External vocabulary service and integration of Agrovoc with work beginning for applying concept semantic type to UMLS concepts.
This commit is contained in:
hudajkhan
parent
9fda9d2922
commit
2ea474b6ef
44 changed files with 1387 additions and 557 deletions
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lib/agrovocws-3.0.jar
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lib/agrovocws-3.0.jar
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lib/ehcache-spring-annotations-1.1.3.jar
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lib/owlapi-bin.jar
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lib/owlapi-bin.jar
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lib/skosapi-3-bin.jar
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lib/skosapi-3-bin.jar
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olddeploy.properties
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olddeploy.properties
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# -----------------------------------------------------------------------------
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#
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# VIVO deployment properties
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#
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# This file is provided as example.deploy.properties.
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#
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# Save a copy of this file as deploy.properties, and edit the properties as
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# needed for your deployment.
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#
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# -----------------------------------------------------------------------------
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#
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# This namespace will be used when generating URIs for objects created in the
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# editor. Change it to reflect your own domain. For example, Cornell's
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# namespace is http://vivo.cornell.edu/individual/
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#
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# Note: it is essential that this namespace end with a trailing slash.
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#
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Vitro.defaultNamespace = http://vivo.mannlib.cornell.edu/individual/
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#
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# Where is the Vitro core directory?
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# In most deployments, this is set to ./vitro-core (It is not uncommon for this
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# setting to point elsewhere in development environments).
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# Examples:
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# vitro.core.dir = ./vitro-core
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# vitro.core.dir = ../vitro
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# vitro.core.dir = /usr/local/vitro/trunk
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vitro.core.dir = ../vivovitro
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#
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# The base install directory for your Tomcat server. The VIVO application
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# will be deployed in the /webapps directory below this base.
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#
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tomcat.home = C:/apache/apache-tomcat-7.0.40
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#
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# The name of the VIVO application. This will be used as the name of the
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# subdirectory within your Tomcat server's /webapps directory. It also appears
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# in the URL for the application. For example, http://my.vivo.server/vivo
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#
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webapp.name = vivo
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#
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# The location where the VIVO application will store the data that it creates.
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# This includes uploaded files (usually images) and the Lucene search index.
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#
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vitro.home.directory = C:/Users/hjk54/vivodata
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#
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# SMTP host which the "Contact Us" form can use to send mail. If this is left
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# empty, the "Contact Us" form will be disabled.
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#
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Vitro.smtpHost =appsmtp.mail.cornell.edu
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#Added these per Jim's instructions, TO DO: try without smtpHost line
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email.smtpHost = appsmtp.mail.cornell.edu
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email.replyTo = hjk54@cornell.edu
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#
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# The basic parameters for a database connection. Change the end of the
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# URL to reflect your database name (if it is not "vitro"). Change the username
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# and password to match the authorized database user you created. Increase the
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# maximum size of the database connection pool if you need to serve a greater
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# number of concurrent page requests.
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#
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#Test Empty database
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#VitroConnection.DataSource.url = jdbc:mysql://localhost/testvivo
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VitroConnection.DataSource.url = jdbc:mysql://localhost/vivodb
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VitroConnection.DataSource.username = vivouser
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VitroConnection.DataSource.password = vivopass
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#test migration
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#VitroConnection.DataSource.url = jdbc:mysql://localhost/migratetest
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#VitroConnection.DataSource.username = migrateuser
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#VitroConnection.DataSource.password = migratepassword
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#
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# The Jena triple store technology to use. SDB is Jena's SPARQL database;
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# this setting allows RDF data to scale beyond the limits of the JVM heap.
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# Set to RDB to use the older Jena RDB store with in-memory caching.
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#
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VitroConnection.DataSource.tripleStoreType = SDB
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#
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# The maximum number of active connections in the database connection pool.
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# Increase this value to support a greater number of concurrent page requests
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# with SDB. It is not necessary to adjust this value when using the
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# RDB configuration.
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#
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VitroConnection.DataSource.pool.maxActive = 40
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#
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# The maximum number of database connections that will be allowed
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# to remain idle in the connection pool. Default is 25%
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# of the maximum number of active connections.
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#
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VitroConnection.DataSource.pool.maxIdle = 10
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#
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# Parameters to change in order to use VIVO with a database other than
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# MySQL.
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#
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VitroConnection.DataSource.dbtype = MySQL
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VitroConnection.DataSource.driver = com.mysql.jdbc.Driver
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VitroConnection.DataSource.validationQuery = SELECT 1
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#
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# The name of your first admin user for the VIVO application. The password
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# for this user is initially set to "defaultAdmin", but you will be asked to
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# change the password the first time you log in.
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#
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initialAdminUser = defaultAdmin
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rootUser.emailAddress = hjk54@cornell.edu
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#
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# How is a logged-in user associated with a particular Individual? One way is
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# for the Individual to have a property whose value is the username of the user.
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# This value should be the URI for that property.
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#
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selfEditing.idMatchingProperty = http://vivo.mannlib.cornell.edu/ns#networkId
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#
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# If an external authentication system like Shibboleth or CUWebAuth is to be
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# used, these properties say how the login button should be labeled, and which
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# HTTP header will contain the user ID from the authentication system. If such
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# a system is not to be used, leave these commented out. Consult the
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# installation instructions for more details.
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#
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#externalAuth.buttonText = Log in using BearCat Shibboleth
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#externalAuth.netIdHeaderName = remote_userID
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#
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# The temporal graph visualization can require extensive machine resources.
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# This can have a particularly noticable impact on memory usage if
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# - VIVO is configured to use Jena SDB,
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# - The organization tree is deep,
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# - The number of grants and publications is large.
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# VIVO release 1.2 guards against this impact by disabling the temporal graph
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# visualization unless the "visualization.temporal" flag is set to "enabled".
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#
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# visualization.temporal = enabled
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#
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# The temporal graph visualization is used to compare different organizations/people
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# within an organization on parameters like number of publications or grants.
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# By default, the app will attempt to make its best guess at the top level
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# organization in your instance. If you're unhappy with this selection, uncomment out
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# the property below and set it to the URI of the organization individual you want to
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# identify as the top level organization. It will be used as the default whenever the
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# temporal graph visualization is rendered without being passed an explicit org.
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# For example, to use "Ponce School of Medicine" as the top organization:
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# visualization.topLevelOrg = http://vivo.psm.edu/individual/n2862
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#
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# visualization.topLevelOrg = http://vivo.mydomain.edu/individual/topLevelOrgURI
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#
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# Default type(s) for Google Refine Reconciliation Service
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# The format for this property is id, name; id1, name1; id2, name2 etc.
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# See Service Metadata from this page http://code.google.com/p/google-refine/wiki/ReconciliationServiceApi
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# for more information.
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Vitro.reconcile.defaultTypeList = http://vivoweb.org/ontology/core#Course, Course; http://vivoweb.org/ontology/core#Grant, Grant; http://aims.fao.org/aos/geopolitical.owl, Location; http://xmlns.com/foaf/0.1/Organization, Organization; http://xmlns.com/foaf/0.1/Person, Person; http://purl.org/ontology/bibo/Article, Publication
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#solr
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vitro.local.solr.url = http://localhost:8080/vivosolr
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ontology/public/catalog-v001.xml
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ontology/public/catalog-v001.xml
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<?xml version="1.0" encoding="UTF-8" standalone="no"?>
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<catalog prefer="public" xmlns="urn:oasis:names:tc:entity:xmlns:xml:catalog">
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<uri id="User Entered Import Resolution" name="http://vivoweb.org/ontology/core/vivo-c4o-public-1.5.owl" uri="vivo-core-public-1.5.owl"/>
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<group id="Folder Repository, directory=, recursive=true, Auto-Update=true, version=2" prefer="public" xml:base=""/>
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</catalog>
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<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
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<#-- $This file is distributed under the terms of the license in /doc/license.txt$ -->
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<#-- List of positions for the individual -->
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<#-- List of positions for the individual --> <h3>Positions!${core}personInPosition</h3>
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<#assign positions = propertyGroups.pullProperty("${core}personInPosition")!>
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<#assign positions = propertyGroups.pullProperty("${core}personInPosition")!>
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<#if positions?has_content> <#-- true when the property is in the list, even if not populated (when editing) -->
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<#if positions?has_content> <#-- true when the property is in the list, even if not populated (when editing) -->
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<#assign localName = positions.localName>
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<#assign localName = positions.localName>
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<#-- List of research areas for the individual -->
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<#-- List of research areas for the individual -->
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<#assign researchAreas = propertyGroups.pullProperty("${core}hasResearchArea")!>
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<#assign researchAreas = propertyGroups.pullProperty("${core}hasResearchArea")!>
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<#assign concepts = propertyGroups.pullProperty("${core}hasAssociatedConcept")!>
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<#if concepts?has_content> concepts has content <#else> concepts dont have content</#if>
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<h2>RESEARCH AREAS: ${core}hasResearchArea</h2>
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<#if researchAreas?has_content> <#-- true when the property is in the list, even if not populated (when editing) -->
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<#if researchAreas?has_content> <#-- true when the property is in the list, even if not populated (when editing) -->
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<#assign localName = researchAreas.localName>
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<#assign localName = researchAreas.localName>
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<h2 id="${localName}" class="mainPropGroup">
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<h2 id="${localName}" class="mainPropGroup">
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</h2>
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</h2>
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<ul id="individual-${localName}" role="list" >
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<ul id="individual-${localName}" role="list" >
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<@p.objectProperty researchAreas editable />
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<@p.objectProperty researchAreas editable />
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</ul>
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</ul> <#else> Research areas does not have content
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</#if>
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</#if>
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<input type="hidden" id="conceptNode" name="conceptNode" value=""/> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="conceptNode" name="conceptNode" value=""/> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="conceptLabel" name="conceptLabel" value="" /> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="conceptLabel" name="conceptLabel" value="" /> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="conceptSource" name="conceptSource" value="" /> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="conceptSource" name="conceptSource" value="" /> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="conceptSemanticTypeURI" name="conceptSemanticTypeURI" value="" /> <!-- Field value populated by JavaScript -->
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<input type="hidden" id="conceptSemanticTypeLabel" name="conceptSemanticTypeLabel" value="" /> <!-- Field value populated by JavaScript -->
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<div id="selectedConcept" name="selectedConcept" class="acSelection">
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<div id="selectedConcept" name="selectedConcept" class="acSelection">
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<p class="inline">
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<p class="inline">
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</p>
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</p>
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@ -54,6 +54,7 @@ var addConceptForm = {
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this.externalConceptURI = $('#conceptNode');
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this.externalConceptURI = $('#conceptNode');
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this.externalConceptLabel = $('#conceptLabel');
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this.externalConceptLabel = $('#conceptLabel');
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this.externalConceptSource = $('#conceptSource');
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this.externalConceptSource = $('#conceptSource');
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this.externalConceptSemanticTypeLabel = $("#conceptSemanticTypeLabel");
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//remove links
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//remove links
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this.removeConceptLinks = $('a.remove');
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this.removeConceptLinks = $('a.remove');
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this.errors = $('#errors');
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this.errors = $('#errors');
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@ -236,23 +237,27 @@ var addConceptForm = {
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}
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}
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var i;
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var i;
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var len = checkedElements.length;
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var len = checkedElements.length;
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var checkedConcept, checkedConceptElement, conceptLabel, conceptSource;
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var checkedConcept, checkedConceptElement, conceptLabel, conceptSource, conceptSemanticType;
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var conceptNodes = [];
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var conceptNodes = [];
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var conceptLabels = [];
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var conceptLabels = [];
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var conceptSources = [];
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var conceptSources = [];
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var conceptSemanticTypes = [];
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checkedElements.each(function() {
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checkedElements.each(function() {
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checkedConceptElement = $(this);
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checkedConceptElement = $(this);
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checkedConcept = checkedConceptElement.val();
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checkedConcept = checkedConceptElement.val();
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conceptLabel = checkedConceptElement.attr("label");
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conceptLabel = checkedConceptElement.attr("label");
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conceptSource = checkedConceptElement.attr("conceptDefinedBy");
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conceptSource = checkedConceptElement.attr("conceptDefinedBy");
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conceptSemanticType = checkedConceptElement.attr("conceptType");
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conceptNodes.push(checkedConcept);
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conceptNodes.push(checkedConcept);
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conceptLabels.push(conceptLabel);
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conceptLabels.push(conceptLabel);
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conceptSources.push(conceptSource);
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conceptSources.push(conceptSource);
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conceptSemanticTypes.push(conceptSemanticType);
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});
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});
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this.externalConceptURI.val(conceptNodes);
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this.externalConceptURI.val(conceptNodes);
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this.externalConceptLabel.val(conceptLabels);
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this.externalConceptLabel.val(conceptLabels);
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this.externalConceptSource.val(conceptSources);
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this.externalConceptSource.val(conceptSources);
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this.externalConceptSemanticTypeLabel.val(conceptSemanticTypes);
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return true;
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return true;
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},
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},
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generateIndividualConceptDisplay: function(cuiURI, label, definition, type, definedBy, isBestMatch) {
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generateIndividualConceptDisplay: function(cuiURI, label, definition, type, definedBy, isBestMatch) {
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27
src/edu/cornell/mannlib/semservices/bo/BaseObject.java
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src/edu/cornell/mannlib/semservices/bo/BaseObject.java
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package edu.cornell.mannlib.semservices.bo;
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public class BaseObject {
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/**
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* Simple JavaBean domain object with an id property.
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* Used as a base class for objects needing this property.
