Pull request #183: RSS-127: Added report for rss poc 2
Merge in RED/redaction-report-service from RSS-127 to master * commit '174a7e88b451adf0082284eb33c39315f1b89e1e': RSS-127: Added report for rss poc 2
This commit is contained in:
Dominique Eiflaender
commit
72f9767c2f
@ -6,7 +6,7 @@ import org.springframework.web.bind.annotation.RestController;
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import com.iqser.red.service.redaction.report.v1.api.model.rss.RSSResponse;
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import com.iqser.red.service.redaction.report.v1.api.resource.RSSResource;
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import com.iqser.red.service.redaction.report.v1.server.service.RSSService;
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import com.iqser.red.service.redaction.report.v1.server.service.RSSPoc2Service;
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import lombok.RequiredArgsConstructor;
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@ -14,7 +14,7 @@ import lombok.RequiredArgsConstructor;
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@RequiredArgsConstructor
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public class RSSController implements RSSResource {
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private final RSSService rSSService;
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private final RSSPoc2Service rSSService;
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public RSSResponse getRSS(@PathVariable(DOSSIER_ID) String dossierId, @RequestParam(value = "fileId", required = false) String fileId) {
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@ -41,7 +41,7 @@ public class GeneratePlaceholderService {
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private final FileAttributesConfigClient fileAttributesClient;
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private final DossierAttributesClient dossierAttributesClient;
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private final DossierAttributesConfigClient dossierAttributesConfigClient;
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private final RSSService rSSService;
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private final RSSPoc2Service rSSService;
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public PlaceholderModel buildPlaceholders(Dossier dossier) {
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@ -0,0 +1,347 @@
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package com.iqser.red.service.redaction.report.v1.server.service;
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import java.text.BreakIterator;
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import java.util.ArrayList;
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import java.util.Comparator;
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import java.util.HashMap;
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import java.util.HashSet;
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import java.util.Iterator;
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import java.util.List;
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import java.util.Locale;
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import java.util.Map;
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import java.util.Set;
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import java.util.TreeMap;
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import java.util.stream.Collectors;
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import javax.annotation.PostConstruct;
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import org.springframework.stereotype.Service;
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import com.iqser.red.service.persistence.service.v1.api.model.dossiertemplate.dossier.file.FileModel;
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import com.iqser.red.service.redaction.report.v1.api.model.rss.RSSFileResponse;
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import com.iqser.red.service.redaction.report.v1.api.model.rss.RSSResponse;
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import com.iqser.red.service.redaction.report.v1.server.client.FileStatusClient;
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import com.iqser.red.service.redaction.report.v1.server.client.RedactionLogClient;
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import com.iqser.red.service.redaction.v1.model.ChangeType;
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import com.iqser.red.service.redaction.v1.model.RedactionLog;
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import com.iqser.red.service.redaction.v1.model.RedactionLogEntry;
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import lombok.RequiredArgsConstructor;
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@Service
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@RequiredArgsConstructor
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public class RSSPoc2Service {
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private final RedactionLogClient redactionLogClient;
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private final FileStatusClient statusClient;
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private final Map<String, Set<String>> guidelineMapping = new HashMap<>();
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@PostConstruct
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public void init() {
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guidelineMapping.put("Nº 425: Acute oral Toxicity - Up-and-Down Procedure (03/10/2008)", Set.of("OECD 425 (2008)", "OECD No. 425 (2008)"));
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guidelineMapping.put("Nº 425: Acute oral Toxicity - Up-and-Down Procedure (17/12/2001)", Set.of("OECD 425 (2001)", "OECD No. 425 (2001)"));
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guidelineMapping.put("Nº 402: Acute Dermal Toxicity (09/10/2017)", Set.of("OECD 402 (2017)", "OECD No. 402 (2017)"));
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guidelineMapping.put("Nº 402: Acute Dermal Toxicity (24/02/1987)", Set.of("OECD 402 (1987)", "OECD No. 402 (1987)"));
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guidelineMapping.put("Nº 403: Acute Inhalation Toxicity (08/09/2009)", Set.of("OECD 403 (2009)", "OECD No. 403 (2009)"));
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guidelineMapping.put("Nº 403: Acute Inhalation Toxicity (12/05/1981)", Set.of("OECD 403 (1981)", "OECD No. 403 (1981)"));
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guidelineMapping.put("Nº 433: Acute Inhalation Toxicity: Fixed Concentration Procedure (27/06/2018)", Set.of("OECD 433 (2018)", "OECD No. 433 (2018)"));
