[Fix #95] robust handling of DOIs

Added DOI regex function to utils.py which is called in add_cmd.py
upon specifying a new DOI.  DOI validation applies directly on
argument parsing by using a custom argparse.Action.

pubs/commands/add_cmd.py

@@ -1,3 +1,4 @@
+import argparse
 from ..uis import get_ui
 from .. import bibstruct
 from .. import content
@@ -7,13 +8,21 @@ from .. import templates
 from .. import apis
 from .. import color
 from .. import pretty
+from .. import utils
 
+class ValidateDOI(argparse.Action):
+    def __call__(self, parser, namespace, values, option_string=None):
+        doi = values
+        new_doi = utils.standardize_doi(doi)
+        if not new_doi:
+            raise ValueError("Not a valid doi: %s", doi)
+        setattr(namespace, self.dest, new_doi)
 
 def parser(subparsers, conf):
     parser = subparsers.add_parser('add', help='add a paper to the repository')
     parser.add_argument('bibfile', nargs='?', default=None,
                         help='bibtex file')
-    parser.add_argument('-D', '--doi', help='doi number to retrieve the bibtex entry, if it is not provided', default=None)
+    parser.add_argument('-D', '--doi', help='doi number to retrieve the bibtex entry, if it is not provided', default=None, action=ValidateDOI)
     parser.add_argument('-I', '--isbn', help='isbn number to retrieve the bibtex entry, if it is not provided', default=None)
     parser.add_argument('-d', '--docfile', help='pdf or ps file', default=None)
     parser.add_argument('-t', '--tags', help='tags associated to the paper, separated by commas',

pubs/utils.py

@@ -1,5 +1,7 @@
 # Function here may belong somewhere else. In the mean time...
 
+import re
+
 from . import color
 from . import pretty
 
@@ -44,3 +46,36 @@ def resolve_citekey_list(repo, citekeys, ui=None, exit_on_fail=True):
         ui.exit()
     else:
         return keys
+
+def standardize_doi(doi):
+    """
+    Given a putative doi, attempts to always return it in the form of
+    10.XXXX/...  Specifically designed to handle these cases:
+    -   https://doi.org/<doi>
+    -   http://doi.org/<doi>
+    -   https://dx.doi.org/<doi>
+    -   http://dx.doi.org/<doi>
+    -   dx.doi.org/<doi>
+    -   doi.org/<doi>
+    and attempts to verify doi adherence to DOI handbook standards and
+    crossref.org advice:
+    https://www.doi.org/doi_handbook/2_Numbering.html
+    https://www.crossref.org/blog/dois-and-matching-regular-expressions/"""
+    """ :returns standardized doi """
+    doi_regexes = (
+        re.compile(r'(10\.\d{4,9}/[-._;()/:A-z0-9\>\<]+)'),
+        re.compile(r'(10.1002/[^\s]+)'),
+        re.compile(r'(10\.\d{4}/\d+-\d+X?(\d+)\d+<[\d\w]+:[\d\w]*>\d+.\d+.\w+;\d)'),
+        re.compile(r'(10\.1021/\w\w\d+\+)'),
+        re.compile(r'(10\.1207/[\w\d]+\&\d+_\d+)')
+        )
+
+    for doi_regex in doi_regexes:
+        match = doi_regex.search(doi)
+        if match:
+            new_doi = match.group(0)
+            break
+    else:
+        new_doi = None
+
+    return new_doi

tests/test_doi.py

@@ -0,0 +1,80 @@
+# coding: utf8
+
+from __future__ import unicode_literals
+import unittest
+
+from pubs.p3 import ustr
+from pubs.utils import standardize_doi
+
+class TestDOIStandardization(unittest.TestCase):
+
+    def setUp(self):
+        # some of these come from
+        # https://stackoverflow.com/questions/27910/finding-a-doi-in-a-document-or-page
+        self.crossref_dois = (
+            '10.2310/JIM.0b013e31820bab4c',
+            '10.1007/978-3-642-28108-2_19',
+            '10.1016/S0735-1097(98)00347-7',
+        )
+
+        self.hard_dois = (
+            '10.1175/1520-0485(2002)032<0870:CT>2.0.CO;2',
+            '10.1002/(SICI)1522-2594(199911)42:5<952::AID-MRM16>3.0.CO;2-S',
+            '10.1579/0044-7447(2006)35\[89:RDUICP\]2.0.CO;2',
+        )
+
+        self.currently_not_supported = (
+            '10.1007.10/978-3-642-28108-2_19',
+            '10.1000.10/123456',
+            '10.1016.12.31/nature.S0735-1097(98)2000/12/31/34:7-7',
+        )
+
+    def test_http_dxdoi_org(self):
+        doi = 'http://dx.doi.org/10.1109/5.771073'
+        sdoi = standardize_doi(doi)
+        self.assertEqual(sdoi, '10.1109/5.771073')
+
+    def test_https_dxdoi_org(self):
+        doi = 'https://dx.doi.org/10.1109/5.771073'
+        sdoi = standardize_doi(doi)
+        self.assertEqual(sdoi, '10.1109/5.771073')
+
+    def test_http_doi_org(self):
+        doi = 'http://doi.org/10.1109/5.771073'
+        sdoi = standardize_doi(doi)
+        self.assertEqual(sdoi, '10.1109/5.771073')
+
+    def test_https_doi_org(self):
+        doi = 'https://doi.org/10.1109/5.771073'
+        sdoi = standardize_doi(doi)
+        self.assertEqual(sdoi, '10.1109/5.771073')
+
+    def test_doi_org(self):
+        doi = 'doi.org/10.1109/5.771073'
+        sdoi = standardize_doi(doi)
+        self.assertEqual(sdoi, '10.1109/5.771073')
+
+    def test_dxdoi_org(self):
+        doi = 'dx.doi.org/10.1109/5.771073'
+        sdoi = standardize_doi(doi)
+        self.assertEqual(sdoi, '10.1109/5.771073')
+
+    def test_doi_colon_org(self):
+        doi = 'doi:10.1109/5.771073'
+        sdoi = standardize_doi(doi)
+        self.assertEqual(sdoi, '10.1109/5.771073')
+
+    def test_crossref_dois(self):
+        for doi in self.crossref_dois:
+            sdoi = standardize_doi(doi)
+            self.assertEqual(doi, sdoi)
+
+    def test_hard_dois(self):
+        for doi in self.hard_dois:
+            sdoi = standardize_doi(doi)
+            self.assertEqual(doi, sdoi)
+
+    def test_currently_not_supported(self):
+        for doi in self.currently_not_supported:
+            sdoi = standardize_doi(doi)
+            self.assertIs(sdoi, None)