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[hg] galaxy 2964: Eliminate printing PYTHONPATH to stderr in the...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0d534da7f0ff changeset: 2964:0d534da7f0ff user: Greg Von Kuster <greg(a)bx.psu.edu> date: Wed Nov 04 13:09:37 2009 -0500 description: Eliminate printing PYTHONPATH to stderr in the cleanup_datasets.py script. diffstat: scripts/cleanup_datasets/cleanup_datasets.py | 1 - 1 files changed, 0 insertions(+), 1 deletions(-) diffs (11 lines): diff -r fdf07565eedf -r 0d534da7f0ff scripts/cleanup_datasets/cleanup_datasets.py --- a/scripts/cleanup_datasets/cleanup_datasets.py Wed Nov 04 12:58:48 2009 -0500 +++ b/scripts/cleanup_datasets/cleanup_datasets.py Wed Nov 04 13:09:37 2009 -0500 @@ -387,7 +387,6 @@ class CleanupDatasetsApplication( object ): """Encapsulates the state of a Universe application""" def __init__( self, database_connection=None, file_path=None ): - print >> sys.stderr, "python path is: " + ", ".join( sys.path ) if database_connection is None: raise Exception( "CleanupDatasetsApplication requires a database_connection value" ) if file_path is None:

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[hg] galaxy 2961: Quick fix for maf_utilities.src_split.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/adfcd8bb13d1 changeset: 2961:adfcd8bb13d1 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Nov 04 12:21:13 2009 -0500 description: Quick fix for maf_utilities.src_split. diffstat: lib/galaxy/tools/util/maf_utilities.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (12 lines): diff -r 91a3bbb52d7a -r adfcd8bb13d1 lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py Wed Nov 04 12:15:53 2009 -0500 +++ b/lib/galaxy/tools/util/maf_utilities.py Wed Nov 04 12:21:13 2009 -0500 @@ -23,7 +23,7 @@ fields = src.split( SRC_SPLIT_CHAR, 1 ) spec = fields.pop( 0 ) if fields: - chrom = fields + chrom = fields.pop( 0 ) else: chrom = spec return spec, chrom

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[hg] galaxy 2962: Fixed a bug in user info - adding new address
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/92d395c8614b changeset: 2962:92d395c8614b user: rc date: Wed Nov 04 12:30:36 2009 -0500 description: Fixed a bug in user info - adding new address diffstat: lib/galaxy/web/controllers/user.py | 114 +++++++++++++++++++++++--------------- templates/user/edit_address.mako | 2 +- templates/user/info.mako | 2 +- templates/user/new_address.mako | 33 +++++++++++ 4 files changed, 104 insertions(+), 47 deletions(-) diffs (200 lines): diff -r adfcd8bb13d1 -r 92d395c8614b lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Wed Nov 04 12:21:13 2009 -0500 +++ b/lib/galaxy/web/controllers/user.py Wed Nov 04 12:30:36 2009 -0500 @@ -272,7 +272,7 @@ user_address.country = util.restore_text(params.get('field_%i_country' % index, '')) user_address.phone = util.restore_text(params.get('field_%i_phone' % index, '')) user_address.flush() - trans.user.refresh() + trans.sa_session.refresh( user ) values.append(int(user_address.id)) elif value == unicode('none'): values.append('') @@ -618,57 +618,81 @@ # User not logged in, history group must be only public return trans.show_error_message( "You must be logged in to change your default permitted actions." ) @web.expose - def new_address( self, trans, short_desc='', name='', institution='', address1='', - address2='', city='', state='', postal_code='', country='', phone='' ): - if trans.app.config.require_login: - refresh_frames = [ 'masthead', 'history', 'tools' ] - else: - refresh_frames = [ 'masthead', 'history' ] + def new_address( self, trans, **kwd ): + params = util.Params( kwd ) + msg = util.restore_text( params.get( 'msg', '' ) ) + messagetype = params.get( 'messagetype', 'done' ) + admin_view = params.get( 'admin_view', 'False' ) + error = '' + user = trans.sa_session.query( trans.app.model.User ).get( int( params.get( 'user_id', None ) ) ) if not trans.app.config.allow_user_creation and not trans.user_is_admin(): return trans.show_error_message( 'User registration is disabled. Please contact your Galaxy administrator for an account.' ) - short_desc_error = name_error = institution_error = address1_error = city_error = None - address2_error = state_error = postal_code_error = country_error = phone_error = None - if short_desc: - if not len( short_desc ): - short_desc_error = 'Enter a short description for this address' - elif not len( name ): - name_error = 'Enter the full name' - elif not len( institution ): - institution_error = 'Enter the institution associated with the user' - elif not len ( address1 ): - address1_error = 'Enter the address' - elif not len( city ): - city_error = 'Enter the city' - elif not len( state ): - state_error = 'Enter the state/province/region' - elif not len( postal_code ): - postal_code_error = 'Enter the postal code' - elif not len( country ): - country_error = 'Enter the country' + if params.get( 'save_new_address_button', None ) == 'Save': + if not len( util.restore_text( params.get( 'short_desc', '' ) ) ): + error = 'Enter a short description for this address' + elif not len( util.restore_text( params.get( 'name', '' ) ) ): + error = 'Enter the full name' + elif not len( util.restore_text( params.get( 'institution', '' ) ) ): + error = 'Enter the institution associated with the user' + elif not len ( util.restore_text( params.get( 'address1', '' ) ) ): + error = 'Enter the address' + elif not len( util.restore_text( params.get( 'city', '' ) ) ): + error = 'Enter the city' + elif not len( util.restore_text( params.get( 'state', '' ) ) ): + error = 'Enter the state/province/region' + elif not len( util.restore_text( params.get( 'postal_code', '' ) ) ): + error = 'Enter the postal code' + elif not len( util.restore_text( params.get( 'country', '' ) ) ): + error = 'Enter the country' else: - user_address = trans.app.model.UserAddress( user=trans.user, desc=short_desc, - name=name, institution=institution, - address=address1+' '+address2, city=city, - state=state, postal_code=postal_code, - country=country, phone=phone) + user_address = trans.app.model.UserAddress( user=user ) + user_address.desc = util.restore_text( params.get( 'short_desc', '' ) ) + user_address.name = util.restore_text( params.get( 'name', '' ) ) + user_address.institution = util.restore_text( params.get( 'institution', '' ) ) + user_address.address = util.restore_text( params.get( 'address1', '' ) )+' '+util.restore_text( params.get( 'address2', '' ) ) + user_address.city = util.restore_text( params.get( 'city', '' ) ) + user_address.state = util.restore_text( params.get( 'state', '' ) ) + user_address.postal_code = util.restore_text( params.get( 'postal_code', '' ) ) + user_address.country = util.restore_text( params.get( 'country', '' ) ) + user_address.phone = util.restore_text( params.get( 'phone', '' ) ) user_address.flush() + msg = 'Address <b>%s</b> has been added' % user_address.desc + if admin_view == 'True': + return trans.response.send_redirect( web.url_for( controller='user', + action='show_info', + admin_view=True, + user_id=user.id, + msg=msg, + messagetype='done') ) return trans.response.send_redirect( web.url_for( controller='user', action='show_info', - msg='Address <b>%s</b> has been added' % user_address.desc, + msg=msg, messagetype='done') ) - - return trans.show_form( - web.FormBuilder( web.url_for(), "New address", submit_text="Save" ) - .add_text( "short_desc", "Short address description", value=short_desc, error=short_desc_error ) - .add_text( "name", "Name", value=name, error=name_error ) - .add_text( "institution", "Institution", value=institution, error=institution_error ) - .add_text( "address1", "Address Line 1", value=address1, error=address1_error ) - .add_text( "address2", "Address Line 2", value=address2, error=address2_error ) - .add_text( "city", "City", value=city, error=city_error ) - .add_text( "state", "State/Province/Region", value=state, error=state_error ) - .add_text( "postal_code", "Postal Code", value=postal_code, error=postal_code_error ) - .add_text( "country", "Country", value=country, error=country_error ) - .add_text( "phone", "Phone", value=phone, error=phone_error ) ) + else: + # show the address form with the current values filled in + # create the widgets for each address field + widgets = [] + widgets.append(dict(label='Short description', + widget=TextField( 'short_desc', 40, '' ) ) ) + widgets.append(dict(label='Name', + widget=TextField( 'name', 40, '' ) ) ) + widgets.append(dict(label='Institution', + widget=TextField( 'institution', 40, '' ) ) ) + widgets.append(dict(label='Address Line 1', + widget=TextField( 'address1', 40, '' ) ) ) + widgets.append(dict(label='City', + widget=TextField( 'city', 40, '' ) ) ) + widgets.append(dict(label='State', + widget=TextField( 'state', 40, '' ) ) ) + widgets.append(dict(label='Postal Code', + widget=TextField( 'postal_code', 40, '' ) ) ) + widgets.append(dict(label='Country', + widget=TextField( 'country', 40, '' ) ) ) + widgets.append(dict(label='Phone', + widget=TextField( 'phone', 40, '' ) ) ) + return trans.fill_template( 'user/new_address.mako', user=user, + admin_view=admin_view, + widgets=widgets, msg=msg, messagetype=messagetype) @web.expose def edit_address( self, trans, **kwd ): params = util.Params( kwd ) diff -r adfcd8bb13d1 -r 92d395c8614b templates/user/edit_address.mako --- a/templates/user/edit_address.mako Wed Nov 04 12:21:13 2009 -0500 +++ b/templates/user/edit_address.mako Wed Nov 04 12:30:36 2009 -0500 @@ -11,7 +11,7 @@ <ul class="manage-table-actions"> <li> - <a class="action-button" href="${h.url_for( controller='user', action='show_info')}"> + <a class="action-button" href="${h.url_for( controller='user', action='show_info', admin_view=admin_view, user_id=user.id)}"> <span>Manage User Information</span></a> </li> </ul> diff -r adfcd8bb13d1 -r 92d395c8614b templates/user/info.mako --- a/templates/user/info.mako Wed Nov 04 12:21:13 2009 -0500 +++ b/templates/user/info.mako Wed Nov 04 12:30:36 2009 -0500 @@ -99,7 +99,7 @@ </div> </form> %endif - <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address' )}" method="post" > + <form name="user_info" id="user_info" action="${h.url_for( controller='user', action='new_address', user_id=user.id, admin_view=admin_view )}" method="post" > <div class="toolFormTitle">User Addresses</div> <div class="toolFormBody"> %if user.addresses: diff -r adfcd8bb13d1 -r 92d395c8614b templates/user/new_address.mako --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/templates/user/new_address.mako Wed Nov 04 12:30:36 2009 -0500 @@ -0,0 +1,33 @@ +<%inherit file="/base.mako"/> +<%namespace file="/message.mako" import="render_msg" /> + + +%if msg: + ${render_msg( msg, messagetype )} +%endif +</br> +</br> +<h3>New address</h3> + +<ul class="manage-table-actions"> + <li> + <a class="action-button" href="${h.url_for( controller='user', action='show_info', admin_view=admin_view, user_id=user.id)}"> + <span>Manage User Information</span></a> + </li> +</ul> +<div class="toolForm"> +<form name="login_info" id="login_info" action="${h.url_for( controller='user', action='new_address', admin_view=admin_view, user_id=user.id )}" method="post" > + <div class="toolFormTitle">New address</div> + <div class="toolFormBody"> + %for field in widgets: + <div class="form-row"> + <label>${field[ 'label' ]}</label> + ${field[ 'widget' ].get_html()} + </div> + %endfor + <div class="form-row"> + <input type="submit" name="save_new_address_button" value="Save"> + </div> + </div> +</form> +</div> \ No newline at end of file

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[hg] galaxy 2963: Add the GeneTrack egg. Also includes some enh...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/fdf07565eedf changeset: 2963:fdf07565eedf user: Nate Coraor <nate(a)bx.psu.edu> date: Wed Nov 04 12:58:48 2009 -0500 description: Add the GeneTrack egg. Also includes some enhancements and cleanup of the eggs/fetch/scramble code. diffstat: dist-eggs.ini | 4 + eggs.ini | 5 +- lib/galaxy/config.py | 13 +++ lib/galaxy/eggs/__init__.py | 149 ++++++++++++++---------------------- scripts/fetch_eggs.py | 36 ++++---- scripts/scramble.py | 28 +++--- scripts/scramble/scripts/GeneTrack.py | 52 +++++++++++++ 7 files changed, 164 insertions(+), 123 deletions(-) diffs (490 lines): diff -r 92d395c8614b -r fdf07565eedf dist-eggs.ini --- a/dist-eggs.ini Wed Nov 04 12:30:36 2009 -0500 +++ b/dist-eggs.ini Wed Nov 04 12:58:48 2009 -0500 @@ -57,3 +57,7 @@ all = py2.4-all py2.5-all py2.6-all ; default hosts for platform-inspecific eggs noplatform = py2.4-linux-i686-ucs4 py2.5-linux-i686-ucs4 py2.6-linux-i686-ucs4 + +[ignore] +; Don't build these eggs on these platforms: +GeneTrack = py2.4-noplatform diff -r 92d395c8614b -r fdf07565eedf eggs.ini --- a/eggs.ini Wed Nov 04 12:30:36 2009 -0500 +++ b/eggs.ini Wed Nov 04 12:58:48 2009 -0500 @@ -9,7 +9,7 @@ [general] repository = http://eggs.g2.bx.psu.edu ; these eggs must be scrambled for your local environment -no_download = pbs_python DRMAA_python +no_auto = pbs_python DRMAA_python [eggs:platform] bx_python = 0.5.0 @@ -31,6 +31,7 @@ decorator = 3.1.2 docutils = 0.4 elementtree = 1.2.6_20050316 +GeneTrack = 2.0.0_beta_1 lrucache = 0.2 ;lsprof - james Mako = 0.2.5 @@ -61,6 +62,7 @@ python_lzo = _static flup = .dev_r2311 bx_python = _dev_r4bf1f32e6b76 +GeneTrack = _dev_raa786e9fc131d998e532a1aef39d108850c9e93d ; nose = .dev_r7156749efc58 ; source location, necessary for scrambling @@ -81,6 +83,7 @@ decorator = http://pypi.python.org/packages/source/d/decorator/decorator-3.1.2.tar.gz docutils = http://downloads.sourceforge.net/docutils/docutils-0.4.tar.gz elementtree = http://effbot.org/downloads/elementtree-1.2.6-20050316.tar.gz +GeneTrack = http://github.com/ialbert/genetrack-central/tarball/aa786e9fc131d998e532a1a… lrucache = http://evan.prodromou.name/lrucache/lrucache-0.2.tar.gz Mako = http://www.makotemplates.org/downloads/Mako-0.2.5.tar.gz MyghtyUtils = http://cheeseshop.python.org/packages/source/M/MyghtyUtils/MyghtyUtils-0.52… diff -r 92d395c8614b -r fdf07565eedf lib/galaxy/config.py --- a/lib/galaxy/config.py Wed Nov 04 12:30:36 2009 -0500 +++ b/lib/galaxy/config.py Wed Nov 04 12:58:48 2009 -0500 @@ -8,6 +8,9 @@ import ConfigParser from galaxy.util import string_as_bool +from galaxy import eggs +import pkg_resources + log = logging.getLogger( __name__ ) def resolve_path( path, root ): @@ -126,6 +129,16 @@ for path in self.tool_config, self.datatypes_config: if not os.path.isfile(path): raise ConfigurationError("File not found: %s" % path ) + # Check job runners so the admin can scramble dependent egg. + if self.start_job_runners is not None: + runner_to_egg = dict( pbs = 'pbs_python', sge = 'DRMAA_python' ) + for runner in self.start_job_runners.split( ',' ): + try: + pkg_resources.require( runner_to_egg[runner] ) + except eggs.EggNotFetchable, e: + raise eggs.EggNotFetchable( 'You must scramble the %s egg to use the %s job runner. Instructions are available at:\n http://bitbucket.org/galaxy/galaxy-central/wiki/Config/Cluster' % ( runner_to_egg[runner], runner ) ) + except KeyError: + raise Exception( 'No such job runner: %s. Please double-check the value of start_job_runners in universe_wsgi.ini' % runner ) def is_admin_user( self,user ): """ diff -r 92d395c8614b -r fdf07565eedf lib/galaxy/eggs/__init__.py --- a/lib/galaxy/eggs/__init__.py Wed Nov 04 12:30:36 2009 -0500 +++ b/lib/galaxy/eggs/__init__.py Wed Nov 04 12:58:48 2009 -0500 @@ -14,11 +14,12 @@ # within tools. i don't know of any way around this. -ndc galaxy_dir = os.path.abspath( os.path.join( os.path.dirname( __file__ ), "..", "..", ".." ) ) -class NewEgg( Exception ): - pass - class EggNotFetchable( Exception ): - pass + def __init__( self, eggs ): + if type( eggs ) in ( list, tuple ): + self.eggs = eggs + else: + self.eggs = [ eggs ] class PlatformNotSupported( Exception ): pass @@ -157,6 +158,14 @@ # scramble helper methods def get_archive_path( self, url ): return os.path.join( Egg.archive_dir, (url.rsplit( '/', 1 ))[1] ) + def get_tld( self, names ): + tld = names[0].split( os.path.sep, 1 )[0] + for name in names: + try: + assert tld == name.split( os.path.sep, 1 )[0] + except: + raise Exception( "get_tld(): Archive contains multiple top-level directories!" ) + return tld def fetch_source( self ): if not os.access( Egg.archive_dir, os.F_OK ): os.makedirs( Egg.archive_dir ) @@ -195,7 +204,7 @@ log.warning( " %s" % self.buildpath ) def unpack_zip( self, source_path, unpack_path ): z = zipfile.ZipFile( source_path, "r" ) - tld = ( z.namelist()[0].split( os.path.sep, 1 ) )[0] + tld = self.get_tld( z.namelist() ) cur = os.getcwd() os.chdir( unpack_path ) for fn in z.namelist(): @@ -211,12 +220,12 @@ os.chdir( cur ) def unpack_tar( self, source_path, unpack_path ): t = tarfile.open( source_path, "r" ) - tld = ( t.getnames()[0].split( os.path.sep, 1 ) )[0] + members = filter( lambda x: "ez_setup" not in x.name and "pax_global_header" != x.name, t.getmembers() ) + tld = self.get_tld( [ x.name for x in members ] ) cur = os.getcwd() os.chdir( unpack_path ) - for member in t.getmembers(): - if "ez_setup" not in member.name: - t.extract( member ) + for member in members: + t.extract( member ) t.close() os.rename( tld, self.name ) os.chdir( cur ) @@ -265,7 +274,7 @@ self.eggs = {} self.config = CSConfigParser() self.repo = None - self.no_download = [] + self.no_auto = [] self.platform = { 'peak' : get_platform( platform=True, peak=True ), 'galaxy' : get_platform( platform=True, peak=False ) } self.noplatform = { 'peak' : get_platform( platform=False, peak=True ), 'galaxy' : get_platform( platform=False, peak=False ) } def parse( self ): @@ -273,7 +282,7 @@ raise Exception( "unable to read egg config from %s" % Crate.config_file ) try: self.repo = self.config.get( "general", "repository" ) - self.no_download = self.config.get( "general", "no_download" ).split() + self.no_auto = self.config.get( "general", "no_auto" ).split() except ConfigParser.NoSectionError: raise Exception( "eggs.ini is missing required section [general]" ) #except ConfigParser.NoOptionError: @@ -316,19 +325,19 @@ return True def fetch( self, ignore=[] ): """ - Fetch all eggs in the crate (ignoring any that you want to - ignore). If your platform isn't available, it'll attempt to - download all the noplatform eggs before failing. + Fetch all eggs in the crate (ignoring any that you want to + ignore). If your platform isn't available, it'll attempt to + download all the noplatform eggs before failing. """ skip_platform = False - ignore.extend( self.no_download ) + ignore.extend( self.no_auto ) + missing = [] try: f = urllib2.urlopen( "%s/%s" % ( self.repo, self.platform['galaxy'] ) ) f.close() except urllib2.HTTPError, e: if e.code == 404: skip_platform = True - missing = [] for egg in self.eggs.itervalues(): if ignore is not None: if egg.name in ignore: @@ -336,11 +345,18 @@ if skip_platform and egg.platform['galaxy'] == self.platform['galaxy']: missing.append( egg.name ) continue - egg.fetch() + try: + egg.fetch() + except EggNotFetchable: + missing.append( egg.name ) if skip_platform: raise PlatformNotSupported( self.platform['galaxy'] ) + if missing: + raise EggNotFetchable( missing ) return True def scramble( self, ignore=None ): + # Crate-scrambling the no_auto eggs makes no sense + ignore.extend( self.no_auto ) for egg in self.eggs.itervalues(): if ignore is not None: if egg.name in ignore: @@ -379,21 +395,14 @@ if self.config.read( DistCrate.dist_config_file ) == []: raise Exception( "unable to read dist egg config from %s" % DistCrate.dist_config_file ) try: - self.hosts = self.dictize_list_of_tuples( self.config.items( "hosts" ) ) - self.groups = self.dictize_list_of_tuples( self.config.items( "groups" ) ) + self.hosts = dict( self.config.items( "hosts" ) ) + self.groups = dict( self.config.items( "groups" ) ) + self.ignore = dict( self.config.items( "ignore" ) ) except ConfigParser.NoSectionError, e: raise Exception( "eggs.ini is missing required section: %s" % e ) self.platforms = self.get_platforms( self.build_on ) self.noplatforms = self.get_platforms( 'noplatform' ) Crate.parse( self ) - def dictize_list_of_tuples( self, lot ): - """ - Makes a list of 2-value tuples into a dict. - """ - d = {} - for k, v in lot: - d[k] = v - return d def get_platforms( self, wanted ): # find all the members of a group and process them if self.groups.has_key( wanted ): @@ -409,8 +418,8 @@ raise Exception( "unknown platform: %s" % wanted ) def parse_egg_section( self, eggs, type ): """ - Overrides the base class's method. Here we use the third arg - to find out what type of egg we'll be building. + Overrides the base class's method. Here we use the third arg + to find out what type of egg we'll be building. """ if type == "platform": platforms = self.platforms @@ -418,14 +427,16 @@ platforms = self.noplatforms for name, version in eggs: for platform in platforms: - # can't use the regular methods here because we're not - # actually ON the target platform + # can't use the regular methods here because we're not + # actually ON the target platform if type == "platform": gplat = platform pplat = platform.rsplit('-', 1)[0] elif type == "noplatform": gplat = "%s-noplatform" % platform.split('-', 1)[0] pplat = platform.split('-', 1)[0] + if name in self.ignore and gplat in self.ignore[name].split(): + continue egg = Egg() try: egg.tag = self.config.get( "tags", name ) @@ -448,75 +459,31 @@ class GalaxyConfig: config_file = os.path.join( galaxy_dir, "universe_wsgi.ini" ) + always_conditional = ( 'GeneTrack', ) def __init__( self ): self.config = ConfigParser.ConfigParser() if self.config.read( GalaxyConfig.config_file ) == []: raise Exception( "error: unable to read Galaxy config from %s" % GalaxyConfig.config_file ) # TODO: conditionals should really be handled better than this def check_conditional( self, egg_name ): - if egg_name == "psycopg2": + if egg_name == "pysqlite": + # SQLite is different since it can be specified in two config vars and defaults to True try: - if self.config.get( "app:main", "database_connection" ).startswith( "postgres://" ): - return True - else: - return False + return self.config.get( "app:main", "database_connection" ).startswith( "sqlite://" ) + except: + return True + else: + try: + return { "psycopg2": lambda: self.config.get( "app:main", "database_connection" ).startswith( "postgres://" ), + "MySQL_python": lambda: self.config.get( "app:main", "database_connection" ).startswith( "mysql://" ), + "DRMAA_python": lambda: "sge" in self.config.get( "app:main", "start_job_runners" ).split(","), + "pbs_python": lambda: "pbs" in self.config.get( "app:main", "start_job_runners" ).split(","), + "threadframe": lambda: self.config.get( "app:main", "use_heartbeat" ), + "guppy": lambda: self.config.get( "app:main", "use_memdump" ), + "GeneTrack": lambda: sys.version_info[:2] >= ( 2, 5 ), + }.get( egg_name, lambda: True )() except: return False - elif egg_name == "pysqlite": - try: - # database connection is the sqlite alchemy dialect (not really - # a documented usage in Galaxy, but it would work) - if self.config.get( "app:main", "database_connection" ).startswith( "sqlite://" ): - return True - else: - return False - # database connection is unset, so sqlite is the default - except: - return True - elif egg_name == "DRMAA_python": - try: - runners = self.config.get( "app:main", "start_job_runners" ).split(",") - if "sge" in runners: - return True - else: - return False - except: - return False - elif egg_name == "pbs_python": - try: - runners = self.config.get( "app:main", "start_job_runners" ).split(",") - if "pbs" in runners: - return True - else: - return False - except: - return False - elif egg_name == "threadframe": - try: - if self.config.get( "app:main", "use_heartbeat" ): - return True - else: - return False - except: - return False - elif egg_name == "guppy": - try: - if self.config.get( "app:main", "use_memdump" ): - return True - else: - return False - except: - return False - elif egg_name == "MySQL_python": - try: - if self.config.get( "app:main", "database_connection" ).startswith( "mysql://" ): - return True - else: - return False - except: - return False - else: - return True def require( pkg ): # add the egg dirs to sys.path if they're not already there diff -r 92d395c8614b -r fdf07565eedf scripts/fetch_eggs.py --- a/scripts/fetch_eggs.py Wed Nov 04 12:30:36 2009 -0500 +++ b/scripts/fetch_eggs.py Wed Nov 04 12:58:48 2009 -0500 @@ -25,26 +25,28 @@ c.platform = { 'peak' : sys.argv[2].rsplit('-',1)[0], 'galaxy' : sys.argv[2] } c.parse() try: + galaxy_config = GalaxyConfig() + names = [] if len( sys.argv ) == 1: - galaxy_config = GalaxyConfig() - ignore = [] - for name in c.get_names(): - if not galaxy_config.check_conditional( name ): - ignore.append( name ) - c.fetch( ignore=ignore ) + names = c.get_names() + elif sys.argv[1] == 'all': + names = galaxy_config.always_conditional else: - if sys.argv[1] == 'all': - c.fetch() - else: - egg = c.get( sys.argv[1] ) - if egg is None: - print "error: %s not in eggs.ini" % sys.argv[1] - sys.exit( 1 ) - egg.fetch() + # Fetch a specific egg + egg = c.get( sys.argv[1] ) + if egg is None: + print "error: %s not in eggs.ini" % sys.argv[1] + sys.exit( 1 ) + egg.fetch() + sys.exit( 0 ) + ignore = filter( lambda x: not galaxy_config.check_conditional( x ), list( names ) ) + c.fetch( ignore ) except EggNotFetchable, e: - print "One of the python eggs necessary to run Galaxy couldn't be downloaded" - print "automatically. You may want to try building it by hand with:" - print " python scripts/scramble.py %s" % e + print "One or more of the python eggs necessary to run Galaxy couldn't be" + print "downloaded automatically. You may want to try building them by" + print "hand with:" + for egg in e.eggs: + print " python scripts/scramble.py %s" % egg sys.exit( 1 ) except PlatformNotSupported, e: print "Your platform (%s) is not supported." % e diff -r 92d395c8614b -r fdf07565eedf scripts/scramble.py --- a/scripts/scramble.py Wed Nov 04 12:30:36 2009 -0500 +++ b/scripts/scramble.py Wed Nov 04 12:58:48 2009 -0500 @@ -18,19 +18,19 @@ c = Crate() c.parse() +galaxy_config = GalaxyConfig() +names = [] if len( sys.argv ) == 1: - galaxy_config = GalaxyConfig() - ignore = [] - for name in c.get_names(): - if not galaxy_config.check_conditional( name ): - ignore.append( name ) - c.scramble( ignore=ignore ) + names = c.get_names() +elif sys.argv[1] == 'all': + names = galaxy_config.always_conditional else: - if sys.argv[1] == 'all': - c.scramble() - else: - egg = c.get( sys.argv[1] ) - if egg is None: - print "error: %s not in eggs.ini" % sys.argv[1] - sys.exit( 1 ) - egg.scramble() +# Scramble a specific egg + egg = c.get( sys.argv[1] ) + if egg is None: + print "error: %s not in eggs.ini" % sys.argv[1] + sys.exit( 1 ) + egg.scramble() + sys.exit( 0 ) +ignore = filter( lambda x: not galaxy_config.check_conditional( x ), list( names ) ) +c.scramble( ignore=ignore ) diff -r 92d395c8614b -r fdf07565eedf scripts/scramble/scripts/GeneTrack.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/scripts/scramble/scripts/GeneTrack.py Wed Nov 04 12:58:48 2009 -0500 @@ -0,0 +1,52 @@ +import os, sys, shutil + +# change back to the build dir +if os.path.dirname( sys.argv[0] ) != "": + os.chdir( os.path.dirname( sys.argv[0] ) ) + +# find setuptools +scramble_lib = os.path.join( "..", "..", "..", "lib" ) +sys.path.append( scramble_lib ) +from ez_setup import use_setuptools +use_setuptools( download_delay=8, to_dir=scramble_lib ) +from setuptools import * + +# get the tag +if os.access( ".galaxy_tag", os.F_OK ): + tagfile = open( ".galaxy_tag", "r" ) + tag = tagfile.readline().strip() +else: + tag = None + +# in case you're running this by hand from a dirty module source dir +for dir in [ "build", "dist" ]: + if os.access( dir, os.F_OK ): + print "scramble.py: removing dir:", dir + shutil.rmtree( dir ) + +# reset args for distutils +me = sys.argv[0] +sys.argv = [ me ] +sys.argv.append( "egg_info" ) +if tag is not None: + #sys.argv.append( "egg_info" ) + sys.argv.append( "--tag-build=%s" %tag ) +# svn revision (if any) is handled directly in tag-build +sys.argv.append( "--no-svn-revision" ) +sys.argv.append( "bdist_egg" ) + +print "scramble.py: Creating setup.py for GeneTrack" +setup_py = """from setuptools import setup, find_packages +setup( + name = "GeneTrack", + version = "2.0.0-beta-1", + package_data = {'':["*.*"]}, + packages = find_packages(), + zip_safe = True, +) +""" +open( 'setup.py', 'w' ).write( setup_py ) + + +# do it +execfile( "setup.py", globals(), locals() )

1 0

[hg] galaxy 2960: Fix maf_utilities.src_split. Should resolve ti...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/91a3bbb52d7a changeset: 2960:91a3bbb52d7a user: Dan Blankenberg <dan(a)bx.psu.edu> date: Wed Nov 04 12:15:53 2009 -0500 description: Fix maf_utilities.src_split. Should resolve tickets #200, #215 and #220. Note: Do not use bx.align.src_split in Galaxy. diffstat: lib/galaxy/datatypes/converters/maf_to_interval_converter.py | 2 +- lib/galaxy/datatypes/converters/maf_to_interval_converter.xml | 2 +- lib/galaxy/tools/util/maf_utilities.py | 11 +++++++---- 3 files changed, 9 insertions(+), 6 deletions(-) diffs (49 lines): diff -r 4bca8f8ed94d -r 91a3bbb52d7a lib/galaxy/datatypes/converters/maf_to_interval_converter.py --- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.py Wed Nov 04 11:35:50 2009 -0500 +++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.py Wed Nov 04 12:15:53 2009 -0500 @@ -21,7 +21,7 @@ for block in bx.align.maf.Reader( open( input_name, 'r' ) ): for c in maf_utilities.iter_components_by_src_start( block, species ): if c is not None: - out.write( "%s\t%i\t%i\t%s\n" % ( bx.align.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) ) + out.write( "%s\t%i\t%i\t%s\n" % ( maf_utilities.src_split( c.src )[-1], c.get_forward_strand_start(), c.get_forward_strand_end(), c.strand ) ) count += 1 except Exception, e: print >> sys.stderr, "There was a problem processing your input: %s" % e diff -r 4bca8f8ed94d -r 91a3bbb52d7a lib/galaxy/datatypes/converters/maf_to_interval_converter.xml --- a/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Wed Nov 04 11:35:50 2009 -0500 +++ b/lib/galaxy/datatypes/converters/maf_to_interval_converter.xml Wed Nov 04 12:15:53 2009 -0500 @@ -1,4 +1,4 @@ -<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals" version="1.0.1"> +<tool id="CONVERTER_maf_to_interval_0" name="Convert MAF to Genomic Intervals" version="1.0.2">  <command interpreter="python">maf_to_interval_converter.py $output1 $input1 ${input1.metadata.dbkey}</command> <inputs> diff -r 4bca8f8ed94d -r 91a3bbb52d7a lib/galaxy/tools/util/maf_utilities.py --- a/lib/galaxy/tools/util/maf_utilities.py Wed Nov 04 11:35:50 2009 -0500 +++ b/lib/galaxy/tools/util/maf_utilities.py Wed Nov 04 12:15:53 2009 -0500 @@ -20,9 +20,12 @@ SRC_SPLIT_CHAR = '.' def src_split( src ): - spec, chrom = bx.align.maf.src_split( src ) - if None in [ spec, chrom ]: - spec = chrom = src + fields = src.split( SRC_SPLIT_CHAR, 1 ) + spec = fields.pop( 0 ) + if fields: + chrom = fields + else: + chrom = spec return spec, chrom def src_merge( spec, chrom, contig = None ): @@ -530,7 +533,7 @@ if suffix: header = "%s%s" % ( header, suffix ) else: - header = "%s%s" % ( header, bx.align.src_split( component.src )[ 0 ] ) + header = "%s%s" % ( header, src_split( component.src )[ 0 ] ) return header def get_attributes_from_fasta_header( header ):

1 0

[hg] galaxy 2958: Fixed the ordering in selectboxes
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/0e78d558fe57 changeset: 2958:0e78d558fe57 user: rc date: Wed Nov 04 10:16:20 2009 -0500 description: Fixed the ordering in selectboxes Fixed a bug in editing samples in the request page diffstat: lib/galaxy/model/mapping.py | 3 ++- lib/galaxy/web/controllers/forms.py | 4 +++- lib/galaxy/web/controllers/requests.py | 9 +++++---- lib/galaxy/web/controllers/requests_admin.py | 22 ++++++++++++---------- templates/admin/requests/show_request.mako | 2 +- templates/requests/show_request.mako | 4 ---- test/base/twilltestcase.py | 2 +- 7 files changed, 24 insertions(+), 22 deletions(-) diffs (191 lines): diff -r 5b2d593d9aed -r 0e78d558fe57 lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Wed Nov 04 10:04:51 2009 -0500 +++ b/lib/galaxy/model/mapping.py Wed Nov 04 10:16:20 2009 -0500 @@ -652,7 +652,8 @@ primaryjoin=( Request.table.c.user_id == User.table.c.id ), backref="requests" ), samples=relation( Sample, - primaryjoin=( Request.table.c.id == Sample.table.c.request_id ) ), + primaryjoin=( Request.table.c.id == Sample.table.c.request_id ), + order_by=asc(Sample.table.c.update_time) ), folder=relation( LibraryFolder, primaryjoin=( Request.table.c.folder_id == LibraryFolder.table.c.id ) ), library=relation( Library, diff -r 5b2d593d9aed -r 0e78d558fe57 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Wed Nov 04 10:04:51 2009 -0500 +++ b/lib/galaxy/web/controllers/forms.py Wed Nov 04 10:16:20 2009 -0500 @@ -60,7 +60,9 @@ form_type_selectbox.add_option('Select one', 'none', selected=True) else: form_type_selectbox.add_option('Select one', 'none') - for ft in trans.app.model.FormDefinition.types.items(): + fd_types = trans.app.model.FormDefinition.types.items() + fd_types.sort() + for ft in fd_types: if selected == ft[1]: form_type_selectbox.add_option(ft[1], ft[1], selected=True) else: diff -r 5b2d593d9aed -r 0e78d558fe57 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Wed Nov 04 10:04:51 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Wed Nov 04 10:16:20 2009 -0500 @@ -304,8 +304,7 @@ s = trans.app.model.Sample(sample_name, '', request, form_values) s.flush() else: - for index in range(len(current_samples)): - sample_index = index + for sample_index in range(len(current_samples)): sample_name = current_samples[sample_index][0] new_sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] @@ -379,8 +378,10 @@ details=details, edit_mode=edit_mode) def __select_request_type(self, trans, rtid): + requesttype_list = trans.sa_session.query( trans.app.model.RequestType )\ + .order_by( trans.app.model.RequestType.name.asc() ) rt_ids = ['none'] - for rt in trans.sa_session.query( trans.app.model.RequestType ): + for rt in requesttype_list: if not rt.deleted: rt_ids.append(str(rt.id)) select_reqtype = SelectField('select_request_type', @@ -390,7 +391,7 @@ select_reqtype.add_option('Select one', 'none', selected=True) else: select_reqtype.add_option('Select one', 'none') - for rt in trans.sa_session.query( trans.app.model.RequestType ): + for rt in requesttype_list: if not rt.deleted: if rtid == rt.id: select_reqtype.add_option(rt.name, rt.id, selected=True) diff -r 5b2d593d9aed -r 0e78d558fe57 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Wed Nov 04 10:04:51 2009 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Wed Nov 04 10:16:20 2009 -0500 @@ -266,8 +266,10 @@ #---- Request Creation ---------------------------------------------------------- # def __select_request_type(self, trans, rtid): + requesttype_list = trans.sa_session.query( trans.app.model.RequestType )\ + .order_by( trans.app.model.RequestType.name.asc() ) rt_ids = ['none'] - for rt in trans.sa_session.query( trans.app.model.RequestType ): + for rt in requesttype_list: if not rt.deleted: rt_ids.append(str(rt.id)) select_reqtype = SelectField('select_request_type', @@ -277,7 +279,7 @@ select_reqtype.add_option('Select one', 'none', selected=True) else: select_reqtype.add_option('Select one', 'none') - for rt in trans.sa_session.query( trans.app.model.RequestType ): + for rt in requesttype_list: if not rt.deleted: if rtid == rt.id: select_reqtype.add_option(rt.name, rt.id, selected=True) @@ -799,7 +801,7 @@ # save all the new/unsaved samples entered by the user if edit_mode == 'False': for index in range(len(current_samples)-len(request.samples)): - sample_index = index + len(request.samples) + sample_index = len(request.samples) sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] for field_index in range(len(request.type.sample_form.fields)): @@ -992,7 +994,7 @@ bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, '')) # check for empty bar code if not bar_code.strip(): - msg = 'Please fill the bar code for sample <b>%s</b>.' % request.samples[index].name + msg = 'Please fill the barcode for sample <b>%s</b>.' % request.samples[index].name break # check all the unsaved bar codes count = 0 @@ -1000,8 +1002,8 @@ if bar_code == util.restore_text(params.get('sample_%i_bar_code' % i, '')): count = count + 1 if count > 1: - msg = '''The bar code <b>%s</b> of sample <b>%s</b> already belongs - another sample in this request. The sample bar codes must + msg = '''The barcode <b>%s</b> of sample <b>%s</b> belongs + another sample in this request. The sample barcodes must be unique throughout the system''' % \ (bar_code, request.samples[index].name) break @@ -1009,7 +1011,7 @@ all_samples = trans.sa_session.query( trans.app.model.Sample ) for sample in all_samples: if bar_code == sample.bar_code: - msg = '''The bar code <b>%s</b> of sample <b>%s</b> already + msg = '''The bar code <b>%s</b> of sample <b>%s</b> belongs another sample. The sample bar codes must be unique throughout the system''' % \ (bar_code, request.samples[index].name) @@ -1044,7 +1046,7 @@ return trans.response.send_redirect( web.url_for( controller='requests_admin', action='bar_codes', request_id=request.id, - msg='Bar codes has been saved for this request', + msg='Bar codes have been saved for this request', messagetype='done')) def __set_request_state(self, request): @@ -1162,8 +1164,8 @@ if params.get( 'create', False ): return trans.fill_template( '/admin/requests/create_request_type.mako', request_forms=get_all_forms( trans, - filter=dict(deleted=False), - form_type=trans.app.model.FormDefinition.types.REQUEST ), + filter=dict(deleted=False), + form_type=trans.app.model.FormDefinition.types.REQUEST ), sample_forms=get_all_forms( trans, filter=dict(deleted=False), form_type=trans.app.model.FormDefinition.types.SAMPLE ), diff -r 5b2d593d9aed -r 0e78d558fe57 templates/admin/requests/show_request.mako --- a/templates/admin/requests/show_request.mako Wed Nov 04 10:04:51 2009 -0500 +++ b/templates/admin/requests/show_request.mako Wed Nov 04 10:16:20 2009 -0500 @@ -195,7 +195,7 @@ <div class="toolForm"> ##<div class="toolFormTitle">Samples (${len(request.samples)})</div> - <form id="edit_form" name="edit_form" action="${h.url_for( controller='requests_admin', action='show_request' )}" enctype="multipart/form-data" method="post" > + <form id="show_request" name="show_request" action="${h.url_for( controller='requests_admin', action='show_request', edit_mode=edit_mode )}" enctype="multipart/form-data" method="post" > <div class="form-row"> %if current_samples: %if not request.type.sample_form.layout: diff -r 5b2d593d9aed -r 0e78d558fe57 templates/requests/show_request.mako --- a/templates/requests/show_request.mako Wed Nov 04 10:04:51 2009 -0500 +++ b/templates/requests/show_request.mako Wed Nov 04 10:16:20 2009 -0500 @@ -224,20 +224,16 @@ %endif </td> <td> - ##<div class="form-row"> <label>Import from csv file</label> <input type="file" name="file_data" /> <input type="submit" name="import_samples_button" value="Import samples"/> - ##</div> </td> <td> - ##<div class="form-row"> %if current_samples: <label>Copy from sample</label> ${sample_copy.get_html()} %endif <input type="submit" name="add_sample_button" value="Add New"/> - ##</div> </td> </div> </tr> diff -r 5b2d593d9aed -r 0e78d558fe57 test/base/twilltestcase.py --- a/test/base/twilltestcase.py Wed Nov 04 10:04:51 2009 -0500 +++ b/test/base/twilltestcase.py Wed Nov 04 10:16:20 2009 -0500 @@ -1272,7 +1272,7 @@ for index, bar_code in enumerate(bar_codes): tc.fv( "1", "sample_%i_bar_code" % index, bar_code ) tc.submit( "save_bar_codes" ) - self.check_page_for_string( 'Bar codes has been saved for this request' ) + self.check_page_for_string( 'Bar codes have been saved for this request' ) def change_sample_state( self, sample_name, sample_id, new_state_id, new_state_name, comment='' ): self.home() self.visit_url( "%s/requests_admin/show_events?sample_id=%i" % (self.url, sample_id) )

