Releases · OHDSI/Atlas (original) (raw)

ATLAS v2.15.0

Main Features

• Concept Set annotations
• Temporal/Annual Prevalence in Cohort Characterization
• Cohort Demographics
• Shiny App packaging
• Caching of Permissions and Cohort / Concept Set lists to improve performance.

Specific documentation for the above features will be provided at a later time. The PRs and issues related to the above features can be found under the next section.

What's Changed

• Bypass refreshToken() when authentication is not enabled. by @chrisknoll in #2900
• Optimize Permission handling on ui by @chrisknoll in #2912
• Allow Observation Period in censor events. by @chrisknoll in #2931
• #2916 - Improvements to Docker Configurability of Atlas Application by @qcaas-nhs-sjt in #2917
• fix The Korean sentence order in Authorship description by @tandara0 in #2947
• Data Sources reports bug fixes by @amarsan in #2972
• Update nginx to 1.27.2 by @jmvizcainoio in #2974
• Clearer table boundaries on generate UI by @anthonysena in #2977
• Change concept set display in patient profile - fixes #2815 by @anthonysena in #2976
• IR generation button fixes by @anthonysena in #2979
• Allow read-only custom feature browsing by @anthonysena in #2975
• Have the Clear Server Cache button clear the cdm_cache and achilles_cache tables by @amarsan in #2980
• Extending a Concept Set with a new tab 'Annotations' by @alex-odysseus in #2971
• Switch clear-server cache button to clear webapi cache. by @chrisknoll in #2986
• Update cohort editor and viewer to render new fields from CIRCE 1.12.0 by @chrisknoll in #2989
• Fixed typos in criteria types for issue #2988. by @chrisknoll in #2992
• Adding UI to map non-Standard Concepts to the Standard ones to streamline Concept Set creation by @alex-odysseus in #2978
• Tools module functionality by @alex-odysseus in #2951
• Initial support for InterSystems IRIS data sources by @bdeboe in #2987
• Extending Cohort generation results with simple demographics available in Cohort Characterization by @alex-odysseus in #2959
• Removed duplicated modules. by @chrisknoll in #2998
• Cohort and analyses execution / generation listings extensions with a button to publish/download Shiny applications by @alex-odysseus in #2957
• Show left/right censor of cohort read-only view. by @chrisknoll in #3006
• Refresh auth token if user is actively using the Atlas UI by @pieterlukasse in #3002
• Fix: adjust attribute name "disable" to match what is defined in multi-select.js by @pieterlukasse in #3014
• Add better caching instruction to headers by @pieterlukasse in #3000
• Temporal annual distribution functionality and temporal FeatureExtraction capability enablement by @alex-odysseus in #2950

New Contributors

• @qcaas-nhs-sjt made their first contribution in #2917
• @tandara0 made their first contribution in #2947
• @amarsan made their first contribution in #2972
• @jmvizcainoio made their first contribution in #2974
• @bdeboe made their first contribution in #2987
• @pieterlukasse made their first contribution in #3002

Full Changelog: v2.14.0...v2.15.0

ATLAS v2.14.1

ATLAS v2.14.0

What's Changed

• Check for empty data condition. by @chrisknoll in #2834
• Concept added to a concept set has no Exclude/Descendants/Mapped flag #2838 by @anton-abushkevich in #2839
• Pinned and updated dependency versions by @chgl in #2683
• "Place of service distance" criteria for a Visit Occurrence criteria is misfunctional #2814 by @anton-abushkevich in #2841
• Move databindings loading to application bootstrap. by @chrisknoll in #2852
• Adds ability to disable browser check via config by @alondhe in #2863
• Correct vocabulary for person counts is used by @ssuvorov-fls in #2860
• Add option to force authentication by @RowanErasmus in #2861
• Fixed name of downloaded file by @ssuvorov-fls in #2864
• Fix terms and conditions content by @jack5mil in #2765
• Fixed PLE editor text for i18n. by @chrisknoll in #2871
• Make indexMessage respond to observable changes. by @chrisknoll in #2853
• Add read permissions (#2849) by @chrisknoll in #2879
• Reduce polling to /user/refresh by @chrisknoll in #2835
• Circe date offsets by @chrisknoll in #2880
• Ensure prism loads in correct order. by @chrisknoll in #2877
• Prevent multiple calls to concept set list when loading cohort editor by @anthonysena in #2888
• Reset feature analyses parameters after submission by @jack5mil in #2768

