bugfix: inputs/.TNRS/schema.sql: map_taxonomic_status(): need to use accepted name instead of scrubbed name (which also includes no-opinion names), as described at http://wiki.vegpath.org/2013-11-14_conference_call#taxonomic-fields. this used to be the accepted name, but got switched when the concatenated name was also used to store the matched name for no-opinion names.

inputs/.TNRS/schema.sql: MatchedTaxon: documented how to modify it (using util.force_recreate())

inputs/.TNRS/schema.sql: MatchedTaxon, etc.: added accepted_morphospecies_binomial derived field

inputs/.TNRS/schema.sql: MatchedTaxon.Accepted_name_species: mapped to accepted_species_binomial

fix: inputs/.TNRS/schema.sql: COMMENTs: always include newline before and after

bugfix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: undid rename of accepted name columns to scrubbed_* (r13435), because these are actually not the same (scrubbed_* is the combination of accepted and no-opinion names). the accepted name columns will now be named accepted_*, following the standard naming scheme.

fix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: scrubbed_*: use columns from MatchedTaxon whenever possible, to as much as possible avoid the need to join to taxon_scrub.scrubbed_unique_taxon_name.*

bugfix: inputs/.TNRS/grants.sql: added GRANT statements from schema.sql because these aren't run by `make inputs/.TNRS/reinstall`

bugfix: inputs/input.Makefile: $(datasrc_schema_exists): need to use $(datasrc), not $(schema), as $schema is only what this var is called in the runscripts

bugfix: inputs/analytical_db/: need dummy table.run file to cause a schema to be created for this datasource

fix: inputs/input.Makefile: $(sortFile): don't print the "add any missing tables to $(sortFile)" message every time the Makefile is run

bugfix: inputs/input.Makefile: install: only run this for datasource dirs

inputs/input.Makefile: install: use ./run's install target for clarity

bugfix: inputs/input.Makefile: install: made it idempotent (using new $(datasrc_schema_exists)) so that it could be run by `make install` on an existing system

bugfix: inputs/input.Makefile: $(datasrc_schema_exists): need to use $(shell ...)

inputs/input.Makefile: added $(datasrc_schema_exists)

added inputs/VegBank/verify/outputBien.log.url

inputs/input.Makefile: add: verify/: also svn:ignore *.log

bugfix: inputs/input.Makefile: %/postprocess: invoke runscript if it exists

lib/runscripts/validations.pg.sql.run: export_(): make the export idempotent for easier re-runnability

fix: lib/runscripts/file.pg.sql.run: removed include of in_datasrc_dir.run, because this location does not apply to all .sql export scripts

bugfix: inputs/input.Makefile: validations.sql must be in a subdir so it won't get run by sql/install

bugfix: inputs/input.Makefile: validations.sql must be in a subdir so it won't get run by sql/install

inputs/input.Makefile: install: also run validate/install

inputs/input.Makefile: added validate/install

lib/runscripts/validations.pg.sql.run: export_(): make the export idempotent for easier re-runnability

bugfix: inputs/SALVIAS/validations.sql: need to cast character varying to text so that the types of each side of if() match

bugfix: **/postprocess.sql: don't use the public schema, because this creates an unsatisfied dependency while the database is being installed, and breaks `make install`

inputs/GBIF/_MySQL/.rsync_ignore: added GBIFPortalDB-*.data.sql.gz, because these are intermediate files

inputs/Madidi/_src/: set svn:ignore

fix: inputs/SALVIAS/projects/postprocess.sql: remove private data that should not be publicly visible: preserve datasets with ipr_specific = '', because they are actually redistributable, according to Brad (http://wiki.vegpath.org/2014-04-17_conference_call#conditions-of-use)

bugfix: inputs/NY/validations.sql: _specimens_07_list_of_verbatim_subspecific_taxa_with_author: updated filter condition to match output query

inputs/NY/run: `make inputs/NY/validate`: updated runtime (8 min, with added queries)

fix: inputs/NY/Ecatalog_all/map.csv, postprocess.sql: remapped substrate, vegetation to locationRemarks

fix: inputs/NY/Ecatalog_all/map.csv, postprocess.sql: remapped substrate, vegetation to locationRemarks

bugfix: inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13*: also need to include coordinate pairs which have one of their coordinates NULL, by using OR instead of AND

bugfix: inputs/NY/validations.sql: _specimens_13b_list_of_all_decimal_lat_long: matched column types to output query

bugfix: inputs/NY/validations.sql: _specimens_13a_list_of_all_verbatim_lat_long: matched column types to output query

inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: added breakdowns _specimens_13a_list_of_all_verbatim_lat_long, _specimens_13b_list_of_all_decimal_lat_long to help troubleshoot the diff

fix: inputs/NY/validations.sql, schemas/vegbien.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: count lat/longs together instead of separately, because the DISTINCT is by coordinate pair, not individual coordinate value (which wouldn't make much sense)

