commit/galaxy-central: greg: Automatically create missing required tool shed files from samples when startign the tool shed server.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/2a34f751c32c/
changeset: 2a34f751c32c
user: greg
date: 2013-01-31 17:47:32
summary: Automatically create missing required tool shed files from samples when startign the tool shed server.
affected #: 1 file
diff -r 5e60f2efceafaec9973ed1aa312cd66a0a11b3e8 -r 2a34f751c32cb9b4ab271d1f14c99406b9d04a54 run_community.sh
--- a/run_community.sh
+++ b/run_community.sh
@@ -1,4 +1,37 @@
#!/bin/sh
cd `dirname $0`
+
+SAMPLES="
+ community_wsgi.ini.sample
+ datatypes_conf.xml.sample
+ external_service_types_conf.xml.sample
+ migrated_tools_conf.xml.sample
+ reports_wsgi.ini.sample
+ shed_tool_conf.xml.sample
+ tool_conf.xml.sample
+ shed_tool_data_table_conf.xml.sample
+ tool_data_table_conf.xml.sample
+ tool_sheds_conf.xml.sample
+ openid_conf.xml.sample
+ universe_wsgi.ini.sample
+ tool-data/shared/ncbi/builds.txt.sample
+ tool-data/shared/ensembl/builds.txt.sample
+ tool-data/shared/ucsc/builds.txt.sample
+ tool-data/shared/ucsc/publicbuilds.txt.sample
+ tool-data/shared/igv/igv_build_sites.txt.sample
+ tool-data/shared/rviewer/rviewer_build_sites.txt.sample
+ tool-data/*.sample
+ static/welcome.html.sample
+"
+
+# Create any missing config/location files
+for sample in $SAMPLES; do
+ file=`echo $sample | sed -e 's/\.sample$//'`
+ if [ ! -f "$file" -a -f "$sample" ]; then
+ echo "Initializing $file from `basename $sample`"
+ cp $sample $file
+ fi
+done
+
python ./scripts/paster.py serve community_wsgi.ini --pid-file=community_webapp.pid --log-file=community_webapp.log $@
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Uncomment the default sqlite database connection string in community_wsgi.ini.sample.
by Bitbucket
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/
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commit/galaxy-central: greg: Allow a Galaxy admin to select a shed-related tool panel config file whose tool_path setting will be used to installed repositories into Galaxy for those repositories with which a tool panel selection is not necessary.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/f48d3ebce23e/
changeset: f48d3ebce23e
user: greg
date: 2013-01-31 17:33:15
summary: Allow a Galaxy admin to select a shed-related tool panel config file whose tool_path setting will be used to installed repositories into Galaxy for those repositories with which a tool panel selection is not necessary.
affected #: 4 files
diff -r 1605621deee25ec1ae8e7a72f4c1dc4f257f6760 -r f48d3ebce23e422d9bf9d87851460ba0976a5094 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -2088,10 +2088,7 @@
label = "-1:%s" % changeset_revision
return rev, label
def get_shed_tool_conf_dict( app, shed_tool_conf ):
- """
- Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry
- in the shed_tool_conf_dict associated with the file.
- """
+ """Return the in-memory version of the shed_tool_conf file, which is stored in the config_elems entry in the shed_tool_conf_dict associated with the file."""
for index, shed_tool_conf_dict in enumerate( app.toolbox.shed_tool_confs ):
if shed_tool_conf == shed_tool_conf_dict[ 'config_filename' ]:
return index, shed_tool_conf_dict
diff -r 1605621deee25ec1ae8e7a72f4c1dc4f257f6760 -r f48d3ebce23e422d9bf9d87851460ba0976a5094 lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -1199,6 +1199,7 @@
return trans.show_error_message( message )
message = kwd.get( 'message', '' )
status = kwd.get( 'status', 'done' )
+ shed_tool_conf = kwd.get( 'shed_tool_conf', None )
tool_shed_url = kwd[ 'tool_shed_url' ]
# Handle repository dependencies.
has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) )
@@ -1229,16 +1230,9 @@
includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) )
encoded_repo_info_dicts = util.listify( repo_information_dict.get( 'repo_info_dicts', [] ) )
repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ]
- if ( not includes_tools and not has_repository_dependencies ) or \
+ if ( ( not includes_tools and not has_repository_dependencies ) and kwd.get( 'select_shed_tool_panel_config_button', False ) ) or \
( ( includes_tools or has_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ):
install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies )
- if includes_tools:
- shed_tool_conf = kwd[ 'shed_tool_conf' ]
- else:
- # If installing a repository that includes no tools, get the relative tool_path from the file to which the migrated_tools_config
- # setting points.
- # FIXME: default to a temporary file or raise an exception or display an appropriate error message.
- shed_tool_conf = trans.app.config.migrated_tools_config
if includes_tool_dependencies:
install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies )
else:
@@ -1327,14 +1321,7 @@
return trans.response.send_redirect( web.url_for( controller='admin_toolshed',
action='manage_repositories',
**kwd ) )
- if len( trans.app.toolbox.shed_tool_confs ) > 1:
- shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
- shed_tool_conf = None
- else:
- shed_tool_conf_dict = trans.app.toolbox.shed_tool_confs[0]
- shed_tool_conf = shed_tool_conf_dict[ 'config_filename' ]
- shed_tool_conf = shed_tool_conf.replace( './', '', 1 )
- shed_tool_conf_select_field = None
+ shed_tool_conf_select_field = build_shed_tool_conf_select_field( trans )
tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf )
tool_panel_section_select_field = build_tool_panel_section_select_field( trans )
if len( repo_info_dicts ) == 1:
@@ -1387,21 +1374,40 @@
install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked )
# Handle repository dependencies check box.
install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True )
- return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
- encoded_repo_info_dicts=encoded_repo_info_dicts,
- includes_tools=includes_tools,
- includes_tool_dependencies=includes_tool_dependencies,
- install_tool_dependencies_check_box=install_tool_dependencies_check_box,
- has_repository_dependencies=has_repository_dependencies,
- install_repository_dependencies_check_box=install_repository_dependencies_check_box,
- new_tool_panel_section=new_tool_panel_section,
- containers_dict=containers_dict,
- shed_tool_conf=shed_tool_conf,
- shed_tool_conf_select_field=shed_tool_conf_select_field,
- tool_panel_section_select_field=tool_panel_section_select_field,
- tool_shed_url=kwd[ 'tool_shed_url' ],
- message=message,
- status=status )
+ if includes_tools or has_repository_dependencies:
+ return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako',
+ encoded_repo_info_dicts=encoded_repo_info_dicts,
+ includes_tools=includes_tools,
+ includes_tool_dependencies=includes_tool_dependencies,
+ install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+ has_repository_dependencies=has_repository_dependencies,
+ install_repository_dependencies_check_box=install_repository_dependencies_check_box,
+ new_tool_panel_section=new_tool_panel_section,
+ containers_dict=containers_dict,
+ shed_tool_conf=shed_tool_conf,
+ shed_tool_conf_select_field=shed_tool_conf_select_field,
+ tool_panel_section_select_field=tool_panel_section_select_field,
+ tool_shed_url=kwd[ 'tool_shed_url' ],
+ message=message,
+ status=status )
+ else:
+ # If installing repositories that includes no tools and has not repository dependencies, display a page allowing the Galaxy administrator to
+ # select a shed-related tool panel configuration file whose tool_path setting will be the location the repositories will be installed.
