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RED-9348: move component log to mongodb

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This commit is contained in:
Maverick Studer 2024-09-23 16:05:05 +02:00
parent 21775d5a7d
commit ff10bf07c9
8 changed files with 2063 additions and 867 deletions
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1
.gitlab-ci.yml
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@ -24,4 +24,5 @@ deploy:
rules:
- if: $CI_COMMIT_BRANCH == $CI_DEFAULT_BRANCH
- if: $CI_COMMIT_BRANCH =~ /^release/
- if: $CI_COMMIT_BRANCH =~ /^feature/
- if: $CI_COMMIT_TAG

2
redaction-report-service-v1/redaction-report-service-api-v1/build.gradle.kts
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@ -5,7 +5,7 @@ plugins {
description = "redaction-report-service-api-v1"
val persistenceServiceVersion = "2.539.0"
val persistenceServiceVersion = "2.562.0-RED9348.2"
dependencies {
implementation("io.github.openfeign:feign-core:12.2")

2
redaction-report-service-v1/redaction-report-service-server-v1/build.gradle.kts
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@ -17,7 +17,7 @@ val storageCommonsVersion = "2.45.0"
val lifecycleCommonsVersion = "0.4.0"
val poiVersion = "5.2.3"
val metricCommonsVersion = "2.1.0"
val persistenceServiceVersion = "2.539.0"
val persistenceServiceVersion = "2.562.0-RED9348.2"
val springBootStarterVersion = "3.2.3"
configurations {

8
redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ComponentRowsReportService.java
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@ -33,7 +33,7 @@ public class ComponentRowsReportService {
public void addComponentRows(Sheet sheet, FileModel fileModel, ExcelModel excelModel) {
ComponentLog componentLog = componentResource.getComponentLog(fileModel.getDossierId(), fileModel.getId(), true);
ComponentLog componentLog = componentResource.getComponentLog(fileModel.getDossierId(), fileModel.getId());
AtomicInteger rowIndex = new AtomicInteger(excelModel.getRedactionPlaceholderRow());
@ -41,7 +41,7 @@ public class ComponentRowsReportService {
componentLog.getComponentLogEntries().forEach(componentLogEntry -> {
if (componentLogEntry.getComponentValues().isEmpty()) {
if (componentLogEntry.getValues().isEmpty()) {
return;
}
int componentRowIdx = rowIndex.getAndIncrement();
@ -51,8 +51,8 @@ public class ComponentRowsReportService {
Cell componentNameCell = componentRow.createCell(COMPONENT_NAME_COL);
componentNameCell.setCellValue(oecd + "-" + componentLogEntry.getName().replaceAll("_", " "));
for (int valueIdx = 0; valueIdx < componentLogEntry.getComponentValues().size(); valueIdx++) {
String value = componentLogEntry.getComponentValues().get(valueIdx).getValue();
for (int valueIdx = 0; valueIdx < componentLogEntry.getValues().size(); valueIdx++) {
String value = componentLogEntry.getValues().get(valueIdx).getValue();
componentRow.createCell(COMPONENT_VALUE_STARTING_COL + valueIdx).setCellValue(value);
}

6
redaction-report-service-v1/redaction-report-service-server-v1/src/main/java/com/iqser/red/service/redaction/report/v1/server/service/ScmReportService.java
View File

@ -67,7 +67,7 @@ public class ScmReportService {
CellUtil.setAlignment(firstRow.getCell(textColumnIndex), HorizontalAlignment.LEFT);
ComponentLog componentLog = componentResource.getComponentLog(fileModel.getDossierId(), fileModel.getId(), true);
ComponentLog componentLog = componentResource.getComponentLog(fileModel.getDossierId(), fileModel.getId());
AtomicInteger rowIndex = new AtomicInteger(excelModel.getRedactionPlaceholderRow());
