Skip to content

Commit

Permalink
Correct connection to openBIS
Browse files Browse the repository at this point in the history
  • Loading branch information
@fabioacl
fabioacl committed Jul 26, 2024
1 parent 0530453 commit 59471bb
Showing 1 changed file with 42 additions and 91 deletions.
133 changes: 42 additions & 91 deletions notebooks/eln_import.ipynb
View file
Original file line number Diff line number Diff line change
Expand Up @@ -47,9 +47,11 @@
"from aiidalab_widgets_base import viewer\n",
"from traitlets import dlink\n",
"\n",
"from jsonschema import validate, RefResolver, Draft7Validator, ValidationError\n",
"import json\n",
"from pyld import jsonld"
"from pyld import jsonld\n",
"\n",
"import sys\n",
"import os"
]
},
{
Expand All @@ -59,75 +61,16 @@
"metadata": {},
"outputs": [],
"source": [
"def load_json(filepath: str) -> dict:\n",
" return json.load(open(filepath, \"r\"))\n",
"\n",
"def find_refs(obj, refs=None) -> list[str]:\n",
" if refs is None:\n",
" refs = []\n",
" \n",
" if isinstance(obj, dict):\n",
" for key, value in obj.items():\n",
" if key == '$ref':\n",
" refs.append(value[2:])\n",
" else:\n",
" find_refs(value, refs)\n",
" \n",
" return refs\n",
"\n",
"def find_ref_schemas(schemas_filenames: list[str], refs = None):\n",
" if refs is None:\n",
" refs = []\n",
" \n",
" for schema_filename in schemas_filenames:\n",
" schema = load_json(f\"/home/jovyan/aiida-openbis/Notebooks/New_Metadata_Schemas/{schema_filename}\")\n",
" ref_schemas_filenames = find_refs(schema)\n",
" \n",
" if schema_filename not in refs:\n",
" refs.append(schema_filename)\n",
" find_ref_schemas(ref_schemas_filenames, refs)\n",
" \n",
" return refs\n",
"\n",
"def set_up_validator(json_schema_filename):\n",
" schemas_filenames = [json_schema_filename]\n",
" all_schemas_filenames = find_ref_schemas(schemas_filenames)\n",
"\n",
" first_schema = load_json(f\"/home/jovyan/aiida-openbis/Notebooks/New_Metadata_Schemas/{all_schemas_filenames[0]}\")\n",
" resolver = RefResolver(base_uri=\"http://example.com/\", referrer = first_schema)\n",
"\n",
" for referenced_schema_filename in all_schemas_filenames:\n",
" referenced_schema = load_json(f\"/home/jovyan/aiida-openbis/Notebooks/New_Metadata_Schemas/{referenced_schema_filename}\")\n",
" resolver.store[referenced_schema[\"$id\"]] = referenced_schema\n",
"\n",
" validator = Draft7Validator(first_schema, resolver=resolver)\n",
" \n",
" return validator\n",
"\n",
"# Function to expand context terms\n",
"def expand_context(base_context):\n",
" expanded_context = {}\n",
" for key, value in base_context.items():\n",
" if isinstance(value, str) and ':' in value:\n",
" prefix, suffix = value.split(':', 1)\n",
" if prefix in base_context:\n",
" expanded_context[key] = base_context[prefix] + suffix\n",
" else:\n",
" expanded_context[key] = value\n",
" else:\n",
" expanded_context[key] = value\n",
" return expanded_context\n",
"\n",
"def replace_keys_recursive(data, old_key, new_key):\n",
" if isinstance(data, dict):\n",
" for key in list(data.keys()): # Create a copy of keys to avoid RuntimeError\n",
" if key == old_key:\n",
" key = new_key\n",
" data[new_key] = data.pop(old_key)\n",
" replace_keys_recursive(data[key], old_key, new_key)\n",
" elif isinstance(data, list):\n",
" for item in data:\n",
" replace_keys_recursive(item, old_key, new_key)"
"#sys.path.append(os.path.dirname(\"/home/jovyan/aiida-openbis/Notebooks/Metadata_Schemas_LinkML/\"))\n",
"# from materialMLinfo import Molecule, slots\n",
"# def extract_molecule_data_with_linkml(molecule_jsonld):\n",
"# expanded = jsonld.expand(molecule_jsonld)\n",
"# molecule_data = {}\n",
"# for obj in jsonld_object:\n",
"# if '@type' in obj and str(Molecule.class_class_uri) in obj['@type']:\n",
"# molecule_data['name'] = obj.get(str(slots.name.uri), [None])[0]['@value']\n",
"# molecule_data['smiles'] = obj.get(str(slots.smiles.uri), [None])[0]['@value']\n",
"# return molecule_data"
]
},
{
Expand All @@ -137,35 +80,43 @@
"metadata": {},
"outputs": [],
"source": [
"# Extract data from the converted JSON-LD\n",
"def extract_molecule_data(jsonld_object, context):\n",
" expanded = jsonld.expand(molecule_jsonld)\n",
" compacted = jsonld.compact(expanded, context)\n",
" return {\"name\": compacted[\"name\"], \"smiles\": compacted[\"smiles\"]}\n",
"\n",
"def read_json(filepath: str) -> dict:\n",
" return json.load(open(filepath, \"r\"))\n",
"\n",
"url = urlparse.urlsplit(jupyter_notebook_url)\n",
"parsed_url = urlparse.parse_qs(url.query)\n",
"params = {key:value[0] for key, value in parsed_url.items()}\n",
"molecule_jsonld = json.loads(params[\"molecule_info\"])\n",
"\n",
"molecule_json = json.loads(params[\"molecule_info\"])\n",
"molecule_info_valid = False\n",
"\n",
"molecule_validator = set_up_validator(\"molecule.schema.json\")\n",
"schema_context = molecule_validator.schema[\"@context\"]\n",
"schema_context = expand_context(schema_context)\n",
"json_context = expand_context(molecule_json[\"@context\"])\n",
"jsonld_context_filename = os.path.join(\n",
" os.sep, \n",
" \"home\", \n",
" \"jovyan\", \n",
" \"aiida-openbis\", \n",
" \"Notebooks\", \n",
" \"Metadata_Schemas_LinkML\",\n",
" \"materialMLinfoContext.jsonld\"\n",
")\n",
"\n",
"if \"@context\" in molecule_json:\n",
" _ = molecule_json.pop(\"@context\")\n",
" \n",
"for key1, value1 in schema_context.items():\n",
" for key2, value2 in json_context.items():\n",
" if value1 == value2:\n",
" replace_keys_recursive(molecule_json, key2, key1)\n",
" \n",
"molecule_info_valid = False\n",
"\n",
"aiida_context = read_json(jsonld_context_filename)\n",
"\n",
"try:\n",
" molecule_validator.validate(instance = molecule_json)\n",
" molecule_info_valid = True\n",
" params[\"molecule_info\"] = json.dumps(molecule_json)\n",
" molecule_data = extract_molecule_data(molecule_jsonld, aiida_context)\n",
" params[\"molecule_info\"] = json.dumps(molecule_data)\n",
" eln_widget = ElnImportWidget(path_to_root=\"../../\", **params)\n",
"except ValidationError as e:\n",
" message = e.schema[\"error_msg\"] if \"error_msg\" in e.schema else e.message\n",
" print(f'Invalid data: {message}')"
" molecule_info_valid = True\n",
"except ValueError as e:\n",
" print(e)\n",
"\n"
]
},
{
Expand Down

0 comments on commit 59471bb

Please sign in to comment.