From 2742ce49c656c46d9f197e1260c36847fa71d8ee Mon Sep 17 00:00:00 2001
From: shayanaijaz <shayanaijaz@gmail.com>
Date: Thu, 24 Oct 2024 13:03:54 -0500
Subject: [PATCH] Updated implementation

- Updated implementation of fileObj value
- Review pipeline fully functional with tree view
---
 .../DataFilesProjectFileListing.jsx           |   6 +
 .../ReviewProjectStructure.jsx                |  10 +-
 .../DataFilesProjectReview.jsx                |  20 +-
 .../src/redux/reducers/projects.reducers.js   |  35 +++
 client/src/redux/sagas/projects.sagas.js      |  27 ++
 server/portal/apps/_custom/drp/models.py      |  46 ++--
 server/portal/apps/_custom/drp/views.py       |  31 ++-
 server/portal/apps/projects/tasks.py          | 239 ++++++++++--------
 server/portal/apps/projects/views.py          |   6 +-
 .../workspace_operations/graph_operations.py  |  17 --
 .../project_meta_operations.py                | 131 ++++++++--
 .../project_publish_operations.py             |   0
 .../shared_workspace_operations.py            |  49 ++--
 ...licationrequest_review_project_and_more.py |  25 ++
 server/portal/apps/publications/models.py     |   7 +-
 server/portal/apps/publications/urls.py       |   1 +
 server/portal/apps/publications/views.py      |  52 +++-
 server/portal/libs/agave/operations.py        |  51 ++--
 server/portal/settings/settings.py            |   9 +
 19 files changed, 489 insertions(+), 273 deletions(-)
 create mode 100644 server/portal/apps/projects/workspace_operations/project_publish_operations.py
 create mode 100644 server/portal/apps/publications/migrations/0002_alter_publicationrequest_review_project_and_more.py

diff --git a/client/src/components/DataFiles/DataFilesProjectFileListing/DataFilesProjectFileListing.jsx b/client/src/components/DataFiles/DataFilesProjectFileListing/DataFilesProjectFileListing.jsx
index 9fd525809..b3f8c6508 100644
--- a/client/src/components/DataFiles/DataFilesProjectFileListing/DataFilesProjectFileListing.jsx
+++ b/client/src/components/DataFiles/DataFilesProjectFileListing/DataFilesProjectFileListing.jsx
@@ -28,6 +28,12 @@ const DataFilesProjectFileListing = ({ system, path }) => {
       type: 'PROJECTS_GET_METADATA',
       payload: system,
     });
+
+    dispatch({
+      type: 'PROJECTS_GET_PUBLICATION_REQUESTS',
+      payload: system,
+    })
+
   }, [system]);
 
   useEffect(() => {
diff --git a/client/src/components/_custom/drp/DataFilesProjectPublish/DataFilesProjectPublishWizardSteps/ReviewProjectStructure.jsx b/client/src/components/_custom/drp/DataFilesProjectPublish/DataFilesProjectPublishWizardSteps/ReviewProjectStructure.jsx
index 9cdb163fc..863f9f938 100644
--- a/client/src/components/_custom/drp/DataFilesProjectPublish/DataFilesProjectPublishWizardSteps/ReviewProjectStructure.jsx
+++ b/client/src/components/_custom/drp/DataFilesProjectPublish/DataFilesProjectPublishWizardSteps/ReviewProjectStructure.jsx
@@ -30,7 +30,7 @@ const ReviewProjectStructure = ({ projectTree }) => {
 
   useEffect(() => {
     if (projectTree && projectTree.length > 0) {
-      setExpandedNodes([projectTree[0].uuid]);
+      setExpandedNodes([projectTree[0].id]);
     }
   }, [projectTree]);
 
@@ -65,7 +65,7 @@ const ReviewProjectStructure = ({ projectTree }) => {
     const dataType = node.metadata.data_type;
     // reconstruct editFile to mimic SelectedFile object
     const editFile = {
-      id: node.uuid,
+      id: node.id,
       uuid: node.uuid,
       metadata: node.metadata,
       name: node.metadata.name,
@@ -122,8 +122,8 @@ const ReviewProjectStructure = ({ projectTree }) => {
       >
         <div>
           <TreeItem
-            key={node.uuid}
-            nodeId={node.uuid}
+            key={node.id}
+            nodeId={node.id}
             label={
               <div className={styles['node-name-div']}>
                   {node.label ?? node.name}
@@ -139,7 +139,7 @@ const ReviewProjectStructure = ({ projectTree }) => {
             }}
             onLabelClick={() => handleNodeToggle}
           >
-            {expandedNodes.includes(node.uuid) && node.id !== 'NODE_ROOT' && (
+            {expandedNodes.includes(node.id) && node.id !== 'NODE_ROOT' && (
               <div className={styles['metadata-description-div']}>
                 {(canEdit || node.metadata.data_type === 'file') && (
                   <Button
diff --git a/client/src/components/_custom/drp/DataFilesProjectReview/DataFilesProjectReview.jsx b/client/src/components/_custom/drp/DataFilesProjectReview/DataFilesProjectReview.jsx
index 784e88a9d..44cd59e39 100644
--- a/client/src/components/_custom/drp/DataFilesProjectReview/DataFilesProjectReview.jsx
+++ b/client/src/components/_custom/drp/DataFilesProjectReview/DataFilesProjectReview.jsx
@@ -27,18 +27,20 @@ const DataFilesProjectReview = ({ system }) => {
     const { metadata } = useSelector((state) => state.projects);
 
     const fetchTree = useCallback(async () => {
+    if (projectId) {
         try {
-          const response = await fetchUtil({
-            url: `api/${portalName.toLowerCase()}/tree`,
-            params: {
-              project_id: projectId,
-            },
-          });
-          setTree(response);
+            const response = await fetchUtil({
+                url: `api/${portalName.toLowerCase()}/tree`,
+                params: {
+                    project_id: projectId,
+                },
+            });
+            setTree(response);
         } catch (error) {
-          console.error('Error fetching tree data:', error);
-          setTree([]);
+            console.error('Error fetching tree data:', error);
+            setTree([]);
         }
+    }
     }, [portalName, projectId]);
 
     useEffect(() => {
diff --git a/client/src/redux/reducers/projects.reducers.js b/client/src/redux/reducers/projects.reducers.js
index 7f10496c3..b97bffd69 100644
--- a/client/src/redux/reducers/projects.reducers.js
+++ b/client/src/redux/reducers/projects.reducers.js
@@ -119,6 +119,7 @@ export default function projects(state = initialState, action) {
       return {
         ...state,
         metadata: {
+          ...state.metadata,
           ...action.payload,
           loading: false,
           error: null,
@@ -249,6 +250,40 @@ export default function projects(state = initialState, action) {
           result: null,
         },
       };
+    case 'PROJECTS_GET_PUBLICATION_REQUESTS_STARTED':
+      return {
+        ...state,
+        operation: {
+          name: 'getPublicationRequests',
+          loading: true,
+          error: null,
+          result: null,
+        },
+      };
+    case 'PROJECTS_GET_PUBLICATION_REQUESTS_SUCCESS':
+      return {
+        ...state, 
+        metadata: {
+          ...state.metadata,
+          publication_requests: action.payload,
+        },
+        operation: {
+          name: 'getPublicationRequests',
+          loading: false,
+          error: null,
+          result: action.payload,
+        },
+      }
+    case 'PROJECTS_GET_PUBLICATION_REQUESTS_FAILED':
+      return {
+        ...state,
+        operation: {
+          name: 'getPublicationRequests',
+          loading: false,
+          error: action.payload,
+          result: null,
+        },
+      };
     default:
       return state;
   }
diff --git a/client/src/redux/sagas/projects.sagas.js b/client/src/redux/sagas/projects.sagas.js
index 87f2a5875..4173b6cd1 100644
--- a/client/src/redux/sagas/projects.sagas.js
+++ b/client/src/redux/sagas/projects.sagas.js
@@ -215,6 +215,32 @@ export function* createPublicationRequest(action) {
   }
 }
 
