A tkinter GUI to upload files to our Girder.
Project description
Uploading data to Girder using a GUI
Getting Started
Prerequisites
1. Install python3
Any python above 3.6 should be fine. Python 3.8 is recommended. You can install python3 from one of the following:
- Download from the python official website here.
- Install python3 using brew if you are using macOS
brew install python@3.8
- Install python3 using
pyenv
. See here.
NOTE
If you used pyenv
to install Python on a Mac, tkinter
might not be integrated by default. To install tkinter
lib, you have to first uninstall your current python (if python is already installed), then reinstall it with:
PYTHON_CONFIGURE_OPTS="--with-tcltk-includes='-I/usr/local/opt/tcl-tk/include' --with-tcltk-libs='-L/usr/local/opt/tcl-tk/lib -ltcl8.6 -ltk8.6'"
pyenv install {your python version}
2. Create Girder API key
A Girder API Key is needed in order to Login the Girder System.
- Login NutritionalLungImmunity. Create an account if you don't have one.
- Click your username on the top right -> MyAccount -> API Keys Tab -> Create new key. Keep this key private!
3. Create a Zotero API Key (optional)
If you want to attach Zotero Item with the tag list from Girder, a Zotero API Key is needed.
- Login Zotero. Go to account setting page.
- Click
Create new private key
. - Under
Personal Library
, check all options. UnderDefault Group Permissions
, selectRead/Write
. Then clickSave key
. - Mark down the pop-up API key. Save it in a safe place.
Installation
-
Cloning The GitHub Repository
git clone https://github.com/NutritionalLungImmunity/data-management.git
If you don't have
git
yet, see Getting Started - Installing Git. -
Navigate to the package dir
cd data-management
-
Install the virtual environment package
python3 -m pip install virtualenv
(on Windows add.exe
topython3
)If you have trouble with permission issues installing any packages system-wide, you may have more luck by installing them as user-local packages:
python3 -m pip install --user virtualenv
-
Create a virtual environment
virtualenv -p python3 venv
(on Windows add.exe
tovirtualenv
) -
Enter the virtual environment:
. venv/bin/activate
on Windows:
.\venv\bin\activate.bat
-
Install the uploader into the virtual environment
python3 -m pip install -e .
-
Launching the uploader
nli_data_management
Note: To re-launch the program, perform steps 2, 5, and 7.
Note2: The virtual environment is optional and serves to simplify potential package dependency problems. If you wish to install the uploader outside the virtual environment, perform all steps except 3 through 5. Re-launch is done via step 7.
Initialize Connection
Connect to Girder
- Click
Upload to Girder
and a new setting window will pop up. - Under
Add new Girder instance
:- Give the new Girder instance a name.
- For
Host
, typedata.nutritionallungimmunity.org
- Copy and paste your Girder API Key in the
API Key
- Click the
add
button - Select the new added Girder instance and click
Connect
Connect to Zotero
- Click
Upload to Zotero
- Add a new Girder Instance, if you haven't done it yet.
- Under
Add new zotero Instance
:- Give the new Zotero instance a name.
- For
Library ID
, type2345225
- For
Library Type
, typegroup
- Copy and paste your Zotero API Key in the
API Key
- Click the
add
button - Select both Girder instance and Zotero instance. Click
Connect
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