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# Date Author Comment
14538 08/21/2014 08:49 AM Aaron Marcuse-Kubitza

lib/strings.py: added unesc_quotes() and helper functions

14537 08/21/2014 08:49 AM Aaron Marcuse-Kubitza

lib/strings.py: added json_decode()

14536 08/21/2014 08:38 AM Aaron Marcuse-Kubitza

/README.TXT: To re-run geoscrubbing: updated runtimes

14535 08/21/2014 08:25 AM Aaron Marcuse-Kubitza

exports/*_GBIF.csv.run: documented compress_() runtime (20 min-1 h)

14534 08/20/2014 11:12 PM Aaron Marcuse-Kubitza

lib/runscripts/extract.run: export_(): also compress created file

14533 08/20/2014 11:11 PM Aaron Marcuse-Kubitza

lib/sh/archives.sh: added compress(), expand(), which handle compression of individual files

14532 08/20/2014 04:26 PM Aaron Marcuse-Kubitza

bugfix: inputs/input.Makefile: sql/install: ";" for commands inside $(if) blocks need to be inside the $(if) block, too, because otherwise there will be dangling ";" without a statement (bash does not support empty statements containing just ";")

14531 08/20/2014 11:29 AM Aaron Marcuse-Kubitza

/README.TXT: Full database import: converted database commands to command-line commands to make them easier to run

14530 08/20/2014 11:28 AM Aaron Marcuse-Kubitza

/README.TXT: Full database import: converted database commands to command-line commands to make them easier to run

14529 08/20/2014 10:55 AM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks: added instructions for how to enable automatic restart on power loss for the UPS (which isn't accessible in the GUI)

14528 08/19/2014 05:13 PM Aaron Marcuse-Kubitza

fix: schemas/util.sql: contained_within_approx(point geocoord, region postgis.geography): use util.geography() instead of implicit cast to suppress "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" NOTICEs

14527 08/19/2014 05:10 PM Aaron Marcuse-Kubitza

schemas/util.sql: added geography(util.geocoord), which suppresses "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" NOTICEs

14526 08/19/2014 04:48 PM Aaron Marcuse-Kubitza

exports/native_status_resolver.csv.run: updated export_() runtime (5 min, now that we're using the narrower New World criterion)

14525 08/19/2014 04:39 PM Aaron Marcuse-Kubitza

fix: schemas/public_.sql: native_status_resolver: don't include rows with New World coordinates that don't also have New World country names, since the NSR only uses the country name

14524 08/19/2014 04:26 PM Aaron Marcuse-Kubitza

schemas/public_.sql: native_status_resolver: removed rows with is_geovalid NULL, at Brad's request. note that this removes valid rows with standardized country names.

14523 08/19/2014 04:01 PM Aaron Marcuse-Kubitza

exports/native_status_resolver.csv.run: updated export_() runtime (30 min)

14522 08/19/2014 03:28 PM Aaron Marcuse-Kubitza

fix: schemas/public_.sql: native_status_resolver: added country IS NOT NULL filter requested by Brad

14521 08/19/2014 02:35 PM Aaron Marcuse-Kubitza

fix: schemas/public_.sql: native_status_resolver: remove the id because this prevents SELECT DISTINCT from having the desired effect. instead, the results will be joined back using the other columns.

14520 08/19/2014 02:25 PM Aaron Marcuse-Kubitza

exports/native_status_resolver.csv.run: upload_(): documented runtime (2.5 min)

14519 08/19/2014 02:18 PM Aaron Marcuse-Kubitza

bugfix: exports/native_status_resolver.csv.run: upload_(): $live must be exported

14518 08/19/2014 02:15 PM Aaron Marcuse-Kubitza

exports/native_status_resolver.csv.run: upload_(): use `live=1` instead for consistency with other invocations of put

14517 08/19/2014 02:14 PM Aaron Marcuse-Kubitza

fix: exports/native_status_resolver.csv.run: upload_(): need `l=1`

14516 08/19/2014 02:12 PM Aaron Marcuse-Kubitza

exports/native_status_resolver.csv.run: documented export_() runtime (45 min)

14515 08/19/2014 01:48 PM Aaron Marcuse-Kubitza

exports/native_status_resolver.csv.run: added upload_() to get the file onto nimoy

