Activity
From 03/02/2012 to 03/31/2012
03/29/2012
- 10:33 PM Revision 1710: streams.py: Added FilterStream. Changed TracedStream to use FilterStream.
- 10:24 PM Revision 1709: Moved parse_str() from xml_dom.py to xml_parse.py
- 10:24 PM Revision 1708: Added xml_parse.py
- 10:21 PM Revision 1707: streams.py: CaptureStream: Ignore start_str when recording and end_str when not recording
- 10:13 PM Revision 1706: streams.py: CaptureStream: Get each match as a separate array elem instead of concatenated together
- 09:59 PM Revision 1705: 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.
- 09:57 PM Revision 1704: 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().
- 09:55 PM Revision 1703: input.Makefile: Use with_cat instead of with_cat_csv for XML sources
- 09:54 PM Revision 1702: Renamed inputs/XAL/src/digir.xml.make to digir.specimens.xml.make so it would generate an output file with the proper table name
- 08:53 PM Revision 1701: bin/map: Support concatenated XML documents for XML inputs
- 08:46 PM Revision 1700: bin/map: Merged XML inputs with and without a map into the in_is_xml section
- 08:33 PM Revision 1699: digir_client: Output profiling information
- 08:21 PM Revision 1698: Added inputs/XAL/src/digir.xml.make
- 08:21 PM Revision 1697: digir_client: Import http to take advantage of httplib modifications to deal with IncompleteRead errors
- 08:20 PM Revision 1696: Added http.py with httplib modifications to deal with IncompleteRead errors
- 07:46 PM Revision 1695: 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
- 07:28 PM Revision 1694: input.Makefile: Removed no longer needed "ifneq ($(wildcard test/),)" guard around Testing section because all inputs now have a test subdir
- 07:25 PM Revision 1693: Added inputs/XAL
- 07:22 PM Revision 1692: 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.
- 07:13 PM Revision 1691: 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
- 07:07 PM Revision 1690: digir_client: Repeatedly retrieve data in chunks. Provide match count. Added section comments.
- 06:52 PM Revision 1689: xpath.py: Added get_value() to run get_1() and returns the value of any result node
- 06:51 PM Revision 1688: xml_dom.py: Added parse_str()
- 06:13 PM Revision 1687: digir_client: Use new streams.copy() to copy returned data to stdout
- 06:13 PM Revision 1686: streams.py: Added copy(). Added section comment for traced streams.
- 06:06 PM Revision 1685: digir_client: Label debugging output
- 05:54 PM Revision 1684: streams.py: Renamed LineCountOutputStream to LineCountStream since TracedStream now works on both input and output streams
- 05:52 PM Revision 1683: digir_client: Capture diagnostics for later use in determining next start/count values
- 05:51 PM Revision 1682: 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.
- 05:23 PM Revision 1681: 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().
- 05:21 PM Revision 1680: strings.py: Added with_prefixes()
- 04:56 PM Revision 1679: digir_client: Made schema customizable
- 04:35 PM Revision 1678: digir_client: Set header sendTime, source dynamically. In debug mode, print the request XML.
- 04:03 PM Revision 1677: Added local_ip to get local IP address
- 03:48 PM Revision 1676: bin/map: Added prefixes support for XML inputs
03/28/2012
- 11:12 PM Revision 1675: digir_client: Filter by darwin:Kingdom=PLANTAE because presumably all records will have this. Don't debug-print URL.
- 11:07 PM Revision 1674: Added initial bin/digir_client
- 07:58 PM Revision 1673: Renamed timeout.py to timeouts.py. Renamed timeout_ vars to timeout.
- 07:52 PM Revision 1672: opts.py: get_env_var(): default defaults to None
- 06:35 PM Revision 1671: inputs/SpeciesLink: Accepted test outputs for new TAPIR download
- 06:03 PM Revision 1670: 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
- 05:52 PM Revision 1669: 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
03/27/2012
- 11:10 PM Revision 1668: input.Makefile: import/rotate: Add "." before the date
- 11:08 PM Revision 1667: input.Makefile: Added targets for editing import: import/rotate, import/rm
- 09:41 PM Revision 1666: 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.
- 09:07 PM Revision 1665: main Makefile: php-Darwin: Added instruction to set PHPRC if needed
- 09:03 PM Revision 1664: Added inputs/SpeciesLink/src/tapir.make
- 09:03 PM Revision 1663: 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`
- 09:00 PM Revision 1662: input.Makefile: `src/%: src/%.make`: Name the log file using the make_script name instead of the output file name
- 08:31 PM Revision 1661: cat_csv: If dialect == None, ignore that file because it's empty
- 08:30 PM Revision 1660: csvs.py: stream_info(): If header_line == '', set dialect to None rather than trying (and failing) to auto-detect it
- 08:19 PM Revision 1659: 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
- 08:18 PM Revision 1658: Added sort_filenames to sort a list of filenames, comparing embedded numbers numerically instead of lexicographically
- 07:18 PM Revision 1657: schemas/postgresql.conf: Decreased shared_buffers again because 4000MB wasn't enough less than 4GB SHMMAX
- 07:16 PM Revision 1656: schemas/postgresql.conf: Expressed shared_buffers in MB, since decimal GB doesn't seem to work anymore on 9.1
- 07:14 PM Revision 1655: schemas/postgresql.conf: Decreased shared_buffers to 3.9GB, slightly less than SHMMAX
- 07:11 PM Revision 1654: schemas/postgresql.conf: Optimized again using same changes as were applied to 8.4 version
- 07:10 PM Revision 1653: schemas/postgresql.conf: Replaced with original 9.1 version
- 07:03 PM Revision 1652: schemas/postgresql.conf: Optimized using analogous settings as postgresql.nimoy.conf
- 06:43 PM Revision 1651: 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.
- 05:50 PM Revision 1650: 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.
- 05:41 PM Revision 1649: 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
- 05:40 PM Revision 1648: profiling.py ItersProfiler, exc.py ExPercentTracker: Only output fraction of rows with errors if self.iter_ct > 0, to avoid divide-by-zero error
- 04:55 PM Revision 1647: 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.
- 04:40 PM Revision 1646: inputs/REMIB/src/nodes.make: Support custom starting node ID and # nodes processed via env vars
- 04:29 PM Revision 1645: 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
- 04:27 PM Revision 1644: 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".
- 04:21 PM Revision 1643: inputs/REMIB/src/nodes.all.specimens.csv.make: Write each node to a separate output file
- 04:00 PM Revision 1642: 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
- 03:56 PM Revision 1641: 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
- 03:55 PM Revision 1640: schemas/postgresql.nimoy.conf: Increased shared_buffers to 1.5GB since kernel.shmmax has been increased to 2GB
03/26/2012
- 11:07 PM Revision 1639: Renamed inputs/REMIB/src/remib_raw.0.header.specimens.txt to nodes.all.0.header.specimens.csv
- 10:57 PM Revision 1638: inputs/REMIB/src/nodes.all.specimens.csv.make: Increased read timeout
- 10:55 PM Revision 1637: inputs/REMIB/src/nodes.all.specimens.csv.make: Timeout stuck reads because sometimes nodes are offline, etc.
- 10:53 PM Revision 1636: exc.py: str_(): Strip trailing whitespace. print_ex(): Since str_() now strips trailing whitespace, strings.ensure_newl() is no longer necessary.
- 10:43 PM Revision 1635: streams.py: Added TimeoutInputStream and WrapStream. Changed StreamIter to use new WrapStream.
- 10:42 PM Revision 1634: Added timeout.py
- 10:25 PM Revision 1633: 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.
- 10:17 PM Revision 1632: input.Makefile: `src/%: src/%.make`: Append stderr to log file
- 09:21 PM Revision 1631: Added inputs/REMIB/src/nodes.all.specimens.csv.make to download REMIB data for all nodes
- 09:20 PM Revision 1630: Added streams.py for I/O, which contains StreamIter, TracedOutputStream, and LineCountOutputStream
- 09:20 PM Revision 1629: term.py: Added clear_line. Corrected file comment.
