 +92,14 @@ galaxy.util.dictifiable module
:undoc-members:
:show-inheritance:
galaxy.util.dynamic module
--------------------------
.. automodule:: galaxy.util.dynamic
:members:
:undoc-members:
:show-inheritance:
galaxy.util.expressions module
------------------------------
@@ -116,14 +132,6 @@ galaxy.util.form\_builder module
:undoc-members:
:show-inheritance:
galaxy.util.getargspec module
-----------------------------
.. automodule:: galaxy.util.getargspec
:members:
:undoc-members:
:show-inheritance:
galaxy.util.hash\_util module
-----------------------------
@@ -188,14 +196,6 @@ galaxy.util.monitors module
:undoc-members:
:show-inheritance:
galaxy.util.object\_wrapper module
----------------------------------
.. automodule:: galaxy.util.object_wrapper
:members:
:undoc-members:
:show-inheritance:
galaxy.util.odict module
------------------------
@@ -244,6 +244,14 @@ galaxy.util.renamed\_temporary\_file module
:undoc-members:
:show-inheritance:
galaxy.util.resources module
----------------------------
.. automodule:: galaxy.util.resources
:members:
:undoc-members:
:show-inheritance:
galaxy.util.rules\_dsl module
-----------------------------
@@ -324,6 +332,14 @@ galaxy.util.submodules module
:undoc-members:
:show-inheritance:
galaxy.util.task module
-----------------------
.. automodule:: galaxy.util.task
:members:
:undoc-members:
:show-inheritance:
galaxy.util.template module
---------------------------
doc/source/lib/galaxy.web.framework.middleware.rst
-8
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@@ -49,14 +49,6 @@ galaxy.web.framework.middleware.request\_id module
:undoc-members:
:show-inheritance:
galaxy.web.framework.middleware.sentry module
---------------------------------------------
.. automodule:: galaxy.web.framework.middleware.sentry
:members:
:undoc-members:
:show-inheritance:
galaxy.web.framework.middleware.sqldebug module
-----------------------------------------------
doc/source/lib/galaxy.web.rst
-16
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@@ -35,22 +35,6 @@ galaxy.web.form\_builder module
:undoc-members:
:show-inheritance:
galaxy.web.formatting module
----------------------------
.. automodule:: galaxy.web.formatting
:members:
:undoc-members:
:show-inheritance:
galaxy.web.params module
------------------------
.. automodule:: galaxy.web.params
:members:
:undoc-members:
:show-inheritance:
galaxy.web.statsd\_client module
--------------------------------
doc/source/lib/galaxy.web_stack.rst
+8
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@@ -9,6 +9,14 @@ galaxy.web\_stack package
Submodules
----------
galaxy.web\_stack.gunicorn\_config module
-----------------------------------------
.. automodule:: galaxy.web_stack.gunicorn_config
:members:
:undoc-members:
:show-inheritance:
galaxy.web\_stack.handlers module
---------------------------------
doc/source/lib/galaxy.webapps.base.rst
+8
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@@ -9,6 +9,14 @@ galaxy.webapps.base package
Submodules
----------
galaxy.webapps.base.api module
------------------------------
.. automodule:: galaxy.webapps.base.api
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.base.controller module
-------------------------------------
doc/source/lib/galaxy.webapps.galaxy.api.rst
+16
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@@ -41,6 +41,14 @@ galaxy.webapps.galaxy.api.cloudauthz module
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.common module
---------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.common
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.configuration module
----------------------------------------------
@@ -313,6 +321,14 @@ galaxy.webapps.galaxy.api.roles module
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.sanitize\_allow module
------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.api.sanitize_allow
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.api.search module
---------------------------------------
doc/source/lib/galaxy.webapps.galaxy.controllers.rst
-8
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@@ -97,14 +97,6 @@ galaxy.webapps.galaxy.controllers.library module
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.controllers.openid module
-----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.controllers.openid
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.controllers.page module
---------------------------------------------
doc/source/lib/galaxy.webapps.galaxy.rst
+17
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@@ -14,6 +14,7 @@ Subpackages
galaxy.webapps.galaxy.api
galaxy.webapps.galaxy.controllers
galaxy.webapps.galaxy.services
Submodules
----------
@@ -33,3 +34,19 @@ galaxy.webapps.galaxy.fast\_app module
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.fast\_factory module
------------------------------------------
.. automodule:: galaxy.webapps.galaxy.fast_factory
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.workers module
------------------------------------
.. automodule:: galaxy.webapps.galaxy.workers
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.webapps.galaxy.services.rst
+106
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@@ -0,0 +1,106 @@
galaxy.webapps.galaxy.services package
======================================
.. automodule:: galaxy.webapps.galaxy.services
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy.webapps.galaxy.services.base module
------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.base
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.dataset\_collections module
----------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.dataset_collections
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.datasets module
----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.datasets
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.histories module
-----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.histories
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.history\_contents module
-------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.history_contents
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.libraries module
-----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.libraries
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.library\_folder\_contents module
---------------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.library_folder_contents
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.library\_folders module
------------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.library_folders
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.pages module
-------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.pages
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.quotas module
--------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.quotas
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.sharable module
----------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.sharable
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.galaxy.services.visualizations module
----------------------------------------------------
.. automodule:: galaxy.webapps.galaxy.services.visualizations
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.webapps.reports.api.rst
+7
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@@ -0,0 +1,7 @@
galaxy.webapps.reports.api package
==================================
.. automodule:: galaxy.webapps.reports.api
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy.webapps.reports.rst
+17
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@@ -12,6 +12,7 @@ Subpackages
.. toctree::
:maxdepth: 4
galaxy.webapps.reports.api
galaxy.webapps.reports.controllers
Submodules
@@ -40,3 +41,19 @@ galaxy.webapps.reports.config module
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.reports.fast\_app module
---------------------------------------
.. automodule:: galaxy.webapps.reports.fast_app
:members:
:undoc-members:
:show-inheritance:
galaxy.webapps.reports.fast\_factory module
