RSS-194: Sort in order from flora order, added more components etc.
This commit is contained in:
deiflaender
parent
f4bf290194
commit
c27bd544ab
@ -5,11 +5,11 @@ import java.util.ArrayList;
|
||||
import java.util.Comparator;
|
||||
import java.util.HashMap;
|
||||
import java.util.Iterator;
|
||||
import java.util.LinkedHashMap;
|
||||
import java.util.List;
|
||||
import java.util.Locale;
|
||||
import java.util.Map;
|
||||
import java.util.Set;
|
||||
import java.util.TreeMap;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import javax.annotation.PostConstruct;
|
||||
@ -32,6 +32,46 @@ import lombok.RequiredArgsConstructor;
|
||||
@RequiredArgsConstructor
|
||||
public class RSSPoc2Service {
|
||||
|
||||
public static final String STUDY_TYPE_NUMBER = "Study_Type_Number";
|
||||
public static final String STUDY_TITLE = "Study_Title";
|
||||
public static final String REPORT_NUMBER = "Report_Number";
|
||||
public static final String PERFORMING_LABORATORY = "Performing_Laboratory";
|
||||
public static final String EXPERIMENTAL_STARTING_DATE = "Experimental_Starting_Date";
|
||||
public static final String EXPERIMENTAL_COMPLETION_DATE = "Experimental_Completion_Date";
|
||||
public static final String GLP_STUDY = "GLP_Study";
|
||||
public static final String CERTIFICATE_OF_ANALYSIS_BATCH_IDENTIFICATION = "Certificate_of_Analysis_Batch_Identification";
|
||||
public static final String TEST_GUIDELINE_1 = "Test_Guideline_1";
|
||||
public static final String TEST_GUIDELINE_2 = "Test_Guideline_2";
|
||||
public static final String STUDY_CONCLUSION = "Study_Conclusion";
|
||||
public static final String DEVIATION_FROM_THE_GUIDELINE_SENTENCE = "Deviation_from_the_Guideline_";
|
||||
public static final String SPECIES = "Species";
|
||||
public static final String STRAIN = "Strain";
|
||||
public static final String CONCLUSION_LD_50_MG_PER_MG = "Conclusion_LD50_mg_per_mg";
|
||||
public static final String CONCLUSION_LD_50_GREATER_THAN = "Conclusion_LD50_Greater_than";
|
||||
public static final String CONCLUSION_MINIMUM_CONFIDENCE = "Conclusion_Minimum_Confidence";
|
||||
public static final String CONCLUSION_MAXIMUM_CONFIDENCE = "Conclusion_Maximum_Confidence";
|
||||
public static final String NECROPSY_FINDINGS = "Necropsy_Findings";
|
||||
public static final String NECROPSY_FINDINGS_SENTENCE = "Necropsy_findings_";
|
||||
public static final String CONDUCTED_WITHIN_4_HOURS_OF_EXPOSURE = "Conducted_within_4_Hours_of_Exposure";
|
||||
public static final String STUDY_DESIGN = "Study_Design";
|
||||
public static final String RESULTS_AND_CONCLUSIONS = "Results_and_Conclusions";
|
||||
public static final String WEIGHT_BEHAVIOR_CHANGES_SENTENCE = "Weight_Behavior_Changes_";
|
||||
public static final String MORTALITY_STATEMENT = "Mortality_Statement";
|
||||
public static final String CLINICAL_OBSERVATIONS_SENTENCE = "Clinical_Observations_";
|
||||
public static final String BODY_WEIGHT_CHANGES_SENTENCE = "Body_Weight_Changes_";
|
||||
public static final String DETAILING_OF_REPORTED_CHANGES = "Detailing_of_Reported_Changes";
|
||||
public static final String SEX = "Sex";
|
||||
public static final String NUMBER_OF_ANIMALS = "Number_of_Animals";
|
||||
public static final String CLINCAL_SIGNS_SENTENCE = "Clincal_Signs_";
|
||||
public static final String MORTALITY = "Mortality";
|
||||
