Project

General

Profile

Statistics
| Revision:

# Date Author Comment
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.

9948 06/19/2013 08:45 PM Aaron Marcuse-Kubitza

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

9947 06/19/2013 08:24 PM Aaron Marcuse-Kubitza

lib/runscripts/table.run: import(): also run remake_VegBIEN_mappings() to accept the test output. this function was previously unused, but was left in for future use when lib/import.sh was translated to lib/runscripts/table.run (it was used in its import.sh form in inputs/FIA/occurrence_all/import).

9946 06/19/2013 08:21 PM Aaron Marcuse-Kubitza

bugfix: lib/runscripts/table.run: remake_VegBIEN_mappings(): need to change to $top_dir before running `rm header.csv map.csv`

9945 06/19/2013 08:18 PM Aaron Marcuse-Kubitza

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

9944 06/19/2013 08:00 PM Aaron Marcuse-Kubitza

lib/runscripts/table.run: remake_VegBIEN_mappings(): only remake header.csv, map.csv if this target is being run directly, to avoid needing to remake them every time. for tables that are views, this instead requires them to be explicitly remade when the view columns change.

9943 06/19/2013 07:07 PM Aaron Marcuse-Kubitza

bugfix: lib/runscripts/subdir.run: subdir_make(): only remake if $remake has been explicitly propagated to subdir_make() by using self_make

9942 06/19/2013 06:51 PM Aaron Marcuse-Kubitza

lib/sh/make.sh: added deferred_check_target_exists alias and use it in check_fake_target_exists

9941 06/19/2013 06:41 PM Aaron Marcuse-Kubitza

added lib/sh/web.sh with curl wrapper

9940 06/19/2013 06:41 PM Aaron Marcuse-Kubitza

lib/sh/make.sh: added check_wildcard_target_exists alias

9939 06/19/2013 06:37 PM Aaron Marcuse-Kubitza

lib/sh/util.sh: added wildcard1 alias

9938 06/19/2013 06:37 PM Aaron Marcuse-Kubitza

lib/sh/util.sh: added echo1()

9937 06/19/2013 06:32 PM Aaron Marcuse-Kubitza

lib/runscripts/table.run: load_data(): first make sure schema is installed

9936 06/19/2013 06:31 PM Aaron Marcuse-Kubitza

lib/runscripts/table.run: added datasrc_make_install()

9935 06/19/2013 06:31 PM Aaron Marcuse-Kubitza

table_make_install(): take $install_log as an overridable kw param to support install logs in different locations

9934 06/19/2013 05:55 PM Aaron Marcuse-Kubitza

lib/runscripts/table.run: load_data(): split noclobber functionality into separate table_make_install() function, which can be used by other install-related targets

9933 06/19/2013 03:27 PM Aaron Marcuse-Kubitza

added schemas/VegBIEN/taxonomy/higherPlantGroup.xlsx.src.txt with Brad's description of how the names were chosen

9932 06/19/2013 02:37 PM Aaron Marcuse-Kubitza

added schemas/VegBIEN/taxonomy/higherPlantGroup.xlsx

9931 06/19/2013 01:50 PM Aaron Marcuse-Kubitza

schemas/VegBIEN/planning/taxonomy/: moved non-VegBIEN-specific resources to planning/resources/taxonomy/. this includes Brad's all-important Nomenclature_excerpt.ppt with the Latin taxonomic hierarchy suffixes on slide 5.

9930 06/19/2013 11:02 AM Aaron Marcuse-Kubitza

bugfix: schemas/vegbien.sql: taxon_trait_view: use the TNRS-scrubbed name from ScrubbedTaxon when available

9929 06/19/2013 10:36 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: split geoscrub_input_view's new-row-only filtering into separate view geoscrub_input_new, so that the full geoscrub_input rows are still available. the reduction in geoscrub_input from eliminating the already-scrubbed rows was only 280,000 (5076500 - 4799173) out of a possible 1.7 million (1707970), so it makes sense to just run geoscrubbing on the full input. (the lower-than-expected reduction is most likely due to rows from pre-refresh data being present in the original geoscrub_output table, which have been replaced by different, post-refresh input rows.)

