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RED-6093: Prototype find entities in rules

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*added a prototype paragraph rule
This commit is contained in:
Kilian Schuettler 2023-02-15 16:51:16 +01:00 committed by Kilian Schuettler
parent 525b8d6434
commit 56d7fa950c
5 changed files with 344 additions and 304 deletions
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61
redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/model/Paragraph.java Normal file
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@ -0,0 +1,61 @@
package com.iqser.red.service.redaction.v1.server.redaction.model;
import static com.iqser.red.service.redaction.v1.server.redaction.model.SearchableText.buildString;
import java.util.List;
import com.iqser.red.service.redaction.v1.server.classification.model.TextBlock;
import com.iqser.red.service.redaction.v1.server.parsing.model.RedTextPosition;
import com.iqser.red.service.redaction.v1.server.parsing.model.TextPositionSequence;
import lombok.Getter;
@Getter
public class Paragraph {
private final String searchText;
private final List<RedTextPosition> textPositions;
private final int[] searchTextToPositions;
private final int sectionNumber;
private final int start;
private final int end;
public Paragraph(TextBlock textBlock, int sectionNumber, int start, int end) {
textPositions = textBlock.getSequences().stream().map(TextPositionSequence::getTextPositions).flatMap(List::stream).toList();
this.searchTextToPositions = new int[textPositions.size()];
this.searchText = buildString(textBlock.getSequences());
this.start = start;
this.end = end;
this.sectionNumber = sectionNumber;
}
public boolean containsEntity(Entity entity) {
return entity.getStart() >= start && entity.getEnd() <= end;
}
private String buildSearchText() {
StringBuilder searchTextBuilder = new StringBuilder();
int numberOfNormalCharacters = 0;
for (int i = 0; i < textPositions.size(); ++i) {
if (isNormalText(textPositions.get(i).getUnicode())) {
searchTextBuilder.append(textPositions.get(i).getUnicode());
this.searchTextToPositions[numberOfNormalCharacters] = i;
++numberOfNormalCharacters;
}
}
return searchTextBuilder.toString();
}
private boolean isNormalText(String unicode) {
return !unicode.equals("\n") && //
!unicode.equals("");
}
}

16
redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/model/SectionSearchableTextPair.java
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@ -1,16 +0,0 @@
package com.iqser.red.service.redaction.v1.server.redaction.model;
import java.util.List;
import lombok.AllArgsConstructor;
import lombok.Data;
@Data
@AllArgsConstructor
public class SectionSearchableTextPair {
private Section section;
private SearchableText searchableText;
private List<Integer> cellStarts;
}

26
redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/service/DroolsExecutionService.java
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@ -1,5 +1,13 @@
package com.iqser.red.service.redaction.v1.server.redaction.service;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
import java.util.HashMap;
import java.util.HashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.io.ByteArrayInputStream;
import java.io.InputStream;
import java.nio.charset.StandardCharsets;
@ -16,6 +24,15 @@ import org.kie.api.runtime.KieContainer;
import org.kie.api.runtime.KieSession;
import org.springframework.stereotype.Service;
import com.iqser.red.service.redaction.v1.server.client.RulesClient;
import com.iqser.red.service.redaction.v1.server.exception.RulesValidationException;
import com.iqser.red.service.redaction.v1.server.redaction.model.Dictionary;
import com.iqser.red.service.redaction.v1.server.redaction.model.Entity;
import com.iqser.red.service.redaction.v1.server.redaction.model.Paragraph;
import com.iqser.red.service.redaction.v1.server.redaction.model.Section;
import io.micrometer.core.annotation.Timed;
import lombok.RequiredArgsConstructor;
import com.google.common.cache.CacheBuilder;
import com.google.common.cache.CacheLoader;
import com.google.common.cache.LoadingCache;
@ -71,15 +88,16 @@ public class DroolsExecutionService {
@Timed("redactmanager_executeRules")
public Section executeRules(KieContainer kieContainer, Section section) {
public List<Section> executeRules(KieContainer kieContainer, List<Section> sections, List<Paragraph> paragraphs, Dictionary dictionary) {
Set<Entity> entities = new HashSet<>();
KieSession kieSession = kieContainer.newKieSession();
