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# Date Author Comment
7668 02/26/2013 10:39 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: latitude/longitude_deg,min,sec: Also mapped to the geoscrub coordinates entry

7667 02/26/2013 10:34 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: latitude/longitude_sec: Fixed name, which had been incorrectly automapped to verbatim*

7666 02/26/2013 10:31 AM Aaron Marcuse-Kubitza

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.

7665 02/26/2013 10:22 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_deg,min,sec

7664 02/26/2013 10:15 AM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Merged coordinateUncertainty and coordinatePrecision, since datasources often use these interchangeably (the only difference is the DwC-recommended units).

7663 02/26/2013 10:08 AM Aaron Marcuse-Kubitza

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).

7662 02/26/2013 09:58 AM Aaron Marcuse-Kubitza

inputs/SpeciesLink/Specimen/map.csv: conceptual_darwin_2003_1_0_CoordinatePrecision: Remapped to coordinateUncertaintyInMeters, assuming units based on the range and precision of values

7661 02/26/2013 09:53 AM Aaron Marcuse-Kubitza

inputs/HVAA/Specimen/map.csv: Remapped coordinatePrecision to UNUSED

7660 02/26/2013 09:50 AM Aaron Marcuse-Kubitza

inputs/ARIZ/omoccurrences/map.csv: Remapped coordinatePrecision to UNUSED

7659 02/26/2013 09:05 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added _dms_to_dd()

7658 02/26/2013 08:49 AM Aaron Marcuse-Kubitza

inputs/bien2_traits/TraitObservation/map.csv: Remapped Source to sourceType

7657 02/26/2013 08:43 AM Aaron Marcuse-Kubitza

Added inputs/TEX/

7656 02/26/2013 08:42 AM Aaron Marcuse-Kubitza

units.py: convert(): Support ranges

7655 02/26/2013 08:35 AM Aaron Marcuse-Kubitza

Moved parse_range() from xml_func.py to units.py

7654 02/26/2013 08:02 AM Aaron Marcuse-Kubitza

units.py: conversions: Added ft->m conversion

7653 02/26/2013 07:12 AM Aaron Marcuse-Kubitza

src_map: Reopen stdin (/dev/stdin) in universal newlines mode to support files with \r as the line ending

7652 02/26/2013 06:51 AM Aaron Marcuse-Kubitza

csv2db: Open input stream in universal newlines mode to support files with \r as the line ending

7651 02/22/2013 11:15 PM Aaron Marcuse-Kubitza

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).

7650 02/22/2013 11:09 PM Aaron Marcuse-Kubitza

input.Makefile: $(exts): Added .tab

7649 02/22/2013 10:29 PM Aaron Marcuse-Kubitza

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.

7648 02/22/2013 09:29 PM Aaron Marcuse-Kubitza

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.

7647 02/22/2013 08:47 PM Aaron Marcuse-Kubitza

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.

7646 02/22/2013 08:17 PM Aaron Marcuse-Kubitza

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).

7645 02/22/2013 08:00 PM Aaron Marcuse-Kubitza

inputs/NY/Ecatalog_all/test.xml.ref: Updated inserted row count

7644 02/21/2013 05:13 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: scientificName_verbatim: Use the taxonname (which omits the family and author) instead when available, at Brad's request

7643 02/21/2013 04:02 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Disambiguated taxonlabel.taxonomicname, taxonverbatim.taxonomicname, and taxonverbatim.taxonname

7642 02/21/2013 03:14 PM Aaron Marcuse-Kubitza

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

7641 02/21/2013 02:05 PM Aaron Marcuse-Kubitza

to_do/timeline.2013.xls: Obtain and load any additional new data: Extended beyond April because it's ongoing

7640 02/21/2013 02:02 PM Aaron Marcuse-Kubitza

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

7639 02/21/2013 11:13 AM Aaron Marcuse-Kubitza

to_do/timeline.2013.xls: Reload existing data in need of refresh: Added additional cell because this is still in progress

7638 02/21/2013 11:11 AM Aaron Marcuse-Kubitza

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.

