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# Date Author Comment
8598 04/19/2013 12:29 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: specimen: replaced specimen_holder_institutions with specimen_holder_institution many:many table. added fkeys for the various institution fields. collection: removed name because this is already a required field in source. event_participant: removed *_id suffixes from fields.

8597 04/19/2013 11:55 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: replaced party_list with event_participant many:many table, since the nature of each type of party_list (ordered, not, etc.) may differ between tables that HAVE-A party_list, and because it is not possible to create an fkey to a column that is not unique in the referenced table (as is the case for party_list.list_id)

8596 04/19/2013 11:41 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8595 04/19/2013 11:28 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: made first_publisher a field of source (fkey to party) instead of a subclass of it, because a source can be both an aggregator for some datasets and a first publisher for others and which one it is depends on the dataset

8594 04/19/2013 11:06 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: added organization

8593 04/19/2013 11:01 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: added party_list

8592 04/19/2013 10:29 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: regenerated exports

8591 04/19/2013 10:09 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8590 04/19/2013 09:50 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon_presence, aggregate_observation: added required taxon field to identify (distinguish) the observation itself. this is expected to be the same as the first taxon_determination applied to the observation.

8589 04/19/2013 09:21 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: collection: renamed code to name because the collection code is often the full name of the collection, rather than just an abbreviation. made name required.

8588 04/19/2013 09:17 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: source: added name

8587 04/18/2013 04:54 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: set page size to fit the ERD contents. this cannot be done through the GUI, so instead you need to use the following steps:

$ unzip ERD.mwb document.mwb.xml
open document.mwb.xml and search for "this ERD"
units are mm
$ zip -u ERD.mwb document.mwb.xml...

8586 04/17/2013 05:28 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed split connector

8585 04/17/2013 05:25 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed inheritance lines

8584 04/17/2013 05:22 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: source: added contact field (fkey to party)

8583 04/17/2013 05:17 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: party: inherit from record instead of source, because a party is defined by and scoped by a datasource but isn't a datasource itself (however, a named datasource can have an associated admin party)

8582 04/17/2013 05:12 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: moved tables to make more room between specimen and taxon tables

8581 04/17/2013 04:45 PM Aaron Marcuse-Kubitza

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).

8580 04/17/2013 02:32 PM Aaron Marcuse-Kubitza

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.

8579 04/17/2013 01:04 PM Aaron Marcuse-Kubitza

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.

8578 04/17/2013 11:38 AM Aaron Marcuse-Kubitza

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.

8577 04/17/2013 11:29 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: renamed taxon_observation to taxon_presence for clarity and to distinguish it better from taxon_occurrence

8576 04/17/2013 11:25 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon_determination: added identified_date and unique index on identifying columns

8575 04/17/2013 11:15 AM Aaron Marcuse-Kubitza

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

8574 04/17/2013 10:38 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon tables: added catch-all hstores for custom columns

8573 04/17/2013 10:17 AM Aaron Marcuse-Kubitza

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.

8572 04/17/2013 08:38 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon tables: added nonidentifying columns

8571 04/17/2013 06:55 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: regenerated exports

8570 04/17/2013 06:51 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: categories: updated box sizes

8569 04/17/2013 06:45 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8568 04/17/2013 06:40 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: validatable_place: added unique index on identifying columns

8567 04/17/2013 06:38 AM Aaron Marcuse-Kubitza

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).

8566 04/17/2013 06:06 AM Aaron Marcuse-Kubitza

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

8565 04/17/2013 05:33 AM Aaron Marcuse-Kubitza

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

8564 04/17/2013 05:20 AM Aaron Marcuse-Kubitza

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)

8563 04/17/2013 05:13 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: removed invisible U+FEFF Unicode character

8562 04/17/2013 05:10 AM Aaron Marcuse-Kubitza

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)

8561 04/17/2013 05:03 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: labeled TNRS taxonomic scrubbing steps

8560 04/17/2013 04:42 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: labeled TNRS taxonomic scrubbing steps

8559 04/17/2013 03:52 AM Aaron Marcuse-Kubitza

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)

8558 04/17/2013 03:43 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: regenerated exports

8557 04/17/2013 03:39 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8556 04/17/2013 03:30 AM Aaron Marcuse-Kubitza

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

8555 04/17/2013 03:04 AM Aaron Marcuse-Kubitza

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.

8554 04/17/2013 02:57 AM Aaron Marcuse-Kubitza

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.

8553 04/17/2013 02:48 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: added taxon_name, which is used by taxon_concept

8552 04/17/2013 02:37 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: added taxon_string, which is used by taxon_assertion

8551 04/17/2013 02:15 AM Aaron Marcuse-Kubitza

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.

8550 04/17/2013 01:49 AM Aaron Marcuse-Kubitza

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).

