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Pull request #185: RSS-171: Changed report to new SCM excel file requirements

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Merge in RED/redaction-report-service from RSS-171 to master

* commit 'fdb97646c8f17d0e9eb89295d77f4dc62c842435':
  RSS-171: Changed report to new SCM excel file requirements
This commit is contained in:
Dominique Eiflaender 2022-11-07 13:22:26 +01:00
commit a67ac701d1
1 changed files with 99 additions and 64 deletions
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163
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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@ -65,6 +65,14 @@ public class RSSPoc2Service {
guidelineMapping.put("Nº 442B: Skin Sensitization (27/06/2018)", Set.of("ÖECD 442B (2018)", "ÖECD No. 442B (2018)"));
guidelineMapping.put("Nº 471: Bacterial Reverse Mutation Test (21/07/1997)", Set.of("OECD 471 (1997)", "OECD No. 471 (1997)"));
guidelineMapping.put("Nº 471: Bacterial Reverse Mutation Test (26/06/2020)", Set.of("OECD 471 (2020)", "OECD No. 471 (2020)"));
guidelineMapping.put("Nº 406: Skin Sensitisation (1992)", Set.of("OECD 406 (1992)", "OECD No. 406 (1992)"));
guidelineMapping.put("Nº 428: Split-Thickness Skin test (2004)", Set.of("OECD 428 (2004)", "OECD No. 428 (2004)"));
guidelineMapping.put("Nº 438: Eye Irritation (26/06/2018)", Set.of("OECD 438 (2018)", "OECD No. 438 (2018)"));
guidelineMapping.put("Nº 439: Skin Irritation (2019)", Set.of("OECD 439 (2019)", "OECD No. 439 (2019)"));
guidelineMapping.put("Nº 474: Micronucleus Bone Marrow Cells Rat (2016)", Set.of("OECD 474 (2016)", "OECD No. 474 (2016)"));
guidelineMapping.put("Nº 487: Micronucleus Human Lymphocytes (2016)", Set.of("OECD 487 (2016)", "OECD No. 487 (2016)"));
}
@ -87,100 +95,112 @@ public class RSSPoc2Service {
redactionLog.getRedactionLogEntry().removeIf(r -> !r.isRedacted() || r.getChanges().get(r.getChanges().size() - 1).getType().equals(ChangeType.REMOVED));
resultMap.put("TEST_GUIDELINE(S):_1", getTestGuideline1(redactionLog));
resultMap.put(oecd + "-Study_Title", getTitle(redactionLog));
resultMap.put(oecd + "-Report_Number:", getReportNumber(redactionLog));
resultMap.put(oecd + "-PERFORMING_LABORATORY:", getPerformingLaboratory(redactionLog));
resultMap.put(oecd + "-Experimental_Starting_Date:", getExperimentalStartDate(redactionLog));
resultMap.put(oecd + "-Experimental_Completion_Date:", getExperimentalEndDate(redactionLog));
resultMap.put(oecd + "-GLP_Study", getGlpStudy(redactionLog));
resultMap.put(oecd + "-Certificate_of_Analysis,_Batch_Identification", getBatchNumber(redactionLog));
resultMap.put(oecd + "-TEST_GUIDELINE(S):_1", getTestGuideline1(redactionLog));
var testGuideline2 = getTestGuideline2(redactionLog);
resultMap.put("TEST_GUIDELINE(S):_2", testGuideline2 == null ? "" : testGuideline2);
resultMap.put(oecd + "-TEST_GUIDELINE(S):_2", testGuideline2 == null ? "" : testGuideline2);
resultMap.put("Report_Number:", getReportNumber(redactionLog));
resultMap.put("Experimental_Starting_Date:", getExperimentalStartDate(redactionLog));
resultMap.put("Experimental_Completion_Date:", getExperimentalEndDate(redactionLog));
resultMap.put("Species", getSpecies(redactionLog));
resultMap.put("Strain", getStrain(redactionLog));
if (oecdIn(oecd, Set.of("402", "403", "404", "405", "425", "429", "436", "471"))) {
var macroscopicFindingSentences = getAsSentences(redactionLog, "macroscopic_findings");
int i = 1;
for (String macroscopicFindingSentence : macroscopicFindingSentences) {
resultMap.put("Macroscopic_Findings_" + i, macroscopicFindingSentence);
i++;
}
resultMap.put(oecd + "-Study_Conclusion", getStudyConclusion(redactionLog));
resultMap.put("Study_Title", getTitle(redactionLog));
resultMap.put("GLP_Study", getGlpStudy(redactionLog));
resultMap.put("Certificate_of_Analysis,_Batch_Identification", getBatchNumber(redactionLog));
var clinicalSignsSentences = getAsSentences(redactionLog, "clinical_signs");
i = 1;
for (String clinicalSignsSentence : clinicalSignsSentences) {
resultMap.put("Clincal_Signs_" + i, clinicalSignsSentence);
i++;
}
if (oecd != null && oecd.equals("425")) {
resultMap.put("Dosages", getDosages(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;
int i = 1;
for (String guidelineDeviationSentence : guidelineDeviationSentences) {
