QGIS processing.run() standalone script does not write .prj and .cpg output files of shapefile?

Question

I've created a python standalone script to clip two shapefiles with qgis. I've installed qgis3 with OSgeo4W. The logic is as follows:

import qgis
from qgis.core import *
from qgis.core import QgsApplication
from qgis.core import QgsProject
from qgis.core import QgsProcessingFeedback
from qgis.core import QgsVectorLayer
from qgis.analysis import QgsNativeAlgorithms
import processing
from processing.core.Processing import Processing
path_qgis_installation = "C:/OSGeo4W64/apps/qgis"
QgsApplication.setPrefixPath(path_qgis_installation, True)
qgs = QgsApplication([], False)
qgs.initQgis()
Processing.initialize()
QgsApplication.processingRegistry().addProvider(QgsNativeAlgorithms()) 
input_file = QgsVectorLayer('.../file_name.shp')
overlay_file = QgsVectorLayer('.../file_name.shp')
output_fil = '.../file_name.shp'
processing.run(
 "native:clip", 
 {
 'INPUT':input_file,
 'OVERLAY':overlay_file,
 'OUTPUT':output_fil
 }
)
qgs.exitQgis()

My problem is that when I run the command (only the processing.run()) in the python console in qgis or in the osgeo shell, everything works.

When I however run it with my python console (bat script), I only get the following (corrupted) files written to disc: .dbf, .shp, .shp. Missing are .prj and .shx for a complete shapefile.

My suspition is that is has something to do with the paths. At one point I executed C:/OSGeo4W64/bin/o4w_env.bat from a location outside of C:/OSGeo464) which then even procued the same problem whilst running on the osgeo shell.

Any suggestion what I am missing to load?

• Fran Raga: Look at this answer in case it can help you gis.stackexchange.com/a/289964/49538

Answer 1

Thank you @Fran Raga. I was able to solve the issue based on your reference question. For full disclosure, my working code looks like this.

set OSGEO4W_ROOT=C:/OSGeo4W64
call "%OSGEO4W_ROOT%/bin/o4w_env.bat"
call "%OSGEO4W_ROOT%/bin/qt5_env.bat"
call "%OSGEO4W_ROOT%/bin/py3_env.bat"
path %OSGEO4W_ROOT%/apps/qgis/bin;%PATH%
set GDAL_FILENAME_IS_UTF8=YES
set VSI_CACHE=TRUE
set VSI_CACHE_SIZE=1000000
set QT_PLUGIN_PATH=%OSGEO4W_ROOT%/apps/qgis/qtplugins;%OSGEO4W_ROOT%/apps/qt5/plugins
set PYTHONPATH=%OSGEO4W_ROOT%/apps/qgis/python
set PYTHONHOME=%OSGEO4W_ROOT%/apps/Python37
set PYTHONPATH=%OSGEO4W_ROOT%/apps/Python37/lib/site-packages;%PYTHONPATH%
set QT_QPA_PLATFORM_PLUGIN_PATH=%OSGEO4W_ROOT%/apps/Qt5/plugins/platforms
set QGIS_PREFIX_PATH=%OSGEO4W_ROOT%/apps/qgis
cd /d %~dp0
call ...path/to/shell_scrit.sh

The shell script looks like this:

python path/to/python/script.py

The python script looks like this:

import os
import sys
import qgis
from qgis.core import *
from qgis.core import QgsApplication
from qgis.core import QgsProject
from qgis.core import QgsProcessingFeedback
from qgis.core import QgsVectorLayer
from qgis.analysis import QgsNativeAlgorithms
path_qgis_installation = "C:/OSGeo4W64/apps/qgis"
os.environ['path_qgis_installation'] = path_qgis_installation
QgsApplication.setPrefixPath(os.environ['path_qgis_installation'], True)
qgs = QgsApplication([], False)
qgs.initQgis()
sys.path.append(r'C:\OSGeo4W64\apps\qgis\python\plugins')
import processing
from processing.core.Processing import Processing
Processing.initialize()
QgsApplication.processingRegistry().addProvider(QgsNativeAlgorithms())
input_file = QgsVectorLayer('.../file_name.shp')
overlay_file = QgsVectorLayer('.../file_name.shp')
output_fil = '.../file_name.shp'
processing.run(
 "native:clip", 
 {
 'INPUT':input_file,
 'OVERLAY':overlay_file,
 'OUTPUT':output_fil
 }
)
feedback = QgsProcessingFeedback()
res = processing.run("native:extractvertices", params, feedback=feedback)
qgs.exitQgis()

• Fran Raga: Fine! you are welcome ;)