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Release Notes
Specify 6.3.00
09 June 2011
Specify Software Project

New or Enhanced Features:

  1. Specify WorkBench Validates Data Uploads: The WorkBench is a versatile tool for new data entry, it allows specimen data to be keystroked into a spreadsheet grid or a customized form view. The WorkBench is also great for importing collection records from Excel files. In Specify 6.3 we introduce powerful validation functions which inspect the data in WorkBench fields and evaluate them against the contents of your Specify database. The WorkBench does this as you type in new records or in batch mode once a Data Set is ready for uploading to Specify. Through color coding the WorkBench indicates which data values are new to your database, as well as highlighting formatting errors or data type mismatches. These validation functions immediately indicate which data values need further attention--either to be corrected or accepted as valid new database entries. WorkBench validation of incoming data records keeps misspellings in data types such as taxon or geographical, or collectors' (Agent) names, out of your database and greatly facilitates accurate and consistent data entry.
  2. Containers Organize Specimens: Specify 6.3 now supports Containers which can be substrates or physical containers in a collection. For example, a microscope slide upon which one or more algal specimens are mounted can now be linked to the algal collection object records. The slide may optionally be given a catalog number itself. Containers contain specimens or even other containers. A lichen specimen on the surface of a wood sample would be cataloged as a collection object, while the piece of wood could be recorded as a Container. A Container might also be a box of specimens (Collection Objects) that needs to be cataloged to be curated. Catalog Numbers are optional for Containers, some collections use them, some don't.
  3. Documenting Biological Relationships: Relationships can now be expressed between two collections in order to document biological relationships between collection objects. Predator/prey, pollinator/plant, host/parasite relationships between cataloged collection objects (e.g. a specimen in a herbarium database and an insect in an entomology collection), can now be linked, searched and displayed across collections within Specify.
  4. New Tree Merge Function Improves Data Quality: Data managed in Specify's tree windows (Taxon, Geography, Storage Locality, Chronostratigraphy and Lithostratigraphy) can now be merged across tree entries or nodes. This capability is highly useful for rapid data cleanup when new data entry has introduced misspellings or unwanted variant terms. Nodes at the same rank in a tree can be merged to consolidate duplicate child nodes and preserve all distinct child nodes under the target term. For example, if a Geography Tree has Country rank nodes for "Columbia" and "Colombia", with Colombian Departments listed beneath them, dragging "Columbia" to "Colombia" in a Geography tree will merge all Department nodes, eliminating any redundant Department entries but preserving unique Department names. No information is lost, and all linked Collection Object records then point to "Colombia" and to the appropriate Departments at the next lower rank. Drag-and-drop node merging is a powerful and efficient work flow tool for improving data consistency.
  5. Distributing Data Entry and Mobilizing Records: Specify users can create Record Sets of Collection Objects in their database and then export copies of those records to a Data Set usable by the Specify WorkBench. From there data can be exported to Excel format files. Those Excel files can in turn be imported into other WorkBenches as Data Sets at other institutions or collections, and then re-imported into Specify. Moving Specify records around in this way creates opportunities for collaborative or distributed cataloging as well as for transporting records in Excel for portability and remote use.
  6. Data Cloning Function Speeds Data Entry: Query Combo Boxes are used on Specify's data forms to find and link to existing data in related data tables. For example you may have a Query Combo Box for looking up and scrolling through Locality or Collecting Event records to match one with a new specimen record. If you find an existing Locality or Collecting Event that is close but not identical to the information you need to enter, Specify 6.3's cloning function enables selecting an existing record, quickly duplicating it to make any changes and then saving it. With new data entry, there is no need to link to Locality or Collecting Event data that are different from what you need-- just find an existing record, clone, edit, and save. (This new capability works with any Query Combo Box representing a Many-to-One relationship between data types.)
  7. Batch Identify (or Batch Determination) Accelerates Name Updates: With Batch Identify one can identify a batch of specimens and then change their Current Determination in one action instead of one specimen at a time.
  8. Series Data Entry Creates New Specimens in Batches: Some disciplines such as entomology often computerize a large number of specimens within a single series. With Specify 6.3 one can now enter a range of Catalog Numbers, enter data in one Collection Object form and then with one mouse click, save a series of sequentially-numbered Collection Objects with the entered data.
  9. Pick List Import/Export: Data Form Pick Lists which standardize data values for fields by presenting a small number of valid values, can now be exchanged among Specify installations and collections with Specify 6.3's import/export capabilities. This is useful for collaborators who need to standardize term value options across two or more collection databases. Most Specify data fields can be configured as Pick Lists.
