Past News

2017-08-16

Check out the newest Wildbook: Giraffespotter. Giraffespotter might be our best looking Wildbook yet and represents a consortium of collaborative researchers studying endangered giraffes in Africa.

2017-07-27

Check out our video on National Geographic's Chasing Genius challenge: http://www.natgeochasinggenius.com/video/645

2017-07-22

Wildbook 7.0 development has kicked off, including a new computer vision API for multiple algorithms, a new data curation interface, and new data structures for tracking effort.

2016-07-22

Wildbook 6.0 beta testing has begun. We anticipate an August release. Flukebook.org is featuring the new code, which will also be migrated to other Wildbooks quickly. Wildbook 6 merges the IBEIS.org and Wildbook.org projects into a single project re-using the name “Wildbook”!

2016-05-21

Check out the new humpback fluke matcher developed with Wildbook under the IBEIS.org project! This is one of two matchers we have coming out.

2016-04-02

Wildbook 5.5 has been released!

New features and fixes in Wildbook 5.5 include:

  • MOD: Standardization of PostgreSQL as the required database for Wildbook and removal of Derby and other database support. While Wildbook can technically support a wide array of databases and J2EE servers, we're standardizing on Tomcat and PostgreSQL for Wildbook 5.5 and all versions moving forward. We are also now highly recommending running Wildbook on Ubuntu Linux servers in Amazon's EC2 service. This also means that PostgreSQL must be installed and preconfigured for Wildbook to run.
  • MOD: JavaScript library dependency reductions.
  • FIX/MOD: Broad database connection improvements and fixes to better manage and close multiple database threads under higher usage.
  • FIX: Switch to full support of Encounter.individualID as NULL (upgrade fix script required for previous Wildbooks)
  • NEW: Make Google Map on main landing page (index.jsp) fully responsive for better mobile display
  • MOD: Remove automatic date filtering on Encounter Search default display
  • FIX: Better exception handling in spot matching grid
  • FIX: Make email templates more generic (remove project-specific branding) for reuse across projects
  • MOD: Persistence layer upgrade to DataNucleus 4.2
  • FIX: Improve sub-object REST/JSON display for typed Collections
  • NEW: Google reCAPTCHA integrated to prevent spurious data submission (upgrade requires getting Google key for your web site)
  • MOD: Switch to wildbook_data_dir as default data directory (check your configuration on upgrade)
  • MOD: change default username and password for database connections (now wildbook/wildbook)
  • MOD: Set logging directory relative to POM artifact to help prevent startup log errors
  • NEW: Add alternateID support for top bar Site Search of MarkedIndividuals
  • MOD: Better Java collection typing (MantaMatcher code contribution from Giles Winstanley)
  • FIX: Many minor HTML and CSS fixes

2016-02-22

We're testing Wildbook 5.5 even while Wildbook 6.0 development under IBEIS.org is under way.

New features and fixes in Wildbook 5.5 will include:

  • FIX: Switch to full support of Encounter.individualID as NULL (upgrade fix script required)
  • NEW: Make Google Map on main landing page (index.jsp) fully responsive for better mobile display
  • MOD: Remove automatic date filtering on Encounter Search default display
  • FIX: Better exception handling in spot matching grid
  • FIX: Prevent open database connections after login
  • FIX: Make email templates more generic (remove project-specific branding) for reuse across projects
  • MOD: Persistence layer upgrade to DataNucleus 4.2
  • FIX: Improve sub-object REST/JSON display for Collections
  • NEW: Google reCAPTCHA integrated to prevent spurious data submission (upgrade requires getting Google key for your web site)
  • MOD: Switch to wildbook_data_dir as default data directory (check your configuration on upgrade)
  • MOD: Set logging directory relative to POM artifact to help prevent startup log errors
  • NEW: Add alternateID support for top bat Site Search of MarkedIndividuals
  • MOD: Better collection typing (MantaMatcher code contribution from Giles Winstanley)
  • FIX: Many minor HTML and CSS fixes

2015-09-01

We are pleased to announce a complete visual redesign and new version of Wildbook: v5.4!

New features and fixes:

  • NEW: Modify emailing system to support: HTML template, localization, project-specific overrides
  • MOD: Prevent spurious future date submissions
  • NEW: Password reset
  • FIX: Remove keyword from all media before deleting Keyword object
  • FIX: Reset measurement values did not work
  • NEW: OAuth sign in (Facebook, FLickr, etc.)
  • NEW: OAuth image upload from social media (Flickr, Facebook, etc.)
  • NEW: Spot matching client performance improvement under the Amazon EC2 grid
  • NEW: Componentization of Encounter Search Analysis for reuse as an embeddedable component
    • Embed on My Account page for user-specific details (done)
  • FIX: Fixed bug preventing backup of deleted encounters, and improved reporting in event of failure.
  • NEW: HTML5 responsive design!
  • NEW: typeahead in the search bar for Individual IDs and Location IDs

News

2015-08-04

Wildbook is getting a fancy, new responsive design! Check out the first site to use it in the upcoming Wildbook 5.4 version: MantaMatcher

2015-04-04

We are pleased to release Wildbook 5.3.0 with the following new fixes and features!