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*
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* @author Ken Krebs
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* @author Juergen Hoeller
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*/
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private Integer id;
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public void setId(Integer id) {
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this.id = id;
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}
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public Integer getId() {
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return id;
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}
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public boolean isNew() {
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return (this.id == null);
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}
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}
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/* $This file is distributed under the terms of the license in /doc/license.txt$ */
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package edu.cornell.mannlib.semservices.bo;
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package edu.cornell.mannlib.semservices.bo;
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import java.util.ArrayList;
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import java.util.List;
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public class Concept {
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public class Concept {
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private String definedBy;
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private String definedBy;
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@ -11,13 +12,22 @@ public class Concept {
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private String type;
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private String type;
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private String definition;
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private String definition;
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private String uri;
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private String uri;
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private String schemeURI;
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private List<String> broaderURIList;
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private List<String> narrowerURIList;
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private List<String> exactMatchURIList;
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private List<String> closeMatchURIList;
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/**
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/**
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* default constructor
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* default constructor
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*/
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*/
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public Concept() {
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public Concept() {
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this.broaderURIList = new ArrayList<String>();
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this.narrowerURIList = new ArrayList<String>();
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this.exactMatchURIList = new ArrayList<String>();
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this.closeMatchURIList = new ArrayList<String>();
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}
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}
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/**
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/**
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* @return the conceptId
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* @return the conceptId
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*/
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*/
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@ -90,6 +100,18 @@ public class Concept {
|
||||||
public void setDefinedBy(String definedBy) {
|
public void setDefinedBy(String definedBy) {
|
||||||
this.definedBy = definedBy;
|
this.definedBy = definedBy;
|
||||||
}
|
}
|
||||||
|
/**
|
||||||
|
* @return the schemeURI
|
||||||
|
*/
|
||||||
|
public String getSchemeURI() {
|
||||||
|
return schemeURI;
|
||||||
|
}
|
||||||
|
/**
|
||||||
|
* @param schemeURI the schemeURI to set
|
||||||
|
*/
|
||||||
|
public void setSchemeURI(String schemeURI) {
|
||||||
|
this.schemeURI = schemeURI;
|
||||||
|
}
|
||||||
/**
|
/**
|
||||||
* @return the bestMatch
|
* @return the bestMatch
|
||||||
*/
|
*/
|
||||||
|
|
@ -102,5 +124,29 @@ public class Concept {
|
||||||
public void setBestMatch(String bestMatch) {
|
public void setBestMatch(String bestMatch) {
|
||||||
this.bestMatch = bestMatch;
|
this.bestMatch = bestMatch;
|
||||||
}
|
}
|
||||||
|
public List<String> getBroaderURIList() {
|
||||||
|
return broaderURIList;
|
||||||
|
}
|
||||||
|
public void setBroaderURIList(List<String> broaderURIList) {
|
||||||
|
this.broaderURIList = broaderURIList;
|
||||||
|
}
|
||||||
|
public List<String> getNarrowerURIList() {
|
||||||
|
return narrowerURIList;
|
||||||
|
}
|
||||||
|
public void setNarrowerURIList(List<String> narrowerURIList) {
|
||||||
|
this.narrowerURIList = narrowerURIList;
|
||||||
|
}
|
||||||
|
public List<String> getExactMatchURIList() {
|
||||||
|
return exactMatchURIList;
|
||||||
|
}
|
||||||
|
public void setExactMatchURIList(List<String> exactMatchURIList) {
|
||||||
|
this.exactMatchURIList = exactMatchURIList;
|
||||||
|
}
|
||||||
|
public List<String> getCloseMatchURIList() {
|
||||||
|
return closeMatchURIList;
|
||||||
|
}
|
||||||
|
public void setCloseMatchURIList(List<String> closeMatchURIList) {
|
||||||
|
this.closeMatchURIList = closeMatchURIList;
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.bo;
|
package edu.cornell.mannlib.semservices.bo;
|
||||||
|
|
||||||
|
|
||||||
|
|
@ -8,8 +6,7 @@ import java.util.List;
|
||||||
|
|
||||||
public class ConceptInfo extends SemanticServicesInfoBase {
|
public class ConceptInfo extends SemanticServicesInfoBase {
|
||||||
|
|
||||||
private List<Concept> conceptList;
|
private List<?> conceptList;
|
||||||
|
|
||||||
/**
|
/**
|
||||||
*
|
*
|
||||||
*/
|
*/
|
||||||
|
|
@ -18,17 +15,16 @@ public class ConceptInfo extends SemanticServicesInfoBase {
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @return the vivoDepartmentList
|
* @return the conceptList
|
||||||
*/
|
*/
|
||||||
public List<Concept> getConceptList() {
|
public List<?> getConceptList() {
|
||||||
return conceptList;
|
return conceptList;
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @param vivoDepartmentList the vivoDepartmentList to set
|
* @param conceptList the conceptList to set
|
||||||
*/
|
*/
|
||||||
public void setConceptList(List<Concept> inputConceptList) {
|
public void setConceptList(List<?> conceptList) {
|
||||||
this.conceptList = inputConceptList;
|
this.conceptList = conceptList;
|
||||||
}
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.bo;
|
package edu.cornell.mannlib.semservices.bo;
|
||||||
|
|
||||||
import java.util.Calendar;
|
import java.util.Calendar;
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.bo;
|
package edu.cornell.mannlib.semservices.bo;
|
||||||
|
|
||||||
public class SemanticServicesError {
|
public class SemanticServicesError {
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.bo;
|
package edu.cornell.mannlib.semservices.bo;
|
||||||
|
|
||||||
public class SemanticServicesInfoBase {
|
public class SemanticServicesInfoBase {
|
||||||
|
|
|
||||||
208
src/edu/cornell/mannlib/semservices/bo/SparqlFeed.java
Normal file
208
src/edu/cornell/mannlib/semservices/bo/SparqlFeed.java
Normal file
|
|
@ -0,0 +1,208 @@
|
||||||
|
package edu.cornell.mannlib.semservices.bo;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.Map;
|
||||||
|
|
||||||
|
public class SparqlFeed extends BaseObject implements Serializable {
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
private static final long serialVersionUID = 6024170338796859330L;
|
||||||
|
private String name;
|
||||||
|
private String endpoint;
|
||||||
|
private String repository;
|
||||||
|
private String query;
|
||||||
|
private int mapperId;
|
||||||
|
private int fetcherId;
|
||||||
|
private Map<String, String> parameterMap;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* Constructor
|
||||||
|
*/
|
||||||
|
public SparqlFeed() {
|
||||||
|
super();
|
||||||
|
parameterMap = new HashMap<String, String>();
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the name
|
||||||
|
*/
|
||||||
|
public String getName() {
|
||||||
|
return name;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param name the name to set
|
||||||
|
*/
|
||||||
|
public void setName(String name) {
|
||||||
|
this.name = name;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the endpoint
|
||||||
|
*/
|
||||||
|
public String getEndpoint() {
|
||||||
|
return endpoint;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param endpoint the endpoint to set
|
||||||
|
*/
|
||||||
|
public void setEndpoint(String endpoint) {
|
||||||
|
this.endpoint = endpoint;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the repository
|
||||||
|
*/
|
||||||
|
public String getRepository() {
|
||||||
|
return repository;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param repository the repository to set
|
||||||
|
*/
|
||||||
|
public void setRepository(String repository) {
|
||||||
|
this.repository = repository;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the query
|
||||||
|
*/
|
||||||
|
public String getQuery() {
|
||||||
|
return query;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param query the query to set
|
||||||
|
*/
|
||||||
|
public void setQuery(String query) {
|
||||||
|
this.query = query;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the mapperId
|
||||||
|
*/
|
||||||
|
public int getMapperId() {
|
||||||
|
return mapperId;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param mapperId the mapperId to set
|
||||||
|
*/
|
||||||
|
public void setMapperId(int mapperId) {
|
||||||
|
this.mapperId = mapperId;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the fetcherId
|
||||||
|
*/
|
||||||
|
public int getFetcherId() {
|
||||||
|
return fetcherId;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param fetcherId the fetcherId to set
|
||||||
|
*/
|
||||||
|
public void setFetcherId(int fetcherId) {
|
||||||
|
this.fetcherId = fetcherId;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the parameterMap
|
||||||
|
*/
|
||||||
|
public Map<String, String> getParameterMap() {
|
||||||
|
return parameterMap;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param parameterMap the parameterMap to set
|
||||||
|
*/
|
||||||
|
public void setParameterMap(Map<String, String> parameterMap) {
|
||||||
|
this.parameterMap = parameterMap;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* (non-Javadoc)
|
||||||
|
* @see java.lang.Object#hashCode()
|
||||||
|
*/
|
||||||
|
@Override
|
||||||
|
public int hashCode() {
|
||||||
|
final int prime = 31;
|
||||||
|
int result = 1;
|
||||||
|
result = prime * result + ((endpoint == null) ? 0 : endpoint.hashCode());
|
||||||
|
result = prime * result + fetcherId;
|
||||||
|
result = prime * result + mapperId;
|
||||||
|
result = prime * result + ((name == null) ? 0 : name.hashCode());
|
||||||
|
result = prime * result
|
||||||
|
+ ((parameterMap == null) ? 0 : parameterMap.hashCode());
|
||||||
|
result = prime * result + ((query == null) ? 0 : query.hashCode());
|
||||||
|
result = prime * result
|
||||||
|
+ ((repository == null) ? 0 : repository.hashCode());
|
||||||
|
return result;
|
||||||
|
}
|
||||||
|
|
||||||
|
/* (non-Javadoc)
|
||||||
|
* @see java.lang.Object#equals(java.lang.Object)
|
||||||
|
*/
|
||||||
|
@Override
|
||||||
|
public boolean equals(Object obj) {
|
||||||
|
if (this == obj) {
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
if (obj == null) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
if (getClass() != obj.getClass()) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
SparqlFeed other = (SparqlFeed) obj;
|
||||||
|
if (endpoint == null) {
|
||||||
|
if (other.endpoint != null) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
} else if (!endpoint.equals(other.endpoint)) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
if (fetcherId != other.fetcherId) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
if (mapperId != other.mapperId) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
if (name == null) {
|
||||||
|
if (other.name != null) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
} else if (!name.equals(other.name)) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
if (parameterMap == null) {
|
||||||
|
if (other.parameterMap != null) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