@ -77,7 +77,7 @@ public class ScmReportService {
componentLog.getComponentLogEntries().forEach(componentLogEntry -> {
if (componentLogEntry.getComponentValues().isEmpty()) {
if (componentLogEntry.getValues().isEmpty()) {
return;
}
@ -132,7 +132,7 @@ public class ScmReportService {
// FileAttributes cells
addFileAttribute(row, fileModel, fileAttributeModels);
var iterator = componentLogEntry.getComponentValues().iterator();
var iterator = componentLogEntry.getValues().iterator();
while (iterator.hasNext()) {
ComponentLogEntryValue componentLogEntryValue = iterator.next();
Cell indexCell = row.createCell(valueIndexColumn);

2
redaction-report-service-v1/redaction-report-service-server-v1/src/test/java/com/iqser/red/service/redaction/report/v1/server/RedactionReportIntegrationTest.java
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@ -614,7 +614,7 @@ public class RedactionReportIntegrationTest {
Map<String, String> mapOfEntityDisplayName = createEntityDisplayNames(entityLog);
List<ReportRedactionEntry> reportEntries = entityLogConverterService.convertAndSort(DOSSIER_ID, FILE_ID, entityLog, legalBasisMapping, mapOfEntityDisplayName);
when(componentClient.getComponentLog(dossier.getId(), fileModel.getId(), true)).thenReturn(componentLog);
when(componentClient.getComponentLog(dossier.getId(), fileModel.getId())).thenReturn(componentLog);
when(fileAttributesConfigClient.getFileAttributeConfigs(dossier.getDossierTemplateId())).thenReturn(fileAttributeConfigs);
ClassPathResource templateResource = new ClassPathResource("templates/scm_report.xlsx");

1248
redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/files/scm/componentLog.json
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File diff suppressed because it is too large Load Diff

859
redaction-report-service-v1/redaction-report-service-server-v1/src/test/resources/files/scm/oldComponentLog.json Normal file
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@ -0,0 +1,859 @@
{
"analysisNumber": 2,
"componentRulesVersion": 1,
"componentLogEntries": [
{
"name": "Study_Title",
"componentValues": [
{
"value": "SYN545192 EC (A15457H) - Acute Dermal Toxicity Study in Rats",
"originalValue": "SYN545192 EC (A15457H) - Acute Dermal Toxicity Study in Rats",
"valueDescription": "First found value of type title or else ''",
"componentRuleId": "StudyTitle.0.0",
"componentLogEntityReferences": [
{
"id": "fdc33ec238d48f3f5c9611ea4ba3ae1b",
"type": "title",
"entityRuleId": "DOC.6.1",
"page": 1
}
]
}
]
},
{
"name": "Performing_Laboratory",
"componentValues": [
{
"value": "CiToxLAB Hungary Ltd., Hungary",
"originalValue": "CiToxLAB Hungary Ltd., Hungary",
"valueDescription": "Laboratory name and country found!",
"componentRuleId": "PerformingLaboratory.1.0",
"componentLogEntityReferences": [
{
"id": "f872738237a85170cb073b6220b98e65",
"type": "laboratory_name",
"entityRuleId": "DOC.7.2",
"page": 1
},
{
"id": "1c6dade9e8ea1a6f5e1b83da05f11368",
"type": "laboratory_country",
"entityRuleId": "DOC.7.2",
"page": 1
}
]
}
]
},
{
"name": "Report_Number",
"componentValues": [
{
"value": "12/063-002P",
"originalValue": "12/063-002P",
"valueDescription": "First found value of type report_number or else ''",
"componentRuleId": "ReportNumber.0.0",
"componentLogEntityReferences": [
{
"id": "8ac7d1ad2d1614527bbb055cebb3824f",
"type": "report_number",
"entityRuleId": "DOC.2.0",
"page": 1
}
]
}
]
},
{
"name": "GLP_Study",
"componentValues": [
{
"value": "Yes",
"originalValue": "Yes",
"valueDescription": "Yes if present, No if not",
