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/NCU/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource
inputs/NCU/Specimen/map.csv: OwnerInstitution: remapped to specimenOwner rather than specimenHolderInstitutions. OwnerInstitution, CatalogSeriesPrefix: documented the VegCore SQL dotpath (http://wiki.vegpath.org/SQL_dotpaths) that would be used to refer to the field. this specifies the destination field at a much finer level of detail than the one-size-fits-all denormalized name.
mappings/VegCore-VegBIEN.csv: mapped municipality
inputs/NCU/Specimen/map.csv: CityLocality: remapped to municipality because this is a placename, not a verbatim locality description
inputs/NCU/Specimen/: translated single-column filters 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/NCU/Specimen/map.csv: cultivated: Map false (0) to NULL because cultivated can only be true or NULL, not false
mappings/VegCore-VegBIEN.csv: institutionCode list->sourcename mapping: _split(): Also match ; as a separator, and match separators with or without a following space
mappings/VegCore-VegBIEN.csv: Mapped recordNumber to new specimenreplicate.collectionnumber
schemas/vegbien.sql: plantobservation: Renamed collectionnumber to authorplantcode since this number, which identifies the plant, is actually different from the collectionnumber that identifies the specimen collected from it. This distinction is meaningful for plots data, but generally not for specimens data.
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: Removed TNRS input taxonlabels meant to cross-link to taxonlabels added by the TNRS import, because TNRS taxondeterminations are now created instead
mappings/VegCore-VegBIEN.csv: institutionCode: Removed mapping to sourcename.matched_source_id, which is now autopopulated. Split any list of institutionCodes apart using new _split().
schemas/vegbien.sql: Allow multiple institutionCodes for each specimenreplicate by linking new sourcelist table many-to-many to source via sourcename (which is now a linking table)
inputs/NCU/: Refreshed data with new export from Bob
Renamed inputs/NCU-NCSC/ to NCU because this is the primary herbarium contained in the data
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: Mapped acceptedCounty, county to the matched place
schemas/vegbien.sql: coordinates: Changed coordinates.coordsaccuracy_deg units to m
mappings/VegCore-VegBIEN.csv: Removed _date/date, because _date using a string date argument is no longer supported under plpython3u (dateutil is missing). Note that PostgreSQL's own date parsing is sufficient for most dates, so this use of _date is not strictly necessary and removing it will improve import times.
schemas/vegbien.sql: Renamed reference -> source to make this table more broadly applicable, and because this now stores the datasource metadata
mappings/VegCore-VegBIEN.csv: matched place's coordinates: Fixed bug where coordinates entry itself needed to have its datasource (reference) set to geoscrub, in addition to the place entry that uses it, in order to match up properly with geoscrub's corresponding input place (whose coordinates as well as place are owned by the geoscrub datasource)
mappings/VegCore-VegBIEN.csv: decimalLatitude/Longitude->geoscrub input coordinates: Also set to NULL if 0 here, not just for the coordinates linked to the datasource's place instance
mappings/VegCore-VegBIEN.csv: matched place: Also map verbatim place's geoscrub-related fields to the matched place, to link up with geoscrub's corresponding input place
mappings/VegCore-VegBIEN.csv: Renamed creator_ids to reference_id since they are now fkeys to reference
schemas/vegbien.sql: Made creator_ids an fkey to reference instead of party, so that datasources are stored separately from people and to allow adding reference-type metadata (URL, copyright, etc.) for each datasource
schemas/vegbien.sql: taxonverbatim: Renamed binomial to taxonname because this field is actually the taxonomic name without the author, not just the genus+specific epithet binomial
mappings/VegCore-VegBIEN.csv: Remapped latitude/longitude to new coordinates table
schemas/vegbien.sql: Renamed placepath to place since this contains primary information about the place, including the reference to the canonical place
schemas/vegbien.sql: Link taxondetermination to taxonverbatim (which is a subclass of taxonlabel) instead of directly to taxonlabel. This will enable later having multiple taxonverbatims for one taxonlabel.
schemas/vegbien.sql: taxonlabel: Renamed identifyingtaxonomicname to taxonomicname because the taxonomicname provided by the datasource is now in taxonverbatim, so there is no name collision. Note that both of these fields store the same type of information, but taxonlabel's is autogenerated while taxonverbatim's is verbatim (and is only set if provided by the datasource).
