November 2009 - galaxy-dev - lists.galaxyproject.org

[hg] galaxy 2978: Remove tool conf typo
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/840255033ab0 changeset: 2978:840255033ab0 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Nov 06 14:36:36 2009 -0500 description: Remove tool conf typo diffstat: tool_conf.xml.sample | 1 - 1 files changed, 0 insertions(+), 1 deletions(-) diffs (11 lines): diff -r b08d426dc57f -r 840255033ab0 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Nov 06 14:23:21 2009 -0500 +++ b/tool_conf.xml.sample Fri Nov 06 14:36:36 2009 -0500 @@ -128,7 +128,6 @@ <tool file="visualization/genetrack_indexer.xml" /> <tool file="visualization/genetrack_peak_prediction.xml" /> </section> - </section> <section name="Regional Variation" id="regVar"> <tool file="regVariation/windowSplitter.xml" /> <tool file="regVariation/featureCounter.xml" />

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[hg] galaxy 2977: Fix for GeneTrack egg
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b08d426dc57f changeset: 2977:b08d426dc57f user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Nov 06 14:23:21 2009 -0500 description: Fix for GeneTrack egg diffstat: scripts/scramble/scripts/GeneTrack.py | 18 ++++++++++++------ 1 files changed, 12 insertions(+), 6 deletions(-) diffs (33 lines): diff -r 4a7f9fdead89 -r b08d426dc57f scripts/scramble/scripts/GeneTrack.py --- a/scripts/scramble/scripts/GeneTrack.py Fri Nov 06 14:22:44 2009 -0500 +++ b/scripts/scramble/scripts/GeneTrack.py Fri Nov 06 14:23:21 2009 -0500 @@ -35,17 +35,23 @@ sys.argv.append( "--no-svn-revision" ) sys.argv.append( "bdist_egg" ) -print "scramble.py: Creating setup.py for GeneTrack" -setup_py = """from setuptools import setup, find_packages +if not os.access( 'setup.py', os.F_OK ): + print "scramble.py: Creating setup.py for GeneTrack" + setup_py = """from os import walk +from os.path import join +from setuptools import setup, find_packages +def walk_files( top ): + for dir, dirs, files in walk( top ): + yield( dir, [ join( dir, f ) for f in files ] ) setup( name = "GeneTrack", version = "2.0.0-beta-1", - package_data = {'':["*.*"]}, - packages = find_packages(), - zip_safe = True, + packages = ['genetrack','genetrack.scripts'], + data_files = [ f for f in walk_files('tests') ], + zip_safe = False ) """ -open( 'setup.py', 'w' ).write( setup_py ) + open( 'setup.py', 'w' ).write( setup_py ) # do it

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[hg] galaxy 2979: Commented out second test for SAM-to-BAM so te...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/b54c37f53d53 changeset: 2979:b54c37f53d53 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Nov 06 16:52:00 2009 -0500 description: Commented out second test for SAM-to-BAM so tests will pass, because it relies on using a built-in dbkey that doesn't exist in builds.txt diffstat: tools/samtools/sam_to_bam.xml | 5 +++-- 1 files changed, 3 insertions(+), 2 deletions(-) diffs (23 lines): diff -r 840255033ab0 -r b54c37f53d53 tools/samtools/sam_to_bam.xml --- a/tools/samtools/sam_to_bam.xml Fri Nov 06 14:36:36 2009 -0500 +++ b/tools/samtools/sam_to_bam.xml Fri Nov 06 16:52:00 2009 -0500 @@ -36,16 +36,17 @@ <tests> <test> <param name="indexSource" value="history" /> - <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" /> + <param name="input1" value="sam_to_bam_in1.sam" ftype="sam" dbkey="chrM" /> <param name="ref_file" value="chrM.fa" ftype="fasta" /> <output name="output1" file="sam_to_bam_out1.bam" /> </test> + </tests> <help>

