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# Date Author Comment
11970 01/20/2014 11:33 AM Aaron Marcuse-Kubitza

moved everything into /trunk/ to create the standard svn layout, for use with tools that require this (eg. git-svn). IMPORTANT: do NOT do an `svn up`. instead, re-use your working copy's existing files with `svn switch` (http://svnbook.red-bean.com/en/1.6/svn.ref.svn.c.switch.html).

11396 10/21/2013 07:14 PM Aaron Marcuse-Kubitza

fix: bin/map: put template: comment out the "Put template:" label so that the output is valid XML, and displays properly in a browser rather than showing a syntax error

10866 09/04/2013 11:06 PM Aaron Marcuse-Kubitza

inputs/*/*/test.xml.ref: updated source.shortname for new datasource name, which now starts out with .new suffix

10242 07/10/2013 10:07 PM Aaron Marcuse-Kubitza

inputs/*/Source/VegBIEN.csv: regenerated for new-style import, which uses a symlink to mappings/VegCore-VegBIEN.csv instead of a custom mapping using the original column names

10199 07/09/2013 04:44 PM Aaron Marcuse-Kubitza

bugfix: inputs/*/Source/map.csv: added missing row_num entry, which is needed by the staging table column renaming to make the order of the map.csv columns match the order in the staging table. the staging table column renaming is now used by all Source tables.

10174 07/06/2013 03:55 PM Aaron Marcuse-Kubitza

bugfix: inputs/input.Makefile: %/VegBIEN.csv: for new-style datasources, use a symlink to mappings/VegCore-VegBIEN.csv directly instead of prefiltering VegCore-VegBIEN.csv to include only the columns in map.csv. prefiltering used to be performed as part of mapping the map.csv VegCore output terms to VegBIEN using bin/join, but is no longer needed because the staging table columns are now VegCore terms. instead, the full VegCore-VegBIEN.csv is needed so that derived columns added in stage I or II validations are detected by bin/map (rather than just the original source columns in map.csv).

10166 07/06/2013 11:29 AM Aaron Marcuse-Kubitza

bugfix: inputs/*/Source/data.csv for new-style datasources: need to include a blank row (plus a blank header) so that the metadata values are imported at least once instead of zero times, now that there is an installed staging table that will be iterated over. the blank row did not used to be necessary, because db_xml.put_table() has a special case for metadata-only tables with no installed table, which avoids iterating over the table's rows.

10163 07/03/2013 10:20 PM Aaron Marcuse-Kubitza

inputs/*/Source/ for new-style datasources: use an actual staging table instead of a metadata-only table, so that metadata values can be stored in the staging table instead of the map.csv (as will be required by new-style import)

10050 06/26/2013 07:54 AM Aaron Marcuse-Kubitza

added blank runscripts inputs/GBIF/Source/run, Specimen/run because they are in import_order.txt (used by lib/runscripts/datasrc_dir.run)

8801 05/02/2013 08:53 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files

8176 03/25/2013 09:01 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: %/.map.csv.last_cleanup: Run fix_line_endings after canon/translate to standardize Python's \r\n line endings back to \n. This prevents issues with mixed line endings because LibreOffice (and probably Excel) treat all cell-internal line endings as \n but row line endings as whatever the file had, while text editors like jEdit translate all line endings to whatever the autodetected line ending is. (This creates spurious line ending diffs when a map spreadsheet containing multiline cells is edited in a text editor.)

7646 02/22/2013 08:17 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Documentation has been added on how to choose term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming) and how to form globally unique ID values (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Forming-IDs). Source and Specimen terms have been renamed to be self-explanatory and unambiguous (the DwC equivalents remain as synonyms). Short definitions of Source terms have been added to explain the differences between them. Source, Specimen, and Collection terms have been shortened according to the new instructions for choosing preferred term names (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/VegCore#Naming).

7469 02/05/2013 04:32 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv, inputs/*/*/map.csv: Applied term renamings from the new dynamically generated Veg+-VegCore.csv, which reflects the current state of the data dictionary. (Permanently switching to the new Veg+-VegCore.csv will be a separate change.) Updates to VegCore term names that have occurred since the data dictionary was created are now able to take effect, which involves remapping and inferring units on several fields.

6788 12/11/2012 10:40 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed sampletype to observationtype to match the VegCore term

6777 12/11/2012 08:32 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: Renamed sampletype to observationtype to match the VegCore term

6774 12/11/2012 08:01 AM Aaron Marcuse-Kubitza

mappings/VegCore.csv: Renamed sampleType to observationType to match the SALVIAS term it's derived from

6756 12/11/2012 04:37 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Don't forward specimenreplicate IDs to location for plots data (where the specimenreplicate IDs apply only to the specimen)

6509 11/30/2012 05:09 PM Aaron Marcuse-Kubitza

inputs/*/Source/map.csv for non-herbaria: Mapped sampleType

6409 11/24/2012 08:29 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: source table mappings: Set shortname to env var $source when it's not explicitly specified, because shortname is a required field of source

6406 11/24/2012 07:50 AM Aaron Marcuse-Kubitza

db_xml.py: put(): _setDefault(): Support setting multiple col_defaults at once by using the param names themselves as the column names

6403 11/24/2012 07:29 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Set the source_id col_default to the datasource name using the new _setDefault() built-in function and _env()

6393 11/24/2012 05:41 AM Aaron Marcuse-Kubitza

Added inputs/GBIF/Source/, containing referenceType metadata