Packaging/publication services and analysis execution results data providers for Shiny applications by alex-odysseus · Pull Request #2399 · OHDSI/WebAPI

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>

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

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.

…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

…nfo parameters for Mean, StdDev, variance calculations

…t Administrator

…shiny. Eliminated usage of an exception for flow control. Added logging of body prefix on exceptions from Posit server to troubleshoot posit (non-http) error codes

oleg-odysseus · 2025-03-17T15:20:48Z

Hi @chrisknoll, I`ve resolved the conflicts and ran this branch locally - looks ok to me, please kindly merge this PR along with the Atlas part if you have no objections, thank you.

alex-odysseus requested review from anthonysena and chrisknoll 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

Closed

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

anthonysena self-assigned this Dec 17, 2024

anthonysena reviewed Dec 27, 2024

View reviewed changes

wivern and others added 13 commits March 12, 2025 19:28

ATL-29 API Support for R Shiny Apps

c05a217

ATL-29 API Support for R Shiny Apps

78987ce

ATL-29 API Support for R Shiny Apps

a92a76e

Migrations

84e3886

Posit API Client updates

e61fd7f

Add data files to manifest before publishing

69adde2

Handling the disabled security case

678e5c4

Adding missing placeholders for Posit Connect and API key

3c138d2

Adds default value for shiny properties

25b700d

ATL-46: Changed filenaming

2fc8edf

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

3e9fa5f

ATL-46: File name changed

dda1459

[IncidenceRate App] Datasource to be read from text file

174420a

oleg-odysseus and others added 22 commits March 12, 2025 19:36

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

6d8c927

…R app

[ATL-49] Implemented Cohort Characterizations Shiny App Publishing

62e29d3

Added SourceKey to Shiny apps Titles

89fad5a

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

cbe86cd

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

266dd10

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

Unified Shiny apps names

1ced688

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

c001113

…ords scenario

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

fe0665c

…n the same metadata as used by Atlas

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

cf6449e

…ocale formatting of numbers

Unified naming of generation versions for all shiny apps

9c9e2c0

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

6bb99a2

…the generated filenames to the UI

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

4800b2f

…hiny App

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

08cb9ee

Fix for eliminating statefulness between Shiny apps generation calls

d810efb

Added parameters required for the Shiny Apps introduction pages

e45af1e

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

bd5f2a0

…nfo parameters for Mean, StdDev, variance calculations

Added atlas_link to Pathways Shiny App Properties

fc3af38

Combining migration scripts

9a0cc1f

Extracted posit-related DTOs, refactoring

911d864

Implemented Shiny Apps Tagging with existing tags, predefined by Posi…

aef2ae8

…t Administrator

Fixed compilation issues after rebase

d04951a

oleg-odysseus force-pushed the shiny-applications branch from e9d94ac to d04951a Compare March 12, 2025 19:01

oleg-odysseus added 2 commits March 12, 2025 21:57

Added support for multi-line Author Notes (Analysis descriptions) in …

16249de

…shiny. Eliminated usage of an exception for flow control. Added logging of body prefix on exceptions from Posit server to troubleshoot posit (non-http) error codes

resolved merge conflicts

3d9be4f

chrisknoll approved these changes Mar 18, 2025

View reviewed changes

chrisknoll merged commit 3c322d8 into master Mar 18, 2025
2 checks passed

chrisknoll deleted the shiny-applications branch March 18, 2025 12:38

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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
chrisknoll merged 37 commits intomasterfrom
shiny-applications

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