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galaxy-dist commit 2447b9a4dae3: Make "loc files" more flexible by adding "tool data tables". These are
by commits-noreply＠bitbucket.org 20 Aug '10

20 Aug '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User James Taylor <james(a)jamestaylor.org> # Date 1278614219 14400 # Node ID 2447b9a4dae30b17df089290a6471f3401fa5f78 # Parent e683c6995fb5d032660d1c28cff2e1bc578d1298 Make "loc files" more flexible by adding "tool data tables". These are configured at the application level. Specific tabular data files are specified in a application config file and bound to names, the tools then refer to these names. Thus users can configure where location files are located without modifying tool configs. Also: - Simpler column name configuration - Columns can be referred to by name in addition to index in all dynamic option filters - A data table can merge multiple files - Design can support other types of data files --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -46,9 +46,9 @@ class StaticValueFilter( Filter ): Filter.__init__( self, d_option, elem ) self.value = elem.get( "value", None ) assert self.value is not None, "Required 'value' attribute missing from filter" - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter, when loading from file" - self.column = int ( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter, when loading from file" + self.column = d_option.column_spec_to_index( column ) self.keep = string_as_bool( elem.get( "keep", 'True' ) ) def filter_options( self, options, trans, other_values ): rval = [] @@ -81,11 +81,11 @@ class DataMetaFilter( Filter ): d_option.has_dataset_dependencies = True self.key = elem.get( "key", None ) assert self.key is not None, "Required 'key' attribute missing from filter" - self.column = elem.get( "column", None ) - if self.column is None: + column = elem.get( "column", None ) + if column is None: assert self.dynamic_option.file_fields is None and self.dynamic_option.dataset_ref_name is None, "Required 'column' attribute missing from filter, when loading from file" else: - self.column = int ( self.column ) + self.column = d_option.column_spec_to_index( column ) self.multiple = string_as_bool( elem.get( "multiple", "False" ) ) self.separator = elem.get( "separator", "," ) def get_dependency_name( self ): @@ -141,9 +141,9 @@ class ParamValueFilter( Filter ): Filter.__init__( self, d_option, elem ) self.ref_name = elem.get( "ref", None ) assert self.ref_name is not None, "Required 'ref' attribute missing from filter" - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter" - self.column = int ( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter" + self.column = d_option.column_spec_to_index( column ) self.keep = string_as_bool( elem.get( "keep", 'True' ) ) def get_dependency_name( self ): return self.ref_name @@ -168,9 +168,9 @@ class UniqueValueFilter( Filter ): """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter" - self.column = int ( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter" + self.column = d_option.column_spec_to_index( column ) def get_dependency_name( self ): return self.dynamic_option.dataset_ref_name def filter_options( self, options, trans, other_values ): @@ -196,9 +196,9 @@ class MultipleSplitterFilter( Filter ): def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) self.separator = elem.get( "separator", "," ) - self.columns = elem.get( "column", None ) - assert self.columns is not None, "Required 'columns' attribute missing from filter" - self.columns = [ int ( column ) for column in self.columns.split( "," ) ] + columns = elem.get( "column", None ) + assert columns is not None, "Required 'columns' attribute missing from filter" + self.columns = [ d_option.column_spec_to_index( column ) for column in columns.split( "," ) ] def filter_options( self, options, trans, other_values ): rval = [] for fields in options: @@ -302,9 +302,9 @@ class SortByColumnFilter( Filter ): """ def __init__( self, d_option, elem ): Filter.