7637 02/20/2013 05:35 PM Aaron Marcuse-Kubitza

Added inputs/FIA/REF_*/

7636 02/20/2013 05:33 PM Aaron Marcuse-Kubitza

inputs/FIA/_src/Makefile: Table bundling: Also unpack FIADB_REFERENCE/

7635 02/20/2013 05:13 PM Aaron Marcuse-Kubitza

Added inputs/FIA/_src/FIADB_REFERENCE.ZIP.md5, .url

7634 02/20/2013 04:11 PM Aaron Marcuse-Kubitza

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

7633 02/20/2013 02:00 PM Aaron Marcuse-Kubitza

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>

7632 02/20/2013 01:54 PM Aaron Marcuse-Kubitza

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>

7631 02/20/2013 01:53 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: sync_analytical_stem_to_view(): Also drop and re-create new dependent views analytical_plot, analytical_specimen

7630 02/20/2013 01:20 PM Aaron Marcuse-Kubitza

inputs/TEAM/V*/map.csv: Mapped plotArea_ha based on "1ha Plot Number" field name

7629 02/20/2013 01:12 PM Aaron Marcuse-Kubitza

inputs/TEAM/V*/map.csv: Id: Remapped to individualObservationID

7628 02/20/2013 01:10 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. verbatimScientificName, verbatimTaxonName have been merged into concatenatedScientificName, and ID has been disambiguated.

7627 02/20/2013 01:09 PM Aaron Marcuse-Kubitza

inputs/*/*/map.csv: Automapped taxonConfidence

7626 02/20/2013 12:28 PM Aaron Marcuse-Kubitza

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

7625 02/20/2013 12:18 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/plotMetadata_/create.sql: Added primary key

7624 02/20/2013 11:42 AM Aaron Marcuse-Kubitza

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

7623 02/20/2013 11:32 AM Aaron Marcuse-Kubitza

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.

7622 02/20/2013 11:28 AM Aaron Marcuse-Kubitza

inputs/NY/NY_DATA_20130212.~.utils.sql: Added pkey record type for use by Ecatalog_all's generated pkey

7621 02/20/2013 10:47 AM Aaron Marcuse-Kubitza

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.

7620 02/20/2013 09:20 AM Aaron Marcuse-Kubitza

make_analytical_db: Wait for tnrs.make to acquire the tnrs.make lock if being run right after import

7619 02/20/2013 09:13 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: taxonName_matched: Fixed bug where need to use the matched_taxonverbatim instead of the datasource_taxonverbatim

7618 02/20/2013 08:58 AM Aaron Marcuse-Kubitza

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

7617 02/20/2013 08:56 AM Aaron Marcuse-Kubitza

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

7616 02/20/2013 07:59 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_specimen: Removed speciesBinomialWithMorphospecies because it doesn't apply to specimens

7615 02/20/2013 07:58 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added analytical_plot view

7614 02/20/2013 07:55 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added analytical_specimen view

7613 02/20/2013 07:44 AM Aaron Marcuse-Kubitza

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>

7612 02/20/2013 07:40 AM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: Synced with schema

7611 02/20/2013 07:38 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added reproductiveCondition

7610 02/20/2013 07:33 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped reproductiveCondition

7609 02/20/2013 07:28 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: plantobservation: Added reproductivecondition

7608 02/20/2013 05:33 AM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. matched*Fit_fraction has been renamed to matched*Confidence_fraction.

7607 02/20/2013 05:32 AM Aaron Marcuse-Kubitza

inputs/.TNRS/public.unscrubbed_taxondetermination_view/map.csv: Updated for new mappings/VegCore.htm

7606 02/20/2013 05:10 AM Aaron Marcuse-Kubitza

inputs/bien_web/observation/map.csv: Re-automapped taxonMorphospecies

7605 02/20/2013 05:08 AM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Data owner terms and taxon synonyms have been added, and morphospecies has been disambiguated.

7604 02/20/2013 04:51 AM Aaron Marcuse-Kubitza

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>

7603 02/20/2013 02:25 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: Use new concat_delim() instead of array_to_string() surrounded by NULLIF

7602 02/20/2013 02:19 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added concat_delim()

7601 02/20/2013 01:43 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: Removed deprecated taxonNameWithMorphospecies now that we have speciesBinomialWithMorphospecies

7600 02/20/2013 01:17 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: speciesBinomial: Added morphospecies suffix to create speciesBinomialWithMorphospecies

7599 02/20/2013 12:15 AM Aaron Marcuse-Kubitza

inputs/import.stats.xls: Updated import times

7598 02/20/2013 12:06 AM Aaron Marcuse-Kubitza

README.TXT: Full database import: Check that unscrubbed_taxondetermination_view returns no rows: Documented that this takes 90 s with LIMIT 1

7597 02/19/2013 11:16 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: _taxon_family_require_std(): Also allow non-aceae families accepted by TNRS