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guidelineMapping.put("Nº 433: Acute Inhalation Toxicity: Fixed Concentration Procedure (09/10/2017)", Set.of("OECD 433 (2017)", "OECD No. 433 (2017)"));
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guidelineMapping.put("Nº 436: Acute Inhalation Toxicity – Acute Toxic Class Method (08/09/2009)", Set.of("OECD 436 (2009)", "OECD No. 436 (2009)"));
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guidelineMapping.put("Nº 404: Acute Dermal Irritation/Corrosion (12/05/1981)", Set.of("OECD 404 (1981)", "OECD No. 404 (1981)"));
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guidelineMapping.put("Nº 404: Acute Dermal Irritation/Corrosion (17/07/1992)", Set.of("OECD 404 (1992)", "OECD No. 404 (1992)"));
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guidelineMapping.put("Nº 404: Acute Dermal Irritation/Corrosion (24/04/2002)", Set.of("OECD 404 (2002)", "OECD No. 404 (2002)"));
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guidelineMapping.put("Nº 404: Acute Dermal Irritation/Corrosion (28/07/2015)", Set.of("OECD 405 (2017)", "OECD No. 405 (2017)"));
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guidelineMapping.put("Nº 405: Acute Eye Irritation/Corrosion (09/10/2017)", Set.of("OECD 405 (2017)", "OECD No. 405 (2017)"));
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guidelineMapping.put("Nº 405: Acute Eye Irritation/Corrosion (02/10/2012)", Set.of("OECD 405 (2012)", "OECD No. 405 (2012)"));
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guidelineMapping.put("Nº 405: Acute Eye Irritation/Corrosion (24/04/2002)", Set.of("OECD 405 (2002)", "OECD No. 405 (2002)"));
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guidelineMapping.put("Nº 405: Acute Eye Irritation/Corrosion (24/02/1987)", Set.of("OECD 405 (1987)", "OECD No. 405 (1987)"));
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guidelineMapping.put("Nº 429: Skin Sensitisation: Local Lymph Node Assay (24/04/2002)", Set.of("OECD 429 (2002)", "OECD No. 429 (2002)"));
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guidelineMapping.put("Nº 429: Skin Sensitisation (23/07/2010)", Set.of("OECD 429 (2010)", "OECD No. 429 (2010)"));
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guidelineMapping.put("Nº 442A: Skin Sensitization (23/07/2018)", Set.of("ÖECD 442A (2018)", "ÖECD No. 442A (2018)"));
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guidelineMapping.put("Nº 442B: Skin Sensitization (27/06/2018)", Set.of("ÖECD 442B (2018)", "ÖECD No. 442B (2018)"));
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guidelineMapping.put("Nº 471: Bacterial Reverse Mutation Test (21/07/1997)", Set.of("OECD 471 (1997)", "OECD No. 471 (1997)"));
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guidelineMapping.put("Nº 471: Bacterial Reverse Mutation Test (26/06/2020)", Set.of("OECD 471 (2020)", "OECD No. 471 (2020)"));
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}
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public RSSResponse getRSS(String dossierId, String fileId) {
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List<FileModel> files = new ArrayList<>();
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if (fileId != null) {
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files.add(statusClient.getFileStatus(dossierId, fileId));
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} else {
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files.addAll(statusClient.getDossierStatus(dossierId));
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}
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List<RSSFileResponse> rssFileResponses = new ArrayList<>();
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for (FileModel file : files) {
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Map<String, String> resultMap = new TreeMap<>();
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var redactionLog = redactionLogClient.getRedactionLog(dossierId, file.getId(), new ArrayList<>(), true, false);
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redactionLog.getRedactionLogEntry().removeIf(r -> !r.isRedacted() || r.getChanges().get(r.getChanges().size() - 1).getType().equals(ChangeType.REMOVED));
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resultMap.put("TEST_GUIDELINE(S):_1", getTestGuideline1(redactionLog));
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var testGuideline2 = getTestGuideline2(redactionLog);
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if (testGuideline2 != null) {
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resultMap.put("TEST_GUIDELINE(S):_2", testGuideline2);
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}
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resultMap.put("Report_Number:", getReportNumber(redactionLog));
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resultMap.put("Experimental_Starting_Date:", getExperimentalStartDate(redactionLog));
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resultMap.put("Experimental_Completion_Date:", getExperimentalEndDate(redactionLog));
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resultMap.put("Species", getSpecies(redactionLog));
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resultMap.put("Strain", getStrain(redactionLog));
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var macroscopicFindingSentences = getMacroscopicFindings(redactionLog);
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int i = 1;
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for (String macroscopicFindingSentence : macroscopicFindingSentences) {
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resultMap.put("Macroscopic_Findings_" + i, macroscopicFindingSentence);
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i++;
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}
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resultMap.put("Study_Title", getTitle(redactionLog));
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resultMap.put("GLP_Study", getGlpStudy(redactionLog));
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resultMap.put("Certificate_of_Analysis,_Batch_Identification", getBatchNumber(redactionLog));
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var clinicalSignsSentences = getClinicalSigns(redactionLog);
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i = 1;
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for (String clinicalSignsSentence : clinicalSignsSentences) {
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resultMap.put("Clincal_Signs_" + i, clinicalSignsSentence);
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i++;
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}
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resultMap.put("Dosages", getDosages(redactionLog));
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var mortalitySentences = getMortality(redactionLog);
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i = 1;
