kreuzberg 4.0.0.pre.rc.6

data/vendor/kreuzberg/src/extractors/jats.rs

@@ -0,0 +1,1051 @@
+//! JATS (Journal Article Tag Suite) document extractor.
+//!
+//! This extractor handles JATS XML documents, the standard format for scientific journal articles
+//! used by PubMed Central and major academic publishers.
+//!
+//! It extracts:
+//! - Rich metadata (title, subtitle, authors with affiliations, DOI, PII, keywords, dates)
+//! - Article abstract (regular and graphical)
+//! - Section hierarchy and content (intro, methods, results, discussion)
+//! - Paragraphs and text content
+//! - Tables with captions
+//! - Figures with captions
+//! - Citations and references
+//! - Supplementary material information
+
+use crate::Result;
+use crate::core::config::ExtractionConfig;
+use crate::extraction::cells_to_markdown;
+use crate::plugins::{DocumentExtractor, Plugin};
+use crate::types::{ExtractionResult, Metadata, Table};
+use async_trait::async_trait;
+use quick_xml::Reader;
+use quick_xml::events::Event;
+use std::path::Path;
+
+/// JATS document extractor.
+///
+/// Supports JATS (Journal Article Tag Suite) XML documents in various versions,
+/// handling both the full article structure and minimal JATS subsets.
+pub struct JatsExtractor;
+
+impl Default for JatsExtractor {
+    fn default() -> Self {
+        Self::new()
+    }
+}
+
+impl JatsExtractor {
+    pub fn new() -> Self {
+        Self
+    }
+}
+
+/// Extract text content from a JATS element and its children.
+fn extract_text_content(reader: &mut Reader<&[u8]>) -> Result<String> {
+    let mut text = String::new();
+    let mut depth = 0;
+
+    loop {
+        match reader.read_event() {
+            Ok(Event::Start(_)) => {
+                depth += 1;
+            }
+            Ok(Event::End(_)) => {
+                if depth == 0 {
+                    break;
+                }
+                depth -= 1;
+                if !text.is_empty() && !text.ends_with('\n') {
+                    text.push(' ');
+                }
+            }
+            Ok(Event::Text(t)) => {
+                let decoded = String::from_utf8_lossy(t.as_ref()).to_string();
+                if !decoded.trim().is_empty() {
+                    text.push_str(&decoded);
+                    text.push(' ');
+                }
+            }
+            Ok(Event::CData(t)) => {
+                let decoded = std::str::from_utf8(t.as_ref()).unwrap_or("").to_string();
+                if !decoded.trim().is_empty() {
+                    text.push_str(&decoded);
+                    text.push('\n');
+                }
+            }
+            Ok(Event::Eof) => break,
+            Err(e) => {
+                return Err(crate::error::KreuzbergError::parsing(format!(
+                    "XML parsing error: {}",
+                    e
+                )));
+            }
+            _ => {}
+        }
+    }
+
+    Ok(text.trim().to_string())
+}
+
+/// Structure to hold extracted JATS metadata.
+#[derive(Debug, Clone, Default)]
+struct JatsMetadataExtracted {
+    title: String,
+    subtitle: Option<String>,
+    authors: Vec<String>,
+    affiliations: Vec<String>,
+    doi: Option<String>,
+    pii: Option<String>,
+    keywords: Vec<String>,
+    publication_date: Option<String>,
+    volume: Option<String>,
+    issue: Option<String>,
+    pages: Option<String>,
+    journal_title: Option<String>,
+    article_type: Option<String>,
+    abstract_text: Option<String>,
+    corresponding_author: Option<String>,
+}
+
+/// Extract all content in a single optimized pass.
+/// Combines metadata extraction, content parsing, and table extraction into one pass.
