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# Date Author Comment
6086 11/08/2012 03:27 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added reference_by_shortname(). Using this function instead of the manual query should force the query planner to evaluate this expression first, rather than complexly reordering joins to place this nested select as a filter condition.

6085 11/08/2012 03:00 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added threatened_taxonlabel derived table with generating view threatened_taxonlabel_view

6084 11/08/2012 02:48 PM Aaron Marcuse-Kubitza

Updated inputs/UNCC/Specimen/test.xml.ref inserted row count

6083 11/08/2012 01:38 PM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Added threatened

6082 11/08/2012 01:21 PM Aaron Marcuse-Kubitza

inputs/VegBank/vegbank.~.clean_up.sql: Remove private columns (plot.reallatitude, reallongitude) that should not be publicly visible

6081 11/08/2012 01:13 PM Aaron Marcuse-Kubitza

inputs/CVS/Organism/map.csv: Removed now-dropped realLatitude, realLongitude

6080 11/08/2012 01:12 PM Aaron Marcuse-Kubitza

inputs/CVS/Organism/map.csv: Removed now-dropped realLatitude, realLongitude

6079 11/08/2012 01:12 PM Aaron Marcuse-Kubitza

Added inputs/CVS/Organism/postprocess.sql to drop private realLatitude, realLongitude columns

6078 11/08/2012 01:10 PM Aaron Marcuse-Kubitza

input.Makefile: Staging tables installation: Added back postprocess.sql, which is now used for one-time dropping of private columns that should not be publicly visible

6077 11/08/2012 12:47 PM Aaron Marcuse-Kubitza

input.Makefile: Maps building: %/.map.csv.last_cleanup: $(dict) canon/translate: Use new $(translate?)

6076 11/08/2012 12:45 PM Aaron Marcuse-Kubitza

input.Makefile: Maps building: %/.map.csv.last_cleanup: Added $(srcDict) as a prerequisite, so that .last_cleanup will be re-run if it changes. Added empty $(srcDict) target in case it doesn't exist.

6075 11/08/2012 12:39 PM Aaron Marcuse-Kubitza

inputs/bien_web/observation/map.csv: Omit *_index because they are placeholder columns created by the MySQL to PostgreSQL translation

6074 11/08/2012 12:37 PM Aaron Marcuse-Kubitza

input.Makefile: Maps building: %/.map.csv.last_cleanup: Fixed bug where can only canon/translate using $(srcDict) if it exists for the datasource

6073 11/08/2012 12:26 PM Aaron Marcuse-Kubitza

inputs/bien_web/observation/: Regenerated from actual bien_web.observation schema on nimoy, which has additional columns

6072 11/08/2012 12:24 PM Aaron Marcuse-Kubitza

input.Makefile: SVN: $(svnFilesGlob): Added top-level map.csv, which can be used to apply a datasource-global data dictionary to all tables

6071 11/08/2012 12:18 PM Aaron Marcuse-Kubitza

input.Makefile: Maps building: %/.map.csv.last_cleanup: Also apply any map.csv at the top level of the datasource directory. This can be used to apply a datasource-global data dictionary to all tables.

6070 11/08/2012 12:01 PM Aaron Marcuse-Kubitza

my2pg: Also remove column comments. Note that these cannot be translated by sed, because PostgreSQL only allows setting column comments in a separate statement, not inline with the column's entry in the CREATE TABLE statement, and sed can only make replacements contiguous with the input line.

6069 11/08/2012 11:28 AM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Removed incorrect duplicate entry for verbatimSubgenus

6068 11/08/2012 10:58 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: _taxon_family_require_std(): Fixed bug where name needed to be lowercased before checking if it ended in -aceae, to support family names that are uppercase. Note that this resulted in the family not being prepended to the TNRS input name for datasources with uppercase family names, so the next DB import will likely produce a number of unscrubbed TNRS input names which now have the uppercase family prepended.

6067 11/08/2012 10:17 AM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/tnrs.make: Fixed bug where need to reference the log file path relative to the make script itself, because otherwise the log file would go in inputs/.TNRS/logs/tnrs.make.log.sql

6066 11/08/2012 10:07 AM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/tnrs.make: Fixed bug where need to use just the basename of $0 as the log file name

6065 11/08/2012 09:51 AM Aaron Marcuse-Kubitza

Added inputs/IUCN/

6064 11/08/2012 09:51 AM Aaron Marcuse-Kubitza

input.Makefile: SVN: add: Added _src/ (when it exists). $(_svnFilesGlob): Added .url, .pdf files in _src/.