  • FIX: Encounter Search title on haplotype map
  • FIX: Biological samples not showing in encounter.jsp and individuals.jsp
  • NEW: Better stream closing on EXIF data loading for images
  • NEW: Significant performance improvement in image thumbnail display in Encounter Search
  • NEW: Add assigned user filter to Individual Search and set alpha sort order
  • FIX: Encounters menu did not expand on mobile devices
  • NEW: Spot mapping is now performed in the browser!
  • NEW: Support context-based data access through REST data interface

2015-01-29

We released Wildbook 5.2.0 today with the following changes:

  • NEW: Upgrade to DataNucleus 4.0.3
  • FIX: Encounter.dateInMilliseconds off by one hour for Encounters with no date specified, shifting their position in search results back one day
  • FIX: Minor map display zoom and bad data filtering improvements
  • FIX: UUID switch broke reference image comparison in Encounter Search
  • MOD: Improved support to handle valuable but poorly formatted Dates in EncounterForm
  • FIX: Individual new/previous sighting bar chart in Individual Search showing inconsistent values
  • FIX: Date-based search results had variable behavior with results who days exceeded month boundaries
  • FIX: UpdateEmailAddress threw an NPE after a bad merge
  • NEW: 20% speed improvement in Individual Search mapping through gzip compression of GeoJSON results
  • MOD: Allow for null values in Encounter.dateInMilliseconds
  • NEW: Encounter Search filter by date submitted (not date of actual sighting)
  • NEW: Encounter Search Analysis tab: new charts and metrics
    • Bar chart of encounter totals by year submitted
    • Bar chart of total encounters by submission year
    • Pie chart of Encounters by workflow state
    • Additional calculated values (#submitters, # represented marked individuals, etc.)
  • NEW: Encounter Search filter by strings in the Encounter additional comments
  • NEW: REST interface improvements - Part 1 - add new read-only /api REST URL with capability for custom behavior hooks
  • NEW: Convert JSP-based UI to HTML5 and REST/JSON - Part 1
    • NEW: Convert Encounter Search table tab to JSON-based, filterable, sortable JavaScript table
    • NEW: Convert individuals.jsp Encounter list for a marked individual to a sortable table
    • NEW: Convert Individual Search table tab to JSON-based, filterable, sortable JavaScript table
  • FIX: L10N ongoing cleanup of untranslated stragglers

2015-01-25

Happy 2015! Wildbook 5.2 is up on whaleshark.org for testing. All of the code is done, and much of it has already been tested in a production environment. We should have a full release in less than a week!

2014-10-23

We released Wildbook 5.1.0 today with the following changes:

  • FIX: allow data submission if user has cookies disabled
  • MOD: updated the JPEG metadata reader software and centralize the EXIF data reading and display function (done)
    • UPGRADE: XMP and metadata-extractor JAR files need to be added/upgraded
  • MOD: More elegant error handling in resetThumbnail.jsp
  • FIX: support for custom measurement types was lost in the 5.0 upgrade.
  • FIX: “View all sharks” text still appearing in some locations
  • MOD: Switch Encounter.date and Encounter.releaseDate to calendar selector
    • Do not allow future date submissions
    • Preserve existing date value in selector when setting\editing date and release date
  • MOD: Improve file name character filtering
  • FIX: Remove the unused commonConfiguration.properties administration form
  • NEW: Silo security (BETA) (Flukebook)
  • NEW: ImageMajick support for more efficient processing of images outside of the Java JVM
  • MOD: Remove Struts 1 code to reduce risk of DOS attacks
    • UPGRADE: Remove Struts JARs and XML config files in WEB-INF

2014-10-23

We released Wildbook 5.1.0 today with the following changes:

  • FIX: allow data submission if user has cookies disabled
  • MOD: updated the JPEG metadata reader software and centralize the EXIF data reading and display function (done)
    • UPGRADE: XMP and metadata-extractor JAR files need to be added/upgraded
  • MOD: More elegant error handling in resetThumbnail.jsp
  • FIX: support for custom measurement types was lost in the 5.0 upgrade.
  • FIX: “View all sharks” text still appearing in some locations
  • MOD: Switch Encounter.date and Encounter.releaseDate to calendar selector
    • Do not allow future date submissions
    • Preserve existing date value in selector when setting\editing date and release date
  • MOD: Improve file name character filtering
  • FIX: Remove the unused commonConfiguration.properties administration form
  • NEW: Silo security (BETA) (Flukebook)
  • NEW: ImageMajick support for more efficient processing of images outside of the Java JVM
  • MOD: Remove Struts 1 code to reduce risk of DOS attacks
    • UPGRADE: Remove Struts JARs and XML config files in WEB-INF

2014-08-17

We released Wildbook 5.0.5 today with the following changes:

  • FIX: restore UTF-8 support in Encounter submission
  • FIX: Set MarkedIndividual.haplotype in SRGD import
  • FIX: Data submission only worked for context0
  • FIX: Duplicate messaging in confirmSubmit.jsp

2014-08-06

We released Wildbook 5.0.4 today with the following changes:

  • FIX: individuals.jsp displayed a broken link “View all encounters” when no match could be found. Links were switched to prompt the use to try the more advanced Encounter and Individual searches
  • FIX: List supported versions for GridClient to Java 7
  • FIX: Location ID not set from submitActionClass.properties in EncounterForm submission.
  • FIX: Switch from File.mkdir() to File.mkdirs() across multiple files to fix servlet issues resulting from the change to underlying directory GUID-based structures
  • FIX: EXIF data loading for images was broken by new GUID Encounter numbering and image storage
  • MOD: Minor additional L10N work

2014-07-07

We released Wildbook 5.0.3 today with the following changes:

  • FIX: occurrence.jsp would not display due to bad Java logic
  • MOD: The Wildbook version number has been moved to the top bar of the application and centralized in the file contexts.properties. This allows for clearer display of the version and a link for others to follow to learn more about Wildbook.

