Connect Robot Ambient Conditions and Run Data (#15504)

<!--
Thanks for taking the time to open a pull request! Please make sure
you've read the "Opening Pull Requests" section of our Contributing
Guide:


https://github.com/Opentrons/opentrons/blob/edge/CONTRIBUTING.md#opening-pull-requests

To ensure your code is reviewed quickly and thoroughly, please fill out
the sections below to the best of your ability!
-->

# Overview

Adds RH and Temp to ABR Data Sheet

# Test Plan

Ran script with both sheets. Rows updated successfully.
# Changelog

<!--
List out the changes to the code in this PR. Please try your best to
categorize your changes and describe what has changed and why.

Example changelog:
- Fixed app crash when trying to calibrate an illegal pipette
- Added state to API to track pipette usage
- Updated API docs to mention only two pipettes are supported

IMPORTANT: MAKE SURE ANY BREAKING CHANGES ARE PROPERLY COMMUNICATED
-->

# Review requests

<!--
Describe any requests for your reviewers here.
-->

# Risk assessment

<!--
Carefully go over your pull request and look at the other parts of the
codebase it may affect. Look for the possibility, even if you think it's
small, that your change may affect some other part of the system - for
instance, changing return tip behavior in protocol may also change the
behavior of labware calibration.

Identify the other parts of the system your codebase may affect, so that
in addition to your own review and testing, other people who may not
have the system internalized as much as you can focus their attention
and testing there.
-->

Author: rclarke0

abr-testing/Pipfile

@@ -16,6 +16,8 @@ opentrons-hardware = {editable = true, path = "./../hardware", extras=['FLEX']}
 opentrons = {editable = true, path = "./../api", extras=['flex-hardware']}
 slackclient = "*"
 slack-sdk = "*"
+scikit-learn = "*"
+pandas = "*"
 
 [dev-packages]
 atomicwrites = "==1.4.1"

abr-testing/Pipfile.lock

@@ -197,6 +197,27 @@ def share_permissions(self, file_id: str) -> None:
             fileId=file_id, body=new_permission, transferOwnership=False  # type: ignore
         ).execute()
 
+    def download_single_file(
+        self, save_directory: str, file_id: str, file_name: str, mime_type: str
+    ) -> str:
+        """Download single file."""
+        # google sheets: text/csv
+        file_path = ""
+        if mime_type:
+            request = self.drive_service.files().export_media(
+                fileId=file_id, mimeType=mime_type
+            )
+        else:
+            request = self.drive_service.files().get_media(fileId=file_id)
+        file_path = os.path.join(save_directory, file_name)
+        fh = io.FileIO(file_path, "wb")
+        downloader = MediaIoBaseDownload(fh, request)
+        done = False
+        while done is False:
+            status, done = downloader.next_chunk()
+            print(f"Downloading {file_name}... {int(status.progress() * 100)}%")
+        return file_path
+
     def download_files(
         self, files_to_download: List[Dict[str, Any]], save_directory: str
     ) -> None:

abr-testing/abr_testing/automation/google_drive_tool.py

@@ -142,7 +142,7 @@ def column_letter_to_index(column_letter: str) -> int:
                 try:
                     float_value = float(value)
                     user_entered_value = {"numberValue": float_value}
-                except ValueError:
+                except (ValueError, TypeError):
                     user_entered_value = {"stringValue": str(value)}
                 requests.append(
                     {
@@ -172,14 +172,20 @@ def update_cell(
         self.spread_sheet.worksheet(sheet_title).update_cell(row, column, single_data)
         return row, column, single_data
 
-    def get_all_data(self) -> List[Dict[str, Any]]:
+    def get_all_data(
+        self, expected_headers: Optional[Set[str]]
+    ) -> List[Dict[str, Any]]:
         """Get all the Data recorded from worksheet."""
-        return self.worksheet.get_all_records()
+        return self.worksheet.get_all_records(expected_headers=expected_headers)
 
     def get_column(self, column_number: int) -> Set[str]:
         """Get all values in column."""
         return self.worksheet.col_values(column_number)
 