public static final String DOSAGES = "Dosages";
|
||||
public static final String PRELIMINARY_TEST_RESULTS_SENTENCE = "Preliminary_Test_Results_";
|
||||
public static final String TEST_RESULTS = "Test_Results";
|
||||
public static final String WAS_THE_DEFINITIVE_STUDY_CONDUCTED_WITH_POSITIVE_CONTROL = "Was_the_definitive_study_conducted_with_positive_control";
|
||||
public static final String DOSE_MORTALITY_SENTENCE = "Dose_Mortality_";
|
||||
public static final String RESULTS_MAIN_STUDY = "Results_Main_Study";
|
||||
public static final String WHAT_WAS_THE_APPROACH_USED = "What_was_the_approach_used";
|
||||
|
||||
private final RedactionLogClient redactionLogClient;
|
||||
private final FileStatusClient statusClient;
|
||||
|
||||
@ -90,53 +130,53 @@ public class RSSPoc2Service {
|
||||
|
||||
String oecd = getOecdNumber(file);
|
||||
|
||||
Map<String, String> resultMap = new TreeMap<>();
|
||||
Map<String, String> resultMap = new LinkedHashMap<>();
|
||||
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);
|
||||
resultMap.put(STUDY_TYPE_NUMBER, oecd);
|
||||
|
||||
resultMap.put("Study_Title", getTitle(redactionLog));
|
||||
resultMap.put("Report_Number", getReportNumber(redactionLog));
|
||||
resultMap.put("Performing_Laboratory", getPerformingLaboratory(redactionLog));
|
||||
resultMap.put("Experimental_Starting_Date", getExperimentalStartDate(redactionLog));
|
||||
resultMap.put("Experimental_Completion_Date", getExperimentalEndDate(redactionLog));
|
||||
resultMap.put("GLP_Study", getGlpStudy(redactionLog));
|
||||
resultMap.put("Certificate_of_Analysis_Batch_Identification", getBatchNumber(redactionLog));
|
||||
resultMap.put("Test_Guideline_1", getTestGuideline1(redactionLog));
|
||||
resultMap.put(STUDY_TITLE, getTitle(redactionLog));
|
||||
resultMap.put(REPORT_NUMBER, getReportNumber(redactionLog));
|
||||
resultMap.put(PERFORMING_LABORATORY, getPerformingLaboratory(redactionLog));
|
||||
resultMap.put(EXPERIMENTAL_STARTING_DATE, getExperimentalStartDate(redactionLog));
|
||||
resultMap.put(EXPERIMENTAL_COMPLETION_DATE, getExperimentalEndDate(redactionLog));
|
||||
resultMap.put(GLP_STUDY, getGlpStudy(redactionLog));
|
||||
resultMap.put(CERTIFICATE_OF_ANALYSIS_BATCH_IDENTIFICATION, getBatchNumber(redactionLog));
|
||||
resultMap.put(TEST_GUIDELINE_1, getTestGuideline1(redactionLog));
|
||||
var testGuideline2 = getTestGuideline2(redactionLog);
|
||||
resultMap.put("Test_Guideline_2", testGuideline2 == null ? "" : testGuideline2);
|
||||
resultMap.put(TEST_GUIDELINE_2, testGuideline2 == null ? "" : testGuideline2);
|
||||
|
||||
if (oecdIn(oecd, Set.of("402", "403", "404", "405", "425", "429", "436", "471"))) {
|
||||
|
||||
resultMap.put("Study_Conclusion", getStudyConclusion(redactionLog));
|
||||
resultMap.put(STUDY_CONCLUSION, getStudyConclusion(redactionLog));
|
||||
|
||||
var guidelineDeviationSentences = getAsSentences(redactionLog, "guideline_deviation");
|
||||
int i = 1;
|
||||
for (String guidelineDeviationSentence : guidelineDeviationSentences) {
|
||||
resultMap.put("Deviation_from_the_Guideline_" + i, guidelineDeviationSentence);
|
||||
resultMap.put(DEVIATION_FROM_THE_GUIDELINE_SENTENCE + i, guidelineDeviationSentence);
|
||||
i++;
|
||||
}
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("402", "403", "404", "405", "425", "429", "436"))) {
|
