Installing instructions for Tomcat, THREDDS, ncWMS, ERDDAP and GeoServer

This document contains some simple instructions to install a Tomcat server and deploy THREDDS (a.k.a. TDS, a.k.a Thematic Real-time Environmental Distributed Data Services), ncWMS (a.k.a. Godiva2, a.k.a. Godiva3), ERDDAP and GeoServer over.

References:

Tested on the following system: Linux 5.4.0-47-generic x86_64 GNU/Linux

⚠️ ⚠️ ⚠️ Starting with ncWMW2 v2.5 needs Java 11 to run. Most of the thredds code runs fine with Java11/Tomcat9, but the WMS interface (based on the original ncWMS) fails. So the user has to choose between running a full functioning thredds and an earlier version (before v2.5) of ncWMS2 using Java8 and Tomcat8 or running the latest version of ncWMS2 and a thredds without WMS capabilities using Java11 and Tomcat9.

Install Tomcat

The main directory will be /usr/local/tds. There is no need to run the application as root, it's safer to run as a regular user.

sudo mkdir /usr/local/tds
sudo chown my_user:my_user /usr/local/tds

Get latest Java JDK (get the Linux Compressed Archive). At the time this is jdk-8u271-linux-x64.tar.gz. You need to create a Oracle account do download the file, but it is free.

tar -xzvf jdk-8u271-linux-x64.tar.gz -C /usr/local/tds
cd /usr/local/tds
ln -s jdk1.8.0_271 java

Get the latest Tomcat. At the time this is apache-tomcat-8.5.60.tar.gz. Be careful to download the one listed under Binary Distributions -> Core and not one of the others (e.g. Deployer, Source).

tar -xzvf apache-tomcat-8.5.60.tar.gz -C /usr/local/tds
cd /usr/local/tds
ln -s apache-tomcat-8.5.60 tomcat

The directory tree will be:

$ /bin/ls -l /usr/local/tds/

apache-tomcat-8.5.60
java -> jdk1.8.0_271
jdk1.8.0_271
tomcat -> apache-tomcat-8.5.60

Create the file /usr/local/tds/tomcat/bin/setenv.sh. This file defines some configurations necessary for Tomcat/TDS.

#!/bin/sh
#
# ENVARS for Tomcat
#
export CATALINA_HOME="/usr/local/tds/tomcat"

export CATALINA_BASE="/usr/local/tds/tomcat"

export JAVA_HOME="/usr/local/tds/java"

# TDS specific ENVARS
#
# Define where the TDS content directory will live
#   THIS IS CRITICAL and there is NO DEFAULT - the
#   TDS will not start without this.
#
CONTENT_ROOT=-Dtds.content.root.path=/usr/local/tds/tomcat/content

# set java prefs related variables (used by the wms service, for example)
JAVA_PREFS_ROOTS="-Djava.util.prefs.systemRoot=$CATALINA_HOME/content/thredds/javaUtilPrefs \
                  -Djava.util.prefs.userRoot=$CATALINA_HOME/content/thredds/javaUtilPrefs"

#
# Some commonly used JAVA_OPTS settings:
#
NORMAL="-Xmx4096m -Xms512m -server -ea"
HEAP_DUMP="-XX:+HeapDumpOnOutOfMemoryError"
HEADLESS="-Djava.awt.headless=true"

#
# Standard setup.
#
JAVA_OPTS="$CONTENT_ROOT $NORMAL $MAX_PERM_GEN $HEAP_DUMP $HEADLESS $JAVA_PREFS_ROOTS"

export JAVA_OPTS

-Xmx defines the maximum RAM memory available for the server. Change this accordling to the computer resources.

If Tomcat is behind a proxy (usual in a corporate setup), you can configure the server to access the internet using a modified script like the one bellow. This configuration allows the server (and applets) to access the internet if needed, the client (the user's browser) needs it owns configuration to access the external network.