} else if (!parameterMap.equals(other.parameterMap)) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
if (query == null) {
|
||||||
|
if (other.query != null) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
} else if (!query.equals(other.query)) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
if (repository == null) {
|
||||||
|
if (other.repository != null) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
} else if (!repository.equals(other.repository)) {
|
||||||
|
return false;
|
||||||
|
}
|
||||||
|
return true;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
61
src/edu/cornell/mannlib/semservices/bo/SparqlFeedParam.java
Normal file
61
src/edu/cornell/mannlib/semservices/bo/SparqlFeedParam.java
Normal file
|
|
@ -0,0 +1,61 @@
|
||||||
|
package edu.cornell.mannlib.semservices.bo;
|
||||||
|
|
||||||
|
import java.io.Serializable;
|
||||||
|
|
||||||
|
public class SparqlFeedParam extends BaseObject implements Serializable {
|
||||||
|
|
||||||
|
/**
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
private static final long serialVersionUID = 4602167398212576479L;
|
||||||
|
private int sparqlFeedId;
|
||||||
|
private String param;
|
||||||
|
private String value;
|
||||||
|
|
||||||
|
public SparqlFeedParam() {
|
||||||
|
// default constructor
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the sparqlFeedId
|
||||||
|
*/
|
||||||
|
public int getSparqlFeedId() {
|
||||||
|
return sparqlFeedId;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param sparqlFeedId the sparqlFeedId to set
|
||||||
|
*/
|
||||||
|
public void setSparqlFeedId(int sparqlFeedId) {
|
||||||
|
this.sparqlFeedId = sparqlFeedId;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the param
|
||||||
|
*/
|
||||||
|
public String getParam() {
|
||||||
|
return param;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param param the param to set
|
||||||
|
*/
|
||||||
|
public void setParam(String param) {
|
||||||
|
this.param = param;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @return the value
|
||||||
|
*/
|
||||||
|
public String getValue() {
|
||||||
|
return value;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param value the value to set
|
||||||
|
*/
|
||||||
|
public void setValue(String value) {
|
||||||
|
this.value = value;
|
||||||
|
}
|
||||||
|
|
||||||
|
}
|
||||||
54
src/edu/cornell/mannlib/semservices/bo/SparqlPlugin.java
Normal file
54
src/edu/cornell/mannlib/semservices/bo/SparqlPlugin.java
Normal file
|
|
@ -0,0 +1,54 @@
|
||||||
|
package edu.cornell.mannlib.semservices.bo;
|
||||||
|
|
||||||
|
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.Map;
|
||||||
|
|
||||||
|
public class SparqlPlugin extends BaseObject {
|
||||||
|
private String type;
|
||||||
|
private String name;
|
||||||
|
private String classname;
|
||||||
|
|
||||||
|
/**
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
public SparqlPlugin() {
|
||||||
|
super();
|
||||||
|
}
|
||||||
|
/**
|
||||||
|
* @return the name
|
||||||
|
*/
|
||||||
|
public String getName() {
|
||||||
|
return name;
|
||||||
|
}
|
||||||
|
/**
|
||||||
|
* @param name the name to set
|
||||||
|
*/
|
||||||
|
public void setName(String name) {
|
||||||
|
this.name = name;
|
||||||
|
}
|
||||||
|
/**
|
||||||
|
* @return the type
|
||||||
|
*/
|
||||||
|
public String getType() {
|
||||||
|
return type;
|
||||||
|
}
|
||||||
|
/**
|
||||||
|
* @param type the type to set
|
||||||
|
*/
|
||||||
|
public void setType(String type) {
|
||||||
|
this.type = type;
|
||||||
|
}
|
||||||
|
/**
|
||||||
|
* @return the classname
|
||||||
|
*/
|
||||||
|
public String getClassname() {
|
||||||
|
return classname;
|
||||||
|
}
|
||||||
|
/**
|
||||||
|
* @param classname the classname to set
|
||||||
|
*/
|
||||||
|
public void setClassname(String classname) {
|
||||||
|
this.classname = classname;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.bo;
|
package edu.cornell.mannlib.semservices.bo;
|
||||||
|
|
||||||
import java.util.Date;
|
import java.util.Date;
|
||||||
|
|
|
||||||
|
|
@ -0,0 +1,13 @@
|
||||||
|
package edu.cornell.mannlib.semservices.exceptions;
|
||||||
|
|
||||||
|
public class ConceptsNotFoundException extends Exception {
|
||||||
|
/**
|
||||||
|
* An exception that indicates a service could not find a Concept
|
||||||
|
*/
|
||||||
|
private static final long serialVersionUID = -4729465393290022840L;
|
||||||
|
public ConceptsNotFoundException() { }
|
||||||
|
public ConceptsNotFoundException(String message) { super(message); }
|
||||||
|
public ConceptsNotFoundException(Throwable cause) { super(cause); }
|
||||||
|
public ConceptsNotFoundException(String message, Throwable cause) { super(message, cause); }
|
||||||
|
|
||||||
|
}
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.service;
|
package edu.cornell.mannlib.semservices.service;
|
||||||
|
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
@ -7,7 +5,24 @@ import java.util.List;
|
||||||
import edu.cornell.mannlib.semservices.bo.Concept;
|
import edu.cornell.mannlib.semservices.bo.Concept;
|
||||||
|
|
||||||
public interface ExternalConceptService {
|
public interface ExternalConceptService {
|
||||||
// this is the only method that needs to be exposed
|
|
||||||
List<Concept> processResults(String term) throws Exception;
|
/**
|
||||||
|
* @param term
|
||||||
|
* @return
|
||||||
|
*/
|
||||||
|
List<Concept> processResults(String term) throws Exception;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param term
|
||||||
|
* @return
|
||||||
|
* @throws Exception
|
||||||
|
*/
|
||||||
|
List<Concept> getConcepts(String term) throws Exception;
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param uri
|
||||||
|
* @return
|
||||||
|
*/
|
||||||
|
List<Concept> getConceptsByURIWithSparql(String uri) throws Exception;
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -8,18 +8,30 @@ import java.io.IOException;
|
||||||
import java.io.InputStreamReader;
|
import java.io.InputStreamReader;
|
||||||
import java.io.StringWriter;
|
import java.io.StringWriter;
|
||||||
import java.net.MalformedURLException;
|
import java.net.MalformedURLException;
|
||||||
|
import java.net.URI;
|
||||||
|
import java.net.URISyntaxException;
|
||||||
import java.net.URL;
|
import java.net.URL;
|
||||||
import java.rmi.RemoteException;
|
import java.rmi.RemoteException;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
|
import java.util.HashMap;
|
||||||
|
import java.util.Iterator;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
|
|
||||||
import javax.xml.parsers.ParserConfigurationException;
|
import javax.xml.parsers.ParserConfigurationException;
|
||||||
import javax.xml.rpc.ServiceException;
|
import javax.xml.rpc.ServiceException;
|
||||||
|
|
||||||
|
import org.apache.commons.lang.StringUtils;
|
||||||
import org.apache.commons.logging.Log;
|
import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
import org.fao.gilw.aims.webservices.AgrovocWS;
|
import org.fao.www.webservices.AgrovocWS.ACSWWebService;
|
||||||
import org.fao.gilw.aims.webservices.AgrovocWSServiceLocator;
|
import org.fao.www.webservices.AgrovocWS.ACSWWebServiceServiceLocator;
|
||||||
|
import org.semanticweb.skos.SKOSAnnotation;
|
||||||
|
import org.semanticweb.skos.SKOSConcept;
|
||||||
|
import org.semanticweb.skos.SKOSDataset;
|
||||||
|
import org.semanticweb.skos.SKOSEntity;
|
||||||
|
import org.semanticweb.skos.SKOSLiteral;
|
||||||
|
import org.semanticweb.skos.SKOSUntypedLiteral;
|
||||||
|
import org.semanticweb.skosapibinding.SKOSManager;
|
||||||
import org.w3c.dom.Attr;
|
import org.w3c.dom.Attr;
|
||||||
import org.w3c.dom.Document;
|
import org.w3c.dom.Document;
|
||||||
import org.w3c.dom.NamedNodeMap;
|
import org.w3c.dom.NamedNodeMap;
|
||||||
|
|
@ -27,95 +39,190 @@ import org.w3c.dom.Node;
|
||||||
import org.w3c.dom.NodeList;
|
import org.w3c.dom.NodeList;
|
||||||
import org.xml.sax.SAXException;
|
import org.xml.sax.SAXException;
|
||||||
|
|
||||||
|
import com.hp.hpl.jena.query.Query;
|
||||||
|
import com.hp.hpl.jena.query.QueryExecution;
|
||||||
|
import com.hp.hpl.jena.query.QueryExecutionFactory;
|
||||||
|
import com.hp.hpl.jena.query.QueryFactory;
|
||||||
|
import com.hp.hpl.jena.query.QuerySolution;
|
||||||
|
import com.hp.hpl.jena.query.ResultSet;
|
||||||
|
import com.hp.hpl.jena.rdf.model.Literal;
|
||||||
|
import com.hp.hpl.jena.rdf.model.RDFNode;
|
||||||
|
import com.hp.hpl.jena.rdf.model.Resource;
|
||||||
|
|
||||||
import edu.cornell.mannlib.semservices.bo.Concept;
|
import edu.cornell.mannlib.semservices.bo.Concept;
|
||||||
import edu.cornell.mannlib.semservices.service.ExternalConceptService;
|
import edu.cornell.mannlib.semservices.service.ExternalConceptService;
|
||||||
import edu.cornell.mannlib.semservices.util.XMLUtils;
|
import edu.cornell.mannlib.semservices.util.XMLUtils;
|
||||||
|
|
||||||
public class AgrovocService implements ExternalConceptService {
|
public class AgrovocService implements ExternalConceptService {
|
||||||
|
|
||||||
protected final Log logger = LogFactory.getLog(getClass());
|
protected final Log logger = LogFactory.getLog(getClass());
|
||||||
private java.lang.String AgrovocWS_address = "http://www.fao.org/webservices/AgrovocWS";
|
private java.lang.String AgrovocWS_address = "http://agrovoc.fao.org/axis/services/SKOSWS";
|
||||||
|
private final String schemeUri = "http://aims.fao.org/aos/agrovoc/agrovocScheme";
|
||||||
|
private final String baseUri = "http://aims.fao.org/aos/agrovoc/";
|
||||||
|
private final String ontologyName = "agrovoc";
|
||||||
|
private final String format = "SKOS";
|
||||||
|
private final String lang = "en";
|
||||||
|
private final String codeName = "hasCodeAgrovoc";
|
||||||
|
private final String searchMode = "Exact Match";
|
||||||
|
protected final String dbpedia_endpoint = " http://dbpedia.org/sparql";
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public List<Concept> getConcepts(String term) throws Exception {
|
||||||
|
List<Concept> conceptList = new ArrayList<Concept>();
|
||||||
|
//System.out.println("Searching for term: "+ term);
|
||||||
|
String result = getURIByTermAndLangXML(this.ontologyName, term, this.searchMode, this.format, this.lang);
|
||||||
|
// return empty conceptList if conceptUri is empty
|
||||||
|
if (StringUtils.isEmpty(result)) {
|
||||||
|
return conceptList;
|
||||||
|
}
|
||||||
|
|
||||||
|
// First create a new SKOSManager
|
||||||
|
String conceptUri = getConceptURIFromRDF(result);
|
||||||
|
SKOSManager manager = new SKOSManager();
|
||||||
|
|
||||||
|
// return empty conceptList if conceptUri is empty
|
||||||
|
if (StringUtils.isEmpty(conceptUri)) {
|
||||||
|
return conceptList;
|
||||||
|
}
|
||||||
|
URI uri = null;
|
||||||
|
try {
|
||||||
|
uri = new URI(conceptUri);
|
||||||
|
} catch (URISyntaxException e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
return conceptList;
|
||||||
|
}
|
||||||
|
|
||||||
|
System.out.println("uri: "+uri);
|
||||||
|
SKOSDataset dataset = manager.loadDataset(uri);
|
||||||
|
|
||||||
|
for (SKOSConcept skosConcept : dataset.getSKOSConcepts()) {
|
||||||
|
Concept concept = new Concept();
|
||||||
|
System.out.println("Concept: " + skosConcept.getURI());
|
||||||
|
concept.setUri(skosConcept.getURI().toString());
|
||||||
|
concept.setConceptId(stripConceptId(skosConcept.getURI().toString()));
|
||||||
|
concept.setBestMatch("true");
|
||||||
|
concept.setDefinedBy(this.schemeUri);
|
||||||
|
concept.setSchemeURI(this.schemeUri);
|
||||||
|
concept.setType("");
|
||||||
|
String lang = "";
|
||||||
|
|
||||||
|
for (SKOSLiteral literal : skosConcept.getSKOSRelatedConstantByProperty(dataset, manager.getSKOSDataFactory().getSKOSPrefLabelProperty())) {
|
||||||
|
|
||||||
|
if (!literal.isTyped()) {
|
||||||
|
// if it has language
|
||||||
|
SKOSUntypedLiteral untypedLiteral = literal.getAsSKOSUntypedLiteral();
|
||||||
|
if (untypedLiteral.hasLang()) {
|
||||||
|
lang = untypedLiteral.getLang();
|
||||||
|
} else {
|
||||||
|
lang = "";
|
||||||
|
}
|
||||||
|
}
|
||||||
|
if (lang.equals("en")) {
|
||||||
|
//System.out.println("prefLabel: " + literal.getLiteral());
|
||||||
|
|
||||||
|
concept.setLabel(literal.getLiteral());
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
// get the broader property URI
|
||||||
|
List<String> broaderURIList = new ArrayList<String>();
|
||||||
|
for (SKOSAnnotation annotation: skosConcept.getSKOSAnnotationsByURI(dataset, manager.getSKOSDataFactory().getSKOSBroaderProperty().getURI())) {
|
||||||
|
String value = new String();
|
||||||
|
if (annotation.isAnnotationByConstant()) {
|
||||||
|
SKOSLiteral literal = annotation.getAnnotationValueAsConstant();
|
||||||
|
value = literal.getLiteral();
|
||||||
|
//System.out.println("broder uri: "+ value);
|
||||||
|
} else {
|
||||||
|
// annotation is some resource
|
||||||
|
SKOSEntity entity = annotation.getAnnotationValue();
|
||||||
|
value = entity.getURI().toString();
|
||||||
|
}
|
||||||
|
//System.out.println("broader uri: "+value);
|
||||||
|
broaderURIList.add(value);
|
||||||
|
}
|
||||||
|
concept.setBroaderURIList(broaderURIList);
|
||||||
|
|
||||||
|
// get the narrower property URI
|
||||||
|
List<String> narrowerURIList = new ArrayList<String>();
