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Implimented arXivId Parsing for PDF with arXivId #12335

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Jan 20, 2025
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Implimented arXivId Parsing for PDF with arXivId #12335

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220ddac
Implimented arXivId Parsing forPDF with arXivId
ar-rana Dec 24, 2024
32e9867
added Optional parameter
ar-rana Dec 25, 2024
9c80e04
Merge branch 'main' into feature/arXivId
ar-rana Dec 25, 2024
89de378
merged fixes
ar-rana Dec 25, 2024
28755cf
removed csl-styles
ar-rana Dec 25, 2024
06b6bb0
fixed null arxiv issue on external imports
ar-rana Dec 28, 2024
457bb3f
Improved getArxivId Implementation
ar-rana Jan 1, 2025
a653de5
reduced nesting and added arxiv constant
ar-rana Jan 6, 2025
06c771b
reduced nesting
ar-rana Jan 7, 2025
1512d7e
modified testcase
ar-rana Jan 8, 2025
0308a0b
Merge remote-tracking branch 'upstream/main' into feature/arXivId
Siedlerchr Jan 13, 2025
15ac9a2
Merge branch 'main' into feature/arXivId
Siedlerchr Jan 16, 2025
a21f893
fix abbrev repo
Siedlerchr Jan 16, 2025
774ee84
removed unnecessary 'if' clause
ar-rana Jan 17, 2025
148b716
Merge branch 'main' into feature/arXivId
koppor Jan 20, 2025
126cbaa
Use EPRINTTYPE
koppor Jan 20, 2025
03fede4
Update src/main/java/org/jabref/logic/importer/fileformat/PdfContentI…
koppor Jan 20, 2025
cfe1664
WIP
koppor Jan 20, 2025
b3d8556
Add completion using arXiv ID
koppor Jan 20, 2025
18673c8
Adapt test case
koppor Jan 20, 2025
1f112a2
Fix test name
koppor Jan 20, 2025
5e961fa
"Fix2 number and year extraction for arXiv
koppor Jan 20, 2025
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2 changes: 1 addition & 1 deletion buildres/abbrv.jabref.org
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Submodule abbrv.jabref.org updated 2 files
+0 −9 journals/journal_abbreviations_mathematics.csv
+1 −20 journals/journal_abbreviations_ubc.csv
33 changes: 31 additions & 2 deletions src/main/java/org/jabref/logic/importer/fileformat/PdfContentImporter.java
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Original file line number Diff line number Diff line change
Expand Up @@ -24,6 +24,7 @@
import org.jabref.model.entry.BibEntry;
import org.jabref.model.entry.LinkedFile;
import org.jabref.model.entry.field.StandardField;
import org.jabref.model.entry.identifier.ArXivIdentifier;
import org.jabref.model.entry.identifier.DOI;
import org.jabref.model.entry.types.EntryType;
import org.jabref.model.entry.types.StandardEntryType;
Expand Down Expand Up @@ -364,14 +365,18 @@ Optional<BibEntry> getEntryFromPDFContent(String firstpageContents, String lineS
String volume = null;
String number = null;
String pages = null;
String arXivId = null;
// year is a class variable as the method extractYear() uses it;
String publisher = null;

EntryType type = StandardEntryType.InProceedings;
// sometimes ArXiv ID is read before all parameters
getArXivId(null);
if (curString.length() > 4) {
// special case: possibly conference as first line on the page
extractYear();
doi = getDoi(null);
arXivId = getArXivId(arXivId);
if (curString.contains("Conference")) {
fillCurStringWithNonEmptyLines();
conference = curString;
Expand All @@ -387,7 +392,6 @@ Optional<BibEntry> getEntryFromPDFContent(String firstpageContents, String lineS
}
}
}

// start: title
fillCurStringWithNonEmptyLines();
title = streamlineTitle(curString);
Expand Down Expand Up @@ -507,6 +511,7 @@ Optional<BibEntry> getEntryFromPDFContent(String firstpageContents, String lineS
}
} else {
doi = getDoi(doi);
arXivId = getArXivId(arXivId);

if ((publisher == null) && curString.contains("IEEE")) {
// IEEE has the conference things at the end
Expand All @@ -531,6 +536,10 @@ Optional<BibEntry> getEntryFromPDFContent(String firstpageContents, String lineS
}
}

if (arXivId != null && arXivId.contains(year)) {
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year = null;
}

BibEntry entry = new BibEntry();
entry.setType(type);

Expand All @@ -557,20 +566,26 @@ Optional<BibEntry> getEntryFromPDFContent(String firstpageContents, String lineS
if (doi != null) {
entry.setField(StandardField.DOI, doi);
}
if (arXivId != null) {
entry.setField(StandardField.EPRINT, arXivId);
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}
if (series != null) {
entry.setField(StandardField.SERIES, series);
}
if (volume != null) {
entry.setField(StandardField.VOLUME, volume);
}
if (number != null) {
if (number != null && number.chars().allMatch(Character::isDigit)) {
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entry.setField(StandardField.NUMBER, number);
}
if (pages != null) {
entry.setField(StandardField.PAGES, pages);
}
if (year != null) {
entry.setField(StandardField.YEAR, year);
} else if (arXivId != null) {
year = "20" + arXivId.substring(0, 2);
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entry.setField(StandardField.YEAR, year);
}
if (publisher != null) {
entry.setField(StandardField.PUBLISHER, publisher);
Expand All @@ -592,6 +607,20 @@ private String getDoi(String doi) {
return doi;
}

private String getArXivId(String arXivId) {
if (arXivId == null) {
arXivId = ArXivIdentifier.parse(curString).map(ArXivIdentifier::asString).orElse(null);
if (arXivId != null) {
if (curString.length() > arXivId.length() + 7) {
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What does 7 stand for here? If possible, define a constant with a good name for the value 7 in this context.

