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[hg] galaxy 2679: Eliminate buttons from shared history grid tha...
by Greg Von Kuster 15 Sep '09

15 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ed4cbaf23c88 changeset: 2679:ed4cbaf23c88 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Fri Sep 11 09:00:36 2009 -0400 description: Eliminate buttons from shared history grid that were not meant to be committed. 1 file(s) affected in this change: lib/galaxy/web/controllers/history.py diffs (35 lines): diff -r f0adb6152df9 -r ed4cbaf23c88 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Thu Sep 10 21:24:06 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Fri Sep 11 09:00:36 2009 -0400 @@ -104,9 +104,7 @@ ] operations = [ grids.GridOperation( "Clone" ), - grids.GridOperation( "Unshare" ), - grids.GridOperation( "Enable import via link", condition=( lambda item: item.deleted ) ), - grids.GridOperation( "Disable import via link", condition=( lambda item: item.deleted ) ) + grids.GridOperation( "Unshare" ) ] standard_filters = [] def build_initial_query( self, session ): @@ -280,20 +278,6 @@ association.flush() message = "Unshared %d shared histories" % len( ids ) status = 'done' - elif operation == "enable import via link": - if ids: - histories = [ get_history( trans, id ) for id in ids ] - for history in histories: - if not history.importable: - history.importable = True - history.flush() - elif operation == "disable import via link": - if ids: - histories = [ get_history( trans, id ) for id in ids ] - for history in histories: - if history.importable: - history.importable = False - history.flush() # Render the list view return self.shared_list_grid( trans, status=status, message=message, **kwargs ) @web.expose

