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added tests, fixed bug in node retrieval
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@MartinKl
MartinKl committed Nov 21, 2023
1 parent 7b91bc1 commit 645c7fc
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Showing 2 changed files with 205 additions and 14 deletions.
1 change: 1 addition & 0 deletions CHANGELOG.md
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Original file line number Diff line number Diff line change
Expand Up @@ -40,6 +40,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
- relative import and export paths are interpreted as relative to the parent directory of the workflow file
- the spreadsheet importer will use the correct namespace `default_ns` for segmentation ordering relations
- fixed ordering of token nodes in spreadsheet import
- `link` now considers all matching nodes for the same value, so the correct amount of edges is created

### Removed

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218 changes: 204 additions & 14 deletions src/manipulator/link.rs
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Original file line number Diff line number Diff line change
Expand Up @@ -81,6 +81,8 @@ impl Manipulator for LinkNodes {

type NodeBundle = Vec<(Option<AnnoKey>, String)>;

/// This function executes a single query and returns bundled results or an error.
/// A bundled result is the annotation key the node has a match for and the matching node itself.
fn retrieve_nodes_with_values(
cs: &CorpusStorage,
query: String,
Expand Down Expand Up @@ -123,6 +125,8 @@ fn anno_key(qname: &str) -> AnnoKey {
}
}

/// This function queries the corpus graph and returns the relevant match data.
/// The returned data maps an annotation value or a joint value (value) to the nodes holding said value.
fn gather_link_data(
graph: &AnnotationGraph,
cs: &CorpusStorage,
Expand Down Expand Up @@ -162,8 +166,12 @@ fn gather_link_data(
}
target_data.push(link_node_name.to_string());
}
let joined_value = value_segments.join(sep);
data.insert(joined_value, target_data);
let joint_value = value_segments.join(sep);
if let Some(nodes_with_value) = data.get_mut(&joint_value) {
nodes_with_value.extend(target_data);
} else {
data.insert(joint_value, target_data);
}
} else if let Some(sender) = tx {
let message = StatusMessage::Failed(AnnattoError::Manipulator {
reason: format!(
Expand Down Expand Up @@ -204,7 +212,11 @@ impl LinkNodes {

#[cfg(test)]
mod tests {
use std::{collections::BTreeSet, env::temp_dir, sync::mpsc};
use std::{
collections::{BTreeMap, BTreeSet},
env::temp_dir,
sync::mpsc,
};

use graphannis::{
corpusstorage::{QueryLanguage, ResultOrder, SearchQuery},
Expand All @@ -218,18 +230,23 @@ mod tests {
util::join_qname,
};
use itertools::Itertools;
use tempfile::tempdir_in;
use tempfile::{tempdir_in, TempDir};

use crate::manipulator::{link::LinkNodes, Manipulator};
use crate::manipulator::{
link::{gather_link_data, retrieve_nodes_with_values, LinkNodes},
Manipulator,
};

#[test]
fn test_linker_on_disk() {
assert!(main_test(true).is_ok());
let r = main_test(true);
assert!(r.is_ok(), "Error in main test: {:?}", r.err());
}

#[test]
fn test_linker_in_mem() {
assert!(main_test(false).is_ok());
let r = main_test(false);
assert!(r.is_ok(), "Error in main test: {:?}", r.err());
}

fn main_test(on_disk: bool) -> Result<(), Box<dyn std::error::Error>> {
Expand Down Expand Up @@ -348,12 +365,8 @@ mod tests {
("norm:norm ->morphology morph=/I/", 1),
];
let corpus_name = "current";
let tmp_dir_e = tempdir_in(temp_dir())?;
let tmp_dir_g = tempdir_in(temp_dir())?;
e_g.save_to(&tmp_dir_e.path().join(corpus_name))?;
g.save_to(&tmp_dir_g.path().join(corpus_name))?;
let cs_e = CorpusStorage::with_auto_cache_size(&tmp_dir_e.path(), true)?;
let cs_g = CorpusStorage::with_auto_cache_size(&tmp_dir_g.path(), true)?;
let (cs_e, _tmpe) = store_corpus(&mut e_g, corpus_name)?;
let (cs_g, _tmpg) = store_corpus(&mut g, corpus_name)?;
for (query_s, expected_n) in queries {
let query = SearchQuery {
corpus_names: &[corpus_name],
Expand Down Expand Up @@ -386,6 +399,176 @@ mod tests {
Ok(())
}

fn store_corpus(
graph: &mut AnnotationGraph,
corpus_name: &str,
) -> Result<(CorpusStorage, TempDir), Box<dyn std::error::Error>> {
let tmp_dir = tempdir_in(temp_dir())?;
graph.save_to(&tmp_dir.path().join(corpus_name))?;
Ok((
CorpusStorage::with_auto_cache_size(&tmp_dir.path(), true)?,
tmp_dir,
))
}

