IDigBio API v1 Examples: Difference between revisions

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=== Fetch a specific record based on iDigBio GUID ===
=== Three ways to fetch a specific record based on iDigBio GUID ===


The following three examples intend to illustrate the various methods for looking up a unique record in iDigBio and how the output may differ for the same record.
The following three examples intend to illustrate the various methods for looking up a unique record in iDigBio and how the output may differ for the same record.

Revision as of 16:37, 16 May 2014


This document is a list of examples for using the iDigBio API but may not be comprehensive. See IDigBio API for full documentation on the API including all of the available endpoints and parameters.

Viewing JSON Output

Most of the examples provided here will be shown using the curl command-line tool. Here are some of the more commonly used curl options (for descriptions and additional usage information, see the curl man page): 

$ man curl
...
       -s, --silent
       -i, --include
       -v, --verbose
       -X, --request <command>
       -d, --data <data>
...

A short JSON document is returned by the API when calling the GET method (curl's default) against the base URL: 

$ curl -s -i http://api.idigbio.org/
HTTP/1.1 200 OK
Content-Type: application/json
Content-Length: 108
Access-Control-Allow-Origin: *
Access-Control-Allow-Headers: Accept, Accept-Version, Content-Length, Content-MD5, Content-Type, Date, Api-Version, Response-Time
Access-Control-Allow-Methods: GET
Access-Control-Expose-Headers: Api-Version, Request-Id, Response-Time
Connection: Keep-Alive
Content-MD5: airVCXBxEpZm/Wl/DU6tXw==
Date: Fri, 09 May 2014 19:34:26 GMT
Server: restify
Request-Id: ee775220-d7b0-11e3-8828-37453f55c1c8
Response-Time: 2

{"v1":"http://api.idigbio.org/v1/","v0":"http://api.idigbio.org/v0/","check":"http://api.idigbio.org/check"}


It may be useful to format the output of the JSON document using a "pretty printing" feature of some kind. This will make it more readable by humans and also allow it to be more easily filtered using tools such as grep. Two common tools for this available on Unix/Linux are python's json.tool or the json_pp command-line Perl script (JSON::PP). These tools can receive input from a pipe in the normal Unix fashion to chain multiple commands together.

json.tool

$ curl -s http://api.idigbio.org/ | python -m json.tool
{
    "check": "http://api.idigbio.org/check",
    "v0": "http://api.idigbio.org/v0/",
    "v1": "http://api.idigbio.org/v1/"
}

json_pp

$ curl -s http://api.idigbio.org/ | json_pp
{
   "v1" : "http://api.idigbio.org/v1/",
   "check" : "http://api.idigbio.org/check",
   "v0" : "http://api.idigbio.org/v0/"
}

For best viewing of JSON results in a browser, one may wish to use the JSONView Extension for Chrome and Firefox.

JSONView Browser Extension

JSONView extension allows easier viewing in a web browser

simplejson

Some older systems may not include json_pp or python's json.tool. The python simplejson package may solve this problem. Older versions of python also may require a more complicated syntax to invoke the module from the command line. 

$ curl -s http://api.idigbio.org/ | python -c'from simplejson.tool import main; main()'
{
    "check": "http://api.idigbio.org/check", 
    "v0": "http://api.idigbio.org/v0/", 
    "v1": "http://api.idigbio.org/v1/"
}

Three ways to fetch a specific record based on iDigBio GUID

The following three examples intend to illustrate the various methods for looking up a unique record in iDigBio and how the output may differ for the same record.

The data returned by the Elasticsearch interface may differ from the raw API record, especially with regards to field names, since the Elasticsearch data has been normalized and indexed for consumption by the search portal.

For these three examples, consider the iDigBio specimen record identified by the following GUID: 

"idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430"

Use the API

The complete record that was provided to iDigBio is stored in the API and can be retrieved by referencing the iDigBio GUID ("idigbio:uuid") as the entity ID at the '/records/{ID}' endpoint.

