Merge pull request #936 from KevinMenden/fix-create

Fixing bugs in nf-core create
nf-core · Mar 23, 2021 · e0f0d1b · e0f0d1b
2 parents 3dd6427 + 3261493
commit e0f0d1b
Showing 1 changed file with 26 additions and 15 deletions.
diff --git a/nf_core/create.py b/nf_core/create.py
@@ -83,7 +83,8 @@ def render_template(self):
             loader=jinja2.PackageLoader("nf_core", "pipeline-template"), keep_trailing_newline=True
         )
         template_dir = os.path.join(os.path.dirname(__file__), "pipeline-template")
-        binary_ftypes = ["image", "application/java-archive"]
+        binary_ftypes = ["image", "application/java-archive", "application/x-java-archive"]
+        binary_extensions = [".jpeg", ".jpg", ".png", ".zip", ".gz", ".jar", ".tar"]
         object_attrs = vars(self)
         object_attrs["nf_core_version"] = nf_core.__version__
 
@@ -106,23 +107,33 @@ def render_template(self):
             output_path = os.path.join(self.outdir, template_fn)
             os.makedirs(os.path.dirname(output_path), exist_ok=True)
 
-            # Just copy binary files
-            (ftype, encoding) = mimetypes.guess_type(template_fn_path)
-            if encoding is not None or (ftype is not None and any([ftype.startswith(ft) for ft in binary_ftypes])):
-                log.debug(f"Copying binary file: '{output_path}'")
+            try:
+                # Just copy certain file extensions
+                filename, file_extension = os.path.splitext(template_fn_path)
+                if file_extension in binary_extensions:
+                    raise AttributeError(f"File extension: {file_extension}")
+
+                # Try to detect binary files
+                (ftype, encoding) = mimetypes.guess_type(template_fn_path, strict=False)
+                if encoding is not None or (ftype is not None and any([ftype.startswith(ft) for ft in binary_ftypes])):
+                    raise AttributeError(f"Encoding: {encoding}")
+
+                # Got this far - render the template
+                log.debug(f"Rendering template file: '{template_fn}'")
+                j_template = env.get_template(template_fn)
+                rendered_output = j_template.render(object_attrs)
+
+                # Write to the pipeline output file
+                with open(output_path, "w") as fh:
+                    log.debug(f"Writing to output file: '{output_path}'")
+                    fh.write(rendered_output)
+
+            # Copy the file directly instead of using Jinja
+            except (AttributeError, UnicodeDecodeError) as e:
+                log.debug(f"Copying file without Jinja: '{output_path}' - {e}")
                 shutil.copy(template_fn_path, output_path)
                 continue
 
-            # Render the template
-            log.debug(f"Rendering template file: '{template_fn}'")
-            j_template = env.get_template(template_fn)
-            rendered_output = j_template.render(object_attrs)
-
-            # Write to the pipeline output file
-            with open(output_path, "w") as fh:
-                log.debug(f"Writing to output file: '{output_path}'")
-                fh.write(rendered_output)
-
         # Make a logo and save it
         self.make_pipeline_logo()