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
Moved test scripts and files from util to test
xml_func.py: Added _namepart function for extracting parts of names
Finished NYBG mapping to VegBank\!
test_map: Added debug option to print VegBank XML instead of importing it into the database
xpath.py: Created is_positive() function
Further refinements to mappings to support database constraints
xpath.py: Added support for negative attribute assertions with !
Changed mappings to use keys vs. attrs
xpath.py: Fixed creation of attrs so it happens even when node already exists
xpath.py: Added concept of keys vs attrs in XPath elem
Started filling in required values for VegBank fields in mappings. Will need to refactor to move these to metadata for the datasources.
Now allow empty rows. Added support for select statement limit.
Added support for quoted values in XPaths
Fixed name XML function. Fixed accept_test_output.
Added support for name XML function. Added error handling for empty rows.
Made it easier to accept test output
Added NYBG stemCount metadata
Added xml_func.py to process mappings whose output needs postprocessing
Changed VegBank mappings to use XML functions (not implemented yet) to calculate averages and ranges
Added support for mapping datasource metadata
Changed for loops to use enumerate() where the index is also needed
Moved XPath prep code (setting ID, value) to xpath.py
xpath.py: Added deepcopy() before setting value of other branches to traverse
NYSpecimenDataAmericas.test.xml: Updated for new NYBG-VegX.organisms.csv
NYBG-VegX.organisms.csv: Changed voucher (primary key) column to be UniqueNYInternalRecordNumber because CatalogNumber contained an empty value
xpath.py: Added basic support for split paths
Merged xml_xpath.py into xpath.py in preparation for changing the XPath parse tree to be the XML DOM tree itself
Refactored xpath.parse() to use a nested function instead of a class extending Parser
map: Fixed mislocated import for Parser.SyntaxException
Removed SALVIAS voucher_string mapping per conference call discussion
