1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/5e60f2efceaf/
changeset: 5e60f2efceaf
user: greg
date: 2013-01-31 17:39:12
summary: Uncomment the default sqlite database connection string in community_wsgi.ini.sample.
affected #: 1 file
diff -r f48d3ebce23e422d9bf9d87851460ba0976a5094 -r 5e60f2efceafaec9973ed1aa312cd66a0a11b3e8 community_wsgi.ini.sample
--- a/community_wsgi.ini.sample
+++ b/community_wsgi.ini.sample
@@ -22,7 +22,7 @@
log_level = DEBUG
# Database connection
-#database_file = database/community.sqlite
+database_file = database/community.sqlite
# You may use a SQLAlchemy connection string to specify an external database instead
#database_connection = postgres:///community_test?host=/var/run/postgresql
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/1605621deee2/
changeset: 1605621deee2
user: greg
date: 2013-01-31 15:28:40
summary: Restrict the ability to use reserved words in the tool shed for repository names and public user names.
affected #: 2 files
diff -r 04e22199687138a539734d108bc711fe96ab1083 -r 1605621deee25ec1ae8e7a72f4c1dc4f257f6760 lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -951,7 +951,9 @@
if not description:
message = 'Enter a description.'
error = True
- if not error:
+ if error:
+ status = 'error'
+ else:
# Add the repository record to the db
repository = trans.app.model.Repository( name=name,
description=description,
@@ -2458,15 +2460,17 @@
# in length and must contain only lower-case letters, numbers, and the '_' character.
if name in [ 'None', None, '' ]:
return 'Enter the required repository name.'
+ if name in [ 'repos' ]:
+ return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name
for repository in user.active_repositories:
if repository.name == name:
- return "You already have a repository named '%s', so choose a different name." % name
+ return "You already have a repository named <b>%s</b>, so choose a different name." % name
if len( name ) < 4:
return "Repository names must be at least 4 characters in length."
if len( name ) > 80:
return "Repository names cannot be more than 80 characters in length."
if not( VALID_REPOSITORYNAME_RE.match( name ) ):
- return "Repository names must contain only lower-case letters, numbers and underscore '_'."
+ return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>."
return ''
@web.expose
def view_changelog( self, trans, id, **kwd ):
diff -r 04e22199687138a539734d108bc711fe96ab1083 -r 1605621deee25ec1ae8e7a72f4c1dc4f257f6760 lib/galaxy/webapps/galaxy/controllers/user.py
--- a/lib/galaxy/webapps/galaxy/controllers/user.py
+++ b/lib/galaxy/webapps/galaxy/controllers/user.py
@@ -930,8 +930,11 @@
status=status )
def __validate( self, trans, params, email, password, confirm, username ):
# If coming from the community webapp, we'll require a public user name
- if trans.webapp.name == 'community' and not username:
- return "A public user name is required"
+ if trans.webapp.name == 'community':
+ if not username:
+ return "A public user name is required in the tool shed."
+ if username in [ 'repos' ]:
+ return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a public user name." % username
message = validate_email( trans, email )
if not message:
message = validate_password( trans, password, confirm )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/a1d543da698d/
changeset: a1d543da698d
user: james_taylor
date: 2013-01-30 16:32:16
summary: web.framework: remove stray print
affected #: 1 file
diff -r 2fcef846289917ccf394bb2fabba8f36d55d0039 -r a1d543da698d3d127cd9d7fedd61bd1ac5a19872 lib/galaxy/web/framework/__init__.py
--- a/lib/galaxy/web/framework/__init__.py
+++ b/lib/galaxy/web/framework/__init__.py
@@ -278,7 +278,6 @@
if not( fname.startswith( "_" ) ) and fname.endswith( ".py" ):
name = fname[:-3]
module_name = package_name + "." + name
- print package_name, name, module_name
try:
module = import_module( module_name )
except ControllerUnavailable, exc:
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
3 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/fdd9dd36d6e6/
changeset: fdd9dd36d6e6
user: inithello
date: 2013-01-30 20:54:41
summary: Enable specifying the location of the migrated tools' XML file.
affected #: 1 file
diff -r 43fa4cb72e0fdc207a07fc4c6402273ca4bd4fc6 -r fdd9dd36d6e6bdd17ecaa219c15a6afeb047748c lib/galaxy/config.py
--- a/lib/galaxy/config.py
+++ b/lib/galaxy/config.py
@@ -57,7 +57,7 @@
self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root )
# The value of migrated_tools_config is the file reserved for containing only those tools that have been eliminated from the distribution
# and moved to the tool shed.
- self.migrated_tools_config = resolve_path( "migrated_tools_conf.xml", self.root )
+ self.migrated_tools_config = resolve_path( kwargs.get( 'migrated_tools_config', 'migrated_tools_conf.xml' ), self.root )
if 'tool_config_file' in kwargs:
tcf = kwargs[ 'tool_config_file' ]
elif 'tool_config_files' in kwargs:
https://bitbucket.org/galaxy/galaxy-central/commits/8f56f551b194/
changeset: 8f56f551b194
user: inithello
date: 2013-01-30 20:55:08
summary: Enable running tool shed functional tests with run_functional_tests.sh.
