schemas/functions.sql: Added table2hstore()

schemas/functions.sql: Added reset_map_table()

schemas/functions.sql: Added truncate()

schemas/functions.sql: mk_map_table(): Use the sql language instead of plpgsql because EXECUTE is not used directly, so plpgsql is not actually needed

schemas/functions.sql: mk_map_table(): Store map table schema in separate `map` table and extend it using LIKE, for easier maintainability of the map schema

schemas/functions.sql: Added mk_map_table()

schemas/functions.sql: ensure_prefix(): Made it IMMUTABLE instead of STABLE

schemas/functions.sql: Added rename_cols()

inputs/FIA/*/postprocess.sql: Avoid using :table, :table_str so that the commands in the script can also be run by pasting them into pgAdmin

README.TXT: Full database import: Manual steps to run TNRS/remake analytical DB: Added `export version=<version>` to ensure that the import is run into the correct schema. Since these instructions are for running commands separately from the rest of the import, it's important to first ensure that the import environment is set up properly.

schemas/vegbien.ERD.mwb: Added taxon_trait to ERD

schemas/vegbien.ERD.mwb: Regenerated exports

schemas/vegbien.sql: Removed unused analytical_aggregate table, because analytical_stem provides much more detailed, higher-quality data, both in terms of the number or of rows and the number of columns. analytical_aggregate has also long been out of sync with the analytical DB schema, and it doesn't make sense to spend processing time in make_analytical_db to perform the DISTINCT ON if the table isn't being used. We may revisit analytical_aggregate later once we have ID fields for each entity in the DISTINCT ON and can avoid DISTINCTing on all analytical_aggregate columns.

schemas/vegbien.sql: Removed unused analytical_aggregate table, because analytical_stem provides much more detailed, higher-quality data, both in terms of the number or of rows and the number of columns. analytical_aggregate has also long been out of sync with the analytical DB schema, and it doesn't make sense to spend processing time in make_analytical_db to perform the DISTINCT ON if the table isn't being used. We may revisit analytical_aggregate later once we have ID fields for each entity in the DISTINCT ON and can avoid DISTINCTing on all analytical_aggregate columns.

inputs/FIA/*/postprocess.sql: Added index on *.CN (autogen IDs)

README.TXT: Full database import: Added steps to use `screen` to allow recovering from a closed terminal window

inputs/FIA/TREE/postprocess.sql: TREE.unique index: Renamed to TREE.ID because this is on an autogenerated pkey rather than on domain values (for which a set of unique columns has not yet been found and may not exist)

inputs/FIA/REF_SPECIES/postprocess.sql: Matched SPECIES_SYMBOL to .SYMBOL. Added .SYMBOL_TYPE for use in joining to REF_PLANT_DICTIONARY.

Added inputs/FIA/REF_UNIT/postprocess.sql

Added inputs/FIA/REF_RESEARCH_STATION/postprocess.sql

Added inputs/FIA/COUNTY/postprocess.sql

Added inputs/FIA/REF_PLANT_DICTIONARY/postprocess.sql

inputs/FIA/COND/postprocess.sql: Matched COND.HABTYPCD1, COND.HABTYPCD1_PUB_CD to REF_HABTYP_DESCRIPTION

inputs/input.Makefile: Staging tables installation: $(exportHeader): Fixed bug where need to run postprocess.sql before exporting the header, because it can change the column names

inputs/input.Makefile: Staging tables installation: $(exportHeader): export the header before running $(cleanup), because the header is not affected by the data cleanup operations and thus can be generated right away, to allow mapping while the cleanup operations run

inputs/FIA/REF_HABTYP_DESCRIPTION/postprocess.sql: Prepare columns for joining with COND

inputs/input.Makefile: Staging tables installation: $(exportHeader): Fixed bug where need to use psql_script_vegbien instead of the psql_verbose_vegbien used by $(psqlAsBien), to avoid echoing commands as part of the exported header

Added planning/workflow/(de)normalized_import.mappings.png

Added planning/workflow/denormalized_import.png, normalized_import.png

web/main/IH/: Added lowercase alias

Added web/main/IH/

inputs/input.Makefile: Staging tables installation: Added postprocess target, which runs all the postprocess.sql files

inputs/FIA/REF_SPECIES/postprocess.sql: Cast ID column to integer

inputs/FIA/*/postprocess.sql: Cluster tables by their *.unique index for faster joins

inputs/FIA/*/postprocess.sql: Cast ID columns to integer using new functions.set_col_types()

bin/psql_verbose_vegbien: Run with client_min_messages = NOTICE to display notices for debugging. This is supposed to be the default, but apparently isn't.

inputs/input.Makefile: BIEN commands: $(psqlAsBien): Use psql_verbose_vegbien instead of psql_script_vegbien so that timings and notices are displayed, which is useful for profiling and debugging

schemas/functions.sql: Added col_cast and set_col_types()

schemas/functions.sql: Added col_ref, col_type()

schemas/functions.sql: Added cluster_once()

schemas/functions.sql: Added cluster_index()

schemas/functions.sql: create_if_not_exists(): Also handle duplicate_column exceptions

schemas/functions.sql: Added rename_if_exists()

inputs/FIA/COND/postprocess.sql: Renamed oldgrowth to COND.oldgrowth so it wouldn't be renamed by to_global_col_names()

inputs/FIA/COND/postprocess.sql: Added oldgrowth column as part of the postprocessing instead of as part of the view that left joins the core tables together. This avoids needing to regenerate the oldgrowth field whenever the view is queried or materialized.