2014-06-24

We released Wildbook 5.0.2 today with the following changes:

  • FIX: confirmSubmit.jsp would display a blank page if an Encounter was submitted without an image. No data was lost however.
  • NEW: scanTaskAdmin.jsp now defaults to showing only the current user grid tasks but allows the user to expand the list to see all in the queue.
  • FIX: individualMapEmbed.jsp mixed JavaScript and JSP code, causing maps not to display in individuals.jsp

2014-06-15

Wildbook 5.0 is released! And we couldn't be happier. That was a big release, bringing some much needed cloud-scale improvements to Wildbook. New features include:

  • FIX: Fix the Wildbook link in header.jsp
  • MOD: Handle null values in Encounter.informOthers
  • FIX: Adjust CSS used in servletResponseTemplate.htm
  • FIX: Do not allow “View My Submissions” access before login.
  • FIX: Github.com Issue #44 Fix: JDO exception in Individual Search when patterning code is one of multiple parameter selections
  • FIX: Github.com Issue #36 Fix: Enounters → View Images does not increment with Next and Previous buttons
  • NEW: Part 2: Create ShepherdResourceBundles for localization out of shepherd_data_dir, applying this to all .properties file references
    • Upgrade: move all .properties files to shepherd_data_dir (or project equivalent)
  • NEW: Multi-project support in a single Wildbook (GeneGIS)
    • Upgrade: all Role objects need a context=context0 assigned
  • MOD: Move “Find record” field from main page to top bar for global accessibility
  • FIX: Prevent duplicate addition of the same Encounter in MarkedIndividual and Occurrence objects
  • NEW: L10N consolidation part 1: centralize language determination and apply across JSP files.
  • NEW: Support HTTP Basic Authentication to secure the REST URL by default.
  • NEW: Change your own password (EMAIL PLUS SERVLET) for users with login privileges
  • MOD: Finish branding and make more generic the Inerconnect and Grid Client apps bundled inside Wildbook
  • NEW: Add User filtering to Encounter Search and the related pie chart to the results
  • NEW: RESTful API documentation
  • MOD: When editing Contact info, populate the form with the existing data
  • MOD: Make minimum supported Java version 1.7
  • MOD: Upgrade unit testing framework version
  • NEW: TEST Tomcat 8 support
  • FIX: SinglePhotoVideo.correspondingUsername not being correctly populated
  • MOD: Change Encounter.releaseDate to long data type for broader database compatibility
    • Upgrade: migrate from Encounter.releaseDate to Encounter.releaseDateLong
  • NEW: Default SQL Server and SQL Azure support
  • MOD: Upgrade to latest DataNucleus 3.x components
    • Upgrade: new datanucleus JAR files
  • NEW: Storytelling part 1: backend data persistence to support Wild Me Facebook app
  • MOD: Support null values for Encounter.sex and MarkedIndividual.sex
  • NEW: Release with default Spanish L10N
  • NEW: Drag-n-drop image upload via JavaScript (Flukebook)
  • FIX: Individual Search filter on having photos does not work

2014-05-26

We are wrapping up development on Wildbook 5.0! Only one new feature remains: drag and drop image upload. In the mean time, we are testing for quality by running the latest code on our production sites, such as whaleshark.org and flukebook.org. Feature development should wrap up this month with the release occurring in the first week of June.

2014-04-14

We are trying out of some the early feature of Wildbook 5 on http://www.whaleshark.org and http://www.splashcatalog.org/mmuwildbook. On the MMU Wildbook site, check out the multi-project pulldown menu, allowing one Wildbook to serve as the security and data hub for multiple independent projects and their distinct databases. This provides not only a more efficient software architecture to administer and upgrade, but it also supports higher level analyses of projects and coordinated security.

2014-03-09

We are pleased to release Wildbook 4.1.0! This new, large release includes the following features and fixes:

  • NEW: User agreement acceptance via popup at first login (Flukebook/mantamatcher.org request)
  • FIX: Don't display User profile images in Thumbnail Search Results
  • FIX: Searching by user misses usernames with Capitalization
  • NEW: alternateID search behavior in Encounter Search and Individual Search should support partial String matching
  • FIX: Individual Search needs to match on MarkedIndividual.alternateID fragments (CaribWHALE)
  • MOD: Individual Search: improve performance by switching to AJAX and GeoJSON
    • UPGRADE: Need to populate haplotype in existing MarkedIndividual objects
  • NEW: Add multi-species map aspect to Individual Search mapped results
  • NEW: Allow for GeoJSON export from Individual Search
  • NEW: Wild Me integration with on/off configuration
  • NEW: Add MarkedIndividual.timeOfBirth and Individual Search searchability
  • NEW: Add MarkedIndividual.timeOfDeath and Individual Search searchability
  • FIX: Related occurrences not showing for a MarkedIndividual in individuals.jsp
  • NEW: Relationship and Community support (GeneGIS request)
  • NEW: Community search function for Individual Search
  • NEW: Social role search function for Individual Search
  • FIX: Memory leak on missing images when EXIF data read is attempted
  • FIX: Extend CSS styling to servlet template
  • NEW: Kin Select tool (GeneGIS)
  • FIX: prevent the use of special characters (e.g., '#' and '&') in individual IDs, occurrence IDs, and social unit names
  • MOD: Switch Facebook “Like” link to a “Share” link with populated Open Graph metadata
  • NEW: Kinalyzer (http://kinalyzer.cs.uic.edu/index.html) format export from Individual Search.
  • NEW: Individual Search support for matching on one or more MarkedIndividual.individualID values
  • NEW: Encounter Search support for matching on one or more Encounter.individualID values
  • FIX: Support redirect to original URL request after required login, allowing for User Agreement Acceptance interception.
  • NEW: SocialUnit field export for SOCPROG
  • FIX: Removed remaining references to StyledMarker.js, which no longer worked with newer Google Maps developments

2014-02-27

We are pleased to announce the availability of a Wildbook demo web site at: http://www.wildbookdna.org.demo

Please email “jason [at] whaleshark [dot] org” to receive access to the demo site, on which we will maintain the latest released version of Wildbook.

2014-02-20

Wildbook 4.1.0 turned into a very large release! We are currently testing it in three active server environments, including whaleshark.org. Release is scheduled for 2-28-2014.

2014-02-11

We are almost done with Wildbook 4.1 development and testing has been ongoing. Check out our Roadmap for more information about the upcoming features.

2013-12-15

We are about half way through Wildbook 4.1 development. This next release should arrive in February 2014. Check out our Roadmap for more information about upcoming features.

