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commit/galaxy-central: dannon: Remove import *, fix a docstring in actions/admin
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7904535003f/ changeset: f7904535003f user: dannon date: 2013-03-05 22:10:45 summary: Remove import *, fix a docstring in actions/admin affected #: 1 file diff -r dde0e4592530c3be40e4464b4347817b25a6aa62 -r f7904535003fdf8e56588fb78ebcdf9af913cc55 lib/galaxy/actions/admin.py --- a/lib/galaxy/actions/admin.py +++ b/lib/galaxy/actions/admin.py @@ -1,9 +1,10 @@ """ Contains administrative functions """ + import logging from galaxy import util -from galaxy.exceptions import * +from galaxy.exceptions import MessageException log = logging.getLogger( __name__ ) @@ -167,12 +168,14 @@ self.sa_session.flush() message += ', '.join( names ) return message - + def _purge_quota( self, quota, params ): - # This method should only be called for a Quota that has previously been deleted. - # Purging a deleted Quota deletes all of the following from the database: - # - UserQuotaAssociations where quota_id == Quota.id - # - GroupQuotaAssociations where quota_id == Quota.id + """ + This method should only be called for a Quota that has previously been deleted. + Purging a deleted Quota deletes all of the following from the database: + - UserQuotaAssociations where quota_id == Quota.id + - GroupQuotaAssociations where quota_id == Quota.id + """ quotas = util.listify( quota ) names = [] for q in quotas: @@ -194,3 +197,4 @@ self.sa_session.flush() message += ', '.join( names ) return message + 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: dannon: Strip dead test code (that actually threw an exception when enabled due to undefined variables).
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dde0e4592530/ changeset: dde0e4592530 user: dannon date: 2013-03-05 22:07:35 summary: Strip dead test code (that actually threw an exception when enabled due to undefined variables). affected #: 1 file diff -r a7814c5352318f5e81d77315bc9fff413673d483 -r dde0e4592530c3be40e4464b4347817b25a6aa62 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py +++ b/lib/galaxy/security/__init__.py @@ -903,26 +903,10 @@ .filter( and_( trans.app.model.DatasetPermissions.dataset_id.in_( dataset_ids ), trans.app.model.DatasetPermissions.action == self.permitted_actions.DATASET_ACCESS.action ) ) \ .all() - # Every dataset returned has "access" privileges associated with it, # so it's not public. for permission in access_data_perms: datasets_public[ permission.dataset_id ] = False - - # Test code: Check if the results match up with the original: - test_code = False - if test_code: - log.debug( "datasets_are_public test: check datasets_are_public matches dataset_is_public:" ) - test_success = True - for dataset in datasets: - orig_is_public = self.dataset_is_public( dataset ) - if orig_is_public == datasets_public[ dataset.id ]: - log.debug( "\tMatch for dataset %d" % dataset.id ) - else: - success = False - log.error( "\tERROR: Did not match: single is_public: %s; multiple is_public: %s" - % ( single_is_public, datasets_public[ dataset.id ] ) ) - log.debug( "datasets_are_public: test succeeded? %s" % test_success ) return datasets_public 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 05 Mar '13

05 Mar '13

3 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c7fe14570d9a/ changeset: c7fe14570d9a user: dannon date: 2013-03-05 21:58:13 summary: Tools module import cleanup, removal of dead code. affected #: 1 file diff -r 6bc53fd15c629310c425f15e691f23dec4892293 -r c7fe14570d9a3f1823895978efd8e2734489a9a9 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1,47 +1,59 @@ """ Classes encapsulating galaxy tools and tool configuration. """ -import pkg_resources -pkg_resources.require( "simplejson" ) -pkg_resources.require( "MarkupSafe" ) #MarkupSafe must load before mako -pkg_resources.require( "Mako" ) +import binascii +import glob +import logging +import os +import pipes +import re +import shutil +import sys +import tempfile +import traceback +import types +import urllib -import logging, os, string, sys, tempfile, glob, shutil, types, urllib, subprocess, random, math, traceback, re, pipes +from galaxy import eggs +eggs.require( "simplejson" ) +eggs.require( "MarkupSafe" ) #MarkupSafe must load before mako +eggs.require( "Mako" ) + import simplejson -import binascii +from cgi import FieldStorage +from elementtree import ElementTree from mako.template import Template -from UserDict import DictMixin -from galaxy.util.odict import odict -from galaxy.util.bunch import Bunch -from galaxy.util.template import fill_template -from galaxy import util, jobs, model +from paste import httpexceptions +from sqlalchemy import and_ +from copy import deepcopy + +from galaxy import jobs, model +from galaxy.datatypes.metadata import JobExternalOutputMetadataWrapper from galaxy.jobs import ParallelismInfo -from copy import deepcopy -from elementtree import ElementTree -from parameters import * -from parameters.grouping import * -from parameters.output import ToolOutputActionGroup -from parameters.validation import LateValidationError -from parameters.input_translation import ToolInputTranslator -from galaxy.util.expressions import ExpressionContext -from galaxy.tools.test import ToolTestBuilder from galaxy.tools.actions import DefaultToolAction from galaxy.tools.actions.data_manager import DataManagerToolAction from galaxy.tools.deps import DependencyManager -from galaxy.model import directory_hash_id -from galaxy.model.orm import * +from galaxy.tools.parameters import check_param, params_from_strings, params_to_strings +from galaxy.tools.parameters.basic import (BaseURLToolParameter, + DataToolParameter, HiddenToolParameter, LibraryDatasetToolParameter, + SelectToolParameter, ToolParameter, UnvalidatedValue, + IntegerToolParameter, FloatToolParameter) +from galaxy.tools.parameters.grouping import Conditional, ConditionalWhen, Repeat, UploadDataset +from galaxy.tools.parameters.input_translation import ToolInputTranslator +from galaxy.tools.parameters.output import ToolOutputActionGroup +from galaxy.tools.parameters.validation import LateValidationError +from galaxy.tools.test import ToolTestBuilder +from galaxy.util import isinf, listify, parse_xml, rst_to_html, string_as_bool, string_to_object, xml_text, xml_to_string +from galaxy.util.bunch import Bunch +from galaxy.util.expressions import ExpressionContext +from galaxy.util.hash_util import hmac_new from galaxy.util.none_like import NoneDataset -from galaxy.datatypes import sniff -from cgi import FieldStorage -from galaxy.util.hash_util import * -from galaxy.util import listify -import tool_shed.util.shed_util_common +from galaxy.util.odict import odict +from galaxy.util.template import fill_template +from galaxy.visualization.genome.visual_analytics import TracksterConfig from galaxy.web import url_for - -from paste import httpexceptions - -from galaxy.visualization.genome.visual_analytics import TracksterConfig +from tool_shed.util import shed_util_common log = logging.getLogger( __name__ ) @@ -147,7 +159,7 @@ self.sa_session.query( self.app.model.ToolTagAssociation ).delete() self.sa_session.flush() log.info( "Parsing the tool configuration %s" % config_filename ) - tree = util.parse_xml( config_filename ) + tree = parse_xml( config_filename ) root = tree.getroot() tool_path = root.get( 'tool_path' ) if tool_path: @@ -234,7 +246,7 @@ elif key.startswith( 'label_' ): self.tool_panel[ key ] = val elif key.startswith( 'section_' ): - elem = Element( 'section' ) + elem = ElementTree.Element( 'section' ) elem.attrib[ 'id' ] = val.id or '' elem.attrib[ 'name' ] = val.name or '' elem.attrib[ 'version' ] = val.version or '' @@ -262,7 +274,7 @@ be reset when the various tool panel config files are parsed, at which time the tools and workflows are loaded. """ - tree = util.parse_xml( self.integrated_tool_panel_config ) + tree = parse_xml( self.integrated_tool_panel_config ) root = tree.getroot() for elem in root: if elem.tag == 'tool': @@ -291,7 +303,7 @@ def write_integrated_tool_panel_config_file( self ): """ Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators - use this file to manage the tool panel, we'll not use util.xml_to_string() since it doesn't write XML quite right. + use this file to manage the tool panel, we'll not use xml_to_string() since it doesn't write XML quite right. """ fd, filename = tempfile.mkstemp() os.write( fd, '<?xml version="1.0"?>\n' ) @@ -457,7 +469,7 @@ # the tool if it's it was not found in self.tools_by_id, but performing that check did not enable this scenario. self.tools_by_id[ tool.id ] = tool if load_panel_dict: - self.__add_tool_to_tool_panel( tool.id, panel_dict, section=isinstance( panel_dict, galaxy.tools.ToolSection ) ) + self.__add_tool_to_tool_panel( tool.id, panel_dict, section=isinstance( panel_dict, ToolSection ) ) # Always load the tool into the integrated_panel_dict, or it will not be included in the integrated_tool_panel.xml file. if key in integrated_panel_dict or index is None: integrated_panel_dict[ key ] = tool @@ -707,7 +719,7 @@ return rval def _load_and_preprocess_tool_xml(self, config_file): - tree = util.parse_xml(config_file) + tree = parse_xml(config_file) root = tree.getroot() macros_el = root.find('macros') if not macros_el: @@ -779,7 +791,7 @@ return macros def _load_macro_file(self, path, tool_dir): - tree = util.parse_xml(path) + tree = parse_xml(path) root = tree.getroot() return self._load_macros(root, tool_dir) @@ -848,7 +860,7 @@ """ Keeps track of the state of a users interaction with a tool between requests. The default tool state keeps track of the current page (for - multipage "wizard" tools) and the values of all parameters. + multipage "wizard" tools) and the values of all """ def __init__( self ): self.page = 0 @@ -968,7 +980,7 @@ self.input_required = False self.display_interface = True self.require_login = False - # Define a place to keep track of all input parameters. These + # Define a place to keep track of all input These # differ from the inputs dictionary in that inputs can be page # elements like conditionals, but input_params are basic form # parameters like SelectField objects. This enables us to more @@ -1018,7 +1030,7 @@ def tool_shed_repository( self ): # If this tool is included in an installed tool shed repository, return it. if self.tool_shed: - return tool_shed.util.shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, + return shed_util_common.get_tool_shed_repository_by_shed_name_owner_installed_changeset_revision( self.app, self.tool_shed, self.repository_name, self.repository_owner, @@ -1094,13 +1106,13 @@ # For backward compatibility, some tools may not have versions yet. self.version = "1.0.0" # Support multi-byte tools - self.is_multi_byte = util.string_as_bool( root.get( "is_multi_byte", False ) ) + self.is_multi_byte = string_as_bool( root.get( "is_multi_byte", False ) ) # Force history to fully refresh after job execution for this tool. # Useful i.e. when an indeterminate number of outputs are created by # a tool. - self.force_history_refresh = util.string_as_bool( root.get( 'force_history_refresh', 'False' ) ) - self.display_interface = util.string_as_bool( root.get( 'display_interface', str( self.display_interface ) ) ) - self.require_login = util.string_as_bool( root.get( 'require_login', str( self.require_login ) ) ) + self.force_history_refresh = string_as_bool( root.get( 'force_history_refresh', 'False' ) ) + self.display_interface = string_as_bool( root.get( 'display_interface', str( self.display_interface ) ) ) + self.require_login = string_as_bool( root.get( 'require_login', str( self.require_login ) ) ) # Load input translator, used by datasource tools to change names/values of incoming parameters self.input_translator = root.find( "request_param_translation" ) if self.input_translator: @@ -1125,7 +1137,7 @@ else: self.redirect_url_params = '' # Short description of the tool - self.description = util.xml_text(root, "description") + self.description = xml_text(root, "description") # Versioning for tools self.version_string_cmd = None version_cmd = root.find("version_command") @@ -1155,8 +1167,8 @@ if 'job_config' in dir(self.app): self.job_tool_configurations = self.app.job_config.get_job_tool_configurations(self_ids) # Is this a 'hidden' tool (hidden in tool menu) - self.hidden = util.xml_text(root, "hidden") - if self.hidden: self.hidden = util.string_as_bool(self.hidden) + self.hidden = xml_text(root, "hidden") + if self.hidden: self.hidden = string_as_bool(self.hidden) # Load any tool specific code (optional) Edit: INS 5/29/2007, # allow code files to have access to the individual tool's # "module" if it has one. Allows us to reuse code files, etc. @@ -1175,7 +1187,7 @@ for option_elem in root.findall("options"): for option, value in self.options.copy().items(): if isinstance(value, type(False)): - self.options[option] = util.string_as_bool(option_elem.get(option, str(value))) + self.options[option] = string_as_bool(option_elem.get(option, str(value))) else: self.options[option] = option_elem.get(option, str(value)) self.options = Bunch(** self.options) @@ -1243,8 +1255,8 @@ enctypes = set() if input_elem: # Handle properties of the input form - self.check_values = util.string_as_bool( input_elem.get("check_values", self.check_values ) ) - self.nginx_upload = util.string_as_bool( input_elem.get( "nginx_upload", self.nginx_upload ) ) + 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 ) ) self.action = input_elem.get( 'action', self.action ) # If we have an nginx upload, save the action as a tuple instead of # a string. The actual action needs to get url_for run to add any @@ -1283,7 +1295,7 @@ else: raise Exception, "Conflicting required enctypes: %s" % str( enctypes ) # Check if the tool either has no parameters or only hidden (and - # thus hardcoded) parameters. FIXME: hidden parameters aren't + # thus hardcoded) FIXME: hidden parameters aren't # parameters at all really, and should be passed in a different # way, making this check easier. for param in self.inputs.values(): @@ -1305,7 +1317,7 @@ help_pages = self.help.findall( "page" ) help_header = self.help.text try: - self.help = Template( util.rst_to_html(self.help.text), input_encoding='utf-8', + self.help = Template( rst_to_html(self.help.text), input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) except: @@ -1317,7 +1329,7 @@ help_footer = help_footer + help_page.tail # Each page has to rendered all-together because of backreferences allowed by rst try: - self.help_by_page = [ Template( util.rst_to_html( help_header + x + help_footer, + self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) @@ -1342,11 +1354,11 @@ output.format_source = data_elem.get("format_source", None) output.metadata_source = data_elem.get("metadata_source", "") output.parent = data_elem.get("parent", None) - output.label = util.xml_text( data_elem, "label" ) + output.label = xml_text( data_elem, "label" ) output.count = int( data_elem.get("count", 1) ) output.filters = data_elem.findall( 'filter' ) output.from_work_dir = data_elem.get("from_work_dir", None) - output.hidden = util.string_as_bool( data_elem.get("hidden", "") ) + output.hidden = string_as_bool( data_elem.get("hidden", "") ) output.tool = self output.actions = ToolOutputActionGroup( output, data_elem.find( 'actions' ) ) self.outputs[ output.name ] = output @@ -1370,7 +1382,7 @@ for stdio_elem in ( root.findall( 'stdio' ) ): self.parse_stdio_exit_codes( stdio_elem ) self.parse_stdio_regexes( stdio_elem ) - except Exception, e: + except Exception: log.error( "Exception in parse_stdio! " + str(sys.exc_info()) ) def parse_stdio_exit_codes( self, stdio_elem ): @@ -1397,7 +1409,7 @@ self.parse_error_level( exit_code_elem.get( "level" ))) code_range = exit_code_elem.get( "range", "" ) if None == code_range: - code_range = code_elem.get( "value", "" ) + code_range = exit_code_elem.get( "value", "" ) if None == code_range: log.warning( "Tool stdio exit codes must have " + "a range or value" ) @@ -1441,12 +1453,12 @@ # isn't bogus. If we have two infinite values, then # the start must be -inf and the end must be +inf. # So at least warn about this situation: - if ( util.isinf( exit_code.range_start ) and - util.isinf( exit_code.range_end ) ): + if ( isinf( exit_code.range_start ) and + isinf( exit_code.range_end ) ): log.warning( "Tool exit_code range %s will match on " + "all exit codes" % code_range ) self.stdio_exit_codes.append( exit_code ) - except Exception, e: + except Exception: log.error( "Exception in parse_stdio_exit_codes! " + str(sys.exc_info()) ) trace = sys.exc_info()[2] @@ -1514,7 +1526,7 @@ regex.stdout_match = True regex.stderr_match = True self.stdio_regexes.append( regex ) - except Exception, e: + except Exception: log.error( "Exception in parse_stdio_exit_codes! " + str(sys.exc_info()) ) trace = sys.exc_info()[2] @@ -1539,7 +1551,7 @@ return_level = StdioErrorLevel.FATAL else: log.debug( "Error level %s did not match warning/fatal" % err_level ) - except Exception, e: + except Exception: log.error( "Exception in parse_error_level " + str(sys.exc_info() ) ) trace = sys.exc_info()[2] @@ -1636,7 +1648,7 @@ attributes['lines_diff'] = int( attrib.pop( 'lines_diff', '0' ) ) # Allow a file size to vary if sim_size compare attributes['delta'] = int( attrib.pop( 'delta', '10000' ) ) - attributes['sort'] = util.string_as_bool( attrib.pop( 'sort', False ) ) + attributes['sort'] = string_as_bool( attrib.pop( 'sort', False ) ) attributes['extra_files'] = [] attributes['assert_list'] = assert_list if 'ftype' in attrib: @@ -1654,7 +1666,7 @@ extra_attributes['compare'] = extra.get( 'compare', 'diff' ).lower() extra_attributes['delta'] = extra.get( 'delta', '0' ) extra_attributes['lines_diff'] = int( extra.get( 'lines_diff', '0' ) ) - extra_attributes['sort'] = util.string_as_bool( extra.get( 'sort', False ) ) + extra_attributes['sort'] = string_as_bool( extra.get( 'sort', False ) ) attributes['extra_files'].append( ( extra_type, extra_value, extra_name, extra_attributes ) ) test.add_output( name, file, attributes ) except Exception, e: @@ -1671,7 +1683,7 @@ # Display display_elem = input_elem.find("display") if display_elem is not None: - display = util.xml_to_string(display_elem) + display = xml_to_string(display_elem) else: display = None return display, inputs @@ -1704,7 +1716,7 @@ group = Conditional() group.name = elem.get( "name" ) group.value_ref = elem.get( 'value_ref', None ) - group.value_ref_in_group = util.string_as_bool( elem.get( 'value_ref_in_group', 'True' ) ) + group.value_ref_in_group = string_as_bool( elem.get( 'value_ref_in_group', 'True' ) ) value_from = elem.get( "value_from" ) if value_from: value_from = value_from.split( ':' ) @@ -1789,7 +1801,7 @@ self.requirements """ for requirement_elem in requirements_elem.findall( 'requirement' ): - name = util.xml_text( requirement_elem ) + name = xml_text( requirement_elem ) type = requirement_elem.get( "type", "package" ) version = requirement_elem.get( "version", None ) requirement = ToolRequirement( name=name, type=type, version=version ) @@ -1807,7 +1819,7 @@ # right now if self.tool_type.startswith( 'data_source' ): return False - if not util.string_as_bool( root.get( "workflow_compatible", "True" ) ): + if not string_as_bool( root.get( "workflow_compatible", "True" ) ): return False # TODO: Anyway to capture tools that dynamically change their own # outputs? @@ -1873,7 +1885,7 @@ """ Call the function `callback` on each parameter of this tool. Visits grouping parameters recursively and constructs unique prefixes for - each nested set of parameters. The callback method is then called as: + each nested set of The callback method is then called as: `callback( level_prefix, parameter, parameter_value )` """ @@ -1894,7 +1906,7 @@ """ # Get the state or create if not found if "tool_state" in incoming: - encoded_state = util.string_to_object( incoming["tool_state"] ) + encoded_state = string_to_object( incoming["tool_state"] ) state = DefaultToolState() state.decode( encoded_state, self, trans.app ) else: @@ -1911,7 +1923,7 @@ # Process incoming data if not( self.check_values ): # If `self.check_values` is false we don't do any checking or - # processing on input parameters. This is used to pass raw values + # processing on input This is used to pass raw values # through to/from external sites. FIXME: This should be handled # more cleanly, there is no reason why external sites need to # post back to the same URL that the tool interface uses. @@ -2225,7 +2237,7 @@ """ params = [] for input_param in self.input_params: - if isinstance( input_param, basic.SelectToolParameter ) and input_param.is_dynamic: + if isinstance( input_param, SelectToolParameter ) and input_param.is_dynamic: options = input_param.options if options and options.missing_tool_data_table_name and input_param not in params: params.append( input_param ) @@ -2238,7 +2250,7 @@ """ params = [] for input_param in self.input_params: - if isinstance( input_param, basic.SelectToolParameter ) and input_param.is_dynamic: + if isinstance( input_param, SelectToolParameter ) and input_param.is_dynamic: options = input_param.options if options and options.missing_index_file and input_param not in params: params.append( input_param ) @@ -2324,12 +2336,12 @@ else: # Regular tool parameter, no recursion needed try: - check_param = True + ck_param = True if allow_workflow_parameters and isinstance( values[ input.name ], basestring ): if WORKFLOW_PARAMETER_REGULAR_EXPRESSION.search( values[ input.name ] ): - check_param = False + ck_param = False #this will fail when a parameter's type has changed to a non-compatible one: e.g. conditional group changed to dataset input - if check_param: + if ck_param: input.value_from_basic( input.value_to_basic( values[ input.name ], trans.app ), trans.app, ignore_errors=False ) except: messages[ input.name ] = "Value no longer valid for '%s%s', replaced with default" % ( prefix, input.label ) @@ -2381,7 +2393,6 @@ except Exception, e: # Wrap an re-raise any generated error so we can # generate a more informative message - v = input.value_to_display_text( value, self.app ) message = "Failed runtime validation of %s%s (%s)" \ % ( prefix, input.label, e ) raise LateValidationError( message ) @@ -2619,7 +2630,7 @@ command_line = fill_template( self.command, context=param_dict ) # Remove newlines from command line, and any leading/trailing white space command_line = command_line.replace( "\n", " " ).replace( "\r", " " ).strip() - except Exception, e: + except Exception: # Modify exception message to be more clear #e.args = ( 'Error substituting into command line. Params: %r, Command: %s' % ( param_dict, self.command ), ) raise @@ -2822,6 +2833,7 @@ if outdata == dataset: continue # Create new child dataset child_data = child_dataset.copy( parent_id = dataset.id ) + #DBTODO should this be child_data, and not child_dataset here? self.sa_session.add( child_dataset ) self.sa_session.flush() return children @@ -2837,7 +2849,7 @@ line = simplejson.loads( line ) if line.get( 'type' ) == 'new_primary_dataset': new_primary_datasets[ os.path.split( line.get( 'filename' ) )[-1] ] = line - except Exception, e: + except Exception: # This should not be considered an error or warning condition, this file is optional pass # Loop through output file names, looking for generated primary @@ -3117,7 +3129,7 @@ tool_type = 'set_metadata' def exec_after_process( self, app, inp_data, out_data, param_dict, job = None ): for name, dataset in inp_data.iteritems(): - external_metadata = galaxy.datatypes.metadata.JobExternalOutputMetadataWrapper( job ) + external_metadata = JobExternalOutputMetadataWrapper( job ) if external_metadata.external_metadata_set_successfully( dataset, app.model.context ): dataset.metadata.from_JSON_dict( external_metadata.get_output_filenames_by_dataset( dataset, app.model.context ).filename_out ) else: https://bitbucket.org/galaxy/galaxy-central/commits/c95132dc4813/ changeset: c95132dc4813 user: dannon date: 2013-03-05 21:59:06 summary: Fix incorrect addition of child_dataset to sa_session. affected #: 1 file diff -r c7fe14570d9a3f1823895978efd8e2734489a9a9 -r c95132dc4813d1b1bbfd94fcbc2dc3441947d1dd lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2833,8 +2833,7 @@ if outdata == dataset: continue # Create new child dataset child_data = child_dataset.copy( parent_id = dataset.id ) - #DBTODO should this be child_data, and not child_dataset here? - self.sa_session.add( child_dataset ) + self.sa_session.add( child_data ) self.sa_session.flush() return children def collect_primary_datasets( self, output, job_working_directory ): https://bitbucket.org/galaxy/galaxy-central/commits/a7814c535231/ changeset: a7814c535231 user: dannon date: 2013-03-05 21:59:30 summary: Strip whitespace. affected #: 1 file diff -r c95132dc4813d1b1bbfd94fcbc2dc3441947d1dd -r a7814c5352318f5e81d77315bc9fff413673d483 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -61,7 +61,7 @@ # These determine stdio-based error levels from matching on regular expressions # and exit codes. They are meant to be used comparatively, such as showing -# that warning < fatal. This is really meant to just be an enum. +# that warning < fatal. This is really meant to just be an enum. class StdioErrorLevel( object ): NO_ERROR = 0 LOG = 1 @@ -69,9 +69,9 @@ FATAL = 3 MAX = 3 descs = { - NO_ERROR : 'No error', - LOG: 'Log', - WARNING : 'Warning', + NO_ERROR : 'No error', + LOG: 'Log', + WARNING : 'Warning', FATAL : 'Fatal error' } @staticmethod @@ -163,10 +163,10 @@ root = tree.getroot() tool_path = root.get( 'tool_path' ) if tool_path: - # We're parsing a shed_tool_conf file since we have a tool_path attribute. + # We're parsing a shed_tool_conf file since we have a tool_path attribute. parsing_shed_tool_conf = True # Keep an in-memory list of xml elements to enable persistence of the changing tool config. - config_elems = [] + config_elems = [] else: parsing_shed_tool_conf = False # Default to backward compatible config setting. @@ -302,7 +302,7 @@ self.integrated_tool_panel[ key ] = None def write_integrated_tool_panel_config_file( self ): """ - Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators + Write the current in-memory version of the integrated_tool_panel.xml file to disk. Since Galaxy administrators use this file to manage the tool panel, we'll not use xml_to_string() since it doesn't write XML quite right. """ fd, filename = tempfile.mkstemp() @@ -370,7 +370,7 @@ if tool.version == tool_version: return tool #No tool matches by version, simply return the first available tool found - return rval[0] + return rval[0] return None def get_loaded_tools_by_lineage( self, tool_id ): """Get all loaded tools associated by lineage to the tool whose id is tool_id.""" @@ -614,7 +614,7 @@ return message, status def load_workflow( self, workflow_id ): """ - Return an instance of 'Workflow' identified by `id`, + Return an instance of 'Workflow' identified by `id`, which is encoded in the tool panel. """ id = self.app.security.decode_id( workflow_id ) @@ -631,9 +631,9 @@ Returns a SQLAlchemy session """ return self.app.model.context - + def to_dict( self, trans, in_panel=True, trackster=False ): - + def filter_for_panel( item, filters ): """ Filters tool panel elements so that only those that are compatible @@ -648,12 +648,12 @@ if _apply_filter( item, filters[ 'tool' ] ): return item elif isinstance( item, ToolSectionLabel ): - if _apply_filter( item, filters[ 'label' ] ): + if _apply_filter( item, filters[ 'label' ] ): return item elif isinstance( item, ToolSection ): - # Filter section item-by-item. Only show a label if there are + # Filter section item-by-item. Only show a label if there are # non-filtered tools below it. - + if _apply_filter( item, filters[ 'section' ] ): cur_label_key = None tools_under_label = False @@ -666,35 +666,35 @@ else: del filtered_elems[ key ] elif isinstance( section_item, ToolSectionLabel ): - # If there is a label and it does not have tools, + # If there is a label and it does not have tools, # remove it. if ( cur_label_key and not tools_under_label ) or not _apply_filter( section_item, filters[ 'label' ] ): del filtered_elems[ cur_label_key ] - + # Reset attributes for new label. cur_label_key = key tools_under_label = False - - + + # Handle last label. if cur_label_key and not tools_under_label: del filtered_elems[ cur_label_key ] - + # Only return section if there are elements. if len( filtered_elems ) != 0: copy = item.copy() copy.elems = filtered_elems return copy - + return None - - # + + # # Dictify toolbox. - # - + # + if in_panel: panel_elts = [ val for val in self.tool_panel.itervalues() ] - + # Filter if necessary. filters = dict( tool=[ lambda x: not x._is_hidden_for_user( trans.user ) ], section=[], label=[] ) #hidden tools filter if trackster: @@ -705,7 +705,7 @@ if elt: filtered_panel_elts.append( elt ) panel_elts = filtered_panel_elts - + # Produce panel. rval = [] for elt in panel_elts: @@ -826,7 +826,7 @@ self.id = f( elem, 'id' ) self.version = f( elem, 'version' ) self.elems = odict() - + def copy( self ): copy = ToolSection() copy.name = self.name @@ -834,7 +834,7 @@ copy.version = self.version copy.elems = self.elems.copy() return copy - + def to_dict( self, trans, for_link=False ): """ Return a dict that includes section's attributes. """ section_elts = [] @@ -851,16 +851,16 @@ self.text = elem.get( "text" ) self.id = elem.get( "id" ) self.version = elem.get( "version" ) or '' - + def to_dict( self, trans, **kwargs ): """ Return a dict that includes label's attributes. """ return { 'type': 'label', 'id': self.id, 'name': self.text, 'version': self.version } class DefaultToolState( object ): """ - Keeps track of the state of a users interaction with a tool between - requests. The default tool state keeps track of the current page (for - multipage "wizard" tools) and the values of all + Keeps track of the state of a users interaction with a tool between + requests. The default tool state keeps track of the current page (for + multipage "wizard" tools) and the values of all """ def __init__( self ): self.page = 0 @@ -901,10 +901,10 @@ Represents an output datasets produced by a tool. For backward compatibility this behaves as if it were the tuple:: - (format, metadata_source, parent) + (format, metadata_source, parent) """ - def __init__( self, name, format=None, format_source=None, metadata_source=None, + def __init__( self, name, format=None, format_source=None, metadata_source=None, parent=None, label=None, filters = None, actions = None, hidden=False ): self.name = name self.format = format @@ -918,11 +918,11 @@ # Tuple emulation - def __len__( self ): + def __len__( self ): return 3 def __getitem__( self, index ): - if index == 0: + if index == 0: return self.format elif index == 1: return self.metadata_source @@ -933,7 +933,7 @@ def __iter__( self ): return iter( ( self.format, self.metadata_source, self.parent ) ) - + def to_dict( self ): return { 'name': self.name, @@ -954,12 +954,12 @@ class Tool( object ): """ - Represents a computational tool that can be executed through Galaxy. + Represents a computational tool that can be executed through Galaxy. """ - + tool_type = 'default' default_tool_action = DefaultToolAction - + def __init__( self, config_file, root, app, guid=None ): """Load a tool from the config named by `config_file`""" # Determine the full path of the directory where the tool config is @@ -1091,15 +1091,15 @@ """ # Get the (user visible) name of the tool self.name = root.get( "name" ) - if not self.name: + if not self.name: raise Exception, "Missing tool 'name'" - # Get the UNIQUE id for the tool + # Get the UNIQUE id for the tool self.old_id = root.get( "id" ) if guid is None: self.id = self.old_id else: self.id = guid - if not self.id: + if not self.id: raise Exception, "Missing tool 'id'" self.version = root.get( "version" ) if not self.version: @@ -1107,8 +1107,8 @@ self.version = "1.0.0" # Support multi-byte tools self.is_multi_byte = string_as_bool( root.get( "is_multi_byte", False ) ) - # Force history to fully refresh after job execution for this tool. - # Useful i.e. when an indeterminate number of outputs are created by + # Force history to fully refresh after job execution for this tool. + # Useful i.e. when an indeterminate number of outputs are created by # a tool. self.force_history_refresh = string_as_bool( root.get( 'force_history_refresh', 'False' ) ) self.display_interface = string_as_bool( root.get( 'display_interface', str( self.display_interface ) ) ) @@ -1117,7 +1117,7 @@ self.input_translator = root.find( "request_param_translation" ) if self.input_translator: self.input_translator = ToolInputTranslator.from_element( self.input_translator ) - # Command line (template). Optional for tools that do not invoke a local program + # Command line (template). Optional for tools that do not invoke a local program command = root.find("command") if command is not None and command.text is not None: self.command = command.text.lstrip() # get rid of leading whitespace @@ -1138,7 +1138,7 @@ self.redirect_url_params = '' # Short description of the tool self.description = xml_text(root, "description") - # Versioning for tools + # Versioning for tools self.version_string_cmd = None version_cmd = root.find("version_command") if version_cmd is not None: @@ -1304,8 +1304,8 @@ break def parse_help( self, root ): """ - Parse the help text for the tool. Formatted in reStructuredText, but - stored as Mako to allow for dynamic image paths. + Parse the help text for the tool. Formatted in reStructuredText, but + stored as Mako to allow for dynamic image paths. This implementation supports multiple pages. """ # TODO: Allow raw HTML or an external link. @@ -1329,15 +1329,15 @@ help_footer = help_footer + help_page.tail # Each page has to rendered all-together because of backreferences allowed by rst try: - self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, - input_encoding='utf-8', output_encoding='utf-8', + self.help_by_page = [ Template( rst_to_html( help_header + x + help_footer, + input_encoding='utf-8', output_encoding='utf-8', default_filters=[ 'decode.utf8' ], encoding_errors='replace' ) ) for x in self.help_by_page ] except: log.exception( "error in multi-page help for tool %s" % self.name ) # Pad out help pages to match npages ... could this be done better? - while len( self.help_by_page ) < self.npages: + while len( self.help_by_page ) < self.npages: self.help_by_page.append( self.help ) def parse_outputs( self, root ): """ @@ -1366,18 +1366,18 @@ # TODO: Include the tool's name in any parsing warnings. def parse_stdio( self, root ): """ - Parse <stdio> element(s) and fill in self.return_codes, - self.stderr_rules, and self.stdout_rules. Return codes have a range - and an error type (fault or warning). Stderr and stdout rules have + Parse <stdio> element(s) and fill in self.return_codes, + self.stderr_rules, and self.stdout_rules. Return codes have a range + and an error type (fault or warning). Stderr and stdout rules have a regular expression and an error level (fault or warning). """ try: self.stdio_exit_codes = list() self.stdio_regexes = list() - # We should have a single <stdio> element, but handle the case for - # multiples. - # For every stdio element, add all of the exit_code and regex + # We should have a single <stdio> element, but handle the case for + # multiples. + # For every stdio element, add all of the exit_code and regex # subelements that we find: for stdio_elem in ( root.findall( 'stdio' ) ): self.parse_stdio_exit_codes( stdio_elem ) @@ -1388,12 +1388,12 @@ def parse_stdio_exit_codes( self, stdio_elem ): """ Parse the tool's <stdio> element's <exit_code> subelements. - This will add all of those elements, if any, to self.stdio_exit_codes. + This will add all of those elements, if any, to self.stdio_exit_codes. """ try: - # Look for all <exit_code> elements. Each exit_code element must + # Look for all <exit_code> elements. Each exit_code element must # have a range/value. - # Exit-code ranges have precedence over a single exit code. + # Exit-code ranges have precedence over a single exit code. # So if there are value and range attributes, we use the range # attribute. If there is neither a range nor a value, then print # a warning and skip to the next. @@ -1404,7 +1404,7 @@ exit_code.desc = exit_code_elem.get( "desc" ) if None == exit_code.desc: exit_code.desc = exit_code_elem.get( "description" ) - # Parse the error level: + # Parse the error level: exit_code.error_level = ( self.parse_error_level( exit_code_elem.get( "level" ))) code_range = exit_code_elem.get( "range", "" ) @@ -1417,20 +1417,20 @@ # Parse the range. We look for: # :Y # X: - # X:Y - Split on the colon. We do not allow a colon - # without a beginning or end, though we could. + # X:Y - Split on the colon. We do not allow a colon + # without a beginning or end, though we could. # Also note that whitespace is eliminated. - # TODO: Turn this into a single match - it should be + # TODO: Turn this into a single match - it should be # more efficient. code_range = re.sub( "\s", "", code_range ) code_ranges = re.split( ":", code_range ) if ( len( code_ranges ) == 2 ): if ( None == code_ranges[0] or '' == code_ranges[0] ): - exit_code.range_start = float( "-inf" ) + exit_code.range_start = float( "-inf" ) else: exit_code.range_start = int( code_ranges[0] ) if ( None == code_ranges[1] or '' == code_ranges[1] ): - exit_code.range_end = float( "inf" ) + exit_code.range_end = float( "inf" ) else: exit_code.range_end = int( code_ranges[1] ) # If we got more than one colon, then ignore the exit code. @@ -1448,48 +1448,48 @@ log.warning( "Invalid range start for tool's exit_code %s: exit_code ignored" % code_range ) continue exit_code.range_end = exit_code.range_start - # TODO: Check if we got ">", ">=", "<", or "<=": - # Check that the range, regardless of how we got it, - # isn't bogus. If we have two infinite values, then - # the start must be -inf and the end must be +inf. + # TODO: Check if we got ">", ">=", "<", or "<=": + # Check that the range, regardless of how we got it, + # isn't bogus. If we have two infinite values, then + # the start must be -inf and the end must be +inf. # So at least warn about this situation: - if ( isinf( exit_code.range_start ) and + if ( isinf( exit_code.range_start ) and isinf( exit_code.range_end ) ): log.warning( "Tool exit_code range %s will match on " + "all exit codes" % code_range ) self.stdio_exit_codes.append( exit_code ) except Exception: - log.error( "Exception in parse_stdio_exit_codes! " + log.error( "Exception in parse_stdio_exit_codes! " + str(sys.exc_info()) ) trace = sys.exc_info()[2] if ( None != trace ): trace_msg = repr( traceback.format_tb( trace ) ) - log.error( "Traceback: %s" % trace_msg ) + log.error( "Traceback: %s" % trace_msg ) def parse_stdio_regexes( self, stdio_elem ): - """ + """ Look in the tool's <stdio> elem for all <regex> subelements - that define how to look for warnings and fatal errors in + that define how to look for warnings and fatal errors in stdout and stderr. This will add all such regex elements to the Tols's stdio_regexes list. """ try: # Look for every <regex> subelement. The regular expression - # will have "match" and "source" (or "src") attributes. + # will have "match" and "source" (or "src") attributes. for regex_elem in ( stdio_elem.findall( "regex" ) ): # TODO: Fill in ToolStdioRegex - regex = ToolStdioRegex() + regex = ToolStdioRegex() # Each regex has an optional description that can be # part of the "desc" or "description" attributes: regex.desc = regex_elem.get( "desc" ) if None == regex.desc: regex.desc = regex_elem.get( "description" ) - # Parse the error level - regex.error_level = ( + # Parse the error level + regex.error_level = ( self.parse_error_level( regex_elem.get( "level" ) ) ) regex.match = regex_elem.get( "match", "" ) if None == regex.match: - # TODO: Convert the offending XML element to a string + # TODO: Convert the offending XML element to a string log.warning( "Ignoring tool's stdio regex element %s - " "the 'match' attribute must exist" ) continue @@ -1506,7 +1506,7 @@ if None == output_srcs: output_srcs = "output,error" output_srcs = re.sub( "\s", "", output_srcs ) - src_list = re.split( ",", output_srcs ) + src_list = re.split( ",", output_srcs ) # Just put together anything to do with "out", including # "stdout", "output", etc. Repeat for "stderr", "error", # and anything to do with "err". If neither stdout nor @@ -1527,12 +1527,12 @@ regex.stderr_match = True self.stdio_regexes.append( regex ) except Exception: - log.error( "Exception in parse_stdio_exit_codes! " + log.error( "Exception in parse_stdio_exit_codes! " + str(sys.exc_info()) ) trace = sys.exc_info()[2] if ( None != trace ): trace_msg = repr( traceback.format_tb( trace ) ) - log.error( "Traceback: %s" % trace_msg ) + log.error( "Traceback: %s" % trace_msg ) # TODO: This method doesn't have to be part of the Tool class. def parse_error_level( self, err_level ): @@ -1540,24 +1540,24 @@ Parses error level and returns error level enumeration. If unparsable, returns 'fatal' """ - return_level = StdioErrorLevel.FATAL + return_level = StdioErrorLevel.FATAL try: if err_level: if ( re.search( "log", err_level, re.IGNORECASE ) ): return_level = StdioErrorLevel.LOG elif ( re.search( "warning", err_level, re.IGNORECASE ) ): - return_level = StdioErrorLevel.WARNING + return_level = StdioErrorLevel.WARNING elif ( re.search( "fatal", err_level, re.IGNORECASE ) ): return_level = StdioErrorLevel.FATAL else: log.debug( "Error level %s did not match warning/fatal" % err_level ) except Exception: - log.error( "Exception in parse_error_level " + log.error( "Exception in parse_error_level " + str(sys.exc_info() ) ) trace = sys.exc_info()[2] if ( None != trace ): trace_msg = repr( traceback.format_tb( trace ) ) - log.error( "Traceback: %s" % trace_msg ) + log.error( "Traceback: %s" % trace_msg ) return return_level def parse_tests( self, tests_elem ): @@ -1566,9 +1566,9 @@ store in `self.tests`. """ self.tests = [] - # Composite datasets need a unique name: each test occurs in a fresh + # Composite datasets need a unique name: each test occurs in a fresh # history, but we'll keep it unique per set of tests - composite_data_names_counter = 0 + composite_data_names_counter = 0 for i, test_elem in enumerate( tests_elem.findall( 'test' ) ): name = test_elem.get( 'name', 'Test-%d' % (i+1) ) maxseconds = int( test_elem.get( 'maxseconds', '120' ) ) @@ -1584,20 +1584,20 @@ value = None attrib['children'] = list( param_elem.getchildren() ) if attrib['children']: - # At this time, we can assume having children only - # occurs on DataToolParameter test items but this could - # change and would cause the below parsing to change + # At this time, we can assume having children only + # occurs on DataToolParameter test items but this could + # change and would cause the below parsing to change # based upon differences in children items attrib['metadata'] = [] attrib['composite_data'] = [] attrib['edit_attributes'] = [] # Composite datasets need to be renamed uniquely - composite_data_name = None + composite_data_name = None for child in attrib['children']: if child.tag == 'composite_data': attrib['composite_data'].append( child ) if composite_data_name is None: - # Generate a unique name; each test uses a + # Generate a unique name; each test uses a # fresh history composite_data_name = '_COMPOSITE_RENAMED_%i_' \ % ( composite_data_names_counter ) @@ -1609,10 +1609,10 @@ elif child.tag == 'edit_attributes': attrib['edit_attributes'].append( child ) if composite_data_name: - # Composite datasets need implicit renaming; - # inserted at front of list so explicit declarations + # Composite datasets need implicit renaming; + # inserted at front of list so explicit declarations # take precedence - attrib['edit_attributes'].insert( 0, { 'type': 'name', 'value': composite_data_name } ) + attrib['edit_attributes'].insert( 0, { 'type': 'name', 'value': composite_data_name } ) test.add_param( attrib.pop( 'name' ), value, attrib ) for output_elem in test_elem.findall( "output" ): attrib = dict( output_elem.attrib ) @@ -1621,8 +1621,8 @@ raise Exception( "Test output does not have a 'name'" ) assert_elem = output_elem.find("assert_contents") assert_list = None - # Trying to keep testing patch as localized as - # possible, this function should be relocated + # Trying to keep testing patch as localized as + # possible, this function should be relocated # somewhere more conventional. def convert_elem(elem): """ Converts and XML element to a dictionary format, used by assertion checking code. """ @@ -1638,34 +1638,34 @@ for assert_child in list(assert_elem): assert_list.append(convert_elem(assert_child)) file = attrib.pop( 'file', None ) - # File no longer required if an list of assertions was present. + # File no longer required if an list of assertions was present. if assert_list is None and file is None: raise Exception( "Test output does not have a 'file'") attributes = {} # Method of comparison - attributes['compare'] = attrib.pop( 'compare', 'diff' ).lower() - # Number of lines to allow to vary in logs (for dates, etc) - attributes['lines_diff'] = int( attrib.pop( 'lines_diff', '0' ) ) + attributes['compare'] = attrib.pop( 'compare', 'diff' ).lower() + # Number of lines to allow to vary in logs (for dates, etc) + attributes['lines_diff'] = int( attrib.pop( 'lines_diff', '0' ) ) # Allow a file size to vary if sim_size compare - attributes['delta'] = int( attrib.pop( 'delta', '10000' ) ) + attributes['delta'] = int( attrib.pop( 'delta', '10000' ) ) attributes['sort'] = string_as_bool( attrib.pop( 'sort', False ) ) attributes['extra_files'] = [] attributes['assert_list'] = assert_list if 'ftype' in attrib: attributes['ftype'] = attrib['ftype'] for extra in output_elem.findall( 'extra_files' ): - # File or directory, when directory, compare basename + # File or directory, when directory, compare basename # by basename - extra_type = extra.get( 'type', 'file' ) + extra_type = extra.get( 'type', 'file' ) extra_name = extra.get( 'name', None ) assert extra_type == 'directory' or extra_name is not None, \ 'extra_files type (%s) requires a name attribute' % extra_type extra_value = extra.get( 'value', None ) assert extra_value is not None, 'extra_files requires a value attribute' extra_attributes = {} - extra_attributes['compare'] = extra.get( 'compare', 'diff' ).lower() - extra_attributes['delta'] = extra.get( 'delta', '0' ) - extra_attributes['lines_diff'] = int( extra.get( 'lines_diff', '0' ) ) + extra_attributes['compare'] = extra.get( 'compare', 'diff' ).lower() + extra_attributes['delta'] = extra.get( 'delta', '0' ) + extra_attributes['lines_diff'] = int( extra.get( 'lines_diff', '0' ) ) extra_attributes['sort'] = string_as_bool( extra.get( 'sort', False ) ) attributes['extra_files'].append( ( extra_type, extra_value, extra_name, extra_attributes ) ) test.add_output( name, file, attributes ) @@ -1689,7 +1689,7 @@ return display, inputs def parse_input_elem( self, parent_elem, enctypes, context=None ): """ - Parse a parent element whose children are inputs -- these could be + Parse a parent element whose children are inputs -- these could be groups (repeat, conditional) or param elements. Groups will be parsed recursively. """ @@ -1706,11 +1706,11 @@ group.default = int( elem.get( "default", 0 ) ) group.min = int( elem.get( "min", 0 ) ) # Use float instead of int so that 'inf' can be used for no max - group.max = float( elem.get( "max", "inf" ) ) + group.max = float( elem.get( "max", "inf" ) ) assert group.min <= group.max, \ ValueError( "Min repeat count must be less-than-or-equal to the max." ) # Force default to be within min-max range - group.default = min( max( group.default, group.min ), group.max ) + group.default = min( max( group.default, group.min ), group.max ) rval[group.name] = group elif elem.tag == "conditional": group = Conditional() @@ -1729,7 +1729,7 @@ case = ConditionalWhen() case.value = case_value if case_inputs: - case.inputs = self.parse_input_elem( + case.inputs = self.parse_input_elem( ElementTree.XML( "<when>%s</when>" % case_inputs ), enctypes, context ) else: case.inputs = odict() @@ -1751,10 +1751,10 @@ try: possible_cases.remove( case.value ) except: - log.warning( "Tool %s: a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % + log.warning( "Tool %s: a when tag has been defined for '%s (%s) --> %s', but does not appear to be selectable." % ( self.id, group.name, group.test_param.name, case.value ) ) for unspecified_case in possible_cases: - log.warning( "Tool %s: a when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % + log.warning( "Tool %s: a when tag has not been defined for '%s (%s) --> %s', assuming empty inputs." % ( self.id, group.name, group.test_param.name, unspecified_case ) ) case = ConditionalWhen() case.value = unspecified_case @@ -1764,7 +1764,7 @@ elif elem.tag == "upload_dataset": group = UploadDataset() group.name = elem.get( "name" ) - group.title = elem.get( "title" ) + group.title = elem.get( "title" ) group.file_type_name = elem.get( 'file_type_name', group.file_type_name ) group.default_file_type = elem.get( 'default_file_type', group.default_file_type ) group.metadata_ref = elem.get( 'metadata_ref', group.metadata_ref ) @@ -1782,7 +1782,7 @@ return rval def parse_param_elem( self, input_elem, enctypes, context ): """ - Parse a single "<param>" element and return a ToolParameter instance. + Parse a single "<param>" element and return a ToolParameter instance. Also, if the parameter has a 'required_enctype' add it to the set enctypes. """ @@ -1827,8 +1827,8 @@ def new_state( self, trans, all_pages=False ): """ Create a new `DefaultToolState` for this tool. It will be initialized - with default values for inputs. - + with default values for inputs. + Only inputs on the first page will be initialized unless `all_pages` is True, in which case all inputs regardless of page are initialized. """ @@ -1843,17 +1843,17 @@ def fill_in_new_state( self, trans, inputs, state, context=None ): """ Fill in a tool state dictionary with default values for all parameters - in the dictionary `inputs`. Grouping elements are filled in recursively. + in the dictionary `inputs`. Grouping elements are filled in recursively. """ context = ExpressionContext( state, context ) for input in inputs.itervalues(): state[ input.name ] = input.get_initial_value( trans, context ) def get_param_html_map( self, trans, page=0, other_values={} ): """ - Return a dictionary containing the HTML representation of each - parameter. This is used for rendering display elements. It is + Return a dictionary containing the HTML representation of each + parameter. This is used for rendering display elements. It is currently not compatible with grouping constructs. - + NOTE: This should be considered deprecated, it is only used for tools with `display` elements. These should be eliminated. """ @@ -1865,7 +1865,7 @@ return rval def get_param( self, key ): """ - Returns the parameter named `key` or None if there is no such + Returns the parameter named `key` or None if there is no such parameter. """ return self.inputs.get( key, None ) @@ -1886,7 +1886,7 @@ Call the function `callback` on each parameter of this tool. Visits grouping parameters recursively and constructs unique prefixes for each nested set of The callback method is then called as: - + `callback( level_prefix, parameter, parameter_value )` """ # HACK: Yet another hack around check_values -- WHY HERE? @@ -1915,7 +1915,7 @@ # of inputs even when there is no state in the incoming dictionary # by providing either 'runtool_btn' (the name of the submit button # on the standard run form) or "URL" (a parameter provided by - # external data source tools). + # external data source tools). if "runtool_btn" not in incoming and "URL" not in incoming: if not self.display_interface: return 'message.mako', dict( status='info', message="The interface for this tool cannot be displayed", refresh_frames=['everything'] ) @@ -1933,7 +1933,7 @@ # Update state for all inputs on the current page taking new # values from `incoming`. errors = self.update_state( trans, self.inputs_by_page[state.page], state.inputs, incoming, old_errors=old_errors or {} ) - # If the tool provides a `validate_input` hook, call it. + # If the tool provides a `validate_input` hook, call it. validate_input = self.get_hook( 'validate_input' ) if validate_input: validate_input( trans, errors, state.inputs, self.inputs_by_page[state.page] ) @@ -1941,10 +1941,10 @@ # Did the user actually click next / execute or is this just # a refresh? if 'runtool_btn' in incoming or 'URL' in incoming or 'ajax_upload' in incoming: - # If there were errors, we stay on the same page and display + # If there were errors, we stay on the same page and display # error messages if errors: - error_message = "One or more errors were found in the input you provided. The specific errors are marked below." + error_message = "One or more errors were found in the input you provided. The specific errors are marked below." return "tool_form.mako", dict( errors=errors, tool_state=state, incoming=incoming, error_message=error_message ) # If we've completed the last page we can execute the tool elif state.page == self.last_page: @@ -2010,10 +2010,10 @@ log.exception( 'Unable to load precreated dataset (%s) sent in upload form' % id ) continue if trans.user is None and trans.galaxy_session.current_history != data.history: - log.error( 'Got a precreated dataset (%s) but it does not belong to anonymous user\'s current session (%s)' - % ( data.id, trans.galaxy_session.id ) ) + log.error( 'Got a precreated dataset (%s) but it does not belong to anonymous user\'s current session (%s)' + % ( data.id, trans.galaxy_session.id ) ) elif data.history.user != trans.user: - log.error( 'Got a precreated dataset (%s) but it does not belong to current user (%s)' + log.error( 'Got a precreated dataset (%s) but it does not belong to current user (%s)' % ( data.id, trans.user.id ) ) else: data.state = data.states.ERROR @@ -2021,22 +2021,22 @@ self.sa_session.add( data ) self.sa_session.flush() # It's unlikely the user will ever see this. - return 'message.mako', dict( status='error', - message='Your upload was interrupted. If this was uninentional, please retry it.', + return 'message.mako', dict( status='error', + message='Your upload was interrupted. If this was uninentional, please retry it.', refresh_frames=[], cont=None ) def update_state( self, trans, inputs, state, incoming, prefix="", context=None, update_only=False, old_errors={}, item_callback=None ): """ - Update the tool state in `state` using the user input in `incoming`. + Update the tool state in `state` using the user input in `incoming`. This is designed to be called recursively: `inputs` contains the set of inputs being processed, and `prefix` specifies a prefix to add to the name of each input to extract it's value from `incoming`. - + If `update_only` is True, values that are not in `incoming` will not be modified. In this case `old_errors` can be provided, and any errors for parameters which were *not* updated will be preserved. """ - errors = dict() + errors = dict() # Push this level onto the context stack context = ExpressionContext( state, context ) # Iterate inputs and update (recursively) @@ -2045,7 +2045,7 @@ if isinstance( input, Repeat ): group_state = state[input.name] # Create list of empty errors for each previously existing state - group_errors = [ {} for i in range( len( group_state ) ) ] + group_errors = [ {} for i in range( len( group_state ) ) ] group_old_errors = old_errors.get( input.name, None ) any_group_errors = False # Check any removals before updating state -- only one @@ -2062,7 +2062,7 @@ else: group_errors[i] = { '__index__': 'Cannot remove repeat (min size=%i).' % input.min } any_group_errors = True - # Only need to find one that can't be removed due to size, since only + # Only need to find one that can't be removed due to size, since only # one removal is processed at # a time anyway break elif group_old_errors and group_old_errors[i]: @@ -2079,9 +2079,9 @@ else: rep_old_errors = {} rep_errors = self.update_state( trans, - input.inputs, - rep_state, - incoming, + input.inputs, + rep_state, + incoming, prefix=rep_prefix, context=context, update_only=update_only, @@ -2110,8 +2110,8 @@ old_current_case = group_state['__current_case__'] group_prefix = "%s|" % ( key ) # Deal with the 'test' element and see if it's value changed - if input.value_ref and not input.value_ref_in_group: - # We are referencing an existent parameter, which is not + if input.value_ref and not input.value_ref_in_group: + # We are referencing an existent parameter, which is not # part of this group test_param_key = prefix + input.test_param.name else: @@ -2141,10 +2141,10 @@ group_old_errors = dict() else: # Current case has not changed, update children - group_errors = self.update_state( trans, - input.cases[current_case].inputs, + group_errors = self.update_state( trans, + input.cases[current_case].inputs, group_state, - incoming, + incoming, prefix=group_prefix, context=context, update_only=update_only, @@ -2183,9 +2183,9 @@ else: rep_old_errors = {} rep_errors = self.update_state( trans, - input.inputs, - rep_state, - incoming, + input.inputs, + rep_state, + incoming, prefix=rep_prefix, context=context, update_only=update_only, @@ -2224,7 +2224,7 @@ # If a callback was provided, allow it to process the value if item_callback: old_value = state.get( input.name, None ) - value, error = item_callback( trans, key, input, value, error, old_value, context ) + value, error = item_callback( trans, key, input, value, error, old_value, context ) if error: errors[ input.name ] = error state[ input.name ] = value @@ -2245,7 +2245,7 @@ @property def params_with_missing_index_file( self ): """ - Return all parameters that are dynamically generated + Return all parameters that are dynamically generated select lists whose options refer to a missing .loc file. """ params = [] @@ -2257,7 +2257,7 @@ return params def get_static_param_values( self, trans ): """ - Returns a map of parameter names and values if the tool does not + Returns a map of parameter names and values if the tool does not require any user input. Will raise an exception if any parameter does require input. """ @@ -2273,8 +2273,8 @@ def execute( self, trans, incoming={}, set_output_hid=True, history=None, **kwargs ): """ Execute the tool using parameter values in `incoming`. This just - dispatches to the `ToolAction` instance specified by - `self.tool_action`. In general this will create a `Job` that + dispatches to the `ToolAction` instance specified by + `self.tool_action`. In general this will create a `Job` that when run will build the tool's outputs, e.g. `DefaultToolAction`. """ return self.tool_action.execute( self, trans, incoming=incoming, set_output_hid=set_output_hid, history=history, **kwargs ) @@ -2286,7 +2286,7 @@ """ Check that all parameters have values, and fill in with default values where necessary. This could be called after loading values - from a database in case new parameters have been added. + from a database in case new parameters have been added. """ messages = {} self.check_and_update_param_values_helper( self.inputs, values, trans, messages, update_values=update_values, allow_workflow_parameters=allow_workflow_parameters ) @@ -2329,9 +2329,9 @@ messages[ input.test_param.name ] = "No value found for '%s%s', used default" % ( prefix, input.test_param.label ) current_case = group_values['__current_case__'] for child_input in input.cases[current_case].inputs.itervalues(): - messages[ child_input.name ] = "Value no longer valid for '%s%s', replaced with default" % ( prefix, child_input.label ) + messages[ child_input.name ] = "Value no longer valid for '%s%s', replaced with default" % ( prefix, child_input.label ) else: - current = group_values["__current_case__"] + current = group_values["__current_case__"] self.check_and_update_param_values_helper( input.cases[current].inputs, group_values, trans, messages, context, prefix ) else: # Regular tool parameter, no recursion needed @@ -2350,7 +2350,7 @@ def handle_unvalidated_param_values( self, input_values, app ): """ Find any instances of `UnvalidatedValue` within input_values and - validate them (by calling `ToolParameter.from_html` and + validate them (by calling `ToolParameter.from_html` and `ToolParameter.validate`). """ # No validation is done when check_values is False @@ -2363,7 +2363,7 @@ """ context = ExpressionContext( input_values, context ) for input in inputs.itervalues(): - if isinstance( input, Repeat ): + if isinstance( input, Repeat ): for i, d in enumerate( input_values[ input.name ] ): rep_prefix = prefix + "%s %d > " % ( input.title, i + 1 ) self.handle_unvalidated_param_values_helper( input.inputs, d, app, context, rep_prefix ) @@ -2412,8 +2412,8 @@ """ Build the dictionary of parameters for substituting into the command line. Each value is wrapped in a `InputValueWrapper`, which allows - all the attributes of the value to be used in the template, *but* - when the __str__ method is called it actually calls the + all the attributes of the value to be used in the template, *but* + when the __str__ method is called it actually calls the `to_param_dict_string` method of the associated input. """ param_dict = dict() @@ -2426,7 +2426,7 @@ Wraps parameters as neccesary. """ for input in inputs.itervalues(): - if isinstance( input, Repeat ): + if isinstance( input, Repeat ): for d in input_values[ input.name ]: wrap_values( input.inputs, d ) elif isinstance( input, Conditional ): @@ -2438,37 +2438,37 @@ DatasetListWrapper( input_values[ input.name ], datatypes_registry = self.app.datatypes_registry, tool = self, - name = input.name ) + name = input.name ) elif isinstance( input, DataToolParameter ): - ## FIXME: We're populating param_dict with conversions when - ## wrapping values, this should happen as a separate - ## step before wrapping (or call this wrapping step - ## something more generic) (but iterating this same + ## FIXME: We're populating param_dict with conversions when + ## wrapping values, this should happen as a separate + ## step before wrapping (or call this wrapping step + ## something more generic) (but iterating this same ## list twice would be wasteful) # Add explicit conversions by name to current parent for conversion_name, conversion_extensions, conversion_datatypes in input.conversions: - # If we are at building cmdline step, then converters + # If we are at building cmdline step, then converters # have already executed conv_ext, converted_dataset = input_values[ input.name ].find_conversion_destination( conversion_datatypes ) - # When dealing with optional inputs, we'll provide a + # When dealing with optional inputs, we'll provide a # valid extension to be used for None converted dataset if not conv_ext: conv_ext = conversion_extensions[0] - # input_values[ input.name ] is None when optional - # dataset, 'conversion' of optional dataset should + # input_values[ input.name ] is None when optional + # dataset, 'conversion' of optional dataset should # create wrapper around NoneDataset for converter output - if input_values[ input.name ] and not converted_dataset: - # Input that converter is based from has a value, + if input_values[ input.name ] and not converted_dataset: + # Input that converter is based from has a value, # but converted dataset does not exist - raise Exception( 'A path for explicit datatype conversion has not been found: %s --/--> %s' + raise Exception( 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_values[ input.name ].extension, conversion_extensions ) ) else: - # Trick wrapper into using target conv ext (when + # Trick wrapper into using target conv ext (when # None) without actually being a tool parameter input_values[ conversion_name ] = \ DatasetFilenameWrapper( converted_dataset, datatypes_registry = self.app.datatypes_registry, - tool = Bunch( conversion_name = Bunch( extensions = conv_ext ) ), + tool = Bunch( conversion_name = Bunch( extensions = conv_ext ) ), name = conversion_name ) # Wrap actual input dataset input_values[ input.name ] = \ @@ -2477,15 +2477,15 @@ tool = self, name = input.name ) elif isinstance( input, SelectToolParameter ): - input_values[ input.name ] = SelectToolParameterWrapper( + input_values[ input.name ] = SelectToolParameterWrapper( input, input_values[ input.name ], self.app, other_values = param_dict ) - + elif isinstance( input, LibraryDatasetToolParameter ): - input_values[ input.name ] = LibraryDatasetValueWrapper( + input_values[ input.name ] = LibraryDatasetValueWrapper( input, input_values[ input.name ], param_dict ) - + else: - input_values[ input.name ] = InputValueWrapper( + input_values[ input.name ] = InputValueWrapper( input, input_values[ input.name ], param_dict ) # HACK: only wrap if check_values is not false, this deals with external @@ -2494,15 +2494,15 @@ if self.check_values: wrap_values( self.inputs, param_dict ) - ## FIXME: when self.check_values==True, input datasets are being wrapped - ## twice (above and below, creating 2 separate - ## DatasetFilenameWrapper objects - first is overwritten by - ## second), is this necessary? - if we get rid of this way to - ## access children, can we stop this redundancy, or is there + ## FIXME: when self.check_values==True, input datasets are being wrapped + ## twice (above and below, creating 2 separate + ## DatasetFilenameWrapper objects - first is overwritten by + ## second), is this necessary? - if we get rid of this way to + ## access children, can we stop this redundancy, or is there ## another reason for this? - ## - Only necessary when self.check_values is False (==external dataset - ## tool?: can this be abstracted out as part of being a datasouce tool?) - ## - But we still want (ALWAYS) to wrap input datasets (this should be + ## - Only necessary when self.check_values is False (==external dataset + ## tool?: can this be abstracted out as part of being a datasouce tool?) + ## - But we still want (ALWAYS) to wrap input datasets (this should be ## checked to prevent overhead of creating a new object?) # Additionally, datasets go in the param dict. We wrap them such that # if the bare variable name is used it returns the filename (for @@ -2523,7 +2523,7 @@ for child in data.children: param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) for name, hda in output_datasets.items(): - # Write outputs to the working directory (for security purposes) + # Write outputs to the working directory (for security purposes) # if desired. if self.app.config.outputs_to_working_directory: try: @@ -2542,8 +2542,8 @@ param_dict[ "_CHILD___%s___%s" % ( name, child.designation ) ] = DatasetFilenameWrapper( child ) for out_name, output in self.outputs.iteritems(): if out_name not in param_dict and output.filters: - # Assume the reason we lack this output is because a filter - # failed to pass; for tool writing convienence, provide a + # Assume the reason we lack this output is because a filter + # failed to pass; for tool writing convienence, provide a # NoneDataset param_dict[ out_name ] = NoneDataset( datatypes_registry = self.app.datatypes_registry, ext = output.format ) @@ -2557,20 +2557,20 @@ if table_name in self.app.tool_data_tables: return self.app.tool_data_tables[ table_name ].get_entry( query_attr, query_val, return_attr ) - + param_dict['__get_data_table_entry__'] = get_data_table_entry # We add access to app here, this allows access to app.config, etc param_dict['__app__'] = RawObjectWrapper( self.app ) - # More convienent access to app.config.new_file_path; we don't need to - # wrap a string, but this method of generating additional datasets + # More convienent access to app.config.new_file_path; we don't need to + # wrap a string, but this method of generating additional datasets # should be considered DEPRECATED # TODO: path munging for cluster/dataset server relocatability param_dict['__new_file_path__'] = os.path.abspath(self.app.config.new_file_path) - # The following points to location (xxx.loc) files which are pointers + # The following points to location (xxx.loc) files which are pointers # to locally cached data param_dict['__tool_data_path__'] = param_dict['GALAXY_DATA_INDEX_DIR'] = self.app.config.tool_data_path - # For the upload tool, we need to know the root directory and the + # For the upload tool, we need to know the root directory and the # datatypes conf path, so we can load the datatypes registry param_dict['__root_dir__'] = param_dict['GALAXY_ROOT_DIR'] = os.path.abspath( self.app.config.root ) param_dict['__datatypes_config__'] = param_dict['GALAXY_DATATYPES_CONF_FILE'] = self.app.datatypes_registry.integrated_datatypes_configs @@ -2590,7 +2590,7 @@ if type(value) != type([]): value = [ value ] for elem in value: - f.write( '%s=%s\n' % (key, elem) ) + f.write( '%s=%s\n' % (key, elem) ) f.close() param_dict['param_file'] = param_filename return param_filename @@ -2625,7 +2625,7 @@ command_line = None if not self.command: return - try: + try: # Substituting parameters into the command command_line = fill_template( self.command, context=param_dict ) # Remove newlines from command line, and any leading/trailing white space @@ -2671,7 +2671,7 @@ """ if not self.redirect_url_params: return - redirect_url_params = None + redirect_url_params = None # Substituting parameter values into the url params redirect_url_params = fill_template( self.redirect_url_params, context=param_dict ) # Remove newlines @@ -2679,21 +2679,21 @@ return redirect_url_params def parse_redirect_url( self, data, param_dict ): """ - Parse the REDIRECT_URL tool param. Tools that send data to an external + Parse the REDIRECT_URL tool param. Tools that send data to an external application via a redirect must include the following 3 tool params: - + 1) REDIRECT_URL - the url to which the data is being sent - - 2) DATA_URL - the url to which the receiving application will send an + + 2) DATA_URL - the url to which the receiving application will send an http post to retrieve the Galaxy data - + 3) GALAXY_URL - the url to which the external application may post data as a response """ redirect_url = param_dict.get( 'REDIRECT_URL' ) redirect_url_params = self.build_redirect_url_params( param_dict ) - # Add the parameters to the redirect url. We're splitting the param - # string on '**^**' because the self.parse() method replaced white + # Add the parameters to the redirect url. We're splitting the param + # string on '**^**' because the self.parse() method replaced white # space with that separator. params = redirect_url_params.split( '**^**' ) rup_dict = {} @@ -2762,8 +2762,8 @@ file_name = os.path.join(root, f), create = True, preserve_symlinks = True ) - # Clean up after being handled by object store. - # FIXME: If the object (e.g., S3) becomes async, this will + # Clean up after being handled by object store. + # FIXME: If the object (e.g., S3) becomes async, this will # cause issues so add it to the object store functionality? if extra_dir is not None: # there was an extra_files_path dir, attempt to remove it @@ -2776,7 +2776,7 @@ Look for child dataset files, create HDA and attach to parent. """ children = {} - # Loop through output file names, looking for generated children in + # Loop through output file names, looking for generated children in # form of 'child_parentId_designation_visibility_extension' for name, outdata in output.items(): filenames = [] @@ -2825,11 +2825,11 @@ child_dataset.state = outdata.state self.sa_session.add( child_dataset ) self.sa_session.flush() - # Add child to return dict + # Add child to return dict children[name][designation] = child_dataset - # Need to update all associated output hdas, i.e. history was + # Need to update all associated output hdas, i.e. history was # shared with job running - for dataset in outdata.dataset.history_associations: + for dataset in outdata.dataset.history_associations: if outdata == dataset: continue # Create new child dataset child_data = child_dataset.copy( parent_id = dataset.id ) @@ -2838,7 +2838,7 @@ return children def collect_primary_datasets( self, output, job_working_directory ): """ - Find any additional datasets generated by a tool and attach (for + Find any additional datasets generated by a tool and attach (for cases where number of outputs is not known in advance). """ new_primary_datasets = {} @@ -2851,7 +2851,7 @@ except Exception: # This should not be considered an error or warning condition, this file is optional pass - # Loop through output file names, looking for generated primary + # Loop through output file names, looking for generated primary # datasets in form of: # 'primary_associatedWithDatasetID_designation_visibility_extension(_DBKEY)' primary_datasets = {} @@ -2909,48 +2909,48 @@ dataset_att_by_name = dict( ext='extension' ) for att_set in [ 'name', 'info', 'ext', 'dbkey' ]: dataset_att_name = dataset_att_by_name.get( att_set, att_set ) - setattr( primary_data, dataset_att_name, new_primary_datasets_attributes.get( att_set, getattr( primary_data, dataset_att_name ) ) ) + setattr( primary_data, dataset_att_name, new_primary_datasets_attributes.get( att_set, getattr( primary_data, dataset_att_name ) ) ) primary_data.set_meta() primary_data.set_peek() self.sa_session.add( primary_data ) self.sa_session.flush() outdata.history.add_dataset( primary_data ) - # Add dataset to return dict + # Add dataset to return dict primary_datasets[name][designation] = primary_data - # Need to update all associated output hdas, i.e. history was + # Need to update all associated output hdas, i.e. history was # shared with job running - for dataset in outdata.dataset.history_associations: + for dataset in outdata.dataset.history_associations: if outdata == dataset: continue new_data = primary_data.copy() dataset.history.add( new_data ) self.sa_session.add( new_data ) self.sa_session.flush() return primary_datasets - + def _is_hidden_for_user( self, user ): if self.hidden or ( not user and self.require_login ): return True return False - + def to_dict( self, trans, for_link=False, for_display=False ): """ Returns dict of tool. """ - + # Basic information tool_dict = { 'id': self.id, 'name': self.name, 'version': self.version, 'description': self.description } - + if for_link: # Create tool link. if not self.tool_type.startswith( 'data_source' ): link = url_for( '/tool_runner', tool_id=self.id ) else: link = url_for( self.action, **self.get_static_param_values( trans ) ) - + # Basic information - tool_dict.update( { 'type': 'tool', 'link': link, + tool_dict.update( { 'type': 'tool', 'link': link, 'min_width': self.uihints.get( 'minwidth', -1 ), 'target': self.target } ) - + if for_display: # Dictify inputs. inputs = [] @@ -2968,7 +2968,7 @@ value = option[1] # Pack input. - param_dict.update( { 'type' : 'select', + param_dict.update( { 'type' : 'select', 'html' : urllib.quote( input.get_html( trans ) ), 'options': options, 'value': value @@ -2987,12 +2987,12 @@ param_dict.update( { 'type' : '??', 'init_value' : input.value, \ 'html' : urllib.quote( input.get_html( trans ) ) } ) inputs.append( param_dict ) - + tool_dict[ 'inputs' ] = inputs - + # Dictify outputs. pass - + return tool_dict def get_default_history_by_trans( self, trans, create=False ): @@ -3001,7 +3001,7 @@ class OutputParameterJSONTool( Tool ): """ - Alternate implementation of Tool that provides parameters and other values + Alternate implementation of Tool that provides parameters and other values JSONified within the contents of an output dataset """ tool_type = 'output_parameter_json' @@ -3027,14 +3027,14 @@ return rval def exec_before_job( self, app, inp_data, out_data, param_dict=None ): if param_dict is None: - param_dict = {} + param_dict = {} json_params = {} json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? json_params[ 'output_data' ] = [] json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) json_filename = None for i, ( out_name, data ) in enumerate( out_data.iteritems() ): - #use wrapped dataset to access certain values + #use wrapped dataset to access certain values wrapped_data = param_dict.get( out_name ) #allow multiple files to be created file_name = str( wrapped_data ) @@ -3054,11 +3054,11 @@ class DataSourceTool( OutputParameterJSONTool ): """ - Alternate implementation of Tool for data_source tools -- those that + Alternate implementation of Tool for data_source tools -- those that allow the user to query and extract data from another web site. """ tool_type = 'data_source' - + def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '<param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=%s" />' % self.id ) ) def parse_inputs( self, root ): @@ -3073,17 +3073,17 @@ info = param_dict.get( 'info' ) data_type = param_dict.get( 'data_type' ) name = param_dict.get( 'name' ) - + json_params = {} json_params[ 'param_dict' ] = self._prepare_json_param_dict( param_dict ) #it would probably be better to store the original incoming parameters here, instead of the Galaxy modified ones? json_params[ 'output_data' ] = [] json_params[ 'job_config' ] = dict( GALAXY_DATATYPES_CONF_FILE=param_dict.get( 'GALAXY_DATATYPES_CONF_FILE' ), GALAXY_ROOT_DIR=param_dict.get( 'GALAXY_ROOT_DIR' ), TOOL_PROVIDED_JOB_METADATA_FILE=jobs.TOOL_PROVIDED_JOB_METADATA_FILE ) json_filename = None for i, ( out_name, data ) in enumerate( out_data.iteritems() ): - #use wrapped dataset to access certain values + #use wrapped dataset to access certain values wrapped_data = param_dict.get( out_name ) #allow multiple files to be created - cur_base_param_name = 'GALAXY|%s|' % out_name + cur_base_param_name = 'GALAXY|%s|' % out_name cur_name = param_dict.get( cur_base_param_name + 'name', name ) cur_dbkey = param_dict.get( cur_base_param_name + 'dkey', dbkey ) cur_info = param_dict.get( cur_base_param_name + 'info', info ) @@ -3113,7 +3113,7 @@ class AsyncDataSourceTool( DataSourceTool ): tool_type = 'data_source_async' - + def _build_GALAXY_URL_parameter( self ): return ToolParameter.build( self, ElementTree.XML( '<param name="GALAXY_URL" type="baseurl" value="/async/%s" />' % self.id ) ) @@ -3130,23 +3130,23 @@ for name, dataset in inp_data.iteritems(): external_metadata = JobExternalOutputMetadataWrapper( job ) if external_metadata.external_metadata_set_successfully( dataset, app.model.context ): - dataset.metadata.from_JSON_dict( external_metadata.get_output_filenames_by_dataset( dataset, app.model.context ).filename_out ) + dataset.metadata.from_JSON_dict( external_metadata.get_output_filenames_by_dataset( dataset, app.model.context ).filename_out ) else: dataset._state = model.Dataset.states.FAILED_METADATA self.sa_session.add( dataset ) self.sa_session.flush() return - # If setting external metadata has failed, how can we inform the - # user? For now, we'll leave the default metadata and set the state + # If setting external metadata has failed, how can we inform the + # user? For now, we'll leave the default metadata and set the state # back to its original. dataset.datatype.after_setting_metadata( dataset ) if job and job.tool_id == '1.0.0': dataset.state = param_dict.get( '__ORIGINAL_DATASET_STATE__' ) else: # Revert dataset.state to fall back to dataset.dataset.state - dataset._state = None + dataset._state = None # Need to reset the peek, which may rely on metadata - dataset.set_peek() + dataset.set_peek() self.sa_session.add( dataset ) self.sa_session.flush() def job_failed( self, job_wrapper, message, exception = False ): @@ -3156,10 +3156,10 @@ for dataset_assoc in job.input_datasets: inp_data[dataset_assoc.name] = dataset_assoc.dataset return self.exec_after_process( job_wrapper.app, inp_data, {}, job_wrapper.get_param_dict(), job = job ) - + class ExportHistoryTool( Tool ): tool_type = 'export_history' - + class ImportHistoryTool( Tool ): tool_type = 'import_history' @@ -3169,13 +3169,13 @@ class DataManagerTool( OutputParameterJSONTool ): tool_type = 'manage_data' default_tool_action = DataManagerToolAction - + def __init__( self, config_file, root, app, guid=None, data_manager_id=None, **kwds ): self.data_manager_id = data_manager_id super( DataManagerTool, self ).__init__( config_file, root, app, guid=guid, **kwds ) if self.data_manager_id is None: self.data_manager_id = self.id - + def exec_after_process( self, app, inp_data, out_data, param_dict, job = None, **kwds ): #run original exec_after_process super( DataManagerTool, self ).exec_after_process( app, inp_data, out_data, param_dict, job = job, **kwds ) @@ -3186,7 +3186,7 @@ data_manager = self.app.data_managers.get_manager( data_manager_id, None ) assert data_manager is not None, "Invalid data manager (%s) requested. It may have been removed before the job completed." % ( data_manager_id ) data_manager.process_result( out_data ) - + def get_default_history_by_trans( self, trans, create=False ): def _create_data_manager_history( user ): history = trans.app.model.History( name='Data Manager History (automatically created)', user=user ) @@ -3222,7 +3222,7 @@ tool_types[ tool_class.tool_type ] = tool_class # ---- Utility classes to be factored out ----------------------------------- - + class BadValue( object ): def __init__( self, value ): self.value = value @@ -3239,7 +3239,7 @@ self.stdout_match = False self.stderr_match = False # TODO: Define a common class or constant for error level: - self.error_level = "fatal" + self.error_level = "fatal" self.desc = "" class ToolStdioExitCode( object ): @@ -3294,7 +3294,7 @@ return self.value[self.counter-1] def __getattr__( self, key ): return getattr( self.value, key ) - + class InputValueWrapper( ToolParameterValueWrapper ): """ Wraps an input so that __str__ gives the "param_dict" representation. @@ -3313,7 +3313,7 @@ Wraps a SelectTooParameter so that __str__ returns the selected value, but all other attributes are accessible. """ - + class SelectToolParameterFieldWrapper: """ Provide access to any field by name or index for this particular value. @@ -3328,7 +3328,7 @@ if name not in self._fields: self._fields[ name ] = self._input.options.get_field_by_name_for_value( name, self._value, None, self._other_values ) return self._input.separator.join( map( str, self._fields[ name ] ) ) - + def __init__( self, input, value, app, other_values={} ): self.input = input self.value = value @@ -3345,11 +3345,11 @@ Wraps a dataset so that __str__ returns the filename, but all other attributes are accessible. """ - + class MetadataWrapper: """ - Wraps a Metadata Collection to return MetadataParameters wrapped - according to the metadata spec. Methods implemented to match behavior + Wraps a Metadata Collection to return MetadataParameters wrapped + according to the metadata spec. Methods implemented to match behavior of a Metadata Collection. """ def __init__( self, metadata ): @@ -3360,9 +3360,9 @@ if rval is None: rval = self.metadata.spec[name].no_value rval = self.metadata.spec[name].param.to_string( rval ) - # Store this value, so we don't need to recalculate if needed + # Store this value, so we don't need to recalculate if needed # again - setattr( self, name, rval ) + setattr( self, name, rval ) return rval def __nonzero__( self ): return self.metadata.__nonzero__() @@ -3375,7 +3375,7 @@ return default def items( self ): return iter( [ ( k, self.get( k ) ) for k, v in self.metadata.items() ] ) - + def __init__( self, dataset, datatypes_registry = None, tool = None, name = None, false_path = None ): if not dataset: try: @@ -3420,7 +3420,7 @@ return val.encode( "utf8" ) else: return val - + def get_incoming_value( incoming, key, default ): if "__" + key + "__is_composite" in incoming: composite_keys = incoming["__" + key + "__keys"].split() Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/340d626da27a/ changeset: 340d626da27a user: dannon date: 2013-03-05 21:39:22 summary: Base controller import cleanup, remove unused variables. affected #: 1 file diff -r 0a6a4752493eacfac2fb7a537d30be0333a58977 -r 340d626da27af28fab27115c0329ea1a2069048b lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -1,28 +1,29 @@ """ Contains functionality needed in every web interface """ -import os, time, logging, re, string, sys, glob, shutil, tempfile, subprocess, operator -from datetime import date, datetime, timedelta -from time import strftime -from galaxy import config, tools, web, util -from galaxy.util import inflector -from galaxy.util.hash_util import * +import logging +import operator +import os +import re +import pkg_resources +pkg_resources.require("SQLAlchemy >= 0.4") + +from sqlalchemy import func, and_, select +from paste.httpexceptions import HTTPBadRequest, HTTPInternalServerError, HTTPNotImplemented, HTTPRequestRangeNotSatisfiable + +from galaxy import util, web +from galaxy.datatypes.interval import ChromatinInteractions +from galaxy.exceptions import ItemAccessibilityException, ItemDeletionException, ItemOwnershipException, MessageException +from galaxy.security.validate_user_input import validate_publicname from galaxy.util.sanitize_html import sanitize_html -from galaxy.web import error, form, url_for -from galaxy.model.orm import * -from galaxy.workflow.modules import * -from galaxy.web.framework import simplejson +from galaxy.visualization.genome.visual_analytics import get_tool_def +from galaxy.web import error, url_for from galaxy.web.form_builder import AddressField, CheckboxField, SelectField, TextArea, TextField -from galaxy.web.form_builder import WorkflowField, WorkflowMappingField, HistoryField, PasswordField, build_select_field -from galaxy.visualization.genome.visual_analytics import get_tool_def -from galaxy.security.validate_user_input import validate_publicname -from paste.httpexceptions import * -from galaxy.exceptions import * -from galaxy.model import NoConverterException, ConverterDependencyException -from galaxy.datatypes.interval import ChromatinInteractions +from galaxy.web.form_builder import build_select_field, HistoryField, PasswordField, WorkflowField, WorkflowMappingField +from galaxy.workflow.modules import module_factory +from galaxy.model.orm import eagerload, eagerload_all from galaxy.datatypes.data import Text -from Cheetah.Template import Template log = logging.getLogger( __name__ ) @@ -100,6 +101,7 @@ log.exception( "Invalid %s id ( %s ) specified" % ( class_name, id ) ) raise MessageException( "Invalid %s id ( %s ) specified" % ( class_name, id ), type="error" ) if check_ownership or check_accessible: + #DBTODO bug: encoded_id is id self.security_check( trans, item, check_ownership, check_accessible, encoded_id ) if deleted == True and not item.deleted: raise ItemDeletionException( '%s "%s" is not deleted' % ( class_name, getattr( item, 'name', id ) ), type="warning" ) @@ -134,7 +136,7 @@ def get_object( self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None ): try: return BaseController.get_object( self, trans, id, class_name, check_ownership=False, check_accessible=False, deleted=None ) - except MessageException, e: + except MessageException: raise # handled in the caller except: log.exception( "Execption in get_object check for %s %s:" % ( class_name, str( id ) ) ) @@ -228,7 +230,7 @@ # encoded id? dataset_id = trans.security.decode_id( dataset_id ) - except ( AttributeError, TypeError ), err: + except ( AttributeError, TypeError ): # unencoded id dataset_id = int( dataset_id ) @@ -684,6 +686,7 @@ step.state = None # Error dict if step.tool_errors: + #DBTODO BUG: errors doesn't exist in this scope, intent? errors[step.id] = step.tool_errors else: ## Non-tool specific stuff? @@ -943,9 +946,7 @@ def edit_template( self, trans, cntrller, item_type, form_type, **kwd ): # Edit the template itself, keeping existing field contents, if any. params = util.Params( kwd ) - form_id = params.get( 'form_id', 'none' ) message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) edited = util.string_as_bool( params.get( 'edited', False ) ) action = '' # form_type must be one of: RUN_DETAILS_TEMPLATE, LIBRARY_INFO_TEMPLATE @@ -995,8 +996,6 @@ rtra = item.run_details info_association = rtra.run template = info_association.template - info = info_association.info - form_values = trans.sa_session.query( trans.app.model.FormValues ).get( info.id ) if edited: # The form on which the template is based has been edited, so we need to update the # info_association with the current form @@ -1052,7 +1051,6 @@ sample_id = params.get( 'sample_id', None ) sample = trans.sa_session.query( trans.model.Sample ).get( trans.security.decode_id( sample_id ) ) message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) try: if in_library: item, item_desc, action, id = self.get_item_and_stuff( trans, @@ -1250,7 +1248,6 @@ sample_id = params.get( 'sample_id', None ) #id = params.get( 'id', None ) message = util.restore_text( params.get( 'message', '' ) ) - status = params.get( 'status', 'done' ) try: if in_library: item, item_desc, action, id = self.get_item_and_stuff( trans, @@ -1282,7 +1279,6 @@ info_association = item.run_details if not info_association: message = "There is no template for this %s" % item_type - status = 'error' else: if in_library: info_association.deleted = True @@ -1292,7 +1288,6 @@ trans.sa_session.delete( info_association ) trans.sa_session.flush() message = 'The template for this %s has been deleted.' % item_type - status = 'done' new_kwd = dict( action=action, cntrller=cntrller, id=id, @@ -1449,9 +1444,6 @@ def get_item_and_stuff( self, trans, item_type, **kwd ): # Return an item, description, action and an id based on the item_type. Valid item_types are # library, folder, ldda, request_type, sample. - is_admin = kwd.get( 'is_admin', False ) - #message = None - current_user_roles = trans.get_current_user_roles() if item_type == 'library': library_id = kwd.get( 'library_id', None ) id = library_id https://bitbucket.org/galaxy/galaxy-central/commits/1daf0cefe5be/ changeset: 1daf0cefe5be user: dannon date: 2013-03-05 21:41:22 summary: Fix bug introduced in 6028 -- encoded_id should be just 'id' affected #: 1 file diff -r 340d626da27af28fab27115c0329ea1a2069048b -r 1daf0cefe5bed7f972f3e8aeec0d2577811d005c lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -101,8 +101,7 @@ log.exception( "Invalid %s id ( %s ) specified" % ( class_name, id ) ) raise MessageException( "Invalid %s id ( %s ) specified" % ( class_name, id ), type="error" ) if check_ownership or check_accessible: - #DBTODO bug: encoded_id is id - self.security_check( trans, item, check_ownership, check_accessible, encoded_id ) + self.security_check( trans, item, check_ownership, check_accessible, id ) if deleted == True and not item.deleted: raise ItemDeletionException( '%s "%s" is not deleted' % ( class_name, getattr( item, 'name', id ) ), type="warning" ) elif deleted == False and item.deleted: https://bitbucket.org/galaxy/galaxy-central/commits/94272d25279e/ changeset: 94272d25279e user: dannon date: 2013-03-05 21:43:40 summary: Kill unused step error dict - this is handled elsewhere. affected #: 1 file diff -r 1daf0cefe5bed7f972f3e8aeec0d2577811d005c -r 94272d25279e96b866be313c222e9e3a9af57b9d lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -683,10 +683,6 @@ step.upgrade_messages = "Unknown Tool ID" step.module = None step.state = None - # Error dict - if step.tool_errors: - #DBTODO BUG: errors doesn't exist in this scope, intent? - errors[step.id] = step.tool_errors else: ## Non-tool specific stuff? step.module = module_factory.from_workflow_step( trans, step ) https://bitbucket.org/galaxy/galaxy-central/commits/3b4596096549/ changeset: 3b4596096549 user: dannon date: 2013-03-05 21:44:03 summary: Trim whitespace. affected #: 1 file diff -r 94272d25279e96b866be313c222e9e3a9af57b9d -r 3b459609654976c8908a2c3104a080db8f550b61 lib/galaxy/web/base/controller.py --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -194,7 +194,7 @@ self.mimetype = mimetype self.display_in_upload = display_in_upload -# +# # -- Mixins for working with Galaxy objects. -- # @@ -221,7 +221,7 @@ class UsesHistoryDatasetAssociationMixin: """ Mixin for controllers that use HistoryDatasetAssociation objects. """ - + def get_dataset( self, trans, dataset_id, check_ownership=True, check_accessible=False, check_state=True ): """ Get an HDA object by id. """ # DEPRECATION: We still support unencoded ids for backward compatibility @@ -256,13 +256,13 @@ return trans.show_error_message( "Please wait until this dataset finishes uploading " + "before attempting to view it." ) return data - + def get_history_dataset_association( self, trans, history, dataset_id, check_ownership=True, check_accessible=False, check_state=False ): """Get a HistoryDatasetAssociation from the database by id, verifying ownership.""" self.security_check( trans, history, check_ownership=check_ownership, check_accessible=check_accessible ) hda = self.get_object( trans, dataset_id, 'HistoryDatasetAssociation', check_ownership=False, check_accessible=False, deleted=False ) - + if check_accessible: if not trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ): error( "You are not allowed to access this dataset" ) @@ -270,7 +270,7 @@ if check_state and hda.state == trans.model.Dataset.states.UPLOAD: error( "Please wait until this dataset finishes uploading before attempting to view it." ) return hda - + def get_data( self, dataset, preview=True ): """ Gets a dataset's data. """ @@ -290,7 +290,7 @@ # For now, cannot get data from non-text datasets. dataset_data = None return truncated, dataset_data - + def check_dataset_state( self, trans, dataset ): """ Returns a message if dataset is not ready to be used in visualization. @@ -302,7 +302,7 @@ if dataset.state != trans.app.model.Job.states.OK: return dataset.conversion_messages.PENDING return None - + class UsesLibraryMixin: def get_library( self, trans, id, check_ownership=False, check_accessible=True ): @@ -319,10 +319,10 @@ def get_library_dataset( self, trans, id, check_ownership=False, check_accessible=True ): return self.get_object( trans, id, 'LibraryDataset', check_ownership=False, check_accessible=check_accessible ) -class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, +class UsesVisualizationMixin( UsesHistoryDatasetAssociationMixin, UsesLibraryMixinItems ): """ Mixin for controllers that use Visualization objects. """ - + viz_types = [ "trackster" ] def create_visualization( self, trans, type, title="Untitled Genome Vis", slug=None, dbkey=None, annotation=None, config={}, save=True ): @@ -339,26 +339,26 @@ session.flush() return visualization - + def save_visualization( self, trans, config, type, id=None, title=None, dbkey=None, slug=None, annotation=None ): session = trans.sa_session - - # Create/get visualization. + + # Create/get visualization. if not id: # Create new visualization. vis = self._create_visualization( trans, title, type, dbkey, slug, annotation ) else: decoded_id = trans.security.decode_id( id ) vis = session.query( trans.model.Visualization ).get( decoded_id ) - + # Create new VisualizationRevision that will be attached to the viz vis_rev = trans.model.VisualizationRevision() vis_rev.visualization = vis vis_rev.title = vis.title vis_rev.dbkey = dbkey - + # -- Validate config. -- - + if vis.type == 'trackster': def unpack_track( track_json ): """ Unpack a track from its json. """ @@ -436,12 +436,12 @@ # Unpack Trackster config. latest_revision = visualization.latest_revision bookmarks = latest_revision.config.get( 'bookmarks', [] ) - + def pack_track( track_dict ): dataset_id = track_dict['dataset_id'] hda_ldda = track_dict.get('hda_ldda', 'hda') if hda_ldda == 'ldda': - # HACK: need to encode library dataset ID because get_hda_or_ldda + # HACK: need to encode library dataset ID because get_hda_or_ldda # only works for encoded datasets. dataset_id = trans.security.encode_id( dataset_id ) dataset = self.get_hda_or_ldda( trans, hda_ldda, dataset_id ) @@ -452,10 +452,10 @@ prefs = {} track_type, _ = dataset.datatype.get_track_type() - track_data_provider = trans.app.data_provider_registry.get_data_provider( trans, - original_dataset=dataset, + track_data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, source='data' ) - + return { "track_type": track_type, "name": track_dict['name'], @@ -467,7 +467,7 @@ "tool": get_tool_def( trans, dataset ), "tool_state": track_dict.get( 'tool_state', {} ) } - + def pack_collection( collection_dict ): drawables = [] for drawable_dict in collection_dict[ 'drawables' ]: @@ -482,10 +482,10 @@ 'prefs': collection_dict.get( 'prefs', [] ), 'filters': collection_dict.get( 'filters', {} ) } - + def encode_dbkey( dbkey ): - """ - Encodes dbkey as needed. For now, prepends user's public name + """ + Encodes dbkey as needed. For now, prepends user's public name to custom dbkey keys. """ encoded_dbkey = dbkey @@ -493,7 +493,7 @@ if 'dbkeys' in user.preferences and dbkey in user.preferences[ 'dbkeys' ]: encoded_dbkey = "%s:%s" % ( user.username, dbkey ) return encoded_dbkey - + # Set tracks. tracks = [] if 'tracks' in latest_revision.config: @@ -506,12 +506,12 @@ tracks.append( pack_track( drawable_dict ) ) else: tracks.append( pack_collection( drawable_dict ) ) - - config = { "title": visualization.title, + + config = { "title": visualization.title, "vis_id": trans.security.encode_id( visualization.id ), - "tracks": tracks, - "bookmarks": bookmarks, - "chrom": "", + "tracks": tracks, + "bookmarks": bookmarks, + "chrom": "", "dbkey": encode_dbkey( visualization.dbkey ) } if 'viewport' in latest_revision.config: @@ -522,7 +522,7 @@ config = latest_revision.config return config - + def get_new_track_config( self, trans, dataset ): """ Returns track configuration dict for a dataset. @@ -530,13 +530,13 @@ # Get data provider. track_type, _ = dataset.datatype.get_track_type() track_data_provider = trans.app.data_provider_registry.get_data_provider( trans, original_dataset=dataset ) - - + + if isinstance( dataset, trans.app.model.HistoryDatasetAssociation ): hda_ldda = "hda" elif isinstance( dataset, trans.app.model.LibraryDatasetDatasetAssociation ): hda_ldda = "ldda" - + # Get track definition. return { "track_type": track_type, @@ -548,16 +548,16 @@ "tool": get_tool_def( trans, dataset ), "tool_state": {} } - + def get_hda_or_ldda( self, trans, hda_ldda, dataset_id ): """ Returns either HDA or LDDA for hda/ldda and id combination. """ if hda_ldda == "hda": return self.get_dataset( trans, dataset_id, check_ownership=False, check_accessible=True ) else: return self.get_library_dataset_dataset_association( trans, dataset_id ) - + # -- Helper functions -- - + def _create_visualization( self, trans, title, type, dbkey=None, slug=None, annotation=None, save=True ): """ Create visualization but not first revision. Returns Visualization object. """ user = trans.get_user() @@ -573,7 +573,7 @@ if title_err or slug_err: return { 'title_err': title_err, 'slug_err': slug_err } - + # Create visualization visualization = trans.model.Visualization( user=user, title=title, dbkey=dbkey, type=type ) @@ -616,13 +616,13 @@ if isinstance( dataset.datatype, ChromatinInteractions ): source = 'data' - data_provider = trans.app.data_provider_registry.get_data_provider( trans, - original_dataset=dataset, + data_provider = trans.app.data_provider_registry.get_data_provider( trans, + original_dataset=dataset, source=source ) - # HACK: pass in additional params which are used for only some - # types of data providers; level, cutoffs used for summary tree, + # HACK: pass in additional params which are used for only some + # types of data providers; level, cutoffs used for summary tree, # num_samples for BBI, and interchromosomal used for chromatin interactions. - rval = data_provider.get_genome_data( chroms_info, + rval = data_provider.get_genome_data( chroms_info, level=4, detail_cutoff=0, draw_cutoff=0, num_samples=150, interchromosomal=True ) @@ -635,7 +635,7 @@ Returns highest priority message from a list of messages. """ return_message = None - + # For now, priority is: job error (dict), no converter, pending. for message in message_list: if message is not None: @@ -714,14 +714,14 @@ def get_hda_state_counts( self, trans, history, include_deleted=False, include_hidden=False ): """ - Returns a dictionary with state counts for history's HDAs. Key is a + Returns a dictionary with state counts for history's HDAs. Key is a dataset state, value is the number of states in that count. """ # Build query to get (state, count) pairs. - cols_to_select = [ trans.app.model.Dataset.table.c.state, func.count( '*' ) ] + cols_to_select = [ trans.app.model.Dataset.table.c.state, func.count( '*' ) ] from_obj = trans.app.model.HistoryDatasetAssociation.table.join( trans.app.model.Dataset.table ) - + conditions = [ trans.app.model.HistoryDatasetAssociation.table.c.history_id == history.id ] if not include_deleted: # Only count datasets that have not been deleted. @@ -729,7 +729,7 @@ if not include_hidden: # Only count datasets that are visible. conditions.append( trans.app.model.HistoryDatasetAssociation.table.c.visible == True ) - + group_by = trans.app.model.Dataset.table.c.state query = select( columns=cols_to_select, from_obj=from_obj, @@ -740,7 +740,7 @@ state_count_dict = {} for k, state in trans.app.model.Dataset.states.items(): state_count_dict[ state ] = 0 - + # Process query results, adding to count dict. for row in trans.sa_session.execute( query ): state, count = row @@ -1501,13 +1501,13 @@ class SharableMixin: """ Mixin for a controller that manages an item that can be shared. """ - + # -- Implemented methods. -- def _is_valid_slug( self, slug ): """ Returns true if slug is valid. """ return _is_valid_slug( slug ) - + @web.expose @web.require_login( "share Galaxy items" ) def set_public_username( self, trans, id, username, **kwargs ): @@ -1526,7 +1526,7 @@ item = self.get_item( trans, id ) if item: # Only update slug if slug is not already in use. - if trans.sa_session.query( item.