Merge pull request #4 from janvanmansum/DD-1736

DD-1736 Cannot invoke "nl.knaw.dans.lib.dataverse.model.file.FileMeta.getDataFile()" because "file" is null

docs/description.md

@@ -106,10 +106,10 @@ editFiles:
       reason: 'Pending publication'
 ```
 
-The actions specified in this file correspond roughly to the action available in the dropdown menu in the file view of a dataset in Dataverse.
+The actions specified in this file correspond roughly to the actions available in the dropdown menu in the file view of a dataset in Dataverse.
 
-The replacement file is looked up in the bag, under the `data` directory under the same path as the original file has in the dataset. Note that files the
-replacement files will automatically be skipped in the add files step, the deleted files, however, will not. In other words, it is also possible to remove a
+The replacement file is looked up in the bag, under the `data` directory under the same path as the original file has in the dataset. Note that files in 
+`replaceFiles` will automatically be skipped in the add files step, the deleted files, however, will not. In other words, it is also possible to remove a
 file and add a file back to the same location in one deposit. In that case, there will be no continuous history of the file in the dataset.
 
 The `addRestrictedFiles` action is included, because it allows you to add a large number of restricted files in a more efficient way than by updating the file

docs/dev.md

@@ -0,0 +1,24 @@
+Development
+===========
+
+## Local debugging
+
+To locally debug you need to have the following services running:
+
+* A dataverse instance. Internal DANS developers can use the vagrant boxes with development versions of the Data Stations for this. You will need to configure
+  access to the admin interface to use the unblock-key:
+
+        curl -X PUT -d s3kretKey http://localhost:8080/api/admin/settings/:BlockedApiKey
+        curl -X PUT -d unblock-key http://localhost:8080/api/admin/settings/:BlockedApiPolicy
+
+        # When done debugging, you can reset the policy to localhost-only:
+        curl -X PUT -d localhost-only http://localhost:8080/api/admin/settings/:BlockedApiPolicy/?unblock-key=s3kretKey
+
+* [dd-validate-dans-bag]{:target="_blank"}. Note that its `validation.baseFolder` configuration property should point to the deposit area or an ancestor of it.
+
+Calling `dd-dataverse-ingest` is most conveniently done through the [dd-dataverse-ingest-cli]{:target=_blank} command line tool. 
+
+
+
+[dd-validate-dans-bag]: {{ validate_dans_bag_url }}
+[dd-dataverse-ingest-cli]: {{ dataverse_ingest_cli_url }}

mkdocs.yml

@@ -35,6 +35,8 @@ extra:
   bagit_specs_url: https://www.rfc-editor.org/rfc/rfc8493.html
   dans_bag_profile_url: https://dans-knaw.github.io/dans-bagit-profile/versions/1.2.0/
   dataverse_api_url: https://guides.dataverse.org/en/latest/api
+  validate_dans_bag_url: https://github.com/DANS-KNAW/dd-validate-dans-bag
+  dataverse_ingest_cli_url: https://github.com/DANS-KNAW/dd-dataverse-ingest-cli
 
 plugins:
   - markdownextradata

src/main/java/nl/knaw/dans/dvingest/core/bagprocessor/FilesEditor.java

@@ -60,6 +60,8 @@ public class FilesEditor {
     private final Map<String, FileMeta> filesInDataset = new java.util.HashMap<>();
     private boolean filesRetrieved = false;
 
+    private Map<String, String> renameMap;
+
     public void editFiles(String pid) throws IOException, DataverseException {
         /*
          * TODO:
@@ -69,16 +71,15 @@ public void editFiles(String pid) throws IOException, DataverseException {
          *  - updateFileMetas must exist in bag if first version deposit
          */
         if (editFiles == null) {
-            try (var stream = Files.list(dataDir)) {
-                if (stream.findAny().isEmpty()) {
-                    log.debug("No files to edit for deposit {}", depositId);
-                    return;
-                }
+            if (isEmptyDir(dataDir)) {
+                log.debug("No files to edit for deposit {}", depositId);
+                return;
             }
         }
 
         log.debug("Start editing files for deposit {}", depositId);
         this.pid = pid;
+        this.renameMap = getRenameMap();
         if (editFiles != null) {
             deleteFiles();
             replaceFiles();
@@ -93,6 +94,12 @@ public void editFiles(String pid) throws IOException, DataverseException {
         log.debug("End editing files for deposit {}", depositId);
     }
 
+    private boolean isEmptyDir(Path dir) throws IOException {
+        try (var stream = Files.list(dir)) {
+            return stream.findAny().isEmpty();
+        }
+    }
+
     private void deleteFiles() throws IOException, DataverseException {
         log.debug("Start deleting {} files for deposit {}", depositId, editFiles.getDeleteFiles().size());
         for (var file : editFiles.getDeleteFiles()) {
@@ -156,7 +163,7 @@ private Map<String, String> getRenameMap() {
     private void uploadFileBatch(PathIterator iterator, boolean restrict) throws IOException, DataverseException {
         var tempZipFile = utilityServices.createTempZipFile();
         try {
-            var zipFile = utilityServices.createPathIteratorZipperBuilder(getRenameMap())
+            var zipFile = utilityServices.createPathIteratorZipperBuilder(renameMap)
                 .rootDir(dataDir)
                 .sourceIterator(iterator)
                 .targetZipFile(tempZipFile)
@@ -224,10 +231,26 @@ private void addEmbargoes() throws IOException, DataverseException {
             var embargo = new Embargo();
             embargo.setDateAvailable(addEmbargo.getDateAvailable());
             embargo.setReason(addEmbargo.getReason());
-            var fileIds = addEmbargo.getFilePaths().stream().map(filesInDataset::get).mapToInt(file -> file.getDataFile().getId()).toArray();
+            var fileIds = addEmbargo.getFilePaths()
+                .stream()
+                .map(this::renameFile)
+                .map(this::throwIfFileNotInDataset)
+                .map(filesInDataset::get)
+                .mapToInt(file -> file.getDataFile().getId()).toArray();
             embargo.setFileIds(fileIds);
             dataverseService.addEmbargo(pid, embargo);
         }
         log.debug("End adding embargoes for deposit {}", depositId);
     }
+
+    private String renameFile(String file) {
+        return renameMap.getOrDefault(file, file);
+    }
+
+    private String throwIfFileNotInDataset(String file) {
+        if (!filesInDataset.containsKey(file)) {
+            throw new IllegalArgumentException("File not found in dataset: " + file);
+        }
+        return file;
+    }
 }