11:09 a.m.
Hi Greg & Dave,
I really like the new features on the (Test) Tool Shed for searching
my repositories:
* Latest revision missing tool tests
* Latest revision failing tool tests
* Latest revision all tool tests pass
However there are some teething problems. Some of my tools are
listed under "Latest revision failing tool tests", but when I go to look
at them, no test results are shown (passing or failing):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
In some cases there is indeed a failing test, for instance this is
due to a bug in the test framework:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
https://trello.com/c/KdGX3hkh
And here there are missing dependencies (due to restrictive
licensing problems):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
https://trello.com/card/-/506338ce32ae458f6d15e4b3/770
Peter
12:52 p.m.
Hi Peter,
I created the following Trello card for this and things will be fixed as a priority.
Thanks for letting us know!
https://trello.com/card/toolshed-issues-with-functional-test-results/5063...
On May 1, 2013, at 7:09 AM, Peter Cock wrote:
Hi Greg & Dave,
I really like the new features on the (Test) Tool Shed for searching
my repositories:
* Latest revision missing tool tests
* Latest revision failing tool tests
* Latest revision all tool tests pass
However there are some teething problems. Some of my tools are
listed under "Latest revision failing tool tests", but when I go to look
at them, no test results are shown (passing or failing):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
In some cases there is indeed a failing test, for instance this is
due to a bug in the test framework:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
https://trello.com/c/KdGX3hkh
And here there are missing dependencies (due to restrictive
licensing problems):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
https://trello.com/card/-/506338ce32ae458f6d15e4b3/770
Peter
10:50 p.m.
Peter,
Thanks for the data, I am in the process of tracking down the source of
the issue, and I hope to have a fix ready shortly.
--Dave B.
On 2013-05-01 08:52, Greg Von Kuster wrote:
Hi Peter,
I created the following Trello card for this and things will be fixed as a priority.
Thanks for letting us know!
https://trello.com/card/toolshed-issues-with-functional-test-results/5063...
On May 1, 2013, at 7:09 AM, Peter Cock wrote:
> Hi Greg & Dave,
>
> I really like the new features on the (Test) Tool Shed for searching
> my repositories:
>
> * Latest revision missing tool tests
> * Latest revision failing tool tests
> * Latest revision all tool tests pass
>
> However there are some teething problems. Some of my tools are
> listed under "Latest revision failing tool tests", but when I go to look
> at them, no test results are shown (passing or failing):
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
>
> In some cases there is indeed a failing test, for instance this is
> due to a bug in the test framework:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go
> https://trello.com/c/KdGX3hkh
>
> And here there are missing dependencies (due to restrictive
> licensing problems):
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
> https://trello.com/card/-/506338ce32ae458f6d15e4b3/770
>
> Peter
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9:10 a.m.
On 2013-05-01 08:52, Greg Von Kuster wrote:
>
> Hi Peter,
>
> I created the following Trello card for this and things will be fixed as a
> priority. Thanks for letting us know!
>
>
>
https://trello.com/card/toolshed-issues-with-functional-test-results/5063...
On Wed, May 1, 2013 at 11:50 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
Thanks for the data, I am in the process of tracking down the source of the
issue, and I hope to have a fix ready shortly.
--Dave B.
Hi Dave,
I see from the Trello card you've made some progress here - but I am
still seeing odd results on the Test Tool Shed (including not seeing
any test results), which has also been reflected in the RSS feed.
e.g. Conflicting RSS entries:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/fe46...
Functional test results for changeset revision fae4084a0bc0 of
fastq_paired_unpaired
0 tests passed, 0 tests failed, 5 tests missing test components.
vs
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/fe46...
Functional test results for changeset revision fe469503441b of
fastq_paired_unpaired
0 tests passed, 0 tests failed, 0 tests missing test components.
Currently the Test Tool Shed shows me no test information at all
for this example (and sadly many others).
This seems to be part of a larger issue, "Latest revision: failing tool tests"
currently only lists mira_assembler - yet viewing this shows no failure
(or any other results):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
Last week I had numerous failing tests (mostly due to missing tool
dependencies, some due to issues with the text framework). Many
of the (presumably still problematic) repositories are now listed under
"Latest revision: all tool tests pass" yet on viewing them there are no
test results shown at all, e.g.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/54c3d14e5621
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/af317463...
Something seems to have gone wrong on Friday or over the weekend,
Regards,
Peter
12:55 p.m.
Peter,
Yes, there are a few issues that are causing some repositories not to be
tested correctly. I've discovered the problem, but the solution will
require a bit of work. My goal is to have this resolved as soon as possible.
--Dave B.
On 5/6/13 05:10:57.000, Peter Cock wrote:
> On 2013-05-01 08:52, Greg Von Kuster wrote:
>>
>> Hi Peter,
>>
>> I created the following Trello card for this and things will be fixed as a
>> priority. Thanks for letting us know!
>>
>>
>>
https://trello.com/card/toolshed-issues-with-functional-test-results/5063...
On Wed, May 1, 2013 at 11:50 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
> Peter,
>
> Thanks for the data, I am in the process of tracking down the source of the
> issue, and I hope to have a fix ready shortly.
>
> --Dave B.
Hi Dave,
I see from the Trello card you've made some progress here - but I am
still seeing odd results on the Test Tool Shed (including not seeing
any test results), which has also been reflected in the RSS feed.
e.g. Conflicting RSS entries:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/fe46...
Functional test results for changeset revision fae4084a0bc0 of
fastq_paired_unpaired
0 tests passed, 0 tests failed, 5 tests missing test components.
vs
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/fe46...
Functional test results for changeset revision fe469503441b of
fastq_paired_unpaired
0 tests passed, 0 tests failed, 0 tests missing test components.
Currently the Test Tool Shed shows me no test information at all
for this example (and sadly many others).
This seems to be part of a larger issue, "Latest revision: failing tool tests"
currently only lists mira_assembler - yet viewing this shows no failure
(or any other results):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
Last week I had numerous failing tests (mostly due to missing tool
dependencies, some due to issues with the text framework). Many
of the (presumably still problematic) repositories are now listed under
"Latest revision: all tool tests pass" yet on viewing them there are no
test results shown at all, e.g.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/54c3d14e5621
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/af317463...
Something seems to have gone wrong on Friday or over the weekend,
Regards,
Peter
8:50 a.m.
On Mon, May 6, 2013 at 1:55 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
Yes, there are a few issues that are causing some repositories not to be
tested correctly. I've discovered the problem, but the solution will require
a bit of work. My goal is to have this resolved as soon as possible.
--Dave B.
Hi Dave,
Things are looking sensible again on the Test Tool Shed - thanks :)
I have a query which might deserve discussion: Currently my
some of my BLAST+ tools have missing tests and some are
failing (due in part to limitations of the test framework) yet
the repository is only listed under missing tool tests:
Latest revision: missing tool tests - includes ncbi_blast_plus
Latest revision: failing tool tests - omits ncbi_blast_plus
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
As the yellow description makes clear, this is deliberate,
but I would prefer to have ncbi_blast_plus listed in both
places. In this case I know there are missing tests, but
would hope there are no failing tests - yet the Tool Shed
interface is effectively 'hiding' these failures from the
prominent listing.
(Right now the failures are unexpected, it seems my
changes to the automated installation were not successful
- but that's why I'm testing them here to check this)
What does everyone else think?
Thanks,
Peter
9:59 a.m.
Hi Peter,
This change would be simple to make, but it would result in the inclusion of all
repositories with missing test components to be included in the list of failing tests.
There are currently 2 filters that provide the information to categorize these
repositories: missing test components ( True / False ) and tools functionally correct (
True / False ). I'm not sure it makes sense to add a 3rd filter, but if we can come
up with a sensible one, I would be happy to add it. If not, do you want the list of
failing tool tests to include repositories that are missing test components?
Thanks!
Greg
On May 7, 2013, at 4:50 AM, Peter Cock wrote:
On Mon, May 6, 2013 at 1:55 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> Yes, there are a few issues that are causing some repositories not to be
> tested correctly. I've discovered the problem, but the solution will require
> a bit of work. My goal is to have this resolved as soon as possible.
>
> --Dave B.
Hi Dave,
Things are looking sensible again on the Test Tool Shed - thanks :)
I have a query which might deserve discussion: Currently my
some of my BLAST+ tools have missing tests and some are
failing (due in part to limitations of the test framework) yet
the repository is only listed under missing tool tests:
Latest revision: missing tool tests - includes ncbi_blast_plus
Latest revision: failing tool tests - omits ncbi_blast_plus
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
As the yellow description makes clear, this is deliberate,
but I would prefer to have ncbi_blast_plus listed in both
places. In this case I know there are missing tests, but
would hope there are no failing tests - yet the Tool Shed
interface is effectively 'hiding' these failures from the
prominent listing.
(Right now the failures are unexpected, it seems my
changes to the automated installation were not successful
- but that's why I'm testing them here to check this)
What does everyone else think?
Thanks,
Peter
___________________________________________________________
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1:10 p.m.
On Tue, May 7, 2013 at 10:59 AM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
Hi Peter,
This change would be simple to make, but it would result in the inclusion
of all repositories with missing test components to be included in the list
of failing tests. There are currently 2 filters that provide the
information to categorize these repositories: missing test components ( True
/ False ) and tools functionally correct ( True / False ). I'm not sure it
makes sense to add a 3rd filter, but if we can come up with a sensible one,
I would be happy to add it. If not, do you want the list of failing tool
tests to include repositories that are missing test components?
By missing test components do you mean things like missing a test input
or output file? If so, that would be fine. If I've written a test but
not included
the sample data, then to me that is just a special case of a failing test that
needs fixing (and it should be a trivial fix).
Currently (according to the yellow notes on the Test Tool Shed),
Latest revision: missing tool tests:
* you are authorized to update them
* the latest installable revision contains at least 1 tool with no
defined tests OR:
* the latest installable revision contains at least 1 tool with a
test that requires a missing test data file
Latest revision: failing tool tests:
* you are authorized to update them
* the latest installable revision contains at least 1 tool
* the latest installable revision is not missing any tool test components
* the latest installable revision has at least 1 tool test that fails
My suggestion would be to treat missing test data files as a failing
test, something like this:
Latest revision: missing tool tests:
* you are authorized to update them
* the latest installable revision contains at least 1 tool with no
defined tests
Latest revision: failing tool tests:
* you are authorized to update them
* the latest installable revision has at least 1 tool test that fails
OR requires a missing test data file
Under this scheme, right now on the Test Tool Shed my ncbi_blast_plus
repository would appear on both lists due to missing tests for tools like
ncbi_rpsblast_wrapper, and failing tests like ncbi_blastn_wrapper (due
to a glitch in the dependency installation changes I made).
Peter
6:02 p.m.
Hi Peter,
On May 7, 2013, at 9:10 AM, Peter Cock wrote:
On Tue, May 7, 2013 at 10:59 AM, Greg Von Kuster
<greg(a)bx.psu.edu> wrote:
> Hi Peter,
>
> This change would be simple to make, but it would result in the inclusion
> of all repositories with missing test components to be included in the list
> of failing tests. There are currently 2 filters that provide the
> information to categorize these repositories: missing test components ( True
> / False ) and tools functionally correct ( True / False ). I'm not sure it
> makes sense to add a 3rd filter, but if we can come up with a sensible one,
> I would be happy to add it. If not, do you want the list of failing tool
> tests to include repositories that are missing test components?
By missing test components do you mean things like missing a test input
or output file? If so, that would be fine. If I've written a test but
not included
the sample data, then to me that is just a special case of a failing test that
needs fixing (and it should be a trivial fix).
Missing test components implies a tool config that does not define a test (i.e, a missing
test definition) or a tool config that defines a test, but the test's input or output
files are missing from the repository.
Currently (according to the yellow notes on the Test Tool Shed),
Latest revision: missing tool tests:
* you are authorized to update them
* the latest installable revision contains at least 1 tool with no
defined tests OR:
* the latest installable revision contains at least 1 tool with a
test that requires a missing test data file
Latest revision: failing tool tests:
* you are authorized to update them
* the latest installable revision contains at least 1 tool
* the latest installable revision is not missing any tool test components
* the latest installable revision has at least 1 tool test that fails
My suggestion would be to treat missing test data files as a failing
test, something like this:
Latest revision: missing tool tests:
* you are authorized to update them
* the latest installable revision contains at least 1 tool with no
defined tests
I don't see the benefit of the above where you place tools missing tests into a
different category than tools with defined tests, but missing test data. If any of the
test components (test definition or required input or output files) are missing, then the
test cannot be executed, so defining it as a failing test in either case is a bit
misleading. It is actually a tool that is missing test components that are required for
execution which will result in a pass / fail status.
It would be much simpler to change the filter for failing tests to include those that are
missing test components so that the list of missing test components is a subset of the
list of failing tests.
Latest revision: failing tool tests:
* you are authorized to update them
* the latest installable revision has at least 1 tool test that fails
OR requires a missing test data file
Under this scheme, right now on the Test Tool Shed my ncbi_blast_plus
repository would appear on both lists due to missing tests for tools like
ncbi_rpsblast_wrapper, and failing tests like ncbi_blastn_wrapper (due
to a glitch in the dependency installation changes I made).
Peter
10:45 a.m.
On Tue, May 7, 2013 at 7:02 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
Hi Peter,
Missing test components implies a tool config that does not define a
test (i.e, a missing test definition) or a tool config that defines a test,
but the test's input or output files are missing from the repository.
This seems to be our point of confusion: I don't understand combining
these two categories - it seems unhelpful to me.
Tools missing a test definition clearly can't be tested - but since we'd
like every tool to have tests having this as an easily view listing is
useful both for authors and reviewers. It highlights tools which need
some work - or in some cases work on the Galaxy test framework itself.
