DigiVol Release 6.1.11

 - DG-87, DG-142 (#471) Fixed issue where image dimensions were being misred
 - DG-96 Fixed error with Elastic Search throwing errors when attempting to query more than 10000 user transcriptions
 - DG-82 Updated user notebook to display map pins for user transcriptions with analog geo coordinates
 - DG-144 Fixed broken link for Admin user list
 - DG-131 Fixed search bar in main top menu bar
 - DG-66, DG-67 (#530) Fixed issue with 'See Similar Expeditions' button on finished expedition displaying no results
 - DG-90 (#518) Fixed broken images in Wildlife Spotter expeditions
 - DG-70 (#577) Updated expedition list summary cards to display short description instead of long description truncated
 - DG-94 Added a character counter to short description field in expedition settings
 - DG-146 Removed view button/link from user's notebook

Author: cdausmus

.travis.yml

@@ -7,6 +7,7 @@ branches:
   only:
   - master
   - develop
+  - qa
   - /^feature\/.*$/
   - /^hotfix\/.*$/
 services:

build.gradle

@@ -24,7 +24,7 @@ plugins {
     id "com.github.erdi.webdriver-binaries" version "3.2"
 }
 
-version "6.1.10"
+version "6.1.11"
 group "au.org.ala"
 description "Digivol application"
 
@@ -161,7 +161,7 @@ dependencies {
     implementation 'com.github.ben-manes.caffeine:caffeine:3.1.3' // old: 2.8.0
     implementation 'org.apache.commons:commons-compress:1.11'
     implementation 'org.apache.commons:commons-pool2:2.11.1' // old: 2.4.2
-    implementation group: 'commons-io', name: 'commons-io', version: '2.11.0' //''2.5'
+    implementation group: 'commons-io', name: 'commons-io', version: '2.17.0' //''2.5'
     implementation 'org.elasticsearch:elasticsearch:2.4.6'
     // optional for elastic search, version should match elastic search optional dep
     implementation group: 'org.apache.lucene', name: 'lucene-expressions', version: '4.9.1' //6.0.0 for ES 5.0, 8.11.1 for ES 7.17

grails-app/assets/javascripts/digivol-notebook.js

@@ -69,10 +69,16 @@ var notebook = {
      * @param id
      */
     function load_content(marker, id) {
+      const taskViewUrl = $('#map').attr('taskview-url');
       $.ajax($('#map').attr('infowindow-url') + "/" + id).done(function(data) {
         var content =
-          "<div style='font-size:12px;line-height:1.3em;'>Catalogue No.: " + data.cat + "<br/>Taxon: " + data.name + "<br/>Transcribed by: " + data.transcriber +
-          "</div>";
+            "<div style='font-size:12px;line-height:1.3em;'>" +
+            "Task: " + id +
+            "<br />File: ";
+        if (taskViewUrl !== "") content += "<a href=\"" + taskViewUrl + "/" + id + "\" target=\"_blank\">" + data.filename + "</a>";
+        else content += data.filename;
+        if (data.name !== "" && data.name !== undefined && data.name !== null) content += "<br />Taxon: " + data.name
+        content += "</div>";
         notebook.infowindow.close();
         notebook.infowindow.setContent(content);
         notebook.infowindow.open(notebook.map, marker);

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

@@ -2,6 +2,7 @@ package au.org.ala.volunteer
 
 import grails.converters.JSON
 import org.apache.catalina.connector.ClientAbortException
+import org.apache.commons.io.FilenameUtils
 
 import javax.imageio.ImageIO
 
@@ -27,8 +28,17 @@ class ImageController {
 
         format = format.toLowerCase()
         if (!FORMATS.contains(format)) {
-            render([error: "${format} not supported"] as JSON, status: SC_BAD_REQUEST)
-            return
+            // Did the extension get screwed up? Check if the file does exist:
+            File fileCheck = findImage(encodedPrefix, encodedName)
+            if (fileCheck) {
+                // Image is there with a different extension.
+                log.debug("Found file under different file extension (or broken input): ${fileCheck.name}")
+                format = FilenameUtils.getExtension(fileCheck.name)?.toLowerCase()
+            } else {
+                log.debug("No file found with supported extension: ${encodedName}.${format}")
+                render([error: "${format} not supported"] as JSON, status: SC_BAD_REQUEST)
+                return
+            }
         }
 
