schemas/VegCore/ERD/VegCore.ERD.mwb: party_list: added array field, which stores an array combining all the list entries. if specified, a trigger will autogenerate party_list_entries from this field. if not specified, it will be autopopulated whenever a party_list_entry is added.
schemas/VegCore/ERD/VegCore.ERD.mwb: added data_owner subclass of party_list_entry, which stores use_conditions for each data_owner of a dataset. dataset: added access_rights (public, private, etc.), use_conditions (citation requirements, etc.).
schemas/VegCore/ERD/VegCore.ERD.mwb.run: record.authors: clarified that this should include all parties who helped create the data record, making it a superset of dataset.data_owners, who receive attribution. clarified that record-specific authors such as collectors and identifiers generally do not receive attribution, although dataset-level authors do (this field includes both).
schemas/VegCore/ERD/VegCore.ERD.mwb.run: record.id_within_dataset: removed instruction to also put this in source.name, because source.name is now optional, and this would not make sense because source does not have a parent pointer
schemas/VegCore/ERD/VegCore.ERD.mwb.run: documented that schema COMMENTs cannot contain ' (used in contractions such as "don't"), because MySQL Workbench cannot escape these properly
schemas/VegCore/ERD/VegCore.ERD.mwb: record: added authors, which stores the people who helped create the data record. this is Brad's data author term (Brad.vegpath.org?attribution.data_author), but actually belongs to the individual data record rather than to an entire data*set* because records may have different authors (collectors, identifiers, etc.). note that schema COMMENTs apparently cannot contain ' (used in contractions such as "don't"), because MySQL Workbench cannot escape these properly.
schemas/VegCore/ERD/VegCore.ERD.mwb: dataset.data_owners: documented that this includes all aggregators through which the data has passed, so that this is equivalent to Brad's data indexers (Brad.vegpath.org?attribution.data_indexer)
fix: schemas/VegCore/ERD/VegCore.ERD.mwb: dataset.parent: fixed example to indicate that the GBIF.ARIZ dataset is contained within a specific GBIF dataset (the parent), but was obtained from the GBIF organization (the dataset_source). ARIZ is then the first_publisher, not the dataset_source.
schemas/VegCore/ERD/VegCore.ERD.mwb: dataset: renamed data_source to dataset_source for clarity
schemas/VegCore/ERD/VegCore.ERD.mwb: dataset.contacts: documented that this is the contact person(s) to ask about attribution questions. there should always be at least one contact person. if unknown, the person loading the data should set this to themselves.
added schemas/VegCore/Brad_Boyle/BIEN 3 data use and attribution.docx symlink to schemas/VegBIEN/attribution/BIEN 3 data use and attribution.docx, so that all of Brad's attribution-related terms are in one place
schemas/VegCore/ERD/VegCore.ERD.mwb: dataset.contacts: make this required, so that anyone adding data to a VegCore DB always provides at least one contact person, possibly themselves, to ask about attribution questions (as suggested by Brad in BIEN 3 data use and attribution.docx)
schemas/VegCore/ERD/VegCore.ERD.mwb: dataset.first_publisher: allow this to be any kind of source, rather than just a party (i.e. an organization). this is possible now that party inherits from source.
schemas/VegCore/ERD/VegCore.ERD.mwb: dataset: linked to Brad's synonyms for dataset_source (Brad.vegpath.org?attribution.proximate_data_provider), first_publisher (Brad.vegpath.org?attribution.data_publisher, Brad.vegpath.org?data_provenance.primarydataprovider)
bugfix: web/people/Brad_Boyle/.htaccess: only forward requests for a term defined by Brad to the attribution/ subdir, so that Brad.vegpath.org shows a directory listing instead of forwarding right to the attribution doc
bugfix: web/people/Brad_Boyle/.htaccess: set %{ENV:innermost_dir} to Brad_Boyle
added web/people/Brad_Boyle/data_provenance/ (BIEN database entities related to data provenance and ownership.docx)
bugfix: web/people/Brad_Boyle/attribution/.htaccess: \-escape the %s so that they aren't treated as backreferences. set the [redirect] flag so that the downloaded file has the correct filename (BIEN 3 data use and attribution.docx instead of attribution).
