I happened to copy Peter's .travis.yml for running tests for some of my packages. However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype : https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
Saket
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com wrote:
I happened to copy Peter's .travis.yml for running tests for some of my packages.
Background information: http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype : https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Regards,
Peter
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com wrote:
I happened to copy Peter's .travis.yml for running tests for some of my packages.
Background information: http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype : https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
Regards,
Peter
I don't see anywhere in your Travis YAML file where you are modifying Galaxy's datatypes (like Peter does for instance on these lines https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml#L166). If those datatypes are not defined you cannot upload a tool with a specific type. Am I missing something?
-John
On Thu, Apr 17, 2014 at 7:33 AM, Saket Choudhary saketkc@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com wrote:
I happened to copy Peter's .travis.yml for running tests for some of my packages.
Background information: http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype : https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
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/
Just to add, that is the case with all the tests:
$ sh run_functional_tests.sh Ran 436 tests in 19.153s
FAILED (errors=434)
All tests fail locally and hence I decided to rely on travis. https://wiki.galaxyproject.org/Admin/RunningTests#Functional_Tests says it might be due to conflicting version of paste in my PYTHONPATH. But it happens even if I run these under a virtualenv.
Saket
On 17 April 2014 18:03, Saket Choudhary saketkc@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com wrote:
I happened to copy Peter's .travis.yml for running tests for some of my packages.
Background information: http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype : https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
Regards,
Peter
Hi John,
My tool's input datatype is tabular. I do not have any custom datatypes defined.
Saket
On 17 April 2014 18:10, John Chilton jmchilton@gmail.com wrote:
I don't see anywhere in your Travis YAML file where you are modifying Galaxy's datatypes (like Peter does for instance on these lines https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml#L166). If those datatypes are not defined you cannot upload a tool with a specific type. Am I missing something?
-John
On Thu, Apr 17, 2014 at 7:33 AM, Saket Choudhary saketkc@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com wrote:
I happened to copy Peter's .travis.yml for running tests for some of my packages.
Background information: http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype : https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
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/
Oppps, duh sorry I thought condel_input.tabular was a datatype not a file. That makes sense. I'll look some more.
-John
On Thu, Apr 17, 2014 at 7:45 AM, Saket Choudhary saketkc@gmail.com wrote:
Hi John,
My tool's input datatype is tabular. I do not have any custom datatypes defined.
Saket
On 17 April 2014 18:10, John Chilton jmchilton@gmail.com wrote:
I don't see anywhere in your Travis YAML file where you are modifying Galaxy's datatypes (like Peter does for instance on these lines https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml#L166). If those datatypes are not defined you cannot upload a tool with a specific type. Am I missing something?
-John
On Thu, Apr 17, 2014 at 7:33 AM, Saket Choudhary saketkc@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com wrote:
I happened to copy Peter's .travis.yml for running tests for some of my packages.
Background information: http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype : https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
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/
Hi, Saket - 436 tests in 19.153 seconds means something odd (or fast) with your setup? What errors do you see?
Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
On Thu, Apr 17, 2014 at 10:43 PM, Saket Choudhary saketkc@gmail.com wrote:
Just to add, that is the case with all the tests:
$ sh run_functional_tests.sh Ran 436 tests in 19.153s
FAILED (errors=434)
All tests fail locally and hence I decided to rely on travis. https://wiki.galaxyproject.org/Admin/RunningTests#Functional_Tests says it might be due to conflicting version of paste in my PYTHONPATH. But it happens even if I run these under a virtualenv.
Saket
On 17 April 2014 18:03, Saket Choudhary saketkc@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com
wrote:
I happened to copy Peter's .travis.yml for running tests for some of my packages.
Background information:
http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype :
https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
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/
Culprit: System Proxy.
I am behind a proxy and have my http_proxy, https_proxy variables set. The trick is to unset them. Because I am relying on John's template[1] for testing, I had to just unset http_proxy ONLY.
Maybe I should add this to the wiki?
[1] https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0117.sqli...
