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ADAGUC is a geographical information system to visualize netCDF files via the web. The software consists of a server side C++ application and a client side JavaScript application. The software provides several features to access and visualize data over the web, it uses OGC standards for data dissemination.

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README.md

ADAGUC / adaguc-server

ADAGUC is a geographical information system to visualize netCDF files via the web. The software consists of a server side C++ application (ADAGUC-Server) and a client side JavaScript application (ADAGUC-Viewer). The software provides several features to access and visualize data over the web, it uses OGC standards for data dissemination.

Useful links

  • https://dev.knmi.nl/projects/adagucserver/wiki - For adaguc-server documentation
  • https://dev.knmi.nl/projects/adagucserver/wiki/Configuration - For configuration details.
  • https://github.com/KNMI/adaguc-viewer - ADAGUC-viewer, a WMS client which can connect to ADAGUC-server
  • https://knmi.github.io/adaguc-server/ - Gitbook documentation, currently information about supported data formats is written
  • docker rm -f my-adaguc-server - For stopping and removing your docker container, useful when you want to start it with other arguments
  • docker exec -i -t my-adaguc-server /adaguc/adaguc-server-updatedatasets.sh - For updating adaguc-server datasets.
  • docker exec --env ADAGUC_DATASET_MASK='^eprofile_L0_[0-9]{5}-[A-Z]\.xml$' -i -t my-adaguc-server /adaguc/adaguc-server-updatedatasets.sh - For updating adaguc-server datasets where the datasetname matches the provided ADAGUC_DATASET_MASK.
  • docker exec -i -t my-adaguc-server /adaguc/adaguc-server-checkfile.sh <file in autowms folder, e.g. testdata.nc> - For generating reports about your files, provides feedback on what decisions adaguc-server makes based on your file metadata.

Docker for adaguc-server:

A docker image for adaguc-server is available from dockerhub. This image enables you to quickstart with adaguc-server, everything is configured and pre-installed. You can mount your own directories and configuration files from your workstation inside the docker container. This allows you to use and configure your own data from your workstation. Inside the docker container the paths for data and configuration files are always the same, this is useful for sharing dataset configuration files between different instances because configuration files can be the same across different environments. You can check the docker-compose.yml file to quickstart with both adaguc-server and adaguc-viewer at the same time.

Directories and data

The most important directories are:

  • adaguc-data: Put your NetCDF, HDF5, GeoJSON or PNG files inside this directory, these are referenced by your dataset configurations.
  • adaguc-datasets: These are your dataset configuration files, defining a service. These are small XML files allowing you to customize the styling and aggregation of datafiles. See satellite imagery example below. It is good practice to configure datasets to read data from the /data/adaguc-data folder, which can be mounted from your host machine. This ensures that dataset configurations will work on different environments where paths to the data can differ. Datasets are referenced in the WMS service by the dataset= keyword.
  • adaguc-autowms: Put your files here you want to have visualised automatically without any scanning.

Start adaguc via Docker (compose)

Adaguc comprises the following components run in separate containers:

  1. adaguc-server
  2. adaguc-viewer
  3. nginx webserver
  4. postgresql database

To start adaguc run the following command from the folder ${SRC_ROOT_DIR}/Docker

To get an instance online with docker compose:

git clone https://github.com/KNMI/adaguc-server/
export ADAGUCHOME=$HOME
mkdir -p $ADAGUCHOME/adaguc-data
mkdir -p $ADAGUCHOME/adaguc-datasets
mkdir -p $ADAGUCHOME/adaguc-autowms

cd adaguc-server/Docker

# Generate environment for adaguc:
bash docker-compose-generate-env.sh \
  -a $ADAGUCHOME/adaguc-autowms \
  -d $ADAGUCHOME/adaguc-datasets \
  -f $ADAGUCHOME/adaguc-data \
  -p 443
# You can view or edit the file ./.env

docker-compose pull
docker-compose build
docker-compose up -d && sleep 10

# Visit the url as configured in the .env file under EXTERNALADDRESS
# The server runs with a self signed certificate, this means you get a warning. Add an exception.

Scanning datasets

Datasets can be scanned using a separate container image, or by the built in scanner script of the adaguc-server container.

