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From 05/05/2014 to 06/03/2014

06/03/2014

11:13 PM Revision 13613: web/index.php: subpath@host? redirects: also support multiple @ and nested . in prefix: a@b.c@host? -> host?b.c.a
Aaron Marcuse-Kubitza
11:01 PM Revision 13612: web/index.php: support prefix redirect of the form subpath@host? , which is better than subpath.host because case is preserved and special chars allowed. (must require trailing ? for redirect, to avoid needing login to view the page itself.)
Aaron Marcuse-Kubitza
10:47 PM Revision 13611: bugfix: web/index.php: full directory index: appending query string: need to use $_SERVER["QUERY_STRING"], not $_SERVER["HTTP_AUTHORIZATION"] for this
Aaron Marcuse-Kubitza
03:24 PM Task #934 (New): Data Dictionary
Define the Data Dictionary terms for VegBIEN and associated tables.
# -First define the (approximately 60) terms nee...
Martha Narro
11:36 AM Revision 13610: schemas/public_.sql: sync_*(): renamed to *_modify() to facilitate finding these functions when modifying the corresponding view (using the new naming convention for a view's on-modify function)
Aaron Marcuse-Kubitza
10:36 AM Revision 13609: bugfix: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): updated to include taxon_scrub derived fields
Aaron Marcuse-Kubitza
10:25 AM Revision 13608: bugfix: schemas/util.sql: mk_drop_from_create(): need to match first rather than last CREATE
Aaron Marcuse-Kubitza
10:21 AM Revision 13607: inputs/.TNRS/schema.sql: *_modify(): allow running without a view_query, as recreate_view() now supports this
Aaron Marcuse-Kubitza
09:52 AM Revision 13606: schemas/util.sql: recreate_view(): support omitting the view_query if the view has already been modified (eg. for public.*_view, which allow changing the view as a separate step)
Aaron Marcuse-Kubitza
08:56 AM Revision 13605: fix: schemas/public_.sql: sync_*(): use util.copy() instead of CREATE TABLE AS so that table and column comments are also copied. this avoids the need to separately add the same comments to the view *and* its materialized table.
Aaron Marcuse-Kubitza
08:52 AM Revision 13604: bugfix: schemas/util.sql: recreate(): need to handle case where util.mk_drop_from_create() is NULL
Aaron Marcuse-Kubitza
08:45 AM Revision 13603: bugfix: schemas/util.sql: mk_drop_from_create(): only match CREATE if no custom DROP came before it
Aaron Marcuse-Kubitza
08:29 AM Revision 13602: bugfix: schemas/public_.sql: sync_geoscrub_input_to_view(): `CREATE TABLE geoscrub_input AS __`: needs `LIMIT 0`
Aaron Marcuse-Kubitza
08:19 AM Revision 13601: fix: schemas/util.sql: explain2notice_msg_if_can(): also need to catch invalid_cursor_definition ("cannot open multi-query plan as cursor")
Aaron Marcuse-Kubitza
08:15 AM Revision 13600: schemas/public_.sql: sync_analytical_stem_to_view(): removed DROP TABLE IF EXISTS because this is now done automatically by util.recreate()
Aaron Marcuse-Kubitza
07:39 AM Revision 13599: schemas/util.sql: added copy()
Aaron Marcuse-Kubitza
07:36 AM Revision 13598: schemas/util.sql: added copy_data()
Aaron Marcuse-Kubitza

06/02/2014

04:24 PM Revision 13597: fix: lib/tnrs.py: Constrain by Source: turn it on so that the download settings reflect what TNRS actually used, while this is broken
Aaron Marcuse-Kubitza
06:19 AM Revision 13596: fix: lib/tnrs.py: max_names: reduced back to 500 because even 5000 crashes the dev TNRS server
Aaron Marcuse-Kubitza
05:52 AM Revision 13595: lib/tnrs.py: max_names: reduced to 5000 because 100,000 causes an internal server error
Aaron Marcuse-Kubitza
05:25 AM Revision 13594: bugfix: /README.TXT: Full database import: To run TNRS: to rescrub all names: also need to re-create public-schema views that were cascadingly deleted
Aaron Marcuse-Kubitza
05:23 AM Revision 13593: /README.TXT: Full database import: To run TNRS: added steps to rescrub all names
Aaron Marcuse-Kubitza
04:59 AM Revision 13592: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
04:50 AM Revision 13591: lib/tnrs.py: switched to downloading all matches per name, as is needed to implement #917. note that this will break the parts of the schema that use the tnrs table, until Brad's match-picking algorithm can be implemented, but this tradeoff is necessary to be able to begin scrubbing sooner (Martha; wiki.vegpath.org/2014-05-29_conference_call#TNRS)
Aaron Marcuse-Kubitza
04:35 AM Revision 13590: schemas/vegbien.sql: tnrs_input_name: don't scrub accepted names, as using multiple matches per name no longer provides a single accepted name to scrub. instead, the Accepted_* fields can be whitespace-split to generate the same columns that would have been generated by the scrubbing (and without the overhead of the extra TNRS call).
Aaron Marcuse-Kubitza
04:27 AM Revision 13589: fix: inputs/.TNRS/schema.sql: added back index on Name_submitted, which is needed for tnrs_input_name to work properly (now that there is no automatic index created by a unique constraint)
Aaron Marcuse-Kubitza
04:08 AM Revision 13588: schemas/vegbien.sql: tnrs_input_name: don't scrub accepted names, as using multiple matches per name no longer provides a single accepted name to scrub. instead, the Accepted_* fields can be whitespace-split to generate the same columns that would have been generated by the scrubbing (and without the overhead of the extra TNRS call).
Aaron Marcuse-Kubitza
03:43 AM Revision 13587: fix: inputs/.TNRS/schema.sql: tnrs: removed unique constraint on Name_submitted, Name_matched because there can be more than one match with the same Name_matched (but different accepted names, etc.)
Aaron Marcuse-Kubitza

