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RSS-171: Fixed report findings and added finished components

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deiflaender 2022-11-02 15:07:12 +01:00
parent 72f9767c2f
commit b2645a4b44
1 changed files with 262 additions and 85 deletions
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347
redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/RSSPoc2Service.java
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@ -4,7 +4,6 @@ import java.text.BreakIterator;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.List;
import java.util.Locale;
@ -20,6 +19,7 @@ import org.springframework.stereotype.Service;
import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.dossier.file.FileModel;
import com.iqser.red.service.redaction.report.v1.api.model.rss.RSSFileResponse;
import com.iqser.red.service.redaction.report.v1.api.model.rss.RSSResponse;
import com.iqser.red.service.redaction.report.v1.server.client.FileAttributesConfigClient;
import com.iqser.red.service.redaction.report.v1.server.client.FileStatusClient;
import com.iqser.red.service.redaction.report.v1.server.client.RedactionLogClient;
import com.iqser.red.service.redaction.v1.model.ChangeType;
@ -36,6 +36,7 @@ public class RSSPoc2Service {
private final FileStatusClient statusClient;
private final Map<String, Set<String>> guidelineMapping = new HashMap<>();
private final FileAttributesConfigClient fileAttributesClient;
@PostConstruct
@ -78,6 +79,9 @@ public class RSSPoc2Service {
List<RSSFileResponse> rssFileResponses = new ArrayList<>();
for (FileModel file : files) {
String oecd = getOecdNumber(file);
Map<String, String> resultMap = new TreeMap<>();
var redactionLog = redactionLogClient.getRedactionLog(dossierId, file.getId(), new ArrayList<>(), true, false);
@ -86,9 +90,7 @@ public class RSSPoc2Service {
resultMap.put("TEST_GUIDELINE(S):_1", getTestGuideline1(redactionLog));
var testGuideline2 = getTestGuideline2(redactionLog);
if (testGuideline2 != null) {
resultMap.put("TEST_GUIDELINE(S):_2", testGuideline2);
}
resultMap.put("TEST_GUIDELINE(S):_2", testGuideline2 == null ? "" : testGuideline2);
resultMap.put("Report_Number:", getReportNumber(redactionLog));
resultMap.put("Experimental_Starting_Date:", getExperimentalStartDate(redactionLog));
@ -96,7 +98,7 @@ public class RSSPoc2Service {
resultMap.put("Species", getSpecies(redactionLog));
resultMap.put("Strain", getStrain(redactionLog));
var macroscopicFindingSentences = getMacroscopicFindings(redactionLog);
var macroscopicFindingSentences = getAsSentences(redactionLog, "macroscopic_findings");
int i = 1;
for (String macroscopicFindingSentence : macroscopicFindingSentences) {
resultMap.put("Macroscopic_Findings_" + i, macroscopicFindingSentence);
@ -107,22 +109,80 @@ public class RSSPoc2Service {
resultMap.put("GLP_Study", getGlpStudy(redactionLog));
resultMap.put("Certificate_of_Analysis,_Batch_Identification", getBatchNumber(redactionLog));
var clinicalSignsSentences = getClinicalSigns(redactionLog);
var clinicalSignsSentences = getAsSentences(redactionLog, "clinical_signs");
i = 1;
for (String clinicalSignsSentence : clinicalSignsSentences) {
resultMap.put("Clincal_Signs_" + i, clinicalSignsSentence);
i++;
}
resultMap.put("Dosages", getDosages(redactionLog));
if (oecd != null && oecd.equals("425")) {
resultMap.put("Dosages", getDosages(redactionLog));
}
var mortalitySentences = getMortality(redactionLog);
var mortalitySentences = getAsSentences(redactionLog, "mortality");
i = 1;
for (String mortalitySentence : mortalitySentences) {
resultMap.put("Mortality_" + i, mortalitySentence);
i++;
}
resultMap.put("PERFORMING_LABORATORY:", getPerformingLaboratory(redactionLog));
if (oecd != null && (oecd.equals("402") || oecd.equals("403") || oecd.equals("425"))) {
resultMap.put("Conclusion_-_LD50_(mg/L)", getLd50Value(redactionLog));
resultMap.put("Conclusion_-_Minimum_Confidence", getConfidenceMinimal(redactionLog));
resultMap.put("Conclusion_-_Maximum_Confidence", getConfidenceMaximal(redactionLog));
}
if (oecd != null && (oecd.equals("402") || oecd.equals("403") || oecd.equals("404") || oecd.equals("405") || oecd.equals("425") || oecd.equals("429") || oecd.equals(
"471"))) {
var guidelineDeviationSentences = getAsSentences(redactionLog, "guideline_deviation");
i = 1;
for (String guidelineDeviationSentence : guidelineDeviationSentences) {
resultMap.put("Deviation_from_the_Guideline_(Study_Plan)_" + i, guidelineDeviationSentence);
i++;
}
}
if (oecd != null && (oecd.equals("402") || oecd.equals("403") || oecd.equals("404") || oecd.equals("405") || oecd.equals("425") || oecd.equals("429") || oecd.equals(
"471"))) {
resultMap.put("Study_Conclusion", getStudyConclusion(redactionLog));
}
if (oecd != null && oecd.equals("402")) {
