add features for delete and api updates

cameo/src/main/java/org/openmbee/mms/cameo/services/CameoNodeService.java

@@ -96,7 +96,7 @@ public MountJson getProjectUsages(String projectId, String refId, String commitI
             boolean restrictOnPermissions) {
         saw.add(Pair.of(projectId, refId));
         List<ElementJson> mounts = getNodePersistence().findAllByNodeType(projectId, refId, commitId,
-            CameoNodeType.PROJECTUSAGE.getValue());
+            CameoNodeType.PROJECTUSAGE.getValue(), false);
 
         Authentication auth = SecurityContextHolder.getContext().getAuthentication();
         List<MountJson> mountValues = new ArrayList<>();

cameo/src/main/java/org/openmbee/mms/cameo/services/CameoViewService.java

@@ -19,6 +19,7 @@
 import org.openmbee.mms.core.objects.ElementsResponse;
 import org.openmbee.mms.core.services.NodeChangeInfo;
 import org.openmbee.mms.core.services.NodeGetInfo;
+import org.openmbee.mms.crud.CrudConstants;
 import org.openmbee.mms.crud.domain.JsonDomain;
 import org.openmbee.mms.json.ElementJson;
 import org.openmbee.mms.view.services.PropertyData;
@@ -30,9 +31,10 @@ public class CameoViewService extends CameoNodeService implements ViewService {
 
     @Override
     public ElementsResponse getDocuments(String projectId, String refId, Map<String, String> params) {
+        Boolean deleted = Boolean.parseBoolean(params.getOrDefault(CrudConstants.DELETED, "false"));
         String commitId = params.getOrDefault(CameoConstants.COMMITID, null);
         List<ElementJson> documents = getNodePersistence().findAllByNodeType(projectId, refId,
-            commitId, CameoNodeType.DOCUMENT.getValue());
+            commitId, CameoNodeType.DOCUMENT.getValue(), deleted);
         ElementsResponse res = this.getViews(projectId, refId, buildRequestFromJsons(documents), params);
         for (ElementJson e: res.getElements()) {
             Optional<ElementJson> parent = getFirstRelationshipOfType(projectId, refId, commitId, e,
@@ -83,9 +85,10 @@ public void addChildViews(ElementsResponse res, Map<String, String> params) {
     }
 
     public ElementsResponse getGroups(String projectId, String refId, Map<String, String> params) {
+        Boolean deleted = Boolean.parseBoolean(params.getOrDefault(CrudConstants.DELETED, "false"));
         String commitId = params.getOrDefault(CameoConstants.COMMITID, null);
         List<ElementJson> groups = getNodePersistence().findAllByNodeType(projectId, refId, commitId,
-            CameoNodeType.GROUP.getValue());
+            CameoNodeType.GROUP.getValue(), deleted);
 
         ElementsResponse res = new ElementsResponse().setElements(groups);
         for (ElementJson e: groups) {

core/src/main/java/org/openmbee/mms/core/config/Constants.java

@@ -24,6 +24,8 @@ public class Constants {
     public static final String FALSE = "false";
     public static final String LIMIT = "limit";
 
+    public static final String HOME_SUFFIX = "-home";
+
     public static final String MASTER_BRANCH = "master";
 
     public static final Pattern BRANCH_ID_VALID_PATTERN = Pattern.compile("^[\\w-]+$");

core/src/main/java/org/openmbee/mms/core/dao/NodePersistence.java

@@ -23,13 +23,13 @@ public interface NodePersistence {
 
     NodeGetInfo findById(String projectId, String refId, String commitId, String elementId);
 
-    List<ElementJson> findAllByNodeType(String projectId, String refId, String commitId, int nodeType);
+    List<ElementJson> findAllByNodeType(String projectId, String refId, String commitId, int nodeType, Boolean deleted);
 
     NodeGetInfo findAll(String projectId, String refId, String commitId, List<ElementJson> elements);
 
-    List<ElementJson> findAll(String projectId, String refId, String commitId);
+    List<ElementJson> findAll(String projectId, String refId, String commitId, Boolean deleted);
 
