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
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
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)
web/vegpath/util.php: partition(): Fixed bug where strpos() returns false rather than -1 on no match
web/vegpath/util.php: partition(): Fixed bug where strpos() takes the search-for param first rather than second
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
web/vegpath/index.php: BIEN2: Fixed to use phpMyAdmin with correct URL instead of vegbiendev phpPgAdmin placeholder
web/vegpath/index.php: Added phpMyAdmin()
web/vegpath/.htaccess: mod_rewrite: RewriteBase: Changed to / now that VegPath is hosted at vegbiendev.nceas.ucsb.edu
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
web/vegpath/.htaccess: unknown paths: Removed no longer accurate VegRef from comment header
vegpath/.htaccess: DirectorySlash: Lowercased On for consistency with other boolean directives
Added web/vegpath.conf with Apache VirtualHost config
vegpath/index.php: VegBank(): Fixed bug where name had incorrectly been replaced with $name
vegpath/index.php: phpPgAdmin(): Factored out appending of "&subject="
vegpath/: Archived no longer used vegpath/index.htm
vegpath/index.*: IH: URL-encode ' in search URL to avoid needing to backslash-escape it
vegpath/index.php: IH: Fixed search URL to undo incorrect search-and-replace of + with .
vegpath/index.*: Changed "Supported URLs" to "Supported URL patterns" because the provided short URLs take parameters that are filled into the destination URL
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
vegpath/index.*: Changed tagline to emphasize that the shortened URLs are especially intended to be human-readable, e.g. for use as column names
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>)
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
web/VegRef/.htaccess: Turned off RewriteEngine temporarily because it was preventing the internal VegRef redirection from working
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.
inputs/NCU/Specimen/map.csv: cultivated: Map false (0) to NULL because cultivated can only be true or NULL, not false
inputs/CTFS/_src/_README.TXT: Added e-mails from Brad Boyle about issues with species aggregation methods
inputs/UNCC/Specimen/map.csv: Populated specimenHolderInstitutions
Added planning/goals/BIEN3_derived_data_products.docx.url
Added planning/goals/BIEN3_derived_data_products.docx
inputs/ARIZ/omoccurrences/map.csv: cultivationStatus: Map to NULL if it's false, because cultivated can only be true or NULL
schemas/vegbien.sql: analytical_stem_view: Merged taxonName_verbatim and scientificNameAuthorship_verbatim into scientificName_verbatim
schemas/vegbien.sql: analytical_plot: Added specimens fields at the end, for use by plots data that also tracks specimens (e.g. Madidi, SALVIAS)
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
mappings/VegCore.htm: Regenerated from wiki. Renamed specimenDonor to specimenDonorInstitution to clarify that this is an institution, not a collector.
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
make_analytical_db: Support the $log flag, which toggles output to the terminal or a log file
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!
import_times: When there are no matching logs, exit with status 0 instead of 1 because this is a normal condition
import_times: Fixed bug where sed would wait for user input from stdin when there were no matching logs
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
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
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
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.)
inputs/ACAD/Specimen/map.csv: institutionCode: Replace "Acadia University" with the IH code ACAD
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
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)
schemas/vegbien.sql: tnrs_input_name: accepted_name subquery: Renamed to the VegCore table name AcceptedTaxon
schemas/vegbien.sql: tnrs_input_name: taxonlabel.taxonomicname subquery: Use new MatchedTaxon view, which use VegCore column names where possible
schemas/vegbien.sql: tnrs_input_name: accepted_name subquery: Use new MatchedTaxon, AcceptedTaxon views, which use VegCore column names where possible
README.TXT: Full database import: Added instructions to run TNRS and view the TNRS log
README.TXT: Full database import: Removed no longer necessary command to scrub unscrubbed taxondeterminations
*.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
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
schemas/vegbien.sql: Removed no longer needed unscrubbed_taxondetermination_view. Use taxonlabel joined to ScrubbedTaxon instead.
inputs/.TNRS/schema.sql: ScrubbedTaxon: Include only matches with a match score of at least 0.8 (score_ok())
inputs/.TNRS/schema.sql: Added back score_ok() and tnrs.tnrs_score_ok index
*.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)
inputs/U/Specimen/map.csv: Populated specimenHolderInstitutions
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.
