[23.2] Backport model store fixes

lib/galaxy/model/__init__.py

@@ -4674,12 +4674,14 @@ def get_converted_dataset(self, trans, target_ext, target_context=None, history=
                 ).values()
             )
         )
+        return self.attach_implicitly_converted_dataset(trans.sa_session, new_dataset, target_ext)
+
+    def attach_implicitly_converted_dataset(self, session, new_dataset, target_ext: str):
         new_dataset.name = self.name
         self.copy_attributes(new_dataset)
         assoc = ImplicitlyConvertedDatasetAssociation(
             parent=self, file_type=target_ext, dataset=new_dataset, metadata_safe=False
         )
-        session = trans.sa_session
         session.add(new_dataset)
         session.add(assoc)
         with transaction(session):
@@ -6016,7 +6018,7 @@ def inheritable(self):
         return True  # always allow inheriting, used for replacement
 
 
-class ImplicitlyConvertedDatasetAssociation(Base, RepresentById):
+class ImplicitlyConvertedDatasetAssociation(Base, Serializable):
     __tablename__ = "implicitly_converted_dataset_association"
 
     id = Column(Integer, primary_key=True)
@@ -6054,22 +6056,34 @@ class ImplicitlyConvertedDatasetAssociation(Base, RepresentById):
     )
 
     def __init__(
-        self, id=None, parent=None, dataset=None, file_type=None, deleted=False, purged=False, metadata_safe=True
+        self,
+        id=None,
+        parent=None,
+        dataset=None,
+        file_type=None,
+        deleted=False,
+        purged=False,
+        metadata_safe=True,
+        for_import=False,
     ):
         self.id = id
         add_object_to_object_session(self, dataset)
         if isinstance(dataset, HistoryDatasetAssociation):
             self.dataset = dataset
         elif isinstance(dataset, LibraryDatasetDatasetAssociation):
             self.dataset_ldda = dataset
-        else:
+        elif not for_import:
             raise AttributeError(f"Unknown dataset type provided for dataset: {type(dataset)}")
+            # else if for import - these connections might not have been included in the store,
+            # recover the data we can?
         if isinstance(parent, HistoryDatasetAssociation):
             self.parent_hda = parent
         elif isinstance(parent, LibraryDatasetDatasetAssociation):
             self.parent_ldda = parent
-        else:
+        elif not for_import:
             raise AttributeError(f"Unknown dataset type provided for parent: {type(parent)}")
+            # else if for import - these connections might not have been included in the store,
+            # recover the data we can?
         self.type = file_type
         self.deleted = deleted
         self.purged = purged
@@ -6089,6 +6103,18 @@ def clear(self, purge=False, delete_dataset=True):
             except Exception as e:
                 log.error(f"Failed to purge associated file ({self.get_file_name()}) from disk: {unicodify(e)}")
 
+    def _serialize(self, id_encoder, serialization_options):
+        rval = dict_for(
+            self,
+            file_type=self.type,
+        )
+        if self.parent_hda:
+            rval["parent_hda"] = serialization_options.get_identifier(id_encoder, self.parent_hda)
+        if self.dataset:
+            rval["hda"] = serialization_options.get_identifier(id_encoder, self.dataset)
+        serialization_options.attach_identifier(id_encoder, self, rval)
+        return rval
+
 
 DEFAULT_COLLECTION_NAME = "Unnamed Collection"
 

lib/galaxy/model/store/__init__.py

@@ -133,12 +133,14 @@
 ATTRS_FILENAME_LIBRARIES = "libraries_attrs.txt"
 ATTRS_FILENAME_LIBRARY_FOLDERS = "library_folders_attrs.txt"
 ATTRS_FILENAME_INVOCATIONS = "invocation_attrs.txt"
+ATTRS_FILENAME_CONVERSIONS = "implicit_dataset_conversions.txt"
 TRACEBACK = "traceback.txt"
 GALAXY_EXPORT_VERSION = "2"
 
 DICT_STORE_ATTRS_KEY_HISTORY = "history"
 DICT_STORE_ATTRS_KEY_DATASETS = "datasets"
 DICT_STORE_ATTRS_KEY_COLLECTIONS = "collections"
+DICT_STORE_ATTRS_KEY_CONVERSIONS = "implicit_dataset_conversions"
 DICT_STORE_ATTRS_KEY_JOBS = "jobs"
 DICT_STORE_ATTRS_KEY_IMPLICIT_COLLECTION_JOBS = "implicit_collection_jobs"
 DICT_STORE_ATTRS_KEY_LIBRARIES = "libraries"
@@ -296,6 +298,10 @@ def invocations_properties(self) -> List[Dict[str, Any]]:
     def collections_properties(self) -> List[Dict[str, Any]]:
         """Return a list of HDCA properties."""
 
