Bug/cite 229 - Checking access of an upload in progress should be possible with the upload id.

citesphere/src/main/java/edu/asu/diging/citesphere/api/v1/user/CheckAccessController.java

@@ -31,9 +31,12 @@ public class CheckAccessController extends V1Controller {
     @Autowired
     private IGroupManager groupManager;
 
-    @RequestMapping(value = { "/files/giles/{documentId}/access/check", "/files/giles/progress/{progressId}/access/check" }, produces = {
-        MediaType.APPLICATION_JSON_VALUE })
-    public ResponseEntity<String> checkAccess(@PathVariable(value="documentId", required = false) String documentId, @PathVariable(value="progressId", required = false) String progressId, @RequestParam("username") String username, Principal principal) {
+    @RequestMapping(value = { "/files/giles/{documentId}/access/check", "/files/giles/progress/{progressId}/access/check",
+        "/files/giles/upload/{uploadId}/access/check"}, produces = { MediaType.APPLICATION_JSON_VALUE })
+    public ResponseEntity<String> checkAccess(@PathVariable(value="documentId", required = false) String documentId, 
+            @PathVariable(value="progressId", required = false) String progressId, 
+            @PathVariable(value="uploadId", required = false) String uploadId,
+            @RequestParam("username") String username, Principal principal) {
 
         List<String> authorities = ((OAuth2Authentication)principal).getAuthorities().stream().map(a -> a.getAuthority()).collect(Collectors.toList());
         if (!authorities.contains(Role.TRUSTED_CLIENT.toString())) {
@@ -49,6 +52,8 @@ public ResponseEntity<String> checkAccess(@PathVariable(value="documentId", requ
             citations = citationStore.findByGilesDocumentId(documentId);
         } else if (progressId != null) {
             citations = citationStore.findByGilesProgressId(progressId);
+        } else if (uploadId != null) {
+            citations = citationStore.findByGilesUploadId(uploadId);
         } else {
             return new ResponseEntity<>(HttpStatus.BAD_REQUEST);
         }

citesphere/src/main/java/edu/asu/diging/citesphere/core/service/ICitationStore.java

@@ -40,4 +40,5 @@ public interface ICitationStore {
 
     List<ICitation> findByGilesProgressId(String progressId);
 
+    List<ICitation> findByGilesUploadId(String uploadId);
 }

citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesCheckUploadResponse.java

@@ -1,8 +1,13 @@
 package edu.asu.diging.citesphere.core.service.giles.impl;
 
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
+
+@JsonIgnoreProperties(ignoreUnknown = true)
 public class GilesCheckUploadResponse {
 
     private String msg;
+    private String uploadUrl;
+    private String uploadId;
     private String msgCode;
 
     public String getMsg() {
@@ -11,6 +16,18 @@ public String getMsg() {
     public void setMsg(String msg) {
         this.msg = msg;
     }
+    public String getUploadUrl() {
+        return uploadUrl;
+    }
+    public void setUploadUrl(String uploadUrl) {
+        this.uploadUrl = uploadUrl;
+    }
+    public String getUploadId() {
+        return uploadId;
+    }
+    public void setUploadId(String uploadId) {
+        this.uploadId = uploadId;
+    }
     public String getMsgCode() {
         return msgCode;
     }

citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesUploadCheckerImpl.java

@@ -220,6 +220,21 @@ private Set<IGilesUpload> getFileStatus(IGilesUpload upload, IUser user) {
             // Giles is still procoessing
             logger.debug("Upload " + upload.getProgressId()
                     + " still being processed.");
+
+            // Try to parse as GilesCheckUploadResponse to extract upload ID if available
+            ObjectMapper mapper = new ObjectMapper();
+            String jsonBody = response.getBody();
+            try {
+                GilesCheckUploadResponse checkResponse = mapper.readValue(jsonBody, GilesCheckUploadResponse.class);
+                if (checkResponse.getUploadId() != null && !checkResponse.getUploadId().trim().isEmpty()) {
+                    if (upload.getUploadId() == null || upload.getUploadId().trim().isEmpty()) {
+                        upload.setUploadId(checkResponse.getUploadId());
+                    }
+                }
+            } catch (IOException e) {
+                logger.debug("Could not parse in-progress response as GilesCheckUploadResponse, continuing without upload ID extraction.", e);
+            }
+
             checkedUploads.add(upload);
         } else if (response.getStatusCode() == HttpStatus.OK) {
             logger.debug("Upload " + upload.getProgressId() + " is done.");

citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/UploadResponse.java

@@ -1,11 +1,9 @@
 package edu.asu.diging.citesphere.core.service.giles.impl;
 
-import java.util.List;
-
 class UploadResponse {
     private String id;
     private String checkUrl;
-    private List<String> documentIds;
+    private String documentIds;
 
     public String getId() {
         return id;
@@ -23,11 +21,11 @@ public void setCheckUrl(String checkUrl) {
         this.checkUrl = checkUrl;
     }
 
-    public List<String> getDocumentIds() {
+    public String getDocumentIds() {
         return documentIds;
     }
 
-    public void setDocumentIds(List<String> documentIds) {
+    public void setDocumentIds(String documentIds) {
         this.documentIds = documentIds;
     }
 }

citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationStore.java

@@ -2,6 +2,8 @@
 
 import java.util.List;
 import java.util.Optional;
+import java.util.stream.Collectors;
+import java.util.stream.StreamSupport;
 
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Service;
@@ -11,6 +13,7 @@
 import edu.asu.diging.citesphere.core.sync.ExtraData;
 import edu.asu.diging.citesphere.data.bib.CitationRepository;
 import edu.asu.diging.citesphere.model.bib.ICitation;
+import edu.asu.diging.citesphere.model.bib.IGilesUpload;
 import edu.asu.diging.citesphere.model.bib.ItemType;
 import edu.asu.diging.citesphere.model.bib.impl.Citation;
 
@@ -83,4 +86,15 @@ public List<ICitation> findByGilesDocumentId(String documentId) {
     public List<ICitation> findByGilesProgressId(String progressId) {
         return citationRepository.findByGilesUploadsProgressId(progressId);
     }
+
+    @Override
+    public List<ICitation> findByGilesUploadId(String uploadId) {
+        Iterable<Citation> allCitations = citationRepository.findAll();
+        return StreamSupport.stream(allCitations.spliterator(), false)
+                .filter(citation -> citation.getGilesUploads() != null && 
+                        citation.getGilesUploads().stream()
+                                .anyMatch(upload -> uploadId.equals(upload.getUploadId())))
+                .map(citation -> (ICitation) citation)
+                .collect(Collectors.toList());
+    }
 }