Merge pull request #30 from c-martinez/readme

Readme

README.md

@@ -3,35 +3,34 @@
 [![Coverage Status](https://coveralls.io/repos/github/c-martinez/FAIRDataPoint/badge.svg?branch=dev)](https://coveralls.io/github/c-martinez/FAIRDataPoint?branch=dev)
 
 
-### FAIR Data Point (FDP)
+# FAIR Data Point (FDP)
 
 Python implementation of FAIR Data Point.
 
 FDP is a RESTful web service that enables data owners to describe and to expose their datasets (metadata) as well as data users to discover more information about available datasets according to the [FAIR Data Guiding Principles](http://www.force11.org/group/fairgroup/fairprinciples). In particular, FDP addresses the findability or discoverability of data by providing machine-readable descriptions (metadata) at four hierarchical levels:
 
 *FDP->catalogs->datasets->distributions*
 
-FDP software specification can be found [here](https://dtl-fair.atlassian.net/wiki/spaces/FDP/pages/6127622/FAIR+Data+Point+Software+Specification).
+FDP software specification can be found [here](https://github.com/FAIRDataTeam/FAIRDataPoint-Spec/blob/master/spec.md)
 
 FDP has been implemented in:
-* [Python](https://github.com/NLeSC/ODEX-FAIRDataPoint/)
+* [Python](https://github.com/NLeSC/FAIRDataPoint/)
 * [Java](https://github.com/DTL-FAIRData/FAIRDataPoint)
 
 ## Installation
-------------
 
-To install fdp, do:
+To install FDP, do
 
 ```bash
-git clone https://github.com/NLeSC/ODEX-FAIRDataPoint.git
-cd ODEX-FAIRDataPoint
+git clone https://github.com/NLeSC/fairdatapoint.git
+cd fairdatapoint
 pip install .
 ```
-TODO: register on pypi and change this to `pip install fairdatapoint`
+TODO: update it when there is a release on pypi
 
 ## Running
 ```bash
-fdp-run samples/plant_breeding_group.ttl
+fdp-run localhost 8080
 ```
 
 Then visit from your browser: http://localhost:8080/
@@ -40,104 +39,86 @@ Then visit from your browser: http://localhost:8080/
 Run tests (including coverage) with:
 
 ```bash
-python setup.py test
+pip install .[tests]
+pytest
 ```
 
 TODO: Include a link to your project's full documentation here.
 
-## Contributing
-
-If you want to contribute to the development of FAIR Data Point,
-have a look at the [contribution guidelines](CONTRIBUTING.rst).
-
-## License
-
-Copyright (c) 2019,
-
-Licensed under the Apache License, Version 2.0 (the "License");
-you may not use this file except in compliance with the License.
-You may obtain a copy of the License at
-
-http://www.apache.org/licenses/LICENSE-2.0
-
-Unless required by applicable law or agreed to in writing, software
-distributed under the License is distributed on an "AS IS" BASIS,
-WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-See the License for the specific language governing permissions and
-limitations under the License.
 
 ## Deploy with Docker
-TODO: update docker deployment
-
-`docker run -p 8080:8080 -d nlesc/odex-fairdatapoint`
-
-## Deploy without Docker
-TODO: update this section
-
-Clone this repo.
 
+Download the `docker-compose.prod.yml` from this repo, change the `HOSTNAME` in the file to a proper host, and then run the command
 ```
-git clone https://github.com/NLeSC/ODEX-FAIRDataPoint.git
-cd ODEX-FAIRDataPoint/fdp-api/python
+docker-compose -f docker-compose.prod.yml up -d
 ```
 
-Install FDP into ENV.
+## Deploy without Docker
+
+Before deploying FDP, it's necessary to first have a running SPARQL database.
 
 ```
-python -m venv ENV
-source /ENV/bin/activate
+git clone https://github.com/NLeSC/fairdatapoint.git
+cd fairdatapoint
+pip install .
 
-make install
-# make clean # removes files from doc dir (except swagger.json)
+# fdp-run <host> <port> --db=<sparql-endpoint>
+fdp example.com 8080 --db='http://dbpedia.org/sparql'
 ```
 
-Edit metadata in `config.ini`.
+## Web API documentation
 
-```
-# in development
-make serve-dev # with default HOST=127.0.0.1:8080
-make test
-# in production
-make -e serve-prod HOST=example.com
-```
+FAIR Data Point (FDP) exposes the following endpoints (URL paths):
 
