Compare commits
20
Commits
| Author | SHA1 | Date | |
|---|---|---|---|
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6483e637c6 | ||
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272c7cc228 | ||
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5586531c33 | ||
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559c421542 | ||
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d026f4e1db | ||
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38ddb1d9c8 | ||
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92f0af9d21 | ||
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b24922aa60 | ||
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afa26895c8 | ||
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baa703928f | ||
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85667c91e4 | ||
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8a471d0771 | ||
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bb1112d0d7 | ||
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00a960ee23 | ||
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8c08bb3664 | ||
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14b4f4ab8a | ||
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4206e708a2 | ||
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c4164b57fb | ||
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76369f13f8 | ||
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89ef8234d2 |
@@ -5,7 +5,7 @@
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||||
<parent>
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||||
<artifactId>platform-dependency</artifactId>
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<groupId>com.iqser.red</groupId>
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||||
<version>1.0.1</version>
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<version>1.0.2</version>
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</parent>
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<modelVersion>4.0.0</modelVersion>
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|
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@@ -32,21 +32,21 @@
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<dependency>
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<groupId>com.iqser.red</groupId>
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<artifactId>platform-commons-dependency</artifactId>
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<version>1.0.0</version>
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||||
<version>1.1.0</version>
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<scope>import</scope>
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||||
<type>pom</type>
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</dependency>
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||||
|
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<dependency>
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<groupId>org.apache.pdfbox</groupId>
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<artifactId>pdfbox</artifactId>
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||||
<version>${pdfbox.version}</version>
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</dependency>
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<dependency>
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<groupId>org.apache.pdfbox</groupId>
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<artifactId>pdfbox-tools</artifactId>
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<version>${pdfbox.version}</version>
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</dependency>
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<dependency>
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<groupId>org.apache.pdfbox</groupId>
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<artifactId>pdfbox</artifactId>
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<version>${pdfbox.version}</version>
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</dependency>
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<dependency>
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<groupId>org.apache.pdfbox</groupId>
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<artifactId>pdfbox-tools</artifactId>
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<version>${pdfbox.version}</version>
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</dependency>
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</dependencies>
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+4
@@ -3,11 +3,15 @@ package com.iqser.red.service.redaction.v1.model;
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import java.util.ArrayList;
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import java.util.List;
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import lombok.AllArgsConstructor;
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import lombok.Builder;
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import lombok.Data;
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import lombok.NoArgsConstructor;
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@Data
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@Builder
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@NoArgsConstructor
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@AllArgsConstructor
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public class RedactionLogEntry {
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private String id;
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@@ -63,15 +63,15 @@
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</dependency>
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<!-- commons -->
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<dependency>
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<groupId>com.iqser.gin4.commons</groupId>
