dlebauer

lat,lon,yield,longitude_0,latitude_0,geojson
48.930439,-122.4427032,31.38,-122.4427032,48.930439,"{""type"":""Point"",""coordinates"":[-122.4427,48.93044]}"
33.79605865,-117.3647003,0.20,-117.3647003,33.79605865,"{""type"":""Point"",""coordinates"":[-117.3647,33.79606]}"
45.18630981,-119.2369003,2.35,-119.2369003,45.18630981,"{""type"":""Point"",""coordinates"":[-119.2369,45.18631]}"
48.11856842,-116.4271011,11.38,-116.4271011,48.11856842,"{""type"":""Point"",""coordinates"":[-116.4271,48.11857]}"
46.77112961,-114.8928986,1.55,-114.8928986,46.77112961,"{""type"":""Point"",""coordinates"":[-114.8929,46.77113]}"
47.70011902,-114.1678009,6.55,-114.1678009,47.70011902,"{""type"":""Point"",""coordinates"":[-114.1678,47.70012]}"
34.33436966,-110.25,0.02,-110.25,34.33436966,"{""type"":""Point"",""coordinates"":[-110.25,34.33437]}"
38.07836914,-108.2764969,0.04,-108.2764969,38.07836914,"{""type"":""Point"",""coordinates"":[-108.2765,38.07837]}"
39.52045059,-107.1908035,0.01,-107.1908035,39.52045059,"{""type"":""Point

dlebauer

int time(time) ;
       time:long_name = "Time axis" ;
       time:units = "seconds since YYYY-01-01 00:00:00" ;
       time:calendar = "gregorian" ;
       time:time_origin = "YYYY-01-01 00:00:00" ;
int timestp(time) ;
       timestp:long_name = "Time step axis" ;
       timestp:units = "timesteps since YYYY-01-01 00:00:00" ;
       timestp:tstep_sec = 3600. ;
       timestp:time_origin = "YYYY-01-01 00:00:00" ;

dlebauer

<VirtualHost *:80>

  <Proxy *>
    Allow from localhost
  </Proxy>

  ProxyPass        /rstudio/ http://localhost:8787/
  ProxyPassReverse /rstudio/ http://localhost:8787/
  RedirectMatch permanent ^/rstudio$ /rstudio/

dlebauer

[dlebauer@biocluster vars2]$ ncdump -h all.nc
netcdf all {
dimensions:
        lat = 360 ;
        lon = 720 ;
        time = 160708 ;
        nv = 2 ;
        points_terre = 62482 ;
variables:
        int crs ;

dlebauer

"# David LeBauer, Dan Wang, and Michael Dietze, 2010.  Biofuel Ecophysiological Traits and Yields Database Version 1.0.  Energy Biosciences Institute, Urbana, IL"
#
# Contact:,[email protected]
#
# SQL query:,"SELECT ""traits_and_yields_view"".* FROM ""traits_and_yields_view"" WHERE (access_level >= 4) AND ((LOWER(traits_and_yields_view.scientificname) LIKE '%switchgrass%' OR LOWER(traits_and_yields_view.commonname) LIKE '%switchgrass%' OR LOWER(traits_and_yields_view.trait) LIKE '%switchgrass%' OR LOWER(traits_and_yields_view.trait_description) LIKE '%switchgrass%' OR LOWER(traits_and_yields_view.city) LIKE '%switchgrass%' OR LOWER(traits_and_yields_view.sitename) LIKE '%switchgrass%'))"
#
# Date of query:,2014-04-11 00:42:35 -0500
#
sitename,city,lat,lon,scientificname,commonname,genus,author,citation_year,treatment,date,month,year,dateloc,trait,mean,units,n,statname,stat,notes
Grassland Soil & Water Research Laboratory,Temple,31.05,-97.35,Panicum virgatum,switchgrass,Panicum,Kiniry,1999,Switch1,1995-06

dlebauer

ALTER TABLE "traits" ADD CONSTRAINT "fk_traits_species_1" FOREIGN KEY ("specie_id") REFERENCES "species" ("id");
ALTER TABLE "yields" ADD CONSTRAINT "fk_yields_species_1" FOREIGN KEY ("specie_id") REFERENCES "species" ("id");
ALTER TABLE "traits" ADD CONSTRAINT "fk_traits_sites_1" FOREIGN KEY ("site_id") REFERENCES "sites" ("id");
ALTER TABLE "yields" ADD CONSTRAINT "fk_yields_sites_1" FOREIGN KEY ("site_id") REFERENCES "sites" ("id");
ALTER TABLE "traits" ADD CONSTRAINT "fk_traits_citations_1" FOREIGN KEY ("citation_id") REFERENCES "citations" ("id");
ALTER TABLE "yields" ADD CONSTRAINT "fk_yields_citations_1" FOREIGN KEY ("citation_id") REFERENCES "citations" ("id");
ALTER TABLE "traits" ADD CONSTRAINT "fk_traits_cultivars_1" FOREIGN KEY ("cultivar_id") REFERENCES "cultivars" ("id");
ALTER TABLE "yields" ADD CONSTRAINT "fk_yields_cultivars_1" FOREIGN KEY ("cultivar_id") REFERENCES "cultivars" ("id");
ALTER TABLE "traits" ADD CONSTRAINT "fk_traits_treatments_1" FOREIGN KEY ("treatment_id") REFERENCES "treatm

dlebauer

CREATE TABLE "citations" (
"id" int4 NOT NULL DEFAULT nextval('citations_id_seq'::regclass),
"author" varchar(255) COLLATE "default" NOT NULL,
"year" int4 NOT NULL,
"title" varchar(255) COLLATE "default" NOT NULL,
"journal" varchar(255) COLLATE "default",
"vol" int4,
"pg" varchar(255) COLLATE "default",
"url" varchar(512) COLLATE "default",
"pdf" varchar(255) COLLATE "default",

dlebauer

update sites set geometry=ST_SetSRID(ST_MakePoint(44.28,  -96.68,  495), 4326), notes = 'elevation queried from lat lon using R geonames::GNstrm3', updated_at = now() where id=  12;
update sites set geometry=ST_SetSRID(ST_MakePoint(29.72,  -95.4,  22), 4326), notes = 'elevation queried from lat lon using R geonames::GNstrm3', updated_at = now() where id=  100;
update sites set geometry=ST_SetSRID(ST_MakePoint(47.17,  -122.17,  167), 4326), notes = 'elevation queried from lat lon using R geonames::GNstrm3', updated_at = now() where id=  156;
update sites set geometry=ST_SetSRID(ST_MakePoint(50.63,  -3.45,  3), 4326), notes = 'elevation queried from lat lon using R geonames::GNstrm3', updated_at = now() where id=  186;
update sites set geometry=ST_SetSRID(ST_MakePoint(52.42,  0.11,  -1), 4326), notes = 'experimental site; elevation queried from lat lon using R geonames::GNstrm3', updated_at = now() where id=  199;
update sites set geometry=ST_SetSRID(ST_MakePoint(52.79,  7.09,  13), 4326), notes = 'elevation qu

dlebauer

<?xml version="1.0"?>
<pecan>
  <outdir>/tmp/biocrotest/</outdir>
  <pfts>
    <pft>
      <name>salix</name>
    </pft>
  </pfts>
  <database>
    <bety>

dlebauer

Importing from production database
----------------------------------

```{bash}
mysql -u dlebauer -p"bety" ebi_production < ebi_productiondump.sql
```

```{sql}
delete from traits where user_id not = 15;
```