schemas/vegbien.sql: taxonconcept: Renamed canon_taxonconcept_id to canon_concept_id to shorten the name, which is used often

sql.py: mk_update(): in_place: Convert columns of type character varying to text so that they can be merge-joined with text columns. Note that these two types are equivalent but not aliases of one another, so the explicit type change is needed.

sql_gen.py: Added canon_type()

sql.py: mk_update(): in_place: Factored retrieval of column type out into separate statement for clarity

schemas/functions.sql: _join*(): Fixed bug where was returning '' instead of NULL when only NULL inputs were provided, because array_to_string() always returns a non-NULL string. Functions must always return NULL in place of '' to ensure that empty strings do not find their way into VegBIEN, and to prevent inconsistencies between row-based and column-based import (row-based import folds empty strings to NULL while column-based import relies on having a clean input table).

sql_io.py: cleanup_table(): Use sql.table_pkey_col() instead of sql.pkey_col() so that only an actual pkey column is removed from the list of columns to clean. This fixes a bug where the first column in the table was not cleaned up if there was no pkey. Note that this bug only affected newly re-created staging tables, because staging tables previously had a special row_num pkey column added if they did not already have a pkey. The row_num column is now added by column-based import instead.

sql.py: table_pkey_col(): Raise a DoesNotExistException if the table has no pkey

sql.py: pkey_col(): Call table_pkey_col() directly rather than via pkey_name(). pkey_name(): Call pkey_col() instead of table_pkey_col() now that pkey_col() calls table_pkey_col().

sql.py: pkey_col(): Documented that if there is no pkey, returns the first column in the table

sql.py: pkey_col(): Specify recover directly as a kw_arg because it's the only kw_arg passed to pkey_name()

sql.py: Added table_pkey_col() and use it in pkey_name()

sql.py: Renamed pkey() to pkey_name()

sql.py: Renamed pkey_col_() to pkey_col()

sql.py: Removed no longer used pkey_col

db_xml.py: cleanup_table(): Inline sql.pkey_col ('row_num') because this is the only place it's used

cleanup_table(): Use new sql.table_cols() instead of sql.table_col_names()

sql.py: Added table_cols()

db_xml.py: put(): Fixed bug where needed to avoid truncating the pkeys_loc table, in case it's the same as one of the in_tables. This occurs now that sql_io.put_table() passes through the actual input column instead of the joined-together input table's column when ignoring all rows.

sql_io.py: put_table(): Resolving default value column: If ignoring all rows, use input cols directly instead of cols from joined-together input table. In addition to being simpler, this prevents the returned column's name from growing longer and longer as each iteration prepends its input table table name to the default value column name.

sql_io.py: put_table(): Moved changing the table of the default value column from Resolving the default value column to Setting pkeys of missing rows, because the table change is only needed in this section

sql_io.py: put_table(): Resolving default value column: Always call sql_gen.remove_col_rename() because it will just pass the value through if it's not a column

sql_gen.py: simplify_parens(): Removed extra simplify_parens() at end because it is done in the final iteration that performs no other replacements, so it is not necessary to also do it explicitly

sql_io.py: put_table(): Replaced limit_ref integer with ignore_all_ref boolean, because it is no longer used as a select statement limit

sql_io.py: put_table(): remove_all_rows(): Corrected "just create an empty pkeys table" comment to "just return the default value column"

sql_io.py: put_table(): mk_main_select(): Removed setting limit to limit_ref⁰, because an empty pkeys table is no longer created when ignoring all rows

sql_io.py: put_table(): Setting pkeys of missing rows: Removed "limit_ref⁰ == 0" check because this code is never reached in that case

sql_io.py: put_table(): Ignoring all rows for unrecoverable errors: Even in multi-row mode, just return whatever the default value or column was, instead of creating an output table containing the default value filled in for every row. This also assists the optimization to skip empty levels of taxonconcepts, because it folds the empty level to that level's parent level rather than creating a whole new temp table with ultimately the same contents.

sql_gen.py: not_false_re, not_true_re: Appended \b to ensure that true/false is only matched as a single word

sql_gen.py: simplify_expr(): Also simplify "NOT false" to true

sql_gen.py: simplify_expr(): Also simplify "NOT true" to false

sql_io.py: put_table(): ignore_cond(): Changed "Ignoring rows where" message with the negated (filter-out) condition to "Ignoring rows that don't satisfy" with the filter condition for clarity

sql_io.py: put_table(): ignore_cond(): If cond simplifies to false, remove all rows instead of filtering out individual rows which will all be filtered out. This optimization should improve import times of tables, such as taxonconcept, which use a check constraint instead of NOT NULL constraints to prevent empty rows. The taxonomic schema refactoring caused the creation of many more levels of taxonconcepts, many of which (such as variety, forma, cultivar) are empty for most datasources, so this optimization should also reduce overall import times for datasources that have any empty levels of taxonconcept. Note that this optimization is only possible now that sql_gen.simplify_expr() is able to simplify all the way to a single boolean value for the taxonconcept_required_key constraint.

