Activity
From 08/07/2014 to 09/05/2014
09/05/2014
- 10:51 PM Revision 14670: /README.TXT: to synchronize vegbiendev, jupiter, and your local machine: avoid extraneous diffs when rsyncing: clarified the machines that the command should be run on
- 10:47 PM Revision 14669: web/links/index.htm: updated to Firefox bookmarks: removed broken favicons
- 10:45 PM Revision 14668: web/links/index.htm: updated to Firefox bookmarks: updated favicons
- 10:43 PM Revision 14667: fix: /README.TXT: to backup files not in Time Machine: need to use 2 TB external hard drive instead of Time Machine drive because Time Machine drive does not have ~/Documents/BIEN/ in a location where it can be hardlinked against
- 10:02 PM Revision 14666: web/links/index.htm: updated to Firefox bookmarks: categorized uncategorized bookmarks
- 10:00 PM Revision 14665: web/links/index.htm: updated to Firefox bookmarks: updated favicons
- 09:55 PM Revision 14664: web/links/index.htm: updated to Firefox bookmarks: local machine phpPgAdmin: removed this so the Mac won't get woken up on network access whenever someone opens the links page, which attempts to load the favicon from the local machine. the previous solution of manually deleting the favicon (r13406) doesn't work because the favicon will just get re-added whenever this bookmark is visited.
- 09:37 PM Revision 14663: web/links/index.htm: updated to Firefox bookmarks: find: added instructions for searching by <>, not just =
- 08:48 PM Revision 14662: /README.TXT: Datasource setup: For MS Access databases: added that one should use the settings in the associated .ini file where available
- 08:46 PM Revision 14661: /README.TXT: Datasource setup: For MS Access databases: program link: added page subsections
- 07:44 PM Revision 14660: /README.TXT: to backup files not in Time Machine: note that Time Machine dereferences hard links: added commands documenting that this is the case
- 05:12 PM Revision 14659: fix: /README.TXT: to backup files not in Time Machine: on first run, create parent dirs: added mkdir for Postgres
- 05:11 PM Revision 14658: bugfix: /README.TXT: to backup files not in Time Machine: on first run, create parent dirs: mkdir: need sudo
- 05:07 PM Revision 14657: /README.TXT: to backup files not in Time Machine: moved to root/ subdir to group the multiple top-level dirs together
- 04:53 PM Revision 14656: /README.TXT: to backup files not in Time Machine: added the vegbiendev archival backups, which cannot be backed up by Time Machine because it dereferences hard links
- 04:51 PM Bug #950 (Resolved): fix view_full_occurrence_individual_view rows with is_geovalid NULL
- h3. test case
eg. this happens for CVS rows:
|datasource|country|state_province|county|latitude|longitude|is_ge... - 04:12 PM Revision 14655: /README.TXT: to backup files not in Time Machine: documented why Postgres cannot be backed up by Time Machine
09/04/2014
- 11:52 AM Revision 14654: /README.TXT: Single datasource refresh: added steps to place the updated extract and extracted flat file(s)
- 11:48 AM Revision 14653: /README.TXT: Single datasource refresh: connect to vegbiendev first, even though steps before it have their own step to do this
- 11:47 AM Revision 14652: /README.TXT: Single datasource refresh: reimport_scrub: added step to view progress
- 11:45 AM Revision 14651: /README.TXT: Single datasource refresh: moved to top since these steps are performed more often
- 10:23 AM Revision 14650: added planning/workflow/BIEN data workflow-2_bje.png export
- 10:05 AM Revision 14649: planning/meetings/BIEN conference call availability.xlsx: updated
- 10:04 AM Bug #948 (Resolved): fix duplicated rows in view_full_occurrence_individual
- 10:03 AM Revision 14648: planning/workflow/BIEN data workflow-2_bje.pptx: updated with Martha's changes and changes during conference call
- 08:10 AM Revision 14647: bugfix: web/BIEN3/Redmine/.htaccess: subpath redirect: also redirect dirs, so that empty-subdir main-page redirects (eg. wiki.vegpath.org) work properly
- 07:55 AM Revision 14646: bugfix: web/BIEN3/Redmine/.htaccess: main page should continue to redirect to wiki, not Redmine project page
- 07:44 AM Revision 14645: schemas/public_.sql: *_view: re-ran *_view_modify(), which use the new non-blocking rematerialize_view()
- 07:41 AM Revision 14644: schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's and Martha's request (e-mails from Martha on 2014-8-12 at 17:37PT, and from Brian M on 2014-8-13 at 16:21PT). note that this change has already been made on vegbiendev.
