Merge branch 'development' into 'master'

Release 4.4.2

See merge request rml/proc/rmlmapper-java!60

.gitattributes

@@ -0,0 +1 @@
+docs/apidocs/* binary

.github/no-response.yml

@@ -0,0 +1,13 @@
+# Configuration for probot-no-response - https://github.com/probot/no-response
+
+# Number of days of inactivity before an Issue is closed for lack of response
+daysUntilClose: 28
+# Label requiring a response
+responseRequiredLabel: more-information-needed
+# Comment to post when closing an Issue for lack of response. Set to `false` to disable
+closeComment: >
+  This issue has been automatically closed because there has been no response
+  to our request for more information from the original author. With only the
+  information that is currently in the issue, we don't have enough information
+  to take action. Please reach out if you have or find the answers we need so
+  that we can investigate further.

CHANGELOG.md

@@ -7,6 +7,20 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 
 ## Unreleased
 
+## [4.4.2] - 2019-07-15
+
+### Added
+
+- Configure [no-response bot](https://github.com/probot/no-response) for Github ([issue 35](https://github.com/RMLio/rmlmapper-java/issues/35))
+- Dockerfile
+- Add table of contents to README
+- Refactor data access and records
+- Test case for CSV with special characters
+
+### Fixed
+
+- Base IRI is read from the mapping doc when using CLI
+
 ## [4.4.1] - 2019-06-17
 
 ### Added
@@ -183,6 +197,7 @@ and this project adheres to [Semantic Versioning](http://semver.org/spec/v2.0.0.
 - support for accessing remote files (via HTTP GET)
 - basic support for functions
 
+[4.4.2]: https://github.com/RMLio/rmlmapper-java/compare/v4.4.1...v4.4.2
 [4.4.1]: https://github.com/RMLio/rmlmapper-java/compare/v4.4.0...v4.4.1
 [4.4.0]: https://github.com/RMLio/rmlmapper-java/compare/v4.3.3...v4.4.0
 [4.3.3]: https://github.com/RMLio/rmlmapper-java/compare/v4.3.2...v4.3.3

Dockerfile

@@ -0,0 +1,11 @@
+FROM openjdk:8-alpine
+
+RUN apk add --no-cache git maven
+ADD . /rmlmapper-java
+
+WORKDIR rmlmapper-java
+RUN mvn clean install -DskipTests=true
+RUN mv `find target/ -iname rmlmapper*.jar;` /rmlmapper.jar
+WORKDIR /data
+
+ENTRYPOINT ["java", "-jar", "/rmlmapper.jar"]

README.md

@@ -4,6 +4,21 @@ The RMLMapper execute RML rules to generate Linked Data.
 It is a Java library, which is available via the command line ([API docs online](https://rmlio.github.io/rmlmapper-java/apidocs/)).
 The RMLMapper loads all data in memory, so be aware when working with big datasets.
 
+## Table of contents
+
+- [Features](#features)
+- [Build](#build)
+- [Usage](#usage)
+  - [CLI](#cli)
+  - [Library](#library)
+  - [Docker](#docker)
+  - [Including functions](#including-functions)
+- [Testing](#testing)
+- [Dependencies](#dependencies)
+- [Remarks](#remarks)
+- [Documentation](#documentation)
+  - [UML Diagrams](#uml-diagrams)
+
 ## Features
 
 ### Supported
@@ -73,7 +88,6 @@ import org.eclipse.rdf4j.model.Model;
 import org.eclipse.rdf4j.rio.RDFFormat;
 import org.eclipse.rdf4j.rio.Rio;
 
-import be.ugent.rml.DataFetcher;
 import be.ugent.rml.Executor;
 import be.ugent.rml.records.RecordsFactory;
 import be.ugent.rml.store.RDF4JStore;
@@ -89,27 +103,37 @@ class Main {
 