+ return trans.fill_template( '/admin/tool_shed_repository/select_shed_tool_panel_config.mako',
+ encoded_repo_info_dicts=encoded_repo_info_dicts,
+ includes_tools=includes_tools,
+ includes_tool_dependencies=includes_tool_dependencies,
+ install_tool_dependencies_check_box=install_tool_dependencies_check_box,
+ has_repository_dependencies=has_repository_dependencies,
+ install_repository_dependencies_check_box=install_repository_dependencies_check_box,
+ new_tool_panel_section=new_tool_panel_section,
+ containers_dict=containers_dict,
+ shed_tool_conf=shed_tool_conf,
+ shed_tool_conf_select_field=shed_tool_conf_select_field,
+ tool_panel_section_select_field=tool_panel_section_select_field,
+ tool_shed_url=kwd[ 'tool_shed_url' ],
+ message=message,
+ status=status )
@web.expose
@web.require_admin
def reinstall_repository( self, trans, **kwd ):
diff -r 1605621deee25ec1ae8e7a72f4c1dc4f257f6760 -r f48d3ebce23e422d9bf9d87851460ba0976a5094 templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
--- /dev/null
+++ b/templates/admin/tool_shed_repository/select_shed_tool_panel_config.mako
@@ -0,0 +1,114 @@
+<%inherit file="/base.mako"/>
+<%namespace file="/message.mako" import="render_msg" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="render_dependencies_section" />
+<%namespace file="/admin/tool_shed_repository/common.mako" import="render_readme_section" />
+<%namespace file="/webapps/community/repository/common.mako" import="*" />
+
+<%def name="stylesheets()">
+ ${parent.stylesheets()}
+ ${h.css( "library" )}
+</%def>
+
+<%def name="javascripts()">
+ ${parent.javascripts()}
+ ${h.js("libs/jquery/jquery.rating", "libs/jquery/jstorage" )}
+ ${container_javascripts()}
+</%def>
+
+<%
+ # Handle the case where an uninstalled repository encountered errors during the process of being reinstalled. In
+ # this case, the repository metadata is an empty dictionary, but one or both of has_repository_dependencies
+ # and includes_tool_dependencies may be True. If either of these are True but we have no metadata, we cannot install
+ # repository dependencies on this pass.
+ if has_repository_dependencies:
+ repository_dependencies = containers_dict[ 'repository_dependencies' ]
+ missing_repository_dependencies = containers_dict[ 'missing_repository_dependencies' ]
+ if repository_dependencies or missing_repository_dependencies:
+ can_display_repository_dependencies = True
+ else:
+ can_display_repository_dependencies = False
+ else:
+ can_display_repository_dependencies = False
+ if includes_tool_dependencies:
+ tool_dependencies = containers_dict[ 'tool_dependencies' ]
+ missing_tool_dependencies = containers_dict[ 'missing_tool_dependencies' ]
+ if tool_dependencies or missing_tool_dependencies:
+ can_display_tool_dependencies = True
+ else:
+ can_display_tool_dependencies = False
+ else:
+ can_display_tool_dependencies = False
+%>
+
+%if message:
+ ${render_msg( message, status )}
+%endif
+
+<div class="warningmessage">
+ <p>
+ The core Galaxy development team does not maintain the contents of many Galaxy tool shed repositories. Some repository tools
+ may include code that produces malicious behavior, so be aware of what you are installing.
+ </p>
+ <p>
+ If you discover a repository that causes problems after installation, contact <a href="http://wiki.g2.bx.psu.edu/Support" target="_blank">Galaxy support</a>,
+ sending all necessary information, and appropriate action will be taken.
+ </p>
+ <p>
+ <a href="http://wiki.g2.bx.psu.edu/Tool%20Shed#Contacting_the_owner_of_a_repository" target="_blank">Contact the repository owner</a> for
+ general questions or concerns.
+ </p>
+</div>
+<div class="toolForm">
+ <div class="toolFormBody">
+ <form name="select_shed_tool_panel_config" id="select_shed_tool_panel_config" action="${h.url_for( controller='admin_toolshed', action='prepare_for_install', tool_shed_url=tool_shed_url, encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, includes_tool_dependencies=includes_tool_dependencies )}" method="post" >
+ <div style="clear: both"></div>
+ <% readme_files_dict = containers_dict.get( 'readme_files', None ) %>
+ %if readme_files_dict:
+ <div class="form-row">
+ <table class="colored" width="100%">
+ <th bgcolor="#EBD9B2">Repository README file - may contain important installation or license information</th>
+ </table>
+ </div>
+ ${render_readme_section( containers_dict )}
+ <div style="clear: both"></div>
+ %endif
+ %if can_display_repository_dependencies or can_display_tool_dependencies:
+ <div class="form-row">
+ <table class="colored" width="100%">
+ <th bgcolor="#EBD9B2">Confirm dependency installation</th>
+ </table>
+ </div>
+ ${render_dependencies_section( install_repository_dependencies_check_box, install_tool_dependencies_check_box, containers_dict )}
+ <div style="clear: both"></div>
+ %endif
+ <div class="form-row">
+ <table class="colored" width="100%">
+ <th bgcolor="#EBD9B2">Choose the configuration file whose tool_path setting will be used for installing repositories</th>
+ </table>
+ </div>
+ %if shed_tool_conf_select_field:
+ <%
+ if len( shed_tool_conf_select_field.options ) == 1:
+ select_help = "Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be "
+ select_help += "installed using it's <b>tool_path</b> setting."
+ else:
+ select_help = "Your Galaxy instance is configured with %d shed-related tool configuration files, " % len( shed_tool_conf_select_field.options )
+ select_help += "so select the file whose <b>tool_path</b> setting you want used for installing repositories."
+ %>
+ <div class="form-row">
+ <label>Shed tool configuration file:</label>
+ ${shed_tool_conf_select_field.get_html()}
+ <div class="toolParamHelp" style="clear: both;">
+ ${select_help}
+ </div>
+ </div>
+ <div style="clear: both"></div>
+ %else:
+ <input type="hidden" name="shed_tool_conf" value="${shed_tool_conf}"/>
+ %endif
+ <div class="form-row">
+ <input type="submit" name="select_shed_tool_panel_config_button" value="Install"/>
+ </div>
+ </form>
+ </div>
+</div>
diff -r 1605621deee25ec1ae8e7a72f4c1dc4f257f6760 -r f48d3ebce23e422d9bf9d87851460ba0976a5094 templates/admin/tool_shed_repository/select_tool_panel_section.mako
--- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako
+++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako
@@ -87,12 +87,19 @@
</table></div>
%if shed_tool_conf_select_field:
+ <%
+ if len( shed_tool_conf_select_field.options ) == 1:
+ select_help = "Your Galaxy instance is configured with 1 shed-related tool configuration file, so repositories will be "
+ select_help += "installed using it's <b>tool_path</b> setting."
+ else:
+ select_help = "Your Galaxy instance is configured with %d shed-related tool configuration files, " % len( shed_tool_conf_select_field.options )
+ select_help += "so select the file whose <b>tool_path</b> setting you want used for installing repositories."
+ %><div class="form-row"><label>Shed tool configuration file:</label>
${shed_tool_conf_select_field.get_html()}
<div class="toolParamHelp" style="clear: both;">
- Your Galaxy instance is configured with ${len( shed_tool_conf_select_field.options )} shed tool configuration files,
- so choose one in which to configure the installed tools.
