def init_kb(root, exist_ok=False, config=None) -> bool:
success = False
try:
root = Config.get_root(root)
os.makedirs(str(root), exist_ok=exist_ok)
Config.create(root=root, config=config)
KB(root=root)
success = True
except FileExistsError as e:
logger.error(e)
return success
def sync_config(root: Optional[Path] = typer.Option(None)):
""" Update configuration while keeping the current Secret Key. """
root = Config.get_root(root)
config = Config.create(root=root)
old_json = config.json(indent=4)
typer.echo(f"Getting current config: {config.file_path}")
# retain the secret key
default_config.secret_key = config.secret_key
# write the new config
with config.file_path.open(mode="w") as fp:
new_json = default_config.json(indent=4)
fp.write(new_json)
fp.write("\n")
typer.echo(f"Config updated: {config.file_path}")
diff_gen = Differ().compare(old_json.splitlines(), new_json.splitlines())
typer.echo("\n".join(diff_gen))
def __init__(self, root=None):
self.config = Config.create(root=root)
self.user_store = self.config.create_user_store()
self.normalizer = self.config.create_normalizer()
self.tokenizer = self.config.create_tokenizer()
self.graph = self.config.create_graph(normalizer=self.normalizer)
self.pipelines = {}
for name, pipeline_config in self.config.pipelines.items():
pipeline = pipeline_config.create_pipeline(self)
self.pipelines[name] = pipeline
def clear(
root: Optional[Path] = typer.Option(None),
force: bool = typer.Option(False, "--force", "-f"),
):
""" Clear local KB """
root = Config.get_root(root)
if root.exists():
if not force:
typer.confirm(f"Clearing {root}. Are you sure?", abort=True)
kb = KB(root=root)
kb.clear()
services.finish("Clear", True)
def bootstrap(
root: Optional[Path] = typer.Option(None),
dry_run: bool = typer.Option(False, "--dry-run"),
wipe: bool = typer.Option(False, "--wipe"),
):
""" Load HopeIQ local data store. """
root = Config.get_root(root)
typer.echo(f"Initializing kb: `{root}`")
services.init_kb(root=root, exist_ok=True, config=default_config)
if wipe:
typer.echo(f"Clearing kb: `{root}`")
commands.clear(root=root, force=True)
file_name = "igniteiq.jsonl.gz"
igniteiq_jsonl = Path(__file__).parent.parent.parent / "iiq" / file_name
if not igniteiq_jsonl.exists():
igniteiq_jsonl = Path("/data/iiq/") / file_name
assert igniteiq_jsonl.exists(), f"Could not find {file_name}"
commands.load(
in_file=igniteiq_jsonl,
root=root,
file_format="jsonl",
dry_run=dry_run,
skip_reindex=True,
)
commands.load(
in_file=code_path / "hope_ontologies.xlsx",
root=root,
file_format="ontologies",
dry_run=dry_run,
skip_reindex=True,
is_binary=True,
)
# reindex
if not dry_run:
commands.reindex(root=root)
from urllib.parse import unquote
from fastapi import APIRouter, Body, security, Depends
from entitykb import (
ProxyKB,
models,
Config,
Direction,
exceptions,
User,
UserToken,
)
router = APIRouter()
config = Config.create()
kb = ProxyKB()
# nodes
@router.get("/nodes/{key}", tags=["nodes"])
def get_node(key: str) -> dict:
""" Parse text and return document object. """
key = unquote(key)
return kb.get_node(key)
@router.post("/nodes", tags=["nodes"])
async def save_node(node: dict = Body(...)) -> dict:
""" Saves nodes to graph and terms to index. """
default_config = Config(
graph="entitykb.Graph",
modules=["ontologykb", "hopeiq"],
normalizer="entitykb.LatinLowercaseNormalizer",
searcher="entitykb.DefaultSearcher",
tokenizer="ontologykb.PathTokenizer",
pipelines={
"default": {
"extractor":
"entitykb.DefaultExtractor",
"resolvers": [
"entitykb.TermResolver",
"entitykb.contrib.date.DateResolver",
"ontologykb.PersonResolver",
"ontologykb.MutationGrammarResolver",
"ontologykb.IntensityResolver",
"ontologykb.ClockPositionResolver",
"ontologykb.MeasurementResolver",
"ontologykb.pathology_stage.PathologyStageResolver",
"ontologykb.SystemIDResolver",
"ontologykb.LymphNodesResolver",
],
"filterers": ["ontologykb.CombinedFilterer"],
},
"mm": {
"extractor":
"entitykb.DefaultExtractor",
"resolvers": [
"entitykb.TermResolver",
"entitykb.contrib.date.DateResolver",
"ontologykb.MeasurementResolver",
],
"filterers": ["hopeiq.MMFilterer"]
}
},
)