Activity
From 04/24/2013 to 05/23/2013
05/23/2013
- 11:40 PM Revision 9550: lib/sh/util.sh: $sed_cmd: don't use `command`, which causes sed calls (which are usually internal) to always be logged. instead, use echo_run wherever sed needs to be logged.
- 11:38 PM Revision 9549: lib/sh/util.sh: echo_run(): added trailing-space alias to alias-expand next word, which is a command
- 11:31 PM Revision 9548: lib/sh/binsearch.sh: binsearch(): echo $i at log_level 1 so it's displayed by default, as a progress indicator
- 11:30 PM Revision 9547: lib/sh/binsearch.sh: binsearch(): echo $i at log_level 1 so it's displayed by default, as a progress indicator
- 11:29 PM Revision 9546: lib/sh/binsearch.sh: binsearch(): echo the command being run using new echo_run()
- 11:25 PM Revision 9545: lib/sh/util.sh: log+: set PS4 from $log_level instead of relative to its previous value. this allows PS4 to work properly at negative log_levels, in spite of the inability to store a "negative" value in a prefix string.
- 11:23 PM Revision 9544: lib/sh/util.sh: added float_set_min()
- 11:22 PM Revision 9543: lib/sh/util.sh: log+(): log_level: set it using simpler $(()), since log_level will never be fractional (although verbosity can be). log_level may of course be fractional in invoked scripts, but that does not affect util.sh.
- 10:44 PM Revision 9542: lib/sh/util.sh: log++: also track a numeric log_level var, which follows the PS4 prefix
- 10:35 PM Revision 9541: inputs/.TNRS/schema.sql: MatchedTaxon: matchedFamily: use Accepted_family when the Name_matched_accepted_family is not provided, as it's omitted by the current TNRS CSV schema
- 09:54 PM Revision 9540: lib/sh/util.sh: log+(): PS4: split if statement onto multiple lines for clarity
- 09:44 PM Revision 9539: lib/sh/util.sh: added back echo_run(), usable for internal commands where command() would be used for external commands
- 09:33 PM Revision 9538: lib/sh/util.sh: added int2bool()
- 09:25 PM Revision 9537: *{.sh,run}: use new `|| ignore` instead of ignore_e/end_try
- 09:25 PM Revision 9536: lib/sh/util.sh: added ignore(), which uses ||-syntax
- 09:13 PM Revision 9535: lib/sh/util.sh: ignore(): renamed to ignore_e() so ignore() can be used for a simpler, ||-based command
- 09:09 PM Revision 9534: bugfix: lib/sh/util.sh: catch(): need && between test and e=0 so e=0 is only run if $e was equal to the desired value
- 08:22 PM Revision 9533: added lib/sh/binsearch.sh
- 06:27 PM Revision 9532: bugfix: README.TXT: Full database import: screen: need to unset TMOUT, version *after* running `screen` rather than before so they take effect within the `screen` shell
- 06:25 PM Revision 9531: README.TXT: Full database import: after running `screen`: run `set -o ignoreeof` to prevent Ctrl+D from exiting `screen` to keep attached jobs
- 04:40 PM Revision 9530: 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.
- 03:33 PM Revision 9529: inputs/.TNRS/schema.sql, data.sql: updated TNRS CSV columns to preserve Name_matched_accepted_family even though it isn't present in the current TNRS CSVs. this way, Name_matched_accepted_family can still be used for previously-scrubbed names, and family_matched can be added back to analytical_stem_view. (now that bin/tnrs_db uses an explicit columns list in COPY TO, the absence of a column in the CSV is no longer a problem.)
- 03:28 PM Revision 9528: README.TXT: updating TNRS CSV columns: use the entire "COPY tnrs ..." statement instead of just the body of it so that the explicit columns list is included. this way, the COPY statement will cause an error if the TNRS schema was changed but inputs/.TNRS/data.sql was not yet updated.
- 03:00 PM Revision 9527: bin/tnrs_db: removed unused imports
- 02:55 PM Revision 9526: 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).
- 02:53 PM Revision 9525: lib/tnrs.py: single_tnrs_request(): added support for a cumulative profiler using the cumulative_profiler kw param
- 02:53 PM Revision 9524: lib/profiling.py: Profiler: added add_subprofiler(), for use with cumulative profilers
- 02:48 PM Revision 9523: lib/profiling.py: Profiler: added add_time() and use it instead of `self.total +=`
- 02:38 PM Revision 9522: 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
- 02:36 PM Revision 9521: 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
- 02:32 PM Revision 9520: 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.)
- 02:30 PM Revision 9519: lib/tnrs.py: tnrs_request(): renamed to single_tnrs_request() to distinguish it from repeated_tnrs_request()
- 02:25 PM Revision 9518: 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.
- this also removes clutter in tnrs_db, making it clearer what operations it performs that the library function tnrs.re...
- 02:14 PM Revision 9517: 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.
- 02:09 PM Revision 9516: 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.
- 02:05 PM Revision 9515: 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)
- 01:56 PM Revision 9514: bin/tnrs_db: Iterate over unscrubbed verbatim taxonlabels: put loop body in a function (which returns whether or not the loop should continue), so that the loop body can easily be wrapped in a transaction using sql.with_savepoint()
- 01:19 PM Revision 9513: inputs/.TNRS/schema.sql: tnrs.Time_submitted: set default to now() (the timestamp of the start of the current transaction, http://www.postgresql.org/docs/9.1/static/functions-datetime.html) so that it would automatically be populated when rows are added. note that because the start of the current transaction instead of the exact time at insertion is used, all rows inserted in the same transaction (e.g. as part of the same batch) will have the same value for this, linking them together.
- 01:10 PM Revision 9512: inputs/.TNRS/schema.sql: tnrs_populate_derived_fields(): renamed to tnrs_populate_fields() so it can be used to populate other fields as well
- 01:07 PM Revision 9511: bin/tnrs_db: removed no longer needed explicit appending of derived cols, and instead use append_csv()'s new support for importing CSVs whose columns are a subset of the full table
- 12:56 PM Revision 9510: bin/tnrs_db: ColInsertFilters: use the simpler literal value option for the mk_value param
- 12:55 PM Revision 9509: lib/csvs.py: ColInsertFilter: support using a literal value instead of a function for the mk_value param, since this is the most common use case
- 12:43 PM Revision 9508: lib/sql_io.py: append_csv(): support importing CSVs whose columns are a subset of the full table and/or in a different order. when the header exactly matches the columns, the explicit column list will still be omitted as an optimization. this uses code from r4927.
- 12:15 PM Revision 9507: bugfix: lib/runscripts/util.run: need to include sh/make.sh for all runscripts that use make-style commands
- 12:12 PM Revision 9506: *{.sh,run}: use new top_make instead of `make --directory="$top_dir"`
- 12:11 PM Revision 9505: lib/sh/make.sh: added top_make()
- 11:54 AM Revision 9504: inputs/import.stats.xls: Postprocessing: populated entries for analytical DB for last 4 imports, and for backup, backup test for last import. note that the combined import time for the last import is 3.5 days, compared to 3 days for the column-based import portion.
05/22/2013
05/21/2013
- 11:18 PM Revision 9502: inputs/GBIF/Specimen/postprocess.sql, inputs/REMIB/Specimen/postprocess.sql: updated for providers in r9459, which adds TEX
- 11:10 PM Revision 9501: inputs/*/*/postprocess.sql: Remove institutions that we have direct data for: query to obtain list: updated for current schema
- 10:49 PM Revision 9500: inputs/import.stats.xls: Updated import times. GBIF has been refreshed (with the range modeling column subset), and column-based import now takes 3 days for 88.4 million rows.
- 10:27 PM Revision 9499: README.TXT: Full database import: added warning to perform *every single* step listed, to avoid breaking column-based import
- 10:26 PM Revision 9498: README.TXT: Full database import: Publish the new import: added warning to be sure you have done *every single* verification step before proceeding. otherwise, a previous valid import could incorrectly be overwritten with a broken one.
- 09:07 PM Revision 9497: bugfix: README.TXT: Full database import: To run TNRS/remake analytical DB: need to run `export version=<version>` *before* the command which uses it rather than after
- 08:26 PM Revision 9496: added backups/*.md5
- 08:22 PM Revision 9495: added backups/TNRS.2013-5-21.backup.md5
- 07:42 PM Revision 9494: README.TXT: Datasource setup: For MySQL inputs: For .sql exports: added steps to grant privileges to the bien user. the privileges list *excludes* UPDATE, DELETE, ALTER, DROP to prevent bugs in the import scripts from accidentally deleting data.
- 07:37 PM Revision 9493: inputs/.TNRS/schema.sql, data.sql: updated for new TNRS CSV columns (see bug at https://pods.iplantcollaborative.org/jira/browse/TNRS-183). note that these columns may eventually change back (comment by Naim at https://pods.iplantcollaborative.org/jira/browse/TNRS-183#comment-34444).
- 07:33 PM Revision 9492: README.TXT: Full database import: added steps to check that TNRS ran successfully, and fix errors (due to column changes in the TNRS CSV) if it didn't
- 07:24 PM Revision 9491: inputs/test_taxonomic_names/test_scrub: use sh's -e (errexit) mode so errors in an invoked script cause the script to abort instead of burying the error in more output
- 07:19 PM Revision 9490: inputs/test_taxonomic_names/test_scrub: documented that `make schemas/"$public"/uninstall` removes the previous results (since it may be confusing why it's prompting the user to uninstall the schema that is an output of the program)
- 07:16 PM Revision 9489: inputs/test_taxonomic_names/test_scrub: don't need to run the import twice anymore because the accepted names are now included in the tnrs_input_name view that TNRS runs on
- 07:09 PM Revision 9488: inputs/test_taxonomic_names/test_scrub: updated for current TNRS schema
- 06:47 PM Revision 9487: bugfix: inputs/test_taxonomic_names/test_scrub: unset $n so it doesn't limit the # rows. it is set to 2 in the default test environment, so must be unset for n-sensitive programs that should be unlimited.
- 06:40 PM Revision 9486: inputs/test_taxonomic_names/test_scrub: updated for current TNRS schema
- 01:44 PM Revision 9485: inputs/GBIF/raw_occurrence_record/run: herbaria_filter.table/make(): also include the exported plant_fraction herbaria
- 01:43 PM Revision 9484: inputs/GBIF/raw_occurrence_record/run: added herbaria_filter.plant_fraction.csv_/make(), which exports the plant_fraction herbaria whose plant_fraction >= 0.8
- 01:42 PM Revision 9483: inputs/GBIF/raw_occurrence_record/run: added plant_fraction.table/make(), which contains the plant fraction for each herbarium
- 01:37 PM Revision 9482: lib/sh/db.sh: added mk_drop()
- 01:00 PM Revision 9481: lib/sh/util.sh: to_file(): log $stdout so users can tell which file is being created by the command. for some reason, can't use `local redirs=(">$stdout")` because the redirections don't seem to be applied. can't yet use `log+ -2 echo_vars stdout` because log+ does not yet support negative adjustments (they cause PS4 to be emptied out before being re-prepended to).
- 12:54 PM Revision 9480: bugfix: lib/sh/util.sh: log+(): adjustment < 0: need to enclose -$1 in $(()) so it gets evaluated before being used as an array index
- 12:16 PM Revision 9479: lib/sh/local.sh: psql(): documented that --output is actually for query *results*, not echoed statements (and thus must be redirected back to fd 1 while fd 1 with the statements gets sent to the logging port)
- 12:14 PM Revision 9478: lib/sh/local.sh: psql(): documented why can't use fd 11
- 12:09 PM Revision 9477: lib/sh/local.sh: use @redirs instead of manual redirection to set up --output fd, so that the redirection will be echoed along with the command. for some reason, this requires switching to fd 13 instead of 11, because fd 11 gives a "/dev/fd/11: Bad file descriptor" error when 11 is set with exec right before the command instead of on the subshell the command is executed in. (13 was chosen rather than 12 because *2 is for errors, while *3 (or 3*) is for logging.)
- 04:18 AM Revision 9476: bugfix: lib/sh/db.sh: pg_export_table_to_dir_no_header(): inlined $(pg_header) so setting $cols wouldn't affect pg_export_table_no_header(), which uses it as a kw param
05/20/2013
- 10:44 PM Revision 9475: bugfix: lib/sh/util.sh: to_file(): require_not_exists check: missing `test` in `if "$if_not_exists"`
- 10:39 PM Revision 9474: lib/sh/util.sh: command(): log the function call using echo_func to assist debugging. (use a higher log_level because it's internal.)
- 09:29 PM Revision 9473: lib/sh/util.sh: command(): support custom redirections, which will be echoed along with the command
- 08:48 PM Revision 9472: lib/sh/util.sh: to_file(): reworded confusing || conditional for require_not_exists into an if statement
- 08:21 PM Revision 9471: bugfix: inputs/GBIF/raw_occurrence_record/run: herbaria_filter.table/make(): need to use append=1 with mysql_import so the output table doesn't get re-truncated when additional parts are added
- 07:28 PM Revision 9470: bugfix: lib/sh/db.sh: load new aliases before mk_select(), which uses mk_table_esc
- 07:27 PM Revision 9469: lib/runscripts/table.run: include make.sh so runscripts based on it can use make-related utils
- 06:52 PM Revision 9468: lib/sh/db.sh: added mk_select() and use it in mk_select_var
- 06:46 PM Revision 9467: lib/sh/db.sh: added limit() and use it instead of `${limit:+LIMIT $limit}`
- 06:44 PM Revision 9466: lib/sh/db.sh: added mysql_truncate() and use it instead of `mk_truncate|mysql_ANSI`
- 06:42 PM Revision 9465: lib/sh/db.sh: truncate(): renamed to mk_truncate() because it actually just creates a TRUNCATE statement, rather than also executing it
- 06:38 PM Revision 9464: lib/sh/db.sh: use_local/use_remote: unset $prefix after using it so it isn't unintentionally applied as a kw param for a later function
- 04:18 PM Revision 9463: lib/sh/db.sh: mk_select: renamed to mk_select_var since it actually sets a var in the local context rather than returning a query
- 03:40 PM Revision 9462: inputs/GBIF/raw_occurrence_record/run: herbaria_filter.table/make(): specify the different parts used to create the table in an array
- 03:19 PM Revision 9461: inputs/GBIF/raw_occurrence_record/run: renamed herbaria_filter.csv_ to herbaria_filter.ih.csv_ to allow for other tables that get combined into herbaria_filter
- 03:13 PM Revision 9460: bugfix: lib/sh/db.sh: mk_select: ensure newline before LIMIT clause, in case caller provided custom query which did not have trailing newline
05/17/2013
- 06:00 PM Revision 9459: bugfix: mappings/VegCore-VegBIEN.csv: place.geovalid: added missing /1 after _alt
- 05:55 PM Revision 9458: bugfix: lib/sql.py: parse_exception(): typed_name_re: added back matching of names without "", since these are used by some error messages (ones that contain () after the function name)
- 05:41 PM Revision 9457: bugfix: lib/sql.py: parse_exception(): typed_name_re: need to allow " within the matched name, since there are now "" around the entire identifer that was passed to Postgres, which may itself include " . always require "" around the matched name, to ensure that the whole name is matched by .+? e.g. when followed by () for a function call. the version of Postgres we currently use apparently no longer has error messages without the "", so we don't need a separate regexp for quoted and unquoted names.
- 03:43 PM Revision 9456: lib/sh/db.sh: mysql_import(): automatically ensure the table is empty (i.e. using truncate()), unless append=1 is specified. extra calls to truncate() now that this happens automatically have also been removed.
- 01:13 PM Revision 9455: bin/map: by_col: ensure verbosity is at least 2 in live mode (using new ints.set_min() instead of max() for clarity). documented that live column-based import MUST be run with verbosity 2+ (3 preferred) to provide debugging information for often-complex errors. without this, debugging is effectively impossible.
- 01:08 PM Revision 9454: added lib/ints.py with renamings of max()->set_*min*(), min()->set_*max*() for easier understandability of the set-ceiling/set-floor use cases of min()/max()
- 12:57 PM Revision 9453: bin/map: Set default verbosity: by_col: documented that showing all queries is primarily to assist *debugging*, not profiling
- 11:59 AM Revision 9452: lib/sh/util.sh: logging: named it `log++`
- 11:59 AM Revision 9451: lib/sh/util.sh: logging: verbosities: level 0: documented that log++ also suppresses external command output for full support of cron jobs
- 11:57 AM Revision 9450: lib/sh/util.sh: logging: documented `make` equivalents of the various verbosities, where available. (many of the verbosities, such as level 1, are sorely needed in make to avoid excessive output.)
- # verbosities (and `make` equivalents):
# 0: just print errors. useful for cron jobs.
# vs. make: equivalent to --... - 04:03 AM Revision 9449: lib/sh/util.sh: die_e(): benign errors: increase log_level so that a benign non-zero exit status will only be displayed at debug verbosities (2+) (it is confusing otherwise)
- 03:36 AM Revision 9448: lib/sh/util.sh: try(): always run the command with benign_error=1 so that any die_e() doesn't prematurely indicate that a particular exit status was an error
- 03:34 AM Revision 9447: lib/sh/util.sh: die_e(): support benign errors using $benign_error flag that should be logged as info messages instead of errors
- 03:30 AM Revision 9446: lib/sh/util.sh: die(): documented that msg can't use $() (because it would reset $?)
- 03:19 AM Revision 9445: inputs/bien_web/observation/VegBIEN.csv, unmapped_terms.csv: regenerated
- 03:01 AM Revision 9444: lib/sh/util.sh: command(): 2>&$err_fd: add to _redirs *after* echoing command so it isn't echoed at the end of every command (since this redirection is frequently applied)
- 02:55 AM Revision 9443: lib/sh/util.sh: sed: use case statement instead of test to determine flag letter, to easily allow matching multiple `uname` OSes or adding additional flag letters
- 02:46 AM Revision 9442: lib/sh/util.sh: die(): documented that its msg can use $?, because it has not yet been overridden by another command
- 02:45 AM Revision 9441: lib/sh/util.sh: die_e(): use die(), which performs the necessary save_e/rethrow. this requires using $? instead of $e for the exit status, because $e has not yet been set.
