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//! Element extraction (title, abstract, body, references, tables).
use super::metadata::JatsMetadataExtracted;
use super::parser::extract_text_content;
use crate::Result;
use crate::extraction::cells_to_markdown;
use crate::types::Table;
use quick_xml::Reader;
use quick_xml::events::Event;
/// Extract all content in a single optimized pass.
/// Combines metadata extraction, content parsing, and table extraction into one pass.
pub(super) 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(§ion_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(¤t_table);
tables.push(Table {
cells: current_table.clone(),
markdown,
page_number: table_index + 1,
bounding_box: None,
});
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))
}