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for (String mortalitySentence : mortalitySentences) {
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resultMap.put("Mortality_" + i, mortalitySentence);
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i++;
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}
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rssFileResponses.add(new RSSFileResponse(file.getFilename(), resultMap));
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}
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rssFileResponses.sort(Comparator.comparing(RSSFileResponse::getFilename));
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return new RSSResponse(rssFileResponses);
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}
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private String getDosages(RedactionLog redactionLog) {
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var dosages = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("dosages")).map(RedactionLogEntry::getValue).findFirst();
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return dosages.orElse("");
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}
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private List<String> getMortality(RedactionLog redactionLog) {
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List<String> mortality = new ArrayList<>();
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var mortalityString = redactionLog.getRedactionLogEntry()
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.stream()
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.filter(r -> r.getType().equals("mortality"))
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.map(RedactionLogEntry::getValue)
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.findFirst();
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if (!mortalityString.isPresent()) {
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return mortality;
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}
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String source = mortalityString.get();
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BreakIterator iterator = BreakIterator.getSentenceInstance(Locale.US);
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iterator.setText(source);
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int start = iterator.first();
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for (int end = iterator.next(); end != BreakIterator.DONE; start = end, end = iterator.next()) {
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mortality.add(source.substring(start, end));
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}
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return mortality;
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}
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private List<String> getClinicalSigns(RedactionLog redactionLog) {
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List<String> clinicalSigns = new ArrayList<>();
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var clinicalSignsString = redactionLog.getRedactionLogEntry()
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.stream()
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.filter(r -> r.getType().equals("clinical_signs"))
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.map(RedactionLogEntry::getValue)
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.findFirst();
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if (!clinicalSignsString.isPresent()) {
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return clinicalSigns;
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}
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String source = clinicalSignsString.get();
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BreakIterator iterator = BreakIterator.getSentenceInstance(Locale.US);
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iterator.setText(source);
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int start = iterator.first();
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for (int end = iterator.next(); end != BreakIterator.DONE; start = end, end = iterator.next()) {
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clinicalSigns.add(source.substring(start, end));
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}
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return clinicalSigns;
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}
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private String getBatchNumber(RedactionLog redactionLog) {
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var batchNumber = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("batch_number")).map(RedactionLogEntry::getValue).findFirst();
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return batchNumber.orElse("");
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}
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private String getGlpStudy(RedactionLog redactionLog) {
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var glpStudy = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("glp_study")).map(RedactionLogEntry::getValue).findFirst();
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if (glpStudy.isPresent()) {
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return "Yes";
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}
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return "No";
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}
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private String getTitle(RedactionLog redactionLog) {
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var title = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("title")).map(RedactionLogEntry::getValue).findFirst();
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return title.orElse("");
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}
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private List<String> getMacroscopicFindings(RedactionLog redactionLog) {
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List<String> macroscopicFindings = new ArrayList<>();
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var macroscopicFindingString = redactionLog.getRedactionLogEntry()
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.stream()
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.filter(r -> r.getType().equals("macroscopic_findings"))
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.map(RedactionLogEntry::getValue)
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.findFirst();
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if (!macroscopicFindingString.isPresent()) {
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return macroscopicFindings;
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}
