galaxy-commits September 2011

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commit/galaxy-central: 6 new changesets
by Bitbucket 01 Sep '11

01 Sep '11

6 new changesets in galaxy-central: http://bitbucket.org/galaxy/galaxy-central/changeset/5ed1946867e3/ changeset: 5ed1946867e3 user: jmchilton date: 2011-05-17 22:29:02 summary: Enhancements to Galaxy's functional testing framework as outlined in issue 490. https://bitbucket.org/galaxy/galaxy-central/issue/490/enabling-iterative-te… affected #: 6 files (10.7 KB) --- a/lib/galaxy/tools/__init__.py Tue May 17 13:14:15 2011 -0400 +++ b/lib/galaxy/tools/__init__.py Tue May 17 15:29:02 2011 -0500 @@ -662,8 +662,31 @@ name = attrib.pop( 'name', None ) if name is None: 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 + # somewhere more conventional. + def convert_elem(elem): + """ Converts and XML element to a dictionary format, used by assertion checking code. """ + tag = elem.tag + attributes = dict( elem.attrib ) + child_elems = list( elem.getchildren() ) + converted_children = [] + for child_elem in child_elems: + converted_children.append( convert_elem(child_elem) ) + return {"tag" : tag, "attributes" : attributes, "children" : converted_children} + + if assert_elem is not None: + assert_list = [] + for assert_child in list(assert_elem): + assert_list.append(convert_elem(assert_child)) + + file = attrib.pop( 'file', None ) - if file is None: + # 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 @@ -674,6 +697,9 @@ attributes['delta'] = int( attrib.pop( 'delta', '10000' ) ) attributes['sort'] = util.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' ): --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/base/asserts/__init__.py Tue May 17 15:29:02 2011 -0500 @@ -0,0 +1,76 @@ +import inspect +import logging +import sys +log = logging.getLogger( __name__ ) + +assertion_module_names = ['text', 'tabular', 'xml'] + +# Code for loading modules containing assertion checking functions, to +# create a new module of assertion functions, create the needed python +# source file "test/base/asserts/<MODULE_NAME>.py" and add +# <MODULE_NAME> to the list of assertion module names defined above. +assertion_modules = [] +for assertion_module_name in assertion_module_names: + full_assertion_module_name = 'base.asserts.' + assertion_module_name + log.debug(full_assertion_module_name) + try: + #Dynamically import module + __import__(full_assertion_module_name) + assertion_module = sys.modules[full_assertion_module_name] + assertion_modules.append(assertion_module) + except Exception, e: + log.exception( 'Failed to load assertion module: %s %s' % (assertion_module_name, str(e))) + +def verify_assertions(data, assertion_description_list): + """ This function takes a list of assertions and a string to check + these assertions against. """ + for assertion_description in assertion_description_list: + verify_assertion(data, assertion_description) + +def verify_assertion(data, assertion_description): + tag = assertion_description["tag"] + assert_function_name = "assert_" + tag + assert_function = None + for assertion_module in assertion_modules: + if hasattr(assertion_module, assert_function_name): + assert_function = getattr(assertion_module, assert_function_name) + + if assert_function is None: + errmsg = "Unable to find test function associated with XML tag '%s'. Check your tool file syntax." % tag + raise AssertionError(errmsg) + + assert_function_args = inspect.getargspec(assert_function).args + args = {} + for attribute, value in assertion_description["attributes"].iteritems(): + if attribute in assert_function_args: + args[attribute] = value + + # Three special arguments automatically populated independently of + # tool XML attributes. output is passed in as the contents of the + # output file. verify_assertions_function is passed in as the + # verify_assertions function defined above, this allows + # recursively checking assertions on subsections of + # output. children is the parsed version of the child elements of + # the XML element describing this assertion. See + # assert_element_text in test/base/asserts/xml.py as an example of + # how to use verify_assertions_function and children in conjuction + # to apply assertion checking to a subset of the input. The parsed + # version of an elements child elements do not need to just define + # assertions, developers of assertion