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From 06/21/2014 to 07/20/2014

07/20/2014

11:59 PM Revision 14234: bugfix: schemas/util.sql: canon_sql(): need to include the enclosing () because the DB includes them
Aaron Marcuse-Kubitza
11:42 PM Revision 14233: fix: schemas/util.sql: canon_sql(): use explain()'s verbose mode to facilitate debugging
Aaron Marcuse-Kubitza
11:38 PM Revision 14232: bugfix: schemas/util.sql: explain(): need to restore NOTICEs in verbose mode
Aaron Marcuse-Kubitza
11:22 PM Revision 14231: schemas/util.sql: explain(): support running in verbose mode
Aaron Marcuse-Kubitza
11:19 PM Revision 14230: bugfix: schemas/util.sql: check_constraint_replace(): need to canon the expr, using new util.canon_sql(), so it can be compared with the expr in the DB
Aaron Marcuse-Kubitza
11:18 PM Revision 14229: schemas/util.sql: added canon_sql(expr text, table_ regclass)
Aaron Marcuse-Kubitza
10:45 PM Revision 14228: fix: schemas/util.sql: check_constraint view: *don't* use pretty-print mode, because this format does not match util.canon_sql()
Aaron Marcuse-Kubitza
10:43 PM Revision 14227: fix: schemas/util.sql: check_constraint_expr_enable(), derived_col_expr_from_check_constraint(): trim parens in order to support non-pretty-print mode, which is needed with canon_sql()
Aaron Marcuse-Kubitza
09:27 PM Revision 14226: schemas/util.sql: added canon_sql(expr text)
Aaron Marcuse-Kubitza
09:21 PM Revision 14225: schemas/util.sql: added trim_parens()
Aaron Marcuse-Kubitza
08:19 PM Revision 14224: schemas/util.sql: added copy_struct(from_ regtype, to_ text) and copy_data(from_ regtype, to_ text), and use these in a general-purpose copy()
Aaron Marcuse-Kubitza
08:02 PM Revision 14223: bugfix: schemas/util.sql: copy(from_ regtype, to_ text): must be declared STRICT to handle NULL properly
Aaron Marcuse-Kubitza
07:58 PM Revision 14222: schemas/util.sql: added copy(from_ regtype, to_ text)
Aaron Marcuse-Kubitza
07:39 PM Revision 14221: fix: schemas/util.sql: is_raise_condition(): should be called is_log_level()
Aaron Marcuse-Kubitza
07:36 PM Revision 14220: schemas/util.sql: raise(): support SQLSTATE values
Aaron Marcuse-Kubitza
07:33 PM Revision 14219: bugfix: schemas/util.sql: raise_expr(raise_type): only treat as raise condition if not SQLSTATE, to allow custom SQLSTATEs
Aaron Marcuse-Kubitza
07:30 PM Revision 14218: schemas/util.sql: raise(): support SQLSTATE values
Aaron Marcuse-Kubitza
07:28 PM Revision 14217: schemas/util.sql: added raise_expr(raise_type)
Aaron Marcuse-Kubitza
07:28 PM Revision 14216: schemas/util.sql: added is_raise_condition()
Aaron Marcuse-Kubitza
07:14 PM Revision 14215: schemas/util.sql: added is_sqlstate()
Aaron Marcuse-Kubitza
06:44 PM Revision 14214: schemas/util.sql: typeof(expr text, table_ regtype): use simpler util.eval2val() instead of EXECUTE
Aaron Marcuse-Kubitza
06:13 PM Revision 14213: fix: schemas/util.sql: derived_col_constraint_initially_enabled(): also should be initially enabled if expr unchanged, to avoid re-running constraint on all rows
Aaron Marcuse-Kubitza
06:09 PM Revision 14212: schemas/util.sql: derived_col_update(): use new util.derived_col_constraint_initially_enabled()
Aaron Marcuse-Kubitza
06:09 PM Revision 14211: schemas/util.sql: added derived_col_constraint_initially_enabled()
Aaron Marcuse-Kubitza
06:05 PM Revision 14210: schemas/util.sql: added derived_col_expr(col)
Aaron Marcuse-Kubitza
05:56 PM Revision 14209: derived_col_constraint_enable(): documented that this now avoids re-running constraint on all rows if already enabled
Aaron Marcuse-Kubitza
05:43 PM Revision 14208: fix: check_constraint_replace(): avoid re-running the constraint on all rows if expr hasn't changed
Aaron Marcuse-Kubitza
05:40 PM Revision 14207: schemas/util.sql: check_constraint_replace(): shortened param to `def` for readability
Aaron Marcuse-Kubitza
05:39 PM Revision 14206: schemas/util.sql: added check_constraint_expr(constraint_ table_item)
Aaron Marcuse-Kubitza
04:34 PM Revision 14205: schemas/util.sql: added derived_col_update()
Aaron Marcuse-Kubitza
04:31 PM Revision 14204: schemas/util.sql: check_constraint__disabled(): made disabled configurable (renaming func to check_constraint())
Aaron Marcuse-Kubitza
04:20 PM Revision 14203: schemas/util.sql: added derived_col_constraint_expr()
Aaron Marcuse-Kubitza
04:07 PM Revision 14202: schemas/util.sql: derived_col_constraints_enable(): use new derived_col_constraint_enable()
Aaron Marcuse-Kubitza
04:06 PM Revision 14201: schemas/util.sql: added derived_col_constraint_enable()
Aaron Marcuse-Kubitza
03:52 PM Revision 14200: schemas/util.sql: added table_has_data()
Aaron Marcuse-Kubitza
03:47 PM Revision 14199: schemas/util.sql: added col_add(derived_col_def)
Aaron Marcuse-Kubitza
03:44 PM Revision 14198: schemas/util.sql: added typeof(text, regclass)
Aaron Marcuse-Kubitza
03:40 PM Revision 14197: bugfix: /README.TXT: Full database import: added warnings that you should not run backups/pg_snapshot while the import is running, nor until the previous import has been replaced
Aaron Marcuse-Kubitza
03:22 PM Revision 14196: schemas/util.sql: added regtype(regclass)
Aaron Marcuse-Kubitza
02:52 PM Revision 14195: schemas/util.sql: added col_add()
Aaron Marcuse-Kubitza
02:32 PM Revision 14194: schemas/util.sql: added col_def type
Aaron Marcuse-Kubitza
07:22 AM Revision 14193: schemas/util.sql: derived_cols_populate(): only run if needed
Aaron Marcuse-Kubitza
07:09 AM Revision 14192: schemas/util.sql: added derived_cols_populated()
Aaron Marcuse-Kubitza
07:09 AM Revision 14191: schemas/util.sql: added derived_cols_populated()
Aaron Marcuse-Kubitza
07:08 AM Revision 14190: schemas/util.sql: added derived_col_populated()
Aaron Marcuse-Kubitza
07:07 AM Revision 14189: schemas/util.sql: added check_constraint_enabled()
Aaron Marcuse-Kubitza
06:46 AM Revision 14188: schemas/util.sql: remove_prefix(), remove_suffix(): use new starts_with(), ends_with()
Aaron Marcuse-Kubitza
06:45 AM Revision 14187: schemas/util.sql: added starts_with(), ends_with()
Aaron Marcuse-Kubitza
05:57 AM Revision 14186: schemas/util.sql: derived_cols_populate(): also run util.derived_col_constraints_enable() once populated
Aaron Marcuse-Kubitza
05:55 AM Revision 14185: schemas/util.sql: added derived_col_constraints_enable()
Aaron Marcuse-Kubitza
05:28 AM Revision 14184: schemas/util.sql: added check_constraint__disabled(), which creates a CHECK constraint which is initially disabled
Aaron Marcuse-Kubitza
05:27 AM Revision 14183: schemas/util.sql: added check_constraint__disabled(), which creates a CHECK constraint which is initially disabled
Aaron Marcuse-Kubitza
05:07 AM Revision 14182: fix: schemas/util.sql: run_triggers(): need to re-sort rows if table needs this
Aaron Marcuse-Kubitza
05:05 AM Revision 14181: schemas/util.sql: added try_cluster()
Aaron Marcuse-Kubitza
04:05 AM Revision 14180: schemas/util.sql: added derived_cols_populate()
Aaron Marcuse-Kubitza
04:04 AM Revision 14179: schemas/util.sql: added run_triggers(regclass)
Aaron Marcuse-Kubitza
04:00 AM Revision 14178: schemas/util.sql: added first_col(regclass)
Aaron Marcuse-Kubitza
02:42 AM Revision 14177: fix: schemas/util.sql: read-only functions should be STABLE rather than VOLATILE
Aaron Marcuse-Kubitza
02:42 AM Revision 14176: bugfix: schemas/util.sql: functions that access the DB must be STABLE rather than IMMUTABLE
Aaron Marcuse-Kubitza
02:23 AM Revision 14175: bugfix: schemas/util.sql: derived_col_defs(): derived columns *must* be returned in table order (which should = dependency order), so that they are populated in dependency order
Aaron Marcuse-Kubitza
02:17 AM Revision 14174: bugfix: schemas/util.sql: remove_prefix(), remove_suffix(): must be declared STRICT to handle NULL properly
Aaron Marcuse-Kubitza
02:16 AM Revision 14173: bugfix: schemas/util.sql: remove_suffix(): need to use quote_nullable(str) so a NULL str doesn't NULL out the entire message
Aaron Marcuse-Kubitza
02:10 AM Revision 14172: bugfix: schemas/util.sql: remove_prefix(): need to use quote_nullable(str) so a NULL str doesn't NULL out the entire message
Aaron Marcuse-Kubitza
02:09 AM Revision 14171: bugfix: schemas/util.sql: raise(): use new quote_as_str() to avoid "RAISE statement option cannot be null" errors
Aaron Marcuse-Kubitza
02:08 AM Revision 14170: schemas/util.sql: added quote_as_str()
Aaron Marcuse-Kubitza