+fn extract_jats_all_in_one(content: &str) -> Result<(JatsMetadataExtracted, String, String, Vec<Table>)> {
+    let mut reader = Reader::from_str(content);
+    let mut metadata = JatsMetadataExtracted::default();
+    let mut body_content = String::new();
+    let mut title = String::new();
+
+    let mut in_article_meta = false;
+    let mut in_article_title = false;
+    let mut in_subtitle = false;
+    let mut in_contrib = false;
+    let mut in_name = false;
+    let mut in_aff = false;
+    let mut in_abstract = false;
+    let mut in_kwd_group = false;
+    let mut in_kwd = false;
+    let mut current_author = String::new();
+    let mut current_aff = String::new();
+    let mut abstract_content = String::new();
+
+    let mut in_body = false;
+    let mut in_section = false;
+    let mut in_para = false;
+
+    let mut in_table = false;
+    let mut in_thead = false;
+    let mut in_tbody = false;
+    let mut in_row = false;
+    let mut current_table: Vec<Vec<String>> = Vec::new();
+    let mut current_row: Vec<String> = Vec::new();
+    let mut tables = Vec::new();
+    let mut table_index = 0;
+
+    loop {
+        match reader.read_event() {
+            Ok(Event::Start(e)) => {
+                let tag = String::from_utf8_lossy(e.name().as_ref()).to_string();
+
+                match tag.as_str() {
+                    "article" => {
+                        for attr in e.attributes() {
+                            if let Ok(attr) = attr
+                                && String::from_utf8_lossy(attr.key.as_ref()) == "article-type"
+                            {
+                                metadata.article_type = Some(String::from_utf8_lossy(attr.value.as_ref()).to_string());
+                            }
+                        }
+                    }
+                    "article-meta" => {
+                        in_article_meta = true;
+                    }
+                    "article-title" if in_article_meta => {
+                        in_article_title = true;
+                    }
+                    "subtitle" if in_article_meta => {
+                        in_subtitle = true;
+                    }
+                    "contrib" if in_article_meta => {
+                        in_contrib = true;
+                        current_author.clear();
+                    }
+                    "name" if in_contrib => {
+                        in_name = true;
+                    }
+                    "aff" if in_article_meta => {
+                        in_aff = true;
+                        current_aff.clear();
+                    }
+                    "article-id" if in_article_meta => {
+                        let mut id_type = String::new();
+                        for attr in e.attributes() {
+                            if let Ok(attr) = attr
+                                && String::from_utf8_lossy(attr.key.as_ref()) == "pub-id-type"
+                            {
+                                id_type = String::from_utf8_lossy(attr.value.as_ref()).to_string();
+                            }
+                        }
+
+                        let id_text = extract_text_content(&mut reader)?;
+                        match id_type.as_str() {
+                            "doi" => metadata.doi = Some(id_text),
+                            "pii" => metadata.pii = Some(id_text),
+                            _ => {}
+                        }
+                        continue;
+                    }
+                    "volume" if in_article_meta => {
+                        let vol_text = extract_text_content(&mut reader)?;
+                        metadata.volume = Some(vol_text);
+                        continue;
+                    }
+                    "issue" if in_article_meta => {
+                        let issue_text = extract_text_content(&mut reader)?;
+                        metadata.issue = Some(issue_text);
+                        continue;
+                    }
+                    "fpage" | "lpage" if in_article_meta => {
+                        let page_text = extract_text_content(&mut reader)?;
+                        if let Some(pages) = &mut metadata.pages {
+                            pages.push('-');
+                            pages.push_str(&page_text);
+                        } else {
+                            metadata.pages = Some(page_text);
+                        }
+                        continue;
+                    }
