Changed how postexecution errors are handled in algorithms caling external apps

Improved R error messages

python/plugins/sextante/core/AlgorithmProvider.py

@@ -83,23 +83,7 @@ class AlgorithmProvider():
 
     def getDescription(self):
         '''Returns the full name of the provider'''
-        return "Generic algorithm provider"
+        return "Generic algorithm provider"   
-
-    def getPostProcessingErrorMessage(self, wrongLayers):
-        '''Returns the message to be shown to the user when after running an algorithm for this provider,
-        there is a problem loading the resulting layer.
-        This method should analyze if the problem is caused by wrong entry data, a wrong or missing
-        installation of a required 3rd party app, or any other cause, and create an error response accordingly.
-        Message is provided as an HTML code that will be displayed to the user, and which might contains
-        links to installation paths for missing 3rd party apps.
-        - wrongLayers: a list of Output objects that could not be loaded.'''
-
-        html ="<p>Oooops! SEXTANTE could not open the following output layers</p><ul>\n"
-        for layer in wrongLayers:
-            html += '<li>' + layer.description + ': <font size=3 face="Courier New" color="ff0000">' + layer.value + "</font></li>\n"
-        html +="</ul><p>The above files could not be opened, which probably indicates that they were not correctly produced by the executed algorithm</p>"
-        html +="<p>Checking the log information might help you see why those layers were not created as expected</p>"
-        return html
 
     def getIcon(self):
         return QtGui.QIcon(os.path.dirname(__file__) + "/../images/alg.png")

python/plugins/sextante/core/GeoAlgorithm.py

@@ -408,5 +408,21 @@ class GeoAlgorithm:
                 s+=out.getValueAsCommandLineParameter() + ","
         s= s[:-1] + ")"
         return s
+    
+    def getPostProcessingErrorMessage(self, wrongLayers):
+        '''Returns the message to be shown to the user when, after running this algorithm,
+        there is a problem loading the resulting layer.
+        This method should analyze if the problem is caused by wrong entry data, a wrong or missing
+        installation of a required 3rd party app, or any other cause, and create an error response accordingly.
+        Message is provided as an HTML code that will be displayed to the user, and which might contains
+        links to installation paths for missing 3rd party apps.
+        - wrongLayers: a list of Output objects that could not be loaded.'''
+
+        html ="<p>Oooops! SEXTANTE could not open the following output layers</p><ul>\n"
+        for layer in wrongLayers:
+            html += '<li>' + layer.description + ': <font size=3 face="Courier New" color="ff0000">' + layer.value + "</font></li>\n"
+        html +="</ul><p>The above files could not be opened, which probably indicates that they were not correctly produced by the executed algorithm</p>"
+        html +="<p>Checking the log information might help you see why those layers were not created as expected</p>"
+        return html
 
 

python/plugins/sextante/grass/GrassAlgorithm.py

@@ -449,7 +449,7 @@ class GrassAlgorithm(GeoAlgorithm):
         if msg is not None:
             html = ("<p>This algorithm requires GRASS to be run."
             "Unfortunately, it seems that GRASS is not installed in your system, or it is not correctly configured to be used from QGIS</p>")
-            html += '<p><a href= "http://docs.qgis.org/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure GRASS to be used with SEXTANTE</p>'
+            html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure GRASS to be used with SEXTANTE</p>'
             return html
 
 
@@ -463,3 +463,16 @@ class GrassAlgorithm(GeoAlgorithm):
             func = getattr(module,'checkParameterValuesBeforeExecuting')
             return func(self)
 