- 07:21 AM Revision 14643: schemas/public_.sql: view_full_occurrence_individual: re-ran view_full_occurrence_individual_view_modify(), which uses the new non-blocking rematerialize_view()
- 07:20 AM Revision 14642: schemas/util.sql: rematerialize_view(): made it non-blocking, so that it would allow full access to the original materialized table during the operation
- 07:11 AM Revision 14641: schemas/util.sql: added identifier_replace()
- 07:08 AM Revision 14640: schemas/util.sql: added relation_replace()
- 01:50 AM Revision 14639: /README.TXT: Single datasource import: renamed to Single datasource refresh since it works on existing datasources
- 01:45 AM Revision 14638: /README.TXT: Single datasource import: also need to reload staging tables
- 01:42 AM Revision 14637: /README.TXT: Single datasource import: added steps to re-run geoscrubbing and back up the vegbiendev database
09/03/2014
- 02:43 AM Revision 14636: planning/workflow/BIEN data workflow-2_bje.pptx: fixed text alignment
- 02:35 AM Revision 14635: planning/workflow/BIEN data workflow-2_bje.pptx: answered questions asked in the diagram
- 02:19 AM Revision 14634: added planning/workflow/BIEN data workflow-2_bje.pptx from Martha/Brian E (in Asana)
08/29/2014
- 03:55 PM Revision 14633: added inputs/CVS/verify/Review of CVS data in BIEN3.docx
- 12:40 AM Revision 14632: backups/*retention_policy*: added explanations
- 12:39 AM Revision 14631: backups/*retention_policy*: on jupiter: backups further back: removed "if disk space permits" because this is already labeled "optionally"
- 12:38 AM Revision 14630: backups/*retention_policy*: changed to require retaining *.backup of the last 2 successful imports on all machines
- 12:25 AM Revision 14629: backups/*retention_policy*: allow keeping *.backup of the last 2 successful imports on all machines, not just jupiter
- 12:17 AM Revision 14628: **: renamed 2TB drive's BIEN3 partition to BIEN3.**SAVE** since one might not see the **SAVE** file in it
- 12:13 AM Revision 14627: **: renamed 2TB drive's BIEN3 partition to BIEN3.**SAVE** since one might not see the **SAVE** file in it
- 12:09 AM Revision 14626: **/"**DO_NOT_DELETE**": renamed to shorter **SAVE**
- 12:04 AM Revision 14625: added backups/*retention_policies*/ with retention policy files for each partition
08/28/2014
- 11:58 PM Revision 14624: backups/README.TXT: renamed to *retention_policy* to match the naming convention of the retention policy files in the various partitions
- 11:42 PM Revision 14623: /README.TXT: to back up the local machine's hard drive: also exclude *-files indicating the (differing) retention statuses of the partitions involved
- 08:13 PM Revision 14622: lib/tnrs.py single_tnrs_request(), bin/tnrs_client: use_tnrs_export: default to False because this mode uses incorrect selected matches (vegpath.org/issues/943), and the JSON mode that fixes this is now available
- 08:05 PM Revision 14621: bin/tnrs_db: tnrs.tnrs_request() call: explicitly set use_tnrs_export=True so that this continues to work if the default value is changed
- 07:57 PM Revision 14620: bugfix: lib/csvs.py: JsonReader: need to pass col_order to row_dict_to_list_reader
- 07:43 PM Revision 14619: config/VirtualBox_VMs/vegbiendev/README.TXT: ~/Documents/BIEN/vegbiendev.2014-2-2_1-07-32PT.+VirtualBox_changes/: renamed to vegbiendev.2014-2-2_1-07-32PT.VirtualBox/ to make clear that this is the VirtualBox version of vegbiendev
- 07:12 PM Revision 14618: bugfix: lib/tnrs.py: JSON output: need to stringify arrays so they match what is output in TSV-export mode
- 07:10 PM Revision 14617: lib/csvs.py: JsonReader: added support for values that are arrays
- 07:05 PM Revision 14616: lib/csvs.py: MultiFilter: inherit from WrapReader instead of Filter to avoid needing to define a no-op filter_() function
- 06:49 PM Revision 14615: bugfix: lib/csvs.py: row_dict_to_list_reader: need to override next() directly instead of just using Filter, because Filter doesn't support returning multiple rows for one input row (in this case, prepending a header row). this caused the 1st data row to be missing.
- 06:47 PM Revision 14614: lib/csvs.py: Filter: inherit from WrapReader, which separates out the CSV-reader API code
- 06:43 PM Revision 14613: lib/csvs.py: added WrapReader
- 06:43 PM Revision 14612: lib/csvs.py: added Reader
- 06:00 PM Revision 14611: schemas/public_.sql: views that use view_full_occurrence_individual_view: use the view_full_occurrence_individual table instead, now that this is materialized.