- 08:06 PM Revision 1628: Makefiles: Let subdir's Makefile decide whether to delete on error
- 08:05 PM Revision 1627: input.Makefile: Save partial outputs of aborted src make scripts
- 06:44 PM Revision 1626: input.Makefile: Fixed bug in `%: %.make` rule to use $< instead of $*
- 06:20 PM Revision 1625: mappings/DwC2-VegBIEN.specimens.csv: minimumElevationInMeters: Remove any "ca." prefix
- 06:19 PM Revision 1624: xml_func.py: _replace: Strip whitespace from the returned string
- 06:09 PM Revision 1623: 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.
- 06:06 PM Revision 1622: 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.
- 04:40 PM Revision 1621: 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().
- 03:45 PM Revision 1620: 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
03/24/2012
- 10:31 PM Revision 1619: count_error_rows: Allow input to be specified as last arg(s) in addition to as stdin
- 10:30 PM Revision 1618: exc.py: ExPercentTracker: When diplaying fraction of iters that had errors, don't duplicate the iter_text ("row", etc.) in the numerator
- 10:27 PM Revision 1617: bin/map: Use new ExPercentTracker iter_num tracking to track distinct row #s with errors
- 10:27 PM Revision 1616: exc.py: ExPercentTracker: Track iter_nums of Exceptions as well, to distinguish how many distinct iters had errors
- 10:10 PM Revision 1615: Added bin/count_error_rows to count distinct rows with errors in `map` error messages
- 09:06 PM Revision 1614: 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.
- 09:01 PM Revision 1613: 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)
- 08:57 PM Revision 1612: xml_func.py: Renamed SyntaxException to SyntaxError because it's a user error signaling invalid mappings syntax
- 08:55 PM Revision 1611: 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
- 08:54 PM Revision 1610: exc.py: ExceptionWithCause: Prepend msg to cause's msg separated by ': ' instead of '\ncause: '
- 08:47 PM Revision 1609: xml_func.py: Changed SyntaxException to FormatException where the error was with the input data format rather than the mapping syntax
- 08:41 PM Revision 1608: mappings/VegX-VegBIEN.organisms.csv: slopeaspect: Apply new conversion _compass
- 08:40 PM Revision 1607: xml_func.py: Added _compass to convert a compass direction (N, NE, NNE, etc.) into a degree heading
- 08:38 PM Revision 1606: Added angles.py
- 07:37 PM Revision 1605: inputs/SpeciesLink/maps: Updated to use new TAPIR download
- 07:29 PM Revision 1604: 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.
- 07:23 PM Revision 1603: 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
- 07:03 PM Revision 1602: xml_func.py: _map: Factored replacing code out into new function repl(), which can also be used by other XML funcs
- 06:46 PM Revision 1601: 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
- 03:41 PM Revision 1600: main Makefile: Added instructions to install PHP PEAR and HTTP_Request on Mac OS X
- 03:10 PM Revision 1599: Makefile: Added PHP section, which installs php-http-request
- 03:05 PM Revision 1598: Moved _archive/tapir2flatClient/trunk/client/ to bin/tapir/
- 03:03 PM Revision 1597: _archive/tapir2flatClient/trunk/client/tapir2flat.php: Upgraded to use fputcsv(). This should fix errors caused by embedded delimeters. configurableParams.php: Set default delimeter to ','.
- 02:42 PM Revision 1596: 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
- 02:39 PM Revision 1595: mappings/verify.specimens.sql: # species: Fixed to join separately on plantname_ancestor for genus and species
- 02:14 PM Revision 1594: input.Makefile: Moved log and trace files to new import subdir. Moved subdir-adding code from inputs/Makefile to input.Makefile.
- 01:49 PM Revision 1593: mappings/verify.specimens.sql: Updated for schema changes
- 01:36 PM Revision 1592: inputs/*: Added any missing standard subdirs
- 01:35 PM Revision 1591: inputs/Makefile: Added %/-add to re-add existing dirs
- 01:29 PM Revision 1590: inputs/Makefile: %-add: `svn mkdir` the datasource's standard subdirs
03/23/2012
- 06:52 PM Revision 1589: schemas/postgresql.nimoy.conf: Increased work_mem (for sorting) and maintenance_work_mem (for vacuum)
- 06:45 PM Revision 1588: 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
- 06:33 PM Revision 1587: schemas/postgresql.nimoy.conf: Set shared_buffers to SHMMAX
- 06:27 PM Revision 1586: Optimized schemas/postgresql.nimoy.conf
- 06:04 PM Revision 1585: Added schemas/postgresql.nimoy.conf
- 05:59 PM Revision 1584: bin/map: When profiling, print the profile_to destination file
- 05:53 PM Revision 1583: Added schemas/postgresql.conf
- 05:38 PM Revision 1582: xml_func.py: _date: When converting month name to number, wrap any ValueError in a SyntaxException
- 05:33 PM Revision 1581: 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.
- 05:22 PM Revision 1580: xml_func.py: _date: Use format.str2int instead of int to convert date parts to int so that strange formatting will be parsed correctly
- 05:21 PM Revision 1579: format.py: clean_numeric(): Also fix some OCR errors
- 05:15 PM Revision 1578: filter_errors: Default to outputing only the first match
- 04:59 PM Revision 1577: 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.
- 04:27 PM Revision 1576: 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.
- 03:53 PM Revision 1575: input.Makefile: import: Removed verbose=1 because verbose mode is now automatically on (except in test mode)
- 03:52 PM Revision 1574: bin/map: verbose mode defaults to off in test mode and on otherwise
- 03:48 PM Revision 1573: bin/map: In verbose mode, print which input rows will be processed
- 03:40 PM Revision 1572: 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).
- 03:32 PM Revision 1571: 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.
- 03:31 PM Revision 1570: 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.
- 03:29 PM Revision 1569: inputs/SALVIAS*/maps/VegX.plots.csv: Updated _units for % -> decimal conversion to use new syntax
- 03:20 PM Revision 1568: inputs/SALVIAS*/maps/VegX.plots.csv: Updated _units for % -> decimal conversion to use new syntax
- 03:19 PM Revision 1567: xml_func.py: _units: If value can't be converted to float, wrap the ValueError in a SyntaxException
- 03:18 PM Revision 1566: 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.
- 03:03 PM Revision 1565: 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)
- 02:51 PM Revision 1564: inputs/SALVIAS*/maps/VegX.organisms.csv: Habit: Ignore invalid values instead of generating a SyntaxException
- 02:47 PM Revision 1563: 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.
- 02:39 PM Revision 1562: xml_func.py: Made everything Unicode-safe by using strings.ustr instead of str
- 02:15 PM Task #369 (Resolved): get CTFS data dictionary
- 02:14 PM Task #384 (Resolved): prototype tree traversal algorithm
- 02:14 PM Task #385 (Resolved): implement mechanism to determine which specimenreplicates refer to the same specimen
- 12:48 PM Revision 1561: schemas/tree_cross-links.sql: Added comment for how to get the namedplace trigger from the provided plantname trigger
- 12:44 PM Revision 1560: 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
- 12:39 PM Revision 1559: 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
- 12:28 PM Revision 1558: Added separate SQL file for tree cross-links code. A link to this can be e-mailed to people to review.
- 12:21 PM Revision 1557: 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.
03/22/2012
- 07:08 PM Revision 1556: README.TXT: Added instructions how to stop all running imports
- 06:59 PM Revision 1555: vegbien.sql: Added namedplace_update_ancestors and plantname_update_ancestors triggers to populate ancestor cross-links in new namedplace_ancestor and plantname_ancestor tables
- 06:07 PM Revision 1554: sql.py: insert() (and try_insert()): Added optional returning param to provide name of an inserted column (usually pkey) to return
- 05:41 PM Revision 1553: env_password: Print Usage message if run without initial "."
- 05:34 PM Revision 1552: Added bin/stop_imports to stop all running imports
- 05:33 PM Revision 1551: import_all: Print Usage message if was run without initial "."