6063 11/08/2012 07:47 AM Aaron Marcuse-Kubitza

psql_vegbien: Use bash because it supports substitutions

6062 11/08/2012 07:46 AM Aaron Marcuse-Kubitza

psql_vegbien: Set the search_path to $out_schemas set by vegbien_dest. This will enable running any psql_vegbien script on a schema other than public.

6061 11/08/2012 07:07 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: Changed inner joins on non-datasource taxonlabels to LEFT JOINs, to ensure that an entry is included in the analytical DB even if there was no matched taxonlabel. In theory, this shouldn't be necessary, because every taxonlabel should have a canonical taxonlabel since canon_label_id is auto-populated to the taxonlabel_id if there is no matched_label_id; there should be a taxonverbatim for every datasource and accepted taxonlabel because datasources link to taxonlabel via taxonverbatim and TNRS populates a taxonverbatim for every accepted taxonlabel; and there should be a parsed taxonlabel for every datasource taxonlabel because the mappings populate it.

6060 11/08/2012 06:56 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: Removed join on specimenreplicate, because it isn't used in the analytical DB. Each specimen will still get an entry in analytical_*, because it gets its own location.

6059 11/08/2012 06:45 AM Aaron Marcuse-Kubitza

README.TXT: Data import: Before starting import, added step to run `make inputs/upload` and reinstall newly-uploaded datasources

6058 11/08/2012 03:22 AM Aaron Marcuse-Kubitza

README.TXT: Schema changes: Remember to update the following files with any renamings: Added mappings/verify.*.sql

6057 11/08/2012 02:21 AM Aaron Marcuse-Kubitza

README.TXT: Data import: make_analytical_db: Documented how to view progress in log file

6056 11/08/2012 02:18 AM Aaron Marcuse-Kubitza

make_analytical_db: Run all commands synchronously so the log file output doesn't become jumbled

6055 11/08/2012 02:16 AM Aaron Marcuse-Kubitza

make_analytical_db: Fixed bug where log file needed to be appended to instead of overwritten

6054 11/08/2012 02:15 AM Aaron Marcuse-Kubitza

make_analytical_db: Wrap each individual command in `set -x` to avoid echoing low-level commands such as sleep, wait

6053 11/08/2012 02:02 AM Aaron Marcuse-Kubitza

make_analytical_db: Moved log file to inputs/analytical_db/logs/make_analytical_db.log.sql so it would be synced along with the other import logs

6052 11/08/2012 01:57 AM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/tnrs.make: Output the time at which it's run, so this is included in the log file

6051 11/08/2012 01:53 AM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/tnrs.make: Moved log file to logs/tnrs.make.log.sql so it would automatically be synced along with the other import logs

6050 11/08/2012 01:49 AM Aaron Marcuse-Kubitza

make_analytical_db: Moved log file to inputs/analytical_db/logs/make_analytical_db.log.sql so it would be synced along with the other import logs

6049 11/08/2012 01:40 AM Aaron Marcuse-Kubitza

inputs/Makefile: Import logs: $(rsyncLogs): Always download the TNRS daemon log, rather than requiring tnrs_log=1 to be specified to download it

6048 11/08/2012 01:37 AM Aaron Marcuse-Kubitza

make_analytical_db: Output the time at which it's run, so this is included in the log file

6047 11/08/2012 01:36 AM Aaron Marcuse-Kubitza

make_analytical_db: Store output in schemas/make_analytical_db.log

6046 11/08/2012 01:24 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Removed no longer used make_analytical_db(). Use bin/make_analytical_db instead.

6045 11/08/2012 01:23 AM Aaron Marcuse-Kubitza

make_analytical_db: Use new psql_verbose_vegbien

6044 11/08/2012 01:22 AM Aaron Marcuse-Kubitza

Added psql_verbose_vegbien

6043 11/08/2012 01:18 AM Aaron Marcuse-Kubitza

make_analytical_db: Use psql_script_vegbien, which contains the necessary psq options, instead of setting those options manually

6042 11/08/2012 01:15 AM Aaron Marcuse-Kubitza

make_analytical_db: Run the SQL commands directly with psql instead of using the make_analytical_db() function. This provides incremental results and avoids running all commands in one transaction, thus preventing pgAdmin from freezing when the user attempts to access a table used in analytical DB creation (because the TRUNCATE statement fully locks the table until the entire analytical DB is built).

6041 11/08/2012 12:46 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: make_analytical_db(): Added make_family_higher_plant_group()

6040 11/08/2012 12:17 AM Aaron Marcuse-Kubitza

inputs/import.stats.xls: Updated import times. Fixed input row counts and import times to include derived data, such as TNRS and geoscrub, which adds to the import time and therefore should be considered in the import's speed. (TNRS was already being included in the import time for some, but not all, imports.)