         String cwd = "/home/rml"; //path to default directory for local files
         String mappingFile = "/home/rml/mapping.rml.ttl"; //path to the mapping file that needs to be executed
-        
+
         try {
             InputStream mappingStream = new FileInputStream(mappingFile);
             Model model = Rio.parse(mappingStream, "", RDFFormat.TURTLE);
             RDF4JStore rmlStore = new RDF4JStore(model);
 
-            Executor executor = new Executor(rmlStore, new RecordsFactory(new DataFetcher(cwd, rmlStore)));
+            Executor executor = new Executor(rmlStore, new RecordsFactory(cwd));
             QuadStore result = executor.execute(null);
         } catch (Exception e) {
             System.out.println(e.getMessage());
         }
-    } 
+    }
 }
 ```
 
+### Docker
+
+You can use Docker to run the RMLMapper by following these steps:
+
+- Build the Docker image: `docker build -t rmlmapper .`.
+- Run a Docker container: `docker run --rm -v $(pwd):/data rmlmapper -m mapping.ttl`.
+
+The same parameters are available as via the CLI.
+The RMLMapper is executed in the `/data` folder in the Docker container.
+
 ### Including functions
 
 There are two ways to include (new) functions within the RML Mapper
   * dynamic loading: you add links to java files or jar files, and those files are loaded dynamically at runtime
   * preloading: you register functionality via code, and you need to rebuild the mapper to use that functionality
-  
+
 Registration of functions is done using a Turtle file, which you can find in `src/main/resources/functions.ttl`
 
 The snippet below for example links an fno:function to a library, provided by a jar-file (`GrelFunctions.jar`).
@@ -173,8 +197,8 @@ class Main {
             // execute mapping file
             File mappingFile = Utils.getFile(mapPath);
             QuadStore rmlStore = Utils.readTurtle(mappingFile);
-            
-            Executor executor = new Executor(rmlStore, new RecordsFactory(new DataFetcher(mappingFile.getParent(), rmlStore)),
+
+            Executor executor = new Executor(rmlStore, new RecordsFactory(mappingFile.getParent()),
                 functionLoader);
             QuadStore result = executor.execute(null);
         } catch (Exception e) {
@@ -184,12 +208,12 @@ class Main {
 }
 ```
 
-### Testing
+## Testing
 
-#### RDBs
+### RDBs
 Make sure you have [Docker](https://www.docker.com) running.
 
-##### Problems
+#### Problems
 * A problem with Docker (can't start the container) causes the SQLServer tests to fail locally. These tests will always succeed locally.
 * A problem with Docker (can't start the container) causes the PostgreSQL tests to fail locally on Windows 7 machines.
 
@@ -227,24 +251,24 @@ However, the RMLMapper can be easily adapted to use a different XML parsing impl
 The processor checks whether correct language tags are not, using a regular expression.
 The regex has no support for languages of length 5-8, but this currently only applies to 'qaa..qtz'.
 
-# Documentation
+## Documentation
 Generate static files at /docs/apidocs with:
 ```
 mvn javadoc:javadoc
 ```
 
-# UML Diagrams
+### UML Diagrams
 
-## Architecture UML Diagram
-### How to generate with IntelliJ IDEA
+#### Architecture UML Diagram
+##### How to generate with IntelliJ IDEA
 (Requires Ultimate edition)
 
 * Right click on package: "be.ugent.rml"
 * Diagrams > Show Diagram > Java Class Diagrams
 * Choose what properties of the classes you want to show in the upper left corner
 * Export to file > .png  | Save diagram > .uml
 
