feat!: Add passthrough param to the compress_list and expand_list fun…

…ctions (default to true for python and JS bindings)

js/src/api.rs

@@ -156,12 +156,19 @@ impl ConverterJs {
     // TODO: Use Vec<String> instead of JsValue possible?
     /// Expand a list of CURIEs to URIs
     #[wasm_bindgen(js_name = expandList)]
-    pub fn expand_list(&self, curies: JsValue) -> Result<JsValue, JsValue> {
+    pub fn expand_list(
+        &self,
+        curies: JsValue,
+        passthrough: Option<bool>,
+    ) -> Result<JsValue, JsValue> {
         let curies_vec: Vec<String> = serde_wasm_bindgen::from_value(curies)
             .map_err(|e| JsValue::from_str(&format!("Error converting CURIEs list: {}", e)))?;
         let js_array = self
             .converter
-            .expand_list(curies_vec.iter().map(String::as_str).collect())
+            .expand_list(
+                curies_vec.iter().map(String::as_str).collect(),
+                passthrough.unwrap_or(true),
+            )
             .into_iter()
             .map(JsValue::from)
             .collect::<Array>();
@@ -170,12 +177,19 @@ impl ConverterJs {
 
     /// Compress a list of URIs to CURIEs
     #[wasm_bindgen(js_name = compressList)]
-    pub fn compress_list(&self, curies: JsValue) -> Result<JsValue, JsValue> {
+    pub fn compress_list(
+        &self,
+        curies: JsValue,
+        passthrough: Option<bool>,
+    ) -> Result<JsValue, JsValue> {
         let curies_vec: Vec<String> = serde_wasm_bindgen::from_value(curies)
             .map_err(|e| JsValue::from_str(&format!("Error converting URIs list: {}", e)))?;
         let js_array = self
             .converter
-            .compress_list(curies_vec.iter().map(String::as_str).collect())
+            .compress_list(
+                curies_vec.iter().map(String::as_str).collect(),
+                passthrough.unwrap_or(true),
+            )
             .into_iter()
             .map(JsValue::from)
             .collect::<Array>();

js/tests/curies.test.ts

@@ -14,14 +14,14 @@ describe('Tests for the curies npm package', () => {
     expect(converter.expandList(["OBO:1234", "DOID:1234", "Wrong:1"])).toEqual([
       "http://purl.obolibrary.org/obo/1234",
       "http://purl.obolibrary.org/obo/DOID_1234",
-      undefined
+      "Wrong:1"
     ]);
     expect(converter.compress("http://purl.obolibrary.org/obo/1234")).toBe("OBO:1234");
     expect(converter.compressList([
       "http://purl.obolibrary.org/obo/1234",
       "http://purl.obolibrary.org/obo/DOID_1234",
       "http://identifiers.org/DOID:1234"
-    ])).toEqual(["OBO:1234", "DOID:1234", undefined]);
+    ])).toEqual(["OBO:1234", "DOID:1234", "http://identifiers.org/DOID:1234"]);
     expect(converter.getPrefixes().length).toBe(2)
     expect(converter.getUriPrefixes().length).toBe(2)
 
@@ -43,13 +43,13 @@ describe('Tests for the curies npm package', () => {
     expect(converter.expandList(["OBO:1234", "DOID:1234", "Wrong:1"])).toEqual([
       "http://purl.obolibrary.org/obo/1234",
       "http://purl.obolibrary.org/obo/DOID_1234",
-      undefined
+      "Wrong:1",
     ]);
     expect(converter.compressList([
       "http://purl.obolibrary.org/obo/1234",
       "http://purl.obolibrary.org/obo/DOID_1234",
       "http://identifiers.org/DOID:1234"
-    ])).toEqual(["OBO:1234", "DOID:1234", undefined]);
+    ])).toEqual(["OBO:1234", "DOID:1234", "http://identifiers.org/DOID:1234"]);
   });
 
   test('from JSON-LD', async () => {

lib/src/api.rs

@@ -157,6 +157,8 @@ impl Converter {
     /// assert_eq!(curie, "DOID:1234");
     /// ```
     pub async fn from_prefix_map<T: PrefixMapSource>(prefix_map: T) -> Result<Self, CuriesError> {
+        // TODO: better error handling. We should show all the errors at once instead of stopping at the first one
+        // cf. original python implementation
         let prefix_map: HashMap<String, Value> = prefix_map.fetch().await?;
         let mut converter = Converter::default();
         for (prefix, uri_prefix) in prefix_map {
@@ -598,22 +600,35 @@ impl Converter {
     }
 
