nathandunn · nathandunn · Jun 2, 2020 · Jun 2, 2020 · Jun 3, 2020 · Jun 3, 2020
diff --git a/build.gradle b/build.gradle
@@ -5,7 +5,7 @@ buildscript {
     }
     dependencies {
         classpath "org.grails:grails-gradle-plugin:$grailsVersion"
-        classpath "org.grails.plugins:hibernate5:${gormVersion-".RELEASE"}"
+//        classpath "org.grails.plugins:hibernate5:${gormVersion-".RELEASE"}"
         classpath "com.bertramlabs.plugins:asset-pipeline-gradle:2.15.1"
         classpath "gradle.plugin.com.energizedwork.webdriver-binaries:webdriver-binaries-gradle-plugin:$webdriverBinariesVersion"
     }
@@ -43,18 +43,27 @@ repositories {
 // In this section you declare the dependencies for your production and test code
 dependencies {
     // START added dependencies
+
+    // Neo4j stuff
+//    implementation 'io.micronaut.configuration:micronaut-neo4j-gorm:2.0.0.M2'
+//    compile "org.grails.plugins:neo4j"
+    compile "org.grails.plugins:neo4j:$gormNeo4jVersion"
+
+
+    compile group: 'io.swagger.core.v3', name: 'swagger-annotations', version: '2.1.2'
 //    compile 'org.grails.plugins:swagger:1.0.1'
 //    annotationProcessor "io.micronaut.configuration:micronaut-openapi:1.5.0"
 //    compile "io.swagger.core.v3:swagger-annotations:2.1.1"
 //    implementation "io.swagger.core.v3:swagger-annotations"
 //    compileOnly "io.micronaut.configuration:micronaut-openapi:1.4.0"
-    annotationProcessor "io.micronaut.configuration:micronaut-openapi:1.5.0"
 //    compile "io.swagger.core.v3:swagger-annotations:2.1.1"
-    compile "io.swagger.core.v3:swagger-annotations:2.1.1"
-    compileOnly "io.micronaut.configuration:micronaut-openapi:1.5.0"
+//    annotationProcessor "io.micronaut.configuration:micronaut-openapi:1.5.0"
+//    compile "io.swagger.core.v3:swagger-annotations:2.1.1"
+//    compileOnly "io.micronaut.configuration:micronaut-openapi:1.5.0"
+
 
 //    runtime 'mysql:mysql-connector-java:5.1.49'
-    runtime 'org.postgresql:postgresql:9.4.1212'
+//    runtime 'org.postgresql:postgresql:9.4.1212'
 
 
     // HTSJDK
@@ -83,6 +92,10 @@ dependencies {
 //    compile 'org.grails.plugins:spring-security-core:4.0.0'
 //    compile 'org.grails.plugins:spring-security-core:3.3.1'
 
+    // let's add micronaut stuff
+    compile "io.micronaut:micronaut-http-client"
+    compileOnly "io.micronaut:micronaut-inject-groovy"
+
 
     // END added dependencies
 
@@ -103,14 +116,15 @@ dependencies {
     compile "org.grails.plugins:async"
     compile "org.grails.plugins:scaffolding"
     compile "org.grails.plugins:events"
-    compile "org.grails.plugins:hibernate5"
-    compile "org.hibernate:hibernate-core:5.4.16.Final"
+//    compile "org.grails.plugins:hibernate5:$hibernateDatastoreVersion"
+//    compile "org.hibernate:hibernate-ehcache:$hibernateEhcacheVersion"
+//    compile "org.hibernate:hibernate-core:5.4.16.Final"
     compile "org.hibernate:hibernate-validator:6.1.5.Final"
     compile "org.grails.plugins:gsp"
     console "org.grails:grails-console"
     profile "org.grails.profiles:web"
     runtime "org.glassfish.web:el-impl:2.1.2-b03"
-    runtime "com.h2database:h2"
+//    runtime "com.h2database:h2"
     runtime "org.apache.tomcat:tomcat-jdbc"
     runtime "com.bertramlabs.plugins:asset-pipeline-grails:2.15.1"
     testCompile "org.grails:grails-gorm-testing-support"
@@ -120,6 +134,10 @@ dependencies {
 //    testCompile "org.grails:grails-test-mixins:3.3.0"
 //    testRuntime "org.seleniumhq.selenium:selenium-htmlunit-driver:2.47.1"
     testRuntime "net.sourceforge.htmlunit:htmlunit:2.18"
+//    testRuntime "org.neo4j.test:neo4j-harness:3.5.0"
+    runtime "org.neo4j.test:neo4j-harness:$neo4jVersion"
+
+
 //    testRuntime "org.seleniumhq.selenium:selenium-chrome-driver:2.47.1"
 
