schemas/util.sql: added array_length(anyarray), which does not require a second dimension argument

lib/sql_io.py: put_table(): documented that PostgreSQL 9.1+ now provides a way to implement insert/on duplicate select just once for each table (instead of dynamically for each insert) using the new INSTEAD OF triggers (http://www.postgresql.org/docs/9.1/static/plpgsql-trigger.html). INSTEAD OF triggers were not used when put_table() was developed, because it was necessary to support PostgreSQL 9.0, which was installed on the Mac and not easily upgradeable. it was eventually upgraded to add PostGIS, which required a complete reinstall of the DB from the staging tables, with the associated staging table reload bugs, as well as complete removal of the old Postgres version.

inputs/Madidi/: switched to new-style import

schemas/VegCore/VegCore.ERD.mwb: regenerated exports

schemas/VegCore/VegCore.ERD.mwb: categories: fixed position of place to match where it now is in the diagram. lined up boxes so that there is a visible line between the place- and occurrence-related categories.

inputs/Madidi/IndividualObservation/map.csv: translated 1:many mappings ( FieldFamilyFullName->{family,originalFamily} ) to derived columns (in postprocess.sql) to work with new-style import, which must have a 1:1 relationship between input and output columns

schemas/util.sql: added reset_col_names(), the counterpart to set_col_names(). note that this alters the map table, so it will need to be repopulated after running this function.

schemas/util.sql: mk_derived_col(): support using this function to overwrite an existing column (i.e. as a general-purpose function to perform in-place update with ALTER COLUMN TYPE USING)

lib/sh/db.sh: psql(): display stack traces and DETAIL sections of error messages at verbosity 2+, to help debugging (previously they were always turned off). in particular, the DETAIL section of a "duplicate key value violates unique constraint" error is useful because it contains the duplicated key.

inputs/.TNRS/: switched to new-style import. because this does not have data subdirs (data comes from the TNRS client), this is just a matter of adding ./run.

inputs/.TNRS/Source/: switched to new-style import. this had been missed when all the Source/ subdirs were batch-switched to new-style import.

inputs/*/*/map.csv: replaced /_first filter with mapping to DUPLICATE special term (VegCore.vegpath.org?DUPLICATE). this removes collisions that don't need a postprocessing formula to combine the columns.

inputs/Madidi/map.csv: removed filters on columns from before the refresh (which are not in active use), so that they don't show up in a search for map.csvs with filters (indicating collisions)

inputs/Madidi/IndividualObservation/map.csv: SeniorCollector: don't prepend it to the CollectorString because the CollectorString already contains it. this may be a change between the BIEN2 and refreshed Madidi data (which uses a significantly different schema).

mappings/VegCore.htm: regenerated from wiki. Special terms: added instructions for adding a distinguishing suffix to each special term in the format special_term#suffix. this is needed for new-style import to make the resulting column name unique within the staging table.

mappings/VegCore-VegBIEN.csv: mapped DUPLICATE to nothing so that it would not be treated as an unmapped term

mappings/VegCore.htm: regenerated from wiki. Special terms: added DUPLICATE.

/README.TXT: Maintenance: regenerate mappings/VegCore.csv: commit command: use single quotes ' instead of double quotes " to avoid needing to \-escape every special char (single quotes ' still need to be escaped)

mappings/VegCore.htm: regenerated from wiki. moved UNUSED, PRIVATE underneath OMIT as subterms.

mappings/VegCore.htm: Regenerated from wiki

bugfix: bin/*: spell out [:alnum:] as [a-zA-Z0-9] because Python unfortunately doesn't support character classes

web/links/index.htm: updated to Firefox bookmarks. moved Linux, Mac into Unix folder. added instructions to remove old Linux kernels, which fill up the /boot partition. added instructions to force sed to use raw binary mode instead of UTF-8 when UTF-8 is set in the environment. added methods of implementing DB disk space quotas in Postgres. added comparison on my Mac's CPU (2.66 GHz Intel Core i5) with vegbiendev's (2.44 GHz AMD Phenom X4). my Mac's seems to be much faster, so it might make sense to check that the Thor CPUs are faster than the Vis Lab computers' CPUs the next time it gets upgraded. (these diffs can be seen in WinMerge with Moved block detection on. see /README.TXT > WinMerge setup for details.)