9928 06/19/2013 10:18 AM Aaron Marcuse-Kubitza

added exports/_archive/

9927 06/19/2013 10:17 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: genus->taxonlabel.taxonomicname: use new _filter_genus() (see r9882)

9926 06/19/2013 10:15 AM Aaron Marcuse-Kubitza

backups/TNRS.backup.md5: updated

9925 06/19/2013 09:43 AM Aaron Marcuse-Kubitza

bin/make_analytical_db: use new mk_table() instead of TRUNCATE/INSERT

9924 06/19/2013 09:41 AM Aaron Marcuse-Kubitza

bin/make_analytical_db: added mk_table() and use it in mk_analytical_table()

9923 06/19/2013 09:30 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: higher_plant_group_nodes: ferns and allies: added Lycopodiophyta node, as requested by Brad in the conference call (wiki.vegpath.org/2013-06-13_conference_call)

9922 06/19/2013 09:30 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: geoscrub_input_view: exclude rows that have already been geoscrubbed, by anti-joining on geoscrub_output

9921 06/19/2013 09:11 AM Aaron Marcuse-Kubitza

inputs/.geoscrub/geoscrub_output/postprocess.sql: set decimallatitude, decimallongitude types to double precision to facilitate joining with other double precision values

9920 06/19/2013 09:02 AM Aaron Marcuse-Kubitza

inputs/.geoscrub/geoscrub_output/postprocess.sql: coords index: added rest of input columns so this can be used to check the existence of a result by input. added runtime (55 s). use idempotent create_if_not_exists().

9919 06/19/2013 08:17 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: higher_plant_group_nodes: ferns and allies: added Lycopodiophyta node, as requested by Brad in the conference call (wiki.vegpath.org/2013-06-13_conference_call)

9918 06/19/2013 08:08 AM Aaron Marcuse-Kubitza

bugfix: schemas/vegbien.sql: higher_plant_group_nodes: removed ferns and allies nodes Anthocerotophyta, Marchantiophyta, Bryophyta, which were incorrectly said to be part of this clade in the BIEN2 analytical DB overview (/planning/workflow/validation/BIEN2_Analytical_DB_overview.docx > p. 13 bottom > last ΒΆ). see http://wiki.vegpath.org/2013-06-13_conference_call#fix-higher_plant_group_nodes-mapping .

9917 06/19/2013 07:58 AM Aaron Marcuse-Kubitza

bugfix: /Makefile: postgres-Linux: phpPgAdmin: added steps to configure it for Apache 2.4

9916 06/18/2013 07:49 PM Aaron Marcuse-Kubitza

/run: geoscrub_input/make(): documented runtime (40 s)

9915 06/18/2013 06:22 PM Aaron Marcuse-Kubitza

bin/make_analytical_db: added `/run export_` to make the geoscrub_input CSV export

9914 06/18/2013 06:21 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs_populate_fields(): removed no longer needed casts of *_score to double precision

9913 06/18/2013 06:06 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: *_score: changed type to double precision because these fields are always floats. this also avoids the need to manually cast them to double precision each time they are used.

9912 06/18/2013 05:55 PM Aaron Marcuse-Kubitza

lib/tnrs.py: HTTP requests: rewrapped lines

9911 06/18/2013 05:53 PM Aaron Marcuse-Kubitza

lib/tnrs.py: updated HTTP requests to match current web app

9910 06/18/2013 05:51 PM Aaron Marcuse-Kubitza

bugfix: lib/tnrs.py: download_request_template: changed dirty to true (to match the current web app), which is apparently needed to apply the source_sorting setting to the downloaded TSV in addition to the GUI results

9909 06/18/2013 05:29 PM Aaron Marcuse-Kubitza

lib/tnrs.py: retrieval_request_template: turned source_sorting back off, because it causes any match from the first source to always be used, even if it has a lower match score than the match from the other source. (Brad confirms that this should be off.) I think we had this on originally to ensure that only Tropicos results were used when available, rather than USDA when it was a better match. * note that due to a bug in the web app, this change will not actually be effective, because the source_sorting option is only applied to the GUI results, not the downloaded TSV. *

9908 06/18/2013 04:27 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: Name_number: changed type to integer so it would sort numerically

9907 06/18/2013 04:24 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added pkey on Time_submitted, Name_number

9906 06/18/2013 04:21 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: changed Name_submitted pkey to a unique constraint to allow adding a pkey on Time_submitted, Name_number instead

9905 06/18/2013 04:14 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: Time_submitted, Name_number: added NOT NULL constraints so that they can be used in a unique constraint

9904 06/18/2013 02:21 PM Aaron Marcuse-Kubitza

lib/tnrs.py: submission_request_template: include GCC in addition to Tropicos, because it provides more synonyms than Tropicos for Asteraceae, and the accepted names still match the Tropicos backbone (https://projects.nceas.ucsb.edu/nceas/projects/bien/wiki/2013-06-13_conference_call#include-GCC-when-running-TNRS)

