schemas/VegCore/VegCore.ERD.mwb: split taxon_occurrence into taxon_occurrence and taxon_observation, because a taxon_*occurrence* is actually the thing on which a taxon_*observation* is made, not the observation itself. rearranged tables significantly to put observations next to the things they observe, and to make the ERD less wide so it will fit on a small screen without as much scaling (allowing a bigger font size when the ERD is shrunk to fit the screen).
schemas/VegCore/VegCore.ERD.mwb: added primary columns. changed VARCHAR columns to TEXT and also set default type in ERD so future columns won't need to be changed.
schemas/VegCore/VegCore.ERD.mwb: added primary columns, including catch-all hstores for custom columns. made stem inherit from individual and stem_observation from individual_observation because any stem can have individual-level traits and identifying info.
schemas/VegCore/VegCore.ERD.mwb: replaced trait table with traits hstore on taxon_occurrence, since the trait table is basically just a way of allowing the user to add arbitrary measurement columns to the taxon_occurrence. units can be indicated by storing a record with the quantity and units, converted to a string, and parsing it back out as a record upon retrieval.
schemas/VegCore/VegCore.ERD.mwb: renamed taxon_observation to taxon_presence for clarity and to distinguish it better from taxon_occurrence
schemas/VegCore/VegCore.ERD.mwb: taxon_determination: added identified_date and unique index on identifying columns
schemas/VegCore/VegCore.ERD.mwb: taxon_determination: added identified_by. rearranged taxon tables to visually differentiate between inheritance relationships (1:1) and directional HAS-A arrows
schemas/VegCore/VegCore.ERD.mwb: taxon tables: added catch-all hstores for custom columns
schemas/VegCore/VegCore.ERD.mwb: split taxon_concept into taxon_name (containing the components of a name) and taxon_concept (containing the taxon's formal specification and relationships to other taxon_concepts). this avoids requiring a taxon_concept entry for names that are not true taxon concepts. taxon_name: added taxon name/author-related components. TNRS taxonomic scrubbing steps: added dummy id column to avoid sync problems with empty tables.
schemas/VegCore/VegCore.ERD.mwb: taxon tables: added nonidentifying columns
schemas/VegCore/VegCore.ERD.mwb: regenerated exports
schemas/VegCore/VegCore.ERD.mwb: categories: updated box sizes
schemas/VegCore/VegCore.ERD.mwb: fixed lines
schemas/VegCore/VegCore.ERD.mwb: validatable_place: added unique index on identifying columns
schemas/VegCore/VegCore.ERD.mwb: made place_path and coordinates globally-scoped rather than per-datasource, so that there is only one geovalidation row for each combination of them rather than one per datasource place. added globally-scoped validatable_place table that stores combinations of place_path and coordinates, and made geovalidation extend it (since geovalidation provides optional fields and is 1:1 with it).
schemas/VegCore/VegCore.ERD.mwb: made geovalidation extend place_path instead of being pointed to by it, because it provides a set of optional fields a (geovalidated) place_path may have
schemas/VegCore/VegCore.ERD.mwb: made place_path extend place instead of place having a place_path, because place_path now provides an optional set of fields that a place may provide, rather than being a completely separate entity
schemas/VegCore/VegCore.ERD.mwb: renamed named_place to place_path since place now serves the purpose that named_place used to (i.e. representing geographical areas)
schemas/VegCore/VegCore.ERD.mwb: removed invisible U+FEFF Unicode character
schemas/VegCore/VegCore.ERD.mwb: renamed location to place because any place can be a location, not just a plot or point (e.g. Barro Colorado Island is a CTFS "plot" but definitely much larger than the typical plot)
schemas/VegCore/VegCore.ERD.mwb: labeled TNRS taxonomic scrubbing steps
schemas/VegCore/VegCore.ERD.mwb: geovalidation: put named_place before coordinates so they would be in path order (one named_place can have many coordinates in it)
schemas/VegCore/VegCore.ERD.mwb: taxon_assertion: added fkey to taxon_concept/taxon_path to store any parsed taxonomic fields provided by the data provider
schemas/VegCore/VegCore.ERD.mwb: linked taxon_concept directly to taxon_string rather than to child table taxon_name, because it creates unnecessary confusion to have two tables storing taxonomic strings. a taxon_string is anything that can be used as input to TNRS, and may or may not include a cf_aff.
