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Merge branch 'rel-1.12.0-RC' into main

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This commit is contained in:
Ralph O'Flinn 2021-07-21 07:09:36 -05:00
commit 9f6b545b84
39 changed files with 7842 additions and 293 deletions
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2
.github/workflows/build.yml vendored
View file

@ -28,4 +28,4 @@ jobs:
java-version: 11
- name: Maven Build
run: mvn clean install
run: mvn clean package -s installer/example-settings.xml

2
.github/workflows/deploy.yml vendored
View file

@ -35,7 +35,7 @@ jobs:
server-password: MAVEN_PASSWORD
- name: Maven Deploy
run: mvn --batch-mode deploy
run: mvn --batch-mode deploy -Pskip
env:
MAVEN_USERNAME: ${{ secrets.OSSRH_USERNAME }}
MAVEN_PASSWORD: ${{ secrets.OSSRH_TOKEN }}

2
.github/workflows/docker.yml vendored
View file

@ -32,7 +32,7 @@ jobs:
java-version: 11
- name: Maven Build
run: mvn clean install
run: mvn clean package -s installer/example-settings.xml
- name: Set up QEMU
uses: docker/setup-qemu-action@v1

12
Dockerfile
View file

@ -1,20 +1,18 @@
FROM tomcat:9-jdk11-openjdk
ARG SOLR_URL=http://localhost:8983/solr/vivocore
ARG VIVO_DIR=/opt/vivo/home
ARG VIVO_DIR=/usr/local/vivo/home
ARG TDB_FILE_MODE=direct
ENV SOLR_URL=${SOLR_URL}
ENV JAVA_OPTS="${JAVA_OPTS} -Dvivo-dir=$VIVO_DIR -Dtdb:fileMode=$TDB_FILE_MODE"
ENV JAVA_OPTS="${JAVA_OPTS} -Dtdb:fileMode=$TDB_FILE_MODE"
RUN mkdir /opt/vivo
RUN mkdir /opt/vivo/home
RUN mkdir /usr/local/vivo
RUN mkdir /usr/local/vivo/home
COPY ./installer/home/target/vivo /vivo-home
COPY ./installer/webapp/target/vivo.war /usr/local/tomcat/webapps/ROOT.war
COPY ./home/src/main/resources/config/default.applicationSetup.n3 /applicationSetup.n3
COPY ./home/src/main/resources/config/default.runtime.properties /runtime.properties
COPY start.sh /start.sh
EXPOSE 8080

2
LICENSE
View file

@ -1,4 +1,4 @@
Copyright (c) 2018, Cornell University
Copyright (c) 2021, Cornell University
All rights reserved.
Redistribution and use in source and binary forms, with or without

25
README.md
View file

@ -19,7 +19,7 @@ https://wiki.duraspace.org/display/VIVO/
### Installation Instructions
Installation instructions for the latest release can be found at this location on the wiki:
https://wiki.duraspace.org/display/VIVODOC110x/Installing+VIVO
https://wiki.duraspace.org/display/VIVODOC112x/Installing+VIVO
### Docker
@ -27,7 +27,7 @@ VIVO docker container is available at [vivoweb/vivo](https://hub.docker.com/repo
### Docker Compose
Docker Compose environment variables.
Docker Compose environment variables:
.env defaults
```
@ -36,14 +36,27 @@ RESET_HOME=false
RESET_CORE=false
```
- `LOCAL_VIVO_HOME`: VIVO home directory on your host machine which will mount to volume in docker container.
- `RESET_HOME`: Convinience to reset VIVO home when starting container. **Caution** will delete local configuration, content, and configuration model.
- `RESET_CORE`: Convinience to reset VIVO Solr core when starting container. **Caution** will require complete reindex.
- `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.
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. You will also need to clone (and switch to the appropriate branch) of [Vitro-languages](https://github.com/vivo-project/Vitro-languages) and [VIVO-languages](https://github.com/vivo-project/VIVO-languages).
Build and start VIVO.
1. In Vitro-languages, run:
```
mvn clean install
mvn install
```
2. In VIVO-languages, run:
```
mvn install
```
3. In VIVO (with Vitro cloned alongside it), run:
```
mvn clean package -s installer/example-settings.xml
docker-compose up
```

4
api/pom.xml
View file

@ -7,13 +7,13 @@
<groupId>org.vivoweb</groupId>
<artifactId>vivo-api</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<packaging>jar</packaging>
<parent>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-project</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>

22
api/src/main/java/edu/cornell/mannlib/semservices/service/impl/UMLSService.java
View file

@ -4,12 +4,18 @@ package edu.cornell.mannlib.semservices.service.impl;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.http.HttpVersion;
import org.apache.http.client.fluent.Form;
import org.apache.http.client.fluent.Request;
import org.apache.http.client.utils.URIBuilder;
import org.springframework.util.StringUtils;
import com.fasterxml.jackson.databind.node.ArrayNode;
import com.fasterxml.jackson.databind.node.ObjectNode;
@ -18,11 +24,6 @@ import edu.cornell.mannlib.semservices.bo.Concept;
import edu.cornell.mannlib.semservices.exceptions.ConceptsNotFoundException;
import edu.cornell.mannlib.semservices.service.ExternalConceptService;
import edu.cornell.mannlib.vitro.webapp.utils.json.JacksonUtils;
import org.apache.http.HttpVersion;
import org.apache.http.client.fluent.Form;
import org.apache.http.client.fluent.Request;
import org.apache.http.client.utils.URIBuilder;
import org.springframework.util.StringUtils;
/**
* @author jaf30
@ -54,11 +55,13 @@ public class UMLSService implements ExternalConceptService {
private static String UMLS_AUTH_USER_URL = "https://utslogin.nlm.nih.gov/cas/v1/tickets";
private static String UMLS_AUTH_KEY_URL = "https://utslogin.nlm.nih.gov/cas/v1/api-key";
private static String UTS_SERVICE_URL = "http://umlsks.nlm.nih.gov";
private static final String UMLS_PROPERTIES = "/umls.properties";
private static final Log log = LogFactory.getLog(UMLSService.class);
{
if (username == null || apikey == null) {
final Properties properties = new Properties();
try (InputStream stream = getClass().getResourceAsStream("/umls.properties")) {
try (InputStream stream = getClass().getResourceAsStream(UMLS_PROPERTIES)) {
properties.load(stream);
username = properties.getProperty("username");
password = properties.getProperty("password");
@ -73,12 +76,19 @@ public class UMLSService implements ExternalConceptService {
}
}
} catch (Exception e) {
log.error(e, e);
}
} catch (IOException e) {
log.error(e, e);
}
}
}
public static boolean configurationFileExists() {
URL config = UMLSService.class.getResource(UMLS_PROPERTIES);
return (config != null);
}
public boolean isConfigured() {
return !(StringUtils.isEmpty(username) && StringUtils.isEmpty(apikey));
}

