Releases: OHDSI/WebAPI
WebAPI v2.9.1
Fixes
#1890: BadRequestException: sample parameter size must fall in the range (1, 500)
#1892: Data tables error if we try to save concept set with a concept which is not included in default vocabulary source
#1896: Added missing title for condition occurrence status
#1897: ConceptNot ExistException should be validated (user-readable message)
#1902: javax.ws.rs.ForbiddenException in alert if user does not have vocabulary data source role
WebAPI v2.9.0
New Features
#1821: Localization feature was introduced including translations to Korean and Chinese languages. Thanks to IQVIA and APAC for their contribution.
MS SQL JDBC driver version was updated.
Fixes
#1782: Replacement for RANDOM keyword was added for Netezza
#1797: Sequence used for sec_permission table was changed
#1791: Permissions to view evidence were added
#1800: Fixed missing BigQuery libraries
#1799: Fix caching keys
#1817: Permission checking for priority daimon has been added
#1829: Changes how users are registered
#1822: Checking of age value was added
#1836: Fixed filter jobParameters in notifications
#1841: Quotes have been removed from source keys
#1840: Prevent stacktrace input from endpoint
#1813: Fixed calculation for standard mean difference
#1847: FEAggregate serialization fixes
#1863: Unable to copy Pathway Analysis
#1867: NotFoundException after clicking Pathway analysis in notification
WebAPI v2.8.2
Fixes
#1739: Vulnerabilities in dom4j
#1814: SqlRender version has been updated to 1.7.0
#1817: Permission checking for priority daimon has been added
#1833: Update geospatial dependency to release 1.0.1
#1836: Filter jobParameters in notifications
#1839: Check endpoint and prevent any stacktrace output
#1841: Remove quotes from list with source keys
#1853: Broken URL(undefined) after clicking PLP/PLE analysis in notification
WebAPI v2.8.1
Fixes
Raised versions of vulnerable dependencies (#1728, #1727, #1737,#1697, #1726, #1743, #1775)
#1754 : Update CIRCE to 1.9.1
#1730 : ORA-00933: SQL command not properly ended
#1729: PLP/PLE Analysis result file missed analysis executable code
#1720: WebAPI fails to start with enabled webapi-hive profile
#1733: WebAPI 2.8.0 build error - .git directory is not found! Please specify a valid [dotGitDirectory] in your pom.xml
#1759: ancestorAndDescendant:get permission is not added to new sources
#1765: Failed to export IR analysis to CSV on Hive DS (UndeclaredThrowableException)
a721214: Fix sql server migration.
#1772: [Geospatial] Map or geospatial tab should not be shown for "non-geo" data sources
#1791: Not enough permissions for evidence
v2.8.0
New Features
Important note: The 2.8 line of WebAPI will be the last release to support Oracle and MS Sql as the WebAPI database platform. (Note CDM databases are not impacted by this). So, for future major/minor releases, you will need to install a Postgres instance. We can look into community driven support for other platforms, but going forward official support will be limited to Postgresql for WebAPI.
Added validation mechanism to different domain entities of WebAPI: IR Analysis, Cohort Characterization, Pathways, etc). These validation messages are presented in the Atlas UI.
Cohort Characterization: new design element 'Distribution Criteria' allowing the creation of distribution statistics from criteria expressions. (#1449)
Data Sources - Data Density: Added Measurement data over time to Data Density Plot. (#1620)
Cohort Pathways: Allow Repeats option allows pathway segments to repeat in the result. By default, this is disabled. (#1692)
Geospatial functionality (#1445)
Use Dockerfile to facilitate development (#1384)
Cohort Sampling: samples can be created for a given cohort definition on a specific source. (#1657) (Thank you Andries Purnal (Andries.Purnal@ucb.com), Florence Giesen (Florence.Giesen@ucb.com), @MaximMoinat and The Hyve
Vocabulary Service: Added endpoitns for cocnept ancestor (#1664)
Server-Side rendering of cohort expressions: Circe expressions are converted into Markdown using Freemarker templates (#1655).