kieSession.setGlobal("section", section);
kieSession.insert(section);
sections.forEach(kieSession::insert);
paragraphs.forEach(kieSession::insert);
kieSession.fireAllRules();
kieSession.dispose();
return section;
return sections;
}

2
redaction-service-v1/redaction-service-server-v1/src/main/java/com/iqser/red/service/redaction/v1/server/redaction/utils/EntitySearchUtils.java
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@ -99,7 +99,7 @@ public final class EntitySearchUtils {
List<Entity> orderedEntities = entitiesByWord.get(word).stream().sorted(Comparator.comparing(Entity::getStart)).collect(Collectors.toList());
Entity firstEntity = orderedEntities.get(0);
List<EntityPositionSequence> positionSequences = text.getSequences(firstEntity.getWord().trim(),
List<EntityPositionSequence> positionSequences = text.getSequences(word.trim(),
dictionary == null || dictionary.isCaseInsensitiveDictionary(firstEntity.getType()),
firstEntity.getTargetSequences());

543
redaction-service-v1/redaction-service-server-v1/src/test/resources/drools/rules.drl
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@ -1,413 +1,390 @@
package drools
import com.iqser.red.service.redaction.v1.server.redaction.model.Section
global Section section
import com.iqser.red.service.redaction.v1.server.redaction.model.*
// --------------------------------------- CBI rules -------------------------------------------------------------------
//rule "0: Expand CBI Authors with firstname initials"
// when
// Section(matchesType("CBI_author"))
// then
// section.expandByRegEx("CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1);
// end
rule "-1: Find dictionary entries"
// --------------------------------------- AI rules -------------------------------------------------------------------
rule "-1: find entities from dictionary"
salience 100
no-loop true
when
Section(findDictionaryEntities());
section: Section(!text.isEmpty())
then
end
section.findDictionaryEntities();
update(section);
end
rule "0: Add CBI_author from ai"
when
Section(aiMatchesType("CBI_author"))
section: Section(aiMatchesType("CBI_author"))
then
section.addAiEntities("CBI_author", "CBI_author");
end
rule "0: Combine ai types CBI_author from ai"
rule "0: Combine address parts from ai to CBI_address (org is mandatory)"
when
Section(aiMatchesType("ORG"))
section: Section(aiMatchesType("ORG"))
then
section.combineAiTypes("ORG", "STREET,POSTAL,COUNTRY,CARDINAL,CITY,STATE", 20, "CBI_address", 3, false);
end
rule "0: Expand CBI Authors with firstname initials"
rule "0: Combine address parts from ai to CBI_address (street is mandatory)"
when
Section(matchesType("CBI_author"))
section: Section(aiMatchesType("STREET"))
then
section.expandByRegEx("CBI_author", "(,? [A-Z]\\.?( ?[A-Z]\\.?)?( ?[A-Z]\\.?)?\\b\\.?)", false, 1, "[^\\s]+");
section.combineAiTypes("STREET", "ORG,POSTAL,COUNTRY,CARDINAL,CITY,STATE", 20, "CBI_address", 3, false);
end
rule "0: Expand CBI_author and PII matches with salutation prefix"
rule "0: Combine address parts from ai to CBI_address (city is mandatory)"
when
Section((matchesType("CBI_author") || matchesType("PII")) && (
searchText.contains("Mr")
|| searchText.contains("Mrs")
|| searchText.contains("Ms")
|| searchText.contains("Miss")
|| searchText.contains("Sir")
|| searchText.contains("Madam")
|| searchText.contains("Madame")
|| searchText.contains("Mme")
))
section: Section(aiMatchesType("CITY"))
then
section.expandByPrefixRegEx("CBI_author", "\\b(Mrs?|Ms|Miss|Sir|Madame?|Mme)\\s?\\.?\\s*", false, 0);
section.expandByPrefixRegEx("PII", "\\b(Mrs?|Ms|Miss|Sir|Madame?|Mme)\\s?\\.?\\s*", false, 0);
section.combineAiTypes("CITY", "ORG,STREET,POSTAL,COUNTRY,CARDINAL,STATE", 20, "CBI_address", 3, false);
end
rule "1: Redacted because Section contains Vertebrate"
// --------------------------------------- CBI rules -------------------------------------------------------------------
rule "1: Redact CBI Authors (Non vertebrate study)"
when
Section(matchesType("vertebrate"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && matchesType("CBI_author"))
then
section.redact("CBI_author", 1, "Vertebrate found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redact("CBI_address", 1, "Vertebrate found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redact("CBI_author", 1, "Author found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "2: Redact CBI Authors (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && matchesType("CBI_author"))
then