2
api/src/main/java/edu/cornell/mannlib/vitro/webapp/controller/freemarker/ManagePublicationsForIndividualController.java
View file

@ -69,7 +69,7 @@ public class ManagePublicationsForIndividualController extends FreemarkerHttpSer
+ "PREFIX core: <http://vivoweb.org/ontology/core#> \n"
+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
+ "PREFIX vitro: <http://vitro.mannlib.cornell.edu/ns/vitro/0.7#> \n"
+ "SELECT DISTINCT ?subclass ?authorship (str(?label) as ?title) ?pub ?hideThis WHERE { \n"
+ "SELECT DISTINCT ?subclass ?authorship (?label as ?title) ?pub ?hideThis WHERE { \n"
+ " ?subject core:relatedBy ?authorship . \n"
+ " ?authorship a core:Authorship . \n"
+ " OPTIONAL { \n "

63
api/src/main/java/edu/cornell/mannlib/vitro/webapp/edit/n3editing/configuration/generators/ManageLabelsForPersonGenerator.java
View file

@ -15,6 +15,7 @@ import java.util.HashSet;
import java.util.List;
import java.util.Locale;
import java.util.Map;
import java.util.Set;
import javax.servlet.http.HttpSession;
@ -41,6 +42,7 @@ import edu.cornell.mannlib.vitro.webapp.edit.n3editing.VTwo.fields.FieldVTwo;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.FoafNameToRdfsLabelPreprocessor;
import edu.cornell.mannlib.vitro.webapp.edit.n3editing.configuration.preprocessors.ManageLabelsForPersonPreprocessor;
import edu.cornell.mannlib.vitro.webapp.i18n.selection.SelectedLocale;
import edu.cornell.mannlib.vitro.webapp.rdfservice.filter.LanguageFilteringUtils;
import edu.cornell.mannlib.vitro.webapp.web.templatemodels.individual.DataPropertyStatementTemplateModel;
/**
@ -246,12 +248,12 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
private void addFormSpecificData(EditConfigurationVTwo config,
VitroRequest vreq) {
//Get all language codes/labels in the system, and this list is sorted by language name
List<HashMap<String, String>> locales = this.getLocales(vreq);
ArrayList<Literal> existingLabels = this.getExistingLabels(config.getSubjectUri(), vreq);
//Get language codes/labels for existing labels, and this list is sorted by language name
List<HashMap<String, String>> locales = this.getLocales(vreq, existingLabels);
//Get code to label hashmap - we use this to get the language name for the language code returned in the rdf literal
HashMap<String, String> localeCodeToNameMap = this.getFullCodeToLanguageNameMap(locales);
//the labels already added by the user
ArrayList<Literal> existingLabels = this.getExistingLabels(config.getSubjectUri(), vreq);
int numberExistingLabels = existingLabels.size();
//existing labels keyed by language name and each of the list of labels is sorted by language name
HashMap<String, List<LabelInformation>> existingLabelsByLanguageName = this.getLabelsSortedByLanguageName(existingLabels, localeCodeToNameMap, config, vreq);
@ -439,21 +441,20 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
ArrayList<Literal> labels = new ArrayList<Literal>();
try {
//We want to get the labels for all the languages, not just the display language
ResultSet results = QueryUtils.getLanguageNeutralQueryResults(queryStr, vreq);
// No longer retrieving language-neutral results here, so that
// language editing is consistent with other editing forms.
// Editable values depend on the interface's locale selector.
ResultSet results = QueryUtils.getQueryResults(queryStr, vreq);
while (results.hasNext()) {
QuerySolution soln = results.nextSolution();
Literal nodeLiteral = soln.get("label").asLiteral();
labels.add(nodeLiteral);
}
} catch (Exception e) {
log.error(e, e);
}
return labels;
}
}
//Putting this into a method allows overriding it in subclasses
@ -467,30 +468,32 @@ public class ManageLabelsForPersonGenerator extends BaseEditConfigurationGenerat
return template;
}
//get locales present in list of literals
public List<HashMap<String, String>> getLocales(VitroRequest vreq,
List<Literal> existingLiterals) {
Set<Locale> locales = new HashSet<Locale>();
for(Literal literal : existingLiterals) {
String language = literal.getLanguage();
if(!StringUtils.isEmpty(language)) {
locales.add(LanguageFilteringUtils.languageToLocale(language));
}
}
if (locales.isEmpty()) {
return Collections.emptyList();
}
List<HashMap<String, String>> list = new ArrayList<HashMap<String, String>>();
Locale currentLocale = SelectedLocale.getCurrentLocale(vreq);
for (Locale locale : locales) {
try {
list.add(buildLocaleMap(locale, currentLocale));
} catch (FileNotFoundException e) {
log.warn("Can't show locale '" + locale + "': " + e);
}
}
//get locales
public List<HashMap<String, String>> getLocales(VitroRequest vreq) {
List<Locale> selectables = SelectedLocale.getSelectableLocales(vreq);
if (selectables.isEmpty()) {
return Collections.emptyList();
}
List<HashMap<String, String>> list = new ArrayList<HashMap<String, String>>();
Locale currentLocale = SelectedLocale.getCurrentLocale(vreq);
for (Locale locale : selectables) {
try {
list.add(buildLocaleMap(locale, currentLocale));
} catch (FileNotFoundException e) {
log.warn("Can't show the Locale selector for '" + locale
+ "': " + e);
}
}
return list;
return list;
}
public HashMap<String, String> getFullCodeToLanguageNameMap(List<HashMap<String, String>> localesList) {
HashMap<String, String> codeToLanguageMap = new HashMap<String, String>();
for(Map<String, String> locale: localesList) {

6
api/src/main/java/edu/cornell/mannlib/vitro/webapp/utils/ConceptSearchService/ConceptSearchServiceUtils.java
View file