inputs/bien_web/observation/VegBIEN.csv: regenerated now that *_index dummy columns have been removed

inputs/.TNRS/schema.sql: tnrs_populate_fields(): updated runtimes. it now takes 25 min instead of 16 min to regenerate the derived cols.

inputs/IRMNG/_README.TXT: added note that when refreshing this datasource, remember to regenerate the TNRS derived cols using the instructions in inputs/.TNRS/schema.sql > tnrs_populate_fields()

bin/*: replaced confusing regexp constructs involving \W inside [] with the much clearer explicit character class [:alnum:] . this avoids adding or subtracting from an inverted class in order to reach a subset of the corresponding positive class, because the subset can just be named explicitly instead.

bugfix: bin/repl: doesn't make sense to use other chars in a [^\W_] regexp, because they will have no effect since \w doesn't include the other chars to begin with. this is a result of confusion with the ^ and \W double negative.

lib/runscripts/table.run: postprocess(): propagate the $remake flag to remake_VegBIEN_mappings using self_make, so that a remake=1 on postprocess will cause map.csv to be regenerated as it would for a remake=1 directly on remake_VegBIEN_mappings

bugfix: postprocess(): moved $can_test flag from import() to this function because it is used here

lib/runscripts/table.run: import(): moved postprocessing commands to separate postprocess() function that can be invoked on an already-imported staging table to avoid running the load_data() target. this is especially useful when running the postprocessing on a working copy without the unversioned data files, for datasources whose load_data() target would otherwise try to download the files because they don't already exist.

lib/runscripts/table.run: postprocess(): renamed to custom_postprocess() since this runs only the datasource's custom postprocessing commands, not all the postprocessing commands including map_table, mk_derived

lib/runscripts/util.run: added , function, which treats each of the command-line args as commands the way make does (instead of as args to the same command, the way runscripts do)

lib/sh/util.sh: moved runscript-related commands to lib/runscripts/util.run because these only apply to runscripts

bugfix: inputs/*/*/map.csv (e.g. inputs/GBIF/raw_occurrence_record_plants/map.csv): remapped author to scientificNameAuthorship rather than authors, which it had gotten incorrectly automapped to. note that the VegCore term authors has now been renamed to data_authors to avoid ambiguity, but incorrect automappings resulting from it had not yet been fixed.

bugfix: inputs/GBIF/raw_occurrence_record_plants/run: updated herbaria.ih column names for staging table column renaming

bugfix: inputs/GBIF/table.run: need to include lib/runscripts/mysql.table.run instead of table.run (table.run was accidentally substituted when inputs/.NCBI/table.run was copied to all new-style datasources

backups/Makefile: %.backup/restore: documented runtime (11 h; ~5 h to insert data). note that this is still much shorter than re-running column-based import.

planning/workflow/bien3_architecture.pptx: exported from bien3_architecture.odp, as requested by Martha. the .pptx format is buggy and doesn't show the slide thumbnails on the slide notes view, but will have to do as .ppt (the older MS PowerPoint format) doesn't support the graphics.

planning/workflow/bien3_architecture.odp: added wiki page notes (wiki.vegpath.org/2013-06-20_conference_call, wiki.vegpath.org/2013-06-27_conference_call) in the slide notes

planning/workflow/bien3_architecture.odp: added responses to the red-highlighted questions (from e-mails to the list) in the slide notes

planning/timeline/timeline.2013.xls: fixed formatting: removed internal cell borders in spacer lines

added planning/workflow/bien3_architecture.odp with changes from Skype call with Martha, which include wiki page notes (wiki.vegpath.org/2013-06-20_conference_call) about the refactor-in-place method in the Notes area

planning/timeline/timeline.2013.xls: updated with changes from Skype call with Martha

inputs/*/ which do not contain any explicit collisions (wiki.vegpath.org/2013-06-27_conference_call#To-do-for-Aaron > #3.2 > the following datasources ...): switched to new-style import, which adds the staging table column renaming

inputs/newWorld/: switched to new-style import, which adds the staging table column renaming. these tables are used by the public schema (schemas/vegbien.sql), so the renamings are applied there as well.

inputs/bien_web/bien_web.schema.sql: regenerated using bin/my2pg, to remove the *_index dummy columns so they don't create lots of OMIT#... staging table columns