8549 04/17/2013 01:36 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8548 04/17/2013 01:35 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: taxon_assertion: removed fkey to taxon_concept because only parsed_taxon_assertions have a corresponding taxon_concept

8547 04/17/2013 01:31 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed table positions

8546 04/17/2013 01:25 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: lined up tables

8545 04/17/2013 01:24 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8544 04/17/2013 01:21 AM Aaron Marcuse-Kubitza

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

8543 04/17/2013 01:18 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed inheritance lines

8542 04/17/2013 01:17 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: added taxon_path

8541 04/17/2013 01:10 AM Aaron Marcuse-Kubitza

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

8540 04/17/2013 01:01 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: renamed fkeys to match renamed tables

8539 04/17/2013 12:34 AM Aaron Marcuse-Kubitza

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

8538 04/17/2013 12:15 AM Aaron Marcuse-Kubitza

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.

8537 04/16/2013 11:00 PM Aaron Marcuse-Kubitza

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.

8536 04/16/2013 10:38 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: categories: added stratum

8535 04/16/2013 10:29 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: categories: put categories on the same halves of the legend as they are in the ERD

8534 04/16/2013 10:23 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8533 04/16/2013 10:23 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: added stratum, plot_stratum

8532 04/16/2013 06:14 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: added plot subclass of location

8531 04/16/2013 05:49 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed inheritance lines

8530 04/16/2013 05:45 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8529 04/16/2013 05:34 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8528 04/16/2013 05:31 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8527 04/16/2013 05:28 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: removed redundant "DEFAULT NULL" clauses on nullable fields

8526 04/16/2013 05:24 PM Aaron Marcuse-Kubitza

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

8525 04/16/2013 04:34 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: fixed lines

8524 04/16/2013 04:33 PM Aaron Marcuse-Kubitza

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.

8523 04/16/2013 04:25 PM Aaron Marcuse-Kubitza

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".

8522 04/16/2013 02:30 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.my.sql: removed default_schema qualifier from names because all objects are in the same schema

8521 04/16/2013 02:29 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.my.sql: regenerated from ERD

8520 04/16/2013 09:25 AM Aaron Marcuse-Kubitza

bugfix: schemas/VegCore/VegCore.ERD.mwb: fixed pkey names to match table names

8519 04/16/2013 09:18 AM Aaron Marcuse-Kubitza

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

8518 04/16/2013 09:05 AM Aaron Marcuse-Kubitza

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

8517 04/16/2013 08:43 AM Aaron Marcuse-Kubitza

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.

8516 04/16/2013 08:28 AM Aaron Marcuse-Kubitza

README.TXT: Maintenance: to backup the Ubuntu VM: removed invisible U+FEFF Unicode character

8515 04/16/2013 08:26 AM Aaron Marcuse-Kubitza

README.TXT: added steps to backup the Ubuntu VM

8514 04/16/2013 07:48 AM Aaron Marcuse-Kubitza

bugfix: schemas/.htaccess: corrected $innermost_dir

8513 04/16/2013 07:46 AM Aaron Marcuse-Kubitza

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.

8512 04/16/2013 07:14 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: ensured that inheritance relationships are drawn as 1:1

8511 04/16/2013 07:00 AM Aaron Marcuse-Kubitza

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)

8510 04/14/2013 09:30 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.png: Regenerated again because some tables were highlighted when it was exported, causing the highlighting to appear in the PNG

8509 04/14/2013 09:27 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: Regenerated exports

8508 04/14/2013 09:26 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: shortened embedded ERD URL using new abbreviations

8507 04/14/2013 09:19 PM Aaron Marcuse-Kubitza

web/**/.htaccess: RewriteRules: ensured flags are in alphabetical order

8506 04/14/2013 09:10 PM Aaron Marcuse-Kubitza

removed no longer needed web/dotpath.php. use web/.htaccess's parse-dotpath RewriteRule instead.

8505 04/14/2013 09:07 PM Aaron Marcuse-Kubitza

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.

8504 04/14/2013 08:54 PM Aaron Marcuse-Kubitza

web/.htaccess: renamed REQUEST_URI_no_/ to REQUEST_URI_no_extra_/ to clarify that only an excess / is removed

8503 04/14/2013 08:52 PM Aaron Marcuse-Kubitza

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

8502 04/14/2013 08:44 PM Aaron Marcuse-Kubitza

web/.htaccess: setting REQUEST_URI_no_/: use one RewriteCond instead of two since the regexps can be combined

8501 04/14/2013 02:50 PM Aaron Marcuse-Kubitza

web/.htaccess: parse dotpath in query string: removed dotpath auto-detection code because this is now handled by a separate RewriteRule

8500 04/14/2013 02:49 PM Aaron Marcuse-Kubitza

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.

8499 04/14/2013 02:01 PM Aaron Marcuse-Kubitza

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.