1 0

[hg] galaxy 2959: Fix tool test specification by id
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/4bca8f8ed94d changeset: 2959:4bca8f8ed94d user: James Taylor <james(a)jamestaylor.org> date: Wed Nov 04 11:35:50 2009 -0500 description: Fix tool test specification by id diffstat: test/functional/test_toolbox.py | 2 +- 1 files changed, 1 insertions(+), 1 deletions(-) diffs (9 lines): diff -r 0e78d558fe57 -r 4bca8f8ed94d test/functional/test_toolbox.py --- a/test/functional/test_toolbox.py Wed Nov 04 10:16:20 2009 -0500 +++ b/test/functional/test_toolbox.py Wed Nov 04 11:35:50 2009 -0500 @@ -128,4 +128,4 @@ for j, testdef in enumerate( tool.tests ): name = "%s ( %s ) > %s" % ( tool.name, tool.id, testdef.name ) testcase = get_case( testdef, name ) - G[ 'testcase_%d_%d' % ( i, j ) ] = testcase + G[ testcase.__name__ ] = testcase

1 0

[hg] galaxy 2953: Added 'History' column to HDA grid.
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/14e178f656ba changeset: 2953:14e178f656ba user: jeremy goecks <jeremy.goecks(a)emory.edu> date: Tue Nov 03 16:53:14 2009 -0500 description: Added 'History' column to HDA grid. diffstat: lib/galaxy/web/controllers/dataset.py | 26 +++++++++++++++++++------- templates/dataset/grid.mako | 11 ++++++++--- templates/root/history_common.mako | 2 +- 3 files changed, 28 insertions(+), 11 deletions(-) diffs (116 lines): diff -r 6491acd0bef2 -r 14e178f656ba lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Nov 03 15:39:51 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Nov 03 16:53:14 2009 -0500 @@ -45,6 +45,11 @@ """ class HistoryDatasetAssociationListGrid( grids.Grid ): + # Custom columns for grid. + class HistoryColumn( grids.GridColumn ): + def get_value( self, trans, grid, hda): + return hda.history.name + class StatusColumn( grids.GridColumn ): def get_value( self, trans, grid, hda ): if hda.deleted: @@ -52,6 +57,7 @@ return "" def get_link( self, trans, grid, hda ): return None + class TagsColumn( grids.GridColumn ): def __init__(self, col_name, key, filterable): grids.GridColumn.__init__(self, col_name, key=key, filterable=filterable) @@ -107,14 +113,16 @@ return accepted_filters # Grid definition - title = "Stored Datasets" + title = "Saved Datasets" model_class = model.HistoryDatasetAssociation template='/dataset/grid.mako' default_sort_key = "-create_time" columns = [ - grids.GridColumn( "Name", key="name", - # Link name to dataset's history. + grids.GridColumn( "Name", key="name", + # Link name to dataset's history. link=( lambda item: iff( item.history.deleted, None, dict( operation="switch", id=item.id ) ) ) ), + HistoryColumn( "History", key="history", + link=( lambda item: iff( item.history.deleted, None, dict( operation="switch_history", id=item.id ) ) ) ), TagsColumn( "Tags", key="tags", filterable=True ), StatusColumn( "Status", key="deleted", attach_popup=False ), grids.GridColumn( "Created", key="create_time", format=time_ago ), @@ -285,8 +293,9 @@ log.warn( "Invalid history_dataset_association id '%r' passed to list", hda_id ) if hdas: - - if operation == "switch": + if operation == "switch" or operation == "switch_history": + # Switch to a history that the HDA resides in. + # Convert hda to histories. histories = [] for hda in hdas: @@ -295,8 +304,11 @@ # Use history controller to switch the history. TODO: is this reasonable? status, message = trans.webapp.controllers['history']._list_switch( trans, histories ) - # Current history changed, refresh history frame - trans.template_context['refresh_frames'] = ['history'] + # Current history changed, refresh history frame; if switching to a dataset, set hda seek. + trans.template_context['refresh_frames'] = ['history'] + if operation == "switch": + hda_ids = [ trans.security.encode_id( hda.id ) for hda in hdas ] + trans.template_context[ 'seek_hda_ids' ] = hda_ids # Render the list view return self.stored_list_grid( trans, status=status, message=message, **kwargs ) diff -r 6491acd0bef2 -r 14e178f656ba templates/dataset/grid.mako --- a/templates/dataset/grid.mako Tue Nov 03 15:39:51 2009 -0500 +++ b/templates/dataset/grid.mako Tue Nov 03 16:53:14 2009 -0500 @@ -92,8 +92,6 @@ t.autocomplete("${h.url_for( controller='tag', action='tag_autocomplete_data', item_class='HistoryDatasetAssociation' )}", autocomplete_options); - //t.addClass("tag-input"); - return t; }); ## Can this be moved into base.mako? @@ -110,7 +108,14 @@ %endif %if 'history' in refresh_frames: if ( parent.frames && parent.frames.galaxy_history ) { - parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=str(ids) )}"; + ## If available, include HDA ids to seek to in history request. + <% + hda_id = None + if seek_hda_ids: + hda_id = str( seek_hda_ids[0] ) # Use only the first id. + print hda_id + %> + parent.frames.galaxy_history.location.href="${h.url_for( controller='root', action='history', hda_id=hda_id )}"; if ( parent.force_right_panel ) { parent.force_right_panel( 'show' ); } diff -r 6491acd0bef2 -r 14e178f656ba templates/root/history_common.mako --- a/templates/root/history_common.mako Tue Nov 03 15:39:51 2009 -0500 +++ b/templates/root/history_common.mako Tue Nov 03 16:53:14 2009 -0500 @@ -1,6 +1,7 @@ <% _=n_ %> ## Render the dataset `data` as history item, using `hid` as the displayed id <%def name="render_dataset( data, hid, show_deleted_on_refresh = False, user_owns_dataset = True )"> + <a name="${trans.security.encode_id( data.id )}"></a> <% if data.state in ['no state','',None]: data_state = "queued" @@ -21,7 +22,6 @@ %endif ## Header row for history items (name, state, action buttons) - <a name="${trans.security.encode_id(data.id)}"></a> <div style="overflow: hidden;" class="historyItemTitleBar"> <div class="historyItemButtons"> %if data_state == "upload":

