inputs/REMIB/src/nodes.all.specimens.csv.make: Write each node to a separate output file

inputs/REMIB/src/nodes.all.specimens.csv.make: Raise InputException instead of AssertionError if invalid metadata row, so that it will be caught and printed instead of aborting the program

inputs/REMIB/src/nodes.all.specimens.csv.make: Moved header reading code inside TimeoutException try-except block since read sometimes times out before the header is even read

schemas/postgresql.nimoy.conf: Increased shared_buffers to 1.5GB since kernel.shmmax has been increased to 2GB

Renamed inputs/REMIB/src/remib_raw.0.header.specimens.txt to nodes.all.0.header.specimens.csv

inputs/REMIB/src/nodes.all.specimens.csv.make: Increased read timeout

inputs/REMIB/src/nodes.all.specimens.csv.make: Timeout stuck reads because sometimes nodes are offline, etc.

exc.py: str_(): Strip trailing whitespace. print_ex(): Since str_() now strips trailing whitespace, strings.ensure_newl() is no longer necessary.

streams.py: Added TimeoutInputStream and WrapStream. Changed StreamIter to use new WrapStream.

Added timeout.py

inputs/REMIB/src/nodes.all.specimens.csv.make: Download from all prefixes of all nodes. Stop when a node produces an empty response (not even an error), which indicates no more nodes. Changed status messages.

input.Makefile: `src/%: src/%.make`: Append stderr to log file

Added inputs/REMIB/src/nodes.all.specimens.csv.make to download REMIB data for all nodes

Added streams.py for I/O, which contains StreamIter, TracedOutputStream, and LineCountOutputStream

term.py: Added clear_line. Corrected file comment.

Makefiles: Let subdir's Makefile decide whether to delete on error

input.Makefile: Save partial outputs of aborted src make scripts

input.Makefile: Fixed bug in `%: %.make` rule to use $< instead of $*

mappings/DwC2-VegBIEN.specimens.csv: minimumElevationInMeters: Remove any "ca." prefix

xml_func.py: _replace: Strip whitespace from the returned string

csvs.py: Added TsvReader to support TSV quirks. Added reader_class(). reader_and_header(): Use reader_class() to automatically use TsvReader instead of csv.reader for TSVs. Added is_tsv() and use it where `dialect.delimiter == '\t'` was used.

strings.py: Added extract_line_ending() and remove_line_ending(). ensure_newl(): Use new remove_line_ending(). Moved Parsing section to top since it is used by the other sections.

csvs.py: stream_info(): Set dialect.quoting = csv.QUOTE_NONE for TSVs because they usually don't quote fields. Factored dialect detecting code into new function sniff().

input.Makefile: verify: Added reverify option, which can be turned off to prevent regenerating the verify/%.out file from the DB (which can be time-consuming), and instead just diff verify/%.out with verify/%.ref

count_error_rows: Allow input to be specified as last arg(s) in addition to as stdin

exc.py: ExPercentTracker: When diplaying fraction of iters that had errors, don't duplicate the iter_text ("row", etc.) in the numerator

bin/map: Use new ExPercentTracker iter_num tracking to track distinct row #s with errors

exc.py: ExPercentTracker: Track iter_nums of Exceptions as well, to distinguish how many distinct iters had errors

Added bin/count_error_rows to count distinct rows with errors in `map` error messages

input.Makefile: Changed "%.out: .make" rule to ": %.make" so that any file can be built from a corresponding .make file. This will allow flat files to be retrieved dynamically by running an associated .make file.

xml_func.py: FormatException: Inherit from ExceptionWithCause instead of SyntaxError because a FormatException signals a different kind of error condition (related to the input value rather than the function syntax)

xml_func.py: Renamed SyntaxException to SyntaxError because it's a user error signaling invalid mappings syntax

xml_func.py: SyntaxException: Use ExceptionWithCause to combine msg and cause's msg because it now combines them on one line, which is needed for bin/error_stats to work properly

exc.py: ExceptionWithCause: Prepend msg to cause's msg separated by ': ' instead of '\ncause: '

xml_func.py: Changed SyntaxException to FormatException where the error was with the input data format rather than the mapping syntax

mappings/VegX-VegBIEN.organisms.csv: slopeaspect: Apply new conversion _compass

xml_func.py: Added _compass to convert a compass direction (N, NE, NNE, etc.) into a degree heading

Added angles.py

inputs/SpeciesLink/maps: Updated to use new TAPIR download

input.Makefile: All targets can be specified with an optional trailing slash. This enables using tab completion to complete a target name which is also a subdir name, since tab completion appends a trailing slash.

bin/tapir/tapir2flat.php: Fixed bug in row assembly where XML elements that weren't found were left out of the array, causing the columns to shift to the left

xml_func.py: _map: Factored replacing code out into new function repl(), which can also be used by other XML funcs

bin/tapir/tapir2flat.php: Turned off exiting after 3 successive failures, because it causes the import to abort and it doesn't seem to restart where it left off

main Makefile: Added instructions to install PHP PEAR and HTTP_Request on Mac OS X

Makefile: Added PHP section, which installs php-http-request

Moved _archive/tapir2flatClient/trunk/client/ to bin/tapir/

_archive/tapir2flatClient/trunk/client/tapir2flat.php: Upgraded to use fputcsv(). This should fix errors caused by embedded delimeters. configurableParams.php: Set default delimeter to ','.

