March 2013 - galaxy-commits - lists.galaxyproject.org

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/1da2068fa58c/ changeset: 1da2068fa58c user: dannon date: 2013-03-05 22:15:54 summary: Fix workflow modules imports. affected #: 1 file diff -r f7904535003fdf8e56588fb78ebcdf9af913cc55 -r 1da2068fa58c5f1ac9d4bee510644a1dce20e814 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -1,13 +1,20 @@ +""" +Modules used in building workflows +""" + +import logging import re + from elementtree.ElementTree import Element + +import galaxy.tools from galaxy import web -from galaxy.tools.parameters import DataToolParameter, DummyDataset, RuntimeValue, check_param, visit_input_values -import galaxy.tools +from galaxy.jobs.actions.post import ActionBox +from galaxy.model import PostJobAction +from galaxy.tools.parameters import check_param, DataToolParameter, DummyDataset, RuntimeValue, visit_input_values from galaxy.util.bunch import Bunch from galaxy.util.json import from_json_string, to_json_string -from galaxy.jobs.actions.post import ActionBox -from galaxy.model import PostJobAction -import logging + log = logging.getLogger( __name__ ) https://bitbucket.org/galaxy/galaxy-central/commits/26006e793a32/ changeset: 26006e793a32 user: dannon date: 2013-03-05 22:18:16 summary: Workflow modules: Adjust spacing to new guidelines. affected #: 1 file diff -r 1da2068fa58c5f1ac9d4bee510644a1dce20e814 -r 26006e793a32a35328d941f6cea573b0108faab7 lib/galaxy/workflow/modules.py --- a/lib/galaxy/workflow/modules.py +++ b/lib/galaxy/workflow/modules.py @@ -15,8 +15,8 @@ from galaxy.util.bunch import Bunch from galaxy.util.json import from_json_string, to_json_string +log = logging.getLogger( __name__ ) -log = logging.getLogger( __name__ ) class WorkflowModule( object ): @@ -31,6 +31,7 @@ Create a new instance of the module with default state """ return Class( trans ) + @classmethod def from_dict( Class, trans, d ): """ @@ -38,6 +39,7 @@ dictionary `d`. """ return Class( trans ) + @classmethod def from_workflow_step( Class, trans, step ): return Class( trans ) @@ -51,10 +53,13 @@ def get_type( self ): return self.type + def get_name( self ): return self.name + def get_tool_id( self ): return None + def get_tooltip( self, static_path='' ): return None @@ -62,14 +67,19 @@ def get_state( self ): return None + def get_errors( self ): return None + def get_data_inputs( self ): return [] + def get_data_outputs( self ): return [] + def update_state( self ): pass + def get_config_form( self ): raise TypeError( "Abstract method" ) @@ -84,18 +94,23 @@ def get_runtime_inputs( self ): raise TypeError( "Abstract method" ) + def get_runtime_state( self ): raise TypeError( "Abstract method" ) + def encode_runtime_state( self, trans, state ): raise TypeError( "Abstract method" ) + def decode_runtime_state( self, trans, string ): raise TypeError( "Abstract method" ) + def update_runtime_state( self, trans, state, values ): raise TypeError( "Abstract method" ) def execute( self, trans, state ): raise TypeError( "Abstract method" ) + class InputDataModule( WorkflowModule ): type = "data_input" name = "Input dataset" @@ -105,12 +120,14 @@ module = Class( trans ) module.state = dict( name="Input Dataset" ) return module + @classmethod def from_dict( Class, trans, d, secure=True ): module = Class( trans ) state = from_json_string( d["tool_state"] ) module.state = dict( name=state.get( "name", "Input Dataset" ) ) return module + @classmethod def from_workflow_step( Class, trans, step ): module = Class( trans ) @@ -172,6 +189,7 @@ def execute( self, trans, state ): return None, dict( output=state.inputs['input']) + class ToolModule( WorkflowModule ): type = "tool" @@ -286,6 +304,7 @@ def get_data_inputs( self ): data_inputs = [] + def callback( input, value, prefixed_name, prefixed_label ): if isinstance( input, DataToolParameter ): data_inputs.append( dict( @@ -293,6 +312,7 @@ label=prefixed_label, multiple=input.multiple, extensions=input.extensions ) ) + visit_input_values( self.tool.inputs, self.state.inputs, callback ) return data_inputs @@ -338,6 +358,7 @@ make_runtime_key = incoming.get( 'make_runtime', None ) make_buildtime_key = incoming.get( 'make_buildtime', None ) + def item_callback( trans, key, input, value, error, old_value, context ): # Dummy value for Data parameters if isinstance( input, DataToolParameter ): @@ -354,6 +375,7 @@ return value, None else: return value, error + # Update state using incoming values errors = self.tool.update_state( self.trans, self.tool.inputs, self.state.inputs, incoming, item_callback=item_callback ) self.errors = errors or None @@ -370,6 +392,7 @@ input_connections_by_name = {} # Any connected input needs to have value DummyDataset (these # are not persisted so we need to do it every time) + def callback( input, value, prefixed_name, prefixed_label ): replacement = None if isinstance( input, DataToolParameter ): @@ -379,9 +402,12 @@ else: replacement = DummyDataset() return replacement + visit_input_values( self.tool.inputs, self.state.inputs, callback ) + class WorkflowModuleFactory( object ): + def __init__( self, module_types ): self.module_types = module_types Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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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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