On this GitHub you can find all the information on how to use a HuggingFace machine learning / AI model on the IRIS Framework using python.

1. iris-huggingface

Usage of Machine Learning models in IRIS using Python; For text-to-text, text-to-image or image-to-image models.

Here, models as example :

• https://huggingface.co/gpt2

• https://huggingface.co/Jean-Baptiste/camembert-ner

• https://huggingface.co/bert-base-uncased

• https://huggingface.co/facebook/detr-resnet-50

• https://huggingface.co/facebook/detr-resnet-50-panoptic

• 1. iris-huggingface

• 2. Installation

  • 2.1. Starting the Production
  • 2.

Hi folks!

Just want to introduce you a new util to import CSV into IRIS - csvgenpy!

Install

USER>zpm "install csvgenpy"

Use:

do ##class(shvarov.csvgenpy.csv).Generate("file or url","table","schema")

Example:

USER>do ##class(shvarov.csvgenpy.csv).Generate("https://raw.githubusercontent.com/datasciencedojo/datasets/master/titanic.csv","titanic","data")

This will create table and class data.titanic in IRIS and will load the data.  you can proof it with:

USER>:sql

[SQL]USER>>select * from data.titanic

[SQL]USER>>select * from data.titanic

1. select * from data.

Let me introduce my new project, which is irissqlcli, REPL (Read-Eval-Print Loop)  for InterSystems IRIS SQL 

• Syntax Highlighting
• Suggestions (tables, functions)
• 20+ output formats
• stdin support
• Output to files 

Install it with pip

pip install irissqlcli

Or run with docker

docker run -it caretdev/irissqlcli irissqlcli iris://_SYSTEM:SYS@host.docker.internal:1972/USER

Connect to IRIS

$ irissqlcli iris://_SYSTEM@localhost:1972/USER -W
Password for _SYSTEM:
Server:  InterSystems IRIS Version 2022.3.0.606 xDBC Protocol Version 65
Version: 0.1.0
[SQL]_SYSTEM@localhost:USER> select $ZVERSION
+---------------------------------------------------------------------------------------------------------+
| Expression_1                                                                                            |
+---------------------------------------------------------------------------------------------------------+
| IRIS for UNIX (Ubuntu Server LTS for ARM64 Containers) 2022.3 (Build 606U) Mon Jan 30 2023 09:05:12 EST |
+---------------------------------------------------------------------------------------------------------+
1 row in set
Time: 0.063s
[SQL]_SYSTEM@localhost:USER> help
+----------+-------------------+------------------------------------------------------------+
| Command  | Shortcut          | Description                                                |
+----------+-------------------+------------------------------------------------------------+
| .exit    | \q                | Exit.                                                      |
| .mode    | \T                | Change the table format used to output results.            |
| .once    | \o [-o] filename  | Append next result to an output file (overwrite using -o). |
| .schemas | \ds               | List schemas.                                              |
| .tables  | \dt [schema]      | List tables.                                               |
| \e       | \e                | Edit command with editor (uses $EDITOR).                   |
| help     | \?                | Show this help.                                            |
| nopager  | \n                | Disable pager, print to stdout.                            |
| notee    | notee             | Stop writing results to an output file.                    |
| pager    | \P [command]      | Set PAGER. Print the query results via PAGER.              |
| prompt   | \R                | Change prompt format.                                      |
| quit     | \q                | Quit.                                                      |
| tee      | tee [-o] filename | Append all results to an output file (overwrite using -o). |
+----------+-------------------+------------------------------------------------------------+
Time: 0.012s
[SQL]_SYSTEM@localhost:USER>

The Jupyter Notebook is an open source web application that can be used to create and share documents that contain live text, code, equations and visualizations. It is maintained by the people at Project Jupyter.

Jupyter name comes from the core supported programming languages that it supports: Julia, Python, and R.
It allows users to write code in "cells," which are blocks of code that can be executed individually or together. This makes it easy to test and debug code, as well as to organize and present complex analyses.