bugfix: web/people/Brad_Boyle/attribution/.htaccess: use %20 instead of + because the Apache server apparently doesn't translate + to space correctly
bugfix: web/people/Brad_Boyle/attribution/.htaccess: link to the VegBIEN subdir in /exchange_schemas instead of the main /VegBIEN because there are actually two VegBIEN subdirs, and the main one instead points to /datasources/VegBIEN
added web/people/Brad_Boyle/ with attribution/ subdir for BIEN 3 data use and attribution.docx
inputs/VegBank/plantconcept_/create.sql: documented runtime (21 min)
bugfix: inputs/VegBank/plantconcept_/: added new-style import files
bugfix: inputs/VegBank/import_order.txt: added plantconcept_, because new-style import needs it to be explicitly listed in import_order.txt in order to run it
inputs/VegBank/run: refresh(): added usage
inputs/VegBank/run: refresh(): documented that this should be run on vegbiendev
inputs/VegBank/_archive/2012-8-30/: svn:ignore the data exports
inputs/VegBank/run: added refresh() target
inputs/VegBank/: refreshed VegBank so that all of Mike Lee's sample plots would be included in the input data. (VegBank was last refreshed from the live DB on 2012-8-30.) split vegbank.sql into vegbank.schema.sql and vegbank.data.sql so that the schema can be examined and imported separately, like for MySQL datasources. inputs/VegBank/vegbank.~.clean_up.sql: commented out setting comminterpretation.commname to NOT NULL, because after the refresh it is now NULL in 10 rows, where commconcept_id is also NULL.
lib/runscripts/datasrc_dir.run: import(): added remake (rm=1) mode that reinstalls the datasource before continuing with the subdirs' import actions
lib/runscripts/in_datasrc_dir.run: added datasrc_make(), which runs make in the datasrc dir
inputs/.geoscrub/_src/README.TXT: added e-mail from John Donoghue with general description of the BIEN2 geovalidation workflow
bugfix: schemas/vegbien.sql: plot.**: removed ORDER BY because a SELECT on the view with its own ORDER BY will actually sort the rows twice instead of optimizing away plot.**'s default ORDER BY
schemas/vegbien.sql: added plot.** subset view of analytical_stem_view, used for VegBank validation
planning/timeline/timeline.2013.xls: moved reload core & analytical database out a week because it shouldn't be done until after CVS validation is complete
inputs/.geoscrub/_src/README.TXT: added link to geovalidation description in wiki
added schemas/VegBIEN/attribution/BIEN 3 data use and attribution.docx from Brad
planning/timeline/timeline.2013.xls: updated to reflect that the next week should be spent doing data validations, as decided in the conference call
bugfix: schemas/vegbien.sql: locationevent__communities(): need to use commdescription instead of commname as the communityName because that's where communityName has been mapped to in mappings/VegCore-VegBIEN.csv. (commname instead stores the communityID.)
inputs/VegBank/: added observation__community/
inputs/VegBank/vegbank.~.clean_up.sql: commclass.commcode,commname: rename to prevent collisions
inputs/VegBank/vegbank.~.clean_up.sql: indicate required column comminterpretation.commname
inputs/VegBank/vegbank.~.clean_up.sql: commconcept.commname: rename to prevent collision with commname.commname
planning/timeline/: svn:ignore: added .~* (lock files for .xls)
schemas/vegbien.sql: analytical_stem_view: added instructions for what to do after updating this
schemas/vegbien.sql: analytical_stem_view, analytical_plot: added communities using new locationevent__communities__array()
schemas/vegbien.sql: added locationevent__communities*()
bugfix: schemas/vegbien.sql: locationevent: locationevent__pull_forward_from_parent() trigger: only pull forward the location_id when there is a stratum_id, so that empty locationevents that should be auto-forwarded are not unintentionally made valid by populating the location_id field (which causes a check constraint to become satisfied, and prevents auto-forwarding from working). this fixes a bug in some datasources' automated tests, such as `make inputs/SALVIAS/plotObservations/test`.
lib/sql_io.py: put_table(): default param: documented that this will be used for all missing rows, regardless of which error caused them not to be inserted. this means that auto-forwarding (wiki.vegpath.org/Auto-forwarding) can be used with any type of constraint violation, not just NOT NULL constraints (which it is typically used with).
