Activity
From 02/16/2012 to 03/16/2012
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.
03/01/2012
- 05:55 PM Revision 1209: VegBIEN: stemobservation: Renamed diameter to diameterbreastheight to be more accurate
- 05:45 PM Revision 1208: vegbien.ERD.mwb: Expanded tables where there was room
- 05:34 PM Revision 1207: DwC mappings: Fixed user-defined field mappings according to Brad Boyle's changes
- 05:33 PM Revision 1206: vegbien.sql: Changed specimenreplicate_unique_collectionnumber constraint to include verbatimcollectorname because collection number is assigned by collector
02/28/2012
- 07:41 PM Revision 1205: Regenerated vegbien.ERD exports
- 07:39 PM Revision 1204: vegbien.sql: Changed specimenreplicate_unique_collectionnumber constraint to include verbatimcollectorname because collection number is assigned by collector
- 07:36 PM Revision 1203: VegBIEN: Moved taxonoccurrence.verbatimcollectorname to specimenreplicate and aggregateoccurrence so that it can be used in specimenreplicate duplicate elimination
- 07:21 PM Revision 1202: mappings/DwC1-DwC2.specimens.csv: Notes mapping: Removed extraneous /_merge/1
- 05:51 PM Revision 1201: input.Makefile: svn_props: Removed no longer needed items from input dir svn:ignore
- 05:49 PM Revision 1200: input.Makefile: verify: Fixed bug for inputs without a .ref where $(wildcard) wouldn't recheck the file after verify/%.out is run, so the verify output wasn't printed
- 05:45 PM Revision 1199: input.Makefile: Moved verify files into separate subdir
- 04:46 PM Task #348: 1st draft of schema
- Waiting for confirmation from Bob Peet
- 04:44 PM Task #353 (Resolved): add terms from previous versions of DwC to DwC-BIEN
- @mappings/DwC-VegBIEN.specimens.csv@ now contains duplicate mappings for DwC1 terms, which are automatically added fr...
- 04:43 PM Task #367 (Resolved): get Univ of Arizona DwC data
- See @vegbiendev:/home/bien/svn/inputs/UArizona-CSV/src/ARIZ_DiGIR_21012010.csv.tar.gz@
- 04:30 PM Revision 1198: bin/map: Changed root label data format convention to datasrc[data_format] so datasource names containing hyphens would not have the part after the - treated as the data format
- 04:25 PM Revision 1197: inputs maps: Changed input root labels to match dir names since verify expects these to be the same
- 04:22 PM Revision 1196: input.Makefile: verify: Fixed bug where datasource name was not set for non-DB inputs
- 04:18 PM Revision 1195: input.Makefile: Removed no longer needed default verify action for dirs with no verify.ref's
- 04:15 PM Revision 1194: input.Makefile: verify: Made verifications table-specific
- 03:27 PM Revision 1193: input.Makefile: import: Merged import and import-all because they do the same thing
- 03:26 PM Revision 1192: input.Makefile: verify: Started rearranging to allow different verifies for each table
- 03:19 PM Revision 1191: Moved verify.sql to mappings since it's mapping-related
- 02:31 PM Revision 1190: input.Makefile: Changed option nolog to log so that options aren't specified in the negative
- 01:43 PM Revision 1189: input.Makefile: svn ignore .trace files
- 01:41 PM Revision 1188: input.Makefile: Profile imports into a .trace file unless env var profile=""
- 01:28 PM Revision 1187: xml_func.py: _alt: On empty input, return None instead of raising SyntaxException because empty input should be OK
02/27/2012
- 05:37 PM Revision 1186: xml_func.py: _alt: Fixed bug where not specifying any item would crash the program instead of raising a SyntaxException
- 05:33 PM Revision 1185: Factored verify.sql out into schemas dir
- 05:26 PM Revision 1184: input.Makefile: verify: Print diff in two columns if verbose=1
- 05:03 PM Revision 1183: inputs/SALVIAS/verify.sql: When filtering by datasource name, use an AND clause in the JOIN party's ON condition instead of a separate WHERE statement, so that the datasource filtering code is all on the same line
- 04:58 PM Revision 1182: inputs/SALVIAS/verify.sql: Use new :datasource variable instead of literal 'SALVIAS'
- 04:58 PM Revision 1181: input.Makefile: Provide the verify.sql script a :datasource variable set to the datasource name (in quotes)
- 04:39 PM Revision 1180: vegbien.ERD.mwb: Re-marked aggregateoccurrence:plantobservation relationship as 1:1 in the ERD
- 03:55 PM Revision 1179: bin/map: DB, CSV inputs: Use column indexes instead of column names to look up each field (optimization to avoid repeated dict lookups of the same key)
- 03:47 PM Revision 1178: util.py: ListDict: __str__(): Print each entry on its own line, in the order the keys were provided
- 03:37 PM Revision 1177: NYBG-DwC maps: Filter out MinimumElevation = "."
