class json_schema_factory(eHive.BaseRunnable):
def run(self):
manifest_path = self.param_required("manifest")
errors = []
with open(manifest_path) as manifest_file:
manifest = json.load(manifest_file)
# Check the manifest schema itself
self.dataflow_json("manifest", manifest_path)
# Use dir name from the manifest
for name in manifest:
if "file" in manifest[name]:
file_name = manifest[name]["file"]
manifest[name] = path.join(path.dirname(manifest_path), file_name)
else:
for f in manifest[name]:
if "file" in manifest[name][f]:
file_name = manifest[name][f]["file"]
manifest[name][f] = path.join(path.dirname(manifest_path), file_name)
# Check the other jsons schemas
for metadata_type in ("seq_region", "genome", "functional_annotation"):
if metadata_type in manifest:
self.dataflow_json(metadata_type, manifest[metadata_type])
def dataflow_json(self, metadata_type, metadata_json):
self.dataflow({"metadata_type": metadata_type, "metadata_json": metadata_json}, 2)