web/vegpath/index.php: SALVIAS: Factored out URL to $SALVIAS
web/vegpath/index.php: SALVIAS: Appended Plot_ to dest URL because both data dictionary sections start with this, so it doesn't need to be included in the VegPath
web/vegpath/index.php: XPath resources: Removed # at end of destination URL because the # is now part of the #/XPath suffix (and is added by the user)
web/vegpath/index.php: XPath resources: Added # before XPath because the XPath is actually a location within the resource, and thus resolvable by the client (or user) themselves, rather than part of the redirected URL (which only needs to forward to the XML schema file)
web/vegpath/index.php: Updated $alias to the newly-registered path.vg domain, which is shorter and more intuitive-looking than the previous value j.mp/vegpath (from bitly.com). Note that using a domain also allows redirects without JavaScript, which can be used by any web client (such as a Python script), not just a web browser.
web/vegpath/index.php: Renamed ref to ns to emphasize that the resources in this field are namespaces for the paths
web/vegpath/index.php: add_ref(): Renamed $suffix to $path_pat to distinguish it from the actual suffix string sent in the URL
web/vegpath/index.php: custom_separator(): Marked optional params as such
web/vegpath/index.php: Terms: IH-db: Factored out phpMyAdmin URL into $IH_db
web/vegpath/index.php: Terms: Added IH-db
web/vegpath/index.php: php*Admin(): Added support for a fixed table that doesn't need to be specified in the path
web/: Removed svn:executable permissions from non-executable files
web/vegpath/index.php: Data: Added Institutions subsection
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
web/vegpath/main.css: Added .indent
web/vegpath/index.php: People: Added Brad's VegCore ID terms spreadsheets
web/vegpath/index.php: Factored Redmine svn URLs out into $Redmine_svn
Added schemas/VegCore/Brad_Boyle/ with Brad's VegCore IDs terms spreadsheets
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
web/vegpath/index.php: URL fragment redirect: Fixed bug where need to use parse_mixed_path() instead of parse_dot_path() to support XPaths
web/vegpath/index.php: Terms: Added CTFS
web/vegpath/index.php: URL patterns header: Reworded comment to clarify that the elements that can be left out are in italics
web/vegpath/index.php: URL fragment redirect: Only perform fragment redirect if URL shortener requires it (as indicated by the $alias ending in #)
web/vegpath/index.php: nimoy nodes: Factored nimoy phpMyAdmin() calls out into nimoy_db() function
web/vegpath/index.php: nimoy nodes: Factored nimoy URL prefix out into $nimoy
web/vegpath/index.php: SALVIAS: Added subnodes for each SALVIAS database on nimoy
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
web/vegpath/index.php: BIEN2: Added subnodes for each BIEN2 database on nimoy
web/vegpath/index.php: Inlined VegBank() because it's only used once
web/vegpath/index.php: VegBank(): Use custom_separator()'s new $main_url param
web/vegpath/index.php: custom_separator(): Added $main_url param like in by_prefix(), for use when there is no path
web/vegpath/index.php: VegBank(): Use new custom_separator()
web/vegpath/index.php: Added custom_separator()
web/vegpath/index.php: Add # suffix to $alias instead of adding it in add_ref(), because not all aliases will use a # suffix
web/vegpath/util.php: Added array_non_empty(), join_non_empty()
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
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)
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
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.
web/vegpath/main.css: Added entries for h6
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
web/vegpath/util.php: Path: Made $tail default to ""
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())