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# QC/QA Data Flagging Application # QC/QA Data Flagging Application
This repository hosts a Dash Plotly data flagging app for ACSM data structured in HDF5 format using the DIMA submodule. The provided Jupyter notebooks walk you through the steps to append metadata about diagnostic and target channels, which are necessary for the app to run properly. This repository hosts a Dash Plotly data flagging app for ACSM data structured in HDF5 format using the DIMA submodule. The provided Jupyter notebooks walk you through the steps to append metadata about diagnostic and target channels, which are necessary for the app to run properly.
## Getting Started ## Getting Started
### Requirements ### Requirements
For Windows users, the following are required: For Windows users, the following are required:
1. **Git Bash**: Git Bash will be used to run shell scripts (`.sh` files). 1. **Git Bash**: Git Bash will be used to run shell scripts (`.sh` files).
2. **Conda**: You must have [Anaconda](https://www.anaconda.com/products/individual) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html) installed on your system. Git Bash needs access to Conda to set up the environment properly. Ensure that Conda is added to your system’s PATH during installation. 2. **Conda**: You must have [Anaconda](https://www.anaconda.com/products/individual) or [Miniconda](https://docs.conda.io/en/latest/miniconda.html) installed on your system. Git Bash needs access to Conda to set up the environment properly. Ensure that Conda is added to your system’s PATH during installation.
3. **PSI Network Access (for data retrieval)**: Real data retrieval can only be performed when connected to the PSI network and with the appropriate access rights to the source network drive. 3. **PSI Network Access (for data retrieval)**: Real data retrieval can only be performed when connected to the PSI network and with the appropriate access rights to the source network drive.
## Clone the Repository ## Clone the Repository
Open **Git Bash** and run: Open **Git Bash** and run:
```bash ```bash
cd GitLab cd GitLab
git clone --recurse-submodules https://gitlab.psi.ch/apog/acsmnode.git git clone --recurse-submodules https://gitea.psi.ch/APOG/acsmnode.git
cd acsmnode cd acsmnode
``` ```
## Run the Data Chain App ## Run the Data Chain App
1. Open **PowerShell as Administrator** and navigate to the `acsmnode` repository. 1. Open **PowerShell as Administrator** and navigate to the `acsmnode` repository.
2. Create a `.env` file in the root of `acsmnode/`. 2. Create a `.env` file in the root of `acsmnode/`.
3. **Securely store your network drive access credentials** in the `.env` file by adding the following lines: 3. **Securely store your network drive access credentials** in the `.env` file by adding the following lines:
```plaintext ```plaintext
CIFS_USER=<your-username> CIFS_USER=<your-username>
CIFS_PASS=<your-password> CIFS_PASS=<your-password>
``` ```
**To protect your credentials:** **To protect your credentials:**
- Do not share the .env file with others. - Do not share the .env file with others.
- Ensure the file is excluded from version control by adding .env to your .gitignore and .dockerignore files. - Ensure the file is excluded from version control by adding .env to your .gitignore and .dockerignore files.
4. Open **Docker Desktop**, then build the container image: 4. Open **Docker Desktop**, then build the container image:
```bash ```bash
docker build -t datachain_processor . docker build -t datachain_processor .
``` ```
5. Run the app: 5. Run the app:
```bash ```bash
docker compose --file docker-compose.yaml up datachain_processor docker compose --file docker-compose.yaml up datachain_processor
6. Access: 6. Access:
- **Jupyter Lab**: [http://localhost:8889/lab/tree/notebooks/](http://localhost:8889/lab/tree/notebooks/) - **Jupyter Lab**: [http://localhost:8889/lab/tree/notebooks/](http://localhost:8889/lab/tree/notebooks/)
7. Stop the app: 7. Stop the app:
In the previously open PowerShell terminal, enter: In the previously open PowerShell terminal, enter:
```bash ```bash
Ctrl + C Ctrl + C
``` ```
After the container is properly Stopped, remove the container process as: After the container is properly Stopped, remove the container process as:
```bash ```bash
docker rm $(docker ps -aq --filter ancestor=datachain_processor) docker rm $(docker ps -aq --filter ancestor=datachain_processor)
``` ```
## Set Up the Python Environment ## Set Up the Python Environment
If **Git Bash** lacks a suitable Python interpreter, run: If **Git Bash** lacks a suitable Python interpreter, run:
```bash ```bash
bash env_setup.sh bash env_setup.sh
``` ```
## Run the Dashboard App ## Run the Dashboard App
Run the following command to start the dashboard app: Run the following command to start the dashboard app:
```bash ```bash
python data_flagging_app.py python data_flagging_app.py
``` ```
This command will launch the data flagging app. This command will launch the data flagging app.
## Stop the Dashboard App ## Stop the Dashboard App
Run the following command to stop the dashboard app: Run the following command to stop the dashboard app:
```bash ```bash
CTRL + C CTRL + C
``` ```
This command will terminate the server process running the app. This command will terminate the server process running the app.