07/19/2014

11:23 PM Revision 14169: schemas/util.sql: added CAST (util.col AS util.derived_col_def)
Aaron Marcuse-Kubitza
11:05 PM Revision 14168: schemas/util.sql: derived_col_def(col): use existing util.check_constraint_def()
Aaron Marcuse-Kubitza
11:01 PM Revision 14167: schemas/util.sql: added CAST (util.col AS util.table_item)
Aaron Marcuse-Kubitza
10:50 PM Revision 14166: schemas/util.sql: added derived_col_def(col)
Aaron Marcuse-Kubitza
10:30 PM Revision 14165: schemas/util.sql: added check_constraint_disable()
Aaron Marcuse-Kubitza
10:23 PM Revision 14164: bugfix: schemas/util.sql: check_constraint_drop(): need IF EXISTS
Aaron Marcuse-Kubitza
10:09 PM Revision 14163: schemas/util.sql: added check_constraint_expr_disable()
Aaron Marcuse-Kubitza
09:50 PM Revision 14162: schemas/util.sql: check_constraint_enable(): documented that this is idempotent
Aaron Marcuse-Kubitza
09:21 PM Revision 14161: inputs/.TNRS/schema.sql: taxon_match: documented that whenever columns are renamed, util.derived_cols_sync() should be run
Aaron Marcuse-Kubitza
09:14 PM Revision 14160: schemas/util.sql: derived_cols_sync(): also create trigger, since this is necessary for a complete sync
Aaron Marcuse-Kubitza
09:13 PM Revision 14159: schemas/util.sql: added name(regprocedure)
Aaron Marcuse-Kubitza
09:02 PM Revision 14158: schemas/util.sql: derived_cols_sync(): set the trigger name in a var
Aaron Marcuse-Kubitza
08:52 PM Revision 14157: schemas/util.sql: added check_constraint_enable()
Aaron Marcuse-Kubitza
08:46 PM Revision 14156: schemas/util.sql: added check_constraint_replace()
Aaron Marcuse-Kubitza
08:43 PM Revision 14155: schemas/util.sql: added CAST (util.table_item AS util.check_constraint_def)
Aaron Marcuse-Kubitza
08:38 PM Revision 14154: schemas/util.sql: added check_constraint_drop()
Aaron Marcuse-Kubitza
08:02 PM Revision 14153: schemas/util.sql: derived_col_expr_from_check_constraint(): enable initially-disabled exprs
Aaron Marcuse-Kubitza
08:00 PM Revision 14152: schemas/util.sql: added check_constraint_expr_enable()
Aaron Marcuse-Kubitza
07:42 PM Revision 14151: fix: schemas/util.sql: check_constraint view: def: use pg_get_expr() with pretty-print, to avoid extra () that complicate parsing
Aaron Marcuse-Kubitza
06:54 PM Revision 14150: inputs/.TNRS/schema.sql: taxon_match__fill_derived(): updated using new util.derived_cols_sync()
Aaron Marcuse-Kubitza
06:50 PM Revision 14149: schemas/util.sql: added derived_cols_sync()
Aaron Marcuse-Kubitza
06:45 PM Revision 14148: bugfix: CAST (util.check_constraint_def AS util.derived_col_def): need to extract the derived column expr *from* the CHECK constraint expr
Aaron Marcuse-Kubitza
06:44 PM Revision 14147: schemas/util.sql: added derived_col_expr_from_check_constraint()
Aaron Marcuse-Kubitza
06:39 PM Revision 14146: schemas/util.sql: added extract_str()
Aaron Marcuse-Kubitza
06:34 PM Revision 14145: schemas/util.sql: added remove_suffix()
Aaron Marcuse-Kubitza
06:21 PM Revision 14144: schemas/util.sql: added remove_prefix()
Aaron Marcuse-Kubitza
05:47 PM Revision 14143: schemas/util.sql: added CAST (util.table_item AS util.col)
Aaron Marcuse-Kubitza
05:37 PM Revision 14142: schemas/util.sql: derived_col_defs(): return derived_col_def instead of check_constraint_def
Aaron Marcuse-Kubitza
05:36 PM Revision 14141: schemas/util.sql: added derived_col_def type with cast from util.check_constraint_def
Aaron Marcuse-Kubitza
04:51 PM Revision 14140: schemas/util.sql: added derived_col_defs()
Aaron Marcuse-Kubitza
04:35 PM Revision 14139: schemas/util.sql: check_constraint_defs(): use new util.check_constraint view
Aaron Marcuse-Kubitza
04:30 PM Revision 14138: schemas/util.sql: added check_constraint view
Aaron Marcuse-Kubitza
03:53 PM Revision 14137: schemas/util.sql: added check_constraint_defs()
Aaron Marcuse-Kubitza
03:53 PM Revision 14136: schemas/util.sql: added check_constraint_def type
Aaron Marcuse-Kubitza
03:51 PM Revision 14135: schemas/util.sql: added table_item type
Aaron Marcuse-Kubitza
01:59 PM Revision 14134: schemas/util.sql: col_ref: renamed to just col
Aaron Marcuse-Kubitza
01:38 PM Revision 14133: web/username_prefix.php: remove padding used to visually separate elements: documented that this leaves embedded __ (eg. x__y) untouched
Aaron Marcuse-Kubitza
02:52 AM Revision 14132: fix: inputs/.TNRS/schema.sql: taxon_match: to populate a new column: also need to recluster table so rows are exported in sorted order
Aaron Marcuse-Kubitza
02:47 AM Revision 14131: schemas/util.sql: cluster(): support omitting index to recluster a table
Aaron Marcuse-Kubitza
02:26 AM Revision 14130: schemas/util.sql: cluster_once(): use util.cluster()
Aaron Marcuse-Kubitza
02:24 AM Revision 14129: schemas/util.sql: cluster_once(): documented that this runs cluster only *once* if called repeatedly
Aaron Marcuse-Kubitza
02:24 AM Revision 14128: schemas/util.sql: added cluster(), which reclusters each time
Aaron Marcuse-Kubitza
02:10 AM Revision 14127: schemas/util.sql: cluster_once(): use simpler `LANGUAGE sql` now that we're using util.eval() instead of EXECUTE
Aaron Marcuse-Kubitza
02:03 AM Revision 14126: schemas/util.sql: cluster_once(): use util.eval() instead of EXECUTE to print the CLUSTER statement (if any) it's using
Aaron Marcuse-Kubitza

07/18/2014

11:40 PM Revision 14125: fix: inputs/.TNRS/schema.sql: taxon_match: cluster the table so the rows are always exported in the same order, even when an UPDATE statement is used to run triggers
Aaron Marcuse-Kubitza
11:28 PM Revision 14124: bugfix: schemas/util.sql: cluster_once(): need to use just the name of the index, without the schema prefix
Aaron Marcuse-Kubitza
05:00 PM Revision 14123: schemas/util.sql: cluster_once(): use simpler IS DISTINCT FROM instead of array !=
Aaron Marcuse-Kubitza
03:18 PM Revision 14122: inputs/.TNRS/schema.sql: added __accepted_{genus,specific_epithet} derived column, using the steps at wiki.vegpath.org/Postgres_queries#maintaining-derived-column-formulas-across-column-renames
Aaron Marcuse-Kubitza
02:01 AM Revision 14121: web/username_prefix.php: remove padding used to visually separate elements: documented that this also removes a leading __ that indicates an internal field
Aaron Marcuse-Kubitza

