Merge branch 'main' into feature/jquery-update

gneissone · Mar 22, 2024 · 26b44e5 · 26b44e5
2 parents 933db3f + 80a374f
commit 26b44e5
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diff --git a/.env b/.env
@@ -1,4 +1,22 @@
-LOCAL_VIVO_HOME=./vivo-home
-RESET_HOME=false
-RESET_CORE=false
-VERBOSE=no
+# Variable substitution for docker-compose.yml
+
+# solr service variable substitution
+SOLR_RESET_CORE=false
+SOLR_VERBOSE=no
+
+SOLR_HOST_PORT=8983
+SOLR_CONTAINER_PORT=8983
+
+SOLR_CORES=./vivo-cores
+
+# tomcat service variable substitution
+VIVO_RESET_HOME=false
+VIVO_VERBOSE=no
+
+VIVO_TDB_FILE_MODE=direct
+
+VIVO_HOST_VIVO_HOME=./vivo-home
+VIVO_CONTAINER_VIVO_HOME=/usr/local/vivo/home
+
+VIVO_HOST_PORT=8080
+VIVO_CONTAINER_PORT=8080
diff --git a/.gitignore b/.gitignore
@@ -21,6 +21,7 @@ utilities/rdbmigration/.work
 **/.project
 **/bin/
 
+vivo-cores/
 vivo-home/
 
 .fake

diff --git a/Dockerfile b/Dockerfile
@@ -1,15 +1,16 @@
 FROM tomcat:9-jdk11-openjdk
 
-ARG SOLR_URL=http://localhost:8983/solr/vivocore
-ARG VIVO_DIR=/usr/local/vivo/home
 ARG TDB_FILE_MODE=direct
+ARG VIVO_HOME=/usr/local/vivo/home
+ARG SOLR_URL=http://localhost:8983/solr/vivocore
 
-ENV SOLR_URL=${SOLR_URL}
 ENV JAVA_OPTS="${JAVA_OPTS} -Dtdb:fileMode=$TDB_FILE_MODE"
+ENV VIVO_HOME=${VIVO_HOME}
+ENV SOLR_URL=${SOLR_URL}
 
-RUN mkdir /usr/local/vivo
-RUN mkdir /usr/local/vivo/home
+RUN mkdir -p ${VIVO_HOME}
 
+# Copy VIVO home onto image for backup, initialization, and reset
 COPY ./installer/home/target/vivo /vivo-home
 COPY ./installer/webapp/target/vivo.war /usr/local/tomcat/webapps/ROOT.war
 

diff --git a/README.md b/README.md
@@ -29,18 +29,43 @@ VIVO docker container is available at [vivoweb/vivo](https://hub.docker.com/repo
 
 ### Docker Compose
 
-Docker Compose environment variables:
+Docker Compose variable substitution:
 
 .env defaults
 ```
-LOCAL_VIVO_HOME=./vivo-home
-RESET_HOME=false
-RESET_CORE=false
+SOLR_RESET_CORE=false
+SOLR_VERBOSE=no
+
+SOLR_HOST_PORT=8983
+SOLR_CONTAINER_PORT=8983
+
+SOLR_CORES=./vivo-cores
+
+VIVO_RESET_HOME=false
+VIVO_VERBOSE=no
+
+VIVO_TDB_FILE_MODE=direct
+
+VIVO_HOST_VIVO_HOME=./vivo-home
+VIVO_CONTAINER_VIVO_HOME=/usr/local/vivo/home
+
+VIVO_HOST_PORT=8080
+VIVO_CONTAINER_PORT=8080
 ```
 
