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).
inputs/Madidi/: Refreshed. Note that new export has a completely new schema.
inputs/*/*/map.csv: Remapped recordNumber to new individualCode where applicable
mappings/VegCore-VegBIEN.csv: Mapped individualCode. authortaxoncode: Prefer tag over recordNumber (collectionnumber), because this applies to the plant rather than the specimen.
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.
inputs/*/*/test.xml.ref: Restored inserted row counts, which had gotten auto-accepted from a test run on a non-empty DB
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: 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
inputs/Madidi/Organism/map.csv: Habit: Mapped growth form values
inputs/Madidi/Organism/map.csv: Remapped Habit from verbatimGrowthForm to growthForm, which points to the same place
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: Mapped acceptedCounty, county to the matched place
mappings/VegCore-VegBIEN.csv: verbatimGrowthForm: Removed _map filter, which applied only to SALVIAS and has now been moved to the applicable SALVIAS tables
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
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: 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: Don't populate taxonlabel.creator_id using identifiedBy, because that was meant for creating a taxonconcept when the accordingTo was not specified, but taxonconcepts are now modeled differently using a taxonconcept subclass of taxonlabel with a concept_reference_id
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.csv: Renamed *Binomial to *TaxonName because this field can store more ranks than just the genus+specificEpithet binomial (that goes in speciesBinomial)
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: Map locationID to place.placecode instead when geovalidation columns are provided
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 generate the identifyingtaxonomicname for the original* taxondetermination's 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: taxonlabel: Renamed taxonomicnamewithauthor to taxonomicname because it is equivalent to Darwin Core's scientificName
schemas/vegbien.sql: taxonlabel: Renamed taxonomicname to binomial because it excludes the author
mappings: Renamed *scientificNameWithAuthorship to *scientificName because scientificNameWithAuthorship is actually a synonym of DwC's scientificName ("The full scientific name, with authorship and date information if known" <http://rs.tdwg.org/dwc/terms/#scientificName>)
mappings: Renamed *scientificName to *binomial because DwC defines the scientificName as "The full scientific name, with authorship and date information if known", but many datasources do not include the author in their scientific name, and the fields scientificName is mapped to in VegBIEN assume it does not include 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
mappings/VegCore-VegBIEN.csv: Mapped accordingTo to taxonconcept.creator_id, and have it take the place of identifiedBy when both are present
mappings/VegCore-VegBIEN.csv: Remapped people's names split apart into name components in party to new party.fullname, which does not require splitting or make assumptions about the number of people who may be listed in a particular name field and which components of their name(s) are present
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/Madidi/Organism/map.csv: Total height: Remapped to height_m, assuming units based on the range and precision of values
inputs/Madidi/Organism/map.csv: Subplot X, Subplot Y: Remapped to organismX_m/organismY_m, assuming units based on the size of values relative to the plot area, which has units of ha
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 for taxonconcepts created from original*, verbatim*, and accepted* taxonomic terms
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.
schemas/vegbien.sql: taxonconcept: Renamed definer_id to creator_id to allow merging with datasource_id when datasource_id is renamed to creator_id
mappings/VegCore-VegBIEN.csv: Populated new taxonconcept.definer_id from identifiedBy, or when no identifiedBy is specified, from the datasource itself (using _simplifyPath:[next=datasource_id])
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: Mapped accepted* taxonomic terms
mappings/VegCore-VegBIEN.csv: Don't forward scientificName to taxonoccurrence.authortaxoncode when importing just taxonpaths, as for TNRS
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.csv: Renamed verbatim* taxonomic terms to original* because in most datasources, they are in fact for the original taxon determination of the organism (which can be a completely different name than the primary determination), rather than merely unscrubbed versions of the primary taxonomic name elements. Note that SALVIAS's orig_* terms do appear to be merely unscrubbed versions, but it's not a problem to add an additional taxon determination for them.
mappings/VegCore-VegBIEN.csv: verbatim* taxonomic terms: Added taxonomicnamewithauthor mappings analogous to those for the non-verbatim taxonomic terms
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.
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: Only use institutionCode+collectionCode+catalogNumber as the authorlocationcode (location-scoping ID) if there is actually a catalogNumber. Otherwise, the mapping process would attempt to create one location for each collection in the datasource, when there should be one location for each specimen.
schemas/vegbien.sql: party: Added check constraint to require at least an organizationname or surname. Previously, NULL entries for the collector or identifier incorrectly caused the creation of an empty party entry, hence the lower inserted row counts now that this is no longer created.
schemas/vegbien.sql: taxonpath: Renamed scientificnameauthor to author so the column name doesn't have "scientificname" in it, which made the term look confusingly like scientificname itself. Added descriptive comment that this is the author of the scientific name.
inputs/Madidi/Organism/map.csv: Remapped Diameter from diameterBreastHeight_m to diameterBreastHeight_cm, assuming units based on the range and precision of values
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: 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.
