From ef089655014846c08ba7b7db42b49bd8d673f3b3 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sat, 4 Jul 2020 20:58:01 +0200
Subject: [PATCH] Doc and comment fixes

---
 doc/source/admin/galaxy_options.rst                   | 8 ++++----
 lib/galaxy/config/sample/galaxy.yml.sample            | 2 +-
 lib/galaxy/config/sample/job_conf.xml.sample_advanced | 6 +++---
 lib/galaxy/webapps/galaxy/config_schema.yml           | 2 +-
 test/integration/test_pulsar_embedded_metadata.py     | 4 ++--
 5 files changed, 11 insertions(+), 11 deletions(-)

diff --git a/doc/source/admin/galaxy_options.rst b/doc/source/admin/galaxy_options.rst
index 1682b35b062..ebc6824d962 100644
--- a/doc/source/admin/galaxy_options.rst
+++ b/doc/source/admin/galaxy_options.rst
@@ -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
diff --git a/lib/galaxy/config/sample/galaxy.yml.sample b/lib/galaxy/config/sample/galaxy.yml.sample
index c28ab6fab5b..f14fd7cafe9 100644
--- a/lib/galaxy/config/sample/galaxy.yml.sample
+++ b/lib/galaxy/config/sample/galaxy.yml.sample
@@ -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,
diff --git a/lib/galaxy/config/sample/job_conf.xml.sample_advanced b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
index f44a940a95e..beb5feb3d13 100644
--- a/lib/galaxy/config/sample/job_conf.xml.sample_advanced
+++ b/lib/galaxy/config/sample/job_conf.xml.sample_advanced
@@ -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
diff --git a/lib/galaxy/webapps/galaxy/config_schema.yml b/lib/galaxy/webapps/galaxy/config_schema.yml
index df648f396c3..1eaa2a7f909 100644
--- a/lib/galaxy/webapps/galaxy/config_schema.yml
+++ b/lib/galaxy/webapps/galaxy/config_schema.yml
@@ -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.
 
diff --git a/test/integration/test_pulsar_embedded_metadata.py b/test/integration/test_pulsar_embedded_metadata.py
index 14dc616281d..cd59298a45d 100644
--- a/test/integration/test_pulsar_embedded_metadata.py
+++ b/test/integration/test_pulsar_embedded_metadata.py
@@ -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'