Activity
From 11/05/2013 to 12/04/2013
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.
- 10:00 PM Revision 11826: schemas/vegbien.sql: removed unused function _taxonlabel_set_matched_label_id(), which refers to obsolete fields
- 09:58 PM Revision 11825: schemas/vegbien.sql: synced to DB (the view renderer apparently changed the text of a view)
- 09:44 PM Revision 11824: backups/TNRS.backup: saved copy backups/TNRS.2013-11-18.backup
- 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
- 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
- 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)
- 04:57 PM Revision 11820: inputs/CVS/^taxon_observation.**.sample/create.sql: uncommented identifiedBy since this is now part of taxonObservation_
- 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.
- 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
- 03:42 PM Revision 11817: inputs/CVS/observation_community/header.csv, map.csv: updated input column names for cvs.~.clean_up.sql renamings
- 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.
- 04:19 AM Revision 11815: inputs/CVS/cvs.~.clean_up.sql: commClass, commConcept fields: prepend table name to avoid inter-table collisions upon join
- 03:43 AM Revision 11814: added inputs/CVS/observation_community/, as for VegBank
- 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
12/03/2013
- 04:32 PM Revision 11812: added inputs/CVS/observationContributor_/, which adds the people collecting the plot
- 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
- 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`
- 02:57 PM Revision 11809: fix: inputs/CVS/taxonObservation_/create.sql: mapped identifiedBy, which involves joining to party
- 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
- 01:47 PM Revision 11807: schemas/vegbien.ERD.mwb: regenerated exports
- 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.
- 08:25 AM Revision 11805: inputs/CVS/^taxon_observation.**.sample/map.csv: synced output columns to input columns (which removes the extra *s)
- 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
- 07:58 AM Revision 11803: inputs/CVS/^taxon_observation.**.sample/create.sql: removed parentLocationID, since this is unused in CVS
- 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`
- 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
- 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
- 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)
- 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.
- 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)
- 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... - 12:58 AM Task #501: find out which datasources won't allow their data to be publicly accessible
- see [[Datasource conditions of use]]
12/02/2013
11/27/2013
- 11:16 PM Revision 11795: bugfix: /README.TXT: Full database import: To restart an aborted import for a specific table: added command to remove the temp suffix from the source table entry, which is *not* automatic for importing a specific table (only for importing the entire datasource, at the end of which the datasource is considered completely imported and ready to overwrite any previous import)
- 11:04 PM Revision 11794: inputs/input.Makefile: scrub: clarified that using & (background process) *also* ignores TNRS errors (the primary purpose of & , of course, is to run asynchronously)
- 10:42 PM Revision 11793: bugfix: schemas/Makefile: $(confirmRmPublicSchema): only prompt to delete the schema if it actually exists. this avoids prompting to remove a non-existent schema at the beginning of bin/import_all, which requires user attention. since bin/import_all is often run with a delayed start (e.g. to wait for a staging table reinstall to complete), the user may not be at the terminal when this message is displayed, and without this fix, the import would be prevented from running until they return.
- 09:24 PM Revision 11792: inputs/.geoscrub/geoscrub_output/run: import() runtime: added starscream runtime (20 min)
- 08:48 PM Revision 11791: planning/timeline/timeline.2013.xls: updated for progress
- 08:33 PM Revision 11790: inputs/.geoscrub/geoscrub_output/run: documented import() runtime (15 min)
11/26/2013
- 11:18 PM Revision 11789: inputs/.geoscrub/Source/map.csv: source__modified_date: updated for current run
- 11:11 PM Revision 11788: **/new_terms.csv, unmapped_terms.csv updated (using `make missing_mappings`)
- 11:10 PM Revision 11787: /README.TXT: Full database import: documented that `make schemas/reinstall` requires sudo access
- 11:07 PM Revision 11786: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: updated upload time (30 s)
- 11:00 PM Revision 11785: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: export_(): updated runtime (25 s)
- 10:58 PM Revision 11784: lib/sh/util.sh: import_vars: don't overwrite vars that are already defined, to allow the caller to specify their own values for the vars to create. this requires callers that rely on the overwriting functionality to reverse the order in which they run use_* commands, so that the higher-precedence use_* is applied first and the other one as the default values for the first.
- 10:03 PM Revision 11783: derived/biengeo/README.txt: updated geoscrub.sh runtime
- 09:57 PM Revision 11782: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: make(): derived/biengeo/geoscrub.sh: documented runtime (2.5 h)
- 09:45 PM Revision 11781: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: don't connect to DB as the root user, because this is not needed now that the geoscrub schema is owned by the bien user. this avoids a sudo password prompt at the end of the geoscrubbing run.
- 07:38 PM Revision 11780: planning/timeline/timeline.2013.xls: rescheduled tasks
- 06:51 PM Revision 11779: planning/timeline/timeline.2013.xls: rescheduled tasks
- 06:41 PM Revision 11778: planning/timeline/timeline.2013.xls: updated for progress
- 02:23 PM Revision 11777: bugfix: inputs/input.Makefile: $(import): except in a full-database import, errexit so that the import will stop on an error and not let it scroll by
- 01:55 PM Revision 11776: added inputs/CVS/^taxon_observation.**.sample/, used for the extract. note that the column list is slightly different than for VegBank.