- 02:42 AM Revision 9440: lib/sh/util.sh: inlined log_e() into die_e() because that's the only place it's used
- 02:37 AM Revision 9439: lib/sh/util.sh: command(): print "command exited with error" message using new die_e() if command returns false. this requires removing manual die_e()/log_e() calls elsewhere.
- 02:34 AM Revision 9438: lib/sh/util.sh: command(): moved increase of indent inside () so that error-handling statements after () will use the outer log_level
- 02:31 AM Revision 9437: lib/sh/util.sh: added die_e(), which logs that a command exited with an error
- 02:18 AM Revision 9436: lib/sh/util.sh: command(): determine redirections before echoing the command so they can be logged along with the command, instead of as separate exec statements. (these had a higher log_level to avoid cluttering the output with `exec` lines, which usually suppressed the redirections completely.) inline the command__set_fds() nested func so the redirections are all in one place.
- 01:54 AM Revision 9435: lib/sh/util.sh: use simpler `if can_log; then indent; fi` instead of `can_log && indent || true`. however, the `&& indent || true` syntax is still required in aliases such as echo_func which need to allow prefixing the command with a wrapper command or kw param assignments.
05/16/2013
- 09:28 PM Revision 9434: inputs/GBIF/raw_occurrence_record/run: dynamically generate herbaria_filter.csv_ from herbaria.ih in new target herbaria_filter.csv_/make()
- 09:27 PM Revision 9433: inputs/GBIF/raw_occurrence_record/run: store the herbaria filter in a MySQL table loaded from a CSV instead of getting it from a hardcoded list of IN (...) values
- 09:24 PM Revision 9432: lib/sh/db.sh: added truncate()
- 09:23 PM Revision 9431: lib/sh/make.sh: set_make_vars: set $target_stem
- 08:49 PM Revision 9430: lib/sh/db.sh: added mysql_import()
- 07:02 PM Revision 9429: lib/sh/db.sh: removed no longer used mk_esc_name()
- 07:01 PM Revision 9428: lib/runscripts/table.run: don't mk_esc_name schema, table because these will be mk_esc_name'd by functions that use them
- 06:55 PM Revision 9427: lib/sh/local.sh: psql(): use $schema_esc, $table_esc instead of just putting $schema, $table in ""
- 06:48 PM Revision 9426: lib/sh/db.sh: mk_esc_name_alias(): don't overwrite an already-defined $*_esc, to allow the user to provide an already-escaped value (such as a schema-qualified table) directly
- 06:38 PM Revision 9425: lib/sh/util.sh: rtrim(): increase the log_level of sed to 4+ instead of 2+ because it is usually run as part of a var assignment, and should therefore have a lower log_level than echo_vars
- 06:32 PM Revision 9424: lib/sh/db.sh: mk_esc_name_alias(): echo_vars the *_esc var when it's set
- 06:31 PM Revision 9423: lib/sh/db.sh: added mk_esc_name_alias() and use it to create mk_schema_esc, mk_table_esc
- 05:55 PM Revision 9422: lib/sh/db.sh: mysql(): run with --local-infile=1
- 05:48 PM Revision 9421: bugfix: lib/sh/db.sh: log_sql(): use can_log() instead because the verbosity now gets decremented as the log_level increases, so the threshold to compare to is 0 instead of 2
- 05:46 PM Revision 9420: lib/sh/util.sh: added set_default()
- 05:45 PM Revision 9419: lib/sh/util.sh: rtrim(): run at higher log_level so that sed command is not normally echoed
- 04:40 PM Revision 9418: inputs/GBIF/raw_occurrence_record/run: renamed herbaria.sql to herbaria.data.sql so it wouldn't be added to svn by `make inputs/GBIF/raw_occurrence_record/add` or `make inputs/add`
- 04:38 PM Revision 9417: inputs/input.Makefile: $(svnFiles): also exclude *.data.sql, which should never be in svn
- 04:27 PM Revision 9416: schemas/vegbien.sql: cultivated_family_locations: documented that table is from sftp://nimoy.nceas.ucsb.edu/home/bien/bien2_scripts/geoscrub/cultivated/cult_by_taxon/flag_by_taxa.inc (i.e. not generated by a function)
- 04:15 PM Revision 9415: schemas/vegbien.sql: place.geovalid: added latLongDomainValid to the values to _and together
- 04:09 PM Revision 9414: schemas/vegbien.sql: place.geovalid: require it to be NOT NULL so that it's always a 2-valued boolean (but default it to false since it's not a required field)
- 04:06 PM Revision 9413: mappings/VegCore-VegBIEN.csv: place.geovalid: use false instead of NULL
- 03:46 PM Revision 9412: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): exclude deleted rows (i.e. where the deleted timestamp is non-NULL)
- 03:42 PM Revision 9411: inputs/GBIF/raw_occurrence_record/header.csv: regenerated using ./run. since the table is reimported as a CSV, it uses bin/csv2db, which prepends an additional row_num column.
- 03:09 PM Revision 9410: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): remove explicit cols list to include all cols. the file size of the generated table.tsv will increase by ~3x, but should remain reasonably-sized compared to our available disk space.
- 03:04 PM Revision 9409: bugfix: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): need \ line continuation after vars so they only apply to the command rather than being set as global vars
- 03:02 PM Revision 9408: bugfix: lib/runscripts/table.run: load_data(): use new $verbosity_min instead of running `verbosity_min` so that the command name logging is not output with the new verbosity
- 02:59 PM Revision 9407: lib/sh/util.sh: added $verbosity_min to set a `verbosity_min` value *after* the command name, etc. has been logged, so that the logging itself is not output with the new verbosity
- 02:38 PM Revision 9406: schemas/vegbien.sql: range_modeling_input: include only plants (i.e. rows with higher_plant_group IS NOT NULL)
- 02:36 PM Revision 9405: schemas/vegbien.sql: range_modeling_input: added higher_plant_group, for use in restricting rows to plants
- 02:24 PM Revision 9404: inputs/.geoscrub/geoscrub_output/map.csv: *validity: added definitions of the numeric codes from _src/README.TXT
- 01:11 PM Revision 9403: added planning/workflow/validation/GeoDistKM.sql.txt
- 12:42 PM Revision 9402: planning/goals/BIEN3_derived_data_products.docx: updated to most recent version from Brad's e-mail on 2013-4-16
- 11:18 AM Revision 9401: /README.TXT: Full database import: before running screen: added `unset TMOUT` because TMOUT (autologout) causes screen to exit even with background processes active
- 11:17 AM Revision 9400: /README.TXT: Maintenance: added things to put in your .profile on a live machine (e.g. vegbiendev). in particular, you *MUST NOT* have a TMOUT (autologout) set, because this causes screen to exit even if background processes (e.g. from column-based import) are running
- 11:15 AM Revision 9399: /README.TXT: Maintenance: added things to put in your .profile on a live machine (e.g. vegbiendev). in particular, you *MUST NOT* have a TMOUT (autologout) set, because this causes screen to exit even if background processes (e.g. from column-based import) are running
- 06:15 AM Revision 9398: bugfix: lib/runscripts/table.run: load_data(): need to ensure the verbosity is at least 3 because the install logs require verbose output. (3 is the default for the installer, but is overridden by the runscripts, which instead set the default to 1.)
- 06:13 AM Revision 9397: lib/sh/util.sh: logging: added verbosity_min()
- 06:00 AM Revision 9396: lib/sh/util.sh: logging: added verbosity_int() and use it instead of `round_down "$verbosity"`
- 02:08 AM Revision 9395: bugfix: lib/sh/util.sh: log+ alias: don't expand next word because it's not a cmd
- 01:59 AM Revision 9394: lib/runscripts/table.run: $schema, $table: log the `cd` used to calculate the value at log_level 3 instead of 1 (note that the cd() function call for this will be logged at log_level 5)
- 01:51 AM Revision 9393: lib/sh/util.sh: cd(): trace-log the cd() function call itself (at log_level 3) in addition to the cd builtin call
05/15/2013
- 11:28 PM Revision 9392: lib/runscripts/table.run: import(): added step to load the data into the staging table before postprocessing it
- 11:27 PM Revision 9391: inputs/GBIF/raw_occurrence_record/run: moved table.tsv.md5/make() and invocation of it to inputs/GBIF/table.run because it's general to all tables (which would all use table.tsv for this datasource). use $target_filename in calling table.tsv.md5/make from table.tsv/make.
- 11:21 PM Revision 9390: bugfix: lib/sql.py: parse_exception(): typed_name_re: need to ensure that full name is matched rather than just first character
- 10:26 PM Revision 9389: web/links/index.htm: updated to Firefox bookmarks. Mountain Lion upgrade: added Python psycopg2, Python OrderedDict, X11.
- 07:51 PM Revision 9388: lib/runscripts/table.run: table_make(): run canon_rel_path on the datasrc dir so it's displayed as the direct path to it, without ..
- 07:47 PM Revision 9387: lib/runscripts/table.run: table_make(): moved comment about "${@/#/$table/}" to right after the line it describes
- 07:44 PM Revision 9386: lib/runscripts/table.run: input_make(): renamed to table_make() to make it clear that the target names are relative to the table subdir itself, not the datasrc dir. it was previously called input_make because it used inputs/input.Makefile directly, but now will use any Makefile in the datasrc dir.
- 06:44 PM Revision 9385: added inputs/GBIF/Makefile, which links to ../input.Makefile, to allow running make directly in the datasrc dir (i.e. without --makefile=.../input.Makefile). this is *required* by the runscripts.
- 03:34 PM Revision 9384: inputs/GBIF/raw_occurrence_record/run: table.tsv.md5/make(): don't add extra .md5 extension to $target_filename because it already has the extension as part of the target name (now that this command is run in its own make target rather than in table.tsv/make())
- 03:30 PM Revision 9383: lib/sql_gen.py: import OrderedDict from collections instead of ordereddict for Mac 10.8 Mountain Lion upgrade
- 02:29 PM Revision 9382: lib/sh/util.sh: logging: renamed $log_level_indent to $log_indent_step to avoid confusion with the log_level, which is a different kind of indent (using + signs instead of |s)
- 02:26 PM Revision 9381: lib/sh/util.sh: logging: also export PS4, because it follows verbosity and therefore also needs to be propagated to invoked commands
- 02:21 PM Revision 9380: lib/sh/util.sh: can_log(): support decimal verbosities using round_down()
- 02:21 PM Revision 9379: lib/sh/util.sh: always use echo_export instead of export, even when the verbosity at load time would suppress output, because the verbosity may actually increase during the script due to log-- calls, etc., and vars should then still be echoed as expected
- 02:17 PM Revision 9378: lib/sh/util.sh: log+: inlined PS4_prefix_n alias because there is now room for it
- 02:16 PM Revision 9377: lib/sh/util.sh: log+: $verbosity: support decimal verbosities (but not decimal log_levels) by using new float+int
- 02:13 PM Revision 9376: lib/sh/util.sh: removed no longer used log-. use log+ with a negative argument instead.
- 02:12 PM Revision 9375: bugfix: lib/sh/util.sh: log+: PS4 when $1 < 0: need to negate $1 because now it's a negative number
- 02:06 PM Revision 9374: lib/sh/util.sh: log--: use log+ with -1 instead of log- so we don't need a separate log- function
- 02:04 PM Revision 9373: lib/sh/util.sh: logging: log+: support negative log_level adjustments. log-: use log+ with the negative of its argument
- 01:48 PM Revision 9372: web/links/index.htm: updated to Firefox bookmarks. sorted MySQL and PostgreSQL sections.
- 01:42 PM Revision 9371: web/links/index.htm: updated to Firefox bookmarks
- 01:39 PM Revision 9370: web/links/index.htm: Mac 10.8 Mountain Lion > PostgreSQL: appended tab to name to disambiguate it from the general PostgreSQL section
- 01:33 PM Revision 9369: bugfix: web/links/index.htm.run: prepend __ to the HTML anchors of bookmarks toolbar links so they don't shadow/override folders of the same name: also renamed the corresponding self-anchor hyperlinks
- 01:32 PM Revision 9368: bugfix: web/links/index.htm.run: prepend __ to the HTML anchors of bookmarks toolbar links so they don't shadow/override folders of the same name: need to replace *all* occurrences (using /g option to sed) to include both HTML anchors on the line
- 01:26 PM Revision 9367: web/links/index.htm.run: prepend __ to the HTML anchors of bookmarks toolbar links so they don't shadow/override folders of the same name
- 01:23 PM Revision 9366: lib/sh/util.sh: sed: changed it to an alias so it will also be expanded when passed to an external command (like in_place) that can only run an executable, not a shell function (this occurs as long as the external command is defined as an alias which ends in space, to alias-expand the next word). added associated $sed_cmd var for cases when there is no alias wrapper around the external command, and the literal alias body must be used instead.
- 11:02 AM Revision 9365: lib/sh/util.sh: log+/-(): setting verbosity: added space around operators to support negative numbers
- 10:55 AM Revision 9364: lib/sh/util.sh: added float functions (esp. float+int()) for dealing with decimal verbosities used by sql.py and column-based import
- 10:53 AM Revision 9363: inputs/GBIF/raw_occurrence_record/run: inputs/GBIF/raw_occurrence_record/run: added check_target_exists so you know why make skipped the file (for other, non-silent targets, it would also avoid make's verbose output when the file exists)
- 10:38 AM Revision 9362: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): moved making of table.tsv.md5 to separate function
- 10:30 AM Revision 9361: lib/sh/util.sh: $log_fd: indicated that this is only *initially* stderr (however, the new port will just use stderr if it's not redirected separately)
- 10:28 AM Revision 9360: lib/sh/util.sh: verbosities: 3: added that this includes values of kw params
- 10:25 AM Revision 9359: lib/sh/util.sh: logging: added description of the verbosities available, including what each one does and what it's useful for:
- # verbosities:
# 0: just print errors. useful for cron jobs.
# 1: also external commands run. useful for running at t... - 10:11 AM Revision 9358: lib/sh/util.sh: command__set_fds(): echo the >& line at a higher log_level, because this information (i.e. which fd is used by the command for logging) is primarily for debugging and should not normally be printed
- 10:00 AM Revision 9357: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): also add md5 sum for table.tsv
- 09:50 AM Revision 9356: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): added back filter kw args, which had gotten deleted in a commit without update (although actually, svn should not allow a commit without update, so the working copy may have gotten corrupted)
- 09:27 AM Revision 9355: lib/runscripts/table.run: input_make(): added $silent flag which turns on make's --silent option
- 09:25 AM Revision 9354: lib/sh/make.sh: set_make_vars: usage: added "use $target" to indicate that vars are made available by this alias
- 09:24 AM Revision 9353: lib/sh/make.sh: inline_make(): take the script stdin from caller-provided stdin and get make's stdin from global stdin, so that the caller can just use <<'EOF' rather than having to include a specific fd before the <<
- 08:46 AM Revision 9352: lib/runscripts/table.run: input_make(): documented that it requires a Makefile in the datasrc dir containing `include ../input.Makefile
- 08:41 AM Revision 9351: lib/runscripts/table.run: input_make(): added comment explaining that "${@/#/$table/}" replaces the empty str at the beginning of str (/#) with $table/
- 08:38 AM Revision 9350: lib/runscripts/table.run: put functions on one line where possible
- 08:35 AM Revision 9349: lib/runscripts/table.run: input_make(): use the local make() function instead of external make directly, because it sets $cmd_log_fd appropriately to ensure that all the echoed make commands get properly logged to stdlog/stderr (stdlog is fd 30 when it's redirected to a file)
- 08:22 AM Revision 9348: inputs/GBIF/raw_occurrence_record/run table.tsv/make() and functions used by it: added usage comments for cmd line usage, caller usage, and declaring function usage
- 07:29 AM Revision 9347: web/links/index.htm: updated to Firefox bookmarks
- 07:27 AM Revision 9346: web/links/index.htm: updated to Firefox bookmarks
- 07:00 AM Revision 9345: web/links/index.htm: removed no longer needed - at the beginning of every folder's description
- 07:00 AM Revision 9344: lib/Firefox_bookmarks.reformat.csv: label page's description: don't do this for folders (i.e. descriptions preceded by an <H3> tag) because their descriptions are always author-added rather than from a web page. this avoids needing to add a - at the beginning of every folder's description.
05/14/2013
- 09:43 PM Revision 9343: web/links/index.htm: updated to Firefox bookmarks. upgrading Mac OS X to 10.8 Mountain Lion: put fixes subdirs in order.
- 09:42 PM Revision 9342: web/links/index.htm: updated to Firefox bookmarks. upgrading Mac OS X to 10.8 Mountain Lion: put fixes subdirs in order.
- 08:56 PM Revision 9341: web/links/index.htm: updated to Firefox bookmarks. upgrading Mac OS X to 10.8 Mountain Lion: added fixes for Apache ~/Sites dirs, Apache PHP
- 05:55 PM Revision 9340: web/links/index.htm: updated to Firefox bookmarks. added bookmarks for upgrading Mac OS X to 10.8 Mountain Lion. (WARNING: DO NOT upgrade unless you are prepared to fix several programs broken by the upgrade: svn, PostgreSQL. instructions are in the corresponding bookmark subdirs. these programs will be COMPLETELY UNAVAILABLE until they are manually fixed!)