-------------------------------------------
.. automodule:: galaxy.webapps.reports.fast_factory
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy_test.api.cwl.rst
+7
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@@ -0,0 +1,7 @@
galaxy\_test.api.cwl package
============================
.. automodule:: galaxy_test.api.cwl
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy_test.api.rst
+75 -3
View File
@@ -6,9 +6,33 @@ galaxy\_test.api package
:undoc-members:
:show-inheritance:
Subpackages
-----------
.. toctree::
:maxdepth: 4
galaxy_test.api.cwl
Submodules
----------
galaxy\_test.api.conftest module
--------------------------------
.. automodule:: galaxy_test.api.conftest
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.api.sharable module
--------------------------------
.. automodule:: galaxy_test.api.sharable
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_api\_batch module
----------------------------------------
@@ -57,6 +81,30 @@ galaxy\_test.api.test\_datatypes module
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_display\_applications module
---------------------------------------------------
.. automodule:: galaxy_test.api.test_display_applications
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_folder\_contents module
----------------------------------------------
.. automodule:: galaxy_test.api.test_folder_contents
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_folders module
-------------------------------------
.. automodule:: galaxy_test.api.test_folders
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_framework module
---------------------------------------
@@ -65,10 +113,26 @@ galaxy\_test.api.test\_framework module
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_galaxy\_interactor module
------------------------------------------------
galaxy\_test.api.test\_group\_roles module
------------------------------------------
.. automodule:: galaxy_test.api.test_galaxy_interactor
.. automodule:: galaxy_test.api.test_group_roles
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_group\_users module
------------------------------------------
.. automodule:: galaxy_test.api.test_group_users
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_groups module
------------------------------------
.. automodule:: galaxy_test.api.test_groups
:members:
:undoc-members:
:show-inheritance:
@@ -225,6 +289,14 @@ galaxy\_test.api.test\_workflows module
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_workflows\_cwl module
--------------------------------------------
.. automodule:: galaxy_test.api.test_workflows_cwl
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.api.test\_workflows\_from\_yaml module
---------------------------------------------------
doc/source/lib/galaxy_test.base.rst
+8 -8
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@@ -89,14 +89,6 @@ galaxy\_test.base.rules\_test\_data module
:undoc-members:
:show-inheritance:
galaxy\_test.base.ssh\_util module
----------------------------------
.. automodule:: galaxy_test.base.ssh_util
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.base.testcase module
---------------------------------
@@ -105,6 +97,14 @@ galaxy\_test.base.testcase module
:undoc-members:
:show-inheritance:
galaxy\_test.base.uses\_shed module
-----------------------------------
.. automodule:: galaxy_test.base.uses_shed
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.base.workflow\_fixtures module
-------------------------------------------
doc/source/lib/galaxy_test.driver.rst
+8
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@@ -17,6 +17,14 @@ galaxy\_test.driver.driver\_util module
:undoc-members:
:show-inheritance:
galaxy\_test.driver.integration\_setup module
---------------------------------------------
.. automodule:: galaxy_test.driver.integration_setup
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.driver.integration\_util module
--------------------------------------------
doc/source/lib/galaxy_test.performance.rst
+26
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@@ -0,0 +1,26 @@
galaxy\_test.performance package
================================
.. automodule:: galaxy_test.performance
:members:
:undoc-members:
:show-inheritance:
Submodules
----------
galaxy\_test.performance.conftest module
----------------------------------------
.. automodule:: galaxy_test.performance.conftest
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.performance.test\_workflow\_framework\_performance module
----------------------------------------------------------------------
.. automodule:: galaxy_test.performance.test_workflow_framework_performance
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/galaxy_test.rst
+1
View File
@@ -15,4 +15,5 @@ Subpackages
galaxy_test.api
galaxy_test.base
galaxy_test.driver
galaxy_test.performance
galaxy_test.selenium
doc/source/lib/galaxy_test.selenium.rst
+40
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@@ -17,6 +17,14 @@ Subpackages
Submodules
----------
galaxy\_test.selenium.conftest module
-------------------------------------
.. automodule:: galaxy_test.selenium.conftest
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.selenium.framework module
--------------------------------------
@@ -65,6 +73,14 @@ galaxy\_test.selenium.test\_collection\_builders module
:undoc-members:
:show-inheritance:
galaxy\_test.selenium.test\_collection\_edit module
---------------------------------------------------
.. automodule:: galaxy_test.selenium.test_collection_edit
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.selenium.test\_custom\_builds module
-------------------------------------------------
@@ -73,6 +89,14 @@ galaxy\_test.selenium.test\_custom\_builds module
:undoc-members:
:show-inheritance:
galaxy\_test.selenium.test\_data\_source\_tools module
------------------------------------------------------
.. automodule:: galaxy_test.selenium.test_data_source_tools
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.selenium.test\_histories\_list module
--------------------------------------------------
@@ -97,6 +121,14 @@ galaxy\_test.selenium.test\_history\_dataset\_state module
:undoc-members:
:show-inheritance:
galaxy\_test.selenium.test\_history\_export module
--------------------------------------------------
.. automodule:: galaxy_test.selenium.test_history_export
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.selenium.test\_history\_multi\_view module
-------------------------------------------------------
@@ -312,3 +344,11 @@ galaxy\_test.selenium.test\_workflow\_run module
:members:
:undoc-members:
:show-inheritance:
galaxy\_test.selenium.test\_workflow\_sharing module
----------------------------------------------------
.. automodule:: galaxy_test.selenium.test_workflow_sharing
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/tool_shed.webapp.framework.rst
+11
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@@ -13,3 +13,14 @@ Subpackages
:maxdepth: 4
tool_shed.webapp.framework.middleware
Submodules
----------
tool\_shed.webapp.framework.decorators module
---------------------------------------------
.. automodule:: tool_shed.webapp.framework.decorators
:members:
:undoc-members:
:show-inheritance:
doc/source/lib/tool_shed.webapp.rst
+16
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@@ -46,3 +46,19 @@ tool\_shed.webapp.config module
:members:
:undoc-members:
:show-inheritance:
tool\_shed.webapp.fast\_app module
----------------------------------
.. automodule:: tool_shed.webapp.fast_app
:members:
:undoc-members:
:show-inheritance:
tool\_shed.webapp.fast\_factory module
--------------------------------------
.. automodule:: tool_shed.webapp.fast_factory
:members:
:undoc-members:
:show-inheritance:
doc/source/releases/19.01_announce_user.rst
+1 -1
View File
@@ -68,7 +68,7 @@ Builtin Tool Updates
Release Notes
===========================================================
Please see the `full release notes <19.01_announce.html>`_ for more details.