@ -12,6 +12,7 @@ import org.apache.commons.logging.LogFactory;
import edu.cornell.mannlib.semservices.bo.Concept;
import edu.cornell.mannlib.semservices.service.ExternalConceptService;
import edu.cornell.mannlib.semservices.service.impl.UMLSService;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
/**
* Utilities for search
@ -38,7 +39,9 @@ public class ConceptSearchServiceUtils {
//URL to label
public static HashMap<String, VocabSourceDescription> getVocabSources() {
HashMap<String, VocabSourceDescription> map = new HashMap<String, VocabSourceDescription>();
map.put(UMLSVocabSource, new VocabSourceDescription("UMLS", UMLSVocabSource, "http://www.nlm.nih.gov/research/umls/", "Unified Medical Language System"));
if(UMLSService.configurationFileExists()) {
map.put(UMLSVocabSource, new VocabSourceDescription("UMLS", UMLSVocabSource, "http://www.nlm.nih.gov/research/umls/", "Unified Medical Language System"));
}
//Commenting out agrovoc for now until implementation is updated
map.put(AgrovocVocabSource, new VocabSourceDescription("AGROVOC", AgrovocVocabSource, "http://www.fao.org/agrovoc/", "Agricultural Vocabulary"));
map.put(GemetVocabSource, new VocabSourceDescription("GEMET", GemetVocabSource, "http://www.eionet.europa.eu/gemet", "GEneral Multilingual Environmental Thesaurus"));
@ -53,6 +56,7 @@ public class ConceptSearchServiceUtils {
//Get the hashmap mapping service name to Service class
private static HashMap<String, String> getMapping() {
HashMap<String, String> map = new HashMap<String, String>();
map.put(UMLSVocabSource, "edu.cornell.mannlib.semservices.service.impl.UMLSService");
map.put(AgrovocVocabSource, "edu.cornell.mannlib.semservices.service.impl.AgrovocService");
map.put(GemetVocabSource, "edu.cornell.mannlib.semservices.service.impl.GemetService");

73
api/src/main/java/org/vivoweb/webapp/sitemap/SiteMapServlet.java
View file

@ -2,29 +2,40 @@
package org.vivoweb.webapp.sitemap;
import org.apache.commons.lang3.StringUtils;
import org.apache.jena.query.QuerySolution;
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
import org.apache.commons.io.IOUtils;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
import java.util.List;
import javax.servlet.ServletException;
import javax.servlet.ServletOutputStream;
import javax.servlet.annotation.WebServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import java.io.FileInputStream;
import java.io.IOException;
import java.io.InputStream;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.jena.query.QuerySolution;
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
import edu.cornell.mannlib.vitro.webapp.controller.freemarker.UrlBuilder;
import edu.cornell.mannlib.vitro.webapp.rdfservice.RDFServiceException;
import edu.cornell.mannlib.vitro.webapp.rdfservice.ResultSetConsumer;
import edu.cornell.mannlib.vitro.webapp.visualization.constants.QueryConstants;
@WebServlet(name = "SiteMapServlet", urlPatterns = {"/robots.txt","/sitemap.xml"})
public class SiteMapServlet extends VitroHttpServlet {
private static final int MAX_URLS = 50000; // max URLs per sitemap
private static final Log log = LogFactory.getLog(SiteMapServlet.class);
@Override
protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
String requestURI = request.getRequestURI();
if (requestURI != null) {
@ -60,7 +71,7 @@ public class SiteMapServlet extends VitroHttpServlet {
"WHERE\n" +
"{\n" +
" ?person a foaf:Person .\n" +
"}\n";
"} LIMIT " + MAX_URLS + "\n";
final VitroRequest vreq = new VitroRequest(request);
final ServletOutputStream out = response.getOutputStream();
@ -68,26 +79,31 @@ public class SiteMapServlet extends VitroHttpServlet {
out.println("<?xml version=\"1.0\" encoding=\"UTF-8\"?>");
out.println("<urlset xmlns=\"http://www.sitemaps.org/schemas/sitemap/0.9\">");
List<String> personURIs = new ArrayList<String>();
try {
vreq.getRDFService().sparqlSelectQuery(query, new ResultSetConsumer() {
@Override
protected void processQuerySolution(QuerySolution qs) {
String person = qs.getResource("person").getURI();
String profileUrl = UrlBuilder.getIndividualProfileUrl(person, vreq);
if (!StringUtils.isEmpty(profileUrl)) {
try {
out.println(" <url>");
out.println(" <loc>" + schemeAndServer + profileUrl + "</loc>");
out.println(" <changefreq>weekly</changefreq>");
out.println(" </url>");
} catch (Exception e) {
}
}
personURIs.add(qs.getResource("person").getURI());
}
});
} catch (RDFServiceException rse) {
log.error(rse, rse);
}
for(String person : personURIs) {
String profileUrl = UrlBuilder.getIndividualProfileUrl(person, vreq);
if (!StringUtils.isEmpty(profileUrl)) {
try {
out.println(" <url>");
out.println(" <loc>" + schemeAndServer + profileUrl + "</loc>");
out.println(" <changefreq>weekly</changefreq>");
out.println(" </url>");
} catch (Exception e) {
log.error(e, e);
}
}
}
out.println("</urlset>");
@ -104,7 +120,8 @@ public class SiteMapServlet extends VitroHttpServlet {
if ("http".equalsIgnoreCase(scheme) || "https".equalsIgnoreCase(scheme)) {
StringBuilder builder = new StringBuilder();
builder.append(scheme).append("://").append(serverName);
if (("http".equalsIgnoreCase(scheme) && serverPort != 80) || ("https".equalsIgnoreCase(scheme) && serverPort != 443) ) {
if (("http".equalsIgnoreCase(scheme) && serverPort != 80)
|| ("https".equalsIgnoreCase(scheme) && serverPort != 443) ) {
builder.append(":").append(serverPort);
}

4
docker-compose.yml
View file

@ -19,7 +19,7 @@ services:
context: ./
dockerfile: Dockerfile
args:
- VIVO_DIR=/opt/vivo/home
- VIVO_DIR=/usr/local/vivo/home
- TDB_FILE_MODE=direct
- SOLR_URL=http://solr:8983/solr/vivocore
environment:
@ -28,7 +28,7 @@ services:
ports:
- 8080:8080
volumes:
- ${LOCAL_VIVO_HOME}:/opt/vivo/home
- ${LOCAL_VIVO_HOME}:/usr/local/vivo/home
networks:
- vivo