     testCompile "org.grails.plugins:geb"
@@ -137,8 +155,19 @@ webdriverBinaries {
 }
 
 bootRun {
-    jvmArgs('-Dspring.output.ansi.enabled=always')
-//    addResources = true
+//    systemProperties System.properties
+//    jvmArgs('-Dspring.output.ansi.enabled=always')
+////    addResources = true
+////    String springProfilesActive = 'spring.profiles.active'
+////    systemProperty springProfilesActive, System.getProperty(springProfilesActive)
+//    sourceResources sourceSets.main
+    ignoreExitValue true
+    jvmArgs(
+        '-Dspring.output.ansi.enabled=always',
+        '-noverify',
+        '-XX:TieredStopAtLevel=1',
+        '-Xmx1024m')
+    sourceResources sourceSets.main
     String springProfilesActive = 'spring.profiles.active'
     systemProperty springProfilesActive, System.getProperty(springProfilesActive)
 }

diff --git a/gradle.properties b/gradle.properties
@@ -1,13 +1,18 @@
 #Thu May 28 09:28:15 PDT 2020
-grailsWrapperVersion=1.0.0
-chromeDriverVersion=2.44 
-hibernateCoreVersion=5.4.16.Final
+#grailsWrapperVersion=1.0.0
+#chromeDriverVersion=2.44
+#hibernateCoreVersion=5.4.16.Final
+#hibernateDatastoreVersion=7.1.0.M1
+#hibernateValidatorVersion=6.0.13.Final
+#hibernateEhcacheVersion=5.4.0.Final
 webdriverBinariesVersion=1.4
-groovyVersion=3.0.3
+gormNeo4jVersion=7.1.0.M2
+#groovyVersion=3.0.3
 grailsVersion=4.0.3
 seleniumVersion=3.12.0
-gradleWrapperVersion=5.6.4
-gormVersion=7.0.2
-gebVersion=2.3
-seleniumSafariDriverVersion=3.14.0
-geckodriverVersion=0.23.0 
+#gradleWrapperVersion=5.6.4
+#gormVersion=7.0.2
+#gebVersion=2.3
+#seleniumSafariDriverVersion=3.14.0
+#geckodriverVersion=0.23.0
+neo4jVersion=3.5.18
diff --git a/grails-app/conf/application.groovy b/grails-app/conf/application.groovy
@@ -1,6 +1,6 @@
 
 
-grails.gsp.enable.reload = true
+//grails.gsp.enable.reload = true
 
 // locations to search for config files that get merged into the main config;
 // config files can be ConfigSlurper scripts, Java properties files, or classes

diff --git a/grails-app/conf/application.yml b/grails-app/conf/application.yml
@@ -3,11 +3,26 @@ grails:
     profile: web
     codegen:
         defaultPackage: org.bbop.apollo
+    spring:
+        transactionManagement:
+            proxies: false
     gorm:
         reactor:
             # Whether to translate GORM events into Reactor events
             # Disabled by default for performance reasons
             events: false
+    neo4j:
+#        type: embedded
+        url: bolt://localhost:7687
+        username: neo4j
+        password: testpass
+        flush.mode: AUTO
+        options:
+            maxSessions: 100
+            encryptionLevel: NONE
+            sessionLivenessCheckTimeout: 200
+#            encryption: true
+
 info:
     app:
         name: '@info.app.name@'
@@ -19,6 +34,12 @@ spring:
     groovy:
         template:
             check-template-location: false
+    devtools:
+        restart:
+            exclude:
+                - grails-app/views/**
+                - grails-app/i18n/**
+                - grails-app/conf/**
 
 # Spring Actuator Endpoints are Disabled by Default
 endpoints:
@@ -86,46 +107,46 @@ endpoints:
         unique-names: true
 
