planning/timeline/timeline.2013.xls: extended "revisions to VegBIEN schema" to length of "datasource validations (spot-checking)" because schema changes are expected as we add missing fields
planning/timeline/timeline.2013.xls: crossed out and hid completed tasks ("find out amount remaining in BIEN3 budget")
planning/timeline/timeline.2013.xls: datasource validations (spot-checking): extended through the end of November because data providers' fixes on the remaining 10 datasources (wiki.vegpath.org/2013-10-17_conference_call#validation-order) are likely to add significantly to the issues and feature requests associated with these datasources (e.g. the 2nd-round VegBank validation added 4 issues and 5 feature requests). there is also expected to be wait time while data providers are responding (most likely in multiple rounds of feedback).
planning/timeline/timeline.2013.xls: data provider metadata: removed "iPlant can do" because this actually requires Brad/Brian/Bob/other data providers to provide this info. however, this info may be findable on the web for some datasources.
planning/timeline/timeline.2013.xls: moved "data provider metadata" right after "datasource validations" because this is part of the completed database itself rather than the tools to maintain it
planning/timeline/timeline.2013.xls: split "revisions to schema" into "revisions to VegBIEN schema" (part of datasource validations) and "revisions to normalized VegCore" (part of documentation)
bin/import_all: use just import_scrub, not reimport_scrub, because import_scrub now automatically publishes the datasource's import (i.e. removes the temp suffix)
bugfix: inputs/input.Makefile: import: remove the temp suffix once the import is done, so that the full database import doesn't keep the suffix attached to the datasources that import_all didn't import with reimport. removed unused import_publish target (instead use import_temp to invoke just the import without the temp suffix removal).
planning/timeline/timeline.2013.xls: moved part of "switching to new-style import" under "datasource validations (spot-checking)" because this is necessary to validate CVS
planning/timeline/timeline.2013.xls: moved "simplify process of mapping/adding a new datasource" and "documentation testing" after "usability testing" because these tasks were there to make it possible for people other than me to reload/add to the database, which we have now decided is a lower priority than creating the validated database itself
planning/timeline/timeline.2013.xls: added weeks through the end of the year (12/31)
schemas/VegBIEN/attribution/BIEN 3 data use and attribution.docx: changed dataset definition to the definition in normalized VegCore ("a collection of records from the same place, with the same attribution requirements"), following discussion with Ramona
planning/timeline/timeline.2013.xls: updated for progress
schemas/VegBIEN/attribution/BIEN 3 data use and attribution.docx: updated to Ramona's commented version
inputs/CVS/plot_/map.csv: realLatitude, realLongitude: remapped to UNUSED because these columns are actually empty
inputs/CVS/taxonObservation_/map.csv: collector_ID: remapped it to UNUSED and removed the join to party via it, like in VegBank
inputs/CVS/: deleted stemLocation_, because the CVS stemLocation table is empty (unlike VegBank)
inputs/CVS/import_order.txt: added plantConcept_/ so it would get automapped after switching to new-style import
inputs/CVS/taxonObservation_/map.csv: denorm_{tri,quad}*: mapped to infraspecificRank*, infraspecificEpithet*
inputs/CVS/taxonObservation_/map.csv: infraspecific ranks: remapped to EQUIV#to:species (which is the speciesBinomial), because these actually contain the full taxonomic name at that rank, like VegBank
inputs/CVS/taxonObservation_/map.csv: genus: documented that unlike VegBank, does not include genus author
inputs/CVS/taxonObservation_/map.csv: denorm_* terms _alt-ed with normalized terms: use DUPLICATE#of instead where possible. documented where and why _alt was necessary (this applies to a few rows for division, genus).
bugfix: inputs/CVS/taxonObservation_/map.csv: species: remapped to speciesBinomial, not specificEpithet (like for VegBank). however, note that denorm_species is in fact the epithet, unlike VegBank.
