Activity
From 02/10/2013 to 03/11/2013
03/11/2013
- 11:19 PM Revision 7939: web/vegpath/index.php: Renamed ref to ns to emphasize that the resources in this field are namespaces for the paths
- 11:16 PM Revision 7938: web/vegpath/index.php: add_ref(): Renamed $suffix to $path_pat to distinguish it from the actual suffix string sent in the URL
- 11:09 PM Revision 7937: web/vegpath/index.php: custom_separator(): Marked optional params as such
- 11:07 PM Revision 7936: web/vegpath/index.php: Terms: IH-db: Factored out phpMyAdmin URL into $IH_db
- 11:05 PM Revision 7935: web/vegpath/index.php: Terms: Added IH-db
- 11:05 PM Revision 7934: web/vegpath/index.php: php*Admin(): Added support for a fixed table that doesn't need to be specified in the path
- 10:43 PM Revision 7933: web/: Removed svn:executable permissions from non-executable files
- 10:36 PM Revision 7932: web/vegpath/index.php: Data: Added Institutions subsection
- 10:33 PM Revision 7931: web/vegpath/index.php: Placed Terms and Data sections side-by-side in two columns so that data resources would not need to come after a long list of terms resources
- 10:31 PM Revision 7930: web/vegpath/main.css: Added .indent
- 10:11 PM Revision 7929: web/vegpath/index.php: People: Added Brad's VegCore ID terms spreadsheets
- 10:10 PM Revision 7928: web/vegpath/index.php: Factored Redmine svn URLs out into $Redmine_svn
- 10:06 PM Revision 7927: Added schemas/VegCore/Brad_Boyle/ with Brad's VegCore IDs terms spreadsheets
- 09:51 PM Revision 7926: web/vegpath/index.php: URL fragment redirect: Removed loading indicator (blinking of resource being loaded) because for file downloads, the download will not redirect to a new page and the resource name will instead remain blinking
- 09:48 PM Revision 7925: web/vegpath/index.php: URL fragment redirect: Fixed bug where need to use parse_mixed_path() instead of parse_dot_path() to support XPaths
- 09:48 PM Revision 7924: web/vegpath/index.php: Terms: Added CTFS
- 09:23 PM Revision 7923: web/vegpath/index.php: URL patterns header: Reworded comment to clarify that the elements that can be left out are in italics
- 09:09 PM Revision 7922: web/vegpath/index.php: URL fragment redirect: Only perform fragment redirect if URL shortener requires it (as indicated by the $alias ending in #)
- 09:01 PM Revision 7921: web/vegpath/index.php: nimoy nodes: Factored nimoy phpMyAdmin() calls out into nimoy_db() function
- 08:57 PM Revision 7920: web/vegpath/index.php: nimoy nodes: Factored nimoy URL prefix out into $nimoy
- 08:51 PM Revision 7919: web/vegpath/index.php: SALVIAS: Added subnodes for each SALVIAS database on nimoy
- 08:37 PM Revision 7918: web/vegpath/index.php: VegCore: Changed suffix from .table.column to .term because VegCore terms are globally unique and don't need a table prefix
- 08:36 PM Revision 7917: web/vegpath/index.php: BIEN2: Added subnodes for each BIEN2 database on nimoy
- 08:04 PM Revision 7916: web/vegpath/index.php: Inlined VegBank() because it's only used once
- 08:01 PM Revision 7915: web/vegpath/index.php: VegBank(): Use custom_separator()'s new $main_url param
- 08:00 PM Revision 7914: web/vegpath/index.php: custom_separator(): Added $main_url param like in by_prefix(), for use when there is no path
- 07:55 PM Revision 7913: web/vegpath/index.php: VegBank(): Use new custom_separator()
- 07:55 PM Revision 7912: web/vegpath/index.php: VegBank(): Use new custom_separator()
- 07:53 PM Revision 7911: web/vegpath/index.php: VegBank(): Use new custom_separator()
- 07:53 PM Revision 7910: web/vegpath/index.php: Added custom_separator()
- 07:52 PM Revision 7909: web/vegpath/index.php: Add # suffix to $alias instead of adding it in add_ref(), because not all aliases will use a # suffix
- 07:48 PM Revision 7908: web/vegpath/util.php: Added array_non_empty(), join_non_empty()
- 07:14 PM Revision 7907: web/vegpath/index.php: add_ref(): redirect: Don't display "Loading" as the page itself is not shown to the user when using a Location: header
- 07:12 PM Revision 7906: web/vegpath/index.php: URL fragment redirect: Fixed bug where can't prefix the fragment with / because this won't work if VegPath is not at the top-level of the domain (and in any case is unnecessary to form a relative path)
- 07:09 PM Revision 7905: web/vegpath/index.php: URL fragment redirect: Blink the namespace being loaded, rather than displaying "Loading" at the bottom of the page, to make it clearer what's being loaded
- 06:42 PM Revision 7904: web/vegpath/index.php: add_ref(): Don't display the URL pattern in monospace, because fixed-width font is not needed and variable-width font is easier to read. This requires decreasing the header level because variable-width font is bigger than fixed-width font.
- 06:41 PM Revision 7903: web/vegpath/main.css: Added entries for h6
- 06:28 PM Revision 7902: web/vegpath/index.php: parse_dot_path() calls: Fixed bug where need to test result components using \`!== ""\` instead of just using the value as a boolean because PHP incorrectly interprets the string "0" as false
- 06:24 PM Revision 7901: web/vegpath/util.php: Path: Made $tail default to ""
- 06:20 PM Revision 7900: web/vegpath/index.php: URL fragment redirect: Prepend / instead of ? because filesystem paths are now redirected using .htaccess, removing the need to set the query string
- 06:16 PM Revision 7899: web/vegpath/index.php: phpMyAdmin(): Fixed bug where can't use tbl_alter as the column target page because it requires a token param, which is only obtained after the user logs in
- 06:04 PM Revision 7898: web/vegpath/util.php: partition(): Fixed bug where strpos() actually does take the search-for param second rather than first (but returns false on no match)
- 06:00 PM Revision 7897: web/vegpath/util.php: partition(): Fixed bug where strpos() returns false rather than -1 on no match
- 05:59 PM Revision 7896: web/vegpath/util.php: partition(): Fixed bug where strpos() takes the search-for param first rather than second
- 05:37 PM Revision 7895: web/vegpath/index.php: php*Admin(): Append $target to $url in separate step from returning $url, to make it easier to debug-print the value of $url before returning it
- 05:30 PM Revision 7894: web/vegpath/index.php: BIEN2: Fixed to use phpMyAdmin with correct URL instead of vegbiendev phpPgAdmin placeholder
- 05:20 PM Revision 7893: web/vegpath/index.php: Added phpMyAdmin()
- 04:59 PM Revision 7892: web/vegpath/.htaccess: mod_rewrite: RewriteBase: Changed to / now that VegPath is hosted at vegbiendev.nceas.ucsb.edu
- 04:58 PM Revision 7891: web/vegpath/.htaccess: unknown paths: Don't redirect to index.php if the path already starts with index.php, to help avoid infinite redirect recursion
- 04:54 PM Revision 7890: web/vegpath/.htaccess: unknown paths: Removed no longer accurate VegRef from comment header
- 04:43 PM Revision 7889: vegpath/.htaccess: DirectorySlash: Lowercased On for consistency with other boolean directives
- 04:26 PM Revision 7888: Added web/vegpath.conf with Apache VirtualHost config
- 03:26 PM Revision 7887: vegpath/index.php: VegBank(): Fixed bug where name had incorrectly been replaced with $name
- 03:24 PM Revision 7886: vegpath/index.php: phpPgAdmin(): Factored out appending of "&subject="
- 03:23 PM Revision 7885: vegpath/: Archived no longer used vegpath/index.htm
- 03:05 PM Revision 7884: vegpath/index.*: IH: URL-encode ' in search URL to avoid needing to backslash-escape it
- 03:04 PM Revision 7883: vegpath/index.php: IH: Fixed search URL to undo incorrect search-and-replace of + with .