__init__( self, d_option, elem ) - self.column = elem.get( "column", None ) - assert self.column is not None, "Required 'column' attribute missing from filter" - self.column = int( self.column ) + column = elem.get( "column", None ) + assert column is not None, "Required 'column' attribute missing from filter" + self.column = d_option.column_spec_to_index( column ) def filter_options( self, options, trans, other_values ): rval = [] for i, fields in enumerate( options ): @@ -354,20 +354,25 @@ class DynamicOptions( object ): data_file = elem.get( 'from_file', None ) dataset_file = elem.get( 'from_dataset', None ) from_parameter = elem.get( 'from_parameter', None ) - if data_file is not None or dataset_file is not None or from_parameter is not None: - for column_elem in elem.findall( 'column' ): - name = column_elem.get( 'name', None ) - assert name is not None, "Required 'name' attribute missing from column def" - index = column_elem.get( 'index', None ) - assert index is not None, "Required 'index' attribute missing from column def" - index = int( index ) - self.columns[name] = index - if index > self.largest_index: - self.largest_index = index - assert 'value' in self.columns, "Required 'value' column missing from column def" - if 'name' not in self.columns: - self.columns['name'] = self.columns['value'] + tool_data_table_name = elem.get( 'from_data_table', None ) + + # Options are defined from a data table loaded by the app + self.tool_data_table = None + if tool_data_table_name: + app = tool_param.tool.app + assert tool_data_table_name in app.tool_data_tables, \ + "Data table named '%s' is required by tool but not configured" % tool_data_table_name + self.tool_data_table = app.tool_data_tables[ tool_data_table_name ] + # Column definitions are optional, but if provided override those from the table + if elem.find( "column" ) is not None: + self.parse_column_definitions( elem ) + else: + self.columns = self.tool_data_table.columns + # Options are defined by parsing tabular text data from an data file + # on disk, a dataset, or the value of another parameter + elif data_file is not None or dataset_file is not None or from_parameter is not None: + self.parse_column_definitions( elem ) if data_file is not None: data_file = data_file.strip() if not os.path.isabs( data_file ): @@ -388,6 +393,20 @@ class DynamicOptions( object ): # Load Validators for validator in elem.findall( 'validator' ): self.validators.append( validation.Validator.from_element( self.tool_param, validator ) ) + + def parse_column_definitions( self, elem ): + for column_elem in elem.findall( 'column' ): + name = column_elem.get( 'name', None ) + assert name is not None, "Required 'name' attribute missing from column def" + index = column_elem.get( 'index', None ) + assert index is not None, "Required 'index' attribute missing from column def" + index = int( index ) + self.columns[name] = index + if index > self.largest_index: + self.largest_index = index + assert 'value' in self.columns, "Required 'value' column missing from column def" + if 'name' not in self.columns: + self.columns['name'] = self.columns['value'] def parse_file_fields( self, reader ): rval = [] @@ -421,6 +440,8 @@ class DynamicOptions( object ): assert dataset is not None, "Required dataset '%s' missing from input" % self.dataset_ref_name if not dataset: return [] #no valid dataset in history options = self.parse_file_fields( open( dataset.file_name ) ) + elif self.tool_data_table: + options = self.tool_data_table.get_fields() else: options = list( self.file_fields ) for filter in self.filters: @@ -429,7 +450,7 @@ class DynamicOptions( object ): def get_options( self, trans, other_values ): rval = [] - if self.file_fields is not None or self.dataset_ref_name is not None: + if self.file_fields is not None or self.tool_data_table is not None or self.dataset_ref_name is not None: options = self.get_fields( trans, other_values ) for fields in options: rval.append( ( fields[self.columns['name']], fields[self.columns['value']], False ) ) @@ -437,3 +458,15 @@ class DynamicOptions( object ): for filter in self.filters: rval = filter.filter_options( rval, trans, other_values ) return rval + + def column_spec_to_index( self, column_spec ): + """ + Convert a column specification (as read from the config file), to an + index. A column specification can just be a number, a column name, or + a column alias. + """ + # Name? + if column_spec in self.columns: + return self.columns[column_spec] + # Int? + return