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[hg] galaxy 2678: Streamline history sharing, add a "Manage shar...
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f0adb6152df9 changeset: 2678:f0adb6152df9 user: Greg Von Kuster <greg(a)bx.psu.edu> date: Thu Sep 10 21:24:06 2009 -0400 description: Streamline history sharing, add a "Manage shared histories" section to the History options menu. Also use a better approach to setting peek on datasets. 5 file(s) affected in this change: lib/galaxy/datatypes/data.py lib/galaxy/web/controllers/history.py templates/history/sharing.mako templates/root/index.mako test/functional/test_history_functions.py diffs (482 lines): diff -r 96ccd29277be -r f0adb6152df9 lib/galaxy/datatypes/data.py --- a/lib/galaxy/datatypes/data.py Thu Sep 10 17:48:52 2009 -0400 +++ b/lib/galaxy/datatypes/data.py Thu Sep 10 21:24:06 2009 -0400 @@ -416,8 +416,9 @@ count = 0 file_type = None data_checked = False - for line in file( file_name ): - line = line[:WIDTH] + temp = open( file_name, "U" ) + while count <= LINE_COUNT: + line = temp.readline( WIDTH ) if line and not is_multi_byte and not data_checked: # See if we have a compressed or binary file if line[0:2] == util.gzip_magic: @@ -432,9 +433,8 @@ if file_type in [ 'gzipped', 'binary' ]: break lines.append( line ) - if count == LINE_COUNT: - break count += 1 + temp.close() if file_type in [ 'gzipped', 'binary' ]: text = "%s file" % file_type else: diff -r 96ccd29277be -r f0adb6152df9 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Thu Sep 10 17:48:52 2009 -0400 +++ b/lib/galaxy/web/controllers/history.py Thu Sep 10 21:24:06 2009 -0400 @@ -4,7 +4,7 @@ from galaxy.model.mapping import desc from galaxy.model.orm import * from galaxy.util.json import * -import webhelpers, logging +import webhelpers, logging, operator from datetime import datetime from cgi import escape @@ -31,10 +31,12 @@ return "deleted" elif history.users_shared_with: return "shared" + elif history.importable: + return "importable" return "" def get_link( self, trans, grid, item ): - if item.users_shared_with: - return dict( operation="sharing", id=item.id ) + if item.users_shared_with or item.importable: + return dict( operation="sharing" ) return None # Grid definition title = "Stored histories" @@ -55,9 +57,12 @@ operations = [ grids.GridOperation( "Switch", allow_multiple=False, condition=( lambda item: not item.deleted ) ), grids.GridOperation( "Share", condition=( lambda item: not item.deleted ) ), + grids.GridOperation( "Unshare", condition=( lambda item: not item.deleted ) ), grids.GridOperation( "Rename", condition=( lambda item: not item.deleted ) ), grids.GridOperation( "Delete", condition=( lambda item: not item.deleted ) ), - grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ) + grids.GridOperation( "Undelete", condition=( lambda item: item.deleted ) ), + grids.GridOperation( "Enable import via link", condition=( lambda item: item.deleted ) ), + grids.GridOperation( "Disable import via link", condition=( lambda item: item.deleted ) ) ] standard_filters = [ grids.GridColumnFilter( "Active", args=dict( deleted=False ) ), @@ -99,7 +104,9 @@ ] operations = [ grids.GridOperation( "Clone" ), - grids.GridOperation( "Unshare" ) + grids.GridOperation( "Unshare" ), + grids.GridOperation( "Enable import via link", condition=( lambda item: item.deleted ) ), + grids.GridOperation( "Disable import via link", condition=( lambda item: item.deleted ) ) ] standard_filters = [] def build_initial_query( self, session ): @@ -126,19 +133,19 @@ current_history = trans.get_history() status = message = None if 'operation' in kwargs: - history_ids = util.listify( kwargs.get( 'id', [] ) ) - histories = [] operation = kwargs['operation'].lower() if operation == "share": return self.share( trans, **kwargs ) - elif operation == "rename": + if operation == "rename": return self.rename( trans, **kwargs ) - elif operation == 'sharing': - return self.sharing( trans, id=kwargs['id'] ) + history_ids = util.listify( kwargs.get( 'id', [] ) ) + if operation == "sharing": + return self.sharing( trans, id=history_ids ) # Display no message by default status, message = None, None refresh_history = False # Load the histories and ensure they all belong to the current user + histories = [] for history_id in history_ids: history = get_history( trans, history_id ) if history: @@ -161,6 +168,21 @@ trans.template_context['refresh_frames'] = ['history'] elif operation == "undelete": status, message = self._list_undelete( trans, histories ) + elif operation == "unshare": + for history in histories: + husas = trans.app.model.HistoryUserShareAssociation.filter_by( history=history ).all() + for husa in husas: + husa.delete() + elif operation == "enable import via link": + for history in histories: + if not history.importable: + history.importable = True + elif operation == "disable import via link": + if history_ids: + histories = [ get_history( trans, history_id ) for history_id in history_ids ] + for history in histories: + if history.importable: + history.importable = False trans.sa_session.flush() # Render the list view return self.stored_list_grid( trans, status=status, message=message, **kwargs ) @@ -237,24 +259,20 @@ msg = util.restore_text( kwargs.get( 'msg', '' ) ) status = message = None if 'operation' in kwargs: - id = kwargs.get( 'id', None ) + ids = util.listify( kwargs.get( 'id', [] ) ) operation = kwargs['operation'].lower() if operation == "clone": - if not id: + if not ids: message = "Select a history to clone" return self.shared_list_grid( trans, status='error', message=message, **kwargs ) # When cloning shared histories, only copy active datasets new_kwargs = { 'clone_choice' : 'active' } return self.clone( trans, id, **new_kwargs ) elif operation == 'unshare': - if not id: + if not ids: message = "Select a history to unshare" return self.shared_list_grid( trans, status='error', message=message, **kwargs ) - ids = util.listify( id ) - histories = [] - for history_id in ids: - history = get_history( trans, history_id, check_ownership=False ) - histories.append( history ) + histories = [ get_history( trans, history_id ) for history_id in ids ] for history in histories: # Current user is the user with which the histories were shared association = trans.app.model.HistoryUserShareAssociation.filter_by( user=trans.user, history=history ).one() @@ -262,6 +280,20 @@ association.flush() message = "Unshared %d shared histories" % len( ids ) status = 'done' + elif operation == "enable import via link": + if ids: + histories = [ get_history( trans, id ) for id in ids ] + for history in histories: + if not history.importable: + history.importable = True + history.flush() + elif operation == "disable import via link": + if ids: + histories = [ get_history( trans, id ) for id in ids ] + for history in histories: + if history.importable: + history.importable = False + history.flush() # Render the list view return self.shared_list_grid( trans, status=status, message=message, **kwargs ) @web.expose @@ -622,7 +654,9 @@ params = util.Params( kwd ) msg = util.restore_text ( params.get( 'msg', '' ) ) if id: - histories = [ get_history( trans, id ) ] + ids = util.listify( id ) + if ids: + histories = [ get_history( trans, history_id ) for history_id in ids ] for history in histories: if params.get( 'enable_import_via_link', False ): history.importable = True @@ -635,14 +669,34 @@ if not user: msg = 'History (%s) does not seem to be shared with user (%s)' % ( history.name, user.email ) return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='error' ) - association = trans.app.model.HistoryUserShareAssociation.filter_by( user=user, history=history ).one() - association.delete() - association.flush() - if not id: - shared_msg = "History (%s) now shared with: %d users. " % ( history.name, len( history.users_shared_with ) ) - msg = '%s%s' % ( shared_msg, msg ) + husas = trans.app.model.HistoryUserShareAssociation.filter_by( user=user, history=history ).all() + if husas: + for husa in husas: + husa.delete() + husa.flush() + histories = [] + # Get all histories that have been shared with others + husas = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \ + .join( "history" ) \ + .filter( and_( trans.app.model.History.user == trans.user, + trans.app.model.History.deleted == False ) ) \ + .order_by( trans.app.model.History.table.c.name ) \ + .all() + for husa in husas: + history = husa.history + if history not in histories: + histories.append( history ) + # Get all histories that are importable + importables = trans.sa_session.query( trans.app.model.History ) \ + .filter_by( user=trans.user, importable=True, deleted=False ) \ + .order_by( trans.app.model.History.table.c.name ) \ + .all() + for importable in importables: + if importable not in histories: + histories.append( importable ) + # Sort the list of histories by history.name + histories.sort( key=operator.attrgetter( 'name') ) return trans.fill_template( 'history/sharing.mako', histories=histories, msg=msg, messagetype='done' ) - @web.expose @web.require_login( "rename histories" ) def rename( self, trans, id=None, name=None, **kwd ): diff -r 96ccd29277be -r f0adb6152df9 templates/history/sharing.mako --- a/templates/history/sharing.mako Thu Sep 10 17:48:52 2009 -0400 +++ b/templates/history/sharing.mako Thu Sep 10 21:24:06 2009 -0400 @@ -1,75 +1,63 @@ <%inherit file="/base.mako"/> <%namespace file="/message.mako" import="render_msg" /> -<h2>Public access via link</h2> +##<h2>Import via link</h2> %if msg: ${render_msg( msg, messagetype )} %endif -%for history in histories: - <p> - %if history.importable: - Send the following URL to users as an easy way for them to import the history, making a copy of their own: - <% url = h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id), qualified=True ) %> - <blockquote> - <a href="${url}">${url}</a> - </blockquote> - <br/> - <form