mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Merge pull request #14488 from nsoranzo/release_22.05_fix_docs
[22.05] Doc fixes
This commit is contained in:
Marius van den Beek
@@ -93,7 +93,7 @@ Configuration Basics
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----------------------------
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- Edit ``config/galaxy.yml`` (copy it from ``config/galaxy.yml.sample`` if it does not exist) to make configuration
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changes. This is a `YAML configuration file`_ and should contain one or two sections, one named ``gravity`` for
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changes. This is a YAML configuration file and should contain one or two sections, one named ``gravity`` for
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process management via `Gravity`_ (optional) and one named ``galaxy`` for Galaxy (required).
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- The `gravity` section contain several important options about how to
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@@ -9,22 +9,19 @@ There are two ways in which you can configure logging for Galaxy servers:
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1. Basic/automatic configuration with control over log level and log destination (standard output or a named log file).
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2. More complex configuration using the Python :mod:`logging` module's :func:`logging.config.dictConfig` or :func:`logging.config.fileConfig`.
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By default, Galaxy logs all messages to standard output at the ``DEBUG`` logging level, unless the ``--daemon`` argument
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is passed to ``run.sh``, in which case, output is logged to a location configured in `gravity`_.
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Gravity and related terminology are explained in detail in the :doc:`Scaling and Load Balancing <scaling>` documentation.
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Basic Configuration
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----------------------------
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Basic logging configuration can be used to modify the level of log messages and the file to which Galaxy logs. The level
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is controlled by the ``log_level`` configuration option.
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Basic logging configuration can be used to modify the level of log messages and the file to which Galaxy logs.
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If not set, Galaxy logs all messages at the ``DEBUG`` level (versions prior to 18.01 defaulted to ``INFO`` if unset, but
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the default config file shipped with ``log_level`` explicitly set to ``DEBUG`` for development purposes).
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The logging level is controlled by the ``log_level`` configuration option. By default, Galaxy logs all messages at the
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``DEBUG`` level.
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Galaxy logs all messages to standard output by default if running in the foreground. If running in the background, the
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log is written to a location configured in `gravity`_.
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Galaxy logs all messages to standard output by default if running in the foreground. If running in the background (e.g.
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by passing the ``--daemon`` argument to ``run.sh``), the log is written to a location configured in
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`gravity <https://github.com/galaxyproject/gravity/>`_.
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Gravity and related terminology are explained in detail in the :doc:`Scaling and Load Balancing <scaling>` documentation.
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**Setting the log level:**
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@@ -9,14 +9,6 @@ galaxy.app\_unittest\_utils package
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Submodules
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----------
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galaxy.app\_unittest\_utils.celery\_helper module
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-------------------------------------------------
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.. automodule:: galaxy.app_unittest_utils.celery_helper
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.app\_unittest\_utils.galaxy\_mock module
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-----------------------------------------------
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@@ -1,42 +0,0 @@
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galaxy.containers package
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=========================
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.. automodule:: galaxy.containers
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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galaxy.containers.docker module
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-------------------------------
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.. automodule:: galaxy.containers.docker
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.containers.docker\_decorators module
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-------------------------------------------
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.. automodule:: galaxy.containers.docker_decorators
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.containers.docker\_model module
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--------------------------------------
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.. automodule:: galaxy.containers.docker_model
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.containers.docker\_swarm module
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--------------------------------------
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.. automodule:: galaxy.containers.docker_swarm
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -268,6 +268,14 @@ galaxy.datatypes.proteomics module
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:undoc-members:
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:show-inheritance:
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galaxy.datatypes.qiime2 module
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------------------------------
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.. automodule:: galaxy.datatypes.qiime2
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.datatypes.qualityscore module
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------------------------------------
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@@ -14,3 +14,14 @@ Subpackages
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galaxy.files.sources
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galaxy.files.unittest_utils
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Submodules
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----------
