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https://github.com/atlasoflivingaustralia/spatial-service

Spatial web services and layer administration console
https://github.com/atlasoflivingaustralia/spatial-service

ala-product-spatial ala-systems

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Spatial web services and layer administration console

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README 

        
### [![Build Status](https://travis-ci.org/AtlasOfLivingAustralia/spatial-service.svg?branch=master)](https://travis-ci.org/AtlasOfLivingAustralia/spatial-service)



# spatial-service



####_See also:_  [Integration Test](#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 \%s\"

| | 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](#Authentication)



### 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"