inputs/FIA/TREE/postprocess.sql: Added index on columns that join to parent tables

inputs/FIA/*/postprocess.sql: Removed table prefix from globally-unique columns that should be joined on

schemas/functions.sql: Marked STRICT functions as such

schemas/functions.sql: col_global_names(): Treat any column name that contains . as already being globally unique, and don't prepend the table name. This allows renaming the table columns after running col_global_names(), without causing the table name to be re-prepended the next time col_global_names() is run.

schemas/functions.sql: Added contains()

schemas/functions.sql: Added create_if_not_exists()

inputs/FIA/*/postprocess.sql: Use functions.to_global_col_names() to ensure that all column names are globally unique. This makes it easy to join the tables together without worrying about column name collisions.

inputs/FIA/*/postprocess.sql: Use new functions.create_if_not_exists() to allow re-running postprocess.sql idempotently

inputs/input.Makefile: Staging tables installation: %/install: Use new %.sql/run to run postprocess.sql

inputs/input.Makefile: Staging tables installation: Added %.sql/run to run postprocess.sql, etc. separately from the install targets they are a part of

inputs/input.Makefile: Staging tables installation: Added %.sql/run to run postprocess.sql, etc. separately from the install targets they are a part of

schemas/functions.sql: Added to_global_col_names()

schemas/functions.sql: col_global_names(): Use new functions.ensure_prefix() to only add the table name prefix if it doesn't already exist. This makes the function idempotent.

schemas/functions.sql: Added ensure_prefix()

schemas/functions.sql: Added has_prefix()

schemas/functions.sql: Added col_global_names()

schemas/functions.sql: Added name(regtype)

schemas/functions.sql: Added col_names()

root Makefile: Installation: Fixed bug where need to run schemas/public/install separately because schemas/install installs only the util schemas

root Makefile: Installation: install util schemas (temp functions py_functions) before inputs, so that inputs can use util functions in their postprocess.sql or create.sql scripts. (However, they must not use util functions in views or index functions, because these would be cascadingly deleted whenever the util schemas are reinstalled before an import.)

README.TXT: Single datasource import: Added by_col=1 to all commands

mappings/VegCore-VegBIEN.csv: locationRemarks: Remapped to locationnarrative because location.notespublic is a boolean field

lib/sql_io.py: mk_errors_table(): Create a unique index on the MD5 of the value and error instead of on the values directly, because some strings are too long to index (e.g. row 2537268 of MO.Specimen causes an error "index row size 3032 exceeds maximum 2712 for index [...] Values larger than 1/3 of a buffer page cannot be indexed")

inputs/import.stats.xls: Updated import times

bin/map: No mappings warning: Added explanation that this could also be due to no column name matches, and hint to check if you are importing the correct input table

inputs/MO/: Renamed Specimen.2/ -> now available Specimen/

inputs/MO/: Removed old import in Specimen/

Refreshed MO

csvs.py: TsvReader.next(): Fixed bug where empty line needs to be separately returned as [], because csv.reader would interpret it as EOF since the line ending has already been removed

csvs.py: sniff(): TSVs: Turn off quoting because TSVs use \-escapes instead of quotes to escape delimeters, newlines, etc.

csvs.py: InputRewriter.readline(): Surround function in a try block that prints all exceptions, so that debugging information is available if an error occurs when this stream is used as input for psycopg's copy_expert() (COPY FROM)

Populated inputs/MO/import_order.txt

Refreshed SALVIAS

Added web/main/CTFS/

inputs/SALVIAS/: Regenerated salvias_*.schema.sql from the MySQL version, to take advantage of my2pg improvements. The placeholder *_index columns which take the place of MySQL's inline index definitions have now been replaced by no-op CHECK constraints, so that there are no longer lots of dummy *_index columns in the map spreadsheets.

Added web/main/Redmine/ alias to VegBIEN/Redmine/

Added web/main/VegBIEN/Redmine/

web/main/VegBIEN/.htaccess: Forward to new db/ subdir

Added web/main/VegBIEN/db/

web/main/**/.htaccess: Removed RewriteCond -l tests because one of the -d or -f tests will always also pass, making the -l test unnecessary

web/main.conf: Added tolower RewriteMap

web/main/.htaccess: use separate lowercase version when available: Also support input strings in mixed case which is not the default capitalization, in addition to all-lowercase strings

web/main/.htaccess: use separate lowercase version when available: Generate the new dirname with a separate RewriteCond so its value can be used both in the -d test and in the replacement string, rather than separately for each

web/main/.htaccess: translate dotpaths: Allow an unescaped . at the beginning of a filename, because this will never be a . separator. This adds support for hidden files in dir paths, which now won't be interpreted as dotpaths. However, regular files with extensions still need to have the filename escaped because it will otherwise be interpreted as a dotpath.

web/main/.htaccess: Set Options +FollowSymLinks. It should be on by default ("All options except for MultiViews. This is the default setting." <http://httpd.apache.org/docs/2.2/mod/core.html#options&gt;), but this makes sure it will always be enabled.

web/main/.htaccess: Name the lowercased versions of dirs with a leading . (to make them hidden) instead of a trailing _ , to avoid having each dir listed twice in a row in the dir index

Added web/main/TNRS/

Added web/main/VegBank/

Added web/main/BIEN2/

web/main/index.php: Replaced - with . in namespaces to conform to new dotpath naming convention, which allows nesting of namespaces

web/main/SALVIAS/.htaccess: Forward to new dd/ subdir

Added web/main/SALVIAS/dd/

web/main/DwC/.htaccess: Forward to new terms/ subdir

Added web/main/DwC/terms/

web/main/**/.htaccess: don't redirect subdir paths: Fixed bug where can only match non-empty string, because otherwise the rule would match this directory, which should still have its redirects processed