int( column_spec ) --- a/tools/sr_mapping/bowtie_wrapper.xml +++ b/tools/sr_mapping/bowtie_wrapper.xml @@ -192,10 +192,13 @@ </param><when value="indexed"><param name="index" type="select" label="Select a reference genome" help="if your genome of interest is not listed - contact Galaxy team"> + <options from_data_table="bowtie_indexes"/> + </param></when><when value="history"> --- a/lib/galaxy/util/__init__.py +++ b/lib/galaxy/util/__init__.py @@ -231,13 +231,17 @@ def rst_to_html( s ): log.warn( str ) return docutils.core.publish_string( s, writer=HTMLFragWriter(), settings_overrides=dict( warning_stream=FakeStream() ) ) -def xml_text(root, name): +def xml_text(root, name=None): """Returns the text inside an element""" - # Try attribute first - val = root.get(name) - if val: return val - # Then try as element - elem = root.find(name) + if name is not None: + # Try attribute first + val = root.get(name) + if val: + return val + # Then try as element + elem = root.find(name) + else: + elem = root if elem is not None and elem.text: text = ''.join(elem.text.splitlines()) return text.strip() --- a/setup.sh +++ b/setup.sh @@ -7,6 +7,7 @@ SAMPLES=" datatypes_conf.xml.sample reports_wsgi.ini.sample tool_conf.xml.sample +tool_data_table_conf.xml.sample universe_wsgi.ini.sample tool-data/alignseq.loc.sample tool-data/annotation_profiler_options.xml.sample --- a/tools/sr_mapping/bwa_wrapper.xml +++ b/tools/sr_mapping/bwa_wrapper.xml @@ -34,10 +34,13 @@ </param><when value="indexed"><param name="indices" type="select" label="Select a reference genome"> + <options from_data_table="bwa_indexes"/> + </param></when><when value="history"> --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -2,6 +2,7 @@ import sys, os, atexit from galaxy import config, jobs, util, tools, web import galaxy.tools.search +import galaxy.tools.data from galaxy.web import security import galaxy.model import galaxy.datatypes.registry @@ -36,6 +37,8 @@ class UniverseApplication( object ): self.security = security.SecurityHelper( id_secret=self.config.id_secret ) # Tag handler self.tag_handler = GalaxyTagHandler() + # Tool data tables + self.tool_data_tables = galaxy.tools.data.ToolDataTableManager( self.config.tool_data_table_config_path ) # Initialize the tools self.toolbox = tools.ToolBox( self.config.tool_config, self.config.tool_path, self ) # Search support for tools --- a/lib/galaxy/config.py +++ b/lib/galaxy/config.py @@ -48,6 +48,7 @@ class Configuration( object ): self.tool_data_path = resolve_path( kwargs.get( "tool_data_path", "tool-data" ), os.getcwd() ) self.test_conf = resolve_path( kwargs.get( "test_conf", "" ), self.root ) self.tool_config = resolve_path( kwargs.get( 'tool_config_file', 'tool_conf.xml' ), self.root ) + self.tool_data_table_config_path = resolve_path( kwargs.get( 'tool_data_table_config_path', 'tool_data_table_conf.xml' ), self.root ) self.tool_secret = kwargs.get( "tool_secret", "" ) self.id_secret = kwargs.get( "id_secret", "USING THE DEFAULT IS NOT SECURE!" ) self.set_metadata_externally = string_as_bool( kwargs.get( "set_metadata_externally", "False" ) ) --- a/tools/maf/interval2maf.xml +++ b/tools/maf/interval2maf.xml @@ -32,22 +32,24 @@ </when><when value="cached"><param name="mafType" type="select" label="Choose alignments"> - <options from_file="maf_index.loc"> + <options from_data_table="indexed_maf_files"> +  + <filter type="data_meta" ref="input1" key="dbkey" column="dbkey" multiple="True" separator=","/><validator type="no_options" message="No alignments are available for the build associated with the selected interval file"/></options></param><param name="species" type="select" display="checkboxes" multiple="true" label="Choose species" help="Select species to be included in the final alignment"> - <options from_file="maf_index.loc"> + <options from_data_table="indexed_maf_files"><column name="uid" index="1"/><column name="value" index="3"/><column name="name" index="3"/> - <filter type="param_value" ref="mafType" name="uid" column="1"/> - <filter type="multiple_splitter" column="3" separator=","/> + <filter type="param_value" ref="mafType" column="uid"/> + <filter type="multiple_splitter" column="name" separator=","/></options></param></when>

