New Features
- Phoebe 2.0: Concept Recommendations by @chrisknoll. Install instructions can be found here.
- Improve user tagging usability OHDSI/Atlas#2722 by @anton-abushkevich @ssuvorov-fls in #2067
- Added visit detail entity by @ssuvorov-fls @anton-abushkevich in #2076
- Support storage of more description fields #2058 by @anton-abushkevich @ssuvorov-fls in #2070
- Add valid_start_date and valid_end_date to concept endpoint #2057 by @anton-abushkevich in #2068
- Added isCacheEnabled to Source by @chrisknoll in #2077
- Added OpenTelemetry Java Agent for auto-instrumentation by @chgl in #2082
- configurable scopes for OpenID Connect (OIDC) authentication by @m0nhawk in #2083
- Snowflake dialect support by @ssuvorov-fls in #2096
- Azure Synapse Analytics Dedicated dialect support by @ssuvorov-fls in #2097
- Bump Hydra to v0.3.0 by @anthonysena in #2084
Implementation Notes
Phoebe 2.0
Phoebe 2.0 requires a new table concept_recommended to be created in your OMOP CDM schema. Instructions on creating this table and populating it with the suggested concept recommendations are found in this post: https://forums.ohdsi.org/t/phoebe-2-0/17410
Assigning/unassigning Tags to/from Multiple Assets
Tagging is enabled with the help of <tag.enabled>true</tag.enabled> in the server configuration (WebAPI) and by an entry
config.enableTaggingSection = true; in config-local.js in the client configuration (ATLAS)
Visit Detail as a new Criteria Item
To use this feature your OMOP CDM Data Source should have the optional visit_detail table populated. For more information, please refer to
http://ohdsi.github.io/CommonDataModel/cdm54.html#VISIT_DETAIL
New Dialects Support - Snowflake and Azure Synapse Analytics Dedicated
The following OHDSI repositories have been extended to support the dialects:
OMOP CDM - OMOP CDM DDL scripts can be found there
DatabaseConnector - an R package to connect to a database
DatabaseConnectorJars - an R package which provides external JAR dependencies for the DatabaseConnector package
SqlRender - an R package to translate OHDSI SQL to the corresponding dialect
Achilles - an R package which provides descriptive statistics for an OMOP CDM database
[ARACHNE Commons] (https://github.com/OHDSI/ArachneCommons/tree/1.17.x) (https://github.com/OHDSI/ArachneCommons/tree/master) - a common component used by ATLAS/WebAPI and ARACHNE to share common code
[ARACHNE Execution Engine] (https://github.com/OHDSI/ArachneExecutionEngine) - an application used to execute SQL and R code provided by ATLAS/WebAPI (Patient Level Prediction (PLP), Population Level Effect Estimation (PLE) analyses or [ARACHNE Data Node] (https://github.com/OHDSI/ArachneNodeAPI)
Bug Fixes
- Refresh user names during scheduled user import #2059 by @anton-abushkevich in #2072
- Duplication in logs #2024 by @anton-abushkevich in #2029
- WebAPI v2.11 fails to start with many sources configured #2031 by @anton-abushkevich in #2032
- Achilles Heel report is deprecated in Achilles #2489 by @anton-abushkevich in #2036
- security fixes: add embed tomcat dependency 8.5.81 by @anton-abushkevich in #2044
- Treat pathway combo_id as Long. by @chrisknoll in #2063
Known Issues
- analyses execution on an IBM® Netezza® OMOP CDM Data Source are failing
- PLP and PLE analyses execution on ARACHNE Execution Engine are not supported after updating WebAPI to use Hydra 0.3.0 skeletons - a new release of https://github.com/odysseusinc/DockerEnv is required
- incorrect Cohort counts with a Visit Detail criteria when the corresponding OMOP CDM table is empty #2129
New Contributors
Thanks to @ttemnikova for Quality Assurance
Full Changelog: v2.11.0...v2.12.0