section.redact("CBI_author", 2, "Author found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "2: Not Redacted because Section contains no Vertebrate"
rule "3: Redact not CBI Address (Non vertebrate study)"
when
Section(!matchesType("vertebrate"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && matchesType("CBI_address"))
then
section.redactNot("CBI_author", 2, "No Vertebrate found");
section.redactNot("CBI_address", 2, "No Vertebrate found");
section.redactNot("CBI_address", 3, "Address found for non vertebrate study");
section.ignoreRecommendations("CBI_address");
end
rule "4: Redact CBI Address (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && matchesType("CBI_address"))
then
section.redact("CBI_address", 4, "Address found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "3: Do not redact Names and Addresses if no redaction Indicator is contained"
rule "5: Do not redact genitive CBI_author"
when
Section(matchesType("vertebrate"), matchesType("no_redaction_indicator"))
section: Section(matchesType("CBI_author"))
then
section.redactNot("CBI_author", 3, "Vertebrate and No Redaction Indicator found");
section.redactNot("CBI_address", 3, "Vertebrate and No Redaction Indicator found");
section.expandToFalsePositiveByRegEx("CBI_author", "['’’'ʼˈ´`‘′ʻ’']s", false, 0);
end
rule "4: Redact Names and Addresses if no_redaction_indicator and redaction_indicator is contained"
rule "6: Redact Author(s) cells in Tables with Author(s) header (Non vertebrate study)"
when
Section(matchesType("vertebrate"), matchesType("no_redaction_indicator"), matchesType("redaction_indicator"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && hasTableHeader("Author(s)") && !hasTableHeader("Vertebrate study Y/N"))
then
section.redact("CBI_author", 4, "Vertebrate and Redaction Indicator found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redact("CBI_address", 4, "Vertebrate and Redaction Indicator found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redactCell("Author(s)", 6, "CBI_author", false, "Author found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "7: Redact Author(s) cells in Tables with Author(s) header (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && hasTableHeader("Author(s)") && !hasTableHeader("Vertebrate study Y/N"))
then
section.redactCell("Author(s)", 7, "CBI_author", false, "Author found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "5: Do not redact Names and Addresses if no redaction Indicator is contained"
rule "8: Redact Author cells in Tables with Author header (Non vertebrate study)"
when
Section(matchesType("vertebrate"), matchesType("published_information"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && hasTableHeader("Author") && !hasTableHeader("Vertebrate study Y/N"))
then
section.redactNotAndReference("CBI_author","published_information", 5, "Vertebrate and Published Information found");
section.redactNotAndReference("CBI_address","published_information", 5, "Vertebrate and Published Information found");
section.redactCell("Author", 8, "CBI_author", false, "Author found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "9: Redact Author cells in Tables with Author header (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && hasTableHeader("Author") && !hasTableHeader("Vertebrate study Y/N"))
then
section.redactCell("Author", 9, "CBI_author", false, "Author found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "6: Not redacted because Vertebrate Study = N"
rule "10: Redact and recommand Authors in Tables with Vertebrate study Y/N header (Non vertebrate study)"
when
Section(rowEquals("Vertebrate study Y/N", "N") || rowEquals("Vertebrate study Y/N", "No"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && (rowEquals("Vertebrate study Y/N", "Y") || rowEquals("Vertebrate study Y/N", "Yes") || rowEquals("Vertebrate study Y/N", "N") || rowEquals("Vertebrate study Y/N", "No")))
then
section.redactNotCell("Author(s)", 6, "CBI_author", true, "Not redacted because row is not a vertebrate study");
section.redactNot("CBI_author", 6, "Not redacted because row is not a vertebrate study");
section.redactNot("CBI_address", 6, "Not redacted because row is not a vertebrate study");
section.highlightCell("Vertebrate study Y/N", 6, "hint_only");
section.redactCell("Author(s)", 10, "CBI_author", true, "Author found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "11: Redact and recommand Authors in Tables with Vertebrate study Y/N header (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && (rowEquals("Vertebrate study Y/N", "Y") || rowEquals("Vertebrate study Y/N", "Yes") || rowEquals("Vertebrate study Y/N", "N") || rowEquals("Vertebrate study Y/N", "No")))