03/10/2013
- 06:51 AM Revision 7882: vegpath/index.*: Changed "Supported URLs" to "Supported URL patterns" because the provided short URLs take parameters that are filled into the destination URL
- 06:46 AM Revision 7881: vegpath/index.*: Removed tagline from window title because the window title (which becomes the bookmark name) only needs to be long enough to identify what the page is, and should not be cluttered with descriptions
- 06:43 AM Revision 7880: vegpath/index.*: Changed tagline to emphasize that the shortened URLs are especially intended to be human-readable, e.g. for use as column names
- 06:37 AM Revision 7879: VegRef/: Renamed to VegPath to make it clearer that the purpose of the web service is to provide short, globally unique paths to resources (e.g. for use as global IDs <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs>)
- 06:10 AM Revision 7878: VegRef/.htaccess: URL resolution: mod_rewrite: Fixed bug where also need to consider if %{REQUEST_FILENAME} is a dir or symlink, which occurs e.g. when redirecting to the VegRef/ dir itself
03/09/2013
- 10:50 PM Revision 7877: web/VegRef/.htaccess: Turned off RewriteEngine temporarily because it was preventing the internal VegRef redirection from working
- 10:48 PM Revision 7876: Added web/VegRef/, which provides a URL-shortening service for vegetation references. VegRef URLs are short and human-readable enough to be used as database column names. This also causes Google spreadsheets to display a clickable link for each column name, which takes the user to the data dictionary definition for the term. String row IDs (such as global IDs <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Global_IDs>) can also be clickable VegRef URLs.
03/08/2013
- 10:26 PM Revision 7875: inputs/NCU/Specimen/map.csv: cultivated: Map false (0) to NULL because cultivated can only be true or NULL, not false
- 09:14 PM Revision 7874: inputs/CTFS/_src/_README.TXT: Added e-mails from Brad Boyle about issues with species aggregation methods
03/07/2013
- 06:27 PM Revision 7873: inputs/UNCC/Specimen/map.csv: Populated specimenHolderInstitutions
- 03:21 PM Revision 7872: Added planning/goals/BIEN3_derived_data_products.docx.url
- 03:19 PM Revision 7871: Added planning/goals/BIEN3_derived_data_products.docx
03/06/2013
- 11:00 PM Revision 7870: inputs/ARIZ/omoccurrences/map.csv: cultivationStatus: Map to NULL if it's false, because cultivated can only be true or NULL
- 10:01 PM Revision 7869: schemas/vegbien.sql: analytical_stem_view: Merged taxonName_verbatim and scientificNameAuthorship_verbatim into scientificName_verbatim
- 09:29 PM Revision 7868: schemas/vegbien.sql: analytical_plot: Added specimens fields at the end, for use by plots data that also tracks specimens (e.g. Madidi, SALVIAS)
- 09:21 PM Revision 7867: README.TXT: Full database import: In PostgreSQL: Removed tests related to unscrubbed_taxondetermination_view and TNRS taxondeterminations, which are no longer needed because TNRS is joined directly to analytical_stem_view
- 08:36 PM Revision 7866: mappings/VegCore.htm: Regenerated from wiki. Renamed specimenDonor to specimenDonorInstitution to clarify that this is an institution, not a collector.
- 08:30 PM Revision 7865: inputs/UNCC/Specimen/map.csv: Mapped flower, fruit -> reproductiveCondition using translation is from e-mail conv between Jim Matthews at Habitat Assessment and Bob Peet on 2010-12-2~3
- 08:17 PM Revision 7864: make_analytical_db: Support the $log flag, which toggles output to the terminal or a log file
- 07:50 PM Revision 7863: inputs/import.stats.xls: Updated import times. The core import time has dropped by more than half (!) to ~12 hours, now that the TNRS scrubbing is added using a simple LEFT JOIN, instead of being pushed through the normalized schema. Not since October has the import been this fast!
- 07:27 PM Revision 7862: import_times: When there are no matching logs, exit with status 0 instead of 1 because this is a normal condition
- 07:26 PM Revision 7861: import_times: Fixed bug where sed would wait for user input from stdin when there were no matching logs
- 07:22 PM Revision 7860: README.TXT: Full database import: record the import times in inputs/import.stats.xls: If the row counts do not match up: Added step to get the datasource names from the log file footers
- 07:12 PM Revision 7859: inputs/UNCC/Specimen/map.csv: cultivated: assume anything non-NULL to be cultivated, so that we err on the side of excluding possibly-cultivated specimens
- 06:49 PM Revision 7858: inputs/UNCC/_src/_README.TXT: Added e-mail conv between Jim Matthews at Habitat Assessment and Bob Peet about the meanings of the Leaf, Flower, Fruit, and Root codes
- 05:38 PM Revision 7857: README.TXT: Full database import: Added steps to manually back up the DB. (These steps are specific to the import process, and include filters to exclude previous imports. There are also general backup steps in the Backups > Full DB section.)