#!/bin/sh
#
# ENVARS for Tomcat
#
export CATALINA_HOME="/usr/local/tds/tomcat"

export CATALINA_BASE="/usr/local/tds/tomcat"

export JAVA_HOME="/usr/local/tds/java"

# TDS specific ENVARS
#
# Define where the TDS content directory will live
#   THIS IS CRITICAL and there is NO DEFAULT - the
#   TDS will not start without this.
#
CONTENT_ROOT=-Dtds.content.root.path=/usr/local/tds/tomcat/content

# set java prefs related variables (used by the wms service, for example)
JAVA_PREFS_ROOTS="-Djava.util.prefs.systemRoot=$CATALINA_HOME/content/thredds/javaUtilPrefs \
                  -Djava.util.prefs.userRoot=$CATALINA_HOME/content/thredds/javaUtilPrefs"

#
# Some commonly used JAVA_OPTS settings:
#
NORMAL="-Xmx4096m -Xms512m -server -ea"
HEAP_DUMP="-XX:+HeapDumpOnOutOfMemoryError"
HEADLESS="-Djava.awt.headless=true"

#
# proxy configuration
#
PROXY="-Dhttp.proxySet=true \
       -Dhttp.proxyHost=proxy.mycompany.com \
       -Dhttp.proxyPort=8080 \
       -Dhttp.proxyUser=user \
       -Dhttp.proxyPassword=password \
       -Dhttp.nonProxyHosts='localhost|127.0.0.1|*.mycompany.com' \
       -Dhttps.proxySet=true \
       -Dhttps.proxyHost=proxy.mycompany.com \
       -Dhttps.proxyPort=8080 \
       -Dhttps.proxyUser=user \
       -Dhttps.proxyPassword=password \
       -Dhttps.nonProxyHosts='localhost|127.0.0.1|*.mycompany.com'"

#
# Standard setup.
#
JAVA_OPTS="$CONTENT_ROOT $NORMAL $MAX_PERM_GEN $HEAP_DUMP $HEADLESS $JAVA_PREFS_ROOTS $PROXY"

export JAVA_OPTS

Give execution attributes with:

chmod +x /usr/local/tds/tomcat/bin/setenv.sh

To use Tomcat's manager app, it is mandatory to define some extra roles and an username/password in /usr/local/tds/tomcat/conf/tomcat-users.xml

<tomcat-users ...>

  <role rolename="admin-gui" />
  <role rolename="admin-script" />
  <role rolename="manager-gui" />
  <role rolename="manager-script" />
  <role rolename="manager-jmx" />
  <role rolename="manager-status" />
  <role rolename="ncWMS-admin" />
  <user username="my_user" password="my_password" roles="admin-gui,admin-script,manager-gui,manager-script,manager-jmx,manager-status,ncWMS-admin" />

</tomcat-users>

P.S.: ncWMS-admin will be used to log in ncWMS admin interface.

Following Special note about Tomcat, some special characters used in TDS queries must be allowed in /usr/local/tds/tomcat/conf/server.xml using the relaxedQueryChars parameter in the Connector definition:

    <Connector port="8080" protocol="HTTP/1.1"
               connectionTimeout="20000"
               redirectPort="8443"
               relaxedQueryChars="[]" />

Start Tomcat with:

/usr/local/tds/tomcat/bin/startup.sh

Check if is running with ps aux | grep -i tomcat and going to http://localhost:8080/ in a browser. The manager app is available in http://localhost:8080/manager/html, using the username/password defined in tomcat-users.xml.

To stop Tomcat:

/usr/local/tds/tomcat/bin/shutdown.sh

It may be useful to allow Tomcat to follow symlinks in the system to serve files outside the /usr/local/tds/tomcat/webapps directory. To do this, edit file /usr/local/tds/tomcat/conf/context.xml adding <Resources allowLinking="true" /> inside the Context block and restart Tomcat. Now it is possible to create a link to any place in the file system and have access in Tomcat. E.g.: assuming the file /some/dir/test.txt exists, running

ln -s /some/dir /usr/local/tds/tomcat/webapps/mydir

would permit access to the file in http://localhost:8080/mydir/test.txt.

Also, to allow the users to list the content of a directory instead of getting an error page, edit /usr/local/tds/tomcat/conf/web.xml and set the block

<init-param>
    <param-name>listings</param-name>
    <param-value>false</param-value>
</init-param>

to true. This way, in the previous example the user could access http://localhost:8080/mydir to see the content of the mydir directory (including file test.txt).

Deploy THREDDS

If everything is working, now it is time do deploy the THREDDS server. Download the latest TDS war file from Github or Unidata. At the time this is tds-4.6.15.war. Make a copy of the file following Tomcat naming conventions. If Tomcat is running, the war file will be automatically unpacked.

cp tds-4.6.15.war /usr/local/tds/tomcat/webapps/thredds##4.6.15.war

Go to http://localhost:8080/thredds to check if TDS is up and running.

Now lets change some TDS options. Shutdown Tomcat and edit file /usr/local/tds/tomcat/content/thredds/catalog.xml enabling some additional services.

  <service name="all" base="" serviceType="compound">
    <service name="odap" serviceType="OpenDAP" base="/thredds/dodsC/" />
    <!-- service name="dap4" serviceType="DAP4" base="/thredds/dap4/" /-->
    <service name="http" serviceType="HTTPServer" base="/thredds/fileServer/" />
    <service name="wcs"  serviceType="WCS" base="/thredds/wcs/" />
    <service name="wms"  serviceType="WMS" base="/thredds/wms/" />
    <service name="ncss" serviceType="NetcdfSubset" base="/thredds/ncss/" />
    <service name="ncml" serviceType="NCML" base="/thredds/ncml/" />
    <service name="uddc" serviceType="UDDC" base="/thredds/uddc/" />
    <service name="iso"  serviceType="ISO" base="/thredds/iso/" />
  </service>

In the file /usr/local/tds/tomcat/content/thredds/threddsConfig.xml uncomment and activate (<allow>true</allow>) the following services:

Netcdf Subset Service
WCS
WMS
NCISO

e.g.

  <!--
  The Netcdf Subset Service is off by default. -->
  <NetcdfSubsetService>
    <allow>true</allow>
    <scour>10 min</scour>
    <maxAge>-1 min</maxAge>
  </NetcdfSubsetService>

and set the Aggregation to always use the global attributes of the first file:

  <Aggregation>                                                                                                                                                               
    <typicalDataset>first</typicalDataset>                                
  </Aggregation>

This shows the documentation for the options available in threddsConfig.xml and this shows the actual threddsConfig.xml used in the operational Unidata TDS. As a side note, you can see the current development version of TDS in action here.

Deploy ncWMS

ncWMS is a Web Map Service specialed tailored to serve images/maps reading data from NetCDF files. THREDDS already has a internal version of ncWMS, but installing a standalone version alongside offers some advantages:

in THREDDS each individual dataset has it's own visualization page (Godiva2) where the variables can be analyzed, but comparing different datasets is difficult as each dataset has to be open in different webpage. In a standalone ncWMS installation over Tomcat, the app can be configured to show all the datasets in a single page, making comparisons between datasets much easier.
THREDDS has a earlier implementation of ncWMS (version 1.x) than the one available as standalone (version 2.x).
it is easier to make small changes in the visualization (e.g. basemap, color pallets) in the standalone version.

Download the ncWMS2 war file from Github. The lastest version compatilble with Java8/Tomcat8 is v2.4.2 (see warning above). Make a copy of the file following Tomcat naming conventions. If Tomcat is running, the war file will be automatically unpacked.

cp ncWMS2.war /usr/local/tds/tomcat/webapps/ncWMS2##2.4.2.war

Go to http://localhost:8080/ncWMS2/Godiva3.html to check if ncWMS is up and running. The standard installation comes with no datasets.

You can add new datasets using the "Admin interface" in http://localhost:8080/ncWMS2/ . This interface allows the user to apply some definitions by dataset and variable (e.g. name, color range).