then
section.redactCell("Author(s)", 11, "CBI_author", true, "Author found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "14: Redact and add recommendation for et al. author (Non vertebrate study)"
when
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && searchText.contains("et al"))
then
section.redactAndRecommendByRegEx("\\b([A-ZÄÖÜ][^\\s\\.,]+( [A-ZÄÖÜ]{1,2}\\.?)?( ?[A-ZÄÖÜ]\\.?)?) et al\\.?", false, 1, "CBI_author", 14, "Author found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "15: Redact and add recommendation for et al. author (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && searchText.contains("et al"))
then
section.redactAndRecommendByRegEx("\\b([A-ZÄÖÜ][^\\s\\.,]+( [A-ZÄÖÜ]{1,2}\\.?)?( ?[A-ZÄÖÜ]\\.?)?) et al\\.?", false, 1, "CBI_author", 15, "Author found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "7: Redact if must redact entry is found"
rule "16: Add recommendation for Addresses in Test Organism sections"
when
Section(matchesType("must_redact"))
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && searchText.contains("Species:") && searchText.contains("Source:"))
then
section.redact("CBI_author", 7, "must_redact entry was found.", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redact("CBI_address", 7, "must_redact entry was found.", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.recommendLineAfter("Source:", "CBI_address");
end
rule "8: Redact Authors and Addresses in Reference Table if it is a Vertebrate study"
rule "17: Add recommendation for Addresses in Test Animals sections"
when
Section(rowEquals("Vertebrate study Y/N", "Y") || rowEquals("Vertebrate study Y/N", "Yes"))
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && searchText.contains("Species") && searchText.contains("Source"))
then
section.redactCell("Author(s)", 8, "CBI_author", true, "Redacted because row is a vertebrate study", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redact("CBI_address", 8, "Redacted because row is a vertebrate study", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.highlightCell("Vertebrate study Y/N", 8, "must_redact");
section.recommendLineAfter("Source", "CBI_address");
end
/*
rule "9: Redact sponsor company"
rule "18: Do not redact Names and Addresses if Published Information found"
when
Section(searchText.toLowerCase().contains("batches produced at"))
section: Section(matchesType("published_information"))
then
section.redactIfPrecededBy("batches produced at", "CBI_sponsor", 9, "Redacted because it represents a sponsor company", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.addHintAnnotation("batches produced at", "must_redact");
section.redactNotAndReference("CBI_author","published_information", 18, "Published Information found");
section.redactNotAndReference("CBI_address","published_information", 18, "Published Information found");
end
rule "10: Redact determination of residues"
when
Section((
searchText.toLowerCase.contains("determination of residues") ||
searchText.toLowerCase.contains("determination of total residues")
) && (
searchText.toLowerCase.contains("livestock") ||
searchText.toLowerCase.contains("live stock") ||
searchText.toLowerCase.contains("tissue") ||
searchText.toLowerCase.contains("tissues") ||
searchText.toLowerCase.contains("liver") ||
searchText.toLowerCase.contains("muscle") ||
searchText.toLowerCase.contains("bovine") ||
searchText.toLowerCase.contains("ruminant") ||
searchText.toLowerCase.contains("ruminants")
))
then
section.redact("CBI_author", 10, "Determination of residues was found.", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redact("CBI_address", 10, "Determination of residues was found.", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.addHintAnnotation("determination of residues", "must_redact");
section.addHintAnnotation("livestock", "must_redact");
section.addHintAnnotation("live stock", "must_redact");
section.addHintAnnotation("tissue", "must_redact");
section.addHintAnnotation("tissues", "must_redact");
section.addHintAnnotation("liver", "must_redact");
section.addHintAnnotation("muscle", "must_redact");
section.addHintAnnotation("bovine", "must_redact");
section.addHintAnnotation("ruminant", "must_redact");
section.addHintAnnotation("ruminants", "must_redact");
end
rule "11: Redact if CTL/* or BL/* was found"