schemas/vegbien.sql: taxonlabel: Moved non-scoping fields to new taxonverbatim subclass table, which contains the component parts of the taxonlabel
mappings/VegCore-VegBIEN.csv: Also create the identifyingtaxonomicname on the verbatim taxonlabel supplied by the datasource, in addition to on the TNRS input taxonlabel that the verbatim taxonlabel is matched up with
schemas/vegbien.sql: taxonlabel: Renamed taxonomicname to binomial because it excludes the author
schemas/vegbien.sql: Renamed taxonconcept to taxonlabel per today's conference call, where it was decided that taxonconcept contained too many unrelated fields to be purely a taxon concept
schemas/vegbien.sql: taxonconcept: Renamed canon_concept_id to matched_concept_id, because this is actually the closest-match taxonconcept in the match hierarchy (datasource concept -> parsed concept -> matched concept -> accepted concept) rather than the accepted synonym, which goes in accepted_concept_id
schemas/vegbien.sql: taxonconcept: Renamed canon_taxonconcept_id to canon_concept_id to shorten the name, which is used often
schemas/vegbien.sql: Renamed datasource_id to creator_id so it can apply generally to any entity (such as a person), not just an aggregated datasource. This also enables taxonconcept.datasource_id to merge with creator_id, which now serves the same purpose.
mappings/VegCore-VegBIEN.csv: Fixed bug where needed to set datasource_id=0 on the TNRS party (which concatenated names/TNRS inputs are owned by) in order to make it a datasource (a root party)
schemas/vegbien.sql: Renamed taxonpath -> taxonconcept as part of taxonomic schema refactoring at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/2012-10-03_conference_call#Taxonomic-schema-refactoring>
mappings/VegCore-VegBIEN.csv: taxonoccurrence.authortaxoncode: Only populate if needed to distinguish the taxonoccurrence within a plot
mappings/VegCore-VegBIEN.csv: non-TNRS taxonpaths: Store the concatenated identifyingtaxonomicname in a separate taxonpath owned by the TNRS datasource, so that it will match up with (and create a link to) the corresponding submitted TNRS name's taxonpath. This in turn is linked to the TNRS-determined accepted name, thus creating a three-level hierarchy of datasource name -> concatenated name -> accepted name.
mappings/VegCore-VegBIEN.csv: taxonomic terms: Remapped the concatenated taxonomic name to new identifyingtaxonomicname to use it directly to match up with the TNRS submitted name. Continue to map scientificNameWithAuthorship to taxonomicnamewithauthor.
mappings/VegCore-VegBIEN.csv: Taxonomic terms: Also join terms together in taxonomicnamewithauthor if scientificNameWithAuthorship is not provided, for use by TNRS
schemas/vegbien.sql: Replaced "scientific name" with "taxonomic name" for schema-wide consistency and for consistency with the taxon/taxonomic name vocabulary
mappings/VegCore-VegBIEN.csv: Forward occurrenceID to taxonoccurrence.sourceaccessioncode when there is no other taxonoccurrence.sourceaccessioncode, to ensure that taxonoccurrence is uniquely identified so that there is one taxonoccurrence per organism
mappings/VegCore-VegBIEN.csv: verbatimElevation->elevation_m mapping: Translate units automatically (currently only works in row-based mode). Don't remove any "ca." prefix because this is a datasource-specific filter that does not apply to current datasources with verbatimElevation. Also map verbatimElevation to location.verbatimelevation.
schemas/vegbien.sql: Added units suffix to all core VegBIEN fields that have units. It is the responsibility of the mappings to ensure that all units are properly translated.
schemas/vegbien.sql: Added placepath (analogous to taxonpath), and point locationplace to it instead of directly to namedplace
schemas/vegbien.sql: Split locationdetermination into locationcoords and locationplace, so that coordinate determinations can be made separately from place determinations
schemas/vegbien.sql: Renamed plantconcept to taxonpath for consistency with DwC's Taxon category and to emphasize that the table stores taxonomic paths
mappings/VegCore-VegBIEN.csv: Taxonomic names: Remapped to new denormalized fields in plantconcept
mappings/VegCore-VegBIEN.csv: Removed no longer needed /_simplifyPath:[next=parent_id]/path expressions in specific paths because parent_id forwarding is now set globally for all paths in the map root
mappings/VegCore-VegBIEN.csv: Added /_simplifyPath:[next=parent_id]/path to root so the returned subplot location will be its parent location if there is no subplot name or ID (indicating that that particular plot did not have subplots). Note that this also causes the parent_id forwarding effect to occur for all other tables containing parent_id, which will help prevent similar issues with subplot events, etc. This will hopefully fix the SALVIAS.plotObservations bug where some organisms did not have a subplot #, causing the subplot location to become NULL and causing the corresponding locationevent rows not to match the locationevent_unique_within_location index filter condition (which requires a parent_id), which caused multiple output table pkeys to be returned for those rows, violating the locationevent_pkeys temp table's primary key.