1 0

[hg] galaxy 2955: trackster: much greater resolution for line tr...
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d7c66019de13 changeset: 2955:d7c66019de13 user: Kanwei Li <kanwei(a)gmail.com> date: Tue Nov 03 19:16:01 2009 -0500 description: trackster: much greater resolution for line tracks (might still need to tweak BLOCK_SIZE), fixed stacking issue in feature tracks for features sharing same name) diffstat: lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py | 4 +- lib/galaxy/visualization/tracks/data/array_tree.py | 45 ++++++----- lib/galaxy/visualization/tracks/data/interval_index.py | 6 +- lib/galaxy/web/controllers/tracks.py | 6 +- static/scripts/trackster.js | 46 +++++++---- static/trackster.css | 1 + templates/tracks/browser.mako | 1 + 7 files changed, 65 insertions(+), 44 deletions(-) diffs (293 lines): diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py --- a/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/datatypes/converters/wiggle_to_array_tree_converter.py Tue Nov 03 19:16:01 2009 -0500 @@ -8,6 +8,8 @@ from bx.arrays.array_tree import * from bx.arrays.wiggle import IntervalReader +BLOCK_SIZE = 1000 + def main(): input_fname = sys.argv[1] @@ -16,7 +18,7 @@ reader = IntervalReader( open( input_fname ) ) # Fill array from wiggle - d = array_tree_dict_from_wiggle_reader( reader, {} ) + d = array_tree_dict_from_wiggle_reader( reader, {}, block_size = BLOCK_SIZE ) for value in d.itervalues(): value.root.build_summary() diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/visualization/tracks/data/array_tree.py --- a/lib/galaxy/visualization/tracks/data/array_tree.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/array_tree.py Tue Nov 03 19:16:01 2009 -0500 @@ -31,11 +31,16 @@ f.close() return { 'max': float( max(root_summary.maxs) ), 'min': float( min(root_summary.mins) ) } - def get_data( self, chrom, start, end ): + def get_data( self, chrom, start, end, **kwargs ): start = int( start ) end = int( end ) - level = int( ceil( log( end - start, BLOCK_SIZE ) ) ) - 1 - + resolution = max(1, ceil(float(kwargs['resolution']))) + + level = int( floor( log( resolution, BLOCK_SIZE ) ) ) + level = max( level, 0 ) + stepsize = BLOCK_SIZE ** level + step1 = stepsize * BLOCK_SIZE + # Open the file f = open( self.dataset.file_name ) d = FileArrayTreeDict( f ) @@ -47,22 +52,20 @@ # Is the requested level valid? assert 0 <= level <= chrom_array_tree.levels # Calculate the actual start/range/step of the block we're getting - size = BLOCK_SIZE ** (level+1) - block_start = ( start // BLOCK_SIZE ) * BLOCK_SIZE - block_step = size // BLOCK_SIZE - indexes = range( block_start, block_start + size, block_step ) - # Return either data point or a summary depending on the level - if level > 0: - s = chrom_array_tree.get_summary( start, level ) - f.close() - if s is not None: - return zip( indexes, map( float, s.sums / s.counts ) ) + + results = [] + for block_start in range( start, end, stepsize * BLOCK_SIZE ): + # print block_start + # Return either data point or a summary depending on the level + indexes = range( block_start, block_start + stepsize * BLOCK_SIZE, stepsize ) + if level > 0: + s = chrom_array_tree.get_summary( block_start, level ) + if s is not None: + results.extend( zip( indexes, map( float, s.sums / s.counts ) ) ) else: - return None - else: - v = chrom_array_tree.get_leaf( start ) - f.close() - if v is not None: - return zip( indexes, map( float, v ) ) - else: - return None \ No newline at end of file + v = chrom_array_tree.get_leaf( block_start ) + if v is not None: + results.extend( zip( indexes, map( float, v ) ) ) + + f.close() + return results diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/visualization/tracks/data/interval_index.py --- a/lib/galaxy/visualization/tracks/data/interval_index.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/visualization/tracks/data/interval_index.py Tue Nov 03 19:16:01 2009 -0500 @@ -11,17 +11,18 @@ self.original_dataset = original_dataset self.converted_dataset = converted_dataset - def get_data( self, chrom, start, end ): + def get_data( self, chrom, start, end, **kwargs ): start, end = int(start), int(end) chrom = str(chrom) source = open( self.original_dataset.file_name ) index = Indexes( self.converted_dataset.file_name ) results = [] + uid = 0 for start, end, offset in index.find(chrom, start, end): source.seek(offset) feature = source.readline().split() - payload = { 'start': start, 'end': end, 'name': feature[3] } + payload = { 'uid': uid, 'start': start, 'end': end, 'name': feature[3] } try: payload['strand'] = feature[5] except IndexError: @@ -41,5 +42,6 @@ pass results.append(payload) + uid += 1 return results diff -r 46791b5a653b -r d7c66019de13 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Tue Nov 03 17:16:40 2009 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Tue Nov 03 19:16:01 2009 -0500 @@ -184,7 +184,7 @@ return manifest @web.json - def data( self, trans, dataset_id, track_type, chrom, low, high, stats=False ): + def data( self, trans, dataset_id, track_type, chrom, low, high, **kwargs ): """ Called by the browser to request a block of data """ @@ -216,10 +216,10 @@ data_provider = dataset_type_to_data_provider[ converted_dataset_type ]( converted_dataset, dataset ) # Return stats if we need them - if stats: return data_provider.get_stats( chrom ) + if 'stats' in kwargs: return data_provider.get_stats( chrom ) # Get the requested chunk of data - return data_provider.get_data( chrom, low, high ) + return data_provider.get_data( chrom, low, high, **kwargs ) def __dataset_as_type( self, trans, dataset, type ): """ diff -r 46791b5a653b -r d7c66019de13 static/scripts/trackster.js --- a/static/scripts/trackster.js Tue Nov 03 17:16:40 2009 -0500 +++ b/static/scripts/trackster.js Tue Nov 03 19:16:01 2009 -0500 @@ -1,13 +1,15 @@ /* Trackster 2009, James Taylor, Kanwei Li */ +var DEBUG = false; var DENSITY = 1000, DATA_ERROR = "There was an error in indexing this dataset.", DATA_NONE = "No data for this chrom/contig.", DATA_PENDING = "Currently indexing... please wait", DATA_LOADING = "Loading data...", - CACHED_TILES = 10, + CACHED_TILES_FEATURE = 10, + CACHED_TILES_LINE = 30, CACHED_DATA = 20, CONTEXT = $("<canvas></canvas>").get(0).getContext("2d"), RIGHT_STRAND, LEFT_STRAND; @@ -104,6 +106,9 @@ this.high = Math.ceil(high); this.center = Math.round( this.low + (this.high - this.low) / 2 ); + // 10^log10(range / DENSITY) Close approximation for browser window, assuming DENSITY = window width + this.resolution = Math.pow( 10, Math.ceil( Math.log( (this.high - this.low) / DENSITY ) / Math.LN10 ) ); + // Overview $("#overview-box").css( { left: ( this.low / this.span ) * $("#overview-viewport").width(), @@ -157,18 +162,16 @@ }); var TiledTrack = function() { - this.tile_cache = new Cache(CACHED_TILES); - // this.tile_cache = {}; }; $.extend( TiledTrack.prototype, Track.prototype, { draw: function() { var low = this.view.low, high = this.view.high, - range = high - low; - - var resolution = Math.pow( 10, Math.ceil( Math.log( range / DENSITY ) / Math.log( 10 ) ) ); - resolution = Math.max( resolution, 0.1 ); - resolution = Math.min( resolution, 1000000 ); + range = high - low, + resolution = this.view.resolution; + + + if (DEBUG) { $("#debug").text(resolution); } var parent_element = $("<div style='position: relative;'></div>"); this.content_div.children( ":first" ).remove(); @@ -187,7 +190,7 @@ // console.log("cached tile " + tile_index); var tile_low = tile_index * DENSITY * resolution; cached.css( { - left: ( tile_low - this.view.low ) * w_scale + left: ( tile_low - low ) * w_scale }); // Our responsibility to move the element to the new parent parent_element.append( cached ); @@ -229,6 +232,7 @@ }); var LineTrack = function ( name, dataset_id, height ) { + this.tile_cache = new Cache(CACHED_TILES_LINE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -236,6 +240,7 @@ this.height_px = (height ? height : 100); this.container_div.addClass( "line-track" ); this.dataset_id = dataset_id; + this.data_queue = {}; this.cache = new Cache(CACHED_DATA); // We need to cache some data because of // asynchronous calls }; @@ -282,11 +287,17 @@ low = position * DENSITY * resolution, high = ( position + 1 ) * DENSITY * resolution, key = resolution + "_" + position; - - $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, low: low, high: high, dataset_id: this.dataset_id }, function ( data ) { - track.cache[key] = data; - $(document).trigger( "redraw" ); - }); + + if (!track.data_queue[key]) { + track.data_queue[key] = true; + $.getJSON( data_url, { track_type: this.track_type, chrom: this.view.chrom, + low: low, high: high, dataset_id: this.dataset_id, + resolution: this.view.resolution }, function ( data ) { + track.cache[key] = data; + delete track.data_queue[key]; + track.draw(); + }); + } }, draw_tile: function( resolution, tile_index, parent_element, w_scale ) { if (!this.vertical_range) { // We don't have the necessary information yet @@ -340,6 +351,7 @@ }); var FeatureTrack = function ( name, dataset_id, height ) { + this.tile_cache = new Cache(CACHED_TILES_FEATURE); Track.call( this, name, $("#viewport") ); TiledTrack.call( this ); @@ -409,9 +421,9 @@ if (end_ary[j] === undefined || end_ary[j] < f_start) { end_ary[j] = f_end; if (include_labels) { - this.zi_slots[feature.name] = j; + this.zi_slots[feature.uid] = j; } else { - this.zo_slots[feature.name] = j; + this.zo_slots[feature.uid] = j; } break; } @@ -466,7 +478,7 @@ if (feature.start <= tile_high && feature.end >= tile_low) { var f_start = Math.floor( Math.max(0, (feature.start - tile_low) * w_scale) ), f_end = Math.ceil( Math.min(width, (feature.end - tile_low) * w_scale) ), - y_center = this.slots[feature.name] * this.vertical_gap; + y_center = this.slots[feature.uid] * this.vertical_gap; var thickness, y_start, thick_start = null, thick_end = null; if (feature.thick_start && feature.thick_end) { diff -r 46791b5a653b -r d7c66019de13 static/trackster.css --- a/static/trackster.css Tue Nov 03 17:16:40 2009 -0500 +++ b/static/trackster.css Tue Nov 03 19:16:01 2009 -0500 @@ -25,6 +25,7 @@ font-size: 100%; } +/*canvas{ border-right: 1px solid red; } /* debugging */ #nav { padding: 0.5em 0; background:#cccccc; diff -r 46791b5a653b -r d7c66019de13 templates/tracks/browser.mako --- a/templates/tracks/browser.mako Tue Nov 03 17:16:40 2009 -0500 +++ b/templates/tracks/browser.mako Tue Nov 03 19:16:01 2009 -0500 @@ -122,6 +122,7 @@ <a href="#" onclick="javascript:view.zoom_in();view.redraw();">+</a> <a href="#" onclick="javascript:view.zoom_out();view.redraw();">-</a> </form> + <div id="debug" style="float: right"></div> </div> </div> </div>

1 0

[hg] galaxy 2950: imported patch alchemy05_fixes_02
by Greg Von Kuster 07 Nov '09