__class__ ).filter_by( user=item.user, slug=new_slug, importable=True ).count() == 0: + if trans.sa_session.query( item.__class__ ).filter_by( user=item.user, slug=new_slug, importable=True ).count() == 0: item.slug = new_slug trans.sa_session.flush() @@ -1534,15 +1534,15 @@ def _make_item_accessible( self, sa_session, item ): """ Makes item accessible--viewable and importable--and sets item's slug. - Does not flush/commit changes, however. Item must have name, user, + Does not flush/commit changes, however. Item must have name, user, importable, and slug attributes. """ item.importable = True self.create_item_slug( sa_session, item ) - + def create_item_slug( self, sa_session, item ): - """ Create/set item slug. Slug is unique among user's importable items - for item's class. Returns true if item's slug was set/changed; false - otherwise. + """ Create/set item slug. Slug is unique among user's importable items + for item's class. Returns true if item's slug was set/changed; false + otherwise. """ cur_slug = item.slug @@ -1563,7 +1563,7 @@ else: slug_base = cur_slug - # Using slug base, find a slug that is not taken. If slug is taken, + # Using slug base, find a slug that is not taken. If slug is taken, # add integer to end. new_slug = slug_base count = 1 @@ -1572,13 +1572,13 @@ # handle numerous items with the same name gracefully. new_slug = '%s-%i' % ( slug_base, count ) count += 1 - + # Set slug and return. item.slug = new_slug return item.slug == cur_slug - - # -- Abstract methods. -- - + + # -- Abstract methods. -- + @web.expose @web.require_login( "share Galaxy items" ) def sharing( self, trans, id, **kwargs ): @@ -1595,19 +1595,19 @@ def display_by_username_and_slug( self, trans, username, slug ): """ Display item by username and slug. """ raise "Unimplemented Method" - + @web.json @web.require_login( "get item name and link" ) def get_name_and_link_async( self, trans, id=None ): """ Returns item's name and link. """ raise "Unimplemented Method" - + @web.expose @web.require_login("get item content asynchronously") def get_item_content_async( self, trans, id ): """ Returns item content in HTML format. """ raise "Unimplemented Method" - + def get_item( self, trans, id ): """ Return item based on id. """ raise "Unimplemented Method" https://bitbucket.org/galaxy/galaxy-central/commits/6bc53fd15c62/ changeset: 6bc53fd15c62 user: dannon date: 2013-03-05 21:52:09 summary: Fix spacing between methods in base controller. affected #: 1 file Diff not available. 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: carlfeberhard: Browser testing: add tests (and conv. fns) for working with the history options, history panel
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0a6a4752493e/ changeset: 0a6a4752493e user: carlfeberhard date: 2013-03-05 21:35:59 summary: Browser testing: add tests (and conv. fns) for working with the history options, history panel affected #: 9 files diff -r 592af505e4e673aa891e9163bd237dbbc728ba62 -r 0a6a4752493eacfac2fb7a537d30be0333a58977 test/casperjs/anon-history-tests.js --- a/test/casperjs/anon-history-tests.js +++ b/test/casperjs/anon-history-tests.js @@ -36,6 +36,7 @@ if( spaceghost.fixtureData.testUser ){ email = spaceghost.fixtureData.testUser.email; password = spaceghost.fixtureData.testUser.password; + spaceghost.info( 'Will use fixtureData.testUser: ' + email ); } var galaxyCookieName = 'galaxysession', @@ -174,6 +175,17 @@ }); }); +spaceghost.user.logout(); +spaceghost.thenOpen( spaceghost.baseUrl, function(){ + this.test.comment( 'logging out should create a new, anonymous history' ); + + this.withFrame( this.selectors.frames.history, function(){ + this.test.assertSelectorHasText( nameSelector, unnamedName, 'History name is ' + unnamedName ); + this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, + 'Message contains "' + emptyMsgStr + '"' ); + }); +}); + // =================================================================== spaceghost.run( function(){ diff -r 592af505e4e673aa891e9163bd237dbbc728ba62 -r 0a6a4752493eacfac2fb7a537d30be0333a58977 test/casperjs/casperjs_runner.py --- a/test/casperjs/casperjs_runner.py +++ b/test/casperjs/casperjs_runner.py @@ -9,7 +9,7 @@ * sh run_functional_tests.sh test/casperjs/test_runner * sh run_functional_tests.sh -Note: that you can enable (lots) of debugging info using cli options: +Note: that you can enable (lots of) debugging info using cli options: * casperjs usertests.js --url='http://localhost:8080' --verbose=true --logLevel=debug (see casperjs.org for more information) @@ -94,11 +94,12 @@ while process.poll() == None: stderr_msg = process.stderr.readline() stderr_msg = self.strip_escape_codes( stderr_msg.strip() ) - log.debug( '(%s): %s', rel_script_path, stderr_msg ) - # HACK: this is the last string displayed using the debug settings - afterwards it hangs - # so: bail on this string - if stderr_msg.startswith( self.casper_done_str ): - break + if stderr_msg: + log.debug( '(%s): %s', rel_script_path, stderr_msg ) + # HACK: this is the last string displayed using the debug settings - afterwards it hangs + # so: bail on this string + if stderr_msg.startswith( self.casper_done_str ): + break # stdout is assumed to have the json test data/results ( stdout_output, stderr_output ) = process.communicate() @@ -301,8 +302,12 @@ """User registration tests: register new user, logout, attempt bad registrations. """ # all keywords will be compiled into a single JSON obj and passed to the server - self.run_js_script( 'registration-tests.js', - testuser=test_user ) + #self.run_js_script( 'registration-tests.js', + # # this causes a time out in history-panel-tests: why? + # # also: I can't seem to bump the timeout to an error (using a handler) - causes script to hang + # # removing for the sake of bbot + # testUser=test_user ) + self.run_js_script( 'registration-tests.js' ) #TODO:?? could theoretically do db cleanup, checks here with SQLALX #TODO: have run_js_script return other persistant fixture data (uploaded files, etc.) @@ -310,8 +315,7 @@ def test_20_login( self ): """User log in tests. """ - self.run_js_script( 'login-tests.js', - testuser=test_user ) + self.run_js_script( 'login-tests.js' ) class Test_02_Tools( CasperJSTestCase ): @@ -321,8 +325,7 @@ def test_10_upload( self ): """Tests uploading files """ - self.run_js_script( 'upload-tests.js', - testuser=test_user ) + self.run_js_script( 'upload-tests.js' ) class Test_03_HistoryPanel( CasperJSTestCase ): @@ -332,14 +335,12 @@ def test_00_history_panel( self ): """Test history panel basics (controls, structure, refresh, history options menu, etc.). """ - self.run_js_script( 'history-panel-tests.js', - testuser=test_user ) + self.run_js_script( 'history-panel-tests.js' ) def test_10_anonymous_histories( self ): """Test history panel basics with an anonymous user. """ - self.run_js_script( 'anon-history-tests.js', - testuser=test_user ) + self.run_js_script( 'anon-history-tests.js' ) diff -r 592af505e4e673aa891e9163bd237dbbc728ba62 -r 0a6a4752493eacfac2fb7a537d30be0333a58977 test/casperjs/history-panel-tests.js --- a/test/casperjs/history-panel-tests.js +++ b/test/casperjs/history-panel-tests.js @@ -27,6 +27,7 @@ // =================================================================== /* TODO: + possibly break this file up */ // =================================================================== globals and helpers var email = spaceghost.user.getRandomEmail(), @@ -34,8 +35,8 @@ if( spaceghost.fixtureData.testUser ){ email = spaceghost.fixtureData.testUser.email; password = spaceghost.fixtureData.testUser.password; + spaceghost.info( 'Will use fixtureData.testUser: ' + email ); } -var newHistoryName = "Test History"; var nameSelector = 'div#history-name', unnamedName = 'Unnamed history', @@ -43,7 +44,6 @@ initialSizeStr = '0 bytes', tagIconSelector = '#history-tag.icon-button', annoIconSelector = '#history-annotate.icon-button', - //emptyMsgSelector = '#emptyHistoryMessage'; emptyMsgSelector = '.infomessagesmall', emptyMsgStr = "Your history is empty. Click 'Get Data' on the left pane to start", @@ -51,14 +51,33 @@ nameTooltip = 'Click to rename history', editableTextClass = 'editable-text', - editableTextInputSelector = 'input#renaming-active'; + editableTextInputSelector = 'input#renaming-active', -var historyFrameInfo = {}, + wrapperOkClassName = 'historyItem-ok', + + tagAreaSelector = '#history-tag-area', + annoAreaSelector = '#history-annotation-area', + refreshButtonSelector = 'a#history-refresh-button', + refreshButtonIconSelector = 'span.fa-icon-refresh', + refreshButtonHref = '/history', + + //historyOptionsButtonSelector = '#history-options-button', + //historyOptionsButtonIconSelector = 'span.fa-icon-cog', + includeDeletedOptionsLabel = spaceghost.historyoptions.data.labels.options.includeDeleted; + +function historyOptionXpathByLabel( label ){ + return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' ); +} + +var newHistoryName = "Test History", + filepathToUpload = '../../test-data/1.txt', + historyFrameInfo = {}, testUploadInfo = {}; // =================================================================== TESTS -// ------------------------------------------------------------------- start a new user +// ------------------------------------------------------------------- set up +// start a new user spaceghost.user.loginOrRegisterUser( email, password ); //??: why is a reload needed here? If we don't, loggedInAs === '' ... spaceghost.thenOpen( spaceghost.baseUrl, function(){ @@ -66,13 +85,13 @@ this.test.assert( loggedInAs === email, 'loggedInAs() matches email: "' + loggedInAs + '"' ); }); -// ------------------------------------------------------------------- check structure of empty history // grab the history frame bounds for mouse later tests spaceghost.then( function(){ historyFrameInfo = this.getElementInfo( 'iframe[name="galaxy_history"]' ); //this.debug( 'historyFrameInfo:' + this.jsonStr( historyFrameInfo ) ); }); +// ------------------------------------------------------------------- check structure of empty history spaceghost.thenOpen( spaceghost.baseUrl, function testPanelStructure(){ this.test.comment( 'history panel, new history' ); this.withFrame( this.selectors.frames.history, function(){ @@ -100,7 +119,6 @@ this.test.assertVisible( emptyMsgSelector, 'Empty history message is visible' ); this.test.assertSelectorHasText( emptyMsgSelector, emptyMsgStr, 'Message contains "' + emptyMsgStr + '"' ); - }); }); @@ -163,88 +181,259 @@ }); }); - // ------------------------------------------------------------------- check structure of NON empty history -/* // upload file: 1.txt spaceghost.then( function upload(){ - this.test.comment( 'anon-user should be able to upload files' ); - spaceghost.uploadFile( '../../test-data/1.txt', function uploadCallback( _uploadInfo ){ + this.test.comment( 'should be able to upload files' ); + spaceghost.tools.uploadFile( filepathToUpload, function uploadCallback( _uploadInfo ){ this.debug( 'uploaded HDA info: ' + this.jsonStr( _uploadInfo ) ); var hasHda = _uploadInfo.hdaElement, hasClass = _uploadInfo.hdaElement.attributes[ 'class' ], - hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( 'historyItem-ok' ) !== -1; + hasOkClass = _uploadInfo.hdaElement.attributes[ 'class' ].indexOf( wrapperOkClassName ) !== -1; this.test.assert( ( hasHda && hasClass && hasOkClass ), "Uploaded file: " + _uploadInfo.name ); uploadInfo = _uploadInfo; }); }); -//TODO: for each uploaded file: 1 file per (standard) datatype (or some subset) -// txt, tabular, sam, bam, fasta, fastq, bed, gff, -*/ +spaceghost.then( function checkPanelStructure(){ + this.test.comment( 'checking structure of non-empty panel' ); -// ------------------------------------------------------------------- -//history panel - // structure of empty - // upload file - // structure of not empty - // tags - // annotation - // history refresh - // history options - // structure + this.withFrame( this.selectors.frames.history, function(){ + this.test.comment( "history name should exist, be visible, and have text " + unnamedName ); + this.test.assertExists( nameSelector, nameSelector + ' exists' ); + this.test.assertVisible( nameSelector, 'History name is visible' ); + this.test.assertSelectorHasText( nameSelector, newHistoryName, 'History name is ' + newHistoryName ); - // deleted + this.test.comment( "history subtitle should display size and size should be " + onetxtFilesize + " bytes" ); + var onetxtFilesize = require( 'fs' ).size( this.options.scriptDir + filepathToUpload ), + expectedSubtitle = onetxtFilesize + ' bytes'; + this.test.assertExists( subtitleSelector, 'Found ' + subtitleSelector ); + this.test.assertVisible( subtitleSelector, 'History subtitle is visible' ); + this.test.assertSelectorHasText( subtitleSelector, expectedSubtitle, + 'History subtitle has "' + expectedSubtitle + '"' ); - // hidden + this.test.comment( "tags and annotation icons should be available" ); + this.test.assertExists( tagIconSelector, 'Tag icon button found' ); + this.test.assertExists( annoIconSelector, 'Annotation icon button found' ); - // persistant expansion (or in hdaView?) + this.test.comment( "A message about the current history being empty should NOT be displayed" ); + this.test.assertExists( emptyMsgSelector, emptyMsgSelector + ' exists' ); + this.test.assertNotVisible( emptyMsgSelector, 'Empty history message is NOT visible' ); + }); +}); -//hdaView -// with hpanel: - // (we assume hda is in the ok state) - // with collapsed hda: - // can we see the hid? - // can we see the title? - // three primary action buttons: - // they exist? - // Do they have good hrefs, targets? - // Are they enabled? - // do they have proper tooltips? - // display - // edit - // delete - //??: click through? +// ------------------------------------------------------------------- tags +// keeping this light here - better for it's own test file +spaceghost.then( function openTags(){ + this.test.comment( 'tag area should open when the history panel tag icon is clicked' ); + this.withFrame( this.selectors.frames.history, function(){ + this.mouseEvent( 'click', tagIconSelector ); + this.wait( 1000, function(){ + this.test.assertVisible( tagAreaSelector, 'Tag area is now displayed' ); + }); + }); +}); +spaceghost.then( function closeTags(){ + this.test.comment( 'tag area should close when the history panel tag icon is clicked again' ); + this.withFrame( this.selectors.frames.history, function(){ + this.mouseEvent( 'click', tagIconSelector ); + this.wait( 1000, function(){ + this.test.assertNotVisible( tagAreaSelector, 'Tag area is now hidden' ); + }); + }); +}); - // with expaned hda: - // can we see the hid, title, and primary display buttons? +// ------------------------------------------------------------------- annotation +// keeping this light here - better for it's own test file +spaceghost.then( function openAnnotation(){ + this.test.comment( 'annotation area should open when the history panel annotation icon is clicked' ); + this.withFrame( this.selectors.frames.history, function(){ + this.mouseEvent( 'click', annoIconSelector ); + this.wait( 1000, function(){ + this.test.assertVisible( annoAreaSelector, 'Annotation area is now displayed' ); + }); + }); +}); +spaceghost.then( function closeAnnotation(){ + this.test.comment( 'annotation area should close when the history panel tag icon is clicked again' ); + this.withFrame( this.selectors.frames.history, function bler(){ + this.mouseEvent( 'click', annoIconSelector ); + this.wait( 1000, function(){ + this.test.assertNotVisible( annoAreaSelector, 'Tag area is now hidden' ); + }); + }); +}); - // misc info: no dbkey specified - is there a '?' link leading to edit attr? - // misc info: uploaded sam file - // misc info: format: sam +// ------------------------------------------------------------------- refresh button +spaceghost.then( function refreshButton(){ + this.test.comment( 'History panel should refresh when the history refresh icon is clicked' ); - // secondary actions: - // download - // info - // rerun - // visualizations + this.test.assertExists( refreshButtonSelector, "Found refresh button" ); + this.test.assertVisible( refreshButtonSelector, "Refresh button is visible" ); + this.test.assertVisible( refreshButtonSelector + ' ' + refreshButtonIconSelector, "Refresh icon is visible" ); + this.test.assert( this.getElementAttribute( refreshButtonSelector, 'href' ) === refreshButtonHref, + "Refresh button has href: " + refreshButtonHref ); - // tags and annotations - //TODO: to their own file? tested elsewhere? + this.assertNavigationRequested( refreshButtonHref, "History refreshed when clicking refresh icon", function(){ + this.click( refreshButtonSelector ); + }); +}); - // peek: - // proper headers? - // lines? - // scrollbar? +// ------------------------------------------------------------------- history options menu structure +//NOTE: options menu should be functionally tested elsewhere +spaceghost.then( function historyOptions(){ + this.test.comment( 'History options icon should be in place and menu should have the proper structure' ); - // can re-collapse? + // check the button and icon + this.test.assertExists( this.historyoptions.data.selectors.button, "Found history options button" ); + this.test.assertVisible( this.historyoptions.data.selectors.button, "History options button is visible" ); + this.test.assertVisible( this.historyoptions.data.selectors.buttonIcon, "History options icon is visible" ); + // open the menu + this.click( this.historyoptions.data.selectors.button ); + this.test.assertVisible( this.historyoptions.data.selectors.menu, + "Menu is visible when options button is clicked" ); + // check the options + for( var optionKey in this.historyoptions.data.labels.options ){ + if( this.historyoptions.data.labels.options.hasOwnProperty( optionKey ) ){ + var optionLabel = this.historyoptions.data.labels.options[ optionKey ], + optionXpath = this.historyoptions.data.selectors.optionXpathByLabelFn( optionLabel ); + this.test.assertVisible( optionXpath, 'Option label is visible: ' + optionLabel ); + } + } +}); +// ------------------------------------------------------------------- deleted hdas aren't in the dom +spaceghost.then( function(){ + this.test.comment( 'deleted hdas shouldn\'t be in the history panel DOM' ); + this.historypanel.deleteHda( '#' + uploadInfo.hdaElement.attributes.id, function(){ + this.test.assertDoesntExist( '#' + uploadInfo.hdaElement.attributes.id, "Deleted HDA is not in the DOM" ); + }); +}); +// ------------------------------------------------------------------- options allow showing/hiding deleted hdas +spaceghost.then( function(){ + this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' shows deleted datasets' ); + this.historyoptions.includeDeleted(); + this.withFrame( this.selectors.frames.history, function(){ + this.waitForSelector( nameSelector, function(){ + this.test.assertExists( '#' + uploadInfo.hdaElement.attributes.id, + "Deleted HDA is in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); + this.test.assertVisible( '#' + uploadInfo.hdaElement.attributes.id, + "Deleted HDA is visible again (using history options -> " + includeDeletedOptionsLabel + ")" ); + }); + }); +}); +spaceghost.then( function(){ + this.test.comment( 'History options->' + includeDeletedOptionsLabel + ' (again) re-hides deleted datasets' ); + + this.historyoptions.includeDeleted(); + this.withFrame( this.selectors.frames.history, function(){ + this.waitForSelector( nameSelector, function(){ + this.test.assertDoesntExist( '#' + uploadInfo.hdaElement.attributes.id, + "Deleted HDA is not in the DOM (using history options -> " + includeDeletedOptionsLabel + ")" ); + }); + }); +}); + +// undelete the uploaded file +spaceghost.then( function(){ + this.historyoptions.includeDeleted(); + this.withFrame( this.selectors.frames.history, function(){ + this.waitForSelector( nameSelector, function(){ + //TODO: to conv. fn + this.click( '#' + uploadInfo.hdaElement.attributes.id + ' .historyItemUndelete' ); + }); + }); +}); + +// ------------------------------------------------------------------- hidden hdas aren't shown +// ------------------------------------------------------------------- history options allows showing hidden hdas +// can't test this yet w/o a way to make hdas hidden thru the ui or api + +// ------------------------------------------------------------------- hdas can be expanded by clicking on the hda name +// broken in webkit w/ jq 1.7 +spaceghost.then( function(){ + this.test.comment( 'HDAs can be expanded by clicking on the name' ); + var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + + this.withFrame( this.selectors.frames.history, function(){ + this.click( uploadedSelector + ' .historyItemTitle' ); + this.debug( 'title: ' + this.debugElement( uploadedSelector + ' .historyItemTitle' ) ); + this.debug( 'wrapper: ' + this.debugElement( uploadedSelector ) ); + + this.wait( 1000, function(){ + this.test.assertExists( uploadedSelector + ' .historyItemBody', "Body for uploaded file is found" ); + this.test.assertVisible( uploadedSelector + ' .hda-summary', "hda-summary is visible" ); + }); + }); +}); + +// ------------------------------------------------------------------- expanded hdas are still expanded after a refresh +spaceghost.then( function(){ + this.test.comment( 'Expanded hdas are still expanded after a refresh' ); + var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + + this.click( refreshButtonSelector ); + this.withFrame( this.selectors.frames.history, function(){ + this.waitForSelector( nameSelector, function(){ + this.test.assertExists( uploadedSelector + ' .historyItemBody', "Body for uploaded file is found" ); + this.test.assertVisible( uploadedSelector + ' .hda-summary', "hda-summary is visible" ); + }); + }); + // this will break: webkit + jq 1.7 +}); + +// ------------------------------------------------------------------- expanded hdas collapse by clicking name again +spaceghost.then( function(){ + this.test.comment( 'Expanded hdas collapse by clicking name again' ); + var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + + this.withFrame( this.selectors.frames.history, function(){ + this.click( uploadedSelector + ' .historyItemTitle' ); + + this.wait( 500, function(){ + this.test.assertNotVisible( uploadedSelector + ' .hda-summary', "hda-summary is not visible" ); + }); + }); +}); + +// ------------------------------------------------------------------- collapsed hdas are still collapsed after a refresh +spaceghost.then( function(){ + this.test.comment( 'Expanded hdas are still expanded after a refresh' ); + var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + + this.click( refreshButtonSelector ); + this.withFrame( this.selectors.frames.history, function(){ + this.waitForSelector( nameSelector, function(){ + this.test.assertNotVisible( uploadedSelector + ' .hda-summary', "hda-summary is not visible" ); + }); + }); +}); + +// ------------------------------------------------------------------- history options collapses all expanded hdas +spaceghost.then( function(){ + // expand again + this.withFrame( this.selectors.frames.history, function(){ + this.click( '#' + uploadInfo.hdaElement.attributes.id + ' .historyItemTitle' ); + this.wait( 500, function(){}); + }); +}); +spaceghost.then( function(){ + this.test.comment( 'History option collapses all expanded hdas' ); + var uploadedSelector = '#' + uploadInfo.hdaElement.attributes.id; + + this.historyoptions.collapseExpanded(); + this.wait( 500, function(){ + this.withFrame( this.selectors.frames.history, function(){ + this.test.assertNotVisible( uploadedSelector + ' .hda-summary', "hda-summary is not visible" ); + }); + }); +}); // =================================================================== spaceghost.run( function(){ diff -r 592af505e4e673aa891e9163bd237dbbc728ba62 -r 0a6a4752493eacfac2fb7a537d30be0333a58977 test/casperjs/modules/historyoptions.js --- /dev/null +++ b/test/casperjs/modules/historyoptions.js @@ -0,0 +1,160 @@ +// =================================================================== module object, exports +/** Creates a new historyoptions module object. + * @exported + */ +exports.create = function createHistoryOptions( spaceghost ){ + return new HistoryOptions( spaceghost ); +}; + +/** HistoryOptions object constructor. + * @param {SpaceGhost} spaceghost a spaceghost instance + */ +var HistoryOptions = function HistoryOptions( spaceghost ){ + //??: circ ref? + this.spaceghost = spaceghost; +}; +exports.HistoryOptions = HistoryOptions; + +HistoryOptions.prototype.toString = function toString(){ + return this.spaceghost + '.HistoryOptions'; +}; + +// ------------------------------------------------------------------- +/* TODO: + + +*/ +// =================================================================== API (external) +/** Just open the menu + */ +HistoryOptions.prototype.openMenu = function openMenu(){ + this.spaceghost.click( this.data.selectors.button ); +}; + +/** Click an option by Label + */ +HistoryOptions.prototype.clickOption = function clickOption( optionLabel ){ + this.openMenu(); + // casperjs clickLabel + var optionXpath = this.data.selectors.optionXpathByLabelFn( optionLabel ); + this.spaceghost.click( optionXpath ); +}; + +// ------------------------------------------------------------------- +// these options lead to controller pages - encapsulate those pages here +/** corresponds to history options menu: 'Saved Histories' + * @param {String} historyName the name of the history + */ +//HistoryOptions.prototype.savedHistoryByName = function savedHistoryByName( historyName ){ +//}; +/** corresponds to history options menu: 'Histories Shared with Me' + * @param {String} historyName the name of the history + */ +//HistoryOptions.prototype.sharedHistoryByName = function sharedHistoryByName( historyName ){ +//}; + +/** corresponds to history options menu: 'Create New' + */ +//HistoryOptions.prototype.createNew = function createNew(){ +//}; + +/** corresponds to history options menu: 'Copy History' + */ +//HistoryOptions.prototype.copyHistory = function copyHistory(){ +//}; + +/** corresponds to history options menu: 'Copy Datasets' + */ +//HistoryOptions.prototype.copyDatasets = function copyDatasets(){ +//}; + +/** corresponds to history options menu: 'Extract Workflow' + */ +//HistoryOptions.prototype.extractWorkflow = function extractWorkflow(){ +//}; + +/** corresponds to history options menu: 'Share or Publish' + */ +//HistoryOptions.prototype.shareHistoryViaLink = function shareHistoryViaLink(){ +//}; +/** corresponds to history options menu: 'Share or Publish' + */ +//HistoryOptions.prototype.publishHistory = function publishHistory(){ +//}; +/** corresponds to history options menu: 'Share or Publish' + */ +//HistoryOptions.prototype.shareHistoryWithUser = function shareHistoryWithUser(){ +//}; + +/** corresponds to history options menu: 'Dataset Security' + */ +//HistoryOptions.prototype.managePermissions = function managePermissions(){ +//}; +/** corresponds to history options menu: 'Dataset Security' + */ +//HistoryOptions.prototype.accessPermissions = function accessPermissions(){ +//}; + +/** corresponds to history options menu: 'Resume Paused Jobs' + */ +//HistoryOptions.prototype.resumePausedJobs = function resumePausedJobs(){ +//}; + + +// ------------------------------------------------------------------- +// these are easy, one click options (they don't open a new page) +/** corresponds to history options menu: 'Collapse Expanded Datasets' + */ +HistoryOptions.prototype.collapseExpanded = function collapseExpanded(){ + this.clickOption( this.data.labels.options.collapseExpanded ); +}; +/** corresponds to history options menu: 'Include Deleted Datasets' + */ +HistoryOptions.prototype.includeDeleted = function includeDeleted(){ + this.clickOption( this.data.labels.options.includeDeleted ); +}; +/** corresponds to history options menu: 'Include Hidden Datasets' + */ +HistoryOptions.prototype.includeHidden = function includeHidden(){ + this.clickOption( this.data.labels.options.includeHidden ); +}; + + +// =================================================================== SELECTORS +//TODO: data is not a very good name +HistoryOptions.prototype.data = { + selectors : { + button : '#history-options-button', + buttonIcon : '#history-options-button span.fa-icon-cog', + menu : '#history-options-button-menu', + optionXpathByLabelFn : function optionXpathByLabelFn( label ){ + return xpath( '//ul[@id="history-options-button-menu"]/li/a[text()[contains(.,"' + label + '")]]' ); + } + }, + labels : { + options : { + //History Lists + savedHistories : "Saved Histories", + sharedHistories : "Histories Shared with Me", + //Current History + createNew : "Create New", + copyHistory : "Copy History", + copyDatasets : "Copy Datasets", + shareOrPublish : "Share or Publish", + extractWorkflow : "Extract Workflow", + datasetSecurity : "Dataset Security", + resumePausedJobs : "Resume Paused Jobs", + collapseExpanded : 'Collapse Expanded Datasets', + includeDeleted : 'Include Deleted Datasets', + includeHidden : 'Include Hidden Datasets', + unhideHiddenDatasets : "Unhide Hidden Datasets", + purgeDeletedDatasets : "Purge Deleted Datasets", + showStructure : "Show Structure", + exportToFile : "Export to File", + deleteHistory : "Delete", + deleteHistoryPermanently : "Delete Permanently", + //Other Actions + importFromFile : "Import from File" + } + } +}; diff -r 592af505e4e673aa891e9163bd237dbbc728ba62 -r 0a6a4752493eacfac2fb7a537d30be0333a58977 test/casperjs/modules/historypanel.js --- a/test/casperjs/modules/historypanel.js +++ b/test/casperjs/modules/historypanel.js @@ -1,5 +1,5 @@ // =================================================================== module object, exports -/** Creates a new tools module object. +/** Creates a new historypanel module object. * @exported */ exports.create = function createHistoryPanel( spaceghost ){ @@ -24,13 +24,15 @@ // ------------------------------------------------------------------- /* TODO: - run a tool + conv.fns: + expand hda (click title) + undelete hda + rename history */ // =================================================================== INTERNAL // =================================================================== API (external) -//TODO: to history module /** Find the casper element info of the hda wrapper given the hda title and hid. * NOTE: if more than one is found, will return the first found. * precondition: you should wrap this with withFrame( 'galaxy_history' ) :( @@ -116,3 +118,84 @@ }); }); }; + +/** Find the casper element info of the hda wrapper given the hda title and hid. + * NOTE: if more than one is found, will return the first found. + * precondition: you should wrap this with withFrame( 'galaxy_history' ) :( + * @param {String} title the title of the hda + * @param {Int} hid (optional) the hid of the hda to look for + * @returns {Object|null} ElementInfo of the historyItemWrapper found, null if not found + */ +HistoryPanel.prototype.hdaElementInfoByTitle = function hdaElementInfoByTitle( title, hid ){ + var titleContains = ( hid !== undefined )?( hid + ': ' + title ):( title ), + wrapperInfo = this.spaceghost.elementInfoOrNull( + //TODO??: how to put this in editable json file + xpath( '//span[contains(text(),"' + titleContains + '")]/parent::*/parent::*' ) ); + //this.spaceghost.debug( 'wrapperInfo: ' + this.spaceghost.jsonStr( wrapperInfo ) ); + return wrapperInfo; +}; +//TODO!: this will break if the hda name has single or double quotes (which are permitted in names) + +/** Find the id of the hda wrapper given the hda title and hid. + * @param {String} title the title of the hda + * @param {Int} hid (optional) the hid of the hda to look for + * @returns {String|null} DOM id of the historyItemWrapper found, null if not found + */ +HistoryPanel.prototype.hdaIdByTitle = function hdaIdByTitle( title, hid ){ + var elementInfo = this.hdaElementInfoByTitle( title, hid ); + return (( elementInfo && elementInfo.attributes && elementInfo.attributes.id )? + ( elementInfo.attributes.id ):( null )); +}; + +/** Deletes an hda by finding an hda with the given title and clicking on the delete icon. + * NOTE: if more than one is found, the first found will be deleted. + * @param {String} hdaSelector a css or xpath selector for an historyItemWrapper + * @param {Function} whenDeletedFn function to be called when the hda is deleted (optional) + * @param {Function} timeoutFn function to be called if/when the deleted attempted times out (optional) + */ +HistoryPanel.prototype.deleteHda = function deleteHda( hdaSelector, whenDeletedFn, timeoutFn ){ + whenDeletedFn = whenDeletedFn || function(){}; + var spaceghost = this.spaceghost; + + spaceghost.withFrame( spaceghost.selectors.frames.history, function deletingHda(){ + //precondition: historyItemWrapper's (hda dom elements) should have an id + // we could use the selector directly, but better if it errors before an attempted delete + var hdaId = spaceghost.getElementInfo( hdaSelector ).attributes.id; + spaceghost.debug( 'hda id: ' + spaceghost.jsonStr( hdaId ) ); + + // get the delete icon and click it + //TODO: handle disabled delete icon? + var deleteIconSelector = 'a[id^="historyItemDeleter-"]', + thisDeleteIconSelector = '#' + hdaId + ' ' + deleteIconSelector; + spaceghost.click( thisDeleteIconSelector ); + + spaceghost.waitWhileSelector( '#' + hdaId, + function hdaNoLongerInDom(){ + spaceghost.info( 'hda deleted: ' + hdaSelector ); + whenDeletedFn.call( spaceghost ); + + }, function timeout(){ + if( timeoutFn ){ + timeoutFn.call( spaceghost ); + } else { + throw new spaceghost.GalaxyError( 'HistoryPanelError: ' + + 'timeout attempting to delete hda : ' + hdaSelector ); + } + }); + }); +}; + +/** Expands an HDA. + * @param {String} hdaSelector a css or xpath selector for an historyItemWrapper + */ +HistoryPanel.prototype.expandHda = function expandHda( hdaSelector ){ + var spaceghost = this.spaceghost, + historyFrameInfo = spaceghost.getElementInfo( 'iframe[name="galaxy_history"]' ); + + spaceghost.withFrame( spaceghost.selectors.frames.history, function expandingHda(){ + var titleInfo = spaceghost.getElementInfo( hdaSelector + ' .historyItemTitle' ); + spaceghost.page.sendEvent( 'mousedown', + historyFrameInfo.x + titleInfo.x + 1, historyFrameInfo.y + titleInfo.y - 5 ); + }); + return spaceghost; +}; diff -r 592af505e4e673aa891e9163bd237dbbc728ba62 -r 0a6a4752493eacfac2fb7a537d30be0333a58977 test/casperjs/modules/tools.js --- a/test/casperjs/modules/tools.js +++ b/test/casperjs/modules/tools.js @@ -154,7 +154,7 @@ uploadInfo = {}; // precondition: filepath is relative to scriptDir - filepath = spaceghost.options.scriptDir + '/' + filepath; + filepath = spaceghost.options.scriptDir + filepath; // upload the file erroring if a done message is not displayed, aggregate info about upload spaceghost.info( 'uploading file: ' + filepath + ' (timeout after ' + timeoutAfterMs + ')' ); @@ -179,14 +179,16 @@ spaceghost.debug( 'beginning wait for upload file\'s ok state' ); // get the hda view DOM element from the upload name and hid spaceghost.withFrame( spaceghost.selectors.frames.history, function(){ - var hdaInfo = spaceghost.historypanel.hdaElementInfoByTitle( uploadInfo.name, uploadInfo.hid ); - if( !hdaInfo ){ - throw new spaceghost.GalaxyError( 'Upload Error: uploaded file HDA not found: ' - + uploadInfo.hid + ', ' + uploadInfo.name ); - } - spaceghost.debug( 'hdaInfo: ' + spaceghost.jsonStr( hdaInfo ) ); - uploadInfo.hdaElement = hdaInfo; - // uploadInfo now has filepath, filename, name, hid, and hdaElement + spaceghost.waitForSelector( '#history-name', function(){ + var hdaInfo = spaceghost.historypanel.hdaElementInfoByTitle( uploadInfo.name, uploadInfo.hid ); + if( hdaInfo === null ){ + throw new spaceghost.GalaxyError( 'Upload Error: uploaded file HDA not found: ' + + uploadInfo.hid + ', ' + uploadInfo.name ); + } + spaceghost.debug( 'hdaInfo: ' + spaceghost.jsonStr( hdaInfo ) ); + uploadInfo.hdaElement = hdaInfo; + // uploadInfo now has filepath, filename, name, hid, and hdaElement + }); }); spaceghost.then( function waitForOk(){ @@ -217,5 +219,3 @@ }; //TODO: upload via url //TODO: upload by textarea - - diff -r 592af505e4e673aa891e9163bd237dbbc728ba62 -r 0a6a4752493eacfac2fb7a537d30be0333a58977 test/casperjs/modules/user.js --- a/test/casperjs/modules/user.js +++ b/test/casperjs/modules/user.js @@ -68,7 +68,7 @@ * @param {String} email the users email address * @param {String} password the users password */ -User.prototype._submitLogin = function logoutUser( email, password ){ +User.prototype._submitLogin = function _submitLogin( email, password ){ var spaceghost = this.spaceghost, loginInfo = { //NOTE: keys are used as name selectors in the fill fn - must match the names of the inputs @@ -166,7 +166,7 @@ /** Log out the current user * @returns {SpaceGhost} the spaceghost instance (for chaining) */ -User.prototype.logout = function logoutUser(){ +User.prototype.logout = function logout(){ var spaceghost = this.spaceghost; spaceghost.thenOpen( spaceghost.baseUrl, function(){ //TODO: handle already logged out @@ -205,5 +205,3 @@ domain = domain || 'test.test'; return username + Date.now() + '@' + domain; }; - - diff -r 592af505e4e673aa891e9163bd237dbbc728ba62 -r 0a6a4752493eacfac2fb7a537d30be0333a58977 test/casperjs/page-data/selectors.json --- /dev/null +++ b/test/casperjs/page-data/selectors.json @@ -0,0 +1,35 @@ +{ + "cookies" : { + "galaxyCookieName" : "galaxysession" + }, + + "selectors" : { + "historyPanel" : { + "name" : "div#history-name", + "subtitle" : "div#history-subtitle-area", + "tagIcon" : "#history-tag.icon-button", + "annoIcon" : "#history-annotate.icon-button", + "emptyMsg" : ".infomessagesmall" + }, + + "bootstrap" : { + "activeTooltip" : ".bs-tooltip" + }, + + "editableText" : { + "class" : "editable-text", + "activeInput" : "input#renaming-active" + } + }, + + "text" : { + "historyPanel" : { + "newName" : "Unnamed history", + "initialSizeStr" : "0 bytes", + "emptyMsgStr" : "Your history is empty. Click 'Get Data' on the left pane to start", + "tooltips" : { + "anonUserName" : "You must be logged in to edit your history name" + } + } + } +} diff -r 592af505e4e673aa891e9163bd237dbbc728ba62 -r 0a6a4752493eacfac2fb7a537d30be0333a58977 test/casperjs/spaceghost.js --- a/test/casperjs/spaceghost.js +++ b/test/casperjs/spaceghost.js @@ -2,6 +2,8 @@ Use in test command bug: assertStepsRaise raise errors (all the way) when used in 'casperjs test .' + normalize names of fns that use withFrame or then to 'then<action>' + make any callbacks optional (that can be) Does it run: casperjs usertests.js --url='http://localhost:8080' @@ -174,6 +176,8 @@ /** Set up any SG specific options passed in on the cli. */ SpaceGhost.prototype._processCLIArguments = function _processCLIArguments(){ + //this.debug( 'cli: ' + this.jsonStr( this.cli ) ); + //TODO: init these programmitically var CLI_OPTIONS = { returnJsonOnly : { defaultsTo: false, flag: 'return-json', help: 'send output to stderr, json to stdout' }, @@ -248,7 +252,7 @@ // get any fixture data passed in as JSON in args // (NOTE: currently the 2nd arg (with the url being 1st?) - this.fixtureData = ( this.cli.has( 1 ) )?( JSON.parse( this.cli.get( 1 ) ) ):( {} ); + this.fixtureData = ( this.cli.has( 0 ) )?( JSON.parse( this.cli.get( 0 ) ) ):( {} ); this.debug( 'fixtureData:' + this.jsonStr( this.fixtureData ) ); }; @@ -329,6 +333,14 @@ } }; +/** Event handler for step/casper timeouts - throws PageError + */ +SpaceGhost.prototype._timeoutHandler = function _timeoutHandler(){ + console.debug( 'timeout' ); + //msg = msg.replace( 'PageError: ', '' ); + throw new PageError( 'Timeout occurred' ); +}; + /** Event handler for console messages from the page. */ SpaceGhost.prototype._pageConsoleHandler = function _pageConsoleHandler(){ @@ -372,6 +384,9 @@ // ........................ page errors this.on( 'page.error', this._pageErrorHandler ); //this.on( 'load.failed', this._loadFailedHandler ); + this.on( 'timeout', this._timeoutHandler ); + this.on( 'step.timeout', this._timeoutHandler ); + this.on( 'waitFor.timeout', this._timeoutHandler ); // ........................ page info/debugging // these are already displayed at the casper info level @@ -391,6 +406,7 @@ this.user = require( this.options.scriptDir + 'modules/user' ).create( this ); this.tools = require( this.options.scriptDir + 'modules/tools' ).create( this ); this.historypanel = require( this.options.scriptDir + 'modules/historypanel' ).create( this ); + this.historyoptions = require( this.options.scriptDir + 'modules/historyoptions' ).create( this ); }; // =================================================================== PAGE CONTROL @@ -527,6 +543,32 @@ this.tryStepsCatch( stepsFn, testTheError ); }; +/** Assert that a function causes a navigation request with (at least partially) the given url. + * NOTE: _should_ play well with steps (e.g. then, thenOpen, etc.) + * @param {String} url some portion of the expected url for the nav request + * @param {String} message the assertion message + * @param {Function} fnThatRequests a function that causes a navigation request (e.g. click a link) + */ +SpaceGhost.prototype.assertNavigationRequested = function assertNavigationRequested( expectedUrl, message, + fnThatRequests ){ + var requested = false; + function captureNavReq( url, navigationType, navigationLocked, isMainFrame ){ + this.debug( 'Checking navigation.requested for url: ' + expectedUrl ); + // use || here to handle multiple requests, if any one url works -> test will pass + requested = requested || ( url.indexOf( expectedUrl ) !== -1 ); + } + this.then( function(){ + this.on( 'navigation.requested', captureNavReq ); + }); + this.then( function(){ + fnThatRequests.call( this ); + }); + this.then( function(){ + this.removeListener( 'navigation.requested', captureNavReq ); + this.test.assert( requested, message ); + }); +}; + // =================================================================== CONVENIENCE /** Wraps casper.getElementInfo in try, returning null if element not found instead of erroring. * @param {String} selector css or xpath selector for the element to find @@ -605,6 +647,12 @@ return JSON.stringify( obj, null, 2 ); }; +/** output to debug the JSON of the selector (or null if not found) + */ +SpaceGhost.prototype.debugElement = function debugElement( selector ){ + this.debug( this.jsonStr( this.elementInfoOrNull( selector ) ) ); +}; + /** Debug SG itself */ SpaceGhost.prototype.debugMe = function(){ @@ -720,6 +768,13 @@ return JSON.parse( require( 'fs' ).read( filepath ) ); }; +SpaceGhost.prototype.writeJSONFile = function writeJSONFile( filepath, object, mode ){ + mode = mode || 'w'; + //precondition: filepath is relative to script dir + filepath = this.options.scriptDir + filepath; + return require( 'fs' ).write( filepath, this.jsonStr( object ), mode ); +}; + // =================================================================== EXPORTS /** */ @@ -733,4 +788,3 @@ "use strict"; return new SpaceGhost(options); }; - 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 baseline support for reviewing functional test results for installing repositories and executing functional tests on the contained tool inside a Galaxy instance for tools included in repositories in the tool shed.