06/01/2014

09:00 PM Revision 13586: fix: inputs/.TNRS/schema.sql: tnrs.tnrs__valid_match index: made it non-unique to allow multiple matches per name, as is needed to implement #917
Aaron Marcuse-Kubitza
05:00 AM Revision 13585: bugfix: inputs/.TNRS/schema.sql: tnrs__match_num__fill(): only fill if not set, to support case where tnrs is being restored from a .sql file (where match_num is already set)
Aaron Marcuse-Kubitza
04:36 AM Revision 13584: inputs/.TNRS/schema.sql: tnrs: documented runtime to add a constraint (3 min)
Aaron Marcuse-Kubitza
04:35 AM Revision 13583: inputs/.TNRS/schema.sql: unique constraint on Name_submitted: added Name_matched to allow multiple matches per name, as is needed to implement #917
Aaron Marcuse-Kubitza
03:44 AM Revision 13582: inputs/.TNRS/schema.sql: tnrs: documented how to populate a new column
Aaron Marcuse-Kubitza
03:41 AM Revision 13581: inputs/.TNRS/schema.sql: tnrs: pkey: use match_num instead of Name_number to allow multiple matches per name, as is needed to implement #917
Aaron Marcuse-Kubitza

05/31/2014

10:31 PM Revision 13580: inputs/.TNRS/schema.sql: tnrs.match_num: made it NOT NULL now that it's populated
Aaron Marcuse-Kubitza
10:28 PM Revision 13579: inputs/.TNRS/schema.sql: tnrs: populate match_num
Aaron Marcuse-Kubitza
10:25 PM Revision 13578: inputs/.TNRS/schema.sql: tnrs: populate match_num
Aaron Marcuse-Kubitza
09:50 PM Revision 13577: inputs/.TNRS/schema.sql: tnrs: documented how to add and remove columns
Aaron Marcuse-Kubitza
08:58 PM Revision 13576: inputs/.TNRS/schema.sql: made COMMENTs start on their own line, using the steps at wiki.vegpath.org/Postgres_queries#make-COMMENTs-start-on-their-own-line
Aaron Marcuse-Kubitza
08:58 PM Revision 13575: inputs/.TNRS/schema.sql: made COMMENTs start on their own line, using the steps at wiki.vegpath.org/Postgres_queries#make-COMMENTs-start-on-their-own-line
Aaron Marcuse-Kubitza
08:11 PM Revision 13574: inputs/test_taxonomic_names/_scrub/*: updated to TNRS schema
Aaron Marcuse-Kubitza
08:10 PM Revision 13573: inputs/.TNRS/schema.sql: tnrs: added match_num
Aaron Marcuse-Kubitza
08:06 PM Revision 13572: inputs/.TNRS/data.sql.run: refresh(): documented runtime (1 min)
Aaron Marcuse-Kubitza
08:03 PM Revision 13571: schemas/Makefile: added back rename/%, which *is* used by `inputs/.TNRS/data.sql.run refresh`. updated it to use schema bundles.
Aaron Marcuse-Kubitza
06:44 PM Revision 13570: inputs/.TNRS/schema.sql: added tnrs__match_num__next()
Aaron Marcuse-Kubitza
06:29 PM Revision 13569: inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)
Aaron Marcuse-Kubitza
05:06 AM Revision 13568: exports/2014-3-11.Jeff_Ott.climatic_range_determinants.csv.run: documented export_() runtime (11 min) and rowcount (11 million matching the filter criteria)
Aaron Marcuse-Kubitza

