From 0cd5daa27cb616258b8edfac97763413349258ad Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Fri, 20 Sep 2024 07:10:36 +0200 Subject: [PATCH 1/7] Raise MessageException instead of assertions on rerun problems --- lib/galaxy/tools/actions/__init__.py | 24 ++++++++++++++---------- 1 file changed, 14 insertions(+), 10 deletions(-) diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py index 826b5d54059a..f922e5b858b7 100644 --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -18,6 +18,7 @@ from galaxy import model from galaxy.exceptions import ( + AuthenticationRequired, ItemAccessibilityException, RequestParameterInvalidException, ) @@ -758,19 +759,22 @@ def _remap_job_on_rerun(self, trans, galaxy_session, rerun_remap_job_id, current try: old_job = trans.sa_session.get(Job, rerun_remap_job_id) assert old_job is not None, f"({rerun_remap_job_id}/{current_job.id}): Old job id is invalid" - assert ( - old_job.tool_id == current_job.tool_id - ), f"({old_job.id}/{current_job.id}): Old tool id ({old_job.tool_id}) does not match rerun tool id ({current_job.tool_id})" + if old_job.old_id != current_job.old_id: + raise RequestParameterInvalidException( + f"Old tool id ({old_job.tool_id}) does not match rerun tool id ({current_job.tool_id})" + ) if trans.user is not None: - assert ( - old_job.user_id == trans.user.id - ), f"({old_job.id}/{current_job.id}): Old user id ({old_job.user_id}) does not match rerun user id ({trans.user.id})" + if old_job.user_id != trans.user.id: + raise RequestParameterInvalidException( + "Cannot remap job dependencies for job not created by current user." + ) elif trans.user is None and isinstance(galaxy_session, trans.model.GalaxySession): - assert ( - old_job.session_id == galaxy_session.id - ), f"({old_job.id}/{current_job.id}): Old session id ({old_job.session_id}) does not match rerun session id ({galaxy_session.id})" + if old_job.session_id != galaxy_session.id: + raise RequestParameterInvalidException( + "Cannot remap job dependencies for job not created by current user." + ) else: - raise Exception(f"({old_job.id}/{current_job.id}): Remapping via the API is not (yet) supported") + raise AuthenticationRequired("Authentication required to remap job dependencies") # Start by hiding current job outputs before taking over the old job's (implicit) outputs. current_job.hide_outputs(flush=False) # Duplicate PJAs before remap. From 69a3cda018d4a7f4e7fbe8604949185753808b0f Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Sun, 22 Sep 2024 10:35:13 +0200 Subject: [PATCH 2/7] Fix history import when parent_hda not serialized and make sure we include the parent_hda when exporting histories. Fixes https://sentry.galaxyproject.org/share/issue/20ee27f675ef476588bbe8ff273eaee7/: ``` KeyError: '31e7840b5aedca43523bfcc8e2e9e56f' File "galaxy/jobs/__init__.py", line 2039, in finish task_wrapper = self.tool.exec_after_process( File "galaxy/tools/__init__.py", line 3100, in exec_after_process JobImportHistoryArchiveWrapper(self.app, job.id).cleanup_after_job() File "galaxy/tools/imp_exp/__init__.py", line 81, in cleanup_after_job model_store.perform_import(new_history, job=job, new_history=True) File "galaxy/model/store/__init__.py", line 416, in perform_import self._import_implicit_dataset_conversions(object_import_tracker) File "galaxy/model/store/__init__.py", line 1280, in _import_implicit_dataset_conversions idc.parent_hda = object_import_tracker.hdas_by_key[idc_attrs["parent_hda"]] ``` --- lib/galaxy/model/__init__.py | 1 + lib/galaxy/model/store/__init__.py | 30 +++++++++--- test/unit/data/model/test_model_store.py | 62 +++++++++++++++++++++--- 3 files changed, 78 insertions(+), 15 deletions(-) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 8c04e2ecefb5..6354b3654f0e 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -4546,6 +4546,7 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): copied_from_history_dataset_association: Optional["HistoryDatasetAssociation"] copied_from_library_dataset_dataset_association: Optional["LibraryDatasetDatasetAssociation"] implicitly_converted_datasets: List["ImplicitlyConvertedDatasetAssociation"] + implicitly_converted_parent_datasets: List["ImplicitlyConvertedDatasetAssociation"] validated_states = DatasetValidatedState diff --git a/lib/galaxy/model/store/__init__.py b/lib/galaxy/model/store/__init__.py index a27e8c57b10c..a3bf6a6ec896 100644 --- a/lib/galaxy/model/store/__init__.py +++ b/lib/galaxy/model/store/__init__.py @@ -1023,7 +1023,7 @@ def _reassign_hids(self, object_import_tracker: "ObjectImportTracker", history: if object_import_tracker.copy_hid_for: # in an if to avoid flush if unneeded - for from_dataset, to_dataset in object_import_tracker.copy_hid_for.items(): + for from_dataset, to_dataset in object_import_tracker.copy_hid_for: to_dataset.hid = from_dataset.hid self._session_add(to_dataset) self._flush() @@ -1276,18 +1276,24 @@ def _import_implicit_dataset_conversions(self, object_import_tracker: "ObjectImp metadata_safe = False idc = model.ImplicitlyConvertedDatasetAssociation(metadata_safe=metadata_safe, for_import=True) idc.type = idc_attrs["file_type"] - if idc_attrs.get("parent_hda"): - idc.parent_hda = object_import_tracker.hdas_by_key[idc_attrs["parent_hda"]] + # We may not have exported the parent, so only set the parent_hda attribute if we did. + if (parent_hda_id := idc_attrs.get("parent_hda")) and ( + parent_hda := object_import_tracker.hdas_by_key.get(parent_hda_id) + ): + # exports created prior to 24.2 may not have a parent if the parent had been purged + idc.parent_hda = parent_hda if idc_attrs.get("hda"): idc.dataset = object_import_tracker.hdas_by_key[idc_attrs["hda"]] - # we have a the dataset and the parent, lets ensure they land up with the same HID - if idc.dataset and idc.parent_hda and idc.parent_hda in object_import_tracker.requires_hid: + # we have the dataset and the parent, lets ensure they land up with the same HID + if idc.dataset and idc.parent_hda: try: object_import_tracker.requires_hid.remove(idc.dataset) except ValueError: pass # we wanted to remove it anyway. - object_import_tracker.copy_hid_for[idc.parent_hda] = idc.dataset + # A HDA can be the parent of multiple implicitly converted dataset, + # that's thy we use [(source, target)] here + object_import_tracker.copy_hid_for.append((idc.parent_hda, idc.dataset)) self._session_add(idc) @@ -1370,7 +1376,7 @@ class ObjectImportTracker: hdca_copied_from_sinks: Dict[ObjectKeyType, ObjectKeyType] jobs_by_key: Dict[ObjectKeyType, model.Job] requires_hid: List["HistoryItem"] - copy_hid_for: Dict["HistoryItem", "HistoryItem"] + copy_hid_for: List[Tuple["HistoryItem", "HistoryItem"]] def __init__(self) -> None: self.libraries_by_key = {} @@ -1388,7 +1394,7 @@ def __init__(self) -> None: self.implicit_collection_jobs_by_key: Dict[str, ImplicitCollectionJobs] = {} self.workflows_by_key: Dict[str, model.Workflow] = {} self.requires_hid = [] - self.copy_hid_for = {} + self.copy_hid_for = [] self.new_history: Optional[model.History] = None @@ -2301,6 +2307,14 @@ def add_implicit_conversion_dataset( include_files: bool, conversion: model.ImplicitlyConvertedDatasetAssociation, ) -> None: + parent_hda = conversion.parent_hda + if parent_hda and parent_hda not in self.included_datasets: + # We should always include the parent of an implicit conversion + # to avoid holes in the provenance. + self.included_datasets[parent_hda] = (parent_hda, include_files) + grand_parent_association = parent_hda.implicitly_converted_parent_datasets + if grand_parent_association and (grand_parent_hda := grand_parent_association[0].parent_hda): + self.add_implicit_conversion_dataset(grand_parent_hda, include_files, grand_parent_association[0]) self.included_datasets[dataset] = (dataset, include_files) self.dataset_implicit_conversions[dataset] = conversion diff --git a/test/unit/data/model/test_model_store.py b/test/unit/data/model/test_model_store.py index a30410dd0207..5ea51452e9f9 100644 --- a/test/unit/data/model/test_model_store.py +++ b/test/unit/data/model/test_model_store.py @@ -122,32 +122,80 @@ def test_import_export_history_allow_discarded_data(): assert imported_job.output_datasets[0].dataset == datasets[1] -def test_import_export_history_with_implicit_conversion(): +def setup_history_with_implicit_conversion(): app = _mock_app() u, h, d1, d2, j = _setup_simple_cat_job(app) + intermediate_ext = "bam" + intermediate_implicit_hda = model.HistoryDatasetAssociation( + extension=intermediate_ext, create_dataset=True, flush=False, history=h + ) + intermediate_implicit_hda.hid = d2.hid convert_ext = "fasta" implicit_hda = model.HistoryDatasetAssociation(extension=convert_ext, create_dataset=True, flush=False, history=h) implicit_hda.hid = d2.hid # this adds and flushes the result... - d2.attach_implicitly_converted_dataset(app.model.context, implicit_hda, convert_ext) + intermediate_implicit_hda.attach_implicitly_converted_dataset(app.model.context, implicit_hda, convert_ext) + d2.attach_implicitly_converted_dataset(app.model.context, intermediate_implicit_hda, intermediate_ext) + + app.object_store.update_from_file(intermediate_implicit_hda.dataset, file_name=TEST_PATH_2_CONVERTED, create=True) app.object_store.update_from_file(implicit_hda.dataset, file_name=TEST_PATH_2_CONVERTED, create=True) - assert len(h.active_datasets) == 3 + assert len(h.active_datasets) == 4 + return app, h, implicit_hda + + +def test_import_export_history_with_implicit_conversion(): + app, h, _ = setup_history_with_implicit_conversion() imported_history = _import_export_history(app, h, export_files="copy", include_hidden=True) - assert len(imported_history.active_datasets) == 3 + assert len(imported_history.active_datasets) == 4 recovered_hda_2 = imported_history.active_datasets[1] assert recovered_hda_2.implicitly_converted_datasets - imported_conversion = recovered_hda_2.implicitly_converted_datasets[0] - assert imported_conversion.type == "fasta" - assert imported_conversion.dataset == imported_history.active_datasets[2] + intermediate_conversion = recovered_hda_2.implicitly_converted_datasets[0] + assert intermediate_conversion.type == "bam" + intermediate_hda = intermediate_conversion.dataset + assert intermediate_hda.implicitly_converted_datasets + final_conversion = intermediate_hda.implicitly_converted_datasets[0] + + assert final_conversion.type == "fasta" + assert final_conversion.dataset == imported_history.active_datasets[-1] # implicit conversions have the same HID... ensure this property is recovered... assert imported_history.active_datasets[2].hid == imported_history.active_datasets[1].hid +def test_import_export_history_with_implicit_conversion_parents_purged(): + app, h, implicit_hda = setup_history_with_implicit_conversion() + # Purge parents + parent = implicit_hda.implicitly_converted_parent_datasets[0].parent_hda + parent.dataset.purged = True + grandparent = parent.implicitly_converted_parent_datasets[0].parent_hda + grandparent.dataset.purged = True + app.model.context.commit() + imported_history = _import_export_history(app, h, export_files="copy", include_hidden=True) + + assert len(imported_history.active_datasets) == 2 + assert len(imported_history.datasets) == 4 + imported_implicit_hda = imported_history.active_datasets[1] + assert imported_implicit_hda.extension == "fasta" + + # implicit conversions have the same HID... ensure this property is recovered... + assert imported_implicit_hda.hid == implicit_hda.hid + assert imported_implicit_hda.implicitly_converted_parent_datasets + intermediate_implicit_conversion = imported_implicit_hda.implicitly_converted_parent_datasets[0] + intermediate_hda = intermediate_implicit_conversion.parent_hda + assert intermediate_hda.hid == implicit_hda.hid + assert intermediate_hda.extension == "bam" + assert intermediate_hda.implicitly_converted_datasets + assert intermediate_hda.implicitly_converted_parent_datasets + first_implicit_conversion = intermediate_hda.implicitly_converted_parent_datasets[0] + source_hda = first_implicit_conversion.parent_hda + assert source_hda.hid == implicit_hda.hid + assert source_hda.extension == "txt" + + def test_import_export_history_with_implicit_conversion_and_extra_files(): app = _mock_app() From b70a7637b93140b15ec43e9e1ede998e59c9ffec Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 23 Sep 2024 16:17:53 +0200 Subject: [PATCH 3/7] Fix up exception handling, add test --- lib/galaxy/model/__init__.py | 1 + lib/galaxy/tools/actions/__init__.py | 68 +++++++++++++++++----------- lib/galaxy_test/api/test_jobs.py | 26 +++++++++++ 3 files changed, 68 insertions(+), 27 deletions(-) diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py index 34fd70c56029..85c0c9f4dfc9 100644 --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -4544,6 +4544,7 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable): creating_job_associations: List[Union[JobToOutputDatasetCollectionAssociation, JobToOutputDatasetAssociation]] copied_from_history_dataset_association: Optional["HistoryDatasetAssociation"] copied_from_library_dataset_dataset_association: Optional["LibraryDatasetDatasetAssociation"] + dependent_jobs: List[JobToInputLibraryDatasetAssociation] implicitly_converted_datasets: List["ImplicitlyConvertedDatasetAssociation"] validated_states = DatasetValidatedState diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py index f922e5b858b7..31c7eb76526c 100644 --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -9,6 +9,7 @@ cast, Dict, List, + Optional, Set, TYPE_CHECKING, Union, @@ -700,14 +701,6 @@ def handle_output(name, output, hidden=None): # Remap any outputs if this is a rerun and the user chose to continue dependent jobs # This functionality requires tracking jobs in the database. if app.config.track_jobs_in_database and rerun_remap_job_id is not None: - # Need to flush here so that referencing outputs by id works - session = trans.sa_session() - try: - session.expire_on_commit = False - with transaction(session): - session.commit() - finally: - session.expire_on_commit = True self._remap_job_on_rerun( trans=trans, galaxy_session=galaxy_session, @@ -748,7 +741,14 @@ def handle_output(name, output, hidden=None): return job, out_data, history - def _remap_job_on_rerun(self, trans, galaxy_session, rerun_remap_job_id, current_job, out_data): + def _remap_job_on_rerun( + self, + trans: ProvidesHistoryContext, + galaxy_session: Optional[model.GalaxySession], + rerun_remap_job_id: int, + current_job: Job, + out_data, + ): """ Re-connect dependent datasets for a job that is being rerun (because it failed initially). @@ -756,25 +756,39 @@ def _remap_job_on_rerun(self, trans, galaxy_session, rerun_remap_job_id, current To be able to resume jobs that depend on this jobs output datasets we change the dependent's job input datasets to be those of the job that is being rerun. """ - try: - old_job = trans.sa_session.get(Job, rerun_remap_job_id) - assert old_job is not None, f"({rerun_remap_job_id}/{current_job.id}): Old job id is invalid" - if old_job.old_id != current_job.old_id: + old_job = trans.sa_session.get(Job, rerun_remap_job_id) + if not old_job: + # I don't think that can really happen + raise RequestParameterInvalidException("rerun_remap_job_id parameter is invalid") + old_tool = trans.app.toolbox.get_tool(old_job.tool_id, exact=False) + new_tool = trans.app.toolbox.get_tool(current_job.tool_id, exact=False) + if old_tool and new_tool and old_tool.old_id != new_tool.old_id: + # If we currently only have the old or new tool installed we'll find the other tool anyway with `exact=False`. + # If we don't have the tool at all we'll fail anyway, no need to worry here. + raise RequestParameterInvalidException( + f"Old tool id ({old_job.tool_id}) does not match rerun tool id ({current_job.tool_id})" + ) + if trans.user is not None: + if old_job.user_id != trans.user.id: raise RequestParameterInvalidException( - f"Old tool id ({old_job.tool_id}) does not match rerun tool id ({current_job.tool_id})" + "Cannot remap job dependencies for job not created by current user." ) - if trans.user is not None: - if old_job.user_id != trans.user.id: - raise RequestParameterInvalidException( - "Cannot remap job dependencies for job not created by current user." - ) - elif trans.user is None and isinstance(galaxy_session, trans.model.GalaxySession): - if old_job.session_id != galaxy_session.id: - raise RequestParameterInvalidException( - "Cannot remap job dependencies for job not created by current user." - ) - else: - raise AuthenticationRequired("Authentication required to remap job dependencies") + elif trans.user is None and galaxy_session: + if old_job.session_id != galaxy_session.id: + raise RequestParameterInvalidException( + "Cannot remap job dependencies for job not created by current user." + ) + else: + raise AuthenticationRequired("Authentication required to remap job dependencies") + # Need to flush here so that referencing outputs by id works + session = trans.sa_session() + try: + session.expire_on_commit = False + with transaction(session): + session.commit() + finally: + session.expire_on_commit = True + try: # Start by hiding current job outputs before taking over the old job's (implicit) outputs. current_job.hide_outputs(flush=False) # Duplicate PJAs before remap. @@ -796,7 +810,7 @@ def _remap_job_on_rerun(self, trans, galaxy_session, rerun_remap_job_id, current for jtod in old_job.output_datasets: for job_to_remap, jtid in [(jtid.job, jtid) for jtid in jtod.dataset.dependent_jobs]: if (trans.user is not None and job_to_remap.user_id == trans.user.id) or ( - trans.user is None and job_to_remap.session_id == galaxy_session.id + trans.user is None and galaxy_session and job_to_remap.session_id == galaxy_session.id ): self.__remap_parameters(job_to_remap, jtid, jtod, out_data) trans.sa_session.add(job_to_remap) diff --git a/lib/galaxy_test/api/test_jobs.py b/lib/galaxy_test/api/test_jobs.py index 82f9ecbab416..c904e808f70f 100644 --- a/lib/galaxy_test/api/test_jobs.py +++ b/lib/galaxy_test/api/test_jobs.py @@ -464,6 +464,32 @@ def test_no_hide_on_rerun(self): assert hdca["visible"] assert isoparse(hdca["update_time"]) > (isoparse(first_update_time)) + def test_rerun_exception_handling(self): + with self.dataset_populator.test_history() as history_id: + other_run_response = self.dataset_populator.run_tool( + tool_id="job_properties", + inputs={}, + history_id=history_id, + ) + unrelated_job_id = other_run_response["jobs"][0]["id"] + run_response = self._run_map_over_error(history_id) + job_id = run_response["jobs"][0]["id"] + self.dataset_populator.wait_for_job(job_id) + failed_hdca = self.dataset_populator.get_history_collection_details( + history_id=history_id, + content_id=run_response["implicit_collections"][0]["id"], + assert_ok=False, + ) + assert failed_hdca["visible"] + rerun_params = self._get(f"jobs/{job_id}/build_for_rerun").json() + inputs = rerun_params["state_inputs"] + inputs["rerun_remap_job_id"] = unrelated_job_id + before_rerun_items = self.dataset_populator.get_history_contents(history_id) + rerun_response = self._run_detect_errors(history_id=history_id, inputs=inputs) + assert "does not match rerun tool id" in rerun_response["err_msg"] + after_rerun_items = self.dataset_populator.get_history_contents(history_id) + assert len(before_rerun_items) == len(after_rerun_items) + @skip_without_tool("empty_output") def test_common_problems(self): with self.dataset_populator.test_history() as history_id: From d4705870283176e7d2fd90f69ae49128217ecb6e Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 23 Sep 2024 17:19:45 +0200 Subject: [PATCH 4/7] Fix data_column ref to nested collection --- lib/galaxy/tools/parameters/basic.py | 12 +++++++---- lib/galaxy_test/api/test_tools.py | 30 ++++++++++++++++++++++++++++ lib/galaxy_test/base/populators.py | 4 ++-- 3 files changed, 40 insertions(+), 6 deletions(-) diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py index 279adde7a92e..9eef495cb153 100644 --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1457,8 +1457,8 @@ def get_column_list(self, trans, other_values): # Use representative dataset if a dataset collection is parsed if isinstance(dataset, HistoryDatasetCollectionAssociation): dataset = dataset.to_hda_representative() - if isinstance(dataset, DatasetCollectionElement) and dataset.hda: - dataset = dataset.hda + if isinstance(dataset, DatasetCollectionElement): + dataset = dataset.first_dataset_instance() if isinstance(dataset, HistoryDatasetAssociation) and self.ref_input and self.ref_input.formats: direct_match, target_ext, converted_dataset = dataset.find_conversion_destination( self.ref_input.formats @@ -1553,9 +1553,13 @@ def is_file_empty(self, trans, other_values): for dataset in util.listify(other_values.get(self.data_ref)): # Use representative dataset if a dataset collection is parsed if isinstance(dataset, HistoryDatasetCollectionAssociation): - dataset = dataset.to_hda_representative() + if dataset.populated: + dataset = dataset.to_hda_representative() + else: + # That's fine, we'll check again on execution + return True if isinstance(dataset, DatasetCollectionElement): - dataset = dataset.hda + dataset = dataset.first_dataset_instance() if isinstance(dataset, DatasetInstance): return not dataset.has_data() if is_runtime_value(dataset): diff --git a/lib/galaxy_test/api/test_tools.py b/lib/galaxy_test/api/test_tools.py index 78a4b3e05c92..56fea13f8285 100644 --- a/lib/galaxy_test/api/test_tools.py +++ b/lib/galaxy_test/api/test_tools.py @@ -2481,6 +2481,36 @@ def test_implicit_reduce_with_mapping(self): ) assert output_hdca["collection_type"] == "list" + @skip_without_tool("column_multi_param") + def test_multi_param_column_nested_list(self): + with self.dataset_populator.test_history() as history_id: + hdca = self.dataset_collection_populator.create_list_of_list_in_history( + history_id, ext="tabular", wait=True + ).json() + inputs = { + "input1": {"src": "hdca", "id": hdca["id"]}, + # FIXME: integers don't work here + "col": "1", + } + response = self._run("column_multi_param", history_id, inputs, assert_ok=True) + self.dataset_populator.wait_for_job(job_id=response["jobs"][0]["id"], assert_ok=True) + + @skip_without_tool("column_multi_param") + def test_multi_param_column_nested_list_fails_on_invalid_column(self): + with self.dataset_populator.test_history() as history_id: + hdca = self.dataset_collection_populator.create_list_of_list_in_history( + history_id, ext="tabular", wait=True + ).json() + inputs = { + "input1": {"src": "hdca", "id": hdca["id"]}, + "col": "10", + } + try: + self._run("column_multi_param", history_id, inputs, assert_ok=True) + except AssertionError as e: + exception_raised = e + assert exception_raised, "Expected invalid column selection to fail job" + @skip_without_tool("column_multi_param") def test_implicit_conversion_and_reduce(self): with self.dataset_populator.test_history() as history_id: diff --git a/lib/galaxy_test/base/populators.py b/lib/galaxy_test/base/populators.py index 4d1c46ca5309..014880ebd1e6 100644 --- a/lib/galaxy_test/base/populators.py +++ b/lib/galaxy_test/base/populators.py @@ -2898,7 +2898,7 @@ def __create_payload(self, history_id: str, *args, **kwds): else: return self.