+
+    def getPostProcessingErrorMessage(self, wrongLayers):
+        html = GeoAlgorithm.getPostProcessingErrorMessage(self, wrongLayers)
+        msg = GrassUtils.checkGrassIsInstalled(True)
+        html += ("<p>This algorithm requires GRASS to be run. A test to check if GRASS is correctly installed "
+                "and configured in your system has been performed, with the following result:</p><ul><i>")
+        if msg is None:
+            html += "GRASS seems to be correctly installed and configured</i></li></ul>"
+        else:
+            html += msg + "</i></li></ul>"
+            html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure GRASS to be used with SEXTANTE</p>'
+
+        return html

python/plugins/sextante/grass/GrassAlgorithmProvider.py

@@ -83,19 +83,6 @@ class GrassAlgorithmProvider(AlgorithmProvider):
     def getIcon(self):
         return  QIcon(os.path.dirname(__file__) + "/../images/grass.png")
 
-    def getPostProcessingErrorMessage(self, wrongLayers):
-        html = AlgorithmProvider.getPostProcessingErrorMessage(self, wrongLayers)
-        msg = GrassUtils.checkGrassIsInstalled(True)
-        html += ("<p>This algorithm requires GRASS to be run. A test to check if GRASS is correctly installed "
-                "and configured in your system has been performed, with the following result:</p><ul><i>")
-        if msg is None:
-            html += "GRASS seems to be correctly installed and configured</li></ul>"
-        else:
-            html += msg + "</i></li></ul>"
-            html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure GRASS to be used with SEXTANTE</p>'
-
-        return html
-
     def getSupportedOutputVectorLayerExtensions(self):
         return ["shp"]
 

python/plugins/sextante/grass/GrassUtils.py

@@ -325,7 +325,6 @@ class GrassUtils:
         if not ignoreRegistrySettings:
             if settings.contains(GRASS_INSTALLED):
                 return
-
         try:
             from sextante import runalg
             result = runalg("grass:v.voronoi", points(),False,False,"270778.60198,270855.745301,4458921.97814,4458983.8488",-1,0.0001, 0, None)

python/plugins/sextante/gui/CouldNotLoadResultsDialog.py

@@ -42,7 +42,7 @@ class CouldNotLoadResultsDialog(QtGui.QDialog):
         webView = QtWebKit.QWebView()
         webView.page().setLinkDelegationPolicy(QtWebKit.QWebPage.DelegateAllLinks)
         webView.connect(webView, SIGNAL("linkClicked(const QUrl&)"), self.linkClicked)
-        html = self.alg.provider.getPostProcessingErrorMessage(self.wrongLayers)
+        html = self.alg.getPostProcessingErrorMessage(self.wrongLayers)
         webView.setHtml(html)
         closeButton = QtGui.QPushButton()
         closeButton.setText("Close")

python/plugins/sextante/r/RAlgorithm.py

@@ -270,22 +270,19 @@ class RAlgorithm(GeoAlgorithm):
 
     def getImportCommands(self):
         commands = []
-        # if rgdal is not available, try to install it
+        
         # just use main mirror
         commands.append('options("repos"="http://cran.at.r-project.org/")')
-        rLibDir = "%s/rlibs" % SextanteUtils.userFolder().replace("\\","/")
+        
-        if not os.path.isdir(rLibDir):
+        # try to install packages if needed
-            os.mkdir(rLibDir)
+        packages = RUtils.getRequiredPackages(self.script)
-        # .libPaths("%s") substitutes the personal libPath with "%s"! With '.libPaths(c("%s",deflibloc))' it is added without replacing and we can use all installed R packages!
+        packages.extend(['rgdal', 'raster'])
-        commands.append('deflibloc <- .libPaths()[1]')
+        for p in packages:            
-        commands.append('.libPaths(c("%s",deflibloc))' % rLibDir )
+            commands.append(
-        commands.append(
+                            'tryCatch(find.package("' + p + 
-            'tryCatch(find.package("rgdal"), error=function(e) install.packages("rgdal", dependencies=TRUE, lib="%s"))' % rLibDir)
+                            '"), error=function(e) install.packages("' + p +'", dependencies=TRUE))')        
-        commands.append("library(\"rgdal\")");
+        commands.append('library("raster")')
-        #if not self.useRasterPackage or self.passFileNames:
+        commands.append('library("rgdal")')
-        commands.append(
-                'tryCatch(find.package("raster"), error=function(e) install.packages("raster", dependencies=TRUE, lib="%s"))' % rLibDir)
-        commands.append("library(\"raster\")");
 
