lib/table.run: template: import(): Also pass "$@" to superclass method

lib/table.run: template: Use "$FUNCNAME" instead of hardcoding import

Added inputs/GBIF/MySQL_export, used by ./table.run

lib/util.run: echo_func: Fixed bug where need to use BASH_LINENO⁰ for the line #s to match up with the files. For some reason the required array indexes for BASH_SOURCE (1) and BASH_LINENO (0) differ by one.

inputs/GBIF/run: Use new import.run, which defines all()

lib/table.run: Use new import.run, which defines all()

Added lib/import.run

lib/util.run: echo_func: Include the line # of the function to make it easier to find where the code being run is

lib/table.run: Added all (default target)

lib/util.run: run_cmd: If bash exited with an error, don't run the "$@" command. This test is necessary because `trap run_cmd EXIT` will run run_cmd as the result of any exit from the shell, including an error.

*run: Use -e option to bash on the #! line instead of separate `set -o errexit` line so that there is no issue with the `set -o errexit` line getting separated from the #! line (errexit is required for the scripts to work properly)

lib/util.run: run_cmd: When no command specified, default to running the `all` command, just like make

lib/util.run: Run run_cmd at shell exit (using trap) instead of requiring every runscript to have `run_cmd ` at the end of it

Added inputs/GBIF/run

Added inputs/GBIF/raw_occurrence_record/run

Added inputs/GBIF/table.run

Added inputs/GBIF/_MySQL/run

lib/util.run: fwd: Check that $subdirs is defined. Added $subdirs to usage.

lib/util.run: fwd: Added usage

lib/table.run: Switched from echo_run to echo_func

lib/util.run: run_cmd: Echo the command being run, including the top-level run script. This is in addition to the echoing of the command in the function itself (using echo_func), which provides both the runscript that was run and the file where the invoked command was actually located (which may be different due to includes).

lib/util.run: Echo the command at the beginning of each function using new echo_func, instead of having to type echo_run before every call to a function. Note that because echo_func uses BASH_SOURCE, the path to the file containing the function will be included in the debug message, which greatly facilitates locating which file a command is in.

lib/util.run: Added echo_func

lib/util.run: Added echo_cmd and use it in echo_run

lib/util.run: echo_cmd(): Renamed to echo_run for clarity, because it also runs the command

lib/util.run: Added inline_make()

lib/util.run: Added echo_stdin()

bin/my2pg_export: Put --password first because it's an authentication-related option

Added lib/table.run, which includes the commands in import.sh but uses run scripts to allow running commands other than just import. (For example, map_table or postprocess can be run separately. Uninstall-related commands which would not belong in an import script can also be added, because import is only one of many commands a run script can offer.)

Added lib/util.run with general functions and template for run scripts (a bash-based replacement for make). Unlike make, run scripts support full bash functionality including multiline commands. The run script template also includes syntax for various kinds of relative includes in bash.

lib/common.Makefile: Added $(require_var)

bin/publish_analytical_db: Fixed bug where need to remove `ESCAPED BY '"'` because this would causing " followed by an escape sequence char to be interpreted specially (e.g. "n -> \n). MySQL automatically takes care of quote doubling when you specify `FIELDS OPTIONALLY ENCLOSED BY`.

lib/common.Makefile: Compression: Added `%:: .gz`, `.gz: %`

planning/workflow/import_process_comparison.odg: Moved "staging tables" under the method labels to reduce empty space

planning/workflow/import_process_comparison.odg: Removed margins so the labels would align with the page margin on the Import process wiki page <https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/Import_process>

Added planning/workflow/import_process_comparison.odg and .png export

lib/db_xml.py: put_table(): Fixed bug where command to advance start to fetch next set was unintentionally deleted when removing the is_view check

inputs/UNCC/Specimen/new_terms.csv: Updated for updated VegCore vocab

inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql.md5: Regenerated after appending agent table to GBIFPortalDB-2013-02-20.data.sql

Added inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql.gz.md5

Added inputs/GBIF/raw_occurrence_record/ from refresh

inputs/GBIF/MySQL.schema.sql: Regenerated with inline enum type translated to CHECK constraint

bin/my2pg: Translate inline enum type to CHECK constraint

Added inputs/GBIF/**/MySQL.schema.sql

Added inputs/GBIF/_MySQL/MySQL.*.sql.make

inputs/FIA/: Archived no longer used subdirs from BIEN2 export

inputs/FIA/: Archived no longer used subdirs from BIEN2 export

inputs/input.Makefile: SVN: add: Removed Source/map.csv prerequisite because it is not related to adding unversioned files in the dir. It was originally a prerequisite in order to auto-create it when the datasource dir is first created, but the map.csv recipe does not currently create metadata-only map.csvs. In the future, metadata-only map.csvs will be replaced with constant columns added to the applicable tables.

Added inputs/FIA/_archive

inputs/input.Makefile: %/map.csv: Fixed bug where can only make header.csv if map.csv does not exist, because some subdirs are metadata-only and don't have a corresponding DB table

README.TXT: Datasource setup: Install the staging tables: For a MySQL .sql export: Documented which password to use at each of the two password prompts my2pg_export will give you. You could also embed the value of the 2nd prompt in the _MySQL/*.make file using `--password="$(cat path/to/config/bien_password)"`.

