09 June 2011
Specify Software Project
New or Enhanced Features:
- 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
- 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.
- 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.
- 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.
- 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.
- 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.)
- 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.
- 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.
- 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.
- 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).
- 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.
- 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.
- 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.
- Use a Custom Database Server Port: Specify can be
configured to access a custom network port of a MySQL Server computer.
- Query Results now Display a Maximum of 20,000 Records.
- The Specify WorkBench Data Set Row Limit has been Increased to
List of changes in Specify 6.3
- It is now possible to delete a user permanently in
Security. 2011-01-18 15:17:03 (Bugzilla #7376).
- The Specify Wizard now downloads Taxon Authority Files as needed
from the Specify web site. 2010-09-21
- Uploading the same Data Set twice no longer causes the tree to
rebuild. 2011-01-06 14:25:33 (8065).
- Users can now edit the name of a Collection in
Configuration in the System menu. 2011-03-28
- In the DNA Sequence form, the Residue Counter no longer displays
blank in view mode. 2011-04-27 13:37:15 (8141).
- 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).
- Stratigraphy tables are now available as Query
Creators. 2011-01-06 11:48:57 (8197).
- The Data Set Mapping Editor no longer shows "Taxon" twice instead
of "Taxon" and "Taxon Import Only". 2011-04-22
- 64-bit NASA World Wind libraries have been added to 64-bit
installations of Specify. 2011-02-09
- The GeoLocate button no longer turns into the BioGeomancer button
for no clear reason. 2011-04-22 13:27:44 (8221).
- An issue that allowed user input in an update notification dialog
has been fixed. 2011-04-21 10:53:43 (8245).
- The user name "root" is no longer allowed to be used for the
generation of login keys. 2011-04-11
- 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).
- Tables in grid mode now always have the green plus
button. 2011-03-17 14:05:28 (8269).
- The Security Wizard now shows the correct list of databases to
which the Master user does not have permissions. 2011-04-11
- Pressing "back" in the Security Wizard no longer causes the
cancel button to disappear. 2011-04-11
- The Security Wizard no longer crashes when it asks users to fix
their Master permissions. 2011-04-19
- 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).
- In the Container form, the Collection Object Query Combo Box is
no longer editable in view mode. 2011-04-18
- 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
- An issue that caused an exception to appear when users opened
Preferences has been fixed. 2011-04-15
- 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).
- Feedback now appears when a user attempts to export a Record Set
the type for which no Data Set exists. 2011-04-11
- It is no longer possible to rename a Collection with the name of
another existing Collection. 2011-04-13
- 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).
- An issue that caused an exception to appear upon logging into a
new database has been fixed. 2011-04-07
- Several Record Set usability problems have been fixed in the
Interactions pane. 2011-04-21 10:37:04 (8313).
- 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
- Adding a parent Container to a Container now triggers the save
button. 2011-04-21 10:31:53 (8318).
- Tabbing to the server field in the login screen no longer sends
the mouse focus to the password field. 2011-04-14
- An issue that prevented user login for two or more databases with
the same user name and password is now fixed. 2011-04-15
- 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).
- An issue that caused the Express Search to generate an exception
has been fixed. 2011-04-14 12:29:27 (8323).
- Adding a new pick list from the Schema Configuration now works
correctly. 2011-04-15 12:54:02 (8325).
- 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
- Importing a bad file name with the Pick List Importer no longer
creates an exception. 2011-04-14 12:19:15 (8328).
- An issue that allowed users without sufficient permissions to
use the QueryBuilder is now fixed. 2011-05-03
- The exception generated by clicking the magnifying glass in the
Container sub-form is now fixed. 2011-04-27
- 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).
- Using keyboard shortcuts in Data Entry no longer disables the
save button. 2011-04-27 13:29:38 (8341).
- One can now delete a collection. 2011-05-20
- 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
- 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).
- 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).
- 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).
- 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).
- Exporting a Workbench Data Set no longer causes an
exception. 2011-05-18 13:33:13 (8364).
- The text on the summary page of the Specify Wizard is no longer
editable. 2011-05-16 14:50:22 (8365).
- 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).
- It is no longer possible to make a Container the parent and child
of the same Container. 2011-05-16 14:45:09 (8367).
- Adding and deleting a Determination in the Batch Identify tool no
longer causes an exception. 2011-05-16 14:51:35 (8368).
- The Workbench Schema Configuration window now displays the
correct title. 2011-05-16 14:58:07 (8372).
- Collection Objects can now belong to cataloged
Containers. 2011-05-20 11:41:24 (8375).
- Irrelevant error pop ups have been removed from the Security
Wizard. 2011-05-20 11:01:42 (8376).
- Deleting multiple determinations in the Batch Identify tool no
longer causes an exception. 2011-05-23
- 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
- Clearing cells in WorkBench Data Sets now enables the Save
button. 2011-05-23 10:47:31 (8381).