Added mutator choice for web and cli

README.md

@@ -145,8 +145,7 @@ we click on [example.cpp](http://127.0.0.1:5000/projects/1/files/1), we see the
 
 - Next to "example.cpp", click on ["generate patches"](http://127.0.0.1:5000/projects/1/files/1/generate).
 - Leave "first line" and "last line" empty to mutate the whole file.
-- Right now, none of the check boxes are actually implemented, so you can ignore all of them - all mutations will be
-  used by default.
+- Select check boxes of mutations you want to use. If none is selected, all mutations will be used by default.
 - Click on "Generate patches".
 
 Back in the [project overview](http://127.0.0.1:5000/projects/1), you see that 14 patches have been generated. You can
@@ -275,13 +274,21 @@ venv/bin/python3 cli/add_files.py --project "Example project" /tmp/cmake-example
 ```
 
 ### `generate_patches.py`
-This script will generate patches for all files in a project.
+This script will generate patches for files in a project using selected mutators.
 
 Example usage:
 ```bash
 venv/bin/python3 cli/generate_patches.py --project "Example project"
 ```
 
+Example usage with files and mutators:
+```bash
+venv/bin/python3 cli/generate_patches.py \
+  --project "Example project" \
+  --files /tmp/cmake-example/src/example.cpp:13:-1 \
+  --mutators logicalOperator,lineDeletion
+```
+
 ### `queue_control.py`
 This script allows you to control the queue and view its state.
 
@@ -290,6 +297,26 @@ Example usage:
 venv/bin/python3 cli/queue_control.py start
 ```
 
+## List of mutators
+
+| Mutator | Description |
+|----------|-------------|
+| lineDeletion | Deletes a whole line |
+| logicalOperator | Replaces logical operators (&&, \|\|, and, or, !, not) |
+| comparisonOperator | Replaces comparison operators (==, !=, <, >, <=, >=) |
+| incDecOperator | Swaps increment and decrement operators (++, --) |
+| assignmentOperator | Replaces assignment operators (=, +=, -=, *=, /=, %=) |
+| booleanAssignmentOperator | Replaces Boolean assignment operators (=, &=, \|=, ^=, <<=, >>=) |
+| arithmeticOperator | Replaces arithmetic operators (+, -, *, /, %) |
+| booleanArithmeticOperator | Replaces Boolean arithmetic operators (&, \|, ^, <<, >>) |
+| booleanLiteral | Swaps the Boolean literals true and false |
+| stdInserter | Changes the position where elements are inserted (front_inserter, back_inserter) |
+| stdRangePredicate | Changes the semantics of an STL range predicate (all_of, any_of, none_of) |
+| stdMinMax | Swaps STL minimum by maximum calls (min, max) |
+| decimalNumberLiteral | Replaces decimal number literals with different values |
+| hexNumberLiteral | Replaces hex number literals with different values |
+| iteratorRange | Changes an iterator range (begin, end) |
+
 ## Help!
 
 Mutate++ is in a very early stage, and there is a lot to do. In particular, we are aware of severe limitations:

app/utils/Mutation.py

@@ -339,7 +339,7 @@ def find_mutations(self, line):
         return self.pattern.mutate(line)
 
 
-def get_mutators():
+def get_mutators(mutator_ids=None):
     mutators = [
         LineDeletionMutator(),
         LogicalOperatorMutator(),
@@ -358,4 +358,7 @@ def get_mutators():
         IteratorRangeMutator()
     ]
 
-    return {mutator.mutator_id: mutator for mutator in mutators}
+    if mutator_ids:
+        mutators = [mutator for mutator in mutators if mutator.mutator_id in mutator_ids]
+
+    return {mutator.mutator_id: mutator for mutator in mutators}

app/utils/SourceFile.py

@@ -25,8 +25,8 @@ def __init__(self, file: File, first_line, last_line):
         # read the relevant content
         self.content = '\n'.join(self.full_content[self.first_line - 1:self.last_line])  # type: str
 
-    def generate_patches(self):
-        mutators = get_mutators()
+    def generate_patches(self, mutator_ids):
+        mutators = get_mutators(mutator_ids)
 
         for line_number, line_raw in self.__get_lines():
             for mutator_name, mutator in mutators.items():

app/views.py

@@ -351,8 +351,9 @@ def route_v2_project_project_id_files_file_id_generate(project_id, file_id):
         except ValueError:
             last_line = -1
 
+        mutators = [key for key in request.form if key not in ['first_line', 'last_line']]
         s = SourceFile(file, first_line, last_line)
-        s.generate_patches()
+        s.generate_patches(mutators)
         flash('Successfully created patches.', category='message')
         return redirect(url_for('route_v2_project_project_id', project_id=project.id))
 

cli/generate_patches.py

@@ -19,7 +19,14 @@ def main():
         "--project", type=str, required=True,
         help="The name of the project. If not provided, all projects will be processed."
     )
-    # TODO allow selection of first/last line + which patches to generate
+    argument_parser.add_argument(
+        "--files", type=str,
+        help='File list in format: "file1@start:end;file2@start:end". If not provided, all files in project will be used.'
+    )
+    argument_parser.add_argument(
+        "--mutators", type=str,
+        help="Comma-separated list of mutators to use. If not provided, all mutators will be used."
+    )
     arguments = argument_parser.parse_args()
 
     # Verify that the project exists
@@ -35,10 +42,28 @@ def main():
         print("No files found to process.")
         exit(2)
 
+    # Parse mutators if specified
+    mutator_ids = arguments.mutators.split(',') if arguments.mutators else None
+
+    # Parse file filters if specified
+    file_filters = {}
+    if arguments.files:
+        for file_spec in arguments.files.split(';'):
+            filename, line_range = file_spec.split('@')
+            first_line, last_line = map(int, line_range.split(':'))
+            file_filters[filename] = (first_line, last_line)
+
+    # Process files
     for file in files:
+        if file_filters and file.filename not in file_filters:
+            continue
+
         print(f"Generating patches for '{file.filename}'...")
-        source_file = SourceFile(file, 1, -1)
-        source_file.generate_patches()
+
+        # If file_filters is empty use all lines of every file
+        first_line, last_line = file_filters.get(file.filename, (1, -1))
+        source_file = SourceFile(file, first_line, last_line)
+        source_file.generate_patches(mutator_ids)
 
     print("Done")
     exit(0)