-    void streamAllAtCommit(String projectId, String refId, String commitId, OutputStream outputStream, String separator);
+    void streamAllAtCommit(String projectId, String refId, String commitId, OutputStream outputStream, String separator, Boolean deleted);
 
     void branchElements(RefJson parentBranch, CommitJson parentCommit, RefJson targetBranch);
 }

crud/src/main/java/org/openmbee/mms/crud/CrudConstants.java

@@ -13,4 +13,5 @@ public class CrudConstants {
     public static final String ORG = "Org";
     public static final String CREATED = "created";
     public static final String CREATING = "creating";
+    public static final String DELETED = "deleted";
 }

crud/src/main/java/org/openmbee/mms/crud/controllers/orgs/OrgsController.java

@@ -16,9 +16,11 @@
 import org.openmbee.mms.core.objects.OrganizationsRequest;
 import org.openmbee.mms.core.objects.OrganizationsResponse;
 import org.openmbee.mms.core.objects.Rejection;
+import org.openmbee.mms.core.services.ProjectService;
 import org.openmbee.mms.crud.CrudConstants;
 import org.openmbee.mms.crud.controllers.BaseController;
 import org.openmbee.mms.crud.services.OrgDeleteService;
+import org.openmbee.mms.crud.services.ProjectDeleteService;
 import org.openmbee.mms.core.exceptions.BadRequestException;
 import org.openmbee.mms.core.exceptions.NotFoundException;
 import org.openmbee.mms.json.OrgJson;
@@ -45,6 +47,8 @@ public class OrgsController extends BaseController {
 
     OrgDeleteService orgDeleteService;
 
+    ProjectDeleteService projectDeleteService;
+
     @Autowired
     public OrgsController(OrgPersistence organizationRepository) {
         this.organizationRepository = organizationRepository;
@@ -55,14 +59,19 @@ public void setOrgDeleteService(OrgDeleteService orgDeleteService) {
         this.orgDeleteService = orgDeleteService;
     }
 
+    @Autowired
+    public void setProjectDeleteService(ProjectDeleteService projectDeleteService) {
+        this.projectDeleteService = projectDeleteService;
+    }
+
     @GetMapping
     public OrganizationsResponse getAllOrgs(@RequestParam(required = false, defaultValue = Constants.FALSE) boolean includeArchived, Authentication auth) {
 
         OrganizationsResponse response = new OrganizationsResponse();
         Collection<OrgJson> allOrgs = organizationRepository.findAll();
         for (OrgJson org : allOrgs) {
             if (mss.hasOrgPrivilege(auth, org.getId(), Privileges.ORG_READ.name(), true) 
-                && (!Constants.TRUE.equals(org.getIsArchived()) || includeArchived)) {
+                && (!org.isArchived() || includeArchived)) {
                 response.getOrgs().add(org);
             }
         }
@@ -119,19 +128,31 @@ public OrganizationsResponse createOrUpdateOrgs(
                     org.setCreator(auth.getName());
                 }
             }
-            if (org.getIsArchived() != null && !org.getIsArchived().equals(o.getIsArchived())) {
-                List<ProjectJson> orgProjs = projectPersistence.findAllByOrgId(org.getId()).stream().collect(Collectors.toList());
-                //Un/Archive all projects contained by org
-                for (ProjectJson proj: orgProjs) {
-                    proj.setIsArchived(org.getIsArchived());
-                    projectPersistence.update(proj);
-                }
-            }
             logger.info("Saving organization: {}", org.getId());
             OrgJson saved = organizationRepository.save(org);
             if (newOrg) {
+                // Initialize Org Permissions
                 permissionService.initOrgPerms(org.getId(), auth.getName());
+
+                createOrgHome(org);
+            } else {
+                Collection<ProjectJson> orgProjs = projectPersistence.findAllByOrgId(org.getId());
+                if (!orgProjs.stream().map(ProjectJson::getId).collect(Collectors.toList()).contains(org.getId() + Constants.HOME_SUFFIX)) {
+                    if (org.isArchived() == null) {
+                        org.setIsArchived(o.isArchived());
+                    }
+                    createOrgHome(org);
+                }
+                for (ProjectJson proj: orgProjs) {
+                    if (org.isArchived() != null && !org.isArchived().equals(o.isArchived())) {
+                        //Un/Archive all projects contained by org
+
+                        proj.setIsArchived(org.isArchived());
+                        projectPersistence.update(proj);
+                    }
+                }
             }
+
             response.getOrgs().add(saved);
         }
         if (orgPost.getOrgs().size() == 1) {
@@ -151,10 +172,46 @@ public OrganizationsResponse deleteOrg(
         if (!orgOption.isPresent()) {
             throw new NotFoundException(response.addMessage("Organization not found."));
         }
-        if (!projectPersistence.findAllByOrgId(orgId).isEmpty() && hard) {
-            throw new BadRequestException(response.addMessage("Cannot Hard Delete Organization that contains Projects"));
+        if (hard) {
+            List<ProjectJson> orgProjs = projectPersistence.findAllByOrgId(orgId).stream().collect(Collectors.toList());
+            if (!orgProjs.isEmpty()) {
+                if (orgProjs.size() == 1 && orgProjs.get(0).getId().equals(orgId + Constants.HOME_SUFFIX)) {
+                    projectDeleteService.deleteProject(orgId + Constants.HOME_SUFFIX, hard);
+                } else {
+                    throw new BadRequestException(response.addMessage("Cannot Hard Delete Organization that contains Projects other than its home"));
+                }
+            }
         }
-
         return orgDeleteService.deleteOrg(orgId, hard);
     }
+
+    private ProjectJson createOrgHome(OrgJson org) {
+        // Create New Org "Home" Project
+        ProjectJson homeProj = new ProjectJson();
+        homeProj.setCreated(org.getCreated());
+        homeProj.setType(CrudConstants.PROJECT);
+        homeProj.setCreator(org.getCreator());
+        homeProj.setId(org.getId() + Constants.HOME_SUFFIX);
+        homeProj.setOrgId(org.getId());
+        homeProj.setIsArchived(org.isArchived());
+        homeProj.setName((!org.getName().isEmpty() ? org.getName() : org.getId()) + " Home");
+
+        ProjectService ps = getProjectService(homeProj);
+        ProjectJson savedProj = ps.create(homeProj);
+        permissionService.initProjectPerms(homeProj.getId(), true, org.getCreator());
+        return savedProj;
+    }
+
+    private ProjectService getProjectService(ProjectJson json) {
+        String type = json.getProjectType();
+        if (type == null || type.isEmpty()) {
+            try {
+                type = this.getProjectType(json.getProjectId());
+            } catch (NotFoundException e) {
+                type = CrudConstants.DEFAULT;
+            }
+            json.setProjectType(type);
+        }
+        return serviceFactory.getProjectService(type);
+    }
 }

