diff options
Diffstat (limited to 'main.py')
| -rw-r--r-- | main.py | 70 |
1 files changed, 33 insertions, 37 deletions
@@ -26,7 +26,7 @@ def type_to_heading(type_name): """ Turn a type name like "sampleSchema" from the metadata schema into a human-readable heading. """ - + # Remove camel case decamel = re.sub('([A-Z])', r' \1', type_name) # Split @@ -35,12 +35,12 @@ def type_to_heading(type_name): filtered = [part.capitalize() for part in parts if (part.lower() != 'schema' and part != '')] # Reassemble return ' '.join(filtered) - + def name_to_label(field_name): """ Turn a filed name like "host_health_status" from the metadata schema into a human-readable label. """ - + return string.capwords(field_name.replace('_', ' ')) def generate_form(schema): @@ -50,10 +50,10 @@ def generate_form(schema): form section in the template) or an 'id', 'label', 'type', and 'required' (in which case we make a form field in the template). """ - + # Get the list of form components, one of which is the root components = schema.get('$graph', []) - + # Find the root root_name = None # And also index components by type name @@ -67,8 +67,8 @@ def generate_form(schema): if component.get('documentRoot', False): # Find whichever one is the root root_name = component_name - - + + def walk_fields(type_name, parent_keys=['metadata'], subtree_optional=False): """ Do a traversal of the component tree. @@ -76,14 +76,14 @@ def generate_form(schema): Form IDs are .-separated keypaths for where they are in the structure. parent_keys is the path of field names to where we are in the root record's document tree. """ - + if len(parent_keys) > 1: # First make a heading, if we aren't the very root of the form yield {'heading': type_to_heading(type_name)} - + for field_name, field_type in by_name.get(type_name, {}).get('fields', {}).items(): # For each field - + ref_url = None if not isinstance(field_type, str): # If the type isn't a string @@ -91,7 +91,7 @@ def generate_form(schema): ref_url = field_type.get('jsonldPredicate', {}).get('_id', None) # Grab out its type field field_type = field_type.get('type', '') - + # Decide if the field is optional (type ends in ?) optional = False if len(field_type) > 0 and field_type[-1] == '?': @@ -99,7 +99,7 @@ def generate_form(schema): optional = True # Drop the ? field_type = field_type[:-1] - + if field_type in by_name: # This is a subrecord. We need to recurse for item in walk_fields(field_type, parent_keys + [field_name], subtree_optional or optional): @@ -119,9 +119,9 @@ def generate_form(schema): else: raise NotImplementedError('Unimplemented field type {} in {} in metadata schema'.format(field_type, type_name)) yield record - + return list(walk_fields(root_name)) - + # At startup, we need to load the current metadata schema so we can make a form for it METADATA_SCHEMA = yaml.safe_load(urllib.request.urlopen('https://raw.githubusercontent.com/arvados/bh20-seq-resource/master/bh20sequploader/bh20seq-schema.yml')) FORM_ITEMS = generate_form(METADATA_SCHEMA) @@ -131,23 +131,23 @@ def send_form(): """ Send the file upload form/front page. """ - + return render_template('form.html', fields=FORM_ITEMS) - + class FileTooBigError(RuntimeError): """ Raised when the user gives a file that is too large. """ pass - + def copy_with_limit(in_file, out_file, limit=1024*1024): """ Copy a file stream, and raise FileTooBigError if the file is too big. """ - + bytes_used = 0 buf_size = 65536 - + buf = in_file.read(buf_size) bytes_used += len(buf) while buf: @@ -156,28 +156,28 @@ def copy_with_limit(in_file, out_file, limit=1024*1024): out_file.write(buf) buf = in_file.read(buf_size) bytes_used += len(buf) - + def parse_input(input_string, html_type): """ Parse an input from the given HTML input type into a useful Python type. - + Raise ValueError if something does not parse. Raise NotImplementedError if we forgot to implement a type. """ - + if html_type == 'text': return input_string elif html_type == 'number': return int(input_string) else: raise NotImplementedError('Unimplemented input type: {}'.format(html_type)) - + @app.route('/submit', methods=['POST']) -def recieve_files(): +def receive_files(): """ - Recieve the uploaded files. + Receive the uploaded files. """ - + # We're going to work in one directory per request dest_dir = tempfile.mkdtemp() fasta_dest = os.path.join(dest_dir, 'fasta.fa') @@ -192,7 +192,7 @@ def recieve_files(): except FileTooBigError as e: # Delegate to the 413 error handler return handle_large_file(e) - + if request.form.get('metadata_type', None) == 'upload': if 'metadata' not in request.files: return (render_template('error.html', @@ -206,12 +206,12 @@ def recieve_files(): elif request.form.get('metadata_type', None) == 'fill': # Build a metadata dict metadata = {} - + for item in FORM_ITEMS: # Pull all the field values we wanted from the form if 'heading' in item: continue - + if item['id'] in request.form and len(request.form[item['id']]) > 0: # We have this thing. Make a place in the dict tree for it. parts = item['id'].split('.') @@ -223,7 +223,7 @@ def recieve_files(): if parent not in dest_dict: dest_dict[parent] = {} dest_dict = dest_dict[parent] - + try: # Now finally add the item dest_dict[key] = parse_input(request.form[item['id']], item['type']) @@ -234,18 +234,18 @@ def recieve_files(): elif item['required']: return (render_template('error.html', error_message="You omitted the required metadata item {}".format(item['id'])), 403) - + # Now serialize the file with all the items with open(metadata_dest, 'w') as out_stream: yaml.dump(metadata, out_stream) else: return (render_template('error.html', error_message="You did not include metadata."), 403) - + # Try and upload files to Arvados result = subprocess.run(['bh20-seq-uploader', fasta_dest, metadata_dest], stdout=subprocess.PIPE, stderr=subprocess.PIPE) - + if result.returncode != 0: # It didn't work. Complain. error_message="Upload failed. Uploader returned {} and said:\n{}".format(result.returncode, result.stderr) @@ -255,7 +255,3 @@ def recieve_files(): return render_template('success.html', log=result.stdout.decode('utf-8', errors='replace')) finally: shutil.rmtree(dest_dir) - - - - |