schemas/py_functions.sql: Changed function languages to plpython3u to match the new installed version. Note that plpythonu is not available on Mac under PostgreSQL 9.1.6.
reinstall_all: Fixed bug where also need to include datasources starting with . such as .TNRS/, by using with_all's new $all option
with_all: Added $all option to also include datasources starting with . such as .TNRS/. This is necessary for reinstall_all, which needs to install all datasources.
root Makefile: PostgreSQL: $(pg_ctl-*): Fixed bug where need to pause for a few seconds after restarting PostgreSQL, to wait for the server to be ready to accept connections
root Makefile: Installation: uninstall: Removed inputs/uninstall because the DB will be uninstalled anyway, so the inputs don't need to be individually removed first
schemas/postgresql.Mac.conf: Added back unix_socket_directory setting, which is apparently still needed in PostgreSQL 9.1.6
root Makefile: PostgreSQL: postgres-Linux: Also install postgresql.conf
root Makefile: PostgreSQL: postgres-Darwin: Also install postgresql.Mac.conf
root Makefile: PostgreSQL: $(macUsePostgresLib): Factored out PostgreSQL dir to $(macPostgresDir)
schemas/postgresql.Mac.conf: Updated to PostgreSQL 9.1.6's postgresql.conf
root Makefile: Datasources: inputs/install: Fixed bug where need to `wait` after `. bin/reinstall_all` to wait for inputs to finish installing before installing the public schema. This is necessary because views in the public schema now have dependencies on some datasources, such as TNRS.
root Makefile: PostgreSQL: $(psqlAsAdmin): Use new $(asAdmin)
root Makefile: VegBIEN DB: Schemas: schemas/public/install: Use $(psqlNoSearchPath) instead of $(psqlAsBien) because the search_path is set by vegbien.sql
root Makefile: Datasources: Added inputs/install override which runs `. bin/reinstall_all` instead, in order to install all datasources simultaneously
root Makefile: Python: python-Darwin: Added instructions to install Python 3.2 (Python 2 comes with Mac OS X, but Python 3.2 is needed for plpython3u)
root Makefile: VegBIEN DB: DB and bien user: mk_db: Updated for PostgreSQL 9.1.6 on the Mac, which only provides plpython3u (Python 3)
root Makefile: VegBIEN DB: DB and bien user: mk_db: Updated for PostgreSQL 9.1.6, which requires the DB name to be specified on the command line instead of in the $PGDATABASE env var set by postgres_vegbien. Fixed bug where need to run createlang as postgres superuser, because plpythonu is an untrusted language (with unrestricted access to the entire DB).
root Makefile: PostgreSQL: postgres-Darwin: Updated for PostgreSQL 9.1.6, which requires some /usr/lib/ symlinks to be changed to newer versions installed in the PostgreSQL lib/ dir
input.Makefile: $(psqlAsBien), csv2db: Turn off the automatic search_path where needed, because when the input is installed, the schemas in it may not exist yet
schemas/vegbien.sql: place: Renamed geosource_valid to geovalid. (It had gotten renamed in the reference -> source rename.)
schemas/vegbien.sql: location: Renamed confidentialitystatus->accesslevel, confidentialityreason->accessconditions to match the corresponding fields in source. Note that accessconditions stores more than confidentialityreason did, because it can contain details about the accesslevel in addition to the reason for it.
schemas/vegbien.sql: source.accesslevel, location.confidentialitystatus: Changed type to accesslevel
schemas/vegbien.sql: Added accesslevel enum
inputs/import.stats.xls: Updated import times
Regenerated vegbien.ERD exports
schemas/vegbien.sql: Renamed reference -> source to make this table more broadly applicable, and because this now stores the datasource metadata
schemas/vegbien.sql: referencename: Scope it by top-level datasource, because institutionCodes (which map to this field) are not globally unique. This involves renaming the previous reference_id field, which was for the matched reference, to matched_reference_id, to allow a scoping reference_id field.