14514 08/19/2014 01:25 PM Aaron Marcuse-Kubitza

added exports/native_status_resolver.csv.run

14513 08/19/2014 01:23 PM Aaron Marcuse-Kubitza

schemas/public_.sql: added native_status_resolver view, requested by Brad (wiki.vegpath.org/Data_requests)

14512 08/19/2014 11:47 AM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: udpated

14511 08/19/2014 08:37 AM Aaron Marcuse-Kubitza

lib/tnrs.py: documentation about output of the retrieve step: added that this is also unusable because the array does not contain all the columns and contains no column names

14510 08/19/2014 07:54 AM Aaron Marcuse-Kubitza

removed no longer used web/BIEN3/Redmine/main/. use Redmine/!__ instead.

14509 08/19/2014 07:52 AM Aaron Marcuse-Kubitza

web/BIEN3/Redmine/issues/.htaccess: perform .. redirects using new ! prefix

14508 08/19/2014 07:51 AM Aaron Marcuse-Kubitza

web/BIEN3/Redmine/.htaccess: enable redirects that avoid using a subdir's .htaccess

14507 08/19/2014 07:46 AM Aaron Marcuse-Kubitza

web/BIEN3/Redmine/wiki/.htaccess: removed no longer needed ignore_fs, since the .htaccess does not have RewriteRules that would need this in a RewriteCond

14506 08/19/2014 07:42 AM Aaron Marcuse-Kubitza

web/BIEN3/Redmine/issues/.htaccess: main issues page: added default filter conditions

14505 08/19/2014 07:41 AM Aaron Marcuse-Kubitza

bugfix: web/BIEN3/Redmine/issues/.htaccess: need to redirect to separate URL for individual issues, because they are not located under the issues/ subdir in Redmine

14504 08/19/2014 06:35 AM Aaron Marcuse-Kubitza

added web/.issues symlink and dest dir (needed because Apache does not support dangling symlinks)

14503 08/19/2014 06:35 AM Aaron Marcuse-Kubitza

web/BIEN3/Redmine/wiki/.htaccess: documented that this dir is needed because Apache does not support dangling symlinks

14502 08/19/2014 06:32 AM Aaron Marcuse-Kubitza

bugfix: web/.htaccess: need to expand top-level symlinks to avoid RewriteBase issues

14501 08/19/2014 06:29 AM Aaron Marcuse-Kubitza

web/main.conf: added RewriteMap for readlink

14500 08/19/2014 06:28 AM Aaron Marcuse-Kubitza

added web/readlink

14499 08/19/2014 05:52 AM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks: updated favicons

14498 08/19/2014 05:47 AM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks: updated favicons

14497 08/18/2014 04:52 PM Aaron Marcuse-Kubitza

web/BIEN3/Redmine/wiki/.htaccess: just use this dir as symlink dest, since the dir name is the same as the URL path within Redmine

14496 08/18/2014 04:50 PM Aaron Marcuse-Kubitza

web/.htaccess: don't rewrite existing files/dirs: allow forcing rewrite of existing things with %{ENV:ignore_fs}

14495 08/18/2014 03:41 PM Aaron Marcuse-Kubitza

web/BIEN3/Redmine/svn-web/.htaccess: use Redmine/ instead of main/ subdir

14494 08/18/2014 03:37 PM Aaron Marcuse-Kubitza

web/BIEN3/Redmine/.htaccess: point this to the Redmine root instead of to the wiki, to avoid the need to append /main

14493 08/18/2014 03:21 PM Aaron Marcuse-Kubitza

backups/vegbien.r14089.backup.md5: updated

14492 08/18/2014 01:58 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_best_match_jerry_lu index to facilitate finding names affected by the match-picking bug (#943)

14491 08/17/2014 12:04 PM Aaron Marcuse-Kubitza

backups/TNRS.backup.md5: updated

14490 08/17/2014 07:49 AM Aaron Marcuse-Kubitza

fix: inputs/HVAA/Specimen/postprocess.sql, map.csv: monthCollected/dayCollected: fix indefinite dates (which aren't supported by Postgres), as decided by Bob (https://docs.google.com/spreadsheets/d/1PI8n0CRttN7ttsXs5qfh5OFFzSoAfJj0gSbylgX6vj4/edit#gid=0)

14489 08/17/2014 07:23 AM Aaron Marcuse-Kubitza

schemas/util.sql: added date_part_fix()

14488 08/16/2014 05:55 PM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's and Martha's request (e-mails from Martha on 2014-8-12 at 17:37PT, and from Brian M on 2014-8-13 at 16:21PT). note that this change has already been made on vegbiendev.

