This page describes the Perl scripts and HTML pages that are used for the UCMP Specimen Database. The database design is based on the Go Model.

To implement this database, you will need:

• a UNIX-based web server (we use Apache)
• a UNIX-based relational database (we use MySQL)
• Perl 5.0 or higher
• DBI and the DBD for your database
• paleo.tar.gz, the source code for the database, described below

Contents of paleo.tar.gz are described in the following sections:

These Perl scripts are run by cron, usually nightly. They create the browselists, select lists, administrivia, etc. by doing queries to the database and then creating text lists and/or html pages.

• gaps.p - makes a list of specimen numbers, showing gaps in numbering
• make_select_lists.p - daily counts, menu selections for drop-down lists
• make_invert_browselist.p - public & admin taxonomy lists
• make_micro_browselist.p - public & admin taxonomy lists
• make_plant_browselist.p - public & admin taxonomy lists
• make_vert_browselist.p - public & admin taxonomy lists
• make_loc_browselist.p - public & admin state & country lists
• make_photo_browselist.p - lists of photos

These Perl scripts handle input from the html forms below. They send queries to the database and create html pages that display the results.

• add_locality - add/update/delete a locality
• add_specimen - add/update/delete a specimen
• people_add_update - add/update/delete a person
• batch_update - update publications, taxonomy, etc. for multiple records
• help - runs the Help menu system (pop-up Help on input forms)
• label - prints labels
• query - processes all queries to specimen and locality tables
• myschema.p - contains the SQL table schema and other variables
• myquery_utils.p - contains utilities for web/MySQL interaction
• utils.p - contains assorted utilities for computing, printing, prettying up, etc.

These are the HTML pages for search forms, browse lists, and administrative tasks. The top level directory contains public forms; admin forms are in the admin/ directory.

• index.html - simple query form for specimens
• advanced.html - advanced query form for specimens
• loc.html - query form for localities
• about.shtml - scope, system, searching, credits
• disclaimer.shtml - usage & disclaimer for data
• favicon.ico - bitmap icon for browsers
• robots.txt - search engine exclusions
• query_help.html - help page for queries
• Browse_Countries2.html - browse list of countries (generated by bin/make_loc_browselist.p)
• Browse_US_states2.html - browse list of states (generated by bin/make_loc_browselist.p)
• Invert_orders2.html - browse list of invertebrate orders (generated by bin/make_vert_browselist.p)
• Micro_orders2.html - browse list of microorganism orders (generated by bin/make_micro_browselist.p)
• Plant_orders2.html - browse list of plant orders (generated by bin/make_plant_browselist.p)
• Vert_orders2.html - browse list of vertebrate orders (generated by bin/make_vert_browselist.p)
• title.html - 1 of 4 include files for all static HTML pages
• head1.html - 2 of 4 include files for all static HTML pages
• head2.html - 3 of 4 include files for all static HTML pages
• footer.html - 4 of 4 include files for all static HTML pages

Directories in "html/":

admin/

Administrative forms for adding, editing and deleting specimen and locality records, adding admin users, and other bookkeeping tasks. UCMP does not permit public access to all fields in the database. For example, lat/long data is not available to the public for nearly all records. Therefore, this directory contains its own query and browse forms. The forms that change or delete data require the name and password of an authorized admin user, and new admin users can only be added by the collection managers. UCMP protects this directory with .htaccess and .htpasswd files.

