Merge branch 'edge' into abr-lengthen-protocols

.eslintrc.js

@@ -39,6 +39,7 @@ module.exports = {
     'no-case-declarations': 'warn',
     'prefer-regex-literals': 'warn',
     'react/prop-types': 'warn',
+    'react/jsx-curly-brace-presence': 'warn',
 
     // Enforce notification hooks
     'no-restricted-imports': [

.github/actions/odd-resource-analysis/action/index.js

@@ -5,9 +5,11 @@ async function run() {
   try {
     const mixpanelUser = core.getInput('mixpanel-user', { required: true })
     const mixpanelSecret = core.getInput('mixpanel-secret', { required: true })
-    const mixpanelProjectId = core.getInput('mixpanel-project-id', {
-      required: true,
-    })
+    const mixpanelProjectId = parseInt(
+      core.getInput('mixpanel-project-id', {
+        required: true,
+      })
+    )
     const previousVersionCount = parseInt(
       core.getInput('previous-version-count') || '2'
     )

.github/actions/odd-resource-analysis/action/lib/helpers/mixpanel.js

@@ -33,7 +33,7 @@ async function getMixpanelResourceMonitorDataFor({
   where,
 }) {
   const params = new URLSearchParams({
-    project_id: parseInt(projectId),
+    project_id: projectId,
     from_date: fromDate,
     to_date: toDate,
     event: '["resourceMonitorReport"]',

.github/workflows/api-test-lint-deploy.yaml

@@ -73,8 +73,6 @@ jobs:
     strategy:
       matrix:
         os: ['windows-2022', 'ubuntu-22.04', 'macos-latest']
-        # TODO(mc, 2022-02-24): expand this matrix to 3.8 and 3.9,
-        # preferably in a nightly cronjob on edge or something
         python: ['3.10']
         with-ot-hardware: ['true', 'false']
         exclude:
@@ -128,6 +126,60 @@ jobs:
           files: ./api/coverage.xml
           flags: api
 
+  test-package:
+    name: 'installed package tests on ${{ matrix.os }}'
+    timeout-minutes: 5
+    strategy:
+      matrix:
+        os: ['ubuntu-22.04', 'macos-latest', 'windows-2022']
+    runs-on: '${{ matrix.os }}'
+    steps:
+      - uses: 'actions/checkout@v4'
+      - name: 'Fix actions/checkout odd handling of tags'
+        if: startsWith(github.ref, 'refs/tags')
+        run: |
+          git fetch -f origin ${{ github.ref }}:${{ github.ref }}
+          git checkout ${{ github.ref }}
+      - uses: 'actions/setup-python@v4'
+        with:
+          python-version: '3.10'
+      - name: Set up package-testing
+        id: setup
+        if: ${{ matrix.os != 'windows-2022' }}
+        working-directory: package-testing
+        shell: bash
+        run: make setup
+      - name: Set up package-testing (Windows)
+        id: setup-windows
+        if: ${{ matrix.os == 'windows-2022' }}
+        working-directory: package-testing
+        shell: pwsh
+        run: make setup-windows
+      - name: Run the tests
+        if: ${{ matrix.os != 'windows-2022' }}
+        shell: bash
+        id: test
+        working-directory: package-testing
+        run: make test
+      - name: Run the tests (Windows)
+        shell: pwsh
+        id: test-windows
+        working-directory: package-testing
+        run: make test-windows
+      - name: Save the test results
+        if: ${{ always() && steps.setup.outcome == 'success' || steps.setup-windows.outcome == 'success' }}
+        id: results
+        uses: actions/upload-artifact@v4
+        with:
+          name: package-test-results-${{ matrix.os }}
+          path: package-testing/results
+      - name: Set job summary
+        if: ${{ always() }}
+        run: |
+          echo "## Opentrons Package Test Results ${{matrix.os}}" >> $GITHUB_STEP_SUMMARY
+          echo "### Test Outcome: Unixy ${{ steps.test.outcome }} Windows: ${{ steps.test-windows.outcome }}" >> $GITHUB_STEP_SUMMARY
+          echo "[Download the test results artifact](${{steps.results.outputs.artifact-url}})" >> $GITHUB_STEP_SUMMARY
+
   deploy:
     name: 'deploy opentrons package'
     needs: [test]

.github/workflows/odd-memory-usage-test.yaml

@@ -20,5 +20,5 @@ jobs:
         with:
           mixpanel-user: ${{ secrets.MIXPANEL_INGEST_USER }}
           mixpanel-secret: ${{ secrets.MIXPANEL_INGEST_SECRET }}
-          mixpanel-project-id: ${{ secrets.OT_APP_MIXPANEL_ID }}
+          mixpanel-project-id: ${{ secrets.OT_MIXPANEL_PROJECT_ID }}
           previous-version-count: '2'

