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ndobbndobb
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Docker new (#391)
* API and DB working * Cleaned up old docker compose docs
1 parent 8300d44 commit c65a316

13 files changed

+381
-104
lines changed

‎.dockerignore

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.vscode
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*.bak
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.git
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src/db
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src/ui-client
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src/server/Dockerfile.dev
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src/server/.gitignore
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src/server/.dockerignore
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src/ui-client/node_modules
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src/ui-client/build

‎containerize_leaf.sh

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# Set configurable stuff
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SA_PASSWORD=Th3PA55--8zz # DB password
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DB_SERVER=host.docker.internal # Use 'host.docker.internal' if mac, else '127.0.0.1' if linux
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# see: (https://stackoverflow.com/questions/24319662/from-inside-of-a-docker-container-how-do-i-connect-to-the-localhost-of-the-mach)
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LEAF_ROOT=$(PWD)
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# Check ENV variables
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if [ -z ${LEAFDB_SA_PW+x} ]; then echo "LEAFDB_SA_PW is unset!" exit; fi
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if [ -z ${LEAF_JWT_CERT+x} ]; then echo "LEAF_JWT_CERT is unset!" exit; fi
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if [ -z ${LEAF_JWT_KEY+x} ]; then echo "LEAF_JWT_KEY is unset!" exit; fi
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if [ -z ${LEAF_JWT_KEY+x} ]; then echo "LEAF_JWT_KEY is unset!" exit; fi
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if [ -z ${LEAF_JWT_KEY_PW+x} ]; then echo "LEAF_JWT_KEY_PW is unset!" exit; fi
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if [ -z ${LEAF_JWT_KEY_PW+x} ]; then echo "LEAF_JWT_KEY_PW is unset!" exit; fi
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# Extract cert/key path from ENVs
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KEYS_PATH=`echo $LEAF_JWT_CERT | sed 's/\/cert.pem.*//'`
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if [ -z ${KEYS_PATH+x} ]; then echo "Couldn't find cert+key path! Are you sure LEAF_JWT_CERT is a valid path?" && exit; fi
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#--------------
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# DB
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#--------------
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docker run -d -e "ACCEPT_EULA=Y" -e "SA_PASSWORD=$SA_PASSWORD" -p 1433:1433 --name leaf_db_demo mcr.microsoft.com/mssql/server:2017-latest
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sleep 10s
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# sqlcmd oddly prefers '127.0.0.1' (not 'host.docker.internal'), so use that here
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sqlcmd -S '127.0.0.1' -U SA -P $SA_PASSWORD -i src/db/build/LeafDB.sql
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sqlcmd -S '127.0.0.1' -U SA -P $SA_PASSWORD -d LeafDB -i src/db/build/LeafDB.Init.sql
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sqlcmd -S '127.0.0.1' -U SA -P $SA_PASSWORD -i src/db/build/TestDB.sql
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#--------------
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# API
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#--------------
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cd $LEAF_ROOT/src/server
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docker build -t leaf_api .
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cd $LEAF_ROOT
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docker run \
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-e "LEAF_APP_DB=Server=$DB_SERVER,1433;Database=LeafDB;uid=sa;Password=$SA_PASSWORD" \
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-e "LEAF_CLIN_DB=Server=$DB_SERVER,1433;Database=TestDB;uid=sa;Password=$SA_PASSWORD" \
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-e "LEAF_JWT_KEY_PW=$LEAF_JWT_KEY_PW" \
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-p 5001:5001 \
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-v ${PWD}/src/server:/app \
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-v ${KEYS_PATH}:/.keys \
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-v ${SERILOG_DIR}:/logs \
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--name leaf_api_demo \
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-d \
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leaf_api

‎docker-compose.yml

-68
This file was deleted.

‎docs/docker.md

-7
This file was deleted.

