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/VegBank/taxonobservation_/map.csv, postprocess.sql: mapped identifiedBy (the join_words() of identifiedBy_first, etc.)
inputs/VegBank/taxonobservation_/create.sql: also join party_id to get the identifiedBy (not mapped yet). note that the inserted row count changes, because taxonobservation_ does not yet have a pkey to do a stable ordering with.
inputs/VegBank/vegbank.~.clean_up.sql: taxoninterpretation.party_id: don't rename to taxoninterpretation_party_id, so that this can be used directly in taxonobservation_/create.sql with a USING join
inputs/VegBank/taxonobservation_/create.sql: join taxonobservation to taxoninterpretation (as in CVS) instead of vice versa, since taxonobservation is the primary, operative table. having VegBank and CVS do things the same way helps ensure that fixes in one can transfer easily to the other.
mappings/VegCore-VegBIEN.csv: mapped taxon_determination__is_current, taxon_determination__is_original
inputs/VegBank/taxonobservation_/map.csv: originalinterpretation, currentinterpretation: removed table name prefix so these would automap
fix: inputs/VegBank/taxonobservation_/map.csv: remapped authorplantname to OMIT because these are not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). see wiki.vegpath.org/Spot-checking#2013-10-10 > Mike Lee's conference call feedback.
fix: inputs/VegBank/taxonobservation_/map.csv: remapped int_* to OMIT because these are not specific to the taxoninterpretation row (this is in a separate taxoninterpretation for the original determination instead). see wiki.vegpath.org/Spot-checking#2013-10-10 > Mike Lee's conference call feedback.
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
inputs/VegBank/taxonobservation_/postprocess.sql: added __parent index on locationID to facilitate the LEFT JOINs used to create the validation input
inputs/VegBank/plantconcept_/: mapped columns, since this is now included in import_order.txt and therefore gets processed by the column-renaming runscripts. note that this means that in taxonobservation_/map.csv, the plantconcept_ input column names need to be changed to what they are mapped to.
inputs/VegBank/taxonobservation_/create.sql: updated runtime (20 s)
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.
bugfix: inputs/VegBank/: taxonOccurrenceID: include the aggregateOrganismObservationID in this so that there is one taxonoccurrence for each stratum's taxonImportance. this allows the different strata to have separate taxonoccurrences that are associated with the stratum-specific locationevents, rather than all being lumped into one taxonoccurrence, with only one locationevent.
inputs/VegBank/taxonobservation_/map.csv: taxonomic ranks not in VegCore: removed table prefix so they will be automapped (they are globally unique)
inputs//: don't import joined tables, because they are now imported in the taxon_observation.** left-join instead
inputs/VegBank/taxonobservation_/create.sql: join starting with taxoninterpretation so that we can use the taxoninterpretation_id as the row_num (text strings, formed from concatenated #s cannot be used as a row_num). there is only 1 taxonobservation without a taxoninterpretation, so we can just include one row for each taxoninterpretation.
bugfix: inputs/VegBank/taxonobservation_/test.xml.ref: updated after reloading staging table. this fixed a bug where observationGranularity apparently either did not exist or was not the right type of constant column to be properly inlined the last time the tester was run. the inlining is important for using metadata switches to generate the correct XML import script.
inputs/VegBank/taxonobservation_/postprocess.sql: added primary key. note that the inserted row count changes, most likely because the rows are now in sorted order.
inputs/VegBank/: prepended the table name to each column name to prevent column collisions, using the steps at http://wiki.vegpath.org/Left-joining_a_datasource
inputs/VegBank/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource
bugfix: inputs/VegBank/taxonobservation_/map.csv: put columns in table order, which is needed by new-style import
inputs/VegBank/taxonobservation_/postprocess.sql: scientificName: recorded runtime (15 s)
inputs/VegBank/taxonobservation_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
inputs/*/*/test.xml.ref: updated source.shortname for new datasource name, which now starts out with .new suffix
inputs/VegBank/taxonobservation_/map.csv: plantname: remapped to DUPLICATE#of:plantconcept_plantname because this is an exact duplicate
bugfix: inputs/VegBank/taxonobservation_/map.csv: updated input column names for renamings in inputs/VegBank/vegbank.~.clean_up.sql
inputs/VegBank/taxonobservation_/map.csv: Species and lower ranks: remapped to EQUIV#to:plantname because these contain the taxonomic name at specific ranks, but plantname contains the taxonomic name of the plant itself, which is longer and populated more often
inputs/VegBank/taxonobservation_/create.sql: also join to plantname, since plantconcept.plantname may not always be populated when plantname.plantname is
fix: inputs/VegBank/taxonobservation_/map.csv: Species and below: remapped to _alts of scientificName, because these are actually the full taxonomic name at that rank, not just the epithet. Genus: documented that it includes the genus author.
