Tool Tests failing with "Exception: History in error state."

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Tool Tests failing with "Exception: History in error state."

Peter Cock
Retitling thread,

On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock <[hidden email]> wrote:

> Thanks Dave,
>
> The good news is yes, the tests are running again on the
> Test Tool Shed (although not the main Tool Shed yet), and
> many of my tools now have successful test results from
> last night.
>
> e.g. My new basic mummer tool which now has a full set
> of dependency packages thanks to Bjoern:
> https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer
>
> The bad news is there are many unexpected failures with:
> "Exception: History in error state."
>
> I'm sure you'll learn more once you look over the logs,
>
> Thank you,
>
> Peter

Right now the mummer example given above is passing,
but I am still getting this error on some of my tools, e.g.

https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
tested 2015-01-25 11:21:12

https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
tested 2015-01-25 10:52:03

(Many of my other tools are also currently listed with
different unexpected failures, some of which include
the "Exception: History in error state." traceback.)

Interestingly, I've just got what appears to be the same
exception from a TravisCI test run (following a trivial
change to README files):

https://travis-ci.org/peterjc/galaxy_blast/builds/48893916

e.g. (one of many similar failing tests in this log)
======================================================================
ERROR: test_tool_000000
(functional.test_toolbox.TestForTool_blastxml_to_top_descr)
BLAST top hit descriptions ( blastxml_to_top_descr ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
line 268, in test_tool
    self.do_it( td )
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
line 37, in do_it
    stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 42, in stage_data_in_history
    upload_wait()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 279, in wait
    while not self.__history_ready( history_id ):
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 297, in __history_ready
    return self._state_ready( state, error_msg="History in error state." )
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 356, in _state_ready
    raise Exception( error_msg )
Exception: History in error state.


I do not recall seeing this problem locally when using my
development instllation of galaxy-central.

The TravisCI failure suggests this could be a stochastic
resource contention (I can re-run the TravisCI build and
see if this works second time round?), which is more prone
to fail under the Tool Shed framework?

Peter
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Re: Tool Tests failing with "Exception: History in error state."

Nicola Soranzo-2
Hi Peter,
I was also getting "Exception: History in error state" errors with BioBlend continuous integration testing, but those seem to be fixed with latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d .

Nicola

Il 30.01.2015 17:36 Peter Cock ha scritto:

Retitling thread,

On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock <[hidden email]> wrote:
Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night. e.g. My new basic mummer tool which now has a full set of dependency packages thanks to Bjoern: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there are many unexpected failures with: "Exception: History in error state." I'm sure you'll learn more once you look over the logs, Thank you, Peter
Right now the mummer example given above is passing,
but I am still getting this error on some of my tools, e.g.

https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
tested 2015-01-25 11:21:12

https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
tested 2015-01-25 10:52:03

(Many of my other tools are also currently listed with
different unexpected failures, some of which include
the "Exception: History in error state." traceback.)

Interestingly, I've just got what appears to be the same
exception from a TravisCI test run (following a trivial
change to README files):

https://travis-ci.org/peterjc/galaxy_blast/builds/48893916

e.g. (one of many similar failing tests in this log)
======================================================================
ERROR: test_tool_000000
(functional.test_toolbox.TestForTool_blastxml_to_top_descr)
BLAST top hit descriptions ( blastxml_to_top_descr ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
line 268, in test_tool
    self.do_it( td )
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
line 37, in do_it
    stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 42, in stage_data_in_history
    upload_wait()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 279, in wait
    while not self.__history_ready( history_id ):
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 297, in __history_ready
    return self._state_ready( state, error_msg="History in error state." )
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 356, in _state_ready
    raise Exception( error_msg )
Exception: History in error state.


I do not recall seeing this problem locally when using my
development instllation of galaxy-central.

The TravisCI failure suggests this could be a stochastic
resource contention (I can re-run the TravisCI build and
see if this works second time round?), which is more prone
to fail under the Tool Shed framework?

Peter
___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/



Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo.
E chiami gratis anche i numeri fissi e mobili nel mondo!
Scarica subito l’app Vai su https://www.indoona.com/


___________________________________________________________
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: Tool Tests failing with "Exception: History in error state."