Please see the :doc:`full release notes <19.01_announce>` for more details.
.. include:: 19.01_prs.rst
doc/source/releases/19.05_announce_user.rst
+1 -1
View File
@@ -90,7 +90,7 @@ Builtin Tool Updates
Release Notes
===========================================================
Please see the `full release notes <19.05_announce.html>`_ for more details.
Please see the :doc:`full release notes <19.05_announce>` for more details.
.. include:: 19.05_prs.rst
doc/source/releases/19.09_announce_user.rst
+1 -1
View File
@@ -95,7 +95,7 @@ Builtin Tool Updates
Release Notes
===========================================================
Please see the `full release notes <19.09_announce.html>`_ for more details.
Please see the :doc:`full release notes <19.09_announce>` for more details.
.. include:: 19.09_prs.rst
doc/source/releases/20.01_announce_user.rst
+1 -1
View File
@@ -131,7 +131,7 @@ Builtin Tool Updates
Release Notes
===========================================================
Please see the `full release notes <20.01_announce.html>`_ for more details.
Please see the :doc:`full release notes <20.01_announce>` for more details.
.. include:: 20.01_prs.rst
doc/source/releases/20.05_announce_user.rst
+1 -1
View File
@@ -107,7 +107,7 @@ Builtin Tool Updates
Release Notes
===========================================================
Please see the `full release notes <20.05_announce.html>`_ for more details.
Please see the :doc:`full release notes <20.05_announce>` for more details.
.. include:: 20.05_prs.rst
doc/source/releases/20.09_announce_user.rst
+1 -1
View File
@@ -190,7 +190,7 @@ Builtin Tool Updates
Release Notes
===========================================================
Please see the `full release notes <20.09_announce.html>`_ for more details.
Please see the :doc:`full release notes <20.09_announce>` for more details.
.. include:: 20.09_prs.rst
doc/source/releases/21.01_announce_user.rst
+1 -1
View File
@@ -174,7 +174,7 @@ Builtin Tool Updates
Release Notes
===========================================================
Please see the `full release notes <21.01_announce.html>`_ for more details.
Please see the :doc:`full release notes <21.01_announce>` for more details.
.. include:: 21.01_prs.rst
doc/source/releases/21.01_prs.rst
+2
View File
@@ -20,6 +20,8 @@
.. _Pull Request 11605: https://github.com/galaxyproject/galaxy/pull/11605
.. _Pull Request 11609: https://github.com/galaxyproject/galaxy/pull/11609
.. _Pull Request 11621: https://github.com/galaxyproject/galaxy/pull/11621
.. _Pull Request 8441: https://github.com/galaxyproject/galaxy/pull/8441
.. _Pull Request 8596: https://github.com/galaxyproject/galaxy/pull/8596
.. _Pull Request 9873: https://github.com/galaxyproject/galaxy/pull/9873
.. _Pull Request 10108: https://github.com/galaxyproject/galaxy/pull/10108
.. _Pull Request 10125: https://github.com/galaxyproject/galaxy/pull/10125
doc/source/releases/21.05_announce_user.rst
+1 -1
View File
@@ -86,7 +86,7 @@ A special thanks to the release testing team for testing many of the new feature
Release Notes
===========================================================
Please see the `full release notes <21.05_announce.html>`_ for more details.
Please see the :doc:`full release notes <21.05_announce>` for more details.
.. include:: 21.05_prs.rst
doc/source/releases/21.09_announce_user.rst
+1 -1
View File
@@ -189,7 +189,7 @@ A special thanks to the release testing team for testing many of the new feature
Release Notes
===========================================================
Please see the `full release notes <21.09_announce.html>`_ for more details.
Please see the :doc:`full release notes <21.09_announce>` for more details.
.. include:: 21.09_prs.rst
doc/source/releases/22.01_announce_user.rst
+1 -5
View File
@@ -40,8 +40,6 @@ If you've been trying out the beta history (which will be the default history ne
New Visualizations
===========================================================
.. visualizations
Thanks to `@neoformit <https://github.com/neoformit>`__, a new R shiny app "iSEE" has been added, which provides a UI for visualization of single-cell RNA datasets. See `Pull Request 12650`_ for more information
.. figure:: https://user-images.githubusercontent.com/42562517/136135157-40a46a31-3553-49b3-a975-b518db1374b2.png
@@ -50,7 +48,6 @@ Thanks to `@neoformit <https://github.com/neoformit>`__, a new R shiny app "iSEE
New Datatypes
===========================================================
.. datatypes
* Add datatype iml_dataset subclassing html
(thanks to `@knutwa-ext <https://github.com/knutwa-ext>`__).
`Pull Request 12099`_
@@ -86,7 +83,6 @@ New Datatypes
Builtin Tool Updates
===========================================================
.. tools
* New interactive tool - iSEE
(thanks to `@neoformit <https://github.com/neoformit>`__).
`Pull Request 12650`_
@@ -144,7 +140,7 @@ Release Notes
User facing release notes compiled by `Helena Rasche <https://github.com/hexylena>`_.
