From 40276dac48273313218dc42b14513fb38da1ba72 Mon Sep 17 00:00:00 2001 From: Terry J Hawkins Date: Wed, 24 Apr 2024 09:21:11 -0500 Subject: [PATCH 1/2] - Updated v_snd_addributeData source query view to ensure lookup value attributes are treated as strings (#719) --- .../create_v_snd_attributeData.sql | 29 ++++++++----------- 1 file changed, 12 insertions(+), 17 deletions(-) diff --git a/snprc_ehr/resources/source_queries/create_v_snd_attributeData.sql b/snprc_ehr/resources/source_queries/create_v_snd_attributeData.sql index eb73f5b3..33b0ed18 100644 --- a/snprc_ehr/resources/source_queries/create_v_snd_attributeData.sql +++ b/snprc_ehr/resources/source_queries/create_v_snd_attributeData.sql @@ -23,9 +23,6 @@ GO SET QUOTED_IDENTIFIER ON GO - - - ALTER VIEW [labkey_etl].[v_snd_attributeData] AS -- ========================================================================================== @@ -37,26 +34,26 @@ AS -- 10/11/2018 removing rows that have attribute values that are '' or null. tjh -- 05/13/19 Added a REPLACE to numeric/decimal CAST -- Purpose is to handle numeric data with commas (',') ~line 59 srr +-- 04/23/2024 Lookup values need to be string values by default. tjh -- ========================================================================================== SELECT TOP (99.999999999) PERCENT - cp.ANIMAL_EVENT_ID AS EventId, - sp.PKG_ID AS PkgId, - -- snd.EventData columns - cp.PROC_ID AS EventDataId, - sp.SUPER_PKG_ID AS SuperPkgId, - pbi.SUPER_PKG_ID AS ParentSuperPkgId, - cpa.value AS value, + cp.ANIMAL_EVENT_ID AS EventId, + sp.PKG_ID AS PkgId, + -- snd.EventData columns + cp.PROC_ID AS EventDataId, + sp.SUPER_PKG_ID AS SuperPkgId, + pbi.SUPER_PKG_ID AS ParentSuperPkgId, + cpa.value AS value, -- exp.ObjectProperty columns - ltrim(rtrim(cpa.ATTRIB_KEY)) AS [KEY], + LTRIM(RTRIM(cpa.ATTRIB_KEY)) AS [_KEY], - CASE WHEN (LOWER(pa.DATA_TYPE) = 'numeric' OR - LOWER(pa.DATA_TYPE) = 'decimal') + CASE WHEN ( (LOWER(pa.DATA_TYPE) = 'numeric' OR LOWER(pa.DATA_TYPE) = 'decimal') ) AND pa.LOOKUP_KEY IS NULL THEN CAST (REPLACE(cpa.value,',','') AS FLOAT ) ELSE NULL END AS FloatValue, - CASE WHEN LOWER(pa.DATA_TYPE) = 'string' + CASE WHEN LOWER(pa.DATA_TYPE) = 'string' OR pa.LOOKUP_KEY IS NOT NULL THEN cpa.value ELSE NULL END AS StringValue, - CASE WHEN (LOWER(pa.DATA_TYPE)) = 'string' THEN 's' ELSE 'f' END AS TypeTag, + CASE WHEN ( (LOWER(pa.DATA_TYPE)) = 'string' OR pa.LOOKUP_KEY IS NOT NULL) THEN 's' ELSE 'f' END AS TypeTag, cp.OBJECT_ID AS objectId, ( SELECT MAX(v) FROM ( VALUES (cp.timestamp), (cpa.timestamp)) AS VALUE (v)) AS TIMESTAMP @@ -71,13 +68,11 @@ INNER JOIN dbo.SUPER_PKGS AS sp ON sp.SUPER_PKG_ID = bi.SUPER_PKG_ID INNER JOIN dbo.PKGS AS p ON p.PKG_ID = sp.PKG_ID INNER JOIN dbo.PKG_ATTRIBS AS pa ON pa.PKG_ID = p.PKG_ID AND pa.ATTRIB_KEY = cpa.ATTRIB_KEY - -- select primates only from the TxBiomed colony INNER JOIN labkey_etl.V_DEMOGRAPHICS AS D ON D.id = ae.ANIMAL_ID WHERE LTRIM(RTRIM(cpa.VALUE)) <> '' AND cpa.VALUE IS NOT NULL ORDER BY EventDataId - GO GRANT SELECT ON Labkey_etl.v_snd_attributeData TO z_labkey From a55920db19b27b1768077c5692f6a4a10585cfae Mon Sep 17 00:00:00 2001 From: Terry J Hawkins Date: Thu, 25 Apr 2024 16:43:49 -0500 Subject: [PATCH 2/2] Moved all Sqlmed and APATH ETL and source query files to corresponding deprecated directories in order to remove them from the Data Integration UI page. (#720) --- snprc_ehr/resources/etls/{ => deprecated}/SqlmedMsh.xml | 0 snprc_ehr/resources/etls/{ => deprecated}/SqlmedObr.xml | 0 snprc_ehr/resources/etls/{ => deprecated}/apathDiagnoses.xml | 0 snprc_ehr/resources/etls/{ => deprecated}/apathPathology.xml | 0 snprc_ehr/resources/etls/{ => deprecated}/clinpathruns.xml | 0 snprc_ehr/resources/etls/{ => deprecated}/labworkResults.xml | 0 snprc_ehr/resources/etls/{ => deprecated}/labwork_panels.xml | 0 snprc_ehr/resources/etls/{ => deprecated}/labwork_services.xml | 0 snprc_ehr/resources/etls/{ => deprecated}/labwork_types.xml | 0 .../{HL7 => deprecated}/copy Sqlmed MSH data to LK.sql | 