@201 Add RO-Crate entity filters for targeted lookups

api/openapi.codegen.yaml

@@ -4815,6 +4815,21 @@ paths:
           - integer
           - 'null'
           format: int64
+      - name: file_id
+        in: query
+        required: false
+        schema:
+          type:
+          - integer
+          - 'null'
+          format: int64
+      - name: entity_id
+        in: query
+        required: false
+        schema:
+          type:
+          - string
+          - 'null'
       - name: sort_by
         in: query
         required: false

api/openapi.yaml

@@ -4815,6 +4815,21 @@ paths:
           - integer
           - 'null'
           format: int64
+      - name: file_id
+        in: query
+        required: false
+        schema:
+          type:
+          - integer
+          - 'null'
+          format: int64
+      - name: entity_id
+        in: query
+        required: false
+        schema:
+          type:
+          - string
+          - 'null'
       - name: sort_by
         in: query
         required: false

julia_client/Torc/src/api/apis/api_RoCrateEntitiesApi.jl

@@ -138,11 +138,13 @@ const _returntypes_list_ro_crate_entities_RoCrateEntitiesApi = Dict{Regex,Type}(
     Regex("^" * replace("500", "x"=>".") * "\$") => ErrorResponse,
 )
 
-function _oacinternal_list_ro_crate_entities(_api::RoCrateEntitiesApi, id::Int64; offset=nothing, limit=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing)
+function _oacinternal_list_ro_crate_entities(_api::RoCrateEntitiesApi, id::Int64; offset=nothing, limit=nothing, file_id=nothing, entity_id=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing)
     _ctx = OpenAPI.Clients.Ctx(_api.client, "GET", _returntypes_list_ro_crate_entities_RoCrateEntitiesApi, "/workflows/{id}/ro_crate_entities", [])
     OpenAPI.Clients.set_param(_ctx.path, "id", id)  # type Int64
     OpenAPI.Clients.set_param(_ctx.query, "offset", offset; style="form", is_explode=true)  # type Int64
     OpenAPI.Clients.set_param(_ctx.query, "limit", limit; style="form", is_explode=true)  # type Int64
+    OpenAPI.Clients.set_param(_ctx.query, "file_id", file_id; style="form", is_explode=true)  # type Int64
+    OpenAPI.Clients.set_param(_ctx.query, "entity_id", entity_id; style="form", is_explode=true)  # type String
     OpenAPI.Clients.set_param(_ctx.query, "sort_by", sort_by; style="form", is_explode=true)  # type String
     OpenAPI.Clients.set_param(_ctx.query, "reverse_sort", reverse_sort; style="form", is_explode=true)  # type Bool
     OpenAPI.Clients.set_header_accept(_ctx, ["application/json", ])
@@ -154,18 +156,20 @@ end
 - id::Int64 (required)
 - offset::Int64
 - limit::Int64
+- file_id::Int64
+- entity_id::String
 - sort_by::String
 - reverse_sort::Bool
 
 Return: ListRoCrateEntitiesResponse, OpenAPI.Clients.ApiResponse
 """
-function list_ro_crate_entities(_api::RoCrateEntitiesApi, id::Int64; offset=nothing, limit=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing)
-    _ctx = _oacinternal_list_ro_crate_entities(_api, id; offset=offset, limit=limit, sort_by=sort_by, reverse_sort=reverse_sort, _mediaType=_mediaType)
+function list_ro_crate_entities(_api::RoCrateEntitiesApi, id::Int64; offset=nothing, limit=nothing, file_id=nothing, entity_id=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing)
+    _ctx = _oacinternal_list_ro_crate_entities(_api, id; offset=offset, limit=limit, file_id=file_id, entity_id=entity_id, sort_by=sort_by, reverse_sort=reverse_sort, _mediaType=_mediaType)
     return OpenAPI.Clients.exec(_ctx)
 end
 