inputs/SpeciesLink/Specimen/map.csv: Fixed embedded line endings
inputs/NY/Ecatalog_all/map.csv: PlantFungDescription->occurrenceRemarks: Removed "plant fungus" label because this field actually contains the specimenDescription
inputs/.TNRS/import_order.txt: Removed public.unscrubbed_taxondetermination_view
inputs/.TNRS/: Moved no longer needed public.unscrubbed_taxondetermination_view/ to _archive/
root Makefile: Datasources: scrub: Removed no longer needed scrub-remake, which has been replaced by direct use of TNRS.ScrubbedTaxon
schemas/vegbien.sql: analytical_stem_view: taxondetermination: Fixed bug where need to include only the is_datasource_current taxondetermination
schemas/vegbien.sql: analytical_stem_view: Use new TNRS.ScrubbedTaxon directly instead of the scrubbed taxondeterminations added to the normalized DB
inputs/.TNRS/schema.sql: MatchedTaxon: Renamed matchedTaxonomicStatus to preferred name taxonomicStatus
mappings/VegCore.htm: Regenerated from wiki. Taxon: Moved scrubbing-related terms to MatchedTaxon.
inputs/.TNRS/schema.sql: Added matched* prefix where needed
inputs/.TNRS/schema.sql: MatchedTaxon: Added missing Name_submitted column
inputs/.TNRS/schema.sql: MatchedTaxon: Name_matched: Fixed mapping to matchedTaxonName
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)
inputs/.TNRS/schema.sql: tnrs_populate_derived_fields(): Use new concat_delim()
schemas/functions.sql: _join*(): Use new concat_delim()
schemas/functions.sql: Added concat_delim() (also in public, but this copy is for use by the functions schema)
inputs/.TNRS/schema.sql: Removed no longer used tnrs+accepted. Use ScrubbedTaxon instead.
inputs/.TNRS/schema.sql: Added MatchedTaxon, AcceptedTaxon, ScrubbedTaxon views, which rename the columns to VegCore names
Removed inputs/GBIF/_src/GBIFPortalDB-2012-12-11.dump*, which has been replaced by GBIFPortalDB-2013-02-20.dump
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
schemas/functions.sql: functions._map(): Made function STRICT because it always returns NULL if either argument is NULL
inputs/UNCC/Specimen/map.csv: campus: Mapped to cultivated, interpreting non-NULL values as true
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.
inputs/UNCC/Specimen/map.csv: accession: Removed comment that this is actually the catalogNumber, because they are now synonyms
mappings/VegCore.htm: Regenerated from wiki. Split specimenIndexer into specimenStampingInstitution and specimenDonor (which are often the same).
mappings/VegCore-VegBIEN.csv: Removed specimenIndexer->institutionCode mappings because the institutionCode should refer only to the specimenHolder
Added inputs/GBIF/_src/GBIFPortalDB-2013-02-20.dump.gz (a new download they posted to the FTP site)
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)
inputs/UNCC/Specimen/map.csv: Removed mappings to reproductiveCondition because we don't know what the single-letter codes mean
inputs/UNCC/Specimen/map.csv: Fixed embedded line endings
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
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.
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)
schemas/vegbien.sql: analytical_stem_view: Added temperature_C, precipitation_m for possible use in John Wiens' plant climatic niche evolution project ("how fast is the rate of climatic niche evolution among species compared to projected changes in climate over the next 100 years? How do these rates compare for temperature and precipitation variables?")
mappings/VegCore.htm: Regenerated from wiki. Added specimenDescription.
mappings/VegCore.htm: Regenerated from wiki. Split apart identificationQualifier and taxonFit. Split apart taxonConfidence and identificationVerificationStatus. Moved identificationQualifier to new QualifiedTaxonName table.
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
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)
my2pg.data: Replace \0 (with the backslash) with 0 because \0 isn't allowed in UTF-8
root Makefile: VegBIEN DB: mk_db: Added command to import arbitrary DB users from a config file