4
home/pom.xml
View file

@ -7,13 +7,13 @@
<groupId>org.vivoweb</groupId>
<artifactId>vivo-home</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<packaging>pom</packaging>
<parent>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-project</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>

0
home/src/main/resources/config/default.applicationSetup.n3 → home/src/main/resources/config/example.applicationSetup.n3
View file

57
home/src/main/resources/config/default.runtime.properties → home/src/main/resources/config/example.runtime.properties
View file

@ -19,6 +19,26 @@
# BASIC PROPERTIES
# -----------------------------------------------------------------------------
#
# This namespace will be used when generating URIs for objects created in the
# editor. In order to serve linked data, the default namespace must be composed
# as follows (optional elements in parentheses):
#
# scheme + server_name (+ port) (+ servlet_context) + "/individual/"
#
# For example, Cornell's default namespace is:
#
# http://vivo.cornell.edu/individual/
#
Vitro.defaultNamespace = http://vivo.mydomain.edu/individual/
#
# The email address of the root user for the VIVO application. The password
# for this user is initially set to "rootPassword", but you will be asked to
# change the password the first time you log in.
#
rootUser.emailAddress = vivo_root@mydomain.edu
#
# Argon2 password hashing parameters for time, memory and parallelism required to
# compute a hash.
@ -51,8 +71,12 @@ argon2.time = 1000
# Email parameters which VIVO can use to send mail. If these are left empty,
# the "Contact Us" form will be disabled and users will not be notified of
# changes to their accounts.
# email.smtpHost = smtp.mydomain.edu
# email.replyTo = vivoAdmin@mydomain.edu
# Example:
# email.smtpHost = smtp.mydomain.edu
# email.replyTo = vivoAdmin@mydomain.edu
#
# email.smtpHost =
# email.replyTo =
#
# URL of Solr context used in local VIVO search. This will usually consist of:
@ -90,6 +114,22 @@ selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
#
#externalAuth.netIdHeaderName = remote_userID
# -----------------------------------------------------------------------------
# OPTIMIZING LIST VIEW QUERIES
# -----------------------------------------------------------------------------
#
# Include sections between <precise-subquery></precise-subquery>
# tags when executing 'list view' queries that retrieve data
# for property lists on profile pages.
#
# Including these optional sections does not change the query
# semantics, but may improve performance.
#
# Default is true if not set.
# (Prior to v1.12, default was true for SDB and false for TDB.)
#
# listview.usePreciseSubquery = true
# -----------------------------------------------------------------------------
# TUNING THE DATABASE CONNECTION POOL
@ -108,7 +148,6 @@ selfEditing.idMatchingProperty = http://vivo.mydomain.edu/ns#networkId
#
# VitroConnection.DataSource.pool.maxIdle = 10
# -----------------------------------------------------------------------------
# USING A DIFFERENT DATABASE
# -----------------------------------------------------------------------------
@ -387,7 +426,15 @@ Vitro.reconcile.defaultTypeList = http://vivoweb.org/ontology/core#Role, core:Ro
# If you do not wish to use the claiming interface, set this property to nothing (empty)
createAndLink.providers = doi, pmid
# Triple pattern fragments is a very fast, very simple means for querying a triple store.
# The triple pattern fragments API in VIVO puts little load on the server, providing a simple means for getting data from the triple store. The API has a web interface for manual use, can be used from the command line via curl, and can be used by programs.
# Triple Pattern Fragments is a very fast, very simple means for querying a
# triple store. The Triple Pattern Fragments API in VIVO puts little load on
# the server, providing a simple means for getting data from the triple store.
# The API has a web interface for manual use, can be used from the command
# line via curl, and can be used by programs.
#
# VIVO's Triple Pattern Fragments API does not require authentication and
# makes the full RDF graph available regardless of display or publish levels
# set on particular properties. Enable Triple Pattern Fragments only if your
# VIVO does not contain restricted data that should not be shared with others.
#
# tpf.activeFlag = true

16
home/src/main/resources/rdf/display/everytime/searchIndexerConfigurationVivo.n3
View file

@ -117,6 +117,22 @@
}
""" .
# URI finder that will find the relevant person to update when the
# property linking to the email or preferred title resource is removed
:vivoUriFinder_VCard_2
a searchIndex:indexing.IndexingUriFinder ,
searchIndex:indexing.SelectQueryUriFinder ;
rdfs:label "Preferred title / email person URI finder #2" ;
:hasPredicateRestriction "http://www.w3.org/2006/vcard/ns#hasTitle" ;
:hasPredicateRestriction "http://www.w3.org/2006/vcard/ns#hasEmail" ;
:hasSelectQuery """
PREFIX obo: <http://purl.obolibrary.org/obo/>
SELECT ?uri
WHERE {
?uri obo:ARG_2000028 ?subject .
}
""" .
:vivodocumentModifier_PreferredTitle
a searchIndex:documentBuilding.SelectQueryDocumentModifier ,
searchIndex:documentBuilding.DocumentModifier ;

22
home/src/main/resources/rdf/tbox/firsttime/README.md
View file

@ -1,6 +1,20 @@
This directory contains ontology "TBox" files with class and property definitions.
These are loaded by the VIVO application when it starts for the first time, after
the initial installation or after an upgrade installation that involves changes
to these files.
This directory contains ontology "TBox" files with class and property
definitions or annotations that are intended to be editable in the VIVO GUI.
These files are loaded by the VIVO application when it starts for the first time
and during later restarts if the contents have changed. A triple is updated
if there is no conflicting value for the same subject and predicate that was
added to the triple store via the GUI or data ingest (e.g. SPARQL UPDATE).
The file vitroAnnotations.n3 contains triples with predicates in the vitro
namespace and objects that are not literals with language tags.
The VIVO-languages project contains additional language-specific
vitroAnnotations.n3 files where all of the triples contain language-tagged
literals.
VIVO-languages also provides additional annotation files
(e.g. initialTBoxAnnotations_en_US.n3) containing triples with predicates
in ontologies/voabularies outside the vitro namespace (e.g. rdfs:label).
See ../filegraph/README.md for more information about "TBox" files.