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/592af505e4e6/ changeset: 592af505e4e6 user: greg date: 2013-03-05 18:36:58 summary: Add baseline support for reviewing functional test results for installing repositories and executing functional tests on the contained tool inside a Galaxy instance for tools included in repositories in the tool shed. affected #: 4 files diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 592af505e4e673aa891e9163bd237dbbc728ba62 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 @@ -672,20 +672,32 @@ status='error' ) ) @web.expose - def display_tool_functional_test_errors( self, trans, repository_id, repository_metadata_id, **kwd ): + def display_tool_functional_test_results( self, trans, repository_id, repository_metadata_id, **kwd ): + """ + The test framework in ~/test/install_and_test_tool_shed_repositories can be executed on a regularly defined schedule (e.g., via cron) to install appropriate + repositories from a tool shed into a Galaxy instance and run defined functional tests for the tools included in the repository. This process affects the values + if these columns in the repository_metadata table: tools_functionally_correct, do_not_test, time_last_tested and tool_test_errors. The tool_test_errors is + slightly mis-named (it should have been named tool_test_results) it will contain a dictionary that includes information about the test environment even if all + tests passed and the tools_functionally_correct column is set to True. + The value of the tool_test_errors column will be a dictionary with the key / value pairs: + "test_environment", {"architecture": "i386", "python_version": "2.5.4", "system": "Darwin 10.8.0"} + "test_errors" [ { "test_id":<some test id>, "stdout":<stdout of running the test>, "stderr":<stderr of running the test>, "traceback":<traceback of running the test>] + """ params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) - repository = suc.get_repository_by_id( trans.app, repository_id ) + repository = suc.get_repository_by_id( trans, repository_id ) if repository: repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) changeset_revision = repository_metadata.changeset_revision if repository_metadata: metadata = repository_metadata.metadata if metadata: - return trans.fill_template( '/webapps/tool_shed/repository/display_tool_functional_test_errors.mako', + revision_label = suc.get_revision_label( trans, repository, repository_metadata.changeset_revision ) + return trans.fill_template( '/webapps/tool_shed/repository/display_tool_functional_test_results.mako', repository=repository, repository_metadata=repository_metadata, + revision_label=revision_label, message=message, status=status ) else: @@ -1636,7 +1648,6 @@ downloadable=False ) revision_label = suc.get_revision_label( trans, repository, repository.tip( trans.app ) ) repository_metadata = None - repository_metadata_id = None metadata = None is_malicious = False repository_dependencies = None @@ -1644,7 +1655,6 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: revision_label = suc.get_revision_label( trans, repository, changeset_revision ) - repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious else: @@ -1654,7 +1664,6 @@ repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, previous_changeset_revision ) if repository_metadata: revision_label = suc.get_revision_label( trans, repository, previous_changeset_revision ) - repository_metadata_id = trans.security.encode_id( repository_metadata.id ) metadata = repository_metadata.metadata is_malicious = repository_metadata.malicious if repository_metadata: @@ -1702,7 +1711,7 @@ repo=repo, repository=repository, containers_dict=containers_dict, - repository_metadata_id=repository_metadata_id, + repository_metadata=repository_metadata, changeset_revision=changeset_revision, reviewed_by_user=reviewed_by_user, review_id=review_id, diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 592af505e4e673aa891e9163bd237dbbc728ba62 lib/tool_shed/util/shed_util_common.py --- a/lib/tool_shed/util/shed_util_common.py +++ b/lib/tool_shed/util/shed_util_common.py @@ -2134,13 +2134,12 @@ elif len( repo_info_tuple ) == 7: description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies = repo_info_tuple return description, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_dependencies, tool_dependencies -def get_repository_by_id( app, id ): +def get_repository_by_id( trans, id ): """Get a repository from the database via id.""" - sa_session = app.model.context.current - if app.name == 'galaxy': - return sa_session.query( app.model.ToolShedRepository ).get( id ) + if trans.webapp.name == 'galaxy': + return trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( id ) ) else: - return sa_session.query( app.model.Repository ).get( id ) + return trans.sa_session.query( trans.model.Repository ).get( trans.security.decode_id( id ) ) def get_repository_by_name( app, name ): """Get a repository from the database via name.""" sa_session = app.model.context.current diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 592af505e4e673aa891e9163bd237dbbc728ba62 templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako --- /dev/null +++ b/templates/webapps/tool_shed/repository/display_tool_functional_test_results.mako @@ -0,0 +1,185 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> +<%namespace file="/webapps/tool_shed/common/common.mako" import="*" /> +<%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /> + +<% + from galaxy.web.framework.helpers import time_ago + + changeset_revision = repository_metadata.changeset_revision + has_metadata = repository.metadata_revisions + has_readme = metadata and 'readme' in metadata + is_admin = trans.user_is_admin() + is_new = repository.is_new( trans.app ) + is_deprecated = repository.deprecated + + can_browse_contents = trans.webapp.name == 'tool_shed' and not is_new + can_contact_owner = trans.user and trans.user != repository.user + can_download = not is_new and ( not is_malicious or can_push ) + can_manage = is_admin or repository.user == trans.user + can_push = trans.app.security_agent.can_push( trans.app, trans.user, repository ) + can_rate = repository.user != trans.user + can_review_repository = has_metadata and not is_deprecated and trans.app.security_agent.user_can_review_repositories( trans.user ) + can_upload = can_push + can_view_change_log = trans.webapp.name == 'tool_shed' and not is_new + if repository_metadata.tool_test_errors: + # The tool_test_errors is mis-named (it should have been named tool_test_results) it will contain a dictionary that includes information + # about the test environment even if all tests passed and the repository_metadata.tools_functionally_correct column is set to True. + tool_test_errors = repository_metadata.tool_test_errors + test_environment_dict = tool_test_errors.get( 'test_environment', None ) + test_errors = tool_test_errors.get( 'test_errors', [] ) + else: + tool_test_errors = None + test_environment_dict = {} + test_errors = [] + + if can_push: + browse_label = 'Browse or delete repository tip files' + else: + browse_label = 'Browse repository tip files' +%> + +<%! + def inherit(context): + if context.get('use_panels'): + return '/webapps/tool_shed/base_panels.mako' + else: + return '/base.mako' +%> +<%inherit file="${inherit(context)}"/> + +<br/><br/> +<ul class="manage-table-actions"> + %if is_new: + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> + %else: + <li><a class="action-button" id="repository-${repository.id}-popup" class="menubutton">Repository Actions</a></li> + <div popupmenu="repository-${repository.id}-popup"> + %if can_review_repository: + %if reviewed_by_user: + <a class="action-button" href="${h.url_for( controller='repository_review', action='edit_review', id=review_id )}">Manage my review of this revision</a> + %else: + <a class="action-button" href="${h.url_for( controller='repository_review', action='create_review', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Add a review to this revision</a> + %endif + %endif + %if can_manage: + <a class="action-button" href="${h.url_for( controller='repository', action='manage_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">Manage repository</a> + %else: + <a class="action-button" href="${h.url_for( controller='repository', action='view_repository', id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision )}">View repository</a> + %endif + %if can_upload: + <a class="action-button" href="${h.url_for( controller='upload', action='upload', repository_id=trans.security.encode_id( repository.id ) )}">Upload files to repository</a> + %endif + %if can_view_change_log: + <a class="action-button" href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">View change log</a> + %endif + %if can_browse_contents: + <a class="action-button" href="${h.url_for( controller='repository', action='browse_repository', id=trans.app.security.encode_id( repository.id ) )}">${browse_label}</a> + %endif + %if can_contact_owner: + <a class="action-button" href="${h.url_for( controller='repository', action='contact_owner', id=trans.security.encode_id( repository.id ) )}">Contact repository owner</a> + %endif + %if can_download: + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> + <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='zip' )}">Download as a zip file</a> + %endif + </div> + %endif +</ul> + +%if message: + ${render_msg( message, status )} +%endif + +<div class="toolForm"> + <div class="toolFormTitle">Repository revision</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Revision:</label> + %if can_view_change_log: + <a href="${h.url_for( controller='repository', action='view_changelog', id=trans.app.security.encode_id( repository.id ) )}">${revision_label}</a> + %else: + ${revision_label} + %endif + </div> + </div> +</div> +<p/> +%if can_download: + <div class="toolForm"> + <div class="toolFormTitle">Repository '${repository.name}'</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Clone this repository:</label> + ${render_clone_str( repository )} + </div> + </div> + </div> +%else: + <b>Repository name:</b><br/> + ${repository.name} +%endif +%if tool_test_errors: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Tool functional test results</div> + <div class="toolFormBody"> + <div class="form-row"> + <label>Time tested:</label> + ${time_ago( repository_metadata.time_last_tested ) | h} + </div> + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Test environment</td></tr> + </table> + </div> + <div class="form-row"> + <label>Architecture:</label> + ${test_environment_dict.get( 'architecture', 'unknown' ) | h} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Python version:</label> + ${test_environment_dict.get( 'python_version', 'unknown' ) | h} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <label>Operating system:</label> + ${test_environment_dict.get( 'system', 'unknown' ) | h} + <div style="clear: both"></div> + </div> + <div class="form-row"> + <table width="100%"> + <tr bgcolor="#D8D8D8" width="100%"><td><b>Test results</td></tr> + </table> + </div> + <div class="form-row"> + <table class="grid"> + %for test_results_dict in test_errors: + <tr> + <td bgcolor="#FFFFCC"><b>Test id</b></td> + <td bgcolor="#FFFFCC">${test_results_dict.get( 'test_id', 'unknown' )}</td> + </tr> + %if repository_metadata.tools_functionally_correct: + <tr> + <td><b>Stdout</b></td> + <td>${test_results_dict.get( 'stdout', '' )}</td> + </tr> + %else: + <tr> + <td><b>Stderr</b></td> + <td>${test_results_dict.get( 'stderr', '' )}</td> + </tr> + <tr> + <td><b>Traceback</b></td> + <td>${test_results_dict.get( 'traceback', '' )}</td> + </tr> + %endif + %endfor + </table> + <div style="clear: both"></div> + </div> + </div> + </div> +%endif diff -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 -r 592af505e4e673aa891e9163bd237dbbc728ba62 templates/webapps/tool_shed/repository/manage_repository.mako --- a/templates/webapps/tool_shed/repository/manage_repository.mako +++ b/templates/webapps/tool_shed/repository/manage_repository.mako @@ -26,6 +26,13 @@ can_undeprecate = trans.user and ( is_admin or repository.user == trans.user ) and is_deprecated can_upload = can_push can_view_change_log = not is_new + if repository_metadata: + if repository_metadata.includes_tools and repository_metadata.tool_test_errors is not None: + can_display_tool_functional_test_results = True + else: + can_display_tool_functional_test_results = False + else: + can_display_tool_functional_test_results = False if can_push: browse_label = 'Browse or delete repository tip files' @@ -105,6 +112,9 @@ %if can_undeprecate: <a class="action-button" href="${h.url_for( controller='repository', action='deprecate', id=trans.security.encode_id( repository.id ), mark_deprecated=False )}">Mark repository as not deprecated</a> %endif + %if can_display_tool_functional_test_results: + <a class="action-button" href="${h.url_for( controller='repository', action='display_tool_functional_test_results', repository_id=trans.security.encode_id( repository.id ), repository_metadata_id=trans.security.encode_id( repository_metadata.id ) )}">View tool functional test results</a> + %endif %if can_download: <a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='gz' )}">Download as a .tar.gz file</a><a class="action-button" href="${h.url_for( controller='repository', action='download', repository_id=trans.app.security.encode_id( repository.id ), changeset_revision=changeset_revision, file_type='bz2' )}">Download as a .tar.bz2 file</a> 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 05 Mar '13

05 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b5f22685678d/ changeset: b5f22685678d user: inithello date: 2013-03-05 16:23:21 summary: Script to check repositories and determine whether functional tests are defined for all tools, and set the do_not_test flag accordingly. Cleaned up the install and test framework and functional test common methods. affected #: 3 files diff -r d1f875d0f213c0ba5d858b34ac76d314803a6efb -r b5f22685678d6938467ef17c336e154f88698289 lib/tool_shed/scripts/check_repositories_for_functional_tests.py --- /dev/null +++ b/lib/tool_shed/scripts/check_repositories_for_functional_tests.py @@ -0,0 +1,274 @@ +#!/usr/bin/env python + +import os, sys, logging, tempfile + +new_path = [ os.path.join( os.getcwd(), "lib" ), os.path.join( os.getcwd(), "test" ) ] +new_path.extend( sys.path[1:] ) +sys.path = new_path + +log = logging.getLogger() +log.setLevel( 10 ) +log.addHandler( logging.StreamHandler( sys.stdout ) ) + +from galaxy import eggs +import pkg_resources +pkg_resources.require( "SQLAlchemy >= 0.4" ) +pkg_resources.require( 'mercurial' ) +from mercurial import hg, ui, commands + +import time, ConfigParser, shutil +from datetime import datetime, timedelta +from time import strftime +from optparse import OptionParser + +import galaxy.webapps.tool_shed.config as tool_shed_config +import galaxy.webapps.tool_shed.model.mapping +import sqlalchemy as sa +from galaxy.model.orm import and_, not_, distinct +from galaxy.util.json import from_json_string, to_json_string +from galaxy.web import url_for +from tool_shed.util.shed_util_common import clone_repository, get_configured_ui + +from base.util import get_test_environment + +assert sys.version_info[:2] >= ( 2, 4 ) + +def main(): + '''Script that checks repositories to see if the tools contained within them have functional tests defined.''' + parser = OptionParser() + parser.add_option( "-i", "--info_only", action="store_true", dest="info_only", help="info about the requested action", default=False ) + parser.add_option( "-v", "--verbose", action="store_true", dest="verbose", help="verbose mode, print the name, owner, and changeset revision of each repository", default=False ) + ( options, args ) = parser.parse_args() + ini_file = args[0] + config_parser = ConfigParser.ConfigParser( {'here':os.getcwd()} ) + config_parser.read( ini_file ) + config_dict = {} + for key, value in config_parser.items( "app:main" ): + config_dict[key] = value + config = tool_shed_config.Configuration( **config_dict ) + + now = strftime( "%Y-%m-%d %H:%M:%S" ) + print "#############################################################################" + print "# %s - Checking repositories for tools with functional tests." % now + app = FlagRepositoriesApplication( config ) + + if options.info_only: + print "# Displaying info only ( --info_only )" + if options.verbose: + print "# Displaying extra information ( --verbose )" + + check_and_flag_repositories( app, info_only=options.info_only, verbose=options.verbose ) + +def check_and_flag_repositories( app, info_only=False, verbose=False ): + ''' + This method will iterate through all records in the repository_metadata table, checking each one for tool metadata, + then checking the tool metadata for tests. + Each tool's metadata should look something like: + { + "add_to_tool_panel": true, + "description": "", + "guid": "toolshed.url:9009/repos/owner/name/tool_id/1.2.3", + "id": "tool_wrapper", + "name": "Map with Tool Wrapper", + "requirements": [], + "tests": [ + { + "inputs": [ [ "parameter", "value" ], [ "other_parameter", "other_value" ], ], + "name": "Test-1", + "outputs": [ + [ + "output_field_name", + "output_file_name.bed" + ] + ], + "required_files": [ '1.bed', '2.bed', '3.bed' ] + } + ], + "tool_config": "database/community_files/000/repo_1/tool_wrapper.xml", + "tool_type": "default", + "version": "1.2.3", + "version_string_cmd": null + } + + If the "tests" attribute is missing or empty, this script will mark the metadata record (which is specific to a changeset revision of a repository) + not to be tested. If each "tools" attribute has at least one valid "tests" entry, this script will do nothing, and leave it available for the install + and test repositories script to process. If the tested changeset revision does not have a test-data directory, this script will also mark the revision + not to be tested. + + If any error is encountered, the script will update the repository_metadata.tool_test_errors attribute with the following structure: + { + "test_environment": + { + "python_version": "2.7.2", + "architecture": "x86_64", + "system": "Darwin 12.2.0" + }, + "test_errors": + [ + { + "test_id": "Something that will easily identify what the problem is", + "stdout": "The output of the test, or a more detailed description of what was tested and why it failed." + }, + ] + } + ''' + start = time.time() + repository_ids_to_check = [] + tool_count = 0 + has_tests = 0 + no_tests = 0 + no_tools = 0 + # Get the list of metadata records to check for functional tests and test data. Limit this to records that have not been flagged do_not_test + # or tools_functionally_correct. Also filter out changeset revisions that are not downloadable, because it's redundant to test a revision that + # a user can't install. + metadata_records_to_check = app.sa_session.query( app.model.RepositoryMetadata ) \ + .filter( and_( app.model.RepositoryMetadata.table.c.downloadable == True, + app.model.RepositoryMetadata.table.c.do_not_test == False, + app.model.RepositoryMetadata.table.c.tools_functionally_correct == False ) ) \ + .all() + for metadata_record in metadata_records_to_check: + name = metadata_record.repository.name + owner = metadata_record.repository.user.username + changeset_revision = str( metadata_record.changeset_revision ) + repository_status = {} + # If this changeset revision has no tools, we don't need to do anything here, the install and test script has a filter for returning + # only repositories that contain tools. + if 'tools' not in metadata_record.metadata: + no_tools += 1 + continue + else: + # Initialize the repository_status dict with the test environment, but leave the test_errors empty. + repository_status[ 'test_environment' ] = get_test_environment() + repository_status[ 'test_errors' ] = [] + # Loop through all the tools in this metadata record, checking each one for defined functional tests. + for tool_metadata in metadata_record.metadata[ 'tools' ]: + tool_count += 1 + tool_id = tool_metadata[ 'id' ] + if verbose: + print '# Checking for functional tests in changeset revision %s of %s, tool ID %s.' % \ + ( changeset_revision, name, tool_id ) + # If there are no tests, this tool should not be tested, since the tool functional tests only report failure if the test itself fails, + # not if it's missing or undefined. Filtering out those repositories at this step will reduce the number of "false negatives" the + # automated functional test framework produces. + if 'tests' not in tool_metadata or not tool_metadata[ 'tests' ]: + if verbose: + print '# No functional tests defined for %s.' % tool_id + if 'test_errors' not in repository_status: + repository_status[ 'test_errors' ] = [] + test_id = 'Functional tests for %s' % tool_id + # The repository_metadata.tool_test_errors attribute should always have the following structure: + # { + # "environment": + # { + # "python_version": "2.7.2", + # "architecture": "x86_64", + # "system": "Darwin 12.2.0" + # }, + # "test_errors": + # [ + # { + # "test_id": "Something that will easily identify what the problem is", + # "stdout": "The output of the test, or a more detailed description of what was tested and why it failed." + # }, + # ] + # } + # Optionally, "stderr" and "traceback" may be included in a test_errors dict, if they are relevant. + test_errors = dict( test_id=test_id, + stdout='No functional tests defined in changeset revision %s of repository %s owned by %s.' % \ + ( changeset_revision, name, owner ) ) + repository_status[ 'test_errors' ].append( test_errors ) + no_tests += 1 + else: + has_tests += 1 + if verbose: + if not repository_status[ 'test_errors' ]: + print '# All tools have functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + else: + print '# Some tools missing functional tests in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + has_test_data = False + # Clone the repository up to the changeset revision we're checking. + repo_dir = metadata_record.repository.repo_path( app ) + repo = hg.repository( get_configured_ui(), repo_dir ) + work_dir = tempfile.mkdtemp() + cloned_ok, error_message = clone_repository( repo_dir, work_dir, changeset_revision ) + if cloned_ok: + # Iterate through all the directories in the cloned changeset revision and determine whether there's a + # directory named test-data. If this directory is not present, update the metadata record for the changeset + # revision we're checking. + for root, dirs, files in os.walk( work_dir ): + if '.hg' in dirs: + dirs.remove( '.hg' ) + if 'test-data' in dirs: + has_test_data = True + break + # Remove the cloned path. + if os.path.exists( work_dir ): + shutil.rmtree( work_dir ) + if not has_test_data: + if verbose: + print '# Test data missing in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + repository_status[ 'test_environment' ] = get_test_environment() + test_id = 'Find functional test data for %s' % metadata_record.repository.name + # The repository_metadata.tool_test_errors attribute should always have the following structure: + # { + # "test_environment": + # { + # "python_version": "2.7.2", + # "architecture": "x86_64", + # "system": "Darwin 12.2.0" + # }, + # "test_errors": + # [ + # { + # "test_id": "Something that will easily identify what the problem is", + # "stdout": "The output of the test, or a more detailed description of what was tested and why it failed." + # }, + # ] + # } + # Optionally, "stderr" and "traceback" may be included in a test_errors dict, if they are relevant. + test_errors = dict( test_id=test_id, + stdout='No test data found for changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) ) + repository_status[ 'test_errors' ].append( test_errors ) + else: + if verbose: + print '# Test data found in changeset revision %s of repository %s owned by %s.' % ( changeset_revision, name, owner ) + if not info_only: + if repository_status[ 'test_errors' ]: + metadata_record.do_not_test = True + metadata_record.tools_functionally_correct = False + metadata_record.tool_test_errors = to_json_string( repository_status ) + metadata_record.time_last_tested = datetime.utcnow() + app.sa_session.add( metadata_record ) + app.sa_session.flush() + stop = time.time() + print '# Checked %d tools in %d changeset revisions.' % ( tool_count, len( metadata_records_to_check ) ) + print '# Found %d changeset revisions without tools.' % no_tools + print '# Found %d tools without functional tests.' % no_tests + print '# Found %d tools with functional tests.' % has_tests + if info_only: + print '# Database not updated, info_only set.' + print "# Elapsed time: ", stop - start + print "#############################################################################" + +class FlagRepositoriesApplication( object ): + """Encapsulates the state of a Universe application""" + def __init__( self, config ): + if config.database_connection is False: + config.database_connection = "sqlite:///%s?isolation_level=IMMEDIATE" % config.database + # Setup the database engine and ORM + self.model = galaxy.webapps.tool_shed.model.mapping.init( config.file_path, config.database_connection, engine_options={}, create_tables=False ) + self.hgweb_config_manager = self.model.hgweb_config_manager + self.hgweb_config_manager.hgweb_config_dir = config.hgweb_config_dir + print "# Using configured hgweb.config file: ", self.hgweb_config_manager.hgweb_config + @property + def sa_session( self ): + """ + Returns a SQLAlchemy session -- currently just gets the current + session from the threadlocal session context, but this is provided + to allow migration toward a more SQLAlchemy 0.4 style of use. + """ + return self.model.context.current + def shutdown( self ): + pass + +if __name__ == "__main__": main() diff -r d1f875d0f213c0ba5d858b34ac76d314803a6efb -r b5f22685678d6938467ef17c336e154f88698289 test/base/util.py --- a/test/base/util.py +++ b/test/base/util.py @@ -1,4 +1,4 @@ -import os, sys, logging +import os, sys, logging, platform log = logging.getLogger(__name__) @@ -36,6 +36,14 @@ return None, repository_name, changeset_revision return last_galaxy_test_file_dir, last_tested_repository_name, last_tested_changeset_revision +def get_test_environment(): + rval = {} + rval[ 'python_version' ] = platform.python_version() + rval[ 'architecture' ] = platform.machine() + os, hostname, os_version, uname, arch, processor = platform.uname() + rval[ 'system' ] = '%s %s' % ( os, os_version ) + return rval + def parse_tool_panel_config( config, shed_tools_dict ): """ Parse a shed-related tool panel config to generate the shed_tools_dict. This only happens when testing tools installed from the tool shed. diff -r d1f875d0f213c0ba5d858b34ac76d314803a6efb -r b5f22685678d6938467ef17c336e154f88698289 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -180,7 +180,7 @@ do_not_test='false', downloadable='true', malicious='false', - must_include_tools='true' ) ) + includes_tools='true' ) ) api_url = get_api_url( base=location, parts=[ 'repository_revisions' ], params=params ) if format == 'json': return json_from_url( api_url ) @@ -394,7 +394,7 @@ log.info( "The embedded Galaxy application is running on %s:%s" % ( galaxy_test_host, galaxy_test_port ) ) log.info( "Repositories will be installed from the tool shed at %s" % galaxy_tool_shed_url ) success = False - repository_status = {} + repository_status = dict() try: # Iterate through a list of repository info dicts. log.info( "Retrieving repositories to install from the URL:\n%s\n" % str( galaxy_tool_shed_url ) ) https://bitbucket.org/galaxy/galaxy-central/commits/dbe53e2c1eab/ changeset: dbe53e2c1eab user: inithello date: 2013-03-05 16:23:55 summary: Removed the must_include_tools filter from the repository revisions API controller, since repository_metadata now has a flag includes_tools. affected #: 1 file diff -r b5f22685678d6938467ef17c336e154f88698289 -r dbe53e2c1eab2b377880e87c4d2bd770dc470b80 lib/galaxy/webapps/tool_shed/api/repository_revisions.py --- a/lib/galaxy/webapps/tool_shed/api/repository_revisions.py +++ b/lib/galaxy/webapps/tool_shed/api/repository_revisions.py @@ -47,27 +47,20 @@ do_not_test = kwd.get( 'do_not_test', None ) if do_not_test is not None: clause_list.append( trans.model.RepositoryMetadata.table.c.do_not_test == util.string_as_bool( do_not_test ) ) - # Filter by must_include_tools if received. - must_include_tools = kwd.get( 'must_include_tools', False ) + # Filter by includes_tools if received. + includes_tools = kwd.get( 'includes_tools', None ) + if includes_tools is not None: + clause_list.append( trans.model.RepositoryMetadata.table.c.includes_tools == util.string_as_bool( includes_tools ) ) try: query = trans.sa_session.query( trans.app.model.RepositoryMetadata ) \ .filter( and_( *clause_list ) ) \ .order_by( trans.app.model.RepositoryMetadata.table.c.repository_id ) \ .all() for repository_metadata in query: - if must_include_tools: - metadata = repository_metadata.metadata - if 'tools' in metadata: - ok_to_return = True - else: - ok_to_return = False - else: - ok_to_return = True - if ok_to_return: - item = repository_metadata.get_api_value( view='collection', - value_mapper=default_value_mapper( trans, repository_metadata ) ) - item[ 'url' ] = web.url_for( 'repository_revision', id=trans.security.encode_id( repository_metadata.id ) ) - rval.append( item ) + item = repository_metadata.get_api_value( view='collection', + value_mapper=default_value_mapper( trans, repository_metadata ) ) + item[ 'url' ] = web.url_for( 'repository_revision', id=trans.security.encode_id( repository_metadata.id ) ) + rval.append( item ) except Exception, e: rval = "Error in the Tool Shed repository_revisions API in index: " + str( e ) log.error( rval + ": %s" % str( e ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add white space to the tool shed's admin and repository_review controllers per new Galaxy dev team standards and factor out grid utility methods.
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d1f875d0f213/ changeset: d1f875d0f213 user: greg date: 2013-03-05 15:27:50 summary: Add white space to the tool shed's admin and repository_review controllers per new Galaxy dev team standards and factor out grid utility methods. affected #: 5 files diff -r 19d8ba6eddf37211ca69282f350bb67daa42958c -r d1f875d0f213c0ba5d858b34ac76d314803a6efb lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -93,6 +93,7 @@ changeset_revision=v ) ) # Render the list view return self.repository_grid( trans, **kwd ) + @web.expose @web.require_admin def browse_repository_metadata( self, trans, **kwd ): @@ -113,6 +114,7 @@ action='browse_repositories', **kwd ) ) return self.repository_metadata_grid( trans, **kwd ) + @web.expose @web.require_admin def create_category( self, trans, **kwd ): @@ -144,6 +146,7 @@ description=description, message=message, status=status ) + @web.expose @web.require_admin def delete_repository( self, trans, **kwd ): @@ -180,6 +183,7 @@ action='browse_repositories', message=util.sanitize_text( message ), status=status ) ) + @web.expose @web.require_admin def delete_repository_metadata( self, trans, **kwd ): @@ -204,6 +208,7 @@ action='browse_repository_metadata', message=util.sanitize_text( message ), status=status ) ) + @web.expose @web.require_admin def edit_category( self, trans, **kwd ): @@ -243,6 +248,7 @@ category=category, message=message, status=status ) + @web.expose @web.require_admin def manage_categories( self, trans, **kwd ): @@ -277,6 +283,7 @@ action='edit_category', **kwd ) ) return self.manage_category_grid( trans, **kwd ) + @web.expose @web.require_admin def regenerate_statistics( self, trans, **kwd ): @@ -289,6 +296,7 @@ return trans.fill_template( '/webapps/tool_shed/admin/statistics.mako', message=message, status=status ) + @web.expose @web.require_admin def reset_metadata_on_selected_repositories_in_tool_shed( self, trans, **kwd ): @@ -302,6 +310,7 @@ repositories_select_field=repositories_select_field, message=message, status=status ) + @web.expose @web.require_admin def undelete_repository( self, trans, **kwd ): @@ -341,6 +350,7 @@ action='browse_repositories', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def mark_category_deleted( self, trans, **kwd ): @@ -367,6 +377,7 @@ action='manage_categories', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def purge_category( self, trans, **kwd ): @@ -398,6 +409,7 @@ action='manage_categories', message=util.sanitize_text( message ), status='done' ) ) + @web.expose @web.require_admin def undelete_category( self, trans, **kwd ): diff -r 19d8ba6eddf37211ca69282f350bb67daa42958c -r d1f875d0f213c0ba5d858b34ac76d314803a6efb 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 @@ -8,6 +8,7 @@ import tool_shed.util.shed_util_common as suc 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 galaxy import eggs eggs.require('mercurial') @@ -48,7 +49,8 @@ id=repository_id, changeset_revision=changeset_revision, message=message, - status=status ) ) + status=status ) ) + @web.expose @web.require_login( "browse components" ) def browse_components( self, trans, **kwd ): @@ -59,6 +61,7 @@ action='create_component', **kwd ) ) return self.component_grid( trans, **kwd ) + @web.expose @web.require_login( "browse review" ) def browse_review( self, trans, **kwd ): @@ -75,6 +78,7 @@ review=review, message=message, status=status ) + def copy_review( self, trans, review_to_copy, review ): for component_review in review_to_copy.component_reviews: copied_component_review = trans.model.ComponentReview( repository_review_id=review.id, @@ -89,6 +93,7 @@ review.rating = review_to_copy.rating trans.sa_session.add( review ) trans.sa_session.flush() + @web.expose @web.require_login( "create component" ) def create_component( self, trans, **kwd ): @@ -119,6 +124,7 @@ description=description, message=message, status=status ) + @web.expose @web.require_login( "create review" ) def create_review( self, trans, **kwd ): @@ -183,6 +189,7 @@ return trans.response.send_redirect( web.url_for( controller='repository_review', action='view_or_manage_repository', **kwd ) ) + @web.expose @web.require_login( "edit component" ) def edit_component( self, trans, **kwd ): @@ -213,6 +220,7 @@ component=component, message=message, status=status ) + @web.expose @web.require_login( "edit review" ) def edit_review( self, trans, **kwd ): @@ -324,10 +332,10 @@ selected_value = review.approved else: selected_value = trans.model.ComponentReview.approved_states.NO - revision_approved_select_field = build_approved_select_field( trans, - name='revision_approved', - selected_value=selected_value, - for_component=False ) + revision_approved_select_field = grids_util.build_approved_select_field( trans, + name='revision_approved', + selected_value=selected_value, + for_component=False ) rev, changeset_revision_label = suc.get_rev_label_from_changeset_revision( repo, review.changeset_revision ) return trans.fill_template( '/webapps/tool_shed/repository_review/edit_review.mako', repository=repository, @@ -337,6 +345,7 @@ components_dict=components_dict, message=message, status=status ) + @web.expose @web.require_login( "manage components" ) def manage_components( self, trans, **kwd ): @@ -357,6 +366,7 @@ kwd[ 'message' ] = message kwd[ 'status' ] = status return self.component_grid( trans, **kwd ) + @web.expose @web.require_login( "manage repositories reviewed by me" ) def manage_repositories_reviewed_by_me( self, trans, **kwd ): @@ -371,6 +381,7 @@ **kwd ) ) self.repositories_reviewed_by_me_grid.title = 'Repositories reviewed by me' return self.repositories_reviewed_by_me_grid( trans, **kwd ) + @web.expose @web.require_login( "manage repositories with reviews" ) def manage_repositories_with_reviews( self, trans, **kwd ): @@ -386,6 +397,7 @@ action='view_or_manage_repository', **kwd ) ) return self.repositories_with_reviews_grid( trans, **kwd ) + @web.expose @web.require_login( "manage repositories without reviews" ) def manage_repositories_without_reviews( self, trans, **kwd ): @@ -400,6 +412,7 @@ action='view_or_manage_repository', **kwd ) ) return self.repositories_without_reviews_grid( trans, **kwd ) + @web.expose @web.require_login( "manage repository reviews" ) def manage_repository_reviews( self, trans, mine=False, **kwd ): @@ -447,6 +460,7 @@ mine=mine, message=message, status=status ) + @web.expose @web.require_login( "manage repository reviews of revision" ) def manage_repository_reviews_of_revision( self, trans, **kwd ): @@ -470,6 +484,7 @@ installable=installable, message=message, status=status ) + @web.expose @web.require_login( "repository reviews by user" ) def repository_reviews_by_user( self, trans, **kwd ): @@ -496,6 +511,7 @@ user = suc.get_user( trans, kwd[ 'id' ] ) self.repository_reviews_by_user_grid.title = "All repository revision reviews for user '%s'" % user.username return self.repository_reviews_by_user_grid( trans, **kwd ) + @web.expose @web.require_login( "reviewed repositories i own" ) def reviewed_repositories_i_own( self, trans, **kwd ): @@ -514,6 +530,7 @@ action='view_or_manage_repository', **kwd ) ) return self.reviewed_repositories_i_own_grid( trans, **kwd ) + @web.expose @web.require_login( "select previous review" ) def select_previous_review( self, trans, **kwd ): @@ -533,6 +550,7 @@ previous_reviews_dict=previous_reviews_dict, message=message, status=status ) + @web.expose @web.require_login( "view or manage repository" ) def view_or_manage_repository( self, trans, **kwd ): @@ -545,16 +563,3 @@ return trans.response.send_redirect( web.url_for( controller='repository', action='view_repository', **kwd ) ) - -# ----- Utility methods ----- - -def build_approved_select_field( trans, name, selected_value=None, for_component=True ): - options = [ ( 'No', trans.model.ComponentReview.approved_states.NO ), - ( 'Yes', trans.model.ComponentReview.approved_states.YES ) ] - if for_component: - options.append( ( 'Not applicable', trans.model.ComponentReview.approved_states.NA ) ) - select_field = SelectField( name=name ) - for option_tup in options: - selected = selected_value and option_tup[1] == selected_value - select_field.add_option( option_tup[0], option_tup[1], selected=selected ) - return select_field diff -r 19d8ba6eddf37211ca69282f350bb67daa42958c -r d1f875d0f213c0ba5d858b34ac76d314803a6efb lib/tool_shed/grids/util.py --- a/lib/tool_shed/grids/util.py +++ b/lib/tool_shed/grids/util.py @@ -2,8 +2,18 @@ import tool_shed.util.shed_util_common as suc from galaxy.web.form_builder import SelectField -def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, - downloadable=False, reviewed=False, not_reviewed=False ): +def build_approved_select_field( trans, name, selected_value=None, for_component=True ): + options = [ ( 'No', trans.model.ComponentReview.approved_states.NO ), + ( 'Yes', trans.model.ComponentReview.approved_states.YES ) ] + if for_component: + options.append( ( 'Not applicable', trans.model.ComponentReview.approved_states.NA ) ) + select_field = SelectField( name=name ) + for option_tup in options: + selected = selected_value and option_tup[ 1 ] == selected_value + select_field.add_option( option_tup[ 0 ], option_tup[ 1 ], selected=selected ) + return select_field + +def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, downloadable=False, reviewed=False, not_reviewed=False ): """Build a SelectField whose options are the changeset_rev strings of certain revisions of the received repository.""" options = [] changeset_tups = [] @@ -40,7 +50,7 @@ # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. for changeset_tup in sorted( changeset_tups ): # Display the latest revision first. - options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) + options.insert( 0, ( changeset_tup[ 1 ], changeset_tup[ 2 ] ) ) if add_id_to_name: name = 'changeset_revision_%d' % repository.id else: @@ -49,6 +59,6 @@ refresh_on_change=True, refresh_on_change_values=refresh_on_change_values ) for option_tup in options: - selected = selected_value and option_tup[1] == selected_value - select_field.add_option( option_tup[0], option_tup[1], selected=selected ) + selected = selected_value and option_tup[ 1 ] == selected_value + select_field.add_option( option_tup[ 0 ], option_tup[ 1 ], selected=selected ) return select_field diff -r 19d8ba6eddf37211ca69282f350bb67daa42958c -r d1f875d0f213c0ba5d858b34ac76d314803a6efb templates/webapps/tool_shed/repository_review/edit_review.mako --- a/templates/webapps/tool_shed/repository_review/edit_review.mako +++ b/templates/webapps/tool_shed/repository_review/edit_review.mako @@ -4,7 +4,7 @@ <% from galaxy.web.form_builder import CheckboxField - from galaxy.webapps.tool_shed.controllers.repository_review import build_approved_select_field + from tool_shed.grids.util import build_approved_select_field from galaxy.webapps.tool_shed.util.container_util import STRSEP can_manage_repository = is_admin or repository.user == trans.user %> diff -r 19d8ba6eddf37211ca69282f350bb67daa42958c -r d1f875d0f213c0ba5d858b34ac76d314803a6efb templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako --- a/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako +++ b/templates/webapps/tool_shed/repository_review/reviews_of_changeset_revision.mako @@ -4,7 +4,7 @@ <%namespace file="/webapps/tool_shed/repository/common.mako" import="*" /><% - from galaxy.webapps.tool_shed.controllers.repository_review import build_approved_select_field + from tool_shed.grids.util import build_approved_select_field from galaxy.webapps.tool_shed.util.container_util import STRSEP is_admin = trans.user_is_admin() is_new = repository.is_new( trans.app ) 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 05 Mar '13

05 Mar '13

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9de5110ddf65/ changeset: 9de5110ddf65 user: jmchilton date: 2013-03-04 20:14:08 summary: Add `file_ext` attribute to image classes. Whitespace fixes for same classes. affected #: 1 file diff -r 93f0c6867e3427d582f6fba6ca2877ecf472b6d5 -r 9de5110ddf6573375cc631c703a20ef24e8a72e9 lib/galaxy/datatypes/images.py --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -33,6 +33,7 @@ # we need to ensure that the implementation is such that image files cannot be uploaded # to our main public instance. + class Image( data.Data ): """Class describing an image""" def set_peek( self, dataset, is_multi_byte=False ): @@ -56,94 +57,147 @@ return True else: return False - + + class Jpg( Image ): + file_ext = "jpeg" + def sniff(self, filename, image=None): """Determine if the file is in jpg format.""" return check_image_type( filename, ['JPEG'], image ) + class Png( Image ): + file_ext = "png" + def sniff(self, filename, image=None): """Determine if the file is in png format.""" return check_image_type( filename, ['PNG'], image ) - + + class Tiff( Image ): + file_ext = "tiff" + def sniff(self, filename, image=None): """Determine if the file is in tiff format.""" return check_image_type( filename, ['TIFF'], image ) - + + class Bmp( Image ): + file_ext = "bmp" + def sniff(self, filename, image=None): """Determine if the file is in bmp format.""" return check_image_type( filename, ['BMP'], image ) + class Gif( Image ): + file_ext = "gif" + def sniff(self, filename, image=None): """Determine if the file is in gif format.""" return check_image_type( filename, ['GIF'], image ) + class Im( Image ): + file_ext = "im" + def sniff(self, filename, image=None): """Determine if the file is in im format.""" return check_image_type( filename, ['IM'], image ) + class Pcd( Image ): + file_ext = "pcd" + def sniff(self, filename, image=None): """Determine if the file is in pcd format.""" return check_image_type( filename, ['PCD'], image ) + class Pcx( Image ): + file_ext = "pcx" + def sniff(self, filename, image=None): """Determine if the file is in pcx format.""" return check_image_type( filename, ['PCX'], image ) + class Ppm( Image ): + file_ext = "ppm" + def sniff(self, filename, image=None): """Determine if the file is in ppm format.""" return check_image_type( filename, ['PPM'], image ) + class Psd( Image ): + file_ext = "psd" + def sniff(self, filename, image=None): """Determine if the file is in psd format.""" return check_image_type( filename, ['PSD'], image ) + class Xbm( Image ): + file_ext = "xbm" + def sniff(self, filename, image=None): """Determine if the file is in XBM format.""" return check_image_type( filename, ['XBM'], image ) + class Xpm( Image ): + file_ext = "xpm" + def sniff(self, filename, image=None): """Determine if the file is in XPM format.""" return check_image_type( filename, ['XPM'], image ) + class Rgb( Image ): + file_ext = "rgb" + def sniff(self, filename, image=None): """Determine if the file is in RGB format.""" return check_image_type( filename, ['RGB'], image ) + class Pbm( Image ): + file_ext = "pbm" + def sniff(self, filename, image=None): """Determine if the file is in PBM format""" return check_image_type( filename, ['PBM'], image ) + class Pgm( Image ): + file_ext = "pgm" + def sniff(self, filename, image=None): """Determine if the file is in PGM format""" return check_image_type( filename, ['PGM'], image ) + class Eps( Image ): + file_ext = "eps" + def sniff(self, filename, image=None): """Determine if the file is in eps format.""" return check_image_type( filename, ['EPS'], image ) class Rast( Image ): + file_ext = "rast" + def sniff(self, filename, image=None): """Determine if the file is in rast format""" return check_image_type( filename, ['RAST'], image ) + class Pdf( Image ): + file_ext = "pdf" + def sniff(self, filename): """Determine if the file is in pdf format.""" headers = get_headers(filename, None, 1) https://bitbucket.org/galaxy/galaxy-central/commits/19d8ba6eddf3/ changeset: 19d8ba6eddf3 user: dannon date: 2013-03-05 14:18:39 summary: Merged in galaxyp/galaxy-central-parallelism-refactorings (pull request #133) Add `file_ext` attribute to image classes. Whitespace fixes for same classes. affected #: 1 file diff -r b9af8161548a17653704304a72d392d2a328cc4b -r 19d8ba6eddf37211ca69282f350bb67daa42958c lib/galaxy/datatypes/images.py --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -33,6 +33,7 @@ # we need to ensure that the implementation is such that image files cannot be uploaded # to our main public instance. + class Image( data.Data ): """Class describing an image""" def set_peek( self, dataset, is_multi_byte=False ): @@ -56,94 +57,147 @@ return True else: return False - + + class Jpg( Image ): + file_ext = "jpeg" + def sniff(self, filename, image=None): """Determine if the file is in jpg format.""" return check_image_type( filename, ['JPEG'], image ) + class Png( Image ): + file_ext = "png" + def sniff(self, filename, image=None): """Determine if the file is in png format.""" return check_image_type( filename, ['PNG'], image ) - + + class Tiff( Image ): + file_ext = "tiff" + def sniff(self, filename, image=None): """Determine if the file is in tiff format.""" return check_image_type( filename, ['TIFF'], image ) - + + class Bmp( Image ): + file_ext = "bmp" + def sniff(self, filename, image=None): """Determine if the file is in bmp format.""" return check_image_type( filename, ['BMP'], image ) + class Gif( Image ): + file_ext = "gif" + def sniff(self, filename, image=None): """Determine if the file is in gif format.""" return check_image_type( filename, ['GIF'], image ) + class Im( Image ): + file_ext = "im" + def sniff(self, filename, image=None): """Determine if the file is in im format.""" return check_image_type( filename, ['IM'], image ) + class Pcd( Image ): + file_ext = "pcd" + def sniff(self, filename, image=None): """Determine if the file is in pcd format.""" return check_image_type( filename, ['PCD'], image ) + class Pcx( Image ): + file_ext = "pcx" + def sniff(self, filename, image=None): """Determine if the file is in pcx format.""" return check_image_type( filename, ['PCX'], image ) + class Ppm( Image ): + file_ext = "ppm" + def sniff(self, filename, image=None): """Determine if the file is in ppm format.""" return check_image_type( filename, ['PPM'], image ) + class Psd( Image ): + file_ext = "psd" + def sniff(self, filename, image=None): """Determine if the file is in psd format.""" return check_image_type( filename, ['PSD'], image ) + class Xbm( Image ): + file_ext = "xbm" + def sniff(self, filename, image=None): """Determine if the file is in XBM format.""" return check_image_type( filename, ['XBM'], image ) + class Xpm( Image ): + file_ext = "xpm" + def sniff(self, filename, image=None): """Determine if the file is in XPM format.""" return check_image_type( filename, ['XPM'], image ) + class Rgb( Image ): + file_ext = "rgb" + def sniff(self, filename, image=None): """Determine if the file is in RGB format.""" return check_image_type( filename, ['RGB'], image ) + class Pbm( Image ): + file_ext = "pbm" + def sniff(self, filename, image=None): """Determine if the file is in PBM format""" return check_image_type( filename, ['PBM'], image ) + class Pgm( Image ): + file_ext = "pgm" + def sniff(self, filename, image=None): """Determine if the file is in PGM format""" return check_image_type( filename, ['PGM'], image ) + class Eps( Image ): + file_ext = "eps" + def sniff(self, filename, image=None): """Determine if the file is in eps format.""" return check_image_type( filename, ['EPS'], image ) class Rast( Image ): + file_ext = "rast" + def sniff(self, filename, image=None): """Determine if the file is in rast format""" return check_image_type( filename, ['RAST'], image ) + class Pdf( Image ): + file_ext = "pdf" + def sniff(self, filename): """Determine if the file is in pdf format.""" headers = get_headers(filename, None, 1) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Add links for set_environment tool dependency type in the Tool dependency definitions Galaxy Utilities grid.
