RED-6009 - Document Tree Structure
* fixed rules to include vertebrate study flags
This commit is contained in:
Kilian Schuettler
parent
0443e21858
commit
f0144799c5
@ -66,7 +66,7 @@ rule "0: Recommend CTL/BL laboratory that start with BL or CTL"
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end
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// --------------------------------------- CBI Rules -------------------------------------------------------------------
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rule "1: Redact CBI Authors"
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rule "1: Redact CBI Authors (non vertebrate study)"
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when
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$entity: RedactionEntity(type == "CBI_author", entityType == EntityType.ENTITY)
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@ -74,20 +74,31 @@ rule "1: Redact CBI Authors"
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$entity.setRedaction(true);
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$entity.addMatchedRule(1);
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$entity.setRedactionReason("Author found");
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$entity.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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end
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rule "2: Redact CBI Authors (vertebrate study)"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$entity: RedactionEntity(type == "CBI_author", entityType == EntityType.ENTITY)
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then
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$entity.setRedaction(true);
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$entity.addMatchedRule(2);
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$entity.setRedactionReason("Author found");
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$entity.setLegalBasis("Article 39(e)(2) of Regulation (EC) No 178/2002");
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end
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rule "2: Don't redact CBI Address (Non vertebrate study)"
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rule "3: Don't redact CBI Address (Non vertebrate study)"
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when
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$entity: RedactionEntity(type == "CBI_address", entityType == EntityType.ENTITY)
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then
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$entity.setRedaction(false);
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$entity.addMatchedRule(2);
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$entity.addMatchedRule(3);
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$entity.setRedactionReason("Address found for non vertebrate study");
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end
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rule "3: Redact CBI Address (Vertebrate study)"
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rule "4: Redact CBI Address (Vertebrate study)"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$entity: RedactionEntity(type == "CBI_address", entityType == EntityType.ENTITY)
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@ -107,8 +118,9 @@ rule "5: Add FALSE_POSITIVE Entity for genitive CBI_author"
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insert(falsePositive);
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end
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rule "6: Redact all Cell's with Header Author(s) as CBI_author"
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rule "6: Redact all Cell's with Header Author(s) as CBI_author (non vertebrate study)"
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when
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$table: Table(hasHeader("Author(s)"))
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then
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$table.streamTableCellsWithHeader("Author(s)")
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@ -118,14 +130,32 @@ rule "6: Redact all Cell's with Header Author(s) as CBI_author"
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redactionEntity.addMatchedRule(6);
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redactionEntity.addEngine(Engine.RULE);
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redactionEntity.setRedactionReason("Author(s) found");
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redactionEntity.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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insert(redactionEntity);
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});
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end
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rule "7: Redact all Cell's with Header Author(s) as CBI_author (vertebrate study)"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$table: Table(hasHeader("Author(s)"))
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then
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$table.streamTableCellsWithHeader("Author(s)")
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.map(tableCell -> entityCreationService.bySemanticNode(tableCell, "CBI_author", EntityType.ENTITY))
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.forEach(redactionEntity -> {
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redactionEntity.setRedaction(true);
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redactionEntity.addMatchedRule(7);
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redactionEntity.addEngine(Engine.RULE);
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redactionEntity.setRedactionReason("Author(s) found");
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redactionEntity.setLegalBasis("Article 39(e)(2) of Regulation (EC) No 178/2002");
