Re: [galaxy-dev] Error in creating admin user during tool shed bootstrap
Daniel's instructions did the trick! I tried different combinations, and it seems that I needed to specify the TOOL_SHED_CONFIG_FILE environment variable in addition to including the protocol in the source Tool Shed URL ( *i.e.* https://). Otherwise, I also had to change my password to one without symbols (*i.e.* without non-alphanumerical characters). I even tried URL encoding the password, as I had to do in the PostgreSQL SQLAlchemy database connection string, but that didn't work. Thank you all for your help! Best regards, Bruno On Thu, Nov 13, 2014 at 10:15 AM, Daniel Blankenberg d...@bx.psu.edu wrote: Hi Bruno, You may be able to get it to work if you directly specify the tool_shed.ini file that you want to use and also provide the entire toolshed url including protocol, e.g: TOOL_SHED_CONFIG_FILE=path/to/tool_shed.ini sh run_tool_shed.sh -bootstrap_from_tool_shed https://testtoolshed.g2.bx.psu.edu It does seem as though there is an issue with the automatic resolution of which ini file to use, probably due to the recent /config/ changes. Hope that helps, Dan On Nov 13, 2014, at 12:35 PM, Will Holtz who...@lygos.com wrote: I successfully did the tool shed bootstrapping with postgresql once. But beyond that, I don't think I can offer much advice. -Will On Thu, Nov 13, 2014 at 7:41 AM, John Chilton jmchil...@gmail.com wrote: Hey Bruno, So Greg has moved on new exciting things and I am not sure if there is anyone who now routinely does the tool shed bootstrapping workflow that can help. I tried the bootstrapping process and it worked fine with an sqlite database - maybe it is not compatible with postgres? Want to try sqlite instead - should be fine for testing? -John On Mon, Nov 10, 2014 at 3:42 PM, Bruno Grande bgra...@sfu.ca wrote: I had the brilliant idea of sending the previous email out on a Friday afternoon/evening. I'm just following up with this thread. Best regards, Bruno -- Bruno Grande, B.Sc. (Hons) M.Sc. Candidate Dr. Ryan Morin's Laboratory Molecular Biology and Biochemistry, Simon Fraser University SSB7133, University Drive, Burnaby, BC, Canada, V5A 1S6 On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande bgra...@sfu.ca wrote: I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user. This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists. So, I don't know whether the SQL query is being run against the wrong database (e.g. the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query. I'm using the latest version of Galaxy (revision 83f821c5ecc1). Best regards, Bruno ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at who...@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error in creating admin user during tool shed bootstrap
Hey Bruno, So Greg has moved on new exciting things and I am not sure if there is anyone who now routinely does the tool shed bootstrapping workflow that can help. I tried the bootstrapping process and it worked fine with an sqlite database - maybe it is not compatible with postgres? Want to try sqlite instead - should be fine for testing? -John On Mon, Nov 10, 2014 at 3:42 PM, Bruno Grande bgra...@sfu.ca wrote: I had the brilliant idea of sending the previous email out on a Friday afternoon/evening. I'm just following up with this thread. Best regards, Bruno -- Bruno Grande, B.Sc. (Hons) M.Sc. Candidate Dr. Ryan Morin's Laboratory Molecular Biology and Biochemistry, Simon Fraser University SSB7133, University Drive, Burnaby, BC, Canada, V5A 1S6 On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande bgra...@sfu.ca wrote: I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user. This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists. So, I don't know whether the SQL query is being run against the wrong database (e.g. the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query. I'm using the latest version of Galaxy (revision 83f821c5ecc1). Best regards, Bruno ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error in creating admin user during tool shed bootstrap
I successfully did the tool shed bootstrapping with postgresql once. But beyond that, I don't think I can offer much advice. -Will On Thu, Nov 13, 2014 at 7:41 AM, John Chilton jmchil...@gmail.com wrote: Hey Bruno, So Greg has moved on new exciting things and I am not sure if there is anyone who now routinely does the tool shed bootstrapping workflow that can help. I tried the bootstrapping process and it worked fine with an sqlite database - maybe it is not compatible with postgres? Want to try sqlite instead - should be fine for testing? -John On Mon, Nov 10, 2014 at 3:42 PM, Bruno Grande bgra...@sfu.ca wrote: I had the brilliant idea of sending the previous email out on a Friday afternoon/evening. I'm just following up with this thread. Best regards, Bruno -- Bruno Grande, B.Sc. (Hons) M.Sc. Candidate Dr. Ryan Morin's Laboratory Molecular Biology and Biochemistry, Simon Fraser University SSB7133, University Drive, Burnaby, BC, Canada, V5A 1S6 On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande bgra...@sfu.ca wrote: I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user. This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists. So, I don't know whether the SQL query is being run against the wrong database (e.g. the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query. I'm using the latest version of Galaxy (revision 83f821c5ecc1). Best regards, Bruno ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at who...@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error in creating admin user during tool shed bootstrap
