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# Date Author Comment
14454 08/11/2014 03:40 AM Aaron Marcuse-Kubitza

bugfix: mappings/VegCore-VegBIEN.csv: prefixed taxonomic ranks: use _concat_nullify() so that the prefix is only added if the epithet is non-NULL

14076 07/15/2014 10:07 PM Aaron Marcuse-Kubitza

inputs/TEX/Specimen2/test.xml.ref: updated

13401 05/03/2014 02:03 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: add: verify/: also svn:ignore *.log

12886 03/24/2014 05:35 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: specimenreplicate.institution_id: renamed to duplicate_institutions_sourcelist_id, as decided in the conference calls (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2)

12879 03/24/2014 01:49 AM Aaron Marcuse-Kubitza

mappings/VegCore.htm: regenerated from wiki: rename specimenHolderInstitutions to specimen_duplicate_institutions, as decided in the 2014-03-13 conference call (wiki.vegpath.org/2014-03-13_conference_call#schema-changes-2). note that most schema changes (such as this one) involve mappings changes, which are handled automatically by `inputs/run postprocess; yes|make inputs/{NVS,SALVIAS,TEAM}/test`.

12018 02/02/2014 12:49 AM Aaron Marcuse-Kubitza

inputs/input.Makefile: add!: verify/: also svn:ignore *.tsv, *.txt

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).

11924 12/20/2013 12:28 AM Aaron Marcuse-Kubitza

fix: inputs/TEX/Specimen*/map.csv, postprocess.sql: habitat: also placed in occurrenceRemarks so that this field gets parsed for growth form information, as requested by Brad (wiki.vegpath.org/TEX_validation#2013-2-26)

11923 12/19/2013 11:49 PM Aaron Marcuse-Kubitza

fix: inputs/TEX/Specimen*/map.csv: mapped constant values for specimenHolderInstitutions, country. these have to be added with `rm=1 ./inputs/TEX/Specimen.../run postprocess`.

11922 12/19/2013 11:42 PM Aaron Marcuse-Kubitza

bugfix: inputs/TEX/Specimen2/map.csv: mapped BARCODE to accessionNumber so that we have a unique ID for each row

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

11107 09/29/2013 08:58 PM Aaron Marcuse-Kubitza

bugfix: mappings/VegCore-VegBIEN.csv: nest all taxonoccurrences inside a stratum event, so that the parent locationevent is always fully populated before child locationevents point to it. (previously, a stub parent event was created when the child event was imported first, which blocked the fully-populated parent event from being inserted later on.) this uses auto-folding (for VegBank/CVS) and auto-forwarding (for other datasources) to prune empty stratum events for taxonoccurrences that don't have strata. (see wiki.vegpath.org/Auto-folding, wiki.vegpath.org/Auto-forwarding for more info about these normalization techniques.) note that the inserted row counts stay exactly the same for all datasources except VegBank (which was being fixed), indicating that this signficant change to the mappings did not change the semantics of the import of taxonoccurrences.

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

10625 08/07/2013 04:51 PM Aaron Marcuse-Kubitza

inputs/TEX/: switched to new-style import, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource

10624 08/07/2013 04:44 PM Aaron Marcuse-Kubitza

inputs/TEX/Specimen2/: translated new multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns

10623 08/07/2013 04:41 PM Aaron Marcuse-Kubitza

bugfix: inputs/TEX/Specimen2/map.csv: DETERMINER FIRST NAME/LAST NAME: combined using _join_words() instead of the default _alt()

10622 08/07/2013 04:20 PM Aaron Marcuse-Kubitza

inputs/TEX/Specimen2/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns

10621 08/07/2013 04:13 PM Aaron Marcuse-Kubitza

inputs/TEX/Specimen2/map.csv: MISC NOTES: remapped to locationRemarks since these primarily relate to the coords. PLANT DATA: remapped to occurrenceRemarks since this is the specimenDescription.

