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

[hg] galaxy 2447: Missed adding chrominfo.py, due to my hardcode...
by Greg Von Kuster 16 Jun '09

16 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0cf5c25d1d2b changeset: 2447:0cf5c25d1d2b user: ianschenck(a)Thugunit.local date: Thu Apr 23 14:42:35 2009 -0400 description: Missed adding chrominfo.py, due to my hardcoded paths in test environ. Should be good now? 2 file(s) affected in this change: lib/galaxy/datatypes/chrominfo.py tools/annotation_profiler/annotation_profiler.xml diffs (29 lines): diff -r 854ec7739cfd -r 0cf5c25d1d2b lib/galaxy/datatypes/chrominfo.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/chrominfo.py Thu Apr 23 14:42:35 2009 -0400 @@ -0,0 +1,14 @@ +import data +from galaxy import util +from galaxy.datatypes.sniff import * +from galaxy.web import url_for +from tabular import Tabular +from galaxy.datatypes import metadata +from galaxy.datatypes.metadata import MetadataElement + + +class ChromInfo( Tabular ): + file_ext = "len" + MetadataElement( name="chrom", default=1, desc="Chrom column", param=metadata.ColumnParameter ) + MetadataElement( name="length", default=2, desc="Length column", param=metadata.ColumnParameter ) + diff -r 854ec7739cfd -r 0cf5c25d1d2b tools/annotation_profiler/annotation_profiler.xml --- a/tools/annotation_profiler/annotation_profiler.xml Thu Apr 23 13:46:52 2009 -0400 +++ b/tools/annotation_profiler/annotation_profiler.xml Thu Apr 23 14:42:35 2009 -0400 @@ -1,6 +1,6 @@ <tool id="Annotation_Profiler_0" name="Profile Annotations" Version="1.0.0"> <description>for a set of genomic intervals</description> - <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len -b 3 -t $table_names</command> + <command interpreter="python">annotation_profiler_for_interval.py -i $input1 -c ${input1.metadata.chromCol} -s ${input1.metadata.startCol} -e ${input1.metadata.endCol} -o $out_file1 $keep_empty -p /depot/data2/galaxy/annotation_profiler/$dbkey $summary -l ${chromInfo} -b 3 -t $table_names</command> <inputs> <param format="interval" name="input1" type="data" label="Choose Intervals"> <validator type="dataset_metadata_in_file" filename="annotation_profiler_valid_builds.txt" metadata_name="dbkey" metadata_column="0" message="Profiling is not currently available for this species."/>

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[hg] galaxy 2446: - Performance of indexers much improved.
by Greg Von Kuster 16 Jun '09

