- galaxy-dev - lists.galaxyproject.org

Map of Heavens + Galaxy Dev Conf
by Anton Nekrutenko 10 Feb '10

10 Feb '10

Dear Galaxy Devs: two things: 1. MAP of HEAVENS ----------------- We would like to create a little map of the starry sky by painting locations of existing galaxies on a map. All we need is a URL of your instance. This is, of course, completely voluntary = we will not give this info to Google ;) and galaxy will always be free. 2. Galaxy Dev Conf ------------------ We are running the First Galaxy Developer Conference. Deadline for registration = April 1st. Where and When ============== May 15 - 17 Cold Spring Harbor Laboratory, NY http://www.galaxyproject.org/dev2010 What is Galaxy (well, you probably already know ) ================================================= Galaxy (http://usegalaxy.org) makes it easy to perform analysis interactively through the web, on arbitrarily large datasets. With hundreds of tools there are few limits on what can be done. Now with NGS analysis workflows (including numerous Illumina-, SOLiD-, and 454- specific tools), trackster browser, and collaborative pages you can do more in the Cloud. Galaxy is distributed under BSD-like license. What is Galaxy Developer Conference =================================== The goal of this meeting is to bring together developers, data producers, and tool creators to discuss and implement new way for integration of NGS analysis practices and to create a seamless user experience. We will cover the following aspects of Galaxy framework: The hitchhiker's guide to Galaxy architecture Integration of tools (including NGS analysis tools) and distributed job management Deployment of private Galaxy instances on local resources and on the Cloud Management of large datasets with the Galaxy Library System Using the Galaxy LIMS functionality at NGS sequencing facilities LET US KNOW! THANK YOU! anton + the team Anton Nekrutenko http://usegalaxy.org

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Problem with job & database
by Dijk, F van 10 Feb '10

10 Feb '10

Hi, I have a problem with Galaxy which we're running locally. Somehow we overloaded Galaxy with the jobs which resulted in the database server going down. Now when I try to restart Galaxy the following error is displayed: galaxy.jobs DEBUG 2010-02-08 17:14:08,705 recovering job 1050 in local runner Traceback (most recent call last): File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/web/buildapp.py ", line 61, in app_factory app = UniverseApplication( global_conf = global_conf, **kwargs ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/app.py", line 67, in __init__ self.job_manager = jobs.JobManager( self ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 42, in __init__ self.job_queue = JobQueue( app, self.dispatcher ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 120, in __init__ self.__check_jobs_at_startup() File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 148, in __check_jobs_at_startup self.dispatcher.recover( job, job_wrapper ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 785, in recover self.job_runners[runner_name].recover( job, job_wrapper ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/runners/lo cal.py", line 179, in recover job_wrapper.change_state( model.Job.states.ERROR, info = "This job was killed when Galaxy was restarted. Please retry the job." ) File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.p y", line 460, in change_state dataset.state = state File "/data/home/data/sequences/galaxy/galaxy-dist/lib/galaxy/model/__init__. py", line 478, in set_dataset_state object_session( self ).flush() #flush here, because hda.flush() won't flush the Dataset object File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1356, in flush self._flush(objects) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/session.py", line 1434, in _flush flush_context.execute() File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 261, in execute UOWExecutor().execute(self, tasks) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 753, in execute self.execute_save_steps(trans, task) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 768, in execute_save_steps self.save_objects(trans, task) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/unitofwork.py", line 759, in save_objects task.mapper._save_obj(task.polymorphic_tosave_objects, trans) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/orm/mapper.py", line 1413, in _save_obj c = connection.execute(statement.values(value_params), params) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 896, in __execute_context self._cursor_execute(context.cursor, context.statement, context.parameters[0], context=context) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 950, in _cursor_execute self._handle_dbapi_exception(e, statement, parameters, cursor, context) File "/data/home/data/sequences/galaxy/galaxy-dist/eggs/py2.6-noplatform/SQLA lchemy-0.5.6_dev_r6498-py2.6.egg/sqlalchemy/engine/base.py", line 931, in _handle_dbapi_exception raise exc.DBAPIError.instance(statement, parameters, e, connection_invalidated=is_disconnect) OperationalError: (OperationalError) unable to open database file u'UPDATE dataset SET update_time=?, state=? WHERE dataset.id = ?' ['2010-02-08 16:14:08.738227', 'error', 1084] Do you know how to solve this problem? I hope to hear from you soon. Regards, Freerk van Dijk De inhoud van dit bericht is vertrouwelijk en alleen bestemd voor de geadresseerde(n). Anderen dan de geadresseerde(n) mogen geen gebruik maken van dit bericht, het niet openbaar maken of op enige wijze verspreiden of vermenigvuldigen. Het UMCG kan niet aansprakelijk gesteld worden voor een incomplete aankomst of vertraging van dit verzonden bericht. The contents of this message are confidential and only intended for the eyes of the addressee(s). Others than the addressee(s) are not allowed to use this message, to make it public or to distribute or multiply this message in any way. The UMCG cannot be held responsible for incomplete reception or delay of this transferred message.

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QueuePool error
by SHAUN WEBB 10 Feb '10

10 Feb '10

Hi, our Galaxy server is showing a timeout error: TimeoutError: QueuePool limit of size 10 overflow 20 reached, connection timed out, timeout 30 I assume this is due to overuse as it is consistent with the database settings in the universe.wsgi file. First of all, is there anyway to view and cancel queued jobs? I usually use the admin page but this is not accessible at the moment. Secondly, we plan for Galaxy to be used on a large scale, is there anyway of preventing this type of error in future? I've included the full traceback below. Thanks in advance for any help Shaun Webb URL: http://bifx3.bio.ed.ac.uk:8080/admin Module paste.exceptions.errormiddleware:143 in __call__ << try: __traceback_supplement__ = Supplement, self, environ app_iter = self.application(environ, start_response) return self.make_catching_iter(app_iter, environ) except:>> app_iter = self.application(environ, start_response) Module paste.debug.prints:98 in __call__ << try: status, headers, body = wsgilib.intercept_output( environ, self.app) if status is None: # Some error occurred >> environ, self.app) Module paste.wsgilib:539 in intercept_output << data.append(headers) return output.write app_iter = application(environ, replacement_start_response) if data[0] is None: return (None, None, app_iter)>> app_iter = application(environ, replacement_start_response) Module paste.recursive:80 in __call__ << environ['paste.recursive.script_name'] = my_script_name try: return self.application(environ, start_response) except ForwardRequestException, e: middleware = CheckForRecursionMiddleware(>> return self.application(environ, start_response) Module paste.httpexceptions:632 in __call__ << []).append(HTTPException) try: return self.application(environ, start_response) except HTTPException, exc: return exc(environ, start_response)>> return self.application(environ, start_response) Module galaxy.web.framework.base:99 in __call__ << rc.environ = environ # Setup the transaction trans = self.transaction_factory( environ ) rc.redirect = trans.response.send_redirect # Get the controller class >> trans = self.transaction_factory( environ ) Module galaxy.web.framework:110 in <lambda> << def __init__( self, galaxy_app, session_cookie='galaxysession' ): base.WebApplication.__init__( self ) self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) # Mako support self.mako_template_lookup = mako.lookup.TemplateLookup(>> self.set_transaction_factory( lambda e: UniverseWebTransaction( e, galaxy_app, self, session_cookie ) ) Module galaxy.web.framework:150 in __init__ << self.workflow_building_mode = False # Always have a valid galaxy session self.__ensure_valid_session( session_cookie ) # Prevent deleted users from accessing Galaxy if self.app.config.use_remote_user and self.galaxy_session.user.deleted:>> self.__ensure_valid_session( session_cookie ) Module galaxy.web.framework:279 in __ensure_valid_session << galaxy_session = self.sa_session.query( self.app.model.GalaxySession ) \ .filter( and_( self.app.model.GalaxySession.table.c.session_key==session_key, self.app.model.GalaxySession.table.c.is_valid==True ) ) \ .first() # If remote user is in use it can invalidate the session, so we need to to check some things now. >> self.app.model.GalaxySession.table.c.is_valid==True ) ) Module sqlalchemy.orm.query:1300 in first << ret = list(self)[0:1] else: ret = list(self[0:1]) if len(ret) > 0: return ret[0]>> ret = list(self[0:1]) Module sqlalchemy.orm.query:1221 in __getitem__ << return list(res)[None:None:item.step] else: return list(res) else: return list(self[item:item+1])[0]>> return list(res) Module sqlalchemy.orm.query:1361 in __iter__ << if self._autoflush and not self._populate_existing: self.session._autoflush() return self._execute_and_instances(context) def _execute_and_instances(self, querycontext):>> return self._execute_and_instances(context) Module sqlalchemy.orm.query:1364 in _execute_and_instances << def _execute_and_instances(self, querycontext): result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) return self.instances(result, querycontext)>> result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) Module sqlalchemy.orm.session:754 in execute << engine = self.get_bind(mapper, clause=clause, **kw) return self.__connection(engine, close_with_result=True).execute( clause, params or {})>> return self.__connection(engine, close_with_result=True).execute( Module sqlalchemy.orm.session:721 in __connection << return self.transaction._connection_for_bind(engine) else: return engine.contextual_connect(**kwargs) def execute(self, clause, params=None, mapper=None, **kw):>> return engine.contextual_connect(**kwargs) Module sqlalchemy.engine.base:1229 in contextual_connect << """ return self.Connection(self, self.pool.connect(), close_with_result=close_with_result, **kwargs) def table_names(self, schema=None, connection=None):>> return self.Connection(self, self.pool.connect(), close_with_result=close_with_result, **kwargs) Module sqlalchemy.pool:142 in connect << def connect(self): if not self._use_threadlocal: return _ConnectionFairy(self).checkout() try:>> return _ConnectionFairy(self).checkout() Module sqlalchemy.pool:304 in __init__ << self.__counter = 0 try: rec = self._connection_record = pool.get() conn = self.connection = self._connection_record.get_connection() self._connection_record.backref = weakref.ref(self, lambda ref:_finalize_fairy(conn, rec, pool, ref))>> rec = self._connection_record = pool.get() Module sqlalchemy.pool:161 in get << def get(self): return self.do_get() def do_get(self):>> return self.do_get() Module sqlalchemy.pool:628 in do_get << return self.do_get() else: raise exc.TimeoutError("QueuePool limit of size %d overflow %d reached, connection timed out, timeout %d" % (self.size(), self.overflow(), self._timeout)) if self._overflow_lock is not None:>> raise exc.TimeoutError("QueuePool limit of size %d overflow %d reached, connection timed out, timeout %d" % (self.size(), self.overflow(), self._timeout)) TimeoutError: QueuePool limit of size 10 overflow 20 reached, connection timed out, timeout 30 -- The University of Edinburgh is a charitable body, registered in Scotland, with registration number SC005336.

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[hg] galaxy 3361: Fix for a bug in library uploads introduced wi...
by Nate Coraor 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/606686b073f3 changeset: 3361:606686b073f3 user: Nate Coraor <nate(a)bx.psu.edu> date: Tue Feb 09 13:40:01 2010 -0500 description: Fix for a bug in library uploads introduced with recent PBS job name changes diffstat: lib/galaxy/jobs/__init__.py | 4 +++- 1 files changed, 3 insertions(+), 1 deletions(-) diffs (14 lines): diff -r b4c811246b1d -r 606686b073f3 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Tue Feb 09 11:21:53 2010 -0500 +++ b/lib/galaxy/jobs/__init__.py Tue Feb 09 13:40:01 2010 -0500 @@ -751,7 +751,9 @@ @property def user( self ): job = self.sa_session.query( model.Job ).get( self.job_id ) - if job.history.user is None: + if not job.history: + return 'non_history_job' + elif job.history.user is None: return 'anonymous@' + job.galaxy_session.remote_addr.split()[-1] else: return job.history.user.email

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[hg] galaxy 3360: LIMS: replaced os.system with subprocess to sp...
by Nate Coraor 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b4c811246b1d changeset: 3360:b4c811246b1d user: rc date: Tue Feb 09 11:21:53 2010 -0500 description: LIMS: replaced os.system with subprocess to spawn the data transfer daemon process diffstat: lib/galaxy/web/controllers/forms.py | 2 +- lib/galaxy/web/controllers/requests_admin.py | 42 +++++++++++++++++------ scripts/galaxy_messaging/server/daemon.py | 2 +- scripts/galaxy_messaging/server/data_transfer.py | 13 ++++-- 4 files changed, 40 insertions(+), 19 deletions(-) diffs (145 lines): diff -r 185eab051284 -r b4c811246b1d lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Tue Feb 09 04:16:26 2010 -0500 +++ b/lib/galaxy/web/controllers/forms.py Tue Feb 09 11:21:53 2010 -0500 @@ -137,7 +137,7 @@ msg=msg, messagetype='error', name=util.restore_text( params.get( 'name', '' ) ), - description=util.restore_text( params.get( 'description', '' ) ) ) ) + description=util.restore_text( params.get( 'description', '' ) ) )) self.__get_saved_form( fd ) if self.__imported_from_file: return trans.response.send_redirect( web.url_for( controller='forms', diff -r 185eab051284 -r b4c811246b1d lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Tue Feb 09 04:16:26 2010 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Tue Feb 09 11:21:53 2010 -0500 @@ -4,7 +4,7 @@ from galaxy.datatypes import sniff from galaxy import util from galaxy.util.streamball import StreamBall -import logging, tempfile, zipfile, tarfile, os, sys +import logging, tempfile, zipfile, tarfile, os, sys, subprocess from galaxy.web.form_builder import * from datetime import datetime, timedelta from galaxy.web.controllers.forms import get_all_forms @@ -1526,31 +1526,49 @@ sample_id=trans.security.encode_id(sample.id), messagetype='error', msg=msg)) + error_msg = '' transfer_script = "scripts/galaxy_messaging/server/daemon.py" for index, dataset in enumerate(sample.dataset_files): dfile = dataset[0] status = dataset[1] if status == sample.transfer_status.NOT_STARTED: - cmd = "python %s %s %s %s %s %s %s %s %s" % ( transfer_script, - datatx_info['host'], - datatx_info['username'], - datatx_info['password'], - dfile, - sample.id, - index, - trans.security.encode_id(sample.library.id), - trans.security.encode_id(sample.folder.id)) + cmd = ( "python", + transfer_script, + datatx_info['host'], + datatx_info['username'], + datatx_info['password'], + dfile, + str(sample.id), + str(index), + trans.security.encode_id(sample.library.id), + trans.security.encode_id(sample.folder.id) ) # set the transfer status sample.dataset_files[index][1] = sample.transfer_status.IN_PROGRESS trans.sa_session.add( sample ) trans.sa_session.flush() - os.system(cmd) + try: + retcode = subprocess.call(cmd) + except Exception, e: + error_msg = dfile.split('/')[-1] + ": Data transfer failed. " + str(e) + "<br/>" + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='show_datatx_page', + sample_id=trans.security.encode_id(sample.id), + folder_path=os.path.dirname(dfile), + messagetype='error', + msg=error_msg)) # set the sample state to the last state if sample.current_state().id != sample.request.type.states[-1].id: event = trans.app.model.SampleEvent(sample, sample.request.type.states[-1], - 'The dataset are ready & are being transfered to Galaxy') + 'The dataset is ready and are being transfered to Galaxy') trans.sa_session.add( event ) trans.sa_session.flush() + if error_msg: + return trans.response.send_redirect( web.url_for( controller='requests_admin', + action='show_datatx_page', + sample_id=trans.security.encode_id(sample.id), + folder_path=os.path.dirname(dfile), + messagetype='error', + msg=error_msg)) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='show_datatx_page', sample_id=trans.security.encode_id(sample.id), diff -r 185eab051284 -r b4c811246b1d scripts/galaxy_messaging/server/daemon.py --- a/scripts/galaxy_messaging/server/daemon.py Tue Feb 09 04:16:26 2010 -0500 +++ b/scripts/galaxy_messaging/server/daemon.py Tue Feb 09 11:21:53 2010 -0500 @@ -29,6 +29,6 @@ sys.exit(0) # Exit first parent. except OSError, e: sys.stderr.write("fork #1 failed: (%d) %sn" % (e.errno, e.strerror)) - sys.exit(1) + sys.exit(2) os.execv(os.path.join( os.getcwd(), "scripts/galaxy_messaging/server/data_transfer.py"), sys.argv) diff -r 185eab051284 -r b4c811246b1d scripts/galaxy_messaging/server/data_transfer.py --- a/scripts/galaxy_messaging/server/data_transfer.py Tue Feb 09 04:16:26 2010 -0500 +++ b/scripts/galaxy_messaging/server/data_transfer.py Tue Feb 09 11:21:53 2010 -0500 @@ -41,8 +41,8 @@ curr_dir = os.getcwd() logfile = os.path.join(curr_dir, 'data_transfer.log') -logging.basicConfig(filename=logfile, level=logging.DEBUG, - format="%(asctime)s [%(levelname)s] %(message)s") +logging.basicConfig(filename=sys.stdout, level=logging.DEBUG, + format="%(asctime)s [%(levelname)s] %(message)s") class DataTransferException(Exception): def __init__(self, value): @@ -137,7 +137,9 @@ timeout=10) logging.debug(output) if not os.path.exists(os.path.join(self.server_dir, os.path.basename(self.remote_file))): - raise Exception + raise DataTransferException('Could not find the local file after transfer (%s)' % os.path.join(self.server_dir, os.path.basename(self.remote_file))) + except DataTransferException, (e): + self.error_and_exit(e.msg) except: self.error_and_exit() @@ -192,6 +194,8 @@ raise DataTransferException("The "+email+" user could not logout of Galaxy") except DataTransferException, (e): self.error_and_exit(e.msg) + except: + self.error_and_exit() def update_status(self, status): ''' @@ -202,7 +206,6 @@ df = from_json_string(galaxy.get_sample_dataset_files(self.sample_id)) logging.debug(df) df[self.dataset_index][1] = status - galaxy.set_sample_dataset_files(self.sample_id, to_json_string(df)) logging.debug("######################\n"+str(from_json_string(galaxy.get_sample_dataset_files(self.sample_id))[self.dataset_index])) except: @@ -219,5 +222,5 @@ dt = DataTransfer(sys.argv[1], sys.argv[2], sys.argv[3], sys.argv[4], int(sys.argv[5]), int(sys.argv[6]), sys.argv[7], sys.argv[8]) dt.start() + sys.exit(0) -

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Re: [galaxy-dev] galaxy-dev Digest, Vol 50, Issue 10
by Ross 09 Feb '10

