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BIEN geovalidation notes
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========================
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***** obtain source code:
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svn co https://code.nceas.ucsb.edu/code/projects/bien/derived/biengeo/
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***** install dependencies:
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The only dependencies for running these scripts are PostgreSQL 9.1, postgis 2.0,
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and unzip.
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For postgis installation on Ubuntu 12.04 see:
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http://trac.osgeo.org/postgis/wiki/UsersWikiPostGIS20Ubuntu1204
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Installing these packages on Ubuntu 13.04 should only require these commands:
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sudo apt-get install unzip
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sudo add-apt-repository ppa:ubuntugis/ubuntugis-unstable
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* Note additional install instructions for postgis-2.0 on Ubuntu 13 found here:
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* http://trac.osgeo.org/postgis/wiki/UsersWikiPostGIS20Ubuntu1304
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* Currently, the ubuntugis-unstable sources list needs to change to 'quantal'.
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sudo apt-get update
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sudo apt-get install postgresql-9.1-postgis-2.0-scripts
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***** Notes on running the shell scripts:
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Running any script with the -? or --help option will print a usage message with
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all available options for that script, and then exit.
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The following scripts accept database connection options, similar to psql.
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For example: setup.sh -d dbname -h hostname -U username
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The defaults passed to psql commands, if no options are given to the shell
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scripts, are 'geoscrub' for dbname and 'bien' for username. The -h option is
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not passed to psql commands by default.
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The update_validation_data.sh scripts will only download fresh validation data
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if the directories for GADM data (~/gadm_v2_shp by default) and geonames.org
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data (~/geonames by default) do not already exist or do not contain that data.
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The geoscrub scripts will only download fresh input data if the directory for
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the input data (~/geoscrub_input by default) does not already exist or does not
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contain the geoscrub-corpus.csv input file.
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***** initialize the DB:
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cd <svn_biengeo_root>
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1. setup.sh
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- creates postgis DB and all base tables
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***** update geoscrub validation data:
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runtime: ~40 minutes
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cd <svn_biengeo_root>
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2. update_validation_data.sh [--gadm-data=gadm_dir] [--geonames-data=geonames_dir]
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- runs the following scripts in order to load validation data:
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* update_gadm_data.sh
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runtime: ~15 minutes (not including download time)
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- loads GADM2 data into a new (or re-created) gadm2 table
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* update_geonames_data.sh
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runtime: ~25 minutes (not including download time)
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- loads geonames.org data and adds some custom mapping logic
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* geonames-to-gadm.*.sql
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runtime: ~1 minute
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- contains SQL statements that build linkages between geonames.org
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names and GADM2 names
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***** geoscrub new data:
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WARNING: deletes any previous geoscrubbing results!
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runtime: ~2.5 h
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cd <svn_biengeo_root>
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3. geoscrub.sh [--geoscrub-input=input_dir] [--output-file=geoscrub-output.csv]
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- runs the following scripts in order to load and scrub vegbien input data:
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* load-geoscrub-input.sh
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- dumps geoscrub_input from vegbien and loads it into the geoscrub db
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* geonames.sql
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- contains SQL statements that scrub asserted names and (to the
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extent possible) map them to GADM2
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* geovalidate.sql
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runtime: 2.5 h
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- contains (postgis-extended) SQL statements that score the validity
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of GADM2-scrubbed names against given point coordinates
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- If the --output-file (or -o) option is given, then the final geoscrub table
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will be dumped to the specified output file in CSV format.
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[Also see comments embedded in specific scripts in this directory.]
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The bash and SQL statements contained in the files as ordered above
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should be applied to carry out geographic name scrubbing and
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geovalidation on a given corpus of BIEN location records.
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That said, given the tight deadline under which this was done in order
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to produced a geovalidated BIEN3 corpus in advance of the Nov 2013
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working group meeting, and the corresponding manner in which much of
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this was actually executed piecemeal in an iterative and interactive
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fashion within a bash shell and psql session, I can't guarantee that the
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code in its current state could be run end-to-end without intervention.
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It's close, but probably not bulletproof.
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The resulting 'geoscrub' table is what contains the scrubbed (i.e.,
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GADM2-matched) names and various geovalidation scores.
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Notes/Caveats/Todos:
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* Clearly the SQL statements used in this procedure suffer from a lot of
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redundancy, and it might be worth trying to refactor once we're happy
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with the particular approach taken.
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* Need to pull out more known notes/caveats/todos and highlight them :)
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