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From 08/26/2014 to 09/24/2014

09/24/2014

11:53 PM Revision 14748: fix: /README.TXT: Installation: added instructions for "aaronmk@jupiter's password" prompt
Aaron Marcuse-Kubitza
11:49 PM Revision 14747: /README.TXT: Installation: added step to open a terminal window
Aaron Marcuse-Kubitza
11:48 PM Revision 14746: fix: /README.TXT: Installation: added instructions for "Are you sure you want to continue connecting" prompt
Aaron Marcuse-Kubitza
11:34 PM Revision 14745: inputs/VegBank/run*.log: updated. this adds the function call context in addition to the function location.
Aaron Marcuse-Kubitza
11:28 PM Revision 14744: bugfix: /Makefile: $(uutils_install): need to exit after printing instructions instead of continuing
Aaron Marcuse-Kubitza
11:13 PM Revision 14743: fix: /README.TXT: Installation: need instructions for "reload PATH" prompt
Aaron Marcuse-Kubitza
11:10 PM Revision 14742: fix: /README.TXT: Installation: `apt-get install subversion`: need --yes
Aaron Marcuse-Kubitza
10:58 PM Revision 14741: bugfix: /Makefile: bin/install: uutils: need to reopen terminal window before can proceed with other installation steps
Aaron Marcuse-Kubitza
09:04 PM Revision 14740: /Makefile: python-Linux: removed no longer used installation of pp (Parallel Python). we use Python's multiprocessing package instead.
Aaron Marcuse-Kubitza
07:57 PM Revision 14739: bugfix: /Makefile: install: must be config/download/live, not config/download
Aaron Marcuse-Kubitza
07:52 PM Revision 14738: README.TXT: bin/sync_upload calls as root: don't need to set $USER because this is now set to the correct value in bin/sync_upload's scripts
Aaron Marcuse-Kubitza
07:50 PM Revision 14737: bugfix: lib/sh/local.sh: $sync_remote_url: jupiter user is always aaronmk, not the local user
Aaron Marcuse-Kubitza
07:41 PM Revision 14736: *{.sh,run}: use standard **WARNING** syntax for warning labels
Aaron Marcuse-Kubitza
07:32 PM Revision 14735: bugfix: /Makefile: bin/install: also need to install uutils
Aaron Marcuse-Kubitza
07:26 PM Revision 14734: *{.sh,run}: use standard **WARNING** syntax for warning labels
Aaron Marcuse-Kubitza
07:25 PM Revision 14733: fix: lib/sh/util.sh: verbosity_compat(): documented that this should not be run until right before executing an external command, so that it doesn't mess up the logging mechanism
Aaron Marcuse-Kubitza
07:23 PM Revision 14732: bugfix: bin/make: don't run verbosity_compat until right before executing the external command, so that it doesn't mess up the logging mechanism. this is run automatically by command(), so there is no need to do anything here. note that logging bugs like these can now be troubleshooted much more easily with pst() to narrow down which functions could be causing the problem.
Aaron Marcuse-Kubitza
06:55 PM Revision 14731: bugfix: lib/sh/util.sh: functions called by pst(): commented out/removed logging calls that would have caused infinite recursion when pst()'ing a logging function
Aaron Marcuse-Kubitza
06:38 PM Revision 14730: lib/sh/util.sh: echo_func(): get call context before wrapper(s), which is more useful for debugging. this uses skip_stack_frames()'s lookahead=1 mode.
Aaron Marcuse-Kubitza
06:37 PM Revision 14729: fix: lib/sh/util.sh: skip_stack_frames() callers: updated for new skip_stack_frames rather than get_stack_frame behavior
Aaron Marcuse-Kubitza
06:32 PM Revision 14728: lib/sh/util.sh: skip_stack_frames(): added lookahead support, which looks at entry *after* current to deterine whether to skip current. this is useful for skipping wrappers, by looking at the *calling* function's name.
Aaron Marcuse-Kubitza
06:30 PM Revision 14727: fix: lib/sh/util.sh: skip_stack_frames(): for new skip_stack_frames rather than get_stack_frame behavior, stack frames must be skipped in the caller to preserve the stack frame pointer
Aaron Marcuse-Kubitza
06:26 PM Revision 14726: lib/sh/util.sh: get_stack_frame_after(): renamed to skip_stack_frames() for clarity
Aaron Marcuse-Kubitza
06:25 PM Revision 14725: lib/sh/util.sh: added skip_stack_frame_in_caller, unskip_stack_frame_in_caller
Aaron Marcuse-Kubitza
06:24 PM Revision 14724: lib/sh/util.sh: added prev_stack_frame
Aaron Marcuse-Kubitza
07:04 AM Revision 14723: lib/sh/util.sh: echo_func(): use new format_stack_frame, which adds call context information to what was provided by func_loc
Aaron Marcuse-Kubitza
07:02 AM Revision 14722: fix: lib/sh/util.sh: format_stack_frame(): need to hide canon_rel_path() info using log+
Aaron Marcuse-Kubitza
07:01 AM Revision 14721: lib/sh/util.sh: added get_stack_frame_after()
Aaron Marcuse-Kubitza
06:59 AM Revision 14720: lib/sh/util.sh: added matches()
Aaron Marcuse-Kubitza
06:58 AM Revision 14719: lib/sh/util.sh: next_stack_frame: documented usage
Aaron Marcuse-Kubitza
04:24 AM Revision 14718: fix: lib/runscripts/util.run: runscript template: all(): moved example commands to target(), where they would more likely be located
Aaron Marcuse-Kubitza
02:35 AM Revision 14717: lib/sh/util.sh: format_stack_frame(): support including args
Aaron Marcuse-Kubitza
12:08 AM Revision 14716: lib/sh/util.sh: debugging: added pst() (print_stack_trace)
Aaron Marcuse-Kubitza
12:05 AM Revision 14715: lib/sh/util.sh: added stack_trace(), print_stack_trace()
Aaron Marcuse-Kubitza
12:04 AM Revision 14714: lib/sh/util.sh: added format_stack_frame()
Aaron Marcuse-Kubitza
12:03 AM Revision 14713: lib/sh/util.sh: added get_stack_frame() and helpers
Aaron Marcuse-Kubitza

