Pull request #122 : RED-1055: Enabled to force redact ignore annotations

Merge in RED/redaction-service from RED-1055 to master * commit 'e0fba8d38ce9858235ca84182f4587d472890ef1': RED-1055: Enabled to force redact ignore annotations
RED-1055: Enabled to force redact ignore annotations
2021-02-12 10:55:04 +01:00 · 2021-02-12 10:41:32 +01:00 · 2021-02-11 17:22:55 +01:00 · 2021-02-11 16:53:07 +01:00 · 2021-02-11 14:11:22 +01:00
10 changed files with 130 additions and 33 deletions
@@ -72,14 +72,6 @@ public class PlanSpec {
                        .jobs(new Job("Default Job",
                                new BambooKey("JOB1"))
                                .tasks(
-                                        new ScriptTask()
-                                                .description("Clean")
-                                                .inlineBody("#!/bin/bash\n" +
-                                                        "set -e\n" +
-                                                        "rm -rf ./*"),
-                                        new VcsCheckoutTask()
-                                                .description("Checkout Default Repository")
-                                                .checkoutItems(new CheckoutItem().defaultRepository()),
                                        new ScriptTask()
                                                .description("Clean")
                                                .inlineBody("#!/bin/bash\n" +
@@ -5,7 +5,7 @@
    <parent>
        <artifactId>platform-dependency</artifactId>
        <groupId>com.iqser.red</groupId>
-        <version>1.0.2</version>
+        <version>1.0.3</version>
    </parent>
    <modelVersion>4.0.0</modelVersion>

@@ -0,0 +1,19 @@
+package com.iqser.red.service.redaction.v1.model;
+
+import lombok.AllArgsConstructor;
+import lombok.Builder;
+import lombok.Data;
+import lombok.NoArgsConstructor;
+
+@Data
+@Builder
+@AllArgsConstructor
+@NoArgsConstructor
+public class ManualForceRedact {
+
+    private String id;
+    private String user;
+    private Status status;
+    private String legalBasis;
+
+}
@@ -1,5 +1,5 @@
 package com.iqser.red.service.redaction.v1.model;

 public enum ManualRedactionType {
-    ADD, REMOVE
+    ADD, REMOVE, FORCE_REDACT
 }
@@ -20,6 +20,9 @@ public class ManualRedactions {
    @Builder.Default
    private Set<IdRemoval> idsToRemove = new HashSet<>();

+    @Builder.Default
+    private Set<ManualForceRedact> forceRedacts = new HashSet<>();
+
    @Builder.Default
    private Set<ManualRedactionEntry> entriesToAdd = new HashSet<>();

@@ -140,6 +140,48 @@ public class Section {
    }


+    public void expandToHintAnnotationByRegEx(String type, String pattern, boolean patternCaseInsensitive, int group, String asType) {
+
+        Pattern compiledPattern = Patterns.getCompiledPattern(pattern, patternCaseInsensitive);
+
+        Set<Entity> expanded = new HashSet<>();
+        for (Entity entity : entities) {
+
+            if (!entity.getType().equals(type) || entity.getTextAfter() == null) {
+                continue;
+            }
+
+            Matcher matcher = compiledPattern.matcher(entity.getTextAfter());
+
+            while (matcher.find()) {
+                String match = matcher.group(group);
+                if (StringUtils.isNotBlank(match)) {
+                    expanded.addAll(findEntities(entity.getWord() + match, asType, false, false, 0, null, null));
+                }
+            }
+        }
+
+        EntitySearchUtils.addEntitiesWithHigherRank(entities, expanded, dictionary);
+        EntitySearchUtils.removeEntitiesContainedInLarger(entities);
+    }
+
+
+    public void addHintAnnotationByRegEx(String pattern, boolean patternCaseInsensitive, int group, String asType) {
+
+        Pattern compiledPattern = Patterns.getCompiledPattern(pattern, patternCaseInsensitive);
+
+        Matcher matcher = compiledPattern.matcher(searchText);
+
+        while (matcher.find()) {
+            String match = matcher.group(group);
+            if (StringUtils.isNotBlank(match)) {
+                Set<Entity> found = findEntities(match.trim(), asType, false, false, 0, null, null);
+                EntitySearchUtils.addEntitiesWithHigherRank(entities, found, dictionary);
+            }
+        }
+    }
+
+
    public void redactIfPrecededBy(String prefix, String type, int ruleNumber, String reason, String legalBasis) {