|
||||||
|
for (SKOSAnnotation annotation: skosConcept.getSKOSAnnotationsByURI(dataset, manager.getSKOSDataFactory().getSKOSNarrowerProperty().getURI())) {
|
||||||
|
String value = new String();
|
||||||
|
if (annotation.isAnnotationByConstant()) {
|
||||||
|
SKOSLiteral literal = annotation.getAnnotationValueAsConstant();
|
||||||
|
value = literal.getLiteral();
|
||||||
|
//System.out.println("narrower uri: "+ value);
|
||||||
|
} else {
|
||||||
|
// annotation is some resource
|
||||||
|
SKOSEntity entity = annotation.getAnnotationValue();
|
||||||
|
value = entity.getURI().toString();
|
||||||
|
}
|
||||||
|
//System.out.println("narrower uri: "+value);
|
||||||
|
narrowerURIList.add(value);
|
||||||
|
}
|
||||||
|
concept.setNarrowerURIList(narrowerURIList);
|
||||||
|
|
||||||
|
// exact match
|
||||||
|
List<String> exactMatchURIList = new ArrayList<String>();
|
||||||
|
for (SKOSAnnotation annotation: skosConcept.getSKOSAnnotationsByURI(dataset, manager.getSKOSDataFactory().getSKOSExactMatchProperty().getURI())) {
|
||||||
|
String value = new String();
|
||||||
|
if (annotation.isAnnotationByConstant()) {
|
||||||
|
SKOSLiteral literal = annotation.getAnnotationValueAsConstant();
|
||||||
|
value = literal.getLiteral();
|
||||||
|
//System.out.println("exact match: "+ value);
|
||||||
|
} else {
|
||||||
|
// annotation is some resource
|
||||||
|
SKOSEntity entity = annotation.getAnnotationValue();
|
||||||
|
value = entity.getURI().toString();
|
||||||
|
}
|
||||||
|
//System.out.println("exact match: "+value);
|
||||||
|
exactMatchURIList.add(value);
|
||||||
|
}
|
||||||
|
concept.setExactMatchURIList(exactMatchURIList);
|
||||||
|
|
||||||
|
// close match
|
||||||
|
List<String> closeMatchURIList = new ArrayList<String>();
|
||||||
|
for (SKOSAnnotation annotation: skosConcept.getSKOSAnnotationsByURI(dataset, manager.getSKOSDataFactory().getSKOSCloseMatchProperty().getURI())) {
|
||||||
|
String value = new String();
|
||||||
|
if (annotation.isAnnotationByConstant()) {
|
||||||
|
SKOSLiteral literal = annotation.getAnnotationValueAsConstant();
|
||||||
|
value = literal.getLiteral();
|
||||||
|
//System.out.println("close match: "+ value);
|
||||||
|
} else {
|
||||||
|
// annotation is some resource
|
||||||
|
SKOSEntity entity = annotation.getAnnotationValue();
|
||||||
|
value = entity.getURI().toString();
|
||||||
|
}
|
||||||
|
//System.out.println("close match: "+value);
|
||||||
|
closeMatchURIList.add(value);
|
||||||
|
if (value.startsWith("http://dbpedia.org")) {
|
||||||
|
String description = getDbpediaDescription(value);
|
||||||
|
//System.out.println("description: "+ description);
|
||||||
|
concept.setDefinition(description);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
concept.setCloseMatchURIList(closeMatchURIList);
|
||||||
|
|
||||||
|
conceptList.add(concept);
|
||||||
|
|
||||||
|
|
||||||
|
}
|
||||||
|
return conceptList;
|
||||||
|
}
|
||||||
|
|
||||||
public List<Concept> processResults(String term) throws Exception {
|
public List<Concept> processResults(String term) throws Exception {
|
||||||
List<Concept> conceptList = new ArrayList<Concept>();
|
return getConcepts(term);
|
||||||
|
|
||||||
String termcode;
|
|
||||||
try {
|
|
||||||
termcode = getTermcodeByTerm(term);
|
|
||||||
} catch (Exception e1) {
|
|
||||||
logger.error("Could not get termcode from service", e1);
|
|
||||||
throw e1;
|
|
||||||
}
|
|
||||||
|
|
||||||
String format = "SKOS";
|
|
||||||
// if the termcode is null it means that either the service is not responding
|
|
||||||
// or there was not a match for the string
|
|
||||||
//System.out.println("Got termcode: "+termcode);
|
|
||||||
|
|
||||||
String results = getConceptInfoByTermcodeXML(termcode, format);
|
|
||||||
|
|
||||||
//XMLUtils.prettyPrint(results);
|
|
||||||
|
|
||||||
try {
|
|
||||||
Document doc = XMLUtils.parse(results);
|
|
||||||
String prefLabelQuery = "child::*[@xml:lang='EN']";
|
|
||||||
NodeList nodes = doc.getElementsByTagName("skos:Concept");
|
|
||||||
//System.out.println("Found this many nodes: "+ nodes.getLength());
|
|
||||||
for (int i=0; i < nodes.getLength(); i++) {
|
|
||||||
|
|
||||||
Node node = nodes.item(i);
|
|
||||||
//XMLUtils.serializeNode(node); System.out.println();
|
|
||||||
|
|
||||||
Concept concept = new Concept();
|
|
||||||
concept.setDefinedBy("http://aims.fao.org/aos/agrovoc/agrovocScheme");
|
|
||||||
concept.setConceptId(termcode);
|
|
||||||
|
|
||||||
NamedNodeMap attrs = node.getAttributes();
|
|
||||||
Attr idAttr = (Attr) attrs.getNamedItem("rdf:about");
|
|
||||||
String conceptUri = idAttr.getTextContent();
|
|
||||||
concept.setUri(conceptUri);
|
|
||||||
|
|
||||||
Node prefLabelNode = XMLUtils.getNodeWithXpath(node, prefLabelQuery);
|
|
||||||
if (prefLabelNode != null) {
|
|
||||||
String prefLabel = prefLabelNode.getTextContent();
|
|
||||||
concept.setLabel(prefLabel);
|
|
||||||
}
|
|
||||||
conceptList.add(concept);
|
|
||||||
}
|
|
||||||
} catch (IOException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (SAXException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (ParserConfigurationException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
return conceptList;
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
protected String getAgrovocLanguages() {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.getAgrovocLanguages();
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
|
@Deprecated
|
||||||
protected String getTermcodeByTerm(String term) throws Exception {
|
protected String getTermcodeByTerm(String term) throws Exception {
|
||||||
String result = new String();
|
String result = new String();
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
|
||||||
try {
|
try {
|
||||||
URL url = new URL(AgrovocWS_address);
|
URL url = new URL(AgrovocWS_address);
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
|
||||||
result = agrovoc_service.getTermcodeByTerm(term);
|
result = agrovoc_service.getTermcodeByTerm(term);
|
||||||
} catch (ServiceException e) {
|
} catch (ServiceException e) {
|
||||||
logger.error("service exception", e);
|
logger.error("service exception", e);
|
||||||
|
|
@ -130,275 +237,58 @@ public class AgrovocService implements ExternalConceptService {
|
||||||
return result;
|
return result;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected String getTermcodeByTermXML(String term, String format) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.getTermcodeByTermXML(term, format);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String getTermByLanguage(int termcode, String language) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.getTermByLanguage(termcode, language);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String getTermByLanguageXML(int termcode, String language, String format) {
|
protected String getTermCodeByTermAndLangXML(String ontologyName, String searchString, String lang, String codeName, String format) {
|
||||||
String result = new String();
|
String result = new String();
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
|
||||||
try {
|
try {
|
||||||
URL url = new URL(AgrovocWS_address);
|
URL url = new URL(AgrovocWS_address);
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
|
||||||
result = agrovoc_service.getTermByLanguageXML(termcode, language, format);
|
result = agrovoc_service.getTermCodeByTermAndLangXML(ontologyName, searchString, lang, codeName, format);
|
||||||
} catch (ServiceException e) {
|
} catch (ServiceException e) {
|
||||||
logger.error("service exception", e);
|
logger.error("service exception", e);
|
||||||
e.printStackTrace();
|
e.printStackTrace();
|
||||||
} catch (RemoteException e) {
|
} catch (RemoteException e) {
|
||||||
e.printStackTrace();
|
e.printStackTrace();
|
||||||
} catch (MalformedURLException e) {
|
} catch (MalformedURLException e) {
|
||||||
e.printStackTrace();
|
e.printStackTrace();
|
||||||
}
|
}
|
||||||
|
return result;
|
||||||
|
}
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String getTermsListByLanguage2(String termcodes, String language, String sep) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.getTermsListByLanguage2(termcodes, language, sep);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String getTermsListByLanguageXML(String termcodes, String language, String format) {
|
protected String getURIByTermAndLangXML(String ontologyName, String term,
|
||||||
String result = new String();
|
String searchMode, String format, String lang) {
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
String result = new String();
|
||||||
try {
|
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
|
||||||
URL url = new URL(AgrovocWS_address);
|
try {
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
URL url = new URL(AgrovocWS_address);
|
||||||
result = agrovoc_service.getTermsListByLanguageXML(termcodes, language, format);
|
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
|
||||||
} catch (ServiceException e) {
|
result = agrovoc_service.getURIByTermAndLangXML(ontologyName, term,
|
||||||
logger.error("service exception", e);
|
searchMode, format, lang);
|
||||||
e.printStackTrace();
|
} catch (ServiceException e) {
|
||||||
} catch (RemoteException e) {
|
e.printStackTrace();
|
||||||
e.printStackTrace();
|
} catch (RemoteException e) {
|
||||||
} catch (MalformedURLException e) {
|
e.printStackTrace();
|
||||||
e.printStackTrace();
|
} catch (MalformedURLException e) {
|
||||||
}
|
e.printStackTrace();
|
||||||
|
}
|
||||||
|
|
||||||
return result;
|
return result;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected String getAllLabelsByTermcode2(int termcode, String sep) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.getAllLabelsByTermcode2(termcode, sep);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String getAllLabelsByTermcodeXML(int termcode, String format) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.getAllLabelsByTermcodeXML(termcode, format);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String simpleSearchByMode2(String term, String mode, String sep ) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.simpleSearchByMode2(term, mode, sep);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String simpleSearchByModeXML(String term, String mode, String format) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.simpleSearchByModeXML(term, mode, format);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String searchByTerm2(String term, String sep) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.searchByTerm2(term, sep);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String searchByTermXML(String term, String format) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.searchByTermXML(term, format);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String searchCategoryByMode(String term, String lang, String schemeid, String mode, String sep) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.searchCategoryByMode(term, lang, schemeid, mode, sep);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String searchCategoryByModeXML(String term, String mode, String schemeid, String lang, String format) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.searchCategoryByModeXML(term, mode, schemeid, lang, format);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String[] getConceptInfoByTermcode(String termcode) {
|
|
||||||
String result[] = null;
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.getConceptInfoByTermcode(termcode);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String getConceptInfoByTermcodeXML(String termcode, String format) {
|
protected String getConceptInfoByTermcodeXML(String termcode, String format) {
|
||||||
String result = new String();
|
String result = new String();
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
|
||||||
try {
|
try {
|
||||||
URL url = new URL(AgrovocWS_address);
|
URL url = new URL(AgrovocWS_address);
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
|
||||||
result = agrovoc_service.getConceptInfoByTermcodeXML(termcode, format);
|
result = agrovoc_service.getConceptInfoByTermcodeXML(termcode, format);
|
||||||
} catch (ServiceException e) {
|
} catch (ServiceException e) {
|
||||||
logger.error("service exception", e);
|
logger.error("service exception", e);
|
||||||
|
|
@ -412,69 +302,33 @@ public class AgrovocService implements ExternalConceptService {
|
||||||
return result;
|
return result;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected String[] getDefinitions(int termcode, String lang) {
|
protected String getConceptByKeyword(String ontologyName, String searchString, String format, String searchMode, String lang) {
|
||||||
String[] result = null;
|
String result = new String();
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
ACSWWebServiceServiceLocator locator = new ACSWWebServiceServiceLocator();
|
||||||
try {
|
try {
|
||||||
URL url = new URL(AgrovocWS_address);
|
URL url = new URL(AgrovocWS_address);
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
ACSWWebService agrovoc_service = locator.getACSWWebService(url);
|
||||||
result = agrovoc_service.getDefinitions(termcode, lang);
|
