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jupyter support, fast transfer

Python Gateway for InterSystems Data Platforms.

PythonGateway

Python Gateway for InterSystems Data Platforms. Execute Python code and more from InterSystems IRIS. This projects brings you the power of Python right into your InterSystems IRIS environment:

  • Execute arbitrary Python code
  • Seamlessly transfer data from InterSystems IRIS into Python
  • Build intelligent Interoperability business processes with Python Interoperability Adapter
  • Save, examine, modify and restore Python context from InterSystems IRIS

Webinar - AI Robotization

Machine Learning (ML) Toolkit - a set of extensions to implement machine learning and artificial intelligence on the InterSystems IRIS Data Platform. As part of our webinar, we plan to present an approach to the robotization of these tasks, i.e. to ensure their autonomous adaptive execution proceeds within the parameters and rules you specify. Self-learning neural networks, self-monitoring analytical processes, agency of analytical processes are the main subjects of this webinar.

Webinar is aimed at both experts in Data Science, Data Engineering, Robotic Process Automation - and those who just discover the world of artificial intelligence and machine learning.

We are waiting for you at our event!

The language of the webinar is Russian.

Date: 18 September, 10:00 – 11:00 (GMT+3).

Register.

ML Toolkit user group

ML Toolkit user group is a private GitHub repository set up as part of InterSystems corporate GitHub organization. It is addressed to the external users that are installing, learning or are already using ML Toolkit components. To join ML Toolkit user group, please send a short e-mail at the following address: MLToolkit@intersystems.com and indicate in your e-mail the following details (needed for the group members to get to know and identify you during discussions):

  • GitHub username
  • Full Name (your first name followed by your last name in Latin script)
  • Organization (you are working for, or you study at, or your home office)
  • Position (your actual position in your organization, or “Student”, or “Independent”)
  • Country (you are based in)

Installation

  1. Install Python 3.6.7 64 bit (other Python versions will not work due to ABI incompatibility).
  2. Install dill module: pip install dill (required for context harvesting)
  3. Download latest PythonGateway release and unpack it.
  4. From the InterSystems IRIS terminal, load ObjectScript code. To do that execute: do $system.OBJ.ImportDir("/path/to/unpacked/pythongateway","*.cls","c",,1)) in Production (Ensemble-enabled) namespace. In case you want to Production-enable namespace call: write ##class(%EnsembleMgr).EnableNamespace($Namespace, 1).
  5. Place callout DLL/SO/DYLIB in the bin folder of your InterSystems IRIS installation. Library file should be placed into a path returned by write ##class(isc.py.Callout).GetLib().

Windows

  1. Check that your PYTHONHOME environment variable points to Python 3.6.7.
  2. Check that your SYSTEM PATH environment variable has:
  • %PYTHONHOME% variable (or directory it points to)
  • %PYTHONHOME%\Scripts directory
  1. In the InterSystems IRIS Terminal, run:
  • write $SYSTEM.Util.GetEnviron("PYTHONHOME") and verify it prints out the directory of Python installation
  • write $SYSTEM.Util.GetEnviron("PATH") and verify it prints out the directory of Python installation and Scripts folder inside Python installation.

Linux

  1. Check that your SYSTEM PATH environment variable has /usr/lib and /usr/lib/x86_64-linux-gnu, preferably at the beginning. Use /etc/environment file to set environment variables.
  2. In cause of errors check Troubleshooting section undefined symbol: _Py_TrueStruct and specify PythonLib property.

Mac

  1. Only python 3.6.7 from Python.org. is currently supported. Check PATH variable.

If you modified environment variables restart your InterSystems product.