The following command sends the query as an HTTP GET request: 

$ curl -s https://api.idigbio.org/v1/records/0cec43d8-9ad5-478a-bea1-397ab5cc4430 | json_pp
{
   "idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
   "idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
   "idigbio:links" : {
      "mediarecord" : [
         "http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
      ],
      "owner" : [
         "872733a2-67a3-4c54-aa76-862735a5f334"
      ],
      "recordset" : [
         "http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
      ]
   },
   "idigbio:version" : 1,
   "idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
   "idigbio:recordIds" : [
      "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
   ],
   "idigbio:dateModified" : "2014-04-20T23:11:09.437Z",
   "idigbio:data" : {
      "dwc:catalogNumber" : "ASU0000166",
      "dwc:basisOfRecord" : "PreservedSpecimen",
      "symbiotaverbatimScientificName" : "Abies",
      "dwc:collectionCode" : "Plants",
      "dwc:decimalLongitude" : "-105.859665870667",
      "dcterms:references" : "http://swbiodiversity.org/seinet/collections/individual/index.php?occid=784316",
      "dwc:scientificNameAuthorship" : "P. Mill.",
      "dwc:collectionID" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
      "dwc:minimumElevationInMeters" : "2316",
      "dwc:georeferenceSources" : "georef batch tool 2013-05-10",
      "dwc:georeferenceVerificationStatus" : "reviewed - high confidence",
      "dwc:occurrenceRemarks" : "Tree to 4 m;  occasional in N-facing barranca",
      "dwc:otherCatalogNumbers" : "153418",
      "dwc:rights" : "http://creativecommons.org/licenses/by-nc-sa/3.0/",
      "dwc:decimalLatitude" : "23.5821004818154",
      "dwc:day" : "14",
      "idigbio:recordId" : "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a",
      "dwc:locality" : "Ca. 1 mi N of Hwy 40 between Villa Union and Cd. Durango, and ca. 5 mi W of Durango state border.",
      "dwc:occurrenceID" : "784316",
      "dwc:year" : "1985",
      "dwc:recordedBy" : "T. F. Daniel; ",
      "dwc:family" : "Pinaceae",
      "dwc:scientificName" : "Abies",
      "dwc:georeferencedBy" : "cjsdavis",
      "dwc:recordNumber" : "4031",
      "dcterms:modified" : "2013-05-10 13:39:12",
      "dwc:country" : "Mexico",
      "dwc:eventDate" : "1985-03-14",
      "dwc:verbatimElevation" : "7600ft",
      "dwc:startDayOfYear" : "73",
      "dwc:habitat" : "Pine-oak forest, in N-facing barranca.",
      "dwc:dynamicProperties" : "Tree to 4 m;  occasional in N-facing barranca",
      "dwc:month" : "3",
      "dwc:stateProvince" : "Sinaloa",
      "dwc:genus" : "Abies",
      "dwc:coordinateUncertaintyInMeters" : "1000",
      "dwc:institutionCode" : "ASU"
   }
}

Use Elasticsearch

The normalized and indexed record that is stored in Elasticsearch can be retrieved by referencing the iDigBio GUID ("uuid") as the term provided to the query string parameter.

The list of available terms in the iDigBio index is available at IDigBio_API#Elasticsearch_-_Records.

Use the Elasticsearch URI Search

The following command sends the query as an HTTP GET request: 