-**Web API documentation**
+| Endpoint |  GET  | POST |      DELETE     |
+|--------------|:--------------:|:-----------------:|:--------------:|
+| fdp | Output metadata triples | Remove existing triples for a specific ID, then create new triples with the request data | Not Allowed |
+| catalog/     | Output all IDs   | Remove existing triples for a specific ID, then create new triples with the request data | Remove all IDs |
+| dataset/     | Output all IDs   | Remove existing triples for a specific ID, then create new triples with the request data | Remove all IDs |
+| distribution/  | Output all IDs  | Remove existing triples for a specific ID, then create new triples with the request data | Remove all IDs |
+| catalog/\<catalogID\> | Output metadata triples | Not Allowed | Remove the specific ID |
+| dataset/\<datasetID\> | Output metadata triples | Not Allowed | Remove the specific ID |
+| distribution/\<distributionID\> | Output metadata triples | Not Allowed | Remove the specific ID |
 
-Base URL: `http://127.0.0.1:8080`
 
-**Access endpoints to request metadata programmatically**
+### Access endpoints to request metadata programmatically
 
 FDP: `curl -iH 'Accept: text/turtle' [BASE URL]/fdp`
 
-Catalog: `curl -iH 'Accept: text/turtle' [BASE URL]/catalog/catalog-01`
+Catalog: `curl -iH 'Accept: text/turtle' [BASE URL]/catalog/catalog01`
 
-Dataset: `curl -iH 'Accept: text/turtle' [BASE URL]/dataset/breedb`
+Dataset: `curl -iH 'Accept: text/turtle' [BASE URL]/dataset/dataset01`
 
-Distribution: `curl -iH 'Accept: text/turtle' [BASE URL]/distribution/breedb-sparql`
+Distribution: `curl -iH 'Accept: text/turtle' [BASE URL]/distribution/dist01`
 
-Note: FDP supports the following RDF serializations (MIME-types):
+### FDP supports the following RDF serializations (MIME-types):
 * Turtle: `text/turtle`
 * N-Triples: `application/n-triples`
+* N3: `text/n3`
 * RDF/XML: `application/rdf+xml`
 * JSON-LD: `application/ld+json`
 
 
-## FAIR Data Point specification
+## Contributing
+
+If you want to contribute to the development of FAIR Data Point,
+have a look at the [contribution guidelines](CONTRIBUTING.rst).
+
+## License
 
-FAIR Data Point (FDP) exposes the following endpoints (URL paths):
+Copyright (c) 2019,
+
+Licensed under the Apache License, Version 2.0 (the "License");
+you may not use this file except in compliance with the License.
+You may obtain a copy of the License at
+
+http://www.apache.org/licenses/LICENSE-2.0
 
-| Endpoints | Description |
-| -- | -- |
-| [ /, /doc, /doc/ ]   | Redirects to the API documentation |
-| /fdp                 | Returns FDP metadata |
-| /catalog/{catalogID} | Returns catalog metadata (default: catalog-01) |
-| /dataset/{datasetID} | Returns dataset metadata (default: breedb) |
-| /distribution/{distributionID} | Returns distribution metadata (default: breedb-sparql) |
-
-This services makes use of:
- - [Data Catalog Vocabulary](http://www.w3.org/TR/vocab-dcat/)
- - [Dublin Core Metadata Terms](http://dublincore.org/documents/dcmi-terms/)
- - [DBpedia](http://dbpedia.org/resource/)
+Unless required by applicable law or agreed to in writing, software
+distributed under the License is distributed on an "AS IS" BASIS,
+WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+See the License for the specific language governing permissions and
+limitations under the License.
 
  ## Credits
 

docker-compose.prod.yml

@@ -0,0 +1,17 @@
+version: '3'
+services:
+  fdp:
+    build: .
+    image: ""
+    command: fdp-run HOSTNAME 8080 --db http://db:8890/sparql
+    ports:
+      - "8080:8080"
+    depends_on:
+      - db
+  db:
+    image: "tenforce/virtuoso"
+    ports:
+        - "8890:8890"
+        - "1111:1111"
+    environment:
+        SPARQL_UPDATE: "true"

setup.cfg

@@ -1,10 +1,6 @@
 [metadata]
 description-file = README.rst
 
-[aliases]
-# Define `python setup.py test`
-test=pytest
-
 [coverage:run]
 branch = True
 source = fdp