fix(api): filter get_run_commands

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

@@ -101,9 +101,14 @@ 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]:
+    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."""
-        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]:
@@ -127,6 +132,28 @@ def get_running_command(self) -> Optional[CommandEntry]:
         else:
             return self._commands_by_id[self._running_command_id]
 
+    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_queue_ids(self) -> OrderedSet[str]:
         """Get the IDs of all queued protocol commands, in FIFO order."""
         return self._queued_command_ids

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

@@ -580,18 +580,25 @@ def get_all(self) -> List[Command]:
         return self._state.command_history.get_all_commands()
 
     def get_slice(
-        self,
-        cursor: Optional[int],
-        length: int,
+        self, cursor: Optional[int], length: int, include_fixit_commands: bool
     ) -> CommandSlice:
         """Get a subset of commands around a given cursor.
 
         If the cursor is omitted, a cursor will be selected automatically
         based on the currently running or most recently executed command.
         """
+        command_ids = self._state.command_history.get_filtered_command_ids(
+            command_intents=[
+                CommandIntent.PROTOCOL,
+                CommandIntent.SETUP,
+                CommandIntent.FIXIT,
+            ]
+            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()
-        total_length = self._state.command_history.length()
+        total_length = len(command_ids)
 
         # TODO(mm, 2024-05-17): This looks like it's attempting to do the same thing
         # as self.get_current(), but in a different way. Can we unify them?
@@ -620,7 +627,10 @@ def get_slice(
         # start is inclusive, stop is exclusive
         actual_cursor = max(0, min(cursor, total_length - 1))
         stop = min(total_length, actual_cursor + length)
-        commands = self._state.command_history.get_slice(start=actual_cursor, stop=stop)
+
+        commands = self._state.command_history.get_slice(
+            start=actual_cursor, stop=stop, command_ids=command_ids
+        )
 
         return CommandSlice(
             commands=commands,

api/src/opentrons/protocol_runner/run_orchestrator.py

@@ -257,18 +257,17 @@ 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,
+        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.
+            all_commands: Get all command intents.
         """
         return self._protocol_engine.state_view.commands.get_slice(
-            cursor=cursor, length=length
+            cursor=cursor, length=length, include_fixit_commands=include_fixit_commands
         )
 
     def get_command_error_slice(

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

@@ -13,10 +13,14 @@
 
 
 def create_queued_command_entry(
-    command_id: str = "command-id", index: int = 0
+    command_id: str = "command-id",
+    intent: CommandIntent = CommandIntent.PROTOCOL,
+    index: int = 0,
 ) -> CommandEntry:
     """Create a command entry for a queued command."""
-    return CommandEntry(create_queued_command(command_id=command_id), index)
+    return CommandEntry(
+        create_queued_command(command_id=command_id, intent=intent), index
+    )
 
 
 def create_fixit_command_entry(
@@ -94,6 +98,51 @@ def test_get_all_commands(command_history: CommandHistory) -> None:
     ]
 
 
+def test_get_filtered_commands(command_history: CommandHistory) -> None:
+    """It should return a list of all commands without fixit commands."""
+    assert list(command_history.get_filtered_command_ids()) == []
+    command_entry_1 = create_queued_command(command_id="0")
+    command_entry_2 = create_queued_command(command_id="1")
+    fixit_command_entry_1 = create_queued_command(
+        intent=CommandIntent.FIXIT, command_id="fixit-1"
+    )
+    command_history.append_queued_command(command_entry_1)
+    command_history.append_queued_command(command_entry_2)
+    command_history.append_queued_command(fixit_command_entry_1)
+    assert list(command_history.get_filtered_command_ids()) == ["0", "1"]
+
+
+def test_get_all_filtered_commands(command_history: CommandHistory) -> None:
+    """It should return a list of all commands without fixit commands."""
+    assert (
+        list(
+            command_history.get_filtered_command_ids(
+                command_intents=[
+                    CommandIntent.FIXIT,
+                    CommandIntent.PROTOCOL,
+                    CommandIntent.SETUP,
+                ]
+            )
+        )
+        == []
+    )
+    command_entry_1 = create_queued_command_entry()
+    command_entry_2 = create_queued_command_entry(index=1, intent=CommandIntent.SETUP)
+    fixit_command_entry_1 = create_queued_command_entry(intent=CommandIntent.FIXIT)
+    command_history._add("0", command_entry_1)
+    command_history._add("1", command_entry_2)
+    command_history._add("fixit-1", fixit_command_entry_1)
+    assert list(
+        command_history.get_filtered_command_ids(
+            command_intents=[
+                CommandIntent.FIXIT,
+                CommandIntent.PROTOCOL,
+                CommandIntent.SETUP,
+            ]
+        )
+    ) == ["0", "1", "fixit-1"]
+
+
 def test_get_all_ids(command_history: CommandHistory) -> None:
     """It should return a list of all command IDs."""
     assert command_history.get_all_ids() == []
@@ -119,6 +168,21 @@ def test_get_slice(command_history: CommandHistory) -> None:
     ]
 