09 Feb '10

#3351 should fix this - Juan, can you please try pulling the current code to see if it works for you? Also, some notes on how to maintain a local code repository have also been added to section 6 of http://bitbucket.org/galaxy/galaxy-central/wiki/GetGalaxy - no need to do a fresh clone each time you want to update your local copy. Fixes and comments on the updated notes welcomed... On Mon, Feb 8, 2010 at 12:37 PM, <galaxy-dev-request(a)lists.bx.psu.edu>wrote: > > > Message: 1 > Date: Fri, 5 Feb 2010 18:13:05 -0500 > From: Kanwei Li <kanwei(a)gmail.com> > To: Juan Perin <juanperin(a)gmail.com>, James Taylor > <james.taylor(a)emory.edu> > Cc: galaxy-dev(a)bx.psu.edu > Subject: Re: [galaxy-dev] Python problems > Message-ID: > <1469e4b41002051513o5a21793an348c37646724cb3e(a)mail.gmail.com> > Content-Type: text/plain; charset=UTF-8 > > Hi Juan, > > After some searching it seems that it is an issue with python2.4 and > hashlib. We recently introduced a change that might be responsible for > this (commit 3311) and we'll look into it. > > Thanks, > > Kanwei > > On Fri, Feb 5, 2010 at 12:47 PM, Juan Perin <juanperin(a)gmail.com> wrote: > > I've been working with a much older release of galaxy for a while, and it > > has worked great for the last few months. ?I noticed some progress with > the > > NGS tools, so decided to attempt updating. ?My first mistake was in not > > knowing how to do so, so I essentially decided to start from the hg clone > > step and rebuild galaxy entirely in a new place on the same machine. ? ?I > > stupidly ran the database update script without listening to the warning > > about backing up the original galaxy db. ?So, my original instance won't > > work now... > > So, i'm trying to get the new instance working. ?Copied over my universe > > file and the custom .loc files from tool-data/ . ?everything seems to be > ok, > > however I'm getting a python error that essentially repeats for anything > I > > try to do, I'll paste the full output below for reference. ?I'm using > python > > 2.4 > > Any ideas? > > Thanks in advance. > > URL: http://variome.chop.edu:8082/tool_runner?tool_id=bowtie_wrapperFile > > > '/opt/galaxy-dist/eggs/py2.4-noplatform/WebError-0.8a-py2.4.egg/weberror/evalexception/middleware.py', > > line 364 in respond app_iter = self.application(environ, > > detect_start_response) File > > > '/opt/galaxy-dist/eggs/py2.4-noplatform/Paste-1.6-py2.4.egg/paste/debug/prints.py', > > line 97 in __call__ status, headers, body = wsgilib.intercept_output( > File > > > '/opt/galaxy-dist/eggs/py2.4-noplatform/Paste-1.6-py2.4.egg/paste/wsgilib.py', > > line 539 in intercept_output app_iter = application(environ, > > replacement_start_response) File > > > '/opt/galaxy-dist/eggs/py2.4-noplatform/Paste-1.6-py2.4.egg/paste/recursive.py', > > line 80 in __call__ return self.application(environ, start_response) File > > > '/opt/galaxy-dist/eggs/py2.4-noplatform/Paste-1.6-py2.4.egg/paste/httpexceptions.py', > > line 632 in __call__ return self.application(environ, start_response) > File > > '/opt/galaxy-dist/lib/galaxy/web/framework/base.py', line 125 in __call__ > > body = method( trans, **kwargs ) File > > '/opt/galaxy-dist/lib/galaxy/web/controllers/tool_runner.py', line 61 in > > index return trans.fill_template( template, history=history, > > toolbox=toolbox, tool=tool, util=util, add_frame=add_frame, **vars ) File > > '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 602 in > > fill_template return self.fill_template_mako( filename, **kwargs ) File > > '/opt/galaxy-dist/lib/galaxy/web/framework/__init__.py', line 613 in > > fill_template_mako return template.render( **data ) File > > > '/opt/galaxy-dist/eggs/py2.4-noplatform/Mako-0.2.5-py2.4.egg/mako/template.py', > > line 133 in render return runtime._render(self, self.callable_, args, > data) > > File > > > '/opt/galaxy-dist/eggs/py2.4-noplatform/Mako-0.2.5-py2.4.egg/mako/runtime.py', > > line 364 in _render _render_context(template, callable_, context, *args, > > **_kwargs_for_callable(callable_, data)) File > > > '/opt/galaxy-dist/eggs/py2.4-noplatform/Mako-0.2.5-py2.4.egg/mako/runtime.py', > > line 381 in _render_context _exec_template(inherit, lclcontext, > args=args, > > kwargs=kwargs) File > > > '/opt/galaxy-dist/eggs/py2.4-noplatform/Mako-0.2.5-py2.4.egg/mako/runtime.py', > > line 414 in _exec_template callable_(context, *args, **kwargs) File > > '/opt/galaxy-dist/database/compiled_templates/tool_form.mako.py', line > 103 > > in render_body __M_writer(unicode(util.object_to_string( > tool_state.encode( > > tool, app ) ))) File '/opt/galaxy-dist/lib/galaxy/tools/__init__.py', > line > > 216 in encode a = hmac_new( app.config.tool_secret, value ) File > > '/opt/galaxy-dist/lib/galaxy/util/hash_util.py', line 33 in hmac_new > return > > hmac.new( key, value, sha1 ).hexdigest() File > > '/usr/lib64/python2.4/hmac.py', line 107 in new return HMAC(key, msg, > > digestmod) File '/usr/lib64/python2.4/hmac.py', line 42 in __init__ > > self.outer = digestmod.new() AttributeError: 'builtin_function_or_method' > > object has no attribute 'new' >

1 0

[hg] galaxy 3359: Update tooltips using a modified version of ti...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/185eab051284 changeset: 3359:185eab051284 user: James Taylor <james(a)jamestaylor.org> date: Tue Feb 09 04:16:26 2010 -0500 description: Update tooltips using a modified version of tipsy, these can be used on any page if you include the tipsy script. Also, updating some styles and icons for tags. diffstat: static/images/fugue/tag--plus.png | 0 static/images/fugue/tags.png | 0 static/images/tipsy.gif | 0 static/june_2007_style/autocomplete_tagging.css.tmpl | 6 +- static/june_2007_style/base.css.tmpl | 58 ++++-- static/june_2007_style/blue/autocomplete_tagging.css | 4 +- static/june_2007_style/blue/base.css | 29 ++- static/june_2007_style/blue/history-buttons.png | 0 static/scripts/galaxy.base.js | 10 +- static/scripts/jquery.tipsy.js | 161 +++++++++++++++++++ static/scripts/packed/galaxy.base.js | 2 +- static/scripts/packed/jquery.tipsy.js | 1 + templates/root/history.mako | 44 ++-- templates/tagging_common.mako | 5 +- 14 files changed, 256 insertions(+), 64 deletions(-) diffs (492 lines): diff -r b36c13131ac7 -r 185eab051284 static/images/fugue/tag--plus.png Binary file static/images/fugue/tag--plus.png has changed diff -r b36c13131ac7 -r 185eab051284 static/images/fugue/tags.png Binary file static/images/fugue/tags.png has changed diff -r b36c13131ac7 -r 185eab051284 static/images/tipsy.gif Binary file static/images/tipsy.gif has changed diff -r b36c13131ac7 -r 185eab051284 static/june_2007_style/autocomplete_tagging.css.tmpl --- a/static/june_2007_style/autocomplete_tagging.css.tmpl Mon Feb 08 23:52:56 2010 -0500 +++ b/static/june_2007_style/autocomplete_tagging.css.tmpl Tue Feb 09 04:16:26 2010 -0500 @@ -94,12 +94,12 @@ display: inline-block; cursor: pointer; margin: 0.2em; - border: 0; + border: solid #bbb 1px; padding: 0.1em 0.5em 0.1em 0.5em; -moz-border-radius: .5em; -webkit-border-radius: .5em; border-radius: .5em; - background:#bbb; + background:#eee; } .tag-button img @@ -109,7 +109,7 @@ .tag-button .tag-name:hover { - color: white; + color: black; } .add-tag-button diff -r b36c13131ac7 -r 185eab051284 static/june_2007_style/base.css.tmpl --- a/static/june_2007_style/base.css.tmpl Mon Feb 08 23:52:56 2010 -0500 +++ b/static/june_2007_style/base.css.tmpl Tue Feb 09 04:16:26 2010 -0500 @@ -667,6 +667,9 @@ margin-left: 2px; ## Allow alt text for screen readers text-indent: 20px; + background-repeat:no-repeat; + background-position: 0px 0px; + padding: 0; } .icon-button.display { @@ -700,38 +703,53 @@ } .icon-button.tag { - background-image:url(/static/images/tag-label.png); - background-repeat:no-repeat; - background-position:center; - padding: 0px 0px 0px 0px; + background-image: url(/static/images/tag-label.png); +} + +.icon-button.tags { + background-image: url(/static/images/fugue/tags.png); +} + +.icon-button.tag--plus { + background-image: url(/static/images/fugue/tag--plus.png); } .icon-button.annotate { background-image:url(/static/images/sticky-note-text.png); background-repeat:no-repeat; background-position:center; - padding: 0px 0px 0px 0px; + padding: 0; } -.tooltip { - position: relative; - cursor: pointer; +.tipsy { + padding: 5px; + font-size: 10px; + filter: alpha(opacity=80); + background-repeat: no-repeat; + background-image: url(../images/tipsy.gif); +} +.tipsy-inner { + padding: 5px 8px 4px 8px; + background-color: black; + color: white; + max-width: 200px; + text-align: center; } -span.tip { - display: none +.tipsy-north { + background-position: top center; } -.tooltip:hover span.tip { - font-size: 90%; - display: block; - position: absolute; - left:2em; - bottom:1.75em; - background-color: black; - color: white; - text-align: center; - padding: 0.25em 0.5em; +.tipsy-south { + background-position: bottom center; +} + +.tipsy-east { + background-position: right center; +} + +.tipsy-west { + background-position: left center; } .editable-text { diff -r b36c13131ac7 -r 185eab051284 static/june_2007_style/blue/autocomplete_tagging.css --- a/static/june_2007_style/blue/autocomplete_tagging.css Mon Feb 08 23:52:56 2010 -0500 +++ b/static/june_2007_style/blue/autocomplete_tagging.css Tue Feb 09 04:16:26 2010 -0500 @@ -10,9 +10,9 @@ .individual-tag-area{border:solid 1px #eee;cursor:pointer;} .active-tag-area{background-color:white;} .toggle-link{font-weight:normal;padding:0.3em;margin-bottom:1em;width:100%;padding:0.2em 0em 0.2em 0em;} -.tag-button{width:auto;color:#444;text-decoration:none;display:inline-block;cursor:pointer;margin:0.2em;border:0;padding:0.1em 0.5em 0.1em 0.5em;-moz-border-radius:.5em;-webkit-border-radius:.5em;border-radius:.5em;background:#bbb;} +.tag-button{width:auto;color:#444;text-decoration:none;display:inline-block;cursor:pointer;margin:0.2em;border:solid #bbb 1px;padding:0.1em 0.5em 0.1em 0.5em;-moz-border-radius:.5em;-webkit-border-radius:.5em;border-radius:.5em;background:#eee;} .tag-button img{padding-left:0.4em;} -.tag-button .tag-name:hover{color:white;} +.tag-button .tag-name:hover{color:black;} .add-tag-button{margin-bottom:0.3em;vertical-align:middle;padding:0.3em;} .add-tag-button:hover{cursor:pointer;} .tag-input{vertical-align:bottom;border:none;outline:none;resize:none;} diff -r b36c13131ac7 -r 185eab051284 static/june_2007_style/blue/base.css --- a/static/june_2007_style/blue/base.css Mon Feb 08 23:52:56 2010 -0500 +++ b/static/june_2007_style/blue/base.css Tue Feb 09 04:16:26 2010 -0500 @@ -110,17 +110,22 @@ .text-content fieldset{border-color:#ccc;border:1px solid #ccc;} .text-content th,.text-content td{border-bottom:1px solid #ddd;border-right:1px solid #ccc;} .text-content th,.text-content td{padding:.8em;} -.icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;} -.icon-button.edit{background:url(history-buttons.png) no-repeat 0px -52px;} -.icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -78px;} +.icon-button{width:16px;height:16px;display:block;float:left;margin-left:2px;text-indent:20px;background-repeat:no-repeat;background-position:0px 0px;padding:0;} .icon-button.display{background:url(history-buttons.png) no-repeat 0px -0px;} .icon-button.display:hover{background:url(history-buttons.png) no-repeat 0px -26px;} -.icon-button.delete{background:url(history-buttons.png) no-repeat 0px -104px;} -.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -130px;} -.icon-button.tag{background-image:url(/static/images/tag-label.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} -.icon-button.annotate{background-image:url(/static/images/sticky-note-text.png);background-repeat:no-repeat;background-position:center;padding: 0px 0px 0px 0px;} -.tooltip {position: relative; cursor: pointer} -span.tip{display: none;} -.tooltip:hover span.tip{font-size: 90%; display: block;position: absolute;left:3em;bottom:1.75em; background-color: black;color: white;text-align: center;padding: 0.25em 0.5em;} -.editable-text{cursor:pointer} -.editable-text:hover{background-image:url();background-repeat:no-repeat;background-position:right} \ No newline at end of file +.icon-button.delete{background:url(history-buttons.png) no-repeat 0px -52px;} +.icon-button.delete:hover{background:url(history-buttons.png) no-repeat 0px -78px;} +.icon-button.edit{background:url(history-buttons.png) no-repeat 0px -104px;} +.icon-button.edit:hover{background:url(history-buttons.png) no-repeat 0px -130px;} +.icon-button.tag{background-image:url(/static/images/tag-label.png);} +.icon-button.tags{background-image:url(/static/images/fugue/tags.png);} +.icon-button.tag--plus{background-image:url(/static/images/fugue/tag--plus.png);} +.icon-button.annotate{background-image:url(/static/images/sticky-note-text.png);background-repeat:no-repeat;background-position:center;padding:0;} +.tipsy{padding:5px;font-size:10px;filter:alpha(opacity=80);background-repeat:no-repeat;background-image:url(../images/tipsy.gif);} +.tipsy-inner{padding:5px 8px 4px 8px;background-color:black;color:white;max-width:200px;text-align:center;} +.tipsy-north{background-position:top center;} +.tipsy-south{background-position:bottom center;} +.tipsy-east{background-position:right center;} +.tipsy-west{background-position:left center;} +.editable-text{cursor:pointer;} +.editable-text:hover{background-image:url();background-repeat:no-repeat;background-position:right;} diff -r b36c13131ac7 -r 185eab051284 static/june_2007_style/blue/history-buttons.png Binary file static/june_2007_style/blue/history-buttons.png has changed diff -r b36c13131ac7 -r 185eab051284 static/scripts/galaxy.base.js --- a/static/scripts/galaxy.base.js Mon Feb 08 23:52:56 2010 -0500 +++ b/static/scripts/galaxy.base.js Tue Feb 09 04:16:26 2010 -0500 @@ -14,11 +14,15 @@ }); } -jQuery(document).ready( function() { +$(document).ready( function() { // Links with confirmation - jQuery( "a[confirm]" ).click( function() { - return confirm( jQuery(this).attr( "confirm" ) ) + $( "a[confirm]" ).click( function() { + return confirm( $(this).attr( "confirm" ) ) }); + // Tooltips + if ( $.fn.tipsy ) { + $(".tooltip").tipsy( { gravity: 's' } ); + } // Make popup menus. make_popup_menus(); }); diff -r b36c13131ac7 -r 185eab051284 static/scripts/jquery.tipsy.js --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/static/scripts/jquery.tipsy.js Tue Feb 09 04:16:26 2010 -0500 @@ -0,0 +1,161 @@ +(function($) { + function fixTitle($ele) { + if ($ele.attr('title') || typeof($ele.attr('original-title')) != 'string') { + $ele.attr('original-title', $ele.attr('title') || '').removeAttr('title'); + } + } + + $.fn.tipsy = function(options) { + + options = $.extend({}, $.fn.tipsy.defaults, options); + + return this.each(function() { + + fixTitle($(this)); + var opts = $.fn.tipsy.elementOptions(this, options); + var timeout = null; + + $(this).hover(function() { + var self = this; + timeout = setTimeout(function() { + $.data(self, 'cancel.tipsy', true); + + var tip = $.data(self, 'active.tipsy'); + if (!tip) { + tip = $('<div class="tipsy"><div class="tipsy-inner"/></div>'); + tip.css({position: 'absolute', zIndex: 100000}); + $.data(self, 'active.tipsy', tip); + } + + fixTitle($(self)); + + var title; + if (typeof opts.title == 'string') { + title = $(self).attr(opts.title == 'title' ? 'original-title' : opts.title); + } else if (typeof opts.title == 'function') { + title = opts.title.call(self); + } + + tip.find('.tipsy-inner')[opts.html ? 'html' : 'text'](title || opts.fallback); + + + var pos = $.extend({}, $(self).offset(), {width: self.offsetWidth, height: self.offsetHeight}); + tip.get(0).className = 'tipsy'; // reset classname in case of dynamic gravity + tip.remove().css({top: 0, left: 0, visibility: 'hidden', display: 'block'}).appendTo(document.body); + + tip.css( { width: tip.width() + 1, height: tip.height() } ); + + var actualWidth = tip[0].offsetWidth, actualHeight = tip[0].offsetHeight; + var gravity = (typeof opts.gravity == 'function') ? opts.gravity.call(self) : opts.gravity; + + var top, left; + switch (gravity.charAt(0)) { + case 'n': + top = pos.top + pos.height; + left = pos.left + pos.width / 2 - actualWidth / 2; + tip.addClass('tipsy-north'); + break; + case 's': + top = pos.top - actualHeight; + left = pos.left + pos.width / 2 - actualWidth / 2; + tip.addClass('tipsy-south'); + break; + case 'e': + top = pos.top + pos.height / 2 - actualHeight / 2; + left = pos.left - actualWidth; + tip.addClass('tipsy-east'); + break; + case 'w': + top = pos.top + pos.height / 2 - actualHeight / 2; + left = pos.left + pos.width; + tip.addClass('tipsy-west'); + break; + } + // Shift if off screen + var window = $(window); + + top = Math.max( top, window.scrollTop() ); + top = Math.min( top, window.scrollTop() + window.height() - tip.outerHeight() ); + + var left_shift = 0; + if ( left < window.scrollLeft() ) { + left_shift = left - window.scrollLeft(); + } + var t = window.scrollLeft() + window.width() - tip.outerWidth(); + if ( left > t ) { + left_shift = left - t; + } + + left -= left_shift; + + tip.css( { left: left, top: top } ); + + // Shift background to center over element (not implemented for east/west) + switch (gravity.charAt(0)) { + case 'n': + tip.css( 'background-position', - ( 250 - tip.outerWidth() / 2 ) + left_shift + "px top" ); + break; + case 's': + tip.css( 'background-position', - ( 250 - tip.outerWidth() / 2 ) + left_shift + "px bottom" ); + break; + case 'e': + break; + case 'w': + break; + } + + if (opts.fade) { + tip.stop().css({opacity: 0, display: 'block', visibility: 'visible'}).animate({opacity: opts.opacity}); + } else { + tip.css({visibility: 'visible', opacity: opts.opacity}); + } + }, opts.delayIn); + + }, function() { + $.data(this, 'cancel.tipsy', false); + var self = this; + clearTimeout(timeout); + setTimeout(function() { + if ($.data(this, 'cancel.tipsy')) { return; } + var tip = $.data(self, 'active.tipsy'); + if (opts.fade) { + tip.stop().fadeOut(function() { $(this).remove(); }); + } else if (tip) { + tip.remove(); + } + }, opts.delayOut); + + }); + + }); + + }; + + // Overwrite this method to provide options on a per-element basis. + // For example, you could store the gravity in a 'tipsy-gravity' attribute: + // return $.extend({}, options, {gravity: $(ele).attr('tipsy-gravity') || 'n' }); + // (remember - do not modify 'options' in place!) + $.fn.tipsy.elementOptions = function(ele, options) { + return $.metadata ? $.extend({}, options, $(ele).metadata()) : options; + }; + + $.fn.tipsy.defaults = { + delayIn: 0, + delayOut: 100, + fade: false, + fallback: '', + gravity: 'n', + html: false, + opacity: 0.8, + title: 'title' + }; + + $.fn.tipsy.autoNS = function() { + return $(this).offset().top > ($(document).scrollTop() + $(window).height() / 2) ? 's' : 'n'; + }; + + $.fn.tipsy.autoWE = function() { + return $(this).offset().left > ($(document).scrollLeft() + $(window).width() / 2) ? 'e' : 'w'; + }; + +})(jQuery); diff -r b36c13131ac7 -r 185eab051284 static/scripts/packed/galaxy.base.js --- a/static/scripts/packed/galaxy.base.js Mon Feb 08 23:52:56 2010 -0500 +++ b/static/scripts/packed/galaxy.base.js Tue Feb 09 04:16:26 2010 -0500 @@ -1,1 +1,1 @@ -$.fn.makeAbsolute=function(a){return this.each(function(){var b=$(this);var c=b.position();b.css({position:"absolute",marginLeft:0,marginTop:0,top:c.top,left:c.left,right:$(window).width()-(c.left+b.width())});if(a){b.remove().appendTo("body")}})};jQuery(document).ready(function(){jQuery("a[confirm]").click(function(){return confirm(jQuery(this).attr("confirm"))});make_popup_menus()});function make_popup_menus(){jQuery("div[popupmenu]").each(function(){var c={};$(this).find("a").each(function(){var b=$(this).attr("confirm"),d=$(this).attr("href"),e=$(this).attr("target");c[$(this).text()]=function(){if(!b||confirm(b)){var g=window;if(e=="_parent"){g=window.parent}else{if(e=="_top"){g=window.top}}g.location=d}}});var a=$("#"+$(this).attr("popupmenu"));make_popupmenu(a,c);$(this).remove();a.addClass("popup").show()})}function ensure_popup_helper(){if($("#popup-helper").length==0){$("<div id='popup-helper'/>").css({background:"white",opacity:0,zIndex:15000,position:"absolute",t op:0,left:0,width:"100%",height:"100%"}).appendTo("body").hide()}}function make_popupmenu(d,c){ensure_popup_helper();var a=$(d);var b=$("<ul id='"+d.attr("id")+"-menu'></ul>");$.each(c,function(g,f){if(f){$("<li/>").html(g).click(f).appendTo(b)}else{$("<li class='head'/>").html(g).appendTo(b)}});var e=$("<div class='popmenu-wrapper'>");e.append(b).append("<div class='overlay-border'>").css("position","absolute").appendTo("body").hide();attach_popupmenu(d,e)}function attach_popupmenu(b,d){var a=function(){d.unbind().hide();$("#popup-helper").unbind("click.popupmenu").hide()};var c=function(g){var h=$(b).offset();$("#popup-helper").bind("click.popupmenu",a).show();d.click(a).css({left:0,top:-1000}).show();var f=g.pageX-d.width()/2;f=Math.min(f,$(document).scrollLeft()+$(window).width()-$(d).width()-20);f=Math.max(f,$(document).scrollLeft()+20);d.css({top:g.pageY-5,left:f});return false};$(b).click(c)}var array_length=function(a){if(a.length){return a.length}var b=0;for(element in a){b++}return b};var replace_dbkey_select=function(){var c=$("select[name=dbkey]");var d=c.attr("value");if(c.length!=0){var e=$("<input id='dbkey-input' type='text'></input>");e.attr("size",40);e.attr("name",c.attr("name"));e.click(function(){var g=$(this).attr("value");$(this).attr("value","Loading...");$(this).showAllInCache();$(this).attr("value",g);$(this).select()});var b=new Array();var a=new Object();c.children("option").each(function(){var h=$(this).text();var g=$(this).attr("value");if(g=="?"){return}b.push(h);a[h]=g;if(g==d){e.attr("value",h)}});if(e.attr("value")==""){e.attr("value","Click to Search or Select Build")}var f={selectFirst:false,autoFill:false,mustMatch:false,matchContains:true,max:1000,minChars:0,hideForLessThanMinChars:false};e.autocomplete(b,f);c.replaceWith(e);$("form").submit(function(){var i=$("#dbkey-input");if(i.length!=0){var h=i.attr("value");var g=a[h];if(g!=null&&g!=undefined){i.attr("value",g)}else{if(d!=""){i.attr("value",d)}else{i. attr("value","?")}}}})}};function async_save_text(d,f,e,a,c,h,i,g,b){if(c==null){c=30}if(i==null){i=4}$("#"+d).click(function(){var l=$("#"+f).text();if(h){var j=$("<textarea rows='"+i+"' cols='"+c+"'>"+l+"</textarea>")}else{var j=$("<input type='text' value='"+l+"' size='"+c+"'></input>")}j.blur(function(){$(this).remove();$("#"+f).show();if(m){k.addClass("tooltip")}if(b!=null){b(j)}});var m=$(this).hasClass("tooltip");var k=$(this);j.keyup(function(o){if(o.keyCode==27){$(this).trigger("blur")}else{if(o.keyCode==13){new_text=this.value;$(this).trigger("blur");var n=new Object();n[a]=new_text;$.ajax({url:e,data:n,error:function(){alert("Text editing for elt "+f+" failed")},success:function(p){$("#"+f).text(p);if(b!=null){b(j)}}})}}});if(g!=null){g(j)}$("#"+f).hide();j.insertAfter($("#"+f));j.focus();j.select();$(this).removeClass("tooltip");return false})}; 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\ No newline at end of file diff -r b36c13131ac7 -r 185eab051284 templates/root/history.mako --- a/templates/root/history.mako Mon Feb 08 23:52:56 2010 -0500 +++ b/templates/root/history.mako Tue Feb 09 04:16:26 2010 -0500 @@ -15,7 +15,7 @@ <meta http-equiv="Pragma" content="no-cache"> ${h.css( "base", "history", "autocomplete_tagging" )} -${h.js( "galaxy.base", "jquery", "json2", "jquery.jstore-all", "jquery.autocomplete", "autocomplete_tagging" )} +${h.js( "jquery", "jquery.tipsy", "galaxy.base", "json2", "jquery.jstore-all", "jquery.autocomplete", "autocomplete_tagging" )} <script type="text/javascript"> $(function() { @@ -46,15 +46,25 @@ async_save_text("history-name-container", "history-name", "${h.url_for( controller="/history", action="rename_async", id=trans.security.encode_id(history.id) )}", "new_name", 18); // Tag management. + var historyTagArea = $('#history-tag-area'); $('#history-tag').click( function() { - $('#history-tag-area').toggle("fast"); + if ( historyTagArea.is( ":hidden" ) ) { + historyTagArea.slideDown("fast"); + } else { + historyTagArea.slideUp("fast"); + } return false; }); - // Annotation management. + // Annotation management. + var historyAnnotationArea = $('#history-annotation-area'); $('#history-annotate').click( function() { - $('#history-annotation-area').toggle("fast"); + if ( historyAnnotationArea.is( ":hidden" ) ) { + historyAnnotationArea.slideDown("fast"); + } else { + historyAnnotationArea.slideUp("fast"); + } return false; }); async_save_text("history-annotation-container", "history-annotation", "${h.url_for( controller="/history", action="annotate_async", id=trans.security.encode_id(history.id) )}", "new_annotation", 18, true, 4); @@ -281,15 +291,14 @@ <table width="100%" cellpadding="0" cellspacing="0"> <tr> <td align="left"> - <div id="history-name-container" class="editable-text tooltip"> - <span id="history-name">${history.get_display_name() | h}</span> - <span class="tip">Click to edit</span></a> + <div id="history-name-container" class="editable-text"> + <span id="history-name" class="tooltip" title="Click to rename history">${history.get_display_name() | h}</span> </div> </td> <td align="right" style="width: 40px"> <div style="float: right; white-space: nowrap"> - <a id="history-tag" title="Tag" class="icon-button tag tooltip" target="galaxy_main" href="${h.url_for( controller='history', action='tag' )}"></a> - <a id="history-annotate" title="Annotate" class="icon-button annotate" target="galaxy_main" href="${h.url_for( controller='history', action='annotate' )}"></a> + <a id="history-tag" title="Edit history tags" class="icon-button tags tooltip" target="galaxy_main" href="${h.url_for( controller='history', action='tag' )}"></a> + <a id="history-annotate" title="Edit history annotation" class="icon-button annotate tooltip" target="galaxy_main" href="${h.url_for( controller='history', action='annotate' )}"></a> </div> </td> </tr> @@ -309,8 +318,8 @@ %if trans.get_user() is not None: <div style="margin: 0px 0px 5px 10px"> ## Tagging elt. - <div id="history-tag-area" class="form-row" style="display: none"> - <label>Tags:</label> + <div id="history-tag-area" style="display: none"> + <b>Tags:</b> <style> .tag-area { border: none; @@ -320,15 +329,10 @@ </div> ## Annotation elt. - <div id="history-annotation-area" class="form-row" style="display: none"> - <label>Annotation / Notes:</label> - <div id="history-annotation-container" class="tooltip"> - %if annotation: - <span id="history-annotation">${annotation | h}</span> - %else: - <span id="history-annotation">None</span> - %endif - <span class="tip">Click to edit annotation</span> + <div id="history-annotation-area" style="display: none"> + <b>Annotation / Notes:</b> + <div id="history-annotation-container"> + <span id="history-annotation" class="tooltip" title="Click to edit annotation">${annotation or 'None' | h}</span> </div> </div> diff -r b36c13131ac7 -r 185eab051284 templates/tagging_common.mako --- a/templates/tagging_common.mako Mon Feb 08 23:52:56 2010 -0500 +++ b/templates/tagging_common.mako Tue Feb 09 04:16:26 2010 -0500 @@ -37,7 +37,7 @@ %if use_toggle_link: <a class="toggle-link" href="#">${num_tags} Tag${iff( num_tags == 1, "", "s")}</a> %endif - <div class="tag-area tooltip + <div class="tag-area %if tag_type == 'individual': individual-tag-area %endif @@ -80,9 +80,8 @@ %endif ## Add "add tag" button. %if render_add_tag_button: - <img src='${h.url_for('/static/images/add_icon.png')}' rollover='${h.url_for('/static/images/add_icon_dark.png')}' class="add-tag-button"/> + <img src='${h.url_for('/static/images/fugue/tag--plus.png')}' class="add-tag-button tooltip" title="Add tags"/> %endif - <span class="tip">Click to edit tags</span> %endif </div> </div>