- 03:37 PM Revision 1176: xml_dom.py: NodeTextEntryIter: Filter out empty entries (instead of producing an entry with an explicit None value, which causes problems with XML funcs that can't handle Nones)
- 03:34 PM Revision 1175: NYBG-DwC maps: Map to input fields with XML func appended whenever possible (DwC1->DwC2 translation is done by DwC-VegBIEN.specimens.csv)
- 02:57 PM Revision 1174: vegbien.sql: Renamed methodtaxonclass.description to methodtaxonclass.taxonclass and changed it to a closed list (enum taxonclass). method.description can still be used for freeform taxonclass inclusions/exclusions.
- 02:47 PM Revision 1173: DwC1-DwC2.specimens.csv: Removed no longer needed /_alt/2 XML func from date mappings (you will only ever map either the full date or the year/month/day)
- 02:43 PM Revision 1172: DwC mappings: Moved DwC1's CoordinatePrecision /_noCV/value XML func suffix to DwC2-VegBIEN.specimens.csv
- 02:38 PM Revision 1171: mappings: Removed mappings for XML func suffixes of a path because they are now automatically created heuristically by join
- 02:37 PM Revision 1170: join: Added heuristic search for a match on a parent path, so that every XML func suffix of a path doesn't need its own mapping
- 02:03 PM Revision 1169: Regenerated vegbien.ERD exports
- 02:01 PM Revision 1168: vegbien.sql: Added method.pointsperline. Rearranged ERD after removing role fkeys.
- 02:00 PM Revision 1167: filter_ERD.csv: Remove role fkeys
- 01:45 PM Revision 1166: vegbien.sql: aggregateoccurrence: Added linecover
- 01:37 PM Revision 1165: vegbien.sql: methodtaxonclass: Added description comment with list of values (which may become a closed list)
- 01:10 PM Revision 1164: Regenerated vegbien.ERD exports
- 01:02 PM Revision 1163: vegbien.sql: Changed lengthunits to m in all comments
- 12:56 PM Revision 1162: vegbien.sql: method: Added subplotspacing and subplotmethod_id
- 12:36 PM Revision 1161: vegbien.sql: method: Removed lengthunits and instead require all length- or area-related measurements throughout VegBIEN to be converted to SI base units, e.g. cm -> m, ha -> m^2. Adjusted ERD to avoid some densely packed lines.
- 12:17 PM Revision 1160: vegbien.sql: methodtaxonclass: Added description field for taxon classes that don't fit well into a plantconcept. Made at least one of plantconcept_id or description required. Added unique constraint.
- 12:07 PM Revision 1159: SALVIAS verifications: Use count(DISTINCT) instead of nested SELECT DISTINCT
- 12:05 PM Revision 1158: VegBIEN verifications: Select only the records for the datasource being verified
- 11:46 AM Revision 1157: SALVIAS verifications: Fixed to exclude subplots from locations/location events and uniqify locations based on coords
- 11:25 AM Revision 1156: inputs/SALVIAS/verify.sql: Updated for schema changes
- 10:24 AM Revision 1155: Regenerated vegbien.ERD exports
- 10:22 AM Revision 1154: vegbien.ERD.mwb: Re-marked aggregateoccurrence:plantobservation relationship as 1:1 in the ERD. (I think this will need to be manually re-marked whenever either of those tables is updated.)