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[hg] galaxy 2980: Refactored grid code to (a) generalize numerou...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f520e80ac09c changeset: 2980:f520e80ac09c user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Fri Nov 06 19:04:13 2009 -0500 description: Refactored grid code to (a) generalize numerous column types and (b) fully support multiple, arbitrary, multi-column categorical and free-text queries. Python code provides support for TextColumn and TagColumn objects, and grids_common.mako provides support for programmatically creating free text and categorical filtering UIs. History and HDA grids have been updated to use the refactored code. diffstat: lib/galaxy/model/__init__.py | 2 +- lib/galaxy/web/controllers/dataset.py | 63 ++------------- lib/galaxy/web/controllers/history.py | 129 +++++--------------------------- lib/galaxy/web/controllers/tag.py | 4 +- lib/galaxy/web/framework/helpers/grids.py | 131 +++++++++++++++++++++++++++++++- static/scripts/jquery.wymeditor.js | 92 ++++++++++++++++++++++- static/wymeditor/lang/en.js | 6 +- static/wymeditor/skins/galaxy/icons.png | static/wymeditor/skins/galaxy/skin.css | 1 + templates/dataset/grid.mako | 41 +--------- templates/grid_common.mako | 129 ++++++++++++++++++++++++++++++++ templates/history/grid.mako | 100 +----------------------- 12 files changed, 394 insertions(+), 304 deletions(-) diffs (990 lines): diff -r b54c37f53d53 -r f520e80ac09c lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Fri Nov 06 16:52:00 2009 -0500 +++ b/lib/galaxy/model/__init__.py Fri Nov 06 19:04:13 2009 -0500 @@ -246,7 +246,7 @@ # This needs to be a list return [ hda for hda in self.datasets if not hda.dataset.deleted ] def get_display_name( self ): - ## History name can be either a string or a unicode object. If string, convert to unicode object assuming 'utf-8' format. + """ History name can be either a string or a unicode object. If string, convert to unicode object assuming 'utf-8' format. """ history_name = self.name if isinstance(history_name, str): history_name = unicode(history_name, 'utf-8') diff -r b54c37f53d53 -r f520e80ac09c lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Fri Nov 06 16:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Fri Nov 06 19:04:13 2009 -0500 @@ -1,7 +1,6 @@ import logging, os, string, shutil, re, socket, mimetypes, smtplib, urllib from galaxy.web.base.controller import * -from galaxy.tags.tag_handler import TagHandler from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy import util, datatypes, jobs, web, model from cgi import escape, FieldStorage @@ -49,55 +48,7 @@ class HistoryColumn( grids.GridColumn ): def get_value( self, trans, grid, hda): return hda.history.name - - class StatusColumn( grids.GridColumn ): - def get_value( self, trans, grid, hda ): - if hda.deleted: - return "deleted" - return "" - def get_link( self, trans, grid, hda ): - return None - class TagsColumn( grids.GridColumn ): - def __init__(self, col_name, key, filterable): - grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) - # Tags cannot be sorted. - self.sortable = False - self.tag_elt_id_gen = 0 - def get_value( self, trans, grid, hda ): - self.tag_elt_id_gen += 1 - elt_id="tagging-elt" + str( self.tag_elt_id_gen ) - div_elt = "<div id=%s></div>" % elt_id - return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=hda, - elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) - def filter( self, db_session, query, column_filter ): - """ Modify query to include only hdas with tags in column_filter. """ - if column_filter == "All": - pass - elif column_filter: - # Parse filter to extract multiple tags. - tag_handler = TagHandler() - raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) - for name, value in raw_tags.items(): - tag = tag_handler.get_tag_by_name( db_session, name ) - if tag: - query = query.filter( model.HistoryDatasetAssociation.tags.any( tag_id=tag.id ) ) - if value: - query = query.filter( model.HistoryDatasetAssociation.tags.any( value=value.lower() ) ) - else: - # Tag doesn't exist; unclear what to do here, but the literal thing to do is add the criterion, which - # will then yield a query that returns no results. - query = query.filter( model.HistoryDatasetAssociation.tags.any( user_tname=name ) ) - return query - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = { "All": "All" } - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.items(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters - class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, hda ): if hda.deleted: @@ -118,19 +69,25 @@ template='/dataset/grid.mako' default_sort_key = "-create_time" columns = [ - grids.GridColumn( "Name", key="name", + grids.TextColumn( "Name", key="name", model_class=model.HistoryDatasetAssociation, # Link name to dataset's history. - link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ) ), + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ), filterable="advanced" ), HistoryColumn( "History", key="history", link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), - TagsColumn( "Tags", key="tags", filterable=True ), + grids.TagsColumn( "Tags", "tags", model.HistoryDatasetAssociation, model.HistoryDatasetAssociationTagAssociation, filterable="advanced" ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), ] + columns.append( + grids.MulticolFilterColumn( + "Search", + cols_to_filter=[ columns[0], columns[2] ], + key="free-text-search", visible=False, filterable="default" ) + ) operations = [] standard_filters = [] - default_filter = dict( deleted="False", tags="All" ) + default_filter = dict( name="All", deleted="False", tags="All" ) preserve_state = False use_paging = True num_rows_per_page = 50 diff -r b54c37f53d53 -r f520e80ac09c lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Fri Nov 06 16:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Fri Nov 06 19:04:13 2009 -0500 @@ -2,7 +2,6 @@ from galaxy.web.framework.helpers import time_ago, iff, grids from galaxy import util from galaxy.model.mapping import desc -from galaxy.model import History from galaxy.model.orm import * from galaxy.util.json import * from galaxy.util.odict import odict @@ -19,30 +18,10 @@ class HistoryListGrid( grids.Grid ): # Custom column types - class NameColumn( grids.GridColumn ): - def __init( self, key, link, attach_popup, filterable ): - grids.GridColumn.__init__(self, key, link, attach_popup) - - def get_value( self, trans, grid, history ): + class NameColumn( grids.TextColumn ): + def get_value(self, trans, grid, history): return history.get_display_name() - def filter( self, db_session, query, column_filter ): - """ Modify query to filter histories by name. """ - if column_filter == "All": - pass - elif column_filter: - query = query.filter( func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) ) - return query - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = odict() - accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.iteritems(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters - class DatasetsByStateColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): rval = [] @@ -53,6 +32,7 @@ else: rval.append( '' ) return rval + class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, history ): if history.deleted: @@ -66,44 +46,6 @@ if item.users_shared_with or item.importable: return dict( operation="sharing" ) return None - - class TagsColumn( grids.GridColumn ): - def __init__( self, col_name, key, filterable ): - grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) - # Tags cannot be sorted. - self.sortable = False - self.tag_elt_id_gen = 0 - def get_value( self, trans, grid, history ): - self.tag_elt_id_gen += 1 - elt_id="tagging-elt" + str( self.tag_elt_id_gen ) - div_elt = "<div id=%s></div>" % elt_id - return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=history, - elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) - def filter( self, db_session, query, column_filter ): - """ Modify query to filter histories by tag. """ - if column_filter == "All": - pass - elif column_filter: - # Parse filter to extract multiple tags. - tag_handler = TagHandler() - raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) - for name, value in raw_tags.items(): - if name: - # Search for tag names. - query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) ) - if value: - # Search for tag values. - query = query.filter( History.tags.any( func.lower( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) - return query - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = odict() - accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.iteritems(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters class DeletedColumn( grids.GridColumn ): def get_accepted_filters( self ): @@ -122,12 +64,12 @@ pass elif column_filter: if column_filter == "private": - query = query.filter( History.users_shared_with == None ) - query = query.filter( History.importable == False ) + query = query.filter( model.History.users_shared_with == None ) + query = query.filter( model.History.importable == False ) elif column_filter == "shared": - query = query.filter( History.users_shared_with != None ) + query = query.filter( model.History.users_shared_with != None ) elif column_filter == "importable": - query = query.filter( History.importable == True ) + query = query.filter( model.History.importable == True ) return query def get_accepted_filters( self ): """ Returns a list of accepted filters for this column. """ @@ -141,43 +83,6 @@ args = { self.key: val } accepted_filters.append( grids.GridColumnFilter( label, args) ) return accepted_filters - - class FreeTextSearchColumn( grids.GridColumn ): - def filter( self, db_session, query, column_filter ): - """ Modify query to search tags and history names. """ - if column_filter == "All": - pass - elif column_filter: - # Build tags filter. - tag_handler = TagHandler() - raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) - tags_filter = None - for name, value in raw_tags.items(): - if name: - # Search for tag names. - tags_filter = History.tags.any( func.lower( model.HistoryTagAssociation.user_tname ).like( "%" + name.lower() + "%" ) ) - if value: - # Search for tag values. - tags_filter = and_( tags_filter, func.lower( History.tags.any( model.HistoryTagAssociation.user_value ).like( "%" + value.lower() + "%" ) ) ) - - # Build history name filter. - history_name_filter = func.lower( History.name ).like( "%" + column_filter.lower() + "%" ) - - # Apply filters to query. - if tags_filter: - query = query.filter( or_( tags_filter, history_name_filter ) ) - else: - query = query.filter( history_name_filter ) - return query - def get_accepted_filters( self ): - """ Returns a list of accepted filters for this column. """ - accepted_filter_labels_and_vals = odict() - accepted_filter_labels_and_vals["FREETEXT"] = "FREETEXT" - accepted_filters = [] - for label, val in accepted_filter_labels_and_vals.iteritems(): - args = { self.key: val } - accepted_filters.append( grids.GridColumnFilter( label, args) ) - return accepted_filters # Grid definition title = "Saved Histories" @@ -185,19 +90,25 @@ template='/history/grid.mako' default_sort_key = "-create_time" columns = [ - NameColumn( "Name", key="name", + NameColumn( "Name", key="name", model_class=model.History, link=( lambda history: iff( history.deleted, None, dict( operation="switch", id=history.id ) ) ), - attach_popup=True, filterable=True ), + attach_popup=True, filterable="advanced" ), DatasetsByStateColumn( "Datasets (by state)", ncells=4 ), - TagsColumn( "Tags", key="tags", filterable=True), + grids.TagsColumn( "Tags", "tags", model.History, model.HistoryTagAssociation, filterable="advanced"), StatusColumn( "Status", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), grids.GridColumn( "Last Updated", key="update_time", format=time_ago ), # Columns that are valid for filtering but are not visible. - DeletedColumn( "Deleted", key="deleted", visible=False, filterable=True ), - SharingColumn( "Shared", key="shared", visible=False, filterable=True ), - FreeTextSearchColumn( "Search", key="free-text-search", visible=False ) # Not filterable because it's the default