- 01:42 PM Revision 11775: inputs/CVS/taxonObservation_/map.csv: removed taxonObservation_-- prefix from terms that do not need to be table-specific (like for VegBank)
- 01:32 PM Revision 11774: fix: inputs/CVS/taxonObservation_/map.csv: plantConcept_ columns: synced input and output column names to their names in plantConcept_
- 01:30 PM Revision 11773: fix: inputs/CVS/taxonObservation_/map.csv: plantConcept_ columns: synced input and output column names to their names in plantConcept_
- 01:26 PM Revision 11772: inputs/CVS/plantConcept_/map.csv: removed plantConcept_-- prefix from terms that do not need to be table-specific (like for VegBank)
- 01:22 PM Revision 11771: lib/sh/db.sh: pg_table_exists(): use `SELECT NULL` instead of `SELECT *` to avoid a long column list cluttering up the log output
- 12:47 PM Revision 11770: lib/runscripts/table.run: table_make_install(): simplified the setting of $noclobber since there no longer needs to be a different command for when the log exists
- 12:08 PM Revision 11769: bugfix: lib/runscripts/table.run: need to errexit the make target, so that errors in the SQL install scripts are not suppressed. this requires pre-checking if the table exists (using new pg_table_exists), so that the install target's errexit does not then need to be suppressed for cases when the table already exists.
- 12:01 PM Revision 11768: lib/sh/db.sh: added pg_table_exists()
- 06:48 AM Revision 11767: planning/timeline/timeline.2013.xls: added timespan dots ◦ for supertasks
- 06:46 AM Revision 11766: planning/timeline/timeline.2013.xls: crossed out and hid completed tasks
- 06:20 AM Revision 11765: planning/timeline/timeline.2013.xls: hid previous weeks
- 06:18 AM Revision 11764: planning/timeline/timeline.2013.xls: consolidated legend to take up fewer columns and avoid repeating labels
- 06:09 AM Revision 11763: bugfix: inputs/CVS/import_order.txt: added taxon_observation.**. rescheduled tasks.
- 06:05 AM Revision 11762: planning/timeline/timeline.2013.xls: updated for progress
- 05:56 AM Revision 11761: bugfix: inputs/CVS/import_order.txt: added taxon_observation.**
- 05:54 AM Revision 11760: inputs/CVS/: don't import joined tables, because they are now imported in the taxon_observation.** left-join instead
- 05:53 AM Revision 11759: inputs/CVS/: added taxon_observation.** left-join of the tables, using the steps at http://wiki.vegpath.org/Left-joining_a_datasource. this involves renaming taxonOccurrenceID->taxonOccurrenceID__overall_plot so that it can then be joined together with aggregateOrganismObservationID to create the full taxonOccurrenceID (as in VegBank).
- 05:46 AM Revision 11758: inputs/CVS/stemCount_/map.csv: remapped stratum_ID->*STRATUM_ID so it would match up with stratum.*STRATUM_ID
11/25/2013
- 10:14 PM Revision 11757: inputs/CVS/taxonObservation_/map.csv: mapped TAXONINTERPRETATION_ID to identificationID
- 10:03 PM Revision 11756: added inputs/CVS/stratum/
- 10:02 PM Revision 11755: added inputs/CVS/stratumType/
- 09:43 PM Revision 11754: inputs/CVS/: prepended the table name to each column name to prevent column collisions, using the steps at http://wiki.vegpath.org/Left-joining_a_datasource
- 08:07 PM Revision 11753: bugfix: inputs/CVS/plantConcept_/map.csv: PLANTCONCEPT_ID: remapped without * prefix so that the USING join in inputs/CVS/taxonObservation_/create.sql would continue to work
- 08:05 PM Revision 11752: inputs/CVS/taxonObservation_/header.csv, map.csv: updated to use plantConcept_ renamed columns
- 08:03 PM Revision 11751: bugfix: inputs/CVS/plantConcept_/map.csv: PLANTCONCEPT_ID: remapped without * prefix so that the USING join in inputs/CVS/taxonObservation_/create.sql would continue to work
- 07:59 PM Revision 11750: planning/timeline/timeline.2013.xls: updated for progress
- 07:52 PM Revision 11749: inputs/CVS/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource
- 07:32 PM Revision 11748: inputs/CVS/taxonObservation_/map.csv: updated for CVS refresh
- 07:17 PM Revision 11747: inputs/CVS/taxonObservation_/map.csv: updated input column names to plantConcept_ renamings
- 07:06 PM Revision 11746: inputs/CVS/plantConcept_/header.csv, map.csv: updated for CVS refresh
- 06:51 PM Revision 11745: fix: inputs/CVS/plot_/map.csv: removed filter-less collisions. note that the name county_ is assigned in plot_/create.sql, not cvs.~.clean_up.sql as one might expect, because this is a generated column.
- 06:42 PM Revision 11744: fix: inputs/CVS/plot_/map.csv: removed filter-less collisions
- 06:41 PM Revision 11743: fix: inputs/CVS/plot_/map.csv: removed filter-less collisions
- 05:32 PM Revision 11742: fix: inputs/CVS/taxonObservation_/map.csv: moved inherited derived columns to right after the other columns, because for this table, these are actually real input columns rather than appended derived columns. the column order must match header.csv to avoid mis-renamings.