+export async function fetchPublicationRequestsUtil(system) {
+  const result = await fetchUtil({
+    url: `/api/publications/publication-request/${system}`,
+  });
+  return result.response;
+}
+
+export function* getPublicationRequests(action) {
+
+  yield put({
+    type: 'PROJECTS_GET_PUBLICATION_REQUESTS_STARTED',
+  });
+  try {
+    const publicationRequests = yield call(fetchPublicationRequestsUtil, action.payload);
+    yield put({
+      type: 'PROJECTS_GET_PUBLICATION_REQUESTS_SUCCESS',
+      payload: publicationRequests,
+    });
+  } catch (error) {
+    yield put({
+      type: 'PROJECTS_GET_PUBLICATION_REQUESTS_FAILED',
+      payload: error,
+    });
+  }
+}
+
 export async function createEntityUtil(entityType, projectId, path, data) {
   const result = await fetchUtil({
     url: `/api/projects/${projectId}/entities/create`,
@@ -259,4 +285,5 @@ export function* watchProjects() {
   yield takeLatest('PROJECTS_SET_MEMBER', setMember);
   yield takeLatest('PROJECTS_SET_TITLE_DESCRIPTION', setTitleDescription);
   yield takeLatest('PROJECTS_CREATE_PUBLICATION_REQUEST', createPublicationRequest);
+  yield takeLatest('PROJECTS_GET_PUBLICATION_REQUESTS', getPublicationRequests);
 }
diff --git a/server/portal/apps/_custom/drp/models.py b/server/portal/apps/_custom/drp/models.py
index a057a3ddf..ad521feda 100644
--- a/server/portal/apps/_custom/drp/models.py
+++ b/server/portal/apps/_custom/drp/models.py
@@ -21,6 +21,26 @@ def model_dump(self, *args, **kwargs):
         return partial(super().model_dump, by_alias=True, exclude_none=True)(
             *args, **kwargs
         )
+    
+class DrpFileMetadata(DrpMetadataModel):
+    """Model for DRP File Metadata"""
+
+    model_config = ConfigDict(
+        extra="forbid",
+    ) 
+
+    data_type: Literal['file']
+    name: Optional[str] = None
+    image_type: Optional[Literal[
+        '8_bit', '16_bit_signed', '16_bit_unsigned', '32_bit_signed', '32_bit_unsigned', '32_bit_real', '64_bit_real', 
+        '24_bit_rgb', '24_bit_rgb_planar', '24_bit_bgr', '24_bit_integer', '32_bit_argb', '32_bit_abgr', '1_bit_bitmap',
+    ]] = None
+    height: Optional[int] = None
+    width: Optional[int] = None
+    number_of_images: Optional[int] = None
+    offset_to_first_image: Optional[int] = None
+    gap_between_images: Optional[int] = None
+    byte_order: Optional[Literal['big_endian', 'little_endian']] = None
 
 class FileObj(DrpMetadataModel):
     """Model for associated files"""
@@ -32,6 +52,7 @@ class FileObj(DrpMetadataModel):
     length: Optional[int] = None
     last_modified: Optional[str] = None
     uuid: Optional[str] = None
+    value: Optional[DrpFileMetadata] = None
 
 class PartialEntityWithFiles(DrpMetadataModel):
     """Model for representing an entity with associated files."""
@@ -40,7 +61,6 @@ class PartialEntityWithFiles(DrpMetadataModel):
 
     # file_tags: list[FileTag] = []
     file_objs: list[FileObj] = []
-
 class DrpProjectRelatedDatasets(DrpMetadataModel):
     """Model for DRP Project Related Datasets"""
 
@@ -77,7 +97,6 @@ class DrpProjectRelatedPublications(DrpMetadataModel):
     publication_description: Optional[str] = None
     publication_link: Optional[str] = None
 
-
 class DrpProjectMetadata(DrpMetadataModel):
     """Model for DRP Project Metadata"""
 
@@ -95,8 +114,9 @@ class DrpProjectMetadata(DrpMetadataModel):
     related_software: list[DrpProjectRelatedSoftware] = []
     related_publications: list[DrpProjectRelatedPublications] = []
     publication_date: Optional[str] = None
-    authors: list[str] = []
+    authors: list[dict] = []
     file_objs: list[FileObj] = []
+    is_review_project : Optional[bool] = None
 
 class DrpDatasetMetadata(DrpMetadataModel):
     """Model for Base DRP Dataset Metadata"""
@@ -192,23 +212,3 @@ class DrpAnalysisDatasetMetadata(DrpDatasetMetadata):
     external_uri: Optional[str] = None
     sample: str
     base_origin_data: Optional[str] = None
-
-class DrpFileMetadata(DrpMetadataModel):
-    """Model for DRP File Metadata"""
-
-    model_config = ConfigDict(
-        extra="forbid",
-    ) 
-
-    data_type: Literal['file']
-    name: Optional[str] = None
-    image_type: Optional[Literal[
-        '8_bit', '16_bit_signed', '16_bit_unsigned', '32_bit_signed', '32_bit_unsigned', '32_bit_real', '64_bit_real', 
-        '24_bit_rgb', '24_bit_rgb_planar', '24_bit_bgr', '24_bit_integer', '32_bit_argb', '32_bit_abgr', '1_bit_bitmap',
-    ]] = None
-    height: Optional[int] = None
-    width: Optional[int] = None
-    number_of_images: Optional[int] = None
-    offset_to_first_image: Optional[int] = None
-    gap_between_images: Optional[int] = None
-    byte_order: Optional[Literal['big_endian', 'little_endian']] = None
diff --git a/server/portal/apps/_custom/drp/views.py b/server/portal/apps/_custom/drp/views.py
index 8cb223e88..dd5278468 100644
--- a/server/portal/apps/_custom/drp/views.py
+++ b/server/portal/apps/_custom/drp/views.py
@@ -6,6 +6,7 @@
 from portal.apps.projects.models.project_metadata import ProjectMetadata
 from portal.apps._custom.drp import constants
 import networkx as nx
+from portal.apps.projects.workspace_operations.project_meta_operations import get_ordered_value
 class DigitalRocksSampleView(BaseApiView):
 
     def get(self, request):
@@ -55,8 +56,6 @@ def _get_entity(uuid):
     
     def get(self, request):
 
-        metadata_data_types = ['sample', 'origin_data', 'analysis_data', 'file']
-
         project_id = request.GET.get('project_id')
         full_project_id = f'{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{project_id}'
 
@@ -66,27 +65,31 @@ def get(self, request):
 
         graph = nx.node_link_graph(graph_model.value)
 
