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[hg] galaxy 2433: Allow the uploading of composite datatypes. A...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/73a8b43f1d97 changeset: 2433:73a8b43f1d97 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Jun 08 12:49:26 2009 -0400 description: Allow the uploading of composite datatypes. A new grouping parameter, UploadDataset, is used to contain and process the file_data/url_paste/space_to_tab used to upload a file - multiple sets are displayed when uploading a composite datatype (similar to a repeat). Composite files can now be declared to the datatypes registry (required for proper uploading), but they are stored in the same manner as before (the extra_files_path) and should be backwards compatible. When uploading a composite datatype, only one dataset can be uploaded at a time. The ability to upload multiple datasets (url_paste (contents or urls) + file_data) for non-composite datatypes remains unchanged. A more structured way of storing these files (rather than dumping in a directory) is worth considering. 15 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/datatypes/genetics.py lib/galaxy/datatypes/registry.py lib/galaxy/tools/__init__.py lib/galaxy/tools/actions/upload.py lib/galaxy/tools/parameters/__init__.py lib/galaxy/tools/parameters/basic.py lib/galaxy/tools/parameters/grouping.py lib/galaxy/tools/parameters/validation.py lib/galaxy/util/__init__.py lib/galaxy/web/controllers/tool_runner.py lib/galaxy/web/form_builder.py templates/base_panels.mako templates/tool_form.mako tools/data_source/upload.xml diffs (1641 lines): diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Mon Jun 08 12:49:26 2009 -0400 @@ -1,5 +1,7 @@ import logging, os, sys, time, sets, tempfile from galaxy import util +from galaxy.util.odict import odict +from galaxy.util.bunch import Bunch from cgi import escape import metadata from metadata import MetadataElement #import directly to maintain ease of use in Datatype class definitions @@ -48,10 +50,16 @@ """If False, the peek is regenerated whenever a dataset of this type is copied""" copy_safe_peek = True + #Composite datatypes + composite_type = None + composite_files = odict() + primary_file_name = 'index' + def __init__(self, **kwd): """Initialize the datatype""" object.__init__(self, **kwd) self.supported_display_apps = self.supported_display_apps.copy() + self.composite_files = self.composite_files.copy() def write_from_stream(self, dataset, stream): """Writes data from a stream""" fd = open(dataset.file_name, 'wb') @@ -242,7 +250,49 @@ def after_edit( self, dataset ): """This function is called on the dataset after metadata is edited.""" dataset.clear_associated_files( metadata_safe = True ) - + def __new_composite_file( self, optional = False, mimetype = None, description = None, substitute_name_with_metadata = None, **kwds ): + kwds[ 'optional' ] = optional + kwds[ 'mimetype' ] = mimetype + kwds[ 'description' ] = description + kwds[ 'substitute_name_with_metadata' ] = substitute_name_with_metadata + return Bunch( **kwds ) + def add_composite_file( self, name, **kwds ): + #self.composite_files = self.composite_files.copy() + self.composite_files[ name ] = self.__new_composite_file( **kwds ) + + + def __substitute_composite_key( self, key, composite_file, dataset = None ): + if composite_file.substitute_name_with_metadata: + if dataset: + meta_value = str( dataset.metadata.get( composite_file.substitute_name_with_metadata ) ) + else: + meta_value = self.spec[composite_file.substitute_name_with_metadata].default + return key % meta_value + return key + @property + def writable_files( self, dataset = None ): + files = odict() + if self.composite_type != 'auto_primary_file': + files[ self.primary_file_name ] = self.__new_composite_file() + for key, value in self.get_composite_files( dataset = dataset ).iteritems(): + files[ key ] = value + return files + def get_composite_files( self, dataset = None ): + def substitute_composite_key( key, composite_file ): + if composite_file.substitute_name_with_metadata: + if dataset: + meta_value = str( dataset.metadata.get( composite_file.substitute_name_with_metadata ) ) + else: + meta_value = self.metadata_spec[ composite_file.substitute_name_with_metadata ].default + return key % meta_value + return key + files = odict() + for key, value in self.composite_files.iteritems(): + files[ substitute_composite_key( key, value ) ] = value + return files + def generate_auto_primary_file( self, dataset = None ): + raise Exception( "generate_auto_primary_file is not implemented for this datatype." ) + @property def has_resolution(self): return False diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/datatypes/genetics.py --- a/lib/galaxy/datatypes/genetics.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/datatypes/genetics.py Mon Jun 08 12:49:26 2009 -0400 @@ -117,15 +117,26 @@ """class to use for rgenetics""" """Add metadata elements""" - MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", readonly=True) + MetadataElement( name="base_name", desc="base name for all transformed versions of this genetic dataset", default="galaxy", readonly=True) file_ext="html" - + composite_type = 'auto_primary_file' + def missing_meta( self, dataset ): """Checks for empty meta values""" for key, value in dataset.metadata.items(): if not value: return True return False + + def generate_primary_file( self, dataset = None ): + rval = ['<html><head><title>Files for Composite Dataset (%s)</title></head><p/>This composite dataset is composed of the following files:<p/><ul>' % ( self.file_ext ) ] + for composite_name, composite_file in self.get_composite_files( dataset = dataset ).iteritems(): + opt_text = '' + if composite_file.optional: + opt_text = ' (optional)' + rval.append( '<li><a href="%s">%s</a>%s' % ( composite_name, composite_name, opt_text ) ) + rval.append( '</ul></html>' ) + return "\n".join( rval ) class SNPMatrix(Rgenetics): """fake class to distinguish different species of Rgenetics data collections @@ -148,6 +159,12 @@ """fake class to distinguish different species of Rgenetics data collections """ file_ext="lped" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.ped', description = 'Pedigree File', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.map', description = 'Map File', substitute_name_with_metadata = 'base_name' ) + class Pphe(Rgenetics): """fake class to distinguish different species of Rgenetics data collections @@ -180,11 +197,33 @@ """fake class to distinguish different species of Rgenetics data collections """ file_ext="pbed" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.bim', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.bed', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.fam', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name' ) + class Eigenstratgeno(Rgenetics): """fake class to distinguish different species of Rgenetics data collections """ file_ext="eigenstratgeno" + + def __init__( self, **kwd ): + Rgenetics.__init__( self, **kwd ) + self.add_composite_file( '%s.eigenstratgeno', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.ind', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s.map', substitute_name_with_metadata = 'base_name' ) + self.add_composite_file( '%s_fo.eigenstratgeno', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_fo.ind', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_fo.map', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_oo.eigenstratgeno', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_oo.ind', substitute_name_with_metadata = 'base_name', optional = 'True' ) + self.add_composite_file( '%s_oo.map', substitute_name_with_metadata = 'base_name', optional = 'True' ) + + class Eigenstratpca(Rgenetics): """fake class to distinguish different species of Rgenetics data collections diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Mon Jun 08 12:49:26 2009 -0400 @@ -67,6 +67,15 @@ indexer_config = indexer.get( 'file', None ) if indexer_config: self.indexers.append( (indexer_config, extension) ) + for composite_file in elem.findall( 'composite_file' ): + # add composite files + name = composite_file.get( 'name', None ) + if name is None: + log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) + optional = composite_file.get( 'optional', False ) + mimetype = composite_file.get( 'mimetype', None ) + self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) + except Exception, e: self.log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) ) # Load datatype sniffers from the config @@ -294,3 +303,7 @@ ret_data = None return ( convert_ext, ret_data ) return ( None, None ) + + def get_composite_extensions( self ): + return [ ext for ( ext, d_type ) in self.datatypes_by_extension.iteritems() if d_type.composite_type is not None ] + diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/__init__.py Mon Jun 08 12:49:26 2009 -0400 @@ -591,7 +591,7 @@ group = Repeat() group.name = elem.get( "name" ) group.title = elem.get( "title" ) - group.inputs = self.parse_input_elem( elem, enctypes, context ) + group.inputs = self.parse_input_elem( elem, enctypes, context ) rval[group.name] = group elif elem.tag == "conditional": group = Conditional() @@ -609,6 +609,16 @@ case.inputs = self.parse_input_elem( case_elem, enctypes, context ) group.cases.append( case ) rval[group.name] = group + elif elem.tag == "upload_dataset": + group = UploadDataset() + group.name = elem.get( "name" ) + 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 ) + rval[ group.file_type_name ].refresh_on_change = True + rval[ group.file_type_name ].refresh_on_change_values = self.app.datatypes_registry.get_composite_extensions() + group.inputs = self.parse_input_elem( elem, enctypes, context ) + rval[ group.name ] = group elif elem.tag == "param": param = self.parse_param_elem( elem, enctypes, context ) rval[param.name] = param @@ -951,6 +961,56 @@ group_state['__current_case__'] = current_case # Store the value of the test element group_state[ input.test_param.name ] = value + elif isinstance( input, UploadDataset ): + group_state = state[input.name] + group_errors = [] + group_old_errors = old_errors.get( input.name, None ) + any_group_errors = False + d_type = input.get_datatype( trans, context ) + writable_files = d_type.writable_files + #remove extra files + while len( group_state ) > len( writable_files ): + del group_state[-1] + if group_old_errors: + del group_old_errors[-1] + # Update state + max_index = -1 + for i, rep_state in enumerate( group_state ): + rep_index = rep_state['__index__'] + max_index = max( max_index, rep_index ) + rep_prefix = "%s_%d|" % ( key, rep_index ) + if group_old_errors: + rep_old_errors = group_old_errors[i] + else: + rep_old_errors = {} + rep_errors = self.update_state( trans, + input.inputs, + rep_state, + incoming, + prefix=rep_prefix, + context=context, + update_only=update_only, + old_errors=rep_old_errors, + changed_dependencies=changed_dependencies, + item_callback=item_callback ) + if rep_errors: + any_group_errors = True + group_errors.append( rep_errors ) + else: + group_errors.append( {} ) + #add new fileupload as needed + offset = 1 + while len( writable_files ) > len( group_state ): + new_state = {} + new_state['__index__'] = max_index + offset + offset += 1 + self.fill_in_new_state( trans, input.inputs, new_state, context ) + group_state.append( new_state ) + if any_group_errors: + group_errors.append( {} ) + # Were there *any* errors for any repetition? + if any_group_errors: + errors[input.name] = group_errors else: if key not in incoming \ and "__force_update__" + key not in incoming \ diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Mon Jun 08 12:49:26 2009 -0400 @@ -19,19 +19,15 @@ except: log.exception( 'failure removing temporary file: %s' % filename ) def execute( self, tool, trans, incoming={}, set_output_hid = True ): - data_file = incoming['file_data'] - file_type = incoming['file_type'] - dbkey = incoming['dbkey'] - url_paste = incoming['url_paste'] - is_multi_byte = False - space_to_tab = False - if 'space_to_tab' in incoming: - if incoming['space_to_tab'] not in ["None", None]: - space_to_tab = True + dataset_upload_inputs = [] + for input_name, input in tool.inputs.iteritems(): + if input.type == "upload_dataset": + dataset_upload_inputs.append( input ) + assert dataset_upload_inputs, Exception( "No dataset upload groups were found." ) # Get any precreated datasets (when using asynchronous uploads) async_datasets = [] self.precreated_datasets = [] - if incoming['async_datasets'] not in ["None", "", None]: + if incoming.get( 'async_datasets', None ) not in ["None", "", None]: async_datasets = incoming['async_datasets'].split(',') for id in async_datasets: try: @@ -45,8 +41,39 @@ log.error( 'Got a precreated dataset (%s) but it does not belong to current user (%s)' % ( data.id, trans.user.id ) ) else: self.precreated_datasets.append( data ) - temp_name = "" data_list = [] + for dataset_upload_input in dataset_upload_inputs: + uploaded_datasets = dataset_upload_input.get_uploaded_datasets( trans, incoming ) + for uploaded_dataset in uploaded_datasets: + precreated_dataset = self.get_precreated_dataset( uploaded_dataset.precreated_name ) + dataset = self.add_file( trans, uploaded_dataset.primary_file, uploaded_dataset.name, uploaded_dataset.file_type, uploaded_dataset.is_multi_byte, uploaded_dataset.dbkey, space_to_tab = uploaded_dataset.space_to_tab, info = uploaded_dataset.info, precreated_dataset = precreated_dataset ) + if uploaded_dataset.composite_files: + os.mkdir( dataset.extra_files_path ) #make extra files path + for name, value in uploaded_dataset.composite_files.iteritems(): + #what about binary files here, need to skip converting newlines + if value is None and not dataset.datatype.writable_files[ name ].optional: + dataset.info = "A required composite data file was not provided (%s)" % name + dataset.state = dataset.states.ERROR + break + elif value is not None: + if value.space_to_tab: + sniff.convert_newlines_sep2tabs( value.filename ) + else: + sniff.convert_newlines( value.filename ) + shutil.move( value.filename, os.path.join( dataset.extra_files_path, name ) ) + data_list.append( dataset ) + #clean up extra temp names + uploaded_dataset.clean_up_temp_files() + + #cleanup unclaimed precreated datasets: + for data in self.precreated_datasets: + log.info( 'Cleaned up unclaimed precreated dataset (%s).' % ( data.id ) ) + data.state = data.states.ERROR + data.info = 'No file contents were available.' + + if data_list: + trans.app.model.flush() + # Create the job object job = trans.app.model.Job() job.session_id = trans.get_galaxy_session().id @@ -56,104 +83,14 @@ # For backward compatibility, some tools may not have versions yet. job.tool_version = tool.version except: - job.tool_version = "1.0.0" + job.tool_version = "1.0.1" job.state = trans.app.model.Job.states.UPLOAD job.flush() log.info( 'tool %s created job id %d' % ( tool.id, job.id ) ) trans.log_event( 'created job id %d' % job.id, tool_id=tool.id ) - if 'local_filename' in dir( data_file ): - # Use the existing file - file_name = data_file.filename - file_name = file_name.split( '\\' )[-1] - file_name = file_name.split( '/' )[-1] - precreated_dataset = self.get_precreated_dataset( file_name ) - try: - data_list.append( self.add_file( trans, data_file.local_filename, file_name, file_type, is_multi_byte, dbkey, space_to_tab=space_to_tab, precreated_dataset=precreated_dataset ) ) - except Exception, e: - log.exception( 'exception in add_file using datafile.local_filename %s: %s' % ( data_file.local_filename, str( e ) ) ) - self.remove_tempfile( data_file.local_filename ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - elif 'filename' in dir( data_file ): - file_name = data_file.filename - file_name = file_name.split( '\\' )[-1] - file_name = file_name.split( '/' )[-1] - precreated_dataset = self.get_precreated_dataset( file_name ) - try: - temp_name, is_multi_byte = sniff.stream_to_file( data_file.file, prefix='upload' ) - except Exception, e: - log.exception( 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - try: - data_list.append( self.add_file( trans, temp_name, file_name, file_type, is_multi_byte, dbkey, space_to_tab=space_to_tab, precreated_dataset=precreated_dataset ) ) - except Exception, e: - log.exception( 'exception in add_file using file temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - if url_paste not in [ None, "" ]: - if url_paste.lstrip().lower().startswith( 'http://' ) or url_paste.lstrip().lower().startswith( 'ftp://' ): - # If we were sent a DATA_URL from an external application in a post, NAME and INFO - # values should be in the request - if 'NAME' in incoming and incoming[ 'NAME' ] not in [ "None", None ]: - NAME = incoming[ 'NAME' ] - else: - NAME = '' - if 'INFO' in incoming and incoming[ 'INFO' ] not in [ "None", None ]: - INFO = incoming[ 'INFO' ] - else: - INFO = "uploaded url" - url_paste = url_paste.replace( '\r', '' ).split( '\n' ) - name_set_from_line = False #if we are setting the name from the line, it needs to be the line that creates that dataset - for line in url_paste: - line = line.strip() - if line: - if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ): - continue # non-url line, ignore - if not NAME or name_set_from_line: - NAME = line - name_set_from_line = True - precreated_dataset = self.get_precreated_dataset( NAME ) - try: - temp_name, is_multi_byte = sniff.stream_to_file( urllib.urlopen( line ), prefix='url_paste' ) - except Exception, e: - log.exception( 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - try: - data_list.append( self.add_file( trans, temp_name, NAME, file_type, is_multi_byte, dbkey, info="uploaded url", space_to_tab=space_to_tab, precreated_dataset=precreated_dataset ) ) - except Exception, e: - log.exception( 'exception in add_file using url_paste temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - else: - precreated_dataset = self.get_precreated_dataset( 'Pasted Entry' ) - is_valid = False - for line in url_paste: - line = line.rstrip( '\r\n' ) - if line: - is_valid = True - break - if is_valid: - try: - temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( url_paste ), prefix='strio_url_paste' ) - except Exception, e: - log.exception( 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - try: - data_list.append( self.add_file( trans, temp_name, 'Pasted Entry', file_type, is_multi_byte, dbkey, info="pasted entry", space_to_tab=space_to_tab, precreated_dataset=precreated_dataset ) ) - except Exception, e: - log.exception( 'exception in add_file using StringIO.StringIO( url_paste ) temp_name %s: %s' % ( str( temp_name ), str( e ) ) ) - self.remove_tempfile( temp_name ) - return self.upload_empty( trans, job, "Error:", str( e ), precreated_dataset=precreated_dataset ) - else: - return self.upload_empty( trans, job, "No data error:", "you pasted no data.", precreated_dataset=precreated_dataset ) - if self.empty: - return self.upload_empty( trans, job, "Empty file error:", "you attempted to upload an empty file." ) - elif len( data_list ) < 1: - return self.upload_empty( trans, job, "No data error:", "either you pasted no data, the url you specified is invalid, or you have not specified a file." ) + #if we could make a 'real' job here, then metadata could be set before job.finish() is called - hda = data_list[0] #only our first hda is being added as input for the job, why? + hda = data_list[0] #only our first hda is being added as output for the job, why? job.state = trans.app.model.Job.states.OK file_size_str = datatypes.data.nice_size( hda.dataset.file_size ) job.info = "%s, size: %s" % ( hda.info, file_size_str ) @@ -162,7 +99,7 @@ log.info( 'job id %d ended ok, file size: %s' % ( job.id, file_size_str ) ) trans.log_event( 'job id %d ended ok, file size: %s' % ( job.id, file_size_str ), tool_id=tool.id ) return dict( output=hda ) - + def upload_empty(self, trans, job, err_code, err_msg, precreated_dataset = None): if precreated_dataset is not None: data = precreated_dataset @@ -188,7 +125,7 @@ trans.log_event( 'job id %d ended with errors, err_msg: %s' % ( job.id, err_msg ), tool_id=job.tool_id ) return dict( output=data ) - def add_file( self, trans, temp_name, file_name, file_type, is_multi_byte, dbkey, info=None, space_to_tab=False, precreated_dataset=None ): + def add_file( self, trans, temp_name, file_name, file_type, is_multi_byte, dbkey, info=None, space_to_tab=False, precreated_dataset=None ): data_type = None # See if we have an empty file if not os.path.getsize( temp_name ) > 0: @@ -254,7 +191,7 @@ data_type = 'binary' if not data_type: # We must have a text file - if self.check_html( temp_name ): + if trans.app.datatypes_registry.get_datatype_by_extension( file_type ).composite_type != 'auto_primary_file' and self.check_html( temp_name ): raise BadFileException( "you attempted to upload an inappropriate file." ) if data_type != 'binary' and data_type != 'zip': if space_to_tab: @@ -404,7 +341,7 @@ return self.precreated_datasets.pop( names.index( name ) ) else: return None - + class BadFileException( Exception ): pass diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/parameters/__init__.py --- a/lib/galaxy/tools/parameters/__init__.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/parameters/__init__.py Mon Jun 08 12:49:26 2009 -0400 @@ -20,7 +20,7 @@ be nice to unify all the places that recursively visit inputs. """ for input in inputs.itervalues(): - if isinstance( input, Repeat ): + if isinstance( input, Repeat ) or isinstance( input, UploadDataset ): for i, d in enumerate( input_values[ input.name ] ): index = d['__index__'] new_name_prefix = name_prefix + "%s_%d|" % ( input.name, index ) diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Jun 08 12:49:26 2009 -0400 @@ -23,6 +23,7 @@ def __init__( self, tool, param, context=None ): self.tool = tool self.refresh_on_change = False + self.refresh_on_change_values = [] self.name = param.get("name") self.type = param.get("type") self.label = util.xml_text(param, "label") @@ -301,7 +302,7 @@ self.name = elem.get( 'name' ) self.ajax = str_bool( elem.get( 'ajax-upload' ) ) def get_html_field( self, trans=None, value=None, other_values={} ): - return form_builder.FileField( self.name, self.ajax ) + return form_builder.FileField( self.name, ajax = self.ajax, value = value ) def from_html( self, value, trans=None, other_values={} ): # Middleware or proxies may encode files in special ways (TODO: this # should be pluggable) @@ -325,10 +326,11 @@ """ return "multipart/form-data" def to_string( self, value, app ): - if value is None: + if value in [ None, '' ]: return None - else: - raise Exception( "FileToolParameter cannot be persisted" ) + elif isinstance( value, unicode ) or isinstance( value, str ): + return value + raise Exception( "FileToolParameter cannot be persisted" ) def to_python( self, value, app ): if value is None: return None @@ -401,13 +403,13 @@ >>> print p.name blah >>> print p.get_html() - <select name="blah"> + <select name="blah" last_selected_value="y"> <option value="x">I am X</option> <option value="y" selected>I am Y</option> <option value="z">I am Z</option> </select> >>> print p.get_html( value="z" ) - <select name="blah"> + <select name="blah" last_selected_value="z"> <option value="x">I am X</option> <option value="y">I am Y</option> <option value="z" selected>I am Z</option> @@ -426,13 +428,13 @@ >>> print p.name blah >>> print p.get_html() - <select name="blah" multiple> + <select name="blah" multiple last_selected_value="z"> <option value="x">I am X</option> <option value="y" selected>I am Y</option> <option value="z" selected>I am Z</option> </select> >>> print p.get_html( value=["x","y"]) - <select name="blah" multiple> + <select name="blah" multiple last_selected_value="y"> <option value="x" selected>I am X</option> <option value="y" selected>I am Y</option> <option value="z">I am Z</option> @@ -520,7 +522,7 @@ return form_builder.TextField( self.name, value=(value or "") ) if value is not None: if not isinstance( value, list ): value = [ value ] - field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change ) + field = form_builder.SelectField( self.name, self.multiple, self.display, self.refresh_on_change, refresh_on_change_values = self.refresh_on_change_values ) options = self.get_options( trans, context ) for text, optval, selected in options: if isinstance( optval, UnvalidatedValue ): @@ -676,7 +678,7 @@ >>> # hg17 should be selected by default >>> print p.get_html( trans ) # doctest: +ELLIPSIS - <select name="blah"> + <select name="blah" last_selected_value="hg17"> <option value="?">unspecified (?)</option> ... <option value="hg18">Human Mar. 2006 (hg18)</option> @@ -687,7 +689,7 @@ >>> # If the user selected something else already, that should be used >>> # instead >>> print p.get_html( trans, value='hg18' ) # doctest: +ELLIPSIS - <select name="blah"> + <select name="blah" last_selected_value="hg18"> <option value="?">unspecified (?)</option> ... <option value="hg18" selected>Human Mar. 2006 (hg18)</option> @@ -942,7 +944,7 @@ return form_builder.TextArea( self.name, value=value ) else: return form_builder.TextField( self.name, value=(value or "") ) - return form_builder.DrillDownField( self.name, self.multiple, self.display, self.refresh_on_change, self.get_options( trans, value, other_values ), value ) + return form_builder.DrillDownField( self.name, self.multiple, self.display, self.refresh_on_change, self.get_options( trans, value, other_values ), value, refresh_on_change_values = self.refresh_on_change_values ) def from_html( self, value, trans=None, other_values={} ): if self.need_late_validation( trans, other_values ): @@ -1108,7 +1110,7 @@ if value is not None: if type( value ) != list: value = [ value ] - field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change ) + field = form_builder.SelectField( self.name, self.multiple, None, self.refresh_on_change, refresh_on_change_values = self.refresh_on_change_values ) # CRUCIAL: the dataset_collector function needs to be local to DataToolParameter.get_html_field() def dataset_collector( hdas, parent_hid ): for i, hda in enumerate( hdas ): diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/parameters/grouping.py --- a/lib/galaxy/tools/parameters/grouping.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/parameters/grouping.py Mon Jun 08 12:49:26 2009 -0400 @@ -4,6 +4,14 @@ from basic import ToolParameter from galaxy.util.expressions import ExpressionContext + +import logging +log = logging.getLogger( __name__ ) + +import StringIO, os, urllib +from galaxy.datatypes import sniff +from galaxy.util.bunch import Bunch +from galaxy.util.odict import odict class Group( object ): def __init__( self ): @@ -74,7 +82,322 @@ input.visit_inputs( new_prefix, d[input.name], callback ) def get_initial_value( self, trans, context ): return [] + +class UploadDataset( Group ): + type = "upload_dataset" + def __init__( self ): + Group.__init__( self ) + self.title = None + self.inputs = None + self.file_type_name = 'file_type' + self.default_file_type = 'txt' + self.file_type_to_ext = { 'auto':self.default_file_type } + def get_file_type( self, context ): + return context.get( self.file_type_name, self.default_file_type ) + def get_datatype_ext( self, trans, context ): + ext = self.get_file_type( context ) + if ext in self.file_type_to_ext: + ext = self.file_type_to_ext[ext] #when using autodetect, we will use composite info from 'text', i.e. only the main file + return ext + def get_datatype( self, trans, context ): + ext = self.get_datatype_ext( trans, context ) + return trans.app.datatypes_registry.get_datatype_by_extension( ext ) + @property + def title_plural( self ): + if self.title.endswith( "s" ): + return self.title + else: + return self.title + "s" + def group_title( self, context ): + return "%s (%s)" % ( self.title, context.get( self.file_type_name, self.default_file_type ) ) + def title_by_index( self, trans, index, context ): + d_type = self.get_datatype( trans, context ) + for i, ( composite_name, composite_file ) in enumerate( d_type.writable_files.iteritems() ): + if i == index: + rval = composite_name + if composite_file.description: + rval = "%s (%s)" % ( rval, composite_file.description ) + if composite_file.optional: + rval = "%s [optional]" % rval + return rval + return None + def value_to_basic( self, value, app ): + rval = [] + for d in value: + rval_dict = {} + # Propogate __index__ + if '__index__' in d: + rval_dict['__index__'] = d['__index__'] + for input in self.inputs.itervalues(): + rval_dict[ input.name ] = input.value_to_basic( d[input.name], app ) + rval.append( rval_dict ) + return rval + def value_from_basic( self, value, app, ignore_errors=False ): + rval = [] + for i, d in enumerate( value ): + rval_dict = {} + # If the special __index__ key is not set, create it (for backward + # compatibility) + rval_dict['__index__'] = d.get( '__index__', i ) + # Restore child inputs + for input in self.inputs.itervalues(): + if ignore_errors and input.name not in d: #this wasn't tested + rval_dict[ input.name ] = input.get_initial_value( None, d ) + else: + rval_dict[ input.name ] = input.value_from_basic( d[input.name], app, ignore_errors ) + rval.append( rval_dict ) + return rval + def visit_inputs( self, prefix, value, callback ): + for i, d in enumerate( value ): + for input in self.inputs.itervalues(): + new_prefix = prefix + "%s_%d|" % ( self.name, i ) + if isinstance( input, ToolParameter ): + callback( new_prefix, input, d[input.name], parent = d ) + else: + input.visit_inputs( new_prefix, d[input.name], callback ) + def get_initial_value( self, trans, context ): + d_type = self.get_datatype( trans, context ) + rval = [] + for i, ( composite_name, composite_file ) in enumerate( d_type.writable_files.iteritems() ): + rval_dict = {} + rval_dict['__index__'] = i # create __index__ + for input in self.inputs.itervalues(): + rval_dict[ input.name ] = input.get_initial_value( trans, context ) #input.value_to_basic( d[input.name], app ) + rval.append( rval_dict ) + return rval + def get_uploaded_datasets( self, trans, context, override_name = None, override_info = None ): + def get_data_file_filename( data_file, is_multi_byte = False, override_name = None, override_info = None ): + dataset_name = override_name + dataset_info = override_info + def get_file_name( file_name ): + file_name = file_name.split( '\\' )[-1] + file_name = file_name.split( '/' )[-1] + return file_name + if 'local_filename' in dir( data_file ): + # Use the existing file + return data_file.local_filename, get_file_name( data_file.filename ), is_multi_byte + elif 'filename' in dir( data_file ): + #create a new tempfile + try: + temp_name, is_multi_byte = sniff.stream_to_file( data_file.file, prefix='upload' ) + precreated_name = get_file_name( data_file.filename ) + if not dataset_name: + dataset_name = precreated_name + if not dataset_info: + dataset_info = 'uploaded file' + return temp_name, get_file_name( data_file.filename ), is_multi_byte, dataset_name, dataset_info + except Exception, e: + log.exception( 'exception in sniff.stream_to_file using file %s: %s' % ( data_file.filename, str( e ) ) ) + self.remove_temp_file( temp_name ) + return None, None, is_multi_byte, None, None + def filenames_from_url_paste( url_paste, group_incoming, override_name = None, override_info = None ): + filenames = [] + if url_paste not in [ None, "" ]: + if url_paste.lstrip().lower().startswith( 'http://' ) or url_paste.lstrip().lower().startswith( 'ftp://' ): + url_paste = url_paste.replace( '\r', '' ).split( '\n' ) + for line in url_paste: + line = line.strip() + if line: + if not line.lower().startswith( 'http://' ) and not line.lower().startswith( 'ftp://' ): + continue # non-url line, ignore + precreated_name = line + dataset_name = override_name + if not dataset_name: + dataset_name = line + dataset_info = override_info + if not dataset_info: + dataset_info = 'uploaded url' + try: + temp_name, is_multi_byte = sniff.stream_to_file( urllib.urlopen( line ), prefix='url_paste' ) + except Exception, e: + temp_name = None + precreated_name = str( e ) + log.exception( 'exception in sniff.stream_to_file using url_paste %s: %s' % ( url_paste, str( e ) ) ) + try: + self.remove_temp_file( temp_name ) + except: + pass + yield ( temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info ) + #yield ( None, str( e ), False, dataset_name, dataset_info ) + else: + dataset_name = dataset_info = precreated_name = 'Pasted Entry' #we need to differentiate between various url pastes here + if override_name: + dataset_name = override_name + if override_info: + dataset_info = override_info + is_valid = False + for line in url_paste: #Trim off empty lines from begining + line = line.rstrip( '\r\n' ) + if line: + is_valid = True + break + if is_valid: + try: + temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( url_paste ), prefix='strio_url_paste' ) + except Exception, e: + log.exception( 'exception in sniff.stream_to_file using StringIO.StringIO( url_paste ) %s: %s' % ( url_paste, str( e ) ) ) + temp_name = None + precreated_name = str( e ) + try: + self.remove_temp_file( temp_name ) + except: + pass + yield ( temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info ) + #yield ( None, str( e ), False, dataset_name, dataset_info ) + def get_one_filename( context ): + data_file = context['file_data'] + url_paste = context['url_paste'] + name = context.get( 'NAME', None ) + info = context.get( 'INFO', None ) + warnings = [] + is_multi_byte = False + space_to_tab = False + if context.get( 'space_to_tab', None ) not in ["None", None]: + space_to_tab = True + temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info = get_data_file_filename( data_file, is_multi_byte = is_multi_byte, override_name = name, override_info = info ) + if temp_name: + if url_paste.strip(): + warnings.append( "All file contents specified in the paste box were ignored." ) + else: #we need to use url_paste + #file_names = filenames_from_url_paste( url_paste, context, override_name = name, override_info = info ) + for temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info in filenames_from_url_paste( url_paste, context, override_name = name, override_info = info ):#file_names: + if temp_name: + break + ###this check will cause an additional file to be retrieved and created...so lets not do that + #try: #check to see if additional paste contents were available + # file_names.next() + # warnings.append( "Additional file contents were specified in the paste box, but ignored." ) + #except StopIteration: + # pass + return temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, warnings + + def get_filenames( context ): + rval = [] + data_file = context['file_data'] + url_paste = context['url_paste'] + name = context.get( 'NAME', None ) + info = context.get( 'INFO', None ) + warnings = [] + is_multi_byte = False + space_to_tab = False + if context.get( 'space_to_tab', None ) not in ["None", None]: + space_to_tab = True + temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info = get_data_file_filename( data_file, is_multi_byte = is_multi_byte, override_name = name, override_info = info ) + if temp_name: + rval.append( ( temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info ) ) + for temp_name, precreated_name, is_multi_byte, dataset_name, dataset_info in filenames_from_url_paste( url_paste, context, override_name = name, override_info = info ): + if temp_name: + rval.append( ( temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info ) ) + return rval + class UploadedDataset( Bunch ): + def __init__( self, **kwd ): + Bunch.