details:
http://www.bx.psu.edu/hg/galaxy/rev/ec34b27de1c0
changeset: 3195:ec34b27de1c0
user: Nate Coraor <nate(a)bx.psu.edu>
date: Mon Jan 04 12:51:34 2010 -0500
description:
python run from virtualenv sets up site.py to pull things from the real python's lib
directory, so 'python -S' breaks it. To fix this, have the check_python.py script
check for virtualenv and output the arguments that should be used to start python
('python -E' for virtualenv, 'python -ES' for real), then use these
arguments anywhere 'python -ES' was used in the past.
diffstat:
manage_db.sh | 2 +-
run.sh | 8 +++++---
run_functional_tests.sh | 10 ++++++----
run_reports.sh | 2 +-
run_unit_tests.sh | 2 +-
scripts/check_python.py | 9 +++++++++
set_metadata.sh | 2 +-
setup.sh | 4 ++--
8 files changed, 26 insertions(+), 13 deletions(-)
diffs (145 lines):
diff -r 4743015d9a57 -r ec34b27de1c0 manage_db.sh
--- a/manage_db.sh Wed Dec 23 20:26:01 2009 -0500
+++ b/manage_db.sh Mon Jan 04 12:51:34 2010 -0500
@@ -6,4 +6,4 @@
#######
cd `dirname $0`
-python -ES ./scripts/manage_db.py $@
+`python ./scripts/check_python.py` ./scripts/manage_db.py $@
diff -r 4743015d9a57 -r ec34b27de1c0 run.sh
--- a/run.sh Wed Dec 23 20:26:01 2009 -0500
+++ b/run.sh Mon Jan 04 12:51:34 2010 -0500
@@ -2,16 +2,18 @@
cd `dirname $0`
+CLEAN_PYTHON=`python ./scripts/check_python.py`
+
# explicitly attempt to fetch eggs before running
FETCH_EGGS=1
for arg in "$@"; do
[ "$arg" = "--stop-daemon" ] && FETCH_EGGS=0; break
done
if [ $FETCH_EGGS -eq 1 ]; then
- python -ES ./scripts/check_eggs.py quiet
+ $CLEAN_PYTHON ./scripts/check_eggs.py quiet
if [ $? -ne 0 ]; then
echo "Some eggs are out of date, attempting to fetch..."
- python -ES ./scripts/fetch_eggs.py
+ $CLEAN_PYTHON ./scripts/fetch_eggs.py
if [ $? -eq 0 ]; then
echo "Fetch successful."
else
@@ -20,4 +22,4 @@
fi
fi
fi
-python -ES ./scripts/paster.py serve universe_wsgi.ini $@
+$CLEAN_PYTHON ./scripts/paster.py serve universe_wsgi.ini $@
diff -r 4743015d9a57 -r ec34b27de1c0 run_functional_tests.sh
--- a/run_functional_tests.sh Wed Dec 23 20:26:01 2009 -0500
+++ b/run_functional_tests.sh Mon Jan 04 12:51:34 2010 -0500
@@ -4,8 +4,10 @@
rm -f run_functional_tests.log
+CLEAN_PYTHON=`python ./scripts/check_python.py`
+
if [ ! $1 ]; then
- python -ES ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
run_functional_tests.html --exclude="^get" functional
+ $CLEAN_PYTHON ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
run_functional_tests.html --exclude="^get" functional
elif [ $1 = 'help' ]; then
echo "'run_functional_tests.sh' for testing all the
tools in functional directory"
echo "'run_functional_tests.sh aaa' for testing one test
case of 'aaa' ('aaa' is the file name with path)"
@@ -13,16 +15,16 @@
echo "'run_functional_tests.sh -sid ccc' for testing one
section with sid 'ccc' ('ccc' is the string after
'section::')"
echo "'run_functional_tests.sh -list' for listing all the
tool ids"
elif [ $1 = '-id' ]; then
- python -ES ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$2
--with-nosehtml --html-report-file run_functional_tests.html
+ $CLEAN_PYTHON ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$2
--with-nosehtml --html-report-file run_functional_tests.html
elif [ $1 = '-sid' ]; then
