Activity
From 03/09/2014 to 04/07/2014
04/07/2014
- 06:21 PM Revision 13066: schemas/vegbien.sql: public_validations: specimens queries: added autogenerated ~type tables
- 06:19 PM Revision 13065: inputs/NY/run: `make inputs/NY/validate`: updated runtime (5 min)
- 06:09 PM Revision 13064: validation/aggregating/specimens/qualitative_validations_specimens.sql: removed DDL statements, using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#remove-DDL-statements
- 06:07 PM Revision 13063: schemas/vegbien.sql: public_validations: added specimens queries to pipeline
- 05:51 PM Revision 13062: validation/aggregating/specimens/qualitative_validations_specimens.sql: parameterize queries by datasource
- 05:35 PM Revision 13061: validation/aggregating/**.sql output queries: use `SET join_collapse_limit = 1;` to match public_validations.rematerialize_out_view()
- 05:17 PM Revision 13060: fix: schemas/vegbien.sql: public_validations.rematerialize_out_view(text, regclass): run with join_collapse_limit = 1 to fix query planner issues. this option has been tested on the queries that do not yet use the standard join sequence (plots #11,12,13,14,16,17,18), and all of these queries also work fine with join_collapse_limit = 1. (the standard join sequence is used to ensure *both* correctness of the query and compatibility with join_collapse_limit = 1, but in some cases is not needed for join_collapse_limit.)
- 04:35 PM Revision 13059: validation/aggregating/specimens/qualitative_validations_specimens.sql: _specimens_12_distinct_collector_name_collect_num_date_w_count: turn off join_collapse_limit instead of enable_mergejoin/enable_hashjoin, because join_collapse_limit is something that we will eventually want to turn off for all queries, which would avoid this query needing special handling. (on the other hand, enable_mergejoin/enable_hashjoin may be necessary for some queries and we probably won't turn them off for all queries.)
- 01:43 PM Revision 13058: bugfix: lib/runscripts/table.run: table_make_install(): need to ignore skip_table() errexit
- 10:39 AM Revision 13057: lib/sh/util.sh: import_vars: documented that vars already set will *not* be overwritten
- 09:47 AM Revision 13056: inputs/NY/run: documented `make inputs/NY/validate` runtime (2 min, currently for the input queries)
04/04/2014
04/03/2014
- 07:31 PM Revision 13054: added validation/aggregating/pipeline/validations_on_sparse_datasources.odg
- 04:13 PM Revision 13053: planning/workflow/bien3_architecture/stage_I.png, stages.png: synced to bien3_architecture.pptx
- 04:09 PM Revision 13052: planning/workflow/bien3_architecture.pptx: stage I: made all datasources the same height so that the denormalized VegCore schema boxes would all look exactly the same. widened the denormalized VegCore schema boxes to make it visually clear that they have more columns than the staging tables denormalized together
- 03:40 PM Revision 13051: planning/workflow/bien3_architecture/stage_I.png, stages.png: synced to bien3_architecture.pptx
- 03:39 PM Revision 13050: planning/workflow/bien3_architecture.pptx: updated to reflect decisions made in the 2014-04-03 conference call (wiki.vegpath.org/2014-04-03_conference_call#import-process-2)
- 08:53 AM Revision 13049: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_14_count_of_all_invalid_verbatim_lat_long
- 08:35 AM Revision 13048: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_12_distinct_collector_name_collect_num_date_w_count
- 08:04 AM Revision 13047: validation/aggregating/specimens/qualitative_validations_specimens.sql: _specimens_13_count_of_all_verbatim_and_decimal_lat_long: fixed whitespace
- 07:32 AM Revision 13046: validation/aggregating/specimens/qualitative_validations_specimens.sql: removed trailing whitespace
- 07:31 AM Revision 13045: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_13_count_of_all_verbatim_and_decimal_lat_long
04/02/2014
- 05:55 PM Revision 13044: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_11_list_of_three_standard_political_divisions
- 05:36 PM Revision 13043: validation/aggregating/specimens/qualitative_validations_specimens.sql: *_of_species_binomials: switched back to the old queries that use the split-apart ranks instead of the concatenated taxon name. note that these will not work on all specimens datasources, but now that #6,7 were selected to use the concatenated taxon name, this isn't a problem.
- 05:21 PM Revision 13042: 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
- 05:16 PM Revision 13041: 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
- 05:14 PM Revision 13040: 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
- 05:01 PM Revision 13039: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_10_count_number_of_records_by_institution
- 04:38 PM Revision 13038: 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
- 04:09 PM Revision 13037: 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
- 04:03 PM Revision 13036: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_06_count_of_unique_verb_subsp_taxa_without_author, _specimens_07_list_of_verbatim_subspecific_taxa_without_author
- 03:54 PM Revision 13035: 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
- 03:14 PM Revision 13034: validation/aggregating/specimens/qualitative_validations_specimens.sql: removed extra ; at ends of queries
- 03:13 PM Revision 13033: validation/aggregating/specimens/qualitative_validations_specimens.sql: use the concatenated taxon name instead of concatenating the ranks, as decided in the 2014-03-27 conference call (wiki.vegpath.org/2014-03-27_conference_call#aggregating-validations)
- 03:05 PM Revision 13032: validation/aggregating/specimens/qualitative_validations_specimens.sql: use the concatenated taxon name instead of concatenating the ranks, as decided in the 2014-03-27 conference call (wiki.vegpath.org/2014-03-27_conference_call#aggregating-validations)
- 11:17 AM Revision 13031: /README.TXT: Full database import: disk space: added high-water mark of 1.8 TB @11:15:05
- 10:56 AM Revision 13030: /README.TXT: Full database import: added steps to figure out which datasource tables were not successfully imported due to disk space errors
- 10:45 AM Revision 13029: fix: /README.TXT: Full database import: moved verification of exit statuses before verification of DB contents because there is no point in verifying the DB if the datasources didn't finish importing
- 09:01 AM Revision 13028: /README.TXT: Full database import: disk space: documented that the entire disk again gets used long after the beginning of the import, when only a few datasources are running (ie. it definitely seems to be a recent bug in Postgres, and not a latent problem)
04/01/2014
- 05:40 PM Revision 13027: /README.TXT: Maintenance: added task to regularly re-run full-database import so that bugs in it don't pile up. it needs to be kept in working order so that it works when it's needed.
- 04:24 PM Revision 13026: /README.TXT: Full database import: added steps to manually reimport the applicable datasources if there are errors due to exceeding available disk space
- 04:13 PM Revision 13025: /README.TXT: Full database import: removed extra `ssh -t vegbiendev.nceas.ucsb.edu` before "upload logs", because the previous steps also occur on vegbiendev
- 04:04 PM Revision 13024: /README.TXT: Notes on system stability: added recommendation to maintain a snapshot copy of the VM as it was at the last successful import, for fallback use if a system upgrade breaks anything. system upgrades on the snapshot VM should be disabled completely, and because this will also disable security fixes, the snapshot VM should be disconnected from the internet and all networking interfaces. (this is an unfortunate consequence of modern OSes being written in non-memory-safe languages such as C and C++.)
- 03:43 PM Revision 13023: /README.TXT: Full database import: disk space: documented that a higher high-water mark actually occurs later in the import, so that the disk usage issue actually remains a problem after the very beginning
- 03:37 PM Revision 13022: fix: /README.TXT: Full database import: disk space: increased the minimum free space recommendation to 1 TB, because analysis of the disk usage during the beginning of the import shows that actually close to the entire amount is being used. however, this problem is normally undetectable unless the disk space is specifically checked, because it only manifests itself if the available disk space is exceeded completely.
