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use facet::Facet;
use graphannis::{
model::AnnotationComponentType,
update::{GraphUpdate, UpdateEvent},
};
use graphannis_core::graph::ANNIS_NS;
use itertools::Itertools;
use normpath::PathExt;
use ordered_float::OrderedFloat;
use serde::Serialize;
use serde_derive::Deserialize;
use std::{
collections::{BTreeMap, BTreeSet},
env,
fs::File,
};
use xml::{EventReader, ParserConfig, attribute::OwnedAttribute, reader::XmlEvent};
use super::Importer;
use crate::{
StepID,
error::AnnattoError,
importer::GenericImportConfiguration,
progress::ProgressReporter,
util::graphupdate::{import_corpus_graph_from_files, map_audio_source},
workflow::StatusMessage,
};
/// Import [EXMARaLDA partition editor](https://exmaralda.org/en/partitur-editor-en/)
/// (`.exb`) files.
#[derive(Facet, Deserialize, Serialize, Clone, PartialEq)]
#[serde(deny_unknown_fields)]
pub struct ImportEXMARaLDA {
/// If `true` (the default), events that cover the same timeline items and
/// belong to the same speaker are merged into a single span.
#[serde(default = "default_merge_events")]
merge_events: bool,
}
impl Default for ImportEXMARaLDA {
fn default() -> Self {
Self {
merge_events: default_merge_events(),
}
}
}
fn default_merge_events() -> bool {
true
}
const FILE_EXTENSIONS: [&str; 2] = ["exb", "xml"];
impl Importer for ImportEXMARaLDA {
fn import_corpus(
&self,
input_path: &std::path::Path,
step_id: StepID,
config: GenericImportConfiguration,
tx: Option<crate::workflow::StatusSender>,
) -> Result<graphannis::update::GraphUpdate, Box<dyn std::error::Error>> {
let mut update = GraphUpdate::default();
let all_files = import_corpus_graph_from_files(&mut update, input_path, &config)?;
let progress = ProgressReporter::new(tx.clone(), step_id.clone(), all_files.len())?;
let document_status: Result<Vec<()>, AnnattoError> = all_files
.into_iter()
.map(|(fp, doc_node_name)| {
self.import_document(
&step_id,
&doc_node_name,
fp.as_path(),
&mut update,
&progress,
&tx,
)
})
.collect();
// Check for any errors
document_status?;
Ok(update)
}
fn default_file_extensions(&self) -> &[&str] {
&FILE_EXTENSIONS
}
}
fn attr_vec_to_map(attributes: &[OwnedAttribute]) -> BTreeMap<String, String> {
attributes
.iter()
.map(|attr| (attr.name.to_string(), attr.value.to_string()))
.collect::<BTreeMap<String, String>>()
}
pub const LANGUAGE_SEP: &str = ",";
impl ImportEXMARaLDA {
fn import_document(
&self,
step_id: &StepID,
doc_node_name: &str,
document_path: &std::path::Path,
update: &mut GraphUpdate,
progress: &ProgressReporter,
tx: &Option<crate::workflow::StatusSender>,
) -> crate::error::Result<()> {
// buffers
let mut char_buf = String::new();
let mut timeline = BTreeMap::new();
let mut ordered_tl_nodes: Vec<String> = Vec::new();
let mut speaker_map = BTreeMap::new();
let mut parent_map: BTreeMap<String, BTreeMap<String, String>> = BTreeMap::new();
let mut already_defined: BTreeSet<String> = BTreeSet::new();
let mut named_orderings: BTreeMap<String, Vec<(usize, String)>> = BTreeMap::new();
let mut tlis = Vec::new();
// reader
let f = File::open(document_path)?;
let mut parser_cfg = ParserConfig::new();
parser_cfg.trim_whitespace = true;
let mut reader = EventReader::new_with_config(f, parser_cfg);
let mut errors = Vec::default();
let empty_map = BTreeMap::default();
loop {
match reader.next() {
Ok(XmlEvent::EndDocument) => break,
Ok(XmlEvent::StartDocument { .. }) => {}
Ok(XmlEvent::Characters(value)) => char_buf.push_str(value.as_str()),
Ok(XmlEvent::StartElement {
name, attributes, ..
