Merge pull request #245 from TAMULib/dspace-7_x-sprint5-244-proxy-lic…

…ense-step-extrenal-source-regression

Prevent proxy license step from invoking upload during start submission from external source

dspace/modules/server/src/main/java/org/dspace/app/rest/repository/WorkspaceItemRestRepository.java

@@ -0,0 +1,395 @@
+/**
+ * The contents of this file are subject to the license and copyright
+ * detailed in the LICENSE and NOTICE files at the root of the source
+ * tree and available online at
+ *
+ * http://www.dspace.org/license/
+ */
+package org.dspace.app.rest.repository;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.sql.SQLException;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.UUID;
+import javax.servlet.http.HttpServletRequest;
+
+import org.apache.commons.lang3.StringUtils;
+import org.apache.logging.log4j.Logger;
+import org.dspace.app.rest.Parameter;
+import org.dspace.app.rest.SearchRestMethod;
+import org.dspace.app.rest.converter.WorkspaceItemConverter;
+import org.dspace.app.rest.exception.DSpaceBadRequestException;
+import org.dspace.app.rest.exception.RepositoryMethodNotImplementedException;
+import org.dspace.app.rest.exception.UnprocessableEntityException;
+import org.dspace.app.rest.model.ErrorRest;
+import org.dspace.app.rest.model.WorkspaceItemRest;
+import org.dspace.app.rest.model.patch.Operation;
+import org.dspace.app.rest.model.patch.Patch;
+import org.dspace.app.rest.repository.handler.service.UriListHandlerService;
+import org.dspace.app.rest.submit.SubmissionService;
+import org.dspace.app.rest.submit.UploadableStep;
+import org.dspace.app.rest.utils.Utils;
+import org.dspace.app.util.SubmissionConfig;
+import org.dspace.app.util.SubmissionConfigReaderException;
+import org.dspace.app.util.SubmissionStepConfig;
+import org.dspace.authorize.AuthorizeException;
+import org.dspace.authorize.service.AuthorizeService;
+import org.dspace.content.Collection;
+import org.dspace.content.Item;
+import org.dspace.content.MetadataValue;
+import org.dspace.content.WorkspaceItem;
+import org.dspace.content.service.BitstreamFormatService;
+import org.dspace.content.service.BitstreamService;
+import org.dspace.content.service.CollectionService;
+import org.dspace.content.service.ItemService;
+import org.dspace.content.service.WorkspaceItemService;
+import org.dspace.core.Constants;
+import org.dspace.core.Context;
+import org.dspace.eperson.EPerson;
+import org.dspace.eperson.EPersonServiceImpl;
+import org.dspace.event.Event;
+import org.dspace.importer.external.datamodel.ImportRecord;
+import org.dspace.importer.external.exception.FileMultipleOccurencesException;
+import org.dspace.importer.external.metadatamapping.MetadatumDTO;
+import org.dspace.importer.external.service.ImportService;
+import org.dspace.services.ConfigurationService;
+import org.dspace.submit.factory.SubmissionServiceFactory;
+import org.dspace.submit.service.SubmissionConfigService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
+import org.springframework.security.access.AccessDeniedException;
+import org.springframework.security.access.prepost.PreAuthorize;
+import org.springframework.stereotype.Component;
+import org.springframework.web.multipart.MultipartFile;
+
+
+/**
+ * This is the repository responsible to manage WorkspaceItem Rest object
+ *
+ * @author Andrea Bollini (andrea.bollini at 4science.it)
+ * @author Pasquale Cavallo (pasquale.cavallo at 4science.it)
+ */
+@Component(WorkspaceItemRest.CATEGORY + "." + WorkspaceItemRest.NAME)
+public class WorkspaceItemRestRepository extends DSpaceRestRepository<WorkspaceItemRest, Integer>
+    implements ReloadableEntityObjectRepository<WorkspaceItem, Integer> {
+
+    public static final String OPERATION_PATH_SECTIONS = "sections";
+
+    private static final Logger log = org.apache.logging.log4j.LogManager.getLogger(WorkspaceItemRestRepository.class);
