From 3320f9b2231d8498c267a9e548c6bad2bb5cfe81 Mon Sep 17 00:00:00 2001
From: Pratik Prakash Giri <32401726+PratikGiri@users.noreply.github.com>
Date: Mon, 6 Feb 2023 16:59:34 -0700
Subject: [PATCH 01/10] [CITE-178] Resolving Conflicts

---
 .../core/service/ICitationManager.java        |  4 ++
 .../core/service/impl/CitationManager.java    | 16 +++++
 .../citesphere/web/user/ItemController.java   | 21 ++++++
 .../webapp/WEB-INF/views/auth/group/item.html | 71 ++++++++++++++++++-
 .../service/impl/CitationManagerTest.java     | 19 +++++
 5 files changed, 130 insertions(+), 1 deletion(-)

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/ICitationManager.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/ICitationManager.java
index ebd5edac7..594e180a5 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/ICitationManager.java
+++ b/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 deleteFile(IUser user, String zoteroGroupId, String itemId, String documentId)
+            throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
+            ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException;
+    
 }
\ No newline at end of file
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
index b0b83137b..be36becfa 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
@@ -3,6 +3,7 @@
 import java.time.OffsetDateTime;
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.Iterator;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
@@ -43,6 +44,7 @@
 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;
@@ -494,4 +496,18 @@ public CitationPage getPrevAndNextCitation(IUser user, String groupId, String co
     public void deleteLocalGroupCitations(String groupId) {
         citationStore.deleteCitationByGroupId(groupId);
     }
+
+    @Override
+    public void deleteFile(IUser user, String zoteroGroupId, String itemId, String documentId)
+            throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
+            ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
+        ICitation citation = getCitation(user, zoteroGroupId, itemId);
+
+        for (Iterator<IGilesUpload> gileUpload = citation.getGilesUploads().iterator(); gileUpload.hasNext();) {
+            IGilesUpload g = gileUpload.next();
+            if (g.getDocumentId() != null && g.getDocumentId().equals(documentId))
+                gileUpload.remove();
+        }
+        updateCitation(user, zoteroGroupId, citation);
+    }
 }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java b/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java
index a2b6a692b..b83c56e79 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java
@@ -2,24 +2,33 @@
 
 import java.util.ArrayList;
 import java.util.Arrays;
+import java.util.Iterator;
 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;
+import edu.asu.diging.citesphere.core.service.impl.async.AsyncDeleteCitationsResponse;
 import edu.asu.diging.citesphere.model.bib.ICitation;
 import edu.asu.diging.citesphere.user.IUser;
+import edu.asu.diging.citesphere.model.bib.IGilesUpload;
 
 @Controller
 public class ItemController {
@@ -54,6 +63,7 @@ public String getItem(Authentication authentication, Model model, @PathVariable(
             List<ICitation> notes = citationManager.getNotes((IUser)authentication.getPrincipal(), zoteroGroupId, itemId);
             model.addAttribute("notes", notes);
             model.addAttribute("citation", citation);
+            model.addAttribute("itemId", itemId);
             List<String> fields = new ArrayList<>();
             citationManager.getItemTypeFields((IUser)authentication.getPrincipal(), citation.getItemType()).forEach(f -> fields.add(f.getFilename()));
             model.addAttribute("fields", fields);
@@ -66,4 +76,15 @@ public String getItem(Authentication authentication, Model model, @PathVariable(
         }
         return "auth/group/item";
     }
+
+    @RequestMapping(value = "/auth/group/{zoteroGroupId}/file/delete", 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.deleteFile((IUser) authentication.getPrincipal(), zoteroGroupId, itemId, documentId);
+        return new ResponseEntity<>(HttpStatus.OK);
+    }
 }
diff --git a/citesphere/src/main/webapp/WEB-INF/views/auth/group/item.html b/citesphere/src/main/webapp/WEB-INF/views/auth/group/item.html
index 428bfe38b..50a62f1c2 100644
--- a/citesphere/src/main/webapp/WEB-INF/views/auth/group/item.html
+++ b/citesphere/src/main/webapp/WEB-INF/views/auth/group/item.html
@@ -1,5 +1,7 @@
 <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"/>
 <script th:inline="javascript">
 //# sourceURL=modal.js
 	$(function() {
@@ -85,6 +87,39 @@
 	        });
   
 	    });
+
+		$("#delete-file-button").click(function(e) {
+			e.preventDefault();
+			var fileId = $(this).data("upload-file");
+			$('body').append('<div id="deletingFileDiv" 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/delete|})]",
+				'data': {
+					"documentId": fileId,
+					[[${_csrf.parameterName}]]:[[${_csrf.token}]],
+					"itemId": [[${itemId}]]
+				},
+				'success': function(data) {
+					$("#deletingFileDiv").remove();
+					showNotification("File deleted successfully! ", "success", 10000);
+					location.reload();
+				},
+				'error': function(data) {
+					$("#deletingFileDiv").remove();
+					showNotification("Error while deleting the file!", "danger", 10000)
+				}
+			});
+			$('#file-delete-confirmation').modal("hide");
+			event.preventDefault();
+			$(this).removeData();
+	    });
+
+
+		$(".delete-file").click(function(e) {
+			$("#delete-file-button").attr("data-upload-file", $(this).data("upload-file"));
+			$('#file-delete-confirmation').modal("show");
+		});
 	    
 	    var queryParams = window.location.search;
 	    if(queryParams)  {
@@ -105,6 +140,21 @@
 	    	$(this).text(truncateNote($(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>
 </head>
@@ -360,10 +410,11 @@ <h2 style="margin-top: 0">
         <h3 style="margin-top: 0">Files</h3>
         
