July 2010 - galaxy-commits - lists.galaxyproject.org

galaxy-dist commit ee6aac1b8cba: Bugfix: pick out a language-code from Accept-Language header.
by commits-noreply＠bitbucket.org 16 Jul '10

16 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User MORITA Hideyuki <h-morita(a)esm.co.jp> # Date 1278490499 -32400 # Node ID ee6aac1b8cba0f4d2054df150e5568cad76fa189 # Parent 47411bb09df44719760aac61e4b90de4fd190aad Bugfix: pick out a language-code from Accept-Language header. --- a/lib/galaxy/web/framework/__init__.py +++ b/lib/galaxy/web/framework/__init__.py @@ -27,6 +27,7 @@ import mako.runtime pkg_resources.require( "Babel" ) from babel.support import Translations +from babel import Locale pkg_resources.require( "SQLAlchemy >= 0.4" ) from sqlalchemy import and_ @@ -200,7 +201,7 @@ class GalaxyWebTransaction( base.Default if 'HTTP_ACCEPT_LANGUAGE' in self.environ: # locales looks something like: ['en', 'en-us;q=0.7', 'ja;q=0.3'] locales = self.environ['HTTP_ACCEPT_LANGUAGE'].split( ',' ) - locales = [ l.split( ';' )[0] for l in locales ] + locales = [ Locale.parse(l.split( ';' )[0], sep='-').language for l in locales ] else: # Default to English locales = 'en'

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galaxy-dist commit 41089d12cdd9: Fix typo in documentation of GFFReaderWrapper.
by commits-noreply＠bitbucket.org 16 Jul '10

16 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 1278598278 14400 # Node ID 41089d12cdd9eaaeb8e75e09157d412ccf935eae # Parent 1d604575f89050503ffbc432e41994948181a9e5 Fix typo in documentation of GFFReaderWrapper. --- a/lib/galaxy/tools/util/gff_util.py +++ b/lib/galaxy/tools/util/gff_util.py @@ -13,7 +13,7 @@ class GFFReaderWrapper( NiceReaderWrappe interval = GenomicInterval( self, line.split( "\t" ), self.chrom_col, self.start_col, self.end_col, self.strand_col, self.default_strand, fix_strand=self.fix_strand ) # Change from 1-based to 0-based format. interval.start -= 1 - # Add 1 to end to move from open to closed format for end coordinate. + # Add 1 to end to move from closed to open format for end coordinate. interval.end += 1 return interval

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galaxy-dist commit 1d604575f890: merge i18n fixes
by commits-noreply＠bitbucket.org 16 Jul '10

16 Jul '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 1278527152 14400 # Node ID 1d604575f89050503ffbc432e41994948181a9e5 # Parent a1d152e92eacf882f6e69498ef2fc4f614d4d6ff # Parent d1e86e754b15420ab541e9183139b9243aa989ce merge i18n fixes

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galaxy-dist commit d1e86e754b15: Bugfix: pass the forgotten is_multi_byte argument.
by commits-noreply＠bitbucket.org 16 Jul '10

16 Jul '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User MORITA Hideyuki <h-morita(a)esm.co.jp> # Date 1278491508 -32400 # Node ID d1e86e754b15420ab541e9183139b9243aa989ce # Parent ee6aac1b8cba0f4d2054df150e5568cad76fa189 Bugfix: pass the forgotten is_multi_byte argument. --- a/lib/galaxy/tools/__init__.py +++ b/lib/galaxy/tools/__init__.py @@ -1657,7 +1657,7 @@ class DataSourceTool( Tool ): data.extension = param_dict.get( 'data_type', data.extension ) #TODO: these should be possible as part of data_source.py and external set_meta, see the upload tool: if data.extension in [ 'txt', 'tabular' ]: - data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order ) + data_type = sniff.guess_ext( data.file_name, sniff_order=app.datatypes_registry.sniff_order, is_multi_byte=self.is_multi_byte ) if data.extension != data_type: data.change_datatype( data_type ) elif not isinstance( data.datatype, datatypes.interval.Bed ) and isinstance( data.datatype, datatypes.interval.Interval ):

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galaxy-dist commit 481da3760997: Improvements to history import/export archiving: (a) security checks when opening and/or copying files from imported archive and (b) implemented options to gzip, include/exclude hidden datasets, and include/exclude deleted datasets when exporting to archive.
by commits-noreply＠bitbucket.org 16 Jul '10

