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# Date Author Comment
8825 05/05/2013 10:28 PM Aaron Marcuse-Kubitza

schemas/util.sql: added _lowercase()

8824 05/05/2013 09:05 PM Aaron Marcuse-Kubitza

added inputs/CTFS/ERD/ VegPath location

8823 05/05/2013 11:57 AM Aaron Marcuse-Kubitza

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

8822 05/05/2013 10:59 AM Aaron Marcuse-Kubitza

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.

8821 05/05/2013 10:34 AM Aaron Marcuse-Kubitza

schemas/VegCore/VegCore.ERD.mwb: renamed specimen_holder_institution to specimenholder_institution because specimenholder is one word

8820 05/05/2013 10:12 AM Aaron Marcuse-Kubitza

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)....

8819 05/05/2013 10:00 AM Aaron Marcuse-Kubitza

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).

8818 05/05/2013 04:30 AM Aaron Marcuse-Kubitza

bugfix: /Makefile: apache-Linux: use the standard apt-get syntax for Makefiles (`-sudo apt-get --yes install`) instead of just `apt-get install`

8817 05/05/2013 04:24 AM Aaron Marcuse-Kubitza

/Makefile: added Apache 2.4 installation

8816 05/05/2013 03:57 AM Aaron Marcuse-Kubitza

lib/util.sh: added join ()

8815 05/05/2013 02:58 AM Aaron Marcuse-Kubitza

web/.twiki/data/Main/TWikiPreferences.txt: updated with current settings

8814 05/05/2013 02:55 AM Aaron Marcuse-Kubitza

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.

8813 05/05/2013 02:33 AM Aaron Marcuse-Kubitza

put web/.twiki/data/TWiki/TWikiPreferences.txt under version control

8812 05/05/2013 01:58 AM Aaron Marcuse-Kubitza

inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt: twikibuttons_formats: added blockquote format

8811 05/05/2013 01:47 AM Aaron Marcuse-Kubitza

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.)

8810 05/05/2013 01:26 AM Aaron Marcuse-Kubitza

inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt: theme_advanced_buttons1: added underline, strikethrough buttons

8809 05/05/2013 01:25 AM Aaron Marcuse-Kubitza

put inputs/VegBIEN/TWiki/data/TWiki/TinyMCEPlugin.txt under version control

8808 05/02/2013 11:07 PM Aaron Marcuse-Kubitza

/run: export_ (): pass "$@" to invoked functions since it may contain psql connection or config info

8807 05/02/2013 11:06 PM Aaron Marcuse-Kubitza

lib/util.sh: pg_* (): pass "$@" to invoked functions since it may contain psql connection or config info

8806 05/02/2013 10:59 PM Aaron Marcuse-Kubitza

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!)

8805 05/02/2013 10:53 PM Aaron Marcuse-Kubitza

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.

8804 05/02/2013 10:01 PM Aaron Marcuse-Kubitza

lib/runscripts/import.run: added export_ () command, which is run after import in all ()

8803 05/02/2013 09:57 PM Aaron Marcuse-Kubitza

bin/psql_verbose_vegbien: also echo queries issued by backslash commands (--echo-hidden)

8802 05/02/2013 09:34 PM Aaron Marcuse-Kubitza

/run: make config vars such as $schema overridable by the environment, to allow pointing the export script at a different public schema version

8801 05/02/2013 08:53 PM Aaron Marcuse-Kubitza

inputs/input.Makefile: SVN: add, %/add: */logs: also svn:ignore *.gz, used for compressed log files

8800 05/02/2013 08:50 PM Aaron Marcuse-Kubitza

added inputs/HIBG/Specimen/header.csv

8799 05/02/2013 08:50 PM Aaron Marcuse-Kubitza

added inputs/HVAA/Specimen/Herbario_occur_1360871068.csv.md5

8798 05/02/2013 08:40 PM Aaron Marcuse-Kubitza

exports/: svn:ignore *.csv

8797 05/02/2013 08:39 PM Aaron Marcuse-Kubitza

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.