05/30/2014

06:34 PM Revision 13567: inputs/.TNRS/schema.sql: added tnrs__batch_begin() trigger to populate the match_num (match sort order)
Aaron Marcuse-Kubitza
06:22 PM Revision 13566: schemas/util.sql: added seq__reset()
Aaron Marcuse-Kubitza
06:15 PM Revision 13565: schemas/util.sql: added seq__create()
Aaron Marcuse-Kubitza
06:11 PM Revision 13564: fix: schemas/util.sql: try_cast(), is_castable(): also catch invalid_schema_name, thrown by `'pg_temp.__'::regclass`
Aaron Marcuse-Kubitza
02:49 PM Revision 13563: backups/TNRS.backup.md5: updated
Aaron Marcuse-Kubitza
07:50 AM Revision 13562: lib/tnrs.py: max_names: increased to 100000 because the dev server can handle more names (no simultaneous users), as decided in the conference call (wiki.vegpath.org/2014-05-29_conference_call#TNRS)
Aaron Marcuse-Kubitza
07:42 AM Revision 13561: schemas/vegbien.ERD.mwb: regenerated exports
Aaron Marcuse-Kubitza
07:39 AM Revision 13560: schemas/vegbien.ERD.mwb: re-updated to schemas/vegbien.my.sql, which now recognizes the broken tables. fixed sync issues. vegbien.ERD.mwb is now fully in sync with vegbien.my.sql.
Aaron Marcuse-Kubitza
07:37 AM Revision 13559: fix: lib/PostgreSQL-MySQL.csv: need to replace "double precision" with "double" to work with MySQL Workbench 5.2.47
Aaron Marcuse-Kubitza
06:58 AM Revision 13558: schemas/vegbien.ERD.mwb: updated to schemas/vegbien.my.sql. some tables weren't recognized (likely due to bugs in MySQL Workbench 5.2.47), and have been left as-is (unsynced). note that downgrading to 5.2.35 is not an option, because that is fatally broken by a system upgrade.
Aaron Marcuse-Kubitza
05:58 AM Revision 13557: fix: schemas/vegbien.ERD.mwb: use schemas/vegbien.my.sql instead of schemas/vegbien.my.sql.changes.sql as the sync source
Aaron Marcuse-Kubitza
05:27 AM Revision 13556: schemas/vegbien.ERD.mwb: switched back to MySQL Workbench 6.1.6 version, which also works with MySQL Workbench 5.2.47
Aaron Marcuse-Kubitza
05:17 AM Revision 13555: schemas/vegbien.ERD.mwb: restored version for MySQL Workbench 5.2.35 (undid r13549), as 6.1.6 has bugs in the DDL file sync
Aaron Marcuse-Kubitza
05:05 AM Revision 13554: schemas/vegbien.ERD.mwb: renamed to vegbien.ERD.MySQL_Workbench_6.1.6.mwb to differentiate the versions for different versions of MySQL Workbench
Aaron Marcuse-Kubitza
04:49 AM Revision 13553: removed no longer used config/VirtualBox_VMs/VegCore ERD/. use the Ubuntu 14.04 VM instead, which now has the VegCore ERD setup.
Aaron Marcuse-Kubitza
04:48 AM Revision 13552: config/VirtualBox_VMs/Ubuntu 14.04/Ubuntu 14.04.vbox: added VegCore ERD setup
Aaron Marcuse-Kubitza
03:30 AM Revision 13551: schemas/: svn:ignore *.changes.sql, needed for MySQL Workbench 6.1.6
Aaron Marcuse-Kubitza
03:30 AM Revision 13550: schemas/vegbien.ERD.mwb: updated
Aaron Marcuse-Kubitza
03:16 AM Revision 13549: schemas/vegbien.ERD.mwb: updated layout for MySQL Workbench 6.1.6, which uses a different line spacing
Aaron Marcuse-Kubitza

05/29/2014

11:53 AM Revision 13548: lib/tnrs.py: commented out the value of max_names that is not active, for clarity
Aaron Marcuse-Kubitza

05/28/2014

03:54 PM Revision 13547: config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated: merged post-bootloader installation steps into one snapshot now that eth1 addition is successful
Aaron Marcuse-Kubitza
03:49 PM Revision 13546: config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated, which adds eth1
Aaron Marcuse-Kubitza
03:47 PM Revision 13545: config/VirtualBox_VMs/Ubuntu 12.04/Ubuntu 12.04.vbox: updated
Aaron Marcuse-Kubitza

05/27/2014

11:12 PM Revision 13544: lib/tnrs.py: sources: updated to list/sort order in issue #917
Aaron Marcuse-Kubitza
10:39 PM Revision 13543: added exports/2014-3-11.Jeff_Ott.climatic_range_determinants.csv.run
Aaron Marcuse-Kubitza
10:38 PM Revision 13542: schemas/public_.sql: added 2014-3-11.Jeff_Ott.climatic_range_determinants
Aaron Marcuse-Kubitza
10:17 PM Revision 13541: schemas/public_.sql: analytical_stem_view: added scrubbed_taxon_name_with_author, needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
Aaron Marcuse-Kubitza
10:13 PM Revision 13540: inputs/.TNRS/schema.sql: taxon_scrub.scrubbed_unique_taxon_name.*: added scrubbed_taxon_name_with_author, needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
Aaron Marcuse-Kubitza
10:09 PM Revision 13539: schemas/public_.sql: added scrubbed_specific_epithet, scrubbed_species_binomial, which are needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
Aaron Marcuse-Kubitza
10:08 PM Revision 13538: fix: schemas/public_.sql: sync_analytical_stem_to_view(): removed fkey to source.shortname because this prevents reloading individual datasources
Aaron Marcuse-Kubitza
09:24 PM Task #927 (Resolved): move morphospecies name formation to normalized DB
see [[TNRS derived columns#scrubbed_morphospecies_binomial]] > @scrubbed_morphospecies_binomial@ Aaron Marcuse-Kubitza
09:19 PM Revision 13537: added downloads/
Aaron Marcuse-Kubitza
03:27 AM Revision 13536: schemas/public_.sql: added scrubbed_specific_epithet, scrubbed_species_binomial, which are needed by Jeff Ott's analysis (wiki.vegpath.org/Data_requests)
Aaron Marcuse-Kubitza
03:21 AM Revision 13535: fix: schemas/util.sql: mk_drop_from_create(): also support CREATE queries that include the SELECT statement on the same line as the CREATE
Aaron Marcuse-Kubitza
12:33 AM Revision 13534: schemas/public_.sql: analytical_stem_view: scrubbed_morphospecies_binomial: use new taxon_scrub.scrubbed_morphospecies_binomial
Aaron Marcuse-Kubitza
12:28 AM Revision 13533: inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*
Aaron Marcuse-Kubitza
12:13 AM Revision 13532: inputs/.TNRS/schema.sql: taxon_scrub: added scrubbed_morphospecies_binomial, analogous to accepted_morphospecies_binomial for scrubbed_*
Aaron Marcuse-Kubitza