||||
if (oecdIn(oecd, Set.of("402", "403", "404", "405", "425", "429", "436", "471"))) {
|
||||
|
||||
resultMap.put("Species", getSpecies(redactionLog));
|
||||
resultMap.put("Strain", getStrain(redactionLog));
|
||||
resultMap.put(SPECIES, getSpecies(redactionLog));
|
||||
resultMap.put(STRAIN, getStrain(redactionLog));
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("402", "403", "425", "436"))) {
|
||||
resultMap.put("Conclusion_LD50_mg_per_mg", getLd50Value(redactionLog));
|
||||
resultMap.put("Conclusion_LD50_Greater_than", getLd50GreaterThan(redactionLog));
|
||||
resultMap.put("Conclusion_Minimum_Confidence", getConfidenceMinimal(redactionLog));
|
||||
resultMap.put("Conclusion_Maximum_Confidence", getConfidenceMaximal(redactionLog));
|
||||
resultMap.put(CONCLUSION_LD_50_MG_PER_MG, getLd50Value(redactionLog));
|
||||
resultMap.put(CONCLUSION_LD_50_GREATER_THAN, getLd50GreaterThan(redactionLog));
|
||||
resultMap.put(CONCLUSION_MINIMUM_CONFIDENCE, getConfidenceMinimal(redactionLog));
|
||||
resultMap.put(CONCLUSION_MAXIMUM_CONFIDENCE, getConfidenceMaximal(redactionLog));
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("402"))) {
|
||||
resultMap.put("Necropsy_Findings", getLongestBlock(redactionLog, "necropsy_findings"));
|
||||
resultMap.put(NECROPSY_FINDINGS, getLongestBlock(redactionLog, "necropsy_findings"));
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("403", "436"))) {
|
||||
@ -144,32 +184,32 @@ public class RSSPoc2Service {
|
||||
var sentences = getAsSentences(redactionLog, "necropsy_findings");
|
||||
int i = 1;
|
||||
for (String sentence : sentences) {
|
||||
resultMap.put("Necropsy_findings_" + i, sentence);
|
||||
resultMap.put(NECROPSY_FINDINGS_SENTENCE + i, sentence);
|
||||
i++;
|
||||
}
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("403", "436"))) {
|
||||
resultMap.put("Conducted_within_4_Hours_of_Exposure", getAsOneBlock(redactionLog, "4h_exposure"));
|
||||
resultMap.put(CONDUCTED_WITHIN_4_HOURS_OF_EXPOSURE, getAsOneBlock(redactionLog, "4h_exposure"));
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("404","405", "429" ,"406", "428", "438", "439", "474", "487"))) {
|
||||
resultMap.put("Study_Design", getAsOneBlock(redactionLog, "study_design"));
|
||||
if (oecdIn(oecd, Set.of("404", "405", "429", "406", "428", "438", "439", "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", getJoinedValues(redactionLog, "results_and_conclusion", " "));
|
||||
resultMap.put(RESULTS_AND_CONCLUSIONS, getJoinedValues(redactionLog, "results_and_conclusion", " "));
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("402"))) {
|
||||
var weightBehaviorChangesSentences = getAsSentences(redactionLog, "weight_behavior_changes");
|
||||
int i = 1;
|
||||
for (String sentence : weightBehaviorChangesSentences) {
|
||||
resultMap.put("Weight_Behavior_Changes" + i, sentence);
|
||||
resultMap.put(WEIGHT_BEHAVIOR_CHANGES_SENTENCE + i, sentence);
|
||||
i++;
|
||||
}
|
||||
|
||||
resultMap.put("Mortality_Statement", getAsOneBlock(redactionLog, "mortality_statement"));
|
||||
resultMap.put(MORTALITY_STATEMENT, getAsOneBlock(redactionLog, "mortality_statement"));
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("403"))) {
|
||||
@ -188,14 +228,14 @@ public class RSSPoc2Service {
|
||||
var sentences = getAsSentences(redactionLog, "clinical_observations");