Hey Community,

Watch this video to see how to connect to InterSystems Cloud Services from your Python application using the InterSystems DB-API driver interface:

⏯ Connecting to InterSystems Cloud Services with Python

Let's say you have Python including variable-length arguments methods. How can you call it from ObjectScript? 

def test1(*args):
  return sum(args)
  
def test2(**kwargs):
  a1 = kwargs.get("a1",None)
  a2 = kwargs.get("a2",None)
  return a1+a2

You can call this "a.py" from ObjectScript as below.  For **kwargs argument, create Dynamic Object in ObjectScript and put it into methods with <variablename>... (3 dots) format. 

    set a=##class(%SYS.Python).Import("a")
    write a.test1(1,2,3)   ;; 6
    set req={}
    set req.a1=10
    set req.a2=20
    write a.

Many factors affect a person's quality of life, and one of the most important is sleep. The quality of our sleep determines our ability to function during the day and affects our mental and physical health. Good quality sleep is critical to our overall health and well-being. Therefore, by analyzing indicators preceding sleep, we can determine the quality of our sleep. This is precisely the functionality of the Sheep's Galaxy application.

We have a rule to disable a user account if they have not logged in for a certain number of days. IRIS Audit database logs many events such as login failures for example. It can be configured to log successful logins as well. We have IRIS clusters with many IRIS instances. I like to run queries against audit data from ALL IRIS instances and identify user accounts which have not logged into ANY IRIS instance.

Within IRIS I defined a task to export audit data every day.

I provide some sample files in my GitHub repo.

I wrote ObjectScript code to import all files into otw.audit.consolidator class.

I want to use Python SQLAlchemy, pandas and sqlalchemy-iris (created by Dmitry Maslenikov) to copy consolidated audit data from my consolidator class in my IRIS container to my InterSystems Cloud SQL deployment.

I updated my Dockerfile to pip3 install sqlalchemy-iris and pandas (dataframes).

docker-compose build –no-cache in my personal AWS took 700 seconds.

Hi Community,
In this article, I will introduce my application iris-mlm-explainer

This web application connects to InterSystems Cloud SQL to create, train, validate, and predict ML models, make Predictions and display a dashboard of all the trained models with an explanation of the workings of a fitted machine learning model. The dashboard provides interactive plots on model performance, feature importances, feature contributions to individual predictions, partial dependence plots, SHAP (interaction) values, visualization of individual decision trees, etc.

Overview

Cross-Skilling from IRIS objectScript to Python it becomes clear there are some fascinating differences in syntax.

One of these areas was how Python returns Tuples from a method with automatic unpacking.

Effectively this presents as a method that returns multiple values. What an awesome invention :)

out1, out2 = some_function(in1, in2)

ObjectScript has an alternative approach with ByRef and Output parameters.

Do ##class(some_class).SomeMethod(.inAndOut1, in2, .out2)

Where:

• inAndOut1 is ByRef
• out2 is Output

The leading dot (".") in front of the variable name passes ByRef and for Output.

Named parameters can be achieved with SQLAlchemy :  

from sqlalchemy import create_engine, text,types,engine

_engine = create_engine('iris+emb:///')

with _engine.connect() as conn:
    rs = conn.execute(text("select :some_private_name"), {"some_private_name": 1})
    print(rs.all())

or with native api

from sqlalchemy import create_engine, text,types,engine

# set URL for SQLAlchemy
url = engine.url.URL.create('iris', username='SuperUser', password='SYS', host='localhost', port=33782, database='FHIRSERVER')

_engine = create_engine(url)

with _engine.connect() as conn:
    rs = conn.execute(text("select :some_private_name"), {"some_private_name": 1})
    print(rs.all())

If you are using Python, you can use the built-in venv module to create a virtual environment. This module is the recommended way to create and manage virtual environments.

A virtual environment is a tool that helps to keep dependencies required by different projects separate by creating isolated python virtual environments for them. It solves the “Project X depends on version 1.x but, Project Y needs 4.x” dilemma, and keeps your global site-packages directory clean and manageable.

So if like me you work a lot with Python, you can use the venv module to create a virtual environment for your project. This will allow you to install packages without affecting the global Python installation.