They are neither passing nor failing tests - and it makes sense to list
them separately.
Tools with a test definition should be tested - if they are missing an
input or output file this is just a special case of a test failure (and can
be spotted without actually attempting to run the tool). This is clearly
a broken test and the tool author should be able to fix this easily (by
uploading the missing test data file)
I don't see the benefit of the above where you place tools
missing tests
into a different category than tools with defined tests, but missing test data.
If any of the test components (test definition or required input or output files)
are missing, then the test cannot be executed, so defining it as a failing
test in either case is a bit misleading. It is actually a tool that is missing
test components that are required for execution which will result in a pass
/ fail status.
It is still a failing test (just for the trivial reason of missing a
test data file).
It would be much simpler to change the filter for failing tests to
include
those that are missing test components so that the list of missing test
components is a subset of the list of failing tests.
What I would like is three lists:
Latest revision: missing tool tests
- repositories where at least 1 tool has no test defined
[The medium term TO-DO list for the Tool Author]
Latest revision: failing tool tests
- repositories where at least 1 tool has a failing test (where I include
tests missing their input or output test data files)
[The priority TO-DO list for the Tool Author]
Latest revision: all tool tests pass
- repositories where every tool has tests and they all pass
[The good list, Tool Authors should aim to have everything here]
Right now http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
would appear under both "missing tool tests" and "failing tool
tests",
but I hope to fix this and have this under "missing tool tests" only
(until my current roadblocks with the Galaxy Test Framework are
resolved).
I hope I've managed a clearer explanation this time,
Thanks,
Peter
2:28 p.m.
Hi Peter,
On May 8, 2013, at 6:45 AM, Peter Cock wrote:
On Tue, May 7, 2013 at 7:02 PM, Greg Von Kuster
<greg(a)bx.psu.edu> wrote:
> Hi Peter,
>
> Missing test components implies a tool config that does not define a
> test (i.e, a missing test definition) or a tool config that defines a test,
> but the test's input or output files are missing from the repository.
This seems to be our point of confusion: I don't understand combining
these two categories - it seems unhelpful to me.
I feel this is just a difference of opinion. Combining missing tests and missing test
data into a single category is certainly justifiable. Any repository that falls into this
category clearly states to the owner what is missing, and the owner can easily know that
work is needed to prepare the repository contents for testing, whether that work falls
into the category of adding a missing test or adding missing test data.
Tools missing a test definition clearly can't be tested - but since we'd
like every tool to have tests having this as an easily view listing is
useful both for authors and reviewers.
But is is an easily viewed listing. It is currently very easy to determine if a tool is
missing a defined test, is missing test data, or both.
It highlights tools which need
some work - or in some cases work on the Galaxy test framework itself.
They are neither passing nor failing tests - and it makes sense to list
them separately.
Tools with a test definition should be tested
This is where I disagree. It currently takes a few seconds for our check repositories for
test components to crawl the entire main tool shed and set flags for those repositories
missing test components. However, the separate script that crawls the main tool shed and
installs and tests repositories that are not missing test components currently takes hours
to run even though less than 10% of the repositories are currently tests (due to missing
test components on most of them).
Installing a testing repositories that have tools with defined tests but missing test data
is potentially costly from a time perspective. Let's take a simple example:
Repo A has 1 tool that includes a defined test, but is missing required test data from the
repository. The tool in repo A defines 2 3rd party tool dependencies that must be
installed and compiled. In addition, repo A defines a repository dependency whose
ultimate chain of repository installations results in 4 additional repositories with 16
additional 3rd party tool dependencies, with a total installation time of 2 hours. All of
this time is taken in order to test the tool in repo A when we already know that it will
not succeed because it is missing test data. This is certainly a realistic scenario.
- if they are missing an
input or output file this is just a special case of a test failure (and can
be spotted without actually attempting to run the tool).
Yes, but this is what we are doing now. We are spotting this scenario without installing
the repository or running any defined tests by running the tool.
This is clearly
a broken test and the tool author should be able to fix this easily (by
uploading the missing test data file)
Yes, but this is already possible for them to clearly see without having to install the
repository or run any tests.
> I don't see the benefit of the above where you place tools missing tests
> into a different category than tools with defined tests, but missing test data.
> If any of the test components (test definition or required input or output files)
> are missing, then the test cannot be executed, so defining it as a failing
> test in either case is a bit misleading. It is actually a tool that is missing
> test components that are required for execution which will result in a pass
> / fail status.
It is still a failing test (just for the trivial reason of missing a
test data file).
> It would be much simpler to change the filter for failing tests to include
> those that are missing test components so that the list of missing test
> components is a subset of the list of failing tests.
What I would like is three lists:
Latest revision: missing tool tests
- repositories where at least 1 tool has no test defined
[The medium term TO-DO list for the Tool Author]
Latest revision: failing tool tests
- repositories where at least 1 tool has a failing test (where I include
tests missing their input or output test data files)
[The priority TO-DO list for the Tool Author]
Latest revision: all tool tests pass
- repositories where every tool has tests and they all pass
[The good list, Tool Authors should aim to have everything here]
Right now http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
would appear under both "missing tool tests" and "failing tool
tests",
but I hope to fix this and have this under "missing tool tests" only
(until my current roadblocks with the Galaxy Test Framework are
resolved).
I hope I've managed a clearer explanation this time,
Thanks,
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:
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3:49 p.m.
On Wed, May 8, 2013 at 3:28 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
Hi Peter,
On May 8, 2013, at 6:45 AM, Peter Cock wrote:
> On Tue, May 7, 2013 at 7:02 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
>> Hi Peter,
>>
>> Missing test components implies a tool config that does not define a
>> test (i.e, a missing test definition) or a tool config that defines a test,
>> but the test's input or output files are missing from the repository.
>
> This seems to be our point of confusion: I don't understand combining
> these two categories - it seems unhelpful to me.
I feel this is just a difference of opinion. Combining missing tests and
missing test data into a single category is certainly justifiable. Any
repository that falls into this category clearly states to the owner what
is missing, and the owner can easily know that work is needed to
prepare the repository contents for testing, whether that work falls
into the category of adding a missing test or adding missing test data.
Speaking as a tool author, these are two rather different categories
which should not be merged. I personally would put "tools with defined
tests but missing input/output files" under "failing tests" not under
"missing tests".
> Tools missing a test definition clearly can't be tested - but
since we'd
> like every tool to have tests having this as an easily view listing is
> useful both for authors and reviewers.
But is is an easily viewed listing. It is currently very easy to determine
if a tool is missing a defined test, is missing test data, or both.
No it isn't easily viewable - it is easy to get a combined listing of
repositories with (a) missing tests and/or (b) tests with missing files,
and then very tedious to look at these repositories one by one to see
which it is.
> It highlights tools which need
> some work - or in some cases work on the Galaxy test framework itself.
> They are neither passing nor failing tests - and it makes sense to list
> them separately.
>
> Tools with a test definition should be tested
This is where I disagree. ... <snip>
Installing a testing repositories that have tools with defined tests
but missing test data is potentially costly from a time perspective.
<snip>
I wasn't meaning to suggest you do that though - you're already
able to short cut these cases and mark the test as failed. These
are the quickest possible tests to run - they fail at the first hurdle.
> - if they are missing an input or output
> file this is just a special case of a test failure (and can
> be spotted without actually attempting to run the tool).
Yes, but this is what we are doing now. We are spotting
this scenario without installing the repository or running
any defined tests by running the tool.
Yes, and that is fine - I'm merely talking about how this information
is presented to the Tool Shed viewer.
> This is clearly
> a broken test and the tool author should be able to fix this easily (by
> uploading the missing test data file)
Yes, but this is already possible for them to clearly see without
having to install the repository or run any tests.
Indeed, but it this is a failing test and should (in my view) be
listed under failing tests not under missing tests.
We're just debating where to list such problem tools/repositories
in the Tool Shed's test results interface.
Regards,
Peter
1:10 p.m.
Peter,
As you've already noticed, I've tracked down and fixed the main issue
that was causing inaccurate test results. Thank you again for the data
you provided, which was of great help narrowing down the cause of the
issue.
--Dave B.
On 5/7/13 04:50:23.000, Peter Cock wrote:
On Mon, May 6, 2013 at 1:55 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> Yes, there are a few issues that are causing some repositories not to be
> tested correctly. I've discovered the problem, but the solution will require
> a bit of work. My goal is to have this resolved as soon as possible.
>
> --Dave B.
Hi Dave,
Things are looking sensible again on the Test Tool Shed - thanks :)
I have a query which might deserve discussion: Currently my
some of my BLAST+ tools have missing tests and some are
failing (due in part to limitations of the test framework) yet
the repository is only listed under missing tool tests:
Latest revision: missing tool tests - includes ncbi_blast_plus
Latest revision: failing tool tests - omits ncbi_blast_plus
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
As the yellow description makes clear, this is deliberate,
but I would prefer to have ncbi_blast_plus listed in both
places. In this case I know there are missing tests, but
would hope there are no failing tests - yet the Tool Shed
interface is effectively 'hiding' these failures from the
prominent listing.
(Right now the failures are unexpected, it seems my
changes to the automated installation were not successful
- but that's why I'm testing them here to check this)
What does everyone else think?
Thanks,
Peter
1:16 p.m.
On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
As you've already noticed, I've tracked down and fixed the main issue that
was causing inaccurate test results. Thank you again for the data you
provided, which was of great help narrowing down the cause of the issue.
--Dave B.
I'm glad that's sorted - I should be able to get back into fixing tests
and adding a few more now that I'm getting nightly feedback again :)
Thanks!
Peter
P.S. Is the idea of running the tests whenever a tool is updated likely to
happen in the near future, or is that still a wish list item?
11:09 a.m.
On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
As you've already noticed, I've tracked down and fixed the main issue that
was causing inaccurate test results. Thank you again for the data you
provided, which was of great help narrowing down the cause of the issue.
--Dave B.
Hi Dave,
I've got another problem set for you, some repositories are listed under
"Latest revision: failing tool tests", yet there are no test results are shown
(positive or negative).
Tool shed revision: 9661:cb0432cfcc8a
My clinod wrapper with one test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
Revision 3:a66a914c39b5
My effective T3 wrapper with two tests:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/4567618bebbd
Revision 5:4567618bebbd
My seq_rename tool with one test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/b51633a69a92
Revision 2:b51633a69a92
Regards,
Peter
1:09 p.m.
Peter,
A technical issue prevented the tests from automatically running. I've
resolved the issue and started a manual run, you should be seeing test
results within 2-3 hours.
--Dave B.
On 5/8/13 07:09:28.000, Peter Cock wrote:
On Tue, May 7, 2013 at 2:10 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> As you've already noticed, I've tracked down and fixed the main issue that
> was causing inaccurate test results. Thank you again for the data you
> provided, which was of great help narrowing down the cause of the issue.
>
> --Dave B.
Hi Dave,
I've got another problem set for you, some repositories are listed under
"Latest revision: failing tool tests", yet there are no test results are shown
(positive or negative).
Tool shed revision: 9661:cb0432cfcc8a
My clinod wrapper with one test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
Revision 3:a66a914c39b5
My effective T3 wrapper with two tests:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/4567618bebbd
Revision 5:4567618bebbd
My seq_rename tool with one test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/b51633a69a92
Revision 2:b51633a69a92
Regards,
Peter
9:49 a.m.
On Wed, May 8, 2013 at 2:09 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
A technical issue prevented the tests from automatically running. I've
resolved the issue and started a manual run, you should be seeing test
results within 2-3 hours.
--Dave B.
Hi Dave,
As you hoped, these test now shows up on the tool page (as expected
they are test failures - apparently my install script isn't quite right yet):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
Functional test results for changeset revision a66a914c39b5 of clinod
0 tests passed, 1 tests failed, 0 tests missing test components.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/5644c28cf965
Functional test results for changeset revision 5644c28cf965 of effectivet3
0 tests passed, 2 tests failed, 0 tests missing test components.
This one is more interesting, and appears to be a problem with the
test framework (both tests pass locally via run_functional_tests.sh):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9
Functional test results for changeset revision 16a1a5ae98e9 of seq_rename
0 tests passed, 2 tests failed, 0 tests missing test components.
I'll raise that on a new thread,
Peter
(Sorry for resending this Dave, I left off the mailing list the first time)
9:34 a.m.
On Thu, May 9, 2013 at 10:49 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Wed, May 8, 2013 at 2:09 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> A technical issue prevented the tests from automatically running. I've
> resolved the issue and started a manual run, you should be seeing test
> results within 2-3 hours.
>
> --Dave B.
Hi Dave,
As you hoped, these test now shows up on the tool page (as expected
they are test failures - apparently my install script isn't quite right yet):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
Functional test results for changeset revision a66a914c39b5 of clinod
0 tests passed, 1 tests failed, 0 tests missing test components.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/5644c28cf965
Functional test results for changeset revision 5644c28cf965 of effectivet3
0 tests passed, 2 tests failed, 0 tests missing test components.
This one is more interesting, and appears to be a problem with the
test framework (both tests pass locally via run_functional_tests.sh):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9
Functional test results for changeset revision 16a1a5ae98e9 of seq_rename
0 tests passed, 2 tests failed, 0 tests missing test components.
I'll raise that on a new thread,
Peter
Hi again Dave,
There is something breaking intermittently - my overnight RSS feed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/20e44218fa63
Functional test results for changeset revision 20e44218fa63 of clinod
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)
--> No test results shown (positive or negative), yet it is
listed under "Latest revision: failing tool tests"
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/6e7694a0ae00
Functional test results for changeset revision 6e7694a0ae00 of blast2go
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)
--> Actually one failure due to dependency on main Tool Shed,
correctly listed under "Latest revision: failing tool tests"
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
Functional test results for changeset revision c70df461aae5 of effectivet3
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)
--> No test results shown (positive or negative), yet it is
listed under "Latest revision: failing tool tests"
These were the only three feed entries overnight from:
http://testtoolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owne...
