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# Date Author Comment
8850 05/08/2013 10:15 AM Aaron Marcuse-Kubitza

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

8849 05/08/2013 10:11 AM Aaron Marcuse-Kubitza

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.

8848 05/08/2013 10:01 AM Aaron Marcuse-Kubitza

web/links/index.htm: updated to Firefox bookmarks. added description of the formats supported by PostgreSQL's COPY command and their escape sequences.

8847 05/08/2013 08:44 AM Aaron Marcuse-Kubitza

bugfix: schemas/vegbien.sql: geoscrub_input_view: only include places whose country is not NULL, because at least the country is required for geoscrubbing

8846 05/08/2013 08:34 AM Aaron Marcuse-Kubitza

/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.

8845 05/06/2013 07:10 AM Aaron Marcuse-Kubitza

/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.

8844 05/06/2013 07:05 AM Aaron Marcuse-Kubitza

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.

8843 05/06/2013 06:33 AM Aaron Marcuse-Kubitza

bugfix: /README.TXT: Schema changes: Reinstall staging tables: also need to run `make mk_db` before running reinstall_all

8842 05/06/2013 06:30 AM Aaron Marcuse-Kubitza

/README.TXT: Schema changes: Reinstall staging tables: drop the saved previous DB at the end of the operation

8841 05/06/2013 06:18 AM Aaron Marcuse-Kubitza

/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

8840 05/06/2013 05:57 AM Aaron Marcuse-Kubitza

/README.TXT: Schema changes: Reinstall staging tables: added step to first rename existing vegbien database, so it is not modified in the reinstallation

8839 05/06/2013 05:27 AM Aaron Marcuse-Kubitza

inputs/FIA/: archived no longer used BIEN2 FIA data from the nimoy geoscrub DB

8838 05/06/2013 05:26 AM Aaron Marcuse-Kubitza

inputs/FIA/_archive/: moved FIA_COND_unique, Organism into 2011-10-17/ subdir

8837 05/06/2013 04:44 AM Aaron Marcuse-Kubitza

/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

8836 05/06/2013 04:27 AM Aaron Marcuse-Kubitza

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

8835 05/06/2013 04:25 AM Aaron Marcuse-Kubitza

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

8834 05/06/2013 04:12 AM Aaron Marcuse-Kubitza

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}.

8833 05/06/2013 04:00 AM Aaron Marcuse-Kubitza

*{.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&gt;)

8832 05/06/2013 03:14 AM Aaron Marcuse-Kubitza

schemas/pg_hba*.conf: removed trailing whitespace

8831 05/06/2013 03:10 AM Aaron Marcuse-Kubitza

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.

8830 05/06/2013 02:32 AM Aaron Marcuse-Kubitza

web/links/index.htm: explicitly separate page's description from author comments where needed

8829 05/06/2013 02:29 AM Aaron Marcuse-Kubitza

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

8828 05/06/2013 02:21 AM Aaron Marcuse-Kubitza

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.

8827 05/06/2013 02:17 AM Aaron Marcuse-Kubitza

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

8826 05/05/2013 10:35 PM Aaron Marcuse-Kubitza

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

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= )