fix: inputs/input.Makefile: add!: verify/: also svn:ignore .zip

fix: *Makefile: changed line endings to \n so that `patch` can work with pasted input. use `svn di --extensions --ignore-eol-style` to verify no diff.

inputs/input.Makefile: add: verify/: also svn:ignore *.log

schemas/vegbien.sql: specimenreplicate.institution_id: renamed to duplicate_institutions_sourcelist_id, as decided in the conference calls (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2)

mappings/VegCore.htm: regenerated from wiki: rename specimenHolderInstitutions to specimen_duplicate_institutions, as decided in the 2014-03-13 conference call (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2). note that most schema changes (such as this one) involve mappings changes, which are handled automatically by `inputs/run postprocess; yes|make inputs/{NVS,SALVIAS,TEAM}/test`.

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).

copyright scrub: inputs/: removed data provider-owned schema and documentation files, which are not BIEN copyright and should not be part of what is submitted for open-sourcing. these files will remain accessible via the web interface (fs.vegpath.org), but will not be in the repository.

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

bin/my2pg: comment out COMMENTs instead of removing them so that they will be included in the PostgreSQL translation. COMMENTs contain important metadata about columns, such as definitions and the meanings of integer flag values.

inputs/{.,}*/*.schema.sql: regenerated using the instructions in bin/my2pg. this primarily replaces timestamp with text/*timestamp*/ (to preserve indefinite dates).

bugfix: inputs/BRIT/specimen_flat/postprocess.sql: diameterBreastHeight_cm, height_m: use newly NULL-mapped versions of columns instead of the *_verbatim columns

inputs/BRIT/: switched to new-style import, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource

inputs/BRIT/specimen_flat/: translated multi-column filters with _join() to postprocessing derived columns, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns

inputs/BRIT/specimen_flat/map.csv: Habitat_Summary: remapped to UNUSED

inputs/BRIT/specimen_flat/postprocess.sql: diameterBreastHeight_cm, height_m: updated runtimes

inputs/BRIT/specimen_flat/: DBH_*, Height_*: mapped NULL-equivalent values, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns

inputs/.../: translated multi-column filters with _avg() to postprocessing derived columns, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns

inputs/BRIT/specimen_flat/: translated single-column filters to postprocessing derived columns, using the steps at wiki.vegpath.org/Switching_to_new-style_import#stage-I-source-specific > "translate single-column filters to postprocessing derived columns"

inputs/*/*/map.csv: added distinguishing #... suffix (e.g. UNUSED#institutionID) to the special terms OMIT, PRIVATE, UNUSED (VegCore.vegpath.org#Special-terms) to avoid creating a collision in the staging table renaming

bugfix: inputs/*/*/postprocess.sql: made all operations idempotent, so that postprocess.sql can be run repeatedly (e.g. by new-style import)

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/*/Source/: added missing ./run, which creates the new-style staging tables with the metadata fields as part of the table. this is needed now that these subdirs use installed staging tables instead of metadata-only map.csvs.

inputs/*/: added table.run for use by the table subdirs in new-style import. datasources without table subdirs do not need this.

inputs/*/: added top-level Makefile which includes inputs/input.Makefile, so that make can be run directly on the datasrc dir without needing to specify `--makefile=../input.Makefile` (see input.Makefile $(selfMake))

bugfix: inputs/*/Source/: use installed staging table (with blank-line data.csv) in order to also work with new-style import. this also fixes a benign diff between the by-row and by-col test outputs, where row-based import would not import the Source/ entries because there was not at least one row in the input. note that in order to ensure that all datasources are properly run, you need to check `svn st|sort` against the datasource schema names to see if any are missing.

empty inputs/*/import_order.txt: added subdirs in the order they are used by inputs/input.Makefile, by running make on the inputs to auto-populate import_order.txt. import_order.txt is needed by the runscripts to run the right set of subdirs in the right order.

mappings/VegCore-VegBIEN.csv: genus->taxonlabel.taxonomicname: filter out genera that contain numbers (using new _filter_genus()), which break TNRS and prevent it from matching any other parts of the name. later, these genera can instead be moved to the end of the name, where TNRS will correctly match them as Unmatched_terms.

inputs/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files

inputs/input.Makefile: %/.map.csv.last_cleanup: Run fix_line_endings after canon/translate to standardize Python's \r\n line endings back to \n. This prevents issues with mixed line endings because LibreOffice (and probably Excel) treat all cell-internal line endings as \n but row line endings as whatever the file had, while text editors like jEdit translate all line endings to whatever the autodetected line ending is. (This creates spurious line ending diffs when a map spreadsheet containing multiline cells is edited in a text editor.)

mappings/VegCore.htm: Regenerated from wiki. Renamed specimenHolders to specimenHolderInstitutions to make it obvious that this is a list of institutions, such as would be in institutionCode in a DwC export.

inputs/BRIT/specimen_flat/map.csv: Only map Notes_Plant to occurrenceRemarks if there is a separate Locality_Description, in order to filter out Notes_Plant values that concatenate everything together (often including a herbarium name that would mess up the cultivated flag parsing)

inputs/BRIT/_MySQL/MySQL.*.sql.make: Include all tables, not just specimen_flat

inputs/BRIT/specimen_flat/test.xml.ref: Updated inserted row count

inputs/BRIT/specimen_flat/postprocess.sql: Added primary key

mappings/VegCore.htm: Regenerated from wiki. Remapped organismNotes to be a synonym of occurrenceRemarks, since notes on an organism are more generally notes on an occurrence.

mappings/VegCore-VegBIEN.csv: Mapped occurrenceRemarks

mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions

Mapped inputs/BRIT/

README.TXT: Datasource setup: MySQL inputs: Editing _MySQL/*.make: Set $server to vegbiendev instead so the export command will work from any machine (though it will be faster from vegbiendev itself)

inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where needs to be set to just localhost and --user to bien instead

inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where $server needs to be set to bien@localhost

inputs/BRIT/: Added _MySQL/MySQL.*.sql.make

Added inputs/BRIT/ (not yet translated to PostgreSQL)