• index.html - start page for administrative forms
• coll_mgr_forms.html - extended list of admin forms
• query_spec.html - admin query specimens
• query_loc.html - admin query localities
• batch_updates.html * - batch update publications, taxonomy, museum loc (rack & bay)
• correct_locnum.html * - correct the locality number for an existing record
• correct_specno.html * - correct the specimen number for an existing record
• delete_locnum.html * - delete an existing locality
• delete_specno.html * - delete an existing specimen
• loc_add_update.html * - add or edit a locality
• specimen_add.html * - add or edit a specimen
• people_add_upd.html * - add or edit an authorized admin user
• epoch_period_era.html - a list of accepted epochs & periods
• gaps.html - a list of gaps in specimen numbering (generated by bin/gaps.p)
• htaccess_info.txt - instructions for setting up htaccess
• loc_stds.html - standards used for county, state, country, continent
• public_access.html - notes about public access vs. admin access
• Browse_Countries2.html - browse list of countries (generated by bin/make_loc_browselist.p)
• Browse_US_states2.html - browse list of states (generated by bin/make_loc_browselist.p)
• Invert_orders2.html - browse list of invertebrate orders (generated by bin/make_vert_browselist.p)
• Micro_orders2.html - browse list of microorganism orders (generated by bin/make_micro_browselist.p)
• Plant_orders2.html - browse list of plant orders (generated by bin/make_plant_browselist.p)
• Vert_orders2.html - browse list of vertebrate orders (generated by bin/make_vert_browselist.p)
• template.html - template for static HTML pages
• title.html - 1 of 4 include files for all static HTML pages
• head1.html - 2 of 4 include files for all static HTML pages
• head2.html - 3 of 4 include files for all static HTML pages
• footer.html - 4 of 4 include files for all static HTML pages

* these forms require the name & password of an authorized user

graphics/

Misc. images and icons, etc. - additional images can go here

help/

These ".inc" files are used by many of the forms to create pop-up help windows when the name of a database field is clicked.

maps/

This directory contains configuration files for BerkeleyMapper. This allows database query results to offer the option of displaying results on a map. See the BerkeleyMapper link for more info.

• README.txt - instructions for the configuration files
• ucmp2_admin.xml - displays specimens as points on a map (lat/longs)
• ucmp2_public.xml - displays specimens at county level only
• ucmp_loc2_admin.xml - displays localities as points on a map (lat/longs)
• ucmp_loc2_public.xml - displays localities at county level only

photographers/

These are forms for adding UCMP specimen and locality photos to CalPhotos, provided here for informational purposes only, since they are customized for UCMP use. However, CalPhotos is available for uploading world-wide photos of natural history subjects - see the website for more info.

• index.html - start page for UCMP photographers
• ucmp_add.html - add a new UCMP photo to CalPhotos (a UCMP-specific version of this CalPhotos page.
• ucmp_add_photographers.html - add a new UCMP photographer (a UCMP-specific version of this CalPhotos page.
• ucmp_photographers_policy.html - UCMP's policy on photos

photos/

Public query forms to browse/query photos in CalPhotos where 'collection' is "UCMP".

• index.html - query UCMP photos in CalPhotos (can be modified for use by other CalPhotos collections beside UCMP)
• browse lists - these are informational only; they are generated for UCMP by virtue of the shared database arrangement between CalPhotos and UCMP

select_lists2/

These ".txt" files provide summary lists of what's in the database, such as countries, collector names, periods and epochs, as well as record counts (i.e., number of specimens) from the database. These are used for the drop-down menu selections on HTML forms and for the "total" counts that appear on many of the pages. These text files are generated by bin/make_select_lists.p, which is run nightly by cron.

This directory contains the SQL statements for UCMP's MySQL database tables. Very little modification, if any, would be needed for other relational database vendors, since standard SQL is used. The CREATE TABLE files include indices.

• ucmp2.sql - CREATE TABLE for specimens
• ucmp_loc2.sql - CREATE TABLE for localities
• ucmp_countries.sql - CREATE TABLE for countries & continents
• ucmp_people.sql - CREATE TABLE for people
• ucmp2_deleted.sql - mirrors ucmp2, used by cgi scripts to store deleted specimen records
• ucmp_loc2_deleted.sql - mirrors ucmp_loc2, used by cgi scripts to store deleted locality records
• ucmp_people_deleted.sql - mirrors ucmp_people, used by cgi scripts to store deleted people records
• ucmp_countries.load - load file for ucmp_countries