Executing the main method in AnnotateText.java throws the following exception:

java.io.FileNotFoundException: http://data.bioontology.org/ontologies/OHMI/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FDOID_1909
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1836)
	at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1441)
	at AnnotateText.get(AnnotateText.java:97)
	at AnnotateText.printAnnotations(AnnotateText.java:50)
	at AnnotateText.main(AnnotateText.java:27)
Class details
com.fasterxml.jackson.databind.JsonMappingException: No content to map due to end-of-input
 at [Source: java.io.StringReader@6cd8737; line: 1, column: 1]
	at com.fasterxml.jackson.databind.JsonMappingException.from(JsonMappingException.java:164)
	at com.fasterxml.jackson.databind.ObjectMapper._initForReading(ObjectMapper.java:2836)
	at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:2778)
	at com.fasterxml.jackson.databind.ObjectMapper.readTree(ObjectMapper.java:1659)
	at AnnotateText.jsonToNode(AnnotateText.java:75)
	at AnnotateText.printAnnotations(AnnotateText.java:50)
	at AnnotateText.main(AnnotateText.java:27)
Exception in thread "main" java.lang.NullPointerException
	at AnnotateText.printAnnotations(AnnotateText.java:52)
	at AnnotateText.main(AnnotateText.java:27)

Executing the main method in CreateMapping.java results in the following exception:

java.lang.Exception: {"errors":["Input does not contain classes"],"status":400}
	at CreateMapping.postJSON(CreateMapping.java:98)
	at CreateMapping.main(CreateMapping.java:51)

When I submit a very long text query to NCBO annotator service using Python3.5 on urllib3, it gives me this error.

exceptions.MaxRetryError: HTTPConnectionPool(host='data.bioontology.org', port=80): Max retries exceeded with url: /annotator?text=Prevention+and+Early+Detection+of+ ... (Caused by ProtocolError('Connection aborted.', ConnectionResetError(104, 'Connection reset by peer')))

When I query short text to annotate, it is processed without any problem but when the size of query text is going to be 20Kbyte, it gives me the error.

Presumably, it seems there is certain amount of maximum length of query allowed to the annotator service. If so, can I know how much exactly it is?

For your information, I attached my python code.

Thanks,
Jeongmin

import json
import urllib3
import urllib
import traceback
import sys
import re
import glob
from time import sleep

# user parameters
TEXT_DIR = '../data/text/'
JSON_DIR = '../data/json/'

apikey=''
REST_URL = "http://data.bioontology.org"

ontology_list = 'ICD9CM,LOINC,NDFRT,RXNORM,SNOMEDCT'
tui_list = 'T017,T029,T023'
options = '&longest_only=true&exclude_numbers=false&whole_word_only=true&exclude_synonyms=false' param = '&ontologies=' + ontology_list + '&semantic_types=' + tui_list + options


def get_json(text):
    # create request_url
    request_url = REST_URL + "/annotator?text=" + text.replace(' ','+') + param + "&apikey=" + apikey
    # get data as json type
    http = urllib3.PoolManager() 
    r = http.request('POST', request_url, headers={'Authorization': 'apikey token=' + apikey})
    print('request_url: '+request_url)
    print('http status: '+ str(r.status))
    data_json = json.loads(r.data.decode('utf-8'))
    return data_json

def main():
    for filename in glob.glob(TEXT_DIR+'*.txt'):
        # for each file load file 
        text = ''
        lines = open(filename,"r").read().splitlines()
        for l in lines:
            text = text + l.rstrip()
        # remove special characters
        text = re.sub('[^A-Za-z0-9]+', ' ', text)
        # get json
        data = get_json(text)
        # save to json file
        filename_nodir = filename.split('/')[-1].split('.')[0]
        json_fn = '' + filename_nodir + '.json'
        # print(json_fn)
        with open(JSON_DIR+json_fn, 'w') as outfile:
            json.dump(data, outfile)

if __name__ == "__main__":
    main()

Despite using the correct API key I keep getting this error. Any guidance for how to proceed?