- 02:04 PM Revision 13021: /README.TXT: Full database import: documented that the beginning of the import should be scheduled at a time when the DB will not be needed for other uses, because vegbiendev will be slow for the first few hours of the import due to the import using all the available cores
- 01:36 PM Revision 13020: /README.TXT: Full database import: documented that CPU load warning e-mails can safely be ignored. they happen because the parallel imports use all the available cores.
- 01:31 PM Revision 13019: fix: lib/common.Makefile: $(nice): use an increment of +10 instead of +5 because +5 still leaves the shell sluggish
- 01:29 PM Revision 13018: lib/common.Makefile: added $(nice) and use it everywhere its definition is used
- 01:14 PM Revision 13017: /README.TXT: Full database import: exiting `screen`: clarify that you must use `exit`, as Ctrl+D gets disabled to prevent accidental exits
- 12:47 PM Revision 13016: /README.TXT: Full database import: added step to restart Postgres to free up any disk space used by temp tables from the last import (this is apparently not automatically reclaimed)
- 12:45 PM Revision 13015: /Makefile: postgres_restart-Linux: documented that the manual running of the command is needed because for some reason, pg_ctl does not work when run inside make
- 12:43 PM Revision 13014: fix: /Makefile: postgres_restart-Linux: added pause after telling the user the command to run
- 12:42 PM Revision 13013: /Makefile: $(postgresReload-*): use postgres_restart for the postgres-restarting step
- 12:30 PM Revision 13012: bugfix: /Makefile: postgres_restart: added separate Linux version that deals with Linux-specific issues (as in $(postgresReload-Linux))
- 12:15 PM Revision 13011: /Makefile: added postgres_restart, since this is often invoked separately from the entire postgres_reload target
- 11:40 AM Revision 13010: /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
- 11:37 AM Revision 13009: /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`
- 11:26 AM Revision 13008: backups/TNRS.backup.md5: updated
- 11:23 AM Revision 13007: /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
- 11:08 AM Revision 13006: /README.TXT: Full database import: `unset version`: documented that this is needed because it may have been set in the outer shell
03/30/2014
- 07:54 PM Revision 13005: 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.
- 07:53 PM Revision 13004: fix: lib/sql.py: flatten(): don't warn if can't create pkey, because this just indicates that a set-returning function was used
- 07:52 PM Revision 13003: 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)
- 06:52 PM Revision 13002: /README.TXT: Full database import: disk space: updated schema size (315GB)
- 06:45 PM Revision 13001: /README.TXT: Full database import: removed `up` on jupiter because this is done as part of "do steps under Maintenance > "to synchronize vegbiendev, ..."
- 06:44 PM Revision 13000: /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
- 06:41 PM Revision 12999: /README.TXT: use `up` instead of `svn up --force` for consistency
- 06:40 PM Revision 12998: fix: /README.TXT: always use `up` instead of `svn up` since this includes --force
- 06:39 PM Revision 12997: /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
- 06:38 PM Revision 12996: 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.)
- 06:31 PM Revision 12995: bin/make_analytical_db: removed remake_diff_tables() because this is now done for each datasource in inputs/input.Makefile
- 06:28 PM Revision 12994: bugfix: schemas/vegbien.sql: schemas/vegbien.sql(): need to util.use_schema(schema_anchor) *before* initializing vars that use own-schema functions
- 06:12 PM Revision 12993: inputs/input.Makefile: validate: redirect the output to the log, as for other import-related operations
- 06:08 PM Revision 12992: inputs/input.Makefile: import: validate at the end of the import
- 06:02 PM Revision 12991: inputs/input.Makefile: added new-style aggregating validations (`validate` target)
- 06:02 PM Revision 12990: bin/make_analytical_db: removed no longer needed "${public}_validations" schema qualifier, now that it is in the search_path
- 06:00 PM Revision 12989: fix: bin/vegbien_dest: added public_validations
- 05:41 PM Revision 12988: 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
- 05:39 PM Revision 12987: lib/sh/util.sh: removed end_try_subshell, which now does the same thing as end_try
- 05:38 PM Revision 12986: fix: lib/sh/archives.sh: unzip(): support -p option, which pipes extracted data to stdout
- 05:11 PM Revision 12985: added inputs/GBIF/_src/0001000-131106143450413.zip.header.txt.run
- 05:11 PM Revision 12984: added lib/runscripts/extract_header.run
- 05:09 PM Revision 12983: 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)
- 05:06 PM Revision 12982: fix: lib/runscripts/util.run: to_top_file(): handle $_remake properly, without requiring deferred_check_target_exists to set to_file()'s flags
- 05:03 PM Revision 12981: bugfix: lib/sh/util.sh: die(): usage: documented that if msg uses $(...), save_e is needed
- 04:59 PM Revision 12980: bugfix: lib/sh/util.sh: already_exists_msg(): need to save_e, because new $(mk_hint) call resets $?
- 04:55 PM Revision 12979: lib/sh/util.sh: die(): always errexit even if $e = 0, because die always indicates an error
- 04:53 PM Revision 12978: lib/sh/util.sh: added rethrow!(), which always errexits, even if $e = 0
- 04:53 PM Revision 12977: lib/sh/util.sh: rethrow(): also work in situations where $e is not set
- 04:50 PM Revision 12976: lib/sh/util.sh: rethrow: made it a function since there is now no need for it to be an alias
- 04:47 PM Revision 12975: lib/sh/util.sh: rethrow: removed `test "$e" != 0` since errexit only does anything if $e != 0
- 04:45 PM Revision 12974: lib/sh/util.sh: removed separate rethrow_exit*, rethrow_subshell*, since they now do the same thing as rethrow*
- 04:42 PM Revision 12973: lib/sh/util.sh: rethrow*!: use new errexit, which works in functions *and* subshells
- 04:38 PM Revision 12972: lib/sh/util.sh: added errexit(), used in place of (exit "$1") because a bug in bash prevents subshells from triggering errexit
- 04:18 PM Revision 12971: lib/sh/util.sh: added bool!()
- 03:08 PM Revision 12970: fix: lib/sh/util.sh: redir(): need to indent before invoking an external command (not just in command__exec(), but for all redir() calls)
03/29/2014
- 04:10 AM Revision 12969: lib/sh/make.sh: with_rm(): documented that it only works inside a runscript target that starts w/ begin_target
- 04:06 AM Revision 12968: *{.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.)
- 03:58 AM Revision 12967: 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
03/28/2014
- 07:17 AM Revision 12966: schemas/vegbien.sql: updated _specimens_01_count_of_total_records_specimens_in_source_db
- 07:10 AM Revision 12965: 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)
- 07:03 AM Revision 12964: lib/runscripts/util.run: support conventional main() method as well as `all` target
- 02:39 AM Revision 12963: 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)
- 02:34 AM Revision 12962: fix: inputs/CTFS/AggregateObservation/map.csv: field mapped to occurrenceID: remapped to aggregateOrganismObservationID because these are not specimen occurrences
- 02:32 AM Revision 12961: fix: mappings/VegCore-VegBIEN.csv: taxonoccurrence.sourceaccessioncode: need to populate from aggregateOrganismObservationID when only that is available
- 02:03 AM Revision 12960: 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).