-function list_ro_crate_entities(_api::RoCrateEntitiesApi, response_stream::Channel, id::Int64; offset=nothing, limit=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing)
-    _ctx = _oacinternal_list_ro_crate_entities(_api, id; offset=offset, limit=limit, sort_by=sort_by, reverse_sort=reverse_sort, _mediaType=_mediaType)
+function list_ro_crate_entities(_api::RoCrateEntitiesApi, response_stream::Channel, id::Int64; offset=nothing, limit=nothing, file_id=nothing, entity_id=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing)
+    _ctx = _oacinternal_list_ro_crate_entities(_api, id; offset=offset, limit=limit, file_id=file_id, entity_id=entity_id, sort_by=sort_by, reverse_sort=reverse_sort, _mediaType=_mediaType)
     return OpenAPI.Clients.exec(_ctx, response_stream)
 end
 

julia_client/julia_client/docs/RoCrateEntitiesApi.md

@@ -125,8 +125,8 @@ No authorization required
 [[Back to top]](#) [[Back to API list]](../README.md#api-endpoints) [[Back to Model list]](../README.md#models) [[Back to README]](../README.md)
 
 # **list_ro_crate_entities**
-> list_ro_crate_entities(_api::RoCrateEntitiesApi, id::Int64; offset=nothing, limit=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing) -> ListRoCrateEntitiesResponse, OpenAPI.Clients.ApiResponse <br/>
-> list_ro_crate_entities(_api::RoCrateEntitiesApi, response_stream::Channel, id::Int64; offset=nothing, limit=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing) -> Channel{ ListRoCrateEntitiesResponse }, OpenAPI.Clients.ApiResponse
+> list_ro_crate_entities(_api::RoCrateEntitiesApi, id::Int64; offset=nothing, limit=nothing, file_id=nothing, entity_id=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing) -> ListRoCrateEntitiesResponse, OpenAPI.Clients.ApiResponse <br/>
+> list_ro_crate_entities(_api::RoCrateEntitiesApi, response_stream::Channel, id::Int64; offset=nothing, limit=nothing, file_id=nothing, entity_id=nothing, sort_by=nothing, reverse_sort=nothing, _mediaType=nothing) -> Channel{ ListRoCrateEntitiesResponse }, OpenAPI.Clients.ApiResponse
 
 
 
@@ -143,6 +143,8 @@ Name | Type | Description  | Notes
 ------------- | ------------- | ------------- | -------------
  **offset** | **Int64** |  | [default to nothing]
  **limit** | **Int64** |  | [default to nothing]
+ **file_id** | **Int64** |  | [default to nothing]
+ **entity_id** | **String** |  | [default to nothing]
  **sort_by** | **String** |  | [default to nothing]
  **reverse_sort** | **Bool** |  | [default to nothing]
 

python_client/src/torc/openapi_client/api/ro_crate_entities_api.py

@@ -1128,6 +1128,8 @@ def list_ro_crate_entities(
         id: Annotated[StrictInt, Field(description="Workflow ID")],
         offset: Optional[StrictInt] = None,
         limit: Optional[StrictInt] = None,
+        file_id: Optional[StrictInt] = None,
+        entity_id: Optional[StrictStr] = None,
         sort_by: Optional[StrictStr] = None,
         reverse_sort: Optional[StrictBool] = None,
         _request_timeout: Union[
@@ -1152,6 +1154,10 @@ def list_ro_crate_entities(
         :type offset: int
         :param limit:
         :type limit: int
+        :param file_id:
+        :type file_id: int
+        :param entity_id:
+        :type entity_id: str
         :param sort_by:
         :type sort_by: str
         :param reverse_sort:
@@ -1182,6 +1188,8 @@ def list_ro_crate_entities(
             id=id,
             offset=offset,
             limit=limit,
+            file_id=file_id,
+            entity_id=entity_id,
             sort_by=sort_by,
             reverse_sort=reverse_sort,
             _request_auth=_request_auth,
@@ -1213,6 +1221,8 @@ def list_ro_crate_entities_with_http_info(
         id: Annotated[StrictInt, Field(description="Workflow ID")],
         offset: Optional[StrictInt] = None,
         limit: Optional[StrictInt] = None,
+        file_id: Optional[StrictInt] = None,
+        entity_id: Optional[StrictStr] = None,
         sort_by: Optional[StrictStr] = None,
         reverse_sort: Optional[StrictBool] = None,
         _request_timeout: Union[
@@ -1237,6 +1247,10 @@ def list_ro_crate_entities_with_http_info(
         :type offset: int
         :param limit:
         :type limit: int
+        :param file_id:
+        :type file_id: int
+        :param entity_id:
+        :type entity_id: str
         :param sort_by:
         :type sort_by: str
         :param reverse_sort:
@@ -1267,6 +1281,8 @@ def list_ro_crate_entities_with_http_info(
             id=id,
             offset=offset,
             limit=limit,
+            file_id=file_id,
+            entity_id=entity_id,
             sort_by=sort_by,
             reverse_sort=reverse_sort,
             _request_auth=_request_auth,
@@ -1298,6 +1314,8 @@ def list_ro_crate_entities_without_preload_content(
         id: Annotated[StrictInt, Field(description="Workflow ID")],
         offset: Optional[StrictInt] = None,
         limit: Optional[StrictInt] = None,
+        file_id: Optional[StrictInt] = None,
+        entity_id: Optional[StrictStr] = None,
         sort_by: Optional[StrictStr] = None,
         reverse_sort: Optional[StrictBool] = None,
         _request_timeout: Union[
@@ -1322,6 +1340,10 @@ def list_ro_crate_entities_without_preload_content(
         :type offset: int
         :param limit:
         :type limit: int
+        :param file_id:
+        :type file_id: int
+        :param entity_id:
+        :type entity_id: str
         :param sort_by:
         :type sort_by: str
         :param reverse_sort:
@@ -1352,6 +1374,8 @@ def list_ro_crate_entities_without_preload_content(
             id=id,
             offset=offset,
             limit=limit,
+            file_id=file_id,
+            entity_id=entity_id,
             sort_by=sort_by,
             reverse_sort=reverse_sort,
             _request_auth=_request_auth,
@@ -1378,6 +1402,8 @@ def _list_ro_crate_entities_serialize(
         id,
         offset,
         limit,
+        file_id,
+        entity_id,
         sort_by,
         reverse_sort,
         _request_auth,
@@ -1412,6 +1438,14 @@ def _list_ro_crate_entities_serialize(
 
