Story/CITE-173 : Reprocessing Documents

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

@@ -85,4 +85,8 @@ CloseableIterator<ICitation> getAllGroupItems(IUser user, String groupId, String
 
     void deleteLocalGroupCitations(String groupId);
 
-}
+    void reprocessFile(IUser user, String zoteroGroupId, String itemId, String documentId)
+            throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
+            ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException;
+
+}

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

@@ -1,15 +1,17 @@
 package edu.asu.diging.citesphere.core.service.giles;
 
+import org.springframework.http.HttpMethod;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.client.HttpClientErrorException;
 
 import edu.asu.diging.citesphere.user.IUser;
 
 public interface IGilesConnector {
 
-    <T> ResponseEntity<T> sendRequest(IUser user, String endpoint, Class<T> returnType)
+    <T> ResponseEntity<T> sendRequest(IUser user, String endpoint, Class<T> returnType, HttpMethod httpMethod)
             throws HttpClientErrorException;
 
     byte[] getFile(IUser user, String fileId);
-
-}
+
+    ResponseEntity<String> reprocessDocument(IUser user, String documentId);
+}

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

@@ -8,6 +8,7 @@
 import org.springframework.http.HttpEntity;
 import org.springframework.http.HttpHeaders;
 import org.springframework.http.HttpMethod;
+import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.stereotype.Component;
 import org.springframework.util.MultiValueMap;
@@ -29,6 +30,9 @@ public class GilesConnector implements IGilesConnector {
     @Value("${giles_file_endpoint}")
     private String fileEndpoint;
 
+    @Value("${giles_file_reprocessing_endpoint}")
+    private String reprocessingEndpoint;
+
     @Autowired
     private InternalTokenManager internalTokenManager;
 
@@ -44,7 +48,7 @@ public void init() {
      * @see edu.asu.diging.citesphere.core.service.giles.impl.IGilesConnector#sendRequest(edu.asu.diging.citesphere.user.IUser, java.lang.String, java.lang.Class)
      */
     @Override
-    public <T> ResponseEntity<T> sendRequest(IUser user, String endpoint,Class<T> returnType) throws HttpClientErrorException {
+    public <T> ResponseEntity<T> sendRequest(IUser user, String endpoint,Class<T> returnType, HttpMethod httpMethod) throws HttpClientErrorException {
         String token = internalTokenManager.getAccessToken(user).getValue();
 
         HttpHeaders headers = new HttpHeaders();
@@ -54,15 +58,21 @@ public <T> ResponseEntity<T> sendRequest(IUser user, String endpoint,Class<T> re
 
         return restTemplate.exchange(
                     gilesBaseurl + endpoint,
-                    HttpMethod.GET, requestEntity, returnType);
+                    httpMethod, requestEntity, returnType);
     }
 
     /* (non-Javadoc)
      * @see edu.asu.diging.citesphere.core.service.giles.impl.IGilesConnector#getFile(edu.asu.diging.citesphere.user.IUser, java.lang.String)
      */
     @Override
     public byte[] getFile(IUser user, String fileId) {
-        ResponseEntity<byte[]> content = sendRequest(user, fileEndpoint.replace("{0}",  fileId), byte[].class);
+        ResponseEntity<byte[]> content = sendRequest(user, fileEndpoint.replace("{0}",  fileId), byte[].class, HttpMethod.GET);
         return content.getBody();
     }
+
+    @Override
+    public ResponseEntity<String> reprocessDocument(IUser user, String documentId) {
+        ResponseEntity<String> response = sendRequest(user, reprocessingEndpoint.replace("{0}", documentId), String.class, HttpMethod.POST);
+        return response;
+    }
 }

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

@@ -1,11 +1,15 @@
 package edu.asu.diging.citesphere.core.service.impl;
 
+import java.io.IOException;
 import java.time.OffsetDateTime;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.Set;
 import java.util.concurrent.ExecutionException;
 import java.util.function.BiFunction;
 