mappings/VegCore-VegBIEN.csv: Made taxonoccurrence.verbatimcollectorname an fkey to party, and renamed it to collector_id
inputs/VegBank/taxonobservation_/map.csv: Mapped new givenname, surname (from collector_id's party) to recordedBy
inputs/VegBank/taxonobservation_/create.sql: Also join to collector_id's party to include collector name
inputs/VegBank/vegbank.~.clean_up.sql: Rename taxoninterpretation.party_id to taxoninterpretation_party_id to make it globally unique when joining taxoninterpretation to other tables
inputs/VegBank/vegbank.~.clean_up.sql: Rename party.d_obscount to party_d_obscount to make it globally unique when joining with other tables
input.Makefile: Existing maps discovery: $(allTables): Fixed bug where need to remove extra whitespace before $(tables) when there are no $(joinedTables)
lib/mappings.Makefile: Checking if $(termsSubdirs) defined: Fixed bug where can't use ifndef because that checks if the variable is empty, not undefined. Need to use `ifeq ($(origin var),undefined)` instead.
inputs/TEAM/V*/map.csv: Omit *Method, because it just contains "Derived" for a small fraction of the rows
inputs/SALVIAS/: Updated to new salvias_plots export on nimoy, which has a different schema
inputs/SALVIAS/salvias_plots.~.clean_up.sql: Moved Ensure globally unique column names to end to match VegBank order
my2pg: *int types: Added mediumint
Placed inputs/SALVIAS/_archive/ under version control
inputs/SALVIAS/salvias_plots.~.clean_up.sql: Remove private data that should not be publicly visible, indicated by plotMetadata.AccessCode = 1
inputs/SALVIAS/salvias_plots.~.clean_up.sql: Enable cascading deletes by adding the necessary fkeys
Added inputs/SALVIAS/_src/salvias_data_access_controls.txt
inputs/.geoscrub/import_order.txt: Fixed bug where geoscrub_cultivated needs to be installed after geoscrub_cleaned_unique, not before as it would be with the default alphabetical sort order
inputs/.geoscrub/geoscrub_cultivated/: Use _no_import file to exclude geoscrub_cultivated from the import, because it's used directly as a lookup table by analytical_stem rather than being imported. This ensures that there is no import log or input row count for geoscrub_cultivated in the import times, which would skew the import row count because the row count would be included even though no columns are mapped.
input.Makefile: $(tables): Fixed bug where need to use $(importTables) instead of $(tables) in all places that should use only imported tables, rather than just in the import process itself
input.Makefile: Import to VegBIEN: Added support for tables which should be installed but not imported, but which must be installed after tables which are imported rather than before. This currently applies to geoscrub.geoscrub_cultivated, which depends on geoscrub_cleaned_unique (and therefore must be installed after it), but which should not be imported because it's used directly as a lookup table by analytical_stem.
inputs/VegBank/vegbank.~.clean_up.sql: Documented that plots with confidentialitystatus >= 4 are not deleted if their embargos have already expired. This applies to the Shenandoah NP data, which has confidentialitystatus = 5 but is no longer embargoed according to the embargo table
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.
schemas/vegbien.sql: referencetype: Added terms from reference.referencetype closed list in VegBank data dictionary. Cited sources in comment.
schemas/vegbien.sql: reference.referencetype: Changed type to referencetype enum
schemas/vegbien.sql: Added referencetype enum, containing VegBank's values in reference.referencetype as well as values for bien_web.datasource.aggregatorOrPrimary and bien_web.dataSourceNormalized.isHerbarium,isAggregator
specimenreplicate: Made institution_id an fkey to referencename instead of party, to later be matched up with reference entries for each aggregator's subprovider
schemas/vegbien.sql: referencename: Added referencename_unique unique index on name
schemas/vegbien.sql: referencename: Made reference_id optional so it can be populated later when referencenames are scrubbed
schemas/vegbien.sql: referencename: Renamed identifier to name because it is specifically any name for the reference, not necessarily an ID
schemas/vegbien.sql: Renamed referencealtident to referencename to allow any verbatim reference name to go here, with reference containing the corresponding accepted reference name
schemas/vegbien.sql: reference: Added accesslevel, accessconditions from bien_web.datasource
schemas/vegbien.sql: address: Added street2 from bien_web.party.address2
schemas/vegbien.sql: address: Renamed fields to bien_web.party names
schemas/vegbien.sql: party: Added department from bien_web.party
inputs/SALVIAS/plotMetadata_/map.csv: Mapped lookup_MethodCode_Description to new observationMeasure
schemas/vegbien.sql: method: Made name optional when description or observationmeasure is specified
schemas/vegbien.sql: method: method_unique: Include observationmeasure since the method name sometimes is not globally unique (e.g. in SALVIAS)
mappings/VegCore-VegBIEN.csv: Mapped observationMeasure
mappings/VegCore.csv: observationMeasure: Added source to DwC samplingProtocol
mappings/VegCore.csv: Added observationMeasure
schemas/vegbien.ERD.mwb: Added family_higher_plant_group
schemas/vegbien.sql: Removed VegBank-internal fields starting with d_
schemas/vegbien.ERD.mwb: Moved tables so commclass would have more room. Moved revision back to original spot.
