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July 2014

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commit/galaxy-central: carlfeberhard: Fix to 5c58466: correct margins of dataset messages
by commits-noreply＠bitbucket.org 31 Jul '14

31 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/21d05dda71c7/ Changeset: 21d05dda71c7 User: carlfeberhard Date: 2014-07-31 21:39:04 Summary: Fix to 5c58466: correct margins of dataset messages Affected #: 2 files diff -r a4fc4ba21a254415c6245a23f1842b997c653e31 -r 21d05dda71c74f673b94fcd7c1e34b27ec5e5040 static/style/blue/base.css --- a/static/style/blue/base.css +++ b/static/style/blue/base.css @@ -1735,15 +1735,15 @@ .dataset .details .display-applications .display-application:last-child{margin-bottom:8px} .dataset .details .dataset-peek{margin-bottom:8px;width:100%;margin:0px;border-radius:3px;background:white;color:black;font-size:10px;overflow:auto}.dataset .details .dataset-peek th{color:white;background:#5f6990} .dataset .details .dataset-peek table,.dataset .details .dataset-peek th,.dataset .details .dataset-peek tr,.dataset .details .dataset-peek td{font-family:Monaco,Menlo,Consolas,"Courier New",monospace;font-size:10px} -.history-panel [class$="messagesmall"]{margin:0px} -.history-panel .editable-text{border:solid transparent 1px} -.history-panel .editable-text:hover{cursor:pointer;border:1px dotted #999999} -.history-panel .message-container{cursor:pointer} -.history-panel .message-container [class$=message]{margin:0px;margin-bottom:8px} -.history-panel .history-controls{margin:10px;padding:0px}.history-panel .history-controls .history-search-controls{display:none;padding:0px 0px 8px 0px} +.history-panel .history-controls{margin:10px;padding:0px}.history-panel .history-controls [class$="messagesmall"]{margin:0px} +.history-panel .history-controls .message-container{cursor:pointer} +.history-panel .history-controls .message-container [class$=message]{margin:0px;margin-bottom:8px} +.history-panel .history-controls .history-search-controls{display:none;padding:0px 0px 8px 0px} .history-panel .history-controls .history-title{margin-bottom:8px} .history-panel .history-controls .history-name{word-wrap:break-word;font-weight:bold} .history-panel .history-controls .history-title input{width:100%;margin:-2px 0 -2px -4px;font-weight:bold} +.history-panel .history-controls .editable-text{border:solid transparent 1px} +.history-panel .history-controls .editable-text:hover{cursor:pointer;border:1px dotted #999999} .history-panel .history-controls .history-subtitle{margin-bottom:8px} .history-panel .history-controls .history-size{float:left} .history-panel .history-controls .history-secondary-actions{display:inline-block;float:right}.history-panel .history-controls .history-secondary-actions .icon-btn:not(:last-child){margin:0px;border-radius:0px;border-right:none} diff -r a4fc4ba21a254415c6245a23f1842b997c653e31 -r 21d05dda71c74f673b94fcd7c1e34b27ec5e5040 static/style/src/less/history.less --- a/static/style/src/less/history.less +++ b/static/style/src/less/history.less @@ -525,30 +525,21 @@ // ---------------------------------------------------------------------------- history .history-panel { - [class$="messagesmall"] { - margin: 0px; - } - - .editable-text { - border: solid transparent 1px; - } - .editable-text:hover { - cursor: pointer; - border: 1px dotted #999999; - } - - .message-container { - cursor: pointer; - } - .message-container [class$=message] { - margin: 0px; - margin-bottom: 8px; - } - .history-controls { margin: 10px; padding: 0px; + [class$="messagesmall"] { + margin: 0px; + } + .message-container { + cursor: pointer; + } + .message-container [class$=message] { + margin: 0px; + margin-bottom: 8px; + } + .history-search-controls { display: none; padding: 0px 0px 8px 0px; @@ -567,6 +558,13 @@ margin: -2px 0px -2px -4px; font-weight: bold; } + .editable-text { + border: solid transparent 1px; + } + .editable-text:hover { + cursor: pointer; + border: 1px dotted #999999; + } .history-subtitle { margin-bottom: 8px; 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.

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commit/galaxy-central: greg: Add a UtilityContainerManager class and subclasses for displaying Tool Shed utility containers.
by commits-noreply＠bitbucket.org 31 Jul '14

31 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a4fc4ba21a25/ Changeset: a4fc4ba21a25 User: greg Date: 2014-07-31 21:27:21 Summary: Add a UtilityContainerManager class and subclasses for displaying Tool Shed utility containers. Affected #: 8 files diff -r 4aba2116bc2de405166d46f034c81eb522cfe4e7 -r a4fc4ba21a254415c6245a23f1842b997c653e31 lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -20,13 +20,13 @@ from tool_shed.galaxy_install import dependency_display from tool_shed.metadata import repository_metadata_manager +from tool_shed.utility_containers import ToolShedUtilityContainerManager from tool_shed.tools import tool_validator from tool_shed.tools import tool_version_manager from tool_shed.util import basic_util from tool_shed.util import common_util -from tool_shed.util import container_util from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import metadata_util @@ -1273,12 +1273,12 @@ # Only display repository dependencies if they exist. exclude = [ 'datatypes', 'invalid_repository_dependencies', 'invalid_tool_dependencies', 'invalid_tools', 'readme_files', 'tool_dependencies', 'tools', 'tool_test_results', 'workflows', 'data_manager' ] - containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, - repository, - changeset_revision, - repository_dependencies, - repository_metadata, - exclude=exclude ) + tsucm = ToolShedUtilityContainerManager( trans.app ) + containers_dict = tsucm.build_repository_containers( repository, + changeset_revision, + repository_dependencies, + repository_metadata, + exclude=exclude ) export_repository_dependencies_check_box = CheckboxField( 'export_repository_dependencies', checked=True ) else: containers_dict = None @@ -2458,11 +2458,11 @@ skip_tool_tests_check_box = CheckboxField( 'skip_tool_tests', checked=skip_tool_tests_checked ) categories = suc.get_categories( trans.app ) selected_categories = [ rca.category_id for rca in repository.categories ] - containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, - repository, - changeset_revision, - repository_dependencies, - repository_metadata ) + tsucm = ToolShedUtilityContainerManager( trans.app ) + containers_dict = tsucm.build_repository_containers( repository, + changeset_revision, + repository_dependencies, + repository_metadata ) heads = hg_util.get_repository_heads( repo ) deprecated_repository_dependency_tups = \ metadata_util.get_repository_dependency_tups_from_repository_metadata( trans.app, @@ -2653,11 +2653,11 @@ selected_value=changeset_revision, add_id_to_name=False, downloadable=False ) - containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, - repository, - changeset_revision, - repository_dependencies, - repository_metadata ) + tsucm = ToolShedUtilityContainerManager( trans.app ) + containers_dict = tsucm.build_repository_containers( repository, + changeset_revision, + repository_dependencies, + repository_metadata ) return trans.fill_template( '/webapps/tool_shed/repository/preview_tools_in_changeset.mako', repository=repository, containers_dict=containers_dict, @@ -3360,11 +3360,11 @@ else: message += malicious_error status = 'error' - containers_dict = container_util.build_repository_containers_for_tool_shed( trans.app, - repository, - changeset_revision, - repository_dependencies, - repository_metadata ) + tsucm = ToolShedUtilityContainerManager( trans.app ) + containers_dict = tsucm.build_repository_containers( repository, + changeset_revision, + repository_dependencies, + repository_metadata ) repository_type_select_field = rt_util.build_repository_type_select_field( trans, repository=repository ) heads = hg_util.get_repository_heads( repo ) return trans.fill_template( '/webapps/tool_shed/repository/view_repository.mako', diff -r 4aba2116bc2de405166d46f034c81eb522cfe4e7 -r a4fc4ba21a254415c6245a23f1842b997c653e31 lib/galaxy/webapps/tool_shed/controllers/repository_review.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository_review.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository_review.py @@ -1,17 +1,26 @@ -import os, logging -from galaxy import web, util +import logging +import os + +from sqlalchemy.sql.expression import func + +from galaxy import util +from galaxy import web + +from galaxy.model.orm import and_ +from galaxy.util.odict import odict from galaxy.web.base.controller import BaseUIController -from galaxy.web.form_builder import SelectField, CheckboxField -from sqlalchemy.sql.expression import func -from galaxy.model.orm import and_ +from galaxy.web.form_builder import CheckboxField +from galaxy.web.form_builder import SelectField + from galaxy.webapps.tool_shed.util import ratings_util + +import tool_shed.grids.repository_review_grids as repository_review_grids +import tool_shed.grids.util as grids_util + from tool_shed.util.container_util import STRSEP -import tool_shed.util.shed_util_common as suc from tool_shed.util import hg_util from tool_shed.util import review_util -from galaxy.util.odict import odict -import tool_shed.grids.repository_review_grids as repository_review_grids -import tool_shed.grids.util as grids_util +from tool_shed.util import shed_util_common as suc log = logging.getLogger( __name__ ) diff -r 4aba2116bc2de405166d46f034c81eb522cfe4e7 -r a4fc4ba21a254415c6245a23f1842b997c653e31 lib/tool_shed/dependencies/repository/relation_builder.py --- a/lib/tool_shed/dependencies/repository/relation_builder.py +++ b/lib/tool_shed/dependencies/repository/relation_builder.py @@ -3,6 +3,7 @@ from galaxy.util import asbool from galaxy.util import listify + from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import hg_util diff -r 4aba2116bc2de405166d46f034c81eb522cfe4e7 -r a4fc4ba21a254415c6245a23f1842b997c653e31 lib/tool_shed/galaxy_install/dependency_display.py --- a/lib/tool_shed/galaxy_install/dependency_display.py +++ b/lib/tool_shed/galaxy_install/dependency_display.py @@ -5,6 +5,9 @@ from galaxy import util +from tool_shed.galaxy_install.utility_containers import GalaxyUtilityContainerManager +from tool_shed.utility_containers import utility_container_manager + from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import readme_util @@ -276,22 +279,23 @@ old_container_repository_dependencies_root = old_container_dict[ 'repository_dependencies' ] if old_container_repository_dependencies_root: if repository_dependencies_root_folder is None: - repository_dependencies_root_folder = container_util.Folder( id=folder_id, - key='root', - label='root', - parent=None ) + repository_dependencies_root_folder = utility_container_manager.Folder( id=folder_id, + key='root', + label='root', + parent=None ) folder_id += 1 - repository_dependencies_folder = container_util.Folder( id=folder_id, - key='merged', - label='Repository dependencies', - parent=repository_dependencies_root_folder ) + repository_dependencies_folder = utility_container_manager.Folder( id=folder_id, + key='merged', + label='Repository dependencies', + parent=repository_dependencies_root_folder ) folder_id += 1 # The old_container_repository_dependencies_root will be a root folder containing a single sub_folder. old_container_repository_dependencies_folder = old_container_repository_dependencies_root.folders[ 0 ] # Change the folder id so it won't confict with others being merged. old_container_repository_dependencies_folder.id = folder_id folder_id += 1 - repository_components_tuple = container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) + repository_components_tuple = \ + container_util.get_components_from_key( old_container_repository_dependencies_folder.key ) components_list = suc.extract_components_from_tuple( repository_components_tuple ) name = components_list[ 1 ] # Generate the label by retrieving the repository name. @@ -301,15 +305,15 @@ old_container_tool_dependencies_root = old_container_dict[ 'tool_dependencies' ] if old_container_tool_dependencies_root: if tool_dependencies_root_folder is None: - tool_dependencies_root_folder = container_util.Folder( id=folder_id, - key='root', - label='root', - parent=None ) + tool_dependencies_root_folder = utility_container_manager.Folder( id=folder_id, + key='root', + label='root', + parent=None ) folder_id += 1 - tool_dependencies_folder = container_util.Folder( id=folder_id, - key='merged', - label='Tool dependencies', - parent=tool_dependencies_root_folder ) + tool_dependencies_folder = utility_container_manager.Folder( id=folder_id, + key='merged', + label='Tool dependencies', + parent=tool_dependencies_root_folder ) folder_id += 1 else: td_list = [ td.listify for td in tool_dependencies_folder.tool_dependencies ] @@ -410,23 +414,22 @@ repository_missing_tool_dependencies=missing_tool_dependencies, required_repo_info_dicts=None ) # Most of the repository contents are set to None since we don't yet know what they are. - containers_dict = \ - container_util.build_repository_containers_for_galaxy( app=self.app, - repository=None, - datatypes=None, - invalid_tools=None, - missing_repository_dependencies=missing_repository_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - readme_files_dict=readme_files_dict, - repository_dependencies=installed_repository_dependencies, - tool_dependencies=installed_tool_dependencies, - valid_tools=None, - workflows=None, - valid_data_managers=None, - invalid_data_managers=None, - data_managers_errors=None, - new_install=True, - reinstalling=False ) + gucm = GalaxyUtilityContainerManager( self.app ) + containers_dict = gucm.build_repository_containers( repository=None, + datatypes=None, + invalid_tools=None, + missing_repository_dependencies=missing_repository_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=installed_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + valid_tools=None, + workflows=None, + valid_data_managers=None, + invalid_data_managers=None, + data_managers_errors=None, + new_install=True, + reinstalling=False ) if not updating: # If we installing a new repository and not updaing an installed repository, we can merge # the missing_repository_dependencies container contents to the installed_repository_dependencies @@ -508,23 +511,22 @@ valid_data_managers = metadata['data_manager'].get( 'data_managers', None ) invalid_data_managers = metadata['data_manager'].get( 'invalid_data_managers', None ) data_managers_errors = metadata['data_manager'].get( 'messages', None ) - containers_dict = \ - container_util.build_repository_containers_for_galaxy( app=self.app, - repository=repository, - datatypes=datatypes, - invalid_tools=invalid_tools, - missing_repository_dependencies=missing_repository_dependencies, - missing_tool_dependencies=missing_tool_dependencies, - readme_files_dict=readme_files_dict, - repository_dependencies=installed_repository_dependencies, - tool_dependencies=installed_tool_dependencies, - valid_tools=valid_tools, - workflows=workflows, - valid_data_managers=valid_data_managers, - invalid_data_managers=invalid_data_managers, - data_managers_errors=data_managers_errors, - new_install=False, - reinstalling=reinstalling ) + gucm = GalaxyUtilityContainerManager( self.app ) + containers_dict = gucm.build_repository_containers( repository=repository, + datatypes=datatypes, + invalid_tools=invalid_tools, + missing_repository_dependencies=missing_repository_dependencies, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=installed_repository_dependencies, + tool_dependencies=installed_tool_dependencies, + valid_tools=valid_tools, + workflows=workflows, + valid_data_managers=valid_data_managers, + invalid_data_managers=invalid_data_managers, + data_managers_errors=data_managers_errors, + new_install=False, + reinstalling=reinstalling ) else: containers_dict = dict( datatypes=None, invalid_tools=None, diff -r 4aba2116bc2de405166d46f034c81eb522cfe4e7 -r a4fc4ba21a254415c6245a23f1842b997c653e31 lib/tool_shed/galaxy_install/utility_containers/__init__.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/utility_containers/__init__.py @@ -0,0 +1,145 @@ +import logging +import os +import threading + +from tool_shed.utility_containers import utility_container_manager + +log = logging.getLogger( __name__ ) + + +class GalaxyUtilityContainerManager( utility_container_manager.UtilityContainerManager ): + + def __init__( self, app ): + self.app = app + + def build_repository_containers( self, repository, datatypes, invalid_tools, missing_repository_dependencies, + missing_tool_dependencies, readme_files_dict, repository_dependencies, + tool_dependencies, valid_tools, workflows, valid_data_managers, + invalid_data_managers, data_managers_errors, new_install=False, + reinstalling=False ): + """ + Return a dictionary of containers for the received repository's dependencies and readme files for + display during installation to Galaxy. + """ + containers_dict = dict( datatypes=None, + invalid_tools=None, + missing_tool_dependencies=None, + readme_files=None, + repository_dependencies=None, + missing_repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None, + valid_data_managers=None, + invalid_data_managers=None ) + # Some of the tool dependency folders will include links to display tool dependency information, and + # some of these links require the repository id. However we need to be careful because sometimes the + # repository object is None. + if repository: + repository_id = repository.id + changeset_revision = repository.changeset_revision + else: + repository_id = None + changeset_revision = None + lock = threading.Lock() + lock.acquire( True ) + try: + folder_id = 0 + # Datatypes container. + if datatypes: + folder_id, datatypes_root_folder = self.build_datatypes_folder( folder_id, datatypes ) + containers_dict[ 'datatypes' ] = datatypes_root_folder + # Invalid tools container. + if invalid_tools: + folder_id, invalid_tools_root_folder = \ + self.build_invalid_tools_folder( folder_id, + invalid_tools, + changeset_revision, + repository=repository, + label='Invalid tools' ) + containers_dict[ 'invalid_tools' ] = invalid_tools_root_folder + # Readme files container. + if readme_files_dict: + folder_id, readme_files_root_folder = self.build_readme_files_folder( folder_id, readme_files_dict ) + containers_dict[ 'readme_files' ] = readme_files_root_folder + # Installed repository dependencies container. + if repository_dependencies: + if new_install: + label = 'Repository dependencies' + else: + label = 'Installed repository dependencies' + folder_id, repository_dependencies_root_folder = \ + self.build_repository_dependencies_folder( folder_id=folder_id, + repository_dependencies=repository_dependencies, + label=label, + installed=True ) + containers_dict[ 'repository_dependencies' ] = repository_dependencies_root_folder + # Missing repository dependencies container. + if missing_repository_dependencies: + folder_id, missing_repository_dependencies_root_folder = \ + self.build_repository_dependencies_folder( folder_id=folder_id, + repository_dependencies=missing_repository_dependencies, + label='Missing repository dependencies', + installed=False ) + containers_dict[ 'missing_repository_dependencies' ] = missing_repository_dependencies_root_folder + # Installed tool dependencies container. + if tool_dependencies: + if new_install: + label = 'Tool dependencies' + else: + label = 'Installed tool dependencies' + # We only want to display the Status column if the tool_dependency is missing. + folder_id, tool_dependencies_root_folder = \ + self.build_tool_dependencies_folder( folder_id, + tool_dependencies, + label=label, + missing=False, + new_install=new_install, + reinstalling=reinstalling ) + containers_dict[ 'tool_dependencies' ] = tool_dependencies_root_folder + # Missing tool dependencies container. + if missing_tool_dependencies: + # We only want to display the Status column if the tool_dependency is missing. + folder_id, missing_tool_dependencies_root_folder = \ + self.build_tool_dependencies_folder( folder_id, + missing_tool_dependencies, + label='Missing tool dependencies', + missing=True, + new_install=new_install, + reinstalling=reinstalling ) + containers_dict[ 'missing_tool_dependencies' ] = missing_tool_dependencies_root_folder + # Valid tools container. + if valid_tools: + folder_id, valid_tools_root_folder = self.build_tools_folder( folder_id, + valid_tools, + repository, + changeset_revision, + label='Valid tools' ) + containers_dict[ 'valid_tools' ] = valid_tools_root_folder + # Workflows container. + if workflows: + folder_id, workflows_root_folder = \ + self.build_workflows_folder( folder_id=folder_id, + workflows=workflows, + repository_metadata_id=None, + repository_id=repository_id, + label='Workflows' ) + containers_dict[ 'workflows' ] = workflows_root_folder + if valid_data_managers: + folder_id, valid_data_managers_root_folder = \ + self.build_data_managers_folder( folder_id=folder_id, + data_managers=valid_data_managers, + label='Valid Data Managers' ) + containers_dict[ 'valid_data_managers' ] = valid_data_managers_root_folder + if invalid_data_managers or data_managers_errors: + folder_id, invalid_data_managers_root_folder = \ + self.build_invalid_data_managers_folder( folder_id=folder_id, + data_managers=invalid_data_managers, + error_messages=data_managers_errors, + label='Invalid Data Managers' ) + containers_dict[ 'invalid_data_managers' ] = invalid_data_managers_root_folder + except Exception, e: + log.debug( "Exception in build_repository_containers: %s" % str( e ) ) + finally: + lock.release() + return containers_dict This diff is so big that we needed to truncate the remainder. 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.

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commit/galaxy-central: 22 new changesets
by commits-noreply＠bitbucket.org 31 Jul '14

31 Jul '14

22 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6b0bd93038a8/ Changeset: 6b0bd93038a8 Branch: stable User: natefoo Date: 2014-07-30 16:40:05 Summary: Fix a critical security vulnerability with handling pickled data. Thanks to Inge Alexander Raknes for reporting the isssue. Affected #: 2 files diff -r 6f9d36b726b01606433808fc781df710f755c71b -r 6b0bd93038a843b1585155f0d63f0eea2459c70b lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -400,10 +400,10 @@ return default def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) def get_ucsc_by_build(build): sites = [] diff -r 6f9d36b726b01606433808fc781df710f755c71b -r 6b0bd93038a843b1585155f0d63f0eea2459c70b lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/1cec38142daf/ Changeset: 1cec38142daf Branch: stable User: natefoo Date: 2014-07-30 16:40:27 Summary: Added tag latest_2013.01.13 for changeset 6b0bd93038a8 Affected #: 1 file diff -r 6b0bd93038a843b1585155f0d63f0eea2459c70b -r 1cec38142dafab0174ed42f92d75f3f2606692d1 .hgtags --- /dev/null +++ b/.hgtags @@ -0,0 +1,1 @@ +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 https://bitbucket.org/galaxy/galaxy-central/commits/3e62060b14b9/ Changeset: 3e62060b14b9 Branch: stable User: natefoo Date: 2014-07-30 16:44:41 Summary: Apply 2014.07.30 security fix to release_2013.02.08 Affected #: 3 files diff -r c78e28a5f748e16b0a168d36ba55e5625f322548 -r 3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 .hgtags --- a/.hgtags +++ b/.hgtags @@ -1,2 +1,3 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 diff -r c78e28a5f748e16b0a168d36ba55e5625f322548 -r 3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -400,10 +400,10 @@ return default def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) def get_ucsc_by_build(build): sites = [] diff -r c78e28a5f748e16b0a168d36ba55e5625f322548 -r 3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/58aa61c6c59f/ Changeset: 58aa61c6c59f Branch: stable User: natefoo Date: 2014-07-30 16:44:55 Summary: Added tag latest_2013.02.08 for changeset 3e62060b14b9 Affected #: 1 file diff -r 3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 -r 58aa61c6c59fe116e75426c80a74a5bad824d8fb .hgtags --- a/.hgtags +++ b/.hgtags @@ -1,3 +1,4 @@ a4113cc1cb5eaa68091c9a73375f00555b66dd11 release_2013.01.13 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 https://bitbucket.org/galaxy/galaxy-central/commits/425009b3ff4d/ Changeset: 425009b3ff4d Branch: stable User: natefoo Date: 2014-07-30 16:53:01 Summary: Apply 2014.07.30 security fix to release_2013.04.01 Affected #: 3 files diff -r 03ebba1d1de6f14ccb00e08795ef2f1896135bae -r 425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 .hgtags --- a/.hgtags +++ b/.hgtags @@ -2,3 +2,5 @@ 1c717491139269651bb59687563da9410b84c65d release_2013.02.08 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 diff -r 03ebba1d1de6f14ccb00e08795ef2f1896135bae -r 425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -426,10 +426,10 @@ return default def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) def get_ucsc_by_build(build): sites = [] diff -r 03ebba1d1de6f14ccb00e08795ef2f1896135bae -r 425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/21454fd8bba7/ Changeset: 21454fd8bba7 Branch: stable User: natefoo Date: 2014-07-30 16:53:14 Summary: Added tag latest_2013.04.01 for changeset 425009b3ff4d Affected #: 1 file diff -r 425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 -r 21454fd8bba7b69942b450c761d179bdd50bb36e .hgtags --- a/.hgtags +++ b/.hgtags @@ -4,3 +4,4 @@ 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 https://bitbucket.org/galaxy/galaxy-central/commits/9713d86392ef/ Changeset: 9713d86392ef Branch: stable User: natefoo Date: 2014-07-30 16:55:57 Summary: Apply 2014.07.30 security fix to release_2013.06.03 Affected #: 3 files diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 .hgtags --- a/.hgtags +++ b/.hgtags @@ -3,3 +3,6 @@ 75f09617abaadbc8cc732bb8ee519decaeb56ea7 release_2013.04.01 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -489,10 +489,10 @@ return default def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) def get_ucsc_by_build(build): sites = [] diff -r cd6fec2f5cba878de9943dd00abe816a65dc96db -r 9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/5593110e78c2/ Changeset: 5593110e78c2 Branch: stable User: natefoo Date: 2014-07-30 16:56:05 Summary: Added tag latest_2013.06.03 for changeset 9713d86392ef Affected #: 1 file diff -r 9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 -r 5593110e78c2f1cc7330737b9cddc1bbb102ce86 .hgtags --- a/.hgtags +++ b/.hgtags @@ -6,3 +6,4 @@ 6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 https://bitbucket.org/galaxy/galaxy-central/commits/9ed84cd208e0/ Changeset: 9ed84cd208e0 Branch: stable User: natefoo Date: 2014-07-30 16:57:52 Summary: Apply 2014.07.30 security fix to release_2013.08.12 Affected #: 3 files diff -r e094c73fed4dc66b589932edb83412cb8b827cd3 -r 9ed84cd208e07e8985ec917cb025fcbbb09edcfb .hgtags --- a/.hgtags +++ b/.hgtags @@ -4,3 +4,7 @@ 2cc8d10988e03257dc7b97f8bb332c7df745d1dd security_2013.04.08 524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 diff -r e094c73fed4dc66b589932edb83412cb8b827cd3 -r 9ed84cd208e07e8985ec917cb025fcbbb09edcfb lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -540,10 +540,10 @@ return default def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) def get_ucsc_by_build(build): sites = [] diff -r e094c73fed4dc66b589932edb83412cb8b827cd3 -r 9ed84cd208e07e8985ec917cb025fcbbb09edcfb lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/3fa70507c3bf/ Changeset: 3fa70507c3bf Branch: stable User: natefoo Date: 2014-07-30 16:57:58 Summary: Added tag latest_2013.08.12 for changeset 9ed84cd208e0 Affected #: 1 file diff -r 9ed84cd208e07e8985ec917cb025fcbbb09edcfb -r 3fa70507c3bf43195d691b309fa2617ae6d08ea0 .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,3 +8,4 @@ 3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 https://bitbucket.org/galaxy/galaxy-central/commits/81fbe25bd02e/ Changeset: 81fbe25bd02e Branch: stable User: natefoo Date: 2014-07-30 17:02:23 Summary: Apply 2014.07.30 security fix to release_2013.11.04 Affected #: 3 files diff -r 6c5913a4b701813e823638125fff8bf9fda7354b -r 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 .hgtags --- a/.hgtags +++ b/.hgtags @@ -5,3 +5,8 @@ 524f246ca85395082719ae7a6ff72260d7ad5612 release_2013.06.03 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 diff -r 6c5913a4b701813e823638125fff8bf9fda7354b -r 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -575,10 +575,10 @@ def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) def get_ucsc_by_build(build): sites = [] diff -r 6c5913a4b701813e823638125fff8bf9fda7354b -r 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/22027bfbb8f5/ Changeset: 22027bfbb8f5 Branch: stable User: natefoo Date: 2014-07-30 17:02:24 Summary: Added tag latest_2013.11.04 for changeset 81fbe25bd02e Affected #: 1 file diff -r 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 -r 22027bfbb8f57a536e240208808d0e9ddc468a6a .hgtags --- a/.hgtags +++ b/.hgtags @@ -10,3 +10,4 @@ 425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 +81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 https://bitbucket.org/galaxy/galaxy-central/commits/2a756ca2cb18/ Changeset: 2a756ca2cb18 Branch: stable User: natefoo Date: 2014-07-30 17:04:40 Summary: Apply 2014.07.30 security fix to release_2014.02.10 Affected #: 3 files diff -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc -r 2a756ca2cb1826db7796018e77d12e2dd7b67603 .hgtags --- a/.hgtags +++ b/.hgtags @@ -6,3 +6,9 @@ 1ae95b3aa98d1ccf15b243ac3ce6a895eb7efc53 release_2013.08.12 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 +81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 diff -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc -r 2a756ca2cb1826db7796018e77d12e2dd7b67603 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -686,10 +686,10 @@ def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) def get_ucsc_by_build(build): sites = [] diff -r 9e53251b0b7e93b9563008a2b112f2e815a04bbc -r 2a756ca2cb1826db7796018e77d12e2dd7b67603 lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/50753c5eac3f/ Changeset: 50753c5eac3f Branch: stable User: natefoo Date: 2014-07-30 17:04:48 Summary: Added tag latest_2014.02.10 for changeset 2a756ca2cb18 Affected #: 1 file diff -r 2a756ca2cb1826db7796018e77d12e2dd7b67603 -r 50753c5eac3fa637e442ae1d08ffd7c2e157a63b .hgtags --- a/.hgtags +++ b/.hgtags @@ -12,3 +12,4 @@ 9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 +2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 https://bitbucket.org/galaxy/galaxy-central/commits/9661b9d5d5b3/ Changeset: 9661b9d5d5b3 Branch: stable User: natefoo Date: 2014-07-30 17:07:29 Summary: Apply 2014.07.30 security fix to release_2014.04.14 Affected #: 3 files diff -r ca297d98ab45f650b817acc613050530247c429c -r 9661b9d5d5b330483ae3ad2236410e0efaa7c500 .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,3 +8,10 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 +81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 +2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 diff -r ca297d98ab45f650b817acc613050530247c429c -r 9661b9d5d5b330483ae3ad2236410e0efaa7c500 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -688,10 +688,10 @@ def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) def compare_urls( url1, url2, compare_scheme=True, compare_hostname=True, compare_path=True ): url1 = urlparse( url1 ) diff -r ca297d98ab45f650b817acc613050530247c429c -r 9661b9d5d5b330483ae3ad2236410e0efaa7c500 lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/96e2b84fd947/ Changeset: 96e2b84fd947 Branch: stable User: natefoo Date: 2014-07-30 17:10:33 Summary: Updated tag latest_2014.04.14 for changeset 9661b9d5d5b3 Affected #: 1 file diff -r 9661b9d5d5b330483ae3ad2236410e0efaa7c500 -r 96e2b84fd947912fa742cf366ff89ad3387c4c3e .hgtags --- a/.hgtags +++ b/.hgtags @@ -7,7 +7,7 @@ 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 -68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 +9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 https://bitbucket.org/galaxy/galaxy-central/commits/8c30e91bc9ae/ Changeset: 8c30e91bc9ae Branch: stable User: natefoo Date: 2014-07-30 17:12:05 Summary: Apply 2014.07.30 security fix to release_2014.06.02 Affected #: 3 files diff -r d3b1f484c4b6bbb3daa50fa167eef97a384890b3 -r 8c30e91bc9ae19ee4dc7ec2c22fa825979497108 .hgtags --- a/.hgtags +++ b/.hgtags @@ -7,6 +7,13 @@ 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 -68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02 +9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 +81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 +2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 diff -r d3b1f484c4b6bbb3daa50fa167eef97a384890b3 -r 8c30e91bc9ae19ee4dc7ec2c22fa825979497108 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -688,10 +688,10 @@ def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) def compare_urls( url1, url2, compare_scheme=True, compare_hostname=True, compare_path=True ): url1 = urlparse( url1 ) diff -r d3b1f484c4b6bbb3daa50fa167eef97a384890b3 -r 8c30e91bc9ae19ee4dc7ec2c22fa825979497108 lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/7a4d321c0e38/ Changeset: 7a4d321c0e38 Branch: stable User: natefoo Date: 2014-07-30 17:13:20 Summary: Updated tag latest_2014.06.02 for changeset 8c30e91bc9ae Affected #: 1 file diff -r 8c30e91bc9ae19ee4dc7ec2c22fa825979497108 -r 7a4d321c0e38fa263ea83d29a35a608c3181fcba .hgtags --- a/.hgtags +++ b/.hgtags @@ -8,7 +8,7 @@ 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02 +8c30e91bc9ae19ee4dc7ec2c22fa825979497108 latest_2014.06.02 9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 https://bitbucket.org/galaxy/galaxy-central/commits/adf7bdac8b35/ Changeset: adf7bdac8b35 Branch: next-stable User: natefoo Date: 2014-07-30 17:25:13 Summary: Apply 2014.07.30 security fix to next-stable Affected #: 3 files diff -r 9860d1c6998d38f633a11aae45bd3f667e236cc0 -r adf7bdac8b3502c9f24b899190cdab4f16d2b1fa .hgtags --- a/.hgtags +++ b/.hgtags @@ -7,6 +7,13 @@ 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 -68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02 +8c30e91bc9ae19ee4dc7ec2c22fa825979497108 latest_2014.06.02 +9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 +81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 +2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 diff -r 9860d1c6998d38f633a11aae45bd3f667e236cc0 -r adf7bdac8b3502c9f24b899190cdab4f16d2b1fa lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -714,11 +714,11 @@ def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) class ParamsWithSpecs( collections.defaultdict ): diff -r 9860d1c6998d38f633a11aae45bd3f667e236cc0 -r adf7bdac8b3502c9f24b899190cdab4f16d2b1fa lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/459ec6b67b35/ Changeset: 459ec6b67b35 User: natefoo Date: 2014-07-30 17:25:34 Summary: Apply 2014.07.30 security fix to default Affected #: 3 files diff -r 157adaf92f9c5f06a2ae50a1e7103d0b29543a07 -r 459ec6b67b3593113ee202b7b9418ee7087c1447 .hgtags --- a/.hgtags +++ b/.hgtags @@ -7,6 +7,13 @@ 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 -68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02 +8c30e91bc9ae19ee4dc7ec2c22fa825979497108 latest_2014.06.02 +9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 +81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 +2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 diff -r 157adaf92f9c5f06a2ae50a1e7103d0b29543a07 -r 459ec6b67b3593113ee202b7b9418ee7087c1447 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -714,11 +714,11 @@ def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) class ParamsWithSpecs( collections.defaultdict ): diff -r 157adaf92f9c5f06a2ae50a1e7103d0b29543a07 -r 459ec6b67b3593113ee202b7b9418ee7087c1447 lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/2559a58e62f2/ Changeset: 2559a58e62f2 Branch: next-stable User: natefoo Date: 2014-07-31 20:27:54 Summary: Merge next-stable Affected #: 3 files diff -r 6db9ce7e0415b85ebb833f783458ba6d6e69c242 -r 2559a58e62f292ae537974f8a3fc86ea32ccf8ad .hgtags --- a/.hgtags +++ b/.hgtags @@ -7,6 +7,13 @@ 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 -68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02 +8c30e91bc9ae19ee4dc7ec2c22fa825979497108 latest_2014.06.02 +9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 +81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 +2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 diff -r 6db9ce7e0415b85ebb833f783458ba6d6e69c242 -r 2559a58e62f292ae537974f8a3fc86ea32ccf8ad lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -714,11 +714,11 @@ def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) class ParamsWithSpecs( collections.defaultdict ): diff -r 6db9ce7e0415b85ebb833f783458ba6d6e69c242 -r 2559a58e62f292ae537974f8a3fc86ea32ccf8ad lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): https://bitbucket.org/galaxy/galaxy-central/commits/4aba2116bc2d/ Changeset: 4aba2116bc2d User: natefoo Date: 2014-07-31 20:28:18 Summary: Merge default Affected #: 3 files diff -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 -r 4aba2116bc2de405166d46f034c81eb522cfe4e7 .hgtags --- a/.hgtags +++ b/.hgtags @@ -7,6 +7,13 @@ 26f58e05aa1068761660681583821e21e6cbf7ab release_2013.11.04 5e605ed6069fe4c5ca9875e95e91b2713499e8ca release_2014.02.10 9e53251b0b7e93b9563008a2b112f2e815a04bbc release_2014.04.14 -68a8b0397947c732b28207d465d3f3c4e2a7a8a0 latest_2014.04.14 7e257c7b10badb65772b1528cb61d58175a42e47 release_2014.06.02 -8a863a311a6c9f14b302799bffcf94df9186fef7 latest_2014.06.02 +8c30e91bc9ae19ee4dc7ec2c22fa825979497108 latest_2014.06.02 +9661b9d5d5b330483ae3ad2236410e0efaa7c500 latest_2014.04.14 +6b0bd93038a843b1585155f0d63f0eea2459c70b latest_2013.01.13 +3e62060b14b9afc46f8e0ec02e1a4500d77db9e1 latest_2013.02.08 +425009b3ff4d8b67d2812253b221f3c4f4a8d1e3 latest_2013.04.01 +9713d86392ef985ffcdc39ff0c8ddf51a1f9ce47 latest_2013.06.03 +9ed84cd208e07e8985ec917cb025fcbbb09edcfb latest_2013.08.12 +81fbe25bd02edcd53065e8e4476dd1dfb5a72cf2 latest_2013.11.04 +2a756ca2cb1826db7796018e77d12e2dd7b67603 latest_2014.02.10 diff -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 -r 4aba2116bc2de405166d46f034c81eb522cfe4e7 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -714,11 +714,11 @@ def object_to_string( obj ): - return binascii.hexlify( pickle.dumps( obj, 2 ) ) + return binascii.hexlify( obj ) def string_to_object( s ): - return pickle.loads( binascii.unhexlify( s ) ) + return binascii.unhexlify( s ) class ParamsWithSpecs( collections.defaultdict ): diff -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 -r 4aba2116bc2de405166d46f034c81eb522cfe4e7 lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py --- a/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py +++ b/lib/galaxy/webapps/galaxy/controllers/ucsc_proxy.py @@ -5,6 +5,7 @@ from galaxy.web.base.controller import * import sys +import json from galaxy import web, util import re, urllib, logging @@ -33,7 +34,7 @@ try: store = params.get("__GALAXY__", None) if store: - store = util.string_to_object(store) + store = json.loads(util.string_to_object(store)) else: store = {} UCSC_URL = 'UCSC_URL' @@ -86,7 +87,7 @@ # Serialize store into a form element store_text = "<INPUT TYPE=\"HIDDEN\" NAME=\"__GALAXY__\" ID=\"__GALAXY__\" VALUE=\"" \ - + util.object_to_string(store) + "\" \>" + + json.dumps(util.object_to_string(store)) + "\" \>" # Remove text regions that should not be exposed for key,value in altered_regions.items(): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: Collections view drill-down: (still a work in progress) allow overlay of collection panel view over *current* history panel (not implemented for other history panels), refactoring of history/hda/collections; remove unused init_history_items; pack scripts
by commits-noreply＠bitbucket.org 31 Jul '14