+    @abc.abstractmethod
+    def implicit_dataset_conversion_properties(self) -> List[Dict[str, Any]]:
+        """Return a list of ImplicitlyConvertedDatasetAssociation properties."""
+
     @abc.abstractmethod
     def jobs_properties(self) -> List[Dict[str, Any]]:
         """Return a list of jobs properties."""
@@ -385,6 +391,7 @@ def perform_import(
         self._import_collection_instances(object_import_tracker, collections_attrs, history, new_history)
         self._import_collection_implicit_input_associations(object_import_tracker, collections_attrs)
         self._import_collection_copied_associations(object_import_tracker, collections_attrs)
+        self._import_implicit_dataset_conversions(object_import_tracker)
         self._reassign_hids(object_import_tracker, history)
         self._import_jobs(object_import_tracker, history)
         self._import_implicit_collection_jobs(object_import_tracker)
@@ -1001,6 +1008,13 @@ def _reassign_hids(self, object_import_tracker: "ObjectImportTracker", history:
                 history.stage_addition(obj)
             history.add_pending_items()
 
+            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():
+                    to_dataset.hid = from_dataset.hid
+                    self._session_add(to_dataset)
+                self._flush()
+
     def _import_workflow_invocations(
         self, object_import_tracker: "ObjectImportTracker", history: Optional[model.History]
     ) -> None:
@@ -1239,6 +1253,29 @@ def _import_jobs(self, object_import_tracker: "ObjectImportTracker", history: Op
             if object_key in job_attrs:
                 object_import_tracker.jobs_by_key[job_attrs[object_key]] = imported_job
 
+    def _import_implicit_dataset_conversions(self, object_import_tracker: "ObjectImportTracker") -> None:
+        implicit_dataset_conversion_attrs = self.implicit_dataset_conversion_properties()
+        for idc_attrs in implicit_dataset_conversion_attrs:
+            # I don't know what metadata_safe does per se... should we copy this property or
+            # just set it to False?
+            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"]]
+            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:
+                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
+
+            self._session_add(idc)
+
     def _import_implicit_collection_jobs(self, object_import_tracker: "ObjectImportTracker") -> None:
         object_key = self.object_key
 
@@ -1300,6 +1337,9 @@ def _copied_from_object_key(
     return copied_from_object_key
 
 
+HasHid = Union[model.HistoryDatasetAssociation, model.HistoryDatasetCollectionAssociation]
+
+
 class ObjectImportTracker:
     """Keep track of new and existing imported objects.
 
@@ -1317,7 +1357,8 @@ class ObjectImportTracker:
     hda_copied_from_sinks: Dict[ObjectKeyType, ObjectKeyType]
     hdca_copied_from_sinks: Dict[ObjectKeyType, ObjectKeyType]
     jobs_by_key: Dict[ObjectKeyType, model.Job]
-    requires_hid: List[Union[model.HistoryDatasetAssociation, model.HistoryDatasetCollectionAssociation]]
+    requires_hid: List[HasHid]
+    copy_hid_for: Dict[HasHid, HasHid]
 
     def __init__(self) -> None:
         self.libraries_by_key = {}
@@ -1335,6 +1376,7 @@ 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.new_history: Optional[model.History] = None
 
@@ -1418,6 +1460,9 @@ def datasets_properties(
     def collections_properties(self) -> List[Dict[str, Any]]:
         return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_COLLECTIONS) or []
 
+    def implicit_dataset_conversion_properties(self) -> List[Dict[str, Any]]:
+        return self._store_as_dict.get(DICT_STORE_ATTRS_KEY_CONVERSIONS) or []
+
     def library_properties(
         self,
     ) -> List[Dict[str, Any]]:
@@ -1494,6 +1539,9 @@ def datasets_properties(self) -> List[Dict[str, Any]]:
     def collections_properties(self) -> List[Dict[str, Any]]:
         return self._read_list_if_exists(ATTRS_FILENAME_COLLECTIONS)
 
+    def implicit_dataset_conversion_properties(self) -> List[Dict[str, Any]]:
+        return self._read_list_if_exists(ATTRS_FILENAME_CONVERSIONS)
+
     def library_properties(
         self,
     ) -> List[Dict[str, Any]]:
@@ -1860,6 +1908,7 @@ def __init__(
         )
         self.export_files = export_files
         self.included_datasets: Dict[model.DatasetInstance, Tuple[model.DatasetInstance, bool]] = {}
+        self.dataset_implicit_conversions: Dict[model.DatasetInstance, model.ImplicitlyConvertedDatasetAssociation] = {}
         self.included_collections: List[Union[model.DatasetCollection, model.HistoryDatasetCollectionAssociation]] = []
         self.included_libraries: List[model.Library] = []
         self.included_library_folders: List[model.LibraryFolder] = []
@@ -1928,9 +1977,14 @@ def add(src, dest):
             if not os.path.exists(dir_path):
                 os.makedirs(dir_path)
 