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galaxy-dist commit 6e19bc97f2b8: - Fix dbkey migrate script for downgrade and rare case when config is empty
by commits-noreply＠bitbucket.org 20 Aug '10

20 Aug '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Kanwei Li <kanwei(a)gmail.com> # Date 1280868063 14400 # Node ID 6e19bc97f2b8ba816ab20fc53a88f3504c992e00 # Parent 0366c4a4765631188f1515fbd77fddbbf1532d4f - Fix dbkey migrate script for downgrade and rare case when config is empty - Fix grid sorting in "Visualize in Trackster" modal box - Refactor out sort_order in grids, fixing a bug with sort arrow not showing --- a/templates/tracks/add_to_viz.mako +++ b/templates/tracks/add_to_viz.mako @@ -6,8 +6,3 @@ ${render_grid_header( grid, False )} ${render_grid_table( grid, show_item_checkboxes=True )} -## Initialize the grid. -<script type="text/javascript"> - init_grid_elements(); - init_grid_controls(); -</script> --- a/lib/galaxy/web/framework/helpers/grids.py +++ b/lib/galaxy/web/framework/helpers/grids.py @@ -136,7 +136,6 @@ class Grid( object ): extra_url_args[ "f-" + column.key ] = column_filter.encode("utf-8") # Process sort arguments. sort_key = None - sort_order = None if 'sort' in kwargs: sort_key = kwargs['sort'] elif base_sort_key: @@ -144,11 +143,9 @@ class Grid( object ): encoded_sort_key = sort_key if sort_key: if sort_key.startswith( "-" ): - sort_order = 'desc' # Can't use lower() on timestamp or integer objects, so func.lower() is not used here... query = query.order_by( self.model_class.table.c.get( sort_key[1:] ).desc() ) else: - sort_order = 'asc' # See reason for not using lower() to do case-insensitive search. query = query.order_by( self.model_class.table.c.get( sort_key ).asc() ) extra_url_args['sort'] = encoded_sort_key @@ -226,7 +223,6 @@ class Grid( object ): cur_filter_dict=cur_filter_dict, sort_key=sort_key, encoded_sort_key=encoded_sort_key, - sort_order=sort_order, current_item=current_item, ids = kwargs.get( 'id', [] ), url = url, --- a/templates/grid_base.mako +++ b/templates/grid_base.mako @@ -739,8 +739,8 @@ href = "" extra = "" if column.sortable: - if sort_key == column.key: - if sort_order == "asc": + if sort_key.endswith(column.key): + if not sort_key.startswith("-"): href = url( sort=( "-" + column.key ) ) extra = "↓" else: --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -205,7 +205,7 @@ class UsesVisualization( SharableItemSec # Set dbkey. try: - dbkey = latest_revision.config['dbkey'] + dbkey = latest_revision.dbkey except KeyError: dbkey = None --- a/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py +++ b/lib/galaxy/model/migrate/versions/0054_visualization_dbkey.py @@ -14,13 +14,13 @@ log = logging.getLogger( __name__ ) metadata = MetaData( migrate_engine ) db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) -Visualization_table = Table( "visualization", metadata, autoload=True ) -Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True ) - def upgrade(): print __doc__ metadata.reflect() + + Visualization_table = Table( "visualization", metadata, autoload=True ) + Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True ) # Create dbkey columns. x = Column( "dbkey", TEXT, index=True ) @@ -47,12 +47,16 @@ def upgrade(): for viz in all_viz: viz_id = viz['viz_id'] viz_rev_id = viz['viz_rev_id'] - dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'") - db_session.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id)) - db_session.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id)) + if viz[Visualization_revision_table.c.config]: + dbkey = from_json_string(viz[Visualization_revision_table.c.config]).get('dbkey', "").replace("'", "\\'") + db_session.execute("UPDATE visualization_revision SET dbkey='%s' WHERE id=%s" % (dbkey, viz_rev_id)) + db_session.execute("UPDATE visualization SET dbkey='%s' WHERE id=%s" % (dbkey, viz_id)) def downgrade(): metadata.reflect() + + Visualization_table = Table( "visualization", metadata, autoload=True ) + Visualization_revision_table = Table( "visualization_revision", metadata, autoload=True ) Visualization_table.c.dbkey.drop() Visualization_revision_table.c.dbkey.drop()

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galaxy-dist commit 07e7db914c6d: Modified Group tool by adding Mode function to the list of aggregate operations.