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b9af8161548a/ changeset: b9af8161548a user: greg date: 2013-03-05 01:47:23 summary: Add links for set_environment tool dependency type in the Tool dependency definitions Galaxy Utilities grid. affected #: 1 file diff -r 26315fa894cefb9192a38ee596f3cb93d8c33e3f -r b9af8161548a17653704304a72d392d2a328cc4b lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -843,12 +843,14 @@ # Example: "set_environment": [{"name": "JAVA_JAR_FILE", "type": "set_environment"}] env_dicts = tds_dict[ 'set_environment' ] num_env_dicts = len( env_dicts ) - td_str += '<b>environment:</b> ' - for index, env_dict in enumerate( env_dicts ): - td_str += '%s' % escape_html( env_dict[ 'name' ] ) - if index < num_env_dicts - 1: - td_str += ', ' - td_str += '<br/>' + if num_env_dicts > 0: + td_str += '<a href="browse_datatypes?operation=view_or_manage_repository&id=%s">' % trans.security.encode_id( repository_metadata.id ) + td_str += '<b>environment:</b> ' + for index, env_dict in enumerate( env_dicts ): + td_str += '%s' % escape_html( env_dict[ 'name' ] ) + if index < num_env_dicts - 1: + td_str += ', ' + td_str += '</a><br/>' for index, key in enumerate( sorted_keys ): if key == 'set_environment': continue 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: Better aggangement of Galaxy utility grid columns in the tool shed, and fix for the Repository Dependency link in the Valid repository dependency definitions Galaxy Utilities grid.
by commits-noreply＠bitbucket.org 05 Mar '13

05 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/26315fa894ce/ changeset: 26315fa894ce user: greg date: 2013-03-05 01:39:23 summary: Better aggangement of Galaxy utility grid columns in the tool shed, and fix for the Repository Dependency link in the Valid repository dependency definitions Galaxy Utilities grid. affected #: 1 file diff -r 3254331483381a1f9d4be24a81cc4d88a703f8bb -r 26315fa894cefb9192a38ee596f3cb93d8c33e3f lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -9,6 +9,8 @@ from galaxy import eggs eggs.require('markupsafe') from markupsafe import escape as escape_html +eggs.require('mercurial') +from mercurial import hg, ui, patch, commands log = logging.getLogger( __name__ ) @@ -774,7 +776,14 @@ required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if required_repository: required_repository_id = trans.security.encode_id( required_repository.id ) - rd_str += '<a href="browse_repository_dependencies?operation=view_or_manage_repository&id=%s&changeset_revision=%s">' % ( required_repository_id, changeset_revision ) + required_repository_metadata = suc.get_repository_metadata_by_repository_id_changeset_revision( trans, required_repository_id, changeset_revision ) + if not required_repository_metadata: + repo_dir = required_repository.repo_path( trans.app ) + repo = hg.repository( suc.get_configured_ui(), repo_dir ) + updated_changeset_revision = suc.get_next_downloadable_changeset_revision( required_repository, repo, changeset_revision ) + required_repository_metadata = suc.get_repository_metadata_by_repository_id_changeset_revision( trans, required_repository_id, updated_changeset_revision ) + required_repository_metadata_id = trans.security.encode_id( required_repository_metadata.id ) + rd_str += '<a href="browse_repository_dependencies?operation=view_or_manage_repository&id=%s">' % ( required_repository_metadata_id ) rd_str += 'Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 3 ] ), escape_html( rd_tup[ 2 ] ) ) if required_repository: rd_str += '</a>' @@ -785,6 +794,8 @@ title = "Valid repository dependency definitions in this tool shed" default_sort_key = "Repository.name" columns = [ + RequiredRepositoryColumn( "Repository dependency", + attach_popup=False ), RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -795,12 +806,10 @@ attach_popup=False, key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - RequiredRepositoryColumn( "Repository dependency", - attach_popup=False ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -848,7 +857,9 @@ name = td_dict[ 'name' ] type = td_dict[ 'type' ] version = td_dict[ 'version' ] + td_str += '<a href="browse_datatypes?operation=view_or_manage_repository&id=%s">' % trans.security.encode_id( repository_metadata.id ) td_str += '<b>%s</b> version <b>%s</b>' % ( escape_html( name ), escape_html( version ) ) + td_str += '</a>' if index < num_keys - 1: td_str += '<br/>' return td_str @@ -856,6 +867,8 @@ title = "Tool dependency definitions in this tool shed" default_sort_key = "Repository.name" columns = [ + ToolDependencyColumn( "Tool dependency", + attach_popup=False ), RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -866,12 +879,10 @@ attach_popup=False, key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - ToolDependencyColumn( "Tool dependency", - attach_popup=False ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -910,7 +921,9 @@ for index, tool_tup in enumerate( sorted_tool_tups ): tool_id = tool_tup[ 0 ] version = tool_tup[ 1 ] + tool_str += '<a href="browse_datatypes?operation=view_or_manage_repository&id=%s">' % trans.security.encode_id( repository_metadata.id ) tool_str += '<b>%s:</b> %s' % ( escape_html( tool_id ), escape_html( version ) ) + tool_str += '</a>' if index < num_tool_tups - 1: tool_str += '<br/>' return tool_str @@ -918,6 +931,8 @@ title = "Valid tools in this tool shed" default_sort_key = "Repository.name" columns = [ + ToolsColumn( "Tool id and version", + attach_popup=False ), RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -928,12 +943,10 @@ attach_popup=False, key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - ToolsColumn( "Tool id and version", - attach_popup=False ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) @@ -975,7 +988,9 @@ for index, datatype_tup in enumerate( sorted_datatype_tups ): extension = datatype_tup[ 0 ] dtype = datatype_tup[ 1 ] + datatype_str += '<a href="browse_datatypes?operation=view_or_manage_repository&id=%s">' % trans.security.encode_id( repository_metadata.id ) datatype_str += '<b>%s:</b> %s' % ( escape_html( extension ), escape_html( dtype ) ) + datatype_str += '</a>' if index < num_datatype_tups - 1: datatype_str += '<br/>' return datatype_str @@ -983,6 +998,8 @@ title = "Custom datatypes in this tool shed" default_sort_key = "Repository.name" columns = [ + DatatypesColumn( "Datatype extension and class", + attach_popup=False ), RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), @@ -993,12 +1010,10 @@ attach_popup=False, key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - DatatypesColumn( "Datatype extension and class", - attach_popup=False ) + attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], + cols_to_filter=[ columns[1], columns[2] ], key="free-text-search", visible=False, filterable="standard" ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Speed up the searches for tools and workflows contained in repositories in the tool shed.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/325433148338/ changeset: 325433148338 user: greg date: 2013-03-04 23:21:46 summary: Speed up the searches for tools and workflows contained in repositories in the tool shed. affected #: 1 file diff -r 5705e0578adfb202d1bba0c4b12a9f6344fdd6b7 -r 3254331483381a1f9d4be24a81cc4d88a703f8bb 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 @@ -1927,73 +1927,80 @@ def __search_repository_metadata( self, trans, exact_matches_checked, tool_ids='', tool_names='', tool_versions='', workflow_names='', all_workflows=False ): match_tuples = [] ok = True - for repository_metadata in trans.sa_session.query( model.RepositoryMetadata ): - metadata = repository_metadata.metadata - if tool_ids or tool_names or tool_versions: - if 'tools' in metadata: - tools = metadata[ 'tools' ] - else: - tools = [] - for tool_dict in tools: - if tool_ids and not tool_names and not tool_versions: - for tool_id in tool_ids: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_names and not tool_ids and not tool_versions: - for tool_name in tool_names: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_versions and not tool_ids and not tool_names: - for tool_version in tool_versions: - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif tool_ids and tool_names and not tool_versions: - if len( tool_ids ) == len( tool_names ): - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - elif len( tool_ids ) == 1 or len( tool_names ) == 1: - tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) - match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) - else: - ok = False - elif tool_ids and tool_versions and not tool_names: - if len( tool_ids ) == len( tool_versions ): - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - elif len( tool_ids ) == 1 or len( tool_versions ) == 1: - tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) - match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and not tool_ids: - if len( tool_versions ) == len( tool_names ): - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - elif len( tool_versions ) == 1 or len( tool_names ) == 1: - tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) - match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) - else: - ok = False - elif tool_versions and tool_names and tool_ids: - if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): - for i, tool_version in enumerate( tool_versions ): - tool_name = tool_names[ i ] - tool_id = tool_ids[ i ] - if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + if tool_ids or tool_names or tool_versions: + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.includes_tools == True ) \ + .join( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): + metadata = repository_metadata.metadata + if metadata: + tools = metadata.get( 'tools', [] ) + for tool_dict in tools: + if tool_ids and not tool_names and not tool_versions: + for tool_id in tool_ids: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id ): match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - else: - ok = False - elif workflow_names: - if 'workflows' in metadata: + elif tool_names and not tool_ids and not tool_versions: + for tool_name in tool_names: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_name=tool_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_versions and not tool_ids and not tool_names: + for tool_version in tool_versions: + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif tool_ids and tool_names and not tool_versions: + if len( tool_ids ) == len( tool_names ): + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + elif len( tool_ids ) == 1 or len( tool_names ) == 1: + tool_ids, tool_names = self.__make_same_length( tool_ids, tool_names ) + match_tuples = self.__search_ids_names( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_names ) + else: + ok = False + elif tool_ids and tool_versions and not tool_names: + if len( tool_ids ) == len( tool_versions ): + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + elif len( tool_ids ) == 1 or len( tool_versions ) == 1: + tool_ids, tool_versions = self.__make_same_length( tool_ids, tool_versions ) + match_tuples = self.__search_ids_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_ids, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and not tool_ids: + if len( tool_versions ) == len( tool_names ): + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + elif len( tool_versions ) == 1 or len( tool_names ) == 1: + tool_versions, tool_names = self.__make_same_length( tool_versions, tool_names ) + match_tuples = self.__search_names_versions( tool_dict, exact_matches_checked, match_tuples, repository_metadata, tool_names, tool_versions ) + else: + ok = False + elif tool_versions and tool_names and tool_ids: + if len( tool_versions ) == len( tool_names ) and len( tool_names ) == len( tool_ids ): + for i, tool_version in enumerate( tool_versions ): + tool_name = tool_names[ i ] + tool_id = tool_ids[ i ] + if self.__in_tool_dict( tool_dict, exact_matches_checked, tool_id=tool_id, tool_name=tool_name, tool_version=tool_version ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + else: + ok = False + elif workflow_names or all_workflows: + for repository_metadata in trans.sa_session.query( trans.model.RepositoryMetadata ) \ + .filter( trans.model.RepositoryMetadata.table.c.includes_workflows == True ) \ + .join( trans.model.Repository ) \ + .filter( and_( trans.model.Repository.table.c.deleted == False, + trans.model.Repository.table.c.deprecated == False ) ): + metadata = repository_metadata.metadata + if metadata: # metadata[ 'workflows' ] is a list of tuples where each contained tuple is # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - workflow_tups = metadata[ 'workflows' ] - workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] - else: - workflows = [] - for workflow_dict in workflows: - for workflow_name in workflow_names: - if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) - elif all_workflows and 'workflows' in metadata: - match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + if workflow_names: + workflow_tups = metadata.get( 'workflows', [] ) + workflows = [ workflow_tup[1] for workflow_tup in workflow_tups ] + for workflow_dict in workflows: + for workflow_name in workflow_names: + if self.__in_workflow_dict( workflow_dict, exact_matches_checked, workflow_name ): + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) + elif all_workflows: + match_tuples.append( ( repository_metadata.repository_id, repository_metadata.changeset_revision ) ) return ok, match_tuples @web.expose Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dannon: Update migrate_tools to the correct path.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5705e0578adf/ changeset: 5705e0578adf user: dannon date: 2013-03-04 20:43:41 summary: Update migrate_tools to the correct path. affected #: 1 file diff -r 7010204f7ccda05f806cfe7f30a6a3bc03a5e2d7 -r 5705e0578adfb202d1bba0c4b12a9f6344fdd6b7 lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0114_update_migrate_tools_table_again.py @@ -0,0 +1,44 @@ +""" +Migration script to update the migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * + +import datetime +now = datetime.datetime.utcnow +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import sys, logging +log = logging.getLogger( __name__ ) +log.setLevel(logging.DEBUG) +handler = logging.StreamHandler( sys.stdout ) +format = "%(name)s %(levelname)s %(asctime)s %(message)s" +formatter = logging.Formatter( format ) +handler.setFormatter( formatter ) +log.addHandler( handler ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + # Create the table. + try: + cmd = "UPDATE migrate_tools set repository_path='lib/tool_shed/galaxy_install/migrate';" + db_session.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the new location lib/tool_shed/galaxy_install/migrate failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + try: + cmd = "UPDATE migrate_tools set repository_path='lib/galaxy/tool_shed/migrate';" + db_session.execute( cmd ) + except Exception, e: + log.debug( "Updating migrate_tools.repository_path column to point to the old location lib/galaxy/tool_shed/migrate failed: %s" % str( e ) ) + 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: Fix links in the tool shed's Galaxy utilities grids.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7010204f7ccd/ changeset: 7010204f7ccd user: greg date: 2013-03-04 20:29:23 summary: Fix links in the tool shed's Galaxy utilities grids. affected #: 2 files diff -r 93f0c6867e3427d582f6fba6ca2877ecf472b6d5 -r 7010204f7ccda05f806cfe7f30a6a3bc03a5e2d7 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 @@ -82,10 +82,17 @@ def browse_datatypes( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() + # The received id is a RepositoryMetadata id. + repository_metadata_id = kwd[ 'id' ] + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision + new_kwd = dict( id=repository_id, + changeset_revision=changeset_revision ) if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', - **kwd ) ) + **new_kwd ) ) return self.datatypes_grid( trans, **kwd ) @web.expose @@ -256,34 +263,55 @@ def browse_repository_dependencies( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() + # The received id is a RepositoryMetadata id. + repository_metadata_id = kwd[ 'id' ] + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision + new_kwd = dict( id=repository_id, + changeset_revision=changeset_revision ) if operation == "browse_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='browse_repository', - **kwd ) ) + **new_kwd ) ) if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', - **kwd ) ) + **new_kwd ) ) return self.repository_dependencies_grid( trans, **kwd ) @web.expose def browse_tools( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() + # The received id is a RepositoryMetadata id. + repository_metadata_id = kwd['id' ] + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision + new_kwd = dict( id=repository_id, + changeset_revision=changeset_revision ) if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', - **kwd ) ) + **new_kwd ) ) return self.tools_grid( trans, **kwd ) @web.expose def browse_tool_dependencies( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() + # The received id is a RepositoryMetadata id. + repository_metadata_id = kwd[ 'id' ] + repository_metadata = suc.get_repository_metadata_by_id( trans, repository_metadata_id ) + repository_id = trans.security.encode_id( repository_metadata.repository_id ) + changeset_revision = repository_metadata.changeset_revision + new_kwd = dict( id=repository_id, + changeset_revision=changeset_revision ) if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', - **kwd ) ) + **new_kwd ) ) return self.tool_dependencies_grid( trans, **kwd ) @web.expose diff -r 93f0c6867e3427d582f6fba6ca2877ecf472b6d5 -r 7010204f7ccda05f806cfe7f30a6a3bc03a5e2d7 lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -787,7 +787,7 @@ columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -858,7 +858,7 @@ columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -920,7 +920,7 @@ columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -985,7 +985,7 @@ columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: call_hook: Fix to handle exception.args more gracefully when modifying
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/93f0c6867e34/ changeset: 93f0c6867e34 user: carlfeberhard date: 2013-03-04 19:51:52 summary: call_hook: Fix to handle exception.args more gracefully when modifying affected #: 1 file diff -r 141c99107f8d2a11a1b91c80ad0ce8e264ee806c -r 93f0c6867e3427d582f6fba6ca2877ecf472b6d5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -2715,7 +2715,10 @@ if code: return code( *args, **kwargs ) except Exception, e: - e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, e.args[0] ), ) + original_message = '' + if len( e.args ): + original_message = e.args[0] + e.args = ( "Error in '%s' hook '%s', original message: %s" % ( self.name, hook_name, original_message ), ) raise def exec_before_job( self, app, inp_data, out_data, param_dict={} ): pass 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: Clean up recently introduced tool shed repository Galaxy utilities grids.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/141c99107f8d/ changeset: 141c99107f8d user: greg date: 2013-03-04 19:01:33 summary: Clean up recently introduced tool shed repository Galaxy utilities grids. affected #: 2 files diff -r 8236c09e92011aa2c8c4d4bcd63f0b91de773488 -r 141c99107f8d2a11a1b91c80ad0ce8e264ee806c 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 @@ -280,9 +280,9 @@ def browse_tool_dependencies( self, trans, **kwd ): if 'operation' in kwd: operation = kwd[ 'operation' ].lower() - if operation == "browse_repository": + if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', - action='browse_repository', + action='view_or_manage_repository', **kwd ) ) return self.tool_dependencies_grid( trans, **kwd ) diff -r 8236c09e92011aa2c8c4d4bcd63f0b91de773488 -r 141c99107f8d2a11a1b91c80ad0ce8e264ee806c lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -643,7 +643,10 @@ class ChangesetRevisionColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.changeset_revision ) + repository = repository_metadata.repository + changeset_revision = repository_metadata.changeset_revision + changeset_revision_label = suc.get_revision_label( trans, repository, changeset_revision ) + return escape_html( changeset_revision_label ) class MaliciousColumn( grids.BooleanColumn ): @@ -719,6 +722,7 @@ default_sort_key = "Repository.name" columns = [ RepositoryNameColumn( "Repository name", + key="Repository.name", link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), attach_popup=False ), RepositoryOwnerColumn( "Owner", @@ -743,8 +747,7 @@ .join( model.Repository ) \ .filter( and_( model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class RepositoryDependenciesGrid( RepositoryMetadataGrid ): @@ -767,22 +770,24 @@ for index, rd_tup in enumerate( sorted_rd_tups ): name = rd_tup[ 1 ] owner = rd_tup[ 2 ] + changeset_revision = rd_tup[ 3 ] required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) if required_repository: required_repository_id = trans.security.encode_id( required_repository.id ) - rd_str += '<a href="browse_repository_dependencies?operation=browse_repository&id=%s">' % required_repository_id - rd_str += '<b>name:</b> %s | <b>owner:</b> %s | <b>revision:</b> %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) ) + rd_str += '<a href="browse_repository_dependencies?operation=view_or_manage_repository&id=%s&changeset_revision=%s">' % ( required_repository_id, changeset_revision ) + rd_str += 'Repository <b>%s</b> revision <b>%s</b> owned by <b>%s</b>' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 3 ] ), escape_html( rd_tup[ 2 ] ) ) if required_repository: rd_str += '</a>' if index < num_tups - 1: rd_str += '<br/>' return rd_str - title = "Repository dependency definitions in this tool shed" + title = "Valid repository dependency definitions in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -806,8 +811,7 @@ .filter( and_( model.RepositoryMetadata.table.c.has_repository_dependencies == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class ToolDependenciesGrid( RepositoryMetadataGrid ): @@ -850,10 +854,11 @@ return td_str title = "Tool dependency definitions in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -877,8 +882,7 @@ .filter( and_( model.RepositoryMetadata.table.c.includes_tool_dependencies == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class ToolsGrid( RepositoryMetadataGrid ): @@ -893,21 +897,30 @@ if metadata: tool_dicts = metadata.get( 'tools', [] ) if tool_dicts: - num_tool_dicts = len( tool_dicts ) - for index, tool_dict in enumerate( tool_dicts ): - tool_id = tool_dict[ 'id' ] - name = tool_dict[ 'name' ] - version = tool_dict[ 'version' ] - tool_str += '<b>%s</b> | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) ) - if index < num_tool_dicts - 1: + # Create tuples of the attributes we want so we can sort them by extension. + tool_tups = [] + for tool_dict in tool_dicts: + tool_id = tool_dict.get( 'id', '' ) + version = tool_dict.get( 'version', '' ) + # For now we'll just display tool id and version. + if tool_id and version: + tool_tups.append( ( tool_id, version ) ) + sorted_tool_tups = sorted( tool_tups, key=lambda tool_tup: tool_tup[ 0 ] ) + num_tool_tups = len( sorted_tool_tups ) + for index, tool_tup in enumerate( sorted_tool_tups ): + tool_id = tool_tup[ 0 ] + version = tool_tup[ 1 ] + tool_str += '<b>%s:</b> %s' % ( escape_html( tool_id ), escape_html( version ) ) + if index < num_tool_tups - 1: tool_str += '<br/>' return tool_str title = "Valid tools in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -916,7 +929,7 @@ key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", attach_popup=False ), - ToolsColumn( "Tool id | name | version", + ToolsColumn( "Tool id and version", attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", @@ -931,8 +944,7 @@ .filter( and_( model.RepositoryMetadata.table.c.includes_tools == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) class DatatypesGrid( RepositoryMetadataGrid ): @@ -947,23 +959,33 @@ if metadata: datatype_dicts = metadata.get( 'datatypes', [] ) if datatype_dicts: - num_datatype_dicts = len( datatype_dicts ) - for index, datatype_dict in enumerate( datatype_dicts ): + # Create tuples of the attributes we want so we can sort them by extension. + datatype_tups = [] + for datatype_dict in datatype_dicts: # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} extension = datatype_dict.get( 'extension', '' ) dtype = datatype_dict.get( 'dtype', '' ) mimetype = datatype_dict.get( 'mimetype', '' ) display_in_upload = datatype_dict.get( 'display_in_upload', False ) - datatype_str += '<b>%s</b> | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) - if index < num_datatype_dicts - 1: + # For now we'll just display extension and dtype. + if extension and dtype: + datatype_tups.append( ( extension, dtype ) ) + sorted_datatype_tups = sorted( datatype_tups, key=lambda datatype_tup: datatype_tup[ 0 ] ) + num_datatype_tups = len( sorted_datatype_tups ) + for index, datatype_tup in enumerate( sorted_datatype_tups ): + extension = datatype_tup[ 0 ] + dtype = datatype_tup[ 1 ] + datatype_str += '<b>%s:</b> %s' % ( escape_html( extension ), escape_html( dtype ) ) + if index < num_datatype_tups - 1: datatype_str += '<br/>' return datatype_str title = "Custom datatypes in this tool shed" + default_sort_key = "Repository.name" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id, changeset_revision=item.changeset_revision ) ), attach_popup=False, key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", @@ -972,7 +994,7 @@ key="User.username" ), RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", attach_popup=False ), - DatatypesColumn( "Datatype extension | Type | Mimetype", + DatatypesColumn( "Datatype extension and class", attach_popup=False ) ] columns.append( grids.MulticolFilterColumn( "Search repository name, owner", @@ -987,5 +1009,4 @@ .filter( and_( model.RepositoryMetadata.table.c.includes_datatypes == True, model.Repository.table.c.deleted == False, model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) + .join( model.User.table ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 5 new changesets
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

5 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/32c6537bef27/ changeset: 32c6537bef27 user: jmchilton date: 2013-02-26 06:09:22 summary: Implement equivalent of dataset display through the API. affected #: 4 files diff -r 993c232d34cda550a5605f87d7416467d4e2c33f -r 32c6537bef27b7d481aed08a7189f11c5161a3ee lib/galaxy/web/__init__.py --- a/lib/galaxy/web/__init__.py +++ b/lib/galaxy/web/__init__.py @@ -2,6 +2,6 @@ The Galaxy web application framework """ -from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder, expose_api +from framework import expose, json, json_pretty, require_login, require_admin, url_for, error, form, FormBuilder, expose_api, expose_api_raw from framework.base import httpexceptions diff -r 993c232d34cda550a5605f87d7416467d4e2c33f -r 32c6537bef27b7d481aed08a7189f11c5161a3ee lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -99,7 +99,14 @@ return decorator return argcatcher -def expose_api( func ): +def expose_api_raw( func ): + """ + Expose this function via the API but don't dump the results + to JSON. + """ + return expose_api( func, to_json=False ) + +def expose_api( func, to_json=True ): @wraps(func) def decorator( self, trans, *args, **kwargs ): def error( environ, start_response ): @@ -183,10 +190,12 @@ trans.response.status = 400 return "That user does not exist." try: - if trans.debug: - return simplejson.dumps( func( self, trans, *args, **kwargs ), indent=4, sort_keys=True ) - else: - return simplejson.dumps( func( self, trans, *args, **kwargs ) ) + rval = func( self, trans, *args, **kwargs) + if to_json and trans.debug: + rval = simplejson.dumps( rval, indent=4, sort_keys=True ) + elif to_json: + rval = simplejson.dumps( rval ) + return rval except paste.httpexceptions.HTTPException: raise # handled except: diff -r 993c232d34cda550a5605f87d7416467d4e2c33f -r 32c6537bef27b7d481aed08a7189f11c5161a3ee lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -125,6 +125,33 @@ 'error' : str( exception ) } + @web.expose_api_raw + def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): + """ + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} + Displays history content (dataset). + """ + hda_dict = {} + try: + # for anon users: + #TODO: check login_required? + #TODO: this isn't actually most_recently_used (as defined in histories) + if( ( trans.user == None ) + and ( history_id == trans.security.encode_id( trans.history.id ) ) ): + history = trans.history + #TODO: dataset/hda by id (from history) OR check_ownership for anon user + hda = self.get_history_dataset_association( trans, history, history_content_id, + check_ownership=False, check_accessible=True ) + + else: + history = self.get_history( trans, history_id, + check_ownership=True, check_accessible=True, deleted=False ) + hda = self.get_history_dataset_association( trans, history, history_content_id, + check_ownership=True, check_accessible=True ) + except: + raise + return hda.datatype.display_data(trans, hda, preview, filename, to_ext, chunk, **kwd) + @web.expose_api def show( self, trans, id, history_id, **kwd ): """ diff -r 993c232d34cda550a5605f87d7416467d4e2c33f -r 32c6537bef27b7d481aed08a7189f11c5161a3ee lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -83,6 +83,11 @@ name_prefix='history_', path_prefix='/api/histories/:history_id', parent_resources=dict( member_name='history', collection_name='histories' ) ) + webapp.api_mapper.connect("history_contents_display", + "/api/histories/:history_id/contents/:history_content_id/display", + controller="history_contents", + action="display", + conditions=dict(method=["GET"])) webapp.api_mapper.resource( 'permission', 'permissions', path_prefix='/api/libraries/:library_id', https://bitbucket.org/galaxy/galaxy-central/commits/3284b58ae9fd/ changeset: 3284b58ae9fd user: jmchilton date: 2013-02-26 16:56:15 summary: Update HDA API return value to reflect new API-based path for downloads. affected #: 1 file diff -r 32c6537bef27b7d481aed08a7189f11c5161a3ee -r 3284b58ae9fd65dd276d0faa2ed930f245c9df5d lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -155,7 +155,7 @@ @web.expose_api def show( self, trans, id, history_id, **kwd ): """ - GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display Displays information about a history content (dataset). """ hda_dict = {} @@ -230,14 +230,7 @@ hda_dict[ 'file_name' ] = hda.file_name if not hda_dict[ 'deleted' ]: - # Problem: Method url_for cannot use the dataset controller - # Get the environment from DefaultWebTransaction - # and use default webapp mapper instead of webapp API mapper - web_url_for = routes.URLGenerator( trans.webapp.mapper, trans.environ ) - # http://routes.groovie.org/generating.html - # url_for is being phased out, so new applications should use url - hda_dict[ 'download_url' ] = web_url_for( controller='dataset', action='display', - dataset_id=trans.security.encode_id( hda.id ), to_ext=hda.ext ) + hda_dict[ 'download_url' ] = url_for( 'history_contents_display', history_id = trans.security.encode_id( history.id ), history_content_id = trans.security.encode_id( hda.id ) ) can_access_hda = trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), hda.dataset ) hda_dict[ 'accessible' ] = ( trans.user_is_admin() or can_access_hda ) https://bitbucket.org/galaxy/galaxy-central/commits/440cad876d23/ changeset: 440cad876d23 user: jmchilton date: 2013-02-26 16:59:40 summary: In previous commit, I modified documentation in the wrong place. affected #: 1 file diff -r 3284b58ae9fd65dd276d0faa2ed930f245c9df5d -r 440cad876d23f467bf4ad63ac26a9fe7c4c5eeed lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -128,7 +128,7 @@ @web.expose_api_raw def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): """ - GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display Displays history content (dataset). """ hda_dict = {} @@ -155,7 +155,7 @@ @web.expose_api def show( self, trans, id, history_id, **kwd ): """ - GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id} Displays information about a history content (dataset). """ hda_dict = {} https://bitbucket.org/galaxy/galaxy-central/commits/a2424331a3f9/ changeset: a2424331a3f9 user: jmchilton date: 2013-03-04 17:32:32 summary: Per Jeremy's request I have moved the API history contents dataset display functionality to the dataset controller - https://bitbucket.org/galaxy/galaxy-central/pull-request/131/implement-equi…. affected #: 3 files diff -r 440cad876d23f467bf4ad63ac26a9fe7c4c5eeed -r a2424331a3f929bfadafea1dedbab5fb4b651472 lib/galaxy/webapps/galaxy/api/datasets.py --- a/lib/galaxy/webapps/galaxy/api/datasets.py +++ b/lib/galaxy/webapps/galaxy/api/datasets.py @@ -4,12 +4,12 @@ import logging, os, string, shutil, urllib, re, socket from galaxy import util, datatypes, jobs, web, util from galaxy.visualization.data_providers.genome import FeatureLocationIndexDataProvider -from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin +from galaxy.web.base.controller import BaseAPIController, UsesVisualizationMixin, UsesHistoryDatasetAssociationMixin, UsesHistoryMixin from galaxy.web.framework.helpers import is_true log = logging.getLogger( __name__ ) -class DatasetsController( BaseAPIController, UsesVisualizationMixin ): +class DatasetsController( BaseAPIController, UsesVisualizationMixin, UsesHistoryMixin, UsesHistoryDatasetAssociationMixin ): @web.expose_api def index( self, trans, **kwd ): @@ -191,3 +191,31 @@ data = data_provider.get_data( **kwargs ) return data + + @web.expose_api_raw + def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): + """ + GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display + Displays history content (dataset). + """ + # Huge amount of code overlap with lib/galaxy/webapps/galaxy/api/history_content:show here. + hda_dict = {} + try: + # for anon users: + #TODO: check login_required? + #TODO: this isn't actually most_recently_used (as defined in histories) + if( ( trans.user == None ) + and ( history_id == trans.security.encode_id( trans.history.id ) ) ): + history = trans.history + #TODO: dataset/hda by id (from history) OR check_ownership for anon user + hda = self.get_history_dataset_association( trans, history, history_content_id, + check_ownership=False, check_accessible=True ) + + else: + history = self.get_history( trans, history_id, + check_ownership=True, check_accessible=True, deleted=False ) + hda = self.get_history_dataset_association( trans, history, history_content_id, + check_ownership=True, check_accessible=True ) + except: + raise + return hda.datatype.display_data(trans, hda, preview, filename, to_ext, chunk, **kwd) diff -r 440cad876d23f467bf4ad63ac26a9fe7c4c5eeed -r a2424331a3f929bfadafea1dedbab5fb4b651472 lib/galaxy/webapps/galaxy/api/history_contents.py --- a/lib/galaxy/webapps/galaxy/api/history_contents.py +++ b/lib/galaxy/webapps/galaxy/api/history_contents.py @@ -125,33 +125,6 @@ 'error' : str( exception ) } - @web.expose_api_raw - def display( self, trans, history_content_id, history_id, preview=False, filename=None, to_ext=None, chunk=None, **kwd ): - """ - GET /api/histories/{encoded_history_id}/contents/{encoded_content_id}/display - Displays history content (dataset). - """ - hda_dict = {} - try: - # for anon users: - #TODO: check login_required? - #TODO: this isn't actually most_recently_used (as defined in histories) - if( ( trans.user == None ) - and ( history_id == trans.security.encode_id( trans.history.id ) ) ): - history = trans.history - #TODO: dataset/hda by id (from history) OR check_ownership for anon user - hda = self.get_history_dataset_association( trans, history, history_content_id, - check_ownership=False, check_accessible=True ) - - else: - history = self.get_history( trans, history_id, - check_ownership=True, check_accessible=True, deleted=False ) - hda = self.get_history_dataset_association( trans, history, history_content_id, - check_ownership=True, check_accessible=True ) - except: - raise - return hda.datatype.display_data(trans, hda, preview, filename, to_ext, chunk, **kwd) - @web.expose_api def show( self, trans, id, history_id, **kwd ): """ diff -r 440cad876d23f467bf4ad63ac26a9fe7c4c5eeed -r a2424331a3f929bfadafea1dedbab5fb4b651472 lib/galaxy/webapps/galaxy/buildapp.py --- a/lib/galaxy/webapps/galaxy/buildapp.py +++ b/lib/galaxy/webapps/galaxy/buildapp.py @@ -85,7 +85,7 @@ parent_resources=dict( member_name='history', collection_name='histories' ) ) webapp.api_mapper.connect("history_contents_display", "/api/histories/:history_id/contents/:history_content_id/display", - controller="history_contents", + controller="datasets", action="display", conditions=dict(method=["GET"])) webapp.api_mapper.resource( 'permission', https://bitbucket.org/galaxy/galaxy-central/commits/8236c09e9201/ changeset: 8236c09e9201 user: dannon date: 2013-03-04 18:06:15 summary: Merged in galaxyp/galaxy-central-parallelism-refactorings (pull request #131) Implement equivalent of dataset display through the API. affected #: 5 files Diff not available. 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: Move the tool shed's repository review grid classes out of the repository_review controller and into ~/tool_shed/grids.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cd3270cefc61/ changeset: cd3270cefc61 user: greg date: 2013-03-04 16:07:31 summary: Move the tool shed's repository review grid classes out of the repository_review controller and into ~/tool_shed/grids. affected #: 2 files diff -r 6cd65073a397246e7b6fa8884d2c26760865ffad -r cd3270cefc612315602e43e1a41a17e0f92dec1d 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 @@ -2,15 +2,12 @@ from galaxy import web, util from galaxy.web.base.controller import BaseUIController from galaxy.web.form_builder import SelectField, CheckboxField -from galaxy.webapps.tool_shed import model -from galaxy.web.framework.helpers import grids -from galaxy.model.orm import and_ from sqlalchemy.sql.expression import func from galaxy.webapps.tool_shed.util import common_util from galaxy.webapps.tool_shed.util.container_util import STRSEP -from tool_shed.grids.repository_grids import RepositoryGrid import tool_shed.util.shed_util_common as suc from galaxy.util.odict import odict +import tool_shed.grids.repository_review_grids as repository_review_grids from galaxy import eggs eggs.require('mercurial') @@ -18,259 +15,15 @@ log = logging.getLogger( __name__ ) -class ComponentGrid( grids.Grid ): - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, component ): - return component.name - class DescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, component ): - return component.description - title = "Repository review components" - model_class = model.Component - template='/webapps/tool_shed/repository_review/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - key="Component.name", - link=( lambda item: dict( operation="edit", id=item.id ) ), - attach_popup=False ), - DescriptionColumn( "Description", - key="Component.description", - attach_popup=False ) - ] - default_filter = {} - global_actions = [ - grids.GridAction( "Add new component", - dict( controller='repository_review', action='manage_components', operation='create' ) ) - ] - operations = [] - standard_filters = [] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - -class RepositoriesWithReviewsGrid( RepositoryGrid ): - # This grid filters out repositories that have been marked as either deprecated or deleted. - class WithReviewsRevisionColumn( grids.GridColumn ): - def get_value( self, trans, grid, repository ): - # Restrict to revisions that have been reviewed. - if repository.reviews: - rval = '' - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - for review in repository.reviews: - changeset_revision = review.changeset_revision - rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) - rval += '<a href="manage_repository_reviews_of_revision' - rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) - return rval - return '' - class WithoutReviewsRevisionColumn( grids.GridColumn ): - def get_value( self, trans, grid, repository ): - # Restrict the options to revisions that have not yet been reviewed. - repository_metadata_revisions = suc.get_repository_metadata_revisions_for_review( repository, reviewed=False ) - if repository_metadata_revisions: - rval = '' - for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, - repository_metadata, - repository=repository ) - rval += '<a href="manage_repository_reviews_of_revision' - rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) - return rval - return '' - class ReviewersColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository ): - rval = '' - if repository.reviewers: - for user in repository.reviewers: - rval += '<a class="view-info" href="repository_reviews_by_user?id=%s">' % trans.security.encode_id( user.id ) - rval += '%s</a> | ' % user.username - rval = rval.rstrip( ' | ' ) - return rval - title = "All reviewed repositories" - model_class = model.Repository - template='/webapps/tool_shed/repository_review/grid.mako' - default_sort_key = "Repository.name" - columns = [ - RepositoryGrid.NameColumn( "Repository name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - WithReviewsRevisionColumn( "Reviewed revisions" ), - WithoutReviewsRevisionColumn( "Revisions for review" ), - RepositoryGrid.UserColumn( "Owner", attach_popup=False ), - ReviewersColumn( "Reviewers", attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ - grids.GridOperation( "Inspect repository revisions", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) - ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ - .join( ( model.User.table, model.User.table.c.id == model.Repository.table.c.user_id ) ) \ - .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ - .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) - -class RepositoriesWithoutReviewsGrid( RepositoriesWithReviewsGrid ): - # This grid filters out repositories that have been marked as either deprecated or deleted. - title = "Repositories with no reviews" - columns = [ - RepositoriesWithReviewsGrid.NameColumn( "Repository name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoriesWithReviewsGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), - RepositoriesWithReviewsGrid.UserColumn( "Owner", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ grids.GridOperation( "Inspect repository revisions", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False, - model.Repository.reviews == None ) ) \ - .join( model.User.table ) - -class RepositoriesReviewedByMeGrid( RepositoriesWithReviewsGrid ): - # This grid filters out repositories that have been marked as either deprecated or deleted. - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ - .filter( model.RepositoryReview.table.c.user_id == trans.user.id ) \ - .join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \ - .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ - .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) - -class RepositoryReviewsByUserGrid( grids.Grid ): - # This grid filters out repositories that have been marked as deprecated. - class RepositoryNameColumn( grids.TextColumn ): - def get_value( self, trans, grid, review ): - return review.repository.name - class RepositoryDescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, review ): - return review.repository.description - class RevisionColumn( grids.TextColumn ): - def get_value( self, trans, grid, review ): - encoded_review_id = trans.security.encode_id( review.id ) - rval = '<a class="action-button" href="' - if review.user == trans.user: - rval += 'edit_review' - else: - rval +='browse_review' - rval += '?id=%s">%s</a>' % ( encoded_review_id, suc.get_revision_label( trans, review.repository, review.changeset_revision ) ) - return rval - class RatingColumn( grids.TextColumn ): - def get_value( self, trans, grid, review ): - if review.rating: - rval = '<input ' - rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) - rval += 'type="radio" ' - rval += 'class="community_rating_star star" ' - rval += 'disabled="disabled" ' - rval += 'value="%s"' % str( review.rating ) - rval += '/>' - return rval - return '' - title = "Reviews by user" - model_class = model.RepositoryReview - template='/webapps/tool_shed/repository_review/grid.mako' - default_sort_key = 'repository_id' - columns = [ - RepositoryNameColumn( "Repository Name", - model_class=model.Repository, - key="Repository.name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoryDescriptionColumn( "Description", - model_class=model.Repository, - key="Repository.description", - attach_popup=False ), - RevisionColumn( "Revision", attach_popup=False ), - RatingColumn( "Rating", attach_popup=False ), - ] - # Override these - default_filter = {} - global_actions = [] - operations = [ - grids.GridOperation( "Inspect repository revisions", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) - ] - standard_filters = [] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - def build_initial_query( self, trans, **kwd ): - user_id = trans.security.decode_id( kwd[ 'id' ] ) - return trans.sa_session.query( model.RepositoryReview ) \ - .filter( and_( model.RepositoryReview.table.c.deleted == False, \ - model.RepositoryReview.table.c.user_id == user_id ) ) \ - .join( ( model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ - .filter( model.Repository.table.c.deprecated == False ) - -class ReviewedRepositoriesIOwnGrid( RepositoriesWithReviewsGrid ): - title = "Reviewed repositories I own" - columns = [ - RepositoriesWithReviewsGrid.NameColumn( "Repository name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoriesWithReviewsGrid.WithReviewsRevisionColumn( "Reviewed revisions" ), - RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), - RepositoriesWithReviewsGrid.ReviewersColumn( "Reviewers", attach_popup=False ), - RepositoryGrid.DeprecatedColumn( "Deprecated" ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ - grids.GridOperation( "Inspect repository revisions", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) - ] - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ - .filter( model.Repository.table.c.user_id == trans.user.id ) \ - .join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \ - .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ - .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) class RepositoryReviewController( BaseUIController, common_util.ItemRatings ): - component_grid = ComponentGrid() - repositories_reviewed_by_me_grid = RepositoriesReviewedByMeGrid() - repositories_with_reviews_grid = RepositoriesWithReviewsGrid() - repositories_without_reviews_grid = RepositoriesWithoutReviewsGrid() - repository_reviews_by_user_grid = RepositoryReviewsByUserGrid() - reviewed_repositories_i_own_grid = ReviewedRepositoriesIOwnGrid() + component_grid = repository_review_grids.ComponentGrid() + repositories_reviewed_by_me_grid = repository_review_grids.RepositoriesReviewedByMeGrid() + repositories_with_reviews_grid = repository_review_grids.RepositoriesWithReviewsGrid() + repositories_without_reviews_grid = repository_review_grids.RepositoriesWithoutReviewsGrid() + repository_reviews_by_user_grid = repository_review_grids.RepositoryReviewsByUserGrid() + reviewed_repositories_i_own_grid = repository_review_grids.ReviewedRepositoriesIOwnGrid() @web.expose @web.require_login( "approve repository review" ) diff -r 6cd65073a397246e7b6fa8884d2c26760865ffad -r cd3270cefc612315602e43e1a41a17e0f92dec1d lib/tool_shed/grids/repository_review_grids.py --- /dev/null +++ b/lib/tool_shed/grids/repository_review_grids.py @@ -0,0 +1,258 @@ +import os, logging +from galaxy.webapps.tool_shed import model +from galaxy.web.framework.helpers import grids +from galaxy.model.orm import and_ +from tool_shed.grids.repository_grids import RepositoryGrid +import tool_shed.util.shed_util_common as suc + +from galaxy import eggs +eggs.require('mercurial') +from mercurial import hg, ui, patch, commands + +log = logging.getLogger( __name__ ) + +class ComponentGrid( grids.Grid ): + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, component ): + return component.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, component ): + return component.description + title = "Repository review components" + model_class = model.Component + template='/webapps/tool_shed/repository_review/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="Component.name", + link=( lambda item: dict( operation="edit", id=item.id ) ), + attach_popup=False ), + DescriptionColumn( "Description", + key="Component.description", + attach_popup=False ) + ] + default_filter = {} + global_actions = [ + grids.GridAction( "Add new component", + dict( controller='repository_review', action='manage_components', operation='create' ) ) + ] + operations = [] + standard_filters = [] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + +class RepositoriesWithReviewsGrid( RepositoryGrid ): + # This grid filters out repositories that have been marked as either deprecated or deleted. + class WithReviewsRevisionColumn( grids.GridColumn ): + def get_value( self, trans, grid, repository ): + # Restrict to revisions that have been reviewed. + if repository.reviews: + rval = '' + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + for review in repository.reviews: + changeset_revision = review.changeset_revision + rev, label = suc.get_rev_label_from_changeset_revision( repo, changeset_revision ) + rval += '<a href="manage_repository_reviews_of_revision' + rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) + return rval + return '' + class WithoutReviewsRevisionColumn( grids.GridColumn ): + def get_value( self, trans, grid, repository ): + # Restrict the options to revisions that have not yet been reviewed. + repository_metadata_revisions = suc.get_repository_metadata_revisions_for_review( repository, reviewed=False ) + if repository_metadata_revisions: + rval = '' + for repository_metadata in repository_metadata_revisions: + rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, + repository_metadata, + repository=repository ) + rval += '<a href="manage_repository_reviews_of_revision' + rval += '?id=%s&changeset_revision=%s">%s</a><br/>' % ( trans.security.encode_id( repository.id ), changeset_revision, label ) + return rval + return '' + class ReviewersColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository ): + rval = '' + if repository.reviewers: + for user in repository.reviewers: + rval += '<a class="view-info" href="repository_reviews_by_user?id=%s">' % trans.security.encode_id( user.id ) + rval += '%s</a> | ' % user.username + rval = rval.rstrip( ' | ' ) + return rval + title = "All reviewed repositories" + model_class = model.Repository + template='/webapps/tool_shed/repository_review/grid.mako' + default_sort_key = "Repository.name" + columns = [ + RepositoryGrid.NameColumn( "Repository name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + WithReviewsRevisionColumn( "Reviewed revisions" ), + WithoutReviewsRevisionColumn( "Revisions for review" ), + RepositoryGrid.UserColumn( "Owner", attach_popup=False ), + ReviewersColumn( "Reviewers", attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ + grids.GridOperation( "Inspect repository revisions", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) + ] + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ + .join( ( model.User.table, model.User.table.c.id == model.Repository.table.c.user_id ) ) \ + .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ + .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) + +class RepositoriesWithoutReviewsGrid( RepositoriesWithReviewsGrid ): + # This grid filters out repositories that have been marked as either deprecated or deleted. + title = "Repositories with no reviews" + columns = [ + RepositoriesWithReviewsGrid.NameColumn( "Repository name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoriesWithReviewsGrid.DescriptionColumn( "Synopsis", + key="description", + attach_popup=False ), + RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), + RepositoriesWithReviewsGrid.UserColumn( "Owner", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, description", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ grids.GridOperation( "Inspect repository revisions", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) ] + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False, + model.Repository.reviews == None ) ) \ + .join( model.User.table ) + +class RepositoriesReviewedByMeGrid( RepositoriesWithReviewsGrid ): + # This grid filters out repositories that have been marked as either deprecated or deleted. + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .filter( and_( model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ + .filter( model.RepositoryReview.table.c.user_id == trans.user.id ) \ + .join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \ + .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ + .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) + +class RepositoryReviewsByUserGrid( grids.Grid ): + # This grid filters out repositories that have been marked as deprecated. + class RepositoryNameColumn( grids.TextColumn ): + def get_value( self, trans, grid, review ): + return review.repository.name + class RepositoryDescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, review ): + return review.repository.description + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, review ): + encoded_review_id = trans.security.encode_id( review.id ) + rval = '<a class="action-button" href="' + if review.user == trans.user: + rval += 'edit_review' + else: + rval +='browse_review' + rval += '?id=%s">%s</a>' % ( encoded_review_id, suc.get_revision_label( trans, review.repository, review.changeset_revision ) ) + return rval + class RatingColumn( grids.TextColumn ): + def get_value( self, trans, grid, review ): + if review.rating: + rval = '<input ' + rval += 'name="star1-%s" ' % trans.security.encode_id( review.id ) + rval += 'type="radio" ' + rval += 'class="community_rating_star star" ' + rval += 'disabled="disabled" ' + rval += 'value="%s"' % str( review.rating ) + rval += '/>' + return rval + return '' + title = "Reviews by user" + model_class = model.RepositoryReview + template='/webapps/tool_shed/repository_review/grid.mako' + default_sort_key = 'repository_id' + columns = [ + RepositoryNameColumn( "Repository Name", + model_class=model.Repository, + key="Repository.name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoryDescriptionColumn( "Description", + model_class=model.Repository, + key="Repository.description", + attach_popup=False ), + RevisionColumn( "Revision", attach_popup=False ), + RatingColumn( "Rating", attach_popup=False ), + ] + # Override these + default_filter = {} + global_actions = [] + operations = [ + grids.GridOperation( "Inspect repository revisions", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) + ] + standard_filters = [] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + user_id = trans.security.decode_id( kwd[ 'id' ] ) + return trans.sa_session.query( model.RepositoryReview ) \ + .filter( and_( model.RepositoryReview.table.c.deleted == False, \ + model.RepositoryReview.table.c.user_id == user_id ) ) \ + .join( ( model.Repository.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ + .filter( model.Repository.table.c.deprecated == False ) + +class ReviewedRepositoriesIOwnGrid( RepositoriesWithReviewsGrid ): + title = "Reviewed repositories I own" + columns = [ + RepositoriesWithReviewsGrid.NameColumn( "Repository name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoriesWithReviewsGrid.WithReviewsRevisionColumn( "Reviewed revisions" ), + RepositoriesWithReviewsGrid.WithoutReviewsRevisionColumn( "Revisions for review" ), + RepositoriesWithReviewsGrid.ReviewersColumn( "Reviewers", attach_popup=False ), + RepositoryGrid.DeprecatedColumn( "Deprecated" ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ + grids.GridOperation( "Inspect repository revisions", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) + ] + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .join( ( model.RepositoryReview.table, model.RepositoryReview.table.c.repository_id == model.Repository.table.c.id ) ) \ + .filter( model.Repository.table.c.user_id == trans.user.id ) \ + .join( ( model.User.table, model.User.table.c.id == model.RepositoryReview.table.c.user_id ) ) \ + .outerjoin( ( model.ComponentReview.table, model.ComponentReview.table.c.repository_review_id == model.RepositoryReview.table.c.id ) ) \ + .outerjoin( ( model.Component.table, model.Component.table.c.id == model.ComponentReview.table.c.component_id ) ) + \ No newline at end of file Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: greg: Move the tool shed's administrative grids out of the admin controller and into ~/tool_shed/grids.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/6cd65073a397/ changeset: 6cd65073a397 user: greg date: 2013-03-04 15:47:37 summary: Move the tool shed's administrative grids out of the admin controller and into ~/tool_shed/grids. affected #: 3 files diff -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 -r 6cd65073a397246e7b6fa8884d2c26760865ffad lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -1,12 +1,9 @@ from galaxy.web.base.controller import BaseUIController from galaxy import web, util from galaxy.web.base.controllers.admin import Admin -from galaxy.webapps.tool_shed import model -from galaxy.model.orm import and_ -from galaxy.web.framework.helpers import time_ago, grids from galaxy.util import inflector import tool_shed.util.shed_util_common as suc -from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid +import tool_shed.grids.admin_grids as admin_grids from galaxy import eggs eggs.require( 'mercurial' ) @@ -16,440 +13,15 @@ log = logging.getLogger( __name__ ) -class UserGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. - class UserLoginColumn( grids.TextColumn ): - def get_value( self, trans, grid, user ): - return user.email - class UserNameColumn( grids.TextColumn ): - def get_value( self, trans, grid, user ): - if user.username: - return user.username - return 'not set' - class GroupsColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.groups: - return len( user.groups ) - return 0 - class RolesColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.roles: - return len( user.roles ) - return 0 - class ExternalColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.external: - return 'yes' - return 'no' - class LastLoginColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.galaxy_sessions: - return self.format( user.galaxy_sessions[ 0 ].update_time ) - return 'never' - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, user ): - if user.purged: - return "purged" - elif user.deleted: - return "deleted" - return "" - class EmailColumn( grids.GridColumn ): - def filter( self, trans, user, query, column_filter ): - if column_filter == 'All': - return query - return query.filter( and_( model.Tool.table.c.user_id == model.User.table.c.id, - model.User.table.c.email == column_filter ) ) - title = "Users" - model_class = model.User - template='/admin/user/grid.mako' - default_sort_key = "email" - columns = [ - UserLoginColumn( "Email", - key="email", - link=( lambda item: dict( operation="information", id=item.id ) ), - attach_popup=True, - filterable="advanced" ), - UserNameColumn( "User Name", - key="username", - attach_popup=False, - filterable="advanced" ), - GroupsColumn( "Groups", attach_popup=False ), - RolesColumn( "Roles", attach_popup=False ), - ExternalColumn( "External", attach_popup=False ), - LastLoginColumn( "Last Login", format=time_ago ), - StatusColumn( "Status", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - EmailColumn( "Email", - key="email", - visible=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Create new user", - dict( controller='admin', action='users', operation='create' ) ) - ] - operations = [ - grids.GridOperation( "Manage Roles and Groups", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="manage_roles_and_groups_for_user" ) ), - grids.GridOperation( "Reset Password", - condition=( lambda item: not item.deleted ), - allow_multiple=True, - allow_popup=False, - url_args=dict( action="reset_user_password" ) ) - ] - standard_filters = [ - grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), - grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ), - grids.GridColumnFilter( "Purged", args=dict( purged=True ) ), - grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) - ] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - def get_current_item( self, trans, **kwargs ): - return trans.user - -class RoleGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, role ): - return role.name - class DescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, role ): - if role.description: - return role.description - return '' - class TypeColumn( grids.TextColumn ): - def get_value( self, trans, grid, role ): - return role.type - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, role ): - if role.deleted: - return "deleted" - return "" - class GroupsColumn( grids.GridColumn ): - def get_value( self, trans, grid, role ): - if role.groups: - return len( role.groups ) - return 0 - class UsersColumn( grids.GridColumn ): - def get_value( self, trans, grid, role ): - if role.users: - return len( role.users ) - return 0 - title = "Roles" - model_class = model.Role - template='/admin/dataset_security/role/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="Manage users and groups", id=item.id ) ), - attach_popup=True, - filterable="advanced" ), - DescriptionColumn( "Description", - key='description', - attach_popup=False, - filterable="advanced" ), - TypeColumn( "Type", - key='type', - attach_popup=False, - filterable="advanced" ), - GroupsColumn( "Groups", attach_popup=False ), - UsersColumn( "Users", attach_popup=False ), - StatusColumn( "Status", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) - ] - columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Add new role", - dict( controller='admin', action='roles', operation='create' ) ) - ] - operations = [ grids.GridOperation( "Rename", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="rename_role" ) ), - grids.GridOperation( "Delete", - condition=( lambda item: not item.deleted ), - allow_multiple=True, - url_args=dict( action="mark_role_deleted" ) ), - grids.GridOperation( "Undelete", - condition=( lambda item: item.deleted ), - allow_multiple=True, - url_args=dict( action="undelete_role" ) ), - grids.GridOperation( "Purge", - condition=( lambda item: item.deleted ), - allow_multiple=True, - url_args=dict( action="purge_role" ) ) ] - standard_filters = [ - grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), - grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), - grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) - ] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - def apply_query_filter( self, trans, query, **kwd ): - return query.filter( model.Role.type != model.Role.types.PRIVATE ) - -class GroupGrid( grids.Grid ): - # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, group ): - return group.name - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, group ): - if group.deleted: - return "deleted" - return "" - class RolesColumn( grids.GridColumn ): - def get_value( self, trans, grid, group ): - if group.roles: - return len( group.roles ) - return 0 - class UsersColumn( grids.GridColumn ): - def get_value( self, trans, grid, group ): - if group.members: - return len( group.members ) - return 0 - title = "Groups" - model_class = model.Group - template='/admin/dataset_security/group/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - link=( lambda item: dict( operation="Manage users and roles", id=item.id ) ), - attach_popup=True ), - UsersColumn( "Users", attach_popup=False ), - RolesColumn( "Roles", attach_popup=False ), - StatusColumn( "Status", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) - ] - columns.append( grids.MulticolFilterColumn( "Search", - cols_to_filter=[ columns[0], columns[1], columns[2] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - global_actions = [ - grids.GridAction( "Add new group", - dict( controller='admin', action='groups', operation='create' ) ) - ] - operations = [ grids.GridOperation( "Rename", - condition=( lambda item: not item.deleted ), - allow_multiple=False, - url_args=dict( action="rename_group" ) ), - grids.GridOperation( "Delete", - condition=( lambda item: not item.deleted ), - allow_multiple=True, - url_args=dict( action="mark_group_deleted" ) ), - grids.GridOperation( "Undelete", - condition=( lambda item: item.deleted ), - allow_multiple=True, - url_args=dict( action="undelete_group" ) ), - grids.GridOperation( "Purge", - condition=( lambda item: item.deleted ), - allow_multiple=True, - url_args=dict( action="purge_group" ) ) ] - standard_filters = [ - grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), - grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), - grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) - ] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - -class ManageCategoryGrid( CategoryGrid ): - columns = [ col for col in CategoryGrid.columns ] - # Override the NameColumn to include an Edit link - columns[ 0 ] = CategoryGrid.NameColumn( "Name", - key="Category.name", - link=( lambda item: dict( operation="Edit", id=item.id ) ), - model_class=model.Category, - attach_popup=False ) - global_actions = [ - grids.GridAction( "Add new category", - dict( controller='admin', action='manage_categories', operation='create' ) ) - ] - -class AdminRepositoryGrid( RepositoryGrid ): - class DeletedColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository ): - if repository.deleted: - return 'yes' - return '' - columns = [ RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoryGrid.UserColumn( "Owner", - model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), - attach_popup=False, - key="User.username" ), - RepositoryGrid.DeprecatedColumn( "Deprecated", key="deprecated", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", attach_popup=False ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ operation for operation in RepositoryGrid.operations ] - operations.append( grids.GridOperation( "Delete", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ) - operations.append( grids.GridOperation( "Undelete", - allow_multiple=False, - condition=( lambda item: item.deleted ), - async_compatible=False ) ) - standard_filters = [] - default_filter = {} - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .join( model.User.table ) - -class RepositoryMetadataGrid( grids.Grid ): - class IdColumn( grids.IntegerColumn ): - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.id - class NameColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.name - class OwnerColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.user.username - class RevisionColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - repository = repository_metadata.repository - repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) - ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) - return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) - class ToolsColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - tools_str = '0' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'tools' in metadata: - # We used to display the following, but grid was too cluttered. - #for tool_metadata_dict in metadata[ 'tools' ]: - # tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) - return '%d' % len( metadata[ 'tools' ] ) - return tools_str - class DatatypesColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - datatypes_str = '0' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'datatypes' in metadata: - # We used to display the following, but grid was too cluttered. - #for datatype_metadata_dict in metadata[ 'datatypes' ]: - # datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] - return '%d' % len( metadata[ 'datatypes' ] ) - return datatypes_str - class WorkflowsColumn( grids.TextColumn ): - def get_value( self, trans, grid, repository_metadata ): - workflows_str = '0' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - if 'workflows' in metadata: - # We used to display the following, but grid was too cluttered. - #workflows_str += '<b>Workflows:</b><br/>' - # metadata[ 'workflows' ] is a list of tuples where each contained tuple is - # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] - #workflow_tups = metadata[ 'workflows' ] - #workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] - #for workflow_metadata_dict in workflow_metadata_dicts: - # workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] - return '%d' % len( metadata[ 'workflows' ] ) - return workflows_str - class DeletedColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.repository.deleted: - return 'yes' - return '' - class DeprecatedColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.repository.deprecated: - return 'yes' - return '' - class MaliciousColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.malicious: - return 'yes' - return '' - # Grid definition - title = "Repository Metadata" - model_class = model.RepositoryMetadata - template='/webapps/tool_shed/repository/grid.mako' - default_sort_key = "name" - columns = [ - IdColumn( "Id", - visible=False, - attach_popup=False ), - NameColumn( "Name", - key="name", - model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository_revision", id=item.id ) ), - attach_popup=True ), - OwnerColumn( "Owner", attach_popup=False ), - RevisionColumn( "Revision", attach_popup=False ), - ToolsColumn( "Tools", attach_popup=False ), - DatatypesColumn( "Datatypes", attach_popup=False ), - WorkflowsColumn( "Workflows", attach_popup=False ), - DeletedColumn( "Deleted", attach_popup=False ), - DeprecatedColumn( "Deprecated", attach_popup=False ), - MaliciousColumn( "Malicious", attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ grids.GridOperation( "Delete", - allow_multiple=False, - allow_popup=True, - async_compatible=False, - confirm="Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items." ) ] - standard_filters = [] - default_filter = {} - num_rows_per_page = 50 - preserve_state = False - use_paging = True - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository.table ) class AdminController( BaseUIController, Admin ): - user_list_grid = UserGrid() - role_list_grid = RoleGrid() - group_list_grid = GroupGrid() - manage_category_grid = ManageCategoryGrid() - repository_grid = AdminRepositoryGrid() - repository_metadata_grid = RepositoryMetadataGrid() + user_list_grid = admin_grids.UserGrid() + role_list_grid = admin_grids.RoleGrid() + group_list_grid = admin_grids.GroupGrid() + manage_category_grid = admin_grids.ManageCategoryGrid() + repository_grid = admin_grids.AdminRepositoryGrid() + repository_metadata_grid = admin_grids.RepositoryMetadataGrid() @web.expose @web.require_admin diff -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 -r 6cd65073a397246e7b6fa8884d2c26760865ffad lib/tool_shed/grids/admin_grids.py --- /dev/null +++ b/lib/tool_shed/grids/admin_grids.py @@ -0,0 +1,435 @@ +import os, logging +from galaxy.web.framework.helpers import time_ago, grids +from galaxy.webapps.tool_shed import model +from galaxy.model.orm import and_ +import tool_shed.util.shed_util_common as suc +from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid + +log = logging.getLogger( __name__ ) + + +class UserGrid( grids.Grid ): + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + class UserLoginColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): + return user.email + class UserNameColumn( grids.TextColumn ): + def get_value( self, trans, grid, user ): + if user.username: + return user.username + return 'not set' + class GroupsColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.groups: + return len( user.groups ) + return 0 + class RolesColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.roles: + return len( user.roles ) + return 0 + class ExternalColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.external: + return 'yes' + return 'no' + class LastLoginColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.galaxy_sessions: + return self.format( user.galaxy_sessions[ 0 ].update_time ) + return 'never' + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, user ): + if user.purged: + return "purged" + elif user.deleted: + return "deleted" + return "" + class EmailColumn( grids.GridColumn ): + def filter( self, trans, user, query, column_filter ): + if column_filter == 'All': + return query + return query.filter( and_( model.Tool.table.c.user_id == model.User.table.c.id, + model.User.table.c.email == column_filter ) ) + title = "Users" + model_class = model.User + template='/admin/user/grid.mako' + default_sort_key = "email" + columns = [ + UserLoginColumn( "Email", + key="email", + link=( lambda item: dict( operation="information", id=item.id ) ), + attach_popup=True, + filterable="advanced" ), + UserNameColumn( "User Name", + key="username", + attach_popup=False, + filterable="advanced" ), + GroupsColumn( "Groups", attach_popup=False ), + RolesColumn( "Roles", attach_popup=False ), + ExternalColumn( "External", attach_popup=False ), + LastLoginColumn( "Last Login", format=time_ago ), + StatusColumn( "Status", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + EmailColumn( "Email", + key="email", + visible=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Create new user", + dict( controller='admin', action='users', operation='create' ) ) + ] + operations = [ + grids.GridOperation( "Manage Roles and Groups", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="manage_roles_and_groups_for_user" ) ), + grids.GridOperation( "Reset Password", + condition=( lambda item: not item.deleted ), + allow_multiple=True, + allow_popup=False, + url_args=dict( action="reset_user_password" ) ) + ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True, purged=False ) ), + grids.GridColumnFilter( "Purged", args=dict( purged=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def get_current_item( self, trans, **kwargs ): + return trans.user + +class RoleGrid( grids.Grid ): + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): + return role.name + class DescriptionColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): + if role.description: + return role.description + return '' + class TypeColumn( grids.TextColumn ): + def get_value( self, trans, grid, role ): + return role.type + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): + if role.deleted: + return "deleted" + return "" + class GroupsColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): + if role.groups: + return len( role.groups ) + return 0 + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, role ): + if role.users: + return len( role.users ) + return 0 + title = "Roles" + model_class = model.Role + template='/admin/dataset_security/role/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="Manage users and groups", id=item.id ) ), + attach_popup=True, + filterable="advanced" ), + DescriptionColumn( "Description", + key='description', + attach_popup=False, + filterable="advanced" ), + TypeColumn( "Type", + key='type', + attach_popup=False, + filterable="advanced" ), + GroupsColumn( "Groups", attach_popup=False ), + UsersColumn( "Users", attach_popup=False ), + StatusColumn( "Status", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Add new role", + dict( controller='admin', action='roles', operation='create' ) ) + ] + operations = [ grids.GridOperation( "Rename", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="rename_role" ) ), + grids.GridOperation( "Delete", + condition=( lambda item: not item.deleted ), + allow_multiple=True, + url_args=dict( action="mark_role_deleted" ) ), + grids.GridOperation( "Undelete", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( action="undelete_role" ) ), + grids.GridOperation( "Purge", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( action="purge_role" ) ) ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def apply_query_filter( self, trans, query, **kwd ): + return query.filter( model.Role.type != model.Role.types.PRIVATE ) + +class GroupGrid( grids.Grid ): + # TODO: move this to an admin_common controller since it is virtually the same in the galaxy webapp. + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, group ): + return group.name + class StatusColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): + if group.deleted: + return "deleted" + return "" + class RolesColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): + if group.roles: + return len( group.roles ) + return 0 + class UsersColumn( grids.GridColumn ): + def get_value( self, trans, grid, group ): + if group.members: + return len( group.members ) + return 0 + title = "Groups" + model_class = model.Group + template='/admin/dataset_security/group/grid.mako' + default_sort_key = "name" + columns = [ + NameColumn( "Name", + link=( lambda item: dict( operation="Manage users and roles", id=item.id ) ), + attach_popup=True ), + UsersColumn( "Users", attach_popup=False ), + RolesColumn( "Roles", attach_popup=False ), + StatusColumn( "Status", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + grids.DeletedColumn( "Deleted", + key="deleted", + visible=False, + filterable="advanced" ) + ] + columns.append( grids.MulticolFilterColumn( "Search", + cols_to_filter=[ columns[0], columns[1], columns[2] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + global_actions = [ + grids.GridAction( "Add new group", + dict( controller='admin', action='groups', operation='create' ) ) + ] + operations = [ grids.GridOperation( "Rename", + condition=( lambda item: not item.deleted ), + allow_multiple=False, + url_args=dict( action="rename_group" ) ), + grids.GridOperation( "Delete", + condition=( lambda item: not item.deleted ), + allow_multiple=True, + url_args=dict( action="mark_group_deleted" ) ), + grids.GridOperation( "Undelete", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( action="undelete_group" ) ), + grids.GridOperation( "Purge", + condition=( lambda item: item.deleted ), + allow_multiple=True, + url_args=dict( action="purge_group" ) ) ] + standard_filters = [ + grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), + grids.GridColumnFilter( "Deleted", args=dict( deleted=True ) ), + grids.GridColumnFilter( "All", args=dict( deleted='All' ) ) + ] + num_rows_per_page = 50 + preserve_state = False + use_paging = True + +class ManageCategoryGrid( CategoryGrid ): + columns = [ col for col in CategoryGrid.columns ] + # Override the NameColumn to include an Edit link + columns[ 0 ] = CategoryGrid.NameColumn( "Name", + key="Category.name", + link=( lambda item: dict( operation="Edit", id=item.id ) ), + model_class=model.Category, + attach_popup=False ) + global_actions = [ + grids.GridAction( "Add new category", + dict( controller='admin', action='manage_categories', operation='create' ) ) + ] + +class AdminRepositoryGrid( RepositoryGrid ): + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository ): + if repository.deleted: + return 'yes' + return '' + columns = [ RepositoryGrid.NameColumn( "Name", + key="name", + link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), + attach_popup=True ), + RepositoryGrid.UserColumn( "Owner", + model_class=model.User, + link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), + attach_popup=False, + key="User.username" ), + RepositoryGrid.DeprecatedColumn( "Deprecated", key="deprecated", attach_popup=False ), + # Columns that are valid for filtering but are not visible. + DeletedColumn( "Deleted", key="deleted", attach_popup=False ) ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[0] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ operation for operation in RepositoryGrid.operations ] + operations.append( grids.GridOperation( "Delete", + allow_multiple=False, + condition=( lambda item: not item.deleted ), + async_compatible=False ) ) + operations.append( grids.GridOperation( "Undelete", + allow_multiple=False, + condition=( lambda item: item.deleted ), + async_compatible=False ) ) + standard_filters = [] + default_filter = {} + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.Repository ) \ + .join( model.User.table ) + +class RepositoryMetadataGrid( grids.Grid ): + class IdColumn( grids.IntegerColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.id + class NameColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.name + class OwnerColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + return repository_metadata.repository.user.username + class RevisionColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + repository = repository_metadata.repository + repo = hg.repository( suc.get_configured_ui(), repository.repo_path( trans.app ) ) + ctx = suc.get_changectx_for_changeset( repo, repository_metadata.changeset_revision ) + return "%s:%s" % ( str( ctx.rev() ), repository_metadata.changeset_revision ) + class ToolsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + tools_str = '0' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'tools' in metadata: + # We used to display the following, but grid was too cluttered. + #for tool_metadata_dict in metadata[ 'tools' ]: + # tools_str += '%s <b>%s</b><br/>' % ( tool_metadata_dict[ 'id' ], tool_metadata_dict[ 'version' ] ) + return '%d' % len( metadata[ 'tools' ] ) + return tools_str + class DatatypesColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + datatypes_str = '0' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'datatypes' in metadata: + # We used to display the following, but grid was too cluttered. + #for datatype_metadata_dict in metadata[ 'datatypes' ]: + # datatypes_str += '%s<br/>' % datatype_metadata_dict[ 'extension' ] + return '%d' % len( metadata[ 'datatypes' ] ) + return datatypes_str + class WorkflowsColumn( grids.TextColumn ): + def get_value( self, trans, grid, repository_metadata ): + workflows_str = '0' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + if 'workflows' in metadata: + # We used to display the following, but grid was too cluttered. + #workflows_str += '<b>Workflows:</b><br/>' + # metadata[ 'workflows' ] is a list of tuples where each contained tuple is + # [ <relative path to the .ga file in the repository>, <exported workflow dict> ] + #workflow_tups = metadata[ 'workflows' ] + #workflow_metadata_dicts = [ workflow_tup[1] for workflow_tup in workflow_tups ] + #for workflow_metadata_dict in workflow_metadata_dicts: + # workflows_str += '%s<br/>' % workflow_metadata_dict[ 'name' ] + return '%d' % len( metadata[ 'workflows' ] ) + return workflows_str + class DeletedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.deleted: + return 'yes' + return '' + class DeprecatedColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.repository.deprecated: + return 'yes' + return '' + class MaliciousColumn( grids.BooleanColumn ): + def get_value( self, trans, grid, repository_metadata ): + if repository_metadata.malicious: + return 'yes' + return '' + # Grid definition + title = "Repository Metadata" + model_class = model.RepositoryMetadata + template='/webapps/tool_shed/repository/grid.mako' + default_sort_key = "name" + columns = [ + IdColumn( "Id", + visible=False, + attach_popup=False ), + NameColumn( "Name", + key="name", + model_class=model.Repository, + link=( lambda item: dict( operation="view_or_manage_repository_revision", id=item.id ) ), + attach_popup=True ), + OwnerColumn( "Owner", attach_popup=False ), + RevisionColumn( "Revision", attach_popup=False ), + ToolsColumn( "Tools", attach_popup=False ), + DatatypesColumn( "Datatypes", attach_popup=False ), + WorkflowsColumn( "Workflows", attach_popup=False ), + DeletedColumn( "Deleted", attach_popup=False ), + DeprecatedColumn( "Deprecated", attach_popup=False ), + MaliciousColumn( "Malicious", attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name", + cols_to_filter=[ columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + operations = [ grids.GridOperation( "Delete", + allow_multiple=False, + allow_popup=True, + async_compatible=False, + confirm="Repository metadata records cannot be recovered after they are deleted. Click OK to delete the selected items." ) ] + standard_filters = [] + default_filter = {} + num_rows_per_page = 50 + preserve_state = False + use_paging = True + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository.table ) diff -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 -r 6cd65073a397246e7b6fa8884d2c26760865ffad lib/tool_shed/grids/repository_grids.py --- a/lib/tool_shed/grids/repository_grids.py +++ b/lib/tool_shed/grids/repository_grids.py @@ -10,6 +10,8 @@ eggs.require('markupsafe') from markupsafe import escape as escape_html +log = logging.getLogger( __name__ ) + class CategoryGrid( grids.Grid ): 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: greg: Move the many Grid classes out of the tool shed's repository controller into the new location for tool shed grids: ~/tool_shed/grids.