__init__( self, **kwd ) + self.primary_file = None + self.composite_files = odict() + self.dbkey = None + self.warnings = [] + + self._temp_filenames = [] #store all created filenames here, delete on cleanup + def register_temp_file( self, filename ): + if isinstance( filename, list ): + self._temp_filenames.extend( filename ) + else: + self._temp_filenames.append( filename ) + def remove_temp_file( self, filename ): + try: + os.unlink( filename ) + except Exception, e: + pass + #log.warning( str( e ) ) + def clean_up_temp_files( self ): + for filename in self._temp_filenames: + self.remove_temp_file( filename ) + + file_type = self.get_file_type( context ) + d_type = self.get_datatype( trans, context ) + dbkey = context.get( 'dbkey', None ) + writable_files = d_type.writable_files + writable_files_offset = 0 + groups_incoming = [ None for filename in writable_files ] + for group_incoming in context.get( self.name, [] ): + i = int( group_incoming['__index__'] ) + groups_incoming[ i ] = group_incoming + + if d_type.composite_type is not None: + #handle uploading of composite datatypes + #Only one Dataset can be created + + dataset = UploadedDataset() + dataset.file_type = file_type + dataset.datatype = d_type + dataset.dbkey = dbkey + + temp_name = None + precreated_name = None + is_multi_byte = False + space_to_tab = False + warnings = [] + + dataset_name = None + dataset_info = None + if dataset.datatype.composite_type == 'auto_primary_file': + #replace sniff here with just creating an empty file + temp_name, is_multi_byte = sniff.stream_to_file( StringIO.StringIO( d_type.generate_primary_file() ), prefix='upload_auto_primary_file' ) + precreated_name = dataset_name = 'Uploaded Composite Dataset (%s)' % ( file_type ) + else: + temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, warnings = get_one_filename( groups_incoming[ 0 ] ) + writable_files_offset = 1 + if temp_name is None:#remove this before finish, this should create an empty dataset + raise Exception( 'No primary dataset file was available for composite upload' ) + dataset.primary_file = temp_name + dataset.is_multi_byte = is_multi_byte + dataset.space_to_tab = space_to_tab + dataset.precreated_name = precreated_name + dataset.name = dataset_name + dataset.info = dataset_info + dataset.warnings.extend( warnings ) + dataset.register_temp_file( temp_name ) + + keys = writable_files.keys() + for i, group_incoming in enumerate( groups_incoming[ writable_files_offset : ] ): + key = keys[ i + writable_files_offset ] + if group_incoming is None and not writable_files[ key ].optional: + dataset.warnings.append( "A required composite file (%s) was not specified." % ( key ) ) + dataset.composite_files[ key ] = None + else: + temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, warnings = get_one_filename( group_incoming ) + if temp_name: + dataset.composite_files[ key ] = Bunch( filename = temp_name, precreated_name = precreated_name, is_multi_byte = is_multi_byte, space_to_tab = space_to_tab, warnings = warnings, info = dataset_info, name = dataset_name ) + dataset.register_temp_file( temp_name ) + else: + dataset.composite_files[ key ] = None + if not writable_files[ key ].optional: + dataset.warnings.append( "A required composite file (%s) was not specified." % ( key ) ) + return [ dataset ] + else: + rval = [] + for temp_name, precreated_name, is_multi_byte, space_to_tab, dataset_name, dataset_info, in get_filenames( context[ self.name ][0] ): + dataset = UploadedDataset() + dataset.file_type = file_type + dataset.datatype = d_type + dataset.dbkey = dbkey + dataset.primary_file = temp_name + dataset.is_multi_byte = is_multi_byte + dataset.space_to_tab = space_to_tab + dataset.name = dataset_name + dataset.info = dataset_info + dataset.precreated_name = precreated_name + dataset.register_temp_file( temp_name ) + rval.append( dataset ) + return rval + def remove_temp_file( self, filename ): + try: + os.unlink( filename ) + except Exception, e: + log.warning( str( e ) ) + + class Conditional( Group ): type = "conditional" def __init__( self ): diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/tools/parameters/validation.py --- a/lib/galaxy/tools/parameters/validation.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/tools/parameters/validation.py Mon Jun 08 12:49:26 2009 -0400 @@ -72,14 +72,18 @@ """ @classmethod def from_element( cls, param, elem ): - return cls( elem.get( 'message' ), elem.text ) - def __init__( self, message, expression ): + return cls( elem.get( 'message' ), elem.text, elem.get( 'substitute_value_in_message' ) ) + def __init__( self, message, expression, substitute_value_in_message ): self.message = message + self.substitute_value_in_message = substitute_value_in_message # Save compiled expression, code objects are thread safe (right?) - self.expression = compile( expression, '<string>', 'eval' ) + self.expression = compile( expression, '<string>', 'eval' ) def validate( self, value, history=None ): if not( eval( self.expression, dict( value=value ) ) ): - raise ValueError( self.message ) + message = self.message + if self.substitute_value_in_message: + message = message % value + raise ValueError( message ) class InRangeValidator( Validator ): """ diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/util/__init__.py --- a/lib/galaxy/util/__init__.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/util/__init__.py Mon Jun 08 12:49:26 2009 -0400 @@ -146,6 +146,7 @@ elif isinstance( value, list ): return map(sanitize_text, value) else: + print value raise Exception, 'Unknown parameter type (%s)' % ( type( value ) ) class Params: @@ -222,7 +223,7 @@ pass if not value and not new_value: new_value = tool.param_trans_dict[ key ][1] - if key not in self.NEVER_SANITIZE and sanitize: + if sanitize and not ( key in self.NEVER_SANITIZE or True in [ key.endswith( "|%s" % nonsanitize_parameter ) for nonsanitize_parameter in self.NEVER_SANITIZE ] ): #sanitize check both ungrouped and grouped parameters by name self.__dict__[ new_key ] = sanitize_param( new_value ) else: self.__dict__[ new_key ] = new_value diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/web/controllers/tool_runner.py Mon Jun 08 12:49:26 2009 -0400 @@ -3,6 +3,8 @@ """ from galaxy.web.base.controller import * +from galaxy.util.bunch import Bunch +from galaxy.tools import DefaultToolState import logging log = logging.getLogger( __name__ ) @@ -75,32 +77,51 @@ tool = self.get_toolbox().tools_by_id.get( tool_id, None ) if not tool: return False # bad tool_id - params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool ) + #params = util.Params( kwd, sanitize=tool.options.sanitize, tool=tool ) + if "tool_state" in kwd: + encoded_state = util.string_to_object( kwd["tool_state"] ) + tool_state = DefaultToolState() + tool_state.decode( encoded_state, tool, trans.app ) + else: + tool_state = tool.new_state( trans ) + errors = tool.update_state( trans, tool.inputs, tool_state.inputs, kwd, update_only = True ) datasets = [] - if params.file_data not in [ None, "" ]: - name = params.file_data - if name.count('/'): - name = name.rsplit('/',1)[1] - if name.count('\\'): - name = name.rsplit('\\',1)[1] - datasets.append( create_dataset( name, trans.history ) ) - if params.url_paste not in [ None, "" ]: - url_paste = params.url_paste.replace( '\r', '' ).split( '\n' ) - url = False - for line in url_paste: - line = line.rstrip( '\r\n' ).strip() - if not line: - continue - elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ): - url = True - datasets.append( create_dataset( line, trans.history ) ) - else: - if url: - continue # non-url when we've already processed some urls - else: - # pasted data - datasets.append( create_dataset( 'Pasted Entry', trans.history ) ) - break + dataset_upload_inputs = [] + for input_name, input in tool.inputs.iteritems(): + if input.type == "upload_dataset": + dataset_upload_inputs.append( input ) + assert dataset_upload_inputs, Exception( "No dataset upload groups were found." ) + for dataset_upload_input in dataset_upload_inputs: + d_type = dataset_upload_input.get_datatype( trans, kwd ) + + if d_type.composite_type is not None: + datasets.append( create_dataset( 'Uploaded Composite Dataset (%s)' % dataset_upload_input.get_datatype_ext( trans, kwd ), trans.history ) ) + else: + params = Bunch( ** tool_state.inputs[dataset_upload_input.name][0] ) + if params.file_data not in [ None, "" ]: + name = params.file_data + if name.count('/'): + name = name.rsplit('/',1)[1] + if name.count('\\'): + name = name.rsplit('\\',1)[1] + datasets.append( create_dataset( name, trans.history ) ) + if params.url_paste not in [ None, "" ]: + url_paste = params.url_paste.replace( '\r', '' ).split( '\n' ) + url = False + for line in url_paste: + line = line.rstrip( '\r\n' ).strip() + if not line: + continue + elif line.lower().startswith( 'http://' ) or line.lower().startswith( 'ftp://' ): + url = True + datasets.append( create_dataset( line, trans.history ) ) + else: + if url: + continue # non-url when we've already processed some urls + else: + # pasted data + datasets.append( create_dataset( 'Pasted Entry', trans.history ) ) + break if datasets: trans.model.flush() return [ d.id for d in datasets ] diff -r c0c50620b89d -r 73a8b43f1d97 lib/galaxy/web/form_builder.py --- a/lib/galaxy/web/form_builder.py Mon Jun 08 12:35:38 2009 -0400 +++ b/lib/galaxy/web/form_builder.py Mon Jun 08 12:49:26 2009 -0400 @@ -78,17 +78,21 @@ >>> print FileField( "foo" ).get_html() <input type="file" name="foo"> - >>> print FileField( "foo", True ).get_html() + >>> print FileField( "foo", ajax = True ).get_html() <input type="file" name="foo" galaxy-ajax-upload="true"> """ - def __init__( self, name, ajax=False ): + def __init__( self, name, value = None, ajax=False ): self.name = name self.ajax = ajax + self.value = value def get_html( self, prefix="" ): + value_text = "" + if self.value: + value_text = ' value="%s"' % self.value + ajax_text = "" if self.ajax: - return '<input type="file" name="%s%s" galaxy-ajax-upload="true">' % ( prefix, self.name ) - else: - return '<input type="file" name="%s%s">' % ( prefix, self.name ) + ajax_text = ' galaxy-ajax-upload="true"' + return '<input type="file" name="%s%s"%s%s>' % ( prefix, self.name, ajax_text, value_text ) class HiddenField(BaseField): """ @@ -120,7 +124,7 @@ >>> t.add_option( "automatic", 3 ) >>> t.add_option( "bazooty", 4, selected=True ) >>> print t.get_html() - <select name="bar"> + <select name="bar" last_selected_value="4"> <option value="3">automatic</option> <option value="4" selected>bazooty</option> </select> @@ -140,7 +144,7 @@ <div><input type="checkbox" name="bar" value="3">automatic</div> <div><input type="checkbox" name="bar" value="4" checked>bazooty</div> """ - def __init__( self, name, multiple=None, display=None, refresh_on_change=False ): + def __init__( self, name, multiple=None, display=None, refresh_on_change = False, refresh_on_change_values = [] ): self.name = name self.multiple = multiple or False self.options = list() @@ -152,8 +156,11 @@ raise Exception, "Unknown display type: %s" % display self.display = display self.refresh_on_change = refresh_on_change + self.refresh_on_change_values = refresh_on_change_values if self.refresh_on_change: self.refresh_on_change_text = ' refresh_on_change="true"' + if self.refresh_on_change_values: + self.refresh_on_change_text = '%s refresh_on_change_values="%s"' % ( self.refresh_on_change_text, ",".join( self.refresh_on_change_values ) ) else: self.refresh_on_change_text = '' def add_option( self, text, value, selected = False ): @@ -195,11 +202,17 @@ def get_html_default( self, prefix="" ): if self.multiple: multiple = " multiple" else: multiple = "" - rval = [ '<select name="%s%s"%s%s>' % ( prefix, self.name, multiple, self.refresh_on_change_text ) ] + rval = [] + last_selected_value = "" for text, value, selected in self.options: - if selected: selected_text = " selected" + if selected: + selected_text = " selected" + last_selected_value = value else: selected_text = "" rval.append( '<option value="%s"%s>%s</option>' % ( value, selected_text, text ) ) + if last_selected_value: + last_selected_value = ' last_selected_value="%s"' % last_selected_value + rval.insert( 0, '<select name="%s%s"%s%s%s>' % ( prefix, self.name, multiple, self.refresh_on_change_text, last_selected_value ) ) rval.append( '</select>' ) return "\n".join( rval ) @@ -253,7 +266,7 @@ </li> </ul></div> """ - def __init__( self, name, multiple=None, display=None, refresh_on_change=False, options = [], value = [] ): + def __init__( self, name, multiple=None, display=None, refresh_on_change=False, options = [], value = [], refresh_on_change_values = [] ): self.name = name self.multiple = multiple or False self.options = options @@ -270,8 +283,11 @@ raise Exception, "Unknown display type: %s" % display self.display = display self.refresh_on_change = refresh_on_change + self.refresh_on_change_values = refresh_on_change_values if self.refresh_on_change: self.refresh_on_change_text = ' refresh_on_change="true"' + if self.refresh_on_change_values: + self.refresh_on_change_text = '%s refresh_on_change_values="%s"' % ( self.refresh_on_change_text, ",".join( self.refresh_on_change_values ) ) else: self.refresh_on_change_text = '' def get_html( self, prefix="" ): @@ -308,6 +324,7 @@ rval.append( '</ul></div>' ) return '\n'.join( rval ) + def get_suite(): """Get unittest suite for this module""" import doctest, sys diff -r c0c50620b89d -r 73a8b43f1d97 templates/base_panels.mako --- a/templates/base_panels.mako Mon Jun 08 12:35:38 2009 -0400 +++ b/templates/base_panels.mako Mon Jun 08 12:49:26 2009 -0400 @@ -59,19 +59,19 @@ <script type="text/javascript" src="${h.url_for('/static/scripts/galaxy.panels.js')}"></script> <script type="text/javascript"> - ensure_dd_helper(); + ensure_dd_helper(); - %if self.has_left_panel: + %if self.has_left_panel: var lp = make_left_panel( $("#left"), $("#center"), $("#left-border" ) ); force_left_panel = lp.force_panel; %endif - %if self.has_right_panel: + %if self.has_right_panel: var rp = make_right_panel( $("#right"), $("#center"), $("#right-border" ) ); handle_minwidth_hint = rp.handle_minwidth_hint; force_right_panel = rp.force_panel; %endif - + </script> ## Handle AJAX (actually hidden iframe) upload tool <![if !IE]> @@ -81,34 +81,36 @@ ##$(this.contentDocument).find("input[galaxy-ajax-upload]").each( function() { ##$("iframe")[0].contentDocument.body.innerHTML = "HELLO" ##$(this.contentWindow.document).find("input[galaxy-ajax-upload]").each( function() { - $(this).contents().find("input[galaxy-ajax-upload]").each( function() { - var error_set = false; - $(this).parents("form").submit( function() { - // Make a synchronous request to create the datasets first - var async_datasets; - $.ajax( { - async: false, - type: "POST", - url: "${h.url_for(controller='tool_runner', action='upload_async_create')}", - data: $(this).formSerialize(), - dataType: "json", - success: function( d, s ) { async_datasets = d.join() } - } ); - if (async_datasets == '') { - if (! error_set) { - $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage">No data was entered in the upload form. You may choose to upload a file, paste some data directly in the data box, or enter URL(s) to fetch from.</div><p/>' ); - error_set = true; + $(this).contents().find("form").each( function() { + if ( $(this).find("input[galaxy-ajax-upload]").length > 0 ){ + $(this).submit( function() { + var error_set = false; + // Make a synchronous request to create the datasets first + var async_datasets; + $.ajax( { + async: false, + type: "POST", + url: "${h.url_for(controller='tool_runner', action='upload_async_create')}", + data: $(this).formSerialize(), + dataType: "json", + success: function( d, s ) { async_datasets = d.join() } + } ); + if (async_datasets == '') { + if (! error_set) { + $("iframe#galaxy_main").contents().find("body").prepend( '<div class="errormessage">No data was entered in the upload form. You may choose to upload a file, paste some data directly in the data box, or enter URL(s) to fetch from.</div><p/>' ); + error_set = true; + } + return false; + } else { + $(this).find("input[name=async_datasets]").val( async_datasets ); + $(this).append("<input type='hidden' name='ajax_upload' value='true'>"); } + // iframe submit is required for nginx (otherwise the encoding is wrong) + $(this).ajaxSubmit( { iframe: true } ); + $("iframe#galaxy_main").attr("src","${h.url_for(controller='tool_runner', action='upload_async_message')}"); return false; - } else { - $(this).find("input[name=async_datasets]").val( async_datasets ); - $(this).append("<input type='hidden' name='ajax_upload' value='true'>"); - } - // iframe submit is required for nginx (otherwise the encoding is wrong) - $(this).ajaxSubmit( { iframe: true } ); - $("iframe#galaxy_main").attr("src","${h.url_for(controller='tool_runner', action='upload_async_message')}"); - return false; - }); + }); + } }); }); }); @@ -120,88 +122,88 @@ <%def name="masthead()"> <div class="title" style="float: left;"> - <a target="_blank" href="${app.config.wiki_url}"> - <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> - </a> - Galaxy - %if app.config.brand: - <span class='brand'>/${app.config.brand}</span> - %endif + <a target="_blank" href="${app.config.wiki_url}"> + <img border="0" src="${h.url_for('/static/images/galaxyIcon_noText.png')}" style="width: 26px; vertical-align: top;"> + </a> + Galaxy + %if app.config.brand: + <span class='brand'>/${app.config.brand}</span> + %endif </div> <div style="position: absolute; left: 50%;"> <div class="tab-group" style="position: relative; left: -50%;"> - - <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='' )"> - <% - cls = "tab" - if extra_class: - cls += " " + extra_class - if self.active_view == id: - cls += " active" - style = "" - if not visible: - style = "display: none;" - %> - <span class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></span> - </%def> - ## ${tab( "tracks", "View Data", h.url_for( controller='tracks', action='dbkeys' ), target="galaxy_main")} + <%def name="tab( id, display, href, target='_parent', visible=True, extra_class='' )"> + <% + cls = "tab" + if extra_class: + cls += " " + extra_class + if self.active_view == id: + cls += " active" + style = "" + if not visible: + style = "display: none;" + %> + <span class="${cls}" style="${style}"><a target="${target}" href="${href}">${display}</a></span> + </%def> + + ## ${tab( "tracks", "View Data", h.url_for( controller='tracks', action='dbkeys' ), target="galaxy_main")} - ${tab( "analysis", "Analyze Data", h.url_for( controller='root', action='index' ))} + ${tab( "analysis", "Analyze Data", h.url_for( controller='root', action='index' ))} - ${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))} + ${tab( "workflow", "Workflow", h.url_for( controller='workflow', action='index' ))} ${tab( "libraries", "Libraries", h.url_for( controller='library', action='index' ))} - ${tab( "admin", "Admin", h.url_for( controller='admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - - <span class="tab"> - <a>Help</a> - <div class="submenu"> - <ul> - <li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or suggestions</a></li> - <li><a target="_blank" href="${app.config.get( "wiki_url", "http://g2.trac.bx.psu.edu/" )}">Galaxy Wiki</a></li> - <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" )}">Video tutorials (screencasts)</a></li> - </ul> - </div> - </span> + ${tab( "admin", "Admin", h.url_for( controller='admin', action='index' ), extra_class="admin-only", visible=( trans.user and app.config.is_admin_user( trans.user ) ) )} - <span class="tab"> - <a>User</a> - <% - if trans.user: - user_email = trans.user.email - style1 = "display: none;" - style2 = ""; - else: - user_email = "" - style1 = "" - style2 = "display: none;" - %> - <div class="submenu"> - <ul class="loggedout-only" style="${style1}"> - <li><a target="galaxy_main" href="${h.url_for( controller='user', action='login' )}">Login</a></li> - %if app.config.allow_user_creation: - <li><a target="galaxy_main" href="${h.url_for( controller='user', action='create' )}">Register</a></li> - %endif - </ul> - <ul class="loggedin-only" style="${style2}"> - <li>Logged in as <span id="user-email">${user_email}</span></li> - <li><a target="galaxy_main" href="${h.url_for( controller='user', action='index' )}">Preferences</a></li> - <% - if app.config.require_login: - logout_target = "" - logout_url = h.url_for( controller='root', action='index', m_c='user', m_a='logout' ) - else: - logout_target = "galaxy_main" - logout_url = h.url_for( controller='user', action='logout' ) - %> - <li><a target="${logout_target}" href="${logout_url}">Logout</a></li> - </ul> - </div> - </span> - + <span class="tab"> + <a>Help</a> + <div class="submenu"> + <ul> + <li><a href="${app.config.get( "bugs_email", "mailto:galaxy-bugs@bx.psu.edu" )}">Email comments, bug reports, or suggestions</a></li> + <li><a target="_blank" href="${app.config.get( "wiki_url", "http://g2.trac.bx.psu.edu/" )}">Galaxy Wiki</a></li> + <li><a target="_blank" href="${app.config.get( "screencasts_url", "http://g2.trac.bx.psu.edu/wiki/ScreenCasts" )}">Video tutorials (screencasts)</a></li> + </ul> + </div> + </span> + + <span class="tab"> + <a>User</a> + <% + if trans.user: + user_email = trans.user.email + style1 = "display: none;" + style2 = ""; + else: + user_email = "" + style1 = "" + style2 = "display: none;" + %> + <div class="submenu"> + <ul class="loggedout-only" style="${style1}"> + <li><a target="galaxy_main" href="${h.url_for( controller='user', action='login' )}">Login</a></li> + %if app.config.allow_user_creation: + <li><a target="galaxy_main" href="${h.url_for( controller='user', action='create' )}">Register</a></li> + %endif + </ul> + <ul class="loggedin-only" style="${style2}"> + <li>Logged in as <span id="user-email">${user_email}</span></li> + <li><a target="galaxy_main" href="${h.url_for( controller='user', action='index' )}">Preferences</a></li> + <% + if app.config.require_login: + logout_target = "" + logout_url = h.url_for( controller='root', action='index', m_c='user', m_a='logout' ) + else: + logout_target = "galaxy_main" + logout_url = h.url_for( controller='user', action='logout' ) + %> + <li><a target="${logout_target}" href="${logout_url}">Logout</a></li> + </ul> + </div> + </span> + </div> </div> @@ -213,32 +215,32 @@ <div id="overlay" %if not self.overlay_visible: - style="display: none;" + style="display: none;" %endif > - ## - <div id="overlay-background" style="position: absolute; width: 100%; height: 100%;"></div> - - ## Need a table here for centering in IE6 - <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0" - %if not self.overlay_visible: - style="display: none;" - %endif - ><tr><td> - <div class="dialog-box-wrapper"> - <div class="dialog-box"> - <div class="unified-panel-header"> - <div class="unified-panel-header-inner"><span class='title'>${title}</span></div> - </div> - <div class="body" style="max-height: 600px; overflow: auto;">${content}</div> - <div> - <div class="buttons" style="display: none; float: right;"></div> - <div class="extra_buttons" style="display: none; padding: 5px;"></div> - <div style="clear: both;"></div> - </div> - </div> - </div> - </td></tr></table> + ## + <div id="overlay-background" style="position: absolute; width: 100%; height: 100%;"></div> + + ## Need a table here for centering in IE6 + <table class="dialog-box-container" border="0" cellpadding="0" cellspacing="0" + %if not self.overlay_visible: + style="display: none;" + %endif + ><tr><td> + <div class="dialog-box-wrapper"> + <div class="dialog-box"> + <div class="unified-panel-header"> + <div class="unified-panel-header-inner"><span class='title'>${title}</span></div> + </div> + <div class="body" style="max-height: 600px; overflow: auto;">${content}</div> + <div> + <div class="buttons" style="display: none; float: right;"></div> + <div class="extra_buttons" style="display: none; padding: 5px;"></div> + <div style="clear: both;"></div> + </div> + </div> + </div> + </td></tr></table> </div> </%def> @@ -268,7 +270,7 @@ ${self.message_box_content()} %endif </div> - ${self.overlay()} + ${self.overlay()} %if self.has_left_panel: <div id="left"> ${self.left_panel()} diff -r c0c50620b89d -r 73a8b43f1d97 templates/tool_form.mako --- a/templates/tool_form.mako Mon Jun 08 12:35:38 2009 -0400 +++ b/templates/tool_form.mako Mon Jun 08 12:49:26 2009 -0400 @@ -15,7 +15,39 @@ <script type="text/javascript"> $( function() { $( "select[refresh_on_change='true']").change( function() { - $( "#tool_form" ).submit(); + var refresh = false; + var refresh_on_change_values = $( this )[0].attributes.getNamedItem( 'refresh_on_change_values' ) + if ( refresh_on_change_values ) { + refresh_on_change_values = refresh_on_change_values.value.split( ',' ); + var last_selected_value = $( this )[0].attributes.getNamedItem( 'last_selected_value' ); + for( i= 0; i < refresh_on_change_values.length; i++ ) { + if ( $( this )[0].value == refresh_on_change_values[i] || ( last_selected_value && last_selected_value.value == refresh_on_change_values[i] ) ){ + refresh = true; + break; + } + } + } + else { + refresh = true; + } + if ( refresh ){ + $( ':file' ).each( function() { + var file_value = $( this )[0].value; + if ( file_value ) { + //disable file input, since we don't want to upload the file on refresh + var file_name = $( this )[0].name; + $( this )[0].name = 'replaced_file_input_' + file_name + $( this )[0].disable = true; + //create a new hidden field which stores the filename and has the original name of the file input + var new_file_input = document.createElement( 'input' ); + new_file_input.type = 'hidden'; + new_file_input.value = file_value; + new_file_input.name = file_name; + document.getElementById( 'tool_form' ).appendChild( new_file_input ); + } + } ); + $( "#tool_form" ).submit(); + } }); }); %if not add_frame.debug: @@ -72,6 +104,38 @@ %> ${row_for_param( group_prefix, input.test_param, group_state, group_errors, other_values )} ${do_inputs( input.cases[current_case].inputs, group_state, group_errors, group_prefix, other_values )} + %elif input.type == "upload_dataset": + %if input.get_datatype( trans, other_values ).composite_type is None: #have non-composite upload appear as before + <% + if input.name in errors: + rep_errors = errors[input.name][0] + else: + rep_errors = dict() + %> + ${do_inputs( input.inputs, tool_state[input.name][0], rep_errors, prefix + input.name + "_" + str( 0 ) + "|", other_values )} + %else: + <div class="repeat-group"> + <div class="form-title-row"><b>${input.group_title( other_values )}</b></div> + <% + repeat_state = tool_state[input.name] + %> + %for i in range( len( repeat_state ) ): + <div class="repeat-group-item"> + <% + if input.name in errors: + rep_errors = errors[input.name][i] + else: + rep_errors = dict() + index = repeat_state[i]['__index__'] + %> + <div class="form-title-row"><b>File Contents for ${input.title_by_index( trans, i, other_values )}</b></div> + ${do_inputs( input.inputs, repeat_state[i], rep_errors, prefix + input.name + "_" + str(index) + "|", other_values )} + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_${index}_remove" value="Remove ${input.title} ${i+1}"></div> + </div> + %endfor + ##<div class="form-row"><input type="submit" name="${prefix}${input.name}_add" value="Add new ${input.title}"></div> + </div> + %endif %else: ${row_for_param( prefix, input, tool_state, errors, other_values )} %endif @@ -127,7 +191,7 @@ <br/> %endif -<div class="toolForm" id="$tool.id"> +<div class="toolForm" id="${tool.id}"> %if tool.has_multiple_pages: <div class="toolFormTitle">${tool.name} (step ${tool_state.page+1} of ${tool.npages})</div> %else: diff -r c0c50620b89d -r 73a8b43f1d97 tools/data_source/upload.xml --- a/tools/data_source/upload.xml Mon Jun 08 12:35:38 2009 -0400 +++ b/tools/data_source/upload.xml Mon Jun 08 12:49:26 2009 -0400 @@ -1,17 +1,11 @@ <?xml version="1.0"?> -<tool name="Upload File" id="upload1"> +<tool name="Upload File" id="upload1" version="1.0.1"> <description> from your computer </description> <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> <inputs> - <param name="async_datasets" type="hidden" value="None"/> - <param name="file_data" type="file" size="30" label="File" ajax-upload="true"/> - <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> - <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."> - <option value="Yes">Yes</option> - </param> <param name="file_type" type="select" label="File Format" help="Which format? See help below"> <options from_parameter="tool.app.datatypes_registry.upload_file_formats" transform_lines="[ "%s%s%s" % ( line, self.separator, line ) for line in obj ]"> <column name="value" index="1"/> @@ -20,6 +14,16 @@ <filter type="add_value" name="Auto-detect" value="auto" index="0"/> </options> </param> + <param name="async_datasets" type="hidden" value="None"/> + <upload_dataset name="files" title="Specify Files for Dataset" file_type_name="file_type"> + <param name="file_data" type="file" size="30" label="File" ajax-upload="true"> + <validator type="expression" message="You will need to reselect the file you specified (%s)." substitute_value_in_message="True">not ( ( isinstance( value, unicode ) or isinstance( value, str ) ) and value != "" )</validator>  + </param> + <param name="url_paste" type="text" area="true" size="5x35" label="URL/Text" help="Here you may specify a list of URLs (one per line) or paste the contents of a file."/> + <param name="space_to_tab" type="select" display="checkboxes" multiple="True" label="Convert spaces to tabs" help="Use this option if you are entering intervals by hand."> + <option value="Yes">Yes</option> + </param> + </upload_dataset> <param name="dbkey" type="genomebuild" label="Genome" /> </inputs> <help>

