Fix unit test that did not add the source field to its synthetic test…

… data.

gepi/README.md

@@ -2,7 +2,9 @@
 
 ## Purpose of this software
 
-The core of GePI is a web application for the user-friendly retrieval of descriptions of biomolecular interactions from the scientific literature, [PubMed](https://pubmed.ncbi.nlm.nih.gov/) (PM) and the [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/) (PMC) [open access subset](https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/). To this end, [JCoRe](https://github.com/JULIELab/jcore-base) pipeline components are used to form a number of [UIMA](https://uima.apache.org/) pipelines for the processing of PM and PMC in order to extract the interactions.
+The core of GePI (**Ge**ne and **P**rotein **I**nteractions) is a web application for the user-friendly retrieval of descriptions of biomolecular interactions from the scientific literature, [PubMed](https://pubmed.ncbi.nlm.nih.gov/) (PM) and the [PubMed Central](https://www.ncbi.nlm.nih.gov/pmc/) (PMC) [open access subset](https://www.ncbi.nlm.nih.gov/pmc/tools/openftlist/). To this end, [JCoRe](https://github.com/JULIELab/jcore-base) pipeline components are used to form a number of [UIMA](https://uima.apache.org/) pipelines for the processing of PM and PMC in order to extract the interactions.
+
+The GePI web application is available at https://gepi.coling.uni-jena.de/.
 
 ## Reference for this work
 
@@ -72,8 +74,8 @@ The `production` stage expects that the complete GePI project has been built in
 Run the following commands to create a `development` container:
 
 ```bash
-DOCKER_BUILDKIT=1 docker build -t gepi-dev:1.0.2 --target development .
-docker run -dp 8080:8080 -v {/path/to/gepi/directory}:/var/gepi/dev -e GEPI_CONFIGURATION=<path to config file> --name gepi-dev gepi-dev:1.0.2
+DOCKER_BUILDKIT=1 docker build -t gepi-dev:1.0.3-SNAPSHOT --target development .
+docker run -dp 8080:8080 -v {/path/to/gepi/directory}:/var/gepi/dev -e GEPI_CONFIGURATION=<path to config file> --name gepi-dev gepi-dev:1.0.3-SNAPSHOT
 ```
 
 The first command builds an image of the `development` stage. This will also build the `dependencies` stage where all the Java dependencies of the GePI application are downloaded and cached. This will take a while on the first execution but should be faster afterwards thanks to caching.
@@ -91,8 +93,8 @@ To run the `production` container, run
 
 ```bash
 mvn clean package --projects gepi-webapp --also-make
-DOCKER_BUILDKIT=1 docker build -t gepi:1.0.2 --target production .
-docker run -dp 8080:8080 --name gepi gepi:1.0.2
+DOCKER_BUILDKIT=1 docker build -t gepi:1.0.3-SNAPSHOT --target production .
+docker run -dp 8080:8080 --name gepi gepi:1.0.3-SNAPSHOT
 ```
 
 These commands
@@ -121,7 +123,7 @@ gepi.neo4j.bolt.url=bolt://<host>:<port>
 
 A production environment has a few requirements that are of lesser importance during development. This section explains requirements and solutions that may come up during GePI deployment with the Docker container. While detailed explanations come below, the full Docker `run` command we use for deployment looks like the following:
 ```
-docker run -dp 80:8080 -p 443:8443 -v /host/path/to/certificate.p12:/var/lib/jetty/etc/keystore.p12 -v /host/path/to/configuration.properties:/gepi-webapp-configuration.properties --add-host=host.docker.internal:host-gateway --name gepi -e GEPI_CONFIGURATION=/gepi-webapp-configuration.properties gepi:1.0.2 jetty.sslContext.keyStorePassword=<changeit>
+docker run -dp 80:8080 -p 443:8443 -v /host/path/to/certificate.p12:/var/lib/jetty/etc/keystore.p12 -v /host/path/to/configuration.properties:/gepi-webapp-configuration.properties --add-host=host.docker.internal:host-gateway --name gepi -e GEPI_CONFIGURATION=/gepi-webapp-configuration.properties gepi:1.0.3-SNAPSHOT jetty.sslContext.keyStorePassword=<changeit>
 ```
 Alternatively, the `docker-compose-webapp.yml` file can be used with a few additions.
 