mappings/VegCore-VegBIEN.csv: namedplace elements: _simplifyPath() calls: Removed no longer needed `require` arg, and removed no longer needed table suffix from `next` arg
mappings/VegCore-VegBIEN.csv: Don't map dateCollected to locationevent.obsstartdate/obsenddate because this is the date the specimen was collected, not the date (range) of the entire collection event. This distinction may not be meaningful for specimens data, but VegBIEN should reflect what the data provider designated. This also reduces the number of dateCollected-related mappings needed for any dateCollected-related field, such as year/month/dayCollected.
inputs/UNCC/Specimen/map.csv, inputs/NCU-NCSC/Specimen/map.csv: Remapped cultivated fields directly via new cultivated term, rather than via establishmentMeans
inputs/: Renamed subfolders to VegCSV names, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Rename-subfolders-to-VegCSV-names>
mappings/VegCore-VegBIEN.csv: location.authorlocationcode mappings: Use _first to remove specimens-related alternatives for this field from consideration when plots-related alternatives exist. This avoids unintentionally using specimens-related columns for this field in plots data.
mappings/VegCore-VegBIEN.csv: Changed _merge to _join wherever the duplicate-eliminating functionality of _merge is not needed and a simple concatenation of non-NULL values is sufficient
xml_func.py: simplify(): Added pruning optimization that removes empty children. Empty children are created when some mappings don't apply to the current datasource.
mappings/VegCore-VegBIEN.csv: _simplifyPath() calls: Removed no longer needed `require` arg, and removed no longer needed table suffix from `next` arg
mappings/VegCore-VegBIEN.csv: Primary taxondetermination: Removed [role=identifier] because the role of the entity making the determination is unknown. Added [!isoriginal] filter to those mappings to ensure that primary taxondetermination XPaths map to a different taxondetermination than the [isoriginal=true] determination when both are present.
mappings/VegCore-VegBIEN.csv: taxonomic terms: Removed ":[isoriginal=true]" because there may be multiple determinations for an organism (either in separate rows or, for SALVIAS, in separate columns), and not all will be the original determination
inputs: Move src subdir into main dir, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Move-src-subdir-into-main-dir>
inputs: Moved test outputs into subfolders, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Move-test-outputs-into-subfolders>
mappings/DwC2-VegBIEN.specimens.csv: catalogNumber: Added additional VegCSV mappings for mergability. taxonoccurrence.authortaxoncode: Added alternative mappings from VegCSV for mergability.
xml_func.py: simplify(): Apply pass-through optimizations for _if statements with no condition (which means false). This faciliates automated testing after an _if statement has been added, because the put template provided as part of the automated test will only change for those datasources that actually have a condition entry for the _if statement, which greatly reduces the number of tests that need to be accepted. (Note that the path before the _if will still be included as an empty path if there are no other mappings to that table, because the _if statement does not surround it.)
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: Split occurrenceID into occurrenceID and individualID, where individualID refers to the plant in plots data and occurrenceID refers to the specimen in specimens data. This prevents plant sourceaccessioncodes from being mapped to the specimenreplicate, which was messing up stems mappings for the parent plantobservation. It also avoids mapping the specimenreplicate sourceaccessioncode to additional tables where it isn't needed. (Note that occurrenceID is needed for location to ensure that each specimen gets its own location to make locationdeterminations on. Everything else is directly or indirectly scoped by location when its own sourceaccessioncode isn't specified.)
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: taxonoccurrence: Removed catalogNumber mapping because the catalogNumber applies only to the specimen, not to the occurrence, especially in plots data
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: taxonoccurrence: Map everything except occurrenceID (which is globally unique) to new authortaxoncode, which only needs to be unique within the locationevent
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: occurrenceID: Mapped to location.authorlocationcode instead of sourceaccessioncode so that it would not override any location- or event-related IDs in location.authorlocationcode merely by being mapped to the sourceaccessioncode field (which takes precedence over the authorlocationcode when specified)
mappings/DwC2-VegBIEN.specimens.csv: catalogNumber: Wrapped all mappings in direct voucher _if for mergability with VegCSV
mappings/DwC2-VegBIEN.specimens.csv: catalogNumber: Moved direct/indirect voucher _if inwards to wrap just the value of catalognumber_dwc, not the catalognumber_dwc field node, to match the corresponding VegCSV mapping
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: taxonoccurrence.sourceaccessioncode mappings: Added catalogNumber mapping, which takes precendence over recordNumber and is applicable to specimens data and direct vouchers. recordNumber should only be used as a last resort (before the taxon name) because this is collector-assigned and often not unique within anything.
