From 2e8c52e9b1e1036129d39ba8d5a16f63e37691c8 Mon Sep 17 00:00:00 2001
From: dcarron <daniel.carron@idiap.ch>
Date: Tue, 7 May 2024 13:35:52 +0200
Subject: [PATCH] [cli