schemas/VegCore/VegCore.ERD.mwb: link each taxon_string to a parsed_taxon_assertion. removed verbatim_taxon_assertion because that function is now performed by taxon_string.
schemas/VegCore/VegCore.ERD.mwb: added taxon_name, which is used by taxon_concept
schemas/VegCore/VegCore.ERD.mwb: added taxon_string, which is used by taxon_assertion
schemas/VegCore/VegCore.ERD.mwb: added unique indexes on identifying columns where possible. unique indexes differ from primary keys in that they are generally on multiple columns, while pkeys are on a text field which is the concatenation of the identifying columns.
schemas/VegCore/VegCore.ERD.mwb: hierarchical tables: made parent pointer NOT NULL so that it can be an identifying column. this requires the root(s) of the hierarchy to be indicated with a self-referential parent pointer rather than a NULL value. this also allows materializing parent elements to arbitrary levels without worrying about hitting the root, because the root's ancestors will simlpy be itself for as many levels as are needed (i.e. materializing several levels up the tree is guaranteed to produce a non-NULL entry for all levels).
schemas/VegCore/VegCore.ERD.mwb: taxon_assertion: removed fkey to taxon_concept because only parsed_taxon_assertions have a corresponding taxon_concept
schemas/VegCore/VegCore.ERD.mwb: fixed table positions
schemas/VegCore/VegCore.ERD.mwb: lined up tables
schemas/VegCore/VegCore.ERD.mwb: parsed_taxon_assertion.matched_taxon: changed it to be an fkey to taxon_path, because the parsing must also populate the denormalized path fields in addition to defining a taxon_concept with the concatenated scientific name
schemas/VegCore/VegCore.ERD.mwb: fixed inheritance lines
schemas/VegCore/VegCore.ERD.mwb: added taxon_path
schemas/VegCore/VegCore.ERD.mwb: geological_context: made it the same color as community because it is a type of community for the geological aspects of the location
schemas/VegCore/VegCore.ERD.mwb: renamed fkeys to match renamed tables
schemas/VegCore/VegCore.ERD.mwb: merged synonym_taxon, accepted_taxon into taxon_concept because any taxon_concept can have an accepted taxon which indicates the canonical name for that taxon, not just TNRS match results
schemas/VegCore/VegCore.ERD.mwb: merged taxon_concept and taxon, because every taxon is according to someone (whether that's Weakley, Tropicos, or the person identifying a taxon_occurrence). note that the according_to is usually different from the source (which is the datasource that owns the record), but if there is no specific according_to, the according_to is the datasource itself.
schemas/VegCore/VegCore.ERD.mwb: lightened table colors so dark text is easier to see against them. used colors from VegBank ERD (http://vegpath.org/fs/schemas/VegBank/vegbank.ERD.pdf) where possible, to have a familiar look-and-feel for those who have seen the VegBank ERD.
schemas/VegCore/VegCore.ERD.mwb: categories: added stratum
schemas/VegCore/VegCore.ERD.mwb: categories: put categories on the same halves of the legend as they are in the ERD
schemas/VegCore/VegCore.ERD.mwb: added stratum, plot_stratum
schemas/VegCore/VegCore.ERD.mwb: added plot subclass of location
schemas/VegCore/VegCore.ERD.mwb: removed redundant "DEFAULT NULL" clauses on nullable fields
schemas/VegCore/VegCore.ERD.mwb: renamed taxon_occurrence.*_taxon_determination to taxon_occurrence.*_determination because the column name does not need to be globally unique, and can therefore be shorter while still being unambiguous within the table
schemas/VegCore/VegCore.ERD.mwb: changed all fkeys to CASCADE to support cascading deletes. this allows datasources to be reloaded, because the corresponding source row can be deleted, and the delete will cascade to every record that's part of that datasource.
schemas/VegCore/VegCore.ERD.mwb: changed globally unique column names to locally unique column names, now that the SQL dotpath algorithm (http://vegpath.org/wiki/SQL_dotpaths#Algorithm) can be used to generate globally unique column names automatically according to the fkeys. in particular, this means that the pkeys have all been renamed to "id".