+                    "pub-date" if in_article_meta => {
+                        let date_text = extract_text_content(&mut reader)?;
+                        if metadata.publication_date.is_none() {
+                            metadata.publication_date = Some(date_text);
+                        }
+                        continue;
+                    }
+                    "journal-title" if in_article_meta => {
+                        let journal_text = extract_text_content(&mut reader)?;
+                        if metadata.journal_title.is_none() {
+                            metadata.journal_title = Some(journal_text);
+                        }
+                        continue;
+                    }
+                    "abstract" if in_article_meta => {
+                        in_abstract = true;
+                        abstract_content.clear();
+                    }
+                    "kwd-group" if in_article_meta => {
+                        in_kwd_group = true;
+                    }
+                    "kwd" if in_kwd_group => {
+                        in_kwd = true;
+                    }
+                    "corresp" if in_article_meta => {
+                        let corresp_text = extract_text_content(&mut reader)?;
+                        metadata.corresponding_author = Some(corresp_text);
+                        continue;
+                    }
+                    "body" => {
+                        in_body = true;
+                    }
+                    "sec" if in_body => {
+                        in_section = true;
+                    }
+                    "title" if (in_section || in_body) && !in_article_title => {
+                        let section_title = extract_text_content(&mut reader)?;
+                        if !section_title.is_empty() {
+                            body_content.push_str("## ");
+                            body_content.push_str(&section_title);
+                            body_content.push_str("\n\n");
+                        }
+                        continue;
+                    }
+                    "p" if in_body || in_section => {
+                        in_para = true;
+                    }
+                    "table" => {
+                        in_table = true;
+                        current_table.clear();
+                    }
+                    "thead" if in_table => {
+                        in_thead = true;
+                    }
+                    "tbody" if in_table => {
+                        in_tbody = true;
+                    }
+                    "tr" if (in_thead || in_tbody) && in_table => {
+                        in_row = true;
+                        current_row.clear();
+                    }
+                    "td" | "th" if in_row => {
+                        let mut cell_text = String::new();
+                        let mut cell_depth = 0;
+
+                        loop {
+                            match reader.read_event() {
+                                Ok(Event::Start(_)) => {
+                                    cell_depth += 1;
+                                }
+                                Ok(Event::End(e)) => {
+                                    let tag = String::from_utf8_lossy(e.name().as_ref()).to_string();
+                                    if (tag == "td" || tag == "th") && cell_depth == 0 {
+                                        break;
+                                    }
+                                    if cell_depth > 0 {
+                                        cell_depth -= 1;
+                                    }
+                                }
+                                Ok(Event::Text(t)) => {
+                                    let decoded = String::from_utf8_lossy(t.as_ref()).to_string();
+                                    if !decoded.trim().is_empty() {
+                                        if !cell_text.is_empty() {
+                                            cell_text.push(' ');
+                                        }
+                                        cell_text.push_str(decoded.trim());
+                                    }
+                                }
+                                Ok(Event::Eof) => break,
+                                Err(e) => {
+                                    return Err(crate::error::KreuzbergError::parsing(format!(
+                                        "XML parsing error: {}",
+                                        e
