From b879020c5e651850dedfee8c05e754e2350fd0bc Mon Sep 17 00:00:00 2001 From: vermeul <swen@ethz.ch> Date: Thu, 31 Oct 2019 12:40:59 +0100 Subject: [PATCH] Update DEVELOPER.md --- DEVELOPER.md | 29 +++++++++++++++++++++++++---- 1 file changed, 25 insertions(+), 4 deletions(-) diff --git a/DEVELOPER.md b/DEVELOPER.md index 52642d7..5ec5309 100644 --- a/DEVELOPER.md +++ b/DEVELOPER.md @@ -8,12 +8,12 @@ This Jupyter extension contains of two components: * written in Python * see [jupyter-openbis-extension/](jupyter-openbis-extension) -* is registered with the `jupyter serverextension enable --py jupyter-openbis-extension` command +* serverextension is registered with the `jupyter serverextension enable --py jupyter-openbis-extension` command * registration should happen automatically when installilng via `pip install jupyter-openbis-extension` * this serverextension is loaded whenever a Jupyter server is started – either `jupyter notebook` or `jupyter lab` * serverextension talks to openBIS instances via the [pyBIS module](https://pypi.org/project/PyBIS/) * serverextension also talks to the notebook extension (see below) via https -* serverextension uses an instance of the [tornado webserver](https://www.tornadoweb.org/en/stable/) that is used by Jupyter +* serverextension uses an instance of the [tornado webserver](https://www.tornadoweb.org/en/stable/) that is used by Jupyter server * downloads and uploads dataSets and openBIS metadata **Jupyter notebook extension** (aka Jupyter nbextension) @@ -27,8 +27,29 @@ This Jupyter extension contains of two components: * displays the three prominent buttons (configuration, download, upload) inside a Jupyter notebook * talks to the Jupyter serverextension (see above) via https requests +## Jupyter serverextension +sources see [jupyter-openbis-extension/](jupyter-openbis-extension) +[server.py](jupyter-openbis-extension/server.py) dispatches all requests coming from the nbextension. Currently, following endpoints are present: - - \ No newline at end of file +* GET `/openbis/dataset/(?P<connection_name>.*)?/(?P<permId>.*)?/(?P<downloadPath>.*)` – downloads the files of a dataSet to the disk. +* POST `/openbis/dataset/(?P<connection_name>.*)` – upload of dataSets +* GET `/openbis/datasetTypes/(?P<connection_name>.*)` – receive a list of available dataSet types (including all properties) +* GET `/openbis/sample/(?P<connection_name>.*)?/(?P<identifier>.*)` – receive a list of dataSets for a given sample or experiment identifier (should be *dataSets*, not *sample*) +* GET/POST `/openbis/conns` – receive openBIS connections or create new ones +* PUT `/openbis/conn/(?P<connection_name>.*)` – modifiy an existing openBIS connection + +[connection.py](jupyter-openbis-extension/connection.py) – handles the openBIS connections +[dataset.py](jupyter-openbis-extension/dataset.py) – handles the dataSets (down- and upload) +[sample.py](jupyter-openbis-extension/server.py) – returns the list of available dataSets + + +## Jupyter nbextension + +[main.js](jupyter-openbis-extension/static/main.js) – Main entry point for the nbextension. Registers the connectionDialog, downloadDialog, and uploadDialog +[connectionDialog.js](jupyter-openbis-extension/static/connectionDialog.js) – shows the connection dialog +[downloadDialog.js](jupyter-openbis-extension/static/downloadDialog.js) – shows the download dialog +[uploadDialog.js](jupyter-openbis-extension/static/uploadDialog.js) – shows the upload dialog +[state.js](jupyter-openbis-extension/static/state.js) – stores some state information, e.g. current connection, last downloaded dataSet, last entered metadata etc. +[common.js](jupyter-openbis-extension/static/common.js) – commonly used utilities, e.g. create feedback, create error message, get cookie \ No newline at end of file -- GitLab