-        for node in graph.nodes:
-            node_uuid = graph.nodes[node].get("uuid")
+        for node_id in graph.nodes:
 
-            entity = self._get_entity(node_uuid)
-            metadata = entity.ordered_value
+            node = graph.nodes[node_id]
 
-            file_objs = entity.value.get('fileObjs', [])
+            if node.get('value'):
+                metadata = get_ordered_value(node['name'], node['value'])
+                file_objs = node['value'].get('fileObjs', [])
+            else:
+                node_uuid = node.get("uuid")
+                entity = self._get_entity(node_uuid)
+                metadata = get_ordered_value(entity.name, entity.value)
+                file_objs = entity.value.get('fileObjs', [])
 
             file_objs_dict = []
 
             for file_obj in file_objs:
-                file_obj_entity = self._get_entity(file_obj.get('uuid'))
-                file_obj_metadata = file_obj_entity.ordered_value
 
                 file_objs_dict.append({
                     **file_obj,
-                    'metadata': file_obj_metadata
-            })
-                
-            graph.nodes[node]['metadata'] = metadata
-            graph.nodes[node]['fileObjs'] = file_objs_dict
+                    'id': file_obj.get('uuid'),
+                    'metadata': get_ordered_value(constants.FILE, file_obj.get('value'))
+                })
+
+            node['metadata'] = metadata
+            node['fileObjs'] = file_objs_dict
 
         tree = nx.tree_data(graph, "NODE_ROOT")
 
diff --git a/server/portal/apps/projects/tasks.py b/server/portal/apps/projects/tasks.py
index 6848802ce..2f5d0af12 100644
--- a/server/portal/apps/projects/tasks.py
+++ b/server/portal/apps/projects/tasks.py
@@ -9,140 +9,175 @@
 from portal.libs.agave.utils import user_account, service_account
 from django.contrib.auth import get_user_model
 from django.core.exceptions import ObjectDoesNotExist
+from portal.apps.projects.models.project_metadata import ProjectMetadata
+from portal.apps._custom.drp import constants
+from portal.apps.projects.workspace_operations.project_meta_operations import create_entity_metadata
+from portal.apps.projects.workspace_operations.graph_operations import initialize_project_graph
+import networkx as nx
+import uuid
 
 logger = logging.getLogger(__name__)
 
-@shared_task(bind=True, max_retries=3, queue='default')
-def copy_files_and_metadata(self, user_access_token, source_workspace_id, review_workspace_id, source_system_id, review_system_id):
+def _transfer_files(user_access_token, source_system_id, review_system_id):
+    user_client = user_account(user_access_token)
+    service_client = service_account()
 
-    logger.info(f'Starting copy task for system {source_system_id} to system {review_system_id}')
+    source_system_files = user_client.files.listFiles(systemId=source_system_id, path='/')
 
-    with transaction.atomic(): 
-        # do a system file listing at the root using the client. This will be the list of files to copy
+    transfer_elements = [
+        {
+            'sourceURI': file.url,
+            'destinationURI': f'tapis://{review_system_id}/{file.path}'
+        }
+        for file in source_system_files
+    ]
+
+    transfer = service_client.files.createTransferTask(elements=transfer_elements)
+    return transfer
+
+def _check_transfer_status(service_client, transfer_task_id):
+    transfer_details = service_client.files.getTransferTask(transferTaskId=transfer_task_id)
+    return transfer_details.status
+
+def _create_publication_request(review_system_id, source_system_id, publication_reviewers):
+    review_project = ProjectMetadata.get_project_by_id(review_system_id)
+    source_project = ProjectMetadata.get_project_by_id(source_system_id)
+
+    publication_request = PublicationRequest(
+        review_project=review_project,
+        source_project=source_project,
+    )
+
+    publication_request.save()
+
+    for reviewer in publication_reviewers:
+        try:
+            user = get_user_model().objects.get(username=reviewer)
+            publication_request.reviewers.add(user)
+        except ObjectDoesNotExist:
+            continue
+
+    publication_request.save()
+    logger.info(f'Created publication review for system {review_system_id}')
+
+def _remove_admin_from_workspace(user_client, source_system_id, source_workspace_id, portal_admin_username):
+    user_client.systems.unShareSystem(systemId=source_system_id, users=[portal_admin_username])
+    user_client.systems.revokeUserPerms(systemId=source_system_id, userName=portal_admin_username, permissions=["READ", "MODIFY", "EXECUTE"])
+    user_client.files.deletePermissions(systemId=source_system_id, username=portal_admin_username, path="/")
+    logger.info(f'Removed service account from workspace {source_workspace_id}')
+
+def _add_reviewers_to_workspace(service_client, review_workspace_id, publication_reviewers, review_system_id):
+
+    from portal.apps.projects.workspace_operations.shared_workspace_operations import add_user_to_workspace
+
+    for reviewer in publication_reviewers:
+        add_user_to_workspace(
+            service_client,
+            review_workspace_id,
+            reviewer,
+            "reader",
+            f"{settings.PORTAL_PROJECTS_REVIEW_SYSTEM_PREFIX}.{review_workspace_id}",
+            settings.PORTAL_PROJECTS_ROOT_REVIEW_SYSTEM_NAME,
+        )
+        logger.info(f'Added reviewer {reviewer} to review system {review_system_id}')
+
+def _handle_completed_transfer(user_access_token, source_workspace_id, review_workspace_id, source_system_id, review_system_id, publication_reviewers):
+    service_client = service_account()
+    user_client = user_account(user_access_token)
+    portal_admin_username = settings.PORTAL_ADMIN_USERNAME
+
+    with transaction.atomic():
+        # Create publication request
+        _create_publication_request(review_system_id, source_system_id, publication_reviewers)
+
+        # Remove admin from source workspace
+        _remove_admin_from_workspace(user_client, source_system_id, source_workspace_id, portal_admin_username)
+
+        # Add reviewers to review workspace
+        _add_reviewers_to_workspace(service_client, review_workspace_id, publication_reviewers, review_system_id)
+
+def _add_values_to_tree(project_id):
+    project_meta = ProjectMetadata.get_project_by_id(project_id)
+    prj_entities = ProjectMetadata.get_entities_by_project_id(project_id)
+    
+    entity_map = {entity.uuid: entity for entity in prj_entities}
+
+    publication_tree: nx.DiGraph = nx.node_link_graph(project_meta.project_graph.value)
+    for node_id in publication_tree:
+        uuid = publication_tree.nodes[node_id]["uuid"]
+        if uuid is not None:
+            publication_tree.nodes[node_id]["value"] = entity_map[uuid].value
+            publication_tree.nodes[node_id]["uuid"] = None  # Clear the uuid field
+
+    return publication_tree
 
-        user_client = user_account(user_access_token)
-        service_client = service_account()
+@shared_task(bind=True, max_retries=3, queue='default')
+def copy_graph_and_files(self, user_access_token, source_workspace_id, review_workspace_id, source_system_id, review_system_id):
+    logger.info(f'Starting copy task for system {source_system_id} to system {review_system_id}')
 