1 0

[hg] galaxy 3358: Initial version of DNA code filter tool
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/b36c13131ac7 changeset: 3358:b36c13131ac7 user: Kelly Vincent <kpvincent(a)bx.psu.edu> date: Mon Feb 08 23:52:56 2010 -0500 description: Initial version of DNA code filter tool diffstat: test-data/dna_filter_in1.bed | 49 ++++++++++ test-data/dna_filter_out1.bed | 4 + test-data/dna_filter_out2.bed | 39 ++++++++ test-data/dna_filter_out3.bed | 41 ++++++++ test-data/dna_filter_out4.bed | 24 +++++ tool_conf.xml.sample | 1 + tools/stats/dna_filtering.py | 195 ++++++++++++++++++++++++++++++++++++++++++ tools/stats/dna_filtering.xml | 114 ++++++++++++++++++++++++ 8 files changed, 467 insertions(+), 0 deletions(-) diffs (506 lines): diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_in1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_in1.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,49 @@ +chr1 256 257 A N M N - M N U N N A N D N G N N K N N N +chr1 468 469 C C C N M N N K . N C U N H N G N N M N S +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K +chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A +chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y +chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N +chr2 48073 48074 A G A Y W . N K N N N G N N N G N N N Y N +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N +chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N +chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N +chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N +chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N +chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K +chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N +chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N \ No newline at end of file diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_out1.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out1.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,4 @@ +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_out2.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out2.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,39 @@ +chr1 256 257 A N M N - M N U N N A N D N G N N K N N N +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr1 4792 4793 A A M K N W S S N N Y N N N N N M R N R N +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +chr2 47814 47815 A C A S N X D N N H W N G N Y C N N M R N +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N +chr2 53505 53506 A A A M N N Y N N N N - K N W N N N S N R +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +chr10 56024 56025 A T A N D U N Y B N N X N N Y N T N - N N +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N +chr10 56137 56138 A A A N A Y H . Y N G N . D N N T N N N N +chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N +chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K +chr18 91548 91549 A A A S N X H S R N A K N N N N U A R N N +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_out3.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out3.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,41 @@ +chr1 468 469 C C C N M N N K . N C U N H N G N N M N S +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +chr1 6357 6358 G G N M K N G - N N G U N N N B N N K N S +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +chr1 39160 39161 T T T N N Y N - N N N N N N N V N N N N Y +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +chr1 42100 42101 T T T Y R W N N N V N M R N N G N M Y N K +chr1 45026 45027 C A C N N Y N S Y N N X N A D N N K N N A +chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y +chr2 45407 45408 C N C S B N N N N N C N Y N N T K G N C N +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +chr2 48073 48074 A G A Y W . N K N N N G N N N G N N N Y N +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N +chr2 53130 53131 T C T K R . N B N N T N N M N Y N N Y N N +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +chr2 55607 55608 A N A U S N N H R K N N N Y N N G N N N N +chr10 55659 55660 T N T C N K N N N U N S N N N V C R S N N +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N +chr10 56100 56101 T T A W N N W N S N K M N R N R N R N G N +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N +chr10 56174 56175 A T A Y A N N N N N N N N N . S T Y N B N +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +chr10 68912 68913 G T G R N B R N H N U W Y N N N N N N N T +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +chr18 78200 78201 G G G N N H N N V N G N N N N A A N K X N +chr18 81076 81077 T A T B N N G N N X W N X N V N N D N N N +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +chr18 81216 81217 G A G Y N N D N X N N N N A N S N N N D N +chr18 81398 81399 G T G N - W N N M N G C N K N S N N N N K +chr18 93895 93896 T T T H N N V W Y N N N - N N N N N N Y N +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N diff -r dedb7be9aa44 -r b36c13131ac7 test-data/dna_filter_out4.bed --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/test-data/dna_filter_out4.bed Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,24 @@ +chr1 582 583 G G G N G R N R N - N M N V K N N N G C R +chr1 602 603 G G G N G N Y N R G G N N U N T N A K N R +chr1 6119 6120 G G M N S N N W B N S D N N H V N B W N N +chr1 6433 6434 G G N R N N C N N N . N N . N N N N N R N +chr1 41920 41921 G C G N M C G N A N G N K N W S N N N V N +chr1 45161 45162 C T C . N X H V N N C R N Y N N N N R N Y +chr2 45788 45789 T T T N W S N Y N R Y N S N W M N C T N C +chr2 46243 46244 T T T N W N N B V N U N T N N Y C N U N N +chr2 48633 48634 T T T N G N N N . N N N N S N Y N . N N N +chr2 51304 51305 A G N N C N W - N S Y N . N N G N N N W R +chr2 51324 51325 T T N R N N N N N - N U N W A N N N N N N +chr2 52065 52066 T C T N N N S N . N T N M N S W N T Y C N +chr2 53559 53560 T T T N N V R V N N T N U N N B N M N V Y +chr10 55734 55735 T N T G N C N M M G C N B N . N G N N N N +chr10 55870 55871 C G C N H G - N N N C N H K N M G N N N N +chr10 56120 56121 A - A N A N N Y N N N W V N N Y G N N W N +chr10 59373 59374 A G A N N N N N N T N S N N N G N N N V N +chr10 72946 72947 T A N N N N N N B N N . B D W U N U N D A +chr10 77052 77053 G A R N G N N Y N N N N N N B R N W N N R +chr18 81198 81199 A T A N N N N - N N X N K T N M N K X N W +chr18 98172 98173 T T T N . N N N S N T N Y N N Y X D V N Y +chr18 110904 110905 T - A A N A N A W A N N A X N W N N N N N +chr18 140324 140325 A A A N M N N Y N S N V N N X N C N N . M +chr18 160592 160593 C G G G N G N G N G N N G N N M T N Y N N diff -r dedb7be9aa44 -r b36c13131ac7 tool_conf.xml.sample --- a/tool_conf.xml.sample Mon Feb 08 21:33:12 2010 -0500 +++ b/tool_conf.xml.sample Mon Feb 08 23:52:56 2010 -0500 @@ -49,6 +49,7 @@ <tool file="filters/headWrapper.xml" /> <tool file="filters/tailWrapper.xml" /> <tool file="filters/trimmer.xml" /> + <tool file="stats/dna_filtering.xml" /> </section> <section name="Filter and Sort" id="filter"> <tool file="stats/filtering.xml" /> diff -r dedb7be9aa44 -r b36c13131ac7 tools/stats/dna_filtering.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/dna_filtering.py Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,195 @@ +#!/usr/bin/env python + +""" +This tool takes a tab-delimited text file as input and creates filters on columns based on certain properties. The tool will skip over invalid lines within the file, informing the user about the number of lines skipped. + +usage: %prog [options] + -i, --input=i: tabular input file + -o, --output=o: filtered output file + -c, --cond=c: conditions to filter on + -n, --n_handling=n: how to handle N and X + -l, --columns=l: columns + -t, --col_types=t: column types + +""" + +#from __future__ import division +import os.path, re, string, sys +from galaxy import eggs +import pkg_resources; pkg_resources.require( "bx-python" ) +from bx.cookbook import doc_optparse + +# Older py compatibility +try: + set() +except: + from sets import Set as set + +#assert sys.version_info[:2] >= ( 2, 4 ) + +def get_operands( filter_condition ): + # Note that the order of all_operators is important + items_to_strip = [ '==', '!=', ' and ', ' or ' ] + for item in items_to_strip: + if filter_condition.find( item ) >= 0: + filter_condition = filter_condition.replace( item, ' ' ) + operands = set( filter_condition.split( ' ' ) ) + return operands + +def stop_err( msg ): + sys.stderr.write( msg ) + sys.exit() + +def __main__(): + #Parse Command Line + options, args = doc_optparse.parse( __doc__ ) + input = options.input + output = options.output + cond = options.cond + n_handling = options.n_handling + columns = options.columns + col_types = options.col_types + + try: + in_columns = int( columns ) + assert col_types #check to see that the column types variable isn't null + in_column_types = col_types.split( ',' ) + except: + stop_err( "Data does not appear to be tabular. This tool can only be used with tab-delimited data." ) + + # Unescape if input has been escaped + cond_text = cond.replace( '__eq__', '==' ).replace( '__ne__', '!=' ).replace( '__sq__', "'" ) + orig_cond_text = cond_text + # Expand to allow for DNA codes + dot_letters = [ letter for letter in string.uppercase if letter not in \ + [ 'A', 'T', 'U', 'G', 'C', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X' ] ] + codes = {'A': [ 'A', 'M', 'R', 'W', 'V', 'H', 'D' ], + 'T': [ 'T', 'U', 'K', 'Y', 'W', 'B', 'H', 'D' ], + 'G': [ 'G', 'K', 'R', 'S', 'B', 'V', 'D' ], + 'C': [ 'C', 'M', 'Y', 'S', 'B', 'V', 'H' ], + 'U': [ 'T', 'U', 'K', 'Y', 'W', 'B', 'H', 'D' ], + 'K': [ 'K', 'G', 'T' ], + 'M': [ 'M', 'A', 'C' ], + 'R': [ 'R', 'A', 'G' ], + 'Y': [ 'Y', 'C', 'T' ], + 'S': [ 'S', 'C', 'G' ], + 'W': [ 'W', 'A', 'T' ], + 'B': [ 'B', 'C', 'G', 'T' ], + 'V': [ 'V', 'A', 'C', 'G' ], + 'H': [ 'H', 'A', 'C', 'T' ], + 'D': [ 'D', 'A', 'G', 'T' ], + '.': dot_letters, + '-': [ '-' ]} + # Add handling for N and X + if n_handling == "all": + codes[ 'N' ] = [ 'G', 'A', 'T', 'C', 'U', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X' ] + codes[ 'X' ] = [ 'G', 'A', 'T', 'C', 'U', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X' ] + for code in codes.keys(): + if code != '.' and code != '-': + codes[code].append( 'N' ) + codes[code].append( 'X' ) + else: + codes[ 'N' ] = dot_letters + codes[ 'X' ] = dot_letters + # Expand conditions to allow for DNA codes + try: + match_replace = {} + pat = re.compile( "c\d+\s*[!=]=\s*[\w']+" ) + matches = pat.findall( cond_text ) + for match in matches: + if match.find( '==' ) > 0: + match_parts = match.split( '==' ) + new_match = '(%s in codes[%s] and %s in codes[%s])' % ( match_parts[0], match_parts[1], match_parts[1], match_parts[0] ) + elif match.find( '!=' ) > 0 : + match_parts = match.split( '!=' ) + new_match = '(%s not in codes[%s] or %s not in codes[%s])' % ( match_parts[0], match_parts[1], match_parts[1], match_parts[0] ) + else: + raise Exception + if match_parts[1].find( "'" ) >= 0: + assert match_parts[1].replace( "'", '' ) in [ 'G', 'A', 'T', 'C', 'U', 'K', 'M', 'R', 'Y', 'S', 'W', 'B', 'V', 'H', 'D', 'N', 'X', '-', '.' ] + else: + assert match_parts[1].startswith( 'c' ) + match_replace[match] = new_match + for match in match_replace.keys(): + cond_text = cond_text.replace(match, match_replace[match]) + if len( match_replace ) == 0: + raise Exception + except: + stop_err( "One of your conditions is invalid. Make sure to use only '!=' or '==', valid column numbers, and valid base values." ) + + # Attempt to determine if the condition includes executable stuff and, if so, exit + secured = dir() + operands = get_operands( cond_text ) + for operand in operands: + try: + check = int( operand ) + except: + if operand in secured: + stop_err( "Illegal value '%s' in condition '%s'" % ( operand, cond_text ) ) + + # Prepare the column variable names and wrappers for column data types + cols, type_casts = [], [] + for col in range( 1, in_columns + 1 ): + col_name = "c%d" % col + cols.append( col_name ) + col_type = in_column_types[ col - 1 ] + type_cast = "%s(%s)" % ( col_type, col_name ) + type_casts.append( type_cast ) + + col_str = ', '.join( cols ) # 'c1, c2, c3, c4' + type_cast_str = ', '.join( type_casts ) # 'str(c1), int(c2), int(c3), str(c4)' + assign = "%s = line.split( '\\t' )" % col_str + wrap = "%s = %s" % ( col_str, type_cast_str ) + skipped_lines = 0 + first_invalid_line = 0 + invalid_line = None + lines_kept = 0 + total_lines = 0 + out = open( output, 'wt' ) + # Read and filter input file, skipping invalid lines + code = ''' +for i, line in enumerate( file( input ) ): + total_lines += 1 + line = line.rstrip( '\\r\\n' ) + if not line or line.startswith( '#' ): + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line + continue + try: + %s = line.split( '\\t' ) + %s = %s + if %s: + lines_kept += 1 + print >> out, line + except Exception, e: + skipped_lines += 1 + if not invalid_line: + first_invalid_line = i + 1 + invalid_line = line +''' % ( col_str, col_str, type_cast_str, cond_text ) + + valid_filter = True + try: + exec code + except Exception, e: + out.close() + if str( e ).startswith( 'invalid syntax' ): + valid_filter = False + stop_err( 'Filter condition "%s" likely invalid. See tool tips, syntax and examples.' % orig_cond_text ) + else: + stop_err( str( e ) ) + + if valid_filter: + out.close() + valid_lines = total_lines - skipped_lines + print 'Filtering with %s, ' % orig_cond_text + if valid_lines > 0: + print 'kept %4.2f%% of %d lines.' % ( 100.0*lines_kept/valid_lines, total_lines ) + else: + print 'Possible invalid filter condition "%s" or non-existent column referenced. See tool tips, syntax and examples.' % orig_cond_text + if skipped_lines > 0: + print 'Skipped %d invalid lines starting at line #%d: "%s"' % ( skipped_lines, first_invalid_line, invalid_line ) + +if __name__ == "__main__" : __main__() diff -r dedb7be9aa44 -r b36c13131ac7 tools/stats/dna_filtering.xml --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/tools/stats/dna_filtering.xml Mon Feb 08 23:52:56 2010 -0500 @@ -0,0 +1,114 @@ +<tool id="dna_filter" name="DNA Filter" version="1.0.0"> + <description>filter column data on DNA ambiguity codes using simple expressions</description> + <command interpreter="python"> + dna_filtering.py + --input=$input + --output=$out_file1 + --cond="$cond" + --n_handling=$n_handling + --columns=${input.metadata.columns} + --col_types="${input.metadata.column_types}" + </command> + <inputs> + <param format="tabular" name="input" type="data" label="Filter" help="Query missing? See TIP below."/> + <param name="cond" size="40" type="text" value="c8=='G'" label="With following condition" help="Double equal signs, ==, must be used as shown above. To filter for an arbitrary string, use the Select tool."> + <validator type="empty_field" message="Enter a valid filtering condition, see syntax and examples below."/> + </param> + <param name="n_handling" type="select" label="Do you want N (and X) to match A or C or G or T OR nothing?"> + <option value="all">N = A or C or G or T</option> + <option value="none">N = nothing</option> + </param> + </inputs> + <outputs> + <data format="input" name="out_file1" metadata_source="input"/> + </outputs> + <tests> + <test> + <param name="input" value="dna_filter_in1.bed" /> + <param name="cond" value="c8=='G'" /> + <param name="n_handling" value="all" /> + <output name="out_file1" file="dna_filter_out1.bed" /> + </test> + <test> + <param name="input" value="dna_filter_in1.bed" /> + <param name="cond" value="(c10==c11 or c17==c18) and c6!='C' and c23=='R'" /> + <param name="n_handling" value="all" /> + <output name="out_file1" file="dna_filter_out2.bed" /> + </test> + <test> + <param name="input" value="dna_filter_in1.bed" /> + <param name="cond" value="c4=='B' or c9==c10" /> + <param name="n_handling" value="none" /> + <output name="out_file1" file="dna_filter_out3.bed" /> + </test> + <test> + <param name="input" value="dna_filter_in1.bed" /> + <param name="cond" value="c7!='Y' and c9!='U'" /> + <param name="n_handling" value="none" /> + <output name="out_file1" file="dna_filter_out4.bed" /> + </test> + </tests> + <help> + +.. class:: warningmark + +Double equal signs, ==, must be used as *"equal to"* (e.g., **c1 == 'G'**) + +.. class:: infomark + +**TIP:** If your data is not TAB delimited, use *Text Manipulation->Convert* + +.. class:: infomark + +**TIP:** This tool is intended primarily for comparing column values (such as "c5==c12"), although it is also possible to filter on specific values (like "c6!='G'"). Be aware that when searching for specific values, any possible match is considered. So if you search on "c6!='G'", rows will be excluded when c6 is G, K, R, S, B, V, or D (plus N or X if you set that to equal "all"), because it is possible those values could be G. + +----- + +**Syntax** + +The filter tool allows you to restrict the dataset using simple conditional statements. + +- Columns are referenced with **c** and a **number**. For example, **c1** refers to the first column of a tab-delimited file +- Make sure that multi-character operators contain no white space ( e.g., **!=** is valid while **! =** is not valid ) +- When using 'equal-to' operator **double equal sign '==' must be used** ( e.g., **c1=='chr1'** ) +- Non-numerical values must be included in single or double quotes ( e.g., **c6=='C'** ) +- Filtering condition can include logical operators, but **make sure operators are all lower case** ( e.g., **(c1!='chrX' and c1!='chrY') or c6=='+'** ) + +----- + +**DNA Codes** + +The following are the DNA codes used for filtering:: + + Code Meaning + ---- --------------------------- + A A + T T + U T + G G + C C + K G or T + M A or C + R A or G + Y C or T + S C or G + W A or T + B C, G or T + V A, C or G + H A, C or T + D A, G or T + X A, C, G or T + N A, C, G or T + . not (A, C, G or T) + - gap of indeterminate length + +----- + +**Example** + +- **c8=='A'** selects lines in which the eighth column is A, M, R, W, V, H, D and N or X if appropriate +- **c12==c15** selects lines where the value in the twelfth column could be the same as the fifteenth and the fifteenth column could be the same as the twelfth column (based on appropriate codes) +- **c9!=c19** selects lines where column nine could not be the same as column nineteen and column nineteen could not be the same as column nine (using appropriate codes) + +</help> +</tool>