Please see the `full release notes <22.01_announce.html>`_ for more details.
Please see the :doc:`full release notes <22.01_announce>` for more details.
.. include:: 22.01_prs.rst
lib/galaxy/datatypes/binary.py
+11
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@@ -130,6 +130,7 @@ class Cel(Binary):
def sniff(self, filename):
"""
Try to guess if the file is a Cel file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('affy_v_agcc.cel')
>>> Cel().sniff(fname)
@@ -221,6 +222,7 @@ class Meryldb(CompressedArchive):
def sniff(self, filename):
"""
Try to guess if the file is a Cel file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('affy_v_agcc.cel')
>>> Meryldb().sniff(fname)
@@ -1025,6 +1027,7 @@ class Loom(H5):
class Anndata(H5):
"""
Class describing an HDF5 anndata files: http://anndata.rtfd.io
>>> from galaxy.datatypes.sniff import get_test_fname
>>> Anndata().sniff(get_test_fname('pbmc3k_tiny.h5ad'))
True
@@ -3145,6 +3148,7 @@ class Vel(Binary):
class DAA(Binary):
"""
Class describing an DAA (diamond alignment archive) file
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('diamond.daa')
>>> DAA().sniff(fname)
@@ -3168,6 +3172,7 @@ class DAA(Binary):
class RMA6(Binary):
"""
Class describing an RMA6 (MEGAN6 read-match archive) file
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('diamond.rma6')
>>> RMA6().sniff(fname)
@@ -3190,6 +3195,7 @@ class RMA6(Binary):
class DMND(Binary):
"""
Class describing an DMND file
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('diamond_db.dmnd')
>>> DMND().sniff(fname)
@@ -3236,6 +3242,7 @@ class ICM(Binary):
class Parquet(Binary):
"""
Class describing Apache Parquet file (https://parquet.apache.org/)
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('example.parquet')
>>> Parquet().sniff(fname)
@@ -3257,6 +3264,7 @@ class Parquet(Binary):
class BafTar(CompressedArchive):
"""
Base class for common behavior of tar files of directory-based raw file formats
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('brukerbaf.d.tar')
>>> BafTar().sniff(fname)
@@ -3343,6 +3351,7 @@ class MassLynxTar(BafTar):
class WiffTar(BafTar):
"""
A tar'd up .wiff/.scan pair containing Sciex WIFF format data
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('some.wiff.tar')
>>> WiffTar().sniff(fname)
@@ -3371,6 +3380,7 @@ class Pretext(Binary):
"""
PretextMap contact map file
Try to guess if the file is a Pretext file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('sample.pretext')
>>> Pretext().sniff(fname)
@@ -3401,6 +3411,7 @@ class Pretext(Binary):
class JP2(Binary):
"""
JPEG 2000 binary image format
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.jp2')
>>> JP2().sniff(fname)
lib/galaxy/datatypes/constructive_solid_geometry.py
+31 -22
View File
@@ -497,13 +497,16 @@ class STL(data.Data):
class NeperTess(data.Text):
"""
Neper Tessellation File
***tess
**format
format
**general
dim type
**cell
number_of_cells
Example::
***tess
**format
format
**general
dim type
**cell
number_of_cells
"""
file_ext = "neper.tess"
MetadataElement(name="format", default=None, desc="format", readonly=True, visible=True)
@@ -515,7 +518,8 @@ class NeperTess(data.Text):
def sniff_prefix(self, file_prefix: FilePrefix):
"""
Neper tess format startswith:***tess
Neper tess format, starts with ``***tess``
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.neper.tess')
>>> NeperTess().sniff(fname)
@@ -555,18 +559,21 @@ class NeperTess(data.Text):
class NeperTesr(Binary):
"""
Neper Raster Tessellation File
***tesr
**format
format
**general
dimension
size_x size_y [size_z]
voxsize_x voxsize_y [voxsize_z]
[*origin
origin_x origin_y [origin_z]]
[*hasvoid has_void]
[**cell
number_of_cells
Example::
***tesr
**format
format
**general
dimension
size_x size_y [size_z]
voxsize_x voxsize_y [voxsize_z]
[*origin
origin_x origin_y [origin_z]]
[*hasvoid has_void]
[**cell
number_of_cells
"""
file_ext = "neper.tesr"
MetadataElement(name="format", default=None, desc="format", readonly=True, visible=True)
@@ -581,7 +588,8 @@ class NeperTesr(Binary):
def sniff_prefix(self, file_prefix: FilePrefix):
"""
Neper tesr format startswith:***tesr
Neper tesr format, starts with ``***tesr``
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.neper.tesr')
>>> NeperTesr().sniff(fname)
@@ -716,7 +724,8 @@ class GmshMsh(Binary):
def sniff_prefix(self, file_prefix: FilePrefix):
"""
Gmsh msh format startswith:$MeshFormat
Gmsh msh format, starts with ``$MeshFormat``
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.gmsh.msh')
>>> GmshMsh().sniff(fname)
lib/galaxy/datatypes/images.py
+3 -3
View File
@@ -552,9 +552,9 @@ class Star(data.Text):
def sniff_prefix(self, file_prefix: FilePrefix):
"""Each file must have one or more data blocks.
The start of a data block is defined by the keyword
"data_" followed by an optional string for
identification (e.g., "data_images"). All text
before the first "data_" keyword are comments
``data_`` followed by an optional string for
identification (e.g., ``data_images``). All text
before the first ``data_`` keyword are comments
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('1.star')
lib/galaxy/datatypes/microarrays.py
+2
View File
@@ -64,6 +64,7 @@ class Gal(GenericMicroarrayFile):
def sniff_prefix(self, file_prefix: FilePrefix):
"""
Try to guess if the file is a Gal file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.gal')
>>> Gal().sniff(fname)
@@ -105,6 +106,7 @@ class Gpr(GenericMicroarrayFile):
def sniff_prefix(self, file_prefix: FilePrefix):
"""
Try to guess if the file is a Gpr file.