result = agrovoc_service.getConceptByKeyword(ontologyName, searchString, format, searchMode, lang);
|
||||||
} catch (ServiceException e) {
|
} catch (ServiceException e) {
|
||||||
logger.error("service exception", e);
|
logger.error("service exception", e);
|
||||||
e.printStackTrace();
|
e.printStackTrace();
|
||||||
} catch (RemoteException e) {
|
} catch (RemoteException e) {
|
||||||
e.printStackTrace();
|
e.printStackTrace();
|
||||||
} catch (MalformedURLException e) {
|
} catch (MalformedURLException e) {
|
||||||
e.printStackTrace();
|
e.printStackTrace();
|
||||||
}
|
}
|
||||||
|
|
||||||
return result;
|
return result;
|
||||||
}
|
}
|
||||||
|
|
||||||
protected String getDefinitionsXML(int termcode, String lang, String format) {
|
|
||||||
String result = null;
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.getDefinitionsXML(termcode, lang, format);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String getTermExpansion(String aQuery, String langugage) {
|
|
||||||
String result = new String();
|
|
||||||
AgrovocWSServiceLocator locator = new AgrovocWSServiceLocator();
|
|
||||||
try {
|
|
||||||
URL url = new URL(AgrovocWS_address);
|
|
||||||
AgrovocWS agrovoc_service = locator.getAgrovocWS(url);
|
|
||||||
result = agrovoc_service.getTermExpansion(aQuery, langugage);
|
|
||||||
} catch (ServiceException e) {
|
|
||||||
logger.error("service exception", e);
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (RemoteException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
} catch (MalformedURLException e) {
|
|
||||||
e.printStackTrace();
|
|
||||||
}
|
|
||||||
|
|
||||||
return result;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String getWsdl() {
|
protected String getWsdl() {
|
||||||
String result = new String();
|
String result = new String();
|
||||||
try {
|
try {
|
||||||
|
|
||||||
StringWriter sw = new StringWriter();
|
StringWriter sw = new StringWriter();
|
||||||
URL rss = new URL(AgrovocWS_address + "?wsdl");
|
URL rss = new URL(this.AgrovocWS_address + "?wsdl");
|
||||||
|
|
||||||
BufferedReader in = new BufferedReader(new InputStreamReader(rss.openStream()));
|
BufferedReader in = new BufferedReader(new InputStreamReader(rss.openStream()));
|
||||||
String inputLine;
|
String inputLine;
|
||||||
|
|
@ -490,4 +344,139 @@ public class AgrovocService implements ExternalConceptService {
|
||||||
}
|
}
|
||||||
return result;
|
return result;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
public List<Concept> getConceptsByURIWithSparql(String uri) throws Exception {
|
||||||
|
//John Ferreira's original code has implementation
|
||||||
|
List<Concept> newConceptList = new ArrayList<Concept>();
|
||||||
|
return newConceptList;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected String getAgrovocTermCode(String rdf) throws Exception {
|
||||||
|
String termcode = new String();
|
||||||
|
try {
|
||||||
|
Document doc = XMLUtils.parse(rdf);
|
||||||
|
NodeList nodes = doc.getElementsByTagName("hasCodeAgrovoc");
|
||||||
|
if (nodes.item(0) != null) {
|
||||||
|
Node node = nodes.item(0);
|
||||||
|
termcode = node.getTextContent();
|
||||||
|
}
|
||||||
|
|
||||||
|
} catch (SAXException e) {
|
||||||
|
//e.printStackTrace();
|
||||||
|
throw e;
|
||||||
|
} catch (ParserConfigurationException e) {
|
||||||
|
//e.printStackTrace();
|
||||||
|
throw e;
|
||||||
|
} catch (IOException e) {
|
||||||
|
//e.printStackTrace();
|
||||||
|
throw e;
|
||||||
|
}
|
||||||
|
return termcode;
|
||||||
|
}
|
||||||
|
|
||||||
|
protected String getConceptURIFromRDF(String rdf) {
|
||||||
|
String conceptUri = new String();
|
||||||
|
try {
|
||||||
|
Document doc = XMLUtils.parse(rdf);
|
||||||
|
NodeList nodes = doc.getElementsByTagName("skos:Concept");
|
||||||
|
Node node = nodes.item(0);
|
||||||
|
|
||||||
|
NamedNodeMap attrs = node.getAttributes();
|
||||||
|
Attr idAttr = (Attr) attrs.getNamedItem("rdf:about");
|
||||||
|
conceptUri = idAttr.getTextContent();
|
||||||
|
} catch (IOException e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
System.err.println("rdf: "+rdf);
|
||||||
|
} catch (SAXException e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
System.err.println("rdf: "+rdf);
|
||||||
|
} catch (ParserConfigurationException e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
System.err.println("rdf: "+rdf);
|
||||||
|
}
|
||||||
|
return conceptUri;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
protected String getDbpediaDescription(String uri) throws Exception{
|
||||||
|
String description = new String();
|
||||||
|
String qs = ""
|
||||||
|
+ "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> \n"
|
||||||
|
+ "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> \n"
|
||||||
|
+ "PREFIX foaf: <http://xmlns.com/foaf/0.1/> \n"
|
||||||
|
+ "PREFIX dbpedia-owl: <http://dbpedia.org/ontology/>\n"
|
||||||
|
+ "SELECT DISTINCT ?description WHERE { \n" + "<" + uri
|
||||||
|
+ "> rdfs:comment ?description . \n"
|
||||||
|
+ "FILTER (LANG(?description)='en' ) \n" + "}";
|
||||||
|
//System.out.println(qs);
|
||||||
|
List<HashMap> resultList = new ArrayList<HashMap>();
|
||||||
|
QueryExecution qexec = null;
|
||||||
|
try {
|
||||||
|
|
||||||
|
Query query = QueryFactory.create(qs);
|
||||||
|
qexec = QueryExecutionFactory.sparqlService(this.dbpedia_endpoint,
|
||||||
|
query);
|
||||||
|
resultList = new ArrayList<HashMap>();
|
||||||
|
ResultSet resultSet = qexec.execSelect();
|
||||||
|
int resultSetSize = 0;
|
||||||
|
while (resultSet.hasNext()) {
|
||||||
|
resultSetSize++;
|
||||||
|
QuerySolution solution = resultSet.nextSolution();
|
||||||
|
Iterator varnames = solution.varNames();
|
||||||
|
HashMap<String, String> hm = new HashMap<String, String>();
|
||||||
|
while (varnames.hasNext()) {
|
||||||
|
String name = (String) varnames.next();
|
||||||
|
RDFNode rdfnode = solution.get(name);
|
||||||
|
// logger.info("rdf node name, type: "+ name
|
||||||
|
// +", "+getRDFNodeType(rdfnode));
|
||||||
|
if (rdfnode.isLiteral()) {
|
||||||
|
Literal literal = rdfnode.asLiteral();
|
||||||
|
String nodeval = literal.getString();
|
||||||
|
hm.put(name, nodeval);
|
||||||
|
} else if (rdfnode.isResource()) {
|
||||||
|
Resource resource = rdfnode.asResource();
|
||||||
|
String nodeval = resource.toString();
|
||||||
|
hm.put(name, nodeval);
|
||||||
|
}
|
||||||
|
}
|
||||||
|
resultList.add(hm);
|
||||||
|
}
|
||||||
|
description = "";
|
||||||
|
for (HashMap map : resultList) {
|
||||||
|
if (map.containsKey("description")) {
|
||||||
|
description = (String) map.get("description");
|
||||||
|
}
|
||||||
|
}
|
||||||
|
} catch (Exception ex) {
|
||||||
|
throw ex;
|
||||||
|
}
|
||||||
|
return description;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param uri
|
||||||
|
* @return
|
||||||
|
*/
|
||||||
|
protected String stripConceptId(String uri) {
|
||||||
|
String conceptId = new String();
|
||||||
|
int lastslash = uri.lastIndexOf('/');
|
||||||
|
conceptId = uri.substring(lastslash + 1, uri.length());
|
||||||
|
return conceptId;
|
||||||
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param str
|
||||||
|
* @return
|
||||||
|
*/
|
||||||
|
protected String extractConceptId(String str) {
|
||||||
|
try {
|
||||||
|
return str.substring(1, str.length() - 1);
|
||||||
|
} catch (Exception ex) {
|
||||||
|
return "";
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,41 +1,23 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.service.impl;
|
package edu.cornell.mannlib.semservices.service.impl;
|
||||||
|
|
||||||
|
|
||||||
import java.io.BufferedReader;
|
import java.io.BufferedReader;
|
||||||
import java.io.IOException;
|
|
||||||
import java.io.InputStreamReader;
|
import java.io.InputStreamReader;
|
||||||
import java.io.StringWriter;
|
import java.io.StringWriter;
|
||||||
import java.net.MalformedURLException;
|
|
||||||
import java.net.URL;
|
import java.net.URL;
|
||||||
import java.rmi.RemoteException;
|
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
|
|
||||||
import javax.xml.parsers.ParserConfigurationException;
|
|
||||||
import javax.xml.rpc.ServiceException;
|
|
||||||
|
|
||||||
import net.sf.json.JSONArray;
|
import net.sf.json.JSONArray;
|
||||||
import net.sf.json.JSONObject;
|
import net.sf.json.JSONObject;
|
||||||
import net.sf.json.JSONSerializer;
|
import net.sf.json.JSONSerializer;
|
||||||
|
|
||||||
import org.apache.commons.logging.Log;
|
import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
import org.fao.gilw.aims.webservices.AgrovocWS;
|
|
||||||
import org.fao.gilw.aims.webservices.AgrovocWSServiceLocator;
|
|
||||||
import org.w3c.dom.Attr;
|
|
||||||
import org.w3c.dom.Document;
|
|
||||||
import org.w3c.dom.NamedNodeMap;
|
|
||||||
import org.w3c.dom.Node;
|
|
||||||
import org.w3c.dom.NodeList;
|
|
||||||
import org.xml.sax.SAXException;
|
|
||||||
|
|
||||||
import edu.cornell.mannlib.semservices.bo.Concept;
|
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.semservices.service.ExternalConceptService;
|
||||||
import edu.cornell.mannlib.semservices.util.XMLUtils;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
|
|
||||||
|
|
||||||
public class GemetService implements ExternalConceptService {
|
public class GemetService implements ExternalConceptService {
|
||||||
protected final Log logger = LogFactory.getLog(getClass());
|
protected final Log logger = LogFactory.getLog(getClass());
|
||||||
|
|
@ -49,63 +31,112 @@ public class GemetService implements ExternalConceptService {
|
||||||
private final String altLabelUri = "http://www.w3.org/2004/02/skos/core%23altLabel";
|
private final String altLabelUri = "http://www.w3.org/2004/02/skos/core%23altLabel";
|
||||||
private final String exampleUri = "http://www.w3.org/2004/02/skos/core%23example";
|
private final String exampleUri = "http://www.w3.org/2004/02/skos/core%23example";
|
||||||
private final String acronymLabelUri = "http://www.w3.org/2004/02/skos/core%23acronymLabel";
|
private final String acronymLabelUri = "http://www.w3.org/2004/02/skos/core%23acronymLabel";
|
||||||
|
private final String endpoint = "http://cr.eionet.europa.eu/sparql";
|
||||||
|
private final String schemeURI = "http://www.eionet.europa.eu/gemet/gemetThesaurus";
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
@Override
|
||||||
|
public List<Concept> getConcepts(String term) throws Exception {
|
||||||
|
List<Concept> conceptList = new ArrayList<Concept>();
|
||||||
|
try {
|
||||||
|
String results = getConceptsMatchingKeyword(term);
|
||||||
|
//System.out.println(results);
|
||||||
|
conceptList = processOutput(results);
|
||||||
|
|
||||||
|
} catch (Exception ex) {
|
||||||
|
return new ArrayList<Concept>();
|
||||||
|
//ex.printStackTrace();
|
||||||
|
//throw ex;
|
||||||
|
}
|
||||||
|
return conceptList;
|
||||||
|
}
|
||||||
|
|
||||||
public List<Concept> processResults(String term) throws Exception {
|
public List<Concept> processResults(String term) throws Exception {
|
||||||
List<Concept> conceptList = processConceptsAndRelatedMatchingKeyword(term);
|
List<Concept> conceptList = new ArrayList<Concept>();
|
||||||
|
try {
|
||||||
|
String results = getConceptsMatchingKeyword(term);
|
||||||
|
conceptList = processOutput(results);
|
||||||
|
} catch (Exception ex) {
|
||||||
|
//ex.printStackTrace();
|
||||||
|
throw ex;
|
||||||
|
}
|
||||||
return conceptList;
|
return conceptList;
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public List<Concept> getConceptsByURIWithSparql(String uri) throws Exception {
|
||||||
|
//John Ferreira's original code has implementation
|
||||||
|
List<Concept> newConceptList = new ArrayList<Concept>();
|
||||||
|
return newConceptList;
|
||||||
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @param results
|
* @param results
|
||||||
* @return
|
* @return
|
||||||
* By default, concepts set with best match = true
|
|
||||||
*/
|
*/
|
||||||
private List<Concept> processOutput(String results) {
|
private List<Concept> processOutput(String results) throws Exception {
|
||||||
return processOutput(results, "true");
|
|
||||||
|
|
||||||
}
|
List<Concept> conceptList = new ArrayList<Concept>();
|
||||||
|
|
||||||
private List<Concept> processOutput(String results, String bestMatch) {
|
|
||||||
List<Concept> conceptList = new ArrayList<Concept>();
|
|
||||||
try {
|
try {
|
||||||
JSONArray jsonArray = (JSONArray) JSONSerializer.toJSON( results );
|
JSONArray jsonArray = (JSONArray) JSONSerializer.toJSON( results );
|
||||||
|
if (jsonArray.size() == 0) {
|
||||||
|
throw new ConceptsNotFoundException();
|
||||||
|
}
|
||||||
|
|
||||||
for (int i = 0; i < jsonArray.size(); i++) {
|
for (int i = 0; i < jsonArray.size(); i++) {
|
||||||
Concept concept = new Concept();
|
Concept concept = new Concept();
|
||||||
concept
|
concept.setDefinedBy(this.schemeURI);
|
||||||
.setDefinedBy("http://www.eionet.europa.eu/gemet/gemetThesaurus");
|
concept.setBestMatch("true");
|
||||||
concept.setBestMatch(bestMatch);
|
JSONObject json = jsonArray.getJSONObject(i);
|
||||||
JSONObject json = jsonArray.getJSONObject(i);
|
String uri = getJsonValue(json, "uri");
|
||||||
String uri = getJsonValue(json, "uri");
|
|
||||||
|
|
||||||
concept.setUri(uri);
|
concept.setUri(uri);
|
||||||