7232
home/src/main/resources/rdf/tbox/firsttime/vitroAnnotations.n3 Normal file
View file

File diff suppressed because it is too large Load diff

22
installer/example-settings.xml Normal file
View file

@ -0,0 +1,22 @@
<settings xmlns="http://maven.apache.org/SETTINGS/1.1.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/SETTINGS/1.1.0 http://maven.apache.org/xsd/settings-1.1.0.xsd">
<profiles>
<profile>
<id>defaults</id>
<properties>
<app-name>vivo</app-name>
<vivo-dir>/usr/local/vivo/home</vivo-dir>
<tomcat-dir>/usr/local/tomcat</tomcat-dir>
<default-theme>wilma</default-theme>
</properties>
</profile>
</profiles>
<activeProfiles>
<activeProfile>defaults</activeProfile>
</activeProfiles>
</settings>

114
installer/home/pom.xml
View file

@ -7,13 +7,13 @@
<groupId>org.vivoweb</groupId>
<artifactId>vivo-installer-home</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<packaging>pom</packaging>
<parent>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-installer</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
@ -23,24 +23,108 @@
<default-theme>wilma</default-theme>
</properties>
<profiles>
<profile>
<id>package</id>
<activation>
<property><name>vivo-dir</name></property>
</activation>
<build>
<finalName>${app-name}</finalName>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptors>
<descriptor>src/main/assembly/home.xml</descriptor>
</descriptors>
<appendAssemblyId>false</appendAssemblyId>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>install</id>
<activation>
<property><name>vivo-dir</name></property>
</activation>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<configuration>
<descriptors>
<descriptor>src/main/assembly/home.xml</descriptor>
</descriptors>
<appendAssemblyId>false</appendAssemblyId>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<executions>
<execution>
<id>remove-webapp</id>
<phase>verify</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<target>
<delete dir="${vivo-dir}/rdf" />
</target>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<executions>
<execution>
<id>install</id>
<phase>install</phase>
<goals>
<goal>copy-resources</goal>
</goals>
<configuration>
<outputDirectory>${vivo-dir}</outputDirectory>
<resources>
<resource>
<directory>${project.build.directory}/${project.build.finalName}</directory>
</resource>
</resources>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<build>
<plugins>
<plugin>
<artifactId>maven-assembly-plugin</artifactId>
<artifactId>maven-install-plugin</artifactId>
<configuration>
<descriptors>
<descriptor>src/main/assembly/home.xml</descriptor>
</descriptors>
<appendAssemblyId>false</appendAssemblyId>
<skip>true</skip>
</configuration>
<executions>
<execution>
<phase>package</phase>
<goals>
<goal>single</goal>
</goals>
</execution>
</executions>
</plugin>
</plugins>
</build>

1
installer/home/src/main/assembly/home.xml
View file

@ -4,7 +4,6 @@
<id>home</id>
<formats>
<format>dir</format>
<format>tar</format>
</formats>
<includeBaseDirectory>false</includeBaseDirectory>
<dependencySets>

68
installer/pom.xml
View file

@ -7,7 +7,7 @@
<groupId>org.vivoweb</groupId>
<artifactId>vivo-installer</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<packaging>pom</packaging>
<name>VIVO Installer</name>
@ -29,6 +29,12 @@
<encoding>UTF-8</encoding>
</configuration>
</plugin>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-gpg-plugin</artifactId>
@ -142,6 +148,12 @@
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-dependency-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<artifactId>maven-resources-plugin</artifactId>
<version>2.6</version>
@ -165,6 +177,60 @@
</execution>
</executions>
</plugin>
<plugin>
<artifactId>maven-war-plugin</artifactId>
<executions>
<execution>
<id>default-war</id>
<phase/>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>install</id>
<activation>
<property><name>vivo-dir</name></property>
</activation>
<build>
<plugins>
<plugin>
<artifactId>maven-enforcer-plugin</artifactId>
<executions>
<execution>
<id>enforce-properties</id>
<phase>validate</phase>
<goals>
<goal>enforce</goal>
</goals>
<configuration>
<rules>
<requireProperty>
<property>app-name</property>
<message>You must provide an application name (app-name)</message>
</requireProperty>
</rules>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>skip</id>
<build>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-deploy-plugin</artifactId>
<version>2.8.2</version>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
</plugins>
</build>
</profile>

181
installer/webapp/pom.xml
View file

@ -7,21 +7,129 @@
<groupId>org.vivoweb</groupId>
<artifactId>vivo-installer-vivo</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<packaging>war</packaging>
<parent>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-installer</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
<name>VIVO Install Web App</name>
<profiles>
<profile>
<id>package</id>
<activation>
<property><name>app-name</name></property>
</activation>
<build>
<finalName>${app-name}</finalName>
<plugins>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
</manifest>
</archive>
<archiveClasses>false</archiveClasses>
<overlays>
<overlay>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-webapp</artifactId>
<type>war</type>
</overlay>
<!-- Overlays for multilingual support -->
<!-- overlay>
<groupId>org.vivoweb</groupId>
<artifactId>vitro-languages-webapp</artifactId>
<type>war</type>
</overlay>
<overlay>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-languages-webapp</artifactId>
<type>war</type>
</overlay -->
</overlays>
<webResources>
<resource>
<directory>src/main/webResources</directory>
<filtering>true</filtering>
</resource>
</webResources>
</configuration>
</plugin>
</plugins>
</build>
</profile>
<profile>
<id>install</id>
<activation>
<property><name>tomcat-dir</name></property>
</activation>
<build>
<plugins>
<plugin>
<artifactId>maven-antrun-plugin</artifactId>
<executions>
<execution>
<id>remove-webapp</id>
<phase>verify</phase>
<goals>
<goal>run</goal>
</goals>
<configuration>
<target>
<delete dir="${tomcat-dir}/webapps/${project.build.finalName}" />
</target>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<executions>
<execution>
<id>install</id>
<phase>install</phase>
<goals>
<goal>unpack</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>${project.groupId}</groupId>
<artifactId>${project.artifactId}</artifactId>
<version>${project.version}</version>
<type>war</type>
<overWrite>true</overWrite>
<outputDirectory>${tomcat-dir}/webapps/${project.build.finalName}</outputDirectory>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
</plugins>
</build>
</profile>
</profiles>
<build>
<finalName>${app-name}</finalName>
<plugins>
<plugin>
<artifactId>maven-install-plugin</artifactId>
<configuration>
<skip>true</skip>
</configuration>
</plugin>
<plugin>
<artifactId>maven-clean-plugin</artifactId>
<configuration>
@ -32,75 +140,6 @@
</filesets>
</configuration>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-dependency-plugin</artifactId>
<configuration>
<skip>false</skip>
</configuration>
<executions>
<execution>
<id>include-home</id>
<phase>process-resources</phase>
<goals>
<goal>copy</goal>
</goals>
<configuration>
<artifactItems>
<artifactItem>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-installer-home</artifactId>
<version>${project.version}</version>
<type>tar</type>
<destFileName>vivo-home.tar</destFileName>
<outputDirectory>${project.build.directory}/home-files</outputDirectory>
</artifactItem>
</artifactItems>
</configuration>
</execution>
</executions>
</plugin>
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-war-plugin</artifactId>
<configuration>
<archive>
<manifest>
<addClasspath>true</addClasspath>
</manifest>
</archive>
<archiveClasses>false</archiveClasses>
<overlays>
<overlay>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-webapp</artifactId>
<type>war</type>
</overlay>
<!-- Overlays for multilingual support -->
<overlay>
<groupId>org.vivoweb</groupId>
<artifactId>vitro-languages-webapp-core</artifactId>
<type>war</type>
</overlay>
<overlay>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-languages-webapp-core</artifactId>
<type>war</type>
</overlay>
</overlays>
<webResources>
<resource>
<directory>src/main/webResources</directory>
<filtering>true</filtering>
</resource>
<resource>
<directory>${project.build.directory}/home-files/</directory>
<targetPath>WEB-INF/resources/home-files/</targetPath>
</resource>
</webResources>
</configuration>
</plugin>
</plugins>
</build>

