lib/sh/local.sh: added $root_user, $root_password

lib/sh/db.sh: added use_root alias (similar to use_local/use_remote)

added inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.schema.z.clean_up.sql, which removes duplicated and unnecessary indexes in raw_occurrence_record

added inputs/GBIF/_MySQL/GBIFPortalDB-2013-02-20.schema.0.preamble.sql

bugfix: lib/sh/resume_import.sh: sql_preamble(): also stop at first "-- Table structure for table" line (when using a full dumpfile rather than a data-only subset)

lib/sh/resume_import.sh: resume_import(): run connection preamble (first few lines of dumpfile) before continuing with main file at offset, so that connection setting are reapplied

lib/sh/resume_import.sh: is_pkey_imported__int(): use echo_stdout so the user can see the result of the > function in each iteration

added lib/sh/resume_import.sh and use it in inputs/GBIF/_MySQL/MySQL.data.sql.run

inputs/GBIF/_MySQL/MySQL.data.sql.run: is_pkey_imported__int(): made pkey name configurable in $pkey_name

inputs/GBIF/_MySQL/MySQL.data.sql.run: import_resume_pos() run time: removed seconds because the precision is likely only to the nearest half-minute

inputs/GBIF/_MySQL/MySQL.data.sql.run: documented that import_resume_pos() takes 6 min to run, with 37 iterations

added inputs/GBIF/_MySQL/MySQL.data.sql.run, with helper functions for resuming the import to MySQL from where it left off. this is very useful if the import is interrupted for any reason, because otherwise, the entire import would have to be run again from the start, taking 40-50 hours. import_resume_pos() uses new binsearch() to find where in the file the import left off, based on which pkeys have already been imported. (GBIF pkeys are unfortnately not in any order in the input file, nor are they in insertion order in the imported table, because MySQL instead clusters the table by the pkey. this necessitates a much more complex solution to resuming a partial import.)

lib/sh/binsearch.sh: binsearch(): also echo_vars the iter_num, to track how close binsearch is to finding the value (it will always take the same # iters, log2(max - min) )

lib/sh/binsearch.sh: binsearch(): also echo_vars the min/max so these can be used as shortcut inputs if binsearch is run again

bugfix: lib/sh/util.sh: caching: cache_key for function inputs: need to use `declare -p kw_param` instead of "$kw_param" because declare accepts a param name, not value`

lib/sh/binsearch.sh: binsearch(): doc comment: fixed typo in "truncates"

bugfix: lib/sh/util.sh: func_override(): need to match shortest _* suffix instead of longest in case the function being overridden itself contained _

bugfix: lib/sh/util.sh: file_size: Linux: need % in %s

lib/sh/db.sh: mysql(): added $data_only flag which enables --skip-column-names and $output_data

bugfix: lib/sh/util.sh: file_size: need to use --format instead of -f on Linux

added lib/runscripts/table_dir.run and use it in table.run

inputs/GBIF/raw_occurrence_record/run: herbaria_filter.ih.csv_/make(): don't use any outer limit value, so that all the IH herbaria are always used. this also ensures that the first GBIF rows will be from an IH herbarium.

inputs/GBIF/raw_occurrence_record/run: herbaria_filter.table/make(): herbaria_filter: don't explicitly set ENGINE or DEFAULT CHARSET, because these should be set to the database values instead so that collations, etc. match

lib/sh/util.sh: filesystem: added file_size alias

lib/sh/util.sh: exceptions: added signals-related functions ignore_sig(), piped_cmd() and helper sig_e()

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.

lib/sh/util.sh: echo_run(): added trailing-space alias to alias-expand next word, which is a command

lib/sh/binsearch.sh: binsearch(): echo $i at log_level 1 so it's displayed by default, as a progress indicator

lib/sh/binsearch.sh: binsearch(): echo $i at log_level 1 so it's displayed by default, as a progress indicator

lib/sh/binsearch.sh: binsearch(): echo the command being run using new echo_run()

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.

lib/sh/util.sh: added float_set_min()

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.

lib/sh/util.sh: log++: also track a numeric log_level var, which follows the PS4 prefix

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

lib/sh/util.sh: log+(): PS4: split if statement onto multiple lines for clarity

lib/sh/util.sh: added back echo_run(), usable for internal commands where command() would be used for external commands

lib/sh/util.sh: added int2bool()

*{.sh,run}: use new `|| ignore` instead of ignore_e/end_try

lib/sh/util.sh: added ignore(), which uses ||-syntax

lib/sh/util.sh: ignore(): renamed to ignore_e() so ignore() can be used for a simpler, ||-based command

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

added lib/sh/binsearch.sh

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

README.TXT: Full database import: after running `screen`: run `set -o ignoreeof` to prevent Ctrl+D from exiting `screen` to keep attached jobs

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.