- 05:58 PM Revision 14610: planning/meetings/BIEN conference call availability.xlsx: updated
- 08:57 AM Revision 14609: /README.TXT: to back up the local machine's hard drive: renamed backup partition to BIEN3 to make clear what the backup drive contains
- 08:54 AM Revision 14608: fix: /README.TXT: to back up the local machine's hard drive: updated location of `screen` for added commands
- 08:53 AM Revision 14607: /README.TXT: added trailing / on dirs to make clear that they're dirs
- 08:40 AM Revision 14606: config/VirtualBox_VMs/vegbiendev/README.TXT: added instructions to configure the VM to support VirtualBox
- 08:22 AM Revision 14605: config/VirtualBox_VMs/vegbiendev/README.TXT: added instructions to retrieve the contents of the VM, with the VirtualBox changes added
- 07:47 AM Revision 14604: config/VirtualBox_VMs/vegbiendev/README.TXT: to retrieve the original contents of the backup from the VM: added steps to restore the correct VM snapshot
- 07:40 AM Revision 14603: config/VirtualBox_VMs/vegbiendev/README.TXT: also generate list of all the files whose permissions were changed since the backup, but which are extracted with their changed permissions instead of their original ones in the backup
- 07:05 AM Revision 14602: config/VirtualBox_VMs/vegbiendev/README.TXT: added instructions to retrieve the original contents of the backup from the VM
- 05:47 AM Revision 14601: fix: /README.TXT: to back up vegbiendev: also back up /home/aaronmk/bien/ (instead of just symlinking to the local copy), since this can be done space-efficiently with hardlinks. this ensures that the vegbiendev backup will not be modified when the local copy of bien/ is.
- 03:10 AM Revision 14600: lib/csvs.py: JsonReader: factored out row-dict-to-list into new row_dict_to_list_reader so that JSON-specific preprocessing is kept separate from the row format translation
08/27/2014
- 03:17 PM Revision 14599: lib/csvs.py: added MultiFilter, which enables applying multiple filters by nesting
08/26/2014
- 07:57 PM Revision 14598: lib/tnrs.py: single_tnrs_request(): JSON mode: implemented output of JSON data
- 07:53 PM Revision 14597: lib/tnrs.py: single_tnrs_request(): factored out wrapping in TnrsOutputStream, since this is done for both modes
- 07:47 PM Revision 14596: fix: lib/tnrs.py: JSON mode: TSV export columns: need to translate these to JSON column names before they can be used with the JSON data
- 07:44 PM Revision 14595: lib/csvs.py: added JsonReader, which reads parsed JSON data as row tuples
- 07:43 PM Revision 14594: lib/csvs.py: added row_dict_to_list(), which translates a CSV dict-based row to a list-based one
- 07:43 PM Revision 14593: lib/csvs.py: RowNumFilter: added support for filtering the header row as well
- 07:42 PM Revision 14592: lib/csvs.py: ColInsertFilter: added support for filtering the header row as well
- 05:12 PM Revision 14591: lib/csvs.py: InputRewriter: documented that this is also a stream (in addition to inheriting from StreamFilter)
- 05:11 PM Revision 14590: bugfix: lib/csvs.py: InputRewriter: accept a reader, as would be expected, instead of a custom stream whose lines are tuples
- 05:08 PM Revision 14589: fix: lib/sql_io.py: append_csv(): use new csvs.ProgressInputFilter instead of streams.ProgressInputStream(csvs.StreamFilter(__)), so that the input to csvs.InputRewriter is a reader, not a stream. this avoids the need for csvs.InputRewriter to accept a stream whose lines are tuples, instead of the expected reader.
- 05:02 PM Revision 14588: bugfix: inputs/input.Makefile: %/install: $(exportHeader) must come before postprocess because postprocess renames columns
- 04:50 PM Revision 14587: exports/: svn:ignore: added *.gz
- 04:49 PM Revision 14586: lib/csvs.py: added ProgressInputFilter, analogous to streams.ProgressInputStream
- 04:46 PM Revision 14585: lib/sql_io.py: added commented-out debug statement used to troubleshoot copy_expert() errors
- 04:45 PM Revision 14584: lib/dicts.py: added pair_keys(), pair_values()
- 04:15 PM Revision 14583: bugfix: lib/streams.py: CaptureStream: end_idx must also be > start_idx
- 04:07 PM Revision 14582: bugfix: inputs/input.Makefile: $(import_install_): need `set -o pipefail` to enable errexit
- 03:47 AM Revision 14581: /README.TXT: to backup files not in Time Machine: don't need to review diff because command is unidirectional
- 02:59 AM Revision 14580: fix: /README.TXT: to back up the local machine's hard drive: "repeat until only minimal changes" should refer to the first sync command
- 02:52 AM Revision 14579: inputs/.geoscrub/geoscrub_output/run: documented postprocess() rm=1 runtime (6 min)
08/25/2014
- 10:17 PM Revision 14578: lib/tnrs.py: single_tnrs_request(): use_tnrs_export=False: need to obtain export columns
- 10:16 PM Revision 14577: lib/csvs.py: added header(stream)
- 10:16 PM Revision 14576: fix: lib/tnrs.py: single_tnrs_request(): need to `assert name_ct >= 1`, because with no names, TNRS hangs indefinitely
- 09:13 PM Revision 14575: bin/tnrs_client: added env var to configure use_tnrs_export
- 08:18 PM Revision 14574: /README.TXT: to back up vegbiendev: use inplace=1 to speed stopping and resuming transfer
