glciampaglia / knowledge_linker Goto Github PK
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License: Apache License 2.0
Computational Fact Checking from Knowledge Networks
License: Apache License 2.0
Hello,
After running this in console:
python setup.py nosetests
I get the following error
https://drive.google.com/open?id=1NA4KAfjWE98T0MydpUgzjxov3_2jw8mi
I'm running on windows.
Regards,
I'm getting the following error & failures while trying to run the test cases
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/knowledge_linker/knowledge_linker/tests/test_closure.py", line 422, in test_backbone_metric
DG.add_edge(n1, n2, {'weight_sum':sum_path_weights})
TypeError: add_edge() takes exactly 3 arguments (4 given)
Traceback (most recent call last):
File "/usr/lib/python2.7/doctest.py", line 2226, in runTest
raise self.failureException(self.format_failure(new.getvalue()))
AssertionError: Failed doctest test for knowledge_linker.algorithms.closure.closuress
File "/knowledge_linker/knowledge_linker/algorithms/closure.py", line 114, in closuress
Traceback (most recent call last):
File "/usr/local/lib/python2.7/dist-packages/nose/case.py", line 197, in runTest
self.test(*self.arg)
File "/knowledge_linker/knowledge_linker/tests/test_closure.py", line 95, in test_closure_rand
assert np.all(p1 == p2)
AssertionError
REPORT FILE:
https://openload.co/f/dCKlFZq9X6g/docker_kl_report1.txt
After installing the package
python setup.py install
Trying to run klinker
will throw:
Traceback (most recent call last):
File "/home/marvram/anaconda3/envs/p2/bin/klinker", line 11, in <module>
load_entry_point('knowledge-linker==0.1rc0', 'console_scripts', 'klinker')()
File "/home/marvram/anaconda3/envs/p2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 565, in load_entry_point
File "/home/marvram/anaconda3/envs/p2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 2598, in load_entry_point
File "/home/marvram/anaconda3/envs/p2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 2258, in load
File "/home/marvram/anaconda3/envs/p2/lib/python2.7/site-packages/setuptools-27.2.0-py2.7.egg/pkg_resources/__init__.py", line 2264, in resolve
File "build/bdist.linux-x86_64/egg/knowledge_linker/__init__.py", line 31, in <module>
ImportError: cannot import name io
This is because setup.py only specifies packages=['knowledge_linker']
, while it should do packages=find_packages()
.
Per title. See https://guides.github.com/activities/citable-code/
(env-kl) [zkachwal@h2 knowledge_linker]$ pip install .
DEPRECATION: Python 2.7 will reach the end of its life on January 1st, 2020. Please upgrade your Python as Python 2.7 won't be maintained after that date. A future version of pip will drop support for Python 2.7.
Processing /gpfs/home/z/k/zkachwal/Carbonate/knowledge_linker
ERROR: Complete output from command python setup.py egg_info:
ERROR: Traceback (most recent call last):
File "<string>", line 1, in <module>
File "/tmp/pip-req-build-QW1JDC/setup.py", line 20, in <module>
from numpy import get_include
ImportError: No module named numpy
----------------------------------------
ERROR: Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-req-build-QW1JDC/
Fixed by installing numpy.
After installing:
(env-kl) [zkachwal@h2 knowledge_linker]$ klinker -h
Traceback (most recent call last):
File "/N/u/zkachwal/Carbonate/miniconda3/envs/env-kl/bin/klinker", line 6, in <module>
from knowledge_linker.frontend.cmdline import main
File "/N/u/zkachwal/Carbonate/miniconda3/envs/env-kl/lib/python2.7/site-packages/knowledge_linker/frontend/cmdline.py", line 20, in <module>
from . import linkpred
File "/N/u/zkachwal/Carbonate/miniconda3/envs/env-kl/lib/python2.7/site-packages/knowledge_linker/frontend/linkpred.py", line 22, in <module>
import pandas as pd
ImportError: No module named pandas
(env-factcheckgraph) [zkachwal@burns knowledge_linker]$ python --version
Python 3.6.8 :: Anaconda, Inc.
