schemas/VegBIEN/taxonomy/higherPlantGroup.xlsx.src.txt: added Brad's comment that there are some holes in the Embryophyte subclasses list, and we need to validate it

inputs/.TNRS/schema.sql: tnrs: documented that when changing this table's schema, you must also make the same changes on vegbiendev. included sample util.set_col_types() call with runtime (4 min).

inputs/.TNRS/schema.sql: tnrs_populate_fields(): updated runtime (16 min)

bugfix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): need to schema-qualify invoked functions

bugfix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): Is_homonym: use the *_is_homonym flag for whichever of genus or family (in that order) is NOT NULL, rather than horizontal-ORing potentially NULL values together

bugfix: inputs/.TNRS/schema.sql: family_is_homonym(), genus_is_homonym(): need to return NULL instead of false when input family/genus is NULL. EXISTS does not support this, so STRICT is used to provide this functionality automatically.

inputs/.TNRS/schema.sql: added family_is_homonym(), genus_is_homonym() and use them in tnrs_populate_fields()

inputs/.TNRS/schema.sql: score_ok(): changed to IMMUTABLE and STRICT

inputs/.TNRS/schema.sql: tnrs_populate_fields(): updated runtime (16 min)

inputs/.TNRS/schema.sql: tnrs_populate_fields(): never_homonym: use Author_score threshold to exclude matches that are too fuzzy to confirm the presence of a plant name author

bugfix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): *_is_homonym: also need to check that there was no Author_matched (i.e. that it could be a homonym). Is_homonym: use new never_homonym var.

inputs/.TNRS/schema.sql: tnrs_populate_fields(): updated runtime (18 min)

inputs/import.stats.xls: Updated import times

planning/workflow/bien3_architecture.pptx: stage II: removed Step prefix before stage #, which the other slides don't have

added planning/workflow/bien3_architecture/stages.png

added planning/workflow/bien3_architecture/stage_*.png

added planning/workflow/bien3_architecture.pptx

inputs/.TNRS/schema.sql: tnrs_populate_fields(): when changing this function: UPDATE statement: include TNRS schema since it may not be in the search_path

inputs/.TNRS/schema.sql: tnrs_populate_fields(): Is_plant: also consider homonyms using new family_is_homonym, genus_is_homonym (see wiki.vegpath.org/Result_filtering#taxon_is_plant)

inputs/.TNRS/schema.sql: tnrs: added Is_homonym derived col (uses IRMNG.family_homonym_epithet, genus_homonym_epithet)

schemas/vegbien.sql: re-ran `make schemas/public/reinstall; make schemas/remake` cycle, which apparently changed sort order of statements

/README.TXT: Full database import: disk space check: updated minimum (to 300GB) for new import schema size. note that most of the space (166GB) is indexes, and even of the 87GB of data, only 20GB is from GBIF and 15GB from FIA (so most of it is duplication).

added inputs/IRMNG/*_homonym_epithet/map.csv, etc. (created by */run)

bugfix: inputs/input.Makefile: `%/install %/header.csv: %/create.sql`: in noclobber mode, mark %/header.csv as .PRECIOUS so the existing file won't be deleted if the table already exists (causing an error exit)

bugfix: lib/runscripts/table.run: remake_VegBIEN_mappings(): run yes using piped_cmd() so the SIGPIPE doesn't cause an errexit

added inputs/IRMNG/{genus_homonym_epithet,family_homonym_epithet}/run, which inherit from ../table.run so that load_data() (which runs create.sql) is invoked

added inputs/IRMNG/species_homonyms/new_terms.csv

bugfix: added no-op inputs/IRMNG/Source/run so inputs/IRMNG/run would have something to invoke for it

inputs/IRMNG/run: use lib/runscripts/datasrc_dir.run, which now provides import() and $subdirs

lib/runscripts/datasrc_dir.run: extend import.run and provide an import() implementation that runs all the runscripts for import_order.txt subdirs

lib/csvs.py: sniff(): support single-column spreadsheets by defaulting to the Excel dialect when the delimiter can't be determined

inputs/IRMNG/: added family_homonym_epithet, genus_homonym_epithet lookup tables, which use util.all_same() to filter out internal Plantae homonyms

schemas/util.sql: added all_same() aggregate

schemas/util.sql: added not_empty(anyarray)

schemas/util.sql: added not_null() (usable as an aggregate's FINALFUNC)

schemas/util.sql: added not_null() (usable as an aggregate's FINALFUNC)

bugfix: inputs/IRMNG/import_order.txt: need to specify order so that Source is first

bugfix: inputs/IRMNG/*/map.csv: remapped Authority to scientificNameAuthorship instead of authors (now data_authors <VegCore.vegpath.org?data_authors> for clarity)

inputs/IRMNG/map.csv: updated to scrubbed output names from */map.csv (/map.csv does not currently get scrubbed)

bugfix: inputs/IRMNG/species_homonyms/header.csv, map.csv: reset input columns to DSV (delim-separated values) header. they had gotten changed to the output names in running map.csv with remake=1, causing it to be remade from the (renamed) staging tables.