-        source_system_files = user_client.files.listFiles(systemId=source_system_id, path='/')
-        source_system_files_metadata = DataFilesMetadata.objects.filter(project_id=source_system_id).order_by('created_at')
-        review_project = ProjectsMetadata.objects.get(project_id=review_system_id)
-
-        # create new metadata records for each file in the listing
-        for metadata in source_system_files_metadata: 
-            review_system_file_metadata = DataFilesMetadata(
-                name = metadata.name,
-                path = f'{review_system_id}/{metadata.path.split("/", 1)[-1]}',
-                metadata = metadata.metadata,
-                project = review_project
-            )
+    with transaction.atomic():
+        pub_tree = _add_values_to_tree(source_system_id)
 
-            review_system_file_metadata.save()
-
-        # create transfer object for tapis file copy
-        transfer_elements = [
-            {
-                'sourceURI': file.url,
-                'destinationURI': f'tapis://{review_system_id}/{file.path}'
-            }
-            for file in source_system_files
-        ]
-        
-        transfer = service_client.files.createTransferTask(elements=transfer_elements)
-
-        copy_result = {
-            'uuid': transfer.uuid,
-            'status': transfer.status
-        }
+        graph_model_value = nx.node_link_data(pub_tree)
+        review_project = ProjectMetadata.get_project_by_id(review_system_id)
+        ProjectMetadata.objects.update_or_create(
+            name=constants.PROJECT_GRAPH,
+            base_project=review_project,
+            defaults={"value": graph_model_value},
+        )
 
-        logger.info(f'Created transfer task {transfer.uuid} for system {source_system_id} to system {review_system_id}')
+        transfer = _transfer_files(user_access_token, source_system_id, review_system_id)
+
+        logger.info(f'Transfer task submmited with id {transfer.uuid}')
 
         post_file_transfer.apply_async(kwargs={
-            'user_access_token': user_access_token, 
+            'user_access_token': user_access_token,
             'source_workspace_id': source_workspace_id,
             'review_workspace_id': review_workspace_id,
-            'source_system_id': source_system_id, 
+            'source_system_id': source_system_id,
             'review_system_id': review_system_id,
             'transfer_task_id': transfer.uuid
         }, countdown=30)
 
-
 @shared_task(bind=True, max_retries=3, queue='default')
 def post_file_transfer(self, user_access_token, source_workspace_id, review_workspace_id, source_system_id, review_system_id, transfer_task_id):
-
     logger.info(f'Starting post transfer task for transfer id {transfer_task_id} for system {source_system_id} to system {review_system_id}')
 
     try:
-        user_client = user_account(user_access_token)
         service_client = service_account()
-        portal_admin_username = settings.PORTAL_ADMIN_USERNAME
         publication_reviewers = settings.PUBLICATION_REVIEWERS
 
         # Check the transfer status
-        transfer_details = service_client.files.getTransferTask(transferTaskId=transfer_task_id)
-        transfer_status = transfer_details.status
+        transfer_status = _check_transfer_status(service_client, transfer_task_id)
 
-        # Check if the transfer is still pending
+        # Handle pending or in-progress transfer
         if transfer_status in ['PENDING', 'IN_PROGRESS']:
-            # Reschedule the task to check again after 30 seconds
-            logger.info(f'Transfer {transfer_task_id} is still pending, retrying in 30 seconds.')
-            self.apply_async(
-                kwargs={
-                    'user_access_token': user_access_token,
-                    'source_workspace_id': source_workspace_id,
-                    'review_workspace_id': review_workspace_id,
-                    'source_system_id': source_system_id,
-                    'review_system_id': review_system_id,
-                    'transfer_task_id': transfer_task_id
-                }, 
-                countdown=30
-            )
+            logger.info(f'Transfer {transfer_task_id} is still pending with status {transfer_status}, retrying in 30 seconds.')
+            self.apply_async(kwargs={
+                'user_access_token': user_access_token,
+                'source_workspace_id': source_workspace_id,
+                'review_workspace_id': review_workspace_id,
+                'source_system_id': source_system_id,
+                'review_system_id': review_system_id,
+                'transfer_task_id': transfer_task_id
+            }, countdown=30)
             return
+
+        # Handle completed transfer
         elif transfer_status == 'COMPLETED':
             logger.info(f'Transfer {transfer_task_id} completed successfully for system {source_system_id} to system {review_system_id}')
-            from portal.apps.projects.workspace_operations.shared_workspace_operations import add_user_to_workspace
-
-            with transaction.atomic():
-                # create a publication review object
-                review_project = ProjectsMetadata.objects.get(project_id=review_system_id)
-                source_project = ProjectsMetadata.objects.get(project_id=source_system_id)
-
-                publication_request = PublicationRequest(
-                    review_project = review_project,
-                    source_project = source_project,
-                )
-
-                publication_request.save()
-
-                for reviewer in publication_reviewers:
-                    try:
-                        user = get_user_model().objects.get(username=reviewer)
-                        publication_request.reviewers.add(user)
-                    except ObjectDoesNotExist:
-                        continue
-                
-                publication_request.save()
-
-                logger.info(f'Created publication review for system {review_system_id}')
-
-                # remove the service account from the source workspace
-                user_client.systems.unShareSystem(systemId=source_system_id, users=[portal_admin_username])
-                user_client.systems.revokeUserPerms(systemId=source_system_id,
-                                            userName=portal_admin_username,
-                                            permissions=["READ", "MODIFY", "EXECUTE"])
-                user_client.files.deletePermissions(systemId=source_system_id,
-                                            username=portal_admin_username,
-                                            path="/")
-                logger.info(f'Removed service account from workspace {source_workspace_id}')
-
-                # add the reviewers to the review workspace
-                for reviewer in publication_reviewers:
-                    add_user_to_workspace(service_client, review_workspace_id, reviewer, "reader")
-                    logger.info(f'Added reviewer {reviewer} to review system {review_system_id}')
-        else: 
-            logger.error(f'Error processing transfer {transfer_task_id} for system {source_system_id} to system {review_system_id}: Transfer status is {transfer_status}')
+            _handle_completed_transfer(
+                user_access_token,
+                source_workspace_id,
+                review_workspace_id,
+                source_system_id,
+                review_system_id,
+                publication_reviewers
+            )
+        else:
+            logger.error(f'Error processing transfer {transfer_task_id}: Transfer status is {transfer_status}')
             raise Exception(f'Transfer {transfer_task_id} failed with status {transfer_status}')
-        
+    
     except Exception as e:
         logger.error(f'Error processing transfer {transfer_task_id} for system {source_system_id} to system {review_system_id}: {e}')
         self.retry(exc=e, countdown=30)
-
diff --git a/server/portal/apps/projects/views.py b/server/portal/apps/projects/views.py
index 9ee186243..bedbc9fbb 100644
--- a/server/portal/apps/projects/views.py
+++ b/server/portal/apps/projects/views.py
@@ -26,7 +26,7 @@
 from django.db import transaction
 from portal.apps import SCHEMA_MAPPING
 from django.db import models
-from portal.apps.projects.workspace_operations.project_meta_operations import create_entity_metadata, create_project_metdata, patch_file_obj_entity, patch_entity, patch_project_entity
+from portal.apps.projects.workspace_operations.project_meta_operations import create_entity_metadata, create_project_metadata, get_ordered_value, patch_file_obj_entity, patch_entity, patch_project_entity
 from portal.libs.agave.operations import mkdir
 from pathlib import Path
 from portal.apps._custom.drp import constants
@@ -131,7 +131,7 @@ def post(self, request):  # pylint: disable=no-self-use
 