         if (width < 0 || width >  MAX_WIDTH || height < 0 || height > MAX_HEIGHT) {

grails-app/controllers/au/org/ala/volunteer/ProjectController.groovy

@@ -801,6 +801,14 @@ class ProjectController {
                             return false
                         }
                     }
+
+                    if (params.shortDescription) {
+                        if (params.shortDescription.toString().length() > 500) {
+                            project.errors.rejectValue("shortDescription", "project.shortdescription.toolarge",
+                                    "Short Description is too long.")
+                            return false
+                        }
+                    }
                 }
 
                 bindData(project, params)

grails-app/controllers/au/org/ala/volunteer/UserController.groovy

@@ -1,12 +1,15 @@
 package au.org.ala.volunteer
 
 import com.google.common.base.Stopwatch
+import com.google.common.base.Strings
 import grails.converters.JSON
 import grails.gorm.transactions.Transactional
 import org.elasticsearch.action.search.SearchResponse
 import org.elasticsearch.action.search.SearchType
 import org.springframework.dao.DataIntegrityViolationException
 
+import java.util.regex.Pattern
+
 import static org.springframework.http.HttpStatus.NO_CONTENT
 
 class UserController {
@@ -387,7 +390,8 @@ class UserController {
         if (!user) {
             flash.message = message(code: 'default.not.found.message',
                      args: [message(code: 'user.label', default: 'User'), params.id]) as String
-            redirect(action: "list")
+            redirect(action: "adminList")
+            return
         }
 
         def roles = UserRole.findAllByUser(user)
@@ -470,7 +474,7 @@ class UserController {
         else {
             flash.message = message(code: 'default.not.found.message',
                      args: [message(code: 'user.label', default: 'User'), params.id]) as String
-            redirect(action: "list")
+            redirect(action: "adminList")
         }
     }
 
@@ -488,7 +492,7 @@ class UserController {
                 user.delete(flush: true)
                 flash.message = message(code: 'default.deleted.message',
                          args: [message(code: 'user.label', default: 'User'), params.id]) as String
-                redirect(action: "list")
+                redirect(action: "adminList")
             } catch (DataIntegrityViolationException e) {
                 String message = message(code: 'default.not.deleted.message',
                           args: [message(code: 'user.label', default: 'User'), params.id]) as String
@@ -499,7 +503,7 @@ class UserController {
         } else {
             flash.message = message(code: 'default.not.found.message',
                      args: [message(code: 'user.label', default: 'User'), params.id]) as String
-            redirect(action: "list")
+            redirect(action: "adminList")
         }
     }
 
@@ -618,40 +622,74 @@ class UserController {
         log.debug("ajaxGetPoints| Transcription.countByFullyTranscribedBy(): ${sw.toString()}")
         sw.reset().start()
 
-        final query = """{
-  "constant_score": {
-    "filter": {
-      "and": [
-        { "term": { "transcriptions.fullyTranscribedBy": "${userInstance.userId}" } },
-        { "nested" :
-          {
-            "path" : "fields",
-            "filter" : { "term" : { "name": "decimalLongitude"}}
-          }
-        },
-        { "nested" :
-          {
-            "path" : "fields",
-            "filter" : { "term" : { "name": "decimalLongitude"}}
-          }
+        final query = """
+{
+    "query": {
+        "bool": {
+            "must": [
+                {
+                    "term": { 
+                        "transcriptions.fullyTranscribedBy": "${userInstance.userId}" 
+                    }
+                },
+                {
+                    "term": { 
+                        "fields.name": "decimalLongitude" 
+                    }
+                },
+                {
+                    "term": { 
+                        "fields.name": "decimalLatitude" 
+                    }
+                }
+            ]
         }
-      ]
     }
-  }
 }"""
-
-        def searchResponse = fullTextIndexService.rawSearch(query, SearchType.QUERY_THEN_FETCH, taskCount.intValue(), fullTextIndexService.rawResponse)
+        // Elastic Search max value.
+        final int MAX_SEARCH = 10000
+        def searchResponse = fullTextIndexService.rawSearch(query, SearchType.QUERY_THEN_FETCH, MAX_SEARCH, fullTextIndexService.rawResponse)
         sw.stop()
         log.debug("ajaxGetPoints| fullTextIndexService.rawSearch(): ${sw.toString()}")
         sw.reset().start()
 