+ ${select_help}
</div></div><div style="clear: both"></div>
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Restrict the ability to use reserved words in the tool shed for repository names and public user names.
by Bitbucket
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/
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commit/galaxy-central: greg: Dont' assume a complex repository dependency was properly defined.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/04e221996871/
changeset: 04e221996871
user: greg
date: 2013-01-30 22:47:20
summary: Dont' assume a complex repository dependency was properly defined.
affected #: 1 file
diff -r ea3da2000fa733a2d3ff5d5629dec58d3573645c -r 04e22199687138a539734d108bc711fe96ab1083 lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -1223,7 +1223,8 @@
current_rd_tups, error_message = handle_repository_elem( app=app,
repository_elem=sub_elem,
repository_dependencies_tups=None )
- repository_dependency_tup = current_rd_tups[ 0 ]
+ if current_rd_tups:
+ repository_dependency_tup = current_rd_tups[ 0 ]
if requirements_dict:
dependency_key = '%s/%s' % ( package_name, package_version )
tool_dependencies_dict[ dependency_key ] = requirements_dict
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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commit/galaxy-central: greg: Support for installation and administration of complex repository dependencies in Galaxy.
by Bitbucket
1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/ea3da2000fa7/
changeset: ea3da2000fa7
user: greg
date: 2013-01-30 22:29:37
summary: Support for installation and administration of complex repository dependencies in Galaxy.
affected #: 7 files
diff -r 618c34d9b2eab385e092c9ca2d7dd07b9ea31024 -r ea3da2000fa733a2d3ff5d5629dec58d3573645c lib/galaxy/model/__init__.py
--- a/lib/galaxy/model/__init__.py
+++ b/lib/galaxy/model/__init__.py
@@ -3153,6 +3153,11 @@
def can_reinstall_or_activate( self ):
return self.deleted
@property
+ def has_readme_files( self ):
+ if self.metadata:
+ return 'readme_files' in self.metadata
+ return False
+ @property
def has_repository_dependencies( self ):
if self.metadata:
return 'repository_dependencies' in self.metadata
@@ -3176,11 +3181,6 @@
def in_error_state( self ):
return self.status == self.installation_status.ERROR
@property
- def has_readme_files( self ):
- if self.metadata:
- return 'readme_files' in self.metadata
- return False
- @property
def repository_dependencies( self ):
required_repositories = []
for rrda in self.required_repositories:
diff -r 618c34d9b2eab385e092c9ca2d7dd07b9ea31024 -r ea3da2000fa733a2d3ff5d5629dec58d3573645c lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/fabric_util.py
@@ -50,6 +50,7 @@
install_dir = actions_dict[ 'install_dir' ]
package_name = actions_dict[ 'package_name' ]
actions = actions_dict.get( 'actions', None )
+ filtered_actions = []
if actions:
with make_tmp_dir() as work_dir:
with lcd( work_dir ):
@@ -57,6 +58,8 @@
# are currently only two supported processes; download_by_url and clone via a "shell_command" action type.
action_type, action_dict = actions[ 0 ]
if action_type == 'download_by_url':
+ # Eliminate the download_by_url action so remaining actions can be processed correctly.
+ filtered_actions = actions[ 1: ]
url = action_dict[ 'url' ]
if 'target_filename' in action_dict:
downloaded_filename = action_dict[ 'target_filename' ]
@@ -75,15 +78,24 @@
dir = work_dir
elif action_type == 'shell_command':
# <action type="shell_command">git clone --recursive git://github.com/ekg/freebayes.git</action>
+ # Eliminate the shell_command clone action so remaining actions can be processed correctly.
+ filtered_actions = actions[ 1: ]
return_code = handle_command( app, tool_dependency, install_dir, action_dict[ 'command' ] )
if return_code:
return
dir = package_name
+ else:
+ # We're handling a complex repository dependency where we only have a set_environment tag set.
+ # <action type="set_environment">
+ # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+ # </action>
+ filtered_actions = [ a for a in actions ]
+ dir = install_dir
if not os.path.exists( dir ):
os.makedirs( dir )
# The package has been down-loaded, so we can now perform all of the actions defined for building it.
with lcd( dir ):
- for action_tup in actions[ 1: ]:
+ for action_tup in filtered_actions:
action_type, action_dict = action_tup
current_dir = os.path.abspath( os.path.join( work_dir, dir ) )
if action_type == 'make_directory':
@@ -93,6 +105,8 @@
source_dir=os.path.join( action_dict[ 'source_directory' ] ),
destination_dir=os.path.join( action_dict[ 'destination_directory' ] ) )
elif action_type == 'move_file':
+ # TODO: Remove this hack that resets current_dir so that the pre-compiled bwa binary can be found.
+ # current_dir = '/Users/gvk/workspaces_2008/bwa/bwa-0.5.9'
common_util.move_file( current_dir=current_dir,
source=os.path.join( action_dict[ 'source' ] ),
destination_dir=os.path.join( action_dict[ 'destination' ] ) )
diff -r 618c34d9b2eab385e092c9ca2d7dd07b9ea31024 -r ea3da2000fa733a2d3ff5d5629dec58d3573645c lib/galaxy/tool_shed/tool_dependencies/install_util.py
--- a/lib/galaxy/tool_shed/tool_dependencies/install_util.py
+++ b/lib/galaxy/tool_shed/tool_dependencies/install_util.py
@@ -1,8 +1,9 @@
-import sys, os, subprocess, tempfile
+import sys, os, subprocess, tempfile, urllib2
import common_util
import fabric_util
from galaxy.tool_shed import encoding_util
from galaxy.model.orm import and_
+from galaxy.web import url_for
from galaxy import eggs
import pkg_resources
@@ -11,6 +12,9 @@
from elementtree import ElementTree, ElementInclude
from elementtree.ElementTree import Element, SubElement
+def clean_tool_shed_url( base_url ):
+ protocol, base = base_url.split( '://' )
+ return base.rstrip( '/' )
def create_or_update_tool_dependency( app, tool_shed_repository, name, version, type, status, set_status=True ):
# Called from Galaxy (never the tool shed) when a new repository is being installed or when an uninstalled repository is being reinstalled.
sa_session = app.model.context.current
@@ -28,6 +32,64 @@
sa_session.add( tool_dependency )
sa_session.flush()
return tool_dependency
+def create_temporary_tool_dependencies_config( tool_shed_url, name, owner, changeset_revision ):
+ """Make a call to the tool shed to get the required repository's tool_dependencies.xml file."""
+ url = url_join( tool_shed_url,
+ 'repository/get_tool_dependencies_config_contents?name=%s&owner=%s&changeset_revision=%s' % \
+ ( name, owner, changeset_revision ) )
+ response = urllib2.urlopen( url )
+ text = response.read()
+ response.close()
+ if text:
+ # Write the contents to a temporary file on disk so it can be reloaded and parsed.
+ fh = tempfile.NamedTemporaryFile( 'wb' )
+ tmp_filename = fh.name
+ fh.close()
+ fh = open( tmp_filename, 'wb' )
+ fh.write( text )
+ fh.close()
+ return tmp_filename
+ else:
+ message = "Unable to retrieve required tool_dependencies.xml file from the tool shed for revision "
+ message += "%s of installed repository %s owned by %s." % ( str( changeset_revision ), str( name ), str( owner ) )
+ raise Exception( message )
+ return None
+def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ):
+ """Return the absolute path to a specified disk file contained in a repository."""
+ stripped_file_name = strip_path( file_name )
+ file_path = None
+ for root, dirs, files in os.walk( repo_files_dir ):
+ if root.find( '.hg' ) < 0:
+ for name in files:
+ if name == stripped_file_name:
+ return os.path.abspath( os.path.join( root, name ) )
+ return file_path
+def get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( app, tool_shed_url, name, owner, changeset_revision ):
+ sa_session = app.model.context.current
+ tool_shed = clean_tool_shed_url( tool_shed_url )
+ tool_shed_repository = sa_session.query( app.model.ToolShedRepository ) \
+ .filter( and_( app.model.ToolShedRepository.table.c.tool_shed == tool_shed,
+ app.model.ToolShedRepository.table.c.name == name,
+ app.model.ToolShedRepository.table.c.owner == owner,
+ app.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+ .first()
+ if tool_shed_repository:
+ return tool_shed_repository
+ # The tool_shed_repository must have been updated to a newer changeset revision than the one defined in the repository_dependencies.xml file,
+ # so call the tool shed to get all appropriate newer changeset revisions.