0 .../{HL7 => deprecated}/copy Sqlmed NTE data to LK.sql | 0 .../{HL7 => deprecated}/copy Sqlmed OBR data to LK.sql | 0 .../{HL7 => deprecated}/copy Sqlmed OBX data to LK.sql | 0 .../source_queries/{ => deprecated}/create_v_apath_diagnoses.sql | 0 .../source_queries/{ => deprecated}/create_v_apath_pathology.sql | 0 .../source_queries/{ => deprecated}/create_v_clinpathruns.sql | 0 .../{ => deprecated}/create_v_delete_apath_diagnoses.sql | 0 .../{ => deprecated}/create_v_delete_apath_pathology.sql | 0 .../{ => deprecated}/create_v_delete_clinpathruns.sql | 0 .../{ => deprecated}/create_v_delete_labwork_panels.sql | 0 .../{ => deprecated}/create_v_delete_labwork_results.sql | 0 .../{ => deprecated}/create_v_delete_labwork_services.sql | 0 .../{ => deprecated}/create_v_delete_labwork_types.sql | 0 .../source_queries/{ => deprecated}/create_v_labwork_panels.sql | 0 .../source_queries/{ => deprecated}/create_v_labwork_results.sql | 0 .../source_queries/{ => deprecated}/create_v_labwork_services.sql | 0 .../source_queries/{ => deprecated}/create_v_labwork_types.sql | 0 .../source_queries/{HL7 => deprecated}/create_v_sqlmed_msh.sql | 0 .../source_queries/{HL7 => deprecated}/create_v_sqlmed_obr.sql | 0 29 files changed, 0 insertions(+), 0 deletions(-) rename snprc_ehr/resources/etls/{ => deprecated}/SqlmedMsh.xml (100%) rename snprc_ehr/resources/etls/{ => deprecated}/SqlmedObr.xml (100%) rename snprc_ehr/resources/etls/{ => deprecated}/apathDiagnoses.xml (100%) rename snprc_ehr/resources/etls/{ => deprecated}/apathPathology.xml (100%) rename snprc_ehr/resources/etls/{ => deprecated}/clinpathruns.xml (100%) rename snprc_ehr/resources/etls/{ => deprecated}/labworkResults.xml (100%) rename snprc_ehr/resources/etls/{ => deprecated}/labwork_panels.xml (100%) rename snprc_ehr/resources/etls/{ => deprecated}/labwork_services.xml (100%) rename snprc_ehr/resources/etls/{ => deprecated}/labwork_types.xml (100%) rename snprc_ehr/resources/source_queries/{HL7 => deprecated}/copy Sqlmed MSH data to LK.sql (100%) rename snprc_ehr/resources/source_queries/{HL7 => deprecated}/copy Sqlmed NTE data to LK.sql (100%) rename snprc_ehr/resources/source_queries/{HL7 => deprecated}/copy Sqlmed OBR data to LK.sql (100%) rename snprc_ehr/resources/source_queries/{HL7 => deprecated}/copy Sqlmed OBX data to LK.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_apath_diagnoses.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_apath_pathology.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_clinpathruns.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_delete_apath_diagnoses.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_delete_apath_pathology.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_delete_clinpathruns.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_delete_labwork_panels.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_delete_labwork_results.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_delete_labwork_services.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_delete_labwork_types.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_labwork_panels.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_labwork_results.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_labwork_services.sql (100%) rename snprc_ehr/resources/source_queries/{ => deprecated}/create_v_labwork_types.sql (100%) rename snprc_ehr/resources/source_queries/{HL7 => deprecated}/create_v_sqlmed_msh.sql (100%) rename snprc_ehr/resources/source_queries/{HL7 => deprecated}/create_v_sqlmed_obr.sql (100%) diff --git a/snprc_ehr/resources/etls/SqlmedMsh.xml b/snprc_ehr/resources/etls/deprecated/SqlmedMsh.xml similarity index 100% rename from snprc_ehr/resources/etls/SqlmedMsh.xml rename to snprc_ehr/resources/etls/deprecated/SqlmedMsh.xml diff --git a/snprc_ehr/resources/etls/SqlmedObr.xml b/snprc_ehr/resources/etls/deprecated/SqlmedObr.xml similarity index 100% rename from snprc_ehr/resources/etls/SqlmedObr.xml rename to snprc_ehr/resources/etls/deprecated/SqlmedObr.xml