May 2010 - galaxy-dev - lists.galaxyproject.org

about sequencing requests
by Davide Cittaro 24 May '10

24 May '10

Hi there, What are "Data Libraries" and "Folder" in sample request and grid information in sample request edit page? Thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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doesn't authenticate anymore
by Davide Cittaro 24 May '10

24 May '10

Hi all, I was trying a new (almost) clean installation of galaxy... It happens that I cannot authenticate anymore. log files do not suggest anything, who wants to help me in debugging this? thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Tool config Cheetah errors
by Nate Coraor 21 May '10

21 May '10

Hi Amit, Please create a new topic when sending new requests to the mailing list - this ensures that the subject is relevant and threading is correct in the mailing list archives and individuals' mail readers. Modi, Amit wrote: > Hi, > > I have added a few tools in the galaxy.For one of these tools it > sometime gives an error. > but everytime I execute this tool it renders this exception on console. > > Can anybody please help me fix it. > > galaxy.jobs DEBUG 2010-05-21 14:30:03,166 dispatching job 203 to sge > runner > galaxy.jobs.runners.sge ERROR 2010-05-21 14:30:03,508 failure > running job 203 > Traceback (most recent call last): > File > "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/runners/sge.py", > line 120, in queue_job > job_wrapper.prepare() > File > "/export/home/galaxy/galaxy-dist/lib/galaxy/jobs/__init__.py", line > 390, in prepare > self.command_line = self.tool.build_command_line( param_dict ) > File > "/export/home/galaxy/galaxy-dist/lib/galaxy/tools/__init__.py", line > 1343, in build_command_line > command_line = fill_template( self.command, context=param_dict ) > File > "/export/home/galaxy/galaxy-dist/lib/galaxy/util/template.py", line > 9, in fill_template > return str( Template( source=template_text, searchList=[context] ) ) > File > "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", > line 1244, in __init__ > self._compile(source, file, compilerSettings=compilerSettings) > File > "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", > line 1538, in _compile > keepRefToGeneratedCode=True) > File > "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Template.py", > line 745, in compile > compiler.compile() > File > "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Compiler.py", > line 1670, in compile > self._parser.parse() > File > "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", > line 1488, in parse > self.eatDirective() > File > "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", > line 1610, in eatDirective > directiveParser() > File > "/export/home/galaxy/galaxy-dist/eggs/Cheetah-2.2.2-py2.4-linux-x86_64-ucs4.egg/Cheetah/Parser.py", > line 1755, in eatEndDirective > raise ParseError(self, msg='Invalid end directive') > ParseError: > > Invalid end directive > Line 3, column 6 > > Line|Cheetah Code > ----|------------------------------------------------------------- > 2 | #else: #gkelvin $confile.nonmeta > 3 | #end > ^ > 4 | > > galaxy.jobs DEBUG 2010-05-21 14:30:03,509 job 203 dispatched The closing syntax for an 'if' statement in Cheetah is: #end if Also, the : is not necessary after the 'else' statement, and I believe it's deprecated. --nate > > > Regards, > Amit Modi > > ------------------------------------------------------------------------ > > * ----------------------------------------- Confidentiality Notice: The > following mail message, including any attachments, is for the sole use > of the intended recipient(s) and may contain confidential and privileged > information. The recipient is responsible to maintain the > confidentiality of this information and to use the information only for > authorized purposes. If you are not the intended recipient (or > authorized to receive information for the intended recipient), you are > hereby notified that any review, use, disclosure, distribution, copying, > printing, or action taken in reliance on the contents of this e-mail is > strictly prohibited. If you have received this communication in error, > please notify us immediately by reply e-mail and destroy all copies of > the original message. Thank you. * >

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Re: [galaxy-dev] [galaxy-user] Problems installing Galaxy
by Nate Coraor 21 May '10