43
installer/webapp/src/main/webResources/META-INF/context.xml
View file

@ -1,52 +1,9 @@
<Context> <!-- useHttpOnly="false" -->
<!--
# The 'home' property specifies the location of VIVO HOME.
# The system user used to run the VIVO web application must have write access
# to the parent directory of the directory defined in this property, if VIVO HOME
# does not already exist.
# If this directory already exists, the system user used to run the VIVO web application
# must have write access to this directory.
-->
<Environment
type="java.lang.String"
name="vitro/home"
value="${vivo-dir}" override="true"/>
<!--
# The name of the application (possibly not used).
-->
<Environment
type="java.lang.String"
name="vitro/appName"
value="${app-name}" override="true"/>
<!--
# The email address of the root user for the VIVO application. The password
# for this user is initially set to "rootPassword", but you will be asked to
# change the password the first time you log in.
-->
<Environment
type="java.lang.String"
name="vitro/rootUserAddress"
value="vivo_root@mydomain.edu" override="true"/>
<!--
# This namespace will be used when generating URIs for objects created in the
# editor. In order to serve linked data, the default namespace must be composed
# as follows (optional elements in parentheses):
#
# scheme + server_name (+ port) (+ servlet_context) + "/individual/"
#
# For example, Cornell's default namespace is:
#
# http://vivo.cornell.edu/individual/
-->
<Environment
type="java.lang.String"
name="vitro/defaultNamespace"
value="http://vivo.mydomain.edu/individual/" override="true"/>
<!-- Disable persist sessions on shut down.-->
<Manager pathname="" />
</Context>

2
installer/webapp/src/main/webResources/WEB-INF/classes/log4j.properties
View file

@ -24,7 +24,7 @@
# debug.log4j.properties exists will be used instead, if it exists, but is not stored in Subversion.
log4j.appender.AllAppender=org.apache.log4j.RollingFileAppender
log4j.appender.AllAppender.File= ${catalina.base}/logs/vivo.all.log
log4j.appender.AllAppender.File=${catalina.base}/logs/${app-name}.all.log
log4j.appender.AllAppender.MaxFileSize=10MB
log4j.appender.AllAppender.MaxBackupIndex=10
log4j.appender.AllAppender.layout=org.apache.log4j.PatternLayout

62
pom.xml
View file

@ -1,13 +1,11 @@
<project
xmlns="http://maven.apache.org/POM/4.0.0"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
<modelVersion>4.0.0</modelVersion>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-project</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<packaging>pom</packaging>
<name>VIVO</name>
@ -43,11 +41,9 @@
</developer>
</developers>
<!--
The SCM repository location is used by Continuum to update against
when changes have occurred. This spawns a new build cycle and releases
snapshots into the snapshot repository below.
-->
<!-- The SCM repository location is used by Continuum to update against
when changes have occurred. This spawns a new build cycle and releases snapshots
into the snapshot repository below. -->
<scm>
<connection>scm:git:git@github.com:vivo-project/VIVO.git</connection>
<developerConnection>scm:git:git@github.com:vivo-project/VIVO.git</developerConnection>
@ -56,7 +52,6 @@
</scm>
<properties>
<app-name>vivo</app-name>
<vitro-version>${project.version}</vitro-version>
<vivo-dir>${basedir}</vivo-dir>
<maven.build.timestamp.format>yyyy-MM-dd HH:mm:ss</maven.build.timestamp.format>
@ -73,7 +68,29 @@
</modules>
<profiles>
<profile>
<profile>
<id>Vitro-languages</id>
<activation>
<file>
<exists>../Vitro-languages/pom.xml</exists>
</file>
</activation>
<modules>
<module>../Vitro-languages</module>
</modules>
</profile>
<profile>
<id>VIVO-languages</id>
<activation>
<file>
<exists>../VIVO-languages/pom.xml</exists>
</file>
</activation>
<modules>
<module>../VIVO-languages</module>
</modules>
</profile>
<profile>
<id>vitro</id>
<activation>
<file>
@ -336,7 +353,8 @@
</configuration>
</plugin>
<!-- Used to validate all code style rules in source code using Checkstyle -->
<!-- Used to validate all code style rules in source code using
Checkstyle -->
<plugin>
<groupId>org.apache.maven.plugins</groupId>
<artifactId>maven-checkstyle-plugin</artifactId>
@ -344,7 +362,8 @@
<executions>
<execution>
<id>verify-style</id>
<!-- Bind to verify so it runs after package & unit tests, but before install -->
<!-- Bind to verify so it runs after package & unit
tests, but before install -->
<phase>verify</phase>
<goals>
<goal>check</goal>
@ -353,10 +372,10 @@
</executions>
<configuration>
<configLocation>
duraspace-checkstyle/checkstyle.xml
duraspace-checkstyle/checkstyle.xml
</configLocation>
<suppressionsLocation>
vitro-checkstyle/checkstyle-suppressions.xml
vitro-checkstyle/checkstyle-suppressions.xml
</suppressionsLocation>
<encoding>UTF-8</encoding>
<consoleOutput>true</consoleOutput>
@ -476,9 +495,11 @@
<report>test-javadoc</report>
</reports>
</reportSet>
<reportSet><!-- aggregate reportSet, to define in poms having modules -->
<reportSet><!-- aggregate reportSet, to define in poms
having modules -->
<id>aggregate</id>
<inherited>false</inherited><!-- don't run aggregate in child modules -->
<inherited>false</inherited><!-- don't run aggregate
in child modules -->
<reports>
<report>aggregate</report>
</reports>
@ -502,10 +523,9 @@
</plugins>
</reporting>
<!--
Add a custom repository, which is actually just a simple GitHub project
in order to distribute some dependencies that aren't part of Maven central
-->
<!-- Add a custom repository, which is actually just a simple GitHub
project in order to distribute some dependencies that aren't part of Maven
central -->
<repositories>
<repository>
<id>vivo-dependencies</id>

