Activity
From 10/10/2012 to 11/08/2012
11/08/2012
- 06:38 PM Revision 6098: root Makefile: VegBIEN DB: Schemas: Run all schema installs and uninstalls using no_search_path=1, so that the schemas in the automatic search_path are not required for the command to run
- 06:37 PM Revision 6097: psql_vegbien: Added $no_search_path option to turn off the automatic SET search_path directive
- 06:11 PM Revision 6096: schemas/vegbien.sql: taxonverbatim: Added growthform for growthform based on the taxon name rather than provided with the input data's taxonoccurrence
- 06:00 PM Revision 6095: schemas/vegbien.ERD.mwb: Fixed lines
- 05:47 PM Revision 6094: inputs/SALVIAS/plotMetadata/: LEFT JOINed with lookup_MethodCode to create plotMetadata_
- 04:52 PM Revision 6093: schemas/vegbien.sql: threatened_taxonlabel_view: Fixed bug where needed DISTINCT on resulting taxonlabel_id because some descendants apparently appear in multiple threatened taxonlabels' subtrees
- 04:42 PM Revision 6092: schemas/vegbien.sql: analytical_*: Added threatened, using new threatened_taxonlabel lookup table
- 04:12 PM Revision 6091: schemas/vegbien.sql: reference_by_shortname(): Fixed bug where need to use $-syntax to reference params in sql-language functions
- 04:07 PM Revision 6090: schemas/vegbien.sql: threatened_taxonlabel_view: Use new reference_by_shortname()
- 03:45 PM Revision 6089: root Makefile: VegBIEN DB: Schemas: public: schemas/public/uninstall: Fixed bug where need to run psql_vegbien without public in the search_path because it may have already been deleted
- 03:44 PM Revision 6088: root Makefile: VegBIEN DB: Schemas: public: schemas/public/install: Fixed bug where need to run psql_vegbien without public in the search_path because it doesn't exist, by setting public to the empty string (deleting it)
- 03:42 PM Revision 6087: vegbien_dest: $schemas: Don't include the , before $public if it has been set to the empty string (deleted)
- 03:27 PM Revision 6086: 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.
- 03:00 PM Revision 6085: schemas/vegbien.sql: Added threatened_taxonlabel derived table with generating view threatened_taxonlabel_view
- 02:48 PM Revision 6084: Updated inputs/UNCC/Specimen/test.xml.ref inserted row count
- 01:38 PM Revision 6083: mappings/VegCore.csv: Added threatened
- 01:21 PM Revision 6082: inputs/VegBank/vegbank.~.clean_up.sql: Remove private columns (plot.reallatitude, reallongitude) that should not be publicly visible
- 01:13 PM Revision 6081: inputs/CVS/Organism/map.csv: Removed now-dropped realLatitude, realLongitude
- 01:12 PM Revision 6080: inputs/CVS/Organism/map.csv: Removed now-dropped realLatitude, realLongitude
- 01:12 PM Revision 6079: Added inputs/CVS/Organism/postprocess.sql to drop private realLatitude, realLongitude columns
- 01:10 PM Revision 6078: 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
- 12:47 PM Revision 6077: input.Makefile: Maps building: %/.map.csv.last_cleanup: $(dict) canon/translate: Use new $(translate?)
- 12:45 PM Revision 6076: 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.
- 12:39 PM Revision 6075: inputs/bien_web/observation/map.csv: Omit *_index because they are placeholder columns created by the MySQL to PostgreSQL translation
- 12:37 PM Revision 6074: input.Makefile: Maps building: %/.map.csv.last_cleanup: Fixed bug where can only canon/translate using $(srcDict) if it exists for the datasource
- 12:26 PM Revision 6073: inputs/bien_web/observation/: Regenerated from actual bien_web.observation schema on nimoy, which has additional columns
- 12:24 PM Revision 6072: input.Makefile: SVN: $(svnFilesGlob): Added top-level map.csv, which can be used to apply a datasource-global data dictionary to all tables
- 12:18 PM Revision 6071: 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.
- 12:01 PM Revision 6070: 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.
- 11:28 AM Revision 6069: mappings/VegCore.csv: Removed incorrect duplicate entry for verbatimSubgenus
- 10:58 AM Revision 6068: 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.
- 10:17 AM Revision 6067: 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
- 10:07 AM Revision 6066: inputs/.TNRS/tnrs/tnrs.make: Fixed bug where need to use just the basename of $0 as the log file name
- 09:51 AM Revision 6065: Added inputs/IUCN/
- 09:51 AM Revision 6064: input.Makefile: SVN: add: Added _src/ (when it exists). $(_svnFilesGlob): Added .url, .pdf files in _src/.
- 07:47 AM Revision 6063: psql_vegbien: Use bash because it supports substitutions
- 07:46 AM Revision 6062: 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.
- 07:07 AM Revision 6061: 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.
- 06:56 AM Revision 6060: 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.
- 06:45 AM Revision 6059: README.TXT: Data import: Before starting import, added step to run `make inputs/upload` and reinstall newly-uploaded datasources
- 03:56 AM Task #346: add georeferencing support to schema
- Georeferencing information can be stored in the geovalidation place entry, which the original place is linked to via ...
- 03:42 AM Task #292: VegBank metadata query mechanism
- Added possible strategy
- 03:32 AM Task #343 (Resolved): integrate TNRS into VegBIEN
- 03:32 AM Task #308 (Resolved): do a direct transfer of some public data from VegBank
- Core fields in VegBank have been mapped. A recent full export of the live VegBank DB is used as the input.
- 03:31 AM Task #335 (Rejected): Look into using Sybase Powerbuilder or IBM Enterprise Vision to map data
- We are using map spreadsheets and auto-mapping instead, which work well so far and would not be easy to translate to ...
- 03:30 AM Task #312: Finish importing SALVIAS data
- Still need to map methods, probably using LEFT JOIN
- 03:27 AM Task #365 (Rejected): retrieve taxonomic hierarchy in analytical layer by using dynamic queries to external sources
- We're using a fixed version of the NCBI tree of life instead
- 03:26 AM Task #424: Finish translating XML functions to SQL functions for column-based import
- Most translated; still left:
* _map
* _range*
* _avg
* _compass
* a few others - 03:24 AM Task #440: aggregating validations of imports
- Queries work for current schema
- 03:22 AM Task #454 (Resolved): update summarizing queries for current schema
- @make inputs/SALVIAS/verify/@ and @make inputs/NY/verify/@ work again
- 03:22 AM Revision 6058: README.TXT: Schema changes: Remember to update the following files with any renamings: Added mappings/verify.*.sql
- 03:16 AM Task #476 (Rejected): develop map spreadsheet -> header override file translation utility
- Shouldn't do this because it would prevent map spreadsheets from having multiple output locations for the same input ...
- 03:11 AM Task #495 (Resolved): add separate datasource table rather than using party for this
- Now using @reference@ for this
- 03:07 AM Task #521 (Resolved): make place* tables use a structure similar to taxonconcept
- 02:21 AM Revision 6057: README.TXT: Data import: make_analytical_db: Documented how to view progress in log file
- 02:18 AM Revision 6056: make_analytical_db: Run all commands synchronously so the log file output doesn't become jumbled
- 02:16 AM Revision 6055: make_analytical_db: Fixed bug where log file needed to be appended to instead of overwritten
- 02:15 AM Revision 6054: make_analytical_db: Wrap each individual command in `set -x` to avoid echoing low-level commands such as sleep, wait
- 02:02 AM Revision 6053: 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
- 01:57 AM Revision 6052: inputs/.TNRS/tnrs/tnrs.make: Output the time at which it's run, so this is included in the log file
- 01:53 AM Revision 6051: 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
- 01:49 AM Revision 6050: 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
- 01:40 AM Revision 6049: inputs/Makefile: Import logs: $(rsyncLogs): Always download the TNRS daemon log, rather than requiring tnrs_log=1 to be specified to download it
- 01:37 AM Revision 6048: make_analytical_db: Output the time at which it's run, so this is included in the log file
- 01:36 AM Revision 6047: make_analytical_db: Store output in schemas/make_analytical_db.log
- 01:24 AM Revision 6046: schemas/vegbien.sql: Removed no longer used make_analytical_db(). Use bin/make_analytical_db instead.
- 01:23 AM Revision 6045: make_analytical_db: Use new psql_verbose_vegbien
- 01:22 AM Revision 6044: Added psql_verbose_vegbien
- 01:18 AM Revision 6043: make_analytical_db: Use psql_script_vegbien, which contains the necessary psq options, instead of setting those options manually
- 01:15 AM Revision 6042: 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).
- 12:46 AM Revision 6041: schemas/vegbien.sql: make_analytical_db(): Added make_family_higher_plant_group()
- 12:17 AM Revision 6040: 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.)
11/06/2012
- 05:02 PM Revision 6039: schemas/vegbien.sql: analytical_*: Added higherPlantGroup
- 04:06 PM Revision 6038: 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
- 04:05 PM Revision 6037: 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
- 03:40 PM Revision 6036: 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
- 03:23 PM Revision 6035: 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)
- 03:18 PM Revision 6034: inputs/.NCBI/nodes/create.sql: Make name_txt completely globally unique by removing all duplicates, not just duplicate genera
- 03:17 PM Revision 6033: inputs/.NCBI/nodes/create.sql: Make name_txt (mostly) globally unique by removing several other kingdoms/superkingdoms, not just Animalia
- 02:56 PM Revision 6032: 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
- 01:57 PM Revision 6031: schemas/vegbien.sql: Added higher_plant_group_nodes lookup table
- 01:57 PM Revision 6030: schemas/vegbien.sql: Added higher_plant_group_nodes lookup table
- 01:49 PM Revision 6029: schemas/Makefile: DDLs: $(pg_dump): Turn off schema-only mode so that lookup table contents are included as well
- 01:47 PM Revision 6028: pg_dump_vegbien: Except in (raw) data mode, filter out pg_catalog.setval() statements (only lookup table contents should be preserved)
- 01:39 PM Revision 6027: lib/PostgreSQL-MySQL.csv: Remove SELECT pg_catalog.setval() statements
- 01:27 PM Revision 6026: lib/PostgreSQL-MySQL.csv: Remove COPY statements
- 01:18 PM Revision 6025: pg_dump_vegbien: $schema flag defaults to on to export only schema
- 01:08 PM Revision 6024: pg_dump_vegbien: Fixed bug where schema name var can't be named $schema because that would conflict with the $schema flag
- 01:03 PM Revision 6023: 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
- 12:33 PM Revision 6022: 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.
- 12:17 PM Revision 6021: schemas/vegbien.sql: Added higher_plant_group enum
- 11:25 AM Revision 6020: mappings/VegCore.csv: Added higherPlantGroup
- 10:40 AM Revision 6019: schemas/vegbien.sql: analytical_*: Added isNewWorld
- 10:32 AM Revision 6018: mappings/VegCore.csv: Added isNewWorld
- 10:21 AM Revision 6017: inputs/newWorld/: Added geoscrub.schema.~.changes.sql to add a unique constraint on countryNameStd and change isNewWorld's type to boolean
- 09:59 AM Revision 6016: Added inputs/newWorld/
- 09:55 AM Revision 6015: 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
- 09:48 AM Revision 6014: input.Makefile: SVN: add: Also set _MySQL/'s svn:ignore
- 09:30 AM Revision 6013: inputs/SALVIAS/_MySQL/salvias_plots.*.sql.make: Use new my2pg_export
- 09:27 AM Revision 6012: inputs/.geoscrub/_MySQL/geoscrub.*.sql.make: Use new my2pg_export
- 09:25 AM Revision 6011: Added my2pg_export
11/05/2012
- 11:16 PM Revision 6010: Regenerated vegbien.ERD exports
- 11:14 PM Revision 6009: schemas/vegbien.ERD.mwb: Added analytical_stem, analytical_aggregate to ERD
- 10:49 PM Revision 6008: schemas/vegbien.sql: analytical_*: Added georeferenceValid, distanceToCountry_km, distanceToStateProvince_km
- 10:34 PM Revision 6007: schemas/vegbien.sql: Added _m_to_km()
- 10:06 PM Revision 6006: 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)
- 09:54 PM Revision 6005: 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
- 09:15 PM Revision 6004: schemas/vegbien.sql: method: method_unique: Added reference_id to make method unique within the datasource instead of globally unique within VegBIEN
- 09:12 PM Revision 6003: mappings/VegCore.csv: Added samplingProtocolID
- 08:48 PM Revision 6002: 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.
- 08:34 PM Revision 6001: mappings/verify.plots.sql: Added # locations, # location events, which also include subplots
- 08:17 PM Revision 6000: 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
- 08:13 PM Revision 5999: mappings/verify.plots.sql: Added "top-level" to # locations, # location events names because these queries do not include all locations
- 07:52 PM Revision 5998: 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
- 07:34 PM Revision 5997: 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
- 05:30 PM Revision 5996: 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.
- 05:14 PM Revision 5995: 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
- 05:04 PM Revision 5994: inputs/SALVIAS/verify/plots.ref: Regenerated on vegbiendev using the PostgreSQL 9.1 pg_catalog.default collation
- 04:49 PM Revision 5993: 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
- 04:42 PM Revision 5992: 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()
- 04:26 PM Revision 5991: schemas/vegbien.sql: Added geoscrub_input derived table with associated view. Build geoscrub_input as part of make_analytical_db().
- 03:56 PM Revision 5990: sql.py: Added table_has_pkey()
- 03:13 PM Revision 5989: 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.)
- 02:41 PM Revision 5988: sql.py: add_pkey_or_index(): Use new add_pkey_index()
- 02:41 PM Revision 5987: sql.py: Added add_pkey_index()
- 02:29 PM Revision 5986: inputs/import.stats.xls: Updated import times
- 02:15 PM Revision 5985: import_times: Use $'' quoting to expand tab, in order to also work on Mac OS X
11/02/2012
- 06:14 PM Revision 5984: schemas/vegbien.sql: place: Added place_set_canon_place_id_on_*() triggers, analogous to taxonlabel.taxonlabel_2_set_canon_label_id_on_*()
- 06:12 PM Revision 5983: schemas/vegbien.sql: place: Added canon_place_id
- 06:04 PM Revision 5982: mappings/verify.plots.sql, inputs/SALVIAS/verify/plots.ref.sql: Renamed project column to projectname to avoid confusion with the project table
- 06:03 PM Revision 5981: input.Makefile: Verification of import: Fixed bug where needed to make %.ref .PRECIOUS instead of verify/%.ref
- 05:57 PM Revision 5980: inputs/SALVIAS/verify/plots.ref.sql: Use project_name instead of project_id everywhere, not just as the ID to list for each project, to match the corresponding VegBIEN queries
- 05:55 PM Revision 5979: input.Makefile: Verification of import: Make verify/%.ref .PRECIOUS because there must always be a .ref for the make rules to work
- 05:34 PM Revision 5978: inputs/SALVIAS/verify/plots.ref.sql: Use project_name instead of project_id as the ID to list for each project, since the SALVIAS projects table is now mapped to the DB and the project_name is used as project.projectname
- 05:18 PM Revision 5977: mappings/VegCore-VegBIEN.csv: subplots: Also complete the locationevent/location diamond (subplot event -> {subplot location, parent plot event} -> parent plot location) when an eventDate or range is specified, as this is also an identifying field for locationevent. This fixes a bug where subplots data without explicit plot events (such as SALVIAS and TEAM) was not being connected to the appropriate parent plot *event* as well as parent plot location. This should fix the SALVIAS verification # location events, which should include only parent plots' locationevents to correspond with # locations, which only includes parent plots' locations, and uses locationevent.parent_id being NULL to determine what is a parent plot event.