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<groupId>com.iqser.red.commons</groupId>
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<artifactId>spring-commons</artifactId>
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</dependency>
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<dependency>
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<groupId>com.iqser.gin4.commons</groupId>
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<groupId>com.iqser.red.commons</groupId>
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<artifactId>logging-commons</artifactId>
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</dependency>
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<dependency>
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<groupId>com.iqser.gin4.commons</groupId>
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<groupId>com.iqser.red.commons</groupId>
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<artifactId>metric-commons</artifactId>
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</dependency>
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<!-- other external -->
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@@ -104,7 +104,7 @@
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<scope>test</scope>
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</dependency>
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<dependency>
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<groupId>com.iqser.gin4.commons</groupId>
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<groupId>com.iqser.red.commons</groupId>
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<artifactId>test-commons</artifactId>
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<scope>test</scope>
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</dependency>
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+1
-1
@@ -20,7 +20,7 @@ import org.springframework.cloud.openfeign.EnableFeignClients;
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import org.springframework.context.annotation.Bean;
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import org.springframework.context.annotation.Import;
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import com.iqser.gin4.commons.spring.DefaultWebMvcConfiguration;
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import com.iqser.red.commons.spring.DefaultWebMvcConfiguration;
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import com.iqser.red.service.configuration.v1.api.model.RulesResponse;
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import com.iqser.red.service.redaction.v1.server.client.RulesClient;
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import com.iqser.red.service.redaction.v1.server.exception.RulesValidationException;
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+1
-1
@@ -2,13 +2,13 @@ package com.iqser.red.service.redaction.v1.server.controller;
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import java.time.OffsetDateTime;
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import com.iqser.red.commons.spring.ErrorMessage;
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import org.springframework.http.HttpStatus;
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import org.springframework.web.bind.annotation.ExceptionHandler;
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import org.springframework.web.bind.annotation.ResponseBody;
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import org.springframework.web.bind.annotation.ResponseStatus;
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import org.springframework.web.bind.annotation.RestControllerAdvice;
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import com.iqser.gin4.commons.api.errorhandling.ErrorMessage;
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import com.iqser.red.service.redaction.v1.server.exception.RulesValidationException;
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import lombok.extern.slf4j.Slf4j;
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+13
-14
@@ -35,17 +35,12 @@ public class Section {
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private Map<String, TextBlock> tabularData;
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public boolean isVertebrateStudy() {
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return tabularData != null
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&& tabularData.containsKey("Vertebrate study Y/N")
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&& tabularData.get("Vertebrate study Y/N").getText().equals("Y");
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}
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public boolean rowEquals(String headerName, String value){
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String cleanHeaderName = headerName.replaceAll("\n", "")
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.replaceAll(" ", "")
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.replaceAll("-", "");
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public boolean isNotVertebrateStudy() {
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return tabularData != null
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&& tabularData.containsKey("Vertebrate study Y/N")
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&& tabularData.get("Vertebrate study Y/N").getText().equals("N");
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return tabularData != null && tabularData.containsKey(cleanHeaderName) && tabularData.get(cleanHeaderName).getText().equals(value);
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}
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@@ -176,13 +171,17 @@ public class Section {
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}
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public void highlightCell(String cellHeader, int ruleNumber) {
