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

galaxy-dist commit 1dba26a363ab: Enhancements for the library dataset information page: display all metadata elements, and if in the admin view, display all undeleted history items and other undeleted library datasets that use the current library dataset's disk file.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275503359 14400 # Node ID 1dba26a363abfb488b8021f3c86c75651fce81b0 # Parent ea2658d131b4c54fca14cdf2b5a66fbf128eaf40 Enhancements for the library dataset information page: display all metadata elements, and if in the admin view, display all undeleted history items and other undeleted library datasets that use the current library dataset's disk file. --- a/templates/library/common/common.mako +++ b/templates/library/common/common.mako @@ -11,9 +11,9 @@ can_modify = trans.app.security_agent.can_modify_library_item( current_user_roles, item ) %> %if widgets: - <p/> - <div class="toolForm"> - %if editable and ( cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ): + %if editable and ( cntrller=='library_admin' or trans.app.security_agent.can_modify_library_item( current_user_roles, item ) ): + <p/> + <div class="toolForm"><div class="toolFormTitle"> %if inherited: Other information <i>- this is an inherited template and is not required to be used with this ${item_type}</i> @@ -54,20 +54,23 @@ </div></form></div> - %else: - <% contents = False %> - %for i, field in enumerate( widgets ): - %if field[ 'widget' ].value: - <% - contents = True - break - %> - %endif - %endfor - %if contents: - <div class="toolForm"> - <div class="toolFormTitle">Other information about ${item.name}</div> - <div class="toolFormBody"> + </div> + <p/> + %else: + <% contents = False %> + %for i, field in enumerate( widgets ): + %if field[ 'widget' ].value: + <% + contents = True + break + %> + %endif + %endfor + %if contents: + <p/> + <div class="toolForm"> + <div class="toolFormTitle">Other information about ${item.name}</div> + <div class="toolFormBody"> %for i, field in enumerate( widgets ): %if field[ 'widget' ].value: <div class="form-row"> @@ -81,9 +84,10 @@ %endif %endfor </div> - %endif + </div> + <p/> %endif - </div> + %endif %endif </%def> --- a/lib/galaxy/web/controllers/library_common.py +++ b/lib/galaxy/web/controllers/library_common.py @@ -523,6 +523,20 @@ class LibraryCommon( BaseController ): message=util.sanitize_text( message ), status='error' ) ) library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) + if cntrller == 'library_admin': + # Get all associated hdas and lddas that use the same disk file. + associated_hdas = trans.sa_session.query( trans.model.HistoryDatasetAssociation ) \ + .filter( and_( trans.model.HistoryDatasetAssociation.deleted == False, + trans.model.HistoryDatasetAssociation.dataset_id == ldda.dataset_id ) ) \ + .all() + associated_lddas = trans.sa_session.query( trans.model.LibraryDatasetDatasetAssociation ) \ + .filter( and_( trans.model.LibraryDatasetDatasetAssociation.deleted == False, + trans.model.LibraryDatasetDatasetAssociation.dataset_id == ldda.dataset_id, + trans.model.LibraryDatasetDatasetAssociation.id != ldda.id ) ) \ + .all() + else: + associated_hdas = [] + associated_lddas = [] # See if we have any associated templates widgets = [] info_association, inherited = ldda.get_info_association() @@ -534,6 +548,8 @@ class LibraryCommon( BaseController ): use_panels=use_panels, ldda=ldda, library=library, + associated_hdas=associated_hdas, + associated_lddas=associated_lddas, show_deleted=show_deleted, widgets=widgets, current_user_roles=current_user_roles, @@ -702,15 +718,15 @@ class LibraryCommon( BaseController ): if error: status = 'error' trans.response.send_redirect( web.url_for( controller='library_common', - action='upload_library_dataset', - cntrller=cntrller, - library_id=library_id, - folder_id=folder_id, - replace_id=replace_id, - upload_option=upload_option, - show_deleted=show_deleted, - message=util.sanitize_text( message ), - status='error' ) ) + action='upload_library_dataset', + cntrller=cntrller, + library_id=library_id, + folder_id=folder_id, + replace_id=replace_id, + upload_option=upload_option, + show_deleted=show_deleted, + message=util.sanitize_text( message ), + status='error' ) ) else: # See if we have any inherited templates, but do not inherit contents. @@ -722,13 +738,13 @@ class LibraryCommon( BaseController ): template_id = 'None' widgets = [] created_outputs_dict = trans.webapp.controllers[ 'library_common' ].upload_dataset( trans, - cntrller=cntrller, - library_id=library_id, - folder_id=folder_id, - template_id=template_id, - widgets=widgets, - replace_dataset=replace_dataset, - **kwd ) + cntrller=cntrller, + library_id=library_id, + folder_id=folder_id, + template_id=template_id, + widgets=widgets, + replace_dataset=replace_dataset, + **kwd ) if created_outputs_dict: total_added = len( created_outputs_dict.keys() ) ldda_id_list = [ str( v.id ) for k, v in created_outputs_dict.items() ] @@ -1094,6 +1110,8 @@ class LibraryCommon( BaseController ): library = trans.sa_session.query( trans.app.model.Library ).get( trans.security.decode_id( library_id ) ) roles = trans.app.security_agent.get_legitimate_roles( trans, library, cntrller ) return trans.fill_template( "/library/common/upload.mako", + action='add_history_datasets_to_library', + cntrller=cntrller, upload_option=upload_option, library_id=library_id, folder_id=folder_id, @@ -1877,9 +1895,24 @@ def activatable_folders_and_lddas( trans .all() return folders, lddas def branch_deleted( folder ): - # Return True if a folder belongs to a branc that has been deleted + # Return True if a folder belongs to a branch that has been deleted if folder.deleted: return True if folder.parent: return branch_deleted( folder.parent ) return False +def get_containing_library_from_library_dataset( trans, library_dataset ): + """Given a library_dataset, get the containing library""" + folder = library_dataset.folder + parent = folder + while folder.parent: + parent = folder.parent + # We have parent set to the library's root folder, which has the + # same name as the library + for library in trans.sa_session.query( trans.model.Library ) \ + .filter( and_( trans.model.Library.table.c.deleted == False, + trans.model.Library.table.c.name == parent.name ) ): + if library.root_folder == parent: + return library + return None + --- a/templates/library/common/ldda_info.mako +++ b/templates/library/common/ldda_info.mako @@ -3,7 +3,8 @@ <%namespace file="/library/common/common.mako" import="render_template_info" /><% from galaxy import util - from galaxy.web.controllers.library_common import branch_deleted + from galaxy.web.controllers.library_common import branch_deleted, get_containing_library_from_library_dataset + from galaxy.web.framework.helpers import time_ago if ldda == ldda.library_dataset.library_dataset_dataset_association: current_version = True @@ -64,11 +65,13 @@ %endif </div><div class="toolFormBody"> - <div class="form-row"> - <label>Message:</label> - <pre>${ldda.message}</pre> - <div style="clear: both"></div> - </div> + %if ldda.message: + <div class="form-row"> + <label>Message:</label> + <pre>${ldda.message}</pre> + <div style="clear: both"></div> + </div> + %endif <div class="form-row"><label>Uploaded by:</label> ${uploaded_by} @@ -80,6 +83,11 @@ <div style="clear: both"></div></div><div class="form-row"> + <label>File size:</label> + ${ldda.get_size( nice_size=True )} + <div style="clear: both"></div> + </div> + <div class="form-row"><label>Data type:</label> ${ldda.ext} <div style="clear: both"></div> @@ -97,6 +105,20 @@ <div class="form-row"><div>${ldda.blurb}</div></div> + %for name, spec in ldda.metadata.spec.items(): + <div class="form-row"> + <label>${spec.desc.replace( ' (click box & select)', '' )}:</label> + <% + metadata_val = ldda.metadata.get( name ) + if isinstance( metadata_val, trans.model.MetadataFile ): + metadata_val = metadata_val.file_name + elif isinstance( metadata_val, list ): + metadata_val = ', '.join( metadata_val ) + %> + ${metadata_val} + <div style="clear: both"></div> + </div> + %endfor %if ldda.peek != "no peek": <div class="form-row"><div id="info${ldda.id}" class="historyItemBody"> @@ -110,6 +132,79 @@ %if widgets: ${render_template_info( cntrller=cntrller, item_type='ldda', library_id=library_id, widgets=widgets, info_association=info_association, inherited=inherited, folder_id=trans.security.encode_id( ldda.library_dataset.folder.id ), ldda_id=trans.security.encode_id( ldda.id ), editable=False )} %endif +%if cntrller == 'library_admin': + %if associated_hdas: + <p/> + <b>History items that use this library dataset's disk file</b> + <div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>History</th> + <th>History Item</th> + <th>Last Updated</th> + <th>User</th> + </tr> + </thead> + %for hda in associated_hdas: + <tr> + <td><a target="_blank" href="${h.url_for( controller='history', action='view', id=trans.security.encode_id( hda.history.id ) )}">${hda.history.get_display_name()}</a></td> + <td>${hda.get_display_name()}</td> + <td>${time_ago( hda.update_time )}</td> + <td> + %if hda.history.user: + ${hda.history.user.email} + %else: + anonymous + %endif + </td> + </tr> + %endfor + </table> + </div> + <p/> + %endif + %if associated_lddas: + <p/> + <b>Other library datasets that use this library dataset's disk file</b> + <div class="toolForm"> + <table class="grid"> + <thead> + <tr> + <th>Library</th> + <th>Library Folder</th> + <th>Library Dataset</th> + <th>Last Updated</th> + <th>User</th> + </tr> + </thead> + %for copied_ldda in associated_lddas: + <% containing_library = get_containing_library_from_library_dataset( trans, copied_ldda.library_dataset ) %> + <tr> + <td> + %if containing_library: + <a href="${h.url_for( controller='library_common', action='browse_library', id=trans.security.encode_id( containing_library.id ), cntrller=cntrller, use_panels=use_panels )}">${containing_library.get_display_name()}</a> + %else: + error finding library + %endif + </td> + <td>${copied_ldda.library_dataset.folder.get_display_name()}</td> + <td>${copied_ldda.get_display_name()}</td> + <td>${time_ago( copied_ldda.update_time )}</td> + <td> + %if copied_ldda.user: + ${copied_ldda.user.email} + %else: + anonymous + %endif + </td> + </tr> + %endfor + </table> + </div> + <p/> + %endif +%endif %if current_version: <% expired_lddas = [ e_ldda for e_ldda in ldda.library_dataset.expired_datasets ] %> %if expired_lddas:

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galaxy-dist commit ea2658d131b4: Fix for LibraryDatasetDatasetAssociation objects when created by importing a history item iinto a library, the copied_from_history_dataset_association_id will now be kept.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '10

# HG changeset patch -- Bitbucket.org # Project galaxy-dist # URL http://bitbucket.org/galaxy/galaxy-dist/overview # User Greg Von Kuster <greg(a)bx.psu.edu> # Date 1275503088 14400 # Node ID ea2658d131b4c54fca14cdf2b5a66fbf128eaf40 # Parent cea1569d9efd3f89188f455e9eb101ac3ce48594 Fix for LibraryDatasetDatasetAssociation objects when created by importing a history item iinto a library, the copied_from_history_dataset_association_id will now be kept. Add a get_display_name() method to the LibraryDatasetDatasetAssociation class. Fix for the test_forms_and_requests.py functional test script, purge all created libraries created during the tests so following test runs will test correctly. --- a/lib/galaxy/model/__init__.py +++ b/lib/galaxy/model/__init__.py @@ -932,7 +932,7 @@ class LibraryFolder( object ): return [ ld for ld in self.datasets if not ld.library_dataset_dataset_association.dataset.deleted ] @property def active_datasets( self ): - # This needs to be a list + # This needs to be a list return [ ld.library_dataset_dataset_association.dataset for ld in self.datasets if not ld.library_dataset_dataset_association.deleted ] def get_display_name( self ): # Library folder name can be either a string or a unicode object. If string, @@ -997,8 +997,10 @@ class LibraryDatasetDatasetAssociation( # FIXME: sa_session is must be passed to DataSetInstance if the create_dataset # parameter in kwd is True so that the new object can be flushed. Is there a better way? DatasetInstance.__init__( self, sa_session=sa_session, **kwd ) - self.copied_from_history_dataset_association = copied_from_history_dataset_association - self.copied_from_library_dataset_dataset_association = copied_from_library_dataset_dataset_association + if copied_from_history_dataset_association: + self.copied_from_history_dataset_association_id = copied_from_history_dataset_association.id + if copied_from_library_dataset_dataset_association: + self.copied_from_library_dataset_dataset_association_id = copied_from_library_dataset_dataset_association.id self.library_dataset = library_dataset self.user = user def to_history_dataset_association( self, target_history, parent_id = None, add_to_history = False ): @@ -1085,6 +1087,15 @@ class LibraryDatasetDatasetAssociation( else: return template.get_widgets( trans.user ) return [] + def get_display_name( self ): + """ + LibraryDatasetDatasetAssociation name can be either a string or a unicode object. + If string, convert to unicode object assuming 'utf-8' format. + """ + ldda_name = self.name + if isinstance( ldda_name, str ): + ldda_name = unicode( ldda_name, 'utf-8' ) + return ldda_name class LibraryInfoAssociation( object ): def __init__( self, library, form_definition, info, inheritable=False ): --- a/test/functional/test_forms_and_requests.py +++ b/test/functional/test_forms_and_requests.py @@ -382,6 +382,16 @@ class TestFormsAndRequests( TwillTestCas sa_session.delete( a ) sa_session.flush() ################## + # Purge all libraries + ################## + for library in [ library_one ]: + self.delete_library_item( 'library_admin', + self.security.encode_id( library.id ), + self.security.encode_id( library.id ), + library.name, + item_type='library' ) + self.purge_library( self.security.encode_id( library.id ), library.name ) + ################## # Eliminate all non-private roles ################## for role in [ role_one, role_two ]:

1 0

galaxy-dist commit 6d218af7906a: Add history import and export functionality to Galaxy. Options for exporting the current history to a file or importing a history from a file are now listed in the history options menu. Also modified the form builder to support file inputs.
by commits-noreply＠bitbucket.org 07 Jun '10

07 Jun '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 1275581854 14400 # Node ID 6d218af7906af1f9524d02f785885bf1fd508f16 # Parent a12eeed213ff6d8581073ad77914b12dfc26f9bd Add history import and export functionality to Galaxy. Options for exporting the current history to a file or importing a history from a file are now listed in the history options menu. Also modified the form builder to support file inputs. --- a/templates/root/index.mako +++ b/templates/root/index.mako @@ -35,12 +35,19 @@ "Show structure": function() { galaxy_main.location = "${h.url_for( controller='history', action='display_structured' )}"; }, + "Export to File": function() { + galaxy_main.location = "${h.url_for( controller='history', action='export_archive' )}"; + }, "Delete": function() { if ( confirm( "Really delete the current history?" ) ) { galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}"; } + }, + "Other Actions": null, + "Import from File": function() { + galaxy_main.location = "${h.url_for( controller='history', action='import_archive' )}"; } }); }); --- a/templates/form.mako +++ b/templates/form.mako @@ -55,7 +55,18 @@ <div class="form" style="margin: 1em"><div class="form-title">${form.title}</div><div class="form-body"> - <form name="${form.name}" action="${form.action}" method="post" > + <% + has_file_input = False + for input in form.inputs: + if input.type == 'file': + has_file_input = True + break + %> + <form name="${form.name}" action="${form.action}" method="post" + %if has_file_input: + enctype="multipart/form-data" + %endif + > %for input in form.inputs: <% cls = "form-row" --- /dev/null +++ b/database/export/info.txt @@ -0,0 +1,1 @@ +This folder contains the data that can be exported. --- a/lib/galaxy/web/controllers/history.py +++ b/lib/galaxy/web/controllers/history.py @@ -6,9 +6,10 @@ from galaxy.model.mapping import desc from galaxy.model.orm import * from galaxy.util.json import * from galaxy.util.sanitize_html import sanitize_html +from galaxy.tools.actions import upload_common from galaxy.tags.tag_handler import GalaxyTagHandler from sqlalchemy.sql.expression import ClauseElement -import webhelpers, logging, operator +import webhelpers, logging, operator, tempfile, subprocess, shutil from datetime import datetime from cgi import escape @@ -441,6 +442,226 @@ class HistoryController( BaseController, self.add_item_annotation( trans, history, new_annotation ) trans.sa_session.flush() return new_annotation + + @web.expose + def import_archive( self, trans, archived_history=None ): + """ Import a history. """ + + if archived_history is not None: + # Import archived history. + try: + archive_file = archived_history.file + + # Unpack archive in temporary directory. + temp_output_dir = tempfile.mkdtemp() + cmd = "pax -z -r < %s " % archive_file.name + temp_stderr_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name + temp_stderr = open( temp_stderr_name, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=temp_output_dir, stderr=temp_stderr.fileno() ) + returncode = proc.wait() + temp_stderr.close() + + # Read history attributes. + history_attr_in = open( '%s/%s' % ( temp_output_dir, 'history_attrs.txt'), 'rb' ) + history_attr_str = '' + buffsize = 1048576 + try: + while True: + history_attr_str += history_attr_in.read( buffsize ) + if not history_attr_str or len( history_attr_str ) % buffsize != 0: + break + except OverflowError: + pass + history_attrs = from_json_string( history_attr_str ) + + # Create history. + # TODO: set tags, annotations. + new_history = model.History( name='imported: %s' % history_attrs['name'].encode( 'utf-8' ), user=trans.user ) + trans.sa_session.add( new_history ) + trans.sa_session.flush() + # TODO: Ignore hid_counter for now since it just artificially increases the hid for all the history's HDAs. + #new_history.hid_counter = history_attrs['hid_counter'] + new_history.genome_build = history_attrs['genome_build'] + trans.sa_session.flush() + + # Read datasets attributes. + datasets_attr_in = open( '%s/%s' % ( temp_output_dir, 'datasets_attrs.txt'), 'rb' ) + datasets_attr_str = '' + buffsize = 1048576 + try: + while True: + datasets_attr_str += datasets_attr_in.read( buffsize ) + if not datasets_attr_str or len( datasets_attr_str ) % buffsize != 0: + break + except OverflowError: + pass + 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 = trans.app.model.HistoryDatasetAssociation( name = dataset_attrs['name'].encode( 'utf-8' ), + extension = dataset_attrs['extension'], + hid = dataset_attrs['hid'], + info = dataset_attrs['info'].encode( 'utf-8' ), + blurb = dataset_attrs['blurb'], + peek = dataset_attrs['peek'], + designation = dataset_attrs['designation'], + visible = dataset_attrs['visible'], + dbkey = metadata['dbkey'], + metadata = metadata, + history = new_history, + create_dataset = True, + sa_session = trans.sa_session ) + hda.state = hda.states.OK + trans.sa_session.add( hda ) + trans.sa_session.flush() + new_history.add_dataset( hda, genome_build = None ) + 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 ) + + # TODO: set tags, annotations. + + # 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 ) ) + + + return trans.show_form( + 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 ) + ) + + @web.expose + def export_archive( self, trans, id=None ): + """ Export a history. """ + + # Get history to export. + if id: + history = self.get_history( trans, id, check_ownership=False, check_accessible=True ) + else: + # Use current history. + history = trans.history + + if not history: + 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 ) ) + # TODO: for now, always create archive when exporting; this is for debugging purposes. + if True: + # Condition for only creating an archive when history is newer than archive: + #not os.path.exists ( archive_file_name ) or datetime.utcfromtimestamp( os.path.getmtime( archive_file_name ) ) < history.update_time: + + # Create archive and stream back to client. + + # Simple method to convert strings to unicode in utf-8 format. Method should be used for all user input. + def unicode_wrangler( a_string ): + a_string_type = type ( a_string ) + if a_string_type is str: + return unicode( a_string, 'utf-8' ) + elif a_string_type is unicode: + return a_string.encode( 'utf-8' ) + + try: + # Use temporary directory for temp output files. + temp_output_dir = tempfile.mkdtemp() + + # Write history attributes to file. + # TODO: include tags, annotations. + history_attrs = { + "create_time" : history.create_time.__str__(), + "update_time" : history.update_time.__str__(), + "name" : unicode_wrangler( history.name ), + "hid_counter" : history.hid_counter, + "genome_build" : history.genome_build + } + history_attrs_file_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name + history_attrs_out = open( history_attrs_file_name, 'w' ) + history_attrs_out.write( to_json_string( history_attrs ) ) + history_attrs_out.close() + new_name = '%s/%s' % ( temp_output_dir, "history_attrs.txt" ) + os.rename( history_attrs_file_name, new_name ) + history_attrs_file_name = new_name + + # Write datasets' attributes to file. + # TODO: include tags, annotations. + datasets = self.get_history_datasets( trans, history ) + datasets_attrs = [] + for dataset in datasets: + attribute_dict = { + "create_time" : dataset.create_time.__str__(), + "update_time" : dataset.update_time.__str__(), + "hid" : dataset.hid, + "name" : unicode_wrangler( dataset.name ), + "info" : unicode_wrangler( dataset.info ), + "blurb" : dataset.blurb, + "peek" : dataset.peek, + "extension" : dataset.extension, + "metadata" : dict( dataset.metadata.items() ), + "parent_id" : dataset.parent_id, + "designation" : dataset.designation, + "deleted" : dataset.deleted, + "visible" : dataset.visible, + "file_name" : dataset.file_name.split('/')[-1] + } + datasets_attrs.append( attribute_dict ) + 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 ) ) + datasets_attrs_out.close() + new_name = '%s/%s' % ( temp_output_dir, "datasets_attrs.txt" ) + os.rename( datasets_attrs_file_name, new_name ) + datasets_attrs_file_name = new_name + + # Write temp file with all files to archive. These files are (a) history attributes file; (b) datasets attributes file; and (c) + # datasets files. + archive_list_file_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name + archive_list_out = open( archive_list_file_name, 'w' ) + archive_list_out.write( '%s\n' % history_attrs_file_name ) + archive_list_out.write( '%s\n' % datasets_attrs_file_name ) + for dataset in datasets: + archive_list_out.write( '%s\n' % dataset.file_name ) + archive_list_out.close() + + # Use 'pax' to create compressed tar archive of history's datasets. -s options uses a regular expression to replace path + # information. + cmd = "pax -w -s ',.*history_attrs.txt,history_attrs.txt,' -s ',.*datasets_attrs.txt,datasets_attrs.txt,' -s ',/.*/,datasets/,' -x tar -z -f %s.tar.gz < %s" % ( trans.security.encode_id( history.id ), archive_list_file_name ) + temp_stderr_name = tempfile.NamedTemporaryFile( dir=temp_output_dir ).name + temp_stderr = open( temp_stderr_name, 'wb' ) + proc = subprocess.Popen( args=cmd, shell=True, cwd=history_export_dir_name, stderr=temp_stderr.fileno() ) + returncode = proc.wait() + temp_stderr.close() + + # Remove temp directory. + if os.path.exists( temp_output_dir ): + shutil.rmtree( temp_output_dir ) + + except Exception, e: + return trans.show_error_message( 'Error creating history archive. ' + str( e ) ) + + # Stream archive. + archive_file_name = '%s/%s.tar.gz' % ( history_export_dir_name, trans.security.encode_id( history.id ) ) + 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( archive_file_name ) + else: + return @web.expose @web.json

