schemas/vegbien.sql: specimenreplicate.institution_id: renamed to duplicate_institutions_sourcelist_id, as decided in the conference calls (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2)
mappings/VegCore.htm: regenerated from wiki: rename specimenHolderInstitutions to specimen_duplicate_institutions, as decided in the 2014-03-13 conference call (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2). note that most schema changes (such as this one) involve mappings changes, which are handled automatically by `inputs/run postprocess; yes|make inputs/{NVS,SALVIAS,TEAM}/test`.
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/REMIB/: switched to new-style import, using the steps at wiki.vegpath.org/Switching_to_new-style_import#stage-I-source-specific > "run the following for each datasource"
inputs/REMIB/Specimen/: translated single-column filters to postprocessing derived columns, using the steps at wiki.vegpath.org/Switching_to_new-style_import#stage-I-source-specific > "translate single-column filters to postprocessing derived columns". null-mapping filters now use wrappers around new util.map_nulls(). note that the verbatim columns input to the filters need to be renamed to avoid name collisions with their filtered columns, which must be VegCore terms for new-style import.
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/REMIB/Specimen/map.csv: Mapping NULL-equivalent lat/long to NULL: Fixed bug where need special *=* mapping to pass through values not in the map
inputs/REMIB/Specimen/map.csv: Map NULL-equivalent text fields (country, state, etc.) to NULL
inputs/REMIB/Specimen/map.csv: Map NULL-equivalent lat/long to NULL
inputs/REMIB/Specimen/map.csv: Remapped lat/long_deg,min,sec to new latitude/longitude_deg,min,sec, allowing the DMS coordinates to be translated
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: 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: 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)
mappings/VegCore-VegBIEN.csv: Mapped locality description fields to location.iscultivated using _locationnarrative_is_cultivated()
db_xml.py: put(): _setDefault(): Support setting multiple col_defaults at once by using the param names themselves as the column names
mappings/VegCore-VegBIEN.csv: Set the source_id col_default to the datasource name using the new _setDefault() built-in function and _env()
mappings/VegCore-VegBIEN.csv: institutionCode: Also map to the sourcename's matched source, which identifies whether the source is a herbarium
mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place
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
specimenreplicate: Made institution_id an fkey to referencename instead of party, to later be matched up with reference entries for each aggregator's subprovider
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
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
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
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: 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)
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.).
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: Taxonomic terms: Also join terms together in taxonomicnamewithauthor if scientificNameWithAuthorship is not provided, for use by TNRS
inputs/REMIB/Specimen/map.csv: Remapped accession_number to catalogNumber because it is not globally unique, only (usually) unique within the institution providing the data ("acronym"). Note that there are nevertheless 11,869 rows where an accession_number appears multiple times within the same institution.
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.
inputs/REMIB/Specimen/map.csv: Remapped acronym to institutionCode because this is an aggregator, and the field lists the datasource each record was aggregated from. Note that the inserted row count changes because of different duplicate elimination strategies in specimenreplicate and party (which institutionCode is placed in).
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
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/: Moved year/month/dayCollected mappings from Veg+-VegCore.csv to VegCore-VegBIEN.csv so that Veg+-VegCore.csv contains only renamings, not business logic. Note that this allows the year/month/dayCollected values to bypass the additional _dateRangeStart filter that is applied to text dates. The priority of the plain dateCollected field is now higher than the year/month/dayCollected fields when both are specified, because the dateCollected field presumably contains verbatim text while the year/month/dayCollected fields contain parsed date parts.
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/: 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: _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, 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: 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, 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, 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
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
mappings/DwC2-VegBIEN.specimens.csv, VegX-VegBIEN.stems.csv: Removed all manual mappings to datasource_id now that datasource_id is auto-populated, both on the VegBIEN output side and the DwC/VegX input side. This should greatly simplify many of the mappings!
input.Makefile: Testing: Renamed import.*.out tests to end in .xml because they now contain XML import trees for validation, and this extension turns on XML syntax highlighting in a text editor
bin/map: out_is_db: Output the put template to stdout so it will be validated in the automated testing
VegBIEN: Fixing import issue related to duplicate entries in tables with children, where when a new table entry duplicates an existing entry, the 1:1 tables of that table and those tables' children are not merged, causing them to become orphaned. It is described in detail at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Import_issues#Merging-duplicates-with-children>, including the rationale for this solution. Note that this is not a bug in column-based import, it applies to row-based import as well. This commit fixes the issue for specimenreplicate->taxonoccurrence.
schemas/vegbien.sql: location: Dropped unique constraint on lat/long because it covered only some rows, which interfered with column-based import's selection of different insert methods based on the presence or absence of duplicate keys. (With the constraint, locations with coordinates would have duplicates eliminated, but locations without coordinates would not be able to find which row was added for a particular location because there was no lookup key to join on, and would all just use the first inserted row.) The previous behavior didn't make much sense anyway, because it would assert that two locationevents occurred in the same place just because they had the same coordinates, which may not have been precise enough to make this determination. Asserting that two locationevents occurred in the same place is really part of the secondary validation, not the import process.
Added inputs/REMIB/test with accepted test outputs