- 04:51 PM Revision 11741: inputs/CVS/taxonObservation_/map.csv: removed filter functions, which are now performed in plantConcept_
- 04:43 PM Revision 11740: inputs/CVS/taxonObservation_/postprocess.sql: added _parent index to facilitate joins
- 04:24 PM Revision 11739: fix: inputs/CVS/taxonObservation_/header.csv, map.csv: updated for CVS refresh and addition of plantConcept_ derived columns
- 03:22 PM Revision 11738: inputs/CVS/stemCount_/: translated filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#1-Translate-filters-to-postprocessing-derived-columns. note that the inserted row count changes, because there is now a primary key (which the table is auto-sorted by) where previously there was none.
- 02:58 PM Revision 11737: web/links/index.htm: updated to Firefox bookmarks. added API writing links, including the best quotes from a Google developer's PowerPoint on the topic.
- 12:59 AM Revision 11736: schemas/vegbien.sql: collected_dates: documented runtime (2.5 min)
- 12:57 AM Revision 11735: schemas/vegbien.sql: collected_date_min: replaced with collected_dates view that lists all dates we have, so that we can determine which of these may be valid. it turns out that we have data collected from very far back (to the year 1), which are not merely 2-digit years because PostgreSQL will only parse early years when there are 4 digits.
- 12:26 AM Revision 11734: added planning/publication/KNB/submission.published.old_site.maff, submission.published.eml.xml from old KNB site
- 12:18 AM Revision 11733: added planning/publication/KNB/submission.*
11/24/2013
- 11:48 PM Revision 11732: bugfix: schemas/vegbien.sql: collected_date_min: exclude invalid dates < 1000-01-01
- 11:41 PM Revision 11731: bugfix: schemas/vegbien.sql: collected_date_min: exclude -infinity
- 11:13 PM Revision 11730: schemas/vegbien.sql: added collected_date_min view
11/21/2013
- 05:20 PM Revision 11729: inputs/CVS/plot_/: translated column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#1-Translate-filters-to-postprocessing-derived-columns
- 04:59 PM Revision 11728: /README.TXT: Full database import: verifying import: In PostgreSQL: don't include current values of the datasource counts, etc., because these may change and should always be re-checked at wiki.vegpath.org/VegBIEN_contents
- 04:27 PM Revision 11727: inputs/CVS/plot_/postprocess.sql: added pkey from the primary joined table
- 04:11 PM Revision 11726: inputs/CVS/plot_/map.csv: documented assumptions about the units of fields
- 03:52 PM Revision 11725: inputs/CVS/plot_/map.csv: documented assumptions about the units and meaning of numeric codes for fields
- 03:01 PM Revision 11724: inputs/CVS/plantConcept_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#1-Translate-filters-to-postprocessing-derived-columns
- 02:54 PM Revision 11723: inputs/CVS/plantConcept_/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#1-Translate-filters-to-postprocessing-derived-columns
- 01:59 PM Revision 11722: web/links/index.htm: updated to Firefox bookmarks. BIEN: added DataONE compatibility links.
- 01:58 PM Revision 11721: inputs/CVS/plantConcept_/postprocess.sql: added pkey from the primary joined table
- 01:11 PM Revision 11720: inputs/CVS/observation_/postprocess.sql: added pkey from the primary joined table. added _parent index to facilitate joins.
- 01:08 PM Revision 11719: fix: inputs/input.Makefile: $(svnFilesGlob): removed schema and PDF files, since these are owned by the data provider and should not be in the repository that gets open-sourced
- 01:01 PM Revision 11718: bugfix: inputs/CVS/observation_/create.sql: only include one soilObs for each observation (using DISTINCT ON), rather than just left-joining them
- 11:59 AM Revision 11717: inputs/: removed SALVIAS-CSV, because this is a sample datasource which was only there to test the mapping process. it should not be adding records that duplicate SALVIAS, nor should it take up maintenance effort (switching to new-style import, updating to match SALVIAS, etc.).
- 11:52 AM Revision 11716: planning/timeline/timeline.2013.xls: removed the weeks of 12/23, 12/30 because these are during winter break. rescheduled tasks.
- 11:08 AM Revision 11715: inputs/.TNRS/schema.sql: updated runtime (30 min) and rowcount (+2 million)
- 10:23 AM Revision 11714: planning/timeline/timeline.2013.xls: rescheduled tasks
- 10:16 AM Revision 11713: planning/timeline/timeline.2013.xls: crossed out and hid completed tasks
- 10:14 AM Revision 11712: planning/timeline/timeline.2013.xls: updated for progress
- 09:04 AM Revision 11711: fix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): is_valid_match: set this to false if Taxonomic_status is Invalid
- 08:53 AM Revision 11710: schemas/vegbien.sql: analytical_stem_view: added taxonomic_status. notice that PostgreSQL 9.3 puts each view column on a separate line, making it *much* easier to review the svn diff!