concept.setConceptId(uri);
|
concept.setConceptId(stripConceptId(uri));
|
||||||
if (json.has("preferredLabel")) {
|
concept.setSchemeURI(schemeURI);
|
||||||
JSONObject preferredLabelObj = json
|
if (json.has("preferredLabel")) {
|
||||||
.getJSONObject("preferredLabel");
|
JSONObject preferredLabelObj = json
|
||||||
if (preferredLabelObj.has("string")) {
|
.getJSONObject("preferredLabel");
|
||||||
concept.setLabel(getJsonValue(preferredLabelObj,
|
if (preferredLabelObj.has("string")) {
|
||||||
"string"));
|
concept.setLabel(getJsonValue(preferredLabelObj,
|
||||||
}
|
"string"));
|
||||||
}
|
}
|
||||||
if (json.has("definition")) {
|
}
|
||||||
JSONObject definitionObj = json.getJSONObject("definition");
|
if (json.has("definition")) {
|
||||||
if (definitionObj.has("string")) {
|
JSONObject definitionObj = json.getJSONObject("definition");
|
||||||
concept.setDefinition(getJsonValue(definitionObj,
|
if (definitionObj.has("string")) {
|
||||||
"string"));
|
concept.setDefinition(getJsonValue(definitionObj,
|
||||||
}
|
"string"));
|
||||||
}
|
}
|
||||||
conceptList.add(concept);
|
}
|
||||||
|
|
||||||
}
|
String narrower = getRelatedConcepts(uri, "narrower");
|
||||||
|
List<String> narrowerURIList = getRelatedUris(narrower);
|
||||||
|
concept.setNarrowerURIList(narrowerURIList);
|
||||||
|
|
||||||
|
String broader = getRelatedConcepts(uri, "broader");
|
||||||
|
List<String> broaderURIList = getRelatedUris(broader);
|
||||||
|
concept.setBroaderURIList(broaderURIList);
|
||||||
|
|
||||||
|
/*String related = getRelatedConcepts(uri, "related");
|
||||||
|
List<String> relatedURIList = getRelatedUris(related);
|
||||||
|
for (String s: relatedURIList) {
|
||||||
|
System.out.println("related uri: "+s);
|
||||||
|
}*/
|
||||||
|
|
||||||
|
|
||||||
|
conceptList.add(concept);
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
} catch (Exception ex ) {
|
} catch (Exception ex ) {
|
||||||
ex.printStackTrace();
|
//ex.printStackTrace();
|
||||||
logger.error("Could not get concepts", ex);
|
logger.error("Could not get concepts", ex);
|
||||||
|
throw ex;
|
||||||
}
|
}
|
||||||
return conceptList;
|
return conceptList;
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
|
|
@ -123,23 +154,50 @@ public class GemetService implements ExternalConceptService {
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param concept_uri
|
||||||
|
* @return
|
||||||
|
* @throws Exception
|
||||||
|
*/
|
||||||
protected String getAvailableLangs(String concept_uri) throws Exception {
|
protected String getAvailableLangs(String concept_uri) throws Exception {
|
||||||
String result = new String();
|
String result = new String();
|
||||||
String serviceUrl = GemetWS_address + "getAvailableLanguages" +
|
String serviceUrl = GemetWS_address + "getAvailableLanguages" +
|
||||||
"?concept_uri=" + concept_uri;
|
"?concept_uri=" + concept_uri;
|
||||||
result = getGemetResults(serviceUrl);
|
try {
|
||||||
|
result = getGemetResults(serviceUrl);
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
throw e;
|
||||||
|
}
|
||||||
return result;
|
return result;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param concept_uri
|
||||||
|
* @return
|
||||||
|
* @throws Exception
|
||||||
|
*/
|
||||||
protected String getConcept(String concept_uri) throws Exception {
|
protected String getConcept(String concept_uri) throws Exception {
|
||||||
String result = new String();
|
String result = new String();
|
||||||
String serviceUrl = GemetWS_address + "getConcept" +
|
String serviceUrl = GemetWS_address + "getConcept" +
|
||||||
"?concept_uri=" + concept_uri +
|
"?concept_uri=" + concept_uri +
|
||||||
"&language=en";
|
"&language=en";
|
||||||
result = getGemetResults(serviceUrl);
|
try {
|
||||||
|
result = getGemetResults(serviceUrl);
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
throw e;
|
||||||
|
}
|
||||||
return result;
|
return result;
|
||||||
}
|
}
|
||||||
protected String getAllTranslationsForConcept(String concept_uri, String property) throws Exception {
|
|
||||||
|
/**
|
||||||
|
* @param concept_uri
|
||||||
|
* @param property
|
||||||
|
* @return
|
||||||
|
* @throws Exception
|
||||||
|
*/
|
||||||
|
protected String getAllTranslationsForConcept(String concept_uri, String property) throws Exception {
|
||||||
String result = new String();
|
String result = new String();
|
||||||
String property_uri = new String();
|
String property_uri = new String();
|
||||||
if (property.equals("definition")) {
|
if (property.equals("definition")) {
|
||||||
|
|
@ -160,11 +218,23 @@ public class GemetService implements ExternalConceptService {
|
||||||
"?concept_uri=" + concept_uri +
|
"?concept_uri=" + concept_uri +
|
||||||
"&property_uri=" + property_uri +
|
"&property_uri=" + property_uri +
|
||||||
"&language=en";
|
"&language=en";
|
||||||
result = getGemetResults(serviceUrl);
|
|
||||||
|
try {
|
||||||
|
result = getGemetResults(serviceUrl);
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
throw e;
|
||||||
|
}
|
||||||
return result;
|
return result;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param concept_uri
|
||||||
|
* @param relation
|
||||||
|
* @return
|
||||||
|
* @throws Exception
|
||||||
|
*/
|
||||||
protected String getRelatedConcepts(String concept_uri, String relation) throws Exception {
|
protected String getRelatedConcepts(String concept_uri, String relation) throws Exception {
|
||||||
String result = new String();
|
String result = new String();
|
||||||
String relation_uri = new String();
|
String relation_uri = new String();
|
||||||
|
|
@ -179,41 +249,43 @@ public class GemetService implements ExternalConceptService {
|
||||||
"?concept_uri=" + concept_uri +
|
"?concept_uri=" + concept_uri +
|
||||||
"&relation_uri=" + relation_uri +
|
"&relation_uri=" + relation_uri +
|
||||||
"&language=en";
|
"&language=en";
|
||||||
result = getGemetResults(serviceUrl);
|
try {
|
||||||
|
result = getGemetResults(serviceUrl);
|
||||||
|
} catch (Exception e) {
|
||||||
|
e.printStackTrace();
|
||||||
|
throw e;
|
||||||
|
}
|
||||||
return result;
|
return result;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param keyword
|
||||||
|
* @return
|
||||||
|
* @throws Exception
|
||||||
|
*/
|
||||||
protected String getConceptsMatchingKeyword(String keyword) throws Exception {
|
protected String getConceptsMatchingKeyword(String keyword) throws Exception {
|
||||||
String result = new String();
|
String result = new String();
|
||||||
String serviceUrl = GemetWS_address + "getConceptsMatchingKeyword" +
|
String serviceUrl = GemetWS_address + "getConceptsMatchingKeyword" +
|
||||||
"?keyword=" + URLEncoder.encode(keyword) +
|
"?keyword=" + keyword +
|
||||||
"&search_mode=0" +
|
"&search_mode=0" +
|
||||||
"&thesaurus_uri=http://www.eionet.europa.eu/gemet/concept/" +
|
"&thesaurus_uri=http://www.eionet.europa.eu/gemet/concept/" +
|
||||||
"&language=en";
|
"&language=en";
|
||||||
|
try {
|
||||||
result = getGemetResults(serviceUrl);
|
result = getGemetResults(serviceUrl);
|
||||||
|
} catch (Exception ex) {
|
||||||
|
throw ex;
|
||||||
|
}
|
||||||
return result;
|
return result;
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
//Get concepts matching keyword plus any related concepts
|
/**
|
||||||
protected List<Concept> processConceptsAndRelatedMatchingKeyword(String keyword) throws Exception {
|
* @param url
|
||||||
String result = getConceptsMatchingKeyword(keyword);
|
* @return
|
||||||
//iterate through each of the concepts and add related concepts a well
|
*/
|
||||||
List<Concept> bestMatchConceptList = processOutput(result);
|
protected String getGemetResults(String url) throws Exception {
|
||||||
List<Concept> relatedConceptList = new ArrayList<Concept>();
|
|
||||||
for(Concept c: bestMatchConceptList) {
|
|
||||||
String conceptUri = c.getUri();
|
|
||||||
String resultsRelated = getRelatedConcepts(conceptUri, "related");
|
|
||||||
relatedConceptList.addAll(processOutput(resultsRelated, "false"));
|
|
||||||
}
|
|
||||||
bestMatchConceptList.addAll(relatedConceptList);
|
|
||||||
return bestMatchConceptList;
|
|
||||||
}
|
|
||||||
|
|
||||||
protected String getGemetResults(String url) throws Exception {
|
|
||||||
String results = new String();
|
String results = new String();
|
||||||
//System.out.println("url: "+url);
|
//System.out.println("url: "+url);
|
||||||
try {
|
try {
|
||||||
|
|
@ -232,9 +304,36 @@ public class GemetService implements ExternalConceptService {
|
||||||
|
|
||||||
} catch (Exception ex) {
|
} catch (Exception ex) {
|
||||||
logger.error("error occurred in servlet", ex);
|
logger.error("error occurred in servlet", ex);
|
||||||
|
ex.printStackTrace();
|
||||||
throw ex;
|
throw ex;
|
||||||
}
|
}
|
||||||
return results;
|
return results;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
protected List<String> getRelatedUris(String json) {
|
||||||
|
List<String> uriList = new ArrayList<String>();
|
||||||
|
String uri = new String();
|
||||||
|
JSONArray jsonArray = (JSONArray) JSONSerializer.toJSON( json );
|
||||||
|
if (jsonArray.size() == 0) {
|
||||||
|
return new ArrayList<String>();
|
||||||
|
}
|
||||||
|
for (int i = 0; i < jsonArray.size(); i++) {
|
||||||
|
JSONObject jsonObj = jsonArray.getJSONObject(i);
|
||||||
|
uri = getJsonValue(jsonObj, "uri");
|
||||||
|
uriList.add(uri);
|
||||||
|
}
|
||||||
|
|
||||||
|
return uriList;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
|
protected String stripConceptId(String uri) {
|
||||||
|
String conceptId = new String();
|
||||||
|
int lastslash = uri.lastIndexOf('/');
|
||||||
|
conceptId = uri.substring(lastslash + 1, uri.length());
|
||||||
|
return conceptId;
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,11 +1,10 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.service.impl;
|
package edu.cornell.mannlib.semservices.service.impl;
|
||||||
|
|
||||||
import java.io.BufferedReader;
|
import java.io.BufferedReader;
|
||||||
import java.io.InputStreamReader;
|
import java.io.InputStreamReader;
|
||||||
import java.io.StringWriter;
|
import java.io.StringWriter;
|
||||||
import java.net.URL;
|
import java.net.URL;
|
||||||
|
import java.net.URLEncoder;
|
||||||
import java.util.ArrayList;
|
import java.util.ArrayList;
|
||||||
import java.util.List;
|
import java.util.List;
|
||||||
|
|
||||||
|
|
@ -17,8 +16,8 @@ import org.apache.commons.logging.Log;
|
||||||
import org.apache.commons.logging.LogFactory;
|
import org.apache.commons.logging.LogFactory;
|
||||||
|
|
||||||
import edu.cornell.mannlib.semservices.bo.Concept;
|
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.semservices.service.ExternalConceptService;
|
||||||
import edu.cornell.mannlib.vitro.webapp.web.URLEncoder;
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @author jaf30
|
* @author jaf30
|
||||||
|
|
@ -28,11 +27,48 @@ public class UMLSService implements ExternalConceptService {
|
||||||
protected final Log logger = LogFactory.getLog(getClass());
|
protected final Log logger = LogFactory.getLog(getClass());
|
||||||
private static final String submissionUrl = "http://link.informatics.stonybrook.edu/MeaningLookup/MlServiceServlet?";
|
private static final String submissionUrl = "http://link.informatics.stonybrook.edu/MeaningLookup/MlServiceServlet?";
|
||||||
private static final String baseUri = "http://link.informatics.stonybrook.edu/umls/CUI/";
|
private static final String baseUri = "http://link.informatics.stonybrook.edu/umls/CUI/";
|
||||||
|
private static final String endpoint = "http://link.informatics.stonybrook.edu/sparql/";
|
||||||
|
private static final String schemeURI = "http://link.informatics.stonybrook.edu/umls";
|
||||||
|
|
||||||
public List<Concept> processResults(String term) throws Exception{
|
|
||||||
|
@Override
|
||||||
|
public List<Concept> getConcepts(String term) throws Exception {
|
||||||
|
List<Concept> conceptList = new ArrayList<Concept>();
|
||||||
|
|
||||||
|
String results = null;
|
||||||
|
//Format in rdf/xml is possible but would require separate processing method
|
||||||
|
String dataUrl = submissionUrl + "textToProcess="
|
||||||
|
+ URLEncoder.encode(term, "UTF-8")
|
||||||
|
+ "&format=json";
|
||||||
|
|
||||||
|
try {
|
||||||
|
|
||||||
|
StringWriter sw = new StringWriter();
|
||||||
|
URL rss = new URL(dataUrl);
|
||||||
|
|
||||||
|
BufferedReader in = new BufferedReader(new InputStreamReader(
|
||||||
|
rss.openStream()));
|
||||||
|
String inputLine;
|
||||||
|
while ((inputLine = in.readLine()) != null) {
|
||||||
|
sw.write(inputLine);
|
||||||
|
}
|
||||||
|
in.close();
|
||||||
|
|
||||||
|
results = sw.toString();
|
||||||
|
//System.out.println("results before processing: "+results);
|
||||||
|
conceptList = processOutput(results);
|
||||||
|
return conceptList;
|
||||||
|
|
||||||
|
} catch (Exception ex) {
|
||||||
|
logger.error("error occurred in servlet", ex);
|
||||||
|
return null;
|
||||||
|
}
|
||||||
|
}
|
||||||
|
|
||||||
|
public List<Concept> processResults(String term) throws Exception {
|
||||||
String results = null;
|
String results = null;
|
||||||
String dataUrl = submissionUrl + "textToProcess="
|
String dataUrl = submissionUrl + "textToProcess="
|
||||||
+ URLEncoder.encode(term) + "&format=json";