schemas/filter_ERD.csv: Display referencecontributor->party connection in ERD
schemas/vegbien.sql: Removed no longer used table referenceparty
schemas/vegbien.sql: referencecontributor: Point to party instead of referenceparty, which duplicates party
schemas/vegbien.sql: party: Added new suffix field to party_unique unique index
schemas/vegbien.sql: party: Added fields from referenceparty. Note that referenceparty.type is named partytype.
inputs/SALVIAS/salvias_plots.~.clean_up.sql: Rename lookup_MethodCode.Description to lookup_MethodCode_Description to make it globally unique when joined with plotMetadata
input.Makefile: SVN: $(svnFilesGlob): Added root-level .sql files containing ~, which run additional commands after the original data is imported
inputs/SALVIAS/_MySQL/: Updated svn:ignore from running `make inputs/SALVIAS/add`
mappings/VegCore-VegBIEN.csv: matched place's coordinates: Fixed bug where coordinates entry itself needed to have its datasource (reference) set to geoscrub, in addition to the place entry that uses it, in order to match up properly with geoscrub's corresponding input place (whose coordinates as well as place are owned by the geoscrub datasource)
mappings/VegCore-VegBIEN.csv: matched place's coordinates: Fixed bug where coordinates mappings with and without matched_place_id=0 need to sort together in order to be merged, by prepending ".," to the place attrs list
inputs/VegBank/plot_/test.xml.ref: Updated inserted row count
inputs/Makefile: Input data: $(rsyncLogs): Also include logs from the datasource's top-level logs/ dir, which contains make_analytical_db.log.sql
inputs/VegBank/vegbank.~.clean_up.sql: Remove still-embargoed plots
inputs/VegBank/vegbank.~.clean_up.sql: Enable cascading deletes by setting all foreign keys to ON DELETE CASCADE
Added inputs/VegBank/_src/vegbank.schema.sql.make and vegbank.schema.sql
input.Makefile: Staging tables installation: sql/install: Use new pg_dump_limit to remove security and schema-setting commands
Added pg_dump_limit to filter a PostgreSQL DB dump to remove security and schema-setting commands
inputs/.geoscrub/geoscrub_cleaned_unique/create.sql: Removed no longer needed index on latitudeDecimalVerbatim, longitudeDecimalVerbatim, which is now on geoscrub_cultivated instead
schemas/vegbien.sql: analytical_stem_view: Fixed bug where needed to join on new geoscrub_cultivated, not geoscrub, for all geoscrub-related information. geoscrub contains many duplicate records, causing one input row to match many rows in geoscrub, when there should only be one entry for each coordinate pair.
Added inputs/.geoscrub/geoscrub_cultivated/
inputs/.geoscrub/geoscrub_cleaned_unique/create.sql: Added index on latitudeDecimalVerbatim, longitudeDecimalVerbatim for use by analytical_stem_view
inputs/newWorld/geoscrub.schema.~.changes.sql: Change countryNameStd type to text to allow merge-joining with place.country in analytical_stem_view
inputs/newWorld/geoscrub.schema.~.changes.sql: ALTER TABLE ... ALTER COLUMN statement: Reformatted to allow adding additional ALTER COLUMN clauses
inputs/.geoscrub/geoscrub_cleaned_unique/create.sql: Change latitudeDecimalVerbatim, longitudeDecimalVerbatim types to double precision to allow merge-joining with coordinates.latitude_deg, longitude_deg in analytical_stem_view
README.TXT: Data import: Instead of using `make schemas/rotate` and then renaming the public schema to the correct name, just rename directly to the correct name using `make schemas/rename/...`. Use new import_name to determine the import name instead of manually finding the date in the first datasource's log file name.