6039 11/06/2012 05:02 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_*: Added higherPlantGroup

6038 11/06/2012 04:06 PM Aaron Marcuse-Kubitza

pg_dump_vegbien: When not in data mode, use --inserts so the INSERT statements generated can be run directly in pgAdmin, they can be directly translated to MySQL, and an empty COPY FROM statement isn't generated for every table

6037 11/06/2012 04:05 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added family_higher_plant_group lookup table, generated with make_family_higher_plant_group() using the contents of higher_plant_group_nodes

6036 11/06/2012 03:40 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added family_higher_plant_group lookup table, generated with make_family_higher_plant_group() using the contents of higher_plant_group_nodes

6035 11/06/2012 03:23 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Always map taxonNameOrEpithet to taxonomicname, now that it's globally unique at all ranks in the datasource that provides it (NCBI)

6034 11/06/2012 03:18 PM Aaron Marcuse-Kubitza

inputs/.NCBI/nodes/create.sql: Make name_txt completely globally unique by removing all duplicates, not just duplicate genera

6033 11/06/2012 03:17 PM Aaron Marcuse-Kubitza

inputs/.NCBI/nodes/create.sql: Make name_txt (mostly) globally unique by removing several other kingdoms/superkingdoms, not just Animalia

6032 11/06/2012 02:56 PM Aaron Marcuse-Kubitza

inputs/.NCBI/nodes/create.sql: Making genus globally unique: Moved comment with kingdom name to line with DELETE, and put "delete cascades to descendants" comment on its own line

6031 11/06/2012 01:57 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added higher_plant_group_nodes lookup table

6030 11/06/2012 01:57 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added higher_plant_group_nodes lookup table

6029 11/06/2012 01:49 PM Aaron Marcuse-Kubitza

schemas/Makefile: DDLs: $(pg_dump): Turn off schema-only mode so that lookup table contents are included as well

6028 11/06/2012 01:47 PM Aaron Marcuse-Kubitza

pg_dump_vegbien: Except in (raw) data mode, filter out pg_catalog.setval() statements (only lookup table contents should be preserved)

6027 11/06/2012 01:39 PM Aaron Marcuse-Kubitza

lib/PostgreSQL-MySQL.csv: Remove SELECT pg_catalog.setval() statements

6026 11/06/2012 01:27 PM Aaron Marcuse-Kubitza

lib/PostgreSQL-MySQL.csv: Remove COPY statements

6025 11/06/2012 01:18 PM Aaron Marcuse-Kubitza

pg_dump_vegbien: $schema flag defaults to on to export only schema

6024 11/06/2012 01:08 PM Aaron Marcuse-Kubitza

pg_dump_vegbien: Fixed bug where schema name var can't be named $schema because that would conflict with the $schema flag

6023 11/06/2012 01:03 PM Aaron Marcuse-Kubitza

root Makefile: VegBIEN DB: DB and bien user: db: Run inputs/.TNRS/install before schemas/install because public.tnrs_input_name depends on TNRS.tnrs

6022 11/06/2012 12:33 PM Aaron Marcuse-Kubitza

pg_dump_vegbien: Only include just the schema if new $schema flag is set. This causes constant lookup tables to automatically be exported for DB schemas, which was not fully supported by the $data flag because it also forced $owners to be enabled.

6021 11/06/2012 12:17 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added higher_plant_group enum

6020 11/06/2012 11:25 AM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Added higherPlantGroup

6019 11/06/2012 10:40 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_*: Added isNewWorld

6018 11/06/2012 10:32 AM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Added isNewWorld

6017 11/06/2012 10:21 AM Aaron Marcuse-Kubitza

inputs/newWorld/: Added geoscrub.schema.~.changes.sql to add a unique constraint on countryNameStd and change isNewWorld's type to boolean

6016 11/06/2012 09:59 AM Aaron Marcuse-Kubitza

Added inputs/newWorld/

6015 11/06/2012 09:55 AM Aaron Marcuse-Kubitza

README.TXT: Datasource setup: Moved Auto-create the map spreadsheets after Install the staging tables, because for DB-only tables, creating the map spreadsheets requires the header.csv generated by the staging tables install

6014 11/06/2012 09:48 AM Aaron Marcuse-Kubitza

input.Makefile: SVN: add: Also set _MySQL/'s svn:ignore

6013 11/06/2012 09:30 AM Aaron Marcuse-Kubitza

inputs/SALVIAS/_MySQL/salvias_plots.*.sql.make: Use new my2pg_export

6012 11/06/2012 09:27 AM Aaron Marcuse-Kubitza

inputs/.geoscrub/_MySQL/geoscrub.*.sql.make: Use new my2pg_export

6011 11/06/2012 09:25 AM Aaron Marcuse-Kubitza

Added my2pg_export

6010 11/05/2012 11:16 PM Aaron Marcuse-Kubitza

Regenerated vegbien.ERD exports

6009 11/05/2012 11:14 PM Aaron Marcuse-Kubitza

schemas/vegbien.ERD.mwb: Added analytical_stem, analytical_aggregate to ERD

6008 11/05/2012 10:49 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_*: Added georeferenceValid, distanceToCountry_km, distanceToStateProvince_km

