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# Date Author Comment
13676 06/06/2014 04:57 AM Aaron Marcuse-Kubitza

fix: web/index.php: directory index: don't append QUERY_STRING, as this is not used by /all

13675 06/06/2014 04:57 AM Aaron Marcuse-Kubitza

web/.htaccess: username-based prefix subpaths: removed usernames_disabled env var because the bug that appeared to require this has now been fixed

13674 06/06/2014 04:56 AM Aaron Marcuse-Kubitza

bugfix: web/.htaccess: username-based prefix subpaths: also need to check original URL (REDIRECT_REQUEST_URI), in addition to current URL (REQUEST_URI) to see if usernames should be disabled

13673 06/06/2014 04:39 AM Aaron Marcuse-Kubitza

web/.htaccess: username-based prefix subpaths: allow explicitly disabling in a RewriteRule to handle special cases

13672 06/06/2014 04:28 AM Aaron Marcuse-Kubitza

web/.htaccess: auto-detect dotpath: removed handling of no longer used @ prefix (used to be used by username-based prefix subpaths)

13671 06/06/2014 04:20 AM Aaron Marcuse-Kubitza

bugfix: web/index.php: directory index: use QUERY_STRING, not HTTP_AUTHORIZATION (HTTP_AUTHORIZATION was probably left over from a previous attempt to provide username-based prefix subpaths)

13670 06/06/2014 02:44 AM Aaron Marcuse-Kubitza

fix: schemas/public_.sql: analytical_stem_view: vegpath.org links: use ; instead of : between link and definition, because it makes more grammatical sense

13669 06/06/2014 02:42 AM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view: vegpath.org links: removed no longer needed // suffix

13668 06/06/2014 02:38 AM Aaron Marcuse-Kubitza

web/.htaccess, username_prefix.php: username-based prefix subpaths: don't require the // at the end , to avoid clutter. IMPORTANT: in order to access the home page after visiting a URL with a username, you must now append "." to the host ("vegpath.org.") (other pages are not affected by this problem). since vegpath.org is a URL shortener, this is a worthwhile tradeoff to avoid needing the // suffixes everywhere.

13667 06/06/2014 02:19 AM Aaron Marcuse-Kubitza

bugfix: web/.htaccess: subdomains: each path element must be non-empty, to avoid matching a trailing . incorrectly

13666 06/06/2014 01:18 AM Aaron Marcuse-Kubitza

web/.htaccess: username-based prefix subpaths: updated documentation to use leading // instead of trailing ? or ?@

13665 06/06/2014 01:14 AM Aaron Marcuse-Kubitza

web/username_prefix.php: $_SERVER["PHP_AUTH_USER"] test: factored $_SERVER["SCRIPT_URL"] out of both branches of if statement

13664 06/06/2014 12:36 AM Aaron Marcuse-Kubitza

web/username_prefix.php: don't remove @ from query string because that is no longer a special character

13663 06/06/2014 12:08 AM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view: added links and definitions for half a dozen of the terms from various sources

13662 06/05/2014 11:46 PM Aaron Marcuse-Kubitza

fix: web/.htaccess: username-based prefix subpaths: changed format to subpath@host//path because the trailing ? makes it look like the sentence the URL is in is a question

13661 06/05/2014 08:38 PM Aaron Marcuse-Kubitza

web/.phpPgAdmin/.htaccess: action redirect: only append ? if adding to the query string

13660 06/05/2014 01:17 PM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13659 06/05/2014 01:17 PM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13658 06/05/2014 12:27 PM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13657 06/05/2014 12:12 PM Aaron Marcuse-Kubitza

inputs/publishable datasources.xlsx: updated

13656 06/05/2014 11:33 AM Aaron Marcuse-Kubitza

web/.phpPgAdmin/.htaccess: view: default to displaying the columns rather than the definition

13655 06/05/2014 09:02 AM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view: indicated provenance of the rest of the terms

