Fixes #50 - Add the possibility to generate an Allotrope from a singl…

…e .ch file - ChemStationToAllotropeMapper is now more customizable - In addition to the time-zone, users can now customize the date-time format and the names of the necessary files for conversion - More metadata is read from .ch files - Add a merge strategy option if metadata read from .ch and other files differ Fix ChemStationToAllotropeMapper
ifpen · Dec 17, 2024 · 45c2635 · 45c2635
1 parent 6cb5c6e
commit 45c2635
Show file tree

Hide file tree

Showing 22 changed files with 757 additions and 1,782 deletions.
diff --git a/README.md b/README.md
@@ -1,31 +1,67 @@
 # GC2ASM
 
-[![Maven Central Version](https://img.shields.io/maven-central/v/fr.ifpen.allotropeconverters/gc2asm)][maven-central]
-[![License CeCILL 2.1](https://img.shields.io/badge/License-CeCILL_2.1-green)][license]
+[![Maven Central Version][maven-central-badge]][maven-central]
+[![License CeCILL 2.1][license-badge]][cecill-2.1]
 
+A Java converter from GC proprietary data to Allotrope's ASM data.
 
-
-A Java converter from GC proprietary data to Allotrope's ASM data
-
-A project from [IFP Energies Nouvelles](https://www.ifpenergiesnouvelles.com/), a public research, innovation and training organization in the fields of energy, transport and the environment
+A project from [IFP Energies Nouvelles][ifpen], a public research, innovation and
+training organization in the fields of energy, transport and the environment.
 
 ## Usage
+
 ```java
-        String filePath = pathToGCFile;
-        GcToAllotropeJsonConverter converter = new GcToAllotropeJsonConverter();
-        ObjectNode result = converter.convertFile(filePath);
+import fr.ifpen.allotropeconverters.gc.GcToAllotropeJsonConverter;
+import fr.ifpen.allotropeconverters.gc.chemstation.ChemStationToAllotropeMapper;
+import fr.ifpen.allotropeconverters.gc.chemstation.ChemStationToAllotropeMapperBuilder;
+
+String folderPath = "path to folder containing .ch, .xml and .txt files";
+String filePath = "path to .ch file";
+
+// Using default mapper
+GcToAllotropeJsonConverter converter = new GcToAllotropeJsonConverter();
+
+// Conversion from folder to Allotrope JSON
+ObjectNode allotropeFromFolder = converter.convertFolderToAllotrope(folderPath);
+
+// Conversion from .ch file to Allotrope JSON
+ObjectNode allotropeFromFile = converter.convertChFileToAllotrope(filePath);
+
+
+// ChemStation to Allotrope mapper can be customized
+ChemStationToAllotropeMapperBuilder builder = new ChemStationToAllotropeMapperBuilder();
+ChemStationToAllotropeMapper mapper = builder.withZoneId(ZoneId.of("Europe/Paris"))
+                                             .withChFileName("file.ch")
+                                             .withXmlFileName("file.xml")
+                                             .build();
+GcToAllotropeJsonConverter customizedConverter = new GcToAllotropeJsonConverter(mapper);
+
+// Convert folders and files
+// [...]
 ```
 
 ## Supported files
+
 - Chemstation V179
 - Chemstation V181
 
 ## Roadmap
+
 Support for Thermo's Chromeleon data.
 
 ## License
-The code is available under the [CeCILL 2.1](https://cecill.info/licences/Licence_CeCILL_V2.1-fr.txt) licence, which is compatible with GNU GPL, GNU Affero GPL and EUPL.
-The [ASM JSON schemas](https://www.allotrope.org/asm) are available under [CC-BY-NC 4.0](https://creativecommons.org/licenses/by-nc/4.0/) terms.
+
+The code is available under the [CeCILL 2.1][cecill-2.1] license, 
+which is compatible with GNU GPL, GNU Affero GPL and EUPL.  
+The [ASM JSON schemas][asm] are available under [CC-BY-NC 4.0][cc-by-nc-4.0] terms.
+
+[//]: # (@formatter:off)
+
+[maven-central-badge]: https://img.shields.io/maven-central/v/fr.ifpen.allotropeconverters/gc2asm
+[license-badge]: https://img.shields.io/badge/License-CeCILL_2.1-green
 
 [maven-central]: https://central.sonatype.com/artifact/fr.ifpen.allotropeconverters/gc2asm
-[license]: https://opensource.org/license/cecill-2-1
+[cecill-2.1]: https://opensource.org/license/cecill-2-1
+[ifpen]: https://www.ifpenergiesnouvelles.com/
+[asm]: https://www.allotrope.org/asm
+[cc-by-nc-4.0]: https://creativecommons.org/licenses/by-nc/4.0/
diff --git a/pom.xml b/pom.xml
@@ -87,6 +87,12 @@
             <version>4.3.1</version>
         </dependency>
 