07/17/2014

07:18 PM Revision 14120: web/links/index.htm: updated to Firefox bookmarks: Quick links: added VegBIEN data dictionary spreadsheet, TNRS data dictionary.
Aaron Marcuse-Kubitza
06:15 PM Revision 14119: fix: web/username_prefix.php: transposes: changed recommended syntax to _y~x@url so that _y~ lines up vertically with [y_] paths
Aaron Marcuse-Kubitza
06:11 PM Revision 14118: web/username_prefix.php: removed special category comments syntax because this is now handled by transposes and insertion comments
Aaron Marcuse-Kubitza
06:10 PM Revision 14117: web/username_prefix.php: added support for transposes ( y~x_@url -> x_y@url , Y~x@url -> xY@url ), which can be used to put the category in a column name first without duplicating the category
Aaron Marcuse-Kubitza
05:35 PM Revision 14116: web/username_prefix.php: removed linewraps code because Google spreadsheets no longer supports wrapping on a - , and because a shorter syntax for category comments is now available
Aaron Marcuse-Kubitza
05:32 PM Revision 14115: web/username_prefix.php: category comments: moved _-_ outside [] in comparison example since it will be deleted separately
Aaron Marcuse-Kubitza
05:27 PM Revision 14114: bugfix: web/username_prefix.php: category comments: need /__/ around regexp
Aaron Marcuse-Kubitza
05:24 PM Revision 14113: web/username_prefix.php: category comments: added support for a shorter syntax than [x_-_]y@url : x+y@url -> y@url
Aaron Marcuse-Kubitza
04:14 PM Revision 14112: schemas/vegbien.ERD.mwb: updated
Aaron Marcuse-Kubitza
04:13 PM Revision 14111: fix: inputs/.TNRS/schema.sql: taxon_match: added back * prefixes on TNRS-namespace column names
Aaron Marcuse-Kubitza
03:34 PM Revision 14110: inputs/.TNRS/schema.sql: MatchedTaxon: taxon_best_match: don't alias to `s` since this is no longer a nested select
Aaron Marcuse-Kubitza
03:32 PM Revision 14109: inputs/.TNRS/schema.sql: MatchedTaxon: nested select: use just taxon_best_match since this no longer performs renamings
Aaron Marcuse-Kubitza
03:27 PM Revision 14108: inputs/.TNRS/schema.sql: MatchedTaxon: renamed output columns to match input columns, so that the nested select would not be performing any renamings
Aaron Marcuse-Kubitza
03:05 PM Revision 14107: fix: inputs/.TNRS/schema.sql: MatchedTaxon: added all columns from taxon_match (some of them apparently hadn't been included in MatchedTaxon)
Aaron Marcuse-Kubitza
03:01 PM Revision 14106: fix: inputs/.TNRS/schema.sql: reordered columns to match taxon_match
Aaron Marcuse-Kubitza
02:38 PM Revision 14105: fix: inputs/.TNRS/schema.sql: MatchedTaxon: added all columns from taxon_match (some of them apparently hadn't been included in MatchedTaxon)
Aaron Marcuse-Kubitza
01:02 PM Revision 14104: fix: inputs/.TNRS/schema.sql: added back Family_matched, which had gotten merged with Name_matched_accepted_family when TNRS temporarily stopped populating Name_matched_accepted_family
Aaron Marcuse-Kubitza
12:32 PM Revision 14103: inputs/.TNRS/schema.sql: MatchedTaxon: taxonomicStatus: moved outside the inner SELECT so that the inner SELECT would consist solely of renamings
Aaron Marcuse-Kubitza
12:12 PM Revision 14102: inputs/.TNRS/schema.sql: MatchedTaxon: removed unneeded "Name_matched." prefix on source-specific names (only the * is needed because there is only one table)
Aaron Marcuse-Kubitza
12:10 PM Revision 14101: bugfix: schemas/util.sql: view_is_subset(): auto-updatable views that are *not* plain subsets: include ones with WHERE clauses
Aaron Marcuse-Kubitza
12:03 PM Revision 14100: bugfix: schemas/util.sql: view_is_subset(): also need to handle auto-updatable views that are *not* plain subsets (there are some of these)
Aaron Marcuse-Kubitza
09:05 AM Revision 14099: bin/import_all: hidden_srcs(): removed `by_col=1` because these should be done in the same mode as the main datasources
Aaron Marcuse-Kubitza

07/16/2014

07:55 PM Revision 14098: schemas/public_.sql: removed no longer used threatened_taxonlabel. use iucn_red_list instead.
Aaron Marcuse-Kubitza
07:39 PM Revision 14097: fix: schemas/public_.sql: analytical_stem_view: don't use threatened_taxonlabel, which was never populated correctly. instead, this can eventually be rewritten to use new iucn_red_list.
Aaron Marcuse-Kubitza
07:13 PM Revision 14096: bin/make_analytical_db: removed threatened_taxonlabel because this is now handled by iucn_red_list
Aaron Marcuse-Kubitza
07:12 PM Revision 14095: bin/make_analytical_db: added iucn_red_list_view_modify()
Aaron Marcuse-Kubitza
06:48 PM Revision 14094: bin/make_analytical_db: removed unused code to create views in the analytical_db schema
Aaron Marcuse-Kubitza
06:35 PM Revision 14093: bin/make_analytical_db: merged mk_table and mk_analytical_table since they now do the same thing
Aaron Marcuse-Kubitza
06:34 PM Revision 14092: bin/make_analytical_db: removed unused code to create views in the analytical_db schema
Aaron Marcuse-Kubitza
05:05 PM Revision 14091: /README.TXT: Notes on system stability: added warning that when shutting down the VM, one should always first stop Postgres, to prevent the OS from SIGKILLing it
Aaron Marcuse-Kubitza
05:04 PM Revision 14090: inputs/SALVIAS/Source/header.csv: updated
Aaron Marcuse-Kubitza
03:50 PM Revision 14089: bugfix: bin/with_all: isset(): need to use `&>/dev/null` instead of `>&-`, etc because closing an fd causes declare to return false
Aaron Marcuse-Kubitza
03:31 PM Revision 14088: bugfix: bin/with_all, import_all: don't disown processes because they should be auto-killed if the shell is (disown was only needed before we used screen)
Aaron Marcuse-Kubitza
03:24 PM Revision 14087: bugfix: Full database import: need nested shell to prevent errexit from closing the window
Aaron Marcuse-Kubitza
01:24 PM Revision 14086: bugfix: schemas/public_.sql: analytical_stem_view_modify(): added columns: need to include COMMENT statements
Aaron Marcuse-Kubitza
01:21 PM Revision 14085: bugfix: schemas/util.sql: comment(element oid): need `objsubid = 0` filter so this doesn't use comments for any other objsubids
Aaron Marcuse-Kubitza
12:53 PM Revision 14084: schemas/public_.sql: added iucn_red_list_view_modify() and use it in iucn_red_list_view's "after updating this" instructions
Aaron Marcuse-Kubitza
12:47 PM Revision 14083: bugfix: schemas/util.sql: rematerialize_view(): also need to handle the target table's dependent views
Aaron Marcuse-Kubitza
12:38 PM Revision 14082: bugfix: schemas/util.sql: mk_drop_from_create(): need to use `IF EXISTS` so that the resulting statement also works if the target object does not yet exist
Aaron Marcuse-Kubitza
12:24 PM Revision 14081: schemas/util.sql: mk_drop_from_create(): also support `SELECT util.drop_*()` statements, in addition to DROP
Aaron Marcuse-Kubitza
11:37 AM Revision 14080: inputs/.TNRS/Source/test.xml.ref: updated
Aaron Marcuse-Kubitza

