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Commit 33a68113 authored by Javi Corvi's avatar Javi Corvi
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new results of pipeline

parent ec995dc1
Pipeline #25589 passed with stage
in 1 minute and 43 seconds
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src/main/java/es/bsc/inb/ades/export/json/main/App.java
View file @ 33a68113
......@@ -39,6 +39,7 @@ import com.fasterxml.jackson.core.JsonGenerationException;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import gate.Annotation;
......@@ -172,8 +173,9 @@ public class App {
String fileOutPutName = file.getName();
File outputAbstractFile = new File (outputDirectoryPath + File.separator + fileOutPutName.replace(".xml", "_documents.json"));
File outputAnnotationsFile = new File (outputDirectoryPath + File.separator + fileOutPutName.replace(".xml", "_annotations.json"));
File cvsOutputFile = new File (outputDirectoryPath + File.separator + fileOutPutName.replace(".xml", "_FINDINGS.csv"));
processDocument(file, outputAbstractFile, outputAnnotationsFile, cvsOutputFile, annotationSet, annotationSetRelationExtraction);
File cvsFindingsOutputFile = new File (outputDirectoryPath + File.separator + fileOutPutName.replace(".xml", "_FINDINGS.csv"));
File cvsSRDomainOutputFile = new File (outputDirectoryPath + File.separator + fileOutPutName.replace(".xml", "_SRDOMAIN.csv"));
processDocument(file, outputAbstractFile, outputAnnotationsFile, cvsFindingsOutputFile, cvsSRDomainOutputFile,annotationSet, annotationSetRelationExtraction);
} catch (ResourceInstantiationException e) {
System.out.println("App::process :: error with document " + file.getAbsolutePath());
e.printStackTrace();
......@@ -204,7 +206,7 @@ public class App {
* @throws JsonGenerationException
* @throws InvalidOffsetException
*/
private static void processDocument(File inputFile, File outputTextFile, File outputAnnotationsFile, File cvsOutputFile,String annotationSet, String annotationSetRelationExtraction ) throws ResourceInstantiationException, JsonGenerationException, IOException, InvalidOffsetException{
private static void processDocument(File inputFile, File outputTextFile, File outputAnnotationsFile, File cvsFindingsOutputFile,File cvsSRDomainOutputFile, String annotationSet, String annotationSetRelationExtraction ) throws ResourceInstantiationException, JsonGenerationException, IOException, InvalidOffsetException{
gate.Document doc = Factory.newDocument(inputFile.toURI().toURL(), "UTF-8");
Gson gsonBuilder = new GsonBuilder().create();
JsonObject annotated_document = new JsonObject();
......@@ -232,11 +234,11 @@ public class App {
writer1.flush();
writer1.close();
writer1 = null;
annotated_document=null;
exportCVS(annotated_document, cvsOutputFile);
exportDataCVS(annotated_document, cvsFindingsOutputFile, cvsSRDomainOutputFile);
annotated_document=null;
//document text
DateFormat dateFormat = new SimpleDateFormat("yyyy/MM/dd HH:mm:ss");
Date date = new Date();
......@@ -256,10 +258,136 @@ public class App {
}
private static void exportCVS(JsonObject annotated_document, File cvsOutput) {
private static void exportDataCVS(JsonObject annotated_document, File cvsFindingsOutput, File cvsSRDomainOutput) {
StringBuffer retStr = new StringBuffer("");
retStr.append("SENTENCE|FINDING|STUDY_TESTCD|MANIFESTATION_OF_FINDING|SPECIMEN|SEX|DOSE|GROUP|IS_TREATMENT_RELATED|STATUS");
retStr.append(System.getProperty("line.separator"));
StringBuffer retStr2 = new StringBuffer("");
retStr2.append("STUDYID|DOMAIN|SRSEQ|SRRISK|SPGRPCD|GRPLBL|SRGRPDOS|SRSEX|SRSTDY|SRSTPHSE|SROBSTDY|SRENDY|SRENPHSE|SROBENDY|SRDOMAIN|SRSPEC|SRTSTCD|SRFNDG|SRORES|SROBSV|SROBSQ|SRSEV|SRPCNT|SRSIGF|SRTRTEF|SRCOMNT|STATUS");