>>> from galaxy.datatypes.sniff import get_test_fname
>>> fname = get_test_fname('test.gpr')
>>> Gpr().sniff(fname)
lib/galaxy/datatypes/molecules.py
+2 -3
View File
@@ -228,8 +228,7 @@ class SDF(GenericMolFile):
if idx < 4:
continue
elif idx == 4:
if len(line) != 39 or not(line.endswith(' V2000')
or line.endswith(' V3000')):
if len(line) != 39 or not (line.endswith(" V2000") or line.endswith(" V3000")):
return False
elif not m_end_found:
if line == 'M END':
@@ -988,7 +987,7 @@ class CIF(GenericMolFile):
Try to guess if the file is a CIF file.
The CIF format and the Relion STAR format have a shared origin.
Note therefore that STAR files and the STAR sniffer also use "data_" blocks.
Note therefore that STAR files and the STAR sniffer also use ``data_`` blocks.
STAR files will not pass the CIF sniffer, but CIF files can pass the STAR sniffer.
>>> from galaxy.datatypes.sniff import get_test_fname
lib/galaxy/jobs/runners/util/pykube_util.py
+10 -7
View File
@@ -187,14 +187,17 @@ def ingress_object_dict(params, ingress_name, spec):
def parse_pvc_param_line(pvc_param):
"""
Takes a pvc mount in the format: "pvc-name/subpath/desired:/mountpath/desired[:r]"
and returns {"name": "pvc-name",
"subPath": "subpath/desired",
"mountPath": "/mountpath/desired",
"readOnly": False}
:type pvc_param: str
:param pvc_param: the pvc mount param in the format ``pvc-name/subpath/desired:/mountpath/desired[:r]``
:param pvc_param: the pvc mount param in the format "pvc-name/subpath:/mountpath[:r]"
:return: a dict containing the elements claim, subpath, mountpath and readonly
:rtype: dict
:return: a dict
like::
{"name": "pvc-name",
"subPath": "subpath/desired",
"mountPath": "/mountpath/desired",
"readOnly": False}
"""
claim, _, rest = pvc_param.partition(":")
mount_path, _, mode = rest.partition(":")
lib/galaxy/selenium/has_driver.py
+3 -4
View File
@@ -4,7 +4,7 @@ This should be mixed into classes with a self.driver and self.default_timeout
attribute.
"""
from selenium.common.exceptions import TimeoutException
from selenium.common.exceptions import TimeoutException as SeleniumTimeoutException
from selenium.webdriver.common.action_chains import ActionChains
from selenium.webdriver.common.by import By
from selenium.webdriver.common.keys import Keys
@@ -16,7 +16,6 @@ UNSPECIFIED_TIMEOUT = object()
class HasDriver:
TimeoutException = TimeoutException
driver: WebDriver
def assert_xpath(self, xpath):
@@ -217,7 +216,7 @@ class HasDriver:
timeout_msg = timeout_exception.msg
if timeout_msg:
msg += f" {timeout_msg}"
return TimeoutException(
return SeleniumTimeoutException(
msg=msg,
screen=timeout_exception.screen,
stacktrace=timeout_exception.stacktrace,
@@ -236,5 +235,5 @@ __all__ = (
"exception_indicates_not_clickable",
"exception_indicates_stale_element",
"HasDriver",
"TimeoutException",
"SeleniumTimeoutException",
)
lib/galaxy/selenium/navigates_galaxy.py
+10 -10
View File
@@ -27,7 +27,7 @@ from .has_driver import (
exception_indicates_not_clickable,
exception_indicates_stale_element,
HasDriver,
TimeoutException,
SeleniumTimeoutException,
)
from .smart_components import SmartComponent
@@ -370,7 +370,7 @@ class NavigatesGalaxy(HasDriver):
timeout = self.timeout_for(wait_type=WAIT_TYPES.JOB_COMPLETION)
try:
self.wait(timeout).until(history_has_hid)
except self.TimeoutException as e:
except SeleniumTimeoutException as e:
hids = get_hids()
message = f"Timeout waiting for history {history_id} to have hid {hid} - have hids {hids}"
raise self.prepend_timeout_message(e, message)
@@ -385,7 +385,7 @@ class NavigatesGalaxy(HasDriver):
history_item_selector = self.history_panel_item_component(history_item, hid=hid, multi_history_panel=multi_history_panel)
try:
self.history_item_wait_for(history_item_selector, allowed_force_refreshes)
except self.TimeoutException as e:
except SeleniumTimeoutException as e:
contents_elements = self.find_elements(self.navigation.history_panel.selectors.contents)
div_ids = [f"#{d.get_attribute('id')}" for d in contents_elements]
template = "Failed waiting on history item %d to become visible, visible datasets include [%s]."
@@ -406,7 +406,7 @@ class NavigatesGalaxy(HasDriver):
try:
rval = self.wait_for_visible(history_item_selector, wait_type=WAIT_TYPES.JOB_COMPLETION)
break
except self.TimeoutException:
except SeleniumTimeoutException:
if attempt >= allowed_force_refreshes:
raise
@@ -435,7 +435,7 @@ class NavigatesGalaxy(HasDriver):
history_item_selector_state = history_item_selector.with_data("state", state)
try:
self.history_item_wait_for(history_item_selector_state, allowed_force_refreshes)
except self.TimeoutException as e:
except SeleniumTimeoutException as e:
history_item = self.wait_for_visible(history_item_selector)
current_state = "UNKNOWN"
classes = history_item.get_attribute("class").split(" ")
@@ -577,7 +577,7 @@ class NavigatesGalaxy(HasDriver):
user_menu = self.components.masthead.user_menu.wait_for_visible()
try:
username_element = self.components.masthead.username.wait_for_visible()
except self.TimeoutException as e:
except SeleniumTimeoutException as e:
menu_items = user_menu.find_elements_by_css_selector("li a")
menu_text = [mi.text for mi in menu_items]
message = f"Failed to find logged in message in menu items {', '.join(menu_text)}"
@@ -593,7 +593,7 @@ class NavigatesGalaxy(HasDriver):
def wait_for_logged_in(self):
try:
self.components.masthead.logged_in_only.wait_for_visible()
except self.TimeoutException as e:
except SeleniumTimeoutException as e:
ui_logged_out = self.components.masthead.logged_out_only.is_displayed
if ui_logged_out:
dom_message = "Element a.loggedout-only is present in DOM, indicating Login or Register button still in masthead."