README.TXT: Datasource setup: Install the staging tables: Removed requirement that `make inputs/<datasrc>/reinstall quiet=1 &` be run on vegbiendev for MySQL .sql exports, because the hostname is now set to vegbiendev instead of localhost

inputs/input.Makefile: sql/install: Use psql_script_vegbien instead of $(psqlNoSearchPath) (which uses psql_verbose_vegbien) because the insert statement for each data row should not be echoed

inputs/FIA/occurrence_all/import: Run remake_VegBIEN_mappings at end to keep mappings to next stage of import process up to date

inputs/FIA/occurrence_all/: Accepted new test output

lib/import.sh: remake_VegBIEN_mappings(): Also remake VegBIEN.csv and test.xml.ref use `make test`

lib/import.sh: Added remake_VegBIEN_mappings()

inputs/input.Makefile: %/map.csv: make $*/header.csv first in case it doesn't exist (e.g. if it has been deleted so that it will be remade)

inputs/FIA/occurrence_all/map.csv: Regenerated using new input table mappings

lib/import.sh: Added make() and use it instead of the full make command

inputs/input.Makefile: postprocess: Use %/postprocess instead of %/postprocess.sql/run so $*/import is also run

inputs/FIA/: Ran inputs/FIA/import. This maps to VegCore's commonName.

inputs/input.Makefile: %/postprocess: Also run the $*/import script, if it exists. Note that this is not the same as the %/import make target.

inputs/input.Makefile: %/postprocess.sql/run: Factored out into separate %/postprocess command, which can eventually also perform other actions

inputs/FIA/PLOT/map.csv: ELEV: Remapped to elevation_ft, assuming units based on the actual elevation of the region for a sample plot record

inputs/VegBank/taxonobservation_/map.csv: Mapped int_currplantcommon to vernacularName

mappings/VegCore.htm: Renamed salvias_plots table plotMetadata to PlotMetadata because of SALVIAS refresh on nimoy

mappings/VegCore.htm: Regenerated from wiki. Added flower, fruit, commonName.

mappings/Makefile: $(vocab); bin/redmine_synonyms: Support crossed out (deprecated) terms

README.TXT: Maintenance: VegCore data dictionary: Added steps to update the data dictionary's Tables section if necessary

inputs/GBIF/_MySQL/Makefile: %.data.sql: Added agent table

Added inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.data.sql.md5

Added inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.schema.sql

Added web/main/svn*/, now using .htaccess to forward to Redmine/*

Removed web/main/svn, svn-web symlinks because they need to be .htaccess-es in order for the relative mod_rewrite commands to work correctly

Added web/main/svn, svn-web symlinks to Redmine/* for shorter URLs

Added web/main/Redmine/svn-web/

inputs/GBIF/: Added scripts for subsetting refresh

lib/sql.py: table_order_by(): Documented that it returns None if table is a view, because table_cluster_on() would return None. This is necessary for inputs/FIA/occurrence_all/ sorting to work correctly, because specifying a manual sort order would prevent the query planner from just using fast nested loop joins and instead cause it to perform a slow sort. (This appears to be a bug in the query planner, because when the column list specified matches the joined-on indexes, there should be no need for post-nested loop re-sorting.)

inputs/FIA/occurrence_all/test.xml.ref: Updated inserted row count for new row sort order

lib/db_xml.py: put_table(): Fixed bug where also need to advance start to fetch next set when table is a view, because the views that are now being used with the import (inputs/FIA/occurrence_all/) are static rather than dynamic and do not return different rows after the previous set of rows has been imported

inputs/FIA/occurrence_all/import: Removed no longer applicable comment that directional joins are needed for PostgreSQL query planner to avoid slow sorts

inputs/FIA/TREE/import: Reclustered table by TREE.parent path index, to facilitate path-order joins

inputs/FIA/occurrence_all/import: Changed all RIGHT JOINs to inner joins so that tables would be joined in path order (i.e. general->specific). This optimizes the incremental joins so that the small tables are joined to each other before being joined to the large tables, rather than each row of the large tables being looked up in the small tables. This effect may not be noticeable for small LIMIT values, but would become apparent for large LIMIT values, such as the 1-million-row partitions used by db_xml.put_table() for column-based import. Note that inner joins used to cause the query planner to produce incorrect results containing slow sorts, but now this appears to no longer be an issue, perhaps because the result is not sorted by the TREE.ID index (which is not in the same order as the path indexes *.unique, *.parent).

inputs/FIA/occurrence_all/import: Removed trailing whitespace

Removed unused inputs/FIA/COND_unique/. Use COND instead.

inputs/FIA/import: Use `set -o errexit` instead of putting ` || exit` after each command

lib/import.sh: map_table(): Removed unneeded () around psql. This also fixes a bug where an error exit status from psql would not have aborted the script because `set -o errexit` does not apply to commands enclosed in (). For () you need to use ` || exit` instead (or ` || return` inside a function).

lib/import.sh: Use `set -o errexit` so any command that exits with an error aborts the script. Note that a command's exit status can still be ignored using ` || true`. Removed no longer needed ` || return` in functions.

schemas/util.sql: Renamed rename_if_exists() to try_create() because it can be used to create a column in any way, not just by renaming another column

lib/import.sh: functions: abort if a command encounters an error

schemas/VegCore/mk_derived: Added cultivated from oldGrowth

schemas/util.sql: Added try_mk_derived_col()

inputs/FIA/*/import: Run mk_derived after postprocessing commands

inputs/FIA/import_order.txt: Added occurrence_all/

mappings/VegCore-VegBIEN.csv: subplotID,subplot -> location.sourceaccessioncode: Fixed bug where need /_first to handle the case where both subplotID and subplot are provided

Added inputs/FIA/map.csv, which maps shared columns to VegCore

inputs/FIA/FIA_COND_unique/test.xml.ref: Updated now that PLOT, CONDID have been mapped

inputs/FIA/*/map.csv for pre-refresh tables: Added back * before unmapped column names

lib/csvs.py: stream_info(): Fixed bug where headers with multiline columns were not supported because only the first line (not the first multiline row) is sniffed for the dialect