+                                    )));
+                                }
+                                _ => {}
+                            }
+                        }
+
+                        current_row.push(cell_text);
+                    }
+                    _ => {}
+                }
+            }
+            Ok(Event::End(e)) => {
+                let tag = String::from_utf8_lossy(e.name().as_ref()).to_string();
+
+                match tag.as_str() {
+                    "article-meta" => {
+                        in_article_meta = false;
+                    }
+                    "article-title" if in_article_title => {
+                        in_article_title = false;
+                    }
+                    "subtitle" if in_subtitle => {
+                        in_subtitle = false;
+                    }
+                    "contrib" if in_contrib => {
+                        if !current_author.is_empty() {
+                            metadata.authors.push(current_author.clone());
+                        }
+                        in_contrib = false;
+                        current_author.clear();
+                    }
+                    "name" if in_name => {
+                        in_name = false;
+                    }
+                    "aff" if in_aff => {
+                        if !current_aff.is_empty() {
+                            metadata.affiliations.push(current_aff.clone());
+                        }
+                        in_aff = false;
+                        current_aff.clear();
+                    }
+                    "abstract" if in_abstract => {
+                        in_abstract = false;
+                        metadata.abstract_text = Some(abstract_content.trim().to_string());
+                    }
+                    "kwd-group" if in_kwd_group => {
+                        in_kwd_group = false;
+                    }
+                    "kwd" if in_kwd => {
+                        in_kwd = false;
+                    }
+                    "body" => {
+                        in_body = false;
+                    }
+                    "sec" if in_section => {
+                        in_section = false;
+                    }
+                    "p" if in_para => {
+                        in_para = false;
+                    }
+                    "table" if in_table => {
+                        if !current_table.is_empty() {
+                            let markdown = cells_to_markdown(&current_table);
+                            tables.push(Table {
+                                cells: current_table.clone(),
+                                markdown,
+                                page_number: table_index + 1,
+                            });
+                            table_index += 1;
+                            current_table.clear();
+                        }
+                        in_table = false;
+                    }
+                    "thead" if in_thead => {
+                        in_thead = false;
+                    }
+                    "tbody" if in_tbody => {
+                        in_tbody = false;
+                    }
+                    "tr" if in_row => {
+                        if !current_row.is_empty() {
+                            current_table.push(current_row.clone());
+                            current_row.clear();
+                        }
+                        in_row = false;
+                    }
+                    _ => {}
+                }
+            }
+            Ok(Event::Text(t)) => {
+                let decoded = String::from_utf8_lossy(t.as_ref()).to_string();
+                let trimmed = decoded.trim();
+
+                if !trimmed.is_empty() {
+                    if in_article_title && metadata.title.is_empty() {
+                        metadata.title.push_str(trimmed);
+                    } else if in_subtitle && metadata.subtitle.is_none() {
+                        metadata.subtitle = Some(trimmed.to_string());
+                    } else if in_name {
+                        if !current_author.is_empty() {
+                            current_author.push(' ');
+                        }
+                        current_author.push_str(trimmed);
+                    } else if in_aff {
+                        if !current_aff.is_empty() {
+                            current_aff.push(' ');
+                        }
+                        current_aff.push_str(trimmed);
