Submit endpoint4

.github/workflows/test-backend.yml

@@ -55,3 +55,39 @@ jobs:
       - name: Run tests
         run: |
           tests/test.sh
+
+  sboltestrunner:
+    name: SBOLTestRunner
+    needs: build
+    runs-on: ubuntu-latest
+    timeout-minutes: 180
+    steps:
+      - uses: actions/checkout@v3
+        name: Checkout source tree
+      - uses: actions/download-artifact@v4
+        name: Download Docker image
+        with:
+          name: sbh3-image
+      - name: Import saved Docker image
+        run: |
+          cat sbh3.tar.gz | docker load
+      - name: Install Docker Compose
+        run: |
+          sudo apt-get update
+          sudo apt-get install -y docker-compose
+      - uses: actions/setup-java@v4
+        name: Install Java
+        with:
+          distribution: temurin
+          java-version: '17'
+      - uses: actions/setup-python@v4
+        name: Install Python
+        with:
+          python-version: '3.9'
+      - name: Install test dependencies
+        run: |
+          pip install -r tests/test_requirements.txt
+      - name: Run SBOLTestRunner
+        run: |
+          cd tests
+          bash ./sbolsuite.sh

.gitignore

@@ -171,4 +171,6 @@ tests/Compared/
 tests/Emulated/
 tests/Retrieved/
 tests/SynBioHubRunner/
+tests/Timing/
+tests/sbol_testrunner_result
 tests/logs_from_test_suite/

backend/src/main/java/com/synbiohub/sbh3/controllers/ExposeController.java

@@ -0,0 +1,40 @@
+package com.synbiohub.sbh3.controllers;
+
+import com.synbiohub.sbh3.submit.SubmitExposeRegistry;
+import lombok.RequiredArgsConstructor;
+import org.springframework.core.io.FileSystemResource;
+import org.springframework.core.io.Resource;
+import org.springframework.http.HttpHeaders;
+import org.springframework.http.MediaType;
+import org.springframework.http.ResponseEntity;
+import org.springframework.web.bind.annotation.GetMapping;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RestController;
+
+import java.net.URLConnection;
+import java.nio.file.Files;
+import java.nio.file.Path;
+
+@RestController
+@RequiredArgsConstructor
+public class ExposeController {
+
+    private final SubmitExposeRegistry exposeRegistry;
+
+    @GetMapping("/expose/{token}")
+    public ResponseEntity<Resource> exposeFile(@PathVariable String token) {
+        Path file = exposeRegistry.resolve(token);
+        if (file == null || !Files.isRegularFile(file)) {
+            return ResponseEntity.notFound().build();
+        }
+        String filename = file.getFileName().toString();
+        String contentType = URLConnection.guessContentTypeFromName(filename);
+        MediaType mediaType = contentType != null
+                ? MediaType.parseMediaType(contentType)
+                : MediaType.APPLICATION_OCTET_STREAM;
+        return ResponseEntity.ok()
+                .header(HttpHeaders.CONTENT_DISPOSITION, "inline; filename=\"" + filename + "\"")
+                .contentType(mediaType)
+                .body(new FileSystemResource(file));
+    }
+}

backend/src/main/java/com/synbiohub/sbh3/controllers/SubmitController.java

@@ -1,15 +1,19 @@
 package com.synbiohub.sbh3.controllers;
 
 import com.synbiohub.sbh3.services.SubmitService;
+import com.synbiohub.sbh3.submit.SubmitPayload;
 import io.swagger.v3.oas.annotations.Operation;
 import io.swagger.v3.oas.annotations.tags.Tag;
 import lombok.RequiredArgsConstructor;
 import org.sbolstandard.core2.SBOLDocument;
+import org.sbolstandard.core2.SBOLValidationException;
 import org.springframework.http.HttpStatus;
 import org.springframework.http.MediaType;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.bind.annotation.*;
+import org.springframework.web.multipart.MultipartFile;
 
+import java.io.IOException;
 import java.util.Map;
 
 @Tag(name = "Submissions", description = "Endpoints for creating and submitting registry objects")
@@ -21,17 +25,17 @@ public class SubmitController {
     /**
      * Create a new collection or submit file contents into an existing collection.
      * <p>
-     * String form fields are bound via {@code allParams} (e.g. id, version, name,
-     * description,
-     * citations, overwrite_merge, rootCollections, plugin). The uploaded design
-     * file is bound
-     * separately because multipart files are not included in a
-     * {@code Map<String, String>}.
+     * String form fields are bound via {@code allParams} (e.g. id, version, name, description,
+     * citations, overwrite_merge, rootCollections, plugin). The uploaded design file is bound
+     * separately because multipart files are not included in a {@code Map<String, String>}.
      */
-    @PostMapping(value = "/submit", consumes = MediaType.MULTIPART_FORM_DATA_VALUE, produces = "text/plain; charset=UTF-8")
-    @Operation(summary = "Submit object (stub)", description = "Temporary stub so the branch compiles.")
-    public ResponseEntity<String> submit(@RequestParam Map<String, String> allParams) {
-        return ResponseEntity.ok("Form submitted");
+    @PostMapping(value = "/submit",
+            consumes = MediaType.MULTIPART_FORM_DATA_VALUE,
+            produces = "text/plain; charset=UTF-8")
+    public ResponseEntity<String> submit(
+            @ModelAttribute SubmitPayload allParams,
+            @RequestPart(value = "file", required = false) MultipartFile file) throws IOException, SBOLValidationException {
+        return submitService.submit(allParams, file);
     }
 