2013-11-15

We released a patch release: 4.0.4. This includes some small but important new features and some critical fixes for some export formats. New features and fixes include:

  • NEW: individualSearchResults.jsp performance improvement
  • MOD: Email notification of Users needs to be based on username and not raw email addresses
  • FIX: SOCPROG, CAPTURE, and MARK exports did not receive all URL parameters for filtering
  • NEW: Add a Discovery Curve to the Encounter Search results Analysis tab
  • NEW: Analysis tab of Encounter Search: Show weekly summation of Encounters to help visualize seasonality

In this release, we are especially proud of the new Discovery Curve and Weekly Seasonality charts added to the Encounter Search Analysis tab.

2013-11-3

Hot on the heels of the last release, version 4.1.0 development has begun! This new version will include new feature requests from MantaMatcher, CaribWhale, and geneGIS, plus a lot of administrative improvement and some of our own innovations, such as the dispaly of Discovery Curves. Check out the Roadmap for more information!

2013-11-1

Version 4.0.3 has been released. Critical critical fixes and new features in this release include:

  • MOD: Adding a spot pattern should then redirect you to the bottom of the encounter.jsp page where the pattern is displayed (whaleshark.org request)
  • MOD: offset data display in encounter.jsp with alternating background colors to better show groupings of data and make the page easier on the eye
  • NEW: add Encounter.locationID to submission form (mantamatcher.org request)
  • FIX: OBIS export (after encounter search) show incorrect Scientific Name in downloaded data. (mantamatcher.org request)
  • NEW: Expose Encounter.patterningCode for manual editing and configure in commonConfiguration.properties (mantamatcher.org request)
  • NEW: provide numeric summary of number of users on users.jsp page
  • MOD: Do not all removal of email address without first asking the user to confirm in a JSP (Georgia Aquarium request)

2013-10-30

Wildbook 4.0.3 testing has been extended to mantamatcher.org and apodstrandings.org. So far, everything is testing well. We antiticpate a release on 11/1.

2013-10-24

Wildbook 4.0.3 is code complete and in testing on whaleshark.org. It should be released in 1-2 weeks. We will also be testing it on mantamatcher.org before release.

2013-9-27

Version 4.0.2 has been released. Critical fixes in this release include:

  • FIX: Fix the “Learn More” links that have become broken as a result of the switch to Wildbook branding.
  • FIX: Fix query memory leaks
  • FIX: Null query string handling in Individual Search results pages
  • FIX: MarkedIndividual.maxYearsBetweenResights not being reset when a related encounter's date is changed
  • FIX: More query memory leak areas in Shepherd class
  • MOD: Add JavaScript confirmation dialog box on delete of tissue sample and related genetic analyses
  • FIX: Allow for special characters in the tissue sample ID
  • FIX: TissueSampleSetMicrosatelliteMarkers servlet not protected
  • FIX: Locus object not being persisted due to bad datanucleus metadata

2013-9-15

Wildbook 4.0 has been released! It provides additional user management functions, more workflow and Encounter state configuration, and a LOT of UI improvements. New features and fixes in this release include:

  • FIX: Image-less adoption still shows broken thumbnail
  • MOD: Set GPS from map and allow for map selection of GPS in encounter.jsp
    • Only allow selection if the ?edit= param is set
    • Display note to public if no GPS is set rather than map. Logged in researchers should always have map option.
  • NEW: Allow for direct emailing of submitter(s) and photographer
  • NEW: Add User profile photo upload and display
  • NEW: Add User project name, statement, and URL fields
  • FIX: The Add Adoption link on encounterAdoptionEmbed.jsp is broken
  • MOD: Update the Encounter set assigned user form to be a <select> form element of existing User object accounts rather than an open text field capable of accepting any value
  • FIX: Encounter.occurrenceID not being set properly
  • NEW: Display detailed info and picture for assigned Encounter researcher
  • NEW: Add User.lastLogin data field
  • NEW: individuals.jsp - show all associated Users researching a MarkedIndividual through the Encounter association
  • FIX: IE10 image rendering fixes for publicly-displayed images
  • NEW: Allow project-specific haplotype color codes to be loaded from the shepherd_data_dir
  • MOD: Convert individuals.jsp forms to JQuery UI popup dialogs
  • MOD: Convert occurrence.jsp forms to JQuery UI popup dialogs
  • MOD: Convert encounter.jsp forms to JQuery UI popup dialogs
  • MOD: switch to icon from “edit” menu option in occurrence.jsp, individuals,jsp, and encounter.jsp
  • MOD: Modify Encounter menu to queue off Encounter.state options (GeneGIS)
  • NEW: Add species pie chart to Encounter Search analysis tab
  • NEW: Add country pie chart to Encounter Search analysis tab
  • MOD: Modify servlets to use Encounter.state options
  • NEW: Add “Are you sure…” popup dialogs to confirm execution of data deletion tasks and prevent accidental delete.
  • MOD: userStatement should be LONGVARCHAR
  • MOD: Remove allIndividuals.jsp and point menu at individualSearchResults.jsp (GeneGIS)
  • NEW: Rebrand to Wildbook (
  • FIX: Adjust CAPTURE format export to support online version
  • FIX: Fix TissueSample biomeasurement value getter

2013-8-13

Wildbook 4.0 is now being tested on whaleshark.org! This is a very big release addressing information organization, user management and display, and workflow. These changes set the stage for more powerful versions of Wildbook in the future! The release date for 4.0 is expected to be September 18!

2013-6-24

Wildbook 4.0 (renamed from “Shepherd Project”) development is well underway. We're looking for a mid-July release. This release will focus primarily on research user management, including visual cues to help the public learn more about which researchers are managing which data sets.

2013-6-5

Version 3.3.1 has been released. It provides critical security fixes to the Shepherd Project, refining some of is default security behavior after testing 3.3.0 with the new Apache Shiro security system.

