From 238f02a47c50736d8341e1aa4b9ff5b7e3b9c820 Mon Sep 17 00:00:00 2001 From: Andrei Isvoran Date: Wed, 18 Oct 2023 08:58:13 +0200 Subject: [PATCH] RED-7745 - Use EntityLog in redaction-report-service --- redaction-report-service-v1/pom.xml | 2 +- .../v1/server/client/RedactionLogClient.java | 10 - .../v1/server/controller/RSSController.java | 3 +- ...ce.java => EntityLogConverterService.java} | 98 +- .../service/ExcelReportGenerationService.java | 2 +- .../v1/server/service/RSSPoc2Service.java | 338 +- .../service/ReportGenerationService.java | 4 +- .../service/WordReportGenerationService.java | 6 +- .../server/storage/ReportStorageService.java | 12 + .../RedactionReportIntegrationTest.java | 103 +- .../RedactionReportV2IntegrationTest.java | 22 +- .../EntityLogConverterServiceTest.java | 81 + .../src/test/resources/expected/iuclid.txt | 16 +- .../src/test/resources/files/entityLog.json | 6110 ++ .../files/entityLogWithManualRedactions.json | 6203 ++ .../test/resources/files/redactionLog.json | 47500 ---------------- .../redactionLogWithManualRedactions.json | 6361 --- 17 files changed, 12700 insertions(+), 54171 deletions(-) delete mode 100644 redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/client/RedactionLogClient.java rename redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/{RedactionLogConverterService.java => EntityLogConverterService.java} (68%) create mode 100644 redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/service/EntityLogConverterServiceTest.java create mode 100644 redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/files/entityLog.json create mode 100644 redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/files/entityLogWithManualRedactions.json delete mode 100644 redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/files/redactionLog.json delete mode 100644 redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/files/redactionLogWithManualRedactions.json diff --git a/redaction-report-service-v1/pom.xml b/redaction-report-service-v1/pom.xml index 70b59ae..e16c5c5 100644 --- a/redaction-report-service-v1/pom.xml +++ b/redaction-report-service-v1/pom.xml @@ -24,7 +24,7 @@ - 2.198.0 + 2.217.0 5.2.3 diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/client/RedactionLogClient.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/client/RedactionLogClient.java deleted file mode 100644 index 0714480..0000000 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/client/RedactionLogClient.java +++ /dev/null @@ -1,10 +0,0 @@ -package com.iqser.red.service.redaction.report.v1.server.client; - -import org.springframework.cloud.openfeign.FeignClient; - -import com.iqser.red.service.persistence.service.v1.api.internal.resources.RedactionLogResource; - -@FeignClient(name = "RedactionLogResource", url = "${persistence-service.url}") -public interface RedactionLogClient extends RedactionLogResource { - -} diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/controller/RSSController.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/controller/RSSController.java index defcae3..1d9e55b 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/controller/RSSController.java +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/controller/RSSController.java @@ -43,8 +43,7 @@ public class RSSController implements RSSResource { } fileResponses.add(new RSSFileResponse(fileName, result)); } - RSSResponse rssResponse = new RSSResponse(fileResponses); - return rssResponse; + return new RSSResponse(fileResponses); } diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/RedactionLogConverterService.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/EntityLogConverterService.java similarity index 68% rename from redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/RedactionLogConverterService.java rename to redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/EntityLogConverterService.java index c98cd88..4cf30cb 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/RedactionLogConverterService.java +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/EntityLogConverterService.java @@ -14,18 +14,20 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; import org.springframework.stereotype.Service; -import com.iqser.red.service.persistence.service.v1.api.shared.model.annotations.AnnotationStatus; -import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.Dossier; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.Change; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.ChangeType; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLog; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLogEntry; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLogLegalBasis; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntryState; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntryType; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.ManualRedactionType; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.Position; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.type.Type; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.ManualRedactionType; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.Rectangle; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.RedactionLog; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.RedactionLogEntry; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.RedactionLogLegalBasis; import com.iqser.red.service.redaction.report.v1.server.client.DictionaryClient; import com.iqser.red.service.redaction.report.v1.server.client.DossierClient; -import com.iqser.red.service.redaction.report.v1.server.client.RedactionLogClient; import com.iqser.red.service.redaction.report.v1.server.model.ReportRedactionEntry; +import com.iqser.red.service.redaction.report.v1.server.storage.ReportStorageService; import com.iqser.red.storage.commons.exception.StorageObjectDoesNotExist; import io.micrometer.core.annotation.Timed; @@ -33,33 +35,32 @@ import lombok.RequiredArgsConstructor; @Service @RequiredArgsConstructor -public class RedactionLogConverterService { - - private final RedactionLogClient redactionLogClient; +public class EntityLogConverterService { private final DossierClient dossierClient; private final DictionaryClient dictionaryClient; + private final ReportStorageService reportStorageService; + @Timed("redactmanager_getReportEntries") - public List getReportEntries(String dossierId, String fileId, boolean isExcluded, Dossier dossier) { + public List getReportEntries(String dossierId, String fileId, boolean isExcluded) { if (isExcluded) { return new ArrayList<>(); } - RedactionLog redactionLog; + EntityLog entityLog; Map mapOfEntityDisplayName; try { - redactionLog = redactionLogClient.getRedactionLog(dossierId, fileId, new ArrayList<>(), true, false); + entityLog = reportStorageService.getEntityLog(dossierId, fileId, new ArrayList<>()); mapOfEntityDisplayName = fillMapOfTypeAndEntityDisplayName(dossierId); } catch (StorageObjectDoesNotExist e) { return new ArrayList<>(); } - var legalBasisMappings = redactionLog.getLegalBasis(); - return convertAndSort(redactionLog, legalBasisMappings, mapOfEntityDisplayName, dossier); + return convertAndSort(entityLog, entityLog.getLegalBasis(), mapOfEntityDisplayName); } @@ -80,20 +81,19 @@ public class RedactionLogConverterService { } - public List convertAndSort(RedactionLog redactionLog, - List legalBasisMappings, - Map mapOfEntityDisplayName, - Dossier dossier) { + public List convertAndSort(EntityLog entityLog, + List legalBasisMappings, + Map mapOfEntityDisplayName) { List reportEntries = new ArrayList<>(); - var allTypes = dictionaryClient.getAllTypesForDossierTemplate(dossier.getDossierTemplateId(), false); + entityLog.getEntityLogEntry().forEach(entry -> { + var isSkipped = entry.getState() != EntryState.APPLIED + && !(entry.getEntryType().equals(EntryType.HINT) || entry.getState().equals(EntryState.IGNORED)); - redactionLog.getRedactionLogEntry().forEach(entry -> { - var isSkipped = !entry.isRedacted() && !entry.isHint() && !isHintType(allTypes, entry.getType()); - if (entry.isRedacted() || isSkipped) { + if (entry.getState() == EntryState.APPLIED || isSkipped) { - if (entry.lastChangeIsRemoved()) { + if (lastChangeIsRemoved(entry.getChanges())) { return; } @@ -101,43 +101,42 @@ public class RedactionLogConverterService { return; } - if (entry.isRecommendation()) { + if (entry.getEntryType() == EntryType.RECOMMENDATION) { return; } - if (entry.isFalsePositive()) { + if (entry.getEntryType() == EntryType.FALSE_POSITIVE ) { return; } - if (entry.getManualChanges() != null && entry.getManualChanges().size() != 0 && entry.getManualChanges() - .get(entry.getManualChanges().size() - 1) - .getManualRedactionType() - .equals(ManualRedactionType.ADD_LOCALLY) && entry.getManualChanges() - .get(entry.getManualChanges().size() - 1) - .getAnnotationStatus() - .equals(AnnotationStatus.DECLINED)) { + if (entry.getManualChanges() != null + && entry.getManualChanges().size() != 0 + && entry.getManualChanges() + .get(entry.getManualChanges().size() - 1) + .getManualRedactionType() + .equals(ManualRedactionType.ADD_LOCALLY)) { return; } Set pages = new HashSet<>(); - for (Rectangle position : entry.getPositions()) { + for (Position position : entry.getPositions()) { - if (pages.isEmpty() || !pages.contains(position.getPage())) { - pages.add(position.getPage()); - reportEntries.add(new ReportRedactionEntry(position.getPage(), - position.getTopLeft().getX(), - position.getTopLeft().getY(), + if (pages.isEmpty() || !pages.contains(position.getPageNumber())) { + pages.add(position.getPageNumber()); + reportEntries.add(new ReportRedactionEntry(position.getPageNumber(), + position.x(), + position.y(), getSection(entry, position), checkTextForNull(entry.getLegalBasis()) + " " + legalBasisMappings.stream() .filter(lbm -> lbm.getReason().equalsIgnoreCase(entry.getLegalBasis())) .findAny() - .map(RedactionLogLegalBasis::getDescription) + .map(EntityLogLegalBasis::getDescription) .orElse(""), entry.getLegalBasis(), legalBasisMappings.stream() .filter(lbm -> lbm.getReason().equalsIgnoreCase(entry.getLegalBasis())) .findAny() - .map(RedactionLogLegalBasis::getDescription) + .map(EntityLogLegalBasis::getDescription) .orElse(""), checkTextForNull(entry.getTextBefore()) + entry.getValue() + checkTextForNull(entry.getTextAfter()), entry.getValue(), @@ -174,13 +173,13 @@ public class RedactionLogConverterService { } - private String getSection(RedactionLogEntry entry, Rectangle position) { + private String getSection(EntityLogEntry entry, Position position) { if (StringUtils.isNotBlank(entry.getSection())) { return entry.getSection(); } - if (entry.isImage()) { + if (entry.getEntryType() == EntryType.IMAGE) { return "Image: " + humanize(entry.getType()); } @@ -188,7 +187,7 @@ public class RedactionLogConverterService { return "Non-readable content"; } - return "Text on page " + position.getPage(); + return "Text on page " + position.getPageNumber(); } @@ -224,4 +223,13 @@ public class RedactionLogConverterService { } + private boolean lastChangeIsRemoved(List changes) { + + return last(changes).map(c -> c.getType() == ChangeType.REMOVED).orElse(false); + } + + private Optional last(List list) { + + return list == null || list.isEmpty() ? Optional.empty() : Optional.of(list.get(list.size() - 1)); + } } diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ExcelReportGenerationService.