var weightBehaviorChangesSentences = getAsSentences(redactionLog, "weight_behavior_changes");
i = 1;
for (String sentence : weightBehaviorChangesSentences) {
resultMap.put("Body_weight_changes_" + i, sentence);
i++;
}
}
if (oecd != null && oecd.equals("403")) {
resultMap.put("MMAD", getMmad(redactionLog));
resultMap.put("GSD", getGsd(redactionLog));
var effectiveConcentrations = getEffectiveConcentrations(redactionLog);
Iterator<String> effectiveConcentrationsIterator = effectiveConcentrations.iterator();
i = 1;
while (effectiveConcentrationsIterator.hasNext()) {
String effectiveConcentration = effectiveConcentrationsIterator.next();
resultMap.put("Effective_Concerntration_(mg/L_of_air)_" + i, effectiveConcentration);
i++;
}
}
if (oecd != null && (oecd.equals("438") || oecd.equals("439"))) {
resultMap.put("Results_and_Conclusions", getResultsAndConclusion(redactionLog));
}
if (oecd != null && oecd.equals("404")) {
resultMap.put("Dose_(ml/animal)", getDoseMlPerAnimal(redactionLog));
resultMap.put("Was_there_dilution_of_the_test_substance?", getDilution(redactionLog));
}
rssFileResponses.add(new RSSFileResponse(file.getFilename(), resultMap));
}
@ -132,6 +192,200 @@ public class RSSPoc2Service {
}
private String getOecdNumber(FileModel file) {
var fileAttributesConfig = fileAttributesClient.getFileAttributeConfigs(file.getDossierTemplateId());
var oecdFileAttributeConf = fileAttributesConfig.stream().filter(f -> f.getLabel().equals("OECD Number")).map(f -> f.getId()).findFirst();
if (oecdFileAttributeConf.isPresent()) {
return file.getFileAttributes().get(oecdFileAttributeConf.get());
}
return null;
}
private String getDilution(RedactionLog redactionLog) {
var dilution = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("dilution")).map(RedactionLogEntry::getValue).findFirst();
if (dilution.isPresent()) {
return "Yes";
}
return "No";
}
private String getDoseMlPerAnimal(RedactionLog redactionLog) {
var doseMlPerAnimal = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("dose_(ml_per_animal)")).map(RedactionLogEntry::getValue).findFirst();
return doseMlPerAnimal.orElse("");
}
private String getResultsAndConclusion(RedactionLog redactionLog) {
var resultsAndConclusion = redactionLog.getRedactionLogEntry()
.stream()
.filter(r -> r.getType().equals("results_and_conclusion"))
.map(RedactionLogEntry::getValue)
.collect(Collectors.toList());
StringBuilder stringBuilder = new StringBuilder();
Iterator<String> itty = resultsAndConclusion.iterator();
while (itty.hasNext()) {
stringBuilder.append(itty.next());
if (itty.hasNext()) {
stringBuilder.append(". ");
}
}
return stringBuilder.toString().trim();
}
private Set<String> getEffectiveConcentrations(RedactionLog redactionLog) {
return redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("effective_concentration")).map(RedactionLogEntry::getValue).collect(Collectors.toSet());
}
private String getGsd(RedactionLog redactionLog) {
var uniqueGsd = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("gsd")).map(RedactionLogEntry::getValue).collect(Collectors.toSet());
StringBuilder stringBuilder = new StringBuilder();
Iterator<String> itty = uniqueGsd.iterator();
while (itty.hasNext()) {
stringBuilder.append(itty.next());
if (itty.hasNext()) {
stringBuilder.append(", ");
}
}
return stringBuilder.toString().trim();
}
private String getMmad(RedactionLog redactionLog) {
var uniqueMmad = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("mmad")).map(RedactionLogEntry::getValue).collect(Collectors.toSet());
StringBuilder stringBuilder = new StringBuilder();
Iterator<String> itty = uniqueMmad.iterator();
while (itty.hasNext()) {
stringBuilder.append(itty.next());
if (itty.hasNext()) {
stringBuilder.append(", ");
}
}
return stringBuilder.toString().trim();
}
private String getStudyConclusion(RedactionLog redactionLog) {
var studyConclusion = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("study_conclusion")).map(RedactionLogEntry::getValue).findFirst();
return studyConclusion.orElse("");
}
private List<String> getAsSentences(RedactionLog redactionLog, String type) {
List<String> sentences = new ArrayList<>();
var typeStrings = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).map(RedactionLogEntry::getValue).collect(Collectors.toList());
if (typeStrings.isEmpty()) {
return sentences;
}
for (String typeString : typeStrings) {
BreakIterator iterator = BreakIterator.getSentenceInstance(Locale.US);
iterator.setText(typeString);
int start = iterator.first();
for (int end = iterator.next(); end != BreakIterator.DONE; start = end, end = iterator.next()) {
sentences.add(typeString.substring(start, end).replaceAll("\\n", "").trim());
}
}
return sentences;
}
private String getConfidenceMinimal(RedactionLog redactionLog) {
