Merge branch 'main' into fix-tooltip

.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

.github/PULL_REQUEST_TEMPLATE.md

@@ -25,11 +25,39 @@ A description of what steps someone could take to:
 Any additional information that you think would be helpful when reviewing this PR.
 
 Example:
-* Does this change require documentation to be updated? 
-* Does this change add any new dependencies? 
-* Does this change require any other modifications to be made to the repository? 
+* Does this change require documentation to be updated?
+* Does this change add any new dependencies?
+* Does this change require any other modifications to be made to the repository?
 * Could this change impact execution of existing code?
-* Large pull requests should be avoided. If this PR is large (more than 1,000 lines of codes), please provide short explanation why your contribution can't be decoupled in smaller PRs. 
+* Large pull requests should be avoided. If this PR is large (more than 1,000 lines of codes), please provide short explanation why your contribution can't be decoupled in smaller PRs.
 
 # Interested parties
 Tag (@ mention) interested parties or, if unsure, @VIVO-project/vivo-committers
+
+# Reviewers' expertise
+**Please add any new expertise in the list which might be needed for reviewing your PR or remove any of the listed if it is not needed.**
+
+Candidates for reviewing this PR should have some of the following expertises:
+1. Java
+1. HTML, CSS, JavaScript
+1. FreeMarker
+1. SPARQL
+1. Ontologies
+1. Docker
+1. Natural language knowledge
+    1. English
+    2. German
+    3. Spanish
+    4. French
+    5. Portuguese
+    6. Russian
+    7. Serbian
+
+# Reviewers' report template
+**Please update the following template which should be used by reviewers.**
+## General comment
+A reviewer should provide here comments and suggestions for requested changes if any.
+## Testing
+A reviewer should briefly describe here how it was tested
+## Code reviewing
+A reviewer should briefly describe here which part was code reviewed