|
+ URLEncoder.encode(term, "UTF-8") + "&format=json";
|
||||||
|
|
||||||
try {
|
try {
|
||||||
|
|
||||||
|
|
@ -47,41 +83,57 @@ public class UMLSService implements ExternalConceptService {
|
||||||
in.close();
|
in.close();
|
||||||
|
|
||||||
results = sw.toString();
|
results = sw.toString();
|
||||||
|
//System.out.println("results before processing: "+results);
|
||||||
|
List<Concept> conceptList = processOutput(results);
|
||||||
|
return conceptList;
|
||||||
|
|
||||||
} catch (Exception ex) {
|
} catch (Exception ex) {
|
||||||
logger.error("error occurred in servlet", ex);
|
logger.error("error occurred in servlet", ex);
|
||||||
throw ex;
|
return null;
|
||||||
}
|
}
|
||||||
List<Concept> conceptList = processOutput(results);
|
|
||||||
return conceptList;
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param uri
|
||||||
|
* @return
|
||||||
|
*/
|
||||||
|
public List<Concept> getConceptsByURIWithSparql(String uri) throws Exception {
|
||||||
|
//John Ferreira's original code has implementation
|
||||||
|
List<Concept> newConceptList = new ArrayList<Concept>();
|
||||||
|
return newConceptList;
|
||||||
}
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @param results
|
* @param results
|
||||||
* @return
|
* @return
|
||||||
*/
|
*/
|
||||||
private List<Concept> processOutput(String results) {
|
private List<Concept> processOutput(String results) throws Exception {
|
||||||
|
|
||||||
List<Concept> conceptList = new ArrayList<Concept>();
|
List<Concept> conceptList = new ArrayList<Concept>();
|
||||||
List<String> bestMatchIdList = new ArrayList<String>();
|
List<String> bestMatchIdList = new ArrayList<String>();
|
||||||
String bestMatchId = new String();
|
String bestMatchId = new String();
|
||||||
|
boolean bestMatchFound = false;
|
||||||
|
boolean allFound = false;
|
||||||
|
|
||||||
try {
|
try {
|
||||||
JSONObject json = (JSONObject) JSONSerializer.toJSON( results );
|
JSONObject json = (JSONObject) JSONSerializer.toJSON( results );
|
||||||
|
//System.out.println(json.toString());
|
||||||
if (json.has("Best Match")) {
|
if (json.has("Best Match")) {
|
||||||
|
bestMatchFound = true;
|
||||||
//System.out.println("Best Match");
|
//System.out.println("Best Match");
|
||||||
|
|
||||||
JSONArray bestMatchArray = json.getJSONArray("Best Match");
|
JSONArray bestMatchArray = json.getJSONArray("Best Match");
|
||||||
int len = bestMatchArray.size();
|
int len = bestMatchArray.size();
|
||||||
if (len > 1) {
|
if (len > 1) {
|
||||||
System.out.println("Found this many best matches: "+ len);
|
logger.debug("Found this many best matches: "+ len);
|
||||||
}
|
}
|
||||||
int i;
|
int i;
|
||||||
for (i = 0; i < len; i++) {
|
for (i = 0; i < len; i++) {
|
||||||
JSONObject o = bestMatchArray.getJSONObject(i);
|
JSONObject o = bestMatchArray.getJSONObject(i);
|
||||||
//System.out.println(o.toString());
|
//System.out.println(o.toString());
|
||||||
Concept concept = new Concept();
|
Concept concept = new Concept();
|
||||||
concept.setDefinedBy("http://link.informatics.stonybrook.edu/umls");
|
concept.setDefinedBy(schemeURI);
|
||||||
concept.setBestMatch("true");
|
concept.setBestMatch("true");
|
||||||
String cui = getJsonValue(o, "CUI");
|
String cui = getJsonValue(o, "CUI");
|
||||||
bestMatchIdList.add(cui);
|
bestMatchIdList.add(cui);
|
||||||
|
|
@ -91,11 +143,12 @@ public class UMLSService implements ExternalConceptService {
|
||||||
concept.setType(getJsonValue(o, "type"));
|
concept.setType(getJsonValue(o, "type"));
|
||||||
concept.setDefinition(getJsonValue(o, "definition"));
|
concept.setDefinition(getJsonValue(o, "definition"));
|
||||||
concept.setUri(baseUri + cui);
|
concept.setUri(baseUri + cui);
|
||||||
|
concept.setSchemeURI(schemeURI);
|
||||||
conceptList.add(concept);
|
conceptList.add(concept);
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
if (json.has("All")) {
|
if (json.has("All")) {
|
||||||
|
allFound = true;
|
||||||
JSONArray allArray = json.getJSONArray("All");
|
JSONArray allArray = json.getJSONArray("All");
|
||||||
int len = allArray.size();
|
int len = allArray.size();
|
||||||
//System.out.println("size of best match array: "+ len);
|
//System.out.println("size of best match array: "+ len);
|
||||||
|
|
@ -104,7 +157,7 @@ public class UMLSService implements ExternalConceptService {
|
||||||
JSONObject o = allArray.getJSONObject(i);
|
JSONObject o = allArray.getJSONObject(i);
|
||||||
//System.out.println(o.toString());
|
//System.out.println(o.toString());
|
||||||
Concept concept = new Concept();
|
Concept concept = new Concept();
|
||||||
concept.setDefinedBy("http://link.informatics.stonybrook.edu/umls");
|
concept.setDefinedBy(schemeURI);
|
||||||
String cui = getJsonValue(o, "CUI");
|
String cui = getJsonValue(o, "CUI");
|
||||||
concept.setConceptId(cui);
|
concept.setConceptId(cui);
|
||||||
|
|
||||||
|
|
@ -112,6 +165,7 @@ public class UMLSService implements ExternalConceptService {
|
||||||
concept.setType(getJsonValue(o, "type"));
|
concept.setType(getJsonValue(o, "type"));
|
||||||
concept.setDefinition(getJsonValue(o, "definition"));
|
concept.setDefinition(getJsonValue(o, "definition"));
|
||||||
concept.setUri(baseUri + cui);
|
concept.setUri(baseUri + cui);
|
||||||
|
concept.setSchemeURI(schemeURI);
|
||||||
// prevent duplicate concepts in list
|
// prevent duplicate concepts in list
|
||||||
if (! bestMatchIdList.contains(cui)) {
|
if (! bestMatchIdList.contains(cui)) {
|
||||||
concept.setBestMatch("false");
|
concept.setBestMatch("false");
|
||||||
|
|
@ -122,20 +176,18 @@ public class UMLSService implements ExternalConceptService {
|
||||||
} catch (Exception ex ) {
|
} catch (Exception ex ) {
|
||||||
ex.printStackTrace();
|
ex.printStackTrace();
|
||||||
logger.error("Could not get concepts", ex);
|
logger.error("Could not get concepts", ex);
|
||||||
|
throw ex;
|
||||||
}
|
}
|
||||||
|
if (! bestMatchFound && !allFound) {
|
||||||
|
// we did not get a bestMatch or All element
|
||||||
|
throw new ConceptsNotFoundException();
|
||||||
|
}
|
||||||
|
|
||||||
|
//
|
||||||
return conceptList;
|
return conceptList;
|
||||||
|
|
||||||
//
|
|
||||||
// now serialize the list of Concepts to a JSON String
|
|
||||||
//
|
|
||||||
//JSONObject jsonObject = null;
|
|
||||||
//jsonObject = BeanToJsonSerializer.serializeToJsonObject(conceptList);
|
|
||||||
//System.out.println(jsonObject.toString());
|
|
||||||
//return jsonObject.toString();
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* Get a string from a json object or an empty string if there is no value for the given key
|
* Get a string from a json object or an empty string if there is no value for the given key
|
||||||
* @param obj
|
* @param obj
|
||||||
|
|
@ -150,4 +202,13 @@ public class UMLSService implements ExternalConceptService {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
|
protected String stripConceptId(String uri) {
|
||||||
|
String conceptId = new String();
|
||||||
|
int lastslash = uri.lastIndexOf('/');
|
||||||
|
conceptId = uri.substring(lastslash + 1, uri.length());
|
||||||
|
return conceptId;
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,7 +1,4 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
/*
|
/*
|
||||||
|
|
||||||
* $Id$
|
* $Id$
|
||||||
* CONFIDENTIAL AND PROPRIETARY. ? 2007 Revolution Health Group LLC. All rights reserved.
|
* CONFIDENTIAL AND PROPRIETARY. ? 2007 Revolution Health Group LLC. All rights reserved.
|
||||||
* This source code may not be disclosed to others, used or reproduced without the written permission of Revolution Health Group.
|
* This source code may not be disclosed to others, used or reproduced without the written permission of Revolution Health Group.
|
||||||
|
|
|
||||||
|
|
@ -1,7 +1,4 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
/*
|
/*
|
||||||
|
|
||||||
* $Id: DateConverter.java 50408 2007-03-28 19:14:46Z jdamick $
|
* $Id: DateConverter.java 50408 2007-03-28 19:14:46Z jdamick $
|
||||||
*
|
*
|
||||||
* Copyright 2006- Revolution Health Group. All rights reserved.
|
* Copyright 2006- Revolution Health Group. All rights reserved.
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.util;
|
package edu.cornell.mannlib.semservices.util;
|
||||||
|
|
||||||
import java.text.ParsePosition;
|
import java.text.ParsePosition;
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.util;
|
package edu.cornell.mannlib.semservices.util;
|
||||||
|
|
||||||
|
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.util;
|
package edu.cornell.mannlib.semservices.util;
|
||||||
import java.util.Iterator;
|
import java.util.Iterator;
|
||||||
import javax.xml.XMLConstants;
|
import javax.xml.XMLConstants;
|
||||||
|
|
|
||||||
|
|
@ -264,5 +264,10 @@ public class ObjectUtils {
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public static String nl2br(String text) {
|
||||||
|
return text.replaceAll("\n\n", "<p>").replaceAll("\n", "<br>");
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.util;
|
package edu.cornell.mannlib.semservices.util;
|
||||||
import edu.cornell.mannlib.semservices.bo.Time;
|
import edu.cornell.mannlib.semservices.bo.Time;
|
||||||
import java.util.Date;
|
import java.util.Date;
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,3 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.util;
|
package edu.cornell.mannlib.semservices.util;
|
||||||
import java.sql.Timestamp;
|
import java.sql.Timestamp;
|
||||||
import java.text.SimpleDateFormat;
|
import java.text.SimpleDateFormat;
|
||||||
|
|
|
||||||
|
|
@ -1,5 +1,4 @@
|
||||||
/*
|
/*
|
||||||
|
|
||||||
* $Id: XMLGregorianCalendarConverter.java 28642 2006-10-25 13:41:54Z jdamick $
|
* $Id: XMLGregorianCalendarConverter.java 28642 2006-10-25 13:41:54Z jdamick $
|
||||||
*
|
*
|
||||||
* Copyright 2006- Revolution Health Group. All rights reserved.
|
* Copyright 2006- Revolution Health Group. All rights reserved.
|
||||||
|
|
|
||||||
|
|
@ -1,8 +1,7 @@
|
||||||
/* $This file is distributed under the terms of the license in /doc/license.txt$ */
|
|
||||||
|
|
||||||
package edu.cornell.mannlib.semservices.util;
|
package edu.cornell.mannlib.semservices.util;
|
||||||
|
|
||||||
import java.io.BufferedWriter;
|
import java.io.BufferedWriter;
|
||||||
|
import java.io.ByteArrayOutputStream;
|
||||||
import java.io.IOException;
|
import java.io.IOException;
|
||||||
import java.io.InputStream;
|
import java.io.InputStream;
|
||||||
import java.io.OutputStreamWriter;
|
import java.io.OutputStreamWriter;
|
||||||
|
|
@ -122,6 +121,15 @@ public class XMLUtils {
|
||||||
serializer.serialize(doc);
|
serializer.serialize(doc);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public static String serializeDoctoString(Document doc) throws IOException {
|
||||||
|
XMLSerializer serializer = new XMLSerializer();
|
||||||
|
ByteArrayOutputStream bout = new ByteArrayOutputStream();
|
||||||
|
|
||||||
|
serializer.setOutputByteStream(bout);
|
||||||
|
serializer.serialize(doc);
|
||||||
|
return bout.toString();
|
||||||
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @param xml
|
* @param xml
|
||||||
*/
|
*/
|
||||||
|
|
@ -152,6 +160,36 @@ public class XMLUtils {
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
|
/**
|
||||||
|
* @param xml
|
||||||
|
*/
|
||||||
|
public static String prettyPrintToString(String xml) {
|
||||||
|
Source xmlInput = new StreamSource(new StringReader(xml));
|
||||||
|
StreamResult xmlOutput = new StreamResult(new StringWriter());
|
||||||
|
Transformer transformer = null;
|
||||||
|
try {
|
||||||
|
transformer = TransformerFactory.newInstance().newTransformer();
|
||||||
|
} catch (TransformerConfigurationException e) {
|
||||||
|
// TODO Auto-generated catch block
|
||||||
|
e.printStackTrace();
|
||||||
|
} catch (TransformerFactoryConfigurationError e) {
|
||||||
|
// TODO Auto-generated catch block
|
||||||
|
e.printStackTrace();
|
||||||
|
}
|
||||||
|
//transformer.setOutputProperty(OutputKeys.DOCTYPE_SYSTEM, "testing.dtd");
|
||||||
|
transformer.setOutputProperty(OutputKeys.INDENT, "yes");
|
||||||
|
transformer.setOutputProperty("{http://xml.apache.org/xslt}indent-amount", "2");
|
||||||
|
try {
|
||||||
|
transformer.transform(xmlInput, xmlOutput);
|
||||||
|
} catch (TransformerException e) {
|
||||||
|
// TODO Auto-generated catch block
|
||||||
|
e.printStackTrace();
|
||||||
|
}
|
||||||
|
String formattedxml=xmlOutput.getWriter().toString();
|
||||||
|
return formattedxml;
|
||||||
|
|
||||||
|
}
|
||||||
|
|
||||||
/**
|
/**
|
||||||
* @param node
|
* @param node
|
||||||
*/
|
*/
|
||||||
|
|
|
||||||
|
|
@ -1,4 +1,16 @@
|
||||||
package edu.cornell.mannlib.vitro.webapp.utils.ConceptSearchService;
|
/*
|
||||||
|
* $Id: BeanToJsonSerializer.java 66350 2007-08-20 21:11:41Z xluan $
|
||||||
|
*
|
||||||
|
* Copyright 2006- Revolution Health Group. All rights reserved.
|
||||||
|
*
|
||||||
|
* This software is the confidential and proprietary information
|
||||||
|
* of Revolution Health Group. (Confidential Information).
|
||||||
|
* You shall not disclose such Confidential Information and shall
|
||||||
|
* use it only in accordance with the terms of the license
|
||||||
|
* agreement you entered into with Revolution Health Group.