         <ul class="list-group" >
-	        <li class="list-group-item" th:each="upload:${citation.gilesUploads}">
+	        <li class="list-group-item" th:each="upload,index:${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}|}">[[${upload.uploadedFile?.filename}]]</a>
+			<button th:id="|delete-file-btn-${index.index}|" type="button" th:data-upload-file="${upload.documentId}" class="btn icon-trash delete-file"></button>
 	        </span>
 	        <span th:unless="${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}]])
@@ -479,6 +530,24 @@ <h4 class="modal-title">Upload File</h4>
       </div><!-- /.modal-dialog -->
     </div><!-- /.modal -->
 
+	<div class="modal fade" id="file-delete-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">Delete File</h4>
+			</div>
+			<div class="modal-body">
+			  <p>Are you sure you want to delete this file?</p>
+			</div>
+			<div class="modal-footer">
+			  <button type="button" class="btn btn-default" data-dismiss="modal">No, cancel!</button>
+			  <button id="delete-file-button" data-upload-file="" type="button" class="btn btn-primary">Yes, delete!</button>
+			</div>
+		  </div>
+		</div>
+	</div>
+
     <div id="noteModal" class="modal fade" tabindex="-1" role="dialog">
         <div class="modal-dialog" role="document">
         <div class="modal-content">
diff --git a/citesphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java b/citesphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java
index baac59484..be214827b 100644
--- a/citesphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java
+++ b/citesphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java
@@ -2,9 +2,11 @@
 
 import java.util.ArrayList;
 import java.util.HashMap;
+import java.util.HashSet;
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
+import java.util.Set;
 
 import org.junit.Assert;
 import org.junit.Before;
@@ -28,6 +30,7 @@
 import edu.asu.diging.citesphere.data.bib.ICitationDao;
 import edu.asu.diging.citesphere.model.bib.ICitation;
 import edu.asu.diging.citesphere.model.bib.ICitationGroup;
+import edu.asu.diging.citesphere.model.bib.IGilesUpload;
 import edu.asu.diging.citesphere.model.bib.impl.Citation;
 import edu.asu.diging.citesphere.model.bib.impl.CitationGroup;
 import edu.asu.diging.citesphere.model.bib.impl.CitationResults;
@@ -395,4 +398,20 @@ public void test_getNotes_empty() throws GroupDoesNotExistException, CannotFindC
         List<ICitation> response = managerToTest.getNotes(user, GROUP_ID, EXISTING_ID);
         Assert.assertTrue(response.size() == 0);
     }
+
+    @Test
+    public void test_deleteFile() throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
+        ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
+        String documentId = "43";
+        Set<IGilesUpload> gilesUploads = new HashSet<>();
+        Mockito.when(zoteroManager.getGroupItemVersion(user, GROUP_ID, EXISTING_ID)).thenReturn(currentVersion);
+        existingCitation.setKey(EXISTING_ID);
+        existingCitation.setVersion(currentVersion);
+        existingCitation.setGroup(GROUP_ID);
+        existingCitation.setGilesUploads(gilesUploads);
+        Mockito.when(zoteroManager.updateCitation(user, GROUP_ID, existingCitation)).thenReturn(existingCitation);
+        Mockito.when(citationStore.findById(EXISTING_ID)).thenReturn(Optional.of(existingCitation));
+        managerToTest.deleteFile(user, GROUP_ID, EXISTING_ID, documentId);
+        Mockito.verify(citationStore).save(existingCitation);
+    }
 }

From 2dcc93972c9d75ad07793ed920af5460d06f0689 Mon Sep 17 00:00:00 2001
From: diya17 <diyanna.3@gmail.com>
Date: Thu, 20 Jul 2023 17:00:31 -0700
Subject: [PATCH 02/10] [CITE-178] Adding method for deletion from giles

---
 .../citesphere/core/service/giles/IGilesConnector.java       | 3 ++-
 .../citesphere/core/service/giles/impl/GilesConnector.java   | 5 +++++
 .../diging/citesphere/core/service/impl/CitationManager.java | 5 +++++
 3 files changed, 12 insertions(+), 1 deletion(-)

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
index f18291610..599a659dd 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
@@ -12,4 +12,5 @@ <T> ResponseEntity<T> sendRequest(IUser user, String endpoint, Class<T> returnTy
 
     byte[] getFile(IUser user, String fileId);
 
-}
\ No newline at end of file
+    void deleteDocument(String documentId);
+}
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
index f2f99f420..07686945a 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
@@ -65,4 +65,9 @@ public byte[] getFile(IUser user, String fileId) {
         ResponseEntity<byte[]> content = sendRequest(user, fileEndpoint.replace("{0}",  fileId), byte[].class);
         return content.getBody();
     }
+    
+    @Override
+    public void deleteDocument(String documentId) {
+        
+    }
 }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
index be36becfa..b9b94b688 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
@@ -38,6 +38,7 @@
 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.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;
@@ -85,6 +86,9 @@ public class CitationManager implements ICitationManager {
 
     @Autowired
     private IAsyncCitationProcessor asyncCitationProcessor;
+    
+    @Autowired
+    private IGilesConnector gilesConnector;
 
     private Map<String, BiFunction<ICitation, ICitation, Integer>> sortFunctions;
 
@@ -506,6 +510,7 @@ public void deleteFile(IUser user, String zoteroGroupId, String itemId, String d
         for (Iterator<IGilesUpload> gileUpload = citation.getGilesUploads().iterator(); gileUpload.hasNext();) {
             IGilesUpload g = gileUpload.next();
             if (g.getDocumentId() != null && g.getDocumentId().equals(documentId))
+                gilesConnector.deleteDocument(documentId);
                 gileUpload.remove();
         }
         updateCitation(user, zoteroGroupId, citation);