7596 02/19/2013 09:38 PM Aaron Marcuse-Kubitza

Added inputs/SALVIAS/_archive/salvias_plots.*.sql.zip.md5

7595 02/19/2013 09:35 PM Aaron Marcuse-Kubitza

Added inputs/VegBank/_archive/vegbank_for_bien.tar.gz.url

7594 02/19/2013 09:29 PM Aaron Marcuse-Kubitza

Added inputs/U/UtrechtHerbarium.csv.tar.gz.url

7593 02/19/2013 09:28 PM Aaron Marcuse-Kubitza

Added inputs/TEAM/_archive/ci-team_extract.tar.gz.url

7592 02/19/2013 09:27 PM Aaron Marcuse-Kubitza

Added inputs/SpeciesLink/_archive/specieslink*.txt.gz.url

7591 02/19/2013 09:22 PM Aaron Marcuse-Kubitza

Added inputs/REMIB/_archive/remib_raw.csv.tar.gz.url

7590 02/19/2013 09:19 PM Aaron Marcuse-Kubitza

Added inputs/NY/NYSpecimenDataAmericas.csv.tar.gz.url

7589 02/19/2013 09:17 PM Aaron Marcuse-Kubitza

Added inputs/NCU/_archive/NCU-NCSC_2010-02-12.csv.tar.gz.url

7588 02/19/2013 09:14 PM Aaron Marcuse-Kubitza

Added inputs/MO/mo_digirexport.tar.gz.url

7587 02/19/2013 09:13 PM Aaron Marcuse-Kubitza

Added inputs/Madidi/_archive/2010-1-2/madidi_plots_original_12jan2010.zip.url

7586 02/19/2013 09:11 PM Aaron Marcuse-Kubitza

Added inputs/GBIF/gbif_extract.tar.gz.url

7585 02/19/2013 09:10 PM Aaron Marcuse-Kubitza

Added inputs/FIA/fia_extract.tar.gz.url

7584 02/19/2013 09:08 PM Aaron Marcuse-Kubitza

Added inputs/CVS/_archive/CVS-allTaxonOccurrences_2010-01-12.txt.tar.gz.url

7583 02/19/2013 09:04 PM Aaron Marcuse-Kubitza

Added inputs/ARIZ/ARIZ_DiGIR_21012010.csv.tar.gz.url

7582 02/19/2013 08:55 PM Aaron Marcuse-Kubitza

Added inputs/UNCC/Specimen/UNCC.csv.url, UNCC.csv.md5

7581 02/19/2013 08:45 PM Aaron Marcuse-Kubitza

Added inputs/XAL/_src/digir.xml.gz.md5

7580 02/19/2013 08:39 PM Aaron Marcuse-Kubitza

Added inputs/UNCC/_src/ with UNCC.csv.zip.md5

7579 02/19/2013 08:23 PM Aaron Marcuse-Kubitza

Added inputs/SpeciesLink/_src

7578 02/16/2013 08:24 AM Aaron Marcuse-Kubitza

README.TXT: Datasource setup: MySQL inputs: .sql exports: Use new mysql_bien to connect to the MySQL DB created for the datasource

7577 02/16/2013 08:22 AM Aaron Marcuse-Kubitza

Added mysql_bien, which runs a MySQL command on the local MySQL server

7576 02/16/2013 08:06 AM Aaron Marcuse-Kubitza

Added inputs/GBIF/_src/GBIFPortalDB-2012-12-11.dump.md5 (md5sum of the expanded file)

7575 02/16/2013 08:02 AM Aaron Marcuse-Kubitza

root Makefile: MySQL: mysql-Linux: Also install phpMyAdmin

7574 02/16/2013 08:01 AM Aaron Marcuse-Kubitza

root Makefile: MySQL: mysql-Linux: Split apt-get dependencies into separate commands, like for other apt-get commands, to avoid having one failed dependency prevent the following dependencies from being installed

7573 02/16/2013 07:57 AM Aaron Marcuse-Kubitza

root Makefile: MySQL: *mysql_users: Also add bien_read user

7572 02/16/2013 07:49 AM Aaron Marcuse-Kubitza

root Makefile: MySQL: Renamed *mysql_user to *mysql_users because there can be multiple users

7571 02/16/2013 06:51 AM Aaron Marcuse-Kubitza

inputs/: Added .md5 files for all .zip, .gz

7570 02/16/2013 06:47 AM Aaron Marcuse-Kubitza

Added inputs/HVAA/Specimen/Herbario_occur_1360871068.csv.url

7569 02/16/2013 06:39 AM Aaron Marcuse-Kubitza

lib/common.Makefile: rsync: $(rsync*): Use --no-group because the file group is different depending on the machine