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‎.gitattributes

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* text=auto eol=lf
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*.{cmd,[cC][mM][dD]} text eol=crlf
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*.{bat,[bB][aA][tT]} text eol=crlf

‎.github/workflows/objectscript-quality.yml

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name: objectscriptquality
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on: push
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jobs:
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linux:
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name: Linux build
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runs-on: ubuntu-latest
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steps:
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- name: Execute ObjectScript Quality Analysis
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run: wget https://raw.githubusercontent.com/litesolutions/objectscriptquality-jenkins-integration/master/iris-community-hook.sh && sh ./iris-community-hook.sh

‎.gitignore

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iris/shared/durable
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iris/shared/model/*
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!iris/shared/model/.gitkeep
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iris/shared/HL7Out/*
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!iris/shared/HL7Out/.gitkeep
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iris/shared/in/*
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!iris/shared/in/.gitkeep
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iris/shared/HL7In/*
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!iris/shared/HL7In/.gitkeep
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settings.json
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# Compiled output
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encoder-ui/dist
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encoder-ui/tmp
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encoder-ui/out-tsc
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encoder-ui/bazel-out
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# Node
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encoder-ui/node_modules
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encoder-uinpm-debug.log
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encoder-uiyarn-error.log
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# IDEs and editors
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encoder-ui/.idea/
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encoder-ui/.project
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encoder-ui/.classpath
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encoder-ui/.c9/
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encoder-ui/*.launch
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encoder-ui/.settings/
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encoder-ui/*.sublime-workspace
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# Visual Studio Code
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encoder-ui/.vscode/*
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encoder-ui/!.vscode/settings.json
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encoder-ui/!.vscode/tasks.json
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encoder-ui/!.vscode/launch.json
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encoder-ui/!.vscode/extensions.json
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encoder-ui/.history/*
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# Miscellaneous
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encoder-ui/.angular/cache
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encoder-ui/.sass-cache/
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encoder-ui/connect.lock
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encoder-ui/coverage
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encoder-ui/libpeerconnection.log
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encoder-ui/testem.log
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encoder-ui/typings
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# System files
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encoder-ui/.DS_Store
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encoder-ui/Thumbs.db
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webgateway/shared/durable
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webgateway/shared/CA_Server.srl

‎LICENSE

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MIT License
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Copyright (c) 2019 InterSystems Developer Community
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Permission is hereby granted, free of charge, to any person obtaining a copy
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of this software and associated documentation files (the "Software"), to deal
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in the Software without restriction, including without limitation the rights
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to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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copies of the Software, and to permit persons to whom the Software is
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furnished to do so, subject to the following conditions:
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The above copyright notice and this permission notice shall be included in all
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copies or substantial portions of the Software.
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THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
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FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
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SOFTWARE.

‎README.md

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# Vector Search for MPI
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In this workflow we are going to test the Vector Search functionality applied for the management of an hipotetic Master Patient Index making use of the Vector Storage capabilities of IRIS database.
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.
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# What do you need to install?
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* [Git](https://git-scm.com/downloads)
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* [Docker](https://www.docker.com/products/docker-desktop) (if you are using Windows, make sure you set your Docker installation to use "Linux containers").
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* [Docker Compose](https://docs.docker.com/compose/install/)
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* [Visual Studio Code](https://code.visualstudio.com/download) + [InterSystems ObjectScript VSCode Extension](https://marketplace.visualstudio.com/items?itemName=daimor.vscode-objectscript)
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# Setup
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Build the image we will use during the workshop:
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```console
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$ git clone https://github.com/intersystems-ib/workshop-empi
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$ cd workshop-empi
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$ docker-compose build
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```
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# Introduction
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## What is purpose of this project?
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The main purpose of this project is to develop an interoperability production to generate embeddings for the demographic information of patients received from HL7 messages and to provide possible duplicated patients as the Master Patient Index tools do.
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## How does this project work?
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This project is designed as a docker compose project developed on InterSystems IRIS for Health Community edition and it uses a pre-trained text-similarity model named [all-MiniLM-L6-v2](https://huggingface.co/sentence-transformers/all-MiniLM-L6-v2).
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## Project
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As we said before, our code is developed on InterSystems IRIS for Health leveraging the Embedded Python and Vector Search functionalities. The project is responsible for:
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* Import HL7 file from */shared/in* folder.
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* Transform the PID segment of HL7 message into a custom message.
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* Download model and generate the embeddings for the demographic info using [Embedded Python](https://docs.intersystems.com/irislatest/csp/docbook/DocBook.UI.Page.cls?KEY=AFL_epython) capabilities.
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* Storage of embeddings into IRIS database and generation of response with the list of possible patient duplicates using Vector Search.
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# Testing the project
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* Run the containers to deploy the backend and the frontend:
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```
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docker-compose up -d
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```
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Automatically an IRIS instance will be deployed and a production will be configured and run available to import data to create the prediction model and train it.
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* Open the [Management Portal](http://localhost:52774/csp/sys/%25CSP.Portal.Home.zen?$NAMESPACE=EMPI).
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* Login using the default `superuser`/ `SYS` account.
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* Click on [Production](http://localhost:52774/csp/healthshare/empi/EnsPortal.ProductionConfig.zen?$NAMESPACE=EMPI) to access the production that we are going to use. You can access also through *Interoperability > User > Configure > Production*.

