cherry pick fixes

api/src/opentrons/protocol_engine/state/command_history.py

@@ -97,6 +97,28 @@ def get_all_commands(self) -> List[Command]:
             for command_id in self._all_command_ids
         ]
 
+    def get_filtered_command_ids(
+        self,
+        command_intents: list[CommandIntent] = [
+            CommandIntent.PROTOCOL,
+            CommandIntent.SETUP,
+        ],
+    ) -> List[str]:
+        filtered_command = self._commands_by_id
+        if CommandIntent.FIXIT not in command_intents:
+            filtered_command = {
+                key: val
+                for key, val in self._commands_by_id.items()
+                if val.command.intent != CommandIntent.FIXIT
+            }
+        if CommandIntent.SETUP not in command_intents:
+            filtered_command = {
+                key: val
+                for key, val in filtered_command.items()
+                if val.command.intent != CommandIntent.SETUP
+            }
+        return list(filtered_command.keys())
+
     def get_filtered_queue_ids(self, all_commands: bool) -> list[str]:
         print(list(self.get_fixit_queue_ids()))
         return [
@@ -109,9 +131,15 @@ def get_all_ids(self) -> List[str]:
         """Get all command IDs."""
         return self._all_command_ids
 
-    def get_slice(self, start: int, stop: int) -> List[Command]:
-        """Get a list of commands between start and stop."""
+    def get_slice(
+        self, start: int, stop: int, command_ids: Optional[list[str]] = None
+    ) -> List[Command]:
+        """Get a list of commands between start and stop.""" """Get a list of commands between start and stop."""
         commands = self._all_command_ids[start:stop]
+        selected_command_ids = (
+            command_ids if command_ids is not None else self._all_command_ids
+        )
+        commands = selected_command_ids[start:stop]
         return [self._commands_by_id[command].command for command in commands]
 
     def get_tail_command(self) -> Optional[CommandEntry]:

api/src/opentrons/protocol_engine/state/commands.py

@@ -579,22 +579,8 @@ def get_all(self) -> List[Command]:
         """
         return self._state.command_history.get_all_commands()
 
-    def get_filtered_queue_ids(self, all_commands: bool) -> List[str]:
-        """Get a list of all filtered commands in state.
-
-        Entries are returned in the order of first-added command to last-added command.
-        Replacing a command (to change its status, for example) keeps its place in the
-        ordering.
-
-        If all_commands is True, retunred list will contain all command intents.
-        If False, return list will contain only safe commands.
-        """
-        return self._state.command_history.get_filtered_queue_ids(
-            all_commands=all_commands
-        )
-
     def get_slice(
-        self, cursor: Optional[int], length: int, all_commands: bool
+        self, cursor: Optional[int], length: int, include_fixit_commands: bool
     ) -> CommandSlice:
         """Get a subset of commands around a given cursor.
 
@@ -610,8 +596,8 @@ def get_slice(
             if include_fixit_commands
             else [CommandIntent.PROTOCOL, CommandIntent.SETUP]
         )
-        running_command = self._state.command_history.get_running_command()	        
-        queued_command_ids = self._state.command_history.get_queue_ids()	        
+        running_command = self._state.command_history.get_running_command()
+        queued_command_ids = self._state.command_history.get_queue_ids()
         total_length = len(command_ids)
 
         # TODO(mm, 2024-05-17): This looks like it's attempting to do the same thing

api/src/opentrons/protocol_runner/run_orchestrator.py

@@ -257,7 +257,7 @@ def get_current_command(self) -> Optional[CommandPointer]:
         return self._protocol_engine.state_view.commands.get_current()
 
     def get_command_slice(
-        self, cursor: Optional[int], length: int, all_commands: bool
+        self, cursor: Optional[int], length: int, include_fixit_commands: bool
     ) -> CommandSlice:
         """Get a slice of run commands.
 
@@ -267,7 +267,7 @@ def get_command_slice(
             all_commands: Get all command intents.
         """
         return self._protocol_engine.state_view.commands.get_slice(
-            cursor=cursor, length=length, all_commands=all_commands
+            cursor=cursor, length=length, include_fixit_commands=include_fixit_commands
         )
 
     def get_command_error_slice(

api/tests/opentrons/protocol_engine/state/test_command_view_old.py

@@ -904,7 +904,7 @@ def test_get_current() -> None:
 def test_get_slice_empty() -> None:
     """It should return a slice from the tail if no current command."""
     subject = get_command_view(commands=[])
-    result = subject.get_slice(cursor=0, length=2, all_commands=True)
+    result = subject.get_slice(cursor=0, length=2, include_fixit_commands=True)
 
     assert result == CommandSlice(commands=[], cursor=0, total_length=0)
 
@@ -918,15 +918,15 @@ def test_get_slice() -> None:
 
     subject = get_command_view(commands=[command_1, command_2, command_3, command_4])
 