action="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ) )}" method="POST"> - <input class="action-button" type="submit" name="disable_import_via_link" value="Disable import via link"> - </form> - %else: - This history is currently restricted (only you and the users listed below - can access it). Enabling the following option will generate a URL that you - can give to a user to allow them to import this history. - <br/> - <form action="${h.url_for( action='sharing', id=trans.security.encode_id(history.id) )}" method="POST"> - <input class="action-button" type="submit" name="enable_import_via_link" value="Enable import via link"> - </form> - %endif - </p> - <h2>Sharing with specific users</h2> - %if history.users_shared_with: - <ul class="manage-table-actions"> - <li> - <a class="action-button" href="${h.url_for( controller='history', action='share', id=trans.security.encode_id( history.id ) )}"> - <span>Share with another user</span> - </a> - </li> - </ul> - <p> - The following users will see this history in their list of histories - shared with them by others, and they will be able to create their own copy of it: - </p> - <table class="colored" border="0" cellspacing="0" cellpadding="0" width="100%"> - <tr class="header"> - <th>History '${history.name}' currently shared with</th> - <th></th> - </tr> - %for i, association in enumerate( history.users_shared_with ): - <% user = association.user %> - <tr> - <td> - ${user.email} - <a id="user-${i}-popup" class="popup-arrow" style="display: none;">▼</a> - </td> - <td> - %if len( histories ) == 1: - ## Only allow unsharing if we're dealing with 1 history, otherwise - ## page refreshes screw things up - <div popupmenu="user-${i}-popup"> - <a class="action-button" href="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ), unshare_user=trans.security.encode_id( user.id ) )}">Unshare</a> +<h2>Histories that you've shared with others or enabled to be imported</h2> + +%if not histories: + You have no histories that you've shared with others or enabled to be imported +%else: + %for history in histories: + <div class="toolForm"> + <div class="toolFormTitle">History '${history.name}' shared with</div> + <div class="toolFormBody"> + <div class="form-row"> + <div style="float: right;"> + <a class="action-button" href="${h.url_for( controller='history', action='share', id=trans.security.encode_id( history.id ) )}"> + <span>Share with another user</span> + </a> + </div> + </div> + %if history.users_shared_with: + %for i, association in enumerate( history.users_shared_with ): + <% user = association.user %> + <div class="form-row"> + <a class="action-button" href="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ), unshare_user=trans.security.encode_id( user.id ) )}">Unshare</a> + ${user.email} + </div> + %endfor + %endif + %if history.importable: + <div class="form-row"> + <% url = h.url_for( controller='history', action='imp', id=trans.security.encode_id(history.id), qualified=True ) %> + <a href="${url}">${url}</a> + <div class="toolParamHelp" style="clear: both;"> + Send the above URL to users as an easy way for them to import the history, making a copy of their own + </div> + </div> + <div class="form-row"> + <form action="${h.url_for( controller='history', action='sharing', id=trans.security.encode_id( history.id ) )}" method="POST"> + <div class="form-row"> + <input class="action-button" type="submit" name="disable_import_via_link" value="Disable import via link"> </div> - %endif - </td> - </tr> - %endfor - </table> - %else: - <p>You have not shared this history with any users.</p> - <a class="action-button" href="${h.url_for( controller='history', action='share', id=trans.security.encode_id(history.id) )}"> - <span>Share with another user</span> - </a> - %endif -%endfor + </form> + </div> + %else: + <form action="${h.url_for( action='sharing', id=trans.security.encode_id(history.id) )}" method="POST"> + <div class="form-row"> + <input class="action-button" type="submit" name="enable_import_via_link" value="Enable import via link"> + <div class="toolParamHelp" style="clear: both;"> + Click to generate a URL that you can give to a user to allow them to import this history, making a copy of their own + </div> + </div> + </form> + %endif + </div> + </div> + %endfor +%endif diff -r 96ccd29277be -r f0adb6152df9 templates/root/index.mako --- a/templates/root/index.mako Thu Sep 10 17:48:52 2009 -0400 +++ b/templates/root/index.mako Thu Sep 10 21:24:06 2009 -0400 @@ -9,9 +9,6 @@ "List your histories": null, "Stored by you": function() { galaxy_main.location = "${h.url_for( controller='history', action='list')}"; - }, - "Shared with you": function() { - galaxy_main.location = "${h.url_for( controller='history', action='list_shared')}"; }, "Current History": null, "Create new": function() { @@ -32,10 +29,19 @@ "Show deleted datasets": function() { galaxy_history.location = "${h.url_for( controller='root', action='history', show_deleted=True)}"; }, - "Delete": function() { - if ( confirm( "Really delete the current history?" ) ) { + "Delete": function() + { + if ( confirm( "Really delete the current history?" ) ) + { galaxy_main.location = "${h.url_for( controller='history', action='delete_current' )}"; } + }, + "Manage shared histories": null, + "Shared by you": function() { + galaxy_main.location = "${h.url_for( controller='history', action='list', operation='sharing' )}"; + }, + "Shared with you": function() { + galaxy_main.location = "${h.url_for( controller='history', action='list_shared')}"; } }); }); diff -r 96ccd29277be -r f0adb6152df9 test/functional/test_history_functions.py --- a/test/functional/test_history_functions.py Thu Sep 10 17:48:52 2009 -0400 +++ b/test/functional/test_history_functions.py Thu Sep 10 21:24:06 2009 -0400 @@ -141,14 +141,13 @@ check_str_after_submit='You cannot send histories to yourself.' ) # Share history3 with 1 valid user self.share_current_history( regular_user1.email, - check_str=history3.name, - check_str_after_submit='History (%s) now shared with: 1 users' % history3.name ) + check_str=history3.name ) # Check out list of histories to make sure history3 was shared - self.view_stored_active_histories( check_str='operation=sharing&id=%s">shared' % self.security.encode_id( history3.id ) ) + self.view_stored_active_histories( check_str='operation=sharing">shared' ) # Enable importing history3 via a URL self.enable_import_via_link( self.security.encode_id( history3.id ), check_str='Unshare', - check_str_after_submit='Send the following URL to users' ) + check_str_after_submit='Send the above URL to users' ) # Make sure history3 is now import-able history3.refresh() if not history3.importable: @@ -159,7 +158,7 @@ check_str_after_submit='You cannot import your own history.' ) # Disable the import link for history3 self.disable_import_via_link( self.security.encode_id( history3.id ), - check_str='Send the following URL to users', + check_str='Send the above URL to users', check_str_after_submit='Enable import via link' ) # Try importing history3 after disabling the URL self.import_history_via_url( self.security.encode_id( history3.id ), @@ -274,12 +273,10 @@ self.upload_file( '2.bed', dbkey='hg18' ) ids = '%s,%s' % ( self.security.encode_id( history3.id ), self.security.encode_id( history4.id ) ) emails = '%s,%s' % ( regular_user2.email, regular_user3.email ) - check_str_after_submit = 'History (%s) now shared with: 3 users.' % history3.name self.share_histories_with_users( ids, emails, check_str1='Share 2 histories', - check_str2=history4.name, - check_str_after_submit=check_str_after_submit ) + check_str2=history4.name ) self.logout() self.login( email=regular_user2.email ) # Shared history3 should be in regular_user2's list of shared histories @@ -342,12 +339,10 @@ """Testing sharing a restricted history by making the datasets public""" # Logged in as admin_user action_check_str = 'The following datasets can be shared with %s by updating their permissions' % regular_user1.email - action_check_str_after_submit = 'History (%s) now shared with: 1 users.' % history5.name # Current history is history5 self.share_current_history( regular_user1.email, action='public', - action_check_str=action_check_str, - action_check_str_after_submit=action_check_str_after_submit ) + action_check_str=action_check_str ) self.logout() self.login( email=regular_user1.email ) # Shared history5 should be in regular_user1's list of shared histories @@ -375,12 +370,10 @@ self.upload_file( '2.bed', dbkey='hg18' ) check_str_after_submit = 'The following datasets can be shared with %s with no changes' % regular_user2.email check_str_after_submit2 = 'The following datasets can be shared with %s by updating their permissions' % regular_user2.email - action_check_str_after_submit = 'History (%s) now shared with: 2 users.' % history5.name self.share_current_history( regular_user2.email, check_str_after_submit=check_str_after_submit, check_str_after_submit2=check_str_after_submit2, - action='private', - action_check_str_after_submit=action_check_str_after_submit ) + action='private' ) # We should now have a new sharing role global sharing_role role_name = 'Sharing role for: %s, %s' % ( admin_user.email, regular_user2.email ) @@ -470,12 +463,10 @@ check_str_after_submit = 'The following datasets can be shared with %s with no changes' % email check_str_after_submit2 = 'The following datasets can be shared with %s by updating their permissions' % email # history5 will be shared with regular_user1, regular_user2 and regular_user3 - action_check_str_after_submit = 'History (%s) now shared with: 3 users.' % history5.name self.share_current_history( email, check_str_after_submit=check_str_after_submit, check_str_after_submit2=check_str_after_submit2, - action='share_anyway', - action_check_str_after_submit=action_check_str_after_submit ) + action='share_anyway' ) # Check security on clone of history5 for regular_user2 self.logout() self.login( email=regular_user2.email )

