num-forschungsdatenplattform/num-portal-webapp

num-portal-webapp's Issues

Incorrect rendering of immunization status query in cohort explorer

When choosing the Immunization status inside the cohort explorer, it does not render the data entry fields but shows a message that the parameter is not available.

Expected behavior would be the four parameters as defined in the query:

SELECT
  c0 as Impfstatus
FROM
  EHR e
  contains COMPOSITION c0[openEHR-EHR-COMPOSITION.registereintrag.v1]
  contains (ACTION a1[openEHR-EHR-ACTION.medication.v1]
  and CLUSTER c2[openEHR-EHR-CLUSTER.dosage.v1])
WHERE
  (c0/archetype_details/template_id/value = 'Impfstatus'
  and (a1/description[at0017]/items[at0020]/value/defining_code/code_string = $Impfstoff
  and (a1/description[at0017]/items[at0021]/value/defining_code/code_string = $Impfung_gegen
  and (a1/time/value = $Zeitpunkt
  and c2/items[at0144]/value/magnitude = $Dosismenge))))

You might be able to narrow the error by removing the parameters one by one and see what breaks the UI rendering.

Data Picker not presented in some criteria in cohort explorer

For elements of type DV_DATE and DV_DATETIME, we expect there to be a date picker as shown in this example:

However, this is not showing up reliably for all data fields:

Expected result is the correct and consistent rendering of the date picker whenever a data or date time needs to be chosen. The data picker should also show the right level of detail (only dates when required and full date time including minutes and seconds if required).

Cohort size retrieval not working in all menus

There are different places where you can retrieve a cohort size using the interface - what I tested:

1. Projects -> Create Project - Define Cohort -> Determine Button (ok)
2. While defining a query in the "Criteria Editor" (ok)
3. Search -> Determine Button (what users will generally use - not working)

Using the same search query/criteria the cohort size is correctly displayed in 1 and 2 (398 in this case).
1:

2:

while it does not work in 3.

The Firefox developer console is showing a statuscode 500:

Curiously, the number is displayed correctly again as soon as you click on "next step" and switch to the "data filter" tab:

As openEHR repository we are using the better platform not ehrbase. But since the query works, just not in all places, I think the bug is related to the implementation of the portal.

Cohort Explorer does not provide correct operators for some scores

Using the cohort explorer, it appears that some data types are not properly configured. Here is an example:

The Apgar Score (and other criteria) uses data elements of type "DV_Ordinal", which contain a number and a label. Ordinal explicitly allows to order and compare numbers/scores, so that operators like ">, <, >=, <=" are needed and "=" and "!=" are still useful but not sufficient.

I guess there is only a slight adjustment needed in the cohort explorer backend to push the right operator set to the frontend for this data type.

Not entire AQL which is defined in Criteria will be executed by Retrieve Data

Hi Guys,

we installed num-portal and num-portal-webapp at UKSH to experiment the features and getting connected to our current OpenEHR infrastructure.

Currently, we faced the following issue. After starting a project, by navigating to Data Retrieval and clicking on Retrieve Data, the filter which is defined at Criteria will not be applied correctly.

for example, although the AQL in Criteria is defined like this:

SELECT
  e1/data[at0001]/items[at0002]/value/defining_code/code_string as code
FROM
  EHR e
  contains COMPOSITION c0[openEHR-EHR-COMPOSITION.report.v1]
  contains EVALUATION e1[openEHR-EHR-EVALUATION.problem_diagnosis.v1]
WHERE
  (c0/archetype_details/template_id/value = 'KDS_Diagnose'
  AND e1/data[at0001]/items[at0002]/value/defining_code/code_string LIKE 'I50*')

the UI will send this AQL to num-portal:

SELECT
  c0 as KDS_Diagnose
FROM
  EHR e
  contains COMPOSITION c0[openEHR-EHR-COMPOSITION.report.v1]
WHERE
  c0/archetype_details/template_id/value = 'KDS_Diagnose'

which doesn't contain " code_string LIKE 'I50*' " part and all data will be shown which is not desired. For this example we defined a Criteria, and it will be used for defining a project. But after staring the project, all the data which contains a specific "template_id" (here KDS_Diagnose) will be returned and the other filters will be ignored.

Could you please let us know if this is the way it supposed to behave or where could be the problem.

Thanks!