You will find here two neat alias to create and activate a virtual environment.

Python aliases

alias venv="python3 -m venv .venv; source .venv/bin/activate"
alias irisvenv="python3 -m venv .venv; source .venv/bin/activate; pip install https://github.com/grongierisc/iris-embedded-python-wrapper/releases/download/v0.0.3/iris-0.0.3-py3-none-any.whl"

InterSystems IRIS 2022.2 has Native SDK for Python (https://docs.intersystems.com/iris20222/csp/docbook/Doc.View.cls?KEY=PA…).

We know how to traverse a global data structure using IRIS Object Script $Order function.

SET key=""
   FOR  {
     SET key=$ORDER(^myglobal(key)) 
     QUIT:key=""
     WRITE !,^myglobal(key)
   }

How to do the same from Python using IRIS Native SDK for Python? Here is a code example:

import iris

args = {'hostname':'127.0.0.1', 'port':51772,
    'namespace':'USER', 'username':'_SYSTEM', 'password':'SYS'
    }

conn = iris.

I'm curious about how embedded Python is handled by %CSP classes, particularly in the case of defining REST endpoints on IRIS.
Here is a simple dispatch class for the endpoint /api/pythonapp on my local IRIS instance (2022.3):

Class Python.App.Dispatch Extends %CSP.REST
{

XData UrlMap [ XMLNamespace = "https://www.intersystems.com/urlmap" ]
{
<Routes>
    <Route Url="/test" Method="GET" Call="Hello" />
</Routes>
}

ClassMethod Hello() As %Status [ Language = python ]
{
    import iris

    print('Hello World!

I need connect to cache2016 database by python to get some data, but   I don' t know how to connect by python, did anyone know how to create connection？

If you can provide any python code, that will be better! 

In article

https://community.intersystems.com/print/518106

Traceback (most recent call last):
  File "c:\Users\rochesterd\PythonScripts\fhir_stuff\fhir-client-python-main\fhir-client-python-main\src\client.py", line 57, in <module>
    patient0 = Patient.parse_obj(patients_resources.search(
AttributeError: 'NoneType' object has no attribute 'serialize'

Hi Community,

This article is a continuation of my article about  Getting to know Python Flask Web Framework

In this article, we will cover the basics of topics listed below:

1. Routing in Flask Framework
2. Folder structure for a Flask app (Static and Template)
3. Getting and displaying data in the Flask application from IRIS.

So, let's begin.

Schematron is a rule-based validation language for making assertions about the presence or absence of certain patterns in XML documents. A schematron refers to a collection of one or more rules containing tests. Schematrons are written in a form of XML, making them relatively easy for everyone, even non-programmers, to inspect, understand, and write

So, I know that I can return a SQL Error message from my SQL Procedure written in ObjectScript, with code like this

$ cat <<EOF | irissqlcli iris://_SYSTEM:SYS@localhost:1972/USER
CREATE or REPLACE PROCEDURE test()
LANGUAGE OBJECTSCRIPT
{
 SET %sqlcontext.%SQLCODE = 400
 SET %sqlcontext.%ROWCOUNT = -1
 SET %sqlcontext.%Message = "test error message"
};

CALL test();

EOF
[SQLCODE: <-400>:<Fatal error occurred>]
[Location: <SPFunction>]
[%msg: <test error message>]

But I did not find how to do it with Python. I can't find %sqlcontext variable available there

Iris-python-template

Template project with various Python code to be used with InterSystems IRIS Community Edition with container.

Featuring :

• Notebooks
  • Embedded Python Kernel
  • ObjectScript Kernel
  • Vanilla Python Kernel
• Embedded Python
  • Code example
  • Flask demo
• IRIS Python Native APIs
  • Code example

2. Table of Contents

• 1. iris-python-template
• 2. Table of Contents
• 3. Installation
  • 3.1. Docker
• 4. How to start coding
  • 4.1. Prerequisites
    • 4.1.1. Start coding in ObjectScript
    • 4.1.2. Start coding with Embedded Python
    • 4.1.3. Start coding with Notebooks
• 5. What's inside the repository
  • 5.1.