+        // Regex for detecting traditional latitude/longitude. We will convert to decimal for Google Maps.
+        def regex = Pattern.compile(/(((\d+)°)?)(((\d+)')?)(((\d+)")?)([NnSsEeWw])/)
+
         def data = searchResponse.hits.hits.collect { hit ->
             def field = hit.source['fields']
 
             def pt = field.findAll { value ->
                 value['name'] == 'decimalLongitude' || value['name'] == 'decimalLatitude'
             }.collectEntries { value ->
-                def dVal = value['value']
+                def dVal = value['value'] as String
+                log.debug("ajaxGetPoints| dVal: ${dVal}")
+
+                def matcher = regex.matcher(dVal)
+                if (matcher.find()) {
+                    log.debug("ajaxGetPoints| Group count: ${matcher.groupCount()}")
+                    for (int i = 0; i <= matcher.groupCount(); i++) {
+                        log.debug("match[${i}]: ${matcher.group(i)}")
+                    }
+                    try {
+                        BigDecimal minutes = (getBigDecimalFromString(matcher.group(6).toString()) / new BigDecimal(60))
+                        BigDecimal seconds = (getBigDecimalFromString(matcher.group(9).toString()) / new BigDecimal(3600))
+                        BigDecimal degrees = getBigDecimalFromString(matcher.group(3).toString())
+                        log.debug("Conversion: degrees: [${degrees}], minutes: [${minutes}], seconds: [${seconds}]")
+                        degrees += (minutes + seconds)
+
+                        // Check direction and assign negative if necessary
+                        if (matcher.group(10).equalsIgnoreCase("S") ||
+                                matcher.group(10).equalsIgnoreCase("W")) {
+                            degrees = -degrees
+                        }
+
+                        dVal = degrees.toString()
+                        log.debug("dVal: ${dVal}")
+                    } catch (Exception e) {
+                        log.error("Error attempting to convert degrees, minutes and seconds to a decimal value ${dVal}, skipping.", e)
+                    }
+                }
 
                 if (value['name'] == 'decimalLongitude') {
                     [lng: dVal]
@@ -669,6 +707,19 @@ class UserController {
         render(data as JSON)
     }
 
+    /**
+     * Converts a string value to a BigDecimal, returning 0 if the value isn't parseable.
+     * @param input the value to convert
+     * @return a BigDecimal or 0 if null/empty.
+     */
+    def getBigDecimalFromString(String input) {
+        if (!Strings.isNullOrEmpty(input) && !input.equalsIgnoreCase("null")) {
+            return new BigDecimal(input.toInteger().intValue())
+        } else {
+            return new BigDecimal(0)
+        }
+    }
+
     def notebookMainFragment() {
         def user = User.get(params.int("id"))
         //def simpleTemplateEngine = new SimpleTemplateEngine()

grails-app/i18n/messages.properties

@@ -181,6 +181,7 @@ status.inactive=Inactive
 project.archived.description=Archived expeditions have all their task images removed.
 project.template.notcompatible=The selected template is not compatible with the expedition's type.
 project.template.notavailable=The template {0} is no longer available.
+project.shortdescription.toolarge=You have entered too many characters for the Short Description. It must not exceed 500 characters.
 project.institution.required=An institution is required.
 image.attribution.prefix=Image
 index.heading.line1=Decipher our collections,

grails-app/services/au/org/ala/volunteer/ProjectService.groovy

@@ -402,17 +402,20 @@ class ProjectService implements EventPublisher {
         // Default, if all else fails
         def iconImage = grailsLinkGenerator.resource(file:'/iconLabels.png')
         def iconLabel = 'Specimens'
+        def iconName = 'specimens'
 
         if (project.projectType) {
             iconImage = projectTypeService.getIconURL(project.projectType)
             iconLabel = project.projectType.label
+            iconName = project.projectType.name
         }
 
