Added autoremove
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: unmapped_terms.csv, new_terms.csv: Factored out commands into $(newTerms)
input.Makefile: Maps building: %/.map.csv.last_cleanup: Generate reports on new and unmapped terms in map.csv
Added filter_out_ci
input.Makefile: Maps building: %/.map.csv.last_cleanup: Translate map.csv using $(mappings)/$(via)-VegCore.csv
Added translate
mappings/Veg+-VegCore.csv: Removed no longer used Comments column. Use mappings/Veg+.terms.csv to cite term definitions instead.
mappings/Veg+-VegCore.csv: previousCatalogNumber: Removed no longer needed "According to" comment, because this is now documented in the mappings/Veg+.terms.csv entry. Note that the citation for any mapping is the overlap of the terms' definitions, and thus only the definitions need to be cited, not the mapping itself. (The definitions are provided in the links in mappings/Veg+.terms.csv.)
mappings/Veg+.terms.csv: previousCatalogNumber: Added Source link to DwC history entry, which documents the definition of this term
input.Makefile: Maps building: %/.map.csv.last_cleanup: Canonicalize map.csv using $(mappings)/$(via).vocab.csv
Added canon
mappings/VegCore-VegBIEN.csv: Mapped min/max SlopeAspect/SlopeGradient. Note that this allows the min/maxSlopeAspect values to bypass the additional _compass filter that is applied to slopeAspect.
Added mappings/Veg+.vocab.csv
inputs/GBIF/Specimen/map.csv: Remapped Original fields to new verbatim taxonomic terms
mappings/Veg+.terms.csv: Added min/max SlopeAspect/SlopeGradient
inputs/VegBank/plot_/map.csv: Omit reallatitude/reallongitude because private data should not be placed in a public database
inputs/CVS/Organism/map.csv: Omit realLatitude/realLongitude because private data should not be placed in a public database. Keeping VegBIEN free of restricted-access data allows anyone to run arbitrary queries on the database, without needing an entire security mechanism/front end just to manage users' read-only access to the data (as VegBank has). Note that the private coordinates are still accessible in the staging tables, so they will need to be locked down in order to make VegBIEN secure to public access.
mappings/Veg+-VegCore.csv: Remapped QuadratID to subplotID because the standard definition of an ID term is an ID that's unique within the datasource, and it's just CTFS's usage that makes it unique only within the plot
inputs/CTFS/StemObservation/map.csv: Manually mapped QuadratID to subplot since it is unique only within Site, and thus can't be the subplotID
inputs/CTFS/SubplotObservation/map.csv: Manually mapped QuadratID to subplot since it is unique only within Site, and thus can't be the subplotID
inputs/CTFS/Subplot/map.csv: Manually mapped QuadratID to subplot since it is unique only within Site, and thus can't be the subplotID. Omit QuadratName because QuadratID is used for the same purpose.
mappings/Veg+-VegCore.csv: Removed recordNumber/_alt and recordNumber redirection mappings so that Veg+-VegCore.csv contains only renamings, not business logic. Note that removing the global ordering of these fields does not affect the datasources which contain multiple recordNumber synonyms because they either have a custom ordering or one field is duplicated or unused.
inputs/NY/Specimen/map.csv: Omit CollectorNumber because it is not used, so it does not need to be mapped
inputs/ARIZ/Specimen/map.csv: Omit FieldNumber because it is identical to CollectorNumber, so it does not need to be mapped
inputs/SpeciesLink/Specimen/map.csv: Added manual CollectorNumber mapping which places it after recordNumber/fieldNumber, so that mappings/Veg+-VegCore.csv doesn't need to maintain a global ordering between these fields and just needs to indicate their equivalency
mappings/: Removed no longer needed Veg+-VegCore.to_self.csv, because multiple levels of mappings are no longer needed to get to the VegCore term
mappings/Veg+-VegCore.csv: DescriptionOfSite: Mapped directly to locality rather than to locationNarrative to avoid needing multiple levels of mappings to get to the VegCore term
mappings/Veg+-VegCore.csv: Removed scientificNameAuthorship/_alt and scientificNameAuthorship redirection mappings, which were only used by SpeciesLink but it now has the necessary _alts in its own map.csv
mappings/Veg+-VegCore.csv: Removed dateCollected/_alt and dateCollected redirection mappings, which were only needed when multiple dateCollected fields were being combined in Veg+-VegCore.csv
mappings/: Moved year/month/dayCollected mappings from Veg+-VegCore.csv to VegCore-VegBIEN.csv so that Veg+-VegCore.csv contains only renamings, not business logic. Note that this allows the year/month/dayCollected values to bypass the additional _dateRangeStart filter that is applied to text dates. The priority of the plain dateCollected field is now higher than the year/month/dayCollected fields when both are specified, because the dateCollected field presumably contains verbatim text while the year/month/dayCollected fields contain parsed date parts.