.gitignore

@@ -163,3 +163,5 @@ opentrons-robot-app.tar.gz
 mock_dir
 .npm-cache/
 .eslintcache
+
+package-testing/results

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -11,11 +11,35 @@
 import sys
 import json
 import re
+from pathlib import Path
 import pandas as pd
 from statistics import mean, StatisticsError
 from abr_testing.tools import plate_reader
 
 
+def retrieve_protocol_file(
+    protocol_id: str,
+    robot_ip: str,
+    storage: str,
+) -> Path | str:
+    """Find and copy protocol file on robot with error."""
+    protocol_dir = f"/var/lib/opentrons-robot-server/7.1/protocols/{protocol_id}"
+
+    print(f"FILE TO FIND: {protocol_dir}/{protocol_id}")
+    # Copy protocol file found in robot oto host computer
+    save_dir = Path(f"{storage}/protocol_errors")
+    command = ["scp", "-r", f"root@{robot_ip}:{protocol_dir}", save_dir]
+    try:
+        # If file found and copied return path to file
+        subprocess.run(command, check=True)  # type: ignore
+        print("File transfer successful!")
+        return save_dir
+    except subprocess.CalledProcessError as e:
+        print(f"Error during file transfer: {e}")
+        # Return empty string if file can't be copied
+    return ""
+
+
 def compare_current_trh_to_average(
     robot: str,
     start_time: Any,
@@ -38,9 +62,13 @@ def compare_current_trh_to_average(
     # Find average conditions of errored time period
     df_all_trh = pd.DataFrame(all_trh_data)
     # Convert timestamps to datetime objects
-    df_all_trh["Timestamp"] = pd.to_datetime(
-        df_all_trh["Timestamp"], format="mixed", utc=True
-    ).dt.tz_localize(None)
+    print(f'TIMESTAMP: {df_all_trh["Timestamp"]}')
+    try:
+        df_all_trh["Timestamp"] = pd.to_datetime(
+            df_all_trh["Timestamp"], format="mixed", utc=True
+        ).dt.tz_localize(None)
+    except Exception:
+        print(f'The following timestamp is invalid: {df_all_trh["Timestamp"]}')
     # Ensure start_time is timezone-naive
     start_time = start_time.replace(tzinfo=None)
     relevant_temp_rhs = df_all_trh[
@@ -245,20 +273,24 @@ def get_user_id(user_file_path: str, assignee_name: str) -> str:
     return assignee_id
 
 
-def get_error_runs_from_robot(ip: str) -> List[str]:
+def get_error_runs_from_robot(ip: str) -> Tuple[List[str], List[str]]:
     """Get runs that have errors from robot."""
     error_run_ids = []
+    protocol_ids = []
     response = requests.get(
         f"http://{ip}:31950/runs", headers={"opentrons-version": "3"}
     )
     run_data = response.json()
     run_list = run_data.get("data", [])
     for run in run_list:
         run_id = run["id"]
+        protocol_id = run["protocolId"]
         num_of_errors = len(run["errors"])
         if not run["current"] and num_of_errors > 0:
             error_run_ids.append(run_id)
-    return error_run_ids
+            # Protocol ID will identify the correct folder on the robot of the protocol file
+            protocol_ids.append(protocol_id)
+    return (error_run_ids, protocol_ids)
 
