#IOOS #SOS #OWSLib #MMI Access the AOOS SOS GetCapabilities, issue a sample DescribeSensor request, then parse parts of the response. Includes examples of testing the validity of controlled vocabulary terms vs MMI (using the approach described on the IPython notebook http://nbviewer.ipython.org/6514804). This SOS test complements the one for Get…

AOOS_SOS_SensorML_owslib_AlaskaNDBCBuoy_1.ipynb

{
 "metadata": {
  "name": "AOOS_SOS_SensorML_owslib_AlaskaNDBCBuoy_1"
 },
 "nbformat": 3,
 "nbformat_minor": 0,
 "worksheets": [
  {
   "cells": [
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "# DescribeSensor/SensorML client access tests for IOOS SOS Milestone 1, using the AOOS 52North SOS endpoint\n\nAccess the AOOS SOS GetCapabilities, issue a sample DescribeSensor request, then parse parts of the response. Includes examples of testing the validity of controlled vocabulary terms vs MMI (using the approach [described on this IPython notebook](http://nbviewer.ipython.org/6514804)). This SOS test [complements the one for GetObservations](http://nbviewer.ipython.org/7240742)). 2013/11/4"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "from datetime import datetime\nimport urllib2\nimport json\nimport requests\nfrom owslib.sos import SensorObservationService\nfrom owslib.swe.sensor.sml import SensorML, EventMetadata",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 60
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "# AOOS SOS Tests (GetCap extracted from the AOOS 52N SOS Test Client)\naoossos_gc_url = \"http://sos.aoos.org/sos/sos/kvp?service=SOS&request=GetCapabilities&AcceptVersions=1.0.0\"\naoosxml = urllib2.urlopen(aoossos_gc_url).read()\naoosgc = SensorObservationService(None, xml=aoosxml)",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 61
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "# find wmo 46083 ndbc buoy offering, from the offerings list\nndbcfind = [offering for offering in aoosgc.offerings if '46083' in offering.name.lower()]\naoosoff1 = ndbcfind[0]\nprint aoosoff1.id, aoosoff1.name, aoosoff1.description\nprint aoosoff1.procedures",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "urn_ioos_station_wmo_46083 urn:ioos:station:wmo:46083 None\n['urn:ioos:station:wmo:46083']\n"
      }
     ],
     "prompt_number": 62
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "### Interactions specific to DescribeSensor start here"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "descsen = aoosgc.get_operation_by_name('describesensor')\ndescsen.parameters",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 63,
       "text": "{'outputFormat': {'values': ['text/xml; subtype=\"sensorML/1.0.1\"',\n   'text/xml; subtype=\"sensorML/1.0.1/profiles/ioos_sos/1.0\"']}}"
      }
     ],
     "prompt_number": 63
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "# Set parameters to be used in the DescribeSensor request\noFrmt = 'text/xml;subtype=\"sensorML/1.0.1/profiles/ioos_sos/1.0\"'\nprocedure = aoosoff1.procedures[0]",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 64
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "response = aoosgc.describe_sensor(procedure=procedure, outputFormat=oFrmt)\nprint type(response), len(response)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "<type 'str'> 32302\n"
      }
     ],
     "prompt_number": 65
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "aoosoff1_sml_root = SensorML(response)",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 66
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "To see the structure of the IOOS SOS Milestone 1 SensorML response, see the reference implementation XML at http://code.google.com/p/ioostech/source/browse/trunk/templates/Milestone1.0/SML-DescribeSensor-Station.xml"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "print type(aoosoff1_sml_root), type(aoosoff1_sml_root.systems), len(aoosoff1_sml_root.systems)\naoosoff1_sml = aoosoff1_sml_root.systems[0]\nprint type(aoosoff1_sml)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "<class 'owslib.swe.sensor.sml.SensorML'> <type 'list'> 1\n<class 'owslib.swe.sensor.sml.SystemMetadata'>\n"
      }
     ],
     "prompt_number": 67