when
Section(searchText.contains("CTL/") || searchText.contains("BL/"))
then
section.redact("CBI_author", 11, "Laboraty for vertebrate studies found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redact("CBI_address", 11, "Laboraty for vertebrate studies found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.addHintAnnotation("CTL", "must_redact");
section.addHintAnnotation("BL", "must_redact");
end
rule "12: Redact and add recommendation for et al. author"
when
Section(searchText.contains("et al"))
then
section.redactAndRecommendByRegEx("\\b([A-ZÄÖÜ][^\\s\\.,]+( [A-ZÄÖÜ]{1,2}\\.?)?( ?[A-ZÄÖÜ]\\.?)?) et al\\.?", false, 1, "CBI_author", 12, "Author found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
end
rule "13: Add recommendation for Addresses in Test Organism sections"
when
Section(searchText.contains("Species:") && searchText.contains("Source:"))
then
section.recommendLineAfter("Source:", "CBI_address");
end
rule "14: Add recommendation for Addresses in Test Animals sections"
when
Section(searchText.contains("Species") && searchText.contains("Source"))
then
section.recommendLineAfter("Source", "CBI_address");
end
*/
// --------------------------------------- PII rules -------------------------------------------------------------------
rule "14: Redacted PII Personal Identification Information"
rule "19: Redacted PII Personal Identification Information (Non vertebrate study)"
when
Section(matchesType("PII"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && matchesType("PII"))
then
section.redact("PII", 14, "PII (Personal Identification Information) found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redact("PII", 19, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "20: Redacted PII Personal Identification Information (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && matchesType("PII"))
then
section.redact("PII", 20, "Personal information found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "15: Redact Emails by RegEx"
rule "21: Redact Emails by RegEx (Non vertebrate study)"
when
Section(searchText.contains("@"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && searchText.contains("@"))
then
section.redactByRegEx("\\b[A-Z0-9._%+-]+@[A-Z0-9.-]+\\.[A-Z]{2,4}\\b", true, 0, "PII", 15, "PII (Personal Identification Information) found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactByRegEx("\\b([A-Za-z0-9._%+\\-]+@[A-Za-z0-9.\\-]+\\.[A-Za-z\\-]{1,23}[A-Za-z])\\b", true, 1, "PII", 21, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "22: Redact Emails by RegEx (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && searchText.contains("@"))
then
section.redactByRegEx("\\b([A-Za-z0-9._%+\\-]+@[A-Za-z0-9.\\-]+\\.[A-Za-z\\-]{1,23}[A-Za-z])\\b", true, 1, "PII", 22, "Personal information found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "16: Redact contact information"
rule "23: Redact contact information (Non vertebrate study)"
when
Section(text.contains("Contact point:")
|| text.contains("Phone:")
|| text.contains("Fax:")
|| text.contains("Tel.:")
|| text.contains("Tel:")
|| text.contains("E-mail:")
|| text.contains("Email:")
|| text.contains("e-mail:")
|| text.contains("E-mail address:")
|| text.contains("Alternative contact:")
|| text.contains("Telephone number:")
|| text.contains("Telephone No:")
|| text.contains("Fax number:")
|| text.contains("Telephone:")
|| text.contains("European contact:"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && (text.contains("Contact point:")
|| text.contains("Contact:")
|| text.contains("Alternative contact:")
|| (text.contains("No:") && text.contains("Fax"))
|| (text.contains("Contact:") && text.contains("Tel.:"))
|| text.contains("European contact:")
))
then
section.redactLineAfter("Contact point:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Phone:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Fax:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Tel.:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Tel:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("E-mail:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Email:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("e-mail:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("E-mail address:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Contact:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Alternative contact:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Telephone number:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Telephone No:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Fax number:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Telephone:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactBetween("No:", "Fax", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactBetween("Contact:", "Tel.:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("European contact:", "PII", 16, true, "Contact information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Contact point:", "PII", 23, true, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