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[hg] galaxy 2677: Merge
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/96ccd29277be changeset: 2677:96ccd29277be user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Sep 10 17:48:52 2009 -0400 description: Merge 0 file(s) affected in this change: diffs (69 lines): diff -r f2e4673d784b -r 96ccd29277be cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample Thu Sep 10 17:48:37 2009 -0400 +++ b/cron/updateucsc.sh.sample Thu Sep 10 17:48:52 2009 -0400 @@ -6,7 +6,8 @@ # Edit this line to refer to galaxy's path: GALAXY=/galaxy/path -export PYTHONPATH=${GALAXY}/lib +PYTHONPATH=${GALAXY}/lib +export PYTHONPATH # setup directories echo "Creating required directories." @@ -32,7 +33,11 @@ python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt + diff ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt + fi else echo "Failed to update builds.txt" >&2 fi @@ -42,7 +47,11 @@ python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt + diff ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt + fi else echo "Failed to update builds.txt" >&2 fi @@ -52,7 +61,16 @@ python ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/tool-data/shared/ucsc/chrom/new/ ${GALAXY}/tool-data/shared/ucsc/builds.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len ${GALAXY}/tool-data/shared/ucsc/chrom/ + for src in ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len + do + dst=${GALAXY}/tool-data/shared/ucsc/chrom/`basename $src` + diff $src $dst > /dev/null 2>&1 + if [ $? -ne 0 ] + then + echo "cp -f $src $dst" + cp -f $src $dst + fi + done else echo "Failed to update chromInfo tables." >&2 fi diff -r f2e4673d784b -r 96ccd29277be tools/new_operations/flanking_features.py --- a/tools/new_operations/flanking_features.py Thu Sep 10 17:48:37 2009 -0400 +++ b/tools/new_operations/flanking_features.py Thu Sep 10 17:48:52 2009 -0400 @@ -129,7 +129,7 @@ map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval elif result_up: map(outfields.append, result_up[res_ind].other) - else: + elif result_down: map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval yield outfields

