my2pg: Remove any (#) after bytea
my2pg: Translate binary to bytea
README.TXT: Datasource setup: MySQL inputs: Editing _MySQL/*.make: Set $server to vegbiendev instead so the export command will work from any machine (though it will be faster from vegbiendev itself)
inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where needs to be set to just localhost and --user to bien instead
README.TXT: Datasource setup: MySQL inputs: Editing _MySQL/*.make: Fixed bug where $server needs to be set to just localhost and --user to bien instead.
lib/MySQL.*.sql.make: Added --user option to demonstrate how to set the DB user vs. the ssh user
inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where $server needs to be set to bien@localhost
README.TXT: Datasource setup: MySQL inputs: Editing _MySQL/*.make: Specified that $server needs to be set to bien@localhost. Install the staging tables: Specified that for a MySQL .sql export, this must be done on vegbiendev.
inputs/BRIT/: Added _MySQL/MySQL.*.sql.make
README.TXT: Datasource setup: MySQL inputs: .sql exports: Run mysql_bien in the background
README.TXT: Datasource setup: MySQL inputs: .sql exports: Added steps to sync the export to vegbiendev. Specified that the database for the MySQL export should be created on vegbiendev.
README.TXT: Datasource setup: Update vegbiendev: Updated steps for syncing via jupiter
Added inputs/BRIT/ (not yet translated to PostgreSQL)
mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_DMS to coordinates.latitude_deg using new _dms_to_dd(text)
schemas/functions.sql: Added _dms_to_dd(text)
schemas/functions.sql: _dms_to_dd(): Fixed bug where need to use 1 as the multiplier when dir is NULL
schemas/functions.sql: _dms_to_dd(): Fixed bug where need to apply the sign multiplier after the components are added, because it applies to the DMS as a whole rather than just to the degree component
README.TXT: Full database import: Before running `make inputs/upload`, added step to do ./fix_perms on local machine so that files are not uploaded to jupiter with incorrect permissions
README.TXT: Full database import: Before running `make inputs/upload`, added step to do svn up on jupiter so that unversioned files are not uploaded before their versioned equivalents are checked out from svn (requiring each file to be manually svn-added before the svn up can proceed)
schemas/functions.sql: _dms_to_dd(): Added dir param to specify compass dir suffix, in order to calculate the sign correctly
Moved compass_dir from schemas/vegbien.sql to schemas/functions.sql so it can be used by _dms_to_dd()
Moved _dms_to_dd() from schemas/vegbien.sql to schemas/functions.sql so it can use functions schema functions
schemas/vegbien.sql: Added compass_dir enum
inputs/TEX/Specimen/map.csv: Remapped LAT/LONG_DEGREES,MINUTES,SECONDS to new latitude/longitude_deg,min,sec, allowing the DMS coordinates to be translated
inputs/REMIB/Specimen/map.csv: Remapped lat/long_deg,min,sec to new latitude/longitude_deg,min,sec, allowing the DMS coordinates to be translated
mappings/VegCore-VegBIEN.csv: latitude/longitude_deg,min,sec: Also mapped to the geoscrub coordinates entry
mappings/VegCore-VegBIEN.csv: latitude/longitude_sec: Fixed name, which had been incorrectly automapped to verbatim*
mappings/VegCore.htm: Regenerated from wiki. latitude/longitude: Moved _deg,min,sec components after unit alternatives so that unit alternatives following them wouldn't incorrectly be interpreted as alternatives for the *components instead of for the overall, unitless term.
mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_deg,min,sec
mappings/VegCore.htm: Regenerated from wiki. Merged coordinateUncertainty and coordinatePrecision, since datasources often use these interchangeably (the only difference is the DwC-recommended units).
mappings/VegCore.htm: Regenerated from wiki. Source: Added authors. Renamed creator to firstPublisher. Moved dataOwner to Source as list. Coordinates: latitude/longitude, coordinatePrecision: Added units disambiguation. latitude/longitude_DMS: Added components. Global IDs: Changed "globally unique" tag to "global ID" and hyperlinked it to <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs> (which now includes detailed examples of the various types of global IDs).
