From 14ea7b898b69ebcec3c52078d3e2b2b113a84443 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 4 Mar 2026 17:29:00 +0100 Subject: [PATCH 1/4] Fix AttributeError when requesting invalid metadata file Raise RequestParameterInvalidException instead of crashing when the requested metadata file name doesn't exist in the dataset's metadata spec. Fixes https://github.com/galaxyproject/galaxy/issues/21968 --- lib/galaxy/webapps/galaxy/services/datasets.py | 10 ++++++++-- 1 file changed, 8 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/webapps/galaxy/services/datasets.py b/lib/galaxy/webapps/galaxy/services/datasets.py index bec31edef39..699362d8c65 100644 --- a/lib/galaxy/webapps/galaxy/services/datasets.py +++ b/lib/galaxy/webapps/galaxy/services/datasets.py @@ -734,13 +734,19 @@ class DatasetsService(ServiceBase, UsesVisualizationMixin): """ hda = self.hda_manager.get_accessible(history_content_id, trans.user) self.hda_manager.ensure_dataset_on_disk(trans, hda) - file_ext = hda.metadata.spec.get(metadata_file).get("file_ext", metadata_file) + metadata_spec = hda.metadata.spec.get(metadata_file) + if metadata_spec is None: + raise galaxy_exceptions.RequestParameterInvalidException(f"Unknown metadata file: {metadata_file}") + file_ext = metadata_spec.get("file_ext", metadata_file) fname = "".join(c in util.FILENAME_VALID_CHARS and c or "_" for c in hda.name)[0:150] headers = {} headers["Content-Type"] = "application/octet-stream" headers["Content-Disposition"] = f'attachment; filename="Galaxy{hda.hid}-[{fname}].{file_ext}"' mf = hda.metadata.get(metadata_file) - assert mf + if mf is None: + raise galaxy_exceptions.RequestParameterInvalidException( + f"Metadata file {metadata_file} is not set for this dataset" + ) file_path = mf.get_file_name() if open_file: return open(file_path, "rb"), headers From 00b9b633d41282c29a5fb43a573a86e760586f3a Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 6 Mar 2026 15:28:22 +0100 Subject: [PATCH 2/4] Fix pick_value output inheriting hidden state from input datasets ExpressionTool.exec_after_process calls copy_from() which copies the visible attribute from the input dataset to the output. When pick_value picks from a hidden input (e.g. from a skipped workflow step), the output incorrectly becomes hidden too. Preserve the output's visible state across the copy_from call. --- lib/galaxy/tools/__init__.py | 2 ++ lib/galaxy_test/api/test_workflows.py | 50 +++++++++++++++++++++++++++ 2 files changed, 52 insertions(+) diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py index d13b5702099..234f43cff6d 100644 --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -3310,7 +3310,9 @@ class ExpressionTool(Tool): output.extension if output.extension not in ("data", "expression.json") else copy_object.extension ) require_metadata_regeneration = copy_object.extension != new_ext + visible = output.visible output.copy_from(copy_object, include_metadata=not require_metadata_regeneration) + output.visible = visible output.extension = new_ext if require_metadata_regeneration: if app.config.enable_celery_tasks: diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py index 60ee24bb47f..d2e5bc4e118 100644 --- a/lib/galaxy_test/api/test_workflows.py +++ b/lib/galaxy_test/api/test_workflows.py @@ -8986,6 +8986,56 @@ outer_input: r = self._post("workflows", files={"archive_file": io.StringIO(malformated_yaml)}) assert r.status_code == 400 + def test_pick_value_output_visible_with_hidden_inputs(self): + """Test that pick_value output doesn't inherit hidden state from inputs.""" + with self.dataset_populator.test_history() as history_id: + summary = self._run_workflow( + """class: GalaxyWorkflow +inputs: + input_dataset: + type: data +outputs: + pick_out: + outputSource: pick_value/data_param +steps: + cat_skipped: + tool_id: cat1 + in: + input1: input_dataset + when: $(false) + pick_value: + tool_id: pick_value + tool_state: + style_cond: + pick_style: first + type_cond: + param_type: data + pick_from: + - __index__: 0 + value: + __class__: RuntimeValue + - __index__: 1 + value: + __class__: RuntimeValue + in: + style_cond|type_cond|pick_from_0|value: + source: cat_skipped/out_file1 + style_cond|type_cond|pick_from_1|value: + source: input_dataset +""", + test_data="""input_dataset: + value: 1.bed + type: File +""", + history_id=history_id, + ) + invocation_details = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True) + pick_value_hda = invocation_details["outputs"]["pick_out"] + dataset_details = self.dataset_populator.get_history_dataset_details( + history_id=history_id, content_id=pick_value_hda["id"] + ) + assert dataset_details["visible"], "pick_value output should be visible even when inputs are hidden" + class TestAdminWorkflowsApi(BaseWorkflowsApiTestCase): require_admin_user = True From aead68b0a13bd2cca99a92ee2478678c9614e264 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 6 Mar 2026 15:17:14 +0100 Subject: [PATCH 3/4] Fix NoReplacement handling in workflow callback_helper MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit When an optional text parameter is omitted from a workflow invocation and connected to an expression tool, the callback_helper in visit_input_values could fail to replace unresolved inputs with the tool parameter default. Two issues contributed to this: 1. NoReplacement doesn't implement __eq__, so when the callback returns a different NoReplacement instance than the module-level NO_REPLACEMENT singleton, the equality comparison fails and the raw NoReplacement object gets stored as the input value. 2. The replace_optional_connections path needs to guard replacements with is_runtime_value(value) to avoid clobbering valid tool-state values for unconnected parameters (like select parameters with defaults). Fix both by switching all NoReplacement comparisons to isinstance() checks and restoring the is_runtime_value guard. Add a framework workflow test that connects an optional text parameter to an expression tool converting text→boolean, then uses the boolean as a when condition. --- lib/galaxy/tools/parameters/__init__.py | 26 ++++++++--------- .../optional_text_to_bool.gxwf-tests.yml | 27 +++++++++++++++++ .../workflow/optional_text_to_bool.gxwf.yml | 29 +++++++++++++++++++ .../tools/expression_text_to_bool.xml | 27 +++++++++++++++++ test/functional/tools/sample_tool_conf.xml | 1 + 5 files changed, 97 insertions(+), 13 deletions(-) create mode 100644 lib/galaxy_test/workflow/optional_text_to_bool.gxwf-tests.yml create mode 100644 lib/galaxy_test/workflow/optional_text_to_bool.gxwf.yml create mode 100644 test/functional/tools/expression_text_to_bool.xml diff --git a/lib/galaxy/tools/parameters/__init__.py b/lib/galaxy/tools/parameters/__init__.py index 6e9532f2824..b4fc0defad0 100644 --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -33,7 +33,7 @@ from .grouping import ( ) from .workflow_utils import ( is_runtime_value, - NO_REPLACEMENT, + NoReplacement, runtime_to_json, ) from .wrapped import flat_to_nested_state @@ -179,33 +179,33 @@ def visit_input_values( new_value = callback(**args) # is this good enough ? feels very ugh - if new_value == [no_replacement_value]: + if isinstance(new_value, list) and len(new_value) == 1 and isinstance(new_value[0], NoReplacement): # Single unspecified value in multiple="true" input with a single null input, pretend it's a singular value new_value = no_replacement_value if isinstance(new_value, list): # Maybe mixed input, I guess tool defaults don't really make sense here ? # Would e.g. be default dataset in multiple="true" input, you wouldn't expect the default to be inserted # if other inputs are connected and provided. - new_value = [item if not item == no_replacement_value else None for item in new_value] + new_value = [item if not isinstance(item, NoReplacement) else None for item in new_value] if no_replacement_value is REPLACE_ON_TRUTHY: replace = bool(new_value) else: - replace = new_value != no_replacement_value + replace = not isinstance(new_value, NoReplacement) and new_value != no_replacement_value if replace: input_values[input.name] = new_value elif replace_optional_connections: - # Only used in workflow context - has_default = hasattr(input, "value") - if new_value is value is NO_REPLACEMENT or is_runtime_value(value): - # NO_REPLACEMENT means value was connected but left unspecified - if has_default: - # Use default if we have one + # Only used in workflow context. + # If we reach here the callback returned no_replacement_value, + # meaning the connected step did not produce a value (e.g. an + # omitted optional parameter_input). Only replace sentinel + # values (ConnectedValue, RuntimeValue, NO_REPLACEMENT) with + # the tool parameter's own default — preserve valid tool-state + # values for unconnected inputs. + if