.gitignore

@@ -21,6 +21,7 @@ utilities/rdbmigration/.work
 **/.project
 **/bin/
 
+vivo-cores/
 vivo-home/
 
 .fake

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
 

README.md

@@ -11,7 +11,7 @@ desired information across disciplines.
 ## Resources
 
 ### VIVO Project web site
-http://vivoweb.org/
+[https://vivo.lyrasis.org/](https://vivo.lyrasis.org/)
 
 ### VIVO Project Wiki
 https://wiki.lyrasis.org/display/VIVO/
@@ -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. 
 
@@ -61,31 +86,11 @@ docker build -t vivoweb/vivo:development .
 docker run -p 8080:8080 vivoweb/vivo:development
 ```
 
-## Contact us
-There are several ways to contact the VIVO community. 
-Whatever your interest, we would be pleased to hear from you.
-
-### Contact form 
-https://vivo.lyrasis.org/contact/
-
-### Mailing lists
-
-#### [vivo-all](https://groups.google.com/forum/#!forum/vivo-all) 
-This updates list provides news to the VIVO community of interest to all.
-
-#### [vivo-community](https://groups.google.com/forum/#!forum/vivo-community)  
-Join the VIVO community!  Here you'll find non-technical discussion regarding participation, the VIVO
-conference,  policy, project management, outreach, and engagement. 
-
-#### [vivo-tech](https://groups.google.com/forum/#!forum/vivo-tech)  
-The best place to get your hands dirty in the VIVO Project. 
-Developers and implementers frequent this list to get the latest on feature design, 
-development, implementation, and testing.
+## Community
+There are several ways to contact and join the VIVO community. All of them are listed at https://vivo.lyrasis.org/contact/
 
 ## Contributing Code
-If you would like to contribute code to the VIVO project, please open a ticket 
-in our [JIRA](https://jira.lyrasis.org/projects/VIVO), and prepare a 
-pull request that references your ticket.  Contributors welcome!
+If you would like to contribute code to the VIVO project, please read instructions at [this page](https://github.com/vivo-project/VIVO/wiki/Development-Processes#process-for-suggesting-contribution).  Contributors welcome!
 
 ## Citing VIVO
 If you are using VIVO in your publications or projects, please cite the software paper in the Journal of Open Source Software:

api/pom.xml

@@ -7,13 +7,13 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vivo-api</artifactId>
-    <version>1.14.1-SNAPSHOT</version>
+    <version>1.15.1-SNAPSHOT</version>
     <packaging>jar</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vivo-project</artifactId>
-        <version>1.14.1-SNAPSHOT</version>
+        <version>1.15.1-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>
 

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/AddEditWebpageFormGenerator.java

@@ -3,6 +3,7 @@
 
 import javax.servlet.http.HttpSession;
 
+import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.logging.Log;
 import org.apache.commons.logging.LogFactory;
 
@@ -60,6 +61,7 @@ protected EditConfigurationVTwo setupConfig(VitroRequest vreq, HttpSession sessi
 
 	    config.setVarNameForSubject("subject");
 	    config.setVarNameForObject("vcard");
+	    config.addFormSpecificData("fauxContextUri", vreq.getParameter("fauxContextUri"));
 
 	    config.addNewResource("vcard", DEFAULT_NS_FOR_NEW_RESOURCE);
 	    config.addNewResource("link", DEFAULT_NS_FOR_NEW_RESOURCE);
@@ -238,6 +240,7 @@ private String getUrlPatternToReturnTo(VitroRequest vreq) {
 		String rangeUri = (String) vreq.getParameter("rangeUri");
 		String generatorName = "edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.generators.ManageWebpagesForIndividualGenerator";
 		String editUrl = EditConfigurationUtils.getEditUrlWithoutContext(vreq);
+		String fauxContextUri = vreq.getParameter("fauxContextUri");
 		String returnPath =  editUrl + "?subjectUri=" + UrlBuilder.urlEncode(subjectUri) +
 		"&predicateUri=" + UrlBuilder.urlEncode(predicateUri) +
 		"&editForm=" + UrlBuilder.urlEncode(generatorName);
@@ -247,6 +250,9 @@ private String getUrlPatternToReturnTo(VitroRequest vreq) {
 		if(rangeUri != null && !rangeUri.isEmpty()) {
 			returnPath += "&rangeUri=" + UrlBuilder.urlEncode(rangeUri);
 		}
+		if (StringUtils.isNotBlank(fauxContextUri)) {
+		    returnPath += "&fauxContextUri=" + UrlBuilder.urlEncode(fauxContextUri);
+		}
 		return returnPath;
 
 	}

api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageWebpagesForIndividualGenerator.java

@@ -38,6 +38,8 @@
  * This mainly sets up pageData for the template to use.
  */
 public class ManageWebpagesForIndividualGenerator extends BaseEditConfigurationGenerator implements EditConfigurationGenerator {
+    private static final String OBO_HAS_CONTACT_INFO_URI = "http://purl.obolibrary.org/obo/ARG_2000028";
+
     public static Log log = LogFactory.getLog(ManageWebpagesForIndividualGenerator.class);
 
     @Override
@@ -59,10 +61,12 @@ public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession
         config.addFormSpecificData("rankPredicate", "http://vivoweb.org/ontology/core#rank" );
         config.addFormSpecificData("reorderUrl", "/edit/reorder" );
         config.addFormSpecificData("deleteWebpageUrl", "/edit/primitiveDelete");
+        String fauxContextUri = vreq.getParameter("fauxContextUri");
 
         ParamMap paramMap = new ParamMap();
         paramMap.put("subjectUri", config.getSubjectUri());
         paramMap.put("editForm", this.getEditForm());
+        paramMap.put("fauxContextUri", fauxContextUri);
         paramMap.put("view", "form");
         String path = UrlBuilder.getUrl( UrlBuilder.Route.EDIT_REQUEST_DISPATCH ,paramMap);
 
@@ -76,6 +80,8 @@ public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession
         paramMap.put("predicateUri", config.getPredicateUri());
         paramMap.put("editForm" , this.getEditForm() );
         paramMap.put("cancelTo", "manage");
+        paramMap.put("fauxContextUri", fauxContextUri);
+
         if(domainUri != null && !domainUri.isEmpty()) {
         	paramMap.put("domainUri", domainUri);
         }

api/src/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;

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:

home/pom.xml

@@ -4,13 +4,13 @@
 
     <groupId>org.vivoweb</groupId>
     <artifactId>vivo-home</artifactId>
-    <version>1.14.1-SNAPSHOT</version>
+    <version>1.15.1-SNAPSHOT</version>
     <packaging>pom</packaging>
 
     <parent>
         <groupId>org.vivoweb</groupId>
         <artifactId>vivo-project</artifactId>
-        <version>1.14.1-SNAPSHOT</version>
+        <version>1.15.1-SNAPSHOT</version>
         <relativePath>..</relativePath>
     </parent>