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insert(redactionEntity);
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});
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end
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rule "8: Redact all Cell's with Header Author(s) as CBI_author"
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rule "8: Redact all Cell's with Header Author as CBI_author"
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agenda-group "LOCAL_DICTIONARY_ADDS"
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when
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$table: Table(hasHeader("Author"))
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then
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$table.streamTableCellsWithHeader("Author")
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@ -135,6 +165,24 @@ rule "8: Redact all Cell's with Header Author(s) as CBI_author"
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redactionEntity.addMatchedRule(8);
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redactionEntity.addEngine(Engine.RULE);
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redactionEntity.setRedactionReason("Author found");
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redactionEntity.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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insert(redactionEntity);
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});
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end
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rule "9: Redact all Cell's with Header Author as CBI_author"
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agenda-group "LOCAL_DICTIONARY_ADDS"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$table: Table(hasHeader("Author"))
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then
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$table.streamTableCellsWithHeader("Author")
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.map(tableCell -> entityCreationService.bySemanticNode(tableCell, "CBI_author", EntityType.ENTITY))
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.forEach(redactionEntity -> {
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redactionEntity.setRedaction(true);
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redactionEntity.addMatchedRule(9);
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redactionEntity.addEngine(Engine.RULE);
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redactionEntity.setRedactionReason("Author found");
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redactionEntity.setLegalBasis("Article 39(e)(2) of Regulation (EC) No 178/2002");
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insert(redactionEntity);
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});
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@ -142,22 +190,24 @@ rule "8: Redact all Cell's with Header Author(s) as CBI_author"
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rule "10: Recommend all CBI_author entities in Table with Vertebrate Study Y/N Header"
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agenda-group "LOCAL_DICTIONARY_ADDS"
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salience -1
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when
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$table: Table(hasHeader("Author(s)") && hasHeader("Vertebrate Study Y/N"))
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then
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$table.getEntitiesOfType("CBI_author").forEach(entity -> dictionary.addMultipleAuthorsAsRecommendation(entity));
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end
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rule "14: Add CBI_author with \"et al.\" Regex"
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rule "14: Add CBI_author with \"et al.\" Regex (non vertebrate study)"
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agenda-group "LOCAL_DICTIONARY_ADDS"
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when
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$section: Section(containsString("et al."))
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(containsString("et al."))
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then
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entityCreationService.byRegex("\\b([A-ZÄÖÜ][^\\s\\.,]+( [A-ZÄÖÜ]{1,2}\\.?)?( ?[A-ZÄÖÜ]\\.?)?) et al\\.?", "CBI_author", EntityType.ENTITY, $section)
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entityCreationService.byRegex("\\b([A-ZÄÖÜ][^\\s\\.,]+( [A-ZÄÖÜ]{1,2}\\.?)?( ?[A-ZÄÖÜ]\\.?)?) et al\\.?", "CBI_author", EntityType.ENTITY, $section)
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.forEach(entity -> {
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entity.setRedaction(true);
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entity.setRedactionReason("Author found by \"et al\" regex");
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entity.setLegalBasis("Reg (EC) No 1107/2009 Art. 63 (2g)");
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entity.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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entity.addMatchedRule(14);
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entity.addEngine(Engine.RULE);
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insert(entity);
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@ -165,6 +215,24 @@ rule "14: Add CBI_author with \"et al.\" Regex"
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});
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end
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rule "15: Add CBI_author with \"et al.\" Regex (vertebrate study)"
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agenda-group "LOCAL_DICTIONARY_ADDS"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(containsString("et al."))