  • FIX: Fix EncounterAddComment in encounter.jsp - was not working due to a parameter name change
  • MOD: Do not allow an admin user to delete their own account.
  • NEW: For spot pattern recognition grid, show which completed scans have been assigned to a marked individual (whaleshark.org request)
  • NEW: Allow for the dynamic reloading of commonConfiguration.properties through the Administration page and through the CommonConfiguration class
  • FIX: Provide an access denied“ error message rather than defaulting to an HTTP error code.
  • FIX: Remove lingering, hardcoded requirements for legacy roles

2013-5-31

Version 3.3.1 is being tested! See the Roadmap for more details about all of the features and fixes in the next version. Version 3.4 has now been designated as “4.0”.

2013-5-12

Shepherd Project 3.4 development has kicked off! See the Roadmap for more details about all of the features and fixes in the next version.

2013-5-12

We are pleased to announce the release of Wildbook 3.3.

Summary: Version 3.3 brings user account and role management, removing the need to externally manage these through tomcat-users.xml. We use Apache Shiro to ensure that we are using a quality security system. This new feature reduces the technical complexity of Wildbook and better supports collaborative research.

Features and fixes:

  • NEW: Add Occurrence_ID to SRGD export/import process (GeneGIS)
  • FIX: Fix Time_of_Day hours value in Encounter Search OBIS Excel export format
  • NEW: Bundle MySQL JDBC driver by default (GeneGIS)
  • FIX: encounters/reject.jsp has a non-functional Cancel button
  • FIX: Encounter Search, when selecting the “alive” checkbox, the summary statement still defines the query parameter as “dead”
  • FIX: minutes pulldown menu in submit.jsp has two :15 minutes options. One should be :20.
  • FIX: Do not link “Unassigned” from the table in occurrence.jsp
  • NEW: Integration of Apache Shiro for self-contained AAA security per project (GeneGIS)
  • FIX: Duplicate EncounterSetVerbatimEventDate mapping in web.xml
  • NEW: Support > = and < = operators for measurements and biomeasurements in Encounter Search and Individual Search (Chris Perkins request for white shark research)
  • NEW: Support AND and OR keyword filtering in Encounter Search and Individual Search (Chris Perkins request for white shark research)

2013-4-27

Code development for Wildbook 3.3 is done, and we're prepping for testing on whaleshark.org. This release allows for the internal management of user accounts, rather than configuring these externally in tomcat-users.xml. This is a big usability improvement and a decrease in the complexity of the software overall.

2013-4-4

We are pleased to announce the release of Wildbook version 3.2.0, which can be downloaded from our downloads page. The following new features, fixes, and modifications were made in 3.2 or in the bundled interim release of 3.1.0.

  • NEW: Simple data input format and importer (GeneGIS) - SRGD format
  • NEW: SRGD CSV file export via URL
  • MOD: Gracefully handle null for Encounter.verbatimLocality
  • NEW: Add alive/dead status search filter to Individual Search
  • NEW: DataNucleus 3.2.0 persistence layer upgrade
  • FIX: Change sex and haplotype Encounter Search mapping to workaround a Google Maps issue causing all points to be mapped with one color
  • MOD: Allow for multi-select of photo keyword attributes (MantaMatcher request)
  • NEW: add “has photo/video” option to Individual Search
  • NEW: “Remove All” function to clear out all data to prep for fresh import (GeneGIS)
  • FIX: occurence.jsp mapping showing linked Markedindividual sightings, even if only one encounter is assigned to occurrence
  • NEW: Simple mark-recapture export format from Individual Search
  • MOD: Modify front page “jump to” behavior to more clearly select encounter objects
  • NEW: Add sex and haplotype mapping to Individual Search mapped tab
  • FIX: Ensure encounter dir exists when using EncounterAddImage
  • FIX: Support photoless adoption submission
  • MOD: Move BioMeasurement search field
  • FIX: Remove legacy size measurement field from the calendar display
  • MOD: Further null value handling to support cleaner data imports from legacy projects
  • MOD: Improve null handling of Encounter information to support the import of legacy projects and their data
  • FIX: Search results handle no icon elegantly
  • FIX: Null exception handling improvements for CAPTURE export
  • NEW: Encounter Search: support search for unidentified encounters
  • FIX: Limit behavior field size in Encounter Search
  • NEW: Add behavior filter option to Individual Search - it is date/location dependent
  • MOD: Standardize maximum media upload file size across upload servlets and define its value in commonConfiguration.properties
  • NEW: Support Encounter.country, including submission, editing, and searching capabilities. On/off should also be set through commonConfiguration.properties
  • NEW: Add Encounter Search filter on biological sample ID to provide direct addressability of tissue samples
  • MOD: Limit Fst to four sig. figures
  • NEW: Add documentation link to the base menu
  • NEW: Add connectivity displays to the maps of the Mapped Results of the Individual Search

2013-04-01

Wildbook 3.2 development work is complete, and it is currently being tested on whaleshark.org and other sites before release. Check out the Roadmap for more details.

2013-2-26

Wildbook 3.1 development work is complete, and it is currently being tested on whaleshark.org and other sites before release. Version 3.2 development kicks off tomorrow.

2013-1-18

Wildbook 3.1 development is back in full swing. We're aiming for an end of January release in whaleshark.org and a mid-February release for all projects.

2012-12-16

Check out our new Wildbook installation video for Windows.

Wildbook Installation Video (Windows, 13 minutes)

2012-11-29

We are pleased to announce the release of Wildbook 3.0.2. This release primarily addresses bugs in Google Maps 3.10 that affect mapping.

  • MOD: Upgrade to GeoTools 8.3 and add x,y coordinates to the shapefile attributes table on GIS shapefile export
  • MOD: Refactor andLocationIDs option in IndividualSearch to replace the OR pretty print message
  • MOD: Move mapping above notes in individuals.jsp
  • MOD: Move custom imports above log in encounter.jsp
  • FIX: Fix Google Maps references to use maps v 3.9. In 3.10, all markers take the color of the last defined marker.