- 04:45 PM Revision 5976: input.Makefile: Verification of import: $(verify): Use $(inDatasrc) so that the full standard search_path, including any custom public schema, is made available to the VegBIEN-side verification script
- 04:33 PM Revision 5975: mappings/verify.plots.sql: # locations: Fixed bug where need to use location instead of locationevent
- 04:30 PM Revision 5974: mappings/verify.specimens.sql: Updated for current schema
- 04:26 PM Revision 5973: input.Makefile: Verification of import: verify/%.out: Made the target .PRECIOUS so that partial output will be saved in case of error to help debugging
- 04:13 PM Revision 5972: mappings/verify.plots.sql: Updated for current schema
- 04:01 PM Revision 5971: Updated validation/BIEN2_Analytical_DB_overview.docx with Brad's revision
- 03:58 PM Revision 5970: schemas/vegbien.sql: taxonlabel_set_canon_label_id(): Fixed bug where always need to set canon_label_id on insert (because it must be a self-reference rather than NULL if there is no matched_label_id), but wasn't being set when no matched_label_id because the IS DISTINCT FROM check returned false
- 03:42 PM Revision 5969: mappings/VegCore-VegBIEN.csv: decimalLatitude/Longitude->geoscrub input coordinates: Also set to NULL if 0 here, not just for the coordinates linked to the datasource's place instance
- 03:37 PM Revision 5968: sql_io.py: put_table(): Switched back to using run_query_into()'s add_pkey_ option now that it uses sql.add_pkey_or_index() instead of sql.add_pkey()
- 03:35 PM Revision 5967: sql.py: run_query_into(): add_pkey_: Use add_pkey_or_index() instead of add_pkey(). This should prevent errors for input rows which match multiple output rows in VegBIEN.
- 03:24 PM Revision 5966: README.TXT: Data import: After import, removed steps to reinstall tnrs_accepted, tnrs_other because this would overwrite the versions of these staging tables that were used to build the current version of the database. (The backup should store a snapshot of the database's input data as it was used to build the database.) Note that these tables will still be reinstalled when the next import starts.
- 02:54 PM Revision 5965: Added validation/BIEN2_Analytical_DB_overview.docx
- 02:54 PM Revision 5964: inputs/import.stats.xls: Updated import times
- 12:00 PM Revision 5963: inputs/.TNRS/tnrs_*/create.sql: Fixed bug where need to COALESCE() the WHERE condition with false to ensure that a boolean value, not NULL, is negated by NOT. Otherwise, tnrs_other's query would exclude rows for which the condition returned NULL rather than false.
- 11:43 AM Revision 5962: schemas/vegbien.sql: make_analytical_db(): Truncate tables before (re-)populating them in case make_analytical_db() has already been run
- 11:40 AM Revision 5961: schemas/vegbien.sql: analytical_stem_view: Updated to use reference instead of party to store the datasource name
- 11:28 AM Revision 5960: schemas/vegbien.sql: Renamed make_analytical_stem() back to make_analytical_db()
11/01/2012
- 10:52 AM Revision 5959: import_all: After starting geoscrub import in the background, wait for make commands to scroll by before starting NCBI import
- 10:39 AM Revision 5958: mappings/VegCore-VegBIEN.csv: matched place: Also map verbatim place's geoscrub-related fields to the matched place, to link up with geoscrub's corresponding input place
- 10:22 AM Revision 5957: import_all: Removed explicit by_col=1 from datasources that don't require it for proper import. (It will still be set if the user provides it on the command line.)
- 10:18 AM Revision 5956: schemas/functions.sql: Removed duplicate previous version of _and() with fewer parameters
- 10:14 AM Revision 5955: Regenerated vegbien.ERD exports
- 10:11 AM Revision 5954: schemas/vegbien.sql: method: Made reference_id NOT NULL so the method table would automatically be datasource-scoped
- 10:09 AM Revision 5953: mappings/VegCore-VegBIEN.csv: Renamed creator_ids to reference_id since they are now fkeys to reference
- 10:04 AM Revision 5952: schemas/vegbien.sql: Made creator_ids an fkey to reference instead of party, so that datasources are stored separately from people and to allow adding reference-type metadata (URL, copyright, etc.) for each datasource
- 09:51 AM Revision 5951: schemas/vegbien.sql: reference: Added unique index
- 09:47 AM Revision 5950: mappings/VegCore-VegBIEN.csv: Remapped accordingTo to taxonconcept.concept_reference_id
- 09:46 AM Revision 5949: mappings/VegCore-VegBIEN.csv: Don't populate taxonlabel.creator_id using identifiedBy, because that was meant for creating a taxonconcept when the accordingTo was not specified, but taxonconcepts are now modeled differently using a taxonconcept subclass of taxonlabel with a concept_reference_id
- 09:36 AM Revision 5948: schemas/vegbien.sql: taxonverbatim: Renamed binomial to taxonname because this field is actually the taxonomic name without the author, not just the genus+specific epithet binomial
- 09:29 AM Revision 5947: mappings/VegCore.csv: Renamed *Binomial to *TaxonName because this field can store more ranks than just the genus+specificEpithet binomial (that goes in speciesBinomial)
- 09:22 AM Revision 5946: mappings/VegCore.csv: Renamed taxonName to taxonNameOrEpithet for clarity
- 09:16 AM Revision 5945: schemas/vegbien.sql: analytical_aggregate_view: Added growthForm, cultivated, cultivatedBasis from analytical_stem. Note that this will create multiple entries for a taxon name when some taxonoccurrences are marked as cultivated and others aren't, or different taxonoccurrences have different growthform entries.
- 09:01 AM Revision 5944: import_all: Added geoscrub import, which can happen concurrently with NCBI/TNRS but must come before the main datasources for the matched places to link up properly
- 08:59 AM Revision 5943: import_all: Documented that TNRS import must come after NCBI for cross links to be made
- 08:53 AM Revision 5942: input.Makefile: Staging tables installation: `%.sql: _MySQL/%.sql`, etc.: Only run if target does not exist, to avoid regenerating the target when a .make script which generates the target's prerequisite is checked out from svn (causing its mod time to be newer than the target)
- 08:24 AM Revision 5941: Added inputs/.geoscrub/
- 08:21 AM Revision 5940: input.Makefile: SVN: $(*svnFilesGlob): Added */, _MySQL/ subdirs
- 08:20 AM Revision 5939: lib/common.Makefile: SVN: $(add*): Fixed bug where need to use --depth=empty to ensure directory contents are not added unless explicitly listed
- 08:09 AM Revision 5938: mappings/VegCore-VegBIEN.csv: Mapped georeferenceValid, latLongInCountry, latLongInStateProvince
- 08:05 AM Revision 5937: schemas/functions.sql: Added _and()
- 07:40 AM Revision 5936: mappings/VegCore-VegBIEN.csv: Mapped distanceToCountry_km, distanceToStateProvince_km
- 07:39 AM Revision 5935: schemas/vegbien.sql: Added _km_to_m()
- 07:36 AM Revision 5934: schemas/vegbien.sql: Added _km_to_m()
- 07:31 AM Revision 5933: schemas/vegbien.sql: place: Added georeference_valid, distance_to_country_m, distance_to_state_m
- 07:18 AM Revision 5932: mappings/VegCore-VegBIEN.csv: matched taxonlabel's ancestors: Only create the cross links to NCBI if the name is accepted (taxonIsCanonical)
- 06:55 AM Revision 5931: mappings/VegCore-VegBIEN.csv: accepted* taxonomic terms: If is canonical name, don't populate a separate accepted taxonlabel because the taxonlabel itself is accepted. If is not canonical name, populate matched_label_id directly when the row is created instead of waiting until after all rows are created and using _taxonlabel_set_matched_label_id(). This is possible now that accepted taxonlabels occur only in TNRS's tnrs_accepted table, which is specially marked as taxonIsCanonical. Avoiding _taxonlabel_set_matched_label_id() should fix the slowdown that occurs when it's used on large tables.
- 06:48 AM Revision 5930: mappings/VegCore-VegBIEN.csv: taxonIsCanonical: Moved then=0 into non-identifying _if statement attributes
- 06:41 AM Revision 5929: mappings/VegCore-VegBIEN.csv: Mapped taxonIsCanonical
- 06:41 AM Revision 5928: bin/map: map_rows(): map_table(): Fixed bug where metadata values were being removed prematurely, by passing them through
- 06:40 AM Revision 5927: bin/map: map_rows(): Fixed bug where metadata values were being passed to functions that expected columns, by placing them directly in the XML import tree and then removing them from the mappings
- 05:51 AM Revision 5926: input.Makefile: Maps validation: %/new_terms.csv: Filter out metadata values, which are not new terms even though they are in the same map column as the input columns
- 05:46 AM Revision 5925: inputs/.TNRS/tnrs_accepted/map.csv: Set taxonIsCanonical to true, using new metadata value syntax
- 05:40 AM Revision 5924: mappings/VegCore.csv: Added taxonIsCanonical
- 05:37 AM Revision 5923: input.Makefile: SVN: $(svnFiles): Added _MySQL files that would otherwise be excluded with $(filter-out _% ...)
- 05:34 AM Revision 5922: inputs/*/: Placed all logs/ subdirs and import_order.txt under version control, using `make inputs/.../add`
- 05:31 AM Revision 5921: input.Makefile: SVN: add: Factored list of files to add out into $(svnFiles) var
- 05:30 AM Revision 5920: Added inputs/.TNRS/tnrs/header.csv
- 05:28 AM Revision 5919: input.Makefile: SVN: $(svnFilesGlob): Added *.make
- 05:21 AM Revision 5918: input.Makefile: SVN: add: Fixed bug where _-prefixed dirs (such as _MySQL) were incorrectly being included in the list of files to put under version control
- 05:15 AM Revision 5917: Calls to `make inputs/.TNRS/cleanup`: Do `make inputs/.TNRS/tnrs_accepted/reinstall; make inputs/.TNRS/tnrs_other/reinstall` instead to use new split TNRS tables
- 05:04 AM Revision 5916: inputs/.TNRS/schema.sql: Removed no longer needed tnrs_accepted_names index, now that the accepted names have been split into a separate table
- 05:00 AM Revision 5915: inputs/.TNRS/: Split tnrs table into tnrs_accepted and tnrs_other, with tnrs_accepted imported first. This will eventually allow TNRS data to be imported without needing to use _taxonlabel_set_matched_label_id(), which is extremely slow due to an unknown bug in PostgreSQL's handling of UPDATEs on large tables (possibly limited to UPDATEs inside functions).
- 05:00 AM Revision 5914: input.Makefile: SVN: add: Fixed bug where logs/*.log.sql was incorrectly being included in the list of files to put under version control
- 04:53 AM Revision 5913: lib/common.Makefile: Filesystem: $(wildcard/): Fixed bug where {} exprs weren't handled correctly when some branches contained *, by using `shopt -s nullglob` and bash directly instead of trying to emulate it with grep
- 04:44 AM Revision 5912: input.Makefile: Staging tables installation: `%/install: %/create.sql`: Also provide the schema to create.sql in :schema
- 04:16 AM Revision 5911: bin/map: Added support for including literal metadata values in the map spreadsheet, by prefixing them with ':'
- 03:56 AM Revision 5910: mappings/VegCore.csv: Added distanceToCountry_km, distanceToStateProvince_km
- 03:45 AM Revision 5909: mappings/VegCore.csv: Added distanceToCountry_m, distanceToStateProvince_m
- 03:36 AM Revision 5908: mappings/VegCore-VegBIEN.csv: Mapped acceptedCountry, acceptedStateProvince, acceptedDecimalLatitude/Longitude. Mapped decimalLatitude/Longitude to matched place's coordinates when acceptedDecimalLatitude/Longitude not provided (as is the case for the geoscrub table).
- 03:22 AM Revision 5907: input.Makefile: SVN: $(svnFilesGlob): Added *schema*.sql
- 02:57 AM Revision 5906: mappings/VegCore.csv: Replaced georeferenceInvalid with latLongDomainValid, latLongDomainInvalid because this field is actually just whether the coordinates are in the range of valid decimal values, not whether they are within the named place reference. Re-sourced georeferenceValid to bien_web.observation#isGeovalid rather than isValidLatLong. VegCore-VegBIEN.csv: Replaced now-removed georeferenceInvalid with latLongInCountry for locationID redirection checks.
- 01:54 AM Revision 5905: mappings/VegCore-VegBIEN.csv: Map locationID to place.placecode instead when geovalidation columns are provided
- 01:06 AM Revision 5904: mappings/VegCore-VegBIEN.csv: accepted* taxonlabel: Removed ancestor hierarchy because this is populated, in much greater detail, when the accepted name is imported as an input name and the TNRS-parsed components are available
- 12:55 AM Revision 5903: sql.py: distinct_table(): Use DISTINCT ON instead of a unique index and insert_select()'s ignore mode to remove duplicate rows. This uses whichever sorting method PostgreSQL deems to be fastest instead of requiring the use of a B-tree index. Since most of the slower operations in TNRS's import are distinct_table() calls, this should speed up the TNRS import, which is a bottleneck for the DB import as a whole because the TNRS import must complete before other datasources can be imported.
- 12:36 AM Revision 5902: sql.py: distinct_table(): Changed comment about distinct_on column index to include just the input table, so that the function does not guarantee a unique index on the output table's distinct_on columns
- 12:15 AM Revision 5901: mappings/VegCore.csv: Added acceptedCountry, acceptedStateProvince, acceptedDecimalLatitude/Longitude
10/31/2012
- 11:57 PM Revision 5900: mappings/VegCore.csv: Renamed latLongValid, latLongInvalid to georeferenceValid, georeferenceInvalid to correspond to DwC term georeferenceVerificationStatus
- 11:45 PM Revision 5899: mappings/VegCore.csv: Added latLongValid, latLongInvalid, latLongInCountry, latLongInStateProvince
- 11:14 PM Revision 5898: input.Makefile: Staging tables installation: Treat any .sql file whose name contains (not just ends with) "schema" as a schema file and sort it before other .sql files
- 10:17 PM Revision 5897: schemas/vegbien.sql: Functions containing UPDATE statements: Use quote_nullable() instead of quote_literal() to properly encode NULL values
- 10:10 PM Revision 5896: schemas/vegbien.sql: Functions containing UPDATE statements: Use PL/pgSQL's EXECUTE statement to avoid caching query plans. This is necessary because as the table grows over time, the optimal query plan may change.
- 10:05 PM Revision 5895: sql_io.py: put_table(): ensure_cond(): When deleting rows rows that do not satisfy the condition, handle sql.DoesNotExistExceptions caused by columns in the condition that were not replaced with NULL. These occur when out_table is a function, and the columns of the table the condition relates to therefore can't be found using out_table.
- 09:59 PM Revision 5894: sql_io.py: put_table(): Calling function: Do not cache the function call, because it may be retried after error handling
- 09:58 PM Revision 5893: sql_gen.py: NotCond: Treat a condition that evaluates to NULL as false instead, so that the boolean effect of the condition is completely inverted
- 09:42 PM Revision 5892: sql_gen.py: null_as_str: Use new null instead of hardcoding 'NULL'
- 09:41 PM Revision 5891: sql_gen.py: Added null
- 09:40 PM Revision 5890: sql.py: run_query(): Give failed EXPLAIN approximately the log_level of its query, so that queries which produce an error in the EXPLAIN before the query itself is even run will still be logged
- 08:45 PM Revision 5889: sql_io.py: put_table(): sql.DatabaseErrors: Factored exception-handling code out into handle_unknown_exc(), for use by other exception handlers
- 08:39 PM Revision 5888: sql_io.py: put_table(): ensure_cond(): is_function: Fixed bug where can't replace out_table_cols with NULL because out_table is a function, not a table
10/30/2012
- 04:59 PM Revision 5887: my2pg*: Turn off escape_string_warning because \-escaped strings are standard in MySQL
- 04:58 PM Revision 5886: my2pg.data: Turn off standard_conforming_strings like in my2pg
- 04:42 PM Revision 5885: my2pg: Also remove any CHARACTER SET modifier on a column definition
- 04:26 PM Revision 5884: schemas/vegbien.sql: analytical_aggregate_view: Make size classes cumulative ranges (stems above a certain DBH) rather than bins, per Brad's request
- 04:26 PM Revision 5883: schemas/vegbien.sql: analytical_aggregate_view: Make size classes cumulative ranges (stems above a certain DBH) rather than bins, per Brad's request
- 04:18 PM Revision 5882: input.Makefile: SVN: add: Add header override files with any extension, not just .csv
- 04:15 PM Revision 5881: README.TXT: Datasource setup: Replaced manual `svn add` commands with one `make inputs/<datasrc>/add` before committing to add newly-created files
- 04:00 PM Revision 5880: input.Makefile: SVN: add: Also add any *.sql, *when it's in a subdir*. This applies to create.sql, cleanup.sql, etc.