New Contributors

• @alondhe made their first contribution in #2863
• @RowanErasmus made their first contribution in #2861
• @jack5mil made their first contribution in #2765

Full Changelog: v2.13.0...v2.14.0

ATLAS v2.13.0

New Features

• Tagging Management via UI
• Cohort SQL output enhanced to emulate the SqlRender Shiny application (easy parameters entry and color coding rendering)
• Generation / Executions UI standardized across different Analyses types
• Customized logo and support text allowed ('feedbackContacts', 'feedbackCustomHtmlTemplate', 'companyInfoCustomHtmlTemplate', 'showCompanyInfo' properties in your 'config-local.js')
• Cohort box plots for one and more than two Cohorts in the Cohort Characterization Analysis results
• Shading prevalence data tables in the Cohort Characterization Analysis results
• Data Source selection added to the Concept Set designer together with the person counts (PC) and descendant person counts (DPC) columns
• ACHILLES pre-computed data enriched the Concept page
• The preview button on the Concept page allows previewing the changes of a Concept Set if the Concept will be added as a Concept Set Item
• A Venn diagram has been added for visualization of Concept Sets comparison
• Concept Set comparison enhanced with a possibility to compare Concepts with a list of Concepts in a CSV file of specific structure

What's Changed

• added ability to refresh user names from ldap/ad by @ssuvorov-fls in #2771
• Tags table rendering error #2782 by @anton-abushkevich in #2784
• 403 error when removing IR generation result not displaying properly #2783 by @anton-abushkevich in #2785
• Add venn diagram by @anton-abushkevich in #2794
• Add tagging management through UI #2773 by @anton-abushkevich in #2774
• Add custom logo enhance url support by @anton-abushkevich in #2796
• Add cohorts box plots regardless of selected cohorts by @anton-abushkevich in #2797
• i18n for venn diagram by @TitrS in #2811
• Add highlights sql output by @anton-abushkevich in #2790
• Cohort graphical view - fixed position of tooltip by @anton-abushkevich in #2808
• Add chart drilldown to concept pages by @anton-abushkevich in #2806
• Generation / Executions UI with many data sources #2776 by @anton-abushkevich in #2789
• Add proportional shading to characterization data tables by @anton-abushkevich in #2788
• Add conceptset preview by @anton-abushkevich in #2792
• npm run build fails on master branch #2786 by @anton-abushkevich in #2787
• SQL Export template error on new Cohort #2825 by @anton-abushkevich in #2826
• Add conceptset preview by @anton-abushkevich in #2821
• Add data source selection to cs designer by @anton-abushkevich in #2799
• Add csv for comparison conceptsets by @anton-abushkevich in #2801
• loading record counts was removed from concept drilldown tab by @ssuvorov-fls in #2831

New Contributors

• @TitrS made their first contribution in #2811

Full Changelog: v2.12.0...v2.13.0

ATLAS v2.12.1

A technical release for WebAPI v2.12.1

ATLAS v2.12.0

New Features

• Add visit details criteria by @anton-abushkevich @TitrS in #2737
• Add export button to all visualizations with more export options #2727 by @anton-abushkevich @TitrS in #2736
• Add selection of inclusion rule permutations in Intersection View #2726 by @anton-abushkevich in #2735
• Add description fields for all study asset types #2724 by @anton-abushkevich @TitrS in #2733
• Phoebe 2.0 UI by @chrisknoll in #2751
• Improve user tagging usability #2722 by @anton-abushkevich in #2731
• Add warning message to reusables about using types #2684 by @anton-abushkevich in #2685
• Add notification of generated visuals within “Data Sources” upon drilldown #2725 by @anton-abushkevich @TitrS in #2734
• Add valid_start_date and valid_end_date to concept screens #2723 by @anton-abushkevich in #2732

