Activity
From 04/11/2013 to 05/10/2013
05/10/2013
- 11:59 PM Revision 9097: lib/sh/util.sh: added contains()
- 11:57 PM Revision 9096: lib/sh/util.sh: command alias: also prepend -- to args to prevent a first arg starting with -- from being interpreted as an option to the `command` builtin
- 10:16 PM Revision 9095: lib/sh/db.sh: mysql_cmd(): moved setting of database to specific callers (mysql(), mysqldump()) because the syntax to set it differs between mysql* commands (e.g. mysql uses `--database=` while mysqldump uses `--databases ... --tables`)
- 10:13 PM Revision 9094: lib/sh/db.sh: added set_database alias, and use it in mysql_cmd()
- 10:11 PM Revision 9093: lib/sh/util.sh: import_vars alias and applicable aliases that use it: documented that when used inside another alias 2+ levels deep, it *must* be run inside a function. this is due to a strange bug in bash where $() expressions in 2-level aliases produce a syntax error when the alias is expanded outside a function.
- 10:07 PM Revision 9092: bugfix: lib/sh/util.sh: added back missing echo_func alias, which is needed to also include "$@" in the echoed function call
- 10:05 PM Revision 9091: lib/sh/util.sh: import_vars alias: use new get_prefix_vars()
- 10:04 PM Revision 9090: lib/sh/util.sh: add get_prefix_vars()
- 10:03 PM Revision 9089: lib/sh/util.sh: import_vars alias: use declare instead of local so it can be used outside a function
- 02:47 PM Revision 9088: lib/sh/db.sh: added mk_select alias and use it in pg_export()
- 02:36 PM Revision 9087: lib/sh/db.sh: pg_export(): always include the LIMIT value if specified, rather than only if the caller did not provide a full query
- 02:27 PM Revision 9086: lib/sh/db.sh: pg_export(): rtrim $query
- 02:22 PM Revision 9085: lib/sh/util.sh: added rtrim()
- 01:55 PM Revision 9084: lib/sh/db.sh: pg_export(): for simplicity, always use a SELECT statement as the source. take any source query in \$query without () instead of \$source with (). this will also help make pg_export uniform with MySQL.
- 01:34 PM Revision 9083: lib/sh/db.sh: renamed pg_copy_to() to pg_export() because it is also a general-purpose export command, which could have an analogous counterpart for MySQL
- 01:23 PM Revision 9082: bugfix: lib/sh/util.sh: moved self alias to beginning, before functions that use it
- 12:55 PM Revision 9081: lib/sh/util.sh: added repeat()
- 12:47 PM Revision 9080: lib/sh/util.sh: reverse(): use `i > 0` rather than `i >= 1` to match the `i < length` idiom used in forwards loops
- 12:43 PM Revision 9079: lib/sh/util.sh: moved strings section before verbose output so its commands can be used by the logging functions
- 12:32 PM Revision 9078: lib/sh/util.sh: echo_run() and derivatives (limit_stderr_cmd()): use new `indent` before the invoked command so its own logging messages, if any, are indented
- 12:27 PM Revision 9077: lib/sh/util.sh: propagate indent to invoked commands by exporting PS4
- 12:24 PM Revision 9076: lib/sh/util.sh: verbose output: added indent/outdent aliases and use them in inc_log_level/dec_log_level
- 12:14 PM Revision 9075: *{.sh,run}: replaced extern with command, a shell builtin that does the same thing. this is also part of dash (the Bourne shell on Linux).
- 12:08 PM Revision 9074: *{.sh,run}: removed extra space between function name and (), which is apparently not needed even though `help function` includes it. this greatly improves readability, including when function names are pasted into commit messages!
- 12:03 PM Revision 9073: lib/sh/util.sh: require_exists (): use die/log_info's new support for info messages using $type
- 12:00 PM Revision 9072: lib/sh/util.sh: die (): allow caller to specify a custom log message type (i.e. a suffix for log_* ())
- 11:58 AM Revision 9071: lib/sh/util.sh: log_e (): use new log_err
- 11:57 AM Revision 9070: lib/sh/util.sh: verbose output: added log_custom (), which modifies the symbol in PS4 to indicate the message type, and log_err ()/log_info (), which set specific symbols
- 11:55 AM Revision 9069: lib/sh/util.sh: moved die () into verbose output so it can use logging functions
- 11:53 AM Revision 9068: lib/sh/util.sh: moved functions after verbose output so copy_func () can use logging functions in its input checks
- 11:41 AM Revision 9067: lib/sh/util.sh: moved log_e () to verbose output section so it can use logging functions
- 11:29 AM Revision 9066: lib/sh/db.sh: mysqldump_diffable (): use pipe_delay to ensure that sed is printed after mysqldump
- 11:23 AM Revision 9065: lib/sh/util.sh: echo_cmd (): use new log ()
- 11:21 AM Revision 9064: lib/sh/util.sh: added log ()
- 10:53 AM Revision 9063: lib/sh/util.sh to_file, make.sh check_target_exists: use new require_exists to print message if file skipped because it already exists. this is useful for troubleshooting why certain make commands don't run.
- 10:51 AM Revision 9062: lib/sh/util.sh: added require_exists (), used to skip make commands for existing files
- 10:33 AM Revision 9061: *{.sh,run}: use `test !` instead of `! test` so that the ! is right next to the operator it's negating
- 10:31 AM Revision 9060: /run: geoscrub_input/make (): use new check_fake_target_exists to create the file only if it doesn't exist yet
- 10:31 AM Revision 9059: lib/sh/make.sh: added check_fake_target_exists (analogous to check_target_exists), which defers the target existence check until to_file (when the target name will presumably have been resolved to a path)
- 10:29 AM Revision 9058: lib/sh/util.sh: to_file (): support only running if the file does not exist by setting $if_not_exists
- 10:08 AM Revision 9057: lib/sh/util.sh: limit_stderr_cmd (): run cmd2rel_path explicitly here because echo_run is split apart rather than being run as echo_run ()
- 10:06 AM Revision 9056: lib/sh/util.sh: moved echo_cmd, echo_run before commands that use them
- 10:02 AM Revision 9055: lib/sh/make.sh: check_target_exists: if remaking, consider target not to exist
- 10:01 AM Revision 9054: lib/sh/make.sh: added remaking alias
- 09:45 AM Revision 9053: inputs/GBIF/table.run: table.tsv/make (): use echo_run instead of extern so that the command name is canonicalized properly
- 09:45 AM Revision 9052: lib/sh/util.sh: echo_run (): use new cmd2rel_path to resolve the command ($1)
- 09:44 AM Revision 9051: lib/sh/util.sh: added cmd2rel_path alias, which makes $1 a canon_rel_path if it's a filesystem path. this removes extra .. in the paths of invoked commands.
- 09:06 AM Revision 9050: *{.sh,run}: use shorter `test` instead of `test -n` and `test !` instead of `test -z` (http://www.gnu.org/software/bash/manual/bash.html#Bourne-Shell-Builtins > test)
- 08:52 AM Revision 9049: lib/sh/util.sh: echo_cmd (): don't include leading extern because it clutters up the output and is implied by the log_level
- 08:45 AM Revision 9048: lib/sh/util.sh: to_file (): run echo_func and `echo_vars stdout` to show what file the output is going to, since this information (i.e. redirects) isn't included in the logging output for the command itself
- 08:41 AM Revision 9047: lib/runscripts/table.run: remake_VegBIEN_mappings (): added public_schema_exists check, ported from lib/import.sh
- 08:40 AM Revision 9046: lib/sh/local.sh: added public_schema_exists (), ported from lib/import.sh
- 08:32 AM Revision 9045: *{.sh,run}: use new echo_stdout instead of echo_stdin where applicable, for clarity
- 08:31 AM Revision 9044: lib/sh/util.sh: added echo_stdout (currently just an alias of echo_stdin, because they are usable for the same purpose)
- 08:27 AM Revision 9043: /run: moved geoscrub_input export into separate geoscrub_input/make () target
- 08:24 AM Revision 9042: lib/sh/db.sh: pg_export_table_to_dir_no_header (): use to_file so that the file is autoremoved in case of error
- 07:51 AM Revision 9041: lib/sh/util.sh: let (): renamed to let! so that let can still be used to evaluate whether a numeric value is 0 (yes, an ! is allowed at the end of a command name)
- 07:44 AM Revision 9040: lib/sh/util.sh: moved canon_rel_path () into separate paths section
- 07:39 AM Revision 9039: bugfix: *{.sh,run}: use new func_override for runscript inheritance instead of invoking the overridden function as a (command-line) target of the parent runscript. this ensures that the overridden function is run in the *same* process as the calling function, so that $top_dir keeps the same value and runscript-relative paths continue to work.
- 07:30 AM Revision 9038: lib/sh/util.sh: added func_override (), for use in runscript inheritance
- 07:03 AM Revision 9037: lib/sh/util.sh: copy_func (): check that $from exists and $to does not exist (i.e. don't clobber existing functions). you can always first `unset -f` the function to get around the no-clobber restriction.
- 07:00 AM Revision 9036: lib/sh/util.sh: exceptions: added die ()
- 06:44 AM Revision 9035: lib/sh/util.sh: log_e (): restructured as an error handler to put after save_e rather than as a wrapper around the entire command. this allows it to be used with any kind of expression (such as boolean expressions with !), not just single commands.
- 06:35 AM Revision 9034: lib/sh/util.sh: log_e (): don't export $e to the calling context, since the caller can just use ` || { save_e; ...; }` if they need $e
- 06:31 AM Revision 9033: lib/sh/util.sh: calls to log_e: don't rely on log_e setting $e
- 06:30 AM Revision 9032: lib/sh/util.sh: added save_e, which now sets $e just locally
- 06:28 AM Revision 9031: lib/sh/util.sh: save_e: renamed to export_e because $e overwrites any previous value in the calling context
- 06:26 AM Revision 9030: lib/sh/util.sh: removed no longer used save_e_cmd
- 06:24 AM Revision 9029: lib/sh/util.sh: try (): use simpler save_e instead of save_e_cmd
- 06:19 AM Revision 9028: bugfix: lib/sh/util.sh: bool2int (): need to use try instead of save_e_cmd because save_e_cmd rethrows the error, which should instead just be stored in $e. this bug was not found in testing because bool2int was only used in $(), which errexit does not apply to.
- 06:15 AM Revision 9027: lib/sh/util.sh: exceptions: added save_e, now an alias for e=$?. added save_e/rethrow usage.
- 06:11 AM Revision 9026: lib/sh/util.sh: renamed save_e () to save_e_cmd () since it actually runs a command, in addition to saving $?
- 06:08 AM Revision 9025: lib/sh/util.sh: log_e (): rewrote to avoid using save_e, which will be repurposed
- 05:50 AM Revision 9024: lib/sh/util.sh: added func_exists ()
- 05:50 AM Revision 9023: lib/sh/util.sh: moved copy_func () after exceptions so it can use save_e/rethrow
- 05:44 AM Revision 9022: lib/sh/util.sh: added copy_func ()
- 05:39 AM Revision 9021: lib/sh/util.sh: save_e (): usage: added rethrow example
- 05:26 AM Revision 9020: bugfix: lib/sh/util.sh: bool2int (): need to load new aliases before it so that save_e will be expanded
- 05:24 AM Revision 9019: *{.sh,run}: put functions on one line where possible (and where they are not expected to expand)
- 05:19 AM Revision 9018: lib/sh/util.sh: added separate include guard around the include guard utils so they don't have to be redefined on every include of util.sh
- 05:06 AM Revision 9017: *{.sh,run}: added extra line before new sections to visually separate them. lib/sh/util.sh: added missing section headers.
- 05:01 AM Revision 9016: lib/sh/util.sh: split make utils out into separate make.sh
- 04:38 AM Revision 9015: lib/sh/util.sh: split archive (zip) utils out into separate archives.sh
- 04:24 AM Revision 9014: lib/sh/util.sh: split databases utils out into separate db.sh
- 04:05 AM Revision 9013: moved lib/*.sh to sh/ subdir so it's easier to find the .sh files among all the other lib/ files
- 03:32 AM Revision 9012: lib/util.sh: removed no longer used limit_stderr_extern. use `limit_stderr_cmd extern` instead.
- 03:29 AM Revision 9011: lib/util.sh: specify limit_stderr_cmd just for the (few) commands that need it, rather than for all commands, so that commands that use stderr to print important error messages don't have those error messages hidden when the verbosity is too low. (error messages should always be displayed, regardless of the verbosity.)
- 03:13 AM Revision 9010: lib/util.sh: limit_stderr_cmd (): only echo the command if it starts with echo_run. this requires adding echo_run before commands that use limit_stderr_cmd, such as limit_stderr_extern.
- 03:07 AM Revision 9009: lib/util.sh: limit_stderr_cmd (): remove echo_run from the command to run so that the command name isn't echoed twice
- 02:56 AM Revision 9008: lib/util.sh: limit_stderr_cmd: alias-expand command after it
- 02:53 AM Revision 9007: lib/util.sh: $verbosity: ensure it's an integer using `declare -i`
- 02:45 AM Revision 9006: lib/util.sh: grouped set verbosity statements together and commented them
- 02:43 AM Revision 9005: bugfix: lib/util.sh: verbose output: $verbosity defaults to $verbose (boolean) converted to integer. the previous set-default of $verbosity to $verbose has been removed because it came after `: "${verbosity=3}"` and thus didn't have an effect.
- 02:40 AM Revision 9004: lib/util.sh: added bool2int ()
- 02:32 AM Revision 9003: *{.sh,run}: use new isset
- 02:31 AM Revision 9002: lib/util.sh: added isset ()
- 02:28 AM Revision 9001: *{.sh,run}: use ${var+isset} instead of ${var+t} for clarity
- 02:22 AM Revision 9000: lib/util.sh: propagate the verbosity to invoked commands by exporting it
- 02:20 AM Revision 8999: lib/util.sh: run all commands verbosely by default, not just runscripts. this ensures verbose output for invoked commands like inputs/GBIF/MySQL_export.
