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).
**/new_terms.csv, unmapped_terms.csv updated (using `make missing_mappings`)
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/UNCC/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource
inputs/UNCC/Specimen/: 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. reproductiveCondition: use the suggested values at DwC.vegpath.org?reproductiveCondition instead of just joining together the values in flower and fruit.
inputs/UNCC/Specimen/map.csv: usdaRank, infrarank: documented that they should actually be mapped to infraspecificRank*. it is better to map them to taxonRank for now because infraspecificRank is now mapped to VegBIEN.
mappings/VegCore.htm: regenerated from wiki. added EQUIV (also mapped in mappings/VegCore-VegBIEN.csv).
inputs/UNCC/Specimen/map.csv: infrarank: remapped to EQUIV (of usdaRank). usdaRank, infrarank: documented the VegCore term that each would map to.
inputs/UNCC/Specimen/postprocess.sql: infrarank: remove mismapped values "L." (belong in authors, and are already there)
inputs/UNCC/Specimen/map.csv: loanto, inorout: removed mapping to occurrenceRemarks because this information does not relate to the occurrence. it is also rarely populated.
inputs/UNCC/Specimen/: translated single-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/UNCC/Specimen/new_terms.csv: regenerated
inputs/*/Source/VegBIEN.csv: regenerated for new-style import, which uses a symlink to mappings/VegCore-VegBIEN.csv instead of a custom mapping using the original column names
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
bugfix: inputs/*/Source/map.csv: 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. the staging table column renaming is now used by all Source tables.
bugfix: inputs/*/Source/: added missing ./run, which creates the new-style staging tables with the metadata fields as part of the table. this is needed now that these subdirs use installed staging tables instead of metadata-only map.csvs.
inputs/*/: added table.run for use by the table subdirs in new-style import. datasources without table subdirs do not need this.
inputs/*/: added top-level Makefile which includes inputs/input.Makefile, so that make can be run directly on the datasrc dir without needing to specify `--makefile=../input.Makefile` (see input.Makefile $(selfMake))
mappings/VegCore-VegBIEN.csv: cultivated, oldGrowth: use just cultivated if it's provided, rather than /_alt-ing it back with oldGrowth (which it was generated from)
bugfix: mappings/VegCore-VegBIEN.csv: fixed priority of cultivated and oldGrowth so cultivated is used first if it's available
bugfix: inputs/*/Source/: use installed staging table (with blank-line data.csv) in order to also work with new-style import. this also fixes a benign diff between the by-row and by-col test outputs, where row-based import would not import the Source/ entries because there was not at least one row in the input. note that in order to ensure that all datasources are properly run, you need to check `svn st|sort` against the datasource schema names to see if any are missing.
empty inputs/*/import_order.txt: added subdirs in the order they are used by inputs/input.Makefile, by running make on the inputs to auto-populate import_order.txt. import_order.txt is needed by the runscripts to run the right set of subdirs in the right order.
added inputs/*/*/header.csv for CSV inputs, which are now generated by inputs/input.Makefile %/install
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
inputs/UNCC/Specimen/new_terms.csv: Updated for updated VegCore vocab
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.)
inputs/UNCC/Specimen/map.csv: Populated specimenHolderInstitutions
mappings/VegCore.htm: Regenerated from wiki. Renamed specimenDonor to specimenDonorInstitution to clarify that this is an institution, not a collector.
inputs/UNCC/Specimen/map.csv: Mapped flower, fruit -> reproductiveCondition using translation is from e-mail conv between Jim Matthews at Habitat Assessment and Bob Peet on 2010-12-2~3
inputs/UNCC/Specimen/map.csv: cultivated: assume anything non-NULL to be cultivated, so that we err on the side of excluding possibly-cultivated specimens
inputs/UNCC/_src/_README.TXT: Added e-mail conv between Jim Matthews at Habitat Assessment and Bob Peet about the meanings of the Leaf, Flower, Fruit, and Root codes
inputs/UNCC/Specimen/map.csv: campus: Mapped to cultivated, interpreting non-NULL values as true
inputs/UNCC/Specimen/map.csv: campus: Removed mapping to occurrenceRemarks because this is just a code, not a description. Added definition from Bob's validation comments.
inputs/UNCC/Specimen/map.csv: accession: Removed comment that this is actually the catalogNumber, because they are now synonyms
mappings/VegCore.htm: Regenerated from wiki. Split specimenIndexer into specimenStampingInstitution and specimenDonor (which are often the same).
mappings/VegCore-VegBIEN.csv: Removed specimenIndexer->institutionCode mappings because the institutionCode should refer only to the specimenHolder
inputs/UNCC/Specimen/map.csv: Removed mappings to reproductiveCondition because we don't know what the single-letter codes mean
inputs/UNCC/Specimen/map.csv: Fixed embedded line endings
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
inputs/UNCC/Specimen/map.csv: herbarium->specimenIndexer: Replace UNCCD (UNCC database?) with UNCC
mappings/VegCore.htm: Regenerated from wiki. Source: Added authors. Renamed creator to firstPublisher. Moved dataOwner to Source as list. Coordinates: latitude/longitude, coordinatePrecision: Added units disambiguation. latitude/longitude_DMS: Added components. Global IDs: Changed "globally unique" tag to "global ID" and hyperlinked it to <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs> (which now includes detailed examples of the various types of global IDs).
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-VegBIEN.csv: Mapped reproductiveCondition
Added inputs/UNCC/Specimen/UNCC.csv.url, UNCC.csv.md5
Added inputs/UNCC/_src/ with UNCC.csv.zip.md5
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-VegBIEN.csv: institutionCode list->sourcename mapping: _split(): Also match ; as a separator, and match separators with or without a following space
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>.
inputs/UNCC/Specimen/map.csv: accession: Remapped to catalogNumber per Bob's corrections
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.
*/new_terms.csv, */unmapped_terms.csv: Regenerated using `make missing_mappings`
mappings/VegCore-VegBIEN.csv: Mapped recordNumber to new specimenreplicate.collectionnumber
mappings/VegCore-VegBIEN.csv: Mapped individualCode. authortaxoncode: Prefer tag over recordNumber (collectionnumber), because this applies to the plant rather than the specimen.
schemas/vegbien.sql: plantobservation: Renamed collectionnumber to authorplantcode since this number, which identifies the plant, is actually different from the collectionnumber that identifies the specimen collected from it. This distinction is meaningful for plots data, but generally not for specimens data.
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-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
inputs/*/Source/map.csv without mappings: Added referenceType, etc. mappings. This also ensures that the source table entry for the datasource will be created before the herbaria list is imported, causing all top-level datasources to sort at the top of the source table.
input.Makefile: SVN: add: verify: Also ignore *.xlsx
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: Don't forward specimenreplicate IDs to location for plots data (where the specimenreplicate IDs apply only to the specimen)
inputs/input.Makefile: SVN: add: verify/: Added *.xls to svn:ignore
input.Makefile: SVN: add: Add a Source table to store datasource metadata. This adds a Source table to all herbaria which are listed in .herbaria, and therefore didn't previously need a Source table to indicate their referenceType and sampleType.
inputs/*/verify/: Updated svn:ignore
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: Mapped oldGrowth
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: 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
Updated inputs/UNCC/Specimen/test.xml.ref inserted row count
mappings/VegCore-VegBIEN.csv: Always map taxonNameOrEpithet to taxonomicname, now that it's globally unique at all ranks in the datasource that provides it (NCBI)
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
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)
inputs/*/: Placed all logs/ subdirs and import_order.txt under version control, using `make inputs/.../add`
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
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
