Added correct fields to select to match UNION of other criteria queries. #146
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anthonysena
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Nov 30, 2016
t-abdul-basser
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Jan 11, 2017
* add initial set of refactored class for summary service * Added SQL for summary service functionality. See issue OHDSI/issues/108 * imported SQL file from Achilles Export2JSON, add'l refactoring of CDMResultsService impl * added stub method for retrieval of drug and procedure reports to CDMResultsService * Demographic Criteria Implementation. * Removed BETWEEN usage in criteria A BETWEEN X and Y becomes A >= X and A <= Y. BETWEEN is not consistent between all db platforms. * Incidence Rate Analysis Implementation Implementation of Incidence Rate web services, tasklets and repositories and IR Analysis Report Generation. Added new dependency: apache commons collections v4.1. * Remove BETWEEN expression from numeric and date range criteria input types. * Add null check for correlated criteria end date. Existing cohorts will have this null, so a null check is required. * enhancements for person profile service and cohort comparison service * sql syntax error * Fix to allow more than 1 person per cohort. * Flyway deployment scripts for postgreSQL and Oracle. * adding outcome model retrieval and updates to comparative cohort analysis * Negative controls implementation modified: src/test/java/org/ohdsi/webapi/test/feasibility/StudyInfoTest.java * ConceptSet optimization and comparison utilities * ConceptSet utilties * Moving GenerationStatus enum * Delete concept sets per OHDSI/Atlas#87 * Fixing ir calc flyway script for postgreSql * sql cleanup * Flyway fixes for sql server * Fixed oracle migration scripts. * Added @generated to NegativeControlRecord. JPA will manage this entity's auto-number. * Fix IR Strata TAR. IR Strata was not calculating TAR in years. * resolve interface changes with r packages * logging * resolve missing placeholder * made several sql translation changes * moved mappers and model objects to report package in prep for refactoring. * added DTO to report package and stubbed out service and runner classes. * Use same method (getTreemap) for all (non-temporal) treemaps * Add generic row mapper, text hack impls * new drugService call: http://localhost:8080/WebAPI/OPTUM-PDW/drugexp/personId/33034143174. working as is, but planning to add some fields and allow drug_concept_id to be specified in addition to or instead of person_id * Meant to push this to fork and then make pull request. Reverting. Revert "new drugService call: http://localhost:8080/WebAPI/OPTUM-PDW/drugexp/personId/33034143174. working as is, but planning to add some fields and allow drug_concept_id to be specified in addition to or instead of person_id" This reverts commit 19fee59. * Reverting revert. Will push this to fork instead of ohdsi Revert "Meant to push this to fork and then make pull request. Reverting." This reverts commit 14e1f79. * made the same mistake twice. Revert "Reverting revert. Will push this to fork instead of ohdsi" This reverts commit 5b699ad. * Fix OHDSI#137 Updated criteria group query to left join to @eventTable to capture events that matched 0 of the criteria in the group. * Cohort def optimizations (OHDSI#142) * Make first occurrence of event deterministic. Added order by _date, _id to criteria queries to use the event ID as the tiebreaker. Fixes OHDSI#139. * Cohort Definition Query Optimization Optimized #primary_events and #qualified_events into single query, eliminating one temp table creation. Partitioning on person_id for event_ids allowing MPP architectures to leverage hashing on person_id. Fixes OHDSI#141. * Added proper partitioning on person and event for gain counts. * Switched from qualified_events to included_events for end date selection. * Fixes OHDSI#144. Removed ExceptionHandler from generate cohort step; it was masking the failed job completion status by returning 'COMPLETED' after failure. * Use same method (getTreemap) for all (non-temporal) treemaps * Add generic row mapper, text hack impls * Reformat cdmresults sql scripts * Use AS keyword in all cdm report query aliases * Remove text hack and camel case column names in cdm report queries * Replace all treemap endpoints with a single generic implementation * Rename all treemap CDM report files to treemap.sql * Enquote aliases in CDM report queries to preserve case * Add GenericRowMapper ctor with ObjectMapper for performance * CDMResultsAnalysisRunner.getTreemap returns ArrayNode * Fix condition CDM results queries (by concept) * include conceptId parameter * rename sqlAgeAtFirstDiagnosis to sqlAgeAtFirstOccurrence * modify sqlConditionsByType to check vocabulary_id, not domain_id * cast xCalendarYear to INT in sqlPrevalenceByGenderAgeYear * Fix queries associated with generic drilldown reports * Data types include conditionera, drug, drugera, measurement, observation, procedure, visit * Queries include AgeAtFirstOccurrence, PrevalenceByGenderAgeYear, ByType, ByMonth * Include parameter @conceptId * Cast xCalendarYear to INT (where applicable) * Remove obsoleted code from CDMResultsService (activates observation reports) * Standardize names of "by type" query files for cdm reports to sqlByType.sql Applies to condition, drug, measurement, observation, procedure * Add cdm_database_schema to CDMResultsAnalysisRunner standard columns (for measurement treemap) * Fix typo in sqlVisitDurationByType.sql * added fixes to row mapping in /person and dashboard * implemented /achillesheel, /datadensity started implementation of /death refactored CohortAttributeMapper --> CDMAttributeMapper created new report data objects drop unused/superfluous CDMResultsAnalysisRunner * Fixes for demographic criteria. (OHDSI#146) * Added correct fields to select to match UNION of other criteria queries. * Change IR Analysis strata queries to properly partition by person_id. * Updated sql to match SqlRender SqlRender does not support 'TOP' instruction, changed * HTTP verb normalization POST = create PUT = update Fixes OHDSI#147. * fixed /datadensity * IR Enhancments Calculate distribution of Time At Risk and Time to Outcome. Provide new export to zip function to export definition and raw data from analysis results. * Cohort Definition Correlated Criteria Extends cohort definition criteria to allow specification of a criteria group whose members must result in a true result in order for the criteria to be satisfied. * Allow censoring criteria in cohort definitions. * Gracefully handle empty criteria groups in cohort definitions. Fixes OHDSI#155 * cleaned up and changes /achillesheel --> /heel * Add cdm_database_schema to CDMResultsAnalysisRunner standard columns as per mark-velez/* #e862d53 * changed endpoint signature (/heel -->/achillesheel), fixed summary yob and yob in person report * fixed null totalRecords element in Data Density report * added summary to dashboard report in CDM results service * implemented death report
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