- 01:31 AM Revision 12959: /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
- 01:29 AM Revision 12958: inputs/XAL/Specimen/header.csv: updated
- 12:45 AM Revision 12957: /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
- 12:44 AM Revision 12956: /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
- 12:36 AM Revision 12955: bugfix: lib/sh/sync.sh: don't unintentionally rsync-ignore explicitly-specified files
- 12:32 AM Revision 12954: lib/sh/util.sh: filesystem: added is_*(), could_be_*()
- 12:31 AM Revision 12953: lib/sh/util.sh: added contains_match()
- 12:31 AM Revision 12952: lib/sh/util.sh: added ends_with()
03/27/2014
- 11:13 PM Revision 12951: 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
- 11:11 PM Revision 12950: bugfix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: `svn up` on jupiter: need to use up alias because that adds --force
- 11:10 PM Revision 12949: 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/
- 11:08 PM Revision 12948: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: added `svn up` on jupiter to avoid extraneous diffs when rsyncing
- 10:41 AM Revision 12947: planning/workflow/bien3_architecture/stage_I.png, stages.png: synced to bien3_architecture.pptx
- 10:32 AM Revision 12946: 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*
- 10:29 AM Revision 12945: 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*
- 09:02 AM Revision 12944: bugfix: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: _specimens_16_list_distinct_specimen_descriptions: should use DISTINCT
- 09:01 AM Revision 12943: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_16_list_distinct_specimen_descriptions
- 09:00 AM Revision 12942: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_16_list_distinct_specimen_descriptions
- 08:53 AM Revision 12941: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_15_list_distinct_locality_descriptions
- 08:48 AM Revision 12940: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_09_list_of_unique_verbatim_author_taxa_with_genus
- 08:47 AM Revision 12939: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_08_count_of_unique_verbatim_author_taxa_with_genus
- 08:36 AM Revision 12938: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_05_list_of_verbatim_species_excluding_author
- 08:35 AM Revision 12937: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_04_count_of_unique_verbatim_species_without_author
- 08:23 AM Revision 12936: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_03_list_of_verbatim_families
- 08:18 AM Revision 12935: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_02_count_of_unique_verbatim_families
- 08:06 AM Revision 12934: schemas/vegbien.ERD.mwb: regenerated exports
- 08:04 AM Revision 12933: schemas/vegbien.sql: public_validations: added _specimens_01_count_of_total_records_specimens_in_source_db
- 07:35 AM Revision 12932: validation/aggregating/specimens/qualitative_validations_specimens.sql: implemented _specimens_01_count_of_total_records_specimens_in_source_db
- 07:34 AM Revision 12931: validation/aggregating/specimens/qualitative_validations_specimens.sql: added config statements for datasource and query planner
- 05:06 AM Revision 12930: 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
- 04:43 AM Revision 12929: /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
- 04:43 AM Revision 12928: /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
- 04:40 AM Revision 12927: /README.TXT: Schema changes: changed "update staging table column names" to "update mappings and staging table column names"
- 04:13 AM Revision 12926: 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
- 04:07 AM Revision 12925: 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
- 04:01 AM Revision 12924: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: updated to DB, which pg_dump-formats the views
- 03:57 AM Revision 12923: validation/**.sql: replaced CREATE OR REPLACE VIEW with CREATE VIEW to match pg_dump output for diffing
- 03:36 AM Revision 12922: added inputs/NY/validations*.sql*
- 03:34 AM Revision 12921: 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
- 03:31 AM Revision 12920: 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
- 03:27 AM Revision 12919: 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
03/26/2014
- 09:34 PM Revision 12918: fix: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: decimalLatitude/decimalLongitude: need to cast to double precision for numeric comparisons
- 09:33 PM Revision 12917: fix: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: CollectedDate: updated for refreshed NY data
- 09:30 PM Revision 12916: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: fixed typos in column aliases
- 09:23 PM Revision 12915: 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
- 09:23 PM Revision 12914: fix: bin/repl: text mode (whether all patterns are plain text) should default to on, not off, if matching entire cells in a spreadsheet
- 07:16 PM Revision 12913: 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
- 07:15 PM Revision 12912: 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
- 06:09 PM Revision 12911: validation/aggregating/specimens/qualitative_validations_specimens.sql, NY/qualitative_validations_source_db_NYBG.VegCore.sql: abbreviated view names longer than 63 chars to prevent them from being truncated
- 06:07 PM Revision 12910: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: escape any ' inside '...' by doubling them
- 06:04 PM Revision 12909: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: translated SQL to Postgres
- 05:32 PM Revision 12908: validation/aggregating/specimens/qualitative_validations_specimens.sql, NY/qualitative_validations_source_db_NYBG.VegCore.sql: changed /* */ comments to COMMENT ON comments, using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#prepend-CREATE-VIEW
- 04:58 PM Revision 12907: validation/aggregating/specimens/qualitative_validations_specimens.sql, NY/qualitative_validations_source_db_NYBG.VegCore.sql: removed no longer needed -- comments containing the query name, using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#prepend-CREATE-VIEW
- 03:47 PM Revision 12906: validation/aggregating/specimens/qualitative_validations_specimens.sql: moved notes to comments to after the query
- 03:46 PM Revision 12905: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: moved notes to comments to after the query
- 03:44 PM Revision 12904: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: moved "Check" comments to after the query, using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#translate-to-Postgres
- 03:22 PM Revision 12903: validation/aggregating/specimens/qualitative_validations_specimens.sql: removed "Check: should return [#] rows" comments because these only apply to the NY results, not to all specimens datasources
- 03:16 PM Revision 12902: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: prepended CREATE VIEW, using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#prepend-CREATE-VIEW and the same abbreviations as the output queries (validation/aggregating/specimens/qualitative_validations_specimens.sql)
- 03:01 PM Revision 12901: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: synced "Check" comments to output queries validation/aggregating/specimens/qualitative_validations_specimens.sql
- 02:49 PM Revision 12900: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: enclosed mixed-case identifiers in "" using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#translate-to-Postgres
- 02:37 PM Revision 12899: 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
- 02:29 PM Revision 12898: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: updated to use column names for refreshed NY data
- 02:17 PM Revision 12897: fix: bin/repl: don't consider uppercase SQL keywords to indicate that a word is in a sentence
- 12:02 AM Revision 12896: validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql: use our staging tables instead of the BIEN2 MySQL staging tables
03/25/2014
- 11:52 PM Revision 12895: validation/aggregating/specimens/**.sql: removed trailing whitespace, using the steps at wiki.vegpath.org/Aggregating_validations_refactoring#translate-to-Postgres
- 11:39 PM Revision 12894: archived validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.sql
- 11:39 PM Revision 12893: added validation/aggregating/specimens/NY/qualitative_validations_source_db_NYBG.VegCore.sql, copied from qualitative_validations_source_db_NYBG.sql
- 11:33 PM Revision 12892: validation/aggregating/specimens/qualitative_validations_specimens.sql: added ; at end of `CREATE OR REPLACE VIEW` statements
- 04:18 AM Revision 12891: inputs/run: postprocess(): documented runtime on vegbiendev (1 h)
03/24/2014
- 06:22 PM Revision 12890: validation/aggregating/specimens/qualitative_validations_specimens.sql: removed input-query-specific comments
- 06:21 PM Revision 12889: validation/aggregating/specimens/qualitative_validations_specimens.sql: reworded rowcount check comments to apply to the output queries
- 06:18 PM Revision 12888: validation/aggregating/specimens/qualitative_validations_specimens.sql: shortened view names to fit within the 63-char limit without truncation
- 05:45 PM Revision 12887: /README.TXT: `make inputs/{NVS,SALVIAS,TEAM}/test`: updated runtime (1 min)
- 05:35 PM Revision 12886: 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)
- 05:32 PM Revision 12885: inputs/run: postprocess(): updated runtime (25 min)
- 05:22 PM Revision 12884: fix: validation/aggregating/specimens/qualitative_validations_specimens.sql: changed "Full inner join" to "Full outer join" because a FULL JOIN is a type of outer join, not inner join
- 05:04 PM Revision 12883: /README.TXT: calls to `inputs/run postprocess`: direct user to refer to inputs/run for this, so the runtime doesn't have to be updated in multiple places
- 05:02 PM Revision 12882: inputs/run: postprocess(): updated runtime (20 min)
- 05:01 PM Revision 12881: /README.TXT: Schema changes: added steps to update staging table column names on the local machine and vegbiendev
- 04:50 PM Revision 12880: fix: schemas/VegCore/mk_derived: added `EOF` at end to avoid (benign) "here-document delimited by end-of-file" warnings on Linux
- 01:49 AM Revision 12879: 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`.
