chore: fix typos

Co-authored-by: Nicola Soranzo <[email protected]>
galaxyproject · Oct 13, 2023 · 347e7b8 · 347e7b8
1 parent 26eba22
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Showing 22 changed files with 33 additions and 31 deletions.
diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts
@@ -6914,7 +6914,7 @@ export interface components {
              * Content
              * @description Depending on the `source` it can be:
              * - The encoded id of the source library dataset
-             * - The encoded id of the the HDA
+             * - The encoded id of the HDA
              *
              * @example 0123456789ABCDEF
              */
@@ -18140,10 +18140,10 @@ export interface operations {
              * : The stored workflow's owner's username. (The tag `u` can be used a short hand alias for this tag to filter on this attribute.)
              *
              * `is:published`
-             * : Include only published workflows in the final result. Be sure the the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.
+             * : Include only published workflows in the final result. Be sure the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.
              *
              * `is:share_with_me`
-             * : Include only workflows shared with the requesting user.  Be sure the the query parameter `show_shared` is set to `true` if to include shared workflows.
+             * : Include only workflows shared with the requesting user.  Be sure the query parameter `show_shared` is set to `true` if to include shared workflows.
              *
              * ## Free Text
              *

diff --git a/doc/source/admin/container_resolvers.rst b/doc/source/admin/container_resolvers.rst
@@ -364,7 +364,7 @@ admins might want to control.
 
 .. note::
 
-   For the the execution of jobs Galaxy already implement the `support for using
+   For the execution of jobs Galaxy already implement the `support for using
    tarballs of container images
    <https://github.com/galaxyproject/galaxy/blob/c517e805771cc16807dfe675075a13fe6343f01f/lib/galaxy/tool_util/deps/container_classes.py#L319>`_.
    from ``container_image_cache_path`` (set in galaxy.yml) or the destination

diff --git a/doc/source/admin/jobs.md b/doc/source/admin/jobs.md
@@ -38,7 +38,7 @@ workers
 
 The `<handlers>` configuration elements defines which Galaxy server processes (when [running multiple server processes](scaling.md)) should be used for running jobs, and how to group those processes.
 
-The handlers configuration may define a ``default`` attribute. This is the the handler(s) that should be used if no explicit handler is defined for a job. If unset, any untagged handlers will be used by default.
+The handlers configuration may define a ``default`` attribute. This is the handler(s) that should be used if no explicit handler is defined for a job. If unset, any untagged handlers will be used by default.
 
 The collection contains `<handler>` elements.
 
@@ -316,7 +316,7 @@ The above examples demonstrate that the dynamic job destination framework will p
 
 Also available though less likely useful are ``job_id``.
 
-The above examples demonstrated mapping one tool to one function. Multiple tools may be mapped to the same function, by specifying a function the the dynamic destination:
+The above examples demonstrated mapping one tool to one function. Multiple tools may be mapped to the same function, by specifying a function the dynamic destination:
 
 ```xml
     <destination id="blast_dynamic" runner="dynamic">

diff --git a/doc/source/admin/scaling.md b/doc/source/admin/scaling.md
@@ -534,7 +534,7 @@ Environment=VIRTUAL_ENV=/srv/galaxy/venv PATH=/srv/galaxy/venv/bin:/usr/local/sb
 WantedBy=multi-user.target
 ```
 