31 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5c58466a1bac/ Changeset: 5c58466a1bac User: carlfeberhard Date: 2014-07-31 18:05:26 Summary: Collections view drill-down: (still a work in progress) allow overlay of collection panel view over *current* history panel (not implemented for other history panels), refactoring of history/hda/collections; remove unused init_history_items; pack scripts Affected #: 35 files diff -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js +++ b/static/scripts/galaxy.base.js @@ -463,88 +463,6 @@ }); } -function init_history_items(historywrapper, noinit, nochanges) { - //NOTE: still needed for non-panel history views - - var action = function() { - // Load saved state and show as necessary - try { - var stored = $.jStorage.get("history_expand_state"); - if (stored) { - for (var id in stored) { - $("#" + id + " div.historyItemBody" ).show(); - } - } - } catch(err) { - // Something was wrong with values in storage, so clear storage - $.jStorage.deleteKey("history_expand_state"); - } - - // If Mozilla, hide scrollbars in hidden items since they cause animation bugs - if ( $.browser.mozilla ) { - $( "div.historyItemBody" ).each( function() { - if ( !$(this).is(":visible") ) { $(this).find( "pre.peek" ).css( "overflow", "hidden" ); } - }); - } - - historywrapper.each( function() { - var id = this.id, - body = $(this).children( "div.historyItemBody" ), - peek = body.find( "pre.peek" ); - $(this).find( ".historyItemTitleBar > .historyItemTitle" ).wrap( "<a href='javascript:void(0);'></a>" ) - .click( function() { - var prefs; - if ( body.is(":visible") ) { - // Hiding stuff here - if ( $.browser.mozilla ) { peek.css( "overflow", "hidden" ); } - body.slideUp( "fast" ); - - if (!nochanges) { // Ignore embedded item actions - // Save setting - prefs = $.jStorage.get("history_expand_state"); - if (prefs) { - delete prefs[id]; - $.jStorage.set("history_expand_state", prefs); - } - } - } else { - // Showing stuff here - body.slideDown( "fast", function() { - if ( $.browser.mozilla ) { peek.css( "overflow", "auto" ); } - }); - - if (!nochanges) { - // Save setting - prefs = $.jStorage.get("history_expand_state"); - if (!prefs) { prefs = {}; } - prefs[id] = true; - $.jStorage.set("history_expand_state", prefs); - } - } - return false; - }); - }); - - // Generate 'collapse all' link - $("#top-links > a.toggle").click( function() { - var prefs = $.jStorage.get("history_expand_state"); - if (!prefs) { prefs = {}; } - $( "div.historyItemBody:visible" ).each( function() { - if ( $.browser.mozilla ) { - $(this).find( "pre.peek" ).css( "overflow", "hidden" ); - } - $(this).slideUp( "fast" ); - if (prefs) { - delete prefs[$(this).parent().attr("id")]; - } - }); - $.jStorage.set("history_expand_state", prefs); - }).show(); - }; - - action(); -} - function commatize( number ) { number += ''; // Convert to string var rgx = /(\d+)(\d{3})/; diff -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 static/scripts/mvc/base-mvc.js --- a/static/scripts/mvc/base-mvc.js +++ b/static/scripts/mvc/base-mvc.js @@ -221,10 +221,146 @@ //============================================================================== +var ExpandableView = Backbone.View.extend( LoggableMixin ).extend({ +//TODO: Although the reasoning behind them is different, this shares a lot with HiddenUntilActivated above: combine them + //PRECONDITION: model must have method hasDetails + + initialize : function( attributes ){ + /** are the details of this view expanded/shown or not? */ + this.expanded = attributes.expanded || false; + this.log( '\t expanded:', this.expanded ); + }, + + // ........................................................................ render main +//TODO: for lack of a better place, add rendering logic here + fxSpeed : 'fast', + + /** Render this content, set up ui. + * @param {Integer} speed the speed of the render + * @fires rendered when rendered + * @fires rendered:ready when first rendered and NO running HDAs + * @returns {Object} this HDABaseView + */ + render : function( speed ){ + var $newRender = this._buildNewRender(); + this._queueNewRender( $newRender, speed ); + return this; + }, + + _buildNewRender : function(){ + // create a new render using a skeleton template, render title buttons, render body, and set up events, etc. + var $newRender = $( this.templates.skeleton( this.model.toJSON() ) ); + if( this.expanded ){ + $newRender.children( '.details' ).replaceWith( this._renderDetails() ); + } + this._setUpBehaviors( $newRender ); + return $newRender; + }, + + /** Fade out the old el, replace with new dom, then fade in. + * @param {Boolean} fade whether or not to fade out/in when re-rendering + * @fires rendered when rendered + * @fires rendered:ready when first rendered and NO running HDAs + */ + _queueNewRender : function( $newRender, speed ) { + speed = ( speed === undefined )?( this.fxSpeed ):( speed ); + var view = this; + + $( view ).queue( 'fx', [ + function( next ){ this.$el.fadeOut( speed, next ); }, + function( next ){ + view._swapNewRender( $newRender ); + next(); + }, + function( next ){ this.$el.fadeIn( speed, next ); }, + function( next ){ + this.trigger( 'rendered', view ); + next(); + } + ]); + }, + + _swapNewRender : function( $newRender ){ + return this.$el.empty().attr( 'class', this.className ).append( $newRender.children() ); + }, + + /** set up js behaviors, event handlers for elements within the given container + * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) + */ + _setUpBehaviors : function( $container ){ + $container = $container || this.$el; + // set up canned behavior on children (bootstrap, popupmenus, editable_text, etc.) + make_popup_menus( $container ); + $container.find( '[title]' ).tooltip({ placement : 'bottom' }); + }, + + // ......................................................................... details + _renderDetails : function(){ + // override this + return null; + }, + + // ......................................................................... expansion/details + /** Show or hide the body/details of history content. + * @param {Boolean} expand if true, expand; if false, collapse + */ + toggleExpanded : function( expand ){ + expand = ( expand === undefined )?( !this.expanded ):( expand ); + if( expand ){ + this.expand(); + } else { + this.collapse(); + } + return this; + }, + + /** Render and show the full, detailed body of this view including extra data and controls. + * note: if the model does not have detailed data, fetch that data before showing the body + * @fires expanded when a body has been expanded + */ + expand : function(){ + var view = this; + + function _renderDetailsAndExpand(){ + view.$( '.details' ).replaceWith( view._renderDetails() ); + // needs to be set after the above or the slide will not show + view.expanded = true; + view.$( '.details' ).slideDown( view.fxSpeed, function(){ + view.trigger( 'expanded', view ); + }); + } +//TODO:?? remove + // fetch first if no details in the model + if( !view.model.hasDetails() ){ + // we need the change event on HDCA's for the elements to be processed - so silent == false + view.model.fetch().always( function( model ){ + _renderDetailsAndExpand(); + }); +//TODO: no error handling + } else { + _renderDetailsAndExpand(); + } + }, + + /** Hide the body/details of an HDA. + * @fires collapsed when a body has been collapsed + */ + collapse : function(){ + var view = this; + view.expanded = false; + this.$( '.details' ).slideUp( view.fxSpeed, function(){ + view.trigger( 'collapsed', view ); + }); + } + +}); + +//============================================================================== return { LoggableMixin : LoggableMixin, SessionStorageModel : SessionStorageModel, HiddenUntilActivatedViewMixin : HiddenUntilActivatedViewMixin, - mixin : mixin + mixin : mixin, + ExpandableView : ExpandableView }; }); diff -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 static/scripts/mvc/collection/collection-model.js --- a/static/scripts/mvc/collection/collection-model.js +++ b/static/scripts/mvc/collection/collection-model.js @@ -16,6 +16,7 @@ */ var DatasetCollectionElement = Backbone.Model.extend( BASE_MVC.LoggableMixin ).extend( /** @lends DatasetCollectionElement.prototype */{ + //TODO:?? this model may be unneccessary - it reflects the api structure, but... // if we munge the element with the element.object at parse, we can flatten the entire hierarchy @@ -24,7 +25,6 @@ //logger : console, defaults : { - id : null, model_class : 'DatasetCollectionElement', element_identifier : null, element_index : null, @@ -41,33 +41,48 @@ this.object = this._createObjectModel(); this.on( 'change:object', function(){ - //console.log( 'change:object' ); + //this.log( 'change:object' ); //TODO: prob. better to update the sub-model instead of re-creating it this.object = this._createObjectModel(); }); }, _createObjectModel : function(){ - //console.log( '_createObjectModel', this.get( 'object' ), this.object ); + //this.log( '_createObjectModel', this.get( 'object' ), this.object ); //TODO: same patterns as HDCA _createElementsModel - refactor to BASE_MVC.hasSubModel? if( _.isUndefined( this.object ) ){ this.object = null; } if( !this.get( 'object' ) ){ return this.object; } - var object = this.get( 'object' ); + var object = this.get( 'object' ), + ObjectClass = this._getObjectClass(); this.unset( 'object', { silent: true }); + this.object = new ObjectClass( object ); + return this.object; + }, + + _getObjectClass : function(){ this.debug( 'DCE, element_type:', this.get( 'element_type' ) ); switch( this.get( 'element_type' ) ){ case 'dataset_collection': - this.object = new DatasetCollection( object ); - break; + return DatasetCollection; case 'hda': - this.object = new HDA_MODEL.HistoryDatasetAssociation( object ); - break; - default: - throw new TypeError( 'Unknown element_type: ' + this.get( 'element_type' ) ); + return HDA_MODEL.HistoryDatasetAssociation; } - return this.object; + throw new TypeError( 'Unknown element_type: ' + this.get( 'element_type' ) ); + }, + + toJSON : function(){ + var json = Backbone.Model.prototype.toJSON.call( this ); + if( this.object ){ + json.object = this.object.toJSON(); + } + return json; + }, + + hasDetails : function(){ + return ( this.object !== null + && this.object.hasDetails() ); }, /** String representation. */ @@ -79,6 +94,52 @@ //============================================================================== +/** @class Backbone model for + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var HDADCE = DatasetCollectionElement.extend( +/** @lends DatasetCollectionElement.prototype */{ + + _getObjectClass : function(){ + return HDA_MODEL.HistoryDatasetAssociation; + }, + + /** String representation. */ + toString : function(){ + var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) ); + return ([ 'HDADCE(', objStr, ')' ].join( '' )); + } +}); + + +//============================================================================== +/** @class Backbone model for + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DCDCE = DatasetCollectionElement.extend( +/** @lends DatasetCollectionElement.prototype */{ + + _getObjectClass : function(){ + return DatasetCollection; + }, + + getVisibleContents : function(){ + return this.object? this.object.getVisibleContents(): []; + }, + + /** String representation. */ + toString : function(){ + var objStr = ( this.object )?( '' + this.object ):( this.get( 'element_identifier' ) ); + return ([ 'DCDCE(', objStr, ')' ].join( '' )); + } +}); + + +//============================================================================== /** @class Backbone collection for DCEs. * NOTE: used *only* in second level of list:paired collections (a * collection that contains collections) @@ -87,7 +148,7 @@ * @borrows LoggableMixin#log as #log * @constructs */ -var DatasetCollectionElementCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( +var DCECollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend( /** @lends DatasetCollectionElementCollection.prototype */{ model: DatasetCollectionElement, @@ -112,6 +173,40 @@ //============================================================================== +/** @class Backbone collection for + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var HDADCECollection = DCECollection.extend( +/** @lends DatasetCollectionElementCollection.prototype */{ + model: HDADCE, + + /** String representation. */ + toString : function(){ + return ([ 'HDADCECollection(', this.length, ')' ].join( '' )); + } +}); + + +//============================================================================== +/** @class Backbone collection for + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DCDCECollection = DCECollection.extend( +/** @lends DatasetCollectionElementCollection.prototype */{ + model: DCDCE, + + /** String representation. */ + toString : function(){ + return ([ 'DCDCECollection(', this.length, ')' ].join( '' )); + } +}); + + +//============================================================================== /** @class Backbone model for Dataset Collections. * DCs contain a bbone collection named 'elements' using the class found in * this.collectionClass (gen. DatasetCollectionElementCollection). DCs move @@ -133,7 +228,7 @@ collection_type : 'list' }, - collectionClass : DatasetCollectionElementCollection, + collectionClass : DCECollection, /** */ initialize : function( model, options ){ @@ -159,11 +254,25 @@ return this.elements; }, + toJSON : function(){ + var json = Backbone.Model.prototype.toJSON.call( this ); + if( this.elements ){ + json.elements = this.elements.toJSON(); + } + return json; + }, + hasDetails : function(){ //TODO: this is incorrect for (accidentally) empty collections + this.debug( 'hasDetails:', this.elements.length ); return this.elements.length !== 0; }, + getVisibleContents : function( filters ){ + //TODO: filters unused for now + return this.elements; + }, + // ........................................................................ misc /** String representation */ toString : function(){ @@ -174,37 +283,11 @@ //============================================================================== -/** @class Backbone collection for a collection of collection collections collecting correctly. */ -var DatasetCollectionCollection = Backbone.Collection.extend( BASE_MVC.LoggableMixin ).extend({ - - model: DatasetCollection, - - ///** logger used to record this.log messages, commonly set to console */ - //// comment this out to suppress log output - //logger : console, - - /** Set up. - * @see Backbone.Collection#initialize - */ - initialize : function( models, options ){ - options = options || {}; - this.info( 'DatasetCollectionCollection.initialize:', models, options ); - //this._setUpListeners(); - }, - - /** String representation. */ - toString : function(){ - return ([ 'DatasetCollectionCollection(', this.get( 'name' ), ')' ].join( '' )); - } -}); - - -//NOTE: the following prototypes may not be necessary - but I wanted to specifiy -// them (for now) and allow for the possibility of unique functionality -//============================================================================== var ListDatasetCollection = DatasetCollection.extend( /** @lends ListDatasetCollection.prototype */{ + collectionClass : HDADCECollection, + /** String representation. */ toString : function(){ return ([ 'ListDatasetCollection(', this.get( 'name' ), ')' ].join( '' )); @@ -213,7 +296,7 @@ //============================================================================== -var PairDatasetCollection = DatasetCollection.extend( +var PairDatasetCollection = ListDatasetCollection.extend( /** @lends ListDatasetCollection.prototype */{ /** String representation. */ @@ -227,6 +310,8 @@ var ListPairedDatasetCollection = DatasetCollection.extend( /** @lends ListDatasetCollection.prototype */{ + collectionClass : DCDCECollection, + // list:paired is the only collection that itself contains collections //collectionClass : DatasetCollectionCollection, @@ -239,10 +324,7 @@ //============================================================================== return { - DatasetCollectionElement : DatasetCollectionElement, - DatasetCollectionElementCollection : DatasetCollectionElementCollection, - DatasetCollection : DatasetCollection, - DatasetCollectionCollection : DatasetCollectionCollection, + //DatasetCollection : DatasetCollection, ListDatasetCollection : ListDatasetCollection, PairDatasetCollection : PairDatasetCollection, ListPairedDatasetCollection : ListPairedDatasetCollection diff -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 static/scripts/mvc/collection/collection-panel.js --- a/static/scripts/mvc/collection/collection-panel.js +++ b/static/scripts/mvc/collection/collection-panel.js @@ -1,13 +1,13 @@ define([ "mvc/collection/dataset-collection-base", - "mvc/dataset/hda-base", "mvc/base-mvc", "utils/localization" -], function( DC_BASE, HDA_BASE, BASE_MVC, _l ){ +], function( DC_BASE, BASE_MVC, _l ){ /* ============================================================================= TODO: ============================================================================= */ +// ============================================================================= /** @class non-editable, read-only View/Controller for a dataset collection. * @name CollectionPanel * @@ -18,17 +18,20 @@ */ var CollectionPanel = Backbone.View.extend( BASE_MVC.LoggableMixin ).extend( /** @lends CollectionPanel.prototype */{ + //MODEL is either a DatasetCollection (or subclass) or a DatasetCollectionElement (list of pairs) /** logger used to record this.log messages, commonly set to console */ // comment this out to suppress log output //logger : console, tagName : 'div', - className : 'history-panel', + className : 'dataset-collection-panel', /** (in ms) that jquery effects will use */ fxSpeed : 'fast', + DCEViewClass : DC_BASE.DCEBaseView, + // ......................................................................... SET UP /** Set up the view, set up storage, bind listeners to HistoryContents events * @param {Object} attributes optional settings for the panel @@ -42,7 +45,10 @@ this.log( this + '.initialize:', attributes ); this.hasUser = attributes.hasUser; - this.HDAViewClass = attributes.HDAViewClass || HDA_BASE.HDABaseView; + this.panelStack = []; + this.parentName = attributes.parentName; + + window.collectionPanel = this; }, /** create any event listeners for the panel @@ -74,7 +80,7 @@ this.log( 'render:', speed, callback ); // send a speed of 0 to have no fade in/out performed speed = ( speed === undefined )?( this.fxSpeed ):( speed ); - //console.debug( this + '.render, fxSpeed:', speed ); + //this.debug( this + '.render, fxSpeed:', speed ); var panel = this, $newRender; @@ -123,7 +129,13 @@ */ renderModel : function( ){ // tmp div for final swap in render - var $newRender = $( '<div/>' ).append( CollectionPanel.templates.panel( this.model.toJSON() ) ); +//TODO: ugh - reuse issue - refactor out + var type = this.model.get( 'collection_type' ) || this.model.object.get( 'collection_type' ), + json = _.extend( this.model.toJSON(), { + parentName : this.parentName, + type : type + }), + $newRender = $( '<div/>' ).append( this.templates.panel( json ) ); this._setUpBehaviours( $newRender ); this.renderContents( $newRender ); return $newRender; @@ -154,13 +166,15 @@ * @returns the number of visible hda views */ renderContents : function( $whereTo ){ - //console.debug( 'renderContents, elements:', this.model.elements ); + //this.debug( 'renderContents, elements:', this.model.elements ); $whereTo = $whereTo || this.$el; + this.warn( this + '.renderContents:, model:', this.model ); var panel = this, contentViews = {}, - visibleContents = this.model.elements || []; - //this.log( 'renderContents, visibleContents:', visibleContents, $whereTo ); + //NOTE: no filtering here + visibleContents = this.model.getVisibleContents(); + this.log( 'renderContents, visibleContents:', visibleContents, $whereTo ); this.$datasetsList( $whereTo ).empty(); if( visibleContents && visibleContents.length ){ @@ -168,66 +182,92 @@ var contentId = content.id, contentView = panel._createContentView( content ); contentViews[ contentId ] = contentView; - panel.attachContentView( contentView.render(), $whereTo ); + panel._attachContentView( contentView.render(), $whereTo ); }); } this.contentViews = contentViews; return this.contentViews; }, - /** - * @param {HistoryDatasetAssociation} content - */ + /** */ _createContentView : function( content ){ - //console.debug( 'content json:', JSON.stringify( content, null, ' ' ) ); + //this.debug( 'content json:', JSON.stringify( content, null, ' ' ) ); var contentView = null, ContentClass = this._getContentClass( content ); - //console.debug( 'content.object json:', JSON.stringify( content.object, null, ' ' ) ); - //console.debug( 'ContentClass:', ContentClass ); - //console.debug( 'content:', content ); - //console.debug( 'content.object:', content.object ); + //this.debug( 'content.object json:', JSON.stringify( content.object, null, ' ' ) ); + this.debug( 'ContentClass:', ContentClass ); + //this.debug( 'content:', content ); + this.debug( 'content.object:', content.object ); contentView = new ContentClass({ - model : content.object, + model : content, linkTarget : this.linkTarget, //draggable : true, hasUser : this.hasUser, logger : this.logger }); - //this._setUpHdaListeners( contentView ); + this.debug( 'contentView:', contentView ); + this._setUpContentListeners( contentView ); return contentView; }, + /** */ _getContentClass : function( content ){ + this.debug( this + '._getContentClass:', content ); switch( content.get( 'element_type' ) ){ case 'hda': - return this.HDAViewClass; + return this.DCEViewClass; case 'dataset_collection': - return DC_BASE.NestedDCEBaseView; + return this.DCEViewClass; } throw new TypeError( 'Unknown element type:', content.get( 'element_type' ) ); }, -// /** Set up HistoryPanel listeners for HDAView events. Currently binds: -// * HDAView#body-visible, HDAView#body-hidden to store expanded states -// * @param {HDAView} hdaView HDAView (base or edit) to listen to -// */ -// _setUpHdaListeners : function( hdaView ){ -// var panel = this; -// hdaView.on( 'error', function( model, xhr, options, msg ){ -// panel.errorHandler( model, xhr, options, msg ); -// }); -// // maintain a list of hdas whose bodies are expanded -// hdaView.on( 'body-expanded', function( model ){ -// panel.storage.addExpandedHda( model ); -// }); -// hdaView.on( 'body-collapsed', function( id ){ -// panel.storage.removeExpandedHda( id ); -// }); -// return this; -// }, + /** Set up listeners for content view events. In this override, handle collection expansion. */ + _setUpContentListeners : function( contentView ){ + var panel = this; + if( contentView.model.get( 'element_type' ) === 'dataset_collection' ){ + contentView.on( 'expanded', function( collectionView ){ + panel.info( 'expanded', collectionView ); + panel._addCollectionPanel( collectionView ); + }); + } + }, + + /** */ + _addCollectionPanel : function( collectionView ){ + var currPanel = this, + collectionModel = collectionView.model; + + this.debug( 'collection panel (stack), collectionView:', collectionView ); + this.debug( 'collection panel (stack), collectionModel:', collectionModel ); + var panel = new PairCollectionPanel({ + model : collectionModel, + parentName : this.model.get( 'name' ) + }); + currPanel.panelStack.push( panel ); + + currPanel.$( '.controls' ).add( '.datasets-list' ).hide(); + currPanel.$el.append( panel.$el ); + panel.on( 'close', function(){ + currPanel.render(); + collectionView.collapse(); + currPanel.panelStack.pop(); + }); + + //TODO: to hdca-model, hasDetails + if( !panel.model.hasDetails() ){ + var xhr = panel.model.fetch(); + xhr.done( function(){ + //TODO: (re-)render collection contents + panel.render(); + }); + } else { + panel.render(); + } + }, /** attach an contentView to the panel */ - attachContentView : function( contentView, $whereTo ){ + _attachContentView : function( contentView, $whereTo ){ $whereTo = $whereTo || this.$el; var $datasetsList = this.$datasetsList( $whereTo ); $datasetsList.append( contentView.$el ); @@ -237,90 +277,102 @@ // ------------------------------------------------------------------------ panel events /** event map */ events : { - 'click .panel-navigation-back' : 'close' + 'click .navigation .back' : 'close' }, /** */ close : function( event ){ this.$el.remove(); - this.trigger( 'collection-close' ); + this.trigger( 'close' ); }, // ........................................................................ misc - /** Return a string rep of the history */ + /** string rep */ toString : function(){ return 'CollectionPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; } }); +//----------------------------------------------------------------------------- TEMPLATES +/** underscore templates */ +CollectionPanel.templates = CollectionPanel.prototype.templates = (function(){ +// use closure to run underscore template fn only once at module load + var _panelTemplate = _.template([ + '<div class="controls">', + '<div class="navigation">', + '<a class="back" href="javascript:void(0)">', + '<span class="fa fa-icon fa-angle-left"></span>', + _l( 'Back to ' ), '<%- collection.parentName %>', + '</a>', + '</div>', -//------------------------------------------------------------------------------ TEMPLATES -var _panelTemplate = [ - '<div class="history-controls">', - '<div class="panel-navigation">', - '<a class="panel-navigation-back" href="javascript:void(0)">', _l( 'Back' ), '</a>', + '<div class="title">', + '<div class="name"><%- collection.name || collection.element_identifier %></div>', + '<div class="subtitle">', +//TODO: remove logic from template + '<% if( collection.type === "list" ){ %>', + _l( 'a list of datasets' ), + '<% } else if( collection.type === "paired" ){ %>', + _l( 'a pair of datasets' ), + '<% } else if( collection.type === "list:paired" ){ %>', + _l( 'a list of paired datasets' ), + '<% } %>', + '</div>', + '</div>', '</div>', + // where the datasets/hdas are added + '<div class="datasets-list"></div>' + ].join( '' )); - '<div class="history-title">', - '<% if( collection.name ){ %>', - '<div class="history-name"><%= collection.hid %> : <%= collection.name %></div>', - '<% } %>', - '</div>', + // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within + return { + panel : function( json ){ + return _panelTemplate({ _l: _l, collection: json }); + } + }; +}()); - //'<div class="history-subtitle clear">', - // '<% if( history.nice_size ){ %>', - // '<div class="history-size"><%= history.nice_size %></div>', - // '<% } %>', - // '<div class="history-secondary-actions"></div>', - //'</div>', - // - //'<% if( history.deleted ){ %>', - // '<div class="warningmessagesmall"><strong>', - // _l( 'You are currently viewing a deleted history!' ), - // '</strong></div>', - //'<% } %>', - // - //'<div class="message-container">', - // '<% if( history.message ){ %>', - // // should already be localized - // '<div class="<%= history.status %>message"><%= history.message %></div>', - // '<% } %>', - //'</div>', - // - //'<div class="quota-message errormessage">', - // _l( 'You are over your disk quota' ), '. ', - // _l( 'Tool execution is on hold until your disk usage drops below your allocated quota' ), '.', - //'</div>', - // - //'<div class="tags-display"></div>', - //'<div class="annotation-display"></div>', - //'<div class="history-dataset-actions">', - // '<div class="btn-group">', - // '<button class="history-select-all-datasets-btn btn btn-default"', - // 'data-mode="select">', _l( 'All' ), '</button>', - // '<button class="history-deselect-all-datasets-btn btn btn-default"', - // 'data-mode="select">', _l( 'None' ), '</button>', - // '</div>', - // '<button class="history-dataset-action-popup-btn btn btn-default">', - // _l( 'For all selected' ), '...</button>', - //'</div>', - '</div>', - // end history controls - // where the datasets/hdas are added - '<div class="datasets-list"></div>' +// ============================================================================= +/** @class non-editable, read-only View/Controller for a dataset collection. */ +var ListCollectionPanel = CollectionPanel.extend({ + DCEViewClass : DC_BASE.HDADCEBaseView, + // ........................................................................ misc + /** string rep */ + toString : function(){ + return 'ListCollectionPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; + } +}); -].join( '' ); -CollectionPanel.templates = { - panel : function( JSON ){ - return _.template( _panelTemplate, JSON, { variable: 'collection' }); +// ============================================================================= +/** @class non-editable, read-only View/Controller for a dataset collection. */ +var PairCollectionPanel = ListCollectionPanel.extend({ + // ........................................................................ misc + /** string rep */ + toString : function(){ + return 'PairCollectionPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; } -}; +}); + + +// ============================================================================= +/** @class non-editable, read-only View/Controller for a dataset collection. */ +var ListOfPairsCollectionPanel = CollectionPanel.extend({ + DCEViewClass : DC_BASE.DCDCEBaseView, + // ........................................................................ misc + /** string rep */ + toString : function(){ + return 'ListOfPairsCollectionPanel(' + (( this.model )?( this.model.get( 'name' )):( '' )) + ')'; + } +}); //============================================================================== return { - CollectionPanel: CollectionPanel + CollectionPanel : CollectionPanel, + ListCollectionPanel : ListCollectionPanel, + PairCollectionPanel : PairCollectionPanel, + ListOfPairsCollectionPanel : ListOfPairsCollectionPanel }; }); diff -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 static/scripts/mvc/collection/dataset-collection-base.js --- a/static/scripts/mvc/collection/dataset-collection-base.js +++ b/static/scripts/mvc/collection/dataset-collection-base.js @@ -29,7 +29,82 @@ this.log( 'DCBaseView.initialize:', attributes ); }, -//TODO: render has been removed from the inheritance chain here, so this won't work when called as is + // ........................................................................ render main + /** Render this content, set up ui. + * @param {Boolean} fade whether or not to fade out/in when re-rendering + * @fires rendered when rendered + * @fires rendered:ready when first rendered and NO running HDAs + * @returns {Object} this HDABaseView + */ + render : function( fade ){ + var $newRender = this._buildNewRender(); + this._queueNewRender( $newRender, fade ); + return this; + }, + + _buildNewRender : function(){ + // create a new render using a skeleton template, render title buttons, render body, and set up events, etc. + var $newRender = $( this.templates.skeleton( this.model.toJSON() ) ); + $newRender.find( '.primary-actions' ).append( this._render_primaryActions() ); + this._setUpBehaviors( $newRender ); + //this._renderSelectable( $newRender ); + return $newRender; + }, + + /** Fade out the old el, replace with new dom, then fade in. + * @param {Boolean} fade whether or not to fade out/in when re-rendering + * @fires rendered when rendered + * @fires rendered:ready when first rendered and NO running HDAs + */ + _queueNewRender : function( $newRender, fade ) { + fade = ( fade === undefined )?( true ):( fade ); + var view = this; + + // fade the old render out (if desired) + if( fade ){ + $( view ).queue( function( next ){ this.$el.fadeOut( view.fxSpeed, next ); }); + } + // empty the old render, swap in the new render contents + $( view ).queue( function( next ){ +//TODO:?? change to replaceWith pattern? + this.$el.empty().attr( 'class', view.className ).append( $newRender.children() ); + next(); + }); + // fade the new in + if( fade ){ + $( view ).queue( function( next ){ this.$el.fadeIn( view.fxSpeed, next ); }); + } + // trigger an event to know we're ready + $( view ).queue( function( next ){ + this.trigger( 'rendered', view ); + next(); + }); + }, + + /** set up js behaviors, event handlers for elements within the given container + * @param {jQuery} $container jq object that contains the elements to process (defaults to this.$el) + */ + _setUpBehaviors : function( $container ){ + $container = $container || this.$el; + make_popup_menus( $container ); + $container.find( '[title]' ).tooltip({ placement : 'bottom' }); + }, + + // ........................................................................ titlebar buttons + /** Render icon-button group for the common, most easily accessed actions. + * @returns {jQuery} rendered DOM or null + */ + _render_primaryActions : function(){ + // override + return []; + }, + + // ......................................................................... misc + events : { + 'click .title-bar' : function( event ){ + this.trigger( 'expanded', this ); + } + }, // ......................................................................... misc /** String representation */ @@ -40,37 +115,23 @@ }); /** templates for DCBaseViews (skeleton and body) */ -DCBaseView.templates = (function(){ +DCBaseView.templates = DCBaseView.prototype.templates = (function(){ // use closure to run underscore template fn only once at module load var skeletonTemplate = _.template([ - '<div class="dataset hda">', - '<div class="dataset-warnings">', - '<% if ( collection.deleted ) { %>', - '<div class="dataset-deleted-msg warningmessagesmall"><strong>', - _l( 'This collection has been deleted.' ), - '</div>', - '<% } %>', - '<% if ( !collection.visible ) { %>', - '<div class="dataset-hidden-msg warningmessagesmall"><strong>', - _l( 'This collection has been hidden.' ), - '</div>', - '<% } %>', - '</div>', - '<div class="dataset-primary-actions"></div>', - '<div class="dataset-title-bar clear" tabindex="0">', - '<span class="dataset-state-icon state-icon"></span>', - '<div class="dataset-title">', - '<span class="dataset-name"><%- collection.name %></span>', + '<div class="dataset-collection">', + '<div class="primary-actions"></div>', + '<div class="title-bar clear" tabindex="0">', + '<div class="title">', + '<span class="name"><%- collection.element_identifier %></span>', '</div>', '</div>', - '<div class="dataset-body"></div>', + '<div class="details"></div>', '</div>' ].join( '' )); var bodyTemplate = _.template([ - '<div class="dataset-body">', - '<div class="dataset-summary">', - _l( 'A dataset collection.' ), + '<div class="details">', + '<div class="summary">', _l( 'A dataset collection.' ), '</div>', '</div>' ].join( '' )); @@ -86,66 +147,312 @@ }()); -//TODO: unused -////============================================================================== -///** @class Read only view for DatasetCollectionElement. -// * @name DCEBaseView -// * -// * @augments Backbone.View -// * @borrows LoggableMixin#logger as #logger -// * @borrows LoggableMixin#log as #log -// * @constructs -// */ -//var NestedDCBaseView = DCBaseView.extend({ -// -// logger : console, -// -// /** */ -// initialize : function( attributes ){ -// if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } -// this.warn( this + '.initialize:', attributes ); -// DCBaseView.prototype.initialize.call( this, attributes ); -// }, -// -// _template : function(){ -// this.debug( this.model ); -// this.debug( this.model.toJSON() ); -// return NestedDCBaseView.templates.skeleton( this.model.toJSON() ); -// }, -// -// // ......................................................................... misc -// /** String representation */ -// toString : function(){ -// var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); -// return 'NestedDCBaseView(' + modelString + ')'; -// } -//}); -// -////------------------------------------------------------------------------------ TEMPLATES -////TODO: possibly break these out into a sep. module -//NestedDCBaseView.templates = (function(){ -// var skeleton = _.template([ -// '<div class="dataset hda history-panel-hda state-ok">', -// '<div class="dataset-primary-actions"></div>', -// '<div class="dataset-title-bar clear" tabindex="0">', -// '<div class="dataset-title">', -// '<span class="dataset-name"><%= collection.name %></span>', -// '</div>', -// '</div>', -// '</div>' -// ].join( '' )); -// // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within -// return { -// skeleton : function( json ){ -// return skeleton({ _l: _l, collection: json }); -// } -// }; -//}()); +//============================================================================== +/** @class Read only view for DatasetCollectionElement. + * @name DCBaseView + * + * @augments Backbone.View + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DCEBaseView = BASE_MVC.ExpandableView.extend({ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + /** */ + className : "dataset-collection-element collection-dataset dataset", + /** */ + fxSpeed : 'fast', + + /** */ + initialize : function( attributes ){ + if( attributes.logger ){ this.logger = this.model.logger = attributes.logger; } + this.log( 'DCEBaseView.initialize:', attributes ); + BASE_MVC.ExpandableView.prototype.initialize.call( this, attributes ); + }, + + // ......................................................................... renderers + /** Render the enclosing div of the hda body and, if expanded, the html in the body + * @returns {jQuery} rendered DOM + */ + _renderDetails : function(){ + var $details = $( this.templates.details( this.model.toJSON() ) ); + this._setUpBehaviors( $details ); + // only render the body html if it's being shown + if( this.expanded ){ + $details.show(); + } + return $details; + }, + + // ......................................................................... events + events : { + // expand the body when the title is clicked or when in focus and space or enter is pressed + 'click .title-bar' : '_clickTitleBar', + 'keydown .title-bar' : '_keyDownTitleBar' + }, + + _clickTitleBar : function( event ){ + event.stopPropagation(); + this.toggleExpanded(); + }, + + _keyDownTitleBar : function( event ){ + // bail (with propagation) if keydown and not space or enter + var KEYCODE_SPACE = 32, KEYCODE_RETURN = 13; + if( event && ( event.type === 'keydown' ) + &&( event.keyCode === KEYCODE_SPACE || event.keyCode === KEYCODE_RETURN ) ){ + this.toggleExpanded(); + event.stopPropagation(); + return false; + } + return true; + }, + + // ......................................................................... misc + /** String representation */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'DCEBaseView(' + modelString + ')'; + } +}); + +/** templates for DCBaseViews (skeleton and body) */ +DCEBaseView.templates = DCEBaseView.prototype.templates = (function(){ +// use closure to run underscore template fn only once at module load + var skeletonTemplate = _.template([ + '<div class="dataset-collection-element collection-dataset dataset">', + '<div class="primary-actions"></div>', + '<div class="title-bar clear" tabindex="0">', + '<span class="state-icon"></span>', + '<div class="title">', + '<span class="name"><%- collection.element_identifier %></span>', + '</div>', + '</div>', + '<div class="details"></div>', + '</div>' + ].join( '' )); + + var bodyTemplate = _.template([ + '<div class="details">', + '<div class="summary">', + _l( 'A dataset collection element.' ), + '</div>', + '</div>' + ].join( '' )); + + // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within + return { + skeleton : function( collectionJSON ){ + return skeletonTemplate({ _l: _l, collection: collectionJSON }); + }, + body : function( collectionJSON ){ + return bodyTemplate({ _l: _l, collection: collectionJSON }); + } + }; +}()); + + +//============================================================================== +/** @class Read only view for DatasetCollectionElement. + * @name DCBaseView + * + * @augments Backbone.View + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var HDADCEBaseView = DCEBaseView.extend({ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + // ......................................................................... misc + /** String representation */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'HDADCEBaseView(' + modelString + ')'; + } +}); + +/** templates for DCBaseViews (skeleton and body) */ +HDADCEBaseView.templates = HDADCEBaseView.prototype.templates = (function(){ +// use closure to run underscore template fn only once at module load + var skeletonTemplate = _.template([ + '<div class="dataset-collection-element dataset">', + '<div class="primary-actions"></div>', + '<div class="title-bar clear" tabindex="0">', + '<span class="state-icon"></span>', + '<div class="title">', +//TODO:?? re-check this: in pairs the name and identifier are different - but not otherwise + '<span class="name"><%- element.element_identifier %></span>', + '</div>', +// '<% if( element.element_identifier !== hda.name ){ %>', +// '<div class="subtitle"><%- element.element_identifier %></div>', +// '<% } %>', + '</div>', + '<div class="details"></div>', + '</div>' + ].join( '' )); + + var detailsTemplate = _.template([ + '<div class="details">', + '<div class="summary">', + '<% if( hda.misc_blurb ){ %>', + '<div class="blurb">', + '<span class="value"><%- hda.misc_blurb %></span>', + '</div>', + '<% } %>', + + '<% if( hda.data_type ){ %>', + '<div class="datatype">', + '<label class="prompt">', _l( 'format' ), '</label>', + '<span class="value"><%- hda.data_type %></span>', + '</div>', + '<% } %>', + + '<% if( hda.metadata_dbkey ){ %>', + '<div class="dbkey">', + '<label class="prompt">', _l( 'database' ), '</label>', + '<span class="value">', + '<%- hda.metadata_dbkey %>', + '</span>', + '</div>', + '<% } %>', + + '<% if( hda.misc_info ){ %>', + '<div class="info">', + '<span class="value"><%- hda.misc_info %></span>', + '</div>', + '<% } %>', + '</div>', + // end dataset-summary + + '<div class="actions clear">', + '<div class="left"></div>', + '<div class="right"></div>', + '</div>', + + '<% if( !hda.deleted ){ %>', + '<div class="tags-display"></div>', + '<div class="annotation-display"></div>', + + '<div class="display-applications">', + //TODO: the following two should be compacted + '<% _.each( hda.display_apps, function( app ){ %>', + '<div class="display-application">', + '<span class="display-application-location"><%- app.label %></span> ', + '<span class="display-application-links">', + '<% _.each( app.links, function( link ){ %>', + '<a target="<%= link.target %>" href="<%= link.href %>">', + '<% print( _l( link.text ) ); %>', + '</a> ', + '<% }); %>', + '</span>', + '</div>', + '<% }); %>', + + '<% _.each( hda.display_types, function( app ){ %>', + '<div class="display-application">', + '<span class="display-application-location"><%- app.label %></span> ', + '<span class="display-application-links">', + '<% _.each( app.links, function( link ){ %>', + '<a target="<%= link.target %>" href="<%= link.href %>">', + '<% print( _l( link.text ) ); %>', + '</a> ', + '<% }); %>', + '</span>', + '</div>', + '<% }); %>', + '</div>', + + '<% if( hda.peek ){ %>', + '<pre class="dataset-peek"><%= hda.peek %></pre>', + '<% } %>', + + '<% } %>', + // end if !deleted + + '</div>' + ].join( '' )); + + // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within + return { + skeleton : function( json ){ + return skeletonTemplate({ _l: _l, element: json, hda: json.object }); + }, + details : function( json ){ + return detailsTemplate({ _l: _l, element: json, hda: json.object }); + } + }; +}()); + + +//============================================================================== +/** @class Read only view for DatasetCollectionElement. + * @name DCBaseView + * + * @augments Backbone.View + * @borrows LoggableMixin#logger as #logger + * @borrows LoggableMixin#log as #log + * @constructs + */ +var DCDCEBaseView = DCEBaseView.extend({ + + /** logger used to record this.log messages, commonly set to console */ + // comment this out to suppress log output + //logger : console, + + // ......................................................................... misc + /** String representation */ + expand : function(){ + this.trigger( 'expanded', this ); + }, + + // ......................................................................... misc + /** String representation */ + toString : function(){ + var modelString = ( this.model )?( this.model + '' ):( '(no model)' ); + return 'DCDCEBaseView(' + modelString + ')'; + } +}); + +/** templates for DCBaseViews (skeleton and body) */ +DCDCEBaseView.templates = DCDCEBaseView.prototype.templates = (function(){ +// use closure to run underscore template fn only once at module load + var skeletonTemplate = _.template([ + '<div class="dataset-collection-element dataset-collection">', + '<div class="primary-actions"></div>', + '<div class="title-bar clear" tabindex="0">', + '<span class="state-icon"></span>', + '<div class="title">', + '<span class="name"><%- element.element_identifier %></span>', + '</div>', +//TODO: currently correct, but needs logic if more nested types are added + '<div class="subtitle">', _l( 'paired datasets' ), '</div>', + '</div>', + '<div class="details"></div>', + '</div>' + ].join( '' )); + + // we override here in order to pass the localizer (_L) into the template scope - since we use it as a fn within + return { + skeleton : function( json ){ + return skeletonTemplate({ _l: _l, element: json, collection: json.object }); + } + }; +}()); //============================================================================== return { DCBaseView : DCBaseView, - //NestedDCBaseView : NestedDCBaseView, + DCEBaseView : DCEBaseView, + HDADCEBaseView : HDADCEBaseView, + DCDCEBaseView : DCDCEBaseView }; }); diff -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 static/scripts/mvc/collection/hdca-base.js --- a/static/scripts/mvc/collection/hdca-base.js +++ b/static/scripts/mvc/collection/hdca-base.js @@ -22,8 +22,9 @@ // comment this out to suppress log output //logger : console, +//TODO: not a dataset /** */ - className : "dataset hda history-panel-hda", + className : "dataset hdca history-panel-hda", /** */ initialize : function( attributes ){ @@ -52,6 +53,26 @@ return $body; }, + /** In this override, do not slide down or render any body/details - allow the container to handle it + * @fires expanded when a body has been expanded + */ + expand : function(){ + this.warn( this + '.expand' ); + var contentView = this; + + // fetch first if no details in the model + if( this.model.inReadyState() && !this.model.hasDetails() ){ + // we need the change event on HDCA's for the elements to be processed - so silent == false + this.model.fetch().always( function( model ){ + contentView.expanded = true; + contentView.trigger( 'expanded', contentView ); + }); + } else { + contentView.expanded = true; + contentView.trigger( 'expanded', contentView ); + } + }, + // ......................................................................... misc /** String representation */ toString : function(){ @@ -64,7 +85,8 @@ HDCABaseView.templates = HDCABaseView.prototype.templates = (function(){ // use closure to run underscore template fn only once at module load var skeletonTemplate = _.template([ - '<div class="dataset hda">', +//TODO: not a dataset + '<div class="dataset hdca">', '<div class="dataset-warnings">', '<% if ( collection.deleted ) { %>', '<div class="dataset-deleted-msg warningmessagesmall"><strong>', @@ -77,22 +99,32 @@ '</div>', '<% } %>', '</div>', - '<div class="dataset-selector"><span class="fa fa-2x fa-square-o"></span></div>', - '<div class="dataset-primary-actions"></div>', - '<div class="dataset-title-bar clear" tabindex="0">', - '<span class="dataset-state-icon state-icon"></span>', - '<div class="dataset-title">', - '<span class="hda-hid"><%- collection.hid %></span> ', - '<span class="dataset-name"><%- collection.name %></span>', + '<div class="selector"><span class="fa fa-2x fa-square-o"></span></div>', + '<div class="primary-actions"></div>', + '<div class="title-bar clear" tabindex="0">', + '<span class="state-icon"></span>', + '<div class="title">', + '<span class="hid"><%- collection.hid %></span> ', + '<span class="name"><%- collection.name %></span>', + '</div>', + '<div class="subtitle">', +//TODO: remove from template logic + '<% if( collection.collection_type === "list" ){ %>', + _l( 'a list of datasets' ), + '<% } else if( collection.collection_type === "paired" ){ %>', + _l( 'a pair of datasets' ), + '<% } else if( collection.collection_type === "list:paired" ){ %>', + _l( 'a list of paired datasets' ), + '<% } %>', '</div>', '</div>', - '<div class="dataset-body"></div>', + '<div class="details"></div>', '</div>' ].join( '' )); var bodyTemplate = _.template([ - '<div class="dataset-body">', - '<div class="dataset-summary">', + '<div class="details">', + '<div class="summary">', _l( 'A dataset collection.' ), '</div>' ].join( '' )); diff -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 static/scripts/mvc/collection/hdca-edit.js --- a/static/scripts/mvc/collection/hdca-edit.js +++ b/static/scripts/mvc/collection/hdca-edit.js @@ -23,13 +23,13 @@ // ......................................................................... edit attr, delete /** Render icon-button group for the common, most easily accessed actions. - * Overrides _render_titleButtons to include editing related buttons. + * Overrides _render_primaryActions to include editing related buttons. * @returns {jQuery} rendered DOM */ - _render_titleButtons : function(){ - this.log( this + '._render_titleButtons' ); + _render_primaryActions : function(){ + this.log( this + '._render_primaryActions' ); // render the display, edit attr and delete icon-buttons - return _super.prototype._render_titleButtons.call( this ) + return _super.prototype._render_primaryActions.call( this ) .concat([ this._render_deleteButton() ]); diff -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 static/scripts/mvc/collection/hdca-model.js --- a/static/scripts/mvc/collection/hdca-model.js +++ b/static/scripts/mvc/collection/hdca-model.js @@ -5,20 +5,15 @@ ], function( HISTORY_CONTENT, DC_MODEL, _l ){ //============================================================================== var hcontentMixin = HISTORY_CONTENT.HistoryContentMixin, -/** @class Backbone model for (generic) Dataset Collection within a History. - * @constructs - */ - HistoryDatasetCollection = DC_MODEL.DatasetCollection.extend( hcontentMixin ); + ListDC = DC_MODEL.ListDatasetCollection, + PairDC = DC_MODEL.PairDatasetCollection, + ListPairedDC = DC_MODEL.ListPairedDatasetCollection; - -//NOTE: the following prototypes may not be necessary - but I wanted to specifiy -// them (for now) and allow for the possibility of unique functionality //============================================================================== -var ListDC = DC_MODEL.ListDatasetCollection, /** @class Backbone model for List Dataset Collection within a History. * @constructs */ - HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend( +var HistoryListDatasetCollection = ListDC.extend( hcontentMixin ).extend( /** @lends HistoryListDatasetCollection.prototype */{ initialize : function( model, options ){ @@ -36,11 +31,10 @@ //============================================================================== -var PairDC = DC_MODEL.PairDatasetCollection, /** @class Backbone model for Pair Dataset Collection within a History. * @constructs */ - HistoryPairDatasetCollection = PairDC.extend( hcontentMixin ).extend( +var HistoryPairDatasetCollection = PairDC.extend( hcontentMixin ).extend( /** @lends HistoryPairDatasetCollection.prototype */{ initialize : function( model, options ){ @@ -58,11 +52,10 @@ //============================================================================== -var ListPairedDC = DC_MODEL.ListPairedDatasetCollection, /** @class Backbone model for List of Pairs Dataset Collection within a History. * @constructs */ - HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend( +var HistoryListPairedDatasetCollection = ListPairedDC.extend( hcontentMixin ).extend( /** @lends HistoryListPairedDatasetCollection.prototype */{ initialize : function( model, options ){ @@ -81,7 +74,6 @@ //============================================================================== return { - HistoryDatasetCollection : HistoryDatasetCollection, HistoryListDatasetCollection : HistoryListDatasetCollection, HistoryPairDatasetCollection : HistoryPairDatasetCollection, HistoryListPairedDatasetCollection : HistoryListPairedDatasetCollection diff -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe -r 5c58466a1bacfe265f8dd92b1533f7b9aa9687b9 static/scripts/mvc/dataset/hda-base.js --- a/static/scripts/mvc/dataset/hda-base.js +++ b/static/scripts/mvc/dataset/hda-base.js @@ -23,7 +23,7 @@ //logger : console, tagName : "div", - className : "dataset hda history-panel-hda", + className : "dataset hda history-content", id : function(){ return 'hda-' + this.model.get( 'id' ); }, fxSpeed : 'fast', @@ -96,7 +96,7 @@ /** In this override, render the dataset display button * @returns {jQuery} rendered DOM */ - _render_titleButtons : function(){ + _render_primaryActions : function(){ // render just the display for read-only return [ this._render_displayButton() ]; }, @@ -115,7 +115,7 @@ var displayBtnData = { target : this.linkTarget, - classes : 'dataset-display' + classes : 'display-btn' }; // show a disabled display if the data's been purged @@ -181,7 +181,7 @@ if( _.isEmpty( meta_files ) ){ return $([ '<a href="' + urls.download + '" title="' + _l( 'Download' ) + '" ', - 'class="icon-btn dataset-download-btn">', + 'class="icon-btn download-btn">', '<span class="fa fa-floppy-o"></span>', '</a>' ].join( '' ) ); @@ -206,7 +206,7 @@ '<div class="icon-btn-group">', '<a href="' + urls.download + '" title="' + _l( 'Download' ) + '" ', - 'class="icon-btn dataset-download-btn">', + 'class="icon-btn download-btn">', '<span class="fa fa-floppy-o"></span>', // join these w/o whitespace or there'll be a gap when rendered '</a><a class="icon-btn popup" id="' + menuId + '">', @@ -256,7 +256,7 @@ primaryButtonArray = primaryButtonArray || []; var view = this, $body = $( HDABaseView.templates.body( _.extend( this.model.toJSON(), { body: body }))); - $body.find( '.dataset-actions .left' ).append( + $body.find( '.actions .left' ).append( _.map( primaryButtonArray, function( renderingFn ){ return renderingFn.call( view ); }) @@ -358,7 +358,7 @@ $body = $( HDABaseView.templates.body( this.model.toJSON() ) ), // prepend the download btn to the defaults and render btnRenderers = [ this._render_downloadButton ].concat( this.defaultPrimaryActionButtonRenderers ); - $body.find( '.dataset-actions .left' ).append( + $body.find( '.actions .left' ).append( _.map( btnRenderers, function( renderingFn ){ return renderingFn.call( view ); })); @@ -385,11 +385,11 @@ var hdaView = this; function _renderBodyAndExpand(){ - hdaView.$el.children( '.dataset-body' ).replaceWith( hdaView._renderBody() ); + hdaView.$el.children( '.details' ).replaceWith( hdaView._renderBody() ); //NOTE: needs to be set after the above or the slide will not show hdaView.expanded = true; - hdaView.$el.children( '.dataset-body' ).slideDown( hdaView.fxSpeed, function(){ - hdaView.trigger( 'expanded', hdaView.model ); + hdaView.$el.children( '.details' ).slideDown( hdaView.fxSpeed, function(){ + hdaView.trigger( 'expanded', hdaView ); }); } // fetch first if no details in the model @@ -429,24 +429,24 @@ //TODO: possibly break these out into a sep. module var skeletonTemplate = _.template([ '<div class="dataset hda">', - '<div class="dataset-warnings">', + '<div class="warnings">', // error during index fetch - show error on dataset '<% if( hda.error ){ %>', '<div class="errormessagesmall">', - _l( 'There was an error getting the data for this dataset' ), ':<%- hda.error %>', + _l( 'There was an error getting the data for this dataset' ), ': <%- hda.error %>', '</div>', '<% } %>', '<% if( hda.deleted ){ %>', // purged and deleted '<% if( hda.purged ){ %>', - '<div class="dataset-purged-msg warningmessagesmall"><strong>', + '<div class="purged-msg warningmessagesmall"><strong>', _l( 'This dataset has been deleted and removed from disk' ) + '.', '</strong></div>', // deleted not purged '<% } else { %>', - '<div class="dataset-deleted-msg warningmessagesmall"><strong>', + '<div class="deleted-msg warningmessagesmall"><strong>', _l( 'This dataset has been deleted' ) + '.', '</strong></div>', '<% } %>', @@ -454,61 +454,61 @@ // hidden '<% if( !hda.visible ){ %>', - '<div class="dataset-hidden-msg warningmessagesmall"><strong>', + '<div class="hidden-msg warningmessagesmall"><strong>', _l( 'This dataset has been hidden' ) + '.', '</strong></div>', '<% } %>', '</div>', // multi-select checkbox - '<div class="dataset-selector">', + '<div class="selector">', '<span class="fa fa-2x fa-square-o"></span>', '</div>', // space for title bar buttons - '<div class="dataset-primary-actions"></div>', + '<div class="primary-actions"></div>', // adding a tabindex here allows focusing the title bar and the use of keydown to expand the dataset display - '<div class="dataset-title-bar clear" tabindex="0">', - '<span class="dataset-state-icon state-icon"></span>', - '<div class="dataset-title">', + '<div class="title-bar clear" tabindex="0">', + '<span class="state-icon"></span>', + '<div class="title">', //TODO: remove whitespace and use margin-right - '<span class="hda-hid"><%- hda.hid %></span> ', - '<span class="dataset-name"><%- hda.name %></span>', + '<span class="hid"><%- hda.hid %></span> ', + '<span class="name"><%- hda.name %></span>', '</div>', '</div>', - '<div class="dataset-body"></div>', + '<div class="details"></div>', '</div>' ].join( '' )); var bodyTemplate = _.template([ -'<div class="dataset-body">', +'<div class="details">', '<% if( hda.body ){ %>', - '<div class="dataset-summary">', + '<div class="summary">', '<%= hda.body %>', '</div>', - '<div class="dataset-actions clear">', + '<div class="actions clear">', '<div class="left"></div>', '<div class="right"></div>', '</div>', '<% } else { %>', - '<div class="dataset-summary">', + '<div class="summary">', '<% if( hda.misc_blurb ){ %>', - '<div class="dataset-blurb">', + '<div class="blurb">', '<span class="value"><%- hda.misc_blurb %></span>', '</div>', '<% } %>', '<% if( hda.data_type ){ %>', - '<div class="dataset-datatype">', + '<div class="datatype">', '<label class="prompt">', _l( 'format' ), '</label>', '<span class="value"><%- hda.data_type %></span>', '</div>', '<% } %>', '<% if( hda.metadata_dbkey ){ %>', - '<div class="dataset-dbkey">', + '<div class="dbkey">', '<label class="prompt">', _l( 'database' ), '</label>', '<span class="value">', '<%- hda.metadata_dbkey %>', @@ -517,14 +517,14 @@ '<% } %>', '<% if( hda.misc_info ){ %>', - '<div class="dataset-info">', + '<div class="info">', '<span class="value"><%- hda.misc_info %></span>', '</div>', '<% } %>', '</div>', // end dataset-summary - '<div class="dataset-actions clear">', + '<div class="actions clear">', '<div class="left"></div>', '<div class="right"></div>', '</div>', @@ -533,7 +533,7 @@ '<div class="tags-display"></div>', '<div class="annotation-display"></div>', - '<div class="dataset-display-applications">', + '<div class="display-applications">', //TODO: the following two should be compacted '<% _.each( hda.display_apps, function( app ){ %>', '<div class="display-application">', This diff is so big that we needed to truncate the remainder. 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.