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ExcelReportGenerationService.java index 11c1026..2c16688 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ExcelReportGenerationService.java +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ExcelReportGenerationService.java @@ -157,7 +157,7 @@ public class ExcelReportGenerationService { } } - log.info("Report Generation took: {} for file with id {}, pageCount: {}, redactionLogEntryCount: {}, reportName: {}, className: {}", + log.info("Report Generation took: {} for file with id {}, pageCount: {}, entityLogEntryCount: {}, reportName: {}, className: {}", System.currentTimeMillis() - start, fileModel.getId(), fileModel.getNumberOfPages(), diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/RSSPoc2Service.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/RSSPoc2Service.java index 9b914f0..045385f 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/RSSPoc2Service.java +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/RSSPoc2Service.java @@ -2,27 +2,36 @@ package com.iqser.red.service.redaction.report.v1.server.service; import java.text.DateFormat; import java.text.SimpleDateFormat; -import java.util.*; +import java.util.ArrayList; +import java.util.Comparator; +import java.util.Date; +import java.util.HashMap; +import java.util.LinkedHashMap; +import java.util.List; +import java.util.Locale; +import java.util.Map; +import java.util.Set; import java.util.stream.Collectors; import org.apache.commons.lang3.tuple.Pair; import org.springframework.stereotype.Service; import com.fasterxml.jackson.databind.ObjectMapper; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.ChangeType; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLog; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLogEntry; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntryState; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.Position; import com.iqser.red.service.persistence.service.v1.api.shared.model.component.ComponentsOverrides; +import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileAttributeConfig; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileModel; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileType; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.ChangeType; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.Rectangle; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.RedactionLog; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.RedactionLogEntry; import com.iqser.red.service.redaction.report.v1.api.model.rss.DetailedRSSFileResponse; import com.iqser.red.service.redaction.report.v1.api.model.rss.DetailedRSSResponse; import com.iqser.red.service.redaction.report.v1.api.model.rss.SCMComponent; import com.iqser.red.service.redaction.report.v1.api.model.rss.ScmAnnotation; 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.report.v1.server.storage.ReportStorageService; import jakarta.annotation.PostConstruct; @@ -74,7 +83,6 @@ public class RSSPoc2Service { public static final String WHAT_WAS_THE_APPROACH_USED = "What_was_the_approach_used"; public static final String DOSES_MG_PER_KG_BW = "Doses_mg_per_kg_bw"; - private final RedactionLogClient redactionLogClient; private final FileStatusClient statusClient; private final ReportStorageService reportStorageService; private final ObjectMapper objectMapper; @@ -143,116 +151,116 @@ public class RSSPoc2Service { String oecd = getOecdNumber(file); Map resultMap = new LinkedHashMap<>(); - var redactionLog = redactionLogClient.getRedactionLog(dossierId, file.getId(), new ArrayList<>(), true, false); + var entityLog = reportStorageService.getEntityLog(dossierId, file.getId(), new ArrayList<>()); - sortRedactionLog(redactionLog); + sortEntityLog(entityLog); - redactionLog.getRedactionLogEntry().removeIf(r -> !r.isRedacted() || r.getChanges().get(r.getChanges().size() - 1).getType().equals(ChangeType.REMOVED)); + entityLog.getEntityLogEntry().removeIf(r -> r.getState() != EntryState.APPLIED || r.getChanges().get(r.getChanges().size() - 1).getType().equals(ChangeType.REMOVED)); if(oecd == null){ - resultMap.putAll(getAllEntities(redactionLog)); + resultMap.putAll(getAllEntities(entityLog)); setOverrideValues(dossierId, fileId, resultMap); rssFileResponses.add(new DetailedRSSFileResponse(file.getFilename(), resultMap)); continue; } - resultMap.put(STUDY_TITLE, getFirstEntryOrElse(redactionLog, "title", "")); - resultMap.put(REPORT_NUMBER, getFirstEntryOrElse(redactionLog, "report_number", "")); - resultMap.put(PERFORMING_LABORATORY, getPerformingLaboratory(redactionLog)); - resultMap.put(EXPERIMENTAL_STARTING_DATE, getConvertedDates(redactionLog, "experimental_start_date")); - resultMap.put(EXPERIMENTAL_COMPLETION_DATE, getConvertedDates(redactionLog, "experimental_end_date")); - resultMap.put(GLP_STUDY, ifPresentAddOrElse(redactionLog, "glp_study", "Yes", "No")); - resultMap.put(CERTIFICATE_OF_ANALYSIS_BATCH_IDENTIFICATION, getJoinedUniqueValues(redactionLog, "batch_number", ", ")); - resultMap.put(TEST_GUIDELINE_1, getTestGuideline1(redactionLog)); - resultMap.put(TEST_GUIDELINE_2, getTestGuideline2(redactionLog)); + resultMap.put(STUDY_TITLE, getFirstEntryOrElse(entityLog, "title")); + resultMap.put(REPORT_NUMBER, getFirstEntryOrElse(entityLog, "report_number")); + resultMap.put(PERFORMING_LABORATORY, getPerformingLaboratory(entityLog)); + resultMap.put(EXPERIMENTAL_STARTING_DATE, getConvertedDates(entityLog, "experimental_start_date")); + resultMap.put(EXPERIMENTAL_COMPLETION_DATE, getConvertedDates(entityLog, "experimental_end_date")); + resultMap.put(GLP_STUDY, ifPresentAddOrElse(entityLog, "glp_study", "Yes", "No")); + resultMap.put(CERTIFICATE_OF_ANALYSIS_BATCH_IDENTIFICATION, getJoinedUniqueValues(entityLog, "batch_number")); + resultMap.put(TEST_GUIDELINE_1, getTestGuideline1(entityLog)); + resultMap.put(TEST_GUIDELINE_2, getTestGuideline2(entityLog)); if (oecdIn(oecd, Set.of("402", "403", "404", "405", "425", "429", "436", "471"))) { - resultMap.put(STUDY_CONCLUSION, combineValuesOfFirstFoundSection(redactionLog, "study_conclusion", " ", "")); + resultMap.put(STUDY_CONCLUSION, combineValuesOfFirstFoundSection(entityLog)); - resultMap.putAll(getAsBlockPerAnnotation(redactionLog, "guideline_deviation", DEVIATION_FROM_THE_GUIDELINE)); + resultMap.putAll(getAsBlockPerAnnotation(entityLog, "guideline_deviation", DEVIATION_FROM_THE_GUIDELINE)); } if (oecdIn(oecd, Set.of("402", "403", "404", "405", "425", "429", "436", "471"))) { - resultMap.put(SPECIES, getFirstEntryOrElse(redactionLog, "species", "")); - resultMap.put(STRAIN, getFirstEntryOrElse(redactionLog, "strain", "")); + resultMap.put(SPECIES, getFirstEntryOrElse(entityLog, "species")); + resultMap.put(STRAIN, getFirstEntryOrElse(entityLog, "strain")); } if (oecdIn(oecd, Set.of("402", "403", "425", "436"))) { - resultMap.put(CONCLUSION_LD_50_MG_PER_MG, getJoinedUniqueValues(redactionLog, "ld50_value", ", ")); - resultMap.put(CONCLUSION_LD_50_GREATER_THAN, ifPresentAddOrElse(redactionLog, "ld50_greater", "Greater than", "")); - resultMap.put(CONCLUSION_MINIMUM_CONFIDENCE, getJoinedUniqueValues(redactionLog, "confidence_minimal", ", ")); - resultMap.put(CONCLUSION_MAXIMUM_CONFIDENCE, getJoinedUniqueValues(redactionLog, "confidence_maximal", ", ")); + resultMap.put(CONCLUSION_LD_50_MG_PER_MG, getJoinedUniqueValues(entityLog, "ld50_value")); + resultMap.put(CONCLUSION_LD_50_GREATER_THAN, ifPresentAddOrElse(entityLog, "ld50_greater", "Greater than", "")); + resultMap.put(CONCLUSION_MINIMUM_CONFIDENCE, getJoinedUniqueValues(entityLog, "confidence_minimal")); + resultMap.put(CONCLUSION_MAXIMUM_CONFIDENCE, getJoinedUniqueValues(entityLog, "confidence_maximal")); } if (oecdIn(oecd, Set.of("402"))) { - resultMap.put(NECROPSY_FINDINGS, getLongestCombinedSectionBlockOrElse(redactionLog, "necropsy_findings", "")); - resultMap.put(DOSES_MG_PER_KG_BW, getAsOneBlock(redactionLog, "doses_(mg_kg_bw)")); + resultMap.put(NECROPSY_FINDINGS, getLongestCombinedSectionBlockOrElse(entityLog)); + resultMap.put(DOSES_MG_PER_KG_BW, getAsOneBlock(entityLog, "doses_(mg_kg_bw)")); } if (oecdIn(oecd, Set.of("403", "436"))) { - resultMap.putAll(getAsBlockPerAnnotation(redactionLog, "necropsy_findings", NECROPSY_FINDINGS)); + resultMap.putAll(getAsBlockPerAnnotation(entityLog, "necropsy_findings", NECROPSY_FINDINGS)); } 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(entityLog, "4h_exposure")); } if (oecdIn(oecd, Set.of("404", "405", "429", "406", "428", "438", "439", "474", "487"))) { - resultMap.put(STUDY_DESIGN, getAsOneBlock(redactionLog, "study_design")); + resultMap.put(STUDY_DESIGN, getAsOneBlock(entityLog, "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(entityLog, "results_and_conclusion")); } if (oecdIn(oecd, Set.of("402"))) { - resultMap.putAll(getAsBlockPerAnnotation(redactionLog, "weight_behavior_changes", WEIGHT_BEHAVIOR_CHANGES)); + resultMap.putAll(getAsBlockPerAnnotation(entityLog, "weight_behavior_changes", WEIGHT_BEHAVIOR_CHANGES)); - resultMap.put(MORTALITY_STATEMENT, getAsOneBlock(redactionLog, "mortality_statement")); + resultMap.put(MORTALITY_STATEMENT, getAsOneBlock(entityLog, "mortality_statement")); } if (oecdIn(oecd, Set.of("403"))) { - resultMap.putAll(getAsBlockPerAnnotation(redactionLog, "clinical_observations", CLINICAL_OBSERVATIONS)); - resultMap.putAll(getAsBlockPerAnnotation(redactionLog, "bodyweight_changes", BODY_WEIGHT_CHANGES)); + resultMap.putAll(getAsBlockPerAnnotation(entityLog, "clinical_observations", CLINICAL_OBSERVATIONS)); + resultMap.putAll(getAsBlockPerAnnotation(entityLog, "bodyweight_changes", BODY_WEIGHT_CHANGES)); } if (oecdIn(oecd, Set.of("404", "405"))) { - resultMap.put(DETAILING_OF_REPORTED_CHANGES, getAsOneBlock(redactionLog, "detailing")); + resultMap.put(DETAILING_OF_REPORTED_CHANGES, getAsOneBlock(entityLog, "detailing")); } if (oecdIn(oecd, Set.of("405", "429"))) { - resultMap.put(SEX, getSex(redactionLog)); - resultMap.put(NUMBER_OF_ANIMALS, getNumberOfAnimals(redactionLog)); + resultMap.put(SEX, getSex(entityLog)); + resultMap.put(NUMBER_OF_ANIMALS, getNumberOfAnimals(entityLog)); } if (oecdIn(oecd, Set.of("425"))) { - resultMap.putAll(getAsBlockPerAnnotation(redactionLog, "clinical_signs", CLINCAL_SIGNS)); - resultMap.putAll(getDoseMortality(redactionLog, DOSE_MORTALITY)); + resultMap.putAll(getAsBlockPerAnnotation(entityLog, "clinical_signs", CLINCAL_SIGNS)); + resultMap.putAll(getDoseMortality(entityLog)); - resultMap.put(MORTALITY, getAsOneBlock(redactionLog, "mortality")); - resultMap.put(DOSAGES, getFirstEntryOrElse(redactionLog, "dosages", "")); + resultMap.put(MORTALITY, getAsOneBlock(entityLog, "mortality")); + resultMap.put(DOSAGES, getFirstEntryOrElse(entityLog, "dosages")); } if (oecdIn(oecd, Set.of("429"))) { - resultMap.putAll(getAsBlockPerAnnotation(redactionLog, "preliminary_test_results", PRELIMINARY_TEST_RESULTS)); + resultMap.putAll(getAsBlockPerAnnotation(entityLog, "preliminary_test_results", PRELIMINARY_TEST_RESULTS)); - 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(entityLog, "test_results")); + resultMap.put(WAS_THE_DEFINITIVE_STUDY_CONDUCTED_WITH_POSITIVE_CONTROL, getAsOneBlock(entityLog, "positive_control")); - resultMap.put(RESULTS_MAIN_STUDY, getAsOneBlock(redactionLog, "results_(main_study)")); - resultMap.put(WHAT_WAS_THE_APPROACH_USED, ifPresentAddOrElse(redactionLog, "approach_used", "Group", "Individual")); + resultMap.put(RESULTS_MAIN_STUDY, getAsOneBlock(entityLog, "results_(main_study)")); + resultMap.put(WHAT_WAS_THE_APPROACH_USED, ifPresentAddOrElse(entityLog, "approach_used", "Group", "Individual")); } @@ -296,13 +304,13 @@ public class RSSPoc2Service { } - private Map getAllEntities(RedactionLog redactionLog){ + private Map getAllEntities(EntityLog entityLog){ Map resultMap = new HashMap<>(); - Set existingTypes = redactionLog.getRedactionLogEntry().stream().map(RedactionLogEntry::getType).collect(Collectors.toSet()); + Set existingTypes = entityLog.getEntityLogEntry().stream().map(EntityLogEntry::getType).collect(Collectors.toSet()); existingTypes.forEach(type -> { - resultMap.put(type, getJoinedValues(redactionLog, type, " ")); + resultMap.put(type, getJoinedValues(entityLog, type)); }); return resultMap; @@ -314,43 +322,40 @@ public class RSSPoc2Service { public 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; + var oecdFileAttributeConf = fileAttributesConfig.stream().filter(f -> f.getLabel().equals("OECD Number")).map(FileAttributeConfig::getId).findFirst(); + return oecdFileAttributeConf.map(s -> file.getFileAttributes().get(s)).orElse(null); } - private void sortRedactionLog(RedactionLog redactionLog) { + private void sortEntityLog(EntityLog entityLog) { - 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; + entityLog.getEntityLogEntry().sort((entry1, entry2) -> { + if (entry1.getPositions().get(0).getPageNumber() == entry2.getPositions().get(0).getPageNumber()) { + if (entry1.getPositions().get(0).y() == entry2.getPositions().get(0).y()) { + return entry1.getPositions().get(0).x() <= entry2.getPositions().get(0).x() ? -1 : 1; } else { - return entry1.getPositions().get(0).getTopLeft().getY() <= entry2.getPositions().get(0).getTopLeft().getY() ? 1 : -1; + return entry1.getPositions().get(0).y() <= entry2.getPositions().get(0).y() ? 1 : -1; } } - return entry1.getPositions().get(0).getPage() < entry2.getPositions().get(0).getPage() ? -1 : 1; + return entry1.getPositions().get(0).getPageNumber() < entry2.getPositions().get(0).getPageNumber() ? -1 : 1; }); } - private SCMComponent combineValuesOfFirstFoundSection(RedactionLog redactionLog, String type, String seperator, String elseValue) { + private SCMComponent combineValuesOfFirstFoundSection(EntityLog entityLog) { - String transformation = String.format("Combine paragraphs of '%s' with seperator '%s' in first Section found", type, seperator); + String transformation = String.format("Combine paragraphs of '%s' with separator '%s' in first Section found", "study_conclusion", " "); - var entries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).toList(); + var entries = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("study_conclusion")).toList(); if (entries.isEmpty()) { - return SCMComponent.builder().originalValue(elseValue).transformation(transformation).build(); + return SCMComponent.builder().originalValue("").transformation(transformation).build(); } - int firstSectionNr = entries.get(0).getSectionNumber(); + int firstSectionNr = entries.get(0).getContainingNodeId().get(0); - String value = entries.stream().filter(e -> e.getSectionNumber() == firstSectionNr).map(RedactionLogEntry::getValue).collect(Collectors.joining(seperator)).trim(); + String value = entries.stream().filter(e -> e.getContainingNodeId().get(0) == firstSectionNr).map(EntityLogEntry::getValue).collect(Collectors.joining(" ")).trim(); return SCMComponent.builder() .originalValue(value) @@ -360,11 +365,11 @@ public class RSSPoc2Service { } - private SCMComponent getFirstEntryOrElse(RedactionLog redactionLog, String type, String elseValue) { + private SCMComponent getFirstEntryOrElse(EntityLog entityLog, String type) { - String transformation = String.format("First found value of type '%s' or else '%s'", type, elseValue); + String transformation = String.format("First found value of type '%s' or else '%s'", type, ""); - var firstEntryOptional = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).findFirst(); + var firstEntryOptional = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals(type)).findFirst(); if (firstEntryOptional.isPresent()) { @@ -372,37 +377,35 @@ public class RSSPoc2Service { return SCMComponent.builder().originalValue(firstEntry.getValue()).scmAnnotations(List.of(toScmAnnotations(firstEntry))).transformation(transformation).build(); } - return SCMComponent.builder().originalValue(elseValue).transformation(transformation).build(); + return SCMComponent.builder().originalValue("").transformation(transformation).build(); } - private SCMComponent getPerformingLaboratory(RedactionLog redactionLog) { + private SCMComponent getPerformingLaboratory(EntityLog entityLog) { String transformation = "Value of laboratory_name, combined with laboratory_country if distance is small"; - var laboratoryEntry = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("laboratory_name")).findFirst(); - if (!laboratoryEntry.isPresent()) { + var laboratoryEntry = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("laboratory_name")).findFirst(); + if (laboratoryEntry.isEmpty()) { return getEmptyComponent(transformation); } - var laboratoryCountry = redactionLog.getRedactionLogEntry() + var laboratoryCountry = entityLog.getEntityLogEntry() .stream() - .filter(r -> r.getType().equals("laboratory_country") && Math.abs(laboratoryEntry.get().getPositions().get(0).getTopLeft().getY() - r.getPositions() + .filter(r -> r.getType().equals("laboratory_country") && Math.abs(laboratoryEntry.get().getPositions().get(0).y() - r.getPositions() .get(0) - .getTopLeft() - .getY()) < 80) - .collect(Collectors.toList()); + .y()) < 80) + .toList(); - RedactionLogEntry countryWithSmallestDistance = null; + EntityLogEntry countryWithSmallestDistance = null; for (var entry : laboratoryCountry) { if (countryWithSmallestDistance == null) { countryWithSmallestDistance = entry; - } else if (Math.abs(laboratoryEntry.get().getPositions().get(0).getTopLeft().getY() - entry.getPositions().get(0).getTopLeft().getY()) < Math.abs(laboratoryEntry.get() + } else if (Math.abs(laboratoryEntry.get().getPositions().get(0).y() - entry.getPositions().get(0).y()) < Math.abs(laboratoryEntry.get() .getPositions() .get(0) - .getTopLeft() - .getY() - countryWithSmallestDistance.getPositions().get(0).getTopLeft().getY())) { + .y() - countryWithSmallestDistance.getPositions().get(0).y())) { countryWithSmallestDistance = entry; } @@ -412,9 +415,7 @@ public class RSSPoc2Service { scmAnnotations.add(toScmAnnotations(laboratoryEntry.get())); StringBuilder sb = new StringBuilder(); - if (laboratoryEntry.isPresent()) { - sb.append(laboratoryEntry.get().getValue()); - } + laboratoryEntry.ifPresent(entityLogEntry -> sb.append(entityLogEntry.getValue())); if (countryWithSmallestDistance != null) { sb.append(", ").append(countryWithSmallestDistance.getValue()); scmAnnotations.add(toScmAnnotations(countryWithSmallestDistance)); @@ -424,25 +425,25 @@ public class RSSPoc2Service { } - private SCMComponent getConvertedDates(RedactionLog redactionLog, String type) { + private SCMComponent getConvertedDates(EntityLog entityLog, String type) { - List redactionLogEntries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).collect(Collectors.toList()); + List entityLogEntries = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals(type)).toList(); - String value = redactionLogEntries.stream().map(RedactionLogEntry::getValue).map(this::convertDate).collect(Collectors.joining(", ")); + String value = entityLogEntries.stream().map(EntityLogEntry::getValue).map(this::convertDate).collect(Collectors.joining(", ")); return SCMComponent.builder() .originalValue(value) - .scmAnnotations(redactionLogEntries.stream().map(this::toScmAnnotations).collect(Collectors.toList())) + .scmAnnotations(entityLogEntries.stream().map(this::toScmAnnotations).collect(Collectors.toList())) .transformation(String.format("Convert values of type '%s' to dd/MM/yyyy joined with ', '", type)) .build(); } - private SCMComponent ifPresentAddOrElse(RedactionLog redactionLog, String type, String presentValue, String elseValue) { + private SCMComponent ifPresentAddOrElse(EntityLog entityLog, String type, String presentValue, String elseValue) { String transformation = String.format("If type %s is present than '%s' else '%s'", type, presentValue, elseValue); - var firstEntryOptional = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).findFirst(); + var firstEntryOptional = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals(type)).findFirst(); if (firstEntryOptional.isPresent()) { @@ -454,13 +455,13 @@ public class RSSPoc2Service { } - private SCMComponent getJoinedUniqueValues(RedactionLog redactionLog, String type, String seperator) { + private SCMComponent getJoinedUniqueValues(EntityLog entityLog, String type) { - String transformation = String.format("Combine unique values of '%s' with seperator '%s'", type, seperator); + String transformation = String.format("Combine unique values of '%s' with seperator '%s'", type, ", "); - var uniqueEntries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).collect(Collectors.toSet()); + var uniqueEntries = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals(type)).collect(Collectors.toSet()); - String value = uniqueEntries.stream().map(RedactionLogEntry::getValue).collect(Collectors.toSet()).stream().collect(Collectors.joining(seperator)).trim(); + String value = String.join(", ", uniqueEntries.stream().map(EntityLogEntry::getValue).collect(Collectors.toSet())).trim(); return