21 May '10

Hi Rodolfo, I've moved this over to the galaxy-dev list since it's a local installation issue. Rodolfo Aramayo wrote: > People, > > Apologies for the disturbance. > > On a fresh MacOSX I installed Python, Numpy and Scipy using MacPorts > > I tested both Numpy and Scipy as follows: > > == > python > >>> import numpy > >>> numpy.test('1','10') > >>> import scipy > >>> scipy.test('1','10') > == > > The computer does understand them and processes them as expected. The > tests seem to work? > > However, when I attempt a fresh installation of Galaxy I get the > following error: > >> hg clone http://www.bx.psu.edu/hg/galaxy galaxy_dist > requesting all changes > adding changesets > adding manifests > adding file changes > added 3787 changesets with 17203 changes to 4176 files > updating to branch default > 2691 files updated, 0 files merged, 0 files removed, 0 files unresolved > >> sh setup.sh > Copying datatypes_conf.xml.sample to datatypes_conf.xml > Copying reports_wsgi.ini.sample to reports_wsgi.ini > Copying tool_conf.xml.sample to tool_conf.xml > Copying universe_wsgi.ini.sample to universe_wsgi.ini > Copying tool-data/alignseq.loc.sample to tool-data/alignseq.loc > Copying tool-data/annotation_profiler_options.xml.sample to > tool-data/annotation_profiler_options.xml > Copying tool-data/annotation_profiler_valid_builds.txt.sample to > tool-data/annotation_profiler_valid_builds.txt > Copying tool-data/binned_scores.loc.sample to tool-data/binned_scores.loc > Copying tool-data/blastdb.loc.sample to tool-data/blastdb.loc > Copying tool-data/bowtie_indices.loc.sample to tool-data/bowtie_indices.loc > Copying tool-data/encode_datasets.loc.sample to tool-data/encode_datasets.loc > Copying tool-data/liftOver.loc.sample to tool-data/liftOver.loc > Copying tool-data/maf_index.loc.sample to tool-data/maf_index.loc > Copying tool-data/maf_pairwise.loc.sample to tool-data/maf_pairwise.loc > Copying tool-data/microbial_data.loc.sample to tool-data/microbial_data.loc > Copying tool-data/phastOdds.loc.sample to tool-data/phastOdds.loc > Copying tool-data/quality_scores.loc.sample to tool-data/quality_scores.loc > Copying tool-data/regions.loc.sample to tool-data/regions.loc > Copying tool-data/sam_fa_indices.loc.sample to tool-data/sam_fa_indices.loc > Copying tool-data/sequence_index_base.loc.sample to > tool-data/sequence_index_base.loc > Copying tool-data/sequence_index_color.loc.sample to > tool-data/sequence_index_color.loc > Copying tool-data/twobit.loc.sample to tool-data/twobit.loc > Copying tool-data/shared/ucsc/builds.txt.sample to > tool-data/shared/ucsc/builds.txt > Creating database/files > Creating database/community_files > Creating database/tmp > Creating database/compiled_templates > Creating database/job_working_directory > Creating database/pbs > Creating static/genetrack/plots > Fetched http://eggs.g2.bx.psu.edu/new/Mako/Mako-0.2.5-py2.6.egg > Fetched http://eggs.g2.bx.psu.edu/new/Babel/Babel-0.9.4-py2.6.egg > Fetched http://eggs.g2.bx.psu.edu/new/Tempita/Tempita-0.1-py2.6.egg > Fetched http://eggs.g2.bx.psu.edu/new/lrucache/lrucache-0.2-py2.6.egg > Fetched http://eggs.g2.bx.psu.edu/new/boto/boto-1.8d-py2.6.egg > Fetched http://eggs.g2.bx.psu.edu/new/NoseHTML/NoseHTML-0.3.1-py2.6.egg > Fetched http://eggs.g2.bx.psu.edu/new/pexpect/pexpect-2.4-py2.6.egg > Fetched http://eggs.g2.bx.psu.edu/new/PasteDeploy/PasteDeploy-1.3.3-py2.6.egg > Fetched http://eggs.g2.bx.psu.edu/new/WebHelpers/WebHelpers-0.2-py2.6.egg > Fetched http://eggs.g2.bx.psu.edu/new/docutils/docutils-0.4-py2.6.egg > Traceback (most recent call last): > File "./scripts/fetch_eggs.py", line 31, in <module> > c.resolve() # Only fetch eggs required by the config > File "/Library/WebServer/Documents/galaxy_dist/lib/galaxy/eggs/__init__.py", > line 284, in resolve > egg.resolve() > File "/Library/WebServer/Documents/galaxy_dist/lib/galaxy/eggs/__init__.py", > line 172, in resolve > r = pkg_resources.working_set.resolve( ( > self.distribution.as_requirement(), ), env, self.fetch ) > File "/opt/local/Library/Frameworks/Python.framework/Versions/2.6/lib/python2.6/site-packages/pkg_resources.py", > line 551, in resolve > raise DistributionNotFound(req) > pkg_resources.DistributionNotFound: numpy==1.3.0 > Any Ideas? Galaxy is not directly supported on MacPorts Python, since that version isn't (or wasn't, previously) a "fat" (multiplatform) Framework build. The Apple system-provided Python in Leopard and Snow Leopard, as well as the official releases from python.org are all supported. You may be able to use the MacPorts version by building your own Python Eggs. I'd try first with numpy: % python scripts/scramble.py numpy And see if that works. --nate > > _______________________________________________ > galaxy-user mailing list > galaxy-user(a)lists.bx.psu.edu > http://lists.bx.psu.edu/listinfo/galaxy-user >

