%global _empty_manifest_terminate_build 0 Name: python-termite-toolkit Version: 0.5.6 Release: 1 Summary: scibite-toolkit - python library for calling TERMite, TExpress and other tools, and processing results License: Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License URL: https://github.com/elsevier-health/scibite-toolkit Source0: https://mirrors.nju.edu.cn/pypi/web/packages/87/b8/1f98f9adc77bc6fc0c66e1af2974b289d9d49c06342aaab34f33d75d1f3b/termite_toolkit-0.5.6.tar.gz BuildArch: noarch Requires: python3-requests Requires: python3-pandas Requires: python3-nltk %description ### Project Description scibite-toolkit - 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. %package -n python3-termite-toolkit Summary: scibite-toolkit - python library for calling TERMite, TExpress and other tools, and processing results Provides: python-termite-toolkit BuildRequires: python3-devel BuildRequires: python3-setuptools BuildRequires: python3-pip %description -n python3-termite-toolkit ### Project Description scibite-toolkit - 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. %package help Summary: Development documents and examples for termite-toolkit Provides: python3-termite-toolkit-doc %description help ### Project Description scibite-toolkit - 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. %prep %autosetup -n termite-toolkit-0.5.6 %build %py3_build %install %py3_install install -d -m755 %{buildroot}/%{_pkgdocdir} if [ -d doc ]; then cp -arf doc %{buildroot}/%{_pkgdocdir}; fi if [ -d docs ]; then cp -arf docs %{buildroot}/%{_pkgdocdir}; fi if [ -d example ]; then cp -arf example %{buildroot}/%{_pkgdocdir}; fi if [ -d examples ]; then cp -arf examples %{buildroot}/%{_pkgdocdir}; fi pushd %{buildroot} if [ -d usr/lib ]; then find usr/lib -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/lib64 ]; then find usr/lib64 -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/bin ]; then find usr/bin -type f -printf "/%h/%f\n" >> filelist.lst fi if [ -d usr/sbin ]; then find usr/sbin -type f -printf "/%h/%f\n" >> filelist.lst fi touch doclist.lst if [ -d usr/share/man ]; then find usr/share/man -type f -printf "/%h/%f.gz\n" >> doclist.lst fi popd mv %{buildroot}/filelist.lst . mv %{buildroot}/doclist.lst . %files -n python3-termite-toolkit -f filelist.lst %dir %{python3_sitelib}/* %files help -f doclist.lst %{_docdir}/* %changelog * Thu May 18 2023 Python_Bot - 0.5.6-1 - Package Spec generated