- 01:43 AM Revision 12878: bugfix: lib/runscripts/table.run: schema/make calls: need to use `make schema` instead because old-style datasources don't have a top-level runscript (the absence of this identifies them as old-style so inputs/input.Makefile works correctly)
- 01:21 AM Revision 12877: /README.TXT: Maintenance: VegCore data dictionary: `make inputs/{NVS,SALVIAS,TEAM}/test`: recorded runtime (30 s)
- 01:17 AM Revision 12876: /README.TXT: Maintenance: VegCore data dictionary: `make inputs/{NVS,SALVIAS,TEAM}/test`: prepended `time` to enable obtaining the runtime
- 01:11 AM Revision 12875: /README.TXT: Maintenance: VegCore data dictionary: `inputs/run postprocess`: updated runtime (20 min)
- 12:45 AM Revision 12874: fix: schemas/util.sql: trim(): by default, cascadingly drop dependent columns so that they don't prevent trim() from succeeding. note that this requires the dependent columns to then be manually re-created.
03/23/2014
03/22/2014
- 06:20 AM Revision 12872: bugfix: lib/sh/util.sh: **DON'T** do `shopt -s lastpipe` because this causes a segfault on Linux in stderr_matches(). (it also isn't supported on Mac.) use @PIPESTATUS instead. note that we do not currently need lastpipe, since we use @PIPESTATUS (which actually provides more functionality for our purposes).
- 06:02 AM Revision 12871: fix: lib/sh/util.sh: echo_func(): file/line #: display with regular color because the lighter color actually draws attention *to* rather than *away from* the faded text
- 05:59 AM Revision 12870: lib/sh/util.sh: added plain()
- 05:56 AM Revision 12869: 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).
- 05:50 AM Revision 12868: bugfix: lib/sql_io.py: put_table(): is_literals: `return sql.value(cur): need to use sql.value_or_none() instead to support multi-row functions, such as _split() used in specimens data`
- 05:06 AM Revision 12867: fix: inputs/input.Makefile: don't treat *.xml as data files since these are not currently supported
- 04:55 AM Revision 12866: lib/runscripts/util.run: on_exit(): documented that users can also override gateway()/fallback() to perform other commands (or no commands) after the script is read
- 04:53 AM Revision 12865: bugfix: lib/sh/db.sh: pg_table_exists(): need ! to negate boolean result
- 04:44 AM Revision 12864: fix: lib/runscripts/table.run: table_make_install(): need to inform the user when it skips installing a table, because this is often unexpected
- 04:43 AM Revision 12863: fix: lib/runscripts/util.run: run_args_cmd(): need to indent the output of the target that it's running
- 04:15 AM Revision 12862: lib/runscripts/table.run: removed no longer used datasrc_make_install()
- 04:07 AM Revision 12861: fix: lib/sh/util.sh: fade(): use medium gray instead of light gray because it fades on white *and* black backgrounds
- 03:54 AM Revision 12860: lib/sh/util.sh: echo_func(): fade the file/line # to avoid distracting from the function call in the default log output
- 03:51 AM Revision 12859: lib/sh/util.sh: added fade()
- 03:37 AM Revision 12858: lib/sh/util.sh: highlight_msg(): renamed to highlight_log_msg() to clarify that this contains log++-specific functionality
- 03:35 AM Revision 12857: lib/sh/util.sh: moved terminal formatting commands to own section
- 03:34 AM Revision 12856: lib/sh/util.sh: highlight_msg(): moved formatting code into separate format() function
- 03:21 AM Revision 12855: lib/sh/util.sh: dp(): renamed to ps() to corresponding with pv/pf
- 03:19 AM Revision 12854: lib/sh/make.sh: echo_target: use `log-- echo_func`, which now puts the target name first but also provides much-needed indentation
- 03:16 AM Revision 12853: lib/sh/util.sh: echo_func(): put file/line # *after* function call instead of before so the function name is listed first
- 03:13 AM Revision 12852: lib/sh/util.sh: echo_func(): usage: removed no longer used/implemented minor=1 switch. use log++ instead.
- 03:07 AM Revision 12851: lib/runscripts/datasrc_dir.run: import(): use new schema/make, schema/rm
- 02:59 AM Revision 12850: lib/runscripts/table.run: load_data(): use the much simpler `schema/make` run target, rather than outsourcing to the legacy Makefile via the convoluted datasrc_make_install()/table_make_install()
- 02:26 AM Revision 12849: lib/runscripts/datasrc_dir.run: added schema/rm(), schema/make()
- 02:19 AM Revision 12848: lib/sh/util.sh: ignore_err_msg(): usage: added $ignore_e param from stderr_matches()
- 02:14 AM Revision 12847: lib/runscripts/table.run: psql: always include ; at end of statement
- 01:39 AM Revision 12846: fix: lib/sh/db.sh: pg_cmd(): hide PGPASSWORD at the normal verbosity so that the value of it doesn't appear in any log files
- 01:08 AM Revision 12845: lib/sh/util.sh: log_hint(): renamed to log_err_hint() for clarity, because this applies only to hints for errors
- 01:06 AM Revision 12844: bugfix: lib/sh/util.sh: log_hint!(): use log_err instead of log_info because hints as used here are attached to (possibly benign) errors. for other uses, use mk_hint().
- 01:00 AM Revision 12843: fix: lib/sh/util.sh: highlight_msg(): don't ' '-pad already-formatted text
- 12:57 AM Revision 12842: lib/sh/util.sh: manual terminal escape sequences: use highlight_msg() instead
- 12:53 AM Revision 12841: lib/sh/util.sh: highlight_msg(): auto-add padding around text if there is a background
- 12:51 AM Revision 12840: lib/sh/util.sh: highlight_msg(): use $format itself as the $highlight boolean
- 12:48 AM Revision 12839: lib/sh/util.sh: highlight_msg(): split apart the testing of $format and can_highlight_msg
- 12:39 AM Revision 12838: lib/sh/util.sh: added has_bg()
- 12:28 AM Revision 12837: bugfix: lib/sh/util.sh: highlight_msg(): need to reset any existing formatting before applying new formatting
- 12:25 AM Revision 12836: lib/sh/util.sh: added mk_hint() and use it in log_hint!()
- 12:16 AM Revision 12835: lib/sh/util.sh: bg_cmd(): also log the command being run
- 12:07 AM Revision 12834: fix: lib/sh/util.sh: need `function` before functions that have an alias with the same name
- 12:04 AM Revision 12833: lib/sh/util.sh: log!(): use new log:()
- 12:00 AM Revision 12832: lib/sh/util.sh: added log:(), which sets an explicit log_level. this also simplifies log+().
