web/BIEN3/Redmine/.htaccess: enable redirects that avoid using a subdir's .htaccess

web/BIEN3/Redmine/wiki/.htaccess: removed no longer needed ignore_fs, since the .htaccess does not have RewriteRules that would need this in a RewriteCond

web/BIEN3/Redmine/issues/.htaccess: main issues page: added default filter conditions

bugfix: web/BIEN3/Redmine/issues/.htaccess: need to redirect to separate URL for individual issues, because they are not located under the issues/ subdir in Redmine

added web/.issues symlink and dest dir (needed because Apache does not support dangling symlinks)

web/BIEN3/Redmine/wiki/.htaccess: documented that this dir is needed because Apache does not support dangling symlinks

bugfix: web/.htaccess: need to expand top-level symlinks to avoid RewriteBase issues

web/main.conf: added RewriteMap for readlink

added web/readlink

web/links/index.htm: updated to Firefox bookmarks: updated favicons

web/links/index.htm: updated to Firefox bookmarks: updated favicons

web/BIEN3/Redmine/wiki/.htaccess: just use this dir as symlink dest, since the dir name is the same as the URL path within Redmine

web/.htaccess: don't rewrite existing files/dirs: allow forcing rewrite of existing things with %{ENV:ignore_fs}

web/BIEN3/Redmine/svn-web/.htaccess: use Redmine/ instead of main/ subdir

web/BIEN3/Redmine/.htaccess: point this to the Redmine root instead of to the wiki, to avoid the need to append /main

backups/vegbien.r14089.backup.md5: updated

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_best_match_jerry_lu index to facilitate finding names affected by the match-picking bug (#943)

backups/TNRS.backup.md5: updated

fix: inputs/HVAA/Specimen/postprocess.sql, map.csv: monthCollected/dayCollected: fix indefinite dates (which aren't supported by Postgres), as decided by Bob (https://docs.google.com/spreadsheets/d/1PI8n0CRttN7ttsXs5qfh5OFFzSoAfJj0gSbylgX6vj4/edit#gid=0)

schemas/util.sql: added date_part_fix()

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's and Martha's request (e-mails from Martha on 2014-8-12 at 17:37PT, and from Brian M on 2014-8-13 at 16:21PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: added view_full_occurrence_individual_*GBIF, analytical_stem_*GBIF requested by Mark. note that this change has already been made on vegbiendev.

schemas/VegBIEN/data_dictionary/VegBIEN data dictionary.xlsx: updated

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: view_full_occurrence_individual, analytical_stem: renamed columns to shortened names at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: analytical_stem_view: renamed to analytical_stem since this replaces the materialized analytical_stem table. note that this change has already been made on vegbiendev.

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

schemas/public_.sql: viewFullOccurrence_individual: re-ran viewFullOccurrence_individual_view_modify() to udpate this

bugfix: schemas/util.sql: copy_struct(): also need to util.copy_comment() because CREATE TABLE __ INCLUDING ALL is missing this

schemas/util.sql: added copy_comment(regclass, regclass)

schemas/public_.sql: viewFullOccurrence_individual_view: CREATE INDEX runtime: documented 2-column runtime (~2 h)

exports/analytical_stem_*GBIF.csv.run: documented runtime (40 min-1.2 h)

exports/view_full_occurrence_individual_*GBIF.csv.run: documented runtime (20-30 min)

added exports/analytical_stem_GBIF.csv.run, analytical_stem_non_GBIF.csv.run

added exports/view_full_occurrence_individual_GBIF.csv.run, view_full_occurrence_individual_non_GBIF.csv.run

schemas/public_.sql: viewFullOccurrence_individual_view: added "after updating this" instructions

schemas/public_.sql: viewFullOccurrence_individual_view: documented CREATE INDEX runtime (10 min - 1.5 h depending on the datatype and % populated)

web/links/index.htm: updated to Firefox bookmarks: updated to use frenzy instead of starscream

fix: lib/tnrs.py: retrieval_request_template: source_sorting (Constrain by Source): corrected explanation to reflect that the behavior is actually the same in both modes, since only one match is ever marked as selected, and that match should always come first

planning/meetings/BIEN conference call availability.xlsx: updated

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_name index

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_family index

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_species_binomial index

bugfix: schemas/public_.sql: *_view_modify(): need to set the search_path so that tables are created in the same schema as the function, rather than whichever schema happens to be at the beginning of the search_path

bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to support being used directly instead of via a materialized table

schemas/public_.sql: removed no longer used analytical_stem. use analytical_stem_view or viewFullOccurrence_individual instead.

fix: schemas/public_.sql: viewfulloccurrence_individual_view_modify(): fixed capitalization in function name (needs "" to preserve case)

schemas/public_.sql: other derived views: use viewFullOccurrence_individual instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)

schemas/public_.sql: validation views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)

schemas/public_.sql: derived views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)

bugfix: schemas/util.sql: expansion_min_cols(): increased to properly handle all public-schema views (the largest is currently 2014-6-12.Jeff_Ott.climatic_range_determinants)

schemas/util.sql: view_def_to_orig(): use new expansion_min_cols() for easier configuration

schemas/util.sql: added expansion_min_cols() (the minimum # of cols from the same table to be treated as a * expression)

fix: schemas/public_.sql: analytical_stem_view: regenerated columns list for viewFullOccurrence_individual (instead of viewFullOccurrence_individual_view)

bugfix: mappings/VegCore-VegBIEN.csv: prefixed taxonomic ranks: use _concat_nullify() so that the prefix is only added if the epithet is non-NULL

fix: schemas/util.sql: col_re(): support column names with " in them

schemas/util.sql: added _concat_nullify(), which uses || instead of concat()

bugfix: inputs/FIA/REF_RESEARCH_STATION/map.csv: mapped country, which is not provided in the FIA data

schemas/public_.sql: removed no longer used threatened_taxonlabel_view. use iucn_red_list_view instead.

