Python subprocess gpt gdal error

development python
#1

Dear developers,

When I run gpt directly from Windows cmd all works fine, but when I do the same from Python with subprocess

subprocess.call('gpt -h')

I am getting the following error.

INFO: org.esa.snap.core.gpf.operators.tooladapter.ToolAdapterIO: Initializing external tool adapters
Error: null
java.lang.ExceptionInInitializerError
	at org.esa.s2tbx.dataio.gdal.GDALLoader.initGDAL(GDALLoader.java:54)
	at org.esa.lib.gdal.activator.GDALPlugInActivator.start(GDALPlugInActivator.java:22)
	at org.esa.snap.runtime.Engine.informActivators(Engine.java:222)
	at org.esa.snap.runtime.Engine.lambda$start$0(Engine.java:121)
	at org.esa.snap.runtime.Engine.runClientCode(Engine.java:189)
	at org.esa.snap.runtime.Engine.start(Engine.java:121)
	at org.esa.snap.runtime.Engine.start(Engine.java:90)
	at org.esa.snap.runtime.Launcher.run(Launcher.java:51)
	at org.esa.snap.runtime.Launcher.main(Launcher.java:31)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
	at java.lang.reflect.Method.invoke(Method.java:498)
	at com.exe4j.runtime.LauncherEngine.launch(LauncherEngine.java:84)
	at com.exe4j.runtime.WinLauncher.main(WinLauncher.java:94)
	at com.install4j.runtime.launcher.WinLauncher.main(WinLauncher.java:25)
Caused by: java.nio.file.InvalidPathException: Illegal char <:> at index 48: C:\Miniconda\envs\plot\Library\bin\gdalinfo.exeC:\Program Files\GDAL\gdalinfo.exe
	at sun.nio.fs.WindowsPathParser.normalize(WindowsPathParser.java:182)
	at sun.nio.fs.WindowsPathParser.parse(WindowsPathParser.java:153)
	at sun.nio.fs.WindowsPathParser.parse(WindowsPathParser.java:77)
	at sun.nio.fs.WindowsPath.parse(WindowsPath.java:94)
	at sun.nio.fs.WindowsFileSystem.getPath(WindowsFileSystem.java:255)
	at java.nio.file.Paths.get(Paths.java:84)
	at org.esa.s2tbx.dataio.gdal.OSCategory.getExecutableLocation(OSCategory.java:120)
	at org.esa.s2tbx.dataio.gdal.GDALVersion.retrieveInstalledVersion(GDALVersion.java:166)
	at org.esa.s2tbx.dataio.gdal.GDALVersion.<clinit>(GDALVersion.java:50)
	... 16 more

As far as I could read there is something with two gdal version that I have - from osgeo (Miniconda) and system.

I do not think it is SNAP issue but rather Miniconda, but could you give a hint if you have faced it, please.

#2

It says here there is an illegal character “:”
Caused by: java.nio.file.InvalidPathException: Illegal char <:> at index 48: C:\Miniconda\envs\plot\Library\bin\gdalinfo.exeC:\Program Files\GDAL\gdalinfo.exe

I use Miniconda, Python, and I also call gpt through subprocess. This method works for me.

I think SNAP is confused because somehow you seem to have 2 GDAL installations in your path. How did you install GDAL in your virtual environment?

#3

You can have a look at the option in SNAP Desktop:

image
image738×462 29.9 KB

Maybe you can use the internal version?
If this doesn’t help, then @oana_hogoiu might be able to help you.

#4

Yes, SNAP cannot handle 2 GDAL versions installed on your system.
You can either decide on one of the installed versions, either use the SNAP internal GDAL version, like @marpet suggested.
Also, maybe it helps to delete SNAP cache (on Windows it’s located under C:\Users[username]\AppData\Roaming\SNAP and on unix it’s under ~/.snap/system)

#5

I don’t know how I got it, in other environment there is only one. I was trying to disable Conda’s gdal but I was not able to find environmental path variables of the virtual environment.
Before the last week it was working fine (SNAP 8).

#6

I tried all the things but it didn’t help.
I agree that this is not SNAP but rather a Conda issue, so I am fine like this.
I changed the environment for this command and all worked fine.
Yet, you might find it interesting to fix, if SNAP asks ‘where gdal’ and expects 1 string, but there are two in my bogus case, which SNAP merges into one and complains about the second “:” in the path, which it the beginning of the second path.
Thank you for you fast reply, anyway.

#7

Hi Prikaziuk,
I’m having the same issue. What exactly did you change in the environment for that command?

#8

So in my case there where 2 instances of gdalinfo.exe: one in my Python environment and one that comes with the SNAP installation. I solved it by renaming the one in the Python environment to “gdalinfo.exe.bak”.

The setting in SNAP Desktop as suggested by @marpet did not help in my case.

#9

Hi scheunro,

An elegant workaround, I just activated another conda environment that worked with conda activate another_env_name.