Bug Fixes

• Concept Sets comparison allows to choose from sources unavailable to current user #2705 by @anton-abushkevich in #2706
• Loader icon does not show (font-awesome icon "fa-circle-notch") #2702 by @anton-abushkevich in #2703
• Cohort Builder: Nested Criteria doesn't appear in 'Add Dose Era' and 'Add Observation' #2707 by @anton-abushkevich in #2708
• Achilles Heel report is deprecated in Achilles #2489 by @anton-abushkevich in #2709
• User with human readable name cannot grant access to their PLP and PLE #2714 by @anton-abushkevich in #2717
• Fixed invalid redirect for /atlas without trailing slash by @chgl in #2700
• Changing Data Source does not update the reports on Atlas 2.11.1 #2741 by @anton-abushkevich in #2743
• i18n problem with lodash templates #2745 by @anton-abushkevich in #2746
• Insert from Reusable: change “Any Condition” to “Any Concept Set” #2747 by @anton-abushkevich in #2748
• Patient level prediction covariate settings include/exclude concepts popup broken. #2645 by @anton-abushkevich in #2730
• Typo - Export / Text View - Cohort Exit - suply #2750: fix default i18n by @anton-abushkevich in #2752
• Text View - Copy to Clipboard Errors #2749 by @anton-abushkevich in #2753

New Contributors

• @TitrS made their first contribution in #2736

Thanks to @ttemnikova for Quality Assurance

Full Changelog: v2.11.0...v2.12.0

ATLAS v2.11.1

Fixes

• Concept Sets comparison allows to choose from sources unavailable to the current user #2705
• Loader icon does not show (font-awesome icon "fa-circle-notch") #2702
• Cohort Builder: Nested Criteria doesn't appear in 'Add Dose Era' and 'Add Observation' #2707
• ACHILLES Heel report is deprecated in ACHILLES #2489
• If user's name differs from the login, the user cannot grant access to their PLP and PLE #2714

ATLAS v2.11.0

New Features

• Reusables module #2623
• Font Awesome upgrade #2585
• Import Source Code functionality extended with a possibility to specify a Vocabulary #2653
• Importing a Concept Set from the repository - augmenting the existing expression #2654
• Atlas Charts dependency update #2629

Fixes

• Data Source URLs don't work after authentication #2625
• Correct sorting in the Characterization report #2663
• Cohort Characterization with the large number of Cohorts optimization #2651
• Using the username instead of login in the filter panel #2670
• Listing only user-accessible sources in search results #2672
• Deletion alert messages unification #2680
• Doubled loading indicator when opening a Cohort #2691
• Dependency libraries update #2687
• Missing Characterization result filter options #2619

Acknowledgments

Many thanks to the release contributors @anton-abushkevich @ssuvorov-fls @chrisknoll @anthonysena @alondhe @OdysseusMark @alex-odysseus

ATLAS v2.10.1

Fixes

#2614: Generation results for impala are not visible for incidence rates
#2616: Selecting Censoring event for Payer Plan period fails
#2617: Selecting censoring event for visit creates a specimen entry instead
#2622: Cohort exit date text is wrong in Atlas > Prediction > Population settings

Atlas v2.10.0

New Features

#2589: Tagging capability
#2588: Audit trail
#2592: Versioning of design assets

Fixes

#2501: Disable "Add to New Concept Set" button when no concepts selected
#2539: Fix typo in Included Concept Identifier Export Area
#2514: Messages tab: loader gets stuck if the user leaves IR analysis page and returns back
#2547: Cohort reports are available only after deselecting and selecting a data source
#2548: Add error handling for missing concept from non default vocabulary
#2522: Export JSON and SQL in IR analysis should be generated after saving valid analysis design
#2543: Add back "select all" for concept selection
#2554: Update error message for cohort sampling
#2555: Fix condition status heading in cohort builder
#2557: Added exception handling for absent concept set
#2560: Select all checkbox doesn't work properly with filters
#2563: Inappropriate value in days(Cohort definition)
#2565: Inclusion population visualization shows code as label
#2568: javax.ws.rs.ForbiddenException in alert if user does not have vocabulary data source role
#2572: newThresholdValuePct is not updating in characterization
#2583: "Prevalence" count cannot be changed
#2581: Incorrect domain "provider specialty" in the attributes of the Cohort
#2579: Specimen event missed in censoring events
#2575: Improve docker configuration options

Acknowledgements

Thanks to @anton-abushkevich, @ssuvorov-fls, @chrisknoll, @alex-odysseus, @OdysseusMark, @alondhe, @blootsvoets for their contributions to this release.