"componentRuleId": "GLPStudy.0.0",
"componentLogEntityReferences": [
{
"id": "23cacb7ae621b9cdf987f50e3bdd115b",
"type": "glp_study",
"entityRuleId": "DOC.8.0",
"page": 3
},
{
"id": "fcd231292774563c812cddcf4d78c1f5",
"type": "glp_study",
"entityRuleId": "DOC.8.0",
"page": 25
}
]
}
]
},
{
"name": "Test_Guidelines_1",
"componentValues": [
{
"value": "Nº 402: Acute Dermal Toxicity (24/02/1987)",
"originalValue": "Nº 402: Acute Dermal Toxicity (24/02/1987)",
"valueDescription": "OECD Number and guideline year mapped!",
"componentRuleId": "TestGuideline.0.0",
"componentLogEntityReferences": [
{
"id": "911e8b6737c9529a40590dbf6778c24b",
"type": "oecd_guideline_number",
"entityRuleId": "DOC.1.0",
"page": 1
},
{
"id": "962c4942cd62f0103b1bf5759e2e1b1a",
"type": "oecd_guideline_year",
"entityRuleId": "DOC.1.0",
"page": 1
}
]
}
]
},
{
"name": "Test_Guidelines_2",
"componentValues": [
{
"value": "EPA OPPTS 870.1200 (1998), EC 440/2008 (2008)",
"originalValue": "EPA OPPTS 870.1200 (1998), EC 440/2008 (2008)",
"valueDescription": "Joining all values of type ec_guideline, epa_guideline with ', '",
"componentRuleId": "TestGuideline.2.0",
"componentLogEntityReferences": [
{
"id": "506ef85dd4dcb0a2df24d203ad21d220",
"type": "epa_guideline",
"entityRuleId": "DOC.1.0",
"page": 1
},
{
"id": "09c476952cbc59e3661b03cd38d463e7",
"type": "ec_guideline",
"entityRuleId": "DOC.1.0",
"page": 1
}
]
}
]
},
{
"name": "Experimental_Starting_Date",
"componentValues": [
{
"value": "21/03/2012",
"originalValue": "21/03/2012",
"valueDescription": "Convert values of type 'experimental_start_date' to dd/MM/yyyy joined with ', '",
"componentRuleId": "StartDate.0.0",
"componentLogEntityReferences": [
{
"id": "decf41962064ede79b213035f34862b3",
"type": "experimental_start_date",
"entityRuleId": "DOC.3.0",
"page": 7
}
]
}
]
},
{
"name": "Experimental_Completion_Date",
"componentValues": [
{
"value": "04/04/2012",
"originalValue": "04/04/2012",
"valueDescription": "Convert values of type 'experimental_end_date' to dd/MM/yyyy joined with ', '",
"componentRuleId": "CompletionDate.0.0",
"componentLogEntityReferences": [
{
"id": "346a5ce1bd59081c74885078af715284",
"type": "experimental_end_date",
"entityRuleId": "DOC.4.0",
"page": 7
}
]
}
]
},
{
"name": "Certificate_of_Analysis_Batch_Identification",
"componentValues": [
{
"value": "SMU1LP001",
"originalValue": "SMU1LP001",
"valueDescription": "Joining all unique values of type batch_number with ', '",
"componentRuleId": "AnalysisCertificate.0.0",
"componentLogEntityReferences": [
{
"id": "93b7180cb815e41a53a3f1340776dcf2",
"type": "batch_number",
"entityRuleId": "DOC.9.1",
"page": 12
},
{
"id": "e0cb8bec3a8568335eae3d8776237c8f",
"type": "batch_number",
"entityRuleId": "DOC.9.0",
"page": 23
}
]
}
]
},
{
"name": "Species",
"componentValues": [
{
"value": "rats",
"originalValue": "rats",
"valueDescription": "First found value of type species or else ''",
"componentRuleId": "Species.0.0",
"componentLogEntityReferences": [
{
"id": "b897fbedc847ea1d23f349e5350bc8f1",
"type": "species",
"entityRuleId": "DOC.5.2",
"page": 14
},
{
"id": "f5d80ce83f739506f95420a375c8effa",
"type": "species",
"entityRuleId": "DOC.5.2",
"page": 14
},
{
"id": "4f8b024892a7ee7826a7638833ed0de2",
"type": "species",
"entityRuleId": "DOC.5.2",
"page": 14
}
]
}
]
},
{
"name": "Strain",
"componentValues": [
{
"value": "CRL:(WI)",
"originalValue": "CRL:(WI)",
"valueDescription": "First found value of type strain or else ''",
"componentRuleId": "Strain.0.0",
"componentLogEntityReferences": [
{
