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# Date Author Comment
11970 01/20/2014 11:33 AM Aaron Marcuse-Kubitza

moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).

11396 10/21/2013 07:14 PM Aaron Marcuse-Kubitza

fix: bin/map: put template: comment out the "Put template:" label so that the output is valid XML, and displays properly in a browser rather than showing a syntax error

11107 09/29/2013 08:58 PM Aaron Marcuse-Kubitza

bugfix: mappings/VegCore-VegBIEN.csv: nest all taxonoccurrences inside a stratum event, so that the parent locationevent is always fully populated before child locationevents point to it. (previously, a stub parent event was created when the child event was imported first, which blocked the fully-populated parent event from being inserted later on.) this uses auto-folding (for VegBank/CVS) and auto-forwarding (for other datasources) to prune empty stratum events for taxonoccurrences that don't have strata. (see wiki.vegpath.org/Auto-folding, wiki.vegpath.org/Auto-forwarding for more info about these normalization techniques.) note that the inserted row counts stay exactly the same for all datasources except VegBank (which was being fixed), indicating that this signficant change to the mappings did not change the semantics of the import of taxonoccurrences.

10866 09/04/2013 11:06 PM Aaron Marcuse-Kubitza

inputs/*/*/test.xml.ref: updated source.shortname for new datasource name, which now starts out with .new suffix

10377 07/20/2013 05:09 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: map_nulls() derived cols: documented total runtime (7.5 min on vegbiendev)

10376 07/20/2013 05:07 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: map_nulls() derived cols: updated runtimes for map_nulls() inlining, which created a speed improvement of 7x for the numeric columns and 2.5x for the text columns (292563.362->41929.772 ms and 83640.424->35690.797 ms, respectively). note that the map_nulls__coord__*() calls could be optimized further by combining the successive map_nulls() calls into one, with the hstores merged.

10361 07/20/2013 01:27 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: map_nulls__*(): turned off STRICT to allow dynamic inlining, which speeds up the mk_derived_col() statements by 5x (342799.823 ms -> 71533.252 ms (6 min -> 1 min) for latitude_sec)

10360 07/19/2013 07:23 PM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: runtimes: updated for vegbiendev, before dynamic inlining. the times are about twice as fast as on starscream, so vegbiendev is faster at whatever is the limiting speed factor (probably not CPU, based on other benchmarks).

10350 07/19/2013 02:26 PM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: runtimes: documented the machine the times are from

10349 07/19/2013 01:52 PM Aaron Marcuse-Kubitza

inputs/REMIB/: switched to new-style import, using the steps at wiki.vegpath.org/Switching_to_new-style_import#stage-I-source-specific > "run the following for each datasource"

10341 07/19/2013 08:56 AM Aaron Marcuse-Kubitza

bugfix: inputs/REMIB/Specimen/map.csv: state: changed output column name to stateProvince_verbatim to match the renaming in postprocess.sql

10340 07/19/2013 08:40 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: removed out-of-date rerun time, which applied to doing all the deletes in the same statement (however, the current rerun time is approximately the same). note that index scans are not actually used (as the previous comment incorrectly stated) because the conditions for this filter are prefix-less regexps.

10339 07/19/2013 08:32 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/: translated single-column filters to postprocessing derived columns, using the steps at wiki.vegpath.org/Switching_to_new-style_import#stage-I-source-specific > "translate single-column filters to postprocessing derived columns". null-mapping filters now use wrappers around new util.map_nulls(). note that the verbatim columns input to the filters need to be renamed to avoid name collisions with their filtered columns, which must be VegCore terms for new-style import.

10338 07/19/2013 07:53 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: also filter out non-numbers for long_sec, lat_min, lat_sec

10337 07/19/2013 07:18 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: remove rows where long_min is not a number

10336 07/19/2013 07:15 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: change E'' to regular '' to avoid the need to double \ (instead ' would be doubled). E'' used to be necessary in previous versions of PostgreSQL to avoid a warning about escape string syntax.

10335 07/19/2013 07:09 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: removed unnecessary () around `DELETE FROM :table WHERE long_deg ...`

10334 07/19/2013 07:03 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: removed coll_year, country, long_deg indexes because the frameshift filter conditions on these columns do not use index scans (because their regexp patterns do not contain a fixed prefix). eventually, some regexp patterns may be able to be modified to use prefixes.