On 17 April 2014 18:18, Ross ross.lazarus@gmail.com wrote:
Hi, Saket - 436 tests in 19.153 seconds means something odd (or fast) with your setup? What errors do you see?
Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
On Thu, Apr 17, 2014 at 10:43 PM, Saket Choudhary saketkc@gmail.com wrote:
Just to add, that is the case with all the tests:
$ sh run_functional_tests.sh Ran 436 tests in 19.153s
FAILED (errors=434)
All tests fail locally and hence I decided to rely on travis. https://wiki.galaxyproject.org/Admin/RunningTests#Functional_Tests says it might be due to conflicting version of paste in my PYTHONPATH. But it happens even if I run these under a virtualenv.
Saket
On 17 April 2014 18:03, Saket Choudhary saketkc@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com wrote:
I happened to copy Peter's .travis.yml for running tests for some of my packages.
Background information:
http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype :
https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
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/
HI John, Saket,
Looking at Skaet's .travis.yml he doesn't mess about with the default datatypes_conf.xml(.sample) like I do, so his TravisCI should have all the default Galaxy datatypes (including tabular).
In my more complex .travis.yml I modify this to two reasons, first to add new datatypes, and second for a slight speedup I remove most of the unused datatypes.
Peter
On Thu, Apr 17, 2014 at 1:45 PM, Saket Choudhary saketkc@gmail.com wrote:
Hi John,
My tool's input datatype is tabular. I do not have any custom datatypes defined.
Saket
On 17 April 2014 18:10, John Chilton jmchilton@gmail.com wrote:
I don't see anywhere in your Travis YAML file where you are modifying Galaxy's datatypes (like Peter does for instance on these lines https://github.com/peterjc/pico_galaxy/blob/master/.travis.yml#L166). If those datatypes are not defined you cannot upload a tool with a specific type. Am I missing something?
-John
Apparently my tool itself does a web API call, so the test is bound to fail locally. My best bet is to rely on travis for now, however I still see this failing: https://travis-ci.org/saketkc/galaxy_tools/jobs/23206181#L1721
The input file exists: https://travis-ci.org/saketkc/galaxy_tools/jobs/23206181#L1721
On testtoolshed: http://testtoolshed.g2.bx.psu.edu/view/saketkc/condel
Installation fails, because pycurl fails to install which I shall report in other thread.
Saket
On 17 April 2014 18:45, Saket Choudhary saketkc@gmail.com wrote:
Culprit: System Proxy.
I am behind a proxy and have my http_proxy, https_proxy variables set. The trick is to unset them. Because I am relying on John's template[1] for testing, I had to just unset http_proxy ONLY.
Maybe I should add this to the wiki?
[1] https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0117.sqli...
On 17 April 2014 18:18, Ross ross.lazarus@gmail.com wrote:
Hi, Saket - 436 tests in 19.153 seconds means something odd (or fast) with your setup? What errors do you see?
Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
On Thu, Apr 17, 2014 at 10:43 PM, Saket Choudhary saketkc@gmail.com wrote:
Just to add, that is the case with all the tests:
$ sh run_functional_tests.sh Ran 436 tests in 19.153s
FAILED (errors=434)
All tests fail locally and hence I decided to rely on travis. https://wiki.galaxyproject.org/Admin/RunningTests#Functional_Tests says it might be due to conflicting version of paste in my PYTHONPATH. But it happens even if I run these under a virtualenv.
Saket
On 17 April 2014 18:03, Saket Choudhary saketkc@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com wrote:
I happened to copy Peter's .travis.yml for running tests for some of my packages.
Background information:
http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
However the process has not been smooth at all. See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908
AssertionError: Attempting to set field 'input' to value '['condel_input.tabular']' in form 'tool_form' threw exception: cannot find value/label "condel_input.tabular" in list control
I am already passing it the correct ftype :
https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w...
Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
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/
John pointed out that the error its the upload of the test file itself which is failing. I can locate the input files in test-data/
https://travis-ci.org/saketkc/galaxy_tools/jobs/23238748#L1723
Any clues as to where exactly am I going wrong?