}) => {
parent_map.insert(name.to_string(), attr_vec_to_map(&attributes));
let attr_map = parent_map.get(&name.to_string()).unwrap_or(&empty_map);
match name.to_string().as_str() {
"referenced-file" => {
if let Some(file_url) = attr_vec_to_map(&attributes).get("url") {
if file_url.trim().is_empty() {
continue;
}
if let Some(parent_path) = document_path.parent() {
let audio_path = parent_path.join(file_url);
// only link files, no directories or symlinks
if audio_path.exists() && (audio_path.is_file()) {
let absolute_audio_path = audio_path.normalize()?;
if let Some(rel_path) = pathdiff::diff_paths(
absolute_audio_path,
env::current_dir()?,
) {
if let Some(name_tuple) = doc_node_name.rsplit_once('/')
{
map_audio_source(
update,
rel_path.as_path(),
name_tuple.0,
doc_node_name,
)?;
}
} else {
progress.warn(
format!(
"Could not map linked audio file in \n{}, because no relative path to \n{} could be determined using \n{} as a base.",
doc_node_name,
audio_path.to_string_lossy(),
env::current_dir()?.to_string_lossy()
)
.as_str(),
)?;
}
} else {
let msg = format!(
"Linked file {} could not be found to be linked in document {}",
audio_path.as_path().to_string_lossy(),
&doc_node_name
);
progress.warn(&msg)?;
}
};
}
}
"tli" => {
let time = if let Some(time_value) = attr_map.get("time") {
let time =
if let Ok(t_val) = time_value.parse::<OrderedFloat<f64>>() {
t_val
} else {
let err = AnnattoError::Import {
reason: "Failed to parse tli time value.".to_string(),
importer: step_id.module_name.clone(),
path: document_path.to_path_buf(),
};
return Err(err);
};
Some(time)
} else {
None
};
if let Some(id) = attr_map.get("id") {
tlis.push((id.to_string(), time));
}
}
"language" => {
if !char_buf.is_empty() {
char_buf.push_str(LANGUAGE_SEP);
}
if let Some(lang_value) = attr_map.get("lang") {
char_buf.push_str(lang_value);
}
}
"event" | "abbreviation" | "l1" | "l2" | "comment" | "languages-used"
| "ud-information" => char_buf.clear(),
_ => {}
}
}
Ok(XmlEvent::EndElement { name }) => {
let str_tag_name = name.to_string();
match str_tag_name.as_str() {
"abbreviation" | "l1" | "l2" | "comment" | "languages-used" => {
if let Some(parent) = parent_map.get("speaker")
&& !char_buf.trim().is_empty()
{
let speaker_id = parent["id"].to_string();
if str_tag_name.as_str() == "abbreviation" {
// write speaker name to speaker table
let speaker_name = char_buf.to_string();
speaker_map.insert(speaker_id.to_string(), speaker_name);
}
update.add_event(UpdateEvent::AddNodeLabel {
// speaker table data as document meta annotation
node_name: doc_node_name.to_string(),
anno_ns: speaker_id.to_string(),
anno_name: str_tag_name,
anno_value: char_buf.to_string(),
})?;
}
}
"common-timeline" => {
// check for integrity of timeline
let mut used_time_values = BTreeSet::default();
let mut last = OrderedFloat::from(-1.);
let mut corrupted = false;
for (_, to) in &tlis {
if let Some(t) = to {
if used_time_values.contains(t) {
return Err(AnnattoError::Import {
reason: format!(
"Time value {t} is used more than once."
),
importer: step_id.module_name.to_string(),
path: document_path.to_path_buf(),
});
}
if t <= &last {
if let Some(sender) = &tx {
sender.send(StatusMessage::Warning(
"Unordered timeline, will try to fix ..."
.to_string(),
))?;
}
corrupted = true;
}
last = *t;
used_time_values.insert(*t);
}
}
if corrupted {
if tlis.iter().any(|(_, t_opt)| t_opt.is_none()) {
// impossible, order of mentioning of tlis in xml-file is relevant
return Err(AnnattoError::Import {
reason: "Timeline cannot be fixed automatically."