@@ -18,12 +22,16 @@
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.PropertySource;
 import org.springframework.data.util.CloseableIterator;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
 import org.springframework.social.zotero.api.ZoteroUpdateItemsStatuses;
 import org.springframework.social.zotero.exception.ZoteroConnectionException;
 import org.springframework.stereotype.Service;
 import org.springframework.web.client.HttpClientErrorException;
 
 import com.fasterxml.jackson.core.JsonProcessingException;
+import com.fasterxml.jackson.databind.JsonNode;
+import com.fasterxml.jackson.databind.ObjectMapper;
 
 import edu.asu.diging.citesphere.core.exceptions.AccessForbiddenException;
 import edu.asu.diging.citesphere.core.exceptions.CannotFindCitationException;
@@ -37,16 +45,21 @@
 import edu.asu.diging.citesphere.core.service.ICitationManager;
 import edu.asu.diging.citesphere.core.service.ICitationStore;
 import edu.asu.diging.citesphere.core.service.IGroupManager;
+import edu.asu.diging.citesphere.core.service.giles.GilesUploadChecker;
+import edu.asu.diging.citesphere.core.service.giles.IGilesConnector;
 import edu.asu.diging.citesphere.core.zotero.IZoteroManager;
 import edu.asu.diging.citesphere.data.bib.CitationGroupRepository;
 import edu.asu.diging.citesphere.data.bib.ICitationDao;
+import edu.asu.diging.citesphere.model.bib.GilesStatus;
 import edu.asu.diging.citesphere.model.bib.ICitation;
 import edu.asu.diging.citesphere.model.bib.ICitationCollection;
 import edu.asu.diging.citesphere.model.bib.ICitationGroup;
+import edu.asu.diging.citesphere.model.bib.IGilesUpload;
 import edu.asu.diging.citesphere.model.bib.ItemType;
 import edu.asu.diging.citesphere.model.bib.impl.BibField;
 import edu.asu.diging.citesphere.model.bib.impl.CitationGroup;
 import edu.asu.diging.citesphere.model.bib.impl.CitationResults;
+import edu.asu.diging.citesphere.model.bib.impl.GilesUpload;
 import edu.asu.diging.citesphere.user.IUser;
 
 @Service
@@ -83,6 +96,12 @@ public class CitationManager implements ICitationManager {
 
     @Autowired
     private IAsyncCitationProcessor asyncCitationProcessor;
+
+    @Autowired
+    private IGilesConnector gilesConnector;
+
+    @Autowired
+    private GilesUploadChecker gilesUploadChecker;
 
     private Map<String, BiFunction<ICitation, ICitation, Integer>> sortFunctions;
 
@@ -494,4 +513,77 @@ public CitationPage getPrevAndNextCitation(IUser user, String groupId, String co
     public void deleteLocalGroupCitations(String groupId) {
         citationStore.deleteCitationByGroupId(groupId);
     }
+
+    @Override
+    public void reprocessFile(IUser user, String zoteroGroupId, String itemId, String documentId)
+            throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
+            ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
+        ICitation citation = getCitation(user, zoteroGroupId, itemId);
+        for (Iterator<IGilesUpload> gilesUpload = citation.getGilesUploads().iterator(); gilesUpload.hasNext();) {
+            IGilesUpload upload = gilesUpload.next();
+            if (upload.getDocumentId() != null && upload.getDocumentId().equals(documentId)) {
+                ResponseEntity<String> reprocessingResponse = gilesConnector.reprocessDocument(user, documentId);
+                if (reprocessingResponse.getStatusCode().equals(HttpStatus.OK)) {
+                    IGilesUpload reprocessedUpload = new GilesUpload();
+                    String responseBody = reprocessingResponse.getBody();
+                    ObjectMapper objectMapper = new ObjectMapper();
+                    JsonNode jsonNode;
+                    try {
+                        jsonNode = objectMapper.readTree(responseBody);
+                        String checkUrl = jsonNode.get("checkUrl").asText();
+                        String[] urlSegments = checkUrl.split("/");
+                        String progressId = urlSegments[urlSegments.length - 1];
+                        reprocessedUpload.setUploadingUser(user.getUsername());
+                        reprocessedUpload.setProgressId(progressId);
+                        Set<IGilesUpload> checkedUploads = new HashSet<>();
+                        checkedUploads.add(reprocessedUpload);
+                        updateCitationWithUpdatedGilesUpload(checkedUploads, user, citation, documentId);
+                        gilesUploadChecker.add(citation);
+                    } catch (IOException e) {
+                        logger.error("Could not deserialize response.", e);
+                    }
+                }
+            }
+
+        }
+    }
+
+    private void updateCitationWithUpdatedGilesUpload(Set<IGilesUpload> checkedUploads, IUser user, ICitation citation, String documentId) {
+        ICitation currentCitation = getCurrentCitation(citation, user);
+        if (currentCitation != null) {
+            for (IGilesUpload upload : checkedUploads) {
+                Optional<IGilesUpload> oldUpload = currentCitation
+                        .getGilesUploads().stream()
+                        .filter(u -> u.getDocumentId() != null && u
+                                .getDocumentId().equals(documentId))
+                        .findFirst();
+                if (oldUpload.isPresent()) {
+                    currentCitation.getGilesUploads().remove(oldUpload.get());
+                }
+                currentCitation.getGilesUploads().add(upload);
+            }
+
+            try {
+                updateCitation(user, citation.getGroup(),
+                        currentCitation);
+            } catch (ZoteroConnectionException | CitationIsOutdatedException
+                    | ZoteroHttpStatusException | ZoteroItemCreationFailedException e) {
+                logger.error("Could not update citation.", e);
+            }
+        }
+    }
+
+    private ICitation getCurrentCitation(ICitation citation, IUser user) {
+        try {
+            return getCitation(user,
+                    citation.getGroup(), citation.getKey());
+        } catch (GroupDoesNotExistException e) {
+            logger.error("Could not get citation.", e);
+        } catch (CannotFindCitationException e) {
+            logger.error("Could not get citation.", e);
+        } catch (ZoteroHttpStatusException e) {
+            logger.error("Could not get citation.", e);
+        }
+        return null;
+    }
 }

citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java

@@ -5,16 +5,22 @@
 import java.util.List;
 
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
 import org.springframework.security.core.Authentication;
+import org.springframework.social.zotero.exception.ZoteroConnectionException;
 import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.PathVariable;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 
 import edu.asu.diging.citesphere.core.exceptions.CannotFindCitationException;
+import edu.asu.diging.citesphere.core.exceptions.CitationIsOutdatedException;
 import edu.asu.diging.citesphere.core.exceptions.GroupDoesNotExistException;
 import edu.asu.diging.citesphere.core.exceptions.ZoteroHttpStatusException;
+import edu.asu.diging.citesphere.core.exceptions.ZoteroItemCreationFailedException;
 import edu.asu.diging.citesphere.core.search.service.SearchEngine;
 import edu.asu.diging.citesphere.core.service.ICitationManager;
 import edu.asu.diging.citesphere.core.service.impl.CitationPage;
@@ -66,4 +72,15 @@ public String getItem(Authentication authentication, Model model, @PathVariable(
         }
         return "auth/group/item";
     }
+
+    @RequestMapping(value = "/auth/group/{zoteroGroupId}/file/reprocess", method = RequestMethod.POST)
+    public ResponseEntity<String> deleteFile(Authentication authentication,
+            @PathVariable("zoteroGroupId") String zoteroGroupId,
+            @RequestParam(value = "documentId", required = false) String documentId,
+            @RequestParam(value = "itemId", required = false) String itemId)
+            throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
+            ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
+        citationManager.reprocessFile((IUser) authentication.getPrincipal(), zoteroGroupId, itemId, documentId);
+        return new ResponseEntity<>(HttpStatus.OK);
+    }
 }

citesphere/src/main/resources/config.properties

@@ -88,5 +88,6 @@ elasticsearch.connect.timeout=${elasticsearch.connect.timeout}
 giles_upload_endpoint=/api/v2/files/upload
 giles_check_endpoint=/api/v2/files/upload/check/
 giles_file_endpoint=/api/v2/resources/files/{0}/content
+giles_file_reprocessing_endpoint=/api/v2/resources/documents/{0}/reprocess
 
 javers_default_author=${javers.default.author}

citesphere/src/main/webapp/WEB-INF/views/auth/group/item.html

@@ -1,5 +1,9 @@
 <html layout:decorate="~{layouts/main}">
 <head>
+<script th:src="@{/resources/notify/bootstrap-notify.min.js}"></script>
+<link th:href="@{/resources/notify/animate.css}" rel="stylesheet"/>
+<link th:href="@{/resources/bootstrap/css/word-wrap.css}" type="text/css"
+	rel="stylesheet">
 <script th:inline="javascript">
 //# sourceURL=modal.js
 	$(function() {
@@ -86,6 +90,40 @@
 
 	    });
 
