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From 11/29/2013 to 12/28/2013

12/20/2013

10:45 PM Revision 11939: fix: planning/timeline/timeline.xls: realigned legend
Aaron Marcuse-Kubitza
10:44 PM Revision 11938: planning/timeline/timeline.xls: hid previous weeks
Aaron Marcuse-Kubitza
10:43 PM Revision 11937: planning/timeline/timeline.xls: crossed out and hid completed tasks
Aaron Marcuse-Kubitza
10:41 PM Revision 11936: planning/timeline/timeline.xls: updated for progress
Aaron Marcuse-Kubitza
05:41 PM Revision 11935: web/links/index.htm: updated to Firefox bookmarks. open-sourcing BIEN: added links for VegBank's license (GPLv2), and how these terms apply to us (a diff of our changes is not GPL-ed under GPLv2, although it is claimed to be GPL-ed under GPLv3)
Aaron Marcuse-Kubitza
04:41 PM Revision 11934: inputs/VegBank/^taxon_observation.**.sample/create.sql, map.csv: added new project columns
Aaron Marcuse-Kubitza
04:31 PM Revision 11933: inputs/VegBank/taxon_observation.**/postprocess.sql: added the project table
Aaron Marcuse-Kubitza
04:25 PM Revision 11932: mapped inputs/VegBank/project/, which includes the projectName for attribution
Aaron Marcuse-Kubitza
02:56 PM Revision 11931: inputs/CVS/^taxon_observation.**.sample/create.sql, map.csv: added new project columns
Aaron Marcuse-Kubitza
02:44 PM Revision 11930: inputs/CVS/taxon_observation.**/postprocess.sql: added the project table
Aaron Marcuse-Kubitza
02:42 PM Revision 11929: inputs/CVS/project/map.csv: mapped stopDate->projectEndDate
Aaron Marcuse-Kubitza
02:35 PM Revision 11928: mapped inputs/CVS/project/, which includes the projectName for attribution
Aaron Marcuse-Kubitza
01:25 AM Revision 11927: inputs/VegBIEN/Redmine/svn/.htaccess: updated to use *much* faster direct repository URL rather than Redmine web interface, now that the repository itself is publicly accessible in addition to the Redmine view of it
Aaron Marcuse-Kubitza
01:18 AM Revision 11926: planning/timeline/timeline.xls: updated for progress
Aaron Marcuse-Kubitza
01:13 AM Revision 11925: planning/timeline/timeline.2013.xls: renamed to timeline.xls so that this can continue to be used for 2014 (leaving a symlink from the old filename to preserve permalinks)
Aaron Marcuse-Kubitza
12:28 AM Revision 11924: fix: inputs/TEX/Specimen*/map.csv, postprocess.sql: habitat: also placed in occurrenceRemarks so that this field gets parsed for growth form information, as requested by Brad (wiki.vegpath.org/TEX_validation#2013-2-26)
Aaron Marcuse-Kubitza

12/19/2013

11:49 PM Revision 11923: fix: inputs/TEX/Specimen*/map.csv: mapped constant values for specimenHolderInstitutions, country. these have to be added with `rm=1 ./inputs/TEX/Specimen.../run postprocess`.
Aaron Marcuse-Kubitza
11:42 PM Revision 11922: bugfix: inputs/TEX/Specimen2/map.csv: mapped BARCODE to accessionNumber so that we have a unique ID for each row
Aaron Marcuse-Kubitza
11:11 PM Revision 11921: schemas/vegbien.sql: analytical_stem_view: scientificName_verbatim: don't use taxonverbatim.taxonname+author as the scientificName_verbatim if only the author is provided. (this lead to weird scientificName_verbatims that contain just the author.)
Aaron Marcuse-Kubitza

12/17/2013

08:06 AM Revision 11920: inputs/datasource_release_status.xlsx: updated
Aaron Marcuse-Kubitza
07:28 AM Revision 11919: web/links/index.htm: updated to Firefox bookmarks. added links for fixing the "App Store is temporarily unavailable" error (turn on Spotlight) and modifying a running shell script (unlink it first).
Aaron Marcuse-Kubitza
05:47 AM Revision 11918: bugfix: bin/map: in_is_db: don't ignore errors when the table does not exist, because these prevent an errexit and allow an import to continue when a staging table is missing. suppressing this error had previously been necessary because metadata-only tables (Source/) used to not have installed staging tables, and the program had to react accordingly.
Aaron Marcuse-Kubitza