     /// Compresses a list of URIs to CURIEs
-    pub fn compress_list(&self, uris: Vec<&str>) -> Vec<Option<String>> {
+    pub fn compress_list(&self, uris: Vec<&str>, passthrough: bool) -> Vec<Option<String>> {
+        // TODO: fixed
         uris.into_iter()
             .map(|uri| match self.compress(uri) {
                 Ok(curie) => Some(curie),
-                Err(_) => None,
+                Err(_) => {
+                    if passthrough {
+                        Some(uri.to_string()) // Return the full URI if passthrough is true
+                    } else {
+                        None
+                    }
+                }
             })
             .collect()
     }
 
     /// Expands a list of CURIESs to URIs
-    pub fn expand_list(&self, curies: Vec<&str>) -> Vec<Option<String>> {
+    pub fn expand_list(&self, curies: Vec<&str>, passthrough: bool) -> Vec<Option<String>> {
         curies
             .into_iter()
             .map(|curie| match self.expand(curie) {
                 Ok(uri) => Some(uri),
-                Err(_) => None,
+                Err(_) => {
+                    if passthrough {
+                        Some(curie.to_string()) // Return the full URI if passthrough is true
+                    } else {
+                        None
+                    }
+                }
             })
             .collect()
     }

lib/tests/curies_test.rs

@@ -86,19 +86,41 @@ fn new_empty_converter() -> Result<(), Box<dyn std::error::Error>> {
     );
 
     assert_eq!(
-        converter
-            .compress_list(["http://wrong/1234", "https://identifiers.org/DOID/1234"].to_vec()),
+        converter.compress_list(
+            ["http://wrong/1234", "https://identifiers.org/DOID/1234"].to_vec(),
+            false
+        ),
         [None, Some("doid:1234".to_string())].to_vec()
     );
     assert_eq!(
-        converter.expand_list(["doid:1234", "wrong:1234"].to_vec()),
+        converter.expand_list(["doid:1234", "wrong:1234"].to_vec(), false),
         [
             Some("http://purl.obolibrary.org/obo/DOID_1234".to_string()),
             None
         ]
         .to_vec()
     );
 
+    assert_eq!(
+        converter.compress_list(
+            ["http://wrong/1234", "https://identifiers.org/DOID/1234"].to_vec(),
+            true
+        ),
+        [
+            Some("http://wrong/1234".to_string()),
+            Some("doid:1234".to_string())
+        ]
+        .to_vec()
+    );
+    assert_eq!(
+        converter.expand_list(["doid:1234", "wrong:1234"].to_vec(), true),
+        [
+            Some("http://purl.obolibrary.org/obo/DOID_1234".to_string()),
+            Some("wrong:1234".to_string()),
+        ]
+        .to_vec()
+    );
+
     // Test wrong calls
     assert!(converter
         .add_prefix("doid", "http://purl.obolibrary.org/obo/DOID_")

python/src/api.rs

@@ -190,16 +190,20 @@ impl ConverterPy {
 
     /// Expand a list of CURIEs
     #[pyo3(text_signature = "(curies)")]
-    fn expand_list(&self, curies: Vec<String>) -> Vec<Option<String>> {
-        self.converter
-            .expand_list(curies.iter().map(|s| s.as_str()).collect())
+    fn expand_list(&self, curies: Vec<String>, passthrough: Option<bool>) -> Vec<Option<String>> {
+        self.converter.expand_list(
+            curies.iter().map(|s| s.as_str()).collect(),
+            passthrough.unwrap_or(true),
+        )
     }
 
     /// Compress a list of URIs
     #[pyo3(text_signature = "(uris)")]
-    fn compress_list(&self, uris: Vec<String>) -> Vec<Option<String>> {
-        self.converter
-            .compress_list(uris.iter().map(|s| s.as_str()).collect())
+    fn compress_list(&self, uris: Vec<String>, passthrough: Option<bool>) -> Vec<Option<String>> {
+        self.converter.compress_list(
+            uris.iter().map(|s| s.as_str()).collect(),
+            passthrough.unwrap_or(true),
+        )
     }
 
     /// Standardize prefix