/Makefile: mk_db: config/users.sql: unset ON_ERROR_STOP so user-exists errors don't prevent further user-adds
planning/timeline/timeline.2013.xls: updated for progress
bugfix: schemas/vegbien.sql: analytical_stem_view: plot__collectors: to include plot__collectors for nested stratum events, need to calculate the locationevent__contributors__array() for the locationevent and parent_event separately, and then COALESCE those, instead of just running locationevent__contributors__array() once on the COALESCE of the two IDs
bugfix: schemas/vegbien.sql: locationevent: added pull-forward trigger to populate location_id from the parent event. a pull-forward trigger must be used for this (not a COALESCE in analytical_stem_view) because the locationevent cannot even be found by analytical_stem_view if it does not have an associated location.
schemas/VegCore/ERD/VegCore.ERD.mwb: source: added required url field, which points to the source data and uniquely identifies the source. note that this differs from the id, which is a self-refential pkey (as described at wiki.vegpath.org/Web_interface#Clickable-fkeys).
schemas/VegCore/ERD/VegCore.ERD.mwb: fixed lines
schemas/VegCore/ERD/VegCore.ERD.mwb: regenerated exports and udpated image map
schemas/VegCore/ERD/VegCore.ERD.mwb: source: removed canon, because this would create too much complexity as a result of having multiple copies of the same source with different names. instead, source names will be scrubbed upon insert so that the row always contains the most accurate data, and there is only one copy of each source. this scrubbing may use the assistance of a thesaurus table w/ standard abbreviations, etc.
schemas/VegCore/ERD/VegCore.ERD.mwb: plot.name: merged with inherited name field
schemas/VegCore/ERD/VegCore.ERD.mwb: source: added canon field. when there are multiple names for a source, this points to the canonically-named source. by default, points recursively to itself.
schemas/VegCore/ERD/VegCore.ERD.mwb: taxon_observation.taxon_occurrence: documented that when not provided (and not fillable from another field), a taxon_occurrence will be created with the same id as the taxon_observation. this operation should eventually be perfomed by a trigger.
schemas/VegCore/ERD/VegCore.ERD.mwb: geovalidatable_place.parent_geoplace: renamed to parent so it will merge with the inherited parent field. this is the parent geoplace.
schemas/VegCore/ERD/VegCore.ERD.mwb: individual_observation.specimenholder_institutions: documented that instead, the taxon_occurrence for the individual_observation should have an autogenerated current_observation that merges together all the individual_observations for these institutions' specimens. in this case, each institution's specimen will still have its own individual_observation containing what it believes to be the specimenholder institutions.
schemas/VegCore/ERD/VegCore.ERD.mwb: individual_observation.specimenholder_institutions: documented that when provided, the source (i.e. traceable.source) should be set to the value of this field, because these institutions together provided the data for this entity
schemas/VegCore/ERD/VegCore.ERD.mwb: party_list: inherit from source so that a party_list can be used as the source for a row (e.g. a list of institutions that together provided the data for an individual_observation that has specimens at multiple institutions)
schemas/VegCore/ERD/VegCore.ERD.mwb: reobservable_presence: merged into taxon_determination, so that voucher is directly available to taxon_determination to autopopulate fields when a redetermination is made on the voucher
schemas/VegCore/ERD/VegCore.ERD.mwb: aggregate_observation.sampling_event: merged with inherited sampling_event field
schemas/VegCore/ERD/VegCore.ERD.mwb: taxon_observation.parent: require that this is an fkey to another taxon_observation, since this stores the taxon_observation of the same taxon_occurrence in the parent sampling_event
schemas/VegCore/ERD/VegCore.ERD.mwb: subplot.parent_plot: renamed to parent so it will merge with the inherited parent field. this is the parent plot.
schemas/VegCore/ERD/VegCore.ERD.mwb: individual_count.taxon_presence: renamed to parent so it will merge with the inherited parent field. this is the taxon_presence for the taxon as a whole (not subdivided by size_class, etc.).
schemas/VegCore/ERD/VegCore.ERD.mwb: taxa_sampling_event.method: renamed to subsetting_method for clarity
schemas/VegCore/ERD/VegCore.ERD.mwb: stratum_event.parent_event: renamed to parent so it will merge with the inherited parent field
schemas/VegCore/ERD/VegCore.ERD.mwb: traceable: added alternate pkey id_by_source, which allows referencing a traceable by its source information even when the subclass chose a different value for the pkey
schemas/VegCore/ERD/VegCore.ERD.mwb: taxon_observation.observation_in_parent_place: merged with inherited parent field, documenting that for this table, this contains the observation of the same taxon_occurrence in the parent sampling_event
schemas/VegCore/ERD/VegCore.ERD.mwb: individual_observation.place_observed_at: merged with inherited place field, documenting that for this table, this contains the place the individual was observed at
schemas/VegCore/ERD/VegCore.ERD.mwb: event: reordered date_range, participants, place in the order of how likely they are to be provided. (place was considered more optional than the other two because a project does not usually have a place.)