Hi Bruno, You may be able to get it to work if you directly specify the tool_shed.ini file that you want to use and also provide the entire toolshed url including protocol, e.g: TOOL_SHED_CONFIG_FILE=path/to/tool_shed.ini sh run_tool_shed.sh -bootstrap_from_tool_shed https://testtoolshed.g2.bx.psu.edu It does seem as though there is an issue with the automatic resolution of which ini file to use, probably due to the recent /config/ changes. Hope that helps, Dan On Nov 13, 2014, at 12:35 PM, Will Holtz who...@lygos.com wrote: I successfully did the tool shed bootstrapping with postgresql once. But beyond that, I don't think I can offer much advice. -Will On Thu, Nov 13, 2014 at 7:41 AM, John Chilton jmchil...@gmail.com wrote: Hey Bruno, So Greg has moved on new exciting things and I am not sure if there is anyone who now routinely does the tool shed bootstrapping workflow that can help. I tried the bootstrapping process and it worked fine with an sqlite database - maybe it is not compatible with postgres? Want to try sqlite instead - should be fine for testing? -John On Mon, Nov 10, 2014 at 3:42 PM, Bruno Grande bgra...@sfu.ca wrote: I had the brilliant idea of sending the previous email out on a Friday afternoon/evening. I'm just following up with this thread. Best regards, Bruno -- Bruno Grande, B.Sc. (Hons) M.Sc. Candidate Dr. Ryan Morin's Laboratory Molecular Biology and Biochemistry, Simon Fraser University SSB7133, University Drive, Burnaby, BC, Canada, V5A 1S6 On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande bgra...@sfu.ca wrote: I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user. This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists. So, I don't know whether the SQL query is being run against the wrong database (e.g. the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query. I'm using the latest version of Galaxy (revision 83f821c5ecc1). Best regards, Bruno ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ -- The information contained in this e-mail message or any attachment(s) may be confidential and/or privileged and is intended for use only by the individual(s) to whom this message is addressed. If you are not the intended recipient, any dissemination, distribution, copying, or use is strictly prohibited. If you receive this e-mail message in error, please e-mail the sender at who...@lygos.com and destroy this message and remove the transmission from all computer directories (including e-mail servers). Please consider the environment before printing this email. ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/ ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
Re: [galaxy-dev] Error in creating admin user during tool shed bootstrap
I had the brilliant idea of sending the previous email out on a Friday afternoon/evening. I'm just following up with this thread. Best regards, Bruno -- Bruno Grande, B.Sc. (Hons) M.Sc. Candidate Dr. Ryan Morin's Laboratory Molecular Biology and Biochemistry, Simon Fraser University SSB7133, University Drive, Burnaby, BC, Canada, V5A 1S6 On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande bgra...@sfu.ca wrote: I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post http://gregvonkuster.org/galaxy-tool-shed-june-2-2014-release/. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user. This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists. So, I don't know whether the SQL query is being run against the wrong database (*e.g.* the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query. I'm using the latest version of Galaxy (revision 83f821c5ecc1). Best regards, Bruno ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
[galaxy-dev] Error in creating admin user during tool shed bootstrap
I'm setting up a local development Tool Shed according to Greg Von Kuster's blog post http://gregvonkuster.org/galaxy-tool-shed-june-2-2014-release/. During the bootstrapping process, it seems that the creation of the admin user based on the information in user_info.xml fails because of a SQLAlchemy error (see attached stdout.txt). As a result, I believe the API calls for creating categories and users also fail, because they depend on the existence of admin user. This error seems to be due to a missing repository table in the database. I ran the SQL query against the Tool Shed database within PostgreSQL after the failed bootstrapping command and it returned no error, because the repository table actually exists. So, I don't know whether the SQL query is being run against the wrong database (*e.g.* the Galaxy database) or if the database schema isn't properly set up by the time SQLAlchemy attempts the query. I'm using the latest version of Galaxy (revision 83f821c5ecc1). Best regards, Bruno $ sh ~/galaxy_dist/run_tool_shed.sh -bootstrap_from_tool_shed testtoolshed.g2.bx.psu.edu Bootstrapping from tool shed at testtoolshed.g2.bx.psu.edu. Creating database... done. Creating user 'bgrande' with email address 'bgra...@sfu.ca'...Traceback (most recent call last): File lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py, line 152, in module app = BootstrapApplication( config ) File lib/tool_shed/scripts/bootstrap_tool_shed/create_user_with_api_key.py, line 46, in __init__ create_tables=False ) File /home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/model/mapping.py, line 330, in init result.shed_counter = shed_statistics.ShedCounter( result ) File /home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/util/shed_statistics.py, line 20, in __init__ self.generate_statistics() File /home/galaxy/galaxy_dist/lib/galaxy/webapps/tool_shed/util/shed_statistics.py, line 39, in generate_statistics for repository in self.sa_session.query( self.model.Repository ): File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py, line 2227, in __iter__ File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/orm/query.py, line 2242, in _execute_and_instances File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1449, in execute File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1584, in _execute_clauseelement File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1698, in _execute_context File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/base.py, line 1691, in _execute_context File /home/galaxy/galaxy_dist/eggs/SQLAlchemy-0.7.9-py2.7-linux-x86_64-ucs4.egg/sqlalchemy/engine/default.py, line 331, in do_execute sqlalchemy.exc.OperationalError: (OperationalError) no such table: repository u'SELECT repository.id AS repository_id, repository.create_time AS repository_create_time, repository.update_time AS repository_update_time, repository.name AS repository_name, repository.type AS repository_type, repository.description AS repository_description, repository.long_description AS repository_long_description, repository.user_id AS repository_user_id, repository.private AS repository_private, repository.deleted AS repository_deleted, repository.email_alerts AS repository_email_alerts, repository.times_downloaded AS repository_times_downloaded, repository.deprecated AS repository_deprecated \nFROM repository' () done. Starting tool shed in order to populate users and categories... done. Retrieving admin user's API key from http://127.0.0.1:9009... done. Creating users... done. Creating categories... done. Bootstrap complete, shutting down temporary tool shed process. A log has been saved to tool_shed_bootstrap.log tool_shed_bootstrap.log Description: Binary data ___ Please keep all replies on the list by using reply all in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
