Error in creating admin user during tool shed bootstrap

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Error in creating admin user during tool shed bootstrap

bgrande
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

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stdout.txt (4K) Download Attachment
tool_shed_bootstrap.log (62K) Download Attachment
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Re: Error in creating admin user during tool shed bootstrap

bgrande
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, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6

On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande <[hidden email]> 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


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Re: Error in creating admin user during tool shed bootstrap

John Chilton-4
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 <[hidden email]> 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, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6
>
> On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande <[hidden email]> 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/

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Re: Error in creating admin user during tool shed bootstrap

Will Holtz
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 <[hidden email]> 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 <[hidden email]> 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, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6
>
> On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande <[hidden email]> 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:
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  http://galaxyproject.org/search/mailinglists/



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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 [hidden email] and destroy this message and remove the transmission from all computer directories (including e-mail servers).

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Re: Error in creating admin user during tool shed bootstrap

Daniel Blankenberg
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6
>
> On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande <[hidden email]> 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 [hidden email] 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/


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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:
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Re: Error in creating admin user during tool shed bootstrap

bgrande
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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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 <[hidden email]> 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, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6
>
> On Fri, Nov 7, 2014 at 2:17 PM, Bruno Grande <[hidden email]> 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 [hidden email] 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/