        entities.forEach(entity -> {
@@ -14,6 +14,7 @@ import org.springframework.stereotype.Service;
 import com.iqser.red.service.redaction.v1.model.CellRectangle;
 import com.iqser.red.service.redaction.v1.model.Comment;
 import com.iqser.red.service.redaction.v1.model.IdRemoval;
+import com.iqser.red.service.redaction.v1.model.ManualForceRedact;
 import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
 import com.iqser.red.service.redaction.v1.model.ManualRedactionType;
 import com.iqser.red.service.redaction.v1.model.ManualRedactions;
@@ -136,9 +137,11 @@ public class RedactionLogCreatorService {
                                redactionLogEntry.setRedacted(false);
                                redactionLogEntry.setStatus(Status.APPROVED);
                                manualOverrideReason = entity.getRedactionReason() + ", removed by manual override";
+                                redactionLogEntry.setColor(getColor(entity, ruleSetId, false));
                            } else if (manualRemoval.getStatus().equals(Status.REQUESTED)) {
                                manualOverrideReason = entity.getRedactionReason() + ", requested to remove";
                                redactionLogEntry.setStatus(Status.REQUESTED);
+                                redactionLogEntry.setColor(getColor(entity, ruleSetId, true));
                            } else {
                                redactionLogEntry.setStatus(Status.DECLINED);
                            }
@@ -149,7 +152,34 @@ public class RedactionLogCreatorService {
                            redactionLogEntry.setManualRedactionType(ManualRedactionType.REMOVE);
                        }
                    }
+                }

+                if (manualRedactions != null && !manualRedactions.getForceRedacts().isEmpty()) {
+                    for (ManualForceRedact manualForceRedact : manualRedactions.getForceRedacts()) {
+                        if (manualForceRedact.getId().equals(entityPositionSequence.getId())) {
+                            String manualOverrideReason = null;
+                            if (manualForceRedact.getStatus().equals(Status.APPROVED)) {
+                                entity.setRedaction(true);
+                                redactionLogEntry.setRedacted(true);
+                                redactionLogEntry.setStatus(Status.APPROVED);
+                                redactionLogEntry.setColor(getColor(entity, ruleSetId, false));
+                                manualOverrideReason = entity.getRedactionReason() + ", forced by manual override";
+                                redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
+                            } else if (manualForceRedact.getStatus().equals(Status.REQUESTED)) {
+                                manualOverrideReason = entity.getRedactionReason() + ", requested to force redact";
+                                redactionLogEntry.setStatus(Status.REQUESTED);
+                                redactionLogEntry.setColor(getColor(entity, ruleSetId, true));
+                                redactionLogEntry.setLegalBasis(manualForceRedact.getLegalBasis());
+                            } else {
+                                redactionLogEntry.setStatus(Status.DECLINED);
+                            }
+
+                            entity.setRedactionReason(manualOverrideReason != null ? manualOverrideReason : entity.getRedactionReason());
+                            redactionLogEntry.setReason(manualOverrideReason);
+                            redactionLogEntry.setManual(true);
+                            redactionLogEntry.setManualRedactionType(ManualRedactionType.FORCE_REDACT);
+                        }
+                    }
                }

                if (CollectionUtils.isNotEmpty(entityPositionSequence.getSequences())) {
@@ -51,6 +51,7 @@ import com.iqser.red.service.redaction.v1.model.AnnotateRequest;
 import com.iqser.red.service.redaction.v1.model.AnnotateResponse;
 import com.iqser.red.service.redaction.v1.model.Comment;
 import com.iqser.red.service.redaction.v1.model.IdRemoval;
+import com.iqser.red.service.redaction.v1.model.ManualForceRedact;
 import com.iqser.red.service.redaction.v1.model.ManualRedactionEntry;
 import com.iqser.red.service.redaction.v1.model.ManualRedactions;
 import com.iqser.red.service.redaction.v1.model.Point;
@@ -324,7 +325,6 @@ public class RedactionIntegrationTest {
        recommendationTypeMap.put(PURITY, false);
        recommendationTypeMap.put(IMAGE, false);

