d-michail / python-jgrapht Goto Github PK

Here have some info
`
Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb
return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

File "_ctypes/callbacks.c", line 234, in 'calling callback function'

File "F:\python36\lib\site-packages\jgrapht\algorithms\drawing.py", line 67, in actual_vertex_comparator_cb

return vertex_comparator_cb(v1, v2)

TypeError: 'NoneType' object is not callable

Traceback (most recent call last):

...

Graph.drawing.draw_matplotlib.draw_jgrapht(G)

File "F:\python36\lib\site-packages\jgrapht\drawing\draw_matplotlib.py", line 119, in draw_jgrapht

positions = layout(g, name=kwargs.get('name'))

File "F:\python36\lib\site-packages\jgrapht\drawing\draw_matplotlib.py", line 770, in layout

x, y = result.get_vertex_location(i)

File "F:\python36\lib\site-packages\jgrapht_internals_anyhashableg_drawing.py", line 18, in get_vertex_location

vertex = _vertex_anyhashableg_to_g(self._graph, vertex)

File "F:\python36\lib\site-packages\jgrapht_internals_anyhashableg.py", line 797, in _vertex_anyhashableg_to_g

return graph._vertex_hash_to_id[vertex] if vertex is not None else None

KeyError: 0

`

The Graph vertex is a new class. it can work, but can't drawing.

Since positions are extracted using vertex indices and not values, masked subgraphs are not drawn correctly. This is fixed in pull request #12.

I'm trying to import an edgelist file with no success.

My input file is a single edge; the file is:

0, 1

My code is as follows (<input file> substitutes for the file path):

import jgrapht as j
input_file = <input file>
e = j.io.edgelist.parse_edgelist_csv(input_file, format='edgelist')

I get the following error:

Traceback (most recent call last): 
File "<python file>", line 12, in <module>
    e = j.io.edgelist.parse_edgelist_csv(input_file, format='edgelist')
File "<....>/jgrapht/io/edgelist.py", line 532 in parse_edgelist_csv
    return _import_edgelist_with_string_ids("string_csv", False, input_string, *args)
File "<....>/jgrapht/io/edgelist.py", line 23 in _import_edgelist_with_string_ids
    res = alg_method(filename_or_string_as_bytearray, *args)
File "<....>/jgrapht/backend.py", line 780, in jgrapht_import_edgelist_noattrs_string_csv
    return _backend_jgrapht_import_edgelist_noattrs_string_csv(BYTEARRAY, arg2, arg3, arg4, arg5)
', 'ror: Failed to import CSV graph: line 1:38 mismatched innput '<EOF>' expecting {' 
', SEPARATOR}

I'm running this in a conda environment, Python 3.8, with no other installed packages than those installed when installing jgrapht, on an Ubuntu VM.

I am trying to create an empty graph using jgrapth (latest) inside a job from apscheduler library (version 3.6.3), but I am having a java exception everytime the job is executed:

Error

Fatal error: StackOverflowError: Enabling the yellow zone of the stack did not make any stack space available. Possible reasons for that: 1) A call from native code to Java code provided the wrong JNI environment or the wrong IsolateThread; 2) Frames of native code filled the stack, and now there is not even enough stack space left to throw a regular StackOverflowError; 3) An internal VM error occurred. traveltimeservice | traveltimeservice | JavaFrameAnchor dump: traveltimeservice | traveltimeservice | No anchors traveltimeservice | traveltimeservice | TopFrame info: traveltimeservice | traveltimeservice | TotalFrameSize in CodeInfoTable 32 traveltimeservice | traveltimeservice | VMThreads info: traveltimeservice | traveltimeservice | VMThread 0000000001484120 STATUS_IN_JAVA (safepoints disabled) java.lang.Thread@0x7f12e939fd78 traveltimeservice | traveltimeservice | VM Thread State for current thread 0000000001484120: traveltimeservice | traveltimeservice | 0 (8 bytes): com.oracle.svm.jni.JNIThreadLocalEnvironment.jniFunctions = (bytes) traveltimeservice | 0000000001484120: 00007f12e9036d68 traveltimeservice | traveltimeservice | 8 (32 bytes): com.oracle.svm.core.genscavenge.ThreadLocalAllocation.regularTLAB = (bytes) traveltimeservice | 0000000001484128: 00007f12e7900000 00007f12e7a00000 traveltimeservice | 0000000001484138: 00007f12e79021e8 0000000000000000 traveltimeservice | traveltimeservice | traveltimeservice | 40 (8 bytes): com.oracle.svm.core.heap.NoAllocationVerifier.openVerifiers = (Object) null traveltimeservice | 48 (8 bytes): com.oracle.svm.core.jdk.IdentityHashCodeSupport.hashCodeGeneratorTL = (Object) null traveltimeservice | 56 (8 bytes): com.oracle.svm.core.snippets.ExceptionUnwind.currentException = (Object) null traveltimeservice | 64 (8 bytes): com.oracle.svm.core.thread.JavaThreads.currentThread = (Object) java.lang.Thread 00007f12e939fd78 traveltimeservice | 72 (8 bytes): com.oracle.svm.core.thread.ThreadingSupportImpl.activeTimer = (Object) null traveltimeservice | 80 (8 bytes): com.oracle.svm.jni.JNIObjectHandles.handles = (Object) com.oracle.svm.core.handles.ThreadLocalHandles 00007f12e7901228 traveltimeservice | 88 (8 bytes): com.oracle.svm.jni.JNIThreadLocalPendingException.pendingException = (Object) null traveltimeservice | 96 (8 bytes): com.oracle.svm.jni.JNIThreadLocalPinnedObjects.pinnedObjectsListHead = (Object) null traveltimeservice | 104 (8 bytes): com.oracle.svm.jni.JNIThreadOwnedMonitors.ownedMonitors = (Object) null traveltimeservice | 112 (8 bytes): com.oracle.svm.core.genscavenge.ThreadLocalAllocation.freeList = (Word) 0 0000000000000000 traveltimeservice | 120 (8 bytes): com.oracle.svm.core.graal.snippets.StackOverflowCheckImpl.stackBoundaryTL = (Word) 1 0000000000000001 traveltimeservice | 128 (8 bytes): com.oracle.svm.core.stack.JavaFrameAnchors.lastAnchor = (Word) 0 0000000000000000 traveltimeservice | 136 (8 bytes): com.oracle.svm.core.thread.VMThreads.IsolateTL = (Word) 139719186989056 00007f12e8824000 traveltimeservice | 144 (8 bytes): com.oracle.svm.core.thread.VMThreads.OSThreadHandleTL = (Word) 139719241832256 00007f12ebc71740 traveltimeservice | 152 (8 bytes): com.oracle.svm.core.thread.VMThreads.OSThreadIdTL = (Word) 139719241832256 00007f12ebc71740 traveltimeservice | 160 (8 bytes): com.oracle.svm.core.thread.VMThreads.nextTL = (Word) 0 0000000000000000 traveltimeservice | 168 (4 bytes): com.oracle.svm.core.graal.snippets.StackOverflowCheckImpl.yellowZoneStateTL = (int) -16843010 fefefefe traveltimeservice | 172 (4 bytes): com.oracle.svm.core.snippets.ImplicitExceptions.implicitExceptionsAreFatal = (int) 0 00000000 traveltimeservice | 176 (4 bytes): com.oracle.svm.core.thread.Safepoint.safepointRequested = (int) 2147473738 7fffd94a traveltimeservice | 180 (4 bytes): com.oracle.svm.core.thread.ThreadingSupportImpl.currentPauseDepth = (int) 0 00000000 