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).

bugfix: mappings/VegCore-VegBIEN.csv: main taxondetermination: use [!isoriginal=true] instead of [!isoriginal] so that adding a manual isoriginal field does not prevent this selector from matching

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/*/*/map.csv for IndividualObservation tables: also mapped eventDate,day,month,year to *Collected, because a general date always applies to the observation itself in addition to any parent event which it may be a part of

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/*/*/map.csv for CSV tables with a row_num column: 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

added inputs/*/*/header.csv for CSV inputs, which are now generated by inputs/input.Makefile %/install

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

mappings/VegCore-VegBIEN.csv: subplotID,subplot -> location.sourceaccessioncode: Fixed bug where need /_first to handle the case where both subplotID and subplot are provided

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.)

inputs/TEAM/V*/map.csv: Mapped plotArea_ha based on "1ha Plot Number" field name

inputs/TEAM/V*/map.csv: Id: Remapped to individualObservationID

mappings/VegCore.htm: Regenerated from wiki. Brad's new DwC ID terms spreadsheet has now been added, and a number of the ID terms clarified, disambiguated, and recategorized. In particular, institutionCode has now been split into the custodialInstitutions and collectingInstitution, to differentiate between which institution has the specimen vs. stamped the specimen. This distinction is important because the catalogNumber, stamped on the specimen, is only unique within the collectingInstitution. Most datasources don't unambiguously specify which institution their institutionCode is referring to, so it has been assumed to be custodialInstitutions unless a data dictionary says otherwise (as is the case for UNCC). In addition, a MatchedTaxonDetermination table has been added with the *_matched fields from TNRS.

mappings/VegCore-VegBIEN.csv: datasourceRecordID: Fixed bug where also need to add datasourceRecordID next to occurrenceID for an institutionCode remap switch

inputs/*/Specimen/map.csv: Remapped ID to datasourceRecordID

mappings/VegCore-VegBIEN.csv: Don't create NCBI crosslinks for the matched taxonomic name. These crosslinks are no longer needed now that TNRS provides a separate accepted name on which crosslinks can be made.

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: taxonlabel.taxonomicname: Prepend the family to the rest of the name using new _merge_prefix() instead of _join_words()/_nullIf(), so that any input taxonomic name that includes the family will not have the family duplicated in the combined taxonomic name. Previously, the duplication was removed only when the rest of the input name was equal to the family. This change fixes a bug in the new TNRS import where a pre-concatenated taxonomic name (Accepted_scientific_name) which includes the family is now used instead of Accepted_name, which only includes it when it's equal to the family.

mappings/VegCore-VegBIEN.csv: locationID/locationName + subplot -> location.sourceaccessioncode mapping: Fixed bug where subplot was incorrectly being mapped to this field even when there was no location*. (This field can only be populated if both location* and subplot are specified.) Also only map locationID for this, to avoid inconsistencies where one table supplies locationID+subplot, while another table supplies locationName+subplot, but they both get mapped to the same field, preventing plots from being matched up with their observations when creating the analytical_stem.

mappings/VegCore-VegBIEN.csv: authortaxoncode mappings: Only use authorTaxonCode if there is no plant ID, because an individual plant gets its own taxonoccurrence and thus needs the taxonoccurrence's IDs to be unique to the plant, regardless of what the author designates as the taxonoccurrence code

mappings/VegCore-VegBIEN.csv: Mapped authorTaxonCode

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)

mappings/VegCore-VegBIEN.csv: Don't forward specimenreplicate IDs to location for plots data (where the specimenreplicate IDs apply only to the specimen)

mappings/VegCore.csv: Renamed plotName to locationName because this term also applies to the location of a specimen. This replaces CTFS's definition of locationName as locality.

mappings/VegCore-VegBIEN.csv: Mapped locality description fields to location.iscultivated using _locationnarrative_is_cultivated()

mappings/VegCore-VegBIEN.csv: source table mappings: Set shortname to env var $source when it's not explicitly specified, because shortname is a required field of source

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: institutionCode: Also map to the sourcename's matched source, which identifies whether the source is a herbarium

mappings/VegCore-VegBIEN.csv: institutionCode: Remap to source.shortname when specimen information is not provided, as is the case for geoscrub.herbaria on nimoy

mappings/VegCore-VegBIEN.csv: Concatenated taxonlabel: Don't prepend family if the taxonName/scientificName itself is the family, so that the family is not duplicated in the concatenated taxonomic name

mappings/VegCore-VegBIEN.csv: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot

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: Made taxonoccurrence.verbatimcollectorname an fkey to party, and renamed it to collector_id

inputs/TEAM/V*/map.csv: Omit *Method, because it just contains "Derived" for a small fraction of the rows