On 17 April 2014 19:40, Saket Choudhary saketkc@gmail.com wrote:
Apparently my tool itself does a web API call, so the test is bound to fail locally. My best bet is to rely on travis for now, however I still see this failing: https://travis-ci.org/saketkc/galaxy_tools/jobs/23206181#L1721
The input file exists: https://travis-ci.org/saketkc/galaxy_tools/jobs/23206181#L1721
On testtoolshed: http://testtoolshed.g2.bx.psu.edu/view/saketkc/condel
Installation fails, because pycurl fails to install which I shall report in other thread.
Saket
On 17 April 2014 18:45, Saket Choudhary saketkc@gmail.com wrote:
Culprit: System Proxy.
I am behind a proxy and have my http_proxy, https_proxy variables set. The trick is to unset them. Because I am relying on John's template[1] for testing, I had to just unset http_proxy ONLY.
Maybe I should add this to the wiki?
[1] https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0117.sqli...
On 17 April 2014 18:18, Ross ross.lazarus@gmail.com wrote:
Hi, Saket - 436 tests in 19.153 seconds means something odd (or fast) with your setup? What errors do you see?
Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
On Thu, Apr 17, 2014 at 10:43 PM, Saket Choudhary saketkc@gmail.com wrote:
Just to add, that is the case with all the tests:
$ sh run_functional_tests.sh Ran 436 tests in 19.153s
FAILED (errors=434)
All tests fail locally and hence I decided to rely on travis. https://wiki.galaxyproject.org/Admin/RunningTests#Functional_Tests says it might be due to conflicting version of paste in my PYTHONPATH. But it happens even if I run these under a virtualenv.
Saket
On 17 April 2014 18:03, Saket Choudhary saketkc@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com wrote: > I happened to copy Peter's .travis.yml for running tests for some of > my packages.
Background information:
http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-...
> However the process has not been smooth at all. > See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908 > > AssertionError: Attempting to set field 'input' to value > '['condel_input.tabular']' in form 'tool_form' threw exception: cannot > find value/label "condel_input.tabular" in list control > > I am already passing it the correct ftype : > > https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w... > > Is there something I am missing?
This is similar to (but different) to the error message I recently reported as being unclear when a datatype was not defined: http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html
In your case, this is an input file which seems to be missing, test-data/condel_input.tabular - but I see the line copying the tool's test-data into the main Galaxy test-data folder is there in the .travis.yml file.
I am puzzled too.
The key question I would ask you is: do your tests work locally? If so, are they installed via a (local) Tool Shed, or manually along the same lines of the attempted TravisCI tool installation?
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
Regards,
Peter
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Can I throw in a bounty for this one? ;-)
On 18 April 2014 03:09, Saket Choudhary saketkc@gmail.com wrote:
John pointed out that the error its the upload of the test file itself which is failing. I can locate the input files in test-data/
https://travis-ci.org/saketkc/galaxy_tools/jobs/23238748#L1723
Any clues as to where exactly am I going wrong?
On 17 April 2014 19:40, Saket Choudhary saketkc@gmail.com wrote:
Apparently my tool itself does a web API call, so the test is bound to fail locally. My best bet is to rely on travis for now, however I still see this failing: https://travis-ci.org/saketkc/galaxy_tools/jobs/23206181#L1721
The input file exists: https://travis-ci.org/saketkc/galaxy_tools/jobs/23206181#L1721
On testtoolshed: http://testtoolshed.g2.bx.psu.edu/view/saketkc/condel
Installation fails, because pycurl fails to install which I shall report in other thread.
Saket
On 17 April 2014 18:45, Saket Choudhary saketkc@gmail.com wrote:
Culprit: System Proxy.
I am behind a proxy and have my http_proxy, https_proxy variables set. The trick is to unset them. Because I am relying on John's template[1] for testing, I had to just unset http_proxy ONLY.
Maybe I should add this to the wiki?
[1] https://github.com/jmchilton/galaxy-downloads/raw/master/db_gx_rev_0117.sqli...