Update dependencies

npm WARN deprecated [email protected]: this library is no longer supported
npm WARN deprecated [email protected]: Please update to ini >=1.3.6 to avoid a prototype pollution issue
npm WARN deprecated [email protected]: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
npm WARN deprecated [email protected]: Please upgrade  to version 7 or higher.  Older versions may use Math.random() in certain circumstances, which is known to be problematic.  See https://v8.dev/blog/math-random for details.
npm WARN deprecated [email protected]: Debug versions >=3.2.0 <3.2.7 || >=4 <4.3.1 have a low-severity ReDos regression when used in a Node.js environment. It is recommended you upgrade to 3.2.7 or 4.3.1. (https://github.com/visionmedia/debug/issues/797)
npm WARN deprecated [email protected]: request has been deprecated, see https://github.com/request/request/issues/3142

node_modules/jsdom "version": "15.2.1" depends on [email protected] which depends on those old libraries above.

$ npm audit
# npm audit report

ansi-html  *
Severity: high
Uncontrolled Resource Consumption in ansi-html - https://github.com/advisories/GHSA-whgm-jr23-g3j9
fix available via `npm audit fix --force`
Will install @angular-devkit/[email protected], which is a breaking change
node_modules/ansi-html
  webpack-dev-server  2.0.0-beta - 4.1.0
  Depends on vulnerable versions of ansi-html
  Depends on vulnerable versions of chokidar
  Depends on vulnerable versions of yargs
  node_modules/webpack-dev-server
    @angular-devkit/build-angular  0.8.8 - 13.0.0-rc.3
    Depends on vulnerable versions of webpack
    Depends on vulnerable versions of webpack-dev-server
    node_modules/@angular-devkit/build-angular