search. + DeletedColumn( "Deleted", key="deleted", visible=False, filterable="advanced" ), + SharingColumn( "Shared", key="shared", visible=False, filterable="advanced" ), ] + columns.append( + grids.MulticolFilterColumn( + "Search", + cols_to_filter=[ columns[0], columns[2] ], + key="free-text-search", visible=False, filterable="default" ) + ) + operations = [ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), grids.GridOperation( "Share", condition=( lambda item: not item.deleted ) ), @@ -464,7 +375,7 @@ return ac_data = "" - for history in trans.sa_session.query( History ).filter_by( user=user ).filter( func.lower( History.name ) .like(q.lower() + "%") ): + for history in trans.sa_session.query( model.History ).filter_by( user=user ).filter( func.lower( model.History.name ) .like(q.lower() + "%") ): ac_data = ac_data + history.name + "\n" return ac_data diff -r b54c37f53d53 -r f520e80ac09c lib/galaxy/web/controllers/tag.py --- a/lib/galaxy/web/controllers/tag.py Fri Nov 06 16:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/tag.py Fri Nov 06 19:04:13 2009 -0500 @@ -105,7 +105,7 @@ # Build select statement. cols_to_select = [ item_tag_assoc_class.table.c.tag_id, func.count('*') ] - from_obj = item_tag_assoc_class.table.join(item_class.table).join(Tag) + from_obj = item_tag_assoc_class.table.join(item_class.table).join(Tag.table) where_clause = and_(self._get_column_for_filtering_item_by_user_id(item_class)==trans.get_user().id, Tag.table.c.name.like(q + "%")) order_by = [ func.count("*").desc() ] @@ -154,7 +154,7 @@ # Build select statement. cols_to_select = [ item_tag_assoc_class.table.c.value, func.count('*') ] - from_obj = item_tag_assoc_class.table.join(item_class.table).join(Tag) + from_obj = item_tag_assoc_class.table.join(item_class.table).join(Tag.table) where_clause = and_(self._get_column_for_filtering_item_by_user_id(item_class)==trans.get_user().id, Tag.table.c.id==tag.id, item_tag_assoc_class.table.c.value.like(tag_value + "%")) diff -r b54c37f53d53 -r f520e80ac09c lib/galaxy/web/framework/helpers/grids.py --- a/lib/galaxy/web/framework/helpers/grids.py Fri Nov 06 16:52:00 2009 -0500 +++ b/lib/galaxy/web/framework/helpers/grids.py Fri Nov 06 19:04:13 2009 -0500 @@ -1,6 +1,7 @@ from galaxy.model import * from galaxy.model.orm import * +from galaxy.tags.tag_handler import TagHandler from galaxy.web import url_for from galaxy.util.json import from_json_string, to_json_string @@ -87,18 +88,51 @@ column_filter = kwargs.get( "f-" + column.key ) elif column.key in base_filter: column_filter = base_filter.get( column.key ) - + + # Method (1) combines a mix of strings and lists of strings into a single string and (2) attempts to de-jsonify all strings. + def from_json_string_recurse(item): + decoded_list = [] + if isinstance( item, basestring): + try: + # Not clear what we're decoding, so recurse to ensure that we catch everything. + decoded_item = from_json_string( item ) + if isinstance( decoded_item, list): + decoded_list = from_json_string_recurse( decoded_item ) + else: + decoded_list = [ str( decoded_item ) ] + except ValueError: + decoded_list = [ str( item ) ] + elif isinstance( item, list): + return_val = [] + for element in item: + a_list = from_json_string_recurse( element ) + decoded_list = decoded_list + a_list + return decoded_list + # If column filter found, apply it. if column_filter is not None: + # TextColumns may have a mix of json and strings. + if isinstance( column, TextColumn ): + column_filter = from_json_string_recurse( column_filter ) + if len( column_filter ) == 1: + column_filter = column_filter[0] # Update query. query = column.filter( trans.sa_session, query, column_filter ) # Upate current filter dict. cur_filter_dict[ column.key ] = column_filter - # Carry filter along to newly generated urls; make sure filter is a string so + # Carry filter along to newly generated urls; make sure filter is a string so # that we can encode to UTF-8 and thus handle user input to filters. - if not isinstance( column_filter, basestring ): - column_filter = unicode(column_filter) - extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") + if isinstance( column_filter, list ): + # Filter is a list; process each item. + for filter in column_filter: + if not isinstance( filter, basestring ): + filter = unicode( filter ).encode("utf-8") + extra_url_args[ "f-" + column.key ] = to_json_string( column_filter ) + else: + # Process singleton filter. + if not isinstance( column_filter, basestring ): + column_filter = unicode(column_filter) + extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") # Process sort arguments. sort_key = sort_order = None @@ -218,9 +252,12 @@ return query class GridColumn( object ): - def __init__( self, label, key=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, filterable=False ): + def __init__( self, label, key=None, model_class=None, method=None, format=None, link=None, attach_popup=False, visible=True, ncells=1, + # Valid values for filterable are ['default', 'advanced', None] + filterable=None ): self.label = label self.key = key + self.model_class = model_class self.method = method self.format = format self.link = link @@ -265,6 +302,88 @@ args = { self.key: val } accepted_filters.append( GridColumnFilter( val, args) ) return accepted_filters + +# Generic column that employs freetext and, hence, supports freetext, case-independent filtering. +class TextColumn( GridColumn ): + def filter( self, db_session, query, column_filter ): + """ Modify query to filter using free text, case independence. """ + if column_filter == "All": + pass + elif column_filter: + query = query.filter( self.get_filter( column_filter ) ) + return query + def get_filter( self, column_filter ): + """ Returns a SQLAlchemy criterion derived from column_filter. """ + # This is a pretty ugly way to get the key attribute of model_class. TODO: Can this be fixed? + model_class_key_field = eval( "self.model_class." + self.key ) + + if isinstance( column_filter, basestring ): + return func.lower( model_class_key_field ).like( "%" + column_filter.lower() + "%" ) + elif isinstance( column_filter, list ): + composite_filter = True + for filter in column_filter: + composite_filter = and_( composite_filter, func.lower( model_class_key_field ).like( "%" + filter.lower() + "%" ) ) + return composite_filter + +# Generic column that supports tagging. +class TagsColumn( TextColumn ): + def __init__( self, col_name, key, model_class, model_tag_association_class, filterable ): + GridColumn.__init__(self, col_name, key=key, model_class=model_class, filterable=filterable) + self.model_tag_association_class = model_tag_association_class + # Tags cannot be sorted. + self.sortable = False + self.tag_elt_id_gen = 0 + def get_value( self, trans, grid, item ): + self.tag_elt_id_gen += 1 + elt_id="tagging-elt" + str( self.tag_elt_id_gen ) + div_elt = "<div id=%s></div>" % elt_id + return div_elt + trans.fill_template( "/tagging_common.mako", trans=trans, tagged_item=item, + elt_id = elt_id, in_form="true", input_size="20", tag_click_fn="add_tag_to_grid_filter" ) + def filter( self, db_session, query, column_filter ): + """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ + if column_filter == "All": + pass + elif column_filter: + query = query.filter( self.get_filter( column_filter ) ) + return query + def get_filter( self, column_filter ): + # Parse filter to extract multiple tags. + tag_handler = TagHandler() + if isinstance( column_filter, list ): + # Collapse list of tags into a single string; this is redundant but effective. TODO: fix this by iterating over tags. + column_filter = ",".join( column_filter ) + raw_tags = tag_handler.parse_tags( column_filter.encode("utf-8") ) + filter = True + for name, value in raw_tags.items(): + if name: + # Search for tag names. + filter = and_( filter, self.model_class.tags.any( func.lower( self.model_tag_association_class.user_tname ).like( "%" + name.lower() + "%" ) ) ) + if value: + # Search for tag values. + filter = and_( filter, self.model_class.tags.any( func.lower( self.model_tag_association_class.user_value ).like( "%" + value.lower() + "%" ) ) ) + return filter + +# Column that performs multicolumn filtering. +class MulticolFilterColumn( TextColumn ): + def __init__( self, col_name, cols_to_filter, key, visible, filterable="default" ): + GridColumn.__init__( self, col_name, key=key, visible=visible, filterable=filterable) + self.cols_to_filter = cols_to_filter + def filter( self, db_session, query, column_filter ): + """ Modify query to filter model_class by tag. Multiple filters are ANDed. """ + if column_filter == "All": + return query + if isinstance( column_filter, list): + composite_filter = True + for filter in column_filter: + part_composite_filter = False + for column in self.cols_to_filter: + part_composite_filter = or_( part_composite_filter, column.get_filter( filter ) ) + composite_filter = and_( composite_filter, part_composite_filter ) + else: + composite_filter = False + for column in self.cols_to_filter: + composite_filter = or_( composite_filter, column.get_filter( column_filter ) ) + return query.filter( composite_filter ) class GridOperation( object ): def __init__( self, label, key=None, condition=None, allow_multiple=True, allow_popup=True, target=None, url_args=None ): diff -r b54c37f53d53 -r f520e80ac09c static/scripts/jquery.wymeditor.js --- a/static/scripts/jquery.wymeditor.js Fri Nov 06 16:52:00 2009 -0500 +++ b/static/scripts/jquery.wymeditor.js Fri Nov 06 19:04:13 2009 -0500 @@ -295,6 +295,66 @@ }); +/* + Galaxy code that integrates into the WYM Editor. + */ +var Galaxy = +{ + /* + Galaxy constants for WYM Editor: + TOOLS - A string replaced by the galaxy toolbar's HTML. + TOOLS_ITEMS - A string replaced by the galaxy toolbar items. + INSERT_HISTORY - Command: open the insert history dialog. + INSERT_DATASET - Command: open the insert dataset dialog. + DIALOG_HISTORY - A dialog to insert a history. + DIALOG_DATASET - A dialog to insert a dataset. + */ + TOOLS : "{Galaxy_Tools}", + TOOLS_ITEMS : "{Galaxy_Tools_Items}", + INSERT_HISTORY : "InsertHistory", + INSERT_DATASET : "InsertDataset", + DIALOG_HISTORY : "DialogHistory", + DIALOG_DATASET : "DialogDataset", + + // Tool items overview. + toolsItems: [ + {'name': "InsertHistory", 'title': 'History', 'css': 'galaxy_tools_insert_history_link'}, + {'name': "InsertDataset", 'title': 'Dataset', 'css': 'galaxy_dataset'} + ], + + // Tools HTML. + toolsHtml: "<div class='wym_tools wym_section'>" + + "<h2>" + this.TOOLS + "</h2>" + + "<ul>" + + this.TOOLS_ITEMS + + "</ul>" + + "</div>", + + // Insert history dialog. + dialogHistoryHtml: "<body class='wym_dialog wym_dialog_history'" + + " onload='WYMeditor.INIT_DIALOG(" + WYMeditor.INDEX + ")'" + + ">" + + "<form>" + + "<fieldset>" + + "<input type='hidden' class='wym_dialog_type' value='" + + this.DIALOG_HISTORY + + "' />" + + "<legend>{Link}</legend>" + + "<div class='row'>" + + "<label>{Title}</label>" + + "<input type='text' class='wym_title' value='' size='40' />" + + "</div>" + + "<div class='row row-indent'>" + + "<input class='wym_submit' type='button'" + + " value='{Add}' />" + + "<input class='wym_cancel' type='button'" + + "value='{Cancel}' />" + + "</div>" + + "</fieldset>" + + "</form>" + + "</body>", +}; + /********** JQUERY **********/ @@ -354,6 +414,7 @@ + "<div class='wym_area_right'>" + WYMeditor.CONTAINERS + WYMeditor.CLASSES + + Galaxy.TOOLS + "</div>" + "<div class='wym_area_main'>" + WYMeditor.HTML @@ -384,6 +445,8 @@ + "<h2>{Tools}</h2>" + "<ul>" + WYMeditor.TOOLS_ITEMS + // Add Galaxy Tools. + + Galaxy.TOOLS_ITEMS + "</ul>" + "</div>", @@ -758,6 +821,7 @@ boxHtml = h.replaceAll(boxHtml, WYMeditor.LOGO, this._options.logoHtml); boxHtml = h.replaceAll(boxHtml, WYMeditor.TOOLS, this._options.toolsHtml); + boxHtml = h.replaceAll(boxHtml, Galaxy.TOOLS, Galaxy.toolsHtml); boxHtml = h.replaceAll(boxHtml, WYMeditor.CONTAINERS,this._options.containersHtml); boxHtml = h.replaceAll(boxHtml, WYMeditor.CLASSES, this._options.classesHtml); boxHtml = h.replaceAll(boxHtml, WYMeditor.HTML, this._options.htmlHtml); @@ -781,6 +845,24 @@ } boxHtml = h.replaceAll(boxHtml, WYMeditor.TOOLS_ITEMS, sTools); + + // Construct Galaxy tools list. + var galaxyTools = eval(Galaxy.toolsItems); + sTools = ""; + for(var i = 0; i < galaxyTools.length; i++) { + var galaxyTool = galaxyTools[i]; + if(galaxyTool.name && galaxyTool.title) { + var sTool = this._options.toolsItemHtml; + var sTool = h.replaceAll(sTool, WYMeditor.TOOL_NAME, galaxyTool.name); + sTool = h.replaceAll(sTool, WYMeditor.TOOL_TITLE, this._options.stringDelimiterLeft + + galaxyTool.title + + this._options.stringDelimiterRight); + sTool = h.replaceAll(sTool, WYMeditor.TOOL_CLASS, galaxyTool.css); + sTools += sTool; + } + } + + boxHtml = h.replaceAll(boxHtml, Galaxy.TOOLS_ITEMS, sTools); //construct classes list var aClasses = eval(this._options.classesItems); @@ -947,6 +1029,10 @@ this.dialog(WYMeditor.PREVIEW, this._options.dialogFeaturesPreview); break; + case Galaxy.INSERT_HISTORY: + this.dialog(Galaxy.DIALOG_HISTORY); + break; + default: this._exec(cmd); break; @@ -1153,7 +1239,6 @@ * @description Opens a dialog box */ WYMeditor.editor.prototype.dialog = function( dialogType, dialogFeatures, bodyHtml ) { - var features = dialogFeatures || this._wym._options.dialogFeatures; var wDialog = window.open('', 'dialog', features); @@ -1178,11 +1263,13 @@ case(WYMeditor.PREVIEW): sBodyHtml = this._options.dialogPreviewHtml; break; + case(Galaxy.DIALOG_HISTORY): + sBodyHtml = Galaxy.dialogHistoryHtml; + break; default: sBodyHtml = bodyHtml; } - var h = WYMeditor.Helper; //construct the dialog @@ -1197,7 +1284,6 @@ dialogHtml = h.replaceAll(dialogHtml, WYMeditor.INDEX, this._index); dialogHtml = this.replaceStrings(dialogHtml); - var doc = wDialog.document; doc.write(dialogHtml); doc.close(); diff -r b54c37f53d53 -r f520e80ac09c static/wymeditor/lang/en.js --- a/static/wymeditor/lang/en.js Fri Nov 06 16:52:00 2009 -0500 +++ b/static/wymeditor/lang/en.js Fri Nov 06 19:04:13 2009 -0500 @@ -40,6 +40,10 @@ Containers: 'Containers', Classes: 'Classes', Status: 'Status', - Source_Code: 'Source code' + Source_Code: 'Source code', + + // Galaxy replacements. + History: 'History', + Dataset: 'Dataset', }; diff -r b54c37f53d53 -r f520e80ac09c static/wymeditor/skins/galaxy/icons.png Binary file static/wymeditor/skins/galaxy/icons.png has changed diff -r b54c37f53d53 -r f520e80ac09c static/wymeditor/skins/galaxy/skin.css --- a/static/wymeditor/skins/galaxy/skin.css Fri Nov 06 16:52:00 2009 -0500 +++ b/static/wymeditor/skins/galaxy/skin.css Fri Nov 06 19:04:13 2009 -0500 @@ -109,6 +109,7 @@ .wym_skin_galaxy .wym_buttons li.wym_tools_paste a { background-position: 0 -552px;} .wym_skin_galaxy .wym_buttons li.wym_tools_html a { background-position: 0 -193px;} .wym_skin_galaxy .wym_buttons li.wym_tools_preview a { background-position: 0 -408px;} + .wym_skin_galaxy .wym_buttons li.galaxy_tools_insert_history_link a { background-position: 0 -622px;} /*DECORATION*/ .wym_skin_galaxy .wym_section h2 { background: #f0f0f0; border: solid gray; border-width: 0 0 1px;} diff -r b54c37f53d53 -r f520e80ac09c templates/dataset/grid.mako --- a/templates/dataset/grid.mako Fri Nov 06 16:52:00 2009 -0500 +++ b/templates/dataset/grid.mako Fri Nov 06 19:04:13 2009 -0500 @@ -167,43 +167,12 @@ </style> </%def> -<div class="grid-header"> - <h2>${grid.title}</h2> +<%namespace file="../grid_common.mako" import="*" /> - ## Print grid filter. - <form name="dataset_actions" action="javascript:add_tag_to_grid_filter($('#input-tag-filter').attr('value'))" method="get" > - <strong>Filter:   </strong> - %for column in grid.columns: - %if column.filterable: - <span> by ${column.label.lower()}:</span> - ## For now, include special case to handle tags. - %if column.key == "tags": - %if cur_filter_dict[column.key] != "All": - <span class="filter" "style='font-style: italic'"> - ${cur_filter_dict[column.key]} - </span> - <span>|</span> - %endif - <input id="input-tag-filter" name="f-tags" type="text" value="" size="15"/> - <span>|</span> - %endif - - ## Handle other columns. - %for i, filter in enumerate( column.get_accepted_filters() ): - %if i > 0: - <span>|</span> - %endif - %if cur_filter_dict[column.key] == filter.args[column.key]: - <span class="filter" "style='font-style: italic'">${filter.label}</span> - %else: - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endif - %endfor - <span>     </span> - %endif - %endfor - </form> -</div> +## Print grid header. +${render_grid_filters()} + +## Print grid. <form name="dataset_actions" action="${url()}" method="post" > <table class="grid"> <thead> diff -r b54c37f53d53 -r f520e80ac09c templates/grid_common.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/grid_common.mako Fri Nov 06 19:04:13 2009 -0500 @@ -0,0 +1,129 @@ +<%! from galaxy.web.framework.helpers.grids import TextColumn, GridColumnFilter %> + +## Render a filter UI for a grid column. Filter is rendered as a table row. +<%def name="render_grid_column_filter(column)"> + <tr> + <% + column_label = column.label + if column.filterable == "advanced": + column_label = column_label.lower() + %> + <td align="left" style="padding-left: 10px">${column_label}:</td> + <td> + %if isinstance(column, TextColumn): + <form name="history_actions" action="${url( dict() )}" + method="get" > + ## Carry forward filtering criteria with hidden inputs. + %for temp_column in grid.columns: + %if temp_column.key in cur_filter_dict: + <% value = cur_filter_dict[ temp_column.key ] %> + %if value != "All": + <% + if isinstance( temp_column, TextColumn ): + value = h.to_json_string( value ) + %> + <input type="hidden" id="${temp_column.key}" name="f-${temp_column.key}" value='${value}'/> + %endif + %endif + %endfor + + ## Print current filtering criteria and links to delete. + %if column.key in cur_filter_dict: + <% column_filter = cur_filter_dict[column.key] %> + %if isinstance( column_filter, basestring ): + %if column_filter != "All": + <span style="font-style: italic">${cur_filter_dict[column.key]}</span> + <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + | + %endif + %elif isinstance( column_filter, list ): + %for i, filter in enumerate( column_filter ): + %if i > 0: + , + %endif + <span style="font-style: italic">${filter}</span> + <% + new_filter = list( column_filter ) + del new_filter[ i ] + new_column_filter = GridColumnFilter( "", { column.key : h.to_json_string( new_filter ) } ) + %> + <a href="${url( new_column_filter.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> + %endfor + + %endif + %endif + <span><input id="input-${column.key}-filter" name="f-${column.key}" type="text" value="" size="15"/></span> + </form> + %else: + %for i, filter in enumerate( column.get_accepted_filters() ): + %if i > 0: + <span>|</span> + %endif + %if cur_filter_dict[column.key] == filter.args[column.key]: + <span class="filter" style="font-style: italic">${filter.label}</span> + %else: + <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> + %endif + %endfor + %endif + </td> + </tr> +</%def> + +## Print grid search/filtering UI. +<%def name="render_grid_filters()"> + <div class="grid-header"> + <h2>${grid.title}</h2> + + ## Default search. + <div> + <table><tr> + <td> + <table> + %for column in grid.columns: + %if column.filterable == "default": + ${render_grid_column_filter(column)} + %endif + %endfor + </table> + </td> + <td> + ##| + ##<% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> + ##<a href="${url( filter_all.get_url_args() )}">Clear All</a> + | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> + </td> + </tr></table> + </div> + + + ## Advanced search. + <div id="more-search-options" style="display: none; padding-top: 5px"> + <table style="border: 1px solid gray;"> + <tr><td style="text-align: left" colspan="100"> + Advanced Search | + <a href=""# onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Close</a> | + ## Link to clear all filters. + <% + no_filter = GridColumnFilter("Clear All", default_filter_dict) + %> + <a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> + </td></tr> + %for column in grid.columns: + %if column.filterable == "advanced": + ## Show div if current filter has value that is different from the default filter. + %if column.key in cur_filter_dict and column.key in default_filter_dict and \ + cur_filter_dict[column.key] != default_filter_dict[column.key]: + <script type="text/javascript"> + $('#more-search-options').css("display", "block"); + </script> + %endif + + ${render_grid_column_filter(column)} + %endif + %endfor + </table> + </div> + </div> +</%def> \ No newline at end of file diff -r b54c37f53d53 -r f520e80ac09c templates/history/grid.mako --- a/templates/history/grid.mako Fri Nov 06 16:52:00 2009 -0500 +++ b/templates/history/grid.mako Fri Nov 06 19:04:13 2009 -0500 @@ -1,4 +1,4 @@ -<%! from galaxy.web.framework.helpers.grids import GridColumnFilter %> +<%! from galaxy.web.framework.helpers.grids import TextColumn, GridColumnFilter %> <%inherit file="/base.mako"/> <%def name="title()">${grid.title}</%def> @@ -153,98 +153,12 @@ </style> </%def> -<div class="grid-header"> - <h2>${grid.title}</h2> - - ## Search box and more options filter at top of grid. - <div> - ## Grid search. TODO: use more elegant way to get free text search column. - <% column = grid.columns[-1] %> - <% use_form = False %> - %for i, filter in enumerate( column.get_accepted_filters() ): - %if i > 0: - <span>|</span> - %endif - %if column.key in cur_filter_dict and cur_filter_dict[column.key] == filter.args[column.key]: - <span class="filter" "style='font-style: italic'">${filter.label}</span> - %elif filter.label == "FREETEXT": - <form name="history_actions" - action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),false)" - method="get" > - ${column.label}: - %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": - <span style="font-style: italic">${cur_filter_dict[column.key]}</span> - <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> - | - %endif - <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> - <% use_form = True %> - %else: - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endif - %endfor - | <a href="" onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Advanced Search</a> - %if use_form: - </form> - %endif - </div> - - ## Advanced Search - <div id="more-search-options" style="display: none; padding-top: 5px"> - <table style="border: 1px solid gray;"> - <tr><td style="text-align: left" colspan="100"> - Advanced Search | - <a href=""# onclick="javascript:$('#more-search-options').slideToggle('fast');return false;">Close</a> | - ## Link to clear all filters. - <% - no_filter = GridColumnFilter("Clear All", default_filter_dict) - %> - <a href="${url( no_filter.get_url_args() )}">${no_filter.label}</a> - </td></tr> - %for column in grid.columns: - %if column.filterable: - <tr> - ## Show div if current filter has value that is different from the default filter. - %if cur_filter_dict[column.key] != default_filter_dict[column.key]: - <script type="text/javascript"> - $('#more-search-options').css("display", "block"); - </script> - %endif - <td style="padding-left: 10px">${column.label.lower()}:</td> - <td> - <% use_form = False %> - %for i, filter in enumerate( column.get_accepted_filters() ): - %if i > 0: - <span>|</span> - %endif - %if cur_filter_dict[column.key] == filter.args[column.key]: - <span class="filter" style="font-style: italic">${filter.label}</span> - %elif filter.label == "FREETEXT": - <form name="history_actions" action="javascript:add_condition_to_grid_filter($('#input-${column.key}-filter').attr('name'),$('#input-${column.key}-filter').attr('value'),true)" - method="get" > - %if column.key in cur_filter_dict and cur_filter_dict[column.key] != "All": - <span style="font-style: italic">${cur_filter_dict[column.key]}</span> - <% filter_all = GridColumnFilter( "", { column.key : "All" } ) %> - <a href="${url( filter_all.get_url_args() )}"><img src="${h.url_for('/static/images/delete_tag_icon_gray.png')}"/></a> - | - %endif - <span><input id="input-${column.key}-filter" name="${column.key}" type="text" value="" size="15"/></span> - <% use_form = True %> - %else: - <span class="filter"><a href="${url( filter.get_url_args() )}">${filter.label}</a></span> - %endif - %endfor - %if use_form: - </form> - %endif - </td> - </tr> - %endif - %endfor - </table> - </div> -</div> +<%namespace file="../grid_common.mako" import="*" /> + +## Print grid header. +${render_grid_filters()} + +## Print grid. <form name="history_actions" action="${url()}" method="post" > <input type="hidden" name="page" value="${cur_page_num}"> <table class="grid">