09/23/2014

10:29 PM Revision 14712: lib/sh/util.sh: terminal: moved before errors so it can be used by it
Aaron Marcuse-Kubitza
10:25 PM Revision 14711: lib/sh/util.sh: errors, debugging: moved after datatype sections so their functions can use these
Aaron Marcuse-Kubitza

09/22/2014

05:45 PM Revision 14710: bugfix: lib/sh/util.sh: canon_rel_path() stub: proper no-op requires passing through original path
Aaron Marcuse-Kubitza
05:42 PM Revision 14709: lib/sh/util.sh: canon_rel_path(): fall back to original path if can't resolve, instead of errexiting
Aaron Marcuse-Kubitza
05:39 PM Revision 14708: bugfix: lib/sh/util.sh: canon_rel_path(): don't re-localize $path because this clears it
Aaron Marcuse-Kubitza
05:36 PM Revision 14707: lib/sh/util.sh: canon_rel_path(): import $1 to $path before function body, so that the function body can be moved to a nested function
Aaron Marcuse-Kubitza
03:48 PM Revision 14706: lib/sh/util.sh: added canon_rel_path() stub for use by debugging functions
Aaron Marcuse-Kubitza
03:39 PM Revision 14705: bugfix: /Makefile: install: run bin/install first since config/download depends on it
Aaron Marcuse-Kubitza
03:36 PM Revision 14704: lib/sh/util.sh: moved func_loc() to before debugging section so it can be used by debugging functions
Aaron Marcuse-Kubitza

09/20/2014

02:34 PM Revision 14703: bugfix: lib/sh/util.sh: command__exec(): need to restore $verbosity before calling die_e
Aaron Marcuse-Kubitza