05/13/2013
- 07:43 AM Revision 9339: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): cols: also include scientific_name, which is preferable as a TNRS input because it also contains lower ranks
- 07:40 AM Revision 9338: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): cols: also include id, institution_code, collection_code, catalogue_number
- 07:38 AM Revision 9337: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): added filter for institution_codes in herbaria.ih (in PostgreSQL)
- 07:19 AM Revision 9336: inputs/GBIF/raw_occurrence_record/run: table.tsv/make(): added column subset (from http://vegpath.org/twiki/bin/view/Main/ConfCall20130509#subsetting_strategy > include)
- 07:14 AM Revision 9335: lib/sh/db.sh: mk_select: constructed queries: in ${var:+if_true} syntax, put the newline at the end of the if_true value instead of the beginning, so that each ${var:+if_true} expression starts at the beginning of a line
- 07:10 AM Revision 9334: lib/sh/db.sh: mk_select: constructed queries: support custom columns list using $cols
- 07:07 AM Revision 9333: lib/sh/db.sh: mk_select: constructed queries: support WHERE clause using $filter
- 06:52 AM Revision 9332: lib/sh/util.sh: echo_stdin(): don' increase the log_level, because the input being sent to the command (which is usually a set of interpreted commands itself) is necessary to fully know what action is being performed
- 06:30 AM Revision 9331: bugfix: lib/sh/local.sh: add a manual errexit for $() exprs by embedding them in just a var assignment (*without* local or declare), whose exit status will then equal the of the $(). a `|| return` also needs to be added because errexit does not work on assignment statements. this commit adds them for func_loc(), echo_func(), canon_rel_path(), set_paths(), save_cache, cached realpath(), local.sh global vars
- 06:14 AM Revision 9330: lib/sh/util.sh: shell-variable-based caching: usage: updated alias names
- 05:33 AM Revision 9329: web/links/index.htm: updated to Firefox bookmarks. regenerating also removed extra <a name=...> tags that were added when running index.htm.run on an already-processed index.htm.
- 05:19 AM Revision 9328: bugfix: lib/sh/util.sh: `set -o`: need a -o before *every* option to set
- 05:10 AM Revision 9327: lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links' names: hyperlink the added anchors as clickable paragraph marks (like Redmine), which take you to the HTML anchor. this is analogous to the clickable folder names which take you to *their* anchors.
- 04:52 AM Revision 9326: lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links' *names*, in addition to their URLs
- 04:47 AM Revision 9325: bugfix: lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links' URLs: use .*? instead of .* to match the contents of the <A> tag before the HREF
- 04:45 AM Revision 9324: lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links using the URL itself as the anchor. these can be used to link to the comments attached *to* a bookmark in the bookmarks page, rather than to the bookmark's destination.
- 04:43 AM Revision 9323: lib/Firefox_bookmarks.reformat.csv: add HTML anchors for external links using the URL itself as the anchor. these can be used to link to the comments attached *to* a bookmark in the bookmarks page, rather than to the bookmark's destination.
- 04:35 AM Revision 9322: web/links/index.htm: updated to Firefox bookmarks
- 04:24 AM Revision 9321: lib/sh/util.sh: `set -o`: added pipefail option, to ensure that exit statuses (esp. for errexit) also work with pipelines (a|b)
- 04:13 AM Revision 9320: lib/sh/util.sh: use new log+ with a numeric arg instead of multiple calls to log++
- 04:06 AM Revision 9319: lib/sh/util.sh: use new log+ with a numeric arg instead of multiple calls to log++. use the command form of log-- (`log-- echo_func`) to counter the normal log++ performed by echo_func, for cases when the function name is descriptive and should be output at the same log_level as the commands it runs.
05/12/2013
- 08:33 PM Revision 9318: *{.sh,run}: removed extra space between function name and ()
- 08:13 PM Revision 9317: lib/sh/util.sh: echo_func(): take the FUNCNAME as an argument (auto-added in the echo_func alias) instead of getting it from the FUNCNAME array (which would have produced an inaccurate value if another function call (such as log++) intervened between the caller and echo_func())
- 08:04 PM Revision 9316: lib/sh/util.sh: echo_func(): display where the function was declared (using new func_loc()) instead of where echo_func() was called from. this is more intuitive when debugging, becaues the line # is where the function starts. it also helps remove the dependency on the FUNCNAME/BASH_* arrays, which would produce an inaccurate value if another function call (such as log++) intervened between the caller and echo_func().
- 07:57 PM Revision 9315: lib/sh/util.sh: added func_loc(), which gets where a function was declared in the format file:line, and helper alias set_func_loc
- 07:09 PM Revision 9314: lib/sh/util.sh: str2varname(): use bash's internal ${var//glob/repl} syntax, which supports character classes ([a-z], etc.), instead of sed (which is slower because it's an external command and uses regexps)
- 07:00 PM Revision 9313: lib/sh/util.sh: added support for caching realpath() using the new shell-variable-based caching. this can be enabled via $realpath_cache and defaults to off because it's currently slower than without. note that the cache needs to be cleared in cd() because relative paths will become invalid.
- 06:48 PM Revision 9312: lib/sh/util.sh: added str2varname() and use it in include_guard_var()
- 06:47 PM Revision 9311: lib/sh/util.sh: added shell-variable-based caching functions
- 05:08 PM Revision 9310: lib/sh/util.sh: canon_rel_path(): use $PWD instead of the slower $(pwd -P) now that $PWD has symlinks expanded
- 05:06 PM Revision 9309: lib/sh/util.sh: expand symlinks in $PWD: moved it before canon_rel_path(), which will require it
- 05:03 PM Revision 9308: lib/sh/util.sh: expand symlinks in $PWD using `cd -P .` so it matches the output of realpath
- 05:01 PM Revision 9307: lib/sh/util.sh: cd(): documented what -P option does and why it's used
- 04:55 PM Revision 9306: lib/sh/util.sh: cd(): always run cd with -P (expand symlinks) so that $PWD will contain a canonical path which matches the output of `readlink -f`. however, don't display the added -P in the logging output because it distracts from the directory being changed to.
- 04:29 PM Revision 9305: lib/sh/util.sh: logging: added log+/-, which take a variable log_level step, and use them in log++/--
- 04:16 PM Revision 9304: lib/sh/util.sh: repeat(): for simplicity and speed, just append to a local string var (and echo the result at the end) instead of using printf
- 04:12 PM Revision 9303: bugfix: lib/sh/util.sh: repeat(): need to use %s instead of %q (escaped string) in printf
- 03:59 PM Revision 9302: lib/sh/util.sh: logging: log++/--: comment about the different uses can be performed with one function: clarified that *without a cmd*, "$@" expands to nothing and assignments are applied to the caller
- 03:00 PM Revision 9301: lib/sh/util.sh: log++/--: support running a command with the given log++/-- setting instead of applying it in the calling context. note that with no args, "$@" will expand to nothing and the var assignments will be applied in the calling context instead of to an executed command. this requires using $(()) syntax instead of let! to set the verbosity.
- 02:48 PM Revision 9300: lib/sh/util.sh: logging: inlined PS4 functions into log++/-- because that's the only place they're used and it greatly simplifies the code
- 02:34 PM Revision 9299: lib/sh/util.sh: log++/-- (and helpers PS4++/--): added functions for these so they can also be used in other contexts that don't support aliases. note that direct callers of the functions would still need to localize the PS4/$verbosity values using log_local.
- 02:08 PM Revision 9298: lib/sh/util.sh: run_args_cmd(): moved test of $? to lib/runscripts/util.run on_exit() since it needs to be performed for all run_args_cmd() functions, not just the default implementation. (this test ensures that no commands are executed if the EXIT trap was encountered due to a parsing/loading error).
- 01:54 PM Revision 9297: bugfix: lib/sh/util.sh: fwd(): need to use $top_dir (the runscript's file) instead of "${BASH_SOURCE[1]}" (the caller's file)
- 01:38 PM Revision 9296: lib/sh/util.sh: command__set_fds(): cmd_log_fd = log_fd and can_log: don't call set_fds because no redirection is needed. this also avoids the need to increase the log_level of the set_fds call that used to set cmd_log_fd to itself.
- 01:30 PM Revision 9295: bugfix: lib/sh/util.sh: command__set_fds(): cmd_log_fd = log_fd: need to increase the log_level *after* can_log is checked, to avoid limiting the command output itself
- 01:23 PM Revision 9294: bugfix: lib/sh/util.sh: command__set_fds(): log the command output at the same log_level as the command name (i.e. leave the log_level as-is), to allow nesting verbose commands within one another without the inner commands always getting suppressed
- 01:08 PM Revision 9293: lib/sh/util.sh: command__set_fds(): set the src fd outside of the set_fds call, for clarity
- 01:02 PM Revision 9292: lib/sh/util.sh: command(): if cmd_log_fd = log_fd, log the filtering of cmd_log_fd at 2 log_levels higher (verbosity >= 3)
- 12:57 PM Revision 9291: lib/sh/util.sh: command(): documented that $cmd_log_fd's default (no cmd_log_fd) limits log_fd in case command uses util.sh
- 12:54 PM Revision 9290: bugfix: lib/sh/util.sh: command(): need to make $cmd_log_fd a local var when setting its default value
- 12:49 PM Revision 9289: lib/sh/util.sh: logging: moved indent for call tree to its own section, so it isn't confused with the log_level
- 12:40 PM Revision 9288: lib/sh/util.sh: logging: log_level definition: added instructions to view a message's log_level (count the # of + signs before it in the output)
- 12:39 PM Revision 9287: lib/sh/util.sh: logging: log_level definition: replaced command with message because not just commands can be logged
- 12:38 PM Revision 9286: lib/sh/util.sh: logging: log_level definition: emphasized that the log_level starts with *1*, not 0 (0 has a special meaning, which refers to unfiltered messages)
- 12:34 PM Revision 9285: lib/sh/util.sh: logging: log_level definition: documented that for commands that use can_log(), the log_level starts with 1. for unfiltered commands, the log_level is 0 (i.e. still output at verbosity=0).
- 12:29 PM Revision 9284: lib/sh/util.sh: logging: added definition that the log_level is the minimum verbosity needed to display a command
- 12:22 PM Revision 9283: lib/sh/util.sh: set_global_fds(): documented that the logging output for this is visible at verbosity >= 3
- 12:21 PM Revision 9282: lib/sh/util.sh: set_global_fds(): moved stdlog fd setup to separate setup_log_fd() function, which runs at a much higher log_level (5 instead of 3). because the stdlog fd setup statements *themselves* are logged to fd 2 (because fd 30 is not yet open), you normally don't want to display these, if you are using fd 2 for errors only and fd 30 for logging.
- 12:07 PM Revision 9281: lib/sh/util.sh: command(): $cmd_log_fd: if not set, assume it's a script using util.sh (i.e. with log fd=$log_fd)
- 12:00 PM Revision 9280: lib/sh/util.sh: set_global_fds(): also open stdlog logging stream on fd 30, and use this in the logging functions by setting $log_fd
- 11:51 AM Revision 9279: lib/sh/util.sh: moved streams section before external commands echoing because command() uses set_fds
- 11:50 AM Revision 9278: lib/sh/util.sh: moved echo_eval() to general command echoing section so it can be used by other echoing commands
- 11:45 AM Revision 9277: lib/sh/util.sh: don't load new aliases after defining echo_stdout because it's no longer an alias
- 11:44 AM Revision 9276: lib/sh/util.sh: load new aliases after defining echo_func
- 11:36 AM Revision 9275: lib/sh/util.sh: .(): use "$FUNCNAME" like cd()
- 11:36 AM Revision 9274: lib/sh/util.sh: .(): wrapped lines in the same way as cd()
- 11:34 AM Revision 9273: lib/sh/util.sh: moved functions echoing section before other types of echoing so they can use echo_func()
- 11:28 AM Revision 9272: lib/sh/util.sh: $verbosity: decreased default value to 1 so that normally, only external commands are echoed. this avoids cluttering up the output with the function call tree, which is really only needed for debugging. it also mirrors make's default verbosity (i.e. print external commands and subdir recursions, but not make's internal actions).
- 11:25 AM Revision 9271: *{.sh,run}: put doc comment on next line when possible, so that the function name always comes before it
- 11:22 AM Revision 9270: lib/sh/util.sh: put usage message at end of line when possible, so that the function name always comes before it
- 11:14 AM Revision 9269: bugfix: lib/sh/util.sh: $top_script: need to realpath this before doing any cd so this points to the right place. set and use $top_script_abs for this purpose.
- 10:34 AM Revision 9268: lib/runscripts/util.run: added setting of $top_file, $top_filename to set_paths()
- 10:25 AM Revision 9267: lib/runscripts/util.run: set $top_file, $top_filename in a function (set_paths__util_run())
- 10:21 AM Revision 9266: lib/sh/util.sh: cd(): re-run set_paths() to update $top_script, $top_dir for the new current dir
- 10:13 AM Revision 9265: lib/sh/util.sh: added set_paths(), which sets $top_script, $top_dir
- 10:10 AM Revision 9264: lib/sh/util.sh: moved $top_script, $top_dir before internal commands echoing so they can be reset in cd()
- 10:09 AM Revision 9263: lib/sh/util.sh: moved vars echoing before internal commands echoing so that echo_vars can be used in it
- 09:56 AM Revision 9262: lib/sh/util.sh: use set_fds() instead of `echo_eval exec` for clarity
- 09:53 AM Revision 9261: lib/sh/util.sh: set_fd(): allow setting multiple fds at once, and changed the function name accordingly
- 09:50 AM Revision 9260: lib/sh/util.sh: set_fd(): moved noclobber functionality to fd_set_default() since that is only used by fd_set_default() (whose purpose has become just to run set_fd without clobbering an existing dest fd)
- 09:40 AM Revision 9259: lib/sh/util.sh: shadow_fd(): renamed to fd_set_default() for clarity (since this can't just be used for shadowing stdin/stdout/stderr)
- 09:38 AM Revision 9258: lib/sh/util.sh: set_fd()/shadow_fd(): take the redirect expr as an arg instead of a kw_param because it's the only param
- 09:33 AM Revision 9257: lib/sh/util.sh: set_fd()/shadow_fd(): take just a redirect expr containing the entire dest[<>]src expr, and parse the dest out from it
- 09:29 AM Revision 9256: lib/sh/util.sh: set_fd()/shadow_fd(): updated usage and kw_params
- 09:29 AM Revision 9255: lib/sh/util.sh: set_fd()/shadow_fd(): updated usage and kw_params
- 09:24 AM Revision 9254: lib/sh/util.sh: set_fd()/shadow_fd(): take just a redirect source expr containing the <> and the fd, to allow the caller to specify these in the shell redirection syntax. this also allows using a file (such as /dev/null) as the redirect source.
- 09:11 AM Revision 9253: lib/sh/util.sh: added cd() wrapper that logs itself and indents (indent is permanent within subshell cd was used in)
- 09:04 AM Revision 9252: lib/sh/util.sh: added caller_indent alias
- 08:45 AM Revision 9251: lib/sh/util.sh: log_err(): changed symbol to # instead of * so that it stands out better at the outmost indent level and doesn't blend in with the + that will be prefixing other messages
- 08:40 AM Revision 9250: lib/sh/util.sh: log_info(): changed symbol to : so that it blends in better with the | lines (looking like a dotted segment of the line), but still stands out (because of the dots)
- 08:32 AM Revision 9249: *{.sh,run}: don't use aliases unless it's actually necessary (e.g. to define a var in the calling function, or to alias-expand the next word)
- 08:13 AM Revision 9248: lib/runscripts/util.run: $top_file: also match dir-level runscripts by removing /run suffix
- 08:13 AM Revision 9247: lib/sh/util.sh: shadow_fd(): take a dest fd instead of a prefix to prepend to the src fd, so that the full name of the dest fd is in the function call. this makes it much clearer what fd will be created from a shadow_fd() call.
- 07:59 AM Revision 9246: lib/sh/util.sh: rel_path(): also remove base_dir when path exactly = to it. this involves adding and removing an extra trailing /.
- 07:56 AM Revision 9245: bugfix: lib/sh/util.sh: rel_path(): ensure non-empty by using . if empty
- 07:55 AM Revision 9244: lib/sh/util.sh: split canon_rel_path() into itself and rel_path() helper for clarity
- 07:47 AM Revision 9243: lib/sh/local.sh: $root_dir: run canon_rel_path on it
- 07:37 AM Revision 9242: lib/sh/util.sh: log_custom(): use keyword-args syntax instead of local vars
- 07:36 AM Revision 9241: lib/sh/util.sh: log_custom(): replace all non-whitespace chars in PS4 with $symbol instead of just the first one, so there aren't mixed $symbols and PS4 chars
- 07:28 AM Revision 9240: lib/sh/util.sh: moved paths section after logging so it can use logging functions
- 06:10 AM Revision 9239: *{.sh,run}: echo all global vars (except those defined before echo_vars is available)
- 05:58 AM Revision 9238: web/links/index.htm.run: use the runscript-common $top_file, which is equivalent to $linked_file
- 05:55 AM Revision 9237: *{.sh,run}: use new local_export instead of local...export. this still requires calling echo_vars manually, because local_export is an alias (and must be, to define the var in the caller's context).
- 05:54 AM Revision 9236: lib/sh/util.sh: added local_export alias, which combines the effects of local and export
- 05:36 AM Revision 9235: lib/sh/util.sh: renamed params() to kw_params() to clarify the type of params it handles
- 05:33 AM Revision 9234: lib/sh/util.sh: logging: echo all keyword params by overriding params(). this requires removing manual echo_vars calls.
- 05:31 AM Revision 9233: lib/sh/util.sh: moved functions section right after exceptions, so that other sections can use it. in particular, func_override is needed by verbose output to override non-verbose versions of functions.
- 05:28 AM Revision 9232: lib/sh/util.sh: only try to echo vars that are set, to avoid `declare -p` "not found" errors
- 05:09 AM Revision 9231: *{.sh,run}: use new `params` in all functions that have keyword params, in order to remove their vars from the environment. note that functions that use $? (such as die()) must save it *before* running params, because params will overwrite $?.
- 04:28 AM Revision 9230: web/links/index.htm: updated to Firefox bookmarks. added bash and MySQL-related bookmarks, including MySQL doc subfolder.
- 04:11 AM Revision 9229: lib/sh/util.sh: params(): added doc comment
- 04:10 AM Revision 9228: lib/sh/util.sh: added params(), which removes keyword-param-only vars from the environment
- 03:50 AM Revision 9227: lib/sh/util.sh: added unexport() (note that `declare +x` won't work because it defines the var if it isn't set)
- 03:39 AM Revision 9226: lib/sh/util.sh: moved vars section to beginning so other sections can use it (it does not contain logging statements, so it doesn't need to be after verbose output)
- 03:34 AM Revision 9225: bugfix: lib/sh/util.sh: command(): limit cmd_log_fd directly instead of limiting log_fd (usually fd 2) and then redirecting cmd_log_fd to it. this ensures that stderr is not limited unless it's actually used as the cmd_log_fd, so that a non-logging stderr will still reach the user properly regardless of whether err_fd is set to something other than 2. (previously, without an err_fd at 22, closing fd 2 at the beginning of the set of redirections would leave no fd pointing to a place to echo errors to.)
