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Fix handling of URL in file field (#7347)
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* Add workaround of test not working on Windows

Co-authored-by: Dominik Voigt <dominik.ingo.voigt@gmail.com>

* Change input of throws

Co-authored-by: Dominik Voigt <dominik.ingo.voigt@gmail.com>

* Add link as String as constructor parameter

* Add CHANGELOG entry

* Move tests for FieldFieldParser to FileFieldParserTest (and fix handling of //)

* Fix checkstyle

Co-authored-by: Dominik Voigt <dominik.ingo.voigt@gmail.com>
Co-authored-by: Carl Christian Snethlage <50491877+calixtus@users.noreply.github.com>
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@koppor @DominikVoigt @calixtus
3 people authored Jan 24, 2021
1 parent 7672b2d commit ae43548
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3 changes: 2 additions & 1 deletion CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -34,7 +34,8 @@ Note that this project **does not** adhere to [Semantic Versioning](http://semve
- We fixed an issue where the "Find unlinked files" dialog would freeze JabRef on importing. [#7205](https://github.com/JabRef/jabref/issues/7205)
- We fixed an issue where the "Find unlinked files" would stop importing when importing a single file failed. [#7206](https://github.com/JabRef/jabref/issues/7206)
- We fixed an issue where an exception would be displayed for previewing and preferences when a custom theme has been configured but is missing [#7177](https://github.com/JabRef/jabref/issues/7177)
- We fixed an issue where the regex based file search miss-interpreted specific symbols [#4342](https://github.com/JabRef/jabref/issues/4342)
- We fixed an issue where URLs in `file` fields could not be handled on Windows. [#7359](https://github.com/JabRef/jabref/issues/7359)
- We fixed an issue where the regex based file search miss-interpreted specific symbols. [#4342](https://github.com/JabRef/jabref/issues/4342)
- We fixed an issue where the Harvard RTF exporter used the wrong default file extension. [4508](https://github.com/JabRef/jabref/issues/4508)
- We fixed an issue where the Harvard RTF exporter did not use the new authors formatter and therefore did not export "organization" authors correctly. [4508](https://github.com/JabRef/jabref/issues/4508)
- We fixed an issue where the field `urldate` was not exported to the corresponding fields `YearAccessed`, `MonthAccessed`, `DayAccessed` in MS Office XML [#7354](https://github.com/JabRef/jabref/issues/7354)
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53 changes: 38 additions & 15 deletions src/main/java/org/jabref/logic/importer/util/FileFieldParser.java
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Expand Up @@ -2,6 +2,7 @@

import java.net.MalformedURLException;
import java.net.URL;
import java.nio.file.InvalidPathException;
import java.nio.file.Path;
import java.util.ArrayList;
import java.util.List;
Expand All @@ -17,7 +18,7 @@ public static List<LinkedFile> parse(String value) {
return files;
}

List<String> entry = new ArrayList<>();
List<String> linkedFileData = new ArrayList<>();
StringBuilder sb = new StringBuilder();
boolean inXmlChar = false;
boolean escaped = false;
Expand All @@ -39,30 +40,38 @@ public static List<LinkedFile> parse(String value) {
sb.append(c);
inXmlChar = false;
} else if (!escaped && (c == ':')) {
entry.add(sb.toString());
// We are in the next LinkedFile data element
linkedFileData.add(sb.toString());
sb = new StringBuilder();
} else if (!escaped && (c == ';') && !inXmlChar) {
entry.add(sb.toString());
sb = new StringBuilder();
linkedFileData.add(sb.toString());
files.add(convert(linkedFileData));

files.add(convert(entry));
// next iteration
sb = new StringBuilder();
} else {
sb.append(c);
}
escaped = false;
}
if (sb.length() > 0) {
entry.add(sb.toString());
linkedFileData.add(sb.toString());
}

if (!entry.isEmpty()) {
files.add(convert(entry));
if (!linkedFileData.isEmpty()) {
files.add(convert(linkedFileData));
}