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commit/galaxy-central: dan: Fix for displaying Category name when browsing toolshed repositories by categories.
by commits-noreply＠bitbucket.org 31 Jul '14

31 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6db9ce7e0415/ Changeset: 6db9ce7e0415 Branch: next-stable User: dan Date: 2014-07-31 17:03:27 Summary: Fix for displaying Category name when browsing toolshed repositories by categories. Affected #: 1 file diff -r a12359ac3a8a90f6402f4ec36eb707aa6c5e866f -r 6db9ce7e0415b85ebb833f783458ba6d6e69c242 lib/tool_shed/grids/repository_grid_filter_manager.py --- a/lib/tool_shed/grids/repository_grid_filter_manager.py +++ b/lib/tool_shed/grids/repository_grid_filter_manager.py @@ -27,7 +27,7 @@ return "Certified 2 Repository Suites %s" % trailing_string if filter == self.filters.SUITES: return "Repository Suites %s" % trailing_string - return "%s" % default + return "%s %s" % ( default, trailing_string ) def get_filter( self, trans ): filter = trans.get_cookie( name='toolshedrepogridfilter' ) 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.

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commit/galaxy-central: dan: Fix for displaying Category name when browsing toolshed repositories by categories.
by commits-noreply＠bitbucket.org 31 Jul '14

31 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/51e6a073c4b9/ Changeset: 51e6a073c4b9 User: dan Date: 2014-07-31 17:03:27 Summary: Fix for displaying Category name when browsing toolshed repositories by categories. Affected #: 1 file diff -r 09de83748e247d5c10c9d0e28833a8200606e46c -r 51e6a073c4b93a5df784e876abd17edffd3b0bbe lib/tool_shed/grids/repository_grid_filter_manager.py --- a/lib/tool_shed/grids/repository_grid_filter_manager.py +++ b/lib/tool_shed/grids/repository_grid_filter_manager.py @@ -27,7 +27,7 @@ return "Certified 2 Repository Suites %s" % trailing_string if filter == self.filters.SUITES: return "Repository Suites %s" % trailing_string - return "%s" % default + return "%s %s" % ( default, trailing_string ) def get_filter( self, trans ): filter = trans.get_cookie( name='toolshedrepogridfilter' ) 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.

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commit/galaxy-central: dan: When viewing a repository, make list of categories clickable and include description.
by commits-noreply＠bitbucket.org 31 Jul '14

31 Jul '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/09de83748e24/ Changeset: 09de83748e24 User: dan Date: 2014-07-31 16:55:49 Summary: When viewing a repository, make list of categories clickable and include description. Affected #: 1 file diff -r 15cfed4fb8186252436e64ee671b80e1c31a918b -r 09de83748e247d5c10c9d0e28833a8200606e46c templates/webapps/tool_shed/repository/view_repository.mako --- a/templates/webapps/tool_shed/repository/view_repository.mako +++ b/templates/webapps/tool_shed/repository/view_repository.mako @@ -171,7 +171,7 @@ <div class="toolFormBody"> %for rca in repository.categories: <div class="form-row"> - ${rca.category.name | h} + <a href="${h.url_for( controller='repository', action='browse_repositories_in_category', id=trans.security.encode_id( rca.category.id ) )}">${rca.category.name | h}</a> - ${rca.category.description | h} </div> %endfor <div style="clear: both"></div> 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.