05/26/2014

11:54 PM Revision 13531: inputs/.TNRS/schema.sql: taxon_scrub: documented how to modify it
Aaron Marcuse-Kubitza
11:51 PM Revision 13530: inputs/.TNRS/schema.sql: added taxon_scrub_modify()
Aaron Marcuse-Kubitza
11:41 PM Revision 13529: schemas/util.sql: create_if_not_exists(): print message if already exists, so the function doesn't inexplicably appear not to have run at all
Aaron Marcuse-Kubitza
11:20 PM Revision 13528: inputs/.TNRS/schema.sql: added taxon_scrub_modify()
Aaron Marcuse-Kubitza

05/23/2014

06:17 PM Revision 13527: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): use simpler util.recreate_view()
Aaron Marcuse-Kubitza
06:15 PM Revision 13526: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): documented usage
Aaron Marcuse-Kubitza
06:09 PM Revision 13525: schemas/util.sql: added recreate_view(), a special case of util.recreate()
Aaron Marcuse-Kubitza
04:24 PM Revision 13524: fix: schemas/util.sql: recreate(): usage: use `schema` instead of `schemas`
Aaron Marcuse-Kubitza
04:20 PM Revision 13523: config/VirtualBox_VMs/vegbiendev/vegbiendev.vbox: updated
Aaron Marcuse-Kubitza
03:57 PM Revision 13522: bugfix: schemas/public_.sql: _plots_20_tnrs_names: verbatim_name_with_author: use taxonverbatim.taxonomicname rather than taxonlabel.taxonomicname
Aaron Marcuse-Kubitza
02:16 AM Revision 13521: config/VirtualBox_VMs/Ubuntu */*.vbox: updated
Aaron Marcuse-Kubitza

05/22/2014

04:43 PM Task #932 (New): Discovering BIEN data through iPlant

iPlant will assign DOIs to datasets made public through its infrastructure. For the BIEN db data, the plan is:
* t...
Martha Narro
04:32 PM Task #931 (New): BIEN db at iPlant
Parent issue for tasks related to moving BIEN3 relational database and associated analytical views to iPlant. Martha Narro
04:20 PM Revision 13520: bugfix: config/VirtualBox_VMs/: switched from symlinks to hard links, because svn does not follow symlinks
Aaron Marcuse-Kubitza
02:07 PM Revision 13519: added config/VirtualBox_VMs/, containing the .vbox settings and password.txt (a non-empty password is needed for some system commands)
Aaron Marcuse-Kubitza