6007 11/05/2012 10:34 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added _m_to_km()

6006 11/05/2012 10:06 PM Aaron Marcuse-Kubitza

inputs/.geoscrub/geoscrub_cleaned_unique/map.csv: Removed geoscrubID->locationID mapping because it allowed multiple occurrences of the same placename/coordinates combination, which was causing problems when datasources try to link up to the geoscrub places (and end up matching multiple output rows for each input row)

6005 11/05/2012 09:54 PM Aaron Marcuse-Kubitza

sql_io.py: put_table(): Removed assertion that into's row count be at least full_in_table's row count, because now that DISTINCT ON is used to satisfy the into table pkey, this is no longer necessarily true

6004 11/05/2012 09:15 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: method: method_unique: Added reference_id to make method unique within the datasource instead of globally unique within VegBIEN

6003 11/05/2012 09:12 PM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Added samplingProtocolID

6002 11/05/2012 08:48 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: subplot locationevent: Only populate parent locationevent's location unique IDs if a subplot #/subplotID is actually specified. (The lack of a location unique ID will cause the parent locationevent's location to be removed, as well as the parent locationevent itself if there is no parent locationevent unique ID.) This fixes a bug where top-level plots in datasources that provide a nullable subplot #/subplotID were incorrectly getting connected to parent locationevents.

6001 11/05/2012 08:34 PM Aaron Marcuse-Kubitza

mappings/verify.plots.sql: Added # locations, # location events, which also include subplots

6000 11/05/2012 08:17 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/verify/plots.ref.sql: Standardized line wrapping to put ; on its own line in multi-line queries and at the end of the line in one-line queries

5999 11/05/2012 08:13 PM Aaron Marcuse-Kubitza

mappings/verify.plots.sql: Added "top-level" to # locations, # location events names because these queries do not include all locations

5998 11/05/2012 07:52 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/verify/plots.ref.sql: # locations: Fixed count to include all plotMetadata entries instead of just unique coordinates, because each plotMetadata entry now gets its own location

5997 11/05/2012 07:34 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: matched place: When any of the accepted* names is specified, set matched_place_id=0 (self-reference) to indicate that the matched place is an accepted (scrubbed) place

5996 11/05/2012 05:30 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: Use the canonical (scrubbed) place instead of the datasource's place where available. Note that canon_place_id is always populated (with a self-reference if needed), to enable using a just a LEFT JOIN for this.

5995 11/05/2012 05:14 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: Use datasource_* prefix instead of reference_* prefix that tables had gotten when datasource_id was renamed to reference_id

5994 11/05/2012 05:04 PM Aaron Marcuse-Kubitza

inputs/SALVIAS/verify/plots.ref: Regenerated on vegbiendev using the PostgreSQL 9.1 pg_catalog.default collation

5993 11/05/2012 04:49 PM Aaron Marcuse-Kubitza

sql_io.py: put_table(): Setting pkeys of missing rows: Fixed bug in column-based import where when input rows match multiple output rows in one of this iteration's input tables, the into table's pkey constraint is violated because full_in_table contains multiple entries for an input pkey

5992 11/05/2012 04:42 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: place: Added index on matched_place_id to facilitate looking up places by matched_place_id in place_set_canon_place_id()

5991 11/05/2012 04:26 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Added geoscrub_input derived table with associated view. Build geoscrub_input as part of make_analytical_db().

5990 11/05/2012 03:56 PM Aaron Marcuse-Kubitza

sql.py: Added table_has_pkey()

5989 11/05/2012 03:13 PM Aaron Marcuse-Kubitza

sql.py: table_pkey_col(): For PostgreSQL DBs, use pg_catalog via index_cols() and table_pkey_index(), in order to use the search_path to look up the table. This fixes a bug where the pkey would be selected from information_schema.table_constraints in random order, and this order sometimes returned the corresponding table in the public schema but sometimes in other schemas, such as VegBank. This became a problem now that VegBIEN has a place table, which conflicts with VegBank's place table. (Most other VegBank tables that are mapped to have been renamed in VegBIEN.)

5988 11/05/2012 02:41 PM Aaron Marcuse-Kubitza

sql.py: add_pkey_or_index(): Use new add_pkey_index()

5987 11/05/2012 02:41 PM Aaron Marcuse-Kubitza

sql.py: Added add_pkey_index()