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).
inputs/SpeciesLink/: switched to new-style import, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource
inputs/SpeciesLink/Specimen/map.csv: renamed DUPLICATE#of:... output columns to be <= 63 chars long, in order to be valid PostgreSQL columns without collisions
inputs/SpeciesLink/Specimen/: translated multi-column filters to postprocessing derived columns, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns
inputs/SpeciesLink/Specimen/map.csv: conceptual_darwin_2003_1_0_BoundingBox: remapped to UNUSED
inputs/SpeciesLink/Specimen/map.csv: remapped Darwin Core synonyms to DUPLICATE. this avoids the need to translate these to postprocessing derived columns for new-style import, and also speeds up column-based import because there are less automatic alts to perform to resolve filter-less collisions. the svn diff was verified by replacing DUPLICATE#of:dwc_terms<term>#... with <term>, removing the comment, and checking that this removes the diff (except where VegCore has renamed a DwC term).
bugfix: inputs/SpeciesLink/Specimen/map.csv: *scientificName: remapped to scientificName instead of taxonName to match the DwC term's name (this is the same dwc_terms_scientificName mismapping that was fixed in r10434)
bugfix: inputs/SpeciesLink/Specimen/map.csv: dwc_terms_scientificName: remapped to scientificName instead of taxonName to match that DwC term name, as well as the mappings of other *scientificName terms
inputs/SpeciesLink/Specimen/map.csv: marked dwc_geospatial_VerbatimLatitude,Longitude as exact duplicates of dwc_terms_*
inputs/SpeciesLink/Specimen/map.csv: remapped identical _alt-ed fields to DUPLICATE. this avoids the need to translate these to postprocessing derived columns for new-style import, and also speeds up column-based import because there are less automatic _alts to perform to resolve filter-less collisions.
bugfix: inputs/SpeciesLink/Specimen/map.csv: *CollectorNumber: moved these to the same _alt group as recordNumber, because they are actually duplicates
correction: inputs/SpeciesLink/Specimen/map.csv: FieldNumber: fixed incorrect comment that these fields are identical to recordNumber, when instead they have the same *meaning but not the same values. instead, values are stored under either of the two terms. the previous conclusion had been based on an incorrect query, which used != instead of the NULL-sensitive IS NOT DISTINCT FROM.
bugfix: inputs/*/*/map.csv for specimen tables: remapped eventDate,day,month,year to *Collected, because a general date always applies to the observation itself rather than to any parent event (specimens don't have a parent event)
inputs/SpeciesLink/Specimen/map.csv: remapped *dayOfYear-related terms to UNUSED
bugfix: inputs/SpeciesLink/Specimen/map.csv: remapped conceptual_darwin_2003_1_0_JulianDay, dwc_dwcore_DayOfYear to dayOfYear instead of day (the day of the month)
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.
inputs/SpeciesLink/Specimen/map.csv: Fixed embedded line endings
inputs/SpeciesLink/Specimen/map.csv: dwc_dwcore_Remarks: Remapped to occurrenceRemarks (it had been incorrectly automapped to taxonRemarks). Combined occurrenceRemarks inputs using /_alt.
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.
inputs/SpeciesLink/Specimen/map.csv: conceptual_darwin_2003_1_0_CoordinatePrecision: Remapped to coordinateUncertaintyInMeters, assuming units based on the range and precision of values
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 -)
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
inputs/SpeciesLink/Specimen/map.csv: Documented that dwc_geospatial_VerbatimLatitude/Longitude contain a mix of DMS and other verbatim coordinates
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: 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/SpeciesLink/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/SpeciesLink/Specimen/map.csv: Removed no longer needed duplicate entries for each first letter case, which cause duplicate output mappings now that join is case- and punctuation-insensitive. Note that the `svn diff` hides _alt entry 0, which contains one of the removed duplicate columns that appears in the diff.
inputs/SpeciesLink/Specimen/map.csv: Added manual CollectorNumber mapping which places it after recordNumber/fieldNumber, so that mappings/Veg+-VegCore.csv doesn't need to maintain a global ordering between these fields and just needs to indicate their equivalency
inputs/SpeciesLink/Specimen/map.csv: _alt all scientificNameAuthorship synonyms together in one _alt
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/SpeciesLink/src/specimens/map.csv: Added explicit _alt suffix when multiple terms map to the same place
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/SpeciesLink/maps/DwC.specimens.csv: Remapped fieldNumber to recordNumber because term usage was inconsistent with DwC definition. Datasources often confuse this term, because it seems like the collection number, but is actually the author code for the event (VegBank's authorObsCode).
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/SpeciesLink/src: Added custom header that overwrites existing header so that column names will not be too long for the staging table
union: Omit mappings that are mapped to in the input map, in addition to mappings that were overridden. This prevents multiple outputs being created for both the renamed and original mappings, causing duplicate output nodes when one XML tree is used for all rows.
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/SpeciesLink/maps: Updated to use new TAPIR download
inputs/SpeciesLink/maps/DwC.specimens.csv: Mapped remaining fields
inputs/*/maps/DwC.specimens.csv: Ran through `cols *` to standardize CSV format to that generated by Python
inputs/SpeciesLink: Switched to using flat files instead of DB
Added inputs/SpeciesLink/maps
