chore: Adding neuroglancer utility

ingestion_tools/scripts/neuroglancer_util.py

@@ -0,0 +1,62 @@
+import json
+import urllib.parse
+import webbrowser
+
+import click
+import cryoet_data_portal as cdp
+
+STAGING_GRAPHQL_URL = "https://genuine-satyr.staging-cryoet.staging.czi.team/graphql"
+STAGING_FILESERVER = "https://files.cryoet.staging.si.czi.technology/"
+
+PROD_FILESERVER = "https://files.cryoetdataportal.cziscience.com/"
+
+
+@click.group()
+@click.pass_context
+def cli(ctx):
+    pass
+
+
+def print_neuroglancer_links(run_id: int, client: cdp.Client, dest_fileserver: str, print_link: bool):
+    run = cdp.Run.get_by_id(client, run_id)
+    for tomogram in run.tomograms:
+        if neuroglancer_config := tomogram.neuroglancer_config:
+            new_config = neuroglancer_config.replace(PROD_FILESERVER, dest_fileserver)
+            config_json = json.loads(new_config)
+            ng_url = "https://neuroglancer-demo.appspot.com/#!" + urllib.parse.quote(
+                json.dumps(config_json, separators=(",", ":")),
+            )
+            if print_link:
+                print(f"Tomogram id={tomogram.id} processing={tomogram.processing}")
+                print(ng_url + "\n" * 3)
+            webbrowser.open(ng_url, new=0, autoraise=True)
+
+
+@cli.command()
+@click.argument("run_id", required=True, type=int)
+@click.argument("graphql_url", required=False, type=str, default=STAGING_GRAPHQL_URL)
+@click.argument("output_fileserver", required=False, type=str, default=STAGING_FILESERVER)
+@click.option(
+    "--print-link", type=bool, is_flag=True, default=False, help="print the neuroglancer link to the consoles",
+)
+def translate_env(run_id: int, graphql_url, output_fileserver: str, print_link: bool) -> None:
+    """
+    Translate the neuroglancer links from one environment to another
+
+    @param run_id: id of the run in the environment where we are fetching the neuroglancer config
+
+    @param graphql_url: graphql url of the environment the client should point to, defaults to staging
+
+    @param output_fileserver: fileserver of the environment the client should point to, defaults to staging
+
+    @param print_link: print the neuroglancer link to the consoles
+
+    This can be called from the command line as follows:
+
+      python3 neuroglancer_util.py translate-env 123 --print-link
+    """
+    print_neuroglancer_links(run_id, cdp.Client(graphql_url), output_fileserver, print_link)
+
+
+if __name__ == "__main__":
+    cli()