16 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/854ec7739cfd changeset: 2446:854ec7739cfd user: ianschenck(a)Thugunit.local date: Thu Apr 23 13:46:52 2009 -0400 description: - Performance of indexers much improved. - Indexing for tracks done in background with a visual treatment done to Trackster - DB builds can be uploaded by a user (chromInfo/len extension). - TODO: Add ability to change the dbkey of a dataset to any arbitrary string value. 23 file(s) affected in this change: datatypes_conf.xml.sample lib/galaxy/datatypes/data.py lib/galaxy/datatypes/indexers/coverage.py lib/galaxy/datatypes/indexers/interval.awk lib/galaxy/datatypes/indexers/interval.py lib/galaxy/datatypes/indexers/interval_awk.xml lib/galaxy/datatypes/indexers/wiggle.py lib/galaxy/datatypes/interval.py lib/galaxy/datatypes/metadata.py lib/galaxy/datatypes/registry.py lib/galaxy/tools/actions/__init__.py lib/galaxy/tools/actions/upload.py lib/galaxy/tools/parameters/basic.py lib/galaxy/tracks/store.py lib/galaxy/web/controllers/root.py lib/galaxy/web/controllers/tracks.py lib/galaxy/web/framework/__init__.py static/scripts/trackster.js static/trackster.css templates/dataset/edit_attributes.mako templates/tracks/index.mako tools/data_source/upload.xml tools/new_operations/complement.xml diffs (663 lines): diff -r f7336991d0ee -r 854ec7739cfd datatypes_conf.xml.sample --- a/datatypes_conf.xml.sample Thu Apr 23 09:20:11 2009 -0400 +++ b/datatypes_conf.xml.sample Thu Apr 23 13:46:52 2009 -0400 @@ -8,6 +8,9 @@ <converter file="interval_to_coverage.xml" target_datatype="coverage"/> </datatype> <datatype extension="binseq.zip" type="galaxy.datatypes.images:Binseq" mimetype="application/zip" display_in_upload="true"/> + <datatype extension="len" type="galaxy.datatypes.chrominfo:ChromInfo" display_in_upload="true"> +  + </datatype> <datatype extension="coverage" type="galaxy.datatypes.coverage:LastzCoverage" display_in_upload="true"> <indexer file="coverage.xml" /> </datatype> @@ -31,7 +34,7 @@ <datatype extension="html" type="galaxy.datatypes.images:Html" mimetype="text/html"/> <datatype extension="interval" type="galaxy.datatypes.interval:Interval" display_in_upload="true"> <converter file="interval_to_bed_converter.xml" target_datatype="bed"/> - <indexer file="interval.xml" /> + <indexer file="interval_awk.xml" /> </datatype> <datatype extension="jpg" type="galaxy.datatypes.images:Image" mimetype="image/jpeg"/> <datatype extension="laj" type="galaxy.datatypes.images:Laj"/> diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Thu Apr 23 13:46:52 2009 -0400 @@ -40,7 +40,7 @@ __metaclass__ = DataMeta """Add metadata elements""" - MetadataElement( name="dbkey", desc="Database/Build", default="?", param=metadata.SelectParameter, multiple=False, values=util.dbnames, no_value="?" ) + MetadataElement( name="dbkey", desc="Database/Build", default="?", param=metadata.DBKeyParameter, multiple=False, no_value="?" ) """Stores the set of display applications, and viewing methods, supported by this datatype """ supported_display_apps = {} @@ -242,7 +242,7 @@ def after_edit( self, dataset ): """This function is called on the dataset after metadata is edited.""" dataset.clear_associated_files( metadata_safe = True ) - + @property def has_resolution(self): return False diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/datatypes/indexers/coverage.py --- a/lib/galaxy/datatypes/indexers/coverage.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/datatypes/indexers/coverage.py Thu Apr 23 13:46:52 2009 -0400 @@ -37,7 +37,7 @@ os.rename( fname+".npy", fname ) # Write average - for window in 10, 100, 1000, 10000: + for window in 10, 100, 1000, 10000, 100000: input = scores.copy() size = len( input ) input.resize( ( ( size / window ), window ) ) diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/datatypes/indexers/interval.awk --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/indexers/interval.awk Thu Apr 23 13:46:52 2009 -0400 @@ -0,0 +1,43 @@ +BEGIN { + # from galaxy.utils + mapped_chars[">"] = "__gt__" + mapped_chars["<"] = "__lt__" + mapped_chars["'"] = "__sq__" + mapped_chars["\""] = "__dq__" + mapped_chars["\\["] = "__ob__" + mapped_chars["\\]"] = "__cb__" + mapped_chars["\\{"] = "__oc__" + mapped_chars["\\}"] = "__cc__" + mapped_chars["@"] = "__at__" + # additional, not in galaxy.utils + mapped_chars["/"] = "__fs__" + mapped_chars["^manifest\.tab$"] = "__manifest.tab__" +} +function escape_filename( name ) +{ + for( char in mapped_chars ) { + gsub( char, mapped_chars[char], name ) + } + return name +} +!_[$chrom]++ { + # close files only when we switch to a new one. + fn && close(fn) + fn = storepath "/" escape_filename($1) } +{ + print $0 >> fn; + # the || part is needed to catch 0 length chromosomes, which + # should never happen but... + if ($end > chroms[$chrom] || !chroms[$chrom]) + chroms[$chrom] = $end } +END { + fn = storepath "/manifest.tab" + for( x in chroms ) { + # add line to manifest + print x "\t" chroms[x] >> fn + chromfile = storepath "/" escape_filename(x) + # sort in-place + system( "sort -f -n -k " chrom " -k " start " -k " end " -o " chromfile " " chromfile ) + close(chromfile) + } +} \ No newline at end of file diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/datatypes/indexers/interval.py --- a/lib/galaxy/datatypes/indexers/interval.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/datatypes/indexers/interval.py Thu Apr 23 13:46:52 2009 -0400 @@ -29,13 +29,11 @@ manifest[chrom] = max(manifest.get(chrom,0),line.end) if not lastchrom == chrom: if current_file: - current_file.flush() current_file.close() current_file = open( os.path.join( out_path, "%s" % chrom), "a" ) print >> current_file, "\t".join(line) lastchrom = chrom if current_file: - current_file.flush() current_file.close() return manifest diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/datatypes/indexers/interval_awk.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/datatypes/indexers/interval_awk.xml Thu Apr 23 13:46:52 2009 -0400 @@ -0,0 +1,16 @@ +<tool id="INDEXER_Interval_0" name="Index Interval for Track Viewer"> +  + <command interpreter="awk -f">interval.awk + chrom=${input_dataset.metadata.chromCol} start=${input_dataset.metadata.startCol} + end=${input_dataset.metadata.endCol} strand=${input_dataset.metadata.strandCol} + storepath=${store_path} + $input_dataset 2>&1 + </command> + <inputs> + <page> + <param format="interval" name="input_dataset" type="data" label="Choose intervals"/> + </page> + </inputs> + <help> + </help> +</tool> diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/datatypes/indexers/wiggle.py --- a/lib/galaxy/datatypes/indexers/wiggle.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/datatypes/indexers/wiggle.py Thu Apr 23 13:46:52 2009 -0400 @@ -18,6 +18,8 @@ from numpy import * import tempfile import os +from galaxy.tracks.store import sanitize_name + def write_chrom(max, out_base, instream): @@ -35,7 +37,7 @@ os.rename( fname+".npy", fname ) # Write average - for window in 10, 100, 1000, 10000: + for window in 10, 100, 1000, 10000, 100000: input = scores.copy() size = len( input ) input.resize( ( ( size / window ), window ) ) @@ -60,7 +62,7 @@ LEN[chrom] = max2( LEN.get(chrom,0), pos+1 ) for chrom, stream in chroms.items(): stream.seek(0) - prefix = os.path.join(sys.argv[2], chrom) + prefix = os.path.join(sys.argv[2], sanitize_name(chrom)) write_chrom( LEN[chrom], prefix, stream ) manifest_file = open( os.path.join( sys.argv[2], "manifest.tab" ),"w" ) diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/datatypes/interval.py --- a/lib/galaxy/datatypes/interval.