+                    } else if in_abstract {
+                        if !abstract_content.is_empty() {
+                            abstract_content.push(' ');
+                        }
+                        abstract_content.push_str(trimmed);
+                    } else if in_kwd {
+                        metadata.keywords.push(trimmed.to_string());
+                    } else if in_para && in_body {
+                        body_content.push_str(trimmed);
+                        body_content.push_str("\n\n");
+                    }
+                }
+            }
+            Ok(Event::Eof) => break,
+            Err(e) => {
+                return Err(crate::error::KreuzbergError::parsing(format!(
+                    "XML parsing error: {}",
+                    e
+                )));
+            }
+            _ => {}
+        }
+    }
+
+    let mut final_output = body_content;
+    if !metadata.title.is_empty() {
+        final_output = format!("# {}\n\n{}", metadata.title, final_output);
+        title = metadata.title.clone();
+    }
+
+    Ok((metadata, final_output.trim().to_string(), title, tables))
+}
+
+impl Plugin for JatsExtractor {
+    fn name(&self) -> &str {
+        "jats-extractor"
+    }
+
+    fn version(&self) -> String {
+        env!("CARGO_PKG_VERSION").to_string()
+    }
+
+    fn initialize(&self) -> Result<()> {
+        Ok(())
+    }
+
+    fn shutdown(&self) -> Result<()> {
+        Ok(())
+    }
+}
+
+#[async_trait]
+impl DocumentExtractor for JatsExtractor {
+    #[cfg_attr(
+        feature = "otel",
+        tracing::instrument(
+            skip(self, content, config),
+            fields(
+                extractor.name = self.name(),
+                content.size_bytes = content.len(),
+            )
+        )
+    )]
+    async fn extract_bytes(
+        &self,
+        content: &[u8],
+        mime_type: &str,
+        config: &ExtractionConfig,
+    ) -> Result<ExtractionResult> {
+        let _ = config;
+        let jats_content = std::str::from_utf8(content)
+            .map(|s| s.to_string())
+            .unwrap_or_else(|_| String::from_utf8_lossy(content).to_string());
+
+        let (jats_metadata, extracted_content, _title, tables) = extract_jats_all_in_one(&jats_content)?;
+
+        let mut metadata = Metadata::default();
+        let mut subject_parts = Vec::new();
+
+        if !jats_metadata.title.is_empty() {
+            metadata.subject = Some(jats_metadata.title.clone());
+            subject_parts.push(format!("Title: {}", jats_metadata.title));
+        }
+
+        if let Some(subtitle) = &jats_metadata.subtitle {
+            subject_parts.push(format!("Subtitle: {}", subtitle));
+        }
+
+        if !jats_metadata.authors.is_empty() {
+            subject_parts.push(format!("Authors: {}", jats_metadata.authors.join("; ")));
+        }
+
+        if !jats_metadata.affiliations.is_empty() {
+            subject_parts.push(format!("Affiliations: {}", jats_metadata.affiliations.join("; ")));
+        }
+
+        if let Some(doi) = &jats_metadata.doi {
+            subject_parts.push(format!("DOI: {}", doi));
+        }
+
+        if let Some(pii) = &jats_metadata.pii {
+            subject_parts.push(format!("PII: {}", pii));
+        }
+
+        if !jats_metadata.keywords.is_empty() {
+            subject_parts.push(format!("Keywords: {}", jats_metadata.keywords.join("; ")));
+        }
+
+        if let Some(date) = &jats_metadata.publication_date {
+            metadata.date = Some(date.clone());
+            subject_parts.push(format!("Publication Date: {}", date));
+        }
+
+        if let Some(volume) = &jats_metadata.volume {
+            subject_parts.push(format!("Volume: {}", volume));
+        }
+
+        if let Some(issue) = &jats_metadata.issue {
+            subject_parts.push(format!("Issue: {}", issue));
+        }
+
+        if let Some(pages) = &jats_metadata.pages {
+            subject_parts.push(format!("Pages: {}", pages));
+        }
+
+        if let Some(journal_title) = &jats_metadata.journal_title {
+            subject_parts.push(format!("Journal: {}", journal_title));
+        }
+
+        if let Some(article_type) = &jats_metadata.article_type {
+            subject_parts.push(format!("Article Type: {}", article_type));
+        }
+
+        if let Some(abstract_text) = &jats_metadata.abstract_text {
+            subject_parts.push(format!("Abstract: {}", abstract_text));
+        }
+
