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csv file postfixes added for sideloaded entities
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@hkir-dev
hkir-dev committed Aug 21, 2024
1 parent d0cc00c commit 69d2393
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Showing 5 changed files with 30 additions and 16 deletions.
1 change: 0 additions & 1 deletion pom.xml
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Original file line number Diff line number Diff line change
Expand Up @@ -104,7 +104,6 @@
<groupId>com.github.ben-manes.caffeine</groupId>
<artifactId>caffeine</artifactId>
<version>2.3.3</version>
<scope>provided</scope>
</dependency>

<!-- https://mvnrepository.com/artifact/org.json/json -->
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17 changes: 13 additions & 4 deletions src/main/java/ebi/spot/neo4j2owl/importer/N2OCSVWriter.java
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Expand Up @@ -17,6 +17,7 @@ public class N2OCSVWriter {
private final RelationTypeCounter relationTypeCounter;
private final N2OLog log = N2OLog.getInstance();
private final N2OImportCSVConfig n2OImportCSVConfig = new N2OImportCSVConfig();
private final String csvPostfix;
public enum CSV_TYPE
{
NODES("nodes"), RELATIONSHIPS("relationship");
Expand All @@ -26,10 +27,15 @@ public enum CSV_TYPE
}
}

N2OCSVWriter(N2OImportManager manager, RelationTypeCounter relationTypeCounter, File dir) {
N2OCSVWriter(N2OImportManager manager, RelationTypeCounter relationTypeCounter, File dir, String csvPostfix) {
this.manager = manager;
this.dir = dir;
this.relationTypeCounter = relationTypeCounter;
if(csvPostfix == null) {
this.csvPostfix = "";
}else {
this.csvPostfix = csvPostfix;
}
}

void exportOntologyToCSV() throws N2OException {
Expand All @@ -49,20 +55,20 @@ private void processExportForRelationships() throws N2OException {
Map<String, List<N2OOWLRelationship>> relationships = indexRelationshipsByType();
Map<String, List<String>> dataout_rel = prepareRelationCSVsForExport(relationships);
prepareCyperQueries(dataout_rel, CSV_TYPE.RELATIONSHIPS);
N2OUtils.writeToFile(getImportDir(), dataout_rel, CSV_TYPE.RELATIONSHIPS);
N2OUtils.writeToFile(getImportDir(), dataout_rel, CSV_TYPE.RELATIONSHIPS, csvPostfix);
}

private void processExportForNodes() throws N2OException {
Map<String, List<OWLEntity>> entities = indexEntitiesByType();
Map<String, List<String>> dataout = prepareNodeCSVsForExport(entities);
prepareCyperQueries(dataout, CSV_TYPE.NODES);
N2OUtils.writeToFile(dir, dataout, CSV_TYPE.NODES);
N2OUtils.writeToFile(dir, dataout, CSV_TYPE.NODES, csvPostfix);

}

private void prepareCyperQueries(Map<String, List<String>> dataout, CSV_TYPE csv_type) {
for(String type: dataout.keySet()) {
File f = N2OUtils.constructFileHandle(dir, csv_type.name, type);
File f = N2OUtils.constructFileHandle(dir, csv_type.name, type, csvPostfix);
String cypher = constructCypherQuery(csv_type, f);
this.n2OImportCSVConfig.putImport(cypher, f.getName());
}
Expand All @@ -72,6 +78,9 @@ private String constructCypherQuery(CSV_TYPE csv_type, File f) {
String filename = f.getName();

String type = filename.substring(filename.indexOf("_") + 1).replaceAll(N2OStatic.CSV_EXTENSION, "");
if(!csvPostfix.isEmpty()) {
type = type.replace(csvPostfix + "_" , "");
}
Integer periodic_commit = N2OConfig.getInstance().getPeriodicCommit();
String cypher = "USING PERIODIC COMMIT "+periodic_commit+"\n" +
"LOAD CSV WITH HEADERS FROM \"file:/"+filename+"\" AS cl\n";
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6 changes: 3 additions & 3 deletions src/main/java/ebi/spot/neo4j2owl/importer/N2OImportService.java
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Expand Up @@ -25,10 +25,10 @@ public void prepareConfig(String config, File importdir) throws IOException, N2O
}