- 08:49 AM Revision 11709: inputs/.TNRS/schema.sql: added map_taxonomic_status()
- 08:48 AM Revision 11708: inputs/.TNRS/schema.sql, data.sql: updated for PostgreSQL 9.3
- 08:26 AM Revision 11707: bugfix: inputs/CVS/stemCount_/map.csv: ensure the aggregateoccurrence.sourceaccessioncode is always populated, because this is a required field when using sourceaccessioncodes. without it, the import will exclude rows which lack a value in this field because it cannot deduplicate on it for these rows, leading to the dropping of large numbers of occurrences. this shows up when comparing provider_count to the input table's row count, and produces the following error in the .errors table:
- ---
ERROR: duplicate key value violates unique constraint "aggregateoccurrence_taxonoccurrence_1_to_1"
DETAIL: Key ... - 07:40 AM Revision 11706: fix: schemas/vegbien.sql: taxon_trait_view: include only TNRS-valid names
- 12:24 AM Revision 11705: copyright scrub: inputs/: removed data provider-owned schema and documentation files, which are not BIEN copyright and should not be part of what is submitted for open-sourcing. these files will remain accessible via the web interface (fs.vegpath.org), but will not be in the repository.
- 12:02 AM Revision 11704: added inputs/TEAM/_src/data_cart.tsv, containing the content extracted from data_cart.maff
11/20/2013
- 11:38 PM Revision 11703: web/links/index.htm: updated to Firefox bookmarks. BIEN: open-sourcing: added UArizona and iPlant IP policies, which are relevant to Brad's numerous documentation and schema-modeling contributions in our repository (most done while he was an iPlant employee).
- 10:49 PM Revision 11702: removed inputs/TEAM/_src/data_cart.pdf since this does not contain all the info in data_cart.maff
- 01:21 PM Revision 11701: added planning/legal/open-sourcing/request_to_open_source_software.orig.docx.url
- 01:18 PM Revision 11700: added planning/legal/open-sourcing/, which will contain the "request to open source software" form (this cannot be under version control due to copyright limitations stated in the form)
11/19/2013
- 09:21 PM Revision 11699: web/links/index.htm: updated to Firefox bookmarks. BIEN: open-sourcing: added potential licenses we could use (public domain/CC0, BSD, GNU Verbatim Copying License, *not* CC-BY because incompatible w/ GPL).
- 08:31 PM Revision 11698: web/links/index.htm: updated to Firefox bookmarks. BIEN: added links related to open-sourcing it, including the "Request to Open Source Software" form, the funding sources that need to be included in it, and part of the delegation of authority chain (from the UC Regents) that authorizes the open-sourcing.
11/18/2013
- 11:38 PM Revision 11697: backups/TNRS.backup.md5: updated
- 10:50 PM Task #816 (New): re-run TNRS on mis-scrubbed names
- * temporary workaround for names with an accepted name:
use @Accepted_name_family@ when @Name_matched_accepted_famil... - 05:40 PM Revision 11696: schemas/vegbien.sql: sync_analytical_stem_to_view(): use new util.force_recreate() instead of manually dropping and re-creating every view that uses this. this avoids the need to add several lines to this function every time we add a new scientific view (of which we expect to have many), because force_recreate()'s error parsing handles this automatically. this makes it possible for a non-expert user to add scientific views without compromising the ability to add columns to analytical_stem_view, because they don't need to understand Postgres's dependency error messages when updating analytical_stem with this function.
- 05:32 PM Revision 11695: schemas/util.sql: added force_recreate(), for use by sync_analytical_stem_to_view(). this uses the new `GET STACKED DIAGNOSTICS` in PostgreSQL 9.3 to access the DETAIL section of the dependent_objects_still_exist error.
- 12:10 PM Revision 11694: web/links/index.htm: updated to Firefox bookmarks. upgrading to PostgreSQL 9.3: added Linux pg_upgrade steps and install instructions. added Mac PostGIS, psycopg2 install steps. added note that after installing, you need to restore config values that the upgrade reset: in pgAdmin > Preferences > Query tool > Query editor, set Max characters per column back to -1 (to avoid cells being truncated). (this is *not* a bug in PostgreSQL, only in pgAdmin, and does *not* signal a need to downgrade.)