+    def get_row(self, row_number: int) -> Set[str]:
+        """Get all values in row."""
+        return self.worksheet.row_values(row_number)
+
     def get_cell(self, sheet_title: str, cell: str) -> Any:
         """Get cell value with location ex: 'A1'."""
         return self.spread_sheet.worksheet(sheet_title).acell(cell).value

abr-testing/abr_testing/automation/google_sheets_tool.py

@@ -115,6 +115,8 @@ def create_data_dictionary(
                 plate_measure = {
                     "Plate Measured": plate,
                     "End Volume Accuracy (%)": accuracy,
+                    "Average Temp (oC)": "",
+                    "Average RH(%)": "",
                 }
                 row_for_lpc = {**row, **all_modules, **notes}
                 row_2 = {
@@ -203,6 +205,7 @@ def create_data_dictionary(
     ) = create_data_dictionary(missing_runs_from_gs, storage_directory, "", "", "")
 
     start_row = google_sheet.get_index_row() + 1
+    print(start_row)
     google_sheet.batch_update_cells(transposed_runs_and_robots, "A", start_row, "0")
 
     # Add LPC to google sheet

abr-testing/abr_testing/data_collection/abr_google_drive.py

@@ -255,7 +255,8 @@ 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"
-    parent_key = project_key + "-" + robot[-1]
+    print(robot)
+    parent_key = project_key + "-" + robot.split("ABR")[1]
     # TODO: read board to see if ticket for run id already exists.
     # CREATE TICKET
     issue_key = ticket.create_ticket(

abr-testing/abr_testing/data_collection/abr_robot_error.py

@@ -10,7 +10,8 @@ def remove_duplicate_data() -> None:
     seen = set()
     new_values = []
     row_indices = []
-    sheet_data = google_sheet_lpc.get_all_data()
+    headers = google_sheet_lpc.get_row(1)
+    sheet_data = google_sheet_lpc.get_all_data(headers)
     for i, row in enumerate(sheet_data):
         key = (
             row["Robot"],
@@ -49,8 +50,10 @@ def remove_duplicate_data() -> None:
     except FileNotFoundError:
         print(f"Add credentials.json file to: {storage_directory}.")
         sys.exit()
+
     google_sheet_lpc = google_sheets_tool.google_sheet(credentials_path, "ABR-LPC", 0)
-    print(len(google_sheet_lpc.get_all_data()))
+    headers = google_sheet_lpc.get_row(1)
+    print(len(google_sheet_lpc.get_all_data(headers)))
     remove_duplicate_data()
-    num_of_rows = print(len(google_sheet_lpc.get_all_data()))
+    num_of_rows = print(len(google_sheet_lpc.get_all_data(headers)))
     # TODO: automate data analysis

abr-testing/abr_testing/tools/abr_lpc.py

@@ -42,7 +42,9 @@ def get_all_plate_readings(
 ) -> float:
     """Calculate accuracy of liquid moved on final measurement step."""
     accuracy = 0.0
-    all_data = google_sheet.get_all_data()
+    header_list = google_sheet.get_row(1)
+    all_data = google_sheet.get_all_data(header_list)
+
     # Get mass of first reading
     mass_1_readings = []
     for row in all_data:

abr-testing/abr_testing/tools/abr_scale.py

@@ -0,0 +1,137 @@
+"""Add temperature and humidity data to ABR-run-data sheet."""
+
+from abr_testing.automation import google_sheets_tool
+from abr_testing.automation import google_drive_tool
+import argparse
+import csv
+import sys
+import os
+from typing import Dict, Tuple, Any, List
+from statistics import mean, StatisticsError
+
+
+def add_robot_lifetime(abr_data: List[Dict[str, Any]]) -> None:
+    """Add % Robot Lifetime to each run."""
+    # TODO: add robot lifetime to each run.
+
+
+def compare_run_to_temp_data(
+    abr_data: List[Dict[str, Any]], temp_data: List[Dict[str, Any]], google_sheet: Any
+) -> None:
+    """Read ABR Data and compare robot and timestamp columns to temp data."""
+    row_update = 0
+    for run in abr_data:
+        run_id = run["Run_ID"]
+        try:
+            average_temp = float(run["Average Temp (oC)"])
+        except ValueError:
+            average_temp = 0
+        if len(run_id) < 1 or average_temp > 0:
+            continue
+        else:
+            # Determine which runs do not have average temp/rh data
+            temps = []
+            rel_hums = []
+            for recording in temp_data:
+                temp_robot = recording["Robot"]
+                if len(recording["Timestamp"]) > 1:
+                    timestamp = recording["Timestamp"]
+                    if (
+                        temp_robot == run["Robot"]
+                        and timestamp >= run["Start_Time"]
+                        and timestamp <= run["End_Time"]
+                    ):
+                        temps.append(float(recording["Temp (oC)"]))
+                        rel_hums.append(float(recording["Relative Humidity (%)"]))
+            try:
+                avg_temps = mean(temps)
+                avg_humidity = mean(rel_hums)
+                row_num = google_sheet.get_row_index_with_value(run_id, 2)
+                # Write average temperature
+                google_sheet.update_cell("Sheet1", row_num, 46, avg_temps)
+                # Write average humidity
+                google_sheet.update_cell("Sheet1", row_num, 47, avg_humidity)
+                # TODO: Write averages to google sheet
+                print(f"Updated row {row_num}.")
+            except StatisticsError:
+                avg_temps = None
+                avg_humidity = None
+    print(f"Updated {row_update} rows with temp and RH data.")
+
+
+def read_csv_as_dict(file_path: str) -> List[Dict[str, Any]]:
+    """Read a CSV file and return its content as a list of dictionaries."""
+    with open(file_path, mode="r", newline="", encoding="utf-8") as csvfile:
+        reader = csv.DictReader(csvfile)
+        data = [row for row in reader]
+    return data
+
+
+def connect_and_download(
+    sheets: Dict[str, str], storage_directory: str
+) -> Tuple[List[str], str]:
+    """Connect to google sheet and download."""
+    try:
+        credentials_path = os.path.join(storage_directory, "credentials.json")
+        google_drive = google_drive_tool.google_drive(
+            credentials_path,
+            "1W8S3EV3cIfC-ZoRF3km0ad5XqyVkO3Tu",
+            "[email protected]",
+        )
+        print("connected to gd")
+    except FileNotFoundError:
+        print(f"Add credentials.json file to: {storage_directory}.")
+        sys.exit()
+    file_paths = []
+    for sheet in sheets.items():
+        file_name, file_id = sheet[0], sheet[1]
+        print(file_name)
+        file_path = google_drive.download_single_file(
+            storage_directory, file_id, file_name, "text/csv"
+        )
+        file_paths.append(file_path)
+    return file_paths, credentials_path
+
+
+if __name__ == "__main__":
+    parser = argparse.ArgumentParser(
+        description="Adds average robot ambient conditions to run sheet."
+    )
+    parser.add_argument(
+        "--abr-data-sheet",
+        type=str,
+        default="1M6LSLNwvWuHQOwIwUpblF_Eyx4W5y5gXgdU3rjU2XFk",
+        help="end of url of main data sheet.",
+    )
+    parser.add_argument(
+        "--room-conditions-sheet",
+        type=str,
+        default="1cIjSvK_mPCq4IFqUPB7SgdDuuMKve5kJh0xyH4znAd0",
+        help="end fo url of ambient conditions data sheet",
+    )
+    parser.add_argument(
+        "--storage-directory",
+        type=str,
+        default="C:/Users/Rhyann Clarke/test_folder",
+        help="Path to long term storage directory for run logs.",
+    )
+    args = parser.parse_args()
+    google_sheets_to_download = {
+        "ABR-run-data": args.abr_data_sheet,
+        "ABR Ambient Conditions": args.room_conditions_sheet,
+    }
+    storage_directory = args.storage_directory
+    # Download google sheets.
+    file_paths, credentials_path = connect_and_download(
+        google_sheets_to_download, storage_directory
+    )
+    # TODO: read csvs.
+    abr_data = read_csv_as_dict(file_paths[0])
+    temp_data = read_csv_as_dict(file_paths[1])
+    # TODO: compare robot and timestamps.
+    abr_google_sheet = google_sheets_tool.google_sheet(
+        credentials_path, "ABR-run-data", 0
+    )
+
+    compare_run_to_temp_data(abr_data, temp_data, abr_google_sheet)
+    # TODO: Write average for matching cells.