1 0

[hg] galaxy 2432: Functional test fixes for purging a user.
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c0c50620b89d changeset: 2432:c0c50620b89d user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jun 08 12:35:38 2009 -0400 description: Functional test fixes for purging a user. 2 file(s) affected in this change: test/functional/test_history_functions.py test/functional/test_security_and_libraries.py diffs (215 lines): diff -r 1a24a530a3ae -r c0c50620b89d test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Mon Jun 08 10:31:59 2009 -0400 +++ b/test/functional/test_history_functions.py Mon Jun 08 12:35:38 2009 -0400 @@ -114,11 +114,10 @@ self.login( email=regular_user1.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) + # Need to delete history3_copy1 + self.delete_history( id=str( history3_copy1.id ) ) self.logout() self.login( email=admin_user.email ) - # Need to delete history3_copy1 - history3_copy1.deleted = True - history3_copy1.flush() # Test sharing a history with an invalid user email = 'jack(a)jill.com' check_str = '%s is not a valid Galaxy user.' % email @@ -138,48 +137,55 @@ self.share_history( id, email, check_str ) # We need to keep track of all shared histories so they can later be deleted history3_copy_name = "%s from %s" % ( history3.name, admin_user.email ) - history3_copies = galaxy.model.History \ + history3_to_use_for_regular_user2 = galaxy.model.History \ .filter( and_( galaxy.model.History.table.c.name==history3_copy_name, + galaxy.model.History.table.c.user_id==regular_user2.id, galaxy.model.History.table.c.deleted==False ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .limit( 2 ) \ - .all() - history3_copy2 = history3_copies[0] - history3_copy3 = history3_copies[1] - history4_copy_name = "%s from %s" % ( history4.name, admin_user.email ) - history4_copyies = galaxy.model.History \ - .filter( and_( galaxy.model.History.table.c.name==history4_copy_name, + .first() + assert history3_to_use_for_regular_user2 is not None, "Problem retrieving history3_to_use_for_regular_user2 from database" + history3_to_use_for_regular_user3 = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history3_copy_name, + galaxy.model.History.table.c.user_id==regular_user3.id, galaxy.model.History.table.c.deleted==False ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .limit( 2 ) \ - .all() - history4_copy1 = history4_copyies[0] - history4_copy2 = history4_copyies[1] + .first() + assert history3_to_use_for_regular_user3 is not None, "Problem retrieving history3_to_use_for_regular_user3 from database" + history4_copy_name = "%s from %s" % ( history4.name, admin_user.email ) + history4_to_use_for_regular_user2 = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history4_copy_name, + galaxy.model.History.table.c.user_id==regular_user2.id, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + assert history4_to_use_for_regular_user2 is not None, "Problem retrieving history4_to_use_for_regular_user2 from database" + history4_to_use_for_regular_user3 = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history4_copy_name, + galaxy.model.History.table.c.user_id==regular_user3.id, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + assert history4_to_use_for_regular_user3 is not None, "Problem retrieving history4_to_use_for_regular_user3 from database" self.logout() self.login( email=regular_user2.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) check_str = '%s from %s' % ( history4.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) + # Need to delete the copied histories, so later test runs are valid + self.delete_history( id=str( history3_to_use_for_regular_user2.id ) ) + self.delete_history( id=str( history4_to_use_for_regular_user2.id ) ) self.logout() self.login( email=regular_user3.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) check_str = '%s from %s' % ( history4.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) + # Need to delete the copied histories, so later test runs are valid + self.delete_history( id=str( history3_to_use_for_regular_user3.id ) ) + self.delete_history( id=str( history4_to_use_for_regular_user3.id ) ) self.logout() self.login( email=admin_user.email ) - # Need to delete the copied histories, so later test runs are valid - history3_copy2.deleted = True - history3_copy2.flush() - history3_copy3.deleted = True - history3_copy3.flush() - history4_copy1.deleted = True - history4_copy1.flush() - history4_copy1.deleted = True - history4_copy1.flush() - history4_copy2.deleted = True - history4_copy2.flush() def test_030_change_permissions_on_current_history( self ): """Testing changing permissions on the current history""" global history5 @@ -222,8 +228,7 @@ self.visit_url( "%s/history/list" % self.url ) self.check_page_for_string( history5_copy1.name ) # Need to delete history5_copy1 on the history list page for regular_user1 - history5_copy1.deleted = True - history5_copy1.flush() + self.delete_history( id=str( history5_copy1.id ) ) self.logout() self.login( email=admin_user.email ) def test_040_sharing_history_by_making_new_sharing_role( self ): @@ -278,8 +283,7 @@ # Make sure 2.bed is accessible since it is associated with a sharing role self.display_history_item( str( hda_2_bed.id ), check_str='chr1' ) # Need to delete history5_copy2 on the history list page for regular_user1 - history5_copy2.deleted = True - history5_copy2.flush() + self.delete_history( id=str( history5_copy2.id ) ) def test_045_sharing_private_history_with_multiple_users_by_changing_no_permissions( self ): """Testing sharing a restricted history with multiple users, making no permission changes""" self.logout() @@ -301,47 +305,44 @@ action_check_str=action_check_str ) # We need to keep track of all shared histories so they can later be deleted history5_copy_name = "%s from %s" % ( history5.name, admin_user.email ) - history5_copies = galaxy.model.History \ + history5_to_use_for_regular_user1 = galaxy.model.History \ .filter( and_( galaxy.model.History.table.c.name==history5_copy_name, + galaxy.model.History.table.c.user_id==regular_user1.id, galaxy.model.History.table.c.deleted==False ) ) \ .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ - .limit( 2 ) \ - .all() - history5_copy3 = history5_copies[0] - assert history5_copy3 is not None, "Problem retrieving history5_copy3 from database" - history5_copy4 = history5_copies[1] - assert history5_copy4 is not None, "Problem retrieving history5_copy4 from database" - # Make sure test1(a)bx.psu.edu received a copy of history5 with both datasets accessible - if history5_copy3.user_id == regular_user1.id: - history_to_use_for_regular_user_1 = history5_copy3 - history_to_use_for_regular_user_2 = history5_copy4 - elif history5_copy4.user_id == regular_user1.id: - history_to_use_for_regular_user_1 = history5_copy4 - history_to_use_for_regular_user_2 = history5_copy3 - else: - raise AssertionError, "Copies of history5 were not correctly associated with users" + .first() + assert history5_to_use_for_regular_user1 is not None, "Problem retrieving history5_to_use_for_regular_user1 from database" + history5_to_use_for_regular_user2 = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history5_copy_name, + galaxy.model.History.table.c.user_id==regular_user2.id, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .first() + assert history5_to_use_for_regular_user2 is not None, "Problem retrieving history5_to_use_for_regular_user2 from database" self.logout() self.login( email=regular_user1.email ) check_str = '%s from %s' % ( history5.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) - self.switch_history( id=str( history_to_use_for_regular_user_1.id ), name=history_to_use_for_regular_user_1.name ) + self.switch_history( id=str( history5_to_use_for_regular_user1.id ), name=history5_to_use_for_regular_user1.name ) self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) + # Need to delete the copied histories, so later test runs are valid + self.delete_history( id=str( history5_to_use_for_regular_user1.id ) ) self.logout() # Make sure test2(a)bx.psu.edu received a copy of history5, with only 1.bed accessible self.login( email=regular_user2.email ) self.view_stored_active_histories( check_str=check_str ) - self.switch_history( id=str( history_to_use_for_regular_user_2.id ), name=history_to_use_for_regular_user_2.name ) + self.switch_history( id=str( history5_to_use_for_regular_user2.id ), name=history5_to_use_for_regular_user2.name ) self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) # Get both new hdas from the db that were created for the shared history hda_1_bed = galaxy.model.HistoryDatasetAssociation \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy4.id, + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_to_use_for_regular_user1.id, galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ .first() assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" hda_2_bed = galaxy.model.HistoryDatasetAssociation \ - .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy4.id, + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_to_use_for_regular_user1.id, galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ .first() assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" @@ -355,10 +356,7 @@ pass self.check_history_for_string( 'You do not have permission to view this dataset' ) # Need to delete the copied histories, so later test runs are valid - history5_copy3.deleted = True - history5_copy3.flush() - history5_copy4.deleted = True - history5_copy4.flush() + self.delete_history( id=str( history5_to_use_for_regular_user2.id ) ) def test_050_sharing_private_history_by_choosing_to_not_share( self ): """Testing sharing a restricted history with multiple users by choosing not to share""" self.logout() diff -r 1a24a530a3ae -r c0c50620b89d test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Mon Jun 08 10:31:59 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Mon Jun 08 12:35:38 2009 -0400 @@ -1668,16 +1668,8 @@ history.refresh() if not history.deleted: raise AssertionError( 'User %s has active history id %d after their account was marked as purged.' % ( regular_user3.email, hda.id ) ) - # Make sure HistoryDatasetAssociation deleted - for hda in history.datasets: - hda.refresh() - if not hda.deleted: - raise AssertionError( 'HistoryDatasetAssociation id %d was not deleted.' % hda.id ) - # Make sure Dataset deleted - d = galaxy.model.Dataset.filter( galaxy.model.Dataset.table.c.id==hda.dataset_id ).first() - d.refresh() - if not d.deleted: - raise AssertionError( 'Dataset id %d was not deleted.' % d.id ) + # NOTE: Not all hdas / datasets will be deleted at the time a history is deleted - the cleanup_datasets.py script + # is responsible for this. # Make sure UserGroupAssociations deleted if regular_user3.groups: raise AssertionError( 'User %s has active group id %d after their account was marked as purged.' % ( regular_user3.email, uga.id ) )

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[hg] galaxy 2435: Update the way the testing framework decides w...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/3190f7d6b572 changeset: 2435:3190f7d6b572 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Jun 08 16:52:55 2009 -0400 description: Update the way the testing framework decides whether a refresh_on_change is required. 1 file(s) affected in this change: test/base/twilltestcase.py diffs (30 lines): diff -r 73d8b2acef0a -r 3190f7d6b572 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Jun 08 16:47:01 2009 -0400 +++ b/test/base/twilltestcase.py Mon Jun 08 16:52:55 2009 -0400 @@ -548,22 +548,11 @@ # Check for refresh_on_change attribute, submit a change if required if 'refresh_on_change' in control.attrs.keys(): changed = False - for elem in kwd[control.name]: - # For DataToolParameter, control.value is the index of the DataToolParameter select list, - # but elem is the filename. The following loop gets the filename of that index. - param_text = '' - for param in tc.show().split('<select'): - param = ('<select' + param.split('select>')[0] + 'select>').replace('selected', 'selected="yes"') - if param.find('on_chang') != -1 and param.find('name="%s"' % control.name) != -1: - tree = ElementTree.fromstring(param) - for option in tree.findall('option'): - if option.get('value') in control.value: - param_text = option.text.strip() - break - break - if elem not in control.value and param_text.find(elem) == -1 : + item_labels = [ item.attrs[ 'label' ] for item in control.get_items() if item.selected ] #For DataToolParameter, control.value is the HDA id, but kwd contains the filename. This loop gets the filename/label for the selected values. + for value in kwd[ control.name ]: + if value not in control.value and True not in [ value in item_label for item_label in item_labels ]: changed = True - break + break if changed: # Clear Control and set to proper value control.clear()

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[hg] galaxy 2434: Allow UnvalidatedValues to be used when genera...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/73d8b2acef0a changeset: 2434:73d8b2acef0a user: James Taylor <james(a)jamestaylor.org> date: Mon Jun 08 16:47:01 2009 -0400 description: Allow UnvalidatedValues to be used when generating output labels (fixes issue #59) 1 file(s) affected in this change: lib/galaxy/tools/parameters/basic.py diffs (38 lines): diff -r 73a8b43f1d97 -r 73d8b2acef0a lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Jun 08 12:49:26 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Mon Jun 08 16:47:01 2009 -0400 @@ -535,9 +535,10 @@ def from_html( self, value, trans=None, context={} ): if self.need_late_validation( trans, context ): if self.multiple: - #While it is generally allowed that a select value can be '', - #we do not allow this to be the case in a dynamically generated multiple select list being set in workflow building mode - #we instead treat '' as 'No option Selected' (None) + # While it is generally allowed that a select value can be '', + # we do not allow this to be the case in a dynamically + # generated multiple select list being set in workflow building + # mode we instead treat '' as 'No option Selected' (None) if value == '': value = None else: @@ -565,9 +566,9 @@ if isinstance( value, list ): if not(self.repeat): assert self.multiple, "Multiple values provided but parameter is not expecting multiple values" - return self.separator.join( value ) + return self.separator.join( map( str, value ) ) else: - return value + return str(value) def value_to_basic( self, value, app ): if isinstance( value, UnvalidatedValue ): return { "__class__": "UnvalidatedValue", "value": value.value } @@ -1331,6 +1332,8 @@ """ def __init__( self, value ): self.value = value + def __str__( self ): + return str( self.value ) class RuntimeValue( object ): """

1 0

[hg] galaxy 2427: Add EuPathDb data source tool config.
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/73847f425801 changeset: 2427:73847f425801 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jun 01 10:27:04 2009 -0400 description: Add EuPathDb data source tool config. 1 file(s) affected in this change: tools/data_source/eupathdb.xml diffs (36 lines): diff -r e50551db6e60 -r 73847f425801 tools/data_source/eupathdb.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/data_source/eupathdb.xml Mon Jun 01 10:27:04 2009 -0400 @@ -0,0 +1,32 @@ + +<tool name="EuPathDB" id="eupathdb" tool_type="data_source" url_method="post"> + <description>server</description> + <command interpreter="python">data_source.py $output</command> + <inputs action="http://galaxy.eupathdb.org/eupathdb.galaxy/queries_tools.jsp" check_values="false" method="post"> + <display>go to EuPathDB server $GALAXY_URL</display> + <param name="GALAXY_URL" type="baseurl" value="/tool_runner?tool_id=eupathdb" /> + </inputs> + <request_param_translation> + <request_param galaxy_name="URL" remote_name="URL" missing=""> + <add_to_url> + <param_from_source name="dbkey" missing="?" /> + <param_from_source name="wdk_history_id" missing="" /> + <param_from_source name="wdkReportFormat" missing="tabular" /> + <param_from_source name="selectedFields" missing="" /> + <param_from_source name="includeHeader" missing="yes" /> + <param_from_source name="downloadType" missing="plain" /> + </add_to_url> + </request_param> + <request_param galaxy_name="format" remote_name="wdkReportFormat" missing="tabular" /> + <request_param galaxy_name="dbkey" remote_name="dbkey" missing="?" /> + </request_param_translation> + <uihints minwidth="800"/> + <outputs> + <data name="output" format="txt" /> + </outputs> + <options sanitize="False" refresh="True"/> +</tool>