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User gua110 # Date 1280420469 14400 # Node ID 07e7db914c6d2090ef7579a5e2c0583af50c39f3 # Parent 79baa9583d9390bb6341d3484aa9f55b8e3808f8 Modified Group tool by adding Mode function to the list of aggregate operations. --- a/tools/stats/grouping.py +++ b/tools/stats/grouping.py @@ -23,6 +23,12 @@ def main(): cols.append(var.split()[1]) rounds.append(var.split()[2]) + if 'Mode' in ops: + try: + r.library('prettyR') + except: + stop_err('R package prettyR could not be loaded. Please make sure it is installed.') + """ At this point, ops, cols and rounds will look something like this: ops: ['mean', 'min', 'c'] @@ -46,9 +52,10 @@ def main(): except: stop_err( "Group column not specified." ) + str_ops = ['c', 'length', 'unique', 'random', 'cuniq', 'Mode'] #ops that can handle string/non-numeric inputs for k,col in enumerate(cols): col = int(col)-1 - if ops[k] not in ['c', 'length', 'unique', 'random', 'cuniq']: + if ops[k] not in str_ops: # We'll get here only if the user didn't choose 'Concatenate' or 'Count' or 'Count Distinct' or 'pick randmly', which are the # only aggregation functions that can be used on columns containing strings. try: @@ -109,7 +116,7 @@ def main(): valid = True # Before appending the current value, make sure it is numeric if the # operation for the column requires it. - if ops[i] not in ['c','length', 'unique','random','cuniq']: + if ops[i] not in str_ops: try: float( fields[col].strip()) except: @@ -128,13 +135,14 @@ def main(): due to the sort on group_col we've applied to the data above. """ out_str = prev_item - + multiple_modes = False + mode_index = None for i, op in enumerate( ops ): if op == 'cuniq': rfunc = "r.c" else: rfunc = "r." + op - if op not in ['c','length','unique','random','cuniq']: + if op not in str_ops: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) rout = eval( rfunc )( prev_vals[i] ) @@ -148,7 +156,10 @@ def main(): else: rand_index = random.randint(0,len(prev_vals[i])-1) rout = prev_vals[i][rand_index] - + + if op == 'Mode' and rout == '>1 mode': + multiple_modes = True + mode_index = i if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) @@ -165,8 +176,13 @@ def main(): out_str += "\t" + str(rout) else: out_str += "\t" + str(rout) - - print >>fout, out_str + if multiple_modes and mode_index != None: + out_str_list = out_str.split('\t') + for val in prev_vals[mode_index]: + out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) + print >>fout, out_str.rstrip('\t') + else: + print >>fout, out_str prev_item = item prev_vals = [] @@ -195,14 +211,15 @@ def main(): # Handle the last grouped value out_str = prev_item - + multiple_modes = False + mode_index = None for i, op in enumerate(ops): if op == 'cuniq': rfunc = "r.c" else: rfunc = "r." + op try: - if op not in ['c','length','unique','random','cuniq']: + if op not in str_ops: for j, elem in enumerate( prev_vals[i] ): prev_vals[i][j] = float( elem ) rout = eval( rfunc )( prev_vals[i] ) @@ -216,7 +233,10 @@ def main(): else: rand_index = random.randint(0,len(prev_vals[i])-1) rout = prev_vals[i][rand_index] - + + if op == 'Mode' and rout == '>1 mode': + multiple_modes = True + mode_index = i if op == 'unique': rfunc = "r.length" rout = eval( rfunc )( rout ) @@ -238,7 +258,13 @@ def main(): if not first_invalid_line: first_invalid_line = ii+1 - print >>fout, out_str + if multiple_modes and mode_index != None: + out_str_list = out_str.split('\t') + for val in prev_vals[mode_index]: + out_str = '\t'.join(out_str_list[:mode_index+1]) + '\t' + str(val) + '\t' + '\t'.join(out_str_list[mode_index+2:]) + print >>fout, out_str.rstrip('\t') + else: + print >>fout, out_str # Generate a useful info message. msg = "--Group by c%d: " %(group_col+1) --- a/tools/stats/grouping.xml +++ b/tools/stats/grouping.xml @@ -1,4 +1,4 @@ -<tool id="Grouping1" name="Group" version="1.9.0"> +<tool id="Grouping1" name="Group" version="1.9.1"><description>data by a column and perform aggregate operation on other columns.</description><command interpreter="python"> grouping.py @@ -22,6 +22,7 @@ <param name="optype" type="select" label="Type"><option value="mean">Mean</option><option value="median">Median</option> + <option value="Mode">Mode</option><option value="max">Maximum</option><option value="min">Minimum</option><option value="sum">Sum</option> @@ -77,10 +78,12 @@ **Syntax** -This tool allows you to group the input dataset by a particular column and perform aggregate functions like Mean, Sum, Max, Min and Concatenate on other columns. +This tool allows you to group the input dataset by a particular column and perform aggregate functions like Mean, Median, Mode, Sum, Max, Min, Count, Random draw and Concatenate on other columns. - All invalid, blank and comment lines are skipped when performing the aggregate functions. The number of skipped lines is displayed in the resulting history item. +- If multiple modes are present, all are reported. + ----- **Example**

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galaxy-dist commit 66e03194e2da: lims:
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1280424157 14400 # Node ID 66e03194e2dae00723d446509e077a869f274922 # Parent 07e7db914c6d2090ef7579a5e2c0583af50c39f3 lims: - sample dataset size now appear correctly in the grid. The path of the datasets no longer appears with it. --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -1624,7 +1624,7 @@ class Sample( object ): output = pexpect.run(cmd, events={'.ssword:*': datatx_info['password']+'\r\n', pexpect.TIMEOUT:print_ticks}, timeout=10) - return output.split('\t')[0] + return output.replace(filepath, '').strip() class SampleState( object ): def __init__(self, name=None, desc=None, request_type=None):

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galaxy-dist commit a8ef6a46d622: Added AttributeValueSplitterFilter to tool select parameter filters so that GFF attributes can be read and used as tool inputs. Updated gff_filtering tool to use this filter.
