✨Add typehints and validation

README.md

@@ -1,3 +1,6 @@
 # OMOP: OMOP Common Data Model
 
-Definition of the models: https://github.com/OHDSI/CommonDataModel
+OMOP (Observational Medical Outcomes Partnership) is a common data model (CDM) that standardizes the structure and content of disparate healthcare data for large-scale observational research.
+This schema models the OMOP data model accurately allowing for validation of OMOP modeled data.
+
+More about OMOP can be found at the [OHDSI website](https://ohdsi.org) and on the [OMOP GitHub](https://github.com/OHDSI/CommonDataModel).

docs/quickstart.ipynb

@@ -24,8 +24,8 @@
    },
    "outputs": [],
    "source": [
-    "!wget https://physionet.org/static/published-projects/mimic-iv-demo-omop/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip\n",
-    "!unzip mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip"
+    "!wget -nc https://physionet.org/static/published-projects/mimic-iv-demo-omop/mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip\n",
+    "!unzip -n mimic-iv-demo-data-in-the-omop-common-data-model-0.9.zip"
    ]
   },
   {
@@ -41,7 +41,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "!lamin init --storage ./test-omop --schema omop"
+    "!lamin init --storage ./test-omop --name test-omop --schema omop"
    ]
   },
   {
@@ -57,15 +57,16 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "import omop as oo\n",
+    "import lamindb as ln\n",
+    "import omop as op\n",
     "import pandas as pd"
    ]
   },
   {
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Load the data into a dataframe:"
+    "Load the data into a Pandas DataFrame:"
    ]
   },
   {
@@ -101,16 +102,32 @@
    },
    "outputs": [],
    "source": [
-    "concepts = [oo.Concept(**row.to_dict()) for _, row in df.iterrows()]\n",
+    "concepts = [op.Concept(**row.to_dict()) for _, row in df.iterrows()]\n",
     "for concept in concepts:\n",
     "    concept.save()\n",
-    "oo.Concept.df()"
+    "op.Concept.df()"
+   ]
+  },
+  {
+   "cell_type": "markdown",
+   "metadata": {},
+   "source": [
+    "Perform validation of new data."
+   ]
+  },
+  {
+   "cell_type": "code",
+   "execution_count": null,
+   "metadata": {},
+   "outputs": [],
+   "source": [
+    "op.Concept.validate([\"Stroke Volume Variation\", \"this concept does not exist\"], field=op.Concept.concept_name)"
    ]
   }
  ],
  "metadata": {
   "kernelspec": {
-   "display_name": "py310",
+   "display_name": "lamindb",
    "language": "python",
    "name": "python3"
   },
@@ -124,7 +141,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.10.13"
+   "version": "3.11.7"
   }
  },
  "nbformat": 4,

omop/__init__.py

@@ -49,7 +49,7 @@
    Vocabulary
 """
 
-__version__ = "0.1.1"  # denote a pre-release for 0.1.0 with 0.1rc1
+__version__ = "0.1.2"  # denote a pre-release for 0.1.0 with 0.1rc1
 
 from lamindb_setup import _check_instance_setup