1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/38f8adbf6a47/
Changeset: 38f8adbf6a47
User: dan
Date: 2014-09-02 18:50:37
Summary: Fix for custom dbkeys when chrom count dataset has been deleted.
Affected #: 1 file
diff -r d8eccdf88c8090e7237dca11502c5c62b3388bc0 -r 38f8adbf6a47aa05b64c8dd46ee828c36628df31 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -1680,9 +1680,12 @@
continue
else:
# Set chrom count.
- chrom_count = int( open( chrom_count_dataset.file_name ).readline() )
- attributes[ 'count' ] = chrom_count
- updated = True
+ try:
+ chrom_count = int( open( chrom_count_dataset.file_name ).readline() )
+ attributes[ 'count' ] = chrom_count
+ updated = True
+ except Exception, e:
+ log.error( "Failed to open chrom count dataset: %s", e )
if updated:
user.preferences['dbkeys'] = to_json_string(dbkeys)
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/d8eccdf88c80/
Changeset: d8eccdf88c80
User: jmchilton
Date: 2014-09-02 18:35:33
Summary: Small improvements to JavaScript testing with run_tests.sh.
Add new -j|--casperjs option to run through the casperjs test suite. Ensure grunt is on path before attempting to run qunit tests. A more useful version of this changeset which automatically installed phantomjs, casperjs, grunt, and npm as needed and added the required tools to the tester's path (https://bitbucket.org/jmchilton/galaxy-central-fork-1/commits/0919fc9403933…) proved unpopular because of implementation details - see conversation here https://bitbucket.org/galaxy/galaxy-central/pull-request/461/remove-depreca….
Affected #: 2 files
diff -r 7f729ff2483d6aed19100542e102f14e3f2f11b1 -r d8eccdf88c8090e7237dca11502c5c62b3388bc0 run_tests.sh
--- a/run_tests.sh
+++ b/run_tests.sh
@@ -31,6 +31,19 @@
echo "'${0##*/} -sid ccc' for testing one section with sid 'ccc' ('ccc' is the string after 'section::')"
}
+exists() {
+ type "$1" >/dev/null 2>/dev/null
+}
+
+ensure_grunt() {
+ if ! exists "grunt";
+ then
+ echo "Grunt not on path, cannot run these tests."
+ exit 1
+ fi
+}
+
+
test_script="./scripts/functional_tests.py"
report_file="run_functional_tests.html"
with_framework_test_tools_arg=""
@@ -110,6 +123,12 @@
data_managers_test=1;
shift 1
;;
+ -j|-casperjs|--casperjs)
+ # TODO: Support running casper tests against existing
+ # Galaxy instances.
+ casperjs_test=1;
+ shift
+ ;;
-m|-migrated|--migrated)
migrated_test=1;
shift
@@ -196,6 +215,11 @@
extra_args="$toolshed_script"
elif [ -n "$api_script" ]; then
extra_args="$api_script"
+elif [ -n "$casperjs_test" ]; then
+ # TODO: Ensure specific versions of casperjs and phantomjs are
+ # available. Some option for leveraging npm to automatically
+ # install these dependencies would be nice as well.
+ extra_args="test/casperjs/casperjs_runner.py"
elif [ -n "$section_id" ]; then
extra_args=`python tool_list.py $section_id`
elif [ -n "$test_id" ]; then
@@ -212,6 +236,7 @@
if [ "$driver" = "python" ]; then
python $test_script $coverage_arg -v --with-nosehtml --html-report-file $report_file $with_framework_test_tools_arg $extra_args
else
+ ensure_grunt
if [ -n "$watch" ]; then
grunt_task="watch"
else
diff -r 7f729ff2483d6aed19100542e102f14e3f2f11b1 -r d8eccdf88c8090e7237dca11502c5c62b3388bc0 test/casperjs/casperjs_runner.py
--- a/test/casperjs/casperjs_runner.py
+++ b/test/casperjs/casperjs_runner.py
@@ -6,8 +6,9 @@
* casperjs test mytests.js --url='http://localhost:8080'
* python casperjs_runner.py
* nosetests
-* sh run_functional_tests.sh test/casperjs/casperjs_runner.py
-* sh run_functional_tests.sh
+* sh run_tests.sh -j
+* sh run_tests.sh test/casperjs/casperjs_runner.py
+* sh run_tests.sh
Note: that you can enable (lots of) debugging info using cli options:
* casperjs test api-user-tests.js --url='http://localhost:8080' --verbose=true --logLevel=debug
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/6b26b7df6924/
Changeset: 6b26b7df6924
User: jmchilton
Date: 2014-09-02 17:50:43
Summary: Remove deprecated test running scripts.
