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# Date Author Comment
10048 06/26/2013 12:30 AM Aaron Marcuse-Kubitza

lib/sh/local.sh: added PATH_add= flag to allow turning off the addition of $bin_dir_abs to the PATH. this is useful for wrapper scripts that should not alter the PATH passed to their invoked command.

10047 06/26/2013 12:28 AM Aaron Marcuse-Kubitza

bugfix: lib/sh/make.sh: make(): invoke only the system make command instead of any wrapper for it in the PATH (by using self_sys instead of self), to prevent infinite recursion. single recursion is resolved by nonrecursive=1, but there are cases where mutual recursion occurs due to the presence of two, different bin/makes in the PATH (e.g. if you have two working copies with bin/make, and one is symlinked in your ~/bin/ folder), and these cases can only be resolved by clearing out the PATH completely (since the bin/makes do not know of each other's existence, in order to remove their parent dirs from the PATH).

10046 06/26/2013 12:23 AM Aaron Marcuse-Kubitza

lib/sh/util.sh: self_sys alias: use new sys_cmd() instead of `command -p` so that only the command path resolution is performed with a limited PATH, and the invoked command itself inherits the full PATH

10045 06/26/2013 12:22 AM Aaron Marcuse-Kubitza

lib/sh/util.sh: added sys_cmd(), which runs a system command and allows running a system command of the same name as the script

10044 06/26/2013 12:20 AM Aaron Marcuse-Kubitza

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

10043 06/25/2013 06:37 PM Aaron Marcuse-Kubitza

inputs/.rsync_ignore: test*.xml: turn on syncing again, but always treat the local side of the sync (starscream or vegbiendev) as the authoritative copy since they are the machines the tests can be run on

10042 06/25/2013 05:18 PM Aaron Marcuse-Kubitza

/.rsync_ignore: temp files: hide them on upload so that they are never synced to jupiter. hiding is different than unidirectionally exclude'ing them, because it also causes them to be deleted on the destination if they were uploaded in previous syncs.

10041 06/25/2013 04:57 PM Aaron Marcuse-Kubitza

inputs/VegBIEN/TWiki/.rsync_ignore: /**: turn syncing back on, but only allow it unidirectionally from vegbiendev->jupiter->starscream to avoid clobbering the live site or the jupiter backup. this is probably the only dir whose authoritative copy is always on vegbiendev. for all other dirs, edits can be made wherever convenient, so no copy is authoritative and no sync directions need to be restricted.

10040 06/25/2013 04:27 PM Aaron Marcuse-Kubitza

/README.TXT: Maintenance: synchronization: fixed whitespace

10039 06/25/2013 04:07 PM Aaron Marcuse-Kubitza

inputs/.rsync_ignore: install.log.sql: only exclude this on starscream (the local machine), using new machine-specific .rsync_filters, so that vegbiendev's copies of this will be backed up

10038 06/25/2013 03:46 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: upload(): .rsync_filter: also support machine-specific filters, for cases when different machines produce the same file (e.g. a log file) but only one machine's copy should be backed up

10037 06/25/2013 03:43 PM Aaron Marcuse-Kubitza

/README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: removed filters that are now handled by .rsync_ignores

10036 06/25/2013 03:31 PM Aaron Marcuse-Kubitza

added inputs/GBIF/_src/.rsync_filter.upload,download to prevent old versions of GBIFPortalDB-*.dump.gz from being downloaded to the local machine, while keeping them on jupiter. this avoids the need to store these files in ~/Documents/BIEN/large_files/ with symlinks from inputs/GBIF/_src/ to exclude them from the sync.

10035 06/25/2013 03:17 PM Aaron Marcuse-Kubitza

bugfix: /README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: sync ~/Dropbox/svn/ (the no-unversioned-files working copy) separately from the rest of the files, because .svn/ is now excluded by /.rsync_ignore, so that `svn up` needs to be used to keep the .svn/ dirs in sync. note that .svn/ should generally not be synced between machines, because they may use incompatible versions of the svn working copy format.

10034 06/25/2013 03:02 PM Aaron Marcuse-Kubitza

/README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: use new bin/sync_upload (with $sync_remote_subdir) so that per-dir .rsync_ignores are processed, and to use the default $sync_remote_url

10033 06/25/2013 02:57 PM Aaron Marcuse-Kubitza

lib/sh/local.sh: $sync_remote_url: allow user to override just the sync subdir (not the whole URL) in $sync_remote_subdir. this is useful e.g. for backing up the Mac's files to jupiter.

