mappings/VegCore-VegBIEN.csv: Mapped taxonRank analogously to computer.taxonRank
inputs/SALVIAS*/1.organisms/map.csv: Remapped OrigFamily/OrigGenus/OrigSpecies to new verbatim* taxonomic names. Also remapped cfaff to verbatimIdentificationQualifier, because it was previously mapped to the same taxondetermination as the Orig* terms, but this will later need to be remapped to identificationQualifier (not in this commit because that is a separate change). Note that the switch to the verbatim* taxonomic names removes a concatenated binomial that was part of the previous mappings, which put OrigGenus and OrigSpecies together into one scientificName.
mappings/VegCore-VegBIEN.csv: Mapped verbatimScientificName to taxonoccurrence.authortaxoncode as an alternative to scientificName
mappings/VegCore-VegBIEN.csv: Mapped verbatim* taxonomic terms
mappings/Veg+.terms.csv: Added verbatimIdentificationQualifier
mappings/Veg+.terms.csv: Added verbatimScientificName
schemas/vegbien.sql: taxondetermination: taxondetermination_unique unique index: Added isoriginal so an "original" determination in the same row (as found in SALVIAS) will be seen as distinct from the scrubbed determination, even if they are to the same plant name
mappings/VegCore-VegBIEN.csv: taxonomic terms: Removed ":[isoriginal=true]" because there may be multiple determinations for an organism (either in separate rows or, for SALVIAS, in separate columns), and not all will be the original determination
schemas/vegbien.sql: taxondetermination.role: Default to 'unknown' so that the field is optional
schemas/vegbien.sql: role enum: Added 'unknown' value
mappings/Veg+.terms.csv: Added verbatim* taxonomic terms
inputs/import.stats.xls: Updated with stats from latest import
inputs: Regenerated maps for changes to bin/union, which removes empty mappings. Added /_alt suffix where needed.
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>
input.Makefile: $(tables): Allow datasource to specify custom import order in src/import_order.txt
mappings/Veg+.terms.csv: growthForm: Documented source of standard terms
inputs/SALVIAS*/src/1.organisms/map.csv: Removed no longer applicable comments, which related to mappings that were in effect long ago
inputs/SALVIAS/src/2.stems/map.csv: Added comments from corresponding SALVIAS-CSV organisms columns
inputs/SALVIAS*/src/1.organisms/map.csv: Habit: Mapped to new Veg+ habit term
inputs/SALVIAS*/src/1.organisms/map.csv: Habit: Don't filter out values not part of the provided terms list, because such values should be flagged as invalid in the error maps rather than silently discarded. This also ensures that any valid values which are not part of the provided terms list are kept.
mappings/Veg+-VegCore.csv: habit: Map to new verbatimGrowthForm since this field is not necessarily standardized
mappings/Makefile: Veg+.cs-VegBIEN.csv: Join new Veg+-VegCore.to_self.csv (self-join), instead of Veg+-VegCore.csv, to VegCore-VegBIEN.csv, to support two-level chains of mappings in Veg+-VegCore.csv
mappings/Veg+-VegCore.csv: /_alt pass through mappings: Removed comment because the two-level mapping propagates it to all fields ending in /_alt, even though it doesn't apply to them, causing the main VegBIEN map and several datasources' maps to change unnecessarily. Also, the comment is not completely accurate because /_alt pass throughs are now used primarily to support idempotent self-joins of Veg+-VegCore.csv.
union: Don't eliminate duplicate rows based on matches between map_0's output column and map_1's input column, because union is now being used for self-joins and it is legitimate for a term to appear as both an input and an output
sql_io.py: put_table(): MissingCastException: Use strings.repr_no_u() instead of strings.urepr() in order to remove the u in u'...' for Unicode strings
README.TXT: After a new import: Updated commands for new subdirs layout
Regenerated vegbien.ERD exports
mappings: Added autogen Veg+-VegCore.to_self.csv, which is Veg+-VegCore.csv joined to itself, and use it as an intermediate map to join to VegCore-VegBIEN.csv. This provides support for two-level chains of mappings in Veg+-VegCore.csv.
mappings/Veg+-VegCore.csv: Changed output root to Veg+, to allow mappings/Veg+-VegCore.csv to be joined with itself idempotently, for supporting multi-level chains of mappings
mappings/Veg+-VegCore.csv: Add pass through /_alt mapping for all terms in this map that are merged with _alt, to allow datasource to define custom mappings that don't pass through the default mapping. This also allows mappings/Veg+-VegCore.csv to be joined with itself idempotently, to support multi-level chains of mappings.
