# PHE python script example

See Run phe_upload.py.

- Designed to run on a windows host with Python 3
- TOML format config file initially acts as a rudimentary ruleset for generating lists of files with metadata to upload to iRODS
- Windows filesystem creation date is provided as an optional metadata key value pair
- Add custom key value pairs to the ruleset
- Generated upload_files.toml list is used for subsequent run of the script, this maybe used as a template to target any files with any key value pairs
- Where upload_files.tml exists the config file will only be used iRODS connectivity  

## Python iRODS client

> https://github.com/irods/python-irodsclient

## Windows 10 vitual env setup

```
# setup python venv
cd C:\PHE_iRODS
mkdir venv
python -m venv C:\PHE_iRODS\venv

# enter virtual env
C:\PHE_iRODS\venv\Scripts\Activate.ps1

# install pip packages
pip install --upgrade pip
pip install python-irodsclient
pip install toml

# to save all pip module requirements
pip3 freeze > venv-requirements.txt

# to install requirements on a new venv
pip3 install -r venv-requirements.txt

# exit venv
deactivate
```

## Required PIP packages, should already be installed from venv-requirements

```
pip install python-irodsclient
pip install toml
```

## Run phe_upload.py

* run once to create sample config file
* modify config for your environment
* run again to produce a sample file list based on your modified config
* modify the file list - this maybe wiped and used as a template to include files from any local/mounted path, each entry must have a unique numerical top level key, this is arbritrary and no sequence is required
* run again to upload files
* a log file is produced for each run of the script, containing skipped files that did not meet validation and failed/sucessful uploads
* to run the script without confirmation, pass the argument --confirm