- run_functional_tests.sh can be replaced with the backward compatible run_tests.sh.
- run_unit_tests.sh can be replaced with `run_tests.sh --unit` (or just -u)
- run_tool_shed_functional_tests.sh can be replaced with `./run_tests.sh -toolshed` (or just -t).
In each case run_tests.sh provides better documentation and superior argument parsing.
Affected #: 3 files
diff -r d3e72ceda152bd813cca2ca676a6ad1f3e7deb5a -r 6b26b7df6924de890ee547f96f939fcd73cfe60b run_functional_tests.sh
--- a/run_functional_tests.sh
+++ /dev/null
@@ -1,82 +0,0 @@
-#!/bin/sh
-
-# A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/
-rm -f run_functional_tests.log
-
-if [ ! $1 ]; then
- 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)"
- 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::')"
- echo "'run_functional_tests.sh -api' for running API functional tests"
- 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 -workflow test.xml' for running a workflow test case as defined by supplied workflow xml test file"
- 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'"
- echo "'run_functional_tests.sh -data_managers -id data_manager_id' for testing one Data Manager with id 'data_manager_id'"
-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
- 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::')"
-elif [ $1 = '-migrated' ]; then
- if [ ! $2 ]; then
- python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -migrated
- elif [ $2 = '-id' ]; then
- # TODO: This option is not tested...
- python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$3 --with-nosehtml --html-report-file run_functional_tests.html -migrated
- else
- python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -migrated
- fi
-elif [ $1 = '-installed' ]; then
- if [ ! $2 ]; then
- python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -installed
- elif [ $2 = '-id' ]; then
- # TODO: This option is not tested...
- python ./scripts/functional_tests.py -v functional.test_toolbox:TestForTool_$3 --with-nosehtml --html-report-file run_functional_tests.html -installed
- else
- python ./scripts/functional_tests.py -v functional.test_toolbox --with-nosehtml --html-report-file run_functional_tests.html -installed
- fi
-elif [ $1 = '-toolshed' ]; then
- if [ ! $2 ]; then
- python ./test/tool_shed/functional_tests.py -v --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html ./test/tool_shed/functional
- 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 = '-api' ]; then
- if [ ! $2 ]; then
- python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_api_tests.html ./test/api
- else
- python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_api_tests.html $2
- fi
-elif [ $1 = '-workflow' ]; then
- python ./scripts/functional_tests.py -v functional.workflow:WorkflowTestCase --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html -workflow $2
-elif [ $1 = '-data_managers' ]; then
- if [ ! $2 ]; then
- python ./scripts/functional_tests.py -v functional.test_data_managers --with-nosehtml --html-report-file run_functional_tests.html -data_managers
- elif [ $2 = '-id' ]; then
- python ./scripts/functional_tests.py -v functional.test_data_managers:TestForDataManagerTool_$3 --with-nosehtml --html-report-file run_functional_tests.html -data_managers
- else
- python ./scripts/functional_tests.py -v functional.test_data_managers --with-nosehtml --html-report-file run_functional_tests.html -data_managers
- 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
-
-echo "'run_functional_tests.sh help' for help"
