gCubeSystem
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software-versions-processor-lib
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Generalizing library terminology

This commit is contained in:
luca.frosini 2023-08-30 17:40:18 +02:00
parent e3634904e7
commit e2fb00c34f
12 changed files with 76 additions and 43 deletions
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26
pom.xml
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@ -84,4 +84,30 @@
</dependency>
</dependencies>
<build>
<plugins>
<!-- Sphinx plugin' -->
<plugin>
<groupId>kr.motd.maven</groupId>
<artifactId>sphinx-maven-plugin</artifactId>
<version>2.10.0</version>
<configuration>
<outputDirectory>${project.build.directory}/${project.artifactId}-${project.version}/docs</outputDirectory>
<builder>html</builder>
<configDirectory>${basedir}/docs</configDirectory>
<sourceDirectory>${basedir}/docs</sourceDirectory>
</configuration>
<executions>
<execution>
<phase>process-resources</phase>
<goals>
<goal>generate</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</project>

8
src/main/java/org/gcube/common/software/analyser/Analyser.java
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@ -13,7 +13,7 @@ import org.gcube.com.fasterxml.jackson.databind.JsonNode;
import org.gcube.com.fasterxml.jackson.databind.ObjectMapper;
import org.gcube.com.fasterxml.jackson.databind.node.ArrayNode;
import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
import org.gcube.common.software.export.SoftwareVersionExporter;
import org.gcube.common.software.export.SoftwareArtifactExporter;
import org.gcube.common.software.model.ExporterConfig;
import org.gcube.common.software.model.GlobalConfig;
import org.gcube.common.software.model.SoftwareVersionConfig;
@ -118,7 +118,7 @@ public class Analyser {
GlobalConfig globalConfig = getGlobalConfig(globalConfiguration);
Map<String, Class<? extends SoftwareVersionExporter>> availableExporters = SoftwareVersionExporter.getAvailableExporters();
Map<String, Class<? extends SoftwareArtifactExporter>> availableExporters = SoftwareArtifactExporter.getAvailableExporters();
Map<String,ExporterConfig> requestedExporters = globalConfig.getExporters();
checkExporters(availableExporters.keySet(), requestedExporters.keySet());
@ -148,12 +148,12 @@ public class Analyser {
for(String className : requestedExporters.keySet()) {
logger.debug("Going to export with {}", className);
Class<? extends SoftwareVersionExporter> exporterClass = availableExporters.get(className);
Class<? extends SoftwareArtifactExporter> exporterClass = availableExporters.get(className);
ExporterConfig exporterConfig = requestedExporters.get(className);
exporterConfig = actualizeExporterConfig(exporterConfig, softwareVersionConfig);
SoftwareVersionExporter sve = exporterClass.newInstance();
SoftwareArtifactExporter sve = exporterClass.newInstance();
sve.setOutputDirectory(outputDirectory);
sve.setGlobalConfig(globalConfig);
sve.setSoftwareVersionConfig(softwareVersionConfig);

8
src/main/java/org/gcube/common/software/analyser/AnalyserFactory.java
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@ -15,8 +15,8 @@ public class AnalyserFactory {
public static final String EXPORT_FILENAME_EXTENSION = ".json";
public static final String GLOBAL_PROPERTY_NAME = "global";
public static final String VERSIONS_PROPERTY_NAME = "versions";
public static final String CONFIGURATION_PROPERTY_NAME = "configuration";
public static final String ARTIFACTS_PROPERTY_NAME = "artifacts";
public static Analyser getAnalyser(File jsonFile) throws Exception {
ObjectMapper objectMapper = Utils.getObjectMapper();
@ -32,9 +32,9 @@ public class AnalyserFactory {
public static Analyser getAnalyser(JsonNode jsonNode) throws Exception {
Analyser analyser = new Analyser();
ObjectNode originalGlobal = (ObjectNode) jsonNode.get(GLOBAL_PROPERTY_NAME);
ObjectNode originalGlobal = (ObjectNode) jsonNode.get(CONFIGURATION_PROPERTY_NAME);
analyser.setGlobalConfiguration(originalGlobal);
ArrayNode originalVersions = (ArrayNode) jsonNode.get(VERSIONS_PROPERTY_NAME);
ArrayNode originalVersions = (ArrayNode) jsonNode.get(ARTIFACTS_PROPERTY_NAME);
analyser.setVersionConfigurations(originalVersions);
return analyser;
}

