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Added option to import CFF files #7946

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merged 9 commits into from
Sep 1, 2021
Merged

Added option to import CFF files #7946

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32f7297
Added option to import CFF files
AidanM11 Jul 29, 2021
4ddc414
Added tests, also minor fixes
AidanM11 Aug 16, 2021
119c943
Improved author handling, added identifier support
AidanM11 Aug 20, 2021
b9d3da4
Support for unmapped fields and dataset type, also more tests
AidanM11 Aug 25, 2021
44dd028
Simplified tests, minor fixes
AidanM11 Aug 28, 2021
78eb210
CHANGELOG.md update
AidanM11 Aug 28, 2021
f4bb7e4
Merge branch 'main' into addCffImporter
AidanM11 Aug 30, 2021
33329c8
code style fixes
AidanM11 Sep 1, 2021
4a9d13d
Fixed minor style issues
calixtus Sep 1, 2021
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15 changes: 13 additions & 2 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 @@ -17,6 +17,7 @@
import org.jabref.model.entry.BibEntry;
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;
Expand Down Expand Up @@ -95,14 +96,23 @@ 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<Field, String>();
StandardEntryType entryType = StandardEntryType.Software;

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

// Translate CFF author format to JabRef author format
String authorStr = IntStream.range(0, citation.authors.size())
.mapToObj(citation.authors::get)
.map((author) -> author.vals)
Expand All @@ -112,9 +122,9 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
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 = IntStream.range(0, citation.ids.size())
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.mapToObj(citation.ids::get)
Expand All @@ -125,6 +135,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
}
}

// Select SWHID to keep
if (citation.ids != null) {
List<String> swhIds = IntStream.range(0, citation.ids.size())
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.mapToObj(citation.ids::get)
Expand All @@ -145,7 +156,7 @@ public ParserResult importDatabase(BufferedReader reader) throws IOException {
}
}

BibEntry entry = new BibEntry(StandardEntryType.Software);
BibEntry entry = new BibEntry(entryType);
entry.setField(entryMap);

List<BibEntry> entriesList = new ArrayList<BibEntry>();
Expand Down
122 changes: 121 additions & 1 deletion src/test/java/org/jabref/logic/importer/fileformat/CffImporterTest.java
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Expand Up @@ -11,6 +11,8 @@
import org.jabref.logic.util.StandardFileType;
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.field.StandardField;
import org.jabref.model.entry.field.UnknownField;
import org.jabref.model.entry.types.StandardEntryType;

import org.junit.jupiter.api.BeforeEach;
import org.junit.jupiter.api.Test;
Expand Down Expand Up @@ -66,7 +68,7 @@ public void testIsRecognizedFormatReject() throws IOException, URISyntaxExceptio
}

@Test
public void testImportEntries() throws IOException, URISyntaxException {
public void testImportEntriesBasic() throws IOException, URISyntaxException {
Path file = Path.of(CffImporterTest.class.getResource("CffImporterTestValid.cff").toURI());
List<BibEntry> bibEntries = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
BibEntry entry = bibEntries.get(0);
Expand All @@ -83,4 +85,122 @@ public void testImportEntries() throws IOException, URISyntaxException {
assertEquals(entry.getField(StandardField.VERSION), Optional.of("1.0"));

}

@Test
public void testImportEntriesMultipleAuthors() throws IOException, URISyntaxException {
Path file = Path.of(CffImporterTest.class.getResource("CffImporterTestValidMultAuthors.cff").toURI());
List<BibEntry> bibEntries = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
BibEntry entry = bibEntries.get(0);

assertEquals(entry.getField(StandardField.AUTHOR), Optional.of("Joe van Smith and Bob Jones, Jr."));
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assertEquals(entry.getField(StandardField.TITLE), Optional.of("Test"));
assertEquals(entry.getField(StandardField.URL), Optional.of("www.google.com"));
assertEquals(entry.getField(StandardField.REPOSITORY), Optional.of("www.github.com"));
assertEquals(entry.getField(StandardField.DOI), Optional.of("10.0000/TEST"));
assertEquals(entry.getField(StandardField.DATE), Optional.of("2000-07-02"));
assertEquals(entry.getField(StandardField.COMMENT), Optional.of("Test entry."));
assertEquals(entry.getField(StandardField.ABSTRACT), Optional.of("Test abstract."));
assertEquals(entry.getField(StandardField.LICENSE), Optional.of("MIT"));
assertEquals(entry.getField(StandardField.VERSION), Optional.of("1.0"));

