Fix download linked items into templates

backend/sbs_server/app/downloadTemplates.py

@@ -84,7 +84,7 @@ def sbh_download_template(files):
 
     params_from_request = json.loads(params_file.read())
 
-    required_params = ['template_type', 'sbh_url', 'sbh_token', 'collection_url']
+    required_params = ['template_type', 'sbh_url', 'sbh_prefix', 'sbh_token', 'collection_url']
     for param in required_params:
         if param not in params_from_request:
             return jsonify({"error": f"Parameter {param} not found in request"}), 400
@@ -93,6 +93,7 @@ def sbh_download_template(files):
         return jsonify({"error": "No SBH credentials provided"}), 400
 
     sbh_url = params_from_request['sbh_url']
+    sbh_prefix = params_from_request.get('sbh_prefix')
     sbh_collection_url = params_from_request['collection_url'] 
     sbh_token = params_from_request['sbh_token']
     parts = sbh_collection_url.split("/")
@@ -114,44 +115,44 @@ def sbh_download_template(files):
         wb = load_workbook(BytesIO(template_bytes), keep_vba=True)
 
         if template_type == "synbio.object-type.strains":
-            search_result = sbh_get_subCollection_uris(sbh_url,sbh_token,usergraph,sbh_collection_url,"http://identifiers.org/ncit/NCIT:C14419")
+            search_result = sbh_get_subCollection_uris(sbh_url,sbh_prefix,sbh_token,usergraph,sbh_collection_url,"http://identifiers.org/ncit/NCIT:C14419")
             new_rows = []
             for binding in search_result["results"]["bindings"]:
                 uri = binding["s"]["value"]
                 id = binding["id"]["value"]
                 new_rows.append([id, uri])
             expand_table_in_xlsm(wb,sheet_name="SBH_chassis_collections",table_name="SBH_chassis_collections",new_rows=new_rows)
-            search_result = sbh_get_subCollection_uris(sbh_url,sbh_token,usergraph,sbh_collection_url,"http://identifiers.org/so/SO:0000637")
+            search_result = sbh_get_subCollection_uris(sbh_url,sbh_prefix,sbh_token,usergraph,sbh_collection_url,"http://identifiers.org/so/SO:0000637")
             new_rows = []
             for binding in search_result["results"]["bindings"]:
                 uri = binding["s"]["value"]
                 id = binding["id"]["value"]
                 new_rows.append([id, uri])
             expand_table_in_xlsm(wb,sheet_name="SBH_plasmids_collections",table_name="SBH_plasmids_collections",new_rows=new_rows)
         elif template_type == "synbio.object-type.sample-designs":
-            search_result = sbh_get_subCollection_uris(sbh_url,sbh_token,usergraph,sbh_collection_url,"http://identifiers.org/ncit/NCIT:C48164")
+            search_result = sbh_get_subCollection_uris(sbh_url,sbh_prefix,sbh_token,usergraph,sbh_collection_url,"http://identifiers.org/ncit/NCIT:C48164")
             new_rows = []
             for binding in search_result["results"]["bindings"]:
                 uri = binding["s"]["value"]
                 id = binding["id"]["value"]
                 new_rows.append([id, uri])
             expand_table_in_xlsm(wb,sheet_name="SBH_media_collection",table_name="SBH_media_collection",new_rows=new_rows)
-            search_result = sbh_get_subCollection_uris(sbh_url,sbh_token,usergraph,sbh_collection_url,type="http://www.biopax.org/release/biopax-level3.owl#SmallMolecule")
+            search_result = sbh_get_subCollection_uris(sbh_url,sbh_prefix,sbh_token,usergraph,sbh_collection_url,type="http://www.biopax.org/release/biopax-level3.owl#SmallMolecule")
             new_rows = []
             for binding in search_result["results"]["bindings"]:
                 uri = binding["s"]["value"]
                 id = binding["id"]["value"]
                 new_rows.append([id, uri])
             expand_table_in_xlsm(wb,sheet_name="SBH_chemicals_collection",table_name="SBH_chemicals_collection",new_rows=new_rows)
-            search_result = sbh_get_subCollection_uris(sbh_url,sbh_token,usergraph,sbh_collection_url,"http://purl.obolibrary.org/obo/NCIT_C97158")
+            search_result = sbh_get_subCollection_uris(sbh_url,sbh_prefix,sbh_token,usergraph,sbh_collection_url,"http://purl.obolibrary.org/obo/NCIT_C97158")
             new_rows = []
             for binding in search_result["results"]["bindings"]:
                 uri = binding["s"]["value"]
                 id = binding["id"]["value"]
                 new_rows.append([id, uri])
             expand_table_in_xlsm(wb,sheet_name="SBH_strains_collection",table_name="SBH_strains_collection",new_rows=new_rows)
         elif template_type == "synbio.object-type.study-data":
-            search_result = sbh_get_subCollection_uris(sbh_url,sbh_token,usergraph,sbh_collection_url,"https://wiki.synbiohub.org/wiki/Terms/SynBioSuite#SampleDesign")
+            search_result = sbh_get_subCollection_uris(sbh_url,sbh_prefix,sbh_token,usergraph,sbh_collection_url,"https://wiki.synbiohub.org/wiki/Terms/SynBioSuite#SampleDesign")
             new_rows = []
             for binding in search_result["results"]["bindings"]:
                 uri = binding["s"]["value"]