14487 08/16/2014 05:51 PM Aaron Marcuse-Kubitza

schemas/public_.sql: added view_full_occurrence_individual_*GBIF, analytical_stem_*GBIF requested by Mark. note that this change has already been made on vegbiendev.

14486 08/16/2014 05:37 PM Aaron Marcuse-Kubitza

schemas/VegBIEN/data_dictionary/VegBIEN data dictionary.xlsx: updated

14485 08/16/2014 05:15 PM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

14484 08/16/2014 05:11 PM Aaron Marcuse-Kubitza

schemas/public_.sql: view_full_occurrence_individual, analytical_stem: renamed columns to shortened names at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

14483 08/16/2014 02:58 PM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view: renamed to analytical_stem since this replaces the materialized analytical_stem table. note that this change has already been made on vegbiendev.

14482 08/16/2014 02:35 PM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.

14481 08/16/2014 01:20 PM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_individual: re-ran viewFullOccurrence_individual_view_modify() to udpate this

14480 08/16/2014 01:15 PM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: copy_struct(): also need to util.copy_comment() because CREATE TABLE __ INCLUDING ALL is missing this

14479 08/16/2014 01:11 PM Aaron Marcuse-Kubitza

schemas/util.sql: added copy_comment(regclass, regclass)

14478 08/16/2014 12:29 PM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_individual_view: CREATE INDEX runtime: documented 2-column runtime (~2 h)

14477 08/16/2014 12:06 PM Aaron Marcuse-Kubitza

exports/analytical_stem_*GBIF.csv.run: documented runtime (40 min-1.2 h)

14476 08/16/2014 09:36 AM Aaron Marcuse-Kubitza

exports/view_full_occurrence_individual_*GBIF.csv.run: documented runtime (20-30 min)

14475 08/16/2014 08:37 AM Aaron Marcuse-Kubitza

added exports/analytical_stem_GBIF.csv.run, analytical_stem_non_GBIF.csv.run

14474 08/15/2014 07:15 PM Aaron Marcuse-Kubitza

added exports/view_full_occurrence_individual_GBIF.csv.run, view_full_occurrence_individual_non_GBIF.csv.run

14473 08/15/2014 04:13 PM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_individual_view: added "after updating this" instructions

14472 08/15/2014 04:01 PM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_individual_view: documented CREATE INDEX runtime (10 min - 1.5 h depending on the datatype and % populated)

14471 08/15/2014 03:32 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks: updated to use frenzy instead of starscream

14470 08/14/2014 03:25 PM Aaron Marcuse-Kubitza

fix: lib/tnrs.py: retrieval_request_template: source_sorting (Constrain by Source): corrected explanation to reflect that the behavior is actually the same in both modes, since only one match is ever marked as selected, and that match should always come first

14469 08/14/2014 10:50 AM Aaron Marcuse-Kubitza

planning/meetings/BIEN conference call availability.xlsx: updated

14468 08/11/2014 07:48 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_name index

14467 08/11/2014 07:46 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_family index

14466 08/11/2014 07:10 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_species_binomial index

14465 08/11/2014 05:28 AM Aaron Marcuse-Kubitza

bugfix: schemas/public_.sql: *_view_modify(): need to set the search_path so that tables are created in the same schema as the function, rather than whichever schema happens to be at the beginning of the search_path

14464 08/11/2014 05:19 AM Aaron Marcuse-Kubitza

bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to support being used directly instead of via a materialized table

14463 08/11/2014 05:13 AM Aaron Marcuse-Kubitza

schemas/public_.sql: removed no longer used analytical_stem. use analytical_stem_view or viewFullOccurrence_individual instead.