@@ -727,7 +727,7 @@ class NavigatesGalaxy(HasDriver):
self.wait_for_and_click_selector(build_selector)
try:
self.wait_for_selector_absent_or_hidden(build_selector)
except TimeoutException:
except SeleniumTimeoutException:
# Sometimes the callback in the JS hasn't be registered by the
# time that the build button is clicked. By the time the timeout
# has been registered - it should have been.
@@ -1590,7 +1590,7 @@ class NavigatesGalaxy(HasDriver):
self.components.masthead.logout.wait_for_and_click()
try:
self.components.masthead.logged_out_only.wait_for_visible()
except self.TimeoutException as e:
except SeleniumTimeoutException as e:
message = "Clicked logout button but waiting for 'Login or Registration' button failed, perhaps the logout button was clicked before the handler was setup?"
raise self.prepend_timeout_message(e, message)
assert not self.is_logged_in(), "Clicked to logged out and UI reflects a logout, but API still thinks a user is logged in."
@@ -1846,7 +1846,7 @@ class NavigatesGalaxy(HasDriver):
self.assert_absent_or_hidden(editor)
class NotLoggedInException(TimeoutException):
class NotLoggedInException(SeleniumTimeoutException):
def __init__(self, timeout_exception, user_info, dom_message):
template = "Waiting for UI to reflect user logged in but it did not occur. API indicates no user is currently logged in. %s API response was [%s]. %s"
lib/galaxy/tool_util/lint.py
+20 -22
View File
@@ -3,46 +3,44 @@
LintContext: a container for LintMessages
LintMessage: the actual message and level
The idea is to define a LintContext and to apply a linting function `foo` on a
`target`. The `level` (defined by `LintLevel`) determines which linting messages
are shown.
The idea is to define a LintContext and to apply a linting function ``foo`` on a
``target``. The ``level`` (defined by ``LintLevel``) determines which linting
messages are shown::
```
lint_ctx = LintContext(level) # level is the reporting level
lint_ctx.lint(..., lint_func = foo, lint_target = target, ...)
```
The `lint` function essentially calls `foo(target, self)`. Hence
the function `foo` must have two parameters
lint_ctx = LintContext(level) # level is the reporting level
lint_ctx.lint(..., lint_func = foo, lint_target = target, ...)
The ``lint`` function essentially calls ``foo(target, self)``. Hence
the function ``foo`` must have two parameters:
1. the object to lint
2. the lint context
In `foo` the lint context can be used to add LintMessages to the lint context by
using its `valid`, `info`, `warn`, and `error` functions:
In ``foo`` the lint context can be used to add LintMessages to the lint context
by using its ``valid``, ``info``, ``warn``, and ``error`` functions::
```
lint_foo(target, lint_ctx):
lint_ctx.error("target is screwed")
```
Calling `lint` prints out the messages emmited by the linter
lint_foo(target, lint_ctx):
lint_ctx.error("target is screwed")
Calling ``lint`` prints out the messages emmited by the linter
function immediately. Which messages are shown can be determined with the
`level` argument of the LintContext constructor. If set to `SILENT`,
``level`` argument of the ``LintContext`` constructor. If set to ``SILENT``,
no messages will be printed.
For special lint targets it might be useful to have additional information
in the lint messages. This can be achieved by sublassing `LintMessage`.
See for instance `XMLLintMessageLine` which has an additional agrument `node`
in its constructor which is used to determine the line and filename in
in the lint messages. This can be achieved by subclassing ``LintMessage``.
See for instance ``XMLLintMessageLine`` which has an additional argument
``node`` in its constructor which is used to determine the line and filename in
an XML document that caused the message.
In order to use this.
- the lint context needs to be initialized with the additional parameter
`lint_message_class=XMLLintMessageLine`
``lint_message_class=XMLLintMessageLine``
- the additional parameter needs to be added as well to calls adding messages
to the lint context, e.g. `lint_ctx.error("some message", node=X)`. Note
to the lint context, e.g. ``lint_ctx.error("some message", node=X)``. Note
that the additional properties must be given as keyword arguments.
"""
lib/galaxy/util/bool_expressions.py
+2 -1
View File
@@ -123,8 +123,9 @@ class BooleanExpressionEvaluator:
:param evaluator: The custom TokenEvaluator used to transform any token into a boolean.
:type evaluator: TokenEvaluator
:param token_format: A string of all allowed characters used to form a valid token, defaults to None.
The default value (None) will use DEFAULT_TOKEN_FORMAT which means the allowed characters are [A-Za-z0-9_-@.].
The default value (None) will use DEFAULT_TOKEN_FORMAT which means the allowed characters are ``[A-Za-z0-9_-@.]``.
:type token_format: Optional[str]
"""
action = BoolOperand
lib/galaxy/webapps/galaxy/api/history_contents.py
+35 -24
View File
@@ -690,7 +690,7 @@ class FastAPIHistoryContents:
serialization_params: SerializationParams = Depends(query_serialization_params),
) -> HistoryContentsResult:
"""
**Warning**: For internal use to support the scroller functionality.
.. warning:: For internal use to support the scroller functionality.