- 02:15 AM Revision 8998: lib/util.sh: echo_stdin (): use new pipe_delay
- 02:12 AM Revision 8997: lib/util.sh: added pipe_delay (used as `cmd1 | { pipe_delay; cmd2; }`)
- 02:06 AM Revision 8996: lib/util.sh: limit_stderr_cmd (): echo the command like echo_run so that callers don't have to separately call echo_run. this reduces clutter of the nested aliases, ensures that the command is always echoed *outside* of the inner stderr-limiter (which has a different log_level), and avoids echoing "limit_stderr_cmd" itself as part of the command name.
- 01:47 AM Revision 8995: lib/util.sh: limit_stderr (): increase the log_level so that stderr of verbose commands can be turned off separately from the names of the commands themselves. it will now usually have log_level 2, indicating output that is useful primarily for debugging (this is the same as for shell function calls).
- 01:39 AM Revision 8994: lib/util.sh: renamed log_stderr* to limit_stderr* to reflect that stderr is limited (i.e. controlled) rather than logged
- 01:36 AM Revision 8993: lib/util.sh: echo_run_extern: renamed to log_stderr_extern since controlling stderr is its primary function
- 01:25 AM Revision 8992: inputs/GBIF/MySQL_export: only include WHERE clause if $filter is set. support configuring LIMIT/OFFSET.
- 01:00 AM Revision 8991: inputs/GBIF/table.run: table.tsv/make (): use new to_target to auto-delete $target on error
- 12:59 AM Revision 8990: inputs/GBIF/table.run: table.tsv/make (): use new check_target_exists
- 12:58 AM Revision 8989: lib/util.sh: make: added check_target_exists
- 12:42 AM Revision 8988: lib/util.sh: moved $top_file* to runscripts/util.run because they only apply to runscripts
- 12:36 AM Revision 8987: lib/util.sh: make: added to_target, which uses to_file on $target
- 12:35 AM Revision 8986: lib/util.sh: added to_file (), which auto-removes a command's output file on error (like make's .DELETE_ON_ERROR)
- 12:31 AM Revision 8985: lib/util.sh: echo_run_extern, extern: fixed/added comments to indicate that echo_run_extern echoes and controls stderr of *an* external command, while the extern alias does this for *all* external commands
- 12:28 AM Revision 8984: lib/util.sh: auto-echo common external commands, such as rm
- 12:24 AM Revision 8983: lib/util.sh: echo_run_extern, extern aliases: alias-expand next word (the command) by adding trailing space to alias def
- 12:21 AM Revision 8982: bugfix: lib/util.sh: exceptions: log_e: must include `declare e` in the alias and not when save_e is called, so that $e is a local var *of the caller*. this bug did not appear in testing because the save_e alias, which re-scopes $e within log_e (), was not expanded inside log_e () (since new aliases were not loaded between save_e and log_e ()).
- 12:12 AM Revision 8981: lib/util.sh: exceptions: added log_e (), which prints a "command exited with error" message (like make) when applicable
- 12:09 AM Revision 8980: lib/util.sh: exceptions: try_ (): renamed to try () and use the function keyword to distinguish it from the alias
- 12:06 AM Revision 8979: lib/util.sh: exceptions: try_ (): use new save_e
- 12:05 AM Revision 8978: lib/util.sh: exceptions: added save_e
- 12:01 AM Revision 8977: lib/util.sh: exceptions: end_try* aliases: use new rethrow*
05/09/2013
- 11:59 PM Revision 8976: lib/util.sh: exceptions: added rethrow, rethrow_subshell aliases
- 11:47 PM Revision 8975: lib/util.sh: always use '' rather than "" around alias definitions, to ensure that variables are evaluated at expand time rather than compile time
- 11:44 PM Revision 8974: lib/util.sh: zip_newer/unzip_newer: evaluate $no_force at alias expansion time rather than at alias compile time, so that the $no_force can be overridden in the context the alias is used in
- 11:18 PM Revision 8973: lib/util.sh: use `|| return` instead of `|| exit` because `|| exit` doesn't seem to work inside functions (it does not have the errexit effect). also, `|| return` has the advantage of *not* exiting the program if the caller used || after the command (i.e. as an error handler) to temporarily disable errexit.
- 11:11 PM Revision 8972: lib/runscripts/util.run: tell users to override run_args_cmd rather than this function to perform other commands, so that on_exit () can contain other exit-related processing that should *not* be overriden by the user
- 11:05 PM Revision 8971: lib/util.sh: removed "" around $?, $# because they are guaranteed to always be non-empty and contain no special chars
- 10:17 PM Revision 8970: lib/util.sh: say "last space" instead of "trailing space" so the comment will be more likely to fit at the end of the line
- 06:11 PM Revision 8969: lib/local.sh: removed mysql () since its functionality is now provided by mysql () in util.sh
- 05:59 PM Revision 8968: lib/util.sh: mysql_cmd (): $server: like $ssh_server, clear the value when it's equal to this machine's hostname
- 05:58 PM Revision 8967: lib/util.sh: mysql_cmd (): $ssh_server: use new localize_url to clear the value when it's equal to this machine's hostname
- 05:37 PM Revision 8966: lib/util.sh: added localize_url ()
- 05:36 PM Revision 8965: inputs/GBIF/table.run: table.tsv/make (): use extern so the MySQL_export command is echoed
- 05:24 PM Revision 8964: inputs/GBIF/table.run: table.tsv/make (): don't make the target if it already exists
- 05:16 PM Revision 8963: inputs/GBIF/table.run: table.tsv/make (): create the file directly rather than using inline_make, so that the command to create the file can use shell functions such as mysql
- 05:07 PM Revision 8962: bugfix: inputs/GBIF/table.run: table.tsv/make (): need to use $(target) (target's path *relative to curdir*) instead of just the filename, now that make does not change the directory
- 05:01 PM Revision 8961: inputs/GBIF/table.run: moved table.tsv creation to separate table.tsv/make () function
- 04:59 PM Revision 8960: lib/util.sh: echo_stdin (): display the echoed input after leading output of the echoed-to command, by using sleep with a small fractional # of seconds
- 04:38 PM Revision 8959: *{.sh,run}: put functions on one line where possible (and where they are not expected to expand)
- 04:32 PM Revision 8958: lib/local.sh: root_make (): use make () rather than extern make now that make () does not set its own current dir. using make () also automatically enables \$stdout2stderr, which is needed to redirect the echoed make commands.
- 04:26 PM Revision 8957: lib/util.sh: extern (): use exec to ensure that the executed command is in fact external, and not a shell builtin or other type of non-function command. this also simplifies the code because any shell function for the command does not need to be unset.
- 04:20 PM Revision 8956: lib/util.sh: make (): don't change the directory to $top_dir, because paths used by the caller will instead be relative to the current dir (note that in runscripts, paths are generally *not* absolute because of canon_rel_path ()). this requires manually specifying $top_dir when running make on a physical (rather than inlined) makefile.
- 04:01 PM Revision 8955: lib/util.sh: log_stderr_cmd (): replaced the `|| exit` after the () with `|| return`, for the same reason that this was a problem for extern () (see r8954)
- 03:55 PM Revision 8954: lib/util.sh: extern (): replaced the `|| exit` after the () with `|| return`, because `|| exit` strangely does not use $? as its exit status (even though `|| exit $?` works fine). in a shell function, it is actually sufficient, for errexit purposes, to use `|| return`, because the exit status is checked upon return from the function. it is in fact preferable to use return rather than exit, because then the caller can catch the exception using `|| true`.
- 03:51 PM Revision 8953: lib/util.sh: extern (): removed the `|| exit` inside the (), because this strangely prevents the exit status from being propagated to the exit status of the ()
- 03:44 PM Revision 8952: lib/util.sh: added explicit `set -o errexit` in case caller did not have -e in #! line
- 02:47 PM Revision 8951: inputs/GBIF/table.run: renamed MySQL_export () to export_mysql () to match schemas/VegCore/VegCore.ERD.mwb.run
- 02:21 PM Revision 8950: inputs/GBIF/table.run: renamed MySQL_export () to export_mysql () to match schemas/VegCore/VegCore.ERD.mwb.run
- 02:06 PM Revision 8949: inputs/FIA/_archive/2011-10-17/: set svn:ignore to *
- 01:52 PM Revision 8948: web/links/index.htm: updated to Firefox bookmarks. added Mac upgrade and recovery-related bookmarks.
- 12:07 PM Revision 8947: bugfix: lib/import.sh: remake_VegBIEN_mappings (): don't run if there is no public schema to perform the test on (e.g. if the staging tables have just been reinstalled)
- 12:06 PM Revision 8946: lib/import.sh: added public_schema_exists (), which just calls psql_script_vegbien (i.e. with the default search_path temp, public, etc.) and sees if returns an error
- 11:50 AM Revision 8945: /README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: when changes are made on vegbiendev: added step to download TWiki separately to your machine, to ensure that it gets backed up even if you don't sync the rest of the files. also, TWiki needs to be run with delete enabled to remove old session files, while the rest of the files should be run without delete.
- 08:28 AM Revision 8944: schemas/VegCore/VegCore.ERD.mwb.run: use my2pg's new sql_ascii mode
- 08:27 AM Revision 8943: bin/my2pg: support $sql_ascii mode, where varbinary is translated to text instead of bytea
- 08:27 AM Revision 8942: bin/my2pg: remove any () after text
- 08:23 AM Revision 8941: schemas/VegCore/VegCore.ERD.mwb.run: VegCore.my.sql/make (): leave out the DROP TABLE statements for now using --skip-add-drop-table
- 08:19 AM Revision 8940: added schemas/VegCore/VegCore.pg.sql.run with install () command (also part of all ())
- 08:19 AM Revision 8939: lib/local.sh: added root_make ()
- 08:15 AM Revision 8938: bin/my2pg: unpack custom types set('...')
- 08:12 AM Revision 8937: lib/local.sh: psql (): use fd 4 for the logging output instead of 3 because 3 is generally used for passing inline *input* commands (it is used this way by inline_make)
- 08:05 AM Revision 8936: schemas/VegCore/VegCore.ERD.mwb.run: sync (): don't pass "$@" to export_/import because they do not accept args, and the same set of args would not be meaningful for both
- 08:00 AM Revision 8935: schemas/VegCore/VegCore.ERD.mwb.run: use new $top_filename instead of $archive_filename
- 08:00 AM Revision 8934: lib/util.sh: added $top_script (alias for $0), $top_file, $top_filename. use new $top_file in $top_dir.
- 07:54 AM Revision 8933: schemas/VegCore/VegCore.ERD.mwb.run: put zip_newer/unzip_newer on the same line as the `cd "$top_dir"`
- 07:45 AM Revision 8932: bin/my2pg: translate varbinary to bytea
- 07:42 AM Revision 8931: schemas/VegCore/VegCore.ERD.mwb.run: added export_postgres (), which calls VegCore.pg.sql/make ()
- 07:29 AM Revision 8930: lib/util.sh: wrapper functions of external commands: use new self alias
- 07:28 AM Revision 8929: lib/util.sh: added self alias, for use with wrapper functions of external commands
- 07:18 AM Revision 8928: schemas/VegCore/VegCore.my.sql: regenerated using `VegCore.ERD.mwb.run export_mysql` (also part of the all target). note that this uses mysqldump, so the format and table order is different than it was for MySQL Workbench's custom export script.
- 07:05 AM Revision 8927: schemas/VegCore/VegCore.ERD.mwb.run: added export_mysql (), which runs VegCore.my.sql/make ()
- 07:05 AM Revision 8926: schemas/VegCore/VegCore.ERD.mwb.run: added export_mysql (), which runs VegCore.my.sql/make ()
- 07:03 AM Revision 8925: bugfix: lib/local.sh: $PATH: use $bin_dir_abs so the path will remain valid if the current directory is changed
- 07:02 AM Revision 8924: lib/local.sh: added \$bin_dir_abs
- 06:58 AM Revision 8923: bugfix: lib/util.sh: extern (): added `|| exit` after "$@" in addition to after the (), because this additional `|| exit` is apparently needed in order to propagate the exit status of the command to the exit status of the () and cause an error to abort the script properly
- 06:51 AM Revision 8922: lib/util.sh: echo_vars (): output vars with log_level 3 so they can be excluded separately from function calls to reduce clutter in the logging output. increase the default util.run verbosity so that vars are still printed by default.
- 06:47 AM Revision 8921: bugfix: lib/util.sh: echo_vars (): output each var separately so that each is prefixed by $PS4
- 06:39 AM Revision 8920: lib/util.sh: inc/dec_log_level: indent commands at higher log levels using $log_indent
- 06:39 AM Revision 8919: lib/util.sh: inc/dec_log_level: indent commands at higher log levels using $log_indent
- 06:31 AM Revision 8918: bugfix: lib/util.sh: make (): use stdout2stderr=1 so that commands make runs are properly output to stderr
- 06:21 AM Revision 8917: bugfix: lib/util.sh: include_guard_var (): use extern () when invoking sed so that this internal use of it isn't verbosely logged along with other external commands. note the "" around extern to refer to the function, not the alias.
- 06:16 AM Revision 8916: bugfix: lib/util.sh: zip/unzip (): use new $stdout2stderr instead of >&2 so that the redirect happens in the right order
- 06:15 AM Revision 8915: lib/util.sh: log_stderr_cmd (): support redirecting stdout to stderr *after*setting up the stderr redirect, so that stdout is also subject to that redirect
- 06:11 AM Revision 8914: lib/util.sh: added stdout2stderr ()
- 06:08 AM Revision 8913: lib/util.sh: changed echo_run_extern () to an alias
- 06:04 AM Revision 8912: lib/util.sh: echo_run_extern (): use new log_stderr_cmd
- 06:03 AM Revision 8911: lib/util.sh: added log_stderr_cmd ()
- 05:57 AM Revision 8910: lib/util.sh: use extern instead of env to run external commands, because it's simpler and auto-captures the logging output
- 05:44 AM Revision 8909: lib/util.sh: echo_func (): use the much simpler function keyword to avoid expanding the echo_func alias when defining the function, rather than going through the complex process of unaliasing and realiasing the echo_func alias
- 05:38 AM Revision 8908: lib/util.sh: mark env as always being an external command. it is no longer necessary to automatically echo it using echo_run because the extern alias does this now.
- 05:31 AM Revision 8907: lib/util.sh: automatically echo external commands. this requires using the function keyword when declaring extern () so that the new extern alias is not expanded in the function name.
