Specify Software Project

Release Notes
Specify 6.6.06
12 October 2017

Installation Notes:

  1. This Specify 6 update modifies the MySQL database schema. It is critically important to make a full backup of a Specify database before downloading and running the Specify 6.6.06 updater. During the schema modification process, a momentary failure of network communication or server operation may corrupt a Specify database and make it permanently unusable and unrecoverable. Do not attempt to upgrade to release 6.6.06 without a fresh, full backup of your collection's data.
  2. The Specify 'Admin' or 'IT User' account username and password will be required to complete the Specify 6.6.06 software and database update. After the update is applied to one workstation and after it updates the database schema, all other workstations will need to be updated to release 6.6.06 in order to access the database.
  3. Sites operating Specify 6 and Specify 7 simultaneously must update both platforms to release levels: 6.6.06 and 7.3, in order to provide database access with both platforms.
  4. Additionally, Specify 7 installations will need to update the embedded copy of Specify 6 to 6.6.06 within the server configuration. Information on how to update the Specify 7 server is available in the readme file in the source code repository.
  5. This release is compatible with all Java (JRE) 8.x versions but is not yet adapted to the recently released Oracle Java Runtime Environment.
  6. For Specify 64-bit installations on Windows desktops we increased the amount of RAM allocated to Java to 4 GB in a separate, installed, executable file "Specify4GB.exe". Also in the 64-bit Specify installation, the executable "Specify.exe" uses 1GB of memory for the Java virtual environment. If you have 8 GB or more of RAM on your 64-bit Windows desktop, the 4GB version should give you better performance. For 32-bit installations of Specify on Windows "Specify.exe" uses 768 KB of memory for Java, while "Specify1GB.exe" uses 1 GB. The latter may perform slightly better with the increased memory allocation. The Specify DataExporter.exe app for Windows has also been increased to 4 GB to handle large web server and Darwin Core record exports. We also increased the Java memory space to 4GB for macOS ("Specify") and Linux installations ("Specify4GB").

Database Schema Changes:

  1. With this release, we made Specify compliant with the Global Genome Biodiversity Network's (GGBN) "Material Sample" Darwin Core extension for DNA/RNA extract metadata (https://terms.tdwg.org/wiki/GGBN_Data_Standard). We added the data table “Material Sample” along with data fields in several Specify tables to accommodate DNA Extract and DNA Sequence metadata as defined by the GGBN (http://www.ggbn.org/). Data fields (terms) added are from the GGBN Vocabularies: Amplification, Material Sample, Permit, and Preparation. As before, the existing Specify "Preparation" table describes physical object types, like skins, skeletons, seeds, and tissues. The new Material Sample table describes chemical extract samples derived from Preparations. The existing Specify "DNA Sequence" data table describes molecular information derived (e.g. sequenced) from a Material Sample (in a new relationship to the Material Sample table with this release) or from a Collection Object (the pre-existing Specify relationship to DNA Sequence).  We added a second new table "DNA Primer" to describe primer information for Sanger methods. Specify sites using the DNA Sequence table prior to this release as a child of Collection Object should contact the Specify Project to discuss the possibility of using the Material Sample--DNA Sequence relationship in its place. More information is available on the Specify Project web site about the new (GGBN) Material Sample table and its relationships to the Preparation and DNA Sequence tables. These Specify extensions were done in collaboration with the Global Genome Biodiversity Network and were financially supported by them.
  2. Added several fields for NIH SRA accession numbers to enable linking sample and sequence data from next generation methods deposited in NIH SRA databases to the corresponding DNA Sequence record in Specify. This allows http link-outs to molecular data at NIH, sequenced from specimens/tissues/extracts in the collection.
  3. Existing TDWG Audubon Core standard fields were supplemented with additional commonly used Audubon Core vocabulary terms (fields) for describing and exporting multimedia objects (Attachments in Specify).
  4. Added AdminContact (Agent) field to the Collection table for identifying collections in feedback statistics.
  5. Added long integer fields to Taxon table to allow for assignment of numeric codes to taxa for sorting and ordering taxon names in query results.
  6. Added text fields to Borrow Materials table to allow extended description of borrowed materials.
  7. Added text and logical (yes/no) fields to the Collection Object Attributes table.
  8. Added 4 memo fields, 16 logical fields, 11 string, and 2 integer fields to the Taxon table in response to requests to handle IUCN Red List information on species conservation status.
  9. Expanded the AltCatalogNumber field to 64 characters to better handle long legacy numbering schemes.
  10. Added Geocoordinate error estimate fields to the Workbench Row table to allow them to be imported.
  11. Increased the length of picklist value and title fields from 64 to 128 chars to accommodate user needs for long, formatted selection strings.