From da10306e797d3b166a2df13edd1ec3831141413e Mon Sep 17 00:00:00 2001
From: diya17 <diyanna.3@gmail.com>
Date: Fri, 21 Jul 2023 16:59:23 -0700
Subject: [PATCH 03/10] [CITE-178] Deleting files from giles

---
 .../core/service/giles/IGilesConnector.java       |  6 ++++--
 .../core/service/giles/impl/GilesConnector.java   | 15 ++++++++++-----
 .../core/service/impl/CitationManager.java        | 10 +++++++---
 citesphere/src/main/resources/config.properties   |  1 +
 4 files changed, 22 insertions(+), 10 deletions(-)

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
index 599a659dd..951078e25 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
@@ -1,5 +1,7 @@
 package edu.asu.diging.citesphere.core.service.giles;
 
+import org.springframework.http.HttpMethod;
+import org.springframework.http.HttpStatus;
 import org.springframework.http.ResponseEntity;
 import org.springframework.web.client.HttpClientErrorException;
 
@@ -7,10 +9,10 @@
 
 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);
 
-    void deleteDocument(String documentId);
+    HttpStatus deleteDocument(IUser user, String documentId);
 }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
index 07686945a..1f7f69a4b 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
+++ b/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_document_endpoint}")
+    private String documentEndpoint;
+    
     @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();
@@ -54,7 +58,7 @@ 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)
@@ -62,12 +66,13 @@ public <T> ResponseEntity<T> sendRequest(IUser user, String endpoint,Class<T> re
      */
     @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 void deleteDocument(String documentId) {
-        
+    public HttpStatus deleteDocument(IUser user, String documentId) {
+        ResponseEntity<String> response = sendRequest(user, documentEndpoint.replace("{documentId}",  documentId), String.class, HttpMethod.DELETE);
+        return response.getStatusCode();
     }
 }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
index b9b94b688..bb1625af1 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
@@ -19,6 +19,7 @@
 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.social.zotero.api.ZoteroUpdateItemsStatuses;
 import org.springframework.social.zotero.exception.ZoteroConnectionException;
 import org.springframework.stereotype.Service;
@@ -509,9 +510,12 @@ public void deleteFile(IUser user, String zoteroGroupId, String itemId, String d
 
         for (Iterator<IGilesUpload> gileUpload = citation.getGilesUploads().iterator(); gileUpload.hasNext();) {
             IGilesUpload g = gileUpload.next();
-            if (g.getDocumentId() != null && g.getDocumentId().equals(documentId))
-                gilesConnector.deleteDocument(documentId);
-                gileUpload.remove();
+            if (g.getDocumentId() != null && g.getDocumentId().equals(documentId)) {
+                HttpStatus deletionStatus = gilesConnector.deleteDocument(user, documentId);
+                if (deletionStatus.equals(HttpStatus.OK)) {
+                    gileUpload.remove();
+                }
+            }
         }
         updateCitation(user, zoteroGroupId, citation);
     }
diff --git a/citesphere/src/main/resources/config.properties b/citesphere/src/main/resources/config.properties
index 4ddd8c306..b46b904d9 100644
--- a/citesphere/src/main/resources/config.properties
+++ b/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_document_endpoint=/api/v2/resources/documents/{documentId}
 
 javers_default_author=${javers.default.author}

From bbc620753ce124b5897976f6ae60cd2905c79738 Mon Sep 17 00:00:00 2001
From: diya17 <diyanna.3@gmail.com>
Date: Mon, 24 Jul 2023 16:59:21 -0700
Subject: [PATCH 04/10] [CITE-178] Debugging Giles deletion endpoint and
 javadocs

---
 .../citesphere/core/service/giles/IGilesConnector.java    | 8 ++++++++
 .../core/service/giles/impl/GilesConnector.java           | 4 ++--
 2 files changed, 10 insertions(+), 2 deletions(-)

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
index 951078e25..48f407f64 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
@@ -13,6 +13,14 @@ <T> ResponseEntity<T> sendRequest(IUser user, String endpoint, Class<T> returnTy
             throws HttpClientErrorException;
 
     byte[] getFile(IUser user, String fileId);
+    
+    /**
 
+      * Deletes a document for the given user.
+      * @param user The user performing the document deletion.
+      * @param documentId The ID of the document to be deleted.
+      * @return The HTTP status code indicating the success or failure of the delete operation.
+      * @throws RestClientException if there is an issue sending the delete request to the server.
+    */
     HttpStatus deleteDocument(IUser user, String documentId);
 }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
index 1f7f69a4b..c2b773aed 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
@@ -50,7 +50,7 @@ public void init() {
     @Override
     public <T> ResponseEntity<T> sendRequest(IUser user, String endpoint,Class<T> returnType, HttpMethod httpMethod) throws HttpClientErrorException {
         String token = internalTokenManager.getAccessToken(user).getValue();
-
+        System.out.println(endpoint);
         HttpHeaders headers = new HttpHeaders();
         headers.setBearerAuth(token);
         HttpEntity<MultiValueMap<String, Object>> requestEntity = new HttpEntity<>(
@@ -72,7 +72,7 @@ public byte[] getFile(IUser user, String fileId) {
     
     @Override
     public HttpStatus deleteDocument(IUser user, String documentId) {
-        ResponseEntity<String> response = sendRequest(user, documentEndpoint.replace("{documentId}",  documentId), String.class, HttpMethod.DELETE);
+        ResponseEntity<String> response = sendRequest(user, String.format(documentEndpoint, documentId), String.class, HttpMethod.DELETE);
         return response.getStatusCode();
     }
 }