On 17 April 2014 18:18, Ross ross.lazarus@gmail.com wrote:
Hi, Saket - 436 tests in 19.153 seconds means something odd (or fast) with your setup? What errors do you see?
Ross Lazarus MBBS MPH; Head, Medical Bioinformatics, BakerIDI; Tel: +61 385321444 http://scholar.google.com/citations?hl=en&user=UCUuEM4AAAAJ
On Thu, Apr 17, 2014 at 10:43 PM, Saket Choudhary saketkc@gmail.com wrote:
Just to add, that is the case with all the tests:
$ sh run_functional_tests.sh Ran 436 tests in 19.153s
FAILED (errors=434)
All tests fail locally and hence I decided to rely on travis. https://wiki.galaxyproject.org/Admin/RunningTests#Functional_Tests says it might be due to conflicting version of paste in my PYTHONPATH. But it happens even if I run these under a virtualenv.
Saket
On 17 April 2014 18:03, Saket Choudhary saketkc@gmail.com wrote:
On 17 April 2014 15:34, Peter Cock p.j.a.cock@googlemail.com wrote: > On Thu, Apr 17, 2014 at 12:59 AM, Saket Choudhary saketkc@gmail.com > wrote: >> I happened to copy Peter's .travis.yml for running tests for some of >> my packages. > > Background information: > > http://blastedbio.blogspot.co.uk/2013/09/using-travis-ci-for-testing-galaxy-... > >> However the process has not been smooth at all. >> See : https://travis-ci.org/saketkc/galaxy_tools/jobs/23166678#L908 >> >> AssertionError: Attempting to set field 'input' to value >> '['condel_input.tabular']' in form 'tool_form' threw exception: cannot >> find value/label "condel_input.tabular" in list control >> >> I am already passing it the correct ftype : >> >> https://github.com/saketkc/galaxy_tools/blob/travis-test/condel_web/condel_w... >> >> Is there something I am missing? > > This is similar to (but different) to the error message I recently > reported as being unclear when a datatype was not defined: > http://lists.bx.psu.edu/pipermail/galaxy-dev/2014-April/019090.html > > In your case, this is an input file which seems to be missing, > test-data/condel_input.tabular - but I see the line copying the > tool's test-data into the main Galaxy test-data folder is there > in the .travis.yml file. > > I am puzzled too. > > The key question I would ask you is: do your tests work locally? > If so, are they installed via a (local) Tool Shed, or manually along > the same lines of the attempted TravisCI tool installation? >
Unfortunately No.
TwillAssertionError: code is 500 != 200
I am running Galaxy under virtualenv. Unfortunately I get the same error irrespective of whther my input/output files exits inside test-data/ directory. I forgot to link them to test-data path earlier, but I get the same error even otherwise.
> Regards, > > Peter
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On Thu, Apr 17, 2014 at 10:39 PM, Saket Choudhary saketkc@gmail.com wrote:
John pointed out that the error its the upload of the test file itself which is failing. I can locate the input files in test-data/
https://travis-ci.org/saketkc/galaxy_tools/jobs/23238748#L1723
Any clues as to where exactly am I going wrong?
Very strange. Adding "ls test-data" to the TravisCI list worked, and showed the input file condel_input.tabular was present: https://github.com/saketkc/galaxy_tools/commit/c04ff946db0182de9aca4f6dc36ff... https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239476/log.txt https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239477/log.txt
How about replacing that with "ls -l test-data/condel_input.tabular" to verify the ownership and permissions (although if that was the upload problem, Galaxy could give a clearer error).
Likely unrelated, but I don't think I have bothered to set the ftype when uploading tabular files / using them as test inputs. Did you ever try this without the ftype?
Peter
On 18 April 2014 14:59, Peter Cock p.j.a.cock@googlemail.com wrote:
On Thu, Apr 17, 2014 at 10:39 PM, Saket Choudhary saketkc@gmail.com wrote:
John pointed out that the error its the upload of the test file itself which is failing. I can locate the input files in test-data/
https://travis-ci.org/saketkc/galaxy_tools/jobs/23238748#L1723
Any clues as to where exactly am I going wrong?
