Add new option, tools, and data to functional test framework to test/demonstrate tool framework itself.

Add smaple repeat tool demonstrating some weaknesses of twill-based current framework.

run_functional_tests.sh

@@ -13,6 +13,8 @@ elif [ $1 = 'help' ]; then
 	echo "'run_functional_tests.sh -list'                    for listing all the tool ids"
 	echo "'run_functional_tests.sh -toolshed'                for running all the test scripts in the ./test/tool_shed/functional directory"
 	echo "'run_functional_tests.sh -toolshed testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory"
+	echo "'run_functional_tests.sh -framework'               for running through example tool tests testing framework features in test/functional/tools"    
+	echo "'run_functional_tests.sh -framework -id toolid'    for testing one framework tool (in test/functional/tools/) with id 'toolid'"
 elif [ $1 = '-id' ]; then
 	python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$2 --with-nosehtml --html-report-file run_functional_tests.html
 elif [ $1 = '-sid' ]; then
@@ -46,6 +48,14 @@ elif [ $1 = '-toolshed' ]; then
     else
         python ./test/tool_shed/functional_tests.py -v --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html $2
     fi
+elif [ $1 = '-framework' ]; then
+    if [ ! $2 ]; then
+        python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -framework
+    elif [ $2 = '-id' ]; then
+        python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$3 --with-nosehtml --html-report-file run_functional_tests.html -framework
+    else
+        echo "Invalid test option selected, if -framework first argument to $0, optional second argument must be -id followed a tool id."
+    fi
 else
 	python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html $1
 fi

scripts/functional_tests.py

@@ -178,6 +178,7 @@ def main():
         os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales
     testing_migrated_tools = '-migrated' in sys.argv
     testing_installed_tools = '-installed' in sys.argv
+    datatypes_conf_override = None
 
     if testing_migrated_tools or testing_installed_tools:
         sys.argv.pop()
@@ -197,8 +198,21 @@ def main():
         # Exclude all files except test_toolbox.py.
         ignore_files = ( re.compile( r'^test_[adghlmsu]*' ), re.compile( r'^test_ta*' ) )
     else:
-        tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', 'tool_conf.xml' )
-        galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', default_galaxy_test_file_dir )
+        framework_test = '-framework' in sys.argv  # Run through suite of tests testing framework.
+        if framework_test:
+            sys.argv.pop()
+            framework_tool_dir = os.path.join('test', 'functional', 'tools')
+            tool_conf = os.path.join( framework_tool_dir, 'samples_tool_conf.xml' )
+            datatypes_conf_override = os.path.join( framework_tool_dir, 'sample_datatypes_conf.xml' )
+            test_dir = os.path.join( framework_tool_dir, 'test-data')
+
+            tool_path = framework_tool_dir
+        else:
+            # Use tool_conf.xml toolbox.
+            tool_conf = 'tool_conf.xml'
+            test_dir = default_galaxy_test_file_dir
+        tool_config_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', tool_conf )
+        galaxy_test_file_dir = os.environ.get( 'GALAXY_TEST_FILE_DIR', test_dir )
         if not os.path.isabs( galaxy_test_file_dir ):
             galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir )
         library_import_dir = galaxy_test_file_dir
@@ -338,6 +352,8 @@ def main():
         if use_distributed_object_store:
             kwargs[ 'object_store' ] = 'distributed'
             kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample'
+        if datatypes_conf_override:
+            kwargs[ 'datatypes_config_file' ] = datatypes_conf_override
         # If the user has passed in a path for the .ini file, do not overwrite it.
         galaxy_config_file = os.environ.get( 'GALAXY_TEST_INI_FILE', None )
         if not galaxy_config_file:

test/functional/tools/README.txt

@@ -0,0 +1,3 @@
+This directory contains tools only useful for testing the tool test framework
+and demonstrating it features. Run the driver script 'run_functional_tests.sh'
+with '-installed' as first argument to run through these tests.

test/functional/tools/multi_repeats.xml

@@ -0,0 +1,39 @@
+<tool id="multirepeat" name="multirepeat">
+    <description>tail-to-head</description>
+    <command>
+        cat $input1 #for $q in $queries# ${q.input2} #end for# #for $q in $more_queries# ${q.more_queries_input} #end for# > $out_file1
+    </command>
+    <inputs>
+        <param name="input1" type="data" label="Concatenate Dataset"/>
+        <repeat name="queries" title="Dataset">
+            <param name="input2" type="data" label="Select" />
+        </repeat>
+        <repeat name="more_queries" title="Dataset">
+            <param name="more_queries_input" type="data" label="Select" />
+        </repeat>        
+    </inputs>
+    <outputs>
+        <data name="out_file1" format="input" metadata_source="input1"/>
+    </outputs>
+    <tests>
+        <test>
+            <param name="input1" value="simple_line.txt"/>
+            <param name="input2" value="simple_line.txt"/>
+            <output name="out_file1" file="simple_line_x2.txt"/>
+        </test>
+        <test>
+            <param name="input1" value="simple_line.txt"/>
+            <param name="input2" value="simple_line.txt"/>
+            <param name="input2" value="simple_line.txt"/>
+            <output name="out_file1" file="simple_line_x3.txt"/>
+        </test>
+        <test>
+            <param name="input1" value="simple_line.txt"/>
+            <param name="input2" value="simple_line.txt"/>
+            <param name="input2" value="simple_line.txt"/>
+            <param name="more_queries_input" value="simple_line.txt"/>
+            <param name="more_queries_input" value="simple_line.txt"/>            
+            <output name="out_file1" file="simple_line_x5.txt"/>
+        </test>
+    </tests>
+</tool>

test/functional/tools/sample_datatypes_conf.xml

@@ -0,0 +1,8 @@
+<?xml version="1.0"?>
+<datatypes>
+  <registration converters_path="lib/galaxy/datatypes/converters" display_path="display_applications">
+    <datatype extension="velvet" type="galaxy.datatypes.assembly:Velvet" display_in_upload="true"/>
+    <datatype extension="txt" type="galaxy.datatypes.data:Text" display_in_upload="true"/>
+    <datatype extension="tabular" type="galaxy.datatypes.tabular:Tabular" display_in_upload="true"/>
+  </registration>
+</datatypes>

test/functional/tools/samples_tool_conf.xml

@@ -0,0 +1,5 @@
+<?xml version="1.0"?>
+<toolbox>
+  <tool file="upload.xml"/>
+  <tool file="multi_repeats.xml"/>
+</toolbox>

test/functional/tools/test-data/simple_line.txt

@@ -0,0 +1 @@
+This is a line of text.

test/functional/tools/test-data/simple_line_x2.txt

@@ -0,0 +1,2 @@
+This is a line of text.
+This is a line of text.

test/functional/tools/test-data/simple_line_x3.txt

@@ -0,0 +1,3 @@
+This is a line of text.
+This is a line of text.
+This is a line of text.

test/functional/tools/test-data/simple_line_x5.txt

@@ -0,0 +1,5 @@
+This is a line of text.
+This is a line of text.
+This is a line of text.
+This is a line of text.
+This is a line of text.

test/functional/tools/upload.py

@@ -0,0 +1 @@
+../../../tools/data_source/upload.py

test/functional/tools/upload.xml

@@ -0,0 +1 @@
+../../../tools/data_source/upload.xml