10333 07/19/2013 07:01 AM Aaron Marcuse-Kubitza

bugfix: inputs/REMIB/Specimen/postprocess.sql: remove frameshifted rows: can't OR together conditions to determine rows to delete, because if any condition is NULL instead of true/false, this will NULL out the entire WHERE condition and prevent any other true conditions from causing a deletion. the best way to fix this is to use a separate DELETE statement for each condition, so that NULLs only impact that particular condition's DELETE. unlike using a modified, NULL-insensitive OR, which would prevent the use of index scans, this allows indexes to be used for conditions that support them.

10332 07/19/2013 06:05 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: removed duplicate CREATE INDEX for the acronym column

10331 07/19/2013 05:59 AM Aaron Marcuse-Kubitza

bugfix: inputs/REMIB/Specimen/postprocess.sql: switched back to the input column names, since the renaming to *_verbatim is part of a later step

10330 07/19/2013 05:26 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/create.sql: moved filtering out of frameshifted rows to postprocess.sql, where it can happen in an idempotent DELETE. this allows filters to remove additional rows to easily be added on top of the existing filters, without needing to remake Specimen (which takes a long time, because of the many stage I derived columns that get added). the logical inversion inherent in the DELETE condition has been factored through rather than wrapped in NOT (...), because removal of frameshifted rows is more accurately specified as the detection of specific patterns that indicate frameshifting rather than the validation of all fields.

10326 07/18/2013 06:43 PM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/create.sql: also remove frameshifted rows with invalid long_deg values

10245 07/11/2013 12:55 AM Aaron Marcuse-Kubitza

bugfix: inputs/*/*/postprocess.sql: made all operations idempotent, so that postprocess.sql can be run repeatedly (e.g. by new-style import)

10209 07/10/2013 02:32 AM Aaron Marcuse-Kubitza

inputs/*/*/map.csv for CSV tables with a row_num column: added missing row_num entry, which is needed by the staging table column renaming to make the order of the map.csv columns match the order in the staging table

9882 06/12/2013 10:49 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: genus->taxonlabel.taxonomicname: filter out genera that contain numbers (using new _filter_genus()), which break TNRS and prevent it from matching any other parts of the name. later, these genera can instead be moved to the end of the name, where TNRS will correctly match them as Unmatched_terms.

9502 05/21/2013 11:18 PM Aaron Marcuse-Kubitza

inputs/GBIF/Specimen/postprocess.sql, inputs/REMIB/Specimen/postprocess.sql: updated for providers in r9459, which adds TEX

9501 05/21/2013 11:10 PM Aaron Marcuse-Kubitza

inputs/*/*/postprocess.sql: Remove institutions that we have direct data for: query to obtain list: updated for current schema

8801 05/02/2013 08:53 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files

8176 03/25/2013 09:01 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: %/.map.csv.last_cleanup: Run fix_line_endings after canon/translate to standardize Python's \r\n line endings back to \n. This prevents issues with mixed line endings because LibreOffice (and probably Excel) treat all cell-internal line endings as \n but row line endings as whatever the file had, while text editors like jEdit translate all line endings to whatever the autodetected line ending is. (This creates spurious line ending diffs when a map spreadsheet containing multiline cells is edited in a text editor.)

7841 03/05/2013 09:07 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Renamed specimenHolders to specimenHolderInstitutions to make it obvious that this is a list of institutions, such as would be in institutionCode in a DwC export.

7720 02/26/2013 06:32 PM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/map.csv: Mapping NULL-equivalent lat/long to NULL: Fixed bug where need special *=* mapping to pass through values not in the map

7719 02/26/2013 06:30 PM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/map.csv: Map NULL-equivalent text fields (country, state, etc.) to NULL

7718 02/26/2013 06:23 PM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/map.csv: Map NULL-equivalent lat/long to NULL

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

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).