From 80fd7b69bab6d36d974d7294ca72bbdf37f731b4 Mon Sep 17 00:00:00 2001
From: diya17 <diyanna.3@gmail.com>
Date: Tue, 25 Jul 2023 16:53:53 -0700
Subject: [PATCH 05/10] [CITE-178] Adding IGilesDeletionChecker

---
 .../core/service/giles/IGilesConnector.java       |  1 -
 .../core/service/giles/IGilesDeletionChecker.java | 15 +++++++++++++++
 .../core/service/giles/impl/GilesConnector.java   |  1 -
 3 files changed, 15 insertions(+), 2 deletions(-)
 create mode 100644 citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
index 48f407f64..be97729f0 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesConnector.java
@@ -15,7 +15,6 @@ <T> ResponseEntity<T> sendRequest(IUser user, String endpoint, Class<T> returnTy
     byte[] getFile(IUser user, String fileId);
     
     /**
-
       * Deletes a document for the given user.
       * @param user The user performing the document deletion.
       * @param documentId The ID of the document to be deleted.
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java
new file mode 100644
index 000000000..8819e89d3
--- /dev/null
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java
@@ -0,0 +1,15 @@
+package edu.asu.diging.citesphere.core.service.giles;
+
+import org.springframework.social.zotero.exception.ZoteroConnectionException;
+
+import edu.asu.diging.citesphere.core.exceptions.CitationIsOutdatedException;
+import edu.asu.diging.citesphere.core.exceptions.ZoteroHttpStatusException;
+import edu.asu.diging.citesphere.core.exceptions.ZoteroItemCreationFailedException;
+import edu.asu.diging.citesphere.model.bib.ICitation;
+import edu.asu.diging.citesphere.model.bib.IGilesUpload;
+
+public interface IGilesDeletionChecker {
+    void add(IGilesUpload upload, ICitation citation, String zoteroId);
+    
+    void checkDeletion() throws ZoteroConnectionException, CitationIsOutdatedException, ZoteroHttpStatusException, ZoteroItemCreationFailedException;
+}
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
index c2b773aed..e9778db9b 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
@@ -50,7 +50,6 @@ public void init() {
     @Override
     public <T> ResponseEntity<T> sendRequest(IUser user, String endpoint,Class<T> returnType, HttpMethod httpMethod) throws HttpClientErrorException {
         String token = internalTokenManager.getAccessToken(user).getValue();
-        System.out.println(endpoint);
         HttpHeaders headers = new HttpHeaders();
         headers.setBearerAuth(token);
         HttpEntity<MultiValueMap<String, Object>> requestEntity = new HttpEntity<>(

From f5081e2c9ff8d90c5d2a08edb9a209a62a8eae83 Mon Sep 17 00:00:00 2001
From: diya17 <diyanna.3@gmail.com>
Date: Wed, 26 Jul 2023 16:58:28 -0700
Subject: [PATCH 06/10] [CITE-178] Adding deletion checker component

---
 .../giles/impl/GilesDeletionChecker.java      | 91 +++++++++++++++++++
 .../core/service/impl/CitationManager.java    |  8 +-
 .../src/main/resources/config.properties      |  1 +
 3 files changed, 97 insertions(+), 3 deletions(-)
 create mode 100644 citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
new file mode 100644
index 000000000..ffc4493bb
--- /dev/null
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
@@ -0,0 +1,91 @@
+package edu.asu.diging.citesphere.core.service.giles.impl;
+
+import java.util.HashMap;
+import java.util.Iterator;
+import java.util.Map;
+import java.util.Queue;
+import java.util.concurrent.ConcurrentLinkedQueue;
+
+import javax.annotation.PostConstruct;
+
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Value;
+import org.springframework.context.annotation.PropertySource;
+import org.springframework.http.HttpMethod;
+import org.springframework.http.HttpStatus;
+import org.springframework.http.ResponseEntity;
+import org.springframework.scheduling.annotation.Scheduled;
+import org.springframework.social.zotero.exception.ZoteroConnectionException;
+import org.springframework.stereotype.Component;
+
+import edu.asu.diging.citesphere.core.exceptions.CitationIsOutdatedException;
+import edu.asu.diging.citesphere.core.exceptions.ZoteroHttpStatusException;
+import edu.asu.diging.citesphere.core.exceptions.ZoteroItemCreationFailedException;
+import edu.asu.diging.citesphere.core.service.ICitationManager;
+import edu.asu.diging.citesphere.core.service.giles.IGilesConnector;
+import edu.asu.diging.citesphere.core.service.giles.IGilesDeletionChecker;
+import edu.asu.diging.citesphere.core.user.IUserManager;
+import edu.asu.diging.citesphere.model.bib.ICitation;
+import edu.asu.diging.citesphere.model.bib.IGilesUpload;
+import edu.asu.diging.citesphere.user.IUser;
+
+@Component
+@PropertySource({ "classpath:config.properties",
+    "${appConfigFile:classpath:}/app.properties" })
+public class GilesDeletionChecker implements IGilesDeletionChecker {
+
+    @Autowired
+    private IUserManager userManager;
+    
+    @Autowired
+    private ICitationManager citationManager;
+    
+    @Autowired
+    private IGilesConnector gilesConnector;
+
+    @Value("${giles_document_deletion_check_endpoint}")
+    private String gilesDeletionCheckEndpoint;
+    
+    private Queue<Map<String, String>> deletionQueue;
+    
+    @PostConstruct
+    public void init() {
+        deletionQueue = new ConcurrentLinkedQueue<Map<String, String>>();
+    }
+    
+    @Override
+    public void add(IGilesUpload upload, ICitation citation, String zoteroId) {
+        Map<String, String> documentCitationMap = new HashMap<String, String>();
+        documentCitationMap.put("documentId", upload.getDocumentId());
+        documentCitationMap.put("citationKey", citation.getKey());
+        documentCitationMap.put("userName", upload.getUploadingUser());
+        documentCitationMap.put("zoteroId", zoteroId);
+        if (!deletionQueue.contains(documentCitationMap)) {
+            deletionQueue.add(documentCitationMap);
+        }
+    }
+    
+    @Override
+    @Scheduled(fixedDelay = 60000)
+    public void checkDeletion() throws ZoteroConnectionException, CitationIsOutdatedException, ZoteroHttpStatusException, ZoteroItemCreationFailedException {
+        for (Map<String, String> documentCitationMap: deletionQueue) {
+            String documentId = documentCitationMap.get("documentId");
+            String citationKey = documentCitationMap.get("citationKey");
+            ICitation citation = citationManager.getCitation(citationKey);
+            System.out.println(documentCitationMap.get("userName"));
+            IUser user = userManager.findByUsername(documentCitationMap.get("userName"));
+            ResponseEntity<String> response = gilesConnector.sendRequest(user, String.format(gilesDeletionCheckEndpoint, documentId), String.class, HttpMethod.GET);
+            if(response.getStatusCode().equals(HttpStatus.OK)) {
+                for (Iterator<IGilesUpload> gileUpload = citation.getGilesUploads().iterator(); gileUpload.hasNext();) {
+                    IGilesUpload g = gileUpload.next();
+                    if (g.getDocumentId() != null && g.getDocumentId().equals(documentId)) {
+                        gileUpload.remove();
+                    }
+                }
+                citationManager.updateCitation(user, documentCitationMap.get("zoteroGroupId"), citation);
+                deletionQueue.remove(documentCitationMap);
+            }
+        }
+    }
+
+}
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
index bb1625af1..248cd94b8 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
@@ -40,6 +40,7 @@
 import edu.asu.diging.citesphere.core.service.ICitationStore;
 import edu.asu.diging.citesphere.core.service.IGroupManager;
 import edu.asu.diging.citesphere.core.service.giles.IGilesConnector;
+import edu.asu.diging.citesphere.core.service.giles.IGilesDeletionChecker;
 import edu.asu.diging.citesphere.core.zotero.IZoteroManager;
 import edu.asu.diging.citesphere.data.bib.CitationGroupRepository;
 import edu.asu.diging.citesphere.data.bib.ICitationDao;
@@ -90,6 +91,9 @@ public class CitationManager implements ICitationManager {
     