- 05:28 AM Revision 8906: lib/util.sh: added echo_run_extern (), which automatically runs log_stderr to capture the external command's stderr
- 05:27 AM Revision 8905: lib/util.sh: added extern ()
- 05:05 AM Revision 8904: lib/util.sh: added log_stderr ()
- 04:54 AM Revision 8903: lib/util.sh: added end_try_subshell alias
- 04:29 AM Revision 8902: lib/util.sh: zip/unzip: redirect logging output to stderr
- 04:23 AM Revision 8901: lib/util.sh: use inc_log_level where logging info should only be output for verbosity >= 2: echo_func, echo_vars, echo_stdin
- 04:03 AM Revision 8900: lib/util.sh: verbose output: added inc_log_level, dec_log_level aliases which manipulate $verbosity. note that changes in $log_level are now instead indicated by moving $verbosity in the opposite direction.
- 04:01 AM Revision 8899: lib/util.sh: added let () wrapper that prevents it from triggering error-exit
- 03:16 AM Revision 8898: lib/util.sh: verbose output: use just one var ($verbosity) instead of two ($verbosity and $log_level), to track log level, for simplicity. $verbosity would now be subtracted from to alter the log level instead of $log_level being added to.
- 03:09 AM Revision 8897: lib/util.sh: use new can_log wherever logging info is output to stderr
- 03:05 AM Revision 8896: renamed lib/runscripts/local.run to lib/local.sh since the things it defines are not just for runscripts
- 02:53 AM Revision 8895: lib/util.sh: verbose output: added $log_level (must always be > 0 so verbosity=0 turns off all logging) and can_log (), which compares $log_level to $verbosity
- 02:32 AM Revision 8894: bugfix: lib/local.sh: updated $root_dir
- 02:31 AM Revision 8893: renamed lib/runscripts/local.run to lib/local.sh since the things it defines are not just for runscripts
- 02:22 AM Revision 8892: lib/runscripts/local.run: added mysqldump_local, which uses vegbiendev
- 02:21 AM Revision 8891: lib/runscripts/local.run: use postgres_compat mode because all our MySQL schemas should be usable as inputs to my2pg
- 02:20 AM Revision 8890: lib/runscripts/local.run: added connection vars for local (bien) user
- 02:18 AM Revision 8889: lib/util.sh: moved unalias inside include guard since it is not needed by anything *before* the include guard (even though it is used by commands *outside* the include guard, i.e. when the include guard is temporarily closed and reopened to load/unload aliases)
- 02:06 AM Revision 8888: lib/util.sh: use declare instead of local in aliases so that the aliases can also be used outside a function (declare will create a local var when used inside a function, and a global var otherwise)
- 02:00 AM Revision 8887: lib/util.sh: zip: ignore "zip has nothing to do" exit status as this is not an error
- 01:58 AM Revision 8886: lib/util.sh: added exception-handling (i.e. error-suppressing) functions
- 01:03 AM Revision 8885: bugfix: lib/util.sh: echo_func alias: moved it outside the include guard because the unalias statement is needs to be outside the include guard, and therefore so does the alias statement in order to always restore the alias
- 12:59 AM Revision 8884: lib/util.sh: renamed echo_func_ () back to echo_func () and instead add an unalias statement *before* the if statement containing the function definition. this is necessary because if statements are "compound commands", which have aliases expanded when their definition is read (i.e. at the beginning of the if statement, for the entire if statement), not when they are executed, and any aliases for function names in them need to be unaliased *before* the if statement containing the function definition. this is necessary even if the if statement is *not* executed, because the expansion of such aliases will cause syntax errors in the parsing of the if statement itself.
- ** note that this is preferable to the previous approach, because it causes bash to automatically fall back to the fu...
- 12:45 AM Revision 8883: lib/util.sh: added unalias () override, which doesn't produce an error if the alias is undefined
- 12:04 AM Revision 8882: bugfix: lib/util.sh: renamed echo_func () to echo_func_ (), because you apparently can't have a function with the same name as an alias, even if the function is defined before the alias and an include guard prevents the function from being defined again after the alias is set. there may be some kind of alias-expanding preprocessing pass that bash only does in script mode, or maybe there is some other problem related to our use of aliases inside if statements.
05/08/2013
- 08:02 PM Revision 8881: *{.sh,run}: changed echo_func to an alias that includes the "$@", so that callers don't need to specify the "$@" manually. although the original echo_func function is still there, callers need to switch over to the alias at the same time as it's defined because otherwise the "$@" would be doubled, since echo_func refers to the alias instead.
- 07:21 PM Revision 8880: lib/util.sh: added set_make_vars alias, for use with make-target-style shell functions
- 06:37 PM Revision 8879: lib/util.sh: mysql_cmd (): interpret an empty string for $user, $database as if they were unset
- 06:34 PM Revision 8878: bugfix: lib/util.sh: mysql_cmd (): add --tables after specifying --databases so that future unnamed arguments are correctly interpreted as tables
- 06:33 PM Revision 8877: bugfix: lib/util.sh: mysql_cmd (): need to use `--databases ...` rather than `--database=...` to specify the database as a named argument
- 06:26 PM Revision 8876: bugfix: lib/util.sh: mysql_cmd (): need space before $database in command
- 06:23 PM Revision 8875: lib/util.sh: mysql_cmd (): use $schema as $database when provided
- 06:14 PM Revision 8874: lib/util.sh: mysql_cmd (): accept $database connection var
- 06:02 PM Revision 8873: *{.sh,run}: use just env instead of echo_run env now that env is an auto-echoing alias
- 05:56 PM Revision 8872: lib/util.sh: automatically echo commands that use env
- 05:55 PM Revision 8871: lib/util.sh: moved strings after verbose output so strings commands can use verbose output aliases
- 05:28 PM Revision 8870: lib/util.sh: mysql_cmd (): don't ssh if the ssh_server is this machine
- 05:27 PM Revision 8869: lib/util.sh: mysql_cmd (): allow specifying the ssh_dest as a separate ssh_server and ssh_user
- 05:08 PM Revision 8868: lib/util.sh: using prefixed connection vars: added use_local, use_local_remote aliases
- 04:42 PM Revision 8867: lib/util.sh: added mysqldump_diffable ()
- 04:41 PM Revision 8866: lib/util.sh: added mysqldump () wrapper, which does what my2pg_export does, but integrates with mysql_cmd and allows turning off postgres-compatible mode
- 04:15 PM Revision 8865: lib/util.sh: mysql_cmd (): use ${FUNCNAME[1]} to get the caller's command name instead of requiring the caller to pass the command name explicitly
- 03:56 PM Revision 8864: lib/util.sh: databases: added use_remote alias to use the remote_* connection vars (which uses new import_vars)
- 03:54 PM Revision 8863: lib/util.sh: added import_vars alias
- 03:53 PM Revision 8862: lib/util.sh: mysql_cmd (): added doc comment
- 03:52 PM Revision 8861: lib/util.sh: mysql (): use new mysql_cmd to auto-add connection/login opts when specified
- 03:50 PM Revision 8860: lib/util.sh: added mysql_cmd ()
- 03:48 PM Revision 8859: lib/util.sh: added local_inv alias
- 03:34 PM Revision 8858: lib/util.sh: zip/unzip_newer: support extracting/updating the file even if it has an older mtime by setting $force, using new set_inv to get a var to use to determine whether to include the -u flag
- 03:32 PM Revision 8857: lib/util.sh: added set_inv ()
- 03:30 PM Revision 8856: lib/util.sh: echo_vars (): prefix the declare output with "+ " because it's actually a command, not just an indication of the var's value
- 03:28 PM Revision 8855: lib/util.sh: added sed ()
- 03:23 PM Revision 8854: lib/util.sh: added section labels
- 10:57 AM Revision 8853: web/links/index.htm: removed broken favicons
- 10:55 AM Revision 8852: web/links/index.htm: removed broken favicons. this requires using the SQLite Manager Firefox add-on <https://addons.mozilla.org/en-US/firefox/addon/sqlite-manager/?src=search> to manually remove the favicon entries.
- 10:18 AM Revision 8851: lib/Firefox_bookmarks.reformat.csv: formatting fixes: don't put the src attribute of the favicon image on its own line, because it no longer contains long inline image data
- 10:15 AM Revision 8850: lib/Firefox_bookmarks.reformat.csv: favicon image: remove ICON attributes with inline image data, since these are no longer needed for the favicon images and this avoids cluttering up the svn diff
- 10:11 AM Revision 8849: lib/Firefox_bookmarks.reformat.csv: favicon image: use ICON_URI instead of ICON to fetch the favicon directly from the original site. this allows the favicons to be cached separately from the bookmarks page, so that the inline favicon contents don't need to be re-retrieved every time the bookmarks page is updated. this also avoids cluttering up the svn diff.
- 10:01 AM Revision 8848: web/links/index.htm: updated to Firefox bookmarks. added description of the formats supported by PostgreSQL's COPY command and their escape sequences.
- 08:44 AM Revision 8847: bugfix: schemas/vegbien.sql: geoscrub_input_view: only include places whose country is not NULL, because at least the country is required for geoscrubbing
- 08:34 AM Revision 8846: /README.TXT: Schema changes: Reinstall staging tables: added step to run `make schemas/public/install` after the datasources are installed. note that this must be run *after* the datasources are installed, because views in public depend on some of the datasources.
05/06/2013
- 07:10 AM Revision 8845: /README.TXT: Schema changes: Reinstall staging tables: use `make db` instead of mk_db, which includes the required schemas/install command. some datasources use the util schema in their postprocess scripts, so this must be installed before the staging tables.
- 07:05 AM Revision 8844: bugfix: /Makefile: moved schemas/install from install to db so that it is also run whenever the DB is reinstalled. schemas/install is needed by the staging tables reinstallation performed by reinstall_all.
- 06:33 AM Revision 8843: bugfix: /README.TXT: Schema changes: Reinstall staging tables: also need to run `make mk_db` before running reinstall_all
- 06:30 AM Revision 8842: /README.TXT: Schema changes: Reinstall staging tables: drop the saved previous DB at the end of the operation
- 06:18 AM Revision 8841: /README.TXT: Schema changes: Reinstall staging tables: run all of the local machine steps on vegbiendev, including the vegbien DB rename, to ensure that the existing data is saved in case the reinstall has errors
- 05:57 AM Revision 8840: /README.TXT: Schema changes: Reinstall staging tables: added step to first rename existing vegbien database, so it is not modified in the reinstallation
- 05:27 AM Revision 8839: inputs/FIA/: archived no longer used BIEN2 FIA data from the nimoy geoscrub DB
- 05:26 AM Revision 8838: inputs/FIA/_archive/: moved FIA_COND_unique, Organism into 2011-10-17/ subdir
- 04:44 AM Revision 8837: /README.TXT: Schema changes: Reinstall staging tables: added step to first run this on the local machine to check for any errors, before running it on the live DB, to prevent the live DB from becoming unrestorable in the case of bugs
- 04:27 AM Revision 8836: bugfix: bin/with_all: pipe yes to the command in case it makes any interactive prompts, as in e.g. the TNRS staging tables reinstall
- 04:25 AM Revision 8835: bugfix: inputs/input.Makefile: sql/install: manually specify $no_search_path option to psql_script_vegbien, which is added automatically in $(psqlNoSearchPath) but that uses psql_verbose_vegbien
- 04:12 AM Revision 8834: bugfix: *{.sh,run}: use `local` when setting default values for params to prevent these values from leaking into the calling context, where it may have unexpected effects (e.g. pg_copy_to would permanently set $source, which would then be used on the next invocation of pg_copy_to instead of regenerating $source from the next $table value). this involves using ${var-default} or ${var:-default} to return the value to the local statement instead of setting it directly with ${var=default} or ${var:=default}.
- 04:00 AM Revision 8833: *{.sh,run}: commands that take named arguments: usage messages: changed to use simpler bash syntax for specifying command-specific env vars, which does not require a subshell ("The environment for any simple command or function may be augmented temporarily by prefixing it with parameter assignments" <http://www.gnu.org/software/bash/manual/bash.html#Environment>)
- 03:14 AM Revision 8832: schemas/pg_hba*.conf: removed trailing whitespace
- 03:10 AM Revision 8831: schemas/pg_hba*.conf: allow the bien group to access all databases, including test (on the Mac). note that this does not grant access to the vegbank DB on vegbiendev, because that is owned by postgres.
- 02:32 AM Revision 8830: web/links/index.htm: explicitly separate page's description from author comments where needed
- 02:29 AM Revision 8829: web/links/index.htm: use - instead of --- to separate the page's description from the author comments because it's faster to type and one hyphen is sufficient
- 02:21 AM Revision 8828: lib/Firefox_bookmarks.reformat.csv: labeling page's description: don't match descriptions with a leading blank line as an author comment, because sometimes page descriptions themselves start with a blank line. instead, author comments at the beginning of bookmark descriptions should always start with a " or be preceded by a line containing only hyphens (-). note that it was never reliable to use a blank line for this purpose, because it would be trimmed out upon reimport of the HTML file into Firefox.
- 02:17 AM Revision 8827: web/links/index.htm: updated to Firefox bookmarks
05/05/2013
- 10:35 PM Revision 8826: inputs/NVS/*/map.csv: Taxon Growth Form: use new _lowercase() to avoid needing to manually map each value that is already valid but just needs to be lowercased
- 10:28 PM Revision 8825: schemas/util.sql: added _lowercase()
- 09:05 PM Revision 8824: added inputs/CTFS/ERD/ VegPath location
- 11:57 AM Revision 8823: added inputs/MO/_src/_README.TXT with warning that the refresh provided to us is missing several columns from the original extract: CollectionCode, CatalogNumber, IndividualCount
- 10:59 AM Revision 8822: schemas/VegCore/VegCore.ERD.mwb: reduced MaxColumnsDisplayed to 10 to prevent wide tables from taking up too much space in the ERD. this was a big problem in the VegBIEN ERD, which we are hoping to prevent in the VegCore ERD as first-class columns get added to the tables. note that it's very important to ensure that the first-class columns are sorted *in importance order*, so that the 10 most important are visible in the ERD.