mappings/DwC2-VegBIEN.specimens.csv, DwC1-DwC2.specimens.csv: Split eventDate into eventDate and dateCollected, where eventDate refers only to the date of the sampling event, but dateCollected also refers to the date the particular specimen was collected. (This distinction is important in merging with VegCSV, because in plots data, these two fields are distinct.) Remapped datasources with dateCollected-related fields to new dateCollected.
mappings/DwC2-VegBIEN.specimens.csv: eventDate: Also map to obsstartdate/obsenddate, since the collectiondate is also the event date for specimens data, and for mergability with VegCSV
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: eventDate: collectiondate mapping: Removed _dateRangeStart filter because the eventDate (obsstartdate) is only valid as the date the specimen was collected if it is a single date, not a date range. (It is still valid as the obsstartdate/obsenddate if it's a range.)
mappings/DwC2-VegBIEN.specimens.csv: verbatimLatitude/verbatimLongitude: Fixed mappings to use _alt/2 instead of _alt/1 to avoid collisions with decimalLatitude/decimalLongitude
mappings/DwC2-VegBIEN.specimens.csv: occurrenceID: Added VegCSV mappings for it
mappings/DwC2-VegBIEN.specimens.csv: mappings to /location/sourceaccessioncode: Added _alt to prioritize them properly
mappings/DwC2-VegBIEN.specimens.csv: Remapped institutionCode/collectionCode/catalogNumber location mappings to location.authorlocationcode
mappings/DwC2-VegBIEN.specimens.csv: Mapped verbatimElevation and samplingProtocol, for mergability with VegCSV
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: taxondetermination mappings: Removed iscurrent=true because it is not the role of the mappings to specify which taxondetermination is the current one. Eventually, the order of the determinations will need to be specified using a sort # or similar, and the DB will select the current one for queries to use. Ensure all mappings have :[isoriginal=true] so that they match up between DwC and VegCSV.
mappings/DwC2-VegBIEN.specimens.csv: collectionID: Fixed mapping to point to collectioncode_dwc instead of collectionnumber, as this is an ID of the collection rather than within it
mappings/DwC2-VegBIEN.specimens.csv: establishmentMeans: Removed obsolete mapping to growthform, since growthforms and cultivated/native information are no longer merged into one field in VegBIEN (which they were when this mapping was created)
mappings/DwC2-VegBIEN.specimens.csv: catalogNumber: Added _if wrapper for mergability with VegCSV-VegBIEN.specimens.csv
schemas/vegbien.sql: Removed inheritance link between specimenreplicate and taxonoccurrence, which is not needed now that specimenreplicate is mapped via plantobservation. mappings/DwC2-VegBIEN.specimens.csv: As part of this change, moved mappings to specimenreplicate fields inherited from taxonoccurrence to go directly to taxonoccurrence.
VegBIEN mappings: Wrapped dates in _date() and _dateRangeStart()/_dateRangeEnd(), to assist in importing date and date range values that PostgreSQL cannot parse. This will increase the import time, but hopefully also decrease the # of invalid values in the errors tables. (These functions can later be optimized to reduce the impact on import time.)
mappings/DwC2-VegBIEN.specimens.csv: Remapped eventDate to new aggregateoccurrence.collectiondate, which is a more accurate place than locationevent.obsstartdate/obsenddate because the date refers to a specific specimen. This also makes eventDate compatible with plots data.
mappings/DwC2-VegBIEN.specimens.csv: Mapped specimenreplicate via plantobservation for consistency with plots data. (This change is required for VegCSV table merging to work properly.) This is also a more accurate way of representing the data, because a specimen in fact comes from a plant, and it's natural to place the plant-related data (measurements, etc.) in the plantobservation table.
mappings/DwC2-VegBIEN.specimens.csv: Reversed XPaths so that they start with location instead of specimenreplicate
mappings/DwC2-VegBIEN.specimens.csv: Expanded {} expressions using expand_braces, so that each distinct output for the same input is on its own line, improving readability. This will also help enable search-and-replace reversing of XPaths for the re-rooting to location.
mappings: location: Removed centerlatitude/centerlongitude mappings because the lat/long should be in only one place: the locationdetermination. It is up to the database querier to decide which locationdetermination(s) to use as the coordinates for a plot/specimen.
bin/map: Don't create unneeded /_ignore/inLabel element containing the datasource name because sql_io.put_table() now autopopulates the datasource_id
