Project

General

Profile

Activity

From 01/08/2012 to 02/06/2012

02/06/2012

05:22 PM Revision 869: sql.py: truncate(): Use run_raw_query() instead of run_query() because truncate() does not use the recover functionality of run_query(). Also, in the profiling output, this separates the "normal" SQL statements (which use run_query()) from the "core" SQL statements (which use run_raw_query()).
Aaron Marcuse-Kubitza
05:09 PM Revision 868: vegbien.sql: Added indexes for each field in party used in duplicate elimination (for use by sql.put()'s DuplicateKeyException handler)
Aaron Marcuse-Kubitza
04:58 PM Revision 867: sql.py: run_raw_query(): In debug mode, print query after params have been substituted in
Aaron Marcuse-Kubitza
04:55 PM Revision 866: sql.py: Fixed index_cols() to handle UNIQUE indexes with expressions, whose column names are stored in a different format
Aaron Marcuse-Kubitza
04:04 PM Revision 865: sql.py: Print warning if SELECT statement missing a WHERE, LIMIT, or OFFSET clause. Changed bin/map DB input get-all-rows statement to pass start=0 to suppress this warning for that statement.
Aaron Marcuse-Kubitza
03:51 PM Revision 864: db_xml.py: Added start option to get() that passes through to sql.select()
Aaron Marcuse-Kubitza
03:50 PM Revision 863: sql.py: Added start option to select() to set the OFFSET
Aaron Marcuse-Kubitza
03:27 PM Revision 862: sql.py: If run_raw_query.debug flag is set, print each query executed (on a single line)
Aaron Marcuse-Kubitza
03:25 PM Revision 861: strings.py: Added one_line() function to make a string all on one line
Aaron Marcuse-Kubitza
03:20 PM Revision 860: strings.py: Renamed one_line() to remove_extra_newl() to better reflect what it does
Aaron Marcuse-Kubitza
03:19 PM Revision 859: bin/map: Don't print Done after an action in debug logging mode because it messes up newlines when more debugging info is printed right after it
Aaron Marcuse-Kubitza
02:45 PM Revision 858: input.Makefile: Added nolog option to disable creating a log file, e.g. for debugging runs
Aaron Marcuse-Kubitza
01:57 PM Revision 857: xml_dom.py: Remove extra newlines from single-line strings (bin/map doesn't need to do this itself anymore)
Aaron Marcuse-Kubitza
01:56 PM Revision 856: strings.py: Added is_multiline() and one_line() for removing extra newlines from single-line strings
Aaron Marcuse-Kubitza
01:48 PM Revision 855: bin/map: In debug mode, print input XPath's XML tree all on one line
Aaron Marcuse-Kubitza
01:22 PM Revision 854: sql.py: Switched try_insert() to use index_cols() instead of constraint_cols() for "duplicate key value violates unique constraint" errors because they can also be generated by UNIQUE indexes (and there is a UNIQUE index for every UNIQUE constraint)
Aaron Marcuse-Kubitza
01:14 PM Revision 853: sql.py: Added index_cols() to get cols used by an index (similar to constraint_cols())
Aaron Marcuse-Kubitza
01:00 PM Revision 852: vegbien.sql: Fixed duplicate elimination for party to use a UNIQUE index with COALESCE for nullable fields
Aaron Marcuse-Kubitza
01:00 PM Revision 851: sql.py: Fixed bug in try_insert() where DuplicateKeyException was passed only cols[0] instead of cols array
Aaron Marcuse-Kubitza
12:49 PM Revision 850: vegbien.ERD.mwb: Fixed lines
Aaron Marcuse-Kubitza
12:30 PM Revision 849: Added get_errors to select just the error messages from `map` output
Aaron Marcuse-Kubitza
11:59 AM Revision 848: Added profile_stats to analyze a profiling statistics file
Aaron Marcuse-Kubitza
11:59 AM Revision 847: bin/map: Added profile_to option which turns on profiling to the specified file
Aaron Marcuse-Kubitza
11:13 AM Revision 846: bin/map: Added "if __name__ == '__main__': main()" idiom so file can be included as well as run. This will be useful for profiling.
Aaron Marcuse-Kubitza
11:12 AM Revision 845: dates.py: Fixed strftime() to pad years and days with leading zeros as datetime.strftime() does
Aaron Marcuse-Kubitza
11:01 AM Revision 844: dates.py: Work around strftime() bug that can't deal with 2/29 on a leap year
Aaron Marcuse-Kubitza
10:44 AM Revision 843: xml_func.py: Added FormatException for SyntaxExceptions generated by strftime() (which are often Python bugs)
Aaron Marcuse-Kubitza
10:25 AM Task #317: Direct mapping from VegX to VegBIEN
Mappings have been made for SALVIAS VegX fields Aaron Marcuse-Kubitza
10:23 AM Task #333: add traits table to VegBIEN
VegBank had an existing trait table, which was not included in the ERD. We can modify that table for our needs. Aaron Marcuse-Kubitza
10:23 AM Task #332: switch to VegX 1.5.3
VegX 1.5.3 is available, so we're switching to that instead Aaron Marcuse-Kubitza
10:22 AM Task #313: Import full NYBG data
Almost done with the first full load of the NYBG data. Currently takes 2 days. Aaron Marcuse-Kubitza
09:46 AM Revision 842: Added schemas/vegbank.revised.sql. Initial version has all "character varying" types replaced with text.
Aaron Marcuse-Kubitza
09:45 AM Revision 841: vegbien.sql: Replaced all "character varying" types with text, removing the length limits. Note that in PostgreSQL, text and "character varying" are stored the same way internally, so this does not affect performance or indexes.
Aaron Marcuse-Kubitza

02/04/2012

05:28 PM Revision 840: xml_dom.py: Added documentation labels to each section
Aaron Marcuse-Kubitza
05:21 PM Revision 839: xml_dom.py: Fixed bug in NodeTextEntryIter where an entry containing an element instead of a text node would be returned as the whole entry, instead of the value *of* the entry
Aaron Marcuse-Kubitza
04:56 PM Revision 838: bin/map: Added support for starting import at a specific row. Refactored row-processing code with and without a map to use a common process_rows() function (with the previous process_rows() being renamed to map_rows()).
Aaron Marcuse-Kubitza
04:14 PM Revision 837: bin/map: Use new util.cast()
Aaron Marcuse-Kubitza
04:14 PM Revision 836: util.py: Added cast() to cast a value while passing None through
Aaron Marcuse-Kubitza
04:09 PM Revision 835: bin/map: Print row # of rows with errors
Aaron Marcuse-Kubitza
03:27 PM Task #349: make ERD of full schema
Full ERD is available at [[VegBIEN schema]]. A few tables are not yet included, because their lines to existing table... Aaron Marcuse-Kubitza
03:25 PM Task #354 (Resolved): list of deliverables for next week (2/6-2/10)
See [[2012-02-03 conference call]] Aaron Marcuse-Kubitza
03:22 PM Revision 834: sql.py: Fixed error in pkey() where recover was not passed as a named parameter to run_query()
Aaron Marcuse-Kubitza
03:12 PM Revision 833: sql.py: Added documentation labels to each section
Aaron Marcuse-Kubitza
03:10 PM Revision 832: sql.py: Added documentation labels to each section
Aaron Marcuse-Kubitza
03:03 PM Revision 831: db_xml.py: Used new sql.py recover functionality
Aaron Marcuse-Kubitza
03:03 PM Revision 830: sql.py: Added ability to recover from database errors so you don't get the error "InternalError: current transaction is aborted, commands ignored until end of transaction block"
Aaron Marcuse-Kubitza
02:25 PM Revision 829: vegbien.sql: Removed taxonoccurrence.taxoninferencearea because it's duplicated in aggregateoccurrence.inferencearea
Aaron Marcuse-Kubitza
02:18 PM Revision 828: bin/map: Highlight the "input row" and "output row:" labels in error messages
Aaron Marcuse-Kubitza
02:17 PM Revision 827: xml_func.py: Highlight nodes that were commented out because of errors
Aaron Marcuse-Kubitza
02:17 PM Revision 826: exc.py: Print exceptions with the first line highlighted in red
Aaron Marcuse-Kubitza
02:16 PM Revision 825: term.py: Added emph() and error()
Aaron Marcuse-Kubitza
01:51 PM Revision 824: vegbien.ERD.mwb: Fixed lines
Aaron Marcuse-Kubitza
01:47 PM Revision 823: vegbien.ERD.mwb: Fixed lines
Aaron Marcuse-Kubitza
01:46 PM Revision 822: vegbien.ERD.mwb: Added note, notelink, and revision
Aaron Marcuse-Kubitza
01:43 PM Revision 821: vegbien.ERD.mwb: Added embargo to diagram
Aaron Marcuse-Kubitza
01:27 PM Revision 820: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
01:24 PM Revision 819: vegbien.ERD.mwb: Fixed lines. Added "Core subset" and "Other tables" labels.
Aaron Marcuse-Kubitza
01:03 PM Revision 818: xml_func.py: Changed _date func to use new dates.strftime(), which can handle years before 1900
Aaron Marcuse-Kubitza
01:03 PM Revision 817: Added dates.py to handle date/time manipulation, such as fixing Python's broken strftime() that can't handle years before 1900
Aaron Marcuse-Kubitza
01:02 PM Revision 816: Regenerated mappings/for_review/DwC-VegBIEN.specimens.csv
Aaron Marcuse-Kubitza