03/21/2014
- 11:55 PM Revision 12831: lib/sh/util.sh: log+(): set log_level before PS4 so that the PS4 expr doesn't also need to add to log_level
- 11:51 PM Revision 12830: lib/sh/util.sh: removed no longer needed log+ alias (which had been renamed from clog+)
- 11:48 PM Revision 12829: lib/sh/util.sh: clog*: renamed to log* for clarity (possible now that log* is no longer used for function-local log_level setting)
- 11:44 PM Revision 12828: *{.sh,run}: local setting of log_level: use log_local instead of relying on the log* aliases, so that these aliases can instead be used for wrapping commands (the more common use case)
- 11:40 PM Revision 12827: bugfix: lib/sh/util.sh: verbosity_compat alias: need to use `declare verbosity="$verbosity"` instead of `declare verbosity`, which would just clear $verbosity
- 11:38 PM Revision 12826: bugfix: lib/sh/util.sh: verbosity_min alias: need to use `declare verbosity="$verbosity"` instead of log_local now that verbosity is not one of the vars changed by log++
- 11:30 PM Revision 12825: lib/sh/util.sh: log+(): use easier-to-understand log_local instead of prefix-assignments to limit assignments to the invoked command
- 11:30 PM Revision 12824: lib/sh/util.sh: log+(): use easier-to-understand log_local instead of prefix-assignments to limit assignments to the invoked command
- 10:57 PM Revision 12823: *{.sh,run}: use clog* instead of "log*"
- 10:45 PM Revision 12822: bugfix: lib/sh/util.sh: log+(): removed spurious ; between setting of PS4 and log_level, which was causing erratic mismatches between PS4 and log_level. (the ; caused $PS4 to be set in the *caller* when invoked via one of the clog* aliases, rather than being passed as a command-specific env var.)
- 10:30 PM Revision 12821: lib/sh/util.sh: $verbosity: stay constant at what the user set it to instead of changing in tandem with $log_level, to facilitate debugging verbosity/log_level-related issues
- 10:11 PM Revision 12820: lib/sh/util.sh: log+(): usage: use aliases instead of ""-ed function names
- 06:58 PM Revision 12819: added schemas/VegCore.ERD.pdf symlink for easy access
- 06:50 PM Revision 12818: lib/sh/util.sh: log_err(): use red background for better visibility of errors, in the same way that lib/exc.py print_ex() does for column-based import
- 06:44 PM Revision 12817: bugfix: lib/sh/util.sh: removed echo_func in functions used by log++, to avoid spurious highlighted output
- 06:40 PM Revision 12816: lib/sh/util.sh: added missing clog+ alias
- 06:35 PM Revision 12815: bugfix: lib/sh/util.sh: log_hint(): use the standard log_fd and log_info() format, not err_fd and log_err() format, for hint messages
- 06:27 PM Revision 12814: fix: lib/sh/util.sh: log_msg!(): indent each line, not just the first
- 06:26 PM Revision 12813: lib/sh/util.sh: added split_lines()
- 06:05 PM Revision 12812: lib/sh/util.sh: log(): factored out helper function log_msg!()
- 06:00 PM Revision 12811: fix: lib/sh/util.sh: highlight_msg(): bold instead of underlining because the underlining interferes with the readability of the commands
- 05:57 PM Revision 12810: lib/sh/util.sh: highlight_msg(): allow turning off formatting w/ empty $format
- 05:53 PM Revision 12809: fix: lib/sh/util.sh: log_err() calls: removed manual highlighting
- 05:51 PM Revision 12808: lib/sh/util.sh: log_err(): highlight all error messages using highlight_msg()'s new $format
- 05:45 PM Revision 12807: lib/sh/util.sh: highlight_msg(): support custom format
- 05:35 PM Revision 12806: lib/sh/db.sh: pg_*_exists(): log the DB statements to check this at a higher log_level so that they don't clutter up the log output
- 05:25 PM Revision 12805: lib/sh/util.sh: log(): highlight log_level 1 messages to stand out against other output, for easier debugging
- 04:31 PM Revision 12804: *{.sh,run}: stderr_matches() wrapper calls: removed no longer needed prep_try/rethrow
- 04:12 PM Revision 12803: bugfix: catch(): also need to support $1='' because this is a now a use case of ignore_e()
- 04:02 PM Revision 12802: bugfix: lib/sh/util.sh: ignore_err_msg(): also need to ignore false exit status on no match
- 03:49 PM Revision 12801: lib/sh/util.sh: stderr_matches(): moved prep_try/rethrow into the function itself so that callers don't have to wrap this function in a complex sequence of prep_try/rethrow statements
- 03:42 PM Revision 12800: *{.sh,run}: stderr_matches() wrapper calls: removed no longer needed prep_try/rethrow
- 03:42 PM Revision 12799: lib/sh/util.sh: stderr_matches(): moved prep_try/rethrow into the function itself so that callers don't have to wrap this function in a complex sequence of prep_try/rethrow statements
- 03:25 PM Revision 12798: lib/sh/util.sh: added rethrow_exit alias
- 03:10 PM Revision 12797: fix: lib/sh/db.sh: pg_table_exists(): use stderr_matches() rather than just the exit status. this also avoids highlighting the benign error.
- 03:00 PM Revision 12796: fix: lib/sh/db.sh: pg_table_exists(): use stderr_matches() rather than just the exit status. this also avoids highlighting the benign error.
- 02:16 AM Revision 12795: 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.
- 12:34 AM Revision 12794: 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.)
- 12:31 AM Revision 12793: bugfix: inputs/input.Makefile: $(cleanup): need `set -o pipefail`
- 12:02 AM Revision 12792: inputs/VegBank/run: `rm=1 import()`: updated runtime (1 h)
03/20/2014
- 11:54 PM Revision 12791: inputs/VegBank/taxon_observation.**/test.xml.ref: updated inserted row count
- 11:54 PM Revision 12790: inputs/VegBank/projectcontributor_/test.xml.ref: updated inserted row count
- 10:53 PM Revision 12789: bugfix: schemas/util.sql: is_constant(util.col_ref): updated to include standard newline at beginning of comment (applies to newly-imported staging tables)
- 10:44 PM Revision 12788: bugfix: inputs/VegBank/import_order.txt: added missing project, needed to trigger the staging table renaming for the project table
- 10:42 PM Revision 12787: inputs/VegBank/run: documented `rm=1 import()` runtime (>1.5 h)
- 10:40 PM Revision 12786: inputs/VegBank/run: documented `datasrc_make sql/install` runtime (25 min)
- 08:27 PM Revision 12785: inputs/MO/Specimen/test.xml.ref: updated, which adds dateCollected mappings
- 08:20 PM Revision 12784: inputs/WIN/Specimen/test.xml.ref: updated to map.csv, which has eventDate->dateCollected
- 08:13 PM Revision 12783: inputs/VegBank/plantconcept_/create.sql: updated runtime (25 min, ~same)
- 08:08 PM Revision 12782: lib/sh/make.sh: begin_target: echo all targets to facilitate debugging without needing the verbose stack trace mode
- 08:06 PM Revision 12781: bugfix: lib/sh/make.sh: echo_target: don't include filename/line #, since this is not for the stack trace mode
- 07:59 PM Revision 12780: lib/sh/make.sh: added echo_target
- 07:58 PM Revision 12779: *{.sh,run}: use new begin_target instead of `echo_func; set_make_vars`
- 07:51 PM Revision 12778: lib/runscripts/util.run: runscript template: added sample make target, using new make target template
- 07:48 PM Revision 12777: lib/sh/make.sh: added make target template
- 07:47 PM Revision 12776: inputs/VegBank/plot/postprocess.sql: remove institutions that we have direct data for: CVS: updated runtime (same)
- 07:41 PM Revision 12775: lib/sh/make.sh: added begin_target alias
- 07:17 PM Revision 12774: lib/runscripts/datasrc_dir.run: documented how to reinstall staging tables (`rm=1 .../run import`)
- 07:13 PM Revision 12773: bugfix: *{.sh,run}: stderr_matches() wrapper callers: use the required wrapper caller usage, which now includes rethrow and prep_try
- 07:09 PM Revision 12772: bugfix: lib/sh/util.sh: rethrow*: only `return` if $e is actually nonzero, because rethrow is now being used as a catch-all in situations where there might not be an error
- 07:06 PM Revision 12771: lib/sh/util.sh: prep_try: initialize $e to 0 to simplify error-handling coding
- 06:56 PM Revision 12770: stderr_matches(): wrapper caller usage: added alternative usage when using `||`
- 06:50 PM Revision 12769: lib/sh/util.sh: stderr_matches(): wrapper caller usage: documented usage for a negated condition (ie. prefixed w/ !)
