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galaxy-dist commit 19e07ef6eb25: Tweaked wording for locking the job queue
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 Dannon Baker <dannon.baker(a)emory.edu> # Date 1278788080 14400 # Node ID 19e07ef6eb25ea4bd1531ba42c2187f3f5d384d6 # Parent e5e9f62144336658f80d7c3308e8f44110fdede8 Tweaked wording for locking the job queue --- a/templates/admin/jobs.mako +++ b/templates/admin/jobs.mako @@ -126,7 +126,7 @@ </div> %else: <div class="form-row"> - <p>To prevent new jobs from dispatching, you can lock down the job queue here.</p> + <p>To prevent new jobs from dispatching, you can lock the job queue here.</p><input type='hidden' name='job_lock' value='lock'/></div><div class="form-row">

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galaxy-dist commit e5e9f6214433: Feature: Ability to view hidden datasets in the same fashion as you would deleted ones. Unhiding also works in the same fashion.
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 Dannon Baker <dannon.baker(a)emory.edu> # Date 1278785782 14400 # Node ID e5e9f62144336658f80d7c3308e8f44110fdede8 # Parent 71b1a5920fc12514a9e151770eaf250d6fc6da46 Feature: Ability to view hidden datasets in the same fashion as you would deleted ones. Unhiding also works in the same fashion. --- a/lib/galaxy/web/base/controller.py +++ b/lib/galaxy/web/base/controller.py @@ -279,7 +279,7 @@ class UsesHistory( SharableItemSecurity err+msg( "History not found" ) else: return self.security_check( trans.get_user(), history, check_ownership, check_accessible ) - def get_history_datasets( self, trans, history, show_deleted=False ): + def get_history_datasets( self, trans, history, show_deleted=False, show_hidden=False): """ Returns history's datasets. """ query = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \ .filter( trans.model.HistoryDatasetAssociation.history == history ) \ --- a/lib/galaxy/web/controllers/dataset.py +++ b/lib/galaxy/web/controllers/dataset.py @@ -631,6 +631,26 @@ class DatasetInterface( BaseController, trans.log_event( "Dataset id %s has been undeleted" % str(id) ) return True return False + + def _unhide( self, trans, id ): + try: + id = int( id ) + except ValueError, e: + return False + history = trans.get_history() + data = trans.sa_session.query( self.app.model.HistoryDatasetAssociation ).get( id ) + if data: + # Walk up parent datasets to find the containing history + topmost_parent = data + while topmost_parent.parent: + topmost_parent = topmost_parent.parent + assert topmost_parent in history.datasets, "Data does not belong to current history" + # Mark undeleted + data.mark_unhidden() + trans.sa_session.flush() + trans.log_event( "Dataset id %s has been unhidden" % str(id) ) + return True + return False @web.expose def undelete( self, trans, id ): @@ -639,6 +659,13 @@ class DatasetInterface( BaseController, raise "Error undeleting" @web.expose + def unhide( self, trans, id ): + if self._unhide( trans, id ): + return trans.response.send_redirect( web.url_for( controller='root', action='history', show_hidden = True ) ) + raise "Error unhiding" + + + @web.expose def undelete_async( self, trans, id ): if self._undelete( trans, id ): return "OK" --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -37,6 +37,9 @@ "Show Deleted Datasets": function() { galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; }, + "Show Hidden Datasets": function() { + galaxy_history.location = "${h.url_for( controller='root', action='history', show_hidden=True)}"; + }, "Show structure": function() { galaxy_main.location = "${h.url_for( controller='history', action='display_structured' )}"; }, --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -685,6 +685,11 @@ class DatasetInstance( object ): if include_children: for child in self.children: child.mark_undeleted() + def mark_unhidden( self, include_children=True ): + self.visible = True + if include_children: + for child in self.children: + child.mark_unhidden() def undeletable( self ): if self.purged: return False --- a/templates/root/history.mako +++ b/templates/root/history.mako @@ -338,6 +338,12 @@ div.form-row { </div> %endif +%if show_hidden: +<div class="historyLinks"> + <a href="${h.url_for('history', show_hidden=False)}">${_('hide hidden')}</a> +</div> +%endif + <div id="history-name-area" class="historyLinks"> %if trans.get_user(): @@ -385,7 +391,7 @@ div.form-row { ## Render requested datasets, ordered from newest to oldest %for data in reversed( datasets ): - %if data.visible: + %if data.visible or show_hidden: <div class="historyItemContainer" id="historyItemContainer-${data.id}"> ${render_dataset( data, data.hid, show_deleted_on_refresh = show_deleted, for_editing = True )} </div> --- a/lib/galaxy/web/controllers/root.py +++ b/lib/galaxy/web/controllers/root.py @@ -76,7 +76,7 @@ class RootController( BaseController, Us return trans.fill_template_mako( "/my_data.mako" ) @web.expose - def history( self, trans, as_xml=False, show_deleted=False, hda_id=None ): + def history( self, trans, as_xml=False, show_deleted=False, show_hidden=False, hda_id=None ): """ Display the current history, creating a new history if necessary. NOTE: No longer accepts "id" or "template" options for security reasons. @@ -86,16 +86,21 @@ class RootController( BaseController, Us history = trans.get_history( create=True ) if as_xml: trans.response.set_content_type('text/xml') - return trans.fill_template_mako( "root/history_as_xml.mako", history=history, show_deleted=util.string_as_bool( show_deleted ) ) + return trans.fill_template_mako( "root/history_as_xml.mako", + history=history, + show_deleted=util.string_as_bool( show_deleted ), + show_hidden=util.string_as_bool( show_hidden ) ) else: show_deleted = util.string_as_bool( show_deleted ) - datasets = self.get_history_datasets( trans, history, show_deleted ) + show_hidden = util.string_as_bool( show_hidden ) + datasets = self.get_history_datasets( trans, history, show_deleted, show_hidden ) return trans.stream_template_mako( "root/history.mako", history = history, annotation = self.get_item_annotation_str( trans, trans.user, history ), datasets = datasets, hda_id = hda_id, - show_deleted = show_deleted ) + show_deleted = show_deleted, + show_hidden=show_hidden ) @web.expose def dataset_state ( self, trans, id=None, stamp=None ): --- a/templates/root/history_common.mako +++ b/templates/root/history_common.mako @@ -21,6 +21,13 @@ </div> %endif + %if data.visible is False: + <div class="warningmessagesmall"> + <strong>This dataset has been hidden. Click <a href="${h.url_for( controller='dataset', action='unhide', id=data.id )}" class="historyItemUnhide" id="historyItemUnhider-${data.id}" target="galaxy_history">here</a> to unhide.</strong> + </div> + %endif + + ## Header row for history items (name, state, action buttons) <div style="overflow: hidden;" class="historyItemTitleBar"><div class="historyItemButtons">

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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 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 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 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 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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