Use standard list of model names in Execute SPARQL CONSTRUCT page

[brianjlowe]

VIVO4141:

• Other Relevant Links (Mailing list discussion, related pull requests, etc.)

What does this pull request do?

Uses the same list of available model names in the Execute SPARQL CONSTRUCT page that is used in other ingest tool pages. Fixes current bug where only configuration models are offered as source and destination models on this page.

How should this be tested?

1. Go to Site Admin > Ingest tools > Manage Jena Models .
2. Click the "Main Store Models" button near the top. Note the models available in this list, such as "http://vitro.mannlib.cornell.edu/filegraph/tbox/ontologies.owl".
3. Go to Site Admin > Ingest tools > Execute SPARQL CONSTRUCT.
4. Note that these same models are offered under "Select Source Models" and "Select Destination Model".
5. Return to Site Admin > Ingest tools > Manage Jena Models.
6. Click "Configuration Models".
7. Note that other models, such as "http://vitro.mannlib.cornell.edu/default/interface-i18n", are now listed.
8. Return to Site Admin > Ingest tools > Execute SPARQL CONSTRUCT.
9. Confirm that this new set of models is offered for source and destination models.

Interested parties

@VIVO-project/vivo-committers

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[chenejac]

@brianjlowe thanks for the PR, looks good and works good. I will also ask Folke to confirm this is resolving his issue.

[meyerfo]

The system was previously running VIVO 1.15.1 and a Solr container. I then replaced the VIVO container in the docker-compose file.
After the containers had successfully started, I received the following error message in the browser:

---

FATAL: SearchEngineSmokeTest
Threw unexpected exception
edu.cornell.mannlib.vitro.webapp.servlet.setup.SearchEngineSmokeTest

java.lang.RuntimeException: ESHttpClient wasn't initialized.
	at edu.cornell.mannlib.vitro.webapp.searchengine.elasticsearch.ESHttpClient.execute(ESHttpClient.java:50)
	at edu.cornell.mannlib.vitro.webapp.servlet.setup.SearchEngineSmokeTest.identifyService(SearchEngineSmokeTest.java:37)

`

How did i build the container:

• downloaded VIVO 1.15.1 and Vitro (https://github.com/brianjlowe/Vitro/tree/bugfix/VIVO-4141) from Git.
  Afterwards, I executed the following commands in the VIVO folder.
• mvn clean package -s installer/docker-example-settings.xml
• docker build -t vivoweb4141/vivo .
• docker compose up -d

Docker started without an error from the bash.

[chenejac]

The system was previously running VIVO 1.15.1 and a Solr container. I then replaced the VIVO container in the docker-compose file. After the containers had successfully started, I received the following error message in the browser:

FATAL: SearchEngineSmokeTest Threw unexpected exception edu.cornell.mannlib.vitro.webapp.servlet.setup.SearchEngineSmokeTest

java.lang.RuntimeException: ESHttpClient wasn't initialized.
	at edu.cornell.mannlib.vitro.webapp.searchengine.elasticsearch.ESHttpClient.execute(ESHttpClient.java:50)
	at edu.cornell.mannlib.vitro.webapp.servlet.setup.SearchEngineSmokeTest.identifyService(SearchEngineSmokeTest.java:37)

`

How did i build the container:

• downloaded VIVO 1.15.1 and Vitro (https://github.com/brianjlowe/Vitro/tree/bugfix/VIVO-4141) from Git.
  Afterwards, I executed the following commands in the VIVO folder.
• mvn clean package -s installer/docker-example-settings.xml
• docker build -t vivoweb4141/vivo .
• docker compose up -d

Docker started without an error from the bash.