09/19/2014

03:51 PM Revision 14702: bugfix: /Makefile: install: also need to run config/download to get the necessary passwords
Aaron Marcuse-Kubitza
03:43 PM Revision 14701: config/Makefile: added download target
Aaron Marcuse-Kubitza
03:11 PM Revision 14700: /Makefile: config: renamed to bin/install because config is the name of a directory
Aaron Marcuse-Kubitza
02:53 PM Revision 14699: /README.TXT: Installation: `make install`: added instructions for what to do at each prompt
Aaron Marcuse-Kubitza
02:25 PM Revision 14698: /README.TXT: Installation: Check out svn: need to install svn first as this does not come preinstalled on Ubuntu
Aaron Marcuse-Kubitza

09/18/2014

04:57 PM Revision 14697: fix: inputs/.geoscrub/geoscrub_output/geoscrub.csv.run: make(): added warning that this will truncate the geoscrub database tables
Aaron Marcuse-Kubitza

09/17/2014

09:37 AM Bug #953 (New): CVS and VegBank data
Martha,

Here is a rehash of issues with CVS. Several of these are likely to apply to Vegbank as well. I view th...
Martha Narro

09/16/2014

05:35 PM Revision 14696: /README.TXT: to back up the local machine's hard drive: just do a single pass, to avoid the numerous different steps
Aaron Marcuse-Kubitza
05:25 PM Revision 14695: backups/*retention_policy*: on jupiter: changed to avoid retaining backups further back, as these consume significant disk space on jupiter and are not useful for anything
Aaron Marcuse-Kubitza
05:12 PM Task #952 (New): refresh GBIF so it can be published
see [[conditions of use#GBIF|GBIF conditions of use]] > new portal Aaron Marcuse-Kubitza
04:25 PM Revision 14694: fix: lib/sh/local.sh: $sync_remote_url: need $USER so user can be overridden when running as root
Aaron Marcuse-Kubitza
04:07 PM Revision 14693: fix: /README.TXT: to back up the local machine's settings: to jupiter: need `sudo -E` for new Documents/BIEN/vegbiendev*/
Aaron Marcuse-Kubitza
03:47 PM Revision 14692: /README.TXT: backups of ~/.dropbox/: just pause and resume Dropbox instead of quitting and restarting it
Aaron Marcuse-Kubitza
03:40 PM Revision 14691: /README.TXT: to back up the local machine's settings: to Dropbox: exclude gmvault-db/ to save space in Dropbox
Aaron Marcuse-Kubitza
03:36 PM Revision 14690: /README.TXT: to back up the local machine's settings: don't need to exclude ~/Library/Thunderbird/Profiles/9oo8rcyn.default/global-messages-db.sqlite because the disk that was corrupting this file has been replaced (#907)
Aaron Marcuse-Kubitza
03:33 PM Revision 14689: /README.TXT: to back up e-mails: don't need to also sync aaronmk@nceas.ucsb.edu because these e-mails are also in aaronmk.nceas@gmail.com (auto-forwarded)
Aaron Marcuse-Kubitza
03:16 PM Revision 14688: /README.TXT: Notes on system stability: removed no longer applicable warning about system upgrades, which is now incorrect because the disk space overrun bug (#887) was found *not* to have been caused by a system upgrade
Aaron Marcuse-Kubitza
02:57 PM Revision 14687: web/links/index.htm: updated to Firefox bookmarks: Roundtable: added links for Roundtable on "obstacles faced by researchers who reuse, share and manage data, and strategies for overcoming them"
Aaron Marcuse-Kubitza
02:46 PM Revision 14686: lib/Firefox_bookmarks.reformat.csv: label page's self-description as such: also support quotations enclosed in '
Aaron Marcuse-Kubitza