1 0

[hg] galaxy 2976: Add Genetrack tools and display site
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4a7f9fdead89 changeset: 2976:4a7f9fdead89 user: Nate Coraor <nate(a)bx.psu.edu> date: Fri Nov 06 14:22:44 2009 -0500 description: Add Genetrack tools and display site diffstat: lib/galaxy/datatypes/tracks.py | 22 +- lib/galaxy/web/controllers/genetrack.py | 293 -------------------------- tool-data/shared/genetrack/genetrack_sites.txt | 8 +- tool_conf.xml.sample | 3 + tools/visualization/genetrack.py | 189 ----------------- tools/visualization/genetrack.xml | 72 ------ tools/visualization/genetrack_code.py | 12 - tools/visualization/genetrack_indexer.py | 39 +++ tools/visualization/genetrack_indexer.xml | 54 ++++ tools/visualization/genetrack_peak_prediction.py | 40 +++ tools/visualization/genetrack_peak_prediction.xml | 59 +++++ universe_wsgi.ini.sample | 3 +- 12 files changed, 214 insertions(+), 580 deletions(-) diffs (871 lines): diff -r 411b53d32b78 -r 4a7f9fdead89 lib/galaxy/datatypes/tracks.py --- a/lib/galaxy/datatypes/tracks.py Fri Nov 06 09:57:05 2009 -0500 +++ b/lib/galaxy/datatypes/tracks.py Fri Nov 06 14:22:44 2009 -0500 @@ -20,26 +20,26 @@ class GeneTrack( data.Binary ): file_ext = "genetrack" - MetadataElement( name="hdf", default="data.hdf", desc="HDF DB", readonly=True, visible=True, no_value=0 ) - MetadataElement( name="sqlite", default="features.sqlite", desc="SQLite Features DB", readonly=True, visible=True, no_value=0 ) + MetadataElement( name="genetrack", default="data.genetrack", desc="HDF index", readonly=True, visible=True, no_value=0 ) MetadataElement( name="label", default="Custom", desc="Track Label", readonly=True, visible=True, no_value="Custom" ) def __init__(self, **kwargs): super( GeneTrack, self ).__init__( **kwargs ) - self.add_display_app( 'genetrack', 'View in GeneTrack', '', 'genetrack_link' ) + self.add_display_app( 'genetrack', 'View in', '', 'genetrack_link' ) def get_display_links( self, dataset, type, app, base_url, target_frame='galaxy_main', **kwd ): return data.Binary.get_display_links( self, dataset, type, app, base_url, target_frame=target_frame, **kwd ) def genetrack_link( self, hda, type, app, base_url ): ret_val = [] if hda.has_data: - # Get the disk file name + # Get the disk file name and data id file_name = hda.dataset.get_file_name() + data_id = hda.dataset.id # Make it secure - a = hmac_new( app.config.tool_secret, file_name ) - b = binascii.hexlify( file_name ) - encoded_file_name = "%s:%s" % ( a, b ) - for site_name, site_url in util.get_genetrack_sites(): - if site_name in app.config.genetrack_display_sites: - link = "%s?filename=%s" % ( site_url, encoded_file_name ) - ret_val.append( ( site_name, link ) ) + hashkey = hmac_new( app.config.tool_secret, file_name ) + encoded = binascii.hexlify( file_name ) + for name, url in util.get_genetrack_sites(): + if name.lower() in app.config.genetrack_display_sites: + # send both parameters filename and hashkey + link = "%s?filename=%s&hashkey=%s&id=%s&GALAXY_URL=%s" % ( url, encoded, hashkey, data_id, base_url ) + ret_val.append( ( name, link ) ) return ret_val diff -r 411b53d32b78 -r 4a7f9fdead89 lib/galaxy/web/controllers/genetrack.py --- a/lib/galaxy/web/controllers/genetrack.py Fri Nov 06 09:57:05 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,293 +0,0 @@ -import time, glob, os, sys -from itertools import cycle -from mako import exceptions -from mako.template import Template -from mako.lookup import TemplateLookup -from galaxy.web.base.controller import * -from galaxy.util.hash_util import * - -try: - import pkg_resources - pkg_resources.require("GeneTrack") - import atlas - from atlas import sql - from atlas import hdf - from atlas import util as atlas_utils - from atlas.web import formlib, feature_query, feature_filter - from atlas.web import label_cache as atlas_label_cache - from atlas.plotting.const import * - from atlas.plotting.tracks import prefab - from atlas.plotting.tracks import chart - from atlas.plotting import tracks -except Exception, exc: - raise ControllerUnavailable("GeneTrack could not import a required dependency: %s" % str(exc)) - -pkg_resources.require( "Paste" ) -import paste.httpexceptions - -# Database helpers -SHOW_LABEL_LIMIT = 10000 - -def list_labels(session): - """ - Returns a list of labels that will be plotted in order. - """ - labels = sql.Label - query = session.query(labels).order_by("-id") - return query - -def open_databases( conf ): - """ - A helper function that returns handles to the hdf and sql databases - """ - db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' ) - session = sql.get_session( conf.SQL_URI ) - return db, session - -def hdf_query(db, name, param, autosize=False ): - """ - Schema specific hdf query. - Note that returns data as columns not rows. - """ - if not hdf.has_node(db=db, name=name): - atlas.warn( 'missing label %s' % name ) - return [], [], [], [] - data = hdf.GroupData( db=db, name=name) - istart, iend = data.get_indices(label=param.chrom, start=param.start, stop=param.end) - table = data.get_table(label=param.chrom) - if autosize: - # attempts to reduce the number of points - size = len( table.cols.ix[istart:iend] ) - step = max( [1, size/1200] ) - else: - step = 1 - - ix = table.cols.ix[istart:iend:step].tolist() - wx = table.cols.wx[istart:iend:step].tolist() - cx = table.cols.cx[istart:iend:step].tolist() - ax = table.cols.ax[istart:iend:step].tolist() - return ix, wx, cx, ax - -# Chart helpers -def build_tracks( param, conf, data_label, fit_label, pred_label, strand, show=False ): - """ - Builds tracks - """ - # gets all the labels for a fast lookup - label_cache = atlas_label_cache( conf ) - - # get database handles for hdf and sql - db, session = open_databases( conf ) - - # fetching x and y coordinates for bar and fit (line) for - # each strand plus (p), minus (m), all (a) - bix, bpy, bmy, bay = hdf_query( db=db, name=data_label, param=param ) - fix, fpy, fmy, fay = hdf_query( db=db, name=fit_label, param=param ) - - # close the hdf database - db.close() - - # get all features within the range - all = feature_query( session=session, param=param ) - - # draws the barchart and the nucleosome chart below it - if strand == 'composite': - bar = prefab.composite_bartrack( fix=fix, fay=fay, bix=bix, bay=bay, param=param) - else: - bar = prefab.twostrand_bartrack( fix=fix, fmy=fmy, fpy=fpy, bix=bix, bmy=bmy, bpy=bpy, param=param) - - charts = list() - charts.append( bar ) - - return charts - -def feature_chart(param=None, session=None, label=None, label_dict={}, color=cycle( [LIGHT, WHITE] ) ): - all = feature_filter(feature_query(session=session, param=param), name=label, kdict=label_dict) - flipped = [] - for feature in all: - if feature.strand == "-": - feature.start, feature.end = feature.end, feature.start - flipped.append(feature) - opts = track_options( - xscale=param.xscale, w=param.width, fgColor=PURPLE, - show_labels=param.show_labels, ylabel=str(label), - bgColor=color.next() - ) - return [ - tracks.split_tracks(features=flipped, options=opts, split=param.show_labels, track_type='vector') - ] - -def consolidate_charts( charts, param ): - # create the multiplot - opt = chart_options( w=param.width ) - multi = chart.MultiChart(options=opt, charts=charts) - return multi - -# SETUP Track Builders -import functools -def twostrand_tracks( param=None, conf=None ): - return build_tracks( data_label=conf.LABEL, fit_label=conf.FIT_LABEL, pred_label=conf.PRED_LABEL, param=param, conf=conf, strand='twostrand') -def composite_tracks( param=None, conf=None ): - return build_tracks( data_label=conf.LABEL, fit_label=conf.FIT_LABEL, pred_label=conf.PRED_LABEL, param=param, conf=conf, strand='composite') - -class BaseConf( object ): - """ - Fake web_conf for atlas. - """ - IMAGE_DIR = "static/genetrack/plots/" - LEVELS = [str(x) for x in [ 50, 100, 250, 500, 1000, 2500, 5000, 10000, 20000, 50000, 100000, 200000 ]] - ZOOM_LEVELS = zip(LEVELS, LEVELS) - PLOT_SETUP = [ - ('comp-id', 'Composite' , 'genetrack/index.html', composite_tracks ), - ('two-id' , 'Two Strand', 'genetrack/index.html', twostrand_tracks ), - ] - PLOT_CHOICES = [ (id, name) for (id, name, page, func) in PLOT_SETUP ] - PLOT_MAPPER = dict( [ (id, (page, func)) for (id, name, page, func) in PLOT_SETUP ] ) - - def __init__(self, **kwds): - for key,value in kwds.items(): - setattr( self, key, value) - -class WebRoot(BaseController): - @web.expose - def search(self, trans, word='', dataset_id=None, submit=''): - """ - Default search page - """ - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) - if not data: - raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) - # the main configuration file - conf = BaseConf( - TITLE = "<i>%s</i>: %s" % (data.metadata.dbkey, data.metadata.label), - HDF_DATABASE = os.path.join( data.extra_files_path, data.metadata.hdf ), - SQL_URI = "sqlite:///%s" % os.path.join( data.extra_files_path, data.metadata.sqlite ), - LABEL = data.metadata.label, - FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20), - PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20), - ) - - param = atlas.Param( word=word ) - - # search for a given - try: - session = sql.get_session( conf.SQL_URI ) - except: - return trans.fill_template_mako('genetrack/invalid.html', dataset_id=dataset_id) - - if param.word: - def search_query( word, text ): - query = session.query(sql.Feature).filter( "name LIKE :word or freetext LIKE :text" ).params(word=word, text=text) - query = list(query[:20]) - return query - - # a little heuristics to match most likely target - targets = [ - (param.word+'%', 'No match'), # match beginning - ('%'+param.word+'%', 'No match'), # match name anywhere - ('%'+param.word+'%', '%'+param.word+'%'), # match json anywhere - ] - for word, text in targets: - query = search_query( word=word, text=text) - if query: - break - else: - query = [] - - return trans.fill_template_mako('genetrack/search.html', param=param, query=query, dataset_id=dataset_id) - - @web.expose - def index(self, trans, dataset_id=None, **kwds): - """ - Main request handler - """ - color = cycle( [LIGHT, WHITE] ) - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( dataset_id ) - if not data: - raise paste.httpexceptions.HTTPRequestRangeNotSatisfiable( "Invalid reference dataset id: %s." % str( dataset_id ) ) - # the main configuration file - conf = BaseConf( - TITLE = "<i>%s</i>: %s" % (data.metadata.dbkey, data.metadata.label), - HDF_DATABASE = os.path.join( data.extra_files_path, data.metadata.hdf ), - SQL_URI = "sqlite:///%s" % os.path.join( data.extra_files_path, data.metadata.sqlite ), - LABEL = data.metadata.label, - FIT_LABEL = "%s-SIGMA-%d" % (data.metadata.label, 20), - PRED_LABEL = "PRED-%s-SIGMA-%d" % (data.metadata.label, 20), - ) - - try: - session = sql.get_session( conf.SQL_URI ) - except: - return trans.fill_template_mako('genetrack/invalid.html', dataset_id=dataset_id) - - if os.path.exists( conf.HDF_DATABASE ): - db = hdf.hdf_open( conf.HDF_DATABASE, mode='r' ) - conf.CHROM_FIELDS = [(x,x) for x in hdf.GroupData(db=db, name=conf.LABEL).labels] - db.close() - else: - query = session.execute(sql.select([sql.feature_table.c.chrom]).distinct()) - conf.CHROM_FIELDS = [(x.chrom,x.chrom) for x in query] - - # generate a new form based on the configuration - form = formlib.main_form( conf ) - - # clear the tempdir every once in a while - atlas_utils.clear_tempdir( dir=conf.IMAGE_DIR, days=1, chance=10) - - incoming = form.defaults() - incoming.update( kwds ) - - # manage the zoom and pan requests - incoming = formlib.zoom_change( kdict=incoming, levels=conf.LEVELS) - incoming = formlib.pan_view( kdict=incoming ) - - # process the form - param = atlas.Param( **incoming ) - form.process( incoming ) - - if kwds and form.isSuccessful(): - # adds the sucessfull parameters - param.update( form.values() ) - - # if it was a search word not a number go to search page - try: - center = int( param.feature ) - except ValueError: - # go and search for these - return trans.response.send_redirect( web.url_for( controller='genetrack', action='search', word=param.feature, dataset_id=dataset_id ) ) - - param.width = min( [2000, int(param.img_size)] ) - param.xscale = [ param.start, param.end ] - param.show_labels = ( param.end - param.start ) <= SHOW_LABEL_LIMIT - - # get the template and the function used to generate the tracks - tmpl_name, track_maker = conf.PLOT_MAPPER[param.plot] - - # check against a hash, display an image that already exists if it was previously created. - hash = new_secure_hash() - hash.update(str(dataset_id)) - for key in sorted(kwds.keys()): - hash.update(str(kwds[key])) - fname = "%s.png" % hash.hexdigest() - fpath = os.path.join(conf.IMAGE_DIR, fname) - - charts = [] - param.fname = fname - - # The SHA1 hash should uniquely identify the qs that created the plot... - if os.path.exists(fpath): - os.utime(fpath, (time.time(), time.time())) - return trans.fill_template_mako(tmpl_name, conf=conf, form=form, param=param, dataset_id=dataset_id) - - # If the hashed filename doesn't exist, create it. - if track_maker is not None and os.path.exists( conf.HDF_DATABASE ): - # generate the fit track - charts = track_maker( param=param, conf=conf ) - - for label in list_labels( session ): - charts.extend( feature_chart(param=param, session=session, label=label.name, label_dict={label.name:label.id}, color=color)) - - track_chart = consolidate_charts( charts, param ) - track_chart.save(fname=fpath) - - return trans.fill_template_mako(tmpl_name, conf=conf, form=form, param=param, dataset_id=dataset_id) diff -r 411b53d32b78 -r 4a7f9fdead89 tool-data/shared/genetrack/genetrack_sites.txt --- a/tool-data/shared/genetrack/genetrack_sites.txt Fri Nov 06 09:57:05 2009 -0500 +++ b/tool-data/shared/genetrack/genetrack_sites.txt Fri Nov 06 14:22:44 2009 -0500 @@ -1,3 +1,7 @@ # GeneTrack sites -main http://www.genetrack.org/ -test http://www.test.genetrack.org/ +# +# The key(s) should be added to universe_wsgi.ini as the value of +# genetrack_display_sites +# +# key site url +psu_galaxy http://genetrack.g2.bx.psu.edu/galaxy diff -r 411b53d32b78 -r 4a7f9fdead89 tool_conf.xml.sample --- a/tool_conf.xml.sample Fri Nov 06 09:57:05 2009 -0500 +++ b/tool_conf.xml.sample Fri Nov 06 14:22:44 2009 -0500 @@ -125,6 +125,9 @@ <tool file="visualization/GMAJ.xml" /> <tool file="visualization/LAJ.xml" /> <tool file="visualization/build_ucsc_custom_track.xml" /> + <tool file="visualization/genetrack_indexer.xml" /> + <tool file="visualization/genetrack_peak_prediction.xml" /> + </section> </section> <section name="Regional Variation" id="regVar"> <tool file="regVariation/windowSplitter.xml" /> diff -r 411b53d32b78 -r 4a7f9fdead89 tools/visualization/genetrack.py --- a/tools/visualization/genetrack.py Fri Nov 06 09:57:05 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,189 +0,0 @@ -#!