CaosDB.jl

CaosDB interface for Julia

Currently WIP.

Note (2019-10-15): As XML support in Julia is not working smoothly we are working on providing a json interface. This is currently work in progress.

Update (2020-05-14): Problems with EzXML seem to have been solved. This library is working.

Howto

Import the package:

using CaosDB

Create a connection:

c = CaosDB.Connection("https://demo.indiscale.com/")

The connection stores the address to the CaosDB instance (here: demo.indiscale.com). It is passed on to other functions within the CaosDB package. Note that the trailing slash is important, so "https://demo.indiscale.com" would not work. demo.indiscale.com is the demo instance hosted by IndiScale GmbH. This instance should not be used for writing (e.g. inserting) of data. Please use playground.indiscale.com instead.

Retrieve and Query

Retrieve an Entity by id:

CaosDB.retrieve("281", c)

Do a simple query:

doc = CaosDB.query("Find Analysis", c)

You can access the individual entries using the properties attribute of the entity structs. doc[1] is a RecordType in this case and contains only unset properties:

doc[1].properties[1].value

doc[2] is a Record, so values are set:

doc[2].properties[3].value

Inserting of RecordTypes and Records

Create a simple property:

p = CaosDB.Property(name="a", datatype="INTEGER",
                   description="just a property which we can use for a quick test")

Create a simple record type:

rt = CaosDB.RecordType(name="CoolType", properties=[p])
CaosDB.insert([p, rt], c)

... of course that does not work. Insufficient permissions.

So let's try as admin:

c2 = CaosDB.Connection("https://playground.indiscale.com/")
CaosDB.login("admin", "caosdb", c2)
CaosDB.insert([p, rt], c2)

Ok, that should have worked! If you run this code twice, you end up having multiple of these types (this can be configured on the server).

So, what about records?

r1 = CaosDB.Record(parents=CaosDB.query("Find CoolType", c2),
                   properties=[CaosDB.Property(name="a", value="283")])
res = CaosDB.insert([r1], c2)

Now, that a RecordType and a Record have been inserted, we can easily search for them using CaosDB CQL (See https://gitlab.com/caosdb/caosdb/-/wikis/manuals/CQL/CaosDB%20Query%20Language for details):

search_results = CaosDB.query("Find CoolType", c2)

# Or, if you are only interested in the record:
search_results = CaosDB.query("Find Record CoolType", c2)

# Access your results:
search_results[1].properties[1].value

About CaosDB

CaosDB is an open source research data managament system (RDMS). It consists of a server application (written in Java) and clients that communicate with the server to insert, retrieve, update and query data.

The server can be accessed using either the WebUI (have a look at a demo instance here: https://demo.indiscale.com), or one of the clients.

Key Features

CaosDB has some key features that make it especially useful for scientific data management:

• Data insertion is mostly automatic using the data crawler
• A semantic data model allows for continuous adaption to changes in the scientific workflow (e.g. new devices, new types of computer simulation, new analysis software)
• A special query language (CQL), that is intuitive also for non-programmers, which can be accessed from the WebUI or from all client interfaces.

More Information

Official webpage: https://caosdb.org/

CaosDB article: https://www.mdpi.com/2306-5729/4/2/83/htm

Sourcecode: https://gitlab.com/caosdb

CaosDB-Documentation: https://gitlab.com/caosdb/caosdb/-/wikis/home

Research Group Biomedical Physics Webpage: http://bmp.ds.mpg.de/software/caosdb/

Demo instance hosted by IndiScale: https://demo.indiscale.com