inputs/Makefile: Input data sync: Updated rsync filter for new subdirs layout
README.TXT: Datasource setup: Updated for new subdirs layout
input.Makefile: SVN: add: Updated svn:ignores for new subdirs layout
inputs/Makefile: Import logs: Fixed bug where excluded install logs needed to be renamed according to the new name format (from <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Move-log-files-into-subfolders>)
inputs: Moved log files into subfolders, using steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Move-log-files-into-subfolders>
input.Makefile: Merged Installation and Staging tables sections into Staging tables installation, since no other installation is performed. Removed "import/" prefix from non-file import-related targets.
inputs: Moved test outputs into subfolders, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders#Move-test-outputs-into-subfolders>
input.Makefile: Import to VegBIEN: Removed extra test for $(inputFiles), because when there are no inputs, $(tables) will be empty and import will automatically do nothing. Removed no longer needed $(inputFiles).
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>
strings.py: concat(): Apply length limits by shrinking max_len by new raw_extra_len() of the strings. This also fixes a bug where multi-byte characters in str0 were not properly taken into account, leading to overly long strings. Added doc comment.
strings.py: Added raw_extra_len()
sql_gen.py: NoUnderlyingTableException: Take a (required) parameter for the item that had no underlying table, and provide this wherever a NoUnderlyingTableException is created
strings.py: concat(): Perform substring operation on Unicode strings so that substring does not split Unicode characters. Still use to_raw_str() to calculate the str1 length because Unicode characters can be multi-byte, and length limits often apply to the byte length, not the character length.
exc.py: add_msg(): Fixed bug where needed to convert the Unicode string back into a raw string because Python's top-level exception handler doesn't support Unicode strings as exception messages
inputs/import.stats.xls: Updated with stats from latest import
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>
inputs: Renamed organisms table to 1.organisms 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>
inputs: Renamed plots table to 0.plots 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>
input.Makefile: Mapping: If table subdir contains no input files, print warning instead of aborting. This situation occurs when renaming a version-controlled directory, whose previous version persists as an empty dir until committing.
input.Makefile: Mapping: Removed no longer used $(<in) and test for it in $(map)
input.Makefile: Mapping: $(map): Removed no longer used test for $(mapEnv)
sql.py: run_query(): Exception handling: Fixed bug where PostgreSQL 9.1 PL/Python errors have a different format than PostgreSQL 9.0 which needs to be supported separately. This format was already supported in sql_gen.plpythonu_error_handler, but also needed to be supported for exceptions that propagate back to the client.
inputs/SALVIAS-CSV/src/: Removed source files because they shouldn't be under version control. (They are synchronized via `make inputs/download`.)
inputs: Moved src files into VegCSV subfolders (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV#CSV-representation), with table suffixes removed, using the steps at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCSV_subfolders>
util.py: dict_subset(): Fall back to using dict when OrderedDict is not available, in order to support making the maps on nimoy
mappings/: Removed now-inaccurate ".stems" suffix from VegX-VegCore.stems.csv, which actually applied to all tables
mappings/: Removed no longer used ".specimens" suffix from maps, which is now the same for all maps
mappings/: Removed no longer used plots, organisms, and stems maps, which were copies of the specimens map
input.Makefile: Core maps: Always use the specimens "table", since there are now no longer separate mappings for different tables, and the other tables' maps in mappings/ are merely copies of the specimens table's map
input.Makefile: Removed no longer used custom via maps code, so that map files no longer need a prefix (which is always the same) specifying that they map through Veg+. Veg+ thus serves as the single gateway to VegBIEN, which avoids ever again having to maintain two copies of the mappings, as was the case when DwC and VegX XPaths were separate gateways. This will assist in untying the complex mapping logic in input.Makefile from file naming conventions in mappings/, and simplify the task of grouping each map with the CSV it maps.
input.Makefile: Removed no longer used DB inputs section, because all of our inputs are either CSV or (rarely) XML. This removes a significant amount of dead code that will make it easier to refactor input.Makefile to use custom CSV import orders.
mappings/Veg+-VegCore.specimens.csv: Added mappings for miscellaneous terms
mappings/Veg+.terms.csv: Added miscellaneous terms
to_do/: svn:ignore OpenOffice lock files
inputs/import.stats.xls: Updated with stats from latest import. The import time for SpeciesLink (the slowest datasource) went back down to 9 hours after replacing the slower _merge with _alt.
Added new autogen mappings/VegCore.self.specimens.csv (not currently used)
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>.