(env-factcheckgraph) [zkachwal@burns knowledge_linker]$ python setup.py install
running install
running bdist_egg
running egg_info
writing knowledge_linker.egg-info/PKG-INFO
writing dependency_links to knowledge_linker.egg-info/dependency_links.txt
writing entry points to knowledge_linker.egg-info/entry_points.txt
writing requirements to knowledge_linker.egg-info/requires.txt
writing top-level names to knowledge_linker.egg-info/top_level.txt
reading manifest file 'knowledge_linker.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'LICENSE.txt'
writing manifest file 'knowledge_linker.egg-info/SOURCES.txt'
installing library code to build/bdist.linux-x86_64/egg
running install_lib
running build_py
running build_ext
building 'knowledge_linker.algorithms.heap' extension
gcc -pthread -B /l/cnets/research/factcheckgraph/env-factcheckgraph/compiler_compat -Wl,--sysroot=/ -Wsign-compare -DNDEBUG -g -fwrapv -O3 -Wall -Wstrict-prototypes -fPIC -I/l/cnets/research/factcheckgraph/miniconda3/envs/env-factcheckgraph/lib/python3.6/site-packages/numpy/core/include -I/l/cnets/research/factcheckgraph/miniconda3/envs/env-factcheckgraph/include/python3.6m -c knowledge_linker/algorithms/heap.c -o build/temp.linux-x86_64-3.6/knowledge_linker/algorithms/heap.o
In file included from /l/cnets/research/factcheckgraph/miniconda3/envs/env-factcheckgraph/lib/python3.6/site-packages/numpy/core/include/numpy/ndarraytypes.h:1824,
from /l/cnets/research/factcheckgraph/miniconda3/envs/env-factcheckgraph/lib/python3.6/site-packages/numpy/core/include/numpy/ndarrayobject.h:12,
from /l/cnets/research/factcheckgraph/miniconda3/envs/env-factcheckgraph/lib/python3.6/site-packages/numpy/core/include/numpy/arrayobject.h:4,
from knowledge_linker/algorithms/heap.c:256:
/l/cnets/research/factcheckgraph/miniconda3/envs/env-factcheckgraph/lib/python3.6/site-packages/numpy/core/include/numpy/npy_1_7_deprecated_api.h:17:2: warning: #warning "Using deprecated NumPy API, disable it with " "#define NPY_NO_DEPRECATED_API NPY_1_7_API_VERSION"
/l/cnets/research/factcheckgraph/miniconda3/envs/env-factcheckgraph/lib/python3.6/site-packages/numpy/core/include/numpy/__multiarray_api.h:1463: warning: ‘_import_array’ defined but not used
gcc -pthread -shared -B /l/cnets/research/factcheckgraph/env-factcheckgraph/compiler_compat -L/l/cnets/research/factcheckgraph/env-factcheckgraph/lib -Wl,-rpath=/l/cnets/research/factcheckgraph/env-factcheckgraph/lib -Wl,--no-as-needed -Wl,--sysroot=/ build/temp.linux-x86_64-3.6/knowledge_linker/algorithms/heap.o -o build/lib.linux-x86_64-3.6/knowledge_linker/algorithms/heap.cpython-36m-x86_64-linux-gnu.so
/usr/bin/ld: this linker was not configured to use sysroots
collect2: ld returned 1 exit status
error: command 'gcc' failed with exit status 1
Numpy version 1.15.1
importnt allns.tsv instance_types_en.nt
WARNING: the n-triples file must be already sorted by source, destination!