isinstance(value, NoReplacement) or is_runtime_value(value): + if hasattr(input, "value"): input_values[input.name] = input.value else: - # Should fail if input is not optional and does not have default value - # Effectively however depends on parameter implementation. - # We might want to raise an exception here, instead of depending on a tool parameter value error. input_values[input.name] = None def get_current_case(input, input_values): diff --git a/lib/galaxy_test/workflow/optional_text_to_bool.gxwf-tests.yml b/lib/galaxy_test/workflow/optional_text_to_bool.gxwf-tests.yml new file mode 100644 index 00000000000..0bf59f44d0b --- /dev/null +++ b/lib/galaxy_test/workflow/optional_text_to_bool.gxwf-tests.yml @@ -0,0 +1,27 @@ +- doc: | + Test that omitting an optional text parameter connected to an expression + tool that converts text to boolean produces false, correctly skipping + the conditional downstream step. + job: + required_input: + type: File + value: 1.fasta + outputs: + out: + asserts: + has_text: + text: "null" +- doc: | + Test that providing an optional text parameter connected to an expression + tool that converts text to boolean produces true, so the conditional + downstream step runs. + job: + required_input: + type: File + value: 1.fasta + optional_text: some_value + outputs: + out: + asserts: + has_size: + min: 1 diff --git a/lib/galaxy_test/workflow/optional_text_to_bool.gxwf.yml b/lib/galaxy_test/workflow/optional_text_to_bool.gxwf.yml new file mode 100644 index 00000000000..d0f0957a184 --- /dev/null +++ b/lib/galaxy_test/workflow/optional_text_to_bool.gxwf.yml @@ -0,0 +1,29 @@ +class: GalaxyWorkflow +doc: | + Test that an omitted optional text parameter connected to an expression + tool (text→boolean conversion, like map_param_value) produces false, + allowing conditional (when) steps to be correctly skipped. + Regression test for https://github.com/galaxyproject/iwc/pull/1128 +inputs: + required_input: + type: data + optional_text: + type: text + optional: true +outputs: + out: + outputSource: cat/out_file1 +steps: + text_to_bool: + tool_id: expression_text_to_bool + in: + text_input: + source: optional_text + cat: + tool_id: cat + in: + input1: + source: required_input + when: + source: text_to_bool/bool_out + when: $(inputs.when) diff --git a/test/functional/tools/expression_text_to_bool.xml b/test/functional/tools/expression_text_to_bool.xml new file mode 100644 index 00000000000..26a27f1c9ae --- /dev/null +++ b/test/functional/tools/expression_text_to_bool.xml @@ -0,0 +1,27 @@ + + + { + var value = $job.text_input; + if (value == "false" || value == "False") { + return {'bool_out': false}; + } + return {'bool_out': !!value}; + } + + + + + + + + + + + + + + + + + + diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml index d164f0d4c5f..dc9f2dbba59 100644 --- a/test/functional/tools/sample_tool_conf.xml +++ b/test/functional/tools/sample_tool_conf.xml @@ -228,6 +228,7 @@ + From 7f40e45a7fd3a103e80bf0f54dc285243f532600 Mon Sep 17 00:00:00 2001 From: "Michael R. Crusoe" Date: Thu, 2 Nov 2023 12:35:05 +0100 Subject: [PATCH 4/4] Switch to only MIT license --- LICENSE.txt | 194 +----------------- packages/app/setup.cfg | 3 +- packages/auth/setup.cfg | 3 +- packages/config/setup.cfg | 3 +- packages/data/setup.cfg | 3 +- packages/files/setup.cfg | 3 +- packages/job_execution/setup.cfg | 3 +- packages/job_metrics/setup.cfg | 3 +- packages/meta/setup.cfg | 3 +- packages/navigation/setup.cfg | 3 +- packages/objectstore/setup.cfg | 3 +- packages/schema/setup.cfg | 3 +- packages/selenium/setup.cfg | 3 +- packages/test_api/setup.cfg | 3 +- packages/test_base/setup.cfg | 3 +- packages/test_driver/setup.cfg | 3 +- packages/test_selenium/setup.cfg | 3 +- packages/tool_shed/setup.cfg | 3 +- packages/tool_shed_schema/setup.cfg | 3 +- packages/tool_util/setup.cfg | 3 +- packages/tool_util_models/setup.cfg | 1 - packages/tours/setup.cfg | 3 +- packages/util/setup.cfg | 3 +- packages/web_apps/setup.cfg | 3 +- packages/web_client/setup.cfg | 3 +- packages/web_framework/setup.cfg | 3 +- packages/web_stack/setup.cfg | 3 +- test/functional/tools/bibtex.xml | 2 +- .../tools/mulled_example_multi_1.xml | 2 +- test/integration/test_workflow_refactoring.py | 8 +- 30 files changed, 33 insertions(+), 249 deletions(-) diff --git a/LICENSE.txt b/LICENSE.txt index 12ad720a342..c7cd73da4fd 100644 --- a/LICENSE.txt +++ b/LICENSE.txt @@ -1,11 +1,6 @@ -Copyright (c) 2005-2022 Galaxy Contributors (see CONTRIBUTORS.md) - -Work contributed from 2021-04-07 onwards is licensed under the MIT License. -Work contributed before this date is licensed under the Academic Free License -version 3.0. -See https://github.com/galaxyproject/galaxy/ for the contribution history. -See below for the full text of both licenses. +Copyright (c) 2005-2026 Galaxy Contributors (see CONTRIBUTORS.md) +Galaxy is provided from 2026-02-25 onwards entirely under the MIT License. 