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dfci / matchminer-api

A platform for matching patient-specific genomic profiles to precision cancer medicine clinical trials
https://matchminer.org/
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demo: step "nosetests tests" gives errors: syntax, non-existing attribute and non-existent module 'rfc822' and 'engine' #8

Closed cegg closed 5 years ago

cegg commented 5 years ago

matchminer-api$ nosetests tests

EEEEEE....E

ERROR: Failure: AttributeError (module 'sys' has no attribute 'maxint')

Traceback (most recent call last): File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 235, in load_module return load_source(name, filename, file) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 172, in load_source module = _load(spec) File "", line 693, in _load File "", line 673, in _load_unlocked File "", line 697, in exec_module File "", line 222, in _call_with_frames_removed File "/Users/ipozdnya/matchminer-api/tests/unit/test_api/test_neg_genomic.py", line 5, in from matchminer.database import get_db File "/Users/ipozdnya/matchminer-api/matchminer/database.py", line 4, in from matchminer.settings import File "/Users/ipozdnya/matchminer-api/matchminer/settings.py", line 56, in from matchminer.settings_dev import File "/Users/ipozdnya/matchminer-api/matchminer/settings_dev.py", line 20, in TOKEN_TIMEOUT = sys.maxint AttributeError: module 'sys' has no attribute 'maxint'

====================================================================== ERROR: Failure: ImportError (No module named 'rfc822')

Traceback (most recent call last): File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 235, in load_module return load_source(name, filename, file) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 172, in load_source module = _load(spec) File "", line 693, in _load File "", line 673, in _load_unlocked File "", line 697, in exec_module File "", line 222, in _call_with_frames_removed File "/Users/ipozdnya/matchminer-api/tests/unit/test_api/test_response.py", line 7, in from rfc822 import formatdate ImportError: No module named 'rfc822'

====================================================================== ERROR: Failure: AttributeError (module 'sys' has no attribute 'maxint')

Traceback (most recent call last): File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 235, in load_module return load_source(name, filename, file) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 172, in load_source module = _load(spec) File "", line 693, in _load File "", line 673, in _load_unlocked File "", line 697, in exec_module File "", line 222, in _call_with_frames_removed File "/Users/ipozdnya/matchminer-api/tests/unit/test_api/test_status.py", line 6, in from matchminer.database import get_db File "/Users/ipozdnya/matchminer-api/matchminer/database.py", line 4, in from matchminer.settings import File "/Users/ipozdnya/matchminer-api/matchminer/settings.py", line 56, in from matchminer.settings_dev import File "/Users/ipozdnya/matchminer-api/matchminer/settings_dev.py", line 20, in TOKEN_TIMEOUT = sys.maxint AttributeError: module 'sys' has no attribute 'maxint'

====================================================================== ERROR: Failure: SyntaxError (invalid token (test_trial.py, line 621))

Traceback (most recent call last): File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 235, in load_module return load_source(name, filename, file) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 172, in load_source module = _load(spec) File "", line 693, in _load File "", line 673, in _load_unlocked File "", line 693, in exec_module File "", line 799, in get_code File "", line 759, in source_to_code File "", line 222, in _call_with_frames_removed File "/Users/ipozdnya/matchminer-api/tests/unit/test_api/test_trial.py", line 621 "site": [{"id": [01], "value": "Dana-Farber Cancer Institute"}], ^ SyntaxError: invalid token

====================================================================== ERROR: Failure: AttributeError (module 'sys' has no attribute 'maxint')

Traceback (most recent call last): File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 235, in load_module return load_source(name, filename, file) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 172, in load_source module = _load(spec) File "", line 693, in _load File "", line 673, in _load_unlocked File "", line 697, in exec_module File "", line 222, in _call_with_frames_removed File "/Users/ipozdnya/matchminer-api/tests/unit/test_api/test_utilities.py", line 4, in from matchminer.database import get_db File "/Users/ipozdnya/matchminer-api/matchminer/database.py", line 4, in from matchminer.settings import File "/Users/ipozdnya/matchminer-api/matchminer/settings.py", line 56, in from matchminer.settings_dev import File "/Users/ipozdnya/matchminer-api/matchminer/settings_dev.py", line 20, in TOKEN_TIMEOUT = sys.maxint AttributeError: module 'sys' has no attribute 'maxint'

====================================================================== ERROR: Failure: ImportError (No module named 'engine')

Traceback (most recent call last): File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 235, in load_module return load_source(name, filename, file) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 172, in load_source module = _load(spec) File "", line 693, in _load File "", line 673, in _load_unlocked File "", line 697, in exec_module File "", line 222, in _call_with_frames_removed File "/Users/ipozdnya/matchminer-api/tests/test_cbioengine/test_engine.py", line 4, in from tcm import CBioEngine File "/Users/ipozdnya/matchminer-api/tcm/init.py", line 1, in from engine import CBioEngine ImportError: No module named 'engine'

====================================================================== ERROR: Failure: ImportError (No module named 'rfc822')

Traceback (most recent call last): File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/failure.py", line 39, in runTest raise self.exc_val.with_traceback(self.tb) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/loader.py", line 418, in loadTestsFromName addr.filename, addr.module) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 47, in importFromPath return self.importFromDir(dir_path, fqname) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/site-packages/nose/importer.py", line 94, in importFromDir mod = load_module(part_fqname, fh, filename, desc) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 245, in load_module return load_package(name, filename) File "/Users/ipozdnya/ve_matchminer/lib/python3.5/imp.py", line 217, in load_package return _load(spec) File "", line 693, in _load File "", line 673, in _load_unlocked File "", line 697, in exec_module File "", line 222, in _call_with_frames_removed File "/Users/ipozdnya/matchminer-api/tests/test_matchminer/init.py", line 10, in from rfc822 import formatdate ImportError: No module named 'rfc822'

Looks like it's trying to import python3 packages for some reason even though my python is aliased to 2.7. When I force it to run with python2.7, ( python2.7 -m nose tests ) another error happens:

ERROR: Failure: ImportError (No module named pytest)
----------------------------------------------------------------------
Traceback (most recent call last):
  File "/usr/local/Cellar/numpy/1.15.4_2/libexec/nose/lib/python2.7/site-packages/nose/loader.py", line 418, in loadTestsFromName
    addr.filename, addr.module)
  File "/usr/local/Cellar/numpy/1.15.4_2/libexec/nose/lib/python2.7/site-packages/nose/importer.py", line 47, in importFromPath
    return self.importFromDir(dir_path, fqname)
  File "/usr/local/Cellar/numpy/1.15.4_2/libexec/nose/lib/python2.7/site-packages/nose/importer.py", line 94, in importFromDir
    mod = load_module(part_fqname, fh, filename, desc)
  File "/Users/ipozdnya/Library/Python/2.7/lib/python/site-packages/tests/test_transport_http.py", line 35, in <module>
    import pytest
ImportError: No module named pytest

----------------------------------------------------------------------
Ran 28 tests in 0.963s

I checked for pytest:

$ python2.7 -m pip install pytest
Requirement already satisfied: pytest in /usr/local/lib/python2.7/site-packages (4.1.0)

What am I missing still?

cegg commented 5 years ago

python version mismatch for the most part, closing