Packaging/publication services and analysis execution results data providers for Shiny applications #2399

alex-odysseus · 2024-09-26T21:12:44Z

Addressing #2349

By default the feature is not enabled

There was a new profile added 'webapi-shiny' so that while building an application it should be specified together with a set property 'shiny.app.directory' pointing to a checked out directory on the build server with the Shiny applications source code (a new OHDSI repository to be created @chrisknoll @anthonysena - https://github.com/OHDSI/webapi-shiny)

mvn clean package -s WebAPIConfig/settings.xml -P webapi-postgresql,webapi-shiny -D shiny.app.directory=D:\\webapi\\checkout

The following properties to be specified in settings.xml:

<shiny.connect.url>url-to-your-posit-connect-server</shiny.connect.url>
<shiny.connect.api.key>api-key-to-connect-to-posit-connect-server</shiny.connect.api.key>
<!-- A URL to your ATLAS to navigate back to published artifacts from the Shiny applications -->
<shiny.atlas.url>http://localhost:8080/atlas</shiny.atlas.url>
<!-- A URL to the source code repository with Shiny applications (to be created) to navigate to from the Shiny applications -->
<shiny.repo.link>https://github.com/OHDSI/atlasshinyexport-repository-to-be-created</shiny.repo.link>
<shiny.output.directory>a-directory-on-the-build-server-into-which-shiny-application-placeholder-archives-are-built</shiny.output.directory>
<!-- A timeout to connect to Posit Connect Server -->
<shiny.connect.okhttp.timeout.seconds>10</shiny.connect.okhttp.timeout.seconds>

A specific Spring profile is activated
<spring.profiles.active>default,shiny</spring.profiles.active>

…R app

…es while configuring application Docker container with an --env-file

…ords scenario

…n the same metadata as used by Atlas

…ishing connect/read/write timeout, no changes/limits to the call timeout), Improved shiny apps code design, eliminated duplicate logic, implemented properties propagation into R apps using a single file app.properties

…ocale formatting of numbers

…the generated filenames to the UI

…hiny App

alex-odysseus · 2024-09-26T22:40:58Z

pom.xml

+                    <include>shiny-cohortCounts.zip</include>
+                    <include>shiny-incidenceRates.zip</include>
+                    <include>shiny-cohortCharacterizations.zip</include>
+                  </includes>


We should clean 'shiny-cohortPathways.zip' as well

alex-odysseus · 2024-09-26T22:45:07Z

src/main/java/org/ohdsi/webapi/pathway/PathwayServiceImpl.java

+        return dto;
+    }
+    @Override
+    public PathwayPopulationResultsDTO getGenerationResults(Long generationId) {


Being extracted from PathwayController

alex-odysseus · 2024-09-26T22:55:17Z

src/main/java/org/ohdsi/webapi/shiny/CohortCharacterizationShinyPackagingService.java

+        dataConsumers.getAppProperties().accept("atlas_link", String.format("%s/#/cc/characterizations/%s", atlasUrl, cohortCharacterization.getId()));
+        dataConsumers.getAppProperties().accept("analysis_name", cohortCharacterization.getName());
+
+        generationResults.getReports()


For Cohort Characterization Shiny application report listings export CSV interface has been chosen

alex-odysseus · 2024-09-26T22:58:25Z

src/main/java/org/ohdsi/webapi/shiny/CommonShinyPackagingService.java

+import java.util.stream.Collectors;
+import java.util.stream.Stream;
+
+public abstract class CommonShinyPackagingService {


A Javadoc to be added

alex-odysseus · 2024-09-26T23:02:49Z

src/main/java/org/ohdsi/webapi/shiny/CommonShinyPackagingService.java

+        }
+    }
+
+    public final TemporaryFile packageApp(Integer generationId, String sourceKey, PackagingStrategy packaging) {


As Shiny applications template archives shouldn't have data and a manifest file should be extended properly with new file entries and signatures an application package creation takes place on the fly so that a 'data' folder is populated with analysis execution results

alex-odysseus · 2024-09-26T23:03:56Z

src/main/java/org/ohdsi/webapi/shiny/CommonShinyPackagingService.java

+                CommonFileUtils.unzipFiles(templateArchive, path.toFile());
+                Path manifestPath = path.resolve("manifest.json");
+                if (!Files.exists(manifestPath)) {
+                    throw new PositConnectClientException("manifest.json is not found in the Shiny Application");