diff --git a/snprc_ehr/resources/etls/apathDiagnoses.xml b/snprc_ehr/resources/etls/deprecated/apathDiagnoses.xml similarity index 100% rename from snprc_ehr/resources/etls/apathDiagnoses.xml rename to snprc_ehr/resources/etls/deprecated/apathDiagnoses.xml diff --git a/snprc_ehr/resources/etls/apathPathology.xml b/snprc_ehr/resources/etls/deprecated/apathPathology.xml similarity index 100% rename from snprc_ehr/resources/etls/apathPathology.xml rename to snprc_ehr/resources/etls/deprecated/apathPathology.xml diff --git a/snprc_ehr/resources/etls/clinpathruns.xml b/snprc_ehr/resources/etls/deprecated/clinpathruns.xml similarity index 100% rename from snprc_ehr/resources/etls/clinpathruns.xml rename to snprc_ehr/resources/etls/deprecated/clinpathruns.xml diff --git a/snprc_ehr/resources/etls/labworkResults.xml b/snprc_ehr/resources/etls/deprecated/labworkResults.xml similarity index 100% rename from snprc_ehr/resources/etls/labworkResults.xml rename to snprc_ehr/resources/etls/deprecated/labworkResults.xml diff --git a/snprc_ehr/resources/etls/labwork_panels.xml b/snprc_ehr/resources/etls/deprecated/labwork_panels.xml similarity index 100% rename from snprc_ehr/resources/etls/labwork_panels.xml rename to snprc_ehr/resources/etls/deprecated/labwork_panels.xml diff --git a/snprc_ehr/resources/etls/labwork_services.xml b/snprc_ehr/resources/etls/deprecated/labwork_services.xml similarity index 100% rename from snprc_ehr/resources/etls/labwork_services.xml rename to snprc_ehr/resources/etls/deprecated/labwork_services.xml diff --git a/snprc_ehr/resources/etls/labwork_types.xml b/snprc_ehr/resources/etls/deprecated/labwork_types.xml similarity index 100% rename from snprc_ehr/resources/etls/labwork_types.xml rename to snprc_ehr/resources/etls/deprecated/labwork_types.xml diff --git a/snprc_ehr/resources/source_queries/HL7/copy Sqlmed MSH data to LK.sql b/snprc_ehr/resources/source_queries/deprecated/copy Sqlmed MSH data to LK.sql similarity index 100% rename from snprc_ehr/resources/source_queries/HL7/copy Sqlmed MSH data to LK.sql rename to snprc_ehr/resources/source_queries/deprecated/copy Sqlmed MSH data to LK.sql diff --git a/snprc_ehr/resources/source_queries/HL7/copy Sqlmed NTE data to LK.sql b/snprc_ehr/resources/source_queries/deprecated/copy Sqlmed NTE data to LK.sql similarity index 100% rename from snprc_ehr/resources/source_queries/HL7/copy Sqlmed NTE data to LK.sql rename to snprc_ehr/resources/source_queries/deprecated/copy Sqlmed NTE data to LK.sql diff --git a/snprc_ehr/resources/source_queries/HL7/copy Sqlmed OBR data to LK.sql b/snprc_ehr/resources/source_queries/deprecated/copy Sqlmed OBR data to LK.sql similarity index 100% rename from snprc_ehr/resources/source_queries/HL7/copy Sqlmed OBR data to LK.sql rename to snprc_ehr/resources/source_queries/deprecated/copy Sqlmed OBR data to LK.sql diff --git a/snprc_ehr/resources/source_queries/HL7/copy Sqlmed OBX data to LK.sql b/snprc_ehr/resources/source_queries/deprecated/copy Sqlmed OBX data to LK.sql similarity index 100% rename from snprc_ehr/resources/source_queries/HL7/copy Sqlmed OBX data to LK.sql rename to snprc_ehr/resources/source_queries/deprecated/copy Sqlmed OBX data to LK.sql diff --git a/snprc_ehr/resources/source_queries/create_v_apath_diagnoses.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_apath_diagnoses.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_apath_diagnoses.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_apath_diagnoses.sql diff --git a/snprc_ehr/resources/source_queries/create_v_apath_pathology.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_apath_pathology.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_apath_pathology.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_apath_pathology.sql diff --git a/snprc_ehr/resources/source_queries/create_v_clinpathruns.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_clinpathruns.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_clinpathruns.