$ curl -s "https://search.idigbio.org/idigbio/records/_search?q=uuid:0cec43d8-9ad5-478a-bea1-397ab5cc4430" | json_pp
{
   "hits" : {
      "hits" : [
         {
            "_source" : {
               "collectioncode" : "plants",
               "datecollected" : "1985-03-14",
               "recordids" : [
                  "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
               ],
               "geopoint" : {
                  "lat" : 23.5821004818154,
                  "lon" : -105.859665870667
               },
               "uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
               "locality" : "ca. 1 mi n of hwy 40 between villa union and cd. durango, and ca. 5 mi w of durango state border.",
               "minelevation" : 2316,
               "collectionid" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
               "datecollected_rejected" : false,
               "datemodified_rejected" : false,
               "recordset" : "40250f4d-7aa6-4fcc-ac38-2868fa4846bd",
               "mediarecords" : [
                  "db38f86b-99f5-4dc4-b4a6-a045a9c35323"
               ],
               "stateprovince" : "sinaloa",
               "country" : "mexico",
               "collector" : "t. f. daniel;",
               "geopoint_rejected" : false,
               "hasImage" : true,
               "genus" : "abies",
               "data" : {
                  "idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
                  "idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
                  "idigbio:links" : {
                     "mediarecord" : [
                        "http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
                     ],
                     "owner" : [
                        "872733a2-67a3-4c54-aa76-862735a5f334"
                     ],
                     "recordset" : [
                        "http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
                     ]
                  },
                  "idigbio:version" : 1,
                  "idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
                  "idigbio:recordIds" : [
                     "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
                  ],
                  "idigbio:data" : {
                     "dwc:catalogNumber" : "ASU0000166",
                     "dwc:basisOfRecord" : "PreservedSpecimen",
                     "symbiotaverbatimScientificName" : "Abies",
                     "idigbio:links" : {
                        "mediarecord" : [
                           "http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
                        ],
                        "owner" : [
                           "872733a2-67a3-4c54-aa76-862735a5f334"
                        ],
                        "recordset" : [
                           "http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
                        ]
                     },
                     "dwc:collectionCode" : "Plants",
                     "dwc:decimalLongitude" : "-105.859665870667",
                     "dcterms:references" : "http://swbiodiversity.org/seinet/collections/individual/index.php?occid=784316",
                     "dwc:scientificNameAuthorship" : "P. Mill.",
                     "dwc:collectionID" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
                     "dwc:minimumElevationInMeters" : "2316",
                     "dwc:georeferenceSources" : "georef batch tool 2013-05-10",
                     "dwc:georeferenceVerificationStatus" : "reviewed - high confidence",
                     "dwc:occurrenceRemarks" : "Tree to 4 m;  occasional in N-facing barranca",
                     "dwc:otherCatalogNumbers" : "153418",
                     "dwc:rights" : "http://creativecommons.org/licenses/by-nc-sa/3.0/",
                     "idigbio:version" : 1,
                     "idigbio:recordIds" : [
                        "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
                     ],
                     "dwc:decimalLatitude" : "23.5821004818154",
                     "dwc:day" : "14",
                     "idigbio:recordId" : "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a",
                     "dwc:locality" : "Ca. 1 mi N of Hwy 40 between Villa Union and Cd. Durango, and ca. 5 mi W of Durango state border.",
                     "dwc:occurrenceID" : "784316",
                     "idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
                     "dwc:year" : "1985",
                     "dwc:recordedBy" : "T. F. Daniel; ",
                     "dwc:recordNumber" : "4031",
                     "dwc:georeferencedBy" : "cjsdavis",
                     "dwc:scientificName" : "Abies",
                     "dwc:family" : "Pinaceae",
                     "dcterms:modified" : "2013-05-10 13:39:12",
                     "idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
                     "dwc:country" : "Mexico",
                     "idigbio:dateModified" : "2014-04-20T23:11:09.437Z",
                     "dwc:eventDate" : "1985-03-14",
                     "dwc:verbatimElevation" : "7600ft",
                     "idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
                     "dwc:startDayOfYear" : "73",
                     "dwc:habitat" : "Pine-oak forest, in N-facing barranca.",
                     "dwc:dynamicProperties" : "Tree to 4 m;  occasional in N-facing barranca",
                     "dwc:month" : "3",
                     "dwc:stateProvince" : "Sinaloa",
                     "dwc:genus" : "Abies",
                     "dwc:coordinateUncertaintyInMeters" : "1000",
                     "dwc:institutionCode" : "ASU"
                  },
                  "idigbio:dateModified" : "2014-04-20T23:11:09.437Z"
               },
               "datemodified" : "2014-04-20",
               "scientificname" : "abies",
               "minelevation_rejected" : false,
               "catalognumber" : "asu0000166",
               "etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
               "mindepth_rejected" : false,
               "maxelevation_rejected" : false,
               "maxdepth_rejected" : false,
               "recordnumber" : "4031",
               "family" : "pinaceae",
               "institutioncode" : "asu"
            },
            "_score" : 14.687269,
            "_index" : "idigbio-1.1.0",
            "_id" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
            "_type" : "records"
         }
      ],
      "max_score" : 14.687269,
      "total" : 1
   },
   "timed_out" : false,
   "_shards" : {
      "failed" : 0,
      "successful" : 10,
      "total" : 10
   },
   "took" : 5
}
Use the Elasticsearch Request Body Search

A JSON query document can be specified on the command-line. Again we are searching for the iDigBio GUID in the "uuid" term.