- 03:58 PM Revision 5879: lib/common.Makefile: SVN: Added $(add*)
- 03:55 PM Revision 5878: input.Makefile: SVN: add: Also add any newly-created files which should be under version control
- 03:35 PM Revision 5877: input.Makefile: Fixed bug where _MySQL/%.sql files weren't being built from associated .make files by adding special `%.sql: %.sql.make` rule to override `%.sql: _MySQL/%.sql`
- 03:33 PM Revision 5876: input.Makefile: `%: %.make`: Factored $(if $(wildcard $@)... test out into $(make_script) so all `%: %.make`-like rules could use it directly
- 03:09 PM Revision 5875: lib/forwarding.Makefile: $(subdirs): Use all folders other than ../ ./ .svn/ instead of listing folders that start with . explicitly
- 02:31 PM Revision 5874: schemas/vegbien.sql: analytical_stem_view: Use accepted_taxonlabel.taxonomicname instead of accepted_taxonverbatim.taxonomicname in order to have the family prepended
- 12:41 PM Revision 5873: Regenerated vegbien.ERD exports
- 12:38 PM Revision 5872: schemas/vegbien.sql: placerank: Reordered in path order, using <http://rs.tdwg.org/dwc/terms/#dcindex> and <http://vegbank.org/vegbank/views/dba_fielddescription_detail.jsp?view=detail&wparam=1415&entity=dba_fielddescription¶ms=1415> as a guide. Documented the source of the values.
- 12:26 PM Revision 5871: schemas/vegbien.sql: placename: Removed non-name-related fields, because placename is designed only to store a hierarchy of placenames, not additional place information
- 12:23 PM Revision 5870: schemas/vegbien.sql: Moved placedescription from placename to place (and renamed it to description), because it applies to the place itself, not the name for the place
- 12:16 PM Revision 5869: schemas/vegbien.sql: analytical_aggregate_view: Added coverPercent, which is the sum of all coverPercents for that species
- 12:13 PM Revision 5868: schemas/vegbien.sql: analytical_aggregate_view: Added coverPercent, which is the sum of all coverPercents for that species
- 12:03 PM Revision 5867: schemas/vegbien.sql: analytical_aggregate_view: Include all analytical_stem species, not just those whose stems have non-NULL DBH
- 11:57 AM Revision 5866: schemas/vegbien.sql: Renamed aggregated_analytical_db to analytical_aggregate to match the name of analytical_stem
- 11:55 AM Revision 5865: schemas/vegbien.sql: Renamed analytical_db to analytical_stem since this contains just the individual stems, not the aggregated data in the main analytical DB
- 11:52 AM Revision 5864: schemas/vegbien.sql: Renamed analytical_db to analytical_stem since this contains just the individual stems, not the aggregated data in the main analytical DB
- 11:38 AM Revision 5863: schemas/vegbien.sql: Removed no longer used locationcoords
- 11:35 AM Revision 5862: schemas/vegbien.sql: analytical_db_view: Use new coordinates instead of locationcoords
- 11:23 AM Revision 5861: mappings/VegCore-VegBIEN.csv: Remapped latitude/longitude to new coordinates table
- 11:15 AM Revision 5860: schemas/vegbien.sql: place: Added coordinates_id
- 11:01 AM Revision 5859: schemas/vegbien.sql: Added coordinates table
- 10:40 AM Revision 5858: schemas/vegbien.sql: place: Removed municipality, site because they are not used in the geoscrubbing
- 10:19 AM Revision 5857: schemas/vegbien.sql: place: Place custom hierarchy of placenames in placename table instead of in otherranks field
- 10:04 AM Revision 5856: schemas/vegbien.sql: place.matched_place_id: Changed comment to say that places are linked in a three-level (instead of two-level) hierarchy of datasource place -> verbatim place -> accepted place, and this field contains the closest match
- 09:54 AM Revision 5855: schemas/vegbien.sql: Renamed placepath to place since this contains primary information about the place, including the reference to the canonical place
- 09:42 AM Revision 5854: schemas/vegbien.sql: Renamed place to placename since it refers just to a name for a place, without coordinates
- 07:18 AM Revision 5853: schemas/vegbien.sql: analytical_db_view: Exclude original taxondeterminations, so that there is only one taxondetermination for each taxonoccurrence
- 07:03 AM Revision 5852: schemas/vegbien.sql: make_analytical_db(): Also make new aggregated_analytical_db
- 07:02 AM Revision 5851: schemas/vegbien.sql: sync_analytical_db_to_view(): DROP TABLE: Use IF EXISTS in case analytical_db table has already been deleted, or not yet created
- 07:01 AM Revision 5850: schemas/vegbien.sql: Added aggregated_analytical_db_view and materialized table aggregated_analytical_db (synced using sync_aggregated_analytical_db_to_view())
- 07:01 AM Revision 5849: schemas/vegbien.sql: Added aggregated_analytical_db_view and materialized table aggregated_analytical_db (synced using sync_aggregated_analytical_db_to_view())
- 06:56 AM Revision 5848: lib/PostgreSQL-MySQL.csv: custom types: Also match column names enclosed in ``
- 06:49 AM Revision 5847: schemas/vegbien.sql: Store materialized analytical_db table in schema so aggregating views can reference it. Added sync_analytical_db_to_view() to maintain analytical_db table.
- 06:30 AM Revision 5846: schemas/vegbank.ERD.pdf: Restored to VegBank ERD, which had gotten overwritten when the vegbien.ERD exports were regenerated
- 06:23 AM Revision 5845: schemas/vegbien.sql: analytical_db_view: Reordered columns in path order
- 06:04 AM Revision 5844: schemas/: Moved unit conversion functions from functions.sql to vegbien.sql so the unit conversion functions used by analytical_db_view wouldn't need to be stored both in functions.sql and in vegbien.sql. (All unit conversion functions used by analytical_db_view must be stored in the public schema so that analytical_db_view doesn't get cascadingly deleted when the functions schema is reinstalled.)
- 05:52 AM Revision 5843: schemas/vegbien.sql: analytical_db_view: Use public._m2_to_ha() instead of functions._m2_to_ha()
- 05:51 AM Revision 5842: schemas/vegbien.sql: Copied _m2_to_ha() to public schema for use by analytical_db_view
- 05:40 AM Revision 5841: schemas/vegbien.sql: analytical_db_view: Added diameterBreastHeight_cm
- 05:38 AM Revision 5840: schemas/functions.sql, vegbien.sql: Added _m_to_cm()
- 05:07 AM Revision 5839: schemas/vegbien.sql: Copied _cm_to_m() to public schema for use by new aggregated_analytical_db_view
- 04:19 AM Revision 5838: schemas/vegbien.sql: analytical_db_view: datasource table: Fixed bug where need to filter by creator_id = party_id in order to use just root parties (datasources)
- 03:40 AM Revision 5837: tnrs_db: Fetching names to scrub: Omit sql.select() fields param because it will be filled in with its default value
- 03:29 AM Revision 5836: import_all: Pass command-line args (such as make vars) to all commands, not just with_all, so that a custom public schema is properly used by all commands
- 02:57 AM Revision 5835: inputs/.NCBI/nodes/create.sql: Make genus completely globally unique by removing duplicates. Note that only duplicates with ranks at or below the genus level need be removed, which for this dataset is just genus and subgenus.
- 02:00 AM Revision 5834: schemas/vegbien.sql: taxonlabel: taxonlabel_required_key constraint: Also allow taxonlabels with just a sourceaccessioncode, to support looking up parent taxonlabels using just their sourceaccessioncode (e.g. in NCBI)
- 01:23 AM Revision 5833: mappings/VegCore-VegBIEN.csv: matched taxonlabel: Don't include taxonName in the concatenated taxonomicname. This also prevents the creation of the matched taxonlabel entirely when only the taxonName is provided.
- 01:20 AM Revision 5832: mappings/VegCore-VegBIEN.csv: Don't create matched taxonlabel if taxonName was provided. This fixes a bug where an NCBI node was incorrectly pointing to a TNRS name, when the reference should only be the other way around. This may also fix the TNRS slowdown, if it was caused by circular matched_label_id references.
- 12:47 AM Revision 5831: schemas/vegbien.sql: taxonlabel_2_set_canon_label_id_on_insert(): Fixed bug where also need to set canon_label_id based on matched_label_id here, not just in taxonlabel_2_set_canon_label_id_on_update(), because the matched_label_id could be specified when the taxonlabel is first created
- 12:34 AM Revision 5830: schemas/vegbien.sql: taxonlabel_2_set_canon_label_id_on_*(): Fixed bug where need to use := instead of = to perform assignment of canon_label_id
- 12:17 AM Revision 5829: schemas/tree_cross-links.sql: Updated for schema changes
- 12:16 AM Revision 5828: schemas/vegbien.sql: taxonlabel_update_ancestors(): Include ancestors for both parent_id and matched_label_id rather than just one or the other. This avoids needing to delete existing ancestors for the parent_id when a matched_label_id is added and overrides it. This should reduce the TNRS import time if the slowdown was due to the need to delete parent_id ancestors when later adding a matched_label_id (which only occurs in a separate step in the TNRS datasource).
- 12:07 AM Revision 5827: sql_io.py: put_table(): ensure_cond(): Fixed bug where test if any rows failed cond did not check if cur != None (which is the case when cond == sql_gen.true_expr) before checking cur.rowcount
10/29/2012
- 10:26 PM Revision 5826: sql_gen.py: simplify_expr(): Don't require () around NULL IS NULL and NULL IS NOT NULL because extra parentheses are not provided in index conditions, only in check constraint conditions
- 10:06 PM Revision 5825: inputs/import.stats.xls: Updated import times. The TNRS import has slowed down significantly, possibly due to a bug in the autopopulation of the taxonlabel_relationship table when the input data contains cycles.
- 09:37 PM Revision 5824: sql_io.py: put_table(): Assertion that into and full_in_table have the same row count: Allow into to have more rows than full_in_table, in case an input row matched multiple output rows. This should not happen for a properly-configured database, but seems to happen periodically nevertheless (currently, to the MO datasource) and should not abort the import when it does.
10/26/2012
- 08:18 PM Revision 5823: sql.py: parse_exception(): "could not create unique index" DuplicateKeyException: Fixed bug where can't use make_DuplicateKeyException() because it tries to retrieve information about the index in question, but the index it was trying to create doesn't exist
- 08:10 PM Revision 5822: schemas/vegbien.sql: analytical_db_view: Renamed datasource's taxonverbatim to datasource_taxonverbatim to distinguish it from the other taxonverbatims that are joined on (parsed_taxonverbatim, accepted_taxonverbatim)
- 07:18 PM Revision 5821: inputs/.NCBI/nodes/create.sql: Make genus (mostly) globally unique by removing kingdom Animalia, which has significant genus overlap with plants. This reduces the number of duplicated genera from 578 to 65 (determined with `SELECT name_txt, count(*), array_agg(rank) FROM "NCBI".nodes GROUP BY name_txt HAVING count(*) > 1 AND 'genus' = ALL (array_agg(rank))`).
- 07:08 PM Revision 5820: inputs/.NCBI/nodes/create.sql: Added foreign key on parent tax_id with covering index
- 07:06 PM Revision 5819: input.Makefile: Staging tables installation: Added %/uninstall, %/reinstall to allow reinstalling individual tables
- 06:00 PM Revision 5818: sql_io.py: put_table(): ensure_cond(): When adding the failed condition to the errors table, also include the original, untranslated condition from the DB schema in addition to the translation of the condition into the input schema
- 05:45 PM Revision 5817: sql_io.py: track_data_error(): Fixed bug where errors whose column had no srcs (indicated by () ) were incorrectly being ignored. This affected NOT NULL exceptions where the column was not provided by the dataset.
- 05:38 PM Revision 5816: sql_gen.py: If no cols had srcs, return [] instead of the [()] that itertools.product() would have returned
- 05:38 PM Revision 5815: sql_io.py: track_data_error(): Support errors with no columns by inserting a single entry with column set to NULL
- 05:35 PM Revision 5814: strings.py: Added join()
- 05:00 PM Revision 5813: sql_io.py: mk_errors_table(): Made "column" column nullable, because some errors (such as check constraint violations) don't have any corresponding columns if its columns weren't provided in the input data
- 04:35 PM Revision 5812: inputs/test_taxonomic_names/test_scrub: `make inputs/.TNRS/reinstall`: Use new $schema_only option so that an empty TNRS schema is installed rather than one containing inputs/.TNRS/data.sql
- 04:34 PM Revision 5811: inputs/.TNRS/: Added data.sql containing the test_taxonomic_names TNRS results, so that a new installation of VegBIEN will contain the necessary data to make the tests pass, including the TNRS import test
- 04:32 PM Revision 5810: input.Makefile: Staging tables installation: If $schema_only option is set, only install .sql files ending in schema.sql
- 04:24 PM Revision 5809: inputs/Makefile: $(rsyncLogs): Use $(rsync) instead of $(rsync*) now that it supports excluding just temp files and .svn rather than all .*
- 04:21 PM Revision 5808: lib/common.Makefile: rsync: $(rsync): Exclude .svn, *#, and .DS_Store rather than all .* because dirs beginning with . created by the user (such as .NCBI, .TNRS) should be included in the sync
- 04:18 PM Revision 5807: Added inputs/REMIB/Specimen.src/.map.csv.last_cleanup
- 04:10 PM Revision 5806: Added inputs/bien_web/observation/+header.csv
- 04:09 PM Revision 5805: input.Makefile: Staging tables installation: $(dbExports): When putting schemas first, don't require a . before "schema" to allow the entire filename to be schema.sql
- 03:44 PM Revision 5804: inputs/test_taxonomic_names/_scrub/public.test_taxonomic_names.sql, TNRS.sql: Regenerated with schema and mappings changes
- 03:42 PM Revision 5803: inputs/.TNRS/tnrs/map.csv: Added _nullIf filter to remove "Unknown" values for Accepted_name_family
- 03:35 PM Revision 5802: README.TXT: Generate the local TNRS cache from the test_taxonomic_names rather than syncing it with the vegbiendev TNRS cache, so that the automated test's inserted row count stays the same regardless of the contents of the full-DB TNRS cache
- 03:34 PM Revision 5801: README.TXT: Backups: Added TNRS cache section
- 03:12 PM Revision 5800: inputs/.TNRS/tnrs/test.xml.ref: Accepted inserted row count using TNRS cache created from test_taxonomic_names. Using a standard set of names for the test ensures that the inserted row count will not change when the full-DB TNRS cache changes.
- 02:48 PM Revision 5799: inputs/.TNRS/schema.sql: tnrs_accepted_names: Prepend the Accepted_name_family to the taxonomic name that will be submitted back to TNRS for parsing, because TNRS input names now always include the family when it's provided
- 02:46 PM Revision 5798: inputs/.TNRS/schema.sql: tnrs_accepted_names: Use simpler array_to_string() instead of || and COALESCE() to put together the taxonomic name that will be submitted back to TNRS for parsing. Note that this requires defining an IMMUTABLE wrapper function for array_to_string(), because pg_catalog.array_to_string() is declared STABLE but indexes require functions to be IMMUTABLE (http://www.mail-archive.com/pgsql-hackers@postgresql.org/msg156323.html).
- 02:42 PM Revision 5797: inputs/.TNRS/schema.sql: Don't hardcode the schema name
- 02:40 PM Revision 5796: input.Makefile: Staging tables installation: sql/install: Provide the datasource's schema to the script in :schema, so it can refer to its own elements explicitly when it's not possible to rely on the search_path. This is the case for functions that have the same signature as (and are intended to replace) a pg_catalog function, because the pg_catalog function will be used in preference to the datasource function regardless of the search_path.
- 02:06 PM Revision 5795: input.Makefile: Staging tables installation: $(cleanup): If a cleanup.sql is provided, *only* run it and don't do default cleanup, to allow tables to override rather than just add to default cleanup operations. This prevents the automatic replacement of certain strings (sql_io.null_strs) with NULL on TNRS, and keeps the TNRS cache mostly as it was output by the TNRS service. Note that empty strings are still replaced with NULL by COPY FROM in sql_io.append_csv(). This is necessary for TNRS import to work properly, because although '' generally means NULL, it is not treated that way by PostgreSQL.