07/15/2014

11:14 PM Revision 14079: bugfix: /README.TXT: logs glob: don't unintentionally match . or ..
Aaron Marcuse-Kubitza
10:43 PM Revision 14078: inputs/VegBank/stemlocation_/test.xml.ref: updated
Aaron Marcuse-Kubitza
10:41 PM Revision 14077: /README.TXT: Full database import: `make test by_col=1`: updated runtime (1 h)
Aaron Marcuse-Kubitza
10:07 PM Revision 14076: inputs/TEX/Specimen2/test.xml.ref: updated
Aaron Marcuse-Kubitza
09:35 PM Revision 14075: inputs/GBIF/raw_occurrence_record_plants/test.xml.ref: updated
Aaron Marcuse-Kubitza
05:50 PM Task #887 (Rejected): fix disk space leak that fills the disk and crashes the import
Aaron Marcuse-Kubitza
05:48 PM Task #902 (Resolved): fix bug that causes joining on the wrong columns in the import
Aaron Marcuse-Kubitza
05:47 PM Task #905 (Resolved): narrow down the cause of the import bug (incorrect join columns and disk space leak)
bug fixed in r14074 Aaron Marcuse-Kubitza
05:44 PM Revision 14074: bugfix: lib/sql_io.py: put_table(): handle_MissingCastException(): when updating join_cols, don't add *new* entry for join_cols[out_col], only update existing one. this fixes #902 (import bug), and with #902 fixed, #887 (disk space leak) should no longer occur.
Aaron Marcuse-Kubitza
04:49 PM Revision 14073: bin/import_all: delete_logs(): documented that `trap EXIT` doesn't run until *shell* exit
Aaron Marcuse-Kubitza
04:48 PM Revision 14072: bin/import_all: delete_logs(): print when this happens, so it can be verified that it's happening properly
Aaron Marcuse-Kubitza
04:32 PM Revision 14071: bugfix: bin/import_all: need to run delete_logs manually because `trap EXIT` doesn't run until bg cmds done
Aaron Marcuse-Kubitza
04:28 PM Revision 14070: bin/import_all: delete_logs: moved testing of whether to delete logs to delete_logs() so that delete_logs() can be run regardless of the $delete_logs setting
Aaron Marcuse-Kubitza
03:58 PM Revision 14069: bugfix: bin/import_all: delete_logs(): also need to match log filenames when n=""
Aaron Marcuse-Kubitza
03:11 PM Revision 14068: bugfix: /Makefile: postgres_restart-*: argument to echo always needs quotes
Aaron Marcuse-Kubitza
03:05 PM Revision 14067: bugfix: /Makefile: $(pg_ctl-*): tell user that if it doesn't work, need to run `rm $(macPostgresDir)/postmaster.pid` and retry
Aaron Marcuse-Kubitza
02:57 PM Revision 14066: /Makefile: $(pg_ctl-Darwin): documented the pg_ctl version of this command in case `brew services` doesn't work
Aaron Marcuse-Kubitza
02:39 PM Revision 14065: bugfix: bin/with_all: isset(): need to use `>&- 2>&-` because &> does not work with - as the dest
Aaron Marcuse-Kubitza
01:19 PM Revision 14064: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: determine if the revision works: use the in# of the query instead of waiting an arbitrary time, because this is more accurate in determining whether the import is successful
Aaron Marcuse-Kubitza
12:52 PM Revision 14063: config/VirtualBox_VMs/vegbiendev/README.TXT: regressions that occurred during the revision range: named these "concurrent regressions"
Aaron Marcuse-Kubitza
12:45 PM Revision 14062: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: need to update system time so wait times can be calculated correctly
Aaron Marcuse-Kubitza
12:22 PM Revision 14061: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: documented that the patches are specifically for regressions that occurred during the revision range, not all bugs that were fixed in that range
Aaron Marcuse-Kubitza
12:14 PM Revision 14060: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: waiting for query: increased time to min. 10 min because some revisions take longer
Aaron Marcuse-Kubitza
12:09 PM Revision 14059: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bin/import_all: added step to type y and press ENTER
Aaron Marcuse-Kubitza
12:07 PM Revision 14058: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added steps to determine if the revision works, and then stop the import
Aaron Marcuse-Kubitza
11:27 AM Revision 14057: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: added r12994
Aaron Marcuse-Kubitza
11:09 AM Revision 14056: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: use for loop to avoid needing to repeat the command
Aaron Marcuse-Kubitza
11:05 AM Revision 14055: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: added r12760
Aaron Marcuse-Kubitza
10:54 AM Revision 14054: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: --fuzz apparently needs to be 3 even though we have only 2 lines of context
Aaron Marcuse-Kubitza
10:52 AM Revision 14053: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: use --fuzz to allow patching even when surrounding lines have changed
Aaron Marcuse-Kubitza
10:44 AM Revision 14052: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: sorted by revision #
Aaron Marcuse-Kubitza
10:43 AM Revision 14051: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: added r12865
Aaron Marcuse-Kubitza
10:33 AM Revision 14050: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: patch: need to use --force to avoid prompting user
Aaron Marcuse-Kubitza
10:16 AM Revision 14049: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: `svn revert`: need to use `--depth infinity` when reverting more than a file
Aaron Marcuse-Kubitza
10:14 AM Revision 14048: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: use `patch` instead of `svn merge` because `svn merge` sometimes inexplicably doens't apply patches
Aaron Marcuse-Kubitza
09:43 AM Revision 14047: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bugfixes: `svn revert` all changes instead of specific files, to support bugfixes to other files
Aaron Marcuse-Kubitza
09:42 AM Revision 14046: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: lib/sh/util.sh bugfix: use `svn merge` instead of `sed --in-place` because this can be used for more complex changes
Aaron Marcuse-Kubitza
09:41 AM Revision 14045: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: lib/sh/util.sh bugfix: documented revision
Aaron Marcuse-Kubitza
09:20 AM Revision 14044: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: need to apply r12872 bugfix to lib/sh/util.sh because it occurred after r12025
Aaron Marcuse-Kubitza
09:10 AM Revision 14043: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: `make` commands: use `yes|` to avoid needing to confirm prompts
Aaron Marcuse-Kubitza
09:08 AM Revision 14042: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: `make mk_db ...`: use `yes|` to avoid needing to confirm prompts
Aaron Marcuse-Kubitza
08:56 AM Revision 14041: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: to test a different revision: added step that if any of the commands after `svn up` are broken, try a different revision
Aaron Marcuse-Kubitza
08:46 AM Revision 14040: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: `make db`: need to run `schemas/reinstall` manually because older versions of the codebase just used `schemas/install`
Aaron Marcuse-Kubitza