@litvinovg do you think this commit might be a solution for this issue? Should Brian cherry pick and add that commit on the PR branch

[litvinovg]

The system was previously running VIVO 1.15.1 and a Solr container. I then replaced the VIVO container in the docker-compose file. After the containers had successfully started, I received the following error message in the browser:
FATAL: SearchEngineSmokeTest Threw unexpected exception edu.cornell.mannlib.vitro.webapp.servlet.setup.SearchEngineSmokeTest

java.lang.RuntimeException: ESHttpClient wasn't initialized.
	at edu.cornell.mannlib.vitro.webapp.searchengine.elasticsearch.ESHttpClient.execute(ESHttpClient.java:50)
	at edu.cornell.mannlib.vitro.webapp.servlet.setup.SearchEngineSmokeTest.identifyService(SearchEngineSmokeTest.java:37)

`

How did i build the container:

• downloaded VIVO 1.15.1 and Vitro (https://github.com/brianjlowe/Vitro/tree/bugfix/VIVO-4141) from Git.
  Afterwards, I executed the following commands in the VIVO folder.
• mvn clean package -s installer/docker-example-settings.xml
• docker build -t vivoweb4141/vivo .
• docker compose up -d

Docker started without an error from the bash.

@litvinovg do you think this commit might be a solution for this issue? Should Brian cherry pick and add that commit on the PR branch

Yes, rebasing current PR branch on top of main branch should solve the problem

[meyerfo]

The problem with the elastic search connection is solved. However, the problem with the "select source model" is not solved.

I checked the output from the mvn clean package command. There is the following eror.

Excerpt from: mvn clean package -s installer/ docker-example-settings.xml

ERROR 2026-05-12 07:30:27.551 [main] (IndividualListController) Error retrieving individuals corresponding to intersection multiple classes.[http://myVclass]
java.lang.RuntimeException: ContextModelAccessStub.getOntModelSelector() not implemented.
at stubs.edu.cornell.mannlib.vitro.webapp.modelaccess.ContextModelAccessStub.getOntModelSelector(ContextModelAccessStub.java:118)
at edu.cornell.mannlib.vitro.webapp.search.controller.SearchFiltering.readFilterConfigurations(SearchFiltering.java:262)
at edu.cornell.mannlib.vitro.webapp.search.controller.SearchFiltering.addDefaultFilters(SearchFiltering.java:361)
at edu.cornell.mannlib.vitro.webapp.controller.freemarker.IndividualListController.buildAndExecuteVClassQuery(IndividualListController.java:227)
at edu.cornell.mannlib.vitro.webapp.controller.freemarker.IndividualListController.buildAndExecuteVClassQuery(IndividualListController.java:192)
at edu.cornell.mannlib.vitro.webapp.controller.freemarker.IndividualListController.getResultsForVClassIntersections(IndividualListController.java:181)
at edu.cornell.mannlib.vitro.webapp.controller.json.JsonServlet.getSearchVClassIntersectionResults(JsonServlet.java:113)
at edu.cornell.mannlib.vitro.webapp.controller.json.JsonServlet.getSearchIndividualsByVClass(JsonServlet.java:92)
at edu.cornell.mannlib.vitro.webapp.controller.json.GetSearchIndividualsByVClass.process(GetSearchIndividualsByVClass.java:44)
at edu.cornell.mannlib.vitro.webapp.controller.json.JsonObjectProducer.process(JsonObjectProducer.java:52)

	there are more lines..

[brianjlowe]

Thanks @meyerfo for trying again. The error stack trace during the unit tests looks to be irrelevant to this issue, but thank you for catching that. I've opened an issue: vivo-project/VIVO#4155. Can you confirm that the jenaIngest/sparqlConstruct.jsp file inside your running Docker container matches what's on the PR branch (e.g., no ModelMaker import on line 5)?

[meyerfo]

This are the first 5 lines of the sparqlConstruct file. There is the import of the modelmaker.
`
<%-- $This file is distributed under the terms of the license in LICENSE$ --%>

<%@ page import="org.apache.jena.ontology.Individual"%>
<%@ page import="org.apache.jena.ontology.OntModel"%>
<%@ page import="org.apache.jena.rdf.model.ModelMaker"%>`

as discussed, the following branch was used:
git clone --single-branch https://github.com/brianjlowe/Vitro.git

[meyerfo]

followed https://wiki.lyrasis.org/spaces/VIVODOC115x/pages/298811876/Using+the+Convert+CSV+to+RDF+ingest+tool

Everything fine.