Merge pull request #4 from 403JFW/develop

Develop

.gitignore

@@ -1,6 +1,55 @@
-.DS_Store
+# Byte-compiled / optimized / DLL files
+__pycache__/
+*.py[cod]
+
+# C extensions
+*.so
+
+# Distribution / packaging
+.Python
+env/
+bin/
+build/
+develop-eggs/
+dist/
+eggs/
+lib/
+lib64/
+parts/
+sdist/
+var/
+*.egg-info/
+.installed.cfg
+*.egg
+
+# Installer logs
+pip-log.txt
+pip-delete-this-directory.txt
+
+# Unit test / coverage reports
+htmlcov/
+.tox/
 .coverage
-*.pyc
+.cache
+nosetests.xml
+coverage.xml
+
+# Translations
+*.mo
+
+# Mr Developer
+.mr.developer.cfg
+.project
+.pydevproject
+
+# Rope
+.ropeproject
+
+# Django stuff:
+*.log
+*.pot
+
+# Sphinx documentation
+docs/_build/
+
 *.swp
-akatsuki.egg-info
-dist

.travis.yml

@@ -3,6 +3,7 @@ python:
     - "2.7"
     - "3.2"
     - "3.3"
+    - "3.4"
     - "pypy"
 install:
     - pip install coveralls

akatsuki/bib2html.py

@@ -5,11 +5,12 @@
 
 from akatsuki.exporter import export_html
 from akatsuki.parser import load_bibtex_file
-from akatsuki.utils import sort_by_date
+from akatsuki.utils import pmid_to_url, sort_by_date
 
 
 def main(bibtex_file, html_file):
     """Load BibTeX file and export to HTML file"""
     entries = load_bibtex_file(bibtex_file)
+    entries = pmid_to_url(entries)
     entries = sort_by_date(entries, reverse=True)
     export_html(html_file, entries)

akatsuki/exporter.py

@@ -55,4 +55,6 @@ def _entry_html(entry):
         if 'pages' in entry:
             result += ':%s' % entry['pages']
         result += '.<br>\n'
+    if 'URL' in entry:
+        result += '<a href="{0:s}">{0:s}</a><br>\n'.format(entry['URL'])
     return result

akatsuki/utils.py

@@ -19,6 +19,8 @@
     'DEC': 12
 }
 
+PUBMED_URL = 'http://www.ncbi.nlm.nih.gov/pubmed/'
+
 
 def sort_by_date(entries, reverse=False):
     """Sort entries by year and month of the entry"""
@@ -35,3 +37,12 @@ def sort_by_date(entries, reverse=False):
     return sorted(entries,
                   key=lambda e: int(e['year']) * 100 + int(e['month_n']),
                   reverse=reverse)
+
+
+def pmid_to_url(entries):
+    """Set URL field from pmid"""
+    for entry in entries:
+        pmid = entry['id'].strip()
+        if (pmid[0:4] == 'pmid') and ('URL' not in entry):
+            entry['URL'] = PUBMED_URL + pmid[4:]
+    return entries

setup.py

@@ -7,15 +7,15 @@
 
 
 setup(name='akatsuki',
-      version='0.1',
+      version='0.1.1',
       description='BibTeX to HTML converter',
       author='Yusuke Miyazaki',
       author_email='miyazaki.dev@gmail.com',
       url='https://github.com/403JFW/akatsuki',
       packages=['akatsuki'],
       scripts=['scripts/bib2html'],
       test_suite='tests',
-      install_requires=['bibtexparser>=0.5.2'],
+      install_requires=['bibtexparser==0.5.2'],
       classifiers=[
           'Development Status :: 3 - Alpha',
           'Environment :: Console',
@@ -30,6 +30,7 @@
           'Programming Language :: Python :: 3',
           'Programming Language :: Python :: 3.2',
           'Programming Language :: Python :: 3.3',
+          'Programming Language :: Python :: 3.4',
           'Programming Language :: Python :: Implementation :: PyPy',
           'Topic :: Utilities'
       ])

tests/exporter.py

@@ -23,7 +23,8 @@ def test_entry_html(self):
             'year': '2014',
             'id': 'ku2014',
             'type': 'article',
-            'pages': '121--123'}
+            'pages': '121--123',
+            'URL': 'http://www.google.com/'}
         entry_text = "%s<br>\n" % entry_dict['author']
         entry_text += "%s<br>\n" % entry_dict['title']
         entry_text += "%s %s %s;%s(%s):%s.<br>\n" % (
@@ -33,4 +34,7 @@ def test_entry_html(self):
             entry_dict['volume'],
             entry_dict['number'],
             entry_dict['pages'])
+        if 'URL' in entry_dict:
+            link_text = '<a href="{0:s}">{0:s}</a><br>\n'
+            entry_text += link_text.format(entry_dict['URL'])
         self.assertEqual(entry_text, exporter._entry_html(entry_dict))

tests/utils.py

@@ -47,3 +47,24 @@ def test_sort_by_date(self):
         result = utils.sort_by_date(entries, reverse=True)
         for es in zip(result, expected_result):
             self.assertEqual(es[0], es[1])
+
+    def test_pmid_to_url(self):
+        # Test data
+        entry_first = {
+            'title': 'First',
+            'id': 'aaa'}
+        entry_second = {
+            'title': 'Second',
+            'id': 'pmid24685317'}
+        entry_third = {
+            'title': 'Third',
+            'id': 'pmid24685317',
+            'URL': 'http://www.google.com/'}
+        entries = [entry_first, entry_second, entry_third]
+
+        result = utils.pmid_to_url(entries)
+
+        self.assertFalse('URL' in result[0])
+        self.assertEqual(result[1]['URL'],
+                        'http://www.ncbi.nlm.nih.gov/pubmed/24685317')
+        self.assertEqual(result[2]['URL'], entry_third['URL'])