16 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 1278421808 14400 # Node ID 481da37609972064346f7a91853686533dcea84c # Parent 40bfc0def292da5d1c83ea3c55ee9915b7fdbf74 Improvements to history import/export archiving: (a) security checks when opening and/or copying files from imported archive and (b) implemented options to gzip, include/exclude hidden datasets, and include/exclude deleted datasets when exporting to archive. --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -10,7 +10,7 @@ from galaxy.tools.parameters.basic impor from galaxy.tools.actions import upload_common from galaxy.tags.tag_handler import GalaxyTagHandler from sqlalchemy.sql.expression import ClauseElement -import webhelpers, logging, operator, tempfile, subprocess, shutil, tarfile +import webhelpers, logging, operator, os, tempfile, subprocess, shutil, tarfile from datetime import datetime from cgi import escape @@ -443,28 +443,31 @@ class HistoryController( BaseController, self.add_item_annotation( trans, history, new_annotation ) trans.sa_session.flush() return new_annotation - - def import_archive( self, trans, archived_history=None ): + + def import_archive( self, trans, archived_history=None, gzip=True ): """ Import a history. """ + def file_in_dir( file_path, a_dir ): + """ Returns true if file is in directory. """ + abs_file_path = os.path.abspath( file_path ) + return os.path.split( abs_file_path )[0] == a_dir + if archived_history is not None: try: history_archive_file = tarfile.open( archived_history.file.name ) - - # Security check: make sure that members are relative, not absolute. - for tarinfo in history_archive_file.getmembers(): - if tarinfo.name.startswith("/") or tarinfo.name.find("..") != -1: - return trans.show_error_message( 'Error importing history archive: archive file is invalid.' ) - + # Unpack archive in temporary directory. temp_output_dir = tempfile.mkdtemp() history_archive_file.extractall( path=temp_output_dir ) history_archive_file.close() - + # # Create history. # - history_attr_in = open( '%s/%s' % ( temp_output_dir, 'history_attrs.txt'), 'rb' ) + history_attr_file_name = '%s/%s' % ( temp_output_dir, 'history_attrs.txt') + if not file_in_dir( history_attr_file_name, temp_output_dir ): + raise Exception( "Invalid location for history attributes file: %s" % history_attr_file_name ) + history_attr_in = open( history_attr_file_name, 'rb' ) history_attr_str = '' buffsize = 1048576 try: @@ -476,32 +479,35 @@ class HistoryController( BaseController, pass history_attr_in.close() history_attrs = from_json_string( history_attr_str ) - + # Create history. new_history = model.History( name='imported from archive: %s' % history_attrs['name'].encode( 'utf-8' ), user=trans.user ) trans.sa_session.add( new_history ) - + new_history.hid_counter = history_attrs['hid_counter'] new_history.genome_build = history_attrs['genome_build'] trans.sa_session.flush() - + # Builds a tag string for a tag, value pair. def get_tag_str( tag, value ): if not value: return tag else: return tag + ":" + value - + # Add annotation, tags. if trans.user: self.add_item_annotation( trans, new_history, history_attrs[ 'annotation' ] ) for tag, value in history_attrs[ 'tags' ].items(): trans.app.tag_handler.apply_item_tags( trans, trans.user, new_history, get_tag_str( tag, value ) ) - + # # Create datasets. # - datasets_attr_in = open( '%s/%s' % ( temp_output_dir, 'datasets_attrs.txt'), 'rb' ) + datasets_attrs_file_name = '%s/%s' % ( temp_output_dir, 'datasets_attrs.txt') + if not file_in_dir( datasets_attrs_file_name, temp_output_dir ): + raise Exception( "Invalid location for dataset attributes file: %s" % datasets_attrs_file_name ) + datasets_attr_in = open( datasets_attrs_file_name, 'rb' ) datasets_attr_str = '' buffsize = 1048576 try: @@ -513,11 +519,11 @@ class HistoryController( BaseController, pass datasets_attr_in.close() datasets_attrs = from_json_string( datasets_attr_str ) - + # Create datasets. for dataset_attrs in datasets_attrs: metadata = dataset_attrs['metadata'] - + # Create dataset and HDA. hda = model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), extension = dataset_attrs['extension'], @@ -539,24 +545,29 @@ class HistoryController( BaseController, permissions = trans.app.security_agent.history_get_default_permissions( new_history ) trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) trans.sa_session.flush() - - # Copy dataset data. - temp_dataset_name = '%s/datasets/%s' % ( temp_output_dir, dataset_attrs['file_name'] ) - shutil.copyfile( temp_dataset_name, hda.file_name ) - + + # Do security check and copy dataset data. + temp_dataset_file_name = '%s/datasets/%s' % ( temp_output_dir, dataset_attrs['file_name'] ) + if not file_in_dir( temp_dataset_file_name, temp_output_dir + "/datasets" ): + raise Exception( "Invalid dataset path: %s" % temp_dataset_file_name ) + shutil.move( temp_dataset_file_name, hda.file_name ) + # Set tags, annotations. if trans.user: self.add_item_annotation( trans, hda, dataset_attrs[ 'annotation' ] ) for tag, value in dataset_attrs[ 'tags' ].items(): trans.app.tag_handler.apply_item_tags( trans, trans.user, hda, get_tag_str( tag, value ) ) trans.sa_session.flush() - + # # Create jobs. # - + # Read jobs attributes. - jobs_attr_in = open( '%s/%s' % ( temp_output_dir, 'jobs_attrs.txt'), 'rb' ) + jobs_attr_file_name = '%s/%s' % ( temp_output_dir, 'jobs_attrs.txt') + if not file_in_dir( jobs_attr_file_name, temp_output_dir ): + raise Exception( "Invalid location for jobs' attributes file: %s" % jobs_attr_file_name ) + jobs_attr_in = open( jobs_attr_file_name, 'rb' ) jobs_attr_str = '' buffsize = 1048576 try: @@ -567,7 +578,7 @@ class HistoryController( BaseController, except OverflowError: pass jobs_attr_in.close() - + # Decode jobs attributes. def as_hda( obj_dct ): """ Hook to 'decode' an HDA; method uses history and HID to get the HDA represented by @@ -577,7 +588,7 @@ class HistoryController( BaseController, .filter_by( history=new_history, hid=obj_dct['hid'] ).first() return obj_dct jobs_attrs = from_json_string( jobs_attr_str, object_hook=as_hda ) - + # Create each job. for job_attrs in jobs_attrs: imported_job = model.Job() @@ -590,7 +601,7 @@ class HistoryController( BaseController, imported_job.imported = True trans.sa_session.add( imported_job ) trans.sa_session.flush() - + class HistoryDatasetAssociationIDEncoder( simplejson.JSONEncoder ): """ Custom JSONEncoder for a HistoryDatasetAssociation that encodes an HDA as its ID. """ def default( self, obj ): @@ -598,7 +609,7 @@ class HistoryController( BaseController, if isinstance( obj, model.HistoryDatasetAssociation ): return obj.id return simplejson.JSONEncoder.default( self, obj ) - + # Set parameters. May be useful to look at metadata.py for creating parameters. # TODO: there may be a better way to set parameters, e.g.: # for name, value in tool.params_to_strings( incoming, trans.app ).iteritems(): @@ -614,9 +625,9 @@ class HistoryController( BaseController, value = input_hda.id #print "added