From 347e7b8301b4f56c1b2b9b86eed83220ab29dfb5 Mon Sep 17 00:00:00 2001 From: Heinz-Alexander Fuetterer Date: Fri, 13 Oct 2023 15:32:26 +0200 Subject: [PATCH] chore: fix typos Co-authored-by: Nicola Soranzo --- client/src/schema/schema.ts | 6 +++--- doc/source/admin/container_resolvers.rst | 2 +- doc/source/admin/jobs.md | 4 ++-- doc/source/admin/scaling.md | 2 +- lib/galaxy/dependencies/update_lint_requirements.sh | 2 +- lib/galaxy/jobs/runners/pbs.py | 2 +- lib/galaxy/managers/library_datasets.py | 2 +- lib/galaxy/managers/workflows.py | 2 +- lib/galaxy/schema/schema.py | 2 +- lib/galaxy/schema/tasks.py | 2 +- .../repository_dependency_manager.py | 4 ++-- lib/galaxy/tool_util/deps/resolvers/__init__.py | 2 +- lib/galaxy/webapps/galaxy/api/workflows.py | 4 ++-- lib/galaxy/webapps/galaxy/controllers/dataset.py | 4 +--- lib/galaxy/webapps/galaxy/controllers/history.py | 2 +- lib/galaxy_test/selenium/test_workflow_editor.py | 2 +- .../test_0170_complex_prior_installation_required.py | 6 ++++-- .../test_1190_complex_prior_installation_required.py | 6 ++++-- test/unit/app/tools/test_parameter_parsing.py | 2 +- .../config_manage/1607_root_filters/config/galaxy.ini | 2 +- .../config_manage/1607_root_samples/config/galaxy.ini | 2 +- tools/sr_mapping/PerM.xml | 2 +- 22 files changed, 33 insertions(+), 31 deletions(-) diff --git a/client/src/schema/schema.ts b/client/src/schema/schema.ts index 0d7f3b1cb0af..057ea7c8c031 100644 --- 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 index 860506004d42..918088f7e026 100644 --- 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 `_. 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 index 804a95379235..f33ddb670037 100644 --- a/doc/source/admin/jobs.md +++ b/doc/source/admin/jobs.md @@ -38,7 +38,7 @@ workers The `` 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 `` 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 diff --git a/doc/source/admin/scaling.md b/doc/source/admin/scaling.md index 780b20eeed52..6819a74b6599 100644 --- 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 index e1f57a7abf02..6f06089aabf8 100755 --- 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 index fa55751ecbc9..fa22c11b1a70 100644 --- 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 index 091946714041..8b39dc2826a2 100644 --- 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 index 1f1467d5b330..80c33c00b581 100644 --- 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 index 13593d951c22..417c69f83cf0 100644 --- 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 index dab80ba87935..e28c5ef7ca82 100644 --- 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 index 79f9c88dae46..0d6a291e0576 100644 --- 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 index e2a0b012f743..d5e644ad52fd 100644 --- 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 index 2523819056d8..a4438c015203 100644 --- 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 index fe75601e8858..1859ac9858bb 100644 --- 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 index 8f72a7d17e34..8719bf3928e6 100644 --- 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 index 9d3edcbc79c4..5f77001fa332 100644 --- 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 index d0d1b3b1bad4..7d64f6993381 100644 --- 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 index b49ae8998ca2..b4f42d7a8488 100644 --- 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 index abfe41c5c0fe..3f911339e360 100644 --- 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 index 25259f15bb1d..f1eea40eaaf4 100644 --- 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 index 25259f15bb1d..f1eea40eaaf4 100644 --- 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 index 1df2dcd570d4..65d8c54e8005 100644 --- 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::