To change global app configurations, like what is the default color palette used or where the new styles files should be located, the user has to change the file /usr/local/tds/tomcat/webapps/ncWMS2##2.4.2/WEB-INF/web.xml. To change the default color palette to a "rainbow" type palette:

    <context-param>
        <!-- This specifies the default palette to use (i.e. the palette returned by the string "default"). It can be a predefined palette or a string of the form: 0x[AA]RRGGBB,0x[AA]RRGGBB,0x[AA]RRGGBB,... -->
        <param-name>defaultPalette</param-name>
        <!-- <param-value>seq-BuYl</param-value> -->
        <param-value>x-Occam</param-value>
    </context-param>

By default, all the user configuration files are stored in $HOME/.ncWMS2. New color palettes can be created in $HOME/.ncWMS2/.palettes and new plot styles in $HOME/.ncWMS2/.styles. This same folder holds the godiva3.properties file where the user can add extra base or overlay layers in the Godiva3 map. Within this file the user can also change the size of the map from the default (mapHeight=600, mapWidth=750) to a size more fitting a widescreen monitor (e.g. mapHeight=730, mapWidth=1180). If mapHeight or mapWidth are greater than 1024 pixels, you also need to change the maximum allowed width and height in the $HOME/.ncWMS2/config.xml to something like:

        <maxImageWidth>2048</maxImageWidth>
        <maxImageHeight>2048</maxImageHeight>

Add new basemaps and overlay layers

The user can add new basemaps and auxiliary overlay layers following the instructions in $HOME/.ncWMS/godiva3.properties. Bellow a example adding two new baselayers based on Open Street Map. The baselayers use OSM data but are made available as a WMS by the good people at terrestris. The overlay layer is useful to show places names when dealing with atmospheric data that covers the land.

# Color Basemap by Open Street Map provided by https://www.terrestris.de
osmcURL=https://ows.terrestris.de/osm/service?
osmcTitle=OpenStreetMap-terrestris-color
osmcLayers=OSM-WMS
osmcProjection=EPSG:4326
osmcVersion=1.1.1
osmcFormat=image/png
osmcOnByDefault=true
osmcIsOverlay=false

# Gray Basemap by Open Street Map provided by https://www.terrestris.de
osmgURL=https://ows.terrestris.de/osm-gray/service?
osmgTitle=OpenStreetMap-terrestris-gray
osmgLayers=OSM-WMS
osmgProjection=EPSG:4326
osmgVersion=1.1.1
osmgFormat=image/png
osmgOnByDefault=false
osmgIsOverlay=false

# Overlay with places names by Open Street Map provided by https://www.terrestris.de
osmoURL=https://ows.terrestris.de/osm/service?
osmoTitle=OpenStreetMap-terrestris-overlay
osmoLayers=OSM-Overlay-WMS
osmoProjection=EPSG:4326
osmoVersion=1.1.1
osmoFormat=image/png
osmoOnByDefault=false
osmoIsOverlay=true

Color palettes

New color palette files must have the .pal extension and one color per line in hex format. You can get a palette from a site like ColorBrewer or build your own from rbg colors. To convert rgb values to hex in python:

def rgb2hex(r, g, b, alpha=100):

    def clamp(x):
        return max(0, min(x, 255))

    return "#{:02x}{:02x}{:02x}{:02x}".format(
        clamp(int(round(255 * alpha/100))), clamp(r), clamp(g), clamp(b))

Palettes can be in #rrbbgg or #aarrbbgg where aa stands for the alpha (opacity) channel. If omitted the opacity is 100%, e.g.:

#ffffff
#ffffff
#ffffff
#ffffe5
#fff7bc
#fee391
#fec44f
#fe9929
#ec7014
#cc4c02
#993404
#662506

Adding the alpha channel is specially useful to make the lower bound of a scalar field transparent, so that regions with lower values don't stand out too much. Bellow the same palette, but with the first three levels in different levels of opacity (in hex 33=20%, 66=40%, 99=%60) and all the other levels with full (in hex FF=100%) opacity. The blue that shows comes from the background map.