         for param in self.parameters:
             if isinstance(param, ParameterRaster):
@@ -386,28 +383,28 @@ class RAlgorithm(GeoAlgorithm):
             return None
 
     def checkBeforeOpeningParametersDialog(self):
-        if SextanteUtils.isWindows():
+        msg = RUtils.checkRIsInstalled()
-            path = RUtils.RFolder()
+        if msg is not None:
-            if path == "":
+            html = ("<p>This algorithm requires R to be run."
-                return "R folder is not configured.\nPlease configure it before running R scripts."
+            "Unfortunately, it seems that R is not installed in your system, or it is not correctly configured to be used from QGIS</p>")
+            html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure R to be used with SEXTANTE</p>'
+            return html
 
-        R_INSTALLED = "R_INSTALLED"
+
-        settings = QSettings()
+    def getPostProcessingErrorMessage(self, wrongLayers):
-        if settings.contains(R_INSTALLED):
+        html = GeoAlgorithm.getPostProcessingErrorMessage(self, wrongLayers)
-            return
+        msg = RUtils.checkRIsInstalled(True)
-        if SextanteUtils.isWindows():
+        html += ("<p>This algorithm requires R to be run. A test to check if R is correctly installed "
-            if SextanteConfig.getSetting(RUtils.R_USE64):
+                "and configured in your system has been performed, with the following result:</p><ul><i>")
-                execDir = "x64"
+        if msg is None:
-            else:
+            html += "GRASS seems to be correctly installed and configured</i></li></ul>"
-                execDir = "i386"
+            html += "<p>The script you have executed needs the following packages:</p><ul>"
-            command = [RUtils.RFolder() + os.sep + "bin" + os.sep + execDir + os.sep + "R.exe", "--version"]
+            packages = RUtils.getRequiredPackages(self.script)
+            for p in packages:
+                html += '<li>' + p + '</li>'            
+            html += "</ul><p>Make sure they are installed in your R environment before trying to execute this script.</p>"
         else:
-            command = ["R --version"]
+            html += msg + "</i></li></ul>"
-        proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE,stderr=subprocess.STDOUT, universal_newlines=True).stdout
+            html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure R to be used with SEXTANTE</p>'
-
-        for line in iter(proc.readline, ""):
-            if "R version" in line:
-                settings.setValue(R_INSTALLED, True)
-                return
-        return "It seems that R is not correctly installed in your system.\nPlease install it before running R Scripts."
 
+        return html

python/plugins/sextante/r/RUtils.py

@@ -16,6 +16,7 @@
 *                                                                         *
 ***************************************************************************
 """
+import re
 
 __author__ = 'Victor Olaya'
 __date__ = 'August 2012'
@@ -24,6 +25,7 @@ __copyright__ = '(C) 2012, Victor Olaya'
 __revision__ = '$Format:%H$'
 
 from PyQt4.QtGui import *
+from PyQt4.QtCore import *
 from sextante.core.SextanteConfig import SextanteConfig
 import os
 from sextante.core.SextanteUtils import mkdir, SextanteUtils
@@ -123,3 +125,41 @@ class RUtils:
         s+="</font>\n"
 