-## Sequence Diagram
-### Edit on [draw.io](https://www.draw.io)
+#### Sequence Diagram
+##### Edit on [draw.io](https://www.draw.io)
 * Go to [draw.io](https://www.draw.io)
 * Click on 'Open Existing Diagram' and choose the .html file

buildNumber.properties

@@ -1,3 +1,3 @@
 #maven.buildNumber.plugin properties file
-#Mon Jun 17 17:22:16 CEST 2019
-buildNumber0=97
+#Mon Jul 15 13:18:09 CEST 2019
+buildNumber0=129

dependency-reduced-pom.xml

@@ -3,7 +3,7 @@
   <modelVersion>4.0.0</modelVersion>
   <groupId>be.ugent.rml</groupId>
   <artifactId>rmlmapper</artifactId>
-  <version>4.4.1</version>
+  <version>4.4.2</version>
   <scm>
     <connection>scm:git:ssh://[email protected]:RMLio/rmlmapper-java.git</connection>
     <url>https://github.com/RMLio/rmlmapper-java</url>
@@ -176,9 +176,9 @@
     </dependency>
   </dependencies>
   <properties>
-    <maven.compiler.target>8</maven.compiler.target>
     <maven.compiler.source>8</maven.compiler.source>
     <project.build.sourceEncoding>UTF-8</project.build.sourceEncoding>
+    <maven.compiler.target>8</maven.compiler.target>
     <junit.version>4.12</junit.version>
   </properties>
 </project>