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again on multiple server instances
by Davide Cittaro 21 May '10

21 May '10

Hi all, after successful configuration of multiple server instances (web and runner) I've placed everything behind apache proxy (actually I'm trying to). I can see the welcome page and navigate through my history (still I have to delegate the authentication to apache), nevertheless I'm not able to perform any job... getting data from UCSC is waiting for run after a couple of hours, uploading files is stuck... Hence I've tried to disable the proxy thing and still have the same issues. I've then checked at the log files for the five runners and two of them report this: [runner0] serving on http://127.0.0.1:8100 galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,032 RoundRobin queue: user/session did not exist, created new jobqueue for session = 6galaxy.jobs DEBUG 2010-05-21 13:49:09,032 job 13 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,032 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-05-21 13:49:09,032 dispatching job 13 to local runner galaxy.jobs DEBUG 2010-05-21 13:49:09,135 job 13 dispatched galaxy.jobs.runners.local DEBUG 2010-05-21 13:49:09,538 executing: python /data/galaxy_dist/tools/data_source/data_source.py /data/galaxy_dist/database/files /000/dataset_60.dat 0 galaxy.jobs.runners.local ERROR 2010-05-21 13:49:09,761 Uncaught exception running job Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next self.run_job( job_wrapper ) File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 101, in run_job job_wrapper.fail( "failure running job", exception=True ) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail self.sa_session.refresh( job ) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 929, in refresh only_load_props=attribute_names) is None: File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/lib/python2.5/decimal.py", line 541, in __new__ m = _parser(value) OperationalError: could not receive data from server: Error 0 [runner1] serving on http://127.0.0.1:8101 galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,198 RoundRobin queue: user/session did not exist, created new jobqueue for session = 6 galaxy.jobs DEBUG 2010-05-21 13:49:09,199 job 13 put in policy queue galaxy.jobs.schedulingpolicy.roundrobin DEBUG 2010-05-21 13:49:09,199 RoundRobin queue: retrieving job from job queue for session = 6 galaxy.jobs DEBUG 2010-05-21 13:49:09,199 dispatching job 13 to local runner galaxy.jobs DEBUG 2010-05-21 13:49:09,315 job 13 dispatched galaxy.jobs.runners.local ERROR 2010-05-21 13:49:09,741 Uncaught exception running job Traceback (most recent call last): File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 46, in run_next self.run_job( job_wrapper ) File "/data/galaxy_dist/lib/galaxy/jobs/runners/local.py", line 58, in run_job job_wrapper.fail( "failure preparing job", exception=True ) File "/data/galaxy_dist/lib/galaxy/jobs/__init__.py", line 413, in fail self.sa_session.refresh( job ) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/scoping.py", line 127, in do return getattr(self.registry(), name)(*args, **kwargs) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 929, in refresh only_load_props=attribute_names) is None: File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1500, in _get return q.all()[0] File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1267, in all return list(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1361, in __iter__ return self._execute_and_instances(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/query.py", line 1364, in _execute_and_instances result = self.session.execute(querycontext.statement, params=self._params, mapper=self._mapper_zero_or_none()) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/orm/session.py", line 755, in execute clause, params or {}) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 824, in execute return Connection.executors[c](self, object, multiparams, params) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 874, in _execute_clauseelement return self.__execute_context(context) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 901, in __execute_context return context.get_result_proxy() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/databases/postgres.py", line 346, in get_result_proxy return base.BufferedRowResultProxy(self) File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1415, in __init__ self._init_metadata() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1704, in _init_metadata self.__buffer_rows() File "/data/galaxy_dist/eggs/SQLAlchemy-0.5.6_dev_r6498-py2.5.egg/sqlalchemy/engine/base.py", line 1721, in __buffer_rows self.__rowbuffer = self.cursor.fetchmany(size) File "/usr/lib/python2.5/decimal.py", line 541, in __new__ m = _parser(value) OperationalError: could not receive data from server: Error 0 BTW, this is the proxy conf: <IfModule mod_proxy.c> ProxyRequests Off ProxyVia Off <Proxy balancer://galaxy> BalancerMember http://localhost:8080 BalancerMember http://localhost:8081 </Proxy> </IfModule> and the rewrite rules: RewriteEngine on RewriteRule ^/galaxy$ /galaxy/ [R] RewriteRule ^/galaxy/static/style/(.*) /data/galaxy_dist/static/june_2007_style/blue/$1 [L] RewriteRule ^/galaxy/static/(.*) /data/galaxy_dist/static/$1 [L] RewriteRule ^/galaxy/images/(.*) /data/galaxy_dist/static/images/$1 [L] RewriteRule ^/galaxy/favicon.ico /data/galaxy_dist/static/favicon.ico [L] RewriteRule ^/galaxy/robots.txt /data/galaxy_dist/static/robots.txt [L] RewriteRule ^/galaxy(.*) http://127.0.0.1:8080$1 [P] Any hint is appreciated... Thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