58
start.sh
View file

@ -9,43 +9,51 @@ fi
# allow easier reset home with `docker run -e RESET_HOME=true`
if [[ "$RESET_HOME" = "true" ]]; then
echo 'Clearing VIVO HOME /opt/vivo/home'
rm -rf /opt/vivo/home/*
echo 'Clearing VIVO HOME /usr/local/vivo/home'
rm -rf /usr/local/vivo/home/*
fi
# ensure home config directory exists
mkdir -p /opt/vivo/home/config
# generate digest.md5 for existing VIVO home if not already exist
if [ ! -f /opt/vivo/home/digest.md5 ]; then
find /opt/vivo/home -type f | grep -E '^/opt/vivo/home/bin/|^/opt/vivo/home/config/|^/opt/vivo/home/rdf/' | xargs md5sum > /opt/vivo/home/digest.md5
echo "Generated digest.md5 for VIVO home"
cat /opt/vivo/home/digest.md5
# copy home bin if not exists
if [ ! -d /usr/local/vivo/home/bin ]; then
echo "Copying home bin directory to /usr/local/vivo/home/bin"
cp -r /vivo-home/bin /usr/local/vivo/home/bin
fi
# only move runtime.properties first time and if it does not already exist in target home directory
if [ -f /runtime.properties ]; then
# template runtime.properties vitro.local.solr.url value to $SOLR_URL value
echo "Templating runtime.properties vitro.local.solr.url = $SOLR_URL"
sed -i "s,http://localhost:8983/solr/vivocore,$SOLR_URL,g" /runtime.properties
# copy home config if not exists
if [ ! -d /usr/local/vivo/home/config ]; then
echo "Copying home config directory to /usr/local/vivo/home/config"
cp -r /vivo-home/config /usr/local/vivo/home/config
fi
if [ ! -f /opt/vivo/home/config/runtime.properties ]
# copy home rdf if not exists
if [ ! -d /usr/local/vivo/home/rdf ]; then
echo "Copying home rdf directory to /usr/local/vivo/home/rdf"
cp -r /vivo-home/rdf /usr/local/vivo/home/rdf
fi
# copy runtime.properties if it does not already exist in target home directory
if [ -f /usr/local/vivo/home/config/example.runtime.properties ]; then
if [ ! -f /usr/local/vivo/home/config/runtime.properties ]
then
echo "First time: moving /runtime.properties to /opt/vivo/home/config/runtime.properties"
mv -n /runtime.properties /opt/vivo/home/config/runtime.properties
echo "Copying example.runtime.properties to /usr/local/vivo/home/config/runtime.properties"
cp /usr/local/vivo/home/config/example.runtime.properties /usr/local/vivo/home/config/runtime.properties
# template runtime.properties vitro.local.solr.url value to $SOLR_URL value
echo "Templating runtime.properties vitro.local.solr.url = $SOLR_URL"
sed -i "s,http://localhost:8983/solr/vivocore,$SOLR_URL,g" /usr/local/vivo/home/config/runtime.properties
else
echo "Using existing /opt/vivo/home/config/runtime.properties"
echo "Using existing /usr/local/vivo/home/config/runtime.properties"
fi
fi
# only move applicationSetup.n3 first time and if it does not already exist in target home directory
if [ -f /applicationSetup.n3 ]; then
if [ ! -f /opt/vivo/home/config/applicationSetup.n3 ]
# copy applicationSetup.n3 if it does not already exist in target home directory
if [ -f /usr/local/vivo/home/config/example.applicationSetup.n3 ]; then
if [ ! -f /usr/local/vivo/home/config/applicationSetup.n3 ]
then
echo "First time: moving /applicationSetup.n3 to /opt/vivo/home/config/applicationSetup.n3"
mv -n /applicationSetup.n3 /opt/vivo/home/config/applicationSetup.n3
echo "Copying example.applicationSetup.n3 to /usr/local/vivo/home/config/applicationSetup.n3"
cp /usr/local/vivo/home/config/example.applicationSetup.n3 /usr/local/vivo/home/config/applicationSetup.n3
else
echo "Using existing /opt/vivo/home/config/applicationSetup.n3"
echo "Using existing /usr/local/vivo/home/config/applicationSetup.n3"
fi
fi

6
webapp/pom.xml
View file

@ -7,13 +7,13 @@
<groupId>org.vivoweb</groupId>
<artifactId>vivo-webapp</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<packaging>war</packaging>
<parent>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-project</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
<relativePath>..</relativePath>
</parent>
@ -69,7 +69,7 @@
<dependency>
<groupId>org.vivoweb</groupId>
<artifactId>vivo-api</artifactId>
<version>1.11.2-SNAPSHOT</version>
<version>1.12.1-SNAPSHOT</version>
</dependency>
</dependencies>
</project>

4
webapp/src/main/webapp/js/visualization/entitycomparison/util.js
View file

@ -1069,7 +1069,7 @@ function prepareTableForDataTablePagination(jsonData, dataTableParams){
// console.log(processJSONData.currentEntityLevel);
if (processJSONData.currentEntityLevel.toUpperCase() === "ORGANIZATIONS AND PEOPLE") {
if (processJSONData.currentEntityLevel === i18nStringsGuiEvents.organizationsAndPeople) {
$.fn.dataTableExt.afnFiltering.push(DatatableCustomFilters.peopleOrOrganizations);
}
@ -1193,7 +1193,7 @@ function prepareTableForDataTablePagination(jsonData, dataTableParams){
*/
function reloadDataTablePagination(preselectedEntityURIs, jsonData){
if (processJSONData.currentEntityLevel.toUpperCase() === "ORGANIZATIONS AND PEOPLE") {
if (processJSONData.currentEntityLevel === i18nStringsGuiEvents.organizationsAndPeople) {
/*
* This will make sure that duplicate filters are not added.