         if metadata is not None: 
             metadata["projectId"] = workspace_id
-            project_meta = create_project_metdata(metadata)
+            project_meta = create_project_metadata(metadata)
             initialize_project_graph(project_meta.project_id)
             # project_metadata = ProjectsMetadata(
             #     project_id = workspace_id,
@@ -178,7 +178,7 @@ def get(self, request, project_id=None, system_id=None):
 
         try: 
             project = ProjectMetadata.objects.get(models.Q(value__projectId=f"{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{project_id}"))
-            prj.update(project.ordered_value)
+            prj.update(get_ordered_value(project.name, project.value))
             prj["projectId"] = project_id
         except: 
             pass
diff --git a/server/portal/apps/projects/workspace_operations/graph_operations.py b/server/portal/apps/projects/workspace_operations/graph_operations.py
index 013b72413..b62ce20c0 100644
--- a/server/portal/apps/projects/workspace_operations/graph_operations.py
+++ b/server/portal/apps/projects/workspace_operations/graph_operations.py
@@ -114,23 +114,6 @@ def get_root_node(project_id: str) -> Dict[str, Any]:
     project_graph = nx.node_link_graph(graph_model.value)
     return {"id": "NODE_ROOT", **project_graph.nodes["NODE_ROOT"]}
 
-def get_file_association_from_path(project_id: str, path: str) -> Dict[str, Any]:
-    """Return the node ID for the parent of a node with the given path."""
-
-    graph_model = ProjectMetadata.objects.get(
-        name=constants.PROJECT_GRAPH, base_project__value__projectId=project_id
-    )
-    project_graph = nx.node_link_graph(graph_model.value)
-
-    path_parts = path.strip("/").split("/")
-
-    if len(path_parts) == 0 or path_parts[0] == "":
-        return {"id": "NODE_ROOT"}
-    
-    node = traverse_graph(project_graph, "NODE_ROOT", path_parts)
-
-    return node
-
 def update_node_in_project(project_id: str, node_id: str, new_parent: str = None, new_name: str = None):
     """Update the database entry for a project graph to update a node."""
     with transaction.atomic():
diff --git a/server/portal/apps/projects/workspace_operations/project_meta_operations.py b/server/portal/apps/projects/workspace_operations/project_meta_operations.py
index 3fd46f7e6..cc7029c40 100644
--- a/server/portal/apps/projects/workspace_operations/project_meta_operations.py
+++ b/server/portal/apps/projects/workspace_operations/project_meta_operations.py
@@ -1,4 +1,5 @@
 import operator
+import uuid
 from django.db import models, transaction
 from portal.apps import SCHEMA_MAPPING
 from portal.apps._custom.drp import constants
@@ -7,10 +8,16 @@
 from portal.apps._custom.drp.models import PartialEntityWithFiles, FileObj
 from portal.apps.projects.workspace_operations.graph_operations import get_node_from_path, get_root_node, update_node_in_project
 from pathlib import Path
+from typing import get_args, List
+
 
 portal = settings.PORTAL_NAMESPACE.lower()
 
-def create_project_metdata(value):
+def snake_to_camel(snake_str):
+    components = snake_str.split('_')
+    return components[0] + ''.join(x.title() for x in components[1:])
+
+def create_project_metadata(value):
     """Create a project metadata object in the database."""
     schema_model = SCHEMA_MAPPING[constants.PROJECT]
     validated_model = schema_model.model_validate(value)
@@ -33,31 +40,107 @@ def create_entity_metadata(project_id, name, value):
     entity_db_model.save()
     return entity_db_model
 
-def get_entity(project_id, path):
+def create_file_obj(project_id, name, size, path, value):
+    """Create a file object metadata associated with an existing project."""
+    schema_model = SCHEMA_MAPPING[constants.FILE]
+    validated_model = schema_model.model_validate(value)
+
+    file_obj = FileObj(
+        system=project_id,
+        name=name,
+        path=path,
+        type='file',
+        length=size,
+        value=validated_model.model_dump(exclude_none=True),
+        uuid=str(uuid.uuid4())
+    )
+
+    return file_obj
+
+def get_value(project_id, path):
     """Retrieve metadata for a specific entity."""
     try:
         node = get_node_from_path(project_id, path)
 
         if not node or node['id'] == 'NODE_ROOT':
             return None
+        
+        if node.get('value'):
+            return get_ordered_value(node['name'], node['value'])
+
         entity = ProjectMetadata.objects.get(uuid=node['uuid'])
-        # entity = ProjectMetadata.get_entity_by_project_id_and_path(project_id, path)
-        return entity
+        return get_ordered_value(entity.name, entity.value)
+    except ProjectMetadata.DoesNotExist:
+        return None
+
+def get_entity(project_id, path):
+    """Retrieve an entity by its path."""
+    try:
+        node = get_node_from_path(project_id, path)
+
+        if not node or node['id'] == 'NODE_ROOT':
+            return None
+
+        return ProjectMetadata.objects.get(uuid=node['uuid'])
     except ProjectMetadata.DoesNotExist:
         return None
 
-def get_file_association_entity(project_id, path):
-    try: 
+def get_ordered_value(name, value):
+    """
+        Return the metadata in the order defined in the Pydantic model.
+        Also converts camelCase keys to snake_case. This is a temporary workaround until fields in settings_forms.py can be updated to use camelCase.
+        """
+    schema = SCHEMA_MAPPING.get(name)
+
+    if not schema:
+        return value  # Return the field value directly if no schema is found
+
+    ordered_value = {}
+
+    # Iterate through the model fields to preserve the order
+    for field in schema.model_fields.keys():
+        camel_field = snake_to_camel(field)
+        field_value = value.get(camel_field)
+
+        # Skip the field if there is no value (None or not present)
+        if field_value is None:
+            continue
+
+        # if the fiels is a list, then we need to get the model of the list and process it
+        if isinstance(field_value, list):
+            field_annotation = schema.model_fields[field].annotation
+            item_type = get_args(field_annotation)[0] if get_args(field_annotation) else None # returns the model class of the list
+
+            # Check if the item type is a Pydantic model
+            if item_type and hasattr(item_type, "model_fields"):
+                # Re-order each item in the list if it's a list of Pydantic models
+                ordered_value[field] = [
+                    {k: item.get(snake_to_camel(k)) for k in item_type.model_fields.keys()}
+                    for item in field_value
+                ]
+            else:
+                ordered_value[field] = field_value
+        else:
+            ordered_value[field] = field_value
+
+    return ordered_value
+
+def get_file_obj( project_id, path):
+    """Retrieve a file object by its path."""
+    try:
         parent_path = str(Path(path).parent)
 
         parent_node = _get_valid_node(project_id, parent_path)
 
-        parent_entity = ProjectMetadata.objects.get(uuid=parent_node['uuid'])
-        file_objs = parent_entity.value.get('fileObjs', [])
+        if (parent_node.get('value')):
+            file_objs = parent_node['value'].get('fileObjs', [])
+        else:
+            parent_entity = ProjectMetadata.objects.get(uuid=parent_node['uuid'])
+            file_objs = parent_entity.value.get('fileObjs', [])
+
         file_obj = next((f for f in file_objs if f['path'] == path), None)
         if file_obj:
-            entity = ProjectMetadata.objects.get(uuid=file_obj['uuid'])
-            return entity
+            return file_obj
         else:
             return None
     except:
@@ -123,23 +206,23 @@ def patch_file_obj_entity(client, project_id, value, path):
 
     parent_node = _get_valid_node(project_id, parent_path)
 