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[hg] galaxy 2675: Support for (1) ordering tags and (2) page tags.
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/2a15e0eca0b9 changeset: 2675:2a15e0eca0b9 user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Sep 10 16:48:11 2009 -0400 description: Support for (1) ordering tags and (2) page tags. 5 file(s) affected in this change: lib/galaxy/model/__init__.py lib/galaxy/model/mapping.py lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py lib/galaxy/tags/tag_handler.py lib/galaxy/web/controllers/tag.py diffs (249 lines): diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/model/__init__.py --- a/lib/galaxy/model/__init__.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/model/__init__.py Thu Sep 10 16:48:11 2009 -0400 @@ -1145,7 +1145,8 @@ return "Tag(id=%s, type=%i, parent_id=%s, name=%s)" % ( self.id, self.type, self.parent_id, self.name ) class ItemTagAssociation ( object ): - def __init__( self, item_id=None, tag_id=None, user_tname=None, value=None ): + def __init__( self, id=None, item_id=None, tag_id=None, user_tname=None, value=None ): + self.id = id self.item_id = item_id self.tag_id = tag_id self.user_tname = user_tname @@ -1165,6 +1166,8 @@ class HistoryDatasetAssociationTagAssociation ( ItemTagAssociation ): pass +class PageTagAssociation ( ItemTagAssociation ): + pass ## ---- Utility methods ------------------------------------------------------- diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/model/mapping.py Thu Sep 10 16:48:11 2009 -0400 @@ -552,6 +552,7 @@ UniqueConstraint( "name" ) ) HistoryTagAssociation.table = Table( "history_tag_association", metadata, + Column( "id", Integer, primary_key=True ), Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), @@ -559,6 +560,7 @@ Column( "user_value", TrimmedString(255), index=True) ) DatasetTagAssociation.table = Table( "dataset_tag_association", metadata, + Column( "id", Integer, primary_key=True ), Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), @@ -566,7 +568,16 @@ Column( "user_value", TrimmedString(255), index=True) ) HistoryDatasetAssociationTagAssociation.table = Table( "history_dataset_association_tag_association", metadata, + Column( "id", Integer, primary_key=True ), Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +PageTagAssociation.table = Table( "page_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), Column( "user_tname", TrimmedString(255), index=True), Column( "value", TrimmedString(255), index=True), @@ -672,7 +683,7 @@ visible_children=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.parent_id == HistoryDatasetAssociation.table.c.id ) & ( HistoryDatasetAssociation.table.c.visible == True ) ) ), - tags=relation(HistoryDatasetAssociationTagAssociation, backref='history_tag_associations') + tags=relation(HistoryDatasetAssociationTagAssociation, order_by=HistoryDatasetAssociationTagAssociation.table.c.id, backref='history_tag_associations') ) ) assign_mapper( context, Dataset, Dataset.table, @@ -689,7 +700,7 @@ active_library_associations=relation( LibraryDatasetDatasetAssociation, primaryjoin=( ( Dataset.table.c.id == LibraryDatasetDatasetAssociation.table.c.dataset_id ) & ( LibraryDatasetDatasetAssociation.table.c.deleted == False ) ) ), - tags=relation(DatasetTagAssociation, backref='datasets') + tags=relation(DatasetTagAssociation, order_by=DatasetTagAssociation.table.c.id, backref='datasets') ) ) assign_mapper( context, HistoryDatasetAssociationDisplayAtAuthorization, HistoryDatasetAssociationDisplayAtAuthorization.table, @@ -709,7 +720,7 @@ properties=dict( galaxy_sessions=relation( GalaxySessionToHistoryAssociation ), datasets=relation( HistoryDatasetAssociation, backref="history", order_by=asc(HistoryDatasetAssociation.table.c.hid) ), active_datasets=relation( HistoryDatasetAssociation, primaryjoin=( ( HistoryDatasetAssociation.table.c.history_id == History.table.c.id ) & ( not_( HistoryDatasetAssociation.table.c.deleted ) ) ), order_by=asc( HistoryDatasetAssociation.table.c.hid ), viewonly=True ), - tags=relation(HistoryTagAssociation, backref="histories") + tags=relation(HistoryTagAssociation, order_by=HistoryTagAssociation.table.c.id, backref="histories") ) ) assign_mapper( context, HistoryUserShareAssociation, HistoryUserShareAssociation.table, @@ -967,7 +978,8 @@ primaryjoin=( Page.table.c.id == PageRevision.table.c.page_id ) ), latest_revision=relation( PageRevision, post_update=True, primaryjoin=( Page.table.c.latest_revision_id == PageRevision.table.c.id ), - lazy=False ) + lazy=False ), + tags=relation(PageTagAssociation, order_by=PageTagAssociation.table.c.id, backref="pages") ) ) assign_mapper( context, Tag, Tag.table, @@ -988,6 +1000,11 @@ properties=dict( tag=relation(Tag, backref="tagged_history_dataset_associations") ), primary_key=[HistoryDatasetAssociationTagAssociation.table.c.history_dataset_association_id, HistoryDatasetAssociationTagAssociation.table.c.tag_id] ) + +assign_mapper( context, PageTagAssociation, PageTagAssociation.table, + properties=dict( tag=relation(Tag, backref="tagged_pages") ), + primary_key=[PageTagAssociation.table.c.page_id, PageTagAssociation.table.c.tag_id] + ) def db_next_hid( self ): """ diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/lib/galaxy/model/migrate/versions/0018_ordered_tags_and_page_tags.py Thu Sep 10 16:48:11 2009 -0400 @@ -0,0 +1,116 @@ +""" +This migration script provides support for (a) ordering tags by recency and +(b) tagging pages. This script deletes all existing tags. +""" + +from sqlalchemy import * +from sqlalchemy.orm import * +from sqlalchemy.exceptions import * +from migrate import * +import migrate.changeset + +import datetime +now = datetime.datetime.utcnow + +# Need our custom types, but don't import anything else from model +from galaxy.model.custom_types import * + +import logging +log = logging.getLogger( __name__ ) + +metadata = MetaData( migrate_engine ) + +def display_migration_details(): + print "" + print "This migration script provides support for (a) ordering tags by recency and" + print "(b) tagging pages. This script deletes all existing tags." + +HistoryTagAssociation_table = Table( "history_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "history_id", Integer, ForeignKey( "history.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +DatasetTagAssociation_table = Table( "dataset_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "dataset_id", Integer, ForeignKey( "dataset.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +HistoryDatasetAssociationTagAssociation_table = Table( "history_dataset_association_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "history_dataset_association_id", Integer, ForeignKey( "history_dataset_association.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +PageTagAssociation_table = Table( "page_tag_association", metadata, + Column( "id", Integer, primary_key=True ), + Column( "page_id", Integer, ForeignKey( "page.id" ), index=True ), + Column( "tag_id", Integer, ForeignKey( "tag.id" ), index=True ), + Column( "user_tname", TrimmedString(255), index=True), + Column( "value", TrimmedString(255), index=True), + Column( "user_value", TrimmedString(255), index=True) ) + +def upgrade(): + display_migration_details() + metadata.reflect() + + # + # Recreate tables. + # + try: + HistoryTagAssociation_table.drop() + HistoryTagAssociation_table.create() + except Exception, e: + print "Recreating history_tag_association table failed: %s" % str( e ) + log.debug( "Recreating history_tag_association table failed: %s" % str( e ) ) + + try: + DatasetTagAssociation_table.drop() + DatasetTagAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Recreating dataset_tag_association table failed: %s" % str( e ) ) + + try: + HistoryDatasetAssociationTagAssociation_table.drop() + HistoryDatasetAssociationTagAssociation_table.create() + except OperationalError, e: + # Handle error that results from and index name that is too long; this occurs + # in MySQL. + if str(e).find("CREATE INDEX") != -1: + # Manually create index. + i = Index( "ix_hda_ta_history_dataset_association_id", HistoryDatasetAssociationTagAssociation_table.c.history_dataset_association_id ) + try: + i.create() + except Exception, e: + print str(e) + log.debug( "Adding index 'ix_hda_ta_history_dataset_association_id' to table 'history_dataset_association_tag_association' table failed: %s" % str( e ) ) + except Exception, e: + print str(e) + log.debug( "Recreating history_dataset_association_tag_association table failed: %s" % str( e ) ) + + # Create page_tag_association table. + try: + PageTagAssociation_table.create() + except Exception, e: + print str(e) + log.debug( "Creating page_tag_association table failed: %s" % str( e ) ) + +def downgrade(): + metadata.reflect() + + # No need to downgrade other tagging tables. They work fine with verision 16 code. + + # Drop page_tag_association table. + try: + PageTagAssociation_table.drop() + except Exception, e: + print str(e) + log.debug( "Dropping page_tag_association table failed: %s" % str( e ) ) diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/tags/tag_handler.py --- a/lib/galaxy/tags/tag_handler.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/tags/tag_handler.py Thu Sep 10 16:48:11 2009 -0400 @@ -1,4 +1,4 @@ -from galaxy.model import Tag, History, HistoryTagAssociation, Dataset, DatasetTagAssociation, HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation +from galaxy.model import Tag import re class TagHandler( object ): diff -r dbbc63c0630a -r 2a15e0eca0b9 lib/galaxy/web/controllers/tag.py --- a/lib/galaxy/web/controllers/tag.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/web/controllers/tag.py Thu Sep 10 16:48:11 2009 -0400 @@ -1,6 +1,9 @@ """ Tags Controller: handles tagging/untagging of entities and provides autocomplete support. """ + +from galaxy.model import History, HistoryTagAssociation, Dataset, DatasetTagAssociation, \ + HistoryDatasetAssociation, HistoryDatasetAssociationTagAssociation, Page, PageTagAssociation from galaxy.web.base.controller import * from galaxy.tags.tag_handler import *