07 Nov '09

details: http://www.bx.psu.edu/hg/galaxy/rev/d872c1e16afb changeset: 2950:d872c1e16afb user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Nov 03 12:52:01 2009 -0500 description: imported patch alchemy05_fixes_02 diffstat: lib/galaxy/jobs/__init__.py | 6 +++--- lib/galaxy/model/mapping.py | 4 ++-- lib/galaxy/model/mapping_tests.py | 15 ++++++++------- lib/galaxy/model/migrate/versions/0025_user_info.py | 4 ++-- lib/galaxy/tools/actions/__init__.py | 7 ++++--- lib/galaxy/tools/actions/metadata.py | 5 +++-- lib/galaxy/tools/actions/upload_common.py | 4 +++- lib/galaxy/web/controllers/async.py | 6 +++--- lib/galaxy/web/controllers/dataset.py | 4 ++-- lib/galaxy/web/controllers/library.py | 6 +++--- lib/galaxy/web/controllers/library_admin.py | 12 ++++++++---- lib/galaxy/web/controllers/requests.py | 2 +- lib/galaxy/web/controllers/root.py | 10 +++++----- lib/galaxy/web/controllers/tool_runner.py | 2 -- lib/galaxy/web/framework/__init__.py | 23 ++++++++++++++--------- test/functional/test_forms_and_requests.py | 1 + test/functional/test_security_and_libraries.py | 2 +- test/functional/test_user_info.py | 3 ++- tools/data_source/microbial_import_code.py | 6 +++--- tools/filters/lav_to_bed_code.py | 1 - tools/maf/maf_to_bed_code.py | 4 +--- 21 files changed, 69 insertions(+), 58 deletions(-) diffs (567 lines): diff -r 133252175425 -r d872c1e16afb lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -199,7 +199,7 @@ try: # Clear the session for each job so we get fresh states for # job and all datasets - self.sa_session.clear() + self.sa_session.expunge_all() # Get the real job entity corresponding to the wrapper (if we # are tracking in the database this is probably cached in # the session from the origianl query above) @@ -346,7 +346,7 @@ Prepare the job to run by creating the working directory and the config files. """ - self.sa_session.clear() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner + self.sa_session.expunge_all() #this prevents the metadata reverting that has been seen in conjunction with the PBS job runner if not os.path.exists( self.working_directory ): os.mkdir( self.working_directory ) # Restore parameters from the database @@ -477,7 +477,7 @@ the contents of the output files. """ # default post job setup - self.sa_session.clear() + self.sa_session.expunge_all() job = self.sa_session.query( model.Job ).get( self.job_id ) # if the job was deleted, don't finish it if job.state == job.states.DELETED: diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/mapping.py --- a/lib/galaxy/model/mapping.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/mapping.py Tue Nov 03 12:52:01 2009 -0500 @@ -817,7 +817,7 @@ user=relation( User, backref="roles" ), non_private_roles=relation( User, backref="non_private_roles", - primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email & Role.table.c.type == 'private' ) ) ), + primaryjoin=( ( User.table.c.id == UserRoleAssociation.table.c.user_id ) & ( UserRoleAssociation.table.c.role_id == Role.table.c.id ) & not_( Role.table.c.name == User.table.c.email ) ) ), role=relation( Role ) ) ) @@ -1134,7 +1134,7 @@ # Pack everything into a bunch result = Bunch( **globals() ) result.engine = engine - result.flush = lambda *args, **kwargs: Session.flush( *args, **kwargs ) + # model.flush() has been removed. result.session = Session # For backward compatibility with "model.context.current" result.context = Session diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/mapping_tests.py --- a/lib/galaxy/model/mapping_tests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/mapping_tests.py Tue Nov 03 12:52:01 2009 -0500 @@ -19,16 +19,17 @@ d1 = model.HistoryDatasetAssociation( extension="interval", metadata=dict(chromCol=1,startCol=2,endCol=3 ), history=h2, create_dataset=True ) #h2.queries.append( q1 ) #h2.queries.append( model.Query( "h2->q2" ) ) - model.context.current.flush() - model.context.current.clear() + model.session.add_all( ( u, h1, h2, d1 ) ) + model.session.flush() + model.session.expunge_all() # Check - users = model.context.current.query( model.User ).all() + users = model.session.query( model.User ).all() assert len( users ) == 1 assert users[0].email == "james(a)foo.bar.baz" assert users[0].password == "password" assert len( users[0].histories ) == 1 assert users[0].histories[0].name == "History 1" - hists = model.context.current.query( model.History ).all() + hists = model.session.query( model.History ).all() assert hists[0].name == "History 1" assert hists[1].name == ( "H" * 255 ) assert hists[0].user == users[0] @@ -38,9 +39,9 @@ assert hists[1].datasets[0].file_name == os.path.join( "/tmp", *directory_hash_id( id ) ) + ( "/dataset_%d.dat" % id ) # Do an update and check hists[1].name = "History 2b" - model.context.current.flush() - model.context.current.clear() - hists = model.context.current.query( model.History ).all() + model.session.flush() + model.session.expunge_all() + hists = model.session.query( model.History ).all() assert hists[0].name == "History 1" assert hists[1].name == "History 2b" # gvk TODO need to ad test for GalaxySessions, but not yet sure what they should look like. diff -r 133252175425 -r d872c1e16afb lib/galaxy/model/migrate/versions/0025_user_info.py --- a/lib/galaxy/model/migrate/versions/0025_user_info.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0025_user_info.py Tue Nov 03 12:52:01 2009 -0500 @@ -21,7 +21,7 @@ log.addHandler( handler ) metadata = MetaData( migrate_engine ) -db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, transactional=False ) ) +db_session = scoped_session( sessionmaker( bind=migrate_engine, autoflush=False, autocommit=True ) ) def display_migration_details(): print "========================================" @@ -59,4 +59,4 @@ except Exception, e: log.debug( "Adding foreign key constraint 'user_form_values_id_fk' to table 'galaxy_user' failed: %s" % ( str( e ) ) ) def downgrade(): - pass \ No newline at end of file + pass diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -235,7 +235,7 @@ # Store output out_data[ name ] = data # Store all changes to database - trans.app.model.flush() + trans.sa_session.flush() # Add all the top-level (non-child) datasets to the history for name in out_data.keys(): if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created @@ -248,7 +248,7 @@ child_dataset = out_data[ child_name ] parent_dataset.children.append( child_dataset ) # Store data after custom code runs - trans.app.model.flush() + trans.sa_session.flush() # Create the job object job = trans.app.model.Job() job.session_id = trans.get_galaxy_session().id @@ -274,7 +274,8 @@ job.add_input_dataset( name, None ) for name, dataset in out_data.iteritems(): job.add_output_dataset( name, dataset ) - trans.app.model.flush() + trans.sa_session.add( job ) + trans.sa_session.flush() # Some tools are not really executable, but jobs are still created for them ( for record keeping ). # Examples include tools that redirect to other applications ( epigraph ). These special tools must # include something that can be retrieved from the params ( e.g., REDIRECT_URL ) to keep the job diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/metadata.py --- a/lib/galaxy/tools/actions/metadata.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/metadata.py Tue Nov 03 12:52:01 2009 -0500 @@ -26,7 +26,8 @@ job.tool_version = tool.version except: job.tool_version = "1.0.0" - job.flush() #ensure job.id is available + trans.sa_session.add( job ) + trans.sa_session.flush() #ensure job.id is available #add parameters to job_parameter table # Store original dataset state, so we can restore it. A separate table might be better (no chance of 'losing' the original state)? @@ -49,7 +50,7 @@ #Need a special state here to show that metadata is being set and also allow the job to run # i.e. if state was set to 'running' the set metadata job would never run, as it would wait for input (the dataset to set metadata on) to be in a ready state dataset.state = dataset.states.SETTING_METADATA - trans.app.model.flush() + trans.sa_session.flush() # Queue the job for execution trans.app.job_queue.put( job.id, tool ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Tue Nov 03 12:52:01 2009 -0500 @@ -121,6 +121,7 @@ trans.history.add_dataset( hda, genome_build = uploaded_dataset.dbkey ) permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) + trans.sa_session.flush() return hda def new_library_upload( trans, uploaded_dataset, library_bunch, state=None ): @@ -291,7 +292,8 @@ for i, dataset in enumerate( data_list ): job.add_output_dataset( 'output%i' % i, dataset ) job.state = job.states.NEW - trans.app.model.flush() + trans.sa_session.add( job ) + trans.sa_session.flush() # Queue the job for execution trans.app.job_queue.put( job.id, tool ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/async.py Tue Nov 03 12:52:01 2009 -0500 @@ -77,7 +77,7 @@ data.state = data.blurb = jobs.JOB_ERROR data.info = "Error -> %s" % STATUS - trans.model.flush() + trans.sa_session.flush() return "Data %s with status %s received. OK" % (data_id, STATUS) @@ -112,7 +112,7 @@ data.flush() open( data.file_name, 'wb' ).close() #create the file trans.history.add_dataset( data, genome_build=GALAXY_BUILD ) - trans.model.flush() + trans.sa_session.flush() trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id ) try: @@ -132,6 +132,6 @@ data.info = str(e) data.state = data.blurb = data.states.ERROR - trans.model.flush() + trans.sa_session.flush() return trans.fill_template('tool_executed.tmpl', out_data={}, tool=tool, config=self.app.config ) diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Tue Nov 03 12:52:01 2009 -0500 @@ -335,7 +335,7 @@ assert topmost_parent in history.datasets, "Data does not belong to current history" # Mark undeleted data.mark_undeleted() - self.app.model.flush() + trans.sa_session.flush() trans.log_event( "Dataset id %s has been undeleted" % str(id) ) return True return False @@ -407,7 +407,7 @@ hist.add_dataset( data.copy( copy_children = True ) ) if history in target_histories: refresh_frames = ['history'] - trans.app.model.flush() + trans.sa_session.flush() done_msg = "%i datasets copied to %i histories." % ( len( source_dataset_ids ) - invalid_datasets, len( target_histories ) ) trans.sa_session.refresh( history ) elif create_new_history: diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/library.py Tue Nov 03 12:52:01 2009 -0500 @@ -421,7 +421,7 @@ if trans.app.security_agent.can_modify_library_item( user, roles, ldda ): if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() msg = "Data type changed for library dataset '%s'" % ldda.name messagetype = 'done' else: @@ -463,7 +463,7 @@ setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) ldda.metadata.dbkey = dbkey ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' else: @@ -486,7 +486,7 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) ldda.datatype.set_meta( ldda ) ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' else: diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Tue Nov 03 12:52:01 2009 -0500 @@ -432,7 +432,7 @@ # The user clicked the Save button on the 'Change data type' form if ldda.datatype.allow_datatype_change and trans.app.datatypes_registry.get_datatype_by_extension( params.datatype ).allow_datatype_change: trans.app.datatypes_registry.change_datatype( ldda, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() msg = "Data type changed for library dataset '%s'" % ldda.name return trans.fill_template( "/admin/library/ldda_edit_info.mako", ldda=ldda, @@ -469,7 +469,7 @@ setattr( ldda.metadata, name, spec.unwrap( params.get ( name, None ) ) ) ldda.metadata.dbkey = dbkey ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name messagetype = 'done' return trans.fill_template( "/admin/library/ldda_edit_info.mako", @@ -488,7 +488,7 @@ setattr( ldda.metadata, name, spec.unwrap( spec.get( 'default' ) ) ) ldda.datatype.set_meta( ldda ) ldda.datatype.after_edit( ldda ) - trans.app.model.flush() + trans.sa_session.flush() msg = 'Attributes updated for library dataset %s' % ldda.name return trans.fill_template( "/admin/library/ldda_edit_info.mako", ldda=ldda, @@ -674,6 +674,10 @@ replace_id = params.get( 'replace_id', None ) if replace_id not in [ None, 'None' ]: replace_dataset = trans.sa_session.query( trans.app.model.LibraryDataset ).get( int( replace_id ) ) + # The name is separately - by the time the new ldda is created, + # replace_dataset.name will point to the new ldda, not the one it's + # replacing. + replace_dataset_name = replace_dataset.name if not last_used_build: last_used_build = replace_dataset.library_dataset_dataset_association.dbkey # Don't allow multiple datasets to be uploaded when replacing a dataset with a new version @@ -701,7 +705,7 @@ if created_outputs: total_added = len( created_outputs.values() ) if replace_dataset: - msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset.name, folder.name ) + msg = "Added %d dataset versions to the library dataset '%s' in the folder '%s'." % ( total_added, replace_dataset_name, folder.name ) else: if not folder.parent: # Libraries have the same name as their root_folder diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Tue Nov 03 12:52:01 2009 -0500 @@ -294,7 +294,7 @@ # save all the new/unsaved samples entered by the user if edit_mode == 'False': for index in range(len(current_samples)-len(request.samples)): - sample_index = index + len(request.samples) + sample_index = len(request.samples) sample_name = util.restore_text( params.get( 'sample_%i_name' % sample_index, '' ) ) sample_values = [] for field_index in range(len(request.type.sample_form.fields)): diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/root.py Tue Nov 03 12:52:01 2009 -0500 @@ -277,7 +277,7 @@ if not __ok_to_edit_metadata( data.id ): return trans.show_error_message( "This dataset is currently being used as input or output. You cannot change datatype until the jobs have completed or you have canceled them." ) trans.app.datatypes_registry.change_datatype( data, params.datatype ) - trans.app.model.flush() + trans.sa_session.flush() else: return trans.show_error_message( "You are unable to change datatypes in this manner. Changing %s to %s is not allowed." % ( data.extension, params.datatype ) ) elif params.save: @@ -303,7 +303,7 @@ data.datatype.after_edit( data ) else: msg = ' (Metadata could not be changed because this dataset is currently being used as input or output. You must cancel or wait for these jobs to complete before changing metadata.)' - trans.app.model.flush() + trans.sa_session.flush() return trans.show_ok_message( "Attributes updated%s" % msg, refresh_frames=['history'] ) elif params.detect: # The user clicked the Auto-detect button on the 'Edit Attributes' form @@ -322,7 +322,7 @@ msg = 'Attributes updated' data.set_meta() data.datatype.after_edit( data ) - trans.app.model.flush() + trans.sa_session.flush() return trans.show_ok_message( msg, refresh_frames=['history'] ) elif params.convert_data: target_type = kwd.get("target_type", None) @@ -383,7 +383,7 @@ if job.check_if_output_datasets_deleted(): job.mark_deleted() self.app.job_manager.job_stop_queue.put( job.id ) - self.app.model.flush() + trans.sa_session.flush() @web.expose def delete( self, trans, id = None, show_deleted_on_refresh = False, **kwd): @@ -432,7 +432,7 @@ for dataset in history.datasets: dataset.deleted = True dataset.clear_associated_files() - self.app.model.flush() + trans.sa_session.flush() trans.log_event( "History id %s cleared" % (str(history.id)) ) trans.response.send_redirect( url_for("/index" ) ) @web.expose diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/controllers/tool_runner.py --- a/lib/galaxy/web/controllers/tool_runner.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/controllers/tool_runner.py Tue Nov 03 12:52:01 2009 -0500 @@ -198,8 +198,6 @@ # pasted data datasets.append( create_dataset( 'Pasted Entry' ) ) break - if datasets: - trans.model.flush() return [ d.id for d in datasets ] @web.expose diff -r 133252175425 -r d872c1e16afb lib/galaxy/web/framework/__init__.py --- a/lib/galaxy/web/framework/__init__.py Tue Nov 03 12:52:00 2009 -0500 +++ b/lib/galaxy/web/framework/__init__.py Tue Nov 03 12:52:01 2009 -0500 @@ -139,7 +139,7 @@ self.__galaxy_session = NOT_SET base.DefaultWebTransaction.__init__( self, environ ) self.setup_i18n() - self.sa_session.clear() + self.sa_session.expunge_all() self.debug = asbool( self.app.config.get( 'debug', False ) ) # Flag indicating whether we are in workflow building mode (means # that the current history should not be used for parameter values @@ -302,12 +302,12 @@ self.galaxy_session = galaxy_session # Do we need to flush the session? if galaxy_session_requires_flush: - objects_to_flush = [ galaxy_session ] + sa_session.add( galaxy_session ) # FIXME: If prev_session is a proper relation this would not # be needed. if prev_galaxy_session: - objects_to_flush.append( prev_galaxy_session ) - sa_session.flush( objects_to_flush ) + sa_session.add( prev_galaxy_session ) + sa_session.flush() # If the old session was invalid, get a new history with our new session if invalidate_existing_session: self.new_history() @@ -427,7 +427,8 @@ if not last_accessed: # Only set default history permissions if current history is not from a previous session self.app.security_agent.history_set_default_permissions( history, dataset=True, bypass_manage_permission=True ) - self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session, history ] ) + self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session, history ) ) + self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name='galaxysession' ) def handle_user_logout( self ): @@ -439,7 +440,8 @@ prev_galaxy_session = self.galaxy_session prev_galaxy_session.is_valid = False self.galaxy_session = self.__create_new_session( prev_galaxy_session ) - self.sa_session.flush( [ prev_galaxy_session, self.galaxy_session ] ) + self.sa_session.add_all( ( prev_galaxy_session, self.galaxy_session ) ) + self.sa_session.flush() # This method is not called from the Galaxy reports, so the cookie will always be galaxysession self.__update_session_cookie( name='galaxysession' ) @@ -466,7 +468,8 @@ def set_history( self, history ): if history and not history.deleted: self.galaxy_session.current_history = history - self.sa_session.flush( [ self.galaxy_session ] ) + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() history = property( get_history, set_history ) def new_history( self, name=None ): """ @@ -489,7 +492,8 @@ # Set the user's default history permissions self.app.security_agent.history_set_default_permissions( history ) # Save - self.sa_session.flush( [ self.galaxy_session, history ] ) + self.sa_session.add_all( ( self.galaxy_session, history ) ) + self.sa_session.flush() return history def get_user( self ): @@ -498,7 +502,8 @@ def set_user( self, user ): """Set the current user.""" self.galaxy_session.user = user - self.sa_session.flush( [ self.galaxy_session ] ) + self.sa_session.add( self.galaxy_session ) + self.sa_session.flush() user = property( get_user, set_user ) def get_user_and_roles( self ): diff -r 133252175425 -r d872c1e16afb test/functional/test_forms_and_requests.py --- a/test/functional/test_forms_and_requests.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_forms_and_requests.py Tue Nov 03 12:52:01 2009 -0500 @@ -29,6 +29,7 @@ .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) for fdc in fdc_list: + sa_session.refresh( fdc.latest_form ) if form_name == fdc.latest_form.name: return fdc.latest_form return None diff -r 133252175425 -r d872c1e16afb test/functional/test_security_and_libraries.py --- a/test/functional/test_security_and_libraries.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_security_and_libraries.py Tue Nov 03 12:52:01 2009 -0500 @@ -156,7 +156,7 @@ raise AssertionError( '%s not in history id %d default_permissions after they were changed' % ( value.action, latest_history.id ) ) # Add a dataset to the history self.upload_file( '1.bed' ) - latest_dataset = galaxy.model.Dataset.query().order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() + latest_dataset = sa_session.query( galaxy.model.Dataset ).order_by( desc( galaxy.model.Dataset.table.c.create_time ) ).first() # Make sure DatasetPermissionss are correct if len( latest_dataset.actions ) != len( latest_history.default_permissions ): raise AssertionError( '%d DatasetPermissionss were created for dataset id %d when it was created ( should have been %d )' % \ diff -r 133252175425 -r d872c1e16afb test/functional/test_user_info.py --- a/test/functional/test_user_info.py Tue Nov 03 12:52:00 2009 -0500 +++ b/test/functional/test_user_info.py Tue Nov 03 12:52:01 2009 -0500 @@ -14,6 +14,7 @@ .filter( galaxy.model.FormDefinitionCurrent.table.c.deleted==False ) \ .order_by( galaxy.model.FormDefinitionCurrent.table.c.create_time.desc() ) for fdc in fdc_list: + sa_session.refresh( fdc.latest_form ) if form_name == fdc.latest_form.name: return fdc.latest_form return None @@ -146,4 +147,4 @@ self.visit_page('forms/manage?show_filter=Deleted') self.check_page_for_string(form_one_latest.name) self.logout() - \ No newline at end of file + diff -r 133252175425 -r d872c1e16afb tools/data_source/microbial_import_code.py --- a/tools/data_source/microbial_import_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/data_source/microbial_import_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -123,7 +123,7 @@ data = app.datatypes_registry.change_datatype( data, file_type ) data.init_meta() data.set_peek() - app.model.flush() + data.flush() elif fields[0] == "#NewFile": description = fields[1] chr = fields[2] @@ -137,7 +137,7 @@ newdata.flush() app.security_agent.copy_dataset_permissions( base_dataset.dataset, newdata.dataset ) history.add_dataset( newdata ) - app.model.flush() + history.flush() try: copyfile(filepath,newdata.file_name) newdata.info = newdata.name @@ -148,4 +148,4 @@ newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() - app.model.flush() + newdata.flush() diff -r 133252175425 -r d872c1e16afb tools/filters/lav_to_bed_code.py --- a/tools/filters/lav_to_bed_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/filters/lav_to_bed_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -16,4 +16,3 @@ data.flush() except: continue - app.model.flush() \ No newline at end of file diff -r 133252175425 -r d872c1e16afb tools/maf/maf_to_bed_code.py --- a/tools/maf/maf_to_bed_code.py Tue Nov 03 12:52:00 2009 -0500 +++ b/tools/maf/maf_to_bed_code.py Tue Nov 03 12:52:01 2009 -0500 @@ -21,7 +21,6 @@ output_data.dbkey = dbkey output_data.name = basic_name + " (" + dbkey + ")" output_data.flush() - app.model.flush() output_data_list.append(output_data) elif line.startswith("#FILE"): fields = line.split("\t") @@ -36,7 +35,6 @@ app.security_agent.copy_dataset_permissions( output_data.dataset, newdata.dataset ) newdata.flush() history.flush() - app.model.flush() try: move(filepath,newdata.file_name) newdata.info = newdata.name @@ -47,7 +45,7 @@ newdata.dbkey = dbkey newdata.init_meta() newdata.set_peek() - app.model.flush() + newdata.flush() output_data_list.append(newdata) else: new_stdout = new_stdout + line

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