1 0

[hg] galaxy 2429: Revert upload.py - didn't mean to commit it.
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/8ac9be4bd716 changeset: 2429:8ac9be4bd716 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Jun 05 11:33:19 2009 -0400 description: Revert upload.py - didn't mean to commit it. 1 file(s) affected in this change: lib/galaxy/tools/actions/upload.py diffs (28 lines): diff -r 9a71b89082fe -r 8ac9be4bd716 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Fri Jun 05 11:15:25 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Fri Jun 05 11:33:19 2009 -0400 @@ -245,14 +245,12 @@ parts = file_name.split( "." ) if len( parts ) > 1: ext = parts[1].strip().lower() - if not( ext == 'ab1' or ext == 'scf' or ext == 'novoindex' ): + if not( ext == 'ab1' or ext == 'scf' ): raise BadFileException( "you attempted to upload an inappropriate file." ) if ext == 'ab1' and file_type != 'ab1': raise BadFileException( "you must manually set the 'File Format' to 'Ab1' when uploading ab1 files." ) elif ext == 'scf' and file_type != 'scf': raise BadFileException( "you must manually set the 'File Format' to 'Scf' when uploading scf files." ) - elif ext == 'novoindex' and file_type != 'novoindex': - raise BadFileException( "you must manually set the 'File Format' to 'NovoIndex' when uploading novoindex files." ) data_type = 'binary' if not data_type: # We must have a text file @@ -338,7 +336,7 @@ return ( False, False, None ) zip_file = zipfile.ZipFile( temp_name, "r" ) # Make sure the archive consists of valid files. The current rules are: - # 1. Archives can only include .ab1, .scf, or .txt files + # 1. Archives can only include .ab1, .scf or .txt files # 2. All file extensions within an archive must be the same name = zip_file.namelist()[0] test_ext = name.split( "." )[1].strip().lower()

1 0

[hg] galaxy 2430: Functional test fixes.
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/373962edbe90 changeset: 2430:373962edbe90 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Jun 05 16:48:03 2009 -0400 description: Functional test fixes. 2 file(s) affected in this change: test/functional/test_history_functions.py test/functional/test_security_and_libraries.py diffs (173 lines): diff -r 8ac9be4bd716 -r 373962edbe90 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Fri Jun 05 11:33:19 2009 -0400 +++ b/test/functional/test_history_functions.py Fri Jun 05 16:48:03 2009 -0400 @@ -24,9 +24,9 @@ global regular_user3 regular_user3 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test3(a)bx.psu.edu' ).first() assert regular_user3 is not None, 'Problem retrieving user with email "test3(a)bx.psu.edu" from the database' - self.logout() def test_005_deleting_histories( self ): """Testing deleting histories""" + self.logout() self.login( email='test(a)bx.psu.edu' ) global admin_user admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ).first() @@ -104,20 +104,18 @@ check_str = "You can't send histories to yourself." self.share_history( str( history3.id ), 'test(a)bx.psu.edu', check_str ) # Share a history with 1 valid user - name = history3.name - email = 'test1(a)bx.psu.edu' - check_str = 'Histories (%s) have been shared with: %s' % ( name, email ) - self.share_history( str( history3.id ), email, check_str ) + check_str = 'Histories (%s) have been shared with: %s' % ( history3.name, regular_user1.email ) + self.share_history( str( history3.id ), regular_user1.email, check_str ) # We need to keep track of all shared histories so they can later be deleted global history3_copy1 history3_copy1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() assert history3_copy1 is not None, "Problem retrieving history3_copy1 from database" self.logout() - self.login( email='test1(a)bx.psu.edu' ) - check_str = '%s from test(a)bx.psu.edu' % history3.name + self.login( email=regular_user1.email ) + check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) self.logout() - self.login( email='test(a)bx.psu.edu' ) + self.login( email=admin_user.email ) # Need to delete history3_copy1 history3_copy1.deleted = True history3_copy1.flush() @@ -135,7 +133,7 @@ self.upload_file( '2.bed', dbkey='hg18' ) id = '%s,%s' % ( str( history3.id ), str( history4.id ) ) name = '%s,%s' % ( history3.name, history4.name ) - email = 'test2@bx.psu.edu,test3@bx.psu.edu' + email = '%s,%s' % ( regular_user2.email, regular_user3.email ) check_str = 'Histories (%s) have been shared with: %s' % ( name, email ) self.share_history( id, email, check_str ) # We need to keep track of all shared histories so they can later be deleted @@ -158,19 +156,19 @@ history4_copy1 = history4_copyies[0] history4_copy2 = history4_copyies[1] self.logout() - self.login( email='test2(a)bx.psu.edu' ) + self.login( email=regular_user2.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) check_str = '%s from %s' % ( history4.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) self.logout() - self.login( email='test3(a)bx.psu.edu' ) + self.login( email=regular_user3.email ) check_str = '%s from %s' % ( history3.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) check_str = '%s from %s' % ( history4.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) self.logout() - self.login( email='test(a)bx.psu.edu' ) + self.login( email=admin_user.email ) # Need to delete the copied histories, so later test runs are valid history3_copy2.deleted = True history3_copy2.flush() @@ -213,6 +211,7 @@ raise AssertionError, "The 'access' permission is not set for history5_dataset1.actions" def test_035_sharing_history_by_making_datasets_public( self ): """Testing sharing a restricted history by making the datasets public""" + # We're still logged in as admin_user.email check_str = 'The following datasets can be shared with %s by updating their permissions' % regular_user1.email action_check_str = 'Histories (%s) have been shared with: %s' % ( history5.name, regular_user1.email ) self.share_history( str( history5.id ), regular_user1.email, check_str, action='public', action_check_str=action_check_str ) @@ -248,7 +247,13 @@ global sharing_role role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user1.email ) sharing_role = galaxy.model.Role.filter( galaxy.model.Role.table.c.name==role_name ).first() - assert sharing_role is not None, "Problem retrieving sharing_role from the database" + if not sharing_role: + # May have created a sharing role in a previous functional test suite from the opposite direction. + role_name = 'Sharing role for: %s, %s' % ( regular_user1.email, admin_user.email ) + sharing_role = galaxy.model.Role.filter( and_( galaxy.model.Role.table.c.type==role_type, + galaxy.model.Role.table.c.name==role_name ) ).first() + if not sharing_role: + raise AssertionError( "Privately sharing a dataset did not properly create a sharing role" ) self.logout() self.login( email=regular_user1.email ) self.visit_url( "%s/history/list" % self.url ) @@ -275,10 +280,10 @@ # Need to delete history5_copy2 on the history list page for regular_user1 history5_copy2.deleted = True history5_copy2.flush() + def test_045_sharing_private_history_with_multiple_users_by_changing_no_permissions( self ): + """Testing sharing a restricted history with multiple users, making no permission changes""" self.logout() self.login( email=admin_user.email ) - def test_045_sharing_private_history_with_multiple_users_by_changing_no_permissions( self ): - """Testing sharing a restricted history with multiple users, making no permission changes""" # History5 can be shared with any user, since it contains a public dataset. However, only # regular_user1 should be able to access history5's 2.bed dataset since it is associated with a # sharing role, and regular_user2 should be able to access history5's 1.bed, but not 2.bed even @@ -307,17 +312,26 @@ history5_copy4 = history5_copies[1] assert history5_copy4 is not None, "Problem retrieving history5_copy4 from database" # Make sure test1(a)bx.psu.edu received a copy of history5 with both datasets accessible + if history5_copy3.user_id == regular_user1.id: + history_to_use_for_regular_user_1 = history5_copy3 + history_to_use_for_regular_user_2 = history5_copy4 + elif history5_copy4.user_id == regular_user1.id: + history_to_use_for_regular_user_1 = history5_copy4 + history_to_use_for_regular_user_2 = history5_copy3 + else: + raise AssertionError, "Copies of history5 were not correctly associated with users" + self.logout() self.login( email=regular_user1.email ) check_str = '%s from %s' % ( history5.name, admin_user.email ) self.view_stored_active_histories( check_str=check_str ) - self.switch_history( id=str( history5_copy3.id ), name=history5_copy3.name ) + self.switch_history( id=str( history_to_use_for_regular_user_1.id ), name=history_to_use_for_regular_user_1.name ) self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) self.logout() # Make sure test2(a)bx.psu.edu received a copy of history5, with only 1.bed accessible self.login( email=regular_user2.email ) self.view_stored_active_histories( check_str=check_str ) - self.switch_history( id=str( history5_copy4.id ), name=history5_copy4.name ) + self.switch_history( id=str( history_to_use_for_regular_user_2.id ), name=history_to_use_for_regular_user_2.name ) self.check_history_for_string( '1.bed' ) self.check_history_for_string( '2.bed' ) # Get both new hdas from the db that were created for the shared history @@ -340,18 +354,15 @@ except: pass self.check_history_for_string( 'You do not have permission to view this dataset' ) - self.logout() - self.login( email='test(a)bx.psu.edu' ) # Need to delete the copied histories, so later test runs are valid history5_copy3.deleted = True history5_copy3.flush() history5_copy4.deleted = True history5_copy4.flush() - - - def test_050_sharing_private_history_by_choosing_to_not_share( self ): """Testing sharing a restricted history with multiple users by choosing not to share""" + self.logout() + self.login( email=admin_user.email ) self.switch_history( id=str( history5.id ), name=history5.name ) email = '%s,%s' % ( regular_user1.email, regular_user2.email ) check_str = 'The following datasets can be shared with %s with no changes' % email diff -r 8ac9be4bd716 -r 373962edbe90 test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Fri Jun 05 11:33:19 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Fri Jun 05 16:48:03 2009 -0400 @@ -170,6 +170,11 @@ global sharing_role sharing_role = galaxy.model.Role.filter( and_( galaxy.model.Role.table.c.type==role_type, galaxy.model.Role.table.c.name==role_name ) ).first() + if not sharing_role: + # May have created a sharing role in a previous functional test suite from the opposite direction. + role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user1.email ) + sharing_role = galaxy.model.Role.filter( and_( galaxy.model.Role.table.c.type==role_type, + galaxy.model.Role.table.c.name==role_name ) ).first() if not sharing_role: raise AssertionError( "Privately sharing a dataset did not properly create a sharing role" ) if len( sharing_role.users ) != 2:

1 0

[hg] galaxy 2428: Add ability to share histories with multiple u...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/9a71b89082fe changeset: 2428:9a71b89082fe user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Jun 05 11:15:25 2009 -0400 description: Add ability to share histories with multiple users, along with bug fixes and more functional test coverage for history features. 12 file(s) affected in this change: lib/galaxy/security/__init__.py lib/galaxy/tools/actions/upload.py lib/galaxy/web/controllers/history.py lib/galaxy/web/controllers/root.py lib/galaxy/web/framework/__init__.py scripts/cleanup_datasets/cleanup_datasets.py templates/history/rename.mako templates/history/share.mako test/base/twilltestcase.py test/functional/test_history_functions.py test/functional/test_security_and_libraries.py tool_conf.xml.sample diffs (1698 lines): diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/security/__init__.py Fri Jun 05 11:15:25 2009 -0400 @@ -51,6 +51,8 @@ def set_dataset_permission( self, dataset, permission ): raise "Unimplemented Method" def set_all_library_permissions( self, dataset, permissions ): + raise "Unimplemented Method" + def dataset_is_public( self, dataset ): raise "Unimplemented Method" def make_dataset_public( self, dataset ): raise "Unimplemented Method" @@ -296,6 +298,10 @@ # Add the new specific permission on the dataset for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: dp.flush() + def dataset_is_public( self, dataset ): + # A dataset is considered public if there are no "access" actions associated with it. Any + # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. + return self.permitted_actions.DATASET_ACCESS.action not in [ a.action for a in dataset.actions ] def make_dataset_public( self, dataset ): # A dataset is considered public if there are no "access" actions associated with it. Any # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Fri Jun 05 11:15:25 2009 -0400 @@ -245,12 +245,14 @@ parts = file_name.split( "." ) if len( parts ) > 1: ext = parts[1].strip().lower() - if not( ext == 'ab1' or ext == 'scf' ): + if not( ext == 'ab1' or ext == 'scf' or ext == 'novoindex' ): raise BadFileException( "you attempted to upload an inappropriate file." ) if ext == 'ab1' and file_type != 'ab1': raise BadFileException( "you must manually set the 'File Format' to 'Ab1' when uploading ab1 files." ) elif ext == 'scf' and file_type != 'scf': raise BadFileException( "you must manually set the 'File Format' to 'Scf' when uploading scf files." ) + elif ext == 'novoindex' and file_type != 'novoindex': + raise BadFileException( "you must manually set the 'File Format' to 'NovoIndex' when uploading novoindex files." ) data_type = 'binary' if not data_type: # We must have a text file @@ -336,7 +338,7 @@ return ( False, False, None ) zip_file = zipfile.ZipFile( temp_name, "r" ) # Make sure the archive consists of valid files. The current rules are: - # 1. Archives can only include .ab1, .scf or .txt files + # 1. Archives can only include .ab1, .scf, or .txt files # 2. All file extensions within an archive must be the same name = zip_file.namelist()[0] test_ext = name.split( "." )[1].strip().lower() diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Fri Jun 05 11:15:25 2009 -0400 @@ -1,6 +1,7 @@ from galaxy.web.base.controller import * from galaxy.web.framework.helpers import time_ago, iff, grids -import webhelpers +from galaxy import util +import webhelpers, logging from datetime import datetime from cgi import escape @@ -65,7 +66,6 @@ @web.expose def index( self, trans ): return "" - @web.expose def list_as_xml( self, trans ): """ @@ -78,9 +78,7 @@ @web.expose @web.require_login( "work with multiple histories" ) def list( self, trans, **kwargs ): - """ - List all available histories - """ + """List all available histories""" status = message = None if 'operation' in kwargs: operation = kwargs['operation'].lower() @@ -92,9 +90,7 @@ status, message = None, None refresh_history = False # Load the histories and ensure they all belong to the current user - history_ids = kwargs.get( 'id', [] ) - if type( history_ids ) is not list: - history_ids = [ history_ids ] + history_ids = util.listify( kwargs.get( 'id', [] ) ) histories = [] for hid in history_ids: history = model.History.get( hid ) @@ -117,17 +113,13 @@ trans.sa_session.flush() # Render the list view return self.list_grid( trans, status=status, message=message, **kwargs ) - def _list_delete( self, trans, histories ): """Delete histories""" n_deleted = 0 deleted_current = False for history in histories: if not history.deleted: - # Delete DefaultHistoryPermissions - for dhp in history.default_permissions: - dhp.delete() - dhp.flush() + # We'll not eliminate any DefaultHistoryPermissions in case we undelete the history later # Mark history as deleted in db history.deleted = True # If deleting the current history, make a new current. @@ -144,7 +136,6 @@ message_parts.append( "Your active history was deleted, a new empty history is now active.") status = INFO return ( status, " ".join( message_parts ) ) - def _list_undelete( self, trans, histories ): """Undelete histories""" n_undeleted = 0 @@ -154,6 +145,15 @@ n_already_purged += 1 if history.deleted: history.deleted = False + if not history.default_permissions: + # For backward compatibility - for a while we were deleting all DefaultHistoryPermissions on + # the history when we deleted the history. We are no longer doing this. + # Need to add default DefaultHistoryPermissions since they were deleted when the history was deleted + default_action = trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS + private_user_role = trans.app.security_agent.get_private_user_role( history.user ) + default_permissions = {} + default_permissions[ default_action ] = [ private_user_role ] + trans.app.security_agent.history_set_default_permissions( history, default_permissions ) n_undeleted += 1 trans.log_event( "History id %d marked as undeleted" % history.id ) status = SUCCESS @@ -164,7 +164,6 @@ message_parts.append( "%d have already been purged and cannot be undeleted." % n_already_purged ) status = WARNING return status, "".join( message_parts ) - def _list_switch( self, trans, histories ): """Switch to a new different history""" new_history = histories[0] @@ -179,13 +178,9 @@ trans.log_event( "History switched to id: %s, name: '%s'" % (str(new_history.id), new_history.name ) ) # No message return None, None - @web.expose def delete_current( self, trans ): - """ - Delete just the active history -- this does not require a logged - in user. - """ + """Delete just the active history -- this does not require a logged in user.""" history = trans.get_history() if not history.deleted: history.deleted = True @@ -195,7 +190,6 @@ # history active trans.new_history() return trans.show_ok_message( "History deleted, a new history is active" ) - @web.expose def rename_async( self, trans, id=None, new_name=None ): history = model.History.get( id ) @@ -209,11 +203,9 @@ # Rename history.name = new_name trans.sa_session.flush() - - ## These have been moved from 'root' but not cleaned up - @web.expose def imp( self, trans, id=None, confirm=False, **kwd ): + # TODO clean this up and make sure functionally correct msg = "" user = trans.get_user() user_history = trans.get_history() @@ -262,97 +254,159 @@ Warning! If you import this history, you will lose your current history. Click <a href="%s">here</a> to confirm. """ % web.url_for( id=id, confirm=True ) ) - @web.expose @web.require_login( "share histories with other users" ) def share( self, trans, id=None, email="", **kwd ): - send_to_err = "" - if not id: - id = trans.get_history().id - if not isinstance( id, list ): - id = [ id ] - histories = [] - history_names = [] - for hid in id: - histories.append( trans.app.model.History.get( hid ) ) - history_names.append(histories[-1].name) - if not email: - return trans.fill_template("/history/share.mako", histories=histories, email=email, send_to_err=send_to_err) - user = trans.get_user() - send_to_user = trans.app.model.User.filter( trans.app.model.User.table.c.email==email ).first() + # If a history contains both datasets that can be shared and others that cannot be shared with the desired user, + # then the entire history is shared, and the protected datasets will be visible, but inaccessible ( greyed out ) + # in the shared history params = util.Params( kwd ) action = params.get( 'action', None ) if action == "no_share": - trans.response.send_redirect( url_for( action='history_options' ) ) - if not send_to_user: - send_to_err = "No such user" - elif user.email == email: - send_to_err = "You can't send histories to yourself" - else: - if 'history_share_btn' in kwd or action != 'share': - # The user is attempting to share a history whose datasets cannot all be accessed by the other user. In this case, - # the user sharing the history can chose to make the datasets public ( action == 'public' ) if he has the authority - # to do so, or automatically create a new "sharing role" that allows the user to share his private datasets only with the - # desired user ( action == 'private' ). - can_change = {} - cannot_change = {} + trans.response.send_redirect( url_for( controller='root', action='history_options' ) ) + if not id: + id = trans.get_history().id + id = util.listify( id ) + send_to_err = "" + histories = [] + for hid in id: + histories.append( trans.app.model.History.get( hid ) ) + if not email: + return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err ) + user = trans.get_user() + send_to_users = [] + for email_address in util.listify( email ): + email_address = email_address.strip() + if email_address: + if email_address == user.email: + send_to_err += "You can't send histories to yourself. " + else: + send_to_user = trans.app.model.User.filter( trans.app.model.User.table.c.email==email_address ).first() + if send_to_user: + send_to_users.append( send_to_user ) + else: + send_to_err += "%s is not a valid Galaxy user. " % email_address + if not send_to_users: + if not send_to_err: + send_to_err += "%s is not a valid Galaxy user. " % email + return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err ) + if params.get( 'share_proceed_button', False ) and action == 'share': + # We need to filter out all histories that cannot be shared + filtered_histories = {} + for history in histories: + for send_to_user in send_to_users: + # Only deal with datasets that have not been purged + for hda in history.activatable_datasets: + # The history can be shared if it contains at least 1 public dataset or 1 dataset that the + # other user can access. Inaccessible datasets contained in the history will be displayed + # in the shared history, but "greyed out", so they cannot be viewed or used. + if trans.app.security_agent.dataset_is_public( hda.dataset ) or \ + trans.app.security_agent.allow_action( send_to_user, + trans.app.security_agent.permitted_actions.DATASET_ACCESS, + dataset=hda ): + if send_to_user in filtered_histories: + filtered_histories[ send_to_user ].append( history ) + else: + filtered_histories[ send_to_user ] = [ history ] + break + return self._share_histories( trans, user, send_to_users, send_to_err, filtered_histories=filtered_histories ) + elif params.get( 'history_share_btn', False ) or action != 'share': + # The user is attempting to share histories whose datasets cannot all be accessed by other users. In this case, + # the user sharing the histories can: + # 1) action=='public': chose to make the datasets public if he is permitted to do so + # 2) action=='private': automatically create a new "sharing role" allowing protected + # datasets to be accessed only by the desired users + # 3) action=='share': share only what can be shared when no permissions are changed - this case is handled above + # 4) action=='no_share': Do not share anything - this case is handled above. + can_change = {} + cannot_change = {} + no_change_needed = {} + for history in histories: + # Only deal with datasets that have not been purged + for hda in history.activatable_datasets: + if trans.app.security_agent.dataset_is_public( hda.dataset ): + if history not in no_change_needed: + no_change_needed[ history ] = [ hda ] + else: + no_change_needed[ history ].append( hda ) + elif not trans.app.security_agent.allow_action( send_to_user, + trans.app.security_agent.permitted_actions.DATASET_ACCESS, + dataset=hda ): + # The user with which we are sharing the history does not have access permission on the current dataset + if trans.app.security_agent.allow_action( user, + trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, + dataset=hda ) and not hda.dataset.library_associations: + # The current user has authority to change permissions on the current dataset because + # they have permission to manage permissions on the dataset and the dataset is not associated + # with a library. + if action == "private": + trans.app.security_agent.privately_share_dataset( hda.dataset, users=[ user, send_to_user ] ) + elif action == "public": + trans.app.security_agent.make_dataset_public( hda.dataset ) + elif history not in can_change: + # Build the set of histories / datasets on which the current user has authority + # to "manage permissions". This is used in /history/share.mako + can_change[ history ] = [ hda ] + else: + can_change[ history ].append( hda ) + else: + if action in [ "private", "public" ]: + # Don't change stuff that the user doesn't have permission to change + continue + elif history not in cannot_change: + # Build the set of histories / datasets on which the current user does + # not have authority to "manage permissions". This is used in /history/share.mako + cannot_change[ history ] = [ hda ] + else: + cannot_change[ history ].append( hda ) + if can_change or cannot_change: + return trans.fill_template( "/history/share.mako", + histories=histories, + email=email, + send_to_err=send_to_err, + can_change=can_change, + cannot_change=cannot_change, + no_change_needed=no_change_needed ) + return self._share_histories( trans, user, send_to_users, send_to_err, histories=histories ) + return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err ) + def _share_histories( self, trans, user, send_to_users, send_to_err, histories=[], filtered_histories={} ): + msg = "" + if not send_to_users: + msg = "No users have been specified with which to share histories" + sent_to_emails = [] + for sent_to_user in send_to_users: + sent_to_emails.append( sent_to_user.email ) + emails = ",".join( e for e in sent_to_emails ) + if not histories and not filtered_histories: + msg = "No histories can be sent to (%s) without changing dataset permissions associating a sharing role with them" % emails + elif histories: + history_names = [] + for history in histories: + history_names.append( history.name ) + for send_to_user in send_to_users: + new_history = history.copy( target_user=send_to_user ) + new_history.name = history.name + " from " + user.email + new_history.user_id = send_to_user.id + self.app.model.flush() + msg = "Histories (%s) have been shared with: %s. " % ( ",".join( history_names ), emails ) + elif filtered_histories: + # filtered_histories is a dictionary like: { user: [ history, history ], user: [ history ] } + for send_to_user, histories in filtered_histories.items(): + history_names = [] for history in histories: - for hda in history.activatable_datasets: - # Only deal with datasets that have not been purged - if not trans.app.security_agent.allow_action( send_to_user, - trans.app.security_agent.permitted_actions.DATASET_ACCESS, - dataset=hda ): - # The user with which we are sharing the history does not have access permission on the current dataset - if trans.app.security_agent.allow_action( user, - trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS, - dataset=hda ) and not hda.dataset.library_associations: - # The current user has authority to change permissions on the current dataset because - # they have permission to manage permissions on the dataset and the dataset is not associated - # with a library. - if action == "private": - trans.app.security_agent.privately_share_dataset( hda.dataset, users=[ user, send_to_user ] ) - elif action == "public": - trans.app.security_agent.make_dataset_public( hda.dataset ) - elif history not in can_change: - # Build the set of histories / datasets on which the current user has authority - # to "manage permissions". This is used in /history/share.mako - can_change[ history ] = [ hda ] - else: - can_change[ history ].append( hda ) - else: - if action in [ "private", "public" ]: - # Don't change stuff that the user doesn't have permission to change - continue - elif history not in cannot_change: - # Build the set of histories / datasets on which the current user does - # not have authority to "manage permissions". This is used in /history/share.mako - cannot_change[ history ] = [ hda ] - else: - cannot_change[ history ].append( hda ) - if can_change or cannot_change: - return trans.fill_template( "/history/share.mako", - histories=histories, - email=email, - send_to_err=send_to_err, - can_change=can_change, - cannot_change=cannot_change ) - for history in histories: - new_history = history.copy( target_user=send_to_user ) - new_history.name = history.name + " from " + user.email - new_history.user_id = send_to_user.id - trans.log_event( "History share, id: %s, name: '%s': to new id: %s" % ( str( history.id ), history.name, str( new_history.id ) ) ) - self.app.model.flush() - return trans.show_message( "History (%s) has been shared with: %s" % ( ",".join( history_names ),email ) ) - return trans.fill_template( "/history/share.mako", histories=histories, email=email, send_to_err=send_to_err ) - + history_names.append( history.name ) + new_history = history.copy( target_user=send_to_user ) + new_history.name = history.name + " from " + user.email + new_history.user_id = send_to_user.id + self.app.model.flush() + msg += "Histories (%s) have been shared with: %s. " % ( ",".join( history_names ), send_to_user.email ) + if send_to_err: + msg += send_to_err + return trans.show_message( msg ) @web.expose @web.require_login( "rename histories" ) def rename( self, trans, id=None, name=None, **kwd ): - if trans.app.memory_usage: - # Keep track of memory usage - m0 = self.app.memory_usage.memory() user = trans.get_user() - if not isinstance( id, list ): if id != None: id = [ id ] @@ -387,7 +441,4 @@ change_msg = change_msg + "<p>You must specify a valid name for History: "+cur_names[i]+"</p>" else: change_msg = change_msg + "<p>History: "+cur_names[i]+" does not appear to belong to you.</p>" - if self.app.memory_usage: - m1 = trans.app.memory_usage.memory( m0, pretty=True ) - log.info( "End of root/history_rename, memory used increased by %s" % m1 ) - return trans.show_message( "<p>%s" % change_msg, refresh_frames=['history'] ) \ No newline at end of file + return trans.show_message( "<p>%s" % change_msg, refresh_frames=['history'] ) diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Fri Jun 05 11:15:25 2009 -0400 @@ -349,14 +349,12 @@ """Displays a list of history related actions""" return trans.fill_template( "/history/options.mako", user = trans.get_user(), history = trans.get_history() ) - @web.expose def history_delete( self, trans, id ): """ Backward compatibility with check_galaxy script. """ return trans.webapp.controllers['history'].list( trans, id, operation='delete' ) - @web.expose def clear_history( self, trans ): """Clears the history for a user""" @@ -367,7 +365,6 @@ self.app.model.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) - @web.expose def history_import( self, trans, id=None, confirm=False, **kwd ): msg = "" @@ -417,13 +414,11 @@ Warning! If you import this history, you will lose your current history. Click <a href="%s">here</a> to confirm. """ % web.url_for( id=id, confirm=True ) ) - @web.expose - def history_new( self, trans ): - trans.new_history() + def history_new( self, trans, name=None ): + trans.new_history( name=name ) trans.log_event( "Created new History, id: %s." % str(trans.get_history().id) ) return trans.show_message( "New history created", refresh_frames = ['history'] ) - @web.expose def history_add_to( self, trans, history_id=None, file_data=None, name="Data Added to History",info=None,ext="txt",dbkey="?",copy_access_from=None,**kwd ): """Adds a POSTed file to a History""" @@ -455,13 +450,22 @@ except Exception, e: trans.log_event( "Failed to add dataset to history: %s" % ( e ) ) return trans.show_error_message("Adding File to History has Failed") - @web.expose - def history_set_default_permissions( self, trans, **kwd ): - """Sets the user's default permissions for the current history""" + def history_set_default_permissions( self, trans, id=None, **kwd ): + """Sets the permissions on a history""" if trans.user: if 'update_roles_button' in kwd: - history = trans.get_history() + history = None + if id: + try: + id = int( id ) + except: + id = None + if id: + history = trans.app.model.History.get( id ) + if not history: + # If we haven't retrieved a history, use the current one + history = trans.get_history() p = util.Params( kwd ) permissions = {} for k, v in trans.app.model.Dataset.permitted_actions.items(): @@ -478,7 +482,6 @@ else: #user not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change a history's default permissions." ) - @web.expose def dataset_make_primary( self, trans, id=None): """Copies a dataset and makes primary""" diff -r 73847f425801 -r 9a71b89082fe lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Mon Jun 01 10:27:04 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Fri Jun 05 11:15:25 2009 -0400 @@ -432,13 +432,15 @@ self.galaxy_session.current_history = history self.sa_session.flush( [ self.galaxy_session ] ) history = property( get_history, set_history ) - def new_history( self ): + def new_history( self, name=None ): """ Create a new history and associate it with the current session and its associated user (if set). """ # Create new history history = self.app.model.History() + if name: + history.name = name # Associate with session history.add_galaxy_session( self.galaxy_session ) # Make it the session's current history diff -r 73847f425801 -r 9a71b89082fe scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Mon Jun 01 10:27:04 2009 -0400 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Fri Jun 05 11:15:25 2009 -0400 @@ -123,6 +123,11 @@ for dataset_assoc in history.datasets: _purge_dataset_instance( dataset_assoc, app, remove_from_disk, info_only = info_only ) #mark a DatasetInstance as deleted, clear associated files, and mark the Dataset as deleted if it is deletable if not info_only: + # TODO: should the Delete DefaultHistoryPermissions be deleted here? This was incorrectly + # done in the _list_delete() method of the history controller, so copied it here. Not sure + # if we should ever delete info like this from the db though, so commented out for now... + #for dhp in history.default_permissions: + # dhp.delete() history.purged = True print "%d" % history.id history_count += 1 @@ -226,7 +231,6 @@ print "# This Dataset (%i) is not deletable, associated Metadata Files will not be removed.\n" % ( dataset.id ) else: # Mark all associated MetadataFiles as deleted and purged and remove them from disk - print "The following metadata files attached to associations of Dataset '%s' have been purged:" % dataset.id metadata_files = [] #lets create a list of metadata files, then perform actions on them for hda in dataset.history_associations: @@ -236,6 +240,7 @@ for metadata_file in app.model.MetadataFile.filter( app.model.MetadataFile.table.c.lda_id==lda.id ).all(): metadata_files.append( metadata_file ) for metadata_file in metadata_files: + print "# The following metadata files attached to associations of Dataset '%s' have been purged:" % dataset.id if not info_only: if remove_from_disk: try: @@ -248,7 +253,6 @@ print "%s" % metadata_file.file_name print dataset.deleted = True - #dataset.flush() app.model.flush() def _purge_dataset( dataset, remove_from_disk, info_only = False ): @@ -259,6 +263,7 @@ if not info_only: # Remove files from disk and update the database if remove_from_disk: + # TODO: should permissions on the dataset be deleted here? os.unlink( dataset.file_name ) # Remove associated extra files from disk if they exist if dataset.extra_files_path and os.path.exists( dataset.extra_files_path ): @@ -286,6 +291,7 @@ for sub_folder in folder.folders: _purge_folder( sub_folder, app, remove_from_disk, info_only = info_only ) if not info_only: + # TODO: should the folder permissions be deleted here? folder.purged = True folder.flush() diff -r 73847f425801 -r 9a71b89082fe templates/history/rename.mako --- a/templates/history/rename.mako Mon Jun 01 10:27:04 2009 -0400 +++ b/templates/history/rename.mako Fri Jun 05 11:15:25 2009 -0400 @@ -4,17 +4,38 @@ <div class="toolForm"> <div class="toolFormTitle">${_('Rename History')}</div> - <div class="toolFormBody"> - <form action="${h.url_for( controller='history', action='rename' )}" method="post" > - <table> - <tr><th>${_('Current Name')}</th><th>${_('New Name')}</th></tr> - %for history in histories: - <tr><td>${history.name}<input type="hidden" name="id" value="${history.id}"></td><td><input type="text" name="name" value="${history.name}" size="40"></td></tr> - %endfor - <tr><td colspan="2"><input type="submit" name="history_rename_btn" value="${_('Rename Histories')}"></td></tr> - </table> - </form> - </div> + <div class="toolFormBody"> + <form action="${h.url_for( controller='history', action='rename' )}" method="post" > + <table class="grid"> + %for history in histories: + <tr> + <td> + <div class="form-row"> + <input type="hidden" name="id" value="${history.id}"> + <label>${_('Current Name')}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${history.name} + </div> + </div> + </td> + <td> + <div class="form-row"> + <label>${_('New Name')}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="name" value="${history.name}" size="40"> + </div> + </div> + </td> + </tr> + %endfor + <tr> + <td colspan="2"> + <div class="form-row"> + <input type="submit" name="history_rename_btn" value="${_('Rename Histories')}"> + </div> + </td> + </tr> + </table> + </form> + </div> </div> -</body> -</html> \ No newline at end of file diff -r 73847f425801 -r 9a71b89082fe templates/history/share.mako --- a/templates/history/share.mako Mon Jun 01 10:27:04 2009 -0400 +++ b/templates/history/share.mako Fri Jun 05 11:15:25 2009 -0400 @@ -2,117 +2,173 @@ <%inherit file="/base.mako"/> <%def name="title()">Share histories</%def> -%if not can_change and not cannot_change: - <div class="toolForm"> - <div class="toolFormTitle">${_('Share histories')}</div> - <table> +<div class="toolForm"> + <div class="toolFormTitle">Share ${len( histories)} histories</div> + <div class="toolFormBody"> + %if not can_change and not cannot_change: <form action="${h.url_for( controller="history", action='share' )}" method="post" > - <tr><th>${_('History Name:')}</td><th>${_('Number of Datasets:')}</th><th>${_('Share Link')}</th></tr> %for history in histories: - <tr> - <td align="center">${history.name}<input type="hidden" name="id" value="${history.id}"></td> - <td align="center"> - %if len( history.datasets ) < 1: - <div class="warningmark">${_('This history contains no data.')}</div> - %else: - ${len(history.datasets)} - %endif - </td> - <td align="center"><a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">${_('copy link to share')}</a></td> - </tr> + <div class="toolForm"> + <div class="form-row"> + <label>${_('History Name:')}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + ${history.name}<input type="hidden" name="id" value="${history.id}"> + </div> + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>${_('Number of Datasets:')}</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + %if len( history.datasets ) < 1: + <div class="warningmark">${_('This history contains no data.')}</div> + %else: + ${len(history.datasets)} + %endif + </td> + </div> + </div> + ## TODO: this feature is not currently working + ##<div style="clear: both"></div> + ##<div class="form-row"> + ## <label>${_('Share Link')}</label> + ## <div style="float: left; width: 250px; margin-right: 10px;"> + ## <a href="${h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id) )}">${_('copy link to share')}</a> + ## </div> + ##</div> + ##<div style="clear: both"></div> + <p/> + </div> %endfor - <tr><td>${_('Email of User to share with:')}</td><td><input type="text" name="email" value="${email}" size="40"></td></tr> + <p/> + <div style="clear: both"></div> + <div class="form-row"> + <label>Galaxy user emails with which to share histories</label> + <div style="float: left; width: 250px; margin-right: 10px;"> + <input type="text" name="email" value="${email}" size="40"> + </div> + <div class="toolParamHelp" style="clear: both;"> + Enter a Galaxy user email address or a comma-separated list of addresses if sharing with multiple users + </div> + </div> %if send_to_err: - <tr><td colspan="100%"><div class="errormessage">${send_to_err}</div></td></tr> + <div style="clear: both"></div> + <div class="form-row"> + <div class="errormessage">${send_to_err}</div> + </div> %endif - <tr><td colspan="2" align="right"><input type="submit" name="history_share_btn" value="Submit"></td></tr> + <div style="clear: both"></div> + <div class="form-row"> + <input type="submit" name="history_share_btn" value="Submit"> + </div> </form> - </table> + %else: + <form action="${h.url_for( controller='history', action='share' )}" method="post"> + %for history in histories: + <input type="hidden" name="id" value="${history.id}"> + %endfor + <input type="hidden" name="email" value="${email}"> + %if no_change_needed: + <div style="clear: both"></div> + <div class="form-row"> + <div class="donemessage"> + The following datasets can be shared with ${email} with no changes + </div> + </div> + %for history, hdas in no_change_needed.items(): + <div class="form-row"> + <label>History</label> + ${history.name} + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Datasets</label> + </div> + %for hda in hdas: + <div class="form-row"> + ${hda.name} + </div> + %endfor + %endfor + %endif + %if can_change: + <div style="clear: both"></div> + <div class="form-row"> + <div class="warningmessage"> + The following datasets can be shared with ${email} by updating their permissions + </div> + </div> + %for history, hdas in can_change.items(): + <div class="form-row"> + <label>History</label> + ${history.name} + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Datasets</label> + </div> + %for hda in hdas: + <div class="form-row"> + ${hda.name} + </div> + %endfor + %endfor + %endif + %if cannot_change: + <div style="clear: both"></div> + <div class="form-row"> + <div class="errormessage"> + The following datasets cannot be shared with ${email} because you are not authorized to + change the permissions on them + </div> + </div> + %for history, hdas in cannot_change.items(): + <div class="form-row"> + <label>History</label> + ${history.name} + </div> + <div style="clear: both"></div> + <div class="form-row"> + <label>Datasets</label> + </div> + %for hda in hdas: + <div class="form-row"> + ${hda.name} + </div> + %endfor + %endfor + %endif + <div class="form-row"> + <label>How would you like to proceed?</label> + </div> + %if can_change: + <div class="form-row"> + <input type="radio" name="action" value="public"> Make datasets public so anyone can access them + %if cannot_change: + (where possible) + %endif + </div> + <div class="form-row"> + <input type="radio" name="action" value="private"> Make datasets private to me and the user(s) with whom I am sharing + %if cannot_change: + (where possible) + %endif + </div> + %endif + %if no_change_needed: + <div class="form-row"> + <input type="radio" name="action" value="share"> Share anyway + %if can_change: + (don't change any permissions) + %endif + </div> + %endif + <div class="form-row"> + <input type="radio" name="action" value="no_share"> Don't share + </div> + <div class="form-row"> + <input type="submit" name="share_proceed_button" value="Go"><br/> + </div> + </form> + %endif </div> -%else: - <style type="text/css"> - th - { - text-align: left; - } - td - { - vertical-align: top; - } - </style> - <form action="${h.url_for( controller='history', action='share' )}" method="post"> - %for history in histories: - <input type="hidden" name="id" value="${history.id}"> - %endfor - <input type="hidden" name="email" value="${email}"> - <div class="warningmessage"> - The history or histories you've chosen to share contain datasets that the user with which you're sharing does not have permission to access. - These datasets are shown below. Datasets that the user has permission to access are not shown. - </div> - <p/> - %if can_change: - <div class="donemessage"> - The following datasets can be shared with ${email} by updating their permissions: - <p/> - <table cellpadding="0" cellspacing="8" border="0"> - <tr><th>Histories</th><th>Datasets</th></tr> - %for history, datasets in can_change.items(): - <tr> - <td>${history.name}</td> - <td> - %for dataset in datasets: - ${dataset.name}<br/> - %endfor - </td> - </tr> - %endfor - </table> - </div> - <p/> - %endif - %if cannot_change: - <div class="errormessage"> - The following datasets cannot be shared with ${email} because you are not authorized to change the permissions on them. - <p/> - <table cellpadding="0" cellspacing="8" border="0"> - <tr><th>Histories</th><th>Datasets</th></tr> - %for history, datasets in cannot_change.items(): - <tr> - <td>${history.name}</td> - <td> - %for dataset in datasets: - ${dataset.name}<br/> - %endfor - </td> - </tr> - %endfor - </table> - </div> - <p/> - %endif - <div> - <b>How would you like to proceed?