|
||||||
|
*
|
||||||
|
*/
|
||||||
|
package edu.cornell.mannlib.semservices.view;
|
||||||
|
|
||||||
import java.beans.PropertyDescriptor;
|
import java.beans.PropertyDescriptor;
|
||||||
import java.lang.reflect.InvocationTargetException;
|
import java.lang.reflect.InvocationTargetException;
|
||||||
|
|
@ -46,7 +46,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
private Log log = LogFactory.getLog(AddAssociatedConceptGenerator.class);
|
private Log log = LogFactory.getLog(AddAssociatedConceptGenerator.class);
|
||||||
private String template = "addAssociatedConcept.ftl";
|
private String template = "addAssociatedConcept.ftl";
|
||||||
private static String SKOSConceptType = "http://www.w3.org/2004/02/skos/core#Concept";
|
private static String SKOSConceptType = "http://www.w3.org/2004/02/skos/core#Concept";
|
||||||
|
//TODO: Set this to a dynamic mechanism
|
||||||
|
private static String VIVOCore = "http://vivoweb.org/ontology/core#";
|
||||||
|
|
||||||
@Override
|
@Override
|
||||||
public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) {
|
public EditConfigurationVTwo getEditConfiguration(VitroRequest vreq, HttpSession session) {
|
||||||
|
|
@ -168,10 +169,13 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
return n3Required;
|
return n3Required;
|
||||||
}
|
}
|
||||||
|
|
||||||
//Don't think there's any n3 optional here
|
//Optional N3, includes possibility of semantic type which may or may not be included
|
||||||
|
//label and source are independent of semantic type
|
||||||
private List<String> generateN3Optional() {
|
private List<String> generateN3Optional() {
|
||||||
return list("?conceptNode <" + RDFS.label.getURI() + "> ?conceptLabel .\n" +
|
return list("?conceptNode <" + RDFS.label.getURI() + "> ?conceptLabel .\n" +
|
||||||
"?conceptNode <" + RDFS.isDefinedBy.getURI() + "> ?conceptSource ."
|
"?conceptNode <" + RDFS.isDefinedBy.getURI() + "> ?conceptSource .",
|
||||||
|
"?conceptNode <" + VIVOCore + "conceptSemanticType> ?conceptSemanticTypeURI ." +
|
||||||
|
"?conceptSemanticTypeURI <" + RDFS.label.getURI() + "> ?conceptSemanticTypeLabel ."
|
||||||
);
|
);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -185,6 +189,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
HashMap<String, String> newResources = new HashMap<String, String>();
|
HashMap<String, String> newResources = new HashMap<String, String>();
|
||||||
//There are no new resources here, the concept node uri doesn't
|
//There are no new resources here, the concept node uri doesn't
|
||||||
//get created but already exists, and vocab uri should already exist as well
|
//get created but already exists, and vocab uri should already exist as well
|
||||||
|
//Adding concept semantic type uri just to test - note this isn't really on the form at all
|
||||||
|
newResources.put("conceptSemanticTypeURI", null);
|
||||||
return newResources;
|
return newResources;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -233,9 +239,12 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
//The URI of the node that defines the concept
|
//The URI of the node that defines the concept
|
||||||
urisOnForm.add("conceptNode");
|
urisOnForm.add("conceptNode");
|
||||||
urisOnForm.add("conceptSource");
|
urisOnForm.add("conceptSource");
|
||||||
|
urisOnForm.add("conceptSemanticTypeURI");
|
||||||
editConfiguration.setUrisOnform(urisOnForm);
|
editConfiguration.setUrisOnform(urisOnForm);
|
||||||
//Also need to add the label of the concept
|
//Also need to add the label of the concept
|
||||||
literalsOnForm.add("conceptLabel");
|
literalsOnForm.add("conceptLabel");
|
||||||
|
literalsOnForm.add("conceptSemanticTypeLabel");
|
||||||
|
|
||||||
editConfiguration.setLiteralsOnForm(literalsOnForm);
|
editConfiguration.setLiteralsOnForm(literalsOnForm);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
@ -263,6 +272,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
setConceptNodeField(editConfiguration, vreq);
|
setConceptNodeField(editConfiguration, vreq);
|
||||||
setConceptLabelField(editConfiguration, vreq);
|
setConceptLabelField(editConfiguration, vreq);
|
||||||
setVocabURIField(editConfiguration, vreq);
|
setVocabURIField(editConfiguration, vreq);
|
||||||
|
setConceptSemanticTypeURIField(editConfiguration,vreq);
|
||||||
|
setConceptSemanticTypeLabelField(editConfiguration,vreq);
|
||||||
}
|
}
|
||||||
|
|
||||||
//this field will be hidden and include the concept node URI
|
//this field will be hidden and include the concept node URI
|
||||||
|
|
@ -291,6 +302,22 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
);
|
);
|
||||||
}
|
}
|
||||||
|
|
||||||
|
//This will also be a URI
|
||||||
|
private void setConceptSemanticTypeURIField(EditConfigurationVTwo editConfiguration,
|
||||||
|
VitroRequest vreq) {
|
||||||
|
editConfiguration.addField(new FieldVTwo().
|
||||||
|
setName("conceptSemanticTypeURI")
|
||||||
|
);
|
||||||
|
}
|
||||||
|
|
||||||
|
private void setConceptSemanticTypeLabelField(EditConfigurationVTwo editConfiguration,
|
||||||
|
VitroRequest vreq) {
|
||||||
|
editConfiguration.addField(new FieldVTwo().
|
||||||
|
setName("conceptSemanticTypeLabel").
|
||||||
|
setRangeDatatypeUri(XSD.xstring.toString())
|
||||||
|
);
|
||||||
|
}
|
||||||
|
|
||||||
|
|
||||||
//Add preprocessor
|
//Add preprocessor
|
||||||
|
|
||||||
|
|
@ -357,6 +384,7 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
boolean isSKOSConcept = false;
|
boolean isSKOSConcept = false;
|
||||||
String conceptUri = conceptIndividual.getURI();
|
String conceptUri = conceptIndividual.getURI();
|
||||||
String conceptLabel = conceptIndividual.getName();
|
String conceptLabel = conceptIndividual.getName();
|
||||||
|
|
||||||
//Check if SKOS Concept type
|
//Check if SKOS Concept type
|
||||||
List<ObjectPropertyStatement> osl = conceptIndividual.getObjectPropertyStatements(RDF.type.getURI());
|
List<ObjectPropertyStatement> osl = conceptIndividual.getObjectPropertyStatements(RDF.type.getURI());
|
||||||
for(ObjectPropertyStatement os: osl) {
|
for(ObjectPropertyStatement os: osl) {
|
||||||
|
|
@ -367,7 +395,8 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
}
|
}
|
||||||
|
|
||||||
if(isSKOSConcept) {
|
if(isSKOSConcept) {
|
||||||
info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, null, null, SKOSConceptType));
|
//if the concept in question is skos - which would imply a user generated concept
|
||||||
|
info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, null, null, SKOSConceptType, null, null));
|
||||||
} else {
|
} else {
|
||||||
//Get the vocab source and vocab label
|
//Get the vocab source and vocab label
|
||||||
List<ObjectPropertyStatement> vocabList = conceptIndividual.getObjectPropertyStatements(RDFS.isDefinedBy.getURI());
|
List<ObjectPropertyStatement> vocabList = conceptIndividual.getObjectPropertyStatements(RDFS.isDefinedBy.getURI());
|
||||||
|
|
@ -379,7 +408,19 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
//Assuming name will get label
|
//Assuming name will get label
|
||||||
vocabLabel = sourceIndividual.getName();
|
vocabLabel = sourceIndividual.getName();
|
||||||
}
|
}
|
||||||
info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, vocabSource, vocabLabel, null));
|
String conceptSemanticTypeURI = null;
|
||||||
|
String conceptSemanticTypeLabel = null;
|
||||||
|
//Can a concept have multiple semantic types? Currently we are only returning the first one
|
||||||
|
List<ObjectPropertyStatement> semanticTypeStatements = conceptIndividual.getObjectPropertyStatements(VIVOCore + "conceptSemanticType");
|
||||||
|
if(semanticTypeStatements.size() > 0) {
|
||||||
|
conceptSemanticTypeURI = semanticTypeStatements.get(0).getObjectURI();
|
||||||
|
Individual conceptSemanticTypeIndividual = EditConfigurationUtils.getIndividual(vreq, conceptSemanticTypeURI);
|
||||||
|
conceptSemanticTypeLabel = conceptSemanticTypeIndividual.getName();
|
||||||
|
}
|
||||||
|
//get label
|
||||||
|
|
||||||
|
//Assuming this is from an external vocabulary source
|
||||||
|
info.add(new AssociatedConceptInfo(conceptLabel, conceptUri, vocabSource, vocabLabel, null, conceptSemanticTypeURI, conceptSemanticTypeLabel));
|
||||||
|
|
||||||
}
|
}
|
||||||
}
|
}
|
||||||
|
|
@ -392,12 +433,16 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
private String vocabURI;
|
private String vocabURI;
|
||||||
private String vocabLabel;
|
private String vocabLabel;
|
||||||
private String type; //In case of SKOS concept, will have skos concept type
|
private String type; //In case of SKOS concept, will have skos concept type
|
||||||
public AssociatedConceptInfo(String inputLabel, String inputURI, String inputVocabURI, String inputVocabLabel, String inputType) {
|
private String conceptSemanticTypeURI; //For some services, such as UMLS, we have a semantic type associated
|
||||||
|
private String conceptSemanticTypeLabel;
|
||||||
|
public AssociatedConceptInfo(String inputLabel, String inputURI, String inputVocabURI, String inputVocabLabel, String inputType, String inputConceptSemanticTypeURI, String inputConceptSemanticTypeLabel) {
|
||||||
this.conceptLabel = inputLabel;
|
this.conceptLabel = inputLabel;
|
||||||
this.conceptURI = inputURI;
|
this.conceptURI = inputURI;
|
||||||
this.vocabURI = inputVocabURI;
|
this.vocabURI = inputVocabURI;
|
||||||
this.vocabLabel = inputVocabLabel;
|
this.vocabLabel = inputVocabLabel;
|
||||||
this.type = inputType;
|
this.type = inputType;
|
||||||
|
this.conceptSemanticTypeURI = inputConceptSemanticTypeURI;
|
||||||
|
this.conceptSemanticTypeLabel = inputConceptSemanticTypeLabel;
|
||||||
}
|
}
|
||||||
|
|
||||||
//Getters
|
//Getters
|
||||||
|
|
@ -421,6 +466,14 @@ public class AddAssociatedConceptGenerator extends VivoBaseGenerator implements
|
||||||
return type;
|
return type;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
public String getConceptSemanticTypeURI(){
|
||||||
|
return conceptSemanticTypeURI;
|
||||||
|
}
|
||||||
|
|
||||||
|
public String getConceptSemanticTypeLabel(){
|
||||||
|
return conceptSemanticTypeLabel;
|
||||||
|
}
|
||||||
|
|
||||||
}
|
}
|
||||||
|
|
||||||
public class AssociatedConceptInfoComparator implements Comparator<AssociatedConceptInfo>{
|
public class AssociatedConceptInfoComparator implements Comparator<AssociatedConceptInfo>{
|
||||||
|
|
|
||||||
|
|
@ -20,9 +20,9 @@ import org.apache.commons.logging.LogFactory;
|
||||||
import edu.cornell.mannlib.semservices.bo.Concept;
|
import edu.cornell.mannlib.semservices.bo.Concept;
|
||||||
import edu.cornell.mannlib.semservices.bo.ConceptInfo;
|
import edu.cornell.mannlib.semservices.bo.ConceptInfo;
|
||||||
import edu.cornell.mannlib.semservices.bo.SemanticServicesError;
|
import edu.cornell.mannlib.semservices.bo.SemanticServicesError;
|
||||||
|
import edu.cornell.mannlib.semservices.view.BeanToJsonSerializer;
|
||||||
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
|
import edu.cornell.mannlib.vitro.webapp.controller.VitroHttpServlet;
|
||||||
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
|
import edu.cornell.mannlib.vitro.webapp.controller.VitroRequest;
|
||||||
import edu.cornell.mannlib.vitro.webapp.utils.ConceptSearchService.BeanToJsonSerializer;
|
|
||||||
import edu.cornell.mannlib.vitro.webapp.utils.ConceptSearchService.ConceptSearchServiceUtils;
|
import edu.cornell.mannlib.vitro.webapp.utils.ConceptSearchService.ConceptSearchServiceUtils;
|
||||||
|
|
||||||
public class ConceptSearchServlet extends VitroHttpServlet {
|
public class ConceptSearchServlet extends VitroHttpServlet {
|
||||||
|
|
|
||||||
|
|
@ -39,7 +39,7 @@ public class ConceptSearchServiceUtils {
|
||||||
HashMap<String, VocabSourceDescription> map = new HashMap<String, VocabSourceDescription>();
|
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"));
|
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
|
//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(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"));
|
map.put(GemetVocabSource, new VocabSourceDescription("GEMET", GemetVocabSource, "http://www.eionet.europa.eu/gemet", "GEneral Multilingual Environmental Thesaurus"));
|
||||||
return map;
|
return map;
|
||||||
}
|
}
|
||||||
|
|
@ -82,7 +82,7 @@ public class ConceptSearchServiceUtils {
|
||||||
|
|
||||||
//Get search
|
//Get search
|
||||||
String searchTerm = getSearchTerm(vreq);
|
String searchTerm = getSearchTerm(vreq);
|
||||||
List<Concept> conceptResults = conceptServiceClass.processResults(searchTerm);
|
List<Concept> conceptResults = conceptServiceClass.getConcepts(searchTerm);
|
||||||
return conceptResults;
|
return conceptResults;
|
||||||
}
|
}
|
||||||
|
|
||||||
|
|
|
||||||
Loading…
Add table
Reference in a new issue