inputs/SpeciesLink/Specimen/map.csv: conceptual_darwin_2003_1_0_CoordinatePrecision: Remapped to coordinateUncertaintyInMeters, assuming units based on the range and precision of values
inputs/HVAA/Specimen/map.csv: Remapped coordinatePrecision to UNUSED
inputs/ARIZ/omoccurrences/map.csv: Remapped coordinatePrecision to UNUSED
schemas/vegbien.sql: Added _dms_to_dd()
inputs/bien2_traits/TraitObservation/map.csv: Remapped Source to sourceType
Added inputs/TEX/
units.py: convert(): Support ranges
Moved parse_range() from xml_func.py to units.py
units.py: conversions: Added ft->m conversion
src_map: Reopen stdin (/dev/stdin) in universal newlines mode to support files with \r as the line ending
csv2db: Open input stream in universal newlines mode to support files with \r as the line ending
mappings/VegCore.htm: Regenerated from wiki. Moved Forming IDs section to separate Global IDs wiki page (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs).
input.Makefile: $(exts): Added .tab
mappings/VegCore.htm: Regenerated from wiki. Moved preferred ID order to Forming IDs section as examples list. Made examples globally unique by prefixing the outer ID that scopes the value.
mappings/VegCore.htm: Regenerated from wiki. Forming IDs: Added instructions for making a local ID global. Added note that these globally unique IDs are not the same as UUIDs. Forming preferred IDs: Reworded as a set of instructions rather than a definition. Clarified that this becomes the database primary key.
mappings/VegCore.htm: Regenerated from wiki. Added section on forming preferred IDs, which are the ID which is most directly associated with the identified object.
mappings/VegCore.htm: Regenerated from wiki. Documentation has been added on how to choose term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming) and how to form globally unique ID values (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Forming-IDs). Source and Specimen terms have been renamed to be self-explanatory and unambiguous (the DwC equivalents remain as synonyms). Short definitions of Source terms have been added to explain the differences between them. Source, Specimen, and Collection terms have been shortened according to the new instructions for choosing preferred term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming).
inputs/NY/Ecatalog_all/test.xml.ref: Updated inserted row count
schemas/vegbien.sql: analytical_stem_view: scientificName_verbatim: Use the taxonname (which omits the family and author) instead when available, at Brad's request
schemas/vegbien.sql: Disambiguated taxonlabel.taxonomicname, taxonverbatim.taxonomicname, and taxonverbatim.taxonname
schemas/vegbien.sql: taxon_trait_view: Use taxonverbatim.taxonname (the binomial) in preference to taxonverbatim.taxonomicname (the binomial+author) or taxonlabel.taxonomicname (the family+binomial+author), at Mark's request
to_do/timeline.2013.xls: Obtain and load any additional new data: Extended beyond April because it's ongoing
README.TXT: Full database import: On nimoy: Moved analytical_aggregate table creation right after analytical_aggregate..csv download because it can happen while the file is downloaded
to_do/timeline.2013.xls: Reload existing data in need of refresh: Added additional cell because this is still in progress
to_do/timeline.2013.xls: Placed check mark in completed cells. Multi-cell tasks that are partially complete have check marks in part of their cells to indicate this.
Added inputs/FIA/REF_*/
inputs/FIA/_src/Makefile: Table bundling: Also unpack FIADB_REFERENCE/
Added inputs/FIA/_src/FIADB_REFERENCE.ZIP.md5, .url
schemas/vegbien.sql: provider_count_view: Group data by dataprovider and dataset, rather than by each separately, to satisfy the GBIF attribution requirements as described by Brad
schemas/vegbien.sql: analytical_plot/specimen: Moved threatened_bien after growthForm as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#SpeciesLink>
schemas/vegbien.sql: analytical_stem_view: Moved threatened_bien after growthForm as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#SpeciesLink>
schemas/vegbien.sql: sync_analytical_stem_to_view(): Also drop and re-create new dependent views analytical_plot, analytical_specimen
inputs/TEAM/V*/map.csv: Mapped plotArea_ha based on "1ha Plot Number" field name
inputs/TEAM/V*/map.csv: Id: Remapped to individualObservationID
mappings/VegCore.htm: Regenerated from wiki. verbatimScientificName, verbatimTaxonName have been merged into concatenatedScientificName, and ID has been disambiguated.