__create_payload_collection(history_id, *args, **kwds) - def __create_payload_fetch(self, history_id: str, collection_type, **kwds): + def __create_payload_fetch(self, history_id: str, collection_type, ext="txt", **kwds): contents = None if "contents" in kwds: contents = kwds["contents"] @@ -2920,7 +2920,7 @@ def __create_payload_fetch(self, history_id: str, collection_type, **kwds): elements.append(contents_level) continue - element = {"src": "pasted", "ext": "txt"} + element = {"src": "pasted", "ext": ext} # Else older style list of contents or element ID and contents, # convert to fetch API. if isinstance(contents_level, tuple): From af3af5a158a3a95229234eefdb8a9a2296f4778e Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Mon, 23 Sep 2024 19:58:04 +0200 Subject: [PATCH 5/7] Fix loading very old worflows with data inputs Fixes https://sentry.galaxyproject.org/share/issue/d1cad9f916e8466f844ea3b49f52afcb/: ``` AttributeError: 'NoneType' object has no attribute 'get' File "galaxy/web/framework/middleware/error.py", line 167, in __call__ app_iter = self.application(environ, sr_checker) File "galaxy/web/framework/middleware/statsd.py", line 29, in __call__ req = self.application(environ, start_response) File "/cvmfs/main.galaxyproject.org/venv/lib/python3.11/site-packages/paste/httpexceptions.py", line 635, in __call__ return self.application(environ, start_response) File "galaxy/web/framework/base.py", line 176, in __call__ return self.handle_request(request_id, path_info, environ, start_response) File "galaxy/web/framework/base.py", line 271, in handle_request body = method(trans, **kwargs) File "galaxy/web/framework/decorators.py", line 74, in call_and_format rval = func(self, trans, *args, **kwargs) File "galaxy/webapps/galaxy/controllers/workflow.py", line 263, in load_workflow return workflow_contents_manager.workflow_to_dict(trans, stored, style="editor", version=version) File "galaxy/managers/workflows.py", line 926, in workflow_to_dict wf_dict = self._workflow_to_dict_editor(trans, stored, workflow) File "galaxy/managers/workflows.py", line 1239, in _workflow_to_dict_editor self.__set_default_label(step, module, step.tool_inputs) File "galaxy/managers/workflows.py", line 1958, in __set_default_label default_label = new_state.get("name") ``` and https://sentry.galaxyproject.org/share/issue/92e8f30a288341e7b219e2c7c91390da/: ``` AttributeError: 'NoneType' object has no attribute 'get' File "starlette/applications.py", line 123, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/middleware/errors.py", line 186, in __call__ raise exc File "starlette/middleware/errors.py", line 164, in __call__ await self.app(scope, receive, _send) File "starlette_context/middleware/raw_middleware.py", line 92, in __call__ await self.app(scope, receive, send_wrapper) File "starlette/middleware/base.py", line 189, in __call__ with collapse_excgroups(): File "contextlib.py", line 155, in __exit__ self.gen.throw(typ, value, traceback) File "starlette/_utils.py", line 93, in collapse_excgroups raise exc File "starlette/middleware/base.py", line 191, in __call__ response = await self.dispatch_func(request, call_next) File "galaxy/webapps/galaxy/fast_app.py", line 109, in add_x_frame_options response = await call_next(request) File "starlette/middleware/base.py", line 165, in call_next raise app_exc File "starlette/middleware/base.py", line 151, in coro await self.app(scope, receive_or_disconnect, send_no_error) File "starlette/middleware/exceptions.py", line 65, in __call__ await wrap_app_handling_exceptions(self.app, conn)(scope, receive, send) File "starlette/_exception_handler.py", line 64, in wrapped_app raise exc File "starlette/_exception_handler.py", line 53, in wrapped_app await app(scope, receive, sender) File "starlette/routing.py", line 756, in __call__ await self.middleware_stack(scope, receive, send) File "starlette/routing.py", line 776, in app await route.handle(scope, receive, send) File "starlette/routing.py", line 297, in handle await self.app(scope, receive, send) File "starlette/routing.py", line 77, in app await wrap_app_handling_exceptions(app, request)(scope, receive, send) File "starlette/_exception_handler.py", line 64, in wrapped_app raise exc File "starlette/_exception_handler.py", line 53, in wrapped_app await app(scope, receive, sender) File "starlette/routing.py", line 72, in app response = await func(request) File "fastapi/routing.py", line 278, in app raw_response = await run_endpoint_function( File "fastapi/routing.py", line 193, in run_endpoint_function return await run_in_threadpool(dependant.call, **values) File "starlette/concurrency.py", line 42, in run_in_threadpool return await anyio.to_thread.run_sync(func, *args) File "anyio/to_thread.py", line 56, in run_sync return await get_async_backend().run_sync_in_worker_thread( File "anyio/_backends/_asyncio.py", line 2144, in run_sync_in_worker_thread return await future File "anyio/_backends/_asyncio.py", line 851, in run result = context.run(func, *args) File "galaxy/webapps/galaxy/api/workflows.py", line 1159, in show_workflow return self.service.show_workflow(trans, workflow_id, instance, legacy, version) File "galaxy/webapps/galaxy/services/workflows.py", line 243, in show_workflow **self._workflow_contents_manager.workflow_to_dict(trans, stored_workflow, style=style, version=version) File "galaxy/managers/workflows.py", line 930, in workflow_to_dict wf_dict = self._workflow_to_dict_instance(trans, stored, workflow=workflow, legacy=False) File "galaxy/managers/workflows.py", line 1663, in _workflow_to_dict_instance step_label = step.label or step.tool_inputs.get("name") ``` This is for https://usegalaxy.org/workflows/export?id=ea97d3a23e6d38e6 --- lib/galaxy/managers/workflows.py | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py index eabaf60af260..9a9e3fb1ba3c 100644 --- a/lib/galaxy/managers/workflows.py +++ b/lib/galaxy/managers/workflows.py @@ -1645,7 +1645,7 @@ def _workflow_to_dict_instance(self, trans, stored, workflow, legacy=True): inputs = {} for step in workflow.input_steps: step_type = step.type - step_label = step.label or step.tool_inputs.get("name") + step_label = step.label or step.tool_inputs and step.tool_inputs.get("name") if step_label: label = step_label elif step_type == "data_input": @@ -1939,7 +1939,7 @@ def __set_default_label(self, step, module, state): to the actual `label` attribute which is available for all module types, unique, and mapped to its own database column. """ if not module.label and module.type in ["data_input", "data_collection_input"]: - new_state = safe_loads(state) + new_state = safe_loads(state) or {} default_label = new_state.get("name") if default_label and util.unicodify(default_label).lower() not in [ "input dataset", From 04abcd5b342a5ed1f5ac2a3c1836a18deb929fac Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 25 Sep 2024 14:29:26 +0200 Subject: [PATCH 6/7] Create version 24.1.2 --- lib/galaxy/version.py | 2 +- packages/app/HISTORY.rst | 51 ++++++++++++++++++++++++++++-- packages/app/setup.cfg | 2 +- packages/auth/HISTORY.rst | 8 ++--- packages/auth/setup.cfg | 2 +- packages/config/HISTORY.rst | 26 +++++++++++++-- packages/config/setup.cfg | 2 +- packages/data/HISTORY.rst | 32 +++++++++++++++++-- packages/data/setup.cfg | 2 +- packages/files/HISTORY.rst | 8 ++--- packages/files/setup.cfg | 2 +- packages/job_execution/HISTORY.rst | 11 +++++-- packages/job_execution/setup.cfg | 2 +- packages/job_metrics/HISTORY.rst | 8 ++--- packages/job_metrics/setup.cfg | 2 +- packages/navigation/HISTORY.rst | 8 ++--- packages/navigation/setup.cfg | 2 +- packages/objectstore/HISTORY.rst | 11 +++++-- packages/objectstore/setup.cfg | 2 +- packages/schema/HISTORY.rst | 22 +++++++++++-- packages/schema/setup.cfg | 2 +- packages/selenium/HISTORY.rst | 8 ++--- packages/selenium/setup.cfg | 2 +- packages/test_api/HISTORY.rst | 23 ++++++++++++-- packages/test_api/setup.cfg | 2 +- packages/test_base/HISTORY.rst | 13 ++++++-- packages/test_base/setup.cfg | 2 +- packages/test_driver/HISTORY.rst | 8 ++--- packages/test_driver/setup.cfg | 2 +- packages/tool_shed/HISTORY.rst | 8 ++--- packages/tool_shed/setup.cfg | 2 +- packages/tool_util/HISTORY.rst | 18 +++++++++-- packages/tool_util/setup.cfg | 2 +- packages/tours/HISTORY.rst | 8 ++--- packages/tours/setup.cfg | 2 +- packages/util/HISTORY.rst | 18 +++++++++-- packages/util/setup.cfg | 2 +- packages/web_apps/HISTORY.rst | 38 ++++++++++++++++++++-- packages/web_apps/setup.cfg | 2 +- packages/web_framework/HISTORY.rst | 13 ++++++-- packages/web_framework/setup.cfg | 2 +- packages/web_stack/HISTORY.rst | 8 ++--- packages/web_stack/setup.cfg | 2 +- 43 files changed, 298 insertions(+), 94 