fix: mappings/VegCore-VegBIEN.csv: taxonoccurrence.sourceaccessioncode: need to populate from aggregateOrganismObservationID when only that is available
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.
bugfix: inputs/VegBank/: taxonOccurrenceID: include the aggregateOrganismObservationID in this so that there is one taxonoccurrence for each stratum's taxonImportance. this allows the different strata to have separate taxonoccurrences that are associated with the stratum-specific locationevents, rather than all being lumped into one taxonoccurrence, with only one locationevent.
inputs/VegBank/stemcount_/map.csv: stratum_id: removed table prefix so it can be used as a join column
inputs//: don't import joined tables, because they are now imported in the taxon_observation.** left-join instead
inputs/VegBank/stemcount_/postprocess.sql: moved stemcount___parent index before the derived columns section because it does not depend on them
bugfix: inputs/VegBank/stemcount_/postprocess.sql: added missing index on taxonOccurrenceID, needed for the 1:many portion of the taxon_observation.** left-join
inputs/VegBank/stemcount_/postprocess.sql: added primary key. note that the inserted row count changes, most likely because the rows are now in sorted order.
inputs/VegBank/: prepended the table name to each column name to prevent column collisions, using the steps at http://wiki.vegpath.org/Left-joining_a_datasource
inputs/VegBank/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource
inputs/VegBank/stemcount_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
inputs/*/*/test.xml.ref: updated source.shortname for new datasource name, which now starts out with .new suffix
bugfix: inputs/VegBank/stemcount_/map.csv: aggregateOrganismObservationID: prepend taxonimportance_id so that rows with only a taxonimportance entry (no stemcounts) will also have the required sourceaccessioncode
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
inputs/*/*/logs: updated svn:ignore
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-VegBIEN.csv, inputs/*/*/map.csv: Applied term renamings from the new dynamically generated Veg+-VegCore.csv, which reflects the current state of the data dictionary. (Permanently switching to the new Veg+-VegCore.csv will be a separate change.) Updates to VegCore term names that have occurred since the data dictionary was created are now able to take effect, which involves remapping and inferring units on several fields.
mappings/VegCore.csv: Regenerated from wiki
mappings/VegCore-VegBIEN.csv: Removed taxonlabel for original taxondetermination, because the original taxondetermination is not scrubbed by scrub.make (only the most current taxondetermination gets scrubbed, because only a single scrubbed determination is added by scrub.make). This still leaves the original taxondetermination's taxonverbatim, which stores the taxonomic information for historical purposes.
mappings/VegCore-VegBIEN.csv: primary taxonlabel's parent taxonlabel: Fixed bug where a taxonverbatim was incorrectly being created solely to store the taxonRank, even though it was already stored in the taxonlabel's rank field
inputs/VegBank/: Joined together taxonimportance and stemcount tables to create stemcount_, because stemcount actually stores stem abundance by size, rather than grouping stems by organism (http://vegbankdev.nceas.ucsb.edu/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename)
mappings/VegCore-VegBIEN.csv: Mapped locality description fields to location.iscultivated using _locationnarrative_is_cultivated()
db_xml.py: put(): _setDefault(): Support setting multiple col_defaults at once by using the param names themselves as the column names
mappings/VegCore-VegBIEN.csv: Set the source_id col_default to the datasource name using the new _setDefault() built-in function and _env()
mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot
schemas/vegbien.sql: aggregateoccurrence: Made taxonoccurrence_id optional when sourceaccessioncode is specified, so that aggregateoccurrence doesn't get pruned away in datasource tables that link just a stemobservation to a plantobservation (and therefore don't provide a taxonoccurrence to satisfy the previous taxonoccurrence_id NOT NULL constraint)
schemas/vegbien.sql: taxonoccurrence: Added taxonoccurrence_required_key check constraint to ensure that all taxonoccurrences are properly identified, and empty taxonoccurrences are properly pruned. This fixes a bug where taxon-only and stem-only data did not properly prune the taxonoccurrence that would otherwise get created because it's included in the mappings.
inputs/VegBank/stemcount/map.csv: stemheight: Remapped to height_m using units from <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>
schemas/vegbien.sql: taxonoccurrence: taxonoccurrence_unique_within_locationevent unique index: Fixed bug where locationevent_id needed to be enclosed in COALESCE so that the unique constraint also applies to rows with NULL locationevent_ids (there is no other unique constraint handling these rows)
inputs/*/*/map.csv: Prefix a * to every term that's not in Veg+ for easy identification of unmapped terms when editing map.csv. Note that canon will remove the * when it finds a matching Veg+ term.
inputs/VegBank/stemcount/map.csv: Fixed bug where taxonimportance_id needed to point to aggregateOccurrenceID instead of taxonOccurrenceID
mappings/VegCore-VegBIEN.csv: Don't forward individualID to taxonoccurrence.sourceaccessioncode when aggregateOccurrenceID is present
inputs/VegBank/: Added stemcount/