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public void highlightCell(String cellHeader, int ruleNumber, String type) {
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TextBlock value = tabularData.get(cellHeader);
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String cleanHeaderName = cellHeader.replaceAll("\n", "")
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.replaceAll(" ", "")
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.replaceAll("-", "");
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||||
|
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TextBlock value = tabularData.get(cleanHeaderName);
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if (value == null) {
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log.warn("Could not find any data for {}.", cellHeader);
|
||||
} else {
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Entity entity = new Entity(value.getText(), "must_redact", 0, value.getText().length(), headline, sectionNumber);
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Entity entity = new Entity(value.getText(), type, 0, value.getText().length(), headline, sectionNumber);
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entity.setRedaction(false);
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entity.setMatchedRule(ruleNumber);
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entity.setRedactionReason(cellHeader);
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||||
@@ -192,4 +191,4 @@ public class Section {
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||||
|
||||
}
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||||
|
||||
}
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||||
}
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||||
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||||
+7
-3
@@ -60,9 +60,13 @@ public class EntityRedactionService {
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||||
}
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addSectionToManualRedactions(cell.getTextBlocks(), manualRedactions, table.getHeadline(), sectionNumber);
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||||
cell.getHeaderCells().forEach(headerCell -> {
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String headerName = headerCell.getTextBlocks().get(0).getText()
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.replaceAll("\n", " ")
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||||
.replaceAll(" ", " ");
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||||
|
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StringBuilder headerBuilder = new StringBuilder();
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headerCell.getTextBlocks().forEach(textBlock -> headerBuilder.append(textBlock.getText()));
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String headerName = headerBuilder.toString()
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.replaceAll("\n", "")
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||||
.replaceAll(" ", "")
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||||
.replaceAll("-", "");
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tabularData.put(headerName, cell.getTextBlocks().get(0));
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});
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||||
for (TextBlock textBlock : cell.getTextBlocks()) {
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||||
|
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+45
-23
@@ -4,6 +4,7 @@ import java.util.ArrayList;
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||||
import java.util.Collections;
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||||
import java.util.Iterator;
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||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
import org.apache.commons.collections4.CollectionUtils;
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||||
import org.springframework.stereotype.Service;
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||||
@@ -39,22 +40,27 @@ public class SectionsBuilderService {
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||||
current.setPage(page.getPageNumber());
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||||
|
||||
if (prev != null && current.getClassification().startsWith("H ") || !document.isHeadlines()) {
|
||||
Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline, previousTable);
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||||
Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline);
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chunkBlock.setHeadline(lastHeadline);
|
||||
lastHeadline = current.getText();
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||||
if (CollectionUtils.isNotEmpty(chunkBlock.getTables())) {
|
||||
previousTable = chunkBlock.getTables().get(0);
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||||
}
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||||
chunkBlockList.add(chunkBlock);
|
||||
chunkWords = new ArrayList<>();
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||||
if (CollectionUtils.isNotEmpty(chunkBlock.getTables())) {
|
||||
previousTable = chunkBlock.getTables().get(chunkBlock.getTables().size() - 1);
|
||||
}
|
||||
}
|
||||
if (current instanceof Table) {
|
||||
Table table = (Table) current;
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||||
// Distribute header information for subsequent tables
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||||
mergeTableMetadata(table, previousTable);
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||||
previousTable = table;
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||||
}
|
||||
|
||||
chunkWords.add(current);
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||||
prev = current;
|
||||
}
|
||||
}
|
||||
|
||||
Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline, previousTable);