Hi,

When trying out the REST API for classes I found that sometimes adding prefLabel to the include param causes the system to return empty (not found) results.
I have tried both GET and POST (batch request) and two examples are as follow

GET- with prefLabel

GET- without prefLabel

POST - with prefLabel

POST - without prefLabel

There are also some issues when I tried getting classes via general /classes method: sometimes some hundreds elements only contains @id and @type. Some other times, the collection field is simply empty - as follow

Could you please help me by seeing to these issues ?

Many thanks and best regards.
ChinhNK

Please add examples of client code for working with the new API annotator.

When I run the example at: https://github.com/ncbo/ncbo_rest_sample_code/blob/master/java/src/AnnotateText.java
I get the error
java.io.FileNotFoundException: http://data.bioontology.org/ontologies/MP/classes/http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FMPATH_359
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(HttpURLConnection.java:1835)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(HttpURLConnection.java:1440)
at AnnotateText.get(AnnotateText.java:96)
at AnnotateText.printAnnotations(AnnotateText.java:49)
at AnnotateText.main(AnnotateText.java:26)
com.fasterxml.jackson.databind.JsonMappingException: No content to map due to end-of-input
at [Source: java.io.StringReader@30c7da1e; line: 1, column: 1]
at com.fasterxml.jackson.databind.JsonMappingException.from(JsonMappingException.java:164)
at com.fasterxml.jackson.databind.ObjectMapper._initForReading(ObjectMapper.java:2836)
at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:2778)
at com.fasterxml.jackson.databind.ObjectMapper.readTree(ObjectMapper.java:1659)
at AnnotateText.jsonToNode(AnnotateText.java:74)
at AnnotateText.printAnnotations(AnnotateText.java:49)
at AnnotateText.main(AnnotateText.java:26)
Class details
Exception in thread "main" java.lang.NullPointerException
at AnnotateText.printAnnotations(AnnotateText.java:51)
at AnnotateText.main(AnnotateText.java:26)

Hello, I tried to use this Python sample code but found that this code would raise UnicodeEncodeError, and this is because my query includes special characters that can't be encoded by 'ascii' codec. This is because your baseline code for Python uses urllib package and this urllib can only handle ASCII requests.

So, I'd recommend to change this urllib-based scripts to simple requests package, which can handle those kind of special characters. If you don't mind, I can pull request those part after fork this code. If there is a reason to use urllib, then never mind on my issue. Thanks!

AnnotateText.java execution throws an exception. The log is given below:

java.io.IOException: Server returned HTTP response code: 401 for URL: http://data.bioontology.org/annotator?text=Melanoma+is+a+malignant+tumor+of+melanocytes+which+are+found+predominantly+in+skin+but+also+in+the+bowel+and+the+eye.
at sun.net.www.protocol.http.HttpURLConnection.getInputStream0(Unknown Source)
at sun.net.www.protocol.http.HttpURLConnection.getInputStream(Unknown Source)
at org.fit.vocabulary.neologism.OntologyRecommender.LOV.AnnotateText.get(AnnotateText.java:101)
at org.fit.vocabulary.neologism.OntologyRecommender.LOV.AnnotateText.main(AnnotateText.java:30)
com.fasterxml.jackson.databind.JsonMappingException: No content to map due to end-of-input
at [Source: ; line: 1, column: 0]
at com.fasterxml.jackson.databind.JsonMappingException.from(JsonMappingException.java:270)
at com.fasterxml.jackson.databind.ObjectMapper._initForReading(ObjectMapper.java:3854)
at com.fasterxml.jackson.databind.ObjectMapper._readMapAndClose(ObjectMapper.java:3799)
at com.fasterxml.jackson.databind.ObjectMapper.readTree(ObjectMapper.java:2397)
at org.fit.vocabulary.neologism.OntologyRecommender.LOV.AnnotateText.jsonToNode(AnnotateText.java:79)
at org.fit.vocabulary.neologism.OntologyRecommender.LOV.AnnotateText.main(AnnotateText.java:30)
Exception in thread "main" java.lang.NullPointerException
at org.fit.vocabulary.neologism.OntologyRecommender.LOV.AnnotateText.printAnnotations(AnnotateText.java:52)
at org.fit.vocabulary.neologism.OntologyRecommender.LOV.AnnotateText.main(AnnotateText.java:31)