- 02:56 PM Revision 7856: inputs/ACAD/Specimen/map.csv: institutionCode: Replace "Acadia University" with the IH code ACAD
- 02:18 PM Revision 7855: inputs/.TNRS/data.sql: Re-ran TNRS on the test_taxonomic_names so that the sample data would contain all the accepted names under the current acceptedScientificName formula, and would not produce any entries for unscrubbed names in tnrs_input_name
- 01:59 PM Revision 7854: schemas/vegbien.sql: tnrs_input_name: taxonlabel.taxonomicname subquery: Don't exclude taxonlabels with a matched_label_id, because matched_label_id is no longer used to indicate that a name has a scrubbed name (this was used when all of TNRS was imported at the beginning of the import)
- 01:56 PM Revision 7853: schemas/vegbien.sql: tnrs_input_name: accepted_name subquery: Renamed to the VegCore table name AcceptedTaxon
- 01:54 PM Revision 7852: schemas/vegbien.sql: tnrs_input_name: taxonlabel.taxonomicname subquery: Use new MatchedTaxon view, which use VegCore column names where possible
- 01:46 PM Revision 7851: schemas/vegbien.sql: tnrs_input_name: accepted_name subquery: Use new MatchedTaxon, AcceptedTaxon views, which use VegCore column names where possible
- 01:22 PM Revision 7850: README.TXT: Full database import: Added instructions to run TNRS and view the TNRS log
- 10:21 AM Revision 7849: README.TXT: Full database import: Removed no longer necessary command to scrub unscrubbed taxondeterminations
03/05/2013
- 11:07 PM Revision 7848: *.sql: concat_ws() calls: Fixed bug where need to surround it with NULLIF(..., '') because concat_ws() returns '' instead of the required NULL when supplied with only NULL args
- 10:22 PM Revision 7847: schemas/vegbien.sql: analytical_stem_view: concat_ws() calls: Fixed bug where arguments were still enclosed in ARRAY[], because the name had been changed from concat_delim() but PostgreSQL removed the VARIADIC keyword without also removing the ARRAY[] wrapper
- 10:11 PM Revision 7846: schemas/vegbien.sql: Removed no longer needed unscrubbed_taxondetermination_view. Use taxonlabel joined to ScrubbedTaxon instead.
- 10:05 PM Revision 7845: inputs/.TNRS/schema.sql: ScrubbedTaxon: Include only matches with a match score of at least 0.8 (score_ok())
- 09:59 PM Revision 7844: inputs/.TNRS/schema.sql: Added back score_ok() and tnrs.tnrs_score_ok index
- 09:53 PM Revision 7843: *.sql: Replaced concat_delim() with concat_ws(), which is built-in as of PostgreSQL 9.1 (http://stackoverflow.com/questions/1943433/postgresql-concat-ws-like-function)
- 09:08 PM Revision 7842: inputs/U/Specimen/map.csv: Populated specimenHolderInstitutions
- 09:07 PM Revision 7841: 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.
- 09:06 PM Revision 7840: inputs/SpeciesLink/Specimen/map.csv: Fixed embedded line endings
- 08:28 PM Revision 7839: inputs/NY/Ecatalog_all/map.csv: PlantFungDescription->occurrenceRemarks: Removed "plant fungus" label because this field actually contains the specimenDescription
- 08:06 PM Revision 7838: inputs/.TNRS/import_order.txt: Removed public.unscrubbed_taxondetermination_view
- 08:01 PM Revision 7837: inputs/.TNRS/: Moved no longer needed public.unscrubbed_taxondetermination_view/ to _archive/
- 07:52 PM Revision 7836: root Makefile: Datasources: scrub: Removed no longer needed scrub-remake, which has been replaced by direct use of TNRS.ScrubbedTaxon
- 07:46 PM Revision 7835: schemas/vegbien.sql: analytical_stem_view: taxondetermination: Fixed bug where need to include only the is_datasource_current taxondetermination
- 07:43 PM Revision 7834: schemas/vegbien.sql: analytical_stem_view: Use new TNRS.ScrubbedTaxon directly instead of the scrubbed taxondeterminations added to the normalized DB
- 07:20 PM Revision 7833: inputs/.TNRS/schema.sql: MatchedTaxon: Renamed matchedTaxonomicStatus to preferred name taxonomicStatus
- 07:19 PM Revision 7832: mappings/VegCore.htm: Regenerated from wiki. Taxon: Moved scrubbing-related terms to MatchedTaxon.
- 07:16 PM Revision 7831: inputs/.TNRS/schema.sql: Added matched* prefix where needed
- 07:02 PM Revision 7830: inputs/.TNRS/schema.sql: MatchedTaxon: Added missing Name_submitted column
- 06:59 PM Revision 7829: inputs/.TNRS/schema.sql: MatchedTaxon: Name_matched: Fixed mapping to matchedTaxonName
- 06:56 PM Revision 7828: inputs/.TNRS/schema.sql: MatchedTaxon: Fixed bug where can't map Source to source because it refers just to the source of the matched name, rather than of the record (which would be TNRS itself)
- 06:55 PM Revision 7827: inputs/.TNRS/schema.sql: tnrs_populate_derived_fields(): Use new concat_delim()
- 06:43 PM Revision 7826: schemas/functions.sql: _join*(): Use new concat_delim()
- 06:41 PM Revision 7825: schemas/functions.sql: Added concat_delim() (also in public, but this copy is for use by the functions schema)
- 06:37 PM Revision 7824: inputs/.TNRS/schema.sql: Removed no longer used tnrs+accepted. Use ScrubbedTaxon instead.
- 06:22 PM Revision 7823: inputs/.TNRS/schema.sql: Added MatchedTaxon, AcceptedTaxon, ScrubbedTaxon views, which rename the columns to VegCore names
- 05:17 PM Revision 7822: Removed inputs/GBIF/_src/GBIFPortalDB-2012-12-11.dump*, which has been replaced by GBIFPortalDB-2013-02-20.dump
- 05:14 PM Revision 7821: mappings/VegCore.htm: Regenerated from wiki. Renamed MatchedTaxonDetermination/AcceptedTaxonDetermination to MatchedTaxon/AcceptedTaxon because they relate to a taxon *name* rather than to an application of that name to a TaxonOccurrence
- 02:43 PM Revision 7820: schemas/functions.sql: functions._map(): Made function STRICT because it always returns NULL if either argument is NULL
- 02:39 PM Revision 7819: inputs/UNCC/Specimen/map.csv: campus: Mapped to cultivated, interpreting non-NULL values as true
- 02:29 PM Revision 7818: inputs/UNCC/Specimen/map.csv: campus: Removed mapping to occurrenceRemarks because this is just a code, not a description. Added definition from Bob's validation comments.
- 02:19 PM Revision 7817: inputs/UNCC/Specimen/map.csv: accession: Removed comment that this is actually the catalogNumber, because they are now synonyms
- 01:56 PM Revision 7816: mappings/VegCore.htm: Regenerated from wiki. Split specimenIndexer into specimenStampingInstitution and specimenDonor (which are often the same).
- 12:25 PM Revision 7815: mappings/VegCore-VegBIEN.csv: Removed specimenIndexer->institutionCode mappings because the institutionCode should refer only to the specimenHolder
- 12:18 PM Revision 7814: Added inputs/GBIF/_src/GBIFPortalDB-2013-02-20.dump.gz (a new download they posted to the FTP site)
- 12:13 PM Revision 7813: schemas/vegbien.sql: analytical_specimen: Removed growthForm, threatened_bien at Brad's request (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#UNCC > Brad Boyle's comments > growthForm, threatened_bien)
- 11:24 AM Revision 7812: inputs/UNCC/Specimen/map.csv: Removed mappings to reproductiveCondition because we don't know what the single-letter codes mean
- 11:16 AM Revision 7811: inputs/UNCC/Specimen/map.csv: Fixed embedded line endings
- 11:05 AM Revision 7810: schemas/vegbien.sql: _locationnarrative_is_cultivated(): Fixed bug where need to use NULL instead of false (and bool_or() instead of OR) for a non-match, because the absence of a match doesn't mean it's not cultivated
- 03:02 AM Revision 7809: mappings/VegCore.htm: Regenerated from wiki. Editing: Changed ambiguous terms templates to list the name of the alternative itself in the alternatives list, instead of the ambiguous term + a source suffix. This avoids the need to choose a source suffix for each alternative of an ambiguous term, as the ambiguous term itself (without the suffix) can be listed as the synonym. Coordinates: Disambiguated verbatimCoordinateSystem.