- 10:18 AM Revision 1153: vegbien.sql: Removed methodgrowthform and growthform, since growthforms can be accommodated by plantconcept in a similar way as higher-order taxonomic ranks
- 10:09 AM Revision 1152: vegbien.sql: methodgrowthform, methodtaxonclass: Removed "included" default value so it's always obvious whether the author intended the classes to be inclusions or exclusions
- 10:04 AM Revision 1151: vegbien.sql: aggregateoccurrence: Removed unneeded fields. Added aggregateoccurrence->coverindex fkey.
- 09:54 AM Revision 1150: vegbien.sql: Added constraint to enforce 1:1 aggregateoccurrence:plantobservation relationship
02/25/2012
- 08:16 PM Revision 1149: vegbien.sql: Added plantname unique constraint
- 08:01 PM Revision 1148: bin/map: Use new util.ListDict and util.WrapIter to simplify getting rows by column name instead of index, and to enable a row to be printed with its column names in error messages
- 08:00 PM Revision 1147: util.py: Added WrapIter to wrap an iterator and ListDict to view a list as a dict
- 07:38 PM Revision 1146: bin/map: Use new util.list_flip()
- 07:37 PM Revision 1145: util.py: Added list_flip()
- 07:02 PM Revision 1144: env_password: Fixed to set the environment variable in the calling shell. Do this by cc-ing the tty only on messages before the "Enter password" prompt, because the redirect creates a subshell which causes the env var to only be set within that subshell.
- 06:18 PM Revision 1143: inputs/NYBG-CSV/maps/DwC.specimens.csv: Removed mappings that are already present in mappings/DwC1-DwC2.specimens.csv. This map now contains only the mappings where NYBG-CSV differs from standard DwC1.
- 06:14 PM Revision 1142: inputs/NYBG/maps/DwC.specimens.csv: Removed mappings that are already present in mappings/DwC1-DwC2.specimens.csv. This map now contains only the mappings where NYBG differs from standard DwC1.
- 05:58 PM Revision 1141: Remove accidentally-committed temp file inputs/NYBG/DwC.specimens2.csv
- 05:56 PM Revision 1140: mappings/Makefile: Generate DwC.self.specimens.csv from DwC-VegBIEN.specimens.csv for use in creating full via maps for inputs
- 05:40 PM Revision 1139: input.Makefile: Generate full via maps from input via maps by appending mappings from the via format to itself when available
- 04:30 PM Revision 1138: inputs/NYBG/maps/DwC.specimens.csv: Changed label to "NYBG-DwC" to take advantage of automatic filling in of DwC mappings not specified in the NYBG map
- 04:28 PM Revision 1137: subtract: Support custom column numbers to compare on (instead of just input col). Added ignore option to continue even if input columns don't match.
- 04:26 PM Revision 1136: bin/map: DB inputs: Get all rows in one query (hopefully a significant optimization). Allow maps to contain entries for columns that are not in the DB table.
- 04:22 PM Revision 1135: sql.py: select(): Select all fields if fields == None. Replaced col(cur, idx) with col_names(cur) because an iterator is easier to use than getting by index.
- 03:57 PM Revision 1134: bin/map: Fixed bug in previous implementation of allowing maps for CSV inputs to contain entries for columns that are not in the CSV file
- 03:45 PM Revision 1133: bin/map: Allow maps for CSV inputs to contain entries for columns that are not in the CSV file
- 02:54 PM Revision 1132: Use new sort_map instead of manually specifying the sort order
- 02:54 PM Revision 1131: Added sort_map to sort a map spreadsheet in the standard order
- 02:43 PM Revision 1130: Removed no longer needed join_passthru, because join_union_sort now serves its purpose
- 02:42 PM Revision 1129: Don't generate mappings/for_review/DwC-VegBIEN.specimens.csv because it's a derived map with lots of duplicated mappings for the various DwC versions
- 02:41 PM Revision 1128: mappings/Makefile: Generate DwC-VegBIEN.specimens.csv directly from DwC1-DwC2 and DwC2-VegBIEN mappings by using join_union_sort with header_num=1, rather than via intermediate DwC1-VegBIEN.specimens.csv
- 02:37 PM Revision 1127: union: Added header_num option to select which map's header to use as the output header
- 02:28 PM Revision 1126: Rename join_sort to join_union_sort and have it run union in ignore mode. This will automatically append the joined map when the input map is a derivative of the joined map, such as for NYBG-DwC.
