This project is a web front-end of the disease data - a web service to providing the API
- LDAP lncRNA-disease association predictor
- UMLS
- CTDBase
- Disease Ontoloy
- DisGeNet
- Human Phenotype Ontology
- MeSH
- NDF-RT
- Orphanet
- PharmacotherapyDB
- KEGG
- HPO
- Spring
- ElsaticSearch
- Hibernate
- Mongodb
- Disease Web Server
- Kaijie Zhao:[email protected]
- Jianxin Wang: [email protected]
- Min Li: [email protected]
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spring dependency
<!-- Spring data mongodb --> <dependency> <groupId>org.springframework.data</groupId> <artifactId>spring-data-mongodb</artifactId> <version>1.8.4.RELEASE</version> </dependency> <!-- MongoDB Java Driver --> <dependency> <groupId>org.mongodb</groupId> <artifactId>mongo-java-driver</artifactId> <version>3.3.0</version> </dependency> -
the full mongo-client config(spring-data-mongodb V1.7+)
<mongo:mongo-client id="mongoClient" host="${mongo.host}" port="${mongo.port}"> <mongo:client-options connections-per-host="${mongo.connectionsPerHost}" min-connections-per-host="${mongo.minConnectionsPerHost}" threads-allowed-to-block-for-connection-multiplier="${mongo.threadsAllowedToBlockForConnectionMultiplier}" connect-timeout="${mongo.connectTimeout}" max-wait-time="${mongo.maxWaitTime}" socket-keep-alive="${mongo.socketKeepAlive}" socket-timeout="${mongo.socketTimeout}" description="${mongo.description}" max-connection-idle-time="${mongo.maxConnectionIdleTime}" max-connection-life-time="${mongo.maxConnectionLifeTime}" heartbeat-socket-timeout="${mongo.heartbeatSocketTimeout}" heartbeat-connect-timeout="${mongo.heartbeatConnectTimeout}" min-heartbeat-frequency="${mongo.minHeartbeatFrequency}" heartbeat-frequency="${mongo.heartbeatFrequency}" /> </mongo:mongo-client> -
the mini mongo-client config
<!--if auth check, mongo-client attributes add: credentials="${mongo.user}:${mongo.pwd}@${mongo.defaultDbName}" --> <!-- mini client --> <mongo:mongo-client id="mongoClient" host="${mongo.host}" port="${mongo.port}"> <mongo:client-options write-concern="SAFE" /> </mongo:mongo-client>
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the spring dependency
<!-- ELASTICSEARCH --> <dependency> <groupId>org.springframework.data</groupId> <artifactId>spring-data-elasticsearch</artifactId> <version>1.2.0.RELEASE</version> </dependency>
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configure the properties files to spring bean
<!-- all properties --> <bean id="apiProperties" class="com.csu.bio.util.PropertyConfigurer"> <property name="locations"> <list> <value>classpath:umls.properties</value> <value>classpath:mygene.properties</value> <value>classpath:mongo.properties</value> </list> </property> </bean>
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html page
<head> <meta http-equiv="Content-Type" content="text/html; charset=UTF-8"> </head> -
web.xml
<filter> <filter-name>encodingFilter</filter-name> <filter-class>org.springframework.web.filter.CharacterEncodingFilter</filter-class> <init-param> <param-name>encoding</param-name> <param-value>UTF-8</param-value> </init-param> <init-param> <param-name>forceEncoding</param-name> <param-value>true</param-value> </init-param> </filter> <filter-mapping> <filter-name>encodingFilter</filter-name> <url-pattern>/*</url-pattern> </filter-mapping> -
spring-mvc.xml
<bean id="velocityConfigurer" class="org.springframework.web.servlet.view.velocity.VelocityConfigurer"> <property name="resourceLoaderPath" value="/WEB-INF/views" /> <property name="velocityProperties"> <props> <prop key="input.encoding">UTF-8</prop> <prop key="output.encoding">UTF-8</prop> <prop key="contentType">text/html;charset=UTF-8</prop> </props> </property> </bean> -
mysql encoding
mysql> show variables like 'character%'; +--------------------------+----------------------------+ | Variable_name | Value | +--------------------------+----------------------------+ | character_set_client | utf8 | | character_set_connection | utf8 | | character_set_database | utf8 | | character_set_filesystem | binary | | character_set_results | utf8 | | character_set_server | utf8 | | character_set_system | utf8 | | character_sets_dir | /usr/share/mysql/charsets/ | +--------------------------+----------------------------+ 8 rows in set -
tomcat server.xml
<Connector port="8080" protocol="HTTP/1.1" connectionTimeout="20000" redirectPort="8443" URIEncoding="UTF-8" /> <Connector port="8009" protocol="AJP/1.3" redirectPort="8443" URIEncoding="UTF-8"/> -
eclipse workspace
1. Window -> Preference -> Content types UTF-8 2. Java source code Window -> Preference -> Workspace -> Text file encoding Windows default is GBK，Linux default is UTF-8