deletions(-) diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index 127856da436f..8447b0537e06 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ VERSION_MAJOR = "24.1" -VERSION_MINOR = "2.dev0" +VERSION_MINOR = "2" VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "") diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index a01c8a3a25c1..6b4fe789a1f3 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -3,11 +3,56 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= + +* Return generic message for password reset email by `@ahmedhamidawan `_ in `#18479 `_ +* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek `_ in `#18494 `_ +* Prevent job submission if input collection element is deleted by `@mvdbeek `_ in `#18517 `_ +* Strip unicode null from tool stdio by `@mvdbeek `_ in `#18527 `_ +* Fix map over calculation for runtime inputs by `@mvdbeek `_ in `#18535 `_ +* Fix for not-null in 'column_list' object by `@hujambo-dunia `_ in `#18553 `_ +* Also fail ``ensure_dataset_on_disk`` if dataset is in new state by `@mvdbeek `_ in `#18559 `_ +* Fix sqlalchemy statement in tooltagmanager reset output by `@dannon `_ in `#18591 `_ +* Set minimum weasyprint version by `@mvdbeek `_ in `#18606 `_ +* Improve relabel identifiers message when number of columns is not 2 by `@mvdbeek `_ in `#18634 `_ +* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek `_ in `#18661 `_ +* Make sure we set file size also for purged outputs by `@mvdbeek `_ in `#18681 `_ +* File source and object store instance api fixes by `@mvdbeek `_ in `#18685 `_ +* Fix change datatype PJA on expression tool data outputs by `@mvdbeek `_ in `#18691 `_ +* Fill in missing help for cross product tools. by `@jmchilton `_ in `#18698 `_ +* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek `_ in `#18731 `_ +* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek `_ in `#18734 `_ +* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek `_ in `#18751 `_ +* Fix directory get or create logic by `@mvdbeek `_ in `#18752 `_ +* Fix job summary for optional unset job data inputs by `@mvdbeek `_ in `#18754 `_ +* Allow to change only the description of a quota by `@bernt-matthias `_ in `#18775 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Fix unspecified ``oidc_endpoint`` variable overwriting specified ``redirect_url`` by `@bgruening `_ in `#18818 `_ +* Fix wrong celery_app config on job and workflow handlers by `@mvdbeek `_ in `#18819 `_ +* Fix ``named cursor is not valid anymore`` by `@mvdbeek `_ in `#18825 `_ +* Tighten TRS url check by `@mvdbeek `_ in `#18841 `_ +* Fix Workflow index bookmark filter by `@itisAliRH `_ in `#18842 `_ +* Skip metric collection if job working directory doesn't exist by `@mvdbeek `_ in `#18845 `_ +* Extend on disk checks to running, queued and error states by `@mvdbeek `_ in `#18846 `_ +* Raise MessageException instead of assertions on rerun problems by `@mvdbeek `_ in `#18858 `_ +* Fix data_column ref to nested collection by `@mvdbeek `_ in `#18875 `_ +* Fix loading very old workflows with data inputs by `@mvdbeek `_ in `#18876 `_ + +============ +Enhancements +============ +* Include workflow invocation id in exception logs by `@mvdbeek `_ in `#18594 `_ +* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus `_ in `#18670 `_ +* Collect job metrics also when job failed by `@mvdbeek `_ in `#18809 `_ +* prevent "missing refresh_token" errors by supporting also with Keycloak backend by `@ljocha `_ in `#18826 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index cb942f671857..8d067b1afe6d 100644 --- a/packages/app/setup.cfg +++ b/packages/app/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-app url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index c0cbc0c0d8c3..72450a70903e 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ - +------------------- +24.1.2 (2024-09-25) +------------------- +No recorded changes since last release ------------------- 24.1.1 (2024-07-02) diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index 44bac91c764a..25b71dc16efa 100644 --- a/packages/auth/setup.cfg +++ b/packages/auth/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-auth url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index f9cf20c3f0f6..ecf0f191d0e4 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -3,11 +3,31 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + + +========= +Bug fixes +========= + +* Strip whitespace when listifying admin users by `@jdavcs `_ in `#18656 `_ +============ +Enhancements +============ + +* Make `default_panel_view` a `_by_host` option by `@natefoo `_ in `#18471 `_ +* More datatype deprecation warnings by `@mvdbeek `_ in `#18612 `_ +* Implemented the generic OIDC backend from python-social-auth into Gal… by `@Edmontosaurus `_ in `#18670 `_ + +============= +Other changes +============= +* Backport pod5 datatype by `@TomHarrop `_ in `#18507 `_ +* Backport PR 18630 "Add BlobToolkit to the list of interactive tools" to release_24.1 by `@cat-bro `_ in `#18784 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index 8b66d4c8be59..e4bfd764fdef 100644 --- a/packages/config/setup.cfg +++ b/packages/config/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-config url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 5092affb1e05..5a6e54d4e89d 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -3,11 +3,37 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= + +* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek `_ in `#18494 `_ +* Prevent job submission if input collection element is deleted by `@mvdbeek `_ in `#18517 `_ +* Fix shared caches with extended metadata collection. by `@jmchilton `_ in `#18520 `_ +* Also check dataset.deleted when determining if data can be displayed by `@mvdbeek `_ in `#18547 `_ +* Fix for not-null in 'column_list' object by `@hujambo-dunia `_ in `#18553 `_ +* Fix h5ad metadata by `@nilchia `_ in `#18635 `_ +* Don't set file size to zero by `@mvdbeek `_ in `#18653 `_ +* Make sure we set file size also for purged outputs by `@mvdbeek `_ in `#18681 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek `_ in `#18802 `_ +* Make pylibmagic import optional by `@mvdbeek `_ in `#18813 `_ +* Ignore converted datasets in invalid input states by `@mvdbeek `_ in `#18850 `_ +* Fix discovered outputs with directory metadata and distributed object by `@mvdbeek `_ in `#18855 `_ +* Raise MessageException instead of assertions on rerun problems by `@mvdbeek `_ in `#18858 `_ +* Fix wrong final state when init_from is used by `@mvdbeek `_ in `#18871 `_ +* Fix history import when parent_hda not serialized by `@mvdbeek `_ in `#18873 `_ + +============= +Other changes +============= +* Backport pod5 datatype by `@TomHarrop `_ in `#18507 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index 4d8cee887fd9..450a66916897 100644 --- a/packages/data/setup.cfg +++ b/packages/data/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-data url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index 0827590918d1..a1c537b77345 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ - +------------------- +24.1.2 (2024-09-25) +------------------- +No recorded changes since last release ------------------- 24.1.1 (2024-07-02) diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index 198052e2cc25..eabac412a0a8 100644 --- a/packages/files/setup.cfg +++ b/packages/files/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-files url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index c43f9b0c30dc..409df54e7732 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -3,11 +3,16 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= +* Retry container monitor POST if it fails (don't assume it succeeded) by `@natefoo `_ in `#18863 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index d5f7f2bf4379..295f6528b505 100644 --- a/packages/job_execution/setup.cfg +++ b/packages/job_execution/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-job-execution url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 