10620 08/07/2013 03:15 PM Aaron Marcuse-Kubitza

inputs/TEX/Specimen/: translated multi-column filters to postprocessing derived columns, using the steps at http://wiki.vegpath.org/Adding_new-style_import_to_a_datasource#Translating-filters-to-postprocessing-derived-columns

10257 07/11/2013 12:09 PM Aaron Marcuse-Kubitza

inputs/*/*/map.csv: added distinguishing #... suffix (e.g. UNUSED#institutionID) to the special terms OMIT, PRIVATE, UNUSED (VegCore.vegpath.org#Special-terms) to avoid creating a collision in the staging table renaming

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

10209 07/10/2013 02:32 AM Aaron Marcuse-Kubitza

inputs/*/*/map.csv for CSV tables with a row_num column: 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

10200 07/09/2013 05:26 PM Aaron Marcuse-Kubitza

bugfix: inputs/TEX/Specimen/header.csv: generated from staging table (was empty previously)

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.

10192 07/09/2013 01:04 AM Aaron Marcuse-Kubitza

bugfix: inputs/*/Source/: added missing ./run, which creates the new-style staging tables with the metadata fields as part of the table. this is needed now that these subdirs use installed staging tables instead of metadata-only map.csvs.

10179 07/06/2013 05:39 PM Aaron Marcuse-Kubitza

inputs/*/: added table.run for use by the table subdirs in new-style import. datasources without table subdirs do not need this.

10177 07/06/2013 05:17 PM Aaron Marcuse-Kubitza

inputs/*/: added top-level Makefile which includes inputs/input.Makefile, so that make can be run directly on the datasrc dir without needing to specify `--makefile=../input.Makefile` (see input.Makefile $(selfMake))

10170 07/06/2013 02:26 PM Aaron Marcuse-Kubitza

bugfix: inputs/*/Source/: use installed staging table (with blank-line data.csv) in order to also work with new-style import. this also fixes a benign diff between the by-row and by-col test outputs, where row-based import would not import the Source/ entries because there was not at least one row in the input. note that in order to ensure that all datasources are properly run, you need to check `svn st|sort` against the datasource schema names to see if any are missing.

10109 06/28/2013 04:54 PM Aaron Marcuse-Kubitza

empty inputs/*/import_order.txt: added subdirs in the order they are used by inputs/input.Makefile, by running make on the inputs to auto-populate import_order.txt. import_order.txt is needed by the runscripts to run the right set of subdirs in the right order.

10091 06/27/2013 12:28 PM Aaron Marcuse-Kubitza

added inputs/*/*/header.csv for CSV inputs, which are now generated by inputs/input.Makefile %/install

9882 06/12/2013 10:49 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: genus->taxonlabel.taxonomicname: filter out genera that contain numbers (using new _filter_genus()), which break TNRS and prevent it from matching any other parts of the name. later, these genera can instead be moved to the end of the name, where TNRS will correctly match them as Unmatched_terms.

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.)

7799 02/28/2013 03:29 PM Aaron Marcuse-Kubitza

inputs/TEX/Specimen2/map.csv: _join() PLANT DATA and MISC NOTES to form occurrenceRemarks instead of _alt()ing them

7798 02/28/2013 03:27 PM Aaron Marcuse-Kubitza

inputs/TEX/Specimen2/test.xml.ref: Accepted test

7716 02/26/2013 05:47 PM Aaron Marcuse-Kubitza

mappings/VegCore.htm: Regenerated from wiki. Remapped organismNotes to be a synonym of occurrenceRemarks, since notes on an organism are more generally notes on an occurrence.

7713 02/26/2013 05:19 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped occurrenceRemarks

7712 02/26/2013 04:53 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Only use one of collection and collectionURL instead of concatenating them when both are provided (as requested by Brad <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Spot-checking#ACAD&gt;)

7681 02/26/2013 01:35 PM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: Mapped latitude/longitude_DMS to coordinates.latitude_deg using new _dms_to_dd(text)

7670 02/26/2013 10:42 AM Aaron Marcuse-Kubitza

inputs/TEX/Specimen/map.csv: Remapped LAT/LONG_DEGREES,MINUTES,SECONDS to new latitude/longitude_deg,min,sec, allowing the DMS coordinates to be translated

7657 02/26/2013 08:43 AM Aaron Marcuse-Kubitza

Added inputs/TEX/