Software Changes:

  1. PaleoMap, a plug-in that shows the paleo localities of fossils was created and contributed by Tomislav Urban, Texas Advanced Computing Center (TACC) for Specify 7. It was easily embedded within Specify 6 and is now accessible on the Collecting Event form for Paleontology collections new to Specify (with this release). With form configuration it can be added to the user interface for existing Specify paleo databases. We thank Tomislav Urban and TACC for contributing this outstanding plug-in. 2017-08-25  (10297)
  2. Enabled Borrow Materials and Borrow Return Materials data to be viewed as a grid  2017-09-01  (Bugzilla 10336, 10308)
  3. Added Start and End Period default values to Chronostrat records to allow for sorting on tree displays and for use by PaleoMap plug-in. 2017-09-01  (10296)
  4. Changed the default formatter for Collecting Event Query Combo Boxes on Collection Object forms from showing start date, to show Station Field Number, Locality Name, Geography Full Name, and Latitude1/Longitude1. 2017-08-31 (10332)
  5. Passwords are no longer stored where they should not be. (External authentication is in development.) 2017-08-28  (10294)
  6. If the Specify Software Project Update server is offline or inaccessible, Specify continues to startup as expected. 2017-08-23  (10228)
  7. Added AltCatNumber to the list of fields that can be searched with simple search. 2017-08-22  (10307)
  8. One can now upload Reference Work table data through the Specify Workbench without associated Collection Objects. 2017-08-18  (10293)
  9. Added field AdminContactName to the Collection data table and included it in feedback stats. 2017-08-18  (10322)
  10. Drag-and-drop operations in Taxon trees now update TimestampModified field in Taxon table. This fixes the problem of Specify overlooking changes in the Taxon tree while identifying updated records to export to iDigBio or GBIF (through IPT), or to the Specify web portal. 2017-08-18 (10251)
  11. Containers can now be uploaded via Specify Workbench; the capability is configured in the Workbench Import Configuration file. 2017-08-18  (10317)
  12. Appropriate Collecting Event data are associated with Localities in the Google Earth plug-in.  2017-08-17  (10318)
  13. The "-" character is no longer allowed in numeric catalog numbers.  2017-08-16 (10300)
  14. Reference Work records can be deleted when they are associated with a Journal record.  2017-08-16  (10209)
  15. QueryCombo box search windows now use customized field captions found in the form schema.  2017-08-16  (10248)
  16. Uploads of bulk attachments can now be handled for Interaction records (gifts, loans, accessions, exchanges, etc.).  2017-08-15  (10305)
  17. Catalog numbers are only auto-assigned if 'Auto Fill Catalog Numbers' is checked in the Workbench. 2017-07-25  (10302)
  18. Spreadsheet cells that contain only space characters can now be uploaded through the Specify Workbench.  2017-07-17  (10306)
  19. For queries, fields for tree data ranks parameterized with "Empty" or "Not Empty" criteria now filter correctly. 2017-05-19  (10295)
  20. The Specify Workbench Uploader no longer erroneously creates multiple GeoCoordDetail records for an existing locality. (10298)
  21. Checking the status of data export caches in the Data Exporter and Symbiota Exporter to see if records need to be added to export table, is now much quicker. 2017-05-16  (10288)
  22. Clone Locality function will now clone everything in Locality, when PaleoContext is configured as an embedded data object in the Locality form. 2017-03-28  (10292)
  23. Auto incrementing of Catalog Numbers works for any portion of a multi-part catalog number that is numeric and set to auto-increment. 2017-03-15  (10291)
  24. LocalityDetail Text1 field on forms uses the appropriate database field. 2017-09-29 (10348)
  25. When a query for an export data mapping returns zero records the Data Exporter works as expected. 2017-09-25 (10354)
  26. Fixed issues with hiding and showing the Attachments task bar entry. 2017-09-21 (10353)
  27. Updated the URL to Lifemapper for distribution maps. 2017-09-21 (10349)
  28. Data Exporter is now more robust on Macs. 2017-09-26 (10345)