02/03/2012

06:15 PM Revision 815: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
06:12 PM Revision 814: vegbien.ERD.mwb: Added reference and party tables
Aaron Marcuse-Kubitza
05:49 PM Revision 813: vegbien.ERD.mwb: Fixed lines
Aaron Marcuse-Kubitza
05:48 PM Revision 812: filter_ERD.csv: Remove fkeys to heavily-linked tables (reference, party)
Aaron Marcuse-Kubitza
05:33 PM Task #347 (Resolved): revise milestones
Brad and Martha have approved it Aaron Marcuse-Kubitza
03:15 PM Task #347: revise milestones
My revisions are on the wiki under *[[Milestones]]* Aaron Marcuse-Kubitza
01:57 PM Task #347 (Resolved): revise milestones
Aaron Marcuse-Kubitza
05:30 PM Revision 811: Added to_do/milestones.doc
Aaron Marcuse-Kubitza
05:27 PM Revision 810: Renamed milestones.doc to timeline.doc
Aaron Marcuse-Kubitza
05:24 PM Revision 809: Added schemas/filter_ERD.csv and use it when generating vegbien.my.sql
Aaron Marcuse-Kubitza
05:16 PM Revision 808: vegbien.ERD.mwb: Added cover* to main diagram
Aaron Marcuse-Kubitza
04:53 PM Revision 807: vegbien.ERD.mwb: Started adding additional tables "below the fold" on the 2nd page
Aaron Marcuse-Kubitza
04:34 PM Revision 806: vegbien.ERD.mwb: Fixed lines
Aaron Marcuse-Kubitza
04:26 PM Revision 805: vegbien.ERD.mwb: Moved legend to top left to make room for more misc tables. Organized legend by location on diagram.
Aaron Marcuse-Kubitza
04:14 PM Revision 804: vegbien.ERD.mwb: Added soilobs table
Aaron Marcuse-Kubitza
04:07 PM Revision 803: vegbien.ERD.mwb: Added userdefined tables. Fixed lines.
Aaron Marcuse-Kubitza
03:57 PM Revision 802: vegbien.ERD.mwb: Changed location color to match VegBank ERD
Aaron Marcuse-Kubitza
03:53 PM Revision 801: vegbien.ERD.mwb: Added trait to diagram
Aaron Marcuse-Kubitza
03:38 PM Revision 800: vegbien.ERD.mwb: Added plantstatus to diagram. Added margins around diagram.
Aaron Marcuse-Kubitza
03:18 PM Task #320: Convert user-defined VegX fields to first-class fields
Brad's meeting notes on 2012-2-3:
* Aaron to make whatever modifications are needed to match VegBien schema
* Sub...
Aaron Marcuse-Kubitza
02:49 PM Revision 799: Added milestones.doc
Aaron Marcuse-Kubitza
02:04 PM Task #346: add georeferencing support to schema
* support DwC georeferencing fields Aaron Marcuse-Kubitza
01:57 PM Task #346 (New): add georeferencing support to schema
Aaron Marcuse-Kubitza
02:03 PM Task #354 (Resolved): list of deliverables for next week (2/6-2/10)
Aaron Marcuse-Kubitza
02:02 PM Task #353 (Resolved): add terms from previous versions of DwC to DwC-BIEN
Aaron Marcuse-Kubitza
02:02 PM Task #352 (Resolved): create way to represent methods hierarchically in schema
Aaron Marcuse-Kubitza
02:01 PM Task #351 (Resolved): list of fields and method attributes needed to know whether can combine data from different plots
* critical methodological elements Aaron Marcuse-Kubitza
02:00 PM Task #350 (Resolved): implement methods in VegBIEN
* middle ground between descriptions and ontological metadata Aaron Marcuse-Kubitza
01:59 PM Task #349 (New): make ERD of full schema
Aaron Marcuse-Kubitza
01:58 PM Task #348 (Resolved): 1st draft of schema
* plots and specimens data Aaron Marcuse-Kubitza
01:56 PM Task #345 (Resolved): integrate GNRS into VegBIEN
* geovalidation in scope
* georeferencing out of scope unless existing implementation
Aaron Marcuse-Kubitza
01:56 PM Task #344 (Resolved): contact John about GNRS/georeferencing
* Using PostGIS/R? Aaron Marcuse-Kubitza
01:55 PM Task #343 (Resolved): integrate TNRS into VegBIEN
Aaron Marcuse-Kubitza
12:39 PM Revision 798: DwC mappings: Fixed syntax of _date XML funcs to not wrap dates twice in a _date func
Aaron Marcuse-Kubitza
12:38 PM Revision 797: xml_func.py: Fixed bug in SyntaxException constructor where the cause was not passed to ExceptionWithCause
Aaron Marcuse-Kubitza
12:24 PM Revision 796: xml_dom.py: Override Node.__repr__ and Element.__repr__ to make sure self.toprettyxml() is used in all cases where a Node is converted to a string
Aaron Marcuse-Kubitza
11:57 AM Revision 795: util.py: Don't print type name in ConstraintError message because sometimes an entry tuple (e.g. from a dict) is checked, and then the type isn't useful
Aaron Marcuse-Kubitza
11:53 AM Revision 794: xml_func.py: Use conv_items(str, ...) in XML funcs that require strings, but don't otherwise use conv_items()
Aaron Marcuse-Kubitza
11:50 AM Revision 793: xml_func.py: Use xml_dom.TextEntryOnlyIter to check inputs for XML funcs that only handle strings, not whole elements
Aaron Marcuse-Kubitza
11:49 AM Revision 792: xml_dom.py: Added TextEntryOnlyIter to check that values returned by NodeTextEntryIter are strings from text nodes
Aaron Marcuse-Kubitza
11:48 AM Revision 791: util.py: Added is_str() and CheckedIter
Aaron Marcuse-Kubitza

01/31/2012

07:52 PM Revision 790: input.Makefile: Log each import to a new log file named according to the current time
Aaron Marcuse-Kubitza
07:38 PM Revision 789: xml_func.py: SyntaxException: Use exc.ExceptionWithCause
Aaron Marcuse-Kubitza
07:37 PM Revision 788: exc.py: Added str_() to convert an Exception to a string. Use str_() in print_ex().
Aaron Marcuse-Kubitza
07:31 PM Revision 787: xml_func.py: conv_items(): Only trap type conversion errors, not errors in map_items(). A previous bug incorrectly interpreted an error caught by map_items() as a SyntaxException.
Aaron Marcuse-Kubitza
07:23 PM Revision 786: xml_func.py: _date func: Fixed bug where setting defaults of a date part and removing zeros needed to happen after elements were converted to int. Refactored to use conv_items().
Aaron Marcuse-Kubitza
06:58 PM Revision 785: Makefiles: Added documentation labels to each section
Aaron Marcuse-Kubitza
06:55 PM Revision 784: Makefile: Added documentation labels to each section
Aaron Marcuse-Kubitza
06:49 PM Revision 783: input.Makefile: Added documentation labels to each section
Aaron Marcuse-Kubitza
06:44 PM Revision 782: xml_dom.py: Fixed conversion of minidom.Node to a string to use toprettyxml() again
Aaron Marcuse-Kubitza
06:40 PM Revision 781: Added inputs/SALVIAS-CSV/maps/VegBIEN.* maps
Aaron Marcuse-Kubitza
06:39 PM Revision 780: input.Makefile: If a test doesn't yet have accepted output, print its current output
Aaron Marcuse-Kubitza
06:24 PM Revision 779: mappings/Makefile: Only clean up a core map (intermediate format->VegBIEN) when it's modified. Note that the .last_cleanup files need to be under version control to prevent cleanups upon running any map command in a new checkout.
Aaron Marcuse-Kubitza
06:07 PM Revision 778: xml_func.py: Support dates with year/month/day == 0
Aaron Marcuse-Kubitza
06:06 PM Revision 777: input.Makefile: Print informative message if test failure is ignored
Aaron Marcuse-Kubitza
05:47 PM Revision 776: input.Makefile: Print path to test output so you can tell which directory a test is running in
Aaron Marcuse-Kubitza
05:45 PM Revision 775: input.Makefile: Fixed 2-step tests, which were still using $(root)/map when all bin/map calls were supposed to be routed through $(map)
Aaron Marcuse-Kubitza
05:05 PM Revision 774: xml_dom.py: Print simple XML elements on one line
Aaron Marcuse-Kubitza
04:33 PM Revision 773: Added inputs/SALVIAS-CSV/maps
Aaron Marcuse-Kubitza
04:33 PM Revision 772: input.Makefile: Added import support for CSV and XML inputs (no test support yet)
Aaron Marcuse-Kubitza
03:48 PM Revision 771: inputs/SALVIAS-CSV: Added src files
Aaron Marcuse-Kubitza
03:47 PM Revision 770: inputs/SALVIAS-CSV: Added src files
Aaron Marcuse-Kubitza
03:42 PM Revision 769: inputs: Removed no longer needed svn:ignore
Aaron Marcuse-Kubitza
03:41 PM Revision 768: input.Makefile: Coded svn:ignore directly in Makefile
Aaron Marcuse-Kubitza
03:40 PM Revision 767: inputs/Makefile: Added %-add target to add new inputs
Aaron Marcuse-Kubitza
03:35 PM Revision 766: input.Makefile: Added svn_props rule for updating svn:ignore of dir and subdirs
Aaron Marcuse-Kubitza
02:42 PM Revision 765: vegbien.sql: Made aggregateoccurrence:taxonoccurrence relationship 1:1
Aaron Marcuse-Kubitza
02:03 PM Revision 764: Added inputs/CTFS/src, with subset of files that will be in version control
Aaron Marcuse-Kubitza
02:01 PM Revision 763: mappings/for_review/DwC-VegBIEN.specimens.csv: Updated
Aaron Marcuse-Kubitza