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then
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entityCreationService.byRegex("\\b([A-ZÄÖÜ][^\\s\\.,]+( [A-ZÄÖÜ]{1,2}\\.?)?( ?[A-ZÄÖÜ]\\.?)?) et al\\.?", "CBI_author", EntityType.ENTITY, $section)
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.forEach(entity -> {
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entity.setRedaction(true);
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entity.setRedactionReason("Author found by \"et al\" regex");
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entity.setLegalBasis("Article 39(e)(2) of Regulation (EC) No 178/2002");
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entity.addMatchedRule(15);
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entity.addEngine(Engine.RULE);
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insert(entity);
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dictionary.addLocalDictionaryEntry("CBI_author", entity.getValue(), false);
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});
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end
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rule "16: Add recommendation for Addresses in Test Organism sections"
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when
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$section: Section(excludesTables, containsString("Species") && containsString("Source") && !containsString("Species:") && !containsString("Source:"))
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@ -221,8 +289,9 @@ rule "18.1: Do not redact Names and Addresses if published information found in
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// --------------------------------------- PII rules -------------------------------------------------------------------
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rule "19: Redact all PII"
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rule "19: Redact all PII (non vertebrate study)"
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when
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$pii: RedactionEntity(type == "PII", redaction == false)
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then
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$pii.setRedaction(true);
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@ -231,8 +300,20 @@ rule "19: Redact all PII"
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$pii.addMatchedRule(19);
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end
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rule "20: Redact all PII (vertebrate study)"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$pii: RedactionEntity(type == "PII", redaction == false)
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then
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$pii.setRedaction(true);
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$pii.setRedactionReason("Personal Information found");
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$pii.setLegalBasis("Article 39(e)(2) of Regulation (EC) No 178/2002");
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$pii.addMatchedRule(20);
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end
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rule "21: Redact Emails by RegEx (Non vertebrate study)"
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when
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(containsString("@"))
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then
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entityCreationService.byRegex("\\b([A-Za-z0-9._%+\\-]+@[A-Za-z0-9.\\-]+\\.[A-Za-z\\-]{1,23}[A-Za-z])\\b", "PII", EntityType.ENTITY, 1, $section)
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@ -245,9 +326,25 @@ rule "21: Redact Emails by RegEx (Non vertebrate study)"
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});
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end
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rule "25: Redact Phone and Fax by RegEx"
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rule "22: Redact Emails by RegEx (vertebrate study)"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(containsString("@"))
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then
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entityCreationService.byRegex("\\b([A-Za-z0-9._%+\\-]+@[A-Za-z0-9.\\-]+\\.[A-Za-z\\-]{1,23}[A-Za-z])\\b", "PII", EntityType.ENTITY, 1, $section)
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.forEach(emailEntity -> {
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emailEntity.setRedaction(true);
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emailEntity.setRedactionReason("Found by Email Regex");
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emailEntity.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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emailEntity.addMatchedRule(22);
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insert(emailEntity);
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});
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end
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rule "25: Redact Phone and Fax by RegEx (non vertebrate study)"
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when
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(containsString("Contact") ||
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containsString("Telephone") ||
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containsString("Phone") ||
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@ -264,13 +361,14 @@ rule "25: Redact Phone and Fax by RegEx"
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contactEntity.setRedaction(true);
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contactEntity.setRedactionReason("Found by Email Regex");
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contactEntity.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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contactEntity.addMatchedRule(26);
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contactEntity.addMatchedRule(25);
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insert(contactEntity);
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});
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end
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rule "25: Redact Phone and Fax by RegEx"
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rule "26: Redact Phone and Fax by RegEx (vertebrate study)"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(containsString("Contact") ||
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containsString("Telephone") ||
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containsString("Phone") ||
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@ -286,15 +384,16 @@ rule "25: Redact Phone and Fax by RegEx"
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.forEach(contactEntity -> {
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contactEntity.setRedaction(true);
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contactEntity.setRedactionReason("Found by Email Regex");
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contactEntity.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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contactEntity.setLegalBasis("Article 39(e)(2) of Regulation (EC) No 178/2002");
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contactEntity.addMatchedRule(26);
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insert(contactEntity);
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});
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end
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rule "27: Redact AUTHOR(S)"
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rule "27: Redact AUTHOR(S) (non vertebrate study)"
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when
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(excludesTables, containsString("AUTHOR(S):"), containsString("COMPLETION DATE:"), !containsString("STUDY COMPLETION DATE:"))
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then
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entityCreationService.betweenStrings("AUTHOR(S):", "COMPLETION DATE:", "PII", EntityType.ENTITY, $section)