crud/src/main/java/org/openmbee/mms/crud/controllers/projects/ProjectsController.java

@@ -45,7 +45,7 @@ public void setProjectSchemas(ProjectSchemas projectSchemas) {
     }
 
     @GetMapping
-    public ProjectsResponse getAllProjects(Authentication auth, @RequestParam(required = false) String orgId, @RequestParam(required = false, defaultValue = Constants.FALSE) boolean includeArchived) {
+    public ProjectsResponse getAllProjects(Authentication auth, @RequestParam(required = false) String orgId, @RequestParam(required = false, defaultValue = Constants.FALSE) boolean includeArchived, @RequestParam(required = false, defaultValue = Constants.FALSE) boolean includeHomes) {
 
         ProjectsResponse response = new ProjectsResponse();
         Collection<ProjectJson> allProjects =
@@ -54,7 +54,7 @@ public ProjectsResponse getAllProjects(Authentication auth, @RequestParam(requir
             try {
                 if (mss.hasProjectPrivilege(auth, projectJson.getProjectId(), Privileges.PROJECT_READ.name(), true)
                         && projectJson.getDocId() != null
-                        && (!Constants.TRUE.equals(projectJson.getIsArchived()) || includeArchived)) {
+                        && (!projectJson.isArchived() || includeArchived) && (!projectJson.getId().endsWith(Constants.HOME_SUFFIX) || includeHomes)) {
                     response.getProjects().add(projectJson);
                 }
             } catch(NotFoundException ex) {

crud/src/main/java/org/openmbee/mms/crud/domain/DefaultNodeUpdateFilter.java

@@ -22,7 +22,7 @@ public class DefaultNodeUpdateFilter implements NodeUpdateFilter {
     @Override
     public boolean filterUpdate(NodeChangeInfo info, ElementJson updated, ElementJson existing) {
         if (!info.getOverwrite()) {
-            if (Constants.TRUE.equals(existing.getIsArchived()) || isUpdated(updated, existing, info)) {
+            if ((existing.isArchived() != null && existing.isArchived()) || isUpdated(updated, existing, info)) {
                 return diffUpdateJson(updated, existing, info);
             } else {
                 return false;