01/30/2012

07:14 PM Revision 762: inputs/NYBG: Map via DwC instead of VegX
Aaron Marcuse-Kubitza
07:12 PM Revision 761: mappings/DwC-VegBIEN.specimens.csv: Provide schema URLs for namespaces (in the column header)
Aaron Marcuse-Kubitza
07:11 PM Revision 760: input.Makefile: Deal with core maps (the main *-VegBIEN map) whose roots are other than organisms
Aaron Marcuse-Kubitza
07:09 PM Revision 759: bin/map: In the xml_func.process() for XML outputs, pass an on_error that outputs to ex_tracker.track()
Aaron Marcuse-Kubitza
07:08 PM Revision 758: xpath.py: set_id(): Deal with XPaths with an
Aaron Marcuse-Kubitza
07:07 PM Revision 757: xml_dom.py: replace_with_text(): Accept Node inputs for cases where e.g. an XML func with an error has been replaced with a comment
Aaron Marcuse-Kubitza
07:06 PM Revision 756: xml_func.py: _date: Year defaults to 1900
Aaron Marcuse-Kubitza
05:18 PM Revision 755: DwC-VegBIEN.specimens.csv: Output DwC as XML instead of CSV
Aaron Marcuse-Kubitza
05:05 PM Revision 754: xpath.py: Allow XPath names to be quoted literals, just like values. Handle : embedded in a name (even without quotes), often indicating a namespace.
Aaron Marcuse-Kubitza
04:55 PM Revision 753: Removed no longer needed lib/ERD-wiki.csv
Aaron Marcuse-Kubitza
04:54 PM Revision 752: Parser.py: In syntax errors, only print <END> at end of string if error was *at* end of string
Aaron Marcuse-Kubitza
04:50 PM Revision 751: bin/map: Print error message rather than assertion failure for CSV output, which isn't supported yet
Aaron Marcuse-Kubitza
04:47 PM Revision 750: input.Makefile: Don't abort tester if via test fails, because CSV output is not supported yet
Aaron Marcuse-Kubitza
04:15 PM Task #323: map NYBG data
Infrastructure exists to do full NYBG loads, but there are many errors in the import Aaron Marcuse-Kubitza
04:12 PM Task #338 (Resolved): put together samples of SALVIAS data that aggregates individuals and stems in different ways
See [[SALVIAS issues]] Aaron Marcuse-Kubitza
04:02 PM Revision 749: input.Makefile: Deal properly with more than one format that's being mapped via (e.g. DwC and VegX)
Aaron Marcuse-Kubitza
03:49 PM Revision 748: Renamed mappings/DwC-VegBIEN.organisms.csv back to mappings/DwC-VegBIEN.specimens.csv because it now uses /specimenreplicate as the output root
Aaron Marcuse-Kubitza
03:43 PM Revision 747: Renamed mappings/DwC-VegBIEN.organisms.csv back to mappings/DwC-VegBIEN.specimens.csv because it now uses /specimenreplicate as the output root
Aaron Marcuse-Kubitza
03:41 PM Revision 746: mappings/DwC-VegBIEN.organisms.csv: Fixed syntax error in a mapping
Aaron Marcuse-Kubitza
03:35 PM Revision 745: mappings/DwC-VegBIEN.organisms.csv: Sorted
Aaron Marcuse-Kubitza
03:34 PM Revision 744: mappings/Makefile: Sort DwC-VegBIEN.organisms.csv
Aaron Marcuse-Kubitza
03:33 PM Revision 743: inputs/NYBG/maps/VegBIEN.organisms.csv: Regenerated
Aaron Marcuse-Kubitza
03:12 PM Revision 742: mappings/DwC-VegBIEN.organisms.csv: Sort on output column
Aaron Marcuse-Kubitza
03:04 PM Revision 741: Renamed mappings/DwC-VegBIEN.specimens.csv to DwC-VegBIEN.organisms.csv because it (currently) uses /taxonoccurrence as the output root
Aaron Marcuse-Kubitza
03:03 PM Revision 740: Renamed mappings/DwC-VegBIEN.specimens.csv to DwC-VegBIEN.organisms.csv because it (currently) uses /taxonoccurrence as the output root
Aaron Marcuse-Kubitza
03:01 PM Revision 739: Makefile: Support recursing into subdir when no target is specified (e.g. make mappings/)
Aaron Marcuse-Kubitza
02:55 PM Revision 738: union: Merge rows (and column labels) using maps.merge_mappings()
Aaron Marcuse-Kubitza
02:51 PM Revision 737: join: Merge the column labels as well
Aaron Marcuse-Kubitza
02:51 PM Revision 736: maps.py: Eliminate duplicates when merging values in the same column
Aaron Marcuse-Kubitza
02:06 PM Revision 735: join: Moved mappings-specific merge functionality into maps.merge_mappings()
Aaron Marcuse-Kubitza
01:55 PM Revision 734: join: Use merge_rows() from new maps.py
Aaron Marcuse-Kubitza
01:54 PM Revision 733: Added new library maps.py for map spreadsheet manipulation
Aaron Marcuse-Kubitza
01:38 PM Revision 732: join: Merge comments of input map and join map
Aaron Marcuse-Kubitza
01:37 PM Revision 731: join: Report which input mappings are missing a mapping in the join map
Aaron Marcuse-Kubitza
01:03 PM Revision 730: join: Report which input mappings are missing a mapping in the join map
Aaron Marcuse-Kubitza
12:28 PM Revision 729: inputs/NYBG/maps/VegX.organisms.csv: Added note that the primary key has NULL values in some rows
Aaron Marcuse-Kubitza
12:24 PM Revision 728: input.Makefile: Preserve as many intermediate files as possible (make likes to delete intermediates if they aren't marked as .PRECIOUS)
Aaron Marcuse-Kubitza
11:46 AM Revision 727: sort: Sort empty strings last so that inputs with no mapping go at the end of the map spreadsheet
Aaron Marcuse-Kubitza
11:24 AM Revision 726: VegBIEN-VegBank.csv: Updated for recent table renames
Aaron Marcuse-Kubitza
11:21 AM Revision 725: join: For input mappings with no match in the join map, include them in the output map with an empty mapping
Aaron Marcuse-Kubitza
11:05 AM Revision 724: input.Makefile: Generalized to handle mapping via any format, not just VegX
Aaron Marcuse-Kubitza
10:44 AM Revision 723: input.Makefile: Don't print message to accept output for failing 2-step tests, because they use another test's accepted output
Aaron Marcuse-Kubitza

01/28/2012

06:02 PM Revision 722: input.Makefile: Don't abort tester if only 2-step test fails, as it's often finicky
Aaron Marcuse-Kubitza
05:55 PM Revision 721: xml_func.py: Raise xml_func.SyntaxException for ValueErrors generated by date.strftime() (e.g. year out of range due to poor Y2K support in some OS implementations of strftime)
Aaron Marcuse-Kubitza
05:51 PM Revision 720: xml_func.py: Raise xml_func.SyntaxException for ValueErrors generated by datetime.date() (e.g. month out of range)
Aaron Marcuse-Kubitza
05:46 PM Revision 719: vegbien.sql: Added project.reference_id to namespace project names by datasource
Aaron Marcuse-Kubitza
05:39 PM Revision 718: input.Makefile: Import all tables at once by default
Aaron Marcuse-Kubitza
05:11 PM Revision 717: bin/map: Print "Inserted ... new rows into database" message to stdout rather than stderr so it can be stored in the test case output as a validation check
Aaron Marcuse-Kubitza
05:08 PM Revision 716: Accepted initial test output for NYBG/test/import.out.ref
Aaron Marcuse-Kubitza
05:06 PM Revision 715: bin/map: Clean up datasource input values
Aaron Marcuse-Kubitza
05:06 PM Revision 714: strings.py: Added std_newl() to convert line endings and cleanup() to process strings with extra or nonstandard whitespace
Aaron Marcuse-Kubitza
04:46 PM Revision 713: PostgreSQL-MySQL.csv: Deal with custom types
Aaron Marcuse-Kubitza
04:36 PM Revision 712: vegbien.sql: Added aggregateoccurrence.occurrencestatus_dwc field
Aaron Marcuse-Kubitza
04:22 PM Revision 711: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
04:21 PM Revision 710: vegbien.ERD.mwb: Added commclass table to ERD
Aaron Marcuse-Kubitza
04:11 PM Revision 709: vegbien.sql: Removed direct pointer from location to namedplace because locationplace already has this relationship and we don't want to have an extra pointer just for duplicate elimination
Aaron Marcuse-Kubitza
03:56 PM Revision 708: vegbien.ERD.mwb: Added stratummethod to ERD
Aaron Marcuse-Kubitza
03:53 PM Revision 707: vegbien.sql: Removed locationevent.stratummethod_id because the stratummethod is a per-stratum (or technically, per-stratumtype) field
Aaron Marcuse-Kubitza
03:28 PM Revision 706: PostgreSQL-MySQL.csv: Remove CHECK constraints
Aaron Marcuse-Kubitza
03:20 PM Revision 705: PostgreSQL-MySQL.csv: Remove functions and triggers
Aaron Marcuse-Kubitza
03:13 PM Revision 704: vegbien.sql: Ensure that aggregateoccurrence.count == 1 when the aggregateoccurrence has a plantobservation. Use a trigger to do this automatically.
Aaron Marcuse-Kubitza
02:51 PM Revision 703: README.TXT: Added command for reimporting data
Aaron Marcuse-Kubitza
02:48 PM Revision 702: README.TXT: Added instructions to sync ERD with vegbien.sql schema. Organized commands into categories.
Aaron Marcuse-Kubitza
02:23 PM Revision 701: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
02:22 PM Revision 700: Added BIEN_logo.png
Aaron Marcuse-Kubitza
02:19 PM Revision 699: vegbien.ERD.mwb: Added color group legend
Aaron Marcuse-Kubitza
01:59 PM Revision 698: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
01:58 PM Revision 697: vegbien.ERD.mwb: Fixed lines
Aaron Marcuse-Kubitza
01:57 PM Revision 696: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
01:57 PM Revision 695: vegbien.ERD.mwb: Fixed lines and moved plant to its own color category
Aaron Marcuse-Kubitza
01:52 PM Revision 694: vegbien.ERD.mwb: Added colors to ERD
Aaron Marcuse-Kubitza
01:34 PM Revision 693: vegbien.ERD.mwb: Simplified diagram by removing column types
Aaron Marcuse-Kubitza
12:56 PM Revision 692: schemas/Makefile: Don't generate for_ERD DDLs because the ERD is now synced with the full schema
Aaron Marcuse-Kubitza
12:54 PM Revision 691: vegbien.ERD.mwb: Synced with whole schema
Aaron Marcuse-Kubitza
12:54 PM Revision 690: vegbien.sql: Reordered fields in tables truncated in the ERD so that all removed fields are at the end of the table
Aaron Marcuse-Kubitza
12:44 PM Revision 689: schemas/Makefile: Generate MySQL version of vegbien.sql as well as vegbien.for_ERD.sql for eventual use in syncing the ERD with the whole schema
Aaron Marcuse-Kubitza
12:43 PM Revision 688: PostgreSQL-MySQL.csv: Added translations for syntaxes used by pg_dump
Aaron Marcuse-Kubitza
12:41 PM Revision 687: PostgreSQL-MySQL.csv: Added translations for syntaxes used by pg_dump
Aaron Marcuse-Kubitza
12:40 PM Revision 686: repl: All regexps are by default in multiline and ignore case mode
Aaron Marcuse-Kubitza