functions can also use the + # child elements in novel ways to define inputs the assertion + # checking function (for instance consider the following fictional + # assertion function for checking column titles of tabular output + # - <has_column_titles><with_name name="sequence"><with_name + # name="probability"></has_column_titles>.) + if "output" in assert_function_args: + args["output"] = data + + if "verify_assertions_function" in assert_function_args: + args["verify_assertions_function"] = verify_assertions + + if "children" in assert_function_args: + args["children"] = assertion_description["children"] + + # TODO: Verify all needed function arguments are specified. + assert_function(**args) + --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/base/asserts/tabular.py Tue May 17 15:29:02 2011 -0500 @@ -0,0 +1,17 @@ +import re + +def get_first_line(output): + match = re.search("^(.*)$", output, flags = re.MULTILINE) + if match is None: + return None + else: + return match.group(1) + +def assert_has_n_columns(output, n, sep = '\t'): + """ Asserts the tabular output contains n columns. The optional + sep argument specifies the column seperator used to determine the + number of columns.""" + n = int(n) + first_line = get_first_line(output) + assert first_line is not None, "Was expecting output with %d columns, but output was empty." % n + assert len(first_line.split(sep)) == n, "Output does not have %d columns." % n --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/base/asserts/text.py Tue May 17 15:29:02 2011 -0500 @@ -0,0 +1,30 @@ +import re + +def assert_has_text(output, text): + """ Asserts specified output contains the substring specified by + the argument text.""" + assert output.find(text) >= 0, "Output file did not contain expected text '%s' (ouptut '%s')" % (text, output) + +def assert_not_has_text(output, text): + """ Asserts specified output does not contain the substring + specified the argument text.""" + assert output.find(text) < 0, "Output file contains unexpected text '%s'" % text + +def assert_has_line(output, line): + """ Asserts the specified output contains the line specified the + argument line.""" + match = re.search("^%s$" % re.escape(line), output, flags = re.MULTILINE) + assert match != None, "No line of output file was '%s' (output was '%s') " % (line, output) + +def assert_has_text_matching(output, expression): + """ Asserts the specified output contains text matching the + regular expression specified by the argument expression.""" + match = re.search(expression, output) + assert match != None, "No text matching expression '%s' was found in output file." % expression + +def assert_has_line_matching(output, expression): + """ Asserts the specified output contains a line matching the + regular expression specified by the argument expression.""" + match = re.search("^%s$" % expression, output, flags = re.MULTILINE) + assert match != None, "No line matching expression '%s' was found in output file." % expression + --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test/base/asserts/xml.py Tue May 17 15:29:02 2011 -0500 @@ -0,0 +1,77 @@ +import elementtree.ElementTree +import re + +# Helper functions used to work with XML output. +def to_xml(output): + return elementtree.ElementTree.fromstring(output) + +def xml_find_text(output, path): + xml = to_xml(output) + text = xml.findtext(path) + return text + +def xml_find(output, path): + xml = to_xml(output) + return xml.find(path) + +def assert_is_valid_xml(output): + """ Simple assertion that just verifies the specified output + is valid XML.""" + try: + to_xml(output) + except Exception, e: + # TODO: Narrow caught exception to just parsing failure + raise AssertionError("Expected valid XML, but could not parse output. %s" % str(e)) + +def assert_has_element_with_path(output, path): + """ Asserts the specified output has at least one XML element with a + path matching the specified path argument. Valid paths are the + simplified subsets of XPath implemented by elementtree (currently + Galaxy makes use of elementtree 1.2). See + http://effbot.org/zone/element-xpath.htm for more information.""" + if xml_find(output, path) is None: + errmsg = "Expected to find XML element matching expression %s, not such match was found." % path + raise AssertionError(errmsg) + +def assert_has_n_elements_with_path(output, path, n): + """ Asserts the specified output