The following command sends the query as an HTTP POST request: 

$ curl -s https://search.idigbio.org/idigbio/records/_search -d'
{
    "filter" : {
    "term"  :  { "uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430" }
    }
}
' | json_pp

and give the following result: 

{
   "hits" : {
      "hits" : [
         {
            "_source" : {
               "collectioncode" : "plants",
               "datecollected" : "1985-03-14",
               "recordids" : [
                  "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
               ],
               "geopoint" : {
                  "lat" : 23.5821004818154,
                  "lon" : -105.859665870667
               },
               "uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
               "locality" : "ca. 1 mi n of hwy 40 between villa union and cd. durango, and ca. 5 mi w of durango state border.",
               "minelevation" : 2316,
               "collectionid" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
               "datecollected_rejected" : false,
               "datemodified_rejected" : false,
               "recordset" : "40250f4d-7aa6-4fcc-ac38-2868fa4846bd",
               "mediarecords" : [
                  "db38f86b-99f5-4dc4-b4a6-a045a9c35323"
               ],
               "stateprovince" : "sinaloa",
               "country" : "mexico",
               "collector" : "t. f. daniel;",
               "geopoint_rejected" : false,
               "hasImage" : true,
               "genus" : "abies",
               "data" : {
                  "idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
                  "idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
                  "idigbio:links" : {
                     "mediarecord" : [
                        "http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
                     ],
                     "owner" : [
                        "872733a2-67a3-4c54-aa76-862735a5f334"
                     ],
                     "recordset" : [
                        "http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
                     ]
                  },
                  "idigbio:version" : 1,
                  "idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
                  "idigbio:recordIds" : [
                     "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
                  ],
                  "idigbio:data" : {
                     "dwc:catalogNumber" : "ASU0000166",
                     "dwc:basisOfRecord" : "PreservedSpecimen",
                     "symbiotaverbatimScientificName" : "Abies",
                     "idigbio:links" : {
                        "mediarecord" : [
                           "http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
                        ],
                        "owner" : [
                           "872733a2-67a3-4c54-aa76-862735a5f334"
                        ],
                        "recordset" : [
                           "http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
                        ]
                     },
                     "dwc:collectionCode" : "Plants",
                     "dwc:decimalLongitude" : "-105.859665870667",
                     "dcterms:references" : "http://swbiodiversity.org/seinet/collections/individual/index.php?occid=784316",
                     "dwc:scientificNameAuthorship" : "P. Mill.",
                     "dwc:collectionID" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
                     "dwc:minimumElevationInMeters" : "2316",
                     "dwc:georeferenceSources" : "georef batch tool 2013-05-10",
                     "dwc:georeferenceVerificationStatus" : "reviewed - high confidence",
                     "dwc:occurrenceRemarks" : "Tree to 4 m;  occasional in N-facing barranca",
                     "dwc:otherCatalogNumbers" : "153418",
                     "dwc:rights" : "http://creativecommons.org/licenses/by-nc-sa/3.0/",
                     "idigbio:version" : 1,
                     "idigbio:recordIds" : [
                        "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
                     ],
                     "dwc:decimalLatitude" : "23.5821004818154",
                     "dwc:day" : "14",
                     "idigbio:recordId" : "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a",
                     "dwc:locality" : "Ca. 1 mi N of Hwy 40 between Villa Union and Cd. Durango, and ca. 5 mi W of Durango state border.",
                     "dwc:occurrenceID" : "784316",
                     "idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
                     "dwc:year" : "1985",
                     "dwc:recordedBy" : "T. F. Daniel; ",
                     "dwc:recordNumber" : "4031",
                     "dwc:georeferencedBy" : "cjsdavis",
                     "dwc:scientificName" : "Abies",
                     "dwc:family" : "Pinaceae",
                     "dcterms:modified" : "2013-05-10 13:39:12",
                     "idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
                     "dwc:country" : "Mexico",
                     "idigbio:dateModified" : "2014-04-20T23:11:09.437Z",
                     "dwc:eventDate" : "1985-03-14",
                     "dwc:verbatimElevation" : "7600ft",
                     "idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
                     "dwc:startDayOfYear" : "73",
                     "dwc:habitat" : "Pine-oak forest, in N-facing barranca.",
                     "dwc:dynamicProperties" : "Tree to 4 m;  occasional in N-facing barranca",
                     "dwc:month" : "3",
                     "dwc:stateProvince" : "Sinaloa",
                     "dwc:genus" : "Abies",
                     "dwc:coordinateUncertaintyInMeters" : "1000",
                     "dwc:institutionCode" : "ASU"
                  },
                  "idigbio:dateModified" : "2014-04-20T23:11:09.437Z"
               },
               "datemodified" : "2014-04-20",
               "scientificname" : "abies",
               "minelevation_rejected" : false,
               "catalognumber" : "asu0000166",
               "etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
               "mindepth_rejected" : false,
               "maxelevation_rejected" : false,
               "maxdepth_rejected" : false,
               "recordnumber" : "4031",
               "family" : "pinaceae",
               "institutioncode" : "asu"
            },
            "_score" : 1,
            "_index" : "idigbio-1.1.0",
            "_id" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
            "_type" : "records"
         }
      ],
      "max_score" : 1,
      "total" : 1
   },
   "timed_out" : false,
   "_shards" : {
      "failed" : 0,
      "successful" : 10,
      "total" : 10
   },
   "took" : 37
}