resultMap.put("Deviation_from_the_Guideline_(Study_Plan)_" + i, guidelineDeviationSentence);
resultMap.put(oecd + "-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 (oecdIn(oecd, Set.of("402", "403", "404", "405", "425", "429", "436"))) {
resultMap.put(oecd + "-Species", getSpecies(redactionLog));
resultMap.put(oecd + "-Strain", getStrain(redactionLog));
}
if (oecd != null && oecd.equals("402")) {
if (oecdIn(oecd, Set.of("402", "403", "425", "436"))) {
resultMap.put(oecd + "-Conclusion_-_LD50_(mg/L)", getLd50Value(redactionLog));
resultMap.put(oecd + "-Conclusion_-_Minimum_Confidence", getConfidenceMinimal(redactionLog));
resultMap.put(oecd + "-Conclusion_-_Maximum_Confidence", getConfidenceMaximal(redactionLog));
}
if (oecdIn(oecd, Set.of("438", "439"))) {
resultMap.put(oecd + "-Results_and_Conclusions", getResultsAndConclusion(redactionLog));
}
if (oecdIn(oecd, Set.of("402"))) {
var weightBehaviorChangesSentences = getAsSentences(redactionLog, "weight_behavior_changes");
i = 1;
int i = 1;
for (String sentence : weightBehaviorChangesSentences) {
resultMap.put("Body_weight_changes_" + i, sentence);
resultMap.put(oecd + "-Weight_Behavior_Change_" + i, sentence);
i++;
}
}
if (oecd != null && oecd.equals("403")) {
resultMap.put("MMAD", getMmad(redactionLog));
resultMap.put("GSD", getGsd(redactionLog));
if (oecdIn(oecd, Set.of("403"))) {
resultMap.put(oecd + "-MMAD", getMmad(redactionLog));
resultMap.put(oecd + "-GSD", getGsd(redactionLog));
var effectiveConcentrations = getEffectiveConcentrations(redactionLog);
Iterator<String> effectiveConcentrationsIterator = effectiveConcentrations.iterator();
i = 1;
int i = 1;
while (effectiveConcentrationsIterator.hasNext()) {
String effectiveConcentration = effectiveConcentrationsIterator.next();
resultMap.put("Effective_Concerntration_(mg/L_of_air)_" + i, effectiveConcentration);
resultMap.put(oecd + "-Effective_Concentration_(mg/L_of_air)_" + i, effectiveConcentration);
i++;
}
}
if (oecd != null && (oecd.equals("438") || oecd.equals("439"))) {
resultMap.put("Results_and_Conclusions", getResultsAndConclusion(redactionLog));
if (oecdIn(oecd, Set.of("404"))) {
resultMap.put(oecd + "-Dose_(ml/animal)", getDoseMlPerAnimal(redactionLog));
resultMap.put(oecd + "-Was_there_dilution_of_the_test_substance?", getDilution(redactionLog));
resultMap.put(oecd + "-Detailing_of_reported_changes", getAsOneBlock(redactionLog, "detailing"));
}
if (oecd != null && oecd.equals("404")) {
resultMap.put("Dose_(ml/animal)", getDoseMlPerAnimal(redactionLog));
resultMap.put("Was_there_dilution_of_the_test_substance?", getDilution(redactionLog));
if (oecdIn(oecd, Set.of("405"))) {
var sentences = getAsSentences(redactionLog, "detailing");
int i = 1;
for (String sentence : sentences) {
resultMap.put(oecd + "-Detailing_of_reported_changes_" + i, sentence);
i++;
}
}
if (oecdIn(oecd, Set.of("425"))) {
var clinicalSignsSentences = getAsSentences(redactionLog, "clinical_signs");
int i = 1;
for (String clinicalSignsSentence : clinicalSignsSentences) {
resultMap.put(oecd + "-Clincal_Signs_" + i, clinicalSignsSentence);
i++;
}
var mortalitySentences = getAsSentences(redactionLog, "mortality");
i = 1;
for (String mortalitySentence : mortalitySentences) {
resultMap.put(oecd + "-Mortality_" + i, mortalitySentence);
i++;
}
resultMap.put(oecd + "-Dosages", getDosages(redactionLog));
}
if (oecdIn(oecd, Set.of("429"))) {
var sentences = getAsSentences(redactionLog, "preliminary_test_results");
int i = 1;
for (String sentence : sentences) {
resultMap.put(oecd + "-Preliminary_test_results" + i, sentence);
i++;
}
resultMap.put(oecd + "-Test_results", getAsOneBlock(redactionLog, "test_results"));
}
rssFileResponses.add(new RSSFileResponse(file.getFilename(), resultMap));
@ -192,6 +212,21 @@ public class RSSPoc2Service {
}
private String getAsOneBlock(RedactionLog redactionLog, String type) {
return redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).map(RedactionLogEntry::getValue).collect(Collectors.joining(" "));
}
private boolean oecdIn(String oecd, Set<String> oecdsToApply) {
if (oecd != null && oecdsToApply.contains(oecd)) {
return true;
}
return false;
}
private String getOecdNumber(FileModel file) {
var fileAttributesConfig = fileAttributesClient.getFileAttributeConfigs(file.getDossierTemplateId());