         // def volunteer = User.findAll("from User where userId in (select distinct fullyTranscribedBy from Task where project_id = ${project.id})")
 
         def ps = new ProjectSummary(project: project)
         ps.iconImage = iconImage
         ps.iconLabel = iconLabel
+        ps.iconName = iconName
 
         ps.taskCount = taskCount.toLong()
         ps.transcribedCount = transcribedCount.toLong()
@@ -540,7 +543,7 @@ class ProjectService implements EventPublisher {
             // #392 Add Project Type to the tag search (i.e. clicking on Project Type searches by 'tag')
             def tagSearch = []
             def labelJoinTable = context.select([PROJECT_LABELS.PROJECT_ID]).from(PROJECT_LABELS.leftJoin(LABEL).on(PROJECT_LABELS.LABEL_ID.eq(LABEL.ID))).where(LABEL.VALUE.in(tag))
-            def typeJoinTable = context.select([PROJECT.ID]).from(PROJECT.leftJoin(PROJECT_TYPE).on(PROJECT.PROJECT_TYPE_ID.eq(PROJECT_TYPE.ID))).where(PROJECT_TYPE.LABEL.in(tag))
+            def typeJoinTable = context.select([PROJECT.ID]).from(PROJECT.leftJoin(PROJECT_TYPE).on(PROJECT.PROJECT_TYPE_ID.eq(PROJECT_TYPE.ID))).where(PROJECT_TYPE.NAME.in(tag))
 
             tagSearch.add(PROJECT.ID.in(labelJoinTable))
             tagSearch.add(PROJECT.ID.in(typeJoinTable))
@@ -580,7 +583,7 @@ class ProjectService implements EventPublisher {
                 sortCondition = jNvl(INSTITUTION.NAME, PROJECT.FEATURED_OWNER)
                 break
             case 'type':
-                sortCondition = PROJECT_TYPE.LABEL
+                sortCondition = PROJECT_TYPE.NAME
                 break
             default:
                 sortCondition = jLower(PROJECT.FEATURED_LABEL)

grails-app/services/au/org/ala/volunteer/TaskService.groovy

@@ -899,8 +899,12 @@ ORDER BY record_idx, name;
             fileMap.dir = dir.absolutePath
             def file = new File(dir, filename)
             file << conn.inputStream
-            fileMap.raw = file.name
-            fileMap.localPath = file.getAbsolutePath()
+
+            File processedFile = new File(dir, filename)
+            boolean result = ImageUtils.reorientImage(file, processedFile)
+
+            fileMap.raw = processedFile.name
+            fileMap.localPath = processedFile.getAbsolutePath()
             fileMap.localUrlPrefix = urlPrefix + "${projectId}/${taskId}/${multimediaId}/"
             fileMap.contentType = conn.contentType
             return fileMap
@@ -1486,6 +1490,7 @@ ORDER BY record_idx, name;
                 [ id: row.id,
                   externalIdentifier: row.external_identifier,
                   isFullyTranscribed: row.is_fully_transcribed,
+                  fullyTranscribedBy: row.fully_transcribed_by,
                   //fullyValidatedBy: row.validator_display_name,
                   projectId: row.project_id,
                   institutionId: row.institution_id,

grails-app/taglib/au/org/ala/volunteer/VolunteerTagLib.groovy

@@ -1059,17 +1059,17 @@ class VolunteerTagLib {
     def truncate = { attrs, body ->
         final ELLIPSIS = attrs.ellipse ?: '…'
         def maxLength = attrs.maxlength
-        final bodyText = body().replaceAll("<[^>]*>", '') // strip out html tags
+        final bodyText = body().replaceAll("<[^>]*>", '').trim() // strip out html tags and white space
 
         if (maxLength == null || !maxLength.isInteger() || maxLength.toInteger() <= 0) {
-            throw new Exception("The attribute 'maxlength' must an integer greater than 3. Provided value: $maxLength")
+            throw new Exception("The attribute 'maxlength' must be an integer greater than 3. Provided value: $maxLength")
         } else {
             maxLength = maxLength.toInteger()
         }
         if (maxLength <= ELLIPSIS.size()) {
             throw new Exception("The attribute 'maxlength' must be greater than 3. Provided value: $maxLength")
         }
-        if (bodyText.length() > maxLength) {
+        if ((bodyText.length() + (ELLIPSIS.size() + 1)) > maxLength) {
             out << bodyText[0..maxLength - (ELLIPSIS.size() + 1)] + ELLIPSIS
         } else {
             out << bodyText