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Add a new parseJabRefComment with unit test #12145

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Add a new parseJabRefComment with unit test #12145

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56c1bef
add a new parseJabRefComment
leaf-soba Nov 4, 2024
b2646ae
fix logic check string contains a valid json
leaf-soba Nov 4, 2024
e12e655
read json as metadata
leaf-soba Nov 5, 2024
465d6cf
Merge branch 'main' into close-issue-10371
leaf-soba Nov 11, 2024
830e7e6
rewrite metaDataParser.parse
leaf-soba Nov 14, 2024
065a784
fix wrong input
leaf-soba Nov 15, 2024
3c4ee8f
follow the review fix code
leaf-soba Nov 20, 2024
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20 changes: 20 additions & 0 deletions src/main/java/org/jabref/logic/importer/fileformat/BibtexParser.java
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Expand Up @@ -20,6 +20,7 @@
import java.util.Optional;
import java.util.Set;
import java.util.function.Predicate;
import java.util.regex.Matcher;
import java.util.regex.Pattern;

import javax.xml.parsers.DocumentBuilderFactory;
Expand Down Expand Up @@ -58,6 +59,8 @@
import com.dd.plist.BinaryPropertyListParser;
import com.dd.plist.NSDictionary;
import com.dd.plist.NSString;
import com.google.gson.Gson;
import com.google.gson.JsonObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.w3c.dom.Document;
Expand Down Expand Up @@ -354,6 +357,7 @@ private void parseJabRefComment(Map<String, String> meta) {
// We remove all line breaks in the metadata
// These have been inserted to prevent too long lines when the file was saved, and are not part of the data.
String comment = buffer.toString().replaceAll("[\\x0d\\x0a]", "");

if (comment.substring(0, Math.min(comment.length(), MetaData.META_FLAG.length())).equals(MetaData.META_FLAG)) {
if (comment.startsWith(MetaData.META_FLAG)) {
String rest = comment.substring(MetaData.META_FLAG.length());
Expand Down Expand Up @@ -386,7 +390,23 @@ private void parseJabRefComment(Map<String, String> meta) {
} catch (ParseException ex) {
parserResult.addException(ex);
}
} else if (comment.substring(0, Math.min(comment.length(), MetaData.META_FLAG_VERSION_010.length())).equals(MetaData.META_FLAG_VERSION_010)) {
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Java strings support startsWith. I think, this should be used here instead of this complicated thign.

parseCommentToJson(comment, meta);
}
}

private JsonObject parseCommentToJson(String comment, Map<String, String> meta) {
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Remove the map as parameter. It should not be modified.

The JsonObject should be separate - to enable handling v5.x meta data (Map) and v6.x metadata (JSON)

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Moreover, return Optional<JsonObject> (which is more modern Java)

Pattern pattern = Pattern.compile("\\{.*}", Pattern.DOTALL);
Matcher matcher = pattern.matcher(comment);
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I think, just doing comments.substring(MetaData.META_FLAG_VERSION_010) should to the trick. - No need for more checking here.

if (matcher.find()) {
String jsonString = matcher.group();
Gson gson = new Gson();
JsonObject jsonObject = gson.fromJson(jsonString, JsonObject.class);
String jsonResult = gson.toJson(jsonObject);
meta.putIfAbsent(MetaData.META_FLAG_VERSION_010, jsonResult);
return jsonObject;
}
return null;
}

/**
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74 changes: 74 additions & 0 deletions src/main/java/org/jabref/logic/importer/util/MetaDataParser.java
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Expand Up @@ -4,6 +4,7 @@
import java.io.Reader;
import java.io.StringReader;
import java.nio.file.Path;
import java.util.AbstractMap;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashMap;
Expand Down Expand Up @@ -35,6 +36,8 @@
import org.jabref.model.strings.StringUtil;
import org.jabref.model.util.FileUpdateMonitor;

import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

Expand Down Expand Up @@ -97,6 +100,77 @@ public MetaData parse(Map<String, String> data, Character keywordSeparator) thro
return parse(new MetaData(), data, keywordSeparator);
}

public MetaData parse(JsonObject data, Character keywordSeparator) throws ParseException {
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return parse(new MetaData(), data, keywordSeparator);
}

public MetaData parse(MetaData metaData, JsonObject data, Character keywordSeparator) throws ParseException {
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Add JavaDoc - I don't get this.

