Fixes #167 #168
Merged
Fixes #167 #168
Conversation
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
fdefalco
approved these changes
Feb 1, 2017
anthonysena
added a commit
that referenced
this pull request
Feb 22, 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 #108 (#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 #167 (#168) * Fixes #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 #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 #176. * Fixes #177 * Fixes #178
Sign up for free
to join this conversation on GitHub.
Already have an account?
Sign in to comment
Add this suggestion to a batch that can be applied as a single commit.
This suggestion is invalid because no changes were made to the code.
Suggestions cannot be applied while the pull request is closed.
Suggestions cannot be applied while viewing a subset of changes.
Only one suggestion per line can be applied in a batch.
Add this suggestion to a batch that can be applied as a single commit.
Applying suggestions on deleted lines is not supported.
You must change the existing code in this line in order to create a valid suggestion.
Outdated suggestions cannot be applied.
This suggestion has been applied or marked resolved.
Suggestions cannot be applied from pending reviews.
Suggestions cannot be applied on multi-line comments.
Suggestions cannot be applied while the pull request is queued to merge.
Suggestion cannot be applied right now. Please check back later.
The delete command in the original method were causing the following JPA exception:
org.hibernate.StaleStateException: Batch update returned unexpected row count from update [0]; actual row count: 0; expected: 1This was fixed by re-ordering the deletes to clean up records from downstream tables first and then deleting the record from the parent table.