- 06:48 PM Revision 12768: lib/sh/util.sh: stderr_matches(): usage: split into wrapper usage and wrapper caller usage for clarity
- 06:45 PM Revision 12767: fix: *{.sh,run}: stderr_matches() wrappers: usage: added `rethrow`
- 06:45 PM Revision 12766: fix: *{.sh,run}: stderr_matches() wrappers: usage: added `rethrow`
- 06:43 PM Revision 12765: fix: lib/sh/util.sh: stderr_matches(): usage: `rethrow` must be called right after stderr_matches(), to avoid calling running other commands if there is an error
- 06:40 PM Revision 12764: fix: lib/sh/util.sh: stderr_matches(): when using $ignore_e, also set benign_error=1 to suppress the highlighting of the error
- 06:36 PM Revision 12763: bugfix: lib/sh/db.sh: pg_schema_exists(): need to ignore benign error exit status from the "cannot create temporary relation in non-temporary schema" error
- 06:34 PM Revision 12762: lib/sh/util.sh: stderr_matches(): supporting ignoring any benign error exit status associated with the error message being tested for
- 06:18 PM Revision 12761: lib/sh/util.sh: stderr_matches(): usage: documented where any ignore_e statement would go
- 05:37 PM Revision 12760: bugfix: lib/sh/util.sh: stderr_matches(): can't use `try` because this clears the exit status, which is needed for @PIPESTATUS to work. to support this, also need to avoid errexiting since @PIPESTATUS will be used instead.
03/18/2014
- 06:18 PM Revision 12759: lib/sh/util.sh: added dp(), which debug-prints a message
- 05:47 PM Revision 12758: bugfix: inputs/VegBank/plot/postprocess.sql: use CVS.plot_ instead because that has the renamed staging table columns, and is compatible with auto-renaming of the SQL script columns
- 05:41 PM Revision 12757: inputs/CVS/plot_/postprocess.sql: add unique constraint on locationName (analogous to the unique constraint in plot), for use by inputs/VegBank/plot/postprocess.sql in removing inter-datasource duplication
- 05:26 PM Revision 12756: fix: schemas/util.sql: explain2notice_msg(): don't include EXPLAIN output for simple, single-value queries, to avoid cluttering up the log output
- 05:22 PM Revision 12755: schemas/util.sql: added fold_explain_msg()
- 05:22 PM Revision 12754: bugfix: bin/repl: only use excluded_prefix_re/excluded_suffix_re in text mode (used in renaming columns in SQL scripts), to prevent the special coding for column renames from also affecting regular regexp/word replacements
- 05:10 PM Revision 12753: inputs/VegBank/taxon_observation.**/test.xml.ref: updated inserted row count
- 05:34 AM Revision 12752: inputs/run: postprocess(): documented runtime (30 min)
- 05:16 AM Revision 12751: bugfix: inputs/input.Makefile: %/postprocess.sql: don't perform replacements using map.csv, because map.csv is not idempotent. this functionality was only there to facilitate switching to new-style import, which is now largely done. (the remaining datasources NVS, SALVIAS, TEAM contain only 1 postprocess.sql: inputs/SALVIAS/projects/postprocess.sql (`st inputs/{NVS,SALVIAS,TEAM}/*/postprocess.sql`).)
- 04:59 AM Revision 12750: bugfix: bin/repl: text mode: also don't match if it's part of a '-'-separated identifier
- 04:57 AM Revision 12749: bugfix: bin/repl: text mode: also don't match if it's a word in a sentence
- 04:42 AM Revision 12748: bugfix: bin/repl: text mode: turned off the suffix matching, because there are cases where a mapping adds a suffix which would cause the same replacement to be performed repeatedly
- 04:33 AM Revision 12747: inputs/input.Makefile: %/postprocess.sql: *always* run this, not just if the associated map spreadsheets change, to avoid needing to `touch` them to cause %/postprocess.sql to run
- 04:25 AM Revision 12746: bin/repl: text mode: exclude prefixes that should not cause replacement, to avoid doubling leading *
- 04:24 AM Revision 12745: fix: inputs/*/*/postprocess.sql: un-doubled *
- 04:06 AM Revision 12744: bugfix: inputs/input.Makefile: %/postprocess.sql: also need to apply renames from mappings/VegCore.thesaurus.csv, as these have been applied to map.csv
- 04:04 AM Revision 12743: bugfix: lib/runscripts/table.run: custom_postprocess(): need to apply renames to SQL statements in postprocess.sql before it can be run
- 04:03 AM Revision 12742: bin/repl: text mode: also match w/ suffix (eg. _verbatim)
- 02:59 AM Revision 12741: bugfix: /README.TXT: Maintenance: VegCore data dictionary: apply new data dict mappings: need to use postprocess rather than import runscript target, so that the command also works on an svn checkout without the flat files (the flat files are not needed for the staging table renaming)
03/15/2014
- 07:20 PM Revision 12740: lib/sh/db.sh: psql(): $verbose_ok: renamed to $bypass_ok for clarity, because this applies only to the `--output /dev/fd/41` bypass (which when not possible, requires turning off verbose output
- 07:15 PM Revision 12739: fix: lib/sh/db.sh: psql(): added $output_data switch analogous to what mysql() has. this causes query results of eg. void-returning functions to be correctly filtered by the logging mechanism, rather than output to stdout.