I think, this should not be in this PR for now - We only focus on the JSON - and then, we can work on the parsing of the JSON.

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Please, either test this method or remove it - and put it to the next PR.

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This method is should be static, shouldn't it?

CitationKeyPattern defaultCiteKeyPattern = CitationKeyPattern.NULL_CITATION_KEY_PATTERN;
Map<EntryType, CitationKeyPattern> nonDefaultCiteKeyPatterns = new HashMap<>();

// process groups (GROUPSTREE and GROUPSTREE_LEGACY) at the very end (otherwise it can happen that not all dependent data are set)
List<Map.Entry<String, String>> entryList = new ArrayList<>();
for (Map.Entry<String, JsonElement> entry : data.entrySet()) {
// Add each entry to the list, converting JsonElement to String
entryList.add(new AbstractMap.SimpleEntry<>(entry.getKey(), entry.getValue().getAsString()));
}

entryList.sort(groupsLast());

for (Map.Entry<String, String> entry : entryList) {
List<String> values = getAsList(entry.getValue());

if (entry.getKey().startsWith(MetaData.PREFIX_KEYPATTERN)) {
EntryType entryType = EntryTypeFactory.parse(entry.getKey().substring(MetaData.PREFIX_KEYPATTERN.length()));
nonDefaultCiteKeyPatterns.put(entryType, new CitationKeyPattern(getSingleItem(values)));
} else if (entry.getKey().startsWith(MetaData.SELECTOR_META_PREFIX)) {
// edge case, it might be one special field e.g. article from biblatex-apa, but we can't distinguish this from any other field and rather prefer to handle it as UnknownField
metaData.addContentSelector(ContentSelectors.parse(FieldFactory.parseField(entry.getKey().substring(MetaData.SELECTOR_META_PREFIX.length())), StringUtil.unquote(entry.getValue(), MetaData.ESCAPE_CHARACTER)));
} else if (entry.getKey().equals(MetaData.FILE_DIRECTORY)) {
metaData.setLibrarySpecificFileDirectory(parseDirectory(entry.getValue()));
} else if (entry.getKey().startsWith(MetaData.FILE_DIRECTORY + '-')) {
// The user name starts directly after FILE_DIRECTORY + '-'
String user = entry.getKey().substring(MetaData.FILE_DIRECTORY.length() + 1);
metaData.setUserFileDirectory(user, parseDirectory(entry.getValue()));
} else if (entry.getKey().startsWith(MetaData.FILE_DIRECTORY_LATEX)) {
// The user name starts directly after FILE_DIRECTORY_LATEX + '-'
String user = entry.getKey().substring(MetaData.FILE_DIRECTORY_LATEX.length() + 1);
Path path = Path.of(parseDirectory(entry.getValue())).normalize();
metaData.setLatexFileDirectory(user, path);
} else if (entry.getKey().equals(MetaData.SAVE_ACTIONS)) {
metaData.setSaveActions(fieldFormatterCleanupsParse(values));
} else if (entry.getKey().equals(MetaData.DATABASE_TYPE)) {
metaData.setMode(BibDatabaseMode.parse(getSingleItem(values)));
} else if (entry.getKey().equals(MetaData.KEYPATTERNDEFAULT)) {
defaultCiteKeyPattern = new CitationKeyPattern(getSingleItem(values));
} else if (entry.getKey().equals(MetaData.PROTECTED_FLAG_META)) {
if (Boolean.parseBoolean(getSingleItem(values))) {
metaData.markAsProtected();
} else {
metaData.markAsNotProtected();
}
} else if (entry.getKey().equals(MetaData.SAVE_ORDER_CONFIG)) {
metaData.setSaveOrder(SaveOrder.parse(values));
} else if (entry.getKey().equals(MetaData.GROUPSTREE) || entry.getKey().equals(MetaData.GROUPSTREE_LEGACY)) {
metaData.setGroups(GroupsParser.importGroups(values, keywordSeparator, fileMonitor, metaData));
} else if (entry.getKey().equals(MetaData.GROUPS_SEARCH_SYNTAX_VERSION)) {
Version version = Version.parse(getSingleItem(values));
metaData.setGroupSearchSyntaxVersion(version);
} else if (entry.getKey().equals(MetaData.VERSION_DB_STRUCT)) {
metaData.setVersionDBStructure(getSingleItem(values));
} else {
// Keep meta data items that we do not know in the file
metaData.putUnknownMetaDataItem(entry.getKey(), values);
}
}

