Merge pull request #71 from AtlasOfLivingAustralia/develop

Fixes for a 1.0.7 release

.gitignore

@@ -1,6 +1,6 @@
 out
 .gradle
-
+build
 .slcache
 /target
 /.idea

build.gradle

@@ -18,7 +18,7 @@ plugins {
 }
 
 
-version "1.0.6"
+version "1.0.7-SNAPSHOT"
 
 
 group "au.org.ala"
@@ -64,7 +64,7 @@ dependencies {
     compile group: 'org.grails.plugins', name: 'ala-bootstrap3', version: '3.2.1', changing: true
     compile group: 'org.grails.plugins', name: 'ala-admin-plugin', version: '2.1', changing: true
     compile group: 'org.grails.plugins', name: 'ala-auth', version: '3.2.2', changing: true
-    compile group: 'au.org.ala.plugins.grails', name:'images-client-plugin', version: '1.0.1-SNAPSHOT', changing: true
+    compile group: 'au.org.ala.plugins.grails', name:'images-client-plugin', version: '1.1', changing: true
 
     // Added dependencies
     compile 'org.grails.plugins:external-config:1.2.2'    
@@ -81,7 +81,7 @@ dependencies {
     compile ('au.org.ala:image-utils:1.8.6'){
         exclude group: 'org.slf4j', module: 'slf4j-log4j12'
     }
-    compile 'org.grails.plugins:ala-ws-security-plugin:2.0'
+    compile 'org.grails.plugins:ala-ws-security-plugin:2.0.1'
 
     // Swagger
     compile 'org.grails.plugins:swagger:1.0.1'

db-upgrade-0_9_to_1_0.sql

@@ -1,25 +1,38 @@
 alter table image add date_deleted timestamp;
 alter table image add recognised_license_id bigint;
+alter table image add occurrence_id character varying(255);
+alter table image add calibrated_by_user character varying(255);
+
 CREATE TABLE public.license (
-                                id bigint NOT NULL,
-                                version bigint NOT NULL,
-                                url character varying(255) NOT NULL,
-                                name character varying(255) NOT NULL,
-                                image_url character varying(255),
-                                acronym character varying(255) NOT NULL
+    id bigint NOT NULL,
+    version bigint NOT NULL,
+    url character varying(255) NOT NULL,
+    name character varying(255) NOT NULL,
+    image_url character varying(255),
+    acronym character varying(255) NOT NULL
 );
 ALTER TABLE ONLY public.license
     ADD CONSTRAINT license_pkey PRIMARY KEY (id);
 CREATE TABLE public.license_mapping (
-                                        id bigint NOT NULL,
-                                        version bigint NOT NULL,
-                                        value character varying(255) NOT NULL,
-                                        license_id bigint NOT NULL
+    id bigint NOT NULL,
+    version bigint NOT NULL,
+    value character varying(255) NOT NULL,
+    license_id bigint NOT NULL
 );
 ALTER TABLE ONLY public.license_mapping
     ADD CONSTRAINT license_mapping_pkey PRIMARY KEY (id);
 ALTER TABLE ONLY public.license_mapping
     ADD CONSTRAINT fktetx2lihs6cq4swvdhaqeco7s FOREIGN KEY (license_id) REFERENCES public.license(id);
 
 
-update image set mime_type = 'audio/mpeg' where original_filename like '%.mp3';
+update image set mime_type = 'audio/mpeg' where original_filename like '%.mp3';
+
+
+/* Add the occurrence_id to top level table */
+CREATE TEMP TABLE temp_image_occurrence as select image_id, value as occurrence_id from image_meta_data_item imdi where imdi.name='occurrenceId';
+UPDATE image
+SET occurrence_id = subquery.occurrence_id
+FROM (SELECT io.image_id, io.occurrence_id from temp_image_occurrence io) AS subquery
+WHERE image.id = subquery.image_id;
+
+DROP TABLE temp_image_occurrence;

grails-app/conf/application.yml

@@ -91,10 +91,11 @@ dataSource:
 