Alternatively, the JSON-formatted query body can be stored in a file. In this example, the file is named uuid.json and contains the iDigBio GUID in the "uuid" term as before: 

$ cat uuid.json
{
    "filter" : {
    "term"  :  { "uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430" }
    }
}

We tell curl to use the file as the source of the data with the at '@' sign. 

$ curl -s -XGET https://search.idigbio.org/idigbio/records/_search -d@uuid.json | json_pp
{
   "hits" : {
      "hits" : [
         {
            "_source" : {
               "collectioncode" : "plants",
               "datecollected" : "1985-03-14",
               "uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
               "geopoint_geohash_6" : "9shwph",
               "locality" : "ca. 1 mi n of hwy 40 between villa union and cd. durango, and ca. 5 mi w of durango state border.",
               "minelevation" : 231,
               "collectionid" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
               "datecollected_rejected" : false,
               "datemodified_rejected" : false,
               "geopoint_geohash_5" : "9shwp",
               "recordset" : "40250f4d-7aa6-4fcc-ac38-2868fa4846bd",
               "geopoint_rejected" : false,
               "hasImage" : true,
               "data" : {
                  "idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
                  "idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
                  "idigbio:links" : {
                     "mediarecord" : [
                        "http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
                     ],
                     "owner" : [
                        "872733a2-67a3-4c54-aa76-862735a5f334"
                     ],
                     "recordset" : [
                        "http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
                     ]
                  },
                  "idigbio:version" : 1,
                  "idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
                  "idigbio:recordIds" : [
                     "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
                  ],
                  "idigbio:data" : {
                     "dwc:catalogNumber" : "ASU0000166",
                     "dwc:basisOfRecord" : "PreservedSpecimen",
                     "symbiotaverbatimScientificName" : "Abies",
                     "idigbio:links" : {
                        "mediarecord" : [
                           "http://api.idigbio.org/v1/mediarecords/db38f86b-99f5-4dc4-b4a6-a045a9c35323"
                        ],
                        "owner" : [
                           "872733a2-67a3-4c54-aa76-862735a5f334"
                        ],
                        "recordset" : [
                           "http://api.idigbio.org/v1/recordsets/40250f4d-7aa6-4fcc-ac38-2868fa4846bd"
                        ]
                     },
                     "dwc:collectionCode" : "Plants",
                     "dwc:decimalLongitude" : "-105.859665870667",
                     "dcterms:references" : "http://swbiodiversity.org/seinet/collections/individual/index.php?occid=784316",
                     "dwc:scientificNameAuthorship" : "P. Mill.",
                     "dwc:collectionID" : "urn:uuid:a2e32c87-d320-4a01-bafd-a9182ae2e191",
                     "dwc:minimumElevationInMeters" : "2316",
                     "dwc:georeferenceSources" : "georef batch tool 2013-05-10",
                     "dwc:georeferenceVerificationStatus" : "reviewed - high confidence",
                     "dwc:occurrenceRemarks" : "Tree to 4 m;  occasional in N-facing barranca",
                     "dwc:otherCatalogNumbers" : "153418",
