From the GraalVM examples, they have code like this to run a single line of Python code:
context.eval("python", "\nprint('Hello polyglot world Python!');");
Yes that works fine in a Java program.
I can also run a Python program from the command line using the "graalpython" program.
My question is how do I run a python program from the Java example I mentioned above?
context.eval("python", "\nprint('Hello polyglot world Python!');");
I tried using the "file:" argument, but that didn't work or I'm doing something wrong.
For example, this did not work:
context.eval("python", "file: /path_to_python/test.py");
This line of code gives me:
Original Internal Error:
java.lang.RuntimeException: not implemented
So, maybe that answers my question, but I have to believe you can run a python script from a GRAAL program like you can a single line of code. Hence, this posting.
--
Is running a python program from within a Java program using graal "eval" supported? If so, I would very much appreciate an example of usage.
Thanks very much.
You need to build a Source object in order to eval a file:
File file = new File("/path_to_python/test.py");
Source source = Source.newBuilder("python", file).build();
context.eval(source);
Related
I'm trying to write a simple machine learning application in Ada, and also trying to find a good framework to use. My knowledge of one thing is extremely minimal, and of the other is somewhat minimal.
There are several nifty machine learning frameworks out there, and I'd like to leverage one for use with an Ada program, but I guess I'm just...at a loss. Can I use an existing framework written in Python, for instance and wrap (or I guess, bind?) the API calls in Ada? Should I just pass off the scripting capabilities? I'm trying to figure it out.
Case in point: Scikit (sklearn)
https://scikit-learn.org/stable/tutorial/text_analytics/working_with_text_data.html#
This does some neat stuff, and I'd like to be able to leverage this, but with an Ada program. Does anyone have advice from a similar experience?
I am just researching, so I have tried finding information.
http://www.inspirel.com/articles/Ada_Python_Binding.html
https://scikit-learn.org/stable/tutorial/text_analytics/working_with_text_data.html#
The inspirel solution is based on python2.7. If you're using anything from python3.5 onwards a few mods need to be made. On Linux, changing to say python 3.7, you'd just change
--for Default_Switches ("Ada") use ("-lpython2.7");
for Default_Switches ("Ada") use ("-lpython3.7");
but on windows, the libraries aren't dumped in a community lib so gnat doesn't know where to find them. All the packages are kept separately. The -L has to be added to tell the linker where to find the library. Alternatively, you can use for lib_dir. In my case, I did a non-admin install of python, so it looks something like
for Default_Switches ("Ada") use ("-L\Users\StdUser\AppData\Local\Programs\Python\Python37-32\libs", "-lpython37");
Note that on windows, the library is called python37: not python3.7. Use gprbuild instead of gnatmake -p, which has been deprecated. If you do all your mods correctly
gprbuild ada_main.gpr
should give you an executable in obj\ada_main.exe if it builds. If a later version of python is used, some edits need to be made
python_module.py
#print 'Hello from Python module'
print('Hello from Python module')
#print 'Python adding:', a, '+', b
print('Python adding:', a, '+', b)
ada_main.adb
-- Python.Execute_String("print 'Hello from Python!'");
Python.Execute_String("print('Hello from Python!')");
Some routines have been deprecated so the linkage has to change
python.adb
--pragma Import(C, PyInt_AsLong, "PyInt_AsLong");
pragma Import(C, PyInt_AsLong, "PyLong_AsLong");
--pragma Import(C, PyString_FromString, PyString_FromString");
pragma Import(C, PyString_FromString, "PyUnicode_FromString");
Running the build and executable should give
C:\Users\StdUser\My Documents\ada-python>gprbuild ada_main.gpr
Compile
[Ada] ada_main.adb
Bind
[gprbind] ada_main.bexch
[Ada] ada_main.ali
Link
[link] ada_main.adb
C:\Users\StdUser\My Documents\ada-python>obj\ada_main.exe
executing Python directly from Ada:
Hello from Python!
loading external Python module and calling functions from that module:
Hello from Python module!
asking Python to add two integers:
Python adding: 10 + 2
Ada got result from Python: 12
we can try other operations, too:
subtract: 8
multiply: 20
divide : 5
Remember to put the pythonxx.dll somewhere on your path otherwise it won't be able to find the library when it starts executing.