ansi-regex  >2.1.1 <5.0.1
Severity: moderate
 Inefficient Regular Expression Complexity in chalk/ansi-regex - https://github.com/advisories/GHSA-93q8-gq69-wqmw
fix available via `npm audit fix --force`
Will install [email protected], which is a breaking change
node_modules/angular-playground/node_modules/ansi-regex
node_modules/angular-playground/node_modules/string-length/node_modules/ansi-regex
node_modules/jest-junit/node_modules/ansi-regex
node_modules/string-length/node_modules/ansi-regex
node_modules/webpack-dev-server/node_modules/cliui/node_modules/ansi-regex
node_modules/webpack-dev-server/node_modules/string-width/node_modules/ansi-regex
node_modules/webpack-dev-server/node_modules/wrap-ansi/node_modules/ansi-regex
node_modules/wide-align/node_modules/ansi-regex
  pretty-format  20.1.0-alpha.1 - 25.0.0
  Depends on vulnerable versions of ansi-regex
  node_modules/angular-playground/node_modules/pretty-format
    jest-config  20.1.0-alpha.1 - 24.9.0
    Depends on vulnerable versions of @jest/test-sequencer
    Depends on vulnerable versions of jest-jasmine2
    Depends on vulnerable versions of pretty-format
    node_modules/angular-playground/node_modules/jest-config
      @jest/core  <=25.5.4
      Depends on vulnerable versions of @jest/reporters
      Depends on vulnerable versions of jest-config
      Depends on vulnerable versions of strip-ansi
      node_modules/@jest/core
      node_modules/angular-playground/node_modules/jest-cli/node_modules/@jest/core
        angular-playground  5.8.0 - 7.1.1
        Depends on vulnerable versions of @angular-devkit/schematics
        Depends on vulnerable versions of @jest/core
        Depends on vulnerable versions of jest
        node_modules/angular-playground
        jest-cli  20.1.0-alpha.1 - 25.0.0
        Depends on vulnerable versions of @jest/core
        Depends on vulnerable versions of jest-config
        Depends on vulnerable versions of jest-validate
        Depends on vulnerable versions of yargs
        node_modules/angular-playground/node_modules/jest-cli
          jest  24.2.0-alpha.0 - 24.9.0
          Depends on vulnerable versions of jest-cli
          node_modules/angular-playground/node_modules/jest
      jest-runner  21.0.0-alpha.1 - 24.9.0
      Depends on vulnerable versions of jest-config
      Depends on vulnerable versions of jest-jasmine2
      Depends on vulnerable versions of jest-leak-detector
      node_modules/angular-playground/node_modules/jest-runner
        @jest/test-sequencer  <=24.9.0
        Depends on vulnerable versions of jest-runner
        node_modules/angular-playground/node_modules/@jest/test-sequencer
      jest-runtime  20.1.0-alpha.1 - 25.0.0
      Depends on vulnerable versions of jest-config
      Depends on vulnerable versions of jest-snapshot
      Depends on vulnerable versions of jest-validate
      Depends on vulnerable versions of yargs
      node_modules/angular-playground/node_modules/jest-runtime
        @jest/reporters  <=26.4.0
        Depends on vulnerable versions of jest-runtime
        Depends on vulnerable versions of node-notifier
        Depends on vulnerable versions of string-length
        node_modules/@jest/reporters
        node_modules/angular-playground/node_modules/@jest/reporters
        jest-jasmine2  20.1.0-alpha.1 - 24.9.0
        Depends on vulnerable versions of jest-each
        Depends on vulnerable versions of jest-matcher-utils
        Depends on vulnerable versions of jest-runtime
        Depends on vulnerable versions of pretty-format
        node_modules/angular-playground/node_modules/jest-jasmine2
    jest-diff  20.1.0-alpha.1 - 24.9.0
    Depends on vulnerable versions of pretty-format
    node_modules/angular-playground/node_modules/jest-diff
      jest-matcher-utils  20.1.0-alpha.1 - 24.9.0
      Depends on vulnerable versions of jest-diff
      Depends on vulnerable versions of pretty-format
      node_modules/angular-playground/node_modules/jest-matcher-utils
        expect  21.0.0-beta.1 - 24.9.0
        Depends on vulnerable versions of jest-matcher-utils
        node_modules/angular-playground/node_modules/expect
          jest-snapshot  20.1.0-alpha.1 - 24.9.0
          Depends on vulnerable versions of expect
          Depends on vulnerable versions of pretty-format
          node_modules/angular-playground/node_modules/jest-snapshot
            jest-resolve-dependencies  23.0.0-alpha.5 - 24.9.0
            Depends on vulnerable versions of jest-snapshot
            node_modules/angular-playground/node_modules/jest-resolve-dependencies
    jest-each  23.0.1 - 24.9.0
    Depends on vulnerable versions of pretty-format
    node_modules/angular-playground/node_modules/jest-each
    jest-leak-detector  21.3.0-beta.9 - 24.9.0
    Depends on vulnerable versions of pretty-format
    node_modules/angular-playground/node_modules/jest-leak-detector
    jest-validate  20.1.0-alpha.1 - 24.9.0
    Depends on vulnerable versions of pretty-format
    node_modules/angular-playground/node_modules/jest-validate
  strip-ansi  4.0.0 - 5.2.0
  Depends on vulnerable versions of ansi-regex
  node_modules/angular-playground/node_modules/string-length/node_modules/strip-ansi
  node_modules/angular-playground/node_modules/strip-ansi
  node_modules/jest-junit/node_modules/strip-ansi
  node_modules/string-length/node_modules/strip-ansi
  node_modules/webpack-dev-server/node_modules/cliui/node_modules/strip-ansi
  node_modules/webpack-dev-server/node_modules/string-width/node_modules/strip-ansi
  node_modules/webpack-dev-server/node_modules/wrap-ansi/node_modules/strip-ansi
  node_modules/wide-align/node_modules/strip-ansi
    cliui  4.0.0 - 5.0.0
    Depends on vulnerable versions of strip-ansi
    Depends on vulnerable versions of wrap-ansi
    node_modules/angular-playground/node_modules/cliui
    node_modules/webpack-dev-server/node_modules/cliui
      yargs  10.1.0 - 15.0.0
      Depends on vulnerable versions of cliui
      Depends on vulnerable versions of string-width
      node_modules/angular-playground/node_modules/yargs
      node_modules/webpack-dev-server/node_modules/yargs
        webpack-dev-server  2.0.0-beta - 4.1.0
        Depends on vulnerable versions of ansi-html
        Depends on vulnerable versions of chokidar
        Depends on vulnerable versions of yargs
        node_modules/webpack-dev-server
          @angular-devkit/build-angular  0.8.8 - 13.0.0-rc.3
          Depends on vulnerable versions of webpack
          Depends on vulnerable versions of webpack-dev-server
          node_modules/@angular-devkit/build-angular
    jest-junit  2.0.1 - 12.3.0
    Depends on vulnerable versions of strip-ansi
    node_modules/jest-junit
    ora  2.0.0 - 4.0.2
    Depends on vulnerable versions of strip-ansi
    node_modules/angular-playground/node_modules/ora
      @angular-devkit/schematics  9.0.0-next.0 - 9.0.7
      Depends on vulnerable versions of ora
      node_modules/angular-playground/node_modules/@angular-devkit/schematics
        @schematics/angular  9.0.0-next.0 - 9.0.7
        Depends on vulnerable versions of @angular-devkit/schematics
        node_modules/angular-playground/node_modules/@schematics/angular
    string-length  2.0.0 - 3.1.0
    Depends on vulnerable versions of strip-ansi
    node_modules/angular-playground/node_modules/string-length
    node_modules/string-length
      jest-watcher  <=26.0.0-alpha.2
      Depends on vulnerable versions of string-length
      node_modules/angular-playground/node_modules/jest-watcher
      node_modules/jest-watcher
    string-width  2.1.0 - 4.1.0
    Depends on vulnerable versions of strip-ansi
    node_modules/angular-playground/node_modules/string-width
    node_modules/webpack-dev-server/node_modules/string-width
    node_modules/wide-align/node_modules/string-width
      wrap-ansi  3.0.0 - 6.1.0
      Depends on vulnerable versions of string-width
      Depends on vulnerable versions of strip-ansi
      node_modules/angular-playground/node_modules/wrap-ansi
      node_modules/webpack-dev-server/node_modules/wrap-ansi