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galaxy-dist commit cea1569d9efd: add fly_modencode, worm_modencode, and wormbase tools to main
by commits-noreply＠bitbucket.org 01 Jun '10

01 Jun '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 1275405570 14400 # Node ID cea1569d9efd3f89188f455e9eb101ac3ce48594 # Parent f65470ca24068dfb7e8c4539e2c30f64402224c1 add fly_modencode, worm_modencode, and wormbase tools to main --- a/tool_conf.xml.main +++ b/tool_conf.xml.main @@ -9,6 +9,9 @@ <tool file="data_source/biomart.xml" /><tool file="data_source/gramene_mart.xml" /><tool file="data_source/flymine.xml" /> + <tool file="data_source/fly_modencode.xml" /> + <tool file="data_source/worm_modencode.xml" /> + <tool file="data_source/wormbase.xml" /><tool file="data_source/eupathdb.xml" /><tool file="data_source/encode_db.xml" /><tool file="data_source/epigraph_import.xml" />

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galaxy-dist commit bf51b81ec7b2: Add missing location files for buildbot
by commits-noreply＠bitbucket.org 01 Jun '10

01 Jun '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 1274977347 14400 # Node ID bf51b81ec7b25d05676a408d0d12e773d538ef10 # Parent fbb990ec01fa7ee3bd9b13ea3f610c8463ad64b8 Add missing location files for buildbot --- a/buildbot_setup.sh +++ b/buildbot_setup.sh @@ -25,6 +25,7 @@ case "$OSTYPE" in esac LINKS=" +/galaxy/data/location/add_scores.loc /galaxy/data/location/alignseq.loc /galaxy/data/annotation_profiler /galaxy/data/annotation_profiler/annotation_profiler.loc @@ -35,6 +36,7 @@ LINKS=" /galaxy/data/location/bowtie_indices.loc /galaxy/data/location/bowtie_indices_color.loc /galaxy/data/location/bwa_index.loc +/galaxy/data/location/codingSnps.loc /galaxy/data/location/encode_datasets.loc /galaxy/home/universe/encode_feature_partitions /galaxy/data/location/lastz_seqs.loc

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