diff -r d3e72ceda152bd813cca2ca676a6ad1f3e7deb5a -r 6b26b7df6924de890ee547f96f939fcd73cfe60b run_tool_shed_functional_tests.sh
--- a/run_tool_shed_functional_tests.sh
+++ /dev/null
@@ -1,15 +0,0 @@
-#!/bin/sh
-
-# A good place to look for nose info: http://somethingaboutorange.com/mrl/projects/nose/
-#rm -f ./test/tool_shed/run_functional_tests.log
-
-if [ ! $1 ]; then
- python ./test/tool_shed/functional_tests.py -v --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html ./test/tool_shed/functional
-elif [ $1 = 'help' ]; then
- echo "'run_tool_shed_functional_tests.sh' for running all the test scripts in the ./test/tool_shed/functional directory"
- echo "'run_tool_shed_functional_tests.sh testscriptname' for running one test script named testscriptname in the .test/tool_shed/functional directory"
-else
- python ./test/tool_shed/functional_tests.py -v --with-nosehtml --html-report-file ./test/tool_shed/run_functional_tests.html $1
-fi
-
-echo "'sh run_tool_shed_functional_tests.sh help' for help"
diff -r d3e72ceda152bd813cca2ca676a6ad1f3e7deb5a -r 6b26b7df6924de890ee547f96f939fcd73cfe60b run_unit_tests.sh
--- a/run_unit_tests.sh
+++ /dev/null
@@ -1,16 +0,0 @@
-#!/bin/sh
-
-## Excluding controllers due to the problematic genetrack dependency
-## Excluding job runners due to various external dependencies
-
-COVERAGE=`which coverage`
-COVERAGE_ARG=""
-if [ $COVERAGE ]; then
- COVERAGE_ARG="--with-coverage"
-fi
-
-python ./scripts/nosetests.py -v \
- $COVERAGE_ARG \
- --with-nosehtml --html-report-file run_unit_tests.html \
- --with-doctest --exclude=functional --exclude="^get" \
- --exclude=controllers --exclude=runners lib test/unit
https://bitbucket.org/galaxy/galaxy-central/commits/7f729ff2483d/
Changeset: 7f729ff2483d
User: jmchilton
Date: 2014-09-02 17:50:43
Summary: Fixup comments and add README for test/casperjs directory.
Affected #: 2 files
diff -r 6b26b7df6924de890ee547f96f939fcd73cfe60b -r 7f729ff2483d6aed19100542e102f14e3f2f11b1 test/casperjs/README.txt
--- /dev/null
+++ b/test/casperjs/README.txt
@@ -0,0 +1,4 @@
+This directory contains the Galaxy framework written by Carl Eberhard
+for running headless browser tests using CasperJS and PhantomJS.
+
+See notes at the top of casperjs_runner.py for more information.
diff -r 6b26b7df6924de890ee547f96f939fcd73cfe60b -r 7f729ff2483d6aed19100542e102f14e3f2f11b1 test/casperjs/casperjs_runner.py
--- a/test/casperjs/casperjs_runner.py
+++ b/test/casperjs/casperjs_runner.py
@@ -6,16 +6,16 @@
* casperjs test mytests.js --url='http://localhost:8080'
* python casperjs_runner.py
* nosetests
-* sh run_functional_tests.sh test/casperjs/test_runner
+* sh run_functional_tests.sh test/casperjs/casperjs_runner.py
* sh run_functional_tests.sh
Note: that you can enable (lots of) debugging info using cli options:
-* casperjs test usertests.js --url='http://localhost:8080' --verbose=true --logLevel=debug
+* casperjs test api-user-tests.js --url='http://localhost:8080' --verbose=true --logLevel=debug
(see casperjs.org for more information)
-Note: This seems to not work with CasperJS 1.1 (and PhantomJS 1.9) - Casper 1.0.xx and
-PhantomJS 1.8 work for me (John).
+Note: This works with CasperJS 1.1 and PhantomJS 1.9.2 and these libraries seem to break backward
+compatbility a lot.
Note: You can pass in extra data using --data='<some JSON object>'
and it will be available in your script as spaceghost.fixtureData.
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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