Project

General

Profile

Statistics
| Revision:

# Date Author Comment
7714 02/26/2013 05:23 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: Added occurrenceRemarks

7713 02/26/2013 05:19 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped occurrenceRemarks

7712 02/26/2013 04:53 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Only use one of collection and collectionURL instead of concatenating them when both are provided (as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#ACAD&gt;)

7711 02/26/2013 04:53 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions

7710 02/26/2013 04:52 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions

7709 02/26/2013 04:44 PM Aaron Marcuse-Kubitza

inputs/FIA/_src/_README.TXT: Added e-mail from Brad Boyle on 2013-2-8

7708 02/26/2013 04:42 PM Aaron Marcuse-Kubitza

inputs/FIA/_src/: Added attachments from Brad's e-mail on 2013-2-8

7707 02/26/2013 04:37 PM Aaron Marcuse-Kubitza

xml_func.py: Removed no longer used _range(). Use SQL functions._range() instead.

7706 02/26/2013 04:34 PM Aaron Marcuse-Kubitza

schemas/functions.sql: Added _range()

7705 02/26/2013 04:30 PM Aaron Marcuse-Kubitza

xml_func.py: Removed no longer used _avg(). Use SQL functions._avg() instead.

7704 02/26/2013 04:29 PM Aaron Marcuse-Kubitza

schemas/functions.sql: Added _avg()

7703 02/26/2013 04:27 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions

7702 02/26/2013 04:15 PM Aaron Marcuse-Kubitza

schemas/functions.sql: _dms_to_dd(text): Corrected concatenated form to interpret last 5 digits as MMmmm = MM.mmm instead of MMSSS, per Tom Wendt's explanation that this form is "degrees/minutes/decimalminutes"

7701 02/26/2013 04:05 PM Aaron Marcuse-Kubitza

inputs/MO/Specimen/postprocess.sql: Use :table instead of hardcoding "MO"."Specimen"

7700 02/26/2013 04:04 PM Aaron Marcuse-Kubitza

inputs/MO/Specimen/postprocess.sql: Also remove frameshifted rows where InstitutionCode is NULL

7699 02/26/2013 03:44 PM Aaron Marcuse-Kubitza

inputs/UNCC/Specimen/map.csv: herbarium->specimenIndexer: Replace UNCCD (UNCC database?) with UNCC

7698 02/26/2013 03:27 PM Aaron Marcuse-Kubitza

schemas/functions.sql: functions._dms_to_dd(): Added support for DMS values without separators

7697 02/26/2013 03:09 PM Aaron Marcuse-Kubitza

README.TXT: Datasource setup: Update vegbiendev: Removed command to run the tests on vegbiendev because vegbiendev no longer has an empty public schema for running tests on (the public schema instead contains the latest published import)

7696 02/26/2013 03:04 PM Aaron Marcuse-Kubitza

Mapped inputs/BRIT/

7695 02/26/2013 02:36 PM Aaron Marcuse-Kubitza

my2pg: Remove (0) after char

7694 02/26/2013 02:35 PM Aaron Marcuse-Kubitza

my2pg: Remove any (#) after bytea

7693 02/26/2013 02:33 PM Aaron Marcuse-Kubitza

my2pg: Translate binary to bytea

7692 02/26/2013 02:30 PM Aaron Marcuse-Kubitza

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)

7691 02/26/2013 02:28 PM Aaron Marcuse-Kubitza

inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where needs to be set to just localhost and --user to bien instead

7690 02/26/2013 02:27 PM Aaron Marcuse-Kubitza

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.

7689 02/26/2013 02:25 PM Aaron Marcuse-Kubitza

lib/MySQL.*.sql.make: Added --user option to demonstrate how to set the DB user vs. the ssh user

7688 02/26/2013 02:19 PM Aaron Marcuse-Kubitza

inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where $server needs to be set to bien@localhost

7687 02/26/2013 02:18 PM Aaron Marcuse-Kubitza

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.

7686 02/26/2013 02:15 PM Aaron Marcuse-Kubitza

inputs/BRIT/: Added _MySQL/MySQL.*.sql.make

7685 02/26/2013 02:08 PM Aaron Marcuse-Kubitza

README.TXT: Datasource setup: MySQL inputs: .sql exports: Run mysql_bien in the background

7684 02/26/2013 02:03 PM Aaron Marcuse-Kubitza

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.

7683 02/26/2013 01:58 PM Aaron Marcuse-Kubitza

README.TXT: Datasource setup: Update vegbiendev: Updated steps for syncing via jupiter

7682 02/26/2013 01:56 PM Aaron Marcuse-Kubitza

Added inputs/BRIT/ (not yet translated to PostgreSQL)

7681 02/26/2013 01:35 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_DMS to coordinates.latitude_deg using new _dms_to_dd(text)

7680 02/26/2013 01:34 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_DMS to coordinates.latitude_deg using new _dms_to_dd(text)

7679 02/26/2013 01:29 PM Aaron Marcuse-Kubitza

schemas/functions.sql: Added _dms_to_dd(text)

7678 02/26/2013 01:28 PM Aaron Marcuse-Kubitza

schemas/functions.sql: _dms_to_dd(): Fixed bug where need to use 1 as the multiplier when dir is NULL

7677 02/26/2013 01:19 PM Aaron Marcuse-Kubitza

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

7676 02/26/2013 12:58 PM Aaron Marcuse-Kubitza

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

7675 02/26/2013 12:57 PM Aaron Marcuse-Kubitza

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)

7674 02/26/2013 12:30 PM Aaron Marcuse-Kubitza

schemas/functions.sql: _dms_to_dd(): Added dir param to specify compass dir suffix, in order to calculate the sign correctly

7673 02/26/2013 11:05 AM Aaron Marcuse-Kubitza

Moved compass_dir from schemas/vegbien.sql to schemas/functions.sql so it can be used by _dms_to_dd()

7672 02/26/2013 10:56 AM Aaron Marcuse-Kubitza

Moved _dms_to_dd() from schemas/vegbien.sql to schemas/functions.sql so it can use functions schema functions

7671 02/26/2013 10:51 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added compass_dir enum

7670 02/26/2013 10:42 AM Aaron Marcuse-Kubitza

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

7669 02/26/2013 10:40 AM Aaron Marcuse-Kubitza

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

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