Coerce amendment source DOIs to URL form.

This is done when fetching, adding, or updating a taxonomic amendment
via the API (so it "repairs" old amendments on the fly). Addresses #155.

peyotl/api/amendments_api.py

@@ -2,7 +2,7 @@
 from peyotl.amendments.amendments_umbrella import TaxonomicAmendmentStore, TaxonomicAmendmentStoreProxy
 from peyotl.api.wrapper import _WSWrapper, APIWrapper
 from peyotl.amendments import AMENDMENT_ID_PATTERN
-from peyotl.utility import get_logger
+from peyotl.utility import get_logger, doi2url
 import anyjson
 import os
 _LOG = get_logger(__name__)
@@ -121,6 +121,7 @@ def get_amendment(self, amendment_id):
         else:
             assert self._src_code == _GET_API
             r = self._remote_get_amendment(amendment_id)
+        self._coerce_source_dois_to_urls(r.get('data'))
         return r
     @property
     def auth_token(self):
@@ -146,10 +147,25 @@ def _remote_push_failure(self):
     def unmerged_branches(self):
         uri = '{}/amendments/unmerged_branches'.format(self._prefix)
         return self.json_http_get(uri)
+    def _coerce_source_dois_to_urls(self,
+                                    json):
+        # Convert source DOIs to their URL form (when fetching, saving, or
+        # updating an amendment)
+        taxa = json.get('taxa')
+        if isinstance(taxa, list):
+            for taxon in taxa:
+                sources = taxon.get('sources')
+                if isinstance(sources, list):
+                    for src in sources:
+                        if src.get('source_type') == "Link (DOI) to publication":
+                            doi = src.get('source', "")
+                            src.set('source', doi2url(doi) )
+
     def post_amendment(self,
                        json,
                        commit_msg=None):
         assert json is not None
+        self._coerce_source_dois_to_urls(json)
         uri = '{d}/amendment'.format(d=self._prefix)
         params = {'auth_token': self.auth_token}
         if commit_msg:
@@ -163,6 +179,7 @@ def put_amendment(self,
                       starting_commit_sha,
                       commit_msg=None):
         assert json is not None
+        self._coerce_source_dois_to_urls(json)
         uri = '{d}/amendment/{i}'.format(d=self._prefix, i=amendment_id)
         params = {'starting_commit_SHA':starting_commit_sha,
                   'auth_token': self.auth_token}