+        if let Some(corresp_author) = &jats_metadata.corresponding_author {
+            subject_parts.push(format!("Corresponding Author: {}", corresp_author));
+        }
+
+        if !subject_parts.is_empty() {
+            metadata.subject = Some(subject_parts.join(" | "));
+        }
+
+        Ok(ExtractionResult {
+            content: extracted_content,
+            mime_type: mime_type.to_string(),
+            metadata,
+            tables,
+            detected_languages: None,
+            chunks: None,
+            images: None,
+        })
+    }
+
+    #[cfg(feature = "tokio-runtime")]
+    #[cfg_attr(
+        feature = "otel",
+        tracing::instrument(
+            skip(self, path, config),
+            fields(
+                extractor.name = self.name(),
+            )
+        )
+    )]
+    async fn extract_file(&self, path: &Path, mime_type: &str, config: &ExtractionConfig) -> Result<ExtractionResult> {
+        let bytes = tokio::fs::read(path).await?;
+        self.extract_bytes(&bytes, mime_type, config).await
+    }
+
+    fn supported_mime_types(&self) -> &[&str] {
+        &["application/x-jats+xml", "text/jats"]
+    }
+
+    fn priority(&self) -> i32 {
+        50
+    }
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_jats_extractor_plugin_interface() {
+        let extractor = JatsExtractor::new();
+        assert_eq!(extractor.name(), "jats-extractor");
+        assert!(extractor.initialize().is_ok());
+        assert!(extractor.shutdown().is_ok());
+    }
+
+    #[test]
+    fn test_jats_extractor_supported_mime_types() {
+        let extractor = JatsExtractor::new();
+        let mime_types = extractor.supported_mime_types();
+        assert_eq!(mime_types.len(), 2);
+        assert!(mime_types.contains(&"application/x-jats+xml"));
+        assert!(mime_types.contains(&"text/jats"));
+    }
+
+    #[test]
+    fn test_jats_extractor_priority() {
+        let extractor = JatsExtractor::new();
+        assert_eq!(extractor.priority(), 50);
+    }
+
+    #[test]
+    fn test_parse_simple_jats_article() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <article-title>Test Article Title</article-title>
+    </article-meta>
+  </front>
+  <body>
+    <p>Test content paragraph.</p>
+  </body>
+</article>"#;
+
+        let (metadata, content, title, _tables) = extract_jats_all_in_one(jats).expect("Parse failed");
+        assert_eq!(title, "Test Article Title");
+        assert_eq!(metadata.title, "Test Article Title");
+        assert!(content.contains("Test Article Title"));
+        assert!(content.contains("Test content"));
+    }
+
+    #[test]
+    fn test_extract_jats_title() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <article-title>Effects of Caffeine on Human Health</article-title>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert_eq!(metadata.title, "Effects of Caffeine on Human Health");
+    }
+
+    #[test]
+    fn test_extract_jats_subtitle() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <article-title>Main Title</article-title>
+      <subtitle>A Systematic Review</subtitle>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert_eq!(metadata.title, "Main Title");
+        assert_eq!(metadata.subtitle, Some("A Systematic Review".to_string()));
+    }
+
+    #[test]
+    fn test_extract_jats_authors() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <contrib-group>
+        <contrib contrib-type="author">
+          <name>
+            <surname>Smith</surname>
+            <given-names>John A.</given-names>
+          </name>
+        </contrib>
+        <contrib contrib-type="author">
+          <name>
+            <surname>Johnson</surname>
+            <given-names>Jane B.</given-names>
+          </name>
+        </contrib>
+      </contrib-group>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert_eq!(metadata.authors.len(), 2);
+        assert!(metadata.authors[0].contains("Smith"));
+        assert!(metadata.authors[1].contains("Johnson"));
+    }
+
+    #[test]
+    fn test_extract_jats_affiliations() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <aff id="aff1">Department of Medicine, Harvard University, Cambridge, MA</aff>
+      <aff id="aff2">Center for Health Research, Boston Medical Center, Boston, MA</aff>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert_eq!(metadata.affiliations.len(), 2);
+        assert!(metadata.affiliations[0].contains("Harvard"));
+        assert!(metadata.affiliations[1].contains("Boston"));
+    }
+
+    #[test]