section.redactLineAfter("Contact:", "PII", 23, true, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
section.redactLineAfter("Alternative contact:", "PII", 23, true, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
section.redactBetween("No:", "Fax", "PII", 23, true, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
section.redactBetween("Contact:", "Tel.:", "PII", 23, true, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
section.redactLineAfter("European contact:", "PII", 23, true, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "17: Redact contact information if applicant is found"
rule "24: Redact contact information (Vertebrate study)"
when
Section(headlineContainsWord("applicant") || text.contains("Applicant") || headlineContainsWord("Primary contact") || headlineContainsWord("Alternative contact") || text.contains("Telephone number:"))
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && (text.contains("Contact point:")
|| text.contains("Contact:")
|| text.contains("Alternative contact:")
|| (text.contains("No:") && text.contains("Fax"))
|| (text.contains("Contact:") && text.contains("Tel.:"))
|| text.contains("European contact:")
))
then
section.redactLineAfter("Contact point:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Phone:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Fax:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Tel.:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Tel:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("E-mail:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Email:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("e-mail:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("E-mail address:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Contact:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Alternative contact:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Telephone number:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Telephone No:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Fax number:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Telephone:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactBetween("No:", "Fax", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactBetween("Contact:", "Tel.:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("European contact:", "PII", 17, true, "Applicant information was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Contact point:", "PII", 24, true, "Personal information found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
section.redactLineAfter("Contact:", "PII", 24, true, "Personal information found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
section.redactLineAfter("Alternative contact:", "PII", 24, true, "Personal information found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
section.redactBetween("No:", "Fax", "PII", 24, true, "Personal information found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
section.redactBetween("Contact:", "Tel.:", "PII", 24, true, "Personal information found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
section.redactLineAfter("European contact:", "PII", 24, true, "Personal information found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "25: Redact Phone and Fax by RegEx (Non vertebrate study)"
when
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && (
text.contains("Contact")
|| text.contains("Telephone")
|| text.contains("Phone")
|| text.contains("Fax")
|| text.contains("Tel")
|| text.contains("Ter")
|| text.contains("Mobile")
|| text.contains("Fel")
|| text.contains("Fer")
))
then
section.redactByRegEx("\\b(contact|telephone|phone|fax|tel|ter|mobile|fel|fer)[a-zA-Z\\s]{0,10}[:.\\s]{0,3}([\\+\\d\\(][\\s\\d\\(\\)\\-\\/\\.]{4,100}\\d)\\b", true, 2, "PII", 25, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "26: Redact Phone and Fax by RegEx (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && (
text.contains("Contact")
|| text.contains("Telephone")
|| text.contains("Phone")
|| text.contains("Fax")
|| text.contains("Tel")
|| text.contains("Ter")
|| text.contains("Mobile")
|| text.contains("Fel")
|| text.contains("Fer")
))
then
section.redactByRegEx("\\b(contact|telephone|phone|fax|tel|ter|mobile|fel|fer)[a-zA-Z\\s]{0,10}[:.\\s]{0,3}([\\+\\d\\(][\\s\\d\\(\\)\\-\\/\\.]{4,100}\\d)\\b", true, 2, "PII", 26, "Personal information found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "27: Redact AUTHOR(S) (Non vertebrate study)"
when
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes")
&& searchText.contains("AUTHOR(S):")
&& searchText.contains("COMPLETION DATE:")
&& !searchText.contains("STUDY COMPLETION DATE:")
)
then
section.redactLinesBetween("AUTHOR(S):", "COMPLETION DATE:", "PII", 27, true, "Author found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "28: Redact AUTHOR(S) (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes")
&& searchText.contains("AUTHOR(S):")
&& searchText.contains("COMPLETION DATE:")
&& !searchText.contains("STUDY COMPLETION DATE:")
)
then
section.redactLinesBetween("AUTHOR(S):", "COMPLETION DATE:", "PII", 28, true, "AUTHOR(S) was found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "18: Redact contact information if Producer is found"
rule "29: Redact AUTHOR(S) (Non vertebrate study)"
when
Section(text.toLowerCase().contains("producer of the plant protection") || text.toLowerCase().contains("producer of the active substance") || text.contains("Manufacturer of the active substance") || text.contains("Manufacturer:") || text.contains("Producer or producers of the active substance"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes")
&& searchText.contains("AUTHOR(S):")
&& searchText.contains("STUDY COMPLETION DATE:")
)
then
section.redactLineAfter("Contact:", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Telephone:", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Phone:", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Fax:", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("E-mail:", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Contact:", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Fax number:", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Telephone number:", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLineAfter("Tel:", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactBetween("No:", "Fax", "PII", 18, true, "Producer was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactLinesBetween("AUTHOR(S):", "STUDY COMPLETION DATE:", "PII", 29, true, "AUTHOR(S) was found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "30: Redact AUTHOR(S) (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes")
&& searchText.contains("AUTHOR(S):")
&& searchText.contains("STUDY COMPLETION DATE:")
)
then
section.redactLinesBetween("AUTHOR(S):", "STUDY COMPLETION DATE:", "PII", 30, true, "AUTHOR(S) was found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "19: Redact AUTHOR(S)"
rule "31: Redact PERFORMING LABORATORY (Non vertebrate study)"
when
Section(searchText.contains("AUTHOR(S):") && fileAttributeByPlaceholderEquals("{fileattributes.vertebrateStudy}", "true"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes")
&& searchText.contains("PERFORMING LABORATORY:")
)
then
section.redactLinesBetween("AUTHOR(S):", "COMPLETION DATE:", "PII", 19, true, "AUTHOR(S) was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactBetween("PERFORMING LABORATORY:", "LABORATORY PROJECT ID:", "CBI_address", 31, true, "PERFORMING LABORATORY was found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
section.redactNot("CBI_address", 31, "Performing laboratory found for non vertebrate study");
end
rule "20: Redact PERFORMING LABORATORY"
rule "32: Redact PERFORMING LABORATORY (Vertebrate study)"
when
Section(searchText.contains("PERFORMING LABORATORY:"))
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes")
&& searchText.contains("PERFORMING LABORATORY:"))
then
section.redactBetween("PERFORMING LABORATORY:", "LABORATORY PROJECT ID:", "PII", 20, true, "PERFORMING LABORATORY was found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
section.redactBetween("PERFORMING LABORATORY:", "LABORATORY PROJECT ID:", "CBI_address", 32, true, "PERFORMING LABORATORY was found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "21: Redact On behalf of Sequani Ltd.:"
rule "33: Redact study director abbreviation"
when
