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https://github.com/vcityteam/conver-g

This project aims to create a knowledge hub that can store and query a set of RDF datasets with a versioning system. The project is part of the BD team's research efforts within the LIRIS and VCity project. The aim of this POC is to query a set of city version and extract associated knowledge.
https://github.com/vcityteam/conver-g

rdf sparql sql versioning

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This project aims to create a knowledge hub that can store and query a set of RDF datasets with a versioning system. The project is part of the BD team's research efforts within the LIRIS and VCity project. The aim of this POC is to query a set of city version and extract associated knowledge.

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# ConVer-G project



> Which means Concurrent Versioning of knowledge Graphs



This project aims to create a knowledge hub that can store and query a set of RDF datasets with a versioning system.

The project is part of the BD team's research efforts within the [LIRIS](https://liris.cnrs.fr/)

and [VCity project](https://projet.liris.cnrs.fr/vcity/).

The aim of this POC is to query a set of city version and extract associated knowledge.



> This system has a demonstration and its code source is [available on GitHub](https://github.com/VCityTeam/UD-Demo-VCity-Knowledge_Evolution).



## Motivations



### Why create a "SPARQL to SQL" translator rather than a from scratch engine?



Our motivation is to find a method for *retrieving knowledge* from a *set of urban data versions* stored in *RDF

format*.



Motivations for linking SPARQL and SQL are numerous, particularly in the fields of science, technology,

and business, where there is a growing need to integrate increasingly diverse data sources (captors, institutions, ...).

By using a SPARQL to SQL translator, we can enable relational databases to be exposed on the Semantic Web and queried

with SPARQL *(with the same performance as with SQL?)*.

This allows researchers and developers to work with RDF and relational data seamlessly and efficiently while leveraging

the performance optimizations of existing relational databases.



A *"from scratch"* engine that is not based on SPARQL nor SQL *would not be interoperable* with these query systems.

It is more simple than reimplementing the full stack (algebra, including join algorithms, optimisation, efficient

storage and indexing)

and because we think that performance will be comparable to a dedicated implementation.



### Why this experiment?



We want to ensure the **provenance, accuracy, efficiency, and reliability** of querying a condensed representation of

the various version of a dataset with regard to querying each different version represented extensionally,

that is understanding whether our proposal of adding to each quad the set of versions it appears in,

instead of representing each version as a separate dataset, leads to a more efficient way of answering queries across

versions.

A query-scenario of this experiment can be : *"Which city version has the highest number of trees in the district 1?"*



### Notes



Using a SQL as a backend for SPARQL has been done in some cases.



- **[A Mapping of SPARQL Onto Conventional SQL - W3C](https://www.w3.org/2008/07/MappingRules/StemMapping)**

  This paper discusses a semantics for expressing relational data as an RDF graph and an algebra for mapping SPARQL

  SELECT queries over that RDF to SQL queries over the original relational data.

  The goal is to provide a specification for SPARQL tool vendors and a foundation for the Semantic Web. It highlights

  the importance of creating a computable mapping from SPARQL semantics to SQL semantics.

- *

  *[Evaluating SPARQL to SQL Translation in Ontop - Free University of Bozen-Bolzano](https://www.inf.unibz.it/~calvanese/papers/rodr-etal-ORE-2013.pdf)

  **

  This research paper discusses the importance of mapping relational databases into RDF using the R2RML standard.

  It mentions the research focused on translating SPARQL queries into SQL and evaluates the SPARQL to SQL translation in

  the Ontop system.

- *

  *[RDF and SPARQL: Using Semantic Web Technology to Integrate the World's Data - W3C](https://www.w3.org/2007/03/VLDB/)

  **

  This resource explains how RDF and SPARQL can be used to improve access to relational databases. It discusses

  techniques for improving mappings between RDF and relational data and mentions that several query engines map SPARQL

  queries to relational queries,

  either by rewriting them into SQL queries or by compiling them directly into evaluation structures native to the

  database.



## Getting started



### Installation



This project uses Java 21 JDK + Maven and

a [dockerized (make sure that Docker is installed too)](https://www.docker.com/) [PostgreSQL 17 database](https://www.postgresql.org/docs/17/index.html).

