content_uploader

Content Uploader

The Content Uploader is a GUI frontend to the file upload facility provided by the data_service for importing files and classifying them under the correct patient / fraction / category. The files are upoaded via HTTPS and are saved on the filesystem partition where the rest of the database files physically exist.

To use the Content Uploader, it is necessary to have proper authentication and be authorised to be able to import files related to a specific trial from a specific treatment centre. These authorisations are granted to tokens, which are small files containing a digitally signed token ID and other related details. Based to the type of token, it may be assigned a password, which would have to entered while authenticating with the token.

Finally, the user should select the appropriate patient and type of file (and other relevant details such as fraction number etc.) and proceed to uploading them.

Executing the Content Uploader

Invoking as a Python Module

The Content Uploader is a python 3 module, which can be invoked using the following command:

python ContentUploader.py

To make sure that all the required dependencies are available in the Python environment, where it would run, either create a conda environment or a virtual environment using the requirements.txt file to install all the required packages.

Setting up the Python Environment

Please run the following commands to setup your python environment (this is required only once). Please ensure that the correct environment is set before installing the requirements. For example, if using conda, ensure that conda activate <proper_environment_name> has been executed.

Anaconda/Miniconda based install

conda install --file requirements.txt

Pip based install

pip install -r requirements.txt

Building a Portable Executable

The Content Uploader can be built into a self contained executable file using the build_bins.bat script. This uses the pyinstaller module, which is included in the requirements. Such an execuatble is also included in the final release package.

Usage Instructions

Authentication

Upon starting the Content Uploader, it would present an authentication screen to the user similar to the following figure.

For authenticating with the backend, the following steps should be followed as indicated in the above figure:

1. By clicking on the open folder button, select the token file (which can be saved in a local drive or loaded from a USB drive etc.)
2. If the token has an associated password, then enter it in the input field labelled "Secret:"
3. Ensure that the correct service URL is present in the next input field.
4. Finally, press the button labelled "Login".

Upon successful authentication, the authentication window would be replaced by the main screen of the Content Uploader.

Uploading Content

The main screen of the content uploader would be similar to the following figure:

To use the content uploader, the following steps should be followed matching the labels of the above figure:

1. Enter the clinical trial ID of the patient whose files are getting uploaded; this could be an ID issued by TROG etc.
2. Click on the button next to ID input field for the application to fetch the details related to the patient. Verify that the patient sequence, test centre, trial name etc. are corect before proceeding.
3. Select the type of file(s) that are going to be uploaded. Be careful: once this category is assigned and uploaded, it cannot be changed later.
4. If the files are related to a specific fraction, select the fraction (this dropdown field would only be enabled if the file category is related to fractions insted of the overall patient records).
5. Drag and drop either a selection of files or entire folder content from the OS file explorer into the file recieving rectangle. Please ensure that all the files/folders dropped here are only related to the category selected in the above step.
6. Click on the button labelled "Add Files". This would queue the dropped files/ folders to be uploaded.
7. The file upload queue can list multiple set of files for uploading. To add multiple types of files, follow the steps 3 to 6 for each file category.
8. Finally, clicking on the button labelled "upload" would start the file upload process.

The upload process of the files is indicated by a pair of progress indicators, which display the progress of individual files being transferred across the network and the overall progress. The status area at the very bottom would indicate if there are any issues encountered while transferring the files.