- 06:52 AM Revision 11693: planning/timeline/timeline.2013.xls: hid previous weeks
- 06:51 AM Revision 11692: planning/timeline/timeline.2013.xls: rescheduled tasks
- 06:45 AM Revision 11691: planning/timeline/timeline.2013.xls: added timespan checkmarks
- 06:44 AM Revision 11690: planning/timeline/timeline.2013.xls: hid completed tasks
- 06:43 AM Revision 11689: planning/timeline/timeline.2013.xls: updated for progress
- 06:23 AM Revision 11688: inputs/CVS/run: `make .../reinstall`: documented vegbiendev runtime (45 min)
- 05:35 AM Revision 11687: removed inputs/CVS/cvs-archive-2012-12-04.schema.sql, which has been replaced by cvs-eep-archive-2013-10-22-VegBIEN.schema.sql
- 05:05 AM Revision 11686: bugfix: /README.TXT: to backup files not in Time Machine: PostgreSQL: need to run with `overwrite=1` so removed files are also deleted
- 05:02 AM Revision 11685: /README.TXT: to backup files not in Time Machine: PostgreSQL: only stop PostgreSQL after all files have been copied, to minimize the time that the PostgreSQL server is down (the final copy just copies concurrent changes)
- 05:02 AM Revision 11684: /README.TXT: to backup files not in Time Machine: PostgreSQL: only stop PostgreSQL after all files have been copied, to minimize the time that the PostgreSQL server is down (the final copy just copies concurrent changes)
- 04:59 AM Revision 11683: /README.TXT: updated to PostgreSQL 9.3
- 04:54 AM Revision 11682: added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.zip.url
- 04:54 AM Revision 11681: added inputs/CVS/cvs-eep-archive-2013-10-22-VegBIEN.schema.sql
- 04:52 AM Revision 11680: inputs/CVS/run: documented `make .../reinstall` runtime (25 min)
- 04:27 AM Revision 11679: inputs/VegBank/stemlocation_/header.csv: updated from reinstalling stemlocation_
- 04:26 AM Revision 11678: added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.schema.sql
- 04:23 AM Revision 11677: added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.schema.sql.run, which makes the SQL suitable for PostgreSQL
- 03:52 AM Revision 11676: bugfix: inputs/input.Makefile: sql/install: exit on error by using `set -o pipefail`
- 12:43 AM Revision 11675: fix: /Makefile: $(macPostgresLibs): added libpq.5, which is needed by PostgreSQL 9.3
- 12:29 AM Revision 11674: fix: /Makefile: postgres-Darwin: also need to install psycopg2
11/17/2013
- 11:27 PM Revision 11673: /Makefile: postgres-Linux: add the PostgreSQL 9.2 apt-src in case we ever need to downgrade to it
- 10:57 PM Revision 11672: bugfix: /Makefile: postgres-Linux: ignore errors if `sudo apt-get update` returns a non-zero exit status due to unreachable apt sources (which are likely unrelated to PostgreSQL, and should not prevent PostgreSQL configuration from continuing)
- 10:54 PM Revision 11671: bugfix: /Makefile: postgres-Linux: fixed command to create /etc/apt/sources.list.d/pgdg.list
11/15/2013
- 06:29 AM Revision 11670: schemas/*.conf: upgraded to PostgreSQL 9.3, which is needed for proper exception parsing in the auto-re-create-views functionality
- 04:29 AM Revision 11669: /Makefile: postgres-Linux: also install postgresql-#-postgis-scripts, which is used by derived/biengeo/
11/14/2013
- 02:36 PM Revision 11668: bugfix: schemas/vegbien.sql: plantobservation_aggregateoccurrence_count_1(): only default aggregateoccurrence.count to 1 for specimens data, because plots data may have any number of individuals in a taxon_presence record that has no explicit individual_count
- 02:32 PM Revision 11667: schemas/*.sql: updated for PostgreSQL 9.3. this reorders some functions, adds empty comment headers for omitted SEQUENCE SET commands, and (best of all) finally splits view columns onto multiple lines, so that changes in the columns are actually legible (and produce their own svn diff!)
- 01:00 PM Revision 11666: planning/timeline/timeline.2013.xls: added tasks "create high-level workflow diagram" and "load BIEN2 exports directly from raw data", as requested by Martha
- 07:19 AM Revision 11665: bugfix: lib/Firefox_bookmarks.reformat.csv: remove empty <DD> tags (which Firefox now adds for all bookmarks) so they don't create a blank space on the page
- 07:16 AM Revision 11664: bugfix: lib/Firefox_bookmarks.reformat.csv: don't prepend "page's description:" to empty <DD> tags, which Firefox now adds for all bookmarks, even if they don't have a description
- 07:06 AM Revision 11663: web/links/index.htm: updated to Firefox bookmarks. added instructions for upgrading PostgreSQL to 9.3, and some GBIF links.
- 06:44 AM Revision 11662: *Makefile, schemas/*.Mac.conf: upgraded to PostgreSQL 9.3, which is needed for proper exception parsing in the auto-re-create-views functionality. this also removes the Mac 10.8 Mountain Lion quirks, such as renaming the postgres user to _postgres (which messed everything up, but is now back to normal).
- 04:09 AM Revision 11661: /Makefile: postgres-Linux: added steps to install PostgreSQL 9.3, which is needed for proper exception parsing in the auto-re-create-views functionality
- 02:59 AM Revision 11660: schemas/util.sql: added save_drop_views()
- 02:37 AM Revision 11659: schemas/util.sql: added is_empty(anyarray)
- 02:17 AM Revision 11658: added inputs/GBIF/_src/0001000-131106143450413.zip.md5, GBIFPortalDB-2013-09-10.dump.gz.md5
- 02:16 AM Revision 11657: schemas/util.sql: added regexp_matches_group()
- 01:13 AM Revision 11656: schemas/util.sql: show_create_view(): also include GRANT statements, which are necessary to fully re-create the view
- 12:54 AM Revision 11655: schemas/util.sql: added show_grants_for(table_ regclass), for use by show_create_view()
- 12:49 AM Revision 11654: inputs/GBIF/_src/GBIFPortalDB-2013-09-10.dump.gz.url: documented download time (5.5 h for an 18 GB file)
- 12:40 AM Revision 11653: inputs/GBIF/_src/0001000-131106143450413.zip.url: documented download time (only 2 h for an 18 GB file)
11/13/2013
- 08:35 PM Revision 11652: schemas/util.sql: added save_drop_view()
- 08:33 PM Revision 11651: schemas/util.sql: added show_create_view()
- 07:14 PM Revision 11650: added inputs/GBIF/_src/0001000-131106143450413.zip.url (DwC-A export), GBIFPortalDB-2013-09-10.dump.gz.url (raw data), portal_26_feb_2013.war.url (raw data portal)
- 04:50 PM Revision 11649: web/.htaccess: mod_autoindex: show .* files which are normally hidden, because these are important parts of our codebase. (the leading . is not used for access controls.) .svn folders will remain hidden to avoid clutter.