If you don't have Java 21 installed by default, I recommend that you install [SDKMAN!](https://sdkman.io/) and use this

tool to set Java 21 as current session version.



> SDKMAN! is a tool for managing parallel versions of multiple Software Development Kits on most Unix based systems.



Once you have `SDKMAN!` installed, run:



```shell

sdk install java 21.0.1-amzn

sdk use java 21.0.1-amzn

```



Make sure you have Maven installed. If you don't have Maven installed, run: `sudo apt install maven`.



### Maven



#### ⌛ Quads-Loader



This project:



- uses the `jena-arq` library for parsing SPARQL statements in Java,

- uses the `springdoc-openapi-starter-webmvc-ui` library to parse the Swagger API annotations and displays

  the [swagger-ui](http://localhost:8080/swagger-ui/index.html),

- needs a [PostgreSQL 17 database](https://www.postgresql.org/docs/17/index.html), so the `postgresql` driver is

  installed too.



This project has been tested with:



- `sonarqube`, assuring the code quality,

- `JaCoCo`, testing the code coverage.



#### 🦆 Quads-Query



This project:



- uses the `jena-fuseki-server` Apache Jena Fuseki is a SPARQL server,

- needs a [PostgreSQL 17 database](https://www.postgresql.org/docs/17/index.html) if you use this target language, so

  the `postgresql` driver is

  installed too.



This project has been tested with: `junit-jupiter-engine`



### Start the application



#### ⌛ Quads-Loader



```shell

# at the root of the project

# starts the database declared inside the docker-compose.yml file

docker compose up -d



# if you want to hack the import program

cd quads-loader



## wait until the PostgreSQL database is up

## starts the Java Spring application locally (http://localhost:8080/)

java "-DDATASOURCE_URL=" "-DDATASOURCE_USERNAME=" "-DDATASOURCE_PASSWORD=" -jar target/quads-loader-0.0.1-SNAPSHOT.jar

```



#### 🦆 Quads-Query



```shell

# at the root of the project

# starts the database declared inside the docker-compose.yml file

docker compose up -d



# if you want to hack the import program

cd quads-query



## wait until the PostgreSQL database is up

# build the project

mvn package



## starts the Java Spring application locally (http://localhost:8081/)

java "-DDATASOURCE_URL=" "-DDATASOURCE_USERNAME=" "-DDATASOURCE_PASSWORD=" ?"-DTARGET_LANG=" ?"-DCONDENSED_MODE=" -jar quads-query-1.0-SNAPSHOT-jar-with-dependencies.jar