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commit/galaxy-central: 3 new changesets
by commits-noreply＠bitbucket.org 30 Jul '14

30 Jul '14

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7052d8f57837/ Changeset: 7052d8f57837 User: erasche2 Date: 2014-06-13 18:58:23 Summary: Added share button Affected #: 1 file diff -r 8a608db6cf83b653a433f43b501f4047f63d248b -r 7052d8f578378847ff6b5ebf64b694811dd432e8 templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -334,6 +334,12 @@ </div></span> %endif + <span class="pull-right"> + <div class="icon-btn-group"> + <a href="${h.url_for( controller='root', action='index', tool_id=tool.id )}" + target="_blank" class="icon-btn" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a> + </div> + </span></div><div class="toolFormBody"><input type="hidden" name="refresh" value="refresh"> https://bitbucket.org/galaxy/galaxy-central/commits/cdc32b8ba500/ Changeset: cdc32b8ba500 User: jmchilton Date: 2014-07-31 03:34:02 Summary: Merge. Affected #: 1 file diff -r 19859e3e4b1c58217c31d2f3c472359c667c2a7f -r cdc32b8ba500d3c50b5270039f142a224f477cdd templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -337,6 +337,12 @@ </div></span> %endif + <span class="pull-right"> + <div class="icon-btn-group"> + <a href="${h.url_for( controller='root', action='index', tool_id=tool.id )}" + target="_blank" class="icon-btn" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a> + </div> + </span></div><div class="toolFormBody"><input type="hidden" name="refresh" value="refresh"> https://bitbucket.org/galaxy/galaxy-central/commits/15cfed4fb818/ Changeset: 15cfed4fb818 User: jmchilton Date: 2014-07-31 04:01:02 Summary: Modify @erasche2's tool share button to pop-up instructions for copy&pasting URL... ... per @martenson's suggestion and with @erasche2 permission. Wonder if we want to double down on these buttons and convert tool shed link and citations handling to use this mechanism or perhaps add a drop down "gear" menu with these options ala the history panel. Affected #: 2 files diff -r cdc32b8ba500d3c50b5270039f142a224f477cdd -r 15cfed4fb8186252436e64ee671b80e1c31a918b static/scripts/galaxy.tools.js --- a/static/scripts/galaxy.tools.js +++ b/static/scripts/galaxy.tools.js @@ -5,6 +5,14 @@ $("input[name='" + name + "'][type='checkbox']").attr('checked', !!check); } + $(".tool-share-link").each( function() { + var href = $(this).attr("href"); + var href = $(this).attr("data-link"); + $(this).click(function() { + window.prompt("Copy to clipboard: Ctrl+C, Enter", href); + }); + }); + // Inserts the Select All / Unselect All buttons for checkboxes $("div.checkUncheckAllPlaceholder").each( function() { var check_name = $(this).attr("checkbox_name"); diff -r cdc32b8ba500d3c50b5270039f142a224f477cdd -r 15cfed4fb8186252436e64ee671b80e1c31a918b templates/webapps/galaxy/tool_form.mako --- a/templates/webapps/galaxy/tool_form.mako +++ b/templates/webapps/galaxy/tool_form.mako @@ -325,9 +325,9 @@ <div class="toolFormTitle">${tool.name} ${tool_version_select_field.get_html()} %endif + <span class="pull-right"> %if trans.app.config.biostar_url: - ## BioStar links - <span class="pull-right"> + ## BioStar links Help from Biostar <div class="icon-btn-group"><a href="${h.url_for( controller='biostar', action='biostar_tool_tag_redirect', tool_id=tool.id )}" @@ -335,14 +335,12 @@ <a href="${h.url_for( controller='biostar', action='biostar_tool_question_redirect', tool_id=tool.id )}" target="_blank" class="icon-btn" title="Ask a question about this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-question-circle"></a></div> - </span> %endif - <span class="pull-right"> - <div class="icon-btn-group"> - <a href="${h.url_for( controller='root', action='index', tool_id=tool.id )}" - target="_blank" class="icon-btn" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a> - </div> - </span> + <div class="icon-btn-group"> + <a href="#" data-link="${h.url_for( controller='root', action='index', tool_id=tool.id )}" + class="icon-btn tool-share-link" title="Share this tool" data-toggle="tooltip" data-placement="bottom"><span class="fa fa-share"></span></a> + </div> + </span></div><div class="toolFormBody"><input type="hidden" name="refresh" value="refresh"> 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 0

commit/galaxy-central: 7 new changesets
by commits-noreply＠bitbucket.org 30 Jul '14