crud/src/main/java/org/openmbee/mms/crud/domain/NodeChangeDomain.java

@@ -56,6 +56,7 @@ public void processElementAdded(NodeChangeInfo info, ElementJson element) {
 
         element.setCreator(commitJson.getCreator()); //Only set on creation of new element
         element.setCreated(commitJson.getCreated());
+        element.setIsArchived(false);
     }
 
     public boolean processElementUpdated(NodeChangeInfo info, ElementJson element, ElementJson existing) {

crud/src/main/java/org/openmbee/mms/crud/services/DefaultNodeService.java

@@ -59,7 +59,7 @@ public void setEventPublisher(Collection<EventService> eventPublisher) {
     @Override
     public void readAsStream(String projectId, String refId, Map<String, String> params, OutputStream stream,
             String accept) throws IOException {
-
+        Boolean deleted = Boolean.parseBoolean(params.getOrDefault(CrudConstants.DELETED, "false"));
         String commitId = params.getOrDefault(CrudConstants.COMMITID, null);
 
         if (commitId != null && !commitId.isEmpty()) {
@@ -81,7 +81,7 @@ public void readAsStream(String projectId, String refId, Map<String, String> par
             separator = ",";
         }
 
-        nodePersistence.streamAllAtCommit(projectId, refId, commitId, stream, separator);
+        nodePersistence.streamAllAtCommit(projectId, refId, commitId, stream, separator, deleted);
 
         if (!"application/x-ndjson".equals(accept)) {
             stream.write("]}".getBytes(StandardCharsets.UTF_8));
@@ -99,6 +99,7 @@ public ElementsResponse read(String projectId, String refId, String id,
             ElementsRequest req = buildRequest(id);
             return read(projectId, refId, req, params);
         }
+        Boolean deleted = Boolean.parseBoolean(params.getOrDefault(CrudConstants.DELETED, "false"));
         String commitId = params.getOrDefault(CrudConstants.COMMITID, null);
         if (commitId == null) {
             Optional<CommitJson> commitJson = commitPersistence.findLatestByProjectAndRef(projectId, refId);
@@ -111,7 +112,7 @@ public ElementsResponse read(String projectId, String refId, String id,
         ElementsResponse response = new ElementsResponse();
         logger.debug("No ElementId given");
 
-        List<ElementJson> nodes = nodePersistence.findAll(projectId, refId, commitId);
+        List<ElementJson> nodes = nodePersistence.findAll(projectId, refId, commitId, deleted);
         response.getElements().addAll(nodes);
         response.getElements().forEach(v -> v.setRefId(refId));
         response.setCommitId(commitId);

crud/src/main/java/org/openmbee/mms/crud/services/DefaultProjectService.java

@@ -63,7 +63,7 @@ public ProjectJson create(ProjectJson project) {
         try {
             //TODO Transaction start
             ProjectJson savedProjectJson = projectPersistence.save(project);
-            savedProjectJson.setIsArchived("false");
+            savedProjectJson.setIsArchived(false);
             //create and save master branch. We're combining operations with the branch unifiedDAO.
             branchPersistence.save(createMasterRefJson(savedProjectJson));
             //TODO Transaction commit
@@ -112,7 +112,7 @@ public RefJson createMasterRefJson(ProjectJson project) {
         branchJson.setCreated(project.getCreated());
         branchJson.setProjectId(project.getId());
         branchJson.setCreator(project.getCreator());
-        branchJson.setIsArchived("false");
+        branchJson.setIsArchived(false);
         return branchJson;
     }
 }

crud/src/main/java/org/openmbee/mms/crud/services/OrgDeleteService.java

@@ -73,7 +73,7 @@ public OrganizationsResponse deleteOrg(String orgId, boolean hard) {
                 projectDeleteService.deleteProject(proj.getId(), false);
             }
             orgPersistence.archiveById(orgId);
-            orgJson.setIsArchived(Constants.TRUE);
+            orgJson.setIsArchived(true);
         }
 
 

crud/src/main/java/org/openmbee/mms/crud/services/ProjectDeleteService.java

@@ -54,7 +54,7 @@ public ProjectsResponse deleteProject(String projectId, boolean hard) {
             projectJson.setDeleted(true);
         } else {
             projectPersistence.archiveById(projectId);
-            projectJson.setIsArchived(Constants.TRUE);
+            projectJson.setIsArchived(true);
         }
 