1 0

[hg] galaxy 2676: merge
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/f2e4673d784b changeset: 2676:f2e4673d784b user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Thu Sep 10 17:48:37 2009 -0400 description: merge 0 file(s) affected in this change: diffs (151 lines): diff -r 2a15e0eca0b9 -r f2e4673d784b lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Sep 10 16:48:11 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Sep 10 17:48:37 2009 -0400 @@ -502,13 +502,6 @@ context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset ) #should this also be checking library associations? - can a library item be added from a history before the job has ended? - lets not allow this to occur for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running - if context.get( 'path', None ): - # The tool can set an alternate output path for the dataset. - try: - shutil.move( context['path'], dataset.file_name ) - except ( IOError, OSError ): - if not context['stderr']: - context['stderr'] = 'This dataset could not be processed' dataset.blurb = 'done' dataset.peek = 'no peek' dataset.info = context['stdout'] + context['stderr'] @@ -707,6 +700,13 @@ sizes.append( ( outfile, os.stat( outfile ).st_size ) ) return sizes def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, **kwds ): + # extension could still be 'auto' if this is the upload tool. + job = model.Job.get( self.job_id ) + for output_dataset_assoc in job.output_datasets: + if output_dataset_assoc.dataset.ext == 'auto': + context = self.get_dataset_finish_context( dict(), output_dataset_assoc.dataset.dataset ) + output_dataset_assoc.dataset.extension = context.get( 'ext', 'data' ) + mapping.context.current.flush() if tmp_dir is None: #this dir should should relative to the exec_dir tmp_dir = self.app.config.new_file_path @@ -716,7 +716,6 @@ config_root = self.app.config.root if datatypes_config is None: datatypes_config = self.app.config.datatypes_config - job = model.Job.get( self.job_id ) return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], exec_dir = exec_dir, tmp_dir = tmp_dir, dataset_files_path = dataset_files_path, config_root = config_root, datatypes_config = datatypes_config, **kwds ) class DefaultJobDispatcher( object ): diff -r 2a15e0eca0b9 -r f2e4673d784b lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Thu Sep 10 16:48:11 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Thu Sep 10 17:48:37 2009 -0400 @@ -144,7 +144,7 @@ job.add_parameter( name, value ) job.add_parameter( 'paramfile', to_json_string( json_file_path ) ) for i, dataset in enumerate( data_list ): - job.add_output_dataset( i, dataset ) + job.add_output_dataset( 'output%i' % i, dataset ) job.state = trans.app.model.Job.states.NEW trans.app.model.flush() diff -r 2a15e0eca0b9 -r f2e4673d784b tools/data_source/upload.py --- a/tools/data_source/upload.py Thu Sep 10 16:48:11 2009 -0400 +++ b/tools/data_source/upload.py Thu Sep 10 17:48:37 2009 -0400 @@ -115,7 +115,14 @@ return ( True, False, test_ext ) return ( True, True, test_ext ) -def add_file( dataset, json_file ): +def parse_outputs( args ): + rval = {} + for arg in args: + id, path = arg.split( ':', 1 ) + rval[int( id )] = path + return rval + +def add_file( dataset, json_file, output_path ): data_type = None line_count = None @@ -229,16 +236,18 @@ ext = dataset.ext if ext == 'auto': ext = 'data' + # Move the dataset to its "real" path + shutil.move( dataset.path, output_path ) + # Write the job info info = dict( type = 'dataset', dataset_id = dataset.dataset_id, - path = dataset.path, ext = ext, stdout = 'uploaded %s file' % data_type, name = dataset.name, line_count = line_count ) json_file.write( to_json_string( info ) + "\n" ) -def add_composite_file( dataset, json_file ): +def add_composite_file( dataset, json_file, output_path ): if dataset.composite_files: os.mkdir( dataset.extra_files_path ) for name, value in dataset.composite_files.iteritems(): @@ -253,17 +262,21 @@ else: sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] ) shutil.move( dataset.composite_file_paths[ value.name ][ 'path' ], os.path.join( dataset.extra_files_path, name ) ) + # Move the dataset to its "real" path + shutil.move( dataset.primary_file, output_path ) + # Write the job info info = dict( type = 'dataset', dataset_id = dataset.dataset_id, - path = dataset.primary_file, stdout = 'uploaded %s file' % dataset.file_type ) json_file.write( to_json_string( info ) + "\n" ) def __main__(): - if len( sys.argv ) != 2: - print >>sys.stderr, 'usage: upload.py <json paramfile>' + if len( sys.argv ) < 2: + print >>sys.stderr, 'usage: upload.py <json paramfile> <output spec> ...' sys.exit( 1 ) + + output_paths = parse_outputs( sys.argv[2:] ) json_file = open( 'galaxy.json', 'w' ) @@ -271,10 +284,16 @@ dataset = from_json_string( line ) dataset = util.bunch.Bunch( **safe_dict( dataset ) ) + try: + output_path = output_paths[int( dataset.dataset_id )] + except: + print >>sys.stderr, 'Output path for dataset %s not found on command line' % dataset.dataset_id + sys.exit( 1 ) + if dataset.type == 'composite': - add_composite_file( dataset, json_file ) + add_composite_file( dataset, json_file, output_path ) else: - add_file( dataset, json_file ) + add_file( dataset, json_file, output_path ) # clean up paramfile try: diff -r 2a15e0eca0b9 -r f2e4673d784b tools/data_source/upload.xml --- a/tools/data_source/upload.xml Thu Sep 10 16:48:11 2009 -0400 +++ b/tools/data_source/upload.xml Thu Sep 10 17:48:37 2009 -0400 @@ -7,6 +7,12 @@ <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> <command interpreter="python"> upload.py $paramfile + #set $outnum = 0 + #while $varExists('output%i' % $outnum): + #set $output = $getVar('output%i' % $outnum) + #set $outnum += 1 + ${output.dataset.dataset.id}:${output} + #end while </command> <inputs> <param name="file_type" type="select" label="File Format" help="Which format? See help below">