76b0afce976b..65672b77b3a0 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ - +------------------- +24.1.2 (2024-09-25) +------------------- +No recorded changes since last release ------------------- 24.1.1 (2024-07-02) diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index bb20a15f6637..a46a3685f144 100644 --- a/packages/job_metrics/setup.cfg +++ b/packages/job_metrics/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-job-metrics url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index e1fcd22d984f..bf47150055bb 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ - +------------------- +24.1.2 (2024-09-25) +------------------- +No recorded changes since last release ------------------- 24.1.1 (2024-07-02) diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index 6dbcdaafcb19..5875c9eaafe8 100644 --- a/packages/navigation/setup.cfg +++ b/packages/navigation/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-navigation url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index ffcff6f795dc..3eef2e167999 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -3,11 +3,16 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= +* Fix shared caches with extended metadata collection. by `@jmchilton `_ in `#18520 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index 38a0e8cf40b8..d700c8e59f2b 100644 --- a/packages/objectstore/setup.cfg +++ b/packages/objectstore/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-objectstore url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst index 0fafdcb684cd..5f30f1ec9783 100644 --- a/packages/schema/HISTORY.rst +++ b/packages/schema/HISTORY.rst @@ -3,11 +3,27 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= + +* Handle error when workflow is unowned in Invocation view by `@ahmedhamidawan `_ in `#18730 `_ +* Fix datatype validation of newly built collection by `@mvdbeek `_ in `#18738 `_ +* Fix job summary for optional unset job data inputs by `@mvdbeek `_ in `#18754 `_ +* Fix ``TypeError`` from Pydantic 2.9.0 by `@nsoranzo `_ in `#18788 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Make all fields optional for HelpForumPost by `@davelopez `_ in `#18839 `_ + +============ +Enhancements +============ +* Include workflow invocation id in exception logs by `@mvdbeek `_ in `#18594 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index 21987bc30fb4..c6bbf4ec1778 100644 --- a/packages/schema/setup.cfg +++ b/packages/schema/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-schema url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 1b5017e44597..16a90b5b1249 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ - +------------------- +24.1.2 (2024-09-25) +------------------- +No recorded changes since last release ------------------- 24.1.1 (2024-07-02) diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index 799669cc8903..d90a94698378 100644 --- a/packages/selenium/setup.cfg +++ b/packages/selenium/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-selenium url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index 5e9ebad174f1..b45d74ca3ebb 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -3,11 +3,28 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= +* Prevent job submission if input collection element is deleted by `@mvdbeek `_ in `#18517 `_ +* Fix view parameter type in Job index API by `@davelopez `_ in `#18521 `_ +* Fix map over calculation for runtime inputs by `@mvdbeek `_ in `#18535 `_ +* Fix Archive header encoding by `@arash77 `_ in `#18583 `_ +* Don't set file size to zero by `@mvdbeek `_ in `#18653 `_ +* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek `_ in `#18661 `_ +* Fix change datatype PJA on expression tool data outputs by `@mvdbeek `_ in `#18691 `_ +* Fix subworkflow scheduling for delayed subworkflow steps connected to data inputs by `@mvdbeek `_ in `#18731 `_ +* Catch and display exceptions when importing malformatted yaml workflows by `@mvdbeek `_ in `#18734 `_ +* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek `_ in `#18751 `_ +* Fix copying workflow with subworkflow step for step that you own by `@mvdbeek `_ in `#18802 `_ +* Raise MessageException instead of assertions on rerun problems by `@mvdbeek `_ in `#18858 `_ +* Fix data_column ref to nested collection by `@mvdbeek `_ in `#18875 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index 8fc3a5dbc334..680f9b59e788 100644 --- a/packages/test_api/setup.cfg +++ b/packages/test_api/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-test-api url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index 7867cc9a8686..65168be1c061 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -3,11 +3,18 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= +* Fix infinitely delayed workflow scheduling if skipped step creates HDCA by `@mvdbeek `_ in `#18751 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Fix data_column ref to nested collection by `@mvdbeek `_ in `#18875 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index 497247d478d5..26939a4cb6ba 100644 --- a/packages/test_base/setup.cfg +++ b/packages/test_base/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-test-base url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 77740d14fb96..1a7fb845bbc4 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ - +------------------- +24.1.2 (2024-09-25) +------------------- +No recorded changes since last release ------------------- 24.1.1 (2024-07-02) diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index c1de1fed8578..02c0ae6c17f6 100644 --- a/packages/test_driver/setup.cfg +++ b/packages/test_driver/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-test-driver url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index efd9ed446874..404fb4d6db11 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ - +------------------- +24.1.2 (2024-09-25) +------------------- +No recorded changes since last release ------------------- 24.1.1 (2024-07-02) diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg index bb38254a06b8..a85c3bce1b7c 100644 --- a/packages/tool_shed/setup.cfg +++ b/packages/tool_shed/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-tool-shed url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index 16fa70ea4b66..0e630494bed2 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -3,11 +3,23 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= + +* Handle all requests error in ``ApiBiotoolsMetadataSource._raw_get_metadata`` by `@nsoranzo `_ in `#18510 `_ +* xsd: allow `change_format` and `actions` also in statically defined collection elements, and break recursion by `@bernt-matthias `_ in `#18605 `_ + +============ +Enhancements +============ +* Make `default_panel_view` a `_by_host` option by `@natefoo `_ in `#18471 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index 194481687d64..3ab01b2ce843 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-tool-util url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index ebc29d06751a..ff76ec68d04b 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ - +------------------- +24.1.2 (2024-09-25) +------------------- +No recorded changes since last release ------------------- 24.1.1 (2024-07-02) diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index c236c2202b8b..981707752a62 100644 --- a/packages/tours/setup.cfg +++ b/packages/tours/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-tours url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index fed3f29e564a..472ce37790b7 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -3,11 +3,23 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= + +* Fix Archive header encoding by `@arash77 `_ in `#18583 `_ +* File source and object store instance api fixes by `@mvdbeek `_ in `#18685 `_ + +============ +Enhancements +============ +* Use smtplib send_message to support utf-8 chars in to and from by `@mvdbeek `_ in `#18805 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index 