+
+    @Autowired
+    WorkspaceItemService wis;
+
+    @Autowired
+    ItemService itemService;
+
+    @Autowired
+    BitstreamService bitstreamService;
+
+    @Autowired
+    BitstreamFormatService bitstreamFormatService;
+
+    @Autowired
+    ConfigurationService configurationService;
+
+    @Autowired
+    WorkspaceItemConverter workspaceItemConverter;
+
+    @Autowired
+    SubmissionService submissionService;
+
+    @Autowired
+    EPersonServiceImpl epersonService;
+
+    @Autowired
+    CollectionService collectionService;
+
+    @Autowired
+    AuthorizeService authorizeService;
+
+    @Autowired
+    ImportService importService;
+
+    @Autowired
+    private UriListHandlerService uriListHandlerService;
+
+    private SubmissionConfigService submissionConfigService;
+
+    public WorkspaceItemRestRepository() throws SubmissionConfigReaderException {
+        submissionConfigService = SubmissionServiceFactory.getInstance().getSubmissionConfigService();
+    }
+
+    @PreAuthorize("hasPermission(#id, 'WORKSPACEITEM', 'READ')")
+    @Override
+    public WorkspaceItemRest findOne(Context context, Integer id) {
+        WorkspaceItem witem = null;
+        try {
+            witem = wis.find(context, id);
+        } catch (SQLException e) {
+            throw new RuntimeException(e.getMessage(), e);
+        }
+        if (witem == null) {
+            return null;
+        }
+        return converter.toRest(witem, utils.obtainProjection());
+    }
+
+    @PreAuthorize("hasAuthority('ADMIN')")
+    @Override
+    public Page<WorkspaceItemRest> findAll(Context context, Pageable pageable) {
+        try {
+            long total = wis.countTotal(context);
+            List<WorkspaceItem> witems = wis.findAll(context, pageable.getPageSize(),
+                    Math.toIntExact(pageable.getOffset()));
+            return converter.toRestPage(witems, pageable, total, utils.obtainProjection());
+        } catch (SQLException e) {
+            throw new RuntimeException(e.getMessage(), e);
+        }
+    }
+
+    @PreAuthorize("hasPermission(#submitterID, 'EPERSON', 'READ')")
+    @SearchRestMethod(name = "findBySubmitter")
+    public Page<WorkspaceItemRest> findBySubmitter(@Parameter(value = "uuid", required = true) UUID submitterID,
+            Pageable pageable) {
+        try {
+            Context context = obtainContext();
+            EPerson ep = epersonService.find(context, submitterID);
+            long total = wis.countByEPerson(context, ep);
+            List<WorkspaceItem> witems = wis.findByEPerson(context, ep, pageable.getPageSize(),
+                    Math.toIntExact(pageable.getOffset()));
+            return converter.toRestPage(witems, pageable, total, utils.obtainProjection());
+        } catch (SQLException e) {
+            throw new RuntimeException(e.getMessage(), e);
+        }
+    }
+
+    @Override
+    protected WorkspaceItemRest createAndReturn(Context context) throws SQLException, AuthorizeException {
+        WorkspaceItem source = submissionService.createWorkspaceItem(context, getRequestService().getCurrentRequest());
+        return converter.toRest(source, utils.obtainProjection());
+    }
+
+    @Override
+    public Class<WorkspaceItemRest> getDomainClass() {
+        return WorkspaceItemRest.class;
+    }
+
+    @PreAuthorize("hasPermission(#id, 'WORKSPACEITEM', 'WRITE')")
+    @Override
+    public WorkspaceItemRest upload(HttpServletRequest request, String apiCategory, String model, Integer id,
+                                    MultipartFile file) throws SQLException {
+
+        Context context = obtainContext();
+        WorkspaceItemRest wsi = findOne(context, id);
+        WorkspaceItem source = wis.find(context, id);
+        List<ErrorRest> errors = submissionService.uploadFileToInprogressSubmission(context, request, wsi, source,
+                file);
