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Crafting round-trip test for Cff importer/exporter #10957

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Crafting round-trip test for Cff importer/exporter #10957

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8227613
issue #10661 - feat: added option to export in cff
jeanprbt Feb 25, 2024
2121718
issue #10661 - feat: updated CHANGELOG.md
jeanprbt Feb 25, 2024
3ead720
issue #10661 - feat: added date field to cff export
jeanprbt Feb 25, 2024
8216a62
issue #10661 - fix: fixed checkstyle errors
jeanprbt Feb 25, 2024
ca86864
merge branch 'main' into issue/10661
jeanprbt Feb 26, 2024
df182ce
Bump org.apache.lucene:lucene-queries from 9.9.1 to 9.10.0 (#10920)
dependabot[bot] Feb 26, 2024
e147f8a
Fix for delete entries should ask user (#10591)
shawn-jj Feb 26, 2024
00eed62
Fix variable name
koppor Feb 26, 2024
7119c20
Fix duplicate check/merge entries dialog not triggered on import from…
Siedlerchr Feb 27, 2024
e6b3179
merge branch 'main' into issue/10661
jeanprbt Feb 27, 2024
7a9de00
issue #10661 - fix: fixed PR review comments
jeanprbt Feb 27, 2024
d7e8b93
issue #10661 - added preferred citation feild and its test
Raahitya-14 Mar 1, 2024
3fe4d3a
issue #10661_RTT - Added preferred citation field and its test
Raahitya-14 Mar 2, 2024
1e8f3b7
Merge branch 'main' into issue/10661_RTT
koppor Mar 2, 2024
f990a25
issue #10661_RTT - fixed method names and CffImporterTest()
Raahitya-14 Mar 2, 2024
7bf71f1
Merge branch 'issue/10661_RTT' of https://github.com/JEANPRBT/jabref …
Raahitya-14 Mar 2, 2024
ca2e873
Fixed preferred citation, fixed tests and added importCITATION() test
Raahitya-14 Mar 3, 2024
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170 changes: 111 additions & 59 deletions src/main/java/org/jabref/logic/importer/fileformat/CffImporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,22 +6,19 @@
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;

import org.jabref.logic.importer.Importer;
import org.jabref.logic.importer.ParserResult;
import org.jabref.logic.util.StandardFileType;
import org.jabref.model.entry.Author;
import org.jabref.model.entry.AuthorList;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.BiblatexSoftwareField;
import org.jabref.model.entry.field.Field;
import org.jabref.model.entry.field.StandardField;
import org.jabref.model.entry.field.UnknownField;
import org.jabref.model.entry.types.StandardEntryType;

import com.fasterxml.jackson.annotation.JsonAnySetter;
import com.fasterxml.jackson.annotation.JsonProperty;
import com.fasterxml.jackson.databind.JsonNode;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;

Expand Down Expand Up @@ -57,9 +54,23 @@ private static class CffFormat {
@JsonProperty("identifiers")
private List<CffIdentifier> ids;

@JsonProperty("preferred-citation")
private JsonNode preferredCitation;

@JsonProperty("type")
private String type;

public CffFormat() {
}

public JsonNode getPreferredCitation() {
return preferredCitation;
}

public void setPreferredCitation(JsonNode preferredCitation) {
this.preferredCitation = preferredCitation;
}

@JsonAnySetter
private void setValues(String key, String value) {
values.put(key, value);
Expand Down Expand Up @@ -92,73 +103,99 @@ public CffIdentifier() {
public ParserResult importDatabase(BufferedReader reader) throws IOException {
ObjectMapper mapper = new ObjectMapper(new YAMLFactory());
CffFormat citation = mapper.readValue(reader, CffFormat.class);
HashMap<Field, String> entryMap = new HashMap<>();
StandardEntryType entryType = StandardEntryType.Software;

// Map CFF fields to JabRef Fields
HashMap<String, Field> fieldMap = getFieldMappings();
for (Map.Entry<String, String> property : citation.values.entrySet()) {
if (fieldMap.containsKey(property.getKey())) {
entryMap.put(fieldMap.get(property.getKey()), property.getValue());
} else if ("type".equals(property.getKey())) {
if ("dataset".equals(property.getValue())) {
entryType = StandardEntryType.Dataset;
}
} else if (getUnmappedFields().contains(property.getKey())) {
entryMap.put(new UnknownField(property.getKey()), property.getValue());
}
}

// Translate CFF author format to JabRef author format
String authorStr = citation.authors.stream()
.map(author -> author.values)
.map(vals -> vals.get("name") != null ?
new Author(vals.get("name"), "", "", "", "") :
new Author(vals.get("given-names"), null, vals.get("name-particle"),
vals.get("family-names"), vals.get("name-suffix")))
.collect(AuthorList.collect())
.getAsFirstLastNamesWithAnd();
entryMap.put(StandardField.AUTHOR, authorStr);