Also, consider reducing the level of nesting in the code by returning early.

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7 is for the 'arxiv:' prefix in the arxiv string,

If possible, define a constant with a good name for the value 7 in this context.

Also, consider reducing the level of nesting in the code by returning early.

sure, I will work on that.

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In that case, ARXIV_PREFIX_LENGTH = "arxiv:".length() would be a good name.

curString = curString.substring(arXivId.length() + 7);
extractYear();
}
return arXivId;
}
}
return arXivId;
}

private String getFirstPageContents(PDDocument document) throws IOException {
PDFTextStripper stripper = new PDFTextStripper();

Expand Down
2 changes: 1 addition & 1 deletion src/main/java/org/jabref/model/entry/identifier/ArXivIdentifier.java
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Original file line number Diff line number Diff line change
Expand Up @@ -38,7 +38,7 @@ public class ArXivIdentifier extends EprintIdentifier {
}

public static Optional<ArXivIdentifier> parse(String value) {
String identifier = value.replace(" ", "");
String identifier = value.split(" ")[0];
Pattern identifierPattern = Pattern.compile("(" + ARXIV_PREFIX + ")?\\s?:?\\s?(?<id>\\d{4}\\.\\d{4,5})(v(?<version>\\d+))?\\s?(\\[(?<classification>\\S+)\\])?");
Matcher identifierMatcher = identifierPattern.matcher(identifier);
if (identifierMatcher.matches()) {
Expand Down
2 changes: 1 addition & 1 deletion src/main/resources/csl-styles
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Submodule csl-styles updated 20 files
+0 −279 acta-medica-portuguesa.csl
+1 −1 anesthesiology.csl
+0 −5 apa-5th-edition.csl
+0 −5 apa-6th-edition-no-ampersand.csl
+0 −5 apa-6th-edition.csl
+0 −5 apa-annotated-bibliography.csl
+0 −5 apa-cv.csl
+0 −5 apa-no-ampersand.csl
+0 −5 apa-no-doi-no-issue.csl
+0 −5 apa-no-initials.csl
+0 −5 apa-numeric-superscript-brackets.csl
+0 −5 apa-numeric-superscript.csl
+0 −5 apa-old-doi-prefix.csl
+0 −5 apa-single-spaced.csl
+0 −5 apa-with-abstract.csl
+0 −5 apa.csl
+1 −11 bern-university-of-applied-sciences-school-of-agricultural-forest-and-food-sciences-hafl.csl
+0 −416 gayana.csl
+0 −24 royal-society-of-chemistry-with-titles.csl
+1 −1 spec/spec_helper.rb
36 changes: 36 additions & 0 deletions src/test/java/org/jabref/logic/importer/fileformat/PdfContentImporterTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -129,6 +129,42 @@ British Journal of Nutrition (2008), 99, 1–11 doi: 10.1017/S0007114507795296
assertEquals(Optional.of(entry), importer.getEntryFromPDFContent(firstPageContent, "\n", Optional.empty()));
}

@Test
void extractArXivFromPage1() {
BibEntry entry = new BibEntry(StandardEntryType.TechReport)
.withField(StandardField.AUTHOR, "Filippo Riccaa and Alessandro Marchettob and Andrea Stoccoc")
.withField(StandardField.TITLE, "[cs.SE] 12 Aug 2024 A Multi-Year Grey Literature Review on AI-assisted Test Automation")
.withField(StandardField.YEAR, "2024")
.withField(StandardField.EPRINT, "2408.06224v1")
.withField((StandardField.KEYWORDS), "Test Automation Artificial Intelligence AI-assisted Test Automation Grey Literature Automated Test Generation Self-Healing Test Scripts");

String firstPageContent = """
arXiv:2408.06224v1 [cs.SE] 12 Aug 2024
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Is it guaranteed that the arXiv id will be on the first line? If not we need to add at least two more tests.

  • ArXiv id in a middle line (the line begins with the id)
  • ArXiv ID in a middle line (the ID is somewhere in the middle of that line)

You can use JUnit 5 Parameterized Tests to reduce verbosity.

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hello houssem, I checked multiple arXiv papers(10) and all of them had their arxiv string at the last line, here you can see it at the top(sorry for the oversight, will fix that) but moving it at the last also passes the test, and since all these papers have the same format i think the arxiv string would mostly be at the end

A Multi-Year Grey Literature Review on AI-assisted Test Automation

Filippo Riccaa, Alessandro Marchettob and Andrea Stoccoc

aUniversity of Genoa, Via Balbi 5, Genova, 16126, Italy
bUniversity of Trento, Via Sommarive 9, Trento, 38123, Italy
cTechnical University of Munich, Boltzmannstraße 3, Munich, 85748, Germany
dfortiss GmbH, Guerickestraße 25, Munich, 80805, Germany

Keywords:
Test Automation
Artificial Intelligence
AI-assisted Test Automation
Grey Literature
Automated Test Generation
Self-Healing Test Scripts

*Corresponding author
filippo.ricca@unige.it (F. Ricca)
https://person.dibris.unige.it/ricca-filippo/ (F. Ricca)
ORCID(s): 0000-0002-3928-5408 (F. Ricca); 0000-0002-6833-896X (A. Marchetto); 0000-0001-8956-3894 (A. Stocco)""";

assertEquals(Optional.of(entry), importer.getEntryFromPDFContent(firstPageContent, "\n", Optional.empty()));
}

@ParameterizedTest
@MethodSource("providePdfData")
void pdfTitleExtraction(String expectedTitle, String filePath) throws Exception {
Expand Down
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