```



### Implementation



#### Ontology



![The graph versioning ontology](https://www.ldf.fi/service/rdf-grapher?rdf=%40prefix+vers%3A+%3Chttps%3A%2F%2Fgithub.com%2FVCityTeam%2FConVer-G%2F%3E+.%0D%0A%40prefix+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E+.%0D%0A%40prefix+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E+.%0D%0A%40prefix+purl%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Felements%2F1.1%3E+.%0D%0A%0D%0A%3Cvers%3AVersioned-Named-Graph%3E+%3Crdf%3Atype%3E+rdfs%3AResource+.%0D%0A%3Cvers%3AVersioned-Named-Graph%3E+%3Crdfs%3Acomment%3E+%22A+versioned+graph+name%22+.%0D%0A%3Cvers%3AVersioned-Named-Graph%3E+%3Crdfs%3Alabel%3E+%22Versioned+named+graph%22%40en+.%0D%0A%3Cvers%3AVersioned-Named-Graph%3E+%3Crdfs%3Alabel%3E+%22Graphe+nomm%C3%A9+versionn%C3%A9%22%40fr+.%0D%0A%0D%0A%3Cvers%3AVersioned-Named-Graph%3E+%3Cvers%3AVersion%23is-in-version%3E+vers%3AVersion+.%0D%0A%3Cvers%3AVersion%3E+%3Crdf%3Atype%3E+rdfs%3AClass+.%0D%0A%3Cvers%3AVersion%3E+%3Crdfs%3Acomment%3E+%22A+dataset+version%22+.%0D%0A%3Cvers%3AVersion%3E+%3Crdfs%3Alabel%3E+%22Version%22%40en+.%0D%0A%3Cvers%3AVersion%3E+%3Crdfs%3Alabel%3E+%22Version%22%40fr+.%0D%0A%0D%0A%3Cvers%3AVersioned-Named-Graph%3E+%3Cvers%3AVersion%23is-version-of%3E+vers%3ANamed-Graph+.%0D%0A%3Cvers%3ANamed-Graph%3E+%3Crdf%3Atype%3E+rdfs%3AClass+.%0D%0A%3Cvers%3ANamed-Graph%3E+%3Crdfs%3Acomment%3E+%22A+graph+name%22+.%0D%0A%3Cvers%3ANamed-Graph%3E+%3Crdfs%3Alabel%3E+%22Named+graph%22%40en+.%0D%0A%3Cvers%3ANamed-Graph%3E+%3Crdfs%3Alabel%3E+%22Graphe+nomm%C3%A9%22%40fr+.%0D%0A%0D%0A%3Cvers%3AVersioning%3E+%3Crdf%3Atype%3E+%3Chttp%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23Ontology%3E+.%0D%0A%3Cvers%3AVersioning%3E+%3Cpurl%3Atitle%3E+%22The+graph+versioning+vocabulary%22+.%0D%0A%3Cvers%3AVersioning%3E+%3Cpurl%3Adate%3E+%222024-08-26%22+.%0D%0A%3Cvers%3AVersioning%3E+%3Cpurl%3Adescription%3E+%22RDF+schema+of+the+graph+versioning+vocabulary+terms%22+.&from=ttl&to=png)



#### Conceptual model



```mermaid

erDiagram

    VersionedQuad |{--|{ Version: "bitstring index"

    VersionedQuad ||--|{ VersionedNamedGraph: "(named_graph, bitstring index)"

    Version ||--|{ VersionedNamedGraph: "index"

    VersionedQuad {

        text subject

        text predicate

        text object

        text named_graph

        bitstring validity

    }

    VersionedNamedGraph {

        text versioned_named_graph

        int index_version

        text named_graph

    }

    Version {

        int index_version

        text message

        timestamptz transaction_time_start

        timestamptz transaction_time_end

    }

    Metadata {

        text subject

        text predicate

        text object

    }

```



#### Entity–Relationship model



```mermaid

erDiagram

    VersionedQuad ||--|{ ResourceOrLiteral: "subject"

    VersionedQuad ||--|{ ResourceOrLiteral: "object"

    VersionedQuad ||--|{ ResourceOrLiteral: "predicate"

    VersionedQuad ||--|{ ResourceOrLiteral: "named graph"

    VersionedNamedGraph ||--|{ ResourceOrLiteral: "named graph"

    VersionedNamedGraph ||--|{ ResourceOrLiteral: "versioned named graph"

    Metadata }|--|{ ResourceOrLiteral: "subject"

    Metadata }|--|{ ResourceOrLiteral: "object"

    Metadata }|--|{ ResourceOrLiteral: "predicate"

    VersionedQuad ||--|{ VersionedNamedGraph: "foreign key"

    VersionedQuad {

        int id_subject PK, FK

        int id_predicate PK, FK

        int id_object PK, FK

        int id_named_graph FK

        bitstring validity

    }

    VersionedNamedGraph {

        int id_versioned_named_graph PK, FK

        int index_version

        int id_named_graph FK

    }

    ResourceOrLiteral {

        int id_resource_or_literal PK, FK

        text name

        string type "Not null if literal"

    }

    Version {

        int index_version "PK, (FK)"

        text message

        timestamptz transaction_time_start

        timestamptz transaction_time_end

    }

    Metadata {

        int id_subject PK, FK

        int id_predicate PK, FK

        int id_object PK, FK

    }