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: matched place's coordinates: Fixed bug where coordinates mappings with and without matched_place_id=0 need to sort together in order to be merged, by prepending ".," to the place attrs list

mappings/VegCore-VegBIEN.csv: subplot locationevent: Only populate parent locationevent's location unique IDs if a subplot #/subplotID is actually specified. (The lack of a location unique ID will cause the parent locationevent's location to be removed, as well as the parent locationevent itself if there is no parent locationevent unique ID.) This fixes a bug where top-level plots in datasources that provide a nullable subplot #/subplotID were incorrectly getting connected to parent locationevents.

mappings/VegCore-VegBIEN.csv: subplots: Also complete the locationevent/location diamond (subplot event -> {subplot location, parent plot event} -> parent plot location) when an eventDate or range is specified, as this is also an identifying field for locationevent. This fixes a bug where subplots data without explicit plot events (such as SALVIAS and TEAM) was not being connected to the appropriate parent plot event as well as parent plot location. This should fix the SALVIAS verification # location events, which should include only parent plots' locationevents to correspond with # locations, which only includes parent plots' locations, and uses locationevent.parent_id being NULL to determine what is a parent plot event.

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

mappings/VegCore-VegBIEN.csv: matched taxonlabel's ancestors: Only create the cross links to NCBI if the name is accepted (taxonIsCanonical)

mappings/VegCore-VegBIEN.csv: Mapped acceptedCountry, acceptedStateProvince, acceptedDecimalLatitude/Longitude. Mapped decimalLatitude/Longitude to matched place's coordinates when acceptedDecimalLatitude/Longitude not provided (as is the case for the geoscrub table).

mappings/VegCore-VegBIEN.csv: Remapped latitude/longitude to new coordinates table

mappings/VegCore-VegBIEN.csv: Only prepend the family to the concatenated scientificName for TNRS if it ends in -aceae (using _taxon_family_require_std()), to avoid sending unsupported, nonstandard families to TNRS which it will place in Unmatched_terms

mappings/VegCore-VegBIEN.csv: Prepend the family to the concatenated scientificName input to TNRS, so that TNRS can use it to disambiguate the genus

schemas/vegbien.sql: taxonverbatim: Renamed species to specific_epithet to avoid confusion with the scientific meaning of species (genus+specificEpithet), since this field contains just the specific epithet

mappings/VegCore-VegBIEN.csv: location: Populate sourceaccessioncode with locationID + subplot when subplot is unique only within the parent plot, so that location always has a sourceaccessioncode to use as the plotCode in analytical_db_view

mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Do not include rank in the mapping because taxonomicname is globally unique, and thus it isn't used in looking up the NCBI taxonlabel

mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Also attach TNRS genus to NCBI backbone. This causes attachment to be made with as many of family and genus as are provided and have an entry in NCBI.

mappings/VegCore-VegBIEN.csv: Instead of connecting the acceptedFamily to the NCBI backbone, connect the family for the TNRS matched taxonlabel. This connects more families and also connects the same set of fields as will be connected for the genus.

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

mappings/VegCore-VegBIEN.csv: Expanded brace expressions for putting together the identifyingtaxonomicname

mappings/VegCore-VegBIEN.csv: Always generate the concatenated identifyingtaxonomicname, even for higher taxa, to ensure that this field is always populated. Note that this will cause names of higher taxa to be scrubbed by TNRS, but this is usually not a problem because such names either have no match or not a close enough match based on the name only. Naming conventions generally cause names at different ranks to be different, so that collisions with lower ranks should not be a problem.

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 taxonname to taxonepithet for clarity and to be consistent with TCS's use of "epithet" to denote what the taxonname was intended to be (http://www.tdwg.org/standards/117/download/#/UserGuidev_1.3.pdf)

inputs/TEAM/*/map.csv: 1ha Plot X Coordinate, 1ha Plot Y Coordinate: Remapped to organismX_m/organismY_m using units from <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/TEAM-DataPackage-20120920191251_3859/Vegetation+-+Trees+&+Lianas/Vegetation-Tree-and-Liana-Metadata-1.5.pdf>

mappings/VegCore-VegBIEN.csv: identifyingtaxonomicname: Don't create if taxonconcept has an explicit parent, because the taxonName (which is generally only a component of the full taxonomic name, e.g. specificEpithet) is not globally unique. Datasources that provide name components in such a way that levels at or below family can't be directly concatenated cannot currently receive an identifyingtaxonomicname for input to TNRS.