01/27/2012

04:59 PM Revision 685: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
04:59 PM Revision 684: vegbien.sql: Made planttag a child of plantobservation instead of plant, since tags change over time
Aaron Marcuse-Kubitza
04:39 PM Revision 683: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
04:37 PM Revision 682: vegbien.sql: Removed no longer used plantobservation.aggregateoccurrence_id
Aaron Marcuse-Kubitza
04:35 PM Revision 681: VegX-VegBIEN mapping: Link aggregateoccurrence to plantobservation via forward pointer rather than backward child-to-parent pointer
Aaron Marcuse-Kubitza
04:32 PM Revision 680: vegbien.sql: Made plantobservation.aggregateoccurrence_id optional because link will soon be going in the other direction
Aaron Marcuse-Kubitza
04:25 PM Revision 679: vegbien.sql: Removed taxonbinmethod table since its fields are now in aggregateoccurrence
Aaron Marcuse-Kubitza
04:14 PM Revision 678: vegbien.sql: Added taxonbinmethod fields to aggregateoccurrence
Aaron Marcuse-Kubitza
04:10 PM Revision 677: vegbien.sql: Added back aggregateoccurrence.stratum_id
Aaron Marcuse-Kubitza
04:05 PM Revision 676: vegbien.sql: Added stratum.area
Aaron Marcuse-Kubitza
04:03 PM Revision 675: vegbien.sql: Removed denormalized duplicate fields from stratum
Aaron Marcuse-Kubitza
03:58 PM Revision 674: vegbien.sql: Added plant and planttag tables
Aaron Marcuse-Kubitza
03:43 PM Revision 673: VegBIEN: Renamed stem to stemobservation
Aaron Marcuse-Kubitza
03:35 PM Revision 672: vegbien.sql: Removed specimenreplicate:taxonoccurrence 1:1 requirement
Aaron Marcuse-Kubitza
03:32 PM Revision 671: VegBIEN: Renamed individualplant to plantobservation
Aaron Marcuse-Kubitza
03:22 PM Revision 670: vegbien.sql: Updated table comments for specimenreplicate and specimen
Aaron Marcuse-Kubitza
03:19 PM Revision 669: vegbien.sql: Added specimen table to tie specimenreplicates together
Aaron Marcuse-Kubitza
03:12 PM Revision 668: VegBIEN: Renamed specimen to specimenreplicate
Aaron Marcuse-Kubitza
03:06 PM Revision 667: Remerged ERD DDL into ERD
Aaron Marcuse-Kubitza
03:04 PM Task #342 (Resolved): make DwC_BIEN schema
Aaron Marcuse-Kubitza
03:03 PM Task #341 (New): create verbal descriptions of edge cases
test cases for whether model can appropriately accommodate data Aaron Marcuse-Kubitza
02:55 PM Revision 666: Redoing commit that linked aggregateoccurrence forward to individualplant, allowing many taxonoccurrences (e.g. one for each specimen) to point to the same plant (e.g. that those specimens came from)
Aaron Marcuse-Kubitza
12:57 PM Revision 665: Added NYBG input
Aaron Marcuse-Kubitza
12:48 PM Revision 664: input.Makefile: Run tests with verbose output
Aaron Marcuse-Kubitza
12:48 PM Revision 663: bin/map: Fixed bug where verbose/debug flags were ignored and message were always printed.
Aaron Marcuse-Kubitza
12:39 PM Revision 662: bin/map: Added verbose and debug options. Added initial debug info.
Aaron Marcuse-Kubitza
12:39 PM Revision 661: xml_dom.py: Added is_simple() to determine whether every child recursively has no more than one child. Used is_simple() to print condensed XML when simple nodes are converted to a string.
Aaron Marcuse-Kubitza
11:58 AM Revision 660: vegbien.sql: Enforce 1:1 relationship between aggregateoccurrence<->individualplant and taxonoccurrence<->specimen
Aaron Marcuse-Kubitza
11:44 AM Revision 659: vegbien.sql: Changed individualplant UNIQUE constraint to enforce 1:1 relationship between aggregateoccurrence and individualplant
Aaron Marcuse-Kubitza
11:35 AM Revision 658: Undoing previous commit since it would prevent a plant from being tied to a data source, because the aggregateoccurrence pointer goes in the wrong direction
Aaron Marcuse-Kubitza
11:18 AM Revision 657: vegbien.sql: Added aggregateoccurrence.individualplant_id to make a 1:1 relationship between aggregateoccurrence and individualplant
Aaron Marcuse-Kubitza
01:55 AM Revision 656: input.Makefile: Generate VegBIEN.2-step.xml correctly from VegX.xml, by removing DB config env vars passed to map for that test case. Note that this causes the VegBIEN.2-step.xml test to fail, because the 2-step mapping does not yet match the 1-step mapping.
Aaron Marcuse-Kubitza
01:28 AM Revision 655: input.Makefile: Don't need to filter test output since stderr now goes to the screen
Aaron Marcuse-Kubitza
01:21 AM Revision 654: input.Makefile: Don't save *.err outputs for each test because this information is printed to the screen
Aaron Marcuse-Kubitza

01/26/2012

06:50 PM Revision 653: input.Makefile: Send echoed diff command to stdout of the make process (set -x echoes it to stderr)
Aaron Marcuse-Kubitza
06:48 PM Revision 652: input.Makefile: Write test stderr to .err file instead of test output, and tee it to stdout of the make process
Aaron Marcuse-Kubitza
06:29 PM Task #340 (Resolved): put together definitions of abstract BIEN terms
* specimen
* voucher
* taxonoccurrence
Aaron Marcuse-Kubitza
06:08 PM Revision 651: vegbien.sql: Updated name of UNIQUE constraint for specimen collectionnumber. Regenerated vegbien.ERD exports.
Aaron Marcuse-Kubitza
05:49 PM Revision 650: input.Makefile: Don't print "accept test" message when user aborted a test with Ctrl+C
Aaron Marcuse-Kubitza
05:34 PM Revision 649: inputs/SALVIAS/test: Accepted test outputs
Aaron Marcuse-Kubitza
05:33 PM Revision 648: input.Makefile: Also print message for accepting test output when diff fails
Aaron Marcuse-Kubitza
05:23 PM Revision 647: bin/map: Print a message when a database is successfully connected to
Aaron Marcuse-Kubitza
05:20 PM Revision 646: bin/map: Print a message when a database is successfully connected to
Aaron Marcuse-Kubitza
05:03 PM Revision 645: sql.py: Don't enclose PostgreSQL names in quotes because this disables case-insensitivity
Aaron Marcuse-Kubitza
04:58 PM Revision 644: sql.py: Use esc_name() to escape fields in SELECT statements
Aaron Marcuse-Kubitza
04:54 PM Revision 643: sql.py: Added esc_name() to escape identifiers like column names
Aaron Marcuse-Kubitza
04:27 PM Revision 642: vegbien.sql: Added comments to specimen.collectioncode_dwc and collectionnumber to differentiate them
Aaron Marcuse-Kubitza
04:22 PM Revision 641: vegbien.sql: Renamed authorspecimencode to collectionnumber to match its name in source data
Aaron Marcuse-Kubitza
04:18 PM Revision 640: input.Makefile: Use pipefail to cause a test to fail even when the output is filtered by grep. Print message for failing tests with command to run to accept the new test output.
Aaron Marcuse-Kubitza