- 07:54 PM Revision 14573: fix: /README.TXT: to back up the local machine's hard drive: removed --extended-attributes (after initial sync) because rsync apparently has to visit every file for this
- 07:35 PM Revision 14572: fix: /README.TXT: to back up the local machine's hard drive: also need --extended-attributes
- 07:34 PM Revision 14571: /README.TXT: to back up the local machine's hard drive: removed --delete-before now that that partition has been expanded
- 07:16 PM Revision 14570: fix: /README.TXT: to back up vegbiendev: exclude /var/lib/mysql.bak,postgresql.bak because the local machine doesn't need 2 copies of this information
- 07:05 PM Revision 14569: /README.TXT: to back up vegbiendev: removed no longer needed exclude of Dropbox subdir backup
- 06:58 PM Revision 14568: fix: /README.TXT: to back up vegbiendev: also need to do steps under Maintenance > "to synchronize vegbiendev, jupiter, and your local machine" because /home/aaronmk/bien is not synced here
- 06:52 PM Revision 14567: bugfix: /README.TXT: to back up vegbiendev: need `overwrite=1`
- 06:47 PM Revision 14566: /README.TXT: to back up vegbiendev: removed no longer needed exclude of Dropbox subdir backup
- 06:46 PM Revision 14565: /README.TXT: to back up the version history: don't also need this on vegbiendev because it's already on jupiter and the local machine
- 06:43 PM Revision 14564: bugfix: /README.TXT: to back up vegbiendev: need to include Postgres config files
- 06:24 PM Revision 14563: /README.TXT: to back up the local machine's hard drive: don't back up temp files: added /.fseventsd/
- 05:54 PM Revision 14562: fix: /README.TXT: to back up the local machine's hard drive: initial runtime: use range instead because some of the later runtime might have been from the same files
- 05:52 PM Revision 14561: /README.TXT: to back up the local machine's hard drive: updated initial runtime to include additional transferred files (17 h)
- 05:36 PM Revision 14560: fix: /README.TXT: to back up the local machine's hard drive: need to use --delete-before because the backup partition is near capacity
- 05:34 PM Revision 14559: /README.TXT: to back up the local machine's hard drive: don't back up temp files such as /private/var/vm/*
- 05:30 PM Revision 14558: fix: /README.TXT: to back up the local machine's hard drive: back up most Dropbox/Postgres files before stopping processes, to minimize downtime
- 05:17 PM Bug #949 (New): fix shortened view_full_occurrence_individual column names that are now ambiguous
- * some, like @taxon_observation_id@/@taxonobservation_id@, are now ambiguous as a result of the removal of the scopin...
- 04:56 PM Bug #948 (Resolved): fix duplicated rows in view_full_occurrence_individual
- h3. issue
"from Brody":mailto:brody.sandelATbiology.au.dk?Brody_Sandel.2014-8-22-9:43PT:
> SELECT * FROM view_f...
08/21/2014
- 07:35 PM Revision 14557: bugfix: /README.TXT: to back up the local machine's hard drive: can't use ~ with --exclude
- 07:31 PM Revision 14556: fix: inputs/.geoscrub/geoscrub_output/postprocess.sql: map_geovalidity(): unscrubbable names should actually be geo*in*valid, not geovalid=NULL, according to Brad
- 07:24 PM Revision 14555: /README.TXT: to back up the local machine's hard drive: back up the non-Dropbox, non-Postgres files separately to minimize the Dropbox and Postgres downtime
- 06:03 PM Revision 14554: /README.TXT: to back up the vegbiendev databases: don't need to review diff for these as it's always unidirectional
- 05:55 PM Revision 14553: /README.TXT: added instructions to back up vegbiendev
- 05:12 PM Revision 14552: fix: /README.TXT: to back up the local machine's hard drive: also need to repeat backup command until only minimal changes
- 05:11 PM Revision 14551: /README.TXT: to back up the local machine's hard drive: added step to stop Postgres
- 05:10 PM Revision 14550: bugfix: /README.TXT: to back up the local machine's hard drive: also need to stop Dropbox
- 05:06 PM Revision 14549: /README.TXT: to back up the local machine's settings: added step to remove .DS_Store
- 04:47 PM Revision 14548: fix: /README.TXT: to back up the local machine's settings: Dropbox: shoudl not run with `del=`, because the backup should be an exact replica
- 04:25 PM Revision 14547: backups/TNRS.*: removed no longer needed old TNRS backups, which are part of the respective full-database backups in any case
- 02:57 PM Revision 14546: added config/phpMyAdmin/ symlink to schemas/VegCore/phpMyAdmin/
- 12:40 PM Revision 14545: bugfix: lib/sh/archives.sh: compress(): don't include dir prefix in zip archive
- 12:40 PM Revision 14544: lib/sh/util.sh: cd(): use echo_run instead of a manual echo_cmd call
- 12:35 PM Revision 14543: fix: lib/sh/util.sh: cd(): indent after running cd rather than before
- 12:32 PM Revision 14542: lib/sh/util.sh: cd(): support rebasing path vars for the new dir
- 11:51 AM Revision 14541: bugfix: lib/sh/archives.sh: compress(): need to use zip's path syntax to avoid the file in the archive being named "-"
- 08:56 AM Revision 14540: lib/tnrs.py: added option to avoid using TNRS's TSV export feature, which currently returns incorrect selected matches (vegpath.org/issues/943). this has been implemented up through the GWT/JSON decoding.