- 10:34 AM Revision 8821: schemas/VegCore/VegCore.ERD.mwb: renamed specimen_holder_institution to specimenholder_institution because specimenholder is one word
- 10:12 AM Revision 8820: lib/sql_io.py: put_table(): Calling wrapper function: adding pkey or index on the resulting table: don't display warning if a pkey can't be added, because this is actually a legitimate situation when the called function is set-returning and can return multiple rows for one input. having this as a warning results in spurious warnings in the automated tests (which look confusingly like ignored errors because Python warnings include debugging context information). e.g. `make inputs/Madidi/IndividualObservation/test.by_col.xml` causes this error in the sourcelist->sourcename splitting step (which of course can produce multiple specimenholder institutions).
- *** note that a *diff* will continue to be produced (but now without an error message), because row-based import does...
- 10:00 AM Revision 8819: bugfix: lib/sql.py: parse_exception(): typed_name_re (used by MissingCastException, etc.): don't require "" around the value, because function names in "function does not exist" exceptions are (now?) output without them. this exception did *not* occur in the last import, but *does* occur in the automated testing and when running the associated query in pgAdmin (in both Linux and Mac OS X).
- 04:30 AM Revision 8818: bugfix: /Makefile: apache-Linux: use the standard apt-get syntax for Makefiles (`-sudo apt-get --yes install`) instead of just `apt-get install`
- 04:24 AM Revision 8817: /Makefile: added Apache 2.4 installation
- 03:57 AM Revision 8816: lib/util.sh: added join ()
- 02:58 AM Revision 8815: web/.twiki/data/Main/TWikiPreferences.txt: updated with current settings
- 02:55 AM Revision 8814: put web/.twiki/data/Main/TWikiPreferences.txt under version control. note that this file (*Main*/TWikiPreferences.txt) is the correct file to change the settings in, not *TWiki*/TWikiPreferences.txt.
- 02:33 AM Revision 8813: put web/.twiki/data/TWiki/TWikiPreferences.txt under version control
- 01:58 AM Revision 8812: inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt: twikibuttons_formats: added blockquote format
- 01:47 AM Revision 8811: inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt: set inline_styles to false so that markup formatting (underline, strikethrough) gets formatted using HTML tags (<strike>, etc.) instead of CSS styles ("text-decoration: line-through", etc.)
- 01:26 AM Revision 8810: inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt: theme_advanced_buttons1: added underline, strikethrough buttons
- 01:25 AM Revision 8809: put inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt under version control
05/02/2013
- 11:07 PM Revision 8808: /run: export_ (): pass "$@" to invoked functions since it may contain psql connection or config info
- 11:06 PM Revision 8807: lib/util.sh: pg_* (): pass "$@" to invoked functions since it may contain psql connection or config info
- 10:59 PM Revision 8806: bugfix: lib/util.sh: pg_header (): use limit=0 to prevent COPY TO from returning all rows in the table (not an issue for empty tables!)
- 10:53 PM Revision 8805: lib/util.sh: pg_copy_to (): support sources besides whole tables (such as custom queries and tables with columns). support limiting the # of rows retrieved when using whole tables.
- 10:01 PM Revision 8804: lib/runscripts/import.run: added export_ () command, which is run after import in all ()
- 09:57 PM Revision 8803: bin/psql_verbose_vegbien: also echo queries issued by backslash commands (--echo-hidden)
- 09:34 PM Revision 8802: /run: make config vars such as $schema overridable by the environment, to allow pointing the export script at a different public schema version
- 08:53 PM Revision 8801: inputs/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files
- 08:50 PM Revision 8800: added inputs/HIBG/Specimen/header.csv
- 08:50 PM Revision 8799: added inputs/HVAA/Specimen/Herbario_occur_1360871068.csv.md5
- 08:40 PM Revision 8798: exports/: svn:ignore *.csv
- 08:39 PM Revision 8797: added /run, whose export_ command exports DB tables (currently the geoscrub_input table) to CSV. column information is included in the filename when the export format is specified not to contain a header row.
- 08:35 PM Revision 8796: lib/runscripts/local.run: moved log_sql (), pg_* () to lib/util.sh because these do not depend on local external scripts in bin/
- 08:27 PM Revision 8795: lib/runscripts/local.run: added pg_copy_to (), pg_header (), pg_export_table_no_header (), pg_export_table_to_dir_no_header ()
- 08:26 PM Revision 8794: lib/runscripts/local.run: added mk_schema_esc, mk_table_esc aliases as shortcuts for `local *_esc; mk_esc_name *`
- 08:09 PM Revision 8793: lib/util.sh: self_not_included (): added support for loading newly-defined aliases for use in functions in the same file, and documentation for how to do this
- 02:49 PM Revision 8792: lib/runscripts/local.run: psql (): output only the query results to stdout (using --output), and redirect everything else to stderr
- 02:26 PM Revision 8791: added /exports/
- 02:24 PM Revision 8790: lib/runscripts/local.run: added log_sql (). mysql (): don't echo SQL commands when not in verbose mode. this is needed to support commands that use the query result in a $() expression, and should not have echoed commands cluttering up stdout. (unfortunately, the SQL commands are echoed to stdout rather than stderr.)
- 01:52 PM Revision 8789: schemas/vegbien.sql: range_modeling_input: use analytical_stem instead of analytical_stem_view because it takes a long time (~2 min) to get a row from the left-joined view, due to the large number of joins and large number of rows in the joined tables
- 01:41 PM Revision 8788: web/links/index.htm: updated to Firefox bookmarks. grouped related items together.
- 01:28 PM Revision 8787: web/links/index.htm: author comments at beginning of bookmark desc: start with a line containing only dashes (-) rather than a blank line, because a newline will be trimmed away on reimport into Firefox, such that reexporting it will lose the author comment indicator
- 01:24 PM Revision 8786: lib/Firefox_bookmarks.reformat.csv: label page's description: support starting a description with a line containing only dashes (-) to indicate author comments. this is better than a newline, because a newline will be trimmed away on reimport into Firefox, such that reexporting it will lose the author comment indicator
- 01:16 PM Revision 8785: lib/Firefox_bookmarks.reformat.csv: add hyperlinked HTML anchors for folders: switch back to using <a href=...> instead of onclick, but put the <a> tag *around* the <H3> rather than inside it so that Firefox can correctly parse out the folder name when importing the bookmarks
- 12:52 PM Revision 8784: lib/Firefox_bookmarks.reformat.csv: add hyperlinked HTML anchors for folders: use `onclick="javascript:document.location = '#...'"` instead of <a href=...> to allow clicking the header to go to the anchor, so that the <a> tag doesn't prevent Firefox from parsing the folder name
- 12:42 PM Revision 8783: bugfix: lib/Firefox_bookmarks.reformat.csv: add hyperlinked HTML anchors for folders: moved <a name=.../> outside the <H3> so that Firefox can correctly parse out the folder name when importing the bookmarks
- 12:27 PM Revision 8782: web/links/index.htm: updated to Firefox bookmarks. grouped related items together.
- 12:19 PM Revision 8781: lib/Firefox_bookmarks.reformat.csv: indexing: add hyperlinked HTML anchors for folders
- 11:50 AM Revision 8780: web/links/index.htm: updated to Firefox bookmarks
- 08:30 AM Revision 8779: schemas/vegbien.sql: added range_modeling_input view
- 08:21 AM Revision 8778: schemas/vegbien.sql: analytical_stem_view: order by datasource name so that the rows have a predictable rather than random ordering
- 06:14 AM Revision 8777: bugfix: lib/util.sh: moved mysql (), psql () to local.run because they use local commands that are only available after local.run sets the PATH. retain a mysql () function in util.sh that adds the --verbose option to mysql.
- 05:44 AM Revision 8776: lib/util.sh: removed "$bin_dir"/ before commands because the bin dir is now in the PATH
- 05:13 AM Revision 8775: lib/runscripts/table.run: moved general DB commands to lib/util.sh
- 04:47 AM Revision 8774: moved lib/*.run into runscripts/ subdir so runscripts are grouped together and easier to find rather than being scattered throughout lib/
- 04:19 AM Revision 8773: bugfix: lib/util.sh: canon_rel_path (): use $(pwd -P) instead of $PWD because symlinks are resolved by realpath (readlink -f), so they also need to be resolved in the current dir, but $PWD does not contain the symlinks-resolved version of the current dir
- 03:48 AM Revision 8772: inputs/GBIF/MySQL_export: use lib/util.sh instead of util.run now that the non-runscript-specific functions have been separated out into it. this ensures that MySQL_export is not unintentionally treated as a runscript (which functions differently from a normal shell script).
- 02:46 AM Revision 8771: /.htaccess: use canonical URL without symlinks
- 02:44 AM Revision 8770: added /.htaccess to create the right self-referential URL since / is outside the document root (linked from /vegbiendev/fs/)
- 02:14 AM Revision 8769: schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps: moved labels to the *start* of the arrow they label, so that the user can more easily follow the arrows from step to step by looking for an outward-pointing arrow with a label
- 01:48 AM Revision 8768: added inputs/GBIF/_MySQL/MySQL.data.sql.gz.md5
- 12:46 AM Revision 8767: bugfix: lib/common.Makefile: Compression: %.gz <-> %: only run command if target does not exist, to avoid overwriting the target when the compressed or uncompressed version is newer than it. the difference in mtimes can arise when one file is created after the other, and should not cause the opposite operation to be performed to try to make the other file up-to-date (leading to an infinite back-and-forth of creating one file from the other).
04/30/2013
- 11:13 PM Revision 8766: web/links/index.htm: updated to Firefox bookmarks. the VegPath link now includes the new favicon.
- 11:12 PM Revision 8765: added web/favicon.ico generated from schemas/BIEN_logo.png
- 11:01 PM Revision 8764: web/main.conf: added SSL-protected site for use with password-protected areas of the site, so that the user's password is not transmitted in plaintext. (because the SSL certificate is self-signed, it will unfortunately display the Confirm Security Exception message in Firefox.) note that digest authentication cannot be used to avoid plaintext passwords, because it requires knowing the user's original password to generate the digest, but we have only the MD5 sums in /etc/shadow.
- 09:26 PM Revision 8763: web/links/index.htm: updated to Firefox bookmarks
- 08:08 PM Revision 8762: web/links/index.htm: put all bookmarks into one subfolder named BIEN links, to facilitate importing them all into one folder on another machine. this also helps when upgrading to a newer version of the bookmarks, because the previous version must be deleted and this now requires deleting only a single folder.
- 08:02 PM Revision 8761: lib/Firefox_bookmarks.reformat.csv: use <H3 style="font-size: 200%;"> instead of <H1> to make the first folder's name the page title, so that Firefox can reimport the first folder as a bookmarks folder
- 07:42 PM Revision 8760: bugfix: lib/Firefox_bookmarks.reformat.csv: make first folder name the page title: added back replacement string
- 07:40 PM Revision 8759: web/links/index.htm.run: clean_up (): removed command to add page title because this is now done by lib/Firefox_bookmarks.reformat.csv
- 07:40 PM Revision 8758: lib/Firefox_bookmarks.reformat.csv: use page title as window title
- 07:31 PM Revision 8757: lib/Firefox_bookmarks.reformat.csv: remove previous page title
- 07:29 PM Revision 8756: lib/Firefox_bookmarks.reformat.csv: make first folder name the page title
- 07:21 PM Revision 8755: lib/Firefox_bookmarks.reformat.csv: move Bookmarks Toolbar inside first folder instead of before it. this allows storing all bookmarks in one subfolder so that when the web page is imported into another computer's bookmarks, the imported bookmarks are all together in one folder.
- 07:16 PM Revision 8754: bugfix: lib/Firefox_bookmarks.reformat.csv: refactored regexps to account for Python applying (?s) to the entire regexp, even if it appears inside a () subgroup. the Python behavior is in contrast to the standard regexp behavior used by Java, etc. where (?s) applies only to the subgroup it appears in.
- 06:19 PM Revision 8753: web/links/index.htm: updated to Firefox bookmarks. resources: put unsorted links into subfolders.
- 06:11 PM Revision 8752: bugfix: lib/Firefox_bookmarks.reformat.csv: add <style>: format bookmark description as plaintext: use `white-space: pre-wrap` instead of pre in order to wrap long lines
- 06:07 PM Revision 8751: bugfix: lib/Firefox_bookmarks.reformat.csv: favicon images: made replacements idempotent so that the favicons would not be deleted the next time the web/links/index.htm.run is run (due to a newline being added before ICON= )
- 05:52 PM Revision 8750: lib/Firefox_bookmarks.reformat.csv: favicon images: display placeholder favicon image for every link to ensure uniform alignment
- 05:45 PM Revision 8749: added web/links/blank.gif symlink to web/blank.gif for shorter blank.gif URLs
- 05:43 PM Revision 8748: added web/blank.gif
- 05:14 PM Revision 8747: lib/Firefox_bookmarks.reformat.csv: display ICON attributes as separate images. note that this uses the "data:" embedded image contents provided in the bookmarks file, so the images load instantly along with the page instead of needing to be separately retrieved from each server.
- 04:45 PM Revision 8746: lib/Firefox_bookmarks.reformat.csv: instead of removing ICON attributes with favicon contents, put them on their own line so the rest of the line is easier to see
- 04:35 PM Revision 8745: lib/Firefox_bookmarks.reformat.csv: divided replacements into sections
- 04:27 PM Revision 8744: lib/Firefox_bookmarks.reformat.csv: move Bookmarks Toolbar to beginning, remove its desc, and rename it to Quick links
- 04:13 PM Revision 8743: web/links/index.htm: removed extra divider after Recent Tags, Recently Bookmarked because section dividers interfere with regexp matching and the Bookmarks Toolbar is already visually separate from them
- 04:09 PM Revision 8742: web/links/index.htm: moved Recent Tags, Recently Bookmarked special folders to end because they are Firefox-specific and not part of the BIEN links (they also do not work in a browser because they are Firefox-specific query bookmarks instead of actual folders)
- 03:32 PM Revision 8741: web/links/index.htm.run: clean_up (): rename the page title from "Bookmarks" to "BIEN links"
- 03:18 PM Revision 8740: bin/repl: skip header instead of parsing it, since its columns are not used. this also allows using just a blank line as the header when the column names are not important.