                     "dwc:rights" : "http://creativecommons.org/licenses/by-nc-sa/3.0/",
                     "idigbio:version" : 1,
                     "idigbio:recordIds" : [
                        "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a"
                     ],
                     "dwc:decimalLatitude" : "23.5821004818154",
                     "dwc:day" : "14",
                     "idigbio:recordId" : "urn:uuid:5f5e476f-ee39-41c9-8b25-c929f85a773a",
                     "dwc:locality" : "Ca. 1 mi N of Hwy 40 between Villa Union and Cd. Durango, and ca. 5 mi W of Durango state border.",
                     "dwc:occurrenceID" : "784316",
                     "idigbio:etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
                     "dwc:year" : "1985",
                     "dwc:recordedBy" : "T. F. Daniel; ",
                     "dwc:recordNumber" : "4031",
                     "dwc:georeferencedBy" : "cjsdavis",
                     "dwc:scientificName" : "Abies",
                     "dwc:family" : "Pinaceae",
                     "dcterms:modified" : "2013-05-10 13:39:12",
                     "idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
                     "dwc:country" : "Mexico",
                     "idigbio:dateModified" : "2014-04-20T23:11:09.437Z",
                     "dwc:eventDate" : "1985-03-14",
                     "dwc:verbatimElevation" : "7600ft",
                     "idigbio:uuid" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
                     "dwc:startDayOfYear" : "73",
                     "dwc:habitat" : "Pine-oak forest, in N-facing barranca.",
                     "dwc:dynamicProperties" : "Tree to 4 m;  occasional in N-facing barranca",
                     "dwc:month" : "3",
                     "dwc:stateProvince" : "Sinaloa",
                     "dwc:genus" : "Abies",
                     "dwc:coordinateUncertaintyInMeters" : "1000",
                     "dwc:institutionCode" : "ASU"
                  },
                  "idigbio:dateModified" : "2014-04-20T23:11:09.437Z"
               },
               "scientificname" : "abies",
               "minelevation_rejected" : false,
               "etag" : "2682a8f2fb77d59d50442925a80fe58a2ad51e9c",
               "maxdepth_rejected" : false,
               "family" : "pinaceae",
               "institutioncode" : "asu",
               "geopoint" : {
                  "lat" : 23.5821004818154,
                  "lon" : -105.859665870667
               },
               "fieldnumber" : "4031",
               "geopoint_geohash_2" : "9s",
               "stateprovince" : "sinaloa",
               "mediarecords" : [
                  "db38f86b-99f5-4dc4-b4a6-a045a9c35323"
               ],
               "country" : "mexico",
               "collector" : "t. f. daniel;",
               "geopoint_geohash_4" : "9shw",
               "version" : 1,
               "genus" : "abies",
               "geopoint_geohash_3" : "9sh",
               "datemodified" : "2014-04-20",
               "catalognumber" : "asu0000166",
               "mindepth_rejected" : false,
               "maxelevation_rejected" : false
            },
            "_score" : 1,
            "_index" : "idigbio-1.0.0",
            "_id" : "0cec43d8-9ad5-478a-bea1-397ab5cc4430",
            "_type" : "records"
         }
      ],
      "max_score" : 1,
      "total" : 1
   },
   "timed_out" : false,
   "_shards" : {
      "failed" : 0,
      "successful" : 10,
      "total" : 10
   },
   "took" : 64
}

Fetch an Older Version of a Particular Media Record

Consider an iDigBio Media Record "idigbio:uuid" : "ff5fd841-6bc6-4241-80d3-def7e1b6d5e8" with multiple revisions of the record. The API shows that the current version of this particular record is version 1. 