- 02:25 PM Revision 1125: union: Pass through map 0, so that if ignore is set, the input map will still be output. Allow either map's input label to contain the other's input label to enable e.g. appending mappings for an older input version to those for a newer input version.
- 01:43 PM Revision 1124: DwC1-DwC2 mapping: Changed input label to DwC1, which is allowed by the now relaxed label constraints imposed by union
- 01:42 PM Revision 1123: union: Check if two maps can be combined based on whether map 0 column 0 label *contains* map 1 column 0 label instead of being equal. This allows map 0's input 0 root to contain the datasource name as well as a format that allows it to be combined with a more general map. Added ignore flag to not print an error if column labels don't match.
- 01:39 PM Revision 1122: bin/map: Support optional data format tag in map spreadsheet labels, used by union to check if two maps can be combined
- 01:01 PM Revision 1121: mappings: Added DwC1-DwC2.specimens.csv to core maps so it gets cleaned up
- 12:57 PM Revision 1120: Only generate for_review mappings of core maps and end products
- 12:56 PM Revision 1119: Generate DwC-VegBIEN mapping as union of DwC1 and DwC2 mappings
02/24/2012
- 08:00 PM Revision 1118: Generate DwC-VegBIEN mapping as union of DwC1 and DwC2 mappings
- 07:40 PM Revision 1117: NYBG DB mapping: Removed IdentifiedDate and CollectedDate mappings because they are generated from the year/month/day
- 07:39 PM Revision 1116: Added mappings/for_review/DwC1-VegBIEN.specimens.csv
- 07:35 PM Revision 1115: Added DwC1-DwC mapping. Generate DwC1-VegBIEN mapping automatically.
- 07:11 PM Revision 1114: Regenerated vegbien.ERD exports
- 07:08 PM Revision 1113: vegbien.sql: Renamed _keys unique constraints/unique indexes to _unique to better reflect their purpose
- 06:54 PM Revision 1112: vegbien.sql: Added method.diameterheight to store DBH height
- 06:44 PM Revision 1111: VegBIEN: Moved plantstatus.plantlevel to plantname.rank because the taxonomic rank is a property of the name itself
- 06:43 PM Revision 1110: PostgreSQL-MySQL.csv: Fixed custom types translation to match shorter type names
- 06:09 PM Revision 1109: vegbien.sql: Added plantstatus unique constraint
- 06:07 PM Revision 1108: DwC-VegBIEN mapping: Map datasource name via DwC institutionCode
- 05:42 PM Revision 1107: Regenerated vegbien.ERD exports
- 05:40 PM Revision 1106: vegbien.ERD.mwb: Lined up logo and legend with other ERD elements
- 05:35 PM Revision 1105: vegbien.sql: Renamed methodgrowthform.growthformmethod_id to submethod_id. Added methodtaxonclass.submethod_id (similar to methodgrowthform.submethod_id).
- 05:27 PM Revision 1104: vegbien.sql: Added methodgrowthform.growthformmethod_id for specifying a method used by just the growthform
- 05:14 PM Revision 1103: vegbien.ERD.mwb: Rearranged legend to more closely match layout of ERD
- 04:51 PM Revision 1102: vegbien.sql: Reordered plantstatus fields to put the most important fields at the top, which will be visible in the ERD
- 04:42 PM Revision 1101: vegbien.sql: Replaced method.taxonclassincluded,taxonclassexcluded with new many:many methodtaxonclass table. Added methodgrowthform, growthform tables to do the same thing as methodtaxonclass for growth forms.
- 03:53 PM Revision 1100: vegbien.sql: method: Added comment on reference_id
- 03:44 PM Revision 1099: VegBIEN: Moved plotmethod fields to method because they can also apply to strata. Removed no longer used plotmethod table.