- 04:52 PM Revision 1550: Renamed import-all to import_all to match convention of using underscores
- 04:39 PM Revision 1549: inputs/CTFS: Added remaining non-data src files
- 04:35 PM Revision 1548: Added CTFS data dictionary inputs/CTFS/src/ctfs-comments_worksheet.xls
- 04:33 PM Revision 1547: import-all: Fixed to display the datasource name in the job name instead of 'make ${input}import &'
03/20/2012
- 11:13 PM Revision 1546: import-all: disown each new import process to ignore SIGHUP
- 11:06 PM Revision 1545: Added jobspecs to extract jobspecs (%#) from (possibly filtered) `jobs` output
- 11:05 PM Revision 1544: README.TXT: Changed `make import &` to `. bin/import-all`
- 11:05 PM Revision 1543: README.TXT: Changed `make import &` to `. bin/import-all`
- 10:39 PM Revision 1542: main Makefile: import: Before running imports, print message that `. bin/import-all` can be used to import all inputs at once
- 10:38 PM Revision 1541: Added import-all to import all inputs at once
- 10:20 PM Revision 1540: mappings/DwC2-VegBIEN.specimens.csv: Mapped establishmentMeans, which contains growthform, iscultivated, isnative, etc. combined
- 10:11 PM Revision 1539: inputs/SALVIAS-CSV/maps/VegX.organisms.csv: habit: Updated mapping to match equivalent SALVIAS mapping
- 10:10 PM Revision 1538: xml_func.py: _map: Instead of _closed special entry, make all maps closed by default and open them if special entry "*=*" is present. Support using a _map to filter values by interpreting special entry "*=" as removing all values not explicitly specified, and by interpreting special value "*" as keeping input value the same.
- 10:08 PM Revision 1537: xml_func.py: _map: Instead of _closed special entry, make all maps closed by default and open them if special entry "*=*" is present. Support using a _map to filter values by interpreting special entry "*=" as removing all values not explicitly specified, and by interpreting special value "*" as keeping input value the same.
- 09:19 PM Revision 1536: xml_func.py: _date: On error "month must be in 1..12", try swapping month and day
- 09:13 PM Revision 1535: xml_func.py: _date: On error "month must be in 1..12", try swapping month and day
- 08:36 PM Revision 1534: row: Support getting multiple rows. Document that does *not* handle embedded newlines.
- 08:19 PM Revision 1533: mappings/Makefile: Removed no longer needed DwC-VegBIEN.specimens.no_empty.csv
- 08:18 PM Revision 1532: input.Makefile: Removed no longer needed $(join) command
- 08:15 PM Revision 1531: input.Makefile: Removed no longer needed src join maps
- 08:12 PM Revision 1530: input.Makefile: Generate VegBIEN maps from full via maps in order to include all input columns if a src map was provided. This causes the VegBIEN join process to produce *all* the "No join mapping" errors for that datasource, not just those for fields in the (non-full) via map. maps/src.join.*.csv should no longer be needed for producing "No join mapping" errors.
- 08:03 PM Revision 1529: mappings/Makefile: Generate DwC-VegBIEN.specimens.csv from new intermediate DwC.ci-VegBIEN.specimens.csv using $(removeEmpty) so that "No join mapping" errors will be reported when maps are joined to it. Deprecate DwC-VegBIEN.specimens.no_empty.csv because it's now identical to DwC-VegBIEN.specimens.csv.
- 07:45 PM Revision 1528: Added inputs/NY/maps/src.specimens.csv
- 07:41 PM Revision 1527: Added reverse_join to inner-join two map spreadsheets in the opposite order they are specified in
- 07:36 PM Revision 1526: input.Makefile: Intersect the generated VegBIEN and full via maps with the src map, if it exists. This reduces the size of the autogen maps significantly by including only the entries used by the datasource.
- 07:34 PM Revision 1525: intersect: Compare columns based on specified compare_col_nums, just like subtract
- 06:50 PM Revision 1524: input.Makefile: Use var $(selfMap) instead of spelling out $(bin)/cols 0 0
- 06:36 PM Revision 1523: mappings/DwC2-VegBIEN.specimens.csv: Mapped continent
- 06:20 PM Revision 1522: inputs/SpeciesLink/maps/DwC.specimens.csv: Mapped remaining fields
- 06:19 PM Revision 1521: inputs/SpeciesLink/maps/DwC.specimens.csv: Mapped remaining fields
- 06:08 PM Revision 1520: inputs/SpeciesLink/maps/src.specimens.csv: Fixed bug where prefixes had not been removed from fields, which prevented join mappings from being found for any of the fields
- 06:08 PM Revision 1519: main Makefile: Added missing_joins to determine which input fields are missing join mappings
- 05:47 PM Revision 1518: xml_func.py: SyntaxException: Inherit from exc.ExceptionWithCause so the traceback will be populated with the cause's traceback instead of the SyntaxException wrapper's traceback
- 05:35 PM Revision 1517: Added inputs/UNCC/test with accepted test outputs
- 05:35 PM Revision 1516: Added inputs/UNCC/maps
- 05:34 PM Revision 1515: xml_func.py: _date: month: Convert month names to numbers before casting everything to int
- 05:27 PM Revision 1514: xml_func.py: _date: Refactored to convert items to dict right away, and use iteritems() for later type conversion. This will enable month names to be converted before casting everything to int.
- 04:47 PM Revision 1513: mappings/Makefile: Sort mappings/DwC.self.specimens.csv so that entries can more easily be found when using it as a DwC terms reference
03/19/2012
- 09:55 PM Revision 1512: Added inputs/UNCC
- 09:50 PM Revision 1511: Added inputs/U/test with accepted test outputs
- 09:49 PM Revision 1510: inputs/U/maps/DwC.specimens.csv: Mapped most of the remaining fields
- 09:34 PM Revision 1509: input.Makefile: Clean up via maps when they change by subtracting the via format's self map from the via map (the comments column is ignored in determining which entries are redundant, and empty entries with a matching input column are also removed)
- 09:29 PM Revision 1508: subtract: Fixed bug where entries were removed even if maps were not combinable and ignore was off
- 09:27 PM Revision 1507: union: Fixed bug where combinable was not saved for use in deciding whether to add entries in map 1 that weren't already defined
- 09:25 PM Revision 1506: inputs/U/maps: Set svn props
- 09:20 PM Revision 1505: subtract: Also remove nonexplicit empty mappings whose input col is in map 1
- 09:15 PM Revision 1504: maps.py: Added is_nonexplicit_empty_mapping()
- 09:03 PM Revision 1503: subtract: Use new maps.combinable() to compare column headers, which allows more flexibility in combining maps
- 09:01 PM Revision 1502: union: Use new maps.combinable()
- 09:01 PM Revision 1501: maps.py: Added col_label() and combinable()
- 08:54 PM Revision 1500: union: Use new strings.overlaps()
- 08:53 PM Revision 1499: strings.py: Added overlaps()
- 08:46 PM Revision 1498: vegbien.sql: Fixed sytnax error in taxonclass enum: missing comma at end of element
- 08:38 PM Revision 1497: inputs/*/maps/DwC.specimens.csv: Ran through `cols *` to standardize CSV format to that generated by Python
- 08:35 PM Revision 1496: cols: If column number of "*" given, get all columns
- 08:32 PM Revision 1495: bin/subtract: If no compare columns given, compare on all columns instead of column 0
- 08:31 PM Revision 1494: util.py: list_subset(): Support special idxs value None, which returns entire list
- 08:22 PM Revision 1493: cat_csv: Added support for using - to cat stdin
- 08:18 PM Revision 1492: Added inputs/U/maps
- 07:32 PM Revision 1491: Added inputs/U
- 07:29 PM Revision 1490: Put inputs/REMIB/src/remib_raw.0.header.specimens.txt under version control
- 07:24 PM Revision 1489: Added inputs/REMIB/test with accepted test outputs
- 07:22 PM Revision 1488: Added inputs/REMIB/maps
- 07:20 PM Revision 1487: inputs/NCU-NCSC/maps/DwC.specimens.csv: Removed State->StateProvince mapping because that is now in mappings/DwC1-DwC2.specimens.csv
- 07:13 PM Revision 1486: mappings/DwC1-DwC2.specimens.csv: Added common DwC1 fields that are not part of the official DwC1 schema
- 06:51 PM Revision 1485: Added inputs/REMIB
- 06:09 PM Revision 1484: bin/map: Deal with fields that may be in the dataset under more than one prefix by getting all fields and coalesce()ing them (e.g. SpeciesLink has dwcore* and darwin1* columns for the same DwC field)
- 06:06 PM Revision 1483: util.py: Added coalesce()
- 05:40 PM Revision 1482: xpath_func.py: process(): Fixed bug where XPath elem's other_branches were not also processed
- 05:28 PM Revision 1481: row: Don't prepend header row because this feature prevents the program from being used on a pipeline. Sheets may be constructed in a pipeline if multiple segments need to be joined, e.g. with cat_csv.