-
        rankTypeMap.put(FALSE_POSITIVE, 160);
        rankTypeMap.put(PURITY, 155);
        rankTypeMap.put(PII, 150);
@@ -342,7 +342,6 @@ public class RedactionIntegrationTest {
        rankTypeMap.put(RECOMMENDATION_ADDRESS, 30);
        rankTypeMap.put(IMAGE, 30);

-
        colors.setDefaultColor("#acfc00");
        colors.setNotRedacted("#cccccc");
        colors.setRequestAdd("#04b093");
@@ -418,7 +417,6 @@ public class RedactionIntegrationTest {
    }


-
    private List<File> getPathsRecursively(File path) {

        List<File> result = new ArrayList<>();
@@ -446,7 +444,6 @@ public class RedactionIntegrationTest {
 //        91 Trinexapac-ethyl_RAR_01_Volume_1_2018-02-23.pdf
 //        95 Trinexapac-ethyl_RAR_08_Volume_3CA_B-6_2018-01-10.pdf

-
        System.out.println("redactionTest");
        long start = System.currentTimeMillis();
        ClassPathResource pdfFileResource = new ClassPathResource("files/Cyprodinil/49 Cyprodinil - EU AIR3 - MCA Section 8 Supplement - Ecotoxicological studies on the active substance.pdf");
@@ -456,11 +453,13 @@ public class RedactionIntegrationTest {
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
                .build();

-
        AnalyzeResult result = redactionController.analyze(request);

-        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder().document(IOUtils.toByteArray(pdfFileResource.getInputStream())).redactionLog(result.getRedactionLog()).sectionGrid(result.getSectionGrid()).build());
-
+        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .redactionLog(result.getRedactionLog())
+                .sectionGrid(result.getSectionGrid())
+                .build());

        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
            fileOutputStream.write(annotateResponse.getDocument());
@@ -485,11 +484,13 @@ public class RedactionIntegrationTest {
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
                .build();

-
        AnalyzeResult result = redactionController.analyze(request);

-        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder().document(IOUtils.toByteArray(pdfFileResource.getInputStream())).redactionLog(result.getRedactionLog()).sectionGrid(result.getSectionGrid()).build());
-
+        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .redactionLog(result.getRedactionLog())
+                .sectionGrid(result.getSectionGrid())
+                .build());

        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
            fileOutputStream.write(annotateResponse.getDocument());
@@ -504,6 +505,8 @@ public class RedactionIntegrationTest {
    @Test
    public void testManualRedaction() throws IOException {

+//        675eba69b0c2917de55462c817adaa05
+
        System.out.println("testManualRedaction");
        long start = System.currentTimeMillis();
        ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Single Table.pdf");
@@ -518,8 +521,13 @@ public class RedactionIntegrationTest {
                .text("This is a comment test")
                .build();
        manualRedactions.setIdsToRemove(Set.of(IdRemoval.builder()
-                .id("0836727c3508a0b2ea271da69c04cc2f")
-                .status(Status.REQUESTED)
+                .id("5b940b2cb401ed9f5be6fc24f6e77bcf")
+                .status(Status.DECLINED)
+                .build()));
+        manualRedactions.setForceRedacts(Set.of(ManualForceRedact.builder()
+                .id("675eba69b0c2917de55462c817adaa05")
+                .legalBasis("Something")
+                .status(Status.APPROVED)
                .build()));

        manualRedactions.getComments().put("e5be0f1d941bbb92a068e198648d06c4", List.of(comment));
@@ -542,11 +550,13 @@ public class RedactionIntegrationTest {
                .manualRedactions(manualRedactions)
                .build();