/usr/bin/env python -""" -Run GeneTrack(atlas) with a faked conf file to generate GeneTrack data files. - -usage: %prog - -l, --label=N: Data label for fit curve/peak plot - -1, --fits=N/N/N/N/N,...: Data files (interval format) for fit curve/peak plot - -2, --feats=N:M/N/N/N/N/N,...: Data files (interval format) for features. - -d, --data=N: Output path for hdf5 and sqlite databases. - -o, --output=N: Output path for export file. -""" -from galaxy import eggs -import pkg_resources -pkg_resources.require("GeneTrack") -pkg_resources.require("bx-python") - -import commands as oscommands -from atlas import commands -from atlas import sql -from bx.cookbook import doc_optparse -from bx.intervals import io - -import os -import tempfile -from functools import partial - -SIGMA = 20 -WIDTH = 5 * SIGMA -EXCLUSION_ZONE = 147 - -def main(label, fit, feats, data_dir, output): - os.mkdir(data_dir) - conf = DummyConf( - __name__=label, - CLOBBER = True, - DATA_SIZE = 3*10**6, - MINIMUM_PEAK_SIZE = 0.1, - LOADER_ENABLED = False, - FITTER_ENABLED = False, - PREDICTOR_ENABLED = False, - EXPORTER_ENABLED = False, - LOADER = loader, - FITTER = fitter, - PREDICTOR = predictor, - EXPORTER = partial( commands.exporter, formatter=commands.bed_formatter), - HDF_DATABASE = os.path.join( data_dir, "data.hdf" ), - SQL_URI = "sqlite:///%s" % os.path.join( data_dir, "features.sqlite" ), - SIGMA = SIGMA, - WIDTH = WIDTH, - DATA_LABEL = label, - FIT_LABEL = "%s-SIGMA-%d" % ( label,SIGMA ), - PEAK_LABEL = "PRED-%s-SIGMA-%d" % ( label,SIGMA ), - EXCLUSION_ZONE = EXCLUSION_ZONE, - LEFT_SHIFT = EXCLUSION_ZONE / 2, - RIGHT_SHIFT = EXCLUSION_ZONE / 2, - EXPORT_LABELS = [ "PRED-%s-SIGMA-%d" % ( label,SIGMA ) ], - EXPORT_DIR = os.path.join( data_dir ), - DATA_FILE=fit and fit[1] or None, - fit=fit, - feats=feats, - ) - if fit: - # Turn on fit processing. - conf.LOADER_ENABLED = True, - conf.FITTER_ENABLED = True, - conf.PREDICTOR_ENABLED = True, - conf.EXPORTER_ENABLED = True, - for feat in feats: - load_feature_files(conf, feats) - commands.execute(conf) - outname = "%s.%s.txt" % (conf.__name__, conf.EXPORT_LABELS[0] ) - if os.path.exists( os.path.join(data_dir, outname) ): - os.rename( os.path.join(data_dir, outname), output) - -# mod454 seems to be a module without a package. The necessary funcitons are -# stubbed out here until I'm sure of their final home. INS - -def loader( conf ): - from atlas import hdf - from mod454.schema import Mod454Schema as Schema - last_chrom = table = None - db = hdf.hdf_open( conf.HDF_DATABASE, mode='a', title='HDF database') - gp = hdf.create_group( db=db, name=conf.DATA_LABEL, desc='data group', clobber=conf.CLOBBER ) - fit_meta = conf.fit[2] - # iterate over the file and insert into table - for line in open( conf.fit[1], "r" ): - if line.startswith("chrom"): continue #Skip possible header - if line.startswith("#"): continue - fields = line.rstrip('\r\n').split('\t') - chrom = fields[fit_meta.chromCol] - if chrom != last_chrom: - if table: table.flush() - table = hdf.create_table( db=db, name=chrom, where=gp, schema=Schema, clobber=False ) - last_chrom = chrom - try: - position = int(fields[fit_meta.positionCol]) - forward = float(fields[fit_meta.forwardCol]) - reverse = fit_meta.reverseCol > -1 and float(fields[fit_meta.reverseCol]) or 0.0 - row = ( position, forward, reverse, forward+reverse, ) - table.append( [ row ] ) - except ValueError: - # Ignore bad lines - pass - table.flush() - db.close() - -def fitter( conf ): - from mod454.fitter import fitter as mod454_fitter - return mod454_fitter( conf ) - -def predictor( conf ): - from mod454.predictor import predictor as mod454_predictor - return mod454_predictor( conf ) - -def load_feature_files( conf, feats): - """ - Loads features from file names - """ - engine = sql.get_engine( conf.SQL_URI ) - sql.drop_indices(engine) - conn = engine.connect() - for label, fname, col_spec in feats: - label_id = sql.make_label(engine, name=label, clobber=False) - reader = io.NiceReaderWrapper( open(fname,"r"), - chrom_col=col_spec.chromCol, - start_col=col_spec.startCol, - end_col=col_spec.endCol, - strand_col=col_spec.strandCol, - fix_strand=False ) - values = list() - for interval in reader: - print interval - if not type( interval ) is io.GenomicInterval: continue - row = {'label_id':label_id, - 'name':col_spec.nameCol == -1 and "%s-%s" % (str(interval.start), str(interval.end)) or interval.fields[col_spec.nameCol], - 'altname':"", - 'chrom':interval.chrom, - 'start':interval.start, - 'end':interval.end, - 'strand':interval.strand, - 'value':0, - 'freetext':""} - values.append(row) - insert = sql.feature_table.insert() - conn.execute( insert, values) - conn.close() - sql.create_indices(engine) - - -class Bunch( object ): - def __init__(self, **kwargs): - for key,value in kwargs.items(): - setattr( self, key, value ) - -class DummyConf( Bunch ): - """ - Fake conf module for genetrack/atlas. - """ - pass - -if __name__ == "__main__": - options, args = doc_optparse.parse( __doc__ ) - try: - label = options.label - if options.fits: - fit_name, fit_meta = options.fits.split(':')[0], [int(x)-1 for x in options.fits.split(':')[1:]] - fit_meta = Bunch(chromCol=fit_meta[0], positionCol=fit_meta[1], forwardCol=fit_meta[2], reverseCol=fit_meta[3]) - fit = ( label, fit_name, fit_meta, ) - else: - fit = [] - # split apart the string into nested lists, preserves order - if options.feats: - feats = [ ( - feat_label, - fname, - Bunch(chromCol=int(chromCol)-1, startCol=int(startCol)-1, endCol=int(endCol)-1, - strandCol=int(strandCol)-1, nameCol=int(nameCol)-1), - ) - for feat_label, fname, chromCol, startCol, endCol, strandCol, nameCol - in ( feat.split(':') for feat in options.feats.split(',') if len(feat) > 0 )] - else: - feats = [] - data_dir = options.data - output = options.output - except: - doc_optparse.exception() - - main(label, fit, feats, data_dir, output) - diff -r 411b53d32b78 -r 4a7f9fdead89 tools/visualization/genetrack.xml --- a/tools/visualization/genetrack.xml Fri Nov 06 09:57:05 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,73 +0,0 @@ -<tool id="genetrack1" name="GeneTrack"> - - <description>Track creator/viewer</description> - - <code file="genetrack_code.py"> - <hook exec_after_process="exec_after_process" /> - </code> - - <command interpreter="python"> - genetrack.py -l $data_label - #if not str($fit_data) == "None" - -1 - ${fit_data}:${fit_data.metadata.chromCol}:${fit_data.metadata.positionCol}:${fit_data.metadata.forwardCol}:${fit_data.metadata.reverseCol} - #end if - #if $feature_data - -2 - #end if - #for $data in $feature_data - ${data.name}:${data.input}:${data.input.metadata.chromCol}:${data.input.metadata.startCol}:${data.input.metadata.endCol}:${data.input.metadata.strandCol}:${data.input.metadata.nameCol}, - #end for - -d ${genetrack.files_path} - -o ${bed_out} - </command> - - <inputs> - <param name="data_label" type="text" label="Track Label" size="50"> - <validator type="regex" message="Please name the track with only alphanumeric characters.">[a-zA-Z0-9]{1,25}</validator> - </param> - <param name="fit_data" type="data" format="coverage" label="Coverage Dataset (optional)" optional="true" /> - <repeat name="feature_data" title="Features"> - <param name="input" type="data" format="interval" label="Dataset" /> - <param name="name" type="text" label="Feature Type (mRNA, ESTs, ORFs, etc.)" size="25"> - <validator type="regex" message="Please name the feature with only alphanumeric characters.">[a-zA-Z0-9]{1,25}</validator> - </param> - </repeat> - </inputs> - - <outputs> - <data format="genetrack" name="genetrack" /> - <data format="bed" name="bed_out" /> - </outputs> - - <requirements> - <requirement type="python-module">tables</requirement> - <requirement type="python-module">atlas</requirement> - <requirement type="python-module">pychartdir</requirement> - <requirement type="python-module">numpy</requirement> - </requirements> - <help> -This tool takes the input Fit Data and creates a peak and curve plot -showing the reads and fitness on each base pair. Features can be -plotted below as tracks. Fit data is coverage output from tools like -the Lastz tool. Features are simply interval datasets that may be -plotted as tracks below the optional fit data. Both the fit data and -feature datasets are optional, but at least one of either is required -to generate a track. - ------ - -**Syntax** - -- **Track Label** is the name of the generated track. - -- **Fit Data** is the dataset to calculate coverage/reads across - base pairs and generate a curve. This is optional, and tracks may - be created simply showing features. - -- **Features** are datasets (interval format) to be plotted as tracks. - These are also optional, but at least 1 feature track or 1 fit - data is required to generate a track. - -</help> -</tool> diff -r 411b53d32b78 -r 4a7f9fdead89 tools/visualization/genetrack_code.py --- a/tools/visualization/genetrack_code.py Fri Nov 06 09:57:05 2009 -0500 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,12 +0,0 @@ -import os -from galaxy import eggs -from galaxy import jobs -from galaxy.tools.parameters import DataToolParameter - -def exec_after_process(app, inp_data, out_data, param_dict, tool=None, stdout=None, stderr=None): - """ - Copy data_label to genetrack.metadata.label - """ - out_data['genetrack'].metadata.label = param_dict['data_label'] - out_data['genetrack'].info = "Use the link below to view the custom track." - out_data['bed_out'].info = "" diff -r 411b53d32b78 -r 4a7f9fdead89 tools/visualization/genetrack_indexer.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/visualization/genetrack_indexer.py Fri Nov 06 14:22:44 2009 -0500 @@ -0,0 +1,39 @@ +#!/usr/bin/env python + +""" +Wraps genetrack.scripts.tabs2genetrack so the tool can be executed from Galaxy. + +usage: %prog input output shift +""" + +import sys +from galaxy import eggs +import pkg_resources +pkg_resources.require( "GeneTrack" ) + +from genetrack.scripts import tabs2genetrack +from genetrack import logger + +if __name__ == "__main__": + + parser = tabs2genetrack.option_parser() + + options, args = parser.parse_args() + + # uppercase the format + options.format = options.format.upper() + + if options.format not in ('BED', 'GFF'): + sys.stdout = sys.stderr + parser.print_help() + sys.exit(-1) + + logger.disable(options.verbosity) + + # missing file names + if not (options.inpname and options.outname and options.format): + parser.print_help() + sys.exit(-1) + else: + tabs2genetrack.transform(inpname=options.inpname, outname=options.outname,\ + format=options.format, shift=options.shift, index=options.index) diff -r 411b53d32b78 -r 4a7f9fdead89 tools/visualization/genetrack_indexer.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/visualization/genetrack_indexer.xml Fri Nov 06 14:22:44 2009 -0500 @@ -0,0 +1,54 @@ +<tool id="bed2genetrack" name="Visualize BED file"> + + <description> - creates a visualization from a bed file</description> + + <command interpreter="python"> + genetrack_indexer.py -i $input -o $output -s $shift -v 0 -f BED -x + </command> + + <inputs> + + <param format="bed" name="input" type="data" help="Input data"> + <label>Select input bed file</label> + </param> + + <param name="shift" size="4" type="integer" value="0" help="distance in basepairs"> + <label>Shift at 5' end</label> + </param> + +  + + </inputs> + + <outputs> + <data format="genetrack" name="output" /> + </outputs> + +<help> +**Help** + +This tool will create a visualization of the bed file that is selected. + +**Parameters** + +- **Shift at 5' end** should be used when the location of interest is at a fixed distance from + the 5' end for **all sequenced fragments**! + + For example if the sequenced sample consists + mono-nucleosomal DNA (146bp) we should expect that + each nucleosome midpoint is located at 73 bp from the 5' end of the fragment. + Therefore we would enter 73 as the shift parameter. Once corrected the reads + on each strand will coincide and indicate the actual midpoints + of the nucleosomes. + + When shifting the averaging process in GeneTrack is able correct for longer or shorter + than expected fragment sizes as long as the errors are reasonably random. + +</help> + +</tool> diff -r 411b53d32b78 -r 4a7f9fdead89 tools/visualization/genetrack_peak_prediction.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/visualization/genetrack_peak_prediction.py Fri Nov 06 14:22:44 2009 -0500 @@ -0,0 +1,40 @@ +#!/usr/bin/env python + +""" +Wraps genetrack.scripts.peakpred so the tool can be executed from Galaxy. + +usage: %prog input output level sigma mode exclusion strand +""" + +import sys +from galaxy import eggs +import pkg_resources +pkg_resources.require( "GeneTrack" ) + +from genetrack.scripts import peakpred +from genetrack import logger + +if __name__ == "__main__": + + parser = peakpred.option_parser() + + options, args = parser.parse_args() + + logger.disable(options.verbosity) + + from genetrack import conf + + # trigger test mode + if options.test: + options.inpname = conf.testdata('test-hdflib-input.gtrack') + options.outname = conf.testdata('predictions.bed') + + # missing input file name + if not options.inpname and not options.outname: + parser.print_help() + else: + print 'Sigma = %s' % options.sigma + print 'Minimum peak = %s' % options.level + print 'Peak-to-peak = %s' % options.exclude + + peakpred.predict(options.inpname, options.outname, options) diff -r 411b53d32b78 -r 4a7f9fdead89 tools/visualization/genetrack_peak_prediction.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/visualization/genetrack_peak_prediction.xml Fri Nov 06 14:22:44 2009 -0500 @@ -0,0 +1,59 @@ +<tool id="predict2genetrack" name="Peak predictor"> + + <description> - generates peak predictions from an index file</description> + + <command interpreter="python"> + genetrack_peak_prediction.py -i $input -o $output --level=$level --sigma=$sigma --mode=$mode --exclusion=$exclusion --strand=$strand -v 0 + </command> + + <inputs> + + <param format="genetrack" name="input" type="data" help="Input data" label="Select input data"/> + + <param name="method" type="select" label="Smoothing method" help="The function used to average nearby read values"> + <option value="gauss">Gaussian kernel</option> +  + </param> + + <param name="sigma" size="4" type="integer" value="10" label="Smoothing factor" help="The interval over which each read is averaged" /> + + + <param name="mode" type="select" label="Peak prediction" help="Peak prediction method"> + <option value="nolap">Maximal non-overlapping</option> +  + <option value="all">All peaks</option> + </param> + + <param name="exclusion" type="integer" size="4" value="0" help="The minimal distance between peaks" label="Peak-to-peak distance"> + </param> + + <param name="level" size="4" type="float" value="1" label="Threshold" help="Return only peaks above this value" /> + + <param name="strand" type="select" label="Strands" help="Combine strand data or predict on each strand separately"> + <option value="all">Merge strands</option> +  + <option value="two">Separate strands</option> + </param> + + </inputs> + + <outputs> + <data format="bed" name="output" /> + </outputs> + +<help> +**Help** + +This tool will generate genome wide peak prediction from an index file. + +**Parameters** + +- **Smoothing method** the function used to average nearby values + +- **Smoothing value** the factor used in the method + +- **Prediction method** the function used to average nearby values + +</help> + +</tool> diff -r 411b53d32b78 -r 4a7f9fdead89 universe_wsgi.ini.sample --- a/universe_wsgi.ini.sample Fri Nov 06 09:57:05 2009 -0500 +++ b/universe_wsgi.ini.sample Fri Nov 06 14:22:44 2009 -0500 @@ -93,7 +93,8 @@ # Comma separated list of UCSC / gbrowse / GeneTrack browsers to use for viewing ucsc_display_sites = main,test,archaea,ucla gbrowse_display_sites = main,test,tair -genetrack_display_sites = main,test +# Define your GeneTrack servers in tool-data/shared/genetrack/genetrack_sites.txt +#genetrack_display_sites = # Serving static files (needed if running standalone) static_enabled = True