2012-11-16 We released Wildbook 3.0.1 with the following changes:

  • FIX: don't allow Google Maps to zoom in too far in individuals.jsp to zoom levels where no Google map data exists.
  • NEW: Part 1: Create ShepherdResourceBundles for localization out of shepherd_data_dir, applying this to one web page as an example.
  • FIX: Improve thread handling of email notifications to unblock Mac users and deployment
  • MOD: Update Wildbook web.xml file to support deployment on Tomcat 7
  • FIX: Unidentifiable encounter emails not being sent.

2012-11-13

We are testing release 3.0.1 of Wildbook to better support operation on Tomcat 7 and on the Mac OS. Check out the Roadmap for more details.

2012-11-06

Wildbook 3.0 has been running for about a month now on whaleshark.org and is the best release we have ever had. Stability is excellent.

2012-11-02

Wildbook 3.1 development has begun! Check the Roadmap for details.

2012-10-24

We are pleased to release Wildbook 3.0.0 with these new features, fixes, and modifications:

  • NEW: Add measurement and biomeasurement support to Individual Search (done)
  • NEW: provide comprehensive developer documentation for other developers (underway)
  • NEW: create a Web Services API for pluggable pattern recognition algorithms (done)
  • NEW: allow Encounter data fields to be text boxes if values are not pre-defined in commonConfiguration.properties - allows projects to have fields as free form or as a restricted list. (underway)
  • NEW: TissueSample.measurements collection to handle contaminant analysis, stable isotope, fatty acid, etc. (done)
  • MOD: Rename TissueSample class to BiologicalSample and provide limited list capabilities in commConfiguration.properties (done)
  • NEW: Add the “and location ID” option to Search Comparison (done)
  • MOD: Upgrade to DataNucelus 3.1.2 (done)
  • NEW: Test DataNucleus RESTful exposure servlet (again) to see if adequate…YES! (done)
  • FIX: load markers function for map searches needs to be able to create the 'encounter' dir in the data dir area (done)
  • MOD: allow for Encounter.locationID-based delete scan permissions in the scanTaskAdmin.jsp grid control page (done)
  • NEW: Add new/recapture shark distinction in SOCPROG export (done)
  • NEW: Ensure good visualization of minimal, not photo-based CMR catalogs (done)
  • FIX: commonConfiguration.properties loading from shepherd_data_dir (done)
  • NEW: add measurement and biological measurement mean analyses to Encounter Search results (done)
  • FIX: GenePop switches the Search Comparison labels. (done)
  • NEW: add measurement and biomeasurement columns to SOCPROG export (done)
  • NEW: N-measurement comparison in Search Comparison function (done)
  • NEW: allow Encounter data fields to be text boxes if values are not pre-defined in commonConfiguration.properties - allows projects to have fields as free form or as a restricted list. (underway)
  • MOD: support externalization of JDO config parameters (done)

2012-10-19

Wildbook 3.0 is now being tested on mantamatcher.org.

2012-10-09

Wildbook 3.0 is now being tested on whaleshark.org.

2012-8-30

Wildbook 2.4 is released! It contains the following features and fixes.

  • MOD: Improve keyword add/remove UI in encounterImagesEmbed.jsp (done)
  • NEW: Adding mapping to the results of Individual Search (done)
  • NEW: create and display Occurrence class to represent co-occurring encounters (done)
  • NEW: add chevron time pathing to the map displayed in individuals.jsp (done)
  • NEW: support locales.properties point mapping in individualMapEmbed.jsp (done)
  • NEW: export support for GenAlEx from Search Comparison (done)
  • NEW: SOCPROG export from Individual Search (done)
  • NEW: Individual Search Measurement metrics (mean, sex-based, largest, smallest, std. dev.) (done)
  • MOD: Change open source license to GPLv3 (done)

2012-8-23

Wildbook 2.4 is now functionally complete and being tested. Check the roadmap to see the complete set of features.

2012-7-9

Wildbook 2.3 is released! It contains the following new features and fixes.

  • FIX: remove property datanucleus.PersistenceManagerFactoryClass - unused
  • FIX: cannot reset GPS coords if they were first improperly set (e.g., only one of the pair of values was entered). Must block the error condition on submission and fix the update servlet. See A-742 for an example encounter.
  • NEW: location comparison feature
  • FEEDBACK (Scott Baker): Reformat individuals.jsp to better display data types collected per encounter
  • MOD: Upgrade from DataNucelus 3.0.4 to 3.0.9
  • FIX: MarkedIndividual.getMaxDistanceBetweenTwoSightings(…) threw unhandled NullPointerException
  • NEW: GenePop export format out of the Search Comparison feature
  • FIX: Don't try to send an email in confirmSubmit.jsp if configured otherwise.
  • FIX: an adoption on individuals.jsp can force the map to be smaller and cover up the Fullscreen map option. (see A-003). Do this by moving the map out of the column structure and take up the full width of the div.
  • FIX: add charting support for IE8 by removing offending commas from the JavaScript.
  • NEW: Show a measurement as a collected data type in individuals.jsp
  • FIX: Add/remove measurement does not leave an audit trail

2012-7-1

Wildbook 2.3 is up on whaleshark.org. If all goes well there and no issues with performance are revealed, it will be released in a week.

2012-4-23

Here is a sneak peek at the Location Comparison feature being added to Wildbook. This feature has been developed as part of a humpback whale project (GeneGIS) looking at genetic relationships among populations.

2012-3-15

We are pleased to announce the release of Wildbook 2.2, incorporating these new features and fixes:

  • NEW - support 1000+ points in a Google Map by upgrading to Google Maps 3.8
  • NEW - display mapped points in the Encounter Search to improve selection
  • NEW - display mapped points in the Individual Search to improve selection
  • NEW - create a separate search results export tab for Encounter and Individual Searches
  • NEW - Integrate Google Charts API into Encounter and Individual Search results, creating an Analysis tab
  • FIX - Restore filter by sex to Encounter Search
  • NEW/RESTORE re-instate male/female visualization in Google Maps
  • NEW - Provide haplotype mapping in Encounter Search results
  • FIX - Fix cascading measurement problem on submission
  • NEW - add social media links to encounter.jsp and individuals.jsp
  • FIX - InfoWindow image display was broken in Google Earth export with the new external dataDirName feature in 2.1
  • FIX - favicon.ico reference in login.jsp could cause visual login failure
  • FIX - fix a bad Locus constructor
  • MOD - improve MarkedIndividual creation method to greatly improve object creation speed
  • FIX - remove whale shark reference in confirmSubmit.jsp

Here is a preview of some of the advanced mapping and search result analytics added to Wildbook 2.2.0.

