bugfix: /Makefile: postgres_restart: added separate Linux version that deals with Linux-specific issues (as in $(postgresReload-Linux))

/Makefile: added postgres_restart, since this is often invoked separately from the entire postgres_reload target

/README.TXT: Full database import: disk space: increased minimum requirement to 500GB (~200GB extra), as the import may use significant additional space for temp tables

/README.TXT: Full database import: documented that env vars set before invoking `screen` will be inherited by it, so these steps will work even if they come before `screen`

backups/TNRS.backup.md5: updated

/README.TXT: Full database import: added steps to set a custom version, if the auto-assigned one would cause a collision with the last import

/README.TXT: Full database import: `unset version`: documented that this is needed because it may have been set in the outer shell

fix: lib/sql_io.py: put_table(): don't warn if can't create pkey, because this just indicates that a set-returning function was used. this should get rid of the last of the confusing benign warnings in the test output.

fix: lib/sql.py: flatten(): don't warn if can't create pkey, because this just indicates that a set-returning function was used

lib/sql.py: run_query_into() added add_pkey_warn param to support turning off "could not create unique index" warnings, which are sometimes benign (eg. when using set-returning functions with column-based import)

/README.TXT: Full database import: disk space: updated schema size (315GB)

/README.TXT: Full database import: removed `up` on jupiter because this is done as part of "do steps under Maintenance > "to synchronize vegbiendev, ..."

/README.TXT: Full database import: moved "do steps under Maintenance > "to synchronize vegbiendev, ..." outside of "On local machine" because these steps don't only take place on the local machine

/README.TXT: use `up` instead of `svn up --force` for consistency

fix: /README.TXT: always use `up` instead of `svn up` since this includes --force

/README.TXT: Full database import: removed unneeded `ssh -t vegbiendev.nceas.ucsb.edu exec sudo su - aaronmk` at beginning since this is performed again the first time it's needed

fix: /README.TXT: Full database import: removed erroneous line that resulted from a search-and-replace of connection commands in r12396. (it used to read "Follow the steps under Connecting to vegbiendev above, using jupiter instead". this step is now performed on the line below it.)

bin/make_analytical_db: removed remake_diff_tables() because this is now done for each datasource in inputs/input.Makefile

bugfix: schemas/vegbien.sql: schemas/vegbien.sql(): need to util.use_schema(schema_anchor) before initializing vars that use own-schema functions

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)

bin/make_analytical_db: removed no longer needed "${public}_validations" schema qualifier, now that it is in the search_path

fix: bin/vegbien_dest: added public_validations

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

lib/sh/util.sh: removed end_try_subshell, which now does the same thing as end_try

fix: lib/sh/archives.sh: unzip(): support -p option, which pipes extracted data to stdout

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

added lib/runscripts/extract_header.run

fix: lib/sh/make.sh: direct the user to use begin_target instead of set_make_vars (set_make_vars is now used by begin_target)

fix: lib/runscripts/util.run: to_top_file(): handle $_remake properly, without requiring deferred_check_target_exists to set to_file()'s flags

bugfix: lib/sh/util.sh: die(): usage: documented that if msg uses $(...), save_e is needed

bugfix: lib/sh/util.sh: already_exists_msg(): need to save_e, because new $(mk_hint) call resets $?

lib/sh/util.sh: die(): always errexit even if $e = 0, because die always indicates an error

lib/sh/util.sh: added rethrow!(), which always errexits, even if $e = 0

lib/sh/util.sh: rethrow(): also work in situations where $e is not set

lib/sh/util.sh: rethrow: made it a function since there is now no need for it to be an alias

lib/sh/util.sh: rethrow: removed `test "$e" != 0` since errexit only does anything if $e != 0

lib/sh/util.sh: removed separate rethrow_exit*, rethrow_subshell*, since they now do the same thing as rethrow*

lib/sh/util.sh: rethrow*!: use new errexit, which works in functions and subshells

lib/sh/util.sh: added errexit(), used in place of (exit "$1") because a bug in bash prevents subshells from triggering errexit

lib/sh/util.sh: added bool!()

fix: lib/sh/util.sh: redir(): need to indent before invoking an external command (not just in command__exec(), but for all redir() calls)

lib/sh/make.sh: with_rm(): documented that it only works inside a runscript target that starts w/ begin_target

*{.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

schemas/vegbien.sql: updated _specimens_01_count_of_total_records_specimens_in_source_db

validation/aggregating/specimens/qualitative_validations_specimens.sql: use taxonoccurrence instead of location as the table that all specimens should have, as decided in the 2014-03-27 conference call (wiki.vegpath.org/2014-03-27_conference_call#aggregating-validations)

lib/runscripts/util.run: support conventional main() method as well as `all` target

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).

