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swoellauer edited this page Jul 29, 2025 · 44 revisions

Knowledge base

General

Administration

Pointcloud

Raster

R-package

Other

General

Unable to locate package libgdal-java

Reason: Following RSDB install instructions, installation of libgdal-java package fails with message Unable to locate package libgdal-java.
On newer Debian versions, e.g. on Ubuntu 22.04LTS, libgdal-java has been deactiviated, for details see discussion https://bugs.debian.org/cgi-bin/bugreport.cgi?bug=947960

Solution: You need to manually insert the package libgdal-java in the correct version.

First install GDAL:

sudo apt install libgdal-dev

A libgdal-java package for Ubuntu 22.04 LTS is avaiable here gdal-3.4.3%2Bdfsg-java.20220622.tgz origin: http://ftp1.us.debian.org/pub/osgeo/download/livedvd/data/gdal/

Extract the archive:

tar -zxvf *.tgz

Place files in same system folders as in the archive:

/usr/lib/jni/libgdalalljni.so
/usr/share/java/gdal.jar

A libgdal-java package for Ubuntu 24.04 LTS is avaiable here origin: https://download.rasdaman.org/installer/tpinstaller/ubuntu2404/

Extract the archive:

unzip *.zip

Place files in the system folders:

/usr/share/java/gdal.jar
/usr/lib/jni/libgdalalljni.so
/usr/lib/x86_64-linux-gnu/libgdal.so.34.3.8.4   # (optional)

Further Ubuntu versions packages may be available: https://download.rasdaman.org/installer/tpinstaller/

Alternative solution: You may build GDAL from source including Java bindings.

The Web interface is not displayed correctly or some data will not load

Reason: There may be a problem with network connection to RSDB server or RSDB server is not running or not responsive.

Solution:

  • Try reloading the web interface by your browser refresh-button or by pressing the refresh-key ("F5").
  • If RSDB is running locally check if it is actually running.
  • If RSDB is running locally try to stop and start RSDB server again.

RSDB does not start with error: could not listen on port 8081

Reason: The RSDB network port is already used by another application or another instance of RSDB.

Solution: Try to identify the application that is bound to the network port and stop that application and then try to start RSDB server.
To identify the application you may open the port in your browser. e.g. for port 8081 type http://127.0.0.1:8081 and check what application is shown.

Or change RSDB server configuration to a free network port. e.g. "port: 8087" and then try to start RSDB server.

RSDB does not start with error: could not listen on port 80: Permission denied (Bind failed)

Reason: Low port numbers are not allowed for nomal users.

Solution: See Ubuntu network management

I want RSDB URLs without port numbers

Reason: There are default port numbers for HTTP and HTTPS.

Solution: See Ubuntu network management

HTTPS port number is provided but HTTPS is not served

Reason: There may be an error in your certificate setup.
At RSDB start, when there is the message 'WARNING: The certificate key store file 'keystore' does not exist => no HTTPS' the needed keystore file is missing.
At RSDB start, when there is the message 'keystore password was incorrect' or 'failed to decrypt safe contents entry' or 'Given final block not properly padded. Such issues can arise if a bad key is used during decryption.' the yaml entry for the keystore password for the exiting keystore file may be wrong.

Solution: See HTTPS certificate management

Some layers are not listed on the web interface

Reason: The list of layers may be not up to date, e.g. a RSDB task created a new layer.

Solution: At some pages on the web interface is a "layer list reload"-button, e.g. on the "Layers"-tab on the top left. Just click this button.
Alternatively you can reload the web interface by your browser, e.g. by pressing "F5".

Administration

Manually remove RSDB layers

Reason: You created lots of layers in RSDB and you want to remove a large number of the layers.
Note: Single layer removal is supported by the web interface.

Solution: Stop RSDB server. At RSDB folder there are subfolders containing the layers separated by layer type.

RSDB subfolders:

  • pointcloud for PointCloud (point cloud data)
  • pointdb for PointDB (obsolete type of point cloud data)
  • rasterdb for RasterDB (raster data)
  • vectordb for VectorDB (vector data: points, lines, polygons) (ROI and POI layers are implicit vector layers)
  • voxeldb for VoxelDB (voxel data)

Within that subfolders, folders named with the layer IDs are contained.

Delete selected ID-folders to remove unneeded layers. Make sure to only do this when RSDB is not running!

Start RSDB again. RSDB automatically recognizes removed folders and removes cataloging data of that layers.

Rename RSDB layer IDs

Reason: After layer creation the ID of the layer is fixed.
Note: On the web interface layers are displayed by title that is, in difference to ID, changeable at the web interface.

Solution 1: On the web interface TOOLS-tab TASK CREATION apply the task rename on a specific layer.

OR Solution 2:
Stop RSDB server. At RSDB folder there are subfolders containing the layers separated by layer type.

RSDB subfolders:

  • pointcloud for PointCloud (point cloud data)
  • pointdb for PointDB (obsolete type of point cloud data)
  • rasterdb for RasterDB (raster data)
  • vectordb for VectorDB (vector data: points, lines, polygons) (ROI and POI layers are implicit vector layers)
  • voxeldb for VoxelDB (voxel data)

Within that subfolders, folders named with the layer IDs are contained.