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@ -302,14 +401,30 @@ rule "27: Redact AUTHOR(S)"
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authorEntity.setRedaction(true);
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authorEntity.addMatchedRule(27);
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authorEntity.setRedactionReason("AUTHOR(S) was found");
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authorEntity.setLegalBasis("Reg (EC) No 1107/2009 Art. 63 (2e)");
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authorEntity.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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insert(authorEntity);
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});
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end
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rule "28: Redact AUTHOR(S) (vertebrate study)"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(excludesTables, containsString("AUTHOR(S):"), containsString("COMPLETION DATE:"), !containsString("STUDY COMPLETION DATE:"))
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then
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entityCreationService.betweenStrings("AUTHOR(S):", "COMPLETION DATE:", "PII", EntityType.ENTITY, $section)
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.forEach(authorEntity -> {
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authorEntity.setRedaction(true);
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authorEntity.addMatchedRule(28);
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authorEntity.setRedactionReason("AUTHOR(S) was found");
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authorEntity.setLegalBasis("Article 39(e)(2) of Regulation (EC) No 178/2002");
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insert(authorEntity);
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});
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end
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rule "29: Redact AUTHOR(S)"
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rule "29: Redact AUTHOR(S) (non vertebrate study)"
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when
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(excludesTables, containsString("AUTHOR(S):"), containsString("STUDY COMPLETION DATE:"))
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then
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entityCreationService.betweenStrings("AUTHOR(S):", "STUDY COMPLETION DATE:", "PII", EntityType.ENTITY, $section)
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@ -317,12 +432,28 @@ rule "29: Redact AUTHOR(S)"
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authorEntity.setRedaction(true);
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authorEntity.addMatchedRule(29);
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authorEntity.setRedactionReason("AUTHOR(S) was found");
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authorEntity.setLegalBasis("Reg (EC) No 1107/2009 Art. 63 (2e)");
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authorEntity.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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insert(authorEntity);
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});
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end
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rule "30: Redact AUTHOR(S) (vertebrate study)"
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when
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$section: Section(excludesTables, containsString("AUTHOR(S):"), containsString("STUDY COMPLETION DATE:"))
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then
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entityCreationService.betweenStrings("AUTHOR(S):", "STUDY COMPLETION DATE:", "PII", EntityType.ENTITY, $section)
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.forEach(authorEntity -> {
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authorEntity.setRedaction(true);
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authorEntity.addMatchedRule(30);
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authorEntity.setRedactionReason("AUTHOR(S) was found");
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authorEntity.setLegalBasis("Article 39(e)(2) of Regulation (EC) No 178/2002");
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insert(authorEntity);
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});
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end
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rule "31: Redact PERFORMING LABORATORY (Non vertebrate study)"
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agenda-group "LOCAL_DICTIONARY_ADDS"
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when
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not FileAttribute(label == "Vertebrate Study", value == "Yes")
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$section: Section(excludesTables, containsString("PERFORMING LABORATORY:"))
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@ -338,6 +469,7 @@ rule "31: Redact PERFORMING LABORATORY (Non vertebrate study)"
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end
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rule "32: Redact PERFORMING LABORATORY (Vertebrate study)"
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agenda-group "LOCAL_DICTIONARY_ADDS"
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when
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FileAttribute(label == "Vertebrate Study", value == "Yes")
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$section: Section(excludesTables, containsString("PERFORMING LABORATORY:"))
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@ -368,7 +500,7 @@ rule "33: Purity Hint"
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rule "34: Redact signatures (not Vertebrate Study)"
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when
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not FileAttribute(label == "Vertebrate Study", value == "Yes")
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not FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$signature: Image(imageType == ImageType.SIGNATURE)
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then
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$signature.setRedaction(true);
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@ -379,18 +511,19 @@ rule "34: Redact signatures (not Vertebrate Study)"
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rule "35: Redact signatures (Vertebrate Study)"
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when
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FileAttribute(label == "Vertebrate Study", value == "Yes")
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FileAttribute(label == "Vertebrate Study", value.toLowerCase() == "yes")
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$signature: Image(imageType == ImageType.SIGNATURE)
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then
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$signature.setRedaction(true);
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$signature.setMatchedRule(35);
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$signature.setRedactionReason("Signature Found");
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$signature.setLegalBasis("Article 39(e)(3) of Regulation (EC) No 178/2002");
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$signature.setLegalBasis("Article 39(e)(2) of Regulation (EC) No 178/2002");
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end
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rule "36: Redact logos"
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when
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not FileAttribute(label == "Vertbrate Study", value.toLowerCase() == "yes")
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$logo: Image(imageType == ImageType.LOGO)
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then
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$logo.setRedaction(true);
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