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||||
Paragraph chunkBlock = buildTextBlock(chunkWords, lastHeadline);
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||||
chunkBlock.setHeadline(lastHeadline);
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||||
chunkBlockList.add(chunkBlock);
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||||
|
||||
@@ -62,7 +68,39 @@ public class SectionsBuilderService {
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||||
}
|
||||
|
||||
|
||||
private Paragraph buildTextBlock(List<AbstractTextContainer> wordBlockList, String lastHeadline, Table previousTable) {
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||||
private void mergeTableMetadata(Table currentTable, Table previousTable) {
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||||
|
||||
// Distribute header information for subsequent tables
|
||||
if (previousTable != null && hasInvalidHeaderInformation(currentTable) && hasValidHeaderInformation(previousTable)) {
|
||||
List<Cell> previousTableNonHeaderRow = getRowWithNonHeaderCells(previousTable);
|
||||
List<Cell> tableNonHeaderRow = getRowWithNonHeaderCells(currentTable);
|
||||
// Allow merging of tables if header row is separated from first logical non-header row
|
||||
if (previousTableNonHeaderRow.isEmpty() && previousTable.getRowCount() == 1 && previousTable.getRows()
|
||||
.get(0)
|
||||
.size() == tableNonHeaderRow.size()) {
|
||||
previousTableNonHeaderRow = previousTable.getRows().get(0).stream().map(cell -> {
|
||||
Cell fakeCell = new Cell(cell.getPoints()[0], cell.getPoints()[2]);
|
||||
fakeCell.setHeaderCells(Collections.singletonList(cell));
|
||||
return fakeCell;
|
||||
}).collect(Collectors.toList());
|
||||
}
|
||||
if (previousTableNonHeaderRow.size() == tableNonHeaderRow.size()) {
|
||||
for (int i = currentTable.getRows()
|
||||
.size() - 1; i >= 0; i--) { // Non header rows are most likely at bottom of table
|
||||
List<Cell> row = currentTable.getRows().get(i);
|
||||
if (row.size() == tableNonHeaderRow.size() && row.stream()
|
||||
.allMatch(cell -> cell.getHeaderCells().isEmpty())) {
|
||||
for (int j = 0; j < row.size(); j++) {
|
||||
row.get(j).setHeaderCells(previousTableNonHeaderRow.get(j).getHeaderCells());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
private Paragraph buildTextBlock(List<AbstractTextContainer> wordBlockList, String lastHeadline) {
|
||||
|
||||
Paragraph paragraph = new Paragraph();
|
||||
TextBlock textBlock = null;
|
||||
@@ -85,22 +123,6 @@ public class SectionsBuilderService {
|
||||
} else {
|
||||
table.setHeadline("Table in: " + lastHeadline);
|
||||
}
|
||||
// Distribute header information for subsequent tables
|
||||
if (previousTable != null && hasInvalidHeaderInformation(table) && hasValidHeaderInformation(previousTable)) {
|
||||
List<Cell> previousTableNonHeaderRow = getRowWithNonHeaderCells(previousTable);
|
||||
List<Cell> tableNonHeaderRow = getRowWithNonHeaderCells(table);
|
||||
if (previousTableNonHeaderRow.size() == tableNonHeaderRow.size()) {
|
||||
for (int i = table.getRows().size() - 1; i >= 0; i--) { // Non header rows are most likely at bottom of table
|
||||
List<Cell> row = table.getRows().get(i);
|
||||
if (row.size() == previousTableNonHeaderRow.size()
|
||||
&& row.stream().allMatch(cell -> cell.getHeaderCells().isEmpty())) {
|
||||
for (int j = 0; j < row.size(); j++) {
|
||||
row.get(j).setHeaderCells(previousTableNonHeaderRow.get(j).getHeaderCells());
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
if (textBlock != null && !alreadyAdded) {
|
||||
paragraph.getPageBlocks().add(textBlock);
|
||||
|
||||
@@ -8,12 +8,6 @@ spring:
|
||||
profiles:
|
||||
active: kubernetes
|
||||
|
||||
platform.multi-tenancy:
|
||||
enabled: ${multitenancy.enabled:false}
|
||||
tenantFilter:
|
||||
urlPatterns: /redact
|
||||
urlPatternsToIgnore:
|
||||
|
||||
management:
|
||||
endpoint:
|
||||
metrics.enabled: ${monitoring.enabled:false}
|
||||
|
||||
+3
-3
@@ -214,7 +214,7 @@ public class EntityRedactionServiceTest {
|
||||
entityRedactionService.processDocument(classifiedDoc, null);
|
||||
assertThat(classifiedDoc.getEntities()).hasSize(2); // two pages
|
||||
assertThat(classifiedDoc.getEntities().get(1).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(8);
|
||||
assertThat(classifiedDoc.getEntities().get(2).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(4); // FIXME including one false positive "Y"
|
||||
assertThat(classifiedDoc.getEntities().get(2).stream().filter(entity -> entity.getMatchedRule() == 9).count()).isEqualTo(4);
|
||||
}
|
||||
}
|
||||
|
||||
@@ -228,11 +228,11 @@ public class EntityRedactionServiceTest {
|
||||
"global Section section\n" +
|
||||
"rule \"9: Redact Authors and Addresses in Reference Table, if it is a Vertebrate study\"\n" +
|
||||
" when\n" +
|
||||
" Section(isVertebrateStudy())\n" +
|
||||
" Section(rowEquals(\"Vertebrate study Y/N\", \"Y\"))\n" +
|
||||
" then\n" +
|
||||
" section.redact(\"name\", 9, \"Redacted because row is a vertebrate study\");\n" +
|
||||
" section.redact(\"address\", 9, \"Redacted because rows is a vertebrate study\");\n" +
|
||||
" section.highlightCell(\"Vertebrate study Y/N\", 9);\n" +
|
||||
" section.highlightCell(\"Vertebrate study Y/N\", 9, \"must_redact\");\n" +
|
||||
" end";
|
||||
when(rulesClient.getVersion()).thenReturn(1L);
|
||||
when(rulesClient.getRules()).thenReturn(new RulesResponse(tableRules));
|
||||
|
||||
+82
@@ -3,6 +3,7 @@ package com.iqser.red.service.redaction.v1.server.segmentation;
|
||||
import static org.assertj.core.api.Assertions.assertThat;
|
||||
|
||||
import java.io.IOException;
|
||||
import java.util.Collections;
|
||||
import java.util.List;
|
||||
import java.util.stream.Collectors;
|
||||
|
||||
@@ -18,6 +19,7 @@ import org.springframework.test.context.junit4.SpringRunner;
|
||||
|
||||
import com.iqser.red.service.redaction.v1.server.classification.model.Document;
|
||||
