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Doc and comment fixes

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This commit is contained in:
mvdbeek
2020-07-04 20:58:01 +02:00
parent ea3f48a5ec
commit ef08965501
5 changed files with 11 additions and 11 deletions
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doc/source/admin/galaxy_options.rst
+4 -4
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@@ -3570,10 +3570,10 @@
:Description:
Determines how metadata will be set. Valid values are `directory`,
`extended` and `legacy`. In extended mode jobs will decide if a
tool run failed, the object stores configuration is serialized
and made available to the job and is used for writing output
datasets to the object store as part of the job and dynamic
output discovery (e.g. discovered datasets <discover_datasets>,
tool run failed, the object stores configuration is serialized and
made available to the job and is used for writing output datasets
to the object store as part of the job and dynamic output
discovery (e.g. discovered datasets <discover_datasets>,
unpopulated collections, etc) happens as part of the job.
:Default: ``directory``
:Type: str
lib/galaxy/config/sample/galaxy.yml.sample
+1 -1
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@@ -1743,7 +1743,7 @@ galaxy:
# Determines how metadata will be set. Valid values are `directory`,
# `extended` and `legacy`. In extended mode jobs will decide if a tool
# run failed, the object stores configuration is serialized and made
# run failed, the object stores configuration is serialized and made
# available to the job and is used for writing output datasets to the
# object store as part of the job and dynamic output discovery (e.g.
# discovered datasets <discover_datasets>, unpopulated collections,
lib/galaxy/config/sample/job_conf.xml.sample_advanced
+3 -3
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@@ -402,10 +402,10 @@
embedding metadata calculation in job script itself.
-->
<param id="metadata_strategy">directory</param>
<!-- If set overwrites metadata_strategy (configurable in galaxy.yml).
<!-- If set, overwrites metadata_strategy (configurable in galaxy.yml).
Valid values are `directory` (default), `extended` and `legacy`.
Setting metadata_strategy to extended requires that all object stores
that can be written to store datasets by uuid. In extended mode jobs
Setting metadata_strategy to `extended` requires that all object stores
that can be written to store datasets by uuid. In `extended` mode jobs
will decide if a tool run failed, the object stores configuration
is serialized and made available to the job and is used for writing output
datasets to the object store as part of the job and dynamic output discovery
lib/galaxy/webapps/galaxy/config_schema.yml
+1 -1
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@@ -2646,7 +2646,7 @@ mapping:
Determines how metadata will be set. Valid values are `directory`, `extended` and `legacy`.
In extended mode jobs will decide if a tool run failed, the object stores
configuration is serialized and made available to the job and is used for
writing output datasets to the object store as part of the job and dynamic
writing output datasets to the object store as part of the job and dynamic
output discovery (e.g. discovered datasets <discover_datasets>, unpopulated collections,
etc) happens as part of the job.
test/integration/test_pulsar_embedded_metadata.py
+2 -2
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@@ -17,8 +17,8 @@ class EmbeddedMetadataPulsarIntegrationInstance(integration_util.IntegrationInst
def handle_galaxy_config_kwds(cls, config):
config["job_config_file"] = EMBEDDED_PULSAR_JOB_CONFIG_FILE
config['object_store_store_by'] = 'uuid'
# metadata_strategy is being set to directory in embedded_pulsar_metadata_job_conf.yml,
# since extended_metadata doesn't work yet on pulsar
# We set the global metadata_strategy to `extended, but`metadata_strategy is
# being overridden in embedded_pulsar_metadata_job_conf.yml, since extended_metadata does not yet work on pulsar
config['metadata_strategy'] = 'extended'