db_xml.py: put_table(): Place pkeys in temp table

sql.py: mk_insert_select(): Document that embeddable will cause the query to be fully cached, not just if it raises an exception. insert_select(): into != None: Pass recover and cacheable through to each run_query()

sql.py: insert_select(): Support placing RETURNING values in temp table

db_xml.py: put_table(): Support returning pkey from INSERT SELECT

sql.py: mk_insert_select(): Support using an INSERT RETURNING statement as a nested SELECT

sql.py: mk_insert_select(): Removed unused params recover and cacheable

sql.py: Added mogrify()

db_xml.py: put_table(): Corrected @return doc

sql.py: Added mk_insert_select() and use it in insert_select()

db_xml.py: put_table(): Use new insert_select()

sql.py: insert_select(): Changed order of cols and params arguments so select_query and params would be together

sql.py: Added insert_select() and use it in insert()

Calls to sql.esc_name*(): Removed preserve_case=True because it is now the default

sql.py: esc_name_by_module(): Changed preserve_case to ignore_case, which defaults to False

Calls to sql.esc_name*(): Removed preserve_case=True because it is now the default

sql.py: esc_name_by_module(): preserve_case defaults to True

sql.py: mk_select(): Escape all names used (table, column, cond, etc.)

sql.py: esc_name_by_module(): If not enclosing name in quotes, call check_name() on it

sql.py: mk_select(): Support literal values in the list of cols to select

sql.py: mk_select(): Don't escape the table name, because it will either be check_name()d or it's already been escaped

sql.py: Added mk_select(), and use it in select()

bin/map: Always pass qual_name(table) to sql.select(). This is possible now that qual_name() can handle None schemas.

db_xml.py: put_table(): Take separate in_table and in_schema names, instead of in_table and table_is_esc, because the in_schema is needed to scope the temp tables appropriately

sql.py: qual_name(): If schema is None, don't prepend schema

bin/map, sql.py: Turned SQL query caching back on because benchmarks of just the caching on vs. off reveal that it does reduce processing time significantly. However, there is a slowdown that was introduced between the time caching was added and the time the same XML tree was used for each node, which was giving the false indication that the slowdown was due to the caching.

bin/map: Turn SQL query caching off by default

bin/map: Added cache_sql env var to enable SQL query caching

sql.py: Make caching DbConn enablable. Turn caching off by default because recent benchmarks (n=1000) were showing that it slows things down.

bin/map: Added new verbose_errors mode, enabled in test mode and off otherwise, which controls whether the output row and tracebacks are included in error messages. Having this off in import mode will reduce the size of error logs so they don't fill up the vegbiendev hard disk as quickly.

exc.py: print_ex(): Added detail option to turn off traceback

bin/map: Turn parallel processing off by default. This should fix "Cannot allocate memory" errors in large imports.

bin/map: in_is_db: Don't cache the main SELECT query

bin/map: by_col: Use the created template, which already has the column names in it, instead of mapping a sample row

bin/map: Fixed bug where db_xml could not be imported twice, or it was treated as an undefined variable for some reason

bin/map: map_table(): Make each column a db_xml.ColRef instead of a bare index, so that it will appear as the column name when converted to a string. This will provide better debugging info in the template tree and also avoid needing to create a separate sample row in by_col.

db_xml.py: Added ColRef

bin/map: Fixed bug where row count was off by one if all rows in the input were exhausted, because the row that raises StopIteration was counting as a row

main Makefile: VegBIEN DB: mk_db: Use template1 because it has PROCEDURAL LANGUAGE plpgsql already installed and we aren't using an encoding other than UTF8

Moved "CREATE PROCEDURAL LANGUAGE plpgsql" to main Makefile so that it would only run when the DB is created, not when the public schema is reinstalled. This is only relevant on PostgreSQL < 9.x, where the plpgsql language is not part of template0.

Renamed parallel.py to parallelproc.py to avoid conflict with new system parallel module on vegbiendev

Makefile: VegBIEN DB: public schema: Added schemas/rotate

bin/map: Fixed bug in input rows processed count where the count would be off by 1, because the for loop would leave i at the index of the last row instead of one-past-the-last

bin/map: Use the same XML tree for each row in DB outputs, to eliminate time spent creating the tree from the XPaths for each row

bin/map: map_table(): Resolve each prefix into a separate mapping, which is collision-eliminated, instead of resolving values from multiple prefixes when each individual row is mapped

bin/map: Moved collision-prevention code to map_rows() so it would only run if there were mappings, and so that it would run after any mappings preprocessing by map_table() that creates more collisions

bin/map: Prevent collisions if multiple inputs mapping to same output

mappings/DwC1-DwC2.specimens.csv: Mapped collectorNumber and recordNumber to recordNumber with _alt so they wouldn't collide when every input column, even empty ones, are created in the XML tree

bin/map: If out_is_db, in debug mode, print each row's XML tree and each value that it's putting

bin/map: If out_is_db, in debug mode, print the template XML tree used to insert a sample row into the DB

bin/map: map_table(): When translating mappings to column indexes, use appends to a new list instead of deletions from an existing list to simplify the algorithm

union: Omit mappings that are mapped to in the input map, in addition to mappings that were overridden. This prevents multiple outputs being created for both the renamed and original mappings, causing duplicate output nodes when one XML tree is used for all rows.