- 03:05 PM Revision 8739: web/links/index.htm: use initial blank line instead of previous "-" workaround to indicate author comment at start of bookmark desc
- 03:04 PM Revision 8738: web/links/index.htm: use initial blank line to indicate author comment at start of bookmark desc
- 02:59 PM Revision 8737: lib/Firefox_bookmarks.reformat.csv: label page's description: don't label a bookmark desc starting with a blank line (indicating an author-added comment) as a page's description
- 02:51 PM Revision 8736: lib/Firefox_bookmarks.reformat.csv: label page's description: don't label an author-added quotation (which starts with " ) as the page's description
- 02:33 PM Revision 8735: bin/in_place: set the permissions of the new file to the original file when `chmod --reference` is available. this ensures that when a file is marked web-accessible, it stays web-accessible when you run an in_place command on it.
- 02:22 PM Revision 8734: web/links/index.htm: BitTorrent Sync: security warning about data leak: added link to reported bug at http://forum.bittorrent.com/topic/18612-security-hole-in-linux-webui-makes-all-your-files-publicly-accessible/ . updated workaround instructions.
- 01:20 PM Revision 8733: web/links/index.htm: updated to Firefox bookmarks. BitTorrent Sync: added security warning that running btsync on Linux will by default create a *publicly-accessible, unprotected* WebUI, allowing anyone on the web to create a sync folder to view and edit any of your files. to avoid this, always run btsync with a config file which sets a password on the WebUI. if you have already run btsync, run `killall btsync` to turn off the WebUI.
- 12:59 PM Revision 8732: web/links/index.htm: updated to Firefox bookmarks. changes include links about BitTorrent Sync.
- 12:51 PM Revision 8731: lib/Firefox_bookmarks.reformat.csv: label <meta> description: renamed label text to "page's description" to be understandable to non-programmers
- 12:49 PM Revision 8730: lib/Firefox_bookmarks.reformat.csv: label <meta> description: remove any existing description label, to avoid duplicating the description label when the text of the description label changes
- 12:37 PM Revision 8729: lib/Firefox_bookmarks.reformat.csv: label <meta> description as such to avoid confusing it with comments added by the bookmark author, who may not agree with it. the <meta> description is in the 1st paragraph(s), when provided.
- 12:13 PM Revision 8728: lib/Firefox_bookmarks.reformat.csv: remove LAST_MODIFIED attributes, which seem to change whenever the favicon is updated and clutter up the svn diff
- 12:05 PM Revision 8727: lib/Firefox_bookmarks.reformat.csv: remove ICON attributes with favicon contents, which clutter up the svn diffs
- 11:52 AM Revision 8726: added web/links/index.htm.run with clean_up action to run whenever the index.htm bookmarks file is changed (`web/links/index.htm.run clean_up`)
- 11:51 AM Revision 8725: added lib/Firefox_bookmarks.reformat.csv
04/25/2013
- 09:58 PM Revision 8724: README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: exclude only backup files in the Documents/BIEN/svn/backups/ dir (sync the other files)
- 09:53 PM Revision 8723: README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: when changes are made on vegbiendev: don't sync the group, which can be bien on vegbiendev but not on jupiter (where aaronmk is not a member of the bien group)
- 09:51 PM Revision 8722: README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: when changes are made on vegbiendev: include *.md5
- 09:08 PM Revision 8721: README.TXT: Maintenance: removed step to backup the Ubuntu VM, because this is now done as part of the "backup files not in Time Machine" step
- 09:07 PM Revision 8720: README.TXT: Maintenance: added steps to backup files not in Time Machine
- 08:57 PM Revision 8719: README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: back up (almost) all files in the home directory instead of just Library/ (to both jupiter and Dropbox)
- 06:45 PM Revision 8718: README.TXT: put commands: removed unnecessary /** after dirs to exclude
- 06:26 PM Revision 8717: README.TXT: Maintenance: to synchronize a Mac's settings with my testing machine's: added steps to also backup the settings to Dropbox (in addition to jupiter)
- 06:13 PM Revision 8716: lib/util.sh: added realpath () and use it where `readlink -f` is used
- 06:05 PM Revision 8715: lib/util.run: doc comment: changed "run scripts" to "runscripts"
- 06:04 PM Revision 8714: lib/util.run: factored general utils (non-runscript-specific) out into new util.sh
- 05:55 PM Revision 8713: lib/util.run: renamed $verbose to $verbosity because it's an integer level, not a boolean. continue to support specifying the verbosity in $verbose.
- 05:52 PM Revision 8712: lib/util.run: support $verbose="", which is treated as 0
- 05:50 PM Revision 8711: lib/util.run: only automatically echo env vars when they are set if verbosity is >= 2
- 05:49 PM Revision 8710: lib/util.run: added $verbose var to control logging. this is normally set to 0, but defaults to 2 for a runscript.
- 05:41 PM Revision 8709: lib/util.run: moved `shopt -s expand_aliases` inside the include guard so callers can override the setting without it being reset if util.run is included again
- 05:39 PM Revision 8708: lib/local.run: add $bin_dir to the PATH
- 05:15 PM Revision 8707: bin/in_place: don't run if no command to run, because that would erase the file
- 05:10 PM Revision 8706: bin/in_place: use -e (exit on error) option to sh instead of adding `|| exit` after every command
- 04:49 PM Revision 8705: *run: added include guards
- 04:30 PM Revision 8704: bugfix: lib/util.run: added include guard to prevent issues in "diamond includes", where a runscript includes two runscripts and *each* includes util.run, causing the second include of util.run to reset any methods overridden in the first included runscript. this prevents util.run from being included twice in the first place.
- 04:25 PM Revision 8703: lib/util.run: added include_guard_var (), self_not_included () for use by path-based include guards
- 03:40 PM Revision 8702: lib/util.run: echo_stdin (): print a separator before and after the echoed output to help distinguish it from other verbose output
- 03:37 PM Revision 8701: lib/table.run: use new local.run instead of defining $bin_dir, etc. itself
- 03:36 PM Revision 8700: lib/util.run: echo_export (): run the export builtin using `builtin` to avoid recursively calling any export alias or function defined by the user (e.g. `alias export=echo_export`. this causes util.run to be idempotent, such that it can be included multiple times without causing problems due to the redefinition of functions, vars, etc.
- 03:04 PM Revision 8699: added lib/local.run, which links to locally-available resources such as $bin_dir
- 02:50 PM Revision 8698: lib/table.run: added mysql (), mysql_ANSI ()
- 02:41 PM Revision 8697: added web/links/index.htm containing Firefox bookmarks exported to HTML. CSS style information has been added to fix default HTML tag formatting, improve readability, and handle the Firefox bookmarks format. <dd> tags have been manually closed where HTML would not auto-close them properly. note that these changes must be reapplied each time the bookmarks file is reexported (`svn di` will show the changes to make).
- 04:54 AM Revision 8696: lib/table.run: run mk_esc_name for $schema, $table
04/24/2013
- 11:18 PM Revision 8695: lib/table.run: added esc_name (), mk_esc_name ()
- 11:16 PM Revision 8694: lib/util.run: added set_var ()
- 10:58 PM Revision 8693: bugfix: lib/util.run: run_args_cmd (): `set --`: need to use eval so that the output of reverse is interpreted as escaped args rather than split using $IFS
- 10:40 PM Revision 8692: bugfix: lib/util.run: run_args_cmd (): BASH_ARGV is stored in reverse order, so it needs to be reversed to be usable as $@
- 10:38 PM Revision 8691: lib/util.run: added reverse ()
- 02:51 PM Revision 8690: schemas/VegCore/VegCore.ERD.mwb: regenerated exports
- 02:49 PM Revision 8689: schemas/VegCore/VegCore.ERD.mwb: source: renamed contact -> owner because smaller sources may not have an admin/contact person, but would have a copyright holder or other entity with control over the source's distribution
- 02:45 PM Revision 8688: schemas/VegCore/VegCore.ERD.mwb: added table comments from VegCore data dictionary (VegCore.vegpath.org)
- 01:08 PM Revision 8687: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 01:07 PM Revision 8686: schemas/VegCore/VegCore.ERD.mwb: added hstore expansion columns where needed
- 12:54 PM Revision 8685: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 12:34 PM Revision 8684: schemas/VegCore/VegCore.ERD.mwb: specimen: added unique constraint for each set of identifying columns
- 12:25 PM Revision 8683: schemas/VegCore/VegCore.ERD.mwb: collection: added back primary key
- 12:24 PM Revision 8682: schemas/VegCore/VegCore.ERD.mwb: specimen: made owner an fkey to collection instead of organization to correspond with orig_collection and current_collection (and to allow auto-filling it from current_collection in a trigger)
- 12:18 PM Revision 8681: schemas/VegCore/VegCore.ERD.mwb: specimen: reordered columns to group together each method of identifying a specimen
- 12:14 PM Revision 8680: schemas/VegCore/VegCore.ERD.mwb: collection: don't inherit from source, because a collection is a scoping entity, not a dataset. a collection *may* also be used as a dataset, but need not be for the purposes of scoping a specimen's accession_number.
- 12:07 PM Revision 8679: schemas/VegCore/VegCore.ERD.mwb: specimen: removed redundant stamping_institution and donor_institution, because these are now in orig_collection.institution. (it is assumed that stamping_institution and donor_institution are the same, because the first institution to acquire and store a specimen (the donor) is the one that stamps it with an accession_number.)
- 12:01 PM Revision 8678: schemas/VegCore/VegCore.ERD.mwb: specimen: split collection into orig,current_collection because the collection that scoped the accession_number (the orig_collection) is sometimes different than the collection where the specimen is now held (the current_collection, or specimen_holder_institutions), e.g. when the specimen is donated
- 11:49 AM Revision 8677: schemas/VegCore/VegCore.ERD.mwb: collection: added institution, name to identify and scope the collection
- 11:39 AM Revision 8676: schemas/VegCore/VegCore.ERD.mwb: changed taxon_name fkeys to taxon_concept where appropriate, and renamed the referencing columns to *_taxon_concept to clearly indicate the referenced table. taxon_concept fkeys are appropriate whenever a taxon is defined or associated with an observed entity, in which case the assertion is not just to a taxon name but to a defined taxon concept (albeit sometimes an unofficial taxon concept scoped by the collector or identifier).
- 11:08 AM Revision 8675: schemas/VegCore/VegCore.ERD.mwb: specimen: added code_in_individual column
- 10:40 AM Revision 8674: schemas/VegCore/VegCore.ERD.mwb: specimen: added fkey to individual for the individual the specimen was taken from
- 10:30 AM Revision 8673: schemas/VegCore/VegCore.ERD.mwb: individual/stem_observation: made individual/stem nullable because there is not always enough identifying information (stem tag, etc.) to actually associate an identifiable individual with an observation
- 10:27 AM Revision 8672: schemas/VegCore/VegCore.ERD.mwb: moved code from individual to individual_observation because the code is something applied at observation time, rather than something that can be used to track individuals *between observations*
- 10:17 AM Revision 8671: schemas/VegCore/VegCore.ERD.mwb: moved collection_event from taxon_occurrence to specimen because only specimens are actually collected, while other taxon_occurrences (e.g. individuals) must be uniquely identified by some means that are shared between re-observations (e.g. the stem tag)
- 10:03 AM Revision 8670: schemas/VegCore/VegCore.ERD.mwb: moved collector, collector_number from taxon_occurrence to taxon_observation because these are actually attributes that are available or assigned at observation time, rather than being intrinsic to the taxon_occurrence (which can be either an individual or a specimen)
- 09:34 AM Revision 8669: schemas/VegCore/VegCore.ERD.mwb: method: colored it forest green like stratum because these are both tables in the same category (method), and forest green is the color VegBank uses for methods. (the fact that VegBank gives stratum the method color indicates that we are on the right track when we are treating stratum as a type of method that's essentially a height class.)
- 09:27 AM Revision 8668: schemas/VegCore/VegCore.ERD.mwb: method: added parent fkey which can be used to autoinherit attributes from another method, in the same way that event autoinherits a method from its parent
- 09:16 AM Revision 8667: schemas/VegCore/VegCore.ERD.mwb: replaced < event label for diagram half with < place, because the occurrence half actually also includes events (observations), but does not include places
- 09:10 AM Revision 8666: schemas/VegCore/VegCore.ERD.mwb: removed extra empty page used for moving objects around
- 09:08 AM Revision 8665: schemas/VegCore/VegCore.ERD.mwb: swapped position of place and source categories so that the place tables, which users are apt to query often, are at the top, and the attribution information, which is likely to be used less often, is at the bottom. this also moves the plot table closer to taxon_occurrence, which should eventually have an fkey to it.
- 08:19 AM Revision 8664: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 08:05 AM Revision 8663: schemas/VegCore/VegCore.ERD.mwb: record: added source_id_scope and added it to the record_unique unique index
- 08:01 AM Revision 8662: schemas/VegCore/VegCore.ERD.mwb: Default*ColumnType: updated to VARBINARY type used in key columns
04/23/2013
- 11:19 PM Revision 8661: schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps: repositioned arrow labels so they point in the direction of the fkey lines
- 11:06 PM Revision 8660: schemas/VegCore/VegCore.ERD.mwb.run: use new zip/unzip_newer
- 11:06 PM Revision 8659: lib/util.run: added zip/unzip_newer aliases
- 11:05 PM Revision 8658: lib/util.run: added zip/unzip echo_run aliases
- 10:57 PM Revision 8657: schemas/VegCore/VegCore.ERD.mwb.run: export_ (): always overwrite existing files. this option is safe, because -u only extracts files with a newer mtime than their copies on disk.
- 10:55 PM Revision 8656: schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps labels: converted tables to notes, which now have bold formatting so that empty tables aren't needed for formatting purposes
- 10:25 PM Revision 8655: schemas/VegCore/VegCore.ERD.mwb.run: import/export_ (): use zip/unzip's -u flag instead of `make` to auto-sync the zip file contents. the -u flag has the added benefit of preserving the contained file's mtime, at the expense of an mtime lookup in the zip archive's table of contents.
