import requests
import os
from langchain.chains import APIChain
from langchain.chat_models import ChatOpenAIos.environ["OPENAI_API_KEY"] = "API KEY"llm = ChatOpenAI(temperature= 0, model_name="gpt-3.5-turbo", max_tokens = 256, verbose =True)apiSpecs = """API Documentation
base_url: https://api.gbif.org/v1/
Endpoint: occurrence/search
Example API call: https://www.gbif.org/occurrence/search?q=Hemigrapsus%20nudus
"""chain_new = APIChain.from_llm_and_api_docs(llm, apiSpecs, verbose=True)
response = chain_new.run('Please list the most recent occurrence with Tonicella lineata')
print(response)
> Entering new APIChain chain...
https://api.gbif.org/v1/occurrence/search?q=Tonicella%20lineata&limit=1&sort=occurrenceDate desc
{"offset":0,"limit":1,"endOfRecords":false,"count":457899,"results":[{"key":1989898085,"datasetKey":"965bbbd8-f762-11e1-a439-00145eb45e9a","publishingOrgKey":"c76cf030-2a95-11da-9cc1-b8a03c50a862","networkKeys":["17abcf75-2f1e-46dd-bf75-a5b21dd02655"],"installationKey":"60383ab8-f762-11e1-a439-00145eb45e9a","hostingOrganizationKey":"c76cf030-2a95-11da-9cc1-b8a03c50a862","publishingCountry":"DE","protocol":"BIOCASE","lastCrawled":"2023-07-14T22:44:48.042+00:00","lastParsed":"2023-07-15T07:20:55.169+00:00","crawlId":224,"extensions":{},"basisOfRecord":"PRESERVED_SPECIMEN","occurrenceStatus":"PRESENT","taxonKey":2306813,"kingdomKey":1,"phylumKey":52,"classKey":346,"orderKey":8278247,"familyKey":3246305,"genusKey":2306809,"speciesKey":2306813,"acceptedTaxonKey":2306813,"scientificName":"Tonicella lineata (Wood, 1815)","acceptedScientificName":"Tonicella lineata (Wood, 1815)","kingdom":"Animalia","phylum":"Mollusca","order":"Chitonida","family":"Tonicellidae","genus":"Tonicella","species":"Tonicella lineata","genericName":"Tonicella","specificEpithet":"lineata","taxonRank":"SPECIES","taxonomicStatus":"ACCEPTED","iucnRedListCategory":"NE","gadm":{},"issues":["COLLECTION_MATCH_NONE","INSTITUTION_MATCH_FUZZY"],"lastInterpreted":"2023-07-15T07:20:55.169+00:00","license":"http://creativecommons.org/licenses/by/4.0/legalcode","identifiers":[{"identifier":"urn:catalog:SMF:Collection Mollusca:350221"}],"media":[],"facts":[],"relations":[],"institutionKey":"16946ec1-8db3-45b8-b084-7644384cc5f5","isInCluster":false,"class":"Polyplacophora","recordedByIDs":[],"identifiedByIDs":[],"catalogNumber":"350221","institutionCode":"SMF","collectionCode":"Collection Mollusca","gbifID":"1989898085"}],"facets":[]}
> Finished chain.
The most recent occurrence of Tonicella lineata is recorded in the dataset with the key "965bbbd8-f762-11e1-a439-00145eb45e9a". The occurrence is a preserved specimen and is present. The scientific name of the species is "Tonicella lineata (Wood, 1815)" and it belongs to the kingdom Animalia, phylum Mollusca, order Chitonida, family Tonicellidae, genus Tonicella, and species Tonicella lineata. The occurrence was last crawled on July 14, 2023, and last parsed on July 15, 2023. The occurrence is associated with the catalog number "350221" in the institution with the code "SMF" and the collection code "Collection Mollusca".chain_new = APIChain.from_llm_and_api_docs(llm, apiSpecs, verbose=True)
response = chain_new.run('Please list the first occurrence with Hemigrapsus nudus')
print(response)Error in on_chain_start callback: 'name'https://api.gbif.org/v1/occurrence/search?q=Hemigrapsus%20nudus&limit=1