Presumably then other tools were not tested - which makes
sense to save resources if neither the tool nor the tool shed
was updated since the last time a tool was tested.
Peter
12:51 p.m.
Peter,
The automated testing framework consists of a series of scripts that run
in a certain order, so between one script and the next, there may
sometimes be unexpected results displayed. I've had a look at the
repositories you listed, and the results all seem to be in order now.
The RSS feed also seems to be displaying the same results as the web
interface.
A repository is set not to be tested only in a few cases, among those is
when there is a more recent installable changeset revision, and the
revision currently being tested has missing components or does not pass
the tests.
--Dave B.
On 5/10/13 05:34:59.000, Peter Cock wrote:
On Thu, May 9, 2013 at 10:49 AM, Peter Cock
<p.j.a.cock(a)googlemail.com> wrote:
> On Wed, May 8, 2013 at 2:09 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
>> Peter,
>>
>> A technical issue prevented the tests from automatically running. I've
>> resolved the issue and started a manual run, you should be seeing test
>> results within 2-3 hours.
>>
>> --Dave B.
>
> Hi Dave,
>
> As you hoped, these test now shows up on the tool page (as expected
> they are test failures - apparently my install script isn't quite right yet):
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/a66a914c39b5
> Functional test results for changeset revision a66a914c39b5 of clinod
> 0 tests passed, 1 tests failed, 0 tests missing test components.
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/5644c28cf965
> Functional test results for changeset revision 5644c28cf965 of effectivet3
> 0 tests passed, 2 tests failed, 0 tests missing test components.
>
> This one is more interesting, and appears to be a problem with the
> test framework (both tests pass locally via run_functional_tests.sh):
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/16a1a5ae98e9
> Functional test results for changeset revision 16a1a5ae98e9 of seq_rename
> 0 tests passed, 2 tests failed, 0 tests missing test components.
>
> I'll raise that on a new thread,
>
> Peter
Hi again Dave,
There is something breaking intermittently - my overnight RSS feed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/20e44218fa63
Functional test results for changeset revision 20e44218fa63 of clinod
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)
--> No test results shown (positive or negative), yet it is
listed under "Latest revision: failing tool tests"
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/6e7694a0ae00
Functional test results for changeset revision 6e7694a0ae00 of blast2go
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)
--> Actually one failure due to dependency on main Tool Shed,
correctly listed under "Latest revision: failing tool tests"
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
Functional test results for changeset revision c70df461aae5 of effectivet3
0 tests passed, 0 tests failed, 0 tests missing test components.
7:38 AM (2 hours ago)
--> No test results shown (positive or negative), yet it is
listed under "Latest revision: failing tool tests"
These were the only three feed entries overnight from:
http://testtoolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owne...
Presumably then other tools were not tested - which makes
sense to save resources if neither the tool nor the tool shed
was updated since the last time a tool was tested.
Peter
1:30 p.m.
On Fri, May 10, 2013 at 1:51 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
The automated testing framework consists of a series of scripts that run in
a certain order, so between one script and the next, there may sometimes be
unexpected results displayed. I've had a look at the repositories you
listed, and the results all seem to be in order now. The RSS feed also seems
to be displaying the same results as the web interface.
There seems to be some kind of caching problem for me:
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/20e44218fa63
> Functional test results for changeset revision 20e44218fa63 of clinod
> 0 tests passed, 0 tests failed, 0 tests missing test components.
> 7:38 AM (2 hours ago)
>
> --> No test results shown (positive or negative), yet it is
> listed under "Latest revision: failing tool tests"
That URL redirects to here, still no test results shown in my main
browser (Firefox v20.0 on Mac):
http://testtoolshed.g2.bx.psu.edu/repository?repository_id=27e2bf03e13aae...
However, switching to Safari or Firefox on Windows I see the failing
test (Error: Unable to access jarfile ...).
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
> Functional test results for changeset revision c70df461aae5 of effectivet3
> 0 tests passed, 0 tests failed, 0 tests missing test components.
> 7:38 AM (2 hours ago)
>
> --> No test results shown (positive or negative), yet it is
> listed under "Latest revision: failing tool tests"
That URL redirects to here, still no test results in my main browser
(Firefox v20.0 on Mac):
http://testtoolshed.g2.bx.psu.edu/repository?repository_id=26f26c7aa084d3...
Again, switching to Safari or Firefox on Windows I see two failing tests
(Effective T3 model JAR file not found ...).
This suggest some caching problem - but restarting Firefox didn't
solve it, nor did deleting the cache files in Firefox. Puzzling.
Peter
9:08 a.m.
On Fri, May 10, 2013 at 2:30 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Fri, May 10, 2013 at 1:51 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> The automated testing framework consists of a series of scripts that run in
> a certain order, so between one script and the next, there may sometimes be
> unexpected results displayed. I've had a look at the repositories you
> listed, and the results all seem to be in order now. The RSS feed also seems
> to be displaying the same results as the web interface.
There seems to be some kind of caching problem for me:
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/20e44218fa63
>> Functional test results for changeset revision 20e44218fa63 of clinod
>> 0 tests passed, 0 tests failed, 0 tests missing test components.
>> 7:38 AM (2 hours ago)
>>
>> --> No test results shown (positive or negative), yet it is
>> listed under "Latest revision: failing tool tests"
That URL redirects to here, still no test results shown in my main
browser (Firefox v20.0 on Mac):
http://testtoolshed.g2.bx.psu.edu/repository?repository_id=27e2bf03e13aae...
However, switching to Safari or Firefox on Windows I see the failing
test (Error: Unable to access jarfile ...).
Today all those browsers show no test results for clinod :(
Tool test results
Automated test environment
Time tested: ~ 4 hours ago
System: Linux 3.0.0-1-amd64
Architecture: x86_64
Python version: 2.7.2+
Galaxy revision:
Galaxy database version:
Tool shed revision: 9701:65a81aead95e
Tool shed database version: 18
Tool shed mercurial version: 2.2.3
>>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
>> Functional test results for changeset revision c70df461aae5 of effectivet3
>> 0 tests passed, 0 tests failed, 0 tests missing test components.
>> 7:38 AM (2 hours ago)
Failures still showing (good), I've not uploaded the suggested changes
Dave made on Friday yet:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014619.html
But in addition to clinod (above), here are some more repositories where
the test results are currently missing (tested in three browsers over two
machines):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/5835...
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/88f002677c63
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/06e6112091aa
Might there be a timing issue here? Is it possible that when I check
in the morning UK time, the test results haven't yet all been recorded
in the database so the Tool Shed only has partial information - then
when you check in the afternoon UK time (morning in USA) things are
working (although I don't always see this if there is also a cache problem).
Thanks,
Peter
10:09 a.m.
On Mon, May 13, 2013 at 10:08 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
>>>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/c70df461aae5
>>> Functional test results for changeset revision c70df461aae5 of effectivet3
>>> 0 tests passed, 0 tests failed, 0 tests missing test components.
>>> 7:38 AM (2 hours ago)
Failures still showing (good), I've not uploaded the suggested changes
Dave made on Friday yet:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014619.html
I uploaded a minor change which should still fail but with a more helpful
error when running the tests (which confirmed the install script is failing
to create an expected directory):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/b863c4bec840
Using my default browser Firefox (on two machines) the tests are missing,
just:
Tool test results
Automated test environment
Time tested: 28 minutes ago
System: Linux 3.5.0-21-generic
Architecture: x86_64
Python version: 2.7.3
Galaxy revision: 9701:65a81aead95e
Galaxy database version: 115
Tool shed revision:
Tool shed database version:
Tool shed mercurial version:
However, switching to Safari and Chrome I can see the failures here.
I remain puzzled why I am seeing seemingly stochastic missing test
results.
Regards,
Peter
10:26 a.m.
On Mon, May 13, 2013 at 11:09 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
I remain puzzled why I am seeing seemingly stochastic missing test
results.
Hi Dave,
This continues - although I have been making progress with the
tests for some of my tools. Currently there are a number of
repositories reported as failing but I can't see the error (and so
can't do much about fixing it):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
When previously visible this was due to a test framework
limitation testing with composite output files:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014365.html
Given I suspect a cache issue hiding the test failures, it might
help if rather than the current text like "Time tested: ~ 8 hours ago"
this could also state the date and time of the test (in UTC/GMT to
avoid locale confusion).
Thanks,
Peter
----
Other repositories failing with a clear error message:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
Missing dependencies, should have been skipped, see
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014748.html
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
Limitation of test framework, Trello issue open for this,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014366.html
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename
Limitation of test framework, issue raised,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html
http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list
Missing an R/Bioconductor dependency, best practise for handling
this has yet to be agreed.
12:46 p.m.
Peter,
The most likely cause of this is that there is an issue with some
preceding repositories that hang on installation, causing the build
process to time out and not test later repositories in the list. I am in
the process of working out a solution for that situation.
--Dave B.
On 5/21/13 06:26:56.000, Peter Cock wrote:
On Mon, May 13, 2013 at 11:09 AM, Peter Cock
<p.j.a.cock(a)googlemail.com> wrote:
>
> I remain puzzled why I am seeing seemingly stochastic missing test
> results.
>
Hi Dave,
This continues - although I have been making progress with the
tests for some of my tools. Currently there are a number of
repositories reported as failing but I can't see the error (and so
can't do much about fixing it):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
When previously visible this was due to a test framework
limitation testing with composite output files:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014365.html
Given I suspect a cache issue hiding the test failures, it might
help if rather than the current text like "Time tested: ~ 8 hours ago"
this could also state the date and time of the test (in UTC/GMT to
avoid locale confusion).
Thanks,
Peter
----
Other repositories failing with a clear error message:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
Missing dependencies, should have been skipped, see
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014748.html
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
Limitation of test framework, Trello issue open for this,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014366.html
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename
Limitation of test framework, issue raised,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html
http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list
Missing an R/Bioconductor dependency, best practise for handling
this has yet to be agreed.
5:47 p.m.
Peter,
I have implemented a system that will explicitly exclude a defined list
of repositories from the testing framework, so your repositories' tests
should now be running.
--Dave B.
On 5/21/13 06:26:56.000, Peter Cock wrote:
On Mon, May 13, 2013 at 11:09 AM, Peter Cock
<p.j.a.cock(a)googlemail.com> wrote:
>
> I remain puzzled why I am seeing seemingly stochastic missing test
> results.
>
Hi Dave,
This continues - although I have been making progress with the
tests for some of my tools. Currently there are a number of
repositories reported as failing but I can't see the error (and so
can't do much about fixing it):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus
When previously visible this was due to a test framework
limitation testing with composite output files:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014365.html
Given I suspect a cache issue hiding the test failures, it might
help if rather than the current text like "Time tested: ~ 8 hours ago"
this could also state the date and time of the test (in UTC/GMT to
avoid locale confusion).
Thanks,
Peter
----
Other repositories failing with a clear error message:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp
Missing dependencies, should have been skipped, see
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014748.html
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler
Limitation of test framework, Trello issue open for this,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-April/014366.html
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename
Limitation of test framework, issue raised,
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html
http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list
Missing an R/Bioconductor dependency, best practise for handling
this has yet to be agreed.
7:05 p.m.
On Wed, May 22, 2013 at 6:47 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
I have implemented a system that will explicitly exclude a defined list of
repositories from the testing framework, so your repositories' tests should
now be running.
--Dave B.
Looks good - and now I have some more errors to sort out :)
Thank you,
Peter
10:20 a.m.
On Wed, May 22, 2013 at 8:05 PM, Peter Cock <p.j.a.cock(a)googlemail.com>
wrote:
On Wed, May 22, 2013 at 6:47 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> I have implemented a system that will explicitly exclude a defined list
of
> repositories from the testing framework, so your
repositories' tests
should
> now be running.
>
> --Dave B.
Looks good - and now I have some more errors to sort out :)
Hi Dave,
I'm guessing you need to black-list a few more repositories as I'm
again seeing missing test results, e.g.
------------------
On the test Tool Shed page for this revision I see nothing at all
about the tests for clinod:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/04aed2f80910
Functional test results for changeset revision 04aed2f80910 of clinod
0 tests passed, 0 tests failed, 0 tests missing test components.
The RSS entry is cryptic - either tests didn't run at all (due to something
timing out elsewhere in the test suite), or there was an installation error
perhaps?
-----------------
This one is different - there is a minimal test result output but with
no test results or install failures shown:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr
<quote>
Automated tool test results
Tool test results
Automated test environment
*Time tested:* ~ 13 hours ago *System:* Linux 3.0.0-1-amd64 *
Architecture:* x86_64 *Python version:* 2.7.2+ *Galaxy revision:* *Galaxy
database version:* *Tool shed revision:* 9872:31714646a7b4 *Tool shed
database version:* 19 *Tool shed mercurial version:* 2.2.3
</quote>
Regards,
Peter
6:10 a.m.
Hi again Dave,
Have you worked out any possible causes for missing test results?
I do suspect some sort of caching issue is to blame...
Here is the current list of my failing repositories from the Test
Tool Shed,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
- can see test failure, good.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
- shows one passing test (which is odd, where is the failure?)
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
- no test results visible
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
- can see test failure, good.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
- some test results visible, but no failures
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
- no test results visible
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5...
- no test results visible (strange, should be skipping the tests, so
why is this listed as failing?)
http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
- can see test failure, good.