parameter %s-->%s to job %i" % ( name, value, imported_job.id ) imported_job.add_parameter( name, to_json_string( value, cls=HistoryDatasetAssociationIDEncoder ) ) - + # TODO: Connect jobs to input datasets. - + # Connect jobs to output datasets. for output_hid in job_attrs[ 'output_datasets' ]: #print "%s job has output dataset %i" % (imported_job.id, output_hid) @@ -625,11 +636,11 @@ class HistoryController( BaseController, if output_hda: imported_job.add_output_dataset( output_hda.name, output_hda ) trans.sa_session.flush() - + # Cleanup. if os.path.exists( temp_output_dir ): shutil.rmtree( temp_output_dir ) - + return trans.show_ok_message( message="History '%s' has been imported. " % history_attrs['name'] ) except Exception, e: return trans.show_error_message( 'Error importing history archive. ' + str( e ) ) @@ -638,10 +649,18 @@ class HistoryController( BaseController, web.FormBuilder( web.url_for(), "Import a History from an Archive", submit_text="Submit" ) .add_input( "file", "Archived History File", "archived_history", value=None, error=None ) ) - - def export_archive( self, trans, id=None ): + + def export_archive( self, trans, id=None, gzip=True, include_hidden=False, include_deleted=False ): """ Export a history. """ + # Convert options to booleans. + if isinstance( gzip, basestring ): + gzip = ( gzip in [ 'True', 'true', 'T', 't' ] ) + if isinstance( include_hidden, basestring ): + include_hidden = ( include_hidden in [ 'True', 'true', 'T', 't' ] ) + if isinstance( include_deleted, basestring ): + include_deleted = ( include_deleted in [ 'True', 'true', 'T', 't' ] ) + # # Helper methods/classes. # @@ -702,7 +721,9 @@ class HistoryController( BaseController, return trans.show_error_message( "This history does not exist or you cannot export this history." ) history_export_dir_name = "./database/export" - archive_file_name = '%s/%s.tar.gz' % ( history_export_dir_name, trans.security.encode_id( history.id ) ) + archive_file_name = '%s/%s.tar' % ( history_export_dir_name, trans.security.encode_id( history.id ) ) + if gzip: + archive_file_name += '.gz' # # Do export. @@ -717,7 +738,7 @@ class HistoryController( BaseController, try: # Use temporary directory for temp output files. temp_output_dir = tempfile.mkdtemp() - + # # Write history attributes to file. # @@ -734,27 +755,33 @@ class HistoryController( BaseController, history_attrs_out = open( history_attrs_file_name, 'w' ) history_attrs_out.write( to_json_string( history_attrs ) ) history_attrs_out.close() - + # # Write datasets' attributes to file. # datasets = self.get_history_datasets( trans, history ) + included_datasets = [] datasets_attrs = [] for dataset in datasets: + if not dataset.visible and not include_hidden: + continue + if dataset.deleted and not include_deleted: + continue dataset.annotation = self.get_item_annotation_str( trans, history.user, dataset ) datasets_attrs.append( dataset ) + included_datasets.append( dataset ) datasets_attrs_file_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name datasets_attrs_out = open( datasets_attrs_file_name, 'w' ) datasets_attrs_out.write( to_json_string( datasets_attrs, cls=HistoryDatasetAssociationEncoder ) ) datasets_attrs_out.close() - + # # Write jobs attributes file. # - - # Get all jobs associated with HDAs. + + # Get all jobs associated with included HDAs. jobs_dict = {} - for hda in datasets: + for hda in included_datasets: # Get the associated job, if any. If this hda was copied from another, # we need to find the job that created the origial hda job_hda = hda @@ -763,7 +790,7 @@ class HistoryController( BaseController, if not job_hda.creating_job_associations: # No viable HDA found. continue - + # Get the job object. job = None for assoc in job_hda.creating_job_associations: @@ -772,9 +799,9 @@ class HistoryController( BaseController, if not job: # No viable job. continue - + jobs_dict[ job.id ] = job - + # Get jobs' attributes. jobs_attrs = [] for id, job in jobs_dict.items(): @@ -782,7 +809,7 @@ class HistoryController( BaseController, job_attrs[ 'tool_id' ] = job.tool_id job_attrs[ 'tool_version' ] = job.tool_version job_attrs[ 'state' ] = job.state - + # Get the job's parameters try: params_objects = job.get_param_values( trans.app ) @@ -794,52 +821,57 @@ class HistoryController( BaseController, for name, value in params_objects.items(): params_dict[ name ] = value job_attrs[ 'params' ] = params_dict - + # Get input, output datasets. input_datasets = [ assoc.dataset.hid for assoc in job.input_datasets ] job_attrs[ 'input_datasets' ] = input_datasets output_datasets = [ assoc.dataset.hid for assoc in job.output_datasets ] job_attrs[ 'output_datasets' ] = output_datasets - + jobs_attrs.append( job_attrs ) - + jobs_attrs_file_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name jobs_attrs_out = open( jobs_attrs_file_name, 'w' ) jobs_attrs_out.write( to_json_string( jobs_attrs, cls=HistoryDatasetAssociationEncoder ) ) jobs_attrs_out.close() - + # # Write archive and include: (a) history attributes file; (b) datasets attributes file; # (c) jobs attributes file; and (d) datasets files. # - history_archive_name = '%s/%s.tar.gz' % ( history_export_dir_name, trans.security.encode_id( history.id ) ) - history_archive = tarfile.open( history_archive_name, "w:gz" ) + tarfile_mode = "w" + if gzip: + tarfile_mode += ":gz" + history_archive = tarfile.open( archive_file_name, tarfile_mode ) history_archive.add( history_attrs_file_name, arcname="history_attrs.txt" ) history_archive.add( datasets_attrs_file_name, arcname="datasets_attrs.txt" ) history_archive.add( jobs_attrs_file_name, arcname="jobs_attrs.txt" ) - for i, dataset in enumerate( datasets ) : + for i, dataset in enumerate( included_datasets ): history_archive.add( dataset.file_name, arcname="datasets/%s" % dataset.file_name.split('/')[-1] ) history_archive.close() - + # Remove temp directory. if os.path.exists( temp_output_dir ): - shutil.rmtree( temp_output_dir ) - + shutil.rmtree( temp_output_dir ) except Exception, e: return trans.show_error_message( 'Error creating history archive. ' + str( e ) ) # # Stream archive. # - if os.path.exists( history_archive_name ): + if os.path.exists( archive_file_name ): valid_chars = '.,^_-()[]0123456789abcdefghijklmnopqrstuvwxyzABCDEFGHIJKLMNOPQRSTUVWXYZ' hname = history.name hname = ''.join(c in valid_chars and c or '_' for c in hname)[0:150] - trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-History-%s.tar.gz" % ( hname ) - trans.response.set_content_type( 'application/x-gzip' ) - return open( history_archive_name ) + trans.response.headers["Content-Disposition"] = "attachment; filename=Galaxy-History-%s.tar" % ( hname ) + if gzip: + trans.response.headers["Content-Disposition"] += ".gz" + trans.response.set_content_type( 'application/x-gzip' ) + else: + trans.response.set_content_type( 'application/x-tar' ) + return open( archive_file_name ) else: - return + return trans.show_error_message( 'Archive file does not exist.' ) @web.expose @web.json

