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commit/galaxy-central: jmchilton: Fix duplicated names in on_text when using multiple data inputs.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/e0d69ca8be55/ Changeset: e0d69ca8be55 User: jmchilton Date: 2014-05-14 00:47:57 Summary: Fix duplicated names in on_text when using multiple data inputs. Unit tests verifing the fixed, correct behavior included. Bug introduced in e8c84dd715782e7c1d709d8068e6033b835f7f39 as an unintended consequence of duplicating the first dataset in the dictionary of input datasets generated by the tool action code. Fixes https://trello.com/c/LCEKxImR. Affected #: 2 files diff -r c1873e4d23fa2c496990e5bdef83300e929ae40c -r e0d69ca8be55cd8cfd863ad7f128e95a42eabfd3 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py +++ b/lib/galaxy/tools/actions/__init__.py @@ -472,6 +472,15 @@ def on_text_for_names( input_names ): + # input_names may contain duplicates... this is because the first value in + # multiple input dataset parameters will appear twice once as param_name + # and once as param_name1. + unique_names = [] + for name in input_names: + if name not in unique_names: + unique_names.append( name ) + input_names = unique_names + # Build name for output datasets based on tool name and input names if len( input_names ) == 1: on_text = input_names[0] diff -r c1873e4d23fa2c496990e5bdef83300e929ae40c -r e0d69ca8be55cd8cfd863ad7f128e95a42eabfd3 test/unit/tools/test_actions.py --- a/test/unit/tools/test_actions.py +++ b/test/unit/tools/test_actions.py @@ -2,6 +2,7 @@ from galaxy import model from galaxy.tools.actions import DefaultToolAction +from galaxy.tools.actions import on_text_for_names import tools_support @@ -25,6 +26,19 @@ ''' +def test_on_text_for_names(): + def assert_on_text_is( expected, *names ): + on_text = on_text_for_names( names ) + assert on_text == expected, "Wrong on text value %s, expected %s" % ( on_text, expected ) + + assert_on_text_is( "data 1", "data 1" ) + assert_on_text_is( "data 1 and data 2", "data 1", "data 2" ) + assert_on_text_is( "data 1, data 2, and data 3", "data 1", "data 2", "data 3" ) + assert_on_text_is( "data 1, data 2, and others", "data 1", "data 2", "data 3", "data 4" ) + + assert_on_text_is( "data 1 and data 2", "data 1", "data 1", "data 2" ) + + class DefaultToolActionTestCase( unittest.TestCase, tools_support.UsesApp, tools_support.UsesTools ): def setUp( self ): Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dannon: Merge from stable.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/c1873e4d23fa/ Changeset: c1873e4d23fa User: dannon Date: 2014-05-13 23:39:55 Summary: Merge from stable. Affected #: 1 file diff -r b4680b54994ad6c62f05d354a2af5743344152e8 -r c1873e4d23fa2c496990e5bdef83300e929ae40c lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -177,10 +177,16 @@ while external_job_id is None and trynum < 5: try: external_job_id = self.ds.runJob(jt) - except drmaa.InternalException, e: + break + except ( drmaa.InternalException, drmaa.DeniedByDrmException ), e: trynum += 1 log.warning( '(%s) drmaa.Session.runJob() failed, will retry: %s', galaxy_id_tag, e ) time.sleep( 5 ) + else: + log.error( "(%s) All attempts to submit job failed" % galaxy_id_tag ) + job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" ) + self.ds.deleteJobTemplate( jt ) + return else: job_wrapper.change_ownership_for_run() log.debug( '(%s) submitting with credentials: %s [uid: %s]' % ( galaxy_id_tag, job_wrapper.user_system_pwent[0], job_wrapper.user_system_pwent[2] ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Fixes for DRMAA submission failures.