- 08:50 AM Revision 14539: lib/tnrs.py: added gwt_decode()
- 08:49 AM Revision 14538: lib/strings.py: added unesc_quotes() and helper functions
- 08:49 AM Revision 14537: lib/strings.py: added json_decode()
- 08:47 AM Task #947 (New): have all scripts that replace DB items rename the existing item out of the way rather than dropping it
- * entire DB _done in README.TXT but not scripts_
* -full-database import schema-
* -analytical DB-
* -individual d... - 08:38 AM Revision 14536: /README.TXT: To re-run geoscrubbing: updated runtimes
- 08:25 AM Revision 14535: exports/*_GBIF.csv.run: documented compress_() runtime (20 min-1 h)
08/20/2014
- 11:12 PM Revision 14534: lib/runscripts/extract.run: export_(): also compress created file
- 11:11 PM Revision 14533: lib/sh/archives.sh: added compress(), expand(), which handle compression of individual files
- 04:26 PM Revision 14532: bugfix: inputs/input.Makefile: sql/install: ";" for commands inside $(if) blocks need to be inside the $(if) block, too, because otherwise there will be dangling ";" without a statement (bash does not support empty statements containing just ";")
- 11:29 AM Revision 14531: /README.TXT: Full database import: converted database commands to command-line commands to make them easier to run
- 11:28 AM Revision 14530: /README.TXT: Full database import: converted database commands to command-line commands to make them easier to run
- 10:55 AM Revision 14529: web/links/index.htm: updated to Firefox bookmarks: added instructions for how to enable automatic restart on power loss for the UPS (which isn't accessible in the GUI)
08/19/2014
- 05:13 PM Revision 14528: fix: schemas/util.sql: contained_within_approx(point geocoord, region postgis.geography): use util.geography() instead of implicit cast to suppress "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" NOTICEs
- 05:10 PM Revision 14527: schemas/util.sql: added geography(util.geocoord), which suppresses "Coordinate values were coerced into range [-180 -90, 180 90] for GEOGRAPHY" NOTICEs
- 04:48 PM Revision 14526: exports/native_status_resolver.csv.run: updated export_() runtime (5 min, now that we're using the narrower New World criterion)
- 04:39 PM Revision 14525: fix: schemas/public_.sql: native_status_resolver: don't include rows with New World coordinates that don't also have New World country names, since the NSR only uses the country name
- 04:26 PM Revision 14524: schemas/public_.sql: native_status_resolver: removed rows with is_geovalid NULL, at Brad's request. note that this removes valid rows with standardized country names.
- 04:01 PM Revision 14523: exports/native_status_resolver.csv.run: updated export_() runtime (30 min)
- 03:28 PM Revision 14522: fix: schemas/public_.sql: native_status_resolver: added country IS NOT NULL filter requested by Brad
- 02:35 PM Revision 14521: fix: schemas/public_.sql: native_status_resolver: remove the id because this prevents SELECT DISTINCT from having the desired effect. instead, the results will be joined back using the other columns.
- 02:25 PM Revision 14520: exports/native_status_resolver.csv.run: upload_(): documented runtime (2.5 min)
- 02:18 PM Revision 14519: bugfix: exports/native_status_resolver.csv.run: upload_(): $live must be exported
- 02:15 PM Revision 14518: exports/native_status_resolver.csv.run: upload_(): use `live=1` instead for consistency with other invocations of put
- 02:14 PM Revision 14517: fix: exports/native_status_resolver.csv.run: upload_(): need `l=1`
- 02:12 PM Revision 14516: exports/native_status_resolver.csv.run: documented export_() runtime (45 min)
- 01:48 PM Revision 14515: exports/native_status_resolver.csv.run: added upload_() to get the file onto nimoy
- 01:25 PM Revision 14514: added exports/native_status_resolver.csv.run
- 01:23 PM Revision 14513: schemas/public_.sql: added native_status_resolver view, requested by Brad (wiki.vegpath.org/Data_requests)
- 11:47 AM Revision 14512: inputs/publishable datasources.xlsx: udpated
- 11:20 AM Task #946 (New): update the column names in the VegBIEN example queries to reflect Brian M's renamings
- * the VegBIEN example queries are at *[[VegBIEN FAQ#asked-by-Brian-E-on-2014-8-8]] > asked by Brian E on 2014-8-8*
*... - 08:37 AM Revision 14511: lib/tnrs.py: documentation about output of the retrieve step: added that this is also unusable because the array does not contain all the columns and contains no column names
- 07:54 AM Revision 14510: removed no longer used web/BIEN3/Redmine/main/. use Redmine/!__ instead.