-- `LOCAL_VIVO_HOME`: VIVO home directory on your host machine which will mount to volume in docker container. Set this environment variable to persist your VIVO data on your host machine.
-- `RESET_HOME`: Convenience to reset VIVO home when starting container. **Caution**, will delete local configuration, content, and configuration model.
-- `RESET_CORE`: Convenience to reset VIVO Solr core when starting container. **Caution**, will require complete reindex.
+- `SOLR_RESET_CORE`: Convenience to reset VIVO Solr core when starting container. **Caution**, will require complete reindex.
+- `SOLR_VERBOSE`: Increase log verbosity.
+- `SOLR_HOST_PORT`: Host port binding for solr service port mapping.
+- `SOLR_CONTAINER_PORT`: Container port binding for solr service port mapping.
+- `SOLR_CORES`: Solr cores data directories on your host machine which will mount to volume in docker container. Set this environment variable to persist your Solr data on your host machine.
+
+- `VIVO_RESET_HOME`: Convenience to reset VIVO home when starting container. **Caution**, will delete local configuration, content, and configuration model.
+- `VIVO_VERBOSE`: Increase log verbosity.
+- `VIVO_TDB_FILE_MODE`: TDB file mode. See https://jena.apache.org/documentation/tdb/configuration.html#file-access-mode.
+- `VIVO_HOST_VIVO_HOME`: VIVO home directory on your host machine which will mount to volume in docker container. Set this environment variable to persist your VIVO data on your host machine.
+- `VIVO_CONTAINER_VIVO_HOME`: VIVO home directory within the container.
+- `VIVO_HOST_PORT`: Host port binding for VIVO Tomcat service port mapping.
+- `VIVO_CONTAINER_PORT`: Container port binding for VIVO Tomcat service port mapping.
 
 Before building VIVO, you will also need to clone (and switch to the same branch, if other than main) of [Vitro](https://github.com/vivo-project/Vitro). The Vitro project must be cloned to a sibling directory next to VIVO so that it can be found during the build. 
 

diff --git a/...c/main/java/org/vivoweb/webapp/controller/freemarker/CreateAndLinkResourceController.java b/...c/main/java/org/vivoweb/webapp/controller/freemarker/CreateAndLinkResourceController.java
@@ -57,6 +57,9 @@
 import static edu.cornell.mannlib.vitro.webapp.auth.objects.AccessObject.SOME_LITERAL;
 import static edu.cornell.mannlib.vitro.webapp.auth.objects.AccessObject.SOME_PREDICATE;
 import static edu.cornell.mannlib.vitro.webapp.auth.objects.AccessObject.SOME_URI;
+import static edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary.Precision.DAY;
+import static edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary.Precision.MONTH;
+import static edu.cornell.mannlib.vitro.webapp.dao.VitroVocabulary.Precision.YEAR;
 
 import java.io.ByteArrayInputStream;
 import java.io.ByteArrayOutputStream;
@@ -1218,19 +1221,19 @@ protected boolean addDateToResource(VitroRequest vreq, Resource work, ResourceMo
         if (date.month != null) {
             if (date.day != null) {
                 formattedDate = String.format("%04d-%02d-%02dT00:00:00", date.year, date.month, date.day);
-                precision = "http://vivoweb.org/ontology/core#dayPrecision";
+                precision = DAY.uri();
             } else {
                 formattedDate = String.format("%04d-%02d-01T00:00:00", date.year, date.month);
-                precision = "http://vivoweb.org/ontology/core#monthPrecision";
+                precision = MONTH.uri();
             }
         } else {
             formattedDate = String.format("%04d-01-01T00:00:00", date.year);
-            precision = "http://vivoweb.org/ontology/core#yearPrecision";
+            precision = YEAR.uri();
         }
 
         Resource dateResource = model.createResource(getUnusedUri(vreq)).addProperty(RDF.type, model.getResource("http://vivoweb.org/ontology/core#DateTimeValue"));
         dateResource.addProperty(model.createProperty(VIVO_DATETIME), formattedDate);
-        dateResource.addProperty(model.createProperty(VIVO_DATETIMEPRECISION), precision);
+        dateResource.addProperty(model.createProperty(VIVO_DATETIMEPRECISION), model.createResource(precision));
 
         work.addProperty(model.createProperty(VIVO_DATETIMEVALUE), dateResource);
         return true;

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -2,35 +2,47 @@ version: '3.2'
 
 services:
 