|
||||
int i = 1;
|
||||
for (String sentence : sentences) {
|
||||
resultMap.put("Clinical_Observations_" + i, sentence);
|
||||
resultMap.put(CLINICAL_OBSERVATIONS_SENTENCE + i, sentence);
|
||||
i++;
|
||||
}
|
||||
|
||||
sentences = getAsSentences(redactionLog, "bodyweight_changes");
|
||||
i = 1;
|
||||
for (String sentence : sentences) {
|
||||
resultMap.put("Body_Weight_Changes_" + i, sentence);
|
||||
resultMap.put(BODY_WEIGHT_CHANGES_SENTENCE + i, sentence);
|
||||
i++;
|
||||
}
|
||||
}
|
||||
@ -206,12 +246,12 @@ public class RSSPoc2Service {
|
||||
// }
|
||||
|
||||
if (oecdIn(oecd, Set.of("404", "405"))) {
|
||||
resultMap.put("Detailing_of_Reported_Changes", getAsOneBlock(redactionLog, "detailing"));
|
||||
resultMap.put(DETAILING_OF_REPORTED_CHANGES, getAsOneBlock(redactionLog, "detailing"));
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("405", "429"))) {
|
||||
resultMap.put("Sex", getJoinedUniqueValues(redactionLog, "sex", ", "));
|
||||
resultMap.put("Number_of_Animals", getNumberOfAnimals(redactionLog));
|
||||
resultMap.put(SEX, getJoinedUniqueValues(redactionLog, "sex", ", "));
|
||||
resultMap.put(NUMBER_OF_ANIMALS, getNumberOfAnimals(redactionLog));
|
||||
}
|
||||
|
||||
if (oecdIn(oecd, Set.of("425"))) {
|
||||
@ -219,28 +259,39 @@ public class RSSPoc2Service {
|
||||
var clinicalSignsSentences = getAsSentences(redactionLog, "clinical_signs");
|
||||
int i = 1;
|
||||
for (String clinicalSignsSentence : clinicalSignsSentences) {
|
||||
resultMap.put("Clincal_Signs_" + i, clinicalSignsSentence);
|
||||
resultMap.put(CLINCAL_SIGNS_SENTENCE + i, clinicalSignsSentence);
|
||||
i++;
|
||||
}
|
||||
|
||||
resultMap.put("Mortality", getAsOneBlock(redactionLog, "mortality"));
|
||||
var doseMortalitySentences = getDoseMortality(redactionLog);
|
||||
i = 1;
|
||||
for (String sentence : doseMortalitySentences) {
|
||||
resultMap.put(DOSE_MORTALITY_SENTENCE + i, sentence);
|
||||
i++;
|
||||
}
|
||||
|
||||
resultMap.put("Dosages", getDosages(redactionLog));
|
||||
resultMap.put(MORTALITY, getAsOneBlock(redactionLog, "mortality"));
|
||||
|
||||
resultMap.put(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("Preliminary_Test_Results_" + i, sentence);
|
||||
resultMap.put(PRELIMINARY_TEST_RESULTS_SENTENCE + i, sentence);
|
||||
i++;
|
||||
}
|
||||
|
||||
resultMap.put("Test_Results", getAsOneBlock(redactionLog, "test_results"));
|
||||
resultMap.put("Was_the_definitive_study_conducted_with_positive_control", getAsOneBlock(redactionLog, "positive_control"));
|
||||
resultMap.put(TEST_RESULTS, getAsOneBlock(redactionLog, "test_results"));
|
||||
resultMap.put(WAS_THE_DEFINITIVE_STUDY_CONDUCTED_WITH_POSITIVE_CONTROL, getAsOneBlock(redactionLog, "positive_control"));
|
||||
|
||||
resultMap.put(RESULTS_MAIN_STUDY, getAsOneBlock(redactionLog, "results_(main_study)"));
|
||||
resultMap.put(WHAT_WAS_THE_APPROACH_USED, getWhatWasTheApproachUsed(redactionLog));
|
||||
|
||||
}
|
||||
|
||||
rssFileResponses.add(new RSSFileResponse(file.getFilename(), resultMap));
|
||||
rssFileResponses.add(new RSSFileResponse(file.getFilename(), sortInFloraFormOrder(resultMap)));
|
||||
}
|
||||
|
||||
rssFileResponses.sort(Comparator.comparing(RSSFileResponse::getFilename));
|
||||
@ -249,6 +300,168 @@ public class RSSPoc2Service {
|
||||
}
|
||||
|
||||
|
||||
private Map<String, String> sortInFloraFormOrder(Map<String, String> components) {
|
||||
|
||||
Map<String, String> resultMap = new LinkedHashMap<>();
|
||||
|
||||
resultMap.put(STUDY_TITLE, components.get(STUDY_TITLE));
|
||||
resultMap.put(PERFORMING_LABORATORY, components.get(PERFORMING_LABORATORY));
|
||||
resultMap.put(REPORT_NUMBER, components.get(REPORT_NUMBER));
|
||||
resultMap.put(GLP_STUDY, components.get(GLP_STUDY));
|
||||
resultMap.put(TEST_GUIDELINE_1, components.get(TEST_GUIDELINE_1));
|
||||
resultMap.put(TEST_GUIDELINE_2, components.get(TEST_GUIDELINE_2));
|
||||
resultMap.put(EXPERIMENTAL_STARTING_DATE, components.get(EXPERIMENTAL_STARTING_DATE));
|
||||
resultMap.put(EXPERIMENTAL_COMPLETION_DATE, components.get(EXPERIMENTAL_COMPLETION_DATE));
|
||||
resultMap.put(CERTIFICATE_OF_ANALYSIS_BATCH_IDENTIFICATION, components.get(CERTIFICATE_OF_ANALYSIS_BATCH_IDENTIFICATION));
|
||||
|
||||
String oecd = components.get(STUDY_TYPE_NUMBER);
|
||||
|
||||
if (oecd == null || oecd.isEmpty()) {
|
||||
return resultMap;
|
||||
}
|
||||
|
||||
resultMap.put(STUDY_TYPE_NUMBER, oecd);
|
||||
|
||||
switch (oecd) {
|
||||
|
||||
case "439":
|
||||
case "406":
|
||||
case "428":
|
||||
case "438":
|
||||
case "474":
|
||||
case "487":
|
||||
resultMap.put(STUDY_DESIGN, components.get(STUDY_DESIGN));
|
||||
resultMap.put(RESULTS_AND_CONCLUSIONS, components.get(RESULTS_AND_CONCLUSIONS));
|
||||
break;
|
||||
case "425":
|
||||
resultMap.put(SPECIES, components.get(SPECIES));
|
||||
resultMap.put(STRAIN, components.get(STRAIN));
|
||||
resultMap.put(DOSAGES, components.get(DOSAGES));
|
||||
resultMap.put(MORTALITY, components.get(MORTALITY));
|
||||
resultMap.putAll(getKeyContains(components, DOSE_MORTALITY_SENTENCE));
|
||||
resultMap.putAll(getKeyContains(components, CLINCAL_SIGNS_SENTENCE));
|
||||
resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE_SENTENCE));
|
||||
resultMap.put(CONCLUSION_LD_50_GREATER_THAN, components.get(CONCLUSION_LD_50_GREATER_THAN));
|
||||
resultMap.put(CONCLUSION_LD_50_MG_PER_MG, components.get(CONCLUSION_LD_50_MG_PER_MG));
|
||||
resultMap.put(CONCLUSION_MINIMUM_CONFIDENCE, components.get(CONCLUSION_MINIMUM_CONFIDENCE));
|
||||
resultMap.put(CONCLUSION_MAXIMUM_CONFIDENCE, components.get(CONCLUSION_MAXIMUM_CONFIDENCE));
|
||||
resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION));
|
||||
break;
|
||||
case "402":
|
||||
resultMap.put(SPECIES, components.get(SPECIES));
|
||||
resultMap.put(STRAIN, components.get(STRAIN));
|
||||
// resultMap.put(D, components.get(STRAIN)); 402-Dose(s) (mg/Kg bw) TODO
|
||||
resultMap.put(MORTALITY_STATEMENT, components.get(MORTALITY_STATEMENT));
|
||||
resultMap.putAll(getKeyContains(components, WEIGHT_BEHAVIOR_CHANGES_SENTENCE));
|
||||
resultMap.put(NECROPSY_FINDINGS, components.get(NECROPSY_FINDINGS));
|
||||
resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE_SENTENCE));
|
||||
resultMap.put(CONCLUSION_LD_50_GREATER_THAN, components.get(CONCLUSION_LD_50_GREATER_THAN));
|
||||
resultMap.put(CONCLUSION_LD_50_MG_PER_MG, components.get(CONCLUSION_LD_50_MG_PER_MG));
|
||||
resultMap.put(CONCLUSION_MINIMUM_CONFIDENCE, components.get(CONCLUSION_MINIMUM_CONFIDENCE));
|
||||
resultMap.put(CONCLUSION_MAXIMUM_CONFIDENCE, components.get(CONCLUSION_MAXIMUM_CONFIDENCE));
|
||||
resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION));
