feat(cellguide): upload json script (#6426)

scripts/upload_cellguide_descriptions.py

@@ -0,0 +1,102 @@
+"""
+This is a script to upload cellguide descriptions using the /cellguide/v1/upload endpoint.
+
+It requires a csv file to be present in the scripts directory with the following columns:
+Cell Ontology ID, Final version (QC'd), Supporting reference 1, Supporting reference 2, Supporting reference 3, 
+Supporting reference 4, Supporting reference 5
+
+The script will convert the csv to json and post each row to the endpoint.
+Step 1 - Login: python upload_cellguide_descriptions.py --deployment staging login --api_key <api_key>
+Step 2 - Upload: python upload_cellguide_descriptions.py --deployment staging upload --path cl_descriptions.csv
+"""
+
+import csv
+import json
+import os
+
+import click
+import requests
+
+
+@click.group()
+@click.option("--deployment", default="test", show_default=True, help="The name of the deployment to target")
+@click.pass_context
+def cli(ctx, deployment):
+    """
+    Set deployment stage and api base url
+    """
+    os.environ["DEPLOYMENT_STAGE"] = deployment
+    api_base = {
+        "test" or "dev": "https://api.cellxgene.dev.single-cell.czi.technology",
+        "staging": "https://api.cellxgene.staging.single-cell.czi.technology",
+        "production": "https://api.cellxgene.cziscience.com",
+    }
+    ctx.obj = {"api_base": api_base[deployment]}
+
+
+@cli.command()
+@click.pass_context
+@click.option("--api_key", default="", help="curator api key")
+def login(ctx, api_key):
+    """
+    Login using the curator api key
+    """
+    login_url = f"{ctx.obj['api_base']}/curation/v1/auth/token"
+    headers = {"Content-Type": "application/json", "x-api-key": api_key}
+    response = requests.post(login_url, headers=headers)
+    os.environ["API_TOKEN"] = json.loads(response.text)["access_token"]
+    click.echo(f"API_TOKEN has been set to {os.environ['API_TOKEN']}!")
+
+
+@cli.command()
+@click.option("--path", default=".", help="path to csv")
+@click.pass_context
+def upload(ctx, path):
+    """
+    Upload cellguide descriptions
+    """
+    api_token = os.environ.get("API_TOKEN")
+    if not api_token:
+        click.echo("API_TOKEN is not set. Please run login first.")
+        return
+    click.echo(api_token)
+
+    url = f"{ctx.obj['api_base']}/cellguide/v1/upload"
+    headers = {"Content-Type": "application/json", "Authorization": f"Bearer {api_token}"}
+
+    with open(path, "r") as file:
+        reader = csv.DictReader(file)
+        for row in reader:
+            json_row = convert_to_json(row)
+            response = requests.post(url, headers=headers, data=json_row)
+            click.echo(response.text)
+
+
+def convert_to_json(csv_row):
+    """
+    Convert csv row to json
+    """
+    json_row = {
+        "cell_ontology_term_id": csv_row["Cell Ontology ID"].replace(":", "_"),
+        "description": csv_row["Final version (QC'd)"],
+        "references": format_references(csv_row),
+    }
+    return json.dumps(json_row)
+
+
+def format_references(csv_row):
+    """
+    Format references list
+    """
+    references = []
+    for i in range(1, 6):
+        if csv_row[f"Supporting reference {i}"]:
+            url = csv_row[f"Supporting reference {i}"]
+            if not (url.startswith("http://") or url.startswith("https://")):
+                url = "https://www.doi.org/" + url
+            references.append(url)
+    return references
+
+
+if __name__ == "__main__":
+    cli()