sql_gen.py: plpythonu_error_handler: Always raise PL/Python exceptions as data_exception so they go in the errors table, instead of aborting the iteration

sql_gen.py: plpythonu_error_handler: Fixed bug where not all PL/Python exceptions start with "PL/Python: " (e.g. on PostgreSQL 9.1 on vegbiendev), so the PL/Python prefix must be optional. Refactored to put IF clause for non-PL/Python exception at end for a more logical ordering of the conditions.

Added inputs/CVS/

README.TXT: Datasource setup: Added steps to place the relevant files under version control

README.TXT: Datasource setup: Accepting the test cases: Don't auto-accept the initial tests because there could be bugs in the initial mappings that would be revealed upon inspecting the test output

sql_gen.py: plpythonu_error_handler: Added section comment before handler block, so that it's clear in the (very long) wrapper function definition what the block is doing

input.Makefile: Documentation: import/steps.by_col.sql: Added -s to make to avoid echoing make commands to the log file

README.TXT: Moved Reinstall all datasources at once to Schema changes and renamed it to Reinstall staging tables to reflect that it is only necessary when the staging table format is changed

README.TXT: Datasource setup: Updating vegbiendev: Added step to also install the staging tables on vegbiendev

README.TXT: Datasource setup: Moved Install the staging tables before Map each table's columns because the install can run in the background while you're mapping. It must, however, come after Auto-create the map spreadsheets because it uses the filenames of the created maps to determine which staging tables to create.

README.TXT: Datasource setup: Adding a new datasource: Changed <short_name> to <name> to match usage elsewhere. Documented that it may not contain spaces, and should be abbreviated.

README.TXT: Datasource setup: Added steps to update vegbiendev

inputs/Makefile: Input data: Added upload target

README.TXT: Datasource setup: Added steps to accept the test cases and commit

README.TXT: Datasource setup: Added step to install the staging tables

bin/map: in_is_xml: doc2rows(): "Root not found in input" warning: Changed "error" to "warning" to match the type of error condition signaled

bin/map: map_rows(): out_is_db: Changed `id_node != None` assertion to a warning because this is a normal circumstance in the base case where there are no mappings

input.Makefile: Testing: Added test/accept-all

csv2db: COPY FROM: Fixed %-injection bug where column names' %s were not escaped prior to cursor.mogrify(), by changing the code to use inline db.esc_value() instead

bin/map: in_is_xml: doc2rows(): "Root not found in input" error: Changed SystemExit to a warning because this is a normal circumstance in the base case where the input XML file contains no rows

README.TXT: Datasource setup: Documented how to map each table's columns

README.TXT: Datasource setup: Changed "Auto-create the src column spreadsheets" to "Auto-create map spreadsheets" and updated command to bootstrap all maps, including newly-autogeneratable via maps

input.Makefile: Maps building: maps/$(via).%.csv: Auto-create by copying the src map if doesn't exist. Existing maps discovery: Look up via format in src maps' roots if no via map already exists.

src_map: Fixed bug where non-header rows needed to be materialized with empty fields for each column in the header

input.Makefile: Maps building: Via maps cleanup: Match maps/$(via).%.csv with pattern instead of $(viaMaps) var so that a non-existing via map will have the recipe run, too. When auto-creating via maps is later added, this will be required.

inputs/*/maps/src.*.csv: Regenerated using new src_map output format

parallelproc.py: MultiProducerPool: Removed warning if not using parallel processing because this also gets generated when it's explicitly turned off, which is currently the case and clutters up stderr when testing

src_map: Also add columns for the output mappings and comments, so that the src map can be directly copied for use as the via map (DwC.specimens.csv, etc.). The output mapping column name must be provided by the caller, which input.Makefile maps/src.%.csv provides using the new mappings roots.