+ text = get_updated_changeset_revisions_from_tool_shed( tool_shed_url, name, owner, changeset_revision )
+ if text:
+ changeset_revisions = listify( text )
+ for changeset_revision in changeset_revisions:
+ tool_shed_repository = sa_session.query( app.model.ToolShedRepository ) \
+ .filter( and_( app.model.ToolShedRepository.table.c.tool_shed == tool_shed,
+ app.model.ToolShedRepository.table.c.name == name,
+ app.model.ToolShedRepository.table.c.owner == owner,
+ app.model.ToolShedRepository.table.c.changeset_revision == changeset_revision ) ) \
+ .first()
+ if tool_shed_repository:
+ return tool_shed_repository
+ return None
def get_tool_dependency_by_name_type_repository( app, repository, name, type ):
sa_session = app.model.context.current
return sa_session.query( app.model.ToolDependency ) \
@@ -43,23 +105,83 @@
app.model.ToolDependency.table.c.version == version,
app.model.ToolDependency.table.c.type == type ) ) \
.first()
-def get_tool_dependency_install_dir( app, repository, type, name, version ):
- if type == 'package':
+def get_tool_dependency_install_dir( app, repository_name, repository_owner, repository_changeset_revision, tool_dependency_type, tool_dependency_name,
+ tool_dependency_version ):
+ if tool_dependency_type == 'package':
return os.path.abspath( os.path.join( app.config.tool_dependency_dir,
- name,
- version,
- repository.owner,
- repository.name,
- repository.installed_changeset_revision ) )
- if type == 'set_environment':
+ tool_dependency_name,
+ tool_dependency_version,
+ repository_owner,
+ repository_name,
+ repository_changeset_revision ) )
+ if tool_dependency_type == 'set_environment':
return os.path.abspath( os.path.join( app.config.tool_dependency_dir,
'environment_settings',
- name,
- repository.owner,
- repository.name,
- repository.installed_changeset_revision ) )
+ tool_dependency_name,
+ repository_owner,
+ repository_name,
+ repository_changeset_revision ) )
def get_tool_shed_repository_install_dir( app, tool_shed_repository ):
return os.path.abspath( tool_shed_repository.repo_files_directory( app ) )
+def get_updated_changeset_revisions_from_tool_shed( tool_shed_url, name, owner, changeset_revision ):
+ """Get all appropriate newer changeset revisions for the repository defined by the received tool_shed_url / name / owner combination."""
+ url = url_join( tool_shed_url,
+ 'repository/updated_changeset_revisions?name=%s&owner=%s&changeset_revision=%s' % ( name, owner, changeset_revision ) )
+ response = urllib2.urlopen( url )
+ text = response.read()
+ response.close()
+ return text
+def handle_set_environment_entry_for_package( app, install_dir, tool_shed_repository, package_name, package_version, elem ):
+ action_dict = {}
+ actions = []
+ for package_elem in elem:
+ if package_elem.tag == 'install':
+ # Create the tool_dependency record in the database.
+ tool_dependency = create_or_update_tool_dependency( app=app,
+ tool_shed_repository=tool_shed_repository,
+ name=package_name,
+ version=package_version,
+ type='package',
+ status=app.model.ToolDependency.installation_status.INSTALLING,
+ set_status=True )
+ # Get the installation method version from a tag like: <install version="1.0">
+ package_install_version = package_elem.get( 'version', '1.0' )
+ if package_install_version == '1.0':
+ # Since the required tool dependency is installed for a repository dependency, all we need to do
+ # is inspect the <actions> tag set to find the <action type="set_environment"> tag.
+ for actions_elem in package_elem:
+ for action_elem in actions_elem:
+ action_type = action_elem.get( 'type', 'shell_command' )
+ if action_type == 'set_environment':
+ # <action type="set_environment">
+ # <environment_variable name="PYTHONPATH" action="append_to">$INSTALL_DIR/lib/python</environment_variable>
+ # <environment_variable name="PATH" action="prepend_to">$INSTALL_DIR/bin</environment_variable>
+ # </action>
+ env_var_dicts = []
+ for env_elem in action_elem:
+ if env_elem.tag == 'environment_variable':
+ env_var_dict = common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir )
+ if env_var_dict:
+ env_var_dicts.append( env_var_dict )
+ if env_var_dicts:
+ action_dict[ env_elem.tag ] = env_var_dicts
+ actions.append( ( action_type, action_dict ) )
+ return tool_dependency, actions
+ return None, actions
+def install_and_build_package_via_fabric( app, tool_dependency, actions_dict ):
+ sa_session = app.model.context.current
+ try:
+ # There is currently only one fabric method.
+ fabric_util.install_and_build_package( app, tool_dependency, actions_dict )
+ except Exception, e:
+ tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
+ tool_dependency.error_message = str( e )
+ sa_session.add( tool_dependency )
+ sa_session.flush()
+ if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
+ tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED
+ sa_session.add( tool_dependency )
+ sa_session.flush()
def install_package( app, elem, tool_shed_repository, tool_dependencies=None ):
# The value of tool_dependencies is a partial or full list of ToolDependency records associated with the tool_shed_repository.
sa_session = app.model.context.current
@@ -69,18 +191,101 @@
package_version = elem.get( 'version', None )
if package_name and package_version:
if tool_dependencies:
- install_dir = get_tool_dependency_install_dir( app,
- repository=tool_shed_repository,
- type='package',
- name=package_name,
- version=package_version )
+ # Get the installation directory for tool dependencies that will be installed for the received tool_shed_repository.
+ install_dir = get_tool_dependency_install_dir( app=app,
+ repository_name=tool_shed_repository.name,
+ repository_owner=tool_shed_repository.owner,
+ repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
+ tool_dependency_type='package',
+ tool_dependency_name=package_name,
+ tool_dependency_version=package_version )
if not os.path.exists( install_dir ):
for package_elem in elem:
- if package_elem.tag == 'install':
+ if package_elem.tag == 'repository':
+ # We have a complex repository dependency definition.
+ tool_shed = package_elem.attrib[ 'toolshed' ]
+ required_repository_name = package_elem.attrib[ 'name' ]
+ required_repository_owner = package_elem.attrib[ 'owner' ]
+ required_repository_changeset_revision = package_elem.attrib[ 'changeset_revision' ]
+ required_repository = get_tool_shed_repository_by_tool_shed_name_owner_changeset_revision( app,
+ tool_shed,
+ required_repository_name,
+ required_repository_owner,
+ required_repository_changeset_revision )
+ tmp_filename = None
+ if required_repository:
+ # Set this repository's tool dependency env.sh file with a path to the required repository's installed tool dependency package.
+ # We can get everything we need from the discovered installed required_repository.
+ if required_repository.status in [ app.model.ToolShedRepository.installation_status.DEACTIVATED,
+ app.model.ToolShedRepository.installation_status.INSTALLED ]:
+ # Define the installation directory for the required tool dependency in the required repository.
+ required_repository_package_install_dir = \
+ get_tool_dependency_install_dir( app=app,
+ repository_name=required_repository.name,
+ repository_owner=required_repository.owner,
+ repository_changeset_revision=required_repository.installed_changeset_revision,
+ tool_dependency_type='package',
+ tool_dependency_name=package_name,
+ tool_dependency_version=package_version )
+ assert os.path.exists( required_repository_package_install_dir ), \
+ 'Missing required tool dependency directory %s' % str( required_repository_package_install_dir )
+ repo_files_dir = required_repository.repo_files_directory( app )
+ tool_dependencies_config = get_absolute_path_to_file_in_repository( repo_files_dir, 'tool_dependencies.xml' )
+ if tool_dependencies_config:
+ config_to_use = tool_dependencies_config
+ else:
+ message = "Unable to locate required tool_dependencies.xml file for revision %s of installed repository %s owned by %s." % \
+ ( str( required_repository.changeset_revision ), str( required_repository.name ), str( required_repository.owner ) )
+ raise Exception( message )
+ else:
+ # Make a call to the tool shed to get the changeset revision to which the current value of required_repository_changeset_revision
+ # should be updated if it's not current.
+ text = get_updated_changeset_revisions_from_tool_shed( tool_shed_url=tool_shed,
+ name=required_repository_name,
+ owner=required_repository_owner,
+ changeset_revision=required_repository_changeset_revision )
+ if text:
+ updated_changeset_revisions = listify( text )
+ # The list of changeset revisions is in reverse order, so the newest will be first.