05/11/2013
- 11:16 PM Revision 9224: lib/sh/util.sh: disable_logging(): use echo_eval instead of plain eval so the disabling of logging is nevertheless itself logged
- 11:11 PM Revision 9223: lib/sh/util.sh: command(): made usage message an end-of-line comment
- 11:10 PM Revision 9222: lib/sh/util.sh: inlined limit_log_fd into command() since it's only used once
- 10:22 PM Revision 9221: lib/sh/util.sh: log_err(), log_info(): use bolder symbols (*, #) to make the symbol stand out visually from the line of | above and below it
- 10:09 PM Revision 9220: lib/sh/util.sh: $verbosity: lowered the default from 3 to 2 because level 3 output (vars, etc.) is too verbose for the default output and is only needed for debugging
- 10:06 PM Revision 9219: lib/sh/util.sh: $log_level_indent: added space after | to visually separate the nesting levels and make the output look like an expandable tree (similar to a filesystem browser tree)
- 10:04 PM Revision 9218: lib/sh/util.sh: log_custom(): replace every non-whitespace character of $log_indent, and the first character of PS4, with the symbol, to make the symbol stand out on the line instead of the |||... before it
- 09:19 PM Revision 9217: lib/sh/util.sh: removed no longer used stdout2log_fd(). set $cmd_log_fd instead.
- 09:16 PM Revision 9216: lib/sh/util.sh: set $log_level_indent to | because this visually connects commands at the same indent by effectively connecting their + prefixes with a line of |
- 09:14 PM Revision 9215: lib/sh/archives.sh: zip(), unzip(): added missing echo_func
- 09:07 PM Revision 9214: lib/sh/util.sh: command(): use just one control var $cmd_log_fd instead of three flags (limit_log_fd, limit_stdout, stderr_is_errors) that indicated various common fd configurations. this is much clearer (you state which fd the common uses as its logging fd), more configurable (the logging fd can be any fd, not just 1 or 2), and more automatic (redirecting fd 2 to err_fd happens automatically if it isn't used for logging).
- 08:58 PM Revision 9213: bugfix: lib/sh/local.sh: psql(): need to use limit_stdout=1 instead of stderr_is_errors=1 because logging info is output to *stdout*, not *stderr*, in spite of the >&2 redirection, since the >&2 is applied *after* command()'s logging redirects. note that the >&2 can now be removed, because it will be performed by command().
- 08:16 PM Revision 9212: lib/sh/util.sh: added $log_fd and use it instead of 2 where the log_fd is intended
- 08:11 PM Revision 9211: lib/sh/util.sh: moved stdout2log_fd() to command verbose output subsection of verbose output since it is primarily intended for use with external commands
- 08:05 PM Revision 9210: lib/sh/util.sh: renamed limit_stderr to limit_log_fd, stdout2stderr to stdout2log_fd to clarify their purpose. log_fd is currently assumed to be 2.
- 08:00 PM Revision 9209: lib/sh/util.sh: added disable_logging() and use it instead of `exec 2>/dev/null`
- 07:54 PM Revision 9208: lib/sh/util.sh: added $err_fd global var and use it instead of the 22 magic value. it starts out at 2 until fd 22 has been set up, so commands that required 22 will now work before set_global_fds() is called.
- 07:11 PM Revision 9207: lib/sh/util.sh: shadow_fd(): don't require it to be run with log++ and instead let callers apply log++ if needed. in set_global_fds(), log++ can just be applied once for all the shadow_fd() calls.
- 07:09 PM Revision 9206: lib/sh/util.sh: shadow_fd(): instead of applying minor=1 (i.e. an additional log++) to echo_func and then log++ again separately to set_fd, just apply it to the entire function
- 07:07 PM Revision 9205: lib/sh/util.sh: set_fd(): don't increase the log_level for this function, and instead let callers increase it if needed
- 06:48 PM Revision 9204: lib/sh/util.sh: limit_stderr(): inlined log++ with the can_log call because it should only apply to it. this also makes it obvious that log++ should *not* apply outside of this function. this also enables the contents of this function to be used in an alias.
- 06:01 PM Revision 9203: lib/sh/util.sh: command(): use exec instead of `builtin command` to avoid spawning an extra process (since a subshell is already open)
- 05:43 PM Revision 9202: bugfix: lib/sh/util.sh: command(): only indent if command was logged
- 05:39 PM Revision 9201: bugfix: lib/sh/util.sh: .(): only indent if include statement was logged
- 05:29 PM Revision 9200: lib/sh/util.sh: limit_stderr(): moved $stdout2stderr to command() so that limit_stderr()'s only purpose is to log-limit stderr
- 05:23 PM Revision 9199: bugfix: lib/sh/util.sh: limit_stderr(): moved $stderr_is_errors default to command() where it's used
- 05:20 PM Revision 9198: lib/sh/util.sh: limit_stderr(): do stdout2stderr *after* limit_stderr to avoid having two similar `can_log ... >/dev/null` commands
- 05:09 PM Revision 9197: lib/sh/util.sh: echo_cmd(): removed no longer used removal of first builtin or command arg
- 05:07 PM Revision 9196: lib/sh/util.sh: inlined echo_run_prep into command() since it's now only used once
- 05:06 PM Revision 9195: lib/sh/util.sh: command(): removed no longer used $cmd_echoed flag
- 04:57 PM Revision 9194: *{.sh,run}: use new limit_stdout=1 instead of stdout2stderr=1 limit_stderr=1
- 04:56 PM Revision 9193: lib/sh/util.sh: command(): added limit_stdout=1 flag which implies stdout2stderr=1 limit_stderr=1
- 04:41 PM Revision 9192: lib/sh/util.sh: merged limit_stderr_cmd/limit_stdout_cmd into command(), using flag vars to control what limiting actions it needs to perform. in command invocations, this involves setting the appropriate flag vars instead of using a limit_std*_cmd alias.
- 04:37 PM Revision 9191: lib/sh/util.sh: added run_cmd
- 04:04 PM Revision 9190: lib/sh/util.sh: limit_stderr(): moved before command echoing because it does not depend on it and is a separate feature
- 03:47 PM Revision 9189: lib/sh/util.sh: run_args_cmd(): use $top_script instead of `"$(canon_rel_path "$0")"`
- 03:42 PM Revision 9188: lib/sh/util.sh: $top_script: run canon_rel_path on $0
- 03:35 PM Revision 9187: lib/sh/util.sh: use `minor=1 echo_func` instead of echo_minor_func because the syntax is simple enough that you don't need a separate alias for it
- 03:32 PM Revision 9186: lib/sh/util.sh: echo_func: support using minor=1 to increase the log_level that the function call is echoed at. use this in echo_minor_func.
- 03:28 PM Revision 9185: lib/sh/util.sh: echo_*func aliases: use simpler && syntax (with `|| true` to prevent errexit if the condition is false) instead of an if statement. this also allows prefixing the alias with var definitions.
- 03:27 PM Revision 9184: lib/sh/util.sh: echo_*func aliases: use simpler && syntax (with `|| true` to prevent errexit if the condition is false) instead of an if statement. this also allows prefixing the alias with var definitions.
- 03:18 PM Revision 9183: lib/sh/util.sh: echo_func: only indent if the function call was displayed. this avoids confusing extra whitespace when a function call causes an indent but the function call itself isn't printed.
- 03:10 PM Revision 9182: bugfix: lib/sh/util.sh: echo_minor_func: need to include "$@" in echo_func() call
- 03:08 PM Revision 9181: lib/sh/util.sh: echo_func(): added usage
- 03:07 PM Revision 9180: lib/sh/util.sh: echo_func: added usage
- 02:50 PM Revision 9179: lib/sh/util.sh: $log_level_indent: changed to a single space rather than two, to avoid very deep indents as the call tree becomes more deeply nested. due to the + at the beginning of every line, a single space is enough to visualize the structure of the call tree (unlike source code, which requires more whitespace because it doesn't have a call tree structure).
- 02:46 PM Revision 9178: lib/sh/util.sh: echo_*func aliases: increase the indent for the duration of the function call. this causes function calls to be displayed in an indented call-tree structure, which makes the verbose output much easier to understand.
- 02:43 PM Revision 9177: bugfix: lib/sh/util.sh: recursive aliases (i.e. aliases that call a command of the same name): use "" around the command name so it isn't reexpanded if the function using the alias is copied using copy_func(). (aliases will be reexpanded every time a function is redeclared since they appear unquoted in the function definition.) this is a bug in `declare -f` for which there is no fix, necessitating the "" alias workaround instead.
- 02:01 PM Revision 9176: lib/sh/util.sh: moved log-indent-related vars/aliases before they are first used (by log())
- 01:54 PM Revision 9175: lib/sh/util.sh: renamed inc_log_level/dec_log_level to shorter log++/log--
- 01:54 PM Revision 9174: lib/sh/util.sh: renamed inc_log_level/dec_log_level to shorter log++/log--
- 01:51 PM Revision 9173: lib/sh/util.sh: renamed cmd_indent to just indent now that indent is not being used for the PS4 level
- 01:47 PM Revision 9172: *{.sh,run}: multi-command aliases: enclose in {} so the alias can be used after ||
- 01:44 PM Revision 9171: lib/sh/util.sh: renamed indent->PS4++ , outdent->PS4-- because these relate just to the PS4 length, not to the (whitespace-based) log_indent
- 01:38 PM Revision 9170: lib/sh/util.sh: removed no longer used echo_run(). use command() instead.
- 01:36 PM Revision 9169: *{.sh,run}: use command instead of deprecated echo_run (don't prepend anything when the command is already aliased with `command`)
- 01:29 PM Revision 9168: lib/sh/util.sh: command(): perform echo_run_prep itself instead of requiring echo_run to be added in an alias. echo_run_prep will not be performed if limit_stderr_cmd() has performed it already outside the limit_stderr section. this requires using `builtin command` instead of "command" when you don't want the echoing (such as in include_guard_var()).
- 01:07 PM Revision 9167: *{.sh,run}: multi-command aliases: enclose in {} so the alias can be used after ||
- 12:56 PM Revision 9166: bugfix: lib/sh/util.sh: .(): also need to echo the . before the included file
- 12:48 PM Revision 9165: lib/sh/util.sh: added echo_params alias and use it instead of `log "$*"`
- 12:43 PM Revision 9164: lib/sh/util.sh: .(): echo the include at log_level 2 because it's an internal command
- 12:34 PM Revision 9163: lib/sh/util.sh: echo_cmd(): also remove `builtin` before the command name
- 12:32 PM Revision 9162: lib/sh/util.sh: echo_cmd(): don't remove -- after command, because it is added by the command() function instead and does not appear in the command sent to echo_run()
- 12:29 PM Revision 9161: lib/sh/util.sh: command alias: don't alias-expand next word, because the next word should only be interpreted as a command (part of the effect of the `command` builtin)
- 12:27 PM Revision 9160: lib/sh/util.sh: external commands: always use command rather than echo_run to indicate that a command is external, because command() ensures that what it invokes is not a shell function, and sets 2>&22 where needed
- 12:23 PM Revision 9159: lib/sh/util.sh: .(): use echo_run so that included files are echoed as they are included. note that echo_run uses cmd_indent, so the included files' load-time logging output will be indented according to the nesting level of the include.
- 12:20 PM Revision 9158: lib/sh/util.sh: moved .() command echoing > internal commands section
- 12:19 PM Revision 9157: lib/sh/util.sh: moved echo_run() to general command echoing section because it can also be used for internal commands
- 12:09 PM Revision 9156: removed no longer used inputs/GBIF/MySQL_export. use lib/sh/local.sh mysql_export_local() instead.
- 12:07 PM Revision 9155: inputs/GBIF/raw_occurrence_record/run: override table.tsv/make() instead of export_mysql()
- 12:06 PM Revision 9154: inputs/GBIF/table.run: table.tsv/make(): use new mysql_export_local instead of ./MySQL_export
- 12:05 PM Revision 9153: lib/sh/local.sh: added mysql_export_local()
- 12:05 PM Revision 9152: lib/sh/db.sh: added mysql_export(). documented that mysql_export_outfile() supports CSV, but requires the FILE privilege.
- 12:02 PM Revision 9151: lib/sh/db.sh: mysql(): use --column-names to ensure the output is formatted appropriately. note that --column-names is the default, but better to specify it to be sure.
- 12:01 PM Revision 9150: lib/sh/db.sh: mysql(): output_data mode: use --batch to ensure the output is formatted appropriately. note that --batch is the default when stdin is from a pipe, but better to specify it to be sure.
- 11:49 AM Revision 9149: *{.sh,run}: use new limit_stdout_cmd instead of `stdout2stderr=1 limit_stderr_cmd`
- 11:40 AM Revision 9148: lib/sh/util.sh: added limit_stdout_cmd alias
- 07:25 AM Revision 9147: lib/sh/make.sh: added $rm short var for $remake
- 07:22 AM Revision 9146: lib/sh/util.sh: verbosity: removed `declare -i verbosity` because this does not actually ensure that $verbosity is an integer; it only has "arithmetic evaluation [...] done when the variable is assigned to" (`help declare`)
- 07:20 AM Revision 9145: lib/sh/util.sh: verbosity: support setting this in alternate short-name var $vb
- 07:15 AM Revision 9144: lib/sh/util.sh: override the `.` builtin (a.k.a. `source`) and run canon_rel_path on the included script. this removes .. in the path when it's displayed in bash error messages.
- 06:58 AM Revision 9143: lib/sh/util.sh: log_err(): ensure errors are visible by using 2>&22. since this is uses log(), verbosity=1 also needs to be set.
- 06:50 AM Revision 9142: lib/sh/util.sh: $explicit_errors_only: explicitly set verbosity=0 to hide startup logging
- 06:46 AM Revision 9141: lib/sh/util.sh: limit_stderr(): if stdout goes to stderr (i.e. is logging info), assume that stderr_is_errors
- 06:41 AM Revision 9140: lib/sh/util.sh: $explicit_errors_only: documented that this option should only be used for testing the explicit error displaying, as otherwise, important output may be missed
- 06:39 AM Revision 9139: lib/sh/util.sh: $explicit_errors_only: added usage
- 06:38 AM Revision 9138: bugfix: lib/sh/util.sh: command(): updated $errors_only var name to $explicit_errors_only
- 06:27 AM Revision 9137: lib/sh/util.sh: $explicit_errors_only: noted that verbosity=0 displays everything that isn't explicitly hidden
- 06:24 AM Revision 9136: lib/sh/local.sh: psql(): use new stderr_is_errors=1 since psql's logging output comes on stdout, so stderr contains only errors. (the caveat of this is that the query output is normally mixed with logging info on stdout, and needs to be separated out to a different file descriptor using --output.)
- 06:18 AM Revision 9135: lib/sh/util.sh: added $explicit_errors_only env var which shows only explicitly-displayed errors (those which have been redirected to fd 22). note that most of the time, this has the same effect as `verbosity=0 script...`.
- 06:17 AM Revision 9134: lib/sh/util.sh: command(): support ensuring errors are visible by redirecting them to fd 22 (global stderr) when $stderr_is_errors is set
- 05:51 AM Revision 9133: lib/sh/util.sh: `command`: always prepend -- to the args list (to ensure that the command name is not interpreted as a `command` option), not just when the command alias is used
- 05:40 AM Revision 9132: lib/sh/util.sh: set_global_fds(): increase the log_level so the shadow_fd()/set_fd() function names aren't output at the default verbosity (3), and the redirection commands themselves aren't output at verbosity <= 2. set_global_fds() happens at the beginning of every script that uses util.sh, and is fairly predictable, so it isn't necessary to always echo these commands.
- 05:29 AM Revision 9131: lib/sh/local.sh: psql(): use new convention for command-specific alternate stdout
- 05:15 AM Revision 9130: lib/sh/make.sh: inline_make: use new convention for command-specific alternate stdin
- 05:13 AM Revision 9129: *{.sh,run}: removed extra space between function name and ()
- 05:12 AM Revision 9128: lib/sh/util.sh: streams: moved setting of global stdin/stdout/stderr into set_global_fds () function
- 05:05 AM Revision 9127: lib/sh/util.sh: streams: allow commands to access global stdin/stdout/stderr using fd 20/21/22. this works even when /dev/tty isn't available.
- 05:05 AM Revision 9126: lib/sh/util.sh: streams: added convention that fd 10/11/12 should be used for command-specific alternate stdin/stdout/stderr
- 05:04 AM Revision 9125: lib/sh/util.sh: added streams functions fd_exists, set_fd, shadow_fd, and helpers
- 05:01 AM Revision 9124: lib/sh/util.sh: added echo_minor_func alias
- 05:00 AM Revision 9123: lib/sh/util.sh: added echo_eval()
- 04:32 AM Revision 9122: lib/sh/util.sh: renamed require_exists() to require_not_exists() because the command actually checks if the file *doesn't* exist
- 02:26 AM Revision 9121: lib/sh/util.sh: echo_vars(): use log() instead of manually echoing the log indent, so that the log indent string ($log_indent$PS4) doesn't have to be maintained in several different places
- 02:23 AM Revision 9120: lib/sh/util.sh: logging: visually separate the log_level-based indenting from the external command indenting by using the standard `set -x` prefix (1st char of PS4) for log_level indenting and $log_level_indent (i.e. whitespace) for external command indenting
- 02:19 AM Revision 9119: lib/sh/util.sh: logging: separate the log_level-based indenting from the external command indenting so that the log_level-based indenting can use a different prefix. this involves propagating a new var, $log_indent, to invoked commands instead of $PS4, and always prepending $log_indent to $PS4 when printing log messages.
- 01:55 AM Revision 9118: lib/sh/util.sh: propagate $log_level_indent to invoked commands
- 01:54 AM Revision 9117: lib/sh/util.sh: renamed $log_indent to $log_level_indent to indicate that this is the string added at each level, rather than the entire indent
- 01:49 AM Revision 9116: bugfix: lib/sh/util.sh: limit_stderr(): switched back to running inc_log_level inside limit_stderr(), because it should only apply during the function for use by can_log. documented why inc_log_level needs to be inside limit_stderr().