Python has become the most used programming language in the world (source: https://www.tiobe.com/tiobe-index/) and SQL continues to lead the way as a database language. Wouldn't it be great for Python and SQL to work together to deliver new functionality that SQL alone cannot? After all, Python has more than 380,000 published libraries (source: https://pypi.org/) with very interesting capabilities to extend your SQL queries within Python. This article details how to create new SQL Stored Procedures in InterSystems IRIS Database using Embedded Python.

We're having a problem with the way Python modules are being cached in Iris. If we modify some code and then reimport a module it is still processing the old code.

E.g. Create a python file:

helloWorld.py

def helloWorld() :
  return "Hello world"

The run the following in the Iris terminal:

I'm trying to get started with IRIS for Health but every time I got to a step that asks me to install a .whl-package I cant continue. I'm getting an error that the file does not exist.

Here is the complete error message:

PS C:\Users\x\GIT\quickstarts-multimodel-python> pip install nativeAPI_wheel\irisnative-1.0.0-cp39-cp39m-win_amd64.whl    
WARNING: Requirement 'nativeAPI_wheel\\irisnative-1.0.0-cp39-cp39m-win_amd64.whl' looks like a filename, but the file does not exist
ERROR: irisnative-1.0.0-cp39-cp39m-win_amd64.whl is not a supported wheel on this platform.

Am I doing something wrong?

OCR DEMO

This is a demo of the OCR functionality of the pero-ocr library.

It used in the iris application server in python.

Demo

This is an example of input data :

This is the result of the OCR :

In this example you have the following information:

• The text is in the TextEquiv tag
• The confidence is in the conf attribute of the TextEquiv tag
• The coordinates of the text are in the Coords tag

<PcGts xmlns="http://schema.primaresearch.org/PAGE/gts/pagecontent/2019-07-15" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://schema.primaresearch.

ipython-iris-magic

%%iris magic for IPython, can run ObjectScript command in Notebooks

It can be run in any Notebook and does not require any special setup on IRIS or the Notebook.

Demo

Native Api

I have table

CREATE TABLE nodes (
        name VARCHAR(50) NOT NULL, 
        parent VARCHAR(50), 
        PRIMARY KEY (name), 
        FOREIGN KEY(parent) REFERENCES nodes (name) ON UPDATE cascade
);

I put some data

INSERT INTO nodes (name, parent) VALUES ('n1', NULL);
INSERT INTO nodes (name, parent) VALUES ('n11', 'n1');
INSERT INTO nodes (name, parent) VALUES ('n12', 'n1');
INSERT INTO nodes (name, parent) VALUES ('n13', 'n1');

Let's delete all

DELETE FROM nodes;

Nope, no way.

SQL Error [124] [S1000]: [SQLCODE: <-124>:<FOREIGN KEY constraint failed referential check upon DELETE of row in referenced table>]
[Location: <ServerLoop>]
[%msg: <At least 1 Row exists in table 'SQLUser.nodes' which references key 'NODESPKey2' - Foreign Key Constraint 'NODESFKey3', Field(s) 'parent' failed on referential action of NO ACTION>]

Hi Community, 

Let's meet virtually at our Third Community Roundtable! This will be a 60-min discussion on a given topic: Developing with Python. 

Register through >> this Global Masters challenge << 

UPDATE: the roundtable recording is available here.

I have a table, with autoincremented id

CREATE TABLE users (
    id SERIAL NOT NULL,
    name VARCHAR(30) NOT NULL,
    PRIMARY KEY (id)
)

I can add a new item there with an explicit id 

INSERT INTO users (id, name) VALUES (2, 'fred')

And while my id is autoincremented, I can omit it

INSERT INTO users (name) VALUES ('ed')

So, this time, I don't know the id, and I want to somehow get it.

I could do it with LAST_IDENTITY() function, but it just uses %RowID, and have no relation to the primary id

Hi Developers,

Enjoy watching the new video on InterSystems Developers YouTube:

⏯ Using Python with InterSystems IRIS @ Global Summit 2022