affected #: 1 file
diff -r fdd9dd36d6e6bdd17ecaa219c15a6afeb047748c -r 8f56f551b194ef92029b88c5a774bf3d13220af3 run_functional_tests.sh
--- a/run_functional_tests.sh
+++ b/run_functional_tests.sh
@@ -6,11 +6,13 @@
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 -list' for listing all the tool ids"
+ 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 -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"
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
@@ -38,6 +40,12 @@
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
else
python ./scripts/functional_tests.py -v --with-nosehtml --html-report-file run_functional_tests.html $1
fi
https://bitbucket.org/galaxy/galaxy-central/commits/2fcef8462899/
changeset: 2fcef8462899
user: inithello
date: 2013-01-30 20:57:16
summary: Pass in a temporary file as migrated_tools_conf, so repositories without tools end up in the right location.
affected #: 1 file
diff -r 8f56f551b194ef92029b88c5a774bf3d13220af3 -r 2fcef846289917ccf394bb2fabba8f36d55d0039 test/tool_shed/functional_tests.py
--- a/test/tool_shed/functional_tests.py
+++ b/test/tool_shed/functional_tests.py
@@ -124,6 +124,7 @@
galaxy_tool_data_table_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_DATA_TABLE_CONF', os.path.join( tool_shed_test_tmp_dir, 'tool_data_table_conf.xml' ) )
galaxy_tool_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_tool_conf.xml' ) )
galaxy_shed_tool_conf_file = os.environ.get( 'GALAXY_TEST_SHED_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_shed_tool_conf.xml' ) )
+ galaxy_migrated_tool_conf_file = os.environ.get( 'GALAXY_TEST_MIGRATED_TOOL_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_migrated_tool_conf.xml' ) )
galaxy_tool_sheds_conf_file = os.environ.get( 'GALAXY_TEST_TOOL_SHEDS_CONF', os.path.join( tool_shed_test_tmp_dir, 'test_sheds_conf.xml' ) )
if 'GALAXY_TEST_TOOL_DATA_PATH' in os.environ:
tool_data_path = os.environ.get( 'GALAXY_TEST_TOOL_DATA_PATH' )
@@ -141,6 +142,7 @@
new_repos_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir )
galaxy_tempfiles = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir )
galaxy_shed_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir )
+ galaxy_migrated_tool_path = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir )
galaxy_tool_dependency_dir = tempfile.mkdtemp( dir=tool_shed_test_tmp_dir )
os.environ[ 'GALAXY_TEST_TOOL_DEPENDENCY_DIR' ] = galaxy_tool_dependency_dir
if 'TOOL_SHED_TEST_DBURI' in os.environ:
@@ -258,6 +260,9 @@
shed_tool_conf_template_parser = string.Template( shed_tool_conf_xml_template )
shed_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_shed_tool_path )
file( galaxy_shed_tool_conf_file, 'w' ).write( shed_tool_conf_xml )
+ # Generate the migrated_tool_conf.xml file.
+ migrated_tool_conf_xml = shed_tool_conf_template_parser.safe_substitute( shed_tool_path=galaxy_migrated_tool_path )
+ file( galaxy_migrated_tool_conf_file, 'w' ).write( migrated_tool_conf_xml )
os.environ[ 'GALAXY_TEST_SHED_TOOL_CONF' ] = galaxy_shed_tool_conf_file
# ---- Build Galaxy Application --------------------------------------------------
@@ -275,6 +280,7 @@
tool_data_path = tool_data_path,
shed_tool_path = galaxy_shed_tool_path,
update_integrated_tool_panel = False,
+ migrated_tools_config = galaxy_migrated_tool_conf_file,
tool_config_file = [ galaxy_tool_conf_file, galaxy_shed_tool_conf_file ],
tool_sheds_config_file = galaxy_tool_sheds_conf_file,
datatype_converters_config_file = "datatype_converters_conf.xml.sample",
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/43fa4cb72e0f/
changeset: 43fa4cb72e0f
user: dan
date: 2013-01-30 19:49:43
summary: Add a util.move_merge() function that makes moving directories more consistent.
affected #: 1 file
diff -r a9cbfdfeff11e2e2595b37825584216441a7a6d1 -r 43fa4cb72e0fdc207a07fc4c6402273ca4bd4fc6 lib/galaxy/util/__init__.py
--- a/lib/galaxy/util/__init__.py
+++ b/lib/galaxy/util/__init__.py
@@ -2,7 +2,7 @@
Utility functions used systemwide.
"""
-import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp, smtplib, errno
+import logging, threading, random, string, re, binascii, pickle, time, datetime, math, re, os, sys, tempfile, stat, grp, smtplib, errno, shutil
from email.MIMEText import MIMEText
# Older py compatibility
@@ -737,6 +737,18 @@
else:
raise e
+def move_merge( source, target ):
+ #when using shutil and moving a directory, if the target exists,
+ #then the directory is placed inside of it
+ #if the target doesn't exist, then the target is made into the directory
+ #this makes it so that the target is always the target, and if it exists,
+ #the source contents are moved into the target
+ if os.path.isdir( source ) and os.path.exists( target ) and os.path.isdir( target ):
+ for name in os.listdir( source ):
+ move_merge( os.path.join( source, name ), os.path.join( target, name ) )
+ else:
+ return shutil.move( source, target )
+
galaxy_root_path = os.path.join(__path__[0], "..","..","..")
# The dbnames list is used in edit attributes and the upload tool
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving
this because you have the service enabled, addressing the recipient of
this email.