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Merge pull request #2093 from davebx/move_scripts
Move scripts out of lib/tool_shed.
This commit is contained in:
John Chilton
@@ -4,7 +4,7 @@ import sys
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import urllib
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import urllib2
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sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir ) )
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sys.path.insert( 1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir, 'lib' ) )
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from tool_shed.util import hg_util
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from galaxy import util
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@@ -13,7 +13,7 @@ import sys
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import tempfile
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import urllib2
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sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir ) )
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sys.path.insert( 1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir, 'lib' ) )
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from tool_shed.util import basic_util
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from common import display, submit
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+9
-10
@@ -23,9 +23,8 @@ Here is a working example of how to use this script.
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import argparse
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import os
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import sys
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import urllib
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sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir ) )
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sys.path.insert( 1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir, 'lib' ) )
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from galaxy.util import asbool
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from tool_shed.util import hg_util
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@@ -44,14 +43,14 @@ def main( options ):
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test_install_error = str( options.test_install_error )
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tools_functionally_correct = str( options.tools_functionally_correct )
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parts = [ 'repository_revisions' ]
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params = urllib.urlencode( dict( do_not_test=do_not_test,
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downloadable=downloadable,
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includes_tools=includes_tools,
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malicious=malicious,
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missing_test_components=missing_test_components,
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skip_tool_test=skip_tool_test,
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test_install_error=test_install_error,
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tools_functionally_correct=tools_functionally_correct ) )
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params = dict( do_not_test=do_not_test,
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downloadable=downloadable,
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includes_tools=includes_tools,
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malicious=malicious,
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missing_test_components=missing_test_components,
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skip_tool_test=skip_tool_test,
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test_install_error=test_install_error,
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tools_functionally_correct=tools_functionally_correct )
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api_url = get_api_url( base=base_tool_shed_url, parts=parts, params=params )
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baseline_repository_dicts, error_message = json_from_url( api_url )
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if baseline_repository_dicts is None or error_message:
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+8
-8
@@ -11,15 +11,15 @@ stop_err() {
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exit 1
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}
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tool_shed=`./lib/tool_shed/scripts/bootstrap_tool_shed/parse_run_sh_args.sh $@`
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tool_shed=`./scripts/tool_shed/bootstrap_tool_shed/parse_run_sh_args.sh $@`
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if [ $? -ne 0 ] ; then
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exit 0
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fi
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log_file="lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap.log"
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log_file="scripts/tool_shed/bootstrap_tool_shed/bootstrap.log"
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database_result=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute check_db --config_file ${TOOL_SHED_CONFIG_FILE}`
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database_result=`python ./scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py --execute check_db --config_file ${TOOL_SHED_CONFIG_FILE}`
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if [ $? -ne 0 ] ; then
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stop_err "Unable to bootstrap tool shed. $database_result"
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@@ -36,8 +36,8 @@ else
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fi
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if [ $? -eq 0 ] ; then
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user_auth=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute admin_user_info --config_file ${TOOL_SHED_CONFIG_FILE}`
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local_shed_url=`python ./lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_util.py --execute get_url --config_file ${TOOL_SHED_CONFIG_FILE}`
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user_auth=`python ./scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py --execute admin_user_info --config_file ${TOOL_SHED_CONFIG_FILE}`
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local_shed_url=`python ./scripts/tool_shed/bootstrap_tool_shed/bootstrap_util.py --execute get_url --config_file ${TOOL_SHED_CONFIG_FILE}`
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fi
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admin_user_name=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$1 }'`
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@@ -46,7 +46,7 @@ admin_user_password=`echo $user_auth | awk 'BEGIN { FS="__SEP__" } ; { print \$3
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echo -n "Creating user '$admin_user_name' with email address '$admin_user_email'..."
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python ./lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py -c ${TOOL_SHED_CONFIG_FILE} >> $log_file
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python ./scripts/tool_shed/bootstrap_tool_shed/create_user_with_api_key.py -c ${TOOL_SHED_CONFIG_FILE} >> $log_file
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echo " done."
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@@ -94,10 +94,10 @@ echo " done."
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if [ $? -eq 0 ] ; then
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echo -n "Creating users... "
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python lib/tool_shed/scripts/api/create_users.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file
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python scripts/tool_shed/api/create_users.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file
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echo "done."
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echo -n "Creating categories... "
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python lib/tool_shed/scripts/api/create_categories.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file
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python scripts/tool_shed/api/create_categories.py -a $api_key -f $tool_shed -t $local_shed_url >> $log_file
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echo "done."
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else
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stop_err "Error getting API key from local tool shed."
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+2
-2
@@ -4,7 +4,7 @@ import ConfigParser
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import os
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import sys
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sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir ) )
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sys.path.insert( 1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir, 'lib' ) )
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from sqlalchemy.exc import OperationalError, ProgrammingError
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@@ -69,7 +69,7 @@ def check_db( config_parser ):
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def admin_user_info( ):
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user_info_config = os.path.abspath( os.path.join( os.getcwd(), 'lib/tool_shed/scripts/bootstrap_tool_shed', 'user_info.xml' ) )
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user_info_config = os.path.abspath( os.path.join( os.getcwd(), 'scripts/tool_shed/bootstrap_tool_shed', 'user_info.xml' ) )
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tree, error_message = xml_util.parse_xml( user_info_config )
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username = None
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email = None
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+1
-1
@@ -7,7 +7,7 @@ import re
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import sys
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import optparse
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sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir ) )
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sys.path.insert(1, os.path.join( os.path.dirname( __file__ ), os.pardir, os.pardir, os.pardir, 'lib' ) )
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sys.path.insert(1, os.path.join( os.path.dirname( __file__ ) ) )
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import galaxy.webapps.tool_shed.config as tool_shed_config
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