13654 06/05/2014 08:32 AM Aaron Marcuse-Kubitza

schemas/public_.sql: analytical_stem_view: flagged the DwC terms

13653 06/05/2014 08:20 AM Aaron Marcuse-Kubitza

web/.phpPgAdmin/.htaccess: support viewing the columns of a view rather than the definition

13652 06/05/2014 08:16 AM Aaron Marcuse-Kubitza

web/.phpPgAdmin/.htaccess: RewriteRules: use overridable action var

13651 06/05/2014 08:14 AM Aaron Marcuse-Kubitza

web/.phpPgAdmin/.htaccess: support overriding action param in a later RewriteRule

13650 06/05/2014 08:04 AM Aaron Marcuse-Kubitza

web/.phpPgAdmin/.htaccess: removed skip= because this creates a confusing control flow, and prevents using chain

13649 06/05/2014 07:51 AM Aaron Marcuse-Kubitza

backups/TNRS.backup.md5: updated

13648 06/05/2014 07:30 AM Aaron Marcuse-Kubitza

schemas/public_.sql: added plot.**.modify()

13647 06/05/2014 07:24 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()

13646 06/05/2014 07:21 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: *_modify(): removed the need to manually maintain copies of the dependent view definitions with the *s in place, because the *s are now added automatically by view_def_to_orig()

13645 06/05/2014 07:15 AM Aaron Marcuse-Kubitza

fix: schemas/util.sql: view_def_to_orig(): also need to merge .* expressions resulting from a SELECT * of a join, to avoid duplicated columns

13644 06/05/2014 06:52 AM Aaron Marcuse-Kubitza

fix: schemas/util.sql: view_def_to_orig(): require at least 6 cols to avoid false positives in the expansion match pattern

13643 06/05/2014 06:49 AM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: view_def_to_orig(): 1st col: can't prepend \y because it considers only \w chars, not "

13642 06/05/2014 06:35 AM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: view_def_to_orig(): don't match whitespace in the middle of a "" identifier, as this could throw off the parser

13641 06/05/2014 06:34 AM Aaron Marcuse-Kubitza

schemas/util.sql: eval(): restore user's intent by running util.view_def_to_orig() on the query to unexpand expanded * expressions

13640 06/05/2014 05:50 AM Aaron Marcuse-Kubitza

schemas/util.sql: pg_get_viewdef(): use util.view_def_to_orig()

13639 06/05/2014 05:50 AM Aaron Marcuse-Kubitza

schemas/util.sql: added view_def_to_orig()

13638 06/05/2014 05:46 AM Aaron Marcuse-Kubitza

fix: schemas/util.sql: pg_get_viewdef(): should be STABLE because it references system catalogs

13637 06/05/2014 05:44 AM Aaron Marcuse-Kubitza

schemas/util.sql: added pg_get_viewdef() wrapper, which unexpands expanded * expressions

13636 06/05/2014 04:30 AM Aaron Marcuse-Kubitza

lib/tnrs.py: max_names: raised back up to 500 now that a workaround for the Internal Server Errors is in place (https://github.com/iPlantCollaborativeOpenSource/TNRS/issues/7)

13635 06/05/2014 03:57 AM Aaron Marcuse-Kubitza

fix: schemas/public_.sql: tnrs_input_name: added ORDER BY to ensure a stable sort order. this also creates better query plans by enabling merge joins.

13634 06/05/2014 03:50 AM Aaron Marcuse-Kubitza

bugfix: schemas/public_.sql: tnrs_input_name: need to exclude unsafe taxon names as a workaround to #935 (TNRS crashes when scrubbing names with two infraspecific epithets)

13633 06/05/2014 03:45 AM Aaron Marcuse-Kubitza

schemas/public_.sql: taxonlabel: added index on taxonomicname to facilitate retrieving rows from tnrs_input_name

13632 06/05/2014 03:39 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added taxon_name_is_safe()

13631 06/05/2014 03:30 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: added unsafe_taxon_names()

13630 06/04/2014 03:01 PM Aaron Marcuse-Kubitza

fix: lib/tnrs.py: max_names: lowered to 50 because the dev TNRS server is now always crashing with an Internal Server Error when scrubbing 500 names at a time (https://github.com/iPlantCollaborativeOpenSource/TNRS/issues/7)