has exactly n elements matching the + path specified.""" + xml = to_xml(output) + n = int(n) + num_elements = len(xml.findall(path)) + if num_elements != n: + errmsg = "Expected to find %d elements with path %s, but %d were found." % (n, path, num_elements) + raise AssertionError(errmsg) + +def assert_element_text_matches(output, path, expression): + """ Asserts the text of the first element matching the specified + path matches the specified regular expression.""" + text = xml_find_text(output, path) + if re.match(expression, text) is None: + errmsg = "Expected element with path '%s' to contain text matching '%s', instead text '%s' was found." % (path, text, actual_text) + raise AssertionError(errmsg) + +def assert_element_text_is(output, path, text): + """ Asserts the text of the first element matching the specified + path matches exactly the specified text. """ + assert_element_text_matches(output, path, re.escape(text)) + +def assert_attribute_matches(output, path, attribute, expression): + """ Asserts the specified attribute of the first element matching + the specified path matches the specified regular expression.""" + xml = xml_find(output, path) + attribute_value = xml.attrib[attribute] + if re.match(expression, attribute_value) is None: + errmsg = "Expected attribute '%s' on element with path '%s' to match '%s', instead attribute value was '%s'." % (attribute, path, expression, attribute_value) + raise AssertionError(errmsg) + +def assert_attribute_is(output, path, attribute, text): + """ Asserts the specified attribute of the first element matching + the specified path matches exactly the specified text.""" + assert_attribute_matches(output, path, attribute, re.escape(text)) + +def assert_element_text(output, path, verify_assertions_function, children): + """ Recursively checks the specified assertions against the text of + the first element matching the specified path.""" + text = xml_find_text(output, path) + verify_assertions_function(text, children) --- a/test/base/twilltestcase.py Tue May 17 13:14:15 2011 -0400 +++ b/test/base/twilltestcase.py Tue May 17 15:29:02 2011 -0500 @@ -11,6 +11,7 @@ from elementtree import ElementTree from galaxy.web import security from galaxy.web.framework.helpers import iff +from base.asserts import verify_assertions buffer = StringIO.StringIO() @@ -635,7 +636,7 @@ elem = elems[0] self.assertTrue( hid ) self._assert_dataset_state( elem, 'ok' ) - if self.is_zipped( filename ): + if filename is not None and self.is_zipped( filename ): errmsg = 'History item %s is a zip archive which includes invalid files:\n' % hid zip_file = zipfile.ZipFile( filename, "r" ) name = zip_file.namelist()[0] @@ -647,50 +648,59 @@ if ext != test_ext: raise AssertionError( errmsg ) else: - local_name = self.get_filename( filename ) - temp_name = self.makeTfname(fname = filename) self.home() self.visit_page( "display?hid=" + hid ) data = self.last_page() - file( temp_name, 'wb' ).write(data) - if self.keepOutdir > '': - ofn = os.path.join(self.keepOutdir,os.path.basename(local_name)) - shutil.copy(temp_name,ofn) - log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % (self.keepOutdir,ofn)) - try: - # have to nest try-except in try-finally to handle 2.4 + assert_list = attributes["assert_list"] + if assert_list is not None: try: - if attributes is None: - attributes = {} - compare = attributes.get( 'compare', 'diff' ) - if attributes.get( 'ftype', None ) == 'bam': - local_fh, temp_name = self._bam_to_sam( local_name, temp_name ) - local_name = local_fh.name - extra_files = attributes.get( 'extra_files', None ) - if compare == 'diff': - self.files_diff( local_name, temp_name, attributes=attributes ) - elif compare == 're_match': - self.files_re_match( local_name, temp_name, attributes=attributes ) - elif compare == 're_match_multiline': - self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) - elif compare == 'sim_size': - delta = attributes.get('delta','100') - s1 = len(data) - s2 = os.path.getsize(local_name) - if abs(s1-s2) > int(delta): - raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta) - elif compare == "contains": - self.files_contains( local_name, temp_name, attributes=attributes ) - else: - raise Exception, 'Unimplemented Compare type: %s' % compare - if extra_files: - self.verify_extra_files_content( extra_files, elem.get( 'id' ) ) + verify_assertions(data, assert_list) except