/README.TXT: moved "to back up e-mails" and "to back up the version history" before settings backup so that the local backup of these is up to date when everything gets backed up

inputs/XAL/Specimen/header.csv: updated

/README.TXT: to synchronize vegbiendev, jupiter, and your local machine: backups/TNRS.backup: do this before the general sync so that any reverse sync that's needed won't include it

/README.TXT: to synchronize vegbiendev, jupiter, and your local machine: backups/TNRS.backup: use bin/sync_upload now that this works for rsync-ignored files

bugfix: lib/sh/sync.sh: don't unintentionally rsync-ignore explicitly-specified files

lib/sh/util.sh: filesystem: added is_*(), could_be_*()

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

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

fix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: run `up` on all machines, not just jupiter, because all must be up-to-date to avoid extraneous diffs

bugfix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: `svn up` on jupiter: need to use up alias because that adds --force

bugfix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: added `svn up` on jupiter: needs to be in main dir (~/bien), not ~/Dropbox/svn/

/README.TXT: to synchronize vegbiendev, jupiter, and your local machine: added `svn up` on jupiter to avoid extraneous diffs when rsyncing

planning/workflow/bien3_architecture/stage_I.png, stages.png: synced to bien3_architecture.pptx

planning/workflow/bien3_architecture.pptx: stage I: clarified that the database input is intended to be a normalized input, and its corresonding output is intended to be denormalized

validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: stage I: clarified that the database input is intended to be a normalized input, and its corresonding output is intended to be denormalized

bugfix: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: _specimens_16_list_distinct_specimen_descriptions: should use DISTINCT

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_16_list_distinct_specimen_descriptions

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_16_list_distinct_specimen_descriptions

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_15_list_distinct_locality_descriptions

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_09_list_of_unique_verbatim_author_taxa_with_genus

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_08_count_of_unique_verbatim_author_taxa_with_genus

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_05_list_of_verbatim_species_excluding_author

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_04_count_of_unique_verbatim_species_without_author

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_03_list_of_verbatim_families

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_02_count_of_unique_verbatim_families

schemas/vegbien.ERD.mwb: regenerated exports

schemas/vegbien.sql: public_validations: added _specimens_01_count_of_total_records_specimens_in_source_db

validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_01_count_of_total_records_specimens_in_source_db

validation/aggregating/specimens/qualitative_validations_specimens.sql: added config statements for datasource and query planner

web/links/index.htm: updated to Firefox bookmarks: Firefox: added instructions for enabling security.password_lifetime and making all tabs load when the browser is opened

/README.TXT: Schema changes: manually apply schema changes to the live public schema: moved under "update mappings and staging table column names" because this is a necessary part of that step

/README.TXT: Schema changes: manually apply schema changes to the live public schema: moved under "update mappings and staging table column names" because this is a necessary part of that step

/README.TXT: Schema changes: changed "update staging table column names" to "update mappings and staging table column names"

fix: validation/aggregating/specimens/qualitative_validations_specimens.sql: use pg_dump's formatting for COMMENT ON to facilitate diffing against a pg_dump export of the DDL statements

validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: removed DDL statements so that running the query file does not alter the database, using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#remove-DDL-statements

validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: updated to DB, which pg_dump-formats the views

validation/**.sql: replaced CREATE OR REPLACE VIEW with CREATE VIEW to match pg_dump output for diffing

added inputs/NY/validations*.sql*

fix: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: use pg_dump's formatting for COMMENT ON to facilitate diffing against a pg_dump export of the DDL statements

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

fix: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: decimalLatitude/decimalLongitude: need to cast to double precision for numeric comparisons

fix: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: CollectedDate: updated for refreshed NY data

validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: fixed typos in column aliases

validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: translated column names to VegCore, using `bin/in_place validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql env text=1 bin/repl inputs/NY/Ecatalog_all/map.csv` from the steps at wiki.vegpath.org/Aggregating_validations_refactoring#translate-to-Postgres

fix: bin/repl: text mode (whether all patterns are plain text) should default to on, not off, if matching entire cells in a spreadsheet

bugfix: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: need to enclose additional mixed-case identifiers in "", using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#translate-to-Postgres