A malformed or missing manifest.json will result in an error while publishing an application to Posit Connect

anthonysena · 2024-10-16T02:28:17Z

Notes from demo today on ATLAS WG Call:

The configuration of WebAPI controls the ability to show/hide the "Shiny App" button on the Atlas UI. The UI then allows for download/publish but if there is no Posit Connect server, we might want to be able to download only which will require a work-around configuration for now.
Shiny reports are designed for a single analysis (i.e. Pathways) on a single data source (i.e. SynPuf). In the future there may be the ability to have multiple data sources included.

anthonysena · 2024-10-28T19:02:27Z

@alex-odysseus I've set up the https://github.com/OHDSI/webapi-shiny to hold the Shiny application templates your team has developed.

anthonysena · 2024-11-26T14:33:07Z

Converting this to a draft since the necessary Shiny resources are not yet posted to https://github.com/OHDSI/webapi-shiny

…nfo parameters for Mean, StdDev, variance calculations

anthonysena

This looks good but there is a conflict can you resolve @oleg-odysseus?

oleg-odysseus · 2024-12-27T22:54:27Z

This looks good but there is a conflict can you resolve @oleg-odysseus?
I've resolved the conflicts but I`ll need write access to push the merge commit.

wivern and others added 29 commits December 22, 2023 17:08

ATL-29 API Support for R Shiny Apps

47271f0

ATL-29 API Support for R Shiny Apps

34bab7d

ATL-29 API Support for R Shiny Apps

e44462a

Migrations

9a714bd

Posit API Client updates

3246472

Add data files to manifest before publishing

6c0d9a6

Handling the disabled security case

f5e31b4

Adding missing placeholders for Posit Connect and API key

2ac1eb2

Adds default value for shiny properties

57b2cb9

ATL-46: Changed filenaming

9e761fd

[ATL-48] Implemented Incidence Rates Analysis Shiny app publishing

5968034

ATL-46: File name changed

fbdc8db

[IncidenceRate App] Datasource to be read from text file

d41dbd3

[ATL-53] Added datasource export via file to the data folder for the …

535294e

…R app

[ATL-49] Implemented Cohort Characterizations Shiny App Publishing

8e9d15e

Added SourceKey to Shiny apps Titles

88c417c

[ATL-50] Introduced Cohort Pathway Shiny app download and publishing

a763994

Explicitly using the dot instead of the underscore as there were issu…

1b444a4

…es while configuring application Docker container with an --env-file

Unified Shiny apps names

2ae926e

[ATL-48] Fixed issue with Incidence Rates app publishing for a No Rec…

760403c

…ords scenario

[ATL-50] Changed interface of the Cohort Pathways Shiny app to contai…

d99a1e2

…n the same metadata as used by Atlas

Changed MessageFormat to String.format for shiny app names to avoid l…

e6e972e

…ocale formatting of numbers

Unified naming of generation versions for all shiny apps

532fd1d

Added Content-Disposition header to CORS Filter to allow propagating …

63c9d33

…the generated filenames to the UI

Added 'analysis_name' to app.properties for Cohort Characterization S…

364bcce

…hiny App

Added design JSON and chart data JSON files to Cohort Pathways Shiny app

6d91240

Fix for eliminating statefulness between Shiny apps generation calls

35fe824

Merge remote-tracking branch 'remotes/upstream/master' into ATL-29

85266d5

alex-odysseus requested a review from chrisknoll September 26, 2024 21:12

alex-odysseus requested a review from anthonysena September 26, 2024 21:12

alex-odysseus commented Sep 26, 2024

View reviewed changes

anthonysena linked an issue Oct 1, 2024 that may be closed by this pull request

Extend Posit Connect Shiny applications with Analysis Execution Results from WebAPI #2349

Open

anthonysena marked this pull request as draft November 26, 2024 14:33

alex-odysseus marked this pull request as ready for review December 10, 2024 10:43

oleg-odysseus and others added 4 commits December 10, 2024 14:58

Added parameters required for the Shiny Apps introduction pages

4309e66

Exteacted common constants into a separate enum, changed datasource i…

c94aa0c

…nfo parameters for Mean, StdDev, variance calculations

Added atlas_link to Pathways Shiny App Properties

807603a

Combining migration scripts

75cdbd6

anthonysena self-assigned this Dec 17, 2024

anthonysena reviewed Dec 27, 2024

View reviewed changes

Fixed merge conflicts

b5dda3e

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Packaging/publication services and analysis execution results data providers for Shiny applications #2399

Packaging/publication services and analysis execution results data providers for Shiny applications #2399

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