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "print aoosoff1_sml.id, \" || \", aoosoff1_sml.description\nprint \"*** IDENTIFIERS:\\n\", aoosoff1_sml.identifiers\nprint \"*** CLASSIFIERS:\\n\", aoosoff1_sml.classifiers\nprint \"*** CONTACTS:\\n\", aoosoff1_sml.contacts",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "None  ||  Fairweather Grounds 92NM Southeast of Yakutat, AK\n*** IDENTIFIERS:\n{'stationID': <owslib.swe.sensor.sml.IdentifierMetadata object at 0x333b2d0>, 'shortName': <owslib.swe.sensor.sml.IdentifierMetadata object at 0x333b250>, 'uniqueID': <owslib.swe.sensor.sml.IdentifierMetadata object at 0x333b3d0>, 'longName': <owslib.swe.sensor.sml.IdentifierMetadata object at 0x333b350>}\n*** CLASSIFIERS:\n{'operatorSector': <owslib.swe.sensor.sml.ClassifierMetadata object at 0x333b550>, 'publisher': <owslib.swe.sensor.sml.ClassifierMetadata object at 0x333b4d0>, 'parentNetwork': <owslib.swe.sensor.sml.ClassifierMetadata object at 0x333b610>, 'platformType': <owslib.swe.sensor.sml.ClassifierMetadata object at 0x333b510>, 'sponsor': <owslib.swe.sensor.sml.ClassifierMetadata object at 0x333b5d0>}\n*** CONTACTS:\n{None: <owslib.swe.sensor.sml.ContactMetadata object at 0x333b310>}\n"
      }
     ],
     "prompt_number": 68
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "Explore SensorML Identifiers"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "aoosoff1_sml.identifiers.keys()",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 69,
       "text": "['stationID', 'shortName', 'uniqueID', 'longName']"
      }
     ],
     "prompt_number": 69
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "print \"stationID identifier information:\"\nprint \"   OWSLib object type:  \", type(aoosoff1_sml.identifiers['stationID'])\nprint \"   name: \", aoosoff1_sml.identifiers['stationID'].name\nprint \"   definition: \", aoosoff1_sml.identifiers['stationID'].definition\nprint \"   value: \", aoosoff1_sml.identifiers['stationID'].value",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "stationID identifier information:\n   OWSLib object type:   <class 'owslib.swe.sensor.sml.IdentifierMetadata'>\n   name:  stationID\n   definition:  http://mmisw.org/ont/ioos/definition/stationID\n   value:  urn:ioos:station:wmo:46083\n"
      }
     ],
     "prompt_number": 70
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "Explore SensorML Classifiers"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "aoosoff1_sml.classifiers.keys()",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "pyout",
       "prompt_number": 71,
       "text": "['operatorSector', 'publisher', 'parentNetwork', 'platformType', 'sponsor']"
      }
     ],
     "prompt_number": 71
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "def print_classifier_info(sml, classifier_name):\n    classifier = sml.classifiers[classifier_name]\n    print \"%s classifier information:\" % classifier.name\n    print \"   OWSLib object type:  \", type(classifier)\n    print \"   codespace: \", classifier.codespace\n    print \"   name: \", classifier.name\n    print \"   definition: \", classifier.definition\n    print \"   value: \", classifier.value\n    return classifier",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 72
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "platformType = print_classifier_info(aoosoff1_sml, 'platformType')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "platformType classifier information:\n   OWSLib object type:   <class 'owslib.swe.sensor.sml.ClassifierMetadata'>\n   codespace:  http://mmisw.org/ont/ioos/platform\n   name:  platformType\n   definition:  http://mmisw.org/ont/ioos/definition/platformType\n   value:  FIXED MET STATION\n"
      }
     ],
     "prompt_number": 73
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "publisher = print_classifier_info(aoosoff1_sml, 'publisher')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "publisher classifier information:\n   OWSLib object type:   <class 'owslib.swe.sensor.sml.ClassifierMetadata'>\n   codespace:  http://mmisw.org/ont/ioos/organization\n   name:  publisher\n   definition:  http://mmisw.org/ont/ioos/definition/publisher\n   value:  NDBC\n"
      }
     ],
     "prompt_number": 74
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "operatorSector = print_classifier_info(aoosoff1_sml, 'operatorSector')",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "operatorSector classifier information:\n   OWSLib object type:   <class 'owslib.swe.sensor.sml.ClassifierMetadata'>\n   codespace:  http://mmisw.org/ont/ioos/sector\n   name:  operatorSector\n   definition:  http://mmisw.org/ont/ioos/definition/operatorSector\n   value:  gov_federal\n"
      }
     ],
     "prompt_number": 75
    },
    {
     "cell_type": "markdown",
     "metadata": {},