union: Omit mappings that are mapped to in the input map, in addition to mappings that were overridden. This prevents multiple outputs being created for both the renamed and original mappings, causing duplicate output nodes when one XML tree is used for all rows.

input.Makefile: Maps building: Via maps cleanup: subtract: Include comment column so commented mappings are never removed

subtract: Support "ragged rows" that have fewer columns than the specified column numbers

util.py: list_subset(): Added default param to specify the value to use for invalid indexes (if any)

mappings/VegX-VegBIEN.stems.csv: Mappings with multiple inputs for the same output: Use _alt, etc. to map the multiple inputs to different places in the XML tree, so that when using a pregenerated tree, the empty leaves for each input will not collide with each other

mappings/VegX-VegBIEN.stems.csv: Changed XPath references (using "$") to XML function references using _ref where needed to make them work even on a pre-made XML tree used by all rows

xml_func.py: Added _ref to retrieve a value from another XML node

xml_func.py: Made all functions take a 2nd node param, which contains the func node itself

bin/map: If outputting to a DB, also create output XML elements for NULL input values. This will help with the transition to using the same XML tree for all rows.

xml_func.py: _label: return None on empty input

mappings/VegX-VegBIEN.stems.csv: Added _collapse around subtrees that need to be removed if they are created around a NULL value

xml_func.py: Added _collapse to collapse a subtree if the "value" element in it is NULL

schemas/vegbien.sql: definedvalue: Made definedvalue nullable so that each row of a datasource can have a uniform structure in VegBIEN, and to support reusing the same XML DOM tree for each row

xpath.py: Added is_xpath()

xml_dom.py: set_value(): If value is None and node is Element, remove value node entirely instead of setting node's value to None

xml_dom.py: Added value_node(). Use new value_node() in value() and set_value(). set_value(): If the node already has a value node, reuse it instead of appending a new value node.

xpath.py: put_obj(): Return the id_attr_node using get_1() because it should only be one node

xml_func.py: _simplifyPath: Also treat the elem as empty if the required node exists but is empty

db_xml.py: put_table(): Added part of put() code that should be common to both functions

xpath.py: put_obj(): Return a tuple of the inserted node and the id attr node

xpath.py: set_id(): When creating the id_path, use obj() (which deepcopy()s the entire path) because it prevents pointers w/o targets

xpath.py: set_id(): When creating the id_path, deepcopy() the id_elem because its keys will change in the main copy

xpath.py: set_id(): Return the path to the ID attr, which can be used to change the ID

xpath.py: put_obj(): Return the inserted node so it can be used to change the inserted value

main Makefile: Maps validation: Fixed bug where there would be infinite recursion with the Maps validation section before the Subdir forwarding section (it's unknown why this is necessary)

db_xml.py: put_table(): Added commit param to specify whether to commit after each query

bin/map: in_is_db: by_col: Use new put_table() (defined but not implemented yet)

db_xml.py: Added put_table() (without implementation)

xml_func.py: strip(): Remove _ignore XML funcs completely instead of replacing them with their values

bin/map: in_is_db: by_col: Prefix each input column name by "$"

bin/map: in_is_db: by_col: Strip off XML functions

xml_func.py: Added strip(). pop_value(): Support custom name of value param.

bin/map: in_is_db: by_col: Create XML tree of sample row, with the input column names as the values. This tree will guide the sequencing and creation of the column-based queries.

input.Makefile: use_staged env var: defaults to on if by_col is on

bin/map: Only turn on by_col optimization if mapping to same DB, rather than requiring each place that checks by_col to also check whether mapping to same DB

input.Makefile: Testing: Don't abort tester if only staging test fails, in case staging table missing

input.Makefile: Testing: When cleaning up test outputs, remove everything that doesn't end in .ref

input.Makefile: Testing: Added test/import.%.staging.out test to test the staging tables. Sources: cat: Updated Usage comment to include the "inputs/<datasrc>/" prefix the user would need to add when running make.

bin/map: Fixed bug where mapping to same DB wouldn't work because by-column optimization wasn't implemented yet, by turning it off by default and allowing it to be enabled with an env var

bin/map: DB inputs: Use by-column optimization if mapping to same DB (with skeleton code for optimization's implementation)

input.Makefile: Mapping: Use the staging tables instead of any flat files if use_staged is specified

bin/map: Support custom schema name. Support input table/schema override via env vars, in case the map spreadsheet was written for a different input format.

sql.py: qual_name(): Fixed bugs where esc_name() nested func couldn't have same name as outer func, and esc_name() needed to be invoked without the module name because it's in the same module. select(): Support already-escaped table names.

main Makefile: $(psqlAsAdmin): Tell sudo to preserve env vars so PGOPTIONS is passed to psql

root map: Fill in defaults for inputs from VegBIEN, as well as outputs to it

disown_all: Updated to use main function, local vars, $self, etc. like other bash scripts run using "."

vegbien_dest: Fixed bug where it would give a usage error if run from a makefile rule, because the BASH_LINENO would be 0, by also checking if ${BASH_ARGV⁰} is ${BASH_SOURCE⁰}

postgres_vegbien: Fixed bug where interpreter did not match vegbien_dest's new required interpreter of /bin/bash

vegbien_dest: Changed interpreter to /bin/bash. Removed comment that it requires var bien_password.