Scan with the adaguc-server container:

docker exec -i -t my-adaguc-server /adaguc/adaguc-server-updatedatasets.sh <optional datasetname>

Visit the webservice:

The docker-compose-generate-env.sh tells you where you services can be accessed in the browser. Alternatively you can have a look at the ./adaguc-server/Docker/.env file

cat ./adaguc-server/Docker/.env

The webservices should now be accessible via :

https://<your hostname>/

or, if you specified a port other than 443

https://&lt;your hostname&gt;:&lt;port&gt;/

Note:

  • The first time you acces the service, your browser will show a warning that there is a problem with the certificate. Make an exception for this service.

To view logs:

docker logs -f my-adaguc-server

To stop:

## Press CTRL+C
docker-compose down

Visualize a NetCDF file via autowms

# Put a NetCDF testfile into your autowms folder
export ADAGUCHOME=$HOME
curl -kL https://github.com/KNMI/adaguc-server/raw/master/data/datasets/testdata.nc > $ADAGUCHOME/adaguc-autowms/testdata.nc

AutoWMS files are referenced via the source= key value pair in the URL. Filenames must be URLEncoded. Supported files are NetCDF, HDF5 and GeoJSON. This file is now accessible via https://<your hostname>:<port>/adaguc-services/adagucserver?source=testdata.nc&service=WMS&request=GetCapabilities (An XML document about this NetCDF is shown)

A GetMap request looks like https://<your hostname>:<port>/adaguc-services/adagucserver?source=testdata%2Enc&SERVICE=WMS&VERSION=1.3.0&REQUEST=GetMap&LAYERS=testdata&WIDTH=1249&HEIGHT=716&CRS=EPSG%3A4326&BBOX=34.29823486999199,-24.906440270168137,69.33472934198558,36.21169044983186&STYLES=auto%2Fnearest&FORMAT=image/png&TRANSPARENT=TRUE&

You can visualize this link in the adaguc-viewer via "Add data", for example in http://geoservices.knmi.nl/viewer2.0/ or locally in https://<your hostname>:<port>/

Other testdata can be found here: http://opendap.knmi.nl/knmi/thredds/catalog/ADAGUC/catalog.html.

Test your own dataset configuration for styling, aggregations, etc ...

Get a dataset configurationfile:

curl -kL https://raw.githubusercontent.com/KNMI/adaguc-server/master/data/config/datasets/dataset_a.xml > $ADAGUCHOME/adaguc-datasets/dataset_a.xml

Now update the db:

docker exec -i -t my-adaguc-server /adaguc/adaguc-server-updatedatasets.sh dataset_a

Dataset configurations are referenced via the dataset= key value pair in the URL. This dataset is now accessible via https://<your hostname>:<port>/adaguc-services/adagucserver?service=wms&request=getcapabilities&dataset=dataset_a&

Aggregation of hi-res satellite imagery

First download a sequence of satellite data from opendap.knmi.nl:

export ADAGUCHOME=$HOME
cd $ADAGUCHOME/adaguc-data/
wget -nc -r -l2 -A.h5   -I /knmi/thredds/fileServer/,/knmi/thredds/catalog/ 'http://opendap.knmi.nl/knmi/thredds/catalog/ADAGUC/testsets/projectedgrids/meteosat/catalog.html'
ls opendap.knmi.nl/knmi/thredds/fileServer/ADAGUC/testsets/projectedgrids/meteosat/

Create a dataset configuration file named $ADAGUCHOME/adaguc-datasets/sat.xml :

