def generate_webpage(records: List[Record],
results: List[Dict[str, module_results.ModuleResults]],
options: ConfigType) -> None:
""" Generates and writes the HTML itself """
generate_searchgtr_htmls(records, options)
json_records = js.convert_records(records, results, options)
js_domains = []
for i, record in enumerate(records):
json_record = json_records[i]
json_record['seq_id'] = "".join(char for char in json_record['seq_id']
if char in string.printable)
for json_cluster in json_record['clusters']: # json clusters
from antismash import get_analysis_modules # TODO break circular dependency
handlers = find_plugins_for_cluster(get_analysis_modules(),
json_cluster)
for handler in handlers:
# if there's no results for the module, don't let it try
if handler.__name__ not in results[i]:
continue
if "generate_js_domains" in dir(handler):
domains = handler.generate_js_domains(
json_cluster,
record, # type: ignore
results[i][handler.__name__],
options)
if domains:
js_domains.append(domains)
write_geneclusters_js(json_records, options.output_dir, js_domains)
with open(os.path.join(options.output_dir, 'index.html'),
'w') as result_file:
env = Environment(autoescape=True,
trim_blocks=True,
lstrip_blocks=True,
undefined=jinja2.StrictUndefined,
loader=FileSystemLoader(
path.get_full_path(__file__)))
template = env.get_template('index.html')
options_layer = OptionsLayer(options)
record_layers = []
for record, record_results in zip(records, results):
record_layers.append(
RecordLayer(record, record_results, options_layer))
records_written = sum(len(record.get_clusters()) for record in records)
aux = template.render(records=record_layers,
options=options_layer,
version=options.version,
extra_data=js_domains,
records_written=records_written,
config=options)
result_file.write(aux)
def generate_webpage(seq_records, results, options):
generate_searchgtr_htmls(seq_records, options)
json_records = js.convert_records(seq_records, results, options)
extra_data = dict(js_domains=[])
for i, record in enumerate(seq_records):
json_record = json_records[i]
json_record['seq_id'] = "".join(char for char in json_record['seq_id']
if char in string.printable)
for json_cluster in json_record['clusters']: # json clusters
from antismash import get_analysis_modules # TODO break circular dependency
handlers = find_plugins_for_cluster(get_analysis_modules(),
json_cluster)
for handler in handlers:
# if there's no results for the module, don't let it try
if handler.__name__ not in results[i]:
continue
if "generate_js_domains" in dir(handler):
domains = handler.generate_js_domains(
json_cluster, record, results[i][handler.__name__],
options)
if domains:
extra_data['js_domains'].append(domains)
write_geneclusters_js(json_records, options.output_dir, extra_data)
# jinja
with open(os.path.join(options.output_dir, 'index.html'), 'w') as result:
env = Environment(autoescape=True,
trim_blocks=True,
lstrip_blocks=True,
undefined=jinja2.StrictUndefined,
loader=FileSystemLoader(
path.get_full_path(__file__)))
template = env.get_template('index.html')
options_layered = OptionsLayer(options)
records = [
RecordLayer(record, result, options_layered)
for record, result in zip(seq_records, results)
]
records_written = sum(
[len(record.seq_record.get_clusters()) for record in records])
aux = template.render(records=records,
options=options_layered,
version=options.version,
extra_data=extra_data,
records_written=records_written,
config=options)
result.write(aux)
def build_json_data(
records: List[Record],
results: List[Dict[str, module_results.ModuleResults]], options: ConfigType
) -> Tuple[List[Dict[str, Any]], List[Dict[str, Union[str, List[JSONOrf]]]],
Dict[str, Dict[str, Dict[str, Any]]]]:
""" Builds JSON versions of records and domains for use in drawing SVGs with
javascript.
Arguments:
records: a list of Records to convert
results: a dictionary mapping record id to a list of ModuleResults to convert
options: antiSMASH options
Returns:
a tuple of
a list of JSON-friendly dicts representing records
a list of JSON-friendly dicts representing domains
"""
from antismash import get_all_modules # TODO break circular dependency
js_records = js.convert_records(records, results, options)
js_domains: List[Dict[str, Union[str, List[JSONOrf]]]] = []
js_results = {}
for i, record in enumerate(records):
json_record = js_records[i]
json_record['seq_id'] = "".join(char for char in json_record['seq_id']
if char in string.printable)
for region, json_region in zip(record.get_regions(),
json_record['regions']):
handlers = find_plugins_for_cluster(get_all_modules(), json_region)
region_results = {}
for handler in handlers:
# if there's no results for the module, don't let it try
if handler.__name__ not in results[i]:
continue
if "generate_js_domains" in dir(handler):
domains_by_region = handler.generate_js_domains(
region, record)
if domains_by_region:
js_domains.append(domains_by_region)
if hasattr(handler, "generate_javascript_data"):
region_results[
handler.__name__] = handler.generate_javascript_data(
record, region, results[i][handler.__name__])
if region_results:
js_results[RegionLayer.build_anchor_id(
region)] = region_results
return js_records, js_domains, js_results