$ curl -s http://api.idigbio.org/v1/mediarecords/ff5fd841-6bc6-4241-80d3-def7e1b6d5e8 | json_pp | grep version
   "idigbio:version" : 1,

We would like to look at the previous version (version 0) to see what has changed. We do this by adding ?version=0 as a parameter to the URL. 

$ curl -s http://api.idigbio.org/v1/mediarecords/ff5fd841-6bc6-4241-80d3-def7e1b6d5e8?version=0 | json_pp
{
   "idigbio:uuid" : "ff5fd841-6bc6-4241-80d3-def7e1b6d5e8",
   "idigbio:etag" : "0a9effd5fc2803e87e4236e03a33ba3d00c3b305",
   "idigbio:links" : {
      "owner" : [
         "872733a2-67a3-4c54-aa76-862735a5f334"
      ],
      "record" : [
         "http://api.idigbio.org/v1/records/aebc99d6-3ba8-4d55-9434-83364b98d9b6"
      ],
      "recordset" : [
         "http://api.idigbio.org/v1/recordsets/e70af26a-fb9e-43ab-96a0-d62a2df37e6d"
      ]
   },
   "idigbio:version" : "0",
   "idigbio:createdBy" : "872733a2-67a3-4c54-aa76-862735a5f334",
   "idigbio:recordIds" : [
      "e70af26a-fb9e-43ab-96a0-d62a2df37e6d\\media\\urn:catalog:UConn:CONN:Image:CONN00175018"
   ],
   "idigbio:dateModified" : "2014-03-05T23:38:31.326Z",
   "idigbio:data" : {
      "ac:licenseLogoURL" : "http://mirrors.creativecommons.org/presskit/buttons/80x15/png/by-nc-sa.png",
      "ac:metadataLanguage" : "eng",
      "dwc:occurrenceID" : "urn:catalog:UConn:CONN:CONN00175018",
      "xmpRights:WebStatement" : "http://creativecommons.org/licenses/by-nc-sa/4.0/",
      "ac:bestQualityAccessURI" : "http://bgbaseserver.eeb.uconn.edu/DATABASEIMAGES/CONN00175018.JPG",
      "ac:bestQualityFormat" : "image/jpeg",
      "dcterms:creator" : "CONN",
      "dcterms:type" : "StillImage",
      "xmpRights:Owner" : "G. S. Torrey Herbarium, University of Connecticut",
      "dcterms:rights" : "© 2003 University of Connecticut",
      "dcterms:title" : "specimen image",
      "dcterms:identifier" : "urn:catalog:UConn:CONN:Image:CONN00175018"
   }
}

Fetch five MediaRecord IDs (endpoints) from the API

Example URL:

http://api.idigbio.org/v1/mediarecords?limit=5

Example API Results: 