.to_string(),
importer: step_id.to_string(),
path: document_path.to_path_buf(),
});
} else {
tlis.sort_by(|(_, t_opt_a), (_, t_opt_b)| {
t_opt_a
.unwrap_or_default()
.cmp(&t_opt_b.unwrap_or_default())
});
}
}
// build empty toks
for (tli_id, time_opt) in &tlis {
let node_name = format!("{}#{}", &doc_node_name, tli_id);
update.add_event(UpdateEvent::AddNode {
node_name: node_name.to_string(),
node_type: "node".to_string(),
})?;
update.add_event(UpdateEvent::AddNodeLabel {
node_name: node_name.to_string(),
anno_ns: ANNIS_NS.to_string(),
anno_name: "tok".to_string(),
anno_value: " ".to_string(),
})?;
timeline.insert(
tli_id.to_string(),
((*time_opt), node_name.to_string()),
);
update.add_event(UpdateEvent::AddEdge {
source_node: node_name.to_string(),
target_node: doc_node_name.to_string(),
layer: ANNIS_NS.to_string(),
component_type: AnnotationComponentType::PartOf.to_string(),
component_name: "".to_string(),
})?;
}
// order timeline elements / empty toks
ordered_tl_nodes
.extend(tlis.iter().map(|e| e.0.to_string()).collect_vec());
for i in 1..ordered_tl_nodes.len() {
if let Some(source) = &timeline.get(&ordered_tl_nodes[i - 1])
&& let Some(target) = &timeline.get(&ordered_tl_nodes[i])
{
update.add_event(UpdateEvent::AddEdge {
source_node: source.1.to_string(),
target_node: target.1.to_string(),
layer: ANNIS_NS.to_string(),
component_type: AnnotationComponentType::Ordering
.to_string(),
component_name: "".to_string(),
})?;
}
}
}
"event" => {
let text = char_buf.to_string();
let tier_info = if let Some(m) = parent_map.get("tier") {
m
} else {
return Err(AnnattoError::Export {
reason: "Could not determine tier properties".to_string(),
exporter: step_id.module_name.to_string(),
path: document_path.to_path_buf(),
});
};
let speaker_id_opt = tier_info.get("speaker");
let speaker_id = if let Some(speaker_id_val) = speaker_id_opt {
speaker_id_val.as_str()
} else {
""
};
let speaker_name_opt = speaker_map.get(speaker_id);
let speaker_name = if let Some(speaker_name_value) = speaker_name_opt {
speaker_name_value.as_str()
} else if speaker_id.trim().is_empty() {
speaker_id
} else {
let rs = format!(
"Speaker `{speaker_id}` has not been defined in speaker-table."
);
let err = AnnattoError::Import {
reason: rs,
importer: step_id.module_name.clone(),
path: document_path.to_path_buf(),
};
return Err(err);
};
let anno_name_opt = tier_info.get("category");
let anno_name = if let Some(anno_name_value) = anno_name_opt {
anno_name_value
} else {
let rs = "Tier encountered with undefined category attribute.";
let err = AnnattoError::Import {
reason: rs.to_string(),
importer: step_id.module_name.clone(),
path: document_path.to_path_buf(),
};
return Err(err);
};
let tier_type = if let Some(tpe) = tier_info.get("type") {
tpe.as_str()
} else {
let msg = format!(
"Could not determine tier type for {}::{}. Tier will be treated as annotation tier.",
&speaker_id, &anno_name
);
progress.warn(&msg)?;
"a"
};
let event_info = parent_map.get("event").unwrap_or(&empty_map);
let start_id = if let Some(id) = event_info.get("start") {
id
} else {
// send "Failed", but continue to collect potential further errors in the file
let msg = format!(
"Could not determine start id of currently processed event `{text}`. Event will be skipped. Import will fail."
);
let err = AnnattoError::Import {
reason: msg,
importer: step_id.module_name.clone(),
path: document_path.to_path_buf(),
};
errors.push(err);
continue;
};
let end_id = if let Some(id) = event_info.get("end") {
id
} else {
// send "Failed", but continue to collect potential further errors in the file
let msg = format!(
"Could not determine end id of currently processed event `{text}`. Event will be skipped. Import will fail."
);
let err = AnnattoError::Import {
reason: msg,
importer: step_id.module_name.clone(),
path: document_path.to_path_buf(),
};
errors.push(err);
continue;
};
let start_i = if let Some(i_val) =
ordered_tl_nodes.iter().position(|e| e == start_id)
{
i_val
} else {
let err = AnnattoError::Import {
reason: format!("Unknown time line item: {start_id}"),
importer: step_id.module_name.clone(),
path: document_path.to_path_buf(),
};
return Err(err);
};
let end_i = if let Some(i_val) =
ordered_tl_nodes.iter().position(|e| e == end_id)
{
i_val
} else {
let err = AnnattoError::Import {
reason: format!("Unknown time line item: {end_id}"),
importer: step_id.module_name.clone(),
path: document_path.to_path_buf(),
};
return Err(err);
};
if start_i >= end_i {