7547 02/14/2013 08:58 AM Aaron Marcuse-Kubitza

inputs/*/*/VegBIEN.csv: Regenerated from mappings/VegCore-VegBIEN.csv

7527 02/12/2013 01:08 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Brad's new DwC ID terms spreadsheet has now been added, and a number of the ID terms clarified, disambiguated, and recategorized. In particular, institutionCode has now been split into the custodialInstitutions and collectingInstitution, to differentiate between which institution has the specimen vs. stamped the specimen. This distinction is important because the catalogNumber, stamped on the specimen, is only unique within the collectingInstitution. Most datasources don't unambiguously specify which institution their institutionCode is referring to, so it has been assumed to be custodialInstitutions unless a data dictionary says otherwise (as is the case for UNCC). In addition, a MatchedTaxonDetermination table has been added with the *_matched fields from TNRS.

7433 02/04/2013 11:03 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: institutionCode list->sourcename mapping: _split(): Also match ; as a separator, and match separators with or without a following space

7407 01/31/2013 06:08 PM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Regenerated from wiki. This adds Brad's DwC ID terms and their definitions in <https://projects.nceas.ucsb.edu/nceas/attachments/download/621/vegbien_identifier_examples.xlsx&gt;.

7310 01/18/2013 12:43 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Don't create NCBI crosslinks for the matched taxonomic name. These crosslinks are no longer needed now that TNRS provides a separate accepted name on which crosslinks can be made.

7250 01/16/2013 09:21 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/postprocess.sql: Added back ARIZ, NY because some REMIB specimens for these datasources are not yet in the datasources themselves

7249 01/16/2013 08:43 AM Aaron Marcuse-Kubitza

Added inputs/REMIB/Specimen/postprocess.sql to remove institutions that we have direct data for

7162 01/11/2013 02:03 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Removed TNRS input taxonlabels meant to cross-link to taxonlabels added by the TNRS import, because TNRS taxondeterminations are now created instead

7142 01/09/2013 03:59 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonlabel.taxonomicname: Prepend the family to the rest of the name using new _merge_prefix() instead of _join_words()/_nullIf(), so that any input taxonomic name that includes the family will not have the family duplicated in the combined taxonomic name. Previously, the duplication was removed only when the rest of the input name was equal to the family. This change fixes a bug in the new TNRS import where a pre-concatenated taxonomic name (Accepted_scientific_name) which includes the family is now used instead of Accepted_name, which only includes it when it's equal to the family.

6795 12/11/2012 11:41 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: institutionCode: Removed mapping to sourcename.matched_source_id, which is now autopopulated. Split any list of institutionCodes apart using new _split().

6791 12/11/2012 11:11 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Allow multiple institutionCodes for each specimenreplicate by linking new sourcelist table many-to-many to source via sourcename (which is now a linking table)

6756 12/11/2012 04:37 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Don't forward specimenreplicate IDs to location for plots data (where the specimenreplicate IDs apply only to the specimen)

6432 11/24/2012 01:24 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped locality description fields to location.iscultivated using _locationnarrative_is_cultivated()

6409 11/24/2012 08:29 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: source table mappings: Set shortname to env var $source when it's not explicitly specified, because shortname is a required field of source

6406 11/24/2012 07:50 AM Aaron Marcuse-Kubitza

db_xml.py: put(): _setDefault(): Support setting multiple col_defaults at once by using the param names themselves as the column names

6403 11/24/2012 07:29 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Set the source_id col_default to the datasource name using the new _setDefault() built-in function and _env()

6384 11/24/2012 04:19 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: institutionCode: Also map to the sourcename's matched source, which identifies whether the source is a herbarium

6375 11/24/2012 02:10 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: institutionCode: Remap to source.shortname when specimen information is not provided, as is the case for geoscrub.herbaria on nimoy

6359 11/21/2012 11:05 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Concatenated taxonlabel: Don't prepend family if the taxonName/scientificName itself is the family, so that the family is not duplicated in the concatenated taxonomic name

6294 11/19/2012 04:09 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped acceptedCounty, county to the matched place

6179 11/14/2012 06:30 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed reference -> source to make this table more broadly applicable, and because this now stores the datasource metadata

6171 11/14/2012 05:35 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Made taxonoccurrence.verbatimcollectorname an fkey to party, and renamed it to collector_id

6149 11/13/2012 06:23 PM Aaron Marcuse-Kubitza

specimenreplicate: Made institution_id an fkey to referencename instead of party, to later be matched up with reference entries for each aggregator's subprovider

