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).
bugfix: bin/boldify: also match [[]]-style links at the beginning and end of a line
bin/boldify: made it idempotent
bugfix: bin/boldify: fixed extended regular expression syntax, which doesn't support a \] inside [] (you instead have to put the ] right after the opening [^ )
added bin/boldify, which makes Redmine links bold
bugfix: bin/map: in_is_db: don't ignore errors when the table does not exist, because these prevent an errexit and allow an import to continue when a staging table is missing. suppressing this error had previously been necessary because metadata-only tables (Source/) used to not have installed staging tables, and the program had to react accordingly.
bugfix: bin/pg_dump_limit: support errexit by ignoring the nonzero exit status that grep returns when it doesn't match anything
bin/make_analytical_db: don't regenerate family_higher_plant_group from the NCBI data because the lookup table is now prepopulated as part of the schema
bin/import_all: don't import NCBI because the lookup table is now prepopulated as part of the schema
bugfix: bin/import_all: run in errexit mode, so that if the user cancels reinstalling of the import schema, the script will then abort instead of continuing and using the wrong schema
bin/map: support param start="", which indicates the default value. this fixes a bug in inputs/input.Makefile $(restart_row), which outputs "" if an explicit starting row is not found.
bugfix: bin/with_all: @inputs default value: use `local`, so that the default value is only set for the current function and doesn't leak back out into the caller. this fixes a bug in subset imports where import_all's Source/import call to with_all would add the .* datasources, but these would then stay in for the import_scrub call, causing extra .* datasources to incorrectly be imported.
bin/make_analytical_db: removed no longer needed setting of $schema to $public, because this is now done by psql()
bugfix: bin/import_all: restore the working dir when main() is done, in case it started as something other than the root dir
bin/after_import: support turning off the end-of-import backup for imports that are not the full database
bugfix: bin/make_analytical_db: when running into a public schema other than "public", also pass this to `/run export_` (which currently uses $schema instead of $public)
bugfix: bin/import_all: fix $ when .-included without args (which causes bash to put the wrong values in $ instead of leaving it empty)
when .-included without args (which causes bash to put the wrong values in $
bin/import_all: `make schemas/$version/install`: reinstall instead to allow re-running the import to the same custom schema (e.g. 2013-10-18.Brian_Enquist.Canadensys)
bin/import_all: `make schemas/$version/install`: ignore errors if schema exists, to support running with -e
bugfix: bin/import_all: removing inputs/.TNRS/tnrs/tnrs.make.lock: use `"rm" -f` instead of plain "rm" to avoid having an error exit status, which will abort the script if run with the -e flag (as runscripts are)
bin/*_all: *_main(): renamed to just main() because it does not matter that other shell-includes' main() methods will clobber this, because it is only executed once
bugfix: bin/import_all: Source tables: use .../import instead of import_temp because import_temp is only needed when importing all tables, to prevent the temp suffix from being removed yet
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
bugfix: bin/import_all: need to publish datasources that won't be published by `make .../import`, so that the per-datasource import XPaths that refer to TNRS/geoscrub will link up with the TNRS/geoscrub source entry instead of creating a new entry without the metadata (because the entry with the metadata was named TNRS.new/geoscrub.new)
bin/import_all: removed no longer needed import of geoscrub data, because analytical_stem_view is now joined to the geoscrub_output table directly, instead of using the imported canon_place entries
bin/with_all: $all: renamed to $hidden_srcs for clarity, since this now just adds the hidden (.*) datasources, rather than always using all datasources
bugfix: bin/with_all: in $all mode, just prepend the .* datasources to the user-selected (or default) @inputs, so that using $all to add these datasources doesn't inadvertently cause the action to be performed for all datasources
bin/import_all: usage: documented that this can now be run with a custom datasources list (each of the form inputs/src/)
bin/with_all: added support for providing a custom list of inputs to run the command on
bin/import_all: use just import_scrub, not reimport_scrub, because import_scrub now automatically publishes the datasource's import (i.e. removes the temp suffix)
bin/map: usage: documented that verbosity > 3 in commit mode turns on debug_temp mode, which creates real tables instead of temp tables
bugfix: bin/import_all: use reimport_scrub instead of import_scrub so that the temp suffix of the datasource name is removed
bugfix: bin/after_import: run backups/fix_perms right after the backup files are created to make them private
bugfix: bin/make_analytical_db: `/run export_`: don't take input from the terminal, because this causes rm to prompt the user (from a background task) about overwriting the previous export
bin/map: allow user to override the source env var, which is used as the source.shortname value in the DB
bugfix: bin/import_all: `rm inputs/.TNRS/tnrs/tnrs.make.lock`: need to use `"rm"` instead of `rm` so that we don't use any rm alias the user might have in their shell (import_all is run in the calling shell so that the jobs are owned by the calling shell)
bin/import_all: added step to remove any leftover TNRS lockfile (previously done manually)
bin/tnrs_db: add entry to new batch table
bugfix: bin/import_times: filtering out the Source subdirs: need to match 1 at the beginning of the line only
bin/import_times: filter out the Source subdirs, which now have single-row data and therefore are included in the rowcounts list
bin/after_import: usage: documented that it requires $version
bin/import_all: use new bin/after_import
added bin/after_import, which performs post-normalized-import actions separately from bin/import_all
bin/import_all: with_all import_scrub: documented that this step uses $by_col, so that users know to include by_col=1 when running this step separately
bin/import_all: use column-based import (by_col=1) by default, instead of requiring the user to explicitly specify it. instead turn it off explicitly (by_col=) for row-based import.