             _query_params.append(('limit', limit))
 
+        if file_id is not None:
+
+            _query_params.append(('file_id', file_id))
+
+        if entity_id is not None:
+
+            _query_params.append(('entity_id', entity_id))
+
         if sort_by is not None:
 
             _query_params.append(('sort_by', sort_by))

src/client/apis/ro_crate_api.rs

@@ -1,3 +1,5 @@
+use log::warn;
+
 pub use super::ro_crate_entities_api::{
     CreateRoCrateEntityError, DeleteRoCrateEntitiesError, DeleteRoCrateEntityError,
     GetRoCrateEntityError, ListRoCrateEntitiesError, UpdateRoCrateEntityError,
@@ -7,6 +9,94 @@ pub use super::ro_crate_entities_api::{
 use super::{Error, configuration, ro_crate_entities_api};
 use crate::models;
 
+#[allow(clippy::too_many_arguments)]
+pub fn list_ro_crate_entities_with_filters(
+    configuration: &configuration::Configuration,
+    id: i64,
+    offset: Option<i64>,
+    limit: Option<i64>,
+    file_id: Option<i64>,
+    entity_id: Option<&str>,
+    sort_by: Option<&str>,
+    reverse_sort: Option<bool>,
+) -> Result<models::ListRoCrateEntitiesResponse, Error<ListRoCrateEntitiesError>> {
+    ro_crate_entities_api::list_ro_crate_entities(
+        configuration,
+        id,
+        offset,
+        limit,
+        file_id,
+        entity_id,
+        sort_by,
+        reverse_sort,
+    )
+}
+
+fn first_entity_from_filtered_response(
+    response: models::ListRoCrateEntitiesResponse,
+    filter_name: &str,
+    filter_value: impl std::fmt::Display,
+) -> Option<models::RoCrateEntityModel> {
+    if response.total_count > 1 {
+        warn!(
+            "Expected at most one RO-Crate entity for {}={}, found {}. Returning the first match.",
+            filter_name, filter_value, response.total_count
+        );
+    }
+
+    response.items.into_iter().next()
+}
+
+/// Find the first RO-Crate entity linked to a file.
+///
+/// If multiple entities match, logs a warning and returns the first item.
+pub fn find_ro_crate_entity_by_file_id(
+    configuration: &configuration::Configuration,
+    workflow_id: i64,
+    file_id: i64,
+) -> Result<Option<models::RoCrateEntityModel>, Error<ListRoCrateEntitiesError>> {
+    let response = list_ro_crate_entities_with_filters(
+        configuration,
+        workflow_id,
+        Some(0),
+        Some(2),
+        Some(file_id),
+        None,
+        None,
+        None,
+    )?;
+
+    Ok(first_entity_from_filtered_response(
+        response, "file_id", file_id,
+    ))
+}
+
+/// Find the first RO-Crate entity with a matching entity ID.
+///
+/// If multiple entities match, logs a warning and returns the first item.
+pub fn find_ro_crate_entity_by_entity_id(
+    configuration: &configuration::Configuration,
+    workflow_id: i64,
+    entity_id: &str,
+) -> Result<Option<models::RoCrateEntityModel>, Error<ListRoCrateEntitiesError>> {
+    let response = list_ro_crate_entities_with_filters(
+        configuration,
+        workflow_id,
+        Some(0),
+        Some(2),
+        None,
+        Some(entity_id),
+        None,
+        None,
+    )?;
+
+    Ok(first_entity_from_filtered_response(
+        response,
+        "entity_id",
+        entity_id,
+    ))
+}
+
 pub fn delete_ro_crate_entities(
     configuration: &configuration::Configuration,
     id: i64,