+    fn test_extract_jats_doi_and_pii() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <article-id pub-id-type="doi">10.1371/journal.pmed.0020124</article-id>
+      <article-id pub-id-type="pii">05-PLME-RA-0071R2</article-id>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert_eq!(metadata.doi, Some("10.1371/journal.pmed.0020124".to_string()));
+        assert_eq!(metadata.pii, Some("05-PLME-RA-0071R2".to_string()));
+    }
+
+    #[test]
+    fn test_extract_jats_keywords() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <kwd-group>
+        <kwd>caffeine</kwd>
+        <kwd>meta-analysis</kwd>
+        <kwd>systematic review</kwd>
+      </kwd-group>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert_eq!(metadata.keywords.len(), 3);
+        assert!(metadata.keywords.contains(&"caffeine".to_string()));
+        assert!(metadata.keywords.contains(&"meta-analysis".to_string()));
+    }
+
+    #[test]
+    fn test_extract_jats_publication_info() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <pub-date pub-type="epub">
+        <day>18</day>
+        <month>04</month>
+        <year>2005</year>
+      </pub-date>
+      <volume>2</volume>
+      <issue>4</issue>
+      <fpage>e124</fpage>
+      <lpage>e132</lpage>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert!(metadata.publication_date.is_some());
+        assert_eq!(metadata.volume, Some("2".to_string()));
+        assert_eq!(metadata.issue, Some("4".to_string()));
+        assert!(metadata.pages.is_some());
+    }
+
+    #[test]
+    fn test_extract_jats_abstract() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <abstract>
+        <sec>
+          <title>Background</title>
+          <p>This is the background information of the study.</p>
+        </sec>
+        <sec>
+          <title>Methods</title>
+          <p>We used quantitative analysis to evaluate the hypothesis.</p>
+        </sec>
+      </abstract>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert!(metadata.abstract_text.is_some());
+        let abstract_text = metadata.abstract_text.unwrap();
+        assert!(abstract_text.contains("background"));
+        assert!(abstract_text.contains("quantitative"));
+    }
+
+    #[test]
+    fn test_extract_jats_tables_basic() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <body>
+    <table-wrap id="tbl1">
+      <table>
+        <thead>
+          <tr>
+            <th>Study</th>
+            <th>Year</th>
+          </tr>
+        </thead>
+        <tbody>
+          <tr>
+            <td>Study A</td>
+            <td>2003</td>
+          </tr>
+          <tr>
+            <td>Study B</td>
+            <td>2004</td>
+          </tr>
+        </tbody>
+      </table>
+    </table-wrap>
+  </body>
+</article>"#;
+
+        let (_metadata, _content, _title, tables) = extract_jats_all_in_one(jats).expect("Table extraction failed");
+        assert_eq!(tables.len(), 1);
+        assert_eq!(tables[0].cells.len(), 3);
+    }
+
+    #[test]
+    fn test_extract_jats_corresponding_author() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <author-notes>
+        <corresp id="cor1">To whom correspondence should be addressed. E-mail: rwilliams@yale.edu</corresp>
+      </author-notes>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert!(metadata.corresponding_author.is_some());
+        let corresp = metadata.corresponding_author.unwrap();
+        assert!(corresp.contains("rwilliams"));
+    }
+
+    #[test]
+    fn test_extract_jats_section_hierarchy() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <article-title>Article Title</article-title>
+    </article-meta>
+  </front>
+  <body>
+    <sec id="s1">
+      <title>Introduction</title>
+      <p>Intro content.</p>
+    </sec>
+    <sec id="s2">
+      <title>Methods</title>
+      <p>Methods content.</p>
+    </sec>
+    <sec id="s3">
+      <title>Results</title>
+      <p>Results content.</p>
+    </sec>
+  </body>
+</article>"#;
+
+        let (_metadata, content, _title, _tables) = extract_jats_all_in_one(jats).expect("Parse failed");
+        assert!(content.contains("Introduction"));
+        assert!(content.contains("Methods"));
+        assert!(content.contains("Results"));
+    }
+
+    #[test]
+    fn test_jats_extractor_full_metadata_extraction() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <article-title>Sample Article</article-title>
+      <contrib-group>
+        <contrib contrib-type="author">
+          <name>
+            <surname>Smith</surname>