     "source": "## Test the validity of classifiers against MMI vocabularies\nThe MMI term testing function is taken (and illustrated) from my notebook at http://nbviewer.ipython.org/6514804"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "def get_term_ontmeta_jsonurl(termjsonurl):\n    \"\"\" \n    Pass a complete URL for the json response corresponding to an ontology term.\n    It can be from any ontology engine as long as the json is similar to MMI's.\n    eg: 'http://mmisw.org/ont/cf/parameter/wind_speed.json'\n    Parses the json response to return a regularized dictionary as well as the\n    raw json response loaded as a dict.\n    \"\"\"\n    \n    # This is probably not applicable to other ontology repos beyond MMI...\n    param_jsonstr = requests.get(termjsonurl).content\n    # Validate the term URL\n    if param_jsonstr == '[]':  # term URL does not exist; term is invalid\n        return (None, None)\n    \n    #param_jsonstr = urllib2.urlopen(termjsonurl).read()    \n    param_json = json.loads(param_jsonstr)\n    param_extract_all_dct = dict([(param_el[1].split('/')[-1][:-1], param_el[2]) \n                                  for param_el in param_json])\n    \n    # Add handling of more IOOS vocabularies, as needed\n    if 'cf/parameter' in termjsonurl:\n        param_extract_dct = {'vocabulary': 'cf/parameter',\n                             'definition': param_extract_all_dct['core#definition'],\n                             'units':      param_extract_all_dct['canonical_units'],\n                             'units_type': 'canonical units', \n                            }\n    elif 'ioos/parameter' in termjsonurl:\n        param_extract_dct = {'vocabulary': 'ioos/parameter',\n                             'definition': param_extract_all_dct['Definition'],\n                             'units':      param_extract_all_dct['Units'], \n                             'units_type': 'example or common units', \n                            }\n    else:\n        param_extract_dct = param_extract_all_dct\n    \n    return (param_extract_all_dct, param_extract_dct)",
     "language": "python",
     "metadata": {},
     "outputs": [],
     "prompt_number": 76
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "# Test for a term known to be valid\n# Note that get_term_ontmeta_jsonurl() currently is tuned to do special extra handling\n# only with \"parameter\" (observed properties) terms\nterm_url_json = operatorSector.codespace + '/' + operatorSector.value + '.json' \nprint term_url_json\nget_term_ontmeta_jsonurl(term_url_json)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "http://mmisw.org/ont/ioos/sector/gov_federal.json\n"
      },
      {
       "output_type": "pyout",
       "prompt_number": 77,
       "text": "({u'22-rdf-syntax-ns#type': u'<http://mmisw.org/ont/ioos/sector/Organization>',\n  u'description': u'\"Government-Federal\"',\n  u'name': u'\"Government-Federal\"',\n  u'rdf-schema#label': u'\"gov_federal\"',\n  u'term': u'\"gov_federal\"'},\n {u'22-rdf-syntax-ns#type': u'<http://mmisw.org/ont/ioos/sector/Organization>',\n  u'description': u'\"Government-Federal\"',\n  u'name': u'\"Government-Federal\"',\n  u'rdf-schema#label': u'\"gov_federal\"',\n  u'term': u'\"gov_federal\"'})"
      }
     ],
     "prompt_number": 77
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "# Test for a term known to be invalid (doesn't exist on MMI vocabulary)\nterm_url_json = platformType.codespace + '/' + platformType.value + '.json' \nprint term_url_json\nget_term_ontmeta_jsonurl(term_url_json)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "http://mmisw.org/ont/ioos/platform/FIXED MET STATION.json\n"
      },
      {
       "output_type": "pyout",
       "prompt_number": 78,
       "text": "(None, None)"
      }
     ],
     "prompt_number": 78
    },
    {
     "cell_type": "heading",
     "level": 3,
     "metadata": {},
     "source": "Explore SensorML components (including 'parameters')"
    },
    {
     "cell_type": "code",
     "collapsed": false,
     "input": "# Looks like the sensorml doesn't have any \"component\" entries \n# (sensors / observed properties / parameters) yet ...\nprint type(aoosoff1_sml.components), len(aoosoff1_sml.components)",
     "language": "python",
     "metadata": {},
     "outputs": [
      {
       "output_type": "stream",
       "stream": "stdout",
       "text": "<type 'dict'> 0\n"
      }
     ],
     "prompt_number": 79
    }
   ],
   "metadata": {}
  }
 ]
}