-  solr:
+  vivo-solr:
+    container_name: vivo-solr
     image: vivoweb/vivo-solr:latest
     environment:
-      - RESET_CORE=${RESET_CORE}
-      - VERBOSE=${VERBOSE}
+      - RESET_CORE=${SOLR_RESET_CORE}
+      - VERBOSE=${SOLR_VERBOSE}
     ports:
-      - 8983:8983
+      - ${SOLR_HOST_PORT}:${SOLR_CONTAINER_PORT}
+    volumes:
+      - ${SOLR_CORES}:/opt/solr/server/solr/mycores
     networks:
-      - vivo
+      - vivoweb
+    healthcheck:
+      test: ["CMD-SHELL", "wget --no-verbose --tries=1 --spider http://localhost:8983/solr/vivocore/admin/ping || exit 1"]
+      interval: 15s
+      timeout: 5s
+      retries: 3
 
-  tomcat:
+  vivo:
     container_name: vivo
+    image: vivoweb/vivo:latest
     hostname: vivo
     build:
       context: ./
       dockerfile: Dockerfile
       args:
-        - VIVO_DIR=/usr/local/vivo/home
-        - TDB_FILE_MODE=direct
-        - SOLR_URL=http://solr:8983/solr/vivocore
+        - TDB_FILE_MODE=${VIVO_TDB_FILE_MODE}
+        - VIVO_HOME=${VIVO_CONTAINER_VIVO_HOME}
+        - SOLR_URL=http://vivo-solr:${SOLR_CONTAINER_PORT}/solr/vivocore
     environment:
-      - RESET_HOME=${RESET_HOME}
-      - VERBOSE=${VERBOSE}
+      - RESET_HOME=${VIVO_RESET_HOME}
+      - VERBOSE=${VIVO_VERBOSE}
     ports:
-      - 8080:8080
+      - ${VIVO_HOST_PORT}:${VIVO_CONTAINER_PORT}
     volumes:
-      - ${LOCAL_VIVO_HOME}:/usr/local/vivo/home
+      - ${VIVO_HOST_VIVO_HOME}:${VIVO_CONTAINER_VIVO_HOME}
     networks:
-      - vivo
+      - vivoweb
+    depends_on:
+      vivo-solr:
+        condition: service_healthy
 
 networks:
-  vivo:
+  vivoweb:
diff --git a/home/src/main/resources/rdf/accessControl/firsttime/profile_proximity_query.n3 b/home/src/main/resources/rdf/accessControl/firsttime/profile_proximity_query.n3
@@ -7,70 +7,70 @@ access-individual:PersonProfileProximityToResourceUri a access:SparqlSelectValue
     access:id """
     SELECT ?resourceUri WHERE {
         {
-          ?personUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
+          ?profileUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
           ?roleUri a <http://vivoweb.org/ontology/core#AdvisorRole> .
           ?roleUri <http://vivoweb.org/ontology/core#relatedBy> ?resourceUri .
           ?resourceUri a <http://vivoweb.org/ontology/core#AdvisingRelationship> .
         }
         UNION
         {
-          ?personUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
+          ?profileUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
           ?roleUri a <http://vivoweb.org/ontology/core#TeacherRole> .
           ?roleUri <http://purl.obolibrary.org/obo/BFO_0000054> ?resourceUri .
           ?resourceUri a <http://vivoweb.org/ontology/core#Course> .
         }
         UNION
         {
-          ?personUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
+          ?profileUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
           ?roleUri a <http://vivoweb.org/ontology/core#PrincipalInvestigatorRole> .
           ?roleUri <http://vivoweb.org/ontology/core#relatedBy> ?resourceUri .
           ?resourceUri a <http://vivoweb.org/ontology/core#Grant> .
         }
         UNION
         {
-          ?personUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
+          ?profileUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
           ?roleUri a <http://vivoweb.org/ontology/core#CoPrincipalInvestigatorRole> .
           ?roleUri <http://vivoweb.org/ontology/core#relatedBy> ?resourceUri .
           ?resourceUri a <http://vivoweb.org/ontology/core#Grant> .
         }
         UNION
         {
-          ?personUri <http://vivoweb.org/ontology/core#relatedBy> ?roleUri .
+          ?profileUri <http://vivoweb.org/ontology/core#relatedBy> ?roleUri .
           ?roleUri a <http://vivoweb.org/ontology/core#Authorship> .
           ?roleUri <http://vivoweb.org/ontology/core#relates> ?resourceUri .
           ?resourceUri a <http://purl.obolibrary.org/obo/IAO_0000030> .
         }
         UNION
         {
-          ?personUri <http://vivoweb.org/ontology/core#relatedBy> ?roleUri .
+          ?profileUri <http://vivoweb.org/ontology/core#relatedBy> ?roleUri .
           ?roleUri a <http://vivoweb.org/ontology/core#Editorship> .
           ?roleUri <http://vivoweb.org/ontology/core#relates> ?resourceUri .
           ?resourceUri a <http://purl.obolibrary.org/obo/IAO_0000030> .
         }
         UNION
         {
-          ?personUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
+          ?profileUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
           ?roleUri a <http://vivoweb.org/ontology/core#PresenterRole> .
           ?roleUri <http://purl.obolibrary.org/obo/BFO_0000054> ?resourceUri .
           ?resourceUri a <http://vivoweb.org/ontology/core#Presentation> .
         }
         UNION
         {
-          ?personUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
+          ?profileUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
           ?roleUri a <http://vivoweb.org/ontology/core#ClinicalRole> .
           ?roleUri <http://vivoweb.org/ontology/core#contributesTo> ?resourceUri .
           ?resourceUri a <http://vivoweb.org/ontology/core#Project> .
         }
         UNION
         {
-          ?personUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
+          ?profileUri <http://purl.obolibrary.org/obo/RO_0000053> ?roleUri .
           ?roleUri a <http://vivoweb.org/ontology/core#ClinicalRole> .
           ?roleUri <http://vivoweb.org/ontology/core#contributesTo> ?resourceUri .
           ?resourceUri a <http://vivoweb.org/ontology/core#Service> .
         }
         UNION
         { 
-          BIND ( ?personUri as ?resourceUri)
+          BIND ( ?profileUri as ?resourceUri)
         }
     }
     """ .