- 01:53 PM Revision 5794: input.Makefile: Staging tables installation: Moved custom cleanup.sql cleanup operations to main $(cleanup) function, so custom cleanup operations would run whenever any target (such as %/install) invokes $(cleanup), not just manually through %/cleanup
- 01:52 PM Revision 5793: input.Makefile: Staging tables installation: Moved custom cleanup.sql cleanup operations to main $(cleanup) function, so custom cleanup operations would run whenever any target (such as %/install) invokes $(cleanup), not just manually through %/cleanup
10/25/2012
- 05:16 PM Revision 5792: sql.py: parse_exception(): function MissingCastException: If first param's type is anyelement (for polymorphic function, which had mismatched arg types), use type text, as all types can cast to it
- 05:12 PM Revision 5791: sql_io.py: cast(): Set the created function's value param type to anyelement to support any input type, not just text
- 04:53 PM Revision 5790: mappings/VegCore-VegBIEN.csv: Only prepend the family to the concatenated scientificName for TNRS if it ends in -aceae (using _taxon_family_require_std()), to avoid sending unsupported, nonstandard families to TNRS which it will place in Unmatched_terms
- 04:48 PM Revision 5789: schemas/vegbien.sql: Added _taxon_family_require_std()
- 04:09 PM Revision 5788: mappings/VegCore-VegBIEN.csv: Prepend the family to the concatenated scientificName input to TNRS, so that TNRS can use it to disambiguate the genus
- 03:50 PM Revision 5787: tnrs_db: Making TNRS request: Fixed bug where needed to remove else block now that there is no except block
- 03:45 PM Revision 5786: tnrs.py: retrieval_request_template: Turn on taxonomic_constraint (to match family before genus) and source_sorting (to always return any result from the first source before returning results from any other sources, regardless of match %)
- 12:50 PM Revision 5785: Regenerated vegbien.ERD exports
- 12:46 PM Revision 5784: mappings/VegCore.csv: speciesBinomial: Changed definition to genus+specificEpithet, not genus+species, to match the scientific meaning of specificEpithet vs. species
- 12:45 PM Revision 5783: schemas/vegbien.sql: taxonverbatim: Renamed species to specific_epithet to avoid confusion with the scientific meaning of species (genus+specificEpithet), since this field contains just the specific epithet
- 12:30 PM Revision 5782: input.Makefile: Verification of import: verify: Use tables from the verify/*.ref files themselves rather than from the datasource's subdirs, in order to match the tables in mappings/verify.*.sql
- 11:52 AM Revision 5781: schemas/vegbien.sql: analytical_db_view: Added stemobservation.tag, stemobservation.height_m for use in plot change over time analysis <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Plot_change_over_time_analysis>
- 11:45 AM Revision 5780: schemas/vegbien.sql: analytical_db_view: Fixed typo in scientificNameWithMorphospecies
- 11:41 AM Revision 5779: schemas/vegbien.sql: analytical_db_view: Renamed columns to VegCore names (https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/mappings/VegCore.csv)
- 11:36 AM Revision 5778: mappings/VegCore.csv: Added cultivatedBasis
- 11:34 AM Revision 5777: mappings/VegCore.csv: Added scientificNameWithMorphospecies
- 10:55 AM Revision 5776: mappings/VegCore.csv: Added speciesBinomial
- 10:49 AM Revision 5775: schemas/vegbien.sql: analytical_db_view: Generate species by concatenating genus and specific epithet, since according to Brad this field is actually the binomial, not the specificEpithet
- 10:41 AM Revision 5774: schemas/vegbien.sql: Removed no longer used plot_change_over_time view. Use one of the queries at <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Plot_change_over_time_analysis> instead.
- 10:36 AM Revision 5773: mappings/VegCore-VegBIEN.csv: location: Populate sourceaccessioncode with locationID + subplot when subplot is unique only within the parent plot, so that location always has a sourceaccessioncode to use as the plotCode in analytical_db_view
- 10:07 AM Revision 5772: lib/PostgreSQL-MySQL.csv: Remove views because they can contain arbitrary expressions, whose syntax may not be compatible with MySQL
- 10:04 AM Revision 5771: schemas/vegbien.sql: analytical_db_view: Use location.sourceaccessioncode as plotCode instead of authorlocationcode because authorlocationcode isn't globally unique (for subplots, it's only unique within the parent plot)
- 09:48 AM Revision 5770: schemas/vegbien.sql: plantobservation: Made taxonoccurrence_id optional when sourceaccessioncode is specified, so that aggregateoccurrence doesn't get pruned away in datasource tables that link just a stemobservation to a plantobservation (and therefore don't provide a taxonoccurrence to satisfy the previous taxonoccurrence_id NOT NULL constraint)
- 09:47 AM Revision 5769: schemas/vegbien.sql: aggregateoccurrence: Made taxonoccurrence_id optional when sourceaccessioncode is specified, so that aggregateoccurrence doesn't get pruned away in datasource tables that link just a stemobservation to a plantobservation (and therefore don't provide a taxonoccurrence to satisfy the previous taxonoccurrence_id NOT NULL constraint)
- 09:42 AM Revision 5768: schemas/vegbien.sql: aggregateoccurrence: Made taxonoccurrence_id optional when sourceaccessioncode is specified, so that aggregateoccurrence doesn't get pruned away in datasource tables that link just a stemobservation to a plantobservation (and therefore don't provide a taxonoccurrence to satisfy the previous taxonoccurrence_id NOT NULL constraint)
- 09:31 AM Revision 5767: schemas/vegbien.sql: taxonoccurrence: Added taxonoccurrence_required_key check constraint to ensure that all taxonoccurrences are properly identified, and empty taxonoccurrences are properly pruned. This fixes a bug where taxon-only and stem-only data did not properly prune the taxonoccurrence that would otherwise get created because it's included in the mappings.
- 07:51 AM Revision 5766: sql_io.py: put_table(): insert_into_pkeys(): Use new sql.add_pkey_or_index() instead of sql.add_pkey() in order to just print a warning if for some reason there were duplicate entries for an input row in the iteration's pkeys table. This should provide a workaround for bugs (often in the schema itself, related to its unique indexes) that cause an input row to match multiple output rows when joining on the output table using the unique constraint's columns.
- 07:44 AM Revision 5765: sql.py: Added add_pkey_or_index()
- 07:32 AM Revision 5764: sql.py: parse_exception(): Parse "could not create unique index ... Key is duplicated" errors as DuplicateKeyException
- 07:27 AM Revision 5763: sql.py: parse_exception(): DuplicateKeyException: Factored out creation of DuplicateKeyException into helper function
- 07:20 AM Revision 5762: inputs/import.stats.xls: Updated import times
10/24/2012
- 06:31 PM Revision 5761: tnrs_db: Removed tnrs.InvalidResponse exception handler that retries the query because the current query does not track which names have been submitted to but not processed by TNRS, so the error would continue to happen repeatedly
- 06:13 PM Revision 5760: schemas/vegbien.sql: location: Added index on parent_id to speed up plot change over time joins
- 05:45 PM Revision 5759: schemas/vegbien.sql: location: Added index on creator_id to speed up analytical_db_view joins
- 05:15 PM Revision 5758: schemas/vegbien.sql: stemobservation: Added index on plantobservation_id to speed up analytical_db_view joins
10/23/2012
- 01:08 PM Revision 5757: schemas/vegbien.sql: Added initial plot_change_over_time view
- 12:53 PM Revision 5756: Added inputs/bien_web/
- 12:43 PM Revision 5755: schemas/vegbien.sql: analytical_db_view: Reordered taxonoccurrence.growthform to put if after the bien_web.observation fields
- 12:32 PM Revision 5754: schemas/vegbien.sql: analytical_db_view: Include taxonoccurrence.growthform
- 12:27 PM Revision 5753: schemas/vegbien.sql: analytical_db_view: Generate taxonMorphospecies by concatenating the scientificName to the morphospecies
- 12:23 PM Revision 5752: schemas/vegbien.sql: analytical_db_view: Fixed bug where needed to take taxonomic name components from the accepted taxonlabel's taxonverbatim instead of the datasource's taxonverbatim, which does not contain the accepted name
- 12:19 PM Revision 5751: schemas/vegbien.sql: analytical_db_view: identifiedBy: Added NULLIF() to keep empty strings out of the analytical DB
- 12:13 PM Revision 5750: schemas/vegbien.sql: analytical_db_view: Fixed bug where needed to take taxonomic name components from the accepted taxonlabel's taxonverbatim instead of the datasource's taxonverbatim, which does not contain the accepted name
- 12:10 PM Revision 5749: schemas/vegbien.sql: analytical_db_view: Fixed bug where needed to take morphospecies from the parsed taxonlabel's taxonverbatim, where it has been parsed out, instead of the datasource's taxonverbatim, which has it as part of the verbatim input name
- 11:58 AM Revision 5748: analytical_db_view: Added stemobservation.xposition_m, yposition_m
- 11:46 AM Revision 5747: inputs/.TNRS/tnrs/map.csv: Added new Time_submitted field
- 11:45 AM Revision 5746: inputs/REMIB/Specimen/header.csv: Regenerated for new staging tables format
- 11:41 AM Revision 5745: inputs/.TNRS/tnrs/test.xml.ref: Accepted correct inserted row count, which most likely became detached from the primary row count when the TNRS cache was cleared and repopulated with test data
- 11:28 AM Revision 5744: schemas/vegbien.sql: analytical_db_view: Reordered joins in path order, putting datasource before location. This will enable more naturally reusing the SELECT query for other analyses.
- 11:15 AM Revision 5743: mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Do not include rank in the mapping because taxonomicname is globally unique, and thus it isn't used in looking up the NCBI taxonlabel
- 11:05 AM Revision 5742: inputs/test_taxonomic_names/_scrub/public.test_taxonomic_names.sql, TNRS.sql: Regenerated with schema and mappings changes
- 10:49 AM Revision 5741: mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Also attach TNRS genus to NCBI backbone. This causes attachment to be made with as many of family and genus as are provided and have an entry in NCBI.
- 10:45 AM Revision 5740: mappings/VegCore-VegBIEN.csv: family -> NCBI backbone: Removed extra path after _if statement's cond/_exists
- 10:39 AM Revision 5739: mappings/VegCore-VegBIEN.csv: Instead of connecting the acceptedFamily to the NCBI backbone, connect the family for the TNRS matched taxonlabel. This connects more families and also connects the same set of fields as will be connected for the genus.
- 10:01 AM Revision 5738: mappings/VegCore-VegBIEN.csv: TNRS<->NCBI attachment: Fixed bug where needed to attach accepted family to NCBI using taxonomicname, which is globally unique, rather than taxonepithet, which is only unique within the parent taxon
- 09:34 AM Revision 5737: inputs/.TNRS/tnrs/: Added Time_submitted column at beginning and populate it in tnrs_db with the time the batch TNRS request was submitted
- 09:08 AM Revision 5736: csvs.py: RowNumFilter: Use new ColInsertFilter
- 09:08 AM Revision 5735: csvs.py: Added ColInsertFilter
- 08:43 AM Revision 5734: schemas/vegbien.sql: Removed no longer used _is_higher_taxon(). Use _has_taxonomic_name() or _taxonomic_name_is_epithet() instead.
- 08:42 AM Revision 5733: mappings/VegCore-VegBIEN.csv: taxonName->taxonepithet: Use new _taxonomic_name_is_epithet() instead of _is_higher_taxon(), because it's more specific to the filtering task for this field
- 08:36 AM Revision 5732: schemas/vegbien.sql: Added _taxonomic_name_is_epithet()
- 08:33 AM Revision 5731: mappings/VegCore-VegBIEN.csv: taxonName->taxonomicname: Use new _has_taxonomic_name() instead of _is_higher_taxon(), because it's more specific to the filtering task for this field
- 08:30 AM Revision 5730: mappings/VegCore-VegBIEN.csv: taxonName->taxonomicname: Use new _has_taxonomic_name() instead of _is_higher_taxon(), because it's more specific to the filtering task for this field
- 08:25 AM Revision 5729: schemas/vegbien.sql: Added _has_taxonomic_name() for lower taxon ranks that typically have a globally unique taxonomic name
- 08:10 AM Revision 5728: schemas/functions.sql: Removed unit conversion functions that take a text input, since casts to the parameter type (double precision) are now automatically performed by sql_io.put_table(), using sql.parse_exception()'s function MissingCastException parsing
- 08:01 AM Revision 5727: mappings/VegCore-VegBIEN.csv: _is_higher_taxon() calls: Default to true if the rank can't be parsed to a taxonrank enum value
- 07:56 AM Revision 5726: sql_io.py: put_table(): is_function: Moved definition of wrapper function inside try block of main loop because the creation of the empty pkeys table (whose row type is needed for the wrapper function) can itself produce MissingCastExceptions, which must be thrown inside the loop in order to be handled properly
- 07:05 AM Revision 5725: db_xml.py: put(): Indicate no parent_ids_loc using no_parent_ids_loc sentinel instead of None to support parent_ids_locs that are equal to None (e.g. if the parent node had an error). Always forward parent_ids_loc to children with fkeys to parent, even on error, because the parent table may not be required for the child tables to be valid, such as for taxonomic-data-only datasets that nevertheless have nodes for the non-taxonomic tables in their mappings.
- 06:38 AM Revision 5724: sql.py: parse_exception(): types cannot be matched MissingCastException: Use the first type as the type to cast to instead of text
- 05:59 AM Revision 5723: sql.py: parse_exception(): InvalidValueException: Fixed bug in regexp where can't use .*? before (?:...)? surrounding matched value, because it prevents the value from being matched now that it is optional
- 05:52 AM Revision 5722: inputs/.NCBI/nodes/header.csv: Updated for new staging table format, which includes a row_num column in each joined table
- 05:51 AM Revision 5721: inputs/.NCBI/nodes/create.sql: Updated for new src table names
- 05:36 AM Revision 5720: xml_func.py: process(): Pass on_error through to sql_io.put(). This fixes a bug in row-based import where DB errors in the xml_func.process() phase would abort the entire import instead of being tracked and having the return value set to None.
- 05:33 AM Revision 5719: sql_io.py: put(): Pass on_error through to put_table()
- 05:19 AM Revision 5718: sql_io.py: put_table(): log_exc(): Return False if removing all rows and have callers break the main loop so that no further exception-handling code is processed before the main loop is exited
- 05:17 AM Revision 5717: sql.py: parse_exception(): InvalidValueException: Also match exceptions which don't provide a specific value but just indicate that a value was invalid, such as PL/Python's "day is out of range for month"
- 04:39 AM Revision 5716: db_xml.py: put(): Inserting children with fkeys to parent: Don't do this if this node had an error and sql_io.put_table() returned None as the generated pkey. This fixes a bug where a node with an error will still try to create children with fkeys to parent, but pass None as the fkey to parent, which the recursive put() call will then incorrectly treat as there being no field with an fkey to parent at all rather than a field whose value is NULL. This causes function overload resolution to be unable to find the intended function, because it is missing a parameter.
- 04:34 AM Revision 5715: sql.py: parse_exception(): function MissingCastException: Return the actual type of the function's 1st param, using new function_param0_type(), rather than just text
- 04:31 AM Revision 5714: sql.py: parse_exception(): function MissingCastException: Fixed bug where can't return the function name as the name of what was missing the cast, because this must be a column
- 04:28 AM Revision 5713: sql.py: Added function_param0_type()
- 04:26 AM Revision 5712: sql.py: parse_exception(): function MissingCastException: Only treat DoesNotExistException as a MissingCastException if the query that was run did not already include a cast, to avoid infinite exception-handling recursion
- 04:24 AM Revision 5711: sql.py: parse_exception(): function MissingCastException: Fixed bug where determining whether the exception is a MissingCastException rather than a DoesNotExistException needs to check whether the function exists rather than whether it's the same in the exception message as in the query that was run. The exception message will of course copy the function name verbatim from the query, so there is no information in the exception message itself to indicate whether the DoesNotExistException was caused by a missing cast or by a nonexistent function.
- 04:19 AM Revision 5710: sql.py: parse_exception(): function MissingCastException: Documented that the regexp match to extract the function name also checks that a function signature with param types was matched, indicating a function call rather than cast to regproc. This check will also help avoid infinite recursion when function MissingCastException parsing calls database structure introspection functions.
- 04:15 AM Revision 5709: sql.py: parse_exception(): function MissingCastException: Don't match quotes around the function name because this particular exception (incorrect param type) does not include them. Casts to regproc, which also produce a DoesNotExistException, include the quotes but do not indicate a MissingCastException.
- 04:12 AM Revision 5708: sql.py: parse_exception(): function MissingCastException: Fixed bug where the 1st param's type in the exception's function signature is not actually the type the argument needs to have, because this is just the argument's current type
- 04:04 AM Revision 5707: sql.py: parse_exception(): typed_name_re: Also match identifiers without quotes, such as functions in "No function matches the given name and argument types" errors. This fixes a bug where DoesNotExistExceptions could not be parsed as MissingCastExceptions when applicable because the DoesNotExistException pattern would not even match.
