It seems to be happening during upload - so it is not unsurprising that this error would affect multiple tools. I have checked out the exact revision registered in the tests and the uploads seem fine to me. I am having trouble imagining a deployment problem short of an invalid upload tool that might result in this error. Dave B, is it possible that a problematic datatype is being installed by some repository and affecting unrelated tools? -John On Mon, Mar 23, 2015 at 8:27 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Dave,
Now that you've fixed some of the test back log, the bad news is this issue I reported last week appears to be a major regression affecting multiple tools on the Test Tool Shed:
https://testtoolshed.g2.bx.psu.edu/view/peterjc/align_back_trans https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast2go https://testtoolshed.g2.bx.psu.edu/view/peterjc/blastxml_to_top_descr https://testtoolshed.g2.bx.psu.edu/view/peterjc/clinod ... https://testtoolshed.g2.bx.psu.edu/view/peterjc/nlstradamus ... https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs ... https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_select_by_id
These are all recent test runs from 2015-03-18. Note that some tool tests from the same date are passing, e.g.
https://testtoolshed.g2.bx.psu.edu/view/peterjc/blast_rbh https://testtoolshed.g2.bx.psu.edu/view/peterjc/seq_composition https://testtoolshed.g2.bx.psu.edu/view/peterjc/mummer
I have not yet spotted any pattern in this division.
(However this is clearly not linked to the test expect_failure test I'd added to the sample_seqs tool, as I speculated last week.)
Regards,
Peter
On Wed, Mar 18, 2015 at 2:14 PM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
Hi Dave,
The following looks like a regression on the Test Tool Shed, the tests pass locally (using a recent revision), and on TravisCI using the current galaxy dev branch on GitHub: https://travis-ci.org/peterjc/pico_galaxy/builds/54870500
Problem tool: https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
This may be unrelated, but by chance this is the first time I have uploaded a tool to the Tool Shed which uses the new functionality to test the stdout/stderr strings, and more importantly it includes a test expected to fail via <test expect_failure="true" expect_exit_code="1">
Revision on my development repository: https://github.com/peterjc/pico_galaxy/commit/55ebb308b911b4acef912cc3b03f43...
Test Tool Shed output from last night:
Automated test environment Time tested: 2015-03-18 02:46:55 System: Linux 3.13.0-36-generic Architecture: x86_64 Python version: 2.7.6 Galaxy revision: 17050:6395e7035143 Galaxy database version: 128 Tool shed revision: 16867:0468d285f89c Tool shed database version: 25 Tool shed mercurial version: 3.2.4 Tests that failed Tool id: sample_seqs Tool version: sample_seqs Test: test_tool_000000 (functional.test_toolbox.TestForTool_testtoolshed.g2.bx.psu.edu/repos/peterjc/sample_seqs/sample_seqs/0.2.1) Stderr: Traceback: Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 268, in test_tool self.do_it( td ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/functional/test_toolbox.py", line 37, in do_it stage_data_in_history( galaxy_interactor, testdef.test_data(), test_history, shed_tool_id ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 38, in stage_data_in_history upload_wait() File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 279, in wait while not self.__history_ready( history_id ): File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 297, in __history_ready return self._state_ready( state, error_msg="History in error state." ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/test/base/interactor.py", line 356, in _state_ready raise Exception( error_msg ) Exception: History in error state. Traceback (most recent call last): File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/runners/__init__.py", line 158, in prepare_job job_wrapper.prepare() File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/jobs/__init__.py", line 828, in prepare tool_evaluator.set_compute_environment( compute_environment, get_special=get_special ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/evaluation.py", line 53, in set_compute_environment incoming = self.tool.params_from_strings( incoming, self.app ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/__init__.py", line 1873, in params_from_strings return params_from_strings( self.inputs, params, app, ignore_errors ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/__init__.py", line 103, in params_from_strings value = params[key].value_from_basic( value, app, ignore_errors ) File "/tmp/buildslave/buildbot-install-test-test-tool-shed-py27/build/lib/galaxy/tools/parameters/grouping.py", line 512, in value_from_basic raise e KeyError: 'base_name' requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): 127.0.0.1 galaxy.datatypes.metadata: DEBUG: Cleaning up external metadata files requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/c33ffb67c9176a6c?key=ae52a59b996b793c4c06a11fc3c33481 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): 127.0.0.1 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/c33ffb67c9176a6c/contents?key=ae52a59b996b793c4c06a11fc3c33481 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): 127.0.0.1 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9?key=ae52a59b996b793c4c06a11fc3c33481 HTTP/1.1" 200 None requests.packages.urllib3.connectionpool: INFO: Starting new HTTP connection (1): 127.0.0.1 requests.packages.urllib3.connectionpool: DEBUG: "GET /api/histories/c33ffb67c9176a6c/contents/d80a923b055ee8e9/provenance?key=ae52a59b996b793c4c06a11fc3c33481 HTTP/1.1" 200 None
(All the tests for this tool seem to have failed the same way)
Regards,
Peter
On Wed, Mar 18, 2015 at 1:46 PM, Dave Bouvier <dave@bx.psu.edu> wrote:
Gentlemen,
The issue with the nightly testing was due to a stalled test run blocking subsequent tests. I've cleared out that blockage and a manual test run appears to have completed successfully, as should future automated test runs. As always, feel free to let us know if you encounter any additional inexplicable behavior.
--Dave B.
On 03/18/2015 07:00 AM, Peter Cock wrote:
... I can also confirm that the Test Tool Shed example I gave was tested overnight, although it looks like a novel failure: https://testtoolshed.g2.bx.psu.edu/view/peterjc/sample_seqs
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