1 0

[hg] galaxy 2972: trackster: using overlapping tiles, fix featur...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/52c3fa925dac changeset: 2972:52c3fa925dac user: Kanwei Li <kanwei(a)gmail.com> date: Thu Nov 05 17:25:56 2009 -0500 description: trackster: using overlapping tiles, fix feature names being cut off on the left diffstat: static/scripts/trackster.js | 29 +++++++++++++++++------------ static/trackster.css | 17 +++-------------- 2 files changed, 20 insertions(+), 26 deletions(-) diffs (142 lines): diff -r 9561573441a4 -r 52c3fa925dac static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Nov 05 16:28:38 2009 -0500 +++ b/static/scripts/trackster.js Thu Nov 05 17:25:56 2009 -0500 @@ -189,8 +189,12 @@ if ( cached ) { // console.log("cached tile " + tile_index); var tile_low = tile_index * DENSITY * resolution; + var left = ( tile_low - low ) * w_scale; + if (this.left_offset) { + left -= this.left_offset; + } cached.css( { - left: ( tile_low - low ) * w_scale + left: left }); // Our responsibility to move the element to the new parent parent_element.append( cached ); @@ -364,6 +368,7 @@ this.showing_labels = false; this.vertical_gap = 10; this.base_color = "#2C3143"; + this.left_offset = 200; }; $.extend( FeatureTrack.prototype, TiledTrack.prototype, { init: function() { @@ -462,9 +467,9 @@ new_canvas.css({ position: "absolute", top: 0, - left: ( tile_low - this.view.low ) * w_scale + left: ( tile_low - this.view.low ) * w_scale - this.left_offset }); - new_canvas.get(0).width = width; + new_canvas.get(0).width = width + this.left_offset; new_canvas.get(0).height = height; // console.log(( tile_low - this.view.low ) * w_scale, tile_index, w_scale); var ctx = new_canvas.get(0).getContext("2d"); @@ -487,11 +492,11 @@ } if (!this.showing_labels) { // Non-detail levels - ctx.fillRect(f_start, y_center + 5, f_end - f_start, 1); + ctx.fillRect(f_start + this.left_offset, y_center + 5, f_end - f_start, 1); } else { // Showing labels, blocks, details - if (ctx.fillText) { - ctx.fillText(feature.name, f_start - 1, y_center + 8); + if (ctx.fillText && feature.start > tile_low) { + ctx.fillText(feature.name, f_start - 1 + this.left_offset, y_center + 8); // ctx.fillText(commatize(feature.start), f_start - 1, y_center + 8); } var blocks = feature.blocks; @@ -503,7 +508,7 @@ } else if (feature.strand == "-") { ctx.fillStyle = LEFT_STRAND; } - ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillRect(f_start + this.left_offset, y_center, f_end - f_start, 10); ctx.fillStyle = this.base_color; } @@ -511,11 +516,11 @@ var block = blocks[k], block_start = Math.floor( Math.max(0, (block[0] - tile_low) * w_scale) ), block_end = Math.ceil( Math.min(width, (block[1] - tile_low) * w_scale) ); - + if (block_start > block_end) { continue; } // Draw the block thickness = 5; y_start = 3; - ctx.fillRect(block_start, y_center + y_start, block_end - block_start, thickness); + ctx.fillRect(block_start + this.left_offset, y_center + y_start, block_end - block_start, thickness); if (thick_start && (block_start < thick_end || block_end > thick_start) ) { thickness = 9; @@ -523,7 +528,7 @@ var block_thick_start = Math.max(block_start, thick_start), block_thick_end = Math.min(block_end, thick_end); - ctx.fillRect(block_thick_start, y_center + y_start, block_thick_end - block_thick_start, thickness); + ctx.fillRect(block_thick_start + this.left_offset, y_center + y_start, block_thick_end - block_thick_start, thickness); } } @@ -531,14 +536,14 @@ // If there are no blocks, we treat the feature as one big exon thickness = 9; y_start = 1; - ctx.fillRect(f_start, y_center + y_start, f_end - f_start, thickness); + ctx.fillRect(f_start + this.left_offset, y_center + y_start, f_end - f_start, thickness); if ( feature.strand ) { if (feature.strand == "+") { ctx.fillStyle = RIGHT_STRAND_INV; } else if (feature.strand == "-") { ctx.fillStyle = LEFT_STRAND_INV; } - ctx.fillRect(f_start, y_center, f_end - f_start, 10); + ctx.fillRect(f_start + this.left_offset, y_center, f_end - f_start, 10); ctx.fillStyle = this.base_color; } } diff -r 9561573441a4 -r 52c3fa925dac static/trackster.css --- a/static/trackster.css Thu Nov 05 16:28:38 2009 -0500 +++ b/static/trackster.css Thu Nov 05 17:25:56 2009 -0500 @@ -25,7 +25,9 @@ font-size: 100%; } -/*canvas{ border-right: 1px solid red; } /* debugging */ +/*canvas{ + border-left: 1px solid green; + border-right: 1px solid red; } /* debugging */ #nav { padding: 0.5em 0; background:#cccccc; @@ -35,8 +37,6 @@ color:#333;font-weight:bold; } - - #nav-controls { text-align: center; } @@ -51,17 +51,6 @@ -moz-border-radius: 1em; } -/* -#low { - margin-left: 0.1em; - float: left; -} -#high { - margin-right: 0.1em; - float: right; -} -*/ - #overview { width: 100%; margin: 0px;