Rename selected ID-folders to change layer IDs. Make sure to only do this when RSDB is not running!

Start RSDB again. RSDB automatically recognizes changed folders and updates cataloging data of that layers.

Backup RSDB layers or copy layers to different RSDB servers

Stop RSDB server. At RSDB folder there are subfolders containing the layers separated by layer type.

RSDB subfolders:

  • pointcloud for PointCloud (point cloud data)
  • pointdb for PointDB (obsolete type of point cloud data)
  • rasterdb for RasterDB (raster data)
  • vectordb for VectorDB (vector data: points, lines, polygons) (ROI and POI layers are implicit vector layers)
  • voxeldb for VoxelDB (voxel data)

Within that subfolders, folders named with the layer IDs are contained. All data of a layer is contained in that folder.

Note: Layers may be linked to other layers. For example a pointcloud layer 'pointcloud1' may be linked to a visualization raster layer 'pointcloud1_rasterized'. For backup purposes you should make sure to include both layers.

Backup or copy some or all of the subfolders. Make sure to only do this when RSDB is not running!

Start RSDB again. RSDB automatically recognizes inserted/removed folders and updates cataloging data of that layers.

Pointcloud

Supported point cloud import formats

RSDB supports point cloud files for import:

Import of point cloud '.laz' files fails

Reason: Bugs in an external library may lead to failed read of compressed LAZ files. As soon as the external library updates we will update it in RSDB. Uncompressed LAS files, '.las', are read without external library.
Note: With the current RSDB version, we have not encountered any unsupported LAZ files.

Solution: Convert LAZ files to LAS files and import LAS files in RSDB.
laszip is needed for Format conversation from compressed '.laz' to uncompressed '.las'. It can be found here: https://github.com/LAStools/LAStools.github.io/tree/master/download
download file: laszip-cli.exe or laszip.exe or laszip64.exe. It can be run on linux with Wine.

After point cloud file import to a new layer, projection information is missing

Reason: In the source .las or .laz files projection information is missing or in an unsupported format.

Solution: One of the following three solutions:

  • On the web interface set the projection information of the layer after the data import.
  • At data import task specify projection parameters epsg and/or proj4.
  • Use LAStools to set projection information to LAS/LAZ files, e.g. las2las.exe -i *.laz -olaz -epsg 32632. LAStools can be run on linux with Wine.

Raster

Missing projection information

Reason: Raster files or other raster data without projection information have been uploaded into a new raster layer.

Solution: If projection is known

  • At file upload you may specify correct EPSG and/or PROJ4 information.
  • At raster layer details you may specify correct EPSG and/or PROJ4 information.

If projection is unknown or not needed

  • You are able to show raster data in the viewer, but background maps are not available.
  • You can process the data, but reprojection of other data to this layer, e.g. vector data, is no available.

WMS view in QGIS does not show updated raster layer data

Reason: QGIS does cache data received over network and often QGIS does not automatically load updated data.

Solution: In QGIS go to Settings - Options - Network - Cache settings - "reverse arrow"-button (clear cache)
Close QGIS and start it again. Now updated (meta)-data on WMS connections will be loaded.

Layer view shows old data, no pixels at all or view is very slow

Reason: Normally, after data write to the layer the raster pyramid is updated per default. If this was not the case, the pyramid may not contain the newest data.

Solution: Run the RasterDB task rebuild_pyramid to create the pyramid.
On the web interface TOOLS-tab TASK CREATION apply the RasterDB task rebuild_pyramid on a specific layer.
Or by R-script submit the task: remotesensing$submit_task(task=list(task_rasterdb = 'rebuild_pyramid', rasterdb = rasterdb_name))

For WMS or WCS a reprojection different to the layer projection is needed

Reason: You need to use an application to connect by WMS or WCS to RSDB and the application expects a specific projection.

Solution: On the web interface raster layer detail page, section actions, custom WMS or custom WCS-button, set the needed EPSG reprojection.

For WMS or WCS the default processing settings are not suitable

Reason: For example, the WMS dynamic visualisation is not suitable, a static value range visualisation is needed.

Solution: On the web interface raster layer detail page, section actions, custom WMS or custom WCS-button, set the specific settings.

R-package

After R-package update loading the package fails

Reason: You updated to latest version:

if(!require("remotes")) install.packages("remotes")
remotes::install_github("environmentalinformatics-marburg/rsdb/r-package")

And then loading RSDB package fails library(RSDB)

Solution: The RSDB package may be not fully replaced by new version in memory.
Just restart R environment. Then library(RSDB) should work again.
(in RStudio - Session - Terminate R)

Other

Open issues

RSDB issues are managed on GitHub.

If your issue is not listed on this current troubleshooting page check if the issue is listed already on GitHub.
Otherwise you can create a new issue message.

(RSDB wiki)

RSDB wiki
Access control
Layer discoverability
Layer meta data
Point cloud indices
Raster indices
HTTPS certificate management
Ubuntu network management
Troubleshooting

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