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galaxy.files.uris module
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------------------------
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.. automodule:: galaxy.files.uris
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -17,14 +17,6 @@ galaxy.job\_metrics.instrumenters.cgroup module
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:undoc-members:
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:show-inheritance:
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galaxy.job\_metrics.instrumenters.collectl module
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-------------------------------------------------
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.. automodule:: galaxy.job_metrics.instrumenters.collectl
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.job\_metrics.instrumenters.core module
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---------------------------------------------
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@@ -24,3 +24,11 @@ galaxy.job\_metrics.formatting module
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.job\_metrics.safety module
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---------------------------------
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.. automodule:: galaxy.job_metrics.safety
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -273,6 +273,14 @@ galaxy.managers.metrics module
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:undoc-members:
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:show-inheritance:
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galaxy.managers.model\_stores module
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------------------------------------
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.. automodule:: galaxy.managers.model_stores
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.managers.pages module
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----------------------------
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@@ -1,27 +0,0 @@
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galaxy.model.migrate package
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============================
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.. automodule:: galaxy.model.migrate
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:members:
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:undoc-members:
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:show-inheritance:
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Subpackages
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-----------
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.. toctree::
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:maxdepth: 4
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galaxy.model.migrate.triggers
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galaxy.model.migrate.versions
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Submodules
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----------
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galaxy.model.migrate.check module
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---------------------------------
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.. automodule:: galaxy.model.migrate.check
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -1,26 +0,0 @@
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galaxy.model.migrate.triggers package
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=====================================
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.. automodule:: galaxy.model.migrate.triggers
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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galaxy.model.migrate.triggers.history\_update\_time\_field module
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-----------------------------------------------------------------
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.. automodule:: galaxy.model.migrate.triggers.history_update_time_field
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.migrate.triggers.update\_audit\_table module
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---------------------------------------------------------
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.. automodule:: galaxy.model.migrate.triggers.update_audit_table
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:members:
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:undoc-members:
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:show-inheritance:
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File diff suppressed because it is too large
Load Diff
@@ -0,0 +1,26 @@
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galaxy.model.migrations package
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===============================
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.. automodule:: galaxy.model.migrations
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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galaxy.model.migrations.scripts module
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--------------------------------------
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.. automodule:: galaxy.model.migrations.scripts
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.migrations.util module
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-----------------------------------
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.. automodule:: galaxy.model.migrations.util
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -32,3 +32,11 @@ galaxy.model.orm.scripts module
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.orm.util module
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----------------------------
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.. automodule:: galaxy.model.orm.util
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -13,10 +13,11 @@ Subpackages
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:maxdepth: 4
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galaxy.model.dataset_collections
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galaxy.model.migrate
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galaxy.model.migrations
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galaxy.model.orm
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galaxy.model.store
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galaxy.model.tool_shed_install
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galaxy.model.triggers
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galaxy.model.unittest_utils
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galaxy.model.view
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@@ -55,6 +56,22 @@ galaxy.model.database\_utils module
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:undoc-members:
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:show-inheritance:
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galaxy.model.deferred module
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----------------------------
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.. automodule:: galaxy.model.deferred
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.index\_filter\_util module