1 0

[hg] galaxy 3357: Change naming of converter to conversion for 3...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/dedb7be9aa44 changeset: 3357:dedb7be9aa44 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Feb 08 21:33:12 2010 -0500 description: Change naming of converter to conversion for 3356:c64ef44ed4c5 to more properly reflect the function. diffstat: lib/galaxy/tools/__init__.py | 18 ++++++++-------- lib/galaxy/tools/actions/__init__.py | 40 ++++++++++++++++++------------------ lib/galaxy/tools/parameters/basic.py | 8 +++--- 3 files changed, 33 insertions(+), 33 deletions(-) diffs (128 lines): diff -r c64ef44ed4c5 -r dedb7be9aa44 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Feb 08 12:45:28 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Mon Feb 08 21:33:12 2010 -0500 @@ -1198,27 +1198,27 @@ current = values["__current_case__"] wrap_values( input.cases[current].inputs, values ) elif isinstance( input, DataToolParameter ): - ##FIXME: We're populating param_dict with converters when wrapping values, + ##FIXME: We're populating param_dict with conversions when wrapping values, ##this should happen as a separate step before wrapping (or call this wrapping step something more generic) ##(but iterating this same list twice would be wasteful) - #add explicit converters by name to current parent - for converter_name, converter_extensions, converter_datatypes in input.converters: + #add explicit conversions by name to current parent + for conversion_name, conversion_extensions, conversion_datatypes in input.conversions: #if we are at building cmdline step, then converters have already executed - conv_ext, converted_dataset = input_values[ input.name ].find_conversion_destination( converter_datatypes ) + conv_ext, converted_dataset = input_values[ input.name ].find_conversion_destination( conversion_datatypes ) #when dealing with optional inputs, we'll provide a valid extension to be used for None converted dataset if not conv_ext: - conv_ext = converter_extensions[0] + conv_ext = conversion_extensions[0] #input_values[ input.name ] is None when optional dataset, #'conversion' of optional dataset should create wrapper around NoneDataset for converter output if input_values[ input.name ] and not converted_dataset: #input that converter is based from has a value, but converted dataset does not exist - raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_values[ input.name ].extension, converter_extensions ) + raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_values[ input.name ].extension, conversion_extensions ) else: - input_values[ converter_name ] = \ + input_values[ conversion_name ] = \ DatasetFilenameWrapper( converted_dataset, datatypes_registry = self.app.datatypes_registry, - tool = Bunch( converter_name = Bunch( extensions = conv_ext ) ), #trick wrapper into using target conv ext (when None) without actually being a tool parameter - name = converter_name ) + tool = Bunch( conversion_name = Bunch( extensions = conv_ext ) ), #trick wrapper into using target conv ext (when None) without actually being a tool parameter + name = conversion_name ) #wrap actual input dataset input_values[ input.name ] = \ DatasetFilenameWrapper( input_values[ input.name ], diff -r c64ef44ed4c5 -r dedb7be9aa44 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Mon Feb 08 12:45:28 2010 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Mon Feb 08 21:33:12 2010 -0500 @@ -63,41 +63,41 @@ # are stored as name1, name2, ... for i, v in enumerate( value ): input_datasets[ prefix + input.name + str( i + 1 ) ] = process_dataset( v ) - converters = [] - for converter_name, converter_extensions, converter_datatypes in input.converters: - new_data = process_dataset( input_datasets[ prefix + input.name + str( i + 1 ) ], converter_datatypes ) - if not new_data or isinstance( new_data.datatype, converter_datatypes ): - input_datasets[ prefix + converter_name + str( i + 1 ) ] = new_data - converters.append( ( converter_name, new_data ) ) + conversions = [] + for conversion_name, conversion_extensions, conversion_datatypes in input.conversions: + new_data = process_dataset( input_datasets[ prefix + input.name + str( i + 1 ) ], conversion_datatypes ) + if not new_data or isinstance( new_data.datatype, conversion_datatypes ): + input_datasets[ prefix + conversion_name + str( i + 1 ) ] = new_data + conversions.append( ( conversion_name, new_data ) ) else: - raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name + str( i + 1 ) ].extension, converter_extensions ) + raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name + str( i + 1 ) ].extension, conversion_extensions ) if parent: parent[input.name] = input_datasets[ prefix + input.name + str( i + 1 ) ] - for converter_name, converter_data in converters: + for conversion_name, conversion_data in conversions: #allow explicit conversion to be stored in job_parameter table - parent[ converter_name ] = converter_data.id #a more robust way to determine JSONable value is desired + parent[ conversion_name ] = conversion_data.id #a more robust way to determine JSONable value is desired else: param_values[input.name][i] = input_datasets[ prefix + input.name + str( i + 1 ) ] - for converter_name, converter_data in converters: + for conversion_name, conversion_data in conversions: #allow explicit conversion to be stored in job_parameter table - param_values[ converter_name ][i] = converter_data.id #a more robust way to determine JSONable value is desired + param_values[ conversion_name ][i] = conversion_data.id #a more robust way to determine JSONable value is desired else: input_datasets[ prefix + input.name ] = process_dataset( value ) - converters = [] - for converter_name, converter_extensions, converter_datatypes in input.converters: - new_data = process_dataset( input_datasets[ prefix + input.name ], converter_datatypes ) - if not new_data or isinstance( new_data.datatype, converter_datatypes ): - input_datasets[ prefix + converter_name ] = new_data - converters.append( ( converter_name, new_data ) ) + conversions = [] + for conversion_name, conversion_extensions, conversion_datatypes in input.conversions: + new_data = process_dataset( input_datasets[ prefix + input.name ], conversion_datatypes ) + if not new_data or isinstance( new_data.datatype, conversion_datatypes ): + input_datasets[ prefix + conversion_name ] = new_data + conversions.append( ( conversion_name, new_data ) ) else: - raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name ].extension, converter_extensions ) + raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name ].extension, conversion_extensions ) target_dict = parent if not target_dict: target_dict = param_values target_dict[ input.name ] = input_datasets[ prefix + input.name ] - for converter_name, converter_data in converters: + for conversion_name, conversion_data in conversions: #allow explicit conversion to be stored in job_parameter table - target_dict[ converter_name ] = converter_data.id #a more robust way to determine JSONable value is desired + target_dict[ conversion_name ] = conversion_data.id #a more robust way to determine JSONable value is desired tool.visit_inputs( param_values, visitor ) return input_datasets diff -r c64ef44ed4c5 -r dedb7be9aa44 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Feb 08 12:45:28 2010 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Mon Feb 08 21:33:12 2010 -0500 @@ -1168,15 +1168,15 @@ else: self.options = dynamic_options.DynamicOptions( options, self ) self.is_dynamic = self.options is not None - # Load converters required for the dataset input - self.converters = [] - for conv_elem in elem.findall( "converter" ): + # Load conversions required for the dataset input + self.conversions = [] + for conv_elem in elem.findall( "conversion" ): name = conv_elem.get( "name" ) #name for commandline substitution conv_extensions = conv_elem.get( "type" ) #target datatype extension # FIXME: conv_extensions should be able to be an ordered list assert None not in [ name, type ], 'A name (%s) and type (%s) are required for explicit conversion' % ( name, type ) conv_types = tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ).__class__ - self.converters.append( ( name, conv_extensions, conv_types ) ) + self.conversions.append( ( name, conv_extensions, conv_types ) ) def get_html_field( self, trans=None, value=None, other_values={} ): filter_value = None

