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: 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.
bugfix: inputs/CTFS/*/VegBIEN.csv: regenerated from map.csv. they may have gotten out of date because they are marked as _no_import, even though they are in import_order.txt.
bugfix: added missing inputs/MO/Specimen/header.csv
bugfix: added missing inputs/QFA/Specimen/header.csv
bugfix: inputs/TEX/Specimen/header.csv: generated from staging table (was empty previously)
added inputs/newWorld/iso_code_gadm/header.csv
added inputs/analytical_db/table.run
bugfix: inputs/VASCAN/Taxon/map.csv: added missing row_num column added by bin/csv2db
lib/sql_io.py: cleanup_table(): added assertion that the table exists, so that if it doesn't, the error will occur as part of an assertion rather than as part of the util.table_nulls_mapped__get() call, which might confusingly lead users to believe that this is a bug in util.table_nulls_mapped__get() when in fact the problem is that the table is not installed
fix: inputs/import.stats.xls: removed spurious diff comment on total time, which only applied to the previous import
inputs/import.stats.xls: reformatted times longer than one day as a # of days instead of hours, for clarity. the days format is chosen automatically when the # hours exceeds one day.
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.
bin/map: removed no longer used support for map.csv input column prefixes (expand out the prefixes instead). this used to be used by SpeciesLink to use just one mapping for a single term with multiple DwC namespaces, but was replaced with an explicit, ordered rather than implicit, unordered /_alt-ing together of the terms.
bin/map: removed no longer accurate comment that this is case- and punctuation-insensitive, since the case- and punctuation-insensitivity is now instead handled by map.csv preprocessing scripts before the mappings are even provided to bin/map
inputs/.herbaria/: switched to new-style import, which renamed the columns to the VegCore names. this is done using the commands at wiki.vegpath.org/2013-06-27_conference_call#To-do-for-Aaron > "run the following for each datasource".
lib/sql_io.py: cleanup_table(): don't run the slow ALTER TABLE statement again if the table has already been cleaned up. documented that it is idempotent (and actually was before this change as well).
lib/sql_io.py: added table_nulls_mapped__set(), "__get() wrappers around the corresponding util schema functions
lib/sql_gen.py: added table2regclass_text()
schemas/util.sql: added table_nulls_mapped__get(), which gets whether a table's NULL-equivalent strings have been replaced with NULL
schemas/util.sql: added table_flag__get(), which gets whether a status flag is set by the presence of a table constraint
schemas/util.sql: added table_nulls_mapped__set(), which sets that a table's NULL-equivalent strings have been replaced with NULL
schemas/util.sql: added table_flag__set(), which stores a status flag by the presence of a table constraint
schemas/util.sql: create_if_not_exists(): also ignore duplicate_object exceptions, thrown when trying to add a duplicate constraint
inputs/input.Makefile: %/postprocess: removed no longer used invocation of $*/import (precursor to the runscripts used in FIA)
inputs/*/: added table.run for use by the table subdirs in new-style import. datasources without table subdirs do not need this.
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))
added inputs/test_taxonomic_names/Taxon/header.csv