30 Jul '14

7 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e43587ef3817/ Changeset: e43587ef3817 User: jmchilton Date: 2014-07-24 15:35:41 Summary: PEP8 style fixes for SQliteDataProvider. Affected #: 1 file diff -r 4ca1677c8d5bc6486b0b1dff50372a23dfaf307d -r e43587ef3817b1459b73c89dd2e80100bb1349bb lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -704,33 +704,30 @@ super( BGzipTabixDataProvider, self ).__init__( dataset, **kwargs ) - -class SQliteDataProvider ( base.DataProvider ): +class SQliteDataProvider( base.DataProvider ): """ Data provider that uses a sqlite database file as its source. Allows any query to be run and returns the resulting rows as sqlite3 row objects """ settings = { - 'query' : 'str' + 'query': 'str' } def __init__( self, source, query=None, **kwargs ): - self.query=query - self.connection = sqlite3.connect(source.dataset.file_name); + self.query = query + self.connection = sqlite3.connect(source.dataset.file_name) self.connection.row_factory = sqlite3.Row super( SQliteDataProvider, self ).__init__( source, **kwargs ) - def query_matches_whitelist(self,query): - if re.match("select ",query,re.IGNORECASE): - if re.search("^([^\"]|\"[^\"]*\")*?;",query) or re.search("^([^\']|\'[^\']*\')*?;",query): + def query_matches_whitelist(self, query): + if re.match("select ", query, re.IGNORECASE): + if re.search("^([^\"]|\"[^\"]*\")*?;", query) or re.search("^([^\']|\'[^\']*\')*?;", query): return False else: return True return False - - def __iter__( self ): if (self.query is not None) and self.query_matches_whitelist(self.query): for row in self.connection.cursor().execute(self.query): https://bitbucket.org/galaxy/galaxy-central/commits/b2f9400bedd5/ Changeset: b2f9400bedd5 User: jmchilton Date: 2014-07-24 16:24:02 Summary: Create sqlite util module from sqlite data provider code. Write tests against this module to make me feel more confident white-listing is only allowing select statements as well as tests to make me feel more confident that actual SELECT statements cannot be turned into update statements or access external resources. Affected #: 3 files diff -r e43587ef3817b1459b73c89dd2e80100bb1349bb -r b2f9400bedd57b8d691f2470b46f8023bc000cf9 lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -11,7 +11,7 @@ import line import column import external -import sqlite3 +from galaxy.util import sqlite import re from galaxy import eggs @@ -716,20 +716,11 @@ def __init__( self, source, query=None, **kwargs ): self.query = query - self.connection = sqlite3.connect(source.dataset.file_name) - self.connection.row_factory = sqlite3.Row + self.connection = sqlite.connect(source.dataset.file_name) super( SQliteDataProvider, self ).__init__( source, **kwargs ) - def query_matches_whitelist(self, query): - if re.match("select ", query, re.IGNORECASE): - if re.search("^([^\"]|\"[^\"]*\")*?;", query) or re.search("^([^\']|\'[^\']*\')*?;", query): - return False - else: - return True - return False - def __iter__( self ): - if (self.query is not None) and self.query_matches_whitelist(self.query): + if (self.query is not None) and sqlite.is_read_only_query(self.query): for row in self.connection.cursor().execute(self.query): yield row else: diff -r e43587ef3817b1459b73c89dd2e80100bb1349bb -r b2f9400bedd57b8d691f2470b46f8023bc000cf9 lib/galaxy/util/sqlite.py --- /dev/null +++ b/lib/galaxy/util/sqlite.py @@ -0,0 +1,17 @@ +import sqlite3 +import re + + +def connect(path): + connection = sqlite3.connect(path) + connection.row_factory = sqlite3.Row + return connection + + +def is_read_only_query(query): + if re.match("select ", query, re.IGNORECASE): + if re.search("^([^\"]|\"[^\"]*\")*?;", query) or re.search("^([^\']|\'[^\']*\')*?;", query): + return False + else: + return True + return False diff -r e43587ef3817b1459b73c89dd2e80100bb1349bb -r b2f9400bedd57b8d691f2470b46f8023bc000cf9 test/unit/test_sqlite_utils.py --- /dev/null +++ b/test/unit/test_sqlite_utils.py @@ -0,0 +1,59 @@ +from galaxy.util import sqlite + + +def test_query_whitelisting(): + __assert_whitelisted("SELECT * from FOO") + __assert_whitelisted("SELECT f.col1, f.col2 from FOO as f") + __assert_whitelisted("SELECT f.col1, b.col2 from FOO as f inner join BAR as b on f.id = b.foo_id") + __assert_not_whitelisted("UPDATE FOO SET foo=6") + __assert_not_whitelisted("TRUNCATE FOO") + + +def test_sqlite_exploits(): + # This is not really testing any Galaxy code, just experimenting with ways + # to attempt to exploit sqlite3 connections. + + # More info... + # http://atta.cked.me/home/sqlite3injectioncheatsheet + + connection = sqlite.connect(":memory:") + connection.execute("create TABLE FOO (foo1 text)") + __assert_has_n_rows(connection, "select * from FOO", 0) + __assert_query_errors(connection, "select * from FOOX") + + # Make sure sqlite query cannot execute multiple statements + __assert_query_errors(connection, "select * from FOO; select * from FOO") + + # Make sure sqlite cannot select on PRAGMA results + __assert_query_errors(connection, "select * from (PRAGMA database_list)") + + __assert_has_n_rows(connection, "select * from FOO where foo1 in (SELECT foo1 from FOO)", 0) + # Ensure nested queries cannot modify database. + __assert_query_errors(connection, "select * from FOO where foo1 in (INSERT INTO FOO VALUES ('bar')") + + __assert_has_n_rows(connection, "select * from SQLITE_MASTER", 0) + + +def __assert_has_n_rows(connection, query, n): + count = 0 + for row in connection.cursor().execute(query): + count += 1 + assert count == n + + +def __assert_query_errors(connection, query): + exception = False + try: + for row in connection.cursor().execute(query): + pass + except Exception: + exception = True + assert exception + + +def __assert_whitelisted( query ): + assert sqlite.is_read_only_query(query), "Query [%s] fails whitelist." % query + + +def __assert_not_whitelisted( query ): + assert not sqlite.is_read_only_query(query), "Query [%s] incorrectly fails whitelist." % query https://bitbucket.org/galaxy/galaxy-central/commits/e332be1a256f/ Changeset: e332be1a256f User: iracooke Date: 2014-07-25 03:02:53 Summary: Better sqlite query whitelisting via the sqlparse library Affected #: 2 files diff -r b2f9400bedd57b8d691f2470b46f8023bc000cf9 -r e332be1a256f9431d31baa910579a19dacd504b7 lib/galaxy/util/sqlite.py --- a/lib/galaxy/util/sqlite.py +++ b/lib/galaxy/util/sqlite.py @@ -1,4 +1,5 @@ import sqlite3 +import sqlparse import re @@ -9,9 +10,8 @@ def is_read_only_query(query): - if re.match("select ", query, re.IGNORECASE): - if re.search("^([^\"]|\"[^\"]*\")*?;", query) or re.search("^([^\']|\'[^\']*\')*?;", query): - return False - else: - return True - return False + statements = sqlparse.parse(query) + for statement in statements: + if statement.get_type() != "SELECT": + return False + return True \ No newline at end of file diff -r b2f9400bedd57b8d691f2470b46f8023bc000cf9 -r e332be1a256f9431d31baa910579a19dacd504b7 test/unit/test_sqlite_utils.py --- a/test/unit/test_sqlite_utils.py +++ b/test/unit/test_sqlite_utils.py @@ -31,7 +31,8 @@ # Ensure nested queries cannot modify database. __assert_query_errors(connection, "select * from FOO where foo1 in (INSERT INTO FOO VALUES ('bar')") - __assert_has_n_rows(connection, "select * from SQLITE_MASTER", 0) + # Should access to the schema be blacklisted? + # __assert_has_n_rows(connection, "select * from SQLITE_MASTER", 0) def __assert_has_n_rows(connection, query, n): https://bitbucket.org/galaxy/galaxy-central/commits/db12a9c90f0a/ Changeset: db12a9c90f0a User: iracooke Date: 2014-07-25 03:06:45 Summary: Merged galaxy/galaxy-central into default Affected #: 10 files diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -34,6 +34,7 @@ from galaxy.util.bunch import Bunch from galaxy.util.hash_util import new_secure_hash from galaxy.util.directory_hash import directory_hash_id +from galaxy.util.sanitize_html import sanitize_html from galaxy.web.framework.helpers import to_unicode from galaxy.web.form_builder import (AddressField, CheckboxField, HistoryField, PasswordField, SelectField, TextArea, TextField, WorkflowField, @@ -2589,8 +2590,8 @@ class DatasetCollection( object, Dictifiable, UsesAnnotations ): """ """ - dict_collection_visible_keys = ( 'id', 'name', 'collection_type' ) - dict_element_visible_keys = ( 'id', 'name', 'collection_type' ) + dict_collection_visible_keys = ( 'id', 'collection_type' ) + dict_element_visible_keys = ( 'id', 'collection_type' ) def __init__( self, @@ -3703,23 +3704,27 @@ self.country = country self.phone = phone def get_html(self): + # This should probably be deprecated eventually. It should currently + # sanitize. + # TODO Find out where else uses this and replace with + # templates html = '' if self.name: - html = html + self.name + html = html + sanitize_html(self.name) if self.institution: - html = html + '<br/>' + self.institution + html = html + '<br/>' + sanitize_html(self.institution) if self.address: - html = html + '<br/>' + self.address + html = html + '<br/>' + sanitize_html(self.address) if self.city: - html = html + '<br/>' + self.city + html = html + '<br/>' + sanitize_html(self.city) if self.state: - html = html + ' ' + self.state + html = html + ' ' + sanitize_html(self.state) if self.postal_code: - html = html + ' ' + self.postal_code + html = html + ' ' + sanitize_html(self.postal_code) if self.country: - html = html + '<br/>' + self.country + html = html + '<br/>' + sanitize_html(self.country) if self.phone: - html = html + '<br/>' + 'Phone: ' + self.phone + html = html + '<br/>' + 'phone: ' + sanitize_html(self.phone) return html class UserOpenID( object ): diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1391,7 +1391,7 @@ # Load parameters (optional) input_elem = root.find("inputs") enctypes = set() - if input_elem: + if input_elem is not None: # Handle properties of the input form self.check_values = string_as_bool( input_elem.get("check_values", self.check_values ) ) self.nginx_upload = string_as_bool( input_elem.get( "nginx_upload", self.nginx_upload ) ) diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -1712,10 +1712,15 @@ if self.__display_multirun_option(): # Select multiple datasets, run multiple jobs. multirun_key = "%s|__multirun__" % self.name + collection_multirun_key = "%s|__collection_multirun__" % self.name if multirun_key in (other_values or {}): multirun_value = listify( other_values[ multirun_key ] ) if multirun_value and len( multirun_value ) > 1: default_field = "select_multiple" + elif collection_multirun_key in (other_values or {}): + multirun_value = listify( other_values[ collection_multirun_key ] ) + if multirun_value: + default_field = "select_collection" else: multirun_value = value multi_dataset_matcher = DatasetMatcher( trans, self, multirun_value, other_values ) @@ -2014,9 +2019,17 @@ default_field = "select_single_collection" fields = odict() + collection_multirun_key = "%s|__collection_multirun__" % self.name + if collection_multirun_key in (other_values or {}): + multirun_value = other_values[ collection_multirun_key ] + if multirun_value: + default_field = "select_map_over_collections" + else: + multirun_value = value + history = self._get_history( trans ) fields[ "select_single_collection" ] = self._get_single_collection_field( trans=trans, history=history, value=value, other_values=other_values ) - fields[ "select_map_over_collections" ] = self._get_select_dataset_collection_field( trans=trans, history=history, value=value, other_values=other_values ) + fields[ "select_map_over_collections" ] = self._get_select_dataset_collection_field( trans=trans, history=history, value=multirun_value, other_values=other_values ) return self._switch_fields( fields, default_field=default_field ) diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -48,10 +48,10 @@ from .inflection import Inflector, English inflector = Inflector(English) -log = logging.getLogger(__name__) +log = logging.getLogger(__name__) _lock = threading.RLock() -CHUNK_SIZE = 65536 #64k +CHUNK_SIZE = 65536 # 64k DATABASE_MAX_STRING_SIZE = 32768 DATABASE_MAX_STRING_SIZE_PRETTY = '32K' @@ -62,6 +62,7 @@ NULL_CHAR = '\000' BINARY_CHARS = [ NULL_CHAR ] + def is_multi_byte( chars ): for char in chars: try: @@ -69,18 +70,15 @@ except UnicodeDecodeError: # Probably binary return False - if wchartype.is_asian( char ) or \ - wchartype.is_full_width( char ) or \ - wchartype.is_kanji( char ) or \ - wchartype.is_hiragana( char ) or \ - wchartype.is_katakana( char ) or \ - wchartype.is_half_katakana( char ) or \ - wchartype.is_hangul( char ) or \ - wchartype.is_full_digit( char ) or \ - wchartype.is_full_letter( char ): + if ( wchartype.is_asian( char ) or wchartype.is_full_width( char ) or + wchartype.is_kanji( char ) or wchartype.is_hiragana( char ) or + wchartype.is_katakana( char ) or wchartype.is_half_katakana( char ) + or wchartype.is_hangul( char ) or wchartype.is_full_digit( char ) + or wchartype.is_full_letter( char )): return True return False + def is_binary( value, binary_chars=None ): """ File is binary if it contains a null-byte by default (e.g. behavior of grep, etc.). @@ -99,6 +97,7 @@ return True return False + def get_charset_from_http_headers( headers, default=None ): rval = headers.get('content-type', None ) if rval and 'charset=' in rval: @@ -107,16 +106,18 @@ return rval return default + def synchronized(func): """This wrapper will serialize access to 'func' to a single thread. Use it as a decorator.""" def caller(*params, **kparams): - _lock.acquire(True) # Wait + _lock.acquire(True) # Wait try: return func(*params, **kparams) finally: _lock.release() return caller + def file_iter(fname, sep=None): """ This generator iterates over a file and yields its lines @@ -131,6 +132,7 @@ if line and line[0] != '#': yield line.split(sep) + def file_reader( fp, chunk_size=CHUNK_SIZE ): """This generator yields the open fileobject in chunks (default 64k). Closes the file at the end""" while 1: @@ -140,6 +142,7 @@ yield data fp.close() + def unique_id(KEY_SIZE=128): """ Generates an unique id @@ -148,8 +151,8 @@ >>> len(set(ids)) 1000 """ - id = str( random.getrandbits( KEY_SIZE ) ) - return md5(id).hexdigest() + return md5(str( random.getrandbits( KEY_SIZE ) )).hexdigest() + def parse_xml(fname): """Returns a parsed xml tree""" @@ -163,6 +166,7 @@ tree = ElementTree.fromstring(xml_string) return tree + def xml_to_string( elem, pretty=False ): """Returns a string from an xml tree""" if pretty: @@ -170,12 +174,13 @@ try: return ElementTree.tostring( elem ) except TypeError, e: - #assume this is a comment + # we assume this is a comment if hasattr( elem, 'text' ): return "\n" % ( elem.text ) else: raise e + def xml_element_compare( elem1, elem2 ): if not isinstance( elem1, dict ): elem1 = xml_element_to_dict( elem1 ) @@ -183,9 +188,11 @@ elem2 = xml_element_to_dict( elem2 ) return elem1 == elem2 + def xml_element_list_compare( elem_list1, elem_list2 ): return [ xml_element_to_dict( elem ) for elem in elem_list1 ] == [ xml_element_to_dict( elem ) for elem in elem_list2 ] + def xml_element_to_dict( elem ): rval = {} if elem.attrib: @@ -220,7 +227,6 @@ return rval - def pretty_print_xml( elem, level=0 ): pad = ' ' i = "\n" + level * pad @@ -238,26 +244,28 @@ elem.tail = i + pad return elem + def get_file_size( value, default=None ): try: - #try built-in + # try built-in return os.path.getsize( value ) except: try: - #try built-in one name attribute + # try built-in one name attribute return os.path.getsize( value.name ) except: try: - #try tell() of end of object + # try tell() of end of object offset = value.tell() value.seek( 0, 2 ) rval = value.tell() value.seek( offset ) return rval except: - #return default value + # return default value return default + def shrink_stream_by_size( value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False ): rval = '' if get_file_size( value ) > size: @@ -292,6 +300,7 @@ rval += data return rval + def shrink_string_by_size( value, size, join_by="..", left_larger=True, beginning_on_size_error=False, end_on_size_error=False ): if len( value ) > size: len_join_by = len( join_by ) @@ -311,29 +320,30 @@ value = "%s%s%s" % ( value[:left_index], join_by, value[-right_index:] ) return value + def pretty_print_json(json_data, is_json_string=False): if is_json_string: json_data = json.from_json_string(json_data) return json.to_json_string(json_data, sort_keys=True, indent=4) # characters that are valid -valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!") +valid_chars = set(string.letters + string.digits + " -=_.()/+*^,:?!") # characters that are allowed but need to be escaped -mapped_chars = { '>' :'__gt__', - '<' :'__lt__', - "'" :'__sq__', - '"' :'__dq__', - '[' :'__ob__', - ']' :'__cb__', - '{' :'__oc__', - '}' :'__cc__', - '@' : '__at__', - '\n' : '__cn__', - '\r' : '__cr__', - '\t' : '__tc__', - '#' : '__pd__' - } +mapped_chars = { '>': '__gt__', + '<': '__lt__', + "'": '__sq__', + '"': '__dq__', + '[': '__ob__', + ']': '__cb__', + '{': '__oc__', + '}': '__cc__', + '@': '__at__', + '\n': '__cn__', + '\r': '__cr__', + '\t': '__tc__', + '#': '__pd__'} + def restore_text(text): """Restores sanitized text""" @@ -343,6 +353,7 @@ text = text.replace(value, key) return text + def sanitize_text(text): """ Restricts the characters that are allowed in text; accepts both strings @@ -353,6 +364,7 @@ elif isinstance( text, list ): return [ _sanitize_text_helper(t) for t in text ] + def _sanitize_text_helper(text): """Restricts the characters that are allowed in a string""" @@ -363,9 +375,10 @@ elif c in mapped_chars: out.append(mapped_chars[c]) else: - out.append('X') # makes debugging easier + out.append('X') # makes debugging easier return ''.join(out) + def sanitize_param(value): """Clean incoming parameters (strings or lists)""" if isinstance( value, basestring ): @@ -373,10 +386,12 @@ elif isinstance( value, list ): return map(sanitize_text, value) else: - raise Exception, 'Unknown parameter type (%s)' % ( type( value ) ) + raise Exception('Unknown parameter type (%s)' % ( type( value ) )) valid_filename_chars = set( string.ascii_letters + string.digits + '_.' ) invalid_filenames = [ '', '.', '..' ] + + def sanitize_for_filename( text, default=None ): """ Restricts the characters that are allowed in a filename portion; Returns default value or a unique id string if result is not a valid name. @@ -512,7 +527,7 @@ def __init__( self, params, sanitize=True ): if sanitize: for key, value in params.items(): - if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: #sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed. + if key not in self.NEVER_SANITIZE and True not in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ]: # sanitize check both ungrouped and grouped parameters by name. Anything relying on NEVER_SANITIZE should be changed to not require this and NEVER_SANITIZE should be removed. self.__dict__[ key ] = sanitize_param( value ) else: self.__dict__[ key ] = value @@ -525,7 +540,7 @@ """ flat = [] for key, value in self.__dict__.items(): - if type(value) == type([]): + if isinstance(value, list): for v in value: flat.append( (key, v) ) else: @@ -551,16 +566,19 @@ def update(self, values): self.__dict__.update(values) + def rst_to_html( s ): """Convert a blob of reStructuredText to HTML""" log = logging.getLogger( "docutils" ) + class FakeStream( object ): def write( self, str ): if len( str ) > 0 and not str.isspace(): log.warn( str ) return unicodify( docutils.core.publish_string( s, - writer=docutils.writers.html4css1.Writer(), - settings_overrides={ "embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream() } ) ) + writer=docutils.writers.html4css1.Writer(), + settings_overrides={ "embed_stylesheet": False, "template": os.path.join(os.path.dirname(__file__), "docutils_template.txt"), "warning_stream": FakeStream() } ) ) + def xml_text(root, name=None): """Returns the text inside an element""" @@ -582,6 +600,8 @@ # asbool implementation pulled from PasteDeploy truthy = frozenset(['true', 'yes', 'on', 'y', 't', '1']) falsy = frozenset(['false', 'no', 'off', 'n', 'f', '0']) + + def asbool(obj): if isinstance(obj, basestring): obj = obj.strip().lower() @@ -600,6 +620,7 @@ else: return False + def string_as_bool_or_none( string ): """ Returns True, None or False based on the argument: @@ -618,6 +639,7 @@ else: return False + def listify( item, do_strip=False ): """ Make a single item a single item list, or return a list if passed a @@ -635,6 +657,7 @@ else: return [ item ] + def commaify(amount): orig = amount new = re.sub("^(-?\d+)(\d{3})", '\g<1>,\g<2>', amount) @@ -643,7 +666,8 @@ else: return commaify(new) -def roundify(amount, sfs = 2): + +def roundify(amount, sfs=2): """ Take a number in string form and truncate to 'sfs' significant figures. """ @@ -652,6 +676,7 @@ else: return amount[0:sfs] + '0'*(len(amount) - sfs) + def unicodify( value, encoding=DEFAULT_ENCODING, error='replace', default=None ): """ Returns a unicode string or None @@ -691,6 +716,7 @@ def object_to_string( obj ): return binascii.hexlify( pickle.dumps( obj, 2 ) ) + def string_to_object( s ): return pickle.loads( binascii.unhexlify( s ) ) @@ -743,19 +769,23 @@ return False return True + def get_ucsc_by_build(build): sites = [] for site in ucsc_build_sites: if build in site['builds']: - sites.append((site['name'],site['url'])) + sites.append((site['name'], site['url'])) return sites + + def get_gbrowse_sites_by_build(build): sites = [] for site in gbrowse_build_sites: if build in site['builds']: - sites.append((site['name'],site['url'])) + sites.append((site['name'], site['url'])) return sites + def read_dbnames(filename): """ Read build names from file """ class DBNames( list ): @@ -764,48 +794,54 @@ db_names = DBNames() try: ucsc_builds = {} - man_builds = [] #assume these are integers + man_builds = [] # assume these are integers name_to_db_base = {} for line in open(filename): try: - if line[0:1] == "#": continue - fields = line.replace("\r","").replace("\n","").split("\t") - #Special case of unspecified build is at top of list + if line[0:1] == "#": + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") + # Special case of unspecified build is at top of list if fields[0] == "?": - db_names.insert(0,(fields[0],fields[1])) + db_names.insert(0, (fields[0], fields[1])) continue - try: #manual build (i.e. microbes) + try: # manual build (i.e. microbes) int(fields[0]) man_builds.append((fields[1], fields[0])) - except: #UCSC build + except: # UCSC build db_base = fields[0].rstrip('0123456789') if db_base not in ucsc_builds: ucsc_builds[db_base] = [] name_to_db_base[fields[1]] = db_base - #we want to sort within a species numerically by revision number + # we want to sort within a species numerically by revision number build_rev = re.compile(r'\d+$') - try: build_rev = int(build_rev.findall(fields[0])[0]) - except: build_rev = 0 - ucsc_builds[db_base].append((build_rev, fields[0],fields[1])) - except: continue + try: + build_rev = int(build_rev.findall(fields[0])[0]) + except: + build_rev = 0 + ucsc_builds[db_base].append((build_rev, fields[0], fields[1])) + except: + continue sort_names = name_to_db_base.keys() sort_names.sort() for name in sort_names: db_base = name_to_db_base[name] ucsc_builds[db_base].sort() ucsc_builds[db_base].reverse() - ucsc_builds[db_base] = [(build, name) for build_rev, build, name in ucsc_builds[db_base]] + ucsc_builds[db_base] = [(build, name) for _, build, name in ucsc_builds[db_base]] db_names = DBNames( db_names + ucsc_builds[db_base] ) - if len( db_names ) > 1 and len( man_builds ) > 0: db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) ) + if len( db_names ) > 1 and len( man_builds ) > 0: + db_names.append( ( db_names.default_value, '----- Additional Species Are Below -----' ) ) man_builds.sort() - man_builds = [(build, name) for name, build in man_builds] + man_builds = [(build, name) for name, build in man_builds] db_names = DBNames( db_names + man_builds ) except Exception, e: print "ERROR: Unable to read builds file:", e - if len(db_names)<1: + if len(db_names) < 1: db_names = DBNames( [( db_names.default_value, db_names.default_name )] ) return db_names + def read_ensembl( filename, ucsc ): """ Read Ensembl build names from file """ ucsc_builds = [] @@ -814,47 +850,55 @@ ensembl_builds = list() try: for line in open( filename ): - if line[0:1] in [ '#', '\t' ]: continue - fields = line.replace("\r","").replace("\n","").split("\t") - if fields[0] in ucsc_builds: continue + if line[0:1] in [ '#', '\t' ]: + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") + if fields[0] in ucsc_builds: + continue ensembl_builds.append( dict( dbkey=fields[0], release=fields[1], name=fields[2].replace( '_', ' ' ) ) ) except Exception, e: print "ERROR: Unable to read builds file:", e return ensembl_builds + def read_ncbi( filename ): """ Read NCBI build names from file """ ncbi_builds = list() try: for line in open( filename ): - if line[0:1] in [ '#', '\t' ]: continue - fields = line.replace("\r","").replace("\n","").split("\t") + if line[0:1] in [ '#', '\t' ]: + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") ncbi_builds.append( dict( dbkey=fields[0], name=fields[1] ) ) except Exception, e: print "ERROR: Unable to read builds file:", e return ncbi_builds + def read_build_sites( filename, check_builds=True ): """ read db names to ucsc mappings from file, this file should probably be merged with the one above """ build_sites = [] try: for line in open(filename): try: - if line[0:1] == "#": continue - fields = line.replace("\r","").replace("\n","").split("\t") + if line[0:1] == "#": + continue + fields = line.replace("\r", "").replace("\n", "").split("\t") site_name = fields[0] site = fields[1] if check_builds: site_builds = fields[2].split(",") - site_dict = {'name':site_name, 'url':site, 'builds':site_builds} + site_dict = {'name': site_name, 'url': site, 'builds': site_builds} else: - site_dict = {'name':site_name, 'url':site} + site_dict = {'name': site_name, 'url': site} build_sites.append( site_dict ) - except: continue + except: + continue except: - print "ERROR: Unable to read builds for site file %s" %filename + print "ERROR: Unable to read builds for site file %s" % filename return build_sites + def relativize_symlinks( path, start=None, followlinks=False): for root, dirs, files in os.walk( path, followlinks=followlinks ): rel_start = None @@ -871,23 +915,26 @@ os.remove( symlink_file_name ) os.symlink( rel_path, symlink_file_name ) + def stringify_dictionary_keys( in_dict ): - #returns a new dictionary - #changes unicode keys into strings, only works on top level (does not recurse) - #unicode keys are not valid for expansion into keyword arguments on method calls + # returns a new dictionary + # changes unicode keys into strings, only works on top level (does not recurse) + # unicode keys are not valid for expansion into keyword arguments on method calls out_dict = {} for key, value in in_dict.iteritems(): out_dict[ str( key ) ] = value return out_dict + def recursively_stringify_dictionary_keys( d ): if isinstance(d, dict): - return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_dictionary_keys(v)) for k,v in d.iteritems()]) + return dict([(k.encode( DEFAULT_ENCODING ), recursively_stringify_dictionary_keys(v)) for k, v in d.iteritems()]) elif isinstance(d, list): return [recursively_stringify_dictionary_keys(x) for x in d] else: return d + def mkstemp_ln( src, prefix='mkstemp_ln_' ): """ From tempfile._mkstemp_inner, generate a hard link in the same dir with a @@ -904,9 +951,10 @@ return (os.path.abspath(file)) except OSError, e: if e.errno == errno.EEXIST: - continue # try again + continue # try again raise - raise IOError, (errno.EEXIST, "No usable temporary file name found") + raise IOError(errno.EEXIST, "No usable temporary file name found") + def umask_fix_perms( path, umask, unmasked_perms, gid=None ): """ @@ -923,7 +971,7 @@ try: os.chmod( path, perms ) except Exception, e: - log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ), \ + log.warning( 'Unable to honor umask (%s) for %s, tried to set: %s but mode remains %s, error was: %s' % ( oct( umask ), path, oct( perms ), oct( stat.S_IMODE( st.st_mode ) ), @@ -939,11 +987,12 @@ except: desired_group = gid current_group = st.st_gid - log.warning( 'Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % ( desired_group, \ + log.warning( 'Unable to honor primary group (%s) for %s, group remains %s, error was: %s' % ( desired_group, path, current_group, e ) ) + def docstring_trim(docstring): """Trimming python doc strings. Taken from: http://www.python.org/dev/peps/pep-0257/""" if not docstring: @@ -970,6 +1019,7 @@ # Return a single string: return '\n'.join(trimmed) + def nice_size(size): """ Returns a readably formatted string with the size @@ -989,14 +1039,15 @@ except: return '??? bytes' for ind, word in enumerate(words): - step = 1024 ** (ind + 1) + step = 1024 ** (ind + 1) if step > size: size = size / float(1024 ** ind) - if word == 'bytes': # No decimals for bytes + if word == 'bytes': # No decimals for bytes return "%d bytes" % size return "%.1f %s" % (size, word) return '??? bytes' + def size_to_bytes( size ): """ Returns a number of bytes if given a reasonably formatted string with the size @@ -1023,6 +1074,7 @@ elif multiple.startswith( 'b' ): return int( size ) + def send_mail( frm, to, subject, body, config ): """ Sends an email. @@ -1072,6 +1124,7 @@ s.sendmail( frm, to, msg.as_string() ) s.quit() + def force_symlink( source, link_name ): try: os.symlink( source, link_name ) @@ -1082,12 +1135,13 @@ 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 + # 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 ) ) @@ -1103,7 +1157,7 @@ rv |= ord(x) ^ ord(y) return rv == 0 -galaxy_root_path = os.path.join(__path__[0], "..","..","..") +galaxy_root_path = os.path.join(__path__[0], "..", "..", "..") # The dbnames list is used in edit attributes and the upload tool dbnames = read_dbnames( os.path.join( galaxy_root_path, "tool-data", "shared", "ucsc", "builds.txt" ) ) @@ -1114,6 +1168,7 @@ gbrowse_build_sites = read_build_sites( os.path.join( galaxy_root_path, "tool-data", "shared", "gbrowse", "gbrowse_build_sites.txt" ) ) dlnames = dict(ucsc=ucsc_names, ensembl=ensembl_names, ncbi=ncbi_names) + def galaxy_directory(): return os.path.abspath(galaxy_root_path) diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 static/scripts/galaxy.tools.js --- a/static/scripts/galaxy.tools.js +++ b/static/scripts/galaxy.tools.js @@ -86,7 +86,7 @@ }).attr( 'title', selectionType['select_by'] - ); + ).data( "index", iIndex ); view.formRow().find( "label" ).append( button ); } }); @@ -114,11 +114,13 @@ } else { $("div#remap-row").css("display", "none"); } - this.formRow().find( "i" ).each(function(index, iElement) { + this.formRow().find( "i" ).each(function(_, iElement) { + var $iElement = $(iElement); + var index = $iElement.data("index"); if(index == enableIndex) { - $(iElement).css('color', 'black'); + $iElement.css('color', 'black'); } else { - $(iElement).css('color', 'Gray'); + $iElement.css('color', 'Gray'); } }); var $select = this.$( "select" ); diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 static/scripts/viz/trackster.js --- a/static/scripts/viz/trackster.js +++ b/static/scripts/viz/trackster.js @@ -103,8 +103,9 @@ var self = this, menu = create_icon_buttons_menu([ { icon_class: 'plus-button', title: 'Add tracks', on_click: function() { - visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, function(tracks) { - _.each(tracks, function(track) { + visualization.select_datasets(galaxy_config.root + "visualization/list_current_history_datasets", galaxy_config.root + "api/datasets", { 'f-dbkey': view.dbkey }, + function(new_tracks) { + _.each(new_tracks, function(track) { view.add_drawable( tracks.object_from_template(track, view, view) ); }); }); diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 templates/webapps/galaxy/user/manage_info.mako --- a/templates/webapps/galaxy/user/manage_info.mako +++ b/templates/webapps/galaxy/user/manage_info.mako @@ -49,7 +49,7 @@ <div class="form-row"><div class="grid-header"> %for i, filter in enumerate( ['Active', 'Deleted', 'All'] ): - %if i > 0: + %if i > 0: <span>|</span> %endif %if show_filter == filter: @@ -62,11 +62,11 @@ </div><table class="grid"><tbody> - %for index, address in enumerate(addresses): + %for index, address in enumerate(addresses): <tr class="libraryRow libraryOrFolderRow" id="libraryRow"><td> - <div class="form-row"> - <label>${address.desc}:</label> + <div class="form-row"> + <label>${address.desc | h}:</label> ${address.get_html()} </div><div class="form-row"> @@ -82,7 +82,7 @@ </ul></div></td> - </tr> + </tr> %endfor </tbody></table> diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 test/functional/tools/collection_two_paired.xml --- /dev/null +++ b/test/functional/tools/collection_two_paired.xml @@ -0,0 +1,69 @@ +<tool id="collection_two_paired" name="collection_two_paired" version="0.1.0"> + <command> + #if $kind.collection_type == "paired" + cat $kind.f1.forward $kind.f1['reverse'] >> $out1; + cat $kind.f2.forward $kind.f2['reverse'] >> $out1; + #else + #for $i, $_ in enumerate($kind.f1): + cat $kind.f1[$i] $kind.f2[$i] >> $out1; + #end for + #end if + </command> + <inputs> + <conditional name="kind"> + <param type="select" name="collection_type"> + <option value="paired">Paired Datasets</option> + <option value="list">List of Datasets</option> + </param> + <when value="paired"> + <param name="f1" type="data_collection" collection_type="paired" /> + <param name="f2" type="data_collection" collection_type="paired" /> + </when> + <when value="list"> + <param name="f1" type="data_collection" collection_type="list" /> + <param name="f2" type="data_collection" collection_type="list" /> + </when> + </conditional> + </inputs> + <outputs> + <data format="txt" name="out1" /> + </outputs> + <tests> + <test> + <conditional name="kind"> + <param name="collection_type" value="paired" /> + <param name="f1"> + <collection type="paired"> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /> + </collection> + </param> + <param name="f2"> + <collection type="paired"> + <element name="forward" value="simple_line.txt" /> + <element name="reverse" value="simple_line_alternative.txt" /> + </collection> + </param> + </conditional> + <output name="out1" file="simple_lines_interleaved.txt"/> + </test> + <test> + <conditional name="kind"> + <param name="collection_type" value="list" /> + <param name="f1"> + <collection type="list"> + <element name="l11" value="simple_line.txt" /> + <element name="l12" value="simple_line.txt" /> + </collection> + </param> + <param name="f2"> + <collection type="list"> + <element name="l21" value="simple_line_alternative.txt" /> + <element name="l22" value="simple_line_alternative.txt" /> + </collection> + </param> + </conditional> + <output name="out1" file="simple_lines_interleaved.txt"/> + </test> + </tests> +</tool> diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 test/functional/tools/samples_tool_conf.xml --- a/test/functional/tools/samples_tool_conf.xml +++ b/test/functional/tools/samples_tool_conf.xml @@ -21,4 +21,5 @@ <tool file="collection_paired_test.xml" /><tool file="collection_nested_test.xml" /><tool file="collection_mixed_param.xml" /> + <tool file="collection_two_paired.xml" /></toolbox> \ No newline at end of file diff -r e332be1a256f9431d31baa910579a19dacd504b7 -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 test/unit/tools/test_execution.py --- a/test/unit/tools/test_execution.py +++ b/test/unit/tools/test_execution.py @@ -16,13 +16,12 @@ eggs.require( "Paste" ) from paste import httpexceptions -# Tool with a repeat parameter, to test state update. -REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"> +BASE_REPEAT_TOOL_CONTENTS = '''<tool id="test_tool" name="Test Tool"><command>echo "$param1" #for $r in $repeat# "$r.param2" #end for# < $out1</command><inputs><param type="text" name="param1" value="" /><repeat name="repeat1" label="Repeat 1"> - <param type="text" name="param2" value="" /> + %s </repeat></inputs><outputs> @@ -31,6 +30,10 @@ </tool> ''' +# Tool with a repeat parameter, to test state update. +REPEAT_TOOL_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="text" name="param2" value="" />''' +REPEAT_COLLECTION_PARAM_CONTENTS = BASE_REPEAT_TOOL_CONTENTS % '''<param type="data_collection" name="param2" collection_type="paired" />''' + class ToolExecutionTestCase( TestCase, tools_support.UsesApp, tools_support.UsesTools ): @@ -287,13 +290,48 @@ } ) self.__assert_exeuted( template, template_vars ) - def __history_dataset_collection_for( self, hdas, id=1234 ): - collection = galaxy.model.DatasetCollection() + def test_subcollection_multirun_with_state_updates( self ): + self._init_tool( REPEAT_COLLECTION_PARAM_CONTENTS ) + hda1, hda2 = self.__add_dataset( 1 ), self.__add_dataset( 2 ) + collection = self.__history_dataset_collection_for( [ hda1, hda2 ], collection_type="list:paired" ) + collection_id = self.app.security.encode_id( collection.id ) + self.app.dataset_collections_service = Bunch( + match_collections=lambda collections: None + ) + template, template_vars = self.__handle_with_incoming( + repeat1_add="dummy", + ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert len( state.inputs[ "repeat1" ] ) == 1 + template, template_vars = self.__handle_with_incoming( state, **{ + "repeat1_0|param2|__collection_multirun__": "%s|paired" % collection_id, + "repeat1_add": "dummy", + } ) + state = self.__assert_rerenders_tool_without_errors( template, template_vars ) + assert state.inputs[ "repeat1" ][ 0 ][ "param2|__collection_multirun__" ] == "%s|paired" % collection_id + + def __history_dataset_collection_for( self, hdas, collection_type="list", id=1234 ): + collection = galaxy.model.DatasetCollection( + collection_type=collection_type, + ) to_element = lambda hda: galaxy.model.DatasetCollectionElement( collection=collection, element=hda, ) - collection.datasets = map(to_element, hdas) + elements = map(to_element, hdas) + if collection_type == "list:paired": + paired_collection = galaxy.model.DatasetCollection( + collection_type="paired", + ) + paired_collection.elements = elements + list_dce = galaxy.model.DatasetCollectionElement( + collection=collection, + element=paired_collection, + ) + elements = [ list_dce ] + + collection.elements = elements + history_dataset_collection_association = galaxy.model.HistoryDatasetCollectionAssociation( id=id, collection=collection, @@ -349,13 +387,13 @@ self.history.datasets.append( hda ) return hda - def __add_collection_dataset( self, id, *hdas ): + def __add_collection_dataset( self, id, collection_type="paired", *hdas ): hdca = galaxy.model.HistoryDatasetCollectionAssociation() hdca.id = id collection = galaxy.model.DatasetCollection() hdca.collection = collection collection.elements = [ galaxy.model.DatasetCollectionElement(element=self.__add_dataset( 1 )) ] - + collection.type = collection_type self.trans.sa_session.model_objects[ galaxy.model.HistoryDatasetCollectionAssociation ][ id ] = hdca self.history.dataset_collections.append( hdca ) return hdca https://bitbucket.org/galaxy/galaxy-central/commits/899c50175dd4/ Changeset: 899c50175dd4 User: iracooke Date: 2014-07-31 01:58:21 Summary: Merged galaxy/galaxy-central into default Affected #: 99 files diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 .hgignore --- a/.hgignore +++ b/.hgignore @@ -16,6 +16,7 @@ # Database stuff database/beaker_sessions +database/citations database/community_files database/compiled_templates database/files diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 config/plugins/visualizations/charts/static/build-app.js --- a/config/plugins/visualizations/charts/static/build-app.js +++ b/config/plugins/visualizations/charts/static/build-app.js @@ -3,4 +3,4 @@ // (c) 2009-2013 Jeremy Ashkenas, DocumentCloud Inc. // Underscore may be freely distributed under the MIT license. -define("mvc/ui/ui-modal",[],function(){var e=Backbone.View.extend({elMain:"body",optionsDefault:{title:"ui-modal",body:"",backdrop:!0,height:null,width:null,closing_events:!1,closing_callback:null},buttonList:{},initialize:function(e){e&&this._create(e)},show:function(e){this.initialize(e),this.options.height?(this.$body.css("height",this.options.height),this.$body.css("overflow","hidden")):this.$body.css("max-height",$(window).height()/2),this.options.width&&this.$dialog.css("width",this.options.width),this.visible?this.$el.show():this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.visible=!1,this.$el.fadeOut("fast"),this.options.closing_callback&&this.options.closing_callback()},enableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!1)},disableButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).prop("disabled",!0)},showButton:function(e){var t=this.buttonList[e];this.$buttons.find("#"+t).show()},hideButton:function(e){var 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n=this.$el.find("#portlet-content");this.options.scrollable?n.addClass("scroll"):this.options.title?n.addClass("no-scroll"):n.addClass("no-scroll-no-title"),this.options.nopadding&&(n.css("padding","0px"),this.$content.css("padding","0px")),this.$buttons=$(this.el).find("#buttons");if(this.options.buttons){var r=this;$.each(this.options.buttons,function(e,t){t.$el.prop("id",e),r.$buttons.append(t.$el)})}else this.$buttons.remove();this.$operations=$(this.el).find("#operations");if(this.options.operations){var r=this;$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$operations.append(t.$el)})}this.options.body&&this.append(this.options.body)},append:function(t){this.$content.append(e.wrap(t))},content:function(){return this.$content},show:function(){this.$el.fadeIn("fast"),this.visible=!0},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},enableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!1)},disableButton:function(e){this.$buttons.find("#"+e).prop("disabled",!0)},hideOperation:function(e){this.$operations.find("#"+e).hide()},showOperation:function(e){this.$operations.find("#"+e).show()},setOperation:function(e,t){var n=this.$operations.find("#"+e);n.off("click"),n.on("click",t)},title:function(e){var t=this.$title;return e&&t.html(e),t.html()},_template:function(e){var t='<div class="ui-portlet">';return e.title&&(t+='<div id="portlet-header" class="portlet-header"><div id="operations" style="float: right;"></div><h3>',e.icon&&(t+='<i class="icon fa '+e.icon+'"> </i>'),t+='<span id="portlet-header-text">'+e.title+"</span>"+"</h3>"+"</div>"),t+='<div id="portlet-content" class="portlet-content">',e.placement=="top"&&(t+='<div id="buttons" class="buttons"></div>'),t+='<div id="content" class="content"></div>',e.placement=="bottom"&&(t+='<div id="buttons" class="buttons"></div>'),t+="</div></div>",t}});return{View:t}}),define("plugin/library/ui-select",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{id:"",cls:"",empty:"No data available",visible:!0,wait:!1},selected:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.selected=this.options.value,this.setElement(this._template(this.options)),this.$select=this.$el.find("#select"),this.$icon=this.$el.find("#icon");var n=this;this.$select.on("change",function(){n.value(n.$select.val())}),this.on("change",function(){n.options.onchange&&n.options.onchange(n.value())}),this._refresh(),this.options.visible||this.hide(),this.options.wait?this.wait():this.show()},value:function(e){var t=this.selected;e!==undefined&&(this.selected=e,this.$select.val(e));var n=this.selected;return n&&n!=t&&this.options.onchange&&this.options.onchange(n),n},first:function(){var e=this.$select.find("option");return e.length>0?e.val():undefined},text:function(){return this.$select.find("option:selected").text()},show:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-caret-down"),this.$select.show(),this.$el.show()},hide:function(){this.$el.hide()},wait:function(){this.$icon.removeClass(),this.$icon.addClass("fa fa-spinner fa-spin"),this.$select.hide()},disabled:function(){return this.$select.is(":disabled")},enable:function(){this.$select.prop("disabled",!1)},disable:function(){this.$select.prop("disabled",!0)},add:function(e){this.$select.append(this._templateOption(e)),this._refresh()},del:function(e){this.$select.find("option[value="+e+"]").remove(),this.$select.trigger("change"),this._refresh()},update:function(e){this.$select.find("option").remove();for(var t in e)this.$select.append(this._templateOption(e[t]));this._refresh()},setOnChange:function(e){this.options.onchange=e},exists:function(e){return this.$select.find("option[value="+e+"]").length>0},_refresh:function(){this.$select.find("option[value=null]").remove();var e=this.$select.find("option").length;e==0?(this.disable(),this.$select.append(this._templateOption({value:"null",label:this.options.empty}))):this.enable(),this.selected&&this.$select.val(this.selected)},_templateOption:function(e){return'<option value="'+e.value+'">'+e.label+"</option>"},_template:function(e){var t='<div id="'+e.id+'" class="ui-select">'+'<div class="button">'+'<i id="icon"/>'+"</div>"+'<select id="select" class="select '+e.cls+" "+e.id+'">';for(key in e.data){var n=e.data[key],r="";if(n.value==e.value||n.value=="")r="selected";t+='<option value="'+n.value+'" '+r+">"+n.label+"</option>"}return t+="</select></div>",t}});return{View:t}}),define("plugin/library/ui-button-menu",["utils/utils"],function(e){return Backbone.View.extend({optionsDefault:{id:"",title:"","float":"right",icon:null,onclick:null,cls:"icon-btn",tooltip:"",target:"",href:"",onunload:null,visible:!0,tag:""},$menu:null,initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement($(this._template(this.options)));var n=$(this.el).find(".root"),r=this;n.on("click",function(e){$(".tooltip").hide(),e.preventDefault(),r.options.onclick&&r.options.onclick()}),this.options.visible||this.hide(),n.tooltip({title:t.tooltip,placement:"bottom"})},show:function(){$(this.el).show()},hide:function(){$(this.el).hide()},addMenu:function(t){var n={title:"",target:"",href:"",onclick:null,divider:!1,icon:null,cls:"button-menu btn-group"};n=e.merge(t,n),this.$menu||($(this.el).append(this._templateMenu()),this.$menu=$(this.el).find(".menu"));var r=$(this._templateMenuItem(n));r.on("click",function(e){e.preventDefault(),n.onclick&&n.onclick()}),this.$menu.append(r),n.divider&&this.$menu.append($(this._templateDivider()))},_templateMenuItem:function(e){var t='<li><a href="'+e.href+'" target="'+e.target+'">';return e.icon&&(t+='<i class="fa '+e.icon+'"></i>'),t+=" "+e.title+"</a>"+"</li>",t},_templateMenu:function(){return'<ul class="menu dropdown-menu pull-right" role="menu"></ul>'},_templateDivider:function(){return'<li class="divider"></li>'},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon dropdown '+e.cls+'">';return e.title?n+='<div class="root button dropdown-toggle" data-toggle="dropdown"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}})}),define("plugin/library/ui",["utils/utils","plugin/library/ui-select","plugin/library/ui-button-menu","mvc/ui/ui-modal"],function(e,t,n,r){var i=Backbone.View.extend({optionsDefault:{url:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},_template:function(e){return'<img class="ui-image '+e.cls+'" src="'+e.url+'"/>'}}),s=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options))},title:function(e){this.$el.html(e)},_template:function(e){return'<label class="ui-label '+e.cls+'">'+e.title+"</label>"},value:function(){return options.title}}),o=Backbone.View.extend({optionsDefault:{"float":"right",icon:"",tooltip:"",placement:"bottom",title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){return'<div><span class="fa '+e.icon+'" class="ui-icon"/> '+e.title+"</div>"}}),u=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"btn btn-default",icon:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t='<button id="'+e.id+'" type="submit" style="float: '+e.float+';" type="button" class="ui-button '+e.cls+'">';return e.icon&&(t+='<i class="icon fa '+e.icon+'"></i> '),t+=e.title+"</button>",t}}),a=Backbone.View.extend({optionsDefault:{id:null,title:"","float":"right",cls:"icon-btn",icon:"",tooltip:"",onclick:null},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick),$(this.el).tooltip({title:t.tooltip,placement:"bottom"})},_template:function(e){var t="";e.title&&(t="width: auto;");var n='<div id="'+e.id+'" style="float: '+e.float+"; "+t+'" class="ui-button-icon '+e.cls+'">';return e.title?n+='<div class="button"><i class="icon fa '+e.icon+'"/> '+'<span class="title">'+e.title+"</span>"+"</div>":n+='<i class="icon fa '+e.icon+'"/>',n+="</div>",n}}),f=Backbone.View.extend({optionsDefault:{title:"",cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),$(this.el).on("click",t.onclick)},_template:function(e){return'<div><a href="javascript:void(0)" class="ui-anchor '+e.cls+'">'+e.title+"</a></div>"}}),l=Backbone.View.extend({optionsDefault:{message:"",status:"info",persistent:!1},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement("<div></div>")},update:function(t){this.options=e.merge(t,this.optionsDefault);if(t.message!=""){this.$el.html(this._template(this.options)),this.$el.find(".alert").append(t.message),this.$el.fadeIn();if(!t.persistent){var n=this;window.setTimeout(function(){n.$el.is(":visible")?n.$el.fadeOut():n.$el.hide()},3e3)}}else this.$el.fadeOut()},_template:function(e){return'<div class="ui-message alert alert-'+e.status+'"/>'}}),c=Backbone.View.extend({optionsDefault:{onclick:null,searchword:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options));var n=this;this.options.onclick&&this.$el.on("submit",function(e){var t=n.$el.find("#search");n.options.onclick(t.val())})},_template:function(e){return'<div class="ui-search"><form onsubmit="return false;"><input id="search" class="form-control input-sm" type="text" name="search" placeholder="Search..." value="'+e.searchword+'">'+'<button type="submit" class="btn search-btn">'+'<i class="fa fa-search"></i>'+"</button>"+"</form>"+"</div>"}}),h=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<input id="'+e.id+'" type="'+e.type+'" value="'+e.value+'" placeholder="'+e.placeholder+'" class="ui-input '+e.cls+'">'}}),p=Backbone.View.extend({optionsDefault:{value:"",type:"text",placeholder:"",disabled:!1,visible:!0,cls:""},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.disabled&&this.$el.prop("disabled",!0),this.options.visible||this.$el.hide();var n=this;this.$el.on("input",function(){n.options.onchange&&n.options.onchange(n.$el.val())})},value:function(e){return e!==undefined&&this.$el.val(e),this.$el.val()},_template:function(e){return'<textarea id="'+e.id+'" class="ui-textarea '+e.cls+'" rows="5"></textarea>'}}),d=Backbone.View.extend({optionsDefault:{value:"",visible:!0,cls:"",data:[],id:e.uuid()},initialize:function(t){this.options=e.merge(t,this.optionsDefault),this.setElement(this._template(this.options)),this.options.visible||this.$el.hide(),this.options.value&&this.value(this.options.value),this.current=this.options.value;var n=this;this.$el.find("input").on("change",function(){n.value(n._getValue())})},value:function(e){var t=this.current;e!==undefined&&(this.$el.find("label").removeClass("active"),this.$el.find('[value="'+e+'"]').closest("label").addClass("active"),this.current=e);var n=this.current;return n!=t&&this.options.onchange&&this.options.onchange(this.current),this.current},_getValue:function(){var e=this.$el.find(":checked"),t=null;return e.length>0&&(t=e.val()),t},_template:function(e){var t='<div class="btn-group ui-radiobutton" data-toggle="buttons">';for(key in e.data){var n=e.data[key];t+='<label class="btn btn-default"><input type="radio" name="'+e.id+'" value="'+n.value+'" selected>'+n.label+"</label>"}return t+="</div>",t}});return{Anchor:f,Button:u,ButtonIcon:a,ButtonMenu:n,Icon:o,Image:i,Input:h,Label:s,Message:l,Modal:r,RadioButton:d,Searchbox:c,Select:t,Textarea:p}}),define("plugin/library/jobs",["utils/utils"],function(e){return Backbone.Model.extend({initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e,t,n,r,i){var s=this;e.state("wait","Requesting job results...");var o=e.get("dataset_id_job");o!