- 02:30 AM Revision 7808: mappings/Makefile: VegCore.thesaurus.csv: `uniq`ify the map after applying initial translations, to support mappings that appear twice (once as the result of an alternative's synonym entry and again as the result of an ambiguous term's alternatives listing)
03/04/2013
03/01/2013
- 08:17 PM Revision 7806: mappings/VegCore.htm: Regenerated from wiki. Added specimenDescription.
- 08:00 PM Revision 7805: mappings/VegCore.htm: Regenerated from wiki. Split apart identificationQualifier and taxonFit. Split apart taxonConfidence and identificationVerificationStatus. Moved identificationQualifier to new QualifiedTaxonName table.
- 07:48 PM Revision 7804: README.TXT: Full database import: To view progress: Use tail -100 to show more of the log files, and not tail -f to avoid blocking when the user just wants to check the status
- 04:56 PM Revision 7803: inputs/BRIT/specimen_flat/map.csv: Only map Notes_Plant to occurrenceRemarks if there is a separate Locality_Description, in order to filter out Notes_Plant values that concatenate everything together (often including a herbarium name that would mess up the cultivated flag parsing)
- 04:49 PM Revision 7802: my2pg.data: Replace \0 (with the backslash) with 0 because \0 isn't allowed in UTF-8
- 03:53 PM Revision 7801: root Makefile: VegBIEN DB: mk_db: Added command to import arbitrary DB users from a config file
02/28/2013
- 03:31 PM Revision 7800: inputs/import.stats.xls: Updated import times
- 03:29 PM Revision 7799: inputs/TEX/Specimen2/map.csv: _join() PLANT DATA and MISC NOTES to form occurrenceRemarks instead of _alt()ing them
- 03:27 PM Revision 7798: inputs/TEX/Specimen2/test.xml.ref: Accepted test
- 02:58 PM Revision 7797: inputs/BRIT/_MySQL/MySQL.*.sql.make: Include all tables, not just specimen_flat
- 02:57 PM Revision 7796: my2pg: Replace tinytext, mediumtext with text
- 11:48 AM Revision 7795: Added inputs/GBIF/_src/_README.TXT with Brad's GBIF filtering rules
- 11:30 AM Revision 7794: inputs/FIA/TREE/postprocess.sql: Use :table instead of hardcoding the table name
- 11:26 AM Revision 7793: inputs/FIA/*/postprocess.sql: UNIQUE constraint: Added UNITCD because although it may not be needed to scope PLOT, it is present in all the core tables and thus must be part of the joins' USING columns
- 10:58 AM Revision 7792: inputs/FIA/*/postprocess.sql for core tables: Added unique constraint on the datasource's primary key fields
- 02:38 AM Revision 7791: Added inputs/CTFS/AggregateObservation/ from BIEN2 data
- 02:16 AM Revision 7790: inputs/CTFS/: Switched global _no_import to table-specific _no_imports to allow adding new tables that *are* imported
02/27/2013
- 09:54 PM Revision 7789: Added schemas/TAPIR/SpeciesLink.tapir_request.txt symlink
- 09:53 PM Revision 7788: Added inputs/SpeciesLink/_src/tapir_request.txt
- 09:52 PM Revision 7787: Added schemas/TAPIR/
- 09:48 PM Revision 7786: Added planning/use_cases/rare_species.png
- 09:47 PM Revision 7785: Added planning/goals/BIEN deliverables.png
- 09:31 PM Revision 7784: Added planning/resources/iPlant_Overview_BIEN_2011.pdf.url
- 09:29 PM Revision 7783: planning/goals/Enquist_BIEN_Overview_2011.pptx: Replaced with .url file. Note that the Plone site <http://groups.nceas.ucsb.edu/bien/meetings> is not searchable by document filename.
- 09:26 PM Revision 7782: Added planning/workflow/Boyle_BIEN_data_quality.pdf.url
- 09:21 PM Revision 7781: Added planning/goals/BIEN_Science_2011.pptx.url, BIEN-Tech-Oct2011.ppt.url, Enquist_BIEN_Overview_2011.pptx
- 09:00 PM Revision 7780: Added schemas/VegX/run.py
- 08:53 PM Revision 7779: Added schemas/VegBIEN/growth_forms/Barbara_Dobrin.parsing.scripts/
- 08:35 PM Revision 7778: Added schemas/VegX/Veg-X_paper_in_press_Applied_Vegetation_Science.pdf.url
- 08:25 PM Revision 7777: Added schemas/VegX/JVS-VegX.pdf.url
- 08:22 PM Revision 7776: Added schemas/VegBank/VegBank_Data_Model.with_Collections_intro.ppt
- 08:13 PM Revision 7775: Added planning/goals/BIEN_White_Paper.pdf.url
- 08:11 PM Revision 7774: Added planning/meetings/2010-12-08.working_group/BIEN3-plan.docx
- 08:04 PM Revision 7773: Added schemas/VegBIEN/planning/taxonomy/On_the_Use_of_Taxonomic_Concepts_in_Support_of_Biodiversity_Research_and_Taxonomy.pdf.url
- 07:59 PM Revision 7772: Added schemas/BIEN2/ERD/
- 07:54 PM Revision 7771: Added schemas/BIEN2/bien2_core_schema.png
- 07:54 PM Revision 7770: Added schemas/BIEN2/mappings/BIEN2.viewFullOccurrence-DwC.xls
- 07:51 PM Revision 7769: Added schemas/VegBank/mappings/VegBank.observation-VegX.plotObservation.xls
- 07:49 PM Revision 7768: schemas/vegbien.ERD.mwb: Fixed table positions due to plantobservation field addition
- 07:35 PM Revision 7767: Added schemas/DiGIR/gbif-occurrencestore.digir.client.url
- 07:33 PM Revision 7766: Added schemas/DiGIR/gbif-crawler.digir.*.url
- 07:27 PM Revision 7765: inputs/.geoscrub/import_order.txt: Added Source
- 07:09 PM Revision 7764: Added schemas/VegX/
- 07:00 PM Revision 7763: Added schemas/VegBIEN/taxonomy/family_higher_plant_group.sql
- 06:57 PM Revision 7762: Added planning/use_cases/Trait_BIEN_data_use_case.docx
- 06:56 PM Revision 7761: Added planning/workflow/2010.working_group.white_board/
- 06:54 PM Revision 7760: Added planning/milestones/_archive/BIEN3 Milestones and Development Timeline_MLN2.*
- 06:51 PM Revision 7759: Added planning/workflow/BIEN-modArch-Dec2010 NS-SBD 1.4.ppt
- 06:50 PM Revision 7758: Added planning/milestones/_archive/BIEN3_milestones.2011-12-13.doc
- 06:48 PM Revision 7757: Added planning/milestones/BIEN Milestone – feedback.docx
- 06:46 PM Revision 7756: Added schemas/VegBIEN/planning/taxonomy/Nomenclature_excerpt.ppt
- 06:44 PM Revision 7755: Added planning/use_cases/
- 06:42 PM Revision 7754: Added planning/meetings/2012-11-26~30.working_group/
- 06:41 PM Revision 7753: Added schemas/BIEN2/Guide_to_the_BIEN2_database.pdf
- 06:39 PM Revision 7752: Added planning/meetings/2011-10-24~28.working_group/
- 06:36 PM Revision 7751: Added schemas/VegBIEN/planning/BIEN_OctWG-Whtbrd*.jpg
