Installing SubmitCGAP¶

Setting Up a Virtual Environment (OPTIONAL)¶

This is optional. If you use Poetry and do not create a virtual environment, Poetry will make one for you. But there are still good reasons you might want to make your own, so here are three ways to do it:

If you have virtualenvwrapper that knows to use Python 3.6:
```
mkvirtualenv myenv
```
If you have virtualenv but not virtualenvwrapper, and you have python3.6 in your PATH:
```
virtualenv myenv -p python3.6
```
If you are using pyenv to control what environment you use:
```
pyenv exec python -m venv myenv
```

Activating a Virtual Environment¶

You should execute all actions related to this repository from within a virtual environment.

To activate a virtual environment:

source myenv/bin/activate

Deactivating a Virtual Environment¶

It’s rarely necessary to deactivate a virtual environment. One is automatically deactivated if you enter another, and normally they have very little effect on other actions you might take. So it’s normally safe to just leave them activated.

However, if you want to deactivate an active environment, just do:

deactivate

Installing Poetry in a Virtual Environment¶

End Users: Submit-CGAP can be installed with a simple pip install:

pip install submit-cgap

Developers: Once you have created a virtual environment, or have decided to just let Poetry handle that, install with poetry:

poetry install

Setting Up Credentials¶

Credentials can be placed in a file named ~/.cgap-keys.json. The file format is:

{"envname1": {"key": ..., "secret": ..., "server": ...}, "envname2": ..., ...}

For most CGAP environments, the envname to use is the part of the url preceding .hms.harvard.edu, such as cgap-mgb or cgap-devtest. For end users, reach out to your contact on the CGAP team or at cgap-support@hms-dbmi.atlassian.net if you’re not sure which server you need to submit to. A typical file might look like below for end users (replace the example environment and server with your own envname and server):

{
    "cgap-main": {
        "key": "some_key",
        "secret": "some_secret",
        "server": "https://cgap-main.hms.harvard.edu"
    }
}

For developers, the suggested envname to use for local debugging (for developers) is “fourfront-cgaplocal”. You will probably have several keys in your credential file. An example keyfile is shown below (note that the CGAP servers used are just example urls):

{
    "cgap-main": {
        "key": "some_key",
        "secret": "some_secret",
        "server": "https://cgap-main.hms.harvard.edu"
    },
    "fourfront-cgaplocal": {
        "key": "some_other_key",
        "secret": "some_other_secret",
        "server": "http://localhost:8000"
    },
    "cgap-testing": {
        "key": "some_third_key",
        "secret": "some_third_secret",
        "server": "https://cgap-testing.hms.harvard.edu"
    }
}

This file should _not_ be readable by others than yourself. Set its permissions accordingly by using chmod 600, which sets the file to be readable and writable only by yourself, and to give no one else (but the system superuser) any permissions at all:

$ ls -dal ~/.cgap-keys.json
-rw-r--r--  1 jqcgapuser  staff  297 Sep  4 13:14 /Users/jqcgapuser/.cgap-keys.json

$ chmod 600 ~/.cgap-keys.json

$ ls -dal ~/.cgap-keys.json
-rw-------  1 jqcgapuser  staff  297 Sep  4 13:14 /Users/jqcgapuser/.cgap-keys.json