08067a739317..f8ed152bcaeb 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-util url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index a8daf79a97af..de7face2bee5 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -3,11 +3,43 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + + +========= +Bug fixes +========= + +* Return generic message for password reset email by `@ahmedhamidawan `_ in `#18479 `_ +* Fix view parameter type in Job index API by `@davelopez `_ in `#18521 `_ +* Check if dataset has any data before running provider checks by `@mvdbeek `_ in `#18526 `_ +* Raise appropriate exception if ldda not found by `@mvdbeek `_ in `#18569 `_ +* Close install model session when request ends by `@mvdbeek `_ in `#18629 `_ +* Fix resume_paused_jobs if no session provided by `@mvdbeek `_ in `#18640 `_ +* Fix extract workflow from history when implicit collection has no jobs by `@mvdbeek `_ in `#18661 `_ +* Return error when following a link to a non-ready display application by `@mvdbeek `_ in `#18672 `_ +* Only load authnz routes when oidc enabled by `@mvdbeek `_ in `#18683 `_ +* File source and object store instance api fixes by `@mvdbeek `_ in `#18685 `_ +* Fix sorting users in admin by last login by `@jdavcs `_ in `#18694 `_ +* Fix resume paused jobs response handling by `@dannon `_ in `#18733 `_ +* Fix wrong extension on pick data output by `@mvdbeek `_ in `#18798 `_ +* Tighten TRS url check by `@mvdbeek `_ in `#18841 `_ +* Fix Workflow index bookmark filter by `@itisAliRH `_ in `#18842 `_ +* Extend on disk checks to running, queued and error states by `@mvdbeek `_ in `#18846 `_ +============ +Enhancements +============ + +* Make `default_panel_view` a `_by_host` option by `@natefoo `_ in `#18471 `_ + +============= +Other changes +============= +* Fix check dataset check by `@mvdbeek `_ in `#18856 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index dfbb85e86dc0..ceb404777818 100644 --- a/packages/web_apps/setup.cfg +++ b/packages/web_apps/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-web-apps url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index f09158a5f388..cc4a2f4b5d34 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -3,11 +3,18 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ +------------------- +24.1.2 (2024-09-25) +------------------- + +========= +Bug fixes +========= +* Increase API robustness to invalid requests, improve compressed data serving by `@mvdbeek `_ in `#18494 `_ +* Apply statsd arg sanitization to all pages by `@mvdbeek `_ in `#18509 `_ +* Close install model session when request ends by `@mvdbeek `_ in `#18629 `_ ------------------- 24.1.1 (2024-07-02) diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index 083f8622406d..0291ca017c09 100644 --- a/packages/web_framework/setup.cfg +++ b/packages/web_framework/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-web-framework url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index 91460bc9610d..be5f02f07a0a 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -3,11 +3,11 @@ History .. to_doc ------------ -24.1.2.dev0 ------------ - +------------------- +24.1.2 (2024-09-25) +------------------- +No recorded changes since last release ------------------- 24.1.1 (2024-07-02) diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index 2974323c3b3f..b709dc1f6e80 100644 --- a/packages/web_stack/setup.cfg +++ b/packages/web_stack/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-web-stack url = https://github.com/galaxyproject/galaxy -version = 24.1.2.dev0 +version = 24.1.2 [options] include_package_data = True From a788fbdc6de156ef69d0d41cd52b31b726ee25b4 Mon Sep 17 00:00:00 2001 From: Matthias Bernt Date: Wed, 25 Sep 2024 14:29:29 +0200 Subject: [PATCH 7/7] Start work on 24.1.3.dev0 --- lib/galaxy/version.py | 2 +- packages/app/HISTORY.rst | 6 ++++++ packages/app/setup.cfg | 2 +- packages/auth/HISTORY.rst | 6 ++++++ packages/auth/setup.cfg | 2 +- packages/config/HISTORY.rst | 6 ++++++ packages/config/setup.cfg | 2 +- packages/data/HISTORY.rst | 6 ++++++ packages/data/setup.cfg | 2 +- packages/files/HISTORY.rst | 6 ++++++ packages/files/setup.cfg | 2 +- packages/job_execution/HISTORY.rst | 6 ++++++ packages/job_execution/setup.cfg | 2 +- packages/job_metrics/HISTORY.rst | 6 ++++++ packages/job_metrics/setup.cfg | 2 +- packages/navigation/HISTORY.rst | 6 ++++++ packages/navigation/setup.cfg | 2 +- packages/objectstore/HISTORY.rst | 6 ++++++ packages/objectstore/setup.cfg | 2 +- packages/schema/HISTORY.rst | 6 ++++++ packages/schema/setup.cfg | 2 +- packages/selenium/HISTORY.rst | 6 ++++++ packages/selenium/setup.cfg | 2 +- packages/test_api/HISTORY.rst | 6 ++++++ packages/test_api/setup.cfg | 2 +- packages/test_base/HISTORY.rst | 6 ++++++ packages/test_base/setup.cfg | 2 +- packages/test_driver/HISTORY.rst | 6 ++++++ packages/test_driver/setup.cfg | 2 +- packages/tool_shed/HISTORY.rst | 6 ++++++ packages/tool_shed/setup.cfg | 2 +- packages/tool_util/HISTORY.rst | 6 ++++++ packages/tool_util/setup.cfg | 2 +- packages/tours/HISTORY.rst | 6 ++++++ packages/tours/setup.cfg | 2 +- packages/util/HISTORY.rst | 6 ++++++ packages/util/setup.cfg | 2 +- packages/web_apps/HISTORY.rst | 6 ++++++ packages/web_apps/setup.cfg | 2 +- packages/web_framework/HISTORY.rst | 6 ++++++ packages/web_framework/setup.cfg | 2 +- packages/web_stack/HISTORY.rst | 6 ++++++ packages/web_stack/setup.cfg | 2 +- 43 files changed, 148 insertions(+), 22 deletions(-) diff --git a/lib/galaxy/version.py b/lib/galaxy/version.py index 8447b0537e06..d7d7f3f7f491 100644 --- a/lib/galaxy/version.py +++ b/lib/galaxy/version.py @@ -1,3 +1,3 @@ VERSION_MAJOR = "24.1" -VERSION_MINOR = "2" +VERSION_MINOR = "3.dev0" VERSION = VERSION_MAJOR + (f".{VERSION_MINOR}" if VERSION_MINOR else "") diff --git a/packages/app/HISTORY.rst b/packages/app/HISTORY.rst index 6b4fe789a1f3..27a82fd91ccd 100644 --- a/packages/app/HISTORY.rst +++ b/packages/app/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/app/setup.cfg b/packages/app/setup.cfg index 8d067b1afe6d..80e4d38c3d85 100644 --- a/packages/app/setup.cfg +++ b/packages/app/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-app url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/auth/HISTORY.rst b/packages/auth/HISTORY.rst index 72450a70903e..b46693de1bb3 100644 --- a/packages/auth/HISTORY.rst +++ b/packages/auth/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/auth/setup.cfg b/packages/auth/setup.cfg index 25b71dc16efa..ab82a95b3be2 100644 --- a/packages/auth/setup.cfg +++ b/packages/auth/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-auth url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/config/HISTORY.rst b/packages/config/HISTORY.rst index ecf0f191d0e4..e36fc636cb1f 100644 --- a/packages/config/HISTORY.rst +++ b/packages/config/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/config/setup.cfg b/packages/config/setup.cfg index e4bfd764fdef..68a09c9de456 100644 --- a/packages/config/setup.cfg +++ b/packages/config/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-config url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/data/HISTORY.rst b/packages/data/HISTORY.rst index 5a6e54d4e89d..3b7ca75f5722 100644 --- a/packages/data/HISTORY.rst +++ b/packages/data/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/data/setup.cfg b/packages/data/setup.cfg index 450a66916897..809981ea6394 100644 --- a/packages/data/setup.cfg +++ b/packages/data/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-data url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/files/HISTORY.rst b/packages/files/HISTORY.rst index a1c537b77345..8777207afa0f 100644 --- a/packages/files/HISTORY.rst +++ b/packages/files/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/files/setup.cfg b/packages/files/setup.cfg index eabac412a0a8..85b2493e0f5b 100644 --- a/packages/files/setup.cfg +++ b/packages/files/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-files url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/job_execution/HISTORY.rst