traveltimeservice | 184 (4 bytes): com.oracle.svm.core.thread.VMThreads$ActionOnTransitionToJavaSupport.actionTL = (int) 0 00000000 traveltimeservice | 188 (4 bytes): com.oracle.svm.core.thread.VMThreads$StatusSupport.safepointsDisabledTL = (int) 1 00000001 traveltimeservice | 192 (4 bytes): com.oracle.svm.core.thread.VMThreads$StatusSupport.statusTL = (int) 1 00000001 traveltimeservice | traveltimeservice | VMOperation dump: traveltimeservice | traveltimeservice | No VMOperation in progress traveltimeservice | traveltimeservice | Dump Counters: traveltimeservice | traveltimeservice | traveltimeservice | Raw Stacktrace: traveltimeservice | traveltimeservice | 00007f12ded59dc0: 0000000001278288 00007f12e8f3fae8 traveltimeservice | 00007f12ded59dd0: 00007f12e8824000 00007f12e7b64906 traveltimeservice | 00007f12ded59de0: 0000000001286fa8 000000000059b0a2 traveltimeservice | 00007f12ded59df0: 0000000100000007 00007f12e7b64c6a traveltimeservice | 00007f12ded59e00: 0000000000000027 00007f12d40009f8 traveltimeservice | 00007f12ded59e10: 00007f12e93f5fa0 0000000100000290 traveltimeservice | 00007f12ded59e20: ffffffffffffffff ffffffffffffffff traveltimeservice | 00007f12ded59e30: ffffffffffffffff ffffffffffffffff traveltimeservice | 00007f12ded59e40: ffffffffffffffff ffffffffffffffff traveltimeservice | 00007f12ded59e50: 0000000000000098 0000000000000bfc traveltimeservice | 00007f12ded59e60: ffffffffffffffff ffffffffffffffff traveltimeservice | 00007f12ded59e70: 0000000000000000 0000000000000000 traveltimeservice | 00007f12ded59e80: 0000000000000000 0000000000000000 traveltimeservice | 00007f12ded59e90: 2f6465792f6c6d78 733a697378202233 traveltimeservice | 00007f12ded59ea0: 72672f2f3a707474 72672e6c6d687061 traveltimeservice | 00007f12ded59eb0: 74746820736e6c6d 2e7777772f2f3a70 traveltimeservice | 00007f12ded59ec0: 72672f616d656863 2e312f6c6d687061 traveltimeservice | 00007f12ded59ed0: 6c6d68706172673c 223d736e6c6d7820 traveltimeservice | 00007f12ded59ee0: 646920656764653c 326e3a3a326e223d traveltimeservice | 00007f12ded59ef0: 6e3a3a326e3a3a32 6567726174202237 traveltimeservice | 00007f12ded59f00: 00000000008a3850 00007f12ded90108 traveltimeservice | 00007f12ded59f10: 0000000000000000 0000000000000000 traveltimeservice | 00007f12ded59f20: 0000000000000001 00000000ffffffff traveltimeservice | 00007f12ded59f30: 0000000000000001 0000000000000001 traveltimeservice | 00007f12ded59f40: 00007f12ded5a028 0000000000000001 traveltimeservice | 00007f12ded59f50: 00007ffe18c2b000 0000000000000001 traveltimeservice | 00007f12ded59f60: 0000000080000001 00007f12ded5a028 traveltimeservice | 00007f12ded59f70: 0000000000000001 0000000000000001 traveltimeservice | 00007f12ded59f80: 00007f12ded59f90 00007f12e8565b33 traveltimeservice | 00007f12ded59f90: 00007f12e9a37120 0000000000000077 traveltimeservice | 00007f12ded59fa0: 00007f12ded5a028 00007f12e7b2cca6 traveltimeservice | 00007f12ded59fb0: 00007f12eb8b93a8 00007f12e9a05810 traveltimeservice | 00007f12ded59fc0: 00000000008183a0 00007f12ded5a028 traveltimeservice | 00007f12ded59fd0: 0000000100000001 0000000100000001 traveltimeservice | 00007f12ded59fe0: 0000000001484120 0000000080000001 traveltimeservice | 00007f12ded59ff0: 0000000000000001 0000000000000001 traveltimeservice | 00007f12ded5a000: 0000000000000001 00000000ffffffff traveltimeservice | 00007f12ded5a010: 00007f12ded5a028 00007f12e97d062e traveltimeservice | 00007f12ded5a020: 0000000000000008 0000000000000001 traveltimeservice | 00007f12ded5a030: 000000000081f0c0 000000000081f0c0 traveltimeservice | 00007f12ded5a040: 000000000081f0c0 000000000081f0c0 traveltimeservice | 00007f12ded5a050: 00007f12eba7f048 00007f12e02deb38 traveltimeservice | 00007f12ded5a060: 0000000000000000 00007f12e9a35778 traveltimeservice | 00007f12ded5a070: 0000000001bf9fb0 00007f12e97d0540 traveltimeservice | 00007f12ded5a080: 0000000000000000 00000000005ccc42 traveltimeservice | 00007f12ded5a090: 00007f12ded5a1b8 0000000000000004 traveltimeservice | 00007f12ded5a0a0: 00007f1200000001 0000000000000000 traveltimeservice | 00007f12ded5a0b0: 00007f12e9a809d8 00007f12ded5a1c0 traveltimeservice | 00007f12ded5a0c0: 00007f12e9a37120 0000000001bf9fa8 traveltimeservice | 00007f12ded5a0d0: 0000000001bf9fb0 0000000000000004 traveltimeservice | 00007f12ded5a0e0: 00007f12d00016c0 000000000053ecf0 traveltimeservice | 00007f12ded5a0f0: 0000000000000000 00007f12e9a35778 traveltimeservice | 00007f12ded5a100: 000000000081ec40 0000000000000004 traveltimeservice | 00007f12ded5a110: 00007f12e9a1344e 0000000001bf9fd0 traveltimeservice | 00007f12ded5a120: 0000000001bf9e18 0000000000542228 traveltimeservice | 00007f12ded5a130: 00000000000000a1 000000000054653a traveltimeservice | 00007f12ded5a140: 0000000000000000 0000000000000000 traveltimeservice | 00007f12ded5a150: 00007f12e9a13440 00007f12d00016c0 traveltimeservice | 00007f12ded5a160: 0000000001bf9f80 00007f12e9a12508 traveltimeservice | 00007f12ded5a170: 00007f12e9a13470 ffffffff00000000 traveltimeservice | 00007f12ded5a180: 00007f12e9a11a50 0000000001bf9fa0 traveltimeservice | 00007f12ded5a190: 00007f12ded5a240 00007f12e9a05810 traveltimeservice | 00007f12ded5a1a0: 00000000008183a0 00000000ffffffff traveltimeservice | 00007f12ded5a1b0: 00007f12e9a809d8 00007f12e9a37120 (1 liked)​[12:30 PM] Macias, Alan Full Stacktrace: traveltimeservice | traveltimeservice | RSP 00007f12ded59dc0 RIP 00007f12e7b97256 [image code] com.oracle.svm.core.jdk.VMErrorSubstitutions.shutdown(VMErrorSubstitutions.java:111) traveltimeservice | RSP 00007f12ded59dc0 RIP 00007f12e7b97256 [image code] com.oracle.svm.core.util.VMError.shouldNotReachHere(VMError.java:74) traveltimeservice | RSP 00007f12ded59de0 RIP 00007f12e7b64906 [image code] com.oracle.svm.core.util.VMError.shouldNotReachHere(VMError.java:59) traveltimeservice | RSP 00007f12ded59de0 RIP 00007f12e7b64906 [image code] com.oracle.svm.core.graal.snippets.StackOverflowCheckImpl.makeYellowZoneAvailable(StackOverflowCheckImpl.java:157) traveltimeservice | RSP 00007f12ded59e00 RIP 00007f12e7b64c6a [image code] com.oracle.svm.core.graal.snippets.StackOverflowCheckSnippets.throwNewStackOverflowError(StackOverflowCheckImpl.java:347) traveltimeservice | RSP 00007f12ded59f90 RIP 00007f12e8565b33 [image code] org.jgrapht.capi.impl.GraphApi.createGraph(GraphApi.java:98) traveltimeservice | RSP 00007f12ded59fb0 RIP 00007f12e7b2cca6 [image code] com.oracle.svm.core.code.IsolateEnterStub.GraphApi_createGraph_55db92e5a9752f432b95dce58782e288322437ad(IsolateEnterStub.java:0) traveltimeservice | traveltimeservice | [Native image heap boundaries: traveltimeservice | ReadOnly Primitives: 0x7f12e8824008 .. 0x7f12e8da2518 traveltimeservice | ReadOnly References: 0x7f12e8da2f58 .. 0x7f12e9096e40 traveltimeservice | Writable Primitives: 0x7f12e9097000 .. 0x7f12e91fa858 traveltimeservice | Writable References: 0x7f12e91fa870 .. 0x7f12e9596ef0] traveltimeservice | traveltimeservice | traveltimeservice | [Heap: traveltimeservice | [Young generation: traveltimeservice | [youngSpace: traveltimeservice | aligned: 0/0 unaligned: 0/0]] traveltimeservice | [Old generation: traveltimeservice | [fromSpace: traveltimeservice | aligned: 0/0 unaligned: 0/0] traveltimeservice | [toSpace: traveltimeservice | aligned: 0/0 unaligned: 0/0] traveltimeservice | ] traveltimeservice | [Unused: traveltimeservice | aligned: 0/0]] traveltimeservice | traveltimeservice | Fatal error: StackOverflowError: Enabling the yellow zone of the stack did not make any stack space available. Possible reasons for that: 1) A call from native code to Java code provided the wrong JNI environment or the wrong IsolateThread; 2) Frames of native code filled the stack, and now there is not even enough stack space left to throw a regular StackOverflowError; 3) An internal VM error occurred.