fix: inputs/CVS/taxonObservation_/postprocess.sql: removed {} around denorm_genus to match the normalized genus
inputs/CVS/taxonObservation_/map.csv: removed unnecessary alts for terms that don't have a duplicate denorm* or hierarchical field
fix: inputs/CVS/taxonObservation_/postprocess.sql: fix 1 row that has denorm_kingdom != Kingdom (i.e. both NOT NULL but not the same)
bugfix: lib/common.Makefile: $(subMake): don't enclose the target in "" because sometimes the target is empty (i.e. `all`), and nothing should be passed to the sub-make
inputs/VegBank/plot_/create.sql: documented runtime (5 min)
bugfix: inputs/CVS/plot_/create.sql: like for VegBank, need to compare place.*PLOT_ID*, not PLOTPLACE_ID, with plot.PLOT_ID
/README.TXT: Single datasource import: added pointer to instructions to remake the analytical DB (also required after single datasource import)
inputs/VegBank/verify/input_cols.txt, inputs/VegBank/+taxon_observation.**.sample/create.sql: updated to match taxon_observation.** columns
/README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: run all sync_uploads on the svn working copy using --size-only, because the mtimes are based on when the files were last updated by svn and are not meaningful
/README.TXT: Full database import: On local machine: do steps under Maintenance > "to synchronize vegbiendev, jupiter, and your local machine": removed no longer accurate indicator that these steps are above Full database import, since Full database import is now at the beginning of the file
bugfix: inputs/VegBank/+taxon_observation.**.sample/: renamed to ^taxon_observation.**.sample because a leading + has a special meaning to bash (it indicates a shell option, and you will get an error "invalid option name"), as well as to make (it indicates that a recipe command invokes make recursively)
bugfix: inputs/VegBank/taxon_observation.**/header.csv: updated for observation_/map.csv bugfix, which added new hasobservationsynonym field. this fixes a strange test bug caused by the taxon_observation.**/map.csv column list being mismatched/misaligned with what was in the underlying tables. (column mismatches will often cause unexplainable errors in unrelated sections of code the same way that buffer overflows do in C++.)
bugfix: inputs/VegBank/taxon_observation.**.sample/: renamed to +taxon_observation.**.sample so that the -expansion of taxon_observation.* doesn't add taxon_observation.**.sample (which causes it to attempt to install taxon_observation.**.sample before taxon_observation.** is installed)
bugfix: *Makefile: recursive invocation of $(MAKE): enclose targets in "" in case they contain *
bugfix: lib/runscripts/table.run: load_data(): pass $is_view through to `make reinstall` so that DROP VIEW will be used instead of DROP TABLE where applicable
bugfix: inputs/input.Makefile: %/uninstall: allow user to set is_view=1 flag to use DROP VIEW instead of DROP TABLE
lib/sh/util.sh: added instructions for making an export only visible locally
bugfix: inputs/VegBank/observation_/header.csv, map.csv: updated for refresh, which inserts hasobservationsynonym at the end of the observation table
inputs/VegBank/taxon_observation.**.sample/create.sql: reordered columns in the same order as analytical_plot, for easier validation
bugfix: lib/runscripts/table.run: load_data(): in remaking mode, need to remake header.csv in case the columns have changed
web/links/index.htm: updated to Firefox bookmarks. updated favicons.
web/links/index.htm: updated to Firefox bookmarks. sudo: added instructions to turn off incorrect password e-mails.
inputs/VegBank/taxon_observation.**.sample/create.sql: include only the subset of columns that is imported to VegBIEN
inputs/VegBank/taxon_observation.**.sample/test.xml.ref: updated inserted row count (which was most likely generated before the output column names had been set to the input column names)
added inputs/VegBank/verify/input_cols.include.txt, with runscript to generate it
inputs/VegBank/verify/input_cols.unmapped.txt*: renamed to input_cols.exclude.txt* because this now includes mapped columns as well
inputs/VegBank/verify/input_cols.unmapped.txt.run: remove unmapped join columns, since these would be included in the extract
inputs/VegBank/verify/input_cols.unmapped.txt.run: take input directly from input_cols.txt to avoid needing to first copy and paste it into input_cols.unmapped.txt
inputs/VegBank/verify/input_cols.unmapped.txt.run: added back deliberately excluded columns (DUPLICATE#of:..., etc.) so that the # of rows in the file can be subtracted from the total # of columns to get the # of input columns that would be included in the extract
bugfix: inputs/input.Makefile: %/VegBIEN.csv: `ln -s` to create VegBIEN.csv: enclose the filenames in "" since they may contain * (e.g. taxon_observation.**)
added inputs/VegBank/verify/input_cols.txt, input_cols.unmapped.txt (with runscript to filter input_cols.unmapped.txt)
schemas/VegBIEN/attribution/BIEN 3 data use and attribution.docx: made Ramona's corrections with track changes turned on. note that you have to use MS Word for this, not LibreOffice, because LibreOffice can't save the table of contents properly in .docx or .doc format (although it can save it in .odt format).
inputs/VegBank/stratum/postprocess.sql: added pkey
inputs/VegBank/taxonobservation_/postprocess.sql: added __parent index on locationID to facilitate the LEFT JOINs used to create the validation input
inputs/VegBank/observation_/postprocess.sql: added __parent index on locationID to facilitate the LEFT JOINs used to create the validation input
inputs/VegBank/import_order.txt: added taxon_observation.**.sample so it will automatically be kept up to date
inputs/VegBank/taxon_observation.**.sample/create.sql: set runtime (1 s)
inputs/VegBank/: added taxon_observation.**.sample subset of plots to use in the validation. this avoids the need to import all of VegBank just to validate a few of the plots.