+        <dependency>
+            <groupId>org.assertj</groupId>
+            <artifactId>assertj-core</artifactId>
+            <version>3.26.3</version>
+            <scope>test</scope>
+        </dependency>
         <dependency>
             <groupId>org.slf4j</groupId>
             <artifactId>slf4j-nop</artifactId>

diff --git a/src/main/java/fr/ifpen/allotropeconverters/gc/GcToAllotropeJsonConverter.java b/src/main/java/fr/ifpen/allotropeconverters/gc/GcToAllotropeJsonConverter.java
@@ -6,40 +6,82 @@
 import com.fasterxml.jackson.databind.node.ObjectNode;
 import com.fasterxml.jackson.datatype.jsr310.JavaTimeModule;
 import fr.ifpen.allotropeconverters.gc.chemstation.ChemStationToAllotropeMapper;
+import fr.ifpen.allotropeconverters.gc.chemstation.ChemStationToAllotropeMapperBuilder;
 import fr.ifpen.allotropeconverters.gc.schema.GasChromatographyTabularEmbedSchema;
 import jakarta.xml.bind.JAXBException;
 
 import java.io.IOException;
-import java.time.ZoneId;
-import java.time.ZoneOffset;
 
+/**
+ * GcToAllotropeJsonConverter is responsible for converting gas chromatography data
+ * into an Allotrope-compatible JSON structure.
+ * <p>
+ * It supports conversion from .ch files
+ * as well as from folders containing multiple related files (.ch, .xml, and .txt).
+ */
 public class GcToAllotropeJsonConverter {
 
-    private final ZoneId defaultTimeZone;
-    private ChemStationToAllotropeMapper chemstationMapper;
+    private final ChemStationToAllotropeMapper chemstationMapper;
 
+    /**
+     * Creates a GcToAllotropeJsonConverter with a default {@link ChemStationToAllotropeMapper} from {@link ChemStationToAllotropeMapperBuilder}.
+     */
     public GcToAllotropeJsonConverter() {
-        defaultTimeZone = ZoneOffset.UTC;
-        this.createMapper();
+        this(new ChemStationToAllotropeMapperBuilder().build());
     }
 
-    public GcToAllotropeJsonConverter(ZoneId defaultTimeZone) {
-        this.defaultTimeZone = defaultTimeZone;
-        this.createMapper();
+    /**
+     * Creates a GcToAllotropeJsonConverter with a custom {@link ChemStationToAllotropeMapper}.
+     *
+     * @param chemstationMapper
+     *         mapper created from {@link ChemStationToAllotropeMapperBuilder}
+     */
+    public GcToAllotropeJsonConverter(ChemStationToAllotropeMapper chemstationMapper) {
+        this.chemstationMapper = chemstationMapper;
     }
 
-    private void createMapper() {
-        chemstationMapper = new ChemStationToAllotropeMapper(defaultTimeZone);
-    }
-
-    public ObjectNode convertFile(String filePath) throws JAXBException, IOException {
-        GasChromatographyTabularEmbedSchema embedSchema = chemstationMapper.mapToGasChromatographySchema(filePath);
-
+    private static ObjectNode schema(GasChromatographyTabularEmbedSchema embedSchema) {
         ObjectMapper objectMapper = JsonMapper.builder().addModule(new JavaTimeModule()).build();
 
         objectMapper.disable(SerializationFeature.WRITE_DATES_AS_TIMESTAMPS);
         objectMapper.enable(SerializationFeature.INDENT_OUTPUT);
 
         return objectMapper.valueToTree(embedSchema);
     }
+
+    /**
+     * Converts the contents of a specified folder into an Allotrope-compatible JSON representation.
+     *
+     * @param folderPath
+     *         the path to the folder containing the .ch, .xml and .txt files to be converted
+     *
+     * @return an ObjectNode representing the Allotrope-compatible JSON structure
+     *
+     * @throws JAXBException
+     *         if there is an error while processing XML files during the conversion
+     * @throws IOException
+     *         if there is an I/O error while reading the folder or its contents
+     */
+    public ObjectNode convertFolderToAllotrope(String folderPath) throws JAXBException, IOException {
+        GasChromatographyTabularEmbedSchema embedSchema = chemstationMapper.fromFolder(folderPath);
+
+        return schema(embedSchema);
+    }
+
+    /**
+     * Converts the contents of a specified .ch file into an Allotrope-compatible JSON representation.
+     *
+     * @param chFilePath
+     *         the file path to the .ch file to be converted
+     *
+     * @return an ObjectNode representing the Allotrope-compatible JSON structure
+     *
+     * @throws IOException
+     *         if there is an error accessing or reading the required .ch file
+     */
+    public ObjectNode convertChFileToAllotrope(String chFilePath) throws IOException {
+        GasChromatographyTabularEmbedSchema embedSchema = chemstationMapper.fromChFile(chFilePath);
+
+        return schema(embedSchema);
+    }
 }