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/datatypes/interval.py Thu Apr 23 13:46:52 2009 -0400 @@ -792,7 +792,7 @@ # Determine appropriate resolution to plot ~1000 points resolution = ( 10 ** math.ceil( math.log10( range / 1000 ) ) ) # Restrict to valid range - resolution = min( resolution, 10000 ) + resolution = min( resolution, 100000 ) resolution = max( resolution, 1 ) # Memory map the array (don't load all the data) data = numpy.load( data ) @@ -809,7 +809,7 @@ # Determine appropriate resolution to plot ~1000 points resolution = math.ceil( 10 ** math.ceil( math.log10( range / 1000 ) ) ) # Restrict to valid range - resolution = min( resolution, 10000 ) + resolution = min( resolution, 100000 ) resolution = max( resolution, 1 ) return resolution diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/datatypes/metadata.py Thu Apr 23 13:46:52 2009 -0400 @@ -289,7 +289,22 @@ if value is None: return [] if not isinstance( value, list ): return [value] return value - + + +class DBKeyParameter( SelectParameter ): + def get_html_field( self, value=None, context={}, other_values={}, values=None, **kwd): + try: + values = kwd['trans'].db_builds + except AttributeError: pass + return super(DBKeyParameter, self).get_html_field( value, context, other_values, values, **kwd) + + def get_html( self, value=None, context={}, other_values={}, values=None, **kwd): + try: + values = kwd['trans'].db_builds + except AttributeError: pass + return super(DBKeyParameter, self).get_html( value, context, other_values, values, **kwd) + + class RangeParameter( SelectParameter ): def __init__( self, spec ): SelectParameter.__init__( self, spec ) diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/datatypes/registry.py Thu Apr 23 13:46:52 2009 -0400 @@ -3,7 +3,7 @@ """ import os import logging -import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks +import data, tabular, interval, images, sequence, qualityscore, genetics, xml, coverage, tracks, chrominfo import galaxy.util from galaxy.util.odict import odict diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/tools/actions/__init__.py Thu Apr 23 13:46:52 2009 -0400 @@ -107,6 +107,7 @@ out_data = {} # Collect any input datasets from the incoming parameters inp_data = self.collect_input_datasets( tool, incoming, trans ) + # Deal with input dataset names, 'dbkey' and types input_names = [] input_ext = 'data' @@ -119,6 +120,16 @@ data = NoneDataset( datatypes_registry = trans.app.datatypes_registry ) if data.dbkey not in [None, '?']: input_dbkey = data.dbkey + + # Collect chromInfo dataset and add as parameters to incoming + db_datasets = {} + db_dataset = trans.db_dataset_for( input_dbkey ) + if db_dataset: + db_datasets[ "chromInfo" ] = db_dataset + incoming[ "chromInfo" ] = db_dataset.file_name + else: + incoming[ "chromInfo" ] = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % input_dbkey ) + inp_data.update( db_datasets ) # Determine output dataset permission/roles list existing_datasets = [ inp for inp in inp_data.values() if inp ] diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Thu Apr 23 13:46:52 2009 -0400 @@ -21,7 +21,7 @@ def execute( self, tool, trans, incoming={}, set_output_hid = True ): data_file = incoming['file_data'] file_type = incoming['file_type'] - dbkey = incoming['dbkey'] + dbkey = incoming['other_dbkey'] or incoming['dbkey'] url_paste = incoming['url_paste'] is_multi_byte = False space_to_tab = False diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/tools/parameters/basic.py Thu Apr 23 13:46:52 2009 -0400 @@ -657,7 +657,7 @@ >>> # Create a mock transcation with 'hg17' as the current build >>> from galaxy.util.bunch import Bunch - >>> trans = Bunch( history=Bunch( genome_build='hg17' ) ) + >>> trans = Bunch( history=Bunch( genome_build='hg17' ), db_builds=util.dbnames ) >>> p = GenomeBuildParameter( None, XML( ... ''' @@ -692,10 +692,10 @@ """ def get_options( self, trans, other_values ): last_used_build = trans.history.genome_build - for dbkey, build_name in util.dbnames: + for dbkey, build_name in trans.db_builds: yield build_name, dbkey, ( dbkey == last_used_build ) def get_legal_values( self, trans, other_values ): - return set( dbkey for dbkey, _ in util.dbnames ) + return set( dbkey for dbkey, _ in trans.db_builds ) class ColumnListParameter( SelectToolParameter ): """ diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/tracks/store.py --- a/lib/galaxy/tracks/store.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/tracks/store.py Thu Apr 23 13:46:52 2009 -0400 @@ -1,5 +1,17 @@ import os +import re from string import Template +from galaxy.util import sanitize_text + +# extra mappings/escape to keep users from traversing around the +# filesystem and wreaking havoc +extra_mappings = { r"/": "__fs__", r"^manifest.tab$": "__manifest.tab__" } + +def sanitize_name( name ): + name = sanitize_text( name ) + for key, value in extra_mappings.items(): + name = re.sub( key, value, name ) + return name class TemplateSubber( object ): def __init__(self, obj): @@ -56,7 +68,7 @@ fd.close() def _get_object_path( self, chrom, resolution ): - object_name = chrom + object_name = sanitize_name(chrom) if resolution: object_name += "_%d" % resolution return os.path.join( self.path, object_name ) diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/web/controllers/root.py Thu Apr 23 13:46:52 2009 -0400 @@ -234,11 +234,15 @@ if spec.get("readonly"): continue optional = params.get("is_"+name, None) + other = params.get("or_"+name, None) if optional and optional == 'true': # optional element... == 'true' actually means it is NOT checked (and therefore omitted) setattr(data.metadata, name, None) else: - setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) ) + if other: + setattr( data.metadata, name, other ) + else: + setattr( data.metadata, name, spec.unwrap( params.get (name, None) ) ) data.datatype.after_edit( data ) trans.app.model.flush() diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/web/controllers/tracks.py Thu Apr 23 13:46:52 2009 -0400 @@ -1,13 +1,11 @@ -from mako import exceptions -from mako.template import Template -from mako.lookup import TemplateLookup +import math + +import mimeparse +from galaxy.tracks import messages +from galaxy.util.json import to_json_string from galaxy.web.base.controller import * from galaxy.web.framework import simplejson -from galaxy import web -from galaxy.tracks import messages -import mimeparse -from galaxy.util.json import to_json_string -import math + class MultiResponse(object): """ @@ -82,18 +80,19 @@ def build( self, trans, **kwargs ): trans.session["track_sets"] = list(kwargs.keys()) trans.session.save() - waiting = False - for id, value in kwargs.items(): - status = self.data_handler( trans, id ) - if status == messages.PENDING: - waiting = True - if not waiting: - return trans.response.send_redirect( web.url_for( controller='tracks', action='chroms', dbkey=trans.session["track_dbkey"]) ) - return trans.fill_template( 'tracks/build.mako' ) + #waiting = False + #for id, value in kwargs.items(): + # status = self.data_handler( trans, id ) + # if status == messages.PENDING: + # waiting = True + #if not waiting: + return trans.response.send_redirect( web.url_for( controller='tracks/', action='index', chrom="" ) ) + #return trans.fill_template( 'tracks/build.mako' ) @web.expose def index(self, trans, **kwargs): tracks = [] + dbkey = "" for track in trans.session["track_sets"]: dataset = trans.app.model.HistoryDatasetAssociation.get( track ) tracks.append({ @@ -101,17 +100,23 @@ "name": dataset.name, "id": dataset.id }) + dbkey = dataset.dbkey chrom = kwargs.get("chrom","") LEN = self.chroms_handler(trans, trans.session["track_dbkey"]).get(chrom,0) return trans.fill_template( 'tracks/index.mako', - tracks=tracks, chrom=chrom, + tracks=tracks, chrom=chrom, dbkey=dbkey, LEN=LEN ) def chroms_handler(self, trans, dbkey ): - db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey ) + db_manifest = trans.db_dataset_for( dbkey ) + if not db_manifest: + db_manifest = os.path.join( trans.app.config.tool_data_path, 'shared','ucsc','chrom', "%s.len" % dbkey ) + else: + db_manifest = db_manifest.file_name manifest = {} if os.path.exists( db_manifest ): for line in open( db_manifest ): + if line.startswith("#"): continue line = line.rstrip("\r\n") fields = line.split("\t") manifest[fields[0]] = int(fields[1]) diff -r f7336991d0ee -r 854ec7739cfd lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Thu Apr 23 09:20:11 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Thu Apr 23 13:46:52 2009 -0400 @@ -547,6 +547,31 @@ template = Template( source=template_string, searchList=[context or kwargs, dict(caller=self)] ) return str(template) + + @property + def db_builds( self ): + """ + Returns the builds defined by galaxy and the builds defined by + the user (chromInfo in history). + """ + dbnames = list() + datasets = self.app.model.HistoryDatasetAssociation.filter_by(deleted=False, history_id=self.history.id, extension="len").all() + if len(datasets) > 0: + dbnames.append( (util.dbnames.default_value, '--------- User Defined Builds ----------') ) + for dataset in datasets: + dbnames.append( (dataset.dbkey, dataset.name) ) + dbnames.extend( util.dbnames ) + return dbnames + + def db_dataset_for( self, dbkey ): + """ + Returns the db_file dataset associated/needed by `dataset`, or `None`. + """ + datasets = self.app.model.HistoryDatasetAssociation.filter_by(deleted=False, history_id=self.history.id, extension="len").all() + for ds in datasets: + if dbkey == ds.dbkey: + return ds + return None class FormBuilder( object ): """ diff -r f7336991d0ee -r 854ec7739cfd static/scripts/trackster.js --- a/static/scripts/trackster.js Thu Apr 23 09:20:11 2009 -0400 +++ b/static/scripts/trackster.js Thu Apr 23 13:46:52 2009 -0400 @@ -85,7 +85,7 @@ var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); resolution = Math.max( resolution, 1 ); - resolution = Math.min( resolution, 10000 ); + resolution = Math.min( resolution, 100000 ); var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); @@ -152,10 +152,20 @@ var low = position * DENSITY * resolution; var high = ( position + 1 ) * DENSITY * resolution; cache[resolution][position] = { state: "loading" }; - $.getJSON( "data" + this.type, { chr: this.view.chr, low: low, high: high, dataset_id: this.track.dataset_id }, function ( data ) { - cache[resolution][position] = { state: "loaded", values: data }; - $(document).trigger( "redraw" ); - }); + // use closure to preserve this and parameters for getJSON + var fetcher = function (ref) { + return function () { + $.getJSON( "data" + ref.type, { chr: ref.view.chr, low: low, high: high, dataset_id: ref.track.dataset_id }, function ( data ) { + if( data == "pending" ) { + setTimeout( fetcher, 5000 ); + } else { + cache[resolution][position] = { state: "loaded", values: data }; + } + $(document).trigger( "redraw" ); + }); + }; + }(this); + fetcher(); } return cache[resolution][position]; } @@ -288,8 +298,11 @@ var chunk = this.cache.get( resolution, tile_index ); if ( chunk.state == "loading" ) { - return null; - } + parent_element.addClass("loading"); + return null; + } else { + parent_element.removeClass("loading"); + } var values = chunk.values; for ( var index in values ) { diff -r f7336991d0ee -r 854ec7739cfd static/trackster.css --- a/static/trackster.css Thu Apr 23 09:20:11 2009 -0400 +++ b/static/trackster.css Thu Apr 23 13:46:52 2009 -0400 @@ -85,7 +85,10 @@ } .loading { - background: #DDDDDD; + background-image: url("/static/images/loading_large_white_bg.gif"); + background-position: center center; + background-repeat: no-repeat; + min-height: 100px; } .label-track .label { diff -r f7336991d0ee -r 854ec7739cfd templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Thu Apr 23 09:20:11 2009 -0400 +++ b/templates/dataset/edit_attributes.mako Thu Apr 23 13:46:52 2009 -0400 @@ -46,7 +46,7 @@ ${spec.desc}: </label> <div style="float: left; width: 250px; margin-right: 10px;"> - ${data.metadata.get_html_by_name( name )} + ${data.metadata.get_html_by_name( name, trans=trans )} </div> <div style="clear: both"></div> </div> diff -r f7336991d0ee -r 854ec7739cfd templates/tracks/index.mako --- a/templates/tracks/index.mako Thu Apr 23 09:20:11 2009 -0400 +++ b/templates/tracks/index.mako Thu Apr 23 13:46:52 2009 -0400 @@ -17,18 +17,19 @@ ${parent.late_javascripts()} <script type="text/javascript" src="/static/scripts/jquery.event.drag.js"></script> <script type="text/javascript" src="/static/scripts/trackster.js"></script> -<script> +<script type="text/javascript"> - var view = new View( "${chrom}", ${LEN}, 0, ${LEN} ); + var view = new View( "${chrom}", ${LEN}, 0, ${max(LEN,1)} ); var tracks = new TrackLayout( view ); - + var dbkey = "${dbkey}"; + $(function() { tracks.add( new LabelTrack( view, $("#viewport" ) ) ); %for track in tracks: tracks.add( new ${track["type"]}( "${track["name"]}", view, $("#viewport" ), ${track["id"]} ) ); %endfor - + $(document).bind( "redraw", function( e ) { tracks.redraw(); }); @@ -56,9 +57,43 @@ view.high = new_high; tracks.redraw(); }); + tracks.redraw(); + load_chroms(); + }); - tracks.redraw(); - }); + var load_chroms = function () { + var fetcher = function (ref) { + return function () { + $.getJSON( "chroms", { dbkey: dbkey }, function ( data ) { + // Hacky - check length of "object" + var chrom_length = 0; + for (key in data) chrom_length++; + if( chrom_length == 0 ) { + setTimeout( fetcher, 5000 ); + } else { + var chrom_options = ''; + for (key in data) { + if( key == view.chr ) { + chrom_options += '<option value="' + key + '" selected="true">' + key + '</option>'; + } else { + chrom_options += '<option value="' + key + '">' + key + '</option>'; + } + } + $("#chrom").html(chrom_options); + $("#chrom").bind( "change", function ( e ) { + $("#chr").submit(); + }); + if( view.chr == "" ) { + $("#chrom option:first").attr("selected", true); + $("#chrom").trigger( "change" ); + } + } + }); + }; + }(this); + fetcher(); + }; + </script> </%def> @@ -79,11 +114,14 @@ <div id="nav"> <div id="nav-controls"> + <form name="chr" id="chr" method="GET"> <a href="#" onclick="javascript:view.left(5);tracks.redraw();"><<</a> <a href="#" onclick="javascript:view.left(2);tracks.redraw();"><</a> - - <span style="display: inline-block; width: 30em; text-align: center;">Viewing ${chrom}:<span id="low">0</span>-<span id="high">180857866</span></span> - + <span style="display: inline-block; width: 30em; text-align: center;">Viewing + <select id="chrom" name="chrom"> + <option value="">loading</option> + </select> + <span id="low">0</span>-<span id="high">180857866</span></span> <span style="display: inline-block; width: 10em;"> <a href="#" onclick="javascript:view.zoom_in(2);tracks.redraw();">+</a> <a href="#" onclick="javascript:view.zoom_out(2);tracks.redraw();">-</a> @@ -91,6 +129,7 @@ <a href="#" onclick="javascript:view.right(2);tracks.redraw();">></a> <a href="#" onclick="javascript:view.right(5);tracks.redraw();">>></a> + </form> </div> </div> diff -r f7336991d0ee -r 854ec7739cfd tools/data_source/upload.xml --- a/tools/data_source/upload.xml Thu Apr 23 09:20:11 2009 -0400 +++ b/tools/data_source/upload.xml Thu Apr 23 13:46:52 2009 -0400 @@ -21,6 +21,7 @@ </options> </param> <param name="dbkey" type="genomebuild" label="Genome" /> + <param name="other_dbkey" type="text" label="Or user-defined Genome" /> </inputs> <help> diff -r f7336991d0ee -r 854ec7739cfd tools/new_operations/complement.xml --- a/tools/new_operations/complement.xml Thu Apr 23 09:20:11 2009 -0400 +++ b/tools/new_operations/complement.xml Thu Apr 23 13:46:52 2009 -0400 @@ -1,6 +1,6 @@ <tool id="gops_complement_1" name="Complement"> <description>intervals of a query</description> - <command interpreter="python">gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${GALAXY_DATA_INDEX_DIR}/shared/ucsc/chrom/${dbkey}.len $allchroms</command> + <command interpreter="python">gops_complement.py $input1 $output -1 ${input1.metadata.chromCol},${input1.metadata.startCol},${input1.metadata.endCol},${input1.metadata.strandCol} -l ${chromInfo} $allchroms</command> <inputs> <param format="interval" name="input1" type="data"> <label>Complement regions of</label> @@ -58,4 +58,4 @@ .. image:: ../static/operation_icons/gops_complement.gif </help> -</tool> \ No newline at end of file +</tool>

