Orchard Harvest HL7 Integration#484
Merged
spamhurts merged 18 commits intorelease22.7-SNAPSHOTfrom Aug 16, 2022
Merged
Conversation
* - Added remark column to Culture pivot report - fixed foreign key * - Added remark column to Chemistry pivot report * - Added remark column to Hematology pivot report - fixed foreign key * - re-fixed CulturePivot foreign key * - Fixed remark value in MiscPivot - fixed foreign key * - Add remark value to Parasitology pivot - fixed foreign key * - Add remark value to Parasitology O&P pivot - fixed foreign key * - Add remark value to Surveillance pivot - fixed foreign key * - Add remark value to Urinalysis pivot - fixed foreign key
- Updated table names - updated stored procedure for new table names - changed file structure
- Begin adding ETLs to bring Sqlmed data into new table structures - Fixed FK in OBR table in metadata
… new datasets; runs in SSMS -Refactored FK link between assay_labworkResults, labworkTaqman and labworkPanels; FK changed from RowId to ObjectId - added pivot columns to test type specific pivot queries - added metadata for pivot queries - Refactored LabResultsLabworkType.java to use LabworkResultsAll as data source for labwork data - removed unused source queries and ETLs - added serviceTestId column to HL7_OBX table
…DO: remove study.labworkResults from query after data is merged into HL7_MSH, HL7_OBR, and HL7_OBX
…MESSAGE_DATE_TM source column
…eld for HL7 pivots - Updated HL7 pivot queries to use HL7_GroupNTE - added ProcedureName and TestName logic to HL7HematologyPivot.sql - added container column to HL7 tables - added container to Sqlmed migration scripts - added container column to Herme Tech stored procedure
…prcEHRModules into 22.3_fb_HL7Integration
…tored existing queries to include data from new sources.
-Updated clinpathRunsAll.sql to include Orchard sourced data -Added Orchard data to labwork pivot queries in study. e.g., hematologyPivot, chemPivot, culturePivot, etc.. -Added abnormal flags to clinpath pivot queries -Added color highlighting for abnormal test results to labwork history (in animal history > Clinical > Clinical History -Fixed wrong field display for DietDataSource in Clinical History -Fixed diet data source in CurrentDietDemographicsProvider.java and snprcOverrides.js (in animal snapshot view)
…snprc_ehr.labwork_services data is not populated -incremented module version number -renamed module upgrade script to align with new module version
jallentxbiomed
approved these changes
Aug 16, 2022
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
2 participants
Add this suggestion to a batch that can be applied as a single commit.This suggestion is invalid because no changes were made to the code.Suggestions cannot be applied while the pull request is closed.Suggestions cannot be applied while viewing a subset of changes.Only one suggestion per line can be applied in a batch.Add this suggestion to a batch that can be applied as a single commit.Applying suggestions on deleted lines is not supported.You must change the existing code in this line in order to create a valid suggestion.Outdated suggestions cannot be applied.This suggestion has been applied or marked resolved.Suggestions cannot be applied from pending reviews.Suggestions cannot be applied on multi-line comments.Suggestions cannot be applied while the pull request is queued to merge.Suggestion cannot be applied right now. Please check back later.
Rationale
Related Pull Requests
Changes
• Created new tables for HL7 results import
• Added missing remark column to labwork pivot queries
• Added pivot tables for Clinical Path Lab data - Updated table names - updated stored procedure for new table names - changed file path
• Fixed FK in OBR table in metadata
• Added SQL scripts in source_queries to migrate old clinpath data to new datasets; runs in SSMS -Refactored FK link between assay_labworkResults, labworkTaqman and labworkPanels;
• FK changed from RowId to ObjectId - added pivot columns to test type specific pivot queries -
• added metadata for pivot queries -
• Refactored LabResultsLabworkType.java to use LabworkResultsAll as data source for labwork data -
• removed unused source queries and ETLs -
• added serviceTestId column to HL7_OBX table
• new tables for HL7 results import
• Added missing remark column to labwork pivot queries
• Added remark column to Culture pivot report and fixed foreign key
• Added remark column to Chemistry pivot report
• Added remark column to Hematology pivot report and fixed foreign key
• re-fixed CulturePivot foreign key
• Fixed remark value in MiscPivot
• fixed foreign key
• Add remark value to Parasitology pivot
• fixed foreign key
• Add remark value to Parasitology O&P pivot and fixed foreign key
• Add remark value to Surveillance pivot and fixed foreign key
• Add remark value to Urinalysis pivot and fixed foreign key
• Added pivot tables for Clinical Path Lab data
o - Updated table names
o - updated stored procedure for new table names
o - changed file structure
• Added SQL scripts in source_queries to migrate old clinpath data to new datasets; runs in SSMS
• -Refactored FK link between assay_labworkResults, labworkTaqman and labworkPanels;
• FK changed from RowId to ObjectId
• - added pivot columns to test type specific pivot queries
• - added metadata for pivot queries
• - Refactored LabResultsLabworkType.java to use LabworkResultsAll as data source for labwork data
• - removed unused source queries and ETLs
• - added serviceTestId column to HL7_OBX table
• Added study.labworkResults dataset to labworkResultsAll.sql query; TODO: remove study.labworkResults from query after data is merged into HL7_MSH, HL7_OBR, and HL7_OBX
• copy Sqlmed Msh to LK.sql - fixed column order and removed CAST from MESSAGE_DATE_TM source column
• Added HL7_GroupNTE view to concatenate NTE records into a single field for HL7 pivots
• - Updated HL7 pivot queries to use HL7_GroupNTE
• - added ProcedureName and TestName logic to HL7HematologyPivot.sql
• - added container column to HL7 tables
• - added container to Sqlmed migration scripts
• - added container column to Herme Tech stored procedure