Note that for get_orfs_or_cdss and seq_rename, I am trying to
use an automatically installed dependency on Biopython - so
perhaps there is a silent dependency failure which means the
tests are not being run?
Regards,
Peter
8:43 p.m.
Peter,
It turns out that the automated functional testing framework was not
actually running. I suggest having a look in the morning, and if there
are still any missing test results, I'll get them resolved then.
--Dave B.
On 6/25/13 02:10:10.000, Peter Cock wrote:
Hi again Dave,
Have you worked out any possible causes for missing test results?
I do suspect some sort of caching issue is to blame...
Here is the current list of my failing repositories from the Test
Tool Shed,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
- can see test failure, good.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
- shows one passing test (which is odd, where is the failure?)
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
- no test results visible
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
- can see test failure, good.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
- some test results visible, but no failures
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
- no test results visible
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5...
- no test results visible (strange, should be skipping the tests, so
why is this listed as failing?)
http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
- can see test failure, good.
Note that for get_orfs_or_cdss and seq_rename, I am trying to
use an automatically installed dependency on Biopython - so
perhaps there is a silent dependency failure which means the
tests are not being run?
Regards,
Peter
6 a.m.
On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
It turns out that the automated functional testing framework was not
actually running. I suggest having a look in the morning, and if there are
still any missing test results, I'll get them resolved then.
--Dave B.
Thanks Dave,
That has made a difference but there are still a couple of
issues here - at least in my current browser (Safari):
> Here is the current list of my failing repositories from the
Test
> Tool Shed,
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
> - can see test failure, good.
No change, good.
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
> - shows one passing test (which is odd, where is the failure?)
Improved, says there are test failures, but the arrow section fails
to expand with any details. Could this just be a slow connection
issue?
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
> - no test results visible
Tests have passed now :)
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
> - can see test failure, good.
No change, good.
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
> - some test results visible, but no failures
No change, bad. As above, the arrow/section for the failing test
does not expand.
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
> - no test results visible
Can see test failures, good.
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5...
> - no test results visible (strange, should be skipping the tests, so
> why is this listed as failing?)
No change, bad.
>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
> - can see test failure, good.
No change, good.
Regards,
Peter
3:34 p.m.
Peter,
It looks like the failed tests container is being populated, but there
is some odd behavior with displaying it. As soon as we've tracked down
the issue, I'll update you.
--Dave B.
On 6/26/13 02:00:30.000, Peter Cock wrote:
On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> It turns out that the automated functional testing framework was not
> actually running. I suggest having a look in the morning, and if there are
> still any missing test results, I'll get them resolved then.
>
> --Dave B.
Thanks Dave,
That has made a difference but there are still a couple of
issues here - at least in my current browser (Safari):
>> Here is the current list of my failing repositories from the Test
>> Tool Shed,
>>
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
>> - can see test failure, good.
No change, good.
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
>> - shows one passing test (which is odd, where is the failure?)
Improved, says there are test failures, but the arrow section fails
to expand with any details. Could this just be a slow connection
issue?
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
>> - no test results visible
Tests have passed now :)
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
>> - can see test failure, good.
No change, good.
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
>> - some test results visible, but no failures
No change, bad. As above, the arrow/section for the failing test
does not expand.
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
>> - no test results visible
Can see test failures, good.
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5...
>> - no test results visible (strange, should be skipping the tests, so
>> why is this listed as failing?)
No change, bad.
>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
>> - can see test failure, good.
No change, good.
Regards,
Peter
9:01 p.m.
Peter,
The empty failed tests folder issue has been resolved in
10171:eaa5112fefcd, and the test tool shed has been updated to that
revision.
--Dave B.
On 6/26/13 11:34:38.000, Dave Bouvier wrote:
Peter,
It looks like the failed tests container is being populated, but there
is some odd behavior with displaying it. As soon as we've tracked down
the issue, I'll update you.
--Dave B.
On 6/26/13 02:00:30.000, Peter Cock wrote:
> On Tue, Jun 25, 2013 at 9:43 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
>> Peter,
>>
>> It turns out that the automated functional testing framework was not
>> actually running. I suggest having a look in the morning, and if
>> there are
>> still any missing test results, I'll get them resolved then.
>>
>> --Dave B.
>
> Thanks Dave,
>
> That has made a difference but there are still a couple of
> issues here - at least in my current browser (Safari):
>
>>> Here is the current list of my failing repositories from the Test
>>> Tool Shed,
>>>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
>>> - can see test failure, good.
>
> No change, good.
>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
>>> - shows one passing test (which is odd, where is the failure?)
>
> Improved, says there are test failures, but the arrow section fails
> to expand with any details. Could this just be a slow connection
> issue?
>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
>>>
>>> - no test results visible
>
> Tests have passed now :)
>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
>>>
>>> - can see test failure, good.
>
> No change, good.
>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
>>> - some test results visible, but no failures
>
> No change, bad. As above, the arrow/section for the failing test
> does not expand.
>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
>>> - no test results visible
>
> Can see test failures, good.
>
>>>
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5...
>>>
>>> - no test results visible (strange, should be skipping the tests, so
>>> why is this listed as failing?)
>
> No change, bad.
>
>>> http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
>>> - can see test failure, good.
>
> No change, good.
>
> Regards,
>
> Peter
>
___________________________________________________________
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12:58 a.m.
On Wed, Jun 26, 2013 at 10:01 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
The empty failed tests folder issue has been resolved in 10171:eaa5112fefcd,
and the test tool shed has been updated to that revision.
--Dave B.
Great - currently all the missing test failures have been resolved :)
The bad news is there seems to be a new sniffer bug.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
Can see test failures (tool configuration problem).
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
One test pass, on test failure. The failure is a bit odd and
is likely a new sniffer related bug.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
Tests pass.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
Can see test failure, good.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
One pass, one failure - same new failure as effectiveT3 above.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
Can see a failure, also seems to be sniffer related (but
using a different datatype).
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5...
As before, no test results as there are marked as skip - yet
this is still listed under "Latest revision: failing tool tests".
The filter for this needs to exclude repositories marked as
skip testing.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
Can see test failure, good (missing undeclared dependency)
Thanks,
Peter
7:41 a.m.
I'm not seeing anything other than the test environment report in the
failing tests report for
http://testtoolshed.g2.bx.psu.edu/view/fubar/htseq_bams_to_count_matrix -
if you have time to take a look Dave? I'm having a hard time figuring out
what I've done wrong - it builds, installs and tests fine on my test
machine but I've probably forgotten some dependency that I already have
installed on my laptop...
The result for http://testtoolshed.g2.bx.psu.edu/view/fubar/edger_testmakes
me think that one or more of the test input files is missing but it's
hard to tell.
I wonder if overall we need a more or less complete output data spew for
failing tests to make the task of tracking them down easier?
On Thu, Jun 27, 2013 at 8:58 AM, Peter Cock <p.j.a.cock(a)googlemail.com>
wrote:
On Wed, Jun 26, 2013 at 10:01 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
> Peter,
>
> The empty failed tests folder issue has been resolved in
10171:eaa5112fefcd,
> and the test tool shed has been updated to that revision.
>
> --Dave B.
Great - currently all the missing test failures have been resolved :)
The bad news is there seems to be a new sniffer bug.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/f3a61c2cf309
Can see test failures (tool configuration problem).
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/392279f2e120
One test pass, on test failure. The failure is a bit odd and
is likely a new sniffer related bug.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/26ce6e046040
Tests pass.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira_assembler/da604cc07658
Can see test failure, good.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
One pass, one failure - same new failure as effectiveT3 above.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/44b2e489e26f
Can see a failure, also seems to be sniffer related (but
using a different datatype).
http://testtoolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp/4cd848c5...
As before, no test results as there are marked as skip - yet
this is still listed under "Latest revision: failing tool tests".
The filter for this needs to exclude repositories marked as
skip testing.
http://testtoolshed.g2.bx.psu.edu/view/peterjc/venn_list/51fe47a5a803
Can see test failure, good (missing undeclared dependency)
Thanks,
Peter
___________________________________________________________
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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
1:50 p.m.
Hello all,
I'm seeing missing test results again on the Test Tool Shed, e.g.
listed under "Latest revision: failing tool
tests<http://toolshed.g2.bx.psu.edu/repository/browse_my_writable_repo...
I have:
http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
Tool test results
Automated test environment
*Time tested:* ~ 11 hours ago *System:* Linux 3.8.0-25-generic *
Architecture:* x86_64 *Python version:* 2.7.4 *Galaxy
revision:*10265:e19301cc51b9
*Galaxy database version:* 115 *Tool shed revision:* 10098:adee6fc31991 *Tool
shed database version:* 19 *Tool shed mercurial version:* 2.2.3
Tests that passed successfully
*Tool id:* nlstradamus *Tool version:* nlstradamus *Test:*test_tool_000000 (
functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/...
)
Tests that failed
i.e. The failed test isn't shown
http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 - same problem as
above
http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp - should be
skipping tests (as I expect it to fail)
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename - test framework
regression raised here:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-July/015710.html
Thanks,
Peter
2:10 p.m.
Peter,
I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
Most of these look like display issues, the test results are correctly
recorded in the database. I hope to have that and the seq_rename and
tmhmm_and_signalp issues resolved shortly.
--Dave B.
On 7/29/13 09:50:41.000, Peter Cock wrote:
Hello all,
I'm seeing missing test results again on the Test Tool Shed, e.g.
listed under "Latest revision: failing tool tests
<http://toolshed.g2.bx.psu.edu/repository/browse_my_writable_repositories_...
I have:
http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
Tool test results
Automated test environment
*Time tested:* ~ 11 hours ago
*System:* Linux 3.8.0-25-generic
*Architecture:* x86_64
*Python version:* 2.7.4
*Galaxy revision:* 10265:e19301cc51b9
*Galaxy database version:* 115
*Tool shed revision:* 10098:adee6fc31991
*Tool shed database version:* 19
*Tool shed mercurial version:* 2.2.3
Tests that passed successfully
*Tool id:* nlstradamus
*Tool version:* nlstradamus
*Test:* test_tool_000000
(functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/peterjc/...
<http://functional.test_toolbox.TestForTool_toolshed.g2.bx.psu.edu/repos/p...>)
Tests that failed
i.e. The failed test isn't shown
http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3 - same problem as
above
http://toolshed.g2.bx.psu.edu/view/peterjc/tmhmm_and_signalp - should be
skipping tests (as I expect it to fail)
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_rename - test framework
regression raised here:
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-May/014701.html
http://lists.bx.psu.edu/pipermail/galaxy-dev/2013-July/015710.html
Thanks,
Peter
2:50 p.m.
On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
Thanks Dave.
Most of these look like display issues, the test results are
correctly
recorded in the database. I hope to have that and the seq_rename and
tmhmm_and_signalp issues resolved shortly.
--Dave B.
Oh good - that sounds less troublesome than a problem running
the tests themselves.
Cheers,
Peter
4:03 p.m.
Peter,
The issue with seq_rename incorrectly failing functional tests has been
resolved in 10266:fe04978dadac, and the test results will be corrected
the next time the automated testing framework runs. I'm still looking
into the other issues you reported.
--Dave B.
On 7/29/13 10:50:58.000, Peter Cock wrote:
On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> I've created a Trello card where you can track this issue:
> https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
Thanks Dave.
> Most of these look like display issues, the test results are correctly
> recorded in the database. I hope to have that and the seq_rename and
> tmhmm_and_signalp issues resolved shortly.
>
> --Dave B.
Oh good - that sounds less troublesome than a problem running
the tests themselves.
Cheers,
Peter
6:22 p.m.
Peter,
From what I've been able to determine, the tmhmm_and_signalp test
results predate the introduction of the skip tool tests option, and the
script to check repositories for the presence of functional tests and
test data has been updating the last test date every day, hence the
misleading entry for time last tested. I've committed a fix to that
script in 10267:5ad8db7ff748, which will be included in the next
release, at which point the main tool shed should correctly display no
test results for that repository and any others you have specified not
to be tested.
--Dave B.
On 7/29/13 12:03:23.000, Dave Bouvier wrote:
Peter,
The issue with seq_rename incorrectly failing functional tests has been
resolved in 10266:fe04978dadac, and the test results will be corrected
the next time the automated testing framework runs. I'm still looking
into the other issues you reported.
--Dave B.
On 7/29/13 10:50:58.000, Peter Cock wrote:
> On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
>> Peter,
>>
>> I've created a Trello card where you can track this issue:
>> https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
>
> Thanks Dave.
>
>> Most of these look like display issues, the test results are correctly
>> recorded in the database. I hope to have that and the seq_rename and
>> tmhmm_and_signalp issues resolved shortly.
>>
>> --Dave B.
>
> Oh good - that sounds less troublesome than a problem running
> the tests themselves.
>
> Cheers,
>
> 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:
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To search Galaxy mailing lists use the unified search at:
http://galaxyproject.org/search/mailinglists/
10:15 p.m.
On Monday, July 29, 2013, Dave Bouvier wrote:
Peter,
From what I've been able to determine, the tmhmm_and_signalp test results
predate the introduction of the skip tool tests option, and the script to
check repositories for the presence of functional tests and test data has
been updating the last test date every day, hence the misleading entry for
time last tested. I've committed a fix to that script in
10267:5ad8db7ff748, which will be included in the next release, at which
point the main tool shed should correctly display no test results for that
repository and any others you have specified not to be tested.
--Dave B.
Thanks - that probably makes sense for future repositories with similar
issues, I suspect people are going to tick the skip box after getting
unresolvable test failures.
Peter
10:43 a.m.
On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
The issue with seq_rename incorrectly failing functional tests has been
resolved in 10266:fe04978dadac, and the test results will be corrected the
next time the automated testing framework runs. I'm still looking into the
other issues you reported.
