BS-123 | icd-10 extensions outside bahmni reports #82
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…o, build the jar and include it in the execution classpath
…ed back the build branch to default
daviemukungi
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vijayanandtwks
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Aug 10, 2023
sivareddyp
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Aug 10, 2023
gsluthra
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Aug 11, 2023
sivareddyp
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* Removed extensions related code * Update Dockerfile * Update start.sh * Update build_publish.yml * pulled repo online and build warfile * clone git icd10 extensions repo and build the jar file * BS-123 | daviemukungi,vijay | add extensions outside repository * BS-123 | daviemukungi | Added workflows to clone ICD10 extensions repo, build the jar and include it in the execution classpath * Removed extension repo workflows in the dockerfile * updated a temporary branch to test bahmni extensions workflows * BS-123-temp | daviemukungi | Removed unused test resources and reverted back the build branch to default * BS-123 | Removed unused Dockerfile --------- Co-authored-by: vijayanandtwks <[email protected]> Co-authored-by: Siva Reddy <[email protected]>
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* BS-39 | Siva,Vijay | Publish bahmni-reports with SNOMED image tags (#61) * Enhancing Reports to support SNOMED Feature (#67) * BS-55 | David | Introduced snomedDiagnosis Report type and template * BS-55 | Vijay,David | Integrate Diagnosis Report with SNOMED omod Co-authored-by: daviemukungi <[email protected]> * BS-55 | Vijay,David | Fix count error for Diagnosis Report Co-authored-by: daviemukungi <[email protected]> * Testing HTTP URL Connection * BS - 55 | Vijay,David | Add gender report for SNOMED diagnosis count Co-authored-by: daviemukungi <[email protected]> * BS - 55 | Vijay,David | Add unit tests for SNOMED diagnosis Count and Gender Co-authored-by: daviemukungi <[email protected]> * BS - 55 | Vijay,David | Refactor implementation and unit tests for SNOMED diagnosis Count and Gender Co-authored-by: daviemukungi <[email protected]> * BS - 55/51/24 | Vijay,David | Clean up Co-authored-by: daviemukungi <[email protected]> * BS - 55/51/24 | Vijay | probe HttpClient issue * BS - 55/51/24 | Vijay | upgrade bahmniJavaUtils version * BS - 55/51/24 | Vijay | remove stale branch * BS - 55/51/24 | Vijay | remove feature branch * BS - 55/51/24 | Vijay | cleanup files * BS - 55/51/24 | Vijay | trigger pipeline * BS - 55/51/24 | Vijay | incorporate review comments * BS - 55/51/24 | Vijay | remove stale branch --------- Co-authored-by: daviemukungi <[email protected]> * remove unwanted line * daviemukungi | BS-138 | Align report values to fit at the center of a… (#71) Daviemukungi | BS-138 | Align report values to fit at the center of a cell. Also removed unused imports * BS - 141 | Vijay | add summary total and replace short name instead of FSN and rename Total to Count (#72) * BS - 166 | Vijay | fix for diagnosis count not showing results in clinic config (#75) * BS - 166 | Vijay | fix for diagnosis count not showing results in clinic config * BS 54 | Adding Diagnosis line reports for Malaria, Asthma and Covid-19 (#76) * daviemukungi | BS-54 | Added SQL for the terminology service diagnosis line report * Modified the snomed diagnosis line report and re-used the existing diagnosis line reports sqls * BS-54 | Added Line Reports template and configuration , added unit test cases * BS-54 | Added Line Reports template and configuration , added unit test cases * BS-54 | Re-arranged column and updated column names to match sql columns * BS-54 | Added inner join temp table to load only data related to snomed code in the configuration * BS-54 | using hl7_code instead of name for concept reference term source for consistency across standard and clinic environment * BS-54 | converting UTC date to IST * BS-54 | added patient attributes and patient address attributes * BS-54 | re arranged columns * BS-54 | added same columnn style for newly added columns and refactored method name * BS-54 | Added unit test cases for patient and address attributes * BS-54 | Added temp table join for the report * BS - 166 | Vijay | fix for diagnosis count not showing results in clinic config (#75) * BS - 166 | Vijay | fix for diagnosis count not showing results in clinic config * BS 54 | added concept shortname configuration for line report * BS 54 | modified sql for patient attribute * BS 54 | updated test cases for patient attribute helper * BS 54 | renamed existing count report files name to show the intent * BS 54 | updated test cases for the newly introduced ts configuration * BS 54 | renamed test method and mock methods * BS 54 | extracted common properties to generic and extend them for count and line report * BS 54 | extracted common methods to class and extending them to reduce duplicate code * BS 54 | updated apache commons-lang to 3.8.1 and made the null check more readable * BS 54 | renamed property prefix name from ts to terminologyServer --------- Co-authored-by: daviemukungi <[email protected]> Co-authored-by: vijayanandtwks <[email protected]> * BS-120 | Vijay,Mani,David | add ICD10 feature (#79) * daviemukungi | BS-54 | Added SQL for the terminology service diagnosis line report * Modified the snomed diagnosis line report and re-used the existing diagnosis line reports sqls * BS-54 | Added Line Reports template and configuration , added unit test cases * BS-54 | Added Line Reports template and configuration , added unit test cases * BS-54 | Re-arranged column and updated column names to match sql columns * BS-54 | Added inner join temp table to load only data related to snomed code in the configuration * BS-54 | using hl7_code instead of name for concept reference term source for consistency across standard and clinic environment * BS-54 | converting UTC date to IST * BS-54 | added patient attributes and patient address attributes * BS-54 | re arranged columns * BS-54 | added same columnn style for newly added columns and refactored method name * BS-54 | Added unit test cases for patient and address attributes * BS-54 | Added temp table join for the report * BS - 166 | Vijay | fix for diagnosis count not showing results in clinic config (#75) * BS - 166 | Vijay | fix for diagnosis count not showing results in clinic config * BS 54 | added concept shortname configuration for line report * BS 54 | modified sql for patient attribute * BS 54 | updated test cases for patient attribute helper * BS 54 | renamed existing count report files name to show the intent * BS 54 | updated test cases for the newly introduced ts configuration * BS 54 | renamed test method and mock methods * BS 54 | extracted common properties to generic and extend them for count and line report * BS 54 | extracted common methods to class and extending them to reduce duplicate code * BS - 174 | Vijay,Mani | ICD-10 logic * BS - 174 | Vijay,Mani | ICD-10 sorting logic * BS - 174 | Vijay,Mani | ICD-10 rule evaluation logic * BS - 174 | Vijay,Mani | ICD-10 result set logic * BS 174 | Vijay, Mani | updated comparator logic and added eval logic # Conflicts: # src/main/java/org/bahmni/reports/icd10/ICD10Evaluator.java # src/main/resources/icd-response2.json * Endpoint to return mapRules based on the snomedCode * Refactored endpoint for fetching mapRules * BS - 174 | Vijay | refactor result set logic * BS - 174 | Vijay | cleanup unwanted method * BS 174 | Vijay, Mani | updating test cases and refactoring * BS - 174 | Vijay | Include reflection * BS - 174 | Vijay | refactor and cleanup reflection * BS - 174 | Vijay | handle usecase with or without extension * BS 174 | Vijay, Mani | updating test cases for age * BS - 174 | Vijay | add unit test with ICD10 extension * BS 174 | Vijay, Mani | restructured the declaration and removed unwanted code * BS 174 | Vijay, Mani | refactored the code to a package * BS - 174 | Vijay | add unit test ICD10 res end point * BS 174 | Vijay, Mani | testing the resttemplate changes * BS 174 | Vijay, Mani | working solution for rest template * BS 174 | Vijay, Mani | updated the field * BS 174 | Vijay, Mani | Added unit test cases for look up service * BS 174 | Vijay, Mani | Added log messages * BS 174 | Vijay, Mani | Refactored and changes * BS 174 | Vijay, Mani | added total , updated get response logic and test cases * BS 174 | Vijay, Mani | show table headers when no data is present instead of black page * BS-174 | Vijay | Refactor ICD Evaluator and REST endpoint * BS-174 | Vijay, Mani | add edge cases * BS 174 | Vijay, Mani | updated test cases for teh case where mapTarget is empty * BS 174 | Vijay, Mani | updated test cases for teh case where mapTarget is empty * BS-174 | Vijay | refactored test cases * BS-174 | Vijay | refactored test cases * BS-174 | Vijay | refactored peer review comments * BS-174-ICD * BS-174 | Vijay | refactored constant * BS-174 | Vijay | remove auto deployment of current branch * BS 174 | Vijay, Mani | removed the mock response json from resources * BS 174 | Vijay, Mani | Addressed sonar analysis issues --------- Co-authored-by: daviemukungi <[email protected]> Co-authored-by: manimaarans <[email protected]> Co-authored-by: Siva Reddy <[email protected]> * BS-123 | icd-10 extensions outside bahmni reports (#82) * Removed extensions related code * Update Dockerfile * Update start.sh * Update build_publish.yml * pulled repo online and build warfile * clone git icd10 extensions repo and build the jar file * BS-123 | daviemukungi,vijay | add extensions outside repository * BS-123 | daviemukungi | Added workflows to clone ICD10 extensions repo, build the jar and include it in the execution classpath * Removed extension repo workflows in the dockerfile * updated a temporary branch to test bahmni extensions workflows * BS-123-temp | daviemukungi | Removed unused test resources and reverted back the build branch to default * BS-123 | Removed unused Dockerfile --------- Co-authored-by: vijayanandtwks <[email protected]> Co-authored-by: Siva Reddy <[email protected]> * BS-178 | Increased default tomcat timeout (#84) * BS-178 | Increased API request timeout to 30 minutes * BS-178 | Increased API request timeout to 10 minutes * BS-178 | Adding timeout to tomcat * BS-178 | Siva, Vijay , David | Increased tomcat timeout to 10 minutes * Removed unused imports * BS-178 | Set OpenMRS connection properties to defaults --------- Co-authored-by: Siva Reddy <[email protected]> * Removing unnecessary icd10 service config properties * Adding deleted file * BS-258 | Reverting SNOMED specific GHA * Adding descendantCodes.json * BS-258 | Vijay, Siva | Fixing failed tests --------- Co-authored-by: vijayanandtwks <[email protected]> Co-authored-by: daviemukungi <[email protected]> Co-authored-by: manimaarans <[email protected]> Co-authored-by: manimaarans <[email protected]> Co-authored-by: vijayanandtwks <[email protected]>
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Summary
Removed icd-10 extensions related code from the Bahmni reports code.
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JIRA tickets
https://bahmni.atlassian.net/browse/BS-123