-We can now enable and start the the Galaxy services with systemd:
+We can now enable and start the Galaxy services with systemd:
 
 ```console
 # systemctl enable galaxy

diff --git a/lib/galaxy/dependencies/update_lint_requirements.sh b/lib/galaxy/dependencies/update_lint_requirements.sh
@@ -3,7 +3,7 @@
 set -e
 
 # This script updates the pinned requirements for linting.
-# The lint requirements are split from the the other ones due to incompatible
+# The lint requirements are split from the other ones due to incompatible
 # dependencies: flake8 requires importlib-metadata 4.2, while the Galaxy's core
 # dependencies depend on importlib-metadata 4.13.
 

diff --git a/lib/galaxy/jobs/runners/pbs.py b/lib/galaxy/jobs/runners/pbs.py
@@ -122,7 +122,7 @@ def url_to_destination(self, url):
         if not url:
             return
 
-        # Determine the the PBS server
+        # Determine the PBS server
         url_split = url.split("/")
         server = url_split[2]
         if server == "":

diff --git a/lib/galaxy/managers/library_datasets.py b/lib/galaxy/managers/library_datasets.py
@@ -252,7 +252,7 @@ def serialize(self, trans, ld):
         rval["is_unrestricted"] = trans.app.security_agent.dataset_is_public(ldda.dataset)
         rval["tags"] = trans.tag_handler.get_tags_list(ldda.tags)
 
-        #  Manage dataset permission is always attached to the dataset itself, not the the ld or ldda to maintain consistency
+        #  Manage dataset permission is always attached to the dataset itself, not the ld or ldda to maintain consistency
         rval["can_user_manage"] = trans.user_is_admin or trans.app.security_agent.can_manage_dataset(
             current_user_roles, ldda.dataset
         )

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
@@ -339,7 +339,7 @@ def check_security(self, trans, has_workflow, check_ownership=True, check_access
 
         # If given an invocation verify ownership of invocation
         if isinstance(has_workflow, model.WorkflowInvocation):
-            # We use the the owner of the history that is associated to the invocation as a proxy
+            # We use the owner of the history that is associated to the invocation as a proxy
             # for the owner of the invocation.
             if trans.user != has_workflow.history.user and not trans.user_is_admin:
                 raise exceptions.ItemOwnershipException()

diff --git a/lib/galaxy/schema/schema.py b/lib/galaxy/schema/schema.py
@@ -3494,7 +3494,7 @@ class MaterializeDatasetInstanceAPIRequest(Model):
         description=(
             "Depending on the `source` it can be:\n"
             "- The encoded id of the source library dataset\n"
-            "- The encoded id of the the HDA\n"
+            "- The encoded id of the HDA\n"
         ),
     )
 

diff --git a/lib/galaxy/schema/tasks.py b/lib/galaxy/schema/tasks.py
@@ -107,7 +107,7 @@ class MaterializeDatasetInstanceTaskRequest(BaseModel):
         description=(
             "Depending on the `source` it can be:\n"
             "- The encoded id of the source library dataset\n"
-            "- The encoded id of the the HDA\n"
+            "- The encoded id of the HDA\n"
         ),
     )
 

diff --git a/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py b/lib/galaxy/tool_shed/galaxy_install/repository_dependencies/repository_dependency_manager.py
@@ -71,7 +71,7 @@ def build_repository_dependency_relationships(self, repo_info_dicts, tool_shed_r
                         components_list = repository_util.extract_components_from_tuple(repository_components_tuple)
                         d_toolshed, d_name, d_owner, d_changeset_revision = components_list[0:4]
                         for tsr in tool_shed_repositories:
-                            # Get the the tool_shed_repository defined by name, owner and changeset_revision.  This is
+                            # Get the tool_shed_repository defined by name, owner and changeset_revision.  This is
                             # the repository that will be dependent upon each of the tool shed repositories contained in
                             # val.  We'll need to check tool_shed_repository.tool_shed as well if/when repository dependencies
                             # across tool sheds is supported.
@@ -98,7 +98,7 @@ def build_repository_dependency_relationships(self, repo_info_dicts, tool_shed_r
                                 rd_prior_installation_required,
                                 rd_only_if_compiling_contained_td,