-            target_filename = get_export_dataset_filename(as_dict["name"], as_dict["extension"], dataset_hid)
+            conversion = self.dataset_implicit_conversions.get(dataset)
+            conversion_key = (
+                self.serialization_options.get_identifier(self.security, conversion) if conversion else None
+            )
+            target_filename = get_export_dataset_filename(
+                as_dict["name"], as_dict["extension"], dataset_hid, conversion_key=conversion_key
+            )
             arcname = os.path.join(dir_name, target_filename)
-
             src = file_name
             dest = os.path.join(export_directory, arcname)
             add(src, dest)
@@ -1943,7 +1997,10 @@ def add(src, dest):
                 file_list = []
 
             if len(file_list):
-                arcname = os.path.join(dir_name, f"extra_files_path_{dataset_hid}")
+                extra_files_target_filename = get_export_dataset_extra_files_dir_name(
+                    as_dict["name"], as_dict["extension"], dataset_hid, conversion_key=conversion_key
+                )
+                arcname = os.path.join(dir_name, extra_files_target_filename)
                 add(extra_files_path, os.path.join(export_directory, arcname))
                 as_dict["extra_files_path"] = arcname
             else:
@@ -2139,7 +2196,13 @@ def export_history(
             if dataset not in self.included_datasets:
                 if should_include_file:
                     self._ensure_dataset_file_exists(dataset)
-                self.add_dataset(dataset, include_files=should_include_file)
+                if dataset.implicitly_converted_parent_datasets:
+                    # fetching 0th of list but I think this is just a mapping quirk - I can't imagine how there
+                    # would be more than one of these -John
+                    conversion = dataset.implicitly_converted_parent_datasets[0]
+                    self.add_implicit_conversion_dataset(dataset, should_include_file, conversion)
+                else:
+                    self.add_dataset(dataset, include_files=should_include_file)
 
     def export_library(
         self, library: model.Library, include_hidden: bool = False, include_deleted: bool = False
@@ -2218,6 +2281,15 @@ def add_dataset_collection(
         self.collections_attrs.append(collection)
         self.included_collections.append(collection)
 
+    def add_implicit_conversion_dataset(
+        self,
+        dataset: model.DatasetInstance,
+        include_files: bool,
+        conversion: model.ImplicitlyConvertedDatasetAssociation,
+    ) -> None:
+        self.included_datasets[dataset] = (dataset, include_files)
+        self.dataset_implicit_conversions[dataset] = conversion
+
     def add_dataset(self, dataset: model.DatasetInstance, include_files: bool = True) -> None:
         self.included_datasets[dataset] = (dataset, include_files)
 
@@ -2264,6 +2336,10 @@ def to_json(attributes):
         with open(collections_attrs_filename, "w") as collections_attrs_out:
             collections_attrs_out.write(to_json(self.collections_attrs))
 
+        conversions_attrs_filename = os.path.join(export_directory, ATTRS_FILENAME_CONVERSIONS)
+        with open(conversions_attrs_filename, "w") as conversions_attrs_out:
+            conversions_attrs_out.write(to_json(self.dataset_implicit_conversions.values()))
+
         jobs_attrs = []
         for job_id, job_output_dataset_associations in self.job_output_dataset_associations.items():
             output_dataset_mapping: Dict[str, List[Union[str, int]]] = {}
@@ -2387,6 +2463,7 @@ class WriteCrates:
     included_invocations: List[model.WorkflowInvocation]
     export_directory: StrPath
     included_datasets: Dict[model.DatasetInstance, Tuple[model.DatasetInstance, bool]]
+    dataset_implicit_conversions: Dict[model.DatasetInstance, model.ImplicitlyConvertedDatasetAssociation]
     dataset_id_to_path: Dict[int, Tuple[Optional[str], Optional[str]]]
 
     @property
@@ -2891,12 +2968,22 @@ def tar_export_directory(export_directory: StrPath, out_file: StrPath, gzip: boo
             store_archive.add(os.path.join(export_directory, export_path), arcname=export_path)
 
 
-def get_export_dataset_filename(name: str, ext: str, hid: int) -> str:
+def get_export_dataset_filename(name: str, ext: str, hid: int, conversion_key: Optional[str]) -> str:
     """
     Builds a filename for a dataset using its name an extension.
     """
     base = "".join(c in FILENAME_VALID_CHARS and c or "_" for c in name)
-    return f"{base}_{hid}.{ext}"
+    if not conversion_key:
+        return f"{base}_{hid}.{ext}"
+    else:
+        return f"{base}_{hid}_conversion_{conversion_key}.{ext}"
+
+
+def get_export_dataset_extra_files_dir_name(name: str, ext: str, hid: int, conversion_key: Optional[str]) -> str:
+    if not conversion_key:
+        return f"extra_files_path_{hid}"
+    else:
+        return f"extra_files_path_{hid}_conversion_{conversion_key}"
 
 
 def imported_store_for_metadata(

test/unit/data/model/2.txt

@@ -0,0 +1 @@
+converted bed