‎docker-compose.yml

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services:
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# iris
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iris:
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init: true
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container_name: iris
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build:
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context: .
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dockerfile: iris/Dockerfile
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ports:
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- 52774:52773
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- 51774:1972
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volumes:
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- ./iris/shared:/iris-shared
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environment:
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- ISC_DATA_DIRECTORY=/iris-shared/durable
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command: --check-caps false --ISCAgent false
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mem_limit: 30G
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memswap_limit: 32G

‎iris/Dockerfile

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ARG IMAGE=containers.intersystems.com/intersystems/irishealth-community:latest-cd
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FROM $IMAGE
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USER root
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WORKDIR /opt/irisapp
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RUN chown -R irisowner:irisowner /opt/irisapp
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RUN apt-get update && apt-get install -y python3
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# install required packages
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COPY --chown=$ISC_PACKAGE_MGRUSER:$ISC_PACKAGE_IRISGROUP /requirements.txt /
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RUN chmod 777 /requirements.txt
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RUN pip3 install -r /requirements.txt --break-system-packages
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USER irisowner
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# copy files to image
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WORKDIR /opt/irisapp
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COPY --chown=irisowner:irisowner src src
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COPY --chown=$ISC_PACKAGE_MGRUSER:$ISC_PACKAGE_IRISGROUP /iris/irissession.sh /
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RUN chmod +x /irissession.sh
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COPY --chown=$ISC_PACKAGE_MGRUSER:$ISC_PACKAGE_IRISGROUP /iris/iris.cpf /
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RUN chmod +x /iris.cpf
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ENV ISC_CPF_MERGE_FILE=/iris.cpf
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SHELL ["/irissession.sh"]
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RUN \
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zn "EMPI" \
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set sc = $SYSTEM.OBJ.LoadDir("/opt/irisapp/src/EMPI", "ck", , 1)

‎iris/iris.cpf

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[Actions]
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CreateDatabase:Name=EMPI_DATA,Directory=/usr/irissys/mgr/EMPI_DATA
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CreateDatabase:Name=EMPI_CODE,Directory=/usr/irissys/mgr/EMPI_CODE
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CreateNamespace:Name=EMPI,Globals=EMPI_DATA,Routines=EMPI_CODE,Interop=1
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ModifyUser:Name=SuperUser,PasswordHash=9b900b7299f13b10d9aa5f41a8ce98b55f7e99831f988f596f7048e6647e4f2c3ebbcd3c104b9510a4a8707c9b864e6e550a95e269b4b1dffb8613d85c10e313,ae216ebb10fa9b741efa40fe91236be31d06af08569cca75f78cde36afeafd88505c3d4b3092238074cac14087b9c95a08214e3c0ecbf62e0527c29c82ce097d,10000,SHA512

‎iris/irissession.sh

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#!/bin/bash
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iris start $ISC_PACKAGE_INSTANCENAME quietly
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cat << EOF | iris session $ISC_PACKAGE_INSTANCENAME -U %SYS
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do ##class(%SYSTEM.Process).CurrentDirectory("$PWD")
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$@
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if '\$Get(sc, 1) do ##class(%SYSTEM.Process).Terminate(, 1)
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zn "%SYS"
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do ##class(SYS.Container).QuiesceForBundling()
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do ##class(Security.Users).UnExpireUserPasswords("*")
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halt
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EOF
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exit=$?
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iris stop $ISC_PACKAGE_INSTANCENAME quietly
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exit $exit

‎iris/shared/in/.gitkeep

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‎iris/shared/messagea28.txt

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MSH|^~\&|HIS|H12O|EMPI||20240514094951||ADT^A28|788826|P|2.5.1
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EVN|A28|20240514094951|20240514094951|1
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PID|||1556655112^^^SERMAS^SN~556432^^^H12O^PI||MARTÍN SOLÍS^ROBERTO^^^||20150403|M|||PASEO PEDRO ÁLVAREZ^195 1 CENTRO^LEGANÉS^MADRID^28379^SPAIN||555283055^PRN^^JUAN.GARCIA@YAHOO.COM|||||||||||||||||N|
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PV1||N
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AL1|1|MA|^Polen de olivo^|MI^^||20360331040605
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ZBT|AB-
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MSH|^~\&|HIS|H12O|EMPI||20240514094951||ADT^A28|255913|P|2.5.1
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EVN|A28|20240514094951|20240514094951|1
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PID|||1398528318^^^SERMAS^SN~2312421^^^H120^PI||LÓPEZ MARTÍN^MARÍA^^^||19560121|F|||PASEO MARIO FERNÁNDEZ^258 1 DERECHA^MADRID^MADRID^28627^SPAIN||^PRN^^MARIA.LOPEZ@GOOGLE.COM|||||||||||||||||N|
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PV1||N
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DG1|1||V935^ACC EN EMBARCACION SIN ACC A EMBARC, NO AHOGAM O SUMERS, CANOA O KAYAK^||20240514|||||||||||^MARTÍNEZ SOLCHAGA^MARCOS^^^Dr|
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ZBT|AB-

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