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String source = macroscopicFindingString.get();
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BreakIterator iterator = BreakIterator.getSentenceInstance(Locale.US);
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iterator.setText(source);
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int start = iterator.first();
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for (int end = iterator.next(); end != BreakIterator.DONE; start = end, end = iterator.next()) {
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macroscopicFindings.add(source.substring(start, end));
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}
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return macroscopicFindings;
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}
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private String getStrain(RedactionLog redactionLog) {
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var strain = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("strain")).map(RedactionLogEntry::getValue).findFirst();
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return strain.orElse("");
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}
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private String getSpecies(RedactionLog redactionLog) {
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var species = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("species")).map(RedactionLogEntry::getValue).findFirst();
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return species.orElse("");
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}
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private String getExperimentalEndDate(RedactionLog redactionLog) {
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var experimentalEndDate = redactionLog.getRedactionLogEntry()
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.stream()
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.filter(r -> r.getType().equals("experimental_end_date"))
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.map(RedactionLogEntry::getValue)
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.findFirst();
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return experimentalEndDate.orElse("");
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}
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private String getExperimentalStartDate(RedactionLog redactionLog) {
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var experimentalStartDate = redactionLog.getRedactionLogEntry()
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.stream()
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.filter(r -> r.getType().equals("experimental_start_date"))
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.map(RedactionLogEntry::getValue)
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.findFirst();
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return experimentalStartDate.orElse("");
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}
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private String getReportNumber(RedactionLog redactionLog) {
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var reportNumber = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("report_number")).map(RedactionLogEntry::getValue).findFirst();
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return reportNumber.orElse("");
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}
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private String getTestGuideline1(RedactionLog redactionLog) {
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var guideline = redactionLog.getRedactionLogEntry().stream().filter(r -> r.getType().equals("oecd_guideline")).map(RedactionLogEntry::getValue).findFirst();
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if (guideline.isPresent()) {
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return mapGuideline(guideline.get());
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}
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return "";
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}
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private String getTestGuideline2(RedactionLog redactionLog) {
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List<String> guidelines = new ArrayList<>();
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guidelines.addAll(redactionLog.getRedactionLogEntry()
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.stream()
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.filter(r -> r.getType().equals("epa_guideline"))
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.map(RedactionLogEntry::getValue)
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.collect(Collectors.toList()));
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guidelines.addAll(redactionLog.getRedactionLogEntry()
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.stream()
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.filter(r -> r.getType().equals("ec_guideline"))
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.map(RedactionLogEntry::getValue)
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.collect(Collectors.toList()));
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StringBuilder stringBuilder = new StringBuilder();
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Iterator<String> itty = guidelines.iterator();
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while (itty.hasNext()) {
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stringBuilder.append(itty.next());
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if (itty.hasNext()) {
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stringBuilder.append(", ");
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}
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}
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return !stringBuilder.toString().isEmpty() ? stringBuilder.toString() : null;
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}
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private String mapGuideline(String guideline) {
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for (Map.Entry<String, Set<String>> entry : guidelineMapping.entrySet()) {
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if (entry.getValue().contains(guideline)) {
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return entry.getKey();
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}
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}
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return "No mapping found for: " + guideline;
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}
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}
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