1 0

[hg] galaxy 2674: Bug fix for 'Fetch closest feature' tool.
by Greg Von Kuster 11 Sep '09

11 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0a41293e679a changeset: 2674:0a41293e679a user: guru date: Thu Sep 10 17:35:21 2009 -0400 description: Bug fix for 'Fetch closest feature' tool. 1 file(s) affected in this change: tools/new_operations/flanking_features.py diffs (12 lines): diff -r ce8c57840343 -r 0a41293e679a tools/new_operations/flanking_features.py --- a/tools/new_operations/flanking_features.py Thu Sep 10 17:31:05 2009 -0400 +++ b/tools/new_operations/flanking_features.py Thu Sep 10 17:35:21 2009 -0400 @@ -129,7 +129,7 @@ map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval elif result_up: map(outfields.append, result_up[res_ind].other) - else: + elif result_down: map(outfields.append, result_down[-1].other) #The last element of result_down will be the closest element to the given interval yield outfields

1 0

[hg] galaxy 2673: POSIXize/Bournize updateucsc.sh.sample
by Nate Coraor 10 Sep '09

10 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/ce8c57840343 changeset: 2673:ce8c57840343 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Sep 10 17:31:05 2009 -0400 description: POSIXize/Bournize updateucsc.sh.sample 1 file(s) affected in this change: cron/updateucsc.sh.sample diffs (57 lines): diff -r d3fe789e3931 -r ce8c57840343 cron/updateucsc.sh.sample --- a/cron/updateucsc.sh.sample Thu Sep 10 14:52:38 2009 -0400 +++ b/cron/updateucsc.sh.sample Thu Sep 10 17:31:05 2009 -0400 @@ -6,7 +6,8 @@ # Edit this line to refer to galaxy's path: GALAXY=/galaxy/path -export PYTHONPATH=${GALAXY}/lib +PYTHONPATH=${GALAXY}/lib +export PYTHONPATH # setup directories echo "Creating required directories." @@ -32,7 +33,11 @@ python ${GALAXY}/cron/parse_builds.py > ${GALAXY}/tool-data/shared/ucsc/new/builds.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt + diff ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ucsc/new/builds.txt ${GALAXY}/tool-data/shared/ucsc/builds.txt + fi else echo "Failed to update builds.txt" >&2 fi @@ -42,7 +47,11 @@ python ${GALAXY}/cron/parse_builds_3_sites.py > ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt + diff ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt > /dev/null 2>&1 + if [ $? -ne 0 ] + then + cp -f ${GALAXY}/tool-data/shared/ucsc/new/ucsc_build_sites.txt ${GALAXY}/tool-data/shared/ucsc/ucsc_build_sites.txt + fi else echo "Failed to update builds.txt" >&2 fi @@ -52,7 +61,16 @@ python ${GALAXY}/cron/build_chrom_db.py ${GALAXY}/tool-data/shared/ucsc/chrom/new/ ${GALAXY}/tool-data/shared/ucsc/builds.txt if [ $? -eq 0 ] then - cp -uf ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len ${GALAXY}/tool-data/shared/ucsc/chrom/ + for src in ${GALAXY}/tool-data/shared/ucsc/chrom/new/*.len + do + dst=${GALAXY}/tool-data/shared/ucsc/chrom/`basename $src` + diff $src $dst > /dev/null 2>&1 + if [ $? -ne 0 ] + then + echo "cp -f $src $dst" + cp -f $src $dst + fi + done else echo "Failed to update chromInfo tables." >&2 fi

1 0

[hg] galaxy 2672: Get rid of the hacky "alternate path" stuff us...
by Greg Von Kuster 10 Sep '09