return files;
}

private static LinkedFile convert(List<String> entry) {
/**
* Converts the given textual representation of a LinkedFile object
*
* SIDE EFFECT: The given entry list is cleared upon completion
*
* @param entry the list of elements in the linked file textual representation
* @return a LinkedFile object
*/
static LinkedFile convert(List<String> entry) {
// ensure list has at least 3 fields
while (entry.size() < 3) {
entry.add("");
Expand All @@ -71,17 +80,31 @@ private static LinkedFile convert(List<String> entry) {
LinkedFile field = null;
if (LinkedFile.isOnlineLink(entry.get(1))) {
try {
field = new LinkedFile(new URL(entry.get(1)), entry.get(2));
field = new LinkedFile(entry.get(0), new URL(entry.get(1)), entry.get(2));
} catch (MalformedURLException ignored) {
// ignored
// in case the URL is malformed, store it nevertheless
field = new LinkedFile(entry.get(0), entry.get(1), entry.get(2));
}
}

if (field == null) {
field = new LinkedFile(entry.get(0), Path.of(entry.get(1)), entry.get(2));
String pathStr = entry.get(1);
if (pathStr.contains("//")) {
// In case the path contains //, we assume it is a malformed URL, not a malformed path.
// On linux, the double slash would be converted to a single slash.
field = new LinkedFile(entry.get(0), pathStr, entry.get(2));
} else {
try {
// there is no Path.isValidPath(String) method
Path path = Path.of(pathStr);
field = new LinkedFile(entry.get(0), path, entry.get(2));
} catch (InvalidPathException e) {
field = new LinkedFile(entry.get(0), pathStr, entry.get(2));
}
}
}

// link is only mandatory field
// link is the only mandatory field
if (field.getDescription().isEmpty() && field.getLink().isEmpty() && !field.getFileType().isEmpty()) {
field = new LinkedFile("", Path.of(field.getFileType()), "");
} else if (!field.getDescription().isEmpty() && field.getLink().isEmpty() && field.getFileType().isEmpty()) {
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17 changes: 13 additions & 4 deletions src/main/java/org/jabref/model/entry/LinkedFile.java
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Expand Up @@ -33,15 +33,24 @@ public class LinkedFile implements Serializable {
private transient StringProperty fileType = new SimpleStringProperty();

public LinkedFile(String description, Path link, String fileType) {
this(Objects.requireNonNull(description), Objects.requireNonNull(link).toString(), Objects.requireNonNull(fileType));
}

/**
* Constructor for non-valid paths. We need to parse them, because the GUI needs to render it.
*/
public LinkedFile(String description, String link, String fileType) {
this.description.setValue(Objects.requireNonNull(description));
setLink(Objects.requireNonNull(link).toString());
setLink(link);
this.fileType.setValue(Objects.requireNonNull(fileType));
}

public LinkedFile(URL link, String fileType) {
this.description.setValue("");
setLink(Objects.requireNonNull(link).toString());
this.fileType.setValue(Objects.requireNonNull(fileType));
this("", Objects.requireNonNull(link).toString(), Objects.requireNonNull(fileType));
}

public LinkedFile(String description, URL link, String fileType) {
this(description, Objects.requireNonNull(link).toString(), Objects.requireNonNull(fileType));
}

public StringProperty descriptionProperty() {
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129 changes: 4 additions & 125 deletions src/test/java/org/jabref/logic/bibtex/FileFieldWriterTest.java
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Original file line number Diff line number Diff line change
@@ -1,13 +1,7 @@
package org.jabref.logic.bibtex;

import java.net.MalformedURLException;
import java.net.URL;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;

import org.jabref.logic.importer.util.FileFieldParser;
import org.jabref.model.entry.LinkedFile;

import org.junit.jupiter.api.Test;
Expand All @@ -17,121 +11,6 @@

public class FileFieldWriterTest {

@Test
public void emptyListForEmptyInput() {
String emptyInput = "";

assertEquals(Collections.emptyList(), FileFieldParser.parse(emptyInput));
assertEquals(Collections.emptyList(), FileFieldParser.parse(null));
}

@Test
public void parseCorrectInput() {
String input = "Desc:File.PDF:PDF";

assertEquals(
Collections.singletonList(new LinkedFile("Desc", Path.of("File.PDF"), "PDF")),
FileFieldParser.parse(input));
}