- 06:32 PM Revision 7750: Added schemas/BIEN2/
- 06:29 PM Revision 7749: Added schemas/VegBIEN/
- 06:20 PM Revision 7748: Moved schemas/vegbank.* to schemas/VegBank/
- 06:15 PM Revision 7747: Added planning/milestones/BIEN3 - Progress since the 2011 working group.docx
- 06:13 PM Revision 7746: planning/meetings/: Added Martha's conference call notes
- 06:06 PM Revision 7745: Moved planning/milestones.doc to planning/milestones/
- 06:04 PM Revision 7744: Moved planning/timeline.* to timeline/
- 06:01 PM Revision 7743: Renamed to_do/ to planning/
- 05:53 PM Revision 7742: Added schemas/VegCore/
- 05:53 PM Revision 7741: Added schemas/DwC/
- 05:35 PM Revision 7740: Added schemas/BIEN_logo.png from the bien.nceas.ucsb.edu website
- 05:29 PM Revision 7739: Renamed schemas/BIEN_logo.png to BIEN_logo.small.png
- 05:10 PM Revision 7738: Added inputs/SALVIAS/_archive/salvias_bien_19nov2009.tar.gz.url, .md5
- 04:57 PM Revision 7737: Added inputs/REMIB/_archive/remib_raw.0.header.specimens.txt
- 04:53 PM Revision 7736: Added inputs/CTFS/_src/ctfs_extract.tab.url, .md5
- 04:48 PM Revision 7735: Added inputs/NVS/_src/NVS_VegX.XSLT, _src/VegX/
- 04:43 PM Revision 7734: Added inputs/NVS/_src/_README.TXT
- 04:41 PM Revision 7733: Added inputs/TurboVeg/_src/DBASEDIC_rkp2011*.xlsx
- 04:40 PM Revision 7732: Added inputs/TurboVeg/_src/_README.TXT
- 03:45 PM Revision 7731: inputs/import.stats.xls: Updated import times
- 03:36 PM Revision 7730: README.TXT: Full database import: Don't run backups/fix_perms with sudo because owners are not rsynced to jupiter, so fixing them first is unnecessary. (It's not necessary to change the file owner to bien at any other time, either, because commands are not run as the bien user. It's in fact better to leave the file owner as yourself, to allow rsync to set the modification times.)
- 03:24 PM Revision 7729: README.TXT: Full database import: Added steps to set $version in all vegbiendev terminals
- 03:00 PM Revision 7728: lib/common.Makefile: rsync: $(rsync): Also exclude .lk* lock files
- 02:57 PM Revision 7727: README.TXT: Full database import: Updated log file sync steps for syncing via jupiter
- 02:56 PM Revision 7726: inputs/BRIT/specimen_flat/test.xml.ref: Updated inserted row count
02/26/2013
- 08:27 PM Revision 7725: schemas/py_functions.sql: Added _date(year integer, month integer, day integer)
- 08:08 PM Revision 7724: inputs/BRIT/specimen_flat/postprocess.sql: Added primary key
- 07:40 PM Revision 7723: schemas/functions.sql: Added _dms_to_dd() that takes text arguments and casts them to the appropriate type
- 07:11 PM Revision 7722: inputs/HVAA/Specimen/map.csv: Remapped fieldNotes to UNUSED. This also fixes a bug where fieldNotes was colliding with other occurrenceRemarks inputs because it was missing a filter.
- 06:46 PM Revision 7721: schemas/vegbien.sql: analytical_specimen/analytical_plot: Added occurrenceRemarks
- 06:32 PM Revision 7720: 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
- 06:30 PM Revision 7719: inputs/REMIB/Specimen/map.csv: Map NULL-equivalent text fields (country, state, etc.) to NULL
- 06:23 PM Revision 7718: inputs/REMIB/Specimen/map.csv: Map NULL-equivalent lat/long to NULL
- 05:59 PM Revision 7717: inputs/SpeciesLink/Specimen/map.csv: dwc_dwcore_Remarks: Remapped to occurrenceRemarks (it had been incorrectly automapped to taxonRemarks). Combined occurrenceRemarks inputs using /_alt.
- 05:47 PM Revision 7716: mappings/VegCore.htm: Regenerated from wiki. Remapped organismNotes to be a synonym of occurrenceRemarks, since notes on an organism are more generally notes on an occurrence.
- 05:28 PM Revision 7715: inputs/HVAA/Specimen/map.csv: Remapped dynamicProperties to occurrenceRemarks because it contains occurrenceRemarks data
- 05:23 PM Revision 7714: schemas/vegbien.sql: analytical_stem_view: Added occurrenceRemarks
- 05:19 PM Revision 7713: mappings/VegCore-VegBIEN.csv: Mapped occurrenceRemarks
- 04:53 PM Revision 7712: 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>)
- 04:53 PM Revision 7711: mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions
- 04:52 PM Revision 7710: mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions
- 04:44 PM Revision 7709: inputs/FIA/_src/_README.TXT: Added e-mail from Brad Boyle on 2013-2-8
- 04:42 PM Revision 7708: inputs/FIA/_src/: Added attachments from Brad's e-mail on 2013-2-8
- 04:37 PM Revision 7707: xml_func.py: Removed no longer used _range(). Use SQL functions._range() instead.
- 04:34 PM Revision 7706: schemas/functions.sql: Added _range()
- 04:30 PM Revision 7705: xml_func.py: Removed no longer used _avg(). Use SQL functions._avg() instead.
- 04:29 PM Revision 7704: schemas/functions.sql: Added _avg()
- 04:27 PM Revision 7703: mappings/VegCore-VegBIEN.csv: _avg(): Use numeric param names to work with SQL functions
- 04:15 PM Revision 7702: 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"
- 04:05 PM Revision 7701: inputs/MO/Specimen/postprocess.sql: Use :table instead of hardcoding "MO"."Specimen"
- 04:04 PM Revision 7700: inputs/MO/Specimen/postprocess.sql: Also remove frameshifted rows where InstitutionCode is NULL
- 03:44 PM Revision 7699: inputs/UNCC/Specimen/map.csv: herbarium->specimenIndexer: Replace UNCCD (UNCC database?) with UNCC
- 03:27 PM Revision 7698: schemas/functions.sql: functions._dms_to_dd(): Added support for DMS values without separators
- 03:09 PM Revision 7697: 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)
- 03:04 PM Revision 7696: Mapped inputs/BRIT/
- 02:36 PM Revision 7695: my2pg: Remove (0) after char
- 02:35 PM Revision 7694: my2pg: Remove any (#) after bytea
- 02:33 PM Revision 7693: my2pg: Translate binary to bytea
- 02:30 PM Revision 7692: 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)
- 02:28 PM Revision 7691: inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where needs to be set to just localhost and *--user* to bien instead
- 02:27 PM Revision 7690: 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.
