Merge remote-tracking branch 'origin/hotfix'

docs/conf.py

@@ -69,7 +69,7 @@
 # The short X.Y version.
 version = '1.4'
 # The full version, including alpha/beta/rc tags.
-release = '1.4.2'
+release = '1.4.3'
 
 # The language for content autogenerated by Sphinx. Refer to documentation
 # for a list of supported languages.

docs/index.rst

@@ -49,8 +49,14 @@ New in release |release|
 
 This is a hotfix release. It fixes the following issues:
 
-- This releases fixes a concurrency issue with pVACapi/pVACviz that would occurr when
-  users would try to visualize multiple files at the same time
+- IEDB will output a warning if an epitope contains only amino acid symbols
+  that could also be nucleotides. This would cause an error during parsing of
+  the IEDB output files. This version updates the parser to ignore these
+  warnings.
+- We added some improvements to pVACapi regarding database file read
+  speeds and transaction handling. This version also starts enforcing a file
+  size limit (14MB) for result files. Larger files will no longer be
+  visualizable in pVACviz since they take too long to load.
 
 New in version |version|
 ------------------------

docs/releases/1_4.rst

@@ -49,3 +49,17 @@ This is a hotfix release. It fixes the following issues:
 
 - This releases fixes a concurrency issue with pVACapi/pVACviz that would occurr when
   users would try to visualize multiple files at the same time.
+
+1.4.3
+-----
+
+This is a hotfix release. It fixes the following issues:
+
+- IEDB will output a warning if an epitope contains only amino acid symbols
+  that could also be nucleotides. This would cause an error during parsing of
+  the IEDB output files. This version updates the parser to ignore these
+  warnings.
+- We added some improvements to pVACapi regarding database file read
+  speeds and transaction handling. This version also starts enforcing a file
+  size limit (14MB) for result files. Larger files will no longer be
+  visualizable in pVACviz since they take too long to load.

lib/output_parser.py

@@ -490,6 +490,8 @@ def parse_iedb_file(self, tsv_entries):
                 iedb_tsv_reader = csv.DictReader(reader, delimiter='\t')
                 (sample, method, remainder) = os.path.basename(input_iedb_file).split(".", 2)
                 for line in iedb_tsv_reader:
+                    if "Warning: Potential DNA sequence(s)" in line['allele']:
+                        continue
                     protein_label  = int(line['seq_num'])
                     if 'core_peptide' in line and int(line['end']) - int(line['start']) == 8:
                         #Start and end refer to the position of the core peptide

setup.py

@@ -56,7 +56,7 @@
 
 setup(
     name="pvactools",
-    version="1.4.2",
+    version="1.4.3",
     packages=[
         "tools",
         "tools.pvacfuse",
@@ -80,7 +80,7 @@
     install_requires=[
         'PyVCF',
         'requests',
-        'PyYAML',
+        'PyYAML>=5.1',
         'connexion==1.4.2',
         'biopython',
         'networkx',

tests/test_api.py

@@ -1172,6 +1172,11 @@ def check_res(result):
 
             self.assertTrue(check_res(filtered_results))
 
+    def test_max_file_size(self):
+        with unittest.mock.patch('os.path.getsize', return_value=14*1024*1024):
+            from utils.pvacapi.controllers.utils import file_not_max
+            self.assertFalse(file_not_max('arbitrary/file/path'))
+
     #pagination temporarily put on hold.
     """
     def test_pagination(self):