 
+def test_get_slice_with_filtered_list(command_history: CommandHistory) -> None:
+    """It should return a slice of filtered commands."""
+    assert command_history.get_slice(0, 2) == []
+    command_entry_1 = create_queued_command_entry()
+    command_entry_2 = create_queued_command_entry(index=1)
+    command_entry_3 = create_queued_command_entry(index=2)
+    command_history._add("0", command_entry_1)
+    command_history._add("1", command_entry_2)
+    command_history._add("2", command_entry_3)
+    filtered_list = ["0", "1"]
+    assert command_history.get_slice(1, 3, command_ids=filtered_list) == [
+        command_entry_2.command,
+    ]
+
+
 def test_get_tail_command(command_history: CommandHistory) -> None:
     """It should return the tail command."""
     assert command_history.get_tail_command() is None

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)
+    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)
+    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)
+    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)
+    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)
+    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)
+    result = subject.get_slice(cursor=None, length=2, include_fixit_commands=True)
 
     assert result == CommandSlice(
         commands=[command_3, command_4],
@@ -1006,6 +1006,51 @@ def test_get_slice_default_cursor_running() -> None:
     )
 
 
+def test_get_slice_without_fixit() -> None:
+    """It should select a cursor based on the running command, if present."""
+    command_1 = create_succeeded_command(command_id="command-id-1")
+    command_2 = create_succeeded_command(command_id="command-id-2")
+    command_3 = create_running_command(command_id="command-id-3")
+    command_4 = create_queued_command(command_id="command-id-4")
+    command_5 = create_queued_command(command_id="command-id-5")
+    command_6 = create_queued_command(
+        command_id="fixit-id-1", intent=cmd.CommandIntent.FIXIT
+    )
+    command_7 = create_queued_command(
+        command_id="fixit-id-2", intent=cmd.CommandIntent.FIXIT
+    )
+
+    subject = get_command_view(
+        commands=[
+            command_1,
+            command_2,
+            command_3,
+            command_4,
+            command_5,
+            command_6,
+            command_7,
+        ],
+        queued_command_ids=[
+            "command-id-1",
+            "command-id-2",
+            "command-id-3",
+            "command-id-4",
+            "command-id-5",
+            "fixit-id-1",
+            "fixit-id-2",
+        ],
+        queued_fixit_command_ids=["fixit-id-1", "fixit-id-2"],
+    )
+
+    result = subject.get_slice(cursor=None, length=7, include_fixit_commands=False)
+
+    assert result == CommandSlice(
+        commands=[command_1, command_2, command_3, command_4, command_5],
+        cursor=0,
+        total_length=5,
+    )
+
+
 def test_get_errors_slice_empty() -> None:
     """It should return a slice from the tail if no current command."""
     subject = get_command_view(failed_command_errors=[])

robot-server/robot_server/commands/router.py

@@ -154,7 +154,9 @@ 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 +226,11 @@ 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

@@ -271,6 +271,11 @@ async def get_run_commands(
         _DEFAULT_COMMAND_LIST_LENGTH,
         description="The maximum number of commands in the list to return.",
     ),
+    includeFixitCommands: bool = Query(
+        True,
+        description="If `true`, return all commands (protocol, setup, fixit)."
+        " If `false`, only return safe commands (protocol, setup).",
+    ),
     run_data_manager: RunDataManager = Depends(get_run_data_manager),
 ) -> PydanticResponse[MultiBody[RunCommandSummary, CommandCollectionLinks]]:
     """Get a summary of a set of commands in a run.
@@ -279,13 +284,16 @@ async def get_run_commands(
         runId: Requested run ID, from the URL
         cursor: Cursor index for the collection response.
         pageLength: Maximum number of items to return.
+        includeFixitCommands: If `true`, return all commands."
+            " If `false`, only return safe commands.
         run_data_manager: Run data retrieval interface.
     """
     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

@@ -371,20 +371,24 @@ 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: Weather we should 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