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Fixing bugs in nf-core create #936

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Merged
ewels merged 3 commits into from
Mar 23, 2021
+26 −15
Merged

Fixing bugs in nf-core create #936

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6536ed7
started with more robust jinja2 templating
KevinMenden Mar 22, 2021
676cf8f
added check for binary extensions
KevinMenden Mar 22, 2021
3261493
Refactor code for tidyness points
ewels Mar 22, 2021
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41 changes: 26 additions & 15 deletions nf_core/create.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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__

Expand All @@ -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()

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