     @Autowired
     private IGilesConnector gilesConnector;
+    
+    @Autowired
+    private IGilesDeletionChecker gilesDeletionChecker;
 
     private Map<String, BiFunction<ICitation, ICitation, Integer>> sortFunctions;
 
@@ -507,16 +511,14 @@ public void deleteFile(IUser user, String zoteroGroupId, String itemId, String d
             throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
             ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
         ICitation citation = getCitation(user, zoteroGroupId, itemId);
-
         for (Iterator<IGilesUpload> gileUpload = citation.getGilesUploads().iterator(); gileUpload.hasNext();) {
             IGilesUpload g = gileUpload.next();
             if (g.getDocumentId() != null && g.getDocumentId().equals(documentId)) {
                 HttpStatus deletionStatus = gilesConnector.deleteDocument(user, documentId);
                 if (deletionStatus.equals(HttpStatus.OK)) {
-                    gileUpload.remove();
+                    gilesDeletionChecker.add(g, citation, zoteroGroupId);
                 }
             }
         }
-        updateCitation(user, zoteroGroupId, citation);
     }
 }
diff --git a/citesphere/src/main/resources/config.properties b/citesphere/src/main/resources/config.properties
index b46b904d9..855071bba 100644
--- a/citesphere/src/main/resources/config.properties
+++ b/citesphere/src/main/resources/config.properties
@@ -89,5 +89,6 @@ 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_document_endpoint=/api/v2/resources/documents/{documentId}
+giles_document_deletion_check_endpoint=/api/v2/files/deletion/check/{documentId}
 
 javers_default_author=${javers.default.author}

From bcb5eafb5fd7daaed140279862381ee56f43fcda Mon Sep 17 00:00:00 2001
From: diya17 <diyanna.3@gmail.com>
Date: Thu, 27 Jul 2023 16:56:29 -0700
Subject: [PATCH 07/10] [CITE-178] Making changes to fix userName when its null

---
 .../core/service/giles/IGilesDeletionChecker.java     |  3 ++-
 .../core/service/giles/impl/GilesConnector.java       |  4 ++--
 .../core/service/giles/impl/GilesDeletionChecker.java | 11 ++++++++---
 .../citesphere/core/service/impl/CitationManager.java |  2 +-
 4 files changed, 13 insertions(+), 7 deletions(-)

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java
index 8819e89d3..460a5cee1 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java
@@ -7,9 +7,10 @@
 import edu.asu.diging.citesphere.core.exceptions.ZoteroItemCreationFailedException;
 import edu.asu.diging.citesphere.model.bib.ICitation;
 import edu.asu.diging.citesphere.model.bib.IGilesUpload;
+import edu.asu.diging.citesphere.user.IUser;
 
 public interface IGilesDeletionChecker {
-    void add(IGilesUpload upload, ICitation citation, String zoteroId);
+    void add(IGilesUpload upload, ICitation citation, String zoteroId, IUser user);
     
     void checkDeletion() throws ZoteroConnectionException, CitationIsOutdatedException, ZoteroHttpStatusException, ZoteroItemCreationFailedException;
 }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
index e9778db9b..e2f398044 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
@@ -54,7 +54,7 @@ public <T> ResponseEntity<T> sendRequest(IUser user, String endpoint,Class<T> re
         headers.setBearerAuth(token);
         HttpEntity<MultiValueMap<String, Object>> requestEntity = new HttpEntity<>(
                 headers);
-
+        System.out.println(endpoint);
         return restTemplate.exchange(
                     gilesBaseurl + endpoint,
                     httpMethod, requestEntity, returnType);
@@ -71,7 +71,7 @@ public byte[] getFile(IUser user, String fileId) {
     