12/16/2013

07:05 PM Revision 11917: inputs/CVS/^taxon_observation.**.sample/create.sql: added Mike Lee's additional plots used to validate confidentiality-related fields (wiki.vegpath.org/CVS_validation#plots-to-include)
Aaron Marcuse-Kubitza
06:00 PM Revision 11916: bugfix: inputs/CVS/^taxon_observation.**.sample/create.sql: include taxonName in the subset of columns that's imported for the validation, because it is _alt-ed with scientificName for forming the TNRS input name. this is unique to CVS, which is why it was not part of the validation subset copied from the VegBank subset.
Aaron Marcuse-Kubitza
05:46 PM Revision 11915: /README.TXT: Full database import: documented that you should always start with a clean shell, which does not have changes to the env vars. (there have been inexplicable bugs that went away after closing and reopening the terminal window.) note that running `exec bash` is not sufficient to *reset* the env vars.
Aaron Marcuse-Kubitza
04:58 PM Revision 11914: fix: lib/sh/util.sh: verbosity_min(): usage: clarified that '' is a special value that causes $verbosity to be overwritten to ''
Aaron Marcuse-Kubitza
04:45 PM Revision 11913: lib/runscripts/table.run: added test_() target and use it in remake_VegBIEN_mappings() (it would not be clear that remake_VegBIEN_mappings() runs the tests)
Aaron Marcuse-Kubitza
01:43 PM Revision 11912: bugfix: inputs/.TNRS/schema.sql: granted bien_read SELECT access to derived views as well as the core tnrs table
Aaron Marcuse-Kubitza

12/15/2013

05:30 PM Revision 11911: updated inputs/datasource_release_status.xlsx
Aaron Marcuse-Kubitza
05:27 PM Revision 11910: added inputs/datasource_release_status.xlsx, export of Google spreadsheet at https://docs.google.com/spreadsheet/ccc?key=0ArZXrTAXd-TYdDRRb2RxYi11TWZrQVh5bVdKOURCeFE
Aaron Marcuse-Kubitza

12/12/2013

08:57 AM Revision 11909: planning/timeline/timeline.2013.xls: updated for progress
Aaron Marcuse-Kubitza
08:35 AM Revision 11908: bugfix: schemas/vegbien.sql: location: use the place_id from the parent location when no place_id is specified. this fixes a bug in analytical_stem_view where the parent location's place_id was used because it was sometimes missing from the sublocation, but the parent place_id *itself* was sometimes missing instead if sublocations each had their own place information. this way, it is always available directly in the sublocation, populated from the parent location if needed.
Aaron Marcuse-Kubitza
08:27 AM Revision 11907: bugfix: schemas/vegbien.sql: location: added place_id which is autopopulated from the current locationplace. join on this in plot.**, to avoid a 1:many join when a location has multiple locationplaces.
Aaron Marcuse-Kubitza

12/11/2013

11:10 PM Revision 11906: bugfix: schemas/vegbien.sql: locationevent_unique_within_parent_by_location unique index: need COALESCE() around location_id since it's nullable
Aaron Marcuse-Kubitza
10:54 PM Revision 11905: fix: inputs/CVS/^taxon_observation.**.sample/: added _no_import because this table duplicates part of what's imported from taxon_observation.**
Aaron Marcuse-Kubitza
10:42 PM Revision 11904: bugfix: inputs/VegBank/plot/: added _no_import because this table is left-joined and should not be imported separately
Aaron Marcuse-Kubitza
10:40 PM Revision 11903: bugfix: inputs/{.NCBI,CTFS}/*.src/: added _no_import because these tables are left-joined and should not be imported separately
Aaron Marcuse-Kubitza
09:56 PM Revision 11902: inputs/import.stats.xls: removed table names from datasources where only one table is imported
Aaron Marcuse-Kubitza
09:52 PM Revision 11901: fix: inputs/import.stats.xls: removed deleted tables from current import
Aaron Marcuse-Kubitza
09:51 PM Revision 11900: inputs/import.stats.xls: updated import times
Aaron Marcuse-Kubitza
07:56 PM Revision 11899: updated backups/TNRS.backup.md5
Aaron Marcuse-Kubitza
07:56 PM Revision 11898: added backups/vegbien.r11786.backup.md5
Aaron Marcuse-Kubitza
07:53 PM Revision 11897: /README.TXT: Full database import: backups: added step to download backup to local machine
Aaron Marcuse-Kubitza
07:45 PM Revision 11896: bugfix: /Makefile: install: need to run inputs/download in live mode so that the flat files are actually downloaded
Aaron Marcuse-Kubitza
07:43 PM Revision 11895: lib/common.Makefile: added %/live, for use with `make inputs/download`
Aaron Marcuse-Kubitza