                             ) = common_util.parse_repository_dependency_tuple(repository_dependency_components_list)
-                            # Get the the tool_shed_repository defined by rd_name, rd_owner and rd_changeset_revision.  This
+                            # Get the tool_shed_repository defined by rd_name, rd_owner and rd_changeset_revision.  This
                             # is the repository that will be required by the current d_repository.
                             # TODO: Check tool_shed_repository.tool_shed as well when repository dependencies across tool sheds is supported.
                             for tsr in tool_shed_repositories:

diff --git a/lib/galaxy/tool_util/deps/resolvers/__init__.py b/lib/galaxy/tool_util/deps/resolvers/__init__.py
@@ -32,7 +32,7 @@ class DependencyResolver(Dictifiable, metaclass=ABCMeta):
         "can_uninstall_dependencies",
         "read_only",
     ]
-    # A "simple" dependency is one that does not depend on the the tool
+    # A "simple" dependency is one that does not depend on the tool
     # resolving the dependency. Classic tool shed dependencies are non-simple
     # because the repository install context is used in dependency resolution
     # so the same requirement tags in different tools will have very different

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -1171,11 +1171,11 @@ def __encode_invocation(self, invocation, **kwd):
     IndexQueryTag("user", "The stored workflow's owner's username.", "u"),
     IndexQueryTag(
         "is:published",
-        "Include only published workflows in the final result. Be sure the the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.",
+        "Include only published workflows in the final result. Be sure the query parameter `show_published` is set to `true` if to include all published workflows and not just the requesting user's.",
     ),
     IndexQueryTag(
         "is:share_with_me",
-        "Include only workflows shared with the requesting user.  Be sure the the query parameter `show_shared` is set to `true` if to include shared workflows.",
+        "Include only workflows shared with the requesting user.  Be sure the query parameter `show_shared` is set to `true` if to include shared workflows.",
     ),
 ]
 

diff --git a/lib/galaxy/webapps/galaxy/controllers/dataset.py b/lib/galaxy/webapps/galaxy/controllers/dataset.py
@@ -815,9 +815,7 @@ def _purge(self, trans, dataset_id):
             if hda.dataset.user_can_purge:
                 try:
                     hda.dataset.full_delete()
-                    trans.log_event(
-                        f"Dataset id {hda.dataset.id} has been purged upon the the purge of HDA id {hda.id}"
-                    )
+                    trans.log_event(f"Dataset id {hda.dataset.id} has been purged upon the purge of HDA id {hda.id}")
                     trans.sa_session.add(hda.dataset)
                 except Exception:
                     log.exception(f"Unable to purge dataset ({hda.dataset.id}) on purge of HDA ({hda.id}):")

diff --git a/lib/galaxy/webapps/galaxy/controllers/history.py b/lib/galaxy/webapps/galaxy/controllers/history.py
@@ -658,7 +658,7 @@ def purge_deleted_datasets(self, trans):
                     try:
                         hda.dataset.full_delete()
                         trans.log_event(
-                            f"Dataset id {hda.dataset.id} has been purged upon the the purge of HDA id {hda.id}"
+                            f"Dataset id {hda.dataset.id} has been purged upon the purge of HDA id {hda.id}"
                         )
                         trans.sa_session.add(hda.dataset)
                     except Exception:

diff --git a/lib/galaxy_test/selenium/test_workflow_editor.py b/lib/galaxy_test/selenium/test_workflow_editor.py
@@ -1167,7 +1167,7 @@ def workflow_editor_source_sink_terminal_ids(self, source, sink):
     def workflow_editor_add_input(self, item_name="data_input"):
         editor = self.components.workflow_editor
 
-        # Make sure we're on the the workflow editor and not clicking the main tool panel.
+        # Make sure we're on the workflow editor and not clicking the main tool panel.
         editor.canvas_body.wait_for_visible()
 
         editor.tool_menu.wait_for_visible()

diff --git a/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py b/lib/tool_shed/test/functional/test_0170_complex_prior_installation_required.py
@@ -6,14 +6,16 @@
 )
 
 matplotlib_repository_name = "package_matplotlib_1_2_0170"
-matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package."
+matplotlib_repository_description = (
+    "Contains a tool dependency definition that downloads and compiles version 1.2.x of the python matplotlib package."
+)
 matplotlib_repository_long_description = (
     "This repository is intended to be defined as a complex repository dependency within a separate repository."
 )
 
 numpy_repository_name = "package_numpy_1_7_0170"
 numpy_repository_description = (
-    "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package."
+    "Contains a tool dependency definition that downloads and compiles version 1.7 of the python numpy package."
 )
 numpy_repository_long_description = (
     "This repository is intended to be defined as a complex repository dependency within a separate repository."

diff --git a/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py b/lib/tool_shed/test/functional/test_1190_complex_prior_installation_required.py
@@ -6,14 +6,16 @@
 )
 
 matplotlib_repository_name = "package_matplotlib_1_2_0170"
-matplotlib_repository_description = "Contains a tool dependency definition that downloads and compiles version 1.2.x of the the python matplotlib package."
+matplotlib_repository_description = (
+    "Contains a tool dependency definition that downloads and compiles version 1.2.x of the python matplotlib package."
+)
 matplotlib_repository_long_description = (
     "This repository is intended to be defined as a complex repository dependency within a separate repository."
 )
 
 numpy_repository_name = "package_numpy_1_7_0170"
 numpy_repository_description = (
-    "Contains a tool dependency definition that downloads and compiles version 1.7 of the the python numpy package."
+    "Contains a tool dependency definition that downloads and compiles version 1.7 of the python numpy package."
 )
 numpy_repository_long_description = (
     "This repository is intended to be defined as a complex repository dependency within a separate repository."

diff --git a/test/unit/app/tools/test_parameter_parsing.py b/test/unit/app/tools/test_parameter_parsing.py
@@ -50,7 +50,7 @@ class TestParameterParsing(BaseParameterTestCase):
     those tests may need to be updated anyway.
 
     It occurs to me that rewriting this stuff to test to_dict would
-    be much better - since that is a public API of the the tools.
+    be much better - since that is a public API of the tools.
     """
 
     def test_parse_help_and_label(self):

diff --git a/test/unit/config/config_manage/1607_root_filters/config/galaxy.ini b/test/unit/config/config_manage/1607_root_filters/config/galaxy.ini
@@ -636,7 +636,7 @@ nglims_config_file = tool-data/nglims.yaml
 # set that here.
 #dynamic_proxy_session_map=database/session_map.sqlite
 
-# Set the port and IP for the the dynamic proxy to bind to, this must match
+# Set the port and IP for the dynamic proxy to bind to, this must match
 # the external configuration if dynamic_proxy_manage is False.
 #dynamic_proxy_bind_port=8800
 #dynamic_proxy_bind_ip=0.0.0.0

diff --git a/test/unit/config/config_manage/1607_root_samples/config/galaxy.ini b/test/unit/config/config_manage/1607_root_samples/config/galaxy.ini
@@ -636,7 +636,7 @@ nglims_config_file = tool-data/nglims.yaml
 # set that here.
 #dynamic_proxy_session_map=database/session_map.sqlite
 
-# Set the port and IP for the the dynamic proxy to bind to, this must match
+# Set the port and IP for the dynamic proxy to bind to, this must match
 # the external configuration if dynamic_proxy_manage is False.
 #dynamic_proxy_bind_port=8800
 #dynamic_proxy_bind_ip=0.0.0.0

diff --git a/tools/sr_mapping/PerM.xml b/tools/sr_mapping/PerM.xml
@@ -352,7 +352,7 @@ The command-line options::
   --ignoreQS        Ignore the quality scores in fastq or QUAL files.
   --seed {F2 | S11 | F3 | F4}    Specify the seed pattern, which has a specific full sensitivity. Check the algorithm page (link below) for seed patterns to balance the sensitivity and running time.
   --readFormat {fasta | fastq | csfasta | csfastq}    Read in reads in the specified format, instead of guessing according to the extension name.
-  --delimiter CHAR  Which is a character used as the delimiter to separate the the read id, and the additional info in the line with ">" in fasta or csfasta.
+  --delimiter CHAR  Which is a character used as the delimiter to separate the read id, and the additional info in the line with ">" in fasta or csfasta.
 
 Paired reads options::