 ---
-hibernate:
-    cache:
-        queries: false
-        use_second_level_cache: false
-        use_query_cache: false
-dataSource:
-    pooled: true
-    jmxExport: true
-    driverClassName: org.h2.Driver
-    username: sa
-    password: ''
+#hibernate:
+#    cache:
+#        queries: false
+#        use_second_level_cache: false
+#        use_query_cache: false
+#dataSource:
+#    pooled: true
+#    jmxExport: true
+#    driverClassName: org.h2.Driver
+#    username: sa
+#    password: ''
 
-environments:
-    development:
-        dataSource:
-            dbCreate: create-drop
-            url: jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE
-    test:
-        dataSource:
-            dbCreate: update
-            url: jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE
-    production:
-        dataSource:
-            dbCreate: none
-            url: jdbc:h2:./prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE
-            properties:
-                jmxEnabled: true
-                initialSize: 5
-                maxActive: 50
-                minIdle: 5
-                maxIdle: 25
-                maxWait: 10000
-                maxAge: 600000
-                timeBetweenEvictionRunsMillis: 5000
-                minEvictableIdleTimeMillis: 60000
-                validationQuery: SELECT 1
-                validationQueryTimeout: 3
-                validationInterval: 15000
-                testOnBorrow: true
-                testWhileIdle: true
-                testOnReturn: false
-                jdbcInterceptors: ConnectionState
-                defaultTransactionIsolation: 2 # TRANSACTION_READ_COMMITTED
+#environments:
+#    development:
+#        dataSource:
+#            dbCreate: create-drop
+#            url: jdbc:h2:mem:devDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE
+#    test:
+#        dataSource:
+#            dbCreate: update
+#            url: jdbc:h2:mem:testDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE
+#    production:
+#        dataSource:
+#            dbCreate: none
+#            url: jdbc:h2:./prodDb;MVCC=TRUE;LOCK_TIMEOUT=10000;DB_CLOSE_ON_EXIT=FALSE
+#            properties:
+#                jmxEnabled: true
+#                initialSize: 5
+#                maxActive: 50
+#                minIdle: 5
+#                maxIdle: 25
+#                maxWait: 10000
+#                maxAge: 600000
+#                timeBetweenEvictionRunsMillis: 5000
+#                minEvictableIdleTimeMillis: 60000
+#                validationQuery: SELECT 1
+#                validationQueryTimeout: 3
+#                validationInterval: 15000
+#                testOnBorrow: true
+#                testWhileIdle: true
+#                testOnReturn: false
+#                jdbcInterceptors: ConnectionState
+#                defaultTransactionIsolation: 2 # TRANSACTION_READ_COMMITTED
diff --git a/grails-app/controllers/UrlMappings.groovy b/grails-app/controllers/UrlMappings.groovy
@@ -20,6 +20,7 @@ class UrlMappings {
 //        "/"(redirect: '/annotator/index')
         "500"(view: '/error')
 //        "/menu"(view: '/menu')
+        "/proxytest"(controller: "proxy", action: "init")
         "/"(view: '/index')
 //        "/${clientToken}/version.jsp"(controller: 'annotator', view: "version")
 //        "/about"(controller: 'annotator', view: "about")

diff --git a/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy b/grails-app/controllers/org/bbop/apollo/AnnotatorController.groovy
@@ -13,7 +13,7 @@ import org.bbop.apollo.history.FeatureOperation
 import org.bbop.apollo.report.AnnotatorSummary
 import org.grails.web.json.JSONArray
 import org.grails.web.json.JSONObject
-import org.hibernate.FetchMode
+//import org.hibernate.FetchMode
 // import io.swagger.annotations.*
 import org.springframework.http.HttpStatus
 
