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.

postgres_vegbien: Removed no longer needed retrieval of bien_password

vegbien_dest: Get bien_password by searching relative to $self, which we now have a way to get in a bash script (${BASH_SOURCE⁰}), rather than requiring the caller to set it. Provide usage error if run without initial ".".

input.Makefile: Staging tables: import/install-%: Use new quiet option to determine whether to tee output to terminal. Don't use log option because that's always set to true except in test mode, which doesn't apply to installs.

input.Makefile: Staging tables: import/install-%: Use new quiet option to determine whether to tee output to terminal. Don't use log option because that's always set to true except in test mode, which doesn't apply to installs.

main Makefile: PostgreSQL: Edit /etc/phppgadmin/apache.conf to replace "deny from all" with "allow from all", instead of uncommenting an "allow from all" that may not be there

input.Makefile: Sources: Fixed bug where cat was defined before $(tables), by moving Sources after Existing maps discovery and putting just $(inputFiles) and $(dbExport) from Sources at the beginning of Existing maps discovery

sql.py: Made truncate(), tables(), empty_db() schema-aware. Added qual_name(). tables(): Added option to filter tables by a LIKE pattern.

main Makefile: VegBIEN DB: Install public schema in a separate step, so that it can be dropped without dropping the entire DB (which also contains staging tables that shouldn't be dropped when there is a schema change). Added schemas/install, schemas/uninstall, implicit schemas/reinstall to manage the public schema separately from the rest of the DB. Moved Subdir forwarding to the bottom so overridden targets are not forwarded. README.TXT: Since `make reinstall_db` would drop the entire DB, tell user to run new `make schemas/reinstall` instead to reinstall (main) DB from schema.

schemas/postgresql.Mac.conf: Set unix_socket_directory to the new dir it seems to be using, which is now /tmp

csv2db: Fixed bug where extra columns were not truncated in INSERT mode. Replace empty column names with the column # to avoid errors with CSVs that have trailing ","s, etc.

streams.py: StreamIter: Define readline() as a separate method so it can be overridden, and all calls to self.next() will use the overridden readline(). This fixes a bug in ProgressInputStream where incremental counts would not be displayed and it would end with "not all input read" if the StreamIter interface was used instead of readline().

csv2db: Fall back to manually inserting each row (autodetecting the encoding for each field) if COPY FROM doesn't work

streams.py: FilterStream: Inherit from StreamIter so that all descendants automatically have StreamIter functionality

sql.py: insert(): Support using the default value for columns designated with the special value sql.default

sql.py: insert(): Support rows that are just a list of values, with no columns. Support already-escaped table names.

strings.py: Added contains_any()

csvs.py: reader_and_header(): Use make_reader()

Added reinstall_all to reinstall all inputs at once

with_all: Documented that it must be run from the root svn directory

input.Makefile: Staging tables: import/install-%: Only install staging table if input contains only CSV sources. Changed $(isXml) to $(isCsv) (negated) everywhere because rules almost always only run something if input contains only CSV sources, rather than if input contains XML sources.

input.Makefile: Staging tables: import/install-%: Output load status to log file if log option is set

Scripts that are meant to be run in the calling shell: Fixed bug where running the script inside another script would make the script think it was being run as a program, and abort with a usage error

Scripts that are meant to be run in the calling shell: Fixed bug where running the script as a program (without initial ".") wouldn't be able to call return in something that was not a function. Converted all code to a <script_name>_main method so that return would work properly again. Converted all variables to local variables.

env_password: return instead of exit if password not yet stored, in case user is running it from a shell without the initial "-" argument. (This would be the case if the user is just testing out the script, instead of using a command that env_password directs them to run.)

env_password: Use ${BASH_SOURCE⁰} for $self and $self for $0. return instead of exit on usage error in case user is running it from a shell.

stop_imports: Use ${BASH_SOURCE⁰} for $self and $self for $0

import_all: Use new with_all. Use ${BASH_SOURCE⁰} for $self and $self for $0.

Added with_all to run a make target on all inputs at once

Made row #s 1-based to the user to match up with the staging table row #s

bin/map: Fixed bug where limit passed to sql.select() was end instead of the # rows, causing extra rows to be fetched when start > 0. Documented that row #s start with 0.

Removed no longer needed csv2ddl

input.Makefile: Staging tables: import/install-%: Use new csv2db instead of csv2ddl/$(psqlAsBien), because it handles translating encodings properly

Added csv2db to load a command's CSV output stream into a PostgreSQL table

schemas/postgresql.Mac.conf: Set unix_socket_directory to the appropriate Mac OS X dir, since otherwise, the socket is apparently not created and `make reinstall_db` doesn't work

main Makefile: VegBIEN DB: db: Set LC_COLLATE and LC_CTYPE explicitly, to make it easier to change them

Added ProgressInputStream

exc.py: print_ex(): Added plain option to leave out traceback

main Makefile: VegBIEN DB: db: Use template0 to allow encodings other than UTF-8. Because template0 doesn't have plpgsql on PostgreSQL before 9.x, add "CREATE PROCEDURAL LANGUAGE plpgsql;" manually in schemas/vegbien.sql.make, and filter it back out on PostgreSQL after 9.x using db_dump_localize.

PostgreSQL-MySQL.csv: Remove "CREATE PROCEDURAL LANGUAGE" statements

Added db_dump_localize to translate a PostgreSQL DB dump for the local server's version

Added db_dump_localize to translate a PostgreSQL DB dump for the local server's version