retStr2.append(System.getProperty("line.separator"));
try {
createTxtFile("SR-DOMAIN-RESULT.csv", retStr.toString());
JsonArray sentences = annotated_document.getAsJsonArray("relevant_sentences");
for (JsonElement sentence : sentences) {
JsonObject sentenceObj = sentence.getAsJsonObject();
String text_ = sentenceObj.get("text").getAsString();
String inlinedText = text_.replaceAll("\\R", " ");
String text = inlinedText.replaceAll("\\|", ",");
JsonArray findings = sentenceObj.getAsJsonArray("findings");
for (JsonElement finding : findings) {
JsonObject findingObj = finding.getAsJsonObject();
String finding_str = findingObj.get("FINDING")!=null?findingObj.get("FINDING").getAsJsonObject().get("text").getAsString():"";
String specimen_str = findingObj.get("SPECIMEN")!=null?findingObj.get("SPECIMEN").getAsJsonObject().get("text").getAsString():"";
String study_testcd_str = findingObj.get("STUDY_TESTCD")!=null?findingObj.get("STUDY_TESTCD").getAsJsonObject().get("text").getAsString():"";
String sex_str = findingObj.get("SEX")!=null?findingObj.get("SEX").getAsJsonObject().get("text").getAsString():"";
String manifestation_str = findingObj.get("MANIFESTATION_FINDING")!=null?findingObj.get("MANIFESTATION_FINDING").getAsJsonObject().get("text").getAsString():"";
String is_treatment_related_str = findingObj.get("IS_TREATMENT_RELATED")!=null?findingObj.get("IS_TREATMENT_RELATED").getAsJsonObject().get("value").getAsString():"";
String dose_str = findingObj.get("DOSE")!=null?findingObj.get("DOSE").getAsJsonObject().get("text").getAsString():"";
String group_str = findingObj.get("GROUP")!=null?findingObj.get("GROUP").getAsJsonObject().get("text").getAsString():"";
retStr.append(text).append("|");
retStr.append(finding_str).append("|");
retStr.append(study_testcd_str).append("|");
retStr.append(manifestation_str).append("|");
retStr.append(specimen_str).append("|");
retStr.append(sex_str).append("|");
retStr.append(dose_str).append("|");
retStr.append(group_str).append("|");
retStr.append(is_treatment_related_str).append("|");
retStr.append("not_curated").append("\n");
JsonArray srDomainFindings = findingObj.getAsJsonArray("srDomainFindings");
for (JsonElement srDomainFinding : srDomainFindings) {
JsonObject srDomainFindingObj = srDomainFinding.getAsJsonObject();
//STUDYID -- > Study Identifier
retStr2.append(srDomainFindingObj.get("srDomainId").getAsString());
retStr2.append("|");
//DOMAIN -- > Domain Abbreviation, always SR
retStr2.append("SR");
retStr2.append("|");
//SRSEQ -- > Sequence number
retStr2.append(srDomainFindingObj.get("SRSEQ").getAsString());
retStr2.append("|");
//SRRISK --> Effect Level Associated with a Group/Sex, NOEL, LOEL, NOAEL, LOAEL, HNSTD, STD, MTD
retStr2.append(srDomainFindingObj.get("SRRISK").getAsString());
retStr2.append("|");
//SPGRPCD --> Sponsor-defined Group Code, group 1 , A
retStr2.append(srDomainFindingObj.get("SPGRPCD").getAsString());
retStr2.append("|");
//GRPLBL --> Sponsor-defined Group Name, "low dose", "mid dose"
retStr2.append(srDomainFindingObj.get("GRPLBL").getAsString());
retStr2.append("|");
//SRGRPDOS --> Group Dose Level, "20 mg/kg"
retStr2.append(srDomainFindingObj.get("SRGRPDOS").getAsString());
retStr2.append("|");
//SRSEX -- > Sex
retStr2.append(srDomainFindingObj.get("SRSEX").getAsString());
retStr2.append("|");
//SRSTDY --> Study Day of Start of Finding
retStr2.append("");
retStr2.append("|");
//SRSTPHSE --> Study Phase of first Observation, “PRE-DOSING”, “DOSING”, “RECOVERY”
retStr2.append("");
retStr2.append("|");
//SROBSTDY --> Start Phase Day of Observation
retStr2.append("");
retStr2.append("|");
//SRENDY --> ???