fix: inputs/NY/validations.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: use new is_castable(), which is much more accurate than Brad's custom regexp for determining if something is numeric

inputs/NY/validations.-.util.sql: added util.is_castable() wrapper

bugfix: inputs/NY/validations.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: need to include both lat and long in the value to DISTINCT on

fix: inputs/NY/validations.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: need to DISTINCT the values that are being counted, because they are merged by the coordinates_unique unique constraint in the import

inputs/NY/run: `make inputs/NY/validate`: documented slow queries: _specimens_12_distinct_collector_name_collect_num_date_w_count

inputs/SALVIAS/run_: `make inputs/SALVIAS/validate`: documented slow queries (_plots_06a_list_of_stems). these may need to have their query plans rechecked.

inputs/NY/run, inputs/SALVIAS/run_: `make inputs/.../validate`: updated runtime (+2 min)

fix: inputs/NY/validations.sql: specimens*_of_unique_verbatim_author_taxa_with_genus: use scientificName rather than the concatenated ranks, because that is what is imported to taxonlabel.taxonomicname

mappings/VegCore-VegBIEN.csv: mapped subspecies to new taxonverbatim.subspecies for easier access by validations queries

fix: inputs/test_taxonomic_names/Taxon/map.csv: scientificName: remapped to scientificName instead of taxonName as this does include the author for some names

fix: inputs/NY/Ecatalog_all/map.csv: ScientificName: remapped to scientificName instead of taxonName as this does include the author

fix: inputs/NY/validations.sql: specimens*_of_unique_verb_subsp_taxa_with_author: use taxonName instead of concatenating the ranks, as that corresponds to what we use as the concatenated taxonomic name

bugfix: inputs/NY/validations.sql: specimens*_of_verbatim_subspecific_taxa_with_author: need `subspecies IS NOT NULL` filter

bugfix: inputs/NY/validations.sql: _specimens_07_list_of_verbatim_subspecific_taxa_with_author: need to include subspecies (as _specimens_06_count_of_unique_verb_subsp_taxa_with_author does)

bugfix: inputs/NY/validations.sql: specimens*_of_species_binomials: removed incorrect `subspecies IS NOT NULL` filter (this should be on *_of_unique_verb_subsp_taxa_with_author instead)

fix: inputs/NY/validations.sql: _specimens_16_list_distinct_specimen_descriptions: removed duplicated rows using DISTINCT

bugfix: inputs/NY/validations.sql: _specimens_03_list_of_verbatim_families: use family as specified in query description, not as implemented

bugfix: schemas/vegbien.sql, inputs/NY/validations.sql, validation/aggregating/specimens/qualitative_validations_specimens.sql: _specimens_12_distinct_collector_name_collect_num_date_w_count: dateCollected: cast this to text rather than date because some values for this field are not valid dates and will throw an error if cast to date

fix: inputs/NY/validations.sql: _specimens_12_distinct_collector_name_collect_num_date_w_count: dateCollected: matched type to output query

fix: inputs/U/Specimen/map.csv: Genus: remapped to taxonName because this field is actually mislabeled in the original column names

inputs/NY/run: `make inputs/NY/validate`: updated runtime (6.5 min). this increases as more queries are able to run successfully.

inputs/SALVIAS/run_: `make inputs/SALVIAS/validate`: documented runtime (5 min)

inputs/bien2_traits/run: documented `make inputs/bien2_traits/validate` runtime (9 min)

inputs/NY/run: `make inputs/NY/validate`: updated runtime (5 min)

inputs/NY/run: documented `make inputs/NY/validate` runtime (2 min, currently for the input queries)

added inputs/Madidi/_src/ to match wiki steps in wiki.vegpath.org/Adding_a_flat-file_datasource

validation/aggregating/specimens/qualitative_validations_specimens.sql, NY/qualitative_validations_source_db_NYBG.VegCore.sql, inputs/NY/validations.sql: *_of_species_binomials: renamed columns to species_binomial to reflect reverted query name

validation/aggregating/specimens/qualitative_validations_specimens.sql, NY/qualitative_validations_source_db_NYBG.VegCore.sql, inputs/NY/validations.sql: *_of_verbatim_species_excluding_author: renamed to *_species_binomials for clarity

validation/aggregating/specimens/qualitative_validations_specimens.sql, NY/qualitative_validations_source_db_NYBG.VegCore.sql, inputs/NY/validations.sql: _specimens_04_count_of_unique_verbatim_species_with_author, _specimens_05_list_of_unique_verbatim_species_with_author: switched back to original names because #6,7 now do the same thing as #4,5, so we should include the differing result set of #4,5 for datasources that provide it

