Releases: OHDSI/Atlas
Releases · OHDSI/Atlas
Atlas Version 2.7.2
Helpful Resources
- For installation and configuration, please refer to the Atlas Setup Guide
- For an overview of ATLAS please refer to the Atlas Video Tutorials.
Fixes
- Data Sources
- Fixed precision on data density plots (#1535)
- Fixed description on person plot (#1458)
- Fixed rounding in data density box plot (#1536)
- Fixed data source display with security enabled (#1441)
- Removed extraneous calls to WebAPI (#1715)
- Fixed ATC display heading in drug era report (#1897)
- Fixes issue when data source name includes spaces (#1914)
- Vocabulary Search
- Fix column visibility display (#1491)
- Restores advanced search capability (#1570)
- Handle special characters in search string (#1653)
- Selecting all concepts removes previously chosen filters (#1526)
- Retrieve concept counts for non-standard concepts (#1725)
- Fixed display when navigating to concept from ancestor display (#1865)
- Concept Sets
- Added error message when import fails (#1529)
- Ability to import into an open concept set (#667, #1525)
- Fixes included concept display when adding from the vocabulary (#1518)
- Fixed ability to edit a design after copy with security enabled (#1599)
- Fixed importing large lists of concepts (#1532)
- Fixed stale reference to concept set after deletion (#1750)
- Fixed included concepts display after optimization (#1761)
- Fixed negative control link display (#1888)
- Fixed included source codes display (#1852)
- Cohort Definition
- Fixes generation status error when running cohort reporting (#1606)
- Add visual feedback when selecting a concept set (#1615)
- Provide flexibility in how to restrict events based on observation period (#43)
- Fixed export for print friendly to copy the full text (#1547)
- Restructure code in criteria hierarchy (#1681)
- Inclusion criteria for location region (#1669) and location distance filter for visit occurrence (#1697)
- Added labels to attrition view to display the inclusion rule information (#1129)
- Fixes error thrown when switching exit criteria (#1688)
- Fixed timezone display on cohort/characterization lists (#1748)
- Fixed notification link for cohort reporting (#1755)
- Improved sorting performance for large lists of cohort definitions (#1571)
- Fixes adding concepts from included concepts list in a cohort definition (#1850)
- Additional checks for displaying the concept set export button in a cohort definition (#1853)
- Fixes tooltip message for cohort definition generation (#1860)
- Fixes condition & drug era treemap drilldowns in cohort reporting (OHDSI/WebAPI#933)
- Fixed the status panel when generating cohort reports (#1920)
- Cohort Characterization
- Enable re-generation of failed jobs (#1494)
- Prevent execution of characterization with no cohorts specified (#1363)
- Grey out covariates that are < 0.1 in standardized difference (#1144)
- Default sort by standardized difference and median (#1127)
- Fixed ability to edit a design after copy with security enabled (#1612)
- Properly escape double quotes for covariate names (#1698)
- Fixed proportions when using the 'explore' feature (#1692)
- Fixed Feature Analysis Modal (#1744, #1779)
- Revised the "explore" button for navigating results (#1757)
- Fixed the characterization comparison plot display (#1758)
- Fixed prompt message when closing an empty feature analysis (#1875)
- Removed custom 'preset' feature type from feature analysis definition editor (#1925)
- Cohort Pathways
- Incidence Rates
- Profiles
- Estimation/Prediction
- Use a consistent createdBy formatter to prevent problems in estimation and prediction list display (#1705)
- Display an error if import fails (#1683)
- Fix package name entry (#1533)
- Fixes refresh of summary display of study design after editing (#1710)
- Estimation only - fixed max cohort drop down for positive control synthesis (#1658)
- Fixes an error thrown when saving a PLP study (#1708)
- Fixed collapsible area icon (#1756)
- Security
- Added ability to clone/copy/import/export roles (#1269)
- Fixed session expiration message (#1677)
- Display a full user name instead of a login id (#1289)
- Added "RunAs" functionality (#1723)
- Fixed AD Sync Job (#1729)
- Properly handle unsecured pages after logout (#1767)
- Add confirmation dialog for deleting roles (#1873)
- System
- Don't show date/times for tasks which have not started (#1559)
- Added ability to warm the record count cache on demand (#1407)
- Dispose of data table when containing element is disposed (#1636)
- Ensure all entity names are unique (#1307, #1338, OHDSI/WebAPI#1146)
- Added "id" column to list display for characterizations, pathways (#1550)
- Fixed error when editing a BigQuery data source (#1684)
- Fixed notification hyperlinks for characterization and pathways (#1694)
- Use local CSS file for bootstrap-select (#1726)
- Fixed xss vulnerability in data tables (#1765)
- Lock version of bootstrap select to prevent flex markup issues (#1845)
- Disable exporting unsaved entities (#1884, #1864)
- Change the default sort on all design listing display (#1867, #1908)
- Added HemOnc license agreement (#1921)
- Fixed escape content in links (#1924)
Here is the full list of fixes
Acknowledgements
Thanks to @pavgra, @quveex, @AntonStepanof, Sergey Suvorov, @johnSamilin, @vlbe, @ssuvorov-fls, @aklochkova, @chrisknoll, @wivern, @fdefalco for their contributions and reviews as part of this release.