-    parent_entity = ProjectMetadata.objects.get(uuid=parent_node['uuid'])
-    file_objs = parent_entity.value.get('fileObjs', [])
+    entity = ProjectMetadata.objects.get(uuid=parent_node['uuid'])
+    file_objs = entity.value.get('fileObjs', [])
     file_obj = next((f for f in file_objs if f['path'] == path.strip('/')), None)
 
     if not file_obj:
         return None
 
-    entity = ProjectMetadata.objects.get(uuid=file_obj['uuid'])
-
-    schema_model = SCHEMA_MAPPING[entity.name]
+    schema = SCHEMA_MAPPING[constants.FILE]
+    validated_model = schema.model_validate(value)
+    file_obj['value'] = validated_model.model_dump(exclude_none=True)
 
-    patched_metadata = {**value}
+    entity_file_model = PartialEntityWithFiles.model_validate(entity.value)
+    merged_file_objs = _merge_file_objs(entity_file_model.file_objs, [FileObj(**file_obj)])
+    entity.value["fileObjs"] = [f.model_dump() for f in merged_file_objs]
 
-    validated_model = schema_model.model_validate(patched_metadata)
-    entity.value = validated_model.model_dump(exclude_none=True)
     entity.save()
-
+    
     return entity
 
 def delete_entity(uuid: str):
@@ -271,14 +354,12 @@ def patch_file_association(project_id, value, source_path_full, dest_path_full,
     if not file_obj_dict:
         return
 
-    file_obj_dict['name'] = new_name
-    file_obj_dict['path'] = dest_path_full.strip('/')
-    file_obj = FileObj(**file_obj_dict)
-
     if operation == 'move':
+        file_obj_dict['name'] = new_name
+        file_obj_dict['path'] = dest_path_full.strip('/')
+        file_obj = FileObj(**file_obj_dict)
         remove_file_associations(source_entity.uuid, [source_path_full])
         add_file_associations(dest_entity.uuid, [file_obj])
     elif operation == 'copy':
-        new_meta = create_entity_metadata(project_id, getattr(constants, value.get('data_type').upper()), {**value})
-        file_obj.uuid = new_meta.uuid
+        file_obj = create_file_obj(project_id, new_name, file_obj_dict['length'], dest_path_full.strip('/'), file_obj_dict['value'])
         add_file_associations(dest_entity.uuid, [file_obj])
\ No newline at end of file
diff --git a/server/portal/apps/projects/workspace_operations/project_publish_operations.py b/server/portal/apps/projects/workspace_operations/project_publish_operations.py
new file mode 100644
index 000000000..e69de29bb
diff --git a/server/portal/apps/projects/workspace_operations/shared_workspace_operations.py b/server/portal/apps/projects/workspace_operations/shared_workspace_operations.py
index e7bc1cdbc..82d446e0d 100644
--- a/server/portal/apps/projects/workspace_operations/shared_workspace_operations.py
+++ b/server/portal/apps/projects/workspace_operations/shared_workspace_operations.py
@@ -1,11 +1,14 @@
 # from portal.utils.encryption import createKeyPair
 from portal.libs.agave.utils import service_account
+from portal.apps.projects.models.project_metadata import ProjectMetadata
 from tapipy.tapis import Tapis
 from typing import Literal
 from django.db import transaction
 from django.conf import settings
 from django.contrib.auth import get_user_model
 from portal.apps.projects.models.metadata import ProjectsMetadata
+from django.db import models
+from portal.apps.projects.workspace_operations.project_meta_operations import create_project_metadata
 
 import logging
 logger = logging.getLogger(__name__)
@@ -108,16 +111,17 @@ def submit_workspace_acls_job(
     return res
 
 
-def create_workspace_dir(workspace_id: str) -> str:
+def create_workspace_dir(workspace_id: str, system_id=settings.PORTAL_PROJECTS_ROOT_SYSTEM_NAME) -> str:
     client = service_account()
-    system_id = settings.PORTAL_PROJECTS_ROOT_SYSTEM_NAME
     path = f"{workspace_id}"
     client.files.mkdir(systemId=system_id, path=path)
     return path
 
 
-def create_workspace_system(client, workspace_id: str, title: str, description="", owner=None) -> str:
-    system_id = f"{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{workspace_id}"
+def create_workspace_system(client, workspace_id: str, title: str, description="", owner=None, system_id=None, root_dir=None) -> str:
+    system_id = system_id or f"{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{workspace_id}"
+    root_dir = root_dir or f"{settings.PORTAL_PROJECTS_ROOT_DIR}/{workspace_id}"
+
     system_args = {
         "id": system_id,
         "host": settings.PORTAL_PROJECTS_ROOT_HOST,
@@ -125,7 +129,7 @@ def create_workspace_system(client, workspace_id: str, title: str, description="
         "systemType": "LINUX",
         "defaultAuthnMethod": "PKI_KEYS",
         "canExec": False,
-        "rootDir": f"{settings.PORTAL_PROJECTS_ROOT_DIR}/{workspace_id}",
+        "rootDir": root_dir,
         "effectiveUserId": settings.PORTAL_ADMIN_USERNAME,
         "authnCredential": {
             "privateKey": settings.PORTAL_PROJECTS_PRIVATE_KEY,
@@ -196,14 +200,18 @@ def create_shared_workspace(client: Tapis, title: str, owner: str, description="
 def add_user_to_workspace(client: Tapis,
                           workspace_id: str,
                           username: str,
-                          role="writer"):
+                          role="writer",
+                          system_id=None,
+                          system_name=None):
     """
     Give a user POSIX and Tapis permissions on a workspace system.
     """
     service_client = service_account()
-    system_id = f"{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{workspace_id}"
+    system_id = system_id or f"{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{workspace_id}"
+    system_name = system_name or f"{settings.PORTAL_PROJECTS_ROOT_SYSTEM_NAME}"
+
     set_workspace_acls(service_client,
-                       settings.PORTAL_PROJECTS_ROOT_SYSTEM_NAME,
+                       system_name,
                        workspace_id,
                        username,
                        "add",
@@ -221,7 +229,7 @@ def add_user_to_workspace(client: Tapis,
     client.systems.shareSystem(systemId=system_id, users=[username])
     set_workspace_permissions(client, username, system_id, role)
 
-    return get_project(client, workspace_id)
+    return get_project(client, workspace_id, system_id)
 
 
 def change_user_role(client, workspace_id: str, username: str, new_role):
@@ -338,8 +346,8 @@ def list_projects(client):
     return list(serialized_listing)
 
 
-def get_project(client, workspace_id):
-    system_id = f"{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{workspace_id}"
+def get_project(client, workspace_id, system_id=None):
+    system_id = system_id or f"{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{workspace_id}"
     shares = client.systems.getShareInfo(systemId=system_id)
     system = client.systems.getSystem(systemId=system_id)
 
@@ -392,28 +400,23 @@ def create_publication_review_shared_workspace(client, source_workspace_id: str,
     # add admin to the source workspace to allow for file copying
     resp = add_user_to_workspace(client, source_workspace_id, portal_admin_username)
 