 

elastic/src/main/java/org/openmbee/mms/elastic/ProjectElasticImpl.java

@@ -38,7 +38,7 @@ public void create(String projectId) {
         ProjectJson projectJson = newInstance();
         projectJson.setProjectId(projectId);
         projectJson.setType("default");
-        projectJson.setIsArchived("false");
+        projectJson.setIsArchived(true);
         create(projectJson);
     }
 

federatedpersistence/src/main/java/org/openmbee/mms/federatedpersistence/dao/FederatedBranchPersistence.java

@@ -60,7 +60,7 @@ public RefJson save(RefJson refJson) {
         scopedBranch.setTimestamp(Formats.FORMATTER.parse(refJson.getCreated(), Instant::from));
         scopedBranch.setParentRefId(refJson.getParentRefId());
         scopedBranch.setDocId(refJson.getDocId());
-        scopedBranch.setDeleted(Boolean.parseBoolean(refJson.getIsArchived()));
+        scopedBranch.setDeleted(refJson.isArchived());
 
         //Setup global Branch object
         Optional<Project> project = projectDAO.findByProjectId(refJson.getProjectId());
@@ -104,8 +104,8 @@ public RefJson update(RefJson refJson) {
         ContextHolder.setContext(refJson.getProjectId());
         Optional<Branch> optionalExisting = branchDAO.findByBranchId(refJson.getId());
         Branch existing = optionalExisting.get();
-        if (refJson.getIsArchived() != null) {
-            existing.setDeleted(Boolean.parseBoolean(refJson.getIsArchived()));
+        if (refJson.isArchived() != null) {
+            existing.setDeleted(refJson.isArchived());
         }
 
         branchDAO.save(existing);

federatedpersistence/src/main/java/org/openmbee/mms/federatedpersistence/dao/FederatedNodePersistence.java

@@ -110,14 +110,14 @@ public NodeGetInfo findById(String projectId, String refId, String commitId, Str
     }
 
     @Override
-    public List<ElementJson> findAllByNodeType(String projectId, String refId, String commitId, int nodeType) {
+    public List<ElementJson> findAllByNodeType(String projectId, String refId, String commitId, int nodeType, Boolean deleted) {
         ContextHolder.setContext(projectId, refId);
         String commitToPass = checkCommit(refId, commitId);
         List<Node> nodes;
         if (commitToPass != null) {
             nodes = nodeDAO.findAllByNodeType(nodeType);
         } else {
-            nodes = nodeDAO.findAllByDeletedAndNodeType(false, nodeType);
+            nodes = nodeDAO.findAllByDeletedAndNodeType(deleted, nodeType);
         }
         return new ArrayList<>(getNodeGetDomain().processGetJsonFromNodes(nodes, commitToPass).getActiveElementMap().values());
     }
@@ -130,28 +130,28 @@ public NodeGetInfo findAll(String projectId, String refId, String commitId, List
     }
 
     @Override
-    public List<ElementJson> findAll(String projectId, String refId, String commitId) {
+    public List<ElementJson> findAll(String projectId, String refId, String commitId, Boolean deleted) {
         ContextHolder.setContext(projectId, refId);
         List<Node> nodes;
         String commitToPass = checkCommit(refId, commitId);
         if (commitToPass != null) {
             nodes = nodeDAO.findAll();
         } else {
-            nodes = nodeDAO.findAllByDeleted(false);
+            nodes = nodeDAO.findAllByDeleted(deleted);
         }
         return new ArrayList<>(getNodeGetDomain().processGetJsonFromNodes(nodes, commitToPass).getActiveElementMap().values());
     }
 
 
     @Override
-    public void streamAllAtCommit(String projectId, String refId, String commitId, OutputStream stream, String separator) {
+    public void streamAllAtCommit(String projectId, String refId, String commitId, OutputStream stream, String separator, Boolean deleted) {
         ContextHolder.setContext(projectId, refId);
         List<Node> nodes;
         final String commitToPass = checkCommit(refId, commitId);
         if (commitToPass != null) {
             nodes = nodeDAO.findAll();
         } else {
-            nodes = nodeDAO.findAllByDeleted(false);
+            nodes = nodeDAO.findAllByDeleted(deleted);
         }
         AtomicInteger counter = new AtomicInteger();
         batches(nodes, streamLimit).forEach(ns -> {