cherry picked prev branch changes onto edge

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

@@ -97,6 +97,14 @@ def get_all_commands(self) -> List[Command]:
             for command_id in self._all_command_ids
         ]
 
+    def get_filtered_queue_ids(self, all_commands: bool) -> list[str]:
+        print(list(self.get_fixit_queue_ids()))
+        return [
+            i
+            for i in self._all_command_ids
+            if i not in list(self.get_fixit_queue_ids())
+        ]
+
     def get_all_ids(self) -> List[str]:
         """Get all command IDs."""
         return self._all_command_ids

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

@@ -579,19 +579,40 @@ 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,
+        self, cursor: Optional[int], length: int, all_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.
         """
-        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()
+        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 = 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 +641,9 @@ 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, all_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, all_commands=all_commands
         )
 
     def get_command_error_slice(

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

@@ -94,6 +94,17 @@ def test_get_all_commands(command_history: CommandHistory) -> None:
     ]
 
 
+def test_get_all_filtered_commands(command_history: CommandHistory) -> None:
+    """It should return a list of all commapnds."""
+    assert command_history.get_filtered_queue_ids(all_commands=False) == []
+    command_entry_1 = create_queued_command_entry()
+    command_entry_2 = create_queued_command_entry(index=1)
+    command_history._add("0", command_entry_1)
+    command_history._add("1", command_entry_2)
+    command_history._add_to_fixit_queue("1")
+    assert command_history.get_filtered_queue_ids(all_commands=False) == ["0"]
+
+
 def test_get_all_ids(command_history: CommandHistory) -> None:
     """It should return a list of all command IDs."""
     assert command_history.get_all_ids() == []

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, all_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, all_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, all_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, all_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, all_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, all_commands=True)
 
     assert result == CommandSlice(
         commands=[command_3, command_4],