Moved expression transforming functions from sql.py to sql_gen.py because they do not manipulate an actual database and merely generate SQL

sql.py: Added true_expr, false_expr and use them where their values are used

sql.py: simplify_expr(): Also simplify "AND true" expressions

sql.py: simplify_expr(): Also simplify "AND false" expressions

sql.py: Added atom_re and use it in simplify_parens()

sql.py: Added or_re and use it in simplify_expr()

sql.py: logic_op_re(): Added expr_re param for an expr on the other side of the operator

sql.py: simplify_parens(): Use bool_re

sql.py: Removed no longer needed paren_re()

sql.py: true_re, false_re: Removed no longer needed paren_re() because simplify_parens() now handles this

sql.py: simplify_expr(): Removed final simplify_parens() because this is now done by simplify_recursive()

sql.py: simplify_expr(): Use new simplify_recursive(). This also fixes a bug where some logic expressions are not simplified because of extra parens.

sql.py: Added simplify_recursive()

sql.py: simplify_parens(): Also remove parens around true and false

regexp.py: sub_nested(): Use new sub_recursive()

regexp.py: Added sub_recursive()

sql.py: simplify_expr(): Use new simplify_parens()

sql.py: Added simplify_parens()

sql.py: simplify_expr(): Use new regexp.sub_nested()

Added regexp.py

sql.py: simplify_expr(): Use new logic_op_re()

sql.py: Added logic_op_re()

sql.py: bool_re: Use new true_re, false_re

sql.py: Added true_re, false_re

sql.py: bool_re: Use new paren_re()

sql.py: bool_re: Use new paren_re()

sql.py: Added paren_re()

sql.py: simplify_expr(): Combined replacements of bool_re+' OR ' with the value in either order into one replacement

mappings/VegCore-VegBIEN.csv: verbatim* taxonconcept: Don't store Name_submitted in taxonomicnamewithauthor in addition to identifyingtaxonomicname, because the fields other than identifyingtaxonomicname are meant to store parsed values rather than raw, unscrubbed values and TNRS does not directly provide a concatenated taxonomic name with author

mappings/VegCore-VegBIEN.csv: verbatim* taxonconcept: Don't create hierarchy of parent taxonconcepts, because the parsed names (rather than the names for the matched taxonconcept) are from the input taxonomic name, rather than from the official tree of life used by TNRS. Otherwise, if a taxonomic name provides e.g. no family (common), a separate genus taxonconcept would have been created with no parent_id, which would not compare equal to the matched taxonconcept's genus with a parent_id. Continue to store the parsed family, genus, species in the family, genus, species cached fields, because the parsed family is often different from the matched taxonconcept's family when e.g. no family is provided in the taxonomic name.

sql.py: Renamed table_cols() to table_col_names() for clarity, because it does not return sql_gen.Col objects

inputs/.TNRS/tnrs/test.xml.ref: Accepted new inserted row count. The change is most likely from several revisions back, but the cause of the change is unknown (it is not due to the updated TNRS.tnrs table, which is still sorted with the same rows first).

sql_gen.py: is_text_col(): Use new is_text_type()

sql_gen.py: Added is_text_type()

sql_gen.py: ensure_not_null(): Documented that NULL has no type, hence the NoUnderlyingTableException being re-raised

sql_gen.py: ensure_not_null(): Just store the column type in col_type, instead of storing typed_col and using typed_col.type, now that other info in typed_col is no longer needed

sql_gen.py: ensure_not_null(): Use is_nullable() instead of determining nullability itself, for clarity

sql_gen.py: is_nullable(): Fixed bug where non-columns could not be sent to db.col_info()

sql_gen.py: ensure_not_null(): Always remove_col_rename() the column to ensure that it is acceptable by helper functions like is_nullable()

lib/PostgreSQL-MySQL.csv: COMMENT statement: Fixed bug where ending ; could match only when preceded by ' and followed by a newline, to avoid matching ; embedded in the comment

schemas/vegbien.sql: taxonconcept: family, genus, species comments: Changed "scoping" to "identifying" for clarity

schemas/vegbien.sql: taxonconcept: family, genus, species: Added comment that each is a cached field for easy querying and the scoping version of it is stored in the chain of parent_id ancestors

schemas/vegbien.sql: taxonconcept: taxonconcept_unique: Removed family, genus, species because these are now just cached fields for analytical_db_view rather than scoping fields. The scoping versions of these fields are stored in the chain of parent_id ancestors.