This endpoint provides random access to a large history without having
to know exactly how many pages are in the final query. Pick a target HID
@@ -701,23 +701,30 @@ class FastAPIHistoryContents:
The `direction` determines what items are selected:
a) item counts:
- total matches-up: hid < {hid}
- total matches-down: hid > {hid}
- total matches: total matches-up + total matches-down + 1 (+1 for hid == {hid})
- displayed matches-up: hid <= {hid} (hid == {hid} is included)
- displayed matches-down: hid > {hid}
- displayed matches: displayed matches-up + displayed matches-down
- total matches-up: hid < {hid}
- total matches-down: hid > {hid}
- total matches: total matches-up + total matches-down + 1 (+1 for hid == {hid})
- displayed matches-up: hid <= {hid} (hid == {hid} is included)
- displayed matches-down: hid > {hid}
- displayed matches: displayed matches-up + displayed matches-down
b) {limit} history items:
- if direction == before: hid <= {hid}
- if direction == after: hid > {hid}
- if direction == near: "near" {hid}, so that |before| <= limit // 2, |after| <= limit // 2 + 1.
**Note**: This endpoint uses slightly different filter params syntax. Instead of using `q`/`qv` parameters
it uses the following syntax for query parameters:
?[field]-[operator]=[value]
Example:
?update_time-gt=2015-01-29
- if direction == "before": hid <= {hid}
- if direction == "after": hid > {hid}
- if direction == "near": "near" {hid}, so that
n. items before <= limit // 2,
n. items after <= limit // 2 + 1.
.. note:: This endpoint uses slightly different filter params syntax. Instead of using `q`/`qv` parameters,
it uses the following syntax for query parameters::
?[field]-[operator]=[value]
Example::
?update_time-gt=2015-01-29
"""
serialization_params.default_view = serialization_params.default_view or "betawebclient"
@@ -1177,17 +1184,21 @@ class HistoryContentsController(BaseGalaxyAPIController, UsesLibraryMixinItems,
Returns the following data:
a) item counts:
- total matches-up: hid < {hid}
- total matches-down: hid > {hid}
- total matches: total matches-up + total matches-down + 1 (+1 for hid == {hid})
- displayed matches-up: hid <= {hid} (hid == {hid} is included)
- displayed matches-down: hid > {hid}
- displayed matches: displayed matches-up + displayed matches-down
- total matches-up: hid < {hid}
- total matches-down: hid > {hid}
- total matches: total matches-up + total matches-down + 1 (+1 for hid == {hid})
- displayed matches-up: hid <= {hid} (hid == {hid} is included)
- displayed matches-down: hid > {hid}
- displayed matches: displayed matches-up + displayed matches-down
b) {limit} history items:
- if direction == before: hid <= {hid}
- if direction == after: hid > {hid}
- if direction == near: "near" {hid}, so that |before| <= limit // 2, |after| <= limit // 2 + 1.
- if direction == "before": hid <= {hid}
- if direction == "after": hid > {hid}
- if direction == "near": "near" {hid}, so that
n. items before <= limit // 2,
n. items after <= limit // 2 + 1.
Intended purpose: supports scroller functionality.
lib/galaxy/webapps/galaxy/services/history_contents.py
+12 -11
View File
@@ -374,16 +374,14 @@ class HistoriesContentsService(ServiceBase):
"""
Set permissions of the given dataset to the given role ids.
:param payload: dictionary structure containing:
:param action: (required) describes what action should be performed
available actions: make_private, remove_restrictions, set_permissions
:type action: string
:param access_ids[]: list of Role.id defining roles that should have access permission on the dataset
:type access_ids[]: string or list
:param manage_ids[]: list of Role.id defining roles that should have manage permission on the dataset
:type manage_ids[]: string or list
:param modify_ids[]: list of Role.id defining roles that should have modify permission on the library dataset item
:type modify_ids[]: string or list
:type payload: dict
:param payload: dictionary structure containing:
- action: (required) describes what action should be performed.
Available actions: make_private, remove_restrictions, set_permissions
- access_ids[]: list of Role.id defining roles that should have access permission on the dataset
- manage_ids[]: list of Role.id defining roles that should have manage permission on the dataset
- modify_ids[]: list of Role.id defining roles that should have modify permission on the library dataset item
:raises: RequestParameterInvalidException, ObjectNotFound, InsufficientPermissionsException, InternalServerError
RequestParameterMissingException
@@ -638,9 +636,12 @@ class HistoriesContentsService(ServiceBase):
"""
Return {limit} history items "near" the {hid}. The {direction} determines what items
are selected:
- before: select items with hid < {hid}
- after: select items with hid > {hid}
- near: select items "around" {hid}, so that |before| <= limit // 2, |after| <= limit // 2 + 1
- near: select items "around" {hid}, so that
n. items before <= limit // 2,
n. items after <= limit // 2 + 1
Additional counts provided in the HTTP headers.
"""
lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
+3 -3
View File
@@ -120,9 +120,9 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
def test_0020_verify_generated_dependency(self):
'''Verify that matplotlib now has a package tool dependency and a complex repository dependency.
This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool
dependency displays correctly.
'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on
package_numpy_1_7_0170, and that the inherited tool dependency displays correctly.
'Inherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
dependency on the latest revision of package_numpy_1_7_0170.
'''
numpy_repository = self.test_db_util.get_repository_by_name_and_owner(numpy_repository_name, common.test_user_1_name)
lib/tool_shed/test/functional/test_0420_citable_urls_for_repositories.py
+9 -9
View File
@@ -14,10 +14,10 @@ first_changeset_hash = ''
1. Add and populate a repository to the tool shed with change set revision 0 (assume owner is test).
2. Add valid change set revision 1.
3. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1
4. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420
Resulting page should contain change set revision 1
5. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420/<revision 0>
Resulting page should not contain change set revision 1, but should contain change set revision 0.
4. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420 .