- 01:44 AM Revision 9115: bugfix: lib/sh/util.sh: limit_stderr(): stdout2stderr mode: only limit stdout, since stderr may contain error messages (which should always be displayed)
- 01:32 AM Revision 9114: bugfix: lib/sh/util.sh: limit_stderr_cmd(): need to load new aliases before it so limit_stderr is expanded
- 01:31 AM Revision 9113: bugfix: lib/sh/util.sh: limit_stderr alias: need to inc_log_level before rather than after limit_stderr(), so that can_log uses the right verbosity (previously, inc_log_level was part of limit_stderr() itself, but was moved to the alias because its effects were needed outside the function)
- 01:25 AM Revision 9112: lib/sh/util.sh: stdout2stderr(): fixed doc comment after space-before-() search-and-replace
- 01:24 AM Revision 9111: lib/sh/util.sh: usage(): use `return` instead of `(exit ...)`
- 01:23 AM Revision 9110: lib/sh/util.sh: verbose output: put commands into subsections
- 01:10 AM Revision 9109: lib/sh/util.sh: echo_run(): factored prep code out into echo_run_prep alias, which can also be used in commands that mimic it, such as limit_stderr_cmd()
- 01:06 AM Revision 9108: bugfix: lib/sh/util.sh: limit_stderr(): moved indent to echo_run prep, because it only applies to commands invoked with echo_run
- 01:00 AM Revision 9107: bugfix: lib/sh/util.sh: limit_stderr(): need to apply inc_log_level in the caller so it won't get rolled back at the end of the function
- 12:51 AM Revision 9106: lib/sh/db.sh: mysql_export_outfile(): ensure newline between format info ($mysql_load_data_format) and rest of SELECT query
- 12:49 AM Revision 9105: lib/sh/db.sh: mysql_export_outfile(): ensure newline between SELECT columns list and INTO OUTFILE
- 12:44 AM Revision 9104: lib/sh/util.sh: limit_stderr_cmd(): moved stdout2stderr code to limit_stderr() because it is not specific to running limit_stderr on single commands
- 12:33 AM Revision 9103: lib/sh/util.sh: limit_stderr(): fixed doc comment after space-before-() search-and-replace
- 12:29 AM Revision 9102: lib/sh/db.sh: added mysql_export_outfile(), which uses SELECT ... INTO OUTFILE
- 12:22 AM Revision 9101: lib/sh/db.sh: mysql(): added $output_data option that turns off --verbose and uses echo_stdin instead so that queries are not echoed to stdout along with data. in --verbose mode, use limit_stderr_cmd with stdout2stderr=1 to redirect echoed queries through the logging mechanism.
- 12:17 AM Revision 9100: lib/sh/db.sh: mysql_cmd(): removed set_database because this is now performed by each caller before they use $database
- 12:15 AM Revision 9099: lib/sh/db.sh: mysql_cmd: get command name by adding $FUNCNAME in an alias instead of using ${FUNCNAME[1]} in the function, so that callers can also call mysql_cmd via a nested function, etc.
- 12:00 AM Revision 9098: lib/sh/util.sh: added ensure_nested_func()
05/10/2013
- 11:59 PM Revision 9097: lib/sh/util.sh: added contains()
- 11:57 PM Revision 9096: lib/sh/util.sh: command alias: also prepend -- to args to prevent a first arg starting with -- from being interpreted as an option to the `command` builtin
- 10:16 PM Revision 9095: lib/sh/db.sh: mysql_cmd(): moved setting of database to specific callers (mysql(), mysqldump()) because the syntax to set it differs between mysql* commands (e.g. mysql uses `--database=` while mysqldump uses `--databases ... --tables`)
- 10:13 PM Revision 9094: lib/sh/db.sh: added set_database alias, and use it in mysql_cmd()
- 10:11 PM Revision 9093: lib/sh/util.sh: import_vars alias and applicable aliases that use it: documented that when used inside another alias 2+ levels deep, it *must* be run inside a function. this is due to a strange bug in bash where $() expressions in 2-level aliases produce a syntax error when the alias is expanded outside a function.
- 10:07 PM Revision 9092: bugfix: lib/sh/util.sh: added back missing echo_func alias, which is needed to also include "$@" in the echoed function call
- 10:05 PM Revision 9091: lib/sh/util.sh: import_vars alias: use new get_prefix_vars()
- 10:04 PM Revision 9090: lib/sh/util.sh: add get_prefix_vars()
- 10:03 PM Revision 9089: lib/sh/util.sh: import_vars alias: use declare instead of local so it can be used outside a function
- 02:47 PM Revision 9088: lib/sh/db.sh: added mk_select alias and use it in pg_export()
- 02:36 PM Revision 9087: lib/sh/db.sh: pg_export(): always include the LIMIT value if specified, rather than only if the caller did not provide a full query
- 02:27 PM Revision 9086: lib/sh/db.sh: pg_export(): rtrim $query
- 02:22 PM Revision 9085: lib/sh/util.sh: added rtrim()
- 01:55 PM Revision 9084: lib/sh/db.sh: pg_export(): for simplicity, always use a SELECT statement as the source. take any source query in \$query without () instead of \$source with (). this will also help make pg_export uniform with MySQL.
- 01:34 PM Revision 9083: lib/sh/db.sh: renamed pg_copy_to() to pg_export() because it is also a general-purpose export command, which could have an analogous counterpart for MySQL
- 01:23 PM Revision 9082: bugfix: lib/sh/util.sh: moved self alias to beginning, before functions that use it
- 12:55 PM Revision 9081: lib/sh/util.sh: added repeat()
- 12:47 PM Revision 9080: lib/sh/util.sh: reverse(): use `i > 0` rather than `i >= 1` to match the `i < length` idiom used in forwards loops
- 12:43 PM Revision 9079: lib/sh/util.sh: moved strings section before verbose output so its commands can be used by the logging functions
- 12:32 PM Revision 9078: lib/sh/util.sh: echo_run() and derivatives (limit_stderr_cmd()): use new `indent` before the invoked command so its own logging messages, if any, are indented
- 12:27 PM Revision 9077: lib/sh/util.sh: propagate indent to invoked commands by exporting PS4
- 12:24 PM Revision 9076: lib/sh/util.sh: verbose output: added indent/outdent aliases and use them in inc_log_level/dec_log_level
- 12:14 PM Revision 9075: *{.sh,run}: replaced extern with command, a shell builtin that does the same thing. this is also part of dash (the Bourne shell on Linux).
- 12:08 PM Revision 9074: *{.sh,run}: removed extra space between function name and (), which is apparently not needed even though `help function` includes it. this greatly improves readability, including when function names are pasted into commit messages!
- 12:03 PM Revision 9073: lib/sh/util.sh: require_exists (): use die/log_info's new support for info messages using $type
- 12:00 PM Revision 9072: lib/sh/util.sh: die (): allow caller to specify a custom log message type (i.e. a suffix for log_* ())
- 11:58 AM Revision 9071: lib/sh/util.sh: log_e (): use new log_err
- 11:57 AM Revision 9070: lib/sh/util.sh: verbose output: added log_custom (), which modifies the symbol in PS4 to indicate the message type, and log_err ()/log_info (), which set specific symbols
- 11:55 AM Revision 9069: lib/sh/util.sh: moved die () into verbose output so it can use logging functions
- 11:53 AM Revision 9068: lib/sh/util.sh: moved functions after verbose output so copy_func () can use logging functions in its input checks
- 11:41 AM Revision 9067: lib/sh/util.sh: moved log_e () to verbose output section so it can use logging functions
- 11:29 AM Revision 9066: lib/sh/db.sh: mysqldump_diffable (): use pipe_delay to ensure that sed is printed after mysqldump
- 11:23 AM Revision 9065: lib/sh/util.sh: echo_cmd (): use new log ()
- 11:21 AM Revision 9064: lib/sh/util.sh: added log ()
- 10:53 AM Revision 9063: lib/sh/util.sh to_file, make.sh check_target_exists: use new require_exists to print message if file skipped because it already exists. this is useful for troubleshooting why certain make commands don't run.
- 10:51 AM Revision 9062: lib/sh/util.sh: added require_exists (), used to skip make commands for existing files
- 10:33 AM Revision 9061: *{.sh,run}: use `test !` instead of `! test` so that the ! is right next to the operator it's negating
- 10:31 AM Revision 9060: /run: geoscrub_input/make (): use new check_fake_target_exists to create the file only if it doesn't exist yet
- 10:31 AM Revision 9059: lib/sh/make.sh: added check_fake_target_exists (analogous to check_target_exists), which defers the target existence check until to_file (when the target name will presumably have been resolved to a path)
- 10:29 AM Revision 9058: lib/sh/util.sh: to_file (): support only running if the file does not exist by setting $if_not_exists
- 10:08 AM Revision 9057: lib/sh/util.sh: limit_stderr_cmd (): run cmd2rel_path explicitly here because echo_run is split apart rather than being run as echo_run ()
- 10:06 AM Revision 9056: lib/sh/util.sh: moved echo_cmd, echo_run before commands that use them
- 10:02 AM Revision 9055: lib/sh/make.sh: check_target_exists: if remaking, consider target not to exist
- 10:01 AM Revision 9054: lib/sh/make.sh: added remaking alias
- 09:45 AM Revision 9053: inputs/GBIF/table.run: table.tsv/make (): use echo_run instead of extern so that the command name is canonicalized properly
- 09:45 AM Revision 9052: lib/sh/util.sh: echo_run (): use new cmd2rel_path to resolve the command ($1)
- 09:44 AM Revision 9051: lib/sh/util.sh: added cmd2rel_path alias, which makes $1 a canon_rel_path if it's a filesystem path. this removes extra .. in the paths of invoked commands.
- 09:06 AM Revision 9050: *{.sh,run}: use shorter `test` instead of `test -n` and `test !` instead of `test -z` (http://www.gnu.org/software/bash/manual/bash.html#Bourne-Shell-Builtins > test)
- 08:52 AM Revision 9049: lib/sh/util.sh: echo_cmd (): don't include leading extern because it clutters up the output and is implied by the log_level
- 08:45 AM Revision 9048: lib/sh/util.sh: to_file (): run echo_func and `echo_vars stdout` to show what file the output is going to, since this information (i.e. redirects) isn't included in the logging output for the command itself
- 08:41 AM Revision 9047: lib/runscripts/table.run: remake_VegBIEN_mappings (): added public_schema_exists check, ported from lib/import.sh
- 08:40 AM Revision 9046: lib/sh/local.sh: added public_schema_exists (), ported from lib/import.sh
- 08:32 AM Revision 9045: *{.sh,run}: use new echo_stdout instead of echo_stdin where applicable, for clarity
- 08:31 AM Revision 9044: lib/sh/util.sh: added echo_stdout (currently just an alias of echo_stdin, because they are usable for the same purpose)
- 08:27 AM Revision 9043: /run: moved geoscrub_input export into separate geoscrub_input/make () target
- 08:24 AM Revision 9042: lib/sh/db.sh: pg_export_table_to_dir_no_header (): use to_file so that the file is autoremoved in case of error
- 07:51 AM Revision 9041: lib/sh/util.sh: let (): renamed to let! so that let can still be used to evaluate whether a numeric value is 0 (yes, an ! is allowed at the end of a command name)
- 07:44 AM Revision 9040: lib/sh/util.sh: moved canon_rel_path () into separate paths section
- 07:39 AM Revision 9039: bugfix: *{.sh,run}: use new func_override for runscript inheritance instead of invoking the overridden function as a (command-line) target of the parent runscript. this ensures that the overridden function is run in the *same* process as the calling function, so that $top_dir keeps the same value and runscript-relative paths continue to work.
- 07:30 AM Revision 9038: lib/sh/util.sh: added func_override (), for use in runscript inheritance
- 07:03 AM Revision 9037: lib/sh/util.sh: copy_func (): check that $from exists and $to does not exist (i.e. don't clobber existing functions). you can always first `unset -f` the function to get around the no-clobber restriction.
- 07:00 AM Revision 9036: lib/sh/util.sh: exceptions: added die ()
- 06:44 AM Revision 9035: lib/sh/util.sh: log_e (): restructured as an error handler to put after save_e rather than as a wrapper around the entire command. this allows it to be used with any kind of expression (such as boolean expressions with !), not just single commands.
- 06:35 AM Revision 9034: lib/sh/util.sh: log_e (): don't export $e to the calling context, since the caller can just use ` || { save_e; ...; }` if they need $e
- 06:31 AM Revision 9033: lib/sh/util.sh: calls to log_e: don't rely on log_e setting $e
- 06:30 AM Revision 9032: lib/sh/util.sh: added save_e, which now sets $e just locally
- 06:28 AM Revision 9031: lib/sh/util.sh: save_e: renamed to export_e because $e overwrites any previous value in the calling context
- 06:26 AM Revision 9030: lib/sh/util.sh: removed no longer used save_e_cmd
- 06:24 AM Revision 9029: lib/sh/util.sh: try (): use simpler save_e instead of save_e_cmd
- 06:19 AM Revision 9028: bugfix: lib/sh/util.sh: bool2int (): need to use try instead of save_e_cmd because save_e_cmd rethrows the error, which should instead just be stored in $e. this bug was not found in testing because bool2int was only used in $(), which errexit does not apply to.
- 06:15 AM Revision 9027: lib/sh/util.sh: exceptions: added save_e, now an alias for e=$?. added save_e/rethrow usage.
- 06:11 AM Revision 9026: lib/sh/util.sh: renamed save_e () to save_e_cmd () since it actually runs a command, in addition to saving $?
- 06:08 AM Revision 9025: lib/sh/util.sh: log_e (): rewrote to avoid using save_e, which will be repurposed
- 05:50 AM Revision 9024: lib/sh/util.sh: added func_exists ()
- 05:50 AM Revision 9023: lib/sh/util.sh: moved copy_func () after exceptions so it can use save_e/rethrow
- 05:44 AM Revision 9022: lib/sh/util.sh: added copy_func ()
- 05:39 AM Revision 9021: lib/sh/util.sh: save_e (): usage: added rethrow example
- 05:26 AM Revision 9020: bugfix: lib/sh/util.sh: bool2int (): need to load new aliases before it so that save_e will be expanded
- 05:24 AM Revision 9019: *{.sh,run}: put functions on one line where possible (and where they are not expected to expand)
- 05:19 AM Revision 9018: lib/sh/util.sh: added separate include guard around the include guard utils so they don't have to be redefined on every include of util.sh
- 05:06 AM Revision 9017: *{.sh,run}: added extra line before new sections to visually separate them. lib/sh/util.sh: added missing section headers.
- 05:01 AM Revision 9016: lib/sh/util.sh: split make utils out into separate make.sh
- 04:38 AM Revision 9015: lib/sh/util.sh: split archive (zip) utils out into separate archives.sh
- 04:24 AM Revision 9014: lib/sh/util.sh: split databases utils out into separate db.sh
- 04:05 AM Revision 9013: moved lib/*.sh to sh/ subdir so it's easier to find the .sh files among all the other lib/ files
- 03:32 AM Revision 9012: lib/util.sh: removed no longer used limit_stderr_extern. use `limit_stderr_cmd extern` instead.
- 03:29 AM Revision 9011: lib/util.sh: specify limit_stderr_cmd just for the (few) commands that need it, rather than for all commands, so that commands that use stderr to print important error messages don't have those error messages hidden when the verbosity is too low. (error messages should always be displayed, regardless of the verbosity.)
- 03:13 AM Revision 9010: lib/util.sh: limit_stderr_cmd (): only echo the command if it starts with echo_run. this requires adding echo_run before commands that use limit_stderr_cmd, such as limit_stderr_extern.
- 03:07 AM Revision 9009: lib/util.sh: limit_stderr_cmd (): remove echo_run from the command to run so that the command name isn't echoed twice
- 02:56 AM Revision 9008: lib/util.sh: limit_stderr_cmd: alias-expand command after it
- 02:53 AM Revision 9007: lib/util.sh: $verbosity: ensure it's an integer using `declare -i`
- 02:45 AM Revision 9006: lib/util.sh: grouped set verbosity statements together and commented them
- 02:43 AM Revision 9005: bugfix: lib/util.sh: verbose output: $verbosity defaults to $verbose (boolean) converted to integer. the previous set-default of $verbosity to $verbose has been removed because it came after `: "${verbosity=3}"` and thus didn't have an effect.
- 02:40 AM Revision 9004: lib/util.sh: added bool2int ()
- 02:32 AM Revision 9003: *{.sh,run}: use new isset
- 02:31 AM Revision 9002: lib/util.sh: added isset ()
- 02:28 AM Revision 9001: *{.sh,run}: use ${var+isset} instead of ${var+t} for clarity
- 02:22 AM Revision 9000: lib/util.sh: propagate the verbosity to invoked commands by exporting it
- 02:20 AM Revision 8999: lib/util.sh: run all commands verbosely by default, not just runscripts. this ensures verbose output for invoked commands like inputs/GBIF/MySQL_export.
- 02:15 AM Revision 8998: lib/util.sh: echo_stdin (): use new pipe_delay
- 02:12 AM Revision 8997: lib/util.sh: added pipe_delay (used as `cmd1 | { pipe_delay; cmd2; }`)
- 02:06 AM Revision 8996: lib/util.sh: limit_stderr_cmd (): echo the command like echo_run so that callers don't have to separately call echo_run. this reduces clutter of the nested aliases, ensures that the command is always echoed *outside* of the inner stderr-limiter (which has a different log_level), and avoids echoing "limit_stderr_cmd" itself as part of the command name.
- 01:47 AM Revision 8995: lib/util.sh: limit_stderr (): increase the log_level so that stderr of verbose commands can be turned off separately from the names of the commands themselves. it will now usually have log_level 2, indicating output that is useful primarily for debugging (this is the same as for shell function calls).