- 10:17 PM Revision 8654: added schemas/VegCore/VegCore.ERD.mwb.run, which syncs VegCore.ERD.mwb's zip file contents
- 09:58 PM Revision 8653: bugfix: lib/util.run: inline_make (): put echo_func at the top of the function
- 09:58 PM Revision 8652: lib/util.run: inline_make (): pass Makefile commands using /dev/fd/3 (i.e. 3<<'EOF' ...) instead of stdin, to allow stdin to be used by commands that prompt the user
- 09:44 PM Revision 8651: lib/util.run: inline_make (): use <() to pass Makefile commands as a named descriptor rather than using stdin, to allow stdin to be used by commands that prompt the user
- 09:27 PM Revision 8650: bugfix: lib/util.run: echo_vars (): remove any value to set (=*) from the vars, since this is often used with export
- 09:14 PM Revision 8649: bugfix: lib/util.run: echo_export (): set the vars before echoing them
- 08:55 PM Revision 8648: lib/util.run: run_args_cmd (): use new canon_rel_path() to resolve .. in the script path, so it's easier to see where the script is actually located
- 08:52 PM Revision 8647: lib/util.run: echo_func (): use new canon_rel_path() to resolve .. in the script path, so it's easier to see where the script is actually located
- 08:51 PM Revision 8646: lib/util.run: added canon_rel_path ()
- 08:40 PM Revision 8645: lib/util.run: inline_make (): provide $self as make var
- 08:35 PM Revision 8644: lib/util.run: inline_make (): provide self_dir to make as env var instead of as make var, to avoid specifying every make var both as a local var and as a make var in the make command
- 08:31 PM Revision 8643: lib/util.run: export alias: added comment explaining what it does
- 08:30 PM Revision 8642: lib/util.run: aliased export to echo_export so all env vars are automatically echoed when they are set
- 08:29 PM Revision 8641: lib/util.run: added echo_vars (), echo_export ()
- 08:17 PM Revision 8640: lib/util.run: inline_make (): added local $self and use it to create $self_dir
- 08:15 PM Revision 8639: lib/util.run: inline_make (): set $self_dir as a local var before passing it to make, to avoid clutter in the command that invokes make
- 07:54 PM Revision 8638: added schemas/VegCore/document.mwb.xml, so changes to the diagram can be tracked line-by-line. keeping this up-to-date requires running `unzip VegCore.ERD.mwb document.mwb.xml` whenever VegCore.ERD.mwb is changed.
- 07:53 PM Revision 8637: schemas/VegCore/VegCore.ERD.mwb: target MySQL version: updated to 5.5.3
- 07:49 PM Revision 8636: schemas/VegCore/VegCore.ERD.mwb: NoteFigure:TextFont (labels): made it bold to stand out better
- 07:45 PM Revision 8635: schemas/VegCore/VegCore.ERD.mwb: Layer:TitleFont (legends): increased size and made it bold to stand out better
- 07:31 PM Revision 8634: schemas/VegCore/VegCore.ERD.mwb: made stratum extend method, so that any observation event can have an associated stratum. removed no longer needed plot_stratum, since strata are now represented as sampling methods (i.e. using height classes) rather than a variant of subplots.
- 07:21 PM Revision 8633: schemas/VegCore/VegCore.ERD.mwb: VegCore DB: changed collation to utf8_bin to match table collation
- 07:15 PM Revision 8632: schemas/VegCore/VegCore.ERD.mwb: saved settings for publishing schema to vegbiendev phpMyAdmin (vegbiendev.nceas.ucsb.edu/phpmyadmin/index.php?db=VegCore). this adds `DROP TABLE IF EXISTS` before each CREATE TABLE statement, renames the default DB to VegCore, and adds a USE statement to select the VegCore DB.
- 06:29 PM Revision 8631: schemas/VegCore/connections.xml: vegbiendev.nceas.ucsb.edu: set schema (DB) to VegCore
- 06:20 PM Revision 8630: added schemas/VegCore/connections.xml, which should be installed as the connections.xml settings file
- 06:19 PM Revision 8629: schemas/VegCore/VegCore.ERD.mwb: imported database connections from the connections.xml settings file into document.mwb.xml in the .mwb zip file. these connections are not used directly by MySQL Workbench, but instead need to be copied into the connections.xml settings file.
- 05:17 PM Revision 8628: schemas/VegCore/VegCore.ERD.mwb: use Database > Forward Engineer (Ctrl+G) instead of File > Export > Forward Engineer SQL CREATE Script (Ctrl+Shift+G), so that comments will use the max comment length for the *server's* MySQL version rather than MySQL Workbench's internal MySQL version, which has a max comment length of only 60 chars for tables. this commit stores the default export settings for Forward Engineer, which are saved each time it's run.
- 04:31 PM Revision 8627: bugfix: root Makefile: $(postgresReload-Linux): fixed the "shmat(id=...) failed: Cannot allocate memory" error by telling the user to restart PostgreSQL manually from the command line
- 04:29 PM Revision 8626: root Makefile: $(postgresReload-Linux): don't restart Postgres twice, because this does not fix the "shmat(id=...) failed: Cannot allocate memory" error. this error is instead produced whenever PostgreSQL is restarted from *within a Makefile*, but not when it's run directly from the command line or /bin/sh.
- 03:20 PM Revision 8625: root Makefile: $(postgresReload-Linux): restart Postgres twice, because the first time after the postgresql.conf has been udpated, it always produces a "shmat(id=...) failed: Cannot allocate memory" error
- 03:10 PM Revision 8624: schemas/VegCore/VegCore.ERD.mwb: re-synced with VegCore.my.sql: step 2: `DEFAULT NULL` added on all nullable columns
- 03:10 PM Revision 8623: schemas/VegCore/VegCore.ERD.mwb: re-synced with VegCore.my.sql: step 1: table order changed
- 02:54 PM Revision 8622: schemas/VegCore/VegCore.ERD.mwb: relationship: renamed the two fk_relationship_record1 fkeys so their names wouldn't collide
- 02:52 PM Revision 8621: schemas/VegCore/VegCore.ERD.mwb: changed encoding back to utf8/utf8_bin now that latin1 isn't needed to make the key columns satisfy the index length limits. note that the connection encoding must be utf8 on import so that the correct byte sequence is stored in the VARBINARY columns.
- 02:11 PM Revision 8620: schemas/VegCore/VegCore.ERD.mwb: changed VARCHAR BINARY columns to VARBINARY because VARCHAR BINARY is actually only an alias for the *_bin collation of the table's encoding, but still uses multibyte characters if the encoding does. note that VARBINARY will still be displayed as text (in the connection encoding), rather than hex values.
- 02:02 PM Revision 8619: schemas/VegCore/VegCore.ERD.mwb: changed the type of TEXT columns used in indexes to VARCHAR(767) BINARY to satisfy prefix length limits ("a prefix can be up to [...] 767 bytes for InnoDB tables" <http://dev.mysql.com/doc/refman/5.5/en/create-index.html>). the BINARY flag was added to allow storing Unicode values (from UTF-8), which are not representable in the latin1 encoding.
- 01:15 PM Revision 8618: schemas/VegCore/VegCore.ERD.mwb: changed encoding to latin1 to fit more characters in length-limited indexes (indexes treat utf8 as having *3* bytes/character (http://stackoverflow.com/questions/1814532/1071-specified-key-was-too-long-max-key-length-is-767-bytes#comment-18031137), which significantly reduces the max length of an indexed column)
- 01:08 PM Revision 8617: schemas/VegCore/VegCore.ERD.mwb: changed collation to utf8_bin to avoid case-*in*sensitive comparison of case-sensitive strings. (utf8_bin is also much faster than encoding-aware collations because it uses the raw bytes.)
- 12:47 PM Revision 8616: schemas/VegCore/VegCore.ERD.mwb: set DefaultPkColumnType to TEXT to match the type of current pkey columns
- 12:16 PM Revision 8615: schemas/VegCore/VegCore.ERD.mwb: set all tables to use utf8/utf8_unicode_ci rather than latin1/latin1_swedish_ci because our DB is in UTF-8. utf8_unicode_ci is better than utf8_general_ci because it supports international characters better (http://forums.mysql.com/read.php?103,187048,188748)
- 12:10 PM Revision 8614: schemas/VegCore/VegCore.ERD.mwb: TNRS taxonomic scrubbing steps labels: removed fkey columns to the next step since these are not needed and were causing problems with round-trip sync to the .my.sql file
- 11:42 AM Revision 8613: bugfix: schemas/VegCore/VegCore.ERD.mwb: fixed foreign keys without a referenced columns list
- 11:36 AM Revision 8612: schemas/VegCore/VegCore.ERD.mwb: upgraded for MySQL Workbench 5.2.47 (MySQL 5.5), which requires indexes to have different names than fkeys
- 10:25 AM Revision 8611: schemas/postgresql.conf: shared_buffers: reduced again for Ubuntu VM
- 10:22 AM Revision 8610: bugfix: schemas/postgresql.conf: shared_buffers: removed invalid Unicode character U+FEFF
- 02:40 AM Revision 8609: schemas/postgresql.conf: shared_buffers: reduced to work in Ubuntu VM
- 12:58 AM Revision 8608: README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: add * after analytical_aggregate.*.csv to match *.md5 files as well
04/19/2013
- 07:33 PM Revision 8607: inputs/VegBIEN/TWiki/templates/login.tmpl: increased font size further using <span> style. changed text to fit on two lines with the new size.
- 07:26 PM Revision 8606: inputs/VegBIEN/TWiki/templates/login.tmpl: added large text with instructions to register (the TWiki instructions are small and easily missed)
- 07:09 PM Revision 8605: added inputs/VegBIEN/TWiki/templates/login.tmpl
- 05:14 PM Revision 8604: inputs/VegBIEN/TWiki/twiki.conf: main TWiki dir: changed redirect to go directly to the Main TWiki web, so that we don't need to worry about creating different "webs" (subsites) for top-level wiki pages
- 05:03 PM Revision 8603: inputs/VegBIEN/TWiki/twiki.conf: main TWiki dir: redirect shortened wiki page URLs of the form vegpath.org/twiki/Path to do/view/ for use with VegPath
- 04:49 PM Revision 8602: added web/.twiki symlink to datasources/VegBIEN/TWiki/
- 04:48 PM Revision 8601: added inputs/VegBIEN/TWiki/twiki.conf
- 12:58 PM Revision 8600: schemas/VegCore/VegCore.ERD.mwb: coordinates: added latitude_deg, longitude_deg. geovalidation: added lat_long_in_ranks hstore.
- 12:32 PM Revision 8599: schemas/VegCore/VegCore.ERD.mwb: realigned event/occurrence divider. moved method to avoid overlapping the halves.
- 12:29 PM Revision 8598: schemas/VegCore/VegCore.ERD.mwb: specimen: replaced specimen_holder_institutions with specimen_holder_institution many:many table. added fkeys for the various institution fields. collection: removed name because this is already a required field in source. event_participant: removed *_id suffixes from fields.
- 11:55 AM Revision 8597: schemas/VegCore/VegCore.ERD.mwb: replaced party_list with event_participant many:many table, since the nature of each type of party_list (ordered, not, etc.) may differ between tables that HAVE-A party_list, and because it is not possible to create an fkey to a column that is not unique in the referenced table (as is the case for party_list.list_id)
- 11:41 AM Revision 8596: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 11:28 AM Revision 8595: schemas/VegCore/VegCore.ERD.mwb: made first_publisher a field of source (fkey to party) instead of a subclass of it, because a source can be both an aggregator for some datasets and a first publisher for others and which one it is depends on the dataset
- 11:06 AM Revision 8594: schemas/VegCore/VegCore.ERD.mwb: added organization
- 11:01 AM Revision 8593: schemas/VegCore/VegCore.ERD.mwb: added party_list
- 10:29 AM Revision 8592: schemas/VegCore/VegCore.ERD.mwb: regenerated exports
- 10:09 AM Revision 8591: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 09:50 AM Revision 8590: schemas/VegCore/VegCore.ERD.mwb: taxon_presence, aggregate_observation: added required taxon field to identify (distinguish) the observation itself. this is expected to be the same as the first taxon_determination applied to the observation.
- 09:21 AM Revision 8589: schemas/VegCore/VegCore.ERD.mwb: collection: renamed code to name because the collection code is often the full name of the collection, rather than just an abbreviation. made name required.
- 09:17 AM Revision 8588: schemas/VegCore/VegCore.ERD.mwb: source: added name
04/18/2013
- 04:54 PM Revision 8587: schemas/VegCore/VegCore.ERD.mwb: set page size to fit the ERD contents. this cannot be done through the GUI, so instead you need to use the following steps:
- $ unzip ERD.mwb document.mwb.xml
open document.mwb.xml and search for "this ERD"
units are mm
$ zip -u ERD.mwb docume...
04/17/2013
- 05:28 PM Revision 8586: schemas/VegCore/VegCore.ERD.mwb: fixed split connector
- 05:25 PM Revision 8585: schemas/VegCore/VegCore.ERD.mwb: fixed inheritance lines
- 05:22 PM Revision 8584: schemas/VegCore/VegCore.ERD.mwb: source: added contact field (fkey to party)
- 05:17 PM Revision 8583: schemas/VegCore/VegCore.ERD.mwb: party: inherit from record instead of source, because a party is defined by and scoped by a datasource but isn't a datasource itself (however, a named datasource can have an associated admin party)
- 05:12 PM Revision 8582: schemas/VegCore/VegCore.ERD.mwb: moved tables to make more room between specimen and taxon tables
- 04:45 PM Revision 8581: schemas/VegCore/VegCore.ERD.mwb: split taxon_occurrence into taxon_occurrence and taxon_observation, because a taxon_*occurrence* is actually the *thing* on which a taxon_*observation* is made, not the observation itself. rearranged tables significantly to put observations next to the things they observe, and to make the ERD less wide so it will fit on a small screen without as much scaling (allowing a bigger font size when the ERD is shrunk to fit the screen).
- 02:32 PM Revision 8580: schemas/VegCore/VegCore.ERD.mwb: added primary columns. changed VARCHAR(45) columns to TEXT and also set default type in ERD so future columns won't need to be changed.
- 01:04 PM Revision 8579: schemas/VegCore/VegCore.ERD.mwb: added primary columns, including catch-all hstores for custom columns. made stem inherit from individual and stem_observation from individual_observation because any stem can have individual-level traits and identifying info.