schemas/VegCore/VegCore.my.sql: removed default_schema qualifier from names because all objects are in the same schema
schemas/VegCore/VegCore.my.sql: regenerated from ERD
bugfix: schemas/VegCore/VegCore.ERD.mwb: fixed pkey names to match table names
schemas/VegCore/VegCore.ERD.mwb: renamed matched_taxon table to synonym_taxon because it can be used to store any taxon which has a corresponding accepted_taxon, not just the match results from TNRS
schemas/VegCore/VegCore.ERD.mwb: renamed qualified_taxon tables to *taxon_assertion because they are not just a taxon name plus an optional cf/aff qualifier, but an actual operator/value pair that is the right-hand side of a comparison with a taxon or taxon_occurrence
bugfix: schemas/VegCore/VegCore.ERD.mwb: qualified_taxon subclasses: changed HAS-A arrows to point in the other direction, because the many:1 relationship in fact narrows towards the accepted_taxon. the arrows used to be in the opposite direction because of the way the TNRS results are attached incrementally.
README.TXT: Maintenance: to backup the Ubuntu VM: removed invisible U+FEFF Unicode character
README.TXT: added steps to backup the Ubuntu VM
bugfix: schemas/.htaccess: corrected $innermost_dir
added .htaccess files for inputs/, schemas/ because these reside outside the DOCUMENT_ROOT, and therefore need an explicit RewriteBase directive so that RewriteRules in their subdirs can construct self-referential URLs. this ensures that the input URLs to RewriteRules are always URL paths instead of filesystem paths, which tend to mess up the redirects. (mod_rewrite is capable of doing filesystem-only redirects, but the associated RewriteRules require special care to ensure they match and reconstruct the filesystem path properly.) the presence of filesystem paths in RewriteRule inputs had been causing numerous bugs, especially in rules that use %{REQUEST_URI}, and the addition of the RewriteBases will hopefully avoid these types of bugs in the future. note that every path that resides outside the DOCUMENT_ROOT needs an explicit RewriteBase in its top-level .htaccess.
schemas/VegCore/VegCore.ERD.mwb: ensured that inheritance relationships are drawn as 1:1
web/**/.htaccess: appended query strings for external redirects: just use ? rather than ?& when an external redirect will be perfomed, because no dotpath parsing will be performed on the query string first (which would necessitate the & if the new query string looks like a dotpath)
schemas/VegCore/VegCore.ERD.png: Regenerated again because some tables were highlighted when it was exported, causing the highlighting to appear in the PNG
schemas/VegCore/VegCore.ERD.mwb: Regenerated exports
schemas/VegCore/VegCore.ERD.mwb: shortened embedded ERD URL using new abbreviations
web/**/.htaccess: RewriteRules: ensured flags are in alphabetical order
removed no longer needed web/dotpath.php. use web/.htaccess's parse-dotpath RewriteRule instead.
web/.htaccess: parse dotpath in query string: moved parsing from dotpath.php to RewriteRules. with the eventual addition of config env vars, this makes it possible for subdirs to configure their own dotpath parsing, rather than having all levels of the dotpath translated to a URL path. (for inner levels, it may el.g. be more appropriate to parse the dotpath as query params or pass it along to an external URL.) note that it takes only two lines of mod_rewrite (plus a workaround RewriteRule) to replace over a dozen lines of PHP code.
web/.htaccess: renamed REQUEST_URI_no_/ to REQUEST_URI_no_extra_/ to clarify that only an excess / is removed
web/.htaccess: moved set REQUEST_URI_no_/ under translate subdomain to path because it needs to be set right before being used to be accurate
web/.htaccess: setting REQUEST_URI_no_/: use one RewriteCond instead of two since the regexps can be combined
web/.htaccess: parse dotpath in query string: removed dotpath auto-detection code because this is now handled by a separate RewriteRule
web/.htaccess: auto-detect dotpath in query string (having a . before any = ) and mark it using a leading . . this is done as a separate step so that the dotpath is already explicitly marked as such when it's parsed.
web/dotpath.php: just match the QUERY_STRING directly, excluding &, instead of splitting apart the QUERY_STRING and then matching the dotpath portion. this allows the resulting regexp to be used directly in a .htaccess file.
