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oznome-demo's Introduction

oznome-demo

Code for oznome demonstrator

Information

Grails version required: 2.3.11

To run it locally unzip oznome-demo-local-config.zip in your root folder.

Custom events for Region client UI

  • groupSelected: triggered when a species group is selected. It includes the following data:
{
  group: '...'
}
  • subgroupSelected: triggered when a species subgroup is selected. It includes the following data:
{
  group: '...',
  subgroup: '...'
}
  • speciesSelected: triggered when a species is selected. It includes the following data:
{
  group: '...',
  subgroup: '...',
  speciesName: '...'
}

All these event are associted to the document element. Eg:

$(document).on('groupSelected', function(e, data) {
    console.log(data.group);
    ...
});

Patent search

Requires MongoDB to be installed

Service: POST to [url_base]/patents

Sample request

["Acacia sutherlandii", "Acacia melanoxylon"]

Sample response:

{
  "Acacia sutherlandii": [],
  "Acacia melanoxylon": [
    {
      "applicationNumber": "2015900524",
      "title": "Table tennis racket, 100% Australian made using Tasmanian Blackwood (Acacia Melanoxylon) wood for the blade with balsa handle",
      "applicants": "McFadden, Ronald Edward MR",
      "inventors": "McFadden, Ronald Edward",
      "filingDate": "2015-01-26",
      "filingStatus": "FILED"
    },
    {
      "applicationNumber": "2015100081",
      "title": "Table tennis racket, 100% Australian made using Tasmanian Blackwood (Acacia Melanoxylon) wood for the blade with balsa handle",
      "applicants": "McFadden, Ronald Edward MR",
      "inventors": "McFadden, Ronald Edward",
      "filingDate": "2015-01-26",
      "filingStatus": "CONVERTED"
    }
  ]
}

Species/Patent Search

Service: GET to [url_base]/[region_type]/[region_name]/patents Optional parameter: summary=true

Example query: http://localhost:8080/oznome-demo/Indigenous%20protected%20areas/Deen%20Maar/patents Example response

{

    "count": 161,
    "species": [
      {
        "name": "Mus musculus",
        "lsid": "urn:lsid:biodiversity.org.au:afd.taxon:107696b5-063c-4c09-a015-6edfdb6f4d52",
        "commonName": "House Mouse",
        "occurrenceCount": 1,
        "patentCount": 45,
        "patents": [
           {
              "applicationNumber": "2013202235",
              "title": "Use of Hsp70 as a regulator of enzymatic activity",
               "applicants": "Orphazyme ApS",
               "inventors": "Jensen, Thomas Kirkegaard; Jaattela, Marja Helena",
               "filingDate": "2013-04-02",
               "filingStatus": "ACCEPTED"

           },
           ...
        ]
    },
    ...
    {
       "name": "Acanthiza (Acanthiza) pusilla",
       "lsid": "urn:lsid:biodiversity.org.au:afd.taxon:7c747b85-9ef1-4a2c-839d-0efd7e794af4",
       "commonName": "Brown Thornbill",
       "occurrenceCount": 1,
       "patentCount": 0,
       "patents": [ ]

    },
    ...
}

Example query: http://localhost:8080/oznome-demo/Indigenous%20protected%20areas/Deen%20Maar/patents?summary=true Example response

{

    "count": 161,
    "species": [
      {
        "name": "Mus musculus",
        "lsid": "urn:lsid:biodiversity.org.au:afd.taxon:107696b5-063c-4c09-a015-6edfdb6f4d52",
        "commonName": "House Mouse",
        "occurrenceCount": 1,
        "patentCount": 45
    },
    ...
    {
       "name": "Acanthiza (Acanthiza) pusilla",
       "lsid": "urn:lsid:biodiversity.org.au:afd.taxon:7c747b85-9ef1-4a2c-839d-0efd7e794af4",
       "commonName": "Brown Thornbill",
       "occurrenceCount": 1,
       "patentCount": 0,
    },
    ...
}

oznome-demo's People

Contributors

ansell avatar aruizca avatar charvolant avatar m-r-c avatar sadeghim avatar temi avatar

Watchers

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oznome-demo's Issues

Loading full species list generates socket exception

Too many open files. Stacktrace follows:
java.net.SocketException: Too many open files
at java.net.Socket.createImpl(Socket.java:460)
at java.net.Socket.connect(Socket.java:587)
at com.mongodb.DBPort.ensureOpen(DBPort.java:255)
at com.mongodb.DBPort.(DBPort.java:89)
at com.mongodb.DBPortFactory.create(DBPortFactory.java:28)
at com.mongodb.PooledConnectionProvider$ConnectionItemFactory.create(PooledConnectionProvider.java:186)
at com.mongodb.PooledConnectionProvider$ConnectionItemFactory.create(PooledConnectionProvider.java:183)
at com.mongodb.ConcurrentPool.createNewAndReleasePermitIfFailure(ConcurrentPool.java:150)
at com.mongodb.ConcurrentPool.get(ConcurrentPool.java:118)
at com.mongodb.PooledConnectionProvider.get(PooledConnectionProvider.java:75)
at com.mongodb.DefaultServer.getConnection(DefaultServer.java:61)
at com.mongodb.BaseCluster$WrappedServer.getConnection(BaseCluster.java:248)
at com.mongodb.DBTCPConnector$MyPort.getConnection(DBTCPConnector.java:503)
at com.mongodb.DBTCPConnector$MyPort.get(DBTCPConnector.java:451)
at com.mongodb.DBTCPConnector.getPrimaryPort(DBTCPConnector.java:409)
at com.mongodb.DBCollectionImpl.insert(DBCollectionImpl.java:182)
at com.mongodb.DBCollectionImpl.insert(DBCollectionImpl.java:165)
at com.mongodb.DBCollection.insert(DBCollection.java:93)
at com.mongodb.DBCollection.insert(DBCollection.java:78)
at com.mongodb.DBCollection.insert(DBCollection.java:120)
at com.gmongo.internal.Patcher._invoke(Patcher.groovy:49)
at com.gmongo.internal.Patcher$__patchInternal_closure1.doCall(Patcher.groovy:38)
at au.org.ala.regions.PatentService.fetch(PatentService.groovy:64)
at au.org.ala.regions.PatentService$_fetchAll_closure1_closure3.doCall(PatentService.groovy:29)
at groovyx.gpars.pa.GParsPoolUtilHelper$_eachParallelPA_closure8.doCall(GParsPoolUtilHelper.groovy:189)
at groovyx.gpars.extra166y.AbstractParallelAnyArray$OUPap.leafApply(AbstractParallelAnyArray.java:640)
at groovyx.gpars.extra166y.PAS$FJOApply.atLeaf(PAS.java:147)
at groovyx.gpars.extra166y.PAS$FJBase.internalCompute(PAS.java:118)
at groovyx.gpars.extra166y.PAS$FJBase.compute(PAS.java:106)
at jsr166y.RecursiveAction.exec(RecursiveAction.java:148)
at jsr166y.ForkJoinTask.doExec(ForkJoinTask.java:305)
at jsr166y.ForkJoinWorkerThread.execTask(ForkJoinWorkerThread.java:575)
at jsr166y.ForkJoinPool.scan(ForkJoinPool.java:755)
at jsr166y.ForkJoinPool.work(ForkJoinPool.java:617)
at jsr166y.ForkJoinWorkerThread.run(ForkJoinWorkerThread.java:369)
2015-06-03 09:27:05,782 ERROR [GrailsExceptionResolver] Unable to render errors view: Error initializing GroovyPageView
java.lang.RuntimeException: Error initializing GroovyPageView
at com.nerderg.ajaxanywhere.AAFilter.doFilter(AAFilter.java:56)
at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
at org.jasig.cas.client.session.SingleSignOutFilter.doFilter(SingleSignOutFilter.java:65)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
Caused by: org.codehaus.groovy.grails.web.pages.exceptions.GroovyPagesException: I/O error reading stream for resource [URL [file:/home/pal155/src/oznome-demo/grails-app/views/error.gsp]]: /home/pal155/src/oznome-demo/grails-app/views/error.gsp (Too many open files)
... 8 more
Caused by: java.io.FileNotFoundException: /home/pal155/src/oznome-demo/grails-app/views/error.gsp (Too many open files)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
... 8 more
2015-06-03 09:27:05,802 ERROR [[grails]] Servlet.service() for servlet grails threw exception
java.io.FileNotFoundException: /home/pal155/src/oznome-demo/grails-app/views/error.gsp (Too many open files)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at com.nerderg.ajaxanywhere.AAFilter.doFilter(AAFilter.java:56)
at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
at org.jasig.cas.client.session.SingleSignOutFilter.doFilter(SingleSignOutFilter.java:65)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)
2015-06-03 09:27:05,803 ERROR [[default]] Servlet.service() for servlet [default] in context with path [/oznome-demo] threw exception [Request processing failed; nested exception is org.codehaus.groovy.grails.exceptions.GrailsRuntimeException: java.lang.RuntimeException: Error initializing GroovyPageView] with root cause
java.io.FileNotFoundException: /home/pal155/src/oznome-demo/grails-app/views/error.gsp (Too many open files)
at java.io.FileInputStream.open(FileInputStream.java:195)
at java.io.FileInputStream.(FileInputStream.java:138)
at java.io.FileInputStream.(FileInputStream.java:93)
at com.nerderg.ajaxanywhere.AAFilter.doFilter(AAFilter.java:56)
at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
at au.org.ala.cas.client.UriFilter.doFilter(UriFilter.java:200)
at org.jasig.cas.client.session.SingleSignOutFilter.doFilter(SingleSignOutFilter.java:65)
at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1142)
at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:617)
at java.lang.Thread.run(Thread.java:745)

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