1 0

New tool for Galaxy: Cross-Tabulations (a.k.a Pivot Tables)
by Assaf Gordon 16 Jun '09

16 Jun '09

Hello, I'd like to share a new tool for Galaxy: Cross-Tabulations - Reads a tab-delimited file and produces a cross-tabulation table of two or more variables. Sources + XMLs are available here: http://hannonlab.cshl.edu/crosstab/ Screenshots of the galaxy tool: http://hannonlab.cshl.edu/crosstab/galaxy.html There's no limit to the number of input lines - so this tool can create pivot tables of files with more than one million lines (which Excel currently can't do). The tool is free for use. Comments are welcomed, Gordon.

1 0

[hg] galaxy 2445: Restrict the target history list to the users ...
by Greg Von Kuster 11 Jun '09

11 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/c69e55c91036 changeset: 2445:c69e55c91036 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Jun 11 12:06:29 2009 -0400 description: Restrict the target history list to the users active hisstories when copying datasets between histories, clean up the relavent templates ( fixes ticket # 41 ), and add functional tests for copying history items between histories. 5 file(s) affected in this change: lib/galaxy/web/controllers/dataset.py templates/dataset/copy_view.mako templates/dataset/edit_attributes.mako test/base/twilltestcase.py test/functional/test_history_functions.py diffs (369 lines): diff -r 004cd81cff72 -r c69e55c91036 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Wed Jun 10 15:46:26 2009 -0400 +++ b/lib/galaxy/web/controllers/dataset.py Thu Jun 11 12:06:29 2009 -0400 @@ -159,7 +159,8 @@ raise "Error undeleting" @web.expose - def copy_datasets( self, trans, source_dataset_ids = "", target_history_ids = "", new_history_name="", do_copy = False ): + def copy_datasets( self, trans, source_dataset_ids="", target_history_ids="", new_history_name="", do_copy=False, **kwd ): + params = util.Params( kwd ) user = trans.get_user() history = trans.get_history() create_new_history = False @@ -202,7 +203,7 @@ error_msg = error_msg + "You do not have permission to add datasets to %i requested histories. " % ( len( target_history_ids ) - len( target_histories ) ) for data in map( trans.app.model.HistoryDatasetAssociation.get, source_dataset_ids ): if data is None: - error_msg = error_msg + "You tried to copy a non-existant dataset. " + error_msg = error_msg + "You tried to copy a dataset that does not exist. " invalid_datasets += 1 elif data.history != history: error_msg = error_msg + "You tried to copy a dataset which is not in your current history. " @@ -220,8 +221,7 @@ source_datasets = history.active_datasets target_histories = [history] if user: - target_histories = user.histories - + target_histories = user.active_histories return trans.fill_template( "/dataset/copy_view.mako", source_dataset_ids = source_dataset_ids, target_history_ids = target_history_ids, diff -r 004cd81cff72 -r c69e55c91036 templates/dataset/copy_view.mako --- a/templates/dataset/copy_view.mako Wed Jun 10 15:46:26 2009 -0400 +++ b/templates/dataset/copy_view.mako Thu Jun 11 12:06:29 2009 -0400 @@ -5,65 +5,67 @@ ${javascripts()} %if error_msg: -<p> -<div class="errormessage">${error_msg}</div> -<div style="clear: both"></div> -</p> + <p> + <div class="errormessage">${error_msg}</div> + <div style="clear: both"></div> + </p> %endif %if done_msg: -<p> -<div class="donemessage">${done_msg}</div> -<div style="clear: both"></div> -</p> + <p> + <div class="donemessage">${done_msg}</div> + <div style="clear: both"></div> + </p> %endif <p> -<div class="toolForm"> - <form> - <div style="float: left; width: 50%; padding: 0px 0px 0px 0px;"> - <div class="toolFormTitle">Source History Items</div> - <div class="toolFormBody"> - %for data in source_datasets: - <% - checked = "" - if data.id in source_dataset_ids: - checked = " checked" - %> - <div class="form-row"><input type="checkbox" name="source_dataset_ids" value="${data.id}"${checked}/> ${data.hid}: ${data.name}</div> - %endfor - </div> - </div> - <div style="float: right; width: 50%; padding: 0px 0px 0px 0px;"> - <div class="toolFormTitle">Target Histories</div> - <div class="toolFormBody"> - %for i, hist in enumerate( target_histories ): - <% - checked = "" - if hist.id in target_history_ids: - checked = " checked" - cur_history_text = "" - if hist == trans.get_history(): - cur_history_text = " <strong>(current history)</strong>" - %> - <div class="form-row"><input type="checkbox" name="target_history_ids" value="${hist.id}"${checked}/> ${i + 1}${cur_history_text}: ${hist.name}</div> - %endfor - %if trans.get_user(): - <% - checked = "" - if "create_new_history" in target_history_ids: - checked = " checked" - %> - <br> - <div class="form-row"><input type="checkbox" name="target_history_ids" value="create_new_history"${checked}/>New history named: <input type="textbox" name="new_history_name" value="${new_history_name}"/></div> - %endif - </div> - </div> - <div style="clear: both"></div> - <div class="form-row" align="center"><input type="submit" class="primary-button" name="do_copy" value="Copy History Items"/></div> - </form> -</div> + <div class="toolForm"> + <form> + <div style="float: left; width: 50%; padding: 0px 0px 0px 0px;"> + <div class="toolFormTitle">Source History Items</div> + <div class="toolFormBody"> + %for data in source_datasets: + <% + checked = "" + if data.id in source_dataset_ids: + checked = " checked" + %> + <div class="form-row"><input type="checkbox" name="source_dataset_ids" value="${data.id}"${checked}/> ${data.hid}: ${data.name}</div> + %endfor + </div> + </div> + <div style="float: right; width: 50%; padding: 0px 0px 0px 0px;"> + <div class="toolFormTitle">Target Histories</div> + <div class="toolFormBody"> + %for i, hist in enumerate( target_histories ): + <% + checked = "" + if hist.id in target_history_ids: + checked = " checked" + cur_history_text = "" + if hist == trans.get_history(): + cur_history_text = " <strong>(current history)</strong>" + %> + <div class="form-row"><input type="checkbox" name="target_history_ids" value="${hist.id}"${checked}/> ${i + 1}${cur_history_text}: ${hist.name}</div> + %endfor + %if trans.get_user(): + <% + checked = "" + if "create_new_history" in target_history_ids: + checked = " checked" + %> + <br/> + <div class="form-row"><input type="checkbox" name="target_history_ids" value="create_new_history"${checked}/>New history named: <input type="textbox" name="new_history_name" value="${new_history_name}"/></div> + %endif + </div> + </div> + <div style="clear: both"></div> + <div class="form-row" align="center"> + <input type="submit" class="primary-button" name="do_copy" value="Copy History Items"/> + </div> + </form> + </div> </p> <div style="clear: both"></div> <p> -<div class="infomessage">Select any number of source history items and any number of target histories and click on "Copy History Items" to add a copy of each selected dataset to each selected history.</div> -<div style="clear: both"></div> + <div class="infomessage">Select any number of source history items and any number of target histories and click "Copy History Items" to add a copy of each selected history item to each selected target history.</div> + <div style="clear: both"></div> </p> diff -r 004cd81cff72 -r c69e55c91036 templates/dataset/edit_attributes.mako --- a/templates/dataset/edit_attributes.mako Wed Jun 10 15:46:26 2009 -0400 +++ b/templates/dataset/edit_attributes.mako Thu Jun 11 12:06:29 2009 -0400 @@ -157,8 +157,16 @@ %endif <p/> <div class="toolForm"> -<div class="toolFormTitle">Copy History Item</div> -<div class="toolFormBody"> - Click <a href="${h.url_for( controller='dataset', action='copy_datasets', source_dataset_ids=data.id, target_history_ids=data.history_id )}" target="galaxy_main">here</a> to make a copy of this history item. + <div class="toolFormTitle">Copy History Item</div> + <div class="toolFormBody"> + <form name="copy_hda" action="${h.url_for( controller='dataset', action='copy_datasets', source_dataset_ids=data.id, target_history_ids=data.history_id )}" method="post"> + <div class="form-row"> + <input type="submit" name="change" value="Copy history item"/> + </div> + <div class="toolParamHelp" style="clear: both;"> + Make a copy of this history item in your current history or any of your active histories. + </div> + </form> + </div> + </div> </div> -</div> diff -r 004cd81cff72 -r c69e55c91036 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Jun 10 15:46:26 2009 -0400 +++ b/test/base/twilltestcase.py Thu Jun 11 12:06:29 2009 -0400 @@ -181,8 +181,9 @@ self.home() def new_history( self, name=None ): """Creates a new, empty history""" + self.home() if name: - self.visit_url( "%s/history_new?name=%s" % ( self.url, str( name ) ) ) + self.visit_url( "%s/history_new?name=%s" % ( self.url, name ) ) else: self.visit_url( "%s/history_new" % self.url ) self.check_history_for_string('Your history is empty') @@ -191,7 +192,7 @@ """Rename an existing history""" self.home() self.visit_page( "history/rename?id=%s&name=%s" %( id, new_name ) ) - check_str = 'History: %s renamed to: %s' % ( old_name, new_name ) + check_str = 'History: %s renamed to: %s' % ( old_name, urllib.unquote( new_name ) ) self.check_page_for_string( check_str ) self.home() def set_history( self ): @@ -330,7 +331,7 @@ self.check_page_for_string( 'Attributes updated' ) self.home() def convert_format( self, hda_id, target_type ): - """Auto-detect history_dataset_association metadata""" + """Convert format of history_dataset_association""" self.home() self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) self.check_page_for_string( 'This will inspect the dataset and attempt' ) @@ -339,13 +340,36 @@ self.check_page_for_string( 'The file conversion of Convert BED to GFF on data' ) self.home() def change_datatype( self, hda_id, datatype ): - """Auto-detect history_dataset_association metadata""" + """Change format of history_dataset_association""" self.home() self.visit_url( "%s/root/edit?id=%s" % ( self.url, hda_id ) ) self.check_page_for_string( 'This will change the datatype of the existing dataset but' ) tc.fv( 'change_datatype', 'datatype', datatype ) tc.submit( 'change' ) self.check_page_for_string( 'Edit Attributes' ) + self.home() + def copy_history_item( self, source_dataset_ids='', target_history_ids=[], all_target_history_ids=[], deleted_history_ids=[] ): + """Copy 1 or more history_dataset_associations to 1 or more histories""" + self.home() + self.visit_url( "%s/dataset/copy_datasets?source_dataset_ids=%s" % ( self.url, source_dataset_ids ) ) + self.check_page_for_string( 'Source History Items' ) + # Make sure all of users active histories are displayed + for id in all_target_history_ids: + self.check_page_for_string( id ) + # Make sure only active histories are displayed + for id in deleted_history_ids: + try: + self.check_page_for_string( id ) + raise AssertionError, "deleted history id %d displayed in list of target histories" % id + except: + pass + # Check each history to which we want to copy the item + for id in target_history_ids: + tc.fv( '1', 'target_history_ids', id ) + tc.submit( 'do_copy' ) + no_source_ids = len( source_dataset_ids.split( ',' ) ) + check_str = '%d datasets copied to %d histories.' % ( no_source_ids, len( target_history_ids ) ) + self.check_page_for_string( check_str ) self.home() def get_dataset_ids_in_history( self ): """Returns the ids of datasets in a history""" diff -r 004cd81cff72 -r c69e55c91036 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Wed Jun 10 15:46:26 2009 -0400 +++ b/test/functional/test_history_functions.py Thu Jun 11 12:06:29 2009 -0400 @@ -1,3 +1,4 @@ +import urllib import galaxy.model from galaxy.model.orm import * from base.twilltestcase import * @@ -55,7 +56,7 @@ history1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() assert history1 is not None, "Problem retrieving history1 from database" self.upload_file( '1.bed', dbkey='hg18' ) - self.new_history( name='history2' ) + self.new_history( name=urllib.quote( 'history2' ) ) global history2 history2 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() assert history2 is not None, "Problem retrieving history2 from database" @@ -96,7 +97,7 @@ assert history3 is not None, "Problem retrieving history3 from database" if history3.deleted: raise AssertionError, "History id %d deleted when it should not be" % latest_history.id - self.rename_history( str( history3.id ), history3.name, new_name='history3' ) + self.rename_history( str( history3.id ), history3.name, new_name=urllib.quote( 'history 3' ) ) def test_020_history_list( self ): """Testing viewing previously stored histories""" self.view_stored_active_histories() @@ -131,7 +132,7 @@ global history4 history4 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() assert history4 is not None, "Problem retrieving history4 from database" - self.rename_history( str( history4.id ), history4.name, new_name='history4' ) + self.rename_history( str( history4.id ), history4.name, new_name=urllib.quote( 'history 4' ) ) history4.refresh() self.upload_file( '2.bed', dbkey='hg18' ) id = '%s,%s' % ( str( history3.id ), str( history4.id ) ) @@ -195,7 +196,7 @@ global history5 history5 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() assert history5 is not None, "Problem retrieving history5 from database" - self.rename_history( str( history5.id ), history5.name, new_name='history5' ) + self.rename_history( str( history5.id ), history5.name, new_name=urllib.quote( 'history5' ) ) history5.refresh() # Due to the limitations of twill ( not functional with the permissions forms ), we're forced # to do this manually. At this point, we just want to restrict the access permission on history5 @@ -377,7 +378,7 @@ action='no_share' ) def test_055_history_show_and_hide_deleted_datasets( self ): """Testing displaying deleted history items""" - self.new_history( name='temp_history1' ) + self.new_history( name=urllib.quote( 'show hide deleted datasets' ) ) self.upload_file('1.bed', dbkey='hg18') latest_hda = galaxy.model.HistoryDatasetAssociation.query() \ .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() @@ -393,7 +394,7 @@ self.check_page_for_string( 'Your history is empty' ) def test_060_deleting_and_undeleting_history_items( self ): """Testing deleting and un-deleting history items""" - self.new_history( name='temp_history2' ) + self.new_history( name=urllib.quote( 'delete undelete history items' ) ) # Add a new history item self.upload_file( '1.bed', dbkey='hg15' ) self.home() @@ -416,8 +417,54 @@ self.visit_url( "%s/history/?show_deleted=False" % self.url ) self.check_page_for_string( '1.bed' ) self.check_page_for_string( 'hg15' ) - def test_065_reset_data_for_later_test_runs( self ): + def test_065_copying_history_items_between_histories( self ): + """Testing copying history items between histories""" + self.new_history( name=urllib.quote( 'copy history items' ) ) + global history6 + history6 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history6 is not None, "Problem retrieving history6 from database" + self.upload_file( '1.bed', dbkey='hg18' ) + hda1 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda1 is not None, "Problem retrieving hda1 from database" + # We'll just test copying 1 hda + source_dataset_ids=str( hda1.id ) + # The valid list of target histories is only the user's active histories + all_target_history_ids = [ str( hda.id ) for hda in admin_user.active_histories ] + # Since history1 and history2 have been deleted, they should not be displayed in the list of target histories + # on the copy_view.mako form + deleted_history_ids = [ str( history1.id ), str( history2.id ) ] + # Test copying to the current history + target_history_ids=[ str( history6.id ) ] + self.copy_history_item( source_dataset_ids=source_dataset_ids, + target_history_ids=target_history_ids, + all_target_history_ids=all_target_history_ids, + deleted_history_ids=deleted_history_ids ) + history6.refresh() + if len( history6.datasets ) != 2: + raise AssertionError, "Copying hda1 to the current history failed" + # Test copying 1 hda to another history + self.new_history( name=urllib.quote( 'copy history items - 2' ) ) + global history7 + history7 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + assert history7 is not None, "Problem retrieving history7 from database" + # Switch back to our history from which we want to copy + self.switch_history( id=str( history6.id ), name=history6.name ) + target_history_ids=[ str( history7.id ) ] + all_target_history_ids = [ str( hda.id ) for hda in admin_user.active_histories ] + # Test copying to the a history that is not the current history + target_history_ids=[ str( history7.id ) ] + self.copy_history_item( source_dataset_ids=source_dataset_ids, + target_history_ids=target_history_ids, + all_target_history_ids=all_target_history_ids, + deleted_history_ids=deleted_history_ids ) + # Switch to the history to which we copied + self.switch_history( id=str( history7.id ), name=history7.name ) + self.check_history_for_string( hda1.name ) + def test_070_reset_data_for_later_test_runs( self ): """Reseting data to enable later test runs to pass""" self.delete_history( id=str( history3.id ) ) self.delete_history( id=str( history4.id ) ) self.delete_history( id=str( history5.id ) ) + self.delete_history( id=str( history6.id ) ) + self.delete_history( id=str( history7.id ) )

