Shiro mods #2
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Shiro mods #2
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ganisimov
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May 26, 2017
* ignore IntelliJ files add'l characterization/summarization work added SQL files for summary service from Achilles::ExportToJSON added data transfer objects (DTOs) modified CDMResultsService, made several sql translation changes, moved mappers and DTOs to report package in preparation for refactoring. added add'l DTOs to report package and stubbed out service and runner classes. fixed imports in some DTOs and RowMappers * Use same method (getTreemap) for all (non-temporal) treemaps Add generic row mapper, text hack impls made several sql translation-related changes Use same method (getTreemap) for all (non-temporal) treemaps 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 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 fixed /datadensity 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 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 removed superfluous code (imports, methods, etc) Reorganize sql files for cdm drilldowns (to reduce text wrangling) (#2) * Remove sql prefix from files names * Camel-case filename * Move drilldown files to folders * Delete treemap files that were reverted back removed unused method - renderDrillDownSql() changed access modifier on several fields and methods removed unused test and related resource made post-rebase reconciliations in prep for PR
ganisimov
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May 26, 2017
* Apache Shiro integration. * Reflect HTTP verb normalization. * Final updates to Shiro implementation * Added hibernate dialect to POM.xml. * Added schema qualifier for FK references in migraiton scripts * Fixes OHDSI#108 (OHDSI#163) * ignore IntelliJ files add'l characterization/summarization work added SQL files for summary service from Achilles::ExportToJSON added data transfer objects (DTOs) modified CDMResultsService, made several sql translation changes, moved mappers and DTOs to report package in preparation for refactoring. added add'l DTOs to report package and stubbed out service and runner classes. fixed imports in some DTOs and RowMappers * Use same method (getTreemap) for all (non-temporal) treemaps Add generic row mapper, text hack impls made several sql translation-related changes Use same method (getTreemap) for all (non-temporal) treemaps 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 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 fixed /datadensity 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 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 removed superfluous code (imports, methods, etc) Reorganize sql files for cdm drilldowns (to reduce text wrangling) (#2) * Remove sql prefix from files names * Camel-case filename * Move drilldown files to folders * Delete treemap files that were reverted back removed unused method - renderDrillDownSql() changed access modifier on several fields and methods removed unused test and related resource made post-rebase reconciliations in prep for PR * Fixes OHDSI#167 (OHDSI#168) * Fixes OHDSI#170 * removed extraneous folder * Added support for user-defined OP start and end dates. * Route cleanup. Made service routes for CDMResutlsService, CohortResultsService, EvidenceService and Vocabulary service to stem from the url of the service (such as /cdmresults) vs. stemming from a source key. Added a default handler for vocabulary searching as an example of where it's advantageous to use a route of /vocabulary/search/{query} directly instead of coding to a specific source key (which may not always be available). Fixes OHDSI#173. * Exposing default routes for vocabulary service endpoints that previously required a source key. * Added WebAPI endpoint: /info. Currently only contains version information, stored in pom.xml property 'webapi.version'. Fixes OHDSI#176. * Fixes OHDSI#177 * Fixes OHDSI#178
ganisimov
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May 20, 2024
…with ParallelLogger (OHDSI#1181)
ganisimov
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May 20, 2024
…with ParallelLogger (OHDSI#1182)
ganisimov
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May 20, 2024
…int (OHDSI#1293) * Fixes permissions for newly created Source. Fixes "/permission" endpoint * Remove unused line * Preciser role search * Preciser role search #2 * Preciser role search OHDSI#3
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@ganisimov - I've taken the feedback from our other pull request and revised the code which has simplified both my code modifications and the configuration options. Please take a look and let me know if you have any concerns!