- 11:38 AM Revision 8578: schemas/VegCore/VegCore.ERD.mwb: replaced trait table with traits hstore on taxon_occurrence, since the trait table is basically just a way of allowing the user to add arbitrary measurement columns to the taxon_occurrence. units can be indicated by storing a record with the quantity and units, converted to a string, and parsing it back out as a record upon retrieval.
- 11:29 AM Revision 8577: schemas/VegCore/VegCore.ERD.mwb: renamed taxon_observation to taxon_presence for clarity and to distinguish it better from taxon_occurrence
- 11:25 AM Revision 8576: schemas/VegCore/VegCore.ERD.mwb: taxon_determination: added identified_date and unique index on identifying columns
- 11:15 AM Revision 8575: schemas/VegCore/VegCore.ERD.mwb: taxon_determination: added identified_by. rearranged taxon tables to visually differentiate between inheritance relationships (1:1) and directional HAS-A arrows
- 10:38 AM Revision 8574: schemas/VegCore/VegCore.ERD.mwb: taxon tables: added catch-all hstores for custom columns
- 10:17 AM Revision 8573: schemas/VegCore/VegCore.ERD.mwb: split taxon_concept into taxon_name (containing the components of a name) and taxon_concept (containing the taxon's formal specification and relationships to other taxon_concepts). this avoids requiring a taxon_concept entry for names that are not true taxon concepts. taxon_name: added taxon name/author-related components. TNRS taxonomic scrubbing steps: added dummy id column to avoid sync problems with empty tables.
- 08:38 AM Revision 8572: schemas/VegCore/VegCore.ERD.mwb: taxon tables: added nonidentifying columns
- 06:55 AM Revision 8571: schemas/VegCore/VegCore.ERD.mwb: regenerated exports
- 06:51 AM Revision 8570: schemas/VegCore/VegCore.ERD.mwb: categories: updated box sizes
- 06:45 AM Revision 8569: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 06:40 AM Revision 8568: schemas/VegCore/VegCore.ERD.mwb: validatable_place: added unique index on identifying columns
- 06:38 AM Revision 8567: schemas/VegCore/VegCore.ERD.mwb: made place_path and coordinates globally-scoped rather than per-datasource, so that there is only one geovalidation row for each combination of them rather than one per datasource place. added globally-scoped validatable_place table that stores combinations of place_path and coordinates, and made geovalidation extend it (since geovalidation provides optional fields and is 1:1 with it).
- 06:06 AM Revision 8566: schemas/VegCore/VegCore.ERD.mwb: made geovalidation extend place_path instead of being pointed to by it, because it provides a set of optional fields a (geovalidated) place_path may have
- 05:33 AM Revision 8565: schemas/VegCore/VegCore.ERD.mwb: made place_path extend place instead of place having a place_path, because place_path now provides an optional set of fields that a place may provide, rather than being a completely separate entity
- 05:20 AM Revision 8564: schemas/VegCore/VegCore.ERD.mwb: renamed named_place to place_path since place now serves the purpose that named_place used to (i.e. representing geographical areas)
- 05:13 AM Revision 8563: schemas/VegCore/VegCore.ERD.mwb: removed invisible U+FEFF Unicode character
- 05:10 AM Revision 8562: schemas/VegCore/VegCore.ERD.mwb: renamed location to place because any place can be a location, not just a plot or point (e.g. Barro Colorado Island is a CTFS "plot" but definitely much larger than the typical plot)
- 05:03 AM Revision 8561: schemas/VegCore/VegCore.ERD.mwb: labeled TNRS taxonomic scrubbing steps
- 04:42 AM Revision 8560: schemas/VegCore/VegCore.ERD.mwb: labeled TNRS taxonomic scrubbing steps
- 03:52 AM Revision 8559: schemas/VegCore/VegCore.ERD.mwb: geovalidation: put named_place before coordinates so they would be in path order (one named_place can have many coordinates in it)
- 03:43 AM Revision 8558: schemas/VegCore/VegCore.ERD.mwb: regenerated exports
- 03:39 AM Revision 8557: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 03:30 AM Revision 8556: schemas/VegCore/VegCore.ERD.mwb: taxon_assertion: added fkey to taxon_concept/taxon_path to store any parsed taxonomic fields provided by the data provider
- 03:04 AM Revision 8555: schemas/VegCore/VegCore.ERD.mwb: linked taxon_concept directly to taxon_string rather than to child table taxon_name, because it creates unnecessary confusion to have two tables storing taxonomic strings. a taxon_string is anything that can be used as input to TNRS, and may or may not include a cf_aff.
- 02:57 AM Revision 8554: schemas/VegCore/VegCore.ERD.mwb: link each taxon_string to a parsed_taxon_assertion. removed verbatim_taxon_assertion because that function is now performed by taxon_string.
- 02:48 AM Revision 8553: schemas/VegCore/VegCore.ERD.mwb: added taxon_name, which is used by taxon_concept
- 02:37 AM Revision 8552: schemas/VegCore/VegCore.ERD.mwb: added taxon_string, which is used by taxon_assertion
- 02:15 AM Revision 8551: schemas/VegCore/VegCore.ERD.mwb: added unique indexes on identifying columns where possible. unique indexes differ from primary keys in that they are generally on multiple columns, while pkeys are on a text field which is the concatenation of the identifying columns.
- 01:49 AM Revision 8550: schemas/VegCore/VegCore.ERD.mwb: hierarchical tables: made parent pointer NOT NULL so that it can be an identifying column. this requires the root(s) of the hierarchy to be indicated with a self-referential parent pointer rather than a NULL value. this also allows materializing parent elements to arbitrary levels without worrying about hitting the root, because the root's ancestors will simlpy be itself for as many levels as are needed (i.e. materializing several levels up the tree is guaranteed to produce a non-NULL entry for all levels).
- 01:36 AM Revision 8549: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 01:35 AM Revision 8548: schemas/VegCore/VegCore.ERD.mwb: taxon_assertion: removed fkey to taxon_concept because only parsed_taxon_assertions have a corresponding taxon_concept
- 01:31 AM Revision 8547: schemas/VegCore/VegCore.ERD.mwb: fixed table positions
- 01:25 AM Revision 8546: schemas/VegCore/VegCore.ERD.mwb: lined up tables
- 01:24 AM Revision 8545: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 01:21 AM Revision 8544: schemas/VegCore/VegCore.ERD.mwb: parsed_taxon_assertion.matched_taxon: changed it to be an fkey to taxon_path, because the parsing must also populate the denormalized path fields in addition to defining a taxon_concept with the concatenated scientific name
- 01:18 AM Revision 8543: schemas/VegCore/VegCore.ERD.mwb: fixed inheritance lines
- 01:17 AM Revision 8542: schemas/VegCore/VegCore.ERD.mwb: added taxon_path
- 01:10 AM Revision 8541: schemas/VegCore/VegCore.ERD.mwb: geological_context: made it the same color as community because it is a type of community for the geological aspects of the location
- 01:01 AM Revision 8540: schemas/VegCore/VegCore.ERD.mwb: renamed fkeys to match renamed tables
- 12:34 AM Revision 8539: schemas/VegCore/VegCore.ERD.mwb: merged synonym_taxon, accepted_taxon into taxon_concept because *any* taxon_concept can have an accepted taxon which indicates the canonical name for that taxon, not just TNRS match results
- 12:15 AM Revision 8538: schemas/VegCore/VegCore.ERD.mwb: merged taxon_concept and taxon, because every taxon is according to someone (whether that's Weakley, Tropicos, or the person identifying a taxon_occurrence). note that the according_to is usually different from the source (which is the datasource that owns the record), but if there is no specific according_to, the according_to is the datasource itself.
04/16/2013
- 11:00 PM Revision 8537: schemas/VegCore/VegCore.ERD.mwb: lightened table colors so dark text is easier to see against them. used colors from VegBank ERD (http://vegpath.org/fs/schemas/VegBank/vegbank.ERD.pdf) where possible, to have a familiar look-and-feel for those who have seen the VegBank ERD.
- 10:38 PM Revision 8536: schemas/VegCore/VegCore.ERD.mwb: categories: added stratum
- 10:29 PM Revision 8535: schemas/VegCore/VegCore.ERD.mwb: categories: put categories on the same halves of the legend as they are in the ERD
- 10:23 PM Revision 8534: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 10:23 PM Revision 8533: schemas/VegCore/VegCore.ERD.mwb: added stratum, plot_stratum
- 06:14 PM Revision 8532: schemas/VegCore/VegCore.ERD.mwb: added plot subclass of location
- 05:49 PM Revision 8531: schemas/VegCore/VegCore.ERD.mwb: fixed inheritance lines
- 05:45 PM Revision 8530: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 05:34 PM Revision 8529: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 05:31 PM Revision 8528: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 05:28 PM Revision 8527: schemas/VegCore/VegCore.ERD.mwb: removed redundant "DEFAULT NULL" clauses on nullable fields
- 05:24 PM Revision 8526: schemas/VegCore/VegCore.ERD.mwb: renamed taxon_occurrence.*_taxon_determination to taxon_occurrence.*_determination because the column name does not need to be globally unique, and can therefore be shorter while still being unambiguous within the table
- 04:34 PM Revision 8525: schemas/VegCore/VegCore.ERD.mwb: fixed lines
- 04:33 PM Revision 8524: schemas/VegCore/VegCore.ERD.mwb: changed all fkeys to CASCADE to support cascading deletes. this allows datasources to be reloaded, because the corresponding source row can be deleted, and the delete will cascade to every record that's part of that datasource.
- 04:25 PM Revision 8523: schemas/VegCore/VegCore.ERD.mwb: changed globally unique column names to locally unique column names, now that the SQL dotpath algorithm (http://vegpath.org/wiki/SQL_dotpaths#Algorithm) can be used to generate globally unique column names automatically according to the fkeys. in particular, this means that the pkeys have all been renamed to "id".
- 02:30 PM Revision 8522: schemas/VegCore/VegCore.my.sql: removed default_schema qualifier from names because all objects are in the same schema
- 02:29 PM Revision 8521: schemas/VegCore/VegCore.my.sql: regenerated from ERD
- 09:25 AM Revision 8520: bugfix: schemas/VegCore/VegCore.ERD.mwb: fixed pkey names to match table names
- 09:18 AM Revision 8519: schemas/VegCore/VegCore.ERD.mwb: renamed matched_taxon table to synonym_taxon because it can be used to store any taxon which has a corresponding accepted_taxon, not just the match results from TNRS
- 09:05 AM Revision 8518: schemas/VegCore/VegCore.ERD.mwb: renamed qualified_taxon tables to *taxon_assertion because they are not just a taxon name plus an optional cf/aff qualifier, but an actual operator/value pair that is the right-hand side of a comparison with a taxon or taxon_occurrence
- 08:43 AM Revision 8517: bugfix: schemas/VegCore/VegCore.ERD.mwb: qualified_taxon subclasses: changed HAS-A arrows to point in the other direction, because the many:1 relationship in fact narrows towards the accepted_taxon. the arrows used to be in the opposite direction because of the way the TNRS results are attached incrementally.
- 08:28 AM Revision 8516: README.TXT: Maintenance: to backup the Ubuntu VM: removed invisible U+FEFF Unicode character
- 08:26 AM Revision 8515: README.TXT: added steps to backup the Ubuntu VM
- 07:48 AM Revision 8514: bugfix: schemas/.htaccess: corrected $innermost_dir
- 07:46 AM Revision 8513: added .htaccess files for inputs/, schemas/ because these reside outside the DOCUMENT_ROOT, and therefore need an explicit RewriteBase directive so that RewriteRules in their subdirs can construct self-referential URLs. this ensures that the input URLs to RewriteRules are always URL paths instead of filesystem paths, which tend to mess up the redirects. (mod_rewrite is capable of doing filesystem-only redirects, but the associated RewriteRules require special care to ensure they match and reconstruct the filesystem path properly.) the presence of filesystem paths in RewriteRule inputs had been causing numerous bugs, especially in rules that use %{REQUEST_URI}, and the addition of the RewriteBases will hopefully avoid these types of bugs in the future. note that *every* path that resides outside the DOCUMENT_ROOT needs an explicit RewriteBase in its top-level .htaccess.
- 07:14 AM Revision 8512: schemas/VegCore/VegCore.ERD.mwb: ensured that inheritance relationships are drawn as 1:1
- 07:00 AM Revision 8511: web/**/.htaccess: appended query strings for external redirects: just use ? rather than ?& when an external redirect will be perfomed, because no dotpath parsing will be performed on the query string first (which would necessitate the & if the new query string looks like a dotpath)
04/14/2013
- 09:30 PM Revision 8510: schemas/VegCore/VegCore.ERD.png: Regenerated again because some tables were highlighted when it was exported, causing the highlighting to appear in the PNG
- 09:27 PM Revision 8509: schemas/VegCore/VegCore.ERD.mwb: Regenerated exports
- 09:26 PM Revision 8508: schemas/VegCore/VegCore.ERD.mwb: shortened embedded ERD URL using new abbreviations
- 09:19 PM Revision 8507: web/**/.htaccess: RewriteRules: ensured flags are in alphabetical order
- 09:10 PM Revision 8506: removed no longer needed web/dotpath.php. use web/.htaccess's parse-dotpath RewriteRule instead.
- 09:07 PM Revision 8505: web/.htaccess: parse dotpath in query string: moved parsing from dotpath.php to RewriteRules. with the eventual addition of config env vars, this makes it possible for subdirs to configure their own dotpath parsing, rather than having *all* levels of the dotpath translated to a URL path. (for inner levels, it may el.g. be more appropriate to parse the dotpath as query params or pass it along to an external URL.) note that it takes only two lines of mod_rewrite (plus a workaround RewriteRule) to replace over a dozen lines of PHP code.
- 08:54 PM Revision 8504: web/.htaccess: renamed REQUEST_URI_no_/ to REQUEST_URI_no_extra_/ to clarify that only an excess / is removed
- 08:52 PM Revision 8503: web/.htaccess: moved set REQUEST_URI_no_/ under translate subdomain to path because it needs to be set right before being used to be accurate
- 08:44 PM Revision 8502: web/.htaccess: setting REQUEST_URI_no_/: use one RewriteCond instead of two since the regexps can be combined
- 02:50 PM Revision 8501: web/.htaccess: parse dotpath in query string: removed dotpath auto-detection code because this is now handled by a separate RewriteRule
- 02:49 PM Revision 8500: web/.htaccess: auto-detect dotpath in query string (having a . before any = ) and mark it using a leading . . this is done as a separate step so that the dotpath is already explicitly marked as such when it's parsed.