```



#### Flowcharts



##### Query the relational database with a SPARQL query



```mermaid

flowchart BT

    CS[Computer Scientist] -->|Sends the SPARQL query to the endpoint| SE

    SE -->|Sends the quads to the Computer Scientist| CS

    subgraph Server

        SE -->|Sends the SPARQL query for translation| ARQ[SPARQL to SQL translator]

        ARQ -->|Sends the SQL translated query to JDBC| JDBC[Java Database Connectivity]

        JDBC -->|The filtered quads| ARQ

        ARQ -->|The filtered quads| SE



    end

    subgraph Database

        JDBC -->|Sends the SQL query to the database| DB[PostgreSQL]

        DB -->|Sends the result of the SQL query| JDBC

    end

```



##### Store RDF quads inside a relational database



```mermaid

flowchart TB

    CS[Computer Scientist] -->|Sends the files to the import endpoint| SE

    SE -->|Returns the version number via HTTP| CS

    

    subgraph Server

        SE -->|Sends files to import| RIOT[Jena RIOT]

        RIOT -->|Send the quads for insertion| JDBC[Java Database Connectivity]

        

        JDBC -->|Sends the version number| SE

    end

    

    subgraph Database

        JDBC -->|Sends the SQL query to the database| DB[PostgreSQL]

        DB -->|Sends the version information| JDBC

    end

```



### Testing



#### Swagger



The API description is available on the [swagger-ui](http://localhost:8080/swagger-ui/index.html) at runtime.



#### Tests



```shell

# make sure your database is up



# starts the tests

mvn spring-boot:run test

```



#### Code quality and coverage



The code coverage and quality is available on the [Sonarqube server](http://localhost:9000) after running a sonar

inspection.



### Sample data and workflow



This project has been tested with a dataset created by the [UD-Graph Project](https://github.com/VCityTeam/UD-Graph).

This dataset as been transformed to be compatible with the designed conceptual model.



```mermaid

sequenceDiagram

    title Transformation, Import and query workflow

    autonumber



    participant BSBM

    participant Annotation



    System ->>+ BSBM: Ask for a set of versions

    BSBM ->>- System: Generate a set of versions



    loop For each generated version

        System ->>+ Annotation: Send the versionable data to annotate

        Annotation ->>- System: The annotated data with the version index

        System ->>+ Annotation: Send the versionable data to annotate

        Annotation ->>- System: The annotated data with the graph name

    end

    

    participant Triple store



    loop For each Annotated version

        System ->>+ QuaDer: Sends the version to import

        QuaDer ->>+ Database: Inserts the version

        Database ->>- QuaDer: Returns the insert status

        QuaDer ->>- System: Returns the version index

        

        System ->>+ Triple store: Sends the version to import

        Triple store ->>- System: Returns the insert status

    end

    

    System ->>+ Triple store: Sends the theoretical annotations to import

    Triple store ->>- System: Returns the insert status

    

    box QuaQue

        participant SPARQL-SQL translator

        participant SPARQL API

    end

    

    actor User client

    

    User client ->>+ SPARQL API: Sends a SPARQL query

    SPARQL API ->>+ SPARQL-SQL translator: Translates the SPARQL query

    SPARQL-SQL translator ->>- SPARQL API: Returns the SQL query

    SPARQL API ->>+ Database: Sends the SQL query

    Database ->>- SPARQL API: Returns the queried result

    SPARQL API ->>- User client: Returns the result

```



#### Entity linking



Before importing the dataset inside the triple store and the relational database, we transform the data to match the

theoretical model and the implementation.



##### Contextualization



We add a quad for each triple (the graph name).

Its semantic is the link between the triple and the source of the data.

The transformation has been made with the [annotate python program](quads-creator-old/annotate_graph.py).