- 03:13 PM Revision 1098: input.Makefile: input DB creation: Removed "IF NOT EXISTS" because that check is handled by $(dbExists)
- 03:02 PM Revision 1097: input.Makefile: Don't try to recreate an input DB if it already exists
- 03:01 PM Revision 1096: Added UArizona DB input
- 02:42 PM Revision 1095: Renaming UArizona to UArizona-CSV because there is also a DB input in bien2_staging.ariz_raw on nimoy
- 02:31 PM Revision 1094: Added UArizona input
- 02:08 PM Task #330 (Rejected): DwC extension to VegX
- We're mapping DwC data separately from VegX
- 02:07 PM Task #370 (Resolved): create ERD of final schema
- See [[VegBIEN schema]] > Proposed changes for remaining changes
- 02:06 PM Task #369 (Resolved): get CTFS data dictionary
- 02:06 PM Task #368 (Rejected): get TEAM VegX data
- 02:06 PM Task #367 (Resolved): get Univ of Arizona DwC data
- 02:05 PM Task #366 (Rejected): refactor VegX
- 02:04 PM Task #365 (Rejected): retrieve taxonomic hierarchy in analytical layer by using dynamic queries to external sources
- 12:46 PM Revision 1093: env_password: Fixed bug where exit command would not cause it to exit, because pipefail shell option was not set. Moved automatic exiting of the calling script into env_password itself.
- 12:26 PM Revision 1092: map: Exit if password not set
- 12:18 PM Revision 1091: env_password: cc stderr if it's a log file
02/23/2012
- 06:49 PM Revision 1090: env_password: Print all messages to /dev/tty so the user sees them even if stderr is redirected to a log file. Exit if password not already set, because e.g. scripts run in the background will not be able to prompt for it.
- 05:32 PM Revision 1089: input.Makefile: Don't have make import call verify, because the user often runs import as a test and will not want the output cluttered with verification information. Also, the full imports for which this was intended are often run asynchronously, so that the user will not see the output anyway.
- 05:28 PM Revision 1088: input.Makefile: Don't abort on verification errors, which are expected during development
02/21/2012
- 06:21 PM Revision 1087: SALVIAS tests: Fixed invalid accepted test outputs due to not running `make empty_db` before running tests when using the no-redo optimization shortcut
- 06:14 PM Revision 1086: SALVIAS mappings: Fixed plot key mappings to map the correct values to subplot and parent plot
- 05:36 PM Revision 1085: vegbien.sql: locationevent: Added unique constraint for subplots based on subplot location
- 05:02 PM Revision 1084: SALVIAS-db VegX mapping: Map subplots correctly the way SALVIAS-CSV does
- 04:54 PM Revision 1083: SALVIAS verification: Updated to schema changes
- 04:42 PM Revision 1082: input.Makefile: Fixed syntax error in verify %.ref target (outdated variable name)
- 04:33 PM Revision 1081: input.Makefile: Halt psql commands on first error
- 04:27 PM Revision 1080: vegbien.sql: Removed location.authorlocationcode because it's now stored in locationevent as an author-specific setting
- 04:24 PM Revision 1079: vegbien.sql: locationevent: Redid unique constraints to avoid applying authorlocationcode-only duplicate elimination to subplots
- 04:16 PM Revision 1078: SALVIAS mappings: Map SiteCode/plot_code to locationevent.authorlocationcode because locationevent is now the place to store author-specific plot information
- 04:10 PM Revision 1077: SALVIAS mappings: Fixed PlotID mapping to go to locationevent.sourceaccessioncode
- 04:06 PM Revision 1076: VegBIEN: Renamed locationevent.authoreventcode to authorlocationcode to reflect that datasources usually use an author-defined code for a plot rather than a plot event
- 04:03 PM Revision 1075: vegbien.sql: locationevent: Redid unique constraints to handle datasources that treat the authoreventcode as an authorlocationcode. Eventually, authoreventcode will be renamed to authorlocationcode.
- 03:51 PM Revision 1074: vegbien.sql: locationevent: Redid unique constraints to work properly for all fully-specified combinations of keys
- 03:31 PM Revision 1073: VegBIEN mappings: Mapped datasource name to new project.datasource. Fixes project duplicate elimination.
- 03:16 PM Revision 1072: vegbien.sql: Renamed project.reference_id to datasource_id and pointed it to party, to match locationevent, etc.
- 03:02 PM Revision 1071: VegBIEN mappings: Mapped current lat/long to centerlat/long as well so location duplicate elimination will work properly
- 03:01 PM Revision 1070: xpath.py: Added support for common subpath after split path's {}
- 01:30 PM Revision 1069: sql.py: put(): When encountering a DuplicateKeyException, use dict_subset_right_join to fill in explicit NULL values for columns which don't have data. This causes the database to use the UNIQUE constraint's index to look up the record, instead of relying on individual column indexes for the columns that did have data, which may or may not be available.