validation/aggregating/specimens/qualitative_validations_specimens.sql, NY/qualitative_validations_source_db_NYBG.VegCore.sql, inputs/NY/validations.sql: use taxon_name*_with_author everywhere instead of custom column names, for consistency

validation/aggregating/specimens/qualitative_validations_specimens.sql, NY/qualitative_validations_source_db_NYBG.VegCore.sql, inputs/NY/validations.sql: *_of_verbatim_subspecific_taxa_without_author, etc.: renamed to *_with_author because these now use the concatenated name, rather than the without-author name that only some specimens datasources provide

validation/aggregating/specimens/qualitative_validations_specimens.sql, NY/qualitative_validations_source_db_NYBG.VegCore.sql, inputs/NY/validations.sql: *_verbatim_species_without_author, etc.: renamed to *_with_author because these now use the concatenated name, rather than the without-author name that only some specimens datasources provide

lib/common.Makefile: added $(nice) and use it everywhere its definition is used

inputs/input.Makefile: validate: redirect the output to the log, as for other import-related operations

inputs/input.Makefile: import: validate at the end of the import

inputs/input.Makefile: added new-style aggregating validations (`validate` target)

added inputs/GBIF/_src/0001000-131106143450413.zip.header.txt, which is useful to see what fields will be available when we switch to the new GBIF export format

added inputs/GBIF/_src/0001000-131106143450413.zip.header.txt.run

*{.sh,run}: runscript targets: use begin_target instead of echo_func so the target name is properly echoed. note that this requires using with_rm so that $rm is properly progagated to applicable invoked targets. (previously, $rm was progagated to all invoked targets. note that with_rm only works inside a runscript target that starts with begin_target.)

lib/sh/make.sh: self_make(): renamed to with_rm() for clarity, since this is used only to progagate $rm, and does not also invoke a command with the same name as the current function, as the name might suggest

fix: inputs/*/*/map.csv: remapped occurrenceID-mapped fields to dataProviderRecordID when these were not globally unique DwC occurrenceIDs (http://rs.tdwg.org/dwc/terms/#occurrenceID)

fix: inputs/CTFS/AggregateObservation/map.csv: field mapped to occurrenceID: remapped to aggregateOrganismObservationID because these are not specimen occurrences

fix: mappings/VegCore-VegBIEN.csv: taxonoccurrence.sourceaccessioncode: need to populate from aggregateOrganismObservationID when only that is available

bugfix: inputs/NY/Ecatalog_all/map.csv: can't use CatalogNumber as pkey because it's not unique and not always populated. this fixes the NY NULL accessionNumbers bug (wiki.vegpath.org/Aggregating_validations_status#bugs).

inputs/XAL/Specimen/header.csv: updated

added inputs/NY/validations*.sql*

bugfix: lib/common.Makefile: $(add*): need to wrap w/ $(wildcard) to prevent "targets don't exist" error, because svn 1.7 does not suppress this error even with --force

bugfix: inputs/input.Makefile: add!: add* of $(svnFiles): need to ignore errors because svn 1.7 does not suppress the "targets don't exist" error even with --force

inputs/run: postprocess(): documented runtime on vegbiendev (1 h)

schemas/vegbien.sql: specimenreplicate.institution_id: renamed to duplicate_institutions_sourcelist_id, as decided in the conference calls (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2)

inputs/run: postprocess(): updated runtime (25 min)

inputs/run: postprocess(): updated runtime (20 min)

mappings/VegCore.htm: regenerated from wiki: rename specimenHolderInstitutions to specimen_duplicate_institutions, as decided in the 2014-03-13 conference call (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2). note that most schema changes (such as this one) involve mappings changes, which are handled automatically by `inputs/run postprocess; yes|make inputs/{NVS,SALVIAS,TEAM}/test`.

bugfix: inputs/GBIF/table.run: switched to using lib/runscripts/table.run instead of mysql.table.run because some subdirs (Source/) need the regular table.run to work properly. mysql.table.run should instead be used directly by subdirs that use the MySQL install.

inputs/XAL/Specimen/test.xml.ref: updated for sample data.csv, which contains the columns as a CSV. this fixes a bug where a map.csv must be used on a table that contains the same set of columns (ie. not one with no columns if there are any mappings).

fix: inputs/input.Makefile: don't treat *.xml as data files since these are not currently supported

fix: inputs/input.Makefile: removed no longer used special handling of XML inputs, support for which was never added to the Makefile. (bin/map, however, does support importing an XML file into a database.) this fixes a bug in XAL, which used to abort with an error but now just imports an empty table.

fix: inputs/input.Makefile: %/install: don't ignore errors if table does not exist, to ensure a proper errexit. this is now possible because every dir that this target is being run on should be a data dir. (Source/ used to be a metadata-only dir.)

bugfix: inputs/input.Makefile: $(cleanup): need `set -o pipefail`

inputs/VegBank/run: `rm=1 import()`: updated runtime (1 h)