 
 def get_robot_state(
@@ -335,7 +367,7 @@ def get_robot_state(
 
 
 def get_run_error_info_from_robot(
-    ip: str, one_run: str, storage_directory: str
+    ip: str, one_run: str, storage_directory: str, protocol_found: bool
 ) -> Tuple[str, str, str, List[str], List[str], str, str]:
     """Get error information from robot to fill out ticket."""
     description = dict()
@@ -369,6 +401,9 @@ def get_run_error_info_from_robot(
     description["protocol_name"] = results["protocol"]["metadata"].get(
         "protocolName", ""
     )
+
+    # If Protocol was successfully retrieved from the robot
+    description["protocol_found_on_robot"] = protocol_found
     # Get start and end time of run
     start_time = datetime.strptime(
         results.get("startedAt", ""), "%Y-%m-%dT%H:%M:%S.%f%z"
@@ -511,12 +546,21 @@ def get_run_error_info_from_robot(
     users_file_path = ticket.get_jira_users(storage_directory)
     assignee_id = get_user_id(users_file_path, assignee)
     run_log_file_path = ""
+    protocol_found = False
     try:
-        error_runs = get_error_runs_from_robot(ip)
+        error_runs, protocol_ids = get_error_runs_from_robot(ip)
     except requests.exceptions.InvalidURL:
         print("Invalid IP address.")
         sys.exit()
     if len(run_or_other) < 1:
+        # Retrieve the most recently run protocol file
+        protocol_files_path = retrieve_protocol_file(
+            protocol_ids[-1], ip, storage_directory
+        )
+        # Set protocol_found to true if python protocol was successfully copied over
+        if protocol_files_path:
+            protocol_found = True
+
         one_run = error_runs[-1]  # Most recent run with error.
         (
             summary,
@@ -526,7 +570,9 @@ def get_run_error_info_from_robot(
             labels,
             whole_description_str,
             run_log_file_path,
-        ) = get_run_error_info_from_robot(ip, one_run, storage_directory)
+        ) = get_run_error_info_from_robot(
+            ip, one_run, storage_directory, protocol_found
+        )
     else:
         (
             summary,
@@ -566,8 +612,15 @@ def get_run_error_info_from_robot(
     # OPEN TICKET
     issue_url = ticket.open_issue(issue_key)
     # MOVE FILES TO ERROR FOLDER.
+    print(protocol_files_path)
     error_files = [saved_file_path_calibration, run_log_file_path] + file_paths
-    error_folder_path = os.path.join(storage_directory, issue_key)
+
+    # Move protocol file(s) to error folder
+    if protocol_files_path:
+        for file in os.listdir(protocol_files_path):
+            error_files.append(os.path.join(protocol_files_path, file))
+
+    error_folder_path = os.path.join(storage_directory, "issue_key")
     os.makedirs(error_folder_path, exist_ok=True)
     for source_file in error_files:
         try:
@@ -577,7 +630,7 @@ def get_run_error_info_from_robot(
             shutil.move(source_file, destination_file)
         except shutil.Error:
             continue
-    # POST FILES TO TICKET
+    # POST ALL FILES TO TICKET
     list_of_files = os.listdir(error_folder_path)
     for file in list_of_files:
         file_to_attach = os.path.join(error_folder_path, file)

abr-testing/abr_testing/protocols/active_protocols/10_ZymoBIOMICS_Magbead_DNA_Cells_Flex.py

@@ -460,7 +460,6 @@ def wash(vol: float, source: List[Well]) -> None:
                     src = source[whichwash]
                     protocol.comment(f"new wash source {whichwash}")
                     wash_volume_tracker = 0.0
-
         m1000.drop_tip() if TIP_TRASH else m1000.return_tip()
         helpers.set_hs_speed(protocol, h_s, heater_shaker_speed * 0.9, wash_time, True)
 

abr-testing/abr_testing/protocols/active_protocols/6_Omega_HDQ_DNA_Cells-Flex_96_channel.py

@@ -237,6 +237,7 @@ def protocol_function() -> None:
         if not dry_run:
             h_s.set_and_wait_for_temperature(55)
         protocol.delay(
+
             minutes=10 if not dry_run else 0.25,
             msg="Please allow another 10 minutes of 55C incubation to complete lysis.",
         )
@@ -423,6 +424,7 @@ def clean() -> None:
 
     for i in range(number_of_runs):
         protocol_function()
+
         pip.reset_tipracks()
         if i < number_of_runs - 1:
             setup()
@@ -431,3 +433,4 @@ def clean() -> None:
     if deactivate_modules:
         helpers.deactivate_modules(protocol)
     helpers.find_liquid_height_of_all_wells(protocol, pip, [liquid_waste["A1"]])
+

abr-testing/abr_testing/protocols/liquid_setups/10_ZymoBIOMICS Magbead Liquid Setup.py

@@ -36,6 +36,7 @@ def run(protocol: protocol_api.ProtocolContext) -> None:
     wash2 = 9800 / 8
     wash2_list = [wash2] * 12
     final_elution = 7500 / 8
+
     # Fill up Plates
     # Res1
     p1000.transfer(

abr-testing/abr_testing/protocols/test_protocols/tc_lid_x_offset_test.py

@@ -73,11 +73,13 @@ def run(protocol: ProtocolContext) -> None:
     # Load Parameters
     lids_in_stack: int = protocol.params.lids_in_a_stack  # type: ignore[attr-defined]
     num_offset = protocol.params.num_offset  # type: ignore[attr-defined]
+
     offset = protocol.params.offset  # type: ignore[attr-defined]
     negative = protocol.params.negative  # type: ignore[attr-defined]
     thermocycler_bool = protocol.params.thermocycler_bool  # type: ignore[attr-defined]
     if negative:
         num_offset = num_offset * -1
+
     # Thermocycler
     if thermocycler_bool:
         thermocycler: ThermocyclerContext = protocol.load_module(

abr-testing/abr_testing/tools/abr_setup.py

@@ -54,6 +54,8 @@ def clean_sheet(sheet_name: str, credentials: str) -> Any:
         print("deleted rows")
     except Exception:
         print("could not delete rows")
+        return
+
     clean_sheet(sheet_name, credentials)