8796 05/02/2013 08:35 PM Aaron Marcuse-Kubitza

lib/runscripts/local.run: moved log_sql (), pg_* () to lib/util.sh because these do not depend on local external scripts in bin/

8795 05/02/2013 08:27 PM Aaron Marcuse-Kubitza

lib/runscripts/local.run: added pg_copy_to (), pg_header (), pg_export_table_no_header (), pg_export_table_to_dir_no_header ()

8794 05/02/2013 08:26 PM Aaron Marcuse-Kubitza

lib/runscripts/local.run: added mk_schema_esc, mk_table_esc aliases as shortcuts for `local *_esc; mk_esc_name *`

8793 05/02/2013 08:09 PM Aaron Marcuse-Kubitza

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

8792 05/02/2013 02:49 PM Aaron Marcuse-Kubitza

lib/runscripts/local.run: psql (): output only the query results to stdout (using --output), and redirect everything else to stderr

8791 05/02/2013 02:26 PM Aaron Marcuse-Kubitza

added /exports/

8790 05/02/2013 02:24 PM Aaron Marcuse-Kubitza

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.)

8789 05/02/2013 01:52 PM Aaron Marcuse-Kubitza

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

8788 05/02/2013 01:41 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks. grouped related items together.

8787 05/02/2013 01:28 PM Aaron Marcuse-Kubitza

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

8786 05/02/2013 01:24 PM Aaron Marcuse-Kubitza

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

8785 05/02/2013 01:16 PM Aaron Marcuse-Kubitza

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

8784 05/02/2013 12:52 PM Aaron Marcuse-Kubitza

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

8783 05/02/2013 12:42 PM Aaron Marcuse-Kubitza

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

8782 05/02/2013 12:27 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks. grouped related items together.

8781 05/02/2013 12:19 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: indexing: add hyperlinked HTML anchors for folders

8780 05/02/2013 11:50 AM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks

8779 05/02/2013 08:30 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: added range_modeling_input view

8778 05/02/2013 08:21 AM Aaron Marcuse-Kubitza

schemas/vegbien.sql: analytical_stem_view: order by datasource name so that the rows have a predictable rather than random ordering

8777 05/02/2013 06:14 AM Aaron Marcuse-Kubitza

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.

8776 05/02/2013 05:44 AM Aaron Marcuse-Kubitza

lib/util.sh: removed "$bin_dir"/ before commands because the bin dir is now in the PATH

8775 05/02/2013 05:13 AM Aaron Marcuse-Kubitza

lib/runscripts/table.run: moved general DB commands to lib/util.sh

8774 05/02/2013 04:47 AM Aaron Marcuse-Kubitza

moved lib/*.run into runscripts/ subdir so runscripts are grouped together and easier to find rather than being scattered throughout lib/

8773 05/02/2013 04:19 AM Aaron Marcuse-Kubitza

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

8772 05/02/2013 03:48 AM Aaron Marcuse-Kubitza

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).

8771 05/02/2013 02:46 AM Aaron Marcuse-Kubitza

/.htaccess: use canonical URL without symlinks

8770 05/02/2013 02:44 AM Aaron Marcuse-Kubitza

added /.htaccess to create the right self-referential URL since / is outside the document root (linked from /vegbiendev/fs/)

8769 05/02/2013 02:14 AM Aaron Marcuse-Kubitza

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

8768 05/02/2013 01:48 AM Aaron Marcuse-Kubitza

added inputs/GBIF/_MySQL/MySQL.data.sql.gz.md5

8767 05/02/2013 12:46 AM Aaron Marcuse-Kubitza

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).

8766 04/30/2013 11:13 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks. the VegPath link now includes the new favicon.

8765 04/30/2013 11:12 PM Aaron Marcuse-Kubitza

added web/favicon.ico generated from schemas/BIEN_logo.png

8764 04/30/2013 11:01 PM Aaron Marcuse-Kubitza

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.