+ required_repository_changeset_revision = updated_changeset_revisions[ 0 ]
+ # Define the installation directory for the required tool dependency in the required repository.
+ required_repository_package_install_dir = \
+ get_tool_dependency_install_dir( app=app,
+ repository_name=required_repository_name,
+ repository_owner=required_repository_owner,
+ repository_changeset_revision=required_repository_changeset_revision,
+ tool_dependency_type='package',
+ tool_dependency_name=package_name,
+ tool_dependency_version=package_version )
+ # Make a call to the tool shed to get the required repository's tool_dependencies.xml file.
+ tmp_filename = create_temporary_tool_dependencies_config( tool_shed,
+ required_repository_name,
+ required_repository_owner,
+ required_repository_changeset_revision )
+ config_to_use = tmp_filename
+ tool_dependency, actions_dict = populate_actions_dict( app=app,
+ dependent_install_dir=install_dir,
+ required_install_dir=required_repository_package_install_dir,
+ tool_shed_repository=tool_shed_repository,
+ package_name=package_name,
+ package_version=package_version,
+ tool_dependencies_config=config_to_use )
+ if tmp_filename:
+ try:
+ os.remove( tmp_filename )
+ except:
+ pass
+ # Install and build the package via fabric.
+ install_and_build_package_via_fabric( app, tool_dependency, actions_dict )
+ else:
+ message = "Unable to locate required tool shed repository named %s owned by %s with revision %s." % \
+ ( str( name ), str( owner ), str( changeset_revision ) )
+ raise Exception( message )
+ elif package_elem.tag == 'install':
# <install version="1.0">
package_install_version = package_elem.get( 'version', '1.0' )
- tool_dependency = create_or_update_tool_dependency( app,
- tool_shed_repository,
+ tool_dependency = create_or_update_tool_dependency( app=app,
+ tool_shed_repository=tool_shed_repository,
name=package_name,
version=package_version,
type='package',
@@ -168,7 +373,7 @@
if env_elem.tag == 'environment_variable':
env_var_dict = common_util.create_env_var_dict( env_elem, tool_dependency_install_dir=install_dir )
if env_var_dict:
- env_var_dicts.append( env_var_dict )
+ env_var_dicts.append( env_var_dict )
if env_var_dicts:
action_dict[ env_elem.tag ] = env_var_dicts
else:
@@ -183,18 +388,56 @@
# run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=package_name )
raise Exception( 'Tool dependency installation using proprietary fabric scripts is not yet supported.' )
else:
- try:
- # There is currently only one fabric method.
- fabric_util.install_and_build_package( app, tool_dependency, actions_dict )
- except Exception, e:
- tool_dependency.status = app.model.ToolDependency.installation_status.ERROR
- tool_dependency.error_message = str( e )
- sa_session.add( tool_dependency )
- sa_session.flush()
- if tool_dependency.status != app.model.ToolDependency.installation_status.ERROR:
- tool_dependency.status = app.model.ToolDependency.installation_status.INSTALLED
- sa_session.add( tool_dependency )
- sa_session.flush()
+ install_and_build_package_via_fabric( app, tool_dependency, actions_dict )
+def listify( item ):
+ """
+ Make a single item a single item list, or return a list if passed a
+ list. Passing a None returns an empty list.
+ """
+ if not item:
+ return []
+ elif isinstance( item, list ):
+ return item
+ elif isinstance( item, basestring ) and item.count( ',' ):
+ return item.split( ',' )
+ else:
+ return [ item ]
+def populate_actions_dict( app, dependent_install_dir, required_install_dir, tool_shed_repository, package_name, package_version, tool_dependencies_config ):
+ """
+ Populate an actions dictionary that can be sent to fabric_util.install_and_build_package. This method handles the scenario where a tool_dependencies.xml
+ file defines a complex repository dependency. In this case, the tool dependency package will be installed in a separate repository and the tool dependency
+ defined for the dependent repository will use an environment_variable setting defined in it's env.sh file to locate the required package. This method
+ basically does what the install_via_fabric method does, but restricts it's activity to the <action type="set_environment"> tag set within the required
+ repository's tool_dependencies.xml file.
+ """
+ sa_session = app.model.context.current
+ if not os.path.exists( dependent_install_dir ):
+ os.makedirs( dependent_install_dir )
+ actions_dict = dict( install_dir=dependent_install_dir )
+ if package_name:
+ actions_dict[ 'package_name' ] = package_name
+ tool_dependency = None
+ action_dict = {}
+ if tool_dependencies_config:
+ required_td_tree = parse_xml( tool_dependencies_config )
+ required_td_root = required_td_tree.getroot()
+ for required_td_elem in required_td_root:
+ # Find the appropriate package name and version.
+ if required_td_elem.tag == 'package':
+ # <package name="bwa" version="0.5.9">
+ required_td_package_name = required_td_elem.get( 'name', None )
+ required_td_package_version = required_td_elem.get( 'version', None )
+ if required_td_package_name==package_name and required_td_package_version==package_version:
+ tool_dependency, actions = handle_set_environment_entry_for_package( app=app,
+ install_dir=required_install_dir,
+ tool_shed_repository=tool_shed_repository,
+ package_name=package_name,
+ package_version=package_version,
+ elem=required_td_elem )
+ if actions:
+ actions_dict[ 'actions' ] = actions
+ break
+ return tool_dependency, actions_dict
def run_proprietary_fabric_method( app, elem, proprietary_fabfile_path, install_dir, package_name=None, **kwd ):
"""
TODO: Handle this using the fabric api.
@@ -248,6 +491,10 @@
tmp_stderr = open( tmp_name, 'rb' )
message = '%s\n' % str( tmp_stderr.read() )
tmp_stderr.close()
+ try:
+ os.remove( tmp_name )
+ except:
+ pass
return returncode, message
def set_environment( app, elem, tool_shed_repository ):
"""
@@ -258,6 +505,11 @@
<environment_variable name="R_SCRIPT_PATH" action="set_to">$REPOSITORY_INSTALL_DIR</environment_variable></set_environment>
"""
+ # TODO: Add support for a repository dependency definition within this tool dependency type's tag set. This should look something like
+ # the following. See the implementation of support for this in the tool dependency package type's method above.
+ # <set_environment version="1.0">
+ # <repository toolshed="<tool shed>" name="<repository name>" owner="<repository owner>" changeset_revision="<changeset revision>" />
+ # </set_environment>
sa_session = app.model.context.current
tool_dependency = None
env_var_version = elem.get( 'version', '1.0' )
@@ -267,18 +519,20 @@
env_var_name = env_var_elem.get( 'name', None )
env_var_action = env_var_elem.get( 'action', None )
if env_var_name and env_var_action:
- install_dir = get_tool_dependency_install_dir( app,
- repository=tool_shed_repository,
- type='set_environment',
- name=env_var_name,
- version=None )
+ install_dir = get_tool_dependency_install_dir( app=app,
+ repository_name=tool_shed_repository.name,
+ repository_owner=tool_shed_repository.owner,
+ repository_changeset_revision=tool_shed_repository.installed_changeset_revision,
+ tool_dependency_type='set_environment',
+ tool_dependency_name=env_var_name,
+ tool_dependency_version=None )
tool_shed_repository_install_dir = get_tool_shed_repository_install_dir( app, tool_shed_repository )
env_var_dict = common_util.create_env_var_dict( env_var_elem, tool_shed_repository_install_dir=tool_shed_repository_install_dir )
if env_var_dict:
if not os.path.exists( install_dir ):
os.makedirs( install_dir )
- tool_dependency = create_or_update_tool_dependency( app,
- tool_shed_repository,
+ tool_dependency = create_or_update_tool_dependency( app=app,
+ tool_shed_repository=tool_shed_repository,
name=env_var_name,
version=None,
type='set_environment',
@@ -294,3 +548,22 @@
sa_session.add( tool_dependency )
sa_session.flush()
print 'Environment variable ', env_var_name, 'set in', install_dir
+def strip_path( fpath ):
+ if not fpath:
+ return fpath
+ try:
+ file_path, file_name = os.path.split( fpath )
+ except:
+ file_name = fpath
+ return file_name
+def parse_xml( file_name ):
+ """Returns a parsed xml tree."""