+	    $("#reprocess-file-button").click(function(e) {
+			e.preventDefault();
+			var fileId = $(this).data("upload-file");
+			$('body').append('<div id="reprocessFileDiv" class="modal-backdrop" style="opacity:0.5"><i class="icon-spinner spinner" style="position:fixed; top:50%; left:50%"></i></div>');
+			$.ajax({
+				'type': "POST",
+				'url': "[(@{|/auth/group/${zoteroGroupId}/file/reprocess|})]",
+				'data': {
+					"documentId": fileId,
+					[[${_csrf.parameterName}]]:[[${_csrf.token}]],
+					"itemId": [[${itemId}]]
+
+				},
+				'success': function(data) {
+					$("#reprocessFileDiv").remove();
+					showNotification("File submitted successfully for reprocessing! ", "success", 10000);
+					location.reload();
+				},
+				'error': function(data) {
+					$("#reprocessFileDiv").remove();
+					showNotification("Error while reprocessing the file!", "danger", 10000)
+				}
+			});
+			$('#file-reprocess-confirmation').modal("hide");
+			event.preventDefault();
+			$(this).removeData();
+	    });
+
+
+		$(".reprocess-file").click(function(e) {
+			$("#reprocess-file-button").attr("data-upload-file", $(this).data("upload-file"));
+			$('#file-reprocess-confirmation').modal("show");
+		});
+
 	    var queryParams = window.location.search;
 	    if(queryParams)  {
 	        var params = new URLSearchParams(queryParams);
@@ -104,6 +142,21 @@
 	    $('.note-info').each(function() {
 	    	$(this).text(truncateNote($(this).attr('data-note-text')));
 	    })
+
+	    function showNotification(message, status, time){
+			$.notify('<i class="fas fa-exclamation-circle"></i>'+message, {
+				type: status,
+				offset: {
+					x: 50,
+					y: 90
+				},
+				timer: time,
+				animate: {
+					enter: 'animated fadeInRight',
+					exit: 'animated fadeOutRight'
+				},
+			});
+		}
 	});
 
 </script>
@@ -360,17 +413,18 @@ <h2 style="margin-top: 0">
         <h3 style="margin-top: 0">Files</h3>
 
         <ul class="list-group" >
-	        <li class="list-group-item" th:each="upload:${citation.gilesUploads}">
+	        <li class="list-group-item word-wrap" th:each="upload,index:${citation.gilesUploads}">
 	        <i class="icon-giles"></i>
 	        <span th:if="${upload.uploadedFile?.filename}">
-	        <a th:href="@{|/auth/group/${zoteroGroupId}/items/${citation.key}/giles/${upload.uploadedFile?.id}|}">[[${upload.uploadedFile?.filename}]]</a>
+	        	<a th:href="@{|/auth/group/${zoteroGroupId}/items/${citation.key}/giles/${upload.uploadedFile?.id}|}">[[${upload.uploadedFile?.filename}]]</a>
 	        </span>
 	        <span th:unless="${upload.documentStatus != null && (upload.documentStatus != T(edu.asu.diging.citesphere.model.bib.GilesStatus).SUBMITTED || T(edu.asu.diging.citesphere.model.bib.GilesStatus).NEW)}">
 	        File is being processed... ([[${upload.progressId}]])
 	        </span>
 	        <span th:if="${upload.documentStatus == T(edu.asu.diging.citesphere.model.bib.GilesStatus).FAILED}" class="label label-danger">Failed [[${upload.progressId}]]</span>
 	        <span th:if="${upload.documentStatus == T(edu.asu.diging.citesphere.model.bib.GilesStatus).NEW}" class="label label-default">In Queue</span>
 	        <span th:if="${upload.documentStatus == T(edu.asu.diging.citesphere.model.bib.GilesStatus).SUBMITTED}" class="label label-default">Processing</span>
+	        <button th:id="|reprocess-file-btn-${index.index}|" type="button" th:data-upload-file="${upload.documentId}" class="fa fa-redo fa-xs reprocess-file"></button>
 	        </li>
         </ul>
 
@@ -489,6 +543,24 @@ <h4 class="modal-title">Upload File</h4>
         </div>
       </div>
     </div>
+
+    <div class="modal fade" id="file-reprocess-confirmation" tabindex="-1" role="dialog">
+		<div class="modal-dialog" role="document">
+		  <div class="modal-content">
+			<div class="modal-header">
+			  <button type="button" class="close" data-dismiss="modal" aria-label="Close"><span aria-hidden="true">&times;</span></button>
+			  <h4 class="modal-title">Reprocess File</h4>
+			</div>
+			<div class="modal-body">
+			  <p>Are you sure you want to reprocess this file?</p>
+			</div>
+			<div class="modal-footer">
+			  <button type="button" class="btn btn-default" data-dismiss="modal">No, cancel!</button>
+			  <button id="reprocess-file-button" data-upload-file="" type="button" class="btn btn-primary">Yes, reprocess!</button>
+			</div>
+		  </div>
+		</div>
+	</div>
 </div>
 </body>
-</html>
+</html>