Added mappings/roots for use in creating src maps

input.Makefile: Maps building: maps/src.%.csv: Clean up by passing through `$(bin)/cols '*'` whenever it's changed. This ensures that the CSV dialect is always consistently Python's Excel dialect. (Note that this dialect actually uses \r\n as the line ending. The \n line endings were from src maps generated by a previous version of bin/src_map.)

input.Makefile: Maps building: maps/$(via).%.full.csv: Removed alternate rule when $(srcMap) doesn't exist, because this effect is actually achieved by the no-prereqs rule for maps/src.%.csv, which causes make to think it exists when matching pattern rules even if its recipe doesn't actually create it

input.Makefile: Maps building: maps/$(via).%.full.csv: Added alternate rule when $(srcMap) doesn't exist

inputs/CTFS/maps/: Removed unneeded src.organisms.csv since there is an way to deal with it not existing in input.Makefile

inputs/CTFS/maps/: Removed unneeded .VegX.plots.csv.last_cleanup

inputs/*/maps/src.*.csv: Standardized line endings to \n

input.Makefile: Maps building: maps/$(via).%.full.csv: Added the src map as a prerequisite so it would be rebuilt when the src map changes. This is possible now that every datasource has at least an empty src map. (An empty src map is now treated the same way as a non-existing one.)

inputs/*/maps/src.*.csv: Removed extraneous quotes around fields, which are added by Excel but not by Python

inputs/*/maps/src.*.csv: Removed extraneous quotes around fields, which are added by Excel but not by Python

inputs/CTFS: Added empty maps/src.organisms.csv so that every table of every datasource has a src map

README.TXT: Datasource setup: Documented how to populate the src/ subdir with input data

Added inputs/CVS/

sql_gen.py: plpythonu_error_handler: Translate specific Python exception types to PostgreSQL error codes (ValueError -> data_exception) instead of assuming everything is a data_exception. When removing the PL/Python prefix, preserve the Python exception class in a DETAIL message. Support non-PL/Python internal_errors by re-raising them.

sql_gen.py: Added reraise_exc

schemas/py_functions.sql: _date(): Raise (or pass through) ValueErrors directly instead of wrapping them in FormatExceptions, to simplify the code. This will also enable later translation of ValueErrors to data_exceptions. When year is required and missing, output a parsable 'null value in column year violates not-null constraint' error.

sql_io.py: put_table(): log_exc(): Handle infinite loops from repeated exceptions by removing all rows, instead of just aborting with a failed assertion

sql_io.py: put_table(): is_function: Fixed bug where special case for unrecoverable errors needed to avoid creating an empty output pkeys table because function mode defines the returned pkeys table separately

sql_io.py: put_table(): is_function: Factored defining the error handling wrapper function out of the main loop because it only needs to run once. Don't log "Trying to insert new rows" in function mode because it's inaccurate.

sql_gen.py: Exceptions: Added suppress_exc and use it in ExcHandler.to_str()

README.TXT: Backups: After a new import: Added step to delete previous imports so they won't bloat the full DB backup. (Note that these imports have already been backed up, and only the most recent import needs to be live in the DB.)

README.TXT: Backups: Documented what to do after a new import

backups/Makefile: Full DB: Added vegbien.backup/all to run both test and rotate

README.TXT: Renamed Maintenance section to Backups for clarity

backups/Makefile: .sql: When testing, turn it off so make won't skip `.sql: %` in favor of it

backups/Makefile: Split %.backup and %.sql into separate targets for clarity

inputs/import.stats.xls: Updated with stats from latest import. Note that this import adds data provider feedback for SQL functions as well as additional date processing using _date().

schemas/py_functions.sql: _date(): Re-enabled now that exceptions thrown are properly handled. FormatException: Support raising parsable data_exceptions when provided with the value that was invalid. Date parsing mode: Return date as the value in FormatException so it can be filtered out automatically by column-based import.

sql_io.py: put_table(): is_function: Creating error handling wrapper function: Fixed bug where needed to cast NULL returned in error handler to appropriate type, because it's contained within a SELECT query which does not do implicit casts from type unknown

sql_gen.py: Cast: Support types which are Code objects

sql_io.py: func_wrapper_exception_handler(): Use new sql_gen.merge_not_null() to try to ensure that NULL values are not folded (which would cause the concatenated values not to match up with the concatenated column names). Note that this adds a dependency on the db object, which callers must now provide.

