Adding a fix for cases when the residue API returns more than one entity per chain label

.gitignore

@@ -1,3 +1,4 @@
 .idea*
 .cache*
-*vcs.xml
+*vcs.xml
+sample_data/*

data/test_data_multichain.json

@@ -0,0 +1,71 @@
+{
+  "data_resource": "ProKinO",
+  "resource_version": "2.0",
+  "software_version": "2.0",
+  "resource_entry_url": "http://vulcan.cs.uga.edu/prokino/",
+  "release_date": "10/02/2017",
+  "pdb_id": "1yj9",
+  "chains": [
+    {
+      "residues": [
+        {
+          "pdb_res_label": "0",
+          "aa_type": "MET",
+          "site_data": [
+            {
+              "confidence_score": 1,
+              "site_id_ref": 1,
+              "confidence_classification": "high",
+              "raw_score": 1
+            }
+          ]
+        },
+        {
+          "pdb_res_label": "1",
+          "aa_type": "GLY",
+          "site_data": [
+            {
+              "confidence_score": 1,
+              "site_id_ref": 2,
+              "confidence_classification": "high",
+              "raw_score": 1
+            }
+          ]
+        },
+        {
+          "pdb_res_label": "2",
+          "aa_type": "ARG",
+          "site_data": [
+            {
+              "confidence_score": 1,
+              "site_id_ref": 2,
+              "confidence_classification": "high",
+              "raw_score": 1
+            }
+          ]
+        }
+      ],
+      "chain_label": "A"
+    }
+  ],
+  "sites": [
+    {
+      "site_id": 1,
+      "label": "HRD motif"
+    },
+    {
+      "site_id": 2,
+      "label": "HRD motif"
+    },
+    {
+      "site_id": 3,
+      "label": "HRD motif"
+    }
+  ],
+  "evidence_code_ontology": [
+    {
+      "eco_term": "computational combinatorial evidence",
+      "eco_code": "ECO_0000246"
+    }
+  ]
+}

tests/test_residue_index.py

@@ -23,6 +23,9 @@ from validator.residue_index import ResidueIndexes
 with open("data/test_data.json", "r") as mock_data_file:
     mock_data = json.load(mock_data_file)
 
+with open("data/test_data_multichain.json", "r") as mock_data_file_multichain:
+    mock_data_multichain = json.load(mock_data_file_multichain)
+
 mock_data_no_pdb_id = {"foo": "bar"}
 
 mock_data_bad_numbering = {"pdb_id": "2aqa",
@@ -101,4 +104,9 @@ class TestCheckResidueIndices(TestCase):
         self.assertFalse(result)
         result = self.cri._process_residues(
             [{"author_residue_number": 1, "residue_name": "ALA", "author_insertion_code": ""}], "1", "HIS")
-        self.assertFalse(result)
+        self.assertFalse(result)
+
+    def test_with_multichain(self):
+        self.cri = ResidueIndexes(mock_data_multichain)
+        result = self.cri.check_every_residue()
+        self.assertTrue(result)

validator/residue_index.py

@@ -116,13 +116,15 @@ class ResidueIndexes(object):
         :param depositor_aa_type: Residue amino acid code provided by user
         :return: True is residue numbering is valid, False if not
         """
+        flag = None
         for item in data:
             sub_data = item[label]
             if label == "chains":
-                return self._recursive_loop(sub_data, "residues", depositor_residue_number, depositor_aa_type)
+                flag = self._recursive_loop(sub_data, "residues", depositor_residue_number, depositor_aa_type)
             elif label == "residues":
                 return self._process_residues(sub_data, depositor_residue_number, depositor_aa_type)
-            return False
+        if label == "chains":
+            return flag
 
     def _process_residues(self, residues, depositor_residue_number, depositor_aa_type):
         """