SCMComponent.builder() .originalValue(value) @@ -470,12 +471,12 @@ public class RSSPoc2Service { } - private SCMComponent getTestGuideline1(RedactionLog redactionLog) { + private SCMComponent getTestGuideline1(EntityLog entityLog) { String transformation = "If 'oecd_guideline_number' and 'oecd_guideline_year' are present than mapped by provided mapping table else value of 'oecd_guideline' if present or else ''"; - var guidelineNumber = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("oecd_guideline_number")).findFirst(); - var guidelineYear = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("oecd_guideline_year")).findFirst(); + var guidelineNumber = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("oecd_guideline_number")).findFirst(); + var guidelineYear = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("oecd_guideline_year")).findFirst(); if (guidelineNumber.isPresent() && guidelineYear.isPresent()) { var guidelinePair = Pair.of(guidelineNumber.get().getValue(), guidelineYear.get().getValue()); @@ -489,7 +490,7 @@ public class RSSPoc2Service { } } - var guideline = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("oecd_guideline")).findFirst(); + var guideline = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("oecd_guideline")).findFirst(); if (guideline.isPresent()) { return SCMComponent.builder() @@ -503,15 +504,15 @@ public class RSSPoc2Service { } - private SCMComponent getTestGuideline2(RedactionLog redactionLog) { + private SCMComponent getTestGuideline2(EntityLog entityLog) { String transformation = "Combine values of 'epa_guideline' and 'ec_guideline' with seperator ', '"; - List guidelines = new ArrayList<>(); - guidelines.addAll(redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("epa_guideline")).collect(Collectors.toList())); - guidelines.addAll(redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("ec_guideline")).collect(Collectors.toList())); + List guidelines = new ArrayList<>(); + guidelines.addAll(entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("epa_guideline")).toList()); + guidelines.addAll(entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("ec_guideline")).toList()); - String value = guidelines.stream().map(RedactionLogEntry::getValue).collect(Collectors.joining(", ")); + String value = guidelines.stream().map(EntityLogEntry::getValue).collect(Collectors.joining(", ")); if (!value.isEmpty()) { return SCMComponent.builder() @@ -531,14 +532,14 @@ public class RSSPoc2Service { } - private Map getAsBlockPerAnnotation(RedactionLog redactionLog, String type, String componentKey) { + private Map getAsBlockPerAnnotation(EntityLog entityLog, String type, String componentKey) { String transformation = String.format("Values of type '%s'", type); List scmComponents = new ArrayList<>(); - var typeStringsEntries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).collect(Collectors.toList()); + var typeStringsEntries = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals(type)).toList(); - for (RedactionLogEntry typeStringEntry : typeStringsEntries) { + for (EntityLogEntry typeStringEntry : typeStringsEntries) { scmComponents.add(SCMComponent.builder() .originalValue(typeStringEntry.getValue().replaceAll("\\n", "").trim()) @@ -551,24 +552,24 @@ public class RSSPoc2Service { } - private SCMComponent getLongestCombinedSectionBlockOrElse(RedactionLog redactionLog, String type, String elseValue) { + private SCMComponent getLongestCombinedSectionBlockOrElse(EntityLog entityLog) { - String transformation = String.format("Longest combined section value of type '%s' if present or else '%s'", type, elseValue); + String transformation = String.format("Longest combined section value of type '%s' if present or else '%s'", "necropsy_findings", ""); - Map> entriesPerSection = new HashMap<>(); - redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).forEach(e -> { - entriesPerSection.computeIfAbsent(e.getSectionNumber(), (x) -> new ArrayList<>()).add(e); + Map> entriesPerSection = new HashMap<>(); + entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("necropsy_findings")).forEach(e -> { + entriesPerSection.computeIfAbsent(e.getContainingNodeId().get(0), (x) -> new ArrayList<>()).add(e); }); if (entriesPerSection.isEmpty()) { - return SCMComponent.builder().originalValue(elseValue).transformation(transformation).build(); + return SCMComponent.builder().originalValue("").transformation(transformation).build(); } int sectionNrOfLongestValue = 0; String longestValue = ""; - for (Map.Entry> sectionEntry : entriesPerSection.entrySet()) { + for (Map.Entry> sectionEntry : entriesPerSection.entrySet()) { - String value = sectionEntry.getValue().stream().map(RedactionLogEntry::getValue).collect(Collectors.joining(" ")).trim(); + String value = sectionEntry.getValue().stream().map(EntityLogEntry::getValue).collect(Collectors.joining(" ")).trim(); if (value.length() > longestValue.length()) { longestValue = value; sectionNrOfLongestValue = sectionEntry.getKey(); @@ -583,13 +584,13 @@ public class RSSPoc2Service { } - private SCMComponent getAsOneBlock(RedactionLog redactionLog, String type) { + private SCMComponent getAsOneBlock(EntityLog entityLog, String type) { String transformation = String.format("Combine value of '%s' to one block", type); - var entries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).collect(Collectors.toList()); + var entries = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals(type)).toList(); - String value = entries.stream().map(RedactionLogEntry::getValue).collect(Collectors.joining(" ")); + String value = entries.stream().map(EntityLogEntry::getValue).collect(Collectors.joining(" ")); return SCMComponent.builder() .originalValue(value) @@ -599,13 +600,13 @@ public class RSSPoc2Service { } - private SCMComponent getJoinedValues(RedactionLog redactionLog, String type, String seperator) { + private SCMComponent getJoinedValues(EntityLog entityLog, String type) { - String transformation = String.format("Combine values of '%s' with seperator '%s'", type, seperator); + String transformation = String.format("Combine values of '%s' with separator '%s'", type, " "); - var entries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals(type)).collect(Collectors.toList()); + var entries = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals(type)).toList(); - String value = entries.stream().map(RedactionLogEntry::getValue).collect(Collectors.joining(seperator)).trim(); + String value = entries.stream().map(EntityLogEntry::getValue).collect(Collectors.joining(" ")).trim(); return SCMComponent.builder() .originalValue(value) @@ -615,20 +616,20 @@ public class RSSPoc2Service { } - private SCMComponent getSex(RedactionLog redactionLog) { + private SCMComponent getSex(EntityLog entityLog) { String transformation = "Combine unique values of 'sex', map plural values to singular"; - var entries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("sex")).collect(Collectors.toSet()); + var entries = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("sex")).collect(Collectors.toSet()); - var value = entries.stream().map(RedactionLogEntry::getValue).map(String::toLowerCase).map(s -> { + var value = String.join(", ", entries.stream().map(EntityLogEntry::getValue).map(String::toLowerCase).map(s -> { if (s.equals("females")) { return "female"; } else if (s.equals("males")) { return "male"; } return s; - }).collect(Collectors.toSet()).stream().collect(Collectors.joining(", ")).trim(); + }).collect(Collectors.toSet())).trim(); return SCMComponent.builder() .originalValue(value) @@ -638,11 +639,11 @@ public class RSSPoc2Service { } - private SCMComponent getNumberOfAnimals(RedactionLog redactionLog) { + private SCMComponent getNumberOfAnimals(EntityLog entityLog) { String transformation = "Return value of 'number_of_animals' if present else return sum of unique 'animal_number' or else '' "; - var numberOfAnimals = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("number_of_animals")).findFirst(); + var numberOfAnimals = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("number_of_animals")).findFirst(); if (numberOfAnimals.isPresent()) { return SCMComponent.builder() @@ -652,13 +653,13 @@ public class RSSPoc2Service { .build(); } - var uniqueAnimalNumbers = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("animal_number")).collect(Collectors.toSet()); + var uniqueAnimalNumbers = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("animal_number")).collect(Collectors.toSet()); if (uniqueAnimalNumbers.isEmpty()) { return getEmptyComponent(transformation); } - int size = uniqueAnimalNumbers.stream().map(a -> a.getValue()).collect(Collectors.toSet()).size(); + int size = uniqueAnimalNumbers.stream().map(EntityLogEntry::getValue).collect(Collectors.toSet()).size(); return SCMComponent.builder() .originalValue(String.valueOf(size)) @@ -668,31 +669,29 @@ public class RSSPoc2Service { } - private Map getDoseMortality(RedactionLog redactionLog, String componentKey) { + private Map getDoseMortality(EntityLog entityLog) { String transformation = "Combine values of 'dose_mortality' and 'dose_mortality_dose' of same row with ', ' "; - var doseMortalityEntries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("dose_mortality")).collect(Collectors.toList()); - var doseMortalityDoseEntries = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("dose_mortality_dose")).collect(Collectors.toList()); + var doseMortalityEntries = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("dose_mortality")).toList(); + var doseMortalityDoseEntries = entityLog.getEntityLogEntry().stream().filter(r -> r.getType().equals("dose_mortality_dose")).toList(); List result = new ArrayList<>(); for (var mortality : doseMortalityEntries) { - RedactionLogEntry doseWithSmallestDistance = null; + EntityLogEntry doseWithSmallestDistance = null; for (var dose : doseMortalityDoseEntries) { - if (Math.round(mortality.getPositions().get(0).getTopLeft().getY()) == Math.round(dose.getPositions().get(0).getTopLeft().getY())) { + if (Math.round(mortality.getPositions().get(0).y()) == Math.round(dose.getPositions().get(0).y())) { doseWithSmallestDistance = dose; break; } if (doseWithSmallestDistance == null) { doseWithSmallestDistance = dose; - } else if (Math.abs(Math.round(mortality.getPositions().get(0).getTopLeft().getY()) - Math.round(dose.getPositions() + } else if (Math.abs(Math.round(mortality.getPositions().get(0).y()) - Math.round(dose.getPositions() .get(0) - .getTopLeft() - .getY())) < Math.abs(Math.round(mortality.getPositions().get(0).getTopLeft().getY()) - Math.round(doseWithSmallestDistance.getPositions() + .y())) < Math.abs(Math.round(mortality.getPositions().get(0).y()) - Math.round(doseWithSmallestDistance.getPositions() .get(0) - .getTopLeft() - .getY()))) { + .y()))) { doseWithSmallestDistance = dose; } } @@ -712,7 +711,7 @@ public class RSSPoc2Service { } - return componentListToMap(result, componentKey, transformation); + return componentListToMap(result, RSSPoc2Service.DOSE_MORTALITY, transformation); } @@ -735,17 +734,11 @@ public class RSSPoc2Service { } switch (oecd) { - - case "439": - case "406": - case "428": - case "438": - case "474": - case "487": + case "439", "406", "428", "438", "474", "487" -> { resultMap.put(STUDY_DESIGN, components.get(STUDY_DESIGN)); resultMap.put(RESULTS_AND_CONCLUSIONS, components.get(RESULTS_AND_CONCLUSIONS)); - break; - case "425": + } + case "425" -> { resultMap.put(SPECIES, components.get(SPECIES)); resultMap.put(STRAIN, components.get(STRAIN)); resultMap.put(DOSAGES, components.get(DOSAGES)); @@ -758,8 +751,8 @@ public class RSSPoc2Service { 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": + } + case "402" -> { resultMap.put(SPECIES, components.get(SPECIES)); resultMap.put(STRAIN, components.get(STRAIN)); resultMap.put(DOSES_MG_PER_KG_BW, components.get(DOSES_MG_PER_KG_BW)); @@ -772,9 +765,8 @@ public class RSSPoc2Service { 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": + } + case "403", "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)); @@ -787,8 +779,8 @@ public class RSSPoc2Service { 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": + } + case "405" -> { resultMap.put(SPECIES, components.get(SPECIES)); resultMap.put(STRAIN, components.get(STRAIN)); resultMap.put(SEX, components.get(SEX)); @@ -797,8 +789,8 @@ public class RSSPoc2Service { resultMap.put(DETAILING_OF_REPORTED_CHANGES, components.get(DETAILING_OF_REPORTED_CHANGES)); resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE)); resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION)); - break; - case "429": + } + 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)); @@ -811,20 +803,20 @@ public class RSSPoc2Service { resultMap.put(TEST_RESULTS, components.get(TEST_RESULTS)); resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE)); resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION)); - break; - case "404": + } + 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)); resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION)); - break; - case "471": + } + case "471" -> { resultMap.put(STRAIN, components.get(STRAIN)); resultMap.putAll(getKeyContains(components, DEVIATION_FROM_THE_GUIDELINE)); resultMap.put(STUDY_CONCLUSION, components.get(STUDY_CONCLUSION)); - break; + } } return resultMap; @@ -850,9 +842,9 @@ public class RSSPoc2Service { } - private ScmAnnotation toScmAnnotations(RedactionLogEntry entry) { + private ScmAnnotation toScmAnnotations(EntityLogEntry entry) { - Set pages = entry.getPositions().stream().map(Rectangle::getPage).collect(Collectors.toSet()); + Set pages = entry.getPositions().stream().map(Position::getPageNumber).collect(Collectors.toSet()); return ScmAnnotation.builder().type(entry.getType()).reason(entry.getReason()).pages(pages).ruleIdentifier(entry.getMatchedRule()).build(); } @@ -879,12 +871,12 @@ public class RSSPoc2Service { } - private Map getKeyContains(Map components, String compontentName) { + private Map getKeyContains(Map components, String componentName) { Map resultMap = new LinkedHashMap<>(); for (Map.Entry entry : components.entrySet()) { - if (entry.getKey().contains(compontentName)) { + if (entry.getKey().contains(componentName)) { resultMap.put(entry.getKey(), entry.getValue()); } } diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ReportGenerationService.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ReportGenerationService.java index dcb4e3c..562dd7d 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ReportGenerationService.java +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ReportGenerationService.java @@ -44,7 +44,7 @@ public class ReportGenerationService { private final ReportStorageService reportStorageService; private final WordReportGenerationService wordReportGenerationService; - private final RedactionLogConverterService redactionLogConverterService; + private final EntityLogConverterService entityLogConverterService; private final FileStatusClient fileStatusClient; private final DossierClient dossierClient; private final ReportTemplateClient reportTemplateClient; @@ -78,7 +78,7 @@ public class ReportGenerationService { var fileStatus = fileStatusClient.getFileStatus(dossierId, fileId); generatePlaceholderService.resolveFileAttributeValues(fileStatus, placeholderModel); - List reportEntries = redactionLogConverterService.getReportEntries(dossierId, fileId, fileStatus.isExcluded(), dossier); + List reportEntries = entityLogConverterService.getReportEntries(dossierId, fileId, fileStatus.isExcluded()); generateMultiFileExcelReports(reportTemplates.multiFileWorkbookReportTemplates, placeholderModel, fileStatus, isLastFile, dossierName, reportEntries); diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/WordReportGenerationService.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/WordReportGenerationService.java index 4ba9fbe..188d322 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/WordReportGenerationService.java +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/WordReportGenerationService.java @@ -115,7 +115,7 @@ public class WordReportGenerationService { removePlaceholdersRow(table); } - log.info("Report Generation took: {} for file with id {}, pageCount: {}, redactionLogEntryCount: {}, reportName: {}, className: {}", + log.info("Report Generation took: {} for file with id {}, pageCount: {}, entityLogEntryCount: {}, reportName: {}, className: {}", System.currentTimeMillis() - start, fileModel.getId(), fileModel.getNumberOfPages(), @@ -243,7 +243,7 @@ public class WordReportGenerationService { replacePlaceholderInParagraphAndSplit(doc.getParagraphs(), placeHolderValueMap, doc); for (XWPFTable tbl : doc.getTables()) { if (tableToSkip == tbl) { - // already processed for redactionLog Entries + // already processed for entityLog Entries continue; } for (XWPFTableRow row : tbl.getRows()) { @@ -487,7 +487,7 @@ public class WordReportGenerationService { } if (placeholder.equals(REDACTION_VALUE_PLACEHOLDER)) { foundPlaceholders.add(REDACTION_VALUE_PLACEHOLDER); - return input -> input.getEntry().getValue() != null ? input.getEntry().getValue().replaceAll("\n", " ").replaceAll(" ", " ") : input.getEntry().getEntityDisplayName(); + return input -> input.getEntry().getValue() != null ? input.getEntry().getValue().replaceAll("\n", " ").replaceAll(" {2}", " ") : input.getEntry().getEntityDisplayName(); } if (placeholder.equals(REDACTION_ENTITY_DISPLAY_NAME_PLACEHOLDER)) { foundPlaceholders.add(REDACTION_ENTITY_DISPLAY_NAME_PLACEHOLDER); diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/storage/ReportStorageService.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/storage/ReportStorageService.java index 2ed1e91..803146e 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/storage/ReportStorageService.java +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/storage/ReportStorageService.java @@ -8,12 +8,14 @@ import java.io.InputStream; import java.nio.file.Files; import java.nio.file.Paths; import java.nio.file.StandardOpenOption; +import java.util.ArrayList; import java.util.List; import java.util.UUID; import org.apache.commons.io.IOUtils; import org.springframework.stereotype.Service; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLog; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileType; import com.iqser.red.service.redaction.report.v1.api.model.StoredFileInformation; import com.iqser.red.storage.commons.service.StorageService; @@ -82,4 +84,14 @@ public class ReportStorageService { return Files.newInputStream(Paths.get(destFile.getPath()), StandardOpenOption.DELETE_ON_CLOSE); } + public EntityLog getEntityLog(String dossierId, String fileId, List excludedTypes) { + + EntityLog entityLog; + entityLog = storageService.readJSONObject(TenantContext.getTenantId(), StorageIdUtils.getStorageId(dossierId, fileId, FileType.ENTITY_LOG), EntityLog.class); + if (excludedTypes != null) { + entityLog.getEntityLogEntry().removeIf(entry -> excludedTypes.contains(entry.getType())); + } + return entityLog; + } + } diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/RedactionReportIntegrationTest.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/RedactionReportIntegrationTest.java index 40ab973..0dc825a 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/RedactionReportIntegrationTest.java +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/RedactionReportIntegrationTest.java @@ -31,7 +31,6 @@ import org.apache.poi.xssf.usermodel.XSSFWorkbook; import org.apache.poi.xwpf.usermodel.XWPFDocument; import org.apache.poi.xwpf.usermodel.XWPFParagraph; import org.apache.poi.xwpf.usermodel.XWPFRun; -import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mockito; @@ -49,11 +48,11 @@ import org.springframework.test.context.junit.jupiter.SpringExtension; import com.amazonaws.services.s3.AmazonS3; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLog; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLogLegalBasis; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.Dossier; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileModel; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.type.Type; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.RedactionLog; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.RedactionLogLegalBasis; import com.iqser.red.service.redaction.report.v1.server.client.DictionaryClient; import com.iqser.red.service.redaction.report.v1.server.client.DossierAttributesClient; import com.iqser.red.service.redaction.report.v1.server.client.DossierAttributesConfigClient; @@ -64,9 +63,9 @@ import com.iqser.red.service.redaction.report.v1.server.configuration.MessagingC import com.iqser.red.service.redaction.report.v1.server.model.ImagePlaceholder; import com.iqser.red.service.redaction.report.v1.server.model.PlaceholderModel; import com.iqser.red.service.redaction.report.v1.server.model.ReportRedactionEntry; +import com.iqser.red.service.redaction.report.v1.server.service.EntityLogConverterService; import com.iqser.red.service.redaction.report.v1.server.service.ExcelReportGenerationService; import com.iqser.red.service.redaction.report.v1.server.service.GeneratePlaceholderService; -import com.iqser.red.service.redaction.report.v1.server.service.RedactionLogConverterService; import com.iqser.red.service.redaction.report.v1.server.service.WordReportGenerationService; import com.iqser.red.service.redaction.report.v1.server.storage.ReportStorageService; import com.iqser.red.storage.commons.StorageAutoConfiguration; @@ -112,7 +111,7 @@ public class RedactionReportIntegrationTest { private MessagingConfiguration messagingConfiguration; @Autowired - private RedactionLogConverterService redactionLogConverterService; + private EntityLogConverterService entityLogConverterService; @MockBean private DossierAttributesConfigClient dossierAttributesConfigClient; @@ -153,10 +152,10 @@ public class RedactionReportIntegrationTest { Dossier dossier = prepareDossier(); FileModel fileModel = FileModel.builder().filename("filename").build(); - RedactionLog redactionLog = objectMapper.readValue(new ClassPathResource("files/redactionLog.json").getInputStream(), RedactionLog.class); - List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { }); - List reportEntries = redactionLogConverterService.convertAndSort(redactionLog, legalBasisMapping, new HashMap<>(), dossier); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, new HashMap<>()); var wordTemplateResource = new ClassPathResource("templates/Justification Appendix A1.docx"); var imageResource = new ClassPathResource("files/exampleImage.jpg"); @@ -190,10 +189,10 @@ public class RedactionReportIntegrationTest { Dossier dossier = prepareDossier(); FileModel fileModel = FileModel.builder().filename("filename").build(); - RedactionLog redactionLog = objectMapper.readValue(new ClassPathResource("files/redactionLog.json").getInputStream(), RedactionLog.class); - List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { }); - List reportEntries = redactionLogConverterService.convertAndSort(redactionLog, legalBasisMapping, new HashMap<>(), dossier); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, new HashMap<>()); var wordTemplateResource = new ClassPathResource("templates/Justification Appendix A2.docx"); var imageResource = new ClassPathResource("files/exampleImage.jpg"); @@ -228,9 +227,9 @@ public class RedactionReportIntegrationTest { List paragraphs = doc.getParagraphs(); - assertThat(paragraphs.size()).isEqualTo(19); + assertThat(paragraphs.size()).isEqualTo(11); - List expectedContent = getExpectedContent("expected/iuclid.txt"); + List expectedContent = getExpectedContent(); List contentOfParagraphs = getContentOfParagraphs(paragraphs); @@ -242,12 +241,11 @@ public class RedactionReportIntegrationTest { } - private List getExpectedContent(String path) throws IOException { + private List getExpectedContent() throws IOException { - ClassPathResource classPathResource = new ClassPathResource(path); + ClassPathResource classPathResource = new ClassPathResource("expected/iuclid.txt"); InputStream inputStream = classPathResource.getInputStream(); - List expectedContent = IOUtils.readLines(inputStream, "UTF-8"); - return expectedContent; + return IOUtils.readLines(inputStream, "UTF-8"); } @@ -257,7 +255,7 @@ public class RedactionReportIntegrationTest { for (XWPFParagraph paragraph : paragraphs) { for (XWPFRun run : paragraph.getRuns()) { - res.add(run.text()); + res.add(run.text().trim()); } } return res; @@ -269,10 +267,10 @@ public class RedactionReportIntegrationTest { Dossier dossier = prepareDossier(); FileModel fileStatus = FileModel.builder().filename("filename").build(); - RedactionLog redactionLog = objectMapper.readValue(new ClassPathResource("files/redactionLog.json").getInputStream(), RedactionLog.class); - List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { }); - List reportEntries = redactionLogConverterService.convertAndSort(redactionLog, legalBasisMapping, new HashMap<>(), dossier); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, new HashMap<>()); ClassPathResource templateResource = new ClassPathResource("templates/IUCLID_Template.docx"); XWPFDocument doc = new XWPFDocument(templateResource.getInputStream()); @@ -282,9 +280,8 @@ public class RedactionReportIntegrationTest { wordReportGenerationService.generateWordReport(reportEntries, placeholders, "test", doc, fileStatus, dossier, true); byte[] report = wordReportGenerationService.toByteArray(doc); - XWPFDocument newDoc = new XWPFDocument(new ByteArrayInputStream(report)); - return newDoc; + return new XWPFDocument(new ByteArrayInputStream(report)); } @@ -295,10 +292,10 @@ public class RedactionReportIntegrationTest { Dossier dossier = prepareDossier(); FileModel fileStatus = FileModel.builder().filename("filename").build(); - RedactionLog redactionLog = objectMapper.readValue(new ClassPathResource("files/redactionLog.json").getInputStream(), RedactionLog.class); - List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { }); - List reportEntries = redactionLogConverterService.convertAndSort(redactionLog, legalBasisMapping, new HashMap<>(), dossier); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, new HashMap<>()); ClassPathResource templateResource = new ClassPathResource("templates/Seeds - New Justification Form.docx"); XWPFDocument doc = new XWPFDocument(templateResource.getInputStream()); @@ -321,17 +318,16 @@ public class RedactionReportIntegrationTest { Dossier dossier = prepareDossier(); FileModel fileStatus = FileModel.builder().filename("filename").build(); - RedactionLog redactionLog = objectMapper.readValue(new ClassPathResource("files/redactionLog.json").getInputStream(), RedactionLog.class); - List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { }); - List reportEntries = redactionLogConverterService.convertAndSort(redactionLog, legalBasisMapping, new HashMap<>(), dossier); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, new HashMap<>()); FileModel fileModelSecondFile = FileModel.builder().filename("secondFile").build(); - RedactionLog redactionLogSecondFile = objectMapper.readValue(new ClassPathResource("files/excelReportRedactionLog.json").getInputStream(), RedactionLog.class); - List reportEntriesSecondFile = redactionLogConverterService.convertAndSort(redactionLogSecondFile, + EntityLog entityLogSecondFile = objectMapper.readValue(new ClassPathResource("files/entityLogWithManualRedactions.json").getInputStream(), EntityLog.class); + List reportEntriesSecondFile = entityLogConverterService.convertAndSort(entityLogSecondFile, legalBasisMapping, - new HashMap<>(), - dossier); + new HashMap<>()); ClassPathResource templateResource = new ClassPathResource("templates/Seeds-NewJustificationForm.docx"); XWPFDocument doc = new XWPFDocument(templateResource.getInputStream()); @@ -355,10 +351,10 @@ public class RedactionReportIntegrationTest { Dossier dossier = prepareDossier(); FileModel fileModel = FileModel.builder().filename("filename").build(); - RedactionLog redactionLog = objectMapper.readValue(new ClassPathResource("files/redactionLog.json").getInputStream(), RedactionLog.class); - List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { }); - List reportEntries = redactionLogConverterService.convertAndSort(redactionLog, legalBasisMapping, new HashMap<>(), dossier); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, new HashMap<>()); var wordTemplateResource = new ClassPathResource("templates/6464 appendix_b EFSA dRAR justification.docx"); var imageResource = new ClassPathResource("files/exampleImage.jpg"); @@ -392,11 +388,11 @@ public class RedactionReportIntegrationTest { Dossier dossier = prepareDossier(); FileModel fileModel = FileModel.builder().filename("filename").dossierId(dossier.getDossierId()).fileAttributes(Map.of("TestAttribute", "Lorem Ipsum")).build(); - RedactionLog redactionLog = objectMapper.readValue(new ClassPathResource("files/redactionLogWithManualRedactions.json").getInputStream(), RedactionLog.class); - List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLogWithManualRedactions.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { }); - Map mapOfEntityDisplayName = createEntityDisplayNames(redactionLog); - List reportEntries = redactionLogConverterService.convertAndSort(redactionLog, legalBasisMapping, mapOfEntityDisplayName, dossier); + Map mapOfEntityDisplayName = createEntityDisplayNames(entityLog); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, mapOfEntityDisplayName); ClassPathResource templateResource = new ClassPathResource("templates/Excel Report.xlsx"); @@ -421,11 +417,11 @@ public class RedactionReportIntegrationTest { public void testExcelTemplateReportGenerationMultiFile() { Dossier dossier = prepareDossier(); - RedactionLog redactionLog = objectMapper.readValue(new ClassPathResource("files/redactionLog.json").getInputStream(), RedactionLog.class); - List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { }); - Map mapOfEntityDisplayName = createEntityDisplayNames(redactionLog); - List reportEntries = redactionLogConverterService.convertAndSort(redactionLog, legalBasisMapping, mapOfEntityDisplayName, dossier); + Map mapOfEntityDisplayName = createEntityDisplayNames(entityLog); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, mapOfEntityDisplayName); FileModel fileModel = FileModel.builder().filename("filename").build(); @@ -439,11 +435,10 @@ public class RedactionReportIntegrationTest { writeWorkbook.createSheet("Sheet1"); excelTemplateReportGenerationService.generateExcelReport(reportEntries, placeholders, "test", writeWorkbook, "dossierName", fileModel, excelModel, false); - RedactionLog redactionLogSecondFile = objectMapper.readValue(new ClassPathResource("files/excelReportRedactionLog.json").getInputStream(), RedactionLog.class); - List reportEntriesSecondFile = redactionLogConverterService.convertAndSort(redactionLogSecondFile, + EntityLog entityLogSecondFile = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List reportEntriesSecondFile = entityLogConverterService.convertAndSort(entityLogSecondFile, legalBasisMapping, - mapOfEntityDisplayName, - dossier); + mapOfEntityDisplayName); FileModel fileModelSecondFile = FileModel.builder().filename("secondFile").build(); excelTemplateReportGenerationService.generateExcelReport(reportEntriesSecondFile, placeholders, @@ -466,11 +461,11 @@ public class RedactionReportIntegrationTest { public void testExcelPlaceholders() { Dossier dossier = prepareDossier(); - RedactionLog redactionLog = objectMapper.readValue(new ClassPathResource("files/redactionLog.json").getInputStream(), RedactionLog.class); - List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { }); - Map mapOfEntityDisplayName = createEntityDisplayNames(redactionLog); - List reportEntries = redactionLogConverterService.convertAndSort(redactionLog, legalBasisMapping, mapOfEntityDisplayName, dossier); + Map mapOfEntityDisplayName = createEntityDisplayNames(entityLog); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, mapOfEntityDisplayName); var imageResource = new ClassPathResource("files/exampleImage.jpg"); FileModel fileModel = FileModel.builder().filename("filename").build(); @@ -494,7 +489,7 @@ public class RedactionReportIntegrationTest { } - private Map createEntityDisplayNames(RedactionLog redactionLog) { + private Map createEntityDisplayNames(EntityLog entityLog) { Type t1 = new Type(); t1.setLabel("Type 1"); @@ -510,7 +505,7 @@ public class RedactionReportIntegrationTest { Mockito.when(dictionaryClient.getAllTypesForDossierTemplate(Mockito.any(), Mockito.anyBoolean())).thenReturn(ednList); Map entityDisplayNames = new HashMap<>(); - for (var entry : redactionLog.getRedactionLogEntry()) { + for (var entry : entityLog.getEntityLogEntry()) { if (entry.getType().equals("manual")) { entityDisplayNames.put(entry.getType(), "Manual"); } else { diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/RedactionReportV2IntegrationTest.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/RedactionReportV2IntegrationTest.java index 2de77b8..760d2b5 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/RedactionReportV2IntegrationTest.java +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/RedactionReportV2IntegrationTest.java @@ -35,6 +35,7 @@ import org.springframework.test.context.junit.jupiter.SpringExtension; import com.amazonaws.services.s3.AmazonS3; import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLog; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.DossierAttributeConfig; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.ReportTemplate; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.Dossier; @@ -43,7 +44,7 @@ import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemp import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileAttributeConfig; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileAttributeType; import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileModel; -import com.iqser.red.service.persistence.service.v1.api.shared.model.redactionlog.RedactionLog; +import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.file.FileType; import com.iqser.red.service.redaction.report.v1.api.model.ReportRequestMessage; import com.iqser.red.service.redaction.report.v1.api.model.StoredFileInformation; import com.iqser.red.service.redaction.report.v1.server.client.DictionaryClient; @@ -52,10 +53,11 @@ import com.iqser.red.service.redaction.report.v1.server.client.DossierAttributes import com.iqser.red.service.redaction.report.v1.server.client.DossierClient; 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.report.v1.server.client.ReportTemplateClient; import com.iqser.red.service.redaction.report.v1.server.configuration.MessagingConfiguration; import com.iqser.red.service.redaction.report.v1.server.service.ReportGenerationService; +import com.iqser.red.service.redaction.report.v1.server.storage.ReportStorageService; +import com.iqser.red.service.redaction.report.v1.server.storage.StorageIdUtils; import com.iqser.red.service.redaction.report.v1.server.utils.FileSystemBackedStorageService; import com.iqser.red.service.redaction.report.v1.server.utils.MetricValidationUtils; import com.iqser.red.storage.commons.StorageAutoConfiguration; @@ -107,9 +109,6 @@ public class RedactionReportV2IntegrationTest { @MockBean private FileStatusClient fileStatusClient; - @MockBean - private RedactionLogClient redactionLogClient; - @Autowired private ReportGenerationService reportGenerationService; @@ -122,6 +121,9 @@ public class RedactionReportV2IntegrationTest { @Autowired private PrometheusMeterRegistry prometheusMeterRegistry; + @Autowired + private ReportStorageService reportStorageService; + @SneakyThrows private ReportRequestMessage prepareFlow(int numOfFiles, String... templates) { @@ -156,11 +158,10 @@ public class RedactionReportV2IntegrationTest { .build()); when(fileAttributesConfigClient.getFileAttributeConfigs("dossierTemplateId")).thenReturn(fileAttributeConfig); - var redactionLog = objectMapper.readValue(new ClassPathResource("files/65-S10redactionLogWithRedaction.json").getInputStream(), RedactionLog.class); var fileModels = createFileModels(numOfFiles); for (int i = 1; i <= numOfFiles; i++) { + prepareStorage(i); when(fileStatusClient.getFileStatus("dossierId", "fileId" + i)).thenReturn(fileModels.get(i - 1)); - when(redactionLogClient.getRedactionLog("dossierId", "fileId" + i, new ArrayList<>(), true, false)).thenReturn(redactionLog); } var templateIds = new HashSet(); @@ -219,6 +220,13 @@ public class RedactionReportV2IntegrationTest { } } + @SneakyThrows + private void prepareStorage(int id) { + + var entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + fileSystemBackedStorageService.storeJSONObject(TenantContext.getTenantId(), StorageIdUtils.getStorageId("dossierId", "fileId" + id, FileType.ENTITY_LOG), entityLog); + } + @Test @SneakyThrows diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/service/EntityLogConverterServiceTest.java b/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/service/EntityLogConverterServiceTest.java new file mode 100644 index 0000000..1c39cbd --- /dev/null +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/service/EntityLogConverterServiceTest.java @@ -0,0 +1,81 @@ +package com.iqser.red.service.redaction.report.v1.server.service; + +import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertFalse; +import static org.junit.jupiter.api.Assertions.assertNotNull; +import static org.junit.jupiter.api.Assertions.assertTrue; +import static org.mockito.ArgumentMatchers.eq; +import static org.mockito.Mockito.when; + +import java.util.HashMap; +import java.util.List; + +import org.junit.jupiter.api.Test; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.InjectMocks; +import org.springframework.beans.factory.annotation.Autowired; +import org.springframework.boot.test.context.SpringBootTest; +import org.springframework.boot.test.mock.mockito.MockBean; +import org.springframework.context.annotation.ComponentScan; +import org.springframework.context.annotation.FilterType; +import org.springframework.core.io.ClassPathResource; +import org.springframework.test.context.junit.jupiter.SpringExtension; + +import com.fasterxml.jackson.core.type.TypeReference; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLog; +import com.iqser.red.service.persistence.service.v1.api.shared.model.analysislog.entitylog.EntityLogLegalBasis; +import com.iqser.red.service.persistence.service.v1.api.shared.model.dossiertemplate.dossier.Dossier; +import com.iqser.red.service.redaction.report.v1.server.Application; +import com.iqser.red.service.redaction.report.v1.server.client.DictionaryClient; +import com.iqser.red.service.redaction.report.v1.server.client.DossierClient; +import com.iqser.red.service.redaction.report.v1.server.model.ReportRedactionEntry; +import com.iqser.red.service.redaction.report.v1.server.storage.ReportStorageService; +import com.iqser.red.storage.commons.StorageAutoConfiguration; +import com.knecon.fforesight.tenantcommons.TenantsClient; + +import lombok.SneakyThrows; + +@ExtendWith(SpringExtension.class) +@SpringBootTest(classes = Application.class, webEnvironment = SpringBootTest.WebEnvironment.RANDOM_PORT) +@ComponentScan(excludeFilters = {@ComponentScan.Filter(type = FilterType.ASSIGNABLE_TYPE, value = StorageAutoConfiguration.class)}) +public class EntityLogConverterServiceTest { + + @MockBean + TenantsClient tenantsClient; + + @MockBean + private DossierClient dossierClient; + + @MockBean + private DictionaryClient dictionaryClient; + + @MockBean + private ReportStorageService reportStorageService; + + @InjectMocks + private EntityLogConverterService entityLogConverterService; + + @Autowired + private ObjectMapper objectMapper; + + @Test + @SneakyThrows + public void testConvertAndSort() { + + EntityLog entityLog = objectMapper.readValue(new ClassPathResource("files/entityLog.json").getInputStream(), EntityLog.class); + List legalBasisMapping = objectMapper.readValue(new ClassPathResource("files/legalBasisMapping.json").getInputStream(), new TypeReference<>() { + }); + List reportEntries = entityLogConverterService.convertAndSort(entityLog, legalBasisMapping, new HashMap<>()); + + assertNotNull(reportEntries); + assertFalse(reportEntries.isEmpty()); + assertEquals(reportEntries.size(), 62); + assertEquals(reportEntries.get(0).getPage(), 1); + assertEquals(reportEntries.get(0).getSection(), "[1]: Section: Rule 1/2: Redact CBI"); + assertEquals(reportEntries.get(0).getJustification(), "Article 39(e)(3) of Regulation (EC) No 178/2002 "); + assertEquals(reportEntries.get(0).getJustificationParagraph(), "Article 39(e)(3) of Regulation (EC) No 178/2002"); + assertFalse(reportEntries.get(0).isSkipped()); + } + +} diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/expected/iuclid.txt b/redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/expected/iuclid.txt index fdafa62..5f77f10 100644 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/expected/iuclid.txt +++ b/redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/expected/iuclid.txt @@ -1,19 +1,11 @@ filename -Article 39(e)(1) and Article 39(e)(2) of Regulation (EC) No 178/2002 any other personal data except for - a. the name and address of the applicant; - b. the names of authors of published or publicly available studies supporting such requests; and the names of all participants and observers in meetings of the Scientific Committee and the Scientific Panels, their working groups and any other ad hoc group meeting on the subject matter. -and except for personal data (names and addresses) of individuals involved in testing on vertebrate studies or in obtaining toxicological information +Reg (EC) No 1107/2009 Art. 63 (2e) -relates to: P9 Syngenta Crop Protection AG, P10 Syngenta Crop Protection AG, P10 Syngenta Crop Protection AG, P10 Regina Dorn, P10 +41 (61) 323 6358, P10 +41 (61) 323 6155, P10 regina.dorn@syngenta.com, P10 Syngenta Limited, P13 Syngenta Crop Protection AG, P13 Regina Dorn, P13 +41 (61) 323 6358, P13 +41 (61) 323 6155, P13 regina.dorn@syngenta.com, P13 Syngenta Crop Protection AG, P13 Patrick Gardinal, P13 Syngenta Crop Protection AG, P13 +41 (0) 61 323 60 51, P13 +41 (0) 61 323 61 55, P13 patrick.gardinal@syngenta.com, P21 Meyer, P21 Meyer, P21 Mostert, P22 Moster, P22 Hargeaves, P22 Sole, P22 Vargo, P22 Rezaaiyan, P22 Evans, P22 Hargreaves, P22 Sole, P22 Tribolet, P22 Tribolet, P22 Tribolet, P22 Hargreaves, P22 Sole, P22 Tribolet, P22 Tribolet, P22 Tribolet, P22 Vargo, P22 O’Loughlin, P22 Hazelette, P22 Fankhauser, P22 Fankhauser, P23 Biedermann, P23 Chang, P23 Khalil, P23 Wolf, P23 Gemrot, P23 Gemrot, P23 Hargeaves, P23 Sole, P23 Vargo, P23 Rezaaiyan, P23 Evans, P23 Hargreaves, P23 Sole, P24 Hargreaves, P24 Sole, P24 Vargo, P24 Hargeaves, P24 Sole, P24 Vargo, P24 Rezaaiyan, P24 Evans, P24 Hargreaves, P24 Sole, P24 Hargreaves, P24 Sole, P24 Vargo, P25 Doubovetzky, P25 Garrigue, P25 Garrigue, P25 Hargreaves, P26 Tribolet, P26 Tribolet, P26 Tribolet, P26 Vargo, P26 Meseguer, P28 Class, P28 Richter, P28 Miller, P28 Class, P28 Richter, P28 Giannone, P28 Giannone, P28 Benazeraf, P28 Giannone, P28 Richter, P28 Allen, P28 Richter, P28 Hargreaves, P29 Hargreaves, P29 Sole, P29 Robinson, P29 Hargreaves, P29 Sole, P29 Richardson, P29 Meseguer, P30 Robinson, P30 Wolf, P30 Tribolet, P30 Tribolet, P30 Richter, P30 Class, P30 Richter, P30 Class, P30 Richter, P30 Class, P30 Richter, P30 Class, P30 Richter, P30 Miller, P30 Class, P30 Richter, P30 Class, P30 Richter, P30 Class, P30 Richter, P30 Class, P30 Richter, P30 Miller, P30 Richter, P30 Richter, P30 Richter, P30 Richter, P30 Richter, P30 Richter, P30 Allen, P30 Richter, P30 Richter, P30 Richter, P30 Richter, P30 Allen, P31 Hargreaves, P31 Hargreaves, P31 Hargreaves, P31 Hargreaves, P31 Robinson, P31 Sole, P31 Sole, P31 Richardson, P31 Meseguer, P31 Meseguer, P31 Hargreaves, P31 Hargreaves, P31 Sole, P31 Sole, P31 Meseguer, P31 Meseguer, P31 Robinson, P31 Robinson, P31 Wolf, P31 Wolf, P31 Tribolet, P31 Tribolet, P31 Richter, P31 Richter, P31 Richter, P31 Richter, P31 Meseguer, P31 Anon, P32 Hartnett, P32 Kale, P34 Glaza SM, P34 Schoch M, P34 Winkler G, P34 Matting E, P34 Glaza SM, P34 Holbert MS, P34 Glaza SM, P34 Glaza SM, P34 Marty JH, P34 Glaza SM, P34 Gehrke H, P36 Anon, P37 Fankhauser, P37 Fankhauser, P37 Chang, P37 Fankhauser, P37 Fankhauser, P37 Chang, P37 Hazelette, P37 Mastrocco, P38 Hertner, P38 Sokolowski, P38 Beilstein, P38 Wollny, P38 Strasser, P38 Bohnenberger, P39 Hertner, P39 Dony, P39 Ham, P39 Cifone, P39 Hertner, P39 Tisdell, P39 Tisdell, P40 O’Loughlin, P40 Khalil, P40 Lochry, P40 Gilles, P40 Lightkep, P41 Manton, P41 Argus Laboratories, P41 Lightkep, P41 Manton, P41 Ciba-Geigy laboratory, P41 Gilles, P41 Giknis, P41 Lightkep, P41 Lochry, P42 Charlton, P42 Laville, P42 Aït-Aïssa, P42 Dalton, P42 Mathias, P42 Tisdel, P42 Tisdel, P42 Grennlee, P42 Akkan, P45 Capps, P45 Brown, P45 Mücke, P77 Keller A, P77 Mamouni, P77 Mamouni, P77 Zbaerben&Nicoll ier, P77 Hein W., P77 Mamouni, P78 Mamouni, P78 Zbaerben&Nicoll ier, P78 Morgenroth U, P78 Zbaerben&Nicoll ier, P78 Clark A, P79 Clark A, P79 Fent, P79 Hein W., P79 Zbaerben&Nicoll ier, P79 Kitschmann P, P79 Fent, P80 Kitschmann, P80 Zbaerben&Nicoll ier, P80 Keller, P80 Mamouni, P80 Mamouni, P80 Mamouni, P81 Bond&Ha nd, P81 Bond&Ha nd, P81 Zbaerben&Nicoll ier, P82 Bond&Ha nd, P82 Zbaerben&Nicoll ier, P82 Zbaerben&Nicoll ier, P83 Zbaerben&Nicoll ier, P83 Fent, P83 Zbaerben&Nicoll ier, P84 Bond&Ha nd, P84 Mamouni, P84 Mamouni, P84 Mamouni, P85 Simmonds R, P85 Merritt, A, P85 Simmonds M, P85 Simmonds R, P85 Simmonds M, P85 Simmonds R, P85 Simmonds R, P85 Merritt, A, P86 Mamouni A., P86 Simmonds R, P86 Merritt, A, P86 Mamouni A, P86 Mamouni A, P86 Mamouni A, P86 Kitschmann, P87 Kitschmann P, P87 Hein W., P87 Purdy J., P87 Clark, P87 Morgenroth, P87 Kitschmann, P87 Keller, P87 Simmonds, P87 Simmonds, P87 Lucas, P87 Phaff, P87 Hein, P87 Clark, P87 Keller, P87 Simmonds, P87 Simmonds, P88 Kitschmann, P88 Mamouni, P88 Hein, P88 Nicollier, P88 Nicollier&Glänzel, P90 Clark, P90 Clark, P90 Lucas, P90 Lucas, P90 Lucas, P90 Keller, P90 Keller, P90 Kitschmann, P90 Kitschmann, P90 Kitschmann, P90 Morgenroth, P90 Phaff, P90 Hein, P90 Simmonds, P90 Simmonds, P90 Simmonds, P90 Simmonds, P90 Simmonds, P90 Simmonds, P90 Simmonds, P90 Simmonds, P90 Simmonds, P90 Simmonds, P90 Simmonds, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Phaff, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Clark, P91 Lucas, P91 Simmonds, P91 Simmonds, P91 Simmonds, P91 Simmonds, P92 Keller, P92 Simmonds, P92 Simmonds, P92 Simmonds, P92 Simmonds, P92 Morgenroth, P92 Kitschmann, P92 Lucas, P92 Hein, P92 Kitschmann, P92 Lucas, P92 Kitschmann, P92 Simmonds, P92 Simmonds, P92 Kitschmann, P93 Simmonds, P93 Simmonds, P93 Simmonds, P93 Simmonds, P93 Phaff, P93 Clark, P93 Lucas, P93 Simmonds, P93 Simmonds, P93 Simmonds, P93 Simmonds, P93 Keller, P93 Simmonds, P93 Simmonds, P93 Simmonds, P93 Simmonds, P94 Nicollier, P94 Glänzel, P94 Mamouni, P94 Simmonds, P94 Morgenroth, P94 Kitschmann, P94 Lucas, P94 Hein, P94 Hein, P94 Simmonds, P94 Kitschmann, P94 Nicollier, P94 Glänzel, P94 Lucas, P94 Kitschmann, P95 Nicollier, P95 Glänzel, P95 Simmonds, P95 Simmonds, P95 Simmonds, P95 Simmonds, P95 Phaff, P95 Simmonds, P95 Simmonds, P95 Clark, P95 Lucas, P95 Simmonds, P95 Simmonds, P95 Simmonds, P95 Simmonds, P96 Keller, P96 Simmonds, P96 Simmonds, P96 Simmonds, P96 Simmonds, P96 Kitschmann, P96 Kitschmann, P96 Nicollier, P96 Kitschmann, P96 Lucas, P96 Hein, P96 Kitschmann, P96 Nicollier, P96 Lucas, P96 Kitschmann, P96 Nicollier, P97 Mamouni, P97 Nicollier, P97 Gl änzel, P97 Nicollier, P97 Gl änzel, P97 Nicollier, P97 Gl änzel, P97 Roohi, P97 Roohi, P97 Roohi, P98 Clark, P98 Lucas, P98 Luca, P98 Roohi, P98 Roohi, P98 Roohi, P98 Simmonds, P98 Simmonds, P98 Simmonds, P98 Simmonds, P99 Simmonds, P99 Simmonds, P99 Simmonds, P99 Hein, P99 Simmonds, P99 Mamouni, P99 Merritt, P99 Simmonds, P100 Merritt, P100 Simmonds, P102 Spare, W.C., P102 Ellgehausen, H., P103 Glänzel, A., P103 Nicollier, G., P103 Hein, W., P103 Mamouni, A., P103 Mamouni, P103 Voelkel, W, P104 Spare, W.C., P104 Mamouni, A., P104 Ulbrich, R., P104 Spare, W.C., P104 Voelkel, W, P105 Simmonds, M., P105 Burgess, M, P105 Simmonds, M., P105 Simmonds, M., P106 Spare, P106 MüllerKallert, P106 Plücken, P106 Spare, P106 MüllerKallert, P107 Plücken, P114 Zepp, P114 Cline, P116 Mamouni, P116 Mamouni, P116 Seyfried, P116 Seyfried, P119 Kitschmann, P126 Kitschmann, P128 Bomfim Pestana C., P128 Anas, P128 Beavers, J.B., P128 Beavers, J.B., P128 Anas, P128 Beavers, J.B., P128 Beavers, J.B., P128 Anas, P128 Beavers, J.B., P128 Beavers, J.B., P128 Anas, P128 Taliaferro, P128 Taylor, S., P128 Walton, H., P128 Taliaferro, P128 Taylor, S., P128 Walton, H., P129 Kaczor, M.H., P129 Miller V., P129 Taylor, S., P129 Priestley, S., P129 Schoch, M., P129 Glaza, S.M., P129 Kuhn, P129 O’Loughlin, P131 Buccafusco, P131 Sachsse & Ullmann, P131 Collins, P131 Spare, P131 Liedtke, P131 Collins, P131 Spare, P131 Liedtke, P131 Memmert, P131 Eckenstein, P131 Hoberg, P131 Hefner, P133 Gonzalez-Valero, P134 Engelhard, P134 Wesiak, P134 Neumann, P134 Nienstedt, P134 Nienstedt, P134 Nienstedt, P134 Nienstedt, P134 Candolfi, P134 Candolfi, P134 Candolfi, P134 Candolfi, P135 Wesiak, P135 Neumann, P135 Reber, P135 Großmann, P136 Müther J., P136 Friedrich S., P136 Friedrich S., P136 Friedrich S., P136 Friedrich S., P136 Friedrich S., P136 Friedrich S., P136 Friedrich S., P136 Forster A., P136 Pease G., P136 Milanesi F., P137 Klein O., P137 McCormac, P137 McCormac, P137 McCormac, P137 Friedrich, P137 Friedrich, P137 Friedrich, P137 McCormac, P137 McCormac, P137 Vinall, P137 Vinall, P137 Vinall, P138 Schulz, P138 Schulz, P138 Schulz, P138 Vinall, P138 Vinall, P138 Schulz, L, P138 Grade, R., P138 Grade, R., P138 Seyfried, P138 Hutcheson, P138 Seyfried, P138 Hutcheson, P139 Chetram & Schuster, P139 Chetram & Schuster, P139 Bramby-Gunary, P139 Bramby-Gunary, P140 Boutin, P140 Boutin, P140 Boutin, P141 R. Grade, P141 R.Grade, P141 R. 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Any personal data made public pursuant to Article 38 of this Regulation and this Article shall only be used to ensure the transparency of the risk assessment under this Regulation and shall not be further processed in a manner that is incompatible with these purposes, in accordance with point (b) of Article 5(1) of Regulation (EU) 2016/679 and point (b) of Article 4(1) of Regulation (EU) 2018/1725, as the case may be)", + "reason": "Article 39(e)(3) of Regulation (EC) No 178/2002" + }, + { + "name": "1.2 vertebrate study related personal data (incl. geolocation); Article 39(e)(2)", + "description": "personal data (names and addresses) of individuals involved in testing on vertebrate studies or in obtaining toxicological information", + "reason": "Article 39(e)(2) of Regulation (EC) No 178/2002" + }, + { + "name": "2. manufacturing or production process", + "description": "the manufacturing or production process, including the method and innovative aspects thereof, as well as other technical and industrial specifications inherent to that process or method, except for information which is relevant to the assessment of safety", + "reason": "Article 63(2)(a) of Regulation (EC) No 1107/2009 (making reference to Article 39 of Regulation EC No 178/2002)" + }, + { + "name": "3. links between a producer and applicant", + "description": "commercial links between a producer or importer and the applicant or the authorisation holder, where applicable", + "reason": "Article 63(2)(a) of Regulation (EC) No 1107/2009 (making reference to Article 39 of Regulation EC No 178/2002)" + }, + { + "name": "4. commercial information", + "description": "commercial information revealing sourcing, market shares or business strategy of the applicant", + "reason": "Article 63(2)(a) of Regulation (EC) No 1107/2009 (making reference to Article 39 of Regulation EC No 178/2002)" + }, + { + "name": "5. quantitative composition", + "description": "quantitative composition of the subject matter of the request, except for information which is relevant to the assessment of safety", + "reason": "Article 63(2)(a) of Regulation (EC) No 1107/2009 (making reference to Article 39 of Regulation EC No 178/2002)" + }, + { + "name": "6. specification of impurity", + "description": "the specification of impurity of the active substance and the related methods of analysis for impurities in the active substance as manufactured, except for the impurities that are considered to be toxicologically, ecotoxicologically or environmentally relevant and the related methods of analysis for such impurities", + "reason": "Article 63(2)(b) of Regulation (EC) No 1107/2009" + }, + { + "name": "7. results of production batches", + "description": "results of production batches of the active substance including impurities", + "reason": "Article 63(2)(c) of Regulation (EC) No 1107/2009" + }, + { + "name": "8. composition of a plant protection product", + "description": "information on the complete composition of a plant protection product", + "reason": "Article 63(2)(d) of Regulation (EC) No 1107/2009" + } + ], + "dictionaryVersion": 21, + "dossierDictionaryVersion": 1, + "rulesVersion": 1, + "legalBasisVersion": 2 +} \ No newline at end of file diff --git a/redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/files/redactionLog.json b/redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/files/redactionLog.json deleted file mode 100644 index 46197f0..0000000 --- a/redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/files/redactionLog.json +++ /dev/null @@ -1,47500 +0,0 @@ -{ - 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