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/cc0fe62e54dc/ Changeset: cc0fe62e54dc Branch: stable User: jmchilton Date: 2014-05-12 20:32:34 Summary: Fixes for DRMAA submission failures. Mark job as failed once Galaxy is done attempting to submit the job, catch and retry drmaa.DeniedByDrmException like drmaa.InternalException. Affected #: 1 file diff -r 3534f67acd2a4f84899335326ac2cc8bcf05201d -r cc0fe62e54dc59607c26cd9152ef1ea7c85af625 lib/galaxy/jobs/runners/drmaa.py --- a/lib/galaxy/jobs/runners/drmaa.py +++ b/lib/galaxy/jobs/runners/drmaa.py @@ -177,10 +177,16 @@ while external_job_id is None and trynum < 5: try: external_job_id = self.ds.runJob(jt) - except drmaa.InternalException, e: + break + except ( drmaa.InternalException, drmaa.DeniedByDrmException ), e: trynum += 1 log.warning( '(%s) drmaa.Session.runJob() failed, will retry: %s', galaxy_id_tag, e ) time.sleep( 5 ) + else: + log.error( "(%s) All attempts to submit job failed" % galaxy_id_tag ) + job_wrapper.fail( "Unable to run this job due to a cluster error, please retry it later" ) + self.ds.deleteJobTemplate( jt ) + return else: job_wrapper.change_ownership_for_run() log.debug( '(%s) submitting with credentials: %s [uid: %s]' % ( galaxy_id_tag, job_wrapper.user_system_pwent[0], job_wrapper.user_system_pwent[2] ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: jmchilton: Merged in natefoo/galaxy-central (pull request #392)
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/b4680b54994a/ Changeset: b4680b54994a User: jmchilton Date: 2014-05-13 22:38:04 Summary: Merged in natefoo/galaxy-central (pull request #392) SSL client certificate support for LWR AMQP connections Affected #: 5 files diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -41,6 +41,16 @@  +  +  +  +  + </plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -40,13 +40,17 @@ """ runner_name = "LWRRunner" - def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL ): + def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL, **kwds ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) self.async_status_updates = dict() self._init_monitor_thread() self._init_worker_threads() - client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url} + amqp_connect_ssl_args = {} + for kwd in kwds.keys(): + if kwd.startswith('amqp_connect_ssl_'): + amqp_connect_ssl_args[kwd] = kwds[kwd] + client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url, 'amqp_connect_ssl_args': amqp_connect_ssl_args or None} self.galaxy_url = galaxy_url self.client_manager = build_client_manager(**client_manager_kwargs) diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -30,13 +30,14 @@ name _default_. """ - def __init__(self, url, manager_name, timeout=DEFAULT_TIMEOUT): + def __init__(self, url, manager_name, connect_ssl=None, timeout=DEFAULT_TIMEOUT): """ """ if not kombu: raise Exception(KOMBU_UNAVAILABLE) self.__url = url self.__manager_name = manager_name + self.__connect_ssl = connect_ssl self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) self.__timeout = timeout @@ -46,7 +47,7 @@ def consume(self, queue_name, callback, check=True, connection_kwargs={}): queue = self.__queue(queue_name) - with self.connection(self.__url, **connection_kwargs) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl, **connection_kwargs) as connection: with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): while check: try: @@ -55,7 +56,7 @@ pass def publish(self, name, payload): - with self.connection(self.__url) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl) as connection: with pools.producers[connection].acquire() as producer: key = self.__queue_name(name) producer.publish( diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -13,6 +13,7 @@ from .object_client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager +from .util import parse_amqp_connect_ssl_params from .destination import url_to_destination_params from .amqp_exchange import LwrExchange @@ -76,7 +77,8 @@ def __init__(self, **kwds): self.url = kwds.get('url') self.manager_name = kwds.get("manager", "_default_") - self.exchange = LwrExchange(self.url, self.manager_name) + self.connect_ssl = parse_amqp_connect_ssl_params(kwds.get('amqp_connect_ssl_args', None)) + self.exchange = LwrExchange(self.url, self.manager_name, self.connect_ssl) self.status_cache = {} self.callback_lock = threading.Lock() self.callback_thread = None diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -62,6 +62,21 @@ contents.append(name) return contents +def parse_amqp_connect_ssl_params(params): + ssl = None + rval = None + ssl_options = filter(lambda x: x.startswith('amqp_connect_ssl_'), params.keys()) + if ssl_options: + ssl = __import__('ssl') + rval = {} + for option in ssl_options: + value = params.get(option) + option = option.replace('amqp_connect_ssl_', '', 1) + if option == 'cert_reqs': + value = getattr(ssl, value.upper()) + rval[option] = value + return rval + def filter_destination_params(destination_params, prefix): destination_params = destination_params or {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: 2 new changesets
