Merge pull request #160 from openvax/fix-read-from-json

Fixing serialization of VaccinePeptide objects
openvax · Feb 28, 2018 · 1105c19 · 1105c19
2 parents 75783e5 + b2f7142
commit 1105c19
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Showing 4 changed files with 8 additions and 4 deletions.
diff --git a/.travis.yml b/.travis.yml
@@ -20,6 +20,7 @@ cache:
     - $HOME/.cache/pyensembl/GRCm38/ensembl87/
     - $HOME/.cache/vaxrank
     - $HOME/.cache/pip
+  timeout: 300
 before_install:
   - |
     if [[ "$TRAVIS_PYTHON_VERSION" == "2.7" ]]; then

diff --git a/vaxrank/__init__.py b/vaxrank/__init__.py
@@ -1 +1 @@
-__version__ = "0.7.9"
+__version__ = "0.7.10"
diff --git a/vaxrank/report.py b/vaxrank/report.py
@@ -257,7 +257,7 @@ def _query_wustl(self, predicted_effect, gene_name):
         Returns a link to the WUSTL page for this variant, if present.
         """
         amino_acids = predicted_effect.short_description
-        api_url = "http://docm.genome.wustl.edu/api/v1/variants.json?amino_acids=%s&genes=%s" % (
+        api_url = "http://www.docm.info/api/v1/variants.json?amino_acids=%s&genes=%s" % (
             amino_acids, gene_name.upper())
         logger.info("WUSTL link: %s", api_url)
 

diff --git a/vaxrank/vaccine_peptide.py b/vaxrank/vaccine_peptide.py
@@ -29,6 +29,7 @@
         "wildtype_epitope_predictions",
         "mutant_epitope_score",
         "wildtype_epitope_score",
+        "num_mutant_epitopes_to_keep",
         "manufacturability_scores"])
 
 class VaccinePeptide(VaccinePeptideBase):
@@ -64,6 +65,7 @@ def __new__(
             wildtype_epitope_predictions=wildtype_epitope_predictions,
             mutant_epitope_score=mutant_epitope_score,
             wildtype_epitope_score=wildtype_epitope_score,
+            num_mutant_epitopes_to_keep=num_mutant_epitopes_to_keep,
             manufacturability_scores=ManufacturabilityScores.from_amino_acids(
                 mutant_protein_fragment.amino_acids))
 
@@ -189,8 +191,9 @@ def combined_score(self):
         return self.expression_score * self.mutant_epitope_score
 
     def to_dict(self):
+        epitope_predictions = self.mutant_epitope_predictions + self.wildtype_epitope_predictions
         return {
             "mutant_protein_fragment": self.mutant_protein_fragment,
-            "mutant_epitope_predictions": self.mutant_epitope_predictions,
-            "wildtype_epitope_predictions": self.wildtype_epitope_predictions,
+            "epitope_predictions": epitope_predictions,
+            "num_mutant_epitopes_to_keep": self.num_mutant_epitopes_to_keep,
         }