=""?s._wait(e,r,i):s._submit(e,t,n,r,i)},cleanup:function(t){var n=this,r=t.get("dataset_id_job");r!=""&&(e.request("PUT",config.root+"api/histories/none/contents/"+r,{deleted:!0},function(){n._refreshHdas()}),t.set("dataset_id_job",""))},_submit:function(t,n,r,i,s){var o=this,u=t.id,a=t.get("type"),f=t.definition;data={tool_id:"charts",inputs:{input:{id:t.get("dataset_id"),src:"hda"},module:f.execute,columns:r,settings:n}},t.state("wait","Sending job request..."),e.request("POST",config.root+"api/tools",data,function(e){if(!e.outputs||e.outputs.length==0)t.state("failed","Job submission failed. No response."),s&&s();else{o._refreshHdas();var n=e.outputs[0];t.state("wait","Your job has been queued. You may close the browser window. The job will run in the background."),t.set("dataset_id_job",n.id),this.app.storage.save(),o._wait(t,i,s)}},function(e){var n="";e&&e.message&&e.message.data&&e.message.data.input&&(n=e.message.data.input+"."),t.state("failed","This visualization requires the 'charts' tool. Please make sure it is installed. "+n),s&&s()})},_wait:function(t,n,r){var i=this;e.request("GET",config.root+"api/datasets/"+t.get("dataset_id_job"),{},function(e){var s=!1;switch(e.state){case"ok":t.state("wait","Job completed successfully..."),n&&n(e),s=!0;break;case"error":t.state("failed","Job has failed. Please check the history for details."),r&&r(e),s=!0;break;case"running":t.state("wait","Your job is running. You may close the browser window. The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a 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o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var 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L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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The job will continue in the background.")}s||setTimeout(function(){i._wait(t,n,r)},i.app.config.get("query_timeout"))})},_refreshHdas:function(){Galaxy&&Galaxy.currHistoryPanel&&Galaxy.currHistoryPanel.refreshContents()}})}),define("plugin/library/datasets",["utils/utils"],function(e){return Backbone.Collection.extend({list:{},cache:{},initialize:function(t,n){this.app=t,this.options=e.merge(n,this.optionsDefault)},request:function(e){e.groups?this._get_blocks(e):this._get_dataset(e.id,e.success,e.error)},_get_blocks:function(e){function h(i){c._get(i,function(){var s=!1;for(var o in e.groups){destination_group=e.groups[o],source_group=i.groups[o],destination_group.values||(destination_group.values=[]),destination_group.values=destination_group.values.concat(source_group.values);if(source_group.values.length==0){s=!0;break}}if(++l<a&&!s){n&&n(parseInt(l/a*100));var u=i.start+r;i=$.extend(!0,f,{start:u}),h(i)}else t()})}var t=e.success,n=e.progress,r=this.app.config.get("query_limit"),i=this.app.config.get("query_timeout"),s=e.start||0,o=s+e.query_limit||s+this.app.config.get("query_limit"),u=Math.abs(o-s);if(u<=0){console.debug("FAILED - Datasets::request() - Invalid query range.");return}var a=Math.ceil(u/r)||1,f=$.extend(!0,{},e),l=0,c=this,p=$.extend(!0,f,{start:s});this._get_dataset(e.id,function(){h(p)})},_get_dataset:function(t,n,r){var i=this.list[t];if(i){n(i);return}var s=this;e.request("GET",config.root+"api/datasets/"+t,{},function(e){switch(e.state){case"error":r&&r(e);break;default:s.list[t]=e,n(e)}})},_block_id:function(e,t){return e.id+"_"+e.start+"_"+e.start+this.app.config.get("query_limit")+"_"+t},_get:function(e,t){e.start=e.start||0;var n=[],r={},i=0;for(var s in e.groups){var o=e.groups[s];for(var u in o.columns){var a=o.columns[u].index,f=this._block_id(e,a);if(this.cache[f]||a==="auto"||a==="zero")continue;!r[a]&&a!==undefined&&(r[a]=i,n.push(a),i++)}}if(n.length==0){this._fill_from_cache(e),t(e);return}var l={dataset_id:e.id,start:e.start,columns:n},c=this;this._fetch(l,function(r){for(var i in r){var s=n[i],o=c._block_id(e,s);c.cache[o]=r[i]}c._fill_from_cache(e),t(e)})},_fill_from_cache:function(e){var t=e.start;console.debug("Datasets::_fill_from_cache() - Filling request from cache at "+t+".");var n=0;for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s],u=this._block_id(e,o.index),a=this.cache[u];a&&(n=Math.max(n,a.length))}}n==0&&console.debug("Datasets::_fill_from_cache() - Reached data range limit.");for(var r in e.groups){var i=e.groups[r];i.values=[];for(var f=0;f<n;f++)i.values[f]={x:parseInt(f)+t}}for(var r in e.groups){var i=e.groups[r];for(var s in i.columns){var o=i.columns[s];switch(o.index){case"auto":for(var f=0;f<n;f++){var l=i.values[f];l[s]=parseInt(f)+t}break;case"zero":for(var f=0;f<n;f++){var l=i.values[f];l[s]=0}break;default:var u=this._block_id(e,o.index),a=this.cache[u];for(var f=0;f<n;f++){var l=i.values[f],c=a[f];isNaN(c)&&!o.is_label&&(c=0),l[s]=c}}}}},_fetch:function(t,n){var r=t.start?t.start:0,i=this.app.config.get("query_limit"),s=0;t.columns&&(s=t.columns.length,console.debug("Datasets::_fetch() - Fetching "+s+" column(s) at "+r+".")),s==0&&console.debug("Datasets::_fetch() - No columns requested");var o="";for(var u in t.columns)o+=t.columns[u]+",";o=o.substring(0,o.length-1);var a=this;e.request("GET",config.root+"api/datasets/"+t.dataset_id,{data_type:"raw_data",provider:"dataset-column",limit:i,offset:r,indeces:o},function(e){var t=new Array(s);for(var r=0;r<s;r++)t[r]=[];for(var r in e.data){var i=e.data[r];for(var o in i){var u=i[o];u!==undefined&&u!=2147483647&&t[o].push(u)}}console.debug("Datasets::_fetch() - Fetching complete."),n(t)})}})}),define("plugin/models/group",[],function(){return Backbone.Model.extend({defaults:{key:"Data label",date:""},reset:function(){this.clear({silent:!0}).set(this.defaults),this.trigger("reset",this)}})}),define("plugin/models/groups",["plugin/models/group"],function(e){return Backbone.Collection.extend({model:e})}),define("plugin/models/chart",["plugin/models/groups"],function(e){return Backbone.Model.extend({defaults:{id:null,title:"",type:"",date:null,state:"",state_info:"",modified:!1,dataset_id:"",dataset_id_job:""},initialize:function(t){this.groups=new e,this.settings=new Backbone.Model},reset:function(){this.clear({silent:!0}).set(this.defaults),this.groups.reset(),this.settings.clear(),this.trigger("reset",this)},copy:function(e){var t=this;t.clear({silent:!0}).set(this.defaults),t.set(e.attributes),t.settings=e.settings.clone(),t.groups.reset(),e.groups.each(function(e){t.groups.add(e.clone())}),t.trigger("change",t)},state:function(e,t){this.set("state",e),this.set("state_info",t),this.trigger("set:state"),console.debug("Chart:state() - "+t+" ("+e+")")}})});var Visualization=Backbone.Model.extend({defaults:{config:{}},urlRoot:function(){var e="/api/visualizations";return window.galaxy_config&&galaxy_config.root?galaxy_config.root+e:e},initialize:function(e){_.isObject(e.config)&&_.isObject(this.defaults.config)&&_.defaults(e.config,this.defaults.config),this._setUpListeners()},_setUpListeners:function(){},set:function(e,t){if(e==="config"){var n=this.get("config");_.isObject(n)&&(t=_.extend(_.clone(n),t))}return Backbone.Model.prototype.set.call(this,e,t),this},toString:function(){var e=this.get("id")||"";return this.get("title")&&(e+=":"+this.get("title")),"Visualization("+e+")"}}),VisualizationCollection=Backbone.Collection.extend({model:Visualization,url:function(){return galaxy_config.root+"api/visualizations"},initialize:function(e,t){t=t||{}},set:function(e,t){var n=this;e=_.map(e,function(e){var t=n.get(e.id);if(!t)return e;var r=t.toJSON();return _.extend(r,e),r}),Backbone.Collection.prototype.set.call(this,e,t)},toString:function(){return["VisualizationCollection(",[this.historyId,this.length].join(),")"].join("")}});define("mvc/visualization/visualization-model",function(){}),define("plugin/library/storage",["utils/utils","plugin/models/chart","plugin/models/group","mvc/visualization/visualization-model"],function(e,t,n){return Backbone.Model.extend({vis:null,initialize:function(e){this.app=e,this.chart=this.app.chart,this.options=this.app.options,this.id=this.options.id,this.vis=new Visualization({type:"charts",config:{dataset_id:this.options.config.dataset_id,chart_dict:{}}}),this.id&&(this.vis.id=this.id);var t=this.options.config.chart_dict;t&&(this.vis.get("config").chart_dict=t)},save:function(){var e=this.app.chart;this.vis.get("config").chart_dict={};var t=e.get("title");t!=""&&this.vis.set("title",t);var n={attributes:e.attributes,settings:e.settings.attributes,groups:[]};e.groups.each(function(e){n.groups.push(e.attributes)}),this.vis.get("config").chart_dict=n;var r=this;this.vis.save().fail(function(e,t,n){console.error(e,t,n)}).then(function(e){e&&e.id&&(r.id=e.id)})},load:function(){var e=this.vis.get("config").chart_dict;if(!e.attributes)return!1;var t=e.attributes.type;if(!t)return console.debug("Storage::load() - Chart type not provided. Invalid format."),!1;var r=this.app.types.get(t);if(!r)return console.debug("Storage::load() - Chart type not supported. Please re-configure the chart. Resetting chart."),!1;console.debug("Storage::load() - Loading chart type "+t+"."),this.chart.definition=r,this.chart.set(e.attributes),this.chart.state("ok","Loading saved visualization..."),this.chart.settings.set(e.settings);for(var i in e.groups)this.chart.groups.add(new n(e.groups[i]));return this.chart.set("modified",!1),!0}})}),define("plugin/library/deferred",["utils/utils"],function(e){return Backbone.Model.extend({queue:[],process:{},counter:0,initialize:function(){this.on("refresh",function(){for(var e in this.queue)if(this.counter==0){var t=this.queue[e];this.queue.splice(e,1),t()}})},execute:function(e){this.queue.push(e),this.trigger("refresh")},register:function(){var t=e.uuid();return this.process[t]=!0,this.counter++,console.debug("Deferred:register() - Registering "+t),t},done:function(e){this.process[e]&&(delete this.process[e],this.counter--,console.debug("Deferred:done() - Unregistering "+e),this.trigger("refresh"))},ready:function(){return this.counter==0}})}),define("plugin/views/viewport",["mvc/ui/ui-portlet","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({container_list:[],canvas_list:[],initialize:function(e,t){this.app=e,this.chart=this.app.chart,this.options=n.merge(t,this.optionsDefault),this.setElement($(this._template())),this._fullscreen(this.$el,100),this._createContainer("div");var r=this;this.chart.on("redraw",function(){r._draw(r.chart)}),this.chart.on("set:state",function(){var e=r.$el.find("#info"),t=r.$el.find(".charts-viewport-container"),n=e.find("#icon");n.removeClass(),e.show(),e.find("#text").html(r.chart.get("state_info"));var i=r.chart.get("state");switch(i){case"ok":e.hide(),t.show();break;case"failed":n.addClass("icon fa fa-warning"),t.hide();break;default:n.addClass("icon fa fa-spinner fa-spin"),t.show()}})},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_fullscreen:function(e,t){e.css("height",$(window).height()-t),$(window).resize(function(){e.css("height",$(window).height()-t)})},_createContainer:function(e,t){t=t||1;for(var n in this.container_list)this.container_list[n].remove();this.container_list=[],this.canvas_list=[];for(var n=0;n<t;n++){var r=$(this._templateContainer(e,parseInt(100/t)));this.$el.append(r),this.container_list[n]=r,this.canvas_list[n]=r.find(".charts-viewport-canvas").attr("id")}},_draw:function(e){var t=this,n=this.app.deferred.register(),r=e.get("type");this.chart_definition=e.definition;var i=1;e.settings.get("use_panels")==="true"&&(i=e.groups.length),this._createContainer(this.chart_definition.tag,i),e.state("wait","Please wait...");if(!this.chart_definition.execute||this.chart_definition.execute&&e.get("modified"))this.app.jobs.cleanup(e),e.set("modified",!1);var t=this;require(["plugin/charts/"+this.app.chartPath(r)+"/wrapper"],function(r){if(t.chart_definition.execute)t.app.jobs.request(e,t._defaultSettingsString(e),t._defaultRequestString(e),function(){var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})},function(){this.app.deferred.done(n)});else var i=new r(t.app,{process_id:n,chart:e,request_dictionary:t._defaultRequestDictionary(e),canvas_list:t.canvas_list})})},_defaultRequestString:function(e){var t="",n=0,r=this;return e.groups.each(function(e){n++;for(var i in r.chart_definition.columns)t+=i+"_"+n+":"+(parseInt(e.get(i))+1)+", "}),t.substring(0,t.length-2)},_defaultSettingsString:function(e){var t="";for(key in e.settings.attributes)t+=key+":"+e.settings.get(key)+", ";return t.substring(0,t.length-2)},_defaultRequestDictionary:function(e){var t={groups:[]};this.chart_definition.execute?t.id=e.get("dataset_id_job"):t.id=e.get("dataset_id");var r=0,i=this;return e.groups.each(function(e){var s={};for(var o in i.chart_definition.columns){var u=i.chart_definition.columns[o];s[o]=n.merge({index:e.get(o)},u)}t.groups.push({key:++r+":"+e.get("key"),columns:s})}),t},_template:function(){return'<div class="charts-viewport"><div id="info" class="info"><span id="icon" class="icon"/><span id="text" class="text" /></div></div>'},_templateContainer:function(e,t){return'<div class="charts-viewport-container" style="width:'+t+'%;">'+'<div id="menu"/>'+"<"+e+' id="'+n.uuid()+'" class="charts-viewport-canvas">'+"</div>"}})}),define("plugin/library/screenshot",["libs/underscore"],function(e){function t(e){e.$el.find("svg").length>0?r(e):n(e)}function n(e){try{var t=e.$el.find(".jqplot-target"),n=t.jqplotToImageStr({});n&&(window.location.href=n.replace("image/png","image/octet-stream"))}catch(r){console.debug("FAILED - Screenshot::_fromCanvas() - "+r),e.error&&e.error("Please reduce your chart to a single panel and try again.")}}function r(e){var t=e.$el,n=e.url,r=e.name,s=new XMLSerializer,o=document.createElement("canvas"),u=$(o),a=t.find("svg").length,f=t.find("svg").first(),l=parseInt(f.css("height")),c=parseInt(f.css("width"));u.attr("width",c*a),u.attr("height",l),(!o.getContext||!o.getContext("2d"))&&alert("Your browser doesn't support this feature, please use a modern browser");var h=o.getContext("2d"),p=0;t.find("svg").each(function(){var e=$(this);e.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:c,height:l});var t=s.serializeToString(this);h.drawSvg(t,p,0,c,l),p+=c}),window.location.href=i(o,o.getContext("2d"),"white").replace("image/png","image/octet-stream")}function i(e,t,n){var r=e.width,i=e.height,s;if(n){s=t.getImageData(0,0,r,i);var o=t.globalCompositeOperation;t.globalCompositeOperation="destination-over",t.fillStyle=n,t.fillRect(0,0,r,i)}var u=e.toDataURL("image/png");return n&&(t.clearRect(0,0,r,i),t.putImageData(s,0,0),t.globalCompositeOperation=o),u}function s(e){window.location.href="data:none/none;base64,"+btoa(a(e).string)}function o(e){for(var t in document.styleSheets){var n=document.styleSheets[t],r=n.cssRules;if(r)for(var i=0,s=r.length;i<s;i++)try{e.find(r[i].selectorText).each(function(e,t){t.style.cssText+=r[i].style.cssText})}catch(o){}}}function u(e){var t=a(e),n={filename:name||"chart",type:"application/pdf",height:t.height,width:t.width,scale:2,svg:t.string},r=$("body"),i=r.find("#viewport-form");i.length===0&&(i=$("<form>",{id:"viewport-form",method:"post",action:"http://export.highcharts.com/",display:"none"}),r.append(i)),i.empty();for(name in n){var s=$("<input/>",{type:"hidden",name:name,value:n[name]});i.append(s)}try{i.submit()}catch(o){console.log(o)}}function a(e){if(e.$el.find("svg").length==0&&e.error){e.error("No SVG found. This chart type does not support SVG/PDF export.");return}var t=e.$el,n=t.find("svg").length,r=parseInt(t.find("svg").first().css("height")),i=parseInt(t.find("svg").first().css("width")),s=new XMLSerializer,u=$("<svg/>");u.attr({version:"1.1",xmlns:"http://www.w3.org/2000/svg",width:i*n,height:r});var a="",f=0;return t.find("svg").each(function(){var e=$(this).clone();o(e);var t=$('<g transform="translate('+f+', 0)">');t.append(e.find("g").first()),u.append(t),f+=i}),{string:s.serializeToString(u[0]),height:r,width:i}}return{createPNG:t,createSVG:s,createPDF:u}}),define("plugin/views/viewer",["utils/utils","plugin/library/ui","mvc/ui/ui-portlet","plugin/views/viewport","plugin/library/screenshot"],function(e,t,n,r,i){return Backbone.View.extend({initialize:function(e,s){this.app=e,this.chart=this.app.chart,this.viewport_view=new r(e);var o=this;this.message=new t.Message;var u=new t.ButtonMenu({icon:"fa-camera",title:"Screenshot",tooltip:"Download as PNG, SVG or PDF file"});u.addMenu({id:"button-png",title:"Save as PNG",icon:"fa-file",onclick:function(){o._wait(o.chart,function(){i.createPNG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-svg",title:"Save as SVG",icon:"fa-file-text-o",onclick:function(){o._wait(o.chart,function(){i.createSVG({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}),u.addMenu({id:"button-png",title:"Save as PDF",icon:"fa-file-o",onclick:function(){o.app.modal.show({title:"Send chart data for PDF creation",body:"Galaxy does not provide integrated PDF export scripts. You may click 'Continue' to create the PDF by using a 3rd party service (https://export.highcharts.com)",buttons:{Cancel:function(){o.app.modal.hide()},Continue:function(){o.app.modal.hide(),o._wait(o.chart,function(){i.createPDF({$el:o.viewport_view.$el,title:o.chart.get("title"),error:function(e){o.message.update({message:e,status:"danger"})}})})}}})}}),this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Viewport",scrollable:!1,operations:{edit_button:new t.ButtonIcon({icon:"fa-edit",tooltip:"Customize this chart",title:"Editor",onclick:function(){o._wait(o.chart,function(){o.app.go("editor")})}}),picture_button_menu:u}}),this.portlet.append(this.message.$el),this.portlet.append(this.viewport_view.$el),this.setElement(this.portlet.$el);var o=this;this.chart.on("change:title",function(){o._refreshTitle()})},show:function(){this.$el.show(),$(window).trigger("resize")},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e)},_wait:function(e,t){this.app.deferred.ready()?t():this.message.update({message:"Your chart is currently being processed. Please wait and try again."})}})}),define("mvc/ui/ui-tabs",["utils/utils"],function(e){var t=Backbone.View.extend({optionsDefault:{title_new:"",operations:null,onnew:null},initialize:function(t){this.visible=!1,this.$nav=null,this.$content=null,this.first_tab=null,this.options=e.merge(t,this.optionsDefault);var n=$(this._template(this.options));this.$nav=n.find(".tab-navigation"),this.$content=n.find(".tab-content"),this.setElement(n),this.list={};var r=this;this.options.operations&&$.each(this.options.operations,function(e,t){t.$el.prop("id",e),r.$nav.find(".operations").append(t.$el)});if(this.options.onnew){var i=$(this._template_tab_new(this.options));this.$nav.append(i),i.tooltip({title:"Add a new tab",placement:"bottom",container:r.$el}),i.on("click",function(e){i.tooltip("hide"),r.options.onnew()})}},add:function(e){var t=this,n=e.id,r=$(this._template_tab(e)),i=$(this._template_tab_content(e));this.list[n]=e.ondel?!0:!1,this.options.onnew?this.$nav.find("#new-tab").before(r):this.$nav.append(r),i.append(e.$el),this.$content.append(i),_.size(this.list)==1&&(r.addClass("active"),i.addClass("active"),this.first_tab=n);if(e.ondel){var s=r.find("#delete");s.tooltip({title:"Delete this tab",placement:"bottom",container:t.$el}),s.on("click",function(){return s.tooltip("destroy"),t.$el.find(".tooltip").remove(),e.ondel(),!1})}r.on("click",function(r){r.preventDefault(),e.onclick?e.onclick():t.show(n)})},del:function(e){this.$el.find("#tab-"+e).remove(),this.$el.find("#tab-content-"+e).remove(),this.first_tab==e&&(this.first_tab=null),this.first_tab!=null&&this.show(this.first_tab)},delRemovable:function(){for(var e in this.list)this.list[e]&&this.del(e)},show:function(e){this.$el.fadeIn("fast"),this.visible=!0,e&&(this.$el.find(".tab-element").removeClass("active"),this.$el.find(".tab-pane").removeClass("active"),this.$el.find("#tab-"+e).addClass("active"),this.$el.find("#tab-content-"+e).addClass("active"))},hide:function(){this.$el.fadeOut("fast"),this.visible=!1},hideOperation:function(e){this.$nav.find("#"+e).hide()},showOperation:function(e){this.$nav.find("#"+e).show()},setOperation:function(e,t){var n=this.$nav.find("#"+e);n.off("click"),n.on("click",t)},title:function(e,t){var n=this.$el.find("#tab-title-text-"+e);return t&&n.html(t),n.html()},_template:function(e){return'<div class="ui-tabs tabbable tabs-left"><ul id="tab-navigation" class="tab-navigation nav nav-tabs"><div class="operations" style="float: right; margin-bottom: 4px;"></div></ul><div id="tab-content" class="tab-content"/></div>'},_template_tab_new:function(e){return'<li id="new-tab"><a href="javascript:void(0);"><i class="ui-tabs-add fa fa-plus-circle"/>'+e.title_new+"</a>"+"</li>"},_template_tab:function(e){var t='<li id="tab-'+e.id+'" class="tab-element">'+'<a id="tab-title-link-'+e.id+'" title="" href="#tab-content-'+e.id+'" data-original-title="">'+'<span id="tab-title-text-'+e.id+'">'+e.title+"</span>";return e.ondel&&(t+='<i id="delete" class="ui-tabs-delete fa fa-minus-circle"/>'),t+="</a></li>",t},_template_tab_content:function(e){return'<div id="tab-content-'+e.id+'" class="tab-pane"/>'}});return{View:t}}),define("plugin/library/ui-table",["utils/utils"],function(e){var t=Backbone.View.extend({row:null,row_count:0,optionsDefault:{content:"No content available.",onchange:null,ondblclick:null,onconfirm:null,cls:""},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(t){this.options=e.merge(t,this.optionsDefault);var n=$(this._template(t));this.$thead=n.find("thead"),this.$tbody=n.find("tbody"),this.$tmessage=n.find("tmessage"),this.setElement(n),this.row=$("<tr></tr>")},addHeader:function(e){var t=$("<th></th>");t.append(e),this.row.append(t)},appendHeader:function(){this.$thead.append(this.row),this.row=$("<tr></tr>")},add:function(e,t,n){var r=$("<td></td>");t&&r.css("width",t),n&&r.css("text-align",n),r.append(e),this.row.append(r)},append:function(e){this._commit(e)},prepend:function(e){this._commit(e,!0)},get:function(e){return this.$el.find("#"+e)},del:function(e){var t=this.$tbody.find("#"+e);t.length>0&&(t.remove(),this.row_count--,this._refresh())},delAll:function(){this.$tbody.empty(),this.row_count=0,this._refresh()},value:function(e){this.before=this.$tbody.find(".current").attr("id"),e!==undefined&&(this.$tbody.find("tr").removeClass("current"),e&&this.$tbody.find("#"+e).addClass("current"));var t=this.$tbody.find(".current").attr("id");return t===undefined?null:(t!=this.before&&this.options.onchange&&this.options.onchange(e),t)},size:function(){return this.$tbody.find("tr").length},_commit:function(e,t){this.del(e),this.row.attr("id",e),t?this.$tbody.prepend(this.row):this.$tbody.append(this.row),this.row=$("<tr></tr>"),this.row_count++,this._refresh()},_onclick:function(e){var t=this.value(),n=$(e.target).closest("tr").attr("id");n!=""&&n&&t!=n&&(this.options.onconfirm?this.options.onconfirm(n):this.value(n))},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_refresh:function(){this.row_count==0?this.$tmessage.show():this.$tmessage.hide()},_template:function(e){return'<div><table class="ui-table '+e.cls+'">'+"<thead></thead>"+'<tbody style="cursor: pointer;"></tbody>'+"</table>"+"<tmessage>"+e.content+"</tmessage>"+"<div>"}});return{View:t}}),define("plugin/views/group",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(r,i){this.app=r;var s=this;this.chart=this.app.chart,this.group=i.group,this.group_key=new t.Input({placeholder:"Data label",onchange:function(e){s.group.set("key",e)}}),this.table=new e.View({content:"No data column."});var o=$("<div/>");o.append(n.wrap((new t.Label({title:"Provide a label:"})).$el)),o.append(n.wrap(this.group_key.$el)),o.append(n.wrap((new t.Label({title:"Select columns:"})).$el)),o.append(n.wrap(this.table.$el)),this.setElement(o);var s=this;this.chart.on("change:dataset_id",function(){s._refreshTable()}),this.chart.on("change:type",function(){s._refreshTable()}),this.group.on("change:key",function(){s._refreshGroupKey()}),this.group.on("change",function(){s._refreshGroup()}),this._refreshTable(),this._refreshGroupKey(),this._refreshGroup()},_refreshTable:function(){var e=this.chart.get("dataset_id"),n=this.chart.get("type");if(!e||!n)return;var r=this,i=this.chart.definition;this.table.delAll();var s={};for(var o in i.columns){var u=i.columns[o];if(!u){console.debug("Group::_refreshTable() - Skipping column definition.");continue}var a=new t.Select.View({id:"select_"+o,wait:!0}),f=u.title;u.is_unique&&(f+=" (all data labels)"),this.table.add(f,"25%"),this.table.add(a.$el),this.table.append(o),s[o]=a}this.chart.state("wait","Loading metadata...");var l=this.app.deferred.register(),c={id:e,success:function(e){for(var t in s)r._addRow(t,e,s,i.columns[t]);r.chart.state("ok","Metadata initialized..."),r.app.deferred.done(l)}};this.app.datasets.request(c)},_addRow:function(e,t,n,r){var i=this,s=r.is_label,o=r.is_auto,u=r.is_numeric,a=r.is_unique,f=r.is_zero,l=[],c=n[e];o&&l.push({label:"Column: Row Number",value:"auto"}),f&&l.push({label:"Column: None",value:"zero"});var h=t.metadata_column_types;for(var p in h){var d=!1;h[p]=="int"||h[p]=="float"?d=u:d=s,d&&l.push({label:"Column: "+(parseInt(p)+1)+" ["+h[p]+"]",value:p})}c.update(l),a&&this.chart.groups.first()&&this.group.set(e,this.chart.groups.first().get(e));if(!c.exists(this.group.get(e))){var v=c.first();console.debug('Group()::_addRow() - Switching model value from "'+this.group.get(e)+'" to "'+v+'".'),this.group.set(e,v)}c.value(this.group.get(e)),this.group.off("change:"+e),this.group.on("change:"+e,function(){c.value(i.group.get(e))}),c.setOnChange(function(t){a?i.chart.groups.each(function(n){n.set(e,t)}):i.group.set(e,t),i.chart.set("modified",!0)}),c.show()},_refreshGroup:function(){this.group.set("date",n.time())},_refreshGroupKey:function(){var e=this.group.get("key");e===undefined&&(e=""),this.group_key.value(e)}})}),define("plugin/library/ui-table-form",["plugin/library/ui-table","plugin/library/ui","utils/utils"],function(e,t,n){var r=Backbone.View.extend({optionsDefault:{title:"",content:"",mode:""},list:[],initialize:function(r,i){this.app=r,this.options=n.merge(i,this.optionsDefault),this.table_title=new t.Label({title:this.options.title}),this.table=new e.View({content:this.options.content});var s=$('<div class="ui-table-form"/>');this.options.title&&s.append(n.wrap(this.table_title.$el)),s.append(n.wrap(this.table.$el)),this.setElement(s)},title:function(e){this.table_title.title(e)},update:function(e,t){this.table.delAll(),this.list=[];for(var n in e)this._add(e[n].id||n,e[n],t);for(var n in this.list)this.list[n].trigger("change")},_add:function(e,n,r){var i=this,s=null,o=n.type;switch(o){case"text":s=new t.Input({id:"field-"+e,placeholder:n.placeholder,value:r.get(e),onchange:function(t){r.set(e,t)}});break;case"radiobutton":s=new t.RadioButton({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"select":s=new t.Select.View({id:"field-"+e,data:n.data,value:r.get(e),onchange:function(t){r.set(e,t);var s=_.findWhere(n.data,{value:t});if(s&&s.operations){var o=s.operations;for(var u in o.show){var a=o.show[u];i.table.get(a).show()}for(var u in o.hide){var a=o.hide[u];i.table.get(a).hide()}}}});break;case"dataset":s=new t.Select.View({id:"field-"+e,onchange:function(t){r.set(e,t)}}),i.app.datasets.on("all",function(){var t=[];i.app.datasets.each(function(e){e.get("datatype_id")==n.data&&t.push({value:e.get("id"),label:e.get("name")})}),s.update(t),r.get(e)||r.set(e,s.first()),s.value(r.get(e))}),i.app.datasets.trigger("all.datasets");break;case"textarea":s=new t.Textarea({id:"field-"+e,onchange:function(){r.set(e,s.value())}});break;case"separator":s=$("<div/>");break;default:s=new t.Input({id:"field-"+e,placeholder:n.placeholder,type:n.type,onchange:function(){r.set(e,s.value())}})}if(o!="separator"){r.get(e)||r.set(e,n.init),s.value(r.get(e)),this.list[e]=s;var u=$("<div/>");u.append(s.$el),n.info&&u.append('<div class="ui-table-form-info">'+n.info+"</div>"),this.options.style=="bold"?(this.table.add((new t.Label({title:n.title,cls:"form-label"})).$el),this.table.add(u)):(this.table.add('<span class="ui-table-form-title">'+n.title+"</span>","25%"),this.table.add(u))}else this.table.add('<div class="ui-table-form-separator">'+n.title+":<div/>"),this.table.add($("<div/>"));this.table.append(e),n.hide&&this.table.get(e).hide()}});return{View:r}}),define("plugin/views/settings",["plugin/library/ui","plugin/library/ui-table-form","utils/utils"],function(e,t,n){return Backbone.View.extend({initialize:function(e,n){this.app=e;var r=this;this.chart=this.app.chart,this.form=new t.View(e,{title:"Configuration",content:"This chart type does not provide any options."}),this.setElement(this.form.$el);var r=this;this.chart.on("change",function(){r._refresh()})},_refresh:function(){var e=this.chart.definition;if(!e)return;this.form.title(e.category+" - "+e.title+":"),this.form.update(e.settings,this.chart.settings)}})}),define("plugin/views/types",["utils/utils","plugin/library/ui"],function(e,t){return Backbone.View.extend({optionsDefault:{onchange:null,ondblclick:null},events:{click:"_onclick",dblclick:"_ondblclick"},initialize:function(n,r){var i=this;this.app=n,this.options=e.merge(r,this.optionsDefault);var s=$('<div class="charts-grid"/>');s.append(e.wrap((new t.Label({title:"How many data points would you like to analyze?"})).$el)),this.library=new t.RadioButton({data:[{label:"Few (<500)",value:"small"},{label:"Some (<10k)",value:"medium"},{label:"Many (>10k)",value:"large"}],onchange:function(e){i._filter(e)}}),s.append(e.wrap(this.library.$el)),this.setElement(s),this._render(),this.library.value("small")},value:function(e){var t=this.$el.find(".current").attr("id");e!==undefined&&(this.$el.find(".current").removeClass("current"),this.$el.find("#"+e).addClass("current"));var n=this.$el.find(".current").attr("id");return n===undefined?null:(n!=t&&this.options.onchange&&this.options.onchange(e),n)},_filter:function(e){this.$el.find(".header").hide();var t=this.app.types.attributes;for(var n in t){var r=t[n],i=this.$el.find("#"+n),s=this.$el.find("#types-header-"+this.categories_index[r.category]),o=r.keywords||"";o.indexOf(e)>=0?(i.show(),s.show()):i.hide()}},_render:function(){this.categories={},this.categories_index={};var t=0,n=this.app.types.attributes;for(var r in n){var i=n[r],s=i.category;this.categories[s]||(this.categories[s]={},this.categories_index[s]=t++),this.categories[s][r]=i}for(var s in this.categories){var o=$('<div style="clear: both;"/>');o.append(e.wrap(this._template_header({id:"types-header-"+this.categories_index[s],title:s})));for(var r in this.categories[s]){var i=this.categories[s][r],u=i.title+" ("+i.library+")";i.zoomable&&(u='<span class="fa fa-search-plus"/>'+u),o.append(e.wrap(this._template_item({id:r,title:u,url:config.app_root+"charts/"+this.app.chartPath(r)+"/logo.png"})))}this.$el.append(e.wrap(o))}},_onclick:function(e){var t=this.value(),n=$(e.target).closest(".item").attr("id");n!=""&&n&&t!=n&&this.value(n)},_ondblclick:function(e){var t=this.value();t&&this.options.ondblclick&&this.options.ondblclick(t)},_template_header:function(e){return'<div id="'+e.id+'" class="header">'+"• "+e.title+"<div>"},_template_item:function(e){return'<div id="'+e.id+'" class="item">'+'<img class="image" src="'+e.url+'">'+'<div class="title">'+e.title+"</div>"+"<div>"}})}),define("plugin/views/editor",["mvc/ui/ui-tabs","plugin/library/ui","mvc/ui/ui-portlet","utils/utils","plugin/models/chart","plugin/models/group","plugin/views/group","plugin/views/settings","plugin/views/types"],function(e,t,n,r,i,s,o,u,a){return Backbone.View.extend({initialize:function(i,s){var o=this;this.app=i,this.chart=this.app.chart,this.message=new t.Message,this.portlet=new n.View({icon:"fa-bar-chart-o",title:"Editor",operations:{save:new t.ButtonIcon({icon:"fa-save",tooltip:"Draw Chart",title:"Draw",onclick:function(){o._saveChart()}}),back:new t.ButtonIcon({icon:"fa-caret-left",tooltip:"Return to Viewer",title:"Cancel",onclick:function(){o.app.go("viewer"),o.app.storage.load()}})}}),this.types=new a(i,{onchange:function(e){var t=o.app.types.get(e);t||console.debug("FAILED - Editor::onchange() - Chart type not supported."),o.chart.definition=t,o.chart.settings.clear(),o.chart.set({type:e}),o.chart.set("modified",!0),console.debug("Editor::onchange() - Switched chart type.")},ondblclick:function(e){o._saveChart()}}),this.tabs=new e.View({title_new:"Add Data",onnew:function(){var e=o._addGroupModel();o.tabs.show(e.id)}}),this.title=new t.Input({placeholder:"Chart title",onchange:function(){o.chart.set("title",o.title.value())}});var f=$("<div/>");f.append(r.wrap((new t.Label({title:"Provide a chart title:"})).$el)),f.append(r.wrap(this.title.$el)),f.append(r.wrap(this.types.$el)),this.tabs.add({id:"main",title:"Start",$el:f}),this.settings=new u(this.app),this.tabs.add({id:"settings",title:"Configuration",$el:this.settings.$el}),this.portlet.append(this.message.$el),this.portlet.append(this.tabs.$el),this.setElement(this.portlet.$el),this.tabs.hideOperation("back");var o=this;this.chart.on("change:title",function(e){o._refreshTitle()}),this.chart.on("change:type",function(e){o.types.value(e.get("type"))}),this.chart.on("reset",function(e){o._resetChart()}),this.app.chart.on("redraw",function(e){o.portlet.showOperation("back")}),this.app.chart.groups.on("add",function(e){o._addGroup(e)}),this.app.chart.groups.on("remove",function(e){o._removeGroup(e)}),this.app.chart.groups.on("reset",function(e){o._removeAllGroups()}),this.app.chart.groups.on("change:key",function(e){o._refreshGroupKey()}),this._resetChart()},show:function(){this.$el.show()},hide:function(){this.$el.hide()},_refreshTitle:function(){var e=this.chart.get("title");this.portlet.title(e),this.title.value(e)},_refreshGroupKey:function(){var e=this,t=0;this.chart.groups.each(function(n){var r=n.get("key","");r==""&&(r="Data label"),e.tabs.title(n.id,++t+": "+r)})},_addGroupModel:function(){var e=new s({id:r.uuid()});return this.chart.groups.add(e),e},_addGroup:function(e){var t=this,n=new o(this.app,{group:e});this.tabs.add({id:e.id,$el:n.$el,ondel:function(){t.chart.groups.remove(e.id)}}),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeGroup:function(e){this.tabs.del(e.id),this._refreshGroupKey(),this.chart.set("modified",!0)},_removeAllGroups:function(e){this.tabs.delRemovable()},_resetChart:function(){this.chart.set("id",r.uuid()),this.chart.set("type","nvd3_bar"),this.chart.set("dataset_id",this.app.options.config.dataset_id),this.chart.set("title","New Chart"),this.portlet.hideOperation("back")},_saveChart:function(){this.chart.set({type:this.types.value(),title:this.title.value(),date:r.time()});if(this.chart.groups.length==0){this.message.update({message:"Please select data columns before drawing the chart."});var e=this._addGroupModel();this.tabs.show(e.id);return}var t=this,n=!0,i=this.chart.definition;this.chart.groups.each(function(e){if(!n)return;for(var r in i.columns)if(e.attributes[r]=="null"){t.message.update({status:"danger",message:"This chart type requires column types not found in your tabular file."}),t.tabs.show(e.id),n=!1;return}});if(!n)return;this.app.go("viewer");var t=this;this.app.deferred.execute(function(){t.app.storage.save(),t.chart.trigger("redraw")})}})}),define("plugin/models/config",[],function(){return Backbone.Model.extend({defaults:{query_limit:500,query_timeout:100}})}),define("plugin/charts/forms/default",[],function(){return{title:"",category:"",library:"",tag:"",keywords:"",query_limit:0,settings:{separator_x:{title:"X axis",type:"separator"},x_axis_label:{title:"Axis label",info:"Provide a label for the axis.",type:"text",init:"X-axis",placeholder:"Axis label"},x_axis_type:{title:"Axis value type",info:"Select the value type of the axis.",type:"select",init:"auto",data:[{label:"-- Do not show values 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axis.",type:"select",init:"auto",data:[{label:"-- Do not show values --",value:"hide",operations:{hide:["y_axis_precision"]}},{label:"Auto",value:"auto",operations:{hide:["y_axis_precision"]}},{label:"Float",value:"f",operations:{show:["y_axis_precision"]}},{label:"Exponent",value:"e",operations:{show:["y_axis_precision"]}},{label:"Integer",value:"d",operations:{hide:["y_axis_precision"]}},{label:"Percentage",value:"p",operations:{show:["y_axis_precision"]}},{label:"SI-prefix",value:"s",operations:{hide:["y_axis_precision"]}}]},y_axis_precision:{title:"Axis tick format",info:"Select the tick format for the axis.",type:"select",init:"1",data:[{label:"0.00001",value:"5"},{label:"0.0001",value:"4"},{label:"0.001",value:"3"},{label:"0.01",value:"2"},{label:"0.1",value:"1"},{label:"1",value:"0"}]},separator_legend:{title:"Others",type:"separator"},show_legend:{title:"Show legend",info:"Would you like to add a legend?",type:"radiobutton",init:"true",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]},use_panels:{title:"Use multi-panels",info:"Would you like to separate your data into individual panels?",type:"radiobutton",init:"false",data:[{label:"Yes",value:"true"},{label:"No",value:"false"}]}}}}),function(){function t(e,t){return(new Date(t,e+1,0)).getDate()}function n(e,t,n){return function(r,i,s){var o=e(r),u=[];o<r&&t(o);if(s>1)while(o<i){var a=new Date(+o);n(a)%s===0&&u.push(a),t(o)}else while(o<i)u.push(new Date(+o)),t(o);return u}}var e=window.nv||{};e.version="1.1.15b",e.dev=!0,window.nv=e,e.tooltip=e.tooltip||{},e.utils=e.utils||{},e.models=e.models||{},e.charts={},e.graphs=[],e.logs={},e.dispatch=d3.dispatch("render_start","render_end"),e.dev&&(e.dispatch.on("render_start",function(t){e.logs.startTime=+(new Date)}),e.dispatch.on("render_end",function(t){e.logs.endTime=+(new 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t=e.models.line(),n=e.models.historicalBar(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.legend(),u={top:30,right:60,bottom:50,left:60},a=null,f=null,l=function(e){return e.x},c=function(e){return e.y},h=e.utils.defaultColor(),p=!0,d=!0,v=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},m,g,y,b={},w=null,E="No Data Available.",S=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState");n.padData(!0),t.clipEdge(!1).padData(!0),r.orient("bottom").tickPadding(7).highlightZero(!1),i.orient("left"),s.orient("right");var x=function(n,o){var u=n.pos[0]+(o.offsetLeft||0),a=n.pos[1]+(o.offsetTop||0),f=r.tickFormat()(t.x()(n.point,n.pointIndex)),l=(n.series.bar?i:s).tickFormat()(t.y()(n.point,n.pointIndex)),c=v(n.series.key,f,l,n,T);e.tooltip.show([u,a],c,n.value<0?"n":"s",null,o)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),n.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+u.left,e.pos[1]+u.top],S.tooltipShow(e)}),n.dispatch.on("elementMouseout.tooltip",function(e){S.tooltipHide(e)}),S.on("tooltipHide",function(){d&&e.tooltip.cleanup()}),T.dispatch=S,T.legend=o,T.lines=t,T.bars=n,T.xAxis=r,T.y1Axis=i,T.y2Axis=s,d3.rebind(T,t,"defined","size","clipVoronoi","interpolate"),T.options=e.utils.optionsFunc.bind(T),T.x=function(e){return arguments.length?(l=e,t.x(e),n.x(e),T):l},T.y=function(e){return arguments.length?(c=e,t.y(e),n.y(e),T):c},T.margin=function(e){return arguments.length?(u.top=typeof e.top!="undefined"?e.top:u.top,u.right=typeof e.right!="undefined"?e.right:u.right,u.bottom=typeof e.bottom!="undefined"?e.bottom:u.bottom,u.left=typeof e.left!="undefined"?e.left:u.left,T):u},T.width=function(e){return arguments.length?(a=e,T):a},T.height=function(e){return arguments.length?(f=e,T):f},T.color=function(t){return arguments.length?(h=e.utils.getColor(t),o.color(h),T):h},T.showLegend=function(e){return arguments.length?(p=e,T):p},T.tooltips=function(e){return arguments.length?(d=e,T):d},T.tooltipContent=function(e){return arguments.length?(v=e,T):v},T.state=function(e){return arguments.length?(b=e,T):b},T.defaultState=function(e){return arguments.length?(w=e,T):w},T.noData=function(e){return arguments.length?(E=e,T):E},T},e.models.lineWithFocusChart=function(){function k(e){return e.each(function(e){function R(e){var t=+(e=="e"),n=t?1:-1,r=O/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function U(){a.empty()||a.extent(w),F.data([a.empty()?g.domain():w]).each(function(e,t){var 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e=k.transitionDuration();k.transitionDuration(0),z(),k.transitionDuration(e)}),w&&a.extent(w);var F=P.select(".nv-brushBackground").selectAll("g").data([w||a.extent()]),I=F.enter().append("g");I.append("rect").attr("class","left").attr("x",0).attr("y",0).attr("height",O),I.append("rect").attr("class","right").attr("x",0).attr("y",0).attr("height",O);var q=P.select(".nv-x.nv-brush").call(a);q.selectAll("rect").attr("height",O),q.selectAll(".resize").append("path").attr("d",R),z(),s.scale(g).ticks(L/100).tickSize(-O,0),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),d3.transition(P.select(".nv-context .nv-x.nv-axis")).call(s),o.scale(y).ticks(O/36).tickSize(-L,0),d3.transition(P.select(".nv-context .nv-y.nv-axis")).call(o),P.select(".nv-context .nv-x.nv-axis").attr("transform","translate(0,"+y.range()[0]+")"),u.dispatch.on("stateChange",function(e){k.update()}),T.on("tooltipShow",function(e){E&&C(e,N.parentNode)})}),k}var t=e.models.line(),n=e.models.line(),r=e.models.axis(),i=e.models.axis(),s=e.models.axis(),o=e.models.axis(),u=e.models.legend(),a=d3.svg.brush(),f={top:30,right:30,bottom:30,left:60},l={top:0,right:30,bottom:20,left:60},c=e.utils.defaultColor(),h=null,p=null,d=100,v,m,g,y,b=!0,w=null,E=!0,S=function(e,t,n,r,i){return"<h3>"+e+"</h3>"+"<p>"+n+" at "+t+"</p>"},x="No Data Available.",T=d3.dispatch("tooltipShow","tooltipHide","brush"),N=0;t.clipEdge(!0),n.interactive(!1),r.orient("bottom").tickPadding(5),i.orient("left"),s.orient("bottom").tickPadding(5),o.orient("left");var C=function(n,s){var o=n.pos[0]+(s.offsetLeft||0),u=n.pos[1]+(s.offsetTop||0),a=r.tickFormat()(t.x()(n.point,n.pointIndex)),f=i.tickFormat()(t.y()(n.point,n.pointIndex)),l=S(n.series.key,a,f,n,k);e.tooltip.show([o,u],l,null,null,s)};return t.dispatch.on("elementMouseover.tooltip",function(e){e.pos=[e.pos[0]+f.left,e.pos[1]+f.top],T.tooltipShow(e)}),t.dispatch.on("elementMouseout.tooltip",function(e){T.tooltipHide(e)}),T.on("tooltipHide",function(){E&&e.tooltip.cleanup()}),k.dispatch=T,k.legend=u,k.lines=t,k.lines2=n,k.xAxis=r,k.yAxis=i,k.x2Axis=s,k.y2Axis=o,d3.rebind(k,t,"defined","isArea","size","xDomain","yDomain","xRange","yRange","forceX","forceY","interactive","clipEdge","clipVoronoi","id"),k.options=e.utils.optionsFunc.bind(k),k.x=function(e){return arguments.length?(t.x(e),n.x(e),k):t.x},k.y=function(e){return arguments.length?(t.y(e),n.y(e),k):t.y},k.margin=function(e){return arguments.length?(f.top=typeof e.top!="undefined"?e.top:f.top,f.right=typeof e.right!="undefined"?e.right:f.right,f.bottom=typeof e.bottom!="undefined"?e.bottom:f.bottom,f.left=typeof e.left!="undefined"?e.left:f.left,k):f},k.margin2=function(e){return arguments.length?(l=e,k):l},k.width=function(e){return arguments.length?(h=e,k):h},k.height=function(e){return arguments.length?(p=e,k):p},k.height2=function(e){return arguments.length?(d=e,k):d},k.color=function(t){return arguments.length?(c=e.utils.getColor(t),u.color(c),k):c},k.showLegend=function(e){return arguments.length?(b=e,k):b},k.tooltips=function(e){return arguments.length?(E=e,k):E},k.tooltipContent=function(e){return arguments.length?(S=e,k):S},k.interpolate=function(e){return arguments.length?(t.interpolate(e),n.interpolate(e),k):t.interpolate()},k.noData=function(e){return arguments.length?(x=e,k):x},k.xTickFormat=function(e){return arguments.length?(r.tickFormat(e),s.tickFormat(e),k):r.tickFormat()},k.yTickFormat=function(e){return arguments.length?(i.tickFormat(e),o.tickFormat(e),k):i.tickFormat()},k.brushExtent=function(e){return arguments.length?(w=e,k):w},k.transitionDuration=function(e){return arguments.length?(N=e,k):N},k},e.models.linePlusBarWithFocusChart=function(){function B(e){return e.each(function(e){function tt(e){var t=+(e=="e"),n=t?1:-1,r=I/3;return"M"+.5*n+","+r+"A6,6 0 0 "+t+" "+6.5*n+","+(r+6)+"V"+(2*r-6)+"A6,6 0 0 "+t+" "+.5*n+","+2*r+"Z"+"M"+2.5*n+","+(r+8)+"V"+(2*r-8)+"M"+4.5*n+","+(r+8)+"V"+(2*r-8)}function nt(){h.empty()||h.extent(x),Y.data([h.empty()?k.domain():x]).each(function(e,t){var n=k(e[0])-k.range()[0],r=k.range()[1]-k(e[1]);d3.select(this).select(".left").attr("width",n<0?0:n),d3.select(this).select(".right").attr("x",k(e[1])).attr("width",r<0?0:r)})}function rt(){x=h.empty()?null:h.extent(),S=h.empty()?k.domain():h.extent(),D.brush({extent:S,brush:h}),nt(),r.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&e[n].bar})),t.width(j).height(F).color(e.map(function(e,t){return e.color||w(e,t)}).filter(function(t,n){return!e[n].disabled&&!e[n].bar}));var n=$.select(".nv-focus .nv-barsWrap").datum(R.length?R.map(function(e,t){return{key:e.key,values:e.values.filter(function(e,t){return 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arguments.length?(m=e,F):m},F.showDistY=function(e){return arguments.length?(g=e,F):g},F.showControls=function(e){return arguments.length?(S=e,F):S},F.showLegend=function(e){return arguments.length?(y=e,F):y},F.showXAxis=function(e){return arguments.length?(b=e,F):b},F.showYAxis=function(e){return arguments.length?(w=e,F):w},F.rightAlignYAxis=function(e){return arguments.length?(E=e,r.orient(e?"right":"left"),F):E},F.fisheye=function(e){return arguments.length?(x=e,F):x},F.xPadding=function(e){return arguments.length?(d=e,F):d},F.yPadding=function(e){return arguments.length?(v=e,F):v},F.tooltips=function(e){return arguments.length?(N=e,F):N},F.tooltipContent=function(e){return arguments.length?(L=e,F):L},F.tooltipXContent=function(e){return arguments.length?(C=e,F):C},F.tooltipYContent=function(e){return arguments.length?(k=e,F):k},F.state=function(e){return arguments.length?(A=e,F):A},F.defaultState=function(e){return arguments.length?(O=e,F):O},F.noData=function(e){return 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t=e.models.scatter(),n=e.models.axis(),r=e.models.axis(),i=e.models.legend(),s=e.models.legend(),o=e.models.distribution(),u=e.models.distribution(),a={top:30,right:20,bottom:50,left:75},f=null,l=null,c=e.utils.defaultColor(),h=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.xScale(),p=d3.fisheye?d3.fisheye.scale(d3.scale.linear).distortion(0):t.yScale(),d=!1,v=!1,m=!0,g=!0,y=!0,b=!1,w=!!d3.fisheye,E=0,S=!1,x=!0,T=function(e,t,n){return"<strong>"+t+"</strong>"},N=function(e,t,n){return"<strong>"+n+"</strong>"},C=function(e,t,n,r){return"<h3>"+e+"</h3>"+"<p>"+r+"</p>"},k={},L=null,A=d3.dispatch("tooltipShow","tooltipHide","stateChange","changeState"),O="No Data Available.",M=0;t.xScale(h).yScale(p),n.orient("bottom").tickPadding(10),r.orient(b?"right":"left").tickPadding(10),o.axis("x"),u.axis("y"),s.updateState(!1);var _,D,P=function(i,s){var o=i.pos[0]+(s.offsetLeft||0),u=i.pos[1]+(s.offsetTop||0),f=i.pos[0]+(s.offsetLeft||0),l=p.range()[0]+a.top+(s.offsetTop||0),c=h.range()[0]+a.left+(s.offsetLeft||0),d=i.pos[1]+(s.offsetTop||0),v=n.tickFormat()(t.x()(i.point,i.pointIndex)),m=r.tickFormat()(t.y()(i.point,i.pointIndex));T!=null&&e.tooltip.show([f,l],T(i.series.key,v,m,i,B),"n",1,s,"x-nvtooltip"),N!=null&&e.tooltip.show([c,d],N(i.series.key,v,m,i,B),"e",1,s,"y-nvtooltip"),C!=null&&e.tooltip.show([o,u],C(i.series.key,v,m,i.point.tooltip,i,B),i.value<0?"n":"s",null,s)},H=[{key:"Magnify",disabled:!0}];return t.dispatch.on("elementMouseout.tooltip",function(e){A.tooltipHide(e),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" .nv-distx-"+e.pointIndex).attr("y1",0),d3.select(".nv-chart-"+t.id()+" .nv-series-"+e.seriesIndex+" 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arguments.length?(d=e,B):d},B.showDistY=function(e){return arguments.length?(v=e,B):v},B.showControls=function(e){return arguments.length?(w=e,B):w},B.showLegend=function(e){return arguments.length?(m=e,B):m},B.showXAxis=function(e){return arguments.length?(g=e,B):g},B.showYAxis=function(e){return arguments.length?(y=e,B):y},B.rightAlignYAxis=function(e){return arguments.length?(b=e,r.orient(e?"right":"left"),B):b},B.fisheye=function(e){return arguments.length?(E=e,B):E},B.tooltips=function(e){return arguments.length?(x=e,B):x},B.tooltipContent=function(e){return arguments.length?(C=e,B):C},B.tooltipXContent=function(e){return arguments.length?(T=e,B):T},B.tooltipYContent=function(e){return arguments.length?(N=e,B):N},B.state=function(e){return arguments.length?(k=e,B):k},B.defaultState=function(e){return arguments.length?(L=e,B):L},B.noData=function(e){return arguments.length?(O=e,B):O},B.transitionDuration=function(e){return arguments.length?(M=e,B):M},B},e.models.sparkline=function(){function d(e){return e.each(function(e){var i=n-t.left-t.right,d=r-t.top-t.bottom,v=d3.select(this);s.domain(l||d3.extent(e,u)).range(h||[0,i]),o.domain(c||d3.extent(e,a)).range(p||[d,0]);var m=v.selectAll("g.nv-wrap.nv-sparkline").data([e]),g=m.enter().append("g").attr("class","nvd3 nv-wrap nv-sparkline"),b=g.append("g"),w=m.select("g");m.attr("transform","translate("+t.left+","+t.top+")");var E=m.selectAll("path").data(function(e){return[e]});E.enter().append("path"),E.exit().remove(),E.style("stroke",function(e,t){return e.color||f(e,t)}).attr("d",d3.svg.line().x(function(e,t){return s(u(e,t))}).y(function(e,t){return o(a(e,t))}));var S=m.selectAll("circle.nv-point").data(function(e){function n(t){if(t!=-1){var n=e[t];return n.pointIndex=t,n}return null}var t=e.map(function(e,t){return a(e,t)}),r=n(t.lastIndexOf(o.domain()[1])),i=n(t.indexOf(o.domain()[0])),s=n(t.length-1);return[i,r,s].filter(function(e){return e!=null})});S.enter().append("circle"),S.exit().remove(),S.attr("cx",function(e,t){return s(u(e,e.pointIndex))}).attr("cy",function(e,t){return o(a(e,e.pointIndex))}).attr("r",2).attr("class",function(e,t){return u(e,e.pointIndex)==s.domain()[1]?"nv-point nv-currentValue":a(e,e.pointIndex)==o.domain()[0]?"nv-point nv-minValue":"nv-point nv-maxValue"})}),d}var t={top:2,right:0,bottom:2,left:0},n=400,r=32,i=!0,s=d3.scale.linear(),o=d3.scale.linear(),u=function(e){return e.x},a=function(e){return e.y},f=e.utils.getColor(["#000"]),l,c,h,p;return d.options=e.utils.optionsFunc.bind(d),d.margin=function(e){return arguments.length?(t.top=typeof e.top!="undefined"?e.top:t.top,t.right=typeof e.right!="undefined"?e.right:t.right,t.bottom=typeof e.bottom!="undefined"?e.bottom:t.bottom,t.left=typeof e.left!="undefined"?e.left:t.left,d):t},d.width=function(e){return arguments.length?(n=e,d):n},d.height=function(e){return arguments.length?(r=e,d):r},d.x=function(e){return arguments.length?(u=d3.functor(e),d):u},d.y=function(e){return arguments.length?(a=d3.functor(e),d):a},d.xScale=function(e){return arguments.length?(s=e,d):s},d.yScale=function(e){return arguments.length?(o=e,d):o},d.xDomain=function(e){return arguments.length?(l=e,d):l},d.yDomain=function(e){return arguments.length?(c=e,d):c},d.xRange=function(e){return arguments.length?(h=e,d):h},d.yRange=function(e){return arguments.length?(p=e,d):p},d.animate=function(e){return arguments.length?(i=e,d):i},d.color=function(t){return arguments.length?