-    source_project = ProjectsMetadata.objects.get(project_id=source_system_id)
+    source_project = ProjectMetadata.get_project_by_id(source_system_id)
 
-    # Create new Project entry for the review system
-    review_project = ProjectsMetadata(
-        project_id = review_system_id,
-        metadata = {
-            **source_project.metadata,
-            "is_review_project": True,
-        } 
-    )
+    review_project = create_project_metadata({**source_project.value, "projectId": review_system_id, "is_review_project": True})
 
     review_project.save()
     
-    create_workspace_dir(review_workspace_id)
+    create_workspace_dir(review_workspace_id, settings.PORTAL_PROJECTS_ROOT_REVIEW_SYSTEM_NAME)
         
     set_workspace_acls(service_client,
-                       settings.PORTAL_PROJECTS_ROOT_SYSTEM_NAME,
+                       settings.PORTAL_PROJECTS_ROOT_REVIEW_SYSTEM_NAME,
                        review_workspace_id,
                        portal_admin_username,
                        "add",
                        "writer")
     
-    system_id = create_workspace_system(service_client, review_workspace_id, title, description)
+    system_id = create_workspace_system(service_client, review_workspace_id, title, description, None, 
+                                        f"{settings.PORTAL_PROJECTS_REVIEW_SYSTEM_PREFIX}.{review_workspace_id}",
+                                        f"{settings.PORTAL_PROJECTS_REVIEW_ROOT_DIR}/{review_workspace_id}")
     
     return system_id
diff --git a/server/portal/apps/publications/migrations/0002_alter_publicationrequest_review_project_and_more.py b/server/portal/apps/publications/migrations/0002_alter_publicationrequest_review_project_and_more.py
new file mode 100644
index 000000000..c41ceda6e
--- /dev/null
+++ b/server/portal/apps/publications/migrations/0002_alter_publicationrequest_review_project_and_more.py
@@ -0,0 +1,25 @@
+# Generated by Django 4.2.16 on 2024-10-22 16:45
+
+from django.db import migrations, models
+import django.db.models.deletion
+
+
+class Migration(migrations.Migration):
+
+    dependencies = [
+        ('projects', '0007_projectmetadata_and_more'),
+        ('publications', '0001_initial'),
+    ]
+
+    operations = [
+        migrations.AlterField(
+            model_name='publicationrequest',
+            name='review_project',
+            field=models.ForeignKey(null=True, on_delete=django.db.models.deletion.SET_NULL, related_name='publication_reviews', to='projects.projectmetadata'),
+        ),
+        migrations.AlterField(
+            model_name='publicationrequest',
+            name='source_project',
+            field=models.ForeignKey(on_delete=django.db.models.deletion.CASCADE, related_name='source_publication_reviews', to='projects.projectmetadata'),
+        ),
+    ]
diff --git a/server/portal/apps/publications/models.py b/server/portal/apps/publications/models.py
index 0f0ac5dfd..99d360cb6 100644
--- a/server/portal/apps/publications/models.py
+++ b/server/portal/apps/publications/models.py
@@ -7,6 +7,7 @@
 from django.conf import settings
 from django.db import models
 from django.utils import timezone
+from portal.apps.projects.models.project_metadata import ProjectMetadata
 
 # pylint: disable=invalid-name
 logger = logging.getLogger(__name__)
@@ -20,8 +21,8 @@ class Status(models.TextChoices):
         APPROVED = 'APPROVED'
         REJECTED = 'REJECTED'
 
-    review_project = models.ForeignKey('projects.ProjectsMetadata', related_name='publication_reviews', on_delete=models.SET_NULL, null=True)
-    source_project = models.ForeignKey('projects.ProjectsMetadata', related_name='source_publication_reviews', on_delete=models.CASCADE)
+    review_project = models.ForeignKey(ProjectMetadata, related_name='publication_reviews', on_delete=models.SET_NULL, null=True)
+    source_project = models.ForeignKey(ProjectMetadata, related_name='source_publication_reviews', on_delete=models.CASCADE)
     reviewers = models.ManyToManyField(settings.AUTH_USER_MODEL, related_name='publication_reviewers')
     status = models.CharField(max_length=255, choices=Status.choices, default=Status.PENDING)
     comments = models.TextField(blank=True, null=True)
@@ -29,4 +30,4 @@ class Status(models.TextChoices):
     last_updated = models.DateTimeField(auto_now=True)
 
     def __str__(self):
-        return f'Review for {self.project.project_id}'
\ No newline at end of file
+        return f'Review for {self.review_project.project_id}'
\ No newline at end of file
diff --git a/server/portal/apps/publications/urls.py b/server/portal/apps/publications/urls.py
index f12a14c0f..ab73238c5 100644
--- a/server/portal/apps/publications/urls.py
+++ b/server/portal/apps/publications/urls.py
@@ -6,4 +6,5 @@
 app_name = 'publications'
 urlpatterns = [
     path('publication-request/', views.PublicationRequestView.as_view(), name='publication_request'),
+    path('publication-request/<str:project_id>/', views.PublicationRequestView.as_view(), name='publication_request_detail'),
 ]
\ No newline at end of file
diff --git a/server/portal/apps/publications/views.py b/server/portal/apps/publications/views.py
index 5d87f65b0..8cccae9f1 100644
--- a/server/portal/apps/publications/views.py
+++ b/server/portal/apps/publications/views.py
@@ -14,29 +14,55 @@
 from portal.apps.projects.workspace_operations.shared_workspace_operations import create_publication_review_shared_workspace
 from portal.apps.projects.models.metadata import ProjectsMetadata
 from django.db import transaction
-from portal.apps.projects.tasks import copy_files_and_metadata
+from portal.apps.projects.tasks import copy_graph_and_files
 from portal.apps.notifications.models import Notification
 from django.http import HttpResponse
 from portal.apps.publications.models import PublicationRequest
+from portal.apps.projects.models.project_metadata import ProjectMetadata
+from django.db import models
+
 
 
 LOGGER = logging.getLogger(__name__)
 
 class PublicationRequestView(BaseApiView):
          
-    def get(self, request):
-        project_id = request.GET.get('project_id')
+    def get(self, request, project_id: str):
         
         if project_id:
             try:
-                project = ProjectsMetadata.objects.get(project_id=project_id)
-                publication_requests = PublicationRequest.objects.filter(source_project=project).values()
+                project = ProjectMetadata.get_project_by_id(project_id)
+                
+                publication_requests = PublicationRequest.objects.filter(
+                     models.Q(source_project=project) | models.Q(review_project=project)
+                )
+
+                publication_requests_data = [
+                    {
+                        'id': pub_request.id,
+                        'status': pub_request.status,
+                        'comments': pub_request.comments,
+                        'reviewers': [
+                            {
+                                'username': reviewer.username,
+                                'email': reviewer.email,
+                                'first_name': reviewer.first_name,
+                                'last_name': reviewer.last_name,
+                            }
+                            for reviewer in pub_request.reviewers.all()
+                        ],
+                        'created_at': pub_request.created_at,
+                        'last_updated': pub_request.last_updated
+                    }
+                    for pub_request in publication_requests
+                ]
+                
             except ProjectsMetadata.DoesNotExist:
                 raise ApiException(f'Project {project_id} not found', status=404)
             