R packages for PLE/PLP were updated to use Hydra (#1643)
Implemented server-side exports of concept sets for Feature Analysis and Cohort Characterization (#1461)
Individual auth providers can be disabled. Additional information can be found in README.md. (#1623)
Several performance improvements on exporting and results retrieval (#1005, #1010)
Notable Fixes
Due to the long duration between 2.7 and 2.8 release, there were too many fixes to list here. A list of fixes can be found here (https://github.com/OHDSI/WebAPI/issues?q=is%3Aissue+is%3Aclosed+milestone%3AV2.8.0)
Migration Notes
Use SqlRender to translate the following SQL for your specific environment and run on all CDM results schemas:
Cohort Caching
Per #1353, users will need to update the results schema to include the new *_cache tables, specifically:
ALTER TABLE @results_schema.cohort_inclusion ADD design_hash int NULL;
ALTER TABLE @results_schema.cc_results ADD aggregate_id int NULL;
ALTER TABLE @results_schema.cc_results ADD aggregate_name varchar(1000);
ALTER TABLE @results_schema.cc_results ADD missing_means_zero int NULL;
IF OBJECT_ID('@results_schema.cohort_cache', 'U') IS NULL
CREATE TABLE @results_schema.cohort_cache (
design_hash int NOT NULL,
SUBJECT_ID bigint NOT NULL,
cohort_start_date date NOT NULL,
cohort_end_date date NOT NULL
);
IF OBJECT_ID('@results_schema.cohort_censor_stats_cache', 'U') IS NULL
CREATE TABLE @results_schema.cohort_censor_stats_cache (
design_hash int NOT NULL,
lost_count BIGINT NOT NULL
);
IF OBJECT_ID('@results_schema.cohort_inclusion_result_cache', 'U') IS NULL
CREATE TABLE @results_schema.cohort_inclusion_result_cache (
design_hash int NOT NULL,
mode_id int NOT NULL,
inclusion_rule_mask bigint NOT NULL,
person_count bigint NOT NULL
);
IF OBJECT_ID('@results_schema.cohort_inclusion_stats_cache', 'U') IS NULL
CREATE TABLE @results_schema.cohort_inclusion_stats_cache (
design_hash int NOT NULL,
rule_sequence int NOT NULL,
mode_id int NOT NULL,
person_count bigint NOT NULL,
gain_count bigint NOT NULL,
person_total bigint NOT NULL
);
IF OBJECT_ID('@results_schema.cohort_summary_stats_cache', 'U') IS NULL
CREATE TABLE @results_schema.cohort_summary_stats_cache (
design_hash int NOT NULL,
mode_id int NOT NULL,
base_count bigint NOT NULL,
final_count bigint NOT NULL
);
IF OBJECT_ID('@results_schema.cohort_sample_element', 'U') IS NULL
CREATE TABLE @results_schema.[cohort_sample_element] (
[cohort_sample_id] int NOT NULL,
[rank_value] int NOT NULL,
[person_id] bigint NOT NULL,
[age] int NULL,
[gender_concept_id] int NULL
);
New cache settings in pom.xml:
cache.generation.invalidAfterDays=${cache.generation.invalidAfterDays}
cache.generation.cleanupInterval=${cache.generation.cleanupInterval}
cache.generation.useAsync=${cache.generation.useAsync}
(cache.generation.useAsync details: https://github.com/OHDSI/WebAPI/pull/1459)
Cohort Sampling
IF OBJECT_ID('@results_schema.cohort_sample_element', 'U') IS NULL
CREATE TABLE @results_schema.cohort_sample_element(
cohort_sample_id int NOT NULL,
rank_value int NOT NULL,
person_id bigint NOT NULL,
age int,
gender_concept_id int
);
Cohort Characterization
The following alters the existing cc_results table, the full definition can be found here (https://github.com/OHDSI/WebAPI/blob/master/src/main/resources/ddl/results/cohort_characterizations.sql)
alter table@results_schema.cc_results ADD aggregate_id int NULL, aggregate_name varchar(1000), missing_means_zero int NULL;
Acknowledgements
Thanks to @pavgra, @ssuvorov-fls, @aklochkova, @AntonStepanof, @chrisknoll, @wivern, @anton-abushkevich, @ekaterinakrivets, @YaroslavTir, @SergeySukhanov, @KSadomtsev, @konstjar, @vlbe, @AnthonyMolinaro, @MaximMoinat (and the team at TheHyve) for their contributions and reviews as part of this release.
v2.7.9
Fixes
- Updated springsource maven URL to use HTTPS.
WebAPI v2.7.8
Fixes
- Fix for users permissions (#1598)
- Impossible to delete Feature Analysis (#1596)
- Concept set opens with an error (#1595)
- PLP/PLE import failed (#1593)
- Characterization import skips features (#1538)
- ACHILLES reports and caching (#1551)
- Application initialization failed for users without "Atlas users " role (#1584)
- Export and import of characterizations are not compatible. (#1497)
- User is not allowed to edit imported concept set which was added after PLE importing (#1546)
- Characterization fails with SQL error in case of wrong Feature Analysis name (#1566)
- WebAPI failed to start in some cases with enabled AD synchronization (#1561)
WebAPI v2.7.7
Fixes
- Growing number of TEMP_COHORT tables in results schema for Netezza DB (#1067)
- Google OAuth component update (#1511)
- WebAPI does not invalidate jobs after restart (#1467)
- Hydra updates for PLP improvements (#1487)
- FATAL ERROR in PLE analysis if the data source name contains a slash (#1542)
- Shiny directory is not created in PLP results (#1541)