--Dave B.
Hi Dave,
The seq_rename test results (apparently) from last night are still failing,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/e440681dd17c
AssertionError: Attempting to set field 'new_column' to value
'['2']'
in form 'tool_form' threw exception: cannot find value/label "2" in
list control control: <SelectControl(new_column=[1])> If the above
control is a DataToolparameter whose data type class does not include
a sniff() method, make sure to include a proper 'ftype' attribute to
the tag for the control within the <test> tag set.
Thanks,
Peter
10:47 a.m.
On Thu, Aug 1, 2013 at 11:43 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Mon, Jul 29, 2013 at 5:03 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> The issue with seq_rename incorrectly failing functional tests has been
> resolved in 10266:fe04978dadac, and the test results will be corrected the
> next time the automated testing framework runs. I'm still looking into the
> other issues you reported.
>
> --Dave B.
Hi Dave,
The seq_rename test results (apparently) from last night are still failing,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/e440681dd17c
AssertionError: Attempting to set field 'new_column' to value
'['2']'
in form 'tool_form' threw exception: cannot find value/label "2" in
list control control: <SelectControl(new_column=[1])> If the above
control is a DataToolparameter whose data type class does not include
a sniff() method, make sure to include a proper 'ftype' attribute to
the tag for the control within the <test> tag set.
Same issue here?,
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/2be36fa7565e
AssertionError: Attempting to set field 'fasta_file' to value
'['empty.fasta']' in form 'tool_form' threw exception: cannot
find
value/label "empty.fasta" in list control control:
<SelectControl(fasta_file=[])> If the above control is a
DataToolparameter whose data type class does not include a sniff()
method, make sure to include a proper 'ftype' attribute to the tag for
the control within the <test> tag set.
Peter
11:11 a.m.
On Mon, Jul 29, 2013 at 3:10 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
I've created a Trello card where you can track this issue:
https://trello.com/c/wHXz9j0v/1018-toolshed-test-result-display-issue
Most of these look like display issues, the test results are correctly
recorded in the database. I hope to have that and the seq_rename and
tmhmm_and_signalp issues resolved shortly.
--Dave B.
Hi Dave,
The good news is it does seem some of the missing test results I
had on Monday have been resolved. However, there are still
others showing with no test results: :(
No test results here (I expect some to pass and some to fail):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/688f3fb09a6a
No test results here (I expect a failure due to a missing R dependency):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/rxlr_venn_workflow/41d8f46...
No test results here (I expect these to pass):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/bc4e...
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/deb6cb2db22b
Thanks,
Peter
2:30 p.m.
On Thu, Aug 1, 2013 at 12:11 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
Hi Dave,
The good news is it does seem some of the missing test results I
had on Monday have been resolved. However, there are still
others showing with no test results: :(
No test results here (I expect some to pass and some to fail):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/688f3fb09a6a
I've been updating the BLAST+ repository - currently it does
show some failures due to missing test, but there seems to be
test information missing here - and also I'm expecting the
installation to fail with BOOST issues:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/5693417851ec
(The other problems from 1 August look OK now)
Thanks,
Peter
12:58 p.m.
Peter,
The automated build prior to this email was executed incorrectly. I've
resolved that status, and the current test results look correct.
--Dave B.
On 8/8/13 10:30:37.000, Peter Cock wrote:
On Thu, Aug 1, 2013 at 12:11 PM, Peter Cock
<p.j.a.cock(a)googlemail.com> wrote:
>
> Hi Dave,
>
> The good news is it does seem some of the missing test results I
> had on Monday have been resolved. However, there are still
> others showing with no test results: :(
>
> No test results here (I expect some to pass and some to fail):
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/688f3fb09a6a
I've been updating the BLAST+ repository - currently it does
show some failures due to missing test, but there seems to be
test information missing here - and also I'm expecting the
installation to fail with BOOST issues:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/5693417851ec
(The other problems from 1 August look OK now)
Thanks,
Peter
3:24 p.m.
Hi Dave,
Progress: I can now see the test failures which suggest that the
underlying binaries did not get installed properly. I guess this
either means:
(a) the dependency install failed but the Tool Shed doesn't say
this (my hunch as recently the NCBI BLAST+ tools had stopped
compiling on the Test Tool Shed due to a BOOST system library
change).
Or,
(b) the dependency installed didn't raise any errors but failed
in some way such as not setting the path (unlikely as the
tool_dependencies.xml content has not changed - it has
just been moved to a dependency package repository)
Or,
(c) there is something amiss with the dependency chain meaning
that the BLAST dependencies are not being added to the PATH.
This looks OK but it is the only thing I have changed recently.
Or some other mode of failure I'm not guessed at yet?
Is this something you can diagnose, or do I need to press
ahead with a local Tool Shed to help me work out what is
amiss?
Thanks,
Peter
On Fri, Aug 9, 2013 at 1:58 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
The automated build prior to this email was executed incorrectly. I've
resolved that status, and the current test results look correct.
--Dave B.
On 8/8/13 10:30:37.000, Peter Cock wrote:
>
> I've been updating the BLAST+ repository - currently it does
> show some failures due to missing test, but there seems to be
> test information missing here - and also I'm expecting the
> installation to fail with BOOST issues:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/5693417851ec
>
> (The other problems from 1 August look OK now)
>
> Thanks,
>
> Peter
>
9:59 a.m.
Hello again,
I've not have any missing test results for a while, on the main
or test Tool Shed, so this was a bit of a surprise:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
This is listed under "Latest revision: failing tool tests", but
I see no test results at all :(
Regards,
Peter
4:27 p.m.
Peter,
Thank you for reporting this. I've been able to determine that there was
an installation error that should have been recorded, but was not. I
hope to have a fix committed shortly.
--Dave B.
On 09/23/2013 05:59 AM, Peter Cock wrote:
Hello again,
I've not have any missing test results for a while, on the main
or test Tool Shed, so this was a bit of a surprise:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
This is listed under "Latest revision: failing tool tests", but
I see no test results at all :(
Regards,
Peter
9:53 a.m.
Thanks Dave,
Looks like the same thing happened again last night, but as this
is on the Main Tool Shed your fix wouldn't be included anyway:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
Any clues about the installation failure would be useful, this is
working nicely on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/d8de...
Additionally, another repository I updated yesterday is missing test
results and this time there are no external dependencies:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls
Regards,
Peter
On Mon, Sep 23, 2013 at 5:27 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
Thank you for reporting this. I've been able to determine that there was an
installation error that should have been recorded, but was not. I hope to
have a fix committed shortly.
--Dave B.
On 09/23/2013 05:59 AM, Peter Cock wrote:
>
> Hello again,
>
> I've not have any missing test results for a while, on the main
> or test Tool Shed, so this was a bit of a surprise:
>
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
>
> This is listed under "Latest revision: failing tool tests", but
> I see no test results at all :(
>
> Regards,
>
> Peter
>
12:44 p.m.
Peter,
The one on the main tool shed is due to an issue Greg and I are in the
process of resolving. As soon as we've tested the fix, I'll schedule a
re-test of that repository and update you on the status.
--Dave B.
On 09/24/2013 05:53 AM, Peter Cock wrote:
Thanks Dave,
Looks like the same thing happened again last night, but as this
is on the Main Tool Shed your fix wouldn't be included anyway:
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
Any clues about the installation failure would be useful, this is
working nicely on the Test Tool Shed:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/d8de...
Additionally, another repository I updated yesterday is missing test
results and this time there are no external dependencies:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls
Regards,
Peter
On Mon, Sep 23, 2013 at 5:27 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
> Peter,
>
> Thank you for reporting this. I've been able to determine that there was an
> installation error that should have been recorded, but was not. I hope to
> have a fix committed shortly.
>
> --Dave B.
>
>
> On 09/23/2013 05:59 AM, Peter Cock wrote:
>>
>> Hello again,
>>
>> I've not have any missing test results for a while, on the main
>> or test Tool Shed, so this was a bit of a surprise:
>>
>>
>> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
>>
>> This is listed under "Latest revision: failing tool tests", but
>> I see no test results at all :(
>>
>> Regards,
>>
>> Peter
>>
>
10:40 a.m.
On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
The one on the main tool shed is due to an issue Greg and I are in the
process of resolving. As soon as we've tested the fix, I'll schedule a
re-test of that repository and update you on the status.
--Dave B.
Looks to be spreading, or linked to the blast_datatypes dependency?
Listed under "Latest revision: failing tool tests"
http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go/0ac3ef59ea93
- missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
- missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
- failed as expected (missing Biopython dependency,
see separate thread about the ALTAS dependency problem)
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/6aae6bc0802d
- failing as expected (missing R dependency)
And over on the Test Tool Shed (which was offline but recently came
back up), listed under "Latest revision: failing tool tests":
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
- missing test results
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls/aabc2852571e
- missing test results
Regards,
Peter
10:47 a.m.
+1
I think it's been a problem with some of my repos for a while on test so
possible not related to blast_datatypes - I sent this privately about 2
weeks ago:
Ross <ross.lazarus(a)gmail.com>
Sep 13 (13 days ago)
to Dave, Greg
Hey Dave - any thoughts on how to fix
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models so
the test results appear?
AFAIK the test works but there's no test results section in the manage
repository sections I can see.
On Thu, Sep 26, 2013 at 8:40 PM, Peter Cock <p.j.a.cock(a)googlemail.com>wrote:
On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> The one on the main tool shed is due to an issue Greg and I are in the
> process of resolving. As soon as we've tested the fix, I'll schedule a
> re-test of that repository and update you on the status.
>
> --Dave B.
Looks to be spreading, or linked to the blast_datatypes dependency?
Listed under "Latest revision: failing tool tests"
http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go/0ac3ef59ea93
- missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
- missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
- failed as expected (missing Biopython dependency,
see separate thread about the ALTAS dependency problem)
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/6aae6bc0802d
- failing as expected (missing R dependency)
And over on the Test Tool Shed (which was offline but recently came
back up), listed under "Latest revision: failing tool tests":
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
- missing test results
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls/aabc2852571e
- missing test results
Regards,
Peter
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10:55 a.m.
There seems to be issues with some repositories which we'll need to track down.
However, I fixed some issues yesterday with styles in the tool shed that kep the tool
tests from displaing, and now test results are displaying at least for this repository:
Repository revision
repository tip
Select a revision to inspect and download versions of Galaxy utilities from this
repository.
Repository 'differential_count_models'
Sharable link to this repository:
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models
Clone this repository:
hg clone http://testtoolshed.g2.bx.psu.edu/repos/fubar/differential_count_models
Name:
differential_count_models
Repository type:
Unrestricted
Synopsis:
edgeR, DESeq2 and voom in one tool
Detailed description:
edgeR, DESeq2 and voom for replicate RNA seq data.
1) TURN OFF HTML SANITIZATION in universe_wsgi.xml or your outputs will lack proper style
sheets and look awful
2) This packages dependencies include R and bioconductor so expect your proxy to time out
during the installation - be patient - it takes 10 to 30 minutes to download and compile
everything, depending on the velocity of your machine and the interwebs - about 20 minutes
on my laptop.
3) make sure you have a $TMP set in your environment or ghostscript gets unhappy -
you'll see a warning every time you run this tool if you've forgotten.
Revision:
31:5b6af671d985
Owner:
fubar
Times downloaded:
15
Dependencies of this repository
Repository dependencies - installation of these additional repositories is required
Tool dependencies - repository tools require handling of these dependencies
Contents of this repository
Valid tools - click the name to preview the tool and use the pop-up menu to inspect all
metadata
Automated tool test results
Tool test results
Automated test environment
Tests that failed
Tool id: rgDifferentialCount
Tool version: rgDifferentialCount
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/fuba...)
Stderr:
Traceback:
Traceback (most recent call last):
File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 171, in test_tool
self.do_it( td, shed_tool_id=shed_tool_id )
File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 102, in do_it
self.verify_dataset_correctness( outfile, hid=elem_hid, maxseconds=testdef.maxseconds,
attributes=attributes, shed_tool_id=shed_tool_id )
File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 855, in verify_dataset_correctness
raise AssertionError( errmsg )
AssertionError: History item 4 different than expected, difference (using diff):
(
/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsubztFQ/testtoolshed.g2.bx.psu.edu/repos/fubar/differential_count_models/5b6af671d985/differential_count_models/differential_count_models/test-data/edgeRtest1out.xls
v.
/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpFGK1x1/tmpCzIKTPedgeRtest1out.xls
)
--- local_file
+++ history_data
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Categories
Statistics
On Sep 26, 2013, at 6:47 AM, Ross <ross.lazarus(a)gmail.com> wrote:
+1
I think it's been a problem with some of my repos for a while on test so possible not
related to blast_datatypes - I sent this privately about 2 weeks ago:
Ross <ross.lazarus(a)gmail.com>
Sep 13 (13 days ago)
to Dave, Greg
Hey Dave - any thoughts on how to fix
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models so the test results
appear?
AFAIK the test works but there's no test results section in the manage repository
sections I can see.
On Thu, Sep 26, 2013 at 8:40 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
> Peter,
>
> The one on the main tool shed is due to an issue Greg and I are in the
> process of resolving. As soon as we've tested the fix, I'll schedule a
> re-test of that repository and update you on the status.
>
> --Dave B.
Looks to be spreading, or linked to the blast_datatypes dependency?
Listed under "Latest revision: failing tool tests"
http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go/0ac3ef59ea93
- missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
- missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
- failed as expected (missing Biopython dependency,
see separate thread about the ALTAS dependency problem)
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/6aae6bc0802d
- failing as expected (missing R dependency)
And over on the Test Tool Shed (which was offline but recently came
back up), listed under "Latest revision: failing tool tests":
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
- missing test results
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls/aabc2852571e
- missing test results
Regards,
Peter
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10:59 a.m.