         return s
+    
+    @staticmethod
+    def checkRIsInstalled(ignoreRegistrySettings=False):
+        if SextanteUtils.isWindows():
+            path = RUtils.RFolder()
+            if path == "":
+                return "R folder is not configured.\nPlease configure it before running R scripts."
+
+        R_INSTALLED = "R_INSTALLED"
+        settings = QSettings()
+        if not ignoreRegistrySettings:
+            if settings.contains(R_INSTALLED):
+                return
+        if SextanteUtils.isWindows():
+            if SextanteConfig.getSetting(RUtils.R_USE64):
+                execDir = "x64"
+            else:
+                execDir = "i386"
+            command = [RUtils.RFolder() + os.sep + "bin" + os.sep + execDir + os.sep + "R.exe", "--version"]
+        else:
+            command = ["R --version"]
+        proc = subprocess.Popen(command, shell=True, stdout=subprocess.PIPE, stdin=subprocess.PIPE,stderr=subprocess.STDOUT, universal_newlines=True).stdout
+
+        for line in iter(proc.readline, ""):
+            if "R version" in line:
+                settings.setValue(R_INSTALLED, True)
+                return
+        html = ("<p>This algorithm requires R to be run."
+            "Unfortunately, it seems that R is not installed in your system, or it is not correctly configured to be used from QGIS</p>"
+            '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a>'
+             'to know more about how to install and configure R to be used with SEXTANTE</p>')
+        return html
+        
+    @staticmethod
+    def getRequiredPackages(code):
+        regex = re.compile('library\("?(.*?)"?\)')
+        return regex.findall(code)
+        

python/plugins/sextante/saga/SagaAlgorithm.py

@@ -362,7 +362,7 @@ class SagaAlgorithm(GeoAlgorithm):
         if msg is not None:
             html = ("<p>This algorithm requires SAGA to be run."
             "Unfortunately, it seems that SAGA is not installed in your system, or it is not correctly configured to be used from QGIS</p>")
-            html += '<p><a href= "http://docs.qgis.org/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure SAGA to be used with SEXTANTE</p>'
+            html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure SAGA to be used with SEXTANTE</p>'
             return html
 
 
@@ -379,7 +379,18 @@ class SagaAlgorithm(GeoAlgorithm):
     def helpFile(self):
         return  os.path.join(os.path.dirname(__file__), "help", self.name.replace(" ", "") + ".html")
 
+    def getPostProcessingErrorMessage(self, wrongLayers):
+        html = GeoAlgorithm.getPostProcessingErrorMessage(self, wrongLayers)
+        msg = SagaUtils.checkSagaIsInstalled(True)
+        html += ("<p>This algorithm requires SAGA to be run. A test to check if SAGA is correctly installed "
+                "and configured in your system has been performed, with the following result:</p><ul><i>")
+        if msg is None:
+            html += "SAGA seems to be correctly installed and configured</li></ul>"
+        else:
+            html += msg + "</i></li></ul>"
+            html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure SAGA to be used with SEXTANTE</p>'
 
+        return html
     #===========================================================================
     # def commandLineName(self):
     #    name = self.provider.getName().lower() + ":" + self.cmdname.lower()

python/plugins/sextante/saga/SagaAlgorithmProvider.py

@@ -99,19 +99,6 @@ class SagaAlgorithmProvider(AlgorithmProvider):
     def getName(self):
         return "saga"
 
-    def getPostProcessingErrorMessage(self, wrongLayers):
-        html = AlgorithmProvider.getPostProcessingErrorMessage(self, wrongLayers)
-        msg = SagaUtils.checkSagaIsInstalled(True)
-        html += ("<p>This algorithm requires SAGA to be run. A test to check if SAGA is correctly installed "
-                "and configured in your system has been performed, with the following result:</p><ul><i>")
-        if msg is None:
-            html += "SAGA seems to be correctly installed and configured</li></ul>"
-        else:
-            html += msg + "</i></li></ul>"
-            html += '<p><a href= "http://docs.qgis.org/2.0/html/en/docs/user_manual/sextante/3rdParty.html">Click here</a> to know more about how to install and configure SAGA to be used with SEXTANTE</p>'
-
-        return html
-
     def getSupportedOutputVectorLayerExtensions(self):
         return ["shp"]