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# Date Author Comment
8686 04/24/2013 01:07 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: added hstore expansion columns where needed

8685 04/24/2013 12:54 PM Aaron Marcuse-Kubitza

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

8684 04/24/2013 12:34 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: specimen: added unique constraint for each set of identifying columns

8683 04/24/2013 12:25 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: collection: added back primary key

8682 04/24/2013 12:24 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: specimen: made owner an fkey to collection instead of organization to correspond with orig_collection and current_collection (and to allow auto-filling it from current_collection in a trigger)

8681 04/24/2013 12:18 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: specimen: reordered columns to group together each method of identifying a specimen

8680 04/24/2013 12:14 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: collection: don't inherit from source, because a collection is a scoping entity, not a dataset. a collection may also be used as a dataset, but need not be for the purposes of scoping a specimen's accession_number.

8679 04/24/2013 12:07 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: specimen: removed redundant stamping_institution and donor_institution, because these are now in orig_collection.institution. (it is assumed that stamping_institution and donor_institution are the same, because the first institution to acquire and store a specimen (the donor) is the one that stamps it with an accession_number.)

8678 04/24/2013 12:01 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: specimen: split collection into orig,current_collection because the collection that scoped the accession_number (the orig_collection) is sometimes different than the collection where the specimen is now held (the current_collection, or specimen_holder_institutions), e.g. when the specimen is donated

8677 04/24/2013 11:49 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: collection: added institution, name to identify and scope the collection

8676 04/24/2013 11:39 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: changed taxon_name fkeys to taxon_concept where appropriate, and renamed the referencing columns to *_taxon_concept to clearly indicate the referenced table. taxon_concept fkeys are appropriate whenever a taxon is defined or associated with an observed entity, in which case the assertion is not just to a taxon name but to a defined taxon concept (albeit sometimes an unofficial taxon concept scoped by the collector or identifier).

8675 04/24/2013 11:08 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: specimen: added code_in_individual column

8674 04/24/2013 10:40 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: specimen: added fkey to individual for the individual the specimen was taken from

8673 04/24/2013 10:30 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: individual/stem_observation: made individual/stem nullable because there is not always enough identifying information (stem tag, etc.) to actually associate an identifiable individual with an observation

8672 04/24/2013 10:27 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: moved code from individual to individual_observation because the code is something applied at observation time, rather than something that can be used to track individuals between observations

8671 04/24/2013 10:17 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: moved collection_event from taxon_occurrence to specimen because only specimens are actually collected, while other taxon_occurrences (e.g. individuals) must be uniquely identified by some means that are shared between re-observations (e.g. the stem tag)

8670 04/24/2013 10:03 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: moved collector, collector_number from taxon_occurrence to taxon_observation because these are actually attributes that are available or assigned at observation time, rather than being intrinsic to the taxon_occurrence (which can be either an individual or a specimen)

8669 04/24/2013 09:34 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: method: colored it forest green like stratum because these are both tables in the same category (method), and forest green is the color VegBank uses for methods. (the fact that VegBank gives stratum the method color indicates that we are on the right track when we are treating stratum as a type of method that's essentially a height class.)

8668 04/24/2013 09:27 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: method: added parent fkey which can be used to autoinherit attributes from another method, in the same way that event autoinherits a method from its parent

8667 04/24/2013 09:16 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: replaced < event label for diagram half with < place, because the occurrence half actually also includes events (observations), but does not include places

8666 04/24/2013 09:10 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: removed extra empty page used for moving objects around

8665 04/24/2013 09:08 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: swapped position of place and source categories so that the place tables, which users are apt to query often, are at the top, and the attribution information, which is likely to be used less often, is at the bottom. this also moves the plot table closer to taxon_occurrence, which should eventually have an fkey to it.