-    result = subject.get_slice(cursor=1, length=3, all_commands=True)
+    result = subject.get_slice(cursor=1, length=3, include_fixit_commands=True)
 
     assert result == CommandSlice(
         commands=[command_2, command_3, command_4],
         cursor=1,
         total_length=4,
     )
 
-    result = subject.get_slice(cursor=-3, length=10, all_commands=True)
+    result = subject.get_slice(cursor=-3, length=10, include_fixit_commands=True)
 
     assert result == CommandSlice(
         commands=[command_1, command_2, command_3, command_4],
@@ -944,7 +944,7 @@ def test_get_slice_default_cursor_no_current() -> None:
 
     subject = get_command_view(commands=[command_1, command_2, command_3, command_4])
 
-    result = subject.get_slice(cursor=None, length=3, all_commands=True)
+    result = subject.get_slice(cursor=None, length=3, include_fixit_commands=True)
 
     assert result == CommandSlice(
         commands=[command_2, command_3, command_4],
@@ -975,7 +975,7 @@ def test_get_slice_default_cursor_failed_command() -> None:
         failed_command=CommandEntry(index=2, command=command_3),
     )
 
-    result = subject.get_slice(cursor=None, length=3, all_commands=True)
+    result = subject.get_slice(cursor=None, length=3, include_fixit_commands=True)
 
     assert result == CommandSlice(
         commands=[command_3, command_4],
@@ -997,7 +997,7 @@ def test_get_slice_default_cursor_running() -> None:
         running_command_id="command-id-3",
     )
 
-    result = subject.get_slice(cursor=None, length=2, all_commands=True)
+    result = subject.get_slice(cursor=None, length=2, include_fixit_commands=True)
 
     assert result == CommandSlice(
         commands=[command_3, command_4],

robot-server/robot_server/commands/router.py

@@ -161,7 +161,9 @@ async def get_commands_list(
         cursor: Cursor index for the collection response.
         pageLength: Maximum number of items to return.
     """
-    cmd_slice = orchestrator.get_command_slice(cursor=cursor, length=pageLength)
+    cmd_slice = orchestrator.get_command_slice(
+        cursor=cursor, length=pageLength, include_fixit_commands=True
+    )
     commands = cast(List[StatelessCommand], cmd_slice.commands)
     meta = MultiBodyMeta(cursor=cmd_slice.cursor, totalLength=cmd_slice.total_length)
 

robot-server/robot_server/maintenance_runs/maintenance_run_orchestrator_store.py

@@ -226,7 +226,9 @@ def get_command_slice(
             cursor: Requested index of first command in the returned slice.
             length: Length of slice to return.
         """
-        return self.run_orchestrator.get_command_slice(cursor=cursor, length=length)
+        return self.run_orchestrator.get_command_slice(
+            cursor=cursor, length=length, include_fixit_commands=False
+        )
 
     def get_current_command(self) -> Optional[CommandPointer]:
         """Get the "current" command, if any."""

robot-server/robot_server/runs/router/commands_router.py

@@ -285,6 +285,11 @@ async def get_run_commands(
             description="The maximum number of commands in the list to return.",
         ),
     ] = _DEFAULT_COMMAND_LIST_LENGTH,
+    includeFixitCommands: bool = Query(
+        True,
+        description="If `true`, return all commands (protocol, setup, fixit)."
+        " If `false`, only return safe commands (protocol, setup).",
+    ),
 ) -> PydanticResponse[MultiBody[RunCommandSummary, CommandCollectionLinks]]:
     """Get a summary of a set of commands in a run.
 
@@ -293,12 +298,15 @@ async def get_run_commands(
         cursor: Cursor index for the collection response.
         pageLength: Maximum number of items to return.
         run_data_manager: Run data retrieval interface.
+        includeFixitCommands: If `true`, return all commands."
+            " If `false`, only return safe commands.
     """
     try:
         command_slice = run_data_manager.get_commands_slice(
             run_id=runId,
             cursor=cursor,
             length=pageLength,
+            include_fixit_commands=includeFixitCommands,
         )
     except RunNotFoundError as e:
         raise RunNotFound.from_exc(e).as_error(status.HTTP_404_NOT_FOUND) from e

robot-server/robot_server/runs/run_data_manager.py

@@ -373,20 +373,24 @@ def get_commands_slice(
         run_id: str,
         cursor: Optional[int],
         length: int,
+        include_fixit_commands: bool,
     ) -> CommandSlice:
         """Get a slice of run commands.
 
         Args:
             run_id: ID of the run.
             cursor: Requested index of first command in the returned slice.
             length: Length of slice to return.
+            include_fixit_commands: Include fixit commands.
 