- 07:52 AM Revision 14509: web/BIEN3/Redmine/issues/.htaccess: perform .. redirects using new ! prefix
- 07:51 AM Revision 14508: web/BIEN3/Redmine/.htaccess: enable redirects that avoid using a subdir's .htaccess
- 07:46 AM Revision 14507: web/BIEN3/Redmine/wiki/.htaccess: removed no longer needed ignore_fs, since the .htaccess does not have RewriteRules that would need this in a RewriteCond
- 07:42 AM Revision 14506: web/BIEN3/Redmine/issues/.htaccess: main issues page: added default filter conditions
- 07:41 AM Revision 14505: bugfix: web/BIEN3/Redmine/issues/.htaccess: need to redirect to separate URL for individual issues, because they are not located under the issues/ subdir in Redmine
- 06:35 AM Revision 14504: added web/.issues symlink and dest dir (needed because Apache does not support dangling symlinks)
- 06:35 AM Revision 14503: web/BIEN3/Redmine/wiki/.htaccess: documented that this dir is needed because Apache does not support dangling symlinks
- 06:32 AM Revision 14502: bugfix: web/.htaccess: need to expand top-level symlinks to avoid RewriteBase issues
- 06:29 AM Revision 14501: web/main.conf: added RewriteMap for readlink
- 06:28 AM Revision 14500: added web/readlink
- 05:52 AM Revision 14499: web/links/index.htm: updated to Firefox bookmarks: updated favicons
- 05:47 AM Revision 14498: web/links/index.htm: updated to Firefox bookmarks: updated favicons
08/18/2014
- 04:52 PM Revision 14497: web/BIEN3/Redmine/wiki/.htaccess: just use this dir as symlink dest, since the dir name is the same as the URL path within Redmine
- 04:50 PM Revision 14496: web/.htaccess: don't rewrite existing files/dirs: allow forcing rewrite of existing things with %{ENV:ignore_fs}
- 03:41 PM Revision 14495: web/BIEN3/Redmine/svn-web/.htaccess: use Redmine/ instead of main/ subdir
- 03:37 PM Revision 14494: web/BIEN3/Redmine/.htaccess: point this to the Redmine root instead of to the wiki, to avoid the need to append /main
- 03:21 PM Revision 14493: backups/vegbien.r14089.backup.md5: updated
- 01:58 PM Revision 14492: inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_best_match_jerry_lu index to facilitate finding names affected by the match-picking bug (#943)
- 10:01 AM Bug #945 (New): incorrect synonym being selected in TNRS
- _this is "TNRS-195":https://pods.iplantcollaborative.org/jira/browse/TNRS-195 on the TNRS JIRA bug tracker_
TNRS's...
08/17/2014
- 12:04 PM Revision 14491: backups/TNRS.backup.md5: updated
- 07:49 AM Revision 14490: fix: inputs/HVAA/Specimen/postprocess.sql, map.csv: monthCollected/dayCollected: fix indefinite dates (which aren't supported by Postgres), as decided by Bob (https://docs.google.com/spreadsheets/d/1PI8n0CRttN7ttsXs5qfh5OFFzSoAfJj0gSbylgX6vj4/edit#gid=0)
- 07:23 AM Revision 14489: schemas/util.sql: added date_part_fix()
08/16/2014
- 05:55 PM Revision 14488: schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's and Martha's request (e-mails from Martha on 2014-8-12 at 17:37PT, and from Brian M on 2014-8-13 at 16:21PT). note that this change has already been made on vegbiendev.
- 05:51 PM Revision 14487: schemas/public_.sql: added view_full_occurrence_individual_*GBIF, analytical_stem_*GBIF requested by Mark. note that this change has already been made on vegbiendev.
- 05:37 PM Revision 14486: schemas/VegBIEN/data_dictionary/VegBIEN data dictionary.xlsx: updated
- 05:15 PM Revision 14485: schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.
- 05:11 PM Revision 14484: schemas/public_.sql: view_full_occurrence_individual, analytical_stem: renamed columns to shortened names at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.
- 02:58 PM Revision 14483: schemas/public_.sql: analytical_stem_view: renamed to analytical_stem since this replaces the materialized analytical_stem table. note that this change has already been made on vegbiendev.
- 02:35 PM Revision 14482: schemas/public_.sql: viewFullOccurrence_*: renamed to view_full_occurrence_* at Brian M's request (e-mail from Martha on 2014-8-12 at 17:37PT). note that this change has already been made on vegbiendev.
- 01:20 PM Revision 14481: schemas/public_.sql: viewFullOccurrence_individual: re-ran viewFullOccurrence_individual_view_modify() to udpate this
- 01:15 PM Revision 14480: bugfix: schemas/util.sql: copy_struct(): also need to util.copy_comment() because CREATE TABLE __ INCLUDING ALL is missing this
- 01:11 PM Revision 14479: schemas/util.sql: added copy_comment(regclass, regclass)
- 12:29 PM Revision 14478: schemas/public_.sql: viewFullOccurrence_individual_view: CREATE INDEX runtime: documented 2-column runtime (~2 h)
- 12:06 PM Revision 14477: exports/analytical_stem_*GBIF.csv.run: documented runtime (40 min-1.2 h)
- 09:36 AM Revision 14476: exports/view_full_occurrence_individual_*GBIF.csv.run: documented runtime (20-30 min)
- 08:37 AM Revision 14475: added exports/analytical_stem_GBIF.csv.run, analytical_stem_non_GBIF.csv.run
08/15/2014
- 07:15 PM Revision 14474: added exports/view_full_occurrence_individual_GBIF.csv.run, view_full_occurrence_individual_non_GBIF.csv.run
- 04:13 PM Revision 14473: schemas/public_.sql: viewFullOccurrence_individual_view: added "after updating this" instructions
- 04:01 PM Revision 14472: schemas/public_.sql: viewFullOccurrence_individual_view: documented CREATE INDEX runtime (10 min - 1.5 h depending on the datatype and % populated)
- 03:32 PM Revision 14471: web/links/index.htm: updated to Firefox bookmarks: updated to use frenzy instead of starscream
08/14/2014
- 03:25 PM Revision 14470: fix: lib/tnrs.py: retrieval_request_template: source_sorting (Constrain by Source): corrected explanation to reflect that the behavior is actually the same in both modes, since only one match is ever marked as selected, and that match should always come first
- 03:03 PM Bug #943: in TNRS, the Constrain by Source option is applied incorrectly to the results download
- there is now a much faster workaround, described in the last paragraph of the issue description
- 10:50 AM Revision 14469: planning/meetings/BIEN conference call availability.xlsx: updated
08/11/2014
- 08:53 AM Bug #944 (New): fix phpPgAdmin bug that crashes the DB when browsing large tables
- use "@provider_count@":http://vegbiendev.nceas.ucsb.edu/VegBIEN/public/provider_count/:display to test this
- 07:48 AM Revision 14468: inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_name index
- 07:46 AM Revision 14467: inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_family index
- 07:10 AM Revision 14466: inputs/.TNRS/schema.sql: taxon_match: added taxon_scrub_by_species_binomial index
- 05:28 AM Revision 14465: bugfix: schemas/public_.sql: *_view_modify(): need to set the search_path so that tables are created in the same schema as the function, rather than whichever schema happens to be at the beginning of the search_path
- 05:19 AM Revision 14464: bugfix: schemas/public_.sql: analytical_stem_view_modify(): updated to support being used directly instead of via a materialized table
- 05:13 AM Revision 14463: schemas/public_.sql: removed no longer used analytical_stem. use analytical_stem_view or viewFullOccurrence_individual instead.
- 05:08 AM Revision 14462: fix: schemas/public_.sql: viewfulloccurrence_individual_view_modify(): fixed capitalization in function name (needs "" to preserve case)
- 05:03 AM Revision 14461: schemas/public_.sql: other derived views: use viewFullOccurrence_individual instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)
- 05:01 AM Revision 14460: schemas/public_.sql: validation views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)
- 04:57 AM Revision 14459: schemas/public_.sql: derived views: use analytical_stem_view instead of analytical_stem because analytical_stem is no longer materialized (viewFullOccurrence_individual_view is materialized instead)
- 04:46 AM Revision 14458: bugfix: schemas/util.sql: expansion_min_cols(): increased to properly handle all public-schema views (the largest is currently 2014-6-12.Jeff_Ott.climatic_range_determinants)
- 04:35 AM Revision 14457: schemas/util.sql: view_def_to_orig(): use new expansion_min_cols() for easier configuration
- 04:33 AM Revision 14456: schemas/util.sql: added expansion_min_cols() (the minimum # of cols from the same table to be treated as a * expression)
- 04:05 AM Revision 14455: fix: schemas/public_.sql: analytical_stem_view: regenerated columns list for viewFullOccurrence_individual (instead of viewFullOccurrence_individual_view)
- 03:40 AM Revision 14454: bugfix: mappings/VegCore-VegBIEN.csv: prefixed taxonomic ranks: use _concat_nullify() so that the prefix is only added if the epithet is non-NULL
- 03:29 AM Revision 14453: fix: schemas/util.sql: col_re(): support column names with " in them
- 02:59 AM Revision 14452: schemas/util.sql: added _concat_nullify(), which uses || instead of concat()
- 02:16 AM Revision 14451: bugfix: inputs/FIA/REF_RESEARCH_STATION/map.csv: mapped country, which is not provided in the FIA data
- 01:46 AM Revision 14450: schemas/public_.sql: removed no longer used threatened_taxonlabel_view. use iucn_red_list_view instead.