Section(searchText.contains("On behalf of Sequani Ltd.: Name Title"))
section: Section((searchText.contains("KATH") || searchText.contains("BECH") || searchText.contains("KML")))
then
section.redactBetween("On behalf of Sequani Ltd.: Name Title", "On behalf of", "PII", 21, false , "PII (Personal Identification Information) found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
end
section.redactWordPartByRegEx("((KATH)|(BECH)|(KML)) ?(\\d{4})", true, 0, 1, "PII", 34, "Personal information found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "22: Redact On behalf of Syngenta Ltd.:"
when
Section(searchText.contains("On behalf of Syngenta Ltd.: Name Title"))
then
section.redactBetween("On behalf of Syngenta Ltd.: Name Title", "Study dates", "PII", 22, false , "PII (Personal Identification Information) found", "Reg (EC) No 1107/2009 Art. 63 (2e)");
end
// --------------------------------------- other rules -------------------------------------------------------------------
rule "25: Redact Purity"
rule "34: Purity Hint"
when
Section(searchText.contains("purity"))
section: Section(searchText.toLowerCase().contains("purity"))
then
section.redactByRegEx("purity ?:? (([\\d\\.]+)( .{0,4}\\.)? ?%)", true, 1, "purity", 17, "Purity found", "Reg (EC) No 1107/2009 Art. 63 (2a)");
section.addHintAnnotationByRegEx("(purity ?( of|\\(.{1,20}\\))?( ?:)?) .{0,5}[\\d\\.]+( .{0,4}\\.)? ?%", true, 1, "hint_only");
end
rule "26: Redact signatures"
rule "35: Redact signatures (Non vertebrate study)"
when
Section(matchesImageType("signature"))
section: Section(!fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && matchesImageType("signature"))
then
section.redactImage("signature", 26, "Signature found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redactImage("signature", 35, "Signature found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end
rule "36: Redact signatures (Vertebrate study)"
when
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && matchesImageType("signature"))
then
section.redactImage("signature", 36, "Signature found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "27: Redact formula"
rule "43: Redact Logos (Vertebrate study)"
when
Section(matchesImageType("formula"))
section: Section(fileAttributeByLabelEqualsIgnoreCase("Vertebrate Study","Yes") && matchesImageType("logo"))
then
section.redactImage("formula", 27, "Formula found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
section.redactImage("logo", 43, "Logo found", "Article 39(e)(2) of Regulation (EC) No 178/2002");
end
rule "28: Redact Logos"
rule "44: Redact Author if contained in paragraph with 'unpublished'"
when
Section(matchesImageType("logo"))
$section: Section()
$entity: Entity(type == "CBI_author") from $section.getEntities()
$publishedEntity: Entity(type == "published_information") from $section.getEntities()
$paragraph: Paragraph(sectionNumber == $section.sectionNumber)
then
section.redactImage("logo", 28, "Logo found", "Reg (EC) No 1107/2009 Art. 63 (2g)");
if ($paragraph.containsEntity($entity) && $paragraph.containsEntity($publishedEntity) ) {
$entity.setRedaction(false);
}
end
rule "29: Redact Dossier Redactions"
when
Section(matchesType("dossier_redactions"))
then
section.redact("dossier_redactions", 29, "Dossier Redaction found", "Article 39(1)(2) of Regulation (EC) No 178/2002");
end
rule "30: Ignore dossier_redactions if confidential"
when
Section(!fileAttributeByLabelEqualsIgnoreCase("Confidentiality","confidential") && matchesType("dossier_redactions"));
then
section.ignore("dossier_redactions");
end
// ex. "New Rules for PAD" - "Annex A" - page 21, page 35 (table without header), page 38 (in-text)
// https://www.regexplanet.com/share/index.html?share=yyyypb71xkr
rule "101: Redact CAS numbers"
when
Section(hasTableHeader("Sample #"))
then
section.redactCell("Sample #", 8, "PII", true, "Redacted because row is a vertebrate study", "Reg (EC) No 1107/2009 Art. 63 (2g)");
end
rule "102: Guidelines FileAttributes"
when
Section((text.contains("DATA REQUIREMENT(S):") || text.contains("TEST GUIDELINE(S):")) && (text.contains("OECD") || text.contains("EPA") || text.contains("OPPTS")))
then
section.addFileAttribute("OECD Number", "OECD (No\\.? )?\\d{3}( \\(\\d{4}\\))?", false, 0);
end
rule "8: Redact Author cells in Tables with Author header (Non vertebrate study)"
when
Section(hasTableHeader("h5.1"))
then
section.redactCell("h5.1", 8, "CBI_author", false, "Author found", "Article 39(e)(3) of Regulation (EC) No 178/2002");
end