         Raises:
             RunNotFoundError: The given run identifier was not found in the database.
         """
         if run_id == self._run_orchestrator_store.current_run_id:
             return self._run_orchestrator_store.get_command_slice(
-                cursor=cursor, length=length
+                cursor=cursor,
+                length=length,
+                include_fixit_commands=include_fixit_commands,
             )
 
         # Let exception propagate

robot-server/robot_server/runs/run_orchestrator_store.py

@@ -330,17 +330,18 @@ def get_current_command(self) -> Optional[CommandPointer]:
         return self.run_orchestrator.get_current_command()
 
     def get_command_slice(
-        self,
-        cursor: Optional[int],
-        length: int,
+        self, cursor: Optional[int], length: int, include_fixit_commands: bool
     ) -> CommandSlice:
         """Get a slice of run commands.
 
         Args:
             cursor: Requested index of first command in the returned slice.
             length: Length of slice to return.
+            include_fixit_commands: Include fixit commands.
         """
-        return self.run_orchestrator.get_command_slice(cursor=cursor, length=length)
+        return self.run_orchestrator.get_command_slice(
+            cursor=cursor, length=length, include_fixit_commands=include_fixit_commands
+        )
 
     def get_command_error_slice(
         self,

robot-server/tests/commands/test_router.py

@@ -137,7 +137,11 @@ async def test_get_commands_list(
             index=0,
         )
     )
-    decoy.when(run_orchestrator.get_command_slice(cursor=1337, length=42)).then_return(
+    decoy.when(
+        run_orchestrator.get_command_slice(
+            cursor=1337, length=42, include_fixit_commands=True
+        )
+    ).then_return(
         CommandSlice(commands=[command_1, command_2], cursor=0, total_length=2)
     )
 

robot-server/tests/runs/router/test_commands_router.py

@@ -345,9 +345,7 @@ async def test_get_run_commands(
     )
     decoy.when(
         mock_run_data_manager.get_commands_slice(
-            run_id="run-id",
-            cursor=None,
-            length=42,
+            run_id="run-id", cursor=None, length=42, include_fixit_commands=True
         )
     ).then_return(CommandSlice(commands=[command], cursor=1, total_length=3))
 
@@ -412,7 +410,9 @@ async def test_get_run_commands_empty(
     """It should return an empty commands list if no commands."""
     decoy.when(mock_run_data_manager.get_current_command("run-id")).then_return(None)
     decoy.when(
-        mock_run_data_manager.get_commands_slice(run_id="run-id", cursor=21, length=42)
+        mock_run_data_manager.get_commands_slice(
+            run_id="run-id", cursor=21, length=42, include_fixit_commands=True
+        )
     ).then_return(CommandSlice(commands=[], cursor=0, total_length=0))
 
     result = await get_run_commands(
@@ -436,7 +436,9 @@ async def test_get_run_commands_not_found(
     not_found_error = RunNotFoundError("oh no")
 
     decoy.when(
-        mock_run_data_manager.get_commands_slice(run_id="run-id", cursor=21, length=42)
+        mock_run_data_manager.get_commands_slice(
+            run_id="run-id", cursor=21, length=42, include_fixit_commands=True
+        )
     ).then_raise(not_found_error)
     decoy.when(mock_run_data_manager.get_current_command(run_id="run-id")).then_raise(
         not_found_error

robot-server/tests/runs/test_run_data_manager.py

@@ -848,7 +848,9 @@ def test_get_commands_slice_from_db(
     decoy.when(
         mock_run_store.get_commands_slice(run_id="run_id", cursor=1, length=2)
     ).then_return(expected_command_slice)
-    result = subject.get_commands_slice(run_id="run_id", cursor=1, length=2)
+    result = subject.get_commands_slice(
+        run_id="run_id", cursor=1, length=2, include_fixit_commands=True
+    )
 
     assert expected_command_slice == result
 
@@ -875,11 +877,11 @@ def test_get_commands_slice_current_run(
         commands=expected_commands_result, cursor=1, total_length=3
     )
     decoy.when(mock_run_orchestrator_store.current_run_id).then_return("run-id")
-    decoy.when(mock_run_orchestrator_store.get_command_slice(1, 2)).then_return(
+    decoy.when(mock_run_orchestrator_store.get_command_slice(1, 2, True)).then_return(
         expected_command_slice
     )
 
-    result = subject.get_commands_slice("run-id", 1, 2)
+    result = subject.get_commands_slice("run-id", 1, 2, include_fixit_commands=True)
 
     assert expected_command_slice == result
 
@@ -929,7 +931,9 @@ def test_get_commands_slice_from_db_run_not_found(
         mock_run_store.get_commands_slice(run_id="run-id", cursor=1, length=2)
     ).then_raise(RunNotFoundError(run_id="run-id"))
     with pytest.raises(RunNotFoundError):
-        subject.get_commands_slice(run_id="run-id", cursor=1, length=2)
+        subject.get_commands_slice(
+            run_id="run-id", cursor=1, length=2, include_fixit_commands=True
+        )
 
 
 def test_get_current_command(