fix: inputs/VegBank/taxonobservation_/map.csv: also mapped plantname to scientificName, since int_currplantscifull is not always provided when this is. (it cannot replace int_currplantscifull, because when int_currplantscifull also provided, this often leaves out lower ranks.) this should fill in taxonomic information for taxonobservations that are currently missing it.
inputs/VegBank/taxonobservation_/map.csv: collector_id: remapped to UNUSED. removed LEFT JOIN collector_id->party since this field is never populated.
inputs/VegBank/taxonobservation_/map.csv: int_origplantscifull: remapped to EQUIV (to authorplantname). this is the scrubbed originalScientificName, but we do our own scrubbing.
fix: inputs/VegBank/taxonobservation_/map.csv: authorplantname: remapped to originalScientificName because it includes the name author
inputs/VegBank/taxonobservation_/map.csv: mapped int_origplant*, int_currplant* to *scientificName/*taxonName/etc.
inputs/*/*/logs: updated svn:ignore
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/VegBank/taxonobservation_/map.csv: Mapped int_currplantcommon to vernacularName
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.)
mappings/VegCore.htm: Regenerated from wiki. Remapped organismNotes to be a synonym of occurrenceRemarks, since notes on an organism are more generally notes on an occurrence.
mappings/VegCore-VegBIEN.csv: Mapped occurrenceRemarks
mappings/VegCore.htm: Regenerated from wiki. Documentation has been added on how to choose term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming) and how to form globally unique ID values (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Forming-IDs). Source and Specimen terms have been renamed to be self-explanatory and unambiguous (the DwC equivalents remain as synonyms). Short definitions of Source terms have been added to explain the differences between them. Source, Specimen, and Collection terms have been shortened according to the new instructions for choosing preferred term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming).
inputs/*/*/map.csv: Automapped taxonConfidence
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, inputs/*/*/map.csv: Applied term renamings from the new dynamically generated Veg+-VegCore.csv, which reflects the current state of the data dictionary. (Permanently switching to the new Veg+-VegCore.csv will be a separate change.) Updates to VegCore term names that have occurred since the data dictionary was created are now able to take effect, which involves remapping and inferring units on several fields.
mappings/VegCore.csv: Regenerated from wiki. This adds Brad's DwC ID terms and their definitions in <https://projects.nceas.ucsb.edu/nceas/attachments/download/621/vegbien_identifier_examples.xlsx>.
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.
schemas/vegbien.sql: taxonlabel: Removed creationdate, which duplicates taxondetermination.determinationdate
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.
mappings/VegCore.csv: Regenerated from wiki
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
mappings/VegCore.csv: Term names: Changed special characters to _ because Redmine doesn't support special characters in HTML anchors (it removes everything except letters, numbers, _, and -)
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)
schemas/vegbien.sql: Renamed sampletype to observationtype to match the VegCore term
mappings/VegCore.csv: Renamed sampleType to observationType to match the SALVIAS term it's derived from
inputs/VegBank/taxonobservation_/map.csv: Fixed bug where need to indicate that data is plots data to prevent the specimenreplicate ID from being forwarded to the location ID
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-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
inputs/VegBank/taxonobservation_/map.csv: Mapped new givenname, surname (from collector_id's party) to recordedBy
inputs/VegBank/taxonobservation_/create.sql: Also join to collector_id's party to include collector name
inputs/VegBank/vegbank.~.clean_up.sql: Rename taxoninterpretation.party_id to taxoninterpretation_party_id to make it globally unique when joining taxoninterpretation to other tables
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
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: 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: 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.
inputs/VegBank/taxonobservation_/create.sql: Removed dropping of row_num column, which is no longer added on non-CSV tables
mappings/VegCore-VegBIEN.csv: Do not include the taxonName in the concatenated taxonomicname because it is NOT globally unique. The same name may be used at different taxonomic ranks and mean different things, and lower taxa may have the name appear in multiple genuses or species, meaning different things.
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 taxonomicname to binomial because it excludes the author
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