<?xml version="1.0" encoding="UTF-8" ?>
<Configuration>
  <!-- Custom styles -->
  <Legend name="gray" type="colorRange">
    <palette index="0"   red="0"   green="0"   blue="0" alpha="255"/>
    <palette index="240" red="255" green="255"   blue="255"/>
  </Legend>
  <Legend name="gray-trans" type="colorRange">
    <palette index="0"   red="0"   green="0"   blue="0" alpha="0"/>
    <palette index="240" red="255" green="255"   blue="255"/>
  </Legend>
  <Style name="hrvis_0till30000">
    <Legend fixed="true">gray</Legend>
    <Min>0</Min>
    <Max>30000</Max>
    <RenderMethod>nearest</RenderMethod>
    <RenderSettings renderer="gd"/>
    <NameMapping name="nearest"        title="Albedo 0-30000" abstract="Albedo values from satellite imagery"/>
  </Style>
  <Style name="hrvis_0till30000_transparent">
    <Legend fixed="true">gray-trans</Legend>
    <Min>0</Min>
    <Max>30000</Max>
    <RenderMethod>nearest</RenderMethod>
    <RenderSettings renderer="cairo"/>
    <NameMapping name="nearest"        title="Albedo 0-30000 transparent" abstract="Albedo values from satellite imagery with the lower values made transparent"/>
  </Style>
  <!-- Layers -->
  <Layer type="database">
    <Projection proj4="+proj=geos +lon_0=0.000000 +lat_0=0 +h=35807.414063 +a=6378.169000 +b=6356.583984"/>
    <Name>HRVIS</Name>
    <Title>HRVIS</Title>
    <Variable>image1.image_data</Variable>
    <FilePath
      filter="^METEOSAT_(8|9|10|11).*EUROPEHVIS.*\.h5">/data/adaguc-data/opendap.knmi.nl/knmi/thredds/fileServer/ADAGUC/testsets/projectedgrids/meteosat/</FilePath>
    <DataReader>HDF5</DataReader>
    <Dimension name="time" interval="PT15M">time</Dimension>
    <Styles>hrvis_0till30000,hrvis_0till30000_transparent</Styles>
  </Layer>
  <Layer type="cascaded" hidden="false">
    <Name force="true">baselayer</Name>
    <Title>NPS - Natural Earth II</Title>
    <WMSLayer service="http://geoservices.knmi.nl/cgi-bin/bgmaps.cgi?" layer="naturalearth2"/>
    <LatLonBox minx="-180"  miny="-90" maxx="180" maxy="90"/>
  </Layer>
  <!-- Layer with name overlay from geoservices.knmi.nl -->
  <Layer type="cascaded" hidden="false">
    <Name force="true">overlay</Name>
    <Title>NPS - Natural Earth II</Title>
    <WMSLayer service="http://geoservices.knmi.nl/cgi-bin/worldmaps.cgi?" layer="world_line_thick"/>
    <LatLonBox minx="-180"  miny="-90" maxx="180" maxy="90"/>
    <WMSFormat name="image/png32"/>
  </Layer>
  <!-- Layer with name grid10 from geoservices.knmi.nl -->
  <Layer type="grid">
    <Name force="true">grid10</Name>
    <Title>grid 10 degrees</Title>
    <Grid resolution="10"/>
    <WMSFormat name="image/png32"/>
  </Layer>
</Configuration>

Now update the db wit the sat dataset:

docker exec -i -t my-adaguc-server /adaguc/adaguc-server-updatedatasets.sh sat

The following URL can be used in the viewer: https://<your hostname>:<port>/adaguc-services/adagucserver?service=wms&request=getcapabilities&dataset=sat&

You can use this URL for example in http://geoservices.knmi.nl/viewer2.0/ or locally in https://<your hostname>:<port>/

Aggregation of ERA interim model data

<?xml version="1.0" encoding="UTF-8"?>
<Configuration>
  <!-- Custom styles -->
  <Legend name="ColorPalette" type="colorRange">
    <palette index="0" red="0" green="0" blue="255" />
    <palette index="80" red="0" green="255" blue="255" />
    <palette index="120" red="0" green="255" blue="0" />
    <palette index="160" red="255" green="255" blue="0" />
    <palette index="240" red="255" green="0" blue="0" />
  </Legend>
  <Style name="era5_style">
    <Legend fixed="true">ColorPalette</Legend>
    <ContourLine width="3" linecolor="#ff0000" textcolor="#ff0000" textformatting="%2.0f" classes="300" />
    <ContourLine width="0.3" linecolor="#444444" textcolor="#444444" textformatting="%2.0f" interval="100" />
    <Min>0</Min>
    <Max>1500</Max>
    <ValueRange min="350" max="10000000" />
    <RenderMethod>nearest,contour,nearestcontour</RenderMethod>
    <NameMapping name="nearest" title="IVT 0-1500" abstract="IVT" />
  </Style>
  <!-- Layer with name baselayer from geoservices.knmi.nl -->
  <Layer type="cascaded" hidden="false">
    <Name force="true">baselayer</Name>
    <Title>NPS - Natural Earth II</Title>
    <WMSLayer service="http://geoservices.knmi.nl/cgi-bin/bgmaps.cgi?" layer="naturalearth2" />
    <LatLonBox minx="-180" miny="-90" maxx="180" maxy="90" />
  </Layer>
  <!-- Layer with name overlay from geoservices.knmi.nl -->
  <Layer type="cascaded" hidden="false">
    <Name force="true">overlay</Name>
    <Title>NPS - Natural Earth II</Title>
    <WMSLayer service="http://geoservices.knmi.nl/cgi-bin/worldmaps.cgi?" layer="world_line_thick" />
    <LatLonBox minx="-180" miny="-90" maxx="180" maxy="90" />
  </Layer>
  <!-- Layer with name grid10 from geoservices.knmi.nl -->
  <Layer type="grid">
    <Name force="true">grid10</Name>
    <Title>grid 10 degrees</Title>
    <Grid resolution="10" />
    <WMSFormat name="image/png32" />
  </Layer>
  <!-- Layer with name ivt (Integrated Water Vapor Transport) with ERA interim data -->
  <Layer type="database">
    <Variable>ivt</Variable>
    <FilePath filter="^IVT.ERAINT.2.*\.nc">/data/adaguc-data/TWEX/ERAInt/</FilePath>
    <Styles>era5_style,auto</Styles>
  </Layer>
</Configuration>

