Fixed when fragment has no molblock

Refs #45

CHANGELOG.md

@@ -5,6 +5,12 @@ Formatted as described on http://keepachangelog.com/.
 
 ## Unreleased
 
+## [2.2.1] - 2017-03-07
+
+### Fixed
+
+- Web service has internal server error when fragment has no molblock (#45)
+
 ## [2.2.0] - 2017-02-23
 
 ### Changed

kripodb/version.py

@@ -12,5 +12,5 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-__version_info__ = ('2', '2', '0')
+__version_info__ = ('2', '2', '1')
 __version__ = '.'.join(__version_info__)

kripodb/webservice/server.py

@@ -14,6 +14,8 @@
 """Kripo datafiles wrapped in a webservice"""
 from __future__ import absolute_import
 
+from _ctypes import ArgumentError
+
 from pkg_resources import resource_filename
 import logging
 
@@ -125,7 +127,8 @@ def get_fragments(fragment_ids=None, pdb_codes=None):
             # connexion.problem is using json.dumps instead of flask custom json encoder, so performing convert myself
             # TODO remove mol2string conversion when https://github.com/zalando/connexion/issues/266 is fixed
             for fragment in fragments:
-                fragment['mol'] = MolToMolBlock(fragment['mol'])
+                if fragment['mol']:
+                    fragment['mol'] = MolToMolBlock(fragment['mol'])
             ext = {'absent_identifiers': missing_ids, 'fragments': fragments}
             return connexion.problem(404, title, description, ext=ext)
         return fragments
@@ -154,6 +157,11 @@ def get_fragment_svg(fragment_id, width, height):
     with FragmentsDb(fragments_db_filename) as fragmentsdb:
         try:
             fragment = fragmentsdb[fragment_id]
+            if not fragment['mol']:
+                title = 'Not Found'
+                description = 'Fragment with identifier \'{0}\' has no molblock'.format(fragment_id)
+                ext = {'identifier': fragment_id}
+                return connexion.problem(404, title, description, ext=ext)
             mol = fragment['mol']
             return mol2svg(mol, width, height)
         except LookupError: