fix: inputs/SALVIAS/validations.sql: _plots_18_list_of_subplots_codes_for_each_plot_for_each_project: changed columns to match output query

fix: inputs/SALVIAS/validations.sql: _plots_15_pct_cover_of_each_verb_taxon_in_each_plot_in_each_pro: changed types to match output query

bugfix: inputs/SALVIAS/validations.sql: _plots_15_pct_cover_of_each_verb_taxon_in_each_plot_in_each_pro: changed summarizing column from mean_cover->totalpercentcover to match output query

bugfix: inputs/SALVIAS/validations.sql: _plots_10a_aggregate_observation_individual_counts: changed individual_id type to match output query

schemas/vegbien.sql, inputs/SALVIAS/validations.sql: added _plots_10a_aggregate_observation_individual_counts, for use in debugging diffs in _plots_10_count_of_individuals_per_plot_in_each_proj

fix: inputs/SALVIAS/validations.sql: renamed SiteCode to plot_code to match output queries

inputs/SALVIAS/validations.sql: use plot_code instead of plotcode for easier readability

bugfix: *.sql: public.source_by_shortname(): need to wrap it in a nested SELECT because Postgres incorrectly does not constant-fold (inline) it, leading to a slowdown when it is therefore run many times. this is done using the steps at wiki.vegpath.org/Postgres_queries#wrap-function-call-in-nested-SELECT .

fix: inputs/SALVIAS/validations.sql: plotMetadata.SiteCode: need to match types with the output query column

fix: inputs/SALVIAS/validations.sql: _plots_02_list_of_project_names: altered column aliases to match output query

inputs/SALVIAS/validations.sql: added Brad's comments from validation/aggregating/plots/SALVIAS/bien3_validations_salvias_db_original.VegCore.sql

added inputs/SALVIAS/validations*.sql

fix: schemas/vegbien.sql: _traits_08_taxonname_trait_and_value_for_first_5000_records: renamed to _traits_08_taxonname_trait_and_value because this actually includes all the records, not just the first 5000. this uses the new public_validations.rename_query_view() to rename all associated tables and views, including handling truncated names.

bugfix: inputs/bien2_traits/validations.sql: _traits_01_count_records: changed column names to match public_validations._traits_01_count_records

bugfix: inputs/bien2_traits/validations.sql: use a wrapper function for util.ifnull() so that the views don't get dropped when the util schema is reinstalled

validation/aggregating/*/*.sql, schemas/vegbien.sql, lib/runscripts/validations.pg.sql.run, inputs/bien2_traits/validations.sql: added _ to beginning of each view name so the validation views would sort at the top in the datasource's tables list. this will also make the validation result sets easily distinguishable from the data tables.

added inputs/bien2_traits/validations.sql, from validation/aggregating/traits/BIEN2_traits/bien3_validations_traits_original_mysql.VegCore.sql

inputs/input.Makefile: $(svnFilesGlob): added validations.sql

added inputs/bien2_traits/validations.sql.run

inputs/import.stats.xls: updated import times

inputs/import.stats.xls: updated import times

fix: inputs/VegBIEN/Redmine/wiki/.htaccess: redirect to new main page when accessed without trailing /

inputs/bien2_traits/TraitObservation/postprocess.sql: remove rows with no taxon name, which are invalid, and which helps simplify the aggregating validations queries

fix: inputs/VegBIEN/Redmine/svn/.htaccess: updated repository URL to point to trunk/

bugfix: inputs/SALVIAS/verify/plots.out.sql: fixed ' quoting syntax to use '' instead of \' to escape '

inputs/input.Makefile: verify/%.out: use a *.sql file in the verify/ directory itself to generate *.out, so that each datasource can have its own set of output queries. for datasources that should share the same set of queries, they can instead be symlinked to the same file.