- 04:16 PM Revision 11648: inputs/GBIF/: added LOA files: _src/use_conditions/LetterOfAgreement_template.doc, BIEN LoA agreement annex.docx
- 02:48 AM Revision 11647: inputs/.TNRS/schema.sql: tnrs_populate_fields(): regenerate the derived cols: updated runtime (40 min)
- 01:07 AM Revision 11646: web/links/index.htm: updated to Firefox bookmarks. added links related to PostgreSQL plain-text pkeys and the GBIF data use agreement (which is apparently much less restrictive than the LoA we signed, and would even allow the data to be public). vegetation data: placed links into subfolders by datasource.
11/10/2013
- 07:09 PM Revision 11645: bugfix: schemas/vegbien.sql: scrubbed_morphospecies_binomial: only append the morphospecies suffix if there is not a scrubbed specific epithet
- 07:08 PM Revision 11644: bugfix: schemas/vegbien.sql: scrubbed_morphospecies_binomial: only populate this from the component ranks; do not put a full taxon name in here if it would otherwise be NULL
- 07:02 PM Revision 11643: inputs/.TNRS/schema.sql: tnrs: removed no longer used Accepted_scientific_name. use scrubbed_unique_taxon_name instead.
- 07:00 PM Revision 11642: inputs/.TNRS/schema.sql: MatchedTaxon, etc.: removed no longer used acceptedScientificName (from tnrs.Accepted_scientific_name). use scrubbed_unique_taxon_name instead.
- 06:43 PM Revision 11641: inputs/.TNRS/schema.sql: removed no longer used AcceptedTaxon. use taxon_scrub.scrubbed_unique_taxon_name.* instead.
- 06:38 PM Revision 11640: bugfix: schemas/vegbien.sql: tnrs_input_name: MatchedTaxon self-join: must use a NOT NULL column for a proper anti-join. this unfortunately requires the more verbose LEFT JOIN ON syntax (which allows using the pkey as the NOT NULL column) instead of NATURAL LEFT JOIN (which requires using another column, which are all nullable)
- 06:34 PM Revision 11639: schemas/vegbien.sql: tnrs_input_name: use plain UNION, which automatically removes duplicates, rather than UNION ALL with a manual EXCEPT-removal of rows in the first SELECT
- 06:14 PM Revision 11638: schemas/vegbien.sql: tnrs_input_name: updated to use taxon_scrub.scrubbed_unique_taxon_name.*, to avoid further dependencies on AcceptedTaxon
- 05:55 PM Revision 11637: inputs/.TNRS/schema.sql: removed no longer used ScrubbedTaxon. use taxon_scrub instead.
- 05:54 PM Revision 11636: schemas/vegbien.sql: taxon_trait_view: updated to use new taxon_scrub
- 05:51 PM Revision 11635: schemas/vegbien.sql: analytical_stem_view: updated to use new taxon_scrub. this avoids the need to manually COALESCE() every accepted* and matched* field, and makes the formulas much clearer
- 04:11 PM Revision 11634: inputs/.TNRS/schema.sql: added taxon_scrub, which combines ValidMatchedTaxon with scrubbed_unique_taxon_name.* instead of AcceptedTaxon
- 03:38 PM Revision 11633: inputs/.TNRS/schema.sql: ValidMatchedTaxon: synced to MatchedTaxon
- 03:22 PM Revision 11632: fix: inputs/.TNRS/schema.sql: scrubbed_taxon_name_with_author: renamed to scrubbed_unique_taxon_name because this also contains the family, and is therefore different from just the taxon name with author
- 01:50 PM Revision 11631: inputs/.TNRS/schema.sql: MatchedTaxon: added scrubbed_taxon_name_with_author
- 01:23 PM Revision 11630: inputs/.TNRS/schema.sql: tnrs: removed Is_homonym, since this did not take into account the never_homonym status (when the author disambiguates) or the ability of a non-homonym at a lower rank to override a homonym at a higher rank. taking these into account just produces the value of is_valid_match.
- 01:19 PM Revision 11629: inputs/.TNRS/schema.sql: tnrs: removed Is_plant, since this functionality is now provided by is_valid_match. note that whether a name is a plant is not meaningful for TNRS, because it can match only plant names (thus a "non-plant" is actually a non-match).
- 01:06 PM Revision 11628: inputs/.TNRS/schema.sql: tnrs: added scrubbed_taxon_name_with_author derived column, which uses the matched name when an accepted name is not available
- 09:44 AM Revision 11627: inputs/.TNRS/schema.sql: tnrs: removed no longer used Max_score. use is_valid_match to determine validity instead.