1 0

How to make Galaxy link to a local installed UCSC database?
by xue dong 11 Jun '09

11 Jun '09

Hallo every one, I am new to Galaxy, I have a idea which maybe not new to people here. I work on arabidopsis. maybe you know that UCSC do not offer the genome assembly for plant. so i will install UCSC locally and built the genome assembly for arabidopsis. this work is half done now. I also installed Galaxy, if i understand correctly, Galaxy has the link to UCSC so the user can get data from UCSC. since what i interested is arabidopsis information, I hope Galaxy can retrive data form the locally installed UCSC in future. I do not know if it is possible to make this idea come ture.maybe some of you have done it. if yes, I am gratefully if you can tell me the how to get it. many thanks, Xue

2 1

[hg] galaxy 2444: Fixes for test_get_data functional test script.
by Greg Von Kuster 11 Jun '09

11 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/004cd81cff72 changeset: 2444:004cd81cff72 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Jun 10 15:46:26 2009 -0400 description: Fixes for test_get_data functional test script. 1 file(s) affected in this change: test/functional/test_get_data.py diffs (152 lines): diff -r 08194c60c290 -r 004cd81cff72 test/functional/test_get_data.py --- a/test/functional/test_get_data.py Wed Jun 10 12:22:49 2009 -0400 +++ b/test/functional/test_get_data.py Wed Jun 10 15:46:26 2009 -0400 @@ -1,87 +1,74 @@ +import galaxy.model +from galaxy.model.orm import * from base.twilltestcase import TwillTestCase -""" Tests are executed in order, sorted by name""" - class UploadData( TwillTestCase ): - def test_00_multi_upload( self ): - """test_get_data.test_multi_upload: Testing multiple uploads""" - self.login() - self.upload_file('1.bed') - self.verify_dataset_correctness('1.bed') - self.upload_file('2.bed', dbkey='hg17') - self.verify_dataset_correctness('2.bed') - self.upload_file('3.bed', dbkey='hg17', ftype='bed') - self.verify_dataset_correctness('3.bed') - self.upload_file('4.bed.gz', dbkey='hg17', ftype='bed') - self.verify_dataset_correctness('4.bed') - self.upload_file('1.scf', ftype='scf') - self.verify_dataset_correctness('1.scf') - self.upload_file('1.scf.zip', ftype='binseq.zip') - self.verify_dataset_correctness('1.scf.zip') + def test_000_upload_files_from_disk( self ): + """Test uploading data files from disk""" + self.logout() + self.login( email='tst(a)bx.psu.edu' ) + history1 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + self.upload_file( '1.bed' ) + hda1 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda1 is not None, "Problem retrieving hda1 from database" + self.verify_dataset_correctness( '1.bed', hid=str( hda1.hid ) ) + self.upload_file( '2.bed', dbkey='hg17' ) + hda2 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda2 is not None, "Problem retrieving hda2 from database" + self.verify_dataset_correctness( '2.bed', hid=str( hda2.hid ) ) + self.upload_file( '3.bed', dbkey='hg17', ftype='bed' ) + hda3 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda3 is not None, "Problem retrieving hda3 from database" + self.verify_dataset_correctness( '3.bed', hid=str( hda3.hid ) ) + self.upload_file( '4.bed.gz', dbkey='hg17', ftype='bed' ) + hda4 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda4 is not None, "Problem retrieving hda4 from database" + self.verify_dataset_correctness( '4.bed', hid=str( hda4.hid ) ) + self.upload_file( '1.scf', ftype='scf' ) + hda5 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda5 is not None, "Problem retrieving hda5 from database" + self.verify_dataset_correctness( '1.scf', hid=str( hda5.hid ) ) + self.upload_file( '1.scf.zip', ftype='binseq.zip' ) + hda6 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda6 is not None, "Problem retrieving hda6 from database" + self.verify_dataset_correctness( '1.scf.zip', hid=str( hda6.hid ) ) + self.delete_history( id=str( history1.id ) ) + def test_005_url_paste( self ): + """Test url paste behavior""" + # Deleting the current history should have created a new history + self.check_history_for_string( 'Your history is empty' ) + history2 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() self.upload_url_paste( 'hello world' ) self.check_history_for_string( 'Pasted Entry' ) self.check_history_for_string( 'hello world' ) - self.delete_history_item( 1 ) - self.delete_history_item( 2 ) - self.delete_history_item( 3 ) - self.delete_history_item( 4 ) - self.delete_history_item( 5 ) - self.delete_history_item( 6 ) - self.delete_history_item( 7 ) self.upload_url_paste( u'hello world' ) self.check_history_for_string( 'Pasted Entry' ) self.check_history_for_string( 'hello world' ) - self.delete_history_item( 8 ) - def test_9999_clean_up( self ): - self.delete_history() - self.logout() - -class GetEncodeData( TwillTestCase ): - - def test_00_get_encode_data( self ): - """test_get_data.test_get_encode_data""" - self.login() - self.run_tool('encode_import_chromatin_and_chromosomes1', hg17=['cc.EarlyRepSeg.20051216.bed'] ) - #hg17=[ "cc.EarlyRepSeg.20051216.bed", "cc.EarlyRepSeg.20051216.gencode_partitioned.bed", "cc.LateRepSeg.20051216.bed", "cc.LateRepSeg.20051216.gencode_partitioned.bed", "cc.MidRepSeg.20051216.bed", "cc.MidRepSeg.20051216.gencode_partitioned.bed" ] ) + self.delete_history( id=str( history2.id ) ) + def test_010_upload_encode_data( self ): + """Test uploading encode data""" + # Deleting the current history should have created a new history + self.check_history_for_string( 'Your history is empty' ) + history3 = galaxy.model.History.query().order_by( desc( galaxy.model.History.table.c.create_time ) ).first() + self.run_tool( 'encode_import_chromatin_and_chromosomes1', hg17=['cc.EarlyRepSeg.20051216.bed'] ) self.wait() - self.verify_dataset_correctness('cc.EarlyRepSeg.20051216.bed', hid=1) - #self.verify_dataset_correctness('cc.EarlyRepSeg.20051216.gencode_partitioned.bed', hid=2) - #self.verify_dataset_correctness('cc.LateRepSeg.20051216.bed', hid=3) - #self.verify_dataset_correctness('cc.LateRepSeg.20051216.gencode_partitioned.bed', hid=4) - #self.verify_dataset_correctness('cc.MidRepSeg.20051216.bed', hid=5) - #self.verify_dataset_correctness('cc.MidRepSeg.20051216.gencode_partitioned.bed', hid=6) + hda7 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda7 is not None, "Problem retrieving hda7 from database" + self.verify_dataset_correctness( 'cc.EarlyRepSeg.20051216.bed', hid=str( hda7.hid ) ) self.run_tool('encode_import_gencode1', hg17=['gencode.CDS.20051206.bed']) self.wait() - self.verify_dataset_correctness('sc_3D_cds.bed', hid=2) - self.delete_history_item( 1 ) - self.delete_history_item( 2 ) - def test_9999_clean_up( self ): - self.delete_history() + hda8 = galaxy.model.HistoryDatasetAssociation.query() \ + .order_by( desc( galaxy.model.HistoryDatasetAssociation.table.c.create_time ) ).first() + assert hda8 is not None, "Problem retrieving hda8 from database" + self.verify_dataset_correctness( 'sc_3D_cds.bed', hid=str( hda8.hid ) ) + self.delete_history( id=str( history3.id ) ) + def test_015_reset_data_for_later_test_runs( self ): + """Reseting data to enable later test runs to pass""" self.logout() - -class DataSources( TwillTestCase ): - - #def test_hbvar(self): - # """Getting hybrid gene mutations from HbVar""" - # #self.load_cookies("hbvar_cookie.txt") - # self.clear_history() - # self.run_tool('hbvar') - # params = dict( - # htyp="any hybrid gene", - # ) - # self.submit_form(form=1, button="Submit Query", **params) - # params = dict( - # display_format="galaxy", - # ) - # self.submit_form(form=1, button="Go", **params) - # params = dict( - # build="hg17", - # ) - # self.submit_form(form=1, button="ok", **params); - # """ - # TODO: Currently fails when using sqlite, although successful when - # using Postgres. Upgrading our version of sqlite may fix this, but - # confirmation is required. - # """ - # self.verify_dataset_correctness('hbvar_hybrid_genes.dat') - pass