- 01:27 PM Revision 1068: util.py: Added DefaultDict to wrap collections.defaultdict with a simple value passed in the constructor, defaulting to None. Added dict_subset_right_join() to fill in None for subset keys that don't exist.
- 01:09 PM Task #351 (Resolved): list of fields and method attributes needed to know whether can combine data from different plots
- 01:08 PM Task #350 (Resolved): implement methods in VegBIEN
- 01:08 PM Task #352 (Resolved): create way to represent methods hierarchically in schema
- 01:08 PM Task #358 (Resolved): make shortlist of 1st-level fields a method should have
- 01:06 PM Revision 1067: vegbien.sql: Added method and plotmethod UNIQUE indexes
- 01:04 PM Revision 1066: vegbien.ERD.mwb: Removed embargo table from ERD because its functionality is provided in location.confidentialitystatus,confidentialityreason
- 12:36 PM Revision 1065: Regenerated vegbien.ERD exports
- 12:34 PM Revision 1064: vegbien.sql: Moved locationevent method fields to plotmethod and method. Added comments to method/plotmethod fields, as provided by Michael Lee.
- 12:15 PM Revision 1063: VegX-VegBIEN mapping: Mapped locationevent.methodnarrative to new plotmethod table
02/18/2012
- 07:18 PM Revision 1062: Regenerated vegbien.ERD exports
- 07:15 PM Revision 1061: VegX-VegBIEN mapping: Map sourceaccessioncode and voucher (catalognumber_dwc) to correct place. SALVIAS mappings: Map SourceVoucher as an alternative to coll_number.
- 06:46 PM Revision 1060: vegbien.sql: Removed VegBank-internal tables (including user account tables) because they do not belong in the ecological database. Any web interface should store user account information, cached queries, etc. in a separate interface-specific database.
- 06:34 PM Revision 1059: VegX-VegBIEN mapping: Mapped stem tags to new stemtag table
- 05:47 PM Revision 1058: vegbien.sql: Renamed planttag to stemtag and made it a child of stemobservation. Removed trait table from ERD because it's not used for the purpose we want to use traits for.
- 05:05 PM Revision 1057: vegbien.sql: Removed no longer used location.reference_id. Datasource scoping is now done on locationevent instead, so that locations can be shared across datasources that refer to the same plot or point.
- 04:56 PM Revision 1056: VegX-VegBIEN mapping: Map datasource name (/_ignore/inLabel) to new locationevent.datasource instead of location.reference
- 04:45 PM Revision 1055: vegbien.sql: Added locationevent.datasource_id
- 04:33 PM Revision 1054: vegbien.sql: locationevent: Removed VegBank-internal interp_* fields
- 04:28 PM Revision 1053: VegBIEN: Renamed specimenreplicate.reference_id to datasource_id and pointed it to party instead of reference, since party is better optimized for storing names
- 04:14 PM Revision 1052: DwC mappings: Mapped datasource name to specimenreplicate.reference instead of location.reference
- 04:08 PM Revision 1051: DwC mappings: Mapped specimen description via fieldNotes instead of custom bien.specimenDescription field
- 03:52 PM Revision 1050: VegBIEN: Moved specimenreplicate.verbatimcollectorname to taxonoccurrence since it can also apply to aggregateoccurrences. Removed no longer needed taxonoccurrence fields which are now in taxondetermination.
- 03:31 PM Revision 1049: SALVIAS mappings: Mapped habit to growthForm (user-defined field) instead of habit
- 03:24 PM Revision 1048: DwC-VegBIEN mapping: Convert latitude/longitude values of exactly zero to NULL
- 03:23 PM Revision 1047: xml_func.py: Added _nullIf
- 03:22 PM Revision 1046: util.py: Fixed cast() to not cast a subclass to a superclass (which doesn't make sense in a dynamically-typed language). Added none_if().
- 02:50 PM Revision 1045: util.py: Removed locale import since it's no longer used by util
- 02:31 PM Revision 1044: NYBG-DwC mappings: Map Vegetation to habitat (merged with Habitat). DwC-VegBIEN mapping: Removed remaining mappings to plantobservation.
