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
Fixed DB input to ignore NULL values
xml_dom.py: Changed all uses of name_of(node) to node.tagName
Made XML node names case-sensitive
mappings to VegBank: Fixed incorrect mappings found after disabling heuristic search for missing fields
test/map: Ignore diff exit status
map: Implemented DB input support for querying a single table
Added SALVIAS_db test accepted output
map: Continued to add DB input support
test/map: Echo command used to import db config
Added support for multiple database engines. Changed SALVIAS_db input to use user-entered password.
map: Allow db config vars to be optional. SALVIAS_db test: Changed to use salvias_plots and XPath mapping syntax.
Renamed SALVIAS_db test input to use organisms table
Re-committed accepted_outputs
Renamed test/map output to remove CSV/DB indicator because that is now specified in the datasource name
map: Started adding database get by XPath functionality
format_for_review: Fixed bug where Comments column would be reformatted in addition to mappings columns
Added human-readable versions of mappings and scripts to generate them
VegX-VegBank mapping: Removed a duplicated mapping
NYBG-VegX mapping: Added conference call feedback
Added Comments column with Brad's and Aaron's comments to mapping spreadsheets
Added stub for SALVIAS database test
test/map: Added support for database input
Preparing map to input from DB
Started preparing map to input from DB
xml_func.py: Added optimization to first check if function name starts with _ before looking it up in the table
Added _alt functions for mappings to VegBank authorPlotCode
xml_func.py: Added _alt function to choose between alternative values and used it for the collector plantName mapping
VegX-VegBank mapping: Added mapping from taxonName/Simple (NYBG ScientificName) to collector plantName so that collector plantName will always have a value
xml_func.py: Added support for decimal years (with day as the fraction)
test/map: Added echoing of commands run
Added psql_vegbank to easily access vegbank db from the command line
Ignore OpenOffice lock files in mappings
Added SALVIAS data CSVs and accepted test output
test/map: Expanded to include all input CSVs in test/input
Removed unneeded joins dir
Moved VegBank mapping joins to main mappings dir so they would have similar paths for the upcoming all-sources tester
