Question: planemo test failure (virtualenv problem?)
0
gravatar for danielfortin86
2.5 years ago by
United States
danielfortin86100 wrote:

When I try to run planemo (v0.21.1) I get an error that seems to involve virtualenv. I followed the instructions for installing planemo using the traditional virtualenv and pip method:

planemo test --no_cleanup --install_galaxy --test_output /home/galaxy/files/013/dataset_13063.dat --test_data /home/galaxy/galaxy-functional-tests/ test.xml

git --git-dir /home/galaxy/.planemo/gx_repo fetch >/dev/null 2>&1
cd /tmp/tmpLNljIH; git clone  --branch 'dev' '/home/galaxy/.planemo/gx_repo' 'galaxy-dev'; cd galaxy-dev; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv;  else GALAXY_VIRTUAL_ENV=/home/galaxy/.planemo/gx_venv; fi; export GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /nfs/sw/.conda/envs/galaxy/bin/virtualenv -p /nfs/sw/.conda/envs/galaxy/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate;  COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--skip-venv --dev-wheels"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; ./scripts/common_startup.sh ${COMMON_STARTUP_ARGS}
Initialized empty Git repository in /tmp/tmpLNljIH/galaxy-dev/.git/
Running virtualenv with interpreter /nfs/sw/.conda/envs/galaxy/bin/python2.7
New python executable in .venv/bin/python2.7
Also creating executable in .venv/bin/python
.venv/bin/python2.7: error while loading shared libraries: libpython2.7.so.1.0:                                     cannot open shared object file: No such file or directory
ERROR: The executable .venv/bin/python2.7 is not functioning
ERROR: It thinks sys.prefix is u'/tmp/tmpLNljIH/galaxy-dev' (should be u'/tmp/tm                                    pLNljIH/galaxy-dev/.venv')
ERROR: virtualenv is not compatible with this system or executable
/bin/sh: .venv/bin/activate: No such file or directory
Testing using galaxy_root /tmp/tmpLNljIH/galaxy-dev
Testing tools with command [cd /tmp/tmpLNljIH/galaxy-dev; COMMON_STARTUP_ARGS=;                                     $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--skip-venv --skip-common-startup"; export COMMON_STARTUP_ARGS; echo "Set COMMON_STARTUP_ARGS to ${COMMON_STARTUP_ARGS}"; if [ -d .venv ] || [ -f dist-eggs.ini ]; then GALAXY_VIRTUAL_ENV=.venv;  else GALAXY_VIRTUAL_ENV=/home/galaxy/.planemo/gx_venv; fi; export                                     GALAXY_VIRTUAL_ENV; if [ ! -e $GALAXY_VIRTUAL_ENV ]; then /nfs/sw/.conda/envs/galaxy/bin/virtualenv -p /nfs/sw/.conda/envs/galaxy/bin/python2.7 $GALAXY_VIRTUAL_ENV; fi; [ -e $GALAXY_VIRTUAL_ENV ] && . $GALAXY_VIRTUAL_ENV/bin/activate; sh run_tests.sh $COMMON_STARTUP_ARGS --report_file /remote/RMS/users/galaxy/files/013/dataset_13063.dat --xunit_report_file /tmp/tmpLNljIH/xunit.xml --structured_data_report_file /remote/home/galaxy/tool_test_output.json functional.test_toolbox                                    ]

 

Set COMMON_STARTUP_ARGS to

/bin/sh: .venv/bin/activate: No such file or directory
Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown.
Warning: Problem with target Galaxy, it did not produce a structured test results files - summary information and planemo reports will be incorrect.

Can anyone give me any hints as to what is wrong?

Thanks!

 

planemo virtualenv • 1.1k views
ADD COMMENTlink modified 2.4 years ago • written 2.5 years ago by danielfortin86100

I did some additional testing using planemo 0.14 and 0.21.1 and galaxy 15.07 and 15.10. Using planemo test only works when using the combination of planemo 0.14 and galaxy 15.07. Hope that helps?

ADD REPLYlink written 2.4 years ago by danielfortin86100
0
gravatar for jmchilton
2.4 years ago by
jmchilton1.1k
United States
jmchilton1.1k wrote:

I've made a number of changes to planemo to continue to try to address recent changes in Galaxy (requiring a virtualenv, using wheels instead of eggs, etc...) I suspect just updating planemo will correct these errors, can you verify?

ADD COMMENTlink written 2.4 years ago by jmchilton1.1k

I just did a pip install planemo --upgrade (version 0.21.1)

I now get this error:

Testing using galaxy_root /nfs/sw/galaxy-test
Testing tools with command [cd /nfs/sw/galaxy-test; COMMON_STARTUP_ARGS=; $(grep -q 'skip-venv' run_tests.sh) && COMMON_STARTUP_ARGS="--skip-venv --skip-common-startup";
Set COMMON_STARTUP_ARGS to 
/bin/sh: .venv/bin/activate: No such file or directory
Cannot locate xUnit report option for tests - update Galaxy for more detailed breakdown.
Warning: Problem with target Galaxy, it did not produce a structured test results files - summary information and planemo reports will be incorrect.
Traceback (most recent call last):
  File "/remote/home/galaxy/.venv/bin/planemo", line 9, in <module>
    load_entry_point('planemo==0.21.1', 'console_scripts', 'planemo')()
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/click/core.py", line 716, in __call__
    return self.main(*args, **kwargs)
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/click/core.py", line 696, in main
    rv = self.invoke(ctx)
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/click/core.py", line 1060, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/click/core.py", line 889, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/click/decorators.py", line 64, in new_func
    return ctx.invoke(f, obj, *args[1:], **kwargs)
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/click/core.py", line 534, in invoke
    return callback(*args, **kwargs)
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/planemo/commands/cmd_test.py", line 61, in cli
    sys.exit(return_value)
  File "/usr/lib64/python2.6/contextlib.py", line 34, in __exit__
    self.gen.throw(type, value, traceback)
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/planemo/galaxy_config.py", line 253, in galaxy_config
    master_api_key,
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/planemo/commands/cmd_test.py", line 59, in cli
    return_value = run_in_config(ctx, config, **kwds)
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/planemo/galaxy_test/actions.py", line 83, in run_in_config
    return_code,
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/planemo/galaxy_test/structures.py", line 166, in __init__
    sd = StructuredData(output_json_path)
  File "/remote/home/galaxy/.venv/lib/python2.6/site-packages/planemo/galaxy_test/structures.py", line 78, in __init__
    self.structured_data = structured_data
UnboundLocalError: local variable 'structured_data' referenced before assignment

ADD REPLYlink written 2.4 years ago by danielfortin86100
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 84 users visited in the last hour