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galaxy-dist commit 67f5a7f16c59: Detect pdf files on upload [Brad Chapman]. Resolves #357
by commits-noreply＠bitbucket.org 16 Jul '10

16 Jul '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 1278108645 14400 # Node ID 67f5a7f16c59d3e3bb68b62d278e037975f1c1af # Parent e5c40bd9c179059344645a9171b7172d74c64a25 Detect pdf files on upload [Brad Chapman]. Resolves #357 --- a/tools/data_source/upload.py +++ b/tools/data_source/upload.py @@ -10,6 +10,7 @@ from galaxy import eggs import galaxy.model from galaxy.datatypes import sniff from galaxy.datatypes.binary import * +from galaxy.datatypes.images import Pdf from galaxy.datatypes.registry import Registry from galaxy import util from galaxy.util.json import * @@ -85,6 +86,8 @@ def check_bam( temp_name ): return Bam().sniff( temp_name ) def check_sff( temp_name ): return Sff().sniff( temp_name ) +def check_pdf( temp_name ): + return Pdf().sniff( temp_name ) def check_gzip( temp_name ): # This method returns a tuple of booleans representing ( is_gzipped, is_valid ) # Make sure we have a gzipped file @@ -160,6 +163,9 @@ def add_file( dataset, json_file, output elif check_sff( dataset.path ): ext = 'sff' data_type = 'sff' + elif check_pdf( dataset.path ): + ext = 'pdf' + data_type = 'pdf' else: # See if we have a gzipped file, which, if it passes our restrictions, we'll uncompress is_gzipped, is_valid = check_gzip( dataset.path ) @@ -215,7 +221,7 @@ def add_file( dataset, json_file, output return if not data_type: if check_binary( dataset.path ): - # We have a binary dataset, but it is not Bam or Sff + # We have a binary dataset, but it is not Bam, Sff or Pdf data_type = 'binary' #binary_ok = False parts = dataset.name.split( "." ) --- a/datatypes_conf.xml.sample +++ b/datatypes_conf.xml.sample @@ -79,7 +79,7 @@ <datatype extension="mafcustomtrack" type="galaxy.datatypes.sequence:MafCustomTrack"><display file="ucsc/maf_customtrack.xml" /></datatype> - <datatype extension="pdf" type="galaxy.datatypes.images:Image" mimetype="application/pdf"/> + <datatype extension="pdf" type="galaxy.datatypes.images:Pdf" mimetype="application/pdf"/><datatype extension="pileup" type="galaxy.datatypes.tabular:Pileup" display_in_upload="true" /><datatype extension="png" type="galaxy.datatypes.images:Image" mimetype="image/png"/><datatype extension="qual" type="galaxy.datatypes.qualityscore:QualityScore" /> @@ -260,6 +260,7 @@ <sniffer type="galaxy.datatypes.sequence:Fastq"/><sniffer type="galaxy.datatypes.interval:Wiggle"/><sniffer type="galaxy.datatypes.images:Html"/> + <sniffer type="galaxy.datatypes.images:Pdf"/><sniffer type="galaxy.datatypes.sequence:Axt"/><sniffer type="galaxy.datatypes.interval:Bed"/><sniffer type="galaxy.datatypes.interval:CustomTrack"/> --- a/lib/galaxy/datatypes/images.py +++ b/lib/galaxy/datatypes/images.py @@ -23,6 +23,19 @@ class Image( data.Data ): dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' +class Pdf( Image ): + def sniff(self, filename): + """Determine if the file is in pdf format. + """ + headers = get_headers(filename, None, 1) + try: + if headers[0][0].startswith("%PDF"): + return True + else: + return False + except IndexError: + return False + def create_applet_tag_peek( class_name, archive, params ): text = """