01/24/2012

06:32 PM Task #339 (New): have "schema showdown"
Discuss different meanings everyone has for various ecological terms, especially:
* taxonoccurrence
* specimen
Aaron Marcuse-Kubitza
06:10 PM Revision 639: VegX-VegBIEN mapping: Map additional taxondetermination.determinationdate input formats straight through
Aaron Marcuse-Kubitza
06:08 PM Revision 638: test/input/SALVIAS_db.sh: Updated DB name
Aaron Marcuse-Kubitza
05:57 PM Revision 637: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
05:55 PM Revision 636: input.Makefile: Added documentation for why import errors for one input do not abort the import process for all inputs
Aaron Marcuse-Kubitza
05:53 PM Revision 635: input.Makefile: Determine DB name from input directory name, rather than DB file name
Aaron Marcuse-Kubitza
05:20 PM Revision 634: input.Makefile: Added documentation for accepting a test output
Aaron Marcuse-Kubitza
05:07 PM Revision 633: mappings/Makefile: Don't delete DwC-VegBIEN.specimens.csv in clean
Aaron Marcuse-Kubitza
05:05 PM Revision 632: VegBIEN: Renamed taxondetermination.*determination to is*
Aaron Marcuse-Kubitza
04:16 PM Revision 631: inputs/SALVIAS/test: Ignore test outputs
Aaron Marcuse-Kubitza
04:12 PM Revision 630: input.Makefile: Added test that generates VegBIEN.2-step.xml by mapping via a VegX.xml
Aaron Marcuse-Kubitza
03:39 PM Revision 629: input.Makefile: Added test that generates VegX.xml
Aaron Marcuse-Kubitza
03:29 PM Revision 628: input.Makefile: Added test that generates VegBIEN.xml
Aaron Marcuse-Kubitza
02:50 PM Revision 627: input.Makefile: Factored test/import.out out of DB section
Aaron Marcuse-Kubitza
02:43 PM Revision 626: input.Makefile: Renamed test/import.ref to import.out.ref. Changed syntax for accepting a test output to work with all types of test outputs.
Aaron Marcuse-Kubitza
02:32 PM Revision 625: Makefiles: Recurse into outermost subdir rather than bypassing it and going directly to innermost subdir
Aaron Marcuse-Kubitza
02:08 PM Revision 624: input.Makefile: Deal with inputs without a DB file, tests, verifications, etc.
Aaron Marcuse-Kubitza
02:07 PM Revision 623: inputs/Makefile: Don't use subdir makefiles because they are no longer needed
Aaron Marcuse-Kubitza
01:28 PM Revision 622: input.Makefile: Detect DB engine automatically from SQL file available in src subdir
Aaron Marcuse-Kubitza
01:00 PM Revision 621: input.Makefile: Factored as much as possible out of section for each DB engine
Aaron Marcuse-Kubitza
12:58 PM Revision 620: input.Makefile: Moved tests into test subdir
Aaron Marcuse-Kubitza
12:51 PM Revision 619: input.Makefile: Moved tests into test subdir
Aaron Marcuse-Kubitza
12:46 PM Revision 618: Added initial DwC-VegBIEN mappings spreadsheet with DwC terms
Aaron Marcuse-Kubitza
12:36 PM Revision 617: inputs/SALVIAS/verify: Updated to use new names for renamed tables
Aaron Marcuse-Kubitza
12:34 PM Revision 616: inputs/SALVIAS/verify: Updated to use new names for renamed tables
Aaron Marcuse-Kubitza
12:18 PM Revision 615: vegbien.sql: Removed no longer needed specimen.collector_id
Aaron Marcuse-Kubitza
12:16 PM Revision 614: VegX-VegBIEN mapping: Map collector name to new verbatimcollectorname field
Aaron Marcuse-Kubitza
12:11 PM Revision 613: vegbien.sql: Removed specimen.collectornumber_dwc and replaced it with verbatimcollectorname to reflect that the collectornumber_dwc is actually an ID of the specimen, and the collector's name is what we want to store
Aaron Marcuse-Kubitza

01/23/2012

05:33 PM Revision 612: mappings/Makefile: Run simplify_xpath on VegX-VegBIEN.organisms.csv
Aaron Marcuse-Kubitza
05:33 PM Revision 611: simplify_xpath: Be case sensitive to handle VegX correctly
Aaron Marcuse-Kubitza
05:18 PM Revision 610: VegX-VegBIEN mapping: Avoid using a dummy taxondetermination with role=collector
Aaron Marcuse-Kubitza
04:50 PM Revision 609: VegX-VegBIEN mapping: Map stem count to new stemcount field
Aaron Marcuse-Kubitza
04:48 PM Revision 608: VegX-VegBIEN mapping: Take advantage of aggregateoccurrence.count being optional
Aaron Marcuse-Kubitza
04:46 PM Revision 607: vegbien.sql: Made aggregateoccurrence.count to handle individuals data (for which count should be dynamically determined from # individual plants inside the aggregateoccurrence)
Aaron Marcuse-Kubitza
04:43 PM Revision 606: NYBG-VegBIEN mapping: Don't map dummy values to locationcode, etc. (e.g. in specimens data) because these tables are no longer required
Aaron Marcuse-Kubitza
04:42 PM Revision 605: vegbien.sql: Made several pointers to parent elements optional to deal with specimens data that might not have a location, etc.
Aaron Marcuse-Kubitza
04:29 PM Revision 604: vegbien.sql: Added taxondetermination UNIQUE constraint
Aaron Marcuse-Kubitza
04:18 PM Revision 603: VegX-VegBIEN mapping: Took advantage of location.confidentialitystatus being optional
Aaron Marcuse-Kubitza
04:16 PM Revision 602: VegX-VegBIEN mapping: Took advantage of userdefined.userdefinedtype being optional
Aaron Marcuse-Kubitza
04:13 PM Revision 601: vegbien.sql: Gave userdefined.userdefinedtype a default value
Aaron Marcuse-Kubitza
04:10 PM Revision 600: VegX-VegBIEN mappings: Took advantage of plantconcept.reference_id becoming optional
Aaron Marcuse-Kubitza
04:07 PM Revision 599: vegbien.sql: Made plantconcept.reference_id optional. Merge plantconcepts with no reference_id when eliminating duplicates.
Aaron Marcuse-Kubitza
04:05 PM Revision 598: PostgreSQL-MySQL.csv: Deal with all non-NOT NULL timestamp fields
Aaron Marcuse-Kubitza
04:00 PM Revision 597: vegbien.sql: Removed confusing plantconcept.plantname field since we are using plantname.plantname instead
Aaron Marcuse-Kubitza
03:54 PM Revision 596: VegBIEN: Renamed aux_role to role
Aaron Marcuse-Kubitza
03:47 PM Revision 595: VegX-VegBIEN mappings: Took advantage of several fields becoming optional
Aaron Marcuse-Kubitza
03:43 PM Revision 594: VegX-VegBIEN mappings: Took advantage of several fields becoming optional
Aaron Marcuse-Kubitza
03:36 PM Revision 593: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
03:36 PM Revision 592: vegbien.sql: taxonbinmethod points to stratumtype instead of stratum because stratumtype is a method table, but stratum is a measurements table. stratum does not point directly to stratummethod because it points to it via stratumtype.
Aaron Marcuse-Kubitza
03:04 PM Revision 591: vegbien.sql: Made taxondetermination.determinationdate optional because some determinations might not have a date
Aaron Marcuse-Kubitza
02:47 PM Revision 590: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
02:46 PM Revision 589: vegbien.sql: Added specimen.authorspecimencode
Aaron Marcuse-Kubitza
02:36 PM Revision 588: Adjusted vegbien.ERD.mwb
Aaron Marcuse-Kubitza
02:34 PM Revision 587: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
02:33 PM Revision 586: VegBIEN: Renamed sourceaccessionnumber to sourceaccessioncode to show that they are the data source's analog of accessioncode. Added sourceaccessioncode to all applicable tables because this is the database pkey, which is distinct from any author*code applied by the collector.
Aaron Marcuse-Kubitza
01:56 PM Revision 585: vegbien.sql: Changed taxonbinmethod_keys to UNIQUE INDEX to take advantage of COALESCE() for dealing with NULL values
Aaron Marcuse-Kubitza
01:43 PM Revision 584: vegbien.sql: Renamed taxonbin to taxonbinmethod to reflect that it does not contain actual organisms (those go in aggregateoccurrence), but rather defined a *method* of aggregating organisms
Aaron Marcuse-Kubitza
01:39 PM Revision 583: vegbien.sql: Removed taxonbin.count because that belongs in aggregateoccurrence and taxonbin is more similar to a sampling method. Added taxonbin UNIQUE constraint.
Aaron Marcuse-Kubitza
01:24 PM Revision 582: vegbien.sql: Do location duplicate elimination independently on code or lat/long, allowing duplicate entries with NULLs to exist when a location is incompletely specified
Aaron Marcuse-Kubitza
01:15 PM Revision 581: vegbien.sql: Require location to have either an authorlocationcode or a lat/long. Distinguish between regular and subplots in UNIQUE constraint.
Aaron Marcuse-Kubitza
01:10 PM Revision 580: vegbien.sql: Renamed location.latitude and longitude to publiclatitude, publiclongitude to reflect that they are not the actual lat/long. Switched to requiring reallatitude/reallongitude.
Aaron Marcuse-Kubitza
01:02 PM Revision 579: Added inputs/TurboVeg
Aaron Marcuse-Kubitza
12:58 PM Revision 578: vegbien.ERD.mwb: Deal with MySQL assuming that a timestamp field is NOT NULL
Aaron Marcuse-Kubitza
12:57 PM Revision 577: PostgreSQL-MySQL.csv: Deal with MySQL assuming that a timestamp field is NOT NULL
Aaron Marcuse-Kubitza
12:53 PM Revision 576: vegbien.sql: Made specimen.taxonoccurrence_id required
Aaron Marcuse-Kubitza
12:47 PM Revision 575: vegbien.sql: Made several fields optional, adding defaults where needed
Aaron Marcuse-Kubitza
12:47 PM Revision 574: PostgreSQL-MySQL.csv: Deal with PostgreSQL-style :: casts
Aaron Marcuse-Kubitza
12:14 PM Revision 573: NYBG mappings: Add mapping for CollectorNumber to specimen.collectornumber_dwc
Aaron Marcuse-Kubitza
12:08 PM Revision 572: vegbien.sql: Added specimen.collectornumber_dwc
Aaron Marcuse-Kubitza
12:03 PM Revision 571: VegBIEN: Renamed sourceid to author*code
Aaron Marcuse-Kubitza
12:01 PM Revision 570: VegBIEN: Renamed sourceid to author*code
Aaron Marcuse-Kubitza
11:44 AM Revision 569: mappings: Map ScientificNameAuthor to plantconcept with rank author
Aaron Marcuse-Kubitza
10:53 AM Revision 568: vegbien.sql: Removed sizeclass.*precision fields
Aaron Marcuse-Kubitza
10:50 AM Revision 567: vegbien.sql: Added count field to taxonBin
Aaron Marcuse-Kubitza
10:47 AM Revision 566: VegBIEN: Renamed place to locationplace
Aaron Marcuse-Kubitza
10:40 AM Revision 565: vegbien.sql.make: Exclude 'CREATE OR REPLACE PROCEDURAL LANGUAGE plpgsql' to avoid restore errors
Aaron Marcuse-Kubitza
10:20 AM Revision 564: repl: When matching words, treat _ as word boundary and ignore case.
Aaron Marcuse-Kubitza