‎src/db/build/LeafDB.sql

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-- This Source Code Form is subject to the terms of the Mozilla Public
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-- License, v. 2.0. If a copy of the MPL was not distributed with this
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-- file, You can obtain one at http://mozilla.org/MPL/2.0/.
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USE [master]
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USE [master]
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GO
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/****** Object: Database [LeafDB] Script Date: ******/
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CREATE DATABASE [LeafDB]

‎src/db/build/TestDB.sql

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USE [master]
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GO
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/**
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* TestDB
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*/
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CREATE DATABASE [TestDB]
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GO
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ALTER DATABASE [TestDB] SET RECOVERY SIMPLE
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GO
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USE [TestDB]
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GO
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SET ANSI_NULLS ON
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GO
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SET QUOTED_IDENTIFIER ON
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GO
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CREATE TABLE [dbo].[person](
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[person_id] [int] NULL,
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[age] [int] NULL,
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[gender] [nvarchar](20) NULL
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) ON [PRIMARY]
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GO
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SET ANSI_NULLS ON
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GO
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SET QUOTED_IDENTIFIER ON
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GO
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CREATE TABLE [dbo].[visit_occurrence](
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[person_id] [int] NULL,
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[visit_occurrence_id] [int] NULL,
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[visit_date] [datetime] NULL,
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[visit_type] [nvarchar](10) NULL
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) ON [PRIMARY]
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GO
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INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (1, 28, N'F')
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GO
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INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (2, 74, N'M')
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GO
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INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (3, 55, N'M')
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GO
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INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (4, 43, N'F')
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GO
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INSERT [dbo].[person] ([person_id], [age], [gender]) VALUES (5, 99, N'F')
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GO
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INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (1, 100, CAST(N'2020-08-14T00:00:00.000' AS DateTime), N'IP')
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GO
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INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (1, 101, CAST(N'2020-09-22T00:00:00.000' AS DateTime), N'OP')
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GO
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INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (2, 102, CAST(N'2018-06-01T00:00:00.000' AS DateTime), N'IP')
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GO
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INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (2, 103, CAST(N'2018-02-28T00:00:00.000' AS DateTime), N'ED')
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GO
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INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (3, 104, CAST(N'2015-01-01T00:00:00.000' AS DateTime), N'OP')
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GO
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INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (4, 105, CAST(N'2022-09-19T00:00:00.000' AS DateTime), N'OP')
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GO
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INSERT [dbo].[visit_occurrence] ([person_id], [visit_occurrence_id], [visit_date], [visit_type]) VALUES (4, 106, CAST(N'2028-01-01T00:00:00.000' AS DateTime), N'IP')
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GO
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USE [LeafDB]
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GO
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DECLARE @user NVARCHAR(20) = 'TestDB.sql'
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DECLARE @yes BIT = 1
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DECLARE @no BIT = 0
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INSERT INTO app.ConceptSqlSet (SqlSetFrom, IsEncounterBased, IsEventBased, SqlFieldDate, Created, CreatedBy, Updated, UpdatedBy)
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SELECT *
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FROM (VALUES ('dbo.person', @no, @no, NULL, GETDATE(), @user, GETDATE(), @user),
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('dbo.visit_occurrence', @yes, @no, '@.visit_date', GETDATE(), @user, GETDATE(), @user)
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) AS X(col1,col2,col3,col4,col5,col6,col7,col8)
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DECLARE @sqlset_person INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.person')
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DECLARE @sqlset_visit_occurrence INT = (SELECT TOP 1 Id FROM LeafDB.app.ConceptSqlSet WHERE SqlSetFrom = 'dbo.visit_occurrence')
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INSERT INTO app.Concept (ExternalId, ExternalParentId, [IsNumeric], IsParent, IsRoot, SqlSetId, SqlSetWhere,
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SqlFieldNumeric, UiDisplayName, UiDisplayText, UiDisplayUnits, UiNumericDefaultText, UiDisplayPatientCount)
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SELECT ExternalId = 'A'
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, ExternalParentId = NULL
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, [IsNumeric] = @no
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, IsParent = @yes
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, IsRoot = @yes
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, SqlSetId = @sqlset_person
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Demographics'
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, UiDisplayText = 'Have demographics'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.person)
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UNION ALL
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SELECT ExternalId = 'A1'
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, ExternalParentId = 'A'
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, [IsNumeric] = @no
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, IsParent = @yes
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = '@.gender IS NOT NULL'