mappings/verify.specimens.sql: # species: Don't join at all on genus because DISTINCT is on the plantname_id rather than the plantname, which is already unique for a given genus because plantname_unique includes parent_id

mappings/verify.specimens.sql: # species: Fixed to join separately on plantname_ancestor for genus and species

input.Makefile: Moved log and trace files to new import subdir. Moved subdir-adding code from inputs/Makefile to input.Makefile.

mappings/verify.specimens.sql: Updated for schema changes

inputs/*: Added any missing standard subdirs

inputs/Makefile: Added %/-add to re-add existing dirs

inputs/Makefile: %-add: `svn mkdir` the datasource's standard subdirs

schemas/postgresql.nimoy.conf: Increased work_mem (for sorting) and maintenance_work_mem (for vacuum)

schemas/postgresql.nimoy.conf: Reset shared_buffers to initial value 24MB because although kernel.shmmax is 32MB, only values up to 26MB seem to work

schemas/postgresql.nimoy.conf: Set shared_buffers to SHMMAX

Optimized schemas/postgresql.nimoy.conf

Added schemas/postgresql.nimoy.conf

bin/map: When profiling, print the profile_to destination file

Added schemas/postgresql.conf

xml_func.py: _date: When converting month name to number, wrap any ValueError in a SyntaxException

xml_func.py: XML functions that assume their last argument is a value (_map, etc.): Use new helper function pop_value() to retrieve this value. Return None if value is None because this indicates the input is empty.

xml_func.py: _date: Use format.str2int instead of int to convert date parts to int so that strange formatting will be parsed correctly

format.py: clean_numeric(): Also fix some OCR errors

filter_errors: Default to outputing only the first match

xpath.py: Added append() to recursively append subpath to every leaf of a path tree. parse(): Use append() to fix bug in split path parsing where subpath was not added to every leaf of the tree, only the main leaf of the main branch and the main leaves of the other branches of the last element.

exc.py: Changed to store multiple tracebacks in an exception, in case an exception is caught and re-raised inside an ExceptionWithCause wrapper. This preserves more of the traceback in this situation, because you get the ExceptionWithCause's traceback as well.

input.Makefile: import: Removed verbose=1 because verbose mode is now automatically on (except in test mode)

bin/map: verbose mode defaults to off in test mode and on otherwise

bin/map: In verbose mode, print which input rows will be processed

bin/map: n option: Defaults to 1 in test mode. Empty string "" is interpreted as None (previously n would have to be unset to specify None).

bin/map: Added section comments to env var config retrieval. Reordered env var config retrieval to put DB config last, since these options are input-type specific and complex, and putting them first hides the more general other options.

bin/map: Added section comments to env var config retrieval. Reordered env var config retrieval to put DB config last, since these options are input-type specific and complex, and putting them first hides the more general other options.

inputs/SALVIAS*/maps/VegX.plots.csv: Updated _units for % -> decimal conversion to use new syntax

inputs/SALVIAS*/maps/VegX.plots.csv: Updated _units for % -> decimal conversion to use new syntax

xml_func.py: _units: If value can't be converted to float, wrap the ValueError in a SyntaxException

units.py: convert(): Added support for unit conversions. Added initial unit conversion for % -> unitless. str2quantity(): Fixed regexp to match % as units. Set Quantity.__repr__ to quantity2str.

units.py: convert(): Put "units None" test after "quantity.units units" test because a destination of no units might require a conversion for some input units (e.g. % -> unitless requires a division by 100)

inputs/SALVIAS*/maps/VegX.organisms.csv: Habit: Ignore invalid values instead of generating a SyntaxException

xml_dom.py: minidom modifications: Escape as many text strings as we use directly. This still leaves the tagName used by xml.dom.minidom.Element.writexml: It uses 'writer.write(indent+"<" + self.tagName)' and doesn't escape the tagName.

xml_func.py: Made everything Unicode-safe by using strings.ustr instead of str

schemas/tree_cross-links.sql: Added comment for how to get the namedplace trigger from the provided plantname trigger

vegbien.sql: Fixed bug in tree cross-link algorithm where recursion to descendants' ancestors did not use new to refer to the current node's plantname_id

vegbien.sql: Fixed bug in tree cross-link algorithm to also insert ancestors for top-level nodes, because they now need an ancestor entry for themselves

Added separate SQL file for tree cross-links code. A link to this can be e-mailed to people to review.

vegbien.sql: Modified tree cross-link algorithm to add an "ancestor" for this node. This is useful for queries, because you don't have to separately test if the leaf node is the one you're looking for, in addition to that leaf node's ancestors.

README.TXT: Added instructions how to stop all running imports

vegbien.sql: Added namedplace_update_ancestors and plantname_update_ancestors triggers to populate ancestor cross-links in new namedplace_ancestor and plantname_ancestor tables

sql.py: insert() (and try_insert()): Added optional returning param to provide name of an inserted column (usually pkey) to return

env_password: Print Usage message if run without initial "."

Added bin/stop_imports to stop all running imports

import_all: Print Usage message if was run without initial "."

Renamed import-all to import_all to match convention of using underscores

inputs/CTFS: Added remaining non-data src files

Added CTFS data dictionary inputs/CTFS/src/ctfs-comments_worksheet.xls

import-all: Fixed to display the datasource name in the job name instead of 'make ${input}import &'

import-all: disown each new import process to ignore SIGHUP

Added jobspecs to extract jobspecs (%#) from (possibly filtered) `jobs` output

README.TXT: Changed `make import &` to `. bin/import-all`