01/20/2012

05:09 PM Revision 563: VegBIEN: Renamed individualplant.height to overallheight
Aaron Marcuse-Kubitza
03:02 PM Task #337 (Closed): VegBIEN table renames
E-mail from Brad on 2012-1-20:
Hi Mike,
You and Aaron have convinced me. Bob & I were advocating a return to th...
Aaron Marcuse-Kubitza
02:34 PM Revision 562: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
02:32 PM Revision 561: PostgreSQL-MySQL.csv: Convert double quotes to backticks (`)
Aaron Marcuse-Kubitza
02:10 PM Revision 560: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
02:09 PM Revision 559: vegbien.for_ERD.sql: Fixed syntax error in stratum table
Aaron Marcuse-Kubitza
02:00 PM Revision 558: Regenerated vegbien.ERD exports
Aaron Marcuse-Kubitza
01:39 PM Revision 557: vegbien.sql: Renamed sizeclass.*accuracy to *precision to reflect intended purpose
Aaron Marcuse-Kubitza
01:33 PM Revision 556: vegbien.sql: Added stem.diameteraccuracy
Aaron Marcuse-Kubitza
01:22 PM Revision 555: vegbien.sql: Removed taxonoccurrence.currentdetermination_id and originaldetermination_id because it's not possible to create a two-way pointer when the child-to-parent pointer is required (chicken-and-egg problem)
Aaron Marcuse-Kubitza
01:05 PM Revision 554: README.TXT: Added make empty_db
Aaron Marcuse-Kubitza
12:52 PM Revision 553: vegbien.sql: Added taxonoccurrence.currentdetermination_id and originaldetermination_id
Aaron Marcuse-Kubitza
12:41 PM Revision 552: vegbien.ERD.mwb: Added stratum and place tables
Aaron Marcuse-Kubitza
12:29 PM Task #338 (Resolved): put together samples of SALVIAS data that aggregates individuals and stems in different ways
* individual count
* stem count
* individuals
* stems
Aaron Marcuse-Kubitza

01/19/2012

06:06 PM Task #337: VegBIEN table renames
"observation" can be confusing, because it's not obvious what it's an observation of (a plot, an organism, a stem?). ... Aaron Marcuse-Kubitza
06:02 PM Task #337 (Closed): VegBIEN table renames
E-mail from Brad:
Conceptual definitions of tables:
observation: permanent attributes of a unit or area of obse...
Aaron Marcuse-Kubitza
05:32 PM Task #336 (Resolved): create VegBIEN ERD
Now live on [[VegBIEN schema]]! Aaron Marcuse-Kubitza
04:56 PM Task #336: create VegBIEN ERD
I discovered that MySQL Workbench can synchronize its model with an existing CREATE script. So, it looks like we can ... Aaron Marcuse-Kubitza
04:54 PM Task #336 (Resolved): create VegBIEN ERD
Aaron Marcuse-Kubitza
05:28 PM Revision 551: Added vegbien.ERD.png
Aaron Marcuse-Kubitza
05:24 PM Revision 550: Added vegbien.ERD.svg
Aaron Marcuse-Kubitza
05:21 PM Revision 549: Added vegbien.ERD.pdf
Aaron Marcuse-Kubitza
05:19 PM Revision 548: Added vegbien ERD
Aaron Marcuse-Kubitza
05:19 PM Revision 547: Ignore *.bak in schemas
Aaron Marcuse-Kubitza
05:07 PM Revision 546: VegBIEN: specimen links directly to taxonoccurrence rather than indirectly via individualplant
Aaron Marcuse-Kubitza
04:43 PM Revision 545: vegbien.sql: Made voucher fields NOT NULL
Aaron Marcuse-Kubitza
04:41 PM Revision 544: vegbien.sql: Added voucher table
Aaron Marcuse-Kubitza
04:26 PM Revision 543: VegBIEN: specimen links directly to taxonoccurrence rather than indirectly via individualplant
Aaron Marcuse-Kubitza
04:22 PM Revision 542: VegBIEN: specimen links directly to taxonoccurrence rather than indirectly via individualplant
Aaron Marcuse-Kubitza
04:12 PM Revision 541: Create schemas/vegbien.for_wiki.sql from schemas/vegbien.for_ERD.sql
Aaron Marcuse-Kubitza
04:11 PM Revision 540: Added lib/ERD-wiki.csv to convert ERD SQL to human-readable wiki format
Aaron Marcuse-Kubitza
04:10 PM Revision 539: schemas/vegbien.for_ERD.sql: Removed VegBank-internal fields from taxonoccurrence
Aaron Marcuse-Kubitza
03:51 PM Revision 538: Removed no longer needed schemas/vegbien.my.sql
Aaron Marcuse-Kubitza
03:51 PM Revision 537: PostgreSQL-MySQL.csv: Use \g<0> instead of \0 in replacements because \0 not supported. Replace fulltext with fulltext__ (note fulltext_ doesn't work).
Aaron Marcuse-Kubitza
01:34 PM Revision 536: Added schemas/vegbien.for_ERD.sql and generated MySQL
Aaron Marcuse-Kubitza
01:34 PM Revision 535: Regenerated schemas/vegbien.for_ERD.sql
Aaron Marcuse-Kubitza
01:33 PM Revision 534: PostgreSQL-MySQL.csv: Deal with serial NOT NULL fields
Aaron Marcuse-Kubitza
01:22 PM Revision 533: Generate MySQL DDL schemas/vegbien.my.sql from vegbien.sql
Aaron Marcuse-Kubitza
01:22 PM Revision 532: Added repl spreadsheet to map PostgreSQL DDL to MySQL
Aaron Marcuse-Kubitza
12:56 PM Revision 531: Ignore src subdirectories in inputs
Aaron Marcuse-Kubitza
12:46 PM Revision 530: VegBIEN: Use stem instead of individualplant to store diameter/dbh
Aaron Marcuse-Kubitza
11:35 AM Task #302 (Resolved): Make changes to VegBIEN schema
Extensive changes have been made Aaron Marcuse-Kubitza
11:33 AM Task #331 (Resolved): use VegX's individualOrganismObservation/relatedItem to model stems
Stems are now modeled in VegX. (Note that _VegBIEN_ stems import not complete yet) Aaron Marcuse-Kubitza
11:32 AM Task #319: Update statistics/lists of user-defined fields in use in VegX and VegBIEN
I've done this for NYBG to VegX Aaron Marcuse-Kubitza
11:31 AM Task #322 (Resolved): get access to raw CTFS data
I have the data from Shash, including a SQL dump Aaron Marcuse-Kubitza
11:30 AM Task #334 (Resolved): which DarwinCore attributes do we want to include in the specimen table?
Desired fields have been added or moved from other tables Aaron Marcuse-Kubitza
11:30 AM Task #314: Import CTFS data
I have data from Shash and am working with her to make sure we can parse it Aaron Marcuse-Kubitza
11:29 AM Task #318 (Resolved): decide whether to switch to VegX 1.5.2
In fact, we will switch to 1.5.3, which is now available Aaron Marcuse-Kubitza

01/18/2012

05:57 PM Revision 529: vegbien.sql: Removed no longer needed taxondetermination.plantname_id
Aaron Marcuse-Kubitza
05:53 PM Revision 528: VegBIEN: Made taxondetermination.plantconcept_id required and plantname_id optional
Aaron Marcuse-Kubitza
04:28 PM Revision 527: vegbien.sql: Added specimen.taxonoccurrence_id fkey
Aaron Marcuse-Kubitza
03:47 PM Revision 526: vegbien.sql: Removed no longer needed taxondetermination.individualplant_id, specimen_id fields
Aaron Marcuse-Kubitza
01:57 PM Revision 525: VegBIEN: Renamed plot to location to reflect that a location can also be used for specimens
Aaron Marcuse-Kubitza
01:29 PM Revision 524: vegbien.sql: Added individualplant.stemcount
Aaron Marcuse-Kubitza
12:38 PM Revision 523: vegbien.sql: Added accessioncode fields to existing, modified tables
Aaron Marcuse-Kubitza
12:21 PM Revision 522: vegbien.sql: Added accessioncode fields to new tables
Aaron Marcuse-Kubitza

01/17/2012

04:56 PM Revision 521: vegbien.sql: Removed no longer needed individualplant.taxonarea
Aaron Marcuse-Kubitza
04:40 PM Revision 520: VegBIEN: Moved taxondetermination.sourceaccessionnumber and museum_id to specimen
Aaron Marcuse-Kubitza
03:32 PM Revision 519: vegbien.sql: Split taxondetermination UNIQUE CONSTRAINT into one constraint for each main key (taxonoccurrence_id, specimen_id, individualplant_id) to deal with Postgres treating a row with NULL in any of those columns as distinct. Added CHECK constraint to require one of taxonoccurrence_id, specimen_id, individualplant_id to be NOT NULL.
Aaron Marcuse-Kubitza
02:47 PM Revision 518: VegBIEN: Renamed museumaccessionnumber to sourceaccessionnumber
Aaron Marcuse-Kubitza
02:42 PM Revision 517: VegBIEN: Renamed authorcode to sourceid
Aaron Marcuse-Kubitza
02:33 PM Revision 516: vegbien.sql: Updated sizeclass to use ranges for parameters and remove taxonarea
Aaron Marcuse-Kubitza