|
||||
break;
|
||||
case "403":
|
||||
case "436":
|
||||
resultMap.put(SPECIES, components.get(SPECIES));
|
||||
resultMap.put(STRAIN, components.get(STRAIN));
|
||||
resultMap.put(CONDUCTED_WITHIN_4_HOURS_OF_EXPOSURE, components.get(CONDUCTED_WITHIN_4_HOURS_OF_EXPOSURE));
|
||||
resultMap.putAll(getKeyContains(components, CLINICAL_OBSERVATIONS_SENTENCE));
|
||||
resultMap.putAll(getKeyContains(components, BODY_WEIGHT_CHANGES_SENTENCE));
|
||||
resultMap.putAll(getKeyContains(components, NECROPSY_FINDINGS_SENTENCE));
|
||||
resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE_SENTENCE));
|
||||
resultMap.put(CONCLUSION_LD_50_GREATER_THAN, components.get(CONCLUSION_LD_50_GREATER_THAN));
|
||||
resultMap.put(CONCLUSION_LD_50_MG_PER_MG, components.get(CONCLUSION_LD_50_MG_PER_MG));
|
||||
resultMap.put(CONCLUSION_MINIMUM_CONFIDENCE, components.get(CONCLUSION_MINIMUM_CONFIDENCE));
|
||||
resultMap.put(CONCLUSION_MAXIMUM_CONFIDENCE, components.get(CONCLUSION_MAXIMUM_CONFIDENCE));
|
||||
resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION));
|
||||
break;
|
||||
case "405":
|
||||
resultMap.put(SPECIES, components.get(SPECIES));
|
||||
resultMap.put(STRAIN, components.get(STRAIN));
|
||||
resultMap.put(SEX, components.get(SEX));
|
||||
resultMap.put(NUMBER_OF_ANIMALS, components.get(NUMBER_OF_ANIMALS));
|
||||
resultMap.put(STUDY_DESIGN, components.get(STUDY_DESIGN));
|
||||
resultMap.put(DETAILING_OF_REPORTED_CHANGES, components.get(DETAILING_OF_REPORTED_CHANGES));
|
||||
resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE_SENTENCE));
|
||||
resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION));
|
||||
break;
|
||||
case "429":
|
||||
resultMap.put(SPECIES, components.get(SPECIES));
|
||||
resultMap.put(STRAIN, components.get(STRAIN));
|
||||
resultMap.put(WAS_THE_DEFINITIVE_STUDY_CONDUCTED_WITH_POSITIVE_CONTROL, components.get(WAS_THE_DEFINITIVE_STUDY_CONDUCTED_WITH_POSITIVE_CONTROL));
|
||||
resultMap.put(STUDY_DESIGN, components.get(STUDY_DESIGN));
|
||||
resultMap.put(RESULTS_MAIN_STUDY, components.get(RESULTS_MAIN_STUDY));
|
||||
resultMap.putAll(getKeyContains(components, PRELIMINARY_TEST_RESULTS_SENTENCE));
|
||||
resultMap.put(WHAT_WAS_THE_APPROACH_USED, components.get(WHAT_WAS_THE_APPROACH_USED));
|
||||
resultMap.put(SEX, components.get(SEX));
|
||||
resultMap.put(NUMBER_OF_ANIMALS, components.get(NUMBER_OF_ANIMALS));
|
||||
resultMap.put(TEST_RESULTS, components.get(TEST_RESULTS));
|
||||
resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE_SENTENCE));
|
||||
resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION));
|
||||
break;
|
||||
case "404":
|
||||
resultMap.put(SPECIES, components.get(SPECIES));
|
||||
resultMap.put(STRAIN, components.get(STRAIN));
|
||||
resultMap.put(STUDY_DESIGN, components.get(STUDY_DESIGN));
|
||||
resultMap.put(DETAILING_OF_REPORTED_CHANGES, components.get(DETAILING_OF_REPORTED_CHANGES));
|
||||
resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE_SENTENCE));
|
||||
resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION));
|
||||
break;
|
||||
case "471":
|
||||
resultMap.put(STRAIN, components.get(STRAIN));
|
||||
resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE_SENTENCE));
|
||||
resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION));
|
||||
break;
|
||||
}
|
||||
|
||||