Docker

  1. To build docker image:
  • Copy iscpython.so into repository root (if it's not there already)
  • Execute in the repository root docker build --force-rm --tag intersystemscommunity/irispy:latest . By default the image is built upon store/intersystems/iris:2019.3.0.302.0-community image, however you can change that by providing IMAGE variable. To build from InterSystems IRIS Community Edition execute: docker build --build-arg IMAGE=store/intersystems/iris:2019.3.0.302.0-community --force-rm --tag intersystemscommunity/irispy:latest .
  1. To run docker image execute (key is not needed for Community based images):
docker run -d \
  -p 52773:52773 \
  -v /<HOST-DIR-WITH-iris.key>/:/mount \
  --name irispy \
  intersystemscommunity/irispy:latest \
  --key /mount/iris.key \
  1. Test process isc.py.test.Process saves image artifact into temp directory. You might want to change that path to a mounted directory. To do that edit annotation for Correlation Matrix: Graph call, specifying valid filepath for f.savefig function.
  2. For terminal access execute: docker exec -it irispy sh.
  3. Access SMP with SuperUser/SYS or Admin/SYS user/password.
  4. To stop container execute: docker stop irispy && docker rm --force irispy.

Use

  1. Call: set sc = ##class(isc.py.Callout).Setup() once per systems start (add to ZSTART: docs, sample routine available in rtn folder).
  2. Call main method (can be called many times, context persists): write ##class(isc.py.Main).SimpleString(code, variable, , .result)
  3. Call: set sc = ##class(isc.py.Callout).Finalize() to free Python context.
  4. Call: set sc = ##class(isc.py.Callout).Unload() to free callout library.
set sc = ##class(isc.py.Callout).Setup() 
set sc = ##class(isc.py.Main).SimpleString("x='HELLO'", "x", , .x)
write x
set sc = ##class(isc.py.Callout).Finalize()
set sc = ##class(isc.py.Callout).Unload()

Terminal API

Generally the main interface to Python is isc.py.Main. It offers these methods (all return %Status), which can be separated into three categories:

  • Code execution
  • Data transfer
  • Auxiliary

Code execution

These methods allow execution of arbitrary Python code:

  • ImportModule(module, .imported, .alias) - import module with alias.
  • SimpleString(code, returnVariable, serialization, .result) - for cases where both code and variable are strings.
  • ExecuteCode(code, variable) - execute code (it may be a stream or string), optionally set result into variable.
  • ExecuteFunction(function, positionalArguments, keywordArguments, variable, serialization, .result) - execute Python function or method, write result into Pyhton variable, return chosen serialization in result.
  • ExecuteFunctionArgs(function, variable, serialization, .result, args...) - execute Python function or method, write result into Pyhton variable, return chosen serialization in result. Builds positionalArguments and keywordArguments and passes them to ExecuteFunction. It's recommended to use ExecuteFunction. More information in Gateway docs.

Data Transfer

Transfer data into and from Python.

Python -> InterSystems IRIS

  • GetVariable(variable, serialization, .stream, useString) - get serialization of variable in stream. If useString is 1 and variable serialization can fit into string then string is returned instead of the stream.
  • GetVariableJson(variable, .stream, useString) - get JSON serialization of variable.
  • GetVariablePickle(variable, .stream, useString, useDill) - get Pickle (or Dill) serialization of variable.

InterSystems IRIS -> Python

  • ExecuteQuery(query, variable, type, namespace) - create resultset (pandas dataframe or list) from sql query and set it into variable. isc.py package must be available in namespace.
  • ExecuteGlobal(global, variable, type, start, end, mask, labels, namespace) - transfer global data (from start to end) to Python variable of type: list of tuples or pandas dataframe. For mask and labels arguments specification check class docs and Data Transfer docs.
  • ExecuteClass(class, variable, type, start, end, properties, namespace) - transfer class data to Python list of tuples or pandas dataframe. properties - comma-separated list of properties to form dataframe from. * and ? wildcards are supported. Defaults to * (all properties). %%CLASSNAME property is ignored. Only stored properties can be used.
  • ExecuteTable(table, variable, type, start, end, properties, namespace) - transfer table data to Python list of tuples or pandas dataframe.

ExecuteQuery is universal (any valid SQL query would be transfered into Python). ExecuteGlobal and its wrappers ExecuteClass and ExecuteTable, however, operate with a number of limitations. But they are much faster (3-5 times faster than ODBC driver and 20 times faster than ExecuteQuery). More information in Data Transfer docs.

Auxiliary

Support methods.