glob-parent  <5.1.2
Severity: high
Regular expression denial of service - https://github.com/advisories/GHSA-ww39-953v-wcq6
fix available via `npm audit fix --force`
Will install @angular-devkit/[email protected], which is a breaking change
node_modules/watchpack-chokidar2/node_modules/glob-parent
node_modules/webpack-dev-server/node_modules/glob-parent
  chokidar  1.0.0-rc1 - 2.1.8
  Depends on vulnerable versions of glob-parent
  node_modules/watchpack-chokidar2/node_modules/chokidar
  node_modules/webpack-dev-server/node_modules/chokidar
    watchpack-chokidar2  *
    Depends on vulnerable versions of chokidar
    node_modules/watchpack-chokidar2
      watchpack  1.7.2 - 1.7.5
      Depends on vulnerable versions of watchpack-chokidar2
      node_modules/watchpack
        webpack  4.44.0 - 4.46.0
        Depends on vulnerable versions of watchpack
        node_modules/webpack
          @angular-devkit/build-angular  0.8.8 - 13.0.0-rc.3
          Depends on vulnerable versions of webpack
          Depends on vulnerable versions of webpack-dev-server
          node_modules/@angular-devkit/build-angular
    webpack-dev-server  2.0.0-beta - 4.1.0
    Depends on vulnerable versions of ansi-html
    Depends on vulnerable versions of chokidar
    Depends on vulnerable versions of yargs
    node_modules/webpack-dev-server

json-schema  <0.4.0
Severity: moderate
json-schema is vulnerable to Prototype Pollution - https://github.com/advisories/GHSA-896r-f27r-55mw
fix available via `npm audit fix`
node_modules/json-schema
  jsprim  0.3.0 - 1.4.1 || 2.0.0 - 2.0.1
  Depends on vulnerable versions of json-schema
  node_modules/jsprim

node-notifier  <8.0.1
Severity: moderate
OS Command Injection in node-notifier - https://github.com/advisories/GHSA-5fw9-fq32-wv5p
fix available via `npm audit fix --force`
Will install [email protected], which is a breaking change
node_modules/angular-playground/node_modules/node-notifier
node_modules/node-notifier
  @jest/reporters  <=26.4.0
  Depends on vulnerable versions of jest-runtime
  Depends on vulnerable versions of node-notifier
  Depends on vulnerable versions of string-length
  node_modules/@jest/reporters
  node_modules/angular-playground/node_modules/@jest/reporters
    @jest/core  <=25.5.4
    Depends on vulnerable versions of @jest/reporters
    Depends on vulnerable versions of jest-config
    Depends on vulnerable versions of strip-ansi
    node_modules/@jest/core
    node_modules/angular-playground/node_modules/jest-cli/node_modules/@jest/core
      angular-playground  5.8.0 - 7.1.1
      Depends on vulnerable versions of @angular-devkit/schematics
      Depends on vulnerable versions of @jest/core
      Depends on vulnerable versions of jest
      node_modules/angular-playground
      jest-cli  20.1.0-alpha.1 - 25.0.0
      Depends on vulnerable versions of @jest/core
      Depends on vulnerable versions of jest-config
      Depends on vulnerable versions of jest-validate
      Depends on vulnerable versions of yargs
      node_modules/angular-playground/node_modules/jest-cli
        jest  24.2.0-alpha.0 - 24.9.0
        Depends on vulnerable versions of jest-cli
        node_modules/angular-playground/node_modules/jest

42 vulnerabilities (34 moderate, 8 high)

To address issues that do not require attention, run:
  npm audit fix

To address all issues (including breaking changes), run:
  npm audit fix --force