10032 06/25/2013 02:28 PM Aaron Marcuse-Kubitza

/README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: use new bin/sync_upload instead of specifying all the filter patterns manually. this replaces several `put` commands with various filters with just a bin/sync_upload each on vegbiendev and your machine (in overwrite=1 mode to force a complete sync).

10031 06/25/2013 02:21 PM Aaron Marcuse-Kubitza

bugfix: backups/.rsync_filter.download: need to prevent existing backups from being deleted on the local side, too, by changing hide patterns to exclude

10030 06/25/2013 02:11 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: upload(): make put's $subpath option relative to the currdir instead, like the --include paths. note that $subpath unfortunately can't be used in subdirs at this point because it will cause rsync to ignore the .rsync_ignores and .rsync_filters in parent dirs, including the essential .rsync_ignore in the sync root dir.

10029 06/25/2013 01:42 PM Aaron Marcuse-Kubitza

/README.TXT: removed unnecessary `env` before kw params, which are treated as such whenever they appear before a command name

10028 06/25/2013 01:22 PM Aaron Marcuse-Kubitza

bugfix: /README.TXT: updated `make backups/download` to `make backups/<file>/download`

10027 06/25/2013 01:21 PM Aaron Marcuse-Kubitza

backups/Makefile: upload: use bin/sync_upload

10026 06/25/2013 01:12 PM Aaron Marcuse-Kubitza

inputs/Makefile: download-logs: use bin/sync_upload like upload/download

10025 06/25/2013 01:07 PM Aaron Marcuse-Kubitza

bugfix: /README.TXT: `make inputs/upload`, `make inputs/download`: added live=1 so that the sync operation runs rather than previewing what will be synced. removed test=1 because this flag is not used by put.

10024 06/25/2013 01:00 PM Aaron Marcuse-Kubitza

bugfix: inputs/Makefile: upload, download: need to exclude files in .rsync_ignore, so that large local-only files, such as inputs/GBIF/raw_occurrence_record_plants/table*.tsv, do not have to be synced before `make inputs/upload` can complete (the corresponding .gz gets extracted instead); and deleted temp files in inputs/VegBIEN/TWiki/, such as active sessions, are not added back to the live copy on vegbiendev. previously, fixing this required extracting the rsync command run by `make inputs/upload`, etc. and manually editing it to exclude the applicable .rsync_ignore files, each time `make inputs/upload`, etc. was run (including before every column-based import).

10023 06/25/2013 12:23 PM Aaron Marcuse-Kubitza

bugfix: bin/make: need to leave bin/, ~/bin/ in the PATH when running make nonrecursively, so that commands invoked by it which are located in these dirs (e.g. put, which will be used by `make inputs/upload`) can still be found. this requires using command()'s new nonrecursive=1 flag instead of running no_PATH_recursion, so that no_PATH_recursion() only affects the resolution of the command path, but does not propagate the filtered PATH to the invoked command itself.

10022 06/25/2013 12:18 PM Aaron Marcuse-Kubitza

lib/sh/util.sh: command(): added nonrecursive=1 flag, which uses cmd2abs_path to run an external command nonrecursively

10021 06/25/2013 12:16 PM Aaron Marcuse-Kubitza

lib/sh/util.sh: added cmd2abs_path, which makes the command in $1 nonrecursive

10020 06/25/2013 11:37 AM Aaron Marcuse-Kubitza

bugfix: lib/sh/util.sh: PATH_rm(): also need to remove adjacent occurrences of the same path (or occurrences which become adjacent when other paths are removed), which :...: matching wasn't doing because the trailing : is consumed, preventing it from being matched at the beginning of the next path. since unlike filesystem paths with /, it is not necessary for a match to span multiple :-separated sections, we can just use new split() to split apart the PATH into an array of paths, filter each path, and join() them back together.

10019 06/25/2013 11:33 AM Aaron Marcuse-Kubitza

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

10018 06/25/2013 10:32 AM Aaron Marcuse-Kubitza

lib/sh/util.sh: auto-echo common external commands: added `which`

10017 06/25/2013 10:32 AM Aaron Marcuse-Kubitza

lib/sh/util.sh: auto-echo common external commands: use simpler echo_run instead of command since logging handling is not needed

10016 06/25/2013 08:50 AM Aaron Marcuse-Kubitza

added backups/vegbien.r9897.backup.md5

10015 06/23/2013 09:30 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: upload(): documented that each --include path is relative to the currdir, not the root dir of the upload ($local_dir). this feature, although previously unintended, is actually better because the user can change to a subdir of the root dir and specify upload paths relative to the dir they are in. however, when invoking upload() from a script with --include paths specified, this means you need to use an absolute path (e.g. "$(dirname "${BASH_SOURCE0}")"/...; or the value that will become $local_dir, which for sync_upload() is $root_dir).