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Gender'
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, UiDisplayText = 'Identify with a gender'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.person)
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UNION ALL
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SELECT ExternalId = 'A11'
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, ExternalParentId = 'A1'
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = '@.gender = ''F'''
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Female'
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, UiDisplayText = 'Identify as Female'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.person WHERE gender = 'F')
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UNION ALL
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SELECT ExternalId = 'A12'
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, ExternalParentId = 'A1'
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = '@.gender = ''M'''
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Male'
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, UiDisplayText = 'Identify as Male'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.person WHERE gender = 'M')
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UNION ALL
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SELECT ExternalId = 'A2'
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, ExternalParentId = 'A'
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, [IsNumeric] = @yes
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_person
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, SqlSetWhere = '@.age IS NOT NULL'
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, SqlFieldNumeric = '@.age'
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, UiDisplayName = 'Age'
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, UiDisplayText = 'Are currently'
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, UiDisplayUnits = 'years of age'
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, UiNumericDefaultText = 'any age'
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.person WHERE age IS NOT NULL)
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UNION ALL
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SELECT ExternalId = 'B'
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, ExternalParentId = NULL
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, [IsNumeric] = @no
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, IsParent = @yes
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, IsRoot = @yes
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, SqlSetId = @sqlset_visit_occurrence
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Encounters'
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, UiDisplayText = 'Had an encounter'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.visit_occurrence)
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UNION ALL
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SELECT ExternalId = 'B1'
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, ExternalParentId = 'B'
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_visit_occurrence
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Inpatient'
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, UiDisplayText = 'Had an Inpatient encounter'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.visit_occurrence WHERE visit_type = 'IP')
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UNION ALL
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SELECT ExternalId = 'B2'
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, ExternalParentId = 'B'
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_visit_occurrence
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Outpatient'
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, UiDisplayText = 'Had an Outpatient encounter'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.visit_occurrence WHERE visit_type = 'OP')
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UNION ALL
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SELECT ExternalId = 'B3'
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, ExternalParentId = 'B'
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, [IsNumeric] = @no
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, IsParent = @no
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, IsRoot = @no
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, SqlSetId = @sqlset_visit_occurrence
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, SqlSetWhere = NULL
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, SqlFieldNumeric = NULL
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, UiDisplayName = 'Emergency'
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, UiDisplayText = 'Had an Emergency Department encounter'
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, UiDisplayUnits = NULL
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, UiNumericDefaultText = NULL
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, UiDisplayPatientCount = (SELECT COUNT(*) FROM TestDB.dbo.visit_occurrence WHERE visit_type = 'ED')
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/**
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* Set ParentId based on ExternalIds
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*/
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UPDATE LeafDB.app.Concept
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SET ParentId = P.Id
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FROM LeafDB.app.Concept AS C
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INNER JOIN (SELECT P.Id, P.ParentId, P.ExternalId
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FROM LeafDB.app.Concept AS P) AS P
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ON C.ExternalParentID = P.ExternalID
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WHERE C.ParentId IS NULL
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/**
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* Set RootIds
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*/
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; WITH roots AS
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(
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SELECT RootId = C.Id
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, RootUiDisplayName = C.UiDisplayName
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, C.IsRoot
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, C.Id
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, C.ParentId
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, C.UiDisplayName
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FROM LeafDB.app.Concept AS C
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WHERE C.IsRoot = 1
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UNION ALL
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SELECT roots.RootId
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, roots.RootUiDisplayName
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, C2.IsRoot
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, C2.Id
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, C2.ParentId
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, C2.UiDisplayName
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FROM roots
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INNER JOIN LeafDB.app.Concept AS C2
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ON C2.ParentId = roots.Id
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)
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UPDATE LeafDB.app.Concept
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SET RootId = roots.RootId
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FROM LeafDB.app.Concept AS C
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INNER JOIN roots
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ON C.Id = roots.Id
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WHERE C.RootId IS NULL

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