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: taxonconcept: taxonconcept_required_key: Removed family and genus because these are now cached fields only, and are not used for scoping a taxonconcept. Instead, *taxonomicname and taxonname+parent_id are used for this purpose. This removes several leaf taxonconcepts with insufficient scoping information to create a taxonconcept separate from the main tree. With the upcoming population of creationdate, some of these taxonconcepts will reappear due to the date's additional distinguishing information.

mappings/VegCore-VegBIEN.csv: taxonconcept: Moved infraspecific taxonconcept to its own level, rather than combining it with the level that contains the full taxonomic name and author (as well as any morphospecies), for consistency with the storage of other ranked taxonomic name components, which each get their own taxonconcept. The infraspecific taxon concept is general to all parties making idenfitications (within a datasource), while the concatenated name and author and any morphospecies are specific to the person who defined the taxonconcept used by a taxondetermination.

mappings/VegCore-VegBIEN.csv: taxonconcepts: Also create the taxonconcept tree if datasource provided separated components of the taxonomic name and/or its own tree of life with higher classifications. This enables storing the datasource's own tree of life to supplement any official tree (TROPICOS, USDA, etc.).

mappings/VegCore-VegBIEN.csv: taxonconcept tree: Don't map infraspecificEpithet+taxonRank to a taxonconcept in the tree of parent concepts because it has already been mapped to the primary, lowest-level taxonconcept

mappings/VegCore-VegBIEN.csv: Remapped taxon hierarchy for accepted taxonconcepts to taxonconcept parent_id hierarchy

mappings/VegCore-VegBIEN.csv: TNRS-only mappings: Switch them on when verbatimScientificNameWithAuthorship is provided rather than when acceptedScientificNameWithAuthorship is provided, because it's the presence of a separate TNRS input name that really determines when TNRS is being mapped

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: Mapped morphospecies

mappings/VegCore-VegBIEN.csv: Also map TNRS-parsed infraspecificEpithet (Infraspecific_epithet_matched) to taxon at the infraspecies rank

mappings/VegCore-VegBIEN.csv: Also map TNRS-parsed taxonomic ranks to the tree of life in the taxon table

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: Changed _first to _alt because some datasources have NULL values in scientificNameWithAuthorship or scientificName, so it can't just be used in place of the joined-together taxonomic ranks

mappings/VegCore-VegBIEN.csv: Taxonomic terms: Also join terms together in taxonomicnamewithauthor if scientificNameWithAuthorship is not provided, for use by TNRS

mappings/VegCore-VegBIEN.csv: Removed unnecessary /_first/# suffix for multiple terms in the same _exists expression, because _exists() only checks whether its node is non-empty, and it does not matter how many child nodes it contains

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.

mappings/VegCore-VegBIEN.csv: Remapped verbatimLatitude/Longitude to locationcoords.verbatimlatitude/longitude because these fields now contain only non-decimal coordinates. This involves removing the _alt suffix on decimalLatitude/Longitude, which causes the VegBIEN.csvs to change.

inputs/*/*/map.csv: Remapped latitude/longitude to decimalLatitude/Longitude because these fields almost always have units of decimal degrees

inputs/TEAM/: Regenerated */new_terms.csv

inputs/TEAM/: Obtained new download of TEAM data. (Note that the new download has a slightly different schema.) Archived old data in _archive/. Added tables to import_order.txt. Renamed TeamPlotMetaData/ to TEAM_Sites/ to correspond with the section header in Vegetation-Tree-and-Liana-Metadata-1.5.pdf. Fixed TEAM_Sites mappings: Remapped CollectionDate to eventDate because it relates to the plot, not the organism. Mapped Name to plotName so TEAM_Sites data will match up with VL, VT data.

inputs/TEAM/VL, VT: Split concatenated flat files apart into separate parts each time a header is duplicated, so that the header would be autoremoved by cat_csv. Changed modified BIEN2 flat file headers back to original headers (the duplicated headers) so the headers of all part files would match up. (This is required for cat_csv header autoremoval to work properly.) This results in changes to the input column names in */map.csv.

inputs/TEAM/*/map.csv: Remapped dbh from diameterBreastHeight_m to diameterBreastHeight_cm, using the units defined in Vegetation-Metadata-1.4.pdf

input.Makefile: Maps validation: %/new_terms.csv: Include the entire map spreadsheet row, so that each new term is listed together with its mapping. This facilitates adding new mappings to mappings/Veg+-VegCore.csv directly from any new_terms.csv. Note that the use of `sort -u` (in lib/mappings.Makefile) causes multiline comments to be separated, leading to spurious lines for each multiline comment line.

mappings/VegCore.csv: Renamed diameterBreastHeight to diameterBreastHeight_m to assert units matching the VegBIEN field

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: taxonoccurrence.authortaxoncode alternatives: Use _first instead of _alt because when one of these fields is present, it can be used directly even if it's sometimes NULL, without needing to spend a lot of time _alting together fields that won't be used. Datasources where the authortaxoncode is sometimes NULL usually have a separate sourceaccessioncode for the taxonoccurrence. (In the rare case that they don't, they should map a non-NULL field to recordNumber or tag to ensure that taxonoccurrences can be uniquely identified.)

mappings/VegCore-VegBIEN.csv: Mapped tag to taxonoccurrence.authortaxoncode when the record is an organism, in case there is no other ID for the taxonoccurrence. This fixes a bug in FIA and TEAM data where all organisms in a plot used the same taxonoccurrence because taxonoccurrence was not properly constrained, causing the loss of individual taxondeterminations on each organism.

mappings/VegCore-VegBIEN.csv: Remapped tag to new stemobservation.tag