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User jeremy goecks <jeremy.goecks(a)emory.edu> # Date 1280439706 14400 # Node ID a8ef6a46d6221d8eb3a7bc919fc3e2b13c1bc2aa # Parent 66e03194e2dae00723d446509e077a869f274922 Added AttributeValueSplitterFilter to tool select parameter filters so that GFF attributes can be read and used as tool inputs. Updated gff_filtering tool to use this filter. --- a/lib/galaxy/tools/parameters/dynamic_options.py +++ b/lib/galaxy/tools/parameters/dynamic_options.py @@ -206,6 +206,40 @@ class MultipleSplitterFilter( Filter ): for field in fields[column].split( self.separator ): rval.append( fields[0:column] + [field] + fields[column:] ) return rval + +class AttributeValueSplitterFilter( Filter ): + """ + Filters a list of attribute-value pairs to be unique attribute names. + + Type: attribute_value_splitter + + Required Attributes: + column: column in options to compare with + Optional Attributes: + pair_separator: Split column by this (,) + name_val_separator: Split name-value pair by this ( whitespace ) + """ + def __init__( self, d_option, elem ): + Filter.__init__( self, d_option, elem ) + self.pair_separator = elem.get( "pair_separator", "," ) + self.name_val_separator = elem.get( "name_val_separator", None ) + self.columns = elem.get( "column", None ) + assert self.columns is not None, "Required 'columns' attribute missing from filter" + self.columns = [ int ( column ) for column in self.columns.split( "," ) ] + def filter_options( self, options, trans, other_values ): + attr_names = [] + rval = [] + for fields in options: + for column in self.columns: + for pair in fields[column].split( self.pair_separator ): + ary = pair.split( self.name_val_separator ) + if len( ary ) == 2: + name, value = ary + if name not in attr_names: + rval.append( fields[0:column] + [name] + fields[column:] ) + attr_names.append( name ) + return rval + class AdditionalValueFilter( Filter ): """ @@ -322,6 +356,7 @@ filter_types = dict( data_meta = DataMet static_value = StaticValueFilter, unique_value = UniqueValueFilter, multiple_splitter = MultipleSplitterFilter, + attribute_value_splitter = AttributeValueSplitterFilter, add_value = AdditionalValueFilter, remove_value = RemoveValueFilter, sort_by = SortByColumnFilter ) --- a/tools/ngs_rna/gff_filtering.xml +++ b/tools/ngs_rna/gff_filtering.xml @@ -5,8 +5,12 @@ </command><inputs><param format="gff" name="input" type="data" label="Filter" help="Query missing? See TIP below."/> - <param name="attribute_name" size="40" type="text" label="Attribute name" help=""> - <validator type="empty_field" message="Enter a valid attribute name."/> + <param name="attribute_name" type="select" label="Attribute name" help=""> + <options from_dataset="input"> + <column name="name" index="8"/> + <column name="value" index="8"/> + <filter type="attribute_value_splitter" pair_separator=";" column="8"/> + </options></param><param name="attribute_type" type="select" label="Attribute type"><option value="float">Float</option>

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galaxy-dist commit c653ccfa1a1e: Allow access to /api without HTTP_REMOTE_USER set if use_remote_user = True, since the API controllers handle authentication internally.