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Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy application (backend) keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index 50be0e6d7cc..2e26c40f52b 100644 --- a/packages/auth/setup.cfg +++ b/packages/auth/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy auth framework and implementations keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index 64c32e32a49..6ffeee7bbaa 100644 --- a/packages/config/setup.cfg +++ b/packages/config/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy configuration keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index dd66573c4e3..4533bebc580 100644 --- a/packages/data/setup.cfg +++ b/packages/data/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy datatype framework and datatypes keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index 3773e5acd12..6cfdcff63ac 100644 --- a/packages/files/setup.cfg +++ b/packages/files/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy file source framework and default plugins keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index 184fefcb320..d92848830cd 100644 --- a/packages/job_execution/setup.cfg +++ b/packages/job_execution/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy job execution runtime utilities keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index efdfde8f6db..5b83bd3ad47 100644 --- a/packages/job_metrics/setup.cfg +++ b/packages/job_metrics/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -22,7 +21,7 @@ classifiers = description = Galaxy job metrics keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/meta/setup.cfg b/packages/meta/setup.cfg index cf3c7ffc0cf..def355320a6 100644 --- a/packages/meta/setup.cfg +++ b/packages/meta/setup.cfg @@ -6,7 +6,6 @@ classifiers = Environment :: Console Intended Audience :: Developers Intended Audience :: Science/Research - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -22,7 +21,7 @@ classifiers = description = Galaxy server metapackage keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index 2f98ba69c62..6019998750a 100644 --- a/packages/navigation/setup.cfg +++ b/packages/navigation/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy client DOM navigation framework keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index deb6788be88..f5d8f4e747d 100644 --- a/packages/objectstore/setup.cfg +++ b/packages/objectstore/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -22,7 +21,7 @@ classifiers = description = Galaxy objectstore framework and plugins keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index a7a34374f5d..7d97b718723 100644 --- a/packages/schema/setup.cfg +++ b/packages/schema/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Pydantic models for Galaxy keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index 9b43f67eaea..7a4299f1eb7 100644 --- a/packages/selenium/setup.cfg +++ b/packages/selenium/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy Selenium interaction framework keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index 8344f74656e..1aff5510df9 100644 --- a/packages/test_api/setup.cfg +++ b/packages/test_api/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy API tests keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index b8592f53237..6763eeacd71 100644 --- a/packages/test_base/setup.cfg +++ b/packages/test_base/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy testing utilities keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index 3f4d57a8b90..0fd1b5ffa6b 100644 --- a/packages/test_driver/setup.cfg +++ b/packages/test_driver/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy test driver keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/test_selenium/setup.cfg b/packages/test_selenium/setup.cfg index 1a9d0c7703d..d78fbf2e036 100644 --- a/packages/test_selenium/setup.cfg +++ b/packages/test_selenium/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy Selenium tests keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg index 1b1e45dc9bb..a3c677f53f5 100644 --- a/packages/tool_shed/setup.cfg +++ b/packages/tool_shed/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy Tool Shed keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/tool_shed_schema/setup.cfg b/packages/tool_shed_schema/setup.cfg index cf223a9d157..0e9687c8584 100644 --- a/packages/tool_shed_schema/setup.cfg +++ b/packages/tool_shed_schema/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Pydantic models for the Galaxy Tool Shed keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index 8d724db6e70..1dc3b8489e4 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -22,7 +21,7 @@ classifiers = description = Galaxy tool and tool dependency utilities keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/tool_util_models/setup.cfg b/packages/tool_util_models/setup.cfg index 8a63bf41e79..bb8603dfb34 100644 --- a/packages/tool_util_models/setup.cfg +++ b/packages/tool_util_models/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index ee0552b54bb..eafd1b54792 100644 --- a/packages/tours/setup.cfg +++ b/packages/tours/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy tours backend framework keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index e5f38a860aa..9d4b8d23b27 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -22,7 +21,7 @@ classifiers = description = Galaxy generic utilities keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index 76625ee1ea5..971ef27e1c2 100644 --- a/packages/web_apps/setup.cfg +++ b/packages/web_apps/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy web apps keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/web_client/setup.cfg b/packages/web_client/setup.cfg index b1ad9d9709c..92fad7ea766 100644 --- a/packages/web_client/setup.cfg +++ b/packages/web_client/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy web client (frontend) keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index 97a95a06966..8672bfdd2c7 100644 --- a/packages/web_framework/setup.cfg +++ b/packages/web_framework/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy web framework keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index 7532c6d525c..d48d16ba25b 100644 --- a/packages/web_stack/setup.cfg +++ b/packages/web_stack/setup.cfg @@ -5,7 +5,6 @@ classifiers = Development Status :: 5 - Production/Stable Environment :: Console Intended Audience :: Developers - License :: OSI Approved :: Academic Free License (AFL) Natural Language :: English Operating System :: POSIX Programming Language :: Python :: 3 @@ -20,7 +19,7 @@ classifiers = description = Galaxy web stack abstraction keywords = Galaxy -license = AFL +license = MIT license_files = LICENSE long_description = file: README.rst, HISTORY.rst diff --git a/test/functional/tools/bibtex.xml b/test/functional/tools/bibtex.xml index 60ba096b981..bb47186bfec 100644 --- a/test/functional/tools/bibtex.xml +++ b/test/functional/tools/bibtex.xml @@ -1,4 +1,4 @@ - + + bedtools samtools diff --git a/test/integration/test_workflow_refactoring.py b/test/integration/test_workflow_refactoring.py index 89e39edcda5..08811e40753 100644 --- a/test/integration/test_workflow_refactoring.py +++ b/test/integration/test_workflow_refactoring.py @@ -70,10 +70,10 @@ class TestWorkflowRefactoringIntegration(integration_util.IntegrationTestCase, U assert response.workflow["annotation"] == "my cool new annotation" actions = [ - {"action_type": "update_license", "license": "AFL-3.0"}, + {"action_type": "update_license", "license": "MIT"}, ] self._refactor(actions) - assert self._latest_workflow.license == "AFL-3.0" + assert self._latest_workflow.license == "MIT" actions = [ {"action_type": "update_creator", "creator": [{"class": "Person", "name": "Mary"}]}, @@ -207,10 +207,10 @@ class TestWorkflowRefactoringIntegration(integration_util.IntegrationTestCase, U assert response.workflow["annotation"] == "my cool new annotation" actions = [ - {"action_type": "update_license", "license": "AFL-3.0"}, + {"action_type": "update_license", "license": "MIT"}, ] response = self._dry_run(actions) - assert response.workflow["license"] == "AFL-3.0" + assert response.workflow["license"] == "MIT" actions = [ {"action_type": "update_creator", "creator": [{"class": "Person", "name": "Mary"}]},