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---------------------------------------
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.. automodule:: galaxy.model.index_filter_util
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.item\_attrs module
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-------------------------------
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@@ -24,3 +24,11 @@ galaxy.model.store.discover module
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.store.load\_objects module
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---------------------------------------
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.. automodule:: galaxy.model.store.load_objects
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -1,26 +0,0 @@
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galaxy.model.tool\_shed\_install.migrate package
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================================================
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.. automodule:: galaxy.model.tool_shed_install.migrate
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:members:
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:undoc-members:
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:show-inheritance:
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Subpackages
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-----------
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.. toctree::
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:maxdepth: 4
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galaxy.model.tool_shed_install.migrate.versions
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Submodules
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----------
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galaxy.model.tool\_shed\_install.migrate.check module
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-----------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.check
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:members:
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:undoc-members:
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:show-inheritance:
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@@ -1,146 +0,0 @@
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galaxy.model.tool\_shed\_install.migrate.versions package
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=========================================================
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions
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:members:
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:undoc-members:
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:show-inheritance:
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Submodules
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----------
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galaxy.model.tool\_shed\_install.migrate.versions.0001\_add\_tool\_shed\_repository\_table module
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-------------------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0001_add_tool_shed_repository_table
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0002\_add\_tool\_shed\_repository\_table\_columns module
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----------------------------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0002_add_tool_shed_repository_table_columns
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0003\_tool\_id\_guid\_map\_table module
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-----------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0003_tool_id_guid_map_table
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0004\_add\_installed\_changeset\_revison\_column module
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---------------------------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0004_add_installed_changeset_revison_column
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0005\_add\_tool\_shed\_repository\_table\_columns module
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----------------------------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0005_add_tool_shed_repository_table_columns
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0006\_add\_tool\_version\_tables module
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-----------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0006_add_tool_version_tables
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0007\_add\_migrate\_tools\_table module
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-----------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0007_add_migrate_tools_table
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0008\_add\_ctx\_rev\_column module
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------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0008_add_ctx_rev_column
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:members:
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:undoc-members:
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:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0009\_add\_tool\_dependency\_table module
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-------------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0009_add_tool_dependency_table
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:members:
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:undoc-members:
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||||
:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0010\_alter\_tool\_dependency\_table\_version\_column module
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--------------------------------------------------------------------------------------------------------------
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0010_alter_tool_dependency_table_version_column
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:members:
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||||
:undoc-members:
|
||||
:show-inheritance:
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galaxy.model.tool\_shed\_install.migrate.versions.0011\_drop\_installed\_changeset\_revision\_column module
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-----------------------------------------------------------------------------------------------------------
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||||
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.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0011_drop_installed_changeset_revision_column
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:members:
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||||
:undoc-members:
|
||||
:show-inheritance:
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||||
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galaxy.model.tool\_shed\_install.migrate.versions.0012\_add\_tool\_dependency\_status\_columns module
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-----------------------------------------------------------------------------------------------------
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||||
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0012_add_tool_dependency_status_columns
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
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||||