I would like to visualize pointcloud in drake-visualizer using python binding.
I imitated how to publish images through lcm from here, and checked out these two issues (14985, 14991). The snippet is as follows :
point_cloud_to_lcm_point_cloud = builder.AddSystem(PointCloudToLcm())
point_cloud_to_lcm_point_cloud.set_name('pointcloud_converter')
builder.Connect(
station.GetOutputPort('camera0_point_cloud'),
point_cloud_to_lcm_point_cloud.get_input_port()
)
point_cloud_lcm_publisher = builder.AddSystem(
LcmPublisherSystem.Make(
channel="DRAKE_POINT_CLOUD_camera0",
lcm_type=lcmt_point_cloud,
lcm=None,
publish_period=0.2,
# use_cpp_serializer=True
)
)
point_cloud_lcm_publisher.set_name('point_cloud_publisher')
builder.Connect(
point_cloud_to_lcm_point_cloud.get_output_port(),
point_cloud_lcm_publisher.get_input_port()
)
However, I got the following runtime error:
RuntimeError: DiagramBuilder::Connect: Mismatched value types while connecting output port lcmt_point_cloud of System pointcloud_converter (type drake::lcmt_point_cloud) to input port lcm_message of System point_cloud_publisher (type drake::pydrake::Object)
When I set 'use_cpp_serializer=True', the error becomes
LcmPublisherSystem.Make(
File "/opt/drake/lib/python3.8/site-packages/pydrake/systems/_lcm_extra.py", line 71, in _make_lcm_publisher
serializer = _Serializer_[lcm_type]()
File "/opt/drake/lib/python3.8/site-packages/pydrake/common/cpp_template.py", line 90, in __getitem__
return self.get_instantiation(param)[0]
File "/opt/drake/lib/python3.8/site-packages/pydrake/common/cpp_template.py", line 159, in get_instantiation
raise RuntimeError("Invalid instantiation: {}".format(
RuntimeError: Invalid instantiation: _Serializer_[lcmt_point_cloud]
I saw the cpp example here, so maybe this issue is specific to python binding.
I also saw this python example, but thought using 'PointCloudToLcm' might be more convenient.
P.S.
I am aware of the development in recent commits on MeshcatVisualizerCpp and MeshcatPointCloudVisualizerCpp, but I am still on the drake-dev stable build 0.35.0-1 and want to stay on drake visualizer until the meshcat c++ is more mature.
The old version in pydrake.systems.meshcat_visualizer.MeshcatVisualizer is a bit too slow on my current use-case (multiple objects drop). I can visualize the pointcloud with this visualization setting, but it took too much machine resources.
Only the message types that are specifically bound in lcm_py_bind_cpp_serializers.cc can be used on an LCM message input/output port connection between C++ and Python. For all other LCM message types, the input/output port connection must be from a Python system to a Python system or a C++ System to a C++ System.
The lcmt_image_array is listed there, but not the lcmt_point_cloud.
If you're stuck using Drake's v0.35.0 capabilities, then I don't see any great solutions. Some options:
(1) Write your own PointCloudToLcm system in Python (by re-working the C++ code into Python, possibly with a narrower set of supported features / channels for simplicity).
(2) Write your own small C++ helper function MakePointCloudPublisherSystem(...) that calls LcmPublisherSystem::Make<lcmt_point_cloud> function in C++, and bind it into Python. Then your Python code can call MakePointCloudPublisherSystem() and successfully connect that to the existing C++ PointCloudToLcm.
I'm fresh to python/biopython and tried blast using biopython like this:
from Bio.Blast import NCBIWWW
fasta_string = open("C:\\xxxx\\xxxx\\xxxx\\abc.fasta").read()
result_handle = NCBIWWW.qblast("blastp", "nr", fasta_string)
print result_handle.read()
I was wondering if it is possible to run igblast using biopython. I have searched for this but it seems no one is really doing this.