07/14/2014

11:30 PM Revision 14039: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: documented the range from within the revision should be chosen
Aaron Marcuse-Kubitza
09:19 PM Revision 14038: fix: inputs/.IRMNG/*/: added _no_import because this datasource is only used as a lookup table and does not need to be imported/scrubbed
Aaron Marcuse-Kubitza
09:18 PM Revision 14037: config/VirtualBox_VMs/vegbiendev/README.TXT: `svn up`: documented runtime (1 min)
Aaron Marcuse-Kubitza
08:24 PM Revision 14036: bugfix: added nodes/_no_import, because the NCBI import doesn't work due to a Postgres 9.3 bug (#859). _no_import used to not be needed because we didn't import the hidden sources.
Aaron Marcuse-Kubitza
08:05 PM Revision 14035: fix: bin/with_all: removed debug statements
Aaron Marcuse-Kubitza
05:19 PM Revision 14034: bugfix: bin/with_all: testing if @inputs is set: `"${inputs+isset}"` syntax doesn't work for empty arrays, so need to use `declare -p` instead
Aaron Marcuse-Kubitza
04:46 PM Revision 14033: bugfix: to set up the VM: to use a database backup: also need to `make rm_initial_public` because initdb creates a non-empty DB
Aaron Marcuse-Kubitza
04:42 PM Revision 14032: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added steps to test a different revision
Aaron Marcuse-Kubitza
04:40 PM Revision 14031: /Makefile: db: use reinstall instead of install to allow running this on an existing DB
Aaron Marcuse-Kubitza
02:49 PM Revision 14030: config/VirtualBox_VMs/vegbiendev/README.TXT: `sudo apt-get dist-upgrade`: documented runtime (12 min)
Aaron Marcuse-Kubitza
02:47 PM Revision 14029: config/VirtualBox_VMs/vegbiendev/README.TXT: updated VM snapshot names
Aaron Marcuse-Kubitza
02:44 PM Revision 14028: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to install system updates: added step to restart, because some system updates require this
Aaron Marcuse-Kubitza
02:34 PM Revision 14027: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: to install system updates: added step to restart, because some system updates require this
Aaron Marcuse-Kubitza
02:29 PM Revision 14026: config/VirtualBox_VMs/vegbiendev/README.TXT: added instructions to install system updates
Aaron Marcuse-Kubitza
01:23 PM Revision 14025: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: bin/import_all: documented runtime (50 min)
Aaron Marcuse-Kubitza
01:07 PM Revision 14024: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added steps to run the import
Aaron Marcuse-Kubitza
12:24 PM Revision 14023: config/VirtualBox_VMs/vegbiendev/README.TXT: to set up the VM: added steps to move vegbiendev.vdi to the internal hard drive
Aaron Marcuse-Kubitza
12:19 PM Revision 14022: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added steps to start the VM
Aaron Marcuse-Kubitza
12:16 PM Revision 14021: config/VirtualBox_VMs/vegbiendev/README.TXT: moved "set up the VM" steps to separate section
Aaron Marcuse-Kubitza
12:06 PM Revision 14020: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: added steps to create a booted snapshot
Aaron Marcuse-Kubitza
12:01 PM Revision 14019: config/VirtualBox_VMs/vegbiendev/README.TXT: moved creation of pg_restore snapshot to be part of just the database backup section
Aaron Marcuse-Kubitza
11:52 AM Revision 14018: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: documented runtime (15 min)
Aaron Marcuse-Kubitza
11:51 AM Revision 14017: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: time the operation
Aaron Marcuse-Kubitza
11:32 AM Revision 14016: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: added name for VM snapshot after this step
Aaron Marcuse-Kubitza
11:31 AM Revision 14015: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: need to run as DB superuser to restore py_util
Aaron Marcuse-Kubitza
11:24 AM Revision 14014: config/VirtualBox_VMs/vegbiendev/README.TXT: rsync: updated runtime (25 min)
Aaron Marcuse-Kubitza
11:24 AM Revision 14013: config/VirtualBox_VMs/vegbiendev/README.TXT: added steps to create snapshot before running pg_restore
Aaron Marcuse-Kubitza
10:55 AM Revision 14012: config/VirtualBox_VMs/vegbiendev/README.TXT: added steps to configure the VM before booting
Aaron Marcuse-Kubitza
10:53 AM Revision 14011: config/VirtualBox_VMs/vegbiendev/README.TXT: added instructions for selecting the initial snapshot and booting the VM
Aaron Marcuse-Kubitza
10:36 AM Revision 14010: config/VirtualBox_VMs/vegbiendev/README.TXT: perform long-running operations inside `screen`
Aaron Marcuse-Kubitza
10:35 AM Revision 14009: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to use a database backup: only run mk_db, not db, to avoid restoring schemas that are part of the backup
Aaron Marcuse-Kubitza
09:33 AM Revision 14008: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: schemas must be in dependency order
Aaron Marcuse-Kubitza
09:21 AM Revision 14007: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: don't restore analytical_db schema because we don't use it and it depends on public, which we're not restoring
Aaron Marcuse-Kubitza
09:16 AM Revision 14006: web/links/index.htm: updated to Firefox bookmarks: WebEx: added steps to join a test meeting. pg_restore: documented that you need to *create* the schema before you restore into it, or else you will get a cryptic error message that it's using pg_catalog instead. added Homebrew links, including instructions for setting psycopg2 up with it. added PostGIS links. username URLs: documented how to enable these in Internet Explorer. TWiki: documented what to do when moving the TWiki install dir.
Aaron Marcuse-Kubitza
09:06 AM Revision 14005: bugfix: lib/Firefox_bookmarks.reformat.csv: updated for new Firefox bookmarks format, which indents the <DD> tag
Aaron Marcuse-Kubitza
08:36 AM Revision 14004: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: pg_restore: need to *create* the schema before you restore into it, to avoid cryptic error messages
Aaron Marcuse-Kubitza
08:33 AM Revision 14003: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: schemas/postgresql.conf: need to decrease shared_buffers to match VM's allocated memory (1 GB)
Aaron Marcuse-Kubitza
08:18 AM Revision 14002: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: schemas/postgresql.conf: need to decrease shared_buffers to match VM's allocated memory (1 GB)
Aaron Marcuse-Kubitza

07/13/2014

11:50 PM Revision 14001: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: need to run `make db` to restore users, which are not part of the backup
Aaron Marcuse-Kubitza
11:40 PM Revision 14000: config/VirtualBox_VMs/vegbiendev/README.TXT: rsync: updated runtime (35 min)
Aaron Marcuse-Kubitza

07/11/2014

04:54 PM Revision 13999: config/VirtualBox_VMs/vegbiendev/README.TXT: turning off of non-ARIZ inputs: removed metadata datasources because these have been renamed to start with ".", and so aren't included in */
Aaron Marcuse-Kubitza
04:48 PM Revision 13998: bugfix: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: pg_restore: need to use for loop because pg_restore doesn't support multiple --schema options (it just uses the last one)
Aaron Marcuse-Kubitza
04:35 PM Revision 13997: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: added step to restore the necessary schemas from the DB
Aaron Marcuse-Kubitza
04:32 PM Revision 13996: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: rsync: documented runtime (13 min)
Aaron Marcuse-Kubitza
04:11 PM Revision 13995: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: added step to fetch the database backup via rsync
Aaron Marcuse-Kubitza
04:04 PM Revision 13994: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: moved steps to enable the user to access VirtualBox shared folders to separate section because VirtualBox shared folders currently don't work, likely because of a bug in VirtualBox Guest Additions when installed on something other than a clean Linux install
Aaron Marcuse-Kubitza
03:54 PM Revision 13993: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: database backup approach: added steps to enable the user to access VirtualBox shared folders
Aaron Marcuse-Kubitza
03:06 PM Revision 13992: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: added section for database backup approach, as alternative to clean database approach
Aaron Marcuse-Kubitza
10:32 AM Revision 13991: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: use ".." instead of - to indicate a range, to avoid this being confused for a minus sign
Aaron Marcuse-Kubitza
10:26 AM Revision 13990: bugfix: /Makefile: postgres_restart-Darwin: need to have the user run the command outside of make because it doesn't appear to do anything when run inside make (this is the same problem as on Linux)
Aaron Marcuse-Kubitza
10:25 AM Revision 13989: /Makefile: $(pg_ctl-Darwin): use simpler `brew services` instead of `launchctl __/homebrew.mxcl.postgresql.plist`
Aaron Marcuse-Kubitza
10:03 AM Revision 13988: bugfix: bin/stop_imports: also need to include `bin/after_import`
Aaron Marcuse-Kubitza
09:56 AM Revision 13987: inputs/.TNRS/Source/map.csv: datasetURL: updated to indicate that this uses the TNRS dev server (the actual URL is private)
Aaron Marcuse-Kubitza
09:46 AM Revision 13986: fix: inputs/VASCAN/Source/map.csv: observationGranularity should not be specimen because this datasource contains only taxa
Aaron Marcuse-Kubitza
09:13 AM Revision 13985: bugfix: bin/import_all: now that always using log files to fix output clutter, need to delete created logs if logging is turned off
Aaron Marcuse-Kubitza
08:45 AM Revision 13984: bugfix: bin/import_all: don't errexit if a background process is Ctrl-C'd
Aaron Marcuse-Kubitza
08:41 AM Revision 13983: bugfix: bin/import_all: was run without initial "." test: don't exit nonzero because this will close the subshell
Aaron Marcuse-Kubitza
08:38 AM Revision 13982: bugfix: bin/import_all: ensure that this is run in a subshell, which is needed so errexits don't close the terminal window
Aaron Marcuse-Kubitza
08:32 AM Revision 13981: bin/import_all: documented that this must be run in a subshell (obtained by running `$0`)
Aaron Marcuse-Kubitza
08:25 AM Revision 13980: bugfix: bin/import_all: need to always use log files for background processes
Aaron Marcuse-Kubitza
08:12 AM Revision 13979: fix: bin/import_all: Source/import: don't use by_col=1 for this because it's slower for small #s of rows. by_col mode is no longer needed for metadata-only tables because these tables now have a single empty row so that they also work in row-based mode.
Aaron Marcuse-Kubitza
08:06 AM Revision 13978: fix: bin/import_all: hidden srcs: use with_all for this to avoid needing to list every source, and to display the backgrounded command with the variables substituted
Aaron Marcuse-Kubitza
07:40 AM Revision 13977: bin/import_all: TNRS, geoscrub: integrated into the list of metadata sources
Aaron Marcuse-Kubitza
07:39 AM Revision 13976: bin/import_all: TNRS, geoscrub: use import rather than publish because the non-imported tables have now been excluded
Aaron Marcuse-Kubitza
07:34 AM Revision 13975: fix: inputs/.geoscrub/geoscrub_output/: added _no_import because these tables are metadata that is used in the analytical DB. this is better than relying on bin/import_all not to import these.
Aaron Marcuse-Kubitza

