diff --git a/biokb/setup.py b/biokb/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..ada1b5cf22c9bf7701b1fba2e0fbee9ca6a127a7
--- /dev/null
+++ b/biokb/setup.py
@@ -0,0 +1,35 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+try:
+ from setuptools import setup, find_packages
+except ImportError:
+ from distutils.core import setup
+
+requirements = [
+ 'SPARQLWrapper==1.8.4',
+ 'rdflib==4.2.2'
+]
+
+test_requirements = [
+ 'coverage'
+]
+
+setup(
+ name='textminingservice-biokb',
+ version='0.0.1',
+ description="BioKB implementation of the common text mining interface",
+ url='',
+ packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
+ package_dir={'textminingservice-biokb':
+ 'textminingservice_biokb'},
+ include_package_data=True,
+ install_requires=requirements,
+ zip_safe=False,
+ classifiers=[
+ 'Development Status :: 2 - Pre-Alpha',
+ 'Natural Language :: English',
+ 'Programming Language :: Python :: 3.7',
+ ],
+ tests_require=test_requirements,
+)
diff --git a/integration/__init__.py b/biokb/textminingservice_biokb/__init__.py
similarity index 100%
rename from integration/__init__.py
rename to biokb/textminingservice_biokb/__init__.py
diff --git a/biokb/biokb.py b/biokb/textminingservice_biokb/biokb.py
similarity index 91%
rename from biokb/biokb.py
rename to biokb/textminingservice_biokb/biokb.py
index 38a63334eaeb604819e5d39a0e6c99aee8d57b02..1b0aecfb59fce3dd8d03c2cbf909add58a455aef 100644
--- a/biokb/biokb.py
+++ b/biokb/textminingservice_biokb/biokb.py
@@ -4,10 +4,10 @@ from typing import List
from SPARQLWrapper import SPARQLWrapper, JSON, POSTDIRECTLY
from SPARQLWrapper.SPARQLExceptions import QueryBadFormed
-from interface.TextMiningService import TextMiningService
-from models.coocurrence import CoOccurrence
-from models.publication import Publication
-from .utils import uri_to_entity_code, standarise_underscored_entity_code
+from textminingservice.TextMiningService import TextMiningService
+from textminingservice.models.coocurrence import CoOccurrence
+from textminingservice.models.publication import Publication
+from textminingservice_biokb.utils import uri_to_entity_code, standardise_underscored_entity_code
logger = logging.getLogger(__name__)
@@ -41,7 +41,7 @@ class BioKBService(TextMiningService):
entity_subquery = ""
for entity in entities:
- entity = standarise_underscored_entity_code(entity)
+ entity = standardise_underscored_entity_code(entity)
entity_subquery += f"?publication <http://lcsb.uni.lu/biokb#containsEntity> <http://lcsb.uni.lu/biokb/entities/{entity}> .\n"
query = """
@@ -70,7 +70,7 @@ class BioKBService(TextMiningService):
types_str = ', '.join((f'<{t}>' for t in types))
entity_types_filter = f'FILTER (?e_type IN ({types_str}) )'
- entity = standarise_underscored_entity_code(entity)
+ entity = standardise_underscored_entity_code(entity)
query = """
select * where {
diff --git a/biokb/utils.py b/biokb/textminingservice_biokb/utils.py
similarity index 85%
rename from biokb/utils.py
rename to biokb/textminingservice_biokb/utils.py
index 270a7ec7c695b12f3b9c59864c28549972db5205..921cd4b672f12f02c8285f22ea0aaa120894eb3b 100644
--- a/biokb/utils.py
+++ b/biokb/textminingservice_biokb/utils.py
@@ -1,4 +1,4 @@
-def standarise_underscored_entity_code(entity_code: str) -> str:
+def standardise_underscored_entity_code(entity_code: str) -> str:
return entity_code.replace(':', '_', 1)
diff --git a/dummy-service/__init__.py b/dummy-service/__init__.py
deleted file mode 100644
index c7dec7f2c5973b985c22ed0f20cf8ee2f9cba909..0000000000000000000000000000000000000000
--- a/dummy-service/__init__.py
+++ /dev/null
@@ -1,2 +0,0 @@
-
-
\ No newline at end of file
diff --git a/dummy-service/setup.py b/dummy-service/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..c1ce58a9ea46de52ef10a88366a130f11923ae5d
--- /dev/null
+++ b/dummy-service/setup.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+try:
+ from setuptools import setup, find_packages
+except ImportError:
+ from distutils.core import setup
+
+requirements = [
+
+]
+
+test_requirements = [
+ 'coverage'
+]
+
+setup(
+ name='textminingservice-dummy',
+ version='0.0.1',
+ description="Dummy implementation of the common text mining interface",
+ url='',
+ packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
+ package_dir={'textminingservice-dummy':
+ 'textminingservice_dummy'},
+ include_package_data=True,
+ install_requires=requirements,
+ zip_safe=False,
+ classifiers=[
+ 'Development Status :: 2 - Pre-Alpha',
+ 'Natural Language :: English',
+ 'Programming Language :: Python :: 3.7',
+ ],
+ tests_require=test_requirements,