inputs/input.Makefile: $(_svnFilesGlob): added *Makefile

/README.TXT: `make inputs/{upload,download}`: first run with test=1 to see what the diffs will be

added inputs/IRMNG/, including runscripts to download the names. this is now the 2nd datasource after GBIF to use runscripts, and the 3rd after FIA/GBIF to use new-style import.

inputs/input.Makefile: $(_svnFilesGlob): added *run (runscripts)

lib/runscripts/table.run: import(): also run remake_VegBIEN_mappings() to accept the test output. this function was previously unused, but was left in for future use when lib/import.sh was translated to lib/runscripts/table.run (it was used in its import.sh form in inputs/FIA/occurrence_all/import).

bugfix: lib/runscripts/table.run: remake_VegBIEN_mappings(): need to change to $top_dir before running `rm header.csv map.csv`

lib/sh/util.sh: added in_top_dir()

lib/runscripts/table.run: remake_VegBIEN_mappings(): only remake header.csv, map.csv if this target is being run directly, to avoid needing to remake them every time. for tables that are views, this instead requires them to be explicitly remade when the view columns change.

bugfix: lib/runscripts/subdir.run: subdir_make(): only remake if $remake has been explicitly propagated to subdir_make() by using self_make

lib/sh/make.sh: added deferred_check_target_exists alias and use it in check_fake_target_exists

added lib/sh/web.sh with curl wrapper

lib/sh/make.sh: added check_wildcard_target_exists alias

lib/sh/util.sh: added wildcard1 alias

lib/sh/util.sh: added echo1()

lib/runscripts/table.run: load_data(): first make sure schema is installed

lib/runscripts/table.run: added datasrc_make_install()

table_make_install(): take $install_log as an overridable kw param to support install logs in different locations

lib/runscripts/table.run: load_data(): split noclobber functionality into separate table_make_install() function, which can be used by other install-related targets

added schemas/VegBIEN/taxonomy/higherPlantGroup.xlsx.src.txt with Brad's description of how the names were chosen

added schemas/VegBIEN/taxonomy/higherPlantGroup.xlsx

schemas/VegBIEN/planning/taxonomy/: moved non-VegBIEN-specific resources to planning/resources/taxonomy/. this includes Brad's all-important Nomenclature_excerpt.ppt with the Latin taxonomic hierarchy suffixes on slide 5.

bugfix: schemas/vegbien.sql: taxon_trait_view: use the TNRS-scrubbed name from ScrubbedTaxon when available

schemas/vegbien.sql: split geoscrub_input_view's new-row-only filtering into separate view geoscrub_input_new, so that the full geoscrub_input rows are still available. the reduction in geoscrub_input from eliminating the already-scrubbed rows was only 280,000 (5076500 - 4799173) out of a possible 1.7 million (1707970), so it makes sense to just run geoscrubbing on the full input. (the lower-than-expected reduction is most likely due to rows from pre-refresh data being present in the original geoscrub_output table, which have been replaced by different, post-refresh input rows.)

added exports/_archive/

mappings/VegCore-VegBIEN.csv: genus->taxonlabel.taxonomicname: use new _filter_genus() (see r9882)

backups/TNRS.backup.md5: updated

bin/make_analytical_db: use new mk_table() instead of TRUNCATE/INSERT

bin/make_analytical_db: added mk_table() and use it in mk_analytical_table()

schemas/vegbien.sql: higher_plant_group_nodes: ferns and allies: added Lycopodiophyta node, as requested by Brad in the conference call (wiki.vegpath.org/2013-06-13_conference_call)

schemas/vegbien.sql: geoscrub_input_view: exclude rows that have already been geoscrubbed, by anti-joining on geoscrub_output

inputs/.geoscrub/geoscrub_output/postprocess.sql: set decimallatitude, decimallongitude types to double precision to facilitate joining with other double precision values

inputs/.geoscrub/geoscrub_output/postprocess.sql: coords index: added rest of input columns so this can be used to check the existence of a result by input. added runtime (55 s). use idempotent create_if_not_exists().

schemas/vegbien.sql: higher_plant_group_nodes: ferns and allies: added Lycopodiophyta node, as requested by Brad in the conference call (wiki.vegpath.org/2013-06-13_conference_call)

bugfix: schemas/vegbien.sql: higher_plant_group_nodes: removed ferns and allies nodes Anthocerotophyta, Marchantiophyta, Bryophyta, which were incorrectly said to be part of this clade in the BIEN2 analytical DB overview (/planning/workflow/validation/BIEN2_Analytical_DB_overview.docx > p. 13 bottom > last ¶). see http://wiki.vegpath.org/2013-06-13_conference_call#fix-higher_plant_group_nodes-mapping .

bugfix: /Makefile: postgres-Linux: phpPgAdmin: added steps to configure it for Apache 2.4

/run: geoscrub_input/make(): documented runtime (40 s)

bin/make_analytical_db: added `/run export_` to make the geoscrub_input CSV export

inputs/.TNRS/schema.sql: tnrs_populate_fields(): removed no longer needed casts of *_score to double precision

inputs/.TNRS/schema.sql: tnrs: *_score: changed type to double precision because these fields are always floats. this also avoids the need to manually cast them to double precision each time they are used.

lib/tnrs.py: HTTP requests: rewrapped lines

lib/tnrs.py: updated HTTP requests to match current web app

bugfix: lib/tnrs.py: download_request_template: changed dirty to true (to match the current web app), which is apparently needed to apply the source_sorting setting to the downloaded TSV in addition to the GUI results

lib/tnrs.py: retrieval_request_template: turned source_sorting back off, because it causes any match from the first source to always be used, even if it has a lower match score than the match from the other source. (Brad confirms that this should be off.) I think we had this on originally to ensure that only Tropicos results were used when available, rather than USDA when it was a better match. * note that due to a bug in the web app, this change will not actually be effective, because the source_sorting option is only applied to the GUI results, not the downloaded TSV. *

inputs/.TNRS/schema.sql: tnrs: Name_number: changed type to integer so it would sort numerically

inputs/.TNRS/schema.sql: added pkey on Time_submitted, Name_number

inputs/.TNRS/schema.sql: changed Name_submitted pkey to a unique constraint to allow adding a pkey on Time_submitted, Name_number instead

inputs/.TNRS/schema.sql: Time_submitted, Name_number: added NOT NULL constraints so that they can be used in a unique constraint

lib/tnrs.py: submission_request_template: include GCC in addition to Tropicos, because it provides more synonyms than Tropicos for Asteraceae, and the accepted names still match the Tropicos backbone (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/2013-06-13_conference_call#include-GCC-when-running-TNRS)

inputs/.TNRS/tnrs/tnrs.make: removed no longer needed end time, now that the total runtime is printed

inputs/.TNRS/tnrs/tnrs.make: print the total runtime using `time`

inputs/.TNRS/tnrs/tnrs.make: include the end time in addition to the start time so that the total runtime can be calculated

lib/sh/util.sh: command-specific alternate stdin/stdout/stderr: choice of 40/41/42: added mnemonic that 4 looks like A for Alternate

bugfix: /README.TXT: Full database import: added step to remove any leftover TNRS lockfile. usually, the PID in it would not exist, but sometimes it now refers to a different, active process which blocks tnrs.make.

schemas/vegbien.sql: allow public_ to view lookup tables (cultivated_family_locations, higher_plant_group_nodes)

added backups/TNRS.backup.md5, vegbien.r9459.backup.md5

bugfix: lib/sh/local.sh: sync_upload(): need to use --no-group to prevent the group from being reset to aaronmk upon download from jupiter (which uses group aaronmk instead of bien). use ./fix_perms to set the group of all files to bien. also use --no-owner in case running as root.

lib/sh/sync.sh: removed sync_download(). use swap=1 sync_upload() instead.

lib/sh/sync.sh: removed download(). use swap=1 upload, or swap=1 upload_caller, instead. this avoids having separate upload()/download() pairs for every caller of upload(), because you can instead just set swap=1.

bugfix: lib/sh/sync.sh: upload(): don't kw_params $swap because this unexports it, preventing put from seeing it. instead, use echo_vars to print it.

added bin/sync_upload, a wrapper around sync_upload()