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galaxy-dist commit a1d152e92eac: Add enable_pages option and documentation to universe config sample file.
by commits-noreply＠bitbucket.org 16 Jul '10

16 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 1278447163 14400 # Node ID a1d152e92eacf882f6e69498ef2fc4f614d4d6ff # Parent 481da37609972064346f7a91853686533dcea84c Add enable_pages option and documentation to universe config sample file. --- a/universe_wsgi.ini.sample +++ b/universe_wsgi.ini.sample @@ -315,6 +315,12 @@ use_interactive = True # Enable Galaxy's built-in visualization module, Trackster. #enable_tracks = False +# Enable Galaxy Pages. Pages are custom webpages that include embedded Galaxy items, +# such as datasets, histories, workflows, and visualizations; pages are useful for +# documenting and sharing multiple analyses or workflows. Pages are created using a +# WYSIWYG editor that is very similar to a word processor. +#enable_pages = False + # Enable the (experimental! beta!) Web API. Documentation forthcoming. #enable_api = False

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galaxy-dist commit 40bfc0def292: Improvements to tool search: (a) search tool title, description, and help and (b) set minimum score for searching to remove very poor results.
by commits-noreply＠bitbucket.org 16 Jul '10

16 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 1278183199 14400 # Node ID 40bfc0def292da5d1c83ea3c55ee9915b7fdbf74 # Parent 67f5a7f16c59d3e3bb68b62d278e037975f1c1af Improvements to tool search: (a) search tool title, description, and help and (b) set minimum score for searching to remove very poor results. --- a/lib/galaxy/tools/search/__init__.py +++ b/lib/galaxy/tools/search/__init__.py @@ -8,7 +8,7 @@ try: from whoosh.index import Index from whoosh.qparser import QueryParser tool_search_enabled = True - schema = Schema( id = STORED, title = TEXT, help = TEXT ) + schema = Schema( id = STORED, title = TEXT, description = TEXT, help = TEXT ) except ImportError, e: tool_search_enabled = False schema = None @@ -40,7 +40,7 @@ class ToolBoxSearch( object ): else: return a_basestr - writer.add_document( id=id, title=to_unicode(tool.name), help=to_unicode(tool.help) ) + writer.add_document( id=id, title=to_unicode(tool.name), description=to_unicode(tool.description), help=to_unicode(tool.help) ) writer.commit() def search( self, query, return_attribute='id' ): @@ -48,5 +48,8 @@ class ToolBoxSearch( object ): return [] searcher = self.index.searcher() parser = QueryParser( "help", schema = schema ) - results = searcher.search( parser.parse( query ) ) + # Set query to search title, description, and help. + query = "title:query OR description:query OR help:query".replace( "query", query ) + results = searcher.search( parser.parse( query ), minscore=1.5 ) + print results.scores return [ result[ return_attribute ] for result in results ]

