Add basic sed capability to wxflow.

src/wxflow/file_utils.py

@@ -1,5 +1,6 @@
 from logging import getLogger
 
+from .executable import which
 from .fsutils import cp, mkdir
 
 __all__ = ['FileHandler']
@@ -17,8 +18,8 @@ class FileHandler:
 
     NOTE
     ----
-    "action" can be one of mkdir", "copy", etc.
-    Corresponding "act" would be ['dir1', 'dir2'], [['src1', 'dest1'], ['src2', 'dest2']]
+    "action" can be one of "mkdir", "copy", "sed_replace", etc.
+    Corresponding "act" would be ['dir1', 'dir2'], [['src1', 'dest1'], ['src2', 'dest2']], [['s/search_term/replace_term/<g>', 'src', 'dest']]
 
     Attributes
     ----------
@@ -37,6 +38,7 @@ def sync(self):
         sync_factory = {
             'copy': self._copy_files,
             'mkdir': self._make_dirs,
+            'sed_replace': self._sed_replace_files
         }
         # loop through the configuration keys
         for action, files in self.config.items():
@@ -75,3 +77,38 @@ def _make_dirs(dirlist):
         for dd in dirlist:
             mkdir(dd)
             logger.info(f'Created {dd}')
+
+    @staticmethod
+    def _sed_replace_files(sedlist):
+        """Function to run sed search and replace on a set of files
+
+        `sedlist` should be in the form:
+        - [s/search/replace/<g>, src, dest]
+
+        Parameters
+        ----------
+        filelist : list
+                List of lists of [pattern, src, dest]
+        """
+
+        sed = which("sed")
+
+        for sublist in sedlist:
+            if len(sublist) != 3:
+                raise Exception(
+                    f"List must be of the form ['pattern', 'src', 'dest'], not {sublist}")
+
+            pattern = sublist[0]
+            src = sublist[1]
+            dest = sublist[2]
+
+            # Check for in-place search/replace
+            if src == dest:
+                arg_list = ["-i", pattern, src]
+                print(arg_list)
+                sed(*arg_list, output=str.split, error=str.split)
+                logger.info(f'Performed sed -i {pattern} {src}')
+            else:
+                arg_list = [pattern, src]
+                output = sed(*arg_list, output=dest, error=str.split)
+                logger.info(f'Performed sed {pattern} {src} > {dest}')

tests/test_file_utils.py

@@ -2,7 +2,6 @@
 
 from wxflow import FileHandler
 
-
 def test_mkdir(tmp_path):
     """
     Test for creating directories:
@@ -65,3 +64,50 @@ def test_copy(tmp_path):
     # Check if files were indeed copied
     for ff in dest_files:
         assert os.path.isfile(ff)
+
+
+def test_sed_replace(tmp_path):
+    """
+    Test for copying files:
+    Parameters
+    ----------
+    tmp_path - pytest fixture
+    """
+
+    input_dir_path = tmp_path / 'my_input_dir'
+
+    # Create the input directory
+    config = {'mkdir': [input_dir_path]}
+    FileHandler(config).sync()
+
+    # Put empty files in input_dir_path
+    src_files = [input_dir_path / 'a.txt', input_dir_path / 'b.txt']
+    for ff in src_files:
+        ff.touch()
+        ff.write_text("Search text")
+
+    # Create output_dir_path and expected file names
+    output_dir_path = tmp_path / 'my_output_dir'
+    config = {'mkdir': [output_dir_path]}
+    FileHandler(config).sync()
+    # Create one new file and replace in place for the second
+    dest_files = [output_dir_path / 'a.txt', input_dir_path / 'b.txt']
+
+    sed_list = []
+    pattern = "s/Search text/Text found and replaced/"
+    for src, dest in zip(src_files, dest_files):
+        sed_list.append([pattern, str(src), str(dest)])
+
+    # Create config object for FileHandler
+    config = {'sed_replace': sed_list}
+
+    # Copy input files to output files
+    FileHandler(config).sync()
+
+    # Check if files were indeed copied
+    for ff in dest_files:
+        assert os.path.isfile(ff)
+        with open(ff) as f:
+            lines = f.readlines()
+            assert len(lines) == 1
+            assert "Text found and replaced" in lines[0]