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1280416580 14400 # Node ID c653ccfa1a1ef7c2a384ee4b3ab72da0b391ae14 # Parent ab48c0e20a948f310ad3b072c23560faa8433aa3 Allow access to /api without HTTP_REMOTE_USER set if use_remote_user = True, since the API controllers handle authentication internally. --- a/lib/galaxy/web/framework/middleware/remoteuser.py +++ b/lib/galaxy/web/framework/middleware/remoteuser.py @@ -75,8 +75,8 @@ class RemoteUser( object ): # Apache sets REMOTE_USER to the string '(null)' when using the # Rewrite* method for passing REMOTE_USER and a user is # un-authenticated. Any other possible values need to go here as well. + path_info = environ.get('PATH_INFO', '') if environ.has_key( 'HTTP_REMOTE_USER' ) and environ[ 'HTTP_REMOTE_USER' ] != '(null)': - path_info = environ.get('PATH_INFO', '') if not environ[ 'HTTP_REMOTE_USER' ].count( '@' ): if self.maildomain is not None: environ[ 'HTTP_REMOTE_USER' ] += '@' + self.maildomain @@ -96,7 +96,7 @@ class RemoteUser( object ): if path_info.startswith( '/user/create' ) and environ[ 'HTTP_REMOTE_USER' ] in self.admin_users: pass # admins can create users elif path_info.startswith( '/user/api_keys' ): - pass + pass # api keys can be managed when remote_user is in use elif path_info.startswith( '/user' ): title = "Access to Galaxy user controls is disabled" message = """ @@ -105,6 +105,9 @@ class RemoteUser( object ): """ return self.error( start_response, title, message ) return self.app( environ, start_response ) + elif path_info.startswith( '/api/' ): + # The API handles its own authentication via keys + return self.app( environ, start_response ) else: title = "Access to Galaxy is denied" message = """

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galaxy-dist commit 8d255150cb3e: Use env for the API example scripts instead of directly referring to /usr/bin/python
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Nate Coraor <nate(a)bx.psu.edu> # Date 1280416695 14400 # Node ID 8d255150cb3e868974777eee030843d2c3e7ad16 # Parent c653ccfa1a1ef7c2a384ee4b3ab72da0b391ae14 Use env for the API example scripts instead of directly referring to /usr/bin/python --- a/scripts/api/library_upload_from_import_dir.py +++ b/scripts/api/library_upload_from_import_dir.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import os, sys sys.path.insert( 0, os.path.dirname( __file__ ) ) --- a/scripts/api/library_create_library.py +++ b/scripts/api/library_create_library.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import os, sys sys.path.insert( 0, os.path.dirname( __file__ ) ) --- a/scripts/api/library_create_folder.py +++ b/scripts/api/library_create_folder.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import os, sys sys.path.insert( 0, os.path.dirname( __file__ ) ) --- a/scripts/api/display.py +++ b/scripts/api/display.py @@ -1,4 +1,4 @@ -#!/usr/bin/python +#!/usr/bin/env python import os, sys sys.path.insert( 0, os.path.dirname( __file__ ) )

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galaxy-dist commit ab48c0e20a94: Merge with 0736d9af9e6e7facef8fad93baa3a303e0cf9526
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1280416325 14400 # Node ID ab48c0e20a948f310ad3b072c23560faa8433aa3 # Parent b0cf8217826e7a289eec88fd31894683818d2bee # Parent 0736d9af9e6e7facef8fad93baa3a303e0cf9526 Merge with 0736d9af9e6e7facef8fad93baa3a303e0cf9526

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galaxy-dist commit 79baa9583d93: lims:
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1280417621 14400 # Node ID 79baa9583d9390bb6341d3484aa9f55b8e3808f8 # Parent 8d255150cb3e868974777eee030843d2c3e7ad16 lims: - fixed a migration script bug when moving the sample datasets info from the 'sample' to 'sample_dataset' table --- a/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py +++ b/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py @@ -61,19 +61,20 @@ def upgrade(): result = db_session.execute( cmd ) for r in result: sample_id = r[0] - dataset_files = from_json_string(r[1]) - for df in dataset_files: - cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')" - cmd = cmd % ( nextval('sample_dataset'), - localtimestamp(), - localtimestamp(), - str(sample_id), - df['name'], - df['filepath'], - df['status'], - df['error_msg'].replace('"', '').replace("'", ""), - df['size'] ) - db_session.execute( cmd ) + if r[1]: + dataset_files = from_json_string(r[1]) + for df in dataset_files: + cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')" + cmd = cmd % ( nextval('sample_dataset'), + localtimestamp(), + localtimestamp(), + str(sample_id), + df['name'], + df['filepath'], + df['status'].replace('"', '').replace("'", ""), + "", + df['size'].replace('"', '').replace("'", "") ) + db_session.execute( cmd ) # Delete the dataset_files column in the Sample table try:

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galaxy-dist commit b0cf8217826e: lims:
by commits-noreply＠bitbucket.org 30 Jul '10

30 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User rc # Date 1280416255 14400 # Node ID b0cf8217826e7a289eec88fd31894683818d2bee # Parent d27912281a74ba74a8df6f5d72db7c553ca846c5 lims: - fixed couple of broken links - comminting the db migrate script (0052) skipped in the previous commit --- /dev/null +++ b/lib/galaxy/model/migrate/versions/0052_sample_dataset_table.py @@ -0,0 +1,92 @@ +""" +Migration script to add the sample_dataset table and remove the 'dataset_files' column +from the 'sample' table +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from migrate import * +from migrate.changeset import * +from sqlalchemy.exc import * + +from galaxy.model.custom_types import * +from galaxy.util.json import from_json_string, to_json_string + +import datetime +now = datetime.datetime.utcnow + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) + + +def nextval( table, col='id' ): + if migrate_engine.name == 'postgres': + return "nextval('%s_%s_seq')" % ( table, col ) + elif migrate_engine.name == 'mysql' or migrate_engine.name == 'sqlite': + return "null" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % migrate_engine.name ) + +def localtimestamp(): + if migrate_engine.name == 'postgres' or migrate_engine.name == 'mysql': + return "LOCALTIMESTAMP" + elif migrate_engine.name == 'sqlite': + return "current_date || ' ' || current_time" + else: + raise Exception( 'Unable to convert data for unknown database type: %s' % db ) + +SampleDataset_table = Table('sample_dataset', metadata, + Column( "id", Integer, primary_key=True ), + Column( "create_time", DateTime, default=now ), + Column( "update_time", DateTime, default=now, onupdate=now ), + Column( "sample_id", Integer, ForeignKey( "sample.id" ), index=True ), + Column( "name", TrimmedString( 255 ), nullable=False ), + Column( "file_path", TrimmedString( 255 ), nullable=False ), + Column( "status", TrimmedString( 255 ), nullable=False ), + Column( "error_msg", TEXT ), + Column( "size", TrimmedString( 255 ) ) ) + +def upgrade(): + print __doc__ + metadata.reflect() + try: + SampleDataset_table.create() + except Exception, e: + log.debug( "Creating sample_dataset table failed: %s" % str( e ) ) + + cmd = "SELECT id, dataset_files FROM sample" + result = db_session.execute( cmd ) + for r in result: + sample_id = r[0] + dataset_files = from_json_string(r[1]) + for df in dataset_files: + cmd = "INSERT INTO sample_dataset VALUES (%s, %s, %s, %s, '%s', '%s', '%s', '%s', '%s')" + cmd = cmd % ( nextval('sample_dataset'), + localtimestamp(), + localtimestamp(), + str(sample_id), + df['name'], + df['filepath'], + df['status'], + df['error_msg'].replace('"', '').replace("'", ""), + df['size'] ) + db_session.execute( cmd ) + + # Delete the dataset_files column in the Sample table + try: + Sample_table = Table( "sample", metadata, autoload=True ) + except NoSuchTableError: + Sample_table = None + log.debug( "Failed loading table sample" ) + if Sample_table: + try: + Sample_table.c.dataset_files.drop() + except Exception, e: + log.debug( "Deleting column 'dataset_files' from the 'sample' table failed: %s" % ( str( e ) ) ) + + +def downgrade(): + pass --- a/templates/requests/common/events.mako +++ b/templates/requests/common/events.mako @@ -4,7 +4,7 @@ <h2>History of Sequencing Request "${request.name}"</h2><ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='show_request', id=trans.security.encode_id(request.id) )}"> + <a class="action-button" href="${h.url_for( controller=cntrller, action='list', operation='show', id=trans.security.encode_id(request.id) )}"><span>Browse this request</span></a></li><li> --- a/templates/admin/requests/reject.mako +++ b/templates/admin/requests/reject.mako @@ -8,12 +8,12 @@ <h2>Reject Sequencing Request "${request.name}"</h2><ul class="manage-table-actions"><li> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id) )}"> - <span>Browse this request</span></a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}"> + <span>Events</span></a></li><li> - <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='events', id=trans.security.encode_id(request.id) )}"> - <span>Events</span></a> + <a class="action-button" href="${h.url_for( controller='requests_admin', action='list', operation='show', id=trans.security.encode_id(request.id) )}"> + <span>Browse this request</span></a></li></ul><h3>User: ${request.user.email}</h3> --- a/templates/admin/requests/datasets_grid.mako +++ b/templates/admin/requests/datasets_grid.mako @@ -4,7 +4,6 @@ <%def name="custom_javascripts()"><script type="text/javascript"> $("#select-dataset-action-button").bind( "click", function(e) { - alert('afdhblvi') $.ajax({ url: "${h.url_for( controller='requests_admin', action='remote_file_browser' )}", data: {id: 6},

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