- 12:09 AM Revision 11626: bugfix: lib/runscripts/file.pg.sql.run: export_(): exclude Source and related tables so that these will be re-created by the staging tables installation instead, ensuring that they are always in sync with the Source/ subdir
- 12:08 AM Revision 11625: inputs/.TNRS/data.sql: updated for new derived columns
- 12:04 AM Revision 11624: bugfix: lib/runscripts/file.pg.sql.run: export_(): exclude Source and related tables so that these will be re-created by the staging tables installation instead, ensuring that they are always in sync with the Source/ subdir
11/09/2013
- 10:22 PM Revision 11623: bugfix: schemas/vegbien.sql: analytical_stem_view: scrubbed_taxon_name_no_author, scrubbed_author: need to COALESCE() these to the matched* when no accepted* is available
- 10:02 PM Revision 11622: schemas/vegbien.sql: analytical_stem_view, etc.: renamed scrubbed fields with the scrubbed_* prefix, to clearly distinguish these from the equivalent fields for other taxon names
- 09:10 PM Revision 11621: bugfix: schemas/vegbien.sql: analytical_stem_view: family, genus: need to COALESCE() these to the matched* when no accepted* is available
- 06:04 PM Revision 11620: backups/TNRS.backup.md5: updated
- 04:47 PM Revision 11619: inputs/.TNRS/schema.sql: removed no longer used score_ok(). use tnrs.Is_plant instead. (the threshold is still documented in tnrs_populate_fields().)
- 04:45 PM Revision 11618: inputs/.TNRS/schema.sql: tnrs_populate_fields(): is_valid_match: don't consider Max_score because Is_plant will always be false when the Max_score is insufficient (<0.8)
- 04:20 PM Revision 11617: inputs/.TNRS/schema.sql: schema comment: added steps to remake schema.sql and back up the new TNRS schema. documented that these steps should be run on vegbiendev.
- 04:16 PM Revision 11616: inputs/.TNRS/schema.sql: schema comment: added steps to determine what changes need to be made on vegbiendev
- 04:01 PM Revision 11615: inputs/.TNRS/schema.sql: tnrs_populate_fields(): regenerate the derived cols: updated runtimes (~same)
- 03:54 PM Revision 11614: inputs/.TNRS/schema.sql: tnrs: moved instructions to apply schema changes on vegbiendev to the TNRS schema, because this applies to all elements in the TNRS schema, not just the tnrs table
- 03:30 PM Revision 11613: inputs/.TNRS/schema.sql: score_ok(): don't make it STRICT because this prevents it from being inlined
- 03:24 PM Revision 11612: inputs/.TNRS/schema.sql: tnrs: removed no longer used tnrs_score_ok index. use tnrs__valid_match instead.
- 03:09 PM Revision 11611: bugfix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): is_valid_match: documented that this excludes homonyms because these are not valid matches (i.e. TNRS provides a name, but the name is not meaningful because it is not unambiguous)
- 03:07 PM Revision 11610: bugfix: inputs/.TNRS/schema.sql: ValidMatchedTaxon: exclude inter-kingdom homonyms because these are not valid matches (i.e. TNRS provides a name, but the name is not meaningful because it is not unambiguous). this uses taxon_scrub__is_valid_match instead of score_ok() to determine whether the result should be included.
- 02:56 PM Revision 11609: inputs/.TNRS/schema.sql: ValidMatchedTaxon: synced to MatchedTaxon
- 02:55 PM Revision 11608: inputs/.TNRS/schema.sql: MatchedTaxon: added is_valid_match
- 02:52 PM Revision 11607: inputs/.TNRS/schema.sql: tnrs: added tnrs__valid_match index to facilitate joining to only valid matches
- 02:48 PM Revision 11606: inputs/.TNRS/schema.sql: tnrs: added is_valid_match derived column, to make it easier to select from only those TNRS results that can safely be used as a scrubbed name
- 02:02 PM Revision 11605: lib/sh/util.sh: already_exists_msg(): added instructions on how to force-remake when the file already exists (prepend `rm=1` to the command)
- 02:20 AM Revision 11604: inputs/VegBank/^taxon_observation.**.sample/test.xml.ref: updated inserted row count, now that CVS plots have been removed
11/08/2013
- 10:57 PM Revision 11603: bugfix: lib/runscripts/view.run: don't do anything in load_data(), to avoid trying to remake header.csv before the view is created. (for views, this instead happens in postprocess().)
- 10:51 PM Revision 11602: lib/runscripts/table.run: reordered functions in the order they are called by import()
- 10:28 PM Revision 11601: bugfix: inputs/VegBank/: need to remove inter-datasource duplicates from plot instead of the left-joined plot_ table, because the fkeys needed to do the cascading deletes are all to the plot table. this requires doing the column-renaming and postprocessing on plot *before* it's left-joined.