07/10/2014

07:25 PM Revision 13974: fix: bin/import_all: updated for new metadata datasource names (see issue #940)
Aaron Marcuse-Kubitza
07:25 PM Revision 13973: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: updated for new metadata datasource names (see issue #940)
Aaron Marcuse-Kubitza
06:41 PM Task #940 (Resolved): resequence datasources in dependency order
Aaron Marcuse-Kubitza
04:22 PM Task #940 (Resolved): resequence datasources in dependency order
* this enables bootstrapping the DB from a VM backup
steps
# put all [[VegBIEN_contents#datasources|metadata da...
Aaron Marcuse-Kubitza
06:32 PM Revision 13972: fix: inputs/IUCN/: renamed to inputs/.IUCN/ (see issue #940)
Aaron Marcuse-Kubitza
06:04 PM Revision 13971: fix: inputs/newWorld/: renamed to inputs/.newWorld/ (see issue #940)
Aaron Marcuse-Kubitza
04:59 PM Revision 13970: bugfix: inputs/IRMNG/: renamed to inputs/.IRMNG/ so that this comes before TNRS, which depends on it (this is a metadata datasource, so it can start with "."). part of issue #940.
Aaron Marcuse-Kubitza
03:52 PM Revision 13969: config/VirtualBox_VMs/vegbiendev/README.TXT: to test the import: set up the VM: added steps to create a VM snapshot when done
Aaron Marcuse-Kubitza
03:37 PM Revision 13968: config/VirtualBox_VMs/vegbiendev/README.TXT: `make`: documented runtime (15 min)
Aaron Marcuse-Kubitza
03:33 PM Revision 13967: fix: config/VirtualBox_VMs/vegbiendev/README.TXT: removed non-applicable step about the MySQL root password, which is not used for this procedure
Aaron Marcuse-Kubitza
03:32 PM Revision 13966: added config/VirtualBox_VMs/vegbiendev/README.TXT with instructions to test the import
Aaron Marcuse-Kubitza
12:17 PM Revision 13965: inputs/GBIF/_MySQL/.rsync_ignore: don't exclude GBIFPortalDB-*.data.sql.gz, even though this is an intermediate file, because it's better to have a backup of it locally. this was excluded in r13316 (2014-4-24) to free up disk space on the local machine.
Aaron Marcuse-Kubitza
10:57 AM Revision 13964: fix: inputs/Madidi/LocationObservation/postprocess.sql: parse Spanish dates
Aaron Marcuse-Kubitza
09:45 AM Revision 13963: validation/completeness/BIENDatesPopulated.xlsx: updated: Martha added Priority column
Aaron Marcuse-Kubitza
08:41 AM Revision 13962: schemas/util.sql: replace_words(): use map_words() to enable inlining the concatenated hstore, so that it doesn't need to be concatenated on *each* function call
Aaron Marcuse-Kubitza
08:39 AM Revision 13961: schemas/util.sql: added map_words()
Aaron Marcuse-Kubitza
08:16 AM Revision 13960: schemas/util.sql: added date_from_spanish()
Aaron Marcuse-Kubitza
08:13 AM Revision 13959: schemas/util.sql: added replace_words()
Aaron Marcuse-Kubitza
08:09 AM Revision 13958: schemas/util.sql: added words(text)
Aaron Marcuse-Kubitza
08:02 AM Revision 13957: schemas/util.sql: spanish_date_words(): switched to using hstore because this is better for the algorithm that will translate these
Aaron Marcuse-Kubitza
07:20 AM Revision 13956: schemas/util.sql: added spanish_date_words()
Aaron Marcuse-Kubitza
07:19 AM Revision 13955: schemas/util.sql: added `replacement` type
Aaron Marcuse-Kubitza
04:09 AM Revision 13954: bugfix: mk_set_relation_metadata(): need to include col comments as well so that these are re-created properly by recreate()
Aaron Marcuse-Kubitza
04:07 AM Revision 13953: schemas/util.sql: added mk_set_comments(regclass)
Aaron Marcuse-Kubitza
04:06 AM Revision 13952: schemas/util.sql: show_set_comment(regclass): renamed to mk_set_comment() to match other mk_set_comment() functions
Aaron Marcuse-Kubitza
04:01 AM Revision 13951: schemas/util.sql: added mk_set_col_comments(regclass)
Aaron Marcuse-Kubitza
03:58 AM Revision 13950: schemas/util.sql: added cols(regclass)
Aaron Marcuse-Kubitza
03:56 AM Revision 13949: schemas/util.sql: added mk_set_comment(col_ref)
Aaron Marcuse-Kubitza
03:18 AM Revision 13948: added validation/completeness/BIENDatesPopulated.xlsx from Google spreadsheets
Aaron Marcuse-Kubitza

07/09/2014

02:50 PM Revision 13947: fix: mappings/VegCore-VegBIEN.csv: mapped DwC year/month/day, which are split-date alternatives to eventDate. this fixes the missing eventDate in FIA.
Aaron Marcuse-Kubitza
02:45 PM Revision 13946: bugfix: inputs/FIA/*/VegBIEN.csv: regenerated, replacing these with symlinks to the file used by new-style import
Aaron Marcuse-Kubitza
02:34 PM Revision 13945: inputs/FIA/taxon_observation.**/test.xml.ref: updated
Aaron Marcuse-Kubitza
02:34 PM Revision 13944: inputs/FIA/TREE/test.xml.ref: updated
Aaron Marcuse-Kubitza
02:29 PM Revision 13943: inputs/FIA/REF_RESEARCH_STATION/test.xml.ref: updated
Aaron Marcuse-Kubitza
02:13 PM Revision 13942: bugfix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: updated to new TWiki/ location
Aaron Marcuse-Kubitza
02:12 PM Revision 13941: bugfix: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: updated to new VegBIEN/ location
Aaron Marcuse-Kubitza
12:14 PM Revision 13940: fix: inputs/bien2_traits/TraitObservation/map.csv: mapped VisitingDate to eventDate
Aaron Marcuse-Kubitza
12:05 PM Revision 13939: fix: inputs/Madidi/LocationObservation/postprocess.sql: populated missing eventDate from PlotInventoryName (authorEventCode)
Aaron Marcuse-Kubitza
09:40 AM Revision 13938: schemas/util.sql: mk_set_comment(table_ regclass, comment text): use new util.mk_set_comment(text, text)
Aaron Marcuse-Kubitza
09:38 AM Revision 13937: schemas/util.sql: added mk_set_comment(col col_ref, comment text)
Aaron Marcuse-Kubitza
09:37 AM Revision 13936: schemas/util.sql: added sql(col_ref)
Aaron Marcuse-Kubitza
09:35 AM Revision 13935: schemas/util.sql: added mk_set_comment(on_ text, comment text)
Aaron Marcuse-Kubitza
07:53 AM Revision 13934: schemas/util.sql: added comment(col_ref)
Aaron Marcuse-Kubitza
07:50 AM Revision 13933: schemas/util.sql: added col_num(col_ref)
Aaron Marcuse-Kubitza
07:03 AM Revision 13932: removed no longer needed inputs/.TNRS/grants.sql, since the grants in schema.sql are now being run
Aaron Marcuse-Kubitza
07:03 AM Revision 13931: bugfix: inputs/input.Makefile: sql/install: schema.sql should not be passed through pg_dump_limit because it contains GRANT statements that need to be run
Aaron Marcuse-Kubitza
06:22 AM Revision 13930: schemas/public_.sql: iucn_red_list_view: documented how to regenerate iucn_red_list from this
Aaron Marcuse-Kubitza

07/08/2014

04:17 PM Revision 13929: exports/2014-6-4.Iara_Lacher.reserve_prioritization.csv.run: documented runtime (7.5 min) and rowcount (3.5 million)
Aaron Marcuse-Kubitza
03:23 PM Revision 13928: bugfix: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: fixed slowdown in materializing the view, which was caused by source__observation_type(), by replacing this with a LEFT JOIN as was done for is_threatened_iucn
Aaron Marcuse-Kubitza

