Specify 6.5

Specify 6.5 and Specify Web Portal

Specify 6.5 Support for Images and Attachments

Specify 6.5 adds robust image and attachment handling enabling easy integration of collection data with images and other types of files. Images can be browsed, discovered through queries, displayed on data forms, and served in the Specify Web Portal. Clicking on a thumbnail in Specify’s new image browser window brings up the full-size image or launches a helper application, such as a PDF viewer to view the entire document. Additional clicks show related database records, global map location, or for some image types like jpegs, metadata from inside the image file.

External files can be linked to records in several tables including: Collection Object, Collecting Event, Agent, Field Notebook, Locality, Loan, Permit, Repository Agreement, Taxon, and others. Files can be attached to collection records one-at-a-time or linked in batches from files in a directory. Batch linking of attachments, whether they be label images, photos from the field, publication PDFs, reports or permits in Word, can be done by either matching media file names to unique IDs in the database (e.g. catalog or field numbers), or by creating a simple two-column table which maps attachment file names with the corresponding unique IDs in Specify.

Attachments are copied from the original source files to a designated repository location. Files may be stored locally on a workstation drive or on a shared server drive and accessed through a directory path.  Alternatively, system administrators may set up a Specify Attachment Server to create a repository for attachment files to be accessed through the web protocols.

Specify Attachment Server

The Specify Attachment Server, an optional component which runs on a network file or asset server, manages attachment file transactions, i.e. uploads, downloads and deletions, and it creates thumbnails from original images. The Attachment Server’s Python code is lightweight, it has been tested on Linux and should run on any platform supported by Python. Authentication allows repository access only from Specify workstations and from the new Specify Web Portal. Access rights for individual files follow the same scoping rules for Divisions, Disciplines, and Collections which govern the use of shared data in the Specify institutional hierarchy. The Specify Attachment Server is a flexible option for storage of collection-related images and documents, particularly for institutions with systems support staff and a mix of workstations.

Java 7

Specify 6.5 uses Java 7. The Java 7 Runtime Environment (JRE) allows Specify to run identically across Windows, Linux and Mac platforms.  Downloading and installing Java is no longer required as the Specify installer puts Java 7 into a Specify program directory. If your systems administrator prefers to install Java 7 at a system level, Specify will detect and use the system copy. Specify does not use a Java web browser plug-in. For Mac users, Java 7 requires an Intel processor and Mac OS X 10.7.3 (Lion) or above. [Update: Subsequent to this, as of release 6.5.04, Specify requires an external installation of the Java 7 JRE on workstations. Java is no longer included within the Specify installation package.] [Update #2: As of release 6.6, December 2014, Specify now requires the Java 8 JRE to be installed.]

Specify 6 Synonym Cleanup Tool

Some collection databases which were converted from Specify 5-to-6 have taxon synonyms linked to the wrong parent in their Specify 6 Taxon Trees. That issue resulted from differences in the way that Specify 5 and Specify 6 store and manage synonyms. Collections which were not converted from Specify 5, but created anew in Specify 6, or migrated from a legacy database to Specify 6, do not benefit from this tool.  Sites with Specify-5-converted databases can run the Synonym Cleanup Report to check for misplaced synonyms and then execute a cleanup operation to correct synonym placement in the Taxon Tree. Additional discussion of this issue can be found on the Specify web site documentation page in the file: “Specify 6 Synonym Cleanup Tool.pdf”.

Globally Unique Identifiers (GUIDS)

Specify 6.5 implements identifiers for several major data tables to uniquely identify collection data objects on a global scale.  Specify uses “UUIDS” or “Universally Unique Identifiers” which are a widely-used type of GUID. The importance of UUIDs is that they allow software processes to unambiguously determine record identity. That capability is useful for data exchange, recurring updates from Specify providers to collection data aggregators, for collaborative authority works and data validation, and ultimately for powerful research integration and analysis utilizing tools of the semantic web. UUIDs are not intended for human consumption or for keystroking, but GUID fields can be added to Specify’s data forms for viewing. Specify stores UUIDs as strings of 36 characters, e.g. f81d4fae-7dec-11d0-a765-00a0c91e6bf6. UUIDs are automatically assigned when new records are created through Specify’s data forms or through the WorkBench. They are permanent, read-only, and do not change when records are edited. Specify has GUID fields in these data tables: Agent, Attachment, Collection, Collecting Event, Collection Object, Determination, Geography, Geologic Time Period, Institution, Journal, Litho Stratigraphy, Locality, Reference Work, and Taxon.