6123 11/13/2012 02:30 PM Aaron Marcuse-Kubitza

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)

6122 11/13/2012 02:22 PM Aaron Marcuse-Kubitza

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

5969 11/02/2012 03:42 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: decimalLatitude/Longitude->geoscrub input coordinates: Also set to NULL if 0 here, not just for the coordinates linked to the datasource's place instance

5958 11/01/2012 10:39 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: matched place: Also map verbatim place's geoscrub-related fields to the matched place, to link up with geoscrub's corresponding input place

5953 11/01/2012 10:09 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Renamed creator_ids to reference_id since they are now fkeys to reference

5952 11/01/2012 10:04 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Made creator_ids an fkey to reference instead of party, so that datasources are stored separately from people and to allow adding reference-type metadata (URL, copyright, etc.) for each datasource

5932 11/01/2012 07:18 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: matched taxonlabel's ancestors: Only create the cross links to NCBI if the name is accepted (taxonIsCanonical)

5908 11/01/2012 03:36 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped acceptedCountry, acceptedStateProvince, acceptedDecimalLatitude/Longitude. Mapped decimalLatitude/Longitude to matched place's coordinates when acceptedDecimalLatitude/Longitude not provided (as is the case for the geoscrub table).

5861 10/30/2012 11:23 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Remapped latitude/longitude to new coordinates table

5855 10/30/2012 09:54 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed placepath to place since this contains primary information about the place, including the reference to the canonical place

5790 10/25/2012 04:53 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Only prepend the family to the concatenated scientificName for TNRS if it ends in -aceae (using _taxon_family_require_std()), to avoid sending unsupported, nonstandard families to TNRS which it will place in Unmatched_terms

5788 10/25/2012 04:09 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Prepend the family to the concatenated scientificName input to TNRS, so that TNRS can use it to disambiguate the genus

5783 10/25/2012 12:45 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonverbatim: Renamed species to specific_epithet to avoid confusion with the scientific meaning of species (genus+specificEpithet), since this field contains just the specific epithet

5746 10/23/2012 11:45 AM Aaron Marcuse-Kubitza

inputs/REMIB/Specimen/header.csv: Regenerated for new staging tables format

5743 10/23/2012 11:15 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Do not include rank in the mapping because taxonomicname is globally unique, and thus it isn't used in looking up the NCBI taxonlabel

5741 10/23/2012 10:49 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Also attach TNRS genus to NCBI backbone. This causes attachment to be made with as many of family and genus as are provided and have an entry in NCBI.

5739 10/23/2012 10:39 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Instead of connecting the acceptedFamily to the NCBI backbone, connect the family for the TNRS matched taxonlabel. This connects more families and also connects the same set of fields as will be connected for the genus.

5695 10/23/2012 12:05 AM Aaron Marcuse-Kubitza

inputs/*/*/header.csv: Regenerated for new staging tables format (which now includes a row_num column on every CSV table), as part of reinstalling staging tables

5657 10/18/2012 04:21 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Link taxondetermination to taxonverbatim (which is a subclass of taxonlabel) instead of directly to taxonlabel. This will enable later having multiple taxonverbatims for one taxonlabel.

5656 10/18/2012 04:04 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonlabel: Renamed identifyingtaxonomicname to taxonomicname because the taxonomicname provided by the datasource is now in taxonverbatim, so there is no name collision. Note that both of these fields store the same type of information, but taxonlabel's is autogenerated while taxonverbatim's is verbatim (and is only set if provided by the datasource).

5655 10/18/2012 03:57 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonlabel: Moved non-scoping fields to new taxonverbatim subclass table, which contains the component parts of the taxonlabel

5646 10/18/2012 01:51 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Also create the identifyingtaxonomicname on the verbatim taxonlabel supplied by the datasource, in addition to on the TNRS input taxonlabel that the verbatim taxonlabel is matched up with

5645 10/18/2012 01:46 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Expanded brace expressions for putting together the identifyingtaxonomicname

5644 10/18/2012 01:21 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Always generate the concatenated identifyingtaxonomicname, even for higher taxa, to ensure that this field is always populated. Note that this will cause names of higher taxa to be scrubbed by TNRS, but this is usually not a problem because such names either have no match or not a close enough match based on the name only. Naming conventions generally cause names at different ranks to be different, so that collisions with lower ranks should not be a problem.