- 03:57 AM Revision 5706: inputs/.NCBI/: Renamed higher_taxa to nodes because it currently doesn't just contain the higher taxa
- 01:24 AM Revision 5705: schemas/vegbien.sql: taxonlabel: taxonlabel_2_set_canon_label_id(): Only run if matched_label_id has actually changed, to avoid infinite recursion when updating canon_label_id on labels that resolve to this label when there are cycles in the data
- 01:21 AM Revision 5704: inputs/.NCBI/: Renamed higher_taxa to nodes because it currently doesn't just contain the higher taxa
- 12:57 AM Revision 5703: inputs/.NCBI/: Renamed higher_taxa to nodes because it currently doesn't just contain the higher taxa
- 12:49 AM Revision 5702: inputs/.NCBI/: Renamed names, nodes to *.src so they wouldn't get an automatic row_num column and can be used in higher_taxa's join
- 12:38 AM Revision 5701: inputs/NCU-NCSC/Specimen/+header.csv: Fixed bug where needed ! at beginning to indicate a header override file, which prevents the following row from being treated as data
- 12:36 AM Revision 5700: units.py: MissingUnitsException: Fixed bug where quantity is a Quantity object, not a string, and thus needs to be converted to a string using strings.ustr()
- 12:25 AM Revision 5699: inputs/FIA/Organism/test.xml.ref: Accepted new test output now that FIA table is sorted in the order of the original CSV after staging table reinstallation
- 12:24 AM Revision 5698: inputs/VegBank/taxonobservation_/create.sql: Removed dropping of row_num column, which is no longer added on non-CSV tables
- 12:22 AM Revision 5697: input.Makefile: Staging tables installation: %/install: Moved "table-scope src table's row_num col" comment outside of define block so it wouldn't be echoed to stdout even when the table is not a src table
- 12:17 AM Revision 5696: Added inputs/NCU-NCSC/Specimen/+header.csv header override to remove empty, unnamed column at end
- 12:05 AM Revision 5695: inputs/*/*/header.csv: Regenerated for new staging tables format (which now includes a row_num column on every CSV table), as part of reinstalling staging tables
10/22/2012
- 11:59 PM Revision 5694: inputs/VegBank/vegbank.~.clean_up.sql: Fixed bug where DROP VIEW statements needed IF EXISTS because CASCADEs on previous DROP VIEWs may have already dropped the view in question
- 11:57 PM Revision 5693: input.Makefile: Staging tables installation: %/install: Fixed bug where a .src table's row_num column needed to have the table name prefixed (making it globally unique) to allow joining the table with other tables
- 11:31 PM Revision 5692: input.Makefile: Staging tables installation: sql/install: Fixed bug where $(logInstall) needed to be called with arguments, so that either > or >> would be used before the install log's filename
- 08:22 PM Revision 5691: tnrs.py: submission_request_template: Use just Tropicos as the name source, as Brad says "GCC is for only one family (Asteraceae)" and USDA's "taxonomy is of lower quality and sometimes conflicts with Tropicos"
10/19/2012
- 06:20 PM Revision 5690: sql.py: parse_exception(): function MissingCastException: Support functions with named parameters
- 06:18 PM Revision 5689: sql.py: parse_exception(): function MissingCastException: Support function names enclosed in quotes on the context line
- 06:15 PM Revision 5688: mappings/VegCore-VegBIEN.csv: taxonName: Place it in taxonomicname instead of taxonepithet for lower taxa, because the only datasource that currently provides this field (NCBI) actually provides the full taxonomicname instead of the epithet at the current rank for lower taxa. (taxonomicname is not applicable to higher taxa because their names are not guaranteed to be globally unique.) taxonName may need to be renamed and/or redefined to account for this ambiguity in NCBI's usage.
- 06:14 PM Revision 5687: mappings/VegCore-VegBIEN.csv: Do not include the taxonName in the concatenated taxonomicname because it is NOT globally unique. The same name may be used at different taxonomic ranks and mean different things, and lower taxa may have the name appear in multiple genuses or species, meaning different things.
- 06:04 PM Revision 5686: mappings/VegCore-VegBIEN.csv: Do not include the taxonName in the concatenated taxonomicname because it is NOT globally unique. The same name may be used at different taxonomic ranks and mean different things, and lower taxa may have the name appear in multiple genuses or species, meaning different things.
- 05:57 PM Revision 5685: schemas/vegbien.sql: Added _is_higher_taxon()
- 05:52 PM Revision 5684: README.TXT: Documentation: To import and scrub just the test taxonomic names: Added `make inputs/.TNRS/cleanup` after `make backups/TNRS.backup/restore` because the PostgreSQL collation may differ between vegbiendev's and the user's DB
- 05:50 PM Revision 5683: sql.py: parse_exception(): DoesNotExistException: If item not found was a function and not found only because of a missing cast, raise MissingCastException instead. This should allow automatic casts to be added on function parameters as well as table columns.
- 05:28 PM Revision 5682: schemas/vegbien.sql: analytical_db_view: Fixed bug where needed to join to taxonverbatim on taxonverbatim_id (the pkey) instead of taxonlabel_id, which used to be the pkey but is now an fkey
- 05:22 PM Revision 5681: inputs/test_taxonomic_names/test_scrub: Remove any previous version of public.test_taxonomic_names before renaming public to it
- 05:19 PM Revision 5680: inputs/test_taxonomic_names/test_scrub: Fixed bug where public.sql export did not include the "CREATE SCHEMA public" statement, because pg_dump doesn't add it to backups, by using new schemas/rename/% make target to first rename the public schema and then exporting it
- 05:12 PM Revision 5679: root Makefile: VegBIEN DB: Schemas: schemas/rotate: Use new schemas/rename/%
- 05:12 PM Revision 5678: root Makefile: VegBIEN DB: Schemas: Added schemas/rename/% to rename the public schema
- 04:54 PM Revision 5677: mappings/VegCore-VegBIEN.csv: Removed filter preventing taxonomicStatus from being placed in taxonlabel if a morphospecies was provided, because the morphospecies actually never goes in the *matched* taxonlabel, only the *verbatim* taxonlabel
- 04:50 PM Revision 5676: mappings/VegCore-VegBIEN.csv: morphospecies: Also place it in the verbatim (input name's) taxonlabel. Note that it does not go in the matched name's taxonlabel, because that contains only fields from the matched name. The verbatim taxonlabel is thus a synonym of the matched taxonlabel where there is no morphospecies, or a child of it if there is a morphospecies.
- 04:36 PM Revision 5675: mappings/VegCore-VegBIEN.csv: Do not place taxonomicStatus in taxonlabel if a morphospecies was provided, to prevent it from being incorrectly marked as accepted
- 04:25 PM Revision 5674: mappings/VegCore-VegBIEN.csv: morphospecies -> taxonverbatim.morphospecies: Fixed bug where needed suffix with _if statement then clause
- 04:23 PM Revision 5673: inputs/test_taxonomic_names/_scrub/public.sql, TNRS.sql: Regenerated with schema changes
- 03:45 PM Revision 5672: pg_dump_vegbien: Added opts env var to allow specifying options to a Makefile command, which does not take positional arguments
- 03:37 PM Revision 5671: README.TXT: Schema changes: files to update with any renamings: Removed tnrs_db because that is now abstracted from the schema through the tnrs_input_name view. Note that PostgreSQL will automatically update tnrs_input_name with any table or column renames, which is the significant advantage of using a view rather than a hardcoded query.
- 03:35 PM Revision 5670: schemas/vegbien.sql: tnrs_input_name: Use DISTINCT instead of DISTINCT ON because there is only one column
- 03:34 PM Revision 5669: tnrs_db: Use new tnrs_input_name view to avoid hardcoding changing schema information
- 03:25 PM Revision 5668: inputs/test_taxonomic_names/test_scrub, README.TXT: Documented that `make schemas/public/reinstall` must come after TNRS restore to recreate the tnrs_input_name view, which has a dependency on the TNRS schema
- 03:23 PM Revision 5667: schemas/vegbien.sql: Added tnrs_input_name view for use by tnrs_db
- 12:53 PM Revision 5666: schemas/vegbien.sql: taxonlabel, taxonverbatim: Updated comments for new taxonlabel/taxonverbatim split
- 12:42 PM Revision 5665: schemas/vegbien.sql: taxonlabel_update_ancestors(): Use aliased types (http://www.postgresql.org/docs/8.3/static/plpgsql-declarations.html#PLPGSQL-DECLARATION-TYPE) where possible
- 12:37 PM Revision 5664: schemas/vegbien.sql: taxonlabel_update_ancestors(): Adding new parent's ancestors: Change unique_violations to warnings so they don't abort the import. unique_violations should never happen unless there are cycles of two or mode nodes, but they seem to be happening nevertheless, so this will provide a workaround to that problem.
- 12:18 PM Revision 5663: inputs/import.stats.xls: Updated import times
10/18/2012
- 04:58 PM Revision 5662: Regenerated vegbien.ERD exports
- 04:55 PM Revision 5661: tnrs_db: Updated with schema changes
- 04:54 PM Revision 5660: schemas/vegbien.sql: taxonverbatim: Removed subclass relationship to taxonlabel in order to allow multiple taxonverbatims to point to the same taxonlabel. This involves adding a taxonverbatim_id serial column and pointing all fkeys to taxonverbatim to that column.
- 04:43 PM Revision 5659: schemas/vegbien.sql: analytical_db_view: Fixed bug where needed to join on taxonverbatim before joining on taxonlabel, now that taxondetermination is linked directly to taxonverbatim. Interestingly, PostgreSQL did not flag this error when the schema was changed, but only when the schema was reloaded from the DDL.
- 04:30 PM Revision 5658: schemas/vegbien.ERD.mwb: Moved taxonlabel to the right of taxonverbatim to make room for taxonverbatim to expand
- 04:21 PM Revision 5657: schemas/vegbien.sql: Link taxondetermination to taxonverbatim (which is a subclass of taxonlabel) instead of directly to taxonlabel. This will enable later having multiple taxonverbatims for one taxonlabel.
- 04:04 PM Revision 5656: schemas/vegbien.sql: taxonlabel: Renamed identifyingtaxonomicname to taxonomicname because the taxonomicname provided by the datasource is now in taxonverbatim, so there is no name collision. Note that both of these fields store the same type of information, but taxonlabel's is autogenerated while taxonverbatim's is verbatim (and is only set if provided by the datasource).
- 03:57 PM Revision 5655: schemas/vegbien.sql: taxonlabel: Moved non-scoping fields to new taxonverbatim subclass table, which contains the component parts of the taxonlabel
- 03:06 PM Revision 5654: schemas/vegbien.sql: taxonlabel: Renamed taxonlabel_2_propagate_canon_label_id() to taxonlabel_2_set_canon_label_id() for clarity
- 03:04 PM Revision 5653: schemas/vegbien.sql: taxonlabel_2_propagate_canon_label_id(): If no matched taxonlabel, make self-reference. This fixes a bug in analytical_db_view where rows without a canon_label_id were excluded because they did not have a corresponding canonical taxonlabel.
- 02:53 PM Revision 5652: schemas/vegbien.sql: taxonlabel_unique unique index: Removed binomial, author, taxonomicname, and morphospecies because these are now part of the identifyingtaxonomicname, which is also in the unique index
- 02:44 PM Revision 5651: schemas/vegbien.sql: taxonlabel: Require either an identifyingtaxonomicname or a taxonepithet. The NCBI inserted row count decreases by one because this prunes off a taxonlabel created for a parent node which was not contained in the first two rows (remember that NCBI taxa are not in dependency order, so parents are often imported after children).
- 02:41 PM Revision 5650: mappings/VegCore-VegBIEN.csv: Also generate the identifyingtaxonomicname for the original* taxondetermination's taxonlabel
- 02:31 PM Revision 5649: schemas/vegbien.sql: taxonlabel: Renamed taxonomicnamewithauthor to taxonomicname because it is equivalent to Darwin Core's scientificName
- 02:25 PM Revision 5648: mappings/VegCore-VegBIEN.csv: Also include morphospecies in the identifyingtaxonomicname, except for the matched TNRS taxonlabel, which should not contain morphospecies information
- 02:14 PM Revision 5647: mappings/VegCore-VegBIEN.csv: Mapped acceptedScientificName
- 01:51 PM Revision 5646: mappings/VegCore-VegBIEN.csv: Also create the identifyingtaxonomicname on the verbatim taxonlabel supplied by the datasource, in addition to on the TNRS input taxonlabel that the verbatim taxonlabel is matched up with
- 01:46 PM Revision 5645: mappings/VegCore-VegBIEN.csv: Expanded brace expressions for putting together the identifyingtaxonomicname
- 01:21 PM Revision 5644: mappings/VegCore-VegBIEN.csv: Always generate the concatenated identifyingtaxonomicname, even for higher taxa, to ensure that this field is always populated. Note that this will cause names of higher taxa to be scrubbed by TNRS, but this is usually not a problem because such names either have no match or not a close enough match based on the name only. Naming conventions generally cause names at different ranks to be different, so that collisions with lower ranks should not be a problem.
- 01:05 PM Revision 5643: tnrs_db: Fixed bug where needed to remove internal identifyingtaxonomicname duplicates as well as duplicates with existing Name_submitted values, to avoid violating the TNRS.tnrs pkey constraint when the scrubbed names are later inserted. Note that the taxonlabel_0_unique_identifying_name unique index is not sufficient to prevent internal duplicates, because it includes the creator_id (and thus allows multiple instances of the same name defined by different creators).
- 01:01 PM Revision 5642: sql.py: mk_select(): Don't add table0 to order_by with no table, because this could cause it not to match a corresponding DISTINCT ON column with no explicit table. PostgreSQL apparently does not treat a column with no explicit table and a column with the applicable table as identical for purposes of ORDER BY/DISTINCT ON checking, even when they refer to the same physical column.
- 12:53 PM Revision 5641: sql.py: mk_select(): order_by defaults to first distinct_on column when distinct_on provided
- 12:36 PM Revision 5640: tnrs_db: Updated with schema changes
- 12:33 PM Revision 5639: schemas/vegbien.sql: taxonlabel: Renamed taxonomicnamewithauthor to taxonomicname because it is equivalent to Darwin Core's scientificName
- 12:25 PM Revision 5638: schemas/vegbien.sql: taxonlabel: Renamed taxonomicname to binomial because it excludes the author
- 12:15 PM Revision 5637: schemas/vegbien.sql: taxonlabel.taxonomicname, taxonomicnamewithauthor comments: Corrected to show that taxonomicnamewithauthor is actually scientificName, while taxonomicname does not directly correspond to a DwC term (but would be the binomial)
- 12:13 PM Revision 5636: schemas/vegbien.sql: taxonlabel.taxonomicnamewithauthor comment: Removed no longer applicable 'Equivalent to "Name sec. x"'. The "sec" is now stored in taxonconcept.concept_reference_id.