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

2 new commits in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/0405422ab342/ Changeset: 0405422ab342 User: natefoo Date: 2014-05-13 22:22:03 Summary: Allow specification of SSL client authentication parameters to the kombu connection. This is done via the `amqp_connect_ssl_*` options in `server.ini`. Affected #: 5 files diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -41,6 +41,16 @@  +  +  +  +  + </plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -40,13 +40,17 @@ """ runner_name = "LWRRunner" - def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL ): + def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL, **kwds ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) self.async_status_updates = dict() self._init_monitor_thread() self._init_worker_threads() - client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url} + amqp_connect_ssl_args = {} + for kwd in kwds.keys(): + if kwd.startswith('amqp_connect_ssl_'): + amqp_connect_ssl_args[kwd] = kwds[kwd] + client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url, 'amqp_connect_ssl_args': amqp_connect_ssl_args or None} self.galaxy_url = galaxy_url self.client_manager = build_client_manager(**client_manager_kwargs) diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -30,13 +30,14 @@ name _default_. """ - def __init__(self, url, manager_name, timeout=DEFAULT_TIMEOUT): + def __init__(self, url, manager_name, connect_ssl=None, timeout=DEFAULT_TIMEOUT): """ """ if not kombu: raise Exception(KOMBU_UNAVAILABLE) self.__url = url self.__manager_name = manager_name + self.__connect_ssl = connect_ssl self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) self.__timeout = timeout @@ -46,7 +47,7 @@ def consume(self, queue_name, callback, check=True, connection_kwargs={}): queue = self.__queue(queue_name) - with self.connection(self.__url, **connection_kwargs) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl, **connection_kwargs) as connection: with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): while check: try: @@ -55,7 +56,7 @@ pass def publish(self, name, payload): - with self.connection(self.__url) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl) as connection: with pools.producers[connection].acquire() as producer: key = self.__queue_name(name) producer.publish( diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -13,6 +13,7 @@ from .object_client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager +from .util import parse_amqp_connect_ssl_params from .destination import url_to_destination_params from .amqp_exchange import LwrExchange @@ -76,7 +77,8 @@ def __init__(self, **kwds): self.url = kwds.get('url') self.manager_name = kwds.get("manager", "_default_") - self.exchange = LwrExchange(self.url, self.manager_name) + self.connect_ssl = parse_amqp_connect_ssl_params(kwds.get('amqp_connect_ssl_args', None)) + self.exchange = LwrExchange(self.url, self.manager_name, self.connect_ssl) self.status_cache = {} self.callback_lock = threading.Lock() self.callback_thread = None diff -r e5b545b85b836b6f1be76164543d7e4613f25d87 -r 0405422ab3422f1b1373c0b00398885a4d8423f6 lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -62,6 +62,21 @@ contents.append(name) return contents +def parse_amqp_connect_ssl_params(params): + ssl = None + rval = None + ssl_options = filter(lambda x: x.startswith('amqp_connect_ssl_'), params.keys()) + if ssl_options: + ssl = __import__('ssl') + rval = {} + for option in ssl_options: + value = params.get(option) + option = option.replace('amqp_connect_ssl_', '', 1) + if option == 'cert_reqs': + value = getattr(ssl, value.upper()) + rval[option] = value + return rval + def filter_destination_params(destination_params, prefix): destination_params = destination_params or {} https://bitbucket.org/galaxy/galaxy-central/commits/b4680b54994a/ Changeset: b4680b54994a User: jmchilton Date: 2014-05-13 22:38:04 Summary: Merged in natefoo/galaxy-central (pull request #392) SSL client certificate support for LWR AMQP connections Affected #: 5 files diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 job_conf.xml.sample_advanced --- a/job_conf.xml.sample_advanced +++ b/job_conf.xml.sample_advanced @@ -41,6 +41,16 @@  +  +  +  +  + </plugin><plugin id="cli" type="runner" load="galaxy.jobs.runners.cli:ShellJobRunner" /><plugin id="condor" type="runner" load="galaxy.jobs.runners.condor:CondorJobRunner" /> diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr.py --- a/lib/galaxy/jobs/runners/lwr.py +++ b/lib/galaxy/jobs/runners/lwr.py @@ -40,13 +40,17 @@ """ runner_name = "LWRRunner" - def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL ): + def __init__( self, app, nworkers, transport=None, cache=None, url=None, galaxy_url=DEFAULT_GALAXY_URL, **kwds ): """Start the job runner """ super( LwrJobRunner, self ).__init__( app, nworkers ) self.async_status_updates = dict() self._init_monitor_thread() self._init_worker_threads() - client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url} + amqp_connect_ssl_args = {} + for kwd in kwds.keys(): + if kwd.startswith('amqp_connect_ssl_'): + amqp_connect_ssl_args[kwd] = kwds[kwd] + client_manager_kwargs = {'transport_type': transport, 'cache': string_as_bool_or_none(cache), "url": url, 'amqp_connect_ssl_args': amqp_connect_ssl_args or None} self.galaxy_url = galaxy_url self.client_manager = build_client_manager(**client_manager_kwargs) diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py --- a/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py +++ b/lib/galaxy/jobs/runners/lwr_client/amqp_exchange.py @@ -30,13 +30,14 @@ name _default_. """ - def __init__(self, url, manager_name, timeout=DEFAULT_TIMEOUT): + def __init__(self, url, manager_name, connect_ssl=None, timeout=DEFAULT_TIMEOUT): """ """ if not kombu: raise Exception(KOMBU_UNAVAILABLE) self.__url = url self.__manager_name = manager_name + self.__connect_ssl = connect_ssl self.__exchange = kombu.Exchange(DEFAULT_EXCHANGE_NAME, DEFAULT_EXCHANGE_TYPE) self.__timeout = timeout @@ -46,7 +47,7 @@ def consume(self, queue_name, callback, check=True, connection_kwargs={}): queue = self.__queue(queue_name) - with self.connection(self.__url, **connection_kwargs) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl, **connection_kwargs) as connection: with kombu.Consumer(connection, queues=[queue], callbacks=[callback], accept=['json']): while check: try: @@ -55,7 +56,7 @@ pass def publish(self, name, payload): - with self.connection(self.__url) as connection: + with self.connection(self.__url, ssl=self.__connect_ssl) as connection: with pools.producers[connection].acquire() as producer: key = self.__queue_name(name) producer.publish( diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/manager.py --- a/lib/galaxy/jobs/runners/lwr_client/manager.py +++ b/lib/galaxy/jobs/runners/lwr_client/manager.py @@ -13,6 +13,7 @@ from .object_client import ObjectStoreClient from .transport import get_transport from .util import TransferEventManager +from .util import parse_amqp_connect_ssl_params from .destination import url_to_destination_params from .amqp_exchange import LwrExchange @@ -76,7 +77,8 @@ def __init__(self, **kwds): self.url = kwds.get('url') self.manager_name = kwds.get("manager", "_default_") - self.exchange = LwrExchange(self.url, self.manager_name) + self.connect_ssl = parse_amqp_connect_ssl_params(kwds.get('amqp_connect_ssl_args', None)) + self.exchange = LwrExchange(self.url, self.manager_name, self.connect_ssl) self.status_cache = {} self.callback_lock = threading.Lock() self.callback_thread = None diff -r d963b05c497cc17d36a16696077e5a0f3158e52b -r b4680b54994ad6c62f05d354a2af5743344152e8 lib/galaxy/jobs/runners/lwr_client/util.py --- a/lib/galaxy/jobs/runners/lwr_client/util.py +++ b/lib/galaxy/jobs/runners/lwr_client/util.py @@ -62,6 +62,21 @@ contents.append(name) return contents +def parse_amqp_connect_ssl_params(params): + ssl = None + rval = None + ssl_options = filter(lambda x: x.startswith('amqp_connect_ssl_'), params.keys()) + if ssl_options: + ssl = __import__('ssl') + rval = {} + for option in ssl_options: + value = params.get(option) + option = option.replace('amqp_connect_ssl_', '', 1) + if option == 'cert_reqs': + value = getattr(ssl, value.upper()) + rval[option] = value + return rval + def filter_destination_params(destination_params, prefix): destination_params = destination_params or {} Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Display line errors in data table registry display encountered when loading a location file.