Fix up some of the validations #69
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yavyx
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Aug 10, 2024
mshadbolt
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Aug 20, 2024
* adding date format to date intervals * addded date format * updated docs * updated test date formats * make exceptions more readable * make exception specific * cleanup * cleanup * Update src/clinical_etl/CSVConvert.py Co-authored-by: Marion <mshadbolt@users.noreply.github.com> * exception when parser fails * update reference date docs * improved error catching in manifest * better error msg * fix month intervals * remove import * minor fixes * add sample redcap files (#67) * add sample redcap files * restructure suggestion * mv sample files * update sample inputs links and info * Update README.md --------- Co-authored-by: Marion <mshadbolt@users.noreply.github.com> * create mohschemav3 class * validate v3 donors * validate primary diagnoses * validate specimens * validation logic fix * validate treatments * treatment validation fix * validate systemic & radiation therapies * validate followups * replace match with if, less indentation * validate exposures & comorbidities * rename v3 to lowercase * sample registration validation (required) * validate surgeries * added missing argument * fix nested schemas * update references to v3 * fix test * fix test, using v2 by default * update default templates * update test data files * manual mapping function changes to csv templates * update test yamls * update tests * add biomarker validation, edit resolution to work * update templates * fix typo * fix missing comma * remove extra staging validation * rename v2 template * added multisheet line for testing * stage group validation fix * validate systemic therapy dates * test systemic therapy date validation * add sample redcap files (#67) * add sample redcap files * restructure suggestion * mv sample files * update sample inputs links and info * Update README.md --------- Co-authored-by: Marion <mshadbolt@users.noreply.github.com> * Fix up some of the validations (#69) * fix for loop * fix keyerror * fix if elses * another fix * update tests * revert elif * update to version 3 (#70) --------- Co-authored-by: Javier Castillo-Arnemann <javiercastilloar@gmail.com> Co-authored-by: Javi <30913679+yavyx@users.noreply.github.com> Co-authored-by: Karen Cranston <karen.cranston@gmail.com>
mshadbolt
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Sep 30, 2024
* adding date format to date intervals * addded date format * updated docs * updated test date formats * make exceptions more readable * make exception specific * cleanup * cleanup * Update src/clinical_etl/CSVConvert.py Co-authored-by: Marion <mshadbolt@users.noreply.github.com> * exception when parser fails * update reference date docs * improved error catching in manifest * better error msg * fix month intervals * remove import * minor fixes * add sample redcap files (#67) * add sample redcap files * restructure suggestion * mv sample files * update sample inputs links and info * Update README.md --------- Co-authored-by: Marion <mshadbolt@users.noreply.github.com> * create mohschemav3 class * validate v3 donors * validate primary diagnoses * validate specimens * validation logic fix * validate treatments * treatment validation fix * validate systemic & radiation therapies * validate followups * replace match with if, less indentation * validate exposures & comorbidities * rename v3 to lowercase * sample registration validation (required) * validate surgeries * added missing argument * fix nested schemas * update references to v3 * fix test * fix test, using v2 by default * update default templates * update test data files * manual mapping function changes to csv templates * update test yamls * update tests * add biomarker validation, edit resolution to work * update templates * fix typo * fix missing comma * remove extra staging validation * rename v2 template * added multisheet line for testing * stage group validation fix * validate systemic therapy dates * test systemic therapy date validation * add sample redcap files (#67) * add sample redcap files * restructure suggestion * mv sample files * update sample inputs links and info * Update README.md --------- Co-authored-by: Marion <mshadbolt@users.noreply.github.com> * Fix up some of the validations (#69) * fix for loop * fix keyerror * fix if elses * another fix * update tests * revert elif * update to version 3 (#70) * Add RedCap export splitting script (#78) * add splitting script * minor refactoring * Update validation and test data for model 3.1 (#80) * fix deceased validation * change bools to single_vals * fix more cause_of_death validations * update test data, fix validations, update template/manifest * update schema urls * more schema changes in v3 templates * DIG-1772 & DIG-1782: Handle -99 and 'Not available' as missing (#83) * numeric not availabe and schema template update * update default url * improve template generation, add not_available to missingness * update v3 template * methods for -99 mappng * update test template and test data * update script and moh_diffs * fix typo in validation * updated mapping functions doc * updates for latest version --------- Co-authored-by: Javier Castillo-Arnemann <javiercastilloar@gmail.com> Co-authored-by: Javi <30913679+yavyx@users.noreply.github.com> Co-authored-by: Karen Cranston <karen.cranston@gmail.com> Co-authored-by: Daisie Huang <daisieh@gmail.com>
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There were some issues with the systemic therapies tests that were resulting in keyerrors, I think this should fix it