by commits-noreply＠bitbucket.org 04 Mar '13

04 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/db8a3bd35841/ changeset: db8a3bd35841 user: greg date: 2013-03-04 15:26:59 summary: Move the many Grid classes out of the tool shed's repository controller into the new location for tool shed grids: ~/tool_shed/grids. affected #: 8 files diff -r 7369eda82e2cf7e10338232569ed9185bc3b526b -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -6,7 +6,7 @@ from galaxy.web.framework.helpers import time_ago, grids from galaxy.util import inflector import tool_shed.util.shed_util_common as suc -from repository import RepositoryGrid, CategoryGrid +from tool_shed.grids.repository_grids import RepositoryGrid, CategoryGrid from galaxy import eggs eggs.require( 'mercurial' ) diff -r 7369eda82e2cf7e10338232569ed9185bc3b526b -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 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 @@ -1,10 +1,10 @@ -import os, logging, re, tempfile, shutil, ConfigParser, string +import os, logging, re, tempfile, ConfigParser, string from time import gmtime, strftime from datetime import date, datetime from galaxy import util, web from galaxy.util.odict import odict from galaxy.web.base.controller import BaseUIController -from galaxy.web.form_builder import CheckboxField, SelectField, build_select_field +from galaxy.web.form_builder import CheckboxField, build_select_field from galaxy.webapps.tool_shed import model from galaxy.webapps.tool_shed.model import directory_hash_id from galaxy.web.framework.helpers import grids @@ -15,12 +15,12 @@ from galaxy.webapps.tool_shed.util import workflow_util from galaxy.webapps.tool_shed.util import common_util import galaxy.tools +import tool_shed.grids.repository_grids as repository_grids +import tool_shed.grids.util as grids_util from galaxy import eggs eggs.require('mercurial') from mercurial import hg, ui, patch, commands -eggs.require('markupsafe') -from markupsafe import escape as escape_html log = logging.getLogger( __name__ ) @@ -29,1003 +29,25 @@ malicious_error_can_push = " Correct this changeset as soon as possible, it potentially produces malicious behavior or contains inappropriate content." -class CategoryGrid( grids.Grid ): - - - class NameColumn( grids.TextColumn ): - - def get_value( self, trans, grid, category ): - return category.name - - - class DescriptionColumn( grids.TextColumn ): - def get_value( self, trans, grid, category ): - return category.description - - - class RepositoriesColumn( grids.TextColumn ): - - def get_value( self, trans, grid, category ): - if category.repositories: - viewable_repositories = 0 - for rca in category.repositories: - if not rca.repository.deleted and not rca.repository.deprecated: - viewable_repositories += 1 - return viewable_repositories - return 0 - - title = "Categories" - model_class = model.Category - template='/webapps/tool_shed/category/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - key="Category.name", - link=( lambda item: dict( operation="repositories_by_category", id=item.id ) ), - attach_popup=False ), - DescriptionColumn( "Description", - key="Category.description", - attach_popup=False ), - RepositoriesColumn( "Repositories", - model_class=model.Repository, - attach_popup=False ) - ] - # Override these - default_filter = {} - global_actions = [] - operations = [] - standard_filters = [] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - -class ValidCategoryGrid( CategoryGrid ): - - - class RepositoriesColumn( grids.TextColumn ): - - def get_value( self, trans, grid, category ): - if category.repositories: - viewable_repositories = 0 - for rca in category.repositories: - repository = rca.repository - if not repository.deleted and not repository.deprecated and repository.downloadable_revisions: - viewable_repositories += 1 - return viewable_repositories - return 0 - - title = "Categories of valid repositories" - model_class = model.Category - template='/webapps/tool_shed/category/valid_grid.mako' - default_sort_key = "name" - columns = [ - CategoryGrid.NameColumn( "Name", - key="Category.name", - link=( lambda item: dict( operation="valid_repositories_by_category", id=item.id ) ), - attach_popup=False ), - CategoryGrid.DescriptionColumn( "Description", - key="Category.description", - attach_popup=False ), - # Columns that are valid for filtering but are not visible. - RepositoriesColumn( "Valid repositories", - model_class=model.Repository, - attach_popup=False ) - ] - # Override these - default_filter = {} - global_actions = [] - operations = [] - standard_filters = [] - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - -class RepositoryGrid( grids.Grid ): - - - class NameColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - return escape_html( repository.name ) - - - class MetadataRevisionColumn( grids.GridColumn ): - - def __init__( self, col_name ): - grids.GridColumn.__init__( self, col_name ) - - def get_value( self, trans, grid, repository ): - """Display a SelectField whose options are the changeset_revision strings of all metadata revisions of this repository.""" - # A repository's metadata revisions may not all be installable, as some may contain only invalid tools. - select_field = build_changeset_revision_select_field( trans, repository, downloadable=False ) - if len( select_field.options ) > 1: - return select_field.get_html() - elif len( select_field.options ) == 1: - return select_field.options[ 0 ][ 0 ] - return '' - - - class TipRevisionColumn( grids.GridColumn ): - - def __init__( self, col_name ): - grids.GridColumn.__init__( self, col_name ) - - def get_value( self, trans, grid, repository ): - """Display the repository tip revision label.""" - return escape_html( repository.revision( trans.app ) ) - - - class DescriptionColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - return escape_html( repository.description ) - - - class CategoryColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - rval = '<ul>' - if repository.categories: - for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=repositories_by_category&id=%s">%s</a></li>' \ - % ( trans.security.encode_id( rca.category.id ), rca.category.name ) - else: - rval += '<li>not set</li>' - rval += '</ul>' - return rval - - - class RepositoryCategoryColumn( grids.GridColumn ): - - def filter( self, trans, user, query, column_filter ): - """Modify query to filter by category.""" - if column_filter == "All": - return query - return query.filter( model.Category.name == column_filter ) - - - class UserColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - if repository.user: - return escape_html( repository.user.username ) - return 'no user' - - - class EmailColumn( grids.TextColumn ): - - def filter( self, trans, user, query, column_filter ): - if column_filter == 'All': - return query - return query.filter( and_( model.Repository.table.c.user_id == model.User.table.c.id, - model.User.table.c.email == column_filter ) ) - - - class EmailAlertsColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - if trans.user and repository.email_alerts and trans.user.email in json.from_json_string( repository.email_alerts ): - return 'yes' - return '' - - - class DeprecatedColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - if repository.deprecated: - return 'yes' - return '' - - title = "Repositories" - model_class = model.Repository - template='/webapps/tool_shed/repository/grid.mako' - default_sort_key = "name" - columns = [ - NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - MetadataRevisionColumn( "Metadata Revisions" ), - TipRevisionColumn( "Tip Revision" ), - CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - attach_popup=False ), - UserColumn( "Owner", - model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), - attach_popup=False, - key="User.username" ), - # Columns that are valid for filtering but are not visible. - EmailColumn( "Email", - model_class=model.User, - key="email", - visible=False ), - RepositoryCategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - visible=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ grids.GridOperation( "Receive email alerts", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] - standard_filters = [] - default_filter = dict( deleted="False" ) - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - - -class RepositoriesByUserGrid( RepositoryGrid ): - title = "Repositories by user" - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.TipRevisionColumn( "Tip Revision" ), - RepositoryGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - RepositoryGrid.CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - attach_popup=False ) - ] - operations = [] - standard_filters = [] - default_filter = dict( deleted="False" ) - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - def build_initial_query( self, trans, **kwd ): - decoded_user_id = trans.security.decode_id( kwd[ 'user_id' ] ) - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False, - model.Repository.table.c.user_id == decoded_user_id ) ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - - -class RepositoriesIOwnGrid( RepositoryGrid ): - title = "Repositories I own" - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.TipRevisionColumn( "Tip Revision" ), - RepositoryGrid.CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - attach_popup=False ), - RepositoryGrid.DeprecatedColumn( "Deprecated" ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ grids.GridOperation( "Mark as deprecated", - allow_multiple=False, - condition=( lambda item: not item.deleted and not item.deprecated ), - async_compatible=False, - confirm="Are you sure that you want to deprecate this repository?" ), - grids.GridOperation( "Mark as not deprecated", - allow_multiple=False, - condition=( lambda item: not item.deleted and item.deprecated ), - async_compatible=False ) ] - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.user_id == trans.user.id ) ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - - -class DeprecatedRepositoriesIOwnGrid( RepositoriesIOwnGrid ): - title = "Deprecated repositories I own" - columns = [ - RepositoriesIOwnGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoriesIOwnGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoriesIOwnGrid.TipRevisionColumn( "Tip Revision" ), - RepositoriesIOwnGrid.CategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - attach_popup=False ), - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.user_id == trans.user.id, - model.Repository.table.c.deprecated == True ) ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - - -class EmailAlertsRepositoryGrid( RepositoryGrid ): - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ), - RepositoryGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - RepositoryGrid.UserColumn( "Owner", - model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), - attach_popup=False, - key="User.username" ), - RepositoryGrid.EmailAlertsColumn( "Alert", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - grids.DeletedColumn( "Deleted", - key="deleted", - visible=False, - filterable="advanced" ) - ] - operations = [ grids.GridOperation( "Receive email alerts", - allow_multiple=True, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] - global_actions = [ - grids.GridAction( "User preferences", dict( controller='user', action='index', cntrller='repository' ) ) - ] - - -class MyWritableRepositoriesGrid( RepositoryGrid ): - # This grid filters out repositories that have been marked as either deprecated or deleted. - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - RepositoryGrid.MetadataRevisionColumn( "Metadata Revisions" ), - RepositoryGrid.TipRevisionColumn( "Tip Revision" ), - RepositoryGrid.UserColumn( "Owner", - model_class=model.User, - link=( lambda item: dict( operation="repositories_by_user", id=item.id ) ), - attach_popup=False, - key="User.username" ), - RepositoryGrid.EmailAlertsColumn( "Alert", attach_popup=False ), - # Columns that are valid for filtering but are not visible. - RepositoryGrid.EmailColumn( "Email", - model_class=model.User, - key="email", - visible=False ), - RepositoryGrid.RepositoryCategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - visible=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name", - cols_to_filter=[ columns[0] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [ grids.GridOperation( "Receive email alerts", - allow_multiple=False, - condition=( lambda item: not item.deleted ), - async_compatible=False ) ] - - def build_initial_query( self, trans, **kwd ): - # TODO: improve performance by adding a db table associating users with repositories for which they have write access. - username = trans.user.username - clause_list = [] - for repository in trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deprecated == False, - model.Repository.table.c.deleted == False ) ): - allow_push = repository.allow_push( trans.app ) - if allow_push: - allow_push_usernames = allow_push.split( ',' ) - if username in allow_push_usernames: - clause_list.append( model.Repository.table.c.id == repository.id ) - if clause_list: - return trans.sa_session.query( model.Repository ) \ - .filter( or_( *clause_list ) ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) - # Return an empty query. - return trans.sa_session.query( model.Repository ) \ - .filter( model.Repository.table.c.id < 0 ) - - -class ValidRepositoryGrid( RepositoryGrid ): - # This grid filters out repositories that have been marked as either deleted or deprecated. - - - class CategoryColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository ): - rval = '<ul>' - if repository.categories: - for rca in repository.categories: - rval += '<li><a href="browse_repositories?operation=valid_repositories_by_category&id=%s">%s</a></li>' \ - % ( trans.security.encode_id( rca.category.id ), rca.category.name ) - else: - rval += '<li>not set</li>' - rval += '</ul>' - return rval - - - class RepositoryCategoryColumn( grids.GridColumn ): - - def filter( self, trans, user, query, column_filter ): - """Modify query to filter by category.""" - if column_filter == "All": - return query - return query.filter( model.Category.name == column_filter ) - - - class RevisionColumn( grids.GridColumn ): - - def __init__( self, col_name ): - grids.GridColumn.__init__( self, col_name ) - - def get_value( self, trans, grid, repository ): - """Display a SelectField whose options are the changeset_revision strings of all download-able revisions of this repository.""" - select_field = build_changeset_revision_select_field( trans, repository, downloadable=True ) - if len( select_field.options ) > 1: - return select_field.get_html() - elif len( select_field.options ) == 1: - return select_field.options[ 0 ][ 0 ] - return '' - - title = "Valid repositories" - columns = [ - RepositoryGrid.NameColumn( "Name", - key="name", - attach_popup=True ), - RepositoryGrid.DescriptionColumn( "Synopsis", - key="description", - attach_popup=False ), - RevisionColumn( "Installable Revisions" ), - RepositoryGrid.UserColumn( "Owner", - model_class=model.User, - attach_popup=False ), - # Columns that are valid for filtering but are not visible. - RepositoryCategoryColumn( "Category", - model_class=model.Category, - key="Category.name", - visible=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [] - - def build_initial_query( self, trans, **kwd ): - if 'id' in kwd: - # The user is browsing categories of valid repositories, so filter the request by the received id, which is a category id. - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.RepositoryMetadata.table ) \ - .join( model.User.table ) \ - .join( model.RepositoryCategoryAssociation.table ) \ - .join( model.Category.table ) \ - .filter( and_( model.Category.table.c.id == trans.security.decode_id( kwd[ 'id' ] ), - model.RepositoryMetadata.table.c.downloadable == True ) ) - # The user performed a free text search on the ValidCategoryGrid. - return trans.sa_session.query( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.RepositoryMetadata.table ) \ - .join( model.User.table ) \ - .outerjoin( model.RepositoryCategoryAssociation.table ) \ - .outerjoin( model.Category.table ) \ - .filter( model.RepositoryMetadata.table.c.downloadable == True ) - - -class MatchedRepositoryGrid( grids.Grid ): - # This grid filters out repositories that have been marked as deprecated. - - - class NameColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.name - - - class DescriptionColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.repository.description - - - class RevisionColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.changeset_revision - - - class UserColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.repository.user: - return repository_metadata.repository.user.username - return 'no user' - - # Grid definition - title = "Matching repositories" - model_class = model.RepositoryMetadata - template='/webapps/tool_shed/repository/grid.mako' - default_sort_key = "Repository.name" - columns = [ - NameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=True ), - DescriptionColumn( "Synopsis", - attach_popup=False ), - RevisionColumn( "Revision" ), - UserColumn( "Owner", - model_class=model.User, - attach_popup=False ) - ] - operations = [ - grids.GridOperation( "Install to Galaxy", allow_multiple=True ) - ] - standard_filters = [] - default_filter = {} - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - def build_initial_query( self, trans, **kwd ): - match_tuples = kwd.get( 'match_tuples', [] ) - clause_list = [] - if match_tuples: - for match_tuple in match_tuples: - repository_id, changeset_revision = match_tuple - clause_list.append( "%s=%d and %s='%s'" % ( model.RepositoryMetadata.table.c.repository_id, - int( repository_id ), - model.RepositoryMetadata.table.c.changeset_revision, - changeset_revision ) ) - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .filter( or_( *clause_list ) ) \ - .order_by( model.Repository.name ) - # Return an empty query - return trans.sa_session.query( model.RepositoryMetadata ) \ - .filter( model.RepositoryMetadata.id < 0 ) - - -class InstallMatchedRepositoryGrid( MatchedRepositoryGrid ): - columns = [ col for col in MatchedRepositoryGrid.columns ] - # Override the NameColumn - columns[ 0 ] = MatchedRepositoryGrid.NameColumn( "Name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ) - - -class RepositoryMetadataGrid( grids.Grid ): - - - class RepositoryNameColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - repository = repository_metadata.repository - return escape_html( repository.name ) - - - class RepositoryOwnerColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - repository = repository_metadata.repository - return escape_html( repository.user.username ) - - - class ChangesetRevisionColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.changeset_revision ) - - - class MaliciousColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.malicious: - return 'yes' - return '' - - - class DownloadableColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.downloadable: - return 'yes' - return '' - - - class ToolsFunctionallyCorrectColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.tools_functionally_correct: - return 'yes' - return '' - - - class DoNotTestColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.do_not_test: - return 'yes' - return '' - - - class TimeLastTestedColumn( grids.DateTimeColumn ): - def get_value( self, trans, grid, repository_metadata ): - return repository_metadata.time_last_tested - - - class HasRepositoryDependenciesColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.has_repository_dependencies: - return 'yes' - return '' - - - class IncludesDatatypesColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.includes_datatypes: - return 'yes' - return '' - - - class IncludesToolsColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.includes_tools: - return 'yes' - return '' - - - class IncludesToolDependenciesColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.includes_tool_dependencies: - return 'yes' - return '' - - - class IncludesWorkflowsColumn( grids.BooleanColumn ): - def get_value( self, trans, grid, repository_metadata ): - if repository_metadata.includes_workflows: - return 'yes' - return '' - - title = "Repository metadata" - model_class = model.RepositoryMetadata - template='/webapps/tool_shed/repository/grid.mako' - default_sort_key = "Repository.name" - columns = [ - RepositoryNameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ), - RepositoryOwnerColumn( "Owner", - model_class=model.User, - attach_popup=False, - key="User.username" ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - operations = [] - standard_filters = [] - default_filter = dict( malicious="False" ) - num_rows_per_page = 50 - preserve_state = False - use_paging = True - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - - -class RepositoryDependenciesGrid( RepositoryMetadataGrid ): - - - class RequiredRepositoryColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - rd_str = '' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - rd_dict = metadata.get( 'repository_dependencies', {} ) - if rd_dict: - rd_tups = rd_dict[ 'repository_dependencies' ] - # "repository_dependencies": [["http://localhost:9009", "bwa059", "test", "a07baa797d53"]] - # Sort rd_tups by by required repository name. - sorted_rd_tups = sorted( rd_tups, key=lambda rd_tup: rd_tup[ 1 ] ) - num_tups = len( sorted_rd_tups ) - for index, rd_tup in enumerate( sorted_rd_tups ): - name = rd_tup[ 1 ] - owner = rd_tup[ 2 ] - required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - if required_repository: - required_repository_id = trans.security.encode_id( required_repository.id ) - rd_str += '<a href="browse_repository_dependencies?operation=browse_repository&id=%s">' % required_repository_id - rd_str += '<b>name:</b> %s | <b>owner:</b> %s | <b>revision:</b> %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) ) - if required_repository: - rd_str += '</a>' - if index < num_tups - 1: - rd_str += '<br/>' - return rd_str - - title = "Repository dependency definitions in this tool shed" - columns = [ - RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), - attach_popup=False, - key="Repository.name" ), - RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", - model_class=model.User, - attach_popup=False, - key="User.username" ), - RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - RequiredRepositoryColumn( "Repository dependency", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.RepositoryMetadata.table.c.has_repository_dependencies == True, - model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - - -class ToolDependenciesGrid( RepositoryMetadataGrid ): - - - class ToolDependencyColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - td_str = '' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - tds_dict = metadata.get( 'tool_dependencies', {} ) - if tds_dict: - # Example: {"bwa/0.5.9": {"name": "bwa", "type": "package", "version": "0.5.9"}} - sorted_keys = sorted( [ k for k in tds_dict.keys() ] ) - num_keys = len( sorted_keys ) - # Handle environment settings first. - if 'set_environment' in sorted_keys: - # Example: "set_environment": [{"name": "JAVA_JAR_FILE", "type": "set_environment"}] - env_dicts = tds_dict[ 'set_environment' ] - num_env_dicts = len( env_dicts ) - td_str += '<b>environment:</b> ' - for index, env_dict in enumerate( env_dicts ): - td_str += '%s' % escape_html( env_dict[ 'name' ] ) - if index < num_env_dicts - 1: - td_str += ', ' - td_str += '<br/>' - for index, key in enumerate( sorted_keys ): - if key == 'set_environment': - continue - td_dict = tds_dict[ key ] - # Example: {"name": "bwa", "type": "package", "version": "0.5.9"} - name = td_dict[ 'name' ] - type = td_dict[ 'type' ] - version = td_dict[ 'version' ] - td_str += '<b>%s</b> version <b>%s</b>' % ( escape_html( name ), escape_html( version ) ) - if index < num_keys - 1: - td_str += '<br/>' - return td_str - - title = "Tool dependency definitions in this tool shed" - columns = [ - RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - model_class=model.Repository, - link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), - attach_popup=False, - key="Repository.name" ), - RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", - model_class=model.User, - attach_popup=False, - key="User.username" ), - RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - ToolDependencyColumn( "Tool dependency", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.RepositoryMetadata.table.c.includes_tool_dependencies == True, - model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - - -class ToolsGrid( RepositoryMetadataGrid ): - - - class ToolsColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - tool_str = '' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - tool_dicts = metadata.get( 'tools', [] ) - if tool_dicts: - num_tool_dicts = len( tool_dicts ) - for index, tool_dict in enumerate( tool_dicts ): - tool_id = tool_dict[ 'id' ] - name = tool_dict[ 'name' ] - version = tool_dict[ 'version' ] - tool_str += '<b>%s</b> | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) ) - if index < num_tool_dicts - 1: - tool_str += '<br/>' - return tool_str - - title = "Valid tools in this tool shed" - columns = [ - RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), - attach_popup=False, - key="Repository.name" ), - RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", - model_class=model.User, - attach_popup=False, - key="User.username" ), - RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - ToolsColumn( "Tool id | name | version", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.RepositoryMetadata.table.c.includes_tools == True, - model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - - -class DatatypesGrid( RepositoryMetadataGrid ): - - - class DatatypesColumn( grids.TextColumn ): - - def get_value( self, trans, grid, repository_metadata ): - datatype_str = '' - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - datatype_dicts = metadata.get( 'datatypes', [] ) - if datatype_dicts: - num_datatype_dicts = len( datatype_dicts ) - for index, datatype_dict in enumerate( datatype_dicts ): - # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} - extension = datatype_dict.get( 'extension', '' ) - dtype = datatype_dict.get( 'dtype', '' ) - mimetype = datatype_dict.get( 'mimetype', '' ) - display_in_upload = datatype_dict.get( 'display_in_upload', False ) - datatype_str += '<b>%s</b> | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) - if index < num_datatype_dicts - 1: - datatype_str += '<br/>' - return datatype_str - - title = "Custom datatypes in this tool shed" - columns = [ - RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - model_class=model.Repository, - link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), - attach_popup=False, - key="Repository.name" ), - RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", - model_class=model.User, - attach_popup=False, - key="User.username" ), - RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", - attach_popup=False ), - DatatypesColumn( "Datatype extension | Type | Mimetype", - attach_popup=False ) - ] - columns.append( grids.MulticolFilterColumn( "Search repository name, owner", - cols_to_filter=[ columns[0], columns[1] ], - key="free-text-search", - visible=False, - filterable="standard" ) ) - - def build_initial_query( self, trans, **kwd ): - return trans.sa_session.query( model.RepositoryMetadata ) \ - .join( model.Repository ) \ - .filter( and_( model.RepositoryMetadata.table.c.includes_datatypes == True, - model.Repository.table.c.deleted == False, - model.Repository.table.c.deprecated == False ) ) \ - .join( model.User.table ) \ - .order_by( model.Repository.name ) - class RepositoryController( BaseUIController, common_util.ItemRatings ): - category_grid = CategoryGrid() - datatypes_grid = DatatypesGrid() - deprecated_repositories_i_own_grid = DeprecatedRepositoriesIOwnGrid() - email_alerts_repository_grid = EmailAlertsRepositoryGrid() - install_matched_repository_grid = InstallMatchedRepositoryGrid() - matched_repository_grid = MatchedRepositoryGrid() - my_writable_repositories_grid = MyWritableRepositoriesGrid() - repositories_by_user_grid = RepositoriesByUserGrid() - repositories_i_own_grid = RepositoriesIOwnGrid() - repository_dependencies_grid = RepositoryDependenciesGrid() - repository_grid = RepositoryGrid() + category_grid = repository_grids.CategoryGrid() + datatypes_grid = repository_grids.DatatypesGrid() + deprecated_repositories_i_own_grid = repository_grids.DeprecatedRepositoriesIOwnGrid() + email_alerts_repository_grid = repository_grids.EmailAlertsRepositoryGrid() + install_matched_repository_grid = repository_grids.InstallMatchedRepositoryGrid() + matched_repository_grid = repository_grids.MatchedRepositoryGrid() + my_writable_repositories_grid = repository_grids.MyWritableRepositoriesGrid() + repositories_by_user_grid = repository_grids.RepositoriesByUserGrid() + repositories_i_own_grid = repository_grids.RepositoriesIOwnGrid() + repository_dependencies_grid = repository_grids.RepositoryDependenciesGrid() + repository_grid = repository_grids.RepositoryGrid() # The repository_metadata_grid is not currently displayed, but is sub-classed by several grids. - repository_metadata_grid = RepositoryMetadataGrid() - tool_dependencies_grid = ToolDependenciesGrid() - tools_grid = ToolsGrid() - valid_category_grid = ValidCategoryGrid() - valid_repository_grid = ValidRepositoryGrid() + repository_metadata_grid = repository_grids.RepositoryMetadataGrid() + tool_dependencies_grid = repository_grids.ToolDependenciesGrid() + tools_grid = repository_grids.ToolsGrid() + valid_category_grid = repository_grids.ValidCategoryGrid() + valid_repository_grid = repository_grids.ValidRepositoryGrid() @web.expose def browse_categories( self, trans, **kwd ): @@ -2579,11 +1601,11 @@ allow_push_select_field = self.__build_allow_push_select_field( trans, current_allow_push_list ) checked = alerts_checked or user.email in email_alerts alerts_check_box = CheckboxField( 'alerts', checked=checked ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False, - downloadable=False ) + changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False, + downloadable=False ) revision_label = suc.get_revision_label( trans, repository, repository.tip( trans.app ) ) repository_metadata = None repository_metadata_id = None @@ -2749,11 +1771,11 @@ metadata = None repository_dependencies = None revision_label = suc.get_revision_label( trans, repository, changeset_revision ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False, - downloadable=False ) + changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False, + downloadable=False ) containers_dict = suc.build_repository_containers_for_tool_shed( trans, repository, changeset_revision, repository_dependencies, repository_metadata ) return trans.fill_template( '/webapps/tool_shed/repository/preview_tools_in_changeset.mako', repository=repository, @@ -3378,11 +2400,11 @@ trans.sa_session.flush() checked = alerts_checked or ( user and user.email in email_alerts ) alerts_check_box = CheckboxField( 'alerts', checked=checked ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False, - downloadable=False ) + changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False, + downloadable=False ) revision_label = suc.get_revision_label( trans, repository, changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans, id, changeset_revision ) if repository_metadata: @@ -3500,11 +2522,11 @@ metadata = None #tool_test_errors = None is_malicious = suc.changeset_is_malicious( trans, repository_id, repository.tip( trans.app ) ) - changeset_revision_select_field = build_changeset_revision_select_field( trans, - repository, - selected_value=changeset_revision, - add_id_to_name=False, - downloadable=False ) + changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, + repository, + selected_value=changeset_revision, + add_id_to_name=False, + downloadable=False ) trans.app.config.tool_data_path = original_tool_data_path reviewed_by_user = suc.changeset_revision_reviewed_by_user( trans, trans.user, repository, changeset_revision ) if reviewed_by_user: @@ -3552,56 +2574,3 @@ metadata=metadata, message=message, status=status ) - -# ----- Utility methods ----- - -def build_changeset_revision_select_field( trans, repository, selected_value=None, add_id_to_name=True, - downloadable=False, reviewed=False, not_reviewed=False ): - """Build a SelectField whose options are the changeset_rev strings of certain revisions of the received repository.""" - options = [] - changeset_tups = [] - refresh_on_change_values = [] - if downloadable: - # Restrict the options to downloadable revisions. - repository_metadata_revisions = repository.downloadable_revisions - elif reviewed: - # Restrict the options to revisions that have been reviewed. - repository_metadata_revisions = [] - metadata_changeset_revision_hashes = [] - for metadata_revision in repository.metadata_revisions: - metadata_changeset_revision_hashes.append( metadata_revision.changeset_revision ) - for review in repository.reviews: - if review.changeset_revision in metadata_changeset_revision_hashes: - repository_metadata_revisions.append( review.repository_metadata ) - elif not_reviewed: - # Restrict the options to revisions that have not yet been reviewed. - repository_metadata_revisions = [] - reviewed_metadata_changeset_revision_hashes = [] - for review in repository.reviews: - reviewed_metadata_changeset_revision_hashes.append( review.changeset_revision ) - for metadata_revision in repository.metadata_revisions: - if metadata_revision.changeset_revision not in reviewed_metadata_changeset_revision_hashes: - repository_metadata_revisions.append( metadata_revision ) - else: - # Restrict the options to all revisions that have associated metadata. - repository_metadata_revisions = repository.metadata_revisions - for repository_metadata in repository_metadata_revisions: - rev, label, changeset_revision = suc.get_rev_label_changeset_revision_from_repository_metadata( trans, repository_metadata, repository=repository ) - changeset_tups.append( ( rev, label, changeset_revision ) ) - refresh_on_change_values.append( changeset_revision ) - # Sort options by the revision label. Even though the downloadable_revisions query sorts by update_time, - # the changeset revisions may not be sorted correctly because setting metadata over time will reset update_time. - for changeset_tup in sorted( changeset_tups ): - # Display the latest revision first. - options.insert( 0, ( changeset_tup[1], changeset_tup[2] ) ) - if add_id_to_name: - name = 'changeset_revision_%d' % repository.id - else: - name = 'changeset_revision' - select_field = SelectField( name=name, - refresh_on_change=True, - refresh_on_change_values=refresh_on_change_values ) - for option_tup in options: - selected = selected_value and option_tup[1] == selected_value - select_field.add_option( option_tup[0], option_tup[1], selected=selected ) - return select_field diff -r 7369eda82e2cf7e10338232569ed9185bc3b526b -r db8a3bd35841ce033aff283510a0f7fe3aec3ab0 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 @@ -8,7 +8,7 @@ from sqlalchemy.sql.expression import func from galaxy.webapps.tool_shed.util import common_util from galaxy.webapps.tool_shed.util.container_util import STRSEP -from repository import RepositoryGrid +from tool_shed.grids.repository_grids import RepositoryGrid import tool_shed.util.shed_util_common as suc from galaxy.util.odict import odict 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: jgoecks: Trackster: (a) handle corner case when feature starts at tile boundary and (b) remove poor tile index usage. Pack script.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/7369eda82e2c/ changeset: 7369eda82e2c user: jgoecks date: 2013-03-01 22:18:23 summary: Trackster: (a) handle corner case when feature starts at tile boundary and (b) remove poor tile index usage. Pack script. affected #: 2 files diff -r 5f20704ea90836a5fa54f63c78ceaa536010c4e8 -r 7369eda82e2cf7e10338232569ed9185bc3b526b static/scripts/packed/viz/trackster/painters.js --- a/static/scripts/packed/viz/trackster/painters.js +++ b/static/scripts/packed/viz/trackster/painters.js @@ -1,1 +1,1 @@ -define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var 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text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(0,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char,x_pos;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];x_pos=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=ref_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&ref_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;var tile_index=1;if(tile_index===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file +define(["libs/underscore"],function(_){var extend=_.extend;var BEFORE=1001,CONTAINS=1002,OVERLAP_START=1003,OVERLAP_END=1004,CONTAINED_BY=1005,AFTER=1006;var compute_overlap=function(first_region,second_region){var first_start=first_region[0],first_end=first_region[1],second_start=second_region[0],second_end=second_region[1],overlap;if(first_start<second_start){if(first_end<=second_start){overlap=BEFORE}else{if(first_end<=second_end){overlap=OVERLAP_START}else{overlap=CONTAINS}}}else{if(first_start>second_end){overlap=AFTER}else{if(first_end<=second_end){overlap=CONTAINED_BY}else{overlap=OVERLAP_END}}}return overlap};var is_overlap=function(first_region,second_region){var overlap=compute_overlap(first_region,second_region);return(overlap!==BEFORE&&overlap!==AFTER)};var dashedLine=function(ctx,x1,y1,x2,y2,dashLen){if(dashLen===undefined){dashLen=4}var dX=x2-x1;var dY=y2-y1;var dashes=Math.floor(Math.sqrt(dX*dX+dY*dY)/dashLen);var dashX=dX/dashes;var dashY=dY/dashes;var q;for(q=0;q<dashes;q++,x1+=dashX,y1+=dashY){if(q%2!==0){continue}ctx.fillRect(x1,y1,dashLen,1)}};var drawDownwardEquilateralTriangle=function(ctx,down_vertex_x,down_vertex_y,side_len){var x1=down_vertex_x-side_len/2,x2=down_vertex_x+side_len/2,y=down_vertex_y-Math.sqrt(side_len*3/2);ctx.beginPath();ctx.moveTo(x1,y);ctx.lineTo(x2,y);ctx.lineTo(down_vertex_x,down_vertex_y);ctx.lineTo(x1,y);ctx.strokeStyle=this.fillStyle;ctx.fill();ctx.stroke();ctx.closePath()};var Scaler=function(default_val){this.default_val=(default_val?default_val:1)};Scaler.prototype.gen_val=function(input){return this.default_val};var Painter=function(data,view_start,view_end,prefs,mode){this.data=data;this.view_start=view_start;this.view_end=view_end;this.prefs=extend({},this.default_prefs,prefs);this.mode=mode};Painter.prototype.default_prefs={};Painter.prototype.draw=function(ctx,width,height,w_scale){};var SummaryTreePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode)};SummaryTreePainter.prototype.default_prefs={show_counts:false};SummaryTreePainter.prototype.draw=function(ctx,width,height,w_scale){var view_start=this.view_start,points=this.data.data,max=(this.prefs.histogram_max?this.prefs.histogram_max:this.data.max),base_y=height;delta_x_px=Math.ceil(this.data.delta*w_scale);ctx.save();for(var i=0,len=points.length;i<len;i++){var x=Math.floor((points[i][0]-view_start)*w_scale);var y=points[i][1];if(!y){continue}var y_px=y/max*height;if(y!==0&&y_px<1){y_px=1}ctx.fillStyle=this.prefs.block_color;ctx.fillRect(x,base_y-y_px,delta_x_px,y_px);var text_padding_req_x=4;if(this.prefs.show_counts&&(ctx.measureText(y).width+text_padding_req_x)<delta_x_px){ctx.fillStyle=this.prefs.label_color;ctx.textAlign="center";ctx.fillText(y,x+(delta_x_px/2),10)}}ctx.restore()};var LinePainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][1])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][1])}this.prefs.max_value=max_value}};LinePainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Histogram",color:"#000",overflow_color:"#F66"};LinePainter.prototype.draw=function(ctx,width,height,w_scale){var in_path=false,min_value=this.prefs.min_value,max_value=this.prefs.max_value,vertical_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data;ctx.save();var y_zero=Math.round(height+min_value/vertical_range*height);if(mode!=="Intensity"){ctx.fillStyle="#aaa";ctx.fillRect(0,y_zero,width,1)}ctx.beginPath();var x_scaled,y,delta_x_px;if(data.length>1){delta_x_px=Math.ceil((data[1][0]-data[0][0])*w_scale)}else{delta_x_px=10}var pref_color=parseInt(this.prefs.color.slice(1),16),pref_r=(pref_color&16711680)>>16,pref_g=(pref_color&65280)>>8,pref_b=pref_color&255;for(var i=0,len=data.length;i<len;i++){ctx.fillStyle=ctx.strokeStyle=this.prefs.color;x_scaled=Math.round((data[i][0]-view_start-0.5)*w_scale);y=data[i][1];var top_overflow=false,bot_overflow=false;if(y===null){if(in_path&&mode==="Filled"){ctx.lineTo(x_scaled,height_px)}in_path=false;continue}if(y<min_value){bot_overflow=true;y=min_value}else{if(y>max_value){top_overflow=true;y=max_value}}if(mode==="Histogram"){y=Math.round(y/vertical_range*height_px);ctx.fillRect(x_scaled,y_zero,delta_x_px,-y)}else{if(mode==="Intensity"){var saturation=(y-min_value)/vertical_range,new_r=Math.round(pref_r+(255-pref_r)*(1-saturation)),new_g=Math.round(pref_g+(255-pref_g)*(1-saturation)),new_b=Math.round(pref_b+(255-pref_b)*(1-saturation));ctx.fillStyle="rgb("+new_r+","+new_g+","+new_b+")";ctx.fillRect(x_scaled,0,delta_x_px,height_px)}else{y=Math.round(height_px-(y-min_value)/vertical_range*height_px);if(in_path){ctx.lineTo(x_scaled,y)}else{in_path=true;if(mode==="Filled"){ctx.moveTo(x_scaled,height_px);ctx.lineTo(x_scaled,y)}else{ctx.moveTo(x_scaled,y)}}}}ctx.fillStyle=this.prefs.overflow_color;if(top_overflow||bot_overflow){var overflow_x;if(mode==="Histogram"||mode==="Intensity"){overflow_x=delta_x_px}else{x_scaled-=2;overflow_x=4}if(top_overflow){ctx.fillRect(x_scaled,0,overflow_x,3)}if(bot_overflow){ctx.fillRect(x_scaled,height_px-3,overflow_x,3)}}ctx.fillStyle=this.prefs.color}if(mode==="Filled"){if(in_path){ctx.lineTo(x_scaled,y_zero);ctx.lineTo(0,y_zero)}ctx.fill()}else{ctx.stroke()}ctx.restore()};var FeaturePositionMapper=function(slot_height){this.feature_positions={};this.slot_height=slot_height;this.translation=0;this.y_translation=0};FeaturePositionMapper.prototype.map_feature_data=function(feature_data,slot,x_start,x_end){if(!this.feature_positions[slot]){this.feature_positions[slot]=[]}this.feature_positions[slot].push({data:feature_data,x_start:x_start,x_end:x_end})};FeaturePositionMapper.prototype.get_feature_data=function(x,y){var slot=Math.floor((y-this.y_translation)/this.slot_height),feature_dict;if(!this.feature_positions[slot]){return null}x+=this.translation;for(var i=0;i<this.feature_positions[slot].length;i++){feature_dict=this.feature_positions[slot][i];if(x>=feature_dict.x_start&&x<=feature_dict.x_end){return feature_dict.data}}};var FeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){Painter.call(this,data,view_start,view_end,prefs,mode);this.alpha_scaler=(alpha_scaler?alpha_scaler:new Scaler());this.height_scaler=(height_scaler?height_scaler:new Scaler())};FeaturePainter.prototype.default_prefs={block_color:"#FFF",connector_color:"#FFF"};extend(FeaturePainter.prototype,{get_required_height:function(rows_required,width){var required_height=this.get_row_height(),y_scale=required_height,mode=this.mode;if(mode==="no_detail"||mode==="Squish"||mode==="Pack"){required_height=rows_required*y_scale}return required_height+this.get_top_padding(width)+this.get_bottom_padding(width)},get_top_padding:function(width){return 0},get_bottom_padding:function(width){return Math.max(Math.round(this.get_row_height()/2),5)},draw:function(ctx,width,height,w_scale,slots){var data=this.data,view_start=this.view_start,view_end=this.view_end;ctx.save();ctx.fillStyle=this.prefs.block_color;ctx.textAlign="right";var y_scale=this.get_row_height(),feature_mapper=new FeaturePositionMapper(y_scale),x_draw_coords;for(var i=0,len=data.length;i<len;i++){var feature=data[i],feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],slot=(slots&&slots[feature_uid]!==undefined?slots[feature_uid]:null);if((feature_start<view_end&&feature_end>view_start)&&(this.mode==="Dense"||slot!==null)){x_draw_coords=this.draw_element(ctx,this.mode,feature,slot,view_start,view_end,w_scale,y_scale,width);feature_mapper.map_feature_data(feature,slot,x_draw_coords[0],x_draw_coords[1])}}ctx.restore();feature_mapper.y_translation=this.get_top_padding(width);return feature_mapper},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){console.log("WARNING: Unimplemented function.");return[0,0]}});var DENSE_TRACK_HEIGHT=10,NO_DETAIL_TRACK_HEIGHT=3,SQUISH_TRACK_HEIGHT=5,PACK_TRACK_HEIGHT=10,NO_DETAIL_FEATURE_HEIGHT=1,DENSE_FEATURE_HEIGHT=9,SQUISH_FEATURE_HEIGHT=3,PACK_FEATURE_HEIGHT=9,LABEL_SPACING=2,CONNECTOR_COLOR="#ccc";var LinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.draw_background_connector=true;this.draw_individual_connectors=false};extend(LinkedFeaturePainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var mode=this.mode,height;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="no_detail"){height=NO_DETAIL_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT}}}return height},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],feature_strand=feature[4],f_start=Math.floor(Math.max(0,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),draw_start=f_start,draw_end=f_end,y_center=(mode==="Dense"?0:(0+slot))*y_scale+this.get_top_padding(width),thickness,y_start,thick_start=null,thick_end=null,block_color=(!feature_strand||feature_strand==="+"||feature_strand==="."?this.prefs.block_color:this.prefs.reverse_strand_color);label_color=this.prefs.label_color;ctx.globalAlpha=this.alpha_scaler.gen_val(feature);if(mode==="Dense"){slot=1}if(mode==="no_detail"){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+5,f_end-f_start,NO_DETAIL_FEATURE_HEIGHT)}else{var feature_ts=feature[5],feature_te=feature[6],feature_blocks=feature[7],full_height=true;if(feature_ts&&feature_te){thick_start=Math.floor(Math.max(0,(feature_ts-tile_low)*w_scale));thick_end=Math.ceil(Math.min(width,Math.max(0,(feature_te-tile_low)*w_scale)))}var thin_height,thick_height;if(mode==="Squish"){thin_height=1;thick_height=SQUISH_FEATURE_HEIGHT;full_height=false}else{if(mode==="Dense"){thin_height=5;thick_height=DENSE_FEATURE_HEIGHT}else{thin_height=5;thick_height=PACK_FEATURE_HEIGHT}}if(!feature_blocks){ctx.fillStyle=block_color;ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height);if(feature_strand&&full_height){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}ctx.fillRect(f_start,y_center+1,f_end-f_start,thick_height)}}else{var cur_y_center,cur_height;if(mode==="Squish"||mode==="Dense"){cur_y_center=y_center+Math.floor(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}else{if(feature_strand){cur_y_center=y_center;cur_height=thick_height}else{cur_y_center+=(SQUISH_FEATURE_HEIGHT/2)+1;cur_height=1}}if(this.draw_background_connector){if(mode==="Squish"||mode==="Dense"){ctx.fillStyle=CONNECTOR_COLOR}else{if(feature_strand){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand")}}}else{ctx.fillStyle=CONNECTOR_COLOR}}ctx.fillRect(f_start,cur_y_center,f_end-f_start,cur_height)}var start_and_height;for(var k=0,k_len=feature_blocks.length;k<k_len;k++){var block=feature_blocks[k],block_start=Math.floor(Math.max(0,(block[0]-tile_low-0.5)*w_scale)),block_end=Math.ceil(Math.min(width,Math.max((block[1]-tile_low-0.5)*w_scale))),last_block_start,last_block_end;if(block_start>block_end){continue}ctx.fillStyle=block_color;ctx.fillRect(block_start,y_center+(thick_height-thin_height)/2+1,block_end-block_start,thin_height);if(thick_start!==undefined&&feature_te>feature_ts&&!(block_start>thick_end||block_end<thick_start)){var block_thick_start=Math.max(block_start,thick_start),block_thick_end=Math.min(block_end,thick_end);ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height);if(feature_blocks.length===1&&mode==="Pack"){if(feature_strand==="+"){ctx.fillStyle=ctx.canvas.manager.get_pattern("right_strand_inv")}else{if(feature_strand==="-"){ctx.fillStyle=ctx.canvas.manager.get_pattern("left_strand_inv")}}if(block_thick_start+14<block_thick_end){block_thick_start+=2;block_thick_end-=2}ctx.fillRect(block_thick_start,y_center+1,block_thick_end-block_thick_start,thick_height)}}if(this.draw_individual_connectors&&last_block_start){this.draw_connector(ctx,last_block_start,last_block_end,block_start,block_end,y_center)}last_block_start=block_start;last_block_end=block_end}if(mode==="Pack"){ctx.globalAlpha=1;ctx.fillStyle="white";var hscale_factor=this.height_scaler.gen_val(feature),new_height=Math.ceil(thick_height*hscale_factor),ws_height=Math.round((thick_height-new_height)/2);if(hscale_factor!==1){ctx.fillRect(f_start,cur_y_center+1,f_end-f_start,ws_height);ctx.fillRect(f_start,cur_y_center+thick_height-ws_height+1,f_end-f_start,ws_height)}}}ctx.globalAlpha=1;if(feature_name&&mode==="Pack"&&feature_start>tile_low){ctx.fillStyle=label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8);draw_end+=ctx.measureText(feature_name).width+LABEL_SPACING}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8);draw_start-=ctx.measureText(feature_name).width+LABEL_SPACING}}}ctx.globalAlpha=1;return[draw_start,draw_end]}});var ReadPainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler,ref_seq,base_color_fn){FeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.ref_seq=(ref_seq?ref_seq.data:null);this.base_color_fn=base_color_fn};extend(ReadPainter.prototype,FeaturePainter.prototype,{get_row_height:function(){var height,mode=this.mode;if(mode==="Dense"){height=DENSE_TRACK_HEIGHT}else{if(mode==="Squish"){height=SQUISH_TRACK_HEIGHT}else{height=PACK_TRACK_HEIGHT;if(this.prefs.show_insertions){height*=2}}}return height},draw_read:function(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,cigar,strand,read_seq){ctx.textAlign="center";var tile_region=[tile_low,tile_high],base_offset=0,seq_offset=0,gap=Math.round(w_scale/2),char_width_px=ctx.canvas.manager.char_width_px,block_color=(strand==="+"?this.prefs.block_color:this.prefs.reverse_strand_color),pack_mode=(mode==="Pack");var draw_last=[];if(!cigar){cigar=[[0,read_seq.length]]}for(var cig_id=0,len=cigar.length;cig_id<len;cig_id++){var cig=cigar[cig_id],cig_op="MIDNSHP=X"[cig[0]],cig_len=cig[1];if(cig_op==="H"||cig_op==="S"){base_offset-=cig_len}var seq_start=feature_start+base_offset,s_start=Math.floor(Math.max(-0.5*w_scale,(seq_start-tile_low-0.5)*w_scale)),s_end=Math.floor(Math.max(0,(seq_start+cig_len-tile_low-0.5)*w_scale));if(s_start===s_end){s_end+=1}switch(cig_op){case"H":break;case"S":case"M":case"=":if(is_overlap([seq_start,seq_start+cig_len],tile_region)){ctx.fillStyle=block_color;ctx.fillRect(s_start,y_center+(pack_mode?1:4),s_end-s_start,(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT));var seq=read_seq.slice(seq_offset,seq_offset+cig_len),ref_char,read_char,x_pos;for(var c=0,str_len=seq.length;c<str_len;c++){if(seq_start+c>=tile_low&&seq_start+c<=tile_high){ref_char=(this.ref_seq?this.ref_seq[seq_start-tile_low+c]:null);read_char=seq[c];x_pos=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));if((ref_char&&(!this.prefs.show_differences||(read_char.toLowerCase!=="n"&&(ref_char.toLowerCase()!==read_char.toLowerCase()))))||(!ref_char&&!this.prefs.show_differences)){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillStyle=this.base_color_fn(seq[c]);if(pack_mode&&w_scale>char_width_px){ctx.fillText(seq[c],c_start,y_center+9)}else{if(w_scale>0.05){ctx.fillRect(c_start,y_center+(pack_mode?1:4),Math.max(1,Math.round(w_scale)),(pack_mode?PACK_FEATURE_HEIGHT:SQUISH_FEATURE_HEIGHT))}}}}}}seq_offset+=cig_len;base_offset+=cig_len;break;case"N":ctx.fillStyle=CONNECTOR_COLOR;ctx.fillRect(s_start,y_center+5,s_end-s_start,1);base_offset+=cig_len;break;case"D":ctx.fillStyle="red";ctx.fillRect(s_start,y_center+4,s_end-s_start,3);base_offset+=cig_len;break;case"P":break;case"I":var insert_x_coord=s_start-gap;if(is_overlap([seq_start,seq_start+cig_len],tile_region)){var seq=read_seq.slice(seq_offset,seq_offset+cig_len);if(this.prefs.show_insertions){var x_center=s_start-(s_end-s_start)/2;if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){ctx.fillStyle="yellow";ctx.fillRect(x_center-gap,y_center-9,s_end-s_start,9);draw_last[draw_last.length]={type:"triangle",data:[insert_x_coord,y_center+4,5]};ctx.fillStyle=CONNECTOR_COLOR;switch(compute_overlap([seq_start,seq_start+cig_len],tile_region)){case (OVERLAP_START):seq=seq.slice(tile_low-seq_start);break;case (OVERLAP_END):seq=seq.slice(0,seq_start-tile_high);break;case (CONTAINED_BY):break;case (CONTAINS):seq=seq.slice(tile_low-seq_start,seq_start-tile_high);break}for(var c=0,str_len=seq.length;c<str_len;c++){var c_start=Math.floor(Math.max(0,(seq_start+c-tile_low)*w_scale));ctx.fillText(seq[c],c_start-(s_end-s_start)/2,y_center)}}else{ctx.fillStyle="yellow";ctx.fillRect(x_center,y_center+(this.mode!=="Dense"?2:5),s_end-s_start,(mode!=="Dense"?SQUISH_FEATURE_HEIGHT:DENSE_FEATURE_HEIGHT))}}else{if((mode==="Pack"||this.mode==="Auto")&&read_seq!