inputs/*/*/map.csv: Automapped taxonConfidence
schemas/vegbien.sql: analytical_stem_view: plotArea_ha: Fixed bug where need to use parent plot's area when subplot's area is not provided
inputs/SALVIAS/plotMetadata_/create.sql: Added primary key
inputs/NY/NY_DATA_20130212.~.utils.sql: pkey: Made table an enum instead of a text field so that Ecatalog_LatLong could be sorted before Ecatalog
inputs/NY/Ecatalog_all/create.sql: primary key: Combine table, key into one value so that the primary key has a single column. This is necessary because multi-column primary keys are not supported by the import algorithm.
inputs/NY/NY_DATA_20130212.~.utils.sql: Added pkey record type for use by Ecatalog_all's generated pkey
inputs/NY/Ecatalog_all/create.sql: Add table column which scopes the key field. Add primary key to allow sorting by it. inputs/NY/Ecatalog_all/map.csv: Documented that UniqueNYInternalRecordNumber is sometimes duplicated.
make_analytical_db: Wait for tnrs.make to acquire the tnrs.make lock if being run right after import
schemas/vegbien.sql: analytical_stem_view: taxonName_matched: Fixed bug where need to use the matched_taxonverbatim instead of the datasource_taxonverbatim
Moved wait on tnrs.make lock from import_all to make_analytical_db, so that running make_analytical_db for a one-time import also waits on the lock
schemas/vegbien.sql: taxondetermination: taxondetermination_unique: Added determinationtype so that when the matched and accepted determinations are the same, they still both get created rather than the second one being removed due to the unique constraint
schemas/vegbien.sql: analytical_specimen: Removed speciesBinomialWithMorphospecies because it doesn't apply to specimens
schemas/vegbien.sql: Added analytical_plot view
schemas/vegbien.sql: Added analytical_specimen view
schemas/vegbien.sql: analytical_stem_view: Moved recordedBy, recordNumber before dateCollected as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#ACAD>
schemas/vegbien.ERD.mwb: Synced with schema
schemas/vegbien.sql: Added reproductiveCondition
mappings/VegCore-VegBIEN.csv: Mapped reproductiveCondition
schemas/vegbien.sql: plantobservation: Added reproductivecondition
mappings/VegCore.htm: Regenerated from wiki. matched*Fit_fraction has been renamed to matched*Confidence_fraction.
inputs/.TNRS/public.unscrubbed_taxondetermination_view/map.csv: Updated for new mappings/VegCore.htm
inputs/bien_web/observation/map.csv: Re-automapped taxonMorphospecies
mappings/VegCore.htm: Regenerated from wiki. Data owner terms and taxon synonyms have been added, and morphospecies has been disambiguated.
schemas/vegbien.sql: analytical_stem_view: Moved identifiedBy, dateIdentified, identificationRemarks right after the *_verbatim terms that they relate to, as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#ACAD>
schemas/vegbien.sql: analytical_stem_view: Use new concat_delim() instead of array_to_string() surrounded by NULLIF
schemas/vegbien.sql: Added concat_delim()
schemas/vegbien.sql: analytical_stem_view: Removed deprecated taxonNameWithMorphospecies now that we have speciesBinomialWithMorphospecies
schemas/vegbien.sql: analytical_stem_view: speciesBinomial: Added morphospecies suffix to create speciesBinomialWithMorphospecies
inputs/import.stats.xls: Updated import times
README.TXT: Full database import: Check that unscrubbed_taxondetermination_view returns no rows: Documented that this takes 90 s with LIMIT 1
schemas/vegbien.sql: _taxon_family_require_std(): Also allow non-aceae families accepted by TNRS
Added inputs/SALVIAS/_archive/salvias_plots.*.sql.zip.md5
Added inputs/VegBank/_archive/vegbank_for_bien.tar.gz.url