12/10/2013

07:44 AM Revision 11894: planning/timeline/timeline.2013.xls: rescheduled tasks
Aaron Marcuse-Kubitza
07:40 AM Revision 11893: planning/timeline/timeline.2013.xls: updated for progress
Aaron Marcuse-Kubitza
07:36 AM Revision 11892: /README.TXT: Full database import: In PostgreSQL: documented that the tables to check are located in the *r# schema*, not public
Aaron Marcuse-Kubitza
07:32 AM Revision 11891: planning/timeline/timeline.2013.xls: updated for progress
Aaron Marcuse-Kubitza
07:32 AM Revision 11890: planning/timeline/timeline.2013.xls: datasource validations: reordered datasources according to Brian Enquist's new validation order (wiki.vegpath.org/Spot-checking_validation_order)
Aaron Marcuse-Kubitza
07:10 AM Revision 11889: fix: schemas/vegbien.sql: analytical_specimen: added specimens-related columns that are in analytical_plot
Aaron Marcuse-Kubitza
06:35 AM Revision 11888: inputs/GBIF/raw_occurrence_record_plants/map.csv: row_num: remapped to plain *row_num, like the other datasources that have this field
Aaron Marcuse-Kubitza
06:31 AM Revision 11887: inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: Remove institutions that we have direct data for: rerun time: noted that this is only fast *after* manual vacuuming of the table (to remove the deleted rows from the index). autovacuum apparently does not run, although it should.
Aaron Marcuse-Kubitza
05:18 AM Revision 11886: planning/timeline/timeline.2013.xls: hid previous weeks
Aaron Marcuse-Kubitza
05:18 AM Revision 11885: planning/timeline/timeline.2013.xls: added timespan dots ◦ for supertasks
Aaron Marcuse-Kubitza
05:15 AM Revision 11884: planning/timeline/timeline.2013.xls: legend: changed to movable text box to avoid needing to erase and repopulate the header columns with the legend cells
Aaron Marcuse-Kubitza
05:03 AM Revision 11883: planning/timeline/timeline.2013.xls: crossed out and hid completed tasks
Aaron Marcuse-Kubitza
04:58 AM Revision 11882: planning/timeline/timeline.2013.xls: updated for progress
Aaron Marcuse-Kubitza