Dannon Baker-2
Yep, the FutureWarning that that commit resolves would have caused the upload job to end up as an error; I'm betting this is what was causing Peter's issues too.

On Fri Jan 30 2015 at 12:18:10 PM Nicola Soranzo <[hidden email]> wrote:
Hi Peter,
I was also getting "Exception: History in error state" errors with BioBlend continuous integration testing, but those seem to be fixed with latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d .

Nicola

Il 30.01.2015 17:36 Peter Cock ha scritto:

Retitling thread,

On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock <[hidden email]> wrote:
Thanks Dave, The good news is yes, the tests are running again on the Test Tool Shed (although not the main Tool Shed yet), and many of my tools now have successful test results from last night. e.g. My new basic mummer tool which now has a full set of dependency packages thanks to Bjoern: https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there are many unexpected failures with: "Exception: History in error state." I'm sure you'll learn more once you look over the logs, Thank you, Peter
Right now the mummer example given above is passing,
but I am still getting this error on some of my tools, e.g.

https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
tested 2015-01-25 11:21:12

https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
tested 2015-01-25 10:52:03

(Many of my other tools are also currently listed with
different unexpected failures, some of which include
the "Exception: History in error state." traceback.)

Interestingly, I've just got what appears to be the same
exception from a TravisCI test run (following a trivial
change to README files):

https://travis-ci.org/peterjc/galaxy_blast/builds/48893916

e.g. (one of many similar failing tests in this log)
======================================================================
ERROR: test_tool_000000
(functional.test_toolbox.TestForTool_blastxml_to_top_descr)
BLAST top hit descriptions ( blastxml_to_top_descr ) > Test-1
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
line 268, in test_tool
    self.do_it( td )
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
line 37, in do_it
    stage_data_in_history( galaxy_interactor, testdef.test_data(),
test_history, shed_tool_id )
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 42, in stage_data_in_history
    upload_wait()
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 279, in wait
    while not self.__history_ready( history_id ):
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 297, in __history_ready
    return self._state_ready( state, error_msg="History in error state." )
  File "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
line 356, in _state_ready
    raise Exception( error_msg )
Exception: History in error state.


I do not recall seeing this problem locally when using my
development instllation of galaxy-central.

The TravisCI failure suggests this could be a stochastic
resource contention (I can re-run the TravisCI build and
see if this works second time round?), which is more prone
to fail under the Tool Shed framework?

Peter
___________________________________________________________
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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/



Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate, le video chiamate e persino le chiamate di gruppo.
E chiami gratis anche i numeri fissi e mobili nel mondo!
Scarica subito l’app Vai su https://www.indoona.com/

___________________________________________________________
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:
  https://lists.galaxyproject.org/

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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
  http://galaxyproject.org/search/mailinglists/
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Re: Tool Tests failing with "Exception: History in error state."

Peter Cock
Hi Dannon, Nicola,

This sounds very promising - I'll rerun the TravisCI job and we can
expect it to work this time :)

https://bitbucket.org/galaxy/galaxy-central/commits/3618b7a91e23096ecf7ce5842c1e16c749251a4d
(half an hour ago!)

When will this reach the Tool Shed and Test Tool Shed? The upload job
failure seems to be the root cause of many of the unexpected test
failures.

Thanks,

Peter

On Fri, Jan 30, 2015 at 5:19 PM, Dannon Baker <[hidden email]> wrote:

> Yep, the FutureWarning that that commit resolves would have caused the
> upload job to end up as an error; I'm betting this is what was causing
> Peter's issues too.
>
>
> On Fri Jan 30 2015 at 12:18:10 PM Nicola Soranzo <[hidden email]>
> wrote:
>>
>> Hi Peter,
>> I was also getting "Exception: History in error state" errors with
>> BioBlend continuous integration testing, but those seem to be fixed with
>> latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d .
>>
>> Nicola
>>
>> Il 30.01.2015 17:36 Peter Cock ha scritto:
>>
>> Retitling thread,
>>
>> On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock <[hidden email]>
>> wrote:
>>
>> Thanks Dave, The good news is yes, the tests are running again on the Test
>> Tool Shed (although not the main Tool Shed yet), and many of my tools now
>> have successful test results from last night. e.g. My new basic mummer tool
>> which now has a full set of dependency packages thanks to Bjoern:
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there
>> are many unexpected failures with: "Exception: History in error state." I'm
>> sure you'll learn more once you look over the logs, Thank you, Peter
>>
>> Right now the mummer example given above is passing,
>> but I am still getting this error on some of my tools, e.g.
>>
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
>> tested 2015-01-25 11:21:12
>>
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
>> tested 2015-01-25 10:52:03
>>
>> (Many of my other tools are also currently listed with
>> different unexpected failures, some of which include
>> the "Exception: History in error state." traceback.)
>>
>> Interestingly, I've just got what appears to be the same
>> exception from a TravisCI test run (following a trivial
>> change to README files):
>>
>> https://travis-ci.org/peterjc/galaxy_blast/builds/48893916
>>
>> e.g. (one of many similar failing tests in this log)
>> ======================================================================
>> ERROR: test_tool_000000
>> (functional.test_toolbox.TestForTool_blastxml_to_top_descr)
>> BLAST top hit descriptions ( blastxml_to_top_descr ) > Test-1
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
>> line 268, in test_tool
>>     self.do_it( td )
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
>> line 37, in do_it
>>     stage_data_in_history( galaxy_interactor, testdef.test_data(),
>> test_history, shed_tool_id )
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 42, in stage_data_in_history
>>     upload_wait()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 279, in wait
>>     while not self.__history_ready( history_id ):
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 297, in __history_ready
>>     return self._state_ready( state, error_msg="History in error state." )
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 356, in _state_ready
>>     raise Exception( error_msg )
>> Exception: History in error state.
>>
>>
>> I do not recall seeing this problem locally when using my
>> development instllation of galaxy-central.
>>
>> The TravisCI failure suggests this could be a stochastic
>> resource contention (I can re-run the TravisCI build and
>> see if this works second time round?), which is more prone
>> to fail under the Tool Shed framework?
>>
>> Peter
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>>
>> Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate,
>> le video chiamate e persino le chiamate di gruppo.
>> E chiami gratis anche i numeri fissi e mobili nel mondo!
>> Scarica subito l’app Vai su https://www.indoona.com/
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> 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:
  https://lists.galaxyproject.org/

To search Galaxy mailing lists use the unified search at:
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Re: Tool Tests failing with "Exception: History in error state."

Dannon Baker-2
I'm actually working on rolling out much better error capturing for the toolshed via sentry (getsentry.org) and expect to update the test toolshed again with it shortly.  I'd guess the main toolshed won't be too far behind.

On Fri Jan 30 2015 at 12:24:47 PM Peter Cock <[hidden email]> wrote:
Hi Dannon, Nicola,

This sounds very promising - I'll rerun the TravisCI job and we can
expect it to work this time :)

https://bitbucket.org/galaxy/galaxy-central/commits/3618b7a91e23096ecf7ce5842c1e16c749251a4d
(half an hour ago!)

When will this reach the Tool Shed and Test Tool Shed? The upload job
failure seems to be the root cause of many of the unexpected test
failures.