09/10/2014

11:07 PM Revision 14685: fix: exports/native_status_resolver.csv.run: added `users_by_name=1` to preserve the file group
Aaron Marcuse-Kubitza
11:00 PM Revision 14684: added inputs/VegBank/run.call_graph.log
Aaron Marcuse-Kubitza
05:45 PM Task #907 (Resolved): troubleshoot rsync verification errors
this problem no longer occurs after the Time Machine restore, so it was most likely a disk corruption issue with the ... Aaron Marcuse-Kubitza
05:03 PM Revision 14683: inputs/VegBank/run.log: updated for echo_vars() changes. the PG* vars, which contain important information, will now not need to be filtered out.
Aaron Marcuse-Kubitza
04:48 PM Revision 14682: lib/sh/util.sh: echo_vars(): merge repeated flags so there aren't flags in between the vars (which is also not valid declare syntax)
Aaron Marcuse-Kubitza
04:15 PM Revision 14681: lib/sh/db.sh: pg_cmd(): log vars on same line to avoid clutter
Aaron Marcuse-Kubitza
04:10 PM Task #887: fix disk space leak that fills the disk and crashes the import
not fixing this because we fixed the bug in our code that was triggering this Postgres bug Aaron Marcuse-Kubitza
03:58 PM Task #476 (New): develop map spreadsheet -> header override file translation utility
multiple output locations for the same input column are now handled by source-specific derived columns, so this is no... Aaron Marcuse-Kubitza
03:56 PM Task #483 (Resolved): rename staging table columns according to map.csv
this was later implemented in a way that avoids needing to reinstall the staging tables Aaron Marcuse-Kubitza
03:49 PM Task #951 (Resolved): test that `make install` is able to fully re-create vegbiendev
h3. steps
# update vegbiendev:...
Aaron Marcuse-Kubitza
03:17 PM Revision 14680: lib/sh/util.sh: echo_vars(): put all the vars on the same line so they don't clutter up the call graph generated at the default verbosity
Aaron Marcuse-Kubitza
01:56 PM Revision 14679: web/links/index.htm: updated to Firefox bookmarks: Mac: added link for VNC client. extended attributes: added link for chflags.
Aaron Marcuse-Kubitza
12:52 PM Revision 14678: added planning/workflow/staging_tables_installation_for_SQL_datasource.odg.src.log
Aaron Marcuse-Kubitza
12:51 PM Revision 14677: added inputs/VegBank/run.log
Aaron Marcuse-Kubitza
12:49 PM Revision 14676: fix: inputs/input.Makefile: $(svnFilesGlob): *.log should be in both the subdirs and the main dir
Aaron Marcuse-Kubitza
12:48 PM Revision 14675: inputs/input.Makefile: $(svnFilesGlob): *.log
Aaron Marcuse-Kubitza

09/09/2014

06:43 PM Revision 14674: inputs/Makefile: install: install an empty VegBIEN schema instead of all the datasources, at Mark's request. this enables loading just a single datasource.
Aaron Marcuse-Kubitza

09/08/2014

04:09 PM Revision 14673: schemas/VegBIEN/data_dictionary/VegBIEN data dictionary.xlsx: updated
Aaron Marcuse-Kubitza
04:01 PM Revision 14672: bugfix: schemas/public_.sql: view_full_occurrence_individual_view and related views: synced to data dictionary spreadsheet, which adds back the links to the definitions (which used to be part of the column name itself)
Aaron Marcuse-Kubitza
03:50 PM Revision 14671: fix: schemas/public_.sql: analytical_plot, analytical_specimen: updated column names to be the same as analytical_stem, which these are a subset of
Aaron Marcuse-Kubitza

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
Aaron Marcuse-Kubitza
10:47 PM Revision 14669: web/links/index.htm: updated to Firefox bookmarks: removed broken favicons
Aaron Marcuse-Kubitza
10:45 PM Revision 14668: web/links/index.htm: updated to Firefox bookmarks: updated favicons
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
10:02 PM Revision 14666: web/links/index.htm: updated to Firefox bookmarks: categorized uncategorized bookmarks
Aaron Marcuse-Kubitza
10:00 PM Revision 14665: web/links/index.htm: updated to Firefox bookmarks: updated favicons
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
09:37 PM Revision 14663: web/links/index.htm: updated to Firefox bookmarks: find: added instructions for searching by <>, not just =
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
08:46 PM Revision 14661: /README.TXT: Datasource setup: For MS Access databases: program link: added page subsections
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
05:11 PM Revision 14658: bugfix: /README.TXT: to backup files not in Time Machine: on first run, create parent dirs: mkdir: need sudo
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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...
Aaron Marcuse-Kubitza
04:12 PM Revision 14655: /README.TXT: to backup files not in Time Machine: documented why Postgres cannot be backed up by Time Machine
Aaron Marcuse-Kubitza