13629 06/04/2014 11:41 AM Aaron Marcuse-Kubitza

web/.htaccess: auto-detect dotpath in query string: also auto-prepend & for query strings appended to a username-based prefix, so that these don't need to have & manually prepended to make them appendable

13628 06/04/2014 11:14 AM Aaron Marcuse-Kubitza

web/.htaccess: auto-detect dotpath in query string: also auto-detect dotpath for query strings appended to a username-based prefix, so that these don't need to have . prepended to make them appendable

13627 06/04/2014 02:25 AM Aaron Marcuse-Kubitza

web/username_prefix.php: no prefix: use $_SERVER["SCRIPT_URL"] instead of rtrimming $_SERVER["REQUEST_URI"]

13626 06/04/2014 02:24 AM Aaron Marcuse-Kubitza

web/username_prefix.php: has prefix: use same expr whether or not it has a query string, because the with-query-string expr works for both cases

13625 06/04/2014 02:20 AM Aaron Marcuse-Kubitza

web/username_prefix.php: use if statements instead of `? :` for clarity

13624 06/04/2014 02:10 AM Aaron Marcuse-Kubitza

web/username_prefix.php: use $subpath instead of $_SERVER["PHP_AUTH_USER"] for clarity

13623 06/04/2014 02:09 AM Aaron Marcuse-Kubitza

bugfix: **/.htaccess: redirects with fragment: qsappend does not support fragment, so append it separately

13622 06/04/2014 01:59 AM Aaron Marcuse-Kubitza

web/.htaccess, username_prefix.php: username-based prefix subpaths: support dotpath in query string (which will be appended verbatim to the prefix). use "__?@__" instead of "__?__&" to signal username-based prefix, so that the query string does not end in a dangling & .

13621 06/04/2014 01:53 AM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/.htaccess: qsappend does not support fragment, so append it separately

13620 06/04/2014 01:06 AM Aaron Marcuse-Kubitza

bugfix: web/.htaccess: auto-detect dotpath in query string: don't exclude dotpaths that come before a normal query string (&k=v...)

13619 06/04/2014 01:05 AM Aaron Marcuse-Kubitza

web/.htaccess: auto-detect dotpath in query string: documented what each RewriteCond does

13618 06/04/2014 01:03 AM Aaron Marcuse-Kubitza

web/.htaccess: auto-detect dotpath in query string: use %{QUERY_STRING} instead of %0 for clarity

13617 06/04/2014 12:48 AM Aaron Marcuse-Kubitza

web/.htaccess, web/username_prefix.php: username-based prefix subpaths: support query strings in addition to paths

13616 06/04/2014 12:18 AM Aaron Marcuse-Kubitza

web/index.php: removed no longer needed redirection of username-based prefix subpaths, which is now handled by web/.htaccess

13615 06/04/2014 12:16 AM Aaron Marcuse-Kubitza

web/.htaccess: handle username-based prefix subpaths (of the form "subpath@url?") for all paths rather than just for the root (which were handled by index.php)

13614 06/04/2014 12:11 AM Aaron Marcuse-Kubitza

added web/username_prefix.php, for use with username-based prefix redirects

13613 06/03/2014 11:13 PM Aaron Marcuse-Kubitza

web/index.php: subpath@host? redirects: also support multiple @ and nested . in prefix: @host? -> host?b.c.a

13612 06/03/2014 11:01 PM Aaron Marcuse-Kubitza

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.)

