Adds support for binary files

runner/runner.py

@@ -8,6 +8,7 @@
 import logging
 import time
 import os
+from base64 import b64decode
 from datetime import datetime
 from abc import ABC, abstractmethod
 from ase import db
@@ -481,7 +482,11 @@ def _write_run_data(self, atoms, tasks, files, status, log_msg):
         """
         # write files
         for i, string in files.items():
-            write_mode = "wb" if isinstance(string, bytes) else "w"
+            if string.startswith("data:application/octet-stream;base64,"):
+                write_mode = "wb"
+                string = b64decode(string[37:].encode())
+            else:
+                write_mode = "w"
             with open(i, write_mode) as file_o:
                 file_o.write(string)
 

runner/utils/runnerdata.py

@@ -1,6 +1,7 @@
 """ Utility to handle runner data"""
 import json
 import os
+from base64 import b64encode
 from copy import copy
 
 from runner.utils.utils import json_keys2int, get_db_connect
@@ -161,7 +162,10 @@ def add_file(self, filename, add_as=None):
             # file is binary
             with open(filename, "rb") as fio:
                 basename = os.path.basename(add_as)
-                self.data["files"][basename] = fio.read()
+                self.data["files"][basename] = (
+                    "data:application/octet-stream;base64,"
+                    + b64encode(fio.read()).decode()
+                )
 
     def add_files(self, filenames, add_as=None):
         """Adds files to runner data

tests/test_baserunner.py

@@ -14,6 +14,8 @@
 def main(atoms, conf=0):
     assert conf == 0, 'bad params'
     assert isinstance(atoms[0], Atoms), 'bad atoms'
+    with open("test.bin", "rb") as fio:
+        assert fio.read() == b"\\xff;:"
     return atoms
 """
 runner = {
@@ -24,7 +26,10 @@ def main(atoms, conf=0):
         ["python", "energy.py", {"conf": 0}],
         ["python", "energy.py", {"conf": 0}, "python3"],
     ],
-    "files": {"energy.py": energy},
+    "files": {
+        "energy.py": energy,
+        "test.bin": "data:application/octet-stream;base64,/zs6",
+    },
 }
 
 

tests/test_runnerdata.py

@@ -260,8 +260,11 @@ def test_to_from_data():
 
     with db.connect("database.db") as fdb:
         fdb.write(Atoms())
+    with open("test.bin", "wb") as fio:
+        fio.write(b"\xff;:")
 
     runner = RunnerData.from_data_dict(success)
+    runner.add_file("test.bin")
     runner.to_db("database.db", 1)
     runner.to_json("database.json")
     runner = RunnerData.from_db("database.db", 1)
@@ -271,6 +274,7 @@ def test_to_from_data():
     assert parents[0] == 1 and parents[1] == 2
     assert isinstance(scheduler_options, dict)
     assert isinstance(files, dict)
+    assert files["test.bin"] == "data:application/octet-stream;base64,/zs6"
     assert "energy.py" in files
     assert len(tasks) == 4
     runner = RunnerData.from_json("database.json")
@@ -280,5 +284,6 @@ def test_to_from_data():
     assert parents[0] == 1 and parents[1] == 2
     assert isinstance(scheduler_options, dict)
     assert isinstance(files, dict)
+    assert files["test.bin"] == "data:application/octet-stream;base64,/zs6"
     assert "energy.py" in files
     assert len(tasks) == 4