5608 10/17/2012 04:12 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed taxonconcept to taxonlabel per today's conference call, where it was decided that taxonconcept contained too many unrelated fields to be purely a taxon concept

5596 10/17/2012 12:43 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonconcept: Renamed taxonname to taxonepithet for clarity and to be consistent with TCS's use of "epithet" to denote what the taxonname was intended to be (http://www.tdwg.org/standards/117/download/#/UserGuidev_1.3.pdf)

5490 10/12/2012 05:07 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: identifyingtaxonomicname: Don't create if taxonconcept has an explicit parent, because the taxonName (which is generally only a component of the full taxonomic name, e.g. specificEpithet) is not globally unique. Datasources that provide name components in such a way that levels at or below family can't be directly concatenated cannot currently receive an identifyingtaxonomicname for input to TNRS.

5465 10/12/2012 05:47 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonconcept: Renamed canon_concept_id to matched_concept_id, because this is actually the closest-match taxonconcept in the match hierarchy (datasource concept -> parsed concept -> matched concept -> accepted concept) rather than the accepted synonym, which goes in accepted_concept_id

5399 10/10/2012 07:55 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonconcept: Renamed canon_taxonconcept_id to canon_concept_id to shorten the name, which is used often

5313 10/08/2012 09:30 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: taxonconcept: taxonconcept_required_key: Removed family and genus because these are now cached fields only, and are not used for scoping a taxonconcept. Instead, *taxonomicname and taxonname+parent_id are used for this purpose. This removes several leaf taxonconcepts with insufficient scoping information to create a taxonconcept separate from the main tree. With the upcoming population of creationdate, some of these taxonconcepts will reappear due to the date's additional distinguishing information.

5306 10/08/2012 08:38 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonconcept: Moved infraspecific taxonconcept to its own level, rather than combining it with the level that contains the full taxonomic name and author (as well as any morphospecies), for consistency with the storage of other ranked taxonomic name components, which each get their own taxonconcept. The infraspecific taxon concept is general to all parties making idenfitications (within a datasource), while the concatenated name and author and any morphospecies are specific to the person who defined the taxonconcept used by a taxondetermination.

5294 10/08/2012 04:35 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonconcepts: Also create the taxonconcept tree if datasource provided separated components of the taxonomic name and/or its own tree of life with higher classifications. This enables storing the datasource's own tree of life to supplement any official tree (TROPICOS, USDA, etc.).

5293 10/08/2012 04:25 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: taxonconcept tree: Don't map infraspecificEpithet+taxonRank to a taxonconcept in the tree of parent concepts because it has already been mapped to the primary, lowest-level taxonconcept

5272 10/05/2012 08:38 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Remapped taxon hierarchy for accepted taxonconcepts to taxonconcept parent_id hierarchy

5255 10/05/2012 05:12 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: TNRS-only mappings: Switch them on when verbatimScientificNameWithAuthorship is provided rather than when acceptedScientificNameWithAuthorship is provided, because it's the presence of a separate TNRS input name that really determines when TNRS is being mapped

5242 10/04/2012 08:26 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed datasource_id to creator_id so it can apply generally to any entity (such as a person), not just an aggregated datasource. This also enables taxonconcept.datasource_id to merge with creator_id, which now serves the same purpose.

5237 10/04/2012 06:51 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Fixed bug where needed to set datasource_id=0 on the TNRS party (which concatenated names/TNRS inputs are owned by) in order to make it a datasource (a root party)

5225 10/04/2012 04:23 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed taxonpath -> taxonconcept as part of taxonomic schema refactoring at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/2012-10-03_conference_call#Taxonomic-schema-refactoring>

5202 10/03/2012 08:11 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped morphospecies

5196 10/03/2012 06:29 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Also map TNRS-parsed infraspecificEpithet (Infraspecific_epithet_matched) to taxon at the infraspecies rank

5195 10/03/2012 06:07 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Also map TNRS-parsed taxonomic ranks to the tree of life in the taxon table