10014 06/23/2013 08:56 PM Aaron Marcuse-Kubitza

backups/.rsync_ignore: replaced with .rsync_filter.upload to allow uploading new backups but not deleting existing backups if they don't exist on the local (rsync-invoking) side; and .rsync_filter.download to avoid downloading backups to the local side. this allows storing older backups just on jupiter, where there is much more disk space. note that this change must be made on the remote side (jupiter) for it to be effective, because these are remote-side rules and are only processed by the remote-side rsync instance.

10013 06/23/2013 08:55 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: upload(): use directional .rsync_filter to supplement .rsync_ignore with all kinds of --filter rules. separate .rsync_filters are needed for the upload (swap=) and download (swap=1) directions because the sender and the receiver are reversed, causing asymmetric rules like protect/hide to change meaning.

10012 06/23/2013 07:48 PM Aaron Marcuse-Kubitza

updated backups/TNRS.backup.md5

10011 06/23/2013 07:48 PM Aaron Marcuse-Kubitza

added backups/TNRS.2013-6-17.backup.md5, TNRS.2013-6-22.backup.md5

10010 06/23/2013 03:58 PM Aaron Marcuse-Kubitza

/README.TXT: Backups: TNRS cache: Back up/Restore: added runtimes (3 min/5.5 min)

10009 06/23/2013 03:52 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: upload(): usage: documented put's swap=1 flag, which downloads instead of uploads

10008 06/23/2013 03:47 PM Aaron Marcuse-Kubitza

added inputs/GBIF/raw_occurrence_record_plants/.rsync_ignore with filters that have previously needed to be manually added whenever `make inputs/upload` was run

10007 06/23/2013 03:46 PM Aaron Marcuse-Kubitza

added inputs/GBIF/_MySQL/.rsync_ignore with filters from /README.TXT > Maintenance > to synchronize vegbiendev, jupiter, and your local machine. these filters will now be used with bin/sync_upload in addition to the periodic backup commands.

10006 06/23/2013 03:45 PM Aaron Marcuse-Kubitza

added inputs/VegBIEN/TWiki/.rsync_ignore with filters from /README.TXT > Maintenance > to synchronize vegbiendev, jupiter, and your local machine. these filters will now be used with bin/sync_upload in addition to the periodic backup commands.

10005 06/23/2013 03:44 PM Aaron Marcuse-Kubitza

added inputs/.rsync_ignore with filters from inputs/Makefile $(rsyncSrcs). these filters will now be used with bin/sync_upload in addition to `make inputs/upload`.

10004 06/23/2013 03:43 PM Aaron Marcuse-Kubitza

added bin/.rsync_ignore with filters from /README.TXT > Maintenance > to synchronize vegbiendev, jupiter, and your local machine. these filters will now be used with bin/sync_upload in addition to the periodic backup commands.

10003 06/23/2013 03:40 PM Aaron Marcuse-Kubitza

added backups/.rsync_ignore with filters from /README.TXT > Maintenance > to synchronize vegbiendev, jupiter, and your local machine. these filters will now be used with bin/sync_upload in addition to the periodic backup commands.

10002 06/23/2013 03:36 PM Aaron Marcuse-Kubitza

/.rsync_ignore: added *.pyc

10001 06/23/2013 03:36 PM Aaron Marcuse-Kubitza

added /.rsync_ignore with filters from lib/common.Makefile $(rsync). these filters will now be used with bin/sync_upload in addition to `make inputs/upload`.

10000 06/23/2013 03:34 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: upload(): use --exclude filters from per-dir .rsync_ignore. note that --exclude-from can't be used for this, because it is relative to the currdir, not the rsync root, and therefore also requires the .rsync_ignore to exist rather than using it only if it exists.

9999 06/22/2013 12:23 AM Aaron Marcuse-Kubitza

bin/tnrs_db: documented total runtime (10 days)

9998 06/21/2013 11:58 PM Aaron Marcuse-Kubitza

bin/tnrs_db: documented current runtime (162 ms/name)

9997 06/20/2013 10:58 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks. sorted NCEAS bookmarks to put homepage and support pages first.