18
src/main/java/org/gcube/common/software/export/SoftwareVersionExporter.java → src/main/java/org/gcube/common/software/export/SoftwareArtifactExporter.java
View File

@ -4,8 +4,8 @@ import java.io.File;
import java.util.HashMap;
import java.util.Map;
import org.gcube.common.software.export.biblatex.BibLaTeXSoftwareVersionExporter;
import org.gcube.common.software.export.zenodo.ZenodoSoftwareVersionExporter;
import org.gcube.common.software.export.biblatex.BibLaTeXExporter;
import org.gcube.common.software.export.zenodo.ZenodoExporter;
import org.gcube.common.software.model.ExporterConfig;
import org.gcube.common.software.model.GlobalConfig;
import org.gcube.common.software.model.SoftwareVersionConfig;
@ -13,21 +13,21 @@ import org.gcube.common.software.model.SoftwareVersionConfig;
/**
* @author Luca Frosini (ISTI - CNR)
*/
public abstract class SoftwareVersionExporter {
public abstract class SoftwareArtifactExporter {
protected static Map<String, Class<? extends SoftwareVersionExporter>> availableExporters;
protected static Map<String, Class<? extends SoftwareArtifactExporter>> availableExporters;
static {
availableExporters = new HashMap<>();
add(ZenodoSoftwareVersionExporter.class);
add(BibLaTeXSoftwareVersionExporter.class);
add(ZenodoExporter.class);
add(BibLaTeXExporter.class);
}
private static void add(Class<? extends SoftwareVersionExporter> clz) {
private static void add(Class<? extends SoftwareArtifactExporter> clz) {
availableExporters.put(clz.getSimpleName(), clz);
}
public static Map<String, Class<? extends SoftwareVersionExporter>> getAvailableExporters() {
public static Map<String, Class<? extends SoftwareArtifactExporter>> getAvailableExporters() {
return availableExporters;
}
@ -41,7 +41,7 @@ public abstract class SoftwareVersionExporter {
protected final String exportFileNameExtension;
protected SoftwareVersionExporter(String exportFileNameExtension) {
protected SoftwareArtifactExporter(String exportFileNameExtension) {
this.exportFileNameExtension = exportFileNameExtension;
}

10
src/main/java/org/gcube/common/software/export/biblatex/BibLaTeXSoftwareVersionExporter.java → src/main/java/org/gcube/common/software/export/biblatex/BibLaTeXExporter.java
View File

@ -9,7 +9,7 @@ import java.util.Set;
import org.gcube.com.fasterxml.jackson.databind.JsonNode;
import org.gcube.com.fasterxml.jackson.databind.node.ArrayNode;
import org.gcube.common.software.export.SoftwareVersionExporter;
import org.gcube.common.software.export.SoftwareArtifactExporter;
import org.gcube.common.software.model.ElaborationType;
import org.gcube.common.software.model.Variables;
import org.gcube.common.software.utils.FileUtils;
@ -20,15 +20,15 @@ import org.slf4j.LoggerFactory;
/**
* @author Luca Frosini (ISTI - CNR)
*/
public class BibLaTeXSoftwareVersionExporter extends SoftwareVersionExporter {
public class BibLaTeXExporter extends SoftwareArtifactExporter {
private static final Logger logger = LoggerFactory.getLogger(BibLaTeXSoftwareVersionExporter.class);
private static final Logger logger = LoggerFactory.getLogger(BibLaTeXExporter.class);
public static final String EXPORT_FILENAME_EXTENSION = ".bib";
public static final String TEMPLATE_FILENAME = "biblatex.template";
public BibLaTeXSoftwareVersionExporter() {
super(BibLaTeXSoftwareVersionExporter.EXPORT_FILENAME_EXTENSION);
public BibLaTeXExporter() {
super(BibLaTeXExporter.EXPORT_FILENAME_EXTENSION);
}
@Override

16
src/main/java/org/gcube/common/software/export/zenodo/ZenodoSoftwareVersionExporter.java → src/main/java/org/gcube/common/software/export/zenodo/ZenodoExporter.java
View File

