spatial-service

####See also: Integration Test

This component provides the bulk of the spatial web services for the Atlas' spatial portal that make use of spatial data in Shape or Grid format.

It includes:

• A management console ingestion of Shape and Grid files
• Flexible field mapping capability allowing grouping of multipolygons by different fields provided in the DBF
• Maxent modelling
• Tabulation
• Species polygon distributions
• Intersection services
• Track...

Architecture

• Grails 4 web application ran in the tomcat 9 or as standalone executable jar
• Open JDK 8
• PostGIS database (9.6 or above)
• Geoserver

Setup environment

Modify configurations in

/data/spatial-service/config/spatial-service-config.yml

The dependent services point to other production servers by default

The default production url is https://spatial.ala.org.au/ws

The default develop url is http://devt.ala.org.au:8080/ws

Minimum configurations in external config file:

    api_key: xxxxxxxxx-xxxx-xxxx-xxxx-xxxxxxxxxxxxx
    google:
        apikey: xxxxxxxxxxxxxx

Set the following configurations if deployed on servers, instead of development/prod environment

grails.serverURL: https://spatial-test.ala.org.au/ws
#grails.server.context: /ws

google:
    apikey: "xxxxxxxxxxxx"

api_key: xxxxxxxxxxxxx
spatialHubUrl: https://spatial-test.ala.org.au/

geoserver:
    url: 'https://spatial-test.ala.org.au/geoserver'
    username: 'admin'
    password: 'xxxxxxxx'

dataSource:
    url: 'jdbc:postgresql://localhost/layersdb'
    username: postgres
    password: xxxxxxxxx

batch_sampling_passwords: ""

# au.org.ala.spatial.process config
spatialService.url: "https://spatial-test.ala.org.au/ws"
shp2pgsql.path: "/usr/bin/shp2pgsql"
gdal.dir: "/usr/bin/"

slaveKey: "xxxxxxxxxxxxxx"
serviceKey: "xxxxxxxxxxxxxx"

layers_store.GEONETWORK_URL: 'https://spatial-test.ala.org.au/geonetwork'

Installation

There are ansible scripts for this applications (and other ALA tools) in the ala-install project. The ansible playbook for the spatial-service is here

You can also run this application locally by following the instructions on its wiki page.

Running it locally

Here are some instructions for running spatial-service locally for development. The assumption here is that you are trying to run spatial-service in an IDE such as IntelliJ

There is a docker-compose YML file under docker folder that can be used to run postgres & geoserver locally for local development purposes. To use, run:

cd ./docker
docker-compose up -d

And to shutdown:

docker-compose -f kill

Geoserver: http://localhost:8079/geoserver

Postgis is under standard 5432 port

There is also a requirement for have GDAL installed locally. This can be done with HomeBrew on Mac OSX

brew install gdal

Note: On Mac OSX, GGDAL tools are installed here /usr/local/bin/ or /opt/homebrew/Cellar/gdal/xxxx-version. You can use the gdal.dir configuration property to specify the location if different.

Configure geoserver with the required postgis layers using spatial-service:

http://localhost:8080/tasks/create?name=InitGeoserver&input=%7B%22postgresqlPath%22:%22postgis%22%7D

Disable authentication when running locally by creating the configuration file /data/spatial-service/config/spatial-service-config.properties with the contents:

security.oidc.enabled=false

PDF area report

Override output by putting edited files from /src/main/resources/areareport/ into /data/spatial-service/config/.

• *.html Edit for internationalization.
• AreaReport.css Edit for style changes.
• header.jpg Edit the default front page header image.
• AreaReportDetails.json Definition of pages and page content in the area report.

The struture of AreaReportDetails.json

[
 {
  type: pageType,
  pageType attributes,
  items: [
   {
    type: itemType,
    itemType attributes
   }
  ]
 }  
]

Pages

pageType	attribute	attribute description
title	image	relative path to the image file
	counts	array of items displayed in the style of a dashboard
general	items	array of items
	subpages	the number of subpages. Each page is identical except for the fq used.
	fqs	array of biocache-service fq terms. One fq is required for each subpage.
	{itemAttribute}{itemNumber}	array of item attribute values.
file	file	relative path to the html file

Items

itemType	attribute	attribute description
table	table	one of: species, expertdistributions, checklists, journalmap, occurrences, tabulation
	value	mandatory for table=tabulation. The field for tabulation, e.g. cl22
	endemic	optional for table=species. true or false (default=false)
text	text	HTML text to display
figure
map	buffer	approximate buffer around the selected area as a % of the area width
	layer	optional layer to add. Use layer short name.
	legendUrl	optional URL to geoserver GetLegendGraphic request
	fq	optional fq
LABELS	type	one of: species, expertdistributions, checklists, journalmap, occurrences
	label	HTML text format. e.g. "label value <b>%s</b>"
	name	mandatory for type=attribute, area attribute: area_km, name
	field	mandatory for type=species, count of unique values in a SOLR field. e.g. names_and_lsid
	endemic	optional for type=species, use endemic species count. true or false (default=false)
	fq	optional for type=species OR type=occurrences

Integration Test

Description

The build is setup to work with Firefox and Chrome.

Have a look at the build.gradle and the src/test/resources/GebConfig.groovy file.

From line 200 in build.gradle, you will find how we pass different test servers and authentication into tests.

Usage

Run with Firefox (default):

./gradlew :integrationTest -Dusername=xxxx -Dpassword=xxxxx

Or store authentication into file:

/data/spatial-service/test/default.properties

then run:

./gradlew :integrationTest

See How to pass authentication in

run with Chrome:

./gradlew :integrationTest -Ddriver=chrome

Chrome driver > 89 is not available for webdirver Use npm to set the chrome driver version and reference the lib path from node_modules.

Add "chromedriver": "89.0.0" to package.json

Run npm install

In ./gebConfig.groovy

if (!System.getProperty("webdriver.chrome.driver")) {
    System.setProperty("webdriver.chrome.driver", "node_modules/chromedriver/bin/chromedriver")
} 

Test other servers:

./gradlew :integrationTest -DbaseUrl=http://spatial-test.ala.org.au/ws

Authentication

Authentication info can be passed through with -Dusername and -Dpassword

/gradlew :integrationTest -Dusername=xxxx -Dpassword=xxxxx

Or stored in a config file. The default config file is located in

/data/spatial-service/test/default.properties

username="[email protected]"
password="xxxxx"

We can change the config file with -DconfigFile

/gradlew :integrationTest -DconfigFile="myconfig.properties"