8664 04/24/2013 08:19 AM Aaron Marcuse-Kubitza

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

8663 04/24/2013 08:05 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: record: added source_id_scope and added it to the record_unique unique index

8662 04/24/2013 08:01 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: Default*ColumnType: updated to VARBINARY type used in key columns

8661 04/23/2013 11:19 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps: repositioned arrow labels so they point in the direction of the fkey lines

8660 04/23/2013 11:06 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb.run: use new zip/unzip_newer

8659 04/23/2013 11:06 PM Aaron Marcuse-Kubitza

lib/util.run: added zip/unzip_newer aliases

8658 04/23/2013 11:05 PM Aaron Marcuse-Kubitza

lib/util.run: added zip/unzip echo_run aliases

8657 04/23/2013 10:57 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb.run: export_ (): always overwrite existing files. this option is safe, because -u only extracts files with a newer mtime than their copies on disk.

8656 04/23/2013 10:55 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps labels: converted tables to notes, which now have bold formatting so that empty tables aren't needed for formatting purposes

8655 04/23/2013 10:25 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb.run: import/export_ (): use zip/unzip's -u flag instead of `make` to auto-sync the zip file contents. the -u flag has the added benefit of preserving the contained file's mtime, at the expense of an mtime lookup in the zip archive's table of contents.

8654 04/23/2013 10:17 PM Aaron Marcuse-Kubitza

added schemas/VegCore/VegCore.ERD.mwb.run, which syncs VegCore.ERD.mwb's zip file contents

8653 04/23/2013 09:58 PM Aaron Marcuse-Kubitza

bugfix: lib/util.run: inline_make (): put echo_func at the top of the function

8652 04/23/2013 09:58 PM Aaron Marcuse-Kubitza

lib/util.run: inline_make (): pass Makefile commands using /dev/fd/3 (i.e. 3<<'EOF' ...) instead of stdin, to allow stdin to be used by commands that prompt the user

8651 04/23/2013 09:44 PM Aaron Marcuse-Kubitza

lib/util.run: inline_make (): use <() to pass Makefile commands as a named descriptor rather than using stdin, to allow stdin to be used by commands that prompt the user

8650 04/23/2013 09:27 PM Aaron Marcuse-Kubitza

bugfix: lib/util.run: echo_vars (): remove any value to set (=*) from the vars, since this is often used with export

8649 04/23/2013 09:14 PM Aaron Marcuse-Kubitza

bugfix: lib/util.run: echo_export (): set the vars before echoing them

8648 04/23/2013 08:55 PM Aaron Marcuse-Kubitza

lib/util.run: run_args_cmd (): use new canon_rel_path() to resolve .. in the script path, so it's easier to see where the script is actually located

8647 04/23/2013 08:52 PM Aaron Marcuse-Kubitza

lib/util.run: echo_func (): use new canon_rel_path() to resolve .. in the script path, so it's easier to see where the script is actually located

8646 04/23/2013 08:51 PM Aaron Marcuse-Kubitza

lib/util.run: added canon_rel_path ()

8645 04/23/2013 08:40 PM Aaron Marcuse-Kubitza

lib/util.run: inline_make (): provide $self as make var

8644 04/23/2013 08:35 PM Aaron Marcuse-Kubitza

lib/util.run: inline_make (): provide self_dir to make as env var instead of as make var, to avoid specifying every make var both as a local var and as a make var in the make command

8643 04/23/2013 08:31 PM Aaron Marcuse-Kubitza

lib/util.run: export alias: added comment explaining what it does

8642 04/23/2013 08:30 PM Aaron Marcuse-Kubitza

lib/util.run: aliased export to echo_export so all env vars are automatically echoed when they are set

8641 04/23/2013 08:29 PM Aaron Marcuse-Kubitza

lib/util.run: added echo_vars (), echo_export ()

8640 04/23/2013 08:17 PM Aaron Marcuse-Kubitza

lib/util.run: inline_make (): added local $self and use it to create $self_dir

8639 04/23/2013 08:15 PM Aaron Marcuse-Kubitza

lib/util.run: inline_make (): set $self_dir as a local var before passing it to make, to avoid clutter in the command that invokes make

8638 04/23/2013 07:54 PM Aaron Marcuse-Kubitza

added schemas/VegCore/document.mwb.xml, so changes to the diagram can be tracked line-by-line. keeping this up-to-date requires running `unzip VegCore.ERD.mwb document.mwb.xml` whenever VegCore.ERD.mwb is changed.