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galaxy.model.tool\_shed\_install.migrate.versions.0013\_add\_tool\_shed\_repository\_status\_columns module
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-----------------------------------------------------------------------------------------------------------
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||||
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||||
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0013_add_tool_shed_repository_status_columns
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:members:
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||||
:undoc-members:
|
||||
:show-inheritance:
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||||
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galaxy.model.tool\_shed\_install.migrate.versions.0014\_add\_repository\_dependency\_tables module
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--------------------------------------------------------------------------------------------------
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||||
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0014_add_repository_dependency_tables
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||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
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||||
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galaxy.model.tool\_shed\_install.migrate.versions.0015\_update\_migrate\_tools\_table module
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--------------------------------------------------------------------------------------------
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||||
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||||
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0015_update_migrate_tools_table
|
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
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||||
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galaxy.model.tool\_shed\_install.migrate.versions.0016\_update\_migrate\_tools\_table\_again module
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---------------------------------------------------------------------------------------------------
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||||
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||||
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0016_update_migrate_tools_table_again
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||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
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||||
galaxy.model.tool\_shed\_install.migrate.versions.0017\_drop\_update\_available\_col\_add\_tool\_shed\_status\_col module
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-------------------------------------------------------------------------------------------------------------------------
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||||
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||||
.. automodule:: galaxy.model.tool_shed_install.migrate.versions.0017_drop_update_available_col_add_tool_shed_status_col
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:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -6,14 +6,6 @@ galaxy.model.tool\_shed\_install package
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||||
:undoc-members:
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||||
:show-inheritance:
|
||||
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||||
Subpackages
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||||
-----------
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||||
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||||
.. toctree::
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||||
:maxdepth: 4
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||||
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||||
galaxy.model.tool_shed_install.migrate
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||||
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||||
Submodules
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||||
----------
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||||
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||||
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||||
@@ -0,0 +1,34 @@
|
||||
galaxy.model.triggers package
|
||||
=============================
|
||||
|
||||
.. automodule:: galaxy.model.triggers
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.model.triggers.history\_update\_time\_field module
|
||||
---------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.triggers.history_update_time_field
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.triggers.update\_audit\_table module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.triggers.update_audit_table
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.triggers.utils module
|
||||
----------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.triggers.utils
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -16,3 +16,11 @@ galaxy.model.unittest\_utils.data\_app module
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.model.unittest\_utils.store\_fixtures module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.model.unittest_utils.store_fixtures
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -18,7 +18,6 @@ Subpackages
|
||||
galaxy.authnz
|
||||
galaxy.celery
|
||||
galaxy.config
|
||||
galaxy.containers
|
||||
galaxy.datatypes
|
||||
galaxy.dependencies
|
||||
galaxy.exceptions
|
||||
|
||||
@@ -9,6 +9,14 @@ galaxy.schema package
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.schema.fetch\_data module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy.schema.fetch_data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.schema.fields module
|
||||
---------------------------
|
||||
|
||||
@@ -33,6 +41,14 @@ galaxy.schema.schema module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.schema.tasks module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.schema.tasks
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.schema.types module
|
||||
--------------------------
|
||||
|
||||
|
||||
@@ -15,7 +15,6 @@ Subpackages
|
||||
galaxy.tool_shed.galaxy_install.datatypes
|
||||
galaxy.tool_shed.galaxy_install.metadata
|
||||
galaxy.tool_shed.galaxy_install.repository_dependencies
|
||||
galaxy.tool_shed.galaxy_install.tool_dependencies
|
||||
galaxy.tool_shed.galaxy_install.tools
|
||||
|
||||
Submodules
|
||||
|
||||
@@ -1,58 +0,0 @@
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe package
|
||||
===================================================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.asynchronous\_reader module
|
||||
---------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.asynchronous_reader
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.env\_file\_builder module
|
||||
-------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.env_file_builder
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.install\_environment module
|
||||
---------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.install_environment
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.recipe\_manager module
|
||||
----------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.recipe_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.step\_handler module
|
||||