12/09/2013

07:24 PM Revision 11881: inputs/GBIF/raw_occurrence_record_plants/test.xml.ref: reran test, which added yearCollected/monthCollected/dayCollected
Aaron Marcuse-Kubitza
07:23 PM Revision 11880: inputs/CVS/plantConcept_/create.sql: documented runtime (3 min)
Aaron Marcuse-Kubitza
06:59 PM Revision 11879: inputs/CTFS/*.src/: added test.xml.ref
Aaron Marcuse-Kubitza
06:58 PM Revision 11878: inputs/CTFS/*.src/: added VegBIEN.csv
Aaron Marcuse-Kubitza
06:56 PM Revision 11877: bugfix: inputs/CTFS/TaxonOccurrence*/map.csv: things mapped to taxonObservationID: remapped to taxonOccurrenceID since taxonObservationID is not mapped to anything in VegBIEN (denormalized VegCore doesn't distinguish between taxon occurrences and taxon observations of them)
Aaron Marcuse-Kubitza
05:46 PM Revision 11876: bugfix: inputs/ARIZ/~.clean_up.sql: prevent "column already exists" errors when there is an input column of the same name as an output column
Aaron Marcuse-Kubitza
05:44 PM Revision 11875: bugfix: lib/runscripts/datasrc_dir.run: import(): don't run `sql/install` if the schema already exists, because this will try to rerun all the schema-creation queries. note that this idempotent functionality was *not* provided by the `make .../install` target that was previously used (idempotency is new with new-style import).
Aaron Marcuse-Kubitza
05:26 PM Revision 11874: bugfix: schemas/vegbien.sql: updated for renamed county_centroids column names
Aaron Marcuse-Kubitza
04:16 PM Revision 11873: inputs/.geoscrub/import_order.txt: added county_centroids so that it would be installed by new-style import
Aaron Marcuse-Kubitza
03:54 PM Revision 11872: bugfix: lib/runscripts/datasrc_dir.run: import(): can't run `datasrc_make reinstall` anymore because this now defers to the runscript for new-style import datasources (which was done so that `make .../install` properly reinstalls all the datasources). instead, call the applicable make targets manually (there are just 2 of them).
Aaron Marcuse-Kubitza
03:37 PM Revision 11871: inputs/FIA/TREE/run: documented import() runtime (1.5 h), which includes table cleanup runtime (1 h)
Aaron Marcuse-Kubitza
03:09 PM Revision 11870: bugfix: bin/pg_dump_limit: support errexit by ignoring the nonzero exit status that grep returns when it doesn't match anything
Aaron Marcuse-Kubitza
02:43 PM Revision 11869: inputs/GBIF/raw_occurrence_record_plants/run: updated import() runtime (same), documented table cleanup runtime (1.5 h)
Aaron Marcuse-Kubitza
02:38 PM Revision 11868: inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: CREATE INDEX ... specimenHolderInstitutions: documented runtime (45 min)
Aaron Marcuse-Kubitza
02:28 PM Revision 11867: inputs/GBIF/raw_occurrence_record_plants/postprocess.sql: Remove institutions that we have direct data for: documented runtime (3.5 min)
Aaron Marcuse-Kubitza
02:27 PM Revision 11866: /README.TXT: Datasource setup: added steps to backup e-mails
Aaron Marcuse-Kubitza

12/06/2013

07:46 AM Revision 11865: bugfix: inputs/CTFS/import_order.txt: added *.src so that these would be installed under new-style import as well. this means that their columns will now be automapped, requiring the names to be renamed to VegCore names in */create.sql. note that VegCore taxonOccurrenceID has been renamed to taxonObservationID since this was last run.
Aaron Marcuse-Kubitza
06:56 AM Revision 11864: inputs/.geoscrub/run: documented import() runtime (20 min)
Aaron Marcuse-Kubitza
06:12 AM Revision 11863: bugfix: inputs/.NCBI/import_order.txt: added nodes.src, names.src so that these would be installed under new-style import as well. this means that their columns will now be automapped, requiring the names to be renamed to VegCore names in nodes/create.sql.
Aaron Marcuse-Kubitza
06:01 AM Revision 11862: fix: /Makefile: inputs/reinstall: commented out to avoid a cascade of "overriding commands for target" warnings. this will revert to the default uninstall, install sequence for this target rather than the simultaneous-reinstall optimization (which can still be invoked manually).
Aaron Marcuse-Kubitza
05:52 AM Revision 11861: lib/sh/local.sh: public_schema_exists(): use a higher log_level for pg_schema_exists, to avoid all the verbose output involved in running the query
Aaron Marcuse-Kubitza
05:44 AM Revision 11860: bugfix: lib/sh/local.sh: public_schema_exists(): can no longer use psql_script_vegbien for this, because using `SET search_path` (called by psql_script_vegbien) with a schema that does not exist no longer produces an error. instead, use new pg_schema_exists(), which uses a different command that does produce an error if the schema does not exist.
Aaron Marcuse-Kubitza
05:38 AM Revision 11859: lib/sh/db.sh: added pg_require_schema()
Aaron Marcuse-Kubitza
05:37 AM Revision 11858: lib/sh/util.sh: stderr2stdout(): documented that this redirects fd 2->1 and log_fd (but *not* back to 2)
Aaron Marcuse-Kubitza
05:34 AM Revision 11857: bugfix: lib/sh/util.sh: stderr2stdout() use `command` before tee, which re-filters log_fd so that stderr itself is also filtered. this allows log-filtering out an otherwise-confusing benign error when using e.g. stderr_matches().
Aaron Marcuse-Kubitza
04:31 AM Revision 11856: lib/sh/util.sh: added not(), for use in prefixing wrapped commands
Aaron Marcuse-Kubitza
04:14 AM Revision 11855: lib/sh/db.sh: added pg_schema_exists()
Aaron Marcuse-Kubitza
04:10 AM Revision 11854: lib/sh/util.sh: added stderr_matches()
Aaron Marcuse-Kubitza
03:59 AM Revision 11853: lib/sh/util.sh: documented that fds 2x/3x should not be used because *we* use these, as opposed to 1x which is used by the shell internally
Aaron Marcuse-Kubitza
03:57 AM Revision 11852: lib/sh/util.sh: added stdout_contains()
Aaron Marcuse-Kubitza
03:34 AM Revision 11851: lib/sh/util.sh: added stderr2stdout()
Aaron Marcuse-Kubitza
02:52 AM Revision 11850: fix: lib/sh/db.sh: pg_table_exists(): usage: documented that $table is actually required for this function
Aaron Marcuse-Kubitza
02:44 AM Revision 11849: bugfix: inputs/input.Makefile: install: for new-style datasources, use the associated runscript instead (the old-style install target will not do everything that's needed for a new-style datasource)
Aaron Marcuse-Kubitza
01:57 AM Revision 11848: bugfix: /Makefile: moved inputs/reinstall to end so it overrides the corresponding subdir forwarding target
Aaron Marcuse-Kubitza
12:51 AM Revision 11847: bugfix: inputs/input.Makefile: install: for new-style datasources, use the associated runscript instead (the old-style install target will not do everything that's needed for a new-style datasource)
Aaron Marcuse-Kubitza
12:27 AM Revision 11846: bugfix: /Makefile: inputs/install: don't run bin/reinstall_all here, because /install targets are supposed to be idempotent, forward-only actions that don't first remove existing data
Aaron Marcuse-Kubitza

12/05/2013

11:55 PM Revision 11845: bugfix: /Makefile: postgres-Darwin: don't prepend $(MAKE) to $(postgresReload-Darwin), because this is now a list of commands
Aaron Marcuse-Kubitza
11:52 PM Revision 11844: bugfix: /Makefile: config: ignore errors if ~/bin/make exists
Aaron Marcuse-Kubitza
11:38 PM Revision 11843: inputs/FIA/COND/postprocess.sql: filtering formula: documented that this was created by Brad, and provided the URL to it on nimoy
Aaron Marcuse-Kubitza
12:27 PM Revision 11842: inputs/CVS/cvs.~.clean_up.sql: remove plot.realLatitude/realLongitude, since this is private data that should not be publicly visible
Aaron Marcuse-Kubitza
12:19 PM Revision 11841: inputs/CVS/cvs.~.clean_up.sql: remove plot.realLatitude/realLongitude, since this is private data that should not be publicly visible
Aaron Marcuse-Kubitza
08:38 AM Revision 11840: bin/make_analytical_db: don't regenerate family_higher_plant_group from the NCBI data because the lookup table is now prepopulated as part of the schema
Aaron Marcuse-Kubitza
08:37 AM Revision 11839: bin/import_all: don't import NCBI because the lookup table is now prepopulated as part of the schema
Aaron Marcuse-Kubitza
08:35 AM Revision 11838: schemas/vegbien.sql: include the family_higher_plant_group lookup table values so that these don't need to be regenerated from the NCBI nodes whenever the DB is reloaded
Aaron Marcuse-Kubitza
07:58 AM Revision 11837: schemas/vegbien.sql: taxonlabel_update_ancestors(): don't do an index scan if the value being scanned for is NULL, to support testing this function without the indexes in place, without extra full-table scans for NULL values affecting things. this can be used to determine if the function is actually using the indexes, by turning them off and seeing if the runtime changes.
Aaron Marcuse-Kubitza
07:03 AM Revision 11836: schemas/util.sql: explain2table(): documented usage:
PERFORM util.explain2table($$
query
$$);
Aaron Marcuse-Kubitza
05:52 AM Revision 11835: schemas/util.sql: explain2table(): by default, use the util.explain table
Aaron Marcuse-Kubitza
05:49 AM Revision 11834: schemas/util.sql: added explain table
Aaron Marcuse-Kubitza
05:47 AM Revision 11833: schemas/util.sql: added explain2notice()
Aaron Marcuse-Kubitza
05:44 AM Revision 11832: schemas/util.sql: added explain2str()
Aaron Marcuse-Kubitza
05:33 AM Revision 11831: schemas/util.sql: added explain2table()
Aaron Marcuse-Kubitza
05:23 AM Revision 11830: schemas/util.sql: added explain()
Aaron Marcuse-Kubitza
01:31 AM Revision 11829: schemas/vegbien.sql: taxonlabel_update_ancestors(): don't create a performance-intensive nested transaction (EXCEPTION block) for each INSERT, because there should no longer be duplicate ancestors, so it's OK to abort the whole transaction if this assertion fails
Aaron Marcuse-Kubitza
01:03 AM Revision 11828: bugfix: schemas/vegbien.sql: taxonlabel_update_ancestors_on_{insert,update}(): only use *either* the matched taxon's ancestors *or* the parent's ancestors, to avoid issues related to duplication between these two ancestors lists. this also fixes a bug where the 2nd taxonlabel_update_ancestors() call assumes that the existing ancestors are for the old *parent*, when in fact they have actually just been set to those for the new *matched taxon* (which horribly confuses taxonlabel_update_ancestors()).
Aaron Marcuse-Kubitza