Great! Thanks!
Don't you ever sleep? It must be some un-allah-ly hour where you are.
On Thu, Sep 26, 2013 at 8:55 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
There seems to be issues with some repositories which we'll need
to track
down. However, I fixed some issues yesterday with styles in the tool shed
that kep the tool tests from displaing, and now test results are displaying
at least for this repository:
Repository revision
31:5b6af671d985 28:c4ee2e69d691 3:fe5c828dee80 *repository tip*
Select a revision to inspect and download versions of Galaxy utilities
from this repository.
Repository 'differential_count_models'
Sharable link to this repository:
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models
Clone this repository:hg clone
http://testtoolshed.g2.bx.psu.edu/repos/fubar/differential_count_models
Name:differential_count_models<http://testtoolshed.g2.bx.psu.edu/repos...
Repository type:Unrestricted
Synopsis:edgeR, DESeq2 and voom in one tool
Detailed description:edgeR, DESeq2 and voom for replicate RNA seq data.
1) TURN OFF HTML SANITIZATION in universe_wsgi.xml or your outputs will lack proper style
sheets and look awful
2) This packages dependencies include R and bioconductor so expect your proxy to time out
during the installation - be patient - it takes 10 to 30 minutes to download and compile
everything, depending on the velocity of your machine and the interwebs - about 20 minutes
on my laptop.
3) make sure you have a $TMP set in your environment or ghostscript gets unhappy -
you'll see a warning every time you run this tool if you've forgotten.
Revision:31:5b6af671d985<http://testtoolshed.g2.bx.psu.edu/repository/...
Owner:fubar
Times downloaded:15
Dependencies of this repository
Repository dependencies* - installation of these additional repositories
is
required*<http://testtoolshed.g2.bx.psu.edu/repository/view_repository...
Tool dependencies* - repository tools require handling of these
dependencies*<http://testtoolshed.g2.bx.psu.edu/repository/view_reposi...
Contents of this repository
Valid tools* - click the name to preview the tool and use the pop-up menu
to inspect all
metadata*<http://testtoolshed.g2.bx.psu.edu/repository/view_repository...
Automated tool test results
Tool test
results<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?s...
Automated test
environment<http://testtoolshed.g2.bx.psu.edu/repository/view_reposito...
Tests that
failed<http://testtoolshed.g2.bx.psu.edu/repository/view_repository?st...
*Tool id:* rgDifferentialCount*Tool version:* rgDifferentialCount*Test:*
test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.
bx.psu.edu/repos/fubar/differential_count_models/rgDifferentialCount/0.21)
*Stderr:*
*Traceback:*
Traceback (most recent call last):
File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 171, in test_tool
self.do_it( td, shed_tool_id=shed_tool_id )
File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 102, in do_it
self.verify_dataset_correctness( outfile, hid=elem_hid,
maxseconds=testdef.maxseconds, attributes=attributes, shed_tool_id=shed_tool_id )
File
"/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 855, in verify_dataset_correctness
raise AssertionError( errmsg )
AssertionError: History item 4 different than expected, difference (using diff):
(
/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/shed_toolsubztFQ/testtoolshed.g2.
bx.psu.edu/repos/fubar/differential_count_models/5b6af671d985/differentia...
v.
/var/opt/buildslaves/buildslave-ec2-1/buildbot-install-test-test-tool-shed-py27/build/test/install_and_test_tool_shed_repositories/tmp/tmpFGK1x1/tmpCzIKTPedgeRtest1out.xls
)
--- local_file
+++ history_data
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>Mir208a</a>
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Categories
Statistics
On Sep 26, 2013, at 6:47 AM, Ross <ross.lazarus(a)gmail.com> wrote:
+1
I think it's been a problem with some of my repos for a while on test so
possible not related to blast_datatypes - I sent this privately about 2
weeks ago:
Ross <ross.lazarus(a)gmail.com>
Sep 13 (13 days ago)
to Dave, Greg
Hey Dave - any thoughts on how to fix
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models so
the test results appear?
AFAIK the test works but there's no test results section in the manage
repository sections I can see.
On Thu, Sep 26, 2013 at 8:40 PM, Peter Cock <p.j.a.cock(a)googlemail.com>wrote:
> On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
> > Peter,
> >
> > The one on the main tool shed is due to an issue Greg and I are in the
> > process of resolving. As soon as we've tested the fix, I'll schedule a
> > re-test of that repository and update you on the status.
> >
> > --Dave B.
>
> Looks to be spreading, or linked to the blast_datatypes dependency?
> Listed under "Latest revision: failing tool tests"
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go/0ac3ef59ea93
> - missing test results
>
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
> - missing test results
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
> - failed as expected (missing Biopython dependency,
> see separate thread about the ALTAS dependency problem)
>
> http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/6aae6bc0802d
> - failing as expected (missing R dependency)
>
> And over on the Test Tool Shed (which was offline but recently came
> back up), listed under "Latest revision: failing tool tests":
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
> - missing test results
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls/aabc2852571e
> - missing test results
>
> Regards,
>
> 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:
> 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
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--
Ross Lazarus MBBS MPH;
Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444
http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
2:29 p.m.
Ross, Peter,
Unfortunately, there are some issues with the automated testing
framework that I am working on resolving. I've created a Trello card to
track my progress:
https://trello.com/c/x8mx7HRB
--Dave B.
On 09/26/2013 06:47 AM, Ross wrote:
+1
I think it's been a problem with some of my repos for a while on test so
possible not related to blast_datatypes - I sent this privately about 2
weeks ago:
Ross <ross.lazarus(a)gmail.com <mailto:ross.lazarus@gmail.com>>
Sep 13 (13 days ago)
to Dave, Greg
Hey Dave - any thoughts on how to fix
http://testtoolshed.g2.bx.psu.edu/view/fubar/differential_count_models so the
test results appear?
AFAIK the test works but there's no test results section in the manage
repository sections I can see.
On Thu, Sep 26, 2013 at 8:40 PM, Peter Cock <p.j.a.cock(a)googlemail.com
<mailto:p.j.a.cock@googlemail.com>> wrote:
On Tue, Sep 24, 2013 at 1:44 PM, Dave Bouvier <dave(a)bx.psu.edu
<mailto:dave@bx.psu.edu>> wrote:
> Peter,
>
> The one on the main tool shed is due to an issue Greg and I are
in the
> process of resolving. As soon as we've tested the fix, I'll
schedule a
> re-test of that repository and update you on the status.
>
> --Dave B.
Looks to be spreading, or linked to the blast_datatypes dependency?
Listed under "Latest revision: failing tool tests"
http://toolshed.g2.bx.psu.edu/view/peterjc/blast2go/0ac3ef59ea93
- missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr/09a68a90...
- missing test results
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
- failed as expected (missing Biopython dependency,
see separate thread about the ALTAS dependency problem)
http://toolshed.g2.bx.psu.edu/view/peterjc/venn_list/6aae6bc0802d
- failing as expected (missing R dependency)
And over on the Test Tool Shed (which was offline but recently came
back up), listed under "Latest revision: failing tool tests":
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
- missing test results
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls/aabc2852571e
- missing test results
Regards,
Peter
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10:11 a.m.
On Thu, Sep 26, 2013 at 3:29 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Ross, Peter,
Unfortunately, there are some issues with the automated testing framework
that I am working on resolving. I've created a Trello card to track my
progress:
https://trello.com/c/x8mx7HRB
--Dave B.
Any joy with that "from fabric.api import env" issue?
Meanwhile the set of tools with missing test failures seems to
change from day to day, right now the following are listed under
"Latest revision: failing tool tests" yet have not test results:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/0d39248a7a9f
(expected to pass)
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
(expected to pass)
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
(expected to pass)
Peter
10:19 a.m.
On Fri, Oct 4, 2013 at 11:11 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Thu, Sep 26, 2013 at 3:29 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Ross, Peter,
>
> Unfortunately, there are some issues with the automated testing framework
> that I am working on resolving. I've created a Trello card to track my
> progress:
>
> https://trello.com/c/x8mx7HRB
>
> --Dave B.
>
Any joy with that "from fabric.api import env" issue?
Meanwhile the set of tools with missing test failures seems to
change from day to day, right now the following are listed under
"Latest revision: failing tool tests" yet have not test results:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/0d39248a7a9f
(expected to pass)
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
(expected to pass)
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
(expected to pass)
Peter
There's a similar set on the main Tool Shed, where I should have the
same version of those three tools, which may be interesting for
tracing the problem(s):
http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
(expected to pass)
http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
(expected to pass)
http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
(expected to pass)
Also missing test results:
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
(this revision is expected to fail if Biopython not present, see other thread
about packaging NumPy and its dependencies)
Regards,
Peter
6:32 p.m.
Peter,
Thanks for the information, it uncovered a problem with the testing
framework that has been resolved in 10817:6b0c3592dde1. The listed
repositories should start showing useful results next time the nightly
tests run.
--Dave B.
On 10/04/2013 06:19 AM, Peter Cock wrote:
On Fri, Oct 4, 2013 at 11:11 AM, Peter Cock
<p.j.a.cock(a)googlemail.com> wrote:
> On Thu, Sep 26, 2013 at 3:29 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
>> Ross, Peter,
>>
>> Unfortunately, there are some issues with the automated testing framework
>> that I am working on resolving. I've created a Trello card to track my
>> progress:
>>
>> https://trello.com/c/x8mx7HRB
>>
>> --Dave B.
>>
>
> Any joy with that "from fabric.api import env" issue?
>
> Meanwhile the set of tools with missing test failures seems to
> change from day to day, right now the following are listed under
> "Latest revision: failing tool tests" yet have not test results:
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod/0d39248a7a9f
> (expected to pass)
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
> (expected to pass)
>
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
> (expected to pass)
>
> Peter
There's a similar set on the main Tool Shed, where I should have the
same version of those three tools, which may be interesting for
tracing the problem(s):
http://toolshed.g2.bx.psu.edu/view/peterjc/clinod
(expected to pass)
http://toolshed.g2.bx.psu.edu/view/peterjc/effectivet3
(expected to pass)
http://toolshed.g2.bx.psu.edu/view/peterjc/nlstradamus
(expected to pass)
Also missing test results:
http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/8c02a91a8680
(this revision is expected to fail if Biopython not present, see other thread
about packaging NumPy and its dependencies)
Regards,
Peter
9:43 a.m.
On Mon, Oct 7, 2013 at 7:32 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
Thanks for the information, it uncovered a problem with the testing
framework that has been resolved in 10817:6b0c3592dde1. The listed
repositories should start showing useful results next time the nightly tests
run.
--Dave B.
Hi Dave,
I must sound like a scratched record (is there a replacement
phrase now that LPs are a cultural artefact?):
Currently listed under "Latest revision: failing tool tests" but
missing any test results:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls
(I've got a lot of fresh failures pointing at a separate issue,
email to follow with a new title).
Peter
1:49 p.m.
Hi Peter,
Here is a new Trello card to track the progress for fixing and stabilizing the tool shed
install and test framework. This card will evolve over the next few days as items are
completed and new issues are uncovered that cause problems in the framework. This work is
our top priority until it is finished.
https://trello.com/c/QWgsgll8/1203-toolshed-automated-test-framework-fixes
Greg Von Kuster
On Oct 22, 2013, at 5:43 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Mon, Oct 7, 2013 at 7:32 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> Thanks for the information, it uncovered a problem with the testing
> framework that has been resolved in 10817:6b0c3592dde1. The listed
> repositories should start showing useful results next time the nightly tests
> run.
>
> --Dave B.
Hi Dave,
I must sound like a scratched record (is there a replacement
phrase now that LPs are a cultural artefact?):
Currently listed under "Latest revision: failing tool tests" but
missing any test results:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls
(I've got a lot of fresh failures pointing at a separate issue,
email to follow with a new title).
Peter
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10:05 a.m.
On Tue, Oct 22, 2013 at 2:49 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
Hi Peter,
Here is a new Trello card to track the progress for fixing and stabilizing the tool shed
install and test framework. This card will evolve over the next few days as items are
completed and new issues are uncovered that cause problems in the framework. This work is
our top priority until it is finished.
https://trello.com/c/QWgsgll8/1203-toolshed-automated-test-framework-fixes
Greg Von Kuster
Hi Greg, Dave,
This is just to comment that there is a (possibly related) oddity in
the RSS feeds, with lots of entries showning missing test results:
"0 tests passed, 0 tests failed, 0 tests missing test components."
Strangely this is reporting multiple revisions of each tool (not in
commit order), and it seems the older revisions show no tests
(possibly true, or simple a sign of no test data?).
Peter
--
e.g.
http://testtoolshed.g2.bx.psu.edu/repository/get_functional_test_rss?owne...
Revision 66d1ca92fb38 of seq_filter_by_id
31 October 2013 22:03
0 tests passed, 0 tests failed, 0 tests missing test components.
Revision b7ec1c9db38d of seq_filter_by_id
31 October 2013 21:14
0 tests passed, 0 tests failed, 0 tests missing test components.
Revision 21a065d5f0e2 of seq_filter_by_id
31 October 2013 22:24
0 tests passed, 0 tests failed, 0 tests missing test components.
Revision 8a34c565a473 of seq_filter_by_id
1 November 2013 09:23
1 tests passed, 0 tests failed, 0 tests missing test components.
Revision 44891766cf9b of seq_filter_by_id
18 October 2013 23:29
0 tests passed, 0 tests failed, 1 tests missing test components.