"id": "b9784d1fa897ade518e807b3e371b275",
"type": "strain",
"entityRuleId": "DOC.5.3",
"page": 14
}
]
}
]
},
{
"name": "Doses_mg_per_kg_bw",
"componentValues": [
{
"value": "A single administration of SYN545192 EC (A15457H) at a dose of 2000 mg/kg body weight was applied dermally to 5 male and 5 female CRL:(WI) rats, followed by a 14-day observation period. The test item was applied as supplied by the Sponsor. The application period was 24 hours. Clinical observations were assessed in all animals at 1 and 5 hours after dosing and daily for 14 days thereafter. Body weight was measured prior to dosing on Day 0 and on Days 7 and 14. All animals were euthanized and subjected to a gross macroscopic examination at the end of the 14-day observation period (Day 14). 14",
"originalValue": "A single administration of SYN545192 EC (A15457H) at a dose of 2000 mg/kg body weight was applied dermally to 5 male and 5 female CRL:(WI) rats, followed by a 14-day observation period. The test item was applied as supplied by the Sponsor. The application period was 24 hours. Clinical observations were assessed in all animals at 1 and 5 hours after dosing and daily for 14 days thereafter. Body weight was measured prior to dosing on Day 0 and on Days 7 and 14. All animals were euthanized and subjected to a gross macroscopic examination at the end of the 14-day observation period (Day 14). 14",
"valueDescription": "Joining all values of type doses_(mg_kg_bw) with ' '",
"componentRuleId": "Necropsy.1.0",
"componentLogEntityReferences": [
{
"id": "c1bf6261c8dc8f8f6aa0d6fe5c6553bd",
"type": "doses_(mg_kg_bw)",
"entityRuleId": "DOC.35.0",
"page": 10
},
{
"id": "ede065ea1725687b77490a484aa2d9e8",
"type": "doses_(mg_kg_bw)",
"entityRuleId": "DOC.35.0",
"page": 10
},
{
"id": "1210a0f7ffd1c0d558d330a09241bc7d",
"type": "doses_(mg_kg_bw)",
"entityRuleId": "DOC.35.0",
"page": 10
}
]
}
]
},
{
"name": "Mortality_Statement",
"componentValues": [
{
"value": "No mortality occurred on the study. 35",
"originalValue": "No mortality occurred on the study. 35",
"valueDescription": "Joining all values of type mortality_statement with ' '",
"componentRuleId": "MortalityStatement.0.0",
"componentLogEntityReferences": [
{
"id": "0ae4b2b53905f238cf17c20df26f209d",
"type": "mortality_statement",
"entityRuleId": "DOC.32.0",
"page": 16
},
{
"id": "849e9e6c36d5c510225587c21d66b18d",
"type": "mortality_statement",
"entityRuleId": "DOC.32.0",
"page": 16
}
]
}
]
},
{
"name": "Weight_Behavior_Changes",
"componentValues": [
{
"value": "No mortality occurred during the study.\nNo adverse clinical signs were observed after treatment with the test item during the 14 day observation period. Erythema was noted in all animals (10/10) on Day 1 only. All animals were symptom free from 2 days after the treatment.\nThere were no treatment related effects on body weight or body weight gain during the observation period.\nThere was no evidence of the test item-related observations at a dose level of 2000 mg/kg bw at necropsy.\n15",
"originalValue": "No mortality occurred during the study.\nNo adverse clinical signs were observed after treatment with the test item during the 14 day observation period. Erythema was noted in all animals (10/10) on Day 1 only. All animals were symptom free from 2 days after the treatment.\nThere were no treatment related effects on body weight or body weight gain during the observation period.\nThere was no evidence of the test item-related observations at a dose level of 2000 mg/kg bw at necropsy.\n15",