inputs/SALVIAS-CSV/Organism/map.csv: Remapped census_date to eventDate, since it is not the start of a range
inputs/Madidi/Plot/map.csv: Remapped First evaluation to eventDate, since it is not necessarily the start of a range
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.)
mappings/VegCore-VegBIEN.csv: Don't map dateCollected to locationevent.obsstartdate/obsenddate because this is the date the specimen was collected, not the date (range) of the entire collection event. This distinction may not be meaningful for specimens data, but VegBIEN should reflect what the data provider designated. This also reduces the number of dateCollected-related mappings needed for any dateCollected-related field, such as year/month/dayCollected.
mappings/Veg+-VegCore.csv: Removed dateIdentified/_alt and dateIdentified redirection mappings, which were only needed when multiple dateIdentified fields were being combined in Veg+-VegCore.csv
mappings/: Moved year/month/dayIdentified mappings from Veg+-VegCore.csv to VegCore-VegBIEN.csv so that Veg+-VegCore.csv contains only renamings, not business logic. Note that this allows the year/month/dayIdentified values to bypass the additional _dateRangeStart filter that is applied to text dates. The priority of the plain dateIdentified field is now higher than the year/month/dayIdentified fields when both are specified, because the dateIdentified field presumably contains verbatim text while the year/month/dayIdentified fields contain parsed date parts.
mappings/: Moved verbatimGrowthForm filter mapping from Veg+-VegCore.csv to VegCore-VegBIEN.csv so that Veg+-VegCore.csv contains only renamings, not business logic
inputs/UNCC/Specimen/map.csv, inputs/NCU-NCSC/Specimen/map.csv: Remapped cultivated fields directly via new cultivated term, rather than via establishmentMeans
sql_io.py: mk_errors_table(): Don't cache the sql.table_exists() query, because the table will be created and its existence must be rechecked
sql.py: table_exists(): Allow caller to set whether query will be cached. This is useful if the table will later be created and its existence should be checked again.
sql.py: tables(): Allow caller to set whether query will be cached
mappings/VegCore-VegBIEN.csv: Mapped cultivated
inputs/TEAM/: Added _src/README.TXT with Brad's comments on which files to use
mappings/Veg+.terms.csv: Added cultivated
input.Makefile: Staging tables installation: `%/install: %/create.sql`: Removed manual VACUUM run because this is done as part of $(exportHeader), which calls $(cleanup)
input.Makefile: Staging tables installation: $(cleanup): Append output to log
schemas/py_functions.sql: Added pass-through _date(timestamp) for datasource date columns that are already timestamps
input.Makefile: Staging tables installation: `%/install: %/create.sql`: Fixed bug where embedded \ in ADD COLUMN statement was not removed by the shell, because single quotes do not remove embedded \s
inputs/VegBank/vegbank.~.clean_up.sql: Also rename taxonobservation.reference_id to taxonobservation_reference_id
input.Makefile: Staging tables installation: $(logInstall*Add): Fixed bug where needed to only add -a flag for tee when tee was actually being used (in verbose mode), not when &> is used instead
inputs/VegBank/taxonobservation_/header.csv: Updated for new renames in vegbank.~.clean_up.sql
input.Makefile: Staging tables installation: `%/install: %/create.sql`: Also log the output of commands run after create.sql
input.Makefile: Staging tables installation: Factored $(call logInstall,$*/) out into $(logInstall*)
schemas/py_functions.sql: Added pass-through _dateRangeStart(timestamp), _dateRangeEnd(timestamp) for datasource date columns that are already timestamps
inputs/VegBank/plantconcept_/header.csv: Updated for new renames in vegbank.~.clean_up.sql
inputs/VegBank/plantconcept_/create.sql: Use new plantconcept_plantnames()
inputs/VegBank/vegbank.~.utils.sql: plantconcept_plantnames(): Use SQL SELECT query and WITH clause (http://www.postgresql.org/docs/8.4/static/queries-with.html) instead of temp table, because PostgreSQL does not support using temp tables inside functions that are called repeatedly (http://archives.postgresql.org/pgsql-general/2006-02/msg00516.php; it results in an "out of shared memory" error)
inputs/VegBank/vegbank.~.utils.sql: Removed hardcoded schema name, which is set dynamically by input.Makefile using `SET search_path`
inputs/VegBank/vegbank.~.utils.sql: Added plantconcept_plantnames()
inputs/VegBank/vegbank.~.utils.sql: plantconcept_ancestors(): Made function STABLE instead of IMMUTABLE because it accesses DB tables
inputs/VegBank/vegbank.~.clean_up.sql: Fixed bug where the original plantconcept table's columns needed to be renamed, rather than the derived table plantconcept_'s. Note that this script runs before any derived tables are created, so this would be the wrong place for these statements if the derived table's columns did need to be renamed.