AssertionError, err: - errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare ) + errmsg = 'History item %s different than expected\n' % (hid) errmsg += str( err ) raise AssertionError( errmsg ) - finally: - os.remove( temp_name ) + if filename is not None: + local_name = self.get_filename( filename ) + temp_name = self.makeTfname(fname = filename) + file( temp_name, 'wb' ).write(data) + if self.keepOutdir > '': + ofn = os.path.join(self.keepOutdir,os.path.basename(local_name)) + shutil.copy(temp_name,ofn) + log.debug('## GALAXY_TEST_SAVE=%s. saved %s' % (self.keepOutdir,ofn)) + try: + # have to nest try-except in try-finally to handle 2.4 + try: + if attributes is None: + attributes = {} + compare = attributes.get( 'compare', 'diff' ) + if attributes.get( 'ftype', None ) == 'bam': + local_fh, temp_name = self._bam_to_sam( local_name, temp_name ) + local_name = local_fh.name + extra_files = attributes.get( 'extra_files', None ) + if compare == 'diff': + self.files_diff( local_name, temp_name, attributes=attributes ) + elif compare == 're_match': + self.files_re_match( local_name, temp_name, attributes=attributes ) + elif compare == 're_match_multiline': + self.files_re_match_multiline( local_name, temp_name, attributes=attributes ) + elif compare == 'sim_size': + delta = attributes.get('delta','100') + s1 = len(data) + s2 = os.path.getsize(local_name) + if abs(s1-s2) > int(delta): + raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta) + elif compare == "contains": + self.files_contains( local_name, temp_name, attributes=attributes ) + else: + raise Exception, 'Unimplemented Compare type: %s' % compare + if extra_files: + self.verify_extra_files_content( extra_files, elem.get( 'id' ) ) + except AssertionError, err: + errmsg = 'History item %s different than expected, difference (using %s):\n' % ( hid, compare ) + errmsg += str( err ) + raise AssertionError( errmsg ) + finally: + os.remove( temp_name ) def _bam_to_sam( self, local_name, temp_name ): temp_local = tempfile.NamedTemporaryFile( suffix='.sam', prefix='local_bam_converted_to_sam_' ) http://bitbucket.org/galaxy/galaxy-central/changeset/4b922a226f58/ changeset: 4b922a226f58 user: jmchilton date: 2011-05-17 22:34:22 summary: $ hg diff lib/galaxy/web/buildapp.py affected #: 2 files (263 bytes) --- a/lib/galaxy/web/buildapp.py Tue May 17 15:29:02 2011 -0500 +++ b/lib/galaxy/web/buildapp.py Tue May 17 15:34:22 2011 -0500 @@ -94,6 +94,8 @@ webapp.add_route( '/async/:tool_id/:data_id/:data_secret', controller='async', action='index', tool_id=None, data_id=None, data_secret=None ) webapp.add_route( '/:controller/:action', action='index' ) webapp.add_route( '/:action', controller='root', action='index' ) + # allow for subdirectories in extra_files_path + webapp.add_route( '/datasets/:dataset_id/display/{filename:.+?}', controller='dataset', action='display', dataset_id=None, filename=None) webapp.add_route( '/datasets/:dataset_id/:action/:filename', controller='dataset', action='index', dataset_id=None, filename=None) webapp.add_route( '/display_application/:dataset_id/:app_name/:link_name/:user_id/:app_action/:action_param', controller='dataset', action='display_application', dataset_id=None, user_id=None, app_name = None, link_name = None, app_action = None, action_param = None ) webapp.add_route( '/u/:username/d/:slug', controller='dataset', action='display_by_username_and_slug' ) --- a/lib/galaxy/web/controllers/dataset.py Tue May 17 15:29:02 2011 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue May 17 15:34:22 2011 -0500 @@ -267,17 +267,18 @@ log.exception( "Unable to add composite parent %s to temporary library download archive" % data.file_name) msg = "Unable to create archive for download, please report this error" messagetype = 'error' - flist = glob.glob(os.path.join(efp,'*.