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Round-Robin Scheduling
by Assaf Gordon 10 Jun '09

10 Jun '09

Hello, I have another question regarding the local job scheduler: Is it possible to limit the number of jobs *per user* ? That is - any given user can have up to X number of jobs running concurrently, regardless of the value of local_job_queue_workers ? Imagine the following situation: local_job_queue_worker = 5 job_scheduler_policy = galaxy.jobs.schedulingpolicy.roundrobin:UserRoundRobin Which means that at any given moment, galaxy can run only five jobs. Now, Galaxy is completely Idle, no jobs are running. One users starts 7 very long running jobs (each jobs will take about two hours). If I understand correctly - since no jobs are running, 5 of the user's job will be started immediately, even with the round-robin policy, right ? And this means that for the next two hours, every other user which starts a job - his/her job will be either new or limbo-running, but none will actually be started, right ? I think I'm experiencing this situation on my galaxy server. Users are complaining their jobs have been running 'forever' or not even starting for a long long time. Close examination shows that there are running 5 jobs (all from the same user) which have been running for three hours, and they are kind of hogging all the worker threads. To make a long story short - I would like to make sure a single user can't hog Galaxy. Is it possible with the local job runner, and if not - is it possible with the SGE job runner ? Thanks for reading so far, Gordon.

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Wrappers for Sequence Alignment Programs
by SHAUN WEBB 10 Jun '09

10 Jun '09

Hi, I am planning on integrating sequence alignment programs to our local instance of Galaxy. I was wondering if anyone else has developed wrappers for the following programs: Maq, Bowtie, Tophat. Also, is there a central repository for any new tools or wrappers that have been created by other developers? It would certainly be a useful resource and if I need to wrap these tools myself I would be happy share the code. Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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[hg] galaxy 2442: Fix missing split/join char in Join tool when ...
by Nate Coraor 10 Jun '09

10 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/46bbe610288a changeset: 2442:46bbe610288a user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Jun 10 11:58:21 2009 -0400 description: Fix missing split/join char in Join tool when filling nonjoined columns. 1 file(s) affected in this change: tools/filters/join.py diffs (20 lines): diff -r c0aa8af62124 -r 46bbe610288a tools/filters/join.py --- a/tools/filters/join.py Tue Jun 09 15:03:04 2009 -0400 +++ b/tools/filters/join.py Wed Jun 10 11:58:21 2009 -0400 @@ -288,12 +288,14 @@ if not written and keep_unmatched: out.write( fill_empty_columns( line1.rstrip( '\r\n' ), split, fill_options.file1_columns ) ) if fill_options: - out.write( fill_empty_columns( "", split, fill_options.file2_columns ) ) + if fill_options.file2_columns: + out.write( "%s%s" % ( split, fill_empty_columns( "", split, fill_options.file2_columns ) ) ) out.write( "\n" ) elif keep_partial: out.write( fill_empty_columns( line1.rstrip( '\r\n' ), split, fill_options.file1_columns ) ) if fill_options: - out.write( fill_empty_columns( "", split, fill_options.file2_columns ) ) + if fill_options.file2_columns: + out.write( "%s%s" % ( split, fill_empty_columns( "", split, fill_options.file2_columns ) ) ) out.write( "\n" ) out.close()

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[hg] galaxy 2443: Remote user bug found and fixed by Morita Hide...
by Nate Coraor 10 Jun '09

10 Jun '09

details: http://www.bx.psu.edu/hg/galaxy/rev/08194c60c290 changeset: 2443:08194c60c290 user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Jun 10 12:22:49 2009 -0400 description: Remote user bug found and fixed by Morita Hideyuki 1 file(s) affected in this change: lib/galaxy/web/framework/__init__.py diffs (12 lines): diff -r 46bbe610288a -r 08194c60c290 lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Wed Jun 10 11:58:21 2009 -0400 +++ b/lib/galaxy/web/framework/__init__.py Wed Jun 10 12:22:49 2009 -0400 @@ -268,7 +268,7 @@ invalidate_existing_session = True user_for_new_session = self.__get_or_create_remote_user( remote_user_email ) log.warning( "User logged in as '%s' externally, but has a cookie as '%s' invalidating session", - remote_user_email, prev_galaxy_session.user.email ) + remote_user_email, galaxy_session.user.email ) else: # No session exists, get/create user for new session user_for_new_session = self.__get_or_create_remote_user( remote_user_email )

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