     @Override
     public HttpStatus deleteDocument(IUser user, String documentId) {
-        ResponseEntity<String> response = sendRequest(user, String.format(documentEndpoint, documentId), String.class, HttpMethod.DELETE);
+        ResponseEntity<String> response = sendRequest(user, documentEndpoint.replace("{documentId}",  documentId), String.class, HttpMethod.DELETE);
         return response.getStatusCode();
     }
 }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
index ffc4493bb..9887713b0 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
@@ -54,11 +54,12 @@ public void init() {
     }
     
     @Override
-    public void add(IGilesUpload upload, ICitation citation, String zoteroId) {
+    public void add(IGilesUpload upload, ICitation citation, String zoteroId, IUser user) {
         Map<String, String> documentCitationMap = new HashMap<String, String>();
+        System.out.println(upload.getUploadingUser());
         documentCitationMap.put("documentId", upload.getDocumentId());
         documentCitationMap.put("citationKey", citation.getKey());
-        documentCitationMap.put("userName", upload.getUploadingUser());
+        documentCitationMap.put("userName", user.getUsername());
         documentCitationMap.put("zoteroId", zoteroId);
         if (!deletionQueue.contains(documentCitationMap)) {
             deletionQueue.add(documentCitationMap);
@@ -69,12 +70,16 @@ public void add(IGilesUpload upload, ICitation citation, String zoteroId) {
     @Scheduled(fixedDelay = 60000)
     public void checkDeletion() throws ZoteroConnectionException, CitationIsOutdatedException, ZoteroHttpStatusException, ZoteroItemCreationFailedException {
         for (Map<String, String> documentCitationMap: deletionQueue) {
+            System.out.println(documentCitationMap.keySet());
             String documentId = documentCitationMap.get("documentId");
             String citationKey = documentCitationMap.get("citationKey");
+            System.out.println(documentId);
+            System.out.println(citationKey);
+            System.out.println("Iamawesome");
             ICitation citation = citationManager.getCitation(citationKey);
             System.out.println(documentCitationMap.get("userName"));
             IUser user = userManager.findByUsername(documentCitationMap.get("userName"));
-            ResponseEntity<String> response = gilesConnector.sendRequest(user, String.format(gilesDeletionCheckEndpoint, documentId), String.class, HttpMethod.GET);
+            ResponseEntity<String> response = gilesConnector.sendRequest(user, gilesDeletionCheckEndpoint.replace("{documentId}",  documentId), String.class, HttpMethod.GET);
             if(response.getStatusCode().equals(HttpStatus.OK)) {
                 for (Iterator<IGilesUpload> gileUpload = citation.getGilesUploads().iterator(); gileUpload.hasNext();) {
                     IGilesUpload g = gileUpload.next();
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
index 248cd94b8..90a6ceece 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
@@ -516,7 +516,7 @@ public void deleteFile(IUser user, String zoteroGroupId, String itemId, String d
             if (g.getDocumentId() != null && g.getDocumentId().equals(documentId)) {
                 HttpStatus deletionStatus = gilesConnector.deleteDocument(user, documentId);
                 if (deletionStatus.equals(HttpStatus.OK)) {
-                    gilesDeletionChecker.add(g, citation, zoteroGroupId);
+                    gilesDeletionChecker.add(g, citation, zoteroGroupId, user);
                 }
             }
         }

From b04bbd3b27f03499572da1637933184882028ddf Mon Sep 17 00:00:00 2001
From: diya17 <diyanna.3@gmail.com>
Date: Mon, 31 Jul 2023 17:00:11 -0700
Subject: [PATCH 08/10] [CITE-178] Debugging zotero id

---
 .../citesphere/core/service/giles/impl/GilesDeletionChecker.java | 1 +
 .../asu/diging/citesphere/core/service/impl/CitationManager.java | 1 +
 .../java/edu/asu/diging/citesphere/web/user/ItemController.java  | 1 +
 3 files changed, 3 insertions(+)

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
index 9887713b0..f270c5456 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
@@ -87,6 +87,7 @@ public void checkDeletion() throws ZoteroConnectionException, CitationIsOutdated
                         gileUpload.remove();
                     }
                 }
+                System.out.println(documentCitationMap.get("zoteroGroupId"));
                 citationManager.updateCitation(user, documentCitationMap.get("zoteroGroupId"), citation);
                 deletionQueue.remove(documentCitationMap);
             }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
index 90a6ceece..d9b2d7ba4 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
@@ -511,6 +511,7 @@ public void deleteFile(IUser user, String zoteroGroupId, String itemId, String d
             throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
             ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
         ICitation citation = getCitation(user, zoteroGroupId, itemId);
+        System.out.println(zoteroGroupId);
         for (Iterator<IGilesUpload> gileUpload = citation.getGilesUploads().iterator(); gileUpload.hasNext();) {
             IGilesUpload g = gileUpload.next();
             if (g.getDocumentId() != null && g.getDocumentId().equals(documentId)) {
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java b/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java
index b83c56e79..3af00fd13 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java
@@ -84,6 +84,7 @@ public ResponseEntity<String> deleteFile(Authentication authentication,
             @RequestParam(value = "itemId", required = false) String itemId)
             throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
             ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
+        System.out.println(zoteroGroupId);
         citationManager.deleteFile((IUser) authentication.getPrincipal(), zoteroGroupId, itemId, documentId);
         return new ResponseEntity<>(HttpStatus.OK);
     }