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d963b05c497c/ Changeset: d963b05c497c User: dan Date: 2014-05-13 22:10:27 Summary: Display line errors in data table registry display encountered when loading a location file. Affected #: 2 files diff -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 -r d963b05c497cc17d36a16696077e5a0f3158e52b lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -285,8 +285,9 @@ filename = corrected_filename found = True + errors = [] if found: - self.data.extend( self.parse_file_fields( open( filename ) ) ) + self.data.extend( self.parse_file_fields( open( filename ), errors=errors ) ) self._update_version() else: self.missing_index_file = filename @@ -294,7 +295,7 @@ if filename not in self.filenames or not self.filenames[ filename ][ 'found' ]: self.filenames[ filename ] = dict( found=found, filename=filename, from_shed_config=from_shed_config, tool_data_path=tool_data_path, - config_element=config_element, tool_shed_repository=repo_info ) + config_element=config_element, tool_shed_repository=repo_info, errors=errors ) else: log.debug( "Filename '%s' already exists in filenames (%s), not adding", filename, self.filenames.keys() ) @@ -353,7 +354,7 @@ if 'name' not in self.columns: self.columns['name'] = self.columns['value'] - def parse_file_fields( self, reader ): + def parse_file_fields( self, reader, errors=None ): """ Parse separated lines from file and return a list of tuples. @@ -371,9 +372,10 @@ if self.largest_index < len( fields ): rval.append( fields ) else: - log.warn( "Line %i in tool data table '%s' is invalid (HINT: " - "'%s' characters must be used to separate fields):\n%s" - % ( ( i + 1 ), self.name, separator_char, line ) ) + line_error = "Line %i in tool data table '%s' is invalid (HINT: '%s' characters must be used to separate fields):\n%s" % ( ( i + 1 ), self.name, separator_char, line ) + if errors is not None: + errors.append( line_error ) + log.warn( line_error ) return rval def get_column_name_list( self ): diff -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 -r d963b05c497cc17d36a16696077e5a0f3158e52b templates/admin/view_data_tables_registry.mako --- a/templates/admin/view_data_tables_registry.mako +++ b/templates/admin/view_data_tables_registry.mako @@ -18,7 +18,7 @@ <th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Filename</th><th bgcolor="#D8D8D8">Tool data path</th> - <th bgcolor="#D8D8D8">Missing index file</th> + <th bgcolor="#D8D8D8">Errors</th></tr> %for data_table_elem_name, data_table in sorted_data_tables: %if ctr % 2 == 1: @@ -35,8 +35,11 @@ <td>${ file_dict.get( 'tool_data_path' ) | h }</td><td> %if not file_dict.get( 'found' ): - missing + file missing %endif + %for error in file_dict.get( 'errors', [] ): + ${ error | h } <br/> + %endfor </td></tr> %endfor Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: More Data Manager UI fixes. Fix for viewing data manager job info when dataset has been deleted.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/d0ab4f31e0e0/ Changeset: d0ab4f31e0e0 User: dan Date: 2014-05-13 21:47:54 Summary: More Data Manager UI fixes. Fix for viewing data manager job info when dataset has been deleted. Affected #: 5 files diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 lib/galaxy/webapps/galaxy/controllers/data_manager.py --- a/lib/galaxy/webapps/galaxy/controllers/data_manager.py +++ b/lib/galaxy/webapps/galaxy/controllers/data_manager.py @@ -55,13 +55,18 @@ data_manager = trans.app.data_managers.get_manager( data_manager_id ) hdas = [ assoc.dataset for assoc in job.get_output_datasets() ] data_manager_output = [] + error_messages = [] for hda in hdas: - data_manager_json = from_json_string( open( hda.get_file_name() ).read() ) + try: + data_manager_json = from_json_string( open( hda.get_file_name() ).read() ) + except Exception, e: + data_manager_json = {} + error_messages.append( "Unable to obtain data_table info for hda (%s): %s" % ( hda.id, e ) ) values = [] for key, value in data_manager_json.get( 'data_tables', {} ).iteritems(): values.append( ( key, value ) ) data_manager_output.append( values ) - return trans.fill_template( "data_manager/view_job.mako", data_manager=data_manager, job=job, view_only=not_is_admin, hdas=hdas, data_manager_output=data_manager_output, message=message, status=status ) + return trans.fill_template( "data_manager/view_job.mako", data_manager=data_manager, job=job, view_only=not_is_admin, hdas=hdas, data_manager_output=data_manager_output, message=message, status=status, error_messages=error_messages ) @web.expose def manage_data_table( self, trans, **kwd ): diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 templates/webapps/galaxy/data_manager/index.mako --- a/templates/webapps/galaxy/data_manager/index.mako +++ b/templates/webapps/galaxy/data_manager/index.mako @@ -51,11 +51,10 @@ <li><a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main"> %if table_name in managed_table_names: - <strong>${ table_name | h }</strong> + </span><strong>${ table_name | h }</strong></a><span class="fa fa-exchange"> %else: - ${ table_name | h } + ${ table_name | h }</a> %endif - </a></li><p/> %endfor diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 templates/webapps/galaxy/data_manager/manage_data_manager.mako --- a/templates/webapps/galaxy/data_manager/manage_data_manager.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_manager.mako @@ -28,7 +28,11 @@ <td>PID/Cluster ID</td></tr> %for job in jobs: - <td><a class="icon-btn" href="${ h.url_for( controller="data_manager", action="view_job", id=trans.security.encode_id( job.id ) ) }" title="View info"><span class="fa fa-info"></span></a></td> + <td> + <div class="icon-btn-group"> + <a class="icon-btn" href="${ h.url_for( controller="data_manager", action="view_job", id=trans.security.encode_id( job.id ) ) }" title="View info"><span class="fa fa-info-circle"></span></a><a class="icon-btn" href="${ h.url_for( controller="tool_runner", action="rerun", job_id=trans.security.encode_id( job.id ) ) }" title="Rerun"><span class="fa fa-refresh"></span></a> + </div> + </td><td>${ job.id | h }</td> %if job.history and job.history.user: <td>${job.history.user.email | h}</td> diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 templates/webapps/galaxy/data_manager/manage_data_table.mako --- a/templates/webapps/galaxy/data_manager/manage_data_table.mako +++ b/templates/webapps/galaxy/data_manager/manage_data_table.mako @@ -1,7 +1,7 @@ <%inherit file="/base.mako"/><%namespace file="/message.mako" import="render_msg" /> -<%def name="title()">Data Table Manager: ${ data_table.name | h }</%def> +<%def name="title()">Tool Data Table: ${ data_table.name | h }</%def> %if message: ${render_msg( message, status )} diff -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 -r d0ab4f31e0e0178f58bd2bafb0b38d7a0fee9913 templates/webapps/galaxy/data_manager/view_job.mako --- a/templates/webapps/galaxy/data_manager/view_job.mako +++ b/templates/webapps/galaxy/data_manager/view_job.mako @@ -8,6 +8,12 @@ ${render_msg( message, status )} %endif +%if error_messages: + %for error_message in error_messages: + ${ render_msg( error_message, 'error' ) } + %endfor +%endif + %if view_only: <p>Not implemented</p> %else: @@ -15,7 +21,7 @@ <table class="tabletip"><thead><tr><th colspan="2" style="font-size: 120%;"> - Data Manager: ${ data_manager.name | h } - ${ data_manager.description | h } + Data Manager: <a href="${ h.url_for( controller='tool_runner', action='index', tool_id=data_manager.tool.id ) }">${ data_manager.name | h }</a> - ${ data_manager.description | h } <a class="icon-btn" href="${ h.url_for( controller="tool_runner", action="rerun", job_id=trans.security.encode_id( job.id ) ) }" title="Rerun" data-placement="bottom"><span class="fa fa-refresh"></span></a></th></tr></thead><tbody> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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commit/galaxy-central: dan: Allow tool_runner rerun to accept a job_id instead of a dataset_id.