-            return JsonResponse(list(publication_requests), safe=False)
+            return JsonResponse({'response': publication_requests_data}, safe=False)
         
-        return JsonResponse([])
+        return JsonResponse({'response': []})
 
     @method_decorator(login_required, name='dispatch')
     def post(self, request):
@@ -46,22 +72,22 @@ def post(self, request):
         client = request.user.tapis_oauth.client
         
         source_workspace_id = data['projectId']
-        review_workspace_id = f"{source_workspace_id}-REVIEW"
+        review_workspace_id = f"{source_workspace_id}"
         source_system_id = f'{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{source_workspace_id}'
-        review_system_id = f"{settings.PORTAL_PROJECTS_SYSTEM_PREFIX}.{review_workspace_id}"
+        review_system_id = f"{settings.PORTAL_PROJECTS_REVIEW_SYSTEM_PREFIX}.{review_workspace_id}"
 
         with transaction.atomic():
             # Update authors for the source project 
-            source_project = ProjectsMetadata.objects.get(project_id=source_system_id)
-            source_project.metadata['authors'] = data['authors']
+            source_project = ProjectMetadata.get_project_by_id(source_system_id)
+            # TODO: use pydantic to validate data
+            source_project.value['authors'] = data['authors']
             source_project.save()
 
         system_id = create_publication_review_shared_workspace(client, source_workspace_id, source_system_id, review_workspace_id, 
                                                    review_system_id, data['title'], data['description'])
 
-
         # Start task to copy files and metadata
-        copy_files_and_metadata.apply_async(kwargs={
+        copy_graph_and_files.apply_async(kwargs={
             'user_access_token': client.access_token.access_token, 
             'source_workspace_id': source_workspace_id,
             'review_workspace_id': review_workspace_id,
diff --git a/server/portal/libs/agave/operations.py b/server/portal/libs/agave/operations.py
index f23844f99..0a70f523a 100644
--- a/server/portal/libs/agave/operations.py
+++ b/server/portal/libs/agave/operations.py
@@ -15,8 +15,8 @@
 from portal.apps.projects.models.metadata import ProjectsMetadata
 from portal.apps.datafiles.models import DataFilesMetadata
 from portal.apps import SCHEMA_MAPPING
-from portal.apps.projects.workspace_operations.project_meta_operations import (add_file_associations, create_entity_metadata, get_entity, 
-                                                                               get_file_association_entity, patch_file_association)
+from portal.apps.projects.workspace_operations.project_meta_operations import (add_file_associations, create_entity_metadata, create_file_obj, get_entity, get_file_obj, get_ordered_value, get_value, 
+                                                                               patch_file_association)
 from portal.apps._custom.drp import constants
 from portal.apps.projects.workspace_operations.graph_operations import add_node_to_project, get_root_node, get_node_from_path
 
@@ -91,19 +91,24 @@ def listing(client, system, path, offset=0, limit=100, *args, **kwargs):
                                          offset=int(offset),
                                          limit=int(limit))
         
-    folder_metadata = get_entity(system, path)
+    folder_entity_value = get_value(system, path)
 
     try:
         # Convert file objects to dicts for serialization.
-
         listing = []
 
         for f in raw_listing: 
-
-            entity = get_entity(system, f.path) if f.type == 'dir' else get_file_association_entity(system, f.path)
+            if f.type == 'dir':
+                value = get_value(system,f.path)
+                entity = get_entity(system, f.path)
+                uuid = entity.to_dict().get('uuid') if entity else None
+            else: 
+                file_obj = get_file_obj(system, f.path)
+                value = get_ordered_value(constants.FILE, file_obj.get('value')) if file_obj else None
+                uuid = file_obj.get('uuid') if file_obj else None
 
             listing.append({
-                'uuid': entity.to_dict().get('uuid') if entity else None,
+                'uuid': uuid,
                 'system': system,
                 'type': 'dir' if f.type == 'dir' else 'file',
                 'format': 'folder' if f.type == 'dir' else 'raw',
@@ -115,30 +120,15 @@ def listing(client, system, path, offset=0, limit=100, *args, **kwargs):
                 '_links': {
                     'self': {'href': f.url}
                 },
-                'metadata': entity.ordered_value if entity else None
+                'metadata': value if value else None
             })
-
-        # listing = list(map(lambda f: {
-        #     'system': system,
-        #     'type': 'dir' if f.type == 'dir' else 'file',
-        #     'format': 'folder' if f.type == 'dir' else 'raw',
-        #     'mimeType': f.mimeType,
-        #     'path': f.path,
-        #     'name': f.name,
-        #     'length': f.size,
-        #     'lastModified': f.lastModified,
-        #     '_links': {
-        #         'self': {'href': f.url}
-        #     },
-        #     'metadata': get_entity_metadata(system, f.path)
-        # }, raw_listing))
     except IndexError:
         # Return [] if the listing is empty.
         listing = []
 
     # Update Elasticsearch after each listing.
     tapis_listing_indexer.delay(listing)
-    return {'listing': listing, 'reachedEnd': len(listing) < int(limit), 'folder_metadata': folder_metadata.ordered_value if folder_metadata else None}
+    return {'listing': listing, 'reachedEnd': len(listing) < int(limit), 'folder_metadata': folder_entity_value}
 
 
 def iterate_listing(client, system, path, limit=100):
@@ -547,20 +537,9 @@ def upload(client, system, path, uploaded_file, metadata=None):
 
     if metadata is not None and getattr(constants, metadata.get('data_type').upper(), None): 
         
-        new_meta = create_entity_metadata(system, getattr(constants, metadata.get('data_type').upper()), {
-            **metadata,
-        })
-
         parent_node = get_node_from_path(system, path)
 
-        file_obj = FileObj(
-            system=system,
-            name=uploaded_file.name,
-            path=dest_path,
-            type='file',
-            length=uploaded_file.size,
-            uuid=new_meta.uuid
-        )
+        file_obj = create_file_obj(system, uploaded_file.name, uploaded_file.size, dest_path, metadata)
 
         if parent_node and parent_node['id'] != 'NODE_ROOT':
             add_file_associations(parent_node['uuid'], [file_obj])
diff --git a/server/portal/settings/settings.py b/server/portal/settings/settings.py
index 70f83ad94..b2b270599 100644
--- a/server/portal/settings/settings.py
+++ b/server/portal/settings/settings.py
@@ -571,6 +571,15 @@
 PORTAL_PROJECTS_ROOT_HOST = settings_custom.\
     _PORTAL_PROJECTS_ROOT_HOST
 
+PORTAL_PROJECTS_REVIEW_SYSTEM_PREFIX = settings_custom.\
+    _PORTAL_PROJECTS_REVIEW_SYSTEM_PREFIX
+
+PORTAL_PROJECTS_REVIEW_ROOT_DIR = settings_custom.\
+    _PORTAL_PROJECTS_REVIEW_ROOT_DIR
+
+PORTAL_PROJECTS_ROOT_REVIEW_SYSTEM_NAME = settings_custom.\
+    _PORTAL_PROJECTS_ROOT_REVIEW_SYSTEM_NAME
+
 PORTAL_PROJECTS_PRIVATE_KEY = settings_secret.\
     _PORTAL_PROJECTS_PRIVATE_KEY