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_clinpathruns.sql diff --git a/snprc_ehr/resources/source_queries/create_v_delete_apath_diagnoses.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_delete_apath_diagnoses.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_delete_apath_diagnoses.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_delete_apath_diagnoses.sql diff --git a/snprc_ehr/resources/source_queries/create_v_delete_apath_pathology.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_delete_apath_pathology.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_delete_apath_pathology.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_delete_apath_pathology.sql diff --git a/snprc_ehr/resources/source_queries/create_v_delete_clinpathruns.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_delete_clinpathruns.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_delete_clinpathruns.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_delete_clinpathruns.sql diff --git a/snprc_ehr/resources/source_queries/create_v_delete_labwork_panels.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_delete_labwork_panels.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_delete_labwork_panels.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_delete_labwork_panels.sql diff --git a/snprc_ehr/resources/source_queries/create_v_delete_labwork_results.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_delete_labwork_results.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_delete_labwork_results.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_delete_labwork_results.sql diff --git a/snprc_ehr/resources/source_queries/create_v_delete_labwork_services.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_delete_labwork_services.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_delete_labwork_services.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_delete_labwork_services.sql diff --git a/snprc_ehr/resources/source_queries/create_v_delete_labwork_types.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_delete_labwork_types.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_delete_labwork_types.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_delete_labwork_types.sql diff --git a/snprc_ehr/resources/source_queries/create_v_labwork_panels.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_labwork_panels.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_labwork_panels.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_labwork_panels.sql diff --git a/snprc_ehr/resources/source_queries/create_v_labwork_results.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_labwork_results.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_labwork_results.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_labwork_results.sql diff --git a/snprc_ehr/resources/source_queries/create_v_labwork_services.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_labwork_services.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_labwork_services.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_labwork_services.sql diff --git a/snprc_ehr/resources/source_queries/create_v_labwork_types.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_labwork_types.sql similarity index 100% rename from snprc_ehr/resources/source_queries/create_v_labwork_types.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_labwork_types.sql diff --git a/snprc_ehr/resources/source_queries/HL7/create_v_sqlmed_msh.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_sqlmed_msh.sql similarity index 100% rename from snprc_ehr/resources/source_queries/HL7/create_v_sqlmed_msh.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_sqlmed_msh.sql diff --git a/snprc_ehr/resources/source_queries/HL7/create_v_sqlmed_obr.sql b/snprc_ehr/resources/source_queries/deprecated/create_v_sqlmed_obr.sql similarity index 100% rename from snprc_ehr/resources/source_queries/HL7/create_v_sqlmed_obr.sql rename to snprc_ehr/resources/source_queries/deprecated/create_v_sqlmed_obr.sql