==undefined&&w_scale>char_width_px){draw_last.push({type:"text",data:[seq.length,insert_x_coord,y_center+9]})}else{}}}seq_offset+=cig_len;break;case"X":seq_offset+=cig_len;break}}ctx.fillStyle="yellow";var item,type,data;for(var i=0;i<draw_last.length;i++){item=draw_last[i];type=item.type;data=item.data;if(type==="text"){ctx.save();ctx.font="bold "+ctx.font;ctx.fillText(data[0],data[1],data[2]);ctx.restore()}else{if(type==="triangle"){drawDownwardEquilateralTriangle(ctx,data[0],data[1],data[2])}}}},draw_element:function(ctx,mode,feature,slot,tile_low,tile_high,w_scale,y_scale,width){var feature_uid=feature[0],feature_start=feature[1],feature_end=feature[2],feature_name=feature[3],f_start=Math.floor(Math.max(-0.5*w_scale,(feature_start-tile_low-0.5)*w_scale)),f_end=Math.ceil(Math.min(width,Math.max(0,(feature_end-tile_low-0.5)*w_scale))),y_center=(mode==="Dense"?0:(0+slot))*y_scale,label_color=this.prefs.label_color;if(feature[5] instanceof Array){var b1_start=Math.floor(Math.max(0,(feature[4][0]-tile_low)*w_scale)),b1_end=Math.ceil(Math.min(width,Math.max(0,(feature[4][1]-tile_low)*w_scale))),b2_start=Math.floor(Math.max(0,(feature[5][0]-tile_low)*w_scale)),b2_end=Math.ceil(Math.min(width,Math.max(0,(feature[5][1]-tile_low)*w_scale))),connector=true;if(feature[4][1]>=tile_low&&feature[4][0]<=tile_high&&feature[4][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[4][0],feature[4][2],feature[4][3],feature[4][4])}else{connector=false}if(feature[5][1]>=tile_low&&feature[5][0]<=tile_high&&feature[5][2]){this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature[5][0],feature[5][2],feature[5][3],feature[5][4])}else{connector=false}if(connector&&b2_start>b1_end){ctx.fillStyle=CONNECTOR_COLOR;dashedLine(ctx,b1_end,y_center+5,b2_start,y_center+5)}}else{this.draw_read(ctx,mode,w_scale,y_center,tile_low,tile_high,feature_start,feature[4],feature[5],feature[6])}if(mode==="Pack"&&feature_start>=tile_low&&feature_name!=="."){ctx.fillStyle=this.prefs.label_color;if(tile_low===0&&f_start-ctx.measureText(feature_name).width<0){ctx.textAlign="left";ctx.fillText(feature_name,f_end+LABEL_SPACING,y_center+8)}else{ctx.textAlign="right";ctx.fillText(feature_name,f_start-LABEL_SPACING,y_center+8)}}return[0,0]}});var ArcLinkedFeaturePainter=function(data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler){LinkedFeaturePainter.call(this,data,view_start,view_end,prefs,mode,alpha_scaler,height_scaler);this.longest_feature_length=this.calculate_longest_feature_length();this.draw_background_connector=false;this.draw_individual_connectors=true};extend(ArcLinkedFeaturePainter.prototype,FeaturePainter.prototype,LinkedFeaturePainter.prototype,{calculate_longest_feature_length:function(){var longest_feature_length=0;for(var i=0,len=this.data.length;i<len;i++){var feature=this.data[i],feature_start=feature[1],feature_end=feature[2];longest_feature_length=Math.max(longest_feature_length,feature_end-feature_start)}return longest_feature_length},get_top_padding:function(width){var view_range=this.view_end-this.view_start,w_scale=width/view_range;return Math.min(128,Math.ceil((this.longest_feature_length/2)*w_scale))},draw_connector:function(ctx,block1_start,block1_end,block2_start,block2_end,y_center){var x_center=(block1_end+block2_start)/2,radius=block2_start-x_center;var angle1=Math.PI,angle2=0;if(radius>0){ctx.beginPath();ctx.arc(x_center,y_center,block2_start-x_center,Math.PI,0);ctx.stroke()}}});var Color=function(rgb,a){if(Array.isArray(rgb)){this.rgb=rgb}else{if(rgb.length==6){this.rgb=rgb.match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{if(rgb.length==7){this.rgb=rgb.substring(1,7).match(/.{2}/g).map(function(c){return parseInt(c,16)})}else{this.rgb=rgb.split("").map(function(c){return parseInt(c+c,16)})}}}this.alpha=typeof(a)==="number"?a:1};Color.prototype={eval:function(){return this},toCSS:function(){if(this.alpha<1){return"rgba("+this.rgb.map(function(c){return Math.round(c)}).concat(this.alpha).join(", ")+")"}else{return"#"+this.rgb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")}},toHSL:function(){var r=this.rgb[0]/255,g=this.rgb[1]/255,b=this.rgb[2]/255,a=this.alpha;var max=Math.max(r,g,b),min=Math.min(r,g,b);var h,s,l=(max+min)/2,d=max-min;if(max===min){h=s=0}else{s=l>0.5?d/(2-max-min):d/(max+min);switch(max){case r:h=(g-b)/d+(g<b?6:0);break;case g:h=(b-r)/d+2;break;case b:h=(r-g)/d+4;break}h/=6}return{h:h*360,s:s,l:l,a:a}},toARGB:function(){var argb=[Math.round(this.alpha*255)].concat(this.rgb);return"#"+argb.map(function(i){i=Math.round(i);i=(i>255?255:(i<0?0:i)).toString(16);return i.length===1?"0"+i:i}).join("")},mix:function(color2,weight){color1=this;var p=weight;var w=p*2-1;var a=color1.toHSL().a-color2.toHSL().a;var w1=(((w*a==-1)?w:(w+a)/(1+w*a))+1)/2;var w2=1-w1;var rgb=[color1.rgb[0]*w1+color2.rgb[0]*w2,color1.rgb[1]*w1+color2.rgb[1]*w2,color1.rgb[2]*w1+color2.rgb[2]*w2];var alpha=color1.alpha*p+color2.alpha*(1-p);return new Color(rgb,alpha)}};var LinearRamp=function(start_color,end_color,start_value,end_value){this.start_color=new Color(start_color);this.end_color=new Color(end_color);this.start_value=start_value;this.end_value=end_value;this.value_range=end_value-start_value};LinearRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);value=(value-this.start_value)/this.value_range;return this.start_color.mix(this.end_color,1-value).toCSS()};var SplitRamp=function(start_color,middle_color,end_color,start_value,end_value){this.positive_ramp=new LinearRamp(middle_color,end_color,0,end_value);this.negative_ramp=new LinearRamp(middle_color,start_color,0,-start_value);this.start_value=start_value;this.end_value=end_value};SplitRamp.prototype.map_value=function(value){value=Math.max(value,this.start_value);value=Math.min(value,this.end_value);if(value>=0){return this.positive_ramp.map_value(value)}else{return this.negative_ramp.map_value(-value)}};var DiagonalHeatmapPainter=function(data,view_start,view_end,prefs,mode){Painter.call(this,data,view_start,view_end,prefs,mode);var i,len;if(this.prefs.min_value===undefined){var min_value=Infinity;for(i=0,len=this.data.length;i<len;i++){min_value=Math.min(min_value,this.data[i][5])}this.prefs.min_value=min_value}if(this.prefs.max_value===undefined){var max_value=-Infinity;for(i=0,len=this.data.length;i<len;i++){max_value=Math.max(max_value,this.data[i][5])}this.prefs.max_value=max_value}};DiagonalHeatmapPainter.prototype.default_prefs={min_value:undefined,max_value:undefined,mode:"Heatmap",pos_color:"#FF8C00",neg_color:"#4169E1"};DiagonalHeatmapPainter.prototype.draw=function(ctx,width,height,w_scale){var min_value=this.prefs.min_value,max_value=this.prefs.max_value,value_range=max_value-min_value,height_px=height,view_start=this.view_start,mode=this.mode,data=this.data,invsqrt2=1/Math.sqrt(2);var ramp=(new SplitRamp(this.prefs.neg_color,"#FFFFFF",this.prefs.pos_color,min_value,max_value));var d,s1,e1,s2,e2,value;var scale=function(p){return(p-view_start)*w_scale};ctx.save();ctx.rotate(-45*Math.PI/180);ctx.scale(invsqrt2,invsqrt2);for(var i=0,len=data.length;i<len;i++){d=data[i];s1=scale(d[1]);e1=scale(d[2]);s2=scale(d[4]);e2=scale(d[5]);value=d[6];ctx.fillStyle=(ramp.map_value(value));ctx.fillRect(s1,s2,(e1-s1),(e2-s2))}ctx.restore()};return{Scaler:Scaler,SummaryTreePainter:SummaryTreePainter,LinePainter:LinePainter,LinkedFeaturePainter:LinkedFeaturePainter,ReadPainter:ReadPainter,ArcLinkedFeaturePainter:ArcLinkedFeaturePainter,DiagonalHeatmapPainter:DiagonalHeatmapPainter}}); \ No newline at end of file diff -r 5f20704ea90836a5fa54f63c78ceaa536010c4e8 -r 7369eda82e2cf7e10338232569ed9185bc3b526b static/scripts/viz/trackster/painters.js --- a/static/scripts/viz/trackster/painters.js +++ b/static/scripts/viz/trackster/painters.js @@ -6,6 +6,7 @@ * Compute the type of overlap between two regions. They are assumed to be on the same chrom/contig. * The overlap is computed relative to the second region; hence, OVERLAP_START indicates that the first * region overlaps the start (but not the end) of the second region. + * NOTE: Coordinates are assumed to be in BED format: half open (start is closed, end is open). */ var BEFORE = 1001, CONTAINS = 1002, OVERLAP_START = 1003, OVERLAP_END = 1004, CONTAINED_BY = 1005, AFTER = 1006; var compute_overlap = function(first_region, second_region) { @@ -14,7 +15,7 @@ second_start = second_region[0], second_end = second_region[1], overlap; if (first_start < second_start) { - if (first_end < second_start) { + if (first_end <= second_start) { overlap = BEFORE; } else if (first_end <= second_end) { @@ -763,7 +764,7 @@ } var seq_start = feature_start + base_offset, // -0.5 to offset sequence between bases. - s_start = Math.floor( Math.max(0, (seq_start - tile_low - 0.5) * w_scale) ), + s_start = Math.floor( Math.max(-0.5 * w_scale, (seq_start - tile_low - 0.5) * w_scale) ), s_end = Math.floor( Math.max(0, (seq_start + cig_len - tile_low - 0.5) * w_scale) ); // Make sure that read is drawn even if it too small to be rendered officially; in this case, @@ -858,7 +859,7 @@ var insert_x_coord = s_start - gap; if (is_overlap([seq_start, seq_start + cig_len], tile_region)) { - var seq = ref_seq.slice(seq_offset, seq_offset + cig_len); + var seq = read_seq.slice(seq_offset, seq_offset + cig_len); // Insertion point is between the sequence start and the previous base: (-gap) moves // back from sequence start to insertion point. if (this.prefs.show_insertions) { @@ -869,7 +870,7 @@ // Draw sequence. // X center is offset + start - <half_sequence_length> var x_center = s_start - (s_end - s_start)/2; - if ( (mode === "Pack" || this.mode === "Auto") && ref_seq !== undefined && w_scale > char_width_px) { + if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { // Draw sequence container. ctx.fillStyle = "yellow"; ctx.fillRect(x_center - gap, y_center - 9, s_end - s_start, 9); @@ -905,7 +906,7 @@ } } else { - if ( (mode === "Pack" || this.mode === "Auto") && ref_seq !== undefined && w_scale > char_width_px) { + if ( (mode === "Pack" || this.mode === "Auto") && read_seq !== undefined && w_scale > char_width_px) { // Show insertions with a single number at the insertion point. draw_last.push( { type: "text", data: [seq.length, insert_x_coord, y_center + 9] } ); } @@ -955,7 +956,7 @@ feature_end = feature[2], feature_name = feature[3], // -0.5 to put element between bases. - f_start = Math.floor( Math.max(0, (feature_start - tile_low - 0.5) * w_scale) ), + f_start = Math.floor( Math.max(-0.5 * w_scale, (feature_start - tile_low - 0.5) * w_scale) ), f_end = Math.ceil( Math.min(width, Math.max(0, (feature_end - tile_low - 0.5) * w_scale)) ), y_center = (mode === "Dense" ? 0 : (0 + slot)) * y_scale, label_color = this.prefs.label_color; @@ -997,12 +998,10 @@ // Read is single. this.draw_read(ctx, mode, w_scale, y_center, tile_low, tile_high, feature_start, feature[4], feature[5], feature[6]); } - if (mode === "Pack" && feature_start > tile_low && feature_name !== ".") { + if (mode === "Pack" && feature_start >= tile_low && feature_name !== ".") { // Draw label. ctx.fillStyle = this.prefs.label_color; - // FIXME: eliminate tile_index - var tile_index = 1; - if (tile_index === 0 && f_start - ctx.measureText(feature_name).width < 0) { + if (tile_low === 0 && f_start - ctx.measureText(feature_name).width < 0) { ctx.textAlign = "left"; ctx.fillText(feature_name, f_end + LABEL_SPACING, y_center + 8); } else { 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: greg: Be conservative when displaying custom datatypes in the tool shed.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/5f20704ea908/ changeset: 5f20704ea908 user: greg date: 2013-03-01 22:13:29 summary: Be conservative when displaying custom datatypes in the tool shed. affected #: 1 file diff -r c7c8316a1d134a19e929a2257a701ec1ebc3a33a -r 5f20704ea90836a5fa54f63c78ceaa536010c4e8 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 @@ -967,9 +967,9 @@ num_datatype_dicts = len( datatype_dicts ) for index, datatype_dict in enumerate( datatype_dicts ): # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} - extension = datatype_dict[ 'extension' ] - dtype = datatype_dict[ 'dtype' ] - mimetype = datatype_dict[ 'mimetype' ] + extension = datatype_dict.get( 'extension', '' ) + dtype = datatype_dict.get( 'dtype', '' ) + mimetype = datatype_dict.get( 'mimetype', '' ) display_in_upload = datatype_dict.get( 'display_in_upload', False ) datatype_str += '<b>%s</b> | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) if index < num_datatype_dicts - 1: 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: greg: Implement more granular grids for valid Galaxy utilities in the tool shed - custom datatypes, tools, tool dependencies and repository dependencies are now accessible.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c7c8316a1d13/ changeset: c7c8316a1d13 user: greg date: 2013-03-01 22:08:25 summary: Implement more granular grids for valid Galaxy utilities in the tool shed - custom datatypes, tools, tool dependencies and repository dependencies are now accessible. affected #: 2 files diff -r 513adadb31a2a4b014b3f03c5af2817919ea1760 -r c7c8316a1d134a19e929a2257a701ec1ebc3a33a 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 @@ -646,13 +646,15 @@ class RepositoryNameColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.repository.name ) + repository = repository_metadata.repository + return escape_html( repository.name ) class RepositoryOwnerColumn( grids.TextColumn ): def get_value( self, trans, grid, repository_metadata ): - return escape_html( repository_metadata.user.username ) + repository = repository_metadata.repository + return escape_html( repository.user.username ) class ChangesetRevisionColumn( grids.TextColumn ): @@ -763,18 +765,53 @@ class RepositoryDependenciesGrid( RepositoryMetadataGrid ): - - title = "Repository dependencies available in this Tool Shed" + + + class RequiredRepositoryColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + rd_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + rd_dict = metadata.get( 'repository_dependencies', {} ) + if rd_dict: + rd_tups = rd_dict[ 'repository_dependencies' ] + # "repository_dependencies": [["http://localhost:9009", "bwa059", "test", "a07baa797d53"]] + # Sort rd_tups by by required repository name. + sorted_rd_tups = sorted( rd_tups, key=lambda rd_tup: rd_tup[ 1 ] ) + num_tups = len( sorted_rd_tups ) + for index, rd_tup in enumerate( sorted_rd_tups ): + name = rd_tup[ 1 ] + owner = rd_tup[ 2 ] + required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) + if required_repository: + required_repository_id = trans.security.encode_id( required_repository.id ) + rd_str += '<a href="browse_repository_dependencies?operation=browse_repository&id=%s">' % required_repository_id + rd_str += '<b>name:</b> %s | <b>owner:</b> %s | <b>revision:</b> %s' % ( escape_html( rd_tup[ 1 ] ), escape_html( rd_tup[ 2 ] ), escape_html( rd_tup[ 3 ] ) ) + if required_repository: + rd_str += '</a>' + if index < num_tups - 1: + rd_str += '<br/>' + return rd_str + + title = "Repository dependency definitions in this tool shed" columns = [ RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", - link=( lambda item: dict( operation="view_or_manage_repository", id=item.id ) ), - attach_popup=False ), + model_class=model.Repository, + link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", model_class=model.User, attach_popup=False, - key="User.username" ) + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + RequiredRepositoryColumn( "Repository dependency", + attach_popup=False ) ] - columns.append( grids.MulticolFilterColumn( "Search repository name, description", + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", cols_to_filter=[ columns[0], columns[1] ], key="free-text-search", visible=False, @@ -790,9 +827,190 @@ .order_by( model.Repository.name ) +class ToolDependenciesGrid( RepositoryMetadataGrid ): + + + class ToolDependencyColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + td_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + tds_dict = metadata.get( 'tool_dependencies', {} ) + if tds_dict: + # Example: {"bwa/0.5.9": {"name": "bwa", "type": "package", "version": "0.5.9"}} + sorted_keys = sorted( [ k for k in tds_dict.keys() ] ) + num_keys = len( sorted_keys ) + # Handle environment settings first. + if 'set_environment' in sorted_keys: + # Example: "set_environment": [{"name": "JAVA_JAR_FILE", "type": "set_environment"}] + env_dicts = tds_dict[ 'set_environment' ] + num_env_dicts = len( env_dicts ) + td_str += '<b>environment:</b> ' + for index, env_dict in enumerate( env_dicts ): + td_str += '%s' % escape_html( env_dict[ 'name' ] ) + if index < num_env_dicts - 1: + td_str += ', ' + td_str += '<br/>' + for index, key in enumerate( sorted_keys ): + if key == 'set_environment': + continue + td_dict = tds_dict[ key ] + # Example: {"name": "bwa", "type": "package", "version": "0.5.9"} + name = td_dict[ 'name' ] + type = td_dict[ 'type' ] + version = td_dict[ 'version' ] + td_str += '<b>%s</b> version <b>%s</b>' % ( escape_html( name ), escape_html( version ) ) + if index < num_keys - 1: + td_str += '<br/>' + return td_str + + title = "Tool dependency definitions in this tool shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + model_class=model.Repository, + link=( lambda item: dict( operation="browse_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + ToolDependencyColumn( "Tool dependency", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.includes_tool_dependencies == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + + +class ToolsGrid( RepositoryMetadataGrid ): + + + class ToolsColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + tool_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + tool_dicts = metadata.get( 'tools', [] ) + if tool_dicts: + num_tool_dicts = len( tool_dicts ) + for index, tool_dict in enumerate( tool_dicts ): + tool_id = tool_dict[ 'id' ] + name = tool_dict[ 'name' ] + version = tool_dict[ 'version' ] + tool_str += '<b>%s</b> | %s | %s' % ( escape_html( tool_id ), escape_html( name ), escape_html( version ) ) + if index < num_tool_dicts - 1: + tool_str += '<br/>' + return tool_str + + title = "Valid tools in this tool shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + model_class=model.Repository, + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + ToolsColumn( "Tool id | name | version", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.includes_tools == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + + +class DatatypesGrid( RepositoryMetadataGrid ): + + + class DatatypesColumn( grids.TextColumn ): + + def get_value( self, trans, grid, repository_metadata ): + datatype_str = '' + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + datatype_dicts = metadata.get( 'datatypes', [] ) + if datatype_dicts: + num_datatype_dicts = len( datatype_dicts ) + for index, datatype_dict in enumerate( datatype_dicts ): + # Example: {"display_in_upload": "true", "dtype": "galaxy.datatypes.blast:BlastXml", "extension": "blastxml", "mimetype": "application/xml"} + extension = datatype_dict[ 'extension' ] + dtype = datatype_dict[ 'dtype' ] + mimetype = datatype_dict[ 'mimetype' ] + display_in_upload = datatype_dict.get( 'display_in_upload', False ) + datatype_str += '<b>%s</b> | %s | %s' % ( escape_html( extension ), escape_html( dtype ), escape_html( mimetype ) ) + if index < num_datatype_dicts - 1: + datatype_str += '<br/>' + return datatype_str + + title = "Custom datatypes in this tool shed" + columns = [ + RepositoryMetadataGrid.RepositoryNameColumn( "Repository name", + model_class=model.Repository, + link=( lambda item: dict( operation="view_or_manage_repository", id=item.repository.id ) ), + attach_popup=False, + key="Repository.name" ), + RepositoryMetadataGrid.RepositoryOwnerColumn( "Owner", + model_class=model.User, + attach_popup=False, + key="User.username" ), + RepositoryMetadataGrid.ChangesetRevisionColumn( "Revision", + attach_popup=False ), + DatatypesColumn( "Datatype extension | Type | Mimetype", + attach_popup=False ) + ] + columns.append( grids.MulticolFilterColumn( "Search repository name, owner", + cols_to_filter=[ columns[0], columns[1] ], + key="free-text-search", + visible=False, + filterable="standard" ) ) + + def build_initial_query( self, trans, **kwd ): + return trans.sa_session.query( model.RepositoryMetadata ) \ + .join( model.Repository ) \ + .filter( and_( model.RepositoryMetadata.table.c.includes_datatypes == True, + model.Repository.table.c.deleted == False, + model.Repository.table.c.deprecated == False ) ) \ + .join( model.User.table ) \ + .order_by( model.Repository.name ) + class RepositoryController( BaseUIController, common_util.ItemRatings ): category_grid = CategoryGrid() + datatypes_grid = DatatypesGrid() deprecated_repositories_i_own_grid = DeprecatedRepositoriesIOwnGrid() email_alerts_repository_grid = EmailAlertsRepositoryGrid() install_matched_repository_grid = InstallMatchedRepositoryGrid() @@ -800,9 +1018,12 @@ my_writable_repositories_grid = MyWritableRepositoriesGrid() repositories_by_user_grid = RepositoriesByUserGrid() repositories_i_own_grid = RepositoriesIOwnGrid() + repository_dependencies_grid = RepositoryDependenciesGrid() repository_grid = RepositoryGrid() # The repository_metadata_grid is not currently displayed, but is sub-classed by several grids. repository_metadata_grid = RepositoryMetadataGrid() + tool_dependencies_grid = ToolDependenciesGrid() + tools_grid = ToolsGrid() valid_category_grid = ValidCategoryGrid() valid_repository_grid = ValidRepositoryGrid() @@ -824,7 +1045,7 @@ pass return self.browse_repositories( trans, **kwd ) if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation in [ "repositories_by_category", "repositories_by_user" ]: # Eliminate the current filters if any exist. for k, v in kwd.items(): @@ -836,6 +1057,16 @@ return self.category_grid( trans, **kwd ) @web.expose + def browse_datatypes( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + return self.datatypes_grid( trans, **kwd ) + + @web.expose def browse_invalid_tools( self, trans, **kwd ): params = util.Params( kwd ) message = util.restore_text( params.get( 'message', '' ) ) @@ -881,7 +1112,7 @@ # We add params to the keyword dict in this method in order to rename the param with an "f-" prefix, simulating filtering by clicking a search # link. We have to take this approach because the "-" character is illegal in HTTP requests. if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation == "view_or_manage_repository": return trans.response.send_redirect( web.url_for( controller='repository', action='view_or_manage_repository', @@ -1000,6 +1231,40 @@ status=status ) @web.expose + def browse_repository_dependencies( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "browse_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + **kwd ) ) + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + return self.repository_dependencies_grid( trans, **kwd ) + + @web.expose + def browse_tools( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "view_or_manage_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='view_or_manage_repository', + **kwd ) ) + return self.tools_grid( trans, **kwd ) + + @web.expose + def browse_tool_dependencies( self, trans, **kwd ): + if 'operation' in kwd: + operation = kwd[ 'operation' ].lower() + if operation == "browse_repository": + return trans.response.send_redirect( web.url_for( controller='repository', + action='browse_repository', + **kwd ) ) + return self.tool_dependencies_grid( trans, **kwd ) + + @web.expose def browse_valid_categories( self, trans, **kwd ): # The request came from Galaxy, so restrict category links to display only valid repository changeset revisions. galaxy_url = kwd.get( 'galaxy_url', None ) @@ -1022,7 +1287,7 @@ pass return self.browse_valid_repositories( trans, **kwd ) if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation in [ "valid_repositories_by_category", "valid_repositories_by_user" ]: # Eliminate the current filters if any exist. for k, v in kwd.items(): @@ -2420,7 +2685,7 @@ message = util.restore_text( params.get( 'message', '' ) ) status = params.get( 'status', 'done' ) if 'operation' in kwd: - operation = kwd['operation'].lower() + operation = kwd[ 'operation' ].lower() if operation == "receive email alerts": if trans.user: if kwd[ 'id' ]: diff -r 513adadb31a2a4b014b3f03c5af2817919ea1760 -r c7c8316a1d134a19e929a2257a701ec1ebc3a33a templates/webapps/tool_shed/index.mako --- a/templates/webapps/tool_shed/index.mako +++ b/templates/webapps/tool_shed/index.mako @@ -67,6 +67,22 @@ <a target="galaxy_main" href="${h.url_for( controller='repository', action='find_workflows' )}">Search for workflows</a></div></div> + <div class="toolSectionPad"></div> + <div class="toolSectionTitle"> + Valid Galaxy Utilities + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_tools' )}">Tools</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_datatypes' )}">Custom datatypes</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_repository_dependencies' )}">Repository dependency definitions</a> + </div> + <div class="toolTitle"> + <a target="galaxy_main" href="${h.url_for( controller='repository', action='browse_tool_dependencies' )}">Tool dependency definitions</a> + </div> %endif <div class="toolSectionPad"></div><div class="toolSectionTitle"> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: inithello: Improved documentation for automated repository installation and testing. Handle cases where a repository is missing test data. Limit the list of repositories to test to those that have tools. Update the parse_tool_panel_config method to return a flag specifying whether test data was found for the specified tool panel entry.
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/513adadb31a2/ changeset: 513adadb31a2 user: inithello date: 2013-03-01 21:13:20 summary: Improved documentation for automated repository installation and testing. Handle cases where a repository is missing test data. Limit the list of repositories to test to those that have tools. Update the parse_tool_panel_config method to return a flag specifying whether test data was found for the specified tool panel entry. affected #: 3 files diff -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a -r 513adadb31a2a4b014b3f03c5af2817919ea1760 scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -321,10 +321,10 @@ if testing_migrated_tools or testing_installed_tools: shed_tools_dict = {} if testing_migrated_tools: - shed_tools_dict = parse_tool_panel_config( migrated_tool_panel_config, shed_tools_dict ) + has_test_data, shed_tools_dict = parse_tool_panel_config( migrated_tool_panel_config, shed_tools_dict ) elif testing_installed_tools: for shed_tool_config in installed_tool_panel_configs: - shed_tools_dict = parse_tool_panel_config( shed_tool_config, shed_tools_dict ) + has_test_data, shed_tools_dict = parse_tool_panel_config( shed_tool_config, shed_tools_dict ) # Persist the shed_tools_dict to the galaxy_tool_shed_test_file. shed_tools_file = open( galaxy_tool_shed_test_file, 'w' ) shed_tools_file.write( to_json_string( shed_tools_dict ) ) diff -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a -r 513adadb31a2a4b014b3f03c5af2817919ea1760 test/base/util.py --- a/test/base/util.py +++ b/test/base/util.py @@ -1,4 +1,6 @@ -import os, sys +import os, sys, logging + +log = logging.getLogger(__name__) cwd = os.getcwd() if cwd not in sys.path: @@ -27,6 +29,8 @@ # Locate the test-data directory. installed_tool_path = os.path.join( installed_tool_path_items[ 0 ], 'repos', repository_owner, repository_name, changeset_revision ) for root, dirs, files in os.walk( os.path.join(tool_path, installed_tool_path )): + if '.hg' in dirs: + dirs.remove( '.hg' ) if 'test-data' in dirs: return os.path.join( root, 'test-data' ), repository_name, changeset_revision return None, repository_name, changeset_revision @@ -40,6 +44,7 @@ last_tested_repository_name = None last_tested_changeset_revision = None tool_path = None + has_test_data = False tree = parse_xml( config ) root = tree.getroot() tool_path = root.get('tool_path') @@ -53,6 +58,8 @@ last_tested_changeset_revision, tool_path ) if galaxy_test_file_dir: + if not has_test_data: + has_test_data = True if galaxy_test_file_dir != last_galaxy_test_file_dir: if not os.path.isabs( galaxy_test_file_dir ): galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) @@ -70,11 +77,13 @@ last_tested_changeset_revision, tool_path ) if galaxy_test_file_dir: + if not has_test_data: + has_test_data = True if galaxy_test_file_dir != last_galaxy_test_file_dir: if not os.path.isabs( galaxy_test_file_dir ): galaxy_test_file_dir = os.path.join( os.getcwd(), galaxy_test_file_dir ) guid = section_elem.get( 'guid' ) shed_tools_dict[ guid ] = galaxy_test_file_dir last_galaxy_test_file_dir = galaxy_test_file_dir - return shed_tools_dict + return has_test_data, shed_tools_dict diff -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a -r 513adadb31a2a4b014b3f03c5af2817919ea1760 test/install_and_test_tool_shed_repositories/functional_tests.py --- a/test/install_and_test_tool_shed_repositories/functional_tests.py +++ b/test/install_and_test_tool_shed_repositories/functional_tests.py @@ -5,6 +5,7 @@ # will execute this script with the appropriate parameters. import os, sys, shutil, tempfile, re, string, urllib, platform +from time import strftime # Assume we are run from the galaxy root directory, add lib to the python path cwd = os.getcwd() @@ -114,6 +115,27 @@ else: galaxy_encode_secret = os.environ[ 'GALAXY_INSTALL_TEST_SECRET' ] +def execute_uninstall_method( repository_dict ): + # Delete any configured tool functional tests from the test_toolbox.__dict__, otherwise nose will find them + # and try to re-run the tests after uninstalling the repository. + tests_to_delete = [] + for key in test_toolbox.__dict__: + if key.startswith( 'TestForTool_' ): + log.info( 'Tool test found in test_toolbox, deleting: %s' % key ) + tests_to_delete.append( key ) + for key in tests_to_delete: + del test_toolbox.__dict__[ key ] + # Generate a test method to uninstall this repository through the embedded Galaxy application's web interface. + test_install_repositories.generate_uninstall_method( repository_dict ) + # Set up nose to run the generated uninstall method as a functional test. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed + # repository and delete it from disk. + result = run_tests( test_config ) + success = result.wasSuccessful() + return success + def get_api_url( base, parts=[], params=None, key=None ): if 'api' in parts and parts.index( 'api' ) != 0: parts.pop( parts.index( 'api' ) ) @@ -187,7 +209,7 @@ return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False ) def register_test_success( url, metadata_id ): - params = dict( tools_functionally_correct='true', do_not_test='false' ) + params = dict( tools_functionally_correct='true', do_not_test='true' ) return update( tool_shed_api_key, '%s' % ( url_join( galaxy_tool_shed_url, 'api', 'repository_revisions', metadata_id ) ), params, return_formatted=False ) def run_tests( test_config ): @@ -209,6 +231,11 @@ galaxy_test_host = os.environ.get( 'GALAXY_INSTALL_TEST_HOST', default_galaxy_test_host ) galaxy_test_port = os.environ.get( 'GALAXY_INSTALL_TEST_PORT', str( default_galaxy_test_port_max ) ) + # Initialize some variables for the summary that will be printed to stdout. + repositories_tested = 0 + repositories_passed = 0 + repositories_failed = 0 + tool_path = os.environ.get( 'GALAXY_INSTALL_TEST_TOOL_PATH', 'tools' ) if 'HTTP_ACCEPT_LANGUAGE' not in os.environ: os.environ[ 'HTTP_ACCEPT_LANGUAGE' ] = default_galaxy_locales @@ -373,132 +400,189 @@ log.info( "Retrieving repositories to install from the URL:\n%s\n" % str( galaxy_tool_shed_url ) ) repositories_to_install = get_repositories_to_install( galaxy_tool_shed_url, source='url' ) log.info( "Retrieved %d repositories to install..." % len( repositories_to_install ) ) + repositories_tested = len( repositories_to_install ) + # This loop will iterate through the list of repositories returned by the above method, skipping any that are marked + # as deleted. For each repository, it will generate a test method that will use Twill to install that repository into the + # embedded Galaxy application that was started up, selecting to install repository and tool dependencies if they are + # defined. If the installation completes successfully, it will then generate a test case for each functional test + # defined for each tool in the repository, and execute the generated test cases. When this completes, it will record + # the result of the tests, and if any failed, the traceback and captured output of the tool that was run. + # After all tests have completed, the repository is uninstalled, so that the previous test cases don't interfere with + # the next repository's functional tests. for repository_to_install_dict in repositories_to_install: """ Each repository_to_install_dict looks something like: - {'repository_id': '175812cd7caaf439', - 'url': '/api/repository_revisions/175812cd7caaf439', - 'malicious': False, - 'downloadable': True, - 'changeset_revision': '2388033730f3', - 'id': '175812cd7caaf439'} + { + "changeset_revision": "13fa22a258b5", + "downloadable": true, + "id": "529fd61ab1c6cc36", + "malicious": false, + "repository_id": "529fd61ab1c6cc36", + "url": "/api/repository_revisions/529fd61ab1c6cc36" + } """ repository_id = repository_to_install_dict.get( 'repository_id', None ) changeset_revision = repository_to_install_dict.get( 'changeset_revision', None ) metadata_revision_id = repository_to_install_dict.get( 'id', None ) + # Add the URL for the tool shed we're installing from, so the automated installation methods go to the right place. repository_to_install_dict[ 'tool_shed_url' ] = galaxy_tool_shed_url + # We need to get some details from the tool shed API, such as repository name and owner, to pass on to the + # module that will generate the install methods. repository_info_dict = get_repository_info_from_api( galaxy_tool_shed_url, repository_to_install_dict ) - # If a repository is deleted or malicious, we don't need to test it. - if repository_info_dict[ 'deleted' ] or repository_info_dict[ 'deprecated' ]: - log.info( "Skipping revision %s of repository id %s since it is either deleted or deprecated..." % ( str( changeset_revision ), str( repository_id ) ) ) + # We are testing deprecated repositories, because it is possible that a deprecated repository contains valid + # and functionally correct tools that someone has previously installed. Deleted repositories have never been installed, + # and therefore do not need to be checked. If they are undeleted, this script will then test them the next time it runs. + if repository_info_dict[ 'deleted' ]: + log.info( "Skipping revision %s of repository id %s since the repository is deleted..." % ( str( changeset_revision ), str( repository_id ) ) ) continue log.info( "Installing and testing revision %s of repository id %s..." % ( str( changeset_revision ), str( repository_id ) ) ) + # Add repository details to the basic repository dict. repository_dict = dict( repository_info_dict.items() + repository_to_install_dict.items() ) """ - Each repository_dict looks something like: - {'repository_id': '175812cd7caaf439', - 'url': '/api/repository_revisions/175812cd7caaf439', - 'malicious': False, - 'downloadable': True, - 'changeset_revision': '2388033730f3', - 'id': '175812cd7caaf439'} + After the addition of the repository details, each repository_dict should now contain something like: + { + "changeset_revision": "13fa22a258b5", + "contents_url": "/api/repositories/529fd61ab1c6cc36/contents", + "deleted": false, + "deprecated": false, + "description": "Convert column case.", + "downloadable": true, + "id": "529fd61ab1c6cc36", + "long_description": "This tool takes the specified columns and converts them to uppercase or lowercase.", + "malicious": false, + "name": "change_case", + "owner": "test", + "private": false, + "repository_id": "529fd61ab1c6cc36", + "times_downloaded": 0, + "tool_shed_url": "http://toolshed.local:10001", + "url": "/api/repository_revisions/529fd61ab1c6cc36", + "user_id": "529fd61ab1c6cc36" + } """ - # Generate the method that will install this repository into the running Galaxy instance. + # Use the repository information dict to generate an install method that will install the repository into the embedded + # Galaxy application, with tool dependencies and repository dependencies, if any. test_install_repositories.generate_install_method( repository_dict ) os.environ[ 'GALAXY_INSTALL_TEST_HOST' ] = galaxy_test_host # Configure nose to run the install method as a test. test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) test_config.configure( sys.argv ) - # Run the configured install method as a test. This method uses the Galaxy web interface to install the specified + # Run the configured install method as a test. This method uses the embedded Galaxy application's web interface to install the specified # repository, with tool and repository dependencies also selected for installation. result = run_tests( test_config ) success = result.wasSuccessful() - # If the installation succeeds, set up and run functional tests for this repository. This is equivalent to + # If the installation succeeds, configure and run functional tests for this repository. This is equivalent to # sh run_functional_tests.sh -installed if success: log.debug( 'Installation of %s succeeded, running all defined functional tests.' % repository_dict[ 'name' ] ) - # Parse the tool panel config to get the test-data path for this repository. - if not os.path.exists( galaxy_shed_tools_dict ): - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) - shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) - # Write this to a file, so the functional test framework can find it. - file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) - # Set up the environment so that test.functional.test_toolbox can find the Galaxy server we configured in this framework. - os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict - os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host - os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port - # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. - test_toolbox.toolbox = app.toolbox - # Generate the test methods for this installed repository. We need to pass in True here, or it will look - # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. - test_toolbox.build_tests( testing_shed_tools=True ) - # Set up nose to run the generated functional tests. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the configured tests. - result = run_tests( test_config ) - success = result.wasSuccessful() - repository_dict[ 'test_environment' ] = get_test_environment() - repository_dict[ 'functional_tests_passed' ] = success - test_errors = [] - if success: - register_test_success( galaxy_tool_shed_url, metadata_revision_id ) - log.debug( 'Repository %s installed and passed functional tests.' % repository_dict[ 'name' ] ) + # Generate the shed_tools_dict that specifies the location of test data contained within this repository. If the repository + # does not have a test-data directory, this will return has_test_data = False, and we will set the do_not_test flag to True, + # and the tools_functionally_correct flag to False, as well as updating tool_test_errors. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( dict() ) ) + has_test_data, shed_tools_dict = parse_tool_panel_config( galaxy_shed_tool_conf_file, from_json_string( file( galaxy_shed_tools_dict, 'r' ).read() ) ) + if not has_test_data: + log.error( 'Test data is missing for this repository. Updating repository and skipping functional tests.' ) + repository_status[ 'test_environment' ] = get_test_environment() + test_id = 'Find functional test data for %s' % repository_dict[ 'name' ] + test_errors = dict( test_id=test_id, + stdout='No test data found for changeset revision %s of repository %s owned by %s.' % \ + ( repository_dict[ 'changeset_revision' ], repository_dict[ 'name' ], repository_dict[ 'owner' ] ) ) + repository_status[ 'test_errors' ] = [ test_errors ] + # Record the status of this repository in the tool shed. + register_test_failure( galaxy_tool_shed_url, metadata_revision_id, repository_status ) + # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the + # repository using Twill. + execute_uninstall_method( repository_dict ) + # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. + test_toolbox.toolbox = app.toolbox + repositories_failed += 1 else: - # If the functional tests fail, log the output and submit it to the tool shed whence the repository was installed. - for failure in result.failures: - test_status = dict( test=str( failure[0] ) ) - log_output = failure[1].replace( '\\n', '\n' ) - log_output = re.sub( r'control \d+:.+', r'', log_output ) - log_output = re.sub( r'\n+', r'\n', log_output ) - appending_to = 'output' - tmp_output = {} - output = {} - for line in log_output.split( '\n' ): - if line.startswith( 'Traceback' ): - appending_to = 'traceback' - elif '>> end captured' in line: - continue - elif 'request returned None from get_history' in line: - continue - elif '>> begin captured logging <<' in line: - appending_to = 'logging' - continue - elif '>> begin captured stdout <<' in line: - appending_to = 'stdout' - continue - elif '>> begin captured stderr <<' in line: - appending_to = 'stderr' - continue - if appending_to not in tmp_output: - tmp_output[ appending_to ] = [] - tmp_output[ appending_to ].append( line ) - for output_type in [ 'stderr', 'stdout', 'traceback' ]: - if output_type in tmp_output: - test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] ) - test_errors.append( test_status ) - if test_errors: - repository_status[ 'test_environment' ] = get_test_environment() - repository_status[ 'test_errors' ] = test_errors - register_test_failure( galaxy_tool_shed_url, metadata_revision_id, repository_status ) - log.debug( 'Repository %s installed, but did not pass functional tests.' % repository_dict[ 'name' ] ) - # Delete the completed tool functional tests from the test_toolbox.__dict__, otherwise nose will find them and try to re-run the - # tests after uninstalling the repository. - tests_to_delete = [] - for key in test_toolbox.__dict__: - if key.startswith( 'TestForTool_' ): - tests_to_delete.append( key ) - for key in tests_to_delete: - del test_toolbox.__dict__[ key ] - # Generate an uninstall method for this repository, so that the next repository has a clean environment for testing. - test_install_repositories.generate_uninstall_method( repository_dict ) - # Set up nose to run the generated uninstall method as a functional test. - test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) - test_config.configure( sys.argv ) - # Run the uninstall method. This method uses the Galaxy web interface to uninstall the previously installed - # repository and delete it from disk. - result = run_tests( test_config ) - success = result.wasSuccessful() + # If the repository does have a test-data directory, we write the generated shed_tools_dict to a file, so the functional + # test framework can find it. + file( galaxy_shed_tools_dict, 'w' ).write( to_json_string( shed_tools_dict ) ) + log.info( 'Saved generated shed_tools_dict to %s\nContents: %s' % ( galaxy_shed_tools_dict, str( shed_tools_dict ) ) ) + # Set the GALAXY_TOOL_SHED_TEST_FILE environment variable to the path of the shed_tools_dict file, so that test.base.twilltestcase.setUp + # will find and parse it properly. + os.environ[ 'GALAXY_TOOL_SHED_TEST_FILE' ] = galaxy_shed_tools_dict + os.environ[ 'GALAXY_TEST_HOST' ] = galaxy_test_host + os.environ[ 'GALAXY_TEST_PORT' ] = galaxy_test_port + # Set the module-level variable 'toolbox', so that test.functional.test_toolbox will generate the appropriate test methods. + test_toolbox.toolbox = app.toolbox + # Generate the test methods for this installed repository. We need to pass in True here, or it will look + # in $GALAXY_HOME/test-data for test data, which may result in missing or invalid test files. + test_toolbox.build_tests( testing_shed_tools=True ) + # Set up nose to run the generated functional tests. + test_config = nose.config.Config( env=os.environ, plugins=nose.plugins.manager.DefaultPluginManager() ) + test_config.configure( sys.argv ) + # Run the configured tests. + result = run_tests( test_config ) + success = result.wasSuccessful() + # Record some information about the environment in which this test was run, in case a failure is specific to a certain processor + # architecture or operating system. + repository_dict[ 'test_environment' ] = get_test_environment() + repository_dict[ 'functional_tests_passed' ] = success + test_errors = [] + if success: + # This repository's tools passed all functional tests. Update the repository_metadata table in the tool shed's database + # to reflect that. Call the register_test_success method, which executes a PUT request to the repository_revisions API + # controller with the status of the test. This also sets the do_not_test and tools_functionally correct flags, and + # updates the time_last_tested field to today's date. + repositories_passed += 1 + register_test_success( galaxy_tool_shed_url, metadata_revision_id ) + log.debug( 'Revision %s of repository %s installed and passed functional tests.' % \ + ( repository_dict[ 'changeset_revision' ], repository_dict[ 'name' ] ) ) + else: + # If the functional tests fail, log the output and update the failed changeset revision's metadata record in the tool shed via the API. + for failure in result.failures: + # Record the twill test identifier, so the repository owner can discover which test is failing. + test_status = dict( test_id=str( failure[0] ) ) + log_output = failure[1].replace( '\\n', '\n' ) + # Remove debug output that the reviewer or owner doesn't need. + log_output = re.sub( r'control \d+:.+', r'', log_output ) + log_output = re.sub( r'\n+', r'\n', log_output ) + appending_to = 'output' + tmp_output = {} + output = {} + # Iterate through the functional test output and extract only the important data. Captured logging is not recorded. + for line in log_output.split( '\n' ): + if line.startswith( 'Traceback' ): + appending_to = 'traceback' + elif '>> end captured' in line or '>> end tool' in line: + continue + elif 'request returned None from get_history' in line: + continue + elif '>> begin captured logging <<' in line: + appending_to = 'logging' + continue + elif '>> begin captured stdout <<' in line: + appending_to = 'stdout' + continue + elif '>> begin captured stderr <<' in line or '>> begin tool stderr <<' in line: + appending_to = 'stderr' + continue + if appending_to not in tmp_output: + tmp_output[ appending_to ] = [] + tmp_output[ appending_to ].append( line ) + for output_type in [ 'stderr', 'stdout', 'traceback' ]: + if output_type in tmp_output: + test_status[ output_type ] = '\n'.join( tmp_output[ output_type ] ) + test_errors.append( test_status ) + if test_errors: + # Only update test_errors for this repository if it's not empty. + repository_status[ 'test_environment' ] = get_test_environment() + repository_status[ 'test_errors' ] = test_errors + # Call the register_test_failure method, which executes a PUT request to the repository_revisions API controller with the failure + # status of the test, and updates tool_test_errors with the relevant log data. + # This also sets the do_not_test and tools_functionally correct flags, and updates the time_last_tested field to today's date. + repositories_failed += 1 + register_test_failure( galaxy_tool_shed_url, metadata_revision_id, repository_status ) + log.debug( 'Revision %s of repository %s installed successfully, but did not pass functional tests.' % \ + ( repository_dict[ 'changeset_revision' ], repository_dict[ 'name' ] ) ) + # Run the cleanup method. This removes tool functional test methods from the test_toolbox module and uninstalls the + # repository using Twill. + execute_uninstall_method( repository_dict ) + # Set the test_toolbox.toolbox module-level variable to the new app.toolbox. + test_toolbox.toolbox = app.toolbox else: log.debug( 'Repository %s failed to install correctly.' % repository_dict[ 'name' ] ) except: @@ -528,10 +612,25 @@ pass else: log.debug( 'GALAXY_INSTALL_TEST_NO_CLEANUP set, not cleaning up.' ) + + now = strftime( "%Y-%m-%d %H:%M:%S" ) + print "####################################################################################" + print "# %s - repository installation and testing script completed." % now + print "# Repository revisions tested: %d" % repositories_tested + if repositories_tested > 0: + print "# Repository revisions passed: %d" % repositories_passed + print "# Repository revisions failed: %d" % repositories_failed + print "####################################################################################" + if success: return 0 else: return 1 if __name__ == "__main__": - sys.exit( main() ) + now = strftime( "%Y-%m-%d %H:%M:%S" ) + print "####################################################################################" + print "# %s - running repository installation and testing script." % now + print "####################################################################################" + return_code = main() + sys.exit( return_code ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: carlfeberhard: fix server_env saved output dir name; clean up prev. debugging statements
by commits-noreply＠bitbucket.org 01 Mar '13

01 Mar '13

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/2454aa4b6e7c/ changeset: 2454aa4b6e7c user: carlfeberhard date: 2013-03-01 18:49:08 summary: fix server_env saved output dir name; clean up prev. debugging statements affected #: 3 files diff -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -45,8 +45,6 @@ self.tool_shed_registry = tool_shed.tool_shed_registry.Registry( self.config.root, self.config.tool_sheds_config ) else: self.tool_shed_registry = None - log.debug( 'self.config.tool_sheds_config: %s, self.tool_shed_registry: %s', - self.config.tool_sheds_config, self.tool_shed_registry ) # Initialize database / check for appropriate schema version. # If this # is a new installation, we'll restrict the tool migration messaging. from galaxy.model.migrate.check import create_or_verify_database diff -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a scripts/functional_tests.py --- a/scripts/functional_tests.py +++ b/scripts/functional_tests.py @@ -42,7 +42,6 @@ import nose.loader import nose.plugins.manager -import pprint log = logging.getLogger( "functional_tests.py" ) default_galaxy_test_host = "localhost" @@ -227,7 +226,6 @@ kwargs[ 'object_store' ] = 'distributed' kwargs[ 'distributed_object_store_config_file' ] = 'distributed_object_store_conf.xml.sample' # Build the Universe Application - print 'app.kwargs:\n%s' %( pprint.pformat( kwargs ) ) app = UniverseApplication( job_queue_workers = 5, id_secret = 'changethisinproductiontoo', template_path = "templates", diff -r 153f7f450f4b7537bc8866f09b5cc3ca57ad25ee -r 2454aa4b6e7c308a90bb6ad7f00c47f6177e992a test/casperjs/server_env.py --- a/test/casperjs/server_env.py +++ b/test/casperjs/server_env.py @@ -29,6 +29,9 @@ @classmethod def instance( cls, config=None ): + """Returns the singleton of TestEnvironment, instantiating it first if it + does not yet exist. + """ # singleton pattern if( ( not cls._instance ) or ( config ) ): @@ -36,25 +39,26 @@ cls._instance = cls( config ) return cls._instance - @classmethod - def get_server_url( cls ): - return cls.instance().url - def __init__( self, env_config_dict=None ): self.config = env_config_dict or {} - self.protocol = self._get_setting_from_config_or_env( 'protocol', self.ENV_PROTOCOL, self.DEFAULT_PROTOCOL ) - self.host = self._get_setting_from_config_or_env( 'host', self.ENV_HOST, self.DEFAULT_HOST ) - self.port = self._get_setting_from_config_or_env( 'port', self.ENV_PORT, self.DEFAULT_PORT ) + self.protocol = self._get_setting_from_config_or_env( + 'protocol', self.ENV_PROTOCOL, self.DEFAULT_PROTOCOL ) + self.host = self._get_setting_from_config_or_env( + 'host', self.ENV_HOST, self.DEFAULT_HOST ) + self.port = self._get_setting_from_config_or_env( + 'port', self.ENV_PORT, self.DEFAULT_PORT ) - self.history_id = self._get_setting_from_config_or_env( 'history_id', self.ENV_HISTORY_ID, default=None ) - self.file_dir = self._get_setting_from_config_or_env( 'file_dir', self.ENV_FILE_DIR, default=None ) + self.history_id = self._get_setting_from_config_or_env( + 'history_id', self.ENV_HISTORY_ID, default=None ) + self.file_dir = self._get_setting_from_config_or_env( + 'file_dir', self.ENV_FILE_DIR, default=None ) self.tool_shed_test_file = self._get_setting_from_config_or_env( 'tool_shed_test_file', self.ENV_TOOL_SHED_TEST_FILE, default=None ) self.shed_tools_dict = self._get_shed_tools_dict() - self.keepOutdir = self._get_setting_from_config_or_env( + self.saved_output_dir = self._get_setting_from_config_or_env( 'saved_output_dir', self.ENV_SAVED_FILES_DIR, default=None ) self._init_saved_files_dir() @@ -62,6 +66,7 @@ """Try to get a setting from (in order): TestEnvironment.config, the os env, or some default (if not False). """ + #TODO: if falsy value needed, use None - not ideal config = self.config.get( config_name, None ) env = os.environ.get( env_name, None ) if( ( not ( config or env ) ) @@ -94,6 +99,8 @@ @property def url( self ): + """Builds and returns the url of the test server. + """ url = '%s://%s' %( self.protocol, self.host ) if self.port and self.port != 80: url += ':%s' %( str( self.port ) ) 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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