+        wsi = converter.toRest(source, utils.obtainProjection());
+
+        if (!errors.isEmpty()) {
+            wsi.getErrors().addAll(errors);
+        }
+
+        context.commit();
+        return wsi;
+    }
+
+    @PreAuthorize("hasPermission(#id, 'WORKSPACEITEM', 'WRITE')")
+    @Override
+    public void patch(Context context, HttpServletRequest request, String apiCategory, String model, Integer id,
+                      Patch patch) throws SQLException, AuthorizeException {
+        List<Operation> operations = patch.getOperations();
+        WorkspaceItemRest wsi = findOne(context, id);
+        WorkspaceItem source = wis.find(context, id);
+        for (Operation op : operations) {
+            //the value in the position 0 is a null value
+            String[] path = op.getPath().substring(1).split("/", 3);
+            if (OPERATION_PATH_SECTIONS.equals(path[0])) {
+                String section = path[1];
+                submissionService.evaluatePatchToInprogressSubmission(context, request, source, wsi, section, op);
+            } else {
+                throw new DSpaceBadRequestException(
+                    "Patch path operation need to starts with '" + OPERATION_PATH_SECTIONS + "'");
+            }
+        }
+        wis.update(context, source);
+    }
+
+    @PreAuthorize("hasPermission(#id, 'WORKSPACEITEM', 'DELETE')")
+    @Override
+    protected void delete(Context context, Integer id) throws AuthorizeException {
+        WorkspaceItem witem = null;
+        try {
+            witem = wis.find(context, id);
+            wis.deleteAll(context, witem);
+            context.addEvent(new Event(Event.DELETE, Constants.ITEM, witem.getItem().getID(), null,
+                itemService.getIdentifiers(context, witem.getItem())));
+        } catch (SQLException | IOException e) {
+            log.error(e.getMessage(), e);
+        }
+    }
+
+    @Override
+    public Iterable<WorkspaceItemRest> upload(Context context, HttpServletRequest request,
+            List<MultipartFile> uploadfiles)
+        throws SQLException, FileNotFoundException, IOException, AuthorizeException {
+        List<WorkspaceItemRest> results = new ArrayList<>();
+
+        String uuid = request.getParameter("owningCollection");
+        if (StringUtils.isBlank(uuid)) {
+            uuid = configurationService.getProperty("submission.default.collection");
+        }
+        Collection collection = null;
+        if (StringUtils.isNotBlank(uuid)) {
+            collection = collectionService.find(context, UUID.fromString(uuid));
+        } else {
+            collection = collectionService.findAuthorizedOptimized(context, Constants.ADD).get(0);
+        }
+
+        SubmissionConfig submissionConfig =
+            submissionConfigService.getSubmissionConfigByCollection(collection.getHandle());
+        List<WorkspaceItem> result = null;
+        List<ImportRecord> records = new ArrayList<>();
+        try {
+            for (MultipartFile mpFile : uploadfiles) {
+                File file = Utils.getFile(mpFile, "upload-loader", "filedataloader");
+                try {
+                    ImportRecord record = importService.getRecord(file, mpFile.getOriginalFilename());
+                    if (record != null) {
+                        records.add(record);
+                        break;
+                    }
+                } catch (Exception e) {
+                    log.error("Error processing data", e);
+                    throw e;
+                } finally {
+                    file.delete();
+                }
+            }
+        } catch (FileMultipleOccurencesException e) {
+            throw new UnprocessableEntityException("Too many entries in file");
+        } catch (Exception e) {
+            log.error("Error importing metadata", e);
+        }
+        WorkspaceItem source = submissionService.
