Fix errors found during additional testing

Makefile

@@ -1,17 +1,22 @@
-build: python-packages links
+build: python-packages links env/bin/srcml
 
 .PHONY: links
 links: env/bin/apply.py
 
 env/bin/apply.py: env
 	ln -s $$(realpath scripts/patch_apply/apply.py) env/bin
 
+env/bin/srcml:
+	if [ -z "$$(which srcml)" ]; then cd env; curl http://gehry.sdml.cs.kent.edu/lmcrs/v1.0.0/srcml_1.0.0-1_ubuntu20.04.tar.gz | tar -zxv ; else ln -s "$$(which srcml)" /env/bin/srcml; fi
+	if [ -f "env/bin/srcml" ]; then mv env/bin/srcml env/bin/srcml-binary; echo '#!/bin/bash\nLD_LIBRARY_PATH=$(CURDIR)/env/lib exec srcml-binary $$*' >env/bin/srcml; chmod +x env/bin/srcml; fi;
+
 .PHONY: python-packages
 python-packages: env
 	@if [ ! -d env/lib/python*/site-packages/diff_match_patch ]; then echo "Installing diff_match_patch"; . env/bin/activate; python3 -m pip install diff_match_patch; fi
 	@if [ ! -d env/lib/python*/site-packages/Levenshtein ]; then echo "Installing Levenshtein"; . env/bin/activate; python3 -m pip install Levenshtein; fi
 	@if [ ! -d env/lib/python*/site-packages/pygments ]; then echo "Installing diff_match_patch"; . env/bin/activate; python3 -m pip install pygments; fi
 	@if [ ! -x env/bin/pytest ]; then echo "Installing pytest"; . env/bin/activate; python3 -m pip install pytest; fi
+	@if [ ! -x env/bin/pytest-cov ]; then echo "Installing pytest-cov"; . env/bin/activate; python3 -m pip install pytest-cov; fi
 
 env:
 	python3 -m venv env

scripts/patch_apply/apply.py

@@ -17,6 +17,10 @@
 import scripts.patch_apply.check_file_exists_elsewhere as check_exist
 from scripts.enums import MatchStatus, natureOfChange, CONTEXT_DECISION, precheckStatus
 
+def indent(text, amount, ch = ' '):
+    padding = amount * ch
+    return ''.join(padding + line for line in text.splitlines(True))
+
 def findGitPrefix(path):
     prefix=''
     resolved=False
@@ -240,7 +244,7 @@ def apply(pathToPatch, **kwargs):
         error_message = patch_file.runResult
         if kwargs['verbose'] > 0:
             print("Patch failed while it was run with git apply with error:")
-            print(error_message)
+            print(indent(error_message, 4))
         else:
             print("Patch failed to apply with git apply.")
 
@@ -250,17 +254,21 @@ def apply(pathToPatch, **kwargs):
         does_not_apply = set()
 
         for line in error_message_lines:
-            print(line)
             split_line = [s.strip() for s in line.split(":")]
             if line[0:2] == "  ":
                 pass
             elif split_line[0] == "error":
                 if split_line[1].startswith("corrupt patch"):
                     line_num = re.findall(r'\d+', split_line[1])
-                    print("The patch is corrupted at line %s, stop processing..." % line_num[0])
+                    print("The patch is corrupted at line %s." % line_num[0])
                     return 1
-
-                if split_line[2] == "patch does not apply":
+                elif split_line[1].startswith("git diff header lacks filename information"):
+                    print("The patch is corrupted at line %s." % line_num[0])
+                    return 1
+                elif split_line[1].startswith("cannot apply binary patch"):
+                    print("Binary patch detected.")
+                    return 1
+                elif split_line[2] == "patch does not apply":
                     does_not_apply.add(split_line[1])
                 elif split_line[2] == "already exists":
                     already_exists.add(split_line[1])
@@ -307,10 +315,10 @@ def apply(pathToPatch, **kwargs):
             gitFileName = os.path.join( findGitPrefix(fileName), fileName )
 
             if see_patches:
-                print("\n" + ":".join([fileName, str(patch._lineschanged[0])]))
+                print("\n" + ":".join([fileName, str(patch._oldStart)]))
                 print(patch)
 
-            subpatch_name = ":".join([fileName, str(patch._lineschanged[0])])
+            subpatch_name = ":".join([fileName, str(patch._oldStart)])
 
             if gitFileName in file_not_found:
                 correct_loc = check_exist.checkFileExistsElsewhere(patch)

scripts/patch_apply/check_file_exists_elsewhere.py

@@ -30,8 +30,8 @@ def checkFileExistsElsewhere(patch):
 
     if len(matched_file_locations) == 0:
         return None
-    else:
-        print("----------------------------------------------------------------------")
+    elif sys.stdout.isatty():
+        print("-" * 70)
         print(
             "Here are the locations of files with the same filename as the following missing file: {}".format(
                 toFind
@@ -44,7 +44,7 @@ def checkFileExistsElsewhere(patch):
             "Select the file you would like to apply the patch to by entering the number next to it. Enter anything else to do nothing\n"
         )
 
-        print("----------------------------------------------------------------------")
+        print("-" * 70)
         try:
             to_apply_file_index = int(to_apply_file_index)
             if 0 <= to_apply_file_index and to_apply_file_index < len(
@@ -53,7 +53,10 @@ def checkFileExistsElsewhere(patch):
                 return matched_file_locations[to_apply_file_index]
         except ValueError:
             return None
-
+    else:
+        print(f"Possible files to apply the patch for {toFind} to:")
+        for i in matched_file_locations:
+            print(f"  {i}")
 
 # Testing
 # patch_file = parse.PatchFile("../vulnerableforks/patches/CVE-2014-8172.patch")