- 12:10 PM Revision 5635: mappings/Makefile: .VegCore.csv.last_cleanup: Remove duplicate entries using uniq
- 12:09 PM Revision 5634: mappings/VegCore.csv: Removed duplicate entries using uniq
- 12:06 PM Revision 5633: mappings/VegCore.csv: Removed *scientificNameWithAuthorship, which are now represented by *scientificName
- 12:04 PM Revision 5632: mappings: Renamed *scientificNameWithAuthorship to *scientificName because scientificNameWithAuthorship is actually a synonym of DwC's scientificName ("The full scientific name, with authorship and date information if known" <http://rs.tdwg.org/dwc/terms/#scientificName>)
- 11:57 AM Revision 5631: mappings: Renamed *scientificName to *binomial because DwC defines the scientificName as "The full scientific name, with authorship and date information if known", but many datasources do not include the author in their scientific name, and the fields scientificName is mapped to in VegBIEN assume it does not include the author
- 11:44 AM Revision 5630: mappings/VegCore.csv: Added verbatimBinomial
- 11:41 AM Revision 5629: mappings/VegCore.csv: Redefined *binomial to "Taxonomic name without author", rather than genus+species
- 11:32 AM Revision 5628: schemas/vegbien.sql: taxonconcept.taxonlabel_id: Changed type from serial to integer because this is a subclass, and therefore each taxonconcept must first have a corresponding entry in taxonlabel
- 11:29 AM Revision 5627: schemas/vegbien.sql: Moved taxonlabel.concept_reference_id to new taxonconcept table, which is a subclass of taxonlabel that adds information about who the taxon concept is according to
- 11:13 AM Revision 5626: taxonlabel: Renamed accepted_label_id to canon_label_id to allow any taxonlabel to be the canonical taxonlabel for this taxonlabel, whether or not its status is accepted
- 11:01 AM Revision 5625: schemas/filter_ERD.csv: Remove the methodtaxonclass.submethod_id fkey to taxonlabel, to make room in the ERD for additional taxon tables
- 10:52 AM Revision 5624: schemas/vegbien.sql: establishmentmeans_dwc: Corrected source comment
- 10:51 AM Revision 5623: schemas/vegbien.sql: taxonomic_status enum: Added source comment
- 10:49 AM Revision 5622: schemas/vegbien.sql: taxonlabel_relationship: Added relationship, with relationship enum
- 10:21 AM Revision 5621: mappings/VegCore-VegBIEN.csv: Mapped taxonomicStatus
- 10:20 AM Revision 5620: inputs/.TNRS/tnrs/test.xml.ref: Updated inserted row count
- 10:15 AM Revision 5619: mappings/VegCore.csv: Removed duplicate entry for taxonomicStatus, which is also a DwC term
- 10:14 AM Revision 5618: mappings/VegCore.csv: Added taxonomicStatus
- 10:13 AM Revision 5617: schemas/vegbien.sql: taxonlabel: Added taxonstatus, with taxonomic_status enum
- 09:40 AM Revision 5616: schemas/vegbien.sql: taxonlabel.creator_id comment: Removed no longer accurate comment that this is the "according to" and "Name sec. x", which is now stored in concept_reference_id
- 09:37 AM Revision 5615: schemas/vegbien.sql: taxonlabel: Added concept_reference_id, which is the entity that defined the taxon concept (who the taxon label is according to)
- 09:22 AM Revision 5614: schemas/vegbien.ERD.mwb: Moved taxonlabel_relationship to the right of taxonlabel to provide room for taxonlabel to grow
10/17/2012
- 04:27 PM Revision 5613: Regenerated vegbien.ERD exports
- 04:25 PM Revision 5612: mappings/VegCore-VegBIEN.csv: Remapped morphospecies to new taxonlabel.morphospecies per today's conference call
- 04:23 PM Revision 5611: schemas/vegbien.sql: taxonlabel: Added separate morphospecies field per today's conference call, where it was decided it could not go in taxonepithet (the lowest-rank component of the name)
- 04:17 PM Revision 5610: schemas/vegbien.sql: Deleted taxonusage table per today's conference call, where it was decided that it was not needed
- 04:14 PM Revision 5609: schemas/vegbien.sql: Renamed taxonlabel_ancestor to taxonlabel_relationship per today's conference call, where it was decided that it would eventually contain asserted relationships (such as synonym and parent) in addition to autopopulated ancestor relationships
- 04:12 PM Revision 5608: schemas/vegbien.sql: Renamed taxonconcept to taxonlabel per today's conference call, where it was decided that taxonconcept contained too many unrelated fields to be purely a taxon concept
- 04:01 PM Revision 5607: inputs/import.stats.xls: Updated import times
- 04:01 PM Revision 5606: inputs/test_taxonomic_names/_scrub/public.sql, TNRS.sql: Regenerated with schema changes
- 01:47 PM Revision 5605: schemas/vegbien.ERD.mwb: Fixed lines
- 01:45 PM Revision 5604: Regenerated vegbien.ERD exports
- 01:44 PM Revision 5603: schemas/vegbien.sql: taxonconcept_ancestor: Renamed taxonconcept_id to descendant_id to emphasize the direction of the relationship between the two taxonconcepts
- 01:35 PM Revision 5602: schemas/vegbien.ERD.mwb: Added taxonconcept_ancestor to the diagram since it is now a core table for storing taxonomic information
- 01:15 PM Revision 5601: mappings/VegCore-VegBIEN.csv: Mapped accordingTo to taxonconcept.creator_id, and have it take the place of identifiedBy when both are present
- 01:12 PM Revision 5600: mappings/VegCore-VegBIEN.csv: Remapped people's names split apart into name components in party to new party.fullname, which does not require splitting or make assumptions about the number of people who may be listed in a particular name field and which components of their name(s) are present
- 01:02 PM Revision 5599: schemas/vegbien.sql: party: Added fullname
- 12:55 PM Revision 5598: mappings/VegCore.csv: Added accordingTo
- 12:47 PM Revision 5597: inputs/.TNRS/tnrs/map.csv: Mapped Name_matched_url to scientificNameID, since the URL uniquely identifies the matched taxonconcept
- 12:43 PM Revision 5596: schemas/vegbien.sql: taxonconcept: Renamed taxonname to taxonepithet for clarity and to be consistent with TCS's use of "epithet" to denote what the taxonname was intended to be (http://www.tdwg.org/standards/117/download/#/UserGuidev_1.3.pdf)
- 12:18 PM Revision 5595: schemas/vegbien.sql: taxonconcept.creator_id: Documented that this is the concept reference for a taxon concept with an "according to", or the identifier's name for a nominal concept, and is equivalent to "Name sec. x"
- 12:02 PM Task #497 (Resolved): create examples of taxonomic names to test the limits of the new taxonomic schema
- See "*testNames.txt*":https://projects.nceas.ucsb.edu/nceas/attachments/download/377/testNames.txt
- 11:50 AM Revision 5594: sql_io.py: import_csv(): Add a row_num column at the beginning of the table, which is autopopulated by csvs.RowNumFilter (it cannot be autopopulated by the serial datatype, because this does not support COPY FROM with a NULL-equivalent value in the serial field). This fixes a bug in csv2db where rows would not stay in inserted order upon querying the table, and would be returned in a different order each query, which prevented LIMIT/OFFSET based subsetting from returning consistent, nonoverlapping results. This occurs because PostgreSQL unfortunately does not return rows in inserted order (or any stable order: "If sorting is not chosen, the rows will be returned in an unspecified order [which] must not be relied on" <http://www.postgresql.org/docs/8.3/static/queries-order.html>), so an explicit ORDER BY is always needed to ensure staging table rows are retrievable in the order they were inserted.
- 11:43 AM Revision 5593: csvs.py: Added RowNumFilter, which adds a row # column at the beginning of each row
- 11:42 AM Revision 5592: streams.py: LineCountStream, LineCountInputStream: Fixed bug where line_num was 1 too high because it started at 1 *and* was incremented *before* each line is returned. It now properly starts at 1, but the initial line_num value is 0 to increment to 1 upon encountering the first line. This off-by-one behavior may have been needed for code that associates an error message with a line #, but such code should add 1 to the line_num to get the line # of the error *if* the error prevents the next line from being read by the LineCount*Stream.
- 11:04 AM Revision 5591: sql_io.py: import_csv(): Take a reader and header rather than a stream to allow callers to pass in a wrapped CSV reader for filtering, etc.
- 11:00 AM Revision 5590: sql_io.py: append_csv(): Take a reader and header rather than a stream_info and stream to allow callers to use the simpler csvs.reader_and_header() function. This also allows callers to pass in a wrapped CSV reader for filtering, etc.
- 10:44 AM Revision 5589: csv2db, tnrs_db: Removed ProgressInputStream wrapper around input stream, which is no longer needed (and causes overlapping output) now that sql_io.append_csv() prints # rows read
- 10:42 AM Revision 5588: sql_io.py: append_csv(): Wrap input stream in a ProgressInputStream that reports rows (rather than lines) read
- 10:40 AM Revision 5587: csvs.py: InputRewriter: Use new StreamFilter to translate StopIteration EOF to ''
- 10:36 AM Revision 5586: csvs.py: Added StreamFilter
- 10:36 AM Revision 5585: csvs.py: InputRewriter: Also support stream inputs which report EOF as '' instead of StopIteration
- 09:55 AM Revision 5584: sql_io.py: append_csv(): Removed no longer used INSERT mode, since all callers now use the default COPY FROM
- 09:53 AM Revision 5583: sql_io.py: import_csv(): Removed no longer needed manual setting of use_copy_from, which defaults to True in append_csv()
- 09:50 AM Revision 5582: csv2db: Removed no longer needed manual setting of use_copy_from, which defaults to True in sql_io.import_csv()
- 09:49 AM Revision 5581: csv2db: Removed no longer needed separate handling of sql.DatabaseErrors, because all recoverable errors caused by COPY FROM (EncodingException and ragged rows) are now handled or avoided
- 09:46 AM Revision 5580: csv2db: Handle EncodingException separately by changing the connection encoding to LATIN1 and retrying
- 09:45 AM Revision 5579: sql.py: DbConn: Added set_encoding()
- 09:32 AM Revision 5578: sql_io.py: append_csv(): Parse any exceptions generated by the COPY FROM using new sql.parse_exception()
- 09:28 AM Revision 5577: sql.py: run_query(): Factored exception parsing out into new parse_exception()
- 09:22 AM Revision 5576: sql.py: Added EncodingException and parse it in run_query()
- 09:14 AM Revision 5575: sql.py: Removed no longer used NameException
- 09:14 AM Revision 5574: csvs.py: Filter: Added empty close() method to support using it as a stream (such as with streams.ProgressInputStream)
- 09:01 AM Revision 5573: sql_io.py: append_csv(): Don't disable COPY FROM for TSVs, which are now supported using csvs.InputRewriter
- 08:59 AM Revision 5572: sql_io.py: append_csv(): COPY FROM: Wrap provided stream in standardizing stream to fix ragged rows (with unequal # columns) and nonstandard CSV dialects (such as TSV with \-escaped newlines)
- 08:56 AM Revision 5571: csvs.py: Added InputRewriter, which wraps a reader, writing each row back to CSV
- 08:54 AM Revision 5570: csvs.py: Added ColCtFilter, which gives all rows the same # columns
- 07:25 AM Revision 5569: sql_io.py: row_num_col_def: Changed type to integer so the row_num can be populated directly by the insert process
- 07:19 AM Revision 5568: sql_io.py: Added row_num_col_def for use by import_csv(). The row_num column will be necessary again because PostgreSQL unfortunately does not return rows in inserted order (or any stable order: "If sorting is not chosen, the rows will be returned in an unspecified order [which] must not be relied on" <http://www.postgresql.org/docs/8.3/static/queries-order.html>), so an explicit ORDER BY is always needed to ensure staging table rows are retrievable in the order they were inserted.
10/16/2012
- 10:58 PM Revision 5567: mappings/VegCore.csv: Removed unit-ambiguous height. Use height_m, height_ft instead.
- 10:57 PM Revision 5566: mappings/Veg+-VegCore.csv: Added height
- 10:57 PM Revision 5565: mappings/Veg+-VegCore.csv: Added height
- 10:52 PM Revision 5564: mappings/VegCore-VegBIEN.csv: Removed no longer used height mapping. Use height_m, height_ft instead.
- 10:39 PM Revision 5563: README.TXT: Data import: import_all: Added NCBI backbone to note about import_all not immediately returning control to the shell
- 10:30 PM Revision 5562: inputs/FIA/Organism/map.csv: Height: Remapped to height_ft, assuming units based on the range of values, the height of the tallest tree, and location inside the U.S.
- 10:23 PM Revision 5561: inputs/FIA/Organism/test.xml.ref: Accepted new inserted row count
- 10:01 PM Revision 5560: mappings/VegCore-VegBIEN.csv: Mapped height_ft
- 09:58 PM Revision 5559: schemas/functions.sql: Added _ft_to_m()
- 09:52 PM Revision 5558: mappings/VegCore.csv: Added height_ft
- 09:38 PM Revision 5557: inputs/SALVIAS/stems/map.csv: stem_height_m: Remapped to height_m using units from <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>
- 09:37 PM Revision 5556: inputs/SALVIAS-CSV/Organism/map.csv: stem_height_m: Re-sourced units to stem_height_m rather than height_m definition in SALVIAS data dictionary
- 09:29 PM Revision 5555: Regenerated vegbien.ERD exports
- 09:23 PM Revision 5554: schemas/vegbien.sql: taxonconcept: taxonconcept_update_ancestors() trigger: Fixed bug where matched_concept_id needed to be changed to NULL when equal to taxonconcept_id, to avoid including the node itself with its parent's ancestors (which would violate the taxonconcept_ancestor pkey)
- 09:19 PM Revision 5553: sql_io.py: put_table(): Ensuring into's out_pkey is different from in_pkey: Prepend "out." instead of out_table to avoid long column names for the output pkey
- 09:18 PM Revision 5552: sql_gen.py: concat(): Allow multiple "column" suffixes with "." when matching the existing suffix
- 08:47 PM Revision 5551: schemas/vegbien.sql: taxonconcept: taxonconcept_update_ancestors() trigger: Corrected comment explaining why we don't need an ON DELETE trigger to say that this is because the foreign key for *taxonconcept_ancestor.ancestor_id*, not taxonconcept.parent_id, is ON DELETE CASCADE. The auto-deletion will also occur if taxonconcept.parent_id is ON DELETE CASCADE, because taxonconcept_ancestor.taxonconcept_id is ON DELETE CASCADE, but it is not actually necessary to have cascading deletes on taxonconcept.parent_id (and SET NULL may in fact sometimes be more appropriate).
- 08:33 PM Revision 5550: schemas/tree_cross-links.sql: Removed header comments added by pgAdmin
- 08:30 PM Revision 5549: schemas/tree_cross-links.sql: Updated for new taxonconcept_update_ancestors() trigger
- 08:21 PM Revision 5548: schemas/vegbien.sql: taxonconcept: Rewrote taxonconcept() trigger to avoid completely reinserting the taxonconcept_ancestor entries of all descendants every time taxonconcept changes or using trigger recursion to find descendants. Instead, just delete the old parent's ancestors from and add the new parent's ancestors to each descendant, using taxonconcept_ancestor itself (with the new taxonconcept_ancestor_descendants index) to find all descendants. As an additional optimization, only update taxonconcept_ancestor if the parent_id or matched_concept_id has actually changed. This fixes a bug in NCBI where inserting taxonconcepts out of dependency order caused taxonconcept_ancestor entries to be repeatedly regenerated, slowing the import down to a crawl.
- 07:42 PM Revision 5547: schemas/vegbien.sql: taxonconcept: Added taxonconcept_3_parent_id_avoid_self_ref() trigger to avoid recursive references in root taxonconcepts (taxonconcepts with no parent). This will simplify the new taxonconcept_update_ancestors() trigger.
- 06:32 PM Revision 5546: schemas/vegbien.sql: taxonconcept_ancestor: Added taxonconcept_ancestor_descendants index to support looking up all the descendants for a taxonconcept. This will be used by the new taxonconcept_update_ancestors() trigger, which will support inserting taxonconcepts out of dependency order (such as for NCBI).
- 04:35 PM Revision 5545: schemas/vegbien.sql: *_update_ancestors(): Made trigger deferred, so that it would run after all rows have been inserted in a bulk insert, such as during column-based import. This ensures that ancestors lists are not populated until all parents are inserted, which may occur out of order for datasources (such as NCBI) whose nodes are not in dependency order. (A node that newly acquires a parent will have to update all its descendants, which will then be updated again when its parent acquires its own parent.)
- 04:28 PM Revision 5544: lib/PostgreSQL-MySQL.csv: Also filter out constraint triggers in addition to regular triggers
10/15/2012
- 05:37 PM Revision 5543: inputs/Madidi/Organism/map.csv: Total height: Remapped to height_m, assuming units based on the range and precision of values
- 05:33 PM Revision 5542: inputs/VegBank/stemcount/map.csv: stemheight: Remapped to height_m using units from <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemcount&entity=dba_tabledescription&where=where_tablename>
- 05:29 PM Revision 5541: inputs/SALVIAS/plotObservations/map.csv, inputs/SALVIAS-CSV/Organism/map.csv: height_m, stem_height_m: Remapped to height_m using units from <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>
- 05:24 PM Revision 5540: mappings/VegCore-VegBIEN.csv: Mapped height_m
- 05:15 PM Revision 5539: mappings/VegCore.csv: Added height_m
- 04:20 PM Revision 5538: mappings/VegCore.csv, VegCore-VegBIEN.csv: Removed no longer used and unit-ambiguous organismX, organismY. Use organismX_m, organismY_m instead.