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.)

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.

bin/tnrs_db: removed unused imports

bin/tnrs_db: cumulative_tnrs_profiler: use tnrs.tnrs_request()'s new cumulative_profiler param instead of doing the profiling manually. this also ensures that there isn't extra time between when the cumulative profiler starts/stops and when the per-request profiler starts/stops (because Profiler's new add_subprofiler() method is used).

lib/tnrs.py: single_tnrs_request(): added support for a cumulative profiler using the cumulative_profiler kw param

lib/profiling.py: Profiler: added add_subprofiler(), for use with cumulative profilers

lib/profiling.py: Profiler: added add_time() and use it instead of `self.total +=`

bin/tnrs_db: tnrs_profiler: renamed to cumulative_tnrs_profiler to distinguish it from the tnrs_profiler used by tnrs.tnrs_request(), which just profiles the current request

bugfix: bin/tnrs_db: cumulative profiler: use len(names) instead of this_ct (cur.rowcount) in case the actual # rows fetched differed from the rowcount

lib/tnrs.py: repeated_tnrs_request(): renamed to tnrs_request() since this is the function that should usually be used, to ensure that debugging information is output in the case of an error. (the TNRS request must be made again to output this information.)

lib/tnrs.py: tnrs_request(): renamed to single_tnrs_request() to distinguish it from repeated_tnrs_request()

bin/tnrs_db: removed no longer used $wait flag (which caused tnrs_db to wait max_pause for new rows to be added), because tnrs_db is now invoked automatically after each import by the import_scrub target (in inputs/input.Makefile) and does not need to run as a daemon. note that when scrub is invoked, it is possible that a previous datasource's import has already scrubbed the names for this import, because tnrs_db runs until all rows in tnrs_input_name are scrubbed....

bin/tnrs_db: removed no longer needed explicit population of the Time_submitted, which is now done automatically by the tnrs table. however, this requires starting the transaction before submitting data, so Time_submitted is correctly set to the submission time rather than the insertion time. the setting of the correct time can be tested by inserting `time.sleep(n_sec)` after the TNRS request and checking that the Time_submitted is close to the time tnrs_db was run instead of n_sec seconds later.

bin/tnrs_db: start transaction before submitting data, so Time_submitted is correctly set to the submission time rather than the insertion time. these may differ by several minutes if TNRS is slow. the setting of the correct time can be tested by inserting `time.sleep(n_sec)` after the TNRS request, removing the explicit setting of Time_submitted, and checking that the Time_submitted is close to the time tnrs_db was run instead of n_sec seconds later.

bugfix: bin/tnrs_db: wrap just the TNRS request and the storing of the response data in a function (undoing part of r9514), because the transaction start time for Time_submitted should not be until the TNRS request is actually made (it often takes several minutes to materialize the next set of input names on a full DB)

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()

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.

inputs/.TNRS/schema.sql: tnrs_populate_derived_fields(): renamed to tnrs_populate_fields() so it can be used to populate other fields as well

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

bin/tnrs_db: ColInsertFilters: use the simpler literal value option for the mk_value param

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

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.

bugfix: lib/runscripts/util.run: need to include sh/make.sh for all runscripts that use make-style commands

*{.sh,run}: use new top_make instead of `make --directory="$top_dir"`

lib/sh/make.sh: added top_make()

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.

inputs/import.stats.xls: Postprocessing: added (empty) entries for analytical DB, backup, backup test

inputs/GBIF/Specimen/postprocess.sql, inputs/REMIB/Specimen/postprocess.sql: updated for providers in r9459, which adds TEX

inputs/*/*/postprocess.sql: Remove institutions that we have direct data for: query to obtain list: updated for current schema

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.

README.TXT: Full database import: added warning to perform every single step listed, to avoid breaking column-based import

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.

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

added backups/*.md5

added backups/TNRS.2013-5-21.backup.md5

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.

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).

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

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

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)

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

inputs/test_taxonomic_names/test_scrub: updated for current TNRS schema

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.

inputs/test_taxonomic_names/test_scrub: updated for current TNRS schema

inputs/GBIF/raw_occurrence_record/run: herbaria_filter.table/make(): also include the exported plant_fraction herbaria

inputs/GBIF/raw_occurrence_record/run: added herbaria_filter.plant_fraction.csv_/make(), which exports the plant_fraction herbaria whose plant_fraction >= 0.8

inputs/GBIF/raw_occurrence_record/run: added plant_fraction.table/make(), which contains the plant fraction for each herbarium

lib/sh/db.sh: added mk_drop()

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).

bugfix: lib/sh/util.sh: log+(): adjustment < 0: need to enclose -$1 in $(()) so it gets evaluated before being used as an array index

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)

lib/sh/local.sh: psql(): documented why can't use fd 11

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.)

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