xml_parse.py: Added support for parsing consecutive XML documents in a stream

Added iters.py

streams.py: Added FilterStream. Changed TracedStream to use FilterStream.

Moved parse_str() from xml_dom.py to xml_parse.py

Added xml_parse.py

streams.py: CaptureStream: Ignore start_str when recording and end_str when not recording

streams.py: CaptureStream: Get each match as a separate array elem instead of concatenated together

ch_root, repl, map: Use new maps.col_info() instead of parsing col name manually. This allows maps with prefixes containing ":" to be supported, without the ":" being misinterpreted as the label-root separator.

maps.py: Added col_info() to get label, root, prefixes from col_name. Added col_formats() for use by combinable(). Use new col_formats() in combinable(). Removed no longer needed col_label().

input.Makefile: Use with_cat instead of with_cat_csv for XML sources

Renamed inputs/XAL/src/digir.xml.make to digir.specimens.xml.make so it would generate an output file with the proper table name

bin/map: Support concatenated XML documents for XML inputs

bin/map: Merged XML inputs with and without a map into the in_is_xml section

digir_client: Output profiling information

Added inputs/XAL/src/digir.xml.make

digir_client: Import http to take advantage of httplib modifications to deal with IncompleteRead errors

Added http.py with httplib modifications to deal with IncompleteRead errors

digir_client: Fixed bug where chunk size was being adjusted even if count == None (indicating no determinable last chunk), causing a type mismatch between None and the integer total

input.Makefile: Removed no longer needed "ifneq ($(wildcard test/),)" guard around Testing section because all inputs now have a test subdir

Added inputs/XAL

digir_client: Made chunk_size a configurable env var. Removed schema env var because schema is always the same for DiGIR (can be different for TAPIR). Make sure output ends in a newline so that consecutive XML documents are on different lines.

digir_client: Fixed bug where chunk_size records would always be retrieved even in the last chunk, which ignored any manual count the user might have set via the "n" option

digir_client: Repeatedly retrieve data in chunks. Provide match count. Added section comments.

xpath.py: Added get_value() to run get_1() and returns the value of any result node

xml_dom.py: Added parse_str()

digir_client: Use new streams.copy() to copy returned data to stdout

streams.py: Added copy(). Added section comment for traced streams.

digir_client: Label debugging output

streams.py: Renamed LineCountOutputStream to LineCountStream since TracedStream now works on both input and output streams

digir_client: Capture diagnostics for later use in determining next start/count values

streams.py: Added CaptureStream to wrap a stream, capturing matching text. Renamed TracedOutputStream to TracedStream and made it work on both input and output streams. Made TracedStream inherit from WrapStream so that close() would be forwarded properly.

bin/map: Changed XML input prefix handling to prepend prefix directly to XPath instead of separating it from the XPath with a "/". Changed get_with_prefix() to use new strings.with_prefixes().

strings.py: Added with_prefixes()

digir_client: Made schema customizable

digir_client: Set header sendTime, source dynamically. In debug mode, print the request XML.

Added local_ip to get local IP address

bin/map: Added prefixes support for XML inputs

digir_client: Filter by darwin:Kingdom=PLANTAE because presumably all records will have this. Don't debug-print URL.

Added initial bin/digir_client

Renamed timeout.py to timeouts.py. Renamed timeout_ vars to timeout.

opts.py: get_env_var(): default defaults to None

inputs/SpeciesLink: Accepted test outputs for new TAPIR download

bin/tapir/tapir2flat.php: Output to specieslink.specimens.csv instead of specieslink.txt so that the output file can be used right away without renaming

inputs/REMIB/src/nodes.make: Stop after a configurable # of empty responses (indicating no more nodes), instead of at a preset node ID, because there seem to be many more nodes than are listed on the web form

input.Makefile: import/rotate: Add "." before the date

input.Makefile: Added targets for editing import: import/rotate, import/rm

bin/tapir/tapir2flat.php: Fixed XML parsing to strip control chars so DOMDocument::loadXML() wouldn't complain about "PCDATA invalid Char value 8 in Entity", etc.

main Makefile: php-Darwin: Added instruction to set PHPRC if needed

Added inputs/SpeciesLink/src/tapir.make

input.Makefile: `src/%: src/%.make`: Don't tee recipe's stderr to make's stderr, because long-running make_scripts usually will be tracked using `tail -f`

input.Makefile: `src/%: src/%.make`: Name the log file using the make_script name instead of the output file name

cat_csv: If dialect == None, ignore that file because it's empty

csvs.py: stream_info(): If header_line == '', set dialect to None rather than trying (and failing) to auto-detect it

input.Makefile: Use new sort_filenames to putmultiple numbered sources in the correct order, dealing correctly with embedded numbers that aren't padded with leading zeros

Added sort_filenames to sort a list of filenames, comparing embedded numbers numerically instead of lexicographically

schemas/postgresql.conf: Decreased shared_buffers again because 4000MB wasn't enough less than 4GB SHMMAX

schemas/postgresql.conf: Expressed shared_buffers in MB, since decimal GB doesn't seem to work anymore on 9.1

schemas/postgresql.conf: Decreased shared_buffers to 3.9GB, slightly less than SHMMAX

schemas/postgresql.conf: Optimized again using same changes as were applied to 8.4 version

schemas/postgresql.conf: Replaced with original 9.1 version

schemas/postgresql.conf: Optimized using analogous settings as postgresql.nimoy.conf

inputs/REMIB/src/nodes.make: Don't abort entire import on empty response, because an empty response is also returned for nodes that are temporarily down, not just nodes that don't exist (assumed to be after the highest numbered node). Instead, stop import after 150 nodes if user did not specify an explicit # nodes.

inputs/REMIB/src/nodes.make: Abort prefix on empty response using break, rather than just done = True, to avoid running any more code except the finally block. Moved metadata row validation outside metadata row retrieval try-except block.

inputs/REMIB/src/nodes.make: If a read times out, abort the entire node rather than just the prefix to avoid waiting 20 sec for each of 26*26 prefixes

profiling.py ItersProfiler, exc.py ExPercentTracker: Only output fraction of rows with errors if self.iter_ct > 0, to avoid divide-by-zero error

inputs/REMIB/src/nodes.make: Fixed bug where row count was output in the middle of the row processing code, instead of after the first row is processed and the row count incremented. This removes "Processed 0 row(s)" messages at the beginning of every prefix.

inputs/REMIB/src/nodes.make: Support custom starting node ID and # nodes processed via env vars

Renamed inputs/REMIB/src/nodes.all.0.header.specimens.csv to node.0.header.specimens.csv so it would sort correctly with the new output file names

Renamed inputs/REMIB/src/nodes.all.specimens.csv.make to inputs/REMIB/src/nodes.make since it will not be used to generate nodes.all.specimens.csv. However, it can still be used with the `src/%.make` make target, but will generate a dummy empty output file "nodes".

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)