#[test]
fn test_retrieve_nodes_with_values() {
let g = source_graph(false);
assert!(g.is_ok());
let mut graph = g.unwrap();
let corpus_name = "current";
let cs_r = store_corpus(&mut graph, corpus_name);
assert!(cs_r.is_ok());
let (cs, _tmp) = cs_r.unwrap();
// 1
let r1 = retrieve_nodes_with_values(&cs, "tok=/.*/".to_string());
assert!(r1.is_ok(), "not Ok: {:?}", r1.err());
let results_1 = r1.unwrap();
assert_eq!(6, results_1.len());
for match_v in results_1 {
assert_eq!(1, match_v.len());
assert!(match_v.get(0).unwrap().0.is_none());
}
// 2
let r2 = retrieve_nodes_with_values(&cs, "norm _=_ pos".to_string());
assert!(r2.is_ok(), "not Ok: {:?}", r2.err());
let results_2 = r2.unwrap();
assert_eq!(4, results_2.len());
for match_v in results_2 {
assert_eq!(2, match_v.len());
assert!(match_v.get(0).unwrap().0.is_some());
}
}

#[test]
fn test_gather_link_data() {
let g = source_graph(false);
assert!(g.is_ok());
let mut graph = g.unwrap();
let corpus_name = "current";
let cs_r = store_corpus(&mut graph, corpus_name);
assert!(cs_r.is_ok());
let (cs, _tmp) = cs_r.unwrap();
let ldr = gather_link_data(
&graph,
&cs,
"norm _=_ pos".to_string(),
1,
&[1, 2],
&" ".to_string(),
&None,
);
assert!(ldr.is_ok(), "not Ok: {:?}", ldr.err());
let link_data = ldr.unwrap();
let expected_link_data: BTreeMap<String, Vec<String>> = vec![
(
"i pron".to_string(),
vec![
"import/exmaralda/test_doc#t_norm_T286-T0".to_string(),
"import/exmaralda/test_doc#t_norm_T286-T0".to_string(),
],
),
(
"am verb".to_string(),
vec![
"import/exmaralda/test_doc#t_norm_T0-T1".to_string(),
"import/exmaralda/test_doc#t_norm_T0-T1".to_string(),
],
),
(
"in adp".to_string(),
vec![
"import/exmaralda/test_doc#t_norm_T1-T2".to_string(),
"import/exmaralda/test_doc#t_norm_T1-T2".to_string(),
],
),
(
"new york propn".to_string(),
vec![
"import/exmaralda/test_doc#t_norm_T2-T4".to_string(),
"import/exmaralda/test_doc#t_norm_T2-T4".to_string(),
],
),
]
.into_iter()
.collect();
assert_eq!(expected_link_data, link_data);
}

#[test]
fn test_link_nodes() {
let g = source_graph(false);
assert!(g.is_ok());
let mut graph = g.unwrap();
let linker = LinkNodes {
source_query: "dummy query -- value not used".to_string(),
source_node: 1, // dummy value
source_value: vec![1], // dummy value
target_query: "dummy query -- value not used".to_string(),
target_node: 1, // dummy value
target_value: vec![1], // dummy value
link_type: AnnotationComponentType::Pointing,
link_layer: "".to_string(),
link_name: "link".to_string(),
value_sep: "dummy value".to_string(),
};
let source_map = vec![
(
"i_am_im".to_string(),
vec!["import/exmaralda/test_doc#t_dipl_T286-T1".to_string()],
),
(
"New_York".to_string(),
vec![
"import/exmaralda/test_doc#t_dipl_T2-T3".to_string(),
"import/exmaralda/test_doc#t_dipl_T3-T4".to_string(),
],
),
]
.into_iter()
.collect();
let target_map = vec![
(
"i_am_im".to_string(),
vec![
"import/exmaralda/test_doc#t_norm_T286-T0".to_string(),
"import/exmaralda/test_doc#t_norm_T0-T1".to_string(),
],
),
(
"New_York".to_string(),
vec!["import/exmaralda/test_doc#t_norm_T2-T4".to_string()],
),
]
.into_iter()
.collect();
let r = linker.link_nodes(source_map, target_map);
assert!(r.is_ok());
let mut u = r.unwrap();
assert!(graph.apply_update(&mut u, |_| {}).is_ok());
let storage_bundle = store_corpus(&mut graph, "current");
assert!(storage_bundle.is_ok());
let (cs, _tmp) = storage_bundle.unwrap();
let queries_with_results = [
("dipl=/I'm/ ->link norm=/I/ . norm=/am/ & #1 ->link #3", 1),
(
"dipl=/New/ . dipl=/York/ & #1 ->link norm=/New York/ & #2 ->link #3",
1,
),
];
for (q, n) in queries_with_results {
let query = SearchQuery {
corpus_names: &["current"],
query: q,
query_language: QueryLanguage::AQL,
timeout: None,
};
let c = cs.count(query);
assert!(c.is_ok());
assert_eq!(n, c.unwrap());
}
}

fn source_graph(on_disk: bool) -> Result<AnnotationGraph, Box<dyn std::error::Error>> {
// copied this from exmaralda test
let mut graph = AnnotationGraph::new(on_disk)?;
Expand Down Expand Up @@ -497,7 +680,14 @@ mod tests {
node_name: node_name.to_string(),
anno_ns: ANNIS_NS.to_string(),
anno_name: "tok".to_string(),
anno_value: "value".to_string(),
anno_value: value.to_string(),
})?;
u.add_event(UpdateEvent::AddEdge {
source_node: node_name.to_string(),
target_node: "import/exmaralda/test_doc".to_string(),
layer: ANNIS_NS.to_string(),
component_type: AnnotationComponentType::PartOf.to_string(),
component_name: "".to_string(),
})?;
if let Some(other_name) = prev {
u.add_event(UpdateEvent::AddEdge {
Expand Down

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