bugfix: inputs/IRMNG/: renamed to inputs/.IRMNG/ so that this comes before TNRS, which depends on it (this is a metadata datasource, so it can start with "."). part of issue #940.
inputs/input.Makefile: add: verify/: also svn:ignore *.log
lib/sh/make.sh: self_make(): renamed to with_rm() for clarity, since this is used only to progagate $rm, and does not also invoke a command with the same name as the current function, as the name might suggest
*{.sh,run}: use new begin_target instead of `echo_func; set_make_vars`
inputs/input.Makefile: add!: verify/: also svn:ignore *.tsv, *.txt
moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).
fix: bin/map: put template: comment out the "Put template:" label so that the output is valid XML, and displays properly in a browser rather than showing a syntax error
bugfix: mappings/VegCore-VegBIEN.csv: nest all taxonoccurrences inside a stratum event, so that the parent locationevent is always fully populated before child locationevents point to it. (previously, a stub parent event was created when the child event was imported first, which blocked the fully-populated parent event from being inserted later on.) this uses auto-folding (for VegBank/CVS) and auto-forwarding (for other datasources) to prune empty stratum events for taxonoccurrences that don't have strata. (see wiki.vegpath.org/Auto-folding, wiki.vegpath.org/Auto-forwarding for more info about these normalization techniques.) note that the inserted row counts stay exactly the same for all datasources except VegBank (which was being fixed), indicating that this signficant change to the mappings did not change the semantics of the import of taxonoccurrences.
inputs/*/*/test.xml.ref: updated source.shortname for new datasource name, which now starts out with .new suffix
inputs/IRMNG/_README.TXT: added note that when refreshing this datasource, remember to regenerate the TNRS derived cols using the instructions in inputs/.TNRS/schema.sql > tnrs_populate_fields()
inputs/*/Source/VegBIEN.csv: regenerated for new-style import, which uses a symlink to mappings/VegCore-VegBIEN.csv instead of a custom mapping using the original column names
bugfix: inputs/*/Source/map.csv: added missing row_num entry, which is needed by the staging table column renaming to make the order of the map.csv columns match the order in the staging table. the staging table column renaming is now used by all Source tables.
bugfix: inputs/input.Makefile: %/VegBIEN.csv: for new-style datasources, use a symlink to mappings/VegCore-VegBIEN.csv directly instead of prefiltering VegCore-VegBIEN.csv to include only the columns in map.csv. prefiltering used to be performed as part of mapping the map.csv VegCore output terms to VegBIEN using bin/join, but is no longer needed because the staging table columns are now VegCore terms. instead, the full VegCore-VegBIEN.csv is needed so that derived columns added in stage I or II validations are detected by bin/map (rather than just the original source columns in map.csv).
bugfix: inputs/*/Source/data.csv for new-style datasources: need to include a blank row (plus a blank header) so that the metadata values are imported at least once instead of zero times, now that there is an installed staging table that will be iterated over. the blank row did not used to be necessary, because db_xml.put_table() has a special case for metadata-only tables with no installed table, which avoids iterating over the table's rows.
inputs/*/Source/ for new-style datasources: use an actual staging table instead of a metadata-only table, so that metadata values can be stored in the staging table instead of the map.csv (as will be required by new-style import)
added inputs/IRMNG/*_homonym_epithet/map.csv, etc. (created by */run)
added inputs/IRMNG/{genus_homonym_epithet,family_homonym_epithet}/run, which inherit from ../table.run so that load_data() (which runs create.sql) is invoked
added inputs/IRMNG/species_homonyms/new_terms.csv
bugfix: added no-op inputs/IRMNG/Source/run so inputs/IRMNG/run would have something to invoke for it
inputs/IRMNG/run: use lib/runscripts/datasrc_dir.run, which now provides import() and $subdirs
inputs/IRMNG/: added family_homonym_epithet, genus_homonym_epithet lookup tables, which use util.all_same() to filter out internal Plantae homonyms
bugfix: inputs/IRMNG/import_order.txt: need to specify order so that Source is first
bugfix: inputs/IRMNG/*/map.csv: remapped Authority to scientificNameAuthorship instead of authors (now data_authors <VegCore.vegpath.org?data_authors> for clarity)
inputs/IRMNG/map.csv: updated to scrubbed output names from */map.csv (/map.csv does not currently get scrubbed)
bugfix: inputs/IRMNG/species_homonyms/header.csv, map.csv: reset input columns to DSV (delim-separated values) header. they had gotten changed to the output names in running map.csv with remake=1, causing it to be remade from the (renamed) staging tables.
inputs/input.Makefile: $(_svnFilesGlob): added *Makefile
added inputs/IRMNG/, including runscripts to download the names. this is now the 2nd datasource after GBIF to use runscripts, and the 3rd after FIA/GBIF to use new-style import.