- 02:25 PM Revision 7689: lib/MySQL.*.sql.make: Added --user option to demonstrate how to set the DB user vs. the ssh user
- 02:19 PM Revision 7688: inputs/BRIT/_MySQL/MySQL.*.sql.make: Fixed bug where $server needs to be set to bien@localhost
- 02:18 PM Revision 7687: 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.
- 02:15 PM Revision 7686: inputs/BRIT/: Added _MySQL/MySQL.*.sql.make
- 02:08 PM Revision 7685: README.TXT: Datasource setup: MySQL inputs: .sql exports: Run mysql_bien in the background
- 02:03 PM Revision 7684: 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.
- 01:58 PM Revision 7683: README.TXT: Datasource setup: Update vegbiendev: Updated steps for syncing via jupiter
- 01:56 PM Revision 7682: Added inputs/BRIT/ (not yet translated to PostgreSQL)
- 01:35 PM Revision 7681: mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_DMS to coordinates.latitude_deg using new _dms_to_dd(text)
- 01:34 PM Revision 7680: mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_DMS to coordinates.latitude_deg using new _dms_to_dd(text)
- 01:29 PM Revision 7679: schemas/functions.sql: Added _dms_to_dd(text)
- 01:28 PM Revision 7678: schemas/functions.sql: _dms_to_dd(): Fixed bug where need to use 1 as the multiplier when dir is NULL
- 01:19 PM Revision 7677: 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
- 12:58 PM Revision 7676: 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
- 12:57 PM Revision 7675: 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)
- 12:30 PM Revision 7674: schemas/functions.sql: _dms_to_dd(): Added dir param to specify compass dir suffix, in order to calculate the sign correctly
- 11:05 AM Revision 7673: Moved compass_dir from schemas/vegbien.sql to schemas/functions.sql so it can be used by _dms_to_dd()
- 10:56 AM Revision 7672: Moved _dms_to_dd() from schemas/vegbien.sql to schemas/functions.sql so it can use functions schema functions
- 10:51 AM Revision 7671: schemas/vegbien.sql: Added compass_dir enum
- 10:42 AM Revision 7670: 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
- 10:40 AM Revision 7669: 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
- 10:39 AM Revision 7668: mappings/VegCore-VegBIEN.csv: latitude/longitude_deg,min,sec: Also mapped to the geoscrub coordinates entry
- 10:34 AM Revision 7667: mappings/VegCore-VegBIEN.csv: latitude/longitude_sec: Fixed name, which had been incorrectly automapped to verbatim*
- 10:31 AM Revision 7666: 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.
- 10:22 AM Revision 7665: mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_deg,min,sec
- 10:15 AM Revision 7664: mappings/VegCore.htm: Regenerated from wiki. Merged coordinateUncertainty and coordinatePrecision, since datasources often use these interchangeably (the only difference is the DwC-recommended units).
- 10:08 AM Revision 7663: 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).
- 09:58 AM Revision 7662: inputs/SpeciesLink/Specimen/map.csv: conceptual_darwin_2003_1_0_CoordinatePrecision: Remapped to coordinateUncertaintyInMeters, assuming units based on the range and precision of values
- 09:53 AM Revision 7661: inputs/HVAA/Specimen/map.csv: Remapped coordinatePrecision to UNUSED
- 09:50 AM Revision 7660: inputs/ARIZ/omoccurrences/map.csv: Remapped coordinatePrecision to UNUSED
- 09:05 AM Revision 7659: schemas/vegbien.sql: Added _dms_to_dd()
- 08:49 AM Revision 7658: inputs/bien2_traits/TraitObservation/map.csv: Remapped Source to sourceType
- 08:43 AM Revision 7657: Added inputs/TEX/
- 08:42 AM Revision 7656: units.py: convert(): Support ranges
- 08:35 AM Revision 7655: Moved parse_range() from xml_func.py to units.py
- 08:02 AM Revision 7654: units.py: conversions: Added ft->m conversion
- 07:12 AM Revision 7653: src_map: Reopen stdin (/dev/stdin) in universal newlines mode to support files with \r as the line ending
- 06:51 AM Revision 7652: csv2db: Open input stream in universal newlines mode to support files with \r as the line ending
02/22/2013
- 11:15 PM Revision 7651: 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).
- 11:09 PM Revision 7650: input.Makefile: $(exts): Added .tab
- 10:29 PM Revision 7649: 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.
- 09:29 PM Revision 7648: 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.
- 08:47 PM Revision 7647: 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.
- 08:17 PM Revision 7646: 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).
- 08:00 PM Revision 7645: inputs/NY/Ecatalog_all/test.xml.ref: Updated inserted row count
02/21/2013
- 05:13 PM Revision 7644: schemas/vegbien.sql: analytical_stem_view: scientificName_verbatim: Use the taxonname (which omits the family and author) instead when available, at Brad's request
- 04:02 PM Revision 7643: schemas/vegbien.sql: Disambiguated taxonlabel.taxonomicname, taxonverbatim.taxonomicname, and taxonverbatim.taxonname
- 03:14 PM Revision 7642: 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
- 02:05 PM Revision 7641: to_do/timeline.2013.xls: Obtain and load any additional new data: Extended beyond April because it's ongoing
- 02:02 PM Revision 7640: 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
- 11:13 AM Revision 7639: to_do/timeline.2013.xls: Reload existing data in need of refresh: Added additional cell because this is still in progress
- 11:11 AM Revision 7638: 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.
02/20/2013
- 05:35 PM Revision 7637: Added inputs/FIA/REF_*/
- 05:33 PM Revision 7636: inputs/FIA/_src/Makefile: Table bundling: Also unpack FIADB_REFERENCE/
- 05:13 PM Revision 7635: Added inputs/FIA/_src/FIADB_REFERENCE.ZIP.md5, .url
- 04:11 PM Revision 7634: 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
- 02:00 PM Revision 7633: 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>
- 01:54 PM Revision 7632: 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>
- 01:53 PM Revision 7631: schemas/vegbien.sql: sync_analytical_stem_to_view(): Also drop and re-create new dependent views analytical_plot, analytical_specimen
- 01:20 PM Revision 7630: inputs/TEAM/V*/map.csv: Mapped plotArea_ha based on "1ha Plot Number" field name
- 01:12 PM Revision 7629: inputs/TEAM/V*/map.csv: Id: Remapped to individualObservationID
- 01:10 PM Revision 7628: mappings/VegCore.htm: Regenerated from wiki. verbatimScientificName, verbatimTaxonName have been merged into concatenatedScientificName, and ID has been disambiguated.