}

@Test
public void testImportEntriesSwhIdSelect1() throws IOException, URISyntaxException {
Path file = Path.of(CffImporterTest.class.getResource("CffImporterTestValidSwhIdSelect1.cff").toURI());
List<BibEntry> bibEntries = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
BibEntry entry = bibEntries.get(0);

assertEquals(entry.getField(StandardField.AUTHOR), Optional.of("Joe van Smith and Bob Jones, Jr."));
assertEquals(entry.getField(StandardField.TITLE), Optional.of("Test"));
assertEquals(entry.getField(StandardField.URL), Optional.of("www.google.com"));
assertEquals(entry.getField(StandardField.REPOSITORY), Optional.of("www.github.com"));
assertEquals(entry.getField(StandardField.DOI), Optional.of("10.0000/TEST"));
assertEquals(entry.getField(StandardField.DATE), Optional.of("2000-07-02"));
assertEquals(entry.getField(StandardField.COMMENT), Optional.of("Test entry."));
assertEquals(entry.getField(StandardField.ABSTRACT), Optional.of("Test abstract."));
assertEquals(entry.getField(StandardField.LICENSE), Optional.of("MIT"));
assertEquals(entry.getField(StandardField.VERSION), Optional.of("1.0"));
assertEquals(entry.getField(StandardField.SWHID), Optional.of("swh:1:rel:22ece559cc7cc2364edc5e5593d63ae8bd229f9f"));

}

@Test
public void testImportEntriesSwhIdSelect2() throws IOException, URISyntaxException {
Path file = Path.of(CffImporterTest.class.getResource("CffImporterTestValidSwhIdSelect2.cff").toURI());
List<BibEntry> bibEntries = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
BibEntry entry = bibEntries.get(0);

assertEquals(entry.getField(StandardField.AUTHOR), Optional.of("Joe van Smith and Bob Jones, Jr."));
assertEquals(entry.getField(StandardField.TITLE), Optional.of("Test"));
assertEquals(entry.getField(StandardField.URL), Optional.of("www.google.com"));
assertEquals(entry.getField(StandardField.REPOSITORY), Optional.of("www.github.com"));
assertEquals(entry.getField(StandardField.DOI), Optional.of("10.0000/TEST"));
assertEquals(entry.getField(StandardField.DATE), Optional.of("2000-07-02"));
assertEquals(entry.getField(StandardField.COMMENT), Optional.of("Test entry."));
assertEquals(entry.getField(StandardField.ABSTRACT), Optional.of("Test abstract."));
assertEquals(entry.getField(StandardField.LICENSE), Optional.of("MIT"));
assertEquals(entry.getField(StandardField.VERSION), Optional.of("1.0"));
assertEquals(entry.getField(StandardField.SWHID), Optional.of("swh:1:cnt:94a9ed024d3859793618152ea559a168bbcbb5e2"));

}

@Test
public void testImportEntriesDataset() throws IOException, URISyntaxException {
Path file = Path.of(CffImporterTest.class.getResource("CffImporterTestDataset.cff").toURI());
List<BibEntry> bibEntries = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
BibEntry entry = bibEntries.get(0);

assertEquals(entry.getField(StandardField.AUTHOR), Optional.of("Joe van Smith and Bob Jones, Jr."));
assertEquals(entry.getField(StandardField.TITLE), Optional.of("Test"));
assertEquals(entry.getField(StandardField.URL), Optional.of("www.google.com"));
assertEquals(entry.getField(StandardField.REPOSITORY), Optional.of("www.github.com"));
assertEquals(entry.getField(StandardField.DOI), Optional.of("10.0000/TEST"));
assertEquals(entry.getField(StandardField.DATE), Optional.of("2000-07-02"));
assertEquals(entry.getField(StandardField.COMMENT), Optional.of("Test entry."));
assertEquals(entry.getField(StandardField.ABSTRACT), Optional.of("Test abstract."));
assertEquals(entry.getField(StandardField.LICENSE), Optional.of("MIT"));
assertEquals(entry.getField(StandardField.VERSION), Optional.of("1.0"));

assertEquals(entry.getType(), StandardEntryType.Dataset);

}

@Test
public void testImportEntriesDoiSelect() throws IOException, URISyntaxException {
Path file = Path.of(CffImporterTest.class.getResource("CffImporterTestDoiSelect.cff").toURI());
List<BibEntry> bibEntries = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
BibEntry entry = bibEntries.get(0);

assertEquals(entry.getField(StandardField.AUTHOR), Optional.of("Joe van Smith and Bob Jones, Jr."));
assertEquals(entry.getField(StandardField.TITLE), Optional.of("Test"));
assertEquals(entry.getField(StandardField.URL), Optional.of("www.google.com"));
assertEquals(entry.getField(StandardField.REPOSITORY), Optional.of("www.github.com"));
assertEquals(entry.getField(StandardField.DOI), Optional.of("10.0000/TEST"));
assertEquals(entry.getField(StandardField.DATE), Optional.of("2000-07-02"));
assertEquals(entry.getField(StandardField.COMMENT), Optional.of("Test entry."));
assertEquals(entry.getField(StandardField.ABSTRACT), Optional.of("Test abstract."));
assertEquals(entry.getField(StandardField.LICENSE), Optional.of("MIT"));
assertEquals(entry.getField(StandardField.VERSION), Optional.of("1.0"));