import com.iqser.red.service.redaction.v1.server.classification.service.BlockificationService;
|
||||
import com.iqser.red.service.redaction.v1.server.tableextraction.model.Cell;
|
||||
import com.iqser.red.service.redaction.v1.server.tableextraction.model.Table;
|
||||
import com.iqser.red.service.redaction.v1.server.tableextraction.service.RulingCleaningService;
|
||||
import com.iqser.red.service.redaction.v1.server.tableextraction.service.TableExtractionService;
|
||||
@@ -64,4 +66,84 @@ public class PdfSegmentationServiceTest {
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testTableExtraction() throws IOException {
|
||||
|
||||
ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Merge Table.pdf");
|
||||
|
||||
try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
|
||||
Document document = pdfSegmentationService.parseDocument(pdDocument);
|
||||
assertThat(document.getParagraphs()
|
||||
.stream()
|
||||
.flatMap(paragraph -> paragraph.getTables().stream())
|
||||
.collect(Collectors.toList())).isNotEmpty();
|
||||
Table firstTable = document.getParagraphs()
|
||||
.stream()
|
||||
.flatMap(paragraph -> paragraph.getTables().stream())
|
||||
.collect(Collectors.toList())
|
||||
.get(0);
|
||||
assertThat(firstTable.getColCount()).isEqualTo(8);
|
||||
assertThat(firstTable.getRowCount()).isEqualTo(1);
|
||||
Table secondTable = document.getParagraphs()
|
||||
.stream()
|
||||
.flatMap(paragraph -> paragraph.getTables().stream())
|
||||
.collect(Collectors.toList())
|
||||
.get(1);
|
||||
assertThat(secondTable.getColCount()).isEqualTo(8);
|
||||
assertThat(secondTable.getRowCount()).isEqualTo(2);
|
||||
List<List<Cell>> firstTableHeaderCells = firstTable.getRows()
|
||||
.get(0)
|
||||
.stream()
|
||||
.map(Collections::singletonList)
|
||||
.collect(Collectors.toList());
|
||||
assertThat(secondTable.getRows().stream()
|
||||
.allMatch(row -> row.stream()
|
||||
.map(Cell::getHeaderCells)
|
||||
.collect(Collectors.toList())
|
||||
.equals(firstTableHeaderCells)))
|
||||
.isTrue();
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
@Test
|
||||
public void testMultiPageMetadataPropagation() throws IOException {
|
||||
|
||||
ClassPathResource pdfFileResource = new ClassPathResource("files/Minimal Examples/Merge Multi Page Table.pdf");
|
||||
|
||||
try (PDDocument pdDocument = PDDocument.load(pdfFileResource.getInputStream())) {
|
||||
Document document = pdfSegmentationService.parseDocument(pdDocument);
|
||||
assertThat(document.getParagraphs()
|
||||
.stream()
|
||||
.flatMap(paragraph -> paragraph.getTables().stream())
|
||||
.collect(Collectors.toList())).isNotEmpty();
|
||||
Table firstTable = document.getParagraphs()
|
||||
.stream()
|
||||
.flatMap(paragraph -> paragraph.getTables().stream())
|
||||
.collect(Collectors.toList())
|
||||
.get(0);
|
||||
assertThat(firstTable.getColCount()).isEqualTo(9);
|
||||
assertThat(firstTable.getRowCount()).isEqualTo(5);
|
||||
Table secondTable = document.getParagraphs()
|
||||
.stream()
|
||||
.flatMap(paragraph -> paragraph.getTables().stream())
|
||||
.collect(Collectors.toList())
|
||||
.get(1);
|
||||
assertThat(secondTable.getColCount()).isEqualTo(9);
|
||||
assertThat(secondTable.getRowCount()).isEqualTo(6);
|
||||
List<List<Cell>> firstTableHeaderCells = firstTable.getRows()
|
||||
.get(firstTable.getRowCount() - 1)
|
||||
.stream()
|
||||
.map(Cell::getHeaderCells)
|
||||
.collect(Collectors.toList());
|
||||
assertThat(secondTable.getRows().stream()
|
||||
.allMatch(row -> row.stream()
|
||||
.map(Cell::getHeaderCells)
|
||||
.collect(Collectors.toList())
|
||||
.equals(firstTableHeaderCells)))
|
||||
.isTrue();
|
||||
}
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
+19
-16
@@ -90,28 +90,31 @@ rule "7: Redact contact information, if Producer is found"
|
||||
section.redactBetween("No:", "Fax", "address", 7, "Producer was found");
|
||||
end
|
||||
|
||||
rule "8: Redact Authors and Addresses in Reference Table, if it is a Vertebrate study"
|
||||
when
|
||||
Section(isVertebrateStudy())
|
||||
then
|
||||
section.redact("name", 8, "Redacted because row is a vertebrate study");
|
||||
section.redact("address", 8, "Redacted because row is a vertebrate study");
|
||||
section.highlightCell("Vertebrate study Y/N", 9);
|
||||
end
|
||||
|
||||
rule "9: Not redacted because Vertebrate Study = N"
|
||||
rule "8: Not redacted because Vertebrate Study = N"
|
||||
when
|
||||
Section(isNotVertebrateStudy())
|
||||
Section(rowEquals("Vertebrate study Y/N", "N"))
|
||||
then
|
||||
section.redactNot("name", 9, "Not redacted because row is not a vertebrate study");
|
||||
section.redactNot("address", 9, "Not redacted because row is not a vertebrate study");
|
||||
section.redactNot("name", 8, "Not redacted because row is not a vertebrate study");
|
||||
section.redactNot("address", 8, "Not redacted because row is not a vertebrate study");
|
||||
section.highlightCell("Vertebrate study Y/N", 8, "hint_only");
|
||||
end
|
||||
|
||||
|
||||
rule "10: Redact if must redact entry is found"
|
||||
rule "9: Redact if must redact entry is found"
|
||||
when
|
||||
eval(section.contains("must_redact")==true);
|
||||
then
|
||||
section.redact("name", 10, "must_redact entry was found.");
|
||||
section.redact("address", 10, "must_redact entry was found.");
|
||||
end
|
||||
section.redact("name", 9, "must_redact entry was found.");
|
||||
section.redact("address", 9, "must_redact entry was found.");
|
||||
end
|
||||
|
||||
|
||||
rule "10: Redact Authors and Addresses in Reference Table, if it is a Vertebrate study"
|
||||
when
|
||||
Section(rowEquals("Vertebrate study Y/N", "Y"))
|
||||
then
|
||||
section.redact("name", 10, "Redacted because row is a vertebrate study");
|
||||
section.redact("address", 10, "Redacted because row is a vertebrate study");
|
||||
section.highlightCell("Vertebrate study Y/N", 10, "must_redact");
|
||||
end
|
||||
|
||||
BIN
Binary file not shown.
Reference in New Issue
Block a user