docs/apidocs/allclasses-frame.html

@@ -2,10 +2,10 @@
 <!-- NewPage -->
 <html lang="en">
 <head>
-<!-- Generated by javadoc (1.8.0_212) on Fri May 03 16:50:48 CEST 2019 -->
+<!-- Generated by javadoc (1.8.0_212) on Mon Jul 15 13:18:22 CEST 2019 -->
 <meta http-equiv="Content-Type" content="text/html; charset=UTF-8">
-<title>All Classes (rmlmapper 4.3.3 API)</title>
-<meta name="date" content="2019-05-03">
+<title>All Classes (rmlmapper 4.4.2 API)</title>
+<meta name="date" content="2019-07-15">
 <link rel="stylesheet" type="text/css" href="stylesheet.css" title="Style">
 <script type="text/javascript" src="script.js"></script>
 </head>
@@ -15,15 +15,16 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <ul>
 <li><a href="be/ugent/rml/functions/AbstractSingleRecordFunctionExecutor.html" title="class in be.ugent.rml.functions" target="classFrame">AbstractSingleRecordFunctionExecutor</a></li>
 <li><a href="be/ugent/rml/term/AbstractTerm.html" title="class in be.ugent.rml.term" target="classFrame">AbstractTerm</a></li>
+<li><a href="be/ugent/rml/access/Access.html" title="interface in be.ugent.rml.access" target="classFrame"><span class="interfaceName">Access</span></a></li>
+<li><a href="be/ugent/rml/access/AccessFactory.html" title="class in be.ugent.rml.access" target="classFrame">AccessFactory</a></li>
 <li><a href="be/ugent/rml/term/BlankNode.html" title="class in be.ugent.rml.term" target="classFrame">BlankNode</a></li>
 <li><a href="be/ugent/rml/termgenerator/BlankNodeGenerator.html" title="class in be.ugent.rml.termgenerator" target="classFrame">BlankNodeGenerator</a></li>
 <li><a href="be/ugent/rml/functions/ConcatFunction.html" title="class in be.ugent.rml.functions" target="classFrame">ConcatFunction</a></li>
 <li><a href="be/ugent/rml/extractor/ConstantExtractor.html" title="class in be.ugent.rml.extractor" target="classFrame">ConstantExtractor</a></li>
-<li><a href="be/ugent/rml/records/CSV.html" title="class in be.ugent.rml.records" target="classFrame">CSV</a></li>
 <li><a href="be/ugent/rml/records/CSVRecord.html" title="class in be.ugent.rml.records" target="classFrame">CSVRecord</a></li>
+<li><a href="be/ugent/rml/records/CSVRecordFactory.html" title="class in be.ugent.rml.records" target="classFrame">CSVRecordFactory</a></li>
 <li><a href="be/ugent/rml/DatabaseType.html" title="class in be.ugent.rml" target="classFrame">DatabaseType</a></li>
 <li><a href="be/ugent/rml/DatabaseType.Database.html" title="enum in be.ugent.rml" target="classFrame">DatabaseType.Database</a></li>
-<li><a href="be/ugent/rml/DataFetcher.html" title="class in be.ugent.rml" target="classFrame">DataFetcher</a></li>
 <li><a href="be/ugent/rml/metadata/DatasetLevelMetadataGenerator.html" title="class in be.ugent.rml.metadata" target="classFrame">DatasetLevelMetadataGenerator</a></li>
 <li><a href="be/ugent/rml/functions/DynamicMultipleRecordsFunctionExecutor.html" title="class in be.ugent.rml.functions" target="classFrame">DynamicMultipleRecordsFunctionExecutor</a></li>
 <li><a href="be/ugent/rml/functions/DynamicSingleRecordFunctionExecutor.html" title="class in be.ugent.rml.functions" target="classFrame">DynamicSingleRecordFunctionExecutor</a></li>
@@ -37,11 +38,11 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="be/ugent/rml/functions/lib/IDLabFunctions.html" title="class in be.ugent.rml.functions.lib" target="classFrame">IDLabFunctions</a></li>
 <li><a href="be/ugent/rml/Initializer.html" title="class in be.ugent.rml" target="classFrame">Initializer</a></li>
 <li><a href="be/ugent/rml/records/IteratorFormat.html" title="class in be.ugent.rml.records" target="classFrame">IteratorFormat</a></li>
-<li><a href="be/ugent/rml/functions/JoinConditionFunctionExecutor.html" title="interface in be.ugent.rml.functions" target="classFrame"><span class="interfaceName">JoinConditionFunctionExecutor</span></a></li>
-<li><a href="be/ugent/rml/records/JSON.html" title="class in be.ugent.rml.records" target="classFrame">JSON</a></li>
 <li><a href="be/ugent/rml/records/JSONRecord.html" title="class in be.ugent.rml.records" target="classFrame">JSONRecord</a></li>
+<li><a href="be/ugent/rml/records/JSONRecordFactory.html" title="class in be.ugent.rml.records" target="classFrame">JSONRecordFactory</a></li>
 <li><a href="be/ugent/rml/term/Literal.html" title="class in be.ugent.rml.term" target="classFrame">Literal</a></li>
 <li><a href="be/ugent/rml/termgenerator/LiteralGenerator.html" title="class in be.ugent.rml.termgenerator" target="classFrame">LiteralGenerator</a></li>