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[hg] galaxy 3356: First pass at allowing explicit datatype conve...
by Greg Von Kuster 09 Feb '10

09 Feb '10

details: http://www.bx.psu.edu/hg/galaxy/rev/c64ef44ed4c5 changeset: 3356:c64ef44ed4c5 user: Dan Blankenberg <dan(a)bx.psu.edu> date: Mon Feb 08 12:45:28 2010 -0500 description: First pass at allowing explicit datatype conversion to be specified. This can be used for e.g. providing a tool with a non-metadata based index file. Defined as part of a DataToolParameter: <param name="input1" type="interval" label="An Interval File"> <converter name='input1_as_a_bed_file' type='bed'/> </param> Both the original input as well as the converted dataset can be accessed like: <command>some_binary $input1 $input1_as_a_bed_file </command> if $input1 is already BED, it will be used for input1_as_a_bed_file. The name is be placed in the dictionary space of the data input parameter's parent; so for Grouping objects, e.g. a repeat: <repeat name="queries" title="Query"> <param name="input2" type="data" label="Select" > <converter name='input2_as_a_bed_file' type='bed'/> </param> </repeat> is accessed like (putting both the original and converted dataset as arguments on the command line): <command> ... #for $q in $queries ${q.input2} ${q.input2_as_a_bed_file} #end for ... </command> See notes in code in commit for additional comments. diffstat: lib/galaxy/tools/__init__.py | 28 ++++++++++++++++++++++++ lib/galaxy/tools/actions/__init__.py | 41 +++++++++++++++++++++++++++++------ lib/galaxy/tools/parameters/basic.py | 13 +++++++++- 3 files changed, 73 insertions(+), 9 deletions(-) diffs (147 lines): diff -r 26f01eafc6bd -r c64ef44ed4c5 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Mon Feb 08 11:20:44 2010 -0500 +++ b/lib/galaxy/tools/__init__.py Mon Feb 08 12:45:28 2010 -0500 @@ -1198,6 +1198,28 @@ current = values["__current_case__"] wrap_values( input.cases[current].inputs, values ) elif isinstance( input, DataToolParameter ): + ##FIXME: We're populating param_dict with converters when wrapping values, + ##this should happen as a separate step before wrapping (or call this wrapping step something more generic) + ##(but iterating this same list twice would be wasteful) + #add explicit converters by name to current parent + for converter_name, converter_extensions, converter_datatypes in input.converters: + #if we are at building cmdline step, then converters have already executed + conv_ext, converted_dataset = input_values[ input.name ].find_conversion_destination( converter_datatypes ) + #when dealing with optional inputs, we'll provide a valid extension to be used for None converted dataset + if not conv_ext: + conv_ext = converter_extensions[0] + #input_values[ input.name ] is None when optional dataset, + #'conversion' of optional dataset should create wrapper around NoneDataset for converter output + if input_values[ input.name ] and not converted_dataset: + #input that converter is based from has a value, but converted dataset does not exist + raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_values[ input.name ].extension, converter_extensions ) + else: + input_values[ converter_name ] = \ + DatasetFilenameWrapper( converted_dataset, + datatypes_registry = self.app.datatypes_registry, + tool = Bunch( converter_name = Bunch( extensions = conv_ext ) ), #trick wrapper into using target conv ext (when None) without actually being a tool parameter + name = converter_name ) + #wrap actual input dataset input_values[ input.name ] = \ DatasetFilenameWrapper( input_values[ input.name ], datatypes_registry = self.app.datatypes_registry, @@ -1212,6 +1234,12 @@ # tools (e.g. UCSC) should really be handled in a special way. if self.check_values: wrap_values( self.inputs, param_dict ) + ###FIXME: when self.check_values==True, input datasets are being wrapped twice + ### (above and below, creating 2 separate DatasetFilenameWrapper objects - first is overwritten by second), + ###is this necessary? - if we get rid of this way to access children, can we stop this redundancy, or is there another reason for this? + ###Only necessary when self.check_values is False (==external dataset tool?: can this be abstracted out as part of being a datasouce tool?) + ### but we still want (ALWAYS) to wrap input datasets + ### (this should be checked to prevent overhead of creating a new object?) # Additionally, datasets go in the param dict. We wrap them such that # if the bare variable name is used it returns the filename (for # backwards compatibility). We also add any child datasets to the diff -r 26f01eafc6bd -r c64ef44ed4c5 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Mon Feb 08 11:20:44 2010 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Mon Feb 08 12:45:28 2010 -0500 @@ -31,11 +31,13 @@ """ input_datasets = dict() def visitor( prefix, input, value, parent = None ): - def process_dataset( data ): - if data and not isinstance( data.datatype, input.formats ): + def process_dataset( data, formats = None ): + if formats is None: + formats = input.formats + if data and not isinstance( data.datatype, formats ): # Need to refresh in case this conversion just took place, i.e. input above in tool performed the same conversion trans.sa_session.refresh( data ) - target_ext, converted_dataset = data.find_conversion_destination( input.formats, converter_safe = input.converter_safe( param_values, trans ) ) + target_ext, converted_dataset = data.find_conversion_destination( formats, converter_safe = input.converter_safe( param_values, trans ) ) if target_ext: if converted_dataset: data = converted_dataset @@ -61,16 +63,41 @@ # are stored as name1, name2, ... for i, v in enumerate( value ): input_datasets[ prefix + input.name + str( i + 1 ) ] = process_dataset( v ) + converters = [] + for converter_name, converter_extensions, converter_datatypes in input.converters: + new_data = process_dataset( input_datasets[ prefix + input.name + str( i + 1 ) ], converter_datatypes ) + if not new_data or isinstance( new_data.datatype, converter_datatypes ): + input_datasets[ prefix + converter_name + str( i + 1 ) ] = new_data + converters.append( ( converter_name, new_data ) ) + else: + raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name + str( i + 1 ) ].extension, converter_extensions ) if parent: parent[input.name] = input_datasets[ prefix + input.name + str( i + 1 ) ] + for converter_name, converter_data in converters: + #allow explicit conversion to be stored in job_parameter table + parent[ converter_name ] = converter_data.id #a more robust way to determine JSONable value is desired else: param_values[input.name][i] = input_datasets[ prefix + input.name + str( i + 1 ) ] + for converter_name, converter_data in converters: + #allow explicit conversion to be stored in job_parameter table + param_values[ converter_name ][i] = converter_data.id #a more robust way to determine JSONable value is desired else: input_datasets[ prefix + input.name ] = process_dataset( value ) - if parent: - parent[input.name] = input_datasets[ prefix + input.name ] - else: - param_values[input.name] = input_datasets[ prefix + input.name ] + converters = [] + for converter_name, converter_extensions, converter_datatypes in input.converters: + new_data = process_dataset( input_datasets[ prefix + input.name ], converter_datatypes ) + if not new_data or isinstance( new_data.datatype, converter_datatypes ): + input_datasets[ prefix + converter_name ] = new_data + converters.append( ( converter_name, new_data ) ) + else: + raise Exception, 'A path for explicit datatype conversion has not been found: %s --/--> %s' % ( input_datasets[ prefix + input.name ].extension, converter_extensions ) + target_dict = parent + if not target_dict: + target_dict = param_values + target_dict[ input.name ] = input_datasets[ prefix + input.name ] + for converter_name, converter_data in converters: + #allow explicit conversion to be stored in job_parameter table + target_dict[ converter_name ] = converter_data.id #a more robust way to determine JSONable value is desired tool.visit_inputs( param_values, visitor ) return input_datasets diff -r 26f01eafc6bd -r c64ef44ed4c5 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Mon Feb 08 11:20:44 2010 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Mon Feb 08 12:45:28 2010 -0500 @@ -50,14 +50,14 @@ def get_html( self, trans=None, value=None, other_values={}): """ - Returns the html widget corresponding to the paramter. + Returns the html widget corresponding to the parameter. Optionally attempt to retain the current value specific by 'value' """ return self.get_html_field( trans, value, other_values ).get_html() def from_html( self, value, trans=None, other_values={} ): """ - Convert a value from an HTML POST into the parameters prefered value + Convert a value from an HTML POST into the parameters preferred value format. """ return value @@ -1168,6 +1168,15 @@ else: self.options = dynamic_options.DynamicOptions( options, self ) self.is_dynamic = self.options is not None + # Load converters required for the dataset input + self.converters = [] + for conv_elem in elem.findall( "converter" ): + name = conv_elem.get( "name" ) #name for commandline substitution + conv_extensions = conv_elem.get( "type" ) #target datatype extension + # FIXME: conv_extensions should be able to be an ordered list + assert None not in [ name, type ], 'A name (%s) and type (%s) are required for explicit conversion' % ( name, type ) + conv_types = tool.app.datatypes_registry.get_datatype_by_extension( conv_extensions.lower() ).__class__ + self.converters.append( ( name, conv_extensions, conv_types ) ) def get_html_field( self, trans=None, value=None, other_values={} ): filter_value = None

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