- 06:42 PM Revision 12738: fix: lib/sh/db.sh: psql(): verbosity=0 (errors only) mode: use `SET client_min_messages = WARNING;` instead of NOTICE to hide verbose messages within psql as well
- 06:31 PM Revision 12737: lib/sh/db.sh: psql(): replaced `test "$verbose_ok" && can_log` with bool var $verbose_
- 06:29 PM Revision 12736: fix: lib/sh/db.sh: psql(): $verbose_: renamed to $verbose_ok for clarity
- 06:13 PM Revision 12735: fix: lib/sh/util.sh: stdout_contains(): add another pipe_delay because the `grep` statement was sometimes getting printed before its filtered output
- 05:47 PM Revision 12734: bugfix: schemas/util.sql: set_col_types(): need to COALESCE() the executed SQL to '' because util.eval() does not support NULL (and shouldn't, because this indicates a missing COALESCE() in constructing the statement)
- 05:43 PM Revision 12733: schemas/util.sql: set_col_types(): use simpler util.eval() instead of manual EXECUTE/util.debug_print_sql()
- 05:37 PM Revision 12732: schemas/util.sql: set_col_types(): use string_agg() instead of array_to_string(ARRAY(...)) for clarity
- 05:28 PM Revision 12731: bugfix: lib/sh/util.sh: die_error_hidden(): min verbosity to display error should not be hardcoded
- 05:18 PM Revision 12730: lib/sh/db.sh: psql(): "to see error details" msg: use new die_error_hidden()
- 05:18 PM Revision 12729: lib/sh/util.sh: added die_error_hidden()
- 05:13 PM Revision 12728: lib/sh/db.sh: psql(): "to see error details" msg: use new log_hint()
- 05:13 PM Revision 12727: lib/sh/util.sh: added log_hint(), whose msg is only displayed if not a benign error
- 05:03 PM Revision 12726: bugfix: lib/sh/db.sh: psql(): "to see error details" msg: also don't print it for benign errors ($benign_error)
- 05:00 PM Revision 12725: schemas/util.sql: added mk_not_null()
- 04:42 PM Revision 12724: lib/sh/db.sh: psql(): on error, display message describing how to see error details (prepend `vb=2` to the command)
- 04:31 PM Revision 12723: bugfix: lib/sh/util.sh: log_err(): don't override verbosity manually, as this will not set log_level or PS4. instead, use new log! , which sets these correctly.
- 04:24 PM Revision 12722: lib/sh/util.sh: added log! , which force-displays next log message
- 03:59 PM Revision 12721: lib/sh/util.sh: save_e: made it idempotent so that it also works if save_e was already called
- 03:57 PM Revision 12720: lib/sh/util.sh: save_e: made it idempotent so that it also works if save_e was already called
- 03:37 PM Revision 12719: lib/sh/util.sh: rethrow: documented why can't use `(exit "$e")` (bash bug that prevents errexit)
03/14/2014
- 09:09 PM Revision 12718: bugfix: /README.TXT: Maintenance: VegCore data dictionary: apply new data dict mappings: need to use import rather than mappings runscript target, to rename the staging tables
- 09:06 PM Revision 12717: bugfix: /README.TXT: Maintenance: VegCore data dictionary: also need to apply new data dict mappings on vegbiendev
- 08:19 PM Revision 12716: fix: /README.TXT: Maintenance: VegCore data dictionary: added steps to apply the new data dictionary mappings to the datasource mappings and staging tables
- 07:53 PM Revision 12715: bugfix: lib/runscripts/util.run: $auto_ignore: need to unexport it so don't pass this to invoked scripts except through fwd()
- 07:35 PM Revision 12714: added inputs/run, which runs all the inputs' runscripts using the new auto-forwarding
- 07:34 PM Revision 12713: bugfix: lib/runscripts/util.run: auto_fwd's fallback() must be set *after* auto_ignore's fallback() to overwrite it (auto_ignore should only apply if an error would otherwise have been generated by the fallback)
- 07:30 PM Revision 12712: lib/runscripts/util.run: fwd(): support subdirs that don't contain a runscript, so that the default value of @subdirs will work in most cases
- 07:29 PM Revision 12711: lib/runscripts/util.run: fwd(): set default @subdirs (`{.,}*/`)
- 07:26 PM Revision 12710: lib/sh/util.sh: added enter_top_dir and use it in in_top_dir
- 07:12 PM Revision 12709: fix: lib/sh/util.sh: commands run inside $(...): need to run with log++ so that these aren't normally debug-printed
- 06:41 PM Revision 12708: lib/sh/util.sh: added pv(), which debug-prints var(s)
- 06:40 PM Revision 12707: lib/sh/util.sh: added wildcard.()
- 06:40 PM Revision 12706: lib/sh/util.sh: added wildcard/()
- 06:40 PM Revision 12705: lib/sh/util.sh: added esc_args()
- 06:33 PM Revision 12704: web/links/index.htm: updated to Firefox bookmarks: Google Drive: listed bugs that make it very difficult to use (the need to re-download all files when reconnecting a client to an account). added recommendation not to use it (unstable).
- 05:25 PM Revision 12703: removed unused inputs/table.run. inputs/*/table.run include lib/runscripts/table.run directly.
- 05:02 PM Revision 12702: lib/runscripts/datasrc_dir.run: removed postprocess(), which now does the same thing its auto-forwarded equivalent would
- 05:01 PM Revision 12701: lib/runscripts/datasrc_dir.run: removed separate @table_subdirs, because the table-only targets can now safely be invoked on all subdirs, being auto-ignored in subdirs that don't support them
- 04:53 PM Revision 12700: lib/runscripts/util.run: fwd(): enable $auto_ignore so that each subdir doesn't have to have a definition for the forwarded target
- 04:52 PM Revision 12699: lib/runscripts/util.run: added $auto_ignore switch, which causes fallback() not to generate an error that a non-existant target doesn't exist
- 03:55 PM Revision 12698: lib/runscripts/datasrc_dir.run: use new fwd_self alias
- 03:55 PM Revision 12697: lib/runscripts/util.run: added fwd_self alias
- 03:49 PM Revision 12696: lib/runscripts/datasrc_dir.run: enable $auto_fwd, to create the functionality of lib/forwarding.Makefile's `%` target
- 03:47 PM Revision 12695: lib/runscripts/util.run: added $auto_fwd switch
- 03:36 PM Revision 12694: bugfix: lib/runscripts/util.run: gateway(): need to use is_callable() rather than func_exists() to check whether the target exists, because external commands (eg. echo) are supported as targets, too
- 03:32 PM Revision 12693: lib/sh/util.sh: added is_callable()
- 03:23 PM Revision 12692: lib/runscripts/util.run: support custom handlers for *all* targets (gateway()) as well as targets w/o function (fallback())
- 03:03 PM Revision 12691: lib/runscripts/table.run: remake_VegBIEN_mappings(): renamed to just mappings() since action make targets should be short names
- 07:32 AM Revision 12690: lib/sh/util.sh: stderr_matches(): inline the stderr_matches alias to avoid needing to quote stderr_matches as "stderr_matches" in the most common use case (with pattern as a prefix env var)
- 07:29 AM Revision 12689: bugfix: lib/sh/util.sh: stderr_matches(): when passing `pattern=...` as a prefix env var, must be invoked as `"stderr_matches"` to avoid the env var applying to the prep_try portion of the stderr_matches alias
- 06:38 AM Revision 12688: added schemas/VegCore/Brad_Boyle/bien3_data_provenance_use_cases.docx* from e-mail from Brad
03/13/2014
- 06:53 PM Revision 12687: schemas/vegbien.sql: _plots_08_list_of_plots_which_use_percent_cover, _plots_15_pct_cover_of_each_verb_taxon_in_each_plot_in_each_pro: reran with fixes, which removes the incorrectly auto-added copies columns. (they were only able to be auto-added because the tables had no rows.)