13611 06/03/2014 10:47 PM Aaron Marcuse-Kubitza

bugfix: web/index.php: full directory index: appending query string: need to use $_SERVER["QUERY_STRING"], not $_SERVER["HTTP_AUTHORIZATION"] for this

13610 06/03/2014 11:36 AM Aaron Marcuse-Kubitza

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)

13609 06/03/2014 10:36 AM Aaron Marcuse-Kubitza

bugfix: inputs/.TNRS/schema.sql: MatchedTaxon_modify(): updated to include taxon_scrub derived fields

13608 06/03/2014 10:25 AM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: mk_drop_from_create(): need to match first rather than last CREATE

13607 06/03/2014 10:21 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: *_modify(): allow running without a view_query, as recreate_view() now supports this

13606 06/03/2014 09:52 AM Aaron Marcuse-Kubitza

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)

13605 06/03/2014 08:56 AM Aaron Marcuse-Kubitza

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.

13604 06/03/2014 08:52 AM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: recreate(): need to handle case where util.mk_drop_from_create() is NULL

13603 06/03/2014 08:45 AM Aaron Marcuse-Kubitza

bugfix: schemas/util.sql: mk_drop_from_create(): only match CREATE if no custom DROP came before it

13602 06/03/2014 08:29 AM Aaron Marcuse-Kubitza

bugfix: schemas/public_.sql: sync_geoscrub_input_to_view(): `CREATE TABLE geoscrub_input AS __`: needs `LIMIT 0`

13601 06/03/2014 08:19 AM Aaron Marcuse-Kubitza

fix: schemas/util.sql: explain2notice_msg_if_can(): also need to catch invalid_cursor_definition ("cannot open multi-query plan as cursor")

13600 06/03/2014 08:15 AM Aaron Marcuse-Kubitza

schemas/public_.sql: sync_analytical_stem_to_view(): removed DROP TABLE IF EXISTS because this is now done automatically by util.recreate()

13599 06/03/2014 07:39 AM Aaron Marcuse-Kubitza

schemas/util.sql: added copy()

13598 06/03/2014 07:36 AM Aaron Marcuse-Kubitza

schemas/util.sql: added copy_data()

13597 06/02/2014 04:24 PM Aaron Marcuse-Kubitza

fix: lib/tnrs.py: Constrain by Source: turn it on so that the download settings reflect what TNRS actually used, while this is broken

13596 06/02/2014 06:19 AM Aaron Marcuse-Kubitza

fix: lib/tnrs.py: max_names: reduced back to 500 because even 5000 crashes the dev TNRS server

13595 06/02/2014 05:52 AM Aaron Marcuse-Kubitza

lib/tnrs.py: max_names: reduced to 5000 because 100,000 causes an internal server error

13594 06/02/2014 05:25 AM Aaron Marcuse-Kubitza

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

13593 06/02/2014 05:23 AM Aaron Marcuse-Kubitza

/README.TXT: Full database import: To run TNRS: added steps to rescrub all names

13592 06/02/2014 04:59 AM Aaron Marcuse-Kubitza

backups/TNRS.backup.md5: updated

13591 06/02/2014 04:50 AM Aaron Marcuse-Kubitza

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)

13590 06/02/2014 04:35 AM Aaron Marcuse-Kubitza

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).

13589 06/02/2014 04:27 AM Aaron Marcuse-Kubitza

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)

13588 06/02/2014 04:08 AM Aaron Marcuse-Kubitza

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).

13587 06/02/2014 03:43 AM Aaron Marcuse-Kubitza

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.)

13586 06/01/2014 09:00 PM Aaron Marcuse-Kubitza

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

13585 06/01/2014 05:00 AM Aaron Marcuse-Kubitza

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)

13584 06/01/2014 04:36 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented runtime to add a constraint (3 min)

13583 06/01/2014 04:35 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: unique constraint on Name_submitted: added Name_matched to allow multiple matches per name, as is needed to implement #917

13582 06/01/2014 03:44 AM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented how to populate a new column

13581 06/01/2014 03:41 AM Aaron Marcuse-Kubitza

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

13580 05/31/2014 10:31 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs.match_num: made it NOT NULL now that it's populated

13579 05/31/2014 10:28 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: populate match_num

13578 05/31/2014 10:25 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: populate match_num

13577 05/31/2014 09:50 PM Aaron Marcuse-Kubitza

inputs/.TNRS/schema.sql: tnrs: documented how to add and remove columns