- 10:10 PM Task #815 (New): auto-prepend table name to columns
- * this avoids the need to add manual renames for every column just to prepend the table name
- 10:08 PM Task #814 (New): rename columns by name, not position
- * this avoids frameshift bugs when columns are added/removed
** this is especially a problem when adding source-spec... - 09:57 PM Revision 11600: inputs/VegBank/plot_/create.sql: updated runtime (5 s) for previous bugfix
- 07:50 PM Revision 11599: exports/2013-7-10.Naia.range_limiting_factors.csv.run: updated export_() runtime and rowcount (~ the same)
- 04:26 PM Revision 11598: bugfix: schemas/vegbien.sql: 2013-7-10.Naia.range_limiting_factors: filter by coordinateUncertaintyInMeters filter: assume true for rows with no coordinateUncertaintyInMeters
- 03:43 PM Revision 11597: schemas/vegbien.sql: 2013-7-10.Naia.range_limiting_factors: filter by coordinateUncertaintyInMeters <= 10 km
11/07/2013
- 04:41 PM Revision 11596: planning/timeline/timeline.2013.xls: updated for progress
- 04:00 PM Revision 11595: inputs/.geoscrub/geoscrub_output/run: load_data(): updated runtime (4 min)
- 08:42 AM Revision 11594: planning/timeline/timeline.2013.xls: updated for progress
- 08:34 AM Revision 11593: bugfix: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: invoking derived/biengeo/geoscrub.sh: need to split the input file into separate dir and filename parts, because $DATAFILE actually is just the filename, not the entire path, and will otherwise get prepended with the default value for $DATADIR
11/06/2013
- 04:57 PM Revision 11592: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: also run geoscrub.sh. added export_() target to run just the export of the result table separately.
- 04:39 PM Revision 11591: derived/biengeo/load-geoscrub-input.sh: allow the caller to override $DATAFILE in the environment, to use a file named other than "geoscrub-corpus.csv"
- 02:41 PM Revision 11590: /run: use new exports/geoscrub_input.csv.run
- 02:40 PM Revision 11589: added exports/geoscrub_input.csv.run
- 02:39 PM Revision 11588: bugfix: lib/sh/make.sh: $remake: need to explicitly propagate this to invoked commands if it was set from $rm
- 12:34 PM Revision 11587: derived/biengeo/load-geoscrub-input.sh: updated $DATA_URL for new input filename
- 12:27 PM Revision 11586: /run geoscrub_input/make(): include a header on the CSV file, so that the column names don't risk getting spliced from the data (and to shorten the CSV filename, which had to contain the column names instead). this requires changing the geoscrubbing scripts to accept a CSV header.
- 11:22 AM Revision 11585: planning/timeline/timeline.2013.xls: updated for progress
- 10:14 AM Revision 11584: exports/2013-7-10.Naia.range_limiting_factors.csv.run: added rowcount (40 million of 80 million observations, filtered w/ cultivated, geovalid, and various fields NOT NULL)
- 01:46 AM Revision 11583: exports/2013-7-10.Naia.range_limiting_factors.csv.run: updated export_() runtime
- 01:30 AM Revision 11582: schemas/vegbien.sql: 2013-7-10.Naia.range_limiting_factors: don't sort the results by occurrence_id, because this is not a meaningful ordering and prevents incremental output from the query
- 01:09 AM Revision 11581: schemas/vegbien.sql: 2013-7-10.Naia.range_limiting_factors: also filter out rows without species
- 12:59 AM Revision 11580: exports/2013-7-10.Naia.range_limiting_factors.csv.run: export_(): documented runtime (10 min)
11/05/2013
- 11:13 PM Revision 11579: lib/sh/db.sh: mk_select(): usage: documented that this also takes a $limit/$n param
- 11:12 PM Revision 11578: lib/sh/db.sh: limit(): also support using $n as the limit param, since this var name is used by other parts of the import process
- 11:08 PM Revision 11577: added backups/vegbien.r11549.backup.md5
- 11:07 PM Revision 11576: lib/sh/db.sh: limit(): usage: documented that this also need a $limit param
- 11:06 PM Revision 11575: backups/TNRS.backup.md5: updated
- 10:47 PM Revision 11574: lib/runscripts/extract.run: added export_sample()
- 10:31 PM Revision 11573: /README.TXT: Full database import: after import: record the import times in inputs/import.stats.xls: documented that this should be run on the local machine, because it needs the Mac filename ordering
- 10:30 PM Revision 11572: planning/timeline/timeline.2013.xls: updated for progress
- 10:19 PM Revision 11571: inputs/import.stats.xls: updated import times
- 08:54 PM Revision 11570: /README.TXT: Full database import: after import: removed step to install analytical_stem on nimoy because the import mechanism is not set up to do this (we don't generate CSV exports of the full analytical_stem table because they take up a lot of space and are not currently used for anything)
- 08:32 PM Revision 11569: /README.TXT: Full database import: after import: In PostgreSQL: added step to check that analytical_stem contains the expected # of rows
- 08:16 PM Revision 11568: /README.TXT: Full database import: after import: In PostgreSQL: added specific instructions for determining which/how many datasources are expected to be included in the provider_count and source tables
- 08:05 PM Revision 11567: added inputs/analytical_db/_archive/
- 07:46 PM Revision 11566: inputs/analytical_db/: removed import-related files (Source/, etc.), since this is actually just a folder used to store make_analytical_db.log.sql, so that it will be synced along with the other logs
- 07:43 PM Revision 11565: inputs/analytical_db/: added _no_import to prevent this from incorrectly being included in the source table
- 07:27 PM Revision 11564: inputs/input.Makefile: $(_svnFilesGlob): also svn-add _no_import in the top-level datasrc dir. (this requires using add! , because the presence of a _no_import file there will normally turn off adding by svnFilesGlob.)
- 11:49 AM Revision 11563: Added an output CSV file option to geoscrub.sh.
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