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

bugfix: inputs/input.Makefile: Staging tables installation: $(allInstalls): don't filter out Source table, because it is now an installed table rather than just a mapping

bin/filter_out_ci, lib/maps.py: simplify(): also remove distinguishing #... suffix from terms (e.g. UNUSED#institutionID), to support mapping multiple columns to the special terms OMIT, PRIVATE, UNUSED (VegCore.vegpath.org#Special-terms), without creating a collision in the staging table renaming. note that this change must not be made to bin/canon, because this would cause suffixed terms to be autorenamed to their *un*suffixed VegCore versions.

backups/Makefile: $(restore): added --verbose to display pg_restore's incremental progress

bugfix: inputs/newWorld/newWorldCountries/postprocess.sql: use UPDATE statement (followed by VACUUM ANALYZE to remove dead tuples) instead of in-place update (ALTER COLUMN TYPE USING), so that the statement can be run even after the public schema has been installed and its views use the columns. (a view using the columns would normally block an ALTER COLUMN TYPE statement on a referenced column.)

bugfix: lib/runscripts/table.run: remake_VegBIEN_mappings(): when remaking, do not remake header.csv, because it should keep the original CSV columns rather than being reset to whatever the current staging table columns happen to be. to force-regenerate this, instead delete it first and then run remake_VegBIEN_mappings(). remake mode will now just regenerate map.csv from header.csv, in case map.csv's columns are incomplete or out of order.

bugfix: lib/runscripts/table.run: remake_VegBIEN_mappings(): when remaking, do not remake header.csv, because it should keep the original CSV columns rather than being reset to whatever the current staging table columns happen to be. to force-regenerate this, instead delete it first and then run remake_VegBIEN_mappings(). remake mode will now just regenerate map.csv from header.csv, in case map.csv's columns are incomplete or out of order.

bugfix: lib/runscripts/table.run: map_table(): do not rename view columns, since their column names come from their (column-renamed) joined tables rather than from a map.csv. header.csv, map.csv for views will generally become out-of-date whenever the joined tables change, so it is better not to generate them at all.

lib/runscripts/table.run: added $is_view

lib/runscripts/table.run: added $postprocess_sql to store postprocess.sql path, and use it in postprocess()

bugfix: lib/sh/local.sh: prevent automated tests when the public schema contains the live DB, so the user doesn't have to explicitly specify can_test= when running the import on vegbiendev

bugfix: lib/runscripts/table.run: import(): allow automated tests (remake_VegBIEN_mappings) to be disabled by setting can_test= if the public schema shouldn't be modified (e.g. if it's the live DB)

bugfix: inputs/*/*/postprocess.sql: made all operations idempotent, so that postprocess.sql can be run repeatedly (e.g. by new-style import)

schemas/util.sql: create_if_not_exists(): also suppress "multiple primary keys are not allowed" error

added inputs/newWorld/iso_code_gadm/.map.csv.last_cleanup

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

inputs/input.Makefile: Staging tables installation: %/install: run %/map_table at end to rename the staging table columns for new-style datasources

inputs/input.Makefile: Staging tables installation: added %/map_table to run the new-style import staging table renaming

inputs/bien2_traits/TraitObservation/map.csv: removed no longer needed mappings of dummy columns to OMIT, which were creating an unnecessary collision of staging table column names

inputs/bien2_traits/bien2_staging.schema.sql: regenerated from MySQL version so that dummy columns (which used to be generated by bin/my2pg) will be replaced with dummy CHECK constraints instead. this avoids needing to map several dummy columns all to OMIT, which was creating an unnecessary collision of staging table column names.

bin/my2pg*: keep MySQL indefinite dates as text strings instead of translating them (to the first of the month or year) to fit into a PostgreSQL timestamp. this allows the application to decide how to handle these values, which otherwise have no corresponding value in PostgreSQL. this requires changing the date/time related types to text instead of leaving them as-is, so that they can store the custom MySQL strings.

planning/timeline/timeline.2013.xls: Geoscrubbing: made it a subtask of Adding derived columns. moved it to July so that it can be run for Naia's new project.

planning/timeline/timeline.2013.xls: reordered tasks approximately in priority order (which corresponds to the month(s) in which they are scheduled). indented subtasks under their parent tasks.

