migration and initialization fixes

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

@@ -50,6 +50,7 @@ class CommandHistory:
 
     def __init__(self) -> None:
         self._all_command_ids = []
+        self._all_failed_command_ids = []
         self._all_command_ids_but_fixit_command_ids = []
         self._queued_command_ids = OrderedSet()
         self._queued_setup_command_ids = OrderedSet()

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

@@ -34,13 +34,12 @@
     QueueStatus,
 )
 
-from opentrons.protocol_engine.state.command_history import CommandEntry
+from opentrons.protocol_engine.state.command_history import CommandEntry, CommandHistory
 
 from opentrons.protocol_engine.errors import ProtocolCommandFailedError, ErrorOccurrence
 
 from opentrons_shared_data.errors.codes import ErrorCodes
 
-from opentrons.protocol_engine.state.command_history import CommandHistory
 from opentrons.protocol_engine.state.update_types import StateUpdate
 
 from .command_fixtures import (
@@ -100,6 +99,8 @@ def get_command_view(  # noqa: C901
                 command_id=command.id,
                 command_entry=CommandEntry(index=index, command=command),
             )
+            if command.error:
+                command_history.append_failed_command_id(command.id)
 
     state = CommandState(
         command_history=command_history,

robot-server/robot_server/persistence/_migrations/v7_to_v8.py

@@ -0,0 +1,86 @@
+"""Migrate the persistence directory from schema 7 to 8.
+
+Summary of changes from schema 7:
+
+- Adds a new command_intent to store the commands intent in the commands table
+- Adds a new source to store the data files origin in the data_files table
+- Adds the `boolean_setting` table.
+"""
+
+import json
+from pathlib import Path
+from contextlib import ExitStack
+import shutil
+from typing import Any
+
+import sqlalchemy
+
+from ..database import sql_engine_ctx, sqlite_rowid
+from ..tables import schema_8
+from .._folder_migrator import Migration
+
+from ..file_and_directory_names import (
+    DB_FILE,
+)
+
+
+class Migration7to8(Migration):  # noqa: D101
+    def migrate(self, source_dir: Path, dest_dir: Path) -> None:
+        """Migrate the persistence directory from schema 6 to 7."""
+        # Copy over all existing directories and files to new version
+        for item in source_dir.iterdir():
+            if item.is_dir():
+                shutil.copytree(src=item, dst=dest_dir / item.name)
+            else:
+                shutil.copy(src=item, dst=dest_dir / item.name)
+
+        dest_db_file = dest_dir / DB_FILE
+
+        # Append the new column to existing protocols and data_files in v6 database
+        with ExitStack() as exit_stack:
+            dest_engine = exit_stack.enter_context(sql_engine_ctx(dest_db_file))
+
+            schema_8.metadata.create_all(dest_engine)
+
+            dest_transaction = exit_stack.enter_context(dest_engine.begin())
+
+            def add_column(
+                engine: sqlalchemy.engine.Engine,
+                table_name: str,
+                column: Any,
+            ) -> None:
+                column_type = column.type.compile(engine.dialect)
+                engine.execute(
+                    f"ALTER TABLE {table_name} ADD COLUMN {column.key} {column_type}"
+                )
+
+            add_column(
+                dest_engine,
+                schema_8.run_command_table.name,
+                schema_8.run_command_table.c.command_error,
+            )
+
+            _migrate_command_table_with_new_command_error_col(
+                dest_transaction=dest_transaction
+            )
+
+
+def _migrate_command_table_with_new_command_error_col(
+    dest_transaction: sqlalchemy.engine.Connection,
+) -> None:
+    """Add a new 'command_intent' column to run_command_table table."""
+    select_commands = sqlalchemy.select(schema_8.run_command_table).order_by(
+        sqlite_rowid
+    )
+    for row in dest_transaction.execute(select_commands).all():
+        data = json.loads(row.command)
+        new_command_error = (
+            # Account for old_row.command["error"] being NULL.
+            None
+            if "error" not in row.command or data["error"] == None  # noqa: E711
+            else data["error"]
+        )
+
+        dest_transaction.execute(
+            f"UPDATE run_command SET command_error='{new_command_error}' WHERE row_id={row.row_id}"
+        )

robot-server/robot_server/persistence/file_and_directory_names.py

@@ -8,7 +8,7 @@
 
 from typing import Final
 
-LATEST_VERSION_DIRECTORY: Final = "7.1"
+LATEST_VERSION_DIRECTORY: Final = "8.1"
 
 DECK_CONFIGURATION_FILE: Final = "deck_configuration.json"
 PROTOCOLS_DIRECTORY: Final = "protocols"

robot-server/robot_server/persistence/persistence_directory.py

@@ -11,7 +11,7 @@
 from anyio import Path as AsyncPath, to_thread
 
 from ._folder_migrator import MigrationOrchestrator
-from ._migrations import up_to_3, v3_to_v4, v4_to_v5, v5_to_v6, v6_to_v7
+from ._migrations import up_to_3, v3_to_v4, v4_to_v5, v5_to_v6, v6_to_v7, v7_to_v8
 from .file_and_directory_names import LATEST_VERSION_DIRECTORY
 
 _TEMP_PERSISTENCE_DIR_PREFIX: Final = "opentrons-robot-server-"
@@ -55,7 +55,8 @@ async def prepare_active_subdirectory(prepared_root: Path) -> Path:
             # Subdirectory "7" was previously used on our edge branch for an in-dev
             # schema that was never released to the public. It may be present on
             # internal robots.
-            v6_to_v7.Migration6to7(subdirectory=LATEST_VERSION_DIRECTORY),
+            v6_to_v7.Migration6to7(subdirectory="7"),
+            v7_to_v8.Migration7to8(subdirectory=LATEST_VERSION_DIRECTORY),
         ],
         temp_file_prefix="temp-",
     )

robot-server/robot_server/runs/run_data_manager.py

@@ -366,6 +366,8 @@ async def update(self, run_id: str, current: Optional[bool]) -> Union[Run, BadRu
 
         if next_current is False:
             run_result = await self._run_orchestrator_store.clear()
+            state_summary = run_result.state_summary
+            parameters = run_result.parameters
             run_resource: Union[
                 RunResource, BadRunResource
             ] = self._run_store.update_run_state(

robot-server/robot_server/runs/run_store.py

@@ -176,6 +176,7 @@ def update_run_state(
             transaction.execute(update_run)
             transaction.execute(delete_existing_commands)
             for command_index, command in enumerate(commands):
+                print(command.error)
                 transaction.execute(
                     insert_command,
                     {