#33ffffff
#66ffffff
#99ffffff
#FFffffe5
#FFfff7bc
#FFfee391
#FFfec44f
#FFfe9929
#FFec7014
#FFcc4c02
#FF993404
#FF662506

Styles

Below a example showing a new style combining colormap and contours. If inserted in the file $HOME/.ncWMS2/.styles/scalar-contour.xml the new style will appear with the name scalar-contour in the drop down list right of the plot.

<?xml version="1.0" encoding="ISO-8859-1"?>
<StyledLayerDescriptor version="1.1.0" xsi:schemaLocation="http://www.opengis.net/sld
StyledLayerDescriptor.xsd" xmlns="http://www.opengis.net/sld" xmlns:ogc="http://www.opengis.net/ogc"
xmlns:se="http://www.opengis.net/se" xmlns:xlink="http://www.w3.org/1999/xlink"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:resc="http://www.resc.reading.ac.uk">

  <NamedLayer>
    <se:Name>$layerName</se:Name>
    <UserStyle>
      <se:CoverageStyle>
        <se:Rule>
          <se:RasterSymbolizer>
            <se:Opacity>$opacity</se:Opacity>
            <se:ColorMap>
              <resc:Segment fallbackValue="$bgColor">
                <se:LookupValue>Rasterdata</se:LookupValue>
                <resc:BelowMinValue>$belowMinColor</resc:BelowMinValue>
                <resc:ValueList>
                  <se:Name>$paletteName</se:Name>
                </resc:ValueList>
                <resc:AboveMaxValue>$aboveMaxColor</resc:AboveMaxValue>
                <resc:Range>
                  <resc:Minimum>$scaleMin</resc:Minimum>
                  <resc:Maximum>$scaleMax</resc:Maximum>
                  <resc:Spacing>$logarithmic</resc:Spacing>
                </resc:Range>
                <resc:NumberOfSegments>$numColorBands</resc:NumberOfSegments>
              </resc:Segment>
            </se:ColorMap>
          </se:RasterSymbolizer>
        </se:Rule>
      </se:CoverageStyle>
    </UserStyle>
  </NamedLayer>

  <NamedLayer>
    <se:Name>$layerName</se:Name>
    <UserStyle>
      <se:CoverageStyle>
        <se:Rule>
          <resc:ContourSymbolizer>
            <se:Opacity>$opacity</se:Opacity>
            <resc:NumberOfContours>5</resc:NumberOfContours>
            <resc:ContourLineColour>black</resc:ContourLineColour>
            <resc:ContourLineWidth>1</resc:ContourLineWidth>
            <resc:ContourLineStyle>SOLID</resc:ContourLineStyle>
            <resc:LabelEnabled>true</resc:LabelEnabled>
            <resc:Range>
              <resc:Minimum>$scaleMin</resc:Minimum>
              <resc:Maximum>$scaleMax</resc:Maximum>
              <resc:Spacing>$logarithmic</resc:Spacing>
            </resc:Range>
            <resc:AutoRangeEnabled>false</resc:AutoRangeEnabled>
          </resc:ContourSymbolizer>
        </se:Rule>
      </se:CoverageStyle>
    </UserStyle>
  </NamedLayer>

</StyledLayerDescriptor>

ncWMS2 even has a tool to test new styles in http://localhost:8080/ncWMS2/sldtest.html. Several examples and references can be found in:

Deploy ERDDAP

@todo

Deploy GeoServer

@todo

marceloandrioni / configure_tomcat_stack Goto Github PK

configure_tomcat_stack's Introduction

Installing instructions for Tomcat, THREDDS, ncWMS, ERDDAP and GeoServer

Install Tomcat

Deploy THREDDS

Deploy ncWMS

Add new basemaps and overlay layers

Color palettes

Styles

Deploy ERDDAP

Deploy GeoServer

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