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
bien_user_create: Print instructions in sequence with password prompts
mappings to VegBIEN: Accounted for remaining ALTER TABLE statements
Renamed format*_for_review to review and added for_review to make clean
mappings: Added mappings to VegBIEN
mappings/Makefile: Simplified
Added vegbien DB admin scripts
join_all_vegbank: Sort output by both columns
mappings/VegX-VegBank.organisms.csv: Sorted by both columns
mappings/Makefile: Sort VegBank-VegBIEN.organisms.csv by both columns
extract_plot_map: Removed because functionality now in Makefile
sort: Can sort on multiple columns
Added basic VegX-VegBIEN mapping
Added union and join_passthru
env_password: Print Usage message to stderr
test/map: Create output dir if it doesn't exist
Converted scripts back to bash that required bash-specific features
Fixed test/map to work with sh
Replaced /bin/bash with /bin/sh
join: Added usage item for repeated joins
join: Changed order of args and redirects to be more intuitive
Renamed ch_map_root to ch_root
Renamed join_maps to join
Merged test Makefile into main scripts Makefile
test/map: Turn off test mode (don't run diff) when env var n (for # rows) is set
Added SALVIAS DB mapping for plots data
VegX-VegBank mapping: Fixed VegBank XPath for commName.commName field
db_xml.py: Use pointer target's name as pointer type where possible. Emphasize that pointer type determined from the pointer name itself is a guess based on common database conventions.
xpath.py: Changed backward (child-to-parent) pointer ID abbr expansion to happen in get() when source node's tag name is known. This deals with XPath elements that are '.' being used as a pointer source.
xpath.py: Moved abbr expansion code to separate function
test/map: Process all tables for a given DB (.sh) input
Removed /'s from DB input mappings
map: Use row's index instead of pkey as ID in XML output
test/map: Compare via-VegX output to direct output
xpath.py: Changed order that main and other branches are processed in so it is consistent with the order the branches are specified in the XPath
map: Handle metadata in order with regular mappings
Accepted VegBank test output for new CSV mapping order
map: Changed CSV input to process mappings in the order they are in the spreadsheet, rather than the order of the CSV columns
map: Added support for XML input
Accepted new test output for sorted SALVIAS_db-VegBank mapping
mappings to VegBank: Sorted by output column to help VegX-VegBank conversion put elements in the same order as source-VegBank
join_all_vegbank: Updated to sort output maps
Added script to sort a spreadsheet
xpath.py: Allowed empty names in XPaths
xpath.py: Added automatic conversion of strings to paths where needed.
xpath.py: Added caching of parsed XPaths. Added automatic conversion of strings to paths where needed.
Added str() method to XML nodes
Fixed VegX-VegBank mapping syntax error
Added faded beginning of string in Parser syntax errors
Updated mappings Makefile
Added Makefiles for scripts and test
Added mappings Makefile
Added human-readable SALVIAS_db mappings
db_xml.get(): Pass limit through to SQL query
Regenerated human-readable mappings
Fixed documentation for xml_funcs
Refactored xml_dom.set_value() to avoid needing a doc parameter for the XML document
xpath.py: Refactored xml_func.py to avoid needing a doc parameter for the XML document
xpath.py: Refactored to avoid needing a doc parameter for the XML document