Very strange. Adding "ls test-data" to the TravisCI list worked, and showed the input file condel_input.tabular was present: https://github.com/saketkc/galaxy_tools/commit/c04ff946db0182de9aca4f6dc36ff... https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239476/log.txt https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239477/log.txt
How about replacing that with "ls -l test-data/condel_input.tabular" to verify the ownership and permissions (although if that was the upload problem, Galaxy could give a clearer error).
Thanks, tried it: https://travis-ci.org/saketkc/galaxy_tools/jobs/23270454#L530
This happens irrespective of using ftype. and the plce where ERROR occurs is this:
galaxy.jobs.runners.local DEBUG 2014-04-17 21:25:53,808 execution finished: GALAXY_SLOTS="1"; export GALAXY_SLOTS; python /home/travis/build/saketkc/galaxy_tools/galaxy-central-master/tools/data_source/upload.py /home/travis/build/saketkc/galaxy_tools/galaxy-central-master /tmp/tmpNenHnc/tmp83XrmN/new_files_path_4s4ndH/tmpvroRLA /tmp/tmpNenHnc/tmp83XrmN/new_files_path_4s4ndH/tmpv9tzOU 1:/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/dataset_1_files:/tmp/tmpNenHnc/tmp83XrmN/database/files/000/dataset_1.dat galaxy.datatypes.metadata INFO 2014-04-17 21:25:55,902 /tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_in_HistoryDatasetAssociation_1_bVl30h,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_kwds_HistoryDatasetAssociation_1_jiQBR3,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_out_HistoryDatasetAssociation_1_aoG7yJ,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_results_HistoryDatasetAssociation_1_JM1wqM,,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_override_HistoryDatasetAssociation_1_ZUFWdn galaxy.jobs.runners DEBUG 2014-04-17 21:25:55,903 executing external set_meta script for job 1: /home/travis/build/saketkc/galaxy_tools/galaxy-central-master/set_metadata.sh /tmp/tmpNenHnc/tmp83XrmN/database/files /tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1 . /tmp/tmpNenHnc/functional_tests_wsgi.ini /tmp/tmpNenHnc/tmp83XrmN/new_files_path_4s4ndH/tmpvroRLA /tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/galaxy.json /tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_in_HistoryDatasetAssociation_1_bVl30h,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_kwds_HistoryDatasetAssociation_1_jiQBR3,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_out_HistoryDatasetAssociation_1_aoG7yJ,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_results_HistoryDatasetAssociation_1_JM1wqM,,/tmp/tmpNenHnc/tmp83XrmN/job_working_directory_AsN2Fs/000/1/metadata_override_HistoryDatasetAssociation_1_ZUFWdn galaxy.jobs.runners DEBUG 2014-04-17 21:25:57,620 execution of external set_meta for job 1 finished galaxy.jobs DEBUG 2014-04-17 21:25:57,727 setting dataset state to ERROR
so my dataset state is set to ERROR, essentially upload failed. But why, is what it doesn't tell me.
Likely unrelated, but I don't think I have bothered to set the ftype when uploading tabular files / using them as test inputs. Did you ever try this without the ftype?
Peter
On Fri, Apr 18, 2014 at 11:47 AM, Saket Choudhary saketkc@gmail.com wrote:
On 18 April 2014 14:59, Peter Cock p.j.a.cock@googlemail.com wrote:
Very strange. Adding "ls test-data" to the TravisCI list worked, and showed the input file condel_input.tabular was present: https://github.com/saketkc/galaxy_tools/commit/c04ff946db0182de9aca4f6dc36ff... https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239476/log.txt https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239477/log.txt
How about replacing that with "ls -l test-data/condel_input.tabular" to verify the ownership and permissions (although if that was the upload problem, Galaxy could give a clearer error).
Thanks, tried it: https://travis-ci.org/saketkc/galaxy_tools/jobs/23270454#L530
I see, that looks fine:
$ ls -l test-data/condel_input.tabular -rwxrwxr-x 1 travis travis 110 Apr 18 10:28 test-data/condel_input.tabular
This happens irrespective of using ftype. and the plce where ERROR occurs is this:
...
so my dataset state is set to ERROR, essentially upload failed. But why, is what it doesn't tell me.
