Metadata-Version: 2.1
Name: termite-toolkit
Version: 0.4.1
Summary: Python library for calling TERMite and TExpress and processing results
Home-page: https://github.com/SciBiteLabs/termite_toolkit
Author: SciBite DataScience
Author-email: joe@scibite.com
License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License
Description: ### Project Description
        
        Python library for making calls to [SciBite](https://www.scibite.com/)'s TERMite, TExpress and DOCstore
        The library also enables post-processing of the JSON returned from such requests.
        
        ## Install
        
        ```
        $ pip3 install termite_toolkit
        ```
        Versions listed on [PyPi](https://pypi.org/project/termite-toolkit/)!
        
        ## Example call to TERMite
        
        ```python
        from termite_toolkit import termite
        from pprint import pprint
        
        
        # specify termite API endpoint
        termite_home = "http://localhost:9090/termite"
        
        # specify entities to annotate
        entities = "DRUG"
        
        # initialise a request builder
        t = termite.TermiteRequestBuilder()
        # individually add items to your TERMite request
        t.set_url(termite_home)
        t.set_fuzzy(True)
        t.set_text("citrate macrophage colony sildenafil stimulating factor influenza hedgehog")
        t.set_entities(entities)
        t.set_subsume(True)
        t.set_input_format("txt")
        t.set_output_format("doc.jsonx")
        t.set_reject_ambiguous(False)
        t.set_options({'fragmentSize': 20})
        
        # execute the request
        termite_response = t.execute(display_request=True)
        
        pprint(termite_response)
        ```
        
        ## Example call to TExpress
        
        ```python
        from pprint import pprint
        from termite_toolkit import texpress
        
        # specify termite API endpoint
        termite_home = "http://localhost:9090/termite"
        # specify the pattern you wish to search for- this can created in the TERMite UI
        pattern = ":(INDICATION):{0,5}:(GENE)"
        
        t = texpress.TexpressRequestBuilder()
        
        # individually add items to your TERMite request
        t.set_url(termite_home)
        t.set_text("breast cancer brca1")
        t.set_subsume(True)
        t.set_input_format("txt")
        t.set_output_format("json")
        t.set_allow_ambiguous(False)
        t.set_pattern(pattern)
        
        # execute the request
        texpress_response = t.execute(display_request=True)
        pprint(texpress_response)
        ```
        
        ## Example call to DOCstore
        
        ```python
        from termite_toolkit import docstore
        
        # Document co-occurrence of a list of entities
        docs = docstore.DocStoreRequestBuilder()
        # specify docstore API endpoint and add authentication if necessary
        docs.set_url('docstore_address')
        docs.set_basic_auth(username='user', password='pw')
        # make call to DOCStore
        docs_json = docs.get_dcc_docs(['id:GENE$HTT', 'id:GENE$EGFR'], '*', {})
        # convert json to df
        df = docstore.get_docstore_dcc_df(docs_json)
        # print titles of hits
        print(df['title'])
        ```
        
        ## License 
        
        Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.
Platform: UNKNOWN
Classifier: Programming Language :: Python :: 3
Classifier: Operating System :: OS Independent
Description-Content-Type: text/markdown