</b> - <p/> - %if can_change: - <input type="radio" name="action" value="public"> Set datasets above to public access - %if cannot_change: - (where possible) - %endif - <br/> - <input type="radio" name="action" value="private"> Set datasets above to private access for me and the user(s) with whom I am sharing - %if cannot_change: - (where possible) - %endif - <br/> - %endif - <input type="radio" name="action" value="share"> Share anyway - %if can_change: - (don't change any permissions) - %endif - <br/> - <input type="radio" name="action" value="no_share"> Don't share<br/> - <br/> - <input type="submit" name="submit" value="Ok"><br/> - </div> - </form> -%endif +</div> diff -r 73847f425801 -r 9a71b89082fe test/base/twilltestcase.py --- a/test/base/twilltestcase.py Mon Jun 01 10:27:04 2009 -0400 +++ b/test/base/twilltestcase.py Fri Jun 05 11:15:25 2009 -0400 @@ -103,41 +103,42 @@ page = self.last_page() if page.find( 'error' ) > -1: raise AssertionError('Errors in the history for user %s' % self.user ) - def check_history_for_string( self, patt ): """Looks for 'string' in history page""" self.home() self.visit_page( "history" ) for subpatt in patt.split(): tc.find(subpatt) - + self.home() def clear_history( self ): """Empties a history of all datasets""" self.visit_page( "clear_history" ) self.check_history_for_string( 'Your history is empty' ) - - def delete_history( self, id=None ): - """Deletes a history""" + self.home() + def delete_history( self, id='' ): + """Deletes one or more histories""" history_list = self.get_histories() self.assertTrue( history_list ) - if id is None: + num_deleted = 1 + if not id: history = history_list[0] id = history.get( 'id' ) - id = str( id ) - self.visit_page( "history/list?operation=delete&id=%s" %(id) ) - + else: + num_deleted = len( id.split( ',' ) ) + self.visit_page( "history/list?operation=delete&id=%s" % ( id ) ) + check_str = 'Deleted %d histories' % num_deleted + self.check_page_for_string( check_str ) + self.home() def get_histories( self ): """Returns all histories""" tree = self.histories_as_xml_tree() data_list = [ elem for elem in tree.findall("data") ] return data_list - def get_history( self, show_deleted=False ): """Returns a history""" tree = self.history_as_xml_tree( show_deleted=show_deleted ) data_list = [ elem for elem in tree.findall("data") ] return data_list - def history_as_xml_tree( self, show_deleted=False ): """Returns a parsed xml object of a history""" self.home() @@ -145,7 +146,6 @@ xml = self.last_page() tree = ElementTree.fromstring(xml) return tree - def histories_as_xml_tree( self ): """Returns a parsed xml object of all histories""" self.home() @@ -153,97 +153,96 @@ xml = self.last_page() tree = ElementTree.fromstring(xml) return tree - - def history_options( self ): + def history_options( self, check_str='', upload=False ): """Mimics user clicking on history options link""" self.visit_page( "history_options" ) - - def new_history( self ): + if check_str: + self.check_page_for_string( check_str ) + else: + self.check_page_for_string( 'Rename</a> current history' ) + self.check_page_for_string( 'List</a> previously stored histories' ) + self.check_page_for_string( 'Construct workflow</a> from the current history' ) + self.check_page_for_string( 'Share</a> current history' ) + # Tests for changing default history permissions are done in test_security_and_libraries.py + self.check_page_for_string( 'Change default permissions</a> for the current history' ) + self.check_page_for_string( 'Show deleted</a> datasets in history' ) + self.check_page_for_string( 'Delete</a> current history' ) + # Need to add a history item in order to create a new empty history + try: + self.check_page_for_string( 'Create</a> a new empty history' ) + raise AssertionError, "Incorrectly able to create a new empty history when the current history is empty." + except: + pass + if upload: + self.upload_file( '1.bed', dbkey='hg18' ) + self.home() + self.visit_page( "history_options" ) + self.check_page_for_string( 'Create</a> a new empty history' ) + self.home() + def new_history( self, name=None ): """Creates a new, empty history""" - self.visit_page( "history_new" ) + if name: + self.visit_url( "%s/history_new?name=%s" % ( self.url, str( name ) ) ) + else: + self.visit_url( "%s/history_new" % self.url ) self.check_history_for_string('Your history is empty') - - def rename_history( self, id=None, name='NewTestHistory' ): + self.home() + def rename_history( self, id, old_name, new_name ): """Rename an existing history""" - history_list = self.get_histories() - self.assertTrue( history_list ) - if id is None: # take last id - elem = history_list[-1] - else: - i = history_list.index( id ) - self.assertTrue( i ) - elem = history_list[i] - id = elem.get( 'id' ) - self.assertTrue( id ) - old_name = elem.get( 'name' ) - self.assertTrue( old_name ) - id = str( id ) - self.visit_page( "history/rename?id=%s&name=%s" %(id, name) ) - return id, old_name, name - + self.home() + self.visit_page( "history/rename?id=%s&name=%s" %( id, new_name ) ) + check_str = 'History: %s renamed to: %s' % ( old_name, new_name ) + self.check_page_for_string( check_str ) + self.home() def set_history( self ): """Sets the history (stores the cookies for this run)""" if self.history_id: self.visit_page( "history?id=%s" % self.history_id ) else: self.new_history() - def share_history( self, id=None, email='test2(a)bx.psu.edu' ): - """Share a history with a different user""" - history_list = self.get_histories() - self.assertTrue( history_list ) - if id is None: # take last id - elem = history_list[-1] - else: - i = history_list.index( id ) - self.assertTrue( i ) - elem = history_list[i] - id = elem.get( 'id' ) - self.assertTrue( id ) - id = str( id ) - name = elem.get( 'name' ) - self.assertTrue( name ) + self.home() + def share_history( self, id, email, check_str, check_str2='', action=None, action_check_str=None ): + """Share a history different users""" self.visit_url( "%s/history/share?id=%s&email=%s&history_share_btn=Submit" % ( self.url, id, email ) ) - self.check_page_for_string( 'History (%s) has been shared with: %s' % ( name, email ) ) - return id, name, email - def share_history_containing_private_datasets( self, history_id, email='test(a)bx.psu.edu' ): - """Attempt to share a history containing private datasets with a different user""" - self.visit_url( "%s/history/share?id=%s&email=%s&history_share_btn=Submit" % ( self.url, history_id, email ) ) - self.last_page() - self.check_page_for_string( "The history or histories you've chosen to share contain datasets" ) - self.check_page_for_string( "How would you like to proceed?" ) + self.check_page_for_string( check_str ) + if check_str2: + self.check_page_for_string( check_str2 ) + if action: + # If we have an action, then we are sharing datasets with users that do not have access permissions on them + tc.fv( '1', 'action', action ) + tc.submit( "share_proceed_button" ) + if action_check_str: + self.check_page_for_string( action_check_str ) self.home() - def make_datasets_public( self, history_id, email='test(a)bx.psu.edu' ): - """Make private datasets public in order to share a history with a different user""" - self.visit_url( "%s/history/share?id=%s&email=%s&action=public&submit=Ok" % ( self.url, history_id, email ) ) - self.last_page() - check_str = "History (Unnamed history) has been shared with: %s" % email - self.check_page_for_string( check_str ) - self.home() - def privately_share_dataset( self, history_id, email='test(a)bx.psu.edu' ): - """Make private datasets public in order to share a history with a different user""" - self.visit_url( "%s/history/share?id=%s&email=%s&action=private&submit=Ok" % ( self.url, history_id, email ) ) - self.last_page() - check_str = "History (Unnamed history) has been shared with: %s" % email - self.check_page_for_string( check_str ) - self.home() - def switch_history( self, hid=None ): + def switch_history( self, id='', name='' ): """Switches to a history in the current list of histories""" data_list = self.get_histories() self.assertTrue( data_list ) - if hid is None: # take last hid - elem = data_list[-1] - hid = elem.get('hid') - if hid < 0: - hid = len(data_list) + hid + 1 - hid = str(hid) - elems = [ elem for elem in data_list if elem.get('hid') == hid ] - self.assertEqual(len(elems), 1) - self.visit_page( "history/list?operation=switch&id=%s" % elems[0].get('id') ) - - def view_stored_histories( self, check_str='' ): + if not id: + history = history_list[0] + id = history.get( 'id' ) + self.visit_url( "%s/history/list?operation=switch&id=%s" % ( self.url, id ) ) + if name: + self.check_history_for_string( name ) + self.home() + def view_stored_active_histories( self, check_str='' ): self.visit_page( "history/list" ) + self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( '<input type="checkbox" name="id" value=' ) + self.check_page_for_string( 'operation=Rename&id' ) + self.check_page_for_string( 'operation=Switch&id' ) + self.check_page_for_string( 'operation=Delete&id' ) if check_str: self.check_page_for_string( check_str ) + self.home() + def view_stored_deleted_histories( self, check_str='' ): + self.visit_page( "history/list?f-deleted=True" ) + self.check_page_for_string( 'Stored histories' ) + self.check_page_for_string( '<input type="checkbox" name="id" value=' ) + self.check_page_for_string( 'operation=Undelete&id' ) + if check_str: + self.check_page_for_string( check_str ) + self.home() # Functions associated with datasets (history items) and meta data def get_job_stderr( self, id ): @@ -299,9 +298,14 @@ self.visit_url( "%s/dataset/undelete?id=%s" % ( self.url, elems[0].get( 'id' ) ) ) if check_str: self.check_page_for_string( check_str ) + def display_history_item( self, id, check_str='' ): + """Displays a history item - simulates eye icon click""" + self.visit_url( '%s/datasets/%s/display/index' % ( self.url, id ) ) + if check_str: + self.check_page_for_string( check_str ) + self.home() def edit_metadata( self, hid=None, form_no=0, **kwd ): - """ - Edits the metadata associated with a history item.""" + """Edits the metadata associated with a history item.""" # There are currently 4 forms on the edit page: # 0. name="edit_attributes" # 1. name="auto_detect" @@ -324,7 +328,6 @@ button = "change" #Change data type form if kwd: self.submit_form( form_no=form_no, button=button, **kwd) - def get_dataset_ids_in_history( self ): """Returns the ids of datasets in a history""" data_list = self.get_history() diff -r 73847f425801 -r 9a71b89082fe test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Mon Jun 01 10:27:04 2009 -0400 +++ b/test/functional/test_history_functions.py Fri Jun 05 11:15:25 2009 -0400 @@ -4,74 +4,367 @@ class TestHistory( TwillTestCase ): - def test_00_history_options_when_not_logged_in( self ): + def test_000_history_options_when_not_logged_in( self ): """Testing history options when not logged in""" - self.logout() #Ensure we are not logged in - self.history_options() - self.check_page_for_string( 'logged in</a> to store or switch histories.' ) - self.login( email='test2(a)bx.psu.edu' ) #Just to make sure we have created this account since it is used to share histories self.logout() - def test_05_new_history_then_delete( self ): - """Testing creating a new history and then deleting it""" - self.login() - self.new_history() - if len(self.get_history()) > 0: - raise AssertionError("test_new_history_then_delete failed") - self.delete_history() - self.check_page_for_string( 'Deleted 1 histories' ) - def test_10_history_options_when_logged_in( self ): + check_str = 'logged in</a> to store or switch histories.' + self.history_options( check_str=check_str ) + # Make sure we have created the following accounts + self.login( email='test1(a)bx.psu.edu' ) + global regular_user1 + regular_user1 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() + assert regular_user1 is not None, 'Problem retrieving user with email "test1(a)bx.psu.edu" from the database' + self.logout() + self.login( email='test2(a)bx.psu.edu' ) + global regular_user2 + regular_user2 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test2(a)bx.psu.edu' ).first() + assert regular_user2 is not None, 'Problem retrieving user with email "test2(a)bx.psu.edu" from the database' + self.logout() + self.login( email='test3(a)bx.psu.edu' ) + global regular_user3 + regular_user3 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test3(a)bx.psu.edu' ).first() + assert regular_user3 is not None, 'Problem retrieving user with email "test3(a)bx.psu.edu" from the database' + self.logout() + def test_005_deleting_histories( self ): + """Testing deleting histories""" + self.login( email='test(a)bx.psu.edu' ) + global admin_user + admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ).first() + assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' + # Get the admin_user private role + global admin_user_private_role + admin_user_private_role = None + for role in admin_user.all_roles(): + if role.name == admin_user.email and role.description == 'Private Role for %s' % admin_user.email: + admin_user_private_role = role + break + if not admin_user_private_role: + raise AssertionError( "Private role not found for user '%s'" % admin_user.email ) + latest_history = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert latest_history is not None, "Problem retrieving latest history from database" + assert not latest_history.deleted, "After login, associated history is deleted" + self.delete_history( str( latest_history.id ) ) + latest_history.refresh() + if not latest_history.deleted: + raise AssertionError, "Problem deleting history id %d" % latest_history.id + # We'll now test deleting a list of histories + # After deleting the current history, a new one should have been created + global history1 + history1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history1 is not None, "Problem retrieving history1 from database" + self.upload_file( '1.bed', dbkey='hg18' ) + self.new_history( name='history2' ) + global history2 + history2 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history2 is not None, "Problem retrieving history2 from database" + self.upload_file( '2.bed', dbkey='hg18' ) + ids = '%s,%s' % ( str( history1.id ), str( history2.id ) ) + self.delete_history( ids ) + try: + self.view_stored_active_histories( check_str=history1.name ) + raise AssertionError, "History %s is displayed in the active history list after it was deleted" % history1.name + except: + pass + self.view_stored_deleted_histories( check_str=history1.name ) + try: + self.view_stored_active_histories( check_str=history2.name ) + raise AssertionError, "History %s is displayed in the active history list after it was deleted" % history2.name + except: + pass + self.view_stored_deleted_histories( check_str=history2.name ) + history1.refresh() + if not history1.deleted: + raise AssertionError, "Problem deleting history id %d" % history1.id + if not history1.default_permissions: + raise AssertionError, "Default permissions were incorrectly deleted from the db for history id %d when it was deleted" % history1.id + history2.refresh() + if not history2.deleted: + raise AssertionError, "Problem deleting history id %d" % history2.id + if not history2.default_permissions: + raise AssertionError, "Default permissions were incorrectly deleted from the db for history id %d when it was deleted" % history2.id + def test_010_history_options_when_logged_in( self ): """Testing history options when logged in""" self.history_options() - self.check_page_for_string( 'Rename</a> current history' ) - self.check_page_for_string( 'List</a> previously stored histories' ) - self.check_page_for_string( 'Construct workflow</a> from the current history' ) - self.check_page_for_string( 'Share</a> current history' ) - # Tests for changing default history permissions are done in test_security_and_libraries.py - self.check_page_for_string( 'Change default permissions</a> for the current history' ) - self.check_page_for_string( 'Show deleted</a> datasets in history' ) - self.check_page_for_string( 'Delete</a> current history' ) - # Need to add a history item in order to create a new empty history + def test_015_history_rename( self ): + """Testing renaming a history""" + global history3 + history3 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history3 is not None, "Problem retrieving history3 from database" + if history3.deleted: + raise AssertionError, "History id %d deleted when it should not be" % latest_history.id + self.rename_history( str( history3.id ), history3.name, new_name='history3' ) + def test_020_history_list( self ): + """Testing viewing previously stored histories""" + self.view_stored_active_histories() + def test_025_history_share( self ): + """Testing sharing histories containing only public datasets""" + history3.refresh() + self.upload_file( '1.bed', dbkey='hg18' ) + # Test sharing a history with yourself + check_str = "You can't send histories to yourself." + self.share_history( str( history3.id ), 'test(a)bx.psu.edu', check_str ) + # Share a history with 1 valid user + name = history3.name + email = 'test1(a)bx.psu.edu' + check_str = 'Histories (%s) have been shared with: %s' % ( name, email ) + self.share_history( str( history3.id ), email, check_str ) + # We need to keep track of all shared histories so they can later be deleted + global history3_copy1 + history3_copy1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history3_copy1 is not None, "Problem retrieving history3_copy1 from database" + self.logout() + self.login( email='test1(a)bx.psu.edu' ) + check_str = '%s from test(a)bx.psu.edu' % history3.name + self.view_stored_active_histories( check_str=check_str ) + self.logout() + self.login( email='test(a)bx.psu.edu' ) + # Need to delete history3_copy1 + history3_copy1.deleted = True + history3_copy1.flush() + # Test sharing a history with an invalid user + email = 'jack(a)jill.com' + check_str = '%s is not a valid Galaxy user.' % email + self.share_history( str( history3.id ), email, check_str ) + # Test sharing multiple histories with multiple users + self.new_history() + global history4 + history4 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history4 is not None, "Problem retrieving history4 from database" + self.rename_history( str( history4.id ), history4.name, new_name='history4' ) + history4.refresh() + self.upload_file( '2.bed', dbkey='hg18' ) + id = '%s,%s' % ( str( history3.id ), str( history4.id ) ) + name = '%s,%s' % ( history3.name, history4.name ) + email = 'test2@bx.psu.edu,test3@bx.psu.edu' + check_str = 'Histories (%s) have been shared with: %s' % ( name, email ) + self.share_history( id, email, check_str ) + # We need to keep track of all shared histories so they can later be deleted + history3_copy_name = "%s from %s" % ( history3.name, admin_user.email ) + history3_copies = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history3_copy_name, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .limit( 2 ) \ + .all() + history3_copy2 = history3_copies[0] + history3_copy3 = history3_copies[1] + history4_copy_name = "%s from %s" % ( history4.name, admin_user.email ) + history4_copyies = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history4_copy_name, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .limit( 2 ) \ + .all() + history4_copy1 = history4_copyies[0] + history4_copy2 = history4_copyies[1] + self.logout() + self.login( email='test2(a)bx.psu.edu' ) + check_str = '%s from %s' % ( history3.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + check_str = '%s from %s' % ( history4.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + self.logout() + self.login( email='test3(a)bx.psu.edu' ) + check_str = '%s from %s' % ( history3.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + check_str = '%s from %s' % ( history4.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + self.logout() + self.login( email='test(a)bx.psu.edu' ) + # Need to delete the copied histories, so later test runs are valid + history3_copy2.deleted = True + history3_copy2.flush() + history3_copy3.deleted = True + history3_copy3.flush() + history4_copy1.deleted = True + history4_copy1.flush() + history4_copy1.deleted = True + history4_copy1.flush() + history4_copy2.deleted = True + history4_copy2.flush() + def test_030_change_permissions_on_current_history( self ): + """Testing changing permissions on the current history""" + global history5 + history5 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history5 is not None, "Problem retrieving history5 from database" + self.rename_history( str( history5.id ), history5.name, new_name='history5' ) + history5.refresh() + # Due to the limitations of twill ( not functional with the permissions forms ), we're forced + # to do this manually. At this point, we just want to restrict the access permission on history5 + # to the admin_user + global access_action + access_action = galaxy.model.Dataset.permitted_actions.DATASET_ACCESS.action + dhp = galaxy.model.DefaultHistoryPermissions( history5, access_action, admin_user_private_role ) + dhp.flush() + self.upload_file( '1.bed', dbkey='hg18' ) + history5_dataset1 = None + for hda in history5.datasets: + if hda.name == '1.bed': + history5_dataset1 = hda.dataset + assert history5_dataset1 is not None, "Problem retrieving history5_dataset1 from the database" + # The permissions on the dataset should be restricted from sharing with anyone due to the + # inherited history permissions + restricted = False + for action in history5_dataset1.actions: + if action.action == access_action: + restricted = True + break + if not restricted: + raise AssertionError, "The 'access' permission is not set for history5_dataset1.actions" + def test_035_sharing_history_by_making_datasets_public( self ): + """Testing sharing a restricted history by making the datasets public""" + check_str = 'The following datasets can be shared with %s by updating their permissions' % regular_user1.email + action_check_str = 'Histories (%s) have been shared with: %s' % ( history5.name, regular_user1.email ) + self.share_history( str( history5.id ), regular_user1.email, check_str, action='public', action_check_str=action_check_str ) + history5_copy1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history5_copy1 is not None, "Problem retrieving history5_copy1 from database" + self.logout() + self.login( email=regular_user1.email ) + self.visit_url( "%s/history/list" % self.url ) + self.check_page_for_string( history5_copy1.name ) + # Need to delete history5_copy1 on the history list page for regular_user1 + history5_copy1.deleted = True + history5_copy1.flush() + self.logout() + self.login( email=admin_user.email ) + def test_040_sharing_history_by_making_new_sharing_role( self ): + """Testing sharing a restricted history by associating a new sharing role with protected datasets""" + self.switch_history( id=str( history5.id ), name=history5.name ) + # At this point, history5 should have 1 item, 1.bed, which is public. We'll add another + # item which will be private to admin_user due to the permissions on history5 + self.upload_file( '2.bed', dbkey='hg18' ) + check_str = 'The following datasets can be shared with %s with no changes' % regular_user1.email + check_str2 = 'The following datasets can be shared with %s by updating their permissions' % regular_user1.email + action_check_str = 'Histories (%s) have been shared with: %s' % ( history5.name, regular_user1.email ) + self.share_history( str( history5.id ), + regular_user1.email, + check_str, + check_str2=check_str2, + action='private', + action_check_str=action_check_str ) + history5_copy2 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history5_copy2 is not None, "Problem retrieving history5_copy2 from database" + # We should now have a new sharing role + global sharing_role + role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user1.email ) + sharing_role = galaxy.model.Role.filter( galaxy.model.Role.table.c.name==role_name ).first() + assert sharing_role is not None, "Problem retrieving sharing_role from the database" + self.logout() + self.login( email=regular_user1.email ) + self.visit_url( "%s/history/list" % self.url ) + self.check_page_for_string( history5_copy2.name ) + self.switch_history( id=str( history5_copy2.id ), name=history5_copy2.name ) + # Make sure both datasets are in the history + self.check_history_for_string( '1.bed' ) + self.check_history_for_string( '2.bed' ) + # Get both new hdas from the db that were created for the shared history + hda_1_bed = galaxy.model.HistoryDatasetAssociation \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ + .first() + assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" + hda_2_bed = galaxy.model.HistoryDatasetAssociation \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy2.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ + .first() + assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" + # Make sure 1.bed is accessible since it is public + self.display_history_item( str( hda_1_bed.id ), check_str='chr1' ) + # Make sure 2.bed is accessible since it is associated with a sharing role + self.display_history_item( str( hda_2_bed.id ), check_str='chr1' ) + # Need to delete history5_copy2 on the history list page for regular_user1 + history5_copy2.deleted = True + history5_copy2.flush() + self.logout() + self.login( email=admin_user.email ) + def test_045_sharing_private_history_with_multiple_users_by_changing_no_permissions( self ): + """Testing sharing a restricted history with multiple users, making no permission changes""" + # History5 can be shared with any user, since it contains a public dataset. However, only + # regular_user1 should be able to access history5's 2.bed dataset since it is associated with a + # sharing role, and regular_user2 should be able to access history5's 1.bed, but not 2.bed even + # though they can see it in their shared history. + self.switch_history( id=str( history5.id ), name=history5.name ) + email = '%s,%s' % ( regular_user1.email, regular_user2.email ) + check_str = 'The following datasets can be shared with %s with no changes' % email + check_str2 = 'The following datasets can be shared with %s by updating their permissions' % email + action_check_str = 'Histories (%s) have been shared with: %s' % ( history5.name, regular_user1.email ) + self.share_history( str( history5.id ), + email, + check_str, + check_str2=check_str2, + action='share', + action_check_str=action_check_str ) + # We need to keep track of all shared histories so they can later be deleted + history5_copy_name = "%s from %s" % ( history5.name, admin_user.email ) + history5_copies = galaxy.model.History \ + .filter( and_( galaxy.model.History.table.c.name==history5_copy_name, + galaxy.model.History.table.c.deleted==False ) ) \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ) \ + .limit( 2 ) \ + .all() + history5_copy3 = history5_copies[0] + assert history5_copy3 is not None, "Problem retrieving history5_copy3 from database" + history5_copy4 = history5_copies[1] + assert history5_copy4 is not None, "Problem retrieving history5_copy4 from database" + # Make sure test1(a)bx.psu.edu received a copy of history5 with both datasets accessible + self.login( email=regular_user1.email ) + check_str = '%s from %s' % ( history5.name, admin_user.email ) + self.view_stored_active_histories( check_str=check_str ) + self.switch_history( id=str( history5_copy3.id ), name=history5_copy3.name ) + self.check_history_for_string( '1.bed' ) + self.check_history_for_string( '2.bed' ) + self.logout() + # Make sure test2(a)bx.psu.edu received a copy of history5, with only 1.bed accessible + self.login( email=regular_user2.email ) + self.view_stored_active_histories( check_str=check_str ) + self.switch_history( id=str( history5_copy4.id ), name=history5_copy4.name ) + self.check_history_for_string( '1.bed' ) + self.check_history_for_string( '2.bed' ) + # Get both new hdas from the db that were created for the shared history + hda_1_bed = galaxy.model.HistoryDatasetAssociation \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='1.bed' ) ) \ + .first() + assert hda_1_bed is not None, "Problem retrieving hda_1_bed from database" + hda_2_bed = galaxy.model.HistoryDatasetAssociation \ + .filter( and_( galaxy.model.HistoryDatasetAssociation.table.c.history_id==history5_copy4.id, + galaxy.model.HistoryDatasetAssociation.table.c.name=='2.bed' ) ) \ + .first() + assert hda_2_bed is not None, "Problem retrieving hda_2_bed from database" + # Make sure 1.bed is accessible since it is public + self.display_history_item( str( hda_1_bed.id ), check_str='chr1' ) + # Make sure 2.bed is not accessible since it is protected try: - self.check_page_for_string( 'Create</a> a new empty history' ) - raise AssertionError, "Incorrectly able to create a new empty history when the current history is empty." + self.display_history_item( str( hda_2_bed.id ), check_str='chr1' ) + raise AssertionError, "History item 2.bed is accessible by user %s when is should not be" % regular_user2.email except: pass - self.upload_file( '1.bed', dbkey='hg18' ) - self.history_options() - self.check_page_for_string( 'Create</a> a new empty history' ) - def test_15_history_rename( self ): - """Testing renaming a history""" - id, old_name, new_name = self.rename_history() - self.check_page_for_string( 'History: %s renamed to: %s' %(old_name, new_name) ) - def test_20_history_list( self ): - """Testing viewing previously stored histories""" - self.view_stored_histories() - self.check_page_for_string( 'Stored histories' ) - self.check_page_for_string( '<input type="checkbox" name="id" value=' ) - self.check_page_for_string( 'operation=Rename&id' ) - self.check_page_for_string( 'operation=Switch&id' ) - self.check_page_for_string( 'operation=Delete&id' ) - def test_25_history_share( self ): - """Testing sharing a history with another user""" - self.upload_file('1.bed', dbkey='hg18') - id, name, email = self.share_history() - self.logout() - self.login( email=email ) - self.home() - check_str = 'Unnamed history from test(a)bx.psu.edu' - self.view_stored_histories( check_str=check_str ) - histories = self.get_histories() - for history in histories: - if history.get( 'name' ) == 'Unnamed history from test(a)bx.psu.edu': - id = history.get( 'id' ) - break - self.assertTrue( id ) - self.delete_history( id ) + self.check_history_for_string( 'You do not have permission to view this dataset' ) self.logout() self.login( email='test(a)bx.psu.edu' ) - def test_30_history_show_and_hide_deleted_datasets( self ): + # Need to delete the copied histories, so later test runs are valid + history5_copy3.deleted = True + history5_copy3.flush() + history5_copy4.deleted = True + history5_copy4.flush() + + + + def test_050_sharing_private_history_by_choosing_to_not_share( self ): + """Testing sharing a restricted history with multiple users by choosing not to share""" + self.switch_history( id=str( history5.id ), name=history5.name ) + email = '%s,%s' % ( regular_user1.email, regular_user2.email ) + check_str = 'The following datasets can be shared with %s with no changes' % email + check_str2 = 'The following datasets can be shared with %s by updating their permissions' % email + action_check_str = 'History Options' + self.share_history( str( history5.id ), + email, + check_str, + check_str2=check_str2, + action='no_share' ) + def test_055_history_show_and_hide_deleted_datasets( self ): """Testing displaying deleted history items""" - self.new_history() + self.new_history( name='temp_history1' ) self.upload_file('1.bed', dbkey='hg18') latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() @@ -85,9 +378,9 @@ self.home() self.visit_url( "%s/history/?show_deleted=False" % self.url ) self.check_page_for_string( 'Your history is empty' ) - def test_35_deleting_and_undeleting_history_items( self ): + def test_060_deleting_and_undeleting_history_items( self ): """Testing deleting and un-deleting history items""" - self.new_history() + self.new_history( name='temp_history2' ) # Add a new history item self.upload_file( '1.bed', dbkey='hg15' ) self.home() @@ -110,6 +403,8 @@ self.visit_url( "%s/history/?show_deleted=False" % self.url ) self.check_page_for_string( '1.bed' ) self.check_page_for_string( 'hg15' ) - def test_9999_clean_up( self ): - self.delete_history() - self.logout() + def test_065_reset_data_for_later_test_runs( self ): + """Reseting data to enable later test runs to pass""" + self.delete_history( id=str( history3.id ) ) + self.delete_history( id=str( history4.id ) ) + self.delete_history( id=str( history5.id ) ) diff -r 73847f425801 -r 9a71b89082fe test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Mon Jun 01 10:27:04 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Fri Jun 05 11:15:25 2009 -0400 @@ -40,7 +40,7 @@ global admin_user admin_user = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test(a)bx.psu.edu' ).first() assert admin_user is not None, 'Problem retrieving user with email "test(a)bx.psu.edu" from the database' - # Get the admin user's privat role for later use + # Get the admin user's private role for later use global admin_user_private_role admin_user_private_role = None for role in admin_user.all_roles(): @@ -136,7 +136,7 @@ dps.append( dp.action ) # Sort actions for later comparison dps.sort() - # Compare DatasetPermissionss with permissions_in - should be the same + # Compare DatasetPermissions with permissions_in - should be the same if dps != actions_in: raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from changed default permissions "%s"' \ % ( str( dps ), latest_dataset.id, str( actions_in ) ) ) @@ -145,14 +145,26 @@ raise AssertionError( 'DatasetPermissionss "%s" for dataset id %d differ from DefaultHistoryPermissions "%s" for history id %d' \ % ( str( dps ), latest_dataset.id, str( dhps ), latest_history.id ) ) # Since the dataset in the history is now private, we can test sharing with another user - self.share_history_containing_private_datasets( str( latest_history.id ), email=admin_user.email ) # Test making the dataset in the history public - self.make_datasets_public( str( latest_history.id ), email=admin_user.email ) + check_str = 'The following datasets can be shared with %s by updating their permissions' % admin_user.email + action_check_str = 'Histories (%s) have been shared with: %s' % ( latest_history.name, admin_user.email ) + self.share_history( str( latest_history.id ), + admin_user.email, + check_str, + action='public', + action_check_str=action_check_str ) # Add another dataset to the history, it should be private since that is now our default self.upload_file( '2.bed' ) - self.share_history_containing_private_datasets( str( latest_history.id ), email=admin_user.email ) - # Test creating a new sharing role for sharing the private datasets - self.privately_share_dataset( str( latest_history.id ), email=admin_user.email ) + # Test creating a new sharing role for the private dataset + check_str = 'The following datasets can be shared with %s with no changes' % admin_user.email + check_str2 = 'The following datasets can be shared with %s by updating their permissions' % admin_user.email + action_check_str = 'Histories (%s) have been shared with: %s' % ( latest_history.name, admin_user.email ) + self.share_history( str( latest_history.id ), + admin_user.email, + check_str, + check_str2=check_str2, + action='private', + action_check_str=action_check_str ) role_type = 'sharing' role_name = 'Sharing role for: %s, %s' % ( regular_user1.email, admin_user.email ) global sharing_role diff -r 73847f425801 -r 9a71b89082fe tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Jun 01 10:27:04 2009 -0400 +++ b/tool_conf.xml.sample Fri Jun 05 11:15:25 2009 -0400 @@ -13,6 +13,7 @@ <tool file="data_source/wormbase_test.xml" /> <tool file="data_source/flymine.xml" /> <tool file="data_source/flymine_test.xml" /> + <tool file="data_source/eupathdb.xml" /> <tool file="data_source/encode_db.xml" /> <tool file="data_source/epigraph_import.xml" /> <tool file="data_source/epigraph_import_test.xml" />