--------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.step_handler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.recipe.tag\_handler module
|
||||
-------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.recipe.tag_handler
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -1,26 +0,0 @@
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies package
|
||||
============================================================
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Subpackages
|
||||
-----------
|
||||
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.tool_shed.galaxy_install.tool_dependencies.recipe
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tool\_shed.galaxy\_install.tool\_dependencies.env\_manager module
|
||||
------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_shed.galaxy_install.tool_dependencies.env_manager
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -67,6 +67,14 @@ galaxy.tool\_util.deps.container\_classes module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.container\_volumes module
|
||||
------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.deps.container_volumes
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.tool\_util.deps.containers module
|
||||
----------------------------------------
|
||||
|
||||
|
||||
@@ -0,0 +1,18 @@
|
||||
galaxy.tool\_util.ontologies package
|
||||
====================================
|
||||
|
||||
.. automodule:: galaxy.tool_util.ontologies
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tool\_util.ontologies.ontology\_data module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.tool_util.ontologies.ontology_data
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -18,6 +18,7 @@ Subpackages
|
||||
galaxy.tool_util.deps
|
||||
galaxy.tool_util.linters
|
||||
galaxy.tool_util.locations
|
||||
galaxy.tool_util.ontologies
|
||||
galaxy.tool_util.parser
|
||||
galaxy.tool_util.toolbox
|
||||
galaxy.tool_util.unittest_utils
|
||||
|
||||
@@ -5,3 +5,14 @@ galaxy.tours package
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.tours.validate module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy.tours.validate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -1,26 +0,0 @@
|
||||
galaxy.util.pastescript package
|
||||
===============================
|
||||
|
||||
.. automodule:: galaxy.util.pastescript
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.util.pastescript.loadwsgi module
|
||||
---------------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.pastescript.loadwsgi
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.pastescript.serve module
|
||||
------------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.pastescript.serve
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -13,7 +13,6 @@ Subpackages
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy.util.custom_logging
|
||||
galaxy.util.pastescript
|
||||
galaxy.util.path
|
||||
galaxy.util.tool_shed
|
||||
|
||||
@@ -388,14 +387,6 @@ galaxy.util.watcher module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.web\_compat module
|
||||
------------------------------
|
||||
|
||||
.. automodule:: galaxy.util.web_compat
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.util.xml\_macros module
|
||||
------------------------------
|
||||
|
||||
|
||||
@@ -17,14 +17,6 @@ galaxy.visualization.plugins.config\_parser module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.visualization.plugins.interactive\_environments module
|
||||
-------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.visualization.plugins.interactive_environments
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.visualization.plugins.plugin module
|
||||
------------------------------------------
|
||||
|
||||
|
||||
@@ -9,14 +9,6 @@ galaxy.web.framework.middleware package
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.framework.middleware.batch module
|
||||
--------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.web.framework.middleware.batch
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.framework.middleware.error module
|
||||
--------------------------------------------
|
||||
|
||||
|
||||
@@ -15,18 +15,11 @@ Subpackages
|
||||
galaxy.web.framework
|
||||
galaxy.web.legacy_framework
|
||||
galaxy.web.proxy
|
||||
galaxy.web.short_term_storage
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.web.buildapp module
|
||||
--------------------------
|
||||
|
||||
.. automodule:: galaxy.web.buildapp
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.web.form\_builder module
|
||||
-------------------------------
|
||||
|
||||
|
||||
@@ -0,0 +1,7 @@
|
||||
galaxy.web.short\_term\_storage package
|
||||
=======================================
|
||||
|
||||
.. automodule:: galaxy.web.short_term_storage
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -337,6 +337,14 @@ galaxy.webapps.galaxy.api.search module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.api.short\_term\_storage module
|
||||
-----------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.short_term_storage
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.api.tags module
|
||||
-------------------------------------
|
||||
|
||||
@@ -345,6 +353,14 @@ galaxy.webapps.galaxy.api.tags module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.api.tasks module
|
||||
--------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.api.tasks
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.api.tool\_data module
|
||||
-------------------------------------------
|
||||
|
||||
|
||||
@@ -81,14 +81,6 @@ galaxy.webapps.galaxy.controllers.history module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.controllers.interactive\_environments module
|
||||
------------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.controllers.interactive_environments
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.controllers.library module
|
||||
------------------------------------------------
|
||||
|
||||
|
||||
@@ -9,6 +9,14 @@ galaxy.webapps.galaxy.services package
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.galaxy.services.authenticate module
|
||||
--------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.services.authenticate
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.services.base module
|
||||
------------------------------------------
|
||||
|
||||
@@ -49,6 +57,22 @@ galaxy.webapps.galaxy.services.history\_contents module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.services.invocations module
|
||||
-------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.services.invocations
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.services.jobs module
|
||||
------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.services.jobs
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.services.libraries module
|
||||
-----------------------------------------------
|
||||
|
||||
@@ -97,6 +121,22 @@ galaxy.webapps.galaxy.services.sharable module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.services.tools module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.services.tools
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.services.users module
|
||||
-------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.services.users
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.services.visualizations module
|
||||
----------------------------------------------------
|
||||
|
||||
@@ -104,3 +144,11 @@ galaxy.webapps.galaxy.services.visualizations module