bin/map: usage: documented that verbosity > 3 in commit mode turns on debug_temp mode, which creates real tables instead of temp tables
schemas/VegCore/ERD/VegCore.ERD.mwb: georeferencing: documented that this stores location determinations (= VegBIEN.vegpath.org?public.locationplace)
inputs/VegBank/taxon_observation.**/: updated for data refresh
inputs/VegBank/plantconcept_/: mapped columns, since this is now included in import_order.txt and therefore gets processed by the column-renaming runscripts. note that this means that in taxonobservation_/map.csv, the plantconcept_ input column names need to be changed to what they are mapped to.
inputs/VegBank/taxonobservation_/create.sql: updated runtime (20 s)
schemas/VegCore/ERD/VegCore.ERD.mwb: regenerated exports and udpated image map
fix: schemas/VegCore/ERD/VegCore.ERD.mwb: project: allow it to have a dataset rather than being one, because projects do not always have separate attribution requirements (e.g. in Madidi they don't). this also fixes a bug where projects whose datasets had a parent dataset (e.g. VegBank) would need a dummy event for that parent dataset so that the fkeys on both dataset.parent->dataset and event.parent->event would be satisfied. added project__unique constraint on name within dataset.
schemas/VegCore/ERD/VegCore.ERD.mwb: taxa_sampling_event.parent (inherited): require this to be a taxa_sampling_event. documented that this is the taxa_sampling_event for the parent stratum.
schemas/VegCore/ERD/VegCore.ERD.mwb: fixed lines
schemas/VegCore/ERD/VegCore.ERD.mwb: place_visit.parent (inherited): added fkey constraint that this must be a place_visit. documented that this is the concurrent observation of the parent place.
schemas/VegCore/ERD/VegCore.ERD.mwb: project: inherit from dataset, since projects generally confer attribution and conditions of use
fix: schemas/VegCore/ERD/VegCore.ERD.mwb: place_visit: fixed synonyms list to "VegX.vegpath.org?plotObservation, VegBank.vegpath.org?observation (which was confusingly named) + some of VegBank.vegpath.org?plot (which is actually 1:1 with observation)"
schemas/VegCore/ERD/VegCore.ERD.mwb: place_observation: renamed to place_visit for clarity, since other tables that point to this use it as a general container, not just a link to the observations about the place
schemas/VegCore/ERD/VegCore.ERD.mwb: merged stratum_event into taxa_sampling_event since they serve the same purpose (separating taxa samplings within the same place_observation by subsetting methodology). merged layer into stratum since strata as we think of them are horizontal, although there are other definitions of stratum (e.g. size class) which are more similar to our method table.
schemas/VegCore/ERD/VegCore.ERD.mwb: event subclasses: subject: added applicable fkey constraints to the inherited field. renamed existing table-specific subject fields to subject to merge with the inherited field.
schemas/VegCore/ERD/VegCore.ERD.mwb: event: added unique constraints for every way that the scoping fields can meaningfully be combined. these correspond to the various unique constraints offered by VegBIEN.locationevent. (the event table's constraints are always tricky because there are many ways to define an event. it is important to include all of them so that there is almost always a way to generate a natural key, without resorting to an artificial key from traceable.id_by_source.)
schemas/VegCore/ERD/VegCore.ERD.mwb: event.place: renamed to subject and allow this to be any traceable, not just a place. this allows taxon_observations to be scoped within their taxon_occurrences just as subplot events are scoped within parent plot events.
schemas/VegCore/ERD/VegCore.ERD.mwb: traceable.authors: documented that this makes traceable mutually recursive with party_list
schemas/VegCore/ERD/VegCore.ERD.mwb: fixed inheritance connectors
schemas/VegCore/ERD/VegCore.ERD.mwb: record.authors: moved to traceable because actually, different sections of a denormalized source record may have separate authors (e.g. participants for taxa_sampling_event, identifiers for taxon_determination)
schemas/VegCore/ERD/VegCore.ERD.mwb: record.dataset: split this into the scoping_dataset (which scopes the id_within_dataset) and the attribution_dataset (which provides attribution information)
schemas/VegCore/ERD/VegCore.ERD.mwb: record.authors: changed this to refer only to original data creators such as collectors and identifiers. this way, there is no need to generate a combined party_list of owners+authors for every record, because the record-specific authors list can just point to the same party_list as the collectors or event participants. this is also closer to Brad's meaning, which is specifically "a person or institution responsible for creating the dataset" [+emph].
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.