Make a movie of the sat dataset

You can use the python script at data/python/createmovie.py

Demo image: http://adaguc.knmi.nl/data/msg_hrvis_demo.gif Loop of MSG HRVIS made with adaguc-server

Opendap services can be visualized

The following OpenDAP URL can be visualized:

http://opendap.knmi.nl/knmi/thredds/dodsC/omi/OMI___OPER_R___TYTRCNO_L3/TYTRCNO/OMI___OPER_R___TYTRCNO_3.nc

To provide it to the source= parameter it must be be URL encoded:

http%3A%2F%2Fopendap.knmi.nl%2Fknmi%2Fthredds%2FdodsC%2Fomi%2FOMI___OPER_R___TYTRCNO_L3%2FTYTRCNO%2FOMI___OPER_R___TYTRCNO_3.nc

The ADAGUC WMS URL becomes:

https://&lt;your hostname&gt;:&lt;port&gt;/adaguc-services/adagucserver?source=http%3A%2F%2Fopendap.knmi.nl%2Fknmi%2Fthredds%2FdodsC%2Fomi%2FOMI___OPER_R___TYTRCNO_L3%2FTYTRCNO%2FOMI___OPER_R___TYTRCNO_3.nc&service=wms&request=getcapabilities

This WMS URL can be visualized in the viewer by using "Add data".

Docker compose with server and viewer:

The compose file is located here: Docker/docker-compose.yml

Prebuilt images are available at https://hub.docker.com/ through openearth:

OpenDAP

Adaguc can serve data via OpenDAP. The format is

http(s)://<yourhost>/adaguc-services/adagucopendap/<dataset_name>/<layer_name>

https://<your hostname>:<port>/adaguc-services/adagucopendap/dataset_a/testdata

Opendap endpoints can be checked by testing the following URL's:

  • https://<your hostname>:<port>/adaguc-services/adagucopendap/dataset_a/testdata.das
  • https://<your hostname>:<port>/adaguc-services/adagucopendap/dataset_a/testdata.dds

You can dump the header or visualize with:

  • ncdump -h https://<your hostname>:<port>/adaguc-services/adagucopendap/dataset_a/testdata
  • ncview https://<your hostname>:<port>/adaguc-services/adagucopendap/dataset_a/testdata

Endpoints

  • https://<your hostname>:<port>/adaguc-services/adagucserver? Will be forwarded automaticall to /wms or /wcs depending on the service type
  • https://<your hostname>:<port>/adaguc-services/wms? For serving Web Map Services
  • https://<your hostname>:<port>/adaguc-services/wcs? For serving Web Coverage Services
  • https://<your hostname>:<port>/adaguc-services/adagucopendap/ For serving OpenDAP services
  • https://<your hostname>:<port>/adaguc-services/autowms? For getting the list of visualizable resources
  • https://<your hostname>:<port>/adaguc-services/adagucload? For getting system load
  • https://<your hostname>:<port>/adaguc-services/servicehealth? For getting overview and status of available datasets

Alternatively there is a dedicated adaguc scanner container:

Installation instructions without docker on Ubuntu 18:

About

ADAGUC is a geographical information system to visualize netCDF files via the web. The software consists of a server side C++ application and a client side JavaScript application. The software provides several features to access and visualize data over the web, it uses OGC standards for data dissemination.

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