sql_gen.py: ValueCond.to_str(): Added value_code param

sql_gen.py: Literal, CompareCond: Implemented to_str(). ValueCond: Autoconvert literal values to Literals.

sql.py: DbConn: Added esc_value()

Moved SQL code generation classes from sql.py to new sql_gen.py. sql_gen.py: Added Code, Literal, ValueCond, and CompareCond. sql.py: Removed Query because we will use a different approach.

sql.py: Added Query, Table, Col

sql.py: get(): Fixed bug where limit=1 needs to be passed to select() as a keyword arg now that the distinct_on param comes before it

sql.py: put_table(): mk_main_select(): Pass outer var conds to mk_select()

sql.py: put_table(): mk_select_(): Fixed bug where it was sometimes being called without distinct_on, causing it to return a different # of rows. Renamed mk_select_() to mk_main_select() for clarity.

sql.py: put_table(): Do inserts and selects in a loop so that it will keep retrying the operation with additional constraints until it succeeds

sql.py: put_table(): mk_select_(): Fixed bug where order_by needed to be None because otherwise it wouldn't match the distinct_on cols if they were specified

sql.py: put_table(): insert_(): Fixed bug where distinct_on was not passed to mk_select_()

sql.py: put_table(): mk_select_(): Fixed bug where distinct_on needed to be passed as a keyword param

sql.py: put_table(): insert_() and mk_select_() take distinct_on param

sql.py: put_table(): Factored out code that inserts into pkeys table into run_query_into_pkeys() helper function

sql.py: mk_select(): Implemented DISTINCT ON according to the distinct_on param

sql.py: mk_select(): Added distinct_on param to set the columns to SELECT DISTINCT ON

sql.py: clean_name(): Convert names to lowercase so that PostgreSQL will behave the same whether the name is escaped with "" or not. This will help avoid bugs in code that uses temp tables created by the sql module.

sql.py: put_table(): Added order_by=None wherever rows were not supposed to be re-ordered. On DuplicateKeyException: Save existing pkeys in temp table for joining on.

db_xml.py: put_table(): Pass limit and start to sql.put_table()

db_xml.py: put_table(): Added limit and start options

sql.py: When creating a temporary entity (table, function, etc.), instead create it as a permanent entity in debug mode so it can be viewed after the program is run

sql.py: DbConn: Store whether in debug mode (log_debug != log_debug_none) for easy use by methods

bin/map: connect_db(): Turn on autocommit mode in debug mode if commit is on, so that incremental results can be seen in the DB

sql.py: DbConn: Use internal autocommit handling instead of DB connection autocommit attr to avoid autocommits inside a savepoint

sql.py: DbConn: Added autocommit option to turn on autocommit mode. Use set_session() instead of SQL command to set isolation level.

sql.py: mk_insert_select(): embeddable: Fixed bug where the function may do different things when run, because the function (and other statements whose cached strings depend on the function name) may be run after the function definition would have changed, by versioning the function name and using CREATE FUNCTION instead of CREATE OR REPLACE FUNCTION so that its definition never changes

sql.py: Parse "function already exists" errors as DuplicateFunctionException

sql.py: mk_select(): joins: Fixed bug where join_not_equal did not do what it was designed for, which is filtering out matches of the join condition (before the bug fix, it effectively did a cross join with matching rows excluded, causing duplication of rows). Renamed join_not_equal to filter_out to reflect its intended use. Support table-scoped column names in the WHERE conds list.

sql.py: put_table(): Fixed bug where ORDER BY column needed to have table0 name prefixed (if it didn't already have a table name), to avoid ambiguous column references

sql.py: mk_select(): Fixed bug in joins where right_col had the table name prepended before it was copied for use with a different table name in join_using and join_not_equal

Mapped some unmapped fields in DwC inputs

Added mappings/for_review/DwC2-VegBIEN.specimens.fields.csv

db_xml.py: put_table(): Fixed bug where didn't commit right after inserting node, but instead waited until children with fkeys to parent (independent of the node itself) were inserted

sql.py: put_table(): insert_(): Use insert_select() instead of run_query_into() if new option pkeys_table_exists is on

sql.py: mk_select(): Support joins with !=

sql.py: mk_select(): Support only some join columns being join_using

sql.py: put_table(): Renamed in_joins to insert_joins and joins to select_joins for clarity

db_xml.py: put_table(): Support children with fkeys to parent

sql.py: mk_select(): Make tuple optional for None literal values

sql.py: put_table(): Removed "SELECT statement missing a WHERE, LIMIT, or OFFSET clause" warnings

bin/map: by_col: row_ct = 0 because it's unknown for now

mk_select(): Support join conditions with literal values

sql.py: mk_insert_select(): embeddable: Don't cache function_query because function def could change and then change back

sql.py: with_savepoint(): Renamed savepoints to have "level" prefix, since the # indicates the level #

sql.py: get_cur_query(): Also accept input params to combine with input_query, and pass input params when get_cur_query() is called

sql.py: DbConn.run_query(): Pass input query to get_cur_query()

sql.py: get_cur_query() and _add_cursor_info(): Support input_query param that will be used if the raw query is None. Pass input_query in DbConn.execute().