README.TXT: Schema changes: Updated filenames of PDF ERD exports
Regenerated vegbien.ERD exports
xpath.py: parse(): _value(): Support '+' as a word character that doesn't need to be quoted
intersect: Fixed bug where test for ignore option needed to be removed, because ignore is not supported by this program
util.py: list_subset(): Fixed bug where using '+' to append the rest of the list didn't work if '+' was the first index, because max() cannot be called on an empty list
mappings/DwC2-VegBIEN.specimens.csv: Added VegCSV mappings, to enable use of one VegCSV-VegBIEN mapping for specimens and plots data
inputs/XAL/maps/DwC.specimens.csv: Remapped FieldNumber to recordNumber because this historical DwC term (http://rs.tdwg.org/dwc/terms/history/index.htm#fieldNumber-2009-04-24) has close to the same meaning as recordNumber, but not the same meaning as the current fieldNumber term
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).
mappings/DwC2-VegBIEN.specimens.csv: catalogNumber: Added additional VegCSV mappings for mergability. taxonoccurrence.authortaxoncode: Added alternative mappings from VegCSV for mergability.
xml_func.py: simplify(): Apply pass-through optimizations for _if statements with no condition (which means false). This faciliates automated testing after an _if statement has been added, because the put template provided as part of the automated test will only change for those datasources that actually have a condition entry for the _if statement, which greatly reduces the number of tests that need to be accepted. (Note that the path before the _if will still be included as an empty path if there are no other mappings to that table, because the _if statement does not surround it.)
mappings/VegCSV-VegBIEN.specimens.csv: Added DwC mappings, to enable use of one VegCSV-VegBIEN mapping for specimens and plots data
schemas/vegbien.sql: Moved collectionnumber from specimenreplicate to plantobservation to replace authorplantcode, since these terms are used analogously in plots and specimens data. This code is really the DwC recordNumber (VegBIEN collectionnumber), which "serves as a link between field notes and an Occurrence record, such as a specimen [or plots data] collector's number" (http://rs.tdwg.org/dwc/terms/#recordNumber). Also, this prevents a specimenreplicate from incorrectly being created when plots data provides an authorplantcode.
mappings/DwC2-VegBIEN.specimens.csv: Mapped individualID for mergability with VegCSV
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: Removed catalogNumber mapping because the catalogNumber applies only to the specimen, not to the occurrence, especially in plots data
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
schemas/vegbien.sql: taxonoccurrence: Renamed taxonoccurrence_locationevent_1_to_1 to taxonoccurrence_unique_within_locationevent and added new authortaxoncode to it
schemas/vegbien.sql: taxonoccurrence: Added authortaxoncode to store unique keys that are unique within the locationevent rather than within the datasource
inputs/SALVIAS-CSV/maps/VegCSV.organisms.csv: Added _alt to height_m, stem_height_m to choose between them when both are specified (rather than having bin/map choose their priority order based on their order in the map). Note that when both of the heights are specified, they are always either the same, or height_m 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>).
bin/map: collision_suffix: Setting back to _alt to test if _merge caused the SpeciesLink slowdown. SpeciesLink contains a huge number of equivalent columns due to each DwC term being present with namespaces for all versions of the DwC schema, and these columns can be combined either using _alt or _merge. _merge is only useful if the values in different versions of the same DwC field are different, which is not likely the case.
inputs/import.stats.xls: Updated with stats from latest import. The import time for SpeciesLink (the slowest datasource) doubled, to 16 hours, most likely due to replacing _alt with the slower _merge, which preserves more input data.
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: occurrenceID: Mapped to location.authorlocationcode instead of sourceaccessioncode so that it would not override any location- or event-related IDs in location.authorlocationcode merely by being mapped to the sourceaccessioncode field (which takes precedence over the authorlocationcode when specified)
mappings/VegCSV-VegBIEN.specimens.csv: occurrenceID: Mapped to specimenreplicate.sourceaccessioncode for mergability with DwC
mappings/VegCSV-VegBIEN.specimens.csv: Mapped voucherType to indirect voucher _if statements' conditions
mappings/VegCSV-VegBIEN.specimens.csv: locationID: location.sourceaccessioncode mapping: Added /_alt suffix for mergability with DwC
mappings/DwC2-VegBIEN.specimens.csv: collectionID: Mapped to location.authorlocationcode as merge with collectionCode, the same way as it is for specimenreplicate.collectioncode_dwc
schemas/vegbien.sql: location: location_unique_within_datasource_by_authorlocationcode unique index: Added `parent_id IS NULL` condition so that an authorlocationcode is not unintentionally treated as globally unique when a parent location is available (which implies that the authorlocationcode is a subplot code)
mappings/VegCSV-VegBIEN.specimens.csv: catalogNumber: Added location.authorlocationcode mapping for mergability with DwC
mappings/DwC2-VegBIEN.specimens.csv: location.authorlocationcode mappings: Added /_alt/3 for mergability with VegCSV mappings to same field
mappings/DwC2-VegBIEN.specimens.csv: catalogNumber: Wrapped all mappings in direct voucher _if for mergability with VegCSV
mappings/DwC2-VegBIEN.specimens.csv: catalogNumber: Moved direct/indirect voucher _if inwards to wrap just the value of catalognumber_dwc, not the catalognumber_dwc field node, to match the corresponding VegCSV mapping
mappings/DwC2-VegBIEN.specimens.csv: Replaced _alt with _merge where applicable to avoid losing source data on import when multiple fields collide
mappings/VegCSV-VegBIEN.specimens.csv: Cleaned up using `make mappings/`
schemas/functions.sql: join_strs_transform(): Use STRICT optimization to avoid needing to manually check if the state value or input value is NULL (http://www.postgresql.org/docs/8.3/static/sql-createaggregate.html#AEN51596)
schemas/functions.sql: join_strs(), join_strs_transform(): Reversed order of params to enable strict optimization, which replaces the state value with the first parameter, which used to be the delimiter (http://www.postgresql.org/docs/8.3/static/sql-createaggregate.html#AEN51596)
Renamed join_strs_transform_preserve_empty() to join_strs_transform() now that there are no other join_strs_transform_...() functions
schemas/functions.sql: Removed no longer used join_strs_transform_fold_empty()
schemas/functions.sql: join_strs() aggregate: Use join_strs_transform_preserve_empty() as an optimization because all our data has already had '' replaced with NULL by sql_io.cleanup_table() in csv2db. This will help speed up _merges now that they are performed on a large scale in the slowest datasource, SpeciesLink.