05/21/2014

07:30 PM Revision 13518: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): removed no longer needed DROP VIEW statement
Aaron Marcuse-Kubitza
07:30 PM Revision 13517: schemas/util.sql: recreate(): perform the correct DROP VIEW in the function itself so that the caller does not have to worry about forming it properly
Aaron Marcuse-Kubitza
07:19 PM Revision 13516: bugfix: schemas/util.sql: mk_drop_from_create(): added `DROP`
Aaron Marcuse-Kubitza
07:18 PM Revision 13515: schemas/util.sql: added mk_drop_from_create()
Aaron Marcuse-Kubitza
06:52 PM Revision 13514: schemas/util.sql: added regexp_match()
Aaron Marcuse-Kubitza
05:58 PM Revision 13513: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza
05:50 PM Revision 13512: fix: schemas/util.sql: force_recreate(): renamed to just recreate(), because "force" normally implies that things will be deleted, which this function does not do
Aaron Marcuse-Kubitza
05:49 PM Revision 13511: fix: schemas/public_.sql: _plots_20_tnrs_names: fixed order of tnrs_taxonomic_status, tnrs_accepted_name_family
Aaron Marcuse-Kubitza
04:45 PM Revision 13510: schemas/public_.sql: _plots_20_tnrs_names: added tnrs_taxonomic_status, as requested in issue #915
Aaron Marcuse-Kubitza
04:34 PM Revision 13509: schemas/public_.sql: analytical_stem_view: taxonomic_status: don't filter with map_taxonomic_status() anymore since this is now done by "TNRS"."MatchedTaxon"
Aaron Marcuse-Kubitza
04:25 PM Revision 13508: fix: inputs/.TNRS/schema.sql: MatchedTaxon.taxonomicStatus: filter using map_taxonomic_status() so that the corrected value is available in the normalized DB, not just analytical_stem
Aaron Marcuse-Kubitza
04:05 PM Revision 13507: inputs/.TNRS/schema.sql: MatchedTaxon: to modify: use new MatchedTaxon_modify(), which eliminates the work of putting together the dependent views
Aaron Marcuse-Kubitza
03:53 PM Revision 13506: inputs/.TNRS/schema.sql: added MatchedTaxon_modify()
Aaron Marcuse-Kubitza
03:44 PM Revision 13505: schemas/util.sql: show_create_view(): use new mk_set_relation_metadata()
Aaron Marcuse-Kubitza
03:41 PM Revision 13504: schemas/util.sql: added mk_set_relation_metadata()
Aaron Marcuse-Kubitza
04:13 AM Revision 13503: bugfix: inputs/.TNRS/schema.sql: map_taxonomic_status(): need to use accepted name instead of scrubbed name (which also includes no-opinion names), as described at http://wiki.vegpath.org/2013-11-14_conference_call#taxonomic-fields. this used to be the accepted name, but got switched when the concatenated name was also used to store the matched name for no-opinion names.
Aaron Marcuse-Kubitza
01:50 AM Revision 13502: schemas/public_.sql: _plots_20_tnrs_names: use accepted_morphospecies_binomial, which is now available directly in the TNRS results, instead of just the morphospecies_suffix, as requested in issue #915
Aaron Marcuse-Kubitza
01:27 AM Revision 13501: inputs/.TNRS/schema.sql: MatchedTaxon: documented how to modify it (using util.force_recreate())
Aaron Marcuse-Kubitza
01:23 AM Revision 13500: fix: lib/PostgreSQL-MySQL.csv: also remove left-behind lines such as `$$);`
Aaron Marcuse-Kubitza
12:59 AM Revision 13499: schemas/util.sql: force_recreate(): documented usage, which is somewhat complex and has several important parts
Aaron Marcuse-Kubitza

05/20/2014

05:46 PM Revision 13498: inputs/.TNRS/schema.sql: MatchedTaxon, etc.: added accepted_morphospecies_binomial derived field
Aaron Marcuse-Kubitza
05:40 PM Revision 13497: bugfix: schemas/util.sql: restore_views(): need to specify view name for a manual existence check, in case the view definition becomes invalid, which would produce a nonstandard (uncatchable) exception
Aaron Marcuse-Kubitza
05:33 PM Revision 13496: bugfix: schemas/util.sql: explain(): don't display any log messages printed by IMMUTABLE functions in the query, which EXPLAIN apparently runs
Aaron Marcuse-Kubitza
05:21 PM Revision 13495: schemas/util.sql: create_if_not_exists(): added relation param, which can be used to ensure that a standard exception is always generated if the relation exists, even if the table definition would be invalid (which generates a variety of exceptions)
Aaron Marcuse-Kubitza
04:26 PM Task #929 (New): change TNRS client to store metadata
* see details in [[2013-06-13 conference call#include-TNRS-version-and-settings-in-TNRS-cache]]
* after implementi...
Aaron Marcuse-Kubitza
04:17 PM Task #928 (New): switch to new TNRS setup
# #927 (part of #915)
# #917
# #916 (using rescrubbed names)
# #915
# -#929 (metadata)- _postponed_
Aaron Marcuse-Kubitza
03:26 PM Task #927 (Resolved): move morphospecies name formation to normalized DB
* currently, it's only in the analytical_stem view Aaron Marcuse-Kubitza
02:39 PM Revision 13494: /README.TXT: to back up the vegbiendev databases: added step to review diff before performing backup, in case the backup scripts break and try to synchronize things incorrectly
Aaron Marcuse-Kubitza

