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
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.
mappings/VegCore-VegBIEN.csv: Mapped reproductiveCondition
schemas/vegbien.sql: stemobservation: Added stemobservation_non_empty CHECK constraint to prevent creating an empty stemobservation for plantobservation rows without stem data but with stem mappings
mappings/VegCore-VegBIEN.csv: morphoname: Remapped to the original rather than current taxondetermination because this is the original name applied by the author
inputs/SALVIAS*/Organism/map.csv: Remapped voucher_string/coll_number to recordNumber instead of catalogNumber, because this number is actually applied by the collector rather than by a herbarium
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.
mappings/VegCore-VegBIEN.csv: Mapped morphoname
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/SALVIAS/*/test.xml.ref: Restored SALVIAS* 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: 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
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.
xml_func.py: _first(): Fixed bug where need to choose the first non-empty param, by first pruning empty child nodes
mappings/VegCore-VegBIEN.csv: authortaxoncode mappings: Only using authorTaxonCode if there is no plant ID: Added individualID, stemID to the terms that cause authorTaxonCode not to be mapped to VegBIEN authortaxoncode
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: 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/SALVIAS/: Mapped unmapped fields with a VegCore/VegBIEN equivalent. plotMetadata_/: Remapped life_zone to communityID because it is now alt-ed together with vegetation*, and thus not just a description with life_zone_code as its globally unique name.
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: 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
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
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)
mappings/VegCore-VegBIEN.csv: Only forward taxonRank to the parent taxonconcept (which stores the infraspecific taxonconcept when the infraspecificEpithet is provided) if there is no explicit parent provided via parentTaxonID/etc.
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: Also map *taxonRank to taxonconcept.rank, so that if it's in the taxonrank enum, it will automatically populate this field
mappings/VegCore-VegBIEN.csv: Remapped *infraspecificEpithet to new taxonconcept.taxonname rather than placing it in subspecies prefixed with the taxonRank, because it isn't necessarily the subspecies and because taxonname is defined to contain the lowest-rank portion of the taxonomic name. Note that when both morphospecies and infraspecificEpithet are provided, infraspecificEpithet takes priority for the taxonname field, because if TNRS leaves unmatched terms (which are tentatively mapped to morphospecies) but also matches an infraspecificEpithet, then the unmatched terms can't be for a morphospecies (because an infraspecificEpithet and therefore also a specificEpithet was matched, so the species is definite and formally named).
mappings/VegCore-VegBIEN.csv: Mapped *taxonRank to new taxonconcept.verbatimrank
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: 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: Don't combine taxonRank with infraspecificEpithet if there is no infraspecificEpithet, because the taxonRank is only the infraspecificEpithet's prefix when there is an actual infraspecificEpithet. Often, taxonRank contains values like "genus" or "species" which cannot be used for this purpose.
mappings/VegCore-VegBIEN.csv: verbatim* taxonomic terms: Added taxonomicnamewithauthor mappings analogous to those for the non-verbatim taxonomic terms
mappings/VegCore-VegBIEN.csv: Use new, more general _join_words() instead of _name()
mappings/VegCore-VegBIEN.csv: Taxonomic terms: Also join terms together in taxonomicnamewithauthor if scientificNameWithAuthorship is not provided, for use by TNRS
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/SALVIAS/plotObservations/map.csv: Remapped temp_dbh from diameterBreastHeight_m to diameterBreastHeight_cm, assuming units based on the units for intercept_cm, which measures the same dimension
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
mappings/VegCore-VegBIEN.csv: Removed no longer used previousTag and the complex mapping logic that attempts to place both tags in VegBIEN in the correct order but does not work for column-based import. tag: Removed iscurrent=true because there is now only one tag field.
inputs/SALVIAS/*/map.csv: Remapped all versions of stem and tree tags to tag, with the second tag superceding the first, to avoid the complex VegCore-VegBIEN mapping logic that attempts to place both tags in VegBIEN in the correct order but does not work for column-based import. inputs/SALVIAS-CSV/Organism/map.csv: stem and tree tags: Made the stem tag supercede the tree tag instead of vice versa, to have as specific of a tag as possible.