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Enabling Pages
by Juan Carlos Perin 21 May '10

21 May '10

Can anyone point me to the directions to enabling or instaling 'pages' in Galaxy? I can't, for the life of me, find any information about how to use this nice feature. Thanks in advance. Juan Perin

2 1

Galaxy Sample Tracking System
by David Sidote 21 May '10

21 May '10

Hi, I have galaxy running on a local machine and I can't seem to figure out how to get the sample tracking system set up. Can anyone give me a little help to get going? Thanks, Dave ____________________________________________________ David Sidote, PhD | Director, Waksman Genomics Core Facility Waksman Institute | Rutgers University 190 Frelinghuysen Road | Piscataway, NJ 08854 dsidote(a)waksman.rutgers.edu | 732.445.4737

2 3

Next gen sample submission patch
by Brad Chapman 21 May '10

21 May '10

Hey all; It was great meeting everyone last weekend at beautiful Cold Spring Harbor. Thanks to all of the helpful conversations with RC, Greg and everyone else, I've gotten the Next gen sample submission interface I described ready for inclusion into Galaxy. I put together a big diff with the changes and attached it as an issue: http://bitbucket.org/galaxy/galaxy-central/issue/335/next-gen-lims-interface Initial documentation on setting it up is here: http://bitbucket.org/galaxy/galaxy-central/wiki/LIMS/nglims This is designed to complement the existing functionality in Galaxy. By default it will not be viewable in the main menu, but can be enabled with a flag in the universe_wsgi.ini file. I hope getting this integrated into Galaxy is the first step in getting more eyes on it for further development. I'm very happy to be contributing this. Let me know what else I can do to make this easy to integrate. Thanks, Brad

1 0

need help on extra servers
by Davide Cittaro 21 May '10

21 May '10

Hi again, I'm trying to implement what has been showed at the devcon, the extra servers stuff... There's only a slide about that (in the scalable galaxy talk), but seems should be pretty easy by adding [server:ROLE_ID] port = XXXX where role is... web or runner? Is this the correct syntax: [server:web_0] port = 8081 [server:web_1] port = 8082 [server:runner_0] port = 8100 [server:runner_1] port = 8101 [server:runner_2] port = 8102 [server:runner_3] port = 8103 [server:runner_4] port = 8104 Anyway, added those to the universe file, netstat says there are not additional ports opened... Thanks d /* Davide Cittaro Cogentech - Consortium for Genomic Technologies via adamello, 16 20139 Milano Italy tel.: +39(02)574303007 e-mail: davide.cittaro(a)ifom-ieo-campus.it */

2 4

Multiple files from external source
by Chris Zaleski 20 May '10

20 May '10

Greetings, We have an existing database with a web interface to control users & permissions, searching, etc. On our Galaxy server, I have implemented "Synchronous data depositing" described here: http://bitbucket.org/galaxy/galaxy-central/wiki/DataSources. This allows us to utilize the existing UI on the database, and works very nicely for users to retrieve data & load it into Galaxy. We now have instances where users need to load many files at a time, so I plan to change the implementation to use the "Asynchronous" method. Is it possible for the user to "Get Data", login & browse the external data source (in this case, my DB), choose *multiple* files, and have them all sent to Galaxy at once? In our case, this would prevent the user from having to walk through a multi-step process for each file. Thanks Chris Zaleski

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