2012-2-11

We are pleased to announce the release of Wildbook 2.1.0. This new version includes:

  • NEW - allow Encounter.locationID to be set from a pre-defined list in commonConfiguration.properties. If no list exists, default to an open-ended text field.
  • NEW - encounter data storage folders on the file system should not be in the encounters directory. This folder should be user-specified relative to the webapp install point. The directory name created is set with the dataDirectoryName property in commonConfiguration.properties.
  • FIX - Ensure MarkedIndividual.maxYearsBetweenResightings does not get calculated from a -1 value and MarkedIndividual.getEarliestSightingYear() does not consider -1 either

Upgrade considerations from 2.0.0

  • move the /encounters, /adoptions, and /individuals data folders into the same structure in the directory defined by dataDirectoryName in commonConfiguration.properties
  • move your custom WEB-INF/classes/bundles/commonConfiguration.properties file into the same directory structured but defined by dataDirectoryName in commonConfiguration.properties. Example: /shepherd_data_dir/WEB-INF/classes/bundles/commonConfiguration.properties. This file will now override the default within Wildbook.

2012-2-7

Wildbook 2.1 is being tested on whaleshark.org. This important release allows data and configuration files to be stored outside of a Wildbook instance, easing and securing the upgrade process.

2012-1-25

MantaMatcher is now live with Wildbook 2.0!

2012-1-12

We're pleased to announce the release of Wildbook 2.0.0. This new version includes:

  • support for version 1.0.x upgrade to 2.0.0 through a separate file (email us if you need it)
  • GeneGIS and PRETOMA support, including:
    • create a DataCollectionEvent class object and refactor Encounter to use it for photos, measurements, and genetic data samples.
    • support n-number of configurable animal measurement attributes as DataCollectionEvent objects: length, width, height, weight, etc.
    • add satellite tag attributes as DataCollectionEvent objects
    • add acoustic tag attributes as DataCollectionEvent objects
    • add collected tissue samples as DataCollectionEvent objects
      • add genetic sex determination as a genetic analysis result for a tissues sample
      • add Mitochondrial DNA as a genetic analysis result for a tissue sample
      • add microsatellite markers as a genetic analysis result for a tissue sample
    • clarify photos as DataCollectionEvent objects
  • DataNucleus 3.0.4 upgrade
  • add Darwin Core lifeStage as an Encounter attribute
  • refactor SinglePhotoVideo classes to contain arrays of Keyword objects. Keywords assigned to photos will be from a fixed list.
  • refactor IndividualSearchQuery to allow for cross-encounter queries
  • decompose encounter.jsp into subcomponent jsp files: edit forms, encounter data display, photo/video/keyword management, spot patterning, etc.
  • Logging: log user logins and logouts
  • Logging: Log new encounter submissions
  • Logging: Log encounter deletes and provide link in log to quickly restore them.
  • rework approved/unapproved/unidentifiable state into a single, open-ended Encounter.state attribute
  • move code for export data functions (Excel, KML, and Shapefile) out of JSP and into individual servlets

Upgrade considerations from 1.0.7

  • migrate Encounter.additionalImageNames vector to SinglePhotoVideo objects in the Encounter.images collection
  • migrate Keywords, applying them to SinglePhotoVideo instances in Encounter.images
  • migrate approved/unapproved/unidentifiable booleans to the new Encounter.state
  • make sure to remove all datanucleus 2.x jar files!
  • migrate Encounter.size to new measurement system
  • remove all encounters from Individual.unapprovedEncounters
  • switch commonConfiguration.properties to: javax.jdo.PersistenceManagerFactoryClass=org.datanucleus.api.jdo.JDOPersistenceManagerFactory

2012-1-2

Happy New Year! We now have Wildbook 2.0.0 running successfully on whaleshark.org. We'll test it in this live environment for awhile and then release it. Stay tuned!

2011-12-31 We are pleased to release version 1.0.7, which includes the following fixes and new features:

  • FEATURE: Add a project/organization field for submissions to the Encounter page. (done)
  • MOD: MarkedIndividual.name should be MarkIndividual.individualID (done)
  • FEATURE: add a standardized “unknown” option for genus/species reporting (done)
  • MOD: move confirmSubmitEmails.properties out of the bundles/en folder (done)
  • MOD: move submitActionClass.properties out of bundles/en (done)
  • MOD: move locales.properties out of bundles/en (done)
  • MOD: move and rename newIndividualNumbers.properties out of bundles/en (done)
  • MOD: remove nav.properties (done)
  • FIX: restore EncounterSetBehavior functionality (done)
  • FEATURE: search through marked individuals by year first identified (done)
  • FIX: EXIF and image metadata were not displaying in encounter.jsp unless the user had the imageProcessor role. Now it supports the admin role (default) as well. (done)
  • FIX: Metadata search on the approved/unapproved/unidentifiable state of encounters did not return correct results. (done)
  • FIX: remove legacy whaleshark.org code (done)
  • FIX: Fix searching on encounter state (e.g., approved, unapproved, unidentifiable) (done)

1.0.7 is the last release in the 1.0.x line. Time to move on to 2.0, which will have a very rich set of new features and some important refactors to support better open source development in the future. Development on 2.0.0 is finished, and we are currently testing it. Release is scheduled for January 2012.

2011-12-10

We are currently testing 1.0.7 on whaleshark.org and mantamatcher.org. After verifying that no regressions were introduced, we will be releasing 1.0.7 officially.

