notebook_proxy

Make Notebook Proxy

This proxy creates a notebook in Google Collab from a template. The parameters extracted from the Scicence on Schema JSON-LD files, and sent to the proxy /mknb

For testing, running locally works well.

In production, a container is utilized. This is created by a github workflow, (containerize.yaml)

Calling the Notebook Proxy

Index

http://localhost:3031/ should return the index.html

is it alive

http://localhost:3031/alive/ will let you know it's working.

generate a notebook

http://localhost:3031/mknb/ This proxy creates a notebook in Google Collab from a template. The parameters extracted from the Scicence on Schema JSON-LD files, and sent to the proxy /mknb

• url - url of the resource
• ext - encoding format of the resource.
• urn - urn geocodes urn.
• template -- name of the template file to render. (optional: default: template.ipynb)

Note about url, urns, ext: A hash in the name of the item causes the rest of the url passed to be ignored. To avoid this, we custom encode '#' as <hash>

so:

ext=http://linked.earth/ontology/core/1.2.0/index-en.html#Dataset

becomes:

ext=http://linked.earth/ontology/core/1.2.0/index-en.html<hash>Dataset

generate jsonld from a graphstore

A call like http://localhost:3031/get_graph/urn:gleaner:summoned:opentopography:0024e35144d902d8b413ffd400ede6a27efe2146/json

several forms can be returned

http://localhost:3031/get_graph/{URN}/jsonld

http://localhost:3031/get_graph/{URN}/framed

http://localhost:3031/get_graph/{URN}/compact

http://localhost:3031/get_graph/{URN}/csv

http://localhost:3031/get_graph/{URN}/tsv

Development:

install ec utiltites in development mode

python -m pip install -e ec ../earthcube_utilities

python -m pip install -e bar @ git+https://github.com/earthcube/earthcube_utilities.git

python -m pip install -e ec /path/to/earthcube_utilities

start

In order to use oauth, you need to setup a github app, and set the following environment variables

GITHUB_OAUTHSECRET = GITHUB APP Secret GITHUB_OAUTHCLIENTID = GIHUB Client ID

cd src/notebook_proxy
flask mknb

this will start it at: http://localhost:5000/

cd src/notebook_proxy
python mknb.py

http://localhost:3031/

Docker

A docker container is built using github actions:

https://hub.docker.com/repository/docker/nsfearthcube/mknb

Note need to update to https://github.com/tiangolo/uwsgi-nginx-flask-docker

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Setting up a developer access token

before use you need a token:

• go to settings>developer settings.
• personal access token
• create a token with gist permissions.

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command to install a container for local use:

docker pull nsfearthcube/mknb:latest

docker run -e GITHUB_CLIENTID={GITHUB OAUTH APP} -e GITHUB_SECRET={GITHUB OAUTH APP SECRET}  -p 127.0.0.1:3031:3031 nsfearthcube/mknb:latest

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For docker compose:

Need notes here.

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Local Build

You can build locally from the earthcube_utilities directory

% docker build .

% docker images

REPOSITORY          TAG       IMAGE ID       CREATED          SIZE
<none>              <none>    1f0ebd17e990   22 minutes ago   959MB

image id is: 1f0ebd17e990

docker run -e GIST_TOKEN={YOUR TOKEN} -e GIST_USERNAME={YOU USERNAME} -p 127.0.0.1:3031:3031 {image id}

Proxy is now running at: http://localhost:3031/

try: http://localhost:3031/mknb?url=http://lipdverse.org/Temp12k/1_0_2/Svartvatnet-Norway.Seppa.2009.lpd&ext=application%2Fzip%20%3B%20http%3A%2F%2Flinked.earth%2Fontology%2Fcore%2F1.2.0%2Findex-en.html%3Chash%3EDataset&urn=urn:gleaner:milled:lipdverse:509e465d0793506b237cea8069c3cb2d276fe9c2&encoding=application%2Fzip%20%3B%20http%3A%2F%2Flinked.earth%2Fontology%2Fcore%2F1.2.0%2Findex-en.html%3Chash%3EDataset&

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Testing and development notes

from raw.github http://localhost:5000/mknb?url=http://lipdverse.org/Temp12k/1_0_2/Svartvatnet-Norway.Seppa.2009.lpd&ext=application%2Fzip%20%3B%20http%3A%2F%2Flinked.earth%2Fontology%2Fcore%2F1.2.0%2Findex-en.html%3Chash%3EDataset&urn=urn:gleaner:milled:lipdverse:509e465d0793506b237cea8069c3cb2d276fe9c2&encoding=application%2Fzip%20%3B%20http%3A%2F%2Flinked.earth%2Fontology%2Fcore%2F1.2.0%2Findex-en.html%3Chash%3EDataset&template=https://raw.githubusercontent.com/earthcube/NotebookTemplates/geocodes_template/GeoCODEStemplates/ARGO/SA_01_Argo_Data_Exploration.ipynb

http://localhost:5000/mknb?url=http://lipdverse.org/Temp12k/Svartvatnet-Norway.Seppa.2009.lpd&ext=application%2Fzip%20%3B%20http%3A%2F%2Flinked.earth%2Fontology%2Fcore%2F1.2.0%2Findex-en.html%3Chash%3EDataset&urn=urn:gleaner:milled:lipdverse:509e465d0793506b237cea8069c3cb2d276fe9c2&encoding=application%2Fzip%20%3B%20http%3A%2F%2Flinked.earth%2Fontology%2Fcore%2F1.2.0%2Findex-en.html%3Chash%3EDataset&template=https://github.com/earthcube/NotebookTemplates/blob/geocodes_template/GeoCODEStemplates/Development/2_numpy.ipynb