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galaxy-dist commit b68cbc002e8a: Remove txtseq and binseq from datatypes.
by commits-noreply＠bitbucket.org 16 Jul '10

16 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 1278088028 14400 # Node ID b68cbc002e8aabb1750d1c82607430124065736f # Parent fad6bc5478fa9a4ac4e9d368bcfae1651528deac Remove txtseq and binseq from datatypes. --- a/lib/galaxy/datatypes/binary.py +++ b/lib/galaxy/datatypes/binary.py @@ -141,28 +141,6 @@ class Bam( Binary ): def get_track_type( self ): return "ReadTrack", {"data": "bai", "index": "summary_tree"} -class Binseq( Binary ): - """Class describing a zip archive of binary sequence files""" - file_ext = "binseq.zip" - - def set_peek( self, dataset, is_multi_byte=False ): - if not dataset.dataset.purged: - zip_file = zipfile.ZipFile( dataset.file_name, "r" ) - num_files = len( zip_file.namelist() ) - dataset.peek = "Archive of %s binary sequence files" % ( str( num_files ) ) - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def display_peek( self, dataset ): - try: - return dataset.peek - except: - return "Binary sequence file archive (%s)" % ( data.nice_size( dataset.get_size() ) ) - def get_mime( self ): - """Returns the mime type of the datatype""" - return 'application/zip' - class Scf( Binary ): """Class describing an scf binary sequence file""" file_ext = "scf" --- a/lib/galaxy/datatypes/data.py +++ b/lib/galaxy/datatypes/data.py @@ -414,27 +414,6 @@ class Text( Data ): dataset.peek = 'file does not exist' dataset.blurb = 'file purged from disk' -class Txtseq( Data ): - """Class describing a zip archive of text sequence files""" - file_ext = "txtseq.zip" - def set_peek( self, dataset, is_multi_byte=False ): - if not dataset.dataset.purged: - zip_file = zipfile.ZipFile( dataset.file_name, "r" ) - num_files = len( zip_file.namelist() ) - dataset.peek = "Archive of %s text sequence files" % ( str( num_files ) ) - dataset.blurb = data.nice_size( dataset.get_size() ) - else: - dataset.peek = 'file does not exist' - dataset.blurb = 'file purged from disk' - def display_peek(self, dataset): - try: - return dataset.peek - except: - return "Text sequence file archive (%s)" % ( data.nice_size( dataset.get_size() ) ) - def get_mime(self): - """Returns the mime type of the datatype""" - return 'application/zip' - class Newick( Text ): pass --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -150,7 +150,6 @@ class Registry( object ): 'axt' : sequence.Axt(), 'bam' : binary.Bam(), 'bed' : interval.Bed(), - 'binseq.zip' : binary.Binseq(), 'blastxml' : xml.BlastXml(), 'coverage' : coverage.LastzCoverage(), 'customtrack' : interval.CustomTrack(), @@ -176,7 +175,6 @@ class Registry( object ): 'tabular' : tabular.Tabular(), 'taxonomy' : tabular.Taxonomy(), 'txt' : data.Text(), - 'txtseq.zip' : data.Txtseq(), 'wig' : interval.Wiggle() } self.mimetypes_by_extension = { @@ -184,7 +182,6 @@ class Registry( object ): 'axt' : 'text/plain', 'bam' : 'application/octet-stream', 'bed' : 'text/plain', - 'binseq.zip' : 'application/zip', 'blastxml' : 'text/plain', 'customtrack' : 'text/plain', 'csfasta' : 'text/plain', @@ -208,7 +205,6 @@ class Registry( object ): 'tabular' : 'text/plain', 'taxonomy' : 'text/plain', 'txt' : 'text/plain', - 'txtseq.zip' : 'application/zip', 'wig' : 'text/plain' } # Default values - the order in which we attempt to determine data types is critical

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galaxy-dist commit b841989e2662: Move trackster.css to common stylesheet folder, fix small error in color
by commits-noreply＠bitbucket.org 16 Jul '10