retStr2.append("");
retStr2.append("|");
//SRENPHSE -->Study Phase of last Observation
retStr2.append("");
retStr2.append("|");
//SROBENDY --> ???
retStr2.append("");
retStr2.append("|");
//SRDOMAIN --> Domain of Finding
retStr2.append(srDomainFindingObj.get("SRDOMAIN").getAsString());
retStr2.append("|");
//SRSPEC --> Specimen of Finding
retStr2.append(srDomainFindingObj.get("SRSPEC").getAsString());
retStr2.append("|");
//SRTSTCD --> Test Short Name
retStr2.append(srDomainFindingObj.get("SRTSTCD").getAsString());
retStr2.append("|");
//SRFNDG --> Finding
retStr2.append(srDomainFindingObj.get("SRFNDG").getAsString());
retStr2.append("|");
//SRORES --> Observation (original result)
retStr2.append(srDomainFindingObj.get("SRORES").getAsString());
retStr2.append("|");
//SROBSV --> Manifestation of Finding, “I” (Increase), “D” (Decrease), “P” (Present) or “A” (Absent)
retStr2.append(srDomainFindingObj.get("SROBSV").getAsString());
retStr2.append("|");
//SROBSQ --> Observation Qualifier, “R” (Reversible), “T” (Transient) or ‘none’
retStr2.append(srDomainFindingObj.get("SROBSQ").getAsString());
retStr2.append("|");
//SRSEV --> Severity of Finding
retStr2.append("");
retStr2.append("|");
//SRPCNT --> Scale of this Finding
retStr2.append("");
retStr2.append("|");
//SRSIGF --> Statistical Significance
retStr2.append(srDomainFindingObj.get("SRSIGF").getAsString());
retStr2.append("|");
//SRTRTEF --> Treatment-Related
retStr2.append(srDomainFindingObj.get("SRTRTEF").getAsString());
retStr2.append("|");
//SRCOMNT --> Comment
retStr2.append(srDomainFindingObj.get("SRCOMNT").getAsString());
retStr2.append("|");
//STATUS --> Comment
retStr2.append("not_curated");
retStr2.append("\n");
}
}
}
createTxtFile(cvsFindingsOutput, retStr.toString());
createTxtFile(cvsSRDomainOutput, retStr2.toString());
} catch (IOException e) {
// TODO Auto-generated catch block
e.printStackTrace();
......@@ -472,7 +600,7 @@ public class App {
}else {
String finding_texto = finding.getFeatures().get("text")==null?"":finding.getFeatures().get("text").toString();
if(finding_texto.equals("")) {
System.out.println("text empty finding");//limtox no tiene text
System.out.println("text empty finding");//No se puede entrar por aqui todos deben tener el feature text en la anotacion
}
srDomainFinding.setSRORES(finding_texto);
}
......@@ -660,6 +788,7 @@ public class App {
return srDomainFindingList;
}
private static void processRelevantSentences(String annotationSet, String annotationSetRelationExtraction, gate.Document doc, JsonObject annotated_document) {
AnnotationSet relevant_sentences_set = doc.getAnnotations(annotationSet).get("PRETOX_REL");
JsonArray relevant_sentences = new JsonArray();
......@@ -713,9 +842,8 @@ public class App {
* @throws FileNotFoundException
* @throws IOException
*/
private static void createTxtFile(String path, String plainText) throws FileNotFoundException, IOException {
File fout = new File(path);
FileOutputStream fos = new FileOutputStream(fout);
private static void createTxtFile(File file, String plainText) throws FileNotFoundException, IOException {
FileOutputStream fos = new FileOutputStream(file);
BufferedWriter bw = new BufferedWriter(new OutputStreamWriter(fos,StandardCharsets.UTF_8));
bw.write(plainText);
bw.flush();
......
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