8637 04/23/2013 07:53 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: target MySQL version: updated to 5.5.3

8636 04/23/2013 07:49 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: NoteFigure:TextFont (labels): made it bold to stand out better

8635 04/23/2013 07:45 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: Layer:TitleFont (legends): increased size and made it bold to stand out better

8634 04/23/2013 07:31 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: made stratum extend method, so that any observation event can have an associated stratum. removed no longer needed plot_stratum, since strata are now represented as sampling methods (i.e. using height classes) rather than a variant of subplots.

8633 04/23/2013 07:21 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: VegCore DB: changed collation to utf8_bin to match table collation

8632 04/23/2013 07:15 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: saved settings for publishing schema to vegbiendev phpMyAdmin (vegbiendev.nceas.ucsb.edu/phpmyadmin/index.php?db=VegCore). this adds `DROP TABLE IF EXISTS` before each CREATE TABLE statement, renames the default DB to VegCore, and adds a USE statement to select the VegCore DB.

8631 04/23/2013 06:29 PM Aaron Marcuse-Kubitza

schemas/VegCore/connections.xml: vegbiendev.nceas.ucsb.edu: set schema (DB) to VegCore

8630 04/23/2013 06:20 PM Aaron Marcuse-Kubitza

added schemas/VegCore/connections.xml, which should be installed as the connections.xml settings file

8629 04/23/2013 06:19 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: imported database connections from the connections.xml settings file into document.mwb.xml in the .mwb zip file. these connections are not used directly by MySQL Workbench, but instead need to be copied into the connections.xml settings file.

8628 04/23/2013 05:17 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: use Database > Forward Engineer (Ctrl+G) instead of File > Export > Forward Engineer SQL CREATE Script (Ctrl+Shift+G), so that comments will use the max comment length for the server's MySQL version rather than MySQL Workbench's internal MySQL version, which has a max comment length of only 60 chars for tables. this commit stores the default export settings for Forward Engineer, which are saved each time it's run.

8627 04/23/2013 04:31 PM Aaron Marcuse-Kubitza

bugfix: root Makefile: $(postgresReload-Linux): fixed the "shmat(id=...) failed: Cannot allocate memory" error by telling the user to restart PostgreSQL manually from the command line

8626 04/23/2013 04:29 PM Aaron Marcuse-Kubitza

root Makefile: $(postgresReload-Linux): don't restart Postgres twice, because this does not fix the "shmat(id=...) failed: Cannot allocate memory" error. this error is instead produced whenever PostgreSQL is restarted from within a Makefile, but not when it's run directly from the command line or /bin/sh.

8625 04/23/2013 03:20 PM Aaron Marcuse-Kubitza

root Makefile: $(postgresReload-Linux): restart Postgres twice, because the first time after the postgresql.conf has been udpated, it always produces a "shmat(id=...) failed: Cannot allocate memory" error

8624 04/23/2013 03:10 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: re-synced with VegCore.my.sql: step 2: `DEFAULT NULL` added on all nullable columns

8623 04/23/2013 03:10 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: re-synced with VegCore.my.sql: step 1: table order changed

8622 04/23/2013 02:54 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: relationship: renamed the two fk_relationship_record1 fkeys so their names wouldn't collide

8621 04/23/2013 02:52 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: changed encoding back to utf8/utf8_bin now that latin1 isn't needed to make the key columns satisfy the index length limits. note that the connection encoding must be utf8 on import so that the correct byte sequence is stored in the VARBINARY columns.

8620 04/23/2013 02:11 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: changed VARCHAR BINARY columns to VARBINARY because VARCHAR BINARY is actually only an alias for the *_bin collation of the table's encoding, but still uses multibyte characters if the encoding does. note that VARBINARY will still be displayed as text (in the connection encoding), rather than hex values.