diff --git a/home/src/main/resources/rdf/i18n/de_DE/display/firsttime/search_individuals_vivo.n3 b/home/src/main/resources/rdf/i18n/de_DE/display/firsttime/search_individuals_vivo.n3
@@ -0,0 +1,11 @@
+@prefix : <https://vivoweb.org/ontology/vitro-search-individual/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+:filter_publication_year rdfs:label "Erscheinungsjahr"@de-DE .
+:field_persons rdfs:label "Personen"@de-DE .
+:range_filter_dates rdfs:label "Dates"@de-DE .
+:filter_organizations rdfs:label "Organisationen"@de-DE .
+:filter_persons rdfs:label "Personen"@de-DE .
+:field_dates rdfs:label "Dates"@de-DE .
+:field_organizations rdfs:label "Organisationen"@de-DE .
+:field_publication_year rdfs:label "Erscheinungsjahr"@de-DE .
diff --git a/home/src/main/resources/rdf/i18n/en_CA/display/firsttime/search_individuals_vivo.n3 b/home/src/main/resources/rdf/i18n/en_CA/display/firsttime/search_individuals_vivo.n3
@@ -0,0 +1,11 @@
+@prefix : <https://vivoweb.org/ontology/vitro-search-individual/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+:filter_publication_year rdfs:label "Publication year"@en-CA .
+:field_persons rdfs:label "Persons"@en-CA .
+:range_filter_dates rdfs:label "Dates"@en-CA .
+:filter_organizations rdfs:label "Organizations"@en-CA .
+:filter_persons rdfs:label "Persons"@en-CA .
+:field_dates rdfs:label "Dates"@en-CA .
+:field_organizations rdfs:label "Organizations"@en-CA .
+:field_publication_year rdfs:label "Publication year"@en-CA .
diff --git a/home/src/main/resources/rdf/i18n/es/display/firsttime/search_individuals_vivo.n3 b/home/src/main/resources/rdf/i18n/es/display/firsttime/search_individuals_vivo.n3
@@ -0,0 +1,11 @@
+@prefix : <https://vivoweb.org/ontology/vitro-search-individual/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+:filter_publication_year rdfs:label "Año de publicación"@es .
+:field_persons rdfs:label "personas"@es .
+:range_filter_dates rdfs:label "fechas"@es .
+:filter_organizations rdfs:label "Organizaciones"@es .
+:filter_persons rdfs:label "personas"@es .
+:field_dates rdfs:label "fechas"@es .
+:field_organizations rdfs:label "Organizaciones"@es .
+:field_publication_year rdfs:label "Año de publicación"@es .
diff --git a/home/src/main/resources/rdf/i18n/fr_CA/display/firsttime/search_individuals_vivo.n3 b/home/src/main/resources/rdf/i18n/fr_CA/display/firsttime/search_individuals_vivo.n3
@@ -0,0 +1,11 @@
+@prefix : <https://vivoweb.org/ontology/vitro-search-individual/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+:filter_publication_year rdfs:label "Année de parution"@fr-CA .