  • GetVariableInfo(variable, serialization, .defined, .type, .length) - get info about variable: is it defined, type and serialized length.
  • GetVariableDefined(variable, .defined) - is variable defined.
  • GetVariableType(variable, .type) - get variable FQCN.
  • GetStatus() - returns last occurred exception in Python and clears it.
  • GetModuleInfo(module, .imported, .alias) - get module alias and is it currently imported.
  • GetFunctionInfo(function, .defined, .type, .docs, .signature, .arguments) - get function information.

Possible Serializations:

  • ##class(isc.py.Callout).SerializationStr - Serialization by str() function
  • ##class(isc.py.Callout).SerializationRepr - Serialization by repr() function

Shell

To open Python shell: do ##class(isc.py.util.Shell).Shell(). To exit press enter.

Context persistence

Python context can be persisted into InterSystems IRIS and restored later on. There are currently three public functions:

  • Save context: set sc = ##class(isc.py.data.Context).SaveContext(.context, maxLength, mask, verbose) where maxLength - maximum length of saved variable. If variable serialization is longer than that, it would be ignored. Set to 0 to get them all, mask - comma separated list of variables to save (special symbols * and ? are recognized), verbose specifies displaying context after saving, and context is a resulting Python context. Get context id with context.%Id()
  • Display context: do ##class(isc.py.data.Context).DisplayContext(id) where id is an id of a stored context. Leave empty to display current context.
  • Restore context: do ##class(isc.py.data.Context).RestoreContext(id, verbose, clear) where clear kills currently loaded context if set to 1.

Context is saved into isc.py.data package and can be viewed/edited by SQL and object methods. Currently modules, functions and variables are saved.

Interoperability adapter

Interoperability adapter isc.py.ens.Operation offers ability to interact with Python process from Interoperability productions. Currently five requests are supported:

  • Execute Python code via isc.py.msg.ExecutionRequest. Returns isc.py.msg.ExecutionResponse with requested variable values
  • Execute Python code via isc.py.msg.StreamExecutionRequest. Returns isc.py.msg.StreamExecutionResponse with requested variable values. Same as above, but accepts and returns streams instead of strings.
  • Set dataset from SQL Query with isc.py.msg.QueryRequest. Returns Ens.Response.
  • Set dataset faster from Global/Class/Table with isc.py.msg.GlobalRequest/isc.py.msg.ClassRequest/isc.py.msg.TableRequest. Returns Ens.Response.
  • Save Python context via isc.py.msg.SaveRequest. Returns Ens.StringResponse with context id.
  • Restore Python context via isc.py.msg.RestoreRequest.

Check request/response classes documentation for details.

Settings:

  • Initializer - select a class implementing isc.py.init.Abstract. It can be used to load functions, modules, classes and so on. It would be executed at process start.
  • PythonLib - (Linux only) if you see loading errors set it to libpython3.6m.so or even to a full path to the shared library.

Note: isc.py.util.BPEmulator class is added to allow easy testing of Python Interoperability business processes. It can execute business process (python parts) in a current job.

Variable substitution

All business processes inheriting from isc.py.ens.ProcessUtils can use GetAnnotation(name) method to get value of activity annotation by activity name. Activity annotation can contain variables which would be calculated on ObjectScript side before being passed to Python. This is the syntax for variable substitution:

  • ${class:method:arg1:...:argN} - execute method
  • #{expr} - execute ObjectScript code

Check test isc.py.test.Process business process for example in Correlation Matrix: Graph activity: f.savefig(r'#{process.WorkDirectory}SHOWCASE${%PopulateUtils:Integer:1:100}.png')

In this example:

  • #{process.WorkDirectory} returns WorkDirectory property of process object which is an instance of isc.py.test.Process class and current business process.
  • ${%PopulateUtils:Integer:1:100} calls Integer method of %PopulateUtils class passing arguments 1 and 100, returning random integer in range 1...100.