schemas/public_.sql: viewFullOccurrence_individual_view: documented materialize time (22 h)

inputs/.TNRS/schema.sql: taxon_match: removed no longer used scrubbed_unique_taxon_name. the scrubbed name ranks are now generated from the other TNRS columns instead.

/README.TXT: Full database import: added steps to re-run geoscrubbing

exports/geoscrub_input.csv.run: export_(): updated runtime (30 s)

fix: exports/viewFullOccurrence_*.csv.run: need to limit # rows to 5000 as requested by Bob

schemas/public_.sql: viewFullOccurrence_*: documented materialize time

bin/make_analytical_db: materialize viewFullOccurrence_individual_view instead of analytical_stem_view because analytical_stem_view is now generatable via a simple join onto viewFullOccurrence_individual_view. this avoids running into potential disk space constraints when materializing and backing up both tables (~50 GB/table * 2 tables * 2 copies (incl. the backup) = 200 GB, which is very close to the available disk space).

schemas/public_.sql: analytical_stem_view: use new materialized viewFullOccurrence_individual

schemas/public_.sql: added viewFullOccurrence_individual by running viewFullOccurrence_individual_view_modify()

schemas/public_.sql: added viewFullOccurrence_individual_view_modify(), analogous to analytical_stem_view_modify()

bin/make_analytical_db: removed extra () around psql_verbose_vegbien

bin/make_analytical_db: removed no longer used mk_table()

bin/make_analytical_db: use more up-to-date *_view_modify() functions instead of mk_table()

inputs/.TNRS/schema.sql: removed no longer used view ValidMatchedTaxon. use taxon_scrub instead.

schemas/public_.sql: iucn_red_list_view: use taxon_scrub instead of ValidMatchedTaxon since they are equivalent

inputs/.TNRS/schema.sql: taxon_scrub: use taxon_best_match directly, to avoid the need for a separate ValidMatchedTaxon view

fix: inputs/.TNRS/schema.sql: taxon_scrub: merged synonymous columns

schemas/vegbien.sql: taxon_scrub: documented steps to merge synonymous columns

inputs/.TNRS/schema.sql: removed no longer used view MatchedTaxon. use taxon_best_match instead.

inputs/.TNRS/schema.sql: ValidMatchedTaxon: use taxon_best_match now that it's equivalent to MatchedTaxon

bugfix: schemas/public_.sql: tnrs_input_name: use taxon_match instead of taxon_best_match because there is no index on taxon_match that includes just the filters used by taxon_best_match

schemas/public_.sql: tnrs_input_name: use taxon_best_match now that it's equivalent to MatchedTaxon

backups/TNRS.backup.md5: updated

fix: inputs/.TNRS/schema.sql: MatchedTaxon: merged synonymous columns

fix: schemas/util.sql: view_is_subset_or_renaming(): views with CASE statements are also not subsets/renamings

inputs/.TNRS/schema.sql: removed no longer used taxon_scrub.scrubbed_unique_taxon_name.* . use taxon_scrub instead.

inputs/.TNRS/schema.sql: taxon_scrub: use taxon_match derived columns instead of the incorrect values in taxon_scrub.scrubbed_unique_taxon_name.* (which does not work with the multi-match strategy)

inputs/.TNRS/schema.sql: MatchedTaxon: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.

inputs/.TNRS/schema.sql: taxon_scrub: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.

added exports/viewFullOccurrence_{CVS,VegBank,NCU}.csv.run

schemas/public_.sql: added viewFullOccurrence_{CVS,VegBank,NCU} for Bob

bugfix: schemas/util.sql: added GRANT USAGE for bien_read, public_ so that util schema functions can be called by other users

inputs/.TNRS/schema.sql: taxon_match: to port derived column changes to vegbiendev: derived_cols_export() code: documented runtime (6 h)

bugfix: inputs/.TNRS/schema.sql: removed no longer used derived column __accepted_infraspecific_label, which had a buggy formula that broke derived_cols_populate()

bugfix: schemas/util.sql: drop_derived_col(): also need to run util.derived_cols_trigger_update()

bugfix: inputs/.TNRS/schema.sql: removed no longer used derived column __accepted_infraspecific_label, which had a buggy formula that broke derived_cols_populate()

fix: inputs/.TNRS/schema.sql: taxon_match: to remove a column: updated instructions

bugfix: lib/sh/util.sh: str2varname(): need to lowercase str because on case-insensitive filesystems, paths sometimes canonicalize to a different capitalization than the original

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

bugfix: lib/sh/util.sh: die(): need stub since this is invoked before it's defined

bugfix: lib/sh/util.sh: setup_log_fd(): don't change $log_fd to stdlog until stdlog is set up, to avoid "Bad file descriptor" errors