  10. New Security Wizard Recovers Credentials: The Security Wizard is a new application which must be run with the Specify IT User account name and password. The Security Wizard can verify the Specify Master User name and password, or reset them. The Security Wizard also can view and edit the list of databases the Specify Master User enables Specify users to access. (The Specify IT User is either the 'root' user on the MySQL database installation, or an account in MySQL with root-level permissions created by a database administrator).
  11. Higher Level Taxonomic Searches: Taxon queries are now able to search for Taxon nodes constrained to a particular tree rank. e.g. show me a list of families in my collection.
  12. Specify WorkBench Schema Mapping: The data field labels in the Data Set Mapping Editor are now editable to more easily keep track of individual field mappings between the WorkBench and Specify.
  13. Minimum Password Length can be Specified: Users can be required to create passwords of a minimum length or larger. The default setting is 8 characters.
  14. Use a Custom Database Server Port: Specify can be configured to access a custom network port of a MySQL Server computer.
  15. Query Results now Display a Maximum of 20,000 Records.
  16. The Specify WorkBench Data Set Row Limit has been Increased to 4,000 Rows.


List of changes in Specify 6.3

  1. It is now possible to delete a user permanently in Security.  2011-01-18 15:17:03  (Bugzilla #7376).
  2. The Specify Wizard now downloads Taxon Authority Files as needed from the Specify web site.  2010-09-21 15:16:14  (8054).
  3. Uploading the same Data Set twice no longer causes the tree to rebuild.  2011-01-06 14:25:33  (8065).
  4. Users can now edit the name of a Collection in Configuration in the System menu.  2011-03-28 15:33:49  (8079).
  5. In the DNA Sequence form, the Residue Counter no longer displays blank in view mode.  2011-04-27 13:37:15  (8141).
  6. The schema update messages that appear when users log into a database with a new version of Specify have been made more informative.  2011-04-27 13:35:16  (8159).
  7. Stratigraphy tables are now available as Query Creators.  2011-01-06 11:48:57  (8197).
  8. The Data Set Mapping Editor no longer shows "Taxon" twice instead of "Taxon" and "Taxon Import Only".  2011-04-22 13:54:19  (8209).
  9. 64-bit NASA World Wind libraries have been added to 64-bit installations of Specify.  2011-02-09 14:35:34  (8219).
  10. The GeoLocate button no longer turns into the BioGeomancer button for no clear reason.  2011-04-22 13:27:44  (8221).
  11. An issue that allowed user input in an update notification dialog has been fixed.  2011-04-21 10:53:43  (8245).
  12. The user name "root" is no longer allowed to be used for the generation of login keys.  2011-04-11 13:23:54  (8252).
  13. The default Tree Rank configuration for some discipline types in the Specify Wizard had subphylum "not included" but "enforced."  2011-04-21 10:45:53  (8267).
  14. Tables in grid mode now always have the green plus button.  2011-03-17 14:05:28  (8269).
  15. The Security Wizard now shows the correct list of databases to which the Master user does not have permissions.  2011-04-11 13:36:55  (8284).
  16. Pressing "back" in the Security Wizard no longer causes the cancel button to disappear.  2011-04-11 13:37:17  (8286).
  17. The Security Wizard no longer crashes when it asks users to fix their Master permissions.  2011-04-19 11:43:36  (8287).
  18. An exception has been resolved that appeared when users edited the name of a Container from the form of that Container's parent.  2011-04-01 14:00:52  (8288).
  19. In the Container form, the Collection Object Query Combo Box is no longer editable in view mode.  2011-04-18 14:50:21  (8289).
  20. In the Container form, users can now delete a relationship to a Collection Object (i.e. they can remove it from the Query Combo Box entitled Collection Object).  2011-04-18 14:47:15  (8290).
  21. An issue that caused an exception to appear when users opened Preferences has been fixed.  2011-04-15 12:49:25  (8291).
  22. A discrepancy in the WorkBench that allowed new values to be added to the Preparation Type pick list on a case insensitive basis but validated on a case sensitive basis has been resolved: now both are insensitive.  2011-04-11 13:41:06  (8293).
  23. Feedback now appears when a user attempts to export a Record Set the type for which no Data Set exists.  2011-04-11 13:42:47  (8294).
  24. It is no longer possible to rename a Collection with the name of another existing Collection.  2011-04-13 10:23:21  (8298).
  25. An issue that caused the Specify SetupWizard to fail on the Create Institution and Admin User step has been fixed.  2011-04-11 13:48:42  (8307).
  26. An issue that caused an exception to appear upon logging into a new database has been fixed.  2011-04-07 16:35:02  (8310).
  27. Several Record Set usability problems have been fixed in the Interactions pane.  2011-04-21 10:37:04  (8313).
  28. In a given user's Security profile, the "Generate Master Key" button is now disabled when the string in the password field is encrypted: otherwise the key is being generated from an already-encrypted string.  2011-04-15 13:53:30  (8316).
  29. Adding a parent Container to a Container now triggers the save button.  2011-04-21 10:31:53  (8318).
  30. Tabbing to the server field in the login screen no longer sends the mouse focus to the password field.  2011-04-14 12:30:59  (8319).
  31. An issue that prevented user login for two or more databases with the same user name and password is now fixed.  2011-04-15 13:02:51  (8320).
  32. The login screen no longer sometimes changes the database name in the field to that of a recently used database when users attempt to login.  2011-04-15 13:01:56  (8321).
  33. An issue that caused the Express Search to generate an exception has been fixed.  2011-04-14 12:29:27  (8323).
  34. Adding a new pick list from the Schema Configuration now works correctly.  2011-04-15 12:54:02  (8325).
  35. Pick lists can now only be edited through the Schema Configuration tool (System---Schema Configuration); pick lists cannot be edited from System---Configuration anymore.  2011-04-15 12:51:30  (8326).
  36. Importing a bad file name with the Pick List Importer no longer creates an exception.  2011-04-14 12:19:15  (8328).
  37. An issue that allowed users without sufficient permissions to use the QueryBuilder is now fixed.  2011-05-03 14:31:32  (8330).
  38. The exception generated by clicking the magnifying glass in the Container sub-form is now fixed.  2011-04-27 13:21:21  (8338).
  39. In the Collection Object form of cataloged Containers, the Container field no longer becomes blank when the user changes to Edit mode.  2011-04-27 13:30:54  (8339).
  40. Using keyboard shortcuts in Data Entry no longer disables the save button.  2011-04-27 13:29:38  (8341).
  41. One can now delete a collection.  2011-05-20 13:51:10  (8345).
  42. Query results on the various component fields of DNA Sequence data objects now display the correct number of, for example, "A's" in the Gene Sequence field.  2011-05-20 13:53:11  (8349).
  43. Saving a batch of Collection Objects when some of the Catalog Numbers of the batch already exist in the database no longer generates a separate error message for each Catalog Number in error.  2011-05-03 15:13:58  (8351).
  44. The Collecting Event and Collecting Information icons no longer switch places and display for the wrong Discipline types.  2011-05-20 13:53:43  (8359).
  45. Georeferencing a Locality form accessed from a Collection Object form no longer fills in the GeoRefDetBy field with a value that has disappeared upon reopening the Locality data object.  2011-05-16 14:42:12  (8360).
  46. On Mac OS X and Linux, the Pick List Exporter tool no longer duplicates the ".xml" extension of the exported file.  2011-05-20 13:55:00  (8362).
  47. Exporting a Workbench Data Set no longer causes an exception.  2011-05-18 13:33:13  (8364).
  48. The text on the summary page of the Specify Wizard is no longer editable.  2011-05-16 14:50:22  (8365).
  49. In the Collection Object form, the Collection Relationship search that uses the magnifying glass no longer causes an exception.  2011-05-20 13:56:20  (8366).
  50. It is no longer possible to make a Container the parent and child of the same Container. 2011-05-16 14:45:09  (8367).
  51. Adding and deleting a Determination in the Batch Identify tool no longer causes an exception. 2011-05-16 14:51:35  (8368).
  52. The Workbench Schema Configuration window now displays the correct title.  2011-05-16 14:58:07  (8372).
  53. Collection Objects can now belong to cataloged Containers.  2011-05-20 11:41:24  (8375).
  54. Irrelevant error pop ups have been removed from the Security Wizard.  2011-05-20 11:01:42  (8376).
  55. Deleting multiple determinations in the Batch Identify tool no longer causes an exception.  2011-05-23 10:51:05  (8378).
  56. For a Collection Relationship, viewing a Source Collection Object from a Destination Collection Object's form now correctly shows the Source Collection Object's Collection Relationship.  2011-05-20 14:15:00  (8380).
  57. Clearing cells in WorkBench Data Sets now enables the Save button.  2011-05-23 10:47:31  (8381).