bin/import_all: don't set $dump_opts until running the backup command that uses it, so that the user can run this backup command separately just by copying the line out of the script (without worrying about env vars that need to be set, other than $version which is visible outside the script)
bin/my2pg: use s!...!...! when either the regexp or the replacement contains / , to avoid unnecessary \-s
bin/my2pg: commenting out table options: added explanatory comment, because it is not obvious from the regexp what this does
bin/my2pg: comment out table options (http://dev.mysql.com/doc/refman/5.5/en/server-sql-mode.html#sqlmode_no_table_options) instead of removing them, because they include table COMMENTs, which contain important metadata such as table definitions. (note that table COMMENTs use a slightly different syntax than column COMMENTs, so the table COMMENTs will not be commented out twice.)
bin/my2pg: comment out COMMENTs instead of removing them so that they will be included in the PostgreSQL translation. COMMENTs contain important metadata about columns, such as definitions and the meanings of integer flag values.
bin/my2pg: added instructions for regenerating *.schema.sql whenever this script is changed
bin/my2pg: COMMENT: also match COMMENTs with embedded ', because there will only be one COMMENT per line, so the contents of the COMMENT can just extend to the last ' on the line
bin/my2pg: replace MySQL ` quotes with " quotes to support exports that were generated without ANSI_QUOTES mode. (this replacement only applies to schema exports, not data.) ANSI_QUOTES is only available with mysqldump --compatible modes that also include NO_TABLE_OPTIONS, which omits important table options such as comments. in particular, these comments are part of schemas/VegCore/VegCore.ERD.mwb but were not being included in VegCore.my.sql.
bugfix: bin/repl: text mode: repurpose this to match SQL identifiers, for use by inputs/input.Makefile %/postprocess.sql. %/postprocess.sql is the only place currently using this mode, so this will not affect other scripts.
bugfix: bin/*: spell out [:alnum:] as [a-zA-Z0-9] because Python unfortunately doesn't support character classes
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.
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.
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.
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
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
bugfix: bin/map: in_is_db: inline metadata value columns (used by new-style import) so that they can be compared by value in XML simplifying functions (lib/xml_func.py)
bin/map: map_table(): Resolve prefixes: combined db_xml.ColRef() constructor call with creation of args (as tuple) for clarity
bin/map: update_in_label(): use in_schema instead of the map spreadsheet column name when available, to allow using one spreadsheet for all datasources (which would not have a datasource-specific spreadsheet column name)
bin/src_map: support custom (or no) new_term_prefix. no new_term_prefix is useful for views whose columns have already been renamed in the underlying tables and should not have * re-prepended.
bin/make: moved $make_filter_active test to lib/sh/make.sh make() so that it's also used when make() is run directly (e.g. in a runscript) rather than via the bin/make wrapper in the PATH
bugfix: bin/make: use separate $make_filter_active flag instead of $is_outermost for avoiding duplicate output filtering, so that an outer runscript, which sets $is_outermost but does not activate the make filter, will not prevent the make filter from being activated when make is invoked
bugfix: bin/make: need to use sys_cmd instead of command so that the system make command is invoked instead of the wrapper (which would cause infinite mutual recursion for the ~/bien working copy, although not for the ~/Dropbox/svn working copy because nonrecursive=1 was able to remove the single recursion)
bin/make: use .rel to do relative includes
bugfix: bin/make: do not alter the PATH passed to the invoked make command, since this is a general-purpose wrapper and is not linked to a specific working copy (it could be used to wrap any make invocation, not just for commands in the svn dir). this uses lib/sh/local.sh's new PATH_add= flag.