I haven't tried them, but I have found:
pyigblast.
PyIgBlast - Open source Parser to call IgBlast and parse results for
high-throughput sequencing. Uses Python multi-processing to get around
bottlenecks of IgBlast multi-threading. Parses blast output to
deliminated files (csv,json) for uploading to databases. Can connect
directly with mysql and mongo instances to insert directly.
The code uses Python 2.7 and BioPython.
PyIR
Immunoglobulin and T-Cell receptor rearrangement software. A Python wrapper for IgBLAST that scales to allow for the parallel processing of millions of reads on shared memory computers. All output is stored in a convenient JSON format.
The code uses Python 3.6 and BioPython.
Both tools use a locally installed igblastn executable. You can install igblastn locally with conda install igblast.
I'm trying to execute a simple erlang program of adding two numbers.
I'm trying to do this in Eclipse on Ubuntu 10.04 LTS.
When i execute this program, I'm getting the error as shown below:
** exception error: undefined function add:addfunc/0
How do i go about solving this error? Thanks in advance.
This program when executed in the erlang shell is working fine. But when it comes to eclipse it's giving me this error. Not this, any program for that matter is giving me the similar error. Guess I would be missing something about the eclipse configuration.
EDIT:
Anyways, This is the sample add program,
-module(add).
-export([addfunc/0]).
addfunc() ->
5 + 6.
This message tells you that module add doesn't have an exported function addfunc/0.
Ensure the function you want to be called has exactly that name, doesn't expect any
parameters, is
exported, the module is
compiled, the search path includes the compiled beam file and that there is no module clashes using code:clash()
Update
It's not clear how erlide (eclipse erlang plug-in you seem to use) compiles and runs a program. Try to compile source using erlc or inside erl shell. That way you'll have much easier controllable environment and you'll better understand what's going on.
I got exactly the same problem -for a tail recursive fibonacci function- below:
-module(math2).
-export([fibonacci/1]).
fibonacci(0) -> 0;
fibonacci(1) -> 1;
fibonacci(M) -> fibonacci(M-1) + fibonacci(M-2).
In the end, had realized that this is a compile-time exception. Then, have opened a new tab on my shell and tried with erlc, instead of erl.
$ erlc math2.erl
Now I am also able to see math2.beam file created.
Called fibonacci with 10:
4> math2:fibonacci(10).
55
and it worked!
I think you have not compiled the code and you are trying to run the program.
In eclipse, using the "Run" icon, trigger the run; which will get you to the erl shell in the console window.
There you do -
cd("C:\Learning_ERL\src").
And you should see output like-
(Learning-ERL#DALAKSHM-MNFSM)7> cd("C:\Learning_ERL\src").
c:/Learning_ERL/src
ok
Then compile the code -
c(add)
you should see something like this on the erl shell-
(Learning-ERL#DALAKSHM-MNFSM)10> c(add).
{ok,add}
Now you should be seeing a new file called - add.beam in the same directory as that of your erl source file - add.erl
add.beam is a bytecode file
Now you should be able to run the program without any error
How do you try to execute your code?
In your editor, right-click and choose "Run as"->"Erlang application". The VM that is launched will have your project loaded automatically and when editing/saving a file it will get reloaded. When launching, a console appears and you can call your code from there.
If it still doesn't work, what message do you get for m(add).?
I'm using the Pascal FC implementation for Windows Vista found on http://www-users.cs.york.ac.uk/burns/pf.html
I'm trying to run the dining philophers problem found on the link but I don't get how to make the compiler work.
Screenshot
In the screen shot, the program appears to be waiting for you to enter the name of the file to use for the compiler output. Enter a file name.
Better yet, use the pfc.bat command and let it choose the output names for you. The batch file will also run the program automatically after it has been compiled. At the command prompt, run the command like this:
C:\pascalfc-vista> pfc philchan.pas