- 01:09 PM Revision 7627: inputs/*/*/map.csv: Automapped taxonConfidence
- 12:28 PM Revision 7626: 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
- 12:18 PM Revision 7625: inputs/SALVIAS/plotMetadata_/create.sql: Added primary key
- 11:42 AM Revision 7624: 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
- 11:32 AM Revision 7623: 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.
- 11:28 AM Revision 7622: inputs/NY/NY_DATA_20130212.~.utils.sql: Added pkey record type for use by Ecatalog_all's generated pkey
- 10:47 AM Revision 7621: 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.
- 09:20 AM Revision 7620: make_analytical_db: Wait for tnrs.make to acquire the tnrs.make lock if being run right after import
- 09:13 AM Revision 7619: schemas/vegbien.sql: analytical_stem_view: taxonName_matched: Fixed bug where need to use the matched_taxonverbatim instead of the datasource_taxonverbatim
- 08:58 AM Revision 7618: 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
- 08:56 AM Revision 7617: 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
- 07:59 AM Revision 7616: schemas/vegbien.sql: analytical_specimen: Removed speciesBinomialWithMorphospecies because it doesn't apply to specimens
- 07:58 AM Revision 7615: schemas/vegbien.sql: Added analytical_plot view
- 07:55 AM Revision 7614: schemas/vegbien.sql: Added analytical_specimen view
- 07:44 AM Revision 7613: 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>
- 07:40 AM Revision 7612: schemas/vegbien.ERD.mwb: Synced with schema
- 07:38 AM Revision 7611: schemas/vegbien.sql: Added reproductiveCondition
- 07:33 AM Revision 7610: mappings/VegCore-VegBIEN.csv: Mapped reproductiveCondition
- 07:28 AM Revision 7609: schemas/vegbien.sql: plantobservation: Added reproductivecondition
- 05:33 AM Revision 7608: mappings/VegCore.htm: Regenerated from wiki. matched*Fit_fraction has been renamed to matched*Confidence_fraction.
- 05:32 AM Revision 7607: inputs/.TNRS/public.unscrubbed_taxondetermination_view/map.csv: Updated for new mappings/VegCore.htm
- 05:10 AM Revision 7606: inputs/bien_web/observation/map.csv: Re-automapped taxonMorphospecies
- 05:08 AM Revision 7605: mappings/VegCore.htm: Regenerated from wiki. Data owner terms and taxon synonyms have been added, and morphospecies has been disambiguated.
- 04:51 AM Revision 7604: 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>
- 02:25 AM Revision 7603: schemas/vegbien.sql: analytical_stem_view: Use new concat_delim() instead of array_to_string() surrounded by NULLIF(..., '')
- 02:19 AM Revision 7602: schemas/vegbien.sql: Added concat_delim()
- 01:43 AM Revision 7601: schemas/vegbien.sql: analytical_stem_view: Removed deprecated taxonNameWithMorphospecies now that we have speciesBinomialWithMorphospecies
- 01:17 AM Revision 7600: schemas/vegbien.sql: analytical_stem_view: speciesBinomial: Added morphospecies suffix to create speciesBinomialWithMorphospecies
- 12:15 AM Revision 7599: inputs/import.stats.xls: Updated import times
- 12:06 AM Revision 7598: README.TXT: Full database import: Check that unscrubbed_taxondetermination_view returns no rows: Documented that this takes 90 s with LIMIT 1
02/19/2013
- 11:16 PM Revision 7597: schemas/vegbien.sql: _taxon_family_require_std(): Also allow non-aceae families accepted by TNRS
- 09:38 PM Revision 7596: Added inputs/SALVIAS/_archive/salvias_plots.*.sql.zip.md5
- 09:35 PM Revision 7595: Added inputs/VegBank/_archive/vegbank_for_bien.tar.gz.url
- 09:29 PM Revision 7594: Added inputs/U/UtrechtHerbarium.csv.tar.gz.url
- 09:28 PM Revision 7593: Added inputs/TEAM/_archive/ci-team_extract.tar.gz.url
- 09:27 PM Revision 7592: Added inputs/SpeciesLink/_archive/specieslink*.txt.gz.url
- 09:22 PM Revision 7591: Added inputs/REMIB/_archive/remib_raw.csv.tar.gz.url
- 09:19 PM Revision 7590: Added inputs/NY/NYSpecimenDataAmericas.csv.tar.gz.url
- 09:17 PM Revision 7589: Added inputs/NCU/_archive/NCU-NCSC_2010-02-12.csv.tar.gz.url
- 09:14 PM Revision 7588: Added inputs/MO/mo_digirexport.tar.gz.url
- 09:13 PM Revision 7587: Added inputs/Madidi/_archive/2010-1-2/madidi_plots_original_12jan2010.zip.url
- 09:11 PM Revision 7586: Added inputs/GBIF/gbif_extract.tar.gz.url
- 09:10 PM Revision 7585: Added inputs/FIA/fia_extract.tar.gz.url
- 09:08 PM Revision 7584: Added inputs/CVS/_archive/CVS-allTaxonOccurrences_2010-01-12.txt.tar.gz.url
- 09:04 PM Revision 7583: Added inputs/ARIZ/ARIZ_DiGIR_21012010.csv.tar.gz.url
- 08:55 PM Revision 7582: Added inputs/UNCC/Specimen/UNCC.csv.url, UNCC.csv.md5
- 08:45 PM Revision 7581: Added inputs/XAL/_src/digir.xml.gz.md5
- 08:39 PM Revision 7580: Added inputs/UNCC/_src/ with UNCC.csv.zip.md5
- 08:23 PM Revision 7579: Added inputs/SpeciesLink/_src
02/16/2013
- 08:24 AM Revision 7578: README.TXT: Datasource setup: MySQL inputs: .sql exports: Use new mysql_bien to connect to the MySQL DB created for the datasource
- 08:22 AM Revision 7577: Added mysql_bien, which runs a MySQL command on the local MySQL server
- 08:06 AM Revision 7576: Added inputs/GBIF/_src/GBIFPortalDB-2012-12-11.dump.md5 (md5sum of the expanded file)
- 08:02 AM Revision 7575: root Makefile: MySQL: mysql-Linux: Also install phpMyAdmin
- 08:01 AM Revision 7574: 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
- 07:57 AM Revision 7573: root Makefile: MySQL: *mysql_users: Also add bien_read user
- 07:49 AM Revision 7572: root Makefile: MySQL: Renamed *mysql_user to *mysql_users because there can be multiple users
- 06:51 AM Revision 7571: inputs/: Added .md5 files for all .zip, .gz
- 06:47 AM Revision 7570: Added inputs/HVAA/Specimen/Herbario_occur_1360871068.csv.url
- 06:39 AM Revision 7569: lib/common.Makefile: rsync: $(rsync*): Use --no-group because the file group is different depending on the machine
- 06:10 AM Revision 7568: input.Makefile: SVN: $(_svnFilesGlob): Also add .md5 files. This allows svn to track where unversioned files should be in the directory tree.