- 01:39 AM Revision 8994: lib/util.sh: renamed log_stderr* to limit_stderr* to reflect that stderr is limited (i.e. controlled) rather than logged
- 01:36 AM Revision 8993: lib/util.sh: echo_run_extern: renamed to log_stderr_extern since controlling stderr is its primary function
- 01:25 AM Revision 8992: inputs/GBIF/MySQL_export: only include WHERE clause if $filter is set. support configuring LIMIT/OFFSET.
- 01:00 AM Revision 8991: inputs/GBIF/table.run: table.tsv/make (): use new to_target to auto-delete $target on error
- 12:59 AM Revision 8990: inputs/GBIF/table.run: table.tsv/make (): use new check_target_exists
- 12:58 AM Revision 8989: lib/util.sh: make: added check_target_exists
- 12:42 AM Revision 8988: lib/util.sh: moved $top_file* to runscripts/util.run because they only apply to runscripts
- 12:36 AM Revision 8987: lib/util.sh: make: added to_target, which uses to_file on $target
- 12:35 AM Revision 8986: lib/util.sh: added to_file (), which auto-removes a command's output file on error (like make's .DELETE_ON_ERROR)
- 12:31 AM Revision 8985: lib/util.sh: echo_run_extern, extern: fixed/added comments to indicate that echo_run_extern echoes and controls stderr of *an* external command, while the extern alias does this for *all* external commands
- 12:28 AM Revision 8984: lib/util.sh: auto-echo common external commands, such as rm
- 12:24 AM Revision 8983: lib/util.sh: echo_run_extern, extern aliases: alias-expand next word (the command) by adding trailing space to alias def
- 12:21 AM Revision 8982: bugfix: lib/util.sh: exceptions: log_e: must include `declare e` in the alias and not when save_e is called, so that $e is a local var *of the caller*. this bug did not appear in testing because the save_e alias, which re-scopes $e within log_e (), was not expanded inside log_e () (since new aliases were not loaded between save_e and log_e ()).
- 12:12 AM Revision 8981: lib/util.sh: exceptions: added log_e (), which prints a "command exited with error" message (like make) when applicable
- 12:09 AM Revision 8980: lib/util.sh: exceptions: try_ (): renamed to try () and use the function keyword to distinguish it from the alias
- 12:06 AM Revision 8979: lib/util.sh: exceptions: try_ (): use new save_e
- 12:05 AM Revision 8978: lib/util.sh: exceptions: added save_e
- 12:01 AM Revision 8977: lib/util.sh: exceptions: end_try* aliases: use new rethrow*
05/09/2013
- 11:59 PM Revision 8976: lib/util.sh: exceptions: added rethrow, rethrow_subshell aliases
- 11:47 PM Revision 8975: lib/util.sh: always use '' rather than "" around alias definitions, to ensure that variables are evaluated at expand time rather than compile time
- 11:44 PM Revision 8974: lib/util.sh: zip_newer/unzip_newer: evaluate $no_force at alias expansion time rather than at alias compile time, so that the $no_force can be overridden in the context the alias is used in
- 11:18 PM Revision 8973: lib/util.sh: use `|| return` instead of `|| exit` because `|| exit` doesn't seem to work inside functions (it does not have the errexit effect). also, `|| return` has the advantage of *not* exiting the program if the caller used || after the command (i.e. as an error handler) to temporarily disable errexit.
- 11:11 PM Revision 8972: lib/runscripts/util.run: tell users to override run_args_cmd rather than this function to perform other commands, so that on_exit () can contain other exit-related processing that should *not* be overriden by the user
- 11:05 PM Revision 8971: lib/util.sh: removed "" around $?, $# because they are guaranteed to always be non-empty and contain no special chars
- 10:17 PM Revision 8970: lib/util.sh: say "last space" instead of "trailing space" so the comment will be more likely to fit at the end of the line
- 06:11 PM Revision 8969: lib/local.sh: removed mysql () since its functionality is now provided by mysql () in util.sh
- 05:59 PM Revision 8968: lib/util.sh: mysql_cmd (): $server: like $ssh_server, clear the value when it's equal to this machine's hostname
- 05:58 PM Revision 8967: lib/util.sh: mysql_cmd (): $ssh_server: use new localize_url to clear the value when it's equal to this machine's hostname
- 05:37 PM Revision 8966: lib/util.sh: added localize_url ()
- 05:36 PM Revision 8965: inputs/GBIF/table.run: table.tsv/make (): use extern so the MySQL_export command is echoed
- 05:24 PM Revision 8964: inputs/GBIF/table.run: table.tsv/make (): don't make the target if it already exists
- 05:16 PM Revision 8963: inputs/GBIF/table.run: table.tsv/make (): create the file directly rather than using inline_make, so that the command to create the file can use shell functions such as mysql
- 05:07 PM Revision 8962: bugfix: inputs/GBIF/table.run: table.tsv/make (): need to use $(target) (target's path *relative to curdir*) instead of just the filename, now that make does not change the directory
- 05:01 PM Revision 8961: inputs/GBIF/table.run: moved table.tsv creation to separate table.tsv/make () function
- 04:59 PM Revision 8960: lib/util.sh: echo_stdin (): display the echoed input after leading output of the echoed-to command, by using sleep with a small fractional # of seconds
- 04:38 PM Revision 8959: *{.sh,run}: put functions on one line where possible (and where they are not expected to expand)
- 04:32 PM Revision 8958: lib/local.sh: root_make (): use make () rather than extern make now that make () does not set its own current dir. using make () also automatically enables \$stdout2stderr, which is needed to redirect the echoed make commands.
- 04:26 PM Revision 8957: lib/util.sh: extern (): use exec to ensure that the executed command is in fact external, and not a shell builtin or other type of non-function command. this also simplifies the code because any shell function for the command does not need to be unset.
- 04:20 PM Revision 8956: lib/util.sh: make (): don't change the directory to $top_dir, because paths used by the caller will instead be relative to the current dir (note that in runscripts, paths are generally *not* absolute because of canon_rel_path ()). this requires manually specifying $top_dir when running make on a physical (rather than inlined) makefile.
- 04:01 PM Revision 8955: lib/util.sh: log_stderr_cmd (): replaced the `|| exit` after the () with `|| return`, for the same reason that this was a problem for extern () (see r8954)
- 03:55 PM Revision 8954: lib/util.sh: extern (): replaced the `|| exit` after the () with `|| return`, because `|| exit` strangely does not use $? as its exit status (even though `|| exit $?` works fine). in a shell function, it is actually sufficient, for errexit purposes, to use `|| return`, because the exit status is checked upon return from the function. it is in fact preferable to use return rather than exit, because then the caller can catch the exception using `|| true`.
- 03:51 PM Revision 8953: lib/util.sh: extern (): removed the `|| exit` inside the (), because this strangely prevents the exit status from being propagated to the exit status of the ()
- 03:44 PM Revision 8952: lib/util.sh: added explicit `set -o errexit` in case caller did not have -e in #! line
- 02:47 PM Revision 8951: inputs/GBIF/table.run: renamed MySQL_export () to export_mysql () to match schemas/VegCore/VegCore.ERD.mwb.run
- 02:21 PM Revision 8950: inputs/GBIF/table.run: renamed MySQL_export () to export_mysql () to match schemas/VegCore/VegCore.ERD.mwb.run
- 02:06 PM Revision 8949: inputs/FIA/_archive/2011-10-17/: set svn:ignore to *
- 01:52 PM Revision 8948: web/links/index.htm: updated to Firefox bookmarks. added Mac upgrade and recovery-related bookmarks.
- 12:07 PM Revision 8947: bugfix: lib/import.sh: remake_VegBIEN_mappings (): don't run if there is no public schema to perform the test on (e.g. if the staging tables have just been reinstalled)
- 12:06 PM Revision 8946: lib/import.sh: added public_schema_exists (), which just calls psql_script_vegbien (i.e. with the default search_path temp, public, etc.) and sees if returns an error
- 11:50 AM Revision 8945: /README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: when changes are made on vegbiendev: added step to download TWiki separately to your machine, to ensure that it gets backed up even if you don't sync the rest of the files. also, TWiki needs to be run with delete enabled to remove old session files, while the rest of the files should be run without delete.
- 08:28 AM Revision 8944: schemas/VegCore/VegCore.ERD.mwb.run: use my2pg's new sql_ascii mode
- 08:27 AM Revision 8943: bin/my2pg: support $sql_ascii mode, where varbinary is translated to text instead of bytea
- 08:27 AM Revision 8942: bin/my2pg: remove any () after text
- 08:23 AM Revision 8941: schemas/VegCore/VegCore.ERD.mwb.run: VegCore.my.sql/make (): leave out the DROP TABLE statements for now using --skip-add-drop-table
- 08:19 AM Revision 8940: added schemas/VegCore/VegCore.pg.sql.run with install () command (also part of all ())
- 08:19 AM Revision 8939: lib/local.sh: added root_make ()
- 08:15 AM Revision 8938: bin/my2pg: unpack custom types set('...')
- 08:12 AM Revision 8937: lib/local.sh: psql (): use fd 4 for the logging output instead of 3 because 3 is generally used for passing inline *input* commands (it is used this way by inline_make)
- 08:05 AM Revision 8936: schemas/VegCore/VegCore.ERD.mwb.run: sync (): don't pass "$@" to export_/import because they do not accept args, and the same set of args would not be meaningful for both
- 08:00 AM Revision 8935: schemas/VegCore/VegCore.ERD.mwb.run: use new $top_filename instead of $archive_filename
- 08:00 AM Revision 8934: lib/util.sh: added $top_script (alias for $0), $top_file, $top_filename. use new $top_file in $top_dir.
- 07:54 AM Revision 8933: schemas/VegCore/VegCore.ERD.mwb.run: put zip_newer/unzip_newer on the same line as the `cd "$top_dir"`
- 07:45 AM Revision 8932: bin/my2pg: translate varbinary to bytea
- 07:42 AM Revision 8931: schemas/VegCore/VegCore.ERD.mwb.run: added export_postgres (), which calls VegCore.pg.sql/make ()
- 07:29 AM Revision 8930: lib/util.sh: wrapper functions of external commands: use new self alias
- 07:28 AM Revision 8929: lib/util.sh: added self alias, for use with wrapper functions of external commands
- 07:18 AM Revision 8928: schemas/VegCore/VegCore.my.sql: regenerated using `VegCore.ERD.mwb.run export_mysql` (also part of the all target). note that this uses mysqldump, so the format and table order is different than it was for MySQL Workbench's custom export script.
- 07:05 AM Revision 8927: schemas/VegCore/VegCore.ERD.mwb.run: added export_mysql (), which runs VegCore.my.sql/make ()
- 07:05 AM Revision 8926: schemas/VegCore/VegCore.ERD.mwb.run: added export_mysql (), which runs VegCore.my.sql/make ()
- 07:03 AM Revision 8925: bugfix: lib/local.sh: $PATH: use $bin_dir_abs so the path will remain valid if the current directory is changed
- 07:02 AM Revision 8924: lib/local.sh: added \$bin_dir_abs
- 06:58 AM Revision 8923: bugfix: lib/util.sh: extern (): added `|| exit` after "$@" in addition to after the (), because this additional `|| exit` is apparently needed in order to propagate the exit status of the command to the exit status of the () and cause an error to abort the script properly
- 06:51 AM Revision 8922: lib/util.sh: echo_vars (): output vars with log_level 3 so they can be excluded separately from function calls to reduce clutter in the logging output. increase the default util.run verbosity so that vars are still printed by default.
- 06:47 AM Revision 8921: bugfix: lib/util.sh: echo_vars (): output each var separately so that each is prefixed by $PS4
- 06:39 AM Revision 8920: lib/util.sh: inc/dec_log_level: indent commands at higher log levels using $log_indent
- 06:39 AM Revision 8919: lib/util.sh: inc/dec_log_level: indent commands at higher log levels using $log_indent
- 06:31 AM Revision 8918: bugfix: lib/util.sh: make (): use stdout2stderr=1 so that commands make runs are properly output to stderr
- 06:21 AM Revision 8917: bugfix: lib/util.sh: include_guard_var (): use extern () when invoking sed so that this internal use of it isn't verbosely logged along with other external commands. note the "" around extern to refer to the function, not the alias.
- 06:16 AM Revision 8916: bugfix: lib/util.sh: zip/unzip (): use new $stdout2stderr instead of >&2 so that the redirect happens in the right order
- 06:15 AM Revision 8915: lib/util.sh: log_stderr_cmd (): support redirecting stdout to stderr *after*setting up the stderr redirect, so that stdout is also subject to that redirect
- 06:11 AM Revision 8914: lib/util.sh: added stdout2stderr ()
- 06:08 AM Revision 8913: lib/util.sh: changed echo_run_extern () to an alias
- 06:04 AM Revision 8912: lib/util.sh: echo_run_extern (): use new log_stderr_cmd
- 06:03 AM Revision 8911: lib/util.sh: added log_stderr_cmd ()
- 05:57 AM Revision 8910: lib/util.sh: use extern instead of env to run external commands, because it's simpler and auto-captures the logging output
- 05:44 AM Revision 8909: lib/util.sh: echo_func (): use the much simpler function keyword to avoid expanding the echo_func alias when defining the function, rather than going through the complex process of unaliasing and realiasing the echo_func alias
- 05:38 AM Revision 8908: lib/util.sh: mark env as always being an external command. it is no longer necessary to automatically echo it using echo_run because the extern alias does this now.
- 05:31 AM Revision 8907: lib/util.sh: automatically echo external commands. this requires using the function keyword when declaring extern () so that the new extern alias is not expanded in the function name.
- 05:28 AM Revision 8906: lib/util.sh: added echo_run_extern (), which automatically runs log_stderr to capture the external command's stderr
- 05:27 AM Revision 8905: lib/util.sh: added extern ()
- 05:05 AM Revision 8904: lib/util.sh: added log_stderr ()
- 04:54 AM Revision 8903: lib/util.sh: added end_try_subshell alias
- 04:29 AM Revision 8902: lib/util.sh: zip/unzip: redirect logging output to stderr
- 04:23 AM Revision 8901: lib/util.sh: use inc_log_level where logging info should only be output for verbosity >= 2: echo_func, echo_vars, echo_stdin
- 04:03 AM Revision 8900: lib/util.sh: verbose output: added inc_log_level, dec_log_level aliases which manipulate $verbosity. note that changes in $log_level are now instead indicated by moving $verbosity in the opposite direction.
- 04:01 AM Revision 8899: lib/util.sh: added let () wrapper that prevents it from triggering error-exit
- 03:16 AM Revision 8898: lib/util.sh: verbose output: use just one var ($verbosity) instead of two ($verbosity and $log_level), to track log level, for simplicity. $verbosity would now be subtracted from to alter the log level instead of $log_level being added to.
- 03:09 AM Revision 8897: lib/util.sh: use new can_log wherever logging info is output to stderr
- 03:05 AM Revision 8896: renamed lib/runscripts/local.run to lib/local.sh since the things it defines are not just for runscripts
- 02:53 AM Revision 8895: lib/util.sh: verbose output: added $log_level (must always be > 0 so verbosity=0 turns off all logging) and can_log (), which compares $log_level to $verbosity
- 02:32 AM Revision 8894: bugfix: lib/local.sh: updated $root_dir
- 02:31 AM Revision 8893: renamed lib/runscripts/local.run to lib/local.sh since the things it defines are not just for runscripts
- 02:22 AM Revision 8892: lib/runscripts/local.run: added mysqldump_local, which uses vegbiendev
- 02:21 AM Revision 8891: lib/runscripts/local.run: use postgres_compat mode because all our MySQL schemas should be usable as inputs to my2pg
- 02:20 AM Revision 8890: lib/runscripts/local.run: added connection vars for local (bien) user
- 02:18 AM Revision 8889: lib/util.sh: moved unalias inside include guard since it is not needed by anything *before* the include guard (even though it is used by commands *outside* the include guard, i.e. when the include guard is temporarily closed and reopened to load/unload aliases)
- 02:06 AM Revision 8888: lib/util.sh: use declare instead of local in aliases so that the aliases can also be used outside a function (declare will create a local var when used inside a function, and a global var otherwise)
- 02:00 AM Revision 8887: lib/util.sh: zip: ignore "zip has nothing to do" exit status as this is not an error
- 01:58 AM Revision 8886: lib/util.sh: added exception-handling (i.e. error-suppressing) functions
- 01:03 AM Revision 8885: bugfix: lib/util.sh: echo_func alias: moved it outside the include guard because the unalias statement is needs to be outside the include guard, and therefore so does the alias statement in order to always restore the alias
- 12:59 AM Revision 8884: lib/util.sh: renamed echo_func_ () back to echo_func () and instead add an unalias statement *before* the if statement containing the function definition. this is necessary because if statements are "compound commands", which have aliases expanded when their definition is read (i.e. at the beginning of the if statement, for the entire if statement), not when they are executed, and any aliases for function names in them need to be unaliased *before* the if statement containing the function definition. this is necessary even if the if statement is *not* executed, because the expansion of such aliases will cause syntax errors in the parsing of the if statement itself.
- ** note that this is preferable to the previous approach, because it causes bash to automatically fall back to the fu...
- 12:45 AM Revision 8883: lib/util.sh: added unalias () override, which doesn't produce an error if the alias is undefined
- 12:04 AM Revision 8882: bugfix: lib/util.sh: renamed echo_func () to echo_func_ (), because you apparently can't have a function with the same name as an alias, even if the function is defined before the alias and an include guard prevents the function from being defined again after the alias is set. there may be some kind of alias-expanding preprocessing pass that bash only does in script mode, or maybe there is some other problem related to our use of aliases inside if statements.
05/08/2013
- 08:02 PM Revision 8881: *{.sh,run}: changed echo_func to an alias that includes the "$@", so that callers don't need to specify the "$@" manually. although the original echo_func function is still there, callers need to switch over to the alias at the same time as it's defined because otherwise the "$@" would be doubled, since echo_func refers to the alias instead.