1 0

[hg] galaxy 2431: Temporarily eliminate access to templates unti...
by Greg Von Kuster 09 Jun '09

09 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/1a24a530a3ae changeset: 2431:1a24a530a3ae user: Greg Von Kuster <greg(a)bx.psu.edu> date: Mon Jun 08 10:31:59 2009 -0400 description: Temporarily eliminate access to templates until new forms are finished, and more fixes for functional tests. 7 file(s) affected in this change: lib/galaxy/web/controllers/admin.py templates/admin/library/browse_library.mako templates/library/browse_library.mako test/base/twilltestcase.py test/functional/test_DNAse_flanked_genes.py test/functional/test_metadata_editing.py test/functional/test_security_and_libraries.py diffs (1339 lines): diff -r 373962edbe90 -r 1a24a530a3ae lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Fri Jun 05 16:48:03 2009 -0400 +++ b/lib/galaxy/web/controllers/admin.py Mon Jun 08 10:31:59 2009 -0400 @@ -553,9 +553,7 @@ # with the user's private role in case we want the ability to unpurge the user # some time in the future. # Purging a deleted User deletes all of the following: - # - DefaultUserPermissions where user_id == User.id EXCEPT FOR THE PRIVATE ROLE # - History where user_id = User.id - # - DefaultHistoryPermissions where history_id == History.id EXCEPT FOR THE PRIVATE ROLE # - HistoryDatasetAssociation where history_id = History.id # - Dataset where HistoryDatasetAssociation.dataset_id = Dataset.id # - UserGroupAssociation where user_id == User.id @@ -568,19 +566,9 @@ msg = "User '%s' has not been deleted, so it cannot be purged." % user.email trans.response.send_redirect( web.url_for( action='users', msg=util.sanitize_text( msg ), messagetype='error' ) ) private_role = trans.app.security_agent.get_private_user_role( user ) - # Delete DefaultUserPermissions EXCEPT FOR THE PRIVATE ROLE - for dup in user.default_permissions: - if dup.role_id != private_role.id: - dup.delete() - dup.flush() # Delete History for h in user.active_histories: h.refresh() - # Delete DefaultHistoryPermissions EXCEPT FOR THE PRIVATE ROLE - for dp in h.default_permissions: - if dp.role_id != private_role.id: - dp.delete() - dp.flush() for hda in h.active_datasets: # Delete HistoryDatasetAssociation d = trans.app.model.Dataset.get( hda.dataset_id ) diff -r 373962edbe90 -r 1a24a530a3ae templates/admin/library/browse_library.mako --- a/templates/admin/library/browse_library.mako Fri Jun 05 16:48:03 2009 -0400 +++ b/templates/admin/library/browse_library.mako Mon Jun 08 10:31:59 2009 -0400 @@ -112,13 +112,14 @@ <a class="action-button" href="${h.url_for( controller='admin', action='library_dataset_dataset_association', library_id=library_id, folder_id=folder.id )}">Add datasets to this folder</a> <a class="action-button" href="${h.url_for( controller='admin', action='folder', new=True, id=folder.id, library_id=library_id )}">Create a new sub-folder in this folder</a> <a class="action-button" href="${h.url_for( controller='admin', action='folder', information=True, id=folder.id, library_id=library_id )}">Edit this folder's information</a> - %if folder.library_folder_info_template_associations: - <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %> - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, id=template.id, edit_template=True )}">Edit this folder's information template</a> - %elif not folder.library_folder_info_associations: - ## Only allow adding a new template to the folder if a previously inherited template has not already been used - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a> - %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##%if folder.library_folder_info_template_associations: + ## <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %> + ## <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, id=template.id, edit_template=True )}">Edit this folder's information template</a> + ##%elif not folder.library_folder_info_associations: + ## ## Only allow adding a new template to the folder if a previously inherited template has not already been used + ## <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library_id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a> + ##%endif <a class="action-button" href="${h.url_for( controller='admin', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a> <a class="action-button" confirm="Click OK to delete the folder '${folder.name}.'" href="${h.url_for( controller='admin', action='delete_library_item', library_id=library_id, library_item_id=folder.id, library_item_type='folder' )}">Delete this folder and its contents</a> </div> @@ -199,21 +200,21 @@ library_item_ids = {} library_item_ids[ 'library' ] = library.id %> - - <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this library's information</a> - %if library.library_info_template_associations: - <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> - %else: - <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> - %endif - <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, permissions=True )}">Edit this library's permissions</a> - <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this library and its contents</a> - %if show_deleted: - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted library items</a> - %else: - <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted library items</a> - %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##<a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, information=True )}">Edit this library's information</a> + ##%if library.library_info_template_associations: + ## <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> + ## <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> + ##%else: + ## <a class="action-button" href="${h.url_for( controller='admin', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> + ##%endif + <a class="action-button" href="${h.url_for( controller='admin', action='library', id=library.id, permissions=True )}">Edit this library's permissions</a> + <a class="action-button" confirm="Click OK to delete the library named '${library.name}'." href="${h.url_for( controller='admin', action='delete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Delete this library and its contents</a> + %if show_deleted: + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=False )}">Hide deleted library items</a> + %else: + <a class="action-button" href="${h.url_for( controller='admin', action='browse_library', id=library.id, show_deleted=True )}">Show deleted library items</a> + %endif %elif not library.purged: <a class="action-button" href="${h.url_for( controller='admin', action='undelete_library_item', library_id=library.id, library_item_id=library.id, library_item_type='library' )}">Undelete this library</a> %endif diff -r 373962edbe90 -r 1a24a530a3ae templates/library/browse_library.mako --- a/templates/library/browse_library.mako Fri Jun 05 16:48:03 2009 -0400 +++ b/templates/library/browse_library.mako Mon Jun 08 10:31:59 2009 -0400 @@ -150,17 +150,18 @@ %else: <a class="action-button" href="${h.url_for( controller='library', action='folder', information=True, id=folder.id, library_id=library_id )}">View this folder's information</a> %endif - %if folder.library_folder_info_template_associations: - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ): - <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %> - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this folder's information template</a> - %endif - %elif not folder.library_folder_info_associations: - ## Only allow adding a new template to the folder if a previously inherited template has not already been used - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ): - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a> - %endif - %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##%if folder.library_folder_info_template_associations: + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=folder ): + ## <% template = folder.get_library_item_info_templates( template_list=[], restrict=True )[0] %> + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this folder's information template</a> + ## %endif + ##%elif not folder.library_folder_info_associations: + ## ## Only allow adding a new template to the folder if a previously inherited template has not already been used + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=folder ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, folder_id=folder.id, new_template=True )}">Add an information template to this folder</a> + ## %endif + ##%endif %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=folder ): <a class="action-button" href="${h.url_for( controller='library', action='folder', permissions=True, id=folder.id, library_id=library_id )}">Edit this folder's permissions</a> %endif @@ -229,17 +230,17 @@ %else: <a class="action-button" href="${h.url_for( controller='library', action='library', information=True, id=library.id )}">View this library's information</a> %endif - - %if library.library_info_template_associations: - <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=template ): - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> - %endif - %else: - %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): - <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> - %endif - %endif + ## TODO: temporarily eliminating templates until we have the new forms features done + ##%if library.library_info_template_associations: + ## <% template = library.get_library_item_info_templates( template_list=[], restrict=False )[0] %> + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MODIFY, library_item=template ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, id=template.id, edit_template=True )}">Edit this library's information template</a> + ## %endif + ##%else: + ## %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_ADD, library_item=library ): + ## <a class="action-button" href="${h.url_for( controller='library', action='info_template', library_id=library.id, new_template=True )}">Add an information template to this library</a> + ## %endif + ##%endif %if trans.app.security_agent.allow_action( trans.user, trans.app.security_agent.permitted_actions.LIBRARY_MANAGE, library_item=library ): <a class="action-button" href="${h.url_for( controller='library', action='library', permissions=True, id=library.id )}">Edit this library's permissions</a> %endif diff -r 373962edbe90 -r 1a24a530a3ae test/base/twilltestcase.py --- a/test/base/twilltestcase.py Fri Jun 05 16:48:03 2009 -0400 +++ b/test/base/twilltestcase.py Mon Jun 08 10:31:59 2009 -0400 @@ -304,30 +304,49 @@ if check_str: self.check_page_for_string( check_str ) self.home() - def edit_metadata( self, hid=None, form_no=0, **kwd ): - """Edits the metadata associated with a history item.""" - # There are currently 4 forms on the edit page: - # 0. name="edit_attributes" - # 1. name="auto_detect" - # 2. name="convert_data" - # 3. name="change_datatype" - data_list = self.get_history() - self.assertTrue( data_list ) - if hid is None: # take last hid - elem = data_list[-1] - hid = int( elem.get('hid') ) - self.assertTrue( hid ) - self.visit_page( 'edit?hid=%d' % hid ) - if form_no == 0: - button = "save" #Edit Attributes form - elif form_no == 1: - button = "detect" #Auto-detect Metadata Attributes - elif form_no == 2: - button = "convert_data" #Convert to new format form - elif form_no == 3: - button = "change" #Change data type form - if kwd: - self.submit_form( form_no=form_no, button=button, **kwd) + def edit_hda_attribute_info( self, hda_id, new_name='', new_info='', new_dbkey='', new_startcol='' ): + """Edit history_dataset_association attribute information""" + self.home() + self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) + self.check_page_for_string( 'Edit Attributes' ) + if new_name: + tc.fv( 'edit_attributes', 'name', new_name ) + if new_info: + tc.fv( 'edit_attributes', 'info', new_info ) + if new_dbkey: + tc.fv( 'edit_attributes', 'dbkey', new_dbkey ) + if new_startcol: + tc.fv( 'edit_attributes', 'startCol', new_startcol ) + tc.submit( 'save' ) + self.check_page_for_string( 'Attributes updated' ) + self.home() + def auto_detect_metadata( self, hda_id ): + """Auto-detect history_dataset_association metadata""" + self.home() + self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) + self.check_page_for_string( 'This will inspect the dataset and attempt' ) + tc.fv( 'auto_detect', 'id', hda_id ) + tc.submit( 'detect' ) + self.check_page_for_string( 'Attributes updated' ) + self.home() + def convert_format( self, hda_id, target_type ): + """Auto-detect history_dataset_association metadata""" + self.home() + self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) + self.check_page_for_string( 'This will inspect the dataset and attempt' ) + tc.fv( 'convert_data', 'target_type', target_type ) + tc.submit( 'convert_data' ) + self.check_page_for_string( 'The file conversion of Convert BED to GFF on data' ) + self.home() + def change_datatype( self, hda_id, datatype ): + """Auto-detect history_dataset_association metadata""" + self.home() + self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) + self.check_page_for_string( 'This will change the datatype of the existing dataset but' ) + tc.fv( 'change_datatype', 'datatype', datatype ) + tc.submit( 'change' ) + self.check_page_for_string( 'Edit Attributes' ) + self.home() def get_dataset_ids_in_history( self ): """Returns the ids of datasets in a history""" data_list = self.get_history() diff -r 373962edbe90 -r 1a24a530a3ae test/functional/test_DNAse_flanked_genes.py --- a/test/functional/test_DNAse_flanked_genes.py Fri Jun 05 16:48:03 2009 -0400 +++ b/test/functional/test_DNAse_flanked_genes.py Mon Jun 08 10:31:59 2009 -0400 @@ -1,16 +1,16 @@ +import galaxy.model +from galaxy.model.orm import * from base.twilltestcase import TwillTestCase """ A sample analysis""" - - class AnalysisDNAseHSSFlankedGenes( TwillTestCase ): - def test_get_DNAseHSS_flanked_genes( self ): self.login() - self.new_history() - + global history1 + history1 = galaxy.model.History.query() \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ).first() track_params = dict( db="hg17", hgta_group="regulation", @@ -24,14 +24,21 @@ output_params = dict( fbQual="whole", ) - + # Test 1 self.run_ucsc_main( track_params, output_params ) self.wait() self.verify_dataset_correctness('DNAseHSS.dat') - - self.edit_metadata( name="DNAse HS" ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + # Due to twill not being able to handle the permissions forms, we'll eliminate + # DefaultHistoryPermissions prior to uploading a dataset so that the permission + # form will not be displayed on ted edit attributes page. + for dp in latest_hda.dataset.actions: + dp.delete() + dp.flush() + latest_hda.dataset.refresh() + self.edit_hda_attribute_info( str( latest_hda.id ), new_name="DNAse HS" ) self.check_metadata_for_string( "DNAse HS" ) - track_params = dict( db="hg17", hgta_group="genes", @@ -45,35 +52,38 @@ output_params = dict( fbQual="whole", ) - + # Test 2 self.run_ucsc_main( track_params, output_params ) self.wait() self.verify_dataset_correctness('hg17chr22KnownGenes.dat') - - self.edit_metadata( name="Genes" ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + for dp in latest_hda.dataset.actions: + dp.delete() + dp.flush() + latest_hda.dataset.refresh() + self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Genes" ) self.check_metadata_for_string( "Genes" ) - - + # Test 3 self.run_tool( 'get_flanks1', input="2", region="whole", direction="Upstream", offset="0", size="500" ) self.wait() self.verify_dataset_correctness( 'knownGeneUpstream500Flanks.dat' ) - - self.edit_metadata( name="Flanks" ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + for dp in latest_hda.dataset.actions: + dp.delete() + dp.flush() + latest_hda.dataset.refresh() + self.edit_hda_attribute_info( str( latest_hda.id ), new_name="Flanks" ) self.check_metadata_for_string( "Flanks" ) - - + # Test 4 self.run_tool( 'gops_join_1', input1="3", input2="1", min="1", fill="none" ) self.wait() - #self.verify_dataset_correctness( 'joinFlanksDNAse.dat' ) #we cannot verify this dataset, because this tool spits out data in a non-deterministic order - - + # We cannot verify this dataset, because this tool spits out data in a non-deterministic order + #self.verify_dataset_correctness( 'joinFlanksDNAse.dat' ) + # Test 5 self.run_tool( 'Filter1', input="4", cond="c17==1000" ) self.wait() self.verify_dataset_correctness( 'filteredJoinedFlanksDNAse.dat' ) - - self.delete_history() self.logout() - - - diff -r 373962edbe90 -r 1a24a530a3ae test/functional/test_metadata_editing.py --- a/test/functional/test_metadata_editing.py Fri Jun 05 16:48:03 2009 -0400 +++ b/test/functional/test_metadata_editing.py Mon Jun 08 10:31:59 2009 -0400 @@ -1,27 +1,45 @@ +import galaxy.model +from galaxy.model.orm import * from base.twilltestcase import TwillTestCase class TestMetadataEdit( TwillTestCase ): - def test_00_metadata_edit(self): + def test_00_metadata_edit( self ): """test_metadata_edit: Testing metadata editing""" - self.login() - self.upload_file('1.bed') - self.check_history_for_string('\? bed') - self.check_metadata_for_string('1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=1) + self.logout() + self.login( email='test(a)bx.psu.edu' ) + self.new_history( name='Test Metadata Edit' ) + global history1 + history1 = galaxy.model.History.query() \ + .order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + self.upload_file( '1.bed' ) + latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + self.home() + # Due to twill not being able to handle the permissions forms, we'll eliminate + # DefaultHistoryPermissions prior to uploading a dataset so that the permission + # form will not be displayed on ted edit attributes page. + for dp in latest_hda.dataset.actions: + dp.delete() + dp.flush() + latest_hda.dataset.refresh() + self.check_history_for_string( '1.bed' ) + self.check_metadata_for_string( '1.bed uploaded file unspecified (\?) chromCol value="1" selected endCol value="3" is_strandCol value="true" checked', hid=1 ) """test editing attributes""" - self.edit_metadata(hid=1, form_no=0, name='Testdata', info="Uploaded my file", dbkey='hg16', startCol='6') - self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=1) + self.edit_hda_attribute_info( hda_id=str( latest_hda.id ), + new_name='Testdata', + new_info="Uploaded my file", + new_dbkey='hg16', + new_startcol='6' ) + self.check_metadata_for_string( 'Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="6" selected', hid=1 ) """test Auto-detecting attributes""" - self.edit_metadata(hid=1, form_no=1) - self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=1) + self.auto_detect_metadata( hda_id=str( latest_hda.id ) ) + self.check_metadata_for_string('Testdata bed Uploaded my file hg16 "bed" selected="yes" "startCol" value="2" selected', hid=1 ) """test converting formats""" - self.edit_metadata(hid=1, form_no=2, target_type='gff') - self.check_history_for_string('hg16 Testdata Convert BED to GFF') - self.check_metadata_for_string('"gff" selected="yes"', hid=1) + self.convert_format( hda_id=str( latest_hda.id ), target_type='gff' ) + self.check_metadata_for_string( '"gff" selected="yes"', hid=1 ) """test changing data type""" - self.edit_metadata(hid=1, form_no=3, datatype='gff3') - self.check_history_for_string('hg16 Testdata Convert BED to GFF format: gff3') - self.delete_history_item( 1 ) - def test_9999_clean_up( self ): - self.delete_history() + self.change_datatype( hda_id=str( latest_hda.id ), datatype='gff3' ) + self.check_metadata_for_string( 'gff3', hid=1 ) + self.delete_history( id=str( history1.id ) ) self.logout() diff -r 373962edbe90 -r 1a24a530a3ae test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Fri Jun 05 16:48:03 2009 -0400 +++ b/test/functional/test_security_and_libraries.py Mon Jun 08 10:31:59 2009 -0400 @@ -51,7 +51,7 @@ raise AssertionError( "Private role not found for user '%s'" % admin_user.email ) # Make sure DefaultUserPermissions are correct if len( admin_user.default_permissions ) > 1: - raise AssertionError( '%d DefaultUserPermissions were created for %s when their account was created ( should have been 1 )' \ + raise AssertionError( '%d DefaultUserPermissions associated with user %s ( should be 1 )' \ % ( len( admin_user.default_permissions ), admin_user.email ) ) dup = galaxy.model.DefaultUserPermissions.filter( galaxy.model.DefaultUserPermissions.table.c.user_id==admin_user.id ).first() if not dup.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: @@ -72,6 +72,8 @@ self.logout() def test_010_login_as_regular_user1( self ): """Testing logging in as regular user test1(a)bx.psu.edu - tests private role creation, changing DefaultHistoryPermissions for new histories, and sharing histories with another user""" + # Some of the history related tests here are similar to some tests in the + # test_history_functions.py script, so we could potentially eliminate 1 or 2 of them. self.login( email='test1(a)bx.psu.edu' ) # test1(a)bx.psu.edu is not an admin user global regular_user1 regular_user1 = galaxy.model.User.filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ).first() @@ -93,7 +95,7 @@ latest_dataset = galaxy.model.Dataset.query().order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() # Make sure DatasetPermissions is correct - default is 'manage permissions' if len( latest_dataset.actions ) > 1: - raise AssertionError( '%d DatasetPermissionss were created for dataset id %d when it was created ( should have been 1 )' \ + raise AssertionError( '%d DatasetPermissions were created for dataset id %d when it was created ( should have been 1 )' \ % ( len( latest_dataset.actions ), latest_dataset.id ) ) dp = galaxy.model.DatasetPermissions.filter( galaxy.model.DatasetPermissions.table.c.dataset_id==latest_dataset.id ).first() if not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: @@ -494,97 +496,100 @@ library_one.refresh() self.rename_library( str( library_one.id ), library_one.name, name=name, description=description ) library_one.refresh() - def test_075_library_template_features( self ): - """Testing adding a template to a library, along with template features on the admin side""" - actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] - actions.sort() - # Add a new information template to the library - template_name = 'Library Template 1' - ele_name_0 = 'Foo' - ele_name_1 = 'Doh' - self.add_library_info_template( library_one.id, library_one.name, name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_name_1=ele_name_1 ) - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( ele_name_0 ) - self.check_page_for_string( ele_name_1 ) - self.home() - # Get the template for later testing - global library_one_template - library_one_template = galaxy.model.LibraryItemInfoTemplate.query().order_by( desc( galaxy.model.LibraryItemInfoTemplate.table.c.id ) ).first() - assert library_one_template is not None, 'Problem retrieving LibraryItemInfoTemplate for library named "%s" from the database' % str( library_one.name ) - # Make sure the library permissions were inherited by the template - template_permissions = galaxy.model.LibraryItemInfoTemplatePermissions \ - .query() \ - .filter( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.library_item_info_template_id == library_one_template.id ) \ - .order_by( desc( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.id ) ) \ - .limit( 3 ) \ - .all() - template_permissions = [ litp_obj.action for litp_obj in template_permissions ] - template_permissions.sort() - assert actions == template_permissions, "Template permissions for template %s not correctly inherited from library %s" \ - % ( library_one_template.name, library_one.name ) - # Make sure that the library permissions were inherited by each of the template elements - for library_item_info in library_one_template.library_item_infos: - info_permissions = galaxy.model.LibraryItemInfoPermissions \ - .filter( galaxy.model.LibraryItemInfoPermissions.table.c.library_item_info_id == library_item_info.id ) \ + """ + ## TODO: temporarily eliminating templates until we have the new forms features done + def test_075_library_template_features( self ): + Testing adding a template to a library, along with template features on the admin side + actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] + actions.sort() + # Add a new information template to the library + template_name = 'Library Template 1' + ele_name_0 = 'Foo' + ele_name_1 = 'Doh' + self.add_library_info_template( library_one.id, library_one.name, name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_name_1=ele_name_1 ) + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( ele_name_0 ) + self.check_page_for_string( ele_name_1 ) + self.home() + # Get the template for later testing + global library_one_template + library_one_template = galaxy.model.LibraryItemInfoTemplate.query().order_by( desc( galaxy.model.LibraryItemInfoTemplate.table.c.id ) ).first() + assert library_one_template is not None, 'Problem retrieving LibraryItemInfoTemplate for library named "%s" from the database' % str( library_one.name ) + # Make sure the library permissions were inherited by the template + template_permissions = galaxy.model.LibraryItemInfoTemplatePermissions \ + .query() \ + .filter( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.library_item_info_template_id == library_one_template.id ) \ + .order_by( desc( galaxy.model.LibraryItemInfoTemplatePermissions.table.c.id ) ) \ + .limit( 3 ) \ .all() - info_permissions = [ liip_obj.action for liip_obj in info_permissions ] - info_permissions.sort() - assert actions == info_permissions, "Permissions for library_item_info id %s not correctly inherited from library %s" \ - % ( library_item_info.id, library_one.name ) - element_ids = [] - if library_one.library_info_associations: - # We have a set of LibraryItemInfoElements - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - if not last_library_item_info_element: - element_ids.append( 0 ) - element_ids.append( 1 ) + template_permissions = [ litp_obj.action for litp_obj in template_permissions ] + template_permissions.sort() + assert actions == template_permissions, "Template permissions for template %s not correctly inherited from library %s" \ + % ( library_one_template.name, library_one.name ) + # Make sure that the library permissions were inherited by each of the template elements + for library_item_info in library_one_template.library_item_infos: + info_permissions = galaxy.model.LibraryItemInfoPermissions \ + .filter( galaxy.model.LibraryItemInfoPermissions.table.c.library_item_info_id == library_item_info.id ) \ + .all() + info_permissions = [ liip_obj.action for liip_obj in info_permissions ] + info_permissions.sort() + assert actions == info_permissions, "Permissions for library_item_info id %s not correctly inherited from library %s" \ + % ( library_item_info.id, library_one.name ) + element_ids = [] + if library_one.library_info_associations: + # We have a set of LibraryItemInfoElements + last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ + .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() + if not last_library_item_info_element: + element_ids.append( 0 ) + element_ids.append( 1 ) + else: + element_ids.append( last_library_item_info_element.id + 1 ) + element_ids.append( last_library_item_info_element.id + 2 ) else: - element_ids.append( last_library_item_info_element.id + 1 ) - element_ids.append( last_library_item_info_element.id + 2 ) - else: - # We only have a set of LibraryItemInfoTemplateElements - for ele in library_one_template.elements: - element_ids.append( ele.id ) - element_ids.sort() - # Add information to the library using the template - ele_1_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[0] ) ) - ele_1_contents = 'hello' - ele_2_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[1] ) ) - ele_2_contents = 'world' - self.edit_library_info( str( library_one.id ), library_one.name, - ele_1_field_name, ele_1_contents, - ele_2_field_name, ele_2_contents ) - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( ele_1_contents ) - self.check_page_for_string( ele_2_contents ) - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( ele_1_contents ) - self.check_page_for_string( ele_2_contents ) - # Edit the template - new_name = 'Library Template 1 renamed' - new_ele_name_1_field = "element_name_%s" % element_ids[0] - new_ele_name_1 = 'wind' - new_ele_desc_1_field = "element_description_%s" % element_ids[0] - ele_desc_1 = 'This is the wind component' - new_ele_name_2_field = "element_name_%s" % element_ids[1] - new_ele_name_2 = 'bag' - new_ele_desc_2_field = "element_description_%s" % element_ids[1] - ele_desc_2 = 'This is the bag component' - self.edit_library_info_template( str( library_one.id ), library_one_template.id, new_name, - new_ele_name_1_field, new_ele_name_1, new_ele_desc_1_field, ele_desc_1, - new_ele_name_2_field, new_ele_name_2, new_ele_desc_2_field, ele_desc_2 ) - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( new_ele_name_1 ) - self.check_page_for_string( ele_desc_1 ) - self.check_page_for_string( ele_1_contents ) - self.check_page_for_string( new_ele_name_2 ) - self.check_page_for_string( ele_desc_2 ) - self.check_page_for_string( ele_2_contents ) + # We only have a set of LibraryItemInfoTemplateElements + for ele in library_one_template.elements: + element_ids.append( ele.id ) + element_ids.sort() + # Add information to the library using the template + ele_1_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[0] ) ) + ele_1_contents = 'hello' + ele_2_field_name = "info_element_%s_%s" % ( str( library_one_template.id ), str( element_ids[1] ) ) + ele_2_contents = 'world' + self.edit_library_info( str( library_one.id ), library_one.name, + ele_1_field_name, ele_1_contents, + ele_2_field_name, ele_2_contents ) + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( ele_1_contents ) + self.check_page_for_string( ele_2_contents ) + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( ele_1_contents ) + self.check_page_for_string( ele_2_contents ) + # Edit the template + new_name = 'Library Template 1 renamed' + new_ele_name_1_field = "element_name_%s" % element_ids[0] + new_ele_name_1 = 'wind' + new_ele_desc_1_field = "element_description_%s" % element_ids[0] + ele_desc_1 = 'This is the wind component' + new_ele_name_2_field = "element_name_%s" % element_ids[1] + new_ele_name_2 = 'bag' + new_ele_desc_2_field = "element_description_%s" % element_ids[1] + ele_desc_2 = 'This is the bag component' + self.edit_library_info_template( str( library_one.id ), library_one_template.id, new_name, + new_ele_name_1_field, new_ele_name_1, new_ele_desc_1_field, ele_desc_1, + new_ele_name_2_field, new_ele_name_2, new_ele_desc_2_field, ele_desc_2 ) + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( new_ele_name_1 ) + self.check_page_for_string( ele_desc_1 ) + self.check_page_for_string( ele_1_contents ) + self.check_page_for_string( new_ele_name_2 ) + self.check_page_for_string( ele_desc_2 ) + self.check_page_for_string( ele_2_contents ) + """ def test_080_add_public_dataset_to_root_folder( self ): """Testing adding a public dataset to the root folder""" actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] @@ -623,7 +628,9 @@ if not dp.action == galaxy.model.Dataset.permitted_actions.DATASET_MANAGE_PERMISSIONS.action: raise AssertionError( 'The DatasetPermissions.action for dataset id %d is "%s", but it should be "manage permissions"' \ % ( ldda_one.dataset.id, dp.action ) ) + ## TODO: temporarily eliminating templates until we have the new forms features done # Make sure the library template was inherited by the ldda + """ self.home() self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) ) @@ -631,6 +638,7 @@ self.check_page_for_string( 'This is the wind component' ) self.check_page_for_string( 'bag' ) self.check_page_for_string( 'This is the bag component' ) + """ # Make sure other users can access the dataset from the Libraries view self.logout() self.login( email=regular_user2.email ) @@ -640,20 +648,23 @@ self.logout() self.login( email=admin_user.email ) self.home() - def test_085_editing_dataset_information( self ): - """Testing editing dataset template element information""" - # Need the current library_item_info_element.id - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - global ldda_one_ele_2_field_name - ldda_one_ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) - ele_2_contents = 'pipe' - global ldda_one_ele_1_field_name - ldda_one_ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) - ele_1_contents = 'blown' - self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), - ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents ) - self.home() + """ + ## TODO: temporarily eliminating templates until we have the new forms features done + def test_085_editing_dataset_information( self ): + Testing editing dataset template element information + # Need the current library_item_info_element.id + last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ + .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() + global ldda_one_ele_2_field_name + ldda_one_ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) + ele_2_contents = 'pipe' + global ldda_one_ele_1_field_name + ldda_one_ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) + ele_1_contents = 'blown' + self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), + ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents ) + self.home() + """ def test_090_add_new_folder_to_root_folder( self ): """Testing adding a folder to a library root folder""" root_folder = library_one.root_folder @@ -669,35 +680,41 @@ self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) self.check_page_for_string( description ) + ## TODO: temporarily eliminating templates until we have the new forms features done # Make sure the library template is inherited + """ self.home() self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) self.check_page_for_string( 'wind' ) self.check_page_for_string( 'This is the wind component' ) self.check_page_for_string( 'bag' ) self.check_page_for_string( 'This is the bag component' ) + """ self.home() - def test_095_add_folder_template( self ): - """Testing adding a new folder template to a folder""" - # Add a new information template to the folder - template_name = 'Folder Template 1' - ele_name_0 = 'Fu' - ele_help_0 = 'This is the Fu component'.replace( ' ', '+' ) - ele_name_1 = 'Bar' - ele_help_1 = 'This is the Bar component'.replace( ' ', '+' ) - self.home() - self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_one.id ), folder_one.name, - name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, - ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) - self.home() - self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) - self.check_page_for_string( ele_name_0 ) - check_str = ele_help_0.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - self.check_page_for_string( ele_name_1 ) - check_str = ele_help_1.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - self.home() + """ + ## TODO: temporarily eliminating templates until we have the new forms features done + def test_095_add_folder_template( self ): + Testing adding a new folder template to a folder + # Add a new information template to the folder + template_name = 'Folder Template 1' + ele_name_0 = 'Fu' + ele_help_0 = 'This is the Fu component'.replace( ' ', '+' ) + ele_name_1 = 'Bar' + ele_help_1 = 'This is the Bar component'.replace( ' ', '+' ) + self.home() + self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_one.id ), folder_one.name, + name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, + ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) + self.home() + self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) + self.check_page_for_string( ele_name_0 ) + check_str = ele_help_0.replace( '+', ' ' ) + self.check_page_for_string( check_str ) + self.check_page_for_string( ele_name_1 ) + check_str = ele_help_1.replace( '+', ' ' ) + self.check_page_for_string( check_str ) + self.home() + """ def test_100_add_subfolder_to_folder( self ): """Testing adding a folder to a library folder""" name = "Folder One's Subfolder" @@ -712,8 +729,10 @@ self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) self.check_page_for_string( description ) + ## TODO: temporarily eliminating templates until we have the new forms features done # Make sure the parent folder's template is inherited self.home() + """ self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) self.check_page_for_string( 'Fu' ) self.check_page_for_string( 'This is the Fu component' ) @@ -726,81 +745,84 @@ except: pass self.home() - def test_105_add_template_element( self ): - """Testing adding a new element to an existing library template""" - library_one_template.refresh() - element_ids = [] - for ele in library_one_template.elements: - element_ids.append( ele.id ) - element_ids.sort() - - name = 'Library Template 1 renamed' - ele_field_name_1 = "element_name_%s" % element_ids[0] - ele_name_1 = 'wind' - ele_field_desc_1 = "element_description_%s" % element_ids[0] - ele_desc_1 = 'This is the wind component' - ele_field_name_2 = "element_name_%s" % element_ids[1] - ele_name_2 = 'bag' - ele_field_desc_2 = "element_description_%s" % element_ids[1] - ele_desc_2 = 'This is the bag component' - new_ele_name = 'Fubar' - new_ele_desc = 'This is the Fubar component' - - self.add_library_info_template_element( str( library_one.id ), - str( library_one_template.id ), - library_one_template.name, - ele_field_name_1, - ele_name_1, - ele_field_desc_1, - ele_desc_1, - ele_field_name_2, - ele_name_2, - ele_field_desc_2, - ele_desc_2, - new_ele_name=new_ele_name, - new_ele_desc=new_ele_desc ) - # Make sure the new template element shows up on the existing library info page - self.home() - self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) - self.check_page_for_string( library_one.name ) - self.check_page_for_string( library_one.description ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'hello' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'world' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - # Make sure the new template element does not show up on existing info pages for folder_one since it has its own template - self.home() - self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) - self.check_page_for_string( 'Fu' ) - self.check_page_for_string( 'This is the Fu component' ) - self.check_page_for_string( 'Bar' ) - self.check_page_for_string( 'This is the Bar component' ) - try: + """ + ## TODO: temporarily eliminating templates until we have the new forms features done + """ + def test_105_add_template_element( self ): + Testing adding a new element to an existing library template + library_one_template.refresh() + element_ids = [] + for ele in library_one_template.elements: + element_ids.append( ele.id ) + element_ids.sort() + + name = 'Library Template 1 renamed' + ele_field_name_1 = "element_name_%s" % element_ids[0] + ele_name_1 = 'wind' + ele_field_desc_1 = "element_description_%s" % element_ids[0] + ele_desc_1 = 'This is the wind component' + ele_field_name_2 = "element_name_%s" % element_ids[1] + ele_name_2 = 'bag' + ele_field_desc_2 = "element_description_%s" % element_ids[1] + ele_desc_2 = 'This is the bag component' + new_ele_name = 'Fubar' + new_ele_desc = 'This is the Fubar component' + self.add_library_info_template_element( str( library_one.id ), + str( library_one_template.id ), + library_one_template.name, + ele_field_name_1, + ele_name_1, + ele_field_desc_1, + ele_desc_1, + ele_field_name_2, + ele_name_2, + ele_field_desc_2, + ele_desc_2, + new_ele_name=new_ele_name, + new_ele_desc=new_ele_desc ) + # Make sure the new template element shows up on the existing library info page + self.home() + self.visit_url( '%s/admin/library?id=%s&information=True' % ( self.url, str( library_one.id ) ) ) + self.check_page_for_string( library_one.name ) + self.check_page_for_string( library_one.description ) + self.check_page_for_string( 'wind' ) + self.check_page_for_string( 'hello' ) + self.check_page_for_string( 'This is the wind component' ) + self.check_page_for_string( 'bag' ) + self.check_page_for_string( 'world' ) + self.check_page_for_string( 'This is the bag component' ) self.check_page_for_string( 'Fubar' ) - raise AssertionError( 'Changed library template inherited by folder "%s" when folder had an associated template of its own' ) - except: - pass - # Make sure the new template element shows up on existing info pages for ldda_one since it is contained in the root folder - self.home() - self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_one.id ) ) ) - # Visiting the above page will have resulted in the creation of a new LibraryItemInfoElement, so we'll retrieve it - # for later use - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - global ldda_one_ele_3_field_name - ldda_one_ele_3_field_name = "info_element_%s" % str( last_library_item_info_element.id ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - self.home() + self.check_page_for_string( 'This is the Fubar component' ) + # Make sure the new template element does not show up on existing info pages for folder_one since it has its own template + self.home() + self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_one.id ), str( library_one.id ) ) ) + self.check_page_for_string( 'Fu' ) + self.check_page_for_string( 'This is the Fu component' ) + self.check_page_for_string( 'Bar' ) + self.check_page_for_string( 'This is the Bar component' ) + try: + self.check_page_for_string( 'Fubar' ) + raise AssertionError( 'Changed library template inherited by folder "%s" when folder had an associated template of its own' ) + except: + pass + # Make sure the new template element shows up on existing info pages for ldda_one since it is contained in the root folder + self.home() + self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_one.id ), str( ldda_one.id ) ) ) + # Visiting the above page will have resulted in the creation of a new LibraryItemInfoElement, so we'll retrieve it + # for later use + last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ + .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() + global ldda_one_ele_3_field_name + ldda_one_ele_3_field_name = "info_element_%s" % str( last_library_item_info_element.id ) + self.check_page_for_string( 'wind' ) + self.check_page_for_string( 'This is the wind component' ) + self.check_page_for_string( 'bag' ) + self.check_page_for_string( 'This is the bag component' ) + self.check_page_for_string( 'Fubar' ) + self.check_page_for_string( 'This is the Fubar component' ) + self.home() + """ def test_110_add_2nd_new_folder_to_root_folder( self ): """Testing adding a 2nd folder to a library root folder""" root_folder = library_one.root_folder @@ -816,7 +838,9 @@ self.visit_url( '%s/admin/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( name ) self.check_page_for_string( description ) + ## TODO: temporarily eliminating templates until we have the new forms features done # Make sure the changed library template is inherited to the new folder + """ self.home() self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) ) self.check_page_for_string( 'wind' ) @@ -825,6 +849,7 @@ self.check_page_for_string( 'This is the bag component' ) self.check_page_for_string( 'Fubar' ) self.check_page_for_string( 'This is the Fubar component' ) + """ self.home() def test_115_add_public_dataset_to_root_folders_2nd_subfolder( self ): """Testing adding a public dataset to the root folder's 2nd sub-folder""" @@ -848,56 +873,59 @@ self.check_page_for_string( "2.bed" ) self.check_page_for_string( message ) self.check_page_for_string( admin_user.email ) - def test_120_add_template_to_root_folders_2nd_subfolder( self ): - """Testing adding a template to the root folder's 2nd sub-folder""" - # Before adding the folder template, the inherited library template should be displayed - self.home() - self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - self.home() - # Add a new folde template - template_name = 'Folder 2 Template' - ele_name_0 = 'kill' - ele_help_0 = 'This is the kill component'.replace( ' ', '+' ) - ele_name_1 = 'bill' - ele_help_1 = 'This is the bill component'.replace( ' ', '+' ) - self.home() - self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_two.id ), folder_two.name, - name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, - ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) - # Make sure the new template id displayed on the folder information page - self.home() - self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) ) - self.check_page_for_string( ele_name_0 ) - check_str = ele_help_0.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - self.check_page_for_string( ele_name_1 ) - check_str = ele_help_1.replace( '+', ' ' ) - self.check_page_for_string( check_str ) - # The library dataset ldda_two had previously inherited the library template prior to the new folder template - # being introduced, so the library template should still be displayed on the ldda information page - self.home() - self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ - ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) - self.check_page_for_string( 'wind' ) - self.check_page_for_string( 'This is the wind component' ) - self.check_page_for_string( 'bag' ) - self.check_page_for_string( 'This is the bag component' ) - self.check_page_for_string( 'Fubar' ) - self.check_page_for_string( 'This is the Fubar component' ) - # Make sure the new folder template is not displayed - try: - self.check_page_for_string( 'kill' ) - raise AssertionError( 'New folder template elements incorrectly included in information page for ldda "%s"' % ldda_two.name ) - except: - pass - self.home() + ## TODO: temporarily eliminating templates until we have the new forms features done + """ + def test_120_add_template_to_root_folders_2nd_subfolder( self ): + Testing adding a template to the root folder's 2nd sub-folder + # Before adding the folder template, the inherited library template should be displayed + self.home() + self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) + self.check_page_for_string( 'wind' ) + self.check_page_for_string( 'This is the wind component' ) + self.check_page_for_string( 'bag' ) + self.check_page_for_string( 'This is the bag component' ) + self.check_page_for_string( 'Fubar' ) + self.check_page_for_string( 'This is the Fubar component' ) + self.home() + # Add a new folde template + template_name = 'Folder 2 Template' + ele_name_0 = 'kill' + ele_help_0 = 'This is the kill component'.replace( ' ', '+' ) + ele_name_1 = 'bill' + ele_help_1 = 'This is the bill component'.replace( ' ', '+' ) + self.home() + self.add_folder_info_template( str( library_one.id ), library_one.name, str( folder_two.id ), folder_two.name, + name=template_name, num_fields='2', ele_name_0=ele_name_0, ele_help_0=ele_help_0, + ele_name_1=ele_name_1, ele_help_1=ele_help_1 ) + # Make sure the new template id displayed on the folder information page + self.home() + self.visit_url( '%s/admin/folder?id=%s&library_id=%s&information=True' % ( self.url, str( folder_two.id ), str( library_one.id ) ) ) + self.check_page_for_string( ele_name_0 ) + check_str = ele_help_0.replace( '+', ' ' ) + self.check_page_for_string( check_str ) + self.check_page_for_string( ele_name_1 ) + check_str = ele_help_1.replace( '+', ' ' ) + self.check_page_for_string( check_str ) + # The library dataset ldda_two had previously inherited the library template prior to the new folder template + # being introduced, so the library template should still be displayed on the ldda information page + self.home() + self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ + ( self.url, str( library_one.id ), str( folder_two.id ), str( ldda_two.id ) ) ) + self.check_page_for_string( 'wind' ) + self.check_page_for_string( 'This is the wind component' ) + self.check_page_for_string( 'bag' ) + self.check_page_for_string( 'This is the bag component' ) + self.check_page_for_string( 'Fubar' ) + self.check_page_for_string( 'This is the Fubar component' ) + # Make sure the new folder template is not displayed + try: + self.check_page_for_string( 'kill' ) + raise AssertionError( 'New folder template elements incorrectly included in information page for ldda "%s"' % ldda_two.name ) + except: + pass + self.home() + """ def test_125_add_2nd_public_dataset_to_root_folders_2nd_subfolder( self ): """Testing adding a 2nd public dataset to the root folder's 2nd sub-folder""" actions = [ v.action for k, v in galaxy.model.Library.permitted_actions.items() ] @@ -920,22 +948,25 @@ self.check_page_for_string( "3.bed" ) self.check_page_for_string( message ) self.check_page_for_string( admin_user.email ) - def test_130_editing_dataset_information_with_new_folder_template( self ): - """Testing editing dataset template element information with new inherited folder template""" - # Need the current library_item_info_element.id - last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ - .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() - # Make sure the changed inherited template is included in the ldda information - ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) - ele_2_contents = 'II' - ele_2_help = 'This is the bill component' - ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) - ele_1_contents = 'Volume' - ele_1_help = 'This is the kill component' - self.edit_ldda_template_element_info( str( library_one.id ), str( folder_two.id ), str( ldda_three.id ), - ldda_three.name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents, - ele_1_help=ele_1_help, ele_2_help=ele_2_help ) - self.home() + ## TODO: temporarily eliminating templates until we have the new forms features done + """ + def test_130_editing_dataset_information_with_new_folder_template( self ): + Testing editing dataset template element information with new inherited folder template + # Need the current library_item_info_element.id + last_library_item_info_element = galaxy.model.LibraryItemInfoElement.query() \ + .order_by( desc( galaxy.model.LibraryItemInfoElement.table.c.id ) ).first() + # Make sure the changed inherited template is included in the ldda information + ele_2_field_name = "info_element_%s" % str( last_library_item_info_element.id ) + ele_2_contents = 'II' + ele_2_help = 'This is the bill component' + ele_1_field_name = "info_element_%s" % ( str( last_library_item_info_element.id - 1 ) ) + ele_1_contents = 'Volume' + ele_1_help = 'This is the kill component' + self.edit_ldda_template_element_info( str( library_one.id ), str( folder_two.id ), str( ldda_three.id ), + ldda_three.name, ele_1_field_name, ele_1_contents, ele_2_field_name, ele_2_contents, + ele_1_help=ele_1_help, ele_2_help=ele_2_help ) + self.home() + """ def test_135_add_dataset_with_private_role_restriction_to_folder( self ): """Testing adding a dataset with a private role restriction to a folder""" # Add a dataset restricted by the following: @@ -954,6 +985,8 @@ message ='This is a test of the fourth dataset uploaded' ele_name_0 = 'Fu' ele_name_1 = 'Bar' + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.add_library_dataset( '4.bed', str( library_one.id ), str( folder_one.id ), @@ -965,6 +998,16 @@ root=False, check_template_str1=ele_name_0, check_template_str2=ele_name_1 ) + """ + self.add_library_dataset( '4.bed', + str( library_one.id ), + str( folder_one.id ), + folder_one.name, + file_format='bed', + dbkey='hg18', + roles=[ str( regular_user1_private_role.id ) ], + message=message.replace( ' ', '+' ), + root=False ) global ldda_four ldda_four = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -1047,27 +1090,30 @@ self.visit_url( '%s/library/browse_library?id=%s' % ( self.url, str( library_one.id ) ) ) self.check_page_for_string( ldda_four.name ) self.home() - def test_150_editing_restricted_datasets_information( self ): - """Testing editing a restricted library dataset's template element information""" - ele_1_contents = '' - ele_2_contents = '' - ele_3_contents = 'Adding Fubar text' - self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), - ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents, - ele_1_help='This is the wind component'.replace( ' ', '+' ), - ele_2_help='This is the bag component'.replace( ' ', '+' ), - ele_3_field_name=ldda_one_ele_3_field_name, ele_3_contents=ele_3_contents.replace( ' ', '+' ) ) - # Check the updated information from the libraries view - self.home() - self.visit_url( '%s/library/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s' \ - % ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) ) - self.check_page_for_string( ele_3_contents ) - try: - self.check_page_for_string( 'blown' ) - raise AssertionError( 'Element contents were not correctly eliminated when the information was edited for ldda %s' % ldda_one.name) - except: - pass - self.home() + ## TODO: temporarily eliminating templates until we have the new forms features done + """ + def test_150_editing_restricted_datasets_information( self ): + Testing editing a restricted library dataset's template element information + ele_1_contents = '' + ele_2_contents = '' + ele_3_contents = 'Adding Fubar text' + self.edit_ldda_template_element_info( str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ), + ldda_one.name, ldda_one_ele_1_field_name, ele_1_contents, ldda_one_ele_2_field_name, ele_2_contents, + ele_1_help='This is the wind component'.replace( ' ', '+' ), + ele_2_help='This is the bag component'.replace( ' ', '+' ), + ele_3_field_name=ldda_one_ele_3_field_name, ele_3_contents=ele_3_contents.replace( ' ', '+' ) ) + # Check the updated information from the libraries view + self.home() + self.visit_url( '%s/library/library_dataset_dataset_association?info=True&library_id=%s&folder_id=%s&id=%s' \ + % ( self.url, str( library_one.id ), str( library_one.root_folder.id ), str( ldda_one.id ) ) ) + self.check_page_for_string( ele_3_contents ) + try: + self.check_page_for_string( 'blown' ) + raise AssertionError( 'Element contents were not correctly eliminated when the information was edited for ldda %s' % ldda_one.name) + except: + pass + self.home() + """ def test_155_add_dataset_with_role_associated_with_group_and_users( self ): """Testing adding a dataset with a role that is associated with a group and users""" self.login( email='test(a)bx.psu.edu' ) @@ -1077,6 +1123,8 @@ message = 'Testing adding a dataset with a role that is associated with a group and users' ele_name_0 = 'Fu' ele_name_1 = 'Bar' + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.add_library_dataset( '5.bed', str( library_one.id ), str( folder_one.id ), @@ -1088,6 +1136,16 @@ root=False, check_template_str1=ele_name_0, check_template_str2=ele_name_1 ) + """ + self.add_library_dataset( '5.bed', + str( library_one.id ), + str( folder_one.id ), + folder_one.name, + file_format='bed', + dbkey='hg17', + roles=[ str( role_two.id ) ], + message=message.replace( ' ', '+' ), + root=False ) global ldda_five ldda_five = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -1194,13 +1252,16 @@ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() assert ldda_six is not None, 'Problem retrieving LibraryDatasetDatasetAssociation ldda_six from the database' # Make sure the correct template was inherited + ## TODO: temporarily eliminating templates until we have the new forms features done self.home() + """ self.visit_url( "%s/admin/library_dataset_dataset_association?edit_info=True&library_id=%s&folder_id=%s&id=%s" % \ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six.id ) ) ) self.check_page_for_string( 'Fu' ) self.check_page_for_string( 'This is the Fu component' ) self.check_page_for_string( 'Bar' ) self.check_page_for_string( 'This is the Bar component' ) + """ def test_170_editing_dataset_attribute_info( self ): """Testing editing a datasets attribute information""" new_ldda_name = '6.bed ( version 1 )' @@ -1213,6 +1274,8 @@ def test_175_uploading_new_dataset_version( self ): """Testing uploading a new version of a dataset""" message = 'Testing uploading a new version of a dataset' + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.upload_new_dataset_version( '6.bed', str( library_one.id ), str( subfolder_one.id ), @@ -1224,6 +1287,16 @@ message=message.replace( ' ', '+' ), check_template_str1='Fu', check_template_str2='Bar' ) + """ + self.upload_new_dataset_version( '6.bed', + str( library_one.id ), + str( subfolder_one.id ), + str( subfolder_one.name ), + str( ldda_six.library_dataset.id ), + ldda_six.name, + file_format='auto', + dbkey='hg18', + message=message.replace( ' ', '+' ) ) global ldda_six_version_two ldda_six_version_two = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -1233,6 +1306,8 @@ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_two.id ) ) ) self.check_page_for_string( 'This is the latest version of this library dataset' ) # Make sure the correct template was inherited + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.check_page_for_string( 'Fu' ) self.check_page_for_string( 'This is the Fu component' ) self.check_page_for_string( 'Bar' ) @@ -1240,6 +1315,7 @@ check_str = 'Expired versions of %s' % ldda_six_version_two.name self.check_page_for_string( check_str ) self.check_page_for_string( ldda_six.name ) + """ self.home() # Make sure th permissions are the same ldda_six.refresh() @@ -1262,6 +1338,8 @@ """Testing uploading new versions of a dataset using a directory of files""" message = 'Testing uploading new versions of a dataset using a directory of files' ldda_six_version_two.refresh() + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.upload_new_dataset_versions( str( library_one.id ), str( subfolder_one.id ), str( subfolder_one.name ), @@ -1272,6 +1350,15 @@ message=message.replace( ' ', '+' ), check_template_str1='Fu', check_template_str2='Bar' ) + """ + self.upload_new_dataset_versions( str( library_one.id ), + str( subfolder_one.id ), + str( subfolder_one.name ), + str( ldda_six_version_two.library_dataset.id ), + ldda_six_version_two.name, + file_format='auto', + dbkey='hg18', + message=message.replace( ' ', '+' ) ) global ldda_six_version_five ldda_six_version_five = galaxy.model.LibraryDatasetDatasetAssociation.query() \ .order_by( desc( galaxy.model.LibraryDatasetDatasetAssociation.table.c.create_time ) ).first() @@ -1281,10 +1368,13 @@ ( self.url, str( library_one.id ), str( subfolder_one.id ), str( ldda_six_version_five.id ) ) ) self.check_page_for_string( 'This is the latest version of this library dataset' ) # Make sure the correct template was inherited + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.check_page_for_string( 'Fu' ) self.check_page_for_string( 'This is the Fu component' ) self.check_page_for_string( 'Bar' ) self.check_page_for_string( 'This is the Bar component' ) + """ check_str = 'Expired versions of %s' % ldda_six_version_five.name self.check_page_for_string( check_str ) self.check_page_for_string( ldda_six.name ) @@ -1309,7 +1399,9 @@ def test_185_upload_datasets_from_library_dir( self ): """Testing uploading 3 datasets from a library directory to a root folder""" message = 'This is a test for uploading a directory of files' - roles_tuple = [ ( str( role_one.id ), role_one.name ) ] + roles_tuple = [ ( str( role_one.id ), role_one.name ) ] + ## TODO: temporarily eliminating templates until we have the new forms features done + """ self.add_datasets_from_library_dir( str( library_one.id ), str( library_one.root_folder.id ), library_one.root_folder.name, @@ -1319,6 +1411,13 @@ check_template_str1='wind', check_template_str2='bag', check_template_str3='Fubar' ) + """ + self.add_datasets_from_library_dir( str( library_one.id ), + str( library_one.root_folder.id ), + library_one.root_folder.name, + roles_tuple=roles_tuple, + message=message.replace( '+', ' ' ), + root=True ) self.home() self.visit_page( 'admin/browse_library?id=%s' % ( str( library_one.id ) ) ) self.check_page_for_string( admin_user.email ) @@ -1552,6 +1651,7 @@ def test_245_purge_user( self ): """Testing purging a user account""" self.mark_user_deleted( user_id=regular_user3.id, email=regular_user3.email ) + regular_user3.refresh() self.purge_user( str( regular_user3.id ), regular_user3.email ) regular_user3.refresh() if not regular_user3.purged: @@ -1565,15 +1665,9 @@ raise AssertionError( 'DefaultUserPermissions for user %s are not related with the private role.' % regular_user3.email ) # Make sure History deleted for history in regular_user3.histories: + history.refresh() if not history.deleted: raise AssertionError( 'User %s has active history id %d after their account was marked as purged.' % ( regular_user3.email, hda.id ) ) - # Make sure DefaultHistoryPermissions deleted EXCEPT FOR THE PRIVATE ROLE - if len( history.default_permissions ) != 1: - raise AssertionError( 'DefaultHistoryPermissions for history id %d were not deleted.' % history.id ) - for dhp in history.default_permissions: - role = galaxy.model.Role.get( dhp.role_id ) - if role.type != 'private': - raise AssertionError( 'DefaultHistoryPermissions for history id %d are not related with the private role.' % history.id ) # Make sure HistoryDatasetAssociation deleted for hda in history.datasets: hda.refresh()