- 06:42 PM Revision 12686: bugfix: drop_column(regclass[]): need to run `SELECT NULL::void;` at end of function to avoid folding away functions called in previous query
- 06:40 PM Revision 12685: fix: schemas/util.sql: diff(regclass, regclass): moved try_create() of copies column in parent table to auto_rm_freq() so that it would only happen if both tables actually contain a copies column (otherwise, the try_create() will create an empty copies column if both tables are empty)
- 06:33 PM Revision 12684: schemas/util.sql: try_create(): also handle "child table is missing column" errors
- 05:33 PM Revision 12683: schemas/util.sql: added coalesce(anyarray), which can be used to force evaluation of all values of a COALESCE()
- 05:14 PM Revision 12682: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB
- 05:13 PM Revision 12681: fix: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: removed `public.` qualifier
- 05:04 PM Revision 12680: schemas/vegbien.sql: implemented _plots_19_count_of_censuses_per_plot_in_each_project
- 05:03 PM Revision 12679: inputs/SALVIAS/validations.sql: implemented _plots_19_count_of_censuses_per_plot_in_each_project
- 09:08 AM Revision 12678: validation/aggregating/plots/FIA/bien3_validations_fia_input.sql: _plots_19_count_of_inventories_per_plot_in_each_project: renamed to _plots_19_count_of_censuses_per_plot_in_each_project for clarity
- 09:00 AM Revision 12677: validation/aggregating/plots/FIA/bien3_validations_fia_input.sql*: updated from Brad's latest e-mail
- 02:06 AM Revision 12676: schemas/util.sql: EXCEPTION blocks with multiple exception types: use OR to merge exception types into one WHEN block
- 01:50 AM Revision 12675: schemas/vegbien.sql: public_validations: schema comment: changed "to sync the queries with schemas/vegbien.sql" to "to reset the queries to what's in schemas/vegbien.sql" for clarity
- 01:46 AM Revision 12674: fix: schemas/vegbien.sql: schema comment: to reset the key and value columns for all validations queries: updated running of custom keys() functions to use keys() types instead
- 01:14 AM Revision 12673: schemas/vegbien.sql: schema comment: to sync the queries with schemas/vegbien.sql: use new public_validations.rm_output_queries() instead of rm_all_queries() to leave the input queries in place
- 01:12 AM Revision 12672: schemas/vegbien.sql: schema comment: documented how to reset the key and value columns for all validations queries
03/12/2014
- 11:56 PM Revision 12671: schemas/util.sql: mk_keys_func(regtype, util.col_cast[]): indicate in the type comment that the keys() type is autogenerated, so it can be distinguished from custom keys() types when bulk-regenerating keys() types
- 11:53 PM Revision 12670: bugfix: schemas/util.sql: show_relations_like(): also need to include composite types, as these are also relations (and are expected to be included by callers of show_relations_like())
- 11:49 PM Revision 12669: bugfix: schemas/vegbien.sql: rm_output_queries(): also need to include keys_* and values__* types, as these are also associated with the query
- 11:40 PM Revision 12668: schemas/util.sql: added debug_print_func_call(text) and use it where applicable
- 11:33 PM Revision 12667: schemas/util.sql: drop_relations_like(): debug-print the regexps so that you can tell which tables it's trying to match
- 06:26 PM Revision 12666: schemas/vegbien.sql: public_validations: regenerated ~type tables, which adds `copies` columns for queries with a mismatch in the # of occurrences of each row
- 06:18 PM Revision 12665: bugfix: schemas/vegbien.sql: public_validations.validation_views(): need to include views with letters after the query # (eg. _plots_06a_list_of_stems)
- 05:41 PM Revision 12664: schemas/util.sql: removed no longer used to_freq(regclass, drop_if_always_1). use to_freq(regclass) and auto_rm_freq() instead.
- 05:40 PM Revision 12663: bugfix: schemas/util.sql: diff(regclass, regclass): only drop freq column if *all* tables have all 1s
- 05:38 PM Revision 12662: schemas/util.sql: auto_rm_freq(): accept multiple tables, so the freq column is only dropped if *all* tables have all 1s
- 05:36 PM Revision 12661: schemas/util.sql: added freq_always_1(regclass[])
- 05:35 PM Revision 12660: schemas/util.sql: added drop_column(regclass[])
- 05:04 PM Revision 12659: schemas/util.sql: added parent(regclass)
- 04:48 PM Revision 12658: schemas/util.sql: try_create(): also handle not_null_violation, which is thrown when trying to add a NOT NULL column to a parent table, which cascades to a child table whose values for the new column will be NULL
- 04:44 PM Revision 12657: bugfix: schemas/util.sql: diff(text, text): also need to cast left_/right_ to base type for the IS DISTINCT FROM filter, because the WHERE clause apparently does *not* use columns from the SELECT list, even though GROUP BY and ORDER BY do
- 04:13 PM Revision 12656: schemas/util.sql: added to_freq(regclass, drop_if_always_1)
- 04:04 PM Revision 12655: schemas/util.sql: added auto_rm_freq(regclass)
- 03:53 PM Revision 12654: schemas/util.sql: added freq_always_1(regclass)
- 03:00 PM Revision 12653: bugfix: schemas/util.sql: diff(regclass, regclass): need to create a diff when the # of copies of a row differs between the tables. this uses new util.to_freq().
- 02:44 PM Revision 12652: schemas/util.sql: added to_freq(regclass)
- 02:43 PM Revision 12651: schemas/util.sql: added populate_table(regclass, text)
- 01:11 PM Revision 12650: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB
- 12:53 PM Revision 12649: schemas/util.sql: added copy_types_and_data(regclass, text)
- 04:44 AM Revision 12648: schemas/vegbien.sql: public_validations schema comment: added instructions to change the key and value columns for a validations query
- 04:41 AM Revision 12647: schemas/vegbien.sql: implemented _plots_16_intercepts_for_each_verb_taxon_in_each_plot_each_proj
- 03:44 AM Revision 12646: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB
- 03:44 AM Revision 12645: fix: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: removed `public.` qualifier
- 03:35 AM Revision 12644: schemas/vegbien.sql: implemented _plots_09_list_of_plots_which_use_line_intercept
- 03:20 AM Revision 12643: schemas/vegbien.sql: public_validations: queries that use EXISTS(): join locationevent.plot_id to plot.plot_id directly instead of going via location.plot_location_id
- 03:04 AM Revision 12642: schemas/vegbien.sql: implemented _plots_08_list_of_plots_which_use_percent_cover
- 12:04 AM Revision 12641: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB
- 12:01 AM Revision 12640: schemas/vegbien.sql: implemented _plots_07_list_of_plots_which_use_counts_of_indiv_per_species
03/11/2014
- 09:57 PM Revision 12639: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB
- 09:56 PM Revision 12638: bugfix: inputs/SALVIAS/validations.sql: _plots_07_list_of_plots_with_counts_of_individuals_per_species: renamed to _plots_07_list_of_plots_*which_use*_... because this query is not intended to include the actual counts, just to say which plots have them (the correct "which use" wording is also used in queries #8, 9)
- 04:05 PM Revision 12637: web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: query planner: documented how to prevent incorrect query plans (`SET enable_seqscan = off;`, etc.)
- 03:38 PM Revision 12636: web/links/index.htm: updated to Firefox bookmarks: PostgreSQL: query planner: documented that incorrect query plans are an ongoing bug in Postgres, because it does not support index hints and by default does not follow the join order. specifically, Postgres often does the following things in query plans which should normally never be done:
- * performs a sequential scan when an index is available (because it incorrectly thinks there are too many dead rows i...
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