(f=e.utils.getColor(t),d):f},d},e.models.sparklinePlus=function(){function v(e){return e.each(function(c){function O(){if(a)return;var e=C.selectAll(".nv-hoverValue").data(u),r=e.enter().append("g").attr("class","nv-hoverValue").style("stroke-opacity",0).style("fill-opacity",0);e.exit().style("stroke-opacity",0).style("fill-opacity",0).remove(),e.attr("transform",function(e){return"translate("+s(t.x()(c[e],e))+",0)"}).style("stroke-opacity",1).style("fill-opacity",1);if(!u.length)return;r.append("line").attr("x1",0).attr("y1",-n.top).attr("x2",0).attr("y2",b),r.append("text").attr("class","nv-xValue").attr("x",-6).attr("y",-n.top).attr("text-anchor","end").attr("dy",".9em"),C.select(".nv-hoverValue .nv-xValue").text(f(t.x()(c[u[0]],u[0]))),r.append("text").attr("class","nv-yValue").attr("x",6).attr("y",-n.top).attr("text-anchor","start").attr("dy",".9em"),C.select(".nv-hoverValue .nv-yValue").text(l(t.y()(c[u[0]],u[0])))}function M(){function r(e,n){var r=Math.abs(t.x()(e[0],0)-n),i=0;for(var s=0;s<e.length;s++)Math.abs(t.x()(e[s],s)-n)<r&&(r=Math.abs(t.x()(e[s],s)-n),i=s);return i}if(a)return;var e=d3.mouse(this)[0]-n.left;u=[r(c,Math.round(s.invert(e)))],O()}var m=d3.select(this),g=(r||parseInt(m.style("width"))||960)-n.left-n.right,b=(i||parseInt(m.style("height"))||400)-n.top-n.bottom;v.update=function(){v(e)},v.container=this;if(!c||!c.length){var w=m.selectAll(".nv-noData").data([d]);return w.enter().append("text").attr("class","nvd3 nv-noData").attr("dy","-.7em").style("text-anchor","middle"),w.attr("x",n.left+g/2).attr("y",n.top+b/2).text(function(e){return e}),v}m.selectAll(".nv-noData").remove();var E=t.y()(c[c.length-1],c.length-1);s=t.xScale(),o=t.yScale();var S=m.selectAll("g.nv-wrap.nv-sparklineplus").data([c]),T=S.enter().append("g").attr("class","nvd3 nv-wrap nv-sparklineplus"),N=T.append("g"),C=S.select("g");N.append("g").attr("class","nv-sparklineWrap"),N.append("g").attr("class","nv-valueWrap"),N.append("g").attr("class","nv-hoverArea"),S.attr("transform","translate("+n.left+","+n.top+")");var k=C.select(".nv-sparklineWrap");t.width(g).height(b),k.call(t);var L=C.select(".nv-valueWrap"),A=L.selectAll(".nv-currentValue").data([E]);A.enter().append("text").attr("class","nv-currentValue").attr("dx",p?-8:8).attr("dy",".9em").style("text-anchor",p?"end":"start"),A.attr("x",g+(p?n.right:0)).attr("y",h?function(e){return o(e)}:0).style("fill",t.color()(c[c.length-1],c.length-1)).text(l(E)),N.select(".nv-hoverArea").append("rect").on("mousemove",M).on("click",function(){a=!a}).on("mouseout",function(){u=[],O()}),C.select(".nv-hoverArea rect").attr("transform",function(e){return"translate("+ -n.left+","+ -n.top+")"}).attr("width",g+n.left+n.right).attr("height",b+n.top)}),v}var t=e.models.sparkline(),n={top:15,right:100,bottom:10,left:50},r=null,i=null,s,o,u=[],a=!1,f=d3.format(",r"),l=d3.format(",.2f"),c=!0,h=!0,p=!1,d="No Data Available.";return v.sparkline=t,d3.rebind(v,t,"x","y","xScale","yScale","color"),v.options=e.utils.optionsFunc.bind(v),v.margin=function(e){return arguments.length?(n.top=typeof e.top!="undefined"?e.top:n.top,n.right=typeof 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db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 config/plugins/visualizations/charts/static/views/settings.js --- a/config/plugins/visualizations/charts/static/views/settings.js +++ b/config/plugins/visualizations/charts/static/views/settings.js @@ -19,6 +19,7 @@ // create settings this.form = new TableForm.View(app, { + title : 'Configuration', content : 'This chart type does not provide any options.' }); diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 config/plugins/visualizations/charts/templates/charts.mako --- a/config/plugins/visualizations/charts/templates/charts.mako +++ b/config/plugins/visualizations/charts/templates/charts.mako @@ -21,6 +21,9 @@ ## shared css ${h.css( 'base' )} + ## crossfilter + ${h.javascript_link( app_root + "plugins/crossfilter/crossfilter.js" )} + ## canvg ${h.javascript_link( app_root + "plugins/canvg/rgbcolor.js" )} ${h.javascript_link( app_root + "plugins/canvg/canvg.js" )} diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 display_applications/igb/bam.xml --- a/display_applications/igb/bam.xml +++ b/display_applications/igb/bam.xml @@ -7,8 +7,8 @@ #set nm=$bam_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bai_file" url="${niceName}.bam.bai" metadata="bam_index" strip_https="True" /> - <param type="data" name="bam_file" url="${niceName}.bam" strip_https="True" /> + <param type="data" name="bai_file" url="${niceName}.bam.bai" metadata="bam_index" /> + <param type="data" name="bam_file" url="${niceName}.bam" /></link></display> diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 display_applications/igb/bb.xml --- a/display_applications/igb/bb.xml +++ b/display_applications/igb/bb.xml @@ -8,7 +8,7 @@ #set nm=$bigbed_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigbed_file" url="${niceName}.bigbed" strip_https="True" /> + <param type="data" name="bigbed_file" url="${niceName}.bigbed" /></link></display> diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 display_applications/igb/bed.xml --- a/display_applications/igb/bed.xml +++ b/display_applications/igb/bed.xml @@ -8,7 +8,7 @@ #set nm=$bed_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bed_file" url="${niceName}.bed" strip_https="True" /> + <param type="data" name="bed_file" url="${niceName}.bed" /><param type="template" name="bioviz" strip="True" > http://bioviz.org/igb/galaxy.html?version=${bed_file.dbkey}&loadresidue… diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 display_applications/igb/bedgraph.xml --- a/display_applications/igb/bedgraph.xml +++ b/display_applications/igb/bedgraph.xml @@ -8,7 +8,7 @@ #set nm=$bedgraph_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bedgraph_file" url="${niceName}.bed.bedgraph" strip_https="True" /> + <param type="data" name="bedgraph_file" url="${niceName}.bed.bedgraph" /><param type="template" name="bioviz" strip="True" > http://bioviz.org/igb/galaxy.html?version=${bedgraph_file.dbkey}&loadre… diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 display_applications/igb/bigwig.xml --- a/display_applications/igb/bigwig.xml +++ b/display_applications/igb/bigwig.xml @@ -8,7 +8,7 @@ #set nm=$bigwig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="bigwig_file" url="${niceName}.bigwig" strip_https="True" /> + <param type="data" name="bigwig_file" url="${niceName}.bigwig" /><!--<param type="template" name="position" strip="True" > #set chrom, start, end = $bigwig_file.datatype.get_estimated_display_viewport( $bigwig_file ) #if $chrom is not None: diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 display_applications/igb/gtf.xml --- a/display_applications/igb/gtf.xml +++ b/display_applications/igb/gtf.xml @@ -8,7 +8,7 @@ #set nm=$gtf_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="gtf_file" url="${niceName}.gtf" strip_https="True" /> + <param type="data" name="gtf_file" url="${niceName}.gtf" /><param type="template" name="bioviz" strip="True" > http://bioviz.org/igb/galaxy.html?version=${gtf_file.dbkey}&loadresidue… diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 display_applications/igb/wig.xml --- a/display_applications/igb/wig.xml +++ b/display_applications/igb/wig.xml @@ -8,7 +8,7 @@ #set nm=$wig_file_for_name.name ${re.sub('\W',"_",nm)} </param> - <param type="data" name="wig_file" url="${niceName}.wig" strip_https="True" /> + <param type="data" name="wig_file" url="${niceName}.wig" /><param type="template" name="position" strip="True" > #set chrom, start, end = $wig_file.datatype.get_estimated_display_viewport( $wig_file ) #if $chrom is not None: diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/config.py --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -64,8 +64,6 @@ tempfile.tempdir = self.new_file_path self.openid_consumer_cache_path = resolve_path( kwargs.get( "openid_consumer_cache_path", "database/openid_consumer_cache" ), self.root ) self.cookie_path = kwargs.get( "cookie_path", "/" ) - self.genome_data_path = kwargs.get( "genome_data_path", "tool-data/genome" ) - self.rsync_url = kwargs.get( "rsync_url", "rsync://datacache.galaxyproject.org/indexes" ) # Galaxy OpenID settings self.enable_openid = string_as_bool( kwargs.get( 'enable_openid', False ) ) self.openid_config = kwargs.get( 'openid_config_file', 'openid_conf.xml' ) @@ -378,6 +376,10 @@ # Default chunk size for chunkable datatypes -- 64k self.display_chunk_size = int( kwargs.get( 'display_chunk_size', 65536) ) + self.citation_cache_type = kwargs.get( "citation_cache_type", "file" ) + self.citation_cache_data_dir = self.resolve_path( kwargs.get( "citation_cache_data_dir", "database/citations/data" ) ) + self.citation_cache_lock_dir = self.resolve_path( kwargs.get( "citation_cache_lock_dir", "database/citations/locks" ) ) + @property def sentry_dsn_public( self ): """ @@ -572,6 +574,10 @@ tool_configs = self.config.tool_configs if self.config.migrated_tools_config not in tool_configs: tool_configs.append( self.config.migrated_tools_config ) + + from galaxy.managers.citations import CitationsManager + self.citations_manager = CitationsManager( self ) + from galaxy import tools self.toolbox = tools.ToolBox( tool_configs, self.config.tool_path, self ) # Search support for tools diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/datatypes/sniff.py --- a/lib/galaxy/datatypes/sniff.py +++ b/lib/galaxy/datatypes/sniff.py @@ -90,19 +90,19 @@ f.close() return False -def convert_newlines( fname, in_place=True ): +def convert_newlines( fname, in_place=True, tmp_dir=None, tmp_prefix=None ): """ Converts in place a file from universal line endings to Posix line endings. >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\r3 4") - >>> convert_newlines(fname) + >>> convert_newlines(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir()) (2, None) >>> file(fname).read() '1 2\\n3 4\\n' """ - fd, temp_name = tempfile.mkstemp() + fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir ) fp = os.fdopen( fd, "wt" ) i = None for i, line in enumerate( file( fname, "U" ) ): @@ -150,20 +150,20 @@ else: return ( i, temp_name ) -def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+" ): +def convert_newlines_sep2tabs( fname, in_place=True, patt="\\s+", tmp_dir=None, tmp_prefix=None ): """ Combines above methods: convert_newlines() and sep2tabs() so that files do not need to be read twice >>> fname = get_test_fname('temp.txt') >>> file(fname, 'wt').write("1 2\\r3 4") - >>> convert_newlines_sep2tabs(fname) + >>> convert_newlines_sep2tabs(fname, tmp_prefix="gxtest", tmp_dir=tempfile.gettempdir()) (2, None) >>> file(fname).read() '1\\t2\\n3\\t4\\n' """ regexp = re.compile( patt ) - fd, temp_name = tempfile.mkstemp() + fd, temp_name = tempfile.mkstemp( prefix=tmp_prefix, dir=tmp_dir ) fp = os.fdopen( fd, "wt" ) for i, line in enumerate( file( fname, "U" ) ): line = line.rstrip( '\r\n' ) diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/managers/citations.py --- /dev/null +++ b/lib/galaxy/managers/citations.py @@ -0,0 +1,170 @@ +import pkg_resources + +import functools +import os +import urllib2 + +pkg_resources.require('Beaker') +from beaker.cache import CacheManager +from beaker.util import parse_cache_config_options + +import logging +log = logging.getLogger( __name__ ) + + +class CitationsManager( object ): + + def __init__( self, app ): + self.app = app + self.doi_cache = DoiCache( app.config ) + + def citations_for_tool( self, tool ): + return tool.citations + + def citations_for_tool_ids( self, tool_ids ): + citation_collection = CitationCollection() + for tool_id in tool_ids: + tool = self._get_tool( tool_id ) + for citation in self.citations_for_tool( tool ): + citation_collection.add( citation ) + return citation_collection.citations + + def parse_citation( self, citation_elem, tool_directory ): + return parse_citation( citation_elem, tool_directory, self ) + + def _get_tool( self, tool_id ): + tool = self.app.toolbox.get_tool( tool_id ) + return tool + + +class DoiCache( object ): + + def __init__( self, config ): + cache_opts = { + 'cache.type': getattr( config, 'citation_cache_type', 'file'), + 'cache.data_dir': getattr( config, 'citation_cache_data_dir', None), + 'cache.lock_dir': getattr( config, 'citation_cache_lock_dir', None), + } + self._cache = CacheManager(**parse_cache_config_options(cache_opts)).get_cache('doi') + + def _raw_get_bibtex( self, doi ): + dx_url = "http://dx.doi.org/" + doi + headers = {'Accept': "text/bibliography; style=bibtex" } + req = urllib2.Request(dx_url, data="", headers=headers) + response = urllib2.urlopen(req) + bibtex = response.read() + return bibtex + + def get_bibtex( self, doi ): + createfunc = functools.partial(self._raw_get_bibtex, doi) + return self._cache.get(key=doi, createfunc=createfunc) + + +def parse_citation( elem, directory, citation_manager ): + """ Parse an abstract citation entry from the specified XML element. + The directory parameter should be used to find external files for this + citation. + """ + citation_type = elem.attrib.get( 'type', None ) + citation_class = CITATION_CLASSES.get( citation_type, None ) + if not citation_class: + log.warn("Unknown or unspecified citation type: %s" % citation_type) + return None + return citation_class( elem, directory, citation_manager ) + + +class CitationCollection( object ): + + def __init__( self ): + self.citations = [] + + def __iter__( self ): + return self.citations.__iter__() + + def __len__( self ): + return len( self.citations ) + + def add( self, new_citation ): + for citation in self.citations: + if citation.equals( new_citation ): + # TODO: We have two equivalent citations, pick the more + # informative/complete/correct. + return False + + self.citations.append( new_citation ) + return True + + +class BaseCitation( object ): + + def to_dict( self, citation_format ): + if citation_format == "bibtex": + return dict( + format="bibtex", + content=self.to_bibtex(), + ) + else: + raise Exception("Unknown citation format %s" % citation_format) + + def equals( self, other_citation ): + if self.has_doi() and other_citation.has_doi(): + return self.doi() == other_citation.doi() + else: + # TODO: Do a better job figuring out if this is the same citation. + return self.to_bibtex() == other_citation.to_bibtex() + + def has_doi( self ): + return False + + +class BibtexCitation( BaseCitation ): + + def __init__( self, elem, directory, citation_manager ): + bibtex_file = elem.attrib.get("file", None) + if bibtex_file: + raw_bibtex = open(os.path.join(directory, bibtex_file), "r").read() + else: + raw_bibtex = elem.text.strip() + self._set_raw_bibtex( raw_bibtex ) + + def _set_raw_bibtex( self, raw_bibtex ): + self.raw_bibtex = raw_bibtex + + def to_bibtex( self ): + return self.raw_bibtex + + +class DoiCitation( BaseCitation ): + BIBTEX_UNSET = object() + + def __init__( self, elem, directory, citation_manager ): + self.__doi = elem.text.strip() + self.doi_cache = citation_manager.doi_cache + self.raw_bibtex = DoiCitation.BIBTEX_UNSET + + def has_doi( self ): + return True + + def doi( self ): + return self.__doi + + def to_bibtex( self ): + if self.raw_bibtex is DoiCitation.BIBTEX_UNSET: + try: + self.raw_bibtex = self.doi_cache.get_bibtex(self.__doi) + except Exception: + log.exception("Failed to fetch bibtex for DOI %s" % self.__doi) + + if self.raw_bibtex is DoiCitation.BIBTEX_UNSET: + return """@MISC{%s, + DOI = '%s', + note = 'Failed to fetch BibTeX for DOI.' + }""" % (self.__doi, self.__doi) + else: + return self.raw_bibtex + + +CITATION_CLASSES = dict( + bibtex=BibtexCitation, + doi=DoiCitation, +) diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -874,7 +874,7 @@ class History( object, Dictifiable, UsesAnnotations, HasName ): dict_collection_visible_keys = ( 'id', 'name', 'published', 'deleted' ) - dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged', 'importable', 'slug' ) + dict_element_visible_keys = ( 'id', 'name', 'published', 'deleted', 'genome_build', 'purged', 'importable', 'slug', 'empty' ) default_name = 'Unnamed history' def __init__( self, id=None, name=None, user=None ): @@ -891,6 +891,10 @@ self.galaxy_sessions = [] self.tags = [] + @property + def empty( self ): + return self.hid_counter == 1 + def _next_hid( self ): # this is overriden in mapping.py db_next_hid() method if len( self.datasets ) == 0: diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -79,6 +79,9 @@ def get_sharable_url( self, app ): tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, self.tool_shed ) if tool_shed_url: + # Append a slash to the tool shed URL, because urlparse.urljoin will eliminate + # the last part of a URL if it does not end with a forward slash. + tool_shed_url = '%s/' % tool_shed_url return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) return tool_shed_url diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1360,6 +1360,9 @@ requirements, containers = parse_requirements_from_xml( root ) self.requirements = requirements self.containers = containers + + self.citations = self._parse_citations( root ) + # Determine if this tool can be used in workflows self.is_workflow_compatible = self.check_workflow_compatible(root) # Trackster configuration. @@ -1686,6 +1689,20 @@ trace_msg = repr( traceback.format_tb( trace ) ) log.error( "Traceback: %s" % trace_msg ) + def _parse_citations( self, root ): + citations = [] + citations_elem = root.find("citations") + if not citations_elem: + return citations + + for citation_elem in citations_elem: + if citation_elem.tag != "citation": + pass + citation = self.app.citations_manager.parse_citation( citation_elem, self.tool_dir ) + if citation: + citations.append( citation ) + return citations + # TODO: This method doesn't have to be part of the Tool class. def parse_error_level( self, err_level ): """ diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -114,6 +114,8 @@ #allow explicit conversion to be stored in job_parameter table target_dict[ conversion_name ] = conversion_data.id # a more robust way to determine JSONable value is desired elif isinstance( input, DataCollectionToolParameter ): + if not value: + return for i, v in enumerate( value.collection.dataset_instances ): data = v current_user_roles = trans.get_current_user_roles() diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py +++ b/lib/galaxy/tools/parameters/__init__.py @@ -53,7 +53,7 @@ value = incoming_value error = None try: - if value is not None or isinstance( param, DataToolParameter ): + if value is not None or isinstance( param, DataToolParameter ) or isinstance( param, DataCollectionToolParameter ): # Convert value from HTML representation if source == 'html': value = param.from_html( value, trans, param_values ) diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py +++ b/lib/galaxy/tools/parameters/basic.py @@ -2078,7 +2078,7 @@ def from_html( self, value, trans, other_values={} ): if not value and not self.optional: - raise ValueError( "History does not include a dataset of the required format / build" ) + raise ValueError( "History does not include a dataset collection of the correct type or containing the correct types of datasets" ) if value in [None, "None"]: return None if isinstance( value, str ) and value.find( "," ) > 0: diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/tools/wrappers.py --- a/lib/galaxy/tools/wrappers.py +++ b/lib/galaxy/tools/wrappers.py @@ -269,6 +269,12 @@ def __init__( self, has_collection, dataset_paths=[], **kwargs ): super(DatasetCollectionWrapper, self).__init__() + if has_collection is None: + self.__input_supplied = False + return + else: + self.__input_supplied = True + if hasattr( has_collection, "name" ): # It is a HistoryDatasetCollectionAssociation collection = has_collection.collection @@ -294,24 +300,41 @@ element_instances[element_identifier] = element_wrapper element_instance_list.append( element_wrapper ) - self.element_instances = element_instances - self.element_instance_list = element_instance_list + self.__element_instances = element_instances + self.__element_instance_list = element_instance_list def keys( self ): - return self.element_instances.keys() + if not self.__input_supplied: + return [] + return self.__element_instances.keys() @property def is_collection( self ): return True + @property + def is_input_supplied( self ): + return self.__input_supplied + def __getitem__( self, key ): + if not self.__input_supplied: + return None if isinstance( key, int ): - return self.element_instance_list[ key ] + return self.__element_instance_list[ key ] else: - return self.element_instances[ key ] + return self.__element_instances[ key ] def __getattr__( self, key ): - return self.element_instances[ key ] + if not self.__input_supplied: + return None + return self.__element_instances[ key ] def __iter__( self ): - return self.element_instance_list.__iter__() + if not self.__input_supplied: + return [].__iter__() + return self.__element_instance_list.__iter__() + + def __nonzero__( self ): + # Fail `#if $param` checks in cheetah is optional input + # not specified or if resulting collection is empty. + return self.__input_supplied and bool( self.__element_instance_list ) diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/webapps/galaxy/api/histories.py --- a/lib/galaxy/webapps/galaxy/api/histories.py +++ b/lib/galaxy/webapps/galaxy/api/histories.py @@ -18,7 +18,7 @@ from galaxy.web.base.controller import ExportsHistoryMixin from galaxy.web.base.controller import ImportsHistoryMixin -from galaxy.managers import histories +from galaxy.managers import histories, citations from galaxy import util from galaxy.util import string_as_bool @@ -34,6 +34,7 @@ def __init__( self, app ): super( HistoriesController, self ).__init__( app ) + self.citations_manager = citations.CitationsManager( app ) self.mgrs = util.bunch.Bunch( histories=histories.HistoryManager() ) @@ -117,6 +118,20 @@ history_data[ 'contents_url' ] = url_for( 'history_contents', history_id=history_id ) return history_data + @expose_api_anonymous + def citations( self, trans, history_id, **kwd ): + history = self.mgrs.histories.get( trans, self._decode_id( trans, history_id ), check_ownership=False, check_accessible=True ) + tool_ids = set([]) + for dataset in history.datasets: + job = dataset.creating_job + if not job: + continue + tool_id = job.tool_id + if not tool_id: + continue + tool_ids.add(tool_id) + return map( lambda citation: citation.to_dict( "bibtex" ), self.citations_manager.citations_for_tool_ids( tool_ids ) ) + @expose_api def set_as_current( self, trans, id, **kwd ): """ diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/webapps/galaxy/api/tools.py --- a/lib/galaxy/webapps/galaxy/api/tools.py +++ b/lib/galaxy/webapps/galaxy/api/tools.py @@ -1,6 +1,8 @@ import urllib +from galaxy import exceptions from galaxy import web, util +from galaxy.web import _future_expose_api_anonymous from galaxy.web.base.controller import BaseAPIController from galaxy.web.base.controller import UsesVisualizationMixin from galaxy.web.base.controller import UsesHistoryMixin @@ -44,7 +46,7 @@ trans.response.status = 500 return { 'error': str( exc ) } - @web.expose_api + @_future_expose_api_anonymous def show( self, trans, id, **kwd ): """ GET /api/tools/{tool_id} @@ -52,18 +54,16 @@ """ io_details = util.string_as_bool( kwd.get( 'io_details', False ) ) link_details = util.string_as_bool( kwd.get( 'link_details', False ) ) - try: - id = urllib.unquote_plus( id ) - tool = self.app.toolbox.get_tool( id ) - if not tool: - trans.response.status = 404 - return { 'error': 'tool not found', 'id': id } - return tool.to_dict( trans, io_details=io_details, link_details=link_details ) + tool = self._get_tool( id ) + return tool.to_dict( trans, io_details=io_details, link_details=link_details ) - except Exception, exc: - log.error( 'could not convert tool (%s) to dictionary: %s', id, str( exc ), exc_info=True ) - trans.response.status = 500 - return { 'error': str( exc ) } + @_future_expose_api_anonymous + def citations( self, trans, id, **kwds ): + tool = self._get_tool( id ) + rval = [] + for citation in tool.citations: + rval.append( citation.to_dict( 'bibtex' ) ) + return rval @web.expose_api_anonymous def create( self, trans, payload, **kwd ): @@ -170,6 +170,12 @@ # # -- Helper methods -- # + def _get_tool( self, id ): + id = urllib.unquote_plus( id ) + tool = self.app.toolbox.get_tool( id ) + if not tool: + raise exceptions.ObjectNotFound("Could not find tool with id '%s'" % id) + return tool def _rerun_tool( self, trans, payload, **kwargs ): """ diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/webapps/galaxy/api/workflows.py --- a/lib/galaxy/webapps/galaxy/api/workflows.py +++ b/lib/galaxy/webapps/galaxy/api/workflows.py @@ -82,11 +82,17 @@ latest_workflow = stored_workflow.latest_workflow inputs = {} for step in latest_workflow.steps: - if step.type == 'data_input': + step_type = step.type + if step_type in ['data_input', 'data_collection_input']: if step.tool_inputs and "name" in step.tool_inputs: - inputs[step.id] = {'label': step.tool_inputs['name'], 'value': ""} + label = step.tool_inputs['name'] + elif step_type == "data_input": + label = "Input Dataset" + elif step_type == "data_collection_input": + label = "Input Dataset Collection" else: - inputs[step.id] = {'label': "Input Dataset", 'value': ""} + raise ValueError("Invalid step_type %s" % step_type) + inputs[step.id] = {'label': label, 'value': ""} else: pass # Eventually, allow regular tool parameters to be inserted and modified at runtime. @@ -194,7 +200,27 @@ # Pull other parameters out of payload. param_map = payload.get( 'parameters', {} ) - ds_map = payload.get( 'ds_map', {} ) + inputs = payload.get( 'inputs', None ) + inputs_by = payload.get( 'inputs_by', None ) + if inputs is None: + # Default to legacy behavior - read ds_map and reference steps + # by unencoded step id (a raw database id). + inputs = payload.get( 'ds_map', {} ) + inputs_by = inputs_by or 'step_id' + else: + inputs = inputs or {} + # New default is to reference steps by index of workflow step + # which is intrinsic to the workflow and independent of the state + # of Galaxy at the time of workflow import. + inputs_by = inputs_by or 'step_index' + + valid_inputs_by = [ 'step_id', 'step_index', 'name' ] + if inputs_by not in valid_inputs_by: + trans.response.status = 403 + error_message_template = "Invalid inputs_by specified '%s' must be one of %s" + error_message = error_message_template % ( inputs_by, valid_inputs_by ) + raise ValueError( error_message ) + add_to_history = 'no_add_to_history' not in payload history_param = payload.get('history', '') @@ -234,33 +260,42 @@ trans.sa_session.flush() # Set workflow inputs. - for k in ds_map: + for k in inputs: try: - if ds_map[k]['src'] == 'ldda': + if inputs[k]['src'] == 'ldda': ldda = trans.sa_session.query(self.app.model.LibraryDatasetDatasetAssociation).get( - trans.security.decode_id(ds_map[k]['id'])) + trans.security.decode_id(inputs[k]['id'])) assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) - hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif ds_map[k]['src'] == 'ld': + content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + elif inputs[k]['src'] == 'ld': ldda = trans.sa_session.query(self.app.model.LibraryDataset).get( - trans.security.decode_id(ds_map[k]['id'])).library_dataset_dataset_association + trans.security.decode_id(inputs[k]['id'])).library_dataset_dataset_association assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), ldda.dataset ) - hda = ldda.to_history_dataset_association(history, add_to_history=add_to_history) - elif ds_map[k]['src'] == 'hda': + content = ldda.to_history_dataset_association(history, add_to_history=add_to_history) + elif inputs[k]['src'] == 'hda': # Get dataset handle, add to dict and history if necessary - hda = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get( - trans.security.decode_id(ds_map[k]['id'])) - assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) + content = trans.sa_session.query(self.app.model.HistoryDatasetAssociation).get( + trans.security.decode_id(inputs[k]['id'])) + assert trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), content.dataset ) + elif inputs[k]['src'] == 'hdca': + content = self.app.dataset_collections_service.get_dataset_collection_instance( + trans, + 'history', + inputs[k]['id'] + ) else: trans.response.status = 400 - return "Unknown dataset source '%s' specified." % ds_map[k]['src'] - if add_to_history and hda.history != history: - hda = hda.copy() - history.add_dataset(hda) - ds_map[k]['hda'] = hda + return "Unknown dataset source '%s' specified." % inputs[k]['src'] + if add_to_history and content.history != history: + content = content.copy() + if isinstance( content, self.app.model.HistoryDatasetAssociation ): + history.add_dataset( content ) + else: + history.add_dataset_collection( content ) + inputs[k]['hda'] = content # TODO: rename key to 'content', prescreen input ensure not populated explicitly except AssertionError: trans.response.status = 400 - return "Invalid Dataset '%s' Specified" % ds_map[k]['id'] + return "Invalid Dataset '%s' Specified" % inputs[k]['id'] # Run each step, connecting outputs to inputs replacement_dict = payload.get('replacement_params', {}) @@ -268,7 +303,8 @@ run_config = WorkflowRunConfig( target_history=history, replacement_dict=replacement_dict, - ds_map=ds_map, + inputs=inputs, + inputs_by=inputs_by, param_map=param_map, ) diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -174,6 +174,7 @@ webapp.mapper.resource( 'ftp_file', 'ftp_files', path_prefix='/api' ) webapp.mapper.resource( 'group', 'groups', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'quota', 'quotas', path_prefix='/api' ) + webapp.mapper.connect( '/api/tools/{id:.+?}/citations', action='citations', controller="tools" ) webapp.mapper.connect( '/api/tools/{id:.+?}', action='show', controller="tools" ) webapp.mapper.resource( 'tool', 'tools', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'user', 'users', path_prefix='/api' ) @@ -181,6 +182,7 @@ webapp.mapper.resource( 'visualization', 'visualizations', path_prefix='/api' ) webapp.mapper.resource( 'workflow', 'workflows', path_prefix='/api' ) webapp.mapper.resource_with_deleted( 'history', 'histories', path_prefix='/api' ) + webapp.mapper.connect( '/api/histories/{history_id}/citations', action='citations', controller="histories" ) webapp.mapper.resource( 'configuration', 'configuration', path_prefix='/api' ) webapp.mapper.resource( 'datatype', 'datatypes', diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/webapps/galaxy/controllers/history.py --- a/lib/galaxy/webapps/galaxy/controllers/history.py +++ b/lib/galaxy/webapps/galaxy/controllers/history.py @@ -448,6 +448,13 @@ # ......................................................................... html @web.expose + def citations( self, trans ): + # Get history + history = trans.history + history_id = trans.security.encode_id( history.id ) + return trans.fill_template( "history/citations.mako", history=history, history_id=history_id ) + + @web.expose def display_structured( self, trans, id=None ): """ Display a history as a nested structure showing the jobs and workflow diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/webapps/tool_shed/app.py --- a/lib/galaxy/webapps/tool_shed/app.py +++ b/lib/galaxy/webapps/tool_shed/app.py @@ -52,6 +52,9 @@ # because the Tool Shed should always have an empty dictionary! self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_path ) self.genome_builds = GenomeBuilds( self ) + # Citation manager needed to load tools. + from galaxy.managers.citations import CitationsManager + self.citations_manager = CitationsManager( self ) # The Tool Shed makes no use of a Galaxy toolbox, but this attribute is still required. self.toolbox = tools.ToolBox( [], self.config.tool_path, self ) # Initialize the Tool Shed security agent. diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/webapps/tool_shed/config.py --- a/lib/galaxy/webapps/tool_shed/config.py +++ b/lib/galaxy/webapps/tool_shed/config.py @@ -130,6 +130,9 @@ if global_conf and "__file__" in global_conf: global_conf_parser.read(global_conf['__file__']) self.running_functional_tests = string_as_bool( kwargs.get( 'running_functional_tests', False ) ) + self.citation_cache_type = kwargs.get( "citation_cache_type", "file" ) + self.citation_cache_data_dir = resolve_path( kwargs.get( "citation_cache_data_dir", "database/tool_shed_citations/data" ), self.root ) + self.citation_cache_lock_dir = resolve_path( kwargs.get( "citation_cache_lock_dir", "database/tool_shed_citations/locks" ), self.root ) def get( self, key, default ): return self.config_dict.get( key, default ) diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/webapps/tool_shed/framework/middleware/hg.py --- a/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py +++ b/lib/galaxy/webapps/tool_shed/framework/middleware/hg.py @@ -22,6 +22,7 @@ CHUNK_SIZE = 65536 + class Hg( object ): def __init__( self, app, config ): @@ -35,12 +36,20 @@ self.db_url = self.config[ 'database_connection' ] else: self.db_url = "sqlite:///%s?isolation_level=IMMEDIATE" % self.config[ 'database_file' ] + # Keep track of whether we're setting repository metadata so that we do not increment the times_downloaded + # count for the repository. + self.setting_repository_metadata = False def __call__( self, environ, start_response ): + if 'PATH_INFO' in environ: + path_info = environ[ 'PATH_INFO' ].lstrip( '/' ) + if path_info == 'repository/reset_all_metadata': + self.setting_repository_metadata = True cmd = self.__get_hg_command( **environ ) # The 'getbundle' command indicates that a mercurial client is getting a bundle of one or more changesets, indicating - # a clone or a pull. - if cmd == 'getbundle': + # a clone or a pull. However, we do not want to increment the times_downloaded count if we're only setting repository + # metadata. + if cmd == 'getbundle' and not self.setting_repository_metadata: common, _ = environ[ 'HTTP_X_HGARG_1' ].split( '&' ) # The 'common' parameter indicates the full sha-1 hash of the changeset the client currently has checked out. If # this is 0000000000000000000000000000000000000000, then the client is performing a fresh checkout. If it has any diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/galaxy/workflow/run.py --- a/lib/galaxy/workflow/run.py +++ b/lib/galaxy/workflow/run.py @@ -32,19 +32,26 @@ target_history. (Defaults to False) :type copy_inputs_to_history: bool - :param ds_map: Map from step ids to dict's containing HDA for these steps. - :type ds_map: dict + :param inputs: Map from step ids to dict's containing HDA for these steps. + :type inputs: dict + + :param inputs_by: How inputs maps to inputs (datasets/collections) to workflows + steps - by unencoded database id ('step_id'), index in workflow + 'step_index' (independent of database), or by input name for + that step ('name'). + :type inputs_by: str :param param_map: Override tool and/or step parameters (see documentation on _update_step_parameters below). :type param_map: """ - def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, ds_map={}, param_map={} ): + def __init__( self, target_history, replacement_dict, copy_inputs_to_history=False, inputs={}, inputs_by='step_id', param_map={} ): self.target_history = target_history self.replacement_dict = replacement_dict self.copy_inputs_to_history = copy_inputs_to_history - self.ds_map = ds_map + self.inputs = inputs + self.inputs_by = inputs_by self.param_map = param_map @@ -66,7 +73,9 @@ self.target_history = workflow_run_config.target_history self.replacement_dict = workflow_run_config.replacement_dict self.copy_inputs_to_history = workflow_run_config.copy_inputs_to_history - self.ds_map = workflow_run_config.ds_map + self.inputs = workflow_run_config.inputs + self.inputs_by = workflow_run_config.inputs_by + self.inputs_by_step_id = {} self.param_map = workflow_run_config.param_map self.outputs = odict() @@ -200,7 +209,7 @@ outputs[ step.id ] = out_data # Web controller may set copy_inputs_to_history, API controller always sets - # ds_map. + # inputs. if self.copy_inputs_to_history: for input_dataset_hda in out_data.values(): content_type = input_dataset_hda.history_content_type @@ -214,8 +223,8 @@ outputs[ step.id ][ 'input_ds_copy' ] = new_hdca else: raise Exception("Unknown history content encountered") - if self.ds_map: - outputs[ step.id ][ 'output' ] = self.ds_map[ str( step.id ) ][ 'hda' ] + if self.inputs: + outputs[ step.id ][ 'output' ] = self.inputs_by_step_id[ step.id ][ 'hda' ] return job @@ -277,14 +286,23 @@ message = "Workflow cannot be run because of step upgrade messages: %s" % step.upgrade_messages raise exceptions.MessageException( message ) else: - # This is an input step. Make sure we have an available input. - if step.type == 'data_input' and str( step.id ) not in self.ds_map: - message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id - raise exceptions.MessageException( message ) - step.module = modules.module_factory.from_workflow_step( self.trans, step ) step.state = step.module.get_runtime_state() + # This is an input step. Make sure we have an available input. + if step.type in [ 'data_input', 'data_collection_input' ]: + if self.inputs_by == "step_id": + key = str( step.id ) + elif self.inputs_by == "name": + key = step.tool_inputs.get( 'name', None ) + else: + key = str( step.order_index ) + if key not in self.inputs: + message = "Workflow cannot be run because an expected input step '%s' has no input dataset." % step.id + raise exceptions.MessageException( message ) + else: + self.inputs_by_step_id[ step.id ] = self.inputs[ key ] + def _update_step_parameters(step, param_map): """ diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/tool_shed/galaxy_install/dependency_display.py --- a/lib/tool_shed/galaxy_install/dependency_display.py +++ b/lib/tool_shed/galaxy_install/dependency_display.py @@ -3,6 +3,8 @@ import os import threading +from galaxy import util + from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import readme_util diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py --- /dev/null +++ b/lib/tool_shed/galaxy_install/migrate/versions/0012_tools.py @@ -0,0 +1,48 @@ +""" +The following tools have been eliminated from the distribution: + +1: Compute an expression on every row +2: Correlation for numeric columns +3: Count GFF Features +4: Filter on ambiguities in polymorphism datasets +5: Generate A Matrix for using PC and LDA +6: Histogram of a numeric column +7: Perform Linear Discriminant Analysis +8: Maximal Information-based Nonparametric Exploration +9: Pearson and apos Correlation between any two numeric columns +10: Convert from pgSnp to gd_snp +11: Draw ROC plot on "Perform LDA" output +12: Scatterplot of two numeric columns +13: snpFreq significant SNPs in case-control data +14: Build custom track for UCSC genome browser +15: VCF to pgSnp + +The tools are now available in the repositories respectively: + +1: column_maker +2: correlation +3: count_gff_features +4: dna_filtering +5: generate_pc_lda_matrix +6: histogram +7: lda_analysis +8: mine +9: pearson_correlation +10: pgsnp2gd_snp +11: plot_from_lda +12: scatterplot +13: snpfreq +14: ucsc_custom_track +15: vcf2pgsnp + +from the main Galaxy tool shed at http://toolshed.g2.bx.psu.edu +and will be installed into your local Galaxy instance at the +location discussed above by running the following command. + +""" + +def upgrade( migrate_engine ): + print __doc__ + +def downgrade( migrate_engine ): + pass diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/tool_shed/metadata/metadata_generator.py --- a/lib/tool_shed/metadata/metadata_generator.py +++ b/lib/tool_shed/metadata/metadata_generator.py @@ -7,6 +7,7 @@ from galaxy.datatypes import checkers from galaxy.model.orm import and_ from galaxy.tools.data_manager.manager import DataManager +from galaxy.tools.test import TestCollectionDef from galaxy.web import url_for from tool_shed.repository_types import util as rt_util @@ -621,7 +622,13 @@ # </test> inputs.append( ( param_name, values ) ) else: - if len( values ) == 1: + if isinstance( values, TestCollectionDef ): + # Nested required files are being populated correctly, + # not sure we need the value here to be anything else? + collection_type = values.collection_type + metadata_display_value = "%s collection" % collection_type + inputs.append( ( param_name, metadata_display_value ) ) + elif len( values ) == 1: inputs.append( ( param_name, values[ 0 ] ) ) else: inputs.append( ( param_name, values ) ) diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh --- a/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh +++ b/lib/tool_shed/scripts/bootstrap_tool_shed/bootstrap_tool_shed.sh @@ -73,12 +73,11 @@ fi done -echo -n "Retrieving admin user's API key..." -api_key_json=`curl -s --user $admin_user_email:$admin_user_password $local_shed_url/api/authenticate/baseauth/` -api_key=`echo $api_key_json | grep api_key | awk 'BEGIN { FS="\"" } ; { print \$4 }' | sed 's/\\s\+//'` +echo -n "Retrieving admin user's API key from $local_shed_url..." +api_key=`curl -s --user $admin_user_email:$admin_user_password $local_shed_url/api/authenticate/baseauth/ | sed 's/.\+api_key[^0-9a-f]\+$[0-9a-f]\+$.\+/\1/'` if [[ -z $api_key && ${api_key+x} ]] ; then - stop_err "Error getting API key for user $admin_user_email." + stop_err "Error getting API key for user $admin_user_email." fi echo " done." diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 run_tests.sh --- a/run_tests.sh +++ b/run_tests.sh @@ -88,7 +88,7 @@ shift 1 fi ;; - -with_framework_test_tools|--with_framework_test_tools) + -with_framework_test_tools|--with_framework_test_tools) with_framework_test_tools_arg="-with_framework_test_tools" shift ;; diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 scripts/migrate_tools/0012_tools.sh --- /dev/null +++ b/scripts/migrate_tools/0012_tools.sh @@ -0,0 +1,4 @@ +#!/bin/sh + +cd `dirname $0`/../.. +python ./scripts/migrate_tools/migrate_tools.py 0012_tools.xml $@ diff -r db12a9c90f0a9b265871b44e0adbb5cbc3415613 -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 scripts/migrate_tools/0012_tools.xml --- /dev/null +++ b/scripts/migrate_tools/0012_tools.xml @@ -0,0 +1,48 @@ +<?xml version="1.0"?> +<toolshed name="toolshed.g2.bx.psu.edu"> + <repository changeset_revision="08a01b2ce4cd" owner="devteam" name="column_maker" description="Compute an expression on every row"> + <tool file="stats/column_maker.xml" id="Add_a_column1" version="1.1.0" /> + </repository> + <repository changeset_revision="24e01abf9e34" owner="devteam" name="correlation" description="Correlation for numeric columns"> + <tool file="stats/cor.xml" id="cor2" version="1.0.0" /> + </repository> + <repository changeset_revision="fabda887a71f" owner="devteam" name="count_gff_features" description="Count GFF Features"> + <tool file="stats/count_gff_features.xml" id="count_gff_features" version="0.1" /> + </repository> + <repository changeset_revision="a6f0d355b05f" owner="devteam" name="dna_filtering" description="Filter on ambiguities in polymorphism datasets"> + <tool file="stats/dna_filtering.xml" id="dna_filter" version="1.0.0" /> + </repository> + <repository changeset_revision="04cdbd00dcec" owner="devteam" name="generate_pc_lda_matrix" description="Generate A Matrix for using PC and LDA"> + <tool file="stats/generate_matrix_for_pca_lda.xml" id="generate_matrix_for_pca_and_lda1" version="1.0.0" /> + </repository> + <repository changeset_revision="6ff47de059a0" owner="devteam" name="histogram" description="Histogram of a numeric column"> + <tool file="plotting/histogram2.xml" id="histogram_rpy" version="1.0.3" /> + </repository> + <repository changeset_revision="f38763b52f33" owner="devteam" name="lda_analysis" description="Perform Linear Discriminant Analysis"> + <tool file="stats/lda_analy.xml" id="lda_analy1" version="1.0.1" /> + </repository> + <repository changeset_revision="783d91de9e6d" owner="devteam" name="mine" description="Maximal Information-based Nonparametric Exploration"> + <tool file="stats/MINE.xml" id="maximal_information_based_nonparametric_exploration" version="0.0.1" /> + </repository> + <repository changeset_revision="5ebbb889236a" owner="devteam" name="pearson_correlation" description="Pearson and apos Correlation between any two numeric columns"> + <tool file="stats/correlation.xml" id="Pearson_and_apos_Correlation1" version="1.0.0" /> + </repository> + <repository changeset_revision="d281062566f9" owner="devteam" name="pgsnp2gd_snp" description="Convert from pgSnp to gd_snp"> + <tool file="phenotype_association/pgSnp2gd_snp.xml" id="pgSnp2gd_snp" version="1.0.0" /> + </repository> + <repository changeset_revision="c5ab37076128" owner="devteam" name="plot_from_lda" description="Draw ROC plot on "Perform LDA" output"> + <tool file="stats/plot_from_lda.xml" id="plot_for_lda_output1" version="1.0.1" /> + </repository> + <repository changeset_revision="c12b0759203b" owner="devteam" name="scatterplot" description="Scatterplot of two numeric columns"> + <tool file="plotting/scatterplot.xml" id="scatterplot_rpy" version="1.0.0" /> + </repository> + <repository changeset_revision="72ea0d13dd66" owner="devteam" name="snpfreq" description="snpFreq significant SNPs in case-control data"> + <tool file="phenotype_association/snpFreq.xml" id="hgv_snpFreq" version="1.0.1" /> + </repository> + <repository changeset_revision="618e56c3109b" owner="devteam" name="ucsc_custom_track" description="Build custom track for UCSC genome browser"> + <tool file="visualization/build_ucsc_custom_track.xml" id="build_ucsc_custom_track_1" version="1.0.0" /> + </repository> + <repository changeset_revision="5fca46616675" owner="devteam" name="vcf2pgsnp" description="VCF to pgSnp"> + <tool file="phenotype_association/vcf2pgSnp.xml" id="vcf2pgSnp" version="1.0.0" /> + </repository> +</toolshed> \ No newline at end of file This diff is so big that we needed to truncate the remainder. https://bitbucket.org/galaxy/galaxy-central/commits/19859e3e4b1c/ Changeset: 19859e3e4b1c User: iracooke Date: 2014-07-31 01:59:53 Summary: Fallback for sql whitelisting when sqlparse is not available Affected #: 1 file diff -r 899c50175dd4d5f0e72a72a3968905bd2e965a52 -r 19859e3e4b1c58217c31d2f3c472359c667c2a7f lib/galaxy/util/sqlite.py --- a/lib/galaxy/util/sqlite.py +++ b/lib/galaxy/util/sqlite.py @@ -1,7 +1,28 @@ import sqlite3 -import sqlparse import re +try: + import sqlparse + def is_read_only_query(query): + statements = sqlparse.parse(query) + for statement in statements: + if statement.get_type() != "SELECT": + return False + return True + +except ImportError: + # Without sqlparse we use a very weak regex check + def is_read_only_query(query): + if re.match("select ", query, re.IGNORECASE): + if re.search("^([^\"]|\"[^\"]*\")*?;", query) or re.search("^([^\']|\'[^\']*\')*?;", query): + return False + else: + return True + return False + + + + def connect(path): connection = sqlite3.connect(path) @@ -9,9 +30,3 @@ return connection -def is_read_only_query(query): - statements = sqlparse.parse(query) - for statement in statements: - if statement.get_type() != "SELECT": - return False - return True \ No newline at end of file https://bitbucket.org/galaxy/galaxy-central/commits/a12359ac3a8a/ Changeset: a12359ac3a8a Branch: next-stable User: jmchilton Date: 2014-07-31 03:30:00 Summary: Merge default sqlite datatype improvements into next-stable. Not quite a bug fix per se, but this more testing/robustness for code in next release so I think it belonds in next-stable (certainly not a new feature at any rate). Affected #: 3 files diff -r 1621b66460e0533de4ee155bf23a5f0fabb43e40 -r a12359ac3a8a90f6402f4ec36eb707aa6c5e866f lib/galaxy/datatypes/dataproviders/dataset.py --- a/lib/galaxy/datatypes/dataproviders/dataset.py +++ b/lib/galaxy/datatypes/dataproviders/dataset.py @@ -11,7 +11,7 @@ import line import column import external -import sqlite3 +from galaxy.util import sqlite import re from galaxy import eggs @@ -704,35 +704,23 @@ super( BGzipTabixDataProvider, self ).__init__( dataset, **kwargs ) - -class SQliteDataProvider ( base.DataProvider ): +class SQliteDataProvider( base.DataProvider ): """ Data provider that uses a sqlite database file as its source. Allows any query to be run and returns the resulting rows as sqlite3 row objects """ settings = { - 'query' : 'str' + 'query': 'str' } def __init__( self, source, query=None, **kwargs ): - self.query=query - self.connection = sqlite3.connect(source.dataset.file_name); - self.connection.row_factory = sqlite3.Row + self.query = query + self.connection = sqlite.connect(source.dataset.file_name) super( SQliteDataProvider, self ).__init__( source, **kwargs ) - def query_matches_whitelist(self,query): - if re.match("select ",query,re.IGNORECASE): - if re.search("^([^\"]|\"[^\"]*\")*?;",query) or re.search("^([^\']|\'[^\']*\')*?;",query): - return False - else: - return True - return False - - - def __iter__( self ): - if (self.query is not None) and self.query_matches_whitelist(self.query): + if (self.query is not None) and sqlite.is_read_only_query(self.query): for row in self.connection.cursor().execute(self.query): yield row else: diff -r 1621b66460e0533de4ee155bf23a5f0fabb43e40 -r a12359ac3a8a90f6402f4ec36eb707aa6c5e866f lib/galaxy/util/sqlite.py --- /dev/null +++ b/lib/galaxy/util/sqlite.py @@ -0,0 +1,32 @@ +import sqlite3 +import re + +try: + import sqlparse + def is_read_only_query(query): + statements = sqlparse.parse(query) + for statement in statements: + if statement.get_type() != "SELECT": + return False + return True + +except ImportError: + # Without sqlparse we use a very weak regex check + def is_read_only_query(query): + if re.match("select ", query, re.IGNORECASE): + if re.search("^([^\"]|\"[^\"]*\")*?;", query) or re.search("^([^\']|\'[^\']*\')*?;", query): + return False + else: + return True + return False + + + + + +def connect(path): + connection = sqlite3.connect(path) + connection.row_factory = sqlite3.Row + return connection + + diff -r 1621b66460e0533de4ee155bf23a5f0fabb43e40 -r a12359ac3a8a90f6402f4ec36eb707aa6c5e866f test/unit/test_sqlite_utils.py --- /dev/null +++ b/test/unit/test_sqlite_utils.py @@ -0,0 +1,60 @@ +from galaxy.util import sqlite + + +def test_query_whitelisting(): + __assert_whitelisted("SELECT * from FOO") + __assert_whitelisted("SELECT f.col1, f.col2 from FOO as f") + __assert_whitelisted("SELECT f.col1, b.col2 from FOO as f inner join BAR as b on f.id = b.foo_id") + __assert_not_whitelisted("UPDATE FOO SET foo=6") + __assert_not_whitelisted("TRUNCATE FOO") + + +def test_sqlite_exploits(): + # This is not really testing any Galaxy code, just experimenting with ways + # to attempt to exploit sqlite3 connections. + + # More info... + # http://atta.cked.me/home/sqlite3injectioncheatsheet + + connection = sqlite.connect(":memory:") + connection.execute("create TABLE FOO (foo1 text)") + __assert_has_n_rows(connection, "select * from FOO", 0) + __assert_query_errors(connection, "select * from FOOX") + + # Make sure sqlite query cannot execute multiple statements + __assert_query_errors(connection, "select * from FOO; select * from FOO") + + # Make sure sqlite cannot select on PRAGMA results + __assert_query_errors(connection, "select * from (PRAGMA database_list)") + + __assert_has_n_rows(connection, "select * from FOO where foo1 in (SELECT foo1 from FOO)", 0) + # Ensure nested queries cannot modify database. + __assert_query_errors(connection, "select * from FOO where foo1 in (INSERT INTO FOO VALUES ('bar')") + + # Should access to the schema be blacklisted? + # __assert_has_n_rows(connection, "select * from SQLITE_MASTER", 0) + + +def __assert_has_n_rows(connection, query, n): + count = 0 + for row in connection.cursor().execute(query): + count += 1 + assert count == n + + +def __assert_query_errors(connection, query): + exception = False + try: + for row in connection.cursor().execute(query): + pass + except Exception: + exception = True + assert exception + + +def __assert_whitelisted( query ): + assert sqlite.is_read_only_query(query), "Query [%s] fails whitelist." % query + + +def __assert_not_whitelisted( query ): + assert not sqlite.is_read_only_query(query), "Query [%s] incorrectly fails whitelist." % query Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 30 Jul '14