+ tree = ElementTree.parse( file_name )
+ root = tree.getroot()
+ ElementInclude.include( root )
+ return tree
+def url_join( *args ):
+ parts = []
+ for arg in args:
+ parts.append( arg.strip( '/' ) )
+ return '/'.join( parts )
diff -r 618c34d9b2eab385e092c9ca2d7dd07b9ea31024 -r ea3da2000fa733a2d3ff5d5629dec58d3573645c lib/galaxy/util/shed_util.py
--- a/lib/galaxy/util/shed_util.py
+++ b/lib/galaxy/util/shed_util.py
@@ -414,7 +414,7 @@
cleaned_repository_clone_url = suc.clean_repository_clone_url( repository_clone_url )
if not owner:
owner = get_repository_owner( cleaned_repository_clone_url )
- tool_shed = cleaned_repository_clone_url.split( 'repos' )[ 0 ].rstrip( '/' )
+ tool_shed = cleaned_repository_clone_url.split( '/repos/' )[ 0 ].rstrip( '/' )
for guid, tool_section_dicts in tool_panel_dict.items():
for tool_section_dict in tool_section_dicts:
tool_section = None
@@ -484,20 +484,6 @@
tool_section_dicts = generate_tool_section_dicts( tool_config=file_name, tool_sections=tool_sections )
tool_panel_dict[ guid ] = tool_section_dicts
return tool_panel_dict
-def generate_tool_path( repository_clone_url, changeset_revision ):
- """
- Generate a tool path that guarantees repositories with the same name will always be installed
- in different directories. The tool path will be of the form:
- <tool shed url>/repos/<repository owner>/<repository name>/<installed changeset revision>
- http://test@bx.psu.edu:9009/repos/test/filter
- """
- tmp_url = suc.clean_repository_clone_url( repository_clone_url )
- # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column
- items = tmp_url.split( 'repos' )
- tool_shed_url = items[ 0 ]
- repo_path = items[ 1 ]
- tool_shed_url = suc.clean_tool_shed_url( tool_shed_url )
- return suc.url_join( tool_shed_url, 'repos', repo_path, changeset_revision )
def generate_tool_section_dicts( tool_config=None, tool_sections=None ):
tool_section_dicts = []
if tool_config is None:
@@ -529,6 +515,18 @@
else:
tool_section = None
return tool_section
+def generate_tool_shed_repository_install_dir( repository_clone_url, changeset_revision ):
+ """
+ Generate a repository installation directory that guarantees repositories with the same name will always be installed in different directories.
+ The tool path will be of the form: <tool shed url>/repos/<repository owner>/<repository name>/<installed changeset revision>
+ """
+ tmp_url = suc.clean_repository_clone_url( repository_clone_url )
+ # Now tmp_url is something like: bx.psu.edu:9009/repos/some_username/column
+ items = tmp_url.split( '/repos/' )
+ tool_shed_url = items[ 0 ]
+ repo_path = items[ 1 ]
+ tool_shed_url = suc.clean_tool_shed_url( tool_shed_url )
+ return suc.url_join( tool_shed_url, 'repos', repo_path, changeset_revision )
def get_config( config_file, repo, ctx, dir ):
"""Return the latest version of config_filename from the repository manifest."""
config_file = suc.strip_path( config_file )
@@ -821,14 +819,14 @@
readme_files_dict = json.from_json_string( raw_text )
return readme_files_dict
def get_repository_owner( cleaned_repository_url ):
- items = cleaned_repository_url.split( 'repos' )
+ items = cleaned_repository_url.split( '/repos/' )
repo_path = items[ 1 ]
if repo_path.startswith( '/' ):
repo_path = repo_path.replace( '/', '', 1 )
return repo_path.lstrip( '/' ).split( '/' )[ 0 ]
def get_repository_owner_from_clone_url( repository_clone_url ):
tmp_url = suc.clean_repository_clone_url( repository_clone_url )
- tool_shed = tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
+ tool_shed = tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' )
return get_repository_owner( tmp_url )
def get_required_repo_info_dicts( tool_shed_url, repo_info_dicts ):
"""
diff -r 618c34d9b2eab385e092c9ca2d7dd07b9ea31024 -r ea3da2000fa733a2d3ff5d5629dec58d3573645c lib/galaxy/util/shed_util_common.py
--- a/lib/galaxy/util/shed_util_common.py
+++ b/lib/galaxy/util/shed_util_common.py
@@ -1202,7 +1202,10 @@
app.config.tool_data_table_config_path = original_tool_data_table_config_path
return metadata_dict, invalid_file_tups
def generate_package_dependency_metadata( app, elem, tool_dependencies_dict ):
- """The value of package_name must match the value of the "package" type in the tool config's <requirements> tag set."""
+ """
+ Generate the metadata for a tool dependencies package defined for a repository. The value of package_name must match the value of the "package"
+ type in the tool config's <requirements> tag set. This method is called from both Galaxy and the tool shed.
+ """
repository_dependency_tup = []
requirements_dict = {}
error_message = ''
@@ -1217,9 +1220,9 @@
requirements_dict[ 'readme' ] = sub_elem.text
elif sub_elem.tag == 'repository':
# We have a complex repository dependency.
- current_rd_tups, error_message = handle_repository_elem_for_tool_shed( app=app,
- repository_elem=sub_elem,
- repository_dependencies_tups=None )
+ current_rd_tups, error_message = handle_repository_elem( app=app,
+ repository_elem=sub_elem,
+ repository_dependencies_tups=None )
repository_dependency_tup = current_rd_tups[ 0 ]
if requirements_dict:
dependency_key = '%s/%s' % ( package_name, package_version )
@@ -1274,7 +1277,7 @@
is_valid = False
if is_valid:
for repository_elem in root.findall( 'repository' ):
- current_rd_tups, error_message = handle_repository_elem_for_tool_shed( app, repository_elem, repository_dependencies_tups )
+ current_rd_tups, error_message = handle_repository_elem( app, repository_elem, repository_dependencies_tups )
if error_message:
log.debug( error_message )
return metadata_dict, error_message
@@ -1477,7 +1480,7 @@
metadata_dict[ 'workflows' ] = [ ( relative_path, exported_workflow_dict ) ]
return metadata_dict
def get_absolute_path_to_file_in_repository( repo_files_dir, file_name ):
- """Return the absolute path to a specified disk file containe in a repository."""
+ """Return the absolute path to a specified disk file contained in a repository."""
stripped_file_name = strip_path( file_name )
file_path = None
for root, dirs, files in os.walk( repo_files_dir ):
@@ -1677,8 +1680,8 @@
return None
def get_next_downloadable_changeset_revision( repository, repo, after_changeset_revision ):
"""
- Return the installable changeset_revision in the repository changelog after to the changeset to which after_changeset_revision
- refers. If there isn't one, return None.
+ Return the installable changeset_revision in the repository changelog after the changeset to which after_changeset_revision refers. If there
+ isn't one, return None.
"""
changeset_revisions = get_ordered_downloadable_changeset_revisions( repository, repo )
if len( changeset_revisions ) == 1:
@@ -2157,7 +2160,7 @@
.first()
def get_tool_shed_from_clone_url( repository_clone_url ):
tmp_url = clean_repository_clone_url( repository_clone_url )
- return tmp_url.split( 'repos' )[ 0 ].rstrip( '/' )
+ return tmp_url.split( '/repos/' )[ 0 ].rstrip( '/' )
def get_updated_changeset_revisions_for_repository_dependencies( trans, key_rd_dicts ):
updated_key_rd_dicts = []
for key_rd_dict in key_rd_dicts:
@@ -2411,6 +2414,67 @@
all_repository_dependencies=all_repository_dependencies,
handled_key_rd_dicts=handled_key_rd_dicts,
circular_repository_dependencies=circular_repository_dependencies )
+def handle_repository_elem( app, repository_elem, repository_dependencies_tups ):
+ """
+ Process the received repository_elem which is a <repository> tag either from a repository_dependencies.xml file or a tool_dependencies.xml file.