web/.htaccess: prepend dir name if it's part of the filename: support MultiViews filenames without the extension, by using a lookahead request -F instead of a regular -f
schemas/VegCore/.htaccess: added RewriteBase to support relative redirects. this enables auto-prepending dir name if it's part of the filename, e.g. VegCore/ERD.pdf -> VegCore/VegCore.ERD.pdf).
web/.htaccess: prepend dir name if it's part of the filename (this works only if the dir supports relative redirects and sets %{ENV:innermost_dir})
schemas/VegCore/VegCore.ERD.mwb: made matched_taxon and accepted_taxon inherit from taxon instead of qualified_taxon because they don't contain the cf_aff (cf_aff.vegpath.org; aka identificationQualifier) that makes a taxon qualified
schemas/VegCore/VegCore.ERD.mwb: removed occurrence table, because it's really a synonym for taxon_occurrence ("specimen, observation, etc." <http://rs.tdwg.org/dwc/terms/#Occurrence>)
schemas/VegCore/VegCore.ERD.mwb: added labels for the left and right halves (event and occurrence). rearranged tables to help separate event- and occurrence-related tables.
schemas/VegCore/VegCore.ERD.mwb: rearranged to leave more space for location_observation, and to put all event-related fields on the left and occurrence-related fields on the left
web/.htaccess: parse dotpath in query string: heuristically detect query strings that don't contain dotpaths (such as mod_autoindex sort conditions), rather than always interpreting the part before the first & as the dotpath. now, the part before the first & will be interpreted as a dotpath if it has a . before any = . (query param names containing . are rare, so this usually works correctly.) note that you can always prepend . to force a dotpath, or & to force a query param.
web/dotpath.php: remove any . prefix which forces interpretation as a dotpath
schemas/VegCore/VegCore.ERD.mwb: taxon_concept: renamed source to according_to
schemas/VegCore/VegCore.ERD.mwb: removed no longer used images from zip archive using `zip -d`. this needs to be done every time an image is deleted from the diagram to remove it from the archive (and reclaim the unused space, since `zip -d` will also shrink the archive). note that you can't just expand and re-zip the files, because there is a header of some sort that indicates to MySQL Workbench that it's a valid .mwb file.
bugfix: schemas/VegCore/VegCore.ERD.mwb: also fixed inheritance relationships to the record table to be 1:1 (by search-and-replacing and then updating document.mwb.xml in the .mwb zip archive using `zip -u`). added separate legend for relationships and connector styles, which now uses example tables instead of screenshot images to ensure accurate sizing at all ERD zoom levels.
bugfix: schemas/VegCore/VegCore.ERD.mwb: fixed inheritance relationships to be 1:1 with optional participation by the derived table, rather than the incorrect 1:many relationshipwhich MySQL Workbench defaults to. (in OOP, each derived instance has its own instance of the base class, because it is a separate object.)
web/**/.htaccess: When there is no external redirect for the directory without the trailing /, instead auto-add the trailing / to ensure mod_autoindex relative links work properly. This must be done manually because the top-level .htaccess will not auto-add the trailing / if the dir has an .htaccess file (to allow the custom external redirects). There are actually only two .htaccess files that this applies to (web/.phpPgAdmin/.htaccess, .phpMyAdmin/.htaccess), indicating that dirs which have any kind of virtual paths (redirects) almost always have a "root" redirect when there is no specific subpath. This root redirect is intended to link to the datasource's own index of its available resources, e.g. the list of tables for a database source.
removed web/aggregators/.htaccess because it was only there to auto-add the trailing /, but this is now done by web/.htaccess
bugfix: web/.htaccess: auto-add trailing /: %{LA-F:REQUEST_FILENAME} lookaheads don't work, because they do not show the externally redirected URL, so we need to use an alternate mechanism instead, which just assumes that any dir containing an .htaccess file may contain a redirect and ignores just those dirs (subdirs are not ignored and will receive a trailing / as expected). To create the trailing / effect when you have a .htaccess without an external redirect, you need to manually tell it to correct the path for just that dir without the / (i.e. match ^/ , because a trailing / causes mod_rewrite to use an absolute filesystem path instead).
web/.htaccess: moved auto-add trailing / to after don't rewrite existing dirs, so that the path will automatically not be rewritten if it contains a trailing / and is a dir