@@ -512,25 +512,45 @@ class AnnotatorController {
                     order('lastUpdated', sortorder)
                 }
                 if (showOnlyGoAnnotations) {
-                    fetchMode 'goAnnotations', FetchMode.JOIN
+                    'goAnnotations'
                 }
-                fetchMode 'owners', FetchMode.JOIN
-                fetchMode 'featureSynonyms', FetchMode.JOIN
-                fetchMode 'featureDBXrefs', FetchMode.JOIN
-                fetchMode 'featureProperties', FetchMode.JOIN
-                fetchMode 'featureLocations', FetchMode.JOIN
-                fetchMode 'featureLocations.sequence', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.childFeature', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.parentFeature', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.childFeature.parentFeatureRelationships', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.childFeature.parentFeatureRelationships.childFeature', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.childFeature.parentFeatureRelationships.childFeature.featureLocations', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.childFeature.parentFeatureRelationships.childFeature.featureLocations.sequence', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.childFeature.childFeatureRelationships', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.childFeature.featureLocations', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.childFeature.featureLocations.sequence', FetchMode.JOIN
-                fetchMode 'parentFeatureRelationships.childFeature.owners', FetchMode.JOIN
+                'owners'
+                'featureSynonyms'
+                'featureDBXrefs'
+                'featureProperties'
+                'featureLocations'
+                'featureLocations.sequence'
+                'parentFeatureRelationships'
+                'parentFeatureRelationships.childFeature'
+                'parentFeatureRelationships.parentFeature'
+                'parentFeatureRelationships.childFeature.parentFeatureRelationships'
+                'parentFeatureRelationships.childFeature.parentFeatureRelationships.childFeature'
+                'parentFeatureRelationships.childFeature.parentFeatureRelationships.childFeature.featureLocations'
+                'parentFeatureRelationships.childFeature.parentFeatureRelationships.childFeature.featureLocations.sequence'
+                'parentFeatureRelationships.childFeature.childFeatureRelationships'
+                'parentFeatureRelationships.childFeature.featureLocations'
+                'parentFeatureRelationships.childFeature.featureLocations.sequence'
+                'parentFeatureRelationships.childFeature.owners'
+//                if (showOnlyGoAnnotations) {
+//                    fetchMode 'goAnnotations', FetchMode.JOIN
+//                }
+//                fetchMode 'owners', FetchMode.JOIN
+//                fetchMode 'featureSynonyms', FetchMode.JOIN
+//                fetchMode 'featureDBXrefs', FetchMode.JOIN
+//                fetchMode 'featureProperties', FetchMode.JOIN
+//                fetchMode 'featureLocations', FetchMode.JOIN
+//                fetchMode 'featureLocations.sequence', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.childFeature', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.parentFeature', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.childFeature.parentFeatureRelationships', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.childFeature.parentFeatureRelationships.childFeature', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.childFeature.parentFeatureRelationships.childFeature.featureLocations', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.childFeature.parentFeatureRelationships.childFeature.featureLocations.sequence', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.childFeature.childFeatureRelationships', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.childFeature.featureLocations', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.childFeature.featureLocations.sequence', FetchMode.JOIN
+//                fetchMode 'parentFeatureRelationships.childFeature.owners', FetchMode.JOIN
             }
             long durationInMilliseconds = System.currentTimeMillis() - start;
             log.debug "criteria query ${durationInMilliseconds}"

diff --git a/grails-app/controllers/org/bbop/apollo/ProxyController.groovy b/grails-app/controllers/org/bbop/apollo/ProxyController.groovy
@@ -1,7 +1,9 @@
 package org.bbop.apollo
 
+import grails.converters.JSON
 import grails.gorm.transactions.Transactional
 import org.bbop.apollo.gwt.shared.PermissionEnum
+import org.grails.web.json.JSONObject
 
 import static org.springframework.http.HttpStatus.*
 
@@ -29,6 +31,24 @@ class ProxyController {
         respond proxyInstance
     }
 
+    @Transactional
+    def init(){
+        println "intting proxy 2"
+        println "asdfasdfC running! "
+        Proxy proxy = new Proxy(
+            referenceUrl: "http://asdf.com",
+            targetUrl: "http://asdf.com",
+            active: true,
+        ).save(failOnError: true,flush: true)
+        def proxies = Proxy.findAllByActive(true)
+        if(proxies){
+            respond proxies
+        }
+//        proxyService.initProxies()
+        println "D"
+        render  new JSONObject() as JSON
+    }
+
     def create() {
         params.active = true
         respond new Proxy(params)

diff --git a/grails-app/domain/org/bbop/apollo/Allele.groovy b/grails-app/domain/org/bbop/apollo/Allele.groovy
@@ -20,7 +20,7 @@ class Allele {
     ]
 
     static mapping = {
-        alleleInfo cascade: 'all-delete-orphan'
+//        alleleInfo cascade: 'all-delete-orphan'
     }
 
 }