8763 04/30/2013 09:26 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks

8762 04/30/2013 08:08 PM Aaron Marcuse-Kubitza

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.

8761 04/30/2013 08:02 PM Aaron Marcuse-Kubitza

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

8760 04/30/2013 07:42 PM Aaron Marcuse-Kubitza

bugfix: lib/Firefox_bookmarks.reformat.csv: make first folder name the page title: added back replacement string

8759 04/30/2013 07:40 PM Aaron Marcuse-Kubitza

web/links/index.htm.run: clean_up (): removed command to add page title because this is now done by lib/Firefox_bookmarks.reformat.csv

8758 04/30/2013 07:40 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: use page title as window title

8757 04/30/2013 07:31 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: remove previous page title

8756 04/30/2013 07:29 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: make first folder name the page title

8755 04/30/2013 07:21 PM Aaron Marcuse-Kubitza

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.

8754 04/30/2013 07:16 PM Aaron Marcuse-Kubitza

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.

8753 04/30/2013 06:19 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks. resources: put unsorted links into subfolders.

8752 04/30/2013 06:11 PM Aaron Marcuse-Kubitza

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

8751 04/30/2013 06:07 PM Aaron Marcuse-Kubitza

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= )

8750 04/30/2013 05:52 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: favicon images: display placeholder favicon image for every link to ensure uniform alignment

8749 04/30/2013 05:45 PM Aaron Marcuse-Kubitza

added web/links/blank.gif symlink to web/blank.gif for shorter blank.gif URLs

8748 04/30/2013 05:43 PM Aaron Marcuse-Kubitza

added web/blank.gif

8747 04/30/2013 05:14 PM Aaron Marcuse-Kubitza

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.

8746 04/30/2013 04:45 PM Aaron Marcuse-Kubitza

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

8745 04/30/2013 04:35 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: divided replacements into sections

8744 04/30/2013 04:27 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: move Bookmarks Toolbar to beginning, remove its desc, and rename it to Quick links

8743 04/30/2013 04:13 PM Aaron Marcuse-Kubitza

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

8742 04/30/2013 04:09 PM Aaron Marcuse-Kubitza

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)

8741 04/30/2013 03:32 PM Aaron Marcuse-Kubitza

web/links/index.htm.run: clean_up (): rename the page title from "Bookmarks" to "BIEN links"

8740 04/30/2013 03:18 PM Aaron Marcuse-Kubitza

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.

8739 04/30/2013 03:05 PM Aaron Marcuse-Kubitza

web/links/index.htm: use initial blank line instead of previous "-" workaround to indicate author comment at start of bookmark desc

8738 04/30/2013 03:04 PM Aaron Marcuse-Kubitza

web/links/index.htm: use initial blank line to indicate author comment at start of bookmark desc

8737 04/30/2013 02:59 PM Aaron Marcuse-Kubitza

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

8736 04/30/2013 02:51 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: label page's description: don't label an author-added quotation (which starts with " ) as the page's description

8735 04/30/2013 02:33 PM Aaron Marcuse-Kubitza

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.

8734 04/30/2013 02:22 PM Aaron Marcuse-Kubitza

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.

8733 04/30/2013 01:20 PM Aaron Marcuse-Kubitza

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.

8732 04/30/2013 12:59 PM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks. changes include links about BitTorrent Sync.

8731 04/30/2013 12:51 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: label <meta> description: renamed label text to "page's description" to be understandable to non-programmers

8730 04/30/2013 12:49 PM Aaron Marcuse-Kubitza

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

8729 04/30/2013 12:37 PM Aaron Marcuse-Kubitza

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.

8728 04/30/2013 12:13 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: remove LAST_MODIFIED attributes, which seem to change whenever the favicon is updated and clutter up the svn diff

8727 04/30/2013 12:05 PM Aaron Marcuse-Kubitza

lib/Firefox_bookmarks.reformat.csv: remove ICON attributes with favicon contents, which clutter up the svn diffs

8726 04/30/2013 11:52 AM Aaron Marcuse-Kubitza

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`)