schemas/VegCore/ERD/VegCore.ERD.mwb: taxon_observation.sampling_event: made it required so that there is always a sampling_event to scope the primary_collector/collector_number when provided. (for specimens, this will have the same event information (date_range, participants, place) as the taxon_observation.)
schemas/VegCore/ERD/VegCore.ERD.mwb: taxon_observation: added unique constraint on sampling_event, primary_collector, collector_number. reordered these columns in constraint order (path order).
schemas/VegCore/ERD/VegCore.ERD.mwb: taxon_observation: added primary_collector, to scope the collector_number. collectors: renamed to all_collectors for clarity, now that there is a primary_collector field.
schemas/VegCore/ERD/VegCore.ERD.mwb: specimen.current_collection, owner_collection: moved to specimen_observation because these may differ each time the specimen is reobserved
schemas/VegCore/ERD/VegCore.ERD.mwb: specimen.code_in_individual: renamed to id_within_individual to match the id_within_* naming convention using elsewhere
schemas/VegCore/ERD/VegCore.ERD.mwb: individual_observation: removed code because this duplicates taxon_observation.collector_number and record.id_within_dataset
schemas/VegCore/ERD/VegCore.ERD.mwb: specimen.specimenholder_institutions: moved to individual_observation because the list of institutions which store a specimen from the plant actually relates to the plant, not a particular specimen (this list should be the same for all specimens taken from the plant)
schemas/VegCore/ERD/VegCore.ERD.mwb: specimen: removed collection_event because this is the same as individual_observation
schemas/VegCore/ERD/VegCore.ERD.mwb: specimen: removed separate fkey to individual because this is linked to from individual_observation
schemas/VegCore/ERD/VegCore.ERD.mwb: place_observation: link to project. taxa_sampling_event: removed link to project since this now happens via place_observation.
schemas/VegCore/ERD/VegCore.ERD.mwb: taxa_sampling_event: merged required within_place into place_observation, which already contains a required fkey to place
schemas/VegCore/ERD/VegCore.ERD.mwb: taxa_sampling_event: added place_observation fkey for the concurrent place_observation, which contains all the info about the place (communities, soil data, etc.). this allows a taxon_observation to be traced to its associated location measurements.
bugfix: mappings/VegCore-VegBIEN.csv: nest all taxonoccurrences inside a stratum event, so that the parent locationevent is always fully populated before child locationevents point to it. (previously, a stub parent event was created when the child event was imported first, which blocked the fully-populated parent event from being inserted later on.) this uses auto-folding (for VegBank/CVS) and auto-forwarding (for other datasources) to prune empty stratum events for taxonoccurrences that don't have strata. (see wiki.vegpath.org/Auto-folding, wiki.vegpath.org/Auto-forwarding for more info about these normalization techniques.) note that the inserted row counts stay exactly the same for all datasources except VegBank (which was being fixed), indicating that this signficant change to the mappings did not change the semantics of the import of taxonoccurrences.
inputs/VegBank/observationcontributor_/test.xml.ref: updated inserted row count
bugfix: mappings/VegCore-VegBIEN.csv: stratum's locationevent: link this to the parent locationevent, so that the parent locationevent's information (such as locationeventcontributors) is accessible to the stratum's locationevent
bugfix: inputs/VegBank/taxon_observation.**/postprocess.sql: inlined _join() so that taxon_observation.** wouldn't get cascadingly deleted whenever the util schema (where this normally resides) gets reinstalled
bugfix: schemas/vegbien.sql: locationeventcontributor: added missing unique constraint (locationeventcontributor_unique)
bugfix: schemas/vegbien.sql: locationeventcontributor.role: made it optional because some locationeventcontributors may not have an associated role
schemas/vegbien.sql: analytical_stem_view, analytical_plot: added plot__collectors, which uses locationevent__contributors__array()