@ -30,7 +30,7 @@ import org.gcube.com.fasterxml.jackson.databind.node.ObjectNode;
import org.gcube.common.gxhttp.request.GXHTTPStringRequest;
import org.gcube.common.software.analyser.AnalyserFactory;
import org.gcube.common.software.config.Config;
import org.gcube.common.software.export.SoftwareVersionExporter;
import org.gcube.common.software.export.SoftwareArtifactExporter;
import org.gcube.common.software.model.ElaborationType;
import org.gcube.common.software.model.SoftwareVersionConfig;
import org.gcube.common.software.model.SoftwareVersionFile;
@ -45,9 +45,9 @@ import org.slf4j.LoggerFactory;
/**
* @author Luca Frosini (ISTI - CNR)
*/
public class ZenodoSoftwareVersionExporter extends SoftwareVersionExporter {
public class ZenodoExporter extends SoftwareArtifactExporter {
private static final Logger logger = LoggerFactory.getLogger(ZenodoSoftwareVersionExporter.class);
private static final Logger logger = LoggerFactory.getLogger(ZenodoExporter.class);
public static final String EXPORT_FILENAME_EXTENSION = ".json";
@ -92,8 +92,8 @@ public class ZenodoSoftwareVersionExporter extends SoftwareVersionExporter {
return map;
}
public ZenodoSoftwareVersionExporter() {
super(ZenodoSoftwareVersionExporter.EXPORT_FILENAME_EXTENSION);
public ZenodoExporter() {
super(ZenodoExporter.EXPORT_FILENAME_EXTENSION);
}
protected void addFilesToDeposition(List<File> files ) throws Exception {
@ -476,7 +476,7 @@ public class ZenodoSoftwareVersionExporter extends SoftwareVersionExporter {
conf = Config.getProperties().getProperty(propertyName);
}
if(conf==null) {
throw new Exception("No configuration '" + propertyName + "' property found.");
throw new Exception("No configuration for '" + propertyName + "' property found.");
}
return conf;
}
@ -540,7 +540,7 @@ public class ZenodoSoftwareVersionExporter extends SoftwareVersionExporter {
protected ObjectNode getObjectNode() throws Exception {
ObjectMapper objectMapper = Utils.getObjectMapper();
ObjectNode toBeExported = objectMapper.createObjectNode();
toBeExported.replace(AnalyserFactory.GLOBAL_PROPERTY_NAME, globalConfig.getOriginalJson().deepCopy());
toBeExported.replace(AnalyserFactory.CONFIGURATION_PROPERTY_NAME, globalConfig.getOriginalJson().deepCopy());
ArrayNode array = objectMapper.createArrayNode();
SoftwareVersionConfig previous = softwareVersionConfig;
boolean firstNode = true;
@ -555,7 +555,7 @@ public class ZenodoSoftwareVersionExporter extends SoftwareVersionExporter {
array.insert(0, node);
previous = previous.getPrevious();
}
toBeExported.replace(AnalyserFactory.VERSIONS_PROPERTY_NAME, array);
toBeExported.replace(AnalyserFactory.ARTIFACTS_PROPERTY_NAME, array);
return toBeExported;
}

1
src/main/java/org/gcube/common/software/model/SoftwareVersionConfig.java
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@ -19,6 +19,7 @@ import org.gcube.common.software.utils.Utils;
/**
* @author Luca Frosini (ISTI - CNR)
* TO BE GENERALIZED
*/
public class SoftwareVersionConfig {

4
src/main/java/org/gcube/common/software/utils/FileUtils.java
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@ -3,7 +3,7 @@ package org.gcube.common.software.utils;
import java.io.File;
import java.net.URL;
import org.gcube.common.software.export.biblatex.BibLaTeXSoftwareVersionExporter;
import org.gcube.common.software.export.biblatex.BibLaTeXExporter;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@ -15,7 +15,7 @@ public class FileUtils {
private static final Logger logger = LoggerFactory.getLogger(FileUtils.class);
public static File getFileFromFilename(String fileName) throws Exception {
URL jsonFileURL = BibLaTeXSoftwareVersionExporter.class.getClassLoader().getResource(fileName);
URL jsonFileURL = BibLaTeXExporter.class.getClassLoader().getResource(fileName);
File file = new File(jsonFileURL.toURI());
logger.trace("File is {}", file.getAbsolutePath());
return file;