From 04b2b7ec52d87350a42240d205e344f5ed237bea Mon Sep 17 00:00:00 2001
From: diya17 <diyanna.3@gmail.com>
Date: Tue, 1 Aug 2023 16:51:47 -0700
Subject: [PATCH 09/10] [CITE-178] Fixing the zoteroGroupId issue and removing
 loggers

---
 .../service/giles/IGilesDeletionChecker.java     |  2 +-
 .../core/service/giles/impl/GilesConnector.java  |  1 -
 .../service/giles/impl/GilesDeletionChecker.java | 16 ++++++----------
 .../core/service/impl/CitationManager.java       |  3 +--
 .../citesphere/web/user/ItemController.java      |  1 -
 5 files changed, 8 insertions(+), 15 deletions(-)

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java
index 460a5cee1..3d330d27e 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/IGilesDeletionChecker.java
@@ -10,7 +10,7 @@
 import edu.asu.diging.citesphere.user.IUser;
 
 public interface IGilesDeletionChecker {
-    void add(IGilesUpload upload, ICitation citation, String zoteroId, IUser user);
+    void addDocumentCitationMap(IGilesUpload upload, ICitation citation, String zoteroId, IUser user);
     
     void checkDeletion() throws ZoteroConnectionException, CitationIsOutdatedException, ZoteroHttpStatusException, ZoteroItemCreationFailedException;
 }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
index e2f398044..223b8713e 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesConnector.java
@@ -54,7 +54,6 @@ public <T> ResponseEntity<T> sendRequest(IUser user, String endpoint,Class<T> re
         headers.setBearerAuth(token);
         HttpEntity<MultiValueMap<String, Object>> requestEntity = new HttpEntity<>(
                 headers);
-        System.out.println(endpoint);
         return restTemplate.exchange(
                     gilesBaseurl + endpoint,
                     httpMethod, requestEntity, returnType);
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
index f270c5456..855e0144b 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
@@ -54,13 +54,13 @@ public void init() {
     }
     
     @Override
-    public void add(IGilesUpload upload, ICitation citation, String zoteroId, IUser user) {
-        Map<String, String> documentCitationMap = new HashMap<String, String>();
-        System.out.println(upload.getUploadingUser());
+    public void addDocumentCitationMap(IGilesUpload upload, ICitation citation, String zoteroId, IUser user) {
+        HashMap<String, String> documentCitationMap = new HashMap<String, String>();
         documentCitationMap.put("documentId", upload.getDocumentId());
         documentCitationMap.put("citationKey", citation.getKey());
         documentCitationMap.put("userName", user.getUsername());
         documentCitationMap.put("zoteroId", zoteroId);
+        System.out.println(documentCitationMap.get("zoteroId"));
         if (!deletionQueue.contains(documentCitationMap)) {
             deletionQueue.add(documentCitationMap);
         }
@@ -70,14 +70,10 @@ public void add(IGilesUpload upload, ICitation citation, String zoteroId, IUser
     @Scheduled(fixedDelay = 60000)
     public void checkDeletion() throws ZoteroConnectionException, CitationIsOutdatedException, ZoteroHttpStatusException, ZoteroItemCreationFailedException {
         for (Map<String, String> documentCitationMap: deletionQueue) {
-            System.out.println(documentCitationMap.keySet());
             String documentId = documentCitationMap.get("documentId");
             String citationKey = documentCitationMap.get("citationKey");
-            System.out.println(documentId);
-            System.out.println(citationKey);
-            System.out.println("Iamawesome");
+            String zoteroId = documentCitationMap.get("zoteroId");
             ICitation citation = citationManager.getCitation(citationKey);
-            System.out.println(documentCitationMap.get("userName"));
             IUser user = userManager.findByUsername(documentCitationMap.get("userName"));
             ResponseEntity<String> response = gilesConnector.sendRequest(user, gilesDeletionCheckEndpoint.replace("{documentId}",  documentId), String.class, HttpMethod.GET);
             if(response.getStatusCode().equals(HttpStatus.OK)) {
@@ -87,8 +83,8 @@ public void checkDeletion() throws ZoteroConnectionException, CitationIsOutdated
                         gileUpload.remove();
                     }
                 }
-                System.out.println(documentCitationMap.get("zoteroGroupId"));
-                citationManager.updateCitation(user, documentCitationMap.get("zoteroGroupId"), citation);
+                System.out.println(zoteroId);
+                citationManager.updateCitation(user, zoteroId, citation);
                 deletionQueue.remove(documentCitationMap);
             }
         }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
index d9b2d7ba4..d85053d6e 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/impl/CitationManager.java
@@ -511,13 +511,12 @@ public void deleteFile(IUser user, String zoteroGroupId, String itemId, String d
             throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
             ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
         ICitation citation = getCitation(user, zoteroGroupId, itemId);
-        System.out.println(zoteroGroupId);
         for (Iterator<IGilesUpload> gileUpload = citation.getGilesUploads().iterator(); gileUpload.hasNext();) {
             IGilesUpload g = gileUpload.next();
             if (g.getDocumentId() != null && g.getDocumentId().equals(documentId)) {
                 HttpStatus deletionStatus = gilesConnector.deleteDocument(user, documentId);
                 if (deletionStatus.equals(HttpStatus.OK)) {
-                    gilesDeletionChecker.add(g, citation, zoteroGroupId, user);
+                    gilesDeletionChecker.addDocumentCitationMap(g, citation, zoteroGroupId, user);
                 }
             }
         }
diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java b/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java
index 3af00fd13..b83c56e79 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/web/user/ItemController.java
@@ -84,7 +84,6 @@ public ResponseEntity<String> deleteFile(Authentication authentication,
             @RequestParam(value = "itemId", required = false) String itemId)
             throws GroupDoesNotExistException, CannotFindCitationException, ZoteroHttpStatusException,
             ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
-        System.out.println(zoteroGroupId);
         citationManager.deleteFile((IUser) authentication.getPrincipal(), zoteroGroupId, itemId, documentId);
         return new ResponseEntity<>(HttpStatus.OK);
     }