8619 04/23/2013 02:02 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: changed the type of TEXT columns used in indexes to VARCHAR BINARY to satisfy prefix length limits ("a prefix can be up to [...] 767 bytes for InnoDB tables" <http://dev.mysql.com/doc/refman/5.5/en/create-index.html&gt;). the BINARY flag was added to allow storing Unicode values (from UTF-8), which are not representable in the latin1 encoding.

8618 04/23/2013 01:15 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: changed encoding to latin1 to fit more characters in length-limited indexes (indexes treat utf8 as having 3 bytes/character (http://stackoverflow.com/questions/1814532/1071-specified-key-was-too-long-max-key-length-is-767-bytes#comment-18031137), which significantly reduces the max length of an indexed column)

8617 04/23/2013 01:08 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: changed collation to utf8_bin to avoid case-*in*sensitive comparison of case-sensitive strings. (utf8_bin is also much faster than encoding-aware collations because it uses the raw bytes.)

8616 04/23/2013 12:47 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: set DefaultPkColumnType to TEXT to match the type of current pkey columns

8615 04/23/2013 12:16 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: set all tables to use utf8/utf8_unicode_ci rather than latin1/latin1_swedish_ci because our DB is in UTF-8. utf8_unicode_ci is better than utf8_general_ci because it supports international characters better (http://forums.mysql.com/read.php?103,187048,188748)

8614 04/23/2013 12:10 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps labels: removed fkey columns to the next step since these are not needed and were causing problems with round-trip sync to the .my.sql file

8613 04/23/2013 11:42 AM Aaron Marcuse-Kubitza

bugfix: schemas/VegCore/VegCore.ERD.mwb: fixed foreign keys without a referenced columns list

8612 04/23/2013 11:36 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: upgraded for MySQL Workbench 5.2.47 (MySQL 5.5), which requires indexes to have different names than fkeys

8611 04/23/2013 10:25 AM Aaron Marcuse-Kubitza

schemas/postgresql.conf: shared_buffers: reduced again for Ubuntu VM

8610 04/23/2013 10:22 AM Aaron Marcuse-Kubitza

bugfix: schemas/postgresql.conf: shared_buffers: removed invalid Unicode character U+FEFF

8609 04/23/2013 02:40 AM Aaron Marcuse-Kubitza

schemas/postgresql.conf: shared_buffers: reduced to work in Ubuntu VM

8608 04/23/2013 12:58 AM Aaron Marcuse-Kubitza

README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: add * after analytical_aggregate.*.csv to match *.md5 files as well

8607 04/19/2013 07:33 PM Aaron Marcuse-Kubitza

inputs/VegBIEN/TWiki/templates/login.tmpl: increased font size further using <span> style. changed text to fit on two lines with the new size.

8606 04/19/2013 07:26 PM Aaron Marcuse-Kubitza

inputs/VegBIEN/TWiki/templates/login.tmpl: added large text with instructions to register (the TWiki instructions are small and easily missed)

8605 04/19/2013 07:09 PM Aaron Marcuse-Kubitza

added inputs/VegBIEN/TWiki/templates/login.tmpl

8604 04/19/2013 05:14 PM Aaron Marcuse-Kubitza

inputs/VegBIEN/TWiki/twiki.conf: main TWiki dir: changed redirect to go directly to the Main TWiki web, so that we don't need to worry about creating different "webs" (subsites) for top-level wiki pages

8603 04/19/2013 05:03 PM Aaron Marcuse-Kubitza

inputs/VegBIEN/TWiki/twiki.conf: main TWiki dir: redirect shortened wiki page URLs of the form vegpath.org/twiki/Path to do/view/ for use with VegPath

8602 04/19/2013 04:49 PM Aaron Marcuse-Kubitza

added web/.twiki symlink to datasources/VegBIEN/TWiki/

8601 04/19/2013 04:48 PM Aaron Marcuse-Kubitza

added inputs/VegBIEN/TWiki/twiki.conf

8600 04/19/2013 12:58 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: coordinates: added latitude_deg, longitude_deg. geovalidation: added lat_long_in_ranks hstore.

8599 04/19/2013 12:32 PM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: realigned event/occurrence divider. moved method to avoid overlapping the halves.

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...