10 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d3fe789e3931 changeset: 2672:d3fe789e3931 user: Nate Coraor <nate(a)bx.psu.edu> date: Thu Sep 10 14:52:38 2009 -0400 description: Get rid of the hacky "alternate path" stuff used by the upload tool and fix setting metadata when using autodetect and set_metadata_externally 4 file(s) affected in this change: lib/galaxy/jobs/__init__.py lib/galaxy/tools/actions/upload.py tools/data_source/upload.py tools/data_source/upload.xml diffs (151 lines): diff -r dbbc63c0630a -r d3fe789e3931 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/jobs/__init__.py Thu Sep 10 14:52:38 2009 -0400 @@ -502,13 +502,6 @@ context = self.get_dataset_finish_context( job_context, dataset_assoc.dataset.dataset ) #should this also be checking library associations? - can a library item be added from a history before the job has ended? - lets not allow this to occur for dataset in dataset_assoc.dataset.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running - if context.get( 'path', None ): - # The tool can set an alternate output path for the dataset. - try: - shutil.move( context['path'], dataset.file_name ) - except ( IOError, OSError ): - if not context['stderr']: - context['stderr'] = 'This dataset could not be processed' dataset.blurb = 'done' dataset.peek = 'no peek' dataset.info = context['stdout'] + context['stderr'] @@ -707,6 +700,13 @@ sizes.append( ( outfile, os.stat( outfile ).st_size ) ) return sizes def setup_external_metadata( self, exec_dir = None, tmp_dir = None, dataset_files_path = None, config_root = None, datatypes_config = None, **kwds ): + # extension could still be 'auto' if this is the upload tool. + job = model.Job.get( self.job_id ) + for output_dataset_assoc in job.output_datasets: + if output_dataset_assoc.dataset.ext == 'auto': + context = self.get_dataset_finish_context( dict(), output_dataset_assoc.dataset.dataset ) + output_dataset_assoc.dataset.extension = context.get( 'ext', 'data' ) + mapping.context.current.flush() if tmp_dir is None: #this dir should should relative to the exec_dir tmp_dir = self.app.config.new_file_path @@ -716,7 +716,6 @@ config_root = self.app.config.root if datatypes_config is None: datatypes_config = self.app.config.datatypes_config - job = model.Job.get( self.job_id ) return self.external_output_metadata.setup_external_metadata( [ output_dataset_assoc.dataset for output_dataset_assoc in job.output_datasets ], exec_dir = exec_dir, tmp_dir = tmp_dir, dataset_files_path = dataset_files_path, config_root = config_root, datatypes_config = datatypes_config, **kwds ) class DefaultJobDispatcher( object ): diff -r dbbc63c0630a -r d3fe789e3931 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Thu Sep 10 10:42:50 2009 -0400 +++ b/lib/galaxy/tools/actions/upload.py Thu Sep 10 14:52:38 2009 -0400 @@ -144,7 +144,7 @@ job.add_parameter( name, value ) job.add_parameter( 'paramfile', to_json_string( json_file_path ) ) for i, dataset in enumerate( data_list ): - job.add_output_dataset( i, dataset ) + job.add_output_dataset( 'output%i' % i, dataset ) job.state = trans.app.model.Job.states.NEW trans.app.model.flush() diff -r dbbc63c0630a -r d3fe789e3931 tools/data_source/upload.py --- a/tools/data_source/upload.py Thu Sep 10 10:42:50 2009 -0400 +++ b/tools/data_source/upload.py Thu Sep 10 14:52:38 2009 -0400 @@ -115,7 +115,14 @@ return ( True, False, test_ext ) return ( True, True, test_ext ) -def add_file( dataset, json_file ): +def parse_outputs( args ): + rval = {} + for arg in args: + id, path = arg.split( ':', 1 ) + rval[int( id )] = path + return rval + +def add_file( dataset, json_file, output_path ): data_type = None line_count = None @@ -229,16 +236,18 @@ ext = dataset.ext if ext == 'auto': ext = 'data' + # Move the dataset to its "real" path + shutil.move( dataset.path, output_path ) + # Write the job info info = dict( type = 'dataset', dataset_id = dataset.dataset_id, - path = dataset.path, ext = ext, stdout = 'uploaded %s file' % data_type, name = dataset.name, line_count = line_count ) json_file.write( to_json_string( info ) + "\n" ) -def add_composite_file( dataset, json_file ): +def add_composite_file( dataset, json_file, output_path ): if dataset.composite_files: os.mkdir( dataset.extra_files_path ) for name, value in dataset.composite_files.iteritems(): @@ -253,17 +262,21 @@ else: sniff.convert_newlines( dataset.composite_file_paths[ value.name ][ 'path' ] ) shutil.move( dataset.composite_file_paths[ value.name ][ 'path' ], os.path.join( dataset.extra_files_path, name ) ) + # Move the dataset to its "real" path + shutil.move( dataset.primary_file, output_path ) + # Write the job info info = dict( type = 'dataset', dataset_id = dataset.dataset_id, - path = dataset.primary_file, stdout = 'uploaded %s file' % dataset.file_type ) json_file.write( to_json_string( info ) + "\n" ) def __main__(): - if len( sys.argv ) != 2: - print >>sys.stderr, 'usage: upload.py <json paramfile>' + if len( sys.argv ) < 2: + print >>sys.stderr, 'usage: upload.py <json paramfile> <output spec> ...' sys.exit( 1 ) + + output_paths = parse_outputs( sys.argv[2:] ) json_file = open( 'galaxy.json', 'w' ) @@ -271,10 +284,16 @@ dataset = from_json_string( line ) dataset = util.bunch.Bunch( **safe_dict( dataset ) ) + try: + output_path = output_paths[int( dataset.dataset_id )] + except: + print >>sys.stderr, 'Output path for dataset %s not found on command line' % dataset.dataset_id + sys.exit( 1 ) + if dataset.type == 'composite': - add_composite_file( dataset, json_file ) + add_composite_file( dataset, json_file, output_path ) else: - add_file( dataset, json_file ) + add_file( dataset, json_file, output_path ) # clean up paramfile try: diff -r dbbc63c0630a -r d3fe789e3931 tools/data_source/upload.xml --- a/tools/data_source/upload.xml Thu Sep 10 10:42:50 2009 -0400 +++ b/tools/data_source/upload.xml Thu Sep 10 14:52:38 2009 -0400 @@ -7,6 +7,12 @@ <action module="galaxy.tools.actions.upload" class="UploadToolAction"/> <command interpreter="python"> upload.py $paramfile + #set $outnum = 0 + #while $varExists('output%i' % $outnum): + #set $output = $getVar('output%i' % $outnum) + #set $outnum += 1 + ${output.dataset.dataset.id}:${output} + #end while </command> <inputs> <param name="file_type" type="select" label="File Format" help="Which format? See help below">

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[hg] galaxy 2671: Updated manual builds will L. major (2005) gen...
by Greg Von Kuster 10 Sep '09

10 Sep '09

details: http://www.bx.psu.edu/hg/galaxy/rev/dbbc63c0630a changeset: 2671:dbbc63c0630a user: guru date: Thu Sep 10 10:42:50 2009 -0400 description: Updated manual builds will L. major (2005) genome. 1 file(s) affected in this change: tool-data/shared/ucsc/manual_builds.txt diffs (8 lines): diff -r c3b40f23a0e0 -r dbbc63c0630a tool-data/shared/ucsc/manual_builds.txt --- a/tool-data/shared/ucsc/manual_builds.txt Wed Sep 09 14:24:11 2009 -0400 +++ b/tool-data/shared/ucsc/manual_builds.txt Thu Sep 10 10:42:50 2009 -0400 @@ -664,3 +664,4 @@ baciAnth_AMES Bacillus anthracis str. Ames chr=5227293 shewOnei Shewanella oneidensis MR-1 plasmid_pMR-1=161613,chr=4969803 15217 Human herpesvirus 1 NC_001806=152261 +lMaj5 Leishmania major 2005 chr1=268984,chr2=355714,chr3=384518,chr4=441313,chr5=465823,chr6=516874,chr7=596348,chr8=574972,chr9=573441,chr10=570864,chr11=582575,chr12=675347,chr13=654604,chr14=622648,chr15=629514,chr16=714659,chr17=684831,chr18=739751,chr19=702212,chr20=742551,chr21=772974,chr22=716608,chr23=772567,chr24=840950,chr25=912849,chr26=1091579,chr27=1130447,chr28=1160128,chr29=1212674,chr30=1403454,chr31=1484336,chr32=1604650,chr33=1583673,chr34=1866754,chr35=2090491,chr36=2682183

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Logging and Debugging
by SHAUN WEBB 10 Sep '09

10 Sep '09

Hi, I am looking for more information on the options in the Logging and Debugging section of the universe_wsgi.ini file, in particular what are specific values to which I can set log_level in the first option "verbosity of log messages". I wish to turn off the debugging messages in the log file. Thanks Shaun Webb -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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