+            createWorkspaceItem(context, getRequestService().getCurrentRequest());
+        merge(context, records, source);
+        result = new ArrayList<>();
+        result.add(source);
+
+        //perform upload of bitstream if there is exact one result and convert workspaceitem to entity rest
+        if (!result.isEmpty()) {
+            for (WorkspaceItem wi : result) {
+                List<ErrorRest> errors = new ArrayList<ErrorRest>();
+                wi.setMultipleFiles(uploadfiles.size() > 1);
+                //load bitstream into bundle ORIGINAL only if there is one result (approximately this is the
+                // right behaviour for pdf file but not for other bibliographic format e.g. bibtex)
+                if (result.size() == 1) {
+                    for (int i = 0; i < submissionConfig.getNumberOfSteps(); i++) {
+                        SubmissionStepConfig stepConfig = submissionConfig.getStep(i);
+                        ClassLoader loader = this.getClass().getClassLoader();
+                        Class stepClass;
+                        try {
+                            stepClass = loader.loadClass(stepConfig.getProcessingClassName());
+                            Object stepInstance = stepClass.newInstance();
+                            // TAMU Customization - proxy license step - respect exclusivity of uploadable step
+                            if (UploadableStep.class.isAssignableFrom(stepClass)
+                                && !((UploadableStep) stepInstance).isExclusiveMatchingStepId()) {
+                            // if (UploadableStep.class.isAssignableFrom(stepClass)) {
+                                UploadableStep uploadableStep = (UploadableStep) stepInstance;
+                                for (MultipartFile mpFile : uploadfiles) {
+                                    ErrorRest err = uploadableStep.upload(context,
+                                        submissionService, stepConfig, wi, mpFile);
+                                    if (err != null) {
+                                        errors.add(err);
+                                    }
+                                }
+                            }
+                        } catch (Exception e) {
+                            log.error(e.getMessage(), e);
+                        }
+                    }
+                }
+                WorkspaceItemRest wsi = converter.toRest(wi, utils.obtainProjection());
+                if (result.size() == 1) {
+                    if (!errors.isEmpty()) {
+                        wsi.getErrors().addAll(errors);
+                    }
+                }
+                results.add(wsi);
+            }
+        }
+        return results;
+    }
+
+    @Override
+    protected WorkspaceItemRest createAndReturn(Context context, List<String> stringList)
+        throws AuthorizeException, SQLException, RepositoryMethodNotImplementedException {
+
+        HttpServletRequest req = getRequestService().getCurrentRequest().getHttpServletRequest();
+        WorkspaceItem workspaceItem = uriListHandlerService.handle(context, req, stringList, WorkspaceItem.class);
+        return converter.toRest(workspaceItem, utils.obtainProjection());
+    }
+
+    /**
+     * This is a search method that will return the WorkspaceItemRest object found through the UUID of an item. It'll
+     * find the Item through the given UUID and try to resolve the WorkspaceItem relevant for that item and return it.
+     * It'll return a 401/403 if the current user isn't allowed to view the WorkspaceItem.
+     * It'll return a 204 if nothing was found
+     * @param itemUuid  The UUID for the Item to be used
+     * @param pageable  The pageable if present
+     * @return          The resulting WorkspaceItem object
+     */
+    @SearchRestMethod(name = "item")
+    public WorkspaceItemRest findByItemUuid(@Parameter(value = "uuid", required = true) UUID itemUuid,
+                                            Pageable pageable) {
+        try {
+            Context context = obtainContext();
+            Item item = itemService.find(context, itemUuid);
+            WorkspaceItem workspaceItem = wis.findByItem(context, item);
+            if (workspaceItem == null) {
+                return null;
+            }
+            if (!authorizeService.authorizeActionBoolean(context, workspaceItem.getItem(), Constants.READ)) {
+                throw new AccessDeniedException("The current user does not have rights to view the WorkflowItem");
+            }
+            return converter.toRest(workspaceItem, utils.obtainProjection());
+        } catch (SQLException e) {
+            throw new RuntimeException(e.getMessage(), e);
+        }
+    }
+
+    @Override
+    public WorkspaceItem findDomainObjectByPk(Context context, Integer id) throws SQLException {
+        return wis.find(context, id);
+    }
+
+    @Override
+    public Class<Integer> getPKClass() {
+        return Integer.class;
+    }
+
+    private void merge(Context context, List<ImportRecord> records, WorkspaceItem item) throws SQLException {
+        for (MetadataValue metadataValue : itemService.getMetadata(
+            item.getItem(), Item.ANY, Item.ANY, Item.ANY, Item.ANY)) {
+            itemService.clearMetadata(context, item.getItem(),
+                metadataValue.getMetadataField().getMetadataSchema().getNamespace(),
+                metadataValue.getMetadataField().getElement(),
+                metadataValue.getMetadataField().getQualifier(),
+                metadataValue.getLanguage());
+        }
+        for (ImportRecord record : records) {
+            if (record != null && record.getValueList() != null) {
+                for (MetadatumDTO metadataValue : record.getValueList()) {
+                    itemService.addMetadata(context, item.getItem(), metadataValue.getSchema(),
+                        metadataValue.getElement(), metadataValue.getQualifier(), null,
+                        metadataValue.getValue());
+                }
+            }
+        }
+    }
+}