07/07/2014

07:33 AM Revision 13927: schemas/util.sql: in_south_america(): optimized by using BETWEEN instead of util.contained_within__no_dateline(). this reduces the filter time for 2014-6-4.Iara_Lacher.reserve_prioritization by about 10%.
Aaron Marcuse-Kubitza
07:26 AM Revision 13926: fix: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: is_threatened_iucn: generate this much faster by doing a LEFT JOIN, which can reuse the same in-memory hash index for every row
Aaron Marcuse-Kubitza
07:04 AM Revision 13925: bugfix: schemas/public_.sql: wrapper functions can't use util-schema types because these will cause the wrapper function to be cascadingly dropped when the util schema is reinstalled
Aaron Marcuse-Kubitza
06:55 AM Revision 13924: bugfix: in_south_america(): must use util.contained_within__no_dateline() instead of util.contained_within_approx() to ensure that the more accurate geometry logic is used
Aaron Marcuse-Kubitza
06:51 AM Revision 13923: bugfix: schemas/public_.sql: source__observation_type(): don't display NOTICEs about the search_path, because this function will be called millions of times
Aaron Marcuse-Kubitza
06:48 AM Revision 13922: bugfix: schemas/public_.sql: in_iucn_red_list(): don't display NOTICEs about the search_path, because this function will be called millions of times
Aaron Marcuse-Kubitza
06:43 AM Revision 13921: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added is_threatened_iucn
Aaron Marcuse-Kubitza
06:37 AM Revision 13920: schemas/public_.sql: added in_iucn_red_list()
Aaron Marcuse-Kubitza
06:36 AM Revision 13919: schemas/public_.sql: added iucn_red_list, materialized from iucn_red_list_view
Aaron Marcuse-Kubitza
06:22 AM Revision 13918: bugfix: schemas/vegbien.sql: iucn_red_list_view: need to include only names with an accepted name, and distinctify on the accepted names
Aaron Marcuse-Kubitza
06:17 AM Revision 13917: schemas/public_.sql: added iucn_red_list
Aaron Marcuse-Kubitza
06:14 AM Revision 13916: schemas/util.sql: materialize_view(): use util.copy() instead of util.materialize_query() so that all view metadata is transferred
Aaron Marcuse-Kubitza
06:02 AM Revision 13915: schemas/public_.sql: iucn_red_list: renamed to iucn_red_list_view since this will be materialized
Aaron Marcuse-Kubitza
06:01 AM Revision 13914: schemas/public_.sql: added iucn_red_list
Aaron Marcuse-Kubitza
05:44 AM Revision 13913: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added collection_type (using source__observation_type())
Aaron Marcuse-Kubitza
05:36 AM Revision 13912: schemas/public_.sql: added source__observation_type()
Aaron Marcuse-Kubitza
05:04 AM Revision 13911: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added accepted_subspecies, and removed accepted_taxon_name_with_author which had been substituting for it
Aaron Marcuse-Kubitza
04:50 AM Revision 13910: schemas/public_.sql: added subspecies() wrapper
Aaron Marcuse-Kubitza
04:38 AM Revision 13909: schemas/util.sql: added subspecies()
Aaron Marcuse-Kubitza
04:10 AM Revision 13908: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: include only coordinates in South America
Aaron Marcuse-Kubitza
03:55 AM Revision 13907: schemas/util.sql: added south_america(), in_south_america()
Aaron Marcuse-Kubitza
03:37 AM Revision 13906: fix: schemas/util.sql: OPERATOR ~@(geocoord, postgis.geometry): renamed to @ because this is not an approximate comparison for geometry
Aaron Marcuse-Kubitza
03:35 AM Revision 13905: fix: schemas/util.sql: contained_within_approx(geocoord, postgis.geometry): renamed to contained_within__no_dateline(__) because this is not an approximate comparison for geometry
Aaron Marcuse-Kubitza
03:30 AM Revision 13904: schemas/util.sql: lat_long_in_new_world(): renamed to just in_new_world() because the lat/long is implied by the param type
Aaron Marcuse-Kubitza
03:08 AM Revision 13903: schemas/util.sql: lat_long_in_new_world(): take a geocoord param instead of separate lat/long params
Aaron Marcuse-Kubitza
03:00 AM Revision 13902: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza

07/06/2014

11:08 PM Revision 13901: schemas/util.sql: added contained_within_approx(geocoord, geometry) and corresponding OPERATOR ~@(geocoord, geometry)
Aaron Marcuse-Kubitza
10:39 PM Revision 13900: schemas/util.sql: added OPERATOR ~@(geocoord, geography)
Aaron Marcuse-Kubitza
10:23 PM Revision 13899: schemas/util.sql: lat_long_in_new_world(): use new contained_within_approx(geocoord, geography)
Aaron Marcuse-Kubitza
10:17 PM Revision 13898: schemas/util.sql: added contained_within_approx(geocoord, postgis.geography), which enables specifying just `(lat, long)` without the ::util.geocoord type specifier
Aaron Marcuse-Kubitza
04:04 PM Revision 13897: schemas/util.sql: OPERATOR @(postgis.geography, postgis.geography): renamed to ~@ because it's approximate
Aaron Marcuse-Kubitza
03:52 PM Revision 13896: schemas/util.sql: contained_within(): renamed to contained_within_approx() because the latitude lines of geography type bounding boxes bulge outward, creating false positives above and below the bounding box
Aaron Marcuse-Kubitza
03:50 PM Revision 13895: schemas/util.sql: added contained_within__no_dateline(geometry, geometry) and corresponding operator @
Aaron Marcuse-Kubitza
02:51 PM Revision 13894: schemas/util.sql: contained_within(): renamed to contained_within_approx() because the latitude lines of geography type bounding boxes bulge outward, creating false positives above and below the bounding box
Aaron Marcuse-Kubitza
05:49 AM Revision 13893: schemas/util.sql: geometry(geocoord): documented that it is not possible to create a cast for this, as a bug in pg_dump prevents the cast from being exported, even when no export filters are applied
Aaron Marcuse-Kubitza

07/05/2014

12:40 PM Revision 13892: schemas/util.sql: point(geocoord): renamed to geometry(geocoord) since this is now a cast
Aaron Marcuse-Kubitza
12:03 PM Revision 13891: schemas/util.sql: point(): return geometry instead of geography to support using points with geometry arithmetic
Aaron Marcuse-Kubitza
11:24 AM Revision 13890: schemas/util.sql: point(): take a single util.geocoord param instead of separate lat/long
Aaron Marcuse-Kubitza
10:45 AM Revision 13889: schemas/util.sql: added geocoord type
Aaron Marcuse-Kubitza

07/04/2014

08:29 PM Revision 13888: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: include only *georeferenced* occurrences (lat/long NOT NULL)
Aaron Marcuse-Kubitza
08:25 PM Revision 13887: schemas/util.sql: bounding_box(): use bounding_box__no_dateline() to construct the postgis.geometry object
Aaron Marcuse-Kubitza
08:23 PM Revision 13886: schemas/util.sql: added bounding_box__no_dateline(), which is more accurate than util.bounding_box() (latitude lines will be straight), but geocoordinate wraparound is not supported
Aaron Marcuse-Kubitza
08:14 PM Revision 13885: schemas/public_.sql: 2014-6-4.Iara_Lacher.reserve_prioritization: added functional traits that we have 1st-class columns for (dbh_cm, height_m)
Aaron Marcuse-Kubitza
12:29 PM Revision 13884: added exports/2014-6-4.Iara_Lacher.reserve_prioritization.csv.run
Aaron Marcuse-Kubitza
11:12 AM Revision 13883: inputs/publishable datasources.xlsx: updated
Aaron Marcuse-Kubitza
08:45 AM Revision 13882: inputs/publishable datasources.xlsx: updated
Aaron Marcuse-Kubitza

07/03/2014

08:13 PM Revision 13881: inputs/.TNRS/schema.sql: matchedFamily: just use Name_matched_accepted_family, because TNRS has now been reloaded so that the names that were missing this have it populated
Aaron Marcuse-Kubitza
09:59 AM Revision 13880: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza
03:47 AM Task #917: TNRS: Instructions for new version with TPL
a single "-" creates strikethrough formatting, so you have to use "--" instead Aaron Marcuse-Kubitza
12:34 AM Revision 13879: inputs/.TNRS/schema.sql: taxon_match: taxon_match__valid_match: replaced with taxon_best_match__valid_match, which also applies taxon_best_match's filters, since taxon_match is now accessed through taxon_best_match
Aaron Marcuse-Kubitza
12:17 AM Revision 13878: fix: inputs/.TNRS/schema.sql: MatchedTaxon: use taxon_best_match instead of taxon_match because this should provide only one match per taxon
Aaron Marcuse-Kubitza

07/02/2014

02:17 AM Revision 13877: bugfix: /README.TXT: Mac settings backup: backup to jupiter: need to exclude ~/software/**/.svn/ because these are different on jupiter
Aaron Marcuse-Kubitza
02:00 AM Revision 13876: /README.TXT: Mac settings backup: backup to jupiter: removed no longer applicable exclude of /VirtualBox VMs/Ubuntu/Ubuntu.vdi
Aaron Marcuse-Kubitza

06/27/2014

03:15 PM Task #917: TNRS: Instructions for new version with TPL
test update now that watcher notifications have been fixed Aaron Marcuse-Kubitza

06/26/2014

06:30 PM Revision 13875: inputs/.TNRS/schema.sql: added taxon_best_match view
Aaron Marcuse-Kubitza
06:12 PM Revision 13874: inputs/.TNRS/schema.sql: taxon_match: added taxon_match__one_selected_match unique index
Aaron Marcuse-Kubitza
05:06 PM Revision 13873: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
09:49 AM Revision 13872: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza
09:25 AM Task #917: TNRS: Instructions for new version with TPL
testing Martha's watcher notifications again after e-mail address fix... Aaron Marcuse-Kubitza
09:23 AM Task #917: TNRS: Instructions for new version with TPL
testing Martha's watcher notifications... Aaron Marcuse-Kubitza
05:41 AM Revision 13871: inputs/.TNRS/schema.sql: taxon_match__fill(): split into separate DECLARE blocks for each field for clarity
Aaron Marcuse-Kubitza
04:58 AM Revision 13870: inputs/.TNRS/data.sql: refreshed
Aaron Marcuse-Kubitza
04:57 AM Revision 13869: fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*
Aaron Marcuse-Kubitza
04:33 AM Revision 13868: fix: inputs/.TNRS/schema.sql: taxon_match: renamed related items to start with taxon_match__*
Aaron Marcuse-Kubitza
04:28 AM Revision 13867: inputs/.TNRS/data.sql: refreshed
Aaron Marcuse-Kubitza
04:11 AM Revision 13866: inputs/.TNRS/schema.sql: taxon_match: insert names via taxon_match_input auto-updatable view instead of directly into taxon_match, to allow the taxon_match columns to be renamed while still supporting inserts using the TNRS column names
Aaron Marcuse-Kubitza
02:43 AM Revision 13865: fix: schemas/Makefile: vegbien.sql: also need to update inputs/.TNRS/data.sql, since its contents change along with this
Aaron Marcuse-Kubitza
02:41 AM Revision 13864: inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name
Aaron Marcuse-Kubitza
02:39 AM Revision 13863: inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name
Aaron Marcuse-Kubitza
02:38 AM Revision 13862: inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name
Aaron Marcuse-Kubitza
02:14 AM Revision 13861: inputs/.TNRS/schema.sql: tnrs_match: renamed to taxon_match to use the normalized VegCore name for this, and to avoid repeating the schema name
Aaron Marcuse-Kubitza

06/25/2014

07:54 PM Revision 13860: lib/tnrs.py: dirty: documented that this actually used to be on in the web app (see r9910, 2013-6-18), but does not appear to be needed (the source_sorting bug alluded to in r9910 is not fixed by enabling the dirty setting)
Aaron Marcuse-Kubitza
07:48 PM Task #917: TNRS: Instructions for new version with TPL
multiple @Selected@ names bug fixed in r13855 Aaron Marcuse-Kubitza
07:46 PM Revision 13859: lib/tnrs.py: requests: also debug-print request URL
Aaron Marcuse-Kubitza
07:44 PM Revision 13858: lib/tnrs.py: Download: include the same debug info as do_request()
Aaron Marcuse-Kubitza
07:41 PM Revision 13857: lib/tnrs.py: do_request(): also debug-print request headers
Aaron Marcuse-Kubitza
07:39 PM Revision 13856: lib/tnrs.py: download_request_template: dirty: documented why this must be off
Aaron Marcuse-Kubitza
07:36 PM Revision 13855: bugfix: lib/tnrs.py: download_request_template: fixed bug where multiple names were being marked as Selected, because dirty was incorrectly set to true unlike in the web app
Aaron Marcuse-Kubitza
07:30 PM Revision 13854: added derived/TNRS/web_app/protocol/
Aaron Marcuse-Kubitza
04:28 PM Revision 13853: inputs/.TNRS/data.sql: refreshed
Aaron Marcuse-Kubitza
04:25 PM Revision 13852: bugfix: inputs/.TNRS/schema.sql: taxon_name_is_safe(): need to use `NOT (_ = ANY(_)) instead of `_ != ANY(_)`, because the != operator is applied to each element
Aaron Marcuse-Kubitza
03:47 PM Revision 13851: inputs/.TNRS/schema.sql: tnrs: renamed to tnrs_match to distinguish it from other TNRS-related tables
Aaron Marcuse-Kubitza
03:33 PM Revision 13850: inputs/.TNRS/schema.sql: tnrs: renamed to tnrs_match to distinguish it from other TNRS-related tables
Aaron Marcuse-Kubitza
02:38 PM Revision 13849: fix: lib/phpPgAdmin.login.php.diff: use relative file path rather than the path the file was at when the patch was created
Aaron Marcuse-Kubitza
02:34 PM Revision 13848: /Makefile, lib/phpPgAdmin.login.php.diff: public_ user: added auto-filled password so that users would not be confused as to what to type in the password field
Aaron Marcuse-Kubitza
02:15 PM Revision 13847: added schemas/VegCore/phpMyAdmin/libraries/plugins/auth/AuthenticationCookie.class.php.diff
Aaron Marcuse-Kubitza
01:19 PM Task #938 (New): Enquist's taxon validation
From Brian Enquist:
I can start by checking the accuracy of the fields, and data for a random subset of plots. To ...
Martha Narro
10:39 AM Revision 13846: inputs/.TNRS/schema.sql: `taxon_scrub.scrubbed_unique_taxon_name.*`: added to-modify instructions
Aaron Marcuse-Kubitza
10:36 AM Revision 13845: inputs/.TNRS/schema.sql: *_modify(): merged these into the "to modify" instructions in the corresponding views, because there is no need to create a separate *_modify() function for every view now that their definitions are all the same
Aaron Marcuse-Kubitza
10:21 AM Revision 13844: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB
Aaron Marcuse-Kubitza
05:15 AM Revision 13843: schemas/public_.sql: analytical_stem_view and related views: updated COMMENTs from data dictionary spreadsheet, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#copy-data-dictionary-definitions-to-database
Aaron Marcuse-Kubitza
04:11 AM Revision 13842: schemas/public_.sql: ran analytical_stem_view_modify(), which transfers the column COMMENTs from analytical_stem_view to analytical_stem
Aaron Marcuse-Kubitza
04:04 AM Revision 13841: bugfix: schemas/util.sql: view_def_to_orig(): need to handle cases when list of cols from the same table is not an expanded * expression
Aaron Marcuse-Kubitza
03:59 AM Revision 13840: schemas/util.sql: added view_is_subset(view_def text)
Aaron Marcuse-Kubitza
03:58 AM Revision 13839: schemas/util.sql: added view_is_automatically_updatable(view_def text)
Aaron Marcuse-Kubitza
03:23 AM Revision 13838: bugfix: schemas/util.sql: show_create_view(): use the overridden version of pg_get_viewdef(), which supports expanded * expressions. this was possibly being used already whenever util happened to be in the search_path.
Aaron Marcuse-Kubitza

06/24/2014

05:03 PM Revision 13837: bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to new analytical_stem_view column names
Aaron Marcuse-Kubitza
05:01 PM Revision 13836: fix: schemas/public_.sql: analytical_stem_view derived and related views: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database but with the current columns of analytical_stem as the left-hand column
Aaron Marcuse-Kubitza
04:36 PM Revision 13835: bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to new analytical_stem_view column names
Aaron Marcuse-Kubitza
04:34 PM Revision 13834: schemas/public_.sql: analytical_stem_view: applied data dictionary renamings, using the steps at wiki.vegpath.org/VegBIEN_schema_refactoring#apply-data-dictionary-renamings-to-database
Aaron Marcuse-Kubitza
03:27 PM Revision 13833: lib/tnrs.py: source_sorting (Constrain by Source): documented the different behavior for this in each match mode (all-matches and best-match)
Aaron Marcuse-Kubitza
 

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