If this were a systematic problem other people should have seen it - but I have tests using tabular input files which still work fine.
I wonder where exactly in the process it is failing... perhaps in the metadata processing which would be consistent with it being some oddity in your sample file which is causing trouble?
Can you upload this file condel_input.tabular into Galaxy via the UI without error?
Peter
On 18 April 2014 18:06, Peter Cock p.j.a.cock@googlemail.com wrote:
On Fri, Apr 18, 2014 at 11:47 AM, Saket Choudhary saketkc@gmail.com wrote:
On 18 April 2014 14:59, Peter Cock p.j.a.cock@googlemail.com wrote:
Very strange. Adding "ls test-data" to the TravisCI list worked, and showed the input file condel_input.tabular was present: https://github.com/saketkc/galaxy_tools/commit/c04ff946db0182de9aca4f6dc36ff... https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239476/log.txt https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239477/log.txt
How about replacing that with "ls -l test-data/condel_input.tabular" to verify the ownership and permissions (although if that was the upload problem, Galaxy could give a clearer error).
Thanks, tried it: https://travis-ci.org/saketkc/galaxy_tools/jobs/23270454#L530
I see, that looks fine:
$ ls -l test-data/condel_input.tabular -rwxrwxr-x 1 travis travis 110 Apr 18 10:28 test-data/condel_input.tabular
This happens irrespective of using ftype. and the plce where ERROR occurs is this:
...
so my dataset state is set to ERROR, essentially upload failed. But why, is what it doesn't tell me.
If this were a systematic problem other people should have seen it - but I have tests using tabular input files which still work fine.
I wonder where exactly in the process it is failing... perhaps in the metadata processing which would be consistent with it being some oddity in your sample file which is causing trouble?
Can you upload this file condel_input.tabular into Galaxy via the UI without error?
Yes, the upload works fine with 'Auto-Detect'. It sets the type to be 'interval'. I am also able to upload if I manually set it to 'tabular', which is anyway expected.
Just to double check I tested it with 'filter1_test5.tab' that comes with galaxy-central and that is failing too: https://travis-ci.org/saketkc/galaxy_tools/jobs/23277155#L1283
I am going to clone your repository and try pushing in my tools to the clone to see if that helps.
Peter
* fork your repository.
On 18 April 2014 18:42, Saket Choudhary saketkc@gmail.com wrote:
On 18 April 2014 18:06, Peter Cock p.j.a.cock@googlemail.com wrote:
On Fri, Apr 18, 2014 at 11:47 AM, Saket Choudhary saketkc@gmail.com wrote:
On 18 April 2014 14:59, Peter Cock p.j.a.cock@googlemail.com wrote:
Very strange. Adding "ls test-data" to the TravisCI list worked, and showed the input file condel_input.tabular was present: https://github.com/saketkc/galaxy_tools/commit/c04ff946db0182de9aca4f6dc36ff... https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239476/log.txt https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239477/log.txt
How about replacing that with "ls -l test-data/condel_input.tabular" to verify the ownership and permissions (although if that was the upload problem, Galaxy could give a clearer error).
Thanks, tried it: https://travis-ci.org/saketkc/galaxy_tools/jobs/23270454#L530
I see, that looks fine:
$ ls -l test-data/condel_input.tabular -rwxrwxr-x 1 travis travis 110 Apr 18 10:28 test-data/condel_input.tabular
This happens irrespective of using ftype. and the plce where ERROR occurs is this:
...
so my dataset state is set to ERROR, essentially upload failed. But why, is what it doesn't tell me.
If this were a systematic problem other people should have seen it - but I have tests using tabular input files which still work fine.
I wonder where exactly in the process it is failing... perhaps in the metadata processing which would be consistent with it being some oddity in your sample file which is causing trouble?
Can you upload this file condel_input.tabular into Galaxy via the UI without error?