src/client/apis/ro_crate_entities_api.rs

@@ -308,13 +308,17 @@ pub fn list_ro_crate_entities(
     id: i64,
     offset: Option<i64>,
     limit: Option<i64>,
+    file_id: Option<i64>,
+    entity_id: Option<&str>,
     sort_by: Option<&str>,
     reverse_sort: Option<bool>,
 ) -> Result<models::ListRoCrateEntitiesResponse, Error<ListRoCrateEntitiesError>> {
     // add a prefix to parameters to efficiently prevent name collisions
     let p_path_id = id;
     let p_query_offset = offset;
     let p_query_limit = limit;
+    let p_query_file_id = file_id;
+    let p_query_entity_id = entity_id;
     let p_query_sort_by = sort_by;
     let p_query_reverse_sort = reverse_sort;
 
@@ -331,6 +335,12 @@ pub fn list_ro_crate_entities(
     if let Some(ref param_value) = p_query_limit {
         req_builder = req_builder.query(&[("limit", &param_value.to_string())]);
     }
+    if let Some(ref param_value) = p_query_file_id {
+        req_builder = req_builder.query(&[("file_id", &param_value.to_string())]);
+    }
+    if let Some(ref param_value) = p_query_entity_id {
+        req_builder = req_builder.query(&[("entity_id", &param_value.to_string())]);
+    }
     if let Some(ref param_value) = p_query_sort_by {
         req_builder = req_builder.query(&[("sort_by", &param_value.to_string())]);
     }

src/client/commands/pagination/ro_crate_entities.rs

@@ -72,6 +72,8 @@ impl Paginatable for RoCrateEntityModel {
             params.workflow_id,
             Some(params.offset),
             Some(limit),
+            None,
+            None,
             params.sort_by(),
             params.reverse_sort(),
         )?;

src/client/commands/workflows.rs

@@ -3090,6 +3090,8 @@ fn handle_export(
         None,
         None,
         None,
+        None,
+        None,
     ) {
         Ok(response) => response.items,
         Err(e) => {

src/client/ro_crate_utils.rs

@@ -223,18 +223,8 @@ pub fn find_entity_for_file(
     workflow_id: i64,
     file_id: i64,
 ) -> Option<RoCrateEntityModel> {
-    match apis::ro_crate_entities_api::list_ro_crate_entities(
-        config,
-        workflow_id,
-        None,
-        None,
-        None,
-        None,
-    ) {
-        Ok(response) => response
-            .items
-            .into_iter()
-            .find(|e| e.file_id == Some(file_id)),
+    match apis::ro_crate_api::find_ro_crate_entity_by_file_id(config, workflow_id, file_id) {
+        Ok(entity) => entity,
         Err(e) => {
             warn!("Failed to check for existing RO-Crate entities: {}", e);
             None
@@ -555,6 +545,8 @@ pub fn create_software_entities(config: &Configuration, workflow_id: i64, run_id
             None,
             None,
             None,
+            None,
+            None,
         ) {
             Ok(response) => response.items.into_iter().map(|e| e.entity_id).collect(),
             Err(e) => {