- 05:09 PM Revision 1480: Added row to get a row of a spreadsheet, preceded by the header row
- 05:09 PM Revision 1479: bin programs: Fixed bug in Usage message where program name was not printed because unset variable $self was used instead of $0
- 05:08 PM Revision 1478: xml_func.py: _nullIf: types_by_name: Use strings.ustr instead of str to support Unicode values
- 04:40 PM Revision 1477: xml_func.py: _nullIf: If value not convertible, return it, because can't equal null. Refactored to store types by name in a dict instead of using if statements.
- 04:31 PM Revision 1476: units.py: convert(): raise MissingUnitsException if quantity doesn't have units. MissingUnitsException: Take Quantity input instead of str.
- 04:27 PM Revision 1475: inputs/NCU-NCSC/maps/DwC.specimens.csv: "Cultivated?": For clarity, use _map instead of _if to translate boolean to "cultivated". Translate "No" to "wild" (the opposite of "cultivated") to store an explicit not-cultivated as such.
- 04:26 PM Revision 1474: inputs/NCU-NCSC/maps/DwC.specimens.csv: "Cultivated?": For clarity, use _map instead of _if to translate boolean to "cultivated". Translate "No" to "wild" (the opposite of "cultivated") to store an explicit not-cultivated as such.
- 04:21 PM Revision 1473: xml_func.py: _map: empty map entry means None
- 04:10 PM Revision 1472: xml_func.py: _avg: Support empty inputs by returning None. Moved _range after _rangeStart/_rangeEnd since it's less frequently used.
- 04:07 PM Revision 1471: units.py: Restructured to use a Quantity object for the units-tagged value and conversion functions quantity2str() and str2quantity() to convert between that and a raw string. Added convert() with basic support for removing units and passing through matching units. xml_func.py: _units: Added "to" attr. VegBIEN mappings: Remove units using new _units "to" attr instead of temporary workaround in _units.
- 03:13 PM Revision 1470: xml_func.py: _units: default units attr renamed to default to clarify that it's not the units you're converting to
- 03:06 PM Revision 1469: xml_func.py: Added documentation labels to each section of XML functions
- 03:01 PM Revision 1468: Moved units-related functions from format.py to new units.py
- 02:55 PM Revision 1467: lib/*.py: Removed svn:executable property to turn execute bit off
- 02:45 PM Revision 1466: vegbien.sql: growthform (and taxonclass) enum: Added options suggested by Michael Lee. Removed "woody". establishmentmeans_dwc (and taxonclass) enum: Reordered to match order of taxonoccurrence boolean fields, and to place each option next to its opposite. taxonclass enum: Moved "woody" to bottom because it's no longer part of growthform.
03/18/2012
- 09:10 PM Revision 1465: VegBIEN mappings: distance fields: Remove units
- 09:08 PM Revision 1464: xml_func.py: _units: Allow value to be NULL
- 08:44 PM Revision 1463: xml_func.py: _units: Use new format.cleanup_units() to do units parsing
- 08:43 PM Revision 1462: format.py: Added clean_numeric(), str2int(), str2float(). Added units-related functions. Added documentation labels to each section.
- 06:42 PM Revision 1461: Added filter_errors to filters `map` error messages
- 06:40 PM Revision 1460: Renamed bin/errors_filter_* to filter_errors_* to sound more natural and to have a different prefix than error_stats so that both can easily be tab-completed at the command line
- 06:27 PM Revision 1459: README.TXT: Testing: Added instructions for testing just mapping process, just map spreadsheet generation, and everything
- 06:26 PM Revision 1458: root Makefile: Added test-all for most complete coverage. Removed extraneous ";" at the end of the prerequisites line of rules with a recipe.
- 06:02 PM Revision 1457: mappings/Makefile: Use new ci_map to make DwC.cs-VegBIEN.specimens.csv case-insensitive
- 06:02 PM Revision 1456: Added ci_map to make a map spreadsheet case-insensitive.
- 05:53 PM Revision 1455: mappings: DwC: Generate case-insensitive map of DwC1 and DwC2 together, rather than just DwC2. DwC1-DwC2.specimens.csv: Make input columns lowercase so that case-insensitization will work properly.
- 05:52 PM Revision 1454: inputs/SpeciesLink: Switched to using flat files instead of DB
- 05:52 PM Revision 1453: inputs/MO: Switched to using flat files instead of DB
- 05:51 PM Revision 1452: mappings: DwC: Generate case-insensitive map of DwC1 and DwC2 together, rather than just DwC2. DwC1-DwC2.specimens.csv: Make input columns lowercase so that case-insensitization will work properly.
- 04:55 PM Revision 1451: input.Makefile: Mapping: Support multiple segments of a source table flat file. Use with_cat_csv if flat file segment(s) are available; otherwise use the input file in $+ or the input database, if any. Don't look for an explicit CSV header file because it can now be handled as the first segment if appropriately named.
- 04:50 PM Revision 1450: Added with_cat_csv
- 04:50 PM Revision 1449: with_cat: Added support for custom cat command in env var
- 04:49 PM Revision 1448: cat_csv: Abort if output stream closed instead of exiting with an IOError
- 04:16 PM Revision 1447: cat_csv: Ignore any duplicated headers instead of requiring each CSV to have a header identical to the first. Rewrote to pass the CSVs through as lines rather than parsing each row. Because the CSVs are not parsed, checked that all CSVs have the same dialect.
- 04:14 PM Revision 1446: csvs.py: Added csv modifications to compare Dialect instances
- 04:13 PM Revision 1445: util.py: Added classes_eq()
03/16/2012
- 06:25 PM Revision 1444: csvs.py: Added stream_info() to return NamedTuple {header_line, dialect} for later use in cat_csv. Changed reader_and_header() to use stream_info().
- 06:23 PM Revision 1443: util.py: Added NamedTuple
- 06:04 PM Revision 1442: csvs.py: reader_and_header(): Restrict delimiters to common delimiters so that e.g. letters are not considered delimiters just because they appear frequently
- 05:38 PM Revision 1441: Renamed inputs/NYBG to inputs/NY to match herbarium code
- 05:35 PM Revision 1440: Renamed inputs/UNC-NCSC to inputs/NCU-NCSC to match herbarium code
- 05:32 PM Revision 1439: Renamed inputs/UArizona to inputs/ARIZ to match herbarium code
- 05:31 PM Revision 1438: Regenerated inputs/MO/maps/src.join.specimens.csv
- 05:26 PM Revision 1437: Renamed inputs/MOBOT to inputs/MO to match herbarium code
- 05:11 PM Revision 1436: Regenerated vegbien.ERD exports
- 05:08 PM Revision 1435: vegbien.sql: taxonoccurrence: Added cultivatedbasis
- 05:03 PM Revision 1434: vegbien.sql: Moved all accessioncode fields to the bottom of their tables. vegbien.ERD.mwb: Adjusted lines to remove overlaps.
- 04:52 PM Revision 1433: vegbien.sql: taxonoccurrence: Added iscultivated, isnative. Moved accessioncode to bottom.
