Merge branch 'edge' into AUTH-843-really-add-transfer-liquid-method

abr-testing/abr_testing/automation/jira_tool.py

@@ -107,6 +107,12 @@ def open_issue(self, issue_key: str) -> str:
         webbrowser.open(url)
         return url
 
+    def get_labels(self) -> List[str]:
+        """Get list of available labels."""
+        url = f"{self.url}/rest/api/3/label"
+        response = requests.request("GET", url, headers=self.headers, auth=self.auth)
+        return response.json()
+
     def create_ticket(
         self,
         summary: str,
@@ -118,18 +124,21 @@ def create_ticket(
         priority: str,
         components: list,
         affects_versions: str,
-        robot: str,
+        labels: list,
+        parent_name: str,
     ) -> Tuple[str, str]:
         """Create ticket."""
         # Check if software version is a field on JIRA, if not replaces with existing version
+        # TODO: automate parent linking
         data = {
             "fields": {
                 "project": {"id": "10273", "key": project_key},
                 "issuetype": {"name": issue_type},
                 "summary": summary,
                 "reporter": {"id": reporter_id},
                 "assignee": {"id": assignee_id},
-                "parent": {"key": robot},
+                # "parent": {"key": parent_name},
+                "labels": labels,
                 "priority": {"name": priority},
                 "components": [{"name": component} for component in components],
                 "description": {
@@ -194,6 +203,7 @@ def post_attachment_to_ticket(self, issue_id: str, attachment_path: str) -> None
 
     def get_project_issues(self, project_key: str) -> Dict[str, Any]:
         """Retrieve all issues for the given project key."""
+        # TODO: add field for ticket type.
         headers = {"Accept": "application/json"}
         query = {"jql": f"project={project_key}"}
         response = requests.request(
@@ -203,7 +213,6 @@ def get_project_issues(self, project_key: str) -> Dict[str, Any]:
             params=query,
             auth=self.auth,
         )
-        response.raise_for_status()
         return response.json()
 
     def get_project_versions(self, project_key: str) -> List[str]:

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -125,15 +125,20 @@ def compare_lpc_to_historical_data(
         & (df_lpc_data["Robot"] == robot)
         & (df_lpc_data["Module"] == labware_dict["Module"])
         & (df_lpc_data["Adapter"] == labware_dict["Adapter"])
-        & (df_lpc_data["Run Ending Error"] < 1)
+        & (df_lpc_data["Run Ending Error"])
+        < 1
     ]
     # Converts coordinates to floats and finds averages.
-    x_float = [float(value) for value in relevant_lpc["X"]]
-    y_float = [float(value) for value in relevant_lpc["Y"]]
-    z_float = [float(value) for value in relevant_lpc["Z"]]
-    current_x = round(labware_dict["X"], 2)
-    current_y = round(labware_dict["Y"], 2)
-    current_z = round(labware_dict["Z"], 2)
+    try:
+        x_float = [float(value) for value in relevant_lpc["X"]]
+        y_float = [float(value) for value in relevant_lpc["Y"]]
+        z_float = [float(value) for value in relevant_lpc["Z"]]
+        current_x = round(labware_dict["X"], 2)
+        current_y = round(labware_dict["Y"], 2)
+        current_z = round(labware_dict["Z"], 2)
+    except (ValueError):
+        x_float, y_float, z_float = [0.0], [0.0], [0.0]
+        current_x, current_y, current_z = 0.0, 0.0, 0.0
     try:
         avg_x = round(mean(x_float), 2)
         avg_y = round(mean(y_float), 2)
@@ -247,7 +252,7 @@ def get_error_runs_from_robot(ip: str) -> List[str]:
         f"http://{ip}:31950/runs", headers={"opentrons-version": "3"}
     )
     run_data = response.json()
-    run_list = run_data["data"]
+    run_list = run_data.get("data", [])
     for run in run_list:
         run_id = run["id"]
         num_of_errors = len(run["errors"])
@@ -258,7 +263,7 @@ def get_error_runs_from_robot(ip: str) -> List[str]:
 