Revision 726dcfa94b2c of seq_select_by_id
31 October 2013 22:17
0 tests passed, 0 tests failed, 0 tests missing test components.
Revision 9e9e3b860aa0 of seq_select_by_id
1 November 2013 09:26
0 tests passed, 1 tests failed, 0 tests missing test components.
Revision 694208ea6c34 of seq_select_by_id
31 October 2013 22:24
0 tests passed, 0 tests failed, 0 tests missing test components.
Revision 2b27279adeff of seq_select_by_id
18 October 2013 23:28
0 tests passed, 0 tests failed, 1 tests missing test components.
12:09 a.m.
On Friday, November 1, 2013, Peter Cock wrote:
On Tue, Oct 22, 2013 at 2:49 PM, Greg Von Kuster
<greg@bx.psu.edu<javascript:;>>
wrote:
> Hi Peter,
>
> Here is a new Trello card to track the progress for fixing and
stabilizing the tool shed install and test framework. This card will
evolve over the next few days as items are completed and new issues are
uncovered that cause problems in the framework. This work is our top
priority until it is finished.
>
>
https://trello.com/c/QWgsgll8/1203-toolshed-automated-test-framework-fixes
>
> Greg Von Kuster
>
Hi Greg, Dave,
This is just to comment that there is a (possibly related) oddity in
the RSS feeds, with lots of entries showning missing test results:
"0 tests passed, 0 tests failed, 0 tests missing test components."
Strangely this is reporting multiple revisions of each tool (not in
commit order), and it seems the older revisions show no tests
(possibly true, or simple a sign of no test data?).
Peter
Looks like Dave's fixed the multiple RSS entries:
https://bitbucket.org/galaxy/galaxy-central/commits/52df185d7552
Thanks,
Peter
10:33 a.m.
On Tue, Oct 22, 2013 at 10:43 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Mon, Oct 7, 2013 at 7:32 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> Thanks for the information, it uncovered a problem with the testing
> framework that has been resolved in 10817:6b0c3592dde1. The listed
> repositories should start showing useful results next time the nightly tests
> run.
>
> --Dave B.
Hi Dave,
I must sound like a scratched record (is there a replacement
phrase now that LPs are a cultural artefact?):
Currently listed under "Latest revision: failing tool tests" but
missing any test results:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/predictnls
(I've got a lot of fresh failures pointing at a separate issue,
email to follow with a new title).
Peter
More "missing test results", yet listed under "Latest revision:
failing tool tests":
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
The common feature is they all depend on Biopython - perhaps that
failed to install, and the tests were skipped?
Over on the main tool shed, those three are all showing errors
relating to a failed Biopython install.
Peter
10:02 a.m.
On Mon, Nov 4, 2013 at 10:33 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
More "missing test results", yet listed under "Latest revision:
failing tool tests":
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
The common feature is they all depend on Biopython - perhaps that
failed to install, and the tests were skipped?
I updated all three of these tools (and others) on the Test Tool
Shed yesterday to address my misconfigured dependencies
(thanks Greg!), e.g.
https://github.com/peterjc/pico_galaxy/commit/399111894d1ea9432a4c24ed041...
(Note that other tools with the same broken dependency setup
did not suffer from the "missing test output" problem - they
were showing the tool's test failures)
The good news is that seq_select_by_id has gone from an
apparent failure with missing test output, to a passing test:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/bedfe8f3d3fb
The bad news is there are still 2 apparently failing tests with
missing test output:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/42bca649ec44
Similarly over on the Main Tool Shed (where I have not yet
updated these two tools).
Regards,
Peter
10:18 a.m.
On Thu, Nov 21, 2013 at 10:02 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
Similarly over on the Main Tool Shed (where I have not yet
updated these two tools).
I currently have three tool repositories on the Main Tool Shed
listed under "Latest revision: failing tool tests" yet with no
test results:
* http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/5208c15805ec
Known dependency mis-configuration, updated version on Test Tool Shed.
I would expect this revision to fail (saying Biopython not installed).
* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/ee5acea162a7
Known dependency mis-configuration, updated version on Test Tool Shed.
I would expect this revision to fail (saying Biopython not installed).
* http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/d4412c04d7b1
Should be identical to the working version on the Test Tool Shed, i.e.
http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/93b8db68dde4
I would expect this revision to pass.
Regards,
Peter
2:19 p.m.
Peter,
As of this morning, all of the repositories you listed below seem to
have the expected results, with the exception of samtools_idxstats on
the main tool shed. That repository was not tested due to an unhandled
unicode error in the testing framework, which has been corrected, and
the main tool shed's test framework is now being re-run with the updated
code.
--Dave B.
On 11/21/2013 05:18 AM, Peter Cock wrote:
On Thu, Nov 21, 2013 at 10:02 AM, Peter Cock
<p.j.a.cock(a)googlemail.com> wrote:
> Similarly over on the Main Tool Shed (where I have not yet
> updated these two tools).
I currently have three tool repositories on the Main Tool Shed
listed under "Latest revision: failing tool tests" yet with no
test results:
* http://toolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/5208c15805ec
Known dependency mis-configuration, updated version on Test Tool Shed.
I would expect this revision to fail (saying Biopython not installed).
* http://toolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/ee5acea162a7
Known dependency mis-configuration, updated version on Test Tool Shed.
I would expect this revision to fail (saying Biopython not installed).
* http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/d4412c04d7b1
Should be identical to the working version on the Test Tool Shed, i.e.
http://toolshed.g2.bx.psu.edu/view/peterjc/samtools_idxstats/93b8db68dde4
I would expect this revision to pass.
Regards,
Peter
2:40 p.m.
On Thu, Nov 21, 2013 at 2:19 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
As of this morning, all of the repositories you listed below seem to have
the expected results, with the exception of samtools_idxstats on the main
tool shed. That repository was not tested due to an unhandled unicode error
in the testing framework, which has been corrected, and the main tool shed's
test framework is now being re-run with the updated code.
--Dave B.
Thanks Dave,
I'll wait for the main Tool Shed to finish the test run, but things look
great on the Test Tool Shed now - I have nothing under "Latest
revision: installation errors" or "Latest revision: failing tool tests" :)
:) :)
One possible glitch though is there are no test results for the BLAST+
suite (yet?), listed under "Latest revision: missing tool tests" as not
all its tools have tests yet:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/f2478dc77ccb
Says:
Tool test results
Automated test environment
Time tested: ~ 4 hours ago
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 11433:e6e9349e8da4
Galaxy database version: 117
Tool shed revision:
Tool shed database version:
Tool shed mercurial version:
(no actual test output)
Regards,
Peter
2:38 p.m.
Peter,
About three weeks ago, we began to focus a higher priority on fixing the
nightly functional test runs. Part of this process was to reschedule the
nightly tests to finish around 9am ET. At the time you sent this email,
the test run had not completed, and you were looking at the previous
day's results. The last test run results (from this morning, finishing
at 8:54am ET) are pasted inline.
--Dave B.
On 11/21/2013 05:02 AM, Peter Cock wrote:
The bad news is there are still 2 apparently failing tests with
missing test output:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
Tool test results
Automated test environment
Time tested: ~ 4 hours ago
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 11433:e6e9349e8da4
Galaxy database version: 117
Tool shed revision:
Tool shed database version:
Tool shed mercurial version:
Tests that passed successfully
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000001
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000002
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000003
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool test results
Automated test environment
Time tested: ~ 4 hours ago
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 11433:e6e9349e8da4
Galaxy database version: 117
Tool shed revision:
Tool shed database version:
Tool shed mercurial version:
Tests that passed successfully
Tool id: seq_primer_clip
Tool version: seq_primer_clip
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: seq_primer_clip
Tool version: seq_primer_clip
Test: test_tool_000001
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: seq_primer_clip
Tool version: seq_primer_clip
Test: test_tool_000002
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: seq_primer_clip
Tool version: seq_primer_clip
Test: test_tool_000003
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: seq_primer_clip
Tool version: seq_primer_clip
Test: test_tool_000004
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: seq_primer_clip
Tool version: seq_primer_clip
Test: test_tool_000005
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Similarly over on the Main Tool Shed (where I have not yet
updated these two tools).
Regards,
Peter
2:47 p.m.
On Thu, Nov 21, 2013 at 2:38 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
Peter,
About three weeks ago, we began to focus a higher priority on fixing the
nightly functional test runs.
And we're starting to see the dividends of this time investment now :)
(And with John extending the test framework to handle <repeats>
and potentially ambiguous parameter names with conditionals etc,
you will soon have even more tools with tests to run....)
Part of this process was to reschedule the
nightly tests to finish around 9am ET. At the time you sent this email, the
test run had not completed, and you were looking at the previous day's
results. The last test run results (from this morning, finishing at 8:54am
ET) are pasted inline.
i.e. The tests are now run at 14:00 UTC/GMT, which is mid afternoon
in Europe?
Given you've been working on the test framework a lot, and running
extra tests sometimes, I think I'd missed this time shift.
Given we have Galaxy tool developers right round the globe (unless
maybe the tests could be run twice a day), whenever they are
scheduled wouldn't suit everyone.
Regards,
Peter
10:44 a.m.
On Thu, Nov 21, 2013 at 2:47 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Thu, Nov 21, 2013 at 2:38 PM, Dave Bouvier <dave(a)bx.psu.edu>
wrote:
> Peter,
>
> About three weeks ago, we began to focus a higher priority on fixing the
> nightly functional test runs.
And we're starting to see the dividends of this time investment now :)
Hi Dave,
For a while almost all my tools were showing as passing their tests,
but sadly something seems to have broken - has the Test Tool Shed
really not run any tests for the last three days? Even if so, the display
is still missing the last test results.
Test Tool Shed, "Latest revision: installation errors", no individual test
results, but says the tests were run ~4 days ago:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/63eb...
Test Tool Shed, "Latest revision: installation errors", but no test results
section at all:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/42bca649ec44
Actual test failure shown, again time tested listed as 4 days ago, but
apparently a framework issue:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/324893f5751e
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/61cec46f6be5
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/bedfe8f3d3fb
(BrowserStateError: cannot go to 'http://None:29009')
Regards,
Peter
9:02 p.m.
Hello Peter,
I've done a significant amount of re-engineering of the Tool Shed's install and
test framework over the past 2 weeks, so the results you are seeing are probably a
reflection of some broken peices during the time frame in which I was making changes. I
believe I have most of the things ironed out in 11545:32205f911e74 which is now running on
the test tool shed.
We will be performing some test runs of thie new framework over the long weekend, so more
correct test results should hopefully be showing up for yours and other repositories.
I've also enhanced the "Tool test results" components to store a
configurable number of test runs instead of just 1. The test tool shed is configured to
store 5 test runs. So from here on you'll begin to see multiple containers in the
Tool test results container - something like this:
Automated tool test results
2013-11-27 15:49:51
Automated test environment
Tests that passed successfully
2013-11-27 15:17:57
Automated test environment
Tests that passed successfully
2013-11-27 14:53:46
Automated test environment
Tests that passed successfully
2013-11-27 14:50:30
Automated test environment
Tests that passed successfully
We'll keep on top of things that need fixing as we proceed with this new framework.
Thanks,
Greg Von Kuster
On Nov 27, 2013, at 5:44 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Thu, Nov 21, 2013 at 2:47 PM, Peter Cock
<p.j.a.cock(a)googlemail.com> wrote:
> On Thu, Nov 21, 2013 at 2:38 PM, Dave Bouvier <dave(a)bx.psu.edu> wrote:
>> Peter,
>>
>> About three weeks ago, we began to focus a higher priority on fixing the
>> nightly functional test runs.
>
> And we're starting to see the dividends of this time investment now :)
>
Hi Dave,
For a while almost all my tools were showing as passing their tests,
but sadly something seems to have broken - has the Test Tool Shed
really not run any tests for the last three days? Even if so, the display
is still missing the last test results.
Test Tool Shed, "Latest revision: installation errors", no individual test
results, but says the tests were run ~4 days ago:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go/8c462f7b2c8d
http://testtoolshed.g2.bx.psu.edu/view/peterjc/effectivet3/1e681e19e35c
http://testtoolshed.g2.bx.psu.edu/view/peterjc/fastq_paired_unpaired/63eb...
Test Tool Shed, "Latest revision: installation errors", but no test results
section at all:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_primer_clip/42bca649ec44
Actual test failure shown, again time tested listed as 4 days ago, but
apparently a framework issue:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus/81cac85fc286
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_filter_by_id/324893f5751e
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_rename/61cec46f6be5
http://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id/bedfe8f3d3fb
(BrowserStateError: cannot go to 'http://None:29009')
Regards,
Peter
9:56 a.m.
On Wed, Nov 27, 2013 at 9:02 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
Hello Peter,
I've done a significant amount of re-engineering of the
Tool Shed's install and test framework over the past 2
weeks, so the results you are seeing are probably a
reflection of some broken peices during the time frame
in which I was making changes. I believe I have most
of the things ironed out in 11545:32205f911e74 which
is now running on the test tool shed.
We will be performing some test runs of thie new
framework over the long weekend, so more correct
test results should hopefully be showing up for yours
and other repositories.
Hi Greg,
Things look much better today on the Test Tool Shed, with
most of my tools under "Latest revision: all tool tests pass"
again - or as expected a few under "Latest revision: missing
tool tests" due to not yet having full test coverage.
I've only spotted one glitch so far, missing test results for:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
I saw a recent commit on galaxy-central addressing a test
time display - that may have explained why yesterday
the Test Tool Shed was claiming the test results were
from four days ago.
I've also enhanced the "Tool test results" components
to store a
configurable number of test runs instead of just 1. The test tool
shed is configured to store 5 test runs. So from here on you'll
begin to see multiple containers in the Tool test results container
- something like this:
That sounds useful when the framework itself is changing
rapidly, or if there is anything stochastic in a test failure.