sql_gen.py: Added merge_not_null()

sql_gen.py: Added try_mk_not_null()

sql_gen.py: Renamed ArrayJoin to ArrayMerge to avoid confusion with Join (a SQL construct)

sql_io.py: put_table(): is_function: Creating error handling wrapper function: Set srcs on row_var so that the column type and nullability info of row_var's columns can be retrieved for use with sql_gen.ensure_not_null()

sql_gen.py: RowExcIgnore.to_str(): Compare self.row_var to global const row_var using == to allow caller to provide a copy of row_var with the underlying table set appropriately

sql_gen.py: underlying_table(): Support derived tables and row vars by obtaining the underlying table from the srcs

sql_io.py: put_table(): Setting pkeys of missing rows: Fixed bug where also needed to do this when is_function if an empty pkeys table was created (due to an error that could not be localized to a row)

sql_io.py: put_table(): After main loop: If is_literals, return immediately to avoid needing to test for is_literals in all the code that follows (which only applies to the normal case)

sql_gen.py: RowExcIgnore: If a custom row_var is used, require it to already be defined. This also allows sql_io.ExcToErrorsTable to place the column var definition in the outer DECLARE, eliminating the extra DECLARE block.

sql_io.py: put_table(): is_function: Creating error handling wrapper function: Use new sql_gen.row_var

sql_gen.py: RowExcIgnore: Created global constant for default row_var for callers to use

sql_gen.py: RowExcIgnore.to_str(): Moved SQL comment explaining the use of an EXCEPTION block for each individual row to Python code to avoid cluttering the logged SQL code

sql_io.py: put_table(): is_function: Creating error handling wrapper function: Handle errors using new func_wrapper_exception_handler(), which saves any data_exceptions in the errors table in addition to handling PL/Python errors

sql_io.py: Added func_wrapper_exception_handler()

sql_gen.py: Added ArrayJoin

sql_gen.py: Added Array and to_Array()

sql_gen.py: Added List and inherit from it in Tuple

sql_gen.py: Renamed Tuple to Row and List to Tuple to more accurately reflect the datatype generated by each class (a Tuple being merely a grouping of values)

sql_gen.py: Moved Composite types to Literal values section as a subsection, since Composite types was really about just the input syntaxes for these types

sql_gen.py: Replaced srcs_str() with cross_join_srcs() which more correctly combines the srcs of each column using a Cartesian product. Eventually, the entire tree of srcs will need to be preserved instead of flattened in order to properly attribute errors to a specific column or set of columns.

sql_gen.py: srcs_str(): Fixed bug where needed to filter out columns with no srcs so that there aren't empty elements in the ","-separated list

sql_gen.py: Added has_srcs()

sql_gen.py: Added NestedExcHandler

sql_gen.py: Added srcs_str()

sql_gen.py: as_Col(): Support non-Code, non-string inputs by making them Literals

sql_gen.py: Added is_col() and use it in is_table_col()

sql_io.py: ExcToErrorsTable: Require users to explicitly specify an expression for the value that caused the error, instead of assuming that a variable named "value" already exists. This allows a value expression to be computed only if needed for error handling.

sql_gen.py: Moved repr() from ExcHandler to BaseExcHandler

sql_gen.py: Added BaseExcHandler and inherit from it in ExcHandlers

sql_io.py: cast(): Determining if will be saving errors: Don't add extra check if isinstance(col, sql_gen.Col) because the special case for sql_gen.Literal handles supported non-columns

sql_io.py: data_exception_handler(): Removed no longer needed db param

sql_io.py: Added ExcToErrorsTable, which separates out the errors table inserting code from the exception handling code. data_exception_handler(): Refactored to use new sql_gen.data_exception_handler() and ExcToErrorsTable.

sql_gen.py: Added data_exception_handler

sql_io.py: data_exception_handler(): Refactored to use new sql_gen.ExcToWarning when not using an errors table

sql_gen.py: Added ExcToWarning

schemas/vegbien.sql: taxondetermination: taxondetermination_taxonoccurrence_id_fkey(): Fixed bug where string containing a \-escape needed an "E" prefix

sql_io.py: data_exception_handler(): Require the caller to provide a statement to return a default value in case of error, rather than assuming the caller can accept a return value of NULL

sql_io.py: data_exception_handler(): Refactored to use new sql.define_func()

sql_io.py: put_table(): is_function: Calling function on input rows: Convert PL/Python exceptions (internal_errors) to data_exceptions using sql_gen.plpythonu_error_handler and an error handling wrapper function

debug2redmine.csv: EXPLAIN comments: Fixed bug where needed to also match whitespace at beginning of line (indent)

Use sql_gen.ReturnQuery where RETURN QUERY was previously manually prepended