05/19/2014

09:08 PM Revision 13493: bugfix: schemas/util.sql: try_cast(), is_castable(): also need to handle syntax_error_or_access_rule_violation, which is thrown by ::regclass
Aaron Marcuse-Kubitza
08:52 PM Revision 13492: schemas/util.sql: added relation_exists()
Aaron Marcuse-Kubitza
08:27 PM Revision 13491: schemas/util.sql: save_drop_views()/restore_views(): store the view path in addition to the definition so it can be used in restoring
Aaron Marcuse-Kubitza
08:24 PM Revision 13490: bugfix: schemas/util.sql: in_reverse(): can't use `SELECT *` for composite types because this expands them
Aaron Marcuse-Kubitza
08:21 PM Revision 13489: bugfix: schemas/util.sql: array_reverse(): can't use `SELECT *` for composite types because this expands them
Aaron Marcuse-Kubitza
07:50 PM Revision 13488: schemas/util.sql: save_drop_views()/restore_views(): use opaque return type so it can be changed without changing the local var type in functions that use this
Aaron Marcuse-Kubitza
07:22 PM Revision 13487: schemas/util.sql: force_recreate(): recreate_users_cmds: renamed to restore_views_info since this is now whatever is needed by util.restore_views()
Aaron Marcuse-Kubitza
07:16 PM Revision 13486: schemas/util.sql: added restore_views() and use it in force_recreate()
Aaron Marcuse-Kubitza
02:07 AM Revision 13485: bugfix: schemas/util.sql: save_drop_views(): views must be *dropped* in reverse dependency order, but *returned* in forward dependency order
Aaron Marcuse-Kubitza
01:36 AM Revision 13484: bugfix: schemas/util.sql: force_recreate(): dependent views need to be re-created in *forward* dependency order. this is done by reversing the dependencies only for save_drop_views().
Aaron Marcuse-Kubitza
12:48 AM Revision 13483: bugfix: schemas/util.sql: mk_set_comment(): need to use VIEW instead of TABLE for views
Aaron Marcuse-Kubitza
12:29 AM Revision 13482: bugfix: schemas/util.sql: show_create_view(): also need to include view comment
Aaron Marcuse-Kubitza
12:24 AM Revision 13481: fix: schemas/util.sql: mk_set_comment(): added ;
Aaron Marcuse-Kubitza
12:20 AM Revision 13480: fix: schemas/util.sql: show_set_comment(): don't display a COMMENT ON statement if no comment, because this will be appended to table defs, etc. and would create clutter
Aaron Marcuse-Kubitza
12:16 AM Revision 13479: bugfix: schemas/util.sql: mk_set_comment(): need to handle NULL comment properly
Aaron Marcuse-Kubitza
12:06 AM Revision 13478: schemas/util.sql: added show_set_comment(regclass)
Aaron Marcuse-Kubitza

05/18/2014

11:57 PM Revision 13477: schemas/util.sql: set_comment(): use util.mk_set_comment()
Aaron Marcuse-Kubitza
11:48 PM Revision 13476: schemas/Makefile: added vegbien/install, vegbien/uninstall which also handle TNRS
Aaron Marcuse-Kubitza

05/17/2014

06:26 PM Revision 13475: fix: schemas/Makefile: vegbien.sql: also remake inputs/.TNRS/schema.sql since its contents change along with vegbien.sql
Aaron Marcuse-Kubitza
06:22 PM Revision 13474: schemas/util.sql: added mk_set_comment()
Aaron Marcuse-Kubitza
06:22 PM Revision 13473: bugfix: lib/runscripts/util.run: $is_runscript: unexport so don't pass it to invoked scripts
Aaron Marcuse-Kubitza
06:01 PM Revision 13472: backups/pg_snapshot: documented runtime for initial backup (4 h)
Aaron Marcuse-Kubitza
05:36 PM Revision 13471: bugfix: schemas/util.sql: force_recreate(): recreate_users_cmds: use create_if_not_exists() rather than eval(), because cmd might manually re-create a deleted dependent view, causing it to already exist
Aaron Marcuse-Kubitza
05:27 PM Revision 13470: bugfix: schemas/util.sql: save_drop_view(): util.show_create_view(): don't include `OR REPLACE` because that causes nonuniform errors (eg. invalid_table_definition), instead of the standard duplicate_table exception caught by util.create_if_not_exists()
Aaron Marcuse-Kubitza
05:25 PM Revision 13469: fix: schemas/util.sql: show_create_view(): removed extra trailing ; because pg_get_viewdef() now includes one
Aaron Marcuse-Kubitza
05:24 PM Revision 13468: schemas/util.sql: show_create_view(): made inclusion of `OR REPLACE` configurable
Aaron Marcuse-Kubitza
05:10 PM Revision 13467: schemas/util.sql: save_drop_view(): use util.drop_view()
Aaron Marcuse-Kubitza
03:40 PM Revision 13466: /README.TXT: Maintenance: added steps to back up the vegbiendev databases
Aaron Marcuse-Kubitza
02:15 PM Revision 13465: bugfix: lib/runscripts/util.run: run_args_cmd(): don't prepend main to args if no args, because for a non-runscript, all args will be passed to main(), leading `main` to be doubled
Aaron Marcuse-Kubitza
01:30 PM Revision 13464: lib/tnrs.py: use the TNRS dev server (with private URL in tnrs.url) instead of the live server, since that contains datasources that we need
Aaron Marcuse-Kubitza
01:29 PM Revision 13463: lib/streams.py: added file_get_contents()
Aaron Marcuse-Kubitza
01:14 PM Revision 13462: lib/tnrs.py: configure the server separately from the base URL
Aaron Marcuse-Kubitza
01:12 PM Revision 13461: lib/: svn:ignore tnrs.url so the TNRS dev server URL does not become public
Aaron Marcuse-Kubitza

05/16/2014

12:03 AM Revision 13460: bugfix: web/.phpPgAdmin/.htaccess: only append subject if non-empty, to avoid confusing redirect.php
Aaron Marcuse-Kubitza

05/15/2014

11:57 PM Revision 13459: bugfix: web/.phpPgAdmin/.htaccess: custom pages: need to handle in query string because .php filename would be treated as path element
Aaron Marcuse-Kubitza
11:32 PM Revision 13458: web/.phpPgAdmin/.htaccess: support custom .php pages
Aaron Marcuse-Kubitza
10:30 AM Revision 13457: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza
09:43 AM Task #917: TNRS: Instructions for new version with TPL
Aaron, for now (next couple of months, this must be done on the development TNRS web app since TPL is only on the dev... Martha Narro