- 04:36 PM Revision 1432: vegbien.sql: Changed taxonoccurrence.growthform type to more specific growthform
- 04:34 PM Revision 1431: vegbien.sql: Added growthform and establishmentmeans_dwc enums using values from taxonclass. Documented that taxonclass is growthform + establishmentmeans_dwc + some other values.
- 04:22 PM Revision 1430: VegBIEN: Moved aggregateoccurrence.growthform to taxonoccurrence
- 04:21 PM Revision 1429: Added inputs/UNC-NCSC/maps/src.join.specimens.csv
- 04:15 PM Revision 1428: VegBIEN: Merged aggregateoccurrence.verbatimcollectorname and specimenreplicate.verbatimcollectorname into taxonoccurrence
- 03:58 PM Revision 1427: xml_func.py: parse_range(): Handle negative numbers by treating them as not a range
- 03:31 PM Revision 1426: Added inputs/UNC-NCSC/test with initial accepted test outputs
- 03:31 PM Revision 1425: Added inputs/UNC-NCSC/maps
- 03:31 PM Revision 1424: xml_func.py: _replace: Fixed bug where value entry was not unpacked
- 02:59 PM Task #387 (New): count how many duplicates between Canadensys and GBIF
- 02:59 PM Task #386 (Resolved): load Canadensys data
- http://data.canadensys.net/ipt/
- 02:58 PM Task #385 (Resolved): implement mechanism to determine which specimenreplicates refer to the same specimen
- * or are the same record, from different data sources
- 02:58 PM Task #384 (Resolved): prototype tree traversal algorithm
- Aaron's alternative algorithm which cross-links each node to its ancestors using a many:many table
- 02:56 PM Task #383 (New): convert VegBank data dictionary to database comments
- * VegBank data dictionary source code is in svn at https://code.ecoinformatics.org/code/vegbank/trunk/docs/xml/db_mod...
- 12:36 PM Revision 1423: Added inputs/UNC-NCSC
03/15/2012
- 07:12 PM Revision 1422: Added inputs/MOBOT/test with initial accepted test outputs
- 07:11 PM Revision 1421: Added inputs/MOBOT/maps
- 06:51 PM Revision 1420: Added inputs/MOBOT
- 06:41 PM Revision 1419: VegX mappings: Updated plot place mappings to VegX 1.5.3 method of place type-tagged place names. This removes the userdef fields in plot.
- 06:18 PM Revision 1418: VegX mappings: Changed userdef xPosition, yPosition to /relativePlotPosition/relativeX, /relativePlotPosition/relativeY
- 06:16 PM Revision 1417: Regenerated mappings/DwC-VegBIEN.specimens.no_empty.csv
- 05:36 PM Revision 1416: bin/map: map_table(): wrap_row(): Use util.list_as_length() to handle CSV rows of different lengths
- 05:35 PM Revision 1415: util.py: Added list_as_length(). Documented that list_set_length() takes a list, not a tuple. Documented that ListDict must have len(list_) == len(keys).
- 05:19 PM Revision 1414: util.py: Added list_set_length(). Changed list_set() to use list_set_length().
03/13/2012
- 07:48 PM Revision 1413: mappings/DwC2-VegBIEN.specimens.csv: Added empty *_id/taxonoccurrence attr to primary keys to ensure that a taxonoccurrence is always created for the specimenreplicate
- 07:41 PM Revision 1412: xml_func.py: _label: Use ustr instead of str when checking types
- 07:41 PM Revision 1411: csvs.py: Set dialect.doublequote to True because Sniffer doesn't turn this on by default
- 07:23 PM Revision 1410: Merged inputs/NYBG-CSV into NYBG
- 07:16 PM Revision 1409: Merged inputs/UArizona-CSV into UArizona
- 07:02 PM Revision 1408: Added inputs/SpeciesLink/test
- 07:02 PM Revision 1407: Added inputs/SpeciesLink/maps
- 07:02 PM Revision 1406: xml_func.py: range-related funcs: Made inputs optional in case they get set to NULL by _nullIf
- 06:48 PM Revision 1405: mappings/DwC1-DwC2.specimens.csv: Added common DwC1 fields that are not part of the official DwC1 schema
- 06:31 PM Revision 1404: bin/map: Added support for getting columns with an optional prefix list for DB/CSV inputs
- 06:21 PM Revision 1403: bin/map: Factored out code common to DB and CSV inputs into map_table()
- 06:00 PM Revision 1402: bin/map: Parse any prefixes in map input column name. They will later be used to check for versions of columns with a prefix added when processing CSV/DB inputs.
- 05:58 PM Revision 1401: strings.py: Added split(), remove_prefix(), remove_suffix(), and remove_prefixes(). Added section comments.
- 05:06 PM Revision 1400: mappings/DwC2-VegBIEN.specimens.csv: minimumElevationInMeters: Handle embedded ranges using _rangeStart and _rangeEnd
- 05:05 PM Revision 1399: xml_func.py: Added _rangeStart and _rangeEnd
- 05:04 PM Revision 1398: xpath.py: parse(): Split paths: Raise a SyntaxException if can't attach a split path because there is no parent element to attach to
- 05:02 PM Revision 1397: Parser.py: Renamed _syntax_err() to syntax_err() to make it a public method
- 04:38 PM Revision 1396: mappings/DwC2-VegBIEN.specimens.csv: Mapped fieldNotes and taxonRemarks to description using _merge. inputs/UArizona*/maps/DwC.specimens.csv: Mapped Remarks to taxonRemarks, which now has a VegBIEN mapping.
- 04:24 PM Revision 1395: Added inputs/GBIF/src with small files that can be under version control
- 04:23 PM Revision 1394: input.Makefile: svn_props: Ignore everything in the src/ subdir that hasn't been explicitly checked in
- 04:18 PM Revision 1393: Added inputs/GBIF/test with accepted test outputs
- 04:18 PM Revision 1392: Added inputs/GBIF/maps
- 04:17 PM Revision 1391: Regenerated inputs/UArizona*/maps VegBIEN maps
- 04:13 PM Revision 1390: Regenerated mappings/DwC-VegBIEN.specimens.no_empty.csv
- 04:09 PM Revision 1389: bin/map: Use new csvs.reader_and_header() to support CSVs/TSVs with other than the default Excel dialect
- 04:08 PM Revision 1388: Added csvs.py for CSV I/O such as automatically detecting the dialect based on the header line
- 04:07 PM Revision 1387: join: Don't append suffix to empty output mappings, so that they stay empty ("NULL")
- 04:00 PM Revision 1386: input.Makefile: Added tsv to $(exts). Strip extra whitespace from $(inputs) so that it's the empty string if $(<in) (and $(<in).header) don't exist, and can be used in $(if ...).
03/12/2012
- 07:08 PM Revision 1385: input.Makefile: Fixed bug in inputFiles wildcard where extensions were manually listed instead of dynamically determined from the $(exts) config var
- 06:56 PM Revision 1384: README.TXT: Tell user to `disown -h %1` after running `make import &` so that it won't be sent a SIGHUP if the user logs out
- 06:55 PM Revision 1383: README.TXT: Tell user to `disown -h %1` after running `make import &` so that it won't be sent a SIGHUP if the user logs out
- 06:39 PM Revision 1382: input.Makefile: Prepend separate CSV header when available
- 06:24 PM Revision 1381: input.Makefile: Use with_cat in map to later support prepending separate CSV headers
- 06:21 PM Revision 1380: Added with_cat to run a command, taking input from the concatenation of files
- 05:48 PM Revision 1379: input.Makefile: Set mapEnv if $(dbEngine) is set, to eventually support pre-existing DB connections
- 05:14 PM Revision 1378: input.Makefile: Changed $(dbFile) to $(dbExport) to make it unambiguous that it refers to a SQL export, not a pre-existing DB, which will be supported later
- 05:10 PM Revision 1377: input.Makefile: Added .txt to list of input file extensions
- 04:34 PM Revision 1376: Added inputs/SpeciesLink
- 03:57 PM Revision 1375: root Makefile: python-Linux: Added pymetrics
- 03:54 PM Revision 1374: bin/map: Consider \N to be None
- 03:49 PM Revision 1373: util.py: none_if(): Allow multiple none_vals using varargs
- 03:36 PM Revision 1372: Added inputs/GBIF
- 03:28 PM Revision 1371: exc.py: Fixed bug in traceback-saving mechanism that didn't deal with nested Exceptions (such as Exceptions with causes in ExceptionWithCause). Renamed add_exc_info() to add_traceback() since we really only need to store the traceback.