12/04/2013

10:06 PM Revision 11827: schemas/vegbien.sql: _taxonlabel_set_parent_id(): just use a plain UPDATE statement, to avoid the significant parsing and stringification overhead of EXECUTE and quote_nullable(). it is not clear that EXECUTE is actually necessary to avoid caching the query plan, because the cache should be invalidated automatically when the table's ANALYZE statistics are regenerated.
Aaron Marcuse-Kubitza
10:00 PM Revision 11826: schemas/vegbien.sql: removed unused function _taxonlabel_set_matched_label_id(), which refers to obsolete fields
Aaron Marcuse-Kubitza
09:58 PM Revision 11825: schemas/vegbien.sql: synced to DB (the view renderer apparently changed the text of a view)
Aaron Marcuse-Kubitza
09:44 PM Revision 11824: backups/TNRS.backup: saved copy backups/TNRS.2013-11-18.backup
Aaron Marcuse-Kubitza
07:26 PM Revision 11823: bugfix: bin/import_all: run in errexit mode, so that if the user cancels reinstalling of the import schema, the script will then abort instead of continuing and using the wrong schema
Aaron Marcuse-Kubitza
06:56 PM Revision 11822: bugfix: schemas/Makefile: %/uninstall: always confirm before removing an existing schema, not just for public and r*, because an auxiliary schema might also be used as $version and reinstalled by bin/import_all
Aaron Marcuse-Kubitza
06:04 PM Revision 11821: schemas/vegbien.sql: analytical_stem_view: scrubbed_author: removed empty COALESCE() around value (left over from when multiple values needed to be combined for many TNRS fields)
Aaron Marcuse-Kubitza
04:57 PM Revision 11820: inputs/CVS/^taxon_observation.**.sample/create.sql: uncommented identifiedBy since this is now part of taxonObservation_
Aaron Marcuse-Kubitza
04:08 PM Revision 11819: fix: inputs/CVS/observation_community/create.sql: communityName: populate from commConcept.commName instead, because commInterpretation.commname is not always populated. this requires left-joining to commConcept.
Aaron Marcuse-Kubitza
03:58 PM Revision 11818: inputs/CVS/observation_community/map.csv: updated output column names to new input column names, to avoid later output column collisions
Aaron Marcuse-Kubitza
03:42 PM Revision 11817: inputs/CVS/observation_community/header.csv, map.csv: updated input column names for cvs.~.clean_up.sql renamings
Aaron Marcuse-Kubitza
03:12 PM Revision 11816: schemas/vegbien.sql: provider_count_view: source totals: use the much faster query developed for Brad (wiki.vegpath.org/VegBIEN_FAQ#from-Brad-on-2013-12-4), which avoids the need to do a GROUP BY on all of analytical_stem. eventually, we will want to apply the same optimization to the first publisher subtotals.
Aaron Marcuse-Kubitza
04:19 AM Revision 11815: inputs/CVS/cvs.~.clean_up.sql: commClass, commConcept fields: prepend table name to avoid inter-table collisions upon join
Aaron Marcuse-Kubitza
03:43 AM Revision 11814: added inputs/CVS/observation_community/, as for VegBank
Aaron Marcuse-Kubitza
03:32 AM Revision 11813: inputs/CVS/cvs.~.clean_up.sql: commClass.dba_src_ID: prepend table name to avoid inter-table collisions upon join
Aaron Marcuse-Kubitza