9903 06/17/2013 08:18 PM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/tnrs.make: removed no longer needed end time, now that the total runtime is printed

9902 06/17/2013 08:17 PM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/tnrs.make: print the total runtime using `time`

9901 06/17/2013 08:14 PM Aaron Marcuse-Kubitza

inputs/.TNRS/tnrs/tnrs.make: include the end time in addition to the start time so that the total runtime can be calculated

9900 06/17/2013 07:59 PM Aaron Marcuse-Kubitza

lib/sh/util.sh: command-specific alternate stdin/stdout/stderr: choice of 40/41/42: added mnemonic that 4 looks like A for Alternate

9899 06/14/2013 07:42 AM Aaron Marcuse-Kubitza

bugfix: /README.TXT: Full database import: added step to remove any leftover TNRS lockfile. usually, the PID in it would not exist, but sometimes it now refers to a different, active process which blocks tnrs.make.

9898 06/13/2013 01:00 PM Aaron Marcuse-Kubitza

schemas/vegbien.sql: allow public_ to view lookup tables (cultivated_family_locations, higher_plant_group_nodes)

9897 06/13/2013 08:13 AM Aaron Marcuse-Kubitza

added backups/TNRS.backup.md5, vegbien.r9459.backup.md5

9896 06/12/2013 02:45 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/local.sh: sync_upload(): need to use --no-group to prevent the group from being reset to aaronmk upon download from jupiter (which uses group aaronmk instead of bien). use ./fix_perms to set the group of all files to bien. also use --no-owner in case running as root.

9895 06/12/2013 02:12 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: removed sync_download(). use swap=1 sync_upload() instead.

9894 06/12/2013 02:11 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: removed download(). use swap=1 upload, or swap=1 upload_caller, instead. this avoids having separate upload()/download() pairs for every caller of upload(), because you can instead just set swap=1.

9893 06/12/2013 01:50 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/sync.sh: upload(): don't kw_params $swap because this unexports it, preventing put from seeing it. instead, use echo_vars to print it.

9892 06/12/2013 01:35 PM Aaron Marcuse-Kubitza

added bin/sync_upload, a wrapper around sync_upload()

9891 06/12/2013 01:23 PM Aaron Marcuse-Kubitza

added bin/sync_upload, a wrapper around sync_upload()

9890 06/12/2013 01:00 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/sync.sh: upload(): only add `--exclude="**"` if there are --includes. this enables running upload() without paths to upload all files.

9889 06/12/2013 12:56 PM Aaron Marcuse-Kubitza

lib/sh/sync.sh: upload(): support passing -- options to put, which will not be run through the path->--include processing

9888 06/12/2013 12:55 PM Aaron Marcuse-Kubitza

bugfix: lib/sh/sync.sh: upload(): added missing `local args=()` initializer

9887 06/12/2013 12:18 PM Aaron Marcuse-Kubitza

/README.TXT: Full database import: On local machine: added step to do steps under Maintenance > "to synchronize vegbiendev, jupiter, and your local machine", which is needed in addition to `make inputs/upload` since that doesn't handle overwrites or deletions

9886 06/12/2013 12:10 PM Aaron Marcuse-Kubitza

/README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: added warning that you should pay careful attention to all files that will be deleted or overwritten (as the three machines are often out of sync)

9885 06/12/2013 11:26 AM Aaron Marcuse-Kubitza

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

9884 06/12/2013 11:17 AM Aaron Marcuse-Kubitza

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

9883 06/12/2013 11:12 AM Aaron Marcuse-Kubitza

/README.TXT: Full database import: `svn up`: use --force to avoid errors about existing files

9882 06/12/2013 10:49 AM Aaron Marcuse-Kubitza

mappings/VegCore-VegBIEN.csv: genus->taxonlabel.taxonomicname: filter out genera that contain numbers (using new _filter_genus()), which break TNRS and prevent it from matching any other parts of the name. later, these genera can instead be moved to the end of the name, where TNRS will correctly match them as Unmatched_terms.

9881 06/12/2013 10:48 AM Aaron Marcuse-Kubitza

bugfix: inputs/VegBIEN/: added _no_import to disable import for this folder, since this is actually just an entry in web/datasources/ with VegPath redirection links, rather than an input to the import process. this fixes "schema "VegBIEN" does not exist" errors generated in `make test`.