- 07:21 PM Revision 8880: lib/util.sh: added set_make_vars alias, for use with make-target-style shell functions
- 06:37 PM Revision 8879: lib/util.sh: mysql_cmd (): interpret an empty string for $user, $database as if they were unset
- 06:34 PM Revision 8878: bugfix: lib/util.sh: mysql_cmd (): add --tables after specifying --databases so that future unnamed arguments are correctly interpreted as tables
- 06:33 PM Revision 8877: bugfix: lib/util.sh: mysql_cmd (): need to use `--databases ...` rather than `--database=...` to specify the database as a named argument
- 06:26 PM Revision 8876: bugfix: lib/util.sh: mysql_cmd (): need space before $database in command
- 06:23 PM Revision 8875: lib/util.sh: mysql_cmd (): use $schema as $database when provided
- 06:14 PM Revision 8874: lib/util.sh: mysql_cmd (): accept $database connection var
- 06:02 PM Revision 8873: *{.sh,run}: use just env instead of echo_run env now that env is an auto-echoing alias
- 05:56 PM Revision 8872: lib/util.sh: automatically echo commands that use env
- 05:55 PM Revision 8871: lib/util.sh: moved strings after verbose output so strings commands can use verbose output aliases
- 05:28 PM Revision 8870: lib/util.sh: mysql_cmd (): don't ssh if the ssh_server is this machine
- 05:27 PM Revision 8869: lib/util.sh: mysql_cmd (): allow specifying the ssh_dest as a separate ssh_server and ssh_user
- 05:08 PM Revision 8868: lib/util.sh: using prefixed connection vars: added use_local, use_local_remote aliases
- 04:42 PM Revision 8867: lib/util.sh: added mysqldump_diffable ()
- 04:41 PM Revision 8866: lib/util.sh: added mysqldump () wrapper, which does what my2pg_export does, but integrates with mysql_cmd and allows turning off postgres-compatible mode
- 04:15 PM Revision 8865: lib/util.sh: mysql_cmd (): use ${FUNCNAME[1]} to get the caller's command name instead of requiring the caller to pass the command name explicitly
- 03:56 PM Revision 8864: lib/util.sh: databases: added use_remote alias to use the remote_* connection vars (which uses new import_vars)
- 03:54 PM Revision 8863: lib/util.sh: added import_vars alias
- 03:53 PM Revision 8862: lib/util.sh: mysql_cmd (): added doc comment
- 03:52 PM Revision 8861: lib/util.sh: mysql (): use new mysql_cmd to auto-add connection/login opts when specified
- 03:50 PM Revision 8860: lib/util.sh: added mysql_cmd ()
- 03:48 PM Revision 8859: lib/util.sh: added local_inv alias
- 03:34 PM Revision 8858: lib/util.sh: zip/unzip_newer: support extracting/updating the file even if it has an older mtime by setting $force, using new set_inv to get a var to use to determine whether to include the -u flag
- 03:32 PM Revision 8857: lib/util.sh: added set_inv ()
- 03:30 PM Revision 8856: lib/util.sh: echo_vars (): prefix the declare output with "+ " because it's actually a command, not just an indication of the var's value
- 03:28 PM Revision 8855: lib/util.sh: added sed ()
- 03:23 PM Revision 8854: lib/util.sh: added section labels
- 10:57 AM Revision 8853: web/links/index.htm: removed broken favicons
- 10:55 AM Revision 8852: web/links/index.htm: removed broken favicons. this requires using the SQLite Manager Firefox add-on <https://addons.mozilla.org/en-US/firefox/addon/sqlite-manager/?src=search> to manually remove the favicon entries.
- 10:18 AM Revision 8851: lib/Firefox_bookmarks.reformat.csv: formatting fixes: don't put the src attribute of the favicon image on its own line, because it no longer contains long inline image data
- 10:15 AM Revision 8850: lib/Firefox_bookmarks.reformat.csv: favicon image: remove ICON attributes with inline image data, since these are no longer needed for the favicon images and this avoids cluttering up the svn diff
- 10:11 AM Revision 8849: lib/Firefox_bookmarks.reformat.csv: favicon image: use ICON_URI instead of ICON to fetch the favicon directly from the original site. this allows the favicons to be cached separately from the bookmarks page, so that the inline favicon contents don't need to be re-retrieved every time the bookmarks page is updated. this also avoids cluttering up the svn diff.
- 10:01 AM Revision 8848: web/links/index.htm: updated to Firefox bookmarks. added description of the formats supported by PostgreSQL's COPY command and their escape sequences.
- 08:44 AM Revision 8847: bugfix: schemas/vegbien.sql: geoscrub_input_view: only include places whose country is not NULL, because at least the country is required for geoscrubbing
- 08:34 AM Revision 8846: /README.TXT: Schema changes: Reinstall staging tables: added step to run `make schemas/public/install` after the datasources are installed. note that this must be run *after* the datasources are installed, because views in public depend on some of the datasources.
05/06/2013
- 07:10 AM Revision 8845: /README.TXT: Schema changes: Reinstall staging tables: use `make db` instead of mk_db, which includes the required schemas/install command. some datasources use the util schema in their postprocess scripts, so this must be installed before the staging tables.
- 07:05 AM Revision 8844: bugfix: /Makefile: moved schemas/install from install to db so that it is also run whenever the DB is reinstalled. schemas/install is needed by the staging tables reinstallation performed by reinstall_all.
- 06:33 AM Revision 8843: bugfix: /README.TXT: Schema changes: Reinstall staging tables: also need to run `make mk_db` before running reinstall_all
- 06:30 AM Revision 8842: /README.TXT: Schema changes: Reinstall staging tables: drop the saved previous DB at the end of the operation
- 06:18 AM Revision 8841: /README.TXT: Schema changes: Reinstall staging tables: run all of the local machine steps on vegbiendev, including the vegbien DB rename, to ensure that the existing data is saved in case the reinstall has errors
- 05:57 AM Revision 8840: /README.TXT: Schema changes: Reinstall staging tables: added step to first rename existing vegbien database, so it is not modified in the reinstallation
- 05:27 AM Revision 8839: inputs/FIA/: archived no longer used BIEN2 FIA data from the nimoy geoscrub DB
- 05:26 AM Revision 8838: inputs/FIA/_archive/: moved FIA_COND_unique, Organism into 2011-10-17/ subdir
- 04:44 AM Revision 8837: /README.TXT: Schema changes: Reinstall staging tables: added step to first run this on the local machine to check for any errors, before running it on the live DB, to prevent the live DB from becoming unrestorable in the case of bugs
- 04:27 AM Revision 8836: bugfix: bin/with_all: pipe yes to the command in case it makes any interactive prompts, as in e.g. the TNRS staging tables reinstall
- 04:25 AM Revision 8835: bugfix: inputs/input.Makefile: sql/install: manually specify $no_search_path option to psql_script_vegbien, which is added automatically in $(psqlNoSearchPath) but that uses psql_verbose_vegbien
- 04:12 AM Revision 8834: bugfix: *{.sh,run}: use `local` when setting default values for params to prevent these values from leaking into the calling context, where it may have unexpected effects (e.g. pg_copy_to would permanently set $source, which would then be used on the next invocation of pg_copy_to instead of regenerating $source from the next $table value). this involves using ${var-default} or ${var:-default} to return the value to the local statement instead of setting it directly with ${var=default} or ${var:=default}.
- 04:00 AM Revision 8833: *{.sh,run}: commands that take named arguments: usage messages: changed to use simpler bash syntax for specifying command-specific env vars, which does not require a subshell ("The environment for any simple command or function may be augmented temporarily by prefixing it with parameter assignments" <http://www.gnu.org/software/bash/manual/bash.html#Environment>)
- 03:14 AM Revision 8832: schemas/pg_hba*.conf: removed trailing whitespace
- 03:10 AM Revision 8831: schemas/pg_hba*.conf: allow the bien group to access all databases, including test (on the Mac). note that this does not grant access to the vegbank DB on vegbiendev, because that is owned by postgres.
- 02:32 AM Revision 8830: web/links/index.htm: explicitly separate page's description from author comments where needed
- 02:29 AM Revision 8829: web/links/index.htm: use - instead of --- to separate the page's description from the author comments because it's faster to type and one hyphen is sufficient
- 02:21 AM Revision 8828: lib/Firefox_bookmarks.reformat.csv: labeling page's description: don't match descriptions with a leading blank line as an author comment, because sometimes page descriptions themselves start with a blank line. instead, author comments at the beginning of bookmark descriptions should always start with a " or be preceded by a line containing only hyphens (-). note that it was never reliable to use a blank line for this purpose, because it would be trimmed out upon reimport of the HTML file into Firefox.
- 02:17 AM Revision 8827: web/links/index.htm: updated to Firefox bookmarks
05/05/2013
- 10:35 PM Revision 8826: inputs/NVS/*/map.csv: Taxon Growth Form: use new _lowercase() to avoid needing to manually map each value that is already valid but just needs to be lowercased
- 10:28 PM Revision 8825: schemas/util.sql: added _lowercase()
- 09:05 PM Revision 8824: added inputs/CTFS/ERD/ VegPath location
- 11:57 AM Revision 8823: added inputs/MO/_src/_README.TXT with warning that the refresh provided to us is missing several columns from the original extract: CollectionCode, CatalogNumber, IndividualCount
- 10:59 AM Revision 8822: schemas/VegCore/VegCore.ERD.mwb: reduced MaxColumnsDisplayed to 10 to prevent wide tables from taking up too much space in the ERD. this was a big problem in the VegBIEN ERD, which we are hoping to prevent in the VegCore ERD as first-class columns get added to the tables. note that it's very important to ensure that the first-class columns are sorted *in importance order*, so that the 10 most important are visible in the ERD.
- 10:34 AM Revision 8821: schemas/VegCore/VegCore.ERD.mwb: renamed specimen_holder_institution to specimenholder_institution because specimenholder is one word
- 10:12 AM Revision 8820: lib/sql_io.py: put_table(): Calling wrapper function: adding pkey or index on the resulting table: don't display warning if a pkey can't be added, because this is actually a legitimate situation when the called function is set-returning and can return multiple rows for one input. having this as a warning results in spurious warnings in the automated tests (which look confusingly like ignored errors because Python warnings include debugging context information). e.g. `make inputs/Madidi/IndividualObservation/test.by_col.xml` causes this error in the sourcelist->sourcename splitting step (which of course can produce multiple specimenholder institutions).
- *** note that a *diff* will continue to be produced (but now without an error message), because row-based import does...
- 10:00 AM Revision 8819: bugfix: lib/sql.py: parse_exception(): typed_name_re (used by MissingCastException, etc.): don't require "" around the value, because function names in "function does not exist" exceptions are (now?) output without them. this exception did *not* occur in the last import, but *does* occur in the automated testing and when running the associated query in pgAdmin (in both Linux and Mac OS X).
- 04:30 AM Revision 8818: bugfix: /Makefile: apache-Linux: use the standard apt-get syntax for Makefiles (`-sudo apt-get --yes install`) instead of just `apt-get install`
- 04:24 AM Revision 8817: /Makefile: added Apache 2.4 installation
- 03:57 AM Revision 8816: lib/util.sh: added join ()
- 02:58 AM Revision 8815: web/.twiki/data/Main/TWikiPreferences.txt: updated with current settings
- 02:55 AM Revision 8814: put web/.twiki/data/Main/TWikiPreferences.txt under version control. note that this file (*Main*/TWikiPreferences.txt) is the correct file to change the settings in, not *TWiki*/TWikiPreferences.txt.
- 02:33 AM Revision 8813: put web/.twiki/data/TWiki/TWikiPreferences.txt under version control
- 01:58 AM Revision 8812: inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt: twikibuttons_formats: added blockquote format
- 01:47 AM Revision 8811: inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt: set inline_styles to false so that markup formatting (underline, strikethrough) gets formatted using HTML tags (<strike>, etc.) instead of CSS styles ("text-decoration: line-through", etc.)
- 01:26 AM Revision 8810: inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt: theme_advanced_buttons1: added underline, strikethrough buttons
- 01:25 AM Revision 8809: put inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt under version control
05/02/2013
- 11:07 PM Revision 8808: /run: export_ (): pass "$@" to invoked functions since it may contain psql connection or config info
- 11:06 PM Revision 8807: lib/util.sh: pg_* (): pass "$@" to invoked functions since it may contain psql connection or config info
- 10:59 PM Revision 8806: bugfix: lib/util.sh: pg_header (): use limit=0 to prevent COPY TO from returning all rows in the table (not an issue for empty tables!)
- 10:53 PM Revision 8805: lib/util.sh: pg_copy_to (): support sources besides whole tables (such as custom queries and tables with columns). support limiting the # of rows retrieved when using whole tables.
- 10:01 PM Revision 8804: lib/runscripts/import.run: added export_ () command, which is run after import in all ()
- 09:57 PM Revision 8803: bin/psql_verbose_vegbien: also echo queries issued by backslash commands (--echo-hidden)
- 09:34 PM Revision 8802: /run: make config vars such as $schema overridable by the environment, to allow pointing the export script at a different public schema version
- 08:53 PM Revision 8801: inputs/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files
- 08:50 PM Revision 8800: added inputs/HIBG/Specimen/header.csv
- 08:50 PM Revision 8799: added inputs/HVAA/Specimen/Herbario_occur_1360871068.csv.md5
- 08:40 PM Revision 8798: exports/: svn:ignore *.csv
- 08:39 PM Revision 8797: added /run, whose export_ command exports DB tables (currently the geoscrub_input table) to CSV. column information is included in the filename when the export format is specified not to contain a header row.
- 08:35 PM Revision 8796: lib/runscripts/local.run: moved log_sql (), pg_* () to lib/util.sh because these do not depend on local external scripts in bin/
- 08:27 PM Revision 8795: lib/runscripts/local.run: added pg_copy_to (), pg_header (), pg_export_table_no_header (), pg_export_table_to_dir_no_header ()
- 08:26 PM Revision 8794: lib/runscripts/local.run: added mk_schema_esc, mk_table_esc aliases as shortcuts for `local *_esc; mk_esc_name *`
- 08:09 PM Revision 8793: lib/util.sh: self_not_included (): added support for loading newly-defined aliases for use in functions in the same file, and documentation for how to do this
- 02:49 PM Revision 8792: lib/runscripts/local.run: psql (): output only the query results to stdout (using --output), and redirect everything else to stderr
- 02:26 PM Revision 8791: added /exports/
- 02:24 PM Revision 8790: lib/runscripts/local.run: added log_sql (). mysql (): don't echo SQL commands when not in verbose mode. this is needed to support commands that use the query result in a $() expression, and should not have echoed commands cluttering up stdout. (unfortunately, the SQL commands are echoed to stdout rather than stderr.)
- 01:52 PM Revision 8789: schemas/vegbien.sql: range_modeling_input: use analytical_stem instead of analytical_stem_view because it takes a long time (~2 min) to get a row from the left-joined view, due to the large number of joins and large number of rows in the joined tables
- 01:41 PM Revision 8788: web/links/index.htm: updated to Firefox bookmarks. grouped related items together.
- 01:28 PM Revision 8787: web/links/index.htm: author comments at beginning of bookmark desc: start with a line containing only dashes (-) rather than a blank line, because a newline will be trimmed away on reimport into Firefox, such that reexporting it will lose the author comment indicator
- 01:24 PM Revision 8786: lib/Firefox_bookmarks.reformat.csv: label page's description: support starting a description with a line containing only dashes (-) to indicate author comments. this is better than a newline, because a newline will be trimmed away on reimport into Firefox, such that reexporting it will lose the author comment indicator
- 01:16 PM Revision 8785: lib/Firefox_bookmarks.reformat.csv: add hyperlinked HTML anchors for folders: switch back to using <a href=...> instead of onclick, but put the <a> tag *around* the <H3> rather than inside it so that Firefox can correctly parse out the folder name when importing the bookmarks
- 12:52 PM Revision 8784: lib/Firefox_bookmarks.reformat.csv: add hyperlinked HTML anchors for folders: use `onclick="javascript:document.location = '#...'"` instead of <a href=...> to allow clicking the header to go to the anchor, so that the <a> tag doesn't prevent Firefox from parsing the folder name
- 12:42 PM Revision 8783: bugfix: lib/Firefox_bookmarks.reformat.csv: add hyperlinked HTML anchors for folders: moved <a name=.../> outside the <H3> so that Firefox can correctly parse out the folder name when importing the bookmarks
- 12:27 PM Revision 8782: web/links/index.htm: updated to Firefox bookmarks. grouped related items together.
- 12:19 PM Revision 8781: lib/Firefox_bookmarks.reformat.csv: indexing: add hyperlinked HTML anchors for folders
- 11:50 AM Revision 8780: web/links/index.htm: updated to Firefox bookmarks
- 08:30 AM Revision 8779: schemas/vegbien.sql: added range_modeling_input view
- 08:21 AM Revision 8778: schemas/vegbien.sql: analytical_stem_view: order by datasource name so that the rows have a predictable rather than random ordering
- 06:14 AM Revision 8777: bugfix: lib/util.sh: moved mysql (), psql () to local.run because they use local commands that are only available after local.run sets the PATH. retain a mysql () function in util.sh that adds the --verbose option to mysql.
- 05:44 AM Revision 8776: lib/util.sh: removed "$bin_dir"/ before commands because the bin dir is now in the PATH
- 05:13 AM Revision 8775: lib/runscripts/table.run: moved general DB commands to lib/util.sh
- 04:47 AM Revision 8774: moved lib/*.run into runscripts/ subdir so runscripts are grouped together and easier to find rather than being scattered throughout lib/
- 04:19 AM Revision 8773: bugfix: lib/util.sh: canon_rel_path (): use $(pwd -P) instead of $PWD because symlinks are resolved by realpath (readlink -f), so they also need to be resolved in the current dir, but $PWD does not contain the symlinks-resolved version of the current dir
- 03:48 AM Revision 8772: inputs/GBIF/MySQL_export: use lib/util.sh instead of util.run now that the non-runscript-specific functions have been separated out into it. this ensures that MySQL_export is not unintentionally treated as a runscript (which functions differently from a normal shell script).