Presumably this shows the last 5 tests against the current
tool revision?
Thank Greg, and enjoy Thanksgiving,
Peter
5:16 p.m.
Hello Peter,
On Nov 28, 2013, at 4:56 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Wed, Nov 27, 2013 at 9:02 PM, Greg Von Kuster
<greg(a)bx.psu.edu> wrote:
>
> Hello Peter,
>
> I've done a significant amount of re-engineering of the
> Tool Shed's install and test framework over the past 2
> weeks, so the results you are seeing are probably a
> reflection of some broken peices during the time frame
> in which I was making changes. I believe I have most
> of the things ironed out in 11545:32205f911e74 which
> is now running on the test tool shed.
>
> We will be performing some test runs of thie new
> framework over the long weekend, so more correct
> test results should hopefully be showing up for yours
> and other repositories.
>
Hi Greg,
Things look much better today on the Test Tool Shed, with
most of my tools under "Latest revision: all tool tests pass"
again - or as expected a few under "Latest revision: missing
tool tests" due to not yet having full test coverage.
I've only spotted one glitch so far, missing test results for:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
The above repository was not displaying the missing test components due to a problem in
the previous test runs which I fixed yesterday. The problem resulted in test result data
that could not be displayed. When I introduced the new feature for stroing and displaying
multiple test runs, I decided to not eliminate the bad data, but just to let enough test
runs proceed that the bad data would eventually be eliminated. I forced new test runs,
and now things should be displaying as expected. Here is the display for the above
repository for the latest run this morning:
Automated tool test results
Automated test environment
Time tested: 2013-11-28 11:29:38
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 11549:5aede225ebef
Tool shed database version: 21
Tool shed mercurial version: 2.2.3
Tools missing tests or test data
Tool id: ncbi_rpstblastn_wrapper
Tool version: 0.0.22
Tool guid:
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_rpstblastn_...
Missing components:
Functional test definitions missing for ncbi_rpstblastn_wrapper.
Tool id: ncbi_blastdbcmd_info
Tool version: 0.0.22
Tool guid:
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastdbcmd_...
Missing components:
Functional test definitions missing for ncbi_blastdbcmd_info.
Tool id: ncbi_makeblastdb
Tool version: 0.0.22
Tool guid:
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_makeblastdb...
Missing components:
One or more test files are missing for tool ncbi_makeblastdb:
four_human_proteins.fasta.log
Tool id: ncbi_blastdbcmd_wrapper
Tool version: 0.0.22
Tool guid:
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_blastdbcmd_...
Missing components:
Functional test definitions missing for ncbi_blastdbcmd_wrapper.
Tool id: ncbi_rpsblast_wrapper
Tool version: 0.0.22
Tool guid:
testtoolshed.g2.bx.psu.edu/repos/peterjc/ncbi_blast_plus/ncbi_rpsblast_wr...
Missing components:
Functional test definitions missing for ncbi_rpsblast_wrapper.
I saw a recent commit on galaxy-central addressing a test
time display - that may have explained why yesterday
the Test Tool Shed was claiming the test results were
from four days ago.
Yes, there is a flag that can be set for testing a repository that eliminates it from
being tested by the install and test framework. This flag had been inappropriately set on
many repositories, including the one to which you are referring. That problem has been
corrected, so testing should be more stable.
> I've also enhanced the "Tool test results" components to store a
> configurable number of test runs instead of just 1. The test tool
> shed is configured to store 5 test runs. So from here on you'll
> begin to see multiple containers in the Tool test results container
> - something like this:
That sounds useful when the framework itself is changing
rapidly, or if there is anything stochastic in a test failure.
Presumably this shows the last 5 tests against the current
tool revision?
It displays the last 5 test runs against any installable revision that is tested. We are
currently restricting testing to the latest installable revision, so the 5 test runs will
be displayed for that revision only.
Thank Greg, and enjoy Thanksgiving,
Thanks Peter, your too!
Peter
5:30 p.m.
On Thu, Nov 28, 2013 at 5:16 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
Hello Peter,
On Nov 28, 2013, at 4:56 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
Hi Greg,
Things look much better today on the Test Tool Shed, with
most of my tools under "Latest revision: all tool tests pass"
again - or as expected a few under "Latest revision: missing
tool tests" due to not yet having full test coverage.
I've only spotted one glitch so far, missing test results for:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
The above repository was not displaying the missing test components due to
a problem in the previous test runs which I fixed yesterday. The problem
resulted in test result data that could not be displayed.
Perhaps a fall back error message would be useful here (e.g. "Test failed
but unable to display data"), which would be better than the "missing"
test
results?
When I introduced the new feature for stroing and displaying multiple
test
runs, I decided to not eliminate the bad data, but just to let enough test
runs proceed that the bad data would eventually be eliminated. I forced
new test runs, and now things should be displaying as expected. Here is
the display for the above repository for the latest run this morning:
Thank you - that alerted me to a missing set of out output files for a
recently added test, hopefully addressed in this revision:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045
But its not all good news - another test is now listed as failing, but with
missing test results:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
Thanks,
Peter
5:56 p.m.
On Thu, Nov 28, 2013 at 5:30 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
Thank you - that alerted me to a missing set of out output files for a
recently added test, hopefully addressed in this revision:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045
But its not all good news - another test is now listed as failing, but with
missing test results:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
Another little oddity, the three test results for mira_bait.xml are missing
(although it correctly tells me mira_4_0_mapping and mira_4_0_de_novo
have no tests):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler/302d13490b23
Peter
7:31 p.m.
Hi Peter,
On Nov 28, 2013, at 12:56 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Thu, Nov 28, 2013 at 5:30 PM, Peter Cock
<p.j.a.cock(a)googlemail.com> wrote:
>
> Thank you - that alerted me to a missing set of out output files for a
> recently added test, hopefully addressed in this revision:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045
>
> But its not all good news - another test is now listed as failing, but with
> missing test results:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
>
Another little oddity, the three test results for mira_bait.xml are missing
(although it correctly tells me mira_4_0_mapping and mira_4_0_de_novo
have no tests):
http://testtoolshed.g2.bx.psu.edu/view/peterjc/mira4_assembler/302d13490b23
Here is what I am seeing for the missing tests. Is this information ot correct? If not,
what is incorrect?
Automated tool test results
Test runs
2013-11-28 13:02:42
Automated test environment
Time tested: 2013-11-28 13:02:42
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 11549:5aede225ebef
Tool shed database version: 21
Tool shed mercurial version: 2.2.3
Tools missing tests or test data
Tool id: mira_4_0_mapping
Tool version: 0.0.2
Tool guid:
testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping...
Missing components:
Functional test definitions missing for mira_4_0_mapping.
Tool id: mira_4_0_de_novo
Tool version: 0.0.2
Tool guid:
testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo...
Missing components:
Functional test definitions missing for mira_4_0_de_novo.
2013-11-28 11:29:49
Automated test environment
Time tested: 2013-11-28 11:29:49
System:
Architecture:
Python version:
Galaxy revision:
Galaxy database version:
Tool shed revision: 11549:5aede225ebef
Tool shed database version: 21
Tool shed mercurial version: 2.2.3
Tools missing tests or test data
Tool id: mira_4_0_mapping
Tool version: 0.0.2
Tool guid:
testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_mapping...
Missing components:
Functional test definitions missing for mira_4_0_mapping.
Tool id: mira_4_0_de_novo
Tool version: 0.0.2
Tool guid:
testtoolshed.g2.bx.psu.edu/repos/peterjc/mira4_assembler/mira_4_0_de_novo...
Missing components:
Functional test definitions missing for mira_4_0_de_novo.
Peter
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7:34 p.m.
Hi Peter,
On Nov 28, 2013, at 12:30 PM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
On Thu, Nov 28, 2013 at 5:16 PM, Greg Von Kuster
<greg(a)bx.psu.edu> wrote:
Hello Peter,
On Nov 28, 2013, at 4:56 AM, Peter Cock <p.j.a.cock(a)googlemail.com> wrote:
> Hi Greg,
>
> Things look much better today on the Test Tool Shed, with
> most of my tools under "Latest revision: all tool tests pass"
> again - or as expected a few under "Latest revision: missing
> tool tests" due to not yet having full test coverage.
>
> I've only spotted one glitch so far, missing test results for:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/b2795652d2b4
The above repository was not displaying the missing test components due to a problem in
the previous test runs which I fixed yesterday. The problem resulted in test result data
that could not be displayed.
Perhaps a fall back error message would be useful here (e.g. "Test failed but unable
to display data"), which would be better than the "missing" test results?
When I introduced the new feature for stroing and displaying multiple test runs, I
decided to not eliminate the bad data, but just to let enough test runs proceed that the
bad data would eventually be eliminated. I forced new test runs, and now things should be
displaying as expected. Here is the display for the above repository for the latest run
this morning:
Thank you - that alerted me to a missing set of out output files for a recently added
test, hopefully addressed in this revision:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/ncbi_blast_plus/1b8a92016045
But its not all good news - another test is now listed as failing, but with missing test
results:
http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
The bad data shoud now be eliminated, and there are 3 test runs displaying for this one.
Do these look crrect to you? The oldest test run has a data of 'unknown' because
I had not implemented the date deature at that point.
Automated tool test results
Test runs
2013-11-28 14:50:44
Automated test environment
Time tested: 2013-11-28 14:50:44
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 11549:5aede225ebef
Galaxy database version: 117
Tool shed revision: 11549:5aede225ebef
Tool shed database version: 21
Tool shed mercurial version: 2.2.3
Tests that passed successfully
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000002
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000003
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tests that failed
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000001
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Stderr:
Traceback:
Traceback (most recent call last):
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 101, in test_tool
self.do_it( td )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 31, in do_it
self.__verify_outputs( testdef, test_history, shed_tool_id, data_list,
galaxy_interactor )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 64, in __verify_outputs
galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes,
shed_tool_id=shed_tool_id, maxseconds=maxseconds )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 303, in verify_output
self.twill_test_case.verify_dataset_correctness( outfile, hid=hid,
attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 814, in verify_dataset_correctness
self.wait( maxseconds=maxseconds ) # wait for job to finish
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1425, in wait
return self.wait_for(lambda: self.get_running_datasets(), **kwds)
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1440, in wait_for
assert slept < maxseconds
AssertionError:
2013-11-28 09:24:20
Automated test environment
Time tested: 2013-11-28 09:24:20
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 11548:7756b29bea29
Galaxy database version: 117
Tool shed revision: 11544:8b613225f1de
Tool shed database version: 21
Tool shed mercurial version: 2.2.3
Tests that passed successfully
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000001
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000002
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000003
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
unknown_2
Automated test environment
Time tested: unknown_2
System: Linux 3.8.0-30-generic
Architecture: x86_64
Python version: 2.7.4
Galaxy revision: 11526:c0384bad246d
Galaxy database version: 117
Tool shed revision:
Tool shed database version:
Tool shed mercurial version:
Tests that passed successfully
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000000
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000001
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000002
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Tests that failed
Tool id: get_orfs_or_cdss
Tool version: get_orfs_or_cdss
Test: test_tool_000003
(functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/pete...)
Stderr:
Traceback:
Traceback (most recent call last):
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 101, in test_tool
self.do_it( td )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 31, in do_it
self.__verify_outputs( testdef, test_history, shed_tool_id, data_list,
galaxy_interactor )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 64, in __verify_outputs
galaxy_interactor.verify_output( history, output_data, outfile, attributes=attributes,
shed_tool_id=shed_tool_id, maxseconds=maxseconds )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 303, in verify_output
self.twill_test_case.verify_dataset_correctness( outfile, hid=hid,
attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 814, in verify_dataset_correctness
self.wait( maxseconds=maxseconds ) # wait for job to finish
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1425, in wait
return self.wait_for(lambda: self.get_running_datasets(), **kwds)
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1440, in wait_for
assert slept < maxseconds
AssertionError
Thanks,
Peter
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11:33 a.m.
On Thu, Nov 28, 2013 at 7:34 PM, Greg Von Kuster <greg(a)bx.psu.edu> wrote:
Hi Peter,
> But its not all good news - another test is now listed as failing, but with
> missing test results:
> http://testtoolshed.g2.bx.psu.edu/view/peterjc/get_orfs_or_cdss/09b5b1af9b8f
The bad data shoud now be eliminated, and there are 3 test runs displaying
for this one. Do these look crrect to you? The oldest test run has a data
of 'unknown' because I had not implemented the date deature at that point.
Most of the tests passed (as expected), but a couple of times there
was some kind of time out error, e.g.
Traceback (most recent call last):
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 101, in test_tool
self.do_it( td )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 31, in do_it
self.__verify_outputs( testdef, test_history, shed_tool_id, data_list,
galaxy_interactor )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py",
line 64, in __verify_outputs
galaxy_interactor.verify_output( history, output_data, outfile,
attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py",
line 303, in verify_output
self.twill_test_case.verify_dataset_correctness( outfile, hid=hid,
attributes=attributes, shed_tool_id=shed_tool_id, maxseconds=maxseconds )
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 814, in verify_dataset_correctness
self.wait( maxseconds=maxseconds ) # wait for job to finish
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1425, in wait
return self.wait_for(lambda: self.get_running_datasets(), **kwds)
File
"/var/opt/buildslaves/buildslave-ec2-2/buildbot-install-test-test-tool-shed-py27/build/test/base/twilltestcase.py",
line 1440, in wait_for
assert slept < maxseconds
AssertionError:
Regards,
Peter
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77 comments
4 participants
participants (4)
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Dave Bouvier -
Greg Von Kuster -
Peter Cock -
Ross