2.0 is almost done as well! We will be releasing a beta before the end of the year.

2011-10-07

We are pleased to release version 1.0.6, which includes the following fixes and new features.

  • FEATURE: display genus and species for a marked individual
  • FEATURE: display genus and species in search results
  • FIX: duplicate emails from NotificationMailer
  • FIX: emails to update submitters of a resight were not being sent. this functionality has been re-written
  • FEATURE: submit.jsp: add config to turn off taxonomy/multi-species option
  • MOD: move commonConfiguration.properties out of a language-specific bundles folder (i.e., “en” folder).
  • FIX: add verbatimEventDate back into encounter.jsp
  • FEATURE: Confirm IPT integration
  • FEATURE: Export shapefile from Encounter Search for GIS applications (e.g., ArcGIS)
  • FEATURE: turn email notifications on and off with a configuration option
  • FIX: EncounterSetDelete did not send email notifications correctly

2011-09-09

We released 1.0.5, which includes some fixes and minor new features:

  • FIX: add more exception handling for jpeg metadata extraction
  • FIX: handle null pointer exception related to size in Excel export
  • FEATURE: add ability to set genus and species for an encounter
  • FEATURE: display genus and species for an encounter
  • FEATURE: add ability search for encounters by genus and species (encounterSearch.jsp modification and EncounterQueryProcessor)
  • FEATURE: add ability to search for marked individuals by genus and species (individualSearch.jsp modifications)
  • FEATURE: set genus and species upon submission (submit.jsp, SubmitForm, and SubmitAction modifications)

2011-08-17

We released 1.0.4, which includes some fixes and minor new features:

  • fixed more size null and number format exception handling in calendar-related servlets
  • fixed locationID display in encounterSearch.jsp and individualSearch.jsp, allowing >=1 location IDs to be displayed (previously only >1 was displayed)
  • removed a legacy ganymede dependency from whaleshark.org branch
  • fixed a map-related regression in encounter.jsp that prevented Google Maps display
  • fixed the name/email string filtering for Encounter Search
  • NEW FEATURE: bundle Javadocs with the WAR file. check the /javadoc URL
  • NEW FEATURE: search by image/video filename in encounterSearch.jsp
  • NEW FEATURE: Added AND query criteria for location ID filtering in the Encounter Search feature, allowing users to search for animals that have been sighted in multiple study locations
  • NEW FEATURE: Version injection in footer.jsp, allowing users to see which version of Wildbook they are running at the bottom of every page.

2011-08-02

We released 1.0.3, which includes some critical fixes:

  • fixed more depth/elevation/size null and number format exception handling in encounter.jsp
  • fixed some login handling in encounter.jsp to be a little more elegant
  • fixed a login-related bug that caused users without permissions for an encounter to not be able to see the encounter's full size photos

2011-07-20

We released 1.0.2, which includes some critical fixes:

  • fixed depth/elevation/size null and number format exception handling
  • restored the CommonConfiguration.showProperty(…) function to allow elevation and depth to be displayed or hidden through a setting in commonConfiguration.properties

2011-06-26

We released 1.0.1, which includes some critical fixes.

2011-06-06

We have released version 1.0.0 of Wildbook!

2011-05-04

whaleshark.org is running well on the new software, and we're making minor fixes and improvements daily. polarbearlibrary.org will be using it soon. This is a great example of how software work for humpback whale mark-recapture, polar bear mark-recapture, and whale shark mark-recapture has resulted in benefits for all three research groups. We're constantly upgrading using lessons learned from other projects.

2011-04-22

Wildbook beta 2 is up and running on whaleshark.org. We're giving it one month of active use by a global research community to help us identify and fix any remaining bugs.

2011-04-10

Beta 1 is available. This release is a massive overhaul, including significant performance improvements and usability improvements around search. We provide no support for Beta 1 and make no guarantee of an upgrade path to Beta 2 or beyond. This release is being incorporated into whaleshark.org. It will become release candidate 1 in the near future.

2010-10-06

A re-release of Alpha2 is available. This release includes a feature allowing submitters to opt out of future database emails. Alpha2 should be a complete, standalone, and superior copy of the functionality available at www.whaleshark.org. However, this project is new, and many changes are scheduled for the near future. We provide no support for alpha2 and make no guarantee of an upgrade path to alpha3/beta1 or beyond.

2010-09-17

A release of Alpha2 is available. This release includes a large number of display changes and bug fixes. Specifically, the various search user interfaces (UIs) were collapsed into two searches: Encounter Search and Individual Search. Animation was added to the UIs, as were additional search parameters. Alpha2 should be a complete, standalone, and superior copy of the functionality available at www.whaleshark.org. However, this project is new, and many changes are scheduled for the near future. We provide no support for alpha2 and make no guarantee of an upgrade path to alpha3/beta1 or beyond.

2010-08-21

A re-release of Alpha1 is available. This re-release includes a large number of display changes and bug fixes. Specifically, image metadata extraction was added and image galleries were added for encounters, marked individuals, and for Encounter Search results. Encounter Search was also converted to use JDOQL wherever possible, and Encounter Search results were broken into four tabs. Alpha1 should be a complete, standalone, generic copy of the functionality available at www.whaleshark.org. However, this project is new, and many changes are scheduled for the near future. We provide no support for alpha1 and make no guarantee of an upgrade path to alpha2 or beyond.

2010-07-10

A re-release of Alpha1 is available. This re-release includes a large number of display and bug fixes. Alpha1 should be a complete, standalone, generic copy of the functionality available at www.whaleshark.org. However, this project is new, and many changes are scheduled for the near future. We provide no support for alpha1 and make no guarantee of an upgrade path to alpha2 or beyond.

2010-06-17

Wildbook Alpha1 is available. This is a first trial run during active development. Alpha1 should be a complete, standalone, generic copy of the functionality available at www.whaleshark.org. However, this project is new, and many changes are scheduled for the near future. We provide no support for alpha1 and make no guarantee of an upgrade path to alpha2 or beyond.