 environments:
     development:
-        hibernate:
-            dialect: org.hibernate.dialect.PostgreSQLDialect
+#        hibernate:
+#            dialect: org.hibernate.dialect.PostgreSQLDialect
         dataSource:
             dbCreate: update
+#            driverClassName: org.postgresql.Driver
             url: jdbc:postgresql://localhost/images?autoReconnect=true&connectTimeout=0&useUnicode=true&characterEncoding=UTF-8
             username: "images"
             password: "images"
@@ -136,6 +137,7 @@ environments:
             dialect: org.hibernate.dialect.PostgreSQLDialect
         dataSource:
             dbCreate: update
+            driverClassName: org.postgresql.Driver
             url: jdbc:postgresql://localhost/images?autoReconnect=true&connectTimeout=0&useUnicode=true&characterEncoding=UTF-8
             properties:
                 jmxEnabled: true
@@ -159,7 +161,7 @@ security:
     cas:
         appServerName: 'http://dev.ala.org.au:8080'
         uriFilterPattern: '/admin/.*,/admin,/admin/,/image/deleteImage/.*'
-        authenticateOnlyIfLoggedInPattern:  ''
+        authenticateOnlyIfLoggedInPattern:  '/ws/createSubimage'
         bypass: false
         disableCAS: false
 

grails-app/controllers/UrlMappings.groovy

@@ -32,6 +32,7 @@ class UrlMappings {
         "/ws"(controller: 'webService', action: 'swagger')
 
         // legacy URLS
+        "/image/imageTooltipFragment"(controller: "image", action: "imageTooltipFragment")
         "/image/proxyImageThumbnail"(controller: "image", action: "proxyImageThumbnail")
         "/image/proxyImageThumbnailLarge"(controller: "image", action: "proxyImageThumbnailLarge")
         "/image/proxyImageTile"(controller: "image", action: "proxyImageTile")

grails-app/controllers/au/org/ala/images/AdminController.groovy

@@ -91,7 +91,7 @@ class AdminController {
         if (storeResult.image) {
             imageService.schedulePostIngestTasks(storeResult.image.id, storeResult.image.imageIdentifier, storeResult.image.originalFilename, userId)
         } else {
-            imageService.scheduleNonImagePostIngestTasks(storeResult.image.id, storeResult.image.imageIdentifier, storeResult.image.originalFilename, userId)
+            imageService.scheduleNonImagePostIngestTasks(storeResult.image.id)
         }
         flash.message = "Image uploaded with identifier: ${storeResult.image?.imageIdentifier}"
         redirect(action:'upload')
@@ -112,23 +112,27 @@ class AdminController {
             def headers = []
             def batch = []
 
-            file.inputStream.eachCsvLine { tokens ->
-                if (lineCount == 0) {
-                    headers = tokens
-                } else {
-                    def m = [:]
-                    for (int i = 0; i < headers.size(); ++i) {
-                        m[headers[i]] = tokens[i]
+            try {
+                file.inputStream.eachCsvLine { tokens ->
+                    if (lineCount == 0) {
+                        headers = tokens
+                    } else {
+                        def m = [:]
+                        for (int i = 0; i < headers.size(); ++i) {
+                            m[headers[i]] = tokens[i]
+                        }
+                        batch << m
                     }
-                    batch << m
+                    lineCount++
                 }
-                lineCount++
+                scheduleImagesUpload(batch, authService.getUserId())
+                renderResults([success: true, message:'Image upload started'])
+            } catch (Exception e){
+                log.error(e.getMessage(), e)
+                renderResults([success: false, message: "Problem reading CSV file. Please check contents."])
             }
-
-            scheduleImagesUpload(batch, '-2')
-            renderResults([success: true, message:'Image upload started'])
         } else {
-            renderResults([success: false, message: "Expected multipart request containing 'csvfile' file parameter"])
+            renderResults([success: false, message: "Problem reading CSV file from upload."])
         }
     }
 
