A few changes that made mutate_cpp working on Ubuntu 16.04

.gitignore

@@ -1,3 +1,4 @@
 .idea
 venv
 *.pyc
+*.db

app/__init__.py

@@ -4,6 +4,10 @@
 from flask_compress import Compress
 from flask_sqlalchemy import SQLAlchemy
 from flask_humanize import Humanize
+import os.path
+import sys
+
+sys.path.append( os.path.dirname( os.path.abspath( __file__ ) ) )
 
 app = Flask(__name__)
 app.config.from_object('config')

app/utils/Executor.py

@@ -4,7 +4,7 @@
 import subprocess
 from threading import Timer, Thread
 import psutil
-from app.models import Patch, Run
+from app.models import Patch, Run, File
 import tempfile
 import os
 import datetime
@@ -74,33 +74,37 @@ def killer(process):
 
     def workflow(self, patch: Patch):
         assert self.__current_patch is None, 'no auto-concurrency!'
-        self.__current_patch = patch
-
-        # step 1: write patch to temp file
-        patchfile = tempfile.NamedTemporaryFile(delete=False, mode='w')
-        patchfile.write(patch.patch)
-        patchfile.close()
-
-        # step 2: apply patch
-        self.__execute_command_timeout('patch -p1 --input={patchfile}'.format(patchfile=patchfile.name), cwd='/')
-
-        # step 3: command pipeline
-        success = self.__apply_command(patch, 'build_command') and \
-                  self.__apply_command(patch, 'quickcheck_command') and \
-                  self.__apply_command(patch, 'test_command')
-
-        if success:
-            patch.state = 'survived'
-            db.session.commit()
-
-        # step 4: revert patch
-        self.__execute_command_timeout('patch -p1 --reverse --input={patchfile}'.format(patchfile=patchfile.name),
+
+        file = File.query.get(patch.file_id)
+
+        if file is not None:
+            self.__current_patch = patch
+
+            # step 1: write patch to temp file
+            patchfile = tempfile.NamedTemporaryFile(delete=False, mode='w')
+            patchfile.write(patch.patch)
+            patchfile.close()
+
+            # step 2: apply patch
+            self.__execute_command_timeout('patch -p1 --input={patchfile} {inputfile}'.format(patchfile=patchfile.name, inputfile=file.filename), cwd='/')
+
+            # step 3: command pipeline
+            success = self.__apply_command(patch, 'build_command') and \
+                      self.__apply_command(patch, 'quickcheck_command') and \
+                      self.__apply_command(patch, 'test_command')
+
+            if success:
+                 patch.state = 'survived'
+                 db.session.commit()
+
+            # step 4: revert patch
+            self.__execute_command_timeout('patch -p1 --reverse --input={patchfile} {inputfile}'.format(patchfile=patchfile.name, inputfile=file.filename),
                                        cwd='/')
 
-        # step 6: delete patch file
-        os.remove(patchfile.name)
+            # step 6: delete patch file
+            os.remove(patchfile.name)
 
-        self.__current_patch = None
+            self.__current_patch = None
 
     def __apply_command(self, patch: Patch, step: str):
         print(patch, step)

app/utils/SourceFile.py

@@ -117,14 +117,14 @@ def __create_patch(self, line_number: int, replacement: Replacement) -> str:
         ))
 
         # lines: context before
-        patch_lines += [' ' + x + '\n' for x in context_before]
+        patch_lines += [' ' + x + "\r\n" for x in context_before]
         # line: the old value
-        patch_lines.append('-' + old_line + '\n')
+        patch_lines.append('-' + old_line + "\r\n")
         # line: the new value
         if replacement.new_val is not None:
-            patch_lines.append('+' + new_line + '\n')
+            patch_lines.append('+' + new_line + "\r\n")
         # lines: context after
-        patch_lines += [' ' + x + '\n' for x in context_after]
+        patch_lines += [' ' + x + "\r\n" for x in context_after]
 
         patch_text = ''.join(patch_lines)
         return patch_text

db_create.py

@@ -1,8 +1,8 @@
 # coding=utf-8
 
 from migrate.versioning import api
-from config import SQLALCHEMY_DATABASE_URI
-from config import SQLALCHEMY_MIGRATE_REPO
+from app.config import SQLALCHEMY_DATABASE_URI
+from app.config import SQLALCHEMY_MIGRATE_REPO
 from app import db
 import os.path
 

db_migrate.py

@@ -3,8 +3,8 @@
 import imp
 from migrate.versioning import api
 from app import db
-from config import SQLALCHEMY_DATABASE_URI
-from config import SQLALCHEMY_MIGRATE_REPO
+from app.config import SQLALCHEMY_DATABASE_URI
+from app.config import SQLALCHEMY_MIGRATE_REPO
 
 if __name__ == '__main__':
     v = api.db_version(SQLALCHEMY_DATABASE_URI, SQLALCHEMY_MIGRATE_REPO)

db_upgrade.py

@@ -1,8 +1,8 @@
 # coding=utf-8
 
 from migrate.versioning import api
-from config import SQLALCHEMY_DATABASE_URI
-from config import SQLALCHEMY_MIGRATE_REPO
+from app.config import SQLALCHEMY_DATABASE_URI
+from app.config import SQLALCHEMY_MIGRATE_REPO
 
 if __name__ == '__main__':
     api.upgrade(SQLALCHEMY_DATABASE_URI, SQLALCHEMY_MIGRATE_REPO)