bugfix: bin/make: need to leave bin/, ~/bin/ in the PATH when running make nonrecursively, so that commands invoked by it which are located in these dirs (e.g. put, which will be used by `make inputs/upload`) can still be found. this requires using command()'s new nonrecursive=1 flag instead of running no_PATH_recursion, so that no_PATH_recursion() only affects the resolution of the command path, but does not propagate the filtered PATH to the invoked command itself.
added bin/.rsync_ignore with filters from /README.TXT > Maintenance > to synchronize vegbiendev, jupiter, and your local machine. these filters will now be used with bin/sync_upload in addition to the periodic backup commands.
bin/tnrs_db: documented total runtime (10 days)
bin/tnrs_db: documented current runtime (162 ms/name)
bin/make_analytical_db: use new mk_table() instead of TRUNCATE/INSERT
bin/make_analytical_db: added mk_table() and use it in mk_analytical_table()
bin/make_analytical_db: added `/run export_` to make the geoscrub_input CSV export
added bin/sync_upload, a wrapper around sync_upload()
bugfix: bin/make: use verbosity_compat because some make-invoked commands (e.g. bin/map) don't support verbosity=""
bugfix: bin/make: include local.sh so that its default verbosity-setting make() override will be used
bin/repl: added unescape_html() filter function, which can be specified as the replacement string
bin/repl: support Unicode characters in the matched portion of the string
bugfix: bin/make: use standard make logging port (1) instead of $log_fd (30) so that the output of bin/make can in turn be filtered by util.sh using the standard cmd_log_fd=1
bin/make: use `readlink -f` on BASH_SOURCE0 so that this script can also be run via a symlink
bin/make: don't print make cmd by default, so that only `make` output is printed at verbosity 1
bin/make: don't reinvoke make() if the make filter has already been set up, as indicated by $is_outermost (instead, invoke make directly using exec)
added bin/make, which runs make, hiding verbose messages about making included Makefiles. this should be used in preference to plain make, to avoid excessive log messages that prevent the user from seeing the core commands that are being run.
bin/tnrs_db: documented how to estimate total runtime. note that our tnrs_db wrapper in inputs/.TNRS/tnrs/tnrs.make uses inputs/.TNRS/tnrs/logs/tnrs.make.log.sql as the log file.
bin/tnrs_db: removed unused imports
bin/tnrs_db: cumulative_tnrs_profiler: use tnrs.tnrs_request()'s new cumulative_profiler param instead of doing the profiling manually. this also ensures that there isn't extra time between when the cumulative profiler starts/stops and when the per-request profiler starts/stops (because Profiler's new add_subprofiler() method is used).
bin/tnrs_db: tnrs_profiler: renamed to cumulative_tnrs_profiler to distinguish it from the tnrs_profiler used by tnrs.tnrs_request(), which just profiles the current request
bugfix: bin/tnrs_db: cumulative profiler: use len(names) instead of this_ct (cur.rowcount) in case the actual # rows fetched differed from the rowcount
lib/tnrs.py: repeated_tnrs_request(): renamed to tnrs_request() since this is the function that should usually be used, to ensure that debugging information is output in the case of an error. (the TNRS request must be made again to output this information.)
bin/tnrs_db: removed no longer used $wait flag (which caused tnrs_db to wait max_pause for new rows to be added), because tnrs_db is now invoked automatically after each import by the import_scrub target (in inputs/input.Makefile) and does not need to run as a daemon. note that when scrub is invoked, it is possible that a previous datasource's import has already scrubbed the names for this import, because tnrs_db runs until all rows in tnrs_input_name are scrubbed....
bin/tnrs_db: removed no longer needed explicit population of the Time_submitted, which is now done automatically by the tnrs table. however, this requires starting the transaction before submitting data, so Time_submitted is correctly set to the submission time rather than the insertion time. the setting of the correct time can be tested by inserting `time.sleep(n_sec)` after the TNRS request and checking that the Time_submitted is close to the time tnrs_db was run instead of n_sec seconds later.
bin/tnrs_db: start transaction before submitting data, so Time_submitted is correctly set to the submission time rather than the insertion time. these may differ by several minutes if TNRS is slow. the setting of the correct time can be tested by inserting `time.sleep(n_sec)` after the TNRS request, removing the explicit setting of Time_submitted, and checking that the Time_submitted is close to the time tnrs_db was run instead of n_sec seconds later.
bugfix: bin/tnrs_db: wrap just the TNRS request and the storing of the response data in a function (undoing part of r9514), because the transaction start time for Time_submitted should not be until the TNRS request is actually made (it often takes several minutes to materialize the next set of input names on a full DB)