1 0

[hg] galaxy 2973: Fix for tools with multiple tests
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/071f12d75369 changeset: 2973:071f12d75369 user: James Taylor <james(a)jamestaylor.org> date: Thu Nov 05 17:55:14 2009 -0500 description: Fix for tools with multiple tests diffstat: test/functional/test_toolbox.py | 50 +++++++++++------------- 1 files changed, 23 insertions(+), 27 deletions(-) diffs (104 lines): diff -r 52c3fa925dac -r 071f12d75369 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Thu Nov 05 17:25:56 2009 -0500 +++ b/test/functional/test_toolbox.py Thu Nov 05 17:55:14 2009 -0500 @@ -10,11 +10,11 @@ class ToolTestCase( TwillTestCase ): """Abstract test case that runs tests based on a `galaxy.tools.test.ToolTest`""" - def do_it( self ): + def do_it( self, testdef ): # If the test generation had an error, raise - if self.testdef.error: - if self.testdef.exception: - raise self.testdef.exception + if testdef.error: + if testdef.exception: + raise testdef.exception else: raise Exception( "Test parse failure" ) # Start with a new history @@ -31,13 +31,13 @@ if len( self.get_history_as_data_list() ) > 0: raise AssertionError("ToolTestCase.do_it failed") # Upload any needed files - for fname, extra in self.testdef.required_files: + for fname, extra in testdef.required_files: self.upload_file( fname, ftype=extra.get( 'ftype', 'auto' ), dbkey=extra.get( 'dbkey', 'hg17' ) ) print "Uploaded file: ", fname, ", ftype: ", extra.get( 'ftype', 'auto' ), ", extra: ", extra # We need to handle the case where we've uploaded a valid compressed file since the upload # tool will have uncompressed it on the fly. all_inputs = {} - for name, value, _ in self.testdef.inputs: + for name, value, _ in testdef.inputs: if value: for end in [ '.zip', '.gz' ]: if value.endswith( end ): @@ -46,27 +46,25 @@ all_inputs[ name ] = value # See if we have a grouping.Repeat element repeat_name = None - for input_name, input_value in self.testdef.tool.inputs_by_page[0].items(): + for input_name, input_value in testdef.tool.inputs_by_page[0].items(): if isinstance( input_value, grouping.Repeat ): repeat_name = input_name break # Do the first page - page_inputs = self.__expand_grouping(self.testdef.tool.inputs_by_page[0], all_inputs) + page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[0], all_inputs) # Run the tool - self.run_tool( self.testdef.tool.id, repeat_name=repeat_name, **page_inputs ) + self.run_tool( testdef.tool.id, repeat_name=repeat_name, **page_inputs ) print "page_inputs (0)", page_inputs # Do other pages if they exist - for i in range( 1, self.testdef.tool.npages ): - page_inputs = self.__expand_grouping(self.testdef.tool.inputs_by_page[i], all_inputs) + for i in range( 1, testdef.tool.npages ): + page_inputs = self.__expand_grouping(testdef.tool.inputs_by_page[i], all_inputs) self.submit_form( **page_inputs ) print "page_inputs (%i)" % i, page_inputs # Check the result - assert len( self.testdef.outputs ) == 1, "ToolTestCase does not deal with multiple outputs properly yet." - for name, file in self.testdef.outputs: + assert len( testdef.outputs ) == 1, "ToolTestCase does not deal with multiple outputs properly yet." + for name, file in testdef.outputs: self.verify_dataset_correctness( file ) self.delete_history( id=self.security.encode_id( latest_history.id ) ) - def shortDescription( self ): - return self.name def __expand_grouping( self, tool_inputs, declared_inputs, prefix='' ): expanded_inputs = {} @@ -103,15 +101,6 @@ expanded_inputs[value.name] = declared_inputs[value.name] return expanded_inputs -def get_case( testdef, name ): - """Dynamically generate a `ToolTestCase` for `testdef`""" - n = "TestForTool_" + testdef.tool.id.replace( ' ', '_' ) - s = ( ToolTestCase, ) - def test_tool( self ): - self.do_it() - d = dict( testdef=testdef, test_tool=test_tool, name=name ) - return new.classobj( n, s, d ) - def build_tests(): """ If the module level variable `toolbox` is set, generate `ToolTestCase` @@ -125,7 +114,14 @@ for i, tool_id in enumerate( toolbox.tools_by_id ): tool = toolbox.tools_by_id[ tool_id ] if tool.tests: + # Create a new subclass of ToolTestCase dynamically adding methods + # names test_tool_XXX that run each test defined in the tool. + n = "TestForTool_" + tool.id.replace( ' ', '_' ) + s = ( ToolTestCase, ) + d = dict() for j, testdef in enumerate( tool.tests ): - name = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) - testcase = get_case( testdef, name ) - G[ testcase.__name__ ] = testcase + def test_tool( self ): + self.do_it( testdef ) + test_tool.__doc__ = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) + d['test_tool_%06d' % j] = test_tool + G[ n ] = new.classobj( n, s, d )

1 0

[hg] galaxy 2974: Fix closure in creation of generated test meth...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/12518f99a2a7 changeset: 2974:12518f99a2a7 user: James Taylor <james(a)jamestaylor.org> date: Fri Nov 06 00:25:02 2009 -0500 description: Fix closure in creation of generated test methods, otherwise the last testdef is used for every test diffstat: test/functional/test_toolbox.py | 11 +++++++---- 1 files changed, 7 insertions(+), 4 deletions(-) diffs (19 lines): diff -r 071f12d75369 -r 12518f99a2a7 test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Thu Nov 05 17:55:14 2009 -0500 +++ b/test/functional/test_toolbox.py Fri Nov 06 00:25:02 2009 -0500 @@ -120,8 +120,11 @@ s = ( ToolTestCase, ) d = dict() for j, testdef in enumerate( tool.tests ): - def test_tool( self ): - self.do_it( testdef ) - test_tool.__doc__ = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) - d['test_tool_%06d' % j] = test_tool + def make_test_method( td ): + def test_tool( self ): + self.do_it( td ) + return test_tool + m = make_test_method( testdef ) + m.__doc__ = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) + d['test_tool_%06d' % j] = m G[ n ] = new.classobj( n, s, d )

1 0

[hg] galaxy 2975: Fixed BWA wrapper tests (inputs need to be spe...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/411b53d32b78 changeset: 2975:411b53d32b78 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Fri Nov 06 09:57:05 2009 -0500 description: Fixed BWA wrapper tests (inputs need to be specified fastqsanger because there's no longer a sniff method for that type) diffstat: tools/sr_mapping/bwa_wrapper.xml | 18 +++++++++--------- 1 files changed, 9 insertions(+), 9 deletions(-) diffs (70 lines): diff -r 12518f99a2a7 -r 411b53d32b78 tools/sr_mapping/bwa_wrapper.xml --- a/tools/sr_mapping/bwa_wrapper.xml Fri Nov 06 00:25:02 2009 -0500 +++ b/tools/sr_mapping/bwa_wrapper.xml Fri Nov 06 09:57:05 2009 -0500 @@ -161,7 +161,7 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in1.fastq" /> + <param name="input1" value="bwa_wrapper_in1.fastq" ftype="fastqsanger" /> <param name="source_select" value="pre_set" /> <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out0.sam" ftype="sam" /> @@ -171,7 +171,7 @@ <param name="refGenomeSource" value="history" /> <param name="ownFile" value="phiX.fa" /> <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in0.fastq" /> + <param name="input1" value="bwa_wrapper_in0.fastq" ftype="fastqsanger" /> <param name="source_select" value="pre_set" /> <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out0b.sam" ftype="sam" /> @@ -181,7 +181,7 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in2.fastq" /> + <param name="input1" value="bwa_wrapper_in2.fastq" ftype="fastqsanger" /> <param name="source_select" value="full" /> <param name="maxEditDist" value="0" /> <param name="fracMissingAligns" value="0.04" /> @@ -208,8 +208,8 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="paired" /> - <param name="input1" value="bwa_wrapper_in3.fastq" /> - <param name="input2" value="bwa_wrapper_in4.fastq" /> + <param name="input1" value="bwa_wrapper_in3.fastq" ftype="fastqsanger" /> + <param name="input2" value="bwa_wrapper_in4.fastq" ftype="fastqsanger" /> <param name="source_select" value="full" /> <param name="maxEditDist" value="0" /> <param name="fracMissingAligns" value="0.04" /> @@ -236,7 +236,7 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="single" /> - <param name="input1" value="bwa_wrapper_in1.fastq" /> + <param name="input1" value="bwa_wrapper_in1.fastq" ftype="fastqsanger" /> <param name="source_select" value="full" /> <param name="maxEditDist" value="0" /> <param name="fracMissingAligns" value="0.04" /> @@ -263,8 +263,8 @@ <param name="refGenomeSource" value="indexed" /> <param name="indices" value="phiX" /> <param name="sPaired" value="paired" /> - <param name="input1" value="bwa_wrapper_in5.fastq" /> - <param name="input2" value="bwa_wrapper_in6.fastq" /> + <param name="input1" value="bwa_wrapper_in5.fastq" ftype="fastqsanger" /> + <param name="input2" value="bwa_wrapper_in6.fastq" ftype="fastqsanger" /> <param name="source_select" value="full" /> <param name="maxEditDist" value="0" /> <param name="fracMissingAligns" value="0.04" /> @@ -285,7 +285,7 @@ <param name="maxOccurPairing" value="100000" /> <param name="suppressHeader" value="true" /> <output name="output" file="bwa_wrapper_out4.sam" ftype="sam" /> - </test> + </test> </tests> <help>

1 0

[hg] galaxy 2970: Refactored the new address functional test
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/731875ce0a36 changeset: 2970:731875ce0a36 user: rc date: Thu Nov 05 14:19:45 2009 -0500 description: Refactored the new address functional test diffstat: lib/galaxy/web/controllers/user.py | 4 ++++ test/base/twilltestcase.py | 17 +++++++++++++++++ test/functional/test_forms_and_requests.py | 8 +------- 3 files changed, 22 insertions(+), 7 deletions(-) diffs (66 lines): diff -r c6a8bd78357a -r 731875ce0a36 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Thu Nov 05 10:39:59 2009 -0500 +++ b/lib/galaxy/web/controllers/user.py Thu Nov 05 14:19:45 2009 -0500 @@ -680,6 +680,8 @@ widget=TextField( 'institution', 40, '' ) ) ) widgets.append(dict(label='Address Line 1', widget=TextField( 'address1', 40, '' ) ) ) + widgets.append(dict(label='Address Line 2', + widget=TextField( 'address2', 40, '' ) ) ) widgets.append(dict(label='City', widget=TextField( 'city', 40, '' ) ) ) widgets.append(dict(label='State', @@ -762,6 +764,8 @@ widget=TextField( 'institution', 40, user_address.institution ) ) ) widgets.append(dict(label='Address Line 1', widget=TextField( 'address1', 40, user_address.address ) ) ) + widgets.append(dict(label='Address Line 2', + widget=TextField( 'address2', 40, '' ) ) ) widgets.append(dict(label='City', widget=TextField( 'city', 40, user_address.city ) ) ) widgets.append(dict(label='State', diff -r c6a8bd78357a -r 731875ce0a36 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Thu Nov 05 10:39:59 2009 -0500 +++ b/test/base/twilltestcase.py Thu Nov 05 14:19:45 2009 -0500 @@ -1281,6 +1281,23 @@ tc.fv( "1", "comment", comment ) tc.submit( "add_event_button" ) self.check_page_for_string( new_state_name ) + def add_user_address( self, user_id, address_dict ): + self.home() + self.visit_url( "%s/user/new_address?admin_view=False&user_id=%i" % ( self.url, user_id ) ) + self.check_page_for_string( 'New address' ) + for field_name, value in address_dict.items(): + tc.fv( "1", field_name, value ) + tc.submit( "save_new_address_button" ) + self.check_page_for_string( 'Address <b>%s</b> has been added' % address_dict[ 'short_desc' ] ) + def add_user_address_as_admin( self, user_id, address_dict ): + self.home() + self.visit_url( "%s/user/new_address?admin_view=True&user_id=%i" % ( self.url, user_id ) ) + self.check_page_for_string( 'New address' ) + for field_name, value in address_dict.items(): + tc.fv( "1", field_name, value ) + tc.submit( "save_new_address_button" ) + self.check_page_for_string( 'Address <b>%s</b> has been added' % address_dict[ 'short_desc' ] ) + # Library stuff def create_library( self, name='Library One', description='This is Library One' ): """Create a new library""" diff -r c6a8bd78357a -r 731875ce0a36 test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Thu Nov 05 10:39:59 2009 -0500 +++ b/test/functional/test_forms_and_requests.py Thu Nov 05 14:19:45 2009 -0500 @@ -168,13 +168,7 @@ # create address self.logout() self.login( email='test1(a)bx.psu.edu' ) - self.home() - url_str = '%s/user/new_address?short_desc=%s&name=%s&institution=%s&address1=%s&address2=%s&city=%s&state=%s&postal_code=%s&country=%s&phone=%s' \ - % ( self.url, address1[ 'short_desc' ], address1[ 'name' ], address1[ 'institution' ], - address1[ 'address1' ], address1[ 'address2' ], address1[ 'city' ], address1[ 'state' ], - address1[ 'postal_code' ], address1[ 'country' ], address1[ 'phone' ] ) - self.visit_url( url_str ) - self.check_page_for_string( 'Address <b>%s</b> has been added' % address1[ 'short_desc' ] ) + self.add_user_address( regular_user1.id, address1 ) global regular_user regular_user = sa_session.query( galaxy.model.User ) \ .filter( galaxy.model.User.table.c.email=='test1(a)bx.psu.edu' ) \

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