From 1b1094be215437c272e241bd4e351ba019ef3e59 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Sun, 21 Apr 2024 11:48:46 +0200
Subject: [PATCH] Set (copied) output hid before queuing job

Otherwise we may end up with a history item that either temporarily or
permanently lacks a hid.

This could currently be encountered via implicit conversion that set
`visible=False` in the when calling `datatype.convert_dataset`.
---
 lib/galaxy/datatypes/data.py                   |  6 +++++-
 .../display_applications/parameters.py         | 18 +-----------------
 lib/galaxy/datatypes/protocols.py              |  2 ++
 lib/galaxy/model/__init__.py                   |  9 +++------
 4 files changed, 11 insertions(+), 24 deletions(-)

diff --git a/lib/galaxy/datatypes/data.py b/lib/galaxy/datatypes/data.py
index cad936f06b1..1c8c5382783 100644
--- a/lib/galaxy/datatypes/data.py
+++ b/lib/galaxy/datatypes/data.py
@@ -842,7 +842,11 @@ class Data(metaclass=DataMeta):
         # Make the target datatype available to the converter
         params["__target_datatype__"] = target_type
         # Run converter, job is dispatched through Queue
-        job, converted_datasets, *_ = converter.execute(trans, incoming=params, set_output_hid=visible, history=history)
+        job, converted_datasets, *_ = converter.execute(
+            trans, incoming=params, set_output_hid=visible, history=history, flush_job=False
+        )
+        for converted_dataset in converted_datasets.values():
+            original_dataset.attach_implicitly_converted_dataset(trans.sa_session, converted_dataset, target_type)
         trans.app.job_manager.enqueue(job, tool=converter)
         if len(params) > 0:
             trans.log_event(f"Converter params: {str(params)}", tool_id=converter.id)
diff --git a/lib/galaxy/datatypes/display_applications/parameters.py b/lib/galaxy/datatypes/display_applications/parameters.py
index 25e90032f24..7d022d38d1f 100644
--- a/lib/galaxy/datatypes/display_applications/parameters.py
+++ b/lib/galaxy/datatypes/display_applications/parameters.py
@@ -11,7 +11,6 @@ from urllib.parse import quote_plus
 
 from galaxy.datatypes.data import Data
 from galaxy.model import DatasetInstance
-from galaxy.model.base import transaction
 from galaxy.schema.schema import DatasetState
 from galaxy.util import string_as_bool
 from galaxy.util.template import fill_template
@@ -182,22 +181,7 @@ class DisplayApplicationDataParameter(DisplayApplicationParameter):
                 if target_ext and not converted_dataset:
                     if isinstance(data, DisplayDataValueWrapper):
                         data = data.value
-                    new_data = next(
-                        iter(
-                            data.datatype.convert_dataset(
-                                trans, data, target_ext, return_output=True, visible=False
-                            ).values()
-                        )
-                    )
-                    new_data.hid = data.hid
-                    new_data.name = data.name
-                    trans.sa_session.add(new_data)
-                    assoc = trans.app.model.ImplicitlyConvertedDatasetAssociation(
-                        parent=data, file_type=target_ext, dataset=new_data, metadata_safe=False
-                    )
-                    trans.sa_session.add(assoc)
-                    with transaction(trans.sa_session):
-                        trans.sa_session.commit()
+                    data.datatype.convert_dataset(trans, data, target_ext, return_output=True, visible=False)
                 elif converted_dataset and converted_dataset.state == DatasetState.ERROR:
                     raise Exception(f"Dataset conversion failed for data parameter: {self.name}")
         return self.get_value(other_values, dataset_hash, user_hash, trans)
diff --git a/lib/galaxy/datatypes/protocols.py b/lib/galaxy/datatypes/protocols.py
index bbd702538b7..5bc07c20c9f 100644
--- a/lib/galaxy/datatypes/protocols.py
+++ b/lib/galaxy/datatypes/protocols.py
@@ -85,5 +85,7 @@ class DatasetProtocol(
 
     def set_peek(self) -> None: ...
 
+    def attach_implicitly_converted_dataset(self, session, new_dataset, target_ext: str) -> None: ...
+
 
 class DatasetHasHidProtocol(DatasetProtocol, HasHid, Protocol): ...
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
index 3e78689a2a3..ade3ed17d68 100644
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -4736,7 +4736,7 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
             raise NoConverterException(f"A dependency ({dependency}) is missing a converter.")
         except KeyError:
             pass  # No deps
-        new_dataset = next(
+        return next(
             iter(
                 self.datatype.convert_dataset(
                     trans,
@@ -4750,7 +4750,6 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
                 ).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
@@ -4760,9 +4759,6 @@ class DatasetInstance(RepresentById, UsesCreateAndUpdateTime, _HasTable):
         )
         session.add(new_dataset)
         session.add(assoc)
-        with transaction(session):
-            session.commit()
-        return new_dataset
 
     def copy_attributes(self, new_dataset):
         """
@@ -5134,7 +5130,8 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
                 self.tags.append(copied_tag)
 
     def copy_attributes(self, new_dataset):
-        new_dataset.hid = self.hid
+        if new_dataset.hid is None:
+            new_dataset.hid = self.hid
 
     def to_library_dataset_dataset_association(
         self,