- 12:41 PM Revision 1370: dates.py: parse_date_range(): Fixed bug where the date parts were not joined back together into a string for each date range element. Use strings.single_space() after the date has been split into range parts so that whitespace around the range separator is removed instead of being replaced with a single space.
- 12:25 PM Revision 1369: xml_func.py: process(): Also catch XML func internal errors to assist in debugging. Use new exc.add_exc_info() to save traceback in case later code throws exception, overwriting exc_info().
- 12:23 PM Revision 1368: exc.py: str_(): Add the traceback at the end of the exception string. Added add_exc_info() and get_exc_info() for providing traceback info for str_().
03/11/2012
- 07:33 PM Revision 1367: mappings/DwC2-VegBIEN.specimens.csv: eventDate, dateIdentified: Use _dateRangeStart and _dateRangeEnd
- 07:32 PM Revision 1366: xml_func.py: Added _dateRangeStart and _dateRangeEnd
- 07:32 PM Revision 1365: dates.py: Added parse_date_range() and helper funcs could_be_year() and could_be_day()
- 07:31 PM Revision 1364: strings.py: Added single_space()
- 06:12 PM Revision 1363: inputs/UArizona*: Map the ScientificNameAuthor to the binomial instead since it contains the binomial in addition to the authority
- 05:28 PM Revision 1362: Added inputs/UArizona-CSV/test
- 05:23 PM Revision 1361: input.Makefile: Use .PRECIOUS to save outputs of failed tests so they can be accepted (needed now that .DELETE_ON_ERROR is turned on globally)
- 05:14 PM Revision 1360: bin/map: Moved string-cleanup code from get_value() to cleanup(), called by process_row(). process_row() now cleans up the string before checking if it's None, because cleanup() uses none_if() to map "" to None.
- 05:12 PM Revision 1359: util.py: Added do_ignore_none()
- 04:25 PM Revision 1358: Added inputs/UArizona-CSV/verify
- 04:24 PM Revision 1357: Added inputs/UArizona-CSV/maps
- 04:23 PM Revision 1356: mappings/DwC2-VegBIEN.specimens.csv: Mapped coordinateUncertaintyInMeters to the same place as coordinatePrecision (input sources generally use only one of these columns, which is most likely the accuracy regardless of what it's named)
- 04:18 PM Revision 1355: join: In error message when map column names don't match, include the actual column names
- 04:17 PM Revision 1354: Makefiles: Added .DELETE_ON_ERROR to delete target if recipe fails
- 03:18 PM Revision 1353: VegBIEN mappings: plantnames: Nest taxons hierarchically using plantname.parent_id. Mappings using _forEach: Append a "," to the `in` list so that mappings will sort from shortest to longest `in` list ("]" comes after "," in ASCII, causing this not to happen without the trailing ",").
- 03:14 PM Revision 1352: xpath.py: parse(): _paths(): Remove trailing ","
- 02:38 PM Revision 1351: xpath_func.py: _forEach: Made syntax more natural-looking by using values instead of names for string args and attrs instead of branches for array args
- 02:36 PM Revision 1350: xpath.py: parse() Fixed bug in _paths() where empty lists would be parsed as a list containing a single empty path, instead of as an empty list
- 01:26 PM Revision 1349: VegBIEN mappings: Place names: Use _forEach to simplify XPaths for recursively nested places
- 01:22 PM Revision 1348: bin/map: In debug mode, print output XPaths
03/09/2012
- 07:51 PM Revision 1347: xpath_func.py: _forEach: Fixed to support _val replacements anywhere, by doing a string-based search-and-replace on a quoted XPath instead of a list-based search-and-replace on an already-parsed XPath
- 07:41 PM Revision 1346: xpath_func.py: Renamed _for to _forEach. Finished implementing _forEach.
- 07:41 PM Revision 1345: xpath.py: Import xpath_func after defining XpathElem because xpath_func depends on XpathElem and it hasn't yet been factored into a separate file
- 07:39 PM Revision 1344: util.py: Added list_replace()
- 07:14 PM Revision 1343: xpath_func.py: Changed XPath function signature to take arguments (args, path), and process() to parse out the args. Implemented basic _for that repeats its do arg as many times as there are in_ elements.
- 06:44 PM Revision 1342: xpath.py: parse(): Run xpath_func.process() on the parsed XPath
- 06:43 PM Revision 1341: Added xpath_func.py for XPath "function" elements that transform their subpaths
- 06:23 PM Revision 1340: VegBIEN mappings: Removed no longer needed taxondetermination.determinationtype values, because they can be determined from the new role closed list
- 06:19 PM Revision 1339: filter_ERD.csv: Removed no longer needed references to role
- 06:18 PM Revision 1338: Regenerated vegbien.ERD exports
- 06:17 PM Revision 1337: VegBIEN: Changed role table to a closed list
- 06:14 PM Revision 1336: PostgreSQL-MySQL.csv: custom types: Consider everything except a set of accepted types to be a custom type
- 05:40 PM Revision 1335: VegBIEN: taxonrank enum: Made values lowercase to match case convention in other enums
- 05:33 PM Revision 1334: Regenerated vegbien.ERD exports
- 05:32 PM Revision 1333: vegbien.sql: Renamed plantconceptscope to plantnamescope because it's now attached to plantname
- 05:26 PM Revision 1332: vegbien.sql: Moved parent_id from plantconcept to plantname, since plantnames themselves are unique according to their parent taxons (a species under one genus is not the same as a species under another genus)
- 05:03 PM Revision 1331: Regenerated vegbien.ERD exports
- 04:59 PM Revision 1330: vegbien.ERD.mwb: Fixed lines
- 04:57 PM Revision 1329: vegbien.sql: Moved scope_id from plantconcept to plantname, since plantnames themselves are scoped, not just the plantconcepts that use them (e.g. "sp. 1" has different meanings in different scopes, so it should not be shared between scopes). plantname: Added accessioncode.
- 04:38 PM Revision 1328: vegbien.sql: Moved plantconcept parent_id from plantstatus to plantconcept. plantconcept: Removed datasource-specific fields to make it globally unique (one plantconcept for each assigned parent taxon of a plantname, of which there will usually be just one)
- 04:22 PM Revision 1327: vegbien.sql: plantname: Removed datasource-specific fields to make this a globally-unique table (the datasource-specific fields belong in plantconcept)
- 04:16 PM Revision 1326: Added inputs/UArizona/verify
- 04:15 PM Revision 1325: mappings/verify.specimens.sql: Updated for schema changes
- 04:06 PM Revision 1324: vegbien.sql: placerank enum: Added "village"
- 04:00 PM Revision 1323: VegBIEN mappings: lat/long locationdetermination: Removed [!namedplace_id] key so that it's merged into the namedplace locationdetermination
- 03:54 PM Revision 1322: VegBIEN mappings: Changed namedplace mappings to use new nested format for storing place containment relationships
- 03:44 PM Revision 1321: xml_func.py: Added _simplifyPath
- 03:25 PM Revision 1320: xpath.py: Added get_1()
- 02:50 PM Revision 1319: vegbien.sql: namedplace: Removed parent_id from unique constraint because some data might be missing intervening links (e.g. state for a county, country), but the place (e.g. county) should still be attached to the existing place of the same name and rank (which will hopefully already have the correct parent_id link)
- 02:46 PM Revision 1318: vegbien.sql: namedplace: Made rank required
- 02:33 PM Revision 1317: vegbien.sql: namedplace: Removed no longer needed placesystem, which has been replaced by rank closed list
- 02:30 PM Revision 1316: VegBIEN mappings: Map namedplaces using new rank field
- 02:25 PM Revision 1315: vegbien.sql: namedplace: Added rank. Do duplicate elimination using rank and parent_id instead of placesystem
- 02:20 PM Revision 1314: vegbien.sql: placerank: Standardized names to DwC/GML
- 01:58 PM Task #378 (New): create automated feedback mechanism
- * triggered when an import is run
- 01:57 PM Task #377 (Resolved): ask NYBG for direct access to server
- 01:06 PM Revision 1313: vegbien.sql: Added placerank enum
- 12:35 PM Revision 1312: vegbien.sql: namedplace: Removed VegBank internal fields and datasource scoping fields (namedplaces are globally unique). Added parent_id to point to containing namedplace.
