Cleaned up

Cleaned up from old TODOS etc.
+added explanation to solution

Author: Thechopsee

src/main/java/cz/it4i/fiji/datastore/rest_client/WriteSequenceToN5.java

@@ -181,7 +181,7 @@ public static void writeN5File(final AbstractSequenceDescription<?, ?, ?> seq,
 		int numCompletedTasks = 0;
 
 		final ExecutorService executorService = Executors.newFixedThreadPool( numCellCreatorThreads );
-		//TODO FIND N5 WRITER AND MAKE HIM CHANGABLE
+
 		try (N5Writer n5 = writerSupplier.get()) {
 			// write image data for all views
 			final int numTimepoints = timepointIds.size();

src/main/java/cz/it4i/fiji/legacy/CloneEmptyDatasetFromN5toZarr.java

@@ -150,7 +150,8 @@ public void run() {
         } catch (IOException | ModuleException e) {
             myLogger.error("Some error accessing the reference service and dataset: "+e.getMessage());
         } catch (ExecutionException e) {
-            e.printStackTrace();
+            myLogger.error(e.getMessage());
+
         } catch (InterruptedException e) {
             //dialog interrupted, do nothing special...
             myLogger.error("eee!? "+e.getMessage());

src/main/java/cz/it4i/fiji/legacy/CreateNewDataset.java

@@ -122,13 +122,17 @@ public void run() {
 		di.timepointResolution = new DatasetInfo.ResolutionWithOwnUnit(time_res, time_unit);
 		di.channelResolution = new DatasetInfo.ResolutionWithOwnUnit(channel_res, channel_unit);
 		di.angleResolution = new DatasetInfo.ResolutionWithOwnUnit(angle_res, angle_unit);
-		//TODO totally random solution
+		//This solution was chosen so that there was no need to change the DatasetDTO object,
+		// so the information about the dataset type is placed after the compression with the delimiter '/',
+		// according to which it is then divided in the registerServiceEndpoint and only the actual value of the compression is stored in the compression.
+		// datasetType is then normally stored in the Dataset class and is used to select a suitable handler.
+		// The most likely solution would be to add the datasetType attribute to the DatasetDTO class, but unfortunately this was not entirely within my power.
 		if(this.datasetType.equals("Zarr")) {
-			di.compression = this.compression.equals("none") ? "raw" : this.compression + "|Zarr";
+			di.compression = this.compression.equals("none") ? "raw" : this.compression + "/Zarr";
 		}
 		else
 		{
-			di.compression = this.compression.equals("none") ? "raw" : this.compression + "|N5";
+			di.compression = this.compression.equals("none") ? "raw" : this.compression + "/N5";
 		}
 		di.versions = Collections.emptyList();
 		di.resolutionLevels = new ArrayList<>(numberOfAllResLevels);

src/main/java/cz/it4i/fiji/legacy/CreateNewDatasetFromImage.java

@@ -137,7 +137,6 @@ public void run() {
 		di.channelResolution = new DatasetInfo.ResolutionWithOwnUnit(channel_res, channel_unit);
 		di.angleResolution = new DatasetInfo.ResolutionWithOwnUnit(angle_res, angle_unit);
 
-		//di.compression = this.compression.equals("none") ? "raw" : this.compression;
 		if(this.datasetType.equals("Zarr")) {
 			di.compression = this.compression.equals("none") ? "raw" : this.compression + "/Zarr";
 		}

src/main/java/cz/it4i/fiji/legacy/CreateNewDatasetFromJSON.java

@@ -45,8 +45,7 @@ public void run() {
 		myLogger = mainLogger.subLogger("HPC CreateDataset", LogLevel.INFO);
 
 		try {
-			String add="/datasets";
-			final HttpURLConnection connection = (HttpURLConnection)new URL("http://"+this.url+add).openConnection();
+			final HttpURLConnection connection = (HttpURLConnection)new URL("http://"+this.url+"/datasets").openConnection();
 			connection.setRequestMethod("POST");
 			connection.setRequestProperty("Content-Type","application/json");
 			connection.setDoOutput(true);

src/main/java/cz/it4i/fiji/legacy/CreateNewDatasetZarr.java

@@ -105,9 +105,7 @@ protected void updateSpatialRanges() {
 	/** updates currentResLevel given the current choice in resolutionLevelsAsStr,
 	    sets currentResLevel to null when resolutionLevelsAsStr is not valid */
 	protected void matchResLevel() {
-		//TODO CLEAR
 		myLogger.info("going to match against: "+resolutionLevelsAsStr);
-		System.out.println(resolutionLevelsAsStr);
 		int i = 0;
 		while (i < di.resolutionLevels.size()) {
 			DatasetInfo.ResolutionLevel l = di.resolutionLevels.get(i);

src/main/java/cz/it4i/fiji/legacy/common/ImagePlusDialogHandler.java

@@ -32,7 +32,6 @@ public class DatasetInfo {
 	public List<Integer> versions;
 	public String label;
 
-
 	/** a common label provider with default fallback response/label */
 	public static final String NO_LABEL_MSG = "(no label is attached)";
 	public String getLabel() {