-
        AnalyzeResult result = redactionController.analyze(request);

-        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder().document(IOUtils.toByteArray(pdfFileResource.getInputStream())).redactionLog(result.getRedactionLog()).sectionGrid(result.getSectionGrid()).build());
-
+        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .redactionLog(result.getRedactionLog())
+                .sectionGrid(result.getSectionGrid())
+                .build());

        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
            fileOutputStream.write(annotateResponse.getDocument());
@@ -640,7 +650,6 @@ public class RedactionIntegrationTest {
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
                .build();

-
        AnalyzeResult result = redactionController.analyze(request);

        result.getRedactionLog().getRedactionLogEntry().forEach(entry -> {
@@ -662,11 +671,13 @@ public class RedactionIntegrationTest {
                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
                .build();

-
        AnalyzeResult result = redactionController.analyze(request);

-        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder().document(IOUtils.toByteArray(pdfFileResource.getInputStream())).redactionLog(result.getRedactionLog()).sectionGrid(result.getSectionGrid()).build());
-
+        AnnotateResponse annotateResponse = redactionController.annotate(AnnotateRequest.builder()
+                .document(IOUtils.toByteArray(pdfFileResource.getInputStream()))
+                .redactionLog(result.getRedactionLog())
+                .sectionGrid(result.getSectionGrid())
+                .build());

        try (FileOutputStream fileOutputStream = new FileOutputStream("/tmp/Annotated.pdf")) {
            fileOutputStream.write(annotateResponse.getDocument());
@@ -316,9 +316,9 @@ rule "26: Redact On behalf of Syngenta Ltd.:"

 // --------------------------------------- other rules -------------------------------------------------------------------

-rule "27: Redact Purity"
+rule "27: Purity Hint"
    when
-        Section(searchText.contains("purity"))
+        Section(searchText.toLowerCase().contains("purity"))
    then
-	    section.redactByRegEx("purity ?:? (([\\d\\.]+)( .{0,4}\\.)? ?%)", true, 1, "purity", 27, "Purity found", "Reg (EC) No 1107/2009 Art. 63 (2a)");
+	    section.addHintAnnotationByRegEx("(purity( of)?( ?:)?) [\\d\\.]+( .{0,4}\\.)? ?%", true, 1, "hint_only");
    end
@@ -10,7 +10,7 @@
        <Root level="warn">
            <AppenderRef ref="CONSOLE" />
        </Root>
-        <Logger name="com.iqser.gin4" level="info" />
+        <Logger name="com.iqser" level="info" />
    </Loggers>

 </Configuration>
Author	SHA1	Message	Date
Dominique Eiflaender	53509f072e	Pull request #122 : RED-1055: Enabled to force redact ignore annotations Merge in RED/redaction-service from RED-1055 to master * commit 'e0fba8d38ce9858235ca84182f4587d472890ef1': RED-1055: Enabled to force redact ignore annotations	2021-02-12 10:55:04 +01:00
Dominique Eifländer	e0fba8d38c	RED-1055: Enabled to force redact ignore annotations	2021-02-12 10:41:32 +01:00
Lena Maldacker	8989191314	Pull request #121 : Add hint annotation by reg-ex and expand to hint annotation by reg-ex Merge in RED/redaction-service from dismissGen to master * commit '0f263c69b8f2eb7201f062cc263c8d06b7a710a1': Add hint annotation by reg-ex and expand to hint annotation by reg-ex	2021-02-11 17:22:55 +01:00
lmaldacker	0f263c69b8	Add hint annotation by reg-ex and expand to hint annotation by reg-ex	2021-02-11 16:53:07 +01:00
Kresnadi Budisantoso	ea1c2898bc	Remove duplicate build tasks in bamboo specs	2021-02-11 14:11:22 +01:00