if (!defaultCiteKeyPattern.equals(CitationKeyPattern.NULL_CITATION_KEY_PATTERN) || !nonDefaultCiteKeyPatterns.isEmpty()) {
metaData.setCiteKeyPattern(defaultCiteKeyPattern, nonDefaultCiteKeyPatterns);
}

return metaData;
}

/**
* Parses the data map and changes the given {@link MetaData} instance respectively.
*
Expand Down
5 changes: 1 addition & 4 deletions src/main/java/org/jabref/model/metadata/MetaData.java
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Expand Up @@ -31,13 +31,12 @@
import com.google.common.eventbus.EventBus;
import com.tobiasdiez.easybind.optional.OptionalBinding;
import com.tobiasdiez.easybind.optional.OptionalWrapper;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;

@AllowedToUseLogic("because it needs access to citation pattern and cleanups")
public class MetaData {

public static final String META_FLAG = "jabref-meta: ";
public static final String META_FLAG_VERSION_010 = "jabref-meta-0.1.0";
public static final String ENTRYTYPE_FLAG = "jabref-entrytype: ";
public static final String SAVE_ORDER_CONFIG = "saveOrderConfig"; // ToDo: Rename in next major version to saveOrder, adapt testbibs
public static final String SAVE_ACTIONS = "saveActions";
Expand All @@ -58,8 +57,6 @@ public class MetaData {
public static final char SEPARATOR_CHARACTER = ';';
public static final String SEPARATOR_STRING = String.valueOf(SEPARATOR_CHARACTER);

private static final Logger LOGGER = LoggerFactory.getLogger(MetaData.class);

private final EventBus eventBus = new EventBus();
private final Map<EntryType, String> citeKeyPatterns = new HashMap<>(); // <BibType, Pattern>
private final Map<String, String> userFileDirectory = new HashMap<>(); // <User, FilePath>
Expand Down
23 changes: 23 additions & 0 deletions src/test/java/org/jabref/logic/importer/fileformat/BibtexParserTest.java
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Expand Up @@ -55,6 +55,7 @@
import org.jabref.model.groups.RegexKeywordGroup;
import org.jabref.model.groups.TexGroup;
import org.jabref.model.groups.WordKeywordGroup;
import org.jabref.model.metadata.MetaData;
import org.jabref.model.metadata.SaveOrder;

import org.junit.jupiter.api.BeforeEach;
Expand Down Expand Up @@ -2238,4 +2239,26 @@ void parseInvalidBibDeskFilesResultsInWarnings() throws IOException {

assertEquals(List.of(firstEntry, secondEntry), result.getDatabase().getEntries());
}

@Test
void parseJabRefSingleJsonComment() throws IOException {
String entries =
"""
@Comment{jabref-meta-0.1.0
{
"saveActions" :
{
"state": true,
"date": ["normalize_date", "action2"],
"pages" : ["normalize_page_numbers"],
"month" : ["normalize_month"]
}
}
}
""";
ParserResult result = parser.parse(new StringReader(entries));
MetaData expectedMetaData = new MetaData();
expectedMetaData.putUnknownMetaDataItem("jabref-meta-0.1.0", List.of("{\"saveActions\":{\"state\":true,\"date\":[\"normalize_date\",\"action2\"],\"pages\":[\"normalize_page_numbers\"],\"month\":[\"normalize_month\"]}}"));
assertEquals(expectedMetaData, result.getMetaData());
}
}
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