05/13/2014

02:32 PM Task #917 (New): TNRS: Instructions for new version with TPL
From Brad:
I’ve given some thought to the TPL matter. The algorithm isn’t hard, but Aaron will have to do the sort...
Martha Narro
11:19 AM Revision 13456: schemas/util.sql: save_drop_views(): return text[] instead of concatenated text so that the queries will be run individually and be easier to debug
Aaron Marcuse-Kubitza
11:00 AM Revision 13455: schemas/util.sql: added eval(queries text[])
Aaron Marcuse-Kubitza
09:43 AM Revision 13454: bugfix: schemas/util.sql: force_recreate(): need to drop users in reverse to avoid dependencies that block the drop
Aaron Marcuse-Kubitza
09:25 AM Revision 13453: schemas/util.sql: added array_reverse()
Aaron Marcuse-Kubitza
09:25 AM Revision 13452: schemas/util.sql: added in_reverse()
Aaron Marcuse-Kubitza
08:39 AM Revision 13451: bugfix: schemas/util.sql: force_recreate(): need to use [[:lower:]], not [:lower:]
Aaron Marcuse-Kubitza
08:34 AM Revision 13450: schemas/util.sql: force_recreate(): debug-print PG_EXCEPTION_DETAIL, users to assist in debugging
Aaron Marcuse-Kubitza
08:33 AM Revision 13449: fix: schemas/util.sql: debug_print_value(): added trailing newline to visually distinguish the printed value
Aaron Marcuse-Kubitza
08:27 AM Revision 13448: schemas/util.sql: added debug_print_var()
Aaron Marcuse-Kubitza
07:06 AM Revision 13447: schemas/util.sql: debug_print_return_value(): use new util.debug_print_value()
Aaron Marcuse-Kubitza
06:59 AM Revision 13446: schemas/util.sql: added debug_print_value()
Aaron Marcuse-Kubitza
05:45 AM Revision 13445: fix: schemas/util.sql: util.force_recreate(): also support dropping things besides tables
Aaron Marcuse-Kubitza
04:50 AM Revision 13444: inputs/.TNRS/schema.sql: MatchedTaxon.Accepted_name_species: mapped to accepted_species_binomial
Aaron Marcuse-Kubitza
04:09 AM Revision 13443: fix: inputs/.TNRS/schema.sql: COMMENTs: always include newline before and after
Aaron Marcuse-Kubitza
03:50 AM Revision 13442: bugfix: schemas/public_.sql: _plots_20_tnrs_names: tnrs_accepted_*: use new accepted_*, *not* scrubbed_*, as scrubbed_* does *not* contain only the accepted name (as implied by the tnrs_accepted_* column name)
Aaron Marcuse-Kubitza
03:46 AM Revision 13441: bugfix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: undid rename of accepted name columns to scrubbed_* (r13435), because these are actually *not* the same (scrubbed_* is the combination of accepted and no-opinion names). the accepted name columns will now be named accepted_*, following the standard naming scheme.
Aaron Marcuse-Kubitza
03:28 AM Revision 13440: bugfix: schemas/public_.sql: _plots_20_tnrs_names: morphospeciesSuffix must still be called morphospecies_suffix, not taxon_morphospecies, because that column has not been updated to the taxon_morphospecies yet (fixes r13435)
Aaron Marcuse-Kubitza
03:13 AM Revision 13439: fix: inputs/.TNRS/schema.sql: taxon_scrub, etc.: scrubbed_*: use columns from MatchedTaxon whenever possible, to as much as possible avoid the need to join to taxon_scrub.scrubbed_unique_taxon_name.*
Aaron Marcuse-Kubitza
02:53 AM Revision 13438: schemas/Makefile: vegbien.sql: exclude the same set of Source tables excluded by inputs/.TNRS/schema.sql, so that reinstalling TNRS doesn't change the contents of this file
Aaron Marcuse-Kubitza
02:29 AM Revision 13437: bugfix: inputs/.TNRS/grants.sql: added GRANT statements from schema.sql because these aren't run by `make inputs/.TNRS/reinstall`
Aaron Marcuse-Kubitza

05/12/2014

07:06 PM Revision 13436: lib/tnrs.py: retrieval_request_template: taxonomic_constraint, source_sorting: documented their meaning and why they need to be on/off
Aaron Marcuse-Kubitza
05:03 PM Task #916: Taxon name validation: VegBank
regarding:
Line 617: TNRS gives a synonym for Aronia prunifolia in a different genus, but this is missed here
L...
Martha Narro
04:35 PM Task #916 (New): Taxon name validation: VegBank
Hi Aaron,
Bob only had time to get part way through the VegBank taxon validation file you sent, but there are some...
Martha Narro
04:28 PM Revision 13435: schemas/public_.sql: _plots_20_tnrs_names: changed to set of columns requested by Martha
Aaron Marcuse-Kubitza
03:13 PM Task #915 (New): Taxon Name Validation
1. Please correct the following in taxonMorphospecies:
1.1. -Family should be included in taxonMorphospecies only ...
Martha Narro