- 01:35 AM Revision 14449: schemas/public_.sql: viewFullOccurrence_individual_view: documented materialize time (22 h)
08/10/2014
- 05:53 AM Revision 14448: inputs/.TNRS/schema.sql: taxon_match: removed no longer used scrubbed_unique_taxon_name. the scrubbed name ranks are now generated from the other TNRS columns instead.
- 05:28 AM Revision 14447: /README.TXT: Full database import: added steps to re-run geoscrubbing
- 05:22 AM Revision 14446: exports/geoscrub_input.csv.run: export_(): updated runtime (30 s)
- 03:57 AM Revision 14445: fix: exports/viewFullOccurrence_*.csv.run: need to limit # rows to 5000 as requested by Bob
- 03:42 AM Revision 14444: schemas/public_.sql: viewFullOccurrence_*: documented materialize time
08/09/2014
- 10:23 PM Revision 14443: bin/make_analytical_db: materialize viewFullOccurrence_individual_view instead of analytical_stem_view because analytical_stem_view is now generatable via a simple join onto viewFullOccurrence_individual_view. this avoids running into potential disk space constraints when materializing and backing up both tables (~50 GB/table * 2 tables * 2 copies (incl. the backup) = 200 GB, which is very close to the available disk space).
- 10:17 PM Revision 14442: schemas/public_.sql: analytical_stem_view: use new materialized viewFullOccurrence_individual
- 10:08 PM Revision 14441: schemas/public_.sql: added viewFullOccurrence_individual by running viewFullOccurrence_individual_view_modify()
- 10:05 PM Revision 14440: schemas/public_.sql: added viewFullOccurrence_individual_view_modify(), analogous to analytical_stem_view_modify()
- 09:52 PM Revision 14439: bin/make_analytical_db: removed extra () around psql_verbose_vegbien
- 09:51 PM Revision 14438: bin/make_analytical_db: removed no longer used mk_table()
- 09:49 PM Revision 14437: bin/make_analytical_db: use more up-to-date *_view_modify() functions instead of mk_table()
- 08:46 PM Revision 14436: inputs/.TNRS/schema.sql: removed no longer used view ValidMatchedTaxon. use taxon_scrub instead.
- 08:44 PM Revision 14435: schemas/public_.sql: iucn_red_list_view: use taxon_scrub instead of ValidMatchedTaxon since they are equivalent
- 08:42 PM Revision 14434: inputs/.TNRS/schema.sql: taxon_scrub: use taxon_best_match directly, to avoid the need for a separate ValidMatchedTaxon view
- 08:25 PM Revision 14433: fix: inputs/.TNRS/schema.sql: taxon_scrub: merged synonymous columns
- 08:11 PM Revision 14432: schemas/vegbien.sql: taxon_scrub: documented steps to merge synonymous columns
- 07:45 PM Revision 14431: inputs/.TNRS/schema.sql: removed no longer used view MatchedTaxon. use taxon_best_match instead.
- 07:43 PM Revision 14430: inputs/.TNRS/schema.sql: ValidMatchedTaxon: use taxon_best_match now that it's equivalent to MatchedTaxon
- 07:38 PM Revision 14429: bugfix: schemas/public_.sql: tnrs_input_name: use taxon_match instead of taxon_best_match because there is no index on taxon_match that includes just the filters used by taxon_best_match
- 07:37 PM Revision 14428: schemas/public_.sql: tnrs_input_name: use taxon_best_match now that it's equivalent to MatchedTaxon
- 07:20 PM Revision 14427: backups/TNRS.backup.md5: updated
- 07:19 PM Revision 14426: fix: inputs/.TNRS/schema.sql: MatchedTaxon: merged synonymous columns
- 07:02 PM Revision 14425: fix: schemas/util.sql: view_is_subset_or_renaming(): views with CASE statements are also not subsets/renamings
- 06:52 PM Revision 14424: inputs/.TNRS/schema.sql: removed no longer used taxon_scrub.scrubbed_unique_taxon_name.* . use taxon_scrub instead.
- 06:50 PM Revision 14423: inputs/.TNRS/schema.sql: taxon_scrub: use taxon_match derived columns instead of the incorrect values in taxon_scrub.scrubbed_unique_taxon_name.* (which does not work with the multi-match strategy)
- 05:54 AM Revision 14422: inputs/.TNRS/schema.sql: MatchedTaxon: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.
- 05:27 AM Revision 14421: inputs/.TNRS/schema.sql: taxon_scrub: use derived columns from taxon_match. this also incorporates the fixes in the new derived columns.
08/08/2014
- 07:14 PM Revision 14420: added exports/viewFullOccurrence_{CVS,VegBank,NCU}.csv.run
- 07:13 PM Revision 14419: schemas/public_.sql: added viewFullOccurrence_{CVS,VegBank,NCU} for Bob
- 02:32 PM Revision 14418: bugfix: schemas/util.sql: added GRANT USAGE for bien_read, public_ so that util schema functions can be called by other users
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