1 0

trouble running galaxy server
by Andrew Stewart 04 Jun '09

04 Jun '09

sh run.sh seems to work okay until hitting this block of report... Any ideas what this socket business is about? It looks to me like possibly something python-specific. Starting server in PID 11963. Traceback (most recent call last): File "./scripts/paster.py", line 27, in ? command.run() File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ PasteScript-1.3.6-py2.4.egg/paste/script/command.py", line 78, in run File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ PasteScript-1.3.6-py2.4.egg/paste/script/command.py", line 117, in invoke File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ PasteScript-1.3.6-py2.4.egg/paste/script/command.py", line 212, in run File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ PasteScript-1.3.6-py2.4.egg/paste/script/serve.py", line 232, in command File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ PasteDeploy-1.3.1-py2.4.egg/paste/deploy/loadwsgi.py", line 139, in server_wrapper File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ PasteDeploy-1.3.1-py2.4.egg/paste/deploy/util/fixtypeerror.py", line 57, in fix_call File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1307, in server_runner File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1257, in serve File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1107, in __init__ File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 1087, in __init__ File "/root/src/galaxy-f7336991d0ee/eggs/py2.4-noplatform/ Paste-1.5.1-py2.4.egg/paste/httpserver.py", line 328, in __init__ File "/usr/lib64/python2.4/SocketServer.py", line 330, in __init__ self.server_bind() File "/usr/lib64/python2.4/BaseHTTPServer.py", line 101, in server_bind SocketServer.TCPServer.server_bind(self) File "/usr/lib64/python2.4/SocketServer.py", line 341, in server_bind self.socket.bind(self.server_address) File "<string>", line 1, in bind socket.error: (98, 'Address already in use') galaxy.jobs INFO 2009-06-05 02:15:43,692 sending stop signal to worker thread galaxy.jobs INFO 2009-06-05 02:15:43,692 job queue stopped galaxy.jobs.runners.local INFO 2009-06-05 02:15:43,693 sending stop signal to worker threads galaxy.jobs.runners.local INFO 2009-06-05 02:15:43,694 local job runner stopped galaxy.jobs INFO 2009-06-05 02:15:43,694 sending stop signal to worker thread galaxy.jobs INFO 2009-06-05 02:15:43,695 job stopper stopped

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