backend/sbs_server/app/synbiohubUpload.py

@@ -49,7 +49,7 @@ def upload_to_sbh(doc, sbh_url, sbh_prefix, sbh_token, usergraph, sbh_collection
     subCollection = sbol2.Collection(importType)
     parts = sbh_collection_url.split("/")
     subCollection_url = "/".join(parts[:6]) + "/" + importType + "/1"
-    search_result = sbh_get_subCollection_uris(sbh_url, sbh_token, usergraph, subCollection_url)
+    search_result = sbh_get_subCollection_uris(sbh_url, sbh_prefix, sbh_token, usergraph, subCollection_url, recursiveMembers=False)
     for binding in search_result["results"]["bindings"]:
         uri = binding["s"]["value"]
         subCollection.members = subCollection.members + [ uri ]

backend/sbs_server/app/utils.py

@@ -69,16 +69,35 @@ def sparql_query(sbh_url, sbh_token, query):
 '''
 Helper function to perform SPARQL queries to fetch URIs from SynBioHub
 '''
-def sbh_get_subCollection_uris(sbh_url, sbh_token, usergraph, collectionUri, role = None, type = None):
-    if role is None and type is None:
-        query = f'PREFIX sbol: <http://sbols.org/v2#> SELECT ?s ?id FROM <{usergraph}> WHERE {{ <{collectionUri}> sbol:member ?s . ?s sbol:displayId ?id }}'
-    elif type is None:
-        query = f'PREFIX sbol: <http://sbols.org/v2#> SELECT ?s ?id FROM <{usergraph}> WHERE {{ ?s sbol:role <{role}> . <{collectionUri}> sbol:member ?s . ?s sbol:displayId ?id }}'
-    elif role is None:
-        query = f'PREFIX sbol: <http://sbols.org/v2#> SELECT ?s ?id FROM <{usergraph}> WHERE {{ ?s sbol:type <{type}> . <{collectionUri}> sbol:member ?s . ?s sbol:displayId ?id }}'
+def sbh_get_subCollection_uris(sbh_url, sbh_prefix, sbh_token, usergraph, collectionUri, 
+                               role = None, type = None, recursiveMembers = True):
+    conditions = []
+    publicgraph = sbh_prefix + '/public'
+    if role is not None:
+        conditions.append(f'?s sbol:role <{role}> .')
+    if type is not None:
+        conditions.append(f'?s sbol:type <{type}> .')
+
+    if recursiveMembers:
+        where_parts = [
+            f'<{collectionUri}> sbol:member* ?s .',
+            'FILTER(?s != <' + collectionUri + '>)',
+            '?s sbol:displayId ?id .'
+        ]
     else:
-        query = f'PREFIX sbol: <http://sbols.org/v2#> SELECT ?s ?id FROM <{usergraph}> WHERE {{ ?s sbol:type <{type}> . ?s sbol:role <{role}> . <{collectionUri}> sbol:member ?s . ?s sbol:displayId ?id }}'
-
+        where_parts = [
+            f'<{collectionUri}> sbol:member ?s .',
+            'FILTER(?s != <' + collectionUri + '>)',
+            '?s sbol:displayId ?id .'
+        ]        
+    where_parts.extend(conditions)
+
+    query = (
+        f'PREFIX sbol: <http://sbols.org/v2#> '
+        f'SELECT DISTINCT ?s ?id FROM <{usergraph}> FROM <{publicgraph}> WHERE {{ '
+        f'{" ".join(where_parts)}'
+        f' }}'
+    )
     return sparql_query(sbh_url, sbh_token, query)
 
 def sbh_get_attachment_uri(sbh_url, sbh_token, usergraph, collectionUri, attachmentName):

frontend/src/API.js

@@ -13,6 +13,7 @@ function capitalizeFirst(str) {
 
 export async function download_template(
     sbh_url,
+    sbh_prefix,
     sbh_token,
     collectionUrl,
     templateType) {
@@ -21,6 +22,7 @@ export async function download_template(
 
         const paramsObj = {
           sbh_url: sbh_url,
+          sbh_prefix: sbh_prefix,
           sbh_token: sbh_token,
           collection_url: collectionUrl,
           template_type: templateType

frontend/src/components/activities/explorer/DownloadMetadata.jsx

@@ -60,14 +60,15 @@ export default function DownloadMetadata({ objectType }) {
         const selectedRepo = jsonData.registryURL;
         const authToken = modalResult.authToken
         const registryAPI = dataSBH.find((repo) => repo.registryURL === selectedRepo)?.registryAPI || selectedRepo
-
+        const registryPrefix = dataSBH.find((repo) => repo.registryURL === selectedRepo)?.registryPrefix || selectedRepo
+
         if (!collectionUrl || !selectedRepo || !authToken) {
             showErrorNotification("Download aborted", "Missing repository, credentials, or collection selection.")
             return
         }
 
         try {
-            const response = await download_template(registryAPI,authToken,collectionUrl,objectType?.id);
+            const response = await download_template(registryAPI,registryPrefix,authToken,collectionUrl,objectType?.id);
             const blob = new Blob([response.data], {
                 type: "application/vnd.ms-excel.sheet.macroEnabled.12"
             });