"valueDescription": "Joining all values of type weight_behavior_changes with '\n'",
"componentRuleId": "WeightBehavior.0.0",
"componentLogEntityReferences": [
{
"id": "952c0822930bf5b8e2026f96cd7d9b37",
"type": "weight_behavior_changes",
"entityRuleId": "DOC.16.0",
"page": 10
},
{
"id": "6ce01344b447329c1afa3f1f846173f0",
"type": "weight_behavior_changes",
"entityRuleId": "DOC.16.0",
"page": 10
},
{
"id": "8ffd807ffd5ca21c759c78f54cd87f4f",
"type": "weight_behavior_changes",
"entityRuleId": "DOC.16.0",
"page": 10
},
{
"id": "9eeb75725d19bc1f13330aa9cdaa3fdc",
"type": "weight_behavior_changes",
"entityRuleId": "DOC.16.0",
"page": 10
},
{
"id": "a74be4f45046f442315f472490e39e59",
"type": "weight_behavior_changes",
"entityRuleId": "DOC.16.0",
"page": 10
}
]
}
]
},
{
"name": "Necropsy_Findings",
"componentValues": [
{
"value": "No treatment related macroscopic findings were observed. There was no evidence of the test item-related observations at a dose level of 2000 mg/kg bw at necropsy. 39",
"originalValue": "No treatment related macroscopic findings were observed. There was no evidence of the test item-related observations at a dose level of 2000 mg/kg bw at necropsy. 39",
"valueDescription": "Joining all values of type necropsy_findings with ' '",
"componentRuleId": "Necropsy.0.0",
"componentLogEntityReferences": [
{
"id": "c0c22ea4e6dda938468d4be3102334ae",
"type": "necropsy_findings",
"entityRuleId": "DOC.17.0",
"page": 16
},
{
"id": "799d19b6a371f575c77e988ba7e23063",
"type": "necropsy_findings",
"entityRuleId": "DOC.17.0",
"page": 16
},
{
"id": "24edc84baf21ef6bb37c5b20801d5e84",
"type": "necropsy_findings",
"entityRuleId": "DOC.17.0",
"page": 16
}
]
}
]
},
{
"name": "Deviation_from_the_Guideline",
"componentValues": [
{
"value": "",
"originalValue": "",
"valueDescription": "Joining all values of type with '\n'",
"componentRuleId": "GuidelineDeviation.0.0",
"componentLogEntityReferences": []
}
]
},
{
"name": "Conclusion_LD50_Greater_than",
"componentValues": [
{
"value": "Greater than",
"originalValue": "Greater than",
"valueDescription": "Entity of type 'ld50_greater' found",
"componentRuleId": "Conclusion.1.0",
"componentLogEntityReferences": [
{
"id": "311a441f815daaffc20453a79712a684",
"type": "ld50_greater",
"entityRuleId": "DOC.10.0",
"page": 10
},
{
"id": "107db9f46656e13234c90b9a3a57b694",
"type": "ld50_greater",
"entityRuleId": "DOC.10.0",
"page": 11
},
{
"id": "2c788c7a7118ef9bb18edf7d5e7dbc7b",
"type": "ld50_greater",
"entityRuleId": "DOC.10.0",
"page": 16
}
]
}
]
},
{
"name": "Conclusion_LD50_mg_per_kg",
"componentValues": [
{
"value": "2000",
"originalValue": "2000",
"valueDescription": "Joining all unique values of type ld50_value with ', '",
"componentRuleId": "Conclusion.0.0",
"componentLogEntityReferences": [
{
"id": "fff9617f8d11bd678e1d17ee330d0eef",
"type": "ld50_value",
"entityRuleId": "DOC.10.0",
"page": 10
},
{
"id": "2ef271bd35871a6266f456a7c4360042",
"type": "ld50_value",
"entityRuleId": "DOC.10.0",
"page": 16
}
]
}
]
},
{
"name": "Conclusion_Minimum_Confidence",
"componentValues": [
{
"value": "",
"originalValue": "",
"valueDescription": "Joining all unique values of type with ', '",
"componentRuleId": "Conclusion.2.0",
"componentLogEntityReferences": []
}
]
},
{
"name": "Conclusion_Maximum_Confidence",
"componentValues": [
{
"value": "",
"originalValue": "",
"valueDescription": "Joining all unique values of type with ', '",
"componentRuleId": "Conclusion.3.0",
"componentLogEntityReferences": []
}
]
},
{
"name": "Study_Conclusion",
"componentValues": [
{