16 Jul '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 1278095180 14400 # Node ID b841989e2662b204fcb4c73931ab3a2b08ef35a0 # Parent b68cbc002e8aabb1750d1c82607430124065736f Move trackster.css to common stylesheet folder, fix small error in color --- a/static/june_2007_style/make_style.py +++ b/static/june_2007_style/make_style.py @@ -20,13 +20,14 @@ def run( cmd ): templates = [ ( "base.css.tmpl", "base.css" ), ( "panel_layout.css.tmpl", "panel_layout.css" ), - ( "masthead.css.tmpl", "masthead.css"), - ( "library.css.tmpl", "library.css"), + ( "masthead.css.tmpl", "masthead.css" ), + ( "library.css.tmpl", "library.css" ), ( "history.css.tmpl", "history.css" ), ( "tool_menu.css.tmpl", "tool_menu.css" ), ( "iphone.css.tmpl", "iphone.css" ), ( "reset.css.tmpl", "reset.css" ), - ( "autocomplete_tagging.css.tmpl", "autocomplete_tagging.css") ] + ( "autocomplete_tagging.css.tmpl", "autocomplete_tagging.css" ), + ( "trackster.css.tmpl", "trackster.css" ) ] # TODO: Are these images still being used? If not, clean this code up! images = [ --- a/templates/display_base.mako +++ b/templates/display_base.mako @@ -71,8 +71,7 @@ <%def name="stylesheets()"> ${parent.stylesheets()} - ${h.css( "autocomplete_tagging", "embed_item" )} - <link rel="stylesheet" type="text/css" href="${h.url_for('/static/trackster.css')}" /> + ${h.css( "autocomplete_tagging", "embed_item", "trackster" )} <style type="text/css"> .page-body { Binary file static/june_2007_style/blue/fugue.png has changed Binary file static/june_2007_style/blue/history-buttons.png has changed --- /dev/null +++ b/static/june_2007_style/trackster.css @@ -0,0 +1,125 @@ +.viewport-container { + overflow-x: hidden; + overflow-y: auto; +} + +/*canvas{ + border-left: 1px solid green; + border-right: 1px solid red; } /* debugging */ +.nav { + padding: 0 0; + color:#333;font-weight:bold; +} + +.nav-controls { + text-align: center; + background:#cccccc; + background-image:url(style/panel_header_bg.png); + background-position:top center; + background-repeat:repeat-x; + padding: 2px 0; +} +.nav-controls input { + margin: 0 5px; +} +.nav-controls a { + padding: 0 0.4em; +} + +.overview { + width: 100%; + margin: 0px; + color: white; + margin-top: -6px; + margin-bottom: -4px; +} + +.overview-viewport { + position: relative; + height: 14px; +/* border-top: solid #666 1px;*/ +/* border-bottom: solid #aaa 1px;*/ + background: white; + border-top: solid gray 1px; + border-bottom: solid gray 1px; + margin: 5px 0; +} +.overview-box { + position: absolute; + margin-top: 0px; + height: 14px; + background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat; + /*border-style: outset;*/ +} + +.viewport { +/* overflow-x: hidden;*/ + background-color: #fff; +/* overflow: scroll;*/ +/* border-bottom: 2px solid black;*/ +} + +.viewport-canvas { + width: 100%; + height: 100px; +} + +.yaxislabel { + color: #777; +} +/* Line track needs borders to show range */ +.line-track .track-content { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; +} + +.track { + /* border-top: solid #DDDDDD 1px; */ + /* border-bottom: solid #DDDDDD 1px; */ + background: white; +} + +.track-header { + text-align: center; + padding: 4px; + color: #666; +} + +.track-content { + overflow: hidden; + text-align: center; +} + +.track.error { + background-color: #ECB4AF; +} +.track.nodata { + background-color: #ddd; +} + +.loading { + min-height: 100px; +} + +.label-track { + /* font-weight: bold; */ + /* font-size: 10px; */ +} +.label-track .label { + border-left: solid #999 1px; + padding: 1px; + display: inline-block; +} +.right-float { + float: right; + margin-left: 5px; +} + +.top-labeltrack { + border-bottom: solid #999 1px; +} + +.nav-labeltrack { + border-top: solid #999 1px; + border-bottom: solid #999 1px; +} --- a/static/june_2007_style/blue/base.css +++ b/static/june_2007_style/blue/base.css @@ -73,7 +73,7 @@ span.toolParameterExpandableCollapsable{ ul.toolParameterExpandableCollapsable{list-style:none;} ul.manage-table-actions{float:right;margin-top:-2.5em;} ul.manage-table-actions li{display:block;float:left;margin-left:0.5em;} -.state-color-new{border-color:#A86030;background:FFB030;} +.state-color-new{border-color:#A86030;background:#FFB030;} .state-color-upload{border-color:#6666AA;background:#CCCCFF;} .state-color-waiting{border-color:#A86030;background:#E8C060;} .state-color-queued{border-color:#888888;background:#EEEEEE;} --- a/templates/tracks/browser.mako +++ b/templates/tracks/browser.mako @@ -12,8 +12,8 @@ <%def name="stylesheets()"> ${parent.stylesheets()} -${h.css( "history", "autocomplete_tagging" )} -<link rel="stylesheet" type="text/css" href="${h.url_for('/static/trackster.css')}" /> +${h.css( "history", "autocomplete_tagging", "trackster" )} + <style type="text/css"> #center { overflow: auto; --- /dev/null +++ b/static/june_2007_style/trackster.css.tmpl @@ -0,0 +1,125 @@ +.viewport-container { + overflow-x: hidden; + overflow-y: auto; +} + +/*canvas{ + border-left: 1px solid green; + border-right: 1px solid red; } /* debugging */ +.nav { + padding: 0 0; + color:#333;font-weight:bold; +} + +.nav-controls { + text-align: center; + background:#cccccc; + background-image:url(panel_header_bg.png); + background-position:top center; + background-repeat:repeat-x; + padding: 2px 0; +} +.nav-controls input { + margin: 0 5px; +} +.nav-controls a { + padding: 0 0.4em; +} + +.overview { + width: 100%; + margin: 0px; + color: white; + margin-top: -6px; + margin-bottom: -4px; +} + +.overview-viewport { + position: relative; + height: 14px; +/* border-top: solid #666 1px;*/ +/* border-bottom: solid #aaa 1px;*/ + background: white; + border-top: solid gray 1px; + border-bottom: solid gray 1px; + margin: 5px 0; +} +.overview-box { + position: absolute; + margin-top: 0px; + height: 14px; + background: #ddd url(../images/visualization/draggable_horizontal.png) center center no-repeat; + /*border-style: outset;*/ +} + +.viewport { +/* overflow-x: hidden;*/ + background-color: #fff; +/* overflow: scroll;*/ +/* border-bottom: 2px solid black;*/ +} + +.viewport-canvas { + width: 100%; + height: 100px; +} + +.yaxislabel { + color: #777; +} +/* Line track needs borders to show range */ +.line-track .track-content { + border-top: 1px solid #ddd; + border-bottom: 1px solid #ddd; +} + +.track { + /* border-top: solid #DDDDDD 1px; */ + /* border-bottom: solid #DDDDDD 1px; */ + background: white; +} + +.track-header { + text-align: center; + padding: 4px; + color: #666; +} + +.track-content { + overflow: hidden; + text-align: center; +} + +.track.error { + background-color: #ECB4AF; +} +.track.nodata { + background-color: #ddd; +} + +.loading { + min-height: 100px; +} + +.label-track { + /* font-weight: bold; */ + /* font-size: 10px; */ +} +.label-track .label { + border-left: solid #999 1px; + padding: 1px; + display: inline-block; +} +.right-float { + float: right; + margin-left: 5px; +} + +.top-labeltrack { + border-bottom: solid #999 1px; +} + +.nav-labeltrack { + border-top: solid #999 1px; + border-bottom: solid #999 1px; +} Binary file static/june_2007_style/blue/history-states.png has changed --- a/static/trackster.css +++ /dev/null @@ -1,125 +0,0 @@ -.viewport-container { - overflow-x: hidden; - overflow-y: auto; -} - -/*canvas{ - border-left: 1px solid green; - border-right: 1px solid red; } /* debugging */ -.nav { - padding: 0 0; - color:#333;font-weight:bold; -} - -.nav-controls { - text-align: center; - background:#cccccc; - background-image:url(style/panel_header_bg.png); - background-position:top center; - background-repeat:repeat-x; - padding: 2px 0; -} -.nav-controls input { - margin: 0 5px; -} -.nav-controls a { - padding: 0 0.4em; -} - -.overview { - width: 100%; - margin: 0px; - color: white; - margin-top: -6px; - margin-bottom: -4px; -} - -.overview-viewport { - position: relative; - height: 14px; -/* border-top: solid #666 1px;*/ -/* border-bottom: solid #aaa 1px;*/ - background: white; - border-top: solid gray 1px; - border-bottom: solid gray 1px; - margin: 5px 0; -} -.overview-box { - position: absolute; - margin-top: 0px; - height: 14px; - background: #ddd url(images/visualization/draggable_horizontal.png) center center no-repeat; - /*border-style: outset;*/ -} - -.viewport { -/* overflow-x: hidden;*/ - background-color: #fff; -/* overflow: scroll;*/ -/* border-bottom: 2px solid black;*/ -} - -.viewport-canvas { - width: 100%; - height: 100px; -} - -.yaxislabel { - color: #777; -} -/* Line track needs borders to show range */ -.line-track .track-content { - border-top: 1px solid #ddd; - border-bottom: 1px solid #ddd; -} - -.track { - /* border-top: solid #DDDDDD 1px; */ - /* border-bottom: solid #DDDDDD 1px; */ - background: white; -} - -.track-header { - text-align: center; - padding: 4px; - color: #666; -} - -.track-content { - overflow: hidden; - text-align: center; -} - -.track.error { - background-color: #ECB4AF; -} -.track.nodata { - background-color: #ddd; -} - -.loading { - min-height: 100px; -} - -.label-track { - /* font-weight: bold; */ - /* font-size: 10px; */ -} -.label-track .label { - border-left: solid #999 1px; - padding: 1px; - display: inline-block; -} -.right-float { - float: right; - margin-left: 5px; -} - -.top-labeltrack { - border-bottom: solid #999 1px; -} - -.nav-labeltrack { - border-top: solid #999 1px; - border-bottom: solid #999 1px; -} --- a/static/june_2007_style/blue_colors.ini +++ b/static/june_2007_style/blue_colors.ini @@ -35,7 +35,7 @@ footer_title_bg=#023858 footer_title_hatch=#000000 # History - these are actually Job states (used in the reports webapp), but the same styles are used for Tool states in the community webapp history_new_border=#A86030 -history_new_bg=FFB030 +history_new_bg=#FFB030 history_upload_border=#990099 history_upload_bg=#D090D0 history_waiting_border=#A86030

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