Integrate ID generation with the Clinical Service. #1094
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ciaranschutte
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Jan 23, 2024
* routing renaming and split into individual files * update missing entity route params * add route * add repo call * update swagger * remove duplicate route file. fix status code * fix route import * update swagger --------- Co-authored-by: Ciaran Schutte <[email protected]>
joneubank
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Jan 30, 2024
* Quick summary of exceptions for future devs * Missing Entity repo with update, get, and list all * Disable indent checking until whole repo converted to tabs * Remove patch core completion endpoint * Move prettier config to dedicated file, switch to tabs * Remove patch endpoint for clinical completion * Remove reference to patch clinical completion * Remove Patch Operations tag * Refactor exceptions dir - property and missing entity exceptions into their own directories - move reusable types into a global dir * Removing Patch core complete functions * Renaming to for consistencywith code base * Migration to remove in completion stats * Remove completion calculation from merge submission * Create update endpoint (#1110) * update swagger * rename routing to nest exceptions * add missing entity exception api call for POST * rename old exception api import * add missing entity exception api * add permissions check * wrap async * update swagger * remove feature flag * move parse bool to util * add create missing entity exception service layer * add 500 status for not implemented GET * simplify bool condition * routing renaming and split into individual files * update missing entity route params * update swagger path names * update swagger * rename * swagger updates * rename index exception route * update util return type * add tsdoc * fix router import --------- Co-authored-by: Ciaran Schutte <[email protected]> * Update completion stats to use missing entity exceptions * Use updated core complete calculation when submitting clinical data - applies to commit and approve workflows - slight refactoring of existing function * Create missing entity exception validation check (#1115) * update swagger * validate request body * move req err handling to top of func * cleanup * update ids ref to parsed result --------- Co-authored-by: Ciaran Schutte <[email protected]> * Feat/#1094 list programs with exceptions (#1112) * routing renaming and split into individual files * update missing entity route params * add route * add repo call * update swagger * remove duplicate route file. fix status code * fix route import * update swagger --------- Co-authored-by: Ciaran Schutte <[email protected]> * Feat/#1095 get single program entity exception (#1113) * routing renaming and split into individual files * update missing entity route params * add route * add data call * update swagger * fix invalid files from rebase * swagger update --------- Co-authored-by: Ciaran Schutte <[email protected]> * Feat/#1096 remove donors from program (#1114) * routing renaming and split into individual files * update missing entity route params * update swagger * add route * add api * add db call * update swagger * clean up & fix filter logic * fix merge conflicts * swagger updatess * update types * fix tag * remove extra index file for exception routing --------- Co-authored-by: Ciaran Schutte <[email protected]> * Refactor completion stat calculation to be consistent across all uses * Completion Stats record if they have missing entity exception * Update import paths in tests * Minor description updates * Comment added with description of migration * let -> const * Use Map instead of lodash Dictionary * Add mock for missing entity repo fetch * remove developer console log * Don't compare core-completion stats in submission/regsitration test * Correct exclude property for `completionStats` --------- Co-authored-by: Ciarán Schütte <[email protected]> Co-authored-by: Ciaran Schutte <[email protected]>
joneubank
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Jan 31, 2024
* Markdown formatting for PR Template * #1082 Numeric Exceptions (#1107) * First Definition Changes * Draft -- Test changes * First Pass -- allow undefined value * Improve Conditional * Remove comment * Use getCurrent Dictionary + Unit Test Updates * Unit Test Clean Up * Revert Type Changes * Check for valueType * Additional Unit Test, Copy Change * Revert use of 'undefined' * Remove comma * Streamline Exception Logic * Remove record references * Revised Unit Tests * Test Empty String * Reusable Schema Filter * Feat/1083 Validate Blank Numeric Exception Fields (#1108) * First Definition Changes * Draft -- Test changes * First Pass -- allow undefined value * Improve Conditional * Remove comment * Use getCurrent Dictionary + Unit Test Updates * Unit Test Clean Up * Revert Type Changes * Check for valueType * Additional Unit Test, Copy Change * Revert use of 'undefined' * Remove comma * Streamline Exception Logic * Remove record references * Revised Unit Tests * Test Empty String * Basic Setup * Add Entity Schema Handling, Update Unit test * Value Check for Blank Numeric Fields * Remove Missing Field Check * Check values for undefined * Remove undefined condition (unnecessary) * Use reusable schema filter * Update comments * Comment text v3 * Use Reusable Function in Submission Service * Reusable Field Filter * Handle Undefined Validation * Test for Undefined * Reusable numericField function * Normalize numeric exceptions as undefined * 🗂️ Feat #1103 Allow Treatment Entity Exceptions (#1116) * First Definition Changes * Draft -- Test changes * First Pass -- allow undefined value * Improve Conditional * Remove comment * Use getCurrent Dictionary + Unit Test Updates * Unit Test Clean Up * Revert Type Changes * Check for valueType * Additional Unit Test, Copy Change * Revert use of 'undefined' * Remove comma * Streamline Exception Logic * Remove record references * Revised Unit Tests * Test Empty String * Basic Setup * Add Entity Schema Handling, Update Unit test * Value Check for Blank Numeric Fields * Remove Missing Field Check * Check values for undefined * Remove undefined condition (unnecessary) * first Comments * Use reusable schema filter * Update comments * Comment text v3 * Use Reusable Function in Submission Service * Reusable Field Filter * Basic Treatment Check * Type Updates * Mongoose Model Update * Updated Mongoose Syntax * Fix Unit Test * Add Treatment to Types * Add Treatment case to entity switch block * Revert Mongo changes * Add Missing Entity Exceptions (#1109) * Quick summary of exceptions for future devs * Missing Entity repo with update, get, and list all * Disable indent checking until whole repo converted to tabs * Remove patch core completion endpoint * Move prettier config to dedicated file, switch to tabs * Remove patch endpoint for clinical completion * Remove reference to patch clinical completion * Remove Patch Operations tag * Refactor exceptions dir - property and missing entity exceptions into their own directories - move reusable types into a global dir * Removing Patch core complete functions * Renaming to for consistencywith code base * Migration to remove in completion stats * Remove completion calculation from merge submission * Create update endpoint (#1110) * update swagger * rename routing to nest exceptions * add missing entity exception api call for POST * rename old exception api import * add missing entity exception api * add permissions check * wrap async * update swagger * remove feature flag * move parse bool to util * add create missing entity exception service layer * add 500 status for not implemented GET * simplify bool condition * routing renaming and split into individual files * update missing entity route params * update swagger path names * update swagger * rename * swagger updates * rename index exception route * update util return type * add tsdoc * fix router import --------- Co-authored-by: Ciaran Schutte <[email protected]> * Update completion stats to use missing entity exceptions * Use updated core complete calculation when submitting clinical data - applies to commit and approve workflows - slight refactoring of existing function * Create missing entity exception validation check (#1115) * update swagger * validate request body * move req err handling to top of func * cleanup * update ids ref to parsed result --------- Co-authored-by: Ciaran Schutte <[email protected]> * Feat/#1094 list programs with exceptions (#1112) * routing renaming and split into individual files * update missing entity route params * add route * add repo call * update swagger * remove duplicate route file. fix status code * fix route import * update swagger --------- Co-authored-by: Ciaran Schutte <[email protected]> * Feat/#1095 get single program entity exception (#1113) * routing renaming and split into individual files * update missing entity route params * add route * add data call * update swagger * fix invalid files from rebase * swagger update --------- Co-authored-by: Ciaran Schutte <[email protected]> * Feat/#1096 remove donors from program (#1114) * routing renaming and split into individual files * update missing entity route params * update swagger * add route * add api * add db call * update swagger * clean up & fix filter logic * fix merge conflicts * swagger updatess * update types * fix tag * remove extra index file for exception routing --------- Co-authored-by: Ciaran Schutte <[email protected]> * Refactor completion stat calculation to be consistent across all uses * Completion Stats record if they have missing entity exception * Update import paths in tests * Minor description updates * Comment added with description of migration * let -> const * Use Map instead of lodash Dictionary * Add mock for missing entity repo fetch * remove developer console log * Don't compare core-completion stats in submission/regsitration test * Correct exclude property for `completionStats` --------- Co-authored-by: Ciarán Schütte <[email protected]> Co-authored-by: Ciaran Schutte <[email protected]> * Fix path for missing entity exception * Clean return types for missing-entity exceptions * Versioning 1.86.0 --------- Co-authored-by: Dan <[email protected]> Co-authored-by: Ciarán Schütte <[email protected]> Co-authored-by: Ciaran Schutte <[email protected]>
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Requirement Doc: https://wiki.oicr.on.ca/display/icgcargotech/Global+Id+Generation+Service
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