The resulting page should contain change set revision 1
5. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420/<revision 0> .
The resulting page should not contain change set revision 1, but should contain change set revision 0.
6. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420/<invalid revision>
7. Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/<invalid repository name>
8. Visit the following url and check for appropriate strings: <tool shed base url>/view/<invalid owner>
@@ -115,8 +115,8 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
'''Load the /view/<user>/<repository> page and check for the appropriate strings.
We are at step 4.
Visit the following url and check for strings: <tool shed base url>/view/user1/filtering_0420
Resulting page should contain change set revision 1
Visit the following url and check for strings: ``<tool shed base url>/view/user1/filtering_0420`` .
The resulting page should contain change set revision 1
'''
repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
@@ -142,8 +142,8 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
'''Load a citable url for a past changeset revision and verify that strings display.
We are at step 5.
Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/filtering_0420/<revision 0>
Resulting page should not contain change set revision 1, but should contain change set revision 0.
Visit the following url and check for appropriate strings: ``<tool shed base url>/view/user1/filtering_0420/<revision 0>`` .
The resulting page should not contain change set revision 1, but should contain change set revision 0.
'''
global first_changeset_hash
repository = self.test_db_util.get_repository_by_name_and_owner(repository_name, common.test_user_1_name)
@@ -189,7 +189,7 @@ class TestRepositoryCitableURLs(ShedTwillTestCase):
def test_0035_load_sharable_url_with_invalid_repository_name(self):
'''Load a citable url with an invalid changeset revision specified.
We are at step 7
We are at step 7.
Visit the following url and check for appropriate strings: <tool shed base url>/view/user1/!!invalid!!
'''
test_user_1 = self.test_db_util.get_user(common.test_user_1_email)
lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
+3 -3
View File
@@ -131,9 +131,9 @@ class TestComplexPriorInstallation(ShedTwillTestCase):
def test_0020_verify_generated_dependency(self):
'''Verify that matplotlib now has a package tool dependency and a complex repository dependency.
This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on package_numpy_1_7_0170, and that the inherited tool
dependency displays correctly.
'Inhherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
This is step 3 - Verify that package_matplotlib_1_2_0170 now depends on
package_numpy_1_7_0170, and that the inherited tool dependency displays correctly.
'Inherited' in this case means that matplotlib should show a package tool dependency on numpy version 1.7, and a repository
dependency on the latest revision of package_numpy_1_7_0170.
'''
numpy_repository = self.test_db_util.get_repository_by_name_and_owner(numpy_repository_name, common.test_user_1_name)
lib/tool_shed/test/functional/test_1450_installing_datatypes_sniffers.py
+11 -10
View File
@@ -90,8 +90,8 @@ class TestInstallDatatypesSniffers(ShedTwillTestCase):
def test_0015_verify_datatypes_count(self):
'''Verify that datatypes were added in the previous step.
This is step 3 - Verify the count of datatypes and sniffers is the previous count + the datatypes
contained within proteomics_datatypes_1450.
This is step 3 - Verify the count of datatypes and sniffers is the
previous count + the datatypes contained within proteomics_datatypes_1450.
Compare the current datatypes registry and sniffers with the values that were retrieved in the previous step.
'''
current_datatypes = self.get_datatypes_count()
@@ -105,8 +105,8 @@ class TestInstallDatatypesSniffers(ShedTwillTestCase):
def test_0020_deactivate_datatypes_repository(self):
'''Deactivate the installed proteomics_datatypes_1450 repository.
This is step 4 - Deactivate proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal to
the count determined in step 1.
This is step 4 - Deactivate proteomics_datatypes_1450, verify the count
of datatypes and sniffers is equal to the count determined in step 1.
Deactivate proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values
determined in the first step.
'''
@@ -124,8 +124,8 @@ class TestInstallDatatypesSniffers(ShedTwillTestCase):
def test_0025_reactivate_datatypes_repository(self):
'''Reactivate the deactivated proteomics_datatypes_1450 repository.
This is step 5 - Reactivate proteomics_datatypes, verify that the count of datatypes and sniffers has been
increased by the contents of the repository.
This is step 5 - Reactivate proteomics_datatypes, verify that the count
of datatypes and sniffers has been increased by the contents of the repository.
'''
repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
global repository_datatypes_count
@@ -143,8 +143,8 @@ class TestInstallDatatypesSniffers(ShedTwillTestCase):
def test_0030_uninstall_datatypes_repository(self):
'''Uninstall the installed proteomics_datatypes_1450 repository.
This is step 6 - Uninstall proteomics_datatypes_1450, verify the count of datatypes and sniffers is equal
to the count determined in step 1.
This is step 6 - Uninstall proteomics_datatypes_1450, verify the count
of datatypes and sniffers is equal to the count determined in step 1.
Uninstall proteomics_datatypes_1450 and check that the in-memory datatypes and sniffers match the base values
determined in the first step.
'''
@@ -161,8 +161,9 @@ class TestInstallDatatypesSniffers(ShedTwillTestCase):
def test_0035_reinstall_datatypes_repository(self):
'''Reinstall the uninstalled proteomics_datatypes_1450 repository.
This is step 7 - Reinstall proteomics_datatypes_1450, verify that the count of datatypes and sniffers has been
increased by the contents of the repository.
This is step 7 - Reinstall proteomics_datatypes_1450, verify that the
count of datatypes and sniffers has been increased by the contents of
the repository.
'''
repository = self.test_db_util.get_installed_repository_by_name_owner(repository_name, common.test_user_1_name)
global repository_datatypes_count
scripts/bootstrap_history.py
+1 -1
View File
@@ -171,7 +171,7 @@ A special thanks to the release testing team for testing many of the new feature
Release Notes
===========================================================
Please see the `full release notes <${release}_announce.html>`_ for more details.
Please see the :doc:`full release notes <${release}_announce>` for more details.
.. include:: ${release}_prs.rst