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: 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/CTFS/: switched to new-style import, using the steps at wiki.vegpath.org/Adding_new-style_import_to_a_datasource
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/CTFS/*/VegBIEN.csv: regenerated from map.csv. they may have gotten out of date because they are marked as _no_import, even though they are in import_order.txt.
added inputs/*/*/header.csv for CSV inputs, which are now generated by inputs/input.Makefile %/install
inputs/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files
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/CTFS/: Switched global _no_import to table-specific _no_imports to allow adding new tables that are imported
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: locationID->location.sourceaccessioncode: Removed restriction that this mapping can't occur if geovalidation information is present. The locationID is no longer mapped to the place.sourceaccessioncode, so this filter is not necessary.
mappings/VegCore-VegBIEN.csv: fieldNumber (authorEventCode): Fixed bug where locationevent.authorlocationcode should be authoreventcode
mappings/VegCore-VegBIEN.csv: locationID/locationName + subplot -> location.sourceaccessioncode mapping: Fixed bug where subplot was incorrectly being mapped to this field even when there was no location*. (This field can only be populated if both location* and subplot are specified.) Also only map locationID for this, to avoid inconsistencies where one table supplies locationID+subplot, while another table supplies locationName+subplot, but they both get mapped to the same field, preventing plots from being matched up with their observations when creating the analytical_stem.
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
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: Mapped acceptedCounty, county to the matched place
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.
mappings/VegCore-VegBIEN.csv: subplot locationevent: Only populate parent locationevent's location unique IDs if a subplot #/subplotID is actually specified. (The lack of a location unique ID will cause the parent locationevent's location to be removed, as well as the parent locationevent itself if there is no parent locationevent unique ID.) This fixes a bug where top-level plots in datasources that provide a nullable subplot #/subplotID were incorrectly getting connected to parent locationevents.
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: Map locationID to place.placecode instead when geovalidation columns are provided
mappings/VegCore-VegBIEN.csv: location: Populate sourceaccessioncode with locationID + subplot when subplot is unique only within the parent plot, so that location always has a sourceaccessioncode to use as the plotCode in analytical_db_view
mappings/VegCore-VegBIEN.csv: taxonoccurrence.authortaxoncode: Only populate if needed to distinguish the taxonoccurrence within a plot
mappings/VegCore-VegBIEN.csv: Removed unnecessary /_first/# suffix for multiple terms in the same _exists expression, because _exists() only checks whether its node is non-empty, and it does not matter how many child nodes it contains
inputs/*/*/map.csv: Prefix a * to every term that's not in Veg+ for easy identification of unmapped terms when editing map.csv. Note that canon will remove the * when it finds a matching Veg+ term.
inputs/: Added unmapped_terms.csv, new_terms.csv which were not already under version control
mappings/VegCore-VegBIEN.csv: taxonoccurrence.authortaxoncode alternatives: Use _first instead of _alt because when one of these fields is present, it can be used directly even if it's sometimes NULL, without needing to spend a lot of time _alting together fields that won't be used. Datasources where the authortaxoncode is sometimes NULL usually have a separate sourceaccessioncode for the taxonoccurrence. (In the rare case that they don't, they should map a non-NULL field to recordNumber or tag to ensure that taxonoccurrences can be uniquely identified.)
mappings/VegCore-VegBIEN.csv: Mapped tag to taxonoccurrence.authortaxoncode when the record is an organism, in case there is no other ID for the taxonoccurrence. This fixes a bug in FIA and TEAM data where all organisms in a plot used the same taxonoccurrence because taxonoccurrence was not properly constrained, causing the loss of individual taxondeterminations on each organism.
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/: Regenerated unmapped_terms.csv, new_terms.csv
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
filter_out_ci: Filter header instead of passing it through, in order to properly support CSVs without a header, such as the unmapped_terms.csv and new_terms.csv files. For CSVs with a header, the header of the vocabulary should be removed before passing it to filter_out_ci.
input.Makefile: Maps building: Removed no longer used %/src.csv, because it is no longer needed to generate map.full.csv from map.csv
input.Makefile: Maps building: Removed no longer used %/map.full.csv
input.Makefile: Maps building: %/map.full.csv: Generate by copying map.csv, because the content of these files now differs only in the sort order of the names
inputs/*/*/map.csv: Changed empty mappings to self mappings, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Map_refactoring#Change-empty-mappings-to-self-mappings>. Note that in map.full.csv and VegBIEN.csv, lines that have changed are always the result of the input field's case being changed to match the case of the datasource's actual column name.
inputs/*/*/map.csv: Added back automapped mappings to map.csv, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Map_refactoring#Add-back-automapped-mappings-to-mapcsv>
mappings/VegCore-VegBIEN.csv: Added /_simplifyPath:[next=parent_id]/path to root so the returned subplot location will be its parent location if there is no subplot name or ID (indicating that that particular plot did not have subplots). Note that this also causes the parent_id forwarding effect to occur for all other tables containing parent_id, which will help prevent similar issues with subplot events, etc. This will hopefully fix the SALVIAS.plotObservations bug where some organisms did not have a subplot #, causing the subplot location to become NULL and causing the corresponding locationevent rows not to match the locationevent_unique_within_location index filter condition (which requires a parent_id), which caused multiple output table pkeys to be returned for those rows, violating the locationevent_pkeys temp table's primary key.
Regenerated/modified inputs/*/*/src.csv to use the self-mapping format used by the new automapping mechanism
input.Makefile: Maps building: %/.map.csv.last_cleanup: $(newTerms): Remove the CSV header from the terms lists so that multiple terms lists can easily be appended together
input.Makefile: Maps building: %/.map.csv.last_cleanup: Generate reports on new and unmapped terms in map.csv
mappings/VegCore-VegBIEN.csv: startDate, endDate mappings: Removed _dateRangeStart/_dateRangeEnd filters because these are assumed to already be start and end dates of a range. (eventDate should be used for concatenated date ranges.)
intersect, union: Made case- and punctuation-insensitive. mappings/Veg+-VegBIEN.csv: Removed no longer needed duplicate entries for each first letter case, which must now be removed for case- and punctuation-insensitive intersect/union to work. Note that the SpeciesLink `svn diff` hides _alt entry 0, which contains one of the removed duplicate columns that appears in the diff.
mappings/VegCore-VegBIEN.csv: if subplot: Also forward locationID and plotName to the location of the parent locationevent (in addition to the parent location of the location), in order to "complete the diamond" connecting subplot locationevent -> (parent plot locationevent, subplot location) -> parent plot location
mappings/VegCore-VegBIEN.csv: Redirect eventID, fieldNumber (authoreventcode) to parent locationevent when subplot columns exist
inputs/CTFS/PlotObservation/: Remade (hadn't been automatically remade because it wasn't part of import_order.txt)
Added inputs/CTFS/PlotObservation/