*')) # glob returns full paths - for fpath in flist: - efp,fname = os.path.split(fpath) - try: - archive.add( fpath,fname ) - except IOError: - error = True - log.exception( "Unable to add %s to temporary library download archive" % fname) - msg = "Unable to create archive for download, please report this error" - messagetype = 'error' - continue + for root, dirs, files in os.walk(efp): + for fname in files: + fpath = os.path.join(root,fname) + rpath = os.path.relpath(fpath,efp) + try: + archive.add( fpath,rpath ) + except IOError: + error = True + log.exception( "Unable to add %s to temporary library download archive" % rpath) + msg = "Unable to create archive for download, please report this error" + messagetype = 'error' + continue if not error: if params.do_action == 'zip': archive.close() http://bitbucket.org/galaxy/galaxy-central/changeset/b8292228e13b/ changeset: b8292228e13b user: jmchilton date: 2011-05-19 22:42:25 summary: Added API for assigning roles to a data library. affected #: 2 files (2.3 KB) --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/web/api/permissions.py Thu May 19 15:42:25 2011 -0500 @@ -0,0 +1,51 @@ +""" +API operations on the permissions of a library. +""" +import logging, os, string, shutil, urllib, re, socket +from cgi import escape, FieldStorage +from galaxy import util, datatypes, jobs, web, util +from galaxy.web.base.controller import * +from galaxy.util.sanitize_html import sanitize_html +from galaxy.model.orm import * + +log = logging.getLogger( __name__ ) + +class PermissionsController( BaseController ): + + # Method not ideally named + @web.expose_api + def create( self, trans, library_id, payload, **kwd ): + """ + POST /api/libraries/{encoded_library_id}/permissions + Updates the library permissions. + """ + if not trans.user_is_admin(): + trans.response.status = 403 + return "You are not authorized to update library permissions." + + params = util.Params( payload ) + try: + decoded_library_id = trans.security.decode_id( library_id ) + except TypeError: + trans.response.status = 400 + return "Malformed library id ( %s ) specified, unable to decode." % str( library_id ) + + try: + library = trans.sa_session.query( trans.app.model.Library ).get( decoded_library_id ) + except: + library = None + + permissions = {} + for k, v in trans.app.model.Library.permitted_actions.items(): + role_params = params.get( k + '_in', [] ) + in_roles = [ trans.sa_session.query( trans.app.model.Role ).get( trans.security.decode_id( x ) ) for x in util.listify( role_params ) ] + permissions[ trans.app.security_agent.get_action( v.action ) ] = in_roles + trans.app.security_agent.set_all_library_permissions( library, permissions ) + trans.sa_session.refresh( library ) + # Copy the permissions to the root folder + trans.app.security_agent.copy_library_permissions( library, library.root_folder ) + message = "Permissions updated for library '%s'." % library.name + + item = library.get_api_value( view='element' ) + return item + --- a/lib/galaxy/web/buildapp.py Tue May 17 15:34:22 2011 -0500 +++ b/lib/galaxy/web/buildapp.py Thu May 19 15:42:25 2011 -0500 @@ -110,6 +110,10 @@ 'contents', path_prefix='/api/libraries/:library_id', parent_resources=dict( member_name='library', collection_name='libraries' ) ) + webapp.api_mapper.resource( 'permission', + 'permissions', + path_prefix='/api/libraries/:library_id', + parent_resources=dict( member_name='library', collection_name='libraries' ) ) webapp.api_mapper.resource( 'library', 'libraries', path_prefix='/api' ) webapp.api_mapper.resource( 'sample', 'samples', path_prefix='/api' ) webapp.api_mapper.resource( 'request', 'requests', path_prefix='/api' ) http://bitbucket.org/galaxy/galaxy-central/changeset/e9c02513efcc/ changeset: e9c02513efcc user: jmchilton date: 2011-07-25 20:13:17 summary: Merged latest galaxy-central changes. affected #: 346 files (1.2 MB) Diff too large to display. http://bitbucket.org/galaxy/galaxy-central/changeset/87b627323347/ changeset: 87b627323347 user: jmchilton date: 2011-08-31 18:08:30 summary: Merged latest galaxy-central. affected #: 244 files (4.0 MB) Diff too large to display. http://bitbucket.org/galaxy/galaxy-central/changeset/9e77d9f39ff9/ changeset: 9e77d9f39ff9 user: jmchilton date: 2011-08-31 18:31:23 summary: Small whitespace fix for bug introduced by last merge. affected #: 1 file (1 byte) --- a/test/base/twilltestcase.py Wed Aug 31 11:08:30 2011 -0500 +++ b/test/base/twilltestcase.py Wed Aug 31 11:31:23 2011 -0500 @@ -691,7 +691,7 @@ delta = attributes.get('delta','100') s1 = len(data) s2 = os.path.getsize(local_name) - if abs(s1-s2) > int(delta): + if abs(s1-s2) > int(delta): raise Exception, 'Files %s=%db but %s=%db - compare (delta=%s) failed' % (temp_name,s1,local_name,s2,delta) elif compare == "contains": self.files_contains( local_name, temp_name, attributes=attributes ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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galaxy-commits September 2011