@@ -145,6 +149,12 @@ class AdminController {
         }
     }
 
+    def scheduleDeletedImagesPurge(){
+        imageService.scheduleBackgroundTask(new DeletedImagesPurgeBackgroundTask(imageService))
+        flash.message = "Deleted images purge started. Refresh dashboard for progress."
+        redirect(action:'dashboard')
+    }
+
     def licences(){}
 
     def updateStoredLicences(){

grails-app/controllers/au/org/ala/images/ImageController.groovy

@@ -365,35 +365,45 @@ class ImageController {
                 flash.errorMessage = "Could not find image with id ${params.int("id") ?: params.imageId }!"
                 redirect(action:'list', controller: 'search')
             } else {
-                def subimages = Subimage.findAllByParentImage(image)*.subimage
-                def sizeOnDisk = imageStoreService.getConsumedSpaceOnDisk(image.imageIdentifier)
-
-                //accessible from cookie
-                def userEmail = AuthenticationUtils.getEmailAddress(request)
-                def userDetails = authService.getUserForEmailAddress(userEmail, true)
-                def userId = userDetails ? userDetails.id : ""
-
-                def isAdmin = false
-                if (userDetails){
-                    if (userDetails.getRoles().contains("ROLE_ADMIN"))
-                        isAdmin = true
-                }
+                getImageModel(image)
+            }
+        }
+    }
 
-                def thumbUrls = imageService.getAllThumbnailUrls(image.imageIdentifier)
+    private def getImageModel(Image image){
+        def subimages = Subimage.findAllByParentImage(image)*.subimage
+        def sizeOnDisk = imageStoreService.getConsumedSpaceOnDisk(image.imageIdentifier)
 
-                boolean isImage = imageService.isImageType(image)
+        //accessible from cookie
+        def userEmail = AuthenticationUtils.getEmailAddress(request)
+        def userDetails = authService.getUserForEmailAddress(userEmail, true)
+        def userId = userDetails ? userDetails.id : ""
 
-                //add additional metadata
-                def resourceLevel = collectoryService.getResourceLevelMetadata(image.dataResourceUid)
+        def isAdmin = false
+        if (userDetails){
+            if (userDetails.getRoles().contains("ROLE_ADMIN"))
+                isAdmin = true
+        }
 
-                if (grailsApplication.config.analytics.trackDetailedView.toBoolean()) {
-                    sendAnalytics(image, 'imagedetailedview')
-                }
+        if (!userId){
+            userId =  authService.getUserId()
+        }
 
-                [imageInstance: image, subimages: subimages, sizeOnDisk: sizeOnDisk,
-                 squareThumbs: thumbUrls, isImage: isImage, resourceLevel: resourceLevel, isAdmin:isAdmin, userId:userId]
-            }
+        def thumbUrls = imageService.getAllThumbnailUrls(image.imageIdentifier)
+
+        boolean isImage = imageService.isImageType(image)
+
+        //add additional metadata
+        def resourceLevel = collectoryService.getResourceLevelMetadata(image.dataResourceUid)
+
+        if (grailsApplication.config.analytics.trackDetailedView.toBoolean()) {
+            sendAnalytics(image, 'imagedetailedview')
         }
+
+        [imageInstance: image, subimages: subimages,
+         parentImage: image.parent,
+         sizeOnDisk: sizeOnDisk,
+         squareThumbs: thumbUrls, isImage: isImage, resourceLevel: resourceLevel, isAdmin:isAdmin, userId:userId]
     }
 
     def view() {
@@ -450,6 +460,12 @@ class ImageController {
         [imageInstance: imageInstance, metaData: metaData?.sort { it.name }, source: source]
     }
 
+    def coreImageMetadataTableFragment() {
+        def imageInstance = imageService.getImageFromParams(params)
+
+        render(view: '_coreImageMetadataFragment', model: getImageModel(imageInstance))
+    }
+
     def imageTooltipFragment() {
         def imageInstance = imageService.getImageFromParams(params)
         [imageInstance: imageInstance]