fix: inputs/CVS/project/: added _no_import since this should not also be imported separately from taxon_observation.**

added inputs/XAL/Specimen/_no_import, since this is a demo-only datasource and there isn't a staging table for it

inputs/.geoscrub/county_centroids/test.xml.ref, inputs/.NCBI/{names.src,nodes.src}/test.xml.ref: accepted test outputs (generated now that these tables are in import_order.txt)

inputs/FIA/taxon_observation.**/header.csv: updated for new REF_RESEARCH_STATION.country metadata value col

inputs/input.Makefile: add!: verify/: also svn:ignore *.tsv, *.txt

inputs/publishable datasources.xlsx: updated

inputs/publishable datasources.xlsx: updated

fix: inputs/SALVIAS/projects/postprocess.sql: remove private data that should not be publicly visible: remove projects that do not have "There are no specific use conditions attached to this dataset"

fix: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Remove private data that should not be publicly visible: also need to remove metadata-only plots

bugfix: inputs/SALVIAS/plotMetadata_/map.csv: things mapped to project_participant: remapped to event__participant because these actually relate to the event, not the project, even though they seem like project-related fields

fix: inputs/SALVIAS/plotMetadata_/map.csv, inputs/Madidi/LocationObservation/map.csv: things mapped to communityID: remapped to communityName, which is what's used in analytical_stem (communityID is for numeric IDs)

inputs/SALVIAS/plotMetadata_/create.sql, map.csv: expanded plot_administrator:party_code_party_ and mapped plot_administrator_name to a 2nd project_participant

mappings/VegCore-VegBIEN.csv: project_participant: use [!...] negative lookahead assertion so that multiple project_participant columns will properly map to separate projectcontributor rows

inputs/SALVIAS/plotMetadata_/map.csv: mapped PrimOwnerID_name->project_participant

inputs/SALVIAS/plotMetadata_/create.sql: added join to PrimOwnerID:party_code_party_

bugfix: inputs/SALVIAS/import_order.txt: added party_code_party_

bugfix: inputs/SALVIAS/party_code_party_/create.sql: need to remove duplicate entries in party_code_party

inputs/SALVIAS/party_code_party_/map.csv: mapped fullname->event_participant_name for use by other tables

mapped inputs/SALVIAS/party_code_party_/

inputs/SALVIAS/_MySQL/salvias_plots.*.sql: refreshed. this adds the party and party_code_party tables Brad provided for mapping the plot contributors.

fix: inputs/SALVIAS/salvias_plots.~.clean_up.sql: Delete rows that do not satisfy foreign key constraints: also need to do this for plotObservations, since the refreshed data contains dangling rows for that as well

inputs/SALVIAS/run_: documented *.sql install runtime (3 min), as separate from the full `datasrc_make reinstall` runtime (3.5 min)

inputs/SALVIAS/run_: refresh(): `datasrc_make reinstall`: updated runtime. documented that runtimes are from starscream.

added inputs/SALVIAS/run_, which includes a refresh() target

moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).

bugfix: inputs/.TNRS/schema.sql: scrubbed_family: Name_matched_accepted_family was missing from the TNRS results at one point, so we are now using Family_matched as a workaround to populate this. the workaround is for accepted names only, as no opinion names do not have an Accepted_name_family to prepend to the scrubbed name to parse.

inputs/.TNRS/schema.sql: reexported from live DB, which changes the element order

inputs/VegBank/import_order.txt: added projectcontributor_

inputs/VegBank/projectcontributor_/map.csv, postprocess.sql: added project_participant

added inputs/VegBank/projectcontributor_/

inputs/VegBank/vegbank.~.clean_up.sql: projectcontributor.surname: prepend table name to avoid join collisions

inputs/VegBank/vegbank.~.clean_up.sql, inputs/CVS/cvs.~.clean_up.sql: Prevent "column name specified more than once" errors when tables are joined: put tables in alphabetical order for consistency

inputs/publishable datasources.xlsx: updated

inputs/datasource_release_status.xlsx: renamed to `publishable datasources.xlsx` to match the spreadsheet title

inputs/VegBank/^taxon_observation.**.sample/create.sql, map.csv: added new project columns

inputs/VegBank/taxon_observation.**/postprocess.sql: added the project table

mapped inputs/VegBank/project/, which includes the projectName for attribution

inputs/CVS/^taxon_observation.**.sample/create.sql, map.csv: added new project columns

inputs/CVS/taxon_observation.**/postprocess.sql: added the project table

inputs/CVS/project/map.csv: mapped stopDate->projectEndDate

mapped inputs/CVS/project/, which includes the projectName for attribution

inputs/VegBIEN/Redmine/svn/.htaccess: updated to use much faster direct repository URL rather than Redmine web interface, now that the repository itself is publicly accessible in addition to the Redmine view of it

fix: inputs/TEX/Specimen*/map.csv, postprocess.sql: habitat: also placed in occurrenceRemarks so that this field gets parsed for growth form information, as requested by Brad (wiki.vegpath.org/TEX_validation#2013-2-26)

fix: inputs/TEX/Specimen*/map.csv: mapped constant values for specimenHolderInstitutions, country. these have to be added with `rm=1 ./inputs/TEX/Specimen.../run postprocess`.

