moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).
bugfix: inputs/XAL/Specimen/, NY/Ecatalog_all/: *JulianDay: remapped to dayOfYear instead of day (the day of the month)
inputs/*/*/map.csv: added distinguishing #... suffix (e.g. UNUSED#institutionID) to the special terms OMIT, PRIVATE, UNUSED (VegCore.vegpath.org#Special-terms) to avoid creating a collision in the staging table renaming
inputs/*/*/map.csv for CSV tables with a row_num column: added missing row_num entry, which is needed by the staging table column renaming to make the order of the map.csv columns match the order in the staging table
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. Renamed specimenHolders to specimenHolderInstitutions to make it obvious that this is a list of institutions, such as would be in institutionCode in a DwC export.
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.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).
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: Terms: Removed namespace prefixes (dcterms:), because VegCore terms are globally unique within VegCore and there should not be multiple versions of the same VegCore term with different namespaces. Provenance is instead indicated in the Sources column, which contains not just a namespace but a full URL to each source term.
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 -)
inputs/XAL/Specimen/map.csv: darwin:FieldNumber: Removed command to determine that field is unused, because UNUSED is a factual assertion that does not need a reason to be specified each time
inputs/XAL/Specimen/map.csv: Remapped darwin:CoordinatePrecision to UNUSED
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: 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
inputs/*/*/map.csv: Remapped latitude/longitude to decimalLatitude/Longitude because these fields almost always have units of decimal degrees
input.Makefile: Maps building: Use new mappings/VegCore.csv as the VegCore vocabulary to canonicalize on, in order to also canonicalize VegCore terms which are not yet mapped to VegBIEN. This results in several DwC terms getting their case standardized according to http://rs.tdwg.org/dwc/terms/. Continue to determine unmapped terms using mappings/VegCore-VegBIEN.csv, because a term should not be considered mapped until it has been mapped all the way through to VegBIEN.
inputs/*/*/map.csv: Remapped all unused terms to special value UNUSED. Remapped all private terms to special value PRIVATE. Remapped all deliberately unmapped terms to special value OMIT.
inputs/*/*/map.csv: Mapped variants of subspecies directly to new subspecies term
inputs/*/*/map.csv: Changed output column header from Veg+ to VegCore because the names will be VegCore names after automapping. This is possible now that we're using new automapping scripts that do not require a particular column header.
inputs/*/*/map.csv: Moved filter suffixes to separate filter column to enable automapping to work on those mappings' terms, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Map_refactoring#Move-filter-suffixes-to-separate-filter-column>. Note that the only changes to VegBIEN.csvs are the (now automapped) names of terms in "No join mapping" comments.
inputs/*/*/map.csv: Added Filter column to contain any suffix added after the term, so that the automapping mechanism does not have to deal with the filter expressions
inputs/*/*/map.csv: Removed no longer needed [Veg+] suffix in root, because the input column is no longer used by old-style map utilities such as union that needed this
inputs/XAL/Specimen/src.csv, map.csv: Switched from using root prefixes to full column names, because the namespace mapping functionality can be handled much better by treating each namespace-qualified term as its own term rather than as a term and a prefix
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>
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 maps into subfolders, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Move-maps-into-subfolders>
inputs: Replaced Veg+ prefix with map on via maps, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Replace-Veg-prefix-with-map-on-via-maps>
Merged DwC (including DwC1) and VegCSV mappings into new Veg+ schema. This involves replacing occurrences of DwC and VegCSV with Veg+ (or sometimes VegCore) everywhere, as described in <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV-DwC_merging>.
inputs/XAL/maps/DwC.specimens.csv: Remapped FieldNumber to recordNumber because this historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber, but not the same meaning as the current fieldNumber term
DwC mappings: Removed ':/list/' root (full version: '::[@xmlns:dcterms=http://purl.org/dc/terms/]/list/') from map spreadsheets to simplify the boilerplate in each file. Since intermediate DwC XML files no longer need to be produced for automated tests, these roots are not needed.
inputs/*/maps/DwC.specimens.csv: Removed extranenous XML meta info from DwC column root, since it now just needs to be present in the core via map mappings/DwC-VegBIEN.specimens.csv
inputs/XAL: Added maps