30 Jul '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1621b66460e0/ Changeset: 1621b66460e0 Branch: next-stable User: davebgx Date: 2014-07-30 20:12:40 Summary: Fix the tool shed URL for tools that have been installed from a tool shed using a proxy prefix. Affected #: 1 file diff -r 60419c47c22f23bee6545f8feaf31d14bc6eefe7 -r 1621b66460e0533de4ee155bf23a5f0fabb43e40 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -79,6 +79,9 @@ def get_sharable_url( self, app ): tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, self.tool_shed ) if tool_shed_url: + # Append a slash to the tool shed URL, because urlparse.urljoin will eliminate + # the last part of a URL if it does not end with a forward slash. + tool_shed_url = '%s/' % tool_shed_url return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) return tool_shed_url https://bitbucket.org/galaxy/galaxy-central/commits/03350a21700c/ Changeset: 03350a21700c User: davebgx Date: 2014-07-30 20:13:07 Summary: Merge with 1621b66460e0533de4ee155bf23a5f0fabb43e40 Affected #: 1 file diff -r 42b8dd13c021b3500e0ebfd416ee2267c28b47a2 -r 03350a21700c83d042a952d82387bb295c25fb73 lib/galaxy/model/tool_shed_install/__init__.py --- a/lib/galaxy/model/tool_shed_install/__init__.py +++ b/lib/galaxy/model/tool_shed_install/__init__.py @@ -79,6 +79,9 @@ def get_sharable_url( self, app ): tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( app, self.tool_shed ) if tool_shed_url: + # Append a slash to the tool shed URL, because urlparse.urljoin will eliminate + # the last part of a URL if it does not end with a forward slash. + tool_shed_url = '%s/' % tool_shed_url return urljoin( tool_shed_url, 'view/%s/%s' % ( self.owner, self.name ) ) return tool_shed_url 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.

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