public N2OCSVWriter prepareCSVFilesForImport(String url, File importdir, N2OImportResult importResults) throws OWLOntologyCreationException, IOException, InterruptedException, ExecutionException, N2OException {
return prepareCSVFilesForImport(url, importdir, importResults, true, null);
return prepareCSVFilesForImport(url, importdir, importResults, true, null, null);
}

public N2OCSVWriter prepareCSVFilesForImport(String url, File importdir, N2OImportResult importResults, Boolean enableReasoning, String annotation_iri) throws OWLOntologyCreationException, IOException, InterruptedException, ExecutionException, N2OException {
public N2OCSVWriter prepareCSVFilesForImport(String url, File importdir, N2OImportResult importResults, Boolean enableReasoning, String annotation_iri, String csvPostfix) throws OWLOntologyCreationException, IOException, InterruptedException, ExecutionException, N2OException {
logger.log("Loading Ontology");
OWLOntology o = OWLManager.createOWLOntologyManager().loadOntologyFromOntologyDocument(getOntologyIRI(url, importdir));
logger.log("Size ontology: " + o.getAxiomCount());
Expand All @@ -38,7 +38,7 @@ public N2OCSVWriter prepareCSVFilesForImport(String url, File importdir, N2OImpo

logger.log("Loading in Database: " + importdir.getAbsolutePath());

N2OCSVWriter csvWriter = new N2OCSVWriter(ontologyImporter.getImportManager(), ontologyImporter.getRelationTypeCounter(), importdir);
N2OCSVWriter csvWriter = new N2OCSVWriter(ontologyImporter.getImportManager(), ontologyImporter.getRelationTypeCounter(), importdir, csvPostfix);
csvWriter.exportOntologyToCSV();
return csvWriter;
}
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6 changes: 5 additions & 1 deletion src/main/java/ebi/spot/neo4j2owl/importer/N2OImporterRunner.java
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Expand Up @@ -14,11 +14,15 @@ public static void main(String[] args) {
File importdir = new File(args[2]);
Boolean enableReasoning = true;
String annotation_iri = null;
String csvPostfix = null;

if (args.length > 3) {
enableReasoning = Boolean.parseBoolean(args[3]);
annotation_iri = args[4];
}
if (args.length > 5) {
csvPostfix = args[5];
}

if (config.equals("none")) {
config = null;
Expand All @@ -28,7 +32,7 @@ public static void main(String[] args) {
N2OImportResult importResults = new N2OImportResult();
try {
importService.prepareConfig(config, importdir);
N2OCSVWriter csvWriter = importService.prepareCSVFilesForImport(url, importdir, importResults, enableReasoning, annotation_iri);
N2OCSVWriter csvWriter = importService.prepareCSVFilesForImport(url, importdir, importResults, enableReasoning, annotation_iri, csvPostfix);
File cypherDir = new File(importdir, "transactions");
if (!cypherDir.isDirectory()) {
boolean created = cypherDir.mkdir();
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16 changes: 9 additions & 7 deletions src/main/java/ebi/spot/neo4j2owl/importer/N2OUtils.java
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Expand Up @@ -62,21 +62,23 @@ public static Object extractValueFromOWLAnnotationValue(OWLAnnotationValue aval)
}
return "neo4j2owl_UnknownValue";
}


public static void writeToFile(File dir, Map<String, List<String>> dataout, N2OCSVWriter.CSV_TYPE nodeclass) throws N2OException {

public static void writeToFile(File dir, Map<String, List<String>> dataout, N2OCSVWriter.CSV_TYPE nodeclass, String csvPostfix) throws N2OException {
for (String type : dataout.keySet()) {
File f = constructFileHandle(dir, nodeclass.name, type);
File f = constructFileHandle(dir, nodeclass.name, type, csvPostfix);
try {
FileUtils.writeLines(f, dataout.get(type));
} catch (IOException e) {
throw new N2OException("Writing to file "+f+" failed..",e);
}
}
}

static File constructFileHandle(File dir, String nodeclass, String type) {
return new File(dir, nodeclass + "_" + type + N2OStatic.CSV_EXTENSION);

static File constructFileHandle(File dir, String nodeclass, String type, String namePostfix) {
if(!namePostfix.isEmpty() && !namePostfix.startsWith("_")) {
namePostfix = "_" + namePostfix;
}
return new File(dir, nodeclass + namePostfix + "_" + type + N2OStatic.CSV_EXTENSION);
}

public static String render(OWLClassExpression ce) {
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