bin/map: collision_suffix: Changed to use _merge instead of _alt to avoid losing source data on import when multiple fields collide
bin/map: Preventing collisions if multiple inputs mapping to same output: Made collision suffix configurable so it can easily be changed
mappings/DwC2-VegBIEN.specimens.csv, VegCSV-VegBIEN.specimens.csv: taxonoccurrence.sourceaccessioncode mappings: Added catalogNumber mapping, which takes precendence over recordNumber and is applicable to specimens data and direct vouchers. recordNumber should only be used as a last resort (before the taxon name) because this is collector-assigned and often not unique within anything.
mappings/VegCSV-VegBIEN.specimens.csv: catalogNumber: Moved direct/indirect voucher _ifs inwards to wrap just the value of catalognumber_dwc, not the catalognumber_dwc field node, so that a future SQL function implementation of _if only needs to concern itself with returning one value or another, not with handling XML subtrees. The previous moving of the _ifs in r3942 was intended to effect this, but the _ifs weren't moved in far enough to wrap just the value.
mappings/VegCSV-VegBIEN.specimens.csv: eventDate mappings: Removed collectiondate mapping because the eventDate refers only to the plot event. Added /_alt suffixes for mergability with DwC.
mappings/DwC2-VegBIEN.specimens.csv, DwC1-DwC2.specimens.csv: Split eventDate into eventDate and dateCollected, where eventDate refers only to the date of the sampling event, but dateCollected also refers to the date the particular specimen was collected. (This distinction is important in merging with VegCSV, because in plots data, these two fields are distinct.) Remapped datasources with dateCollected-related fields to new dateCollected.
bin/map: Run new xml_func.simplify() on the root before printing the put template, so that _alts and _merges with only one element for the current datasource will be printed in their simplified form (with the _alt/_merge removed). This faciliates automated testing after an _alt/_merge suffix has been added, because the put template provided as part of the automated test will only change for those datasources that actually have an entry for both mappings, which greatly reduces the number of tests that need to be accepted.
xml_func.py: Added simplify()
xpath.py: put_obj(): Use new get_values(), so that the returned nodes are not modified by XML tree transformations, such as those performed by xml_func.process()
Added get_values()
xml_dom.py: is_empty(): Treat whitespace-only text nodes (including text nodes containing empty strings) as empty. This will also support None equivalents in text nodes, because they are isspace_none_str, which is considered whitespace.
xml_func.py: _map(): Don't remove None params, because are valid values and must be supported. This will become an issue once empty strings in text nodes are considered equivalent to None.
xml_func.py: _units(): Don't remove None params, because are valid values and must be supported. This will become an issue once empty strings in text nodes are considered equivalent to None.
xml_func.py: _name(): Fixed bug where needed to pass None values through and handle no name parts to properly support NULL propagation
xml_dom.py: value(), set_value(): Use new strings.isspace_none_str as sentinel None equivalent, to support cloning text nodes containing a sentinel None
strings.py: Added isspace_none_str to support clone-safe sentinel str values that pass isspace()
xml_dom.py: is_whitespace(): Also consider empty text nodes to be whitespace
xml_dom.py: is_whitespace(): Support text nodes whose value() is None by using .nodeValue instead
xml_dom.py: set_value(): Don't set the value of a text node to None by removing it, because this prevents the node from being reused. Instead use a sentinel string value to denote None, and map to and from it.
strings.py: Added none_str and helper class NonInternedStr to support sentinel str values
xml_dom.py: set_value(): Support setting the value of a text node to None, by removing it