From 4bd3e55f1c65abb2103f1a9c463e5a1b4b1e3191 Mon Sep 17 00:00:00 2001
From: diya17 <diyanna.3@gmail.com>
Date: Mon, 7 Aug 2023 16:25:28 -0400
Subject: [PATCH 10/10] [CITE-178] : Removing loggers and modifying tests

---
 .../service/giles/impl/GilesDeletionChecker.java |  2 --
 .../core/service/impl/CitationManagerTest.java   | 16 +++++++++++++++-
 2 files changed, 15 insertions(+), 3 deletions(-)

diff --git a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
index 855e0144b..d4172d8c1 100644
--- a/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
+++ b/citesphere/src/main/java/edu/asu/diging/citesphere/core/service/giles/impl/GilesDeletionChecker.java
@@ -60,7 +60,6 @@ public void addDocumentCitationMap(IGilesUpload upload, ICitation citation, Stri
         documentCitationMap.put("citationKey", citation.getKey());
         documentCitationMap.put("userName", user.getUsername());
         documentCitationMap.put("zoteroId", zoteroId);
-        System.out.println(documentCitationMap.get("zoteroId"));
         if (!deletionQueue.contains(documentCitationMap)) {
             deletionQueue.add(documentCitationMap);
         }
@@ -83,7 +82,6 @@ public void checkDeletion() throws ZoteroConnectionException, CitationIsOutdated
                         gileUpload.remove();
                     }
                 }
-                System.out.println(zoteroId);
                 citationManager.updateCitation(user, zoteroId, citation);
                 deletionQueue.remove(documentCitationMap);
             }
diff --git a/citesphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java b/citesphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java
index be214827b..10ad68eb7 100644
--- a/citesphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java
+++ b/citesphere/src/test/java/edu/asu/diging/citesphere/core/service/impl/CitationManagerTest.java
@@ -15,6 +15,7 @@
 import org.mockito.Mock;
 import org.mockito.Mockito;
 import org.mockito.MockitoAnnotations;
+import org.springframework.http.HttpStatus;
 import org.springframework.social.zotero.exception.ZoteroConnectionException;
 import org.springframework.test.util.ReflectionTestUtils;
 
@@ -25,6 +26,8 @@
 import edu.asu.diging.citesphere.core.exceptions.ZoteroItemCreationFailedException;
 import edu.asu.diging.citesphere.core.service.ICitationStore;
 import edu.asu.diging.citesphere.core.service.IGroupManager;
+import edu.asu.diging.citesphere.core.service.giles.IGilesConnector;
+import edu.asu.diging.citesphere.core.service.giles.IGilesDeletionChecker;
 import edu.asu.diging.citesphere.core.zotero.IZoteroManager;
 import edu.asu.diging.citesphere.data.bib.CitationGroupRepository;
 import edu.asu.diging.citesphere.data.bib.ICitationDao;
@@ -34,6 +37,7 @@
 import edu.asu.diging.citesphere.model.bib.impl.Citation;
 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;
 import edu.asu.diging.citesphere.user.impl.User;
 
@@ -54,6 +58,12 @@ public class CitationManagerTest {
     @Mock
     private ICitationDao citationDao;
     
+    @Mock
+    private IGilesConnector gilesConnector;
+    
+    @Mock
+    private IGilesDeletionChecker gilesDeletionChecker;
+    
     @InjectMocks
     private CitationManager managerToTest;
     
@@ -404,6 +414,9 @@ public void test_deleteFile() throws GroupDoesNotExistException, CannotFindCitat
         ZoteroConnectionException, CitationIsOutdatedException, ZoteroItemCreationFailedException {
         String documentId = "43";
         Set<IGilesUpload> gilesUploads = new HashSet<>();
+        IGilesUpload gilesUpload = new GilesUpload();
+        gilesUpload.setDocumentId(documentId);
+        gilesUploads.add(gilesUpload);
         Mockito.when(zoteroManager.getGroupItemVersion(user, GROUP_ID, EXISTING_ID)).thenReturn(currentVersion);
         existingCitation.setKey(EXISTING_ID);
         existingCitation.setVersion(currentVersion);
@@ -411,7 +424,8 @@ public void test_deleteFile() throws GroupDoesNotExistException, CannotFindCitat
         existingCitation.setGilesUploads(gilesUploads);
         Mockito.when(zoteroManager.updateCitation(user, GROUP_ID, existingCitation)).thenReturn(existingCitation);
         Mockito.when(citationStore.findById(EXISTING_ID)).thenReturn(Optional.of(existingCitation));
+        Mockito.when(gilesConnector.deleteDocument(user, documentId)).thenReturn(HttpStatus.OK);
         managerToTest.deleteFile(user, GROUP_ID, EXISTING_ID, documentId);
-        Mockito.verify(citationStore).save(existingCitation);
+        Mockito.verify(gilesDeletionChecker).addDocumentCitationMap(gilesUpload, existingCitation, GROUP_ID, user);
     }
 }