}

@Test
public void testImportEntriesUnknownFields() throws IOException, URISyntaxException {
Path file = Path.of(CffImporterTest.class.getResource("CffImporterTestUnknownFields.cff").toURI());
List<BibEntry> bibEntries = importer.importDatabase(file, StandardCharsets.UTF_8).getDatabase().getEntries();
BibEntry entry = bibEntries.get(0);

assertEquals(entry.getField(StandardField.AUTHOR), Optional.of("Joe van Smith"));
assertEquals(entry.getField(StandardField.TITLE), Optional.of("Test"));
assertEquals(entry.getField(StandardField.URL), Optional.of("www.google.com"));
assertEquals(entry.getField(StandardField.REPOSITORY), Optional.of("www.github.com"));
assertEquals(entry.getField(StandardField.DOI), Optional.of("10.0000/TEST"));
assertEquals(entry.getField(StandardField.DATE), Optional.of("2000-07-02"));
assertEquals(entry.getField(StandardField.COMMENT), Optional.of("Test entry."));
assertEquals(entry.getField(StandardField.ABSTRACT), Optional.of("Test abstract."));
assertEquals(entry.getField(StandardField.LICENSE), Optional.of("MIT"));
assertEquals(entry.getField(StandardField.VERSION), Optional.of("1.0"));
assertEquals(entry.getField(new UnknownField("commit")), Optional.of("10ad"));
}
}
26 changes: 26 additions & 0 deletions src/test/resources/org/jabref/logic/importer/fileformat/CffImporterTestDataset.cff
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@@ -0,0 +1,26 @@
# YAML 1.2
---
abstract: "Test abstract."
authors:
-
family-names: Smith
given-names: Joe
name-particle: van
-
family-names: Jones
given-names: Bob
name-suffix: Jr.
cff-version: "1.1.0"
date-released: 2000-07-02
identifiers:
-
type: doi
value: "10.0000/TEST"
license: MIT
message: "Test entry."
title: Test
version: "1.0"
url: "www.google.com"
repository: "www.github.com"
type: dataset
...
25 changes: 25 additions & 0 deletions src/test/resources/org/jabref/logic/importer/fileformat/CffImporterTestDoiSelect.cff
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@@ -0,0 +1,25 @@
# YAML 1.2
---
abstract: "Test abstract."
authors:
-
family-names: Smith
given-names: Joe
name-particle: van
-
family-names: Jones
given-names: Bob
name-suffix: Jr.
cff-version: "1.1.0"
date-released: 2000-07-02
identifiers:
-
type: doi
value: "10.0000/TEST"
license: MIT
message: "Test entry."
title: Test
version: "1.0"
url: "www.google.com"
repository: "www.github.com"
...
20 changes: 20 additions & 0 deletions src/test/resources/org/jabref/logic/importer/fileformat/CffImporterTestUnknownFields.cff
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@@ -0,0 +1,20 @@
# YAML 1.2
---
abstract: "Test abstract."
authors:
-
family-names: Smith
given-names: Joe
name-particle: van
cff-version: "1.1.0"
date-released: 2000-07-02
doi: "10.0000/TEST"
identifiers:
license: MIT
message: "Test entry."
title: Test
version: "1.0"
url: "www.google.com"
repository: "www.github.com"
commit: 10ad
...
23 changes: 23 additions & 0 deletions src/test/resources/org/jabref/logic/importer/fileformat/CffImporterTestValidMultAuthors.cff
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@@ -0,0 +1,23 @@
# YAML 1.2
---
abstract: "Test abstract."
authors:
-
family-names: Smith
given-names: Joe
name-particle: van
-
family-names: Jones
given-names: Bob
name-suffix: Jr.
cff-version: "1.1.0"
date-released: 2000-07-02
doi: "10.0000/TEST"
identifiers:
license: MIT
message: "Test entry."
title: Test
version: "1.0"
url: "www.google.com"
repository: "www.github.com"
...
29 changes: 29 additions & 0 deletions src/test/resources/org/jabref/logic/importer/fileformat/CffImporterTestValidSwhIdSelect1.cff
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@@ -0,0 +1,29 @@
# YAML 1.2
---
abstract: "Test abstract."
authors:
-
family-names: Smith
given-names: Joe
name-particle: van
-
family-names: Jones
given-names: Bob
name-suffix: Jr.
cff-version: "1.1.0"
date-released: 2000-07-02
doi: "10.0000/TEST"
identifiers:
-
type: swh
value: "swh:1:cnt:94a9ed024d3859793618152ea559a168bbcbb5e2"
-
type: swh
value: "swh:1:rel:22ece559cc7cc2364edc5e5593d63ae8bd229f9f"
license: MIT
message: "Test entry."
title: Test
version: "1.0"
url: "www.google.com"
repository: "www.github.com"
...
26 changes: 26 additions & 0 deletions src/test/resources/org/jabref/logic/importer/fileformat/CffImporterTestValidSwhIdSelect2.cff
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@@ -0,0 +1,26 @@
# YAML 1.2
---
abstract: "Test abstract."
authors:
-
family-names: Smith
given-names: Joe
name-particle: van
-
family-names: Jones
given-names: Bob
name-suffix: Jr.
cff-version: "1.1.0"
date-released: 2000-07-02
doi: "10.0000/TEST"
identifiers:
-
type: swh
value: "swh:1:cnt:94a9ed024d3859793618152ea559a168bbcbb5e2"
license: MIT
message: "Test entry."
title: Test
version: "1.0"
url: "www.google.com"
repository: "www.github.com"
...