Add option to GeoPackage Reader to ignore invalid rows

[koettert]

This problem was reported in the KNIME forum while reading this file. The node should offer an option to enable skipping of invalid lines which is what QGIS is doing. This is the full stacktrace:

  File "C:\KNIME\KNIME_AP\KNIME\plugins\org.knime.python3.nodes_4.7.3.v202305081333\src\main\python\_node_backend_launcher.py", line 457, in execute
    outputs = self._node.execute(exec_context, *inputs)
  File "C:\KNIME\KNIME_AP\KNIME\plugins\sdl.harvard.geospatial_1.1.1.202306211527\src\main\python\src\nodes\io.py", line 250, in execute
    gdf = gp.GeoDataFrame.from_features(src)
  File "C:\KNIME\KNIME_AP\KNIME\plugins\sdl.harvard.geospatial.channel.bin.win32.x86_64_1.1.1.202306211527\env\lib\site-packages\geopandas\geodataframe.py", line 640, in from_features
    "geometry": shape(feature["geometry"]) if feature["geometry"] else None
  File "C:\KNIME\KNIME_AP\KNIME\plugins\sdl.harvard.geospatial.channel.bin.win32.x86_64_1.1.1.202306211527\env\lib\site-packages\shapely\geometry\geo.py", line 106, in shape
    return MultiLineString(ob["coordinates"])
  File "C:\KNIME\KNIME_AP\KNIME\plugins\sdl.harvard.geospatial.channel.bin.win32.x86_64_1.1.1.202306211527\env\lib\site-packages\shapely\geometry\multilinestring.py", line 50, in __new__
    line = linestring.LineString(lines[i])
  File "C:\KNIME\KNIME_AP\KNIME\plugins\sdl.harvard.geospatial.channel.bin.win32.x86_64_1.1.1.202306211527\env\lib\site-packages\shapely\geometry\linestring.py", line 73, in __new__
    geom = shapely.linestrings(coordinates)
  File "C:\KNIME\KNIME_AP\KNIME\plugins\sdl.harvard.geospatial.channel.bin.win32.x86_64_1.1.1.202306211527\env\lib\site-packages\shapely\decorators.py", line 77, in wrapped
    return func(*args, **kwargs)
  File "C:\KNIME\KNIME_AP\KNIME\plugins\sdl.harvard.geospatial.channel.bin.win32.x86_64_1.1.1.202306211527\env\lib\site-packages\shapely\creation.py", line 120, in linestrings
    return lib.linestrings(coords, out=out, **kwargs)
shapely.errors.GEOSException: IllegalArgumentException: point array must contain 0 or >1 elements


2023-07-11 18:40:19,463 : DEBUG : KNIME-Worker-7-GeoPackage Reader 3:1552 :  : Node : GeoPackage Reader : 3:1552 : reset
2023-07-11 18:40:19,463 : ERROR : KNIME-Worker-7-GeoPackage Reader 3:1552 :  : Node : GeoPackage Reader : 3:1552 : Execute failed: IllegalArgumentException: point array must contain 0 or >1 elements

org.knime.python3.nodes.PythonNodeRuntimeException: IllegalArgumentException: point array must contain 0 or >1 elements

	at org.knime.python3.nodes.CloseablePythonNodeProxy$FailureState.throwIfFailure(CloseablePythonNodeProxy.java:475)
	at org.knime.python3.nodes.CloseablePythonNodeProxy.execute(CloseablePythonNodeProxy.java:315)
	at org.knime.python3.nodes.DelegatingNodeModel.lambda$4(DelegatingNodeModel.java:145)
	at org.knime.python3.nodes.DelegatingNodeModel.runWithProxy(DelegatingNodeModel.java:204)
	at org.knime.python3.nodes.DelegatingNodeModel.execute(DelegatingNodeModel.java:143)
	at org.knime.core.node.NodeModel.executeModel(NodeModel.java:549)
	at org.knime.core.node.Node.invokeFullyNodeModelExecute(Node.java:1267)
	at org.knime.core.node.Node.execute(Node.java:1041)
	at org.knime.core.node.workflow.NativeNodeContainer.performExecuteNode(NativeNodeContainer.java:595)
	at org.knime.core.node.exec.LocalNodeExecutionJob.mainExecute(LocalNodeExecutionJob.java:98)
	at org.knime.core.node.workflow.NodeExecutionJob.internalRun(NodeExecutionJob.java:201)
	at org.knime.core.node.workflow.NodeExecutionJob.run(NodeExecutionJob.java:117)
	at org.knime.core.util.ThreadUtils$RunnableWithContextImpl.runWithContext(ThreadUtils.java:367)
	at org.knime.core.util.ThreadUtils$RunnableWithContext.run(ThreadUtils.java:221)
	at java.base/java.util.concurrent.Executors$RunnableAdapter.call(Unknown Source)
	at java.base/java.util.concurrent.FutureTask.run(Unknown Source)
	at org.knime.core.util.ThreadPool$MyFuture.run(ThreadPool.java:123)
	at org.knime.core.util.ThreadPool$Worker.run(ThreadPool.java:246)

[koettert]

Relates to https://github.com/geopandas/geopandas/issues/2791 and might already work with the latest version of Geopandas: https://github.com/geopandas/geopandas/issues/2791#issuecomment-1638806042

[koettert]

Still not fixed in Geopandas so we have to postpone this issue to next milestone and see if it is fixed by then.

[UrbanGISer]

merge this update to pull request #391 update IO nodes by using （ engine="pyogrio", on_invalid="ignore",）in GeoFile Reader and GeoPackage Reader