- 12:21 PM Revision 1311: xml_func.py: Added _dateRangePart with partial implementation (only works on strings with no range)
- 12:20 PM Revision 1310: DwC mappings: Moved date _date filter outside _alt so it would run only on the string that was actually chosen, and not produce date format errors when a pre-parsed year/month/day is already available
03/08/2012
- 06:30 PM Revision 1309: xml_func.py: _date: Map date with only empty fields to NULL (occurs when all fields were e.g. 0 and were filtered to NULL by _nullIf)
- 06:00 PM Revision 1308: xml_func.py: _date: Removed mapping year/month/day of 0 to NULL because that is now handled on a case-by-case basis in the mappings
- 05:58 PM Revision 1307: mappings/DwC1-DwC2.specimens.csv: Map year/month/day of 0 to NULL
- 05:13 PM Revision 1306: inputs/SALVIAS/maps/VegX.organisms.csv: Habit: Fixed syntax error in growthForm map
- 05:11 PM Revision 1305: inputs/SALVIAS/maps/VegX.organisms.csv: Habit: Removed input values from growthForm map that Brad said were invalid
- 05:10 PM Revision 1304: xml_func.py: _map: Added option to make map a closed list
- 04:56 PM Revision 1303: mappings/DwC2-VegBIEN.specimens.csv: Fixed waterdepth mappings to use _avg
03/06/2012
- 06:48 PM Revision 1302: mappings/verify.specimens.sql: Use ORDER BY ... NULLS FIRST to match MySQL
- 06:42 PM Revision 1301: input.Makefile: verify: Time the verification since it can take a long time
- 06:34 PM Revision 1300: specimens verification: Added duplicate catalog numbers test
- 06:27 PM Revision 1299: map: On nimoy, use bien2_staging unless otherwise specified
- 06:21 PM Revision 1298: specimens verification: Added # counties test
- 05:34 PM Revision 1297: specimens verification: Added collection codes and # catalog numbers tests
- 05:33 PM Revision 1296: inputs/SALVIAS/maps/VegX.organisms.csv: Mapped custom Habit values not listed in the SALVIAS data dictionary
- 05:32 PM Revision 1295: strings.py: Added unicode_reader for later use in handling Unicode characters in map spreadsheets
- 03:45 PM Revision 1294: xpath.py: Removed unnecessary copy.deepcopy()'s and instead changed set_value() and set_id() to make copies of any elements they change. This should result in up to a 17% speed increase in the import, because deepcopy() was taking a lot of time. Added documentation to set_value() and set_id() that caller must make a shallow copy of the path to prevent modifications from propagating to other copies of the path. (Previously, a deep copy was needed, but there was no comment specifying this.)
- 03:40 PM Revision 1293: mappings/VegX-VegBIEN.organisms.csv: Removed unneeded lookahead assertions from stemtag mappings. They relied on a bug ("feature"?) in the XPath engine that made the value of the lookahead assertion's path the same as the value of the main path, even though the value is set after the path is parsed.
- 02:45 PM Revision 1292: xml_func.py: _date: For year/month/day dates, require the year (it would not make sense to default to a particular year)
- 01:29 PM Revision 1291: inputs/UArizona: Added test outputs
- 01:28 PM Revision 1290: mappings/DwC1-DwC2.specimens.csv: Fixed to allow datasource to define custom date mappings that don't pass through the default date mapping
03/05/2012
- 05:31 PM Revision 1289: input.Makefile: Generate maps/src.join.*.csv, which can be used to determine which DwC fields for a particular dataset do not yet have a join mapping to VegBIEN
- 05:26 PM Revision 1288: Makefile: Fixed subdir remake target to work for nested subdirs as well
- 04:51 PM Revision 1287: inputs/UArizona: Renamed maps/src.csv to maps/src.specimens.csv because there will be one for each input table
- 04:41 PM Revision 1286: inputs/UArizona: Added maps/src.csv with columns from source data
- 04:40 PM Revision 1285: Added autogen mappings/DwC-VegBIEN.specimens.no_empty.csv, which will be used for determining which DwC fields for a particular dataset do not yet have a join mapping to VegBIEN
- 04:35 PM Revision 1284: Added remove_empty to remove empty mappings in a map spreadsheet
- 04:35 PM Revision 1283: join: Don't raise "No join mapping" error for empty mappings because you only want the error for empty mappings for your particular dataset, which requires more information (namely, the subset of the mappings used by your dataset, some of which will not be in the mappings if standard fields have been subtracted out)
- 04:10 PM Revision 1282: join: Fixed bug in "No join mapping" error generation where rows with no existing comments column would cause an IndexError
- 04:09 PM Revision 1281: util.py: Added list_set() and list_setdefault()
- 03:44 PM Revision 1280: inputs/UArizona/maps/DwC.specimens.csv: Merge FieldNotes and Remarks
- 03:35 PM Revision 1279: inputs/UArizona/maps/DwC.specimens.csv: Finished mappings
- 03:08 PM Revision 1278: inputs/UArizona/maps/DwC.specimens.csv: Removed fields already present in DwC mappings
- 03:05 PM Revision 1277: inputs/NYBG-CSV/maps/DwC.specimens.csv: Removed mappings already present in case-insensitive DwC2 mapping
- 03:03 PM Revision 1276: inputs/NYBG/maps/DwC.specimens.csv: Removed mappings already present in case-insensitive DwC2 mapping
- 02:48 PM Revision 1275: mappings/DwC1-DwC2.specimens.csv: Removed fields already present in DwC2.ci-VegBIEN.specimens.csv
- 02:38 PM Revision 1274: Makefiles: Moved remake into main Makefile. Fixed remake to run `make all` in a new make so that cache of existing files is reset. Have main remake run clean and then all instead of forwarding remake to subdirs, so that everything is cleaned before everything is remade.
- 02:21 PM Revision 1273: input.Makefile: maps: maps/$(via).%.full.csv: Fixed bug where $(selfMap) would be ignored if it had not yet been made
- 02:02 PM Revision 1272: mappings/Makefile: Reorganized into DwC and VegX sections
- 02:02 PM Revision 1271: Added autogenerated mappings/DwC2.ci-VegBIEN.specimens.csv. Use it to include DwC2 fields with first letter uppercased in the full DwC mapping, so that datasources that use DwC2 terms with a different case can still use the DwC2 mapping.
- 01:57 PM Revision 1270: Added autogenerated mappings/DwC2.ci-VegBIEN.specimens.csv. Use it to include DwC2 fields with first letter uppercased in the full DwC mapping, so that datasources that use DwC2 terms with a different case can still use the DwC2 mapping.
- 01:54 PM Revision 1269: inputs/UArizona/maps/DwC.specimens.csv: Mapped CollectedDate to eventDate/_alt/2 even though it's not used because other datasources might copy these mappings and want it already filled in
- 01:52 PM Revision 1268: Added ucase_first to uppercase the first character of columns in a spreadsheet
- 01:21 PM Revision 1267: Added inputs/UArizona/maps/DwC.specimens.csv autogen maps
- 01:20 PM Revision 1266: inputs/UArizona/maps/DwC.specimens.csv: Mapped more fields
- 01:14 PM Revision 1265: mappings/DwC1-DwC2.specimens.csv: Remove date -> date/_alt/2 mappings because they prevent the original DwC2 date field from being mapped to without an extra /_alt/2 appended
- 01:10 PM Revision 1264: xml_func.py: Use new dates.strtotime(). When component date parts specified, year defaults to dates.epoch.year.
