This notebook contains code examples for maintaining, extending and updating the Wikipathways bot

In [24]:

    

from wikidataintegrator import wdi_core, wdi_login
import os
import pandas as pd
import pprint


    

In [13]:

    

def sparql(query, endpoint):
    query=query
    return wdi_core.WDItemEngine.execute_sparql_query(query, endpoint=endpoint)

def sparqlpandas(query, endpoint):
    return wdi_core.WDItemEngine.execute_sparql_query(query, endpoint=endpoint, as_dataframe=True)


    

In [9]:

    

print("Logging in...")
if "WDUSER" in os.environ and "WDPASS" in os.environ:
    WDUSER = os.environ['WDUSER']
    WDPASS = os.environ['WDPASS']
else:
    raise ValueError("WDUSER and WDPASS must be specified in local.py or as environment variables")
login = wdi_login.WDLogin(WDUSER, WDPASS)


    

    




Logging in...
https://www.wikidata.org/w/api.php
Successfully logged in as Andrawaag

In [19]:

    

## Find the Wikidata identifier for WP716
query = """
   SELECT * WHERE {?pathway wdt:P2888 <http://identifiers.org/wikipathways/WP716>}
"""
sparqlpandas(query, endpoint="https://query.wikidata.org/sparql")


    

    
Out[19]:







  

    

      

      
pathway
    
  
  

    

      
0
      
http://www.wikidata.org/entity/Q27436284
    
  

In [20]:

    

wdwpid = sparql(query, endpoint="https://query.wikidata.org/sparql")["results"]["bindings"][0]["pathway"]["value"]
print(wdwpid)


    

    




http://www.wikidata.org/entity/Q27436284

In [32]:

    

wdPage = wdi_core.WDItemEngine(wd_item_id=wdwpid.replace("http://www.wikidata.org/entity/", ""))
#pprint.pprint(wdPage.get_wd_json_representation())


    

In [26]:

    

query = """
prefix dcterms:	<http://purl.org/dc/terms/>
SELECT ?item ?description WHERE { <"""
query += wdwpid + "> " 
query += """wdt:P2410 ?wpid ;
         wdt:P2888 ?wpiri .
  SERVICE <http://sparql.wikipathways.org/> {
      ?version dc:identifier ?wpiri ;
               dcterms:description ?description .
    }
}
"""
sparqlpandas(query, endpoint="https://query.wikidata.org/sparql")


    

    
Out[26]:







  

    

      

      
description
    
  
  

    

      
0
      
This pathway is about carotenoid and vitamin A...
    
  

In [29]:

    

description = sparql(query, endpoint="https://query.wikidata.org/sparql")["results"]["bindings"][0]["description"]["value"]
print(description)


    

    




This pathway is about carotenoid and vitamin A metabolism. The initial version was created by the NuGO focusteam on Carotenoid metabolism. It was used to test a text mining workflow which added some additional entities (see Waagmeester et al. 2009 [https://www.ncbi.nlm.nih.gov/pubmed/19715393]).

In [31]:

    

wdPage.set_description(description, lang="en")
wdPage.write(login)


    

    




Error while writing to Wikidata






    




---------------------------------------------------------------------------
WDApiError                                Traceback (most recent call last)
<ipython-input-31-fe99cc2d8eb0> in <module>
      1 wdPage.set_description(description, lang="en")
----> 2 wdPage.write(login)

/usr/local/lib/python3.7/site-packages/wikidataintegrator/wdi_core.py in write(self, login, bot_account, edit_summary, entity_type, property_datatype, max_retries, retry_after)
    942                     raise NonUniqueLabelDescriptionPairError(json_data)
    943                 else:
--> 944                     raise WDApiError(json_data)
    945             elif 'error' in json_data.keys():
    946                 raise WDApiError(json_data)

WDApiError: {'error': {'code': 'modification-failed', 'info': 'Description must be no more than 250 characters long', 'messages': [{'name': 'wikibase-validator-description-too-long', 'parameters': ['250', 'This pathway is about caroten...'], 'html': {'*': 'Description must be no more than 250 characters long'}}], '*': 'See https://www.wikidata.org/w/api.php for API usage. Subscribe to the mediawiki-api-announce mailing list at &lt;https://lists.wikimedia.org/mailman/listinfo/mediawiki-api-announce&gt; for notice of API deprecations and breaking changes.'}, 'servedby': 'mw1286'}

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