+)
diff --git a/jensenLabService/__init__.py b/dummy-service/textminingservice_dummy/__init__.py
similarity index 100%
rename from jensenLabService/__init__.py
rename to dummy-service/textminingservice_dummy/__init__.py
diff --git a/dummy-service/dummyService.py b/dummy-service/textminingservice_dummy/dummyService.py
similarity index 82%
rename from dummy-service/dummyService.py
rename to dummy-service/textminingservice_dummy/dummyService.py
index 6a9c16d59b84bee92d71fcc21a1ca08b92a25357..7c91ea8373fab4d8fe489efc489bfed79819e0a2 100644
--- a/dummy-service/dummyService.py
+++ b/dummy-service/textminingservice_dummy/dummyService.py
@@ -1,8 +1,9 @@
import logging
from typing import List
-from interface.TextMiningService import TextMiningService, Publication
-from models.coocurrence import CoOccurrence
+from textminingservice.TextMiningService import TextMiningService
+from textminingservice.models.coocurrence import CoOccurrence
+from textminingservice.models.publication import Publication
logger = logging.getLogger(__name__)
@@ -18,7 +19,7 @@ class DummyService(TextMiningService):
values = []
for idx in range(limit):
entity_code = f'{entity}_{idx}'
- count = int(idx*idx)
+ count = int(idx * idx)
co_occur = CoOccurrence(entity_code, count)
values.append(co_occur)
return values
diff --git a/integration/setup.py b/integration/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..95e516bdc79e09ea2ce754404c8331c2805ae1ab
--- /dev/null
+++ b/integration/setup.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+try:
+ from setuptools import setup, find_packages
+except ImportError:
+ from distutils.core import setup
+
+requirements = [
+
+]
+
+test_requirements = [
+ 'coverage'
+]
+
+setup(
+ name='textminingservice-integration',
+ version='0.0.1',
+ description="Example of integrations of several text-mining services",
+ url='',
+ packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
+ package_dir={'textminingservice-integration':
+ 'textminingservice_integration'},
+ include_package_data=True,
+ install_requires=requirements,
+ zip_safe=False,
+ classifiers=[
+ 'Development Status :: 2 - Pre-Alpha',
+ 'Natural Language :: English',
+ 'Programming Language :: Python :: 3.7',
+ ],
+ tests_require=test_requirements,
+)
diff --git a/integration/textminingservice_integration/__init__.py b/integration/textminingservice_integration/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..9c847747453665c332c6dd80107c138189275a80
--- /dev/null
+++ b/integration/textminingservice_integration/__init__.py
@@ -0,0 +1,4 @@
+import logging
+
+logger = logging.getLogger(__name__)
+
\ No newline at end of file
diff --git a/integration/example.py b/integration/textminingservice_integration/example.py
similarity index 59%
rename from integration/example.py
rename to integration/textminingservice_integration/example.py
index 43e1a0c0a7ac7a27dabf5fa31c4f89d90a428b8b..a8fc381f5cf5f3e559dd400b7c7191afb02257aa 100644
--- a/integration/example.py
+++ b/integration/textminingservice_integration/example.py
@@ -1,12 +1,8 @@
-import logging
-
-from biokb.biokb import BioKBService
-from jensenLabService.jensenLabService import JensenLabService
-
-logger = logging.getLogger(__name__)
+from textminingservice_biokb.biokb import BioKBService
+from textminingservice_dummy.dummyService import DummyService
if __name__ == '__main__':
- text_mining_services = [JensenLabService(), BioKBService()]
+ text_mining_services = [DummyService(), BioKBService()]
for text_mining_service in text_mining_services:
print("Using service {}".format(text_mining_service.name))
publications = text_mining_service.get_mentions(
diff --git a/interface/__init__.py b/interface/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/interface/setup.py b/interface/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..63cb137a04091d4fec6a6d204aa2be0da3ab07d0
--- /dev/null
+++ b/interface/setup.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+try:
+ from setuptools import setup, find_packages
+except ImportError:
+ from distutils.core import setup
+
+requirements = [
+
+]
+
+test_requirements = [
+ 'coverage'
+]
+
+setup(
+ name='textminingservice-interface',
+ version='0.0.1',
+ description="Provides common interface to several text-mining services",
+ url='',
+ packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
+ package_dir={'textminingservice':
+ 'textminingservice'},
+ include_package_data=True,
+ install_requires=requirements,
+ zip_safe=False,
+ classifiers=[
+ 'Development Status :: 2 - Pre-Alpha',
+ 'Natural Language :: English',
+ 'Programming Language :: Python :: 3.7',
