mirror of
https://gitea.psi.ch/APOG/acsmnode.git
synced 2025-06-27 03:51:13 +02:00
Update README.md. Changed git clone url to gitea
This commit is contained in:
166
README.md
166
README.md
@ -1,84 +1,84 @@
|
||||
# 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.
|
||||
|
||||
## Getting Started
|
||||
|
||||
### Requirements
|
||||
|
||||
For Windows users, the following are required:
|
||||
|
||||
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.
|
||||
|
||||
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
|
||||
|
||||
Open **Git Bash** and run:
|
||||
|
||||
```bash
|
||||
cd GitLab
|
||||
git clone --recurse-submodules https://gitlab.psi.ch/apog/acsmnode.git
|
||||
cd acsmnode
|
||||
```
|
||||
|
||||
## Run the Data Chain App
|
||||
|
||||
1. Open **PowerShell as Administrator** and navigate to the `acsmnode` repository.
|
||||
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:
|
||||
```plaintext
|
||||
CIFS_USER=<your-username>
|
||||
CIFS_PASS=<your-password>
|
||||
```
|
||||
**To protect your credentials:**
|
||||
- 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.
|
||||
4. Open **Docker Desktop**, then build the container image:
|
||||
```bash
|
||||
docker build -t datachain_processor .
|
||||
```
|
||||
5. Run the app:
|
||||
```bash
|
||||
docker compose --file docker-compose.yaml up datachain_processor
|
||||
6. Access:
|
||||
- **Jupyter Lab**: [http://localhost:8889/lab/tree/notebooks/](http://localhost:8889/lab/tree/notebooks/)
|
||||
|
||||
7. Stop the app:
|
||||
In the previously open PowerShell terminal, enter:
|
||||
```bash
|
||||
Ctrl + C
|
||||
```
|
||||
After the container is properly Stopped, remove the container process as:
|
||||
```bash
|
||||
docker rm $(docker ps -aq --filter ancestor=datachain_processor)
|
||||
```
|
||||
|
||||
## Set Up the Python Environment
|
||||
|
||||
If **Git Bash** lacks a suitable Python interpreter, run:
|
||||
|
||||
```bash
|
||||
bash env_setup.sh
|
||||
```
|
||||
|
||||
|
||||
## Run the Dashboard App
|
||||
Run the following command to start the dashboard app:
|
||||
|
||||
```bash
|
||||
python data_flagging_app.py
|
||||
```
|
||||
|
||||
This command will launch the data flagging app.
|
||||
|
||||
## Stop the Dashboard App
|
||||
|
||||
Run the following command to stop the dashboard app:
|
||||
|
||||
```bash
|
||||
CTRL + C
|
||||
```
|
||||
# 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.
|
||||
|
||||
## Getting Started
|
||||
|
||||
### Requirements
|
||||
|
||||
For Windows users, the following are required:
|
||||
|
||||
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.
|
||||
|
||||
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
|
||||
|
||||
Open **Git Bash** and run:
|
||||
|
||||
```bash
|
||||
cd GitLab
|
||||
git clone --recurse-submodules https://gitea.psi.ch/APOG/acsmnode.git
|
||||
cd acsmnode
|
||||
```
|
||||
|
||||
## Run the Data Chain App
|
||||
|
||||
1. Open **PowerShell as Administrator** and navigate to the `acsmnode` repository.
|
||||
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:
|
||||
```plaintext
|
||||
CIFS_USER=<your-username>
|
||||
CIFS_PASS=<your-password>
|
||||
```
|
||||
**To protect your credentials:**
|
||||
- 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.
|
||||
4. Open **Docker Desktop**, then build the container image:
|
||||
```bash
|
||||
docker build -t datachain_processor .
|
||||
```
|
||||
5. Run the app:
|
||||
```bash
|
||||
docker compose --file docker-compose.yaml up datachain_processor
|
||||
6. Access:
|
||||
- **Jupyter Lab**: [http://localhost:8889/lab/tree/notebooks/](http://localhost:8889/lab/tree/notebooks/)
|
||||
|
||||
7. Stop the app:
|
||||
In the previously open PowerShell terminal, enter:
|
||||
```bash
|
||||
Ctrl + C
|
||||
```
|
||||
After the container is properly Stopped, remove the container process as:
|
||||
```bash
|
||||
docker rm $(docker ps -aq --filter ancestor=datachain_processor)
|
||||
```
|
||||
|
||||
## Set Up the Python Environment
|
||||
|
||||
If **Git Bash** lacks a suitable Python interpreter, run:
|
||||
|
||||
```bash
|
||||
bash env_setup.sh
|
||||
```
|
||||
|
||||
|
||||
## Run the Dashboard App
|
||||
Run the following command to start the dashboard app:
|
||||
|
||||
```bash
|
||||
python data_flagging_app.py
|
||||
```
|
||||
|
||||
This command will launch the data flagging app.
|
||||
|
||||
## Stop the Dashboard App
|
||||
|
||||
Run the following command to stop the dashboard app:
|
||||
|
||||
```bash
|
||||
CTRL + C
|
||||
```
|
||||
This command will terminate the server process running the app.
|
||||
Reference in New Issue
Block a user