- python -ES ./scripts/functional_tests.py --with-nosehtml --html-report-file
run_functional_tests.html -v `python tool_list.py $2`
+ $CLEAN_PYTHON ./scripts/functional_tests.py --with-nosehtml --html-report-file
run_functional_tests.html -v `python tool_list.py $2`
elif [ $1 = '-list' ]; then
python tool_list.py
echo
"==========================================================================================================================================="
echo "'run_functional_tests.sh -id bbb' for testing one tool
with id 'bbb' ('bbb' is the tool id)"
echo "'run_functional_tests.sh -sid ccc' for testing one
section with sid 'ccc' ('ccc' is the string after
'section::')"
else
- python -ES ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
run_functional_tests.html $1
+ $CLEAN_PYTHON ./scripts/functional_tests.py -v --with-nosehtml --html-report-file
run_functional_tests.html $1
fi
echo "'run_functional_tests.sh help' for help"
diff -r 4743015d9a57 -r ec34b27de1c0 run_reports.sh
--- a/run_reports.sh Wed Dec 23 20:26:01 2009 -0500
+++ b/run_reports.sh Mon Jan 04 12:51:34 2010 -0500
@@ -2,4 +2,4 @@
cd `dirname $0`
-python -ES ./scripts/paster.py serve reports_wsgi.ini --pid-file=reports_webapp.pid
--log-file=reports_webapp.log $@
+`python ./scripts/check_python.py` ./scripts/paster.py serve reports_wsgi.ini
--pid-file=reports_webapp.pid --log-file=reports_webapp.log $@
diff -r 4743015d9a57 -r ec34b27de1c0 run_unit_tests.sh
--- a/run_unit_tests.sh Wed Dec 23 20:26:01 2009 -0500
+++ b/run_unit_tests.sh Mon Jan 04 12:51:34 2010 -0500
@@ -2,6 +2,6 @@
## Excluding controllers due to the problematic genetrack dependency
-python -ES ./scripts/nosetests.py -v -w lib \
+`python ./scripts/check_python.py` ./scripts/nosetests.py -v -w lib \
--with-nosehtml --html-report-file run_unit_tests.html \
--with-doctest --exclude=functional --exclude="^get" --exclude=controllers
diff -r 4743015d9a57 -r ec34b27de1c0 scripts/check_python.py
--- a/scripts/check_python.py Wed Dec 23 20:26:01 2009 -0500
+++ b/scripts/check_python.py Mon Jan 04 12:51:34 2010 -0500
@@ -6,6 +6,13 @@
supported version is installed but is not your default,
getgalaxy.org
contains instructions on how to force Galaxy to use a different
version.""" % sys.version[:3]
+def check_virtualenv():
+ try:
+ assert sys.real_prefix
+ return 'python -E'
+ except:
+ return 'python -ES'
+
def check_python():
try:
assert sys.version_info[:2] >= ( 2, 4 ) and sys.version_info[:2] <= ( 2, 6
)
@@ -16,5 +23,7 @@
if __name__ == '__main__':
try:
check_python()
+ print check_virtualenv()
+ sys.exit( 0 )
except:
sys.exit( 1 )
diff -r 4743015d9a57 -r ec34b27de1c0 set_metadata.sh
--- a/set_metadata.sh Wed Dec 23 20:26:01 2009 -0500
+++ b/set_metadata.sh Mon Jan 04 12:51:34 2010 -0500
@@ -1,4 +1,4 @@
#!/bin/sh
cd `dirname $0`
-python -ES ./scripts/set_metadata.py $@
+`python ./scripts/check_python.py` ./scripts/set_metadata.py $@
diff -r 4743015d9a57 -r ec34b27de1c0 setup.sh
--- a/setup.sh Wed Dec 23 20:26:01 2009 -0500
+++ b/setup.sh Mon Jan 04 12:51:34 2010 -0500
@@ -1,6 +1,6 @@
#!/bin/sh
-python ./scripts/check_python.py
+CLEAN_PYTHON=`python ./scripts/check_python.py`
[ $? -ne 0 ] && exit 1
SAMPLES="
@@ -56,4 +56,4 @@
fi
done
-python ./scripts/fetch_eggs.py
+$CLEAN_PYTHON ./scripts/fetch_eggs.py