input.Makefile: Staging tables installation: $(dbExports): Sort each group of .sql files in lexical order, since $(wildcard) apparently does not sort them that way automatically on vegbiendev
inputs/import.stats.xls: Updated with stats from latest import. Corrected input row count of CTFS.TaxonOccurrence, which had been set to the inserted row count (which is right above it in the log file).
schemas/vegbien.sql: taxonrank: Added comment documenting source of values
inputs/VegBank/taxonobservation_/map.csv: Mapped observation_id to eventID
inputs/TEAM/: Added VL
inputs/VegBank/: Added taxonobservation_/
inputs/VegBank/: Added plantconcept_/
input.Makefile: Staging tables installation: `%/install: %/create.sql`: Ignore errors if create.sql already added a primary key
input.Makefile: Staging tables installation: `%/install: %/create.sql`: Provide the table name as a var (:table) to the query
inputs/VegBank/vegbank.~.clean_up.sql: Prevent "column name specified more than once" errors when tables are joined
to_do/timeline.doc: Updated to reflect additional time that validations will take, and analytical DB's dependency on it
Added validation/
input.Makefile: Staging tables installation: `%/install: %/create.sql`: Time the install
inputs/VegBank/vegbank.~.utils.sql: plantconcept_ancestors(): Renamed ancestor_id output param to plantconcept_id for clarity and so it can be directly USING-joined with plantconcept on plantconcept_id
inputs/VegBank/: Added vegbank.~.utils.sql (which runs after vegbank.sql), for use by tables' create.sql scripts
inputs/import.stats.xls: Updated with stats from latest import
inputs/VegBank/: Added observation_/
inputs/VegBank/: Added vegbank.~.clean_up.sql (which runs after vegbank.sql), to prevent "cannot alter type of a column used by a view or rule" errors
inputs/VegBank/: Added plot_/
inputs/VegBank/: Added logs
input.Makefile: Staging tables installation: `%/install: %/create.sql`: Log the output to the install log, just like for other %/install targets
vegbien_dest: schemas: Added public explicitly, even though it's already in the default search_path, in order to shadow any datasource's tables of the same name as a VegBIEN table (such as in VegBank). (VegBIEN tables are referenced without a schema, while datasource tables are referenced with a schema, so collisions are not a problem after this fix.)
input.Makefile: Staging tables installation: sql/install: Fixed bug where needed space before \ at end of line, because one is not automatically added in a recipe command (although it's added elsewhere)
sql.py: run_query(): DuplicateException: Also match "of relation" part of error message, so that parsed column name does not contain "of relation"
subtract: Made it case- and punctuation-insensitive
mappings/: Removed no longer needed Veg+.cs-VegBIEN.csv, which is now the same as Veg+-VegBIEN.csv which was derived from it
join: Documented that it's case- and punctuation-insensitive.
bin/map: map_table(): Refactored to map simplified to original column names first and then determine column index for each original name, in order to avoid trying to recover the original name from a simplified name where multiple original names might collide onto the same simplified name. Documented that it's case- and punctuation-insensitive.
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.
bin/map: map_table(): Resolve all mappings and prefixes after applying maps.simplify()
inputs/SpeciesLink/Specimen/map.csv: _alt all scientificNameAuthorship synonyms together in one _alt
schemas/functions.sql: _alt(): Added extra numbered parameters. Eventually these will need to be converted to variadic args, but this will require special support from column-based import.
join: Use new maps.simplify()
maps.py: Added simplify()
join: Match terms with non-alphanumeric chars removed