Yes, the upload works fine with 'Auto-Detect'. It sets the type to be 'interval'. I am also able to upload if I manually set it to 'tabular', which is anyway expected.
Just to double check I tested it with 'filter1_test5.tab' that comes with galaxy-central and that is failing too: https://travis-ci.org/saketkc/galaxy_tools/jobs/23277155#L1283
I am going to clone your repository and try pushing in my tools to the clone to see if that helps.
Peter
Pushed out this changeset https://bitbucket.org/galaxy/galaxy-central/commits/183668ed911ca0ad937f3ffe... which should allow better reporting of dataset errors in histories.
Make sure export GALAXY_TEST_VERBOSE_ERRORS=True is executed before your tests and then check the output of the API driven version - it should have a breakdown of all datasets in error when it encounters a history that is not ok. This should include the standard error and standard output from the upload tool - which in turn should tell us the exact problem (fingers crossed).
On Fri, Apr 18, 2014 at 8:13 AM, Saket Choudhary saketkc@gmail.com wrote:
- fork your repository.
On 18 April 2014 18:42, Saket Choudhary saketkc@gmail.com wrote:
On 18 April 2014 18:06, Peter Cock p.j.a.cock@googlemail.com wrote:
On Fri, Apr 18, 2014 at 11:47 AM, Saket Choudhary saketkc@gmail.com wrote:
On 18 April 2014 14:59, Peter Cock p.j.a.cock@googlemail.com wrote:
Very strange. Adding "ls test-data" to the TravisCI list worked, and showed the input file condel_input.tabular was present: https://github.com/saketkc/galaxy_tools/commit/c04ff946db0182de9aca4f6dc36ff... https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239476/log.txt https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239477/log.txt
How about replacing that with "ls -l test-data/condel_input.tabular" to verify the ownership and permissions (although if that was the upload problem, Galaxy could give a clearer error).
Thanks, tried it: https://travis-ci.org/saketkc/galaxy_tools/jobs/23270454#L530
I see, that looks fine:
$ ls -l test-data/condel_input.tabular -rwxrwxr-x 1 travis travis 110 Apr 18 10:28 test-data/condel_input.tabular
This happens irrespective of using ftype. and the plce where ERROR occurs is this:
...
so my dataset state is set to ERROR, essentially upload failed. But why, is what it doesn't tell me.
If this were a systematic problem other people should have seen it - but I have tests using tabular input files which still work fine.
I wonder where exactly in the process it is failing... perhaps in the metadata processing which would be consistent with it being some oddity in your sample file which is causing trouble?
Can you upload this file condel_input.tabular into Galaxy via the UI without error?
Yes, the upload works fine with 'Auto-Detect'. It sets the type to be 'interval'. I am also able to upload if I manually set it to 'tabular', which is anyway expected.
Just to double check I tested it with 'filter1_test5.tab' that comes with galaxy-central and that is failing too: https://travis-ci.org/saketkc/galaxy_tools/jobs/23277155#L1283
I am going to clone your repository and try pushing in my tools to the clone to see if that helps.
Peter
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Thanks John,
That really helped:
Exception: History in error state.
-------------------- >> begin captured stdout << ---------------------
History with id adb5f5c93f827949 in error - summary of datasets in error below.
--------------------------------------
| 1 - filter1_test5.tab (HID - NAME)
| Dataset Blurb:
| error
| Dataset Info:
| uploaded tabular file
| /usr/local/lib/python2.7/dist-packages/setuptools-2.2-py2.7.egg/pkg_resources.py:991: UserWarning: /home/travis/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more
| Dataset Job Standard Output:
| *Standard output was empty.*
| Dataset Job Standard Error:
| /usr/local/lib/python2.7/dist-packages/setuptools-2.2-py2.7.egg/pkg_resources.py:991: UserWarning: /home/travis/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
|
--------------------------------------
--------------------- >> end captured stdout << ----------------------
Fixed here: https://travis-ci.org/saketkc/galaxy_tools/jobs/23282261#L1402 with:
before_install: - mkdir "$HOME/.python-eggs" - chmod 700 "$HOME/.python-eggs"
The test is failing, but that I expected it to anyway ;)
Thanks everyone! Especially John and Peter!