@Test
public void parseCorrectOnlineInput() throws MalformedURLException {
String input = ":http\\://arxiv.org/pdf/2010.08497v1:PDF";
String inputURL = "http://arxiv.org/pdf/2010.08497v1";
List<LinkedFile> expected = Collections.singletonList(new LinkedFile(new URL(inputURL), "PDF"));

assertEquals(expected, FileFieldParser.parse(input));
}

@Test
public void parseFaultyOnlineInput() {
String input = ":htt\\://arxiv.org/pdf/2010.08497v1:PDF";
String inputURL = "htt://arxiv.org/pdf/2010.08497v1";
List<LinkedFile> expected = Collections.singletonList(new LinkedFile("", Path.of(inputURL), "PDF"));

assertEquals(expected, FileFieldParser.parse(input));
}

@Test
public void ingoreMissingDescription() {
String input = ":wei2005ahp.pdf:PDF";

assertEquals(
Collections.singletonList(new LinkedFile("", Path.of("wei2005ahp.pdf"), "PDF")),
FileFieldParser.parse(input));
}

@Test
public void interpreteLinkAsOnlyMandatoryField() {
String single = "wei2005ahp.pdf";
String multiple = "wei2005ahp.pdf;other.pdf";

assertEquals(
Collections.singletonList(new LinkedFile("", Path.of("wei2005ahp.pdf"), "")),
FileFieldParser.parse(single));

assertEquals(
Arrays.asList(
new LinkedFile("", Path.of("wei2005ahp.pdf"), ""),
new LinkedFile("", Path.of("other.pdf"), "")),
FileFieldParser.parse(multiple));
}

@Test
public void escapedCharactersInDescription() {
String input = "test\\:\\;:wei2005ahp.pdf:PDF";

assertEquals(
Collections.singletonList(new LinkedFile("test:;", Path.of("wei2005ahp.pdf"), "PDF")),
FileFieldParser.parse(input));
}

@Test
public void handleXmlCharacters() {
String input = "test&#44\\;st\\:\\;:wei2005ahp.pdf:PDF";

assertEquals(
Collections.singletonList(new LinkedFile("test&#44;st:;", Path.of("wei2005ahp.pdf"), "PDF")),
FileFieldParser.parse(input));
}

@Test
public void handleEscapedFilePath() {
String input = "desc:C\\:\\\\test.pdf:PDF";

assertEquals(
Collections.singletonList(new LinkedFile("desc", Path.of("C:\\test.pdf"), "PDF")),
FileFieldParser.parse(input));
}

@Test
public void subsetOfFieldsResultsInFileLink() {
String descOnly = "file.pdf::";
String fileOnly = ":file.pdf";
String typeOnly = "::file.pdf";

assertEquals(
Collections.singletonList(new LinkedFile("", Path.of("file.pdf"), "")),
FileFieldParser.parse(descOnly));

assertEquals(
Collections.singletonList(new LinkedFile("", Path.of("file.pdf"), "")),
FileFieldParser.parse(fileOnly));

assertEquals(
Collections.singletonList(new LinkedFile("", Path.of("file.pdf"), "")),
FileFieldParser.parse(typeOnly));
}

@Test
public void tooManySeparators() {
String input = "desc:file.pdf:PDF:asdf";

assertEquals(
Collections.singletonList(new LinkedFile("desc", Path.of("file.pdf"), "PDF")),
FileFieldParser.parse(input));
}

@Test
public void testQuoteStandard() {
assertEquals("a", FileFieldWriter.quote("a"));
Expand All @@ -154,10 +33,10 @@ public void testQuoteNull() {

@Test
public void testEncodeStringArray() {
assertEquals("a:b;c:d", FileFieldWriter.encodeStringArray(new String[][]{{"a", "b"}, {"c", "d"}}));
assertEquals("a:;c:d", FileFieldWriter.encodeStringArray(new String[][]{{"a", ""}, {"c", "d"}}));
assertEquals("a:" + null + ";c:d", FileFieldWriter.encodeStringArray(new String[][]{{"a", null}, {"c", "d"}}));
assertEquals("a:\\:b;c\\;:d", FileFieldWriter.encodeStringArray(new String[][]{{"a", ":b"}, {"c;", "d"}}));
assertEquals("a:b;c:d", FileFieldWriter.encodeStringArray(new String[][] {{"a", "b"}, {"c", "d"}}));
assertEquals("a:;c:d", FileFieldWriter.encodeStringArray(new String[][] {{"a", ""}, {"c", "d"}}));
assertEquals("a:" + null + ";c:d", FileFieldWriter.encodeStringArray(new String[][] {{"a", null}, {"c", "d"}}));
assertEquals("a:\\:b;c\\;:d", FileFieldWriter.encodeStringArray(new String[][] {{"a", ":b"}, {"c;", "d"}}));
}

@Test
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