// Select DOI to keep
if ((entryMap.get(StandardField.DOI) == null) && (citation.ids != null)) {
List<CffIdentifier> doiIds = citation.ids.stream()
.filter(id -> "doi".equals(id.type))
.collect(Collectors.toList());
if (doiIds.size() == 1) {
entryMap.put(StandardField.DOI, doiIds.getFirst().value);
}
StandardEntryType entryType = StandardEntryType.Misc;
if (citation.type != null) {
entryType = mapType(citation.type);
}
BibEntry entry = new BibEntry(entryType);
HashMap<Field, String> entryMap = new HashMap<>();

// Select SWHID to keep
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if (citation.ids != null) {
List<String> swhIds = citation.ids.stream()
.filter(id -> "swh".equals(id.type))
.map(id -> id.value)
.collect(Collectors.toList());

if (swhIds.size() == 1) {
entryMap.put(BiblatexSoftwareField.SWHID, swhIds.getFirst());
} else if (swhIds.size() > 1) {
List<String> relSwhIds = swhIds.stream()
.filter(id -> id.split(":").length > 3) // quick filter for invalid swhids
.filter(id -> "rel".equals(id.split(":")[2]))
.collect(Collectors.toList());
if (relSwhIds.size() == 1) {
entryMap.put(BiblatexSoftwareField.SWHID, relSwhIds.getFirst());
}
}
if (citation.getPreferredCitation() != null) {
PreferredCitationMethod(citation.getPreferredCitation(), entryMap, entry);
}

BibEntry entry = new BibEntry(entryType);
entry.setField(entryMap);
MainCffContentMethod(citation, entryMap, entry);
entryMap.forEach(entry::setField);

List<BibEntry> entriesList = new ArrayList<>();
entriesList.add(entry);

return new ParserResult(entriesList);
}

private void PreferredCitationMethod(JsonNode preferredCitation, Map<Field, String> entryMap, BibEntry entry) {
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method start with a lower case letter (lower camel case)

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Sure I'll change the method name. Thank you!

if (preferredCitation != null) {
if (preferredCitation.has("title")) {
entryMap.put(StandardField.TITLE, preferredCitation.get("title").asText());
}
if (preferredCitation.has("doi")) {
entryMap.put(StandardField.DOI, preferredCitation.get("doi").asText());
}
if (preferredCitation.has("authors")) {
List<String> authorsList = new ArrayList<>();
preferredCitation.get("authors").forEach(authorNode -> {
String givenName = authorNode.has("given-names") ? authorNode.get("given-names").asText() : "";
String familyName = authorNode.has("family-names") ? authorNode.get("family-names").asText() : "";
authorsList.add((givenName + " " + familyName).trim());
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});
String authors = String.join(" and ", authorsList);
entryMap.put(StandardField.AUTHOR, authors);
}
if (preferredCitation.has("journal")) {
entryMap.put(StandardField.JOURNAL, preferredCitation.get("journal").asText());
}
if (preferredCitation.has("volume")) {
entryMap.put(StandardField.VOLUME, preferredCitation.get("volume").asText());
}
if (preferredCitation.has("issue")) {
entryMap.put(StandardField.ISSUE, preferredCitation.get("issue").asText());
}
if (preferredCitation.has("year")) {
entryMap.put(StandardField.YEAR, preferredCitation.get("year").asText());
}
if (preferredCitation.has("start") && preferredCitation.has("end")) {
String pages = preferredCitation.get("start").asText() + "-" + preferredCitation.get("end").asText();
entryMap.put(StandardField.PAGES, pages);
}
if (preferredCitation.has("type")) {
String typeValue = preferredCitation.get("type").asText();
StandardEntryType entryType = mapType(typeValue);
entry.setType(entryType);
}
}
}

private void MainCffContentMethod(CffFormat citation, Map<Field, String> entryMap, BibEntry entry) {
if (!entryMap.containsKey(StandardField.TITLE) && citation.values.containsKey("title")) {
entryMap.put(StandardField.TITLE, citation.values.get("title"));
}
if (!entryMap.containsKey(StandardField.AUTHOR) && citation.authors != null && !citation.authors.isEmpty()) {
List<String> authorsList = new ArrayList<>();
for (CffAuthor author : citation.authors) {
String givenName = author.values.getOrDefault("given-names", "");
String familyName = author.values.getOrDefault("family-names", "");
authorsList.add((givenName + " " + familyName).trim());
}
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String authors = String.join(" and ", authorsList);
entryMap.put(StandardField.AUTHOR, authors);
}
if (!entryMap.containsKey(StandardField.DOI) && citation.values.containsKey("doi")) {
entryMap.put(StandardField.DOI, citation.values.get("doi"));
}
if (!entryMap.containsKey(StandardField.VERSION) && citation.values.containsKey("version")) {
entryMap.put(StandardField.VERSION, citation.values.get("version"));
}
if (!entryMap.containsKey(StandardField.YEAR) && citation.values.containsKey("date-released")) {
String dateReleased = citation.values.get("date-released");
String year = dateReleased.split("-")[0];
entryMap.put(StandardField.YEAR, year);
}
if (!entryMap.containsKey(StandardField.URL) && citation.values.containsKey("url")) {
entryMap.put(StandardField.URL, citation.values.get("url"));
}
}