9996 06/20/2013 06:21 PM Aaron Marcuse-Kubitza

/README.TXT: Full database import: To run TNRS, etc. after the main import: clarified that you should only run `export version=<version>` if the import is named something other than public (i.e. it has not yet replaced the previous public schema)

9995 06/20/2013 06:14 PM Aaron Marcuse-Kubitza

/README.TXT: Full database import: To run TNRS: removed `by_col=1` because by-column mode is not applicable to running TNRS. it is, however, needed when running import_scrub (i.e. `make inputs/<datasrc>/reimport_scrub by_col=1`).

9994 06/20/2013 06:10 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: vegbiendev update steps: added `make backups/TNRS.backup-remake` to back up TNRS before making changes to it. this provides a more recent restore point than the last import in case the changes mess things up. (however, the last import's backup is usually sufficient unless TNRS has been run since then.)

9993 06/20/2013 05:53 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_populate_fields(): added VACUUM ANALYZE and runtime (50 s)

9992 06/20/2013 05:42 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_populate_fields(): updated runtime (16 min)

9991 06/20/2013 05:09 PM Aaron Marcuse-Kubitza

schemas/VegBIEN/taxonomy/higherPlantGroup.xlsx.src.txt: added Brad's comment that there are some holes in the Embryophyte subclasses list, and we need to validate it

9990 06/20/2013 04:49 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented that when changing this table's schema, you must also make the same changes on vegbiendev. included sample util.set_col_types() call with runtime (4 min).

9989 06/20/2013 03:58 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_populate_fields(): updated runtime (16 min)

9988 06/20/2013 03:32 PM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): need to schema-qualify invoked functions

9987 06/20/2013 03:29 PM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): Is_homonym: use the *_is_homonym flag for whichever of genus or family (in that order) is NOT NULL, rather than horizontal-ORing potentially NULL values together

9986 06/20/2013 03:22 PM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: family_is_homonym(), genus_is_homonym(): need to return NULL instead of false when input family/genus is NULL. EXISTS does not support this, so STRICT is used to provide this functionality automatically.

9985 06/20/2013 03:19 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added family_is_homonym(), genus_is_homonym() and use them in tnrs_populate_fields()

9984 06/20/2013 03:15 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: score_ok(): changed to IMMUTABLE and STRICT

9983 06/20/2013 03:14 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_populate_fields(): updated runtime (16 min)

9982 06/20/2013 02:41 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_populate_fields(): never_homonym: use Author_score threshold to exclude matches that are too fuzzy to confirm the presence of a plant name author

9981 06/20/2013 02:38 PM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: tnrs_populate_fields(): *_is_homonym: also need to check that there was no Author_matched (i.e. that it could be a homonym). Is_homonym: use new never_homonym var.

9980 06/20/2013 02:18 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_populate_fields(): updated runtime (18 min)

9979 06/20/2013 02:17 PM Aaron Marcuse-Kubitza

inputs/import.stats.xls: Updated import times

9978 06/20/2013 02:07 PM Aaron Marcuse-Kubitza

planning/workflow/bien3_architecture.pptx: stage II: removed Step prefix before stage #, which the other slides don't have

9977 06/20/2013 01:57 PM Aaron Marcuse-Kubitza

added planning/workflow/bien3_architecture/stages.png

9976 06/20/2013 01:36 PM Aaron Marcuse-Kubitza

added planning/workflow/bien3_architecture/stage_*.png

9975 06/20/2013 12:54 PM Aaron Marcuse-Kubitza

added planning/workflow/bien3_architecture.pptx

9974 06/20/2013 08:20 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_populate_fields(): when changing this function: UPDATE statement: include TNRS schema since it may not be in the search_path

9973 06/20/2013 08:14 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_populate_fields(): Is_plant: also consider homonyms using new family_is_homonym, genus_is_homonym (see wiki.vegpath.org/Result_filtering#taxon_is_plant)

9972 06/20/2013 08:03 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: added Is_homonym derived col (uses IRMNG.family_homonym_epithet, genus_homonym_epithet)

9971 06/20/2013 07:54 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: re-ran `make schemas/public/reinstall; make schemas/remake` cycle, which apparently changed sort order of statements

9970 06/20/2013 07:11 AM Aaron Marcuse-Kubitza

/README.TXT: Full database import: disk space check: updated minimum (to 300GB) for new import schema size. note that most of the space (166GB) is indexes, and even of the 87GB of data, only 20GB is from GBIF and 15GB from FIA (so most of it is duplication).

9969 06/20/2013 07:07 AM Aaron Marcuse-Kubitza

added inputs/IRMNG/*_homonym_epithet/map.csv, etc. (created by */run)

9968 06/20/2013 07:01 AM Aaron Marcuse-Kubitza

bugfix: inputs/input.Makefile: `%/install %/header.csv: %/create.sql`: in noclobber mode, mark %/header.csv as .PRECIOUS so the existing file won't be deleted if the table already exists (causing an error exit)

9967 06/20/2013 06:54 AM Aaron Marcuse-Kubitza

bugfix: lib/runscripts/table.run: remake_VegBIEN_mappings(): run yes using piped_cmd() so the SIGPIPE doesn't cause an errexit

9966 06/20/2013 06:45 AM Aaron Marcuse-Kubitza

added inputs/IRMNG/{genus_homonym_epithet,family_homonym_epithet}/run, which inherit from ../table.run so that load_data() (which runs create.sql) is invoked

9965 06/20/2013 06:44 AM Aaron Marcuse-Kubitza

added inputs/IRMNG/species_homonyms/new_terms.csv

9964 06/20/2013 06:43 AM Aaron Marcuse-Kubitza

bugfix: added no-op inputs/IRMNG/Source/run so inputs/IRMNG/run would have something to invoke for it

9963 06/20/2013 06:35 AM Aaron Marcuse-Kubitza

inputs/IRMNG/run: use lib/runscripts/datasrc_dir.run, which now provides import() and $subdirs

9962 06/20/2013 06:34 AM Aaron Marcuse-Kubitza

lib/runscripts/datasrc_dir.run: extend import.run and provide an import() implementation that runs all the runscripts for import_order.txt subdirs

9961 06/20/2013 06:20 AM Aaron Marcuse-Kubitza

lib/csvs.py: sniff(): support single-column spreadsheets by defaulting to the Excel dialect when the delimiter can't be determined

9960 06/20/2013 06:09 AM Aaron Marcuse-Kubitza

inputs/IRMNG/: added family_homonym_epithet, genus_homonym_epithet lookup tables, which use util.all_same() to filter out internal Plantae homonyms

9959 06/20/2013 05:44 AM Aaron Marcuse-Kubitza

schemas/util.sql: added all_same() aggregate

9958 06/20/2013 05:31 AM Aaron Marcuse-Kubitza

schemas/util.sql: added not_empty(anyarray)

9957 06/20/2013 12:14 AM Aaron Marcuse-Kubitza

schemas/util.sql: added not_null() (usable as an aggregate's FINALFUNC)

9956 06/20/2013 12:13 AM Aaron Marcuse-Kubitza

schemas/util.sql: added not_null() (usable as an aggregate's FINALFUNC)

9955 06/19/2013 10:18 PM Aaron Marcuse-Kubitza

bugfix: inputs/IRMNG/import_order.txt: need to specify order so that Source is first

9954 06/19/2013 10:16 PM Aaron Marcuse-Kubitza

bugfix: inputs/IRMNG/*/map.csv: remapped Authority to scientificNameAuthorship instead of authors (now data_authors <VegCore.vegpath.org?data_authors> for clarity)

9953 06/19/2013 09:59 PM Aaron Marcuse-Kubitza

inputs/IRMNG/map.csv: updated to scrubbed output names from */map.csv (/map.csv does not currently get scrubbed)

9952 06/19/2013 09:51 PM Aaron Marcuse-Kubitza

bugfix: inputs/IRMNG/species_homonyms/header.csv, map.csv: reset input columns to DSV (delim-separated values) header. they had gotten changed to the output names in running map.csv with remake=1, causing it to be remade from the (renamed) staging tables.

9951 06/19/2013 08:54 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: $(_svnFilesGlob): added *Makefile

9950 06/19/2013 08:51 PM Aaron Marcuse-Kubitza

/README.TXT: `make inputs/{upload,download}`: first run with test=1 to see what the diffs will be

9949 06/19/2013 08:47 PM Aaron Marcuse-Kubitza

added inputs/IRMNG/, including runscripts to download the names. this is now the 2nd datasource after GBIF to use runscripts, and the 3rd after FIA/GBIF to use new-style import.