+ ],
+ tests_require=test_requirements,
+)
diff --git a/interface/TextMiningService.py b/interface/textminingservice/TextMiningService.py
similarity index 89%
rename from interface/TextMiningService.py
rename to interface/textminingservice/TextMiningService.py
index 2c2ac4df901ab1dd6c6a6b2ca079c48ea73a11af..88385ab28a3c95d7fa59c70578e0156044c2d5c7 100644
--- a/interface/TextMiningService.py
+++ b/interface/textminingservice/TextMiningService.py
@@ -1,8 +1,8 @@
from abc import ABCMeta, abstractmethod
from typing import List
-from models.coocurrence import CoOccurrence
-from models.publication import Publication
+from textminingservice.models.coocurrence import CoOccurrence
+from textminingservice.models.publication import Publication
class TextMiningService(metaclass=ABCMeta):
diff --git a/interface/textminingservice/__init__.py b/interface/textminingservice/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..9c847747453665c332c6dd80107c138189275a80
--- /dev/null
+++ b/interface/textminingservice/__init__.py
@@ -0,0 +1,4 @@
+import logging
+
+logger = logging.getLogger(__name__)
+
\ No newline at end of file
diff --git a/biokb/__init__.py b/interface/textminingservice/models/__init__.py
similarity index 100%
rename from biokb/__init__.py
rename to interface/textminingservice/models/__init__.py
diff --git a/models/coocurrence.py b/interface/textminingservice/models/coocurrence.py
similarity index 100%
rename from models/coocurrence.py
rename to interface/textminingservice/models/coocurrence.py
diff --git a/models/publication.py b/interface/textminingservice/models/publication.py
similarity index 100%
rename from models/publication.py
rename to interface/textminingservice/models/publication.py
diff --git a/jensenLabService/setup.py b/jensenLabService/setup.py
new file mode 100644
index 0000000000000000000000000000000000000000..a326077591c725d0298ef81af59c56cd6d08f357
--- /dev/null
+++ b/jensenLabService/setup.py
@@ -0,0 +1,34 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+
+try:
+ from setuptools import setup, find_packages
+except ImportError:
+ from distutils.core import setup
+
+requirements = [
+
+]
+
+test_requirements = [
+ 'coverage'
+]
+
+setup(
+ name='textminingservice-jensenlab',
+ version='0.0.1',
+ description="jensenlab implementation of the common text mining interface",
+ url='',
+ packages=find_packages(exclude=['contrib', 'docs', 'tests*']),
+ package_dir={'textminingservice-jensenlab':
+ 'textminingservice_jensenlab'},
+ include_package_data=True,
+ install_requires=requirements,
+ zip_safe=False,
+ classifiers=[
+ 'Development Status :: 2 - Pre-Alpha',
+ 'Natural Language :: English',
+ 'Programming Language :: Python :: 3.7',
+ ],
+ tests_require=test_requirements,
+)
diff --git a/jensenLabService/textminingservice_jensenlab/__init__.py b/jensenLabService/textminingservice_jensenlab/__init__.py
new file mode 100644
index 0000000000000000000000000000000000000000..9c847747453665c332c6dd80107c138189275a80
--- /dev/null
+++ b/jensenLabService/textminingservice_jensenlab/__init__.py
@@ -0,0 +1,4 @@
+import logging
+
+logger = logging.getLogger(__name__)
+
\ No newline at end of file
diff --git a/jensenLabService/jensenLabService.py b/jensenLabService/textminingservice_jensenlab/jensenlabservice.py
similarity index 95%
rename from jensenLabService/jensenLabService.py
rename to jensenLabService/textminingservice_jensenlab/jensenlabservice.py
index a30eeaafa4b6d4de4d893a6506d53c6c842dbd91..54365fa57639547954e681c2af1a2ad987489e92 100644
--- a/jensenLabService/jensenLabService.py
+++ b/jensenLabService/textminingservice_jensenlab/jensenlabservice.py
@@ -4,8 +4,8 @@ from typing import List
import requests
-from interface.TextMiningService import TextMiningService
-from models.publication import Publication
+from textminingservice.TextMiningService import TextMiningService
+from textminingservice.models.publication import Publication
logger = logging.getLogger(__name__)
diff --git a/models/__init__.py b/models/__init__.py
deleted file mode 100644
index e69de29bb2d1d6434b8b29ae775ad8c2e48c5391..0000000000000000000000000000000000000000
diff --git a/requirements.txt b/requirements.txt
deleted file mode 100644
index 1ae881a0c2f17e73961ceb947aa5443cd29cc50c..0000000000000000000000000000000000000000
--- a/requirements.txt
+++ /dev/null
@@ -1,15 +0,0 @@
-astroid==2.3.3
-autopep8==1.4.4
-isodate==0.6.0
-isort==4.3.21
-lazy-object-proxy==1.4.3
-mccabe==0.6.1
-pep8==1.7.1
-pycodestyle==2.5.0
-pylint==2.4.4
-pyparsing==2.4.5
-rdflib==4.2.2
-six==1.13.0
-SPARQLWrapper==1.8.4
-typed-ast==1.4.0
-wrapt==1.11.2