- 06:07 AM Revision 7567: input.Makefile: SVN: $(_svnFilesGlob): .url, .pdf, and README.TXT in the top-level dir: Fixed bug where had extra / after brace expr
- 06:00 AM Revision 7566: input.Makefile: SVN: $(_svnFilesGlob): Also add .url, .pdf, and README.TXT in the top-level dir
- 05:53 AM Revision 7565: input.Makefile: SVN: $(_svnFilesGlob): Add .url, .pdf, and README.TXT files in all subdirs, not just _src
- 05:25 AM Revision 7564: lib/common.Makefile: remote server: Use jupiter instead of vegbiendev, to ensure that all files get uploaded there rather than only to vegbiendev. This involves adding an extra database import step to download the uploaded files from jupiter onto vegbiendev.
- 02:50 AM Revision 7563: inputs/FIA/_src/Makefile: all: Extract zip files before running tables target, because it requires the created dirs
- 02:40 AM Revision 7562: schemas/vegbien.ERD.mwb: Fixed table sizes
- 01:17 AM Revision 7561: Removed no longer used fix_permissions. Use root fix_perms instead.
- 01:16 AM Revision 7560: Added root fix_perms
02/15/2013
- 11:58 PM Revision 7559: Moved Checksums from backups/Makefile to lib/common.Makefile so all dirs (including inputs/) can use md5sum testing
- 11:08 PM Revision 7558: lib/common.Makefile: $(remote): Made remote basepath configurable in $(remote_basepath)
- 11:04 PM Revision 7557: lib/common.Makefile: Renamed $(src_server) to $(remote_host) and $(src_user) to $(remote_user) for clarity
- 10:16 PM Revision 7556: inputs/GBIF/: Added refresh metadata
02/14/2013
- 11:49 AM Revision 7555: Added inputs/HVAA/
- 11:14 AM Revision 7554: Added inputs/ARIZ/_archive
- 11:13 AM Revision 7553: inputs/ARIZ/: Removed previous data now that it has been refreshed
- 11:08 AM Revision 7552: inputs/ARIZ/: Mapped refresh
- 09:48 AM Revision 7551: Added inputs/ARIZ/import_order.txt
- 09:22 AM Revision 7550: Added inputs/NY/_archive/
- 09:20 AM Revision 7549: inputs/NY/: Removed tables from previous extract
- 08:59 AM Revision 7548: inputs/NY/: Mapped refresh
- 08:58 AM Revision 7547: inputs/*/*/VegBIEN.csv: Regenerated from mappings/VegCore-VegBIEN.csv
- 08:52 AM Revision 7546: Added inputs/NY/import_order.txt
- 02:51 AM Revision 7545: inputs/ARIZ/: Added SQL export for refresh
- 02:33 AM Revision 7544: my2pg.data: Translate indefinite (zero) months which have a definite day. This is unusual, but does appear in some data such as the ARIZ DB.
- 02:28 AM Revision 7543: my2pg.data: Translate indefinite dates (dates with 0 as the month or day)
- 02:23 AM Revision 7542: my2pg: Use my2pg.data to perform data-only replacements, instead of duplicating them in both my2pg and my2pg.data
- 02:01 AM Revision 7541: my2pg: named UNIQUE KEYs: Comment out the name because PostgreSQL requires it to be globally unique, but MySQL only requires it to be unique within the table
- 01:53 AM Revision 7540: my2pg: Translate UNIQUE KEYs instead of removing them
- 01:49 AM Revision 7539: my2pg*: Removed KEYs: Comment out the definition rather than removing it
- 01:45 AM Revision 7538: my2pg*: Remove FOREIGN KEYs because MySQL does not dump tables in dependency order, which prevents PostgreSQL from creating tables whose fkeys refer to a later table
- 01:33 AM Revision 7537: my2pg*: Replacing invalid table elements to remove them: Use a dummy CHECK constraint instead of a boolean field to avoid adding fields to the table. The elements can't always simply be removed because sed can't remove the trailing comma of the previous element, and removing the following comma doesn't work for the last element in the table.
- 12:11 AM Revision 7536: my2pg*: Replace '0000-00-00 00:00:00' with '-infinity'
- 12:04 AM Revision 7535: my2pg: Replace datetime with timestamp
02/13/2013
- 11:59 PM Revision 7534: my2pg: Remove COLLATE field attribute
- 11:56 PM Revision 7533: lib/MySQL.*.sql.make: Documented that $server user/host are for ssh, not the DB
- 11:55 PM Revision 7532: lib/MySQL.*.sql.make: Documented that $server can also contain a username (which will be used by ssh)
- 11:51 PM Revision 7531: my2pg_export: Use the --quick option to facilitate exporting large tables (it avoids retrieving all rows before outputting any of them)
- 11:00 PM Revision 7530: README.TXT: Datasource setup: Added instructions for MS Access databases
- 10:43 PM Revision 7529: README.TXT: Datasource setup: MySQL inputs: Added instruction to skip the Add input data for each table section
- 10:40 PM Revision 7528: inputs/NY/: Added SQL export for refresh
02/12/2013
- 01:08 PM Revision 7527: 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.
- 12:15 PM Revision 7526: inputs/CVS/observation_/map.csv: baseSaturation: Resolved ambiguous term
- 12:09 PM Revision 7525: mappings/Makefile: VegCore.vocab.csv: Ignore leading ? when sorting so that ambiguous terms sort alphabetically with other terms. This prevents terms from moving from their previous location when they become ambiguous.
- 12:07 PM Revision 7524: Added sort_ci to sort a spreadsheet, ignoring leading punctuation
- 12:05 PM Revision 7523: mappings/VegCore.vocab.csv: Changed line endings to \r\n in preparation for having a Python script run on it (which changes the line endings)
- 11:47 AM Revision 7522: mappings/Makefile: VegCore.vocab.csv: Added back ambiguous terms, so that the vocabulary contains all terms defined by VegCore, regardless of whether they are ambiguous or unambiguous terms
- 11:44 AM Revision 7521: mappings/Makefile: VegCore.vocab.csv: Added back synonyms, so that the vocabulary contains all terms defined by VegCore, regardless of whether they are synonyms or primary terms. This also prevents VegCore.vocab.csv from losing entries when terms are renamed, which made it difficult to verify that no terms were lost when refactoring.
- 05:50 AM Revision 7520: inputs/MO/Specimen/postprocess.sql: Remove frameshifted rows by detecting InstitutionCodes without any letters
- 04:59 AM Revision 7519: inputs/ARIZ/Specimen/map.csv: CollectorNumber/FieldNumber: Use /_first to map these identical fields to the same location
- 04:54 AM Revision 7518: inputs/ARIZ/Specimen/map.csv: Fixed bug where the column names for InstitutionCode and CollectionCode were reversed in the source data
- 04:14 AM Revision 7517: inputs/*/Specimen/map.csv for Canadensys sources: Remapped institutionID to UNUSED
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