Fix bug in paired/unpaired.

galaxyproject · Jan 23, 2025 · 3716548 · 3716548
1 parent df0e99f
commit 3716548
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Showing 3 changed files with 18 additions and 15 deletions.
diff --git a/lib/galaxy/model/dataset_collections/adapters.py b/lib/galaxy/model/dataset_collections/adapters.py
@@ -45,7 +45,7 @@ def dataset_instances(self):
     def elements(self):
         raise NotImplementedError()
 
-    def to_adapter_model(self, adapting):
+    def to_adapter_model(self):
         # json kwds to recover state from database after the job has been
         # recorded
         raise NotImplementedError()
@@ -110,12 +110,19 @@ def elements(self):
     def adapting(self):
         return self._dce
 
+    @property
+    def _adapting_src_dict(self):
+        return {
+            "src": "dce",
+            "id": self._dce.id,
+        }
+
 
 class PromoteCollectionElementToCollectionAdapter(DCECollectionAdapter):
     # allow a singleton list element to act as paired_or_unpaired collection
 
-    def to_adapter_model(self, adapting) -> AdaptedDataCollectionPromoteCollectionElementToCollectionRequestInternal:
-        adapting_model = DatasetCollectionElementReference.model_validate(adapting)
+    def to_adapter_model(self) -> AdaptedDataCollectionPromoteCollectionElementToCollectionRequestInternal:
+        adapting_model = DatasetCollectionElementReference.model_validate(self._adapting_src_dict)
         return AdaptedDataCollectionPromoteCollectionElementToCollectionRequestInternal(
             src="CollectionAdapter",
             adapter_type="PromoteCollectionElementToCollection",
@@ -134,7 +141,11 @@ def __init__(self, hda: "HistoryDatasetAssociation", collection_type: str):
         self._hda = hda
         self._collection_type = collection_type
 
-    def to_adapter_model(self, adapting) -> AdaptedDataCollectionPromoteDatasetToCollectionRequestInternal:
+    def to_adapter_model(self) -> AdaptedDataCollectionPromoteDatasetToCollectionRequestInternal:
+        adapting = {
+            "src": "hda",
+            "id": self._hda.id,
+        }
         adapting_model = DataRequestInternalHda.model_validate(adapting)
         return AdaptedDataCollectionPromoteDatasetToCollectionRequestInternal(
             src="CollectionAdapter",
@@ -186,7 +197,7 @@ def __init__(self, elements: List["TransientCollectionAdapterDatasetInstanceElem
         self._collection_type = collection_type
         self._elements = elements
 
-    def to_adapter_model(self, adapting) -> AdaptedDataCollectionPromoteDatasetsToCollectionRequestInternal:
+    def to_adapter_model(self) -> AdaptedDataCollectionPromoteDatasetsToCollectionRequestInternal:
         element_models = []
         for element in self._elements:
             element_model = AdapterElementRequestInternal(

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
@@ -949,7 +949,7 @@ def _record_inputs(self, trans, tool, job, incoming, inp_data, inp_dataset_colle
                     # of datasets -> collection adaption because it isn't clear where to track that
                     # (see elif isinstance(adapting, list) branch below).
                     adapting = adapter.adapting
-                    adapter_model = cast(BaseModel, adapter.to_adapter_model(adapting))
+                    adapter_model = cast(BaseModel, adapter.to_adapter_model())
                     if isinstance(adapting, model.DatasetCollectionElement):
                         job.add_input_dataset_collection_element(
                             name, adapting, adapter_json=adapter_model.model_dump()

diff --git a/lib/galaxy/tools/parameters/basic.py b/lib/galaxy/tools/parameters/basic.py
@@ -2875,13 +2875,7 @@ def history_item_to_json(value, app, use_security):
     collection_adapter: Optional[CollectionAdapter] = None
     if isinstance(value, CollectionAdapter):
         collection_adapter = value
-        value = value.adapting
-        if isinstance(value, list):
-            # if we are not just adapting one thing... skip the rest of this
-            # and just serialize the stuff we know we want anyway. Perhaps all
-            # this should just be the only path through. The CollectionAdapter
-            # should know what to do with just use_security I think?
-            return collection_adapter.to_adapter_model(value).dict()
+        return collection_adapter.to_adapter_model().dict()
     if isinstance(value, MutableMapping) and "src" in value and "id" in value:
         return value
     elif isinstance(value, DatasetCollectionElement):
@@ -2898,6 +2892,4 @@ def history_item_to_json(value, app, use_security):
     if src is not None:
         object_id = cached_id(value)
         rval = {"id": app.security.encode_id(object_id) if use_security else object_id, "src": src}
-        if collection_adapter:
-            rval = collection_adapter.to_adapter_model(rval).dict()
         return rval