return resultMap;
|
||||
}
|
||||
|
||||
|
||||
private Map<String, String> getKeyContains(Map<String, String> components, String compontentName) {
|
||||
|
||||
Map<String, String> resultMap = new LinkedHashMap<>();
|
||||
|
||||
for (Map.Entry<String, String> entry : components.entrySet()) {
|
||||
if (entry.getKey().contains(compontentName)) {
|
||||
resultMap.put(entry.getKey(), entry.getValue());
|
||||
}
|
||||
}
|
||||
|
||||
return resultMap;
|
||||
}
|
||||
|
||||
|
||||
private String getWhatWasTheApproachUsed(RedactionLog redactionLog) {
|
||||
|
||||
var approachUsed = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("approach_used")).map(RedactionLogEntry::getValue).findFirst();
|
||||
if (approachUsed.isPresent()) {
|
||||
return "Group";
|
||||
}
|
||||
return "Individual";
|
||||
}
|
||||
|
||||
|
||||
private List<String> getDoseMortality(RedactionLog redactionLog) {
|
||||
|
||||
var doseMortalityEntries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("dose_mortality")).collect(Collectors.toList());
|
||||
|
||||
Map<Integer, List<String>> perYValue = new HashMap<>();
|
||||
|
||||
for (var entry : doseMortalityEntries) {
|
||||
perYValue.computeIfAbsent(Math.round(entry.getPositions().get(0).getTopLeft().getY()), (x) -> new ArrayList<>()).add(entry.getValue());
|
||||
}
|
||||
|
||||
List<String> result = new ArrayList<>();
|
||||
for (Map.Entry<Integer, List<String>> entry : perYValue.entrySet()) {
|
||||
result.add(entry.getValue().stream().collect(Collectors.joining(", ")));
|
||||
}
|
||||
|
||||
return result;
|
||||
}
|
||||
|
||||
|
||||
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();
|
||||
@ -337,7 +550,6 @@ public class RSSPoc2Service {
|
||||
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();
|
||||
@ -345,7 +557,6 @@ public class RSSPoc2Service {
|
||||
// return doseMlPerAnimal.orElse("");
|
||||
// }
|
||||
|
||||
|
||||
// private Set<String> getEffectiveConcentrations(RedactionLog redactionLog) {
|
||||
//
|
||||
// return redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("effective_concentration")).map(RedactionLogEntry::getValue).collect(Collectors.toSet());
|
||||
@ -484,12 +695,25 @@ public class RSSPoc2Service {
|
||||
|
||||
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();
|
||||
// LAB_NAME = "y": 418.50415 GERMANY_ "y": 390.90417 UNITED_K "y": 253.02429 --> GErmany, not unitedK
|
||||
|
||||
var laboratoryEntry = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("laboratory_name")).findFirst();
|
||||
if (!laboratoryEntry.isPresent()) {
|
||||
return "";
|
||||
}
|
||||
|
||||
var laboratoryCountry = redactionLog.getRedactionLogEntry()
|
||||
.stream()
|
||||
.filter(r -> r.getType().equals("laboratory_country") && laboratoryEntry.get().getPositions().get(0).getTopLeft().getY() - r.getPositions()
|
||||
.get(0)
|
||||
.getTopLeft()
|
||||
.getY() < 80)
|
||||
.map(RedactionLogEntry::getValue)
|
||||
.findFirst();
|
||||
|
||||
StringBuilder sb = new StringBuilder();
|
||||
if (laboratoryName.isPresent()) {
|
||||
sb.append(laboratoryName.get());
|
||||
if (laboratoryEntry.isPresent()) {
|
||||
sb.append(laboratoryEntry.get().getValue());
|
||||
}
|
||||
if (laboratoryCountry.isPresent()) {
|
||||
sb.append(", ").append(laboratoryCountry.get());
|
||||
|
||||
Loading…
x
Reference in New Issue
Block a user