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Pull request #191: RSS-207: Added more compontent, fixed issues for SCM Report

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Merge in RED/redaction-report-service from RSS-207 to master

* commit '5f8fbf6794b30b229a7bb3ca9acdc01d244e0718':
  RSS-207: Added more compontent, fixed issues for SCM Report
This commit is contained in:
Dominique Eiflaender 2022-11-16 12:22:38 +01:00
commit 2cfcd3789a
1 changed files with 65 additions and 33 deletions
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98
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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@ -93,6 +93,8 @@ public class RSSPoc2Service {
Map<String, String> resultMap = new TreeMap<>();
var redactionLog = redactionLogClient.getRedactionLog(dossierId, file.getId(), new ArrayList<>(), true, false);
sortRedactionLog(redactionLog);
redactionLog.getRedactionLogEntry().removeIf(r -> !r.isRedacted() || r.getChanges().get(r.getChanges().size() - 1).getType().equals(ChangeType.REMOVED));
resultMap.put("Study_Type_Number", oecd);
@ -133,7 +135,6 @@ public class RSSPoc2Service {
resultMap.put("Conclusion_Maximum_Confidence", getConfidenceMaximal(redactionLog));
}
if (oecdIn(oecd, Set.of("402", "403", "436"))) {
resultMap.put("Necropsy_findings", getLongestBlock(redactionLog, "necropsy_findings"));
}
@ -142,13 +143,12 @@ public class RSSPoc2Service {
resultMap.put("Conducted_with_4_hours_of_Exposure", getAsOneBlock(redactionLog, "4h_exposure"));
}
if (oecdIn(oecd, Set.of("406", "428", "438", "439", "471", "474", "487"))) {
resultMap.put("Study_Design", getAsOneBlock(redactionLog, "study_design"));
}
if (oecdIn(oecd, Set.of("406", "428", "438", "439", "474", "487"))) {
resultMap.put("Results_and_Conclusions", getResultsAndConclusion(redactionLog));
resultMap.put("Results_and_Conclusions", getJoinedValues(redactionLog, "results_and_conclusion", " "));
}
if (oecdIn(oecd, Set.of("402"))) {
@ -193,16 +193,15 @@ public class RSSPoc2Service {
if (oecdIn(oecd, Set.of("404"))) {
resultMap.put("Dose_ml_per_animal", getDoseMlPerAnimal(redactionLog));
// resultMap.put("Was_there_dilution_of_the_test_substance?", getDilution(redactionLog)); // Out of scope.
}
if (oecdIn(oecd, Set.of("404", "405"))) {
resultMap.put("Detailing_of_reported_changes", getAsOneBlock(redactionLog, "detailing"));
}
if (oecdIn(oecd, Set.of("405"))) {
var sentences = getAsSentences(redactionLog, "detailing");
int i = 1;
for (String sentence : sentences) {
resultMap.put("Detailing_of_reported_changes_" + i, sentence);
i++;
}
if (oecdIn(oecd, Set.of("405", "429"))) {
resultMap.put("Sex", getJoinedUniqueValues(redactionLog, "sex", ", "));
resultMap.put("Number_of_Animals", getNumberOfAnimals(redactionLog));
}
if (oecdIn(oecd, Set.of("425"))) {
@ -245,6 +244,25 @@ public class RSSPoc2Service {
}
private String getJoinedValues(RedactionLog redactionLog, String type, String seperator) {
return redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).map(RedactionLogEntry::getValue).collect(Collectors.joining(seperator)).trim();
}
private String getJoinedUniqueValues(RedactionLog redactionLog, String type, String seperator) {
return redactionLog.getRedactionLogEntry()
.stream()
.filter(r -> r.getType().equals(type))
.map(RedactionLogEntry::getValue)
.collect(Collectors.toSet())
.stream()
.collect(Collectors.joining(seperator))
.trim();
}
private String getLongestBlock(RedactionLog redactionLog, String type) {
return redactionLog.getRedactionLogEntry()
@ -282,7 +300,6 @@ public class RSSPoc2Service {
return null;
}
// private String getDilution(RedactionLog redactionLog) {
//
// var dilution = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("dilution")).map(RedactionLogEntry::getValue).findFirst();
@ -294,6 +311,28 @@ public class RSSPoc2Service {
// }
private String getNumberOfAnimals(RedactionLog redactionLog) {
var numberOfAnimals = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("number_of_animals")).map(RedactionLogEntry::getValue).findFirst();
if (numberOfAnimals.isPresent()) {
return numberOfAnimals.get();
}
var uniqueAnimalNumbers = redactionLog.getRedactionLogEntry()
.stream()
.filter(r -> r.getType().equals("animal_number"))
.map(RedactionLogEntry::getValue)
.collect(Collectors.toSet());
if (uniqueAnimalNumbers.isEmpty()) {
return "";
}
return String.valueOf(uniqueAnimalNumbers.size());
}
private String getDoseMlPerAnimal(RedactionLog redactionLog) {
var doseMlPerAnimal = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("dose_(ml_per_animal)")).map(RedactionLogEntry::getValue).findFirst();
@ -302,32 +341,11 @@ public class RSSPoc2Service {
}
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());
@ -344,7 +362,6 @@ public class RSSPoc2Service {
//
// }
// private String getMmad(RedactionLog redactionLog) {
//
// var uniqueMmad = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("mmad")).map(RedactionLogEntry::getValue).collect(Collectors.toSet());
@ -612,4 +629,19 @@ public class RSSPoc2Service {
return "No mapping found for: " + guideline;
}
private void sortRedactionLog(RedactionLog redactionLog) {
redactionLog.getRedactionLogEntry().sort((entry1, entry2) -> {
if (entry1.getPositions().get(0).getPage() == entry2.getPositions().get(0).getPage()) {
if (entry1.getPositions().get(0).getTopLeft().getY() == entry2.getPositions().get(0).getTopLeft().getY()) {
return entry1.getPositions().get(0).getTopLeft().getX() < entry2.getPositions().get(0).getTopLeft().getX() ? -1 : 1;
} else {
return entry1.getPositions().get(0).getTopLeft().getY() < entry2.getPositions().get(0).getTopLeft().getY() ? 1 : -1;
}
}
return entry1.getPositions().get(0).getPage() < entry2.getPositions().get(0).getPage() ? -1 : 1;
});
}
}