var uniqueConfidenceMinimal = redactionLog.getRedactionLogEntry()
.stream()
.filter(r -> r.getType().equals("confidence_minimal"))
.map(RedactionLogEntry::getValue)
.collect(Collectors.toSet());
StringBuilder stringBuilder = new StringBuilder();
Iterator<String> itty = uniqueConfidenceMinimal.iterator();
while (itty.hasNext()) {
stringBuilder.append(itty.next());
if (itty.hasNext()) {
stringBuilder.append(", ");
}
}
return stringBuilder.toString().trim();
}
private String getConfidenceMaximal(RedactionLog redactionLog) {
var uniqueConfidenceMaximal = redactionLog.getRedactionLogEntry()
.stream()
.filter(r -> r.getType().equals("confidence_maximal"))
.map(RedactionLogEntry::getValue)
.collect(Collectors.toSet());
StringBuilder stringBuilder = new StringBuilder();
Iterator<String> itty = uniqueConfidenceMaximal.iterator();
while (itty.hasNext()) {
stringBuilder.append(itty.next());
if (itty.hasNext()) {
stringBuilder.append(", ");
}
}
return stringBuilder.toString().trim();
}
private String getLd50Value(RedactionLog redactionLog) {
var uniqueLd50 = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("ld50_value")).map(RedactionLogEntry::getValue).collect(Collectors.toSet());
StringBuilder stringBuilder = new StringBuilder();
Iterator<String> itty = uniqueLd50.iterator();
while (itty.hasNext()) {
stringBuilder.append(itty.next());
if (itty.hasNext()) {
stringBuilder.append(", ");
}
}
return stringBuilder.toString().trim();
}
private String getPerformingLaboratory(RedactionLog redactionLog) {
var laboratoryName = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("laboratory_name")).map(RedactionLogEntry::getValue).findFirst();
var laboratoryCountry = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("laboratory_country")).map(RedactionLogEntry::getValue).findFirst();
StringBuilder sb = new StringBuilder();
if (laboratoryName.isPresent()) {
sb.append(laboratoryName.get());
}
if (laboratoryCountry.isPresent()) {
sb.append(", ").append(laboratoryCountry.get());
}
return sb.toString().trim();
}
private String getDosages(RedactionLog redactionLog) {
var dosages = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("dosages")).map(RedactionLogEntry::getValue).findFirst();
@ -140,58 +394,6 @@ public class RSSPoc2Service {
}
private List<String> getMortality(RedactionLog redactionLog) {
List<String> mortality = new ArrayList<>();
var mortalityString = redactionLog.getRedactionLogEntry()
.stream()
.filter(r -> r.getType().equals("mortality"))
.map(RedactionLogEntry::getValue)
.findFirst();
if (!mortalityString.isPresent()) {
return mortality;
}
String source = mortalityString.get();
BreakIterator iterator = BreakIterator.getSentenceInstance(Locale.US);
iterator.setText(source);
int start = iterator.first();
for (int end = iterator.next(); end != BreakIterator.DONE; start = end, end = iterator.next()) {
mortality.add(source.substring(start, end));
}
return mortality;
}
private List<String> getClinicalSigns(RedactionLog redactionLog) {
List<String> clinicalSigns = new ArrayList<>();
var clinicalSignsString = redactionLog.getRedactionLogEntry()
.stream()
.filter(r -> r.getType().equals("clinical_signs"))
.map(RedactionLogEntry::getValue)
.findFirst();
if (!clinicalSignsString.isPresent()) {
return clinicalSigns;
}
String source = clinicalSignsString.get();
BreakIterator iterator = BreakIterator.getSentenceInstance(Locale.US);
iterator.setText(source);
int start = iterator.first();
for (int end = iterator.next(); end != BreakIterator.DONE; start = end, end = iterator.next()) {
clinicalSigns.add(source.substring(start, end));
}
return clinicalSigns;
}
private String getBatchNumber(RedactionLog redactionLog) {
var batchNumber = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("batch_number")).map(RedactionLogEntry::getValue).findFirst();
@ -220,31 +422,6 @@ public class RSSPoc2Service {
}
private List<String> getMacroscopicFindings(RedactionLog redactionLog) {
List<String> macroscopicFindings = new ArrayList<>();
var macroscopicFindingString = redactionLog.getRedactionLogEntry()
.stream()
.filter(r -> r.getType().equals("macroscopic_findings"))
.map(RedactionLogEntry::getValue)
.findFirst();
if (!macroscopicFindingString.isPresent()) {
return macroscopicFindings;
}
String source = macroscopicFindingString.get();
BreakIterator iterator = BreakIterator.getSentenceInstance(Locale.US);
iterator.setText(source);
int start = iterator.first();
for (int end = iterator.next(); end != BreakIterator.DONE; start = end, end = iterator.next()) {
macroscopicFindings.add(source.substring(start, end));
}
return macroscopicFindings;
}
private String getStrain(RedactionLog redactionLog) {
var strain = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("strain")).map(RedactionLogEntry::getValue).findFirst();