01/13/2012

05:25 PM Revision 515: input.Makefile: Fixed verify by making %.out: % rule use %.make instead
Aaron Marcuse-Kubitza
05:24 PM Revision 514: input.Makefile: Moved verifications into one set of verify.* files
Aaron Marcuse-Kubitza
05:18 PM Revision 513: input.Makefile: All tests are run in the same transaction, with output to test.out
Aaron Marcuse-Kubitza
05:04 PM Revision 512: bin/map: Added support for processing multiple map_paths at once in the same transaction
Aaron Marcuse-Kubitza
04:50 PM Revision 511: SALVIAS organisms mapping: Removed redundant PlotCode mapping because the association to plotevent is done with PlotID
Aaron Marcuse-Kubitza
04:49 PM Revision 510: bin/map: Started adding support for multiple map_paths, all run in the same db transaction
Aaron Marcuse-Kubitza
04:35 PM Revision 509: Filled in SALVIAS stems mappings. make test2's stems test fails because we don't wrap the import transaction around all the tests so that organisms are already in the database when stems are imported.
Aaron Marcuse-Kubitza
04:28 PM Revision 508: mappings/Makefile: Corrected stemobservation to stem
Aaron Marcuse-Kubitza
03:46 PM Revision 507: Use baseDistance/complexUserDefined/method to distinguish between different dbhs in VegX
Aaron Marcuse-Kubitza
03:41 PM Revision 506: VegX mappings: Use baseDistance/value instead of baseDistance so we can later use complexUserDefined to distinguish between different types of dbh
Aaron Marcuse-Kubitza
03:28 PM Task #335 (Rejected): Look into using Sybase Powerbuilder or IBM Enterprise Vision to map data
The TACC (Texas Advanced Computing Center) people might have individual licenses they could let us use Aaron Marcuse-Kubitza
03:07 PM Revision 505: VegX-VegBIEN.organisms.csv: Added initial stems mappings
Aaron Marcuse-Kubitza
03:06 PM Revision 504: mappings/Makefile: Updated VegX-VegBIEN.stems.csv input/output roots
Aaron Marcuse-Kubitza
03:05 PM Revision 503: ch_root: Deal with roots followed by something other than \b
Aaron Marcuse-Kubitza
02:41 PM Revision 502: input.Makefile: Remove *.out in new verify and test subdirs
Aaron Marcuse-Kubitza
02:38 PM Revision 501: Moved inputs files into subdirs for maps, verify, and test operations
Aaron Marcuse-Kubitza
02:00 PM Revision 500: vegbien.sql: Removed taxondetermination.collector_id because that's now in specimen
Aaron Marcuse-Kubitza
01:58 PM Revision 499: VegBIEN: Map to specimen.collector_id instead of taxondetermination
Aaron Marcuse-Kubitza
01:27 PM Revision 498: vegbien.sql: Added specimen.collector_id column
Aaron Marcuse-Kubitza
01:20 PM Revision 497: vegbien.sql: Changed taxondetermination.stem_id to individualplant_id
Aaron Marcuse-Kubitza
01:16 PM Revision 496: vegbien.sql: Removed taxondetermination columns that have been moved to specimen
Aaron Marcuse-Kubitza
01:14 PM Revision 495: VegBIEN: Merged specimen.collectionnumber and catalognumber_dwc fields. Removed NOT NULL constraints on several specimen columns because not all specimens have all identifiers. Mapped to new specimen fields.
Aaron Marcuse-Kubitza
12:59 PM Revision 494: VegX-VegBIEN mapping: Map collectiondate to specimen table
Aaron Marcuse-Kubitza
12:55 PM Revision 493: vegbien.sql: Added specimen.collectionnumber and collectiondate fields
Aaron Marcuse-Kubitza
12:50 PM Revision 492: Updated README.TXT to reflect new make targets
Aaron Marcuse-Kubitza

01/12/2012

04:40 PM Task #334 (Resolved): which DarwinCore attributes do we want to include in the specimen table?
Aaron Marcuse-Kubitza
04:37 PM Task #314: Import CTFS data
e-mails on 2012-1-12:
Steve Dolins:
We used the identical aggregate data file used for BIEN I... I think the da...
Aaron Marcuse-Kubitza
04:30 PM Task #333 (Resolved): add traits table to VegBIEN
Aaron Marcuse-Kubitza
04:25 PM Task #318: decide whether to switch to VegX 1.5.2
Brad: Yes! Latest version please, 1.5.2. It's about to get a lot less stable in any case, as we make more changes. Aaron Marcuse-Kubitza
04:10 PM Task #318 (Resolved): decide whether to switch to VegX 1.5.2
We have been mapping to VegX 1.5.1 (the latest stable version) but a release candidate VegX 1.5.2 is also available. ... Aaron Marcuse-Kubitza
04:24 PM Task #332 (Rejected): switch to VegX 1.5.3
Aaron Marcuse-Kubitza
04:22 PM Task #331 (Resolved): use VegX's individualOrganismObservation/relatedItem to model stems
Aaron Marcuse-Kubitza
04:22 PM Task #330 (Rejected): DwC extension to VegX
Aaron Marcuse-Kubitza
04:22 PM Task #329 (New): make website user-protected
Aaron Marcuse-Kubitza
04:21 PM Task #328 (New): get raw data rather than flat file exports from RAINFOR
Aaron Marcuse-Kubitza
04:21 PM Task #327 (Resolved): look into Clio
Aaron Marcuse-Kubitza
04:21 PM Task #326 (Rejected): generic MOU template to request data
Aaron Marcuse-Kubitza
04:21 PM Task #325 (Resolved): map CTFS data
Aaron Marcuse-Kubitza
04:21 PM Task #324 (Resolved): NYBG validations
Aaron Marcuse-Kubitza
04:20 PM Task #323 (Resolved): map NYBG data
Aaron Marcuse-Kubitza
04:20 PM Task #322 (Resolved): get access to raw CTFS data
Aaron Marcuse-Kubitza
04:20 PM Task #321 (Resolved): Convert user-defined VegBIEN fields to first-class fields
Aaron Marcuse-Kubitza
04:20 PM Task #320 (Rejected): Convert user-defined VegX fields to first-class fields
Aaron Marcuse-Kubitza
04:20 PM Task #319 (Resolved): Update statistics/lists of user-defined fields in use in VegX and VegBIEN
Aaron Marcuse-Kubitza
01:25 PM Task #302: Make changes to VegBIEN schema
I have applied most of Bob's changes to the VegBIEN schema, as well as many of Mark's suggestions. I posted a summary... Aaron Marcuse-Kubitza
01:18 PM Revision 491: vegbien.sql: Added sizeclass columns
Aaron Marcuse-Kubitza
01:01 PM Revision 490: VegBIEN: Removed stem* prefix from stem measurements because it's redundant and because these same field names were reused in non-stem tables
Aaron Marcuse-Kubitza
12:51 PM Revision 489: VegBIEN: Renamed stemobservation to stem
Aaron Marcuse-Kubitza
12:49 PM Revision 488: vegbien.sql: Added comments to renamed tables specifying VegBank equivalent
Aaron Marcuse-Kubitza
12:45 PM Revision 487: vegbien.sql: Added comments to new tables
Aaron Marcuse-Kubitza
12:25 PM Revision 486: vegbien.sql: Removed r# prefix from foreign key constraints
Aaron Marcuse-Kubitza
12:21 PM Revision 485: vegbien.sql: Added plot.namedplace_id for theplots which are identified by a namedplace rather than lat/long or name
Aaron Marcuse-Kubitza
12:18 PM Revision 484: vegbien.sql: Made plot.authorcode optional as not all plots have names
Aaron Marcuse-Kubitza
12:16 PM Task #317 (Rejected): Direct mapping from VegX to VegBIEN
When complete, this will be a complete, generic mapping of all elements in VegX to all corresponding elements in VegB... Brad Boyle
12:15 PM Revision 483: vegbien.sql: Added _dwc to specimen columns that are from DwC
Aaron Marcuse-Kubitza
12:12 PM Revision 482: vegbien.sql: Added UNIQUE constraint for specimen table. Made catalognumber required so that all specimens can be uniquely identified.
Aaron Marcuse-Kubitza
12:09 PM Revision 481: vegbien.sql: Made specimen.individualplant_id optional because specimens are not required to have a corresponding plot event (which all individualplants must have)
Aaron Marcuse-Kubitza
12:05 PM Revision 480: VegBIEN-VegBank.csv: Updated to reflect renames
Aaron Marcuse-Kubitza
12:02 PM Revision 479: vegbien.sql: Renamed specimen.code to collectioncode to match DwC term
Aaron Marcuse-Kubitza
11:58 AM Revision 478: vegbien.sql: Added sizeclass table
Aaron Marcuse-Kubitza
11:51 AM Revision 477: vegbien.sql: Renamed collection to specimen to reflect that it's for a single collection specimen
Aaron Marcuse-Kubitza
11:45 AM Revision 476: VegBIEN: Renamed collectiveobservation to aggregateoccurrence to reflect VegX usage of aggregate and the new taxonoccurrence table
Aaron Marcuse-Kubitza

01/11/2012

02:47 PM Revision 475: VegBIEN: Renamed stemobservation.stemcode to authorcode
Aaron Marcuse-Kubitza
02:43 PM Revision 474: vegbien.sql: Renamed individualplant.code to authorcode
Aaron Marcuse-Kubitza
02:41 PM Revision 473: sql.py: Reordered get() args to match put()
Aaron Marcuse-Kubitza
02:40 PM Revision 472: db_xml.py: Use new sql.put() which only eliminates duplicates based on database UNIQUE constraints
Aaron Marcuse-Kubitza
02:38 PM Revision 471: sql.py: Added new function put() and changed get() to use it
Aaron Marcuse-Kubitza
02:32 PM Revision 470: sql.py: Fixed raising of NullValueException to pass array of columns rather than single column
Aaron Marcuse-Kubitza
02:25 PM Revision 469: vegbien.sql: Added UNIQUE constraints to tables used in the mapping so that duplicates are eliminated by the database
Aaron Marcuse-Kubitza
02:23 PM Revision 468: sql.py: ExceptionWithColumn now stores multiple columns so that they can all be used in DuplicateKeyExceptions
Aaron Marcuse-Kubitza
02:22 PM Revision 467: util.py: Fixed dict_subset() to work correctly when a key does not exist
Aaron Marcuse-Kubitza
02:13 PM Revision 466: util.py: Added dict_subset()
Aaron Marcuse-Kubitza
02:07 PM Revision 465: sql.py: Use constraint_cols() to determine DuplicateKeyException column in try_insert()
Aaron Marcuse-Kubitza
01:50 PM Revision 464: sql.py: Added constraint_cols() to get columns of a constraint for use in determining the columns for a DuplicateKeyException
Aaron Marcuse-Kubitza
11:59 AM Revision 463: db_xml.py: Map empty fields to None instead of ignoring them, to ensure that an existing row with a value in that field is not used in the duplicate elimination
Aaron Marcuse-Kubitza
11:56 AM Revision 462: bin/map: Use db_xml.put()'s new on_error handler
Aaron Marcuse-Kubitza
11:53 AM Revision 461: db_xml.py: put(): Added on_error handler. Reordered arguments according to how often they are likely to be used.
Aaron Marcuse-Kubitza
11:31 AM Revision 460: bin/map: Print # input rows processed
Aaron Marcuse-Kubitza
11:08 AM Task #314: Import CTFS data
e-mail from Brad Boyle on 2012-1-10:
Interesting observation. I must admit, I haven't inspected Shash's VegX yet, ...
Aaron Marcuse-Kubitza

