Introduction
UI for Microclimatic data for ecological forecasting
API Reference
Refer to
- [R API ]https://github.com/ajijohn/microclimRapi
- [Python API] https://github.com/ajijohn/microclim-api
API keys are to requested prior to interacting with APIs.
Binder
Requirements
- NodeJs >= 6.x (tested on 10.19)
Configurations
setup auth.js with API Keys for Google/Twitter/LinkedIn
Dependencies
Needs MongoDB
sudo apt install -y mongodb
Verify the service's status:
sudo systemctl status mongodb
To restart MongoDB
sudo systemctl restart mongodb
Use MongoDB shell to create the database and the collections
mongo
- Create a database 'ebm'
- Create collections 'post','requests','sessions','users'
Install
$ git clone git://github.com/ajijohn/ebm.git
$ cd ebm
$ npm install
$ cd ebm
$ npm install
if not found/npm not installed - do the below for Ubuntu
sudo apt update
sudo apt install nodejs
sudo apt install npm
sudo apt install nodejs
sudo apt install npm
Check the node version
nodejs -v
We have tested on 10.19
$ npm start
$ npm install -g forever
$ npm install -g forever
Starting the app
forever start bin/www
Then visit http://localhost:3000/
Communication
Once filtering is done via the microclim.org site, an email will be delivered to your mailbox with the details of the extracted file.
Usage
Note the link from the previous section, and to use the NetCDF file, see the vignette below
# author - Aji John
# credit - http://geog.uoregon.edu/bartlein/courses/geog607/Rmd/netCDF_01.htm
library(chron)
library(RColorBrewer)
library(lattice)
library(ncdf4)
url="http://s3-us-west-2.amazonaws.com/microclim/58741743311c3c0e99dac83d/BGAP_output_interval-daily_aggregation-avg_times-19810101-19810122_created-2017-01-09-2316.nc"
dfile="BGAP_output_interval-daily_aggregation-avg_times-19810101-19810122_created-2017-01-09-2316.nc"
download.file(url, destfile=dfile)
# open a NetCDF file
ncin <- nc_open(dfile)
print(ncin)
lon <- ncvar_get(ncin, "lon")
nlon <- dim(lon)
head(lon)
lat <- ncvar_get(ncin, "lat", verbose = F)
nlat <- dim(lat)
head(lat)
#Number of colums - would be 2 by 2 matrix
print(c(nlon, nlat))
# Number of days multiplied by the granularity (hourly/daily etc)
t <- ncvar_get(ncin, "time")
tunits <- ncatt_get(ncin, "time", "units")
nt <- dim(t)
dname <- "BGAP" # note: specific to the variabe being s seclected
tmp.array <- ncvar_get(ncin, dname)
dlname <- ncatt_get(ncin, dname, "long_name")
dunits <- ncatt_get(ncin, dname, "units")
fillvalue <- ncatt_get(ncin, dname, "_FillValue")
dim(tmp.array)
# print the global variables
# reconfirm what was used to filter
created <- ncatt_get(ncin, 0, "createdOn")
startdate <- ncatt_get(ncin, 0, "startdate")
enddate <- ncatt_get(ncin, 0, "enddate")
varname <- ncatt_get(ncin, 0, "varname")
# credit - http://geog.uoregon.edu/bartlein/courses/geog607/Rmd/netCDF_01.htm
library(chron)
library(RColorBrewer)
library(lattice)
library(ncdf4)
url="http://s3-us-west-2.amazonaws.com/microclim/58741743311c3c0e99dac83d/BGAP_output_interval-daily_aggregation-avg_times-19810101-19810122_created-2017-01-09-2316.nc"
dfile="BGAP_output_interval-daily_aggregation-avg_times-19810101-19810122_created-2017-01-09-2316.nc"
download.file(url, destfile=dfile)
# open a NetCDF file
ncin <- nc_open(dfile)
print(ncin)
lon <- ncvar_get(ncin, "lon")
nlon <- dim(lon)
head(lon)
lat <- ncvar_get(ncin, "lat", verbose = F)
nlat <- dim(lat)
head(lat)
#Number of colums - would be 2 by 2 matrix
print(c(nlon, nlat))
# Number of days multiplied by the granularity (hourly/daily etc)
t <- ncvar_get(ncin, "time")
tunits <- ncatt_get(ncin, "time", "units")
nt <- dim(t)
dname <- "BGAP" # note: specific to the variabe being s seclected
tmp.array <- ncvar_get(ncin, dname)
dlname <- ncatt_get(ncin, dname, "long_name")
dunits <- ncatt_get(ncin, dname, "units")
fillvalue <- ncatt_get(ncin, dname, "_FillValue")
dim(tmp.array)
# print the global variables
# reconfirm what was used to filter
created <- ncatt_get(ncin, 0, "createdOn")
startdate <- ncatt_get(ncin, 0, "startdate")
enddate <- ncatt_get(ncin, 0, "enddate")
varname <- ncatt_get(ncin, 0, "varname")
Tests
$ npm test
DOI
License
Apache