b/packages/job_execution/HISTORY.rst index 409df54e7732..3f2f246b5331 100644 --- a/packages/job_execution/HISTORY.rst +++ b/packages/job_execution/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/job_execution/setup.cfg b/packages/job_execution/setup.cfg index 295f6528b505..1dfa56e605e2 100644 --- a/packages/job_execution/setup.cfg +++ b/packages/job_execution/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-job-execution url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/job_metrics/HISTORY.rst b/packages/job_metrics/HISTORY.rst index 65672b77b3a0..025d1cb59bcf 100644 --- a/packages/job_metrics/HISTORY.rst +++ b/packages/job_metrics/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/job_metrics/setup.cfg b/packages/job_metrics/setup.cfg index a46a3685f144..83ce8bebcf0e 100644 --- a/packages/job_metrics/setup.cfg +++ b/packages/job_metrics/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-job-metrics url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/navigation/HISTORY.rst b/packages/navigation/HISTORY.rst index bf47150055bb..7c2eb4dde9ff 100644 --- a/packages/navigation/HISTORY.rst +++ b/packages/navigation/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/navigation/setup.cfg b/packages/navigation/setup.cfg index 5875c9eaafe8..63851150c254 100644 --- a/packages/navigation/setup.cfg +++ b/packages/navigation/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-navigation url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/objectstore/HISTORY.rst b/packages/objectstore/HISTORY.rst index 3eef2e167999..bbf9af4264fa 100644 --- a/packages/objectstore/HISTORY.rst +++ b/packages/objectstore/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/objectstore/setup.cfg b/packages/objectstore/setup.cfg index d700c8e59f2b..986fd23622e0 100644 --- a/packages/objectstore/setup.cfg +++ b/packages/objectstore/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-objectstore url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/schema/HISTORY.rst b/packages/schema/HISTORY.rst index 5f30f1ec9783..eab78124ea70 100644 --- a/packages/schema/HISTORY.rst +++ b/packages/schema/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/schema/setup.cfg b/packages/schema/setup.cfg index c6bbf4ec1778..d8d9801ffcd5 100644 --- a/packages/schema/setup.cfg +++ b/packages/schema/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-schema url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/selenium/HISTORY.rst b/packages/selenium/HISTORY.rst index 16a90b5b1249..514f1cd8b30d 100644 --- a/packages/selenium/HISTORY.rst +++ b/packages/selenium/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/selenium/setup.cfg b/packages/selenium/setup.cfg index d90a94698378..6e6e3028e5a0 100644 --- a/packages/selenium/setup.cfg +++ b/packages/selenium/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-selenium url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/test_api/HISTORY.rst b/packages/test_api/HISTORY.rst index b45d74ca3ebb..9c111a54405c 100644 --- a/packages/test_api/HISTORY.rst +++ b/packages/test_api/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/test_api/setup.cfg b/packages/test_api/setup.cfg index 680f9b59e788..e12a23480d30 100644 --- a/packages/test_api/setup.cfg +++ b/packages/test_api/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-test-api url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/test_base/HISTORY.rst b/packages/test_base/HISTORY.rst index 65168be1c061..8ff6be4ce45b 100644 --- a/packages/test_base/HISTORY.rst +++ b/packages/test_base/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/test_base/setup.cfg b/packages/test_base/setup.cfg index 26939a4cb6ba..10bf9226dfce 100644 --- a/packages/test_base/setup.cfg +++ b/packages/test_base/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-test-base url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/test_driver/HISTORY.rst b/packages/test_driver/HISTORY.rst index 1a7fb845bbc4..3c7b1543b69a 100644 --- a/packages/test_driver/HISTORY.rst +++ b/packages/test_driver/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/test_driver/setup.cfg b/packages/test_driver/setup.cfg index 02c0ae6c17f6..7b17e7629764 100644 --- a/packages/test_driver/setup.cfg +++ b/packages/test_driver/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-test-driver url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/tool_shed/HISTORY.rst b/packages/tool_shed/HISTORY.rst index 404fb4d6db11..4bbe31d51aa5 100644 --- a/packages/tool_shed/HISTORY.rst +++ b/packages/tool_shed/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/tool_shed/setup.cfg b/packages/tool_shed/setup.cfg index a85c3bce1b7c..7a0edb5c9b86 100644 --- a/packages/tool_shed/setup.cfg +++ b/packages/tool_shed/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-tool-shed url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/tool_util/HISTORY.rst b/packages/tool_util/HISTORY.rst index 0e630494bed2..d82cb227c96a 100644 --- a/packages/tool_util/HISTORY.rst +++ b/packages/tool_util/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg index 3ab01b2ce843..321d9bbfb8e5 100644 --- a/packages/tool_util/setup.cfg +++ b/packages/tool_util/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-tool-util url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/tours/HISTORY.rst b/packages/tours/HISTORY.rst index ff76ec68d04b..7a53137118c6 100644 --- a/packages/tours/HISTORY.rst +++ b/packages/tours/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/tours/setup.cfg b/packages/tours/setup.cfg index 981707752a62..a3dc6338c312 100644 --- a/packages/tours/setup.cfg +++ b/packages/tours/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-tours url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/util/HISTORY.rst b/packages/util/HISTORY.rst index 472ce37790b7..befaeb6789f5 100644 --- a/packages/util/HISTORY.rst +++ b/packages/util/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/util/setup.cfg b/packages/util/setup.cfg index f8ed152bcaeb..fdef15f66594 100644 --- a/packages/util/setup.cfg +++ b/packages/util/setup.cfg @@ -28,7 +28,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-util url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/web_apps/HISTORY.rst b/packages/web_apps/HISTORY.rst index de7face2bee5..4444fe0f88e6 100644 --- a/packages/web_apps/HISTORY.rst +++ b/packages/web_apps/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/web_apps/setup.cfg b/packages/web_apps/setup.cfg index ceb404777818..e1b5a1b3df03 100644 --- a/packages/web_apps/setup.cfg +++ b/packages/web_apps/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-web-apps url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/web_framework/HISTORY.rst b/packages/web_framework/HISTORY.rst index cc4a2f4b5d34..a0bd6b14bb14 100644 --- a/packages/web_framework/HISTORY.rst +++ b/packages/web_framework/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/web_framework/setup.cfg b/packages/web_framework/setup.cfg index 0291ca017c09..818b3bef6076 100644 --- a/packages/web_framework/setup.cfg +++ b/packages/web_framework/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-web-framework url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True diff --git a/packages/web_stack/HISTORY.rst b/packages/web_stack/HISTORY.rst index be5f02f07a0a..e7ebb3235a0a 100644 --- a/packages/web_stack/HISTORY.rst +++ b/packages/web_stack/HISTORY.rst @@ -3,6 +3,12 @@ History .. to_doc +----------- +24.1.3.dev0 +----------- + + + ------------------- 24.1.2 (2024-09-25) ------------------- diff --git a/packages/web_stack/setup.cfg b/packages/web_stack/setup.cfg index b709dc1f6e80..dd04dc39fe43 100644 --- a/packages/web_stack/setup.cfg +++ b/packages/web_stack/setup.cfg @@ -27,7 +27,7 @@ long_description = file: README.rst, HISTORY.rst long_description_content_type = text/x-rst name = galaxy-web-stack url = https://github.com/galaxyproject/galaxy -version = 24.1.2 +version = 24.1.3.dev0 [options] include_package_data = True