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: 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.
Refreshed SALVIAS
inputs/SALVIAS/: Regenerated salvias_*.schema.sql from the MySQL version, to take advantage of my2pg improvements. The placeholder *_index columns which take the place of MySQL's inline index definitions have now been replaced by no-op CHECK constraints, so that there are no longer lots of dummy *_index columns in the map spreadsheets.
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: 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-VegBIEN.csv: Mapped locality description fields to location.iscultivated using _locationnarrative_is_cultivated()
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: Remapped cultivated to location when a TaxonOccurrence is not provided, indicating that the record is a plot
inputs/SALVIAS/: Mapped unmapped fields with a VegCore/VegBIEN equivalent. plotMetadata_/: Remapped life_zone to communityID because it is now alt-ed together with vegetation*, and thus not just a description with life_zone_code as its globally unique name.
inputs/SALVIAS/stems/map.csv: stem_height_m: Remapped to height_m using units from <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>
mappings/VegCore-VegBIEN.csv: taxonoccurrence.authortaxoncode: Only populate if needed to distinguish the taxonoccurrence within a plot
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.
mappings/VegCore-VegBIEN.csv: Don't forward individualID to taxonoccurrence.sourceaccessioncode when aggregateOccurrenceID is present
inputs/SALVIAS/stems/map.csv: Remapped stem_dbh from diameterBreastHeight_m to diameterBreastHeight_cm, assuming units based on the units for plotObservations.intercept_cm, which measures the same dimension
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.
mappings/VegCore-VegBIEN.csv: Remapped tag to new stemobservation.tag
mappings/VegCore-VegBIEN.csv: tag: Removed no longer applicable comment
mappings/VegCore-VegBIEN.csv: Removed no longer used previousTag and the complex mapping logic that attempts to place both tags in VegBIEN in the correct order but does not work for column-based import. tag: Removed iscurrent=true because there is now only one tag field.
inputs/SALVIAS/*/map.csv: Remapped all versions of stem and tree tags to tag, with the second tag superceding the first, to avoid the complex VegCore-VegBIEN mapping logic that attempts to place both tags in VegBIEN in the correct order but does not work for column-based import. inputs/SALVIAS-CSV/Organism/map.csv: stem and tree tags: Made the stem tag supercede the tree tag instead of vice versa, to have as specific of a tag as possible.
inputs/SALVIAS/stems/map.csv: Copied Brad's comments on plotObservations.tag1, tag2 to stem_tag1, stem_tag2
schemas/vegbien.sql: Added units suffix to all core VegBIEN fields that have units. It is the responsibility of the mappings to ensure that all units are properly translated.
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/*/*/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/: Added [Veg+] to via map roots to indicate that the datasource and Veg+ vocabularies are combinable. This is possible now that automapped entries are no longer subtracted when this is in the map root, so there is no concern of losing comments on subtracted automapped rows. Note that this change turns on old-style automapping for these datasources, causing SALVIAS plotMetadata to acquire additional mappings.
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.
inputs/SALVIAS/: Switched to using the DB export's staging tables instead of the exported CSVs
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>
mappings/VegCore-VegBIEN.csv: Mapped taxonOccurrenceID
inputs/SALVIAS/2.stems/map.csv: Mapped stem_id
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/SALVIAS/src/2.stems/map.csv: Added comments from corresponding SALVIAS-CSV organisms columns
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: Renamed stems table to 2.stems so import order would be inherent in the dir name, using steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Rename-subfolders-with-import-order>
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: Split occurrenceID into occurrenceID and individualID, where individualID refers to the plant in plots data and occurrenceID refers to the specimen in specimens data. This prevents plant sourceaccessioncodes from being mapped to the specimenreplicate, which was messing up stems mappings for the parent plantobservation. It also avoids mapping the specimenreplicate sourceaccessioncode to additional tables where it isn't needed. (Note that occurrenceID is needed for location to ensure that each specimen gets its own location to make locationdeterminations on. Everything else is directly or indirectly scoped by location when its own sourceaccessioncode isn't specified.)