- 01:09 PM Revision 1263: dates.py: Added strtotime() to wrap dateutil.parser.parse() with default defaulting to epoch, so that e.g. months with day missing default to day 1 instead of the current day of the month
- 12:38 PM Revision 1262: mappings/DwC1-DwC2.specimens.csv: Map eventDate,dateIdentified using /_alt/2 and year/month/day using /_alt/1 so that inputs with both a date and date parts will select between the two
- 11:43 AM Revision 1261: input.Makefile: Added comment that self map must be made first if it's needed for maps/$(via).%.full.csv
- 11:40 AM Revision 1260: Makefiles: Use .SECONDARY with no prerequisites instead of setting a .PRECIOUS for each intermediate, to simplify turning off automatic deletion of intermediate files
- 11:23 AM Revision 1259: inputs/UArizona: Added initial maps/DwC.specimens.csv
- 11:10 AM Revision 1258: DwC mappings: Map datasource name via institutionID to avoid conflicting with existing institutionCode fields that many DwC data sources have
- 10:57 AM Revision 1257: input.Makefile: Don't profile by default because it appears to slow things down significantly on long imports
- 10:56 AM Revision 1256: Added inputs/UArizona/maps
- 10:33 AM Task #372 (Resolved): talk to Nick about proposed changes to VegX
03/03/2012
- 05:56 PM Revision 1255: Makefile: python-Linux: Added python-profiler
- 05:44 PM Revision 1254: specimens verification: Added # binomials test
- 05:35 PM Revision 1253: vegbien.sql: specimenreplicate: Removed specimenreplicate_unique_collectionnumber index because the collectionnumber (NYBG FieldNumber) is not always unique within a collector, even though it should be. Changed specimenreplicate_unique_catalognumber to only operate on rows with no sourceaccessioncode (of which there are 8 in NYBG).
- 05:09 PM Revision 1252: mappings/verify.specimens.sql: # species test: Fixed to join separately on taxondeterminations for genus and species. # genera test: Removed no longer needed join on party.
- 05:04 PM Revision 1251: vegbien.sql: specimenreplicate: Added fki index on taxonoccurrence_id
- 04:25 PM Revision 1250: vegbien.sql: plantname: Added index on rank to speed up specimens verifications, where the query planner insists on joining from plantname to specimenreplicate instead of the other way around (which takes much longer without the index)
- 03:33 PM Revision 1249: mappings/verify.*: Use nested SELECT instead of JOIN on party to get datasource_id, so that party will not be joined on after other joins have already occurred (which slows things down)
- 03:26 PM Revision 1248: vegbien.sql: party: Changed party_unique_name to ignore NULL values and the organizationname (a first(+middle)+last name is considered unique)
- 03:15 PM Revision 1247: vegbien.sql: party: Added party_unique_organizationname constraint
- 02:11 PM Revision 1246: Specimens verification: Added # genera and # species
- 01:50 PM Revision 1245: input.Makefile: verify: Create target dir if it doesn't exist
- 01:42 PM Revision 1244: inputs/NYBG: Added verify/specimens.ref.sql
- 01:41 PM Revision 1243: Added mappings/verify.specimens.sql
- 01:41 PM Revision 1242: Added inputs/NYBG-CSV/verify/
- 01:40 PM Revision 1241: Makefile: Print done message after verify
- 01:29 PM Revision 1240: VegX-VegBIEN mapping: Use new lookup-only element syntax to ensure that stemtag 1 is not created if it doesn't exist when stemtag 2 tries to set its iscurrent status to false. This should fix the 136 "NullValueException: columns: tag" errors in the SALVIAS organisms import.
- 01:27 PM Revision 1239: xpath.py: get(): Added support for lookup-only elements which are not created if they don't exist
- 01:25 PM Revision 1238: xpath.py: parse(): Added support for lookup-only elements which are not created if they don't exist
- 01:15 PM Revision 1237: VegX-VegBIEN mapping: Map stemtags using [] instead of :[] for attrs that are really keys
03/02/2012
- 07:54 PM Revision 1236: Regenerated vegbien.ERD exports
- 07:52 PM Revision 1235: VegX-VegBIEN mapping: Handle user-defined field voucherType (SALVIAS DetType) by mapping specimenreplicates for voucherTypes other than direct via voucher
- 06:58 PM Revision 1234: xml_func.py: Added _if and _eq. Added cast() to throw SyntaxException if can't cast and use it in conv_items(). _merge: Check types of input using conv_items(strings.ustr, items).
- 06:53 PM Revision 1233: util.py: Added all_not_none() and bool2str()
- 06:52 PM Revision 1232: strings.py: Added ustr() (like built-in str() but converts to unicode object)
- 05:32 PM Revision 1231: PostgreSQL-MySQL.csv: Fixed bug in removal of casts of default values, which treated NOT NULL as part of the datatype
- 05:30 PM Revision 1230: VegBIEN: soilobs: Added default value for horizon. Adjusted mappings to remove now-unecessary horizon value.
- 05:26 PM Revision 1229: repl: Removed automatic case-insensitivity because Python apparently only supports turning *on* case-insensitivity via (?i) but not off via (?-i) (as Java does)
- 05:09 PM Revision 1228: VegBIEN: soilobs: Removed soil* prefix from fields
- 05:05 PM Revision 1227: VegX-VegBIEN mapping: Map to new soilobs fields
- 04:57 PM Revision 1226: SALVIAS inputs: Use new _units:[units="%"] on soil fields that are percents. Replace "<..." values with 0.
- 04:55 PM Revision 1225: xml_func.py: Added _units
- 04:30 PM Revision 1224: vegbien.sql: soilobs: Converted user-defined fields to first-class. Labeled appropriate fields as "fraction".
- 04:08 PM Revision 1223: VegBIEN mappings: Changed tableRecord_ID to tablerecord_id to match PostgreSQL field name
- 04:05 PM Revision 1222: DwC2-VegBIEN mapping: Adjusted user-defined mappings
- 04:00 PM Revision 1221: vegbien.sql: userdefined: Made userdefinedname NOT NULL. userdefined, definedvalue: Added unique constraints.
- 03:54 PM Revision 1220: VegX-VegBIEN mapping: Mapped userdefined fields to new first-class fields
- 03:46 PM Revision 1219: xml_func.py: Added _map and _replace
- 02:33 PM Revision 1218: Regenerated vegbien.ERD exports
- 02:30 PM Revision 1217: vegbien.ERD.mwb: Fixed lines. Expanded truncated tables where there was room.
- 02:01 PM Task #366: refactor VegX
- See [[VegX]] schema
- 02:00 PM Task #370 (Resolved): create ERD of final schema
- Ready for sign off on first draft
- 01:59 PM Task #374 (Resolved): mechanism to export VegBIEN data to flat file
- 01:58 PM Task #373 (Resolved): map all specimens data in raw_data
- 01:58 PM Task #372 (Resolved): talk to Nick about proposed changes to VegX
- 01:58 PM Task #371 (Resolved): formalize proposed changes to VegX
- 12:51 PM Revision 1216: Regenerated vegbien.ERD exports
- 12:51 PM Revision 1215: vegbien.sql: locationevent: Added temperature and precipitation
- 12:45 PM Revision 1214: vegbien.sql: aggregateoccurrence: Added growthform
- 12:39 PM Revision 1213: vegbien.ERD.mwb: Reversed the locations of soiltaxon and soilobs to give soilobs room to add new fields
- 12:36 PM Revision 1212: vegbien.sql: Removed embargo table and emb_* fields because we're using a central field, location.confidentialitystatus, for embargo information and coordinate fuzzing
- 12:22 PM Revision 1211: vegbien.sql: stemobservation: Added heightfirstbranch
- 12:17 PM Revision 1210: vegbien.sql: stemobservation: Added diameteraccuracy. Reordered fields.
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