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)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
11:47 AM Revision 14652: /README.TXT: Single datasource refresh: reimport_scrub: added step to view progress
Aaron Marcuse-Kubitza
11:45 AM Revision 14651: /README.TXT: Single datasource refresh: moved to top since these steps are performed more often
Aaron Marcuse-Kubitza
10:23 AM Revision 14650: added planning/workflow/BIEN data workflow-2_bje.png export
Aaron Marcuse-Kubitza
10:05 AM Revision 14649: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza
10:04 AM Bug #948 (Resolved): fix duplicated rows in view_full_occurrence_individual
Aaron Marcuse-Kubitza
10:03 AM Revision 14648: planning/workflow/BIEN data workflow-2_bje.pptx: updated with Martha's changes and changes during conference call
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:55 AM Revision 14646: bugfix: web/BIEN3/Redmine/.htaccess: main page should continue to redirect to wiki, not Redmine project page
Aaron Marcuse-Kubitza
07:44 AM Revision 14645: schemas/public_.sql: *_view: re-ran *_view_modify(), which use the new non-blocking rematerialize_view()
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
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()
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:11 AM Revision 14641: schemas/util.sql: added identifier_replace()
Aaron Marcuse-Kubitza
07:08 AM Revision 14640: schemas/util.sql: added relation_replace()
Aaron Marcuse-Kubitza
01:50 AM Revision 14639: /README.TXT: Single datasource import: renamed to Single datasource refresh since it works on existing datasources
Aaron Marcuse-Kubitza
01:45 AM Revision 14638: /README.TXT: Single datasource import: also need to reload staging tables
Aaron Marcuse-Kubitza
01:42 AM Revision 14637: /README.TXT: Single datasource import: added steps to re-run geoscrubbing and back up the vegbiendev database
Aaron Marcuse-Kubitza

09/03/2014

02:43 AM Revision 14636: planning/workflow/BIEN data workflow-2_bje.pptx: fixed text alignment
Aaron Marcuse-Kubitza
02:35 AM Revision 14635: planning/workflow/BIEN data workflow-2_bje.pptx: answered questions asked in the diagram
Aaron Marcuse-Kubitza
02:19 AM Revision 14634: added planning/workflow/BIEN data workflow-2_bje.pptx from Martha/Brian E (in Asana)
Aaron Marcuse-Kubitza

08/29/2014

03:55 PM Revision 14633: added inputs/CVS/verify/Review of CVS data in BIEN3.docx
Aaron Marcuse-Kubitza
12:40 AM Revision 14632: backups/*retention_policy*: added explanations
Aaron Marcuse-Kubitza
12:39 AM Revision 14631: backups/*retention_policy*: on jupiter: backups further back: removed "if disk space permits" because this is already labeled "optionally"
Aaron Marcuse-Kubitza
12:38 AM Revision 14630: backups/*retention_policy*: changed to require retaining *.backup of the last 2 successful imports on all machines
Aaron Marcuse-Kubitza
12:25 AM Revision 14629: backups/*retention_policy*: allow keeping *.backup of the last 2 successful imports on all machines, not just jupiter
Aaron Marcuse-Kubitza
12:17 AM Revision 14628: **: renamed 2TB drive's BIEN3 partition to BIEN3.**SAVE** since one might not see the **SAVE** file in it
Aaron Marcuse-Kubitza
12:13 AM Revision 14627: **: renamed 2TB drive's BIEN3 partition to BIEN3.**SAVE** since one might not see the **SAVE** file in it
Aaron Marcuse-Kubitza
12:09 AM Revision 14626: **/"**DO_NOT_DELETE**": renamed to shorter **SAVE**
Aaron Marcuse-Kubitza
12:04 AM Revision 14625: added backups/*retention_policies*/ with retention policy files for each partition
Aaron Marcuse-Kubitza