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: taxonoccurrence: Map everything except occurrenceID (which is globally unique) to new authortaxoncode, which only needs to be unique within the locationevent
mappings/VegCSV-VegBIEN.specimens.csv: occurrenceID: Mapped to specimenreplicate.sourceaccessioncode for mergability with DwC
mappings/VegCSV-VegBIEN.specimens.csv: individualCount: Disambiguated alternate meaning as stem count by changing stem count fields to map to new stemCount term, which maps to plantobservation.stemcount
mappings/VegCSV-VegBIEN.specimens.csv: Removed Source column and source-related comments because this information is now maintained in mappings/Veg+.terms.csv
mappings/VegCSV-VegBIEN.specimens.csv: Comments: Removed no longer applicable comments about XPath syntax added to affect sort order
mappings/VegCSV-VegBIEN.specimens.csv: height: Removed mapping to plantobservation.overallheight, since the height is a stem field rather than a plant field. Note that a height in the organisms table will be mapped to the height in a single stemobservation for that plant, with NULL sourceaccessioncode and authorstemcode. Note also that this change is possible because no mapped datasource yet provides a valid overallheight with multiple stems or that differs from its single stem's height. (Although SALVIAS sometimes provides both a stem height and an organism height, that height is always either the same, or the organism height is invalid. See <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/SALVIAS_issues#Some-organisms-have-one-stem-but-different-heights-in-the-organisms-and-stems-tables>.)
mappings/VegCSV-VegBIEN.specimens.csv: catalogNumber: Split _if apart into separate _ifs for the indirect and direct voucher cases. Moved direct voucher _if inwards so it is just wrapping catalognumber_dwc itself. This will enable this mapping to be used for specimens data, which is always considered a direct voucher and will always have this _if return true. Also moved indirect voucher _if inwards in the same way, so that a future SQL function implementation of _if only needs to concern itself with returning one value or another, not with handling entire XML subtrees. Note that if the indirect voucher _if returns false, NOT NULL and CHECK constraint violations will cause the intervening voucher and specimenreplicate elements to be deleted, thus having the same effect. Use new @name syntax for distinguishing _if statements.
plots inputs: Remapped all VegX via maps to VegCSV. See steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegX-%3EVegCSV>.
mappings/VegX-VegBIEN.stems.csv: _if that maps to specimenreplicate via plantobservation or voucher: Refactored to map right-hand side of _eq in the left-hand side mapping, rather than in all then/else mappings. Distinguish this _if statement from others using new name param.
mappings/VegX-VegBIEN.stems.csv: Reversed XPaths so that they start with location instead of plantobservation
mappings/VegX-VegBIEN.stems.csv: Expanded {} expressions using expand_braces, so that each distinct output for the same input is on its own line, improving readability. This will also help enable search-and-replace reversing of XPaths for the re-rooting to location.
VegBIEN: Reversed aggregateoccurrence<->plantobservation relationship to point from plantobservation->aggregateoccurrence, so plantobservation could be scoped by aggregateoccurrence in the same way as all other core tables are scoped by their parent tables. This reversed direction was an anomaly due to the need to have a trigger auto-set aggregateoccurrence.count to 1 when there was an associated plantobservation. This was most easily accomplished on the aggregateoccurrence table itself, but required the reversed relationship. The trigger has now been reimplemented on plantobservation, which externally updates aggregateoccurrence.count.
mappings/VegX-VegBIEN.stems.csv: plantobservation: sourceaccessioncode, authorplantcode: Removed no longer needed mapping to specimenreplicate.sourceaccessioncode, since specimenreplicate for plots data is now identified by its plantobservation fkey, without needing its own sourceaccessioncode
mappings/VegX-VegBIEN.stems.csv: Replaced "/}" (with unnecessary "/") with "}"
mappings/DwC2-VegBIEN.specimens.csv, VegX-VegBIEN.stems.csv: Removed all manual mappings to datasource_id now that datasource_id is auto-populated, both on the VegBIEN output side and the DwC/VegX input side. This should greatly simplify many of the mappings!
inputs/SALVIAS/maps/VegX.stems.csv: Fixed PlotObsID mapping to point to sourceAccessionCode so that it would map to the same place as organisms' PlotObsID and the entries would be merged. This will hopefully also fix a SALVIAS stems import bug where the specimenreplicate join on existing/inserted rows matched multiple rows, in spite of using the specimenreplicate_unique_catalognumber UNIQUE INDEX.