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/dc74a95853b6/ Changeset: dc74a95853b6 User: dan Date: 2014-05-13 21:12:25 Summary: Allow tool_runner rerun to accept a job_id instead of a dataset_id. Affected #: 1 file diff -r f7de39159497fbcffb3f0ed785f26ecf56b40155 -r dc74a95853b6ebe05f811b78b9a6cfbe43211fc8 lib/galaxy/webapps/galaxy/controllers/tool_runner.py --- a/lib/galaxy/webapps/galaxy/controllers/tool_runner.py +++ b/lib/galaxy/webapps/galaxy/controllers/tool_runner.py @@ -106,33 +106,41 @@ **vars ) @web.expose - def rerun( self, trans, id=None, from_noframe=None, **kwd ): + def rerun( self, trans, id=None, from_noframe=None, job_id=None, **kwd ): """ Given a HistoryDatasetAssociation id, find the job and that created the dataset, extract the parameters, and display the appropriate tool form with parameters already filled in. """ - if not id: - error( "'id' parameter is required" ); - try: - id = int( id ) - - except: - # it's not an un-encoded id, try to parse as encoded + if job_id: try: - id = trans.security.decode_id( id ) + job_id = trans.security.decode_id( job_id ) + job = trans.sa_session.query( trans.app.model.Job ).get( job_id ) except: - error( "Invalid value for 'id' parameter" ) - - # Get the dataset object - data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id ) - #only allow rerunning if user is allowed access to the dataset. - if not ( trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ) ): - error( "You are not allowed to access this dataset" ) - # Get the associated job, if any. - job = data.creating_job - if not job: - raise Exception("Failed to get job information for dataset hid %d" % data.hid) + error( "Invalid value for 'job_id' parameter" ) + param_error_text = "Failed to get parameters for job id %d " % job_id + else: + if not id: + error( "'id' parameter is required" ); + try: + id = int( id ) + except: + # it's not an un-encoded id, try to parse as encoded + try: + id = trans.security.decode_id( id ) + except: + error( "Invalid value for 'id' parameter" ) + + # Get the dataset object + data = trans.sa_session.query( trans.app.model.HistoryDatasetAssociation ).get( id ) + #only allow rerunning if user is allowed access to the dataset. + if not ( trans.user_is_admin() or trans.app.security_agent.can_access_dataset( trans.get_current_user_roles(), data.dataset ) ): + error( "You are not allowed to access this dataset" ) + # Get the associated job, if any. + job = data.creating_job + if not job: + raise Exception("Failed to get job information for dataset hid %d" % data.hid) + param_error_text = "Failed to get parameters for dataset id %d " % data.id # Get the tool object tool_id = job.tool_id tool_version = job.tool_version @@ -172,7 +180,7 @@ try: params_objects = job.get_param_values( trans.app, ignore_errors = True ) except: - raise Exception( "Failed to get parameters for dataset id %d " % data.id ) + raise Exception( param_error_text ) upgrade_messages = tool.check_and_update_param_values( params_objects, trans, update_values=False ) # Need to remap dataset parameters. Job parameters point to original # dataset used; parameter should be the analygous dataset in the Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: More Data Manager UI tweaks.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/f7de39159497/ Changeset: f7de39159497 User: dan Date: 2014-05-13 20:34:57 Summary: More Data Manager UI tweaks. Affected #: 1 file diff -r 1c913c980053c4ce2dc6425cdf102298488242ec -r f7de39159497fbcffb3f0ed785f26ecf56b40155 templates/webapps/galaxy/data_manager/index.mako --- a/templates/webapps/galaxy/data_manager/index.mako +++ b/templates/webapps/galaxy/data_manager/index.mako @@ -12,11 +12,11 @@ %if view_only: <p>Not implemented</p> %elif not data_managers.data_managers: - ${render_msg( "You do not currently have any Data Managers installed.", "warning" ) } + ${ render_msg( 'You do not currently have any Data Managers installed. You can install some from a <a href="%s">ToolShed</a>.' % ( h.url_for( controller="admin_toolshed", action="browse_tool_sheds" ) ), "warning" ) } %else: - <p>Choose your data managing option from below.