+            <given-names>John</given-names>
+          </name>
+        </contrib>
+      </contrib-group>
+      <article-id pub-id-type="doi">10.1234/test</article-id>
+      <kwd-group>
+        <kwd>test</kwd>
+      </kwd-group>
+      <abstract>
+        <p>Test abstract.</p>
+      </abstract>
+    </article-meta>
+  </front>
+  <body>
+    <p>Sample content.</p>
+  </body>
+</article>"#;
+
+        let (metadata_extracted, _content, _title, _tables) =
+            extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert_eq!(metadata_extracted.title, "Sample Article");
+        assert_eq!(metadata_extracted.authors.len(), 1);
+        assert_eq!(metadata_extracted.doi, Some("10.1234/test".to_string()));
+        assert_eq!(metadata_extracted.keywords.len(), 1);
+        assert!(metadata_extracted.abstract_text.is_some());
+    }
+
+    #[test]
+    fn test_jats_extractor_empty_article() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+    </article-meta>
+  </front>
+  <body>
+  </body>
+</article>"#;
+
+        let (metadata, content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert!(metadata.title.is_empty());
+        assert!(content.is_empty() || content.trim().is_empty());
+    }
+
+    #[test]
+    fn test_extract_jats_journal_title() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article>
+  <front>
+    <article-meta>
+      <article-title>Test Article</article-title>
+      <journal-title>Nature Medicine</journal-title>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert_eq!(metadata.journal_title, Some("Nature Medicine".to_string()));
+    }
+
+    #[test]
+    fn test_extract_jats_article_type() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article article-type="research-article">
+  <front>
+    <article-meta>
+      <article-title>Test Article</article-title>
+    </article-meta>
+  </front>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+        assert_eq!(metadata.article_type, Some("research-article".to_string()));
+    }
+
+    #[test]
+    fn test_extract_all_13_metadata_fields() {
+        let jats = r#"<?xml version="1.0" encoding="UTF-8"?>
+<article article-type="research-article">
+  <front>
+    <article-meta>
+      <article-title>Full Metadata Test</article-title>
+      <subtitle>A Complete Example</subtitle>
+      <contrib-group>
+        <contrib contrib-type="author">
+          <name>
+            <surname>Author</surname>
+            <given-names>First</given-names>
+          </name>
+        </contrib>
+      </contrib-group>
+      <aff>Department of Testing, Test University</aff>
+      <article-id pub-id-type="doi">10.1234/full-test</article-id>
+      <article-id pub-id-type="pii">TEST-001</article-id>
+      <kwd-group>
+        <kwd>testing</kwd>
+        <kwd>metadata</kwd>
+      </kwd-group>
+      <pub-date pub-type="epub">
+        <year>2024</year>
+      </pub-date>
+      <volume>5</volume>
+      <issue>3</issue>
+      <fpage>100</fpage>
+      <lpage>110</lpage>
+      <journal-title>Test Journal</journal-title>
+      <abstract>
+        <p>This is a test abstract for all metadata fields.</p>
+      </abstract>
+      <author-notes>
+        <corresp>Correspondence: test@example.com</corresp>
+      </author-notes>
+    </article-meta>
+  </front>
+  <body>
+    <p>Test content.</p>
+  </body>
+</article>"#;
+
+        let (metadata, _content, _title, _tables) = extract_jats_all_in_one(jats).expect("Metadata extraction failed");
+
+        assert_eq!(metadata.title, "Full Metadata Test");
+        assert_eq!(metadata.subtitle, Some("A Complete Example".to_string()));
+        assert_eq!(metadata.authors.len(), 1);
+        assert!(metadata.authors[0].contains("Author"));
+        assert_eq!(metadata.affiliations.len(), 1);
+        assert!(metadata.affiliations[0].contains("Testing"));
+        assert_eq!(metadata.doi, Some("10.1234/full-test".to_string()));
+        assert_eq!(metadata.pii, Some("TEST-001".to_string()));
+        assert_eq!(metadata.keywords.len(), 2);
+        assert!(metadata.publication_date.is_some());
+        assert_eq!(metadata.volume, Some("5".to_string()));
+        assert_eq!(metadata.issue, Some("3".to_string()));
+        assert!(metadata.pages.is_some());
+        assert_eq!(metadata.journal_title, Some("Test Journal".to_string()));
+        assert_eq!(metadata.article_type, Some("research-article".to_string()));
+        assert!(metadata.abstract_text.is_some());
+        assert!(metadata.corresponding_author.is_some());
+    }
+}