@Override
public boolean isRecognizedFormat(BufferedReader reader) throws IOException {

Expand All @@ -173,6 +210,21 @@ public boolean isRecognizedFormat(BufferedReader reader) throws IOException {
}
}

private StandardEntryType mapType(String cffType) {
return switch (cffType) {
case "article", "conference-paper" -> StandardEntryType.Article;
case "book" -> StandardEntryType.Book;
case "conference" -> StandardEntryType.InProceedings;
case "proceedings" -> StandardEntryType.Proceedings;
case "misc" -> StandardEntryType.Misc;
case "manual" -> StandardEntryType.Manual;
case "software" -> StandardEntryType.Software;
case "report" -> StandardEntryType.TechReport;
case "unpublished" -> StandardEntryType.Unpublished;
default -> StandardEntryType.Misc;
};
}

private HashMap<String, Field> getFieldMappings() {
HashMap<String, Field> fieldMappings = new HashMap<>();
fieldMappings.put("title", StandardField.TITLE);
Expand Down
72 changes: 72 additions & 0 deletions src/test/java/org/jabref/logic/importer/CffImporterTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,72 @@
import java.io.BufferedReader;
import java.io.StringReader;
import java.util.List;

import org.jabref.logic.importer.ParserResult;
import org.jabref.logic.importer.fileformat.CffImporter;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.StandardField;

import org.junit.jupiter.api.Test;

import static org.junit.jupiter.api.Assertions.assertEquals;

public class CffImporterTest {
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@Test
public void PreferredCitationTest() throws Exception {
String cffContent = """
cff-version: 1.2.0
message: "If you use this software, please cite it as below."
authors:
- family-names: "Lisa"
given-names: "Mona"
orcid: "https://orcid.org/0000-0000-0000-0000"
- family-names: "Bot"
given-names: "Hew"
orcid: "https://orcid.org/0000-0000-0000-0000"
title: "My Research Software"
version: 2.0.4
doi: 10.5281/zenodo.1234
date-released: 2017-12-18
url: "https://github.com/github-linguist/linguist"
preferred-citation:
type: article
authors:
- family-names: "Lisa"
given-names: "Mona"
orcid: "https://orcid.org/0000-0000-0000-0000"
- family-names: "Bot"
given-names: "Hew"
orcid: "https://orcid.org/0000-0000-0000-0000"
doi: "10.0000/00000"
journal: "Journal Title"
month: 9
start: 1
end: 10
title: "My awesome research software"
issue: 1
volume: 1
year: 2021
""";

CffImporter importer = new CffImporter();
try (BufferedReader reader = new BufferedReader(new StringReader(cffContent))) {
ParserResult result = importer.importDatabase(reader);
List<BibEntry> entries = result.getDatabase().getEntries();

assertEquals(1, entries.size());
BibEntry entry = entries.get(0);

assertEquals("My awesome research software", entry.getField(StandardField.TITLE).orElse(null));
assertEquals("Mona Lisa and Hew Bot", entry.getField(StandardField.AUTHOR).orElse(null));
assertEquals("10.0000/00000", entry.getField(StandardField.DOI).orElse(null));
assertEquals("Journal Title", entry.getField(StandardField.JOURNAL).orElse(null));
assertEquals("1", entry.getField(StandardField.VOLUME).orElse(null));
assertEquals("1", entry.getField(StandardField.ISSUE).orElse(null));
assertEquals("1-10", entry.getField(StandardField.PAGES).orElse(null));
assertEquals("2021", entry.getField(StandardField.YEAR).orElse(null));
System.out.println("Test Successful!");
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Please rewrite using the idea of org.jabref.logic.database.DatabaseMergerTest#mergeAddsNonDuplicateEntries: List.of, BibEntry.withfield...

Please no Println with "test successful". IntelliJ will have green or red indicators. See the last part (marked as "optional") in our guide: https://devdocs.jabref.org/getting-into-the-code/guidelines-for-setting-up-a-local-workspace/intellij-12-build.html

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@Raahitya-14 Raahitya-14 Mar 2, 2024 •
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Sure , I'll make the necessary changes. Thanks for the comments!

}
}
}
4 changes: 3 additions & 1 deletion src/test/java/org/jabref/logic/importer/ImporterTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -6,6 +6,7 @@

import org.jabref.logic.importer.fileformat.BiblioscapeImporter;
import org.jabref.logic.importer.fileformat.BibtexImporter;
import org.jabref.logic.importer.fileformat.CffImporter;
import org.jabref.logic.importer.fileformat.CitaviXmlImporter;
import org.jabref.logic.importer.fileformat.CopacImporter;
import org.jabref.logic.importer.fileformat.EndnoteImporter;
Expand Down Expand Up @@ -126,7 +127,8 @@ public static Stream<Importer> instancesToTest() {
new RepecNepImporter(importFormatPreferences),
new RisImporter(),
new SilverPlatterImporter(),
new CitaviXmlImporter()
new CitaviXmlImporter(),
new CffImporter()
);
// @formatter:on
}
Expand Down
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