2
webapp/src/main/webapp/templates/freemarker/body/individual/individual--foaf-person-2column.ftl
View file

@ -51,7 +51,7 @@
<#else>
<h1 itemprop="name" class="vcard foaf-person fn" <#if !editable>style="float:left;border-right:1px solid #A6B1B0;"</#if>>
<#-- Label -->
<@p.label individual editable labelCount localesCount/>
<@p.label individual editable labelCount localesCount languageCount />
</h1>
<#-- Display preferredTitle if it exists; otherwise mostSpecificTypes -->
<#assign title = propertyGroups.pullProperty("http://purl.obolibrary.org/obo/ARG_2000028","http://www.w3.org/2006/vcard/ns#Title")!>

2
webapp/src/main/webapp/templates/freemarker/body/individual/individual--foaf-person-quickview.ftl
View file

@ -62,7 +62,7 @@
<div id="photo-wrapper">${individualImage}</div>
<h1 itemprop="name" class="vcard foaf-person fn" <#if !editable>style="float:left;border-right:1px solid #A6B1B0;"</#if>>
<#-- Label -->
<@p.label individual editable labelCount localesCount/>
<@p.label individual editable labelCount localesCount languageCount />
</h1>
<#-- Display preferredTitle if it exists; otherwise mostSpecificTypes -->
<#assign title = propertyGroups.pullProperty("http://purl.obolibrary.org/obo/ARG_2000028","http://www.w3.org/2006/vcard/ns#Title")!>

6
webapp/src/main/webapp/templates/freemarker/visualization/entitycomparison/entityComparisonSetup.ftl
View file

@ -34,7 +34,7 @@
<#assign temporalGraphDownloadCSVCommonURL = '${urls.base}${dataVisualizationURLRoot}?uri=${organizationURI}&labelField=label'>
<#assign publicationParameter = { "name": "${i18n().publication?js_string}",
<#assign publicationParameter = { "name": "publication",
"pluralName": "${i18n().publications?js_string}",
"verbName": "${i18n().published?js_string}",
"dropDownText": "${i18n().by_publications?js_string}",
@ -44,7 +44,7 @@
"csvLink": "${temporalGraphDownloadCSVCommonURL}&vis=entity_comparison",
"value": "${i18n().publications?js_string}" }>
<#assign grantParameter = { "name": "${i18n().grant?js_string}",
<#assign grantParameter = { "name": "grant",
"pluralName": "${i18n().grants?js_string}",
"verbName": "${i18n().granted?js_string}",
"dropDownText": "${i18n().by_grants?js_string}",
@ -74,7 +74,7 @@ var activitiesLabel = {
plural: '${i18n().activities?js_string}'
};
var i18nStringsGuiEvents = {
temporalGraphCapped: '${i18n().temporal_graph_capitalized?js_string?js_string},
temporalGraphCapped: '${i18n().temporal_graph_capitalized?js_string?js_string}',
temporalGraphLower: '${i18n().temporal_graph?js_string?js_string}',
viewString: '${i18n().view?js_string}',
entityMaxNote: '${i18n().max_entity_note?js_string}',

2
webapp/src/main/webapp/themes/tenderfoot/templates/body/individual/individual--foaf-person.ftl
View file

@ -65,7 +65,7 @@
<section class="vcard person">
<h1 class="foaf-person">
<#-- Label -->
<span itemprop="name" class="fn"><@p.label individual editable labelCount localesCount/></span>
<span itemprop="name" class="fn"><@p.label individual editable labelCount localesCount languageCount /></span>
</h1>
<section id="preferredTitle">
<#-- Display preferredTitle if it exists; otherwise mostSpecificTypes -->

2
webapp/src/main/webapp/themes/tenderfoot/templates/page/page-home.ftl
View file

@ -15,7 +15,7 @@
<#import "lib-home-page.ftl" as lh>
<!DOCTYPE html>
<html lang="en">
<html lang="${country}">
<head>
<#include "head.ftl">
<#if geoFocusMapsEnabled >

2
webapp/src/main/webapp/themes/tenderfoot/templates/page/page.ftl
View file

@ -3,7 +3,7 @@
<#import "lib-list.ftl" as l>
<!DOCTYPE html>
<html lang="en">
<html lang="${country}">
<head>
<#include "head.ftl">
</head>

2
webapp/src/main/webapp/themes/wilma/templates/individual--foaf-person.ftl
View file

@ -89,7 +89,7 @@
<#else>
<h1 class="foaf-person">
<#-- Label -->
<span itemprop="name" class="fn"><@p.label individual editable labelCount localesCount/></span>
<span itemprop="name" class="fn"><@p.label individual editable labelCount localesCount languageCount /></span>
</h1>
<section id="preferredTitle">
<#-- Display preferredTitle if it exists; otherwise mostSpecificTypes -->

2
webapp/src/main/webapp/themes/wilma/templates/page-home.ftl
View file

@ -15,7 +15,7 @@
<#import "lib-home-page.ftl" as lh>
<!DOCTYPE html>
<html lang="en">
<html lang="${country}">
<head>
<#include "head.ftl">
<#if geoFocusMapsEnabled >

2
webapp/src/main/webapp/themes/wilma/templates/page.ftl
View file

@ -3,7 +3,7 @@
<#import "lib-list.ftl" as l>
<!DOCTYPE html>
<html lang="en">
<html lang="${country}">
<head>
<#include "head.ftl">
</head>