01/10/2012

05:32 PM Revision 459: VegX-VegBIEN mapping: Merge different sources of plot elevation
Aaron Marcuse-Kubitza
05:32 PM Revision 458: vegbien.sql: Added individualplant.code field
Aaron Marcuse-Kubitza
05:10 PM Revision 457: xml_func.py: Expand XML funcs in XML func args
Aaron Marcuse-Kubitza
05:06 PM Revision 456: xml_dom.py: In NodeTextEntryIter, return non-text children as-is instead of ignoring them so that XML functions can use them
Aaron Marcuse-Kubitza
04:46 PM Revision 455: xml_dom.py: Improved readability by separating into sections
Aaron Marcuse-Kubitza
04:41 PM Revision 454: db_xml.py: Ignore only fields that are actually empty (rather than just not having element children), as a field containing anything other than a comment should be flagged as invalid input
Aaron Marcuse-Kubitza
04:41 PM Revision 453: xml_dom.py: Changed is_empty() to consider nodes with only comments to be empty
Aaron Marcuse-Kubitza
04:23 PM Revision 452: bin/map: Add input row to exceptions
Aaron Marcuse-Kubitza
04:22 PM Revision 451: db_xml.py: Ignore empty fields. Fixes bug where a field that's not text but has no Element children will be treated as a table, and an error is triggered because the corresponding table does not exist in the database.
Aaron Marcuse-Kubitza
04:19 PM Revision 450: xml_dom.py: Added has_elems() to check if node has Element children
Aaron Marcuse-Kubitza
03:56 PM Revision 449: bin/map: Use xml_func.process()'s new on_error error handler. Add row to database errors and xml_func.SyntaxExceptions.
Aaron Marcuse-Kubitza
03:54 PM Revision 448: xml_func.py: Changed formatting of comment that node with syntax errors is replaced with so that it starts on its own line
Aaron Marcuse-Kubitza
03:50 PM Revision 447: xml_func.py: Use on_error exception handler to allow caller to print exceptions instead of raising them
Aaron Marcuse-Kubitza
03:41 PM Revision 446: db_xml.py: Add node to any database exceptions generated in put()
Aaron Marcuse-Kubitza
03:09 PM Revision 445: exc.py: Added raise_() wrapper for raise statement
Aaron Marcuse-Kubitza
02:45 PM Revision 444: Ignore .~* (lock files generated by OpenOffice.org) in inputs
Aaron Marcuse-Kubitza
02:44 PM Revision 443: inputs/SALVIAS: Added stems map
Aaron Marcuse-Kubitza
02:43 PM Revision 442: bin/map: Handle empty rows for db output
Aaron Marcuse-Kubitza
02:34 PM Revision 441: mappings: Use stemParent instead of stemOrganism to identify stems so that it's clear that the stemParent is an individualOrganismObservation, not an individualOrganism
Aaron Marcuse-Kubitza
02:25 PM Revision 440: input.Makefile: Include VegX maps not in tablesSort
Aaron Marcuse-Kubitza
02:20 PM Task #314: Import CTFS data
e-mail from Mark Schildhauer on 2012-1-10:
I think tt would be best (and certainly most scaleable) if the elements...
Aaron Marcuse-Kubitza
01:20 PM Task #314: Import CTFS data
Looking at Shash's VegX file, I noticed that she uses different VegX elements than we do for SALVIAS and NYBG data. F... Aaron Marcuse-Kubitza
02:13 PM Revision 439: mappings/Makefile: Generate initial VegX-VegBIEN.stems.csv
Aaron Marcuse-Kubitza
01:36 PM Revision 438: mappings/Makefile: Cleaned up in preparation for adding rule to generate VegX-VegBIEN.stems.csv
Aaron Marcuse-Kubitza
12:51 PM Revision 437: bin/map: Continue with database insertion even if a row had XML func syntax errors, because these errors have been fixed by removing the offending function node
Aaron Marcuse-Kubitza
12:49 PM Revision 436: xml_func.py: Remove function nodes with syntax errors to prevent them from causing DatabaseErrors later
Aaron Marcuse-Kubitza
12:48 PM Revision 435: xml_dom.py: Added remove() function to remove a node
Aaron Marcuse-Kubitza
12:39 PM Revision 434: bin/map: Track Exceptions with ExTracker
Aaron Marcuse-Kubitza
12:38 PM Revision 433: exc.py: Added ExTracker to track printed (suppressed) Exceptions and exit with nonzero status if any were encountered
Aaron Marcuse-Kubitza
12:12 PM Revision 432: bin/map: Parse each output XPath at the beginning so XPath syntax errors are detected right away
Aaron Marcuse-Kubitza
12:03 PM Revision 431: vegbien.sql: Reran renames to capture cases where a name is in the middle of an identifier
Aaron Marcuse-Kubitza
11:47 AM Revision 430: vegbien.sql: Use character varying(255) instead of text or character varying in new tables and columns
Aaron Marcuse-Kubitza
11:35 AM Revision 429: input.Makefile: Print Postgres NULL as NULL instead of empty string to match MySQL output
Aaron Marcuse-Kubitza
11:26 AM Revision 428: VegX-VegBIEN mapping: Fixed syntax error in mapping
Aaron Marcuse-Kubitza

01/09/2012

05:30 PM Revision 427: vegbien.sql: Added trait table
Aaron Marcuse-Kubitza
05:22 PM Revision 426: vegbien.sql: Added columns to stemobservation
Aaron Marcuse-Kubitza
05:13 PM Revision 425: vegbien.sql: Renamed collectiveobservation.stratum_id to taxonbin_id
Aaron Marcuse-Kubitza
04:51 PM Revision 424: vegbien.sql: Added some DarwinCore attributes to collection table
Aaron Marcuse-Kubitza
04:44 PM Task #302: Make changes to VegBIEN schema
Added new tables and moved/updated columns Aaron Marcuse-Kubitza
04:44 PM Task #302: Make changes to VegBIEN schema
I asked Bob a few questions about the new Collection table in the VegBIEN modifications:
* Is the Collection table m...
Aaron Marcuse-Kubitza
04:21 PM Revision 423: Makefiles: Added remake target to run clean and all
Aaron Marcuse-Kubitza
04:04 PM Revision 422: vegbien.sql: Added taxondetermination.collection_id column
Aaron Marcuse-Kubitza
03:56 PM Revision 421: VegBIEN: Made taxondetermination.plantname_id required
Aaron Marcuse-Kubitza
02:59 PM Revision 420: vegbien.sql: Made taxondetermination.plantconcept_id optional
Aaron Marcuse-Kubitza
02:49 PM Revision 419: VegBIEN: Renamed author*code to authorcode
Aaron Marcuse-Kubitza
02:47 PM Revision 418: Makefiles: Added empty rules for targets without a rule so that these rules wouldn't trigger the recursive subdir invocation for the default target
Aaron Marcuse-Kubitza
02:33 PM Revision 417: VegX-VegBIEN mapping: Convereted all database names to lowercase to correspond to their case in the database
Aaron Marcuse-Kubitza
02:04 PM Revision 416: Makefiles: Added empty Makefile target so that Makefiles are not included in the targets recursively run on subdirs
Aaron Marcuse-Kubitza
02:01 PM Revision 415: input.Makefile: Dependencies in other directories are included as prerequisistes. Use tablesSort variable instead of sort order prefix to order tables.
Aaron Marcuse-Kubitza
01:35 PM Revision 414: Makefile: Added default target that recursed into subdirs with Makefiles. Used default target for all and clean.
Aaron Marcuse-Kubitza
01:34 PM Revision 413: Regenerated inputs/SALVIAS/map.VegBIEN.0.plots.csv
Aaron Marcuse-Kubitza
01:32 PM Revision 412: Removed scripts symlink because it was causing Makefile recursion issues
Aaron Marcuse-Kubitza
01:28 PM Revision 411: Makefile: Take advantage of new inputs/Makefile
Aaron Marcuse-Kubitza
01:24 PM Revision 410: Added inputs/Makefile to run input targets recursively on each input
Aaron Marcuse-Kubitza
01:08 PM Revision 409: Makefile: Run inputs-* targets for all and clean
Aaron Marcuse-Kubitza
01:00 PM Revision 408: input.Makefile: all doesn't run import. import runs verify.
Aaron Marcuse-Kubitza
12:41 PM Revision 407: vegbien.sql: Set all FOREIGN KEY constraints to ON UPDATE CASCADE ON DELETE CASCADE
Aaron Marcuse-Kubitza
12:35 PM Revision 406: SALVIAS mappings: use PlotID as authorObsCode to link plot observations and organisms correctly for organisms without a PlotCode
Aaron Marcuse-Kubitza
12:32 PM Revision 405: SALVIAS mappings: use PlotID as authorObsCode to link plot observations and organisms correctly for organisms without a PlotCode
Aaron Marcuse-Kubitza
11:49 AM Revision 404: input.Makefile: Fixed bug in verify's diff rule
Aaron Marcuse-Kubitza
11:40 AM Task #314: Import CTFS data
I uploaded Shash's VegX file to vegbiendev at @/home/bien/svn/inputs/CTFS/src.VegX.xml@ . Aaron Marcuse-Kubitza
11:34 AM Revision 403: Added CTFS input
Aaron Marcuse-Kubitza
 

Also available in: Atom