tnrs_db: Moved "Processing # taxonconcepts" log message to before waiting or exiting if no taxonconcepts left, so that it would be printed right after the query is run and say that no taxonconcepts were found

tnrs_db: Updated comments and log messages for schema changes

tnrs_db: Updated query for schema changes

README.TXT: Schema changes: files to update with renamings: Added bin/tnrs_db

inputs/import.stats.xls: Updated import times

README.TXT: Data import: Changed `inputs/*/*/logs` to `inputs/{.,}*/*/logs` to also include the TNRS names import log

import_all: Added commands to import TNRS names so the user doesn't have to do this manually

sql.py: map_expr(): Fixed bug where names were being matched inside punctuated names replaced in previous calls of map_expr()

schemas/vegbien.sql: party: party_required_key: Only allow NULL organizationname if party is not a root party (i.e. creator_id != party_id)

mappings/VegCore-VegBIEN.csv: Mapped to new taxonconcept.creationdate

schemas/vegbien.sql: taxonconcept: taxonconcept_required_key: Added creationdate as an allowable minimum field when parent_id (containing the associated hierarchical concept) is specified

schemas/vegbien.sql: taxonconcept: taxonconcept_required_key: Removed family and genus because these are now cached fields only, and are not used for scoping a taxonconcept. Instead, *taxonomicname and taxonname+parent_id are used for this purpose. This removes several leaf taxonconcepts with insufficient scoping information to create a taxonconcept separate from the main tree. With the upcoming population of creationdate, some of these taxonconcepts will reappear due to the date's additional distinguishing information.

schemas/vegbien.sql: taxonconcept: Added creationdate (the date the taxonconcept was created or defined), and include it in the taxonconcept_unique unique index

schemas/vegbien.sql: taxonconcept: Added comment with the definition of a taxon: "a group of one (or more) populations of organism(s), which a taxonomist adjudges to be a unit" (http://en.wikipedia.org/wiki/Taxon). This is useful in clarifying that our taxon concepts are intended to serve a similar purpose, by storing one person's defined taxon.

schemas/vegbien.sql: taxonconcept: taxonconcept_required_key: Removed family and genus because these are now cached fields only, and are not used for scoping a taxonconcept. Instead, *taxonomicname and taxonname+parent_id are used for this purpose.

schemas/vegbien.sql: taxonconcept: Moved identifyingtaxonomicname near other full-taxonomic-name-related fields, after the fields that contain just the current level's component of the full name

schemas/vegbien.sql: taxonconcept.canon_taxonconcept_id: Changed four-level hierarchy to use "parsed concept" and "matched concept" instead of concatenated and parsed, because the directly-parsed name components actually go in level 2 of the hierarchy (the TNRS input name), while the name components based on the matched taxon concept go in level 3

schemas/vegbien.sql: taxonconcept.parent_id: Documented that while a taxon name may have multiple parents, a taxon concept has only one, based on the creator's opinion of where that taxonconcept goes in the taxonomic hierarchy

mappings/VegCore-VegBIEN.csv: taxonconcept: Moved infraspecific taxonconcept to its own level, rather than combining it with the level that contains the full taxonomic name and author (as well as any morphospecies), for consistency with the storage of other ranked taxonomic name components, which each get their own taxonconcept. The infraspecific taxon concept is general to all parties making idenfitications (within a datasource), while the concatenated name and author and any morphospecies are specific to the person who defined the taxonconcept used by a taxondetermination.

schemas/vegbien.sql: taxonconcept: Removed no longer used higher- and infraspecific taxonomic rank fields because these terms are now stored in their own taxonconcepts. family, genus, and species have not been removed because these are used to cache names of parent taxa for fast access by analytical_db_view.

schemas/vegbien.sql: analytical_db_view: Changed taxonMorphospecies to use taxonconcept.taxonname, where any morphospecies is now stored

mappings/VegCore-VegBIEN.csv: infraspecific taxonomic terms: Removed mappings to first-class taxonconcept fields because these terms are now stored in their own taxonconcepts, or in the lowest-level taxonconcept as the taxonname and rank

mappings/VegCore-VegBIEN.csv: higher-level taxonomic terms: Removed mappings to first-class taxonconcept fields because these terms are now stored in their own taxonconcepts

schemas/vegbien.sql: taxonconcept: Merged taxonconcept_unique_within_creator_by_name unique index into taxonconcept_unique_within_parent, placed parent_id first, and removed index condition, so that this index can be used as a lookup index by taxonconcept_update_ancestors() (which requires no index condition in order to apply to all taxonconcepts) in addition to as a unique index. Note that an index condition should not be necessary for the index's uniquifying task, because if a set of taxonconcepts provides only the identifyingtaxonomicname, that should collide in the taxonconcept_unique_within_creator_by_identifying_name unique index before this index collides. This assumes that the collision order when multiple indexes collide is alphabetical by the index name.

schemas/vegbien.sql: taxonconcept: taxonconcept_required_key check constraint: Also allow a taxonconcept to have just an author when it has a parent_id, so that an author can uniquely identify a taxon within a more general taxon, such as a species name, that has no author