mappings/Veg+-VegCore.csv: authorPlantCode: Added _alt suffix to create the correct priority
union: Exclude empty rows from the output, so that empty mappings from map_0 aren't included when map_1 contains a non-empty mapping for the same term. Note that this causes "No non-empty join mapping" warnings to turn into "No join mapping".
ci_map: Run join_union_sort in quiet mode so that it doesn't add lots of "No non-empty join mapping" warnings to the Comments column
mappings/Veg+-VegCore.csv: scientificNameAuthor: Added scientificNameAuthorship mapping with /_alt/1, to ensure that it has priority over scientificNameAuthor and to ensure that it has an _alt suffix when a datasource contains both scientificNameAuthor and scientificNameAuthorship (such as SpeciesLink)
inputs/SpeciesLink/src/specimens/map.csv: Added explicit _alt suffix when multiple terms map to the same place
inputs/ARIZ/src/specimens/map.csv: RelatedCatalogItem mappings: Added _alt suffixes
union: Multi-support: When an input appears in both maps, treat an empty mapping as if it didn't exist so that it doesn't overwrite a non-empty mapping in the other map
mappings/Makefile: Veg+.cs-VegBIEN.csv: Join Veg+-VegCore.csv to VegCore-VegBIEN.csv in quiet mode, to avoid adding "No non-empty join mapping" to the Comments column
join: quiet mode: Turn off all warnings, not just "No input mapping" warnings. This is useful when join-unioning a synonymy to a primary map, which may have "No non-empty join mapping" for some terms but this should not be stored in the resulting map's Comments column.
mappings/Makefile: Rewrapped lines
mappings/Veg+-VegCore.csv: Added verbatimGrowthForm mapping
mappings/Veg+.terms.csv: verbatimGrowthForm: Added comment that additional values come from SALVIAS. As other datasources' custom growth form values are added, they can be added to this comment.
mappings/Veg+.terms.csv: Added verbatimGrowthForm
schemas/vegbien.sql: locationdetermination: Added verbatimlatitude, verbatimlongitude, verbatimcoordinates
schemas/functions.sql: Made aggregating functions polymorphic
xml_func.py: Removed no longer used _collapse()
xml_func.py: Removed no longer needed _if(), which has been translated to a SQL function
schemas/functions.sql: Added _if()
sql.py: function_exists(): Support overloaded functions
sql.py: run_query(): Parse "more than one" errors as DuplicateExceptions
xml_func.py: XML function specification documentation: Updated parameters
xml_func.py: Removed no longer needed _eq(), which has been translated to a SQL function
schemas/functions.sql: Added _eq()
sql.py: run_query(): Parse "could not determine polymorphic type because input has type "unknown"" errors as MissingCastExceptions to type text. This adds support for polymorphic SQL functions whose parameters are anyelement, etc.
sql_io.py: put_table(): sql.MissingCastException: Support unknown (None) columns, by casting all columns
sql.py: MissingCastException: Support unknown (None) columns
xml_dom.py: replace_with_text(): Support bool `new` values
input.Makefile: Determine import order from sorted order of all non-hidden subdirs, instead of from fixed constant. This allows datasources to specify arbitrary tables, rather than being limited to 0.plots, 1.organisms, 2.stems, specimens.
lib/common.Makefile: Added $(wildcard/) (needed because builtin $(wildcard) doesn't do / suffix correctly)
input.Makefile: src/%/map.full.csv: Fixed bug where couldn't have $(srcMap) in prerequisites because this would for some reason cause src/%/map.full.csv to always be remade
input.Makefile: Src maps cleanup: Fixed bug where src.csv was using .map.csv.last_cleanup instead of .src.csv.last_cleanup as its .last_cleanup file
input.Makefile: Maps building: Moved src/%/map.full.csv after src/%/map.csv now that the filenames are fixed, so pattern matching order isn't an issue
input.Makefile: Maps building: $(makeFullCsv): Removed no longer needed test for whether the $(coreSelfMap) exists, because Veg+'s self map always exists
inputs/CTFS/src/1.organisms/: Added "_" prefix to prevent it from being treated as a data table subdir, before the DB export is mapped
inputs/CTFS/src/ERD.jpg: Made it a symlink to "STRI2011_DB v5.jpg" instead of a copy of it
Added inputs/CTFS/src/bci_01April2011.zip.url, which contains the original download URL for our copy of the CTFS database
inputs/CTFS/src/: Added "_" prefix to scripts_to_drop_extra_tables subdir to prevent it from being treated as a data table subdir
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: 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