The Specify 6.5 update modifies the Specify database schema and therefore requires the username and password of the Specify “IT User” (a MySQL user with root-level privileges on your Specify database) to complete.  In addition to making schema changes, the update assigns UUID values to records in the tables listed above with the exception of Geography and Taxon. The Specify 6.5 installer does not overwrite data in Specify’s GUID fields. The installer checks for data in GUID fields and if it finds a single record with data, it passes over that data table and no UUIDs are assigned to it. However, new collection data records will be assigned UUID values in all tables with GUID fields (except for Geography and Taxon) when they are created. Collections which previously utilized Specify’s GUID data fields for other purposes should contact the Project for assistance to accommodate that data.

Specify Schema Mapper

The Schema Mapper is a capable, visual tool for organizing data to export.  Collaborative project databases and data aggregators commonly prescribe data field types and column headings for collection data transfers in file formats. Earlier versions of Specify would allow users to export data only into a pre-defined and pre-loaded export file schema templates. The Specify 6.5 Schema Mapper is much more versatile. It allows one to choose which data fields in the Specify database will be represented in the export data file and then enables the names of the export data fields or columns to be changed to match the standards of the destination database. Starting with a pre-defined export schema, like one of the many Darwin Core variants (DwC), it is now possible to adjust which DwC concepts will be mapped to which Specify data fields. The Schema Mapper is also used for exporting data to the new the Specify 6 web portal. The Schema Mapper provides outstanding flexibility for mapping specimen database information to alternate formats for project collaboration and data aggregation.


Specify Web Portal

The new Specify 6 Web Portal is a full-featured web interface for public access to specimen data and images. It is an optional component of a Specify installation. Working from an exported copy of a Specify collection database, the Web Portal provides full-text indexed searches, structured, and spatial queries of specimen holdings. Express searches are fast with full-text indexing on every word in the database. Structured queries allow precise control of the search scope and multi-field queries can be constructed with AND or OR logic. Searches can be qualified to return only records with geo-coordinates or with attached images.

The Specify Web Portal displays specimen information in three views–Records, Images, and Map. On the “Records” tab specimen data are shown in a traditional grid view. The choice and number of data fields to display in the web interface is determined by each collection, and web users can sort and re-arrange data columns during a session. The search panel is customizable with an institutional logo or brand image, and the pages can be embedded into institutional content management systems or web platforms by a web programmer.

The image below shows the Specify Web Portal data display on the “Records” tab. The floating “Detail” popup window appears as a result of clicking on a data record and provides access to detailed information for the specimen, any associated images and a map if the specimen is georeferenced.

Specify Web Portal Data View

In the “Images” tab images linked to records are shown. Clicking on the thumbnail images opens a floating window with a larger view which provides links back to the specimen detail information.

Specify 6.5 Web Portal Image Tab

[Wait – are you new to Specify and just evaluating? Should you use Specify? Bring the above image into the middle of the screen and use your mouse scroll wheel to move up and down 1 wheel click quickly. Let the fish answer.]

In the Web Portal “Map” tab, clicking on an occurrence pin opens a floating window which shows the detail record for that specimen.

Specify Specimen Record Detail

Map-based spatial queries are effected by panning and zooming the map window to an area of interest, and then executing the query with the “Fit to Map’ option checked. In this example, the browser map window was originally sized to the green box, then a query restricted to Family was run. Matching records are those which occurred in the original map area and in the family Percidae. Clicking on the Records and Images tabs would show the tabular data and any attachments for that result set.

Specify Spatial Query Detail Fish

The Specify Web Portal is an effective tool for publishing specimen data–it is configurable and customizable. Specify’s Schema Mapper and Data Export tools make issuing updates from a Specify collection database easy. The Web Portal is intended for institutional web server computers; setup requires the technical expertise of a server or network administrator. Installation information is available on the Specify web site Documentation page in the file: Using the Specify Web Portal (PDF).