Testing Results
We have provided high-level test scripts and results to show how the application was tested for this release. Please see the attachments for this release for more details.
Atlas Version 2.7.1
Fixes
- Fixed editing of IR Analysis after generation @vlbe (#1667)
- Fixed switching between Pathways and IR opened analyses @vlbe (#1649)
- Fixed modal overflow @pavgra
- Fixed Concept Set reload when new concepts picked from vocabulary @anthonysena
- Fixed bundle.js timeouts @vlbe
- Don't display login exp time when it is not available @AntonStepanof (#1622)
- Refresh Sources on configuration screen load @AntonStepanof (#1597)
- Fixed Characterization page on return @vlbe (#1626)
- Fixed permissions refresh for Google IAP @pavgra (#1616)
- Fixed issues with first Source creation @AntonStepanof (#1614)
- Added 403 status handling for IR reports @johnSamilin (#1604)
- Fixed markup for Inclusion criteria @vlbe (#1601)
- Fixed IR generation jobs loading @vlbe (#1609)
- Fixed Sign in label for IAP @pavgra (#1603)
Atlas Version 2.7.0
This release aims to fix bugs from the previous releases and to address functionality gaps from v2.6.0.
Important
To build/release Atlas now, you must use npm which is part of NodeJS. Once you have cloned the Atlas repository, run the following command from root of the Atlas directory:
npm run build
Then copy all of the files from the Atlas repo to your web server - the node_modules folder is now required to resolve all JavaScript dependencies.
New Features
- Characterizations
- Added the ability to add one or more strata to a characterization
- Provides the ability to export cohort characterization results to CSV
- Added the ability to cancel generation of a characterization
- Added a threshold for retrieving cohort characterization results to improve reliability of the results page loading (default is prevalence > 0.01)
- Estimation & Prediction
- Added ability to import/export specifications for transport between ATLAS environments
- Updated utilities tab to provide more guidance to review study choices and to download the R study package
Fixes
There were nearly 150 issues closed in this release and so we've broken them down by functional group:
- Characterizations fixes
- Cohort definition fixes
- Data Sources fixes
- Estimation fixes
- Prediction fixes
Here is the full list of issues closed in the 2.7 release
Acknowledgements
Thanks to @pavgra , @johnSamilin , @aklochkova, @chrisknoll, @wivern, @fdefalco, @mpozhidaeva, @vlbe for their contributions and reviews as part of this release.