sql.py: DbConn.run_query(): Check that query != None

bin/map: out_is_db: Only rollback() and close() out_db if it was connected

sql.py: DbConn: Added connected()

sql.py: Wrapped calls to get_cur_query() that are used as strings in str(), because get_cur_query() can return None

sql.py: next_version(): Versions start from 1, because first existing name was version 0

put_table(): Use short name for temp_suffix now that version # will be added if needed

sql.py: mk_select(): Parse join columns for literal values and table-scoped names as well

mappings/DwC2-VegBIEN.specimens.csv: establishmentMeans: Call _toGrowthform on growthform

schemas/vegbien.sql: Added _toGrowthform

sql.py: put_table(): Changed temp_prefix to a suffix so main name won't be removed if name is truncated

sql.py: mk_select(): fields: Support columns with tables. Changed syntax for literal values so that it wouldn't conflict with new syntax for columns with tables.

iters.py: flatten(): If not an iterable, just return the value

sql.py: put_table(): Pass in_pkeys and out_pkeys to run_query_into() by ref so they will be updated if the table names are changed

sql.py: put_table(): Pass pkeys to run_query_into() by ref so it will be updated if the table name is changed

sql.py: run_query_into(): If CREATE TABLE AS generates a DuplicateTableException, rename the table with a version # prepended

sql.py: run_query_into(): Made into param a reference so that the function can change it, and renamed it to into_ref

sql.py: run_query_into(): Made into param a reference so that the function can change it, and renamed it to into_ref

sql.py: put_table(): If DuplicateKeyException: run_query_into() recoverably, so that DB errors such as DuplicateTableException will be parsed

sql.py: Removed no-longer-needed try_insert()

sql.py: Merged with_parsed_errors() into run_query() so all recoverable queries would automatically benefit from DB error message parsing. DbConn: Moved _add_cursor_info() to DbCursor.execute().

sql.py: with_parsed_errors(): Raise DuplicateTableException for "relation already exists" errors instead of "table name specified more than once" errors

sql.py: run_query_into(): Removed "DROP TABLE IF EXISTS" because sometimes when there are collisions in the temp table names, the code actually uses both "copies" of the temp table. Eventually, this situation will be resolved by adding a counter to the temp table name.

sql.py: Cleaned up DbException's and subclasses' messages

exc.py: ExceptionWithCause: Added cause_newline option to put the cause on its own line instead of on the message line

sql.py: with_parsed_errors(): Also parse "table name specified more than once" errors as DuplicateTableExceptions

sql.py: put_table(): Handle DuplicateKeyExceptions by running a select query on the unique constraint columns

sql.py: mk_select(): Support tuples of tables, not just lists

sql.py: with_parsed_errors(): Support table names that start with "_"

sql.py: DbConn: Added with_savepoint(). with_savepoint(): Use new DbConn.with_savepoint().

schemas/functions.sql: Added _toBool

mappings/DwC2-VegBIEN.specimens.csv: establishmentMeans: Use _toBool on iscultivated, isnative

schemas/functions.sql: Added _toBool

schemas/functions.sql: Made trigger functions IMMUTABLE since they do not modify other tables

sql.py: put_table(): Added support for putting just a window subset of the rows in the table. Removed "SELECT statement missing a WHERE, LIMIT, or OFFSET clause" warnings.

sql.py: put_table(): Return the column where the pkeys are made available (the out_pkey) instead of taking it as an argument

sql.py: put_table(): Get input pkeys corresponding to rows in insert and join together out_pkeys and in_pkeys into final pkeys table

sql.py: put_table(): Fully support multiple in_tables, joined together using the main input table's pkey

sql.py: mk_select(): joins: Fixed bug where USING-based joins did not have closing ")"

db_xml.py: put_table(): Fixed bug where in_table was last in in_tables instead of first, causing it to be ignored by the current put_table() implementation, which only considers the first table name

db_xml.py: put_table(): Fixed bug where pkeys_table returned by recursive call to put_table() needed to be prefixed with $ to be treated as an input column name rather than a literal value

sql.py: mk_select(): Support joins with USING, which can be used to merge multiple input cols into the same output col

sql.py: mk_insert_select(): embeddable: Fixed bug where query that uses function was being sorted by its first column (the default mk_select() setting), when it should be left in its original order

sql.py: put_table(): Take a dict mapping out to in cols instead of separate in and out cols lists

sql.py: mk_select(): Joins: Reversed order of left_col and right_col in the joins dict as well, so the joined table's columns are the keys

sql.py: mk_select(): Joins: Reversed order of left_col and right_col so the column of the table being joined is first, to match the form of a WHERE clause

sql.py: mk_select(): Support joins

sql.py: mk_select(): Accept a list of tables to join together (initial implementation just uses the first table)

sql.py: mk_select(): Support ORDER BY clause. By default, order by the pkey, since PostgreSQL apparently doesn't do this automatically (and this was causing some staging table tests to fail).

bin/map: In debug mode, print the row # and input row just like in error messages

bin/map: verbose_errors also defaults to on in debug mode

sql.py: add_row_num(): Make the row number column the primary key

csv2db: Use new sql.cleanup_table() to map NULL-equivalents to NULL. Consider the empty string to be NULL.

sql.py: Added cleanup_table()