let err_msg = format!(
"Start time is bigger than end time for ids: {start_id}--{end_id} "
);
return Err(AnnattoError::Import {
reason: err_msg,
importer: step_id.module_name.clone(),
path: document_path.to_path_buf(),
});
}
let overlapped = &ordered_tl_nodes[start_i..end_i];
let key = if let Some(k) = overlapped.first() {
k
} else {
if let Some(sender) = tx {
let msg = format!(
"Event {}::{}:{}-{} does not cover any tokens and will be skipped.",
&speaker_id, &anno_name, &start_id, &end_id
);
sender.send(StatusMessage::Warning(msg))?;
}
continue;
};
let node_name = if self.merge_events {
format!(
"{doc_node_name}#{tier_type}_{speaker_id}_{start_id}-{end_id}"
)
} else {
format!(
"{doc_node_name}#{tier_type}_{speaker_id}_{anno_name}_{start_id}-{end_id}"
)
};
if !already_defined.contains(&node_name) {
update.add_event(UpdateEvent::AddNode {
node_name: node_name.to_string(),
node_type: "node".to_string(),
})?;
// part-of
update.add_event(UpdateEvent::AddEdge {
source_node: node_name.to_string(),
target_node: doc_node_name.to_string(),
layer: ANNIS_NS.to_string(),
component_type: AnnotationComponentType::PartOf.to_string(),
component_name: "".to_string(),
})?;
// coverage
for overlapped_id in overlapped {
if let Some((_, target_id)) = timeline.get(overlapped_id) {
update.add_event(UpdateEvent::AddEdge {
source_node: node_name.to_string(),
target_node: target_id.to_string(),
layer: ANNIS_NS.to_string(),
component_type: AnnotationComponentType::Coverage
.to_string(),
component_name: "".to_string(),
})?;
}
}
let node_tpl = if let Some(t_name) = ordered_tl_nodes.get(end_i) {
// timeline and ordered tl nodes are directly dependent on each other, so we can safely unwrap
timeline.get(t_name)
} else {
if let Some(sender) = tx {
let msg = format!(
"Could not determine end time of event {}::{}:{}-{}. Event will be skipped.",
&speaker_id, &anno_name, &start_id, &end_id
);
sender.send(StatusMessage::Info(msg))?;
}
continue;
};
if let Some((Some(start_time), _)) = timeline.get(key)
&& let Some((Some(end_time), _)) = node_tpl
{
update.add_event(UpdateEvent::AddNodeLabel {
node_name: node_name.to_string(),
anno_ns: ANNIS_NS.to_string(),
anno_name: "time".to_string(),
anno_value: format!("{start_time}-{end_time}"),
})?;
already_defined.insert(node_name.to_string());
}
}
update.add_event(UpdateEvent::AddNodeLabel {
node_name: node_name.to_string(),
anno_ns: ANNIS_NS.to_string(),
anno_name: "layer".to_string(),
anno_value: speaker_name.to_string(),
})?;
if tier_type == "t" {
// tokenization
update.add_event(UpdateEvent::AddNodeLabel {
node_name: node_name.to_string(),
anno_ns: ANNIS_NS.to_string(),
anno_name: "tok".to_string(),
anno_value: text.to_string(),
})?;
// order nodes
let order_tpl = (start_i, node_name.to_string());
match named_orderings.entry(anno_name.to_string()) {
std::collections::btree_map::Entry::Vacant(e) => {
e.insert(vec![order_tpl]);
}
std::collections::btree_map::Entry::Occupied(mut e) => {
e.get_mut().push(order_tpl);
}
}
}
update.add_event(UpdateEvent::AddNodeLabel {
node_name: node_name.to_string(),
anno_ns: speaker_name.to_string(),
anno_name: anno_name.to_string(),
anno_value: text.to_string(),
})?;
}
"ud-information" => {
if let Some(anno_name) = parent_map
.get("ud-information")
.unwrap_or(&empty_map)
.get("attribute-name")
{
let ns = if let Some(parent) = parent_map.get("speaker") {
if let Some(speaker_id) = parent.get("id") {
speaker_id.as_str()
} else {
""
}
} else {
""
};
update.add_event(UpdateEvent::AddNodeLabel {
node_name: doc_node_name.to_string(),
anno_ns: ns.to_string(),
anno_name: anno_name.to_string(),
anno_value: char_buf.to_string(),
})?;
}
}
_ => {}
}
parent_map.remove(&name.to_string());
}
Err(_) => {
return Err(AnnattoError::Import {
reason: "Failed parsing EXMARaLDA XML.".to_string(),
importer: step_id.module_name.clone(),
path: document_path.to_path_buf(),
});
}
_ => continue,
}
}
// build order relations
for (name, node_name_vec) in named_orderings {
let mut prev = None;
for (_, node_name) in node_name_vec.into_iter().sorted_by(|a, b| a.0.cmp(&b.0)) {
if let Some(source) = prev {
update.add_event(UpdateEvent::AddEdge {
source_node: source,
target_node: node_name.to_string(),
layer: ANNIS_NS.to_string(),
component_type: AnnotationComponentType::Ordering.to_string(),
component_name: name.to_string(),
})?;
}
prev = Some(node_name);
}
}
if errors.is_empty() {
Ok(())
} else {
Err(AnnattoError::ConversionFailed { errors })
}
}
}
#[cfg(test)]
mod tests;