- 02:22 PM Revision 1043: DwC-VegBIEN mapping: Added datasource name to location.reference using /_ignore/inLabel
- 02:00 PM Revision 1042: profiling.py: Support Python before 2.7 by using new dates.total_seconds(). Also use dates.now() to ensure datetimes always have a timezone.
- 01:59 PM Revision 1041: dates.py: Fixed timestamp() to deal with microseconds correctly by adding them after time.mktime()
- 01:41 PM Revision 1040: dates.py: Deal properly with different timezones by using external dateutil package. Added total_seconds() to replace datetime.timedelta.total_seconds() on Python before 2.7.
- 12:41 PM Revision 1039: vegbien.sql: *method tables: Added table comments
02/17/2012
- 06:08 PM Revision 1038: VegX-VegBIEN mapping: Reordered 2-step-only mappings that use /_ignore/inLabel so they run at the same time as other mappings that set the field that uses /_ignore/inLabel. This fixes almost all of the failing 2-step tests.
- 05:53 PM Revision 1037: Regenerated vegbien.ERD exports
- 05:46 PM Revision 1036: vegbien.sql: method: Added lengthunits field
- 05:36 PM Revision 1035: vegbien.sql: Changed types of numerical plotmethod fields to double precision
- 05:32 PM Revision 1034: vegbien.sql: method, plotmethod: Added comments to fields
- 05:27 PM Revision 1033: vegbien.ERD.mwb: Adjusted lines
- 05:24 PM Revision 1032: vegbien.sql: Added plotmethod. locationevent points to plotmethod instead of directly to method
- 04:47 PM Revision 1031: vegbien.sql: Point to covermethod from method instead of locationevent
- 04:39 PM Revision 1030: vegbien.sql: Removed no longer needed sizeclass table (whose fields are now in method)
- 04:32 PM Revision 1029: vegbien.sql: Replaced stratumtype, stratummethod with method
- 04:25 PM Revision 1028: vegbien.sql: Attach method to aggregateoccurrence instead of taxonoccurrence
- 04:20 PM Revision 1027: vegbien.sql: Removed methodtrait* tables and added first-class method attributes as first-class fields of method. Removed *method tables from the ERD that will be replaced by method.
- 04:04 PM Revision 1026: vegbien.sql: Removed location.dsgpoly because it is now locationdetermination.footprintgeometry_dwc
- 03:59 PM Revision 1025: VegBIEN mappings: Remap to new locationdetermination fields
- 03:44 PM Revision 1024: VegBIEN: Renamed location.reallatitude,reallongitude to centerlatitude,centerlongitude to reflect that it's now a value calculated from the centroid of the current locationdetermination
- 03:35 PM Revision 1023: vegbien.sql: locationdetermination: Reordered fields
- 03:32 PM Revision 1022: vegbien.sql: locationdetermination.coordsaccuracy: Added comment with units
- 03:29 PM Revision 1021: vegbien.sql: locationdetermination: Added determination status columns from taxondetermination
- 03:20 PM Revision 1020: vegbien.sql: locationdetermination: Added coordinates-related fields
- 03:08 PM Revision 1019: VegX-VegBIEN mapping: Include the datasource name (now provided by map in /_ignore/inLabel) in the appropriate places in both VegX and VegBIEN
- 02:47 PM Revision 1018: bin/map: Removed metadata values feature since the syntax used was causing problems with mappings starting with a ":", and metadata can instead be stored as attributes of the primary key's mapping
02/16/2012
- 06:07 PM Revision 1017: xml_dom.py: Fixed bug in parent() where it didn't account for NodeParentIter's first element returned being the current node, not its parent. Refactored parent() to use parentNode directly, and NodeParentIter to use parent(), instead of the other way around.
- 05:38 PM Revision 1016: xml_dom.py: Fixed bug in parent() where incorrect variable name was used
- 05:05 PM Revision 1015: VegX-VegBIEN mapping: Use the input data source's label (e.g. SALVIAS) everywhere a reference is needed
- 05:04 PM Revision 1014: bin/map: Store the input data source's label (e.g. SALVIAS) in the output XML tree for use by references in the mappings
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