inputs/VegBank/stemlocation_/header.csv: updated from reinstalling stemlocation_

added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.schema.sql

added inputs/CVS/_src/cvs-eep-archive-2013-10-22-VegBIEN.schema.sql.run, which makes the SQL suitable for PostgreSQL

bugfix: inputs/input.Makefile: sql/install: exit on error by using `set -o pipefail`

fix: /Makefile: $(macPostgresLibs): added libpq.5, which is needed by PostgreSQL 9.3

fix: /Makefile: postgres-Darwin: also need to install psycopg2

/Makefile: postgres-Linux: add the PostgreSQL 9.2 apt-src in case we ever need to downgrade to it

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)

bugfix: /Makefile: postgres-Linux: fixed command to create /etc/apt/sources.list.d/pgdg.list

schemas/*.conf: upgraded to PostgreSQL 9.3, which is needed for proper exception parsing in the auto-re-create-views functionality

/Makefile: postgres-Linux: also install postgresql-#-postgis-scripts, which is used by derived/biengeo/

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

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!)

planning/timeline/timeline.2013.xls: added tasks "create high-level workflow diagram" and "load BIEN2 exports directly from raw data", as requested by Martha

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

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

web/links/index.htm: updated to Firefox bookmarks. added instructions for upgrading PostgreSQL to 9.3, and some GBIF links.

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).

/Makefile: postgres-Linux: added steps to install PostgreSQL 9.3, which is needed for proper exception parsing in the auto-re-create-views functionality

schemas/util.sql: added save_drop_views()

schemas/util.sql: added is_empty(anyarray)

added inputs/GBIF/_src/0001000-131106143450413.zip.md5, GBIFPortalDB-2013-09-10.dump.gz.md5

schemas/util.sql: added regexp_matches_group()

schemas/util.sql: show_create_view(): also include GRANT statements, which are necessary to fully re-create the view

schemas/util.sql: added show_grants_for(table_ regclass), for use by show_create_view()

inputs/GBIF/_src/GBIFPortalDB-2013-09-10.dump.gz.url: documented download time (5.5 h for an 18 GB file)

inputs/GBIF/_src/0001000-131106143450413.zip.url: documented download time (only 2 h for an 18 GB file)

schemas/util.sql: added save_drop_view()

schemas/util.sql: added show_create_view()

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)

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.

inputs/GBIF/: added LOA files: _src/use_conditions/LetterOfAgreement_template.doc, BIEN LoA agreement annex.docx

inputs/.TNRS/schema.sql: tnrs_populate_fields(): regenerate the derived cols: updated runtime (40 min)

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.

bugfix: schemas/vegbien.sql: scrubbed_morphospecies_binomial: only append the morphospecies suffix if there is not a scrubbed specific epithet

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

inputs/.TNRS/schema.sql: tnrs: removed no longer used Accepted_scientific_name. use scrubbed_unique_taxon_name instead.

inputs/.TNRS/schema.sql: MatchedTaxon, etc.: removed no longer used acceptedScientificName (from tnrs.Accepted_scientific_name). use scrubbed_unique_taxon_name instead.

inputs/.TNRS/schema.sql: removed no longer used AcceptedTaxon. use taxon_scrub.scrubbed_unique_taxon_name.* instead.

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)

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

schemas/vegbien.sql: tnrs_input_name: updated to use taxon_scrub.scrubbed_unique_taxon_name.*, to avoid further dependencies on AcceptedTaxon

inputs/.TNRS/schema.sql: removed no longer used ScrubbedTaxon. use taxon_scrub instead.

schemas/vegbien.sql: taxon_trait_view: updated to use new taxon_scrub

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

inputs/.TNRS/schema.sql: added taxon_scrub, which combines ValidMatchedTaxon with scrubbed_unique_taxon_name.* instead of AcceptedTaxon

inputs/.TNRS/schema.sql: ValidMatchedTaxon: synced to MatchedTaxon

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

inputs/.TNRS/schema.sql: MatchedTaxon: added scrubbed_taxon_name_with_author

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.

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).

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

inputs/.TNRS/schema.sql: tnrs: removed no longer used Max_score. use is_valid_match to determine validity instead.

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

inputs/.TNRS/data.sql: updated for new derived columns

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

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

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

bugfix: schemas/vegbien.sql: analytical_stem_view: family, genus: need to COALESCE these to the matched* when no accepted* is available

backups/TNRS.backup.md5: updated

inputs/.TNRS/schema.sql: removed no longer used score_ok(). use tnrs.Is_plant instead. (the threshold is still documented in tnrs_populate_fields().)

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)

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.

inputs/.TNRS/schema.sql: schema comment: added steps to determine what changes need to be made on vegbiendev

inputs/.TNRS/schema.sql: tnrs_populate_fields(): regenerate the derived cols: updated runtimes (~same)

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

inputs/.TNRS/schema.sql: score_ok(): don't make it STRICT because this prevents it from being inlined

inputs/.TNRS/schema.sql: tnrs: removed no longer used tnrs_score_ok index. use tnrs__valid_match instead.

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)

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.

inputs/.TNRS/schema.sql: ValidMatchedTaxon: synced to MatchedTaxon

inputs/.TNRS/schema.sql: MatchedTaxon: added is_valid_match

inputs/.TNRS/schema.sql: tnrs: added tnrs__valid_match index to facilitate joining to only valid matches

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

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)

inputs/VegBank/^taxon_observation.**.sample/test.xml.ref: updated inserted row count, now that CVS plots have been removed

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().)

lib/runscripts/table.run: reordered functions in the order they are called by import()

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.

inputs/VegBank/plot_/create.sql: updated runtime (5 s) for previous bugfix

exports/2013-7-10.Naia.range_limiting_factors.csv.run: updated export_() runtime and rowcount (~ the same)

bugfix: schemas/vegbien.sql: 2013-7-10.Naia.range_limiting_factors: filter by coordinateUncertaintyInMeters filter: assume true for rows with no coordinateUncertaintyInMeters

schemas/vegbien.sql: 2013-7-10.Naia.range_limiting_factors: filter by coordinateUncertaintyInMeters <= 10 km

planning/timeline/timeline.2013.xls: updated for progress

inputs/.geoscrub/geoscrub_output/run: load_data(): updated runtime (4 min)

planning/timeline/timeline.2013.xls: updated for progress

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

inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: also run geoscrub.sh. added export_() target to run just the export of the result table separately.

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"

/run: use new exports/geoscrub_input.csv.run

added exports/geoscrub_input.csv.run

bugfix: lib/sh/make.sh: $remake: need to explicitly propagate this to invoked commands if it was set from $rm

derived/biengeo/load-geoscrub-input.sh: updated $DATA_URL for new input filename

/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.

planning/timeline/timeline.2013.xls: updated for progress

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)

exports/2013-7-10.Naia.range_limiting_factors.csv.run: updated export_() runtime

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

schemas/vegbien.sql: 2013-7-10.Naia.range_limiting_factors: also filter out rows without species

exports/2013-7-10.Naia.range_limiting_factors.csv.run: export_(): documented runtime (10 min)