From 09ca48c623a41cd13626c5e774c70f409ce8c156 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Thu, 17 Mar 2022 08:27:25 +0100 Subject: [PATCH 1/4] add mzqc datatype needed here https://github.com/galaxyproteomics/tools-galaxyp/pull/653 --- lib/galaxy/config/sample/datatypes_conf.xml.sample | 1 + 1 file changed, 1 insertion(+) diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample index 87dc55d66cd..e5bd249556c 100644 --- a/lib/galaxy/config/sample/datatypes_conf.xml.sample +++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample @@ -287,6 +287,7 @@ + From 4084c77ae5cee441897f470749f876805580f014 Mon Sep 17 00:00:00 2001 From: M Bernt Date: Thu, 17 Mar 2022 08:51:08 +0100 Subject: [PATCH 2/4] Apply suggestions from code review --- lib/galaxy/config/sample/datatypes_conf.xml.sample | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/lib/galaxy/config/sample/datatypes_conf.xml.sample b/lib/galaxy/config/sample/datatypes_conf.xml.sample index e5bd249556c..70dfc59510a 100644 --- a/lib/galaxy/config/sample/datatypes_conf.xml.sample +++ b/lib/galaxy/config/sample/datatypes_conf.xml.sample @@ -287,7 +287,7 @@ - + From 96934420e85bf696880c870cba76bf3bf079b82f Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 16 Mar 2022 19:20:53 +0100 Subject: [PATCH 3/4] Attach dataset source in model store imports Fixes ``` FAILED test/integration_selenium/test_dataset_details_source_transforms.py::DatasetSourceTransformSeleniumIntegrationTestCase::test_displaying_source_transformations_grooming FAILED test/integration_selenium/test_dataset_details_source_transforms.py::DatasetSourceTransformSeleniumIntegrationTestCase::test_displaying_source_transformations_posixlines FAILED test/integration_selenium/test_dataset_details_source_transforms.py::DatasetSourceTransformSeleniumIntegrationTestCase::test_displaying_source_transformations_spaces_to_tabs ``` --- lib/galaxy/model/store/__init__.py | 3 +-- .../test_dataset_details_source_transforms.py | 8 ++++++++ 2 files changed, 9 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py index 482ad75727b..582d80e6711 100644 --- a/lib/galaxy/model/store/__init__.py +++ b/lib/galaxy/model/store/__init__.py @@ -264,8 +264,7 @@ class ModelImportStore(metaclass=abc.ABCMeta): if attribute in dataset_attrs["dataset"]: setattr(dataset_instance.dataset, attribute, dataset_attrs["dataset"][attribute]) self._attach_dataset_hashes(dataset_attrs["dataset"], dataset_instance) - # TODO: Once we have a test... - # self._attach_dataset_sources(dataset_attrs["dataset"], dataset_instance) + self._attach_dataset_sources(dataset_attrs["dataset"], dataset_instance) if 'id' in dataset_attrs["dataset"] and self.import_options.allow_edit: dataset_instance.dataset.id = dataset_attrs["dataset"]['id'] if job: diff --git a/test/integration_selenium/test_dataset_details_source_transforms.py b/test/integration_selenium/test_dataset_details_source_transforms.py index d2bc3fed6c9..41870de33e0 100644 --- a/test/integration_selenium/test_dataset_details_source_transforms.py +++ b/test/integration_selenium/test_dataset_details_source_transforms.py @@ -80,3 +80,11 @@ class DatasetSourceTransformSeleniumIntegrationTestCase(PosixFileSourceSetup, Se def setUp(self): super().setUp() self._write_file_fixtures() + + +class DatasetSourceTransformInModelStoreSeleniumIntegrationTestCase(DatasetSourceTransformSeleniumIntegrationTestCase): + + @classmethod + def handle_galaxy_config_kwds(cls, config): + super().handle_galaxy_config_kwds(config) + config["metadata_strategy"] = "extended" From 21e3ba013decee97eabcf0098201ad43ddb0751b Mon Sep 17 00:00:00 2001 From: Beatriz Serrano-Solano Date: Thu, 24 Mar 2022 19:47:05 +0100 Subject: [PATCH 4/4] Point to GTN tutorial in visualizations readme --- config/plugins/visualizations/README.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/config/plugins/visualizations/README.txt b/config/plugins/visualizations/README.txt index 07ca615cd1e..d037815beb0 100644 --- a/config/plugins/visualizations/README.txt +++ b/config/plugins/visualizations/README.txt @@ -8,7 +8,7 @@ Properly configured and written visualizations will be accessible to the user when they click the 'visualizations' icon for a dataset in their history panel. -For more information, see http://wiki.galaxyproject.org/VisualizationsRegistry +For more information, see https://training.galaxyproject.org/archive/2019-06-01/topics/dev/tutorials/visualization-generic/tutorial.html Sub-directory structure