"value": "The median lethal dose of SYN545192 EC (A15457H) after a single dermal administration was found to be greater than 2000 mg/kg bw in male and female CRL:(WI) rats.",
"originalValue": "The median lethal dose of SYN545192 EC (A15457H) after a single dermal administration was found to be greater than 2000 mg/kg bw in male and female CRL:(WI) rats.",
"valueDescription": "Joining all values of type study_conclusion with ' '",
"componentRuleId": "StudyConclusion.0.0",
"componentLogEntityReferences": [
{
"id": "2fd7f1df547bbea6932344ded3d0a7bb",
"type": "study_conclusion",
"entityRuleId": "DOC.15.0",
"page": 10
}
]
}
]
},
{
"name": "laboratory_country",
"componentValues": [
{
"value": "Hungary",
"originalValue": "Hungary",
"valueDescription": "Unmapped Entity",
"componentRuleId": "DefaultComponents.999.0",
"componentLogEntityReferences": [
{
"id": "d469a79eedff7c52b006ae34b36a7ff8",
"type": "laboratory_country",
"entityRuleId": "DOC.7.2",
"page": 1
}
]
},
{
"value": "Hungary",
"originalValue": "Hungary",
"valueDescription": "Unmapped Entity",
"componentRuleId": "DefaultComponents.999.0",
"componentLogEntityReferences": [
{
"id": "9593a204d3530a8bb90cab1921cf57c1",
"type": "laboratory_country",
"entityRuleId": "DOC.7.2",
"page": 1
}
]
},
{
"value": "United Kingdom",
"originalValue": "United Kingdom",
"valueDescription": "Unmapped Entity",
"componentRuleId": "DefaultComponents.999.0",
"componentLogEntityReferences": [
{
"id": "1b968e9b5ce3e90e4158c5353facb78f",
"type": "laboratory_country",
"entityRuleId": "DOC.7.1",
"page": 1
}
]
}
]
},
{
"name": "oecd_guideline",
"componentValues": [
{
"value": "OECD 402 (1987)",
"originalValue": "OECD 402 (1987)",
"valueDescription": "Unmapped Entity",
"componentRuleId": "DefaultComponents.999.0",
"componentLogEntityReferences": [
{
"id": "0adce062717031fcb3130cb4b5121220",
"type": "oecd_guideline",
"entityRuleId": "DOC.1.0",
"page": 1
}
]
}
]
},
{
"name": "study_conclusion",
"componentValues": [
{
"value": "The median lethal dose of SYN545192 EC (A15457H) after a single dermal administration was found to be greater than 2000 mg/kg bw in male and female CRL:(WI) rats.",
"originalValue": "The median lethal dose of SYN545192 EC (A15457H) after a single dermal administration was found to be greater than 2000 mg/kg bw in male and female CRL:(WI) rats.",
"valueDescription": "Unmapped Entity",
"componentRuleId": "DefaultComponents.999.0",
"componentLogEntityReferences": [
{
"id": "f55749c2ff48055d2c2fa7dd08adde62",
"type": "study_conclusion",
"entityRuleId": "DOC.15.0",
"page": 16
}
]
}
]
},
{
"name": "study_design",
"componentValues": [
{
"value": "A single administration of SYN545192 EC (A15457H) at a dose of 2000 mg/kg body weight was applied dermally to 5 male and 5 female CRL:(WI) rats, followed by a 14-day observation period. The test item was applied as supplied by the Sponsor. The application period was 24 hours.",
"originalValue": "A single administration of SYN545192 EC (A15457H) at a dose of 2000 mg/kg body weight was applied dermally to 5 male and 5 female CRL:(WI) rats, followed by a 14-day observation period. The test item was applied as supplied by the Sponsor. The application period was 24 hours.",
"valueDescription": "Unmapped Entity",
"componentRuleId": "DefaultComponents.999.0",
"componentLogEntityReferences": [
{
"id": "5da351be47fa414cfb7f833d3ca87f5e",
"type": "study_design",
"entityRuleId": "DOC.20.0",
"page": 10
}
]
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{
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