- 02:01 PM Revision 8499: web/dotpath.php: just match the QUERY_STRING directly, excluding &, instead of splitting apart the QUERY_STRING and then matching the dotpath portion. this allows the resulting regexp to be used directly in a .htaccess file.
- 01:08 PM Revision 8498: web/.htaccess: prepend dir name if it's part of the filename: support MultiViews filenames without the extension, by using a lookahead request -F instead of a regular -f
- 01:02 PM Revision 8497: schemas/VegCore/.htaccess: added RewriteBase to support relative redirects. this enables auto-prepending dir name if it's part of the filename, e.g. VegCore/ERD.pdf -> VegCore/VegCore.ERD.pdf).
- 12:59 PM Revision 8496: web/.htaccess: prepend dir name if it's part of the filename (this works only if the dir supports relative redirects and sets %{ENV:innermost_dir})
- 11:44 AM Revision 8495: schemas/VegCore/VegCore.ERD.mwb: made matched_taxon and accepted_taxon inherit from taxon instead of qualified_taxon because they don't contain the cf_aff (cf_aff.vegpath.org; aka identificationQualifier) that makes a taxon qualified
- 11:16 AM Revision 8494: schemas/VegCore/VegCore.ERD.mwb: removed occurrence table, because it's really a synonym for taxon_occurrence ("specimen, observation, etc." <http://rs.tdwg.org/dwc/terms/#Occurrence>)
- 10:48 AM Revision 8493: schemas/VegCore/VegCore.ERD.mwb: added labels for the left and right halves (event and occurrence). rearranged tables to help separate event- and occurrence-related tables.
- 10:17 AM Revision 8492: schemas/VegCore/VegCore.ERD.mwb: rearranged to leave more space for location_observation, and to put all event-related fields on the left and occurrence-related fields on the left
- 09:32 AM Revision 8491: web/.htaccess: parse dotpath in query string: heuristically detect query strings that don't contain dotpaths (such as mod_autoindex sort conditions), rather than always interpreting the part before the first & as the dotpath. now, the part before the first & will be interpreted as a dotpath if it has a . before any = . (query param names containing . are rare, so this usually works correctly.) note that you can always prepend . to force a dotpath, or & to force a query param.
- 09:06 AM Revision 8490: web/dotpath.php: remove any . prefix which forces interpretation as a dotpath
- 07:38 AM Revision 8489: schemas/VegCore/VegCore.ERD.mwb: taxon_concept: renamed source to according_to
- 07:06 AM Revision 8488: schemas/VegCore/VegCore.ERD.mwb: removed no longer used images from zip archive using `zip -d`. this needs to be done every time an image is deleted from the diagram to remove it from the archive (and reclaim the unused space, since `zip -d` will also shrink the archive). note that you can't just expand and re-zip the files, because there is a header of some sort that indicates to MySQL Workbench that it's a valid .mwb file.
- 06:27 AM Revision 8487: bugfix: schemas/VegCore/VegCore.ERD.mwb: also fixed inheritance relationships to the record table to be 1:1 (by search-and-replacing and then updating document.mwb.xml in the .mwb zip archive using `zip -u`). added separate legend for relationships and connector styles, which now uses example tables instead of screenshot images to ensure accurate sizing at all ERD zoom levels.
- 05:17 AM Revision 8486: bugfix: schemas/VegCore/VegCore.ERD.mwb: fixed inheritance relationships to be 1:1 with optional participation by the derived table, rather than the incorrect 1:many relationshipwhich MySQL Workbench defaults to. (in OOP, each derived instance has its *own* instance of the base class, because it is a separate object.)
- 05:07 AM Revision 8485: web/**/.htaccess: When there is *no* external redirect for the directory without the trailing /, instead auto-add the trailing / to ensure mod_autoindex relative links work properly. This must be done manually because the top-level .htaccess will not auto-add the trailing / if the dir has an .htaccess file (to allow the custom external redirects). There are actually only two .htaccess files that this applies to (web/.phpPgAdmin/.htaccess, .phpMyAdmin/.htaccess), indicating that dirs which have any kind of virtual paths (redirects) almost always have a "root" redirect when there is no specific subpath. This root redirect is intended to link to the datasource's *own* index of its available resources, e.g. the list of tables for a database source.
- 04:48 AM Revision 8484: removed web/aggregators/.htaccess because it was only there to auto-add the trailing /, but this is now done by web/.htaccess
- 04:29 AM Revision 8483: bugfix: web/.htaccess: auto-add trailing /: %{LA-F:REQUEST_FILENAME} lookaheads don't work, because they do not show the externally redirected URL, so we need to use an alternate mechanism instead, which just assumes that any dir containing an .htaccess file may contain a redirect and ignores just those dirs (subdirs are not ignored and will receive a trailing / as expected). To create the trailing / effect when you have a .htaccess *without* an external redirect, you need to manually tell it to correct the path for just that dir without the / (i.e. match ^/ , because a trailing / causes mod_rewrite to use an absolute filesystem path instead).
- 04:21 AM Revision 8482: web/.htaccess: moved auto-add trailing / to after don't rewrite existing dirs, so that the path will automatically not be rewritten if it contains a trailing / and is a dir
- 04:18 AM Revision 8481: web/.htaccess: don't rewrite existing paths: only prevent existing dirs *with trailing /* from being rewritten, because dirs without trailing / may be redirected
- 01:31 AM Revision 8480: removed web/**/.htaccess whose only purpose was to auto-add the trailing / (which is now handled by the top-level .htaccess)
- 01:30 AM Revision 8479: web/**/.htaccess: removed no longer needed auto-add of trailing / , which is now implemented for all dirs by the top-level .htaccess
- 01:27 AM Revision 8478: web/.htaccess: auto-add trailing / if not external redirect: added test if `%{REQUEST_FILENAME} -d` in addition to checking %{LA-F:REQUEST_FILENAME}, because there are some cases (e.g. subdirs that are symlinked outside the DOCUMENT_ROOT) where LA-F:REQUEST_FILENAME for some reason appends /home to the REQUEST_FILENAME, but the current REQUEST_FILENAME is fortunately already a dir and can be checked directly
- 01:07 AM Revision 8477: web/.htaccess: auto-add trailing / if not external redirect: removed no longer applicable comment that dir without trailing / is provided as an absolute filesystem path, because this is only true in inner .htaccess files for their top-level dirs
- 01:01 AM Revision 8476: bugfix: web/.htaccess: auto-add trailing / if not external redirect: match any path that does not end in / (and satisfies the -d lookahead), rather than only absolute filesystem paths, which are only applicable in inner .htaccess files (and even then only for the outermost dir they control) but not in the top-level .htaccess file. Note that the inner .htaccess files can still use ^/ to match *their own* dir, just not their *subdirs*, without a trailing / .
- 12:25 AM Revision 8475: bugfix: web/.htaccess: auto-add trailing / if not external redirect: replace with "%{REQUEST_URI}/" instead of the empty string (which gets auto-translated to have a trailing /), because the empty string only works in the top-level dir of the .htaccess file (it redirects to the RewriteBase, which ends in /). The entire REQUEST_URI is needed to do the auto-add in dirs which do not have their own auto-add trailing / rule. Also, using REQUEST_URI avoids the need to (sometimes) set RewriteBase for use by *relative* URLs in replacement strings, because this is an absolute URL instead. Setting RewriteBase manually is best avoided, because it hardcodes the URL path to the .htaccess file, which may change.
- 12:17 AM Revision 8474: bugfix: web/.htaccess: auto-add trailing / if not external redirect: use "%{LA-F:REQUEST_FILENAME} -d" instead of "$0 -F" so that the actual value of REQUEST_FILENAME tested, and $0 can also match strings which are not file paths. This is because only those no-trailing-/-paths *which did not match the RewriteBase* are provided to mod_rewrite as absolute filepaths, but RewriteBase is not an issue in the outermost .htaccess (because the RewriteBase is / , which is always matched). This means the method of testing for ^/ to match a no-trailing-/-path *will only work in inner .htaccess files* (where it is currently used extensively).
04/13/2013
- 05:47 PM Revision 8473: web/.htaccess: bugfix: moved auto-add trailing / if not external redirect to before don't rewrite existing paths because the trailing / also needs to be added on paths which *are* existing paths, but are just missing the trailing /
- 08:56 AM Task #565: partition the TaxonDetermination table by row into the different types of determinations
- changed vertical/horizontal to row/column for clarity
- 06:37 AM Revision 8472: web/.htaccess: auto-add trailing / if not external redirect (limited form of DirectorySlash). this allows URLs without trailing /, for dirs which have a special external redirect to the datasource's homepage when there is no trailing /, but still auto-adds the trailing / for all other dirs.
- 06:17 AM Revision 8471: README.TXT: Debugging: mod_rewrite: cached redirects issue: changed to limit the cache clearing to when a *DirectorySlash*-related redirect is changed, since only those redirects are permanent, not the RewriteRule redirects (unless you explicitly set them as permanent)
- 06:03 AM Revision 8470: README.TXT: Debugging: mod_rewrite: added tip that whenever you change a RewriteRule, you *must* clear your browser's cache to ensure that a cached redirect is not used instead (temporary redirects are not supposed to be cached, but sometimes Firefox caches them anyway)
- 04:41 AM Revision 8469: README.TXT: umask: Removed -S because this causes the new umask to be echoed, and is not needed even when setting a symbolic umask
- 04:18 AM Revision 8468: README.TXT: Datasource setup:: added step to use umask to prevent files from becoming web-accessible
- 04:16 AM Revision 8467: README.TXT: Testing: what to put in your .profile: added `umask -S ug=rwx,o=` to prevent files from becoming web-accessible
- 04:05 AM Revision 8466: README.TXT: fixed leading whitespace
- 02:46 AM Revision 8465: lib/util.run: run_cmd (): renamed to run_args_cmd to clarify that this runs only the command line args command, not any command. added doc comment to clarify this.
- 02:41 AM Revision 8464: lib/util.run: EXIT trap: use on_exit() function which calls run_cmd instead of having run_cmd be the handler, so that users can override this function to perform other commands (or no commands) after the script is read
- 02:28 AM Revision 8463: lib/util.run: echo_func (): use the caller's FUNCNAME via the $FUNCNAME[] array instead of requiring them to pass it in the function args as `echo_func "$FUNCNAME" "$@"`
- 02:11 AM Revision 8462: README.TXT: Maintenance: added steps to synchronize a Mac's settings with my testing machine's
- 02:10 AM Revision 8461: README.TXT: Maintenance: to synchronize vegbiendev, jupiter, and your local machine: moved swap=1 right before src= dest=, which it applies to. aligned whitespace of the various commands.
- 01:49 AM Revision 8460: README.TXT: Maintenance: steps to synchronize vegbiendev, jupiter, and your local machine: added steps to install dependencies
- 01:44 AM Revision 8459: README.TXT: Maintenance: Added steps to synchronize vegbiendev, jupiter, and your local machine when changes are made on vegbiendev
- 01:34 AM Revision 8458: README.TXT: converted spaces to tabs for easier readability in a whitespace-highlighting text editor, and so that pressing backspace deletes an indent rather than just a character (creating a misaligned indent)
04/11/2013
- 10:29 PM Revision 8457: Moved validation/ under planning/workflow/
- 10:28 PM Revision 8456: Moved planning/use_cases/ under planning/goals/
- 10:26 PM Revision 8455: Moved planning/milestones/ under planning/timeline/
- 10:23 PM Revision 8454: Added inputs/VegBIEN/planning shortcut to fs/planning
- 10:16 PM Revision 8453: web/.fs: symlink via datasources/VegBIEN/fs instead
- 10:14 PM Revision 8452: Added inputs/VegBIEN/fs symlink to /servers/vegbiendev/fs
- 05:56 PM Revision 8451: Added web/.gbif shortcut to datasources/GBIF
- 04:52 PM Revision 8450: web/**/.htaccess: Use [qsappend] flag with all RewriteRules to ensure that the original query string is never lost
- 04:30 PM Revision 8449: inputs/VegBank/.htaccess: Added RewriteCond to check that the REQUEST_FILENAME is not an existing dir, which is apparently needed to prevent the verify/ subdir from being interpreted as a redirect
- 02:45 PM Revision 8448: web/**/.htaccess: Removed preprocessing commands that need to run for every dir, because these are now inherited from the outermost .htaccess using InheritBefore. This allows the inner .htaccess files to focus just on the fallback rewrites, without needing lots of boilerplate code (except for the obligatory RewriteEngine/RewriteOptions/SetEnvIf preamble).
- 02:34 PM Revision 8447: web/.htaccess: handle DirectoryIndex subrequests when there is no DirectoryIndex, by deleting the /index filename. This ensures that any fallback redirect is not invoked, and instead the action corresponding to a trailing / (usually the display of a directory listing) is performed.
- 02:07 PM Revision 8446: web/**/.htaccess: Use InheritBefore RewriteOption so that the outermost dir's rules are always run first. This is necessary so that all the HTTP_HOST and dotpath handlers, etc. are applied before any fallback handlers, *without* needing to copy and paste each rule into *every* .htaccess file. (Note that the InheritBefore RewriteOption is only available in Apache 2.4.) The outermost .htaccess file, however, must *not* use InheritBefore because this would inherit rules from the global Apache config, which normally should not be run and which cause an infinite redirect loop.
- 01:56 PM Revision 8445: web/**/.htaccess: fallback rules which should not be inherited by subdirs: Filter using a RewriteCond on %{ENV:innermost_dir} so that the rule is only run if the innermost dir was this dir. (This is needed when using InheritBefore.)
- 01:36 PM Revision 8444: web/**/.htaccess: Added SetEnvIf directives to set the $innermost_dir env var, which is used by InheritBefore RewriteRule inheritance. You can easily populate the current dir name in jEdit by right-clicking the buffer tab and selecting Insert File Path (which requires the BufferTabs plugin), and then picking out the dir right before the .htaccess. If multiple dirs in the dir path have the same name (e.g. a/b/a/), add a distinguishing prefix to the inner dirs (this is rare).
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