12/03/2013

04:32 PM Revision 11812: added inputs/CVS/observationContributor_/, which adds the people collecting the plot
Aaron Marcuse-Kubitza
04:02 PM Revision 11811: inputs/CVS/cvs.~.clean_up.sql: observationContributor.dba_src_ID: prepended table name to avoid collision when left-joining to party
Aaron Marcuse-Kubitza
03:44 PM Revision 11810: bugfix: inputs/input.Makefile: %/header.csv: errexit the command so that errors won't scroll by, which in this case requires `set -o pipefail`
Aaron Marcuse-Kubitza
02:57 PM Revision 11809: fix: inputs/CVS/taxonObservation_/create.sql: mapped identifiedBy, which involves joining to party
Aaron Marcuse-Kubitza
02:35 PM Revision 11808: inputs/CVS/cvs.~.clean_up.sql: don't rename taxonInterpretation.PARTY_ID, so that this can be USING-joined to party in inputs/CVS/taxonObservation_/create.sql
Aaron Marcuse-Kubitza
01:47 PM Revision 11807: schemas/vegbien.ERD.mwb: regenerated exports
Aaron Marcuse-Kubitza
08:58 AM Revision 11806: bin/map: support param start="", which indicates the default value. this fixes a bug in inputs/input.Makefile $(restart_row), which outputs "" if an explicit starting row is not found.
Aaron Marcuse-Kubitza
08:25 AM Revision 11805: inputs/CVS/^taxon_observation.**.sample/map.csv: synced output columns to input columns (which removes the extra *s)
Aaron Marcuse-Kubitza
08:00 AM Revision 11804: fix: inputs/CVS/plot_/postprocess.sql: locality: include the site name (authorLocation), because this is part of the unique specification of the place that was sampled, and Bob wants this to be included in VegBIEN
Aaron Marcuse-Kubitza
07:58 AM Revision 11803: inputs/CVS/^taxon_observation.**.sample/create.sql: removed parentLocationID, since this is unused in CVS
Aaron Marcuse-Kubitza
07:45 AM Revision 11802: bugfix: inputs/input.Makefile: `%/install: %/create.sql`: errexit the command so that errors won't scroll by, which in this case requires `set -o pipefail`
Aaron Marcuse-Kubitza
06:51 AM Revision 11801: inputs/VegBank/plot/postprocess.sql: locality: include the site name (authorlocation), because this is part of the unique specification of the place that was sampled
Aaron Marcuse-Kubitza
06:27 AM Revision 11800: bugfix: /README.TXT: Full database import: To restart an aborted import for a specific table: run the two commands in errexit mode so that the datasource does not incorrectly have the temp suffix removed if the import command exited with an error
Aaron Marcuse-Kubitza
05:19 AM Revision 11799: fix: inputs/CVS/taxon_observation.**/map.csv: omit authorPlantName because it is not specific to the taxonInterpretation row (this is in a separate taxonInterpretation for the original determination instead)
Aaron Marcuse-Kubitza
04:59 AM Revision 11798: web/links/index.htm: updated to Firefox bookmarks. PostgreSQL: added links for troubleshooting out-of-memory errors, which show up (cryptically) as "The database system is in recovery mode" errors in processes running at the time the out-of-memory condition occurred.
Aaron Marcuse-Kubitza
02:31 AM Revision 11797: schemas/postgresql.conf: work_mem: documented that this seemingly small # is *multiplied* by max_connections, i.e. 256 MB * 100 = *26 GB*, which approaches total memory (32 GB)
Aaron Marcuse-Kubitza
01:21 AM Task #831 (New): make tests use their own public schema
* enables the automated tests to be run on vegbiendev
* allows adding a new datasource directly on vegbiendev, witho...
Aaron Marcuse-Kubitza
12:58 AM Task #501: find out which datasources won't allow their data to be publicly accessible
see [[Datasource conditions of use]] Aaron Marcuse-Kubitza

12/02/2013

02:46 PM Revision 11796: fix: inputs/CVS/plot_/map.csv: PARENT_ID: remapped to UNUSED, to clarify that subplots are *not* implemented through this field
Aaron Marcuse-Kubitza
 

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