14462 08/11/2014 05:08 AM Aaron Marcuse-Kubitza

fix: schemas/public_.sql: viewfulloccurrence_individual_view_modify(): fixed capitalization in function name (needs "" to preserve case)

14461 08/11/2014 05:03 AM Aaron Marcuse-Kubitza

schemas/public_.sql: other derived views: use viewFullOccurrence_individual instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)

14460 08/11/2014 05:01 AM Aaron Marcuse-Kubitza

schemas/public_.sql: validation views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)

14459 08/11/2014 04:57 AM Aaron Marcuse-Kubitza

schemas/public_.sql: derived views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)

14458 08/11/2014 04:46 AM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: expansion_min_cols(): increased to properly handle all public-schema views (the largest is currently 2014-6-12.Jeff_Ott.climatic_range_determinants)

14457 08/11/2014 04:35 AM Aaron Marcuse-Kubitza

schemas/util.sql: view_def_to_orig(): use new expansion_min_cols() for easier configuration

14456 08/11/2014 04:33 AM Aaron Marcuse-Kubitza

schemas/util.sql: added expansion_min_cols() (the minimum # of cols from the same table to be treated as a * expression)

14455 08/11/2014 04:05 AM Aaron Marcuse-Kubitza

fix: schemas/public_.sql: analytical_stem_view: regenerated columns list for viewFullOccurrence_individual (instead of viewFullOccurrence_individual_view)

14454 08/11/2014 03:40 AM Aaron Marcuse-Kubitza

bugfix: mappings/VegCore-VegBIEN.csv: prefixed taxonomic ranks: use _concat_nullify() so that the prefix is only added if the epithet is non-NULL

14453 08/11/2014 03:29 AM Aaron Marcuse-Kubitza

fix: schemas/util.sql: col_re(): support column names with " in them

14452 08/11/2014 02:59 AM Aaron Marcuse-Kubitza

schemas/util.sql: added _concat_nullify(), which uses || instead of concat()

14451 08/11/2014 02:16 AM Aaron Marcuse-Kubitza

bugfix: inputs/FIA/REF_RESEARCH_STATION/map.csv: mapped country, which is not provided in the FIA data

14450 08/11/2014 01:46 AM Aaron Marcuse-Kubitza

schemas/public_.sql: removed no longer used threatened_taxonlabel_view. use iucn_red_list_view instead.

14449 08/11/2014 01:35 AM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_individual_view: documented materialize time (22 h)

14448 08/10/2014 05:53 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: taxon_match: removed no longer used scrubbed_unique_taxon_name. the scrubbed name ranks are now generated from the other TNRS columns instead.

14447 08/10/2014 05:28 AM Aaron Marcuse-Kubitza

/README.TXT: Full database import: added steps to re-run geoscrubbing

14446 08/10/2014 05:22 AM Aaron Marcuse-Kubitza

exports/geoscrub_input.csv.run: export_(): updated runtime (30 s)

14445 08/10/2014 03:57 AM Aaron Marcuse-Kubitza

fix: exports/viewFullOccurrence_*.csv.run: need to limit # rows to 5000 as requested by Bob

14444 08/10/2014 03:42 AM Aaron Marcuse-Kubitza

schemas/public_.sql: viewFullOccurrence_*: documented materialize time

14443 08/09/2014 10:23 PM Aaron Marcuse-Kubitza

bin/make_analytical_db: materialize viewFullOccurrence_individual_view instead of analytical_stem_view because analytical_stem_view is now generatable via a simple join onto viewFullOccurrence_individual_view. this avoids running into potential disk space constraints when materializing and backing up both tables (~50 GB/table * 2 tables * 2 copies (incl. the backup) = 200 GB, which is very close to the available disk space).

14442 08/09/2014 10:17 PM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view: use new materialized viewFullOccurrence_individual

14441 08/09/2014 10:08 PM Aaron Marcuse-Kubitza

schemas/public_.sql: added viewFullOccurrence_individual by running viewFullOccurrence_individual_view_modify()

14440 08/09/2014 10:05 PM Aaron Marcuse-Kubitza

schemas/public_.sql: added viewFullOccurrence_individual_view_modify(), analogous to analytical_stem_view_modify()

14439 08/09/2014 09:52 PM Aaron Marcuse-Kubitza

bin/make_analytical_db: removed extra () around psql_verbose_vegbien