Shepherd Project 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.
Shepherd Project 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.
Shepherd Project 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.
Check out our new Shepherd Project installation video for Windows.
We are pleased to announce the release of Shepherd Project 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 Shepherd Project 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 the Shepherd Project web.xml file to support deployment on Tomcat 7
- FIX: Unidentifiable encounter emails not being sent.
We are testing release 3.0.1 of the Shepherd Project to better support operation on Tomcat 7 and on the Mac OS. Check out the Roadmap for more details.
Shepherd Project 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.
Shepherd Project 3.1 development has begun! Check the Roadmap for details.
We are pleased to release Shepherd Project 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)
Shepherd Project 3.0 is now being tested on mantamatcher.org.
Shepherd Project 3.0 is now being tested on whaleshark.org.
Shepherd Project 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)
Shepherd Project 2.4 is now functionally complete and being tested. Check the roadmap to see the complete set of features.
Shepherd Project 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.
- NEW: Show a measurement as a collected data type in individuals.jsp
- FIX: Add/remove measurement does not leave an audit trail
Shepherd Project 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.
Here is a sneak peek at the Location Comparison feature being added to the Shepherd Project. This feature has been developed as part of a humpback whale project (GeneGIS) looking at genetic relationships among populations.
We are pleased to announce the release of Shepherd Project 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 Shepherd Project 2.2.0.
We are pleased to announce the release of Shepherd Project 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 the Shepherd Project.
Shepherd Project 2.1 is being tested on whaleshark.org. This important release allows data and configuration files to be stored outside of a Shepherd Project instance, easing and securing the upgrade process.
MantaMatcher is now live with Shepherd Project 2.0!
We're pleased to announce the release of Shepherd Project 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
Happy New Year! We now have Shepherd Project 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.
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.
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
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)
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 the Shepherd Project they are running at the bottom of every page.
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
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
We released 1.0.1, which includes some critical fixes.
We have released version 1.0.0 of the Shepherd Project!
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.
Shepherd Project 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.
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.
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.
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.
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.
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.
Shepherd Project 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.