Merge branch 'develop' into 'master'

Develop

See merge request SOaAS/dbxref!3

README.md → README.rst

-# DB XREF resolver and retriever tool
+DB XREF resolver and retriever tool
+===================================
 
 A tool that resolves database cross references (dbxrefs). It can return a list of
 locations where the cross reference points to in different formats, like HTML,
@@ -9,40 +10,47 @@ The intended audience for this tool are bioinformatician that need to collect
 data for dbxrefs and postprocess it. By returning everything in json format the
 need for normalization and special parsing of the data is reduced.
 
-# Getting started for development (Setup)
+Getting started for development (Setup)
+---------------------------------------
 
 Prerequisites:
 
 * git
 * python3
 
-Supported bioinformatic databases:
+Supported databases:
 
-* Ontologies
-  * Gene Ontology
+* Enzyme
+* Gene Identifier
+* Uniprot
+* Taxonomy
+* SequenceOntology
+* RFAM
+* Pubmed
+* Protein Families
+* PDB
+* InterPro
+* GeneID
+* Gene Ontology
+* HTTP
 
-Checkout the repository:
 
-~~~~
-git clone git@git.computational.bio.uni-giessen.de:SOaAS/dbxref.git
-~~~~
+Checkout the repository::
 
-Setup a virtualenv for development and install it in editable mode:
+    git clone git@git.computational.bio.uni-giessen.de:SOaAS/dbxref.git
 
-~~~~
-# install in development environment
-virtualenv --python=python3 venv; source venv/bin/activate;
-pip install -e .
+Setup a virtualenv for development and install it in editable mode::
 
-# run tests
-python3 setup.py test
+    # install in development environment
+    virtualenv --python=python3 venv; source venv/bin/activate;
+    pip install -e .
 
-# compile documentation
-python3 setup.py build_sphinx
-~~~~
+    # run tests
+    python3 setup.py test
 
-Use the application:
+    # compile documentation
+    python3 setup.py build_sphinx
 
-~~~~
-dbxref resolve GO:0097281
-~~~~
+Use the application::
+
+    dbxref resolve GO:0097281

dbxref/config.py

@@ -10,7 +10,10 @@ def _load_providers(path):
     data = []
     with open(path) as data_file:
         data = yaml.load(data_file)
-    return normalize_index(index_providers(data))
+    return data
+
+def load_indexed_providers():
+    return normalize_index(index_providers(load_providers()))
 
 def index_providers(providers):
     index = {}
@@ -24,10 +27,10 @@ def normalize_index(index):
     return {k.lower():v for (k,v) in index.items()}
 
 def has_provider(provider):
-    return _has_provider(load_providers(), provider)
+    return _has_provider(load_indexed_providers(), provider)
 
 def _has_provider(providers, provider):
     return provider.lower() in providers
 
 def get_provider(provider):
-    return load_providers()[provider.lower()]
+    return load_indexed_providers()[provider.lower()]

dbxref/main.py

 #!/usr/bin/env python3
 import argparse
+from argparse import RawTextHelpFormatter
 import os
 import logging
-from dbxref import resolver
+from dbxref import resolver, config
+from pbr.version import VersionInfo
 import json
 
+__version__ = VersionInfo('dbxref').semantic_version().release_string()
+
 def main():
-    parser = argparse.ArgumentParser(description='Lookup locations of database cross references and retrieve them as json')
+    parser = argparse.ArgumentParser(description='Version ' + __version__ + '\nLookup locations of database cross references and retrieve them as json', formatter_class=RawTextHelpFormatter)
     parser.set_defaults(func=help)
 
     subparsers = parser.add_subparsers()
     info_parser = subparsers.add_parser('info')
     info_parser.set_defaults(func=info)
-    #TODO implement
 
     resolve_parser = subparsers.add_parser('resolve')
     resolve_parser.add_argument('dbxrefs', nargs=argparse.REMAINDER)
@@ -26,7 +29,7 @@ def main():
     retrieve_parser.add_argument('--verbose', '-v', action='store_true', default=False, help="Show debug output")
 
     args = parser.parse_args()
-    config = {} # TODO implement
+    config = {} # implement when needed
     if ('verbose' in vars(args) and args.verbose):
         logging.basicConfig(level=logging.INFO)
     args.parser = parser
@@ -35,9 +38,15 @@ def main():
 def help(args, config):
     args.parser.print_help()
 
-def info(args, config):
-    #TODO implement
-    print ('info')
+def info(args, cfg):
+    print ('dbxref Version ' + __version__)
+    print ('')
+    print ('Supported dbxref databases:')
+    providers = config.load_providers()
+    for provider in providers:
+      print ('   ' + provider['name'])
+      print ('     Prefixes: ' + str.join(', ', [x for x in provider['prefixes']]))
+      print ('     Formats : ' + str.join(', ', [x for x in provider['resources']]))
 
 def resolve(args, config):
     print(json.dumps(resolver.resolve(resolver.convert_to_dbxrefs(args.dbxrefs), check_existence=args.no_check)))

requirements.txt

+requests
+cachecontrol
+pyyaml
+lockfile
+lxml
+pbr

setup.cfg

+[metadata]
+name = dbxref
+author = Lukas Jelonek
+author-email = Lukas.Jelonek@computational.bio.uni-giessen.de
+description = A library for resolving database cross references
+description-file = README.rst
+project_urls =
+    Source Code = https://git.computational.bio.uni-giessen.de/SOaAS/dbxref
+keywords = dbxref
+license = MIT
+
+[files]
+packages = dbxref
+
+[entry_points]
+console_scripts = 
+    dbxref = dbxref.main:main

setup.py

-from setuptools import setup, find_packages
-from codecs import open
-from os import path
-
-here = path.abspath(path.dirname(__file__))
-
-# Get the long description from the README file
-with open(path.join(here, 'README.md'), encoding='utf-8') as f:
-    long_description = f.read()
+from setuptools import setup
 
 setup(
-    name='dbxref',
-    version='0.1.0',
-    description='A library for resolving database cross references',
-    long_description=long_description, 
-    url='https://git.computational.bio.uni-giessen.de/SOaAS/dbxref',
-    author='Lukas Jelonek',
-    author_email='Lukas.Jelonek@computational.bio.uni-giessen.de',
-    keywords='dbxref',
-    packages=find_packages(exclude=['contrib', 'docs', 'tests']),
-    package_data={'dbxref':['*.yaml']},
-    install_requires=[
-      'requests',
-      'cachecontrol',
-      'pyyaml',
-      'lockfile',
-      'lxml'
-    ],
-    entry_points={ 
-        'console_scripts': [
-          'dbxref=dbxref.main:main',
-        ],
-    },
+  setup_requires=['pbr'],
+  pbr=True
 )