+:field_persons rdfs:label "Personnes"@fr-CA .
+:range_filter_dates rdfs:label "Dates"@fr-CA .
+:filter_organizations rdfs:label "Organisations"@fr-CA .
+:filter_persons rdfs:label "Personnes"@fr-CA .
+:field_dates rdfs:label "Dates"@fr-CA .
+:field_organizations rdfs:label "Organisations"@fr-CA .
+:field_publication_year rdfs:label "Année de parution"@fr-CA .
diff --git a/home/src/main/resources/rdf/i18n/pt_BR/display/firsttime/search_individuals_vivo.n3 b/home/src/main/resources/rdf/i18n/pt_BR/display/firsttime/search_individuals_vivo.n3
@@ -0,0 +1,11 @@
+@prefix : <https://vivoweb.org/ontology/vitro-search-individual/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+:filter_publication_year rdfs:label "Ano de publicação"@pt-BR .
+:field_persons rdfs:label "Pessoas"@pt-BR .
+:range_filter_dates rdfs:label "datas"@pt-BR .
+:filter_organizations rdfs:label "Organizações"@pt-BR .
+:filter_persons rdfs:label "Pessoas"@pt-BR .
+:field_dates rdfs:label "datas"@pt-BR .
+:field_organizations rdfs:label "Organizações"@pt-BR .
+:field_publication_year rdfs:label "Ano de publicação"@pt-BR .
diff --git a/home/src/main/resources/rdf/i18n/ru_RU/display/firsttime/search_individuals_vivo.n3 b/home/src/main/resources/rdf/i18n/ru_RU/display/firsttime/search_individuals_vivo.n3
@@ -0,0 +1,11 @@
+@prefix : <https://vivoweb.org/ontology/vitro-search-individual/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+:filter_publication_year rdfs:label "Год публикации"@ru-RU .
+:field_persons rdfs:label "Персоны"@ru-RU .
+:range_filter_dates rdfs:label "Даты"@ru-RU .
+:filter_organizations rdfs:label "Организации"@ru-RU .
+:filter_persons rdfs:label "Персоны"@ru-RU .
+:field_dates rdfs:label "Даты"@ru-RU .
+:field_organizations rdfs:label "Организации"@ru-RU .
+:field_publication_year rdfs:label "Год публикации"@ru-RU .
diff --git a/home/src/main/resources/rdf/i18n/sr_Latn_RS/display/firsttime/search_individuals_vivo.n3 b/home/src/main/resources/rdf/i18n/sr_Latn_RS/display/firsttime/search_individuals_vivo.n3
@@ -0,0 +1,11 @@
+@prefix : <https://vivoweb.org/ontology/vitro-search-individual/> .
+@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
+
+:filter_publication_year rdfs:label "Godina izdanja"@sr-Latn-RS .
+:field_persons rdfs:label "Osobe"@sr-Latn-RS .
+:range_filter_dates rdfs:label "Datumi"@sr-Latn-RS .
+:filter_organizations rdfs:label "Organizacije"@sr-Latn-RS .
+:filter_persons rdfs:label "Osobe"@sr-Latn-RS .
+:field_dates rdfs:label "Datumi"@sr-Latn-RS .
+:field_organizations rdfs:label "Organizacije"@sr-Latn-RS .
+:field_publication_year rdfs:label "Godina izdanja"@sr-Latn-RS .