We used a virtual environment with pip 23.3.1 from Python 3.10.12.



```shell

# create a virtual environment

python3 -m venv venv



# activate the virtual environment

source venv/bin/activate



# install the dependencies

pip install -r python/requirements.txt



# run the program

cd workflows

/bin/bash workflow-bsbm.sh 2 7500 1000 10 > allout.txt 2>&1



# in another terminal

cd workflows

tail -f allout.txt

```



Let's assume that we have a dataset with 2 versions with the following quads:



**Version 1 (buildings-2015.trig):**



| Subject                       | Predicate | Object | Named Graph                               |

|-------------------------------|-----------|--------|-------------------------------------------|

| http://example.edu/Building#1 | height    | 10.5   | http://example.edu/Named-Graph#Grand-Lyon |

| http://example.edu/Building#2 | height    | 9.1    | http://example.edu/Named-Graph#Grand-Lyon |

| http://example.edu/Building#1 | height    | 11     | http://example.edu/Named-Graph#IGN        |



**Version 2 (buildings-2018.trig):**



| Subject                       | Predicate | Object | Named Graph                               |

|-------------------------------|-----------|--------|-------------------------------------------|

| http://example.edu/Building#1 | height    | 10.5   | http://example.edu/Named-Graph#IGN        |

| http://example.edu/Building#1 | height    | 10.5   | http://example.edu/Named-Graph#Grand-Lyon |

| http://example.edu/Building#3 | height    | 15     | http://example.edu/Named-Graph#Grand-Lyon |



##### Theoretical model



After some transformations, we have the following quads representing the theoretical model:



| Subject                                                              | Predicate                                                   | Object                                                       | Named Graph                                                          | 

|----------------------------------------------------------------------|-------------------------------------------------------------|--------------------------------------------------------------|----------------------------------------------------------------------|

| http://example.edu/Building#1                                        | height                                                      | 10.5                                                         | https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-1 |

| http://example.edu/Building#2                                        | height                                                      | 9.1                                                          | https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-1 |

| http://example.edu/Building#1                                        | height                                                      | 11                                                           | https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-2 |

| https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-1 | https://github.com/VCityTeam/ConVer-G/Version#is-version-of | http://example.edu/Named-Graph#Grand-Lyon                    |                                                                      |

| https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-1 | https://github.com/VCityTeam/ConVer-G/Version#is-in-version | https://github.com/VCityTeam/ConVer-G/Version#buildings-2015 |                                                                      |

| https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-2 | https://github.com/VCityTeam/ConVer-G/Version#is-version-of | http://example.edu/Named-Graph#IGN                           |                                                                      |

| https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-2 | https://github.com/VCityTeam/ConVer-G/Version#is-in-version | https://github.com/VCityTeam/ConVer-G/Version#buildings-2015 |                                                                      |

| http://example.edu/Building#1                                        | height                                                      | 10.5                                                         | https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-3 |

| http://example.edu/Building#3                                        | height                                                      | 15                                                           | https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-3 |

| http://example.edu/Building#1                                        | height                                                      | 10.5                                                         | https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-4 |

| https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-3 | https://github.com/VCityTeam/ConVer-G/Version#is-version-of | http://example.edu/Named-Graph#Grand-Lyon                    |                                                                      |

| https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-3 | https://github.com/VCityTeam/ConVer-G/Version#is-in-version | https://github.com/VCityTeam/ConVer-G/Version#buildings-2018 |                                                                      |

| https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-4 | https://github.com/VCityTeam/ConVer-G/Version#is-version-of | http://example.edu/Named-Graph#IGN                           |                                                                      |

| https://github.com/VCityTeam/ConVer-G/Versioned-Named-Graph#sha256-4 | https://github.com/VCityTeam/ConVer-G/Version#is-in-version | https://github.com/VCityTeam/ConVer-G/Version#buildings-2018 |                                                                      |



##### Implementation



After the import inside the relational database, we have the following quads representing the implementation:



| Subject                       | Predicate | Object | Named Graph                               | Validity |

|-------------------------------|-----------|--------|-------------------------------------------|----------|

| http://example.edu/Building#1 | height    | 10.5   | http://example.edu/Named-Graph#Grand-Lyon | 11       |

| http://example.edu/Building#2 | height    | 9.1    | http://example.edu/Named-Graph#Grand-Lyon | 10       |

| http://example.edu/Building#1 | height    | 11     | http://example.edu/Named-Graph#IGN        | 10       |

| http://example.edu/Building#1 | height    | 10.5   | http://example.edu/Named-Graph#IGN        | 01       |

| http://example.edu/Building#3 | height    | 15     | http://example.edu/Named-Graph#Grand-Lyon | 01       |