File not found error on Windows 10: setup script problem?

[jcrozum]

I cannot get this to work; I get a FileNotFoundError. Here is an example.

PS C:\Users\jcroz\models> python
Python 3.7.9 (tags/v3.7.9:13c94747c7, Aug 17 2020, 16:30:00) [MSC v.1900 64 bit (AMD64)] on win32
Type "help", "copyright", "credits" or "license" for more information.
>>> import stablemotifs
>>> sm = stablemotifs.load("test2.txt")
Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\jcroz\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\stablemotifs\__init__.py", line 112, in load
    stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
  File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.7_3.7.2544.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 800, in __init__
    restore_signals, start_new_session)
  File "C:\Program Files\WindowsApps\PythonSoftwareFoundation.Python.3.7_3.7.2544.0_x64__qbz5n2kfra8p0\lib\subprocess.py", line 1207, in _execute_child
    startupinfo)
FileNotFoundError: [WinError 2] The system cannot find the file specified
>>> quit()
PS C:\Users\jcroz\models> cat test2.txt
xA*= xB
xB*= xA
xC*= xA or not xD
xD*= xC
xE*= xB and xF
xF*= xE

I installed via pip and the setup script output is

PS C:\Users\jcroz\AppData\Roaming> python -m stablemotifs_setup
# checking for stablemotifs
# installing colomoto/stablemotifs in C:\Users\jcroz\AppData\Roaming
downloading http://api.anaconda.org/download/colomoto/stablemotifs/1/noarch/stablemotifs-1-1.tar.bz2
installing C:\Users\jcroz\AppData\Roaming\opt/StableMotifs/README.TXT
installing C:\Users\jcroz\AppData\Roaming\opt/StableMotifs/lib/QuineMcCluskeyAlgorithm.jar
installing C:\Users\jcroz\AppData\Roaming\opt/StableMotifs/lib/FileClasses.jar
installing C:\Users\jcroz\AppData\Roaming\opt/StableMotifs/lib/JohnsonCycleAlgorithm.jar
installing C:\Users\jcroz\AppData\Roaming\opt/StableMotifs/StableMotifs.jar
installing C:\Users\jcroz\AppData\Roaming\opt/StableMotifs/lib/jgrapht-jdk1.6.jar
installing C:\Users\jcroz\AppData\Roaming\bin/StableMotifs

However, the supposedly installed files listed do not exist:

PS C:\Users\jcroz\AppData\Roaming> ls | grep opt
PS C:\Users\jcroz\AppData\Roaming> ls | grep bin
PS C:\Users\jcroz\AppData\Roaming> ls | grep StableMotifs
PS C:\Users\jcroz\AppData\Roaming>

[pauleve]

Thanks for the report. Looks like a windows specific issue..
I've updated the helper script, can you try with it?
You need to install the git colomoto_jupyter beforehand:

pip install --user https://github.com/colomoto/colomoto-jupyter/archive/refs/heads/master.zip

and retry stablemotifs_setup (after git pull)

[jcrozum]

Sorry for the slow reply. I have been doing some testing with Jorge to figure out what's going on with his Java version of stable motifs. I did try this again, and I get a different error now that I am pretty sure this has to do with deprecated Java functions in the stable motifs Java code and not anything with this Python interface. Here is the output:

Filename: SmallTest.txt
Creating Boolean table directory: SmallTest
Exception in thread "main" java.lang.NullPointerException: Cannot invoke "javax.script.ScriptEngine.eval(String)" because "engine" is null
        at stablemotifs.OtherMethods.EvalStr(OtherMethods.java:235)
        at stablemotifs.ReadWriteFiles.createTablesFromBooleanRules(ReadWriteFiles.java:254)
        at stablemotifs.Main.main(Main.java:69)

Traceback (most recent call last):
  File "<stdin>", line 1, in <module>
  File "C:\Users\jcroz\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\stablemotifs\__init__.py", line 122, in load
    return StableMotifsResult(wd, model_name, fixed)
  File "C:\Users\jcroz\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\stablemotifs\results.py", line 23, in __init__
    self.attractors = self._parse_attractors()
  File "C:\Users\jcroz\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\stablemotifs\results.py", line 30, in _parse_attractors
    df = pd.read_csv(inputf, sep='\t', index_col=-1) #index_col=-1 we cheat by making the extra tabs at the end of the rows in the files as the index column, and then resetting it to just natural incrementing integers
  File "C:\Users\jcroz\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\pandas\io\parsers.py", line 676, in parser_f
    return _read(filepath_or_buffer, kwds)
  File "C:\Users\jcroz\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\pandas\io\parsers.py", line 448, in _read
    parser = TextFileReader(fp_or_buf, **kwds)
  File "C:\Users\jcroz\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\pandas\io\parsers.py", line 880, in __init__
    self._make_engine(self.engine)
  File "C:\Users\jcroz\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\pandas\io\parsers.py", line 1114, in _make_engine
    self._engine = CParserWrapper(self.f, **self.options)
  File "C:\Users\jcroz\AppData\Local\Packages\PythonSoftwareFoundation.Python.3.7_qbz5n2kfra8p0\LocalCache\local-packages\Python37\site-packages\pandas\io\parsers.py", line 1891, in __init__
    self._reader = parsers.TextReader(src, **kwds)
  File "pandas\_libs\parsers.pyx", line 374, in pandas._libs.parsers.TextReader.__cinit__
  File "pandas\_libs\parsers.pyx", line 674, in pandas._libs.parsers.TextReader._setup_parser_source
FileNotFoundError: [Errno 2] File C:\Users\jcroz\AppData\Local\Temp\StableMotifs-vcbxch1m\SmallTest-QuasiAttractors.txt does not exist: 'C:\\Users\\jcroz\\AppData\\Local\\Temp\\StableMotifs-vcbxch1m\\SmallTest-QuasiAttractors.txt'

I strongly suspect this is due to Java dropping Nashorn support in JRE/JDK 15. There is an update in the Java stable motifs readme about this: https://github.com/jgtz/StableMotifs. I've been able to work around this by changing the Python Java calls to point to an older JDK version, i.e.,

java_path = "<path to old Java version>\\bin\\java.exe"
jar_path = "<path to stable motifs Java directory>\\dist\\StableMotifs.jar"

def run_stable_motifs(filepath):
    wd = tempfile.mkdtemp(prefix="StableMotifs-")
    def cleanup():
        shutil.rmtree(wd)
    atexit.register(cleanup)

    shutil.copy(filepath, wd)
    base = os.path.basename(filepath)

    argv = [java_path,'-jar',jar_path, base]
    proc = subprocess.Popen(argv, cwd=wd,stdout=subprocess.PIPE, stderr=subprocess.STDOUT)
    result = proc.communicate()
   .
   .
   .

I got this to work with JDK 8 without warnings, but in principle, any version before 15 should work (potentially with lots of warnings about impending deprecation).