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy.webapps.galaxy.services.workflows module
|
||||
-----------------------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.galaxy.services.workflows
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -0,0 +1,18 @@
|
||||
galaxy.webapps.openapi package
|
||||
==============================
|
||||
|
||||
.. automodule:: galaxy.webapps.openapi
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy.webapps.openapi.utils module
|
||||
-----------------------------------
|
||||
|
||||
.. automodule:: galaxy.webapps.openapi.utils
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -14,6 +14,7 @@ Subpackages
|
||||
|
||||
galaxy.webapps.base
|
||||
galaxy.webapps.galaxy
|
||||
galaxy.webapps.openapi
|
||||
galaxy.webapps.reports
|
||||
|
||||
Submodules
|
||||
|
||||
@@ -0,0 +1,18 @@
|
||||
galaxy\_ext.container\_monitor package
|
||||
======================================
|
||||
|
||||
.. automodule:: galaxy_ext.container_monitor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy\_ext.container\_monitor.monitor module
|
||||
---------------------------------------------
|
||||
|
||||
.. automodule:: galaxy_ext.container_monitor.monitor
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
@@ -12,5 +12,6 @@ Subpackages
|
||||
.. toctree::
|
||||
:maxdepth: 4
|
||||
|
||||
galaxy_ext.container_monitor
|
||||
galaxy_ext.expressions
|
||||
galaxy_ext.metadata
|
||||
|
||||
@@ -17,14 +17,6 @@ Subpackages
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy\_test.api.conftest module
|
||||
--------------------------------
|
||||
|
||||
.. automodule:: galaxy_test.api.conftest
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy\_test.api.sharable module
|
||||
--------------------------------
|
||||
|
||||
@@ -33,14 +25,6 @@ galaxy\_test.api.sharable module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy\_test.api.test\_api\_batch module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy_test.api.test_api_batch
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy\_test.api.test\_authenticate module
|
||||
------------------------------------------
|
||||
|
||||
|
||||
@@ -9,14 +9,6 @@ galaxy\_test.performance package
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy\_test.performance.conftest module
|
||||
----------------------------------------
|
||||
|
||||
.. automodule:: galaxy_test.performance.conftest
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy\_test.performance.test\_workflow\_framework\_performance module
|
||||
----------------------------------------------------------------------
|
||||
|
||||
|
||||
@@ -17,3 +17,14 @@ Subpackages
|
||||
galaxy_test.driver
|
||||
galaxy_test.performance
|
||||
galaxy_test.selenium
|
||||
|
||||
Submodules
|
||||
----------
|
||||
|
||||
galaxy\_test.conftest module
|
||||
----------------------------
|
||||
|
||||
.. automodule:: galaxy_test.conftest
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
@@ -97,6 +97,14 @@ galaxy\_test.selenium.test\_data\_source\_tools module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy\_test.selenium.test\_dataset\_metadata\_download module
|
||||
--------------------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy_test.selenium.test_dataset_metadata_download
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy\_test.selenium.test\_histories\_list module
|
||||
--------------------------------------------------
|
||||
|
||||
@@ -185,6 +193,14 @@ galaxy\_test.selenium.test\_history\_structure module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy\_test.selenium.test\_invocation\_grid module
|
||||
---------------------------------------------------
|
||||
|
||||
.. automodule:: galaxy_test.selenium.test_invocation_grid
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
galaxy\_test.selenium.test\_jupyter module
|
||||
------------------------------------------
|
||||
|
||||
|
||||
@@ -441,14 +441,6 @@ tool\_shed.test.functional.test\_1410\_update\_manager module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.test.functional.test\_1420\_tool\_dependency\_environment\_inheritance module
|
||||
----------------------------------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.test.functional.test_1420_tool_dependency_environment_inheritance
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.test.functional.test\_1430\_repair\_installed\_repository module
|
||||
---------------------------------------------------------------------------
|
||||
|
||||
@@ -457,14 +449,6 @@ tool\_shed.test.functional.test\_1430\_repair\_installed\_repository module
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.test.functional.test\_1440\_missing\_env\_sh\_files module
|
||||
---------------------------------------------------------------------
|
||||
|
||||
.. automodule:: tool_shed.test.functional.test_1440_missing_env_sh_files
|
||||
:members:
|
||||
:undoc-members:
|
||||
:show-inheritance:
|
||||
|
||||
tool\_shed.test.functional.test\_1450\_installing\_datatypes\_sniffers module
|
||||
-----------------------------------------------------------------------------
|
||||
|
||||
|
||||
@@ -8,12 +8,13 @@ def add_object_to_object_session(object, object_with_session):
|
||||
https://docs.sqlalchemy.org/en/14/changelog/migration_14.html#cascade-backrefs-behavior-deprecated-for-removal-in-2-0
|
||||
|
||||
This function preserves SQLAlchemy's pre-2.0 logic and should be used when:
|
||||
|
||||
1. foo and bar are model instances, that are associated (via SQLAlchemy's relationship), AND
|
||||
2. bar is assigned to foo's bar relationship (e.g. foo.bar = bar), AND
|
||||
3. bar is in a session and foo is not, AND
|
||||
4. foo is implicitly added to bar's session upon assignment(2), as indicated
|
||||
by a RemovedIn20Warning specifying that the '"foo" object is being merged into a Session
|
||||
along the backref cascade path...'
|
||||
by a RemovedIn20Warning specifying that the '"foo" object is being merged into a Session
|
||||
along the backref cascade path...'
|
||||
"""
|
||||
if object_with_session:
|
||||
session = get_object_session(object_with_session)
|
||||
|
||||
@@ -149,10 +149,10 @@ def query_parameter_as_list(query):
|
||||
"""Used as FastAPI dependable for query parameters that need to behave as a list of values separated by comma
|
||||
or as multiple instances of the same parameter.
|
||||
|
||||
**Important**: the `query` annotation provided must define the `alias` exactly as the name of the actual parameter name.
|
||||
.. important:: the ``query`` annotation provided must define the ``alias`` exactly as the name of the actual parameter name.
|
||||
|
||||
Usage example::
|
||||
|
||||
Usage example:
|
||||
```python
|
||||
ValueQueryParam = Query(
|
||||
default=None,
|
||||
alias="value", # Important! this is the parameter name that will be displayed in the API docs
|
||||
@@ -166,11 +166,11 @@ def query_parameter_as_list(query):
|
||||
values: Optional[List[str]] = Depends(query_parameter_as_list(ValueQueryParam)),
|
||||
):
|
||||
...
|
||||
```
|
||||
|
||||
This will render in the API docs as a single string query parameter but will make the following requests equivalent:
|
||||
- `api/my_route?value=val1,val2,val3`
|
||||
- `api/my_route?value=val1&value=val2&value=val3`
|
||||
|
||||
- ``api/my_route?value=val1,val2,val3``
|
||||
- ``api/my_route?value=val1&value=val2&value=val3``
|
||||
"""
|
||||
|
||||
def parse_elements(
|
||||
|
||||
Reference in New Issue
Block a user