</p> + <p>Choose your data managing option from below. You may install additional Data Managers from a <a href="${ h.url_for( controller='admin_toolshed', action='browse_tool_sheds' ) }">ToolShed</a>.</p><ul> - <li><strong>Run Data Manager Tools</strong> + <li><h3>Run Data Manager Tools</h3><div style="margin-left:1em"><ul> %for data_manager_id, data_manager in sorted( data_managers.data_managers.iteritems(), key=lambda x:x[1].name ): @@ -29,12 +29,12 @@ </div></li><p/> - <li><strong>View Data Manager Jobs</strong> + <li><h3>View Data Manager Jobs</h3><div style="margin-left:1em"><ul> %for data_manager_id, data_manager in sorted( data_managers.data_managers.iteritems(), key=lambda x:x[1].name ): <li> - <a href="${h.url_for( controller='data_manager', action='manage_data_manager', id=data_manager_id)}" target="galaxy_main"><strong>${ data_manager.name | h }</strong></a> - ${ data_manager.description | h }</a> + <a href="${ h.url_for( controller='data_manager', action='manage_data_manager', id=data_manager_id)}" target="galaxy_main"><strong>${ data_manager.name | h }</strong></a> - ${ data_manager.description | h }</a></li><p/> %endfor @@ -43,7 +43,7 @@ </li><p/><p/> - <li><strong>View Tool Data Table Entries</strong> + <li><h3>View Tool Data Table Entries</h3><div style="margin-left:1em"><ul><% managed_table_names = data_managers.managed_data_tables.keys() %> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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commit/galaxy-central: dan: Alphabetize lists of Data Manager elements on index page.
by commits-noreply＠bitbucket.org 13 May '14

13 May '14

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/1c913c980053/ Changeset: 1c913c980053 User: dan Date: 2014-05-13 20:21:08 Summary: Alphabetize lists of Data Manager elements on index page. Affected #: 1 file diff -r a5a7edbe49055c328960eaa5c622a62ecf83b27d -r 1c913c980053c4ce2dc6425cdf102298488242ec templates/webapps/galaxy/data_manager/index.mako --- a/templates/webapps/galaxy/data_manager/index.mako +++ b/templates/webapps/galaxy/data_manager/index.mako @@ -19,7 +19,7 @@ <li><strong>Run Data Manager Tools</strong><div style="margin-left:1em"><ul> - %for data_manager_id, data_manager in data_managers.data_managers.iteritems(): + %for data_manager_id, data_manager in sorted( data_managers.data_managers.iteritems(), key=lambda x:x[1].name ): <li><a href="${ h.url_for( controller='tool_runner', action='index', tool_id=data_manager.tool.id ) }"><strong>${ data_manager.name | h }</strong></a> - ${ data_manager.description | h } </li> @@ -32,7 +32,7 @@ <li><strong>View Data Manager Jobs</strong><div style="margin-left:1em"><ul> - %for data_manager_id, data_manager in data_managers.data_managers.iteritems(): + %for data_manager_id, data_manager in sorted( data_managers.data_managers.iteritems(), key=lambda x:x[1].name ): <li><a href="${h.url_for( controller='data_manager', action='manage_data_manager', id=data_manager_id)}" target="galaxy_main"><strong>${ data_manager.name | h }</strong></a> - ${ data_manager.description | h }</a></li> @@ -46,20 +46,19 @@ <li><strong>View Tool Data Table Entries</strong><div style="margin-left:1em"><ul> - %for table_name, managers in data_managers.managed_data_tables.iteritems(): + <% managed_table_names = data_managers.managed_data_tables.keys() %> + %for table_name in sorted( tool_data_tables.get_tables().keys() ): <li> - <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main"><strong>${ table_name | h }</strong></a> + <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main"> + %if table_name in managed_table_names: + <strong>${ table_name | h }</strong> + %else: + ${ table_name | h } + %endif + </a></li><p/> %endfor - %for table_name in tool_data_tables.get_tables(): - %if table_name not in data_managers.managed_data_tables: - <li> - <a href="${h.url_for( controller='data_manager', action='manage_data_table', table_name=table_name)}" target="galaxy_main">${ table_name | h }</a> - </li> - <p/> - %endif - %endfor </ul></div></li> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.

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