Saket
On 18 April 2014 19:15, John Chilton jmchilton@gmail.com wrote:
Pushed out this changeset https://bitbucket.org/galaxy/galaxy-central/commits/183668ed911ca0ad937f3ffe... which should allow better reporting of dataset errors in histories.
Make sure export GALAXY_TEST_VERBOSE_ERRORS=True is executed before your tests and then check the output of the API driven version - it should have a breakdown of all datasets in error when it encounters a history that is not ok. This should include the standard error and standard output from the upload tool - which in turn should tell us the exact problem (fingers crossed).
On Fri, Apr 18, 2014 at 8:13 AM, Saket Choudhary saketkc@gmail.com wrote:
- fork your repository.
On 18 April 2014 18:42, Saket Choudhary saketkc@gmail.com wrote:
On 18 April 2014 18:06, Peter Cock p.j.a.cock@googlemail.com wrote:
On Fri, Apr 18, 2014 at 11:47 AM, Saket Choudhary saketkc@gmail.com wrote:
On 18 April 2014 14:59, Peter Cock p.j.a.cock@googlemail.com wrote:
Very strange. Adding "ls test-data" to the TravisCI list worked, and showed the input file condel_input.tabular was present: https://github.com/saketkc/galaxy_tools/commit/c04ff946db0182de9aca4f6dc36ff... https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239476/log.txt https://s3.amazonaws.com/archive.travis-ci.org/jobs/23239477/log.txt
How about replacing that with "ls -l test-data/condel_input.tabular" to verify the ownership and permissions (although if that was the upload problem, Galaxy could give a clearer error).
Thanks, tried it: https://travis-ci.org/saketkc/galaxy_tools/jobs/23270454#L530
I see, that looks fine:
$ ls -l test-data/condel_input.tabular -rwxrwxr-x 1 travis travis 110 Apr 18 10:28 test-data/condel_input.tabular
This happens irrespective of using ftype. and the plce where ERROR occurs is this:
...
so my dataset state is set to ERROR, essentially upload failed. But why, is what it doesn't tell me.
If this were a systematic problem other people should have seen it - but I have tests using tabular input files which still work fine.
I wonder where exactly in the process it is failing... perhaps in the metadata processing which would be consistent with it being some oddity in your sample file which is causing trouble?
Can you upload this file condel_input.tabular into Galaxy via the UI without error?
Yes, the upload works fine with 'Auto-Detect'. It sets the type to be 'interval'. I am also able to upload if I manually set it to 'tabular', which is anyway expected.
Just to double check I tested it with 'filter1_test5.tab' that comes with galaxy-central and that is failing too: https://travis-ci.org/saketkc/galaxy_tools/jobs/23277155#L1283
I am going to clone your repository and try pushing in my tools to the clone to see if that helps.
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/
On Fri, Apr 18, 2014 at 3:36 PM, Saket Choudhary saketkc@gmail.com wrote:
Thanks John,
That really helped:
...
| /usr/local/lib/python2.7/dist-packages/setuptools-2.2-py2.7.egg/pkg_resources.py:991: UserWarning: /home/travis/.python-eggs is writable by group/others and vulnerable to attack when used with get_resource_filename. Consider a more secure location (set with .set_extraction_path or the PYTHON_EGG_CACHE environment variable).
Fixed here: https://travis-ci.org/saketkc/galaxy_tools/jobs/23282261#L1402 with:
before_install:
- mkdir "$HOME/.python-eggs"
- chmod 700 "$HOME/.python-eggs"
The test is failing, but that I expected it to anyway ;)
Thanks everyone! Especially John and Peter!
Saket
Ah - that was hard to diagnose, perhaps there used to be a more visible warning because I already had that egg chmod trick in my TravsCI setup?
Well done for solving that - and thank you John for the verbose setting, I think that will be useful in future too.
Peter
galaxy-dev@lists.galaxyproject.org
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John Chilton -
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Saket Choudhary