@@ -159,5 +161,5 @@ Update the new version number in the following places:
   * set `PRODUCTION_MODE` to true for releases
 * the Docker image version in the `docker-compose.yml`
 * the DB version in `gene-database.xml` in the `gepi-concept-database` module
-* in execute `python ../../jcore-misc/jcore-scripts/createMetaDescriptors.py -c -i -r manual -v 1.0 gepi-indexing/gepi-indexing-base` given that `jcore-misc` has been cloned to the same directory as GePI
+* execute `python ../../jcore-misc/jcore-scripts/createMetaDescriptors.py -c -i -r manual -v 1.0 gepi-indexing/gepi-indexing-base` given that `jcore-misc` has been cloned to the same base directory as GePI
   * this updates the description file for the use with the JCoRe pipeline builder

gepi/gepi-core/src/test/java/de/julielab/gepi/core/retrieval/services/EventResponseProcessingServiceTest.java

@@ -13,8 +13,7 @@
 import java.util.Optional;
 import java.util.stream.Stream;
 
-import static de.julielab.gepi.core.retrieval.services.EventRetrievalService.FIELD_EVENT_ARG_TOP_HOMOLOGY_IDS;
-import static de.julielab.gepi.core.retrieval.services.EventRetrievalService.FIELD_NUM_ARGUMENTS;
+import static de.julielab.gepi.core.retrieval.services.EventRetrievalService.*;
 import static org.assertj.core.api.Assertions.assertThat;
 
 public class EventResponseProcessingServiceTest {
@@ -33,7 +32,7 @@ public void highlightMerging() {
     private IElasticServerResponse getESResponseWithHighlighting(Map<String, List<String>> sentenceHighlights) {
         final IElasticServerResponse response = Mockito.mock(IElasticServerResponse.class, inv -> null);
 
-        Mockito.when(response.getDocumentResults()).thenReturn(Stream.of(getSearchServerDocument(Map.of(EventRetrievalService.FIELD_PMID, "1234", EventRetrievalService.FIELD_EVENT_ARG_CONCEPT_IDS, List.of("tid007", "tid006"),FIELD_EVENT_ARG_TOP_HOMOLOGY_IDS, List.of("atid1", "atid2"), FIELD_NUM_ARGUMENTS, 1), sentenceHighlights)));
+        Mockito.when(response.getDocumentResults()).thenReturn(Stream.of(getSearchServerDocument(Map.of(EventRetrievalService.FIELD_PMID, "1234", EventRetrievalService.FIELD_EVENT_ARG_CONCEPT_IDS, List.of("tid007", "tid006"),FIELD_EVENT_ARG_TOP_HOMOLOGY_IDS, List.of("atid1", "atid2"), FIELD_NUM_ARGUMENTS, 1, FIELD_SOURCE, "pubmed"), sentenceHighlights)));
         Mockito.when(response.getNumFound()).thenReturn(1L);
         return response;
     }

gepi/gepi-core/src/test/resources/testconfiguration.properties

@@ -1,7 +1,7 @@
 #The port number is automatically set in de.julielab.gepi.core.retrieval.services.EventRetrievalServiceIntegrationTest
-#Fri Sep 20 11:59:19 CEST 2024
+#Fri Sep 20 14:10:17 CEST 2024
 elasticquery.sockettimeout=-1
 elasticquery.url=localhost
 elasticquery.clustername=gepi_testcluster
-elasticquery.port=56176
+elasticquery.port=56736
 gepi.documents.index.name=gepi_testindex