xml_dom.py: Added minidom.Document write_opening() and write_closing() methods. Changed writexml(writer, node) to use new Node.writeprettyxml() method.
Renamed ex.py to exc.py
Import xml.dom.minidom as minidom
xml_dom.py: Refactored xml.dom.minidom.Element.writexml() to use new write_opening() and write_closing() methods. Use new functions is_elem() and is_text_node() to determine node type. Corrected definition of a text element to be an element that contains a single text node.
bin/map: Factored out input processing code
Commit after inserting each row
Use traceback.print_exc() to print Exceptions for each row instead of exiting
env_password: Allow user to change saved password
env_password: Don't print instructions for storing password for the session if called to store password for the session
env_password: Print absolute path to env_password in case invoking script changed the working directory
env_password: Print instructions for storing password for the session
Updated SALVIAS plots mappings and corresponding VegX-VegBank mappings to parse date_start and date_finish
xml_func.py: Print XML of XML functions with SyntaxExceptions
xml_func.py: Added support for parsing dates
ex.py: repl_msg(): take replacements as keyword args
fix_permissions: Also change user to bien
Makefile: Added python-dateutil dependency
input.Makefile: Renamed from_db-<map_file> target to import-<type> so it can be more easily run as a command-line target rather than just a prerequisite
Added inputs/SALVIAS organisms map
map: Print xml_func.SyntaxExceptions without stack traces by using SystemExit
xml_func.py: Add function name to SyntaxException message
ex.py: Added repl_msg() to format a message with the % operator
xml_func.py: Return string->number conversion errors as xml_func.SyntaxExceptions
psql_vegbien: Fixed comment to vegbien instead of vegbank
psql_vegbien: Use new location of bien_password
Makefile: Fixed paths to mappings dir for new scripts dir location
Renamed util to bin
Moved inputs_Makefile to inputs/input.Makefile
Moved bien_password to new config dir
Moved sample inputs to test dir
Added symlink from scripts to new scripts destination
Removed now-empty scripts dir
Moved everything in scripts to root. inputs_Makefile: Don't run "all" when installing.
Renamed bien_map to map
Moved map to util
fix_permissions: Don't chmod symlinks
inputs_Makefile: Auto-generate map to VegBIEN and import data into vegbien from input DB
inputs/SALVIAS: maps to VegX and VegBIEN
bien_map: Runs map with BIEN defaults
join_sort: Sorts a join on the output col
inputs_Makefile: Require dbEngine var instead of defaulting to MySQL
Moved inputs into svn
Moved pre-BIEN 3 files into _archive folder
test/map: Use db.sh syntax in *.sh tests
inputs_Makefile: Generate db.sh with DB access info
inputs_Makefile: Changed GRANT ALL to GRANT SELECT. Added REVOKE ALL. Added $(db).sql as prerequisite of install in case it needs to be auto-generated.
scripts/Makefile: Added action for postgres-Darwin target
scripts/Makefile: Added postgresql to postgres-Linux apt-get packages
test/map: Changed to work on both nimoy and vegbiendev by selecting the appropriate MySQL user and password
env_password: Added optional message arg
Added uninstallation of inputs to Makefiles
scripts/Makefile: Create bien user w/o prompting for password. Fixed syntax error.
scripts/Makefile: Fixed syntax error
Inputs now include inputs_Makefile to get mysql command, etc.
scripts/Makefile: Use bien MySQL user for installing inputs
scripts/Makefile: Use root MySQL user for creating bien user
scripts/Makefile: Don't use root as MySQL admin user. Removed no-longer-needed sub-makes for setting DB login vars.
Changed vegbien_dest and users of it to use separate bien_password file
fix_permissions: Extend all user permissions to group
scripts/Makefile: Added inputs
mappings/Makefile: Cleaned up
fix_permissions: Don't add group write perms to read-only files
scripts/Makefile: Made read command syntax compatible with /bin/sh
scripts/Makefile: Ignore errors about missing packages
scripts/Makefile: Fixed escape character for /bin/sh
scripts/Makefile: Added dependency installation. Makefiles: Use _not_file instead of FORCE for clarity. Use $(os) var
fix_permissions: Configured output verbosity
Added fix_permissions to set correct permissions on shared bien files
Removed VegBank scripts which are no longer needed
Renamed vegbien_dest.sh to vegbien_dest to reflect that it is also includable by Makefiles
DB user creation: Clarified instructions
scripts/Makefile includes vegbien_dest.sh directly
Moved db user creation to scripts/Makefile. Removed now-unneeded admin scripts.
scripts/Makefile: Added empty_db target which uses vegbien_empty.sql
mappings/Makefile: Fixed bug where var containing prerequisistes needed to be defined before used. Added support for different sed flags to use extended regular expressions.
Added auto-generated vegbien_empty.sql to empty the vegbien db
Test output to VegBIEN instead of VegBank
VegX-VegBIEN.organisms.csv: sort output of repl
review: Added nullglob
review: Don't process replacements spreadsheets
Moved schema replacements from VegBank-VegBIEN.csv to VegBank-VegBIEN.schema.csv
VegBank-VegBIEN.csv: Support PostgreSQL before 8.4
repl: Added support for blank lines. Only add whole word regexp code to inputs w/o any regexp metachars.
Create vegbien db from mappings/schemas/vegbien.sql
VegBank-VegBIEN.csv: Added replacements for SQL create script conversion
Generate vegbien db create SQL from vegbank.sql using repl
repl: Fixed bug in reading arguments
repl: Don't add whole-word regexp for inputs that already have regexp metachars
Removed mappings/VegBank-VegBIEN.organisms.csv because now using replacements spreadsheet
mappings: Generate mappings to VegBIEN using VegBank-VegBIEN.cs replacements spreadsheet
Added repl to perform replacements on a spreadsheet or file
scripts/Makefile: removed extra test-% target
README.TXT: Updated
scripts/Makefile: install/uninstall targets