Test Business Process

Along with callout code and Interoperability adapter there's also a test Interoperability Production and test Business Process. To use them:

  1. In OS bash execute pip install pandas matplotlib seaborn.
  2. Execute: do ##class(isc.py.test.CannibalizationData).Import() to populate test data.
  3. In test Business Process isc.py.test.Process edit annotation for Correlation Matrix: Graph call, specifying valid filepath for f.savefig function.
  4. Save and compile business process.
  5. Start isc.py.test.Production production.
  6. Send empty Ens.Request message to the isc.py.test.Process.

Note: instead of step 3 run: set sc = ##class(isc.py.util.Installer).ConfigureTestProcess(user, password, host, port, namespace) to try adjust process automatically.

Notes

  • If you want to use ODBC connection, on Windows install pyodbc: pip install pyodbc, on Linux install: apt-get install unixodbc unixodbc-dev python-pyodbc.
  • If you want to use JDBC connection, install JayDeBeApi: pip install JayDeBeApi. On Linux you might need to install: apt-get install python-apt beforehand.
  • If you get errors similar to undefined symbol: _Py_TrueStruct in isc.py.ens.Operationoperation set setting PythonLib to libpython3.6m.so or even to a full path of the shared library.
  • In test Business Process isc.py.test.Process edit annotation for ODBC or JDBC calls, specifying correct connection string.
  • In production, for the sample business process isc.py.test.Process set ConnectionType setting to a preferred connection type (defaults to RAW, change only if you need to test xDBC connectivity).

Unit tests

To run tests execute:

set repo = ##class(%SourceControl.Git.Utils).TempFolder()
set ^UnitTestRoot = ##class(%File).SubDirectoryName(##class(%File).SubDirectoryName(##class(%File).SubDirectoryName(repo,"isc"),"py"),"unit",1)
set sc = ##class(%UnitTest.Manager).RunTest(,"/nodelete")

ZLANGC00

Install ZLANG routine from rtn folder to add zpy command:

zpy "import random"
zpy "x=random.random()"
zpy "x"
>0.4157151243124494

Argumentless zpy command opens python shell.

Jupyter

Check jupyter folder for details on how to run Jupyter with PythonGateway.

Limitations

There are several limitations associated with the use of PythonAdapter.

  1. Modules reinitialization. Some modules may only be loaded once during process lifetime (i.e. numpy). While Finalization clears the context of the process, repeated load of such libraries terminates the process. Discussions: 1, 2.
  2. Variables. Do not use these variables: zzz* variables. Please report any leakage of these variables. System code should always clear them.
  3. Functions Do not redefine zzz*() functions.
  4. Context persistence. Only pickled/dill variables could be restored correctly. Module imports are supported.

Development

Development of ObjectScript is done via cache-tort-git in UDL mode. Development of C code is done in Eclipse.

Commits

Commits should follow the pattern: moule: description issue. List of modules:

  • Callout - C and ObjectScript callout interface in isc.py.Callout.
  • API - terminal API, mainly isc.py.Main.
  • Gateway - proxy classes generation.
  • Proxyless Gateway - isc.py.gw.DynamicObject class.
  • Interoperability - support utilities for Interoperability Business Processes.
  • Tests - unit tests and test production.
  • Docker - containers.
  • Docs - documentation.

Building

Windows

  1. Install MinGW-w64 you'll need make and gcc.
  2. Rename mingw32-make.exe to make.exe in mingw64\bin directory.
  3. Set GLOBALS_HOME environment variable to the root of Caché or Ensemble installation.
  4. Set PYTHONHOME environment variable to the root of Python3 installation. Usually C:\Users\<User>\AppData\Local\Programs\Python\Python3<X>
  5. Open MinGW bash (mingw64env.cmd or mingw-w64.bat).
  6. In <Repository>\c\ execute make.

Linux

It's recommended to use Linux OS which uses python3 by default, i.e. Ubuntu 18.04.1 LTS. Skip steps 1 and maybe even 2 if your OS has python 3.6 as default python (python3 --version or python --version or python3.6 --version).