 def get_robot_state(
     ip: str, reported_string: str
-) -> Tuple[Any, Any, Any, List[str], str]:
+) -> Tuple[Any, Any, Any, List[str], List[str], str]:
     """Get robot status in case of non run error."""
     description = dict()
     # Get instruments attached to robot
@@ -274,10 +279,11 @@ def get_robot_state(
         f"http://{ip}:31950/health", headers={"opentrons-version": "3"}
     )
     health_data = response.json()
-    parent = health_data.get("name", "")
+    print(f"health data {health_data}")
+    robot = health_data.get("name", "")
     # Create summary name
-    description["robot_name"] = parent
-    summary = parent + "_" + reported_string
+    description["robot_name"] = robot
+    summary = robot + "_" + reported_string
     affects_version = health_data.get("api_version", "")
     description["affects_version"] = affects_version
     # Instruments Attached
@@ -297,6 +303,12 @@ def get_robot_state(
         description[module["moduleType"]] = module
     components = ["Flex-RABR"]
     components = match_error_to_component("RABR", reported_string, components)
+    if "alpha" in affects_version:
+        components.append("flex internal releases")
+    labels = [robot]
+    if "8.2" in affects_version:
+        labels.append("8_2_0")
+    parent = affects_version + " Bugs"
     print(components)
     end_time = datetime.now()
     print(end_time)
@@ -317,13 +329,14 @@ def get_robot_state(
         parent,
         affects_version,
         components,
+        labels,
         whole_description_str,
     )
 
 
 def get_run_error_info_from_robot(
     ip: str, one_run: str, storage_directory: str
-) -> Tuple[str, str, str, List[str], str, str]:
+) -> Tuple[str, str, str, List[str], List[str], str, str]:
     """Get error information from robot to fill out ticket."""
     description = dict()
     # get run information
@@ -339,16 +352,19 @@ def get_run_error_info_from_robot(
     error_code = error_dict["Error_Code"]
     error_instrument = error_dict["Error_Instrument"]
     # JIRA Ticket Fields
-
+    robot = results.get("robot_name", "")
     failure_level = "Level " + str(error_level) + " Failure"
 
     components = [failure_level, "Flex-RABR"]
     components = match_error_to_component("RABR", str(error_type), components)
-    print(components)
     affects_version = results["API_Version"]
-    parent = results.get("robot_name", "")
-    print(parent)
-    summary = parent + "_" + str(one_run) + "_" + str(error_code) + "_" + error_type
+    if "alpha" in affects_version:
+        components.append("flex internal releases")
+    labels = [robot]
+    if "8.2" in affects_version:
+        labels.append("8_2_0")
+    parent = affects_version + " Bugs"
+    summary = robot + "_" + str(one_run) + "_" + str(error_code) + "_" + error_type
     # Description of error
     description["protocol_name"] = results["protocol"]["metadata"].get(
         "protocolName", ""
@@ -430,6 +446,7 @@ def get_run_error_info_from_robot(
         parent,
         affects_version,
         components,
+        labels,
         whole_description_str,
         saved_file_path,
     )
@@ -503,18 +520,20 @@ def get_run_error_info_from_robot(
         one_run = error_runs[-1]  # Most recent run with error.
         (
             summary,
-            robot,
+            parent,
             affects_version,
             components,
+            labels,
             whole_description_str,
             run_log_file_path,
         ) = get_run_error_info_from_robot(ip, one_run, storage_directory)
     else:
         (
             summary,
-            robot,
+            parent,
             affects_version,
             components,
+            labels,
             whole_description_str,
         ) = get_robot_state(ip, run_or_other)
     # Get Calibration Data
@@ -525,16 +544,8 @@ def get_run_error_info_from_robot(
     print(f"Making ticket for {summary}.")
     # TODO: make argument or see if I can get rid of with using board_id.
     project_key = "RABR"
-    print(robot)
-    try:
-        parent_key = project_key + "-" + robot.split("ABR")[1]
-    except IndexError:
-        parent_key = ""
-
-    # Grab all previous issues
-    all_issues = ticket.issues_on_board(project_key)
-
     # TODO: read board to see if ticket for run id already exists.
+    all_issues = ticket.issues_on_board(project_key)
     # CREATE TICKET
     issue_key, raw_issue_url = ticket.create_ticket(
         summary,
@@ -546,7 +557,8 @@ def get_run_error_info_from_robot(
         "Medium",
         components,
         affects_version,
-        parent_key,
+        labels,
+        parent,
     )
     # Link Tickets
     to_link = ticket.match_issues(all_issues, summary)

abr-testing/abr_testing/protocols/active_protocols/3_Tartrazine Protocol.py

@@ -19,62 +19,94 @@
 
 
 def add_parameters(parameters: ParameterContext) -> None:
-    """Parameters."""
-    helpers.create_single_pipette_mount_parameter(parameters)
+    """Add parameters."""
+    parameters.add_int(
+        variable_name="number_of_plates",
+        display_name="Number of Plates",
+        default=4,
+        minimum=1,
+        maximum=4,
+    )
 