- 02:46 AM Revision 8771: /.htaccess: use canonical URL without symlinks
- 02:44 AM Revision 8770: added /.htaccess to create the right self-referential URL since / is outside the document root (linked from /vegbiendev/fs/)
- 02:14 AM Revision 8769: schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps: moved labels to the *start* of the arrow they label, so that the user can more easily follow the arrows from step to step by looking for an outward-pointing arrow with a label
- 01:48 AM Revision 8768: added inputs/GBIF/_MySQL/MySQL.data.sql.gz.md5
- 12:46 AM Revision 8767: bugfix: lib/common.Makefile: Compression: %.gz <-> %: only run command if target does not exist, to avoid overwriting the target when the compressed or uncompressed version is newer than it. the difference in mtimes can arise when one file is created after the other, and should not cause the opposite operation to be performed to try to make the other file up-to-date (leading to an infinite back-and-forth of creating one file from the other).
04/30/2013
- 11:13 PM Revision 8766: web/links/index.htm: updated to Firefox bookmarks. the VegPath link now includes the new favicon.
- 11:12 PM Revision 8765: added web/favicon.ico generated from schemas/BIEN_logo.png
- 11:01 PM Revision 8764: web/main.conf: added SSL-protected site for use with password-protected areas of the site, so that the user's password is not transmitted in plaintext. (because the SSL certificate is self-signed, it will unfortunately display the Confirm Security Exception message in Firefox.) note that digest authentication cannot be used to avoid plaintext passwords, because it requires knowing the user's original password to generate the digest, but we have only the MD5 sums in /etc/shadow.
- 09:26 PM Revision 8763: web/links/index.htm: updated to Firefox bookmarks
- 08:08 PM Revision 8762: web/links/index.htm: put all bookmarks into one subfolder named BIEN links, to facilitate importing them all into one folder on another machine. this also helps when upgrading to a newer version of the bookmarks, because the previous version must be deleted and this now requires deleting only a single folder.
- 08:02 PM Revision 8761: lib/Firefox_bookmarks.reformat.csv: use <H3 style="font-size: 200%;"> instead of <H1> to make the first folder's name the page title, so that Firefox can reimport the first folder as a bookmarks folder
- 07:42 PM Revision 8760: bugfix: lib/Firefox_bookmarks.reformat.csv: make first folder name the page title: added back replacement string
- 07:40 PM Revision 8759: web/links/index.htm.run: clean_up (): removed command to add page title because this is now done by lib/Firefox_bookmarks.reformat.csv
- 07:40 PM Revision 8758: lib/Firefox_bookmarks.reformat.csv: use page title as window title
- 07:31 PM Revision 8757: lib/Firefox_bookmarks.reformat.csv: remove previous page title
- 07:29 PM Revision 8756: lib/Firefox_bookmarks.reformat.csv: make first folder name the page title
- 07:21 PM Revision 8755: lib/Firefox_bookmarks.reformat.csv: move Bookmarks Toolbar inside first folder instead of before it. this allows storing all bookmarks in one subfolder so that when the web page is imported into another computer's bookmarks, the imported bookmarks are all together in one folder.
- 07:16 PM Revision 8754: bugfix: lib/Firefox_bookmarks.reformat.csv: refactored regexps to account for Python applying (?s) to the entire regexp, even if it appears inside a () subgroup. the Python behavior is in contrast to the standard regexp behavior used by Java, etc. where (?s) applies only to the subgroup it appears in.
- 06:19 PM Revision 8753: web/links/index.htm: updated to Firefox bookmarks. resources: put unsorted links into subfolders.
- 06:11 PM Revision 8752: bugfix: lib/Firefox_bookmarks.reformat.csv: add <style>: format bookmark description as plaintext: use `white-space: pre-wrap` instead of pre in order to wrap long lines
- 06:07 PM Revision 8751: bugfix: lib/Firefox_bookmarks.reformat.csv: favicon images: made replacements idempotent so that the favicons would not be deleted the next time the web/links/index.htm.run is run (due to a newline being added before ICON= )
- 05:52 PM Revision 8750: lib/Firefox_bookmarks.reformat.csv: favicon images: display placeholder favicon image for every link to ensure uniform alignment
- 05:45 PM Revision 8749: added web/links/blank.gif symlink to web/blank.gif for shorter blank.gif URLs
- 05:43 PM Revision 8748: added web/blank.gif
- 05:14 PM Revision 8747: lib/Firefox_bookmarks.reformat.csv: display ICON attributes as separate images. note that this uses the "data:" embedded image contents provided in the bookmarks file, so the images load instantly along with the page instead of needing to be separately retrieved from each server.
- 04:45 PM Revision 8746: lib/Firefox_bookmarks.reformat.csv: instead of removing ICON attributes with favicon contents, put them on their own line so the rest of the line is easier to see
- 04:35 PM Revision 8745: lib/Firefox_bookmarks.reformat.csv: divided replacements into sections
- 04:27 PM Revision 8744: lib/Firefox_bookmarks.reformat.csv: move Bookmarks Toolbar to beginning, remove its desc, and rename it to Quick links
- 04:13 PM Revision 8743: web/links/index.htm: removed extra divider after Recent Tags, Recently Bookmarked because section dividers interfere with regexp matching and the Bookmarks Toolbar is already visually separate from them
- 04:09 PM Revision 8742: web/links/index.htm: moved Recent Tags, Recently Bookmarked special folders to end because they are Firefox-specific and not part of the BIEN links (they also do not work in a browser because they are Firefox-specific query bookmarks instead of actual folders)
- 03:32 PM Revision 8741: web/links/index.htm.run: clean_up (): rename the page title from "Bookmarks" to "BIEN links"
- 03:18 PM Revision 8740: bin/repl: skip header instead of parsing it, since its columns are not used. this also allows using just a blank line as the header when the column names are not important.
- 03:05 PM Revision 8739: web/links/index.htm: use initial blank line instead of previous "-" workaround to indicate author comment at start of bookmark desc
- 03:04 PM Revision 8738: web/links/index.htm: use initial blank line to indicate author comment at start of bookmark desc
- 02:59 PM Revision 8737: lib/Firefox_bookmarks.reformat.csv: label page's description: don't label a bookmark desc starting with a blank line (indicating an author-added comment) as a page's description
- 02:51 PM Revision 8736: lib/Firefox_bookmarks.reformat.csv: label page's description: don't label an author-added quotation (which starts with " ) as the page's description
- 02:33 PM Revision 8735: bin/in_place: set the permissions of the new file to the original file when `chmod --reference` is available. this ensures that when a file is marked web-accessible, it stays web-accessible when you run an in_place command on it.
- 02:22 PM Revision 8734: web/links/index.htm: BitTorrent Sync: security warning about data leak: added link to reported bug at http://forum.bittorrent.com/topic/18612-security-hole-in-linux-webui-makes-all-your-files-publicly-accessible/ . updated workaround instructions.
- 01:20 PM Revision 8733: web/links/index.htm: updated to Firefox bookmarks. BitTorrent Sync: added security warning that running btsync on Linux will by default create a *publicly-accessible, unprotected* WebUI, allowing anyone on the web to create a sync folder to view and edit any of your files. to avoid this, always run btsync with a config file which sets a password on the WebUI. if you have already run btsync, run `killall btsync` to turn off the WebUI.
- 12:59 PM Revision 8732: web/links/index.htm: updated to Firefox bookmarks. changes include links about BitTorrent Sync.
- 12:51 PM Revision 8731: lib/Firefox_bookmarks.reformat.csv: label <meta> description: renamed label text to "page's description" to be understandable to non-programmers
- 12:49 PM Revision 8730: lib/Firefox_bookmarks.reformat.csv: label <meta> description: remove any existing description label, to avoid duplicating the description label when the text of the description label changes
- 12:37 PM Revision 8729: lib/Firefox_bookmarks.reformat.csv: label <meta> description as such to avoid confusing it with comments added by the bookmark author, who may not agree with it. the <meta> description is in the 1st paragraph(s), when provided.
- 12:13 PM Revision 8728: lib/Firefox_bookmarks.reformat.csv: remove LAST_MODIFIED attributes, which seem to change whenever the favicon is updated and clutter up the svn diff
- 12:05 PM Revision 8727: lib/Firefox_bookmarks.reformat.csv: remove ICON attributes with favicon contents, which clutter up the svn diffs
- 11:52 AM Revision 8726: added web/links/index.htm.run with clean_up action to run whenever the index.htm bookmarks file is changed (`web/links/index.htm.run clean_up`)
- 11:51 AM Revision 8725: added lib/Firefox_bookmarks.reformat.csv
04/25/2013
- 09:58 PM Revision 8724: README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: exclude only backup files in the Documents/BIEN/svn/backups/ dir (sync the other files)
- 09:53 PM Revision 8723: README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: when changes are made on vegbiendev: don't sync the group, which can be bien on vegbiendev but not on jupiter (where aaronmk is not a member of the bien group)
- 09:51 PM Revision 8722: README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: when changes are made on vegbiendev: include *.md5
- 09:08 PM Revision 8721: README.TXT: Maintenance: removed step to backup the Ubuntu VM, because this is now done as part of the "backup files not in Time Machine" step
- 09:07 PM Revision 8720: README.TXT: Maintenance: added steps to backup files not in Time Machine
- 08:57 PM Revision 8719: README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: back up (almost) all files in the home directory instead of just Library/ (to both jupiter and Dropbox)
- 06:45 PM Revision 8718: README.TXT: put commands: removed unnecessary /** after dirs to exclude
- 06:26 PM Revision 8717: README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: added steps to also backup the settings to Dropbox (in addition to jupiter)
- 06:13 PM Revision 8716: lib/util.sh: added realpath () and use it where `readlink -f` is used
- 06:05 PM Revision 8715: lib/util.run: doc comment: changed "run scripts" to "runscripts"
- 06:04 PM Revision 8714: lib/util.run: factored general utils (non-runscript-specific) out into new util.sh
- 05:55 PM Revision 8713: lib/util.run: renamed $verbose to $verbosity because it's an integer level, not a boolean. continue to support specifying the verbosity in $verbose.
- 05:52 PM Revision 8712: lib/util.run: support $verbose="", which is treated as 0
- 05:50 PM Revision 8711: lib/util.run: only automatically echo env vars when they are set if verbosity is >= 2
- 05:49 PM Revision 8710: lib/util.run: added $verbose var to control logging. this is normally set to 0, but defaults to 2 for a runscript.
- 05:41 PM Revision 8709: lib/util.run: moved `shopt -s expand_aliases` inside the include guard so callers can override the setting without it being reset if util.run is included again
- 05:39 PM Revision 8708: lib/local.run: add $bin_dir to the PATH
- 05:15 PM Revision 8707: bin/in_place: don't run if no command to run, because that would erase the file
- 05:10 PM Revision 8706: bin/in_place: use -e (exit on error) option to sh instead of adding `|| exit` after every command
- 04:49 PM Revision 8705: *run: added include guards
- 04:30 PM Revision 8704: bugfix: lib/util.run: added include guard to prevent issues in "diamond includes", where a runscript includes two runscripts and *each* includes util.run, causing the second include of util.run to reset any methods overridden in the first included runscript. this prevents util.run from being included twice in the first place.
- 04:25 PM Revision 8703: lib/util.run: added include_guard_var (), self_not_included () for use by path-based include guards
- 03:40 PM Revision 8702: lib/util.run: echo_stdin (): print a separator before and after the echoed output to help distinguish it from other verbose output
- 03:37 PM Revision 8701: lib/table.run: use new local.run instead of defining $bin_dir, etc. itself
- 03:36 PM Revision 8700: lib/util.run: echo_export (): run the export builtin using `builtin` to avoid recursively calling any export alias or function defined by the user (e.g. `alias export=echo_export`. this causes util.run to be idempotent, such that it can be included multiple times without causing problems due to the redefinition of functions, vars, etc.
- 03:04 PM Revision 8699: added lib/local.run, which links to locally-available resources such as $bin_dir
- 02:50 PM Revision 8698: lib/table.run: added mysql (), mysql_ANSI ()
- 02:41 PM Revision 8697: added web/links/index.htm containing Firefox bookmarks exported to HTML. CSS style information has been added to fix default HTML tag formatting, improve readability, and handle the Firefox bookmarks format. <dd> tags have been manually closed where HTML would not auto-close them properly. note that these changes must be reapplied each time the bookmarks file is reexported (`svn di` will show the changes to make).
- 04:54 AM Revision 8696: lib/table.run: run mk_esc_name for $schema, $table
04/24/2013
- 11:18 PM Revision 8695: lib/table.run: added esc_name (), mk_esc_name ()
- 11:16 PM Revision 8694: lib/util.run: added set_var ()
- 10:58 PM Revision 8693: bugfix: lib/util.run: run_args_cmd (): `set --`: need to use eval so that the output of reverse is interpreted as escaped args rather than split using $IFS
- 10:40 PM Revision 8692: bugfix: lib/util.run: run_args_cmd (): BASH_ARGV is stored in reverse order, so it needs to be reversed to be usable as $@
- 10:38 PM Revision 8691: lib/util.run: added reverse ()
- 02:51 PM Revision 8690: schemas/VegCore/VegCore.ERD.mwb: regenerated exports
- 02:49 PM Revision 8689: schemas/VegCore/VegCore.ERD.mwb: source: renamed contact -> owner because smaller sources may not have an admin/contact person, but would have a copyright holder or other entity with control over the source's distribution
- 02:45 PM Revision 8688: schemas/VegCore/VegCore.ERD.mwb: added table comments from VegCore data dictionary (VegCore.vegpath.org)
- 01:08 PM Revision 8687: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 01:07 PM Revision 8686: schemas/VegCore/VegCore.ERD.mwb: added hstore expansion columns where needed
- 12:54 PM Revision 8685: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 12:34 PM Revision 8684: schemas/VegCore/VegCore.ERD.mwb: specimen: added unique constraint for each set of identifying columns
- 12:25 PM Revision 8683: schemas/VegCore/VegCore.ERD.mwb: collection: added back primary key
- 12:24 PM Revision 8682: schemas/VegCore/VegCore.ERD.mwb: specimen: made owner an fkey to collection instead of organization to correspond with orig_collection and current_collection (and to allow auto-filling it from current_collection in a trigger)
- 12:18 PM Revision 8681: schemas/VegCore/VegCore.ERD.mwb: specimen: reordered columns to group together each method of identifying a specimen
- 12:14 PM Revision 8680: schemas/VegCore/VegCore.ERD.mwb: collection: don't inherit from source, because a collection is a scoping entity, not a dataset. a collection *may* also be used as a dataset, but need not be for the purposes of scoping a specimen's accession_number.
- 12:07 PM Revision 8679: schemas/VegCore/VegCore.ERD.mwb: specimen: removed redundant stamping_institution and donor_institution, because these are now in orig_collection.institution. (it is assumed that stamping_institution and donor_institution are the same, because the first institution to acquire and store a specimen (the donor) is the one that stamps it with an accession_number.)
- 12:01 PM Revision 8678: schemas/VegCore/VegCore.ERD.mwb: specimen: split collection into orig,current_collection because the collection that scoped the accession_number (the orig_collection) is sometimes different than the collection where the specimen is now held (the current_collection, or specimen_holder_institutions), e.g. when the specimen is donated
- 11:49 AM Revision 8677: schemas/VegCore/VegCore.ERD.mwb: collection: added institution, name to identify and scope the collection
- 11:39 AM Revision 8676: schemas/VegCore/VegCore.ERD.mwb: changed taxon_name fkeys to taxon_concept where appropriate, and renamed the referencing columns to *_taxon_concept to clearly indicate the referenced table. taxon_concept fkeys are appropriate whenever a taxon is defined or associated with an observed entity, in which case the assertion is not just to a taxon name but to a defined taxon concept (albeit sometimes an unofficial taxon concept scoped by the collector or identifier).
- 11:08 AM Revision 8675: schemas/VegCore/VegCore.ERD.mwb: specimen: added code_in_individual column
- 10:40 AM Revision 8674: schemas/VegCore/VegCore.ERD.mwb: specimen: added fkey to individual for the individual the specimen was taken from
- 10:30 AM Revision 8673: schemas/VegCore/VegCore.ERD.mwb: individual/stem_observation: made individual/stem nullable because there is not always enough identifying information (stem tag, etc.) to actually associate an identifiable individual with an observation
- 10:27 AM Revision 8672: schemas/VegCore/VegCore.ERD.mwb: moved code from individual to individual_observation because the code is something applied at observation time, rather than something that can be used to track individuals *between observations*
- 10:17 AM Revision 8671: schemas/VegCore/VegCore.ERD.mwb: moved collection_event from taxon_occurrence to specimen because only specimens are actually collected, while other taxon_occurrences (e.g. individuals) must be uniquely identified by some means that are shared between re-observations (e.g. the stem tag)
- 10:03 AM Revision 8670: schemas/VegCore/VegCore.ERD.mwb: moved collector, collector_number from taxon_occurrence to taxon_observation because these are actually attributes that are available or assigned at observation time, rather than being intrinsic to the taxon_occurrence (which can be either an individual or a specimen)
- 09:34 AM Revision 8669: schemas/VegCore/VegCore.ERD.mwb: method: colored it forest green like stratum because these are both tables in the same category (method), and forest green is the color VegBank uses for methods. (the fact that VegBank gives stratum the method color indicates that we are on the right track when we are treating stratum as a type of method that's essentially a height class.)
- 09:27 AM Revision 8668: schemas/VegCore/VegCore.ERD.mwb: method: added parent fkey which can be used to autoinherit attributes from another method, in the same way that event autoinherits a method from its parent
- 09:16 AM Revision 8667: schemas/VegCore/VegCore.ERD.mwb: replaced < event label for diagram half with < place, because the occurrence half actually also includes events (observations), but does not include places
- 09:10 AM Revision 8666: schemas/VegCore/VegCore.ERD.mwb: removed extra empty page used for moving objects around
- 09:08 AM Revision 8665: schemas/VegCore/VegCore.ERD.mwb: swapped position of place and source categories so that the place tables, which users are apt to query often, are at the top, and the attribution information, which is likely to be used less often, is at the bottom. this also moves the plot table closer to taxon_occurrence, which should eventually have an fkey to it.
- 08:19 AM Revision 8664: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 08:05 AM Revision 8663: schemas/VegCore/VegCore.ERD.mwb: record: added source_id_scope and added it to the record_unique unique index
- 08:01 AM Revision 8662: schemas/VegCore/VegCore.ERD.mwb: Default*ColumnType: updated to VARBINARY type used in key columns
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