+ If the former, we're generating repository dependencies metadata for a repository in the tool shed. If the latter, we're generating package
+ dependency metadata with in Galaxy or the tool shed.
+ """
+ if repository_dependencies_tups is None:
+ new_rd_tups = []
+ else:
+ new_rd_tups = [ rdt for rdt in repository_dependencies_tups ]
+ error_message = ''
+ sa_session = app.model.context.current
+ toolshed = repository_elem.attrib[ 'toolshed' ]
+ name = repository_elem.attrib[ 'name' ]
+ owner = repository_elem.attrib[ 'owner' ]
+ changeset_revision = repository_elem.attrib[ 'changeset_revision' ]
+ user = None
+ repository = None
+ if app.name == 'galaxy':
+ # We're in Galaxy.
+ try:
+ repository = sa_session.query( app.model.ToolShedRepository ) \
+ .filter( and_( app.model.ToolShedRepository.table.c.name == name,
+ app.model.ToolShedRepository.table.c.owner == owner ) ) \
+ .first()
+ except:
+ error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner )
+ log.debug( error_message )
+ return new_rd_tups, error_message
+ repository_dependencies_tup = ( toolshed, name, owner, changeset_revision )
+ if repository_dependencies_tup not in new_rd_tups:
+ new_rd_tups.append( repository_dependencies_tup )
+ else:
+ # We're in the tool shed.
+ if tool_shed_is_this_tool_shed( toolshed ):
+ try:
+ user = sa_session.query( app.model.User ) \
+ .filter( app.model.User.table.c.username == owner ) \
+ .one()
+ except Exception, e:
+ error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name )
+ log.debug( error_message )
+ return new_rd_tups, error_message
+ try:
+ repository = sa_session.query( app.model.Repository ) \
+ .filter( and_( app.model.Repository.table.c.name == name,
+ app.model.Repository.table.c.user_id == user.id ) ) \
+ .first()
+ except:
+ error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner )
+ log.debug( error_message )
+ return new_rd_tups, error_message
+ repository_dependencies_tup = ( toolshed, name, owner, changeset_revision )
+ if repository_dependencies_tup not in new_rd_tups:
+ new_rd_tups.append( repository_dependencies_tup )
+ else:
+ # Repository dependencies are currentlhy supported within a single tool shed.
+ error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name )
+ error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored."
+ log.debug( error_message )
+ return new_rd_tups, error_message
def handle_sample_files_and_load_tool_from_disk( trans, repo_files_dir, tool_config_filepath, work_dir ):
# Copy all sample files from disk to a temporary directory since the sample files may be in multiple directories.
message = ''
@@ -2487,54 +2551,6 @@
if is_orphan_in_tool_shed:
return True
return False
-def handle_repository_elem_for_tool_shed( app, repository_elem, repository_dependencies_tups ):
- if repository_dependencies_tups is None:
- new_rd_tups = []
- else:
- new_rd_tups = [ rdt for rdt in repository_dependencies_tups ]
- error_message = ''
- sa_session = app.model.context.current
- toolshed = repository_elem.attrib[ 'toolshed' ]
- name = repository_elem.attrib[ 'name' ]
- owner = repository_elem.attrib[ 'owner' ]
- changeset_revision = repository_elem.attrib[ 'changeset_revision' ]
- user = None
- repository = None
- if tool_shed_is_this_tool_shed( toolshed ):
- try:
- user = sa_session.query( app.model.User ) \
- .filter( app.model.User.table.c.username == owner ) \
- .one()
- except Exception, e:
- error_message = "Invalid owner %s defined for repository %s. Repository dependencies will be ignored." % ( owner, name )
- log.debug( error_message )
- return new_rd_tups, error_message
- if user:
- try:
- repository = sa_session.query( app.model.Repository ) \
- .filter( and_( app.model.Repository.table.c.name == name,
- app.model.Repository.table.c.user_id == user.id ) ) \
- .first()
- except:
- error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner )
- log.debug( error_message )
- return new_rd_tups, error_message
- if repository:
- repository_dependencies_tup = ( toolshed, name, owner, changeset_revision )
- if repository_dependencies_tup not in new_rd_tups:
- new_rd_tups.append( repository_dependencies_tup )
- else:
- error_message = "Invalid name %s or owner %s defined for repository. Repository dependencies will be ignored." % ( name, owner )
- log.debug( error_message )
- else:
- error_message = "Invalid owner %s defined for owner of repository %s. Repository dependencies will be ignored." % ( owner, name )
- log.debug( error_message )
- else:
- # Repository dependencies are currentlhy supported within a single tool shed.
- error_message = "Invalid tool shed %s defined for repository %s. " % ( toolshed, name )
- error_message += "Repository dependencies are currently supported within a single tool shed, so your definition will be ignored."
- log.debug( error_message )
- return new_rd_tups, error_message
def has_previous_repository_reviews( trans, repository, changeset_revision ):
"""Determine if a repository has a changeset revision review prior to the received changeset revision."""
repo = hg.repository( get_configured_ui(), repository.repo_path( trans.app ) )
@@ -2588,7 +2604,22 @@
return True
return False
def is_downloadable( metadata_dict ):
- return 'datatypes' in metadata_dict or 'repository_dependencies' in metadata_dict or 'tools' in metadata_dict or 'workflows' in metadata_dict
+ if 'datatypes' in metadata_dict:
+ # We have proprietary datatypes.
+ return True
+ if 'repository_dependencies' in metadata_dict:
+ # We have repository_dependencies.
+ return True
+ if 'tools' in metadata_dict:
+ # We have tools.
+ return True
+ if 'tool_dependencies' in metadata_dict:
+ # We have tool dependencies, and perhaps only tool dependencies!
+ return True
+ if 'workflows' in metadata_dict:
+ # We have exported workflows.
+ return True
+ return False
def initialize_all_repository_dependencies( current_repository_key, repository_dependencies_dict, all_repository_dependencies ):
# Initialize the all_repository_dependencies dictionary. It's safe to assume that current_repository_key in this case will have a value.
all_repository_dependencies[ 'root_key' ] = current_repository_key
@@ -3322,7 +3353,7 @@
return ''.join( translated )
return text
def tool_shed_from_repository_clone_url( repository_clone_url ):
- return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' )
+ return clean_repository_clone_url( repository_clone_url ).split( '/repos/' )[ 0 ].rstrip( '/' )
def tool_shed_is_this_tool_shed( toolshed_base_url ):
return toolshed_base_url.rstrip( '/' ) == str( url_for( '/', qualified=True ) ).rstrip( '/' )
def translate_string( raw_text, to_html=True ):
diff -r 618c34d9b2eab385e092c9ca2d7dd07b9ea31024 -r ea3da2000fa733a2d3ff5d5629dec58d3573645c lib/galaxy/webapps/community/controllers/repository.py
--- a/lib/galaxy/webapps/community/controllers/repository.py
+++ b/lib/galaxy/webapps/community/controllers/repository.py
@@ -1466,7 +1466,7 @@
return repo_info_dict
@web.expose
def get_tool_dependencies( self, trans, **kwd ):
- """Handle a request from a Galaxy instance."""
+ """Handle a request from a Galaxy instance to get the tool_dependencies entry from the metadata for a specified changeset revision."""
params = util.Params( kwd )
name = params.get( 'name', None )
owner = params.get( 'owner', None )
@@ -1481,6 +1481,26 @@
return encoding_util.tool_shed_encode( tool_dependencies )
return ''
@web.expose
+ def get_tool_dependencies_config_contents( self, trans, **kwd ):
+ """Handle a request from a Galaxy instance to get the tool_dependencies.xml file contents for a specified changeset revision."""