 
 def run(ctx: ProtocolContext) -> None:
     """Protocol."""
-    mount_pos_50ul = ctx.params.pipette_mount  # type: ignore[attr-defined]
+    number_of_plates = ctx.params.number_of_plates  # type: ignore [attr-defined]
     # Plate Reader
     plate_reader: AbsorbanceReaderContext = ctx.load_module(
         helpers.abs_mod_str, "A3"
     )  # type: ignore[assignment]
     hs: HeaterShakerContext = ctx.load_module(helpers.hs_str, "A1")  # type: ignore[assignment]
-    hs_adapter = hs.load_adapter("opentrons_96_pcr_adapter")
+    hs_adapter = hs.load_adapter("opentrons_universal_flat_adapter")
     tube_rack = ctx.load_labware(
         "opentrons_10_tuberack_nest_4x50ml_6x15ml_conical", "C2", "Reagent Tube"
     )
     tartrazine_tube = tube_rack["A3"]
-
+    water_tube_1 = tube_rack["A4"]
+    water_tube_2 = tube_rack["B3"]
     sample_plate_1 = ctx.load_labware(
-        "nest_96_wellplate_200ul_flat", "D1", "Sample Plate 1"
+        "corning_96_wellplate_360ul_flat", "D1", "Sample Plate 1"
     )
     sample_plate_2 = ctx.load_labware(
-        "nest_96_wellplate_200ul_flat", "C1", "Sample Plate 2"
+        "corning_96_wellplate_360ul_flat", "D2", "Sample Plate 2"
     )
     sample_plate_3 = ctx.load_labware(
-        "nest_96_wellplate_200ul_flat", "B1", "Sample Plate 3"
+        "corning_96_wellplate_360ul_flat", "C1", "Sample Plate 3"
+    )
+    sample_plate_4 = ctx.load_labware(
+        "corning_96_wellplate_360ul_flat", "B1", "Sample Plate 4"
     )
-    sample_plate_list = [sample_plate_1, sample_plate_2, sample_plate_3]
+
+    sample_plate_list = [sample_plate_1, sample_plate_2, sample_plate_3, sample_plate_4]
     tiprack_50_1 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "D3")
     tiprack_50_2 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "C3")
     tiprack_50_3 = ctx.load_labware("opentrons_flex_96_tiprack_50ul", "B3")
+    tiprack_1000_1 = ctx.load_labware("opentrons_flex_96_tiprack_1000ul", "A2")
     tip_racks = [tiprack_50_1, tiprack_50_2, tiprack_50_3]
 
     # Pipette
-    p50 = ctx.load_instrument("flex_1channel_50", mount_pos_50ul, tip_racks=tip_racks)
+    p50 = ctx.load_instrument("flex_1channel_50", "left", tip_racks=tip_racks)
+    p1000 = ctx.load_instrument(
+        "flex_1channel_1000", "right", tip_racks=[tiprack_1000_1]
+    )
 
     # Probe wells
     liquid_vols_and_wells: Dict[str, List[Dict[str, Well | List[Well] | float]]] = {
-        "Tartrazine": [{"well": tartrazine_tube, "volume": 45.0}]
+        "Tartrazine": [{"well": tartrazine_tube, "volume": 45.0}],
+        "Water": [{"well": [water_tube_1, water_tube_2], "volume": 45.0}],
     }
     helpers.find_liquid_height_of_loaded_liquids(ctx, liquid_vols_and_wells, p50)
 
     i = 0
     all_percent_error_dict = {}
     cv_dict = {}
-    for sample_plate in sample_plate_list:
-        deck_locations = ["D1", "C1", "B1"]
+    vol = 0.0
+    tip_count = 0
+    for sample_plate in sample_plate_list[:number_of_plates]:
+        deck_locations = ["D1", "D2", "C1", "B1"]
+        p1000.pick_up_tip()
         for well in sample_plate.wells():
+            if vol < 45000:
+                tube_of_choice = water_tube_1
+            else:
+                tube_of_choice = water_tube_2
             p50.pick_up_tip()
+            p1000.aspirate(190, tube_of_choice)
+            p1000.air_gap(5)
+            p1000.dispense(5, well.top())
+            p1000.dispense(190, well)
+            vol += 190
             height = helpers.find_liquid_height(p50, tartrazine_tube)
             p50.aspirate(10, tartrazine_tube.bottom(z=height))
             p50.air_gap(5)
             p50.dispense(5, well.top())
             p50.dispense(10, well.bottom(z=0.5))
             p50.blow_out()
             p50.return_tip()
+            tip_count += 1
+            if tip_count >= (96 * 3):
+                p50.reset_tipracks()
+        p1000.return_tip()
         helpers.move_labware_to_hs(ctx, sample_plate, hs, hs_adapter)
         helpers.set_hs_speed(ctx, hs, 1500, 2.0, True)
         hs.open_labware_latch()
@@ -117,7 +149,6 @@ def run(ctx: ProtocolContext) -> None:
         plate_reader.open_lid()
         ctx.move_labware(sample_plate, deck_locations[i], use_gripper=True)
         i += 1
-
     # Print percent error dictionary
     ctx.comment("Percent Error: " + str(all_percent_error_dict))
     # Print cv dictionary