Thanks,

Peter

On Fri, Jan 30, 2015 at 5:19 PM, Dannon Baker <[hidden email]> wrote:
> Yep, the FutureWarning that that commit resolves would have caused the
> upload job to end up as an error; I'm betting this is what was causing
> Peter's issues too.
>
>
> On Fri Jan 30 2015 at 12:18:10 PM Nicola Soranzo <[hidden email]>
> wrote:
>>
>> Hi Peter,
>> I was also getting "Exception: History in error state" errors with
>> BioBlend continuous integration testing, but those seem to be fixed with
>> latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d .
>>
>> Nicola
>>
>> Il 30.01.2015 17:36 Peter Cock ha scritto:
>>
>> Retitling thread,
>>
>> On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock <[hidden email]>
>> wrote:
>>
>> Thanks Dave, The good news is yes, the tests are running again on the Test
>> Tool Shed (although not the main Tool Shed yet), and many of my tools now
>> have successful test results from last night. e.g. My new basic mummer tool
>> which now has a full set of dependency packages thanks to Bjoern:
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there
>> are many unexpected failures with: "Exception: History in error state." I'm
>> sure you'll learn more once you look over the logs, Thank you, Peter
>>
>> Right now the mummer example given above is passing,
>> but I am still getting this error on some of my tools, e.g.
>>
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
>> tested 2015-01-25 11:21:12
>>
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
>> tested 2015-01-25 10:52:03
>>
>> (Many of my other tools are also currently listed with
>> different unexpected failures, some of which include
>> the "Exception: History in error state." traceback.)
>>
>> Interestingly, I've just got what appears to be the same
>> exception from a TravisCI test run (following a trivial
>> change to README files):
>>
>> https://travis-ci.org/peterjc/galaxy_blast/builds/48893916
>>
>> e.g. (one of many similar failing tests in this log)
>> ======================================================================
>> ERROR: test_tool_000000
>> (functional.test_toolbox.TestForTool_blastxml_to_top_descr)
>> BLAST top hit descriptions ( blastxml_to_top_descr ) > Test-1
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
>> line 268, in test_tool
>>     self.do_it( td )
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
>> line 37, in do_it
>>     stage_data_in_history( galaxy_interactor, testdef.test_data(),
>> test_history, shed_tool_id )
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 42, in stage_data_in_history
>>     upload_wait()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 279, in wait
>>     while not self.__history_ready( history_id ):
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 297, in __history_ready
>>     return self._state_ready( state, error_msg="History in error state." )
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 356, in _state_ready
>>     raise Exception( error_msg )
>> Exception: History in error state.
>>
>>
>> I do not recall seeing this problem locally when using my
>> development instllation of galaxy-central.
>>
>> The TravisCI failure suggests this could be a stochastic
>> resource contention (I can re-run the TravisCI build and
>> see if this works second time round?), which is more prone
>> to fail under the Tool Shed framework?
>>
>> Peter
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> To search Galaxy mailing lists use the unified search at:
>>   http://galaxyproject.org/search/mailinglists/
>>
>>
>>
>>
>> Connetti gratis il mondo con la nuova indoona: hai la chat, le chiamate,
>> le video chiamate e persino le chiamate di gruppo.
>> E chiami gratis anche i numeri fissi e mobili nel mondo!
>> Scarica subito l’app Vai su https://www.indoona.com/
>>
>> ___________________________________________________________
>> 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:
>>   https://lists.galaxyproject.org/
>>
>> 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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To search Galaxy mailing lists use the unified search at:
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Re: Tool Tests failing with "Exception: History in error state."

Dannon Baker-2
Slight clarification on that -- main toolshed update is a separate process since it runs #stable, but we're working on getting that updated as well.

On Fri Jan 30 2015 at 12:26:06 PM Dannon Baker <[hidden email]> wrote:
I'm actually working on rolling out much better error capturing for the toolshed via sentry (getsentry.org) and expect to update the test toolshed again with it shortly.  I'd guess the main toolshed won't be too far behind.

On Fri Jan 30 2015 at 12:24:47 PM Peter Cock <[hidden email]> wrote:
Hi Dannon, Nicola,

This sounds very promising - I'll rerun the TravisCI job and we can
expect it to work this time :)

https://bitbucket.org/galaxy/galaxy-central/commits/3618b7a91e23096ecf7ce5842c1e16c749251a4d
(half an hour ago!)

When will this reach the Tool Shed and Test Tool Shed? The upload job
failure seems to be the root cause of many of the unexpected test
failures.