mappings/VegX-VegBIEN.stems.csv: Mapped to taxonoccurrence.sourceaccessioncode to avoid underconstraining taxonoccurrence
mappings/VegX-VegBIEN.stems.csv: Marked aggregateoccurrence as mergeable, in preparation for switching to explicit merging only to avoid unwanted merges
mappings/VegX-VegBIEN.stems.csv: Indirect voucher mappings: Removed no longer needed ":[*_id/taxonoccurrence]" because a specimenreplicate is a taxonoccurrence, so it doesn't need to have an empty taxonoccurrence
mappings/VegX-VegBIEN.stems.csv: Fixing specimenreplicate->taxonoccurrence mapping bug where taxonoccurrence_id is no longer used as an fkey because it's instead a pkey inherited from taxonoccurrence, by instead using the new fkey to plantobservation for direct vouchers. Note that a duplicate aggregateoccurrence is created, because the _if XML function runs after the XPaths have created the initial tree, and thus the nodes it pulls forward do not automatically get merged with adjacent nodes of the same name. This will eventually need to be fixed by auto-merging the nodes.
mappings/VegX-VegBIEN.stems.csv: Removed _collapse where it's no longer needed because sql_io.put() handles that now. Note that each plantobservation will get an empty stemobservation, whether or not there are any stemtags. This can later be used to add further stemtags.
inputs/SALVIAS: Switched to using CSV exports of the DB, so that staging tables could be created for column-based import
mappings/VegX-VegBIEN.stems.csv: Changed XPath references (using "$") to XML function references using _ref where needed to make them work even on a pre-made XML tree used by all rows
mappings/VegX-VegBIEN.stems.csv: Added _collapse around subtrees that need to be removed if they are created around a NULL value
mappings: Build VegX-VegBIEN.organisms.csv from VegX-VegBIEN.stems.csv instead of vice versa. This entails switching the roots around so stem points to organism instead of the other way around, which is a complex operation. Re-rooted VegX-VegBIEN.organisms.csv at /plantobservation instead of /taxonoccurrence to avoid traveling up the hierarchy to taxonoccurrence and back down again to plantobservation, etc. as would otherwise have been the case.
join: Also produce warnings for no input mapping (if no comment explaining why no input mapping), in addition to no join mapping
mappings/VegX-VegBIEN.organisms.csv: Removed unneeded lookahead assertions from stemtag mappings. They relied on a bug ("feature"?) in the XPath engine that made the value of the lookahead assertion's path the same as the value of the main path, even though the value is set after the path is parsed.
VegX-VegBIEN mapping: Use new lookup-only element syntax to ensure that stemtag 1 is not created if it doesn't exist when stemtag 2 tries to set its iscurrent status to false. This should fix the 136 "NullValueException: columns: tag" errors in the SALVIAS organisms import.
VegX-VegBIEN mapping: Map stemtags using [] instead of :[] for attrs that are really keys
VegBIEN mappings: Changed tableRecord_ID to tablerecord_id to match PostgreSQL field name
VegX-VegBIEN mapping: Mapped userdefined fields to new first-class fields
VegBIEN: stemobservation: Renamed diameter to diameterbreastheight to be more accurate
VegX-VegBIEN mapping: Mapped stem tags to new stemtag table
sort: Sort empty strings last so that inputs with no mapping go at the end of the map spreadsheet
join: For input mappings with no match in the join map, include them in the output map with an empty mapping
VegX-VegBIEN mapping: Link aggregateoccurrence to plantobservation via forward pointer rather than backward child-to-parent pointer
VegBIEN: Renamed stem to stemobservation
VegBIEN: Renamed individualplant to plantobservation
VegX-VegBIEN mapping: Map stem count to new stemcount field
VegX-VegBIEN mapping: Took advantage of userdefined.userdefinedtype being optional
VegBIEN: Renamed sourceid to author*code
VegBIEN: Renamed authorcode to sourceid
Filled in SALVIAS stems mappings. make test2's stems test fails because we don't wrap the import transaction around all the tests so that organisms are already in the database when stems are imported.
Moved inputs files into subdirs for maps, verify, and test operations
inputs/SALVIAS: Added stems map
