147 lines
7.4 KiB
Markdown
147 lines
7.4 KiB
Markdown
## Startup:
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1. Open the app using the shortcut in the Submissions folder: L:\Robotics Laboratory Support\Submissions\Submissions App.lnk.
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1. Ignore the large black window of fast scrolling text, it is there for debugging purposes.
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2. The 'Submissions' tab should be open by default.
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3. Default settings (config.yml) will be copied to C:\Users\\{USERNAME}\AppData\Local\submissions\config
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## Logging in New Run:
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*should fit 90% of usage cases*
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1. Ensure a properly formatted Submission Excel form has been filled out.
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a. The program can fill in reagent fields and some other information automatically, but should be checked for accuracy afterwards.
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2. Click on 'File' in the menu bar, followed by 'Import Submission' and use the file dialog to locate the form.
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1. The excel file may also be dragged into the grey area on the left hand side of the screen from Windows File Explorer. If so, skip step 3.
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3. Click 'Ok'.
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4. Most of the fields in the form should be automatically filled in from the form area to the left of the screen.
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5. You may need to maximize the app to ensure you can see all the info.
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6. Any fields that are not automatically filled in can be filled in manually from the drop down menus.
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1. Any reagent lots not found in the drop downs can be typed in manually.
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7. Once you are certain all the information is correct, click 'Submit' at the bottom of the form.
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8. Add in any new reagents the app doesn't have in the database.
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9. Once the new run shows up at the bottom of the Submissions, everything is fine.
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10. In case of any mistakes, the run can be overwritten by a reimport.
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## Adding Equipment to a Run:
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1. Right click on the run in the Submissions Table to access the context menu.
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2. Click on “Add Equipment”.
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3. Select equipment used for each equipment role from the drop down menu.
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1. Any tips associated with a liquid handler will also be available in a separate drop down menu.
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4. Select (or input) the process used on with the equipment.
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1. Equipment that is not necessary may disabled using the check boxes to the left of each entry.
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## Importing PCR results (Wastewater only):
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This is meant to import .xslx files created from the Design & Analysis Software
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1. Click on 'File' -> 'Import PCR Results'.
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2. Use the file dialog to locate the .xlsx file you want to import.
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3. Click 'Okay'.
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## Using the Gel Box (Wastewater Artic only):
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1. Right click on the run in the Submissions Table to access the context menu.
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2. Click on “Gel Box”.
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3. Choose the .jpg file exported from the Egel reader.
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4. Click “Okay”.
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5. If none exists, Enter the DNA Core Submission Number and gel barcode at the top of the window.
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6. Use the histogram slide on the right side of the window to adjust the image contrast.
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7. Use the mouse scroll to zoom in on relevant areas of the image.
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8. Enter the control status in the grid at the bottom of the window.
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9. Add any relevant comments.
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10. Click “Okay”.
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## Check existing Run:
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1. Details of existing runs can be checked by double clicking on the row of interest in the summary sheet on the right of the 'Submissions' tab.
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2. All information available on the run should be available in the resulting text window.
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1. This information can be exported by clicking 'Export DOCX' at the top.
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## Signing Off on a run:
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1. Open the “Submission Details” window (see 7.6 above).
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2. Scroll down to bottom of the details window.
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3. If the current user is authorized a button marked “Sign Off” will appear at the bottom of the page. Click it.
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## Generating a report:
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1. Click on 'Reports' -> 'Make Report' in the menu bar.
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2. Select the start date and the end date you want for the report. Click 'ok'.
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3. Use the file dialog to select a location to save the report.
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a. Both an excel sheet and a pdf should be generated containing summary information for submissions made by each client lab.
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## Exporting a run as an Excel file:
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1. Right click on the run in the Submissions Table to access the context menu.
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2. Select “Export” from the context menu.
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3. Select the folder and input the filename in the “Save File” dialog.
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4. Click “Okay”.
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5. Ensure the resulting Excel workbook contains all the relevant information.
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## Checking Controls:
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1. Controls for bacterial runs are now incorporated directly into the submissions database using webview. (Admittedly this performance is not as good as with a browser, so you will have to triage your data)
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2. Click on the "Controls" tab.
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3. Range of dates for controls can be selected from the date pickers at the top.
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1. If start date is set after end date, the start date will default back to 3 months before end date.
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2. Recommendation is to use less than 6 month date range keeping in mind that higher data density will affect performance (with kraken being the worst so far)
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4. Analysis type and subtype can be set using the drop down menus. (Only kraken has a subtype so far).
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## Adding new Kit:
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1. Click "Add Kit" tab in the tab bar.
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2. Select the Submission type from the drop down menu.
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3. Fill in the kit name (required) and other fields (optional).
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4. For each reagent type in the kit click the "Add Reagent Type" button.
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5. Fill in the name of the reagent type. Alternatively select from already existing types in the drop down.
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6. Fill in the reagent location in the excel submission sheet.
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a. For example if the reagent name is in a sheet called "Reagent Info" in row 12, column 1, type "Reagent Info" in the "Excel Location Sheet Name" field.
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b. Set 12 in the "Name Row" and 1 in the "Name Column".
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c. Repeat 6b for the Lot and the Expiry row and columns.
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7. Click the "Submit" button at the top.
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## Linking Extraction Logs:
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1. Click "Monthly" -> "Link Extraction Logs".
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2. Chose the .csv file taken from the extraction table runlogs folder.
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## Linking PCR Logs:
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1. Click "Monthly" -> "Link PCR Logs".
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2. Chose the .csv file taken from the PCR table runlogs folder.
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## SETUP:
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## Download and Setup:
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*Python v3.11 or greater must be installed on your system for this.*
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1. Clone or download from github.
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2. Enter the downloaded folder.
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3. Open a terminal in the folder with the 'src' folder.
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4. Create a new virtual environment: ```python -m venv .venv```
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5. Activate the virtual environment: (Windows) ```.venv\Scripts\activate.bat```
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6. Install dependencies: ```pip install -r requirements.txt```
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## Database:
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*If using a pre-existing database, skip this.*
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1. Copy 'alembic_default.ini' to 'alembic.ini' in the same folder.
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2. Open 'alembic.ini' and edit 'sqlalchemy.url' to the desired path of the database.
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1. The path by default is sqlite based. Postgresql support is available.
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3. Open a terminal in the folder with the 'src' folder.
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4. Run database migration: ```alembic upgrade head```
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## First Run:
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1. On first run, the application copies src/config.yml to C:\Users\\{USERNAME}\AppData\Local\submissions\config
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2. If this folder cannot be found, C:\Users\\{USERNAME}\Documents\submissions will be used.
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1. If using Postgres, the 'database_path' and other variables will have to be updated manually.
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3. Initially, the config variables are set parsing the 'sqlalchemy.url' variable in alembic.ini
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## Building Portable Application:
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*Download and Setup must have been performed beforehand*
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1. Using pyinstaller, an exe can be created.
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2. Open a terminal in the folder with the 'src' folder.
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3. Activate the virtual environment: (Windows) ```.venv\Scripts\activate.bat```
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4. Enter the following command: ```pyinstaller .\submissions.spec --noconfirm``` |