Atlas Version 2.5.2
Fixes
- Fixed empty new source page (#936) - thanks @mpozhidaeva
- Fixed AD import issues (#946) - thanks @mpozhidaeva
- Fixed age of observation chart with negative ages (#941) - thanks @mpozhidaeva
- Fixed cohort generation duration format (#955) - thanks @mpozhidaeva
- Fixed frozen modal backdrop after page navigation (#1039) - thanks @pavgra @wivern
- Restrict deletion of sources with top-priority daimons into 2.5.2 (#1038) - thanks @pavgra
- Fixes for performance of cohort export to 2.5.2 (#1038) - thanks @vantonov1 @pavgra
- Fixed link to cohort definition generated by UI (#1047) - thanks @pavgra @wivern
- Added browser check bar on top of the window into 2.5.2 (#1147) - thanks @aklochkova @pavgra
- Fixed multiple count requests (#1198) - thanks @johnSamilin @pavgra
- Added proper sorting for tables datetime columns (#1264) - thanks @johnSamilin @pavgra
Atlas Version 2.6.0
New Features
- Cohort Characterization (OHDSI/WebAPI#495) - thanks @pavgra, @chrisknoll, @wivern, @gowthamrao, @davekern
- Cohort Pathways (OHDSI/WebAPI#522) - thanks @chrisknoll, @pavgra, @anthonysena, @pbr6cornell
- New editors for Population Level Effect Estimation & Patient Level Prediction to support large scale study design (OHDSI/WebAPI#568) - thanks @anthonysena, @schuemie, @jreps, @PRijnbeek, @ericaVoss, @pbr6cornell, @pavgra, @chrisknoll
- Added SNOMED Terms & Condition pop-up window (#932) - thanks @johnSamilin, @pavgra
Fixes
- Changed ATLAS project structure (#888, #893, #840, #891, #893, #847) - thanks @johnSamilin, @pavgra, @anthonysena
- Fixed permission and role evaluation (#951) - thanks @aklochkova, @pavgra
- Fixed cohort generation duration format (#955) - thanks @aklochkova, @pavgra
- Fixed AD import issues (#945) - thanks @mpozhidaeva, @pavgra
- Fixed JS library bundling (#942) - thanks @johnSamilin, @pavgra
- Page route status fix (#912) - thanks @johnSamilin, @pavgra
- Fixed expired session handler (#918) - thanks @johnSamilin, @pavgra
- Fixed empty new source page (#937) - thanks @mpozhidaeva, @pavgra
- Fixed authApi not defined error after authentication (#897) - thanks @chen-regen, @pavgra
... and many others which are here: https://github.com/OHDSI/Atlas/milestone/14?closed=1
Additional Information
- Turn off SNOMED Terms & Condition popup using config-local.js: configLocal.enableTermsAndConditions = false
Atlas Version 2.5.1
Fixes
- Fixed removing concept set from cohort causes application error.
- #885: Datasource Key field should be disabled on Datasource Configuration page
Atlas Version 2.5.0
New Features
Allow user to select which analysis to run in cohort reporting.
Added Role Manager for LDAP security integration
Support local build of Atlas for isolated environment support. See 'Local Build Instructions' below.
Enhanced Impala Support
CEM 1.0 Integration: Define negative controls using the Common Evidence Model.
CIRCE 1.6 integration. See OHDSI/Circe-be for details.
Major code refactoring: leveraging ES6 classes and improved project structure. Thank you to Odysseus and team!
Fixes
#722: Cost and Utilization plot fixes
#806: Unable to navigate directly to concept
#844: Fixes for timeouts when accessing external resources in an isolated environment.
#863: Cohort Reporting Condition reports are not appearing
#864: Fix Data Source refresh when different source is selected.
#874 #873: Fixed issues with permissions and copying Incidence Rate analysis projects.
Local Build Instructions:
If you want to have all external resources downloaded and bundled (so that no external resources are accessed), follow the following instructions:
- Execute "npm i"
- Execute "npm run build"
- Update config-local.js to include "config.useBundled3dPartyLibs = true;"
Atlas Version 2.4.4
Fixes
- UX and UI improvements for Cost & Util reports (#835, 9437b6d) @pavgra @agackovka
- Do not display detailed data tables / charts when only summary is calculated for Cost & Util (d99ab6c) @pavgra
- Fixed value=NULL handling for Cost & Util charts (7143967) @pavgra
- Added ability to select whether rollups should be enabled for Cost & Util reports (fe0fb2e) @pavgra
- Selection of periods for generation in Cost util reports (cf471a4) @agackovka
Atlas Version 2.4.3
Fixes
- Log name of a person who kicked off a job (#750) @mpozhidaeva
- Html rendering in tooltips is broken (#772 ) @agackovka
- Data sources list is not refreshed after login (#768) @johnSamilin
- Atlas stucks after navigation to Concept Sets from Cohort (#744) @pavgra
- Fixes for Cost & Util filters (#697) @pavgra
- Histogram data is calculated incorrectly when min X value is greater than zero (#764) @chrisknoll @pavgra
- Atlas PLP fails due to changed PLP package API (#740) @pavgra
Atlas Version 2.4.2
Fixes
- Updated to atlas charts 1.4.1 to address resizing and multi-series tooltips on line plots.