{"offset":0,"limit":1,"endOfRecords":false,"count":40113,"results":[{"key":1065135676,"datasetKey":"005eb8d8-ed94-41be-89cf-e3115a9058e4","publishingOrgKey":"7b8aff00-a9f8-11d8-944b-b8a03c50a862","installationKey":"3b84ff5b-79ce-427c-acb7-b4004e160f66","hostingOrganizationKey":"7b8aff00-a9f8-11d8-944b-b8a03c50a862","publishingCountry":"US","protocol":"EML","lastCrawled":"2023-06-01T04:23:12.378+00:00","lastParsed":"2023-06-07T20:20:50.103+00:00","crawlId":310,"extensions":{},"basisOfRecord":"PRESERVED_SPECIMEN","individualCount":2,"occurrenceStatus":"PRESENT","taxonKey":2225773,"kingdomKey":1,"phylumKey":54,"classKey":229,"orderKey":637,"familyKey":11368965,"genusKey":2225769,"speciesKey":2225773,"acceptedTaxonKey":2225773,"scientificName":"Hemigrapsus nudus (Dana, 1851)","acceptedScientificName":"Hemigrapsus nudus (Dana, 1851)","kingdom":"Animalia","phylum":"Arthropoda","order":"Decapoda","family":"Varunidae","genus":"Hemigrapsus","species":"Hemigrapsus nudus","genericName":"Hemigrapsus","specificEpithet":"nudus","taxonRank":"SPECIES","taxonomicStatus":"ACCEPTED","iucnRedListCategory":"NE","continent":"NORTH_AMERICA","stateProvince":"British Columbia","gadm":{},"issues":["OCCURRENCE_STATUS_INFERRED_FROM_INDIVIDUAL_COUNT","INSTITUTION_MATCH_FUZZY","INSTITUTION_COLLECTION_MISMATCH"],"modified":"2023-03-01T09:11:00.000+00:00","lastInterpreted":"2023-06-07T20:20:50.103+00:00","license":"http://creativecommons.org/publicdomain/zero/1.0/legalcode","identifiers":[{"identifier":"f059351b-c94c-4ddc-82be-6d6d900c381c"}],"media":[],"facts":[],"relations":[],"institutionKey":"e71f36f1-e271-4720-a604-3c5a1418e7aa","isInCluster":false,"datasetID":"invertebrates-25-Apr-2023","class":"Malacostraca","countryCode":"CA","recordedByIDs":[],"identifiedByIDs":[],"country":"Canada","rightsHolder":"The Field Museum of Natural History","identifier":"f059351b-c94c-4ddc-82be-6d6d900c381c","nomenclaturalCode":"ICZN","higherGeography":"North America, Canada: Barelay Sound, British Colombia","institutionID":"FMNH","locality":"Barelay Sound, British Colombia","fieldNumber":"ALB-1701","collectionCode":"Invertebrate Zoology","gbifID":"1065135676","occurrenceID":"f059351b-c94c-4ddc-82be-6d6d900c381c","catalogNumber":"1701","organismID":"560837","institutionCode":"FMNH","locationID":"a56e1046-139d-4125-9045-2f6fd51661e0","ownerInstitutionCode":"FMNH","accessRights":"https://www.fieldmuseum.org/about/copyright-information","collectionID":"Invertebrate Zoology","higherClassification":"Animalia Arthropoda Malacostraca Decapoda Varunidae"}],"facets":[]}
> Finished chain.
The first occurrence of Hemigrapsus nudus is found in the dataset with the key "005eb8d8-ed94-41be-89cf-e3115a9058e4". It was published by the organization with the key "7b8aff00-a9f8-11d8-944b-b8a03c50a862" and hosted by the same organization. The occurrence is a preserved specimen with a count of 2 individuals. The taxonomic classification of the occurrence is as follows: kingdom - Animalia, phylum - Arthropoda, class - Malacostraca, order - Decapoda, family - Varunidae, genus - Hemigrapsus, species - Hemigrapsus nudus. The occurrence is considered present and the taxonomic status is accepted. It was recorded in Barelay Sound, British Columbia, Canada. The occurrence is associated with the identifier "f059351b-c94c-4ddc-82be-6d6d900c381c" and has a catalog number of "1701". The occurrence is part of the Invertebrate Zoology collection at The Field Museum of Natural History.import requests
import json
# GBIF API base URL
base_url = 'https://api.gbif.org/v1/'
# Function to search occurrences of a species
def search_species_occurrences(species_name, year = None):
# GBIF Occurrence Search API endpoint
url = f'{base_url}occurrence/search'
# Parameters for the API request
params = {
'scientificName': species_name,
'limit': 5 # Number of results to retrieve (adjust as needed)
}
if year:
#Add year parameter if provided
params["year"] = year
try:
# Set get request to GBIF API
response = requests.get(url, params=params)
response.raise_for_status()
# Extract the repsonse data as JSON
data = response.json()
if "results" in data:
results = data["results"]
if results:
occurrences = []
for result in results:
# if all(attr in result for attr in ["key", "eventDate", "locality", "decimalLatitude", "decimalLongitude", "recordedBy", "kingdomKey","phylumKey", "waterBody"]):
occurrence_id = result.get("key", "N/A")
occurrence_sciName = result.get("scientificName", "N/A")
occurrence_record = result.get("recordedBy", "N/A")
occurrence_date = result.get("eventDate", "N/A")
occurrence_locality = result.get("locality", "N/A")
occurrence_bodywater = result.get("waterBody", "N/A")
occurrence_depth = result.get("depth", "N/A")
occurrence_elevation = result.get("elevation", "N/A")
occurrence_lat = result.get("decimalLatitude", "N/A")
occurrence_long = result.get("decimalLongitude", "N/A")
occurrence_kingdom = result.get("kingdomKey", "N/A")
occurrence_phylum = result.get("phylumKey", "N/A")
#Create a dictionary for the occurrences
occurrence = {
"occurrence_id": occurrence_id,
"occurrence_sciName": occurrence_sciName,
"occurrence_date": occurrence_date,
"location": occurrence_locality,
"latitude": occurrence_lat,
"longitude": occurrence_long,
"collected by": occurrence_record,
"kingdom": occurrence_kingdom,
"phylum": occurrence_phylum,
"body_water": occurrence_bodywater,
"depth": occurrence_depth,
"elevation": occurrence_elevation
}
#Add the occurrence to the list
occurrences.append(occurrence)
return occurrences
else:
return []
else:
print("Error: Invalid reponse from GBIF API")
return []
except requests.exceptions.HTTPError as err:
print(f"HTTP error occurred: {err}")
except requests.exceptions.RequestException as err:
print(f"An error occurred: {err}")
# Example usage
species_name = "Tonicella lineata" # Replace with your desired species name
year = 2014 #replace with year of article
occurrences = search_species_occurrences(species_name, year)# Print or process the occurrences as needed
for occurrence in occurrences:
print(f"Occurrence ID: {occurrence['occurrence_id']}")
print(f"Scientific Name: {occurrence['occurrence_sciName']}")
print(f"Occurrence Date: {occurrence['occurrence_date']}")
print(f"Recorded by: {occurrence['collected by']}")
print(f"Location: {occurrence['location']}")
print(f"Depth: {occurrence['depth']}")
print(f"Elevation: {occurrence['elevation']}")
print(f"Body of Water: {occurrence['body_water']}")
print(f"Latitude: {occurrence['latitude']}")
print(f"Longitude: {occurrence['longitude']}")
print(f"Kingdom: {occurrence['kingdom']}")
print(f"Phylum: {occurrence['phylum']}")
print("-" * 20)Occurrence ID: 4039335302
Scientific Name: Tonicella lineata (Wood, 1815)
Occurrence Date: 2014-01-11T13:38:33
Recorded by: Kris Liang
Location: N/A
Depth: N/A
Elevation: N/A
Body of Water: N/A
Latitude: 37.520271
Longitude: -122.515915
Kingdom: 1
Phylum: 52
--------------------
Occurrence ID: 3357460927
Scientific Name: Tonicella lineata (Wood, 1815)
Occurrence Date: 2014-01-03T00:00:00
Recorded by: Andy Lamb
Location: Baines Point
Depth: N/A
Elevation: N/A
Body of Water: N/A
Latitude: 49.007465
Longitude: -123.587784
Kingdom: 1
Phylum: 52
--------------------
Occurrence ID: 891052717
Scientific Name: Tonicella lineata (Wood, 1815)
Occurrence Date: 2014-02-27T15:09:28
Recorded by: Liam O'Brien
Location: N/A
Depth: N/A
Elevation: N/A
Body of Water: N/A
Latitude: 37.494351
Longitude: -122.498529
Kingdom: 1
Phylum: 52
--------------------
Occurrence ID: 1837784847
Scientific Name: Tonicella lineata (Wood, 1815)
Occurrence Date: 2014-03-23T12:03:00
Recorded by: Donna Pomeroy
Location: N/A
Depth: N/A
Elevation: N/A
Body of Water: N/A
Latitude: 37.495017
Longitude: -122.499231
Kingdom: 1
Phylum: 52
--------------------
Occurrence ID: 1453541336
Scientific Name: Tonicella lineata (Wood, 1815)
Occurrence Date: 2014-03-23T11:39:02
Recorded by: Robin Gwen Agarwal
Location: N/A
Depth: N/A
Elevation: N/A
Body of Water: N/A
Latitude: 37.494806
Longitude: -122.499397
Kingdom: 1
Phylum: 52
--------------------