05/10/2014

09:32 PM Revision 13434: validation/aggregating/plots/bien3_validations_salvias_vegbien.sql: updated to DB
Aaron Marcuse-Kubitza
09:17 PM Revision 13433: schemas/public_.sql: _plots_20_tnrs_names: added morphospecies suffix in order to also validate it
Aaron Marcuse-Kubitza
09:13 PM Revision 13432: schemas/public_.sql: _plots_20_tnrs_names: added verbatim name in order to also validate the formation of the concatenated name
Aaron Marcuse-Kubitza
08:49 PM Revision 13431: schemas/public_.sql: merged _plots_20_tnrs_input_names, _plots_21_tnrs_output_names into _plots_20_tnrs_names so the input and output names can be compared side-by-side
Aaron Marcuse-Kubitza
08:10 PM Revision 13430: schemas/vegbien.sql: synced to DB, which adds Source.errors table indexes added in the import
Aaron Marcuse-Kubitza

05/09/2014

07:27 PM Revision 13429: /README.TXT: Full database import: for test import, turn off DB backup: added () after after_import to show that it's a function
Aaron Marcuse-Kubitza
07:24 PM Revision 13428: /README.TXT: Full database import: refer to the shell instead of screen because it's also possible to use a nested shell for this
Aaron Marcuse-Kubitza
02:51 AM Revision 13427: bugfix: /README.TXT: Full database import: to import just a subset of the datasources: need to set @inputs separately from declaring it, because declare does not support () on Mac
Aaron Marcuse-Kubitza
02:16 AM Revision 13426: fix: /README.TXT: Full database import: on local machine: need to allow logging output to go to log files
Aaron Marcuse-Kubitza
02:05 AM Revision 13425: /README.TXT: Full database import: for test import, added step to turn off DB backup
Aaron Marcuse-Kubitza
01:48 AM Revision 13424: fix: /README.TXT: Full database import: setting $version: moved to inside screen to avoid affecting the outer shell
Aaron Marcuse-Kubitza
01:46 AM Revision 13423: /README.TXT: Full database import: screen: added alternative for a small import (just use nested shell)
Aaron Marcuse-Kubitza
01:42 AM Revision 13422: fix: /README.TXT: Full database import: clear any limit set in .profile: moved to inside screen because it must happen within screen to avoid affecting the outer shell
Aaron Marcuse-Kubitza
01:40 AM Revision 13421: fix: /README.TXT: Full database import: added step to clear any limit set in .profile (applicable to local machine)
Aaron Marcuse-Kubitza
01:35 AM Revision 13420: bugfix: schemas/Makefile: `%/install: public_.sql`: also need to replace `public` when preceded by ( , as it is in the validations queries
Aaron Marcuse-Kubitza

05/07/2014

08:14 PM Revision 13419: bugfix: /Makefile: install: use schemas/public/*re*install because schemas/public/install would errexit if the public schema already exists
Aaron Marcuse-Kubitza
07:17 PM Revision 13418: bugfix: inputs/input.Makefile: $(datasrc_schema_exists): need to use $(datasrc), not $(schema), as $schema is only what this var is called in the runscripts
Aaron Marcuse-Kubitza
06:48 PM Revision 13417: bugfix: inputs/analytical_db/: need dummy table.run file to cause a schema to be created for this datasource
Aaron Marcuse-Kubitza
06:44 PM Revision 13416: fix: inputs/input.Makefile: $(sortFile): don't print the "add any missing tables to $(sortFile)" message every time the Makefile is run
Aaron Marcuse-Kubitza
06:44 PM Revision 13415: bugfix: inputs/input.Makefile: install: only run this for datasource dirs
Aaron Marcuse-Kubitza
05:18 PM Revision 13414: inputs/input.Makefile: install: use ./run's install target for clarity
Aaron Marcuse-Kubitza
05:18 PM Revision 13413: lib/runscripts/import.run: added install() target
Aaron Marcuse-Kubitza
04:56 PM Revision 13412: bugfix: inputs/input.Makefile: install: made it idempotent (using new $(datasrc_schema_exists)) so that it could be run by `make install` on an existing system
Aaron Marcuse-Kubitza
04:02 PM Revision 13411: bugfix: inputs/input.Makefile: $(datasrc_schema_exists): need to use $(shell ...)
Aaron Marcuse-Kubitza
03:31 PM Revision 13410: inputs/input.Makefile: added $(datasrc_schema_exists)
Aaron Marcuse-Kubitza
03:29 PM Revision 13409: lib/runscripts/in_datasrc_dir.run: use new local.run
Aaron Marcuse-Kubitza
03:25 PM Revision 13408: added lib/runscripts/local.run
Aaron Marcuse-Kubitza

05/06/2014

03:39 PM Revision 13407: web/links/index.htm: updated to Firefox bookmarks: iPlant links: fixed broken links
Aaron Marcuse-Kubitza
03:34 PM Revision 13406: web/links/index.htm: updated to Firefox bookmarks: starscream links: removed favicons so they wouldn't wake the Mac up on network access whenever someone opens the links page
Aaron Marcuse-Kubitza
 

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