 curl -s "http://api.idigbio.org/v1/mediarecords?limit=5" | json_pp
{
   "idigbio:errors" : [],
   "idigbio:links" : {
      "idigbio:nextPage" : "http://api.idigbio.org/v1/mediarecords?limit=5&offset=5"
   },
   "idigbio:items" : [
      {
         "idigbio:links" : {
            "mediarecord" : "http://api.idigbio.org/v1/mediarecords/000003cd-0cca-421b-8f26-f557a26b0393"
         },
         "idigbio:uuid" : "000003cd-0cca-421b-8f26-f557a26b0393",
         "idigbio:version" : 1,
         "idigbio:etag" : "ce3e2f7272ec996bb479c87549ba90c15ba96426",
         "idigbio:dateModified" : "2014-04-21T22:19:27.436Z"
      },
      {
         "idigbio:links" : {
            "mediarecord" : "http://api.idigbio.org/v1/mediarecords/00000728-ffb3-4a68-9f93-137f19961121"
         },
         "idigbio:uuid" : "00000728-ffb3-4a68-9f93-137f19961121",
         "idigbio:version" : 2,
         "idigbio:etag" : "c13b10675b4a83031b1dc7a24c1f5c4e443b1939",
         "idigbio:dateModified" : "2014-04-03T17:43:18.145Z"
      },
      {
         "idigbio:links" : {
            "mediarecord" : "http://api.idigbio.org/v1/mediarecords/00000b03-e208-4d22-983b-506ad2842f7c"
         },
         "idigbio:uuid" : "00000b03-e208-4d22-983b-506ad2842f7c",
         "idigbio:version" : 2,
         "idigbio:etag" : "bc118a7ea53e004c82ab9b7e813e1010ae5f8e17",
         "idigbio:dateModified" : "2014-04-20T05:16:20.389Z"
      },
      {
         "idigbio:links" : {
            "mediarecord" : "http://api.idigbio.org/v1/mediarecords/000010bc-a4d4-483d-b71d-0dbdd4fd2d5a"
         },
         "idigbio:uuid" : "000010bc-a4d4-483d-b71d-0dbdd4fd2d5a",
         "idigbio:version" : 0,
         "idigbio:etag" : "68c441bd3c49507bf930f3b278f2c58f9cb792ec",
         "idigbio:dateModified" : "2014-04-20T21:38:46.679Z"
      },
      {
         "idigbio:links" : {
            "mediarecord" : "http://api.idigbio.org/v1/mediarecords/000012f9-d288-4a14-b898-77430e0a137a"
         },
         "idigbio:uuid" : "000012f9-d288-4a14-b898-77430e0a137a",
         "idigbio:version" : 0,
         "idigbio:etag" : "0357f74dada8b21a69281b042a52f47a172fa33b",
         "idigbio:dateModified" : "2014-01-20T20:19:29.754Z"
      }
   ],
   "idigbio:itemCount" : "2199334"
}



To Do: Provide examples of displaying multiple images accessed via the mediarecord API endpoint.

[broken at this time due to point to symbiota4 in url... check back later, might get fixed]

https://api.idigbio.org/v1/records/4e98d066-f35f-4cc0-ad7c-b5b5f2175521/media?quality=thumbnail

https://api.idigbio.org/v1/mediarecords/4c4c5008-5444-4348-85f5-34112b46169b/media?quality=webview

Advanced Elasticsearch Examples

1. Find all specimen records that meet the following criteia
  • Has an image (mediarecord) associated with the specimen record
  • Is from Hocking County, Ohio or Fairfield County, Ohio.

Note that we are not using georeference data here, we are using the "county" and "stateprovince" fields.

To resolve this criteria, we need the following (expressed in pseudocode):

  1. "hasImage" is true
  2. "county" is either "Hocking" or "Fairfield"
  3. "stateprovince" is equal to "Ohio" (there are multiple Fairfield counties throughout the world so we need to restrict the geography by state)

The essential query parameter string will look something like this: 

?q=hasImage:true+AND+county:(fairfield+OR+hocking)+AND+stateprovince:ohio

In addition, it is possible to request more or fewer records at a time using the "from" and "size" parameters. Below is the full curl example requesting only the first 3 records and grep'ing out only the iDigBio GUID field. Note that we put the URL in quotes to keep the shell from trying to interpret it. 

$ curl -s "http://search.idigbio.org/idigbio/records/_search?from=0&size=3&q=hasImage:true+AND+county:(fairfield+OR+hocking)+AND+stateprovince:ohio" | json_pp  | egrep "\"uuid\"" 
               "uuid" : "20ad60a8-4126-4cc0-9378-411a9a640005",
               "uuid" : "ecf14f53-d225-4eb5-89e6-66379b360781",
               "uuid" : "ff69483e-ab19-4fa7-9ca3-d99089280af6",
2. Search for scientific name
# HERE GOES THE EXAMPLE

Mapping Example

  • coming soon

API Performance

For large numbers of records or bulk data aquisition, please use the Download features available in the Portal. https://www.idigbio.org/portal

See also iDigBio API Performance.

Retrieved from "http://www.idigbio.org/wiki/index.php?title=IDigBio_API_v1_Examples&oldid=9845"