10
src/main/java/org/gcube/common/software/utils/Utils.java
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@ -41,8 +41,14 @@ public class Utils {
return s.replaceAll("\\{\\{" + variableName + "\\}\\}", replace);
}
/*
* Merge all the properties contained in version in concept
/**
* Clone node1 and merge all the properties contained in node2 into the cloned JsonNode.
* In other words, the properties contained in node2
* will replace/add the properties contained in the clone of node1.
* Both node1 and node2 are not modified.
* @param node1 contains the properties to be merged with the properties contained in node2.
* @param node2 contains the properties will replace/add the properties in the clone of node1.
* @return a new JsonNode containing the merged properties.
*/
public static JsonNode merge(JsonNode node1, JsonNode node2) {
ObjectNode cloned = node1.deepCopy();

2
src/test/java/org/gcube/common/software/analyser/AnalyserTest.java
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@ -23,7 +23,7 @@ public class AnalyserTest {
File file = FileUtils.getFileFromFilename(FILENAME);
Analyser analyser = AnalyserFactory.getAnalyser(file);
// analyser.setOutputDirectory(file.getParentFile());
List<File> files =analyser.analyse();
List<File> files = analyser.analyse();
logger.info("Generated the following files {}", files);
}

8
src/test/resources/gcat-from-scratch.json
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@ -1,5 +1,5 @@
{
"global": {
"configuration": {
"name": "gcat",
"group": "data-catalogue",
"title": "gCube Catalogue (gCat) Service {{version}}",
@ -136,17 +136,17 @@
],
"export_filename": "{{name}}",
"exporters": {
"ZenodoSoftwareVersionExporter": {
"ZenodoExporter": {
"elaboration": "NONE",
"skip_grants": ["004260"],
"additional_html_description": "\n\n<p><a href=\"https://www.gcube-system.org/\">gCube</a> is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the <a href=\"https://www.d4science.org/\">D4Science Infrastructure</a>, by favouring the realisation of reuse-oriented policies.</p>\n\n<p><a href=\"https://www.gcube-system.org/\">gCube</a> has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage.</p>\n\n<p><a href=\"https://www.gcube-system.org/\">gCube</a> offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data.</p>\n\n<p><a href=\"https://www.d4science.org/\">D4Science</a> is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube.</p>\n\n<p>&nbsp;</p>\n\n<p>The official source code location of this software version is available at:</p>\n\n<p><a href=\"{{code_location}}\">{{code_location}}</a></p>"
},
"BibLaTeXSoftwareVersionExporter": {
"BibLaTeXExporter": {
"elaboration": "ALL"
}
}
},
"versions": [
"artifacts": [
{
"version": "1.0.0",
"date": "2019-01-10",

8
src/test/resources/gcat-test-sandbox.json
View File

@ -1,5 +1,5 @@
{
"global": {
"configuration": {
"name": "gcat",
"group": "data-catalogue",
"title": "gCube Catalogue (gCat) Service {{version}}",
@ -137,17 +137,17 @@
],
"export_filename": "{{name}}",
"exporters": {
"ZenodoSoftwareVersionExporter": {
"ZenodoExporter": {
"elaboration": "NONE",
"skip_grants": ["004260"],
"additional_html_description": "\n\n<p><a href=\"https://www.gcube-system.org/\">gCube</a> is an open-source software toolkit used for building and operating Hybrid Data Infrastructures enabling the dynamic deployment of Virtual Research Environments, such as the <a href=\"https://www.d4science.org/\">D4Science Infrastructure</a>, by favouring the realisation of reuse-oriented policies.</p>\n\n<p><a href=\"https://www.gcube-system.org/\">gCube</a> has been used to successfully build and operate infrastructures and virtual research environments for application domains ranging from biodiversity to environmental data management and cultural heritage.</p>\n\n<p><a href=\"https://www.gcube-system.org/\">gCube</a> offers components supporting typical data management workflows including data access, curation, processing, and visualisation on a large set of data typologies ranging from primary biodiversity data to geospatial and tabular data.</p>\n\n<p><a href=\"https://www.d4science.org/\">D4Science</a> is a Hybrid Data Infrastructure combining over 500 software components and integrating data from more than 50 different data providers into a coherent and managed system of hardware, software, and data resources. The D4Science infrastructure drastically reduces the cost of ownership, maintenance, and operation thanks to the exploitation of gCube.</p>\n\n<p>&nbsp;</p>\n\n<p>The official source code location of this software version is available at:</p>\n\n<p><a href=\"{{code_location}}\">{{code_location}}</a></p>"
},
"BibLaTeXSoftwareVersionExporter": {
"BibLaTeXExporter": {
"elaboration": "ALL"
}
}
},
"versions": [
"artifacts": [
{
"version": "1.0.0",
"date": "2019-01-10",