+ params = util.Params( kwd )
+ name = params.get( 'name', None )
+ owner = params.get( 'owner', None )
+ changeset_revision = params.get( 'changeset_revision', None )
+ repository = suc.get_repository_by_name_and_owner( trans, name, owner )
+ # TODO: We're currently returning the tool_dependencies.xml file that is available on disk. We need to enhance this process
+ # to retrieve older versions of the tool-dependencies.xml file from the repository manafest.
+ repo_dir = repository.repo_path( trans.app )
+ # Get the tool_dependencies.xml file from disk.
+ tool_dependencies_config = suc.get_config_from_disk( 'tool_dependencies.xml', repo_dir )
+ # Return the encoded contents of the tool_dependencies.xml file.
+ if tool_dependencies_config:
+ tool_dependencies_config_file = open( tool_dependencies_config, 'rb' )
+ contents = tool_dependencies_config_file.read()
+ tool_dependencies_config_file.close()
+ return contents
+ return ''
+ @web.expose
def get_tool_versions( self, trans, **kwd ):
"""
For each valid /downloadable change set (up to the received changeset_revision) in the repository's change log, append the change
@@ -1505,7 +1525,7 @@
return ''
@web.json
def get_updated_repository_information( self, trans, name, owner, changeset_revision, **kwd ):
- """Generate a disctionary that contains the information about a repository that is necessary for installing it into a local Galaxy instance."""
+ """Generate a dictionary that contains the information about a repository that is necessary for installing it into a local Galaxy instance."""
repository = suc.get_repository_by_name_and_owner( trans, name, owner )
repository_id = trans.security.encode_id( repository.id )
repository_clone_url = suc.generate_clone_url_for_repository_in_tool_shed( trans, repository )
@@ -2079,7 +2099,7 @@
repository = suc.get_repository_by_name_and_owner( trans, name, owner )
repo_dir = repository.repo_path( trans.app )
repo = hg.repository( suc.get_configured_ui(), repo_dir )
- # Get the lower bound changeset revision
+ # Get the lower bound changeset revision.
lower_bound_changeset_revision = suc.get_previous_downloadable_changset_revision( repository, repo, changeset_revision )
# Build the list of changeset revision hashes.
changeset_hashes = []
@@ -2404,6 +2424,35 @@
if list:
return ','.join( list )
return ''
+ @web.expose
+ def updated_changeset_revisions( self, trans, **kwd ):
+ """
+ Handle a request from a local Galaxy instance to retrieve the lsit of changeset revisions to which an installed repository can be updated. This
+ method will return a string of comma-separated changeset revision hashes for all available updates to the received changeset revision. Among
+ other things , this method handles the scenario where an installed tool shed repository's tool_dependency definition file defines a changeset
+ revision for a complex repository dependency that is outdated. In other words, a defined changeset revision is older than the current changeset
+ revision for the required repository, making it impossible to discover the repository without knowledge of revisions to which it could have been
+ updated.
+ """
+ params = util.Params( kwd )
+ name = params.get( 'name', None )
+ owner = params.get( 'owner', None )
+ changeset_revision = params.get( 'changeset_revision', None )
+ repository = suc.get_repository_by_name_and_owner( trans, name, owner )
+ repo_dir = repository.repo_path( trans.app )
+ repo = hg.repository( suc.get_configured_ui(), repo_dir )
+ # Get the upper bound changeset revision.
+ upper_bound_changeset_revision = suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision )
+ # Build the list of changeset revision hashes defining each available update up to, but excluding, upper_bound_changeset_revision.
+ changeset_hashes = []
+ for changeset in suc.reversed_lower_upper_bounded_changelog( repo, changeset_revision, upper_bound_changeset_revision ):
+ # Make sure to exclude upper_bound_changeset_revision.
+ if changeset != upper_bound_changeset_revision:
+ changeset_hashes.append( str( repo.changectx( changeset ) ) )
+ if changeset_hashes:
+ changeset_hashes_str = ','.join( changeset_hashes )
+ return changeset_hashes_str
+ return ''
def __validate_repository_name( self, name, user ):
# Repository names must be unique for each user, must be at least four characters
# in length and must contain only lower-case letters, numbers, and the '_' character.
diff -r 618c34d9b2eab385e092c9ca2d7dd07b9ea31024 -r ea3da2000fa733a2d3ff5d5629dec58d3573645c lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
--- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
+++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py
@@ -890,7 +890,7 @@
shed_util.update_tool_shed_repository_status( trans.app, tool_shed_repository, trans.model.ToolShedRepository.installation_status.CLONING )
repo_info_tuple = repo_info_dict[ tool_shed_repository.name ]
description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple
- relative_clone_dir = shed_util.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision )
+ relative_clone_dir = shed_util.generate_tool_shed_repository_install_dir( repository_clone_url, tool_shed_repository.installed_changeset_revision )
clone_dir = os.path.join( tool_path, relative_clone_dir )
relative_install_dir = os.path.join( relative_clone_dir, tool_shed_repository.name )
install_dir = os.path.join( tool_path, relative_install_dir )
@@ -1416,7 +1416,8 @@
install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) )
shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository )
repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository )
- clone_dir = os.path.join( tool_path, shed_util.generate_tool_path( repository_clone_url, tool_shed_repository.installed_changeset_revision ) )
+ clone_dir = os.path.join( tool_path, shed_util.generate_tool_shed_repository_install_dir( repository_clone_url,
+ tool_shed_repository.installed_changeset_revision ) )
relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name )
tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, tool_shed_repository )
tool_section = None
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 8 months
- 1
- 0
commit/galaxy-central: 2 new changesets
by Bitbucket
2 new commits in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/commits/9f2b4091e1e5/
changeset: 9f2b4091e1e5
user: Richard Park
date: 2013-01-30 21:48:54
summary: Fixed error when retrieving workflows via API. Added additional tab to lines 88 and 89, to fix error when trying to refer to variable "step."
affected #: 1 file
diff -r 2fcef846289917ccf394bb2fabba8f36d55d0039 -r 9f2b4091e1e5114c8bfc692ce0e685cc75ada39b lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -85,8 +85,8 @@
'type': step.type,
'tool_id': step.tool_id,
'input_steps': {}}
- for conn in step.input_connections:
- steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id,
+ for conn in step.input_connections:
+ steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id,
'step_output': conn.output_name}
item['steps'] = steps
return item
https://bitbucket.org/galaxy/galaxy-central/commits/618c34d9b2ea/
changeset: 618c34d9b2ea
user: dannon
date: 2013-01-30 21:57:10
summary: Merge Pull Request #114 https://bitbucket.org/galaxy/galaxy-central/pull-request/114/fixed-error-...
Adjusted spacing.
affected #: 1 file
diff -r a1d543da698d3d127cd9d7fedd61bd1ac5a19872 -r 618c34d9b2eab385e092c9ca2d7dd07b9ea31024 lib/galaxy/webapps/galaxy/api/workflows.py
--- a/lib/galaxy/webapps/galaxy/api/workflows.py
+++ b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -85,9 +85,9 @@
'type': step.type,
'tool_id': step.tool_id,
'input_steps': {}}
- for conn in step.input_connections:
- steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id,
- 'step_output': conn.output_name}
+ for conn in step.input_connections:
+ steps[step.id]['input_steps'][conn.input_name] = {'source_step': conn.output_step_id,
+ 'step_output': conn.output_name}
item['steps'] = steps
return item
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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8 years, 8 months
- 1
- 0
commit/galaxy-central: james_taylor: web.framework: remove stray print
by Bitbucket
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/
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8 years, 8 months
- 1
- 0
commit/galaxy-central: 3 new changesets
by Bitbucket
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/
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commit/galaxy-central: dan: Add a util.move_merge() function that makes moving directories more consistent.
by Bitbucket
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/
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