schemas/functions.sql: Renamed _pct_to_frac() to _percent_to_fraction() and _frac_to_pct() to _fraction_to_percent(), for clarity and for consistency with _percent (which is spelled out), as used by SALVIAS (http://salvias.net/Documents/salvias_data_dictionary.html) and elsewhere
schemas/vegbien.sql: Changed _frac units suffix to _fraction for clarity and for consistency with _percent (which is spelled out), as used by SALVIAS (http://salvias.net/Documents/salvias_data_dictionary.html) and elsewhere
inputs/*/*/map.csv: Remapped intercept_cm to new intercept_cm so that units match
mappings/VegCore-VegBIEN.csv: coverPercent: Convert to fraction using _pct_to_frac()
schemas/vegbien.sql: Added units suffix to additional VegBIEN fields that have units
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: 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.
intersect, union: Made case- and punctuation-insensitive. mappings/Veg+-VegBIEN.csv: Removed no longer needed duplicate entries for each first letter case, which must now be removed for case- and punctuation-insensitive intersect/union to work. Note that the SpeciesLink `svn diff` hides _alt entry 0, which contains one of the removed duplicate columns that appears in the diff.
join: Match terms case-insensitively
inputs/SALVIAS/: Switched to using the DB export's staging tables instead of the exported CSVs
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: Placed inside "if subplot" _if statement along with sourceaccessioncode to reduce the number of separate _if statements needing a condition mapping
mappings/VegCore-VegBIEN.csv: Moved "if subplot" _if statement around /location/parent_id and /location/sourceaccessioncode themselves, so that only one _if cond mapping for subplot is needed. Note that this is only possible because this _if statement uses _exists, allowing it to be fully evaluated by the XML template simplifying mechanism, which supports subtrees as arguments to _if.
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.
inputs/SALVIAS*/1.organisms/map.csv: Remapped cfaff to identificationQualifier, because it was previously mapped to the same taxondetermination as the Orig* terms but does not have a corresponding Orig prefix to indicate that it should apply to the original determination instead of the primary TNRS one
inputs/SALVIAS*/1.organisms/map.csv: Removed computer.* prefix from primary (TNRS) taxondetermination, so it would map to the main taxondetermination in VegBIEN
inputs/SALVIAS*/1.organisms/map.csv: Remapped OrigFamily/OrigGenus/OrigSpecies to new verbatim* taxonomic names. Also remapped cfaff to verbatimIdentificationQualifier, because it was previously mapped to the same taxondetermination as the Orig* terms, but this will later need to be remapped to identificationQualifier (not in this commit because that is a separate change). Note that the switch to the verbatim* taxonomic names removes a concatenated binomial that was part of the previous mappings, which put OrigGenus and OrigSpecies together into one scientificName.
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/SALVIAS*/src/1.organisms/map.csv: Habit: Don't filter out values not part of the provided terms list, because such values should be flagged as invalid in the error maps rather than silently discarded. This also ensures that any valid values which are not part of the provided terms list are kept.
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>
inputs: Renamed organisms table to 1.organisms so import order would be inherent in the dir name, using steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Rename-subfolders-with-import-order>
schemas/vegbien.sql: Moved collectionnumber from specimenreplicate to plantobservation to replace authorplantcode, since these terms are used analogously in plots and specimens data. This code is really the DwC recordNumber (VegBIEN collectionnumber), which "serves as a link between field notes and an Occurrence record, such as a specimen [or plots data] collector's number" (http://rs.tdwg.org/dwc/terms/#recordNumber). Also, this prevents a specimenreplicate from incorrectly being created when plots data provides an authorplantcode.
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/VegCSV-VegBIEN.specimens.csv: occurrenceID: Mapped to specimenreplicate.sourceaccessioncode for mergability with DwC
mappings/VegCSV-VegBIEN.specimens.csv: Mapped voucherType to indirect voucher _if statements' conditions