bugfix: inputs/TEX/Specimen2/map.csv: mapped BARCODE to accessionNumber so that we have a unique ID for each row

inputs/datasource_release_status.xlsx: updated

inputs/CVS/^taxon_observation.**.sample/create.sql: added Mike Lee's additional plots used to validate confidentiality-related fields (wiki.vegpath.org/CVS_validation#plots-to-include)

bugfix: inputs/CVS/^taxon_observation.**.sample/create.sql: include taxonName in the subset of columns that's imported for the validation, because it is _alt-ed with scientificName for forming the TNRS input name. this is unique to CVS, which is why it was not part of the validation subset copied from the VegBank subset.

bugfix: inputs/.TNRS/schema.sql: granted bien_read SELECT access to derived views as well as the core tnrs table

updated inputs/datasource_release_status.xlsx

added inputs/datasource_release_status.xlsx, export of Google spreadsheet at https://docs.google.com/spreadsheet/ccc?key=0ArZXrTAXd-TYdDRRb2RxYi11TWZrQVh5bVdKOURCeFE

fix: inputs/CVS/^taxon_observation.**.sample/: added _no_import because this table duplicates part of what's imported from taxon_observation.**

bugfix: inputs/VegBank/plot/: added _no_import because this table is left-joined and should not be imported separately

bugfix: inputs/{.NCBI,CTFS}/*.src/: added _no_import because these tables are left-joined and should not be imported separately

inputs/import.stats.xls: removed table names from datasources where only one table is imported

fix: inputs/import.stats.xls: removed deleted tables from current import

inputs/import.stats.xls: updated import times

inputs/GBIF/raw_occurrence_record_plants/map.csv: row_num: remapped to plain *row_num, like the other datasources that have this field

inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: Remove institutions that we have direct data for: rerun time: noted that this is only fast after manual vacuuming of the table (to remove the deleted rows from the index). autovacuum apparently does not run, although it should.

inputs/GBIF/raw_occurrence_record_plants/test.xml.ref: reran test, which added yearCollected/monthCollected/dayCollected

inputs/CVS/plantConcept_/create.sql: documented runtime (3 min)

inputs/CTFS/*.src/: added test.xml.ref

inputs/CTFS/*.src/: added VegBIEN.csv

bugfix: inputs/CTFS/TaxonOccurrence*/map.csv: things mapped to taxonObservationID: remapped to taxonOccurrenceID since taxonObservationID is not mapped to anything in VegBIEN (denormalized VegCore doesn't distinguish between taxon occurrences and taxon observations of them)

bugfix: inputs/ARIZ/~.clean_up.sql: prevent "column already exists" errors when there is an input column of the same name as an output column

inputs/.geoscrub/import_order.txt: added county_centroids so that it would be installed by new-style import

inputs/FIA/TREE/run: documented import() runtime (1.5 h), which includes table cleanup runtime (1 h)

inputs/GBIF/raw_occurrence_record_plants/run: updated import() runtime (same), documented table cleanup runtime (1.5 h)

inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: CREATE INDEX ... specimenHolderInstitutions: documented runtime (45 min)

inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: Remove institutions that we have direct data for: documented runtime (3.5 min)

bugfix: inputs/CTFS/import_order.txt: added *.src so that these would be installed under new-style import as well. this means that their columns will now be automapped, requiring the names to be renamed to VegCore names in */create.sql. note that VegCore taxonOccurrenceID has been renamed to taxonObservationID since this was last run.

inputs/.geoscrub/run: documented import() runtime (20 min)

bugfix: inputs/.NCBI/import_order.txt: added nodes.src, names.src so that these would be installed under new-style import as well. this means that their columns will now be automapped, requiring the names to be renamed to VegCore names in nodes/create.sql.

bugfix: inputs/input.Makefile: install: for new-style datasources, use the associated runscript instead (the old-style install target will not do everything that's needed for a new-style datasource)