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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:57 PM Revision 14620: bugfix: lib/csvs.py: JsonReader: need to pass col_order to row_dict_to_list_reader
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:10 PM Revision 14617: lib/csvs.py: JsonReader: added support for values that are arrays
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
06:47 PM Revision 14614: lib/csvs.py: Filter: inherit from WrapReader, which separates out the CSV-reader API code
Aaron Marcuse-Kubitza
06:43 PM Revision 14613: lib/csvs.py: added WrapReader
Aaron Marcuse-Kubitza
06:43 PM Revision 14612: lib/csvs.py: added Reader
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
05:58 PM Revision 14610: planning/meetings/BIEN conference call availability.xlsx: updated
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
08:54 AM Revision 14608: fix: /README.TXT: to back up the local machine's hard drive: updated location of `screen` for added commands
Aaron Marcuse-Kubitza
08:53 AM Revision 14607: /README.TXT: added trailing / on dirs to make clear that they're dirs
Aaron Marcuse-Kubitza
08:40 AM Revision 14606: config/VirtualBox_VMs/vegbiendev/README.TXT: added instructions to configure the VM to support VirtualBox
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:05 AM Revision 14602: config/VirtualBox_VMs/vegbiendev/README.TXT: added instructions to retrieve the original contents of the backup from the VM
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza

08/27/2014

03:17 PM Revision 14599: lib/csvs.py: added MultiFilter, which enables applying multiple filters by nesting
Aaron Marcuse-Kubitza

08/26/2014

07:57 PM Revision 14598: lib/tnrs.py: single_tnrs_request(): JSON mode: implemented output of JSON data
Aaron Marcuse-Kubitza
07:53 PM Revision 14597: lib/tnrs.py: single_tnrs_request(): factored out wrapping in TnrsOutputStream, since this is done for both modes
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:44 PM Revision 14595: lib/csvs.py: added JsonReader, which reads parsed JSON data as row tuples
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
07:43 PM Revision 14593: lib/csvs.py: RowNumFilter: added support for filtering the header row as well
Aaron Marcuse-Kubitza
07:42 PM Revision 14592: lib/csvs.py: ColInsertFilter: added support for filtering the header row as well
Aaron Marcuse-Kubitza
05:12 PM Revision 14591: lib/csvs.py: InputRewriter: documented that this is also a stream (in addition to inheriting from StreamFilter)
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
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.
Aaron Marcuse-Kubitza
05:02 PM Revision 14588: bugfix: inputs/input.Makefile: %/install: $(exportHeader) must come before postprocess because postprocess renames columns
Aaron Marcuse-Kubitza
04:50 PM Revision 14587: exports/: svn:ignore: added *.gz
Aaron Marcuse-Kubitza
04:49 PM Revision 14586: lib/csvs.py: added ProgressInputFilter, analogous to streams.ProgressInputStream
Aaron Marcuse-Kubitza
04:46 PM Revision 14585: lib/sql_io.py: added commented-out debug statement used to troubleshoot copy_expert() errors
Aaron Marcuse-Kubitza
04:45 PM Revision 14584: lib/dicts.py: added pair_keys(), pair_values()
Aaron Marcuse-Kubitza
04:15 PM Revision 14583: bugfix: lib/streams.py: CaptureStream: end_idx must also be > start_idx
Aaron Marcuse-Kubitza
04:07 PM Revision 14582: bugfix: inputs/input.Makefile: $(import_install_): need `set -o pipefail` to enable errexit
Aaron Marcuse-Kubitza
03:47 AM Revision 14581: /README.TXT: to backup files not in Time Machine: don't need to review diff because command is unidirectional
Aaron Marcuse-Kubitza
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
Aaron Marcuse-Kubitza
02:52 AM Revision 14579: inputs/.geoscrub/geoscrub_output/run: documented postprocess() rm=1 runtime (6 min)
Aaron Marcuse-Kubitza
 

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