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: inputs/CVS/taxonObservation_/create.sql: mapped identifiedBy, which involves joining to party
inputs/CVS/cvs.~.clean_up.sql: don't rename taxonInterpretation.PARTY_ID, so that this can be USING-joined to party in inputs/CVS/taxonObservation_/create.sql
fix: inputs/CVS/taxon_observation.**/map.csv: omit authorPlantName because it is not specific to the taxonInterpretation row (this is in a separate taxonInterpretation for the original determination instead)
inputs/CVS/taxonObservation_/map.csv: removed taxonObservation_-- prefix from terms that do not need to be table-specific (like for VegBank)
fix: inputs/CVS/taxonObservation_/map.csv: plantConcept_ columns: synced input and output column names to their names in plantConcept_
inputs/CVS/: don't import joined tables, because they are now imported in the taxon_observation.** left-join instead
inputs/CVS/: added taxon_observation.** left-join of the tables, using the steps at http://wiki.vegpath.org/Left-joining_a_datasource. this involves renaming taxonOccurrenceID->taxonOccurrenceID__overall_plot so that it can then be joined together with aggregateOrganismObservationID to create the full taxonOccurrenceID (as in VegBank).
inputs/CVS/taxonObservation_/map.csv: mapped TAXONINTERPRETATION_ID to identificationID
inputs/CVS/: 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/CVS/taxonObservation_/header.csv, map.csv: updated to use plantConcept_ renamed columns
inputs/CVS/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource
inputs/CVS/taxonObservation_/map.csv: updated for CVS refresh
inputs/CVS/taxonObservation_/map.csv: updated input column names to plantConcept_ renamings
fix: inputs/CVS/taxonObservation_/map.csv: moved inherited derived columns to right after the other columns, because for this table, these are actually real input columns rather than appended derived columns. the column order must match header.csv to avoid mis-renamings.
inputs/CVS/taxonObservation_/map.csv: removed filter functions, which are now performed in plantConcept_
inputs/CVS/taxonObservation_/postprocess.sql: added _parent index to facilitate joins
fix: inputs/CVS/taxonObservation_/header.csv, map.csv: updated for CVS refresh and addition of plantConcept_ derived columns
mappings/VegCore-VegBIEN.csv: mapped taxon_determination__is_current, taxon_determination__is_original
bugfix: mappings/VegCore-VegBIEN.csv: main taxondetermination: use [!isoriginal=true] instead of [!isoriginal] so that adding a manual isoriginal field does not prevent this selector from matching
mappings/VegCore.htm: regenerated from wiki. added taxon_determination__is_current, taxon_determination__is_original.
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/CVS/taxonObservation_/map.csv: collector_ID: remapped it to UNUSED and removed the join to party via it, like in VegBank
inputs/CVS/taxonObservation_/map.csv: denorm_{tri,quad}*: mapped to infraspecificRank*, infraspecificEpithet*
inputs/CVS/taxonObservation_/map.csv: infraspecific ranks: remapped to EQUIV#to:species (which is the speciesBinomial), because these actually contain the full taxonomic name at that rank, like VegBank
inputs/CVS/taxonObservation_/map.csv: genus: documented that unlike VegBank, does not include genus author
inputs/CVS/taxonObservation_/map.csv: denorm_* terms _alt-ed with normalized terms: use DUPLICATE#of instead where possible. documented where and why _alt was necessary (this applies to a few rows for division, genus).
bugfix: inputs/CVS/taxonObservation_/map.csv: species: remapped to speciesBinomial, not specificEpithet (like for VegBank). however, note that denorm_species is in fact the epithet, unlike VegBank.
fix: inputs/CVS/taxonObservation_/postprocess.sql: removed {} around denorm_genus to match the normalized genus
inputs/CVS/taxonObservation_/map.csv: removed unnecessary alts for terms that don't have a duplicate denorm* or hierarchical field
fix: inputs/CVS/taxonObservation_/postprocess.sql: fix 1 row that has denorm_kingdom != Kingdom (i.e. both NOT NULL but not the same)
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: mappings/VegCore-VegBIEN.csv: stratum's locationevent: link this to the parent locationevent, so that the parent locationevent's information (such as locationeventcontributors) is accessible to the stratum's locationevent
inputs/*/*/test.xml.ref: updated source.shortname for new datasource name, which now starts out with .new suffix
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
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/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files
mappings/VegCore.htm: Regenerated from wiki. Added flower, fruit, commonName.
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>.
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: 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
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
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 -)
Regenerated inputs/CVS/taxonObservation_/new_terms.csv. Note that it includes mappings to terms which are not in mappings/VegCore-VegBIEN.csv, which are prefixed with *.
inputs/CVS/taxonObservation_/map.csv: Mapped plantname, plantNameWithAuthority
inputs/CVS/cvs.~.utils.sql: plantconcept_plantnames(): Use CVS's taxonLevel values, which are different from the VegBank plantLevel values that the original version of this function used
inputs/CVS/taxonObservation_/map.csv: Use denorm_* denormalized taxonomic ranks in place of the normalized ranks when both are provided
inputs/CVS/taxonObservation_/map.csv: Fixed bug where taxonLevel, not taxonRank, needs to be mapped to taxonRank, because CVS's taxonRank is actually a number, while taxonLevel contains the corresponding text string
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/CVS/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)
inputs/CVS/: Refreshed data with new export from Bob