Traceback (most recent call last):
File "/home/kenv/bin/importnt", line 11, in
load_entry_point('knowledge-linker==0.1rc0', 'console_scripts', 'importnt')()
File "build/bdist.linux-x86_64/egg/knowledge_linker/io/importnt.py", line 127, in main
NameError: global name 'readns' is not defined
When multiple paths with the same proximity are available, sometime the Cython implementation (cclosuress
) returns paths with more hops than the pure Python implementation (closuress
).
This bug was surfaced in knowledge_linker.tests.test_closure.test_closure_rand
; it may be a Cython specific issue since regression shows it was introduced in 31589e6 (464d864fd1979229a8f5412f31ae04a5282d5848
on Github.IU), but it seems that the test started failing only recently when a newer version of Cython was used to regenerate the C extension modules.
Hello,
I am very interested in this project. I have installed and used ontoparse & importnt to create the adjacency matrices.
I am interested in the confmatrix command of klinker but I am a bit confused on what each of the options mean.
uris node uris
graph adjacency matrix
source sources input file
target targets input file
output output file
I know that graph would the adjacency graph, but the other I would love some extra details. Thank you!
When networks are huge (ie., with sparse non-negative records >1e9), the instantiating of multiprocessing.Array(c_int, A.indices)
or A.data
fails in python 2.7:
File "test.py", line 53, in <module>
Bm = backbone(A, kind=kind, start=None, offset=None, nprocs=nprocs)
File "../knowledge_linker/algorithms/closure.py", line 507, in backbone
data = Array(c_double, A.data)
File "../multiprocessing/__init__.py", line 260, in Array
return Array(typecode_or_type, size_or_initializer, **kwds)
File "../multiprocessing/sharedctypes.py", line 120, in Array
obj = RawArray(typecode_or_type, size_or_initializer)
File "../multiprocessing/sharedctypes.py", line 94, in RawArray
result.__init__(*size_or_initializer)
SystemError: Objects/tupleobject.c:54: bad argument to internal function
Weirdly, it seems to work if the lines
indptr = Array(c_uint, A.indptr)
indices = Array(c_uint, A.indices)
data = Array(c_double, A.data)
are modified to
indptr = Array(c_int, len(A.indptr))
indptr[:] = A.indptr
indices = Array(c_int, len(A.indices))
indices[:] = A.indices
data = Array(c_double, len(A.data))
data[:] = A.data
... more to come.
I'm getting the below output while trying to run setup.py file on MacOS Mojave
$ python setup.py nosetests
running nosetests
running egg_info
writing requirements to knowledge_linker.egg-info/requires.txt
writing knowledge_linker.egg-info/PKG-INFO
writing top-level names to knowledge_linker.egg-info/top_level.txt
writing dependency_links to knowledge_linker.egg-info/dependency_links.txt
writing entry points to knowledge_linker.egg-info/entry_points.txt
reading manifest file 'knowledge_linker.egg-info/SOURCES.txt'
reading manifest template 'MANIFEST.in'
warning: no files found matching 'LICENSE.txt'
writing manifest file 'knowledge_linker.egg-info/SOURCES.txt'
building 'knowledge_linker.algorithms._maxmin' extension
cc -fno-strict-aliasing -fno-common -dynamic -g -Os -pipe -fno-common -fno-strict-aliasing -fwrapv -DENABLE_DTRACE -DMACOSX -DNDEBUG -Wall -Wstrict-prototypes -Wshorten-64-to-32 -DNDEBUG -g -fwrapv -Os -Wall -Wstrict-prototypes -DENABLE_DTRACE -arch i386 -arch x86_64 -pipe -I/Library/Python/2.7/site-packages/numpy/core/include -I/usr/include/python2.7 -c knowledge_linker/algorithms/_maxmin.c -o build/temp.macosx-10.14-intel-2.7/knowledge_linker/algorithms/_maxmin.o -fopenmp
clang: error: unsupported option '-fopenmp'
clang: error: unsupported option '-fopenmp'
error: command 'cc' failed with exit status 1
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