Timbuctoo

Bridge to networked research data

Getting Started

Prerequisites

The following prerequisites need to be installed on the machine before running the Timbuctoo program:

• Java

• Maven

• Git

• Docker

• libxml2-utils

Start Timbuctoo without Docker

Installation

After the above requirements are fulfilled you can follow the following instructions to install Timbuctoo:

• Clone the Timbuctoo Github repository into a local directory using the command:

  git clone https://github.com/HuygensING/timbuctoo.git

Starting Timbuctoo

• On the Timbuctoo root directory run the Maven build command:

  mvn clean package

• On the "/devtools/debugrun" directory within your Timbuctoo repository, run:

  ./timbuctoo_only.sh

Start Timbuctoo with Docker

To start Timbuctoo only:

$ (sudo) docker run -p8080:80 huygensing/timbuctoo

To start Timbuctoo with Timbuctoo GUI:

$ (sudo) docker-compose up

Uploading data

• You can run a curl command of the following format to upload data into Timbuctoo:

  curl -v -F "file=@/<complete_path_to_file>/<filename>;type=<filetype>" -F "encoding=UTF-8" -H "Authorization: fake" http://localhost:8080/u33707283d426f900d4d33707283d426f900d4d0d/mydataset/upload/rdf?forceCreation=true

  `u33707283d426f900d4d33707283d426f900d4d0d` the user id of the user when no security is used.
  `mydataset` will be the name of the dataset

• You can use the provided bia_clusius.ttl data as a example dataset. The <filetype> for this is "text/turtle". It is available in the following folder:

  "/<complete path to timbuctoo>/src/test/resources/nl/knaw/huygens/timbuctoo/bia_clusius.ttl"

• Note that the above method forces a creation at upload time. Creating a dataset before doing the upload can be done at path:

  "<host>/dataSets/{userId}/{dataSetId}/create"

Querying data and Applying Mutations

• With Timbuctoo running, you can access the GraphIQL in-browser IDE by pointing your web-browser to the following address:

  http://localhost:8080/static/graphiql

• You can then refer to this Timbuctoo GraphQL API guide for querying and mutation instructions with examples.

FAQs/Q&A

I can’t access my data from the GraphiQL and I get the error "SyntaxError: JSON.parse: unexpected character at line 1 column 1 of the JSON data" on the right pane when I try to query for data.

It is likely that the filepath given while using the curl command to load the dataset was incorrect. Please note that the filepath to the dataset should be given in full (i.e. complete path from root) with a '@' symbol preceding it.

License

Timbuctoo is licensed under the GPL license

Contributing

See the contribution guidelines

Documentation

Read about compiling, installing/running and using/developing timbuctoo in the documentation folder.

Acknowledgements

Timbuctoo is and has been funded by

• The Huygens Institute

• Golden Agents (until 2022)

• CLARIAH.nl (until 2018)

• NDE (funding ends december 2016)

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This repository is available online at https://github.com/HuygensING/timbuctoo