  1. Add Python 3.6 repo: add-apt-repository ppa:jonathonf/python-3.6 and apt-get update
  2. Install: apt install python3.6 python3.6-dev libpython3.6-dev build-essential
  3. Set GLOBALS_HOME environment variable to the root of Caché or Ensemble installation.
  4. Set environment variable PYTHONVER to the python version you want to build, i.e.: export PYTHONVER=3.6
  5. In <Repository>/c/ execute make.

Mac OS X

  1. Install Python 3.6 and gcc compiler.
  2. Set GLOBALS_HOME environment variable to the root of Caché or Ensemble installation.
  3. Set environment variable PYTHONVER to the python version you want to build, i.e.: export PYTHONVER=3.6
  4. In <Repository>/c/ execute:
gcc -Wall -Wextra -fpic -O3 -fno-strict-aliasing -Wno-unused-parameter -I/Library/Frameworks/Python.framework/Versions/${PYTHONVER}/Headers -I${GLOBALS_HOME}/dev/iris-callin/include -c -o iscpython.o iscpython.c

gcc -dynamiclib -L/Library/Frameworks/Python.framework/Versions/${PYTHONVER}/lib -L/usr/lib -lpython${PYTHONVER}m -lpthread -ldl -lutil -lm -Xlinker iscpython.o -o iscpython.dylib

If you have a Mac please update makefile so we can build Mac version via Make.

Troubleshooting

<DYNAMIC LIBRARY LOAD> exception

  1. Check that OS has correct python installed. Open python, execute this script:
import sys
sys.version

The result should contain: Python 3.6.7 and 64 bit. If it's not, install Python 3.6.7 64 bit.

  1. Check OS-specific installation steps. Make sure that path relevant for InterSystems IRIS (usually system) contains Python installation.

  2. Make sure that InterSystems IRIS can access Python installation.

Module not found error

Sometimes you can get module not found error. Here's how to fix it. Each step constitutes a complete solution so restart IRIS and check that the problem is fixed.

  1. Check that OS bash and IRIS use the same python. Open python, execute this script from both, they should be the same.
import sys
ver=sys.version
ver

If they are not the same search for a Python executable that is actually used by InterSystems IRIS.

  1. Check that module is, in fact, installed. Open OS bash, execute python (maybe python3 or python36 on Linux) and inside opened python bash execute import <module>. If it fails with some error run in OS bash pip install <module>. Note that module name for import and module name for pip could be different.
  2. If you're sure that module is installed, compare paths used by python (it's not system path). Get path with:
import sys
path=sys.path
path

They should be the same. If they are not the same read how PYTHONPATH (python) is formed here and adjust your OS environment to form pythonpath (python) correctly, i.e. set PYTHONPATH (system) env var to C:\Users\<USER>\AppData\Roaming\Python\Python36\site-packages or other directories where your modules reside (and other missing directories). 4. Compare python paths again and they are not the same or the problem persists add missing paths explicitly to the isc.py.ens.Operation init code (for interoperability) and on process start (for Callout wrapper):

do ##class(isc.py.Main).SimpleString("import sys")
do ##class(isc.py.Main).SimpleString("sys.path.append('C:\\Users\\<USER>\\AppData\\Roaming\\Python\\Python36\\site-packages')")

undefined symbol: _Py_TrueStruct or similar errors

  1. Check ldconfig and adjust it to point to the directory with Python shared library.
  2. If it fails:
    • For interoperability in isc.py.ens.Operation operation set setting PythonLib to libpython3.6m.so or even to a full path of the shared library.
    • For Callout wrapper on process start call do ##class(isc.py.Callout).Initialize("libpython3.6m.so") alternatively pass a full path of the shared library.

PyODBC on Linux and Mac

  1. Install unixodbc: apt-get install unixodbc-dev
  2. Install PyODBC: pip install pyodbc
  3. Set connection string: cnxn=pyodbc.connect(('Driver=/<IRIS directory>/bin/libirisodbcu35.so;Server=localhost;Port=51773;database=USER;UID=_SYSTEM;PWD=SYS'),autocommit=True)

Some notes. Call set sc = ##class(isc.py.util.Installer).ConfigureTestProcess(user, pass, host, port, namespace) to configure test process automatically.