Thanks,

Peter

On Fri, Jan 30, 2015 at 5:19 PM, Dannon Baker <[hidden email]> wrote:
> Yep, the FutureWarning that that commit resolves would have caused the
> upload job to end up as an error; I'm betting this is what was causing
> Peter's issues too.
>
>
> On Fri Jan 30 2015 at 12:18:10 PM Nicola Soranzo <[hidden email]>
> wrote:
>>
>> Hi Peter,
>> I was also getting "Exception: History in error state" errors with
>> BioBlend continuous integration testing, but those seem to be fixed with
>> latest Dannon's commit 3618b7a91e23096ecf7ce5842c1e16c749251a4d .
>>
>> Nicola
>>
>> Il 30.01.2015 17:36 Peter Cock ha scritto:
>>
>> Retitling thread,
>>
>> On Thu, Nov 6, 2014 at 11:08 AM, Peter Cock <[hidden email]>
>> wrote:
>>
>> Thanks Dave, The good news is yes, the tests are running again on the Test
>> Tool Shed (although not the main Tool Shed yet), and many of my tools now
>> have successful test results from last night. e.g. My new basic mummer tool
>> which now has a full set of dependency packages thanks to Bjoern:
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer The bad news is there
>> are many unexpected failures with: "Exception: History in error state." I'm
>> sure you'll learn more once you look over the logs, Thank you, Peter
>>
>> Right now the mummer example given above is passing,
>> but I am still getting this error on some of my tools, e.g.
>>
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
>> tested 2015-01-25 11:21:12
>>
>> https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
>> tested 2015-01-25 10:52:03
>>
>> (Many of my other tools are also currently listed with
>> different unexpected failures, some of which include
>> the "Exception: History in error state." traceback.)
>>
>> Interestingly, I've just got what appears to be the same
>> exception from a TravisCI test run (following a trivial
>> change to README files):
>>
>> https://travis-ci.org/peterjc/galaxy_blast/builds/48893916
>>
>> e.g. (one of many similar failing tests in this log)
>> ======================================================================
>> ERROR: test_tool_000000
>> (functional.test_toolbox.TestForTool_blastxml_to_top_descr)
>> BLAST top hit descriptions ( blastxml_to_top_descr ) > Test-1
>> ----------------------------------------------------------------------
>> Traceback (most recent call last):
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
>> line 268, in test_tool
>>     self.do_it( td )
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/functional/test_toolbox.py",
>> line 37, in do_it
>>     stage_data_in_history( galaxy_interactor, testdef.test_data(),
>> test_history, shed_tool_id )
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 42, in stage_data_in_history
>>     upload_wait()
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 279, in wait
>>     while not self.__history_ready( history_id ):
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 297, in __history_ready
>>     return self._state_ready( state, error_msg="History in error state." )
>>   File
>> "/home/travis/build/peterjc/galaxy_blast/galaxy-central-master/test/base/interactor.py",
>> line 356, in _state_ready
>>     raise Exception( error_msg )
>> Exception: History in error state.
>>
>>
>> I do not recall seeing this problem locally when using my
>> development instllation of galaxy-central.
>>
>> The TravisCI failure suggests this could be a stochastic
>> resource contention (I can re-run the TravisCI build and
>> see if this works second time round?), which is more prone
>> to fail under the Tool Shed framework?
>>
>> Peter
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>>
>>
>>
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Re: Tool Tests failing with "Exception: History in error state."

Peter Cock
In reply to this post by Peter Cock
On Fri, Jan 30, 2015 at 5:24 PM, Peter Cock <[hidden email]> wrote:
> Hi Dannon, Nicola,
>
> This sounds very promising - I'll rerun the TravisCI job and we can
> expect it to work this time :)
>
> https://bitbucket.org/galaxy/galaxy-central/commits/3618b7a91e23096ecf7ce5842c1e16c749251a4d
> (half an hour ago!)

The second TravisCI run worked (same version of the tools, newer
version of Galaxy with Dannon's fix).

> When will this reach the Tool Shed and Test Tool Shed? The upload job
> failure seems to be the root cause of many of the unexpected test
> failures.

The problem tests with "Exception: History in error state" don't
seem to have been re-run yet? e.g.

https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
Still last tested 2015-01-25 11:21:12

https://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
Still last tested 2015-01-25 10:52:03

Thanks,

Peter
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