planning/timeline/timeline.2013.xls: crossed out completed rows and moved them to the bottom

planning/timeline/timeline.2013.xls: use different-style checkmark because LibreOffice doesn't display the font of the previous one correctly anymore (it may already have been displayed incorrectly on other people's computers)

planning/timeline/timeline.2013.xls: Reload existing data in need of refresh: added Oct because Rick Condit is supposed to provide us with a CTFS refresh that we would be allowed to use (he wouldn't let us use the 2011-4-1 full-DB export)

planning/timeline/timeline.2013.xls: continuous tasks: populated past months

planning/timeline/timeline.2013.xls: added Sep, Oct months and moved tasks into them. moved continuous tasks to separate section at bottom to avoid confusion with discrete tasks.

planning/timeline/timeline.2013.xls: use bullet points (•) instead of background shading to indicate future tasks. this allows cells to easily be cleared by pressing Backspace, rather than having to copy a white-background cell on top of the cell.

planning/timeline/timeline.2013.xls: use 3-letter months to make room for more months

planning/timeline/timeline.2013.xls: added missing tasks: switching to new-style import, importing to normalized VegCore, adding derived columns

planning/timeline/timeline.2013.xls: removed alterate-row color highlighting because it makes it difficult to reorder rows or insert new rows in the middle

bin/my2pg: use util.sh $top_dir instead of setting $selfDir

bin/my2pg*: use the util.sh sed wrapper, which fixes the LANG=*.UTF-8 "illegal byte sequence" errors on invalid UTF-8

/Makefile: mysql-Linux: also install mysql-workbench, for use in modifying the VegCore ERD. (note that it has to be modified on Linux, because the Linux and Mac versions of MySQL Workbench position the lines differently.)

/README.TXT: Maintenance: to backup files not in Time Machine: removed VirtualBox VMs because they are now in Time Machine, and do not need to be backed up separately

/README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: added steps to upload just the VirtualBox VMs

bugfix: /README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: added overwrite=1 so that old snapshots, etc. are also deleted

/README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: use better bin/sync_upload instead of put

/README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: removed no longer needed inplace=1, because the VirtualBox VMs now all use a snapshot covering the full disk, so that the full disk is not altered (removing the need to optimize backing up a large file) and just the diff files need to be backed up each time

bugfix: lib/sh/util.sh: sed: must use alias instead of function because function causes segfault in redir() subshell when used with make.sh make() filter (may be bug in bash?). this involves translating `unset LANG` to `env LANG=` (`env -u` to unset a var isn't supported on Mac, but fortunately sed treats LANG="" the same as unset LANG).

archived planning/goals/BIEN3_derived_data_products.docx and replaced with symlink to new BIEN_3_derived_data_products_NormalizedDB_only.docx

added planning/goals/BIEN_3_derived_data_products_NormalizedDB_only.docx from Brad's e-mail

bugfix: lib/sh/util.sh: sed: unset LANG to avoid "illegal byte sequence" errors on invalid UTF-8 for LANG=*.UTF-8. these occur e.g. with MySQL data that is in Latin-1.

lib/sh/util.sh: sed: use function instead of alias so that env can be set up before calling sed

planning/workflow/bien3_architecture.pptx: updated to Martha's revised version from 2013-7-3

lib/runscripts/table.run: map_table(): run map_table repeatedly until no more renames are made: added command to do this

lib/runscripts/table.run: map_table(): documented that collisions may prevent all renames from being made at once. if this is the case, map_table must be run repeatedly until no more renames are made. collisions may result if the staging table gets messed up (e.g. due to missing input columns in map.csv).

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

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.

bugfix: populated empty inputs/IUCN/European_Red_List_Plants/header.csv

inputs/CTFS/*/map.csv: added *.src.row_num from joined tables so that the map.csv input columns would match the staging table. this is needed for the staging table column renaming, which is positional rather than name-based to work with any existing column name.

bugfix: inputs/input.Makefile: map.csv and derived files: use $(tables) instead of $(importTables) when making them so that the mappings of those tables are still kept up-to-date even though they are marked _no_import (and not imported into the main DB)

inputs/CTFS/*/test.xml.ref: regenerated. these got out of date because even though these tables are included in import_order.txt, they are marked as _no_import, which prevents map.csvs and derived files from being kept up-to-date.