mappings/Makefile: Sort VegX-VegBank organisms mapping automatically when anything that depends on it is remade

Added in_place to run a stream command on a file

join_sort: Use /bin/sh instead of /bin/bash

NYBG-VegX mapping: Removed no longer needed global stem count value

Renamed test/accept_output to accept

VegX-VegBank.organisms.csv: Made stemCount default to 1

bin/map: Print DatabaseErrors without stack traces

exc.py: Added print_ex()

exc.py: Added print_ex()

util.py: Added type_name()

strings.py: Added ensure_newl()

input.Makefile: Save map output in log file

bin/map: Print usage message when run with no arguments

Makefile: Removed unnecessary commenting out of "allow from 127.0.0.0..." lines in /etc/phppgadmin/apache.conf

Makefile: Use --loose-exit-status for ed to avoid failing on no match. In editPhppgadminApacheConf, use ,s/// instead of /.../\ns/// to match lines regardless of position.

Makefile: Use tee instead of ed in sudoAppend. Don't change apache port to 8080 if apache already running on 80.

Makefile: Added phppgadmin apache config

bin/map: Only treat DatabaseErrors as warnings, not all Exceptions

xml_func.py: Print newline before func XML because XML is now pretty-printed with indents

xml_dom.py: Node.__str__() uses toprettyxml() instead of toxml()

util.py: Changed rename_key() not to suppress KeyError, since some callers might want to assert that a key exists

Makefile: Added phpPgAdmin dependency

xml_func.py: _name func doesn't require all name parts to be set. _namePart func throws SyntaxException for invalid name parts.

bin/map: Fixed syntax error where db variable had not been renamed to out_db

xml_func.py: Generate SyntaxExceptions on missing XML func args

VegX-VegBank mapping: Added default soilObs.soilHorizon value

xml_func.py: Changed _date func to try parsing date field, rather than year field, as a decimal. Changed SALVIAS mappings to use new _date func syntax. Fixes SALVIAS plots data syntax error for decimal years.

Removed no longer needed VegBank accepted test outputs

test/map: Abort tester on failed diff

Added accepted test output SALVIAS_db.organisms.VegBIEN.xml

SALVIAS organisms mapping: Use _alt to merge tag1 and tag2. Fixes failing diff due to duplicate stemCodes.

test/map: Added tests to insert VegBIEN XML into VegBIEN db

bin/map: Fixed non-map input to set out_label

bin/map: Fixed row processing when no map is used

bin/map: Refactored to process each row separately when out_is_db

xml_dom.py: Added Node pop() and clear() methods

bin/map: Moved process_rows() exception handling around entire row, rather than each value, so that a broken value will not be ignored only to cause errors when outputing the row

bin/map: Moved process_rows() exception handling around entire row, rather than each value, so that a broken value will not be ignored only to cause errors when outputing the row

db_xml.py: Removed no longer needed xml2db()

bin/map: out_is_db uses use_row instead of xml2db()

bin/map: Added commit and exception-handling code to out_is_db use_row()

bin/map: Merged get_xml() into process_xml(). Renamed process*() functions to distinguish them better.

bin/map: Create separate document for printing XML opening and closing

bin/map: Refactored to print document opening, contents, and closing in separate steps so they can be separated later

xml_dom.py: Added support for integer indents

xml_dom.py: Added NodeIter() and Node.__iter__()

Use new xml_dom.prettyxml_config instead of Node.writeprettyxml because it can be passed as keyword args to any writexml function

xml_dom.py: Removed no longer needed xml_dom.writexml()

bin/map: Use Node.writeprettyxml() instead of xml_dom.writexml()

xml_dom.py: Added minidom.Document write_opening() and write_closing() methods. Changed writexml(writer, node) to use new Node.writeprettyxml() method.

Renamed ex.py to exc.py

Import xml.dom.minidom as minidom

xml_dom.py: Refactored xml.dom.minidom.Element.writexml() to use new write_opening() and write_closing() methods. Use new functions is_elem() and is_text_node() to determine node type. Corrected definition of a text element to be an element that contains a single text node.

bin/map: Factored out input processing code

Commit after inserting each row

Commit after inserting each row

Use traceback.print_exc() to print Exceptions for each row instead of exiting

env_password: Allow user to change saved password

env_password: Don't print instructions for storing password for the session if called to store password for the session

env_password: Print absolute path to env_password in case invoking script changed the working directory

env_password: Print instructions for storing password for the session

Updated SALVIAS plots mappings and corresponding VegX-VegBank mappings to parse date_start and date_finish

xml_func.py: Print XML of XML functions with SyntaxExceptions

xml_func.py: Added support for parsing dates

ex.py: repl_msg(): take replacements as keyword args

fix_permissions: Also change user to bien

Makefile: Added python-dateutil dependency

input.Makefile: Renamed from_db-<map_file> target to import-<type> so it can be more easily run as a command-line target rather than just a prerequisite

Added inputs/SALVIAS organisms map

map: Print xml_func.SyntaxExceptions without stack traces by using SystemExit

xml_func.py: Add function name to SyntaxException message

ex.py: Added repl_msg() to format a message with the % operator

xml_func.py: Return string->number conversion errors as xml_func.SyntaxExceptions

psql_vegbien: Fixed comment to vegbien instead of vegbank

psql_vegbien: Use new location of bien_password

Makefile: Fixed paths to mappings dir for new scripts dir location

Renamed util to bin

Moved inputs_Makefile to inputs/input.Makefile

Moved bien_password to new config dir

Moved sample inputs to test dir

Added symlink from scripts to new scripts destination

Removed now-empty scripts dir

Moved everything in scripts to root. inputs_Makefile: Don't run "all" when installing.

Renamed bien_map to map

Moved map to util

fix_permissions: Don't chmod symlinks

inputs_Makefile: Auto-generate map to VegBIEN and import data into vegbien from input DB

inputs/SALVIAS: maps to VegX and VegBIEN

bien_map: Runs map with BIEN defaults

join_sort: Sorts a join on the output col

inputs_Makefile: Require dbEngine var instead of defaulting to MySQL

Moved inputs into svn

Moved pre-BIEN 3 files into _archive folder

test/map: Use db.sh syntax in *.sh tests

inputs_Makefile: Generate db.sh with DB access info

inputs_Makefile: Changed GRANT ALL to GRANT SELECT. Added REVOKE ALL. Added $(db).sql as prerequisite of install in case it needs to be auto-generated.

scripts/Makefile: Added action for postgres-Darwin target

scripts/Makefile: Added postgresql to postgres-Linux apt-get packages

test/map: Changed to work on both nimoy and vegbiendev by selecting the appropriate MySQL user and password

env_password: Added optional message arg