+<li><a href="be/ugent/rml/access/LocalFileAccess.html" title="class in be.ugent.rml.access" target="classFrame">LocalFileAccess</a></li>
 <li><a href="be/ugent/rml/cli/Main.html" title="class in be.ugent.rml.cli" target="classFrame">Main</a></li>
 <li><a href="be/ugent/rml/Mapping.html" title="class in be.ugent.rml" target="classFrame">Mapping</a></li>
 <li><a href="be/ugent/rml/MappingFactory.html" title="class in be.ugent.rml" target="classFrame">MappingFactory</a></li>
@@ -61,16 +62,18 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="be/ugent/rml/term/ProvenancedTerm.html" title="class in be.ugent.rml.term" target="classFrame">ProvenancedTerm</a></li>
 <li><a href="be/ugent/rml/store/Quad.html" title="class in be.ugent.rml.store" target="classFrame">Quad</a></li>
 <li><a href="be/ugent/rml/store/QuadStore.html" title="class in be.ugent.rml.store" target="classFrame">QuadStore</a></li>
-<li><a href="be/ugent/rml/records/RDBs.html" title="class in be.ugent.rml.records" target="classFrame">RDBs</a></li>
+<li><a href="be/ugent/rml/access/RDBAccess.html" title="class in be.ugent.rml.access" target="classFrame">RDBAccess</a></li>
 <li><a href="be/ugent/rml/store/RDF4JStore.html" title="class in be.ugent.rml.store" target="classFrame">RDF4JStore</a></li>
 <li><a href="be/ugent/rml/records/Record.html" title="class in be.ugent.rml.records" target="classFrame">Record</a></li>
 <li><a href="be/ugent/rml/RecordFunctionExecutorFactory.html" title="class in be.ugent.rml" target="classFrame">RecordFunctionExecutorFactory</a></li>
 <li><a href="be/ugent/rml/records/RecordsFactory.html" title="class in be.ugent.rml.records" target="classFrame">RecordsFactory</a></li>
 <li><a href="be/ugent/rml/extractor/ReferenceExtractor.html" title="class in be.ugent.rml.extractor" target="classFrame">ReferenceExtractor</a></li>
+<li><a href="be/ugent/rml/records/ReferenceFormulationRecordFactory.html" title="interface in be.ugent.rml.records" target="classFrame"><span class="interfaceName">ReferenceFormulationRecordFactory</span></a></li>
+<li><a href="be/ugent/rml/access/RemoteFileAccess.html" title="class in be.ugent.rml.access" target="classFrame">RemoteFileAccess</a></li>
 <li><a href="be/ugent/rml/store/SimpleQuadStore.html" title="class in be.ugent.rml.store" target="classFrame">SimpleQuadStore</a></li>
 <li><a href="be/ugent/rml/functions/SingleRecordFunctionExecutor.html" title="interface in be.ugent.rml.functions" target="classFrame"><span class="interfaceName">SingleRecordFunctionExecutor</span></a></li>
-<li><a href="be/ugent/rml/records/SPARQL.html" title="class in be.ugent.rml.records" target="classFrame">SPARQL</a></li>
-<li><a href="be/ugent/rml/records/SPARQL.ResultFormat.html" title="enum in be.ugent.rml.records" target="classFrame">SPARQL.ResultFormat</a></li>
+<li><a href="be/ugent/rml/access/SPARQLEndpointAccess.html" title="class in be.ugent.rml.access" target="classFrame">SPARQLEndpointAccess</a></li>
+<li><a href="be/ugent/rml/records/SPARQLResultFormat.html" title="enum in be.ugent.rml.records" target="classFrame">SPARQLResultFormat</a></li>
 <li><a href="be/ugent/rml/functions/StaticMultipleRecordsFunctionExecutor.html" title="class in be.ugent.rml.functions" target="classFrame">StaticMultipleRecordsFunctionExecutor</a></li>
 <li><a href="be/ugent/rml/functions/StaticSingleRecordFunctionExecutor.html" title="class in be.ugent.rml.functions" target="classFrame">StaticSingleRecordFunctionExecutor</a></li>
 <li><a href="be/ugent/rml/Template.html" title="class in be.ugent.rml" target="classFrame">Template</a></li>
@@ -82,8 +85,8 @@ <h1 class="bar">All&nbsp;Classes</h1>
 <li><a href="be/ugent/rml/functions/lib/UtilFunctions.html" title="class in be.ugent.rml.functions.lib" target="classFrame">UtilFunctions</a></li>
 <li><a href="be/ugent/rml/Utils.html" title="class in be.ugent.rml" target="classFrame">Utils</a></li>
 <li><a href="be/ugent/rml/ValuedJoinCondition.html" title="class in be.ugent.rml" target="classFrame">ValuedJoinCondition</a></li>
-<li><a href="be/ugent/rml/records/XML.html" title="class in be.ugent.rml.records" target="classFrame">XML</a></li>
 <li><a href="be/ugent/rml/records/XMLRecord.html" title="class in be.ugent.rml.records" target="classFrame">XMLRecord</a></li>
+<li><a href="be/ugent/rml/records/XMLRecordFactory.html" title="class in be.ugent.rml.records" target="classFrame">XMLRecordFactory</a></li>
 </ul>
 </div>
 </body>