     @Operation(summary = "Create new collection (Unimplemented)", description = "Currently an empty stub.", deprecated = true)

backend/src/main/java/com/synbiohub/sbh3/dao/SparqlService.java

@@ -1,5 +1,7 @@
 package com.synbiohub.sbh3.dao;
 
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
 import com.synbiohub.sbh3.repo.SparqlRepository;
 import com.synbiohub.sbh3.sparql.SPARQLQuery;
 import com.synbiohub.sbh3.utils.ConfigUtil;
@@ -12,6 +14,7 @@
 import org.springframework.stereotype.Service;
 
 import java.io.IOException;
+import java.nio.file.Path;
 import java.util.HashMap;
 import java.util.Map;
 import java.util.Objects;
@@ -22,8 +25,85 @@
 public class SparqlService {
 
     private final SparqlRepository sparqlRepository;
+    private final ObjectMapper objectMapper;
     private final JsonUtil jsonUtil;
 
+    /**
+     * Virtuoso DELETE templates return one row per batch; loop until nothing remains.
+     * Legacy {@code sparql.deleteStaggered}.
+     */
+    public void deleteCollection(Map<String, String> params, String graphUri) throws IOException {
+        deleteStaggered(sparqlRepository.REMOVE_COLLECTION_SPARQL, params, graphUri);
+    }
+
+    public void delete(Map<String, String> params, String graphUri) throws IOException {
+        deleteStaggered(sparqlRepository.REMOVE_SPARQL, params, graphUri);
+    }
+
+    public void uploadGraphStore(String graphUri, Path file) throws IOException {
+        sparqlRepository.save(graphUri, file);
+    }
+
+    public void uploadAttachment(Map<String, String> params, String graphUri) throws IOException {
+        String query = new SPARQLQuery(sparqlRepository.ATTACHMENT_UPDATE_SPARQL).loadTemplate(params);
+        sparqlRepository.update(query, graphUri, false);
+    }
+
+    public void update(String query, String graphUri, boolean jsonResults) throws IOException {
+        sparqlRepository.update(query, graphUri, jsonResults);
+    }
+
+    private void deleteStaggered(String queryTemplate, Map<String, String> params, String graphUri) throws IOException {
+        String query = new SPARQLQuery(queryTemplate).loadTemplate(params);
+        while (true) {
+            String raw = sparqlRepository.update(query, graphUri, true);
+            JsonNode bindings = objectMapper.readTree(raw).path("results").path("bindings");
+            if (!bindings.isArray() || bindings.isEmpty()) {
+                break;
+            }
+            String msg = bindings.get(0).path("callret-0").path("value").asText("");
+            if (msg.contains("nothing to do")) {
+                break;
+            }
+        }
+    }
+
+    /** Maps existing {@code sbol:source} values (e.g. {@code file:foo.png}) to attachment URIs. */
+    public Map<String, String> loadAttachmentSources(String collectionUri, String graphUri) throws IOException {
+        String query = new SPARQLQuery(SparqlRepository.GET_ATTACHMENT_SOURCE_SPARQL)
+                .loadTemplate(Map.of("uri", collectionUri));
+        String raw = sparqlRepository.getQuery(query, graphUri);
+        Map<String, String> sources = new HashMap<>();
+        JsonNode bindings = objectMapper.readTree(raw).path("results").path("bindings");
+        if (!bindings.isArray()) {
+            return sources;
+        }
+        for (JsonNode row : bindings) {
+            String source = row.path("source").path("value").asText(null);
+            String attachment = row.path("attachment").path("value").asText(null);
+            if (source != null && attachment != null) {
+                sources.put(source, attachment);
+            }
+        }
+        return sources;
+    }
+
+    public void attachUpload(Map<String, String> params, String graphUri, boolean jsonResults) throws IOException {
+        String query = new SPARQLQuery(sparqlRepository.ATTACH_UPLOAD_SPARQL).loadTemplate(params);
+        update(query, graphUri, false);
+    }
+
+    /** Replaces hash/size on an existing attachment when re-uploading the same {@code file:} source. */
+    public void updateAttachment(String graphUri, String attachmentUri, String uploadHash, long size)
+            throws IOException {
+        String query = new SPARQLQuery(sparqlRepository.UPDATE_ATTACHMENT_SPARQL).loadTemplate(Map.of(
+                "attachmentURI", attachmentUri,
+                "attachmentSource", attachmentUri + "/download",
+                "hash", StringUtil.sparqlStringLiteral(uploadHash),
+                "size", StringUtil.sparqlStringLiteral(Long.toString(size))));
+        update(query, graphUri, false);
+    }
+
     public Map<String, String> buildSearchQuery(Map<String, String> allParams) {
         HashMap<String, String> sparqlArgs = new HashMap<>
                 (Map.of("from", "", "criteria", "", "limit", "", "offset", ""));

backend/src/main/java/com/synbiohub/sbh3/dto/SubmitFileFormat.java

@@ -0,0 +1,5 @@
+package com.synbiohub.sbh3.dto;
+
+public enum SubmitFileFormat {
+    SBOL, GENBANK, FASTA, GFF3, ATTACHMENT
+}