- 04:18 PM Revision 5537: inputs/VegBank/stemlocation/map.csv: stemxposition, stemyposition: Remapped to organismX_m/organismY_m using units from <http://vegbank.org/vegbank/views/dba_tabledescription_detail.jsp?view=detail&wparam=stemlocation&entity=dba_tabledescription&where=where_tablename>
- 04:06 PM Revision 5536: inputs/TEAM/*/map.csv: 1ha Plot X Coordinate, 1ha Plot Y Coordinate: Remapped to organismX_m/organismY_m using units from <https://projects.nceas.ucsb.edu/nceas/projects/bien/repository/raw/inputs/TEAM/_src/TEAM-DataPackage-20120920191251_3859/Vegetation+-+Trees+&+Lianas/Vegetation-Tree-and-Liana-Metadata-1.5.pdf>
- 03:59 PM Revision 5535: inputs/SALVIAS/plotObservations/map.csv, inputs/SALVIAS-CSV/Organism/map.csv: x_position, y_position: Remapped to organismX_m/organismY_m using units from <http://salvias.net/Documents/salvias_data_dictionary.html#Plot+data>
- 03:51 PM Revision 5534: inputs/Madidi/Organism/map.csv: Subplot X, Subplot Y: Remapped to organismX_m/organismY_m, assuming units based on the size of values relative to the plot area, which has units of ha
- 03:44 PM Revision 5533: inputs/CTFS/StemObservation/map.csv: x, y: Remapped to organismX_m/organismY_m, assuming units based on the size of values relative to plot area, which has units of ha
- 03:30 PM Revision 5532: mappings/VegCore-VegBIEN.csv: Mapped organismX_m, organismY_m
- 03:29 PM Revision 5531: mappings/VegCore.csv: Added organismX_m, organismY_m
- 03:23 PM Revision 5530: sql_io.py: put_table(): full_in_table: Create it using new sql.copy_table() instead of sql.run_query_into()
- 03:23 PM Revision 5529: sql.py: Added copy_table()
- 03:14 PM Revision 5528: sql.mk_select() calls: Removed no longer needed order_by=None when limit=0
- 03:11 PM Revision 5527: sql.py: mk_select(): Set order_by to None if limit == 0
- 03:09 PM Revision 5526: inputs/.TNRS/schema.sql: Documented that accepted names must be processed before any names that resolve to them, because the entry for the accepted name contains all the ranks parsed out but the resolved name of another entry contains just some ranks and the taxonomic name. Column-based import will do this automatically when the total # of rows is <= the partition_size (because _taxonconcept_set_matched_concept_id()'s accepted taxonconcept is created after the main taxonconcept), but TNRS has more rows than this so sorting is needed to ensure that all the accepted names are processed in the first partitions.
- 02:52 PM Revision 5525: sql.py: table_order_by(): Cache the order_by in table.order_by and propagate it when a LIKE table is created
- 02:51 PM Revision 5524: sql_gen.py: Table: Added order_by attr to cache the results of table_order_by()
- 02:36 PM Revision 5523: sql.select() calls: Removed order_by=None everywhere that a stable row order is required (i.e. consistent between selects, or consistent between table transformations). This causes several tests to return different inserted row counts, because the input table is now being accessed in pkey order instead of in table order. This fixes a bug where tables with more rows than ~100 would return different results for repeated calls of the same non-ordered select.
- 02:27 PM Revision 5522: sql.py: mk_select(): Use table_order_by() instead of table_pkey_col() to determine what column(s) to order by if order_by is set to order_by_pkey
- 02:26 PM Revision 5521: sql.py: Added table_pkey_index(), index_order_by(), table_cluster_on(), table_order_by()
- 01:10 PM Revision 5520: sql.py: Added index_exprs() and use it in index_cols()
- 01:08 PM Revision 5519: README.TXT: Data import: On local machine: Added `make inputs/.TNRS/cleanup`, which is necessary because the PostgreSQL collation may differ between vegbiendev's and your DB
- 12:24 PM Revision 5518: schemas/vegbien.sql: taxonconcept: taxonconcept_update_ancestors(): Use matched_concept_id's ancestors instead if available. (Recursively applied, this will use the ancestors of the accepted concept.) This facilitates finding all children of and matches to an accepted concept, which will all have an entry for that concept in taxonconcept_ancestor. Note that the concept's own parents will not be indexed in taxonconcept_ancestor, because only accepted ancestors are now stored in taxonconcept_ancestor. Documented that taxonconcept_ancestor now stores the *accepted* ancestors of a taxonconcept.
- 12:14 PM Revision 5517: schemas/vegbien.sql: taxonconcept: taxonconcept_2_propagate_accepted_concept_id(): Also update accepted_concept_id on concepts that resolve to this concept, which may have been created before this concept was marked as accepted if concepts are not imported in dependency order (accepted concepts first). Added index on matched_concept_id to speed up finding concepts that resolve to this concept.
- 12:10 PM Revision 5516: sql.py: mk_select(): order_by is order_by_pkey: Only order by the table's actual pkey, if it has one, rather than using the first column if it doesn't
- 12:08 PM Revision 5515: inputs/.TNRS/tnrs/test.xml.ref: Updated inserted row count
- 10:21 AM Revision 5514: db_xml.py: partition_size: Increased to 1,000,000 (>= NCBI.higher_taxa's size) so NCBI.higher_taxa can be imported completely in one partition. This is necessary because NCBI's taxonconcepts are not in dependency order (parents first), so a later partition cannot rely on the parents of its taxonconcepts having already been imported. Instead, all taxonconcepts must be imported at once and then separately, the parents of all taxonconcepts must be set.
- 10:08 AM Revision 5513: mappings/VegCore-VegBIEN.csv: taxonconcept.parent_id when explicit parent provided: Set taxonconcept.parent_id using new _taxonconcept_set_parent_id() *after* creating the child taxonconcept, so that the parent_id will point to the already-inserted parent taxonconcept instead of creating a new, empty parent taxonconcept. This creates a two-step import, where first the taxonconcepts are imported, and then the parent_ids are matched up. This is necessary for column-based import because all the parent taxonconcepts are imported in a separate iteration from the child taxonconcepts with only their sourceaccessioncode, so this iteration must occur after the child taxonconcept iteration in order to match up with fully-populated taxonconcepts. Row-based import, on the other hand, does not require _taxonconcept_set_parent_id() but does require the taxonconcepts to be provided in dependency order (parents first), which is unfortunately not the case for NCBI.
- 09:57 AM Revision 5512: schemas/vegbien.sql: *_update_ancestors(): Telling immediate children to update their ancestors lists: Exclude self to avoid infinite recursion
- 09:57 AM Revision 5511: schemas/vegbien.sql: *_update_ancestors(): Telling immediate children to update their ancestors lists: Exclude self to avoid infinite recursion
- 09:41 AM Revision 5510: schemas/vegbien.sql: Added _taxonconcept_set_parent_id()
- 09:37 AM Revision 5509: schemas/vegbien.sql: Renamed _set_matched_taxonconcept() to _taxonconcept_set_matched_concept_id() so that the function name is prefixed with the table it applies to
- 09:35 AM Revision 5508: db_xml.py: put(): Treat a child node which is a function (starts with _) as a child with fkey to parent rather than as a field in the table. Such a function accepts the table's pkey as one of its arguments.
- 09:05 AM Revision 5507: sql_gen.py: map_expr(): Don't replace an unquoted name when followed by ",", as it would be in an into table name for a function with multiple arguments (e.g. family in "_join_words(1=Field family, 2=Field name)")
- 08:49 AM Revision 5506: schemas/vegbien.sql: locationevent: Moved obsstartdate, obsenddate to top of table so they would be visible in the ERD
- 08:45 AM Revision 5505: sql_io.py: put_table(): ensure_cond(): track_data_error(): Concatenate the columns in the constraint together using , rather than adding a separate entry for each column, because the constraint is applicable to all columns together rather than to each column separately
- 08:26 AM Revision 5504: sql_io.py: put_table(): Renamed ignore_cond() to ensure_cond() for clarity
- 08:22 AM Revision 5503: import_all: Also import the NCBI tree of life, before the TNRS names
- 08:17 AM Revision 5502: mappings/VegCore-VegBIEN.csv: Also map acceptedFamily to the corresponding NCBI family
- 08:07 AM Revision 5501: lib/PostgreSQL-MySQL.csv: custom types: Also exclude time. Reordered excluded (built-in) types by name.
- 07:57 AM Revision 5500: inputs/import.stats.xls: Updated import times
- 07:50 AM Revision 5499: schemas/vegbien.sql: Changed `timestamp with time zone` fields to `date` because time information is not stored in these fields, and it's confusing to have an arbitrary timezone (the server's timezone) and an arbitrary time (midnight) set for input data that only has a precision to the nearest day
- 07:43 AM Revision 5498: sql_gen.py: null_sentinels: Added entry for date
- 07:40 AM Revision 5497: lib/PostgreSQL-MySQL.csv: custom types: Also exclude date, datetime
- 07:11 AM Revision 5496: README.TXT: Documentation: To import and scrub just the test taxonomic names: Run `make backups/TNRS.backup/restore` in the background because it takes awhile
- 06:45 AM Revision 5495: mappings/VegCore.csv: Re-sourced TaxonomicRankEnum fields to the official TCS schema rather than the TCS version in VegX
- 06:42 AM Revision 5494: schemas/vegbien.sql: taxonrank: Updated source to the TCS schema (rather than VegBank) for the new, expanded list. Note that although the list itself was compiled from the TCS version in VegX, the official TCS download does not differ from the VegX TCS in the TaxonomicRankEnum fields (the xs: namespace has just been replaced with xsd: by VegX).
10/12/2012
- 05:21 PM Revision 5493: schemas/vegbien.sql: analytical_db_view: taxonconcept: Join again on the accepted_concept_id in order to use the accepted taxonconcept rather than the verbatim taxonconcept from the datasource
- 05:14 PM Revision 5492: schemas/: svn:ignore log files
- 05:11 PM Revision 5491: Added inputs/.NCBI/. This uses many of the new schema and mappings features, such as taxonconcept.sourceaccessioncode and parentTaxonID
- 05:07 PM Revision 5490: mappings/VegCore-VegBIEN.csv: identifyingtaxonomicname: Don't create if taxonconcept has an explicit parent, because the taxonName (which is generally only a component of the full taxonomic name, e.g. specificEpithet) is not globally unique. Datasources that provide name components in such a way that levels at or below family can't be directly concatenated cannot currently receive an identifyingtaxonomicname for input to TNRS.
- 04:54 PM Revision 5489: mappings/VegCore-VegBIEN.csv: taxonName->identifyingtaxonomicname: Don't include the rank with the taxonName, because TNRS only allows the rank to be included in the taxonomic name if it's infraspecific (otherwise, it returns no or an invalid match due to the presence of what it sees as an invalid term or a name component)
- 04:48 PM Revision 5488: mappings/VegCore-VegBIEN.csv: Mapped taxonName to the TNRS input taxonconcept's identifyingtaxonomicname
- 04:28 PM Revision 5487: mappings/VegCore-VegBIEN.csv: Only forward taxonRank to the parent taxonconcept (which stores the infraspecific taxonconcept when the infraspecificEpithet is provided) if there is no explicit parent provided via parentTaxonID/etc.
- 04:09 PM Revision 5486: mappings/VegCore-VegBIEN.csv: Mapped parentScientificNameID, parentTaxonConceptID, parentTaxonID
- 04:03 PM Revision 5485: mappings/VegCore.csv: Added parentScientificNameID, parentTaxonConceptID, parentTaxonID
- 03:53 PM Revision 5484: input.Makefile: $(inDatasrc): Also include the vegbien_dest $schemas in the search_path, so that the datasource's SQL scripts (create.sql, etc.) can use VegBIEN functions and types
- 03:44 PM Revision 5483: lib/common.Makefile: Added $(comma)
- 02:41 PM Revision 5482: inputs/test_taxonomic_names/_scrub/public.sql: Regenerated with schema changes
- 02:38 PM Revision 5481: input.Makefile: Maps building: %/.map.csv.last_cleanup: Fixed bug where needed to include $(coreMap) as a prerequisite, because even though it is not used directly in this target's recipe, it is used by targets invoked via recursive make after the main recipe runs. In general, whenever targets forward commands to a recursive make target, they also need to forward those recursive targets' prerequisites by including them in their own prerequisites list.
- 02:29 PM Revision 5480: mappings/VegCore-VegBIEN.csv: Mapped taxonConceptID, taxonID, scientificNameID to taxonconcept.sourceaccessioncode. Note that taxonconcept stores all of these taxonomic entities, using creator_id+creationdate, taxonname+rank+parent_id, and identifyingtaxonomicname, respectively.
- 02:28 PM Revision 5479: mappings/VegCore-VegBIEN.csv: Mapped taxonConceptID, taxonID, scientificNameID to taxonconcept.sourceaccessioncode. Note that taxonconcept stores all of these taxonomic entities, using creator_id+creationdate, taxonname+rank+parent_id, and identifyingtaxonomicname, respectively.
- 02:13 PM Revision 5478: mappings/VegCore-VegBIEN.csv: Mapped taxonName
- 02:11 PM Revision 5477: mappings/VegCore.csv: Added taxonName
- 02:05 PM Revision 5476: schemas/vegbien.ERD.mwb: Fixed lines
- 01:55 PM Revision 5475: schemas/vegbien.sql: Copied functions in the functions schema that are also used by the public schema to the public schema, so that reinstalling the functions schema would not cause anything that depends on a function in it to be cascadingly deleted. Currently, this just affects analytical_db_view, which uses _fraction_to_percent().
- 01:44 PM Revision 5474: inputs/test_taxonomic_names/_scrub/public.sql: Regenerated with schema changes
- 01:36 PM Revision 5473: schemas/vegbien.sql: taxonconcept: Added taxonconcept_2_propagate_accepted_concept_id() trigger to auto-populate the accepted_concept_id
- 12:53 PM Revision 5472: schemas/vegbien.sql: taxonconcept.sourceaccessioncode: Added descriptive comment
- 12:53 PM Revision 5471: schemas/vegbien.sql: taxonconcept.accepted_concept_id: Added descriptive comment
- 12:48 PM Revision 5470: Regenerated vegbien.ERD exports
- 12:47 PM Revision 5469: schemas/vegbien.sql: taxonconcept: Added sourceaccessioncode, and allow it to scope the taxonconcept when provided
- 12:33 PM Revision 5468: inputs/test_taxonomic_names/_scrub/public.sql: Regenerated with schema changes
- 12:29 PM Revision 5467: schemas/vegbien.sql: taxonconcept: Renamed canon_concept_id to matched_concept_id, because this is actually the closest-match taxonconcept in the match hierarchy (datasource concept -> parsed concept -> matched concept -> accepted concept) rather than the accepted synonym, which goes in accepted_concept_id
- 05:51 AM Revision 5466: Regenerated vegbien.ERD exports
- 05:47 AM Revision 5465: schemas/vegbien.sql: taxonconcept: Renamed canon_concept_id to matched_concept_id, because this is actually the closest-match taxonconcept in the match hierarchy (datasource concept -> parsed concept -> matched concept -> accepted concept) rather than the accepted synonym, which goes in accepted_concept_id
- 05:34 AM Revision 5464: schemas/vegbien.sql: taxonconcept: Added accepted_concept_id
- 05:27 AM Revision 5463: schemas/vegbien.sql: taxonconcept.canon_concept_id: comment: Changed "accepted synonym" to "closest match", since canon_concept_id is actually a hierarchy from datasource concept -> parsed concept -> matched concept -> accepted concept
- 05:22 AM Revision 5462: schemas/vegbien.sql: taxonconcept: Added order # to trigger names so they run in a defined order (triggers are run in alphabetical order)
- 05:01 AM Task #498 (Resolved): add definitions to columns in "green tables"
- Definitions have been added on all new tables (currently taxonconcept and taxonconcept_ancestor). Other tables' colum...
- 04:56 AM Task #462 (Resolved): name backups according to svn revision instead of or in addition to the date
- This now happens for backups as well as log files
- 04:53 AM Revision 5461: README.TXT: Use new revision # in log filenames to get all the logs for an import. Changed <datetime> to <version> because the rotated public schema now also includes the svn revision.
- 04:44 AM Revision 5460: lib/common.Makefile: $(version): Include both the svn revision when make was started as well as the svn revision when the command is actually run (when these values differ), in case svn was updated between the time an import was started and the time a particular table started being imported. Because tables within a datasource are imported sequentially, it is possible that an update would have happened before the last table started importing.
- 04:23 AM Revision 5459: Makefile: Moved setting of $(root) before include of lib/common.Makefile because it's used by lib/common.Makefile
- 04:21 AM Revision 5458: Factored OS section out from Makefile, input.Makefile into lib/common.Makefile
- 04:13 AM Revision 5457: Makefile, input.Makefile: Use new $(version), which unlike $(date) also includes the svn revision, to version log files, etc. This way, the working copy can be put back to the way it was at the time of a given import (excluding changes to nonversioned files). This also makes it easier to get all the log files for a particular import when different tables' imports started at different times.
- 04:08 AM Revision 5456: Makefile: Added $(root) for use with $(rootRevision)
- 04:08 AM Revision 5455: lib/common.Makefile: Added $(version), to replace $(date) for versioning log files, etc., and helper function $(rootRevision)
- 04:07 AM Revision 5454: lib/common.Makefile: Added $(revision)
- 04:04 AM Revision 5453: input.Makefile: Removed no longer used $(SED)
- 04:03 AM Revision 5452: lib/common.Makefile: Added $(sed)
- 03:58 AM Revision 5451: Factored $(date) out from Makefile, input.Makefile into lib/common.Makefile
- 03:18 AM Revision 5450: sql_io.py: put_table(): DuplicateKeyException: Fixed bug where indexes with conditions needed to have the input rows filtered by the condition, to prevent trying to retrieve an existing/inserted row using a join on the index columns when the index in fact does not apply. This fixes a bug in the import of taxonconcept where the taxonconcept_0_unique_identifying_name unique index has a condition which was not satisfied for input rows with no identifyingtaxonomicname, causing any input row with NULL in this column to match *all* taxonconcepts with a NULL identifyingtaxonomicname. This uses ignore_cond()'s new support for constraints that did not fail at least once.
- 03:12 AM Revision 5449: sql_io.py: put_table(): ignore_cond(): Added support for constraints that did not fail at least once, and therefore should not be required to simplify to a non-false value. As part of this, only track the failed constraint in the errors table if it actually failed at least once based on the deleted row count or the `failed` param.
- 03:05 AM Revision 5448: sql_gen.py: map_expr(): Fixed bug where names were being replaced when they were inside another name. This occurred with combined names created by sql_io.into_table_name().
- 01:11 AM Revision 5447: sql.py: ConstraintException: message: Wrap condition in strings.as_tt()
- 01:06 AM Task #522 (New): fix deadlock when multiple testers are running simultaneously
- Commands running simultaneously:
* @make inputs/.TNRS/tnrs/test.by_col.xml verbosity=3@
* @make test by_col=1@
... - 12:30 AM Revision 5446: sql.py: run_query(): DuplicateKeyException: Also retrieve the index's condition using new index_cond()
- 12:28 AM Revision 5445: sql.py: Added index_cond()
- 12:11 AM Revision 5444: sql_io.py: put_table(): insert_into_pkeys(): Take a query as the param instead of sql.mk_select()'s params, to allow the caller to pass in any query without needing insert_into_pkeys() to manually pass through those args
10/11/2012
- 11:40 PM Revision 5443: sql.py: constraint_cond(): Fixed NotImplementedError message to apply to this function
- 09:53 PM Task #521 (Resolved): make place* tables use a structure similar to taxonconcept
- 09:36 PM Revision 5442: sql_io.py: put_table(): ignore_cond(): Log message: Replaced don't with do not so it wouldn't mess up syntax highlighting when viewing the log file in a text editor
- 09:07 PM Revision 5441: input.Makefile: Staging tables installation: Don't delete %/header.csv on error, because header.csv is a byproduct rather than the primary output and is created roughly atomically
- 08:40 PM Revision 5440: schemas/vegbien.sql: *_ancestor tables: Added descriptive comment that these are ancestor cross link tables
- 08:23 PM Revision 5439: csvs.py: sniff(): Support multi-char delims using \t, such as \t|\t used by NCBI. Support custom line suffixes, such as \t| used by NCBI.
- 08:18 PM Revision 5438: csvs.py: TsvReader.next(): Remove only the autodetected line ending instead of any standard line ending. Note that this requires all header override files to use the same line ending as the CSV they override, which is now the case.
- 08:15 PM Revision 5437: csvs.py: is_tsv(): Support multi-char delimiters by checking only the first char of the delimiter
- 08:12 PM Revision 5436: csvs.py: sniff(): Also autodetect the line ending
- 08:11 PM Revision 5435: csvs.py: sniff(): Also autodetect the line ending
- 08:02 PM Revision 5434: inputs/test_taxonomic_names/Taxon/+header.txt: Changed line endings to \r\n to match testNames.txt line endings. This will be necessary when the line ending is autodetected by csvs.sniff().
- 07:59 PM Revision 5433: csvs.py: TsvReader.next(): Renamed raw_contents var to line, since this is just the line with the ending removed
- 07:36 PM Revision 5432: strings.py: Replaced no longer used contains_any() with find_any(), which returns any found substring, or None if none of the substrings were found
- 07:22 PM Revision 5431: csvs.py: Modify csv.Dialect._validate() to ignore "delimiter must be a 1-character string" errors, in order to support multi-char delimiters used by TsvReader
- 07:21 PM Revision 5430: csvs.py: Modify csv.Dialect._validate() to ignore "delimiter must be a 1-character string" errors, in order to support multi-char delimiters used by TsvReader
- 06:58 PM Revision 5429: csvs.py: TsvReader: Use str.split() instead of csv.reader().next() to parse the row, for efficiency and to support multi-char delimiters. This is possible because the TSV dialect doesn't use CSV parsing features other than the delimiter and newline-escaping (which is handled separately).
- 06:02 PM Revision 5428: Regenerated vegbien.ERD exports
10/10/2012
- 11:43 AM Revision 5427: input.Makefile: $(exts): Added .dmp
- 11:43 AM Revision 5426: csvs.py: delims: Added |
- 11:28 AM Revision 5425: Removed no longer used inputs/.public/. Use inputs/.TNRS/ and inputs/.TNRS/tnrs/tnrs.make instead.
- 11:23 AM Revision 5424: README.TXT: Documentation: To import and scrub just the test taxonomic names: Added steps to restore the original DB when the test scrub is complete
- 11:22 AM Revision 5423: inputs/test_taxonomic_names/test_scrub: Also export the results to inputs/test_taxonomic_names/_scrub/
- 11:06 AM Revision 5422: inputs/test_taxonomic_names/test_scrub: Use regular for .. in loop with a list of what's being processed in each iteration (match_input_names, parse_accepted_names)
- 10:58 AM Revision 5421: inputs/.TNRS/tnrs/map.csv: Mapped Genus_score, Specific_epithet_score
- 10:56 AM Revision 5420: mappings/VegCore-VegBIEN.csv: Mapped matchedGenusFit_fraction, matchedSpeciesFit_fraction. Reordered canon_concept_fit_fraction _maxs in the order they would be used if _alt were being used instead.
- 10:52 AM Revision 5419: mappings/VegCore.csv: Added matchedSpeciesFit_fraction
- 10:47 AM Revision 5418: mappings/VegCore.csv: matchedFamilyFit_fraction: Source the "matched" to Family_matched, which is a closer fit than Name_matched. matchedGenusFit_fraction: Fixed Genus_matched source to use #detailed_download instead of #simple_download.
- 10:42 AM Revision 5417: mappings/VegCore.csv: Added matchedGenusFit_fraction
- 10:18 AM Revision 5416: README.TXT: Removed extra trailing whitespace
- 10:18 AM Revision 5415: README.TXT: Documentation: To import and scrub just the test taxonomic names: Use new inputs/test_taxonomic_names/test_scrub
- 10:17 AM Revision 5414: Added inputs/test_taxonomic_names/test_scrub
- 10:01 AM Revision 5413: schemas/vegbien.sql: taxonconcept: Renamed canon_taxonconcept_id to canon_concept_id to shorten the name, which is used often
- 09:45 AM Revision 5412: schemas/vegbien.sql: taxonconcept: Added taxonconcept_canon_concept_min_fit() trigger to remove the canon_concept_id link from insufficient matches. These occur when e.g. a name in another language is approximated to a latin name or when the input name is not a proper taxon but TNRS provides a best-guess match anyway.
- 09:42 AM Revision 5411: inputs/.TNRS/tnrs/map.csv: Mapped Family_score to new matchedFamilyFit_fraction
- 09:39 AM Revision 5410: mappings/VegCore-VegBIEN.csv: Use matchedFamilyFit_fraction as canon_concept_fit_fraction when greater than matchedTaxonFit_fraction, because if there is at least a matched family, there is a valid taxonconcept to attach to
- 09:39 AM Revision 5409: xml_func.py: Simplifying functions: Added _min, _max as passthroughs
- 09:34 AM Revision 5408: schemas/functions.sql: Added _max(), _min()
- 09:21 AM Revision 5407: mappings/VegCore.csv: Added matchedFamilyFit_fraction
- 09:04 AM Revision 5406: mappings/VegCore-VegBIEN.csv: Remapped matchedTaxonFit_fraction to the verbatim* taxonconcept, because this is actually for the verbatim* concept's fit to the matched concept, not the matched concept's fit to the accepted concept
- 08:59 AM Revision 5405: inputs/.TNRS/tnrs/map.csv: Restored *-prefixed output terms for unmapped terms that had initially been mapped to OMIT but could reasonably match to something in the future. Continue mapping Name_number to OMIT because it isn't globally unique (it identifies the name only within one TNRS batch).
- 08:45 AM Revision 5404: inputs/.TNRS/tnrs/map.csv: Mapped Overall_score to new matchedTaxonFit_fraction
- 08:44 AM Revision 5403: mappings/VegCore-VegBIEN.csv: Mapped matchedTaxonFit_fraction to _set_canon_taxonconcept(canon_concept_fit_fraction)
- 08:37 AM Revision 5402: mappings/VegCore.csv: Added matchedTaxonFit_fraction
- 08:20 AM Revision 5401: schemas/vegbien.sql: _set_canon_taxonconcept(): Also set the canon_concept_fit_fraction
- 08:10 AM Revision 5400: schemas/vegbien.sql: taxonconcept: Added canon_concept_fit_fraction to store the closeness of fit of the canon_concept
- 07:55 AM Revision 5399: schemas/vegbien.sql: taxonconcept: Renamed canon_taxonconcept_id to canon_concept_id to shorten the name, which is used often
- 07:10 AM Revision 5398: sql.py: mk_update(): in_place: Convert columns of type character varying to text so that they can be merge-joined with text columns. Note that these two types are equivalent but not aliases of one another, so the explicit type change is needed.
- 07:07 AM Revision 5397: sql_gen.py: Added canon_type()
- 06:52 AM Revision 5396: sql.py: mk_update(): in_place: Factored retrieval of column type out into separate statement for clarity
- 06:27 AM Revision 5395: schemas/functions.sql: _join*(): Fixed bug where was returning '' instead of NULL when only NULL inputs were provided, because array_to_string() always returns a non-NULL string. Functions must always return NULL in place of '' to ensure that empty strings do not find their way into VegBIEN, and to prevent inconsistencies between row-based and column-based import (row-based import folds empty strings to NULL while column-based import relies on having a clean input table).
- 06:10 AM Revision 5394: sql_io.py: cleanup_table(): Use sql.table_pkey_col() instead of sql.pkey_col() so that only an actual pkey column is removed from the list of columns to clean. This fixes a bug where the first column in the table was not cleaned up if there was no pkey. Note that this bug only affected newly re-created staging tables, because staging tables previously had a special row_num pkey column added if they did not already have a pkey. The row_num column is now added by column-based import instead.
- 05:51 AM Revision 5393: sql.py: table_pkey_col(): Raise a DoesNotExistException if the table has no pkey
- 05:23 AM Revision 5392: sql.py: pkey_col(): Call table_pkey_col() directly rather than via pkey_name(). pkey_name(): Call pkey_col() instead of table_pkey_col() now that pkey_col() calls table_pkey_col().
- 05:14 AM Revision 5391: sql.py: pkey_col(): Documented that if there is no pkey, returns the first column in the table
- 05:13 AM Revision 5390: sql.py: pkey_col(): Specify recover directly as a kw_arg because it's the only kw_arg passed to pkey_name()
- 05:10 AM Revision 5389: sql.py: Added table_pkey_col() and use it in pkey_name()
- 05:01 AM Revision 5388: sql.py: Renamed pkey() to pkey_name()
- 04:45 AM Revision 5387: sql.py: Renamed pkey_col_() to pkey_col()
- 04:43 AM Revision 5386: sql.py: Removed no longer used pkey_col
- 04:43 AM Revision 5385: db_xml.py: cleanup_table(): Inline sql.pkey_col ('row_num') because this is the only place it's used
- 04:37 AM Revision 5384: cleanup_table(): Use new sql.table_cols() instead of sql.table_col_names()
- 04:36 AM Revision 5383: sql.py: Added table_cols()
- 04:16 AM Revision 5382: db_xml.py: put(): Fixed bug where needed to avoid truncating the pkeys_loc table, in case it's the same as one of the in_tables. This occurs now that sql_io.put_table() passes through the actual input column instead of the joined-together input table's column when ignoring all rows.
- 03:33 AM Revision 5381: sql_io.py: put_table(): Resolving default value column: If ignoring all rows, use input cols directly instead of cols from joined-together input table. In addition to being simpler, this prevents the returned column's name from growing longer and longer as each iteration prepends its input table table name to the default value column name.
- 03:07 AM Revision 5380: sql_io.py: put_table(): Moved changing the table of the default value column from Resolving the default value column to Setting pkeys of missing rows, because the table change is only needed in this section
- 03:04 AM Revision 5379: sql_io.py: put_table(): Resolving default value column: Always call sql_gen.remove_col_rename() because it will just pass the value through if it's not a column
- 02:41 AM Revision 5378: sql_gen.py: simplify_parens(): Removed extra simplify_parens() at end because it is done in the final iteration that performs no other replacements, so it is not necessary to also do it explicitly
- 02:30 AM Revision 5377: sql_io.py: put_table(): Replaced limit_ref integer with ignore_all_ref boolean, because it is no longer used as a select statement limit
- 02:29 AM Revision 5376: sql_io.py: put_table(): remove_all_rows(): Corrected "just create an empty pkeys table" comment to "just return the default value column"
- 02:27 AM Revision 5375: sql_io.py: put_table(): mk_main_select(): Removed setting limit to limit_ref[0], because an empty pkeys table is no longer created when ignoring all rows
- 02:19 AM Revision 5374: sql_io.py: put_table(): Setting pkeys of missing rows: Removed "limit_ref[0] == 0" check because this code is never reached in that case
- 02:16 AM Revision 5373: sql_io.py: put_table(): Ignoring all rows for unrecoverable errors: Even in multi-row mode, just return whatever the default value or column was, instead of creating an output table containing the default value filled in for every row. This also assists the optimization to skip empty levels of taxonconcepts, because it folds the empty level to that level's parent level rather than creating a whole new temp table with ultimately the same contents.
- 01:57 AM Revision 5372: sql_gen.py: not_false_re, not_true_re: Appended \b to ensure that true/false is only matched as a single word
- 01:56 AM Revision 5371: sql_gen.py: simplify_expr(): Also simplify "NOT false" to true
- 01:53 AM Revision 5370: sql_gen.py: simplify_expr(): Also simplify "NOT true" to false
- 01:24 AM Revision 5369: sql_io.py: put_table(): ignore_cond(): Changed "Ignoring rows where" message with the negated (filter-out) condition to "Ignoring rows that don't satisfy" with the filter condition for clarity
- 01:22 AM Revision 5368: sql_io.py: put_table(): ignore_cond(): If cond simplifies to false, remove all rows instead of filtering out individual rows which will all be filtered out. This optimization should improve import times of tables, such as taxonconcept, which use a check constraint instead of NOT NULL constraints to prevent empty rows. The taxonomic schema refactoring caused the creation of many more levels of taxonconcepts, many of which (such as variety, forma, cultivar) are empty for most datasources, so this optimization should also reduce overall import times for datasources that have any empty levels of taxonconcept. Note that this optimization is only possible now that sql_gen.simplify_expr() is able to simplify all the way to a single boolean value for the taxonconcept_required_key constraint.
- 12:55 AM Revision 5367: Moved expression transforming functions from sql.py to sql_gen.py because they do not manipulate an actual database and merely generate SQL
- 12:38 AM Revision 5366: sql.py: Added true_expr, false_expr and use them where their values are used
- 12:34 AM Revision 5365: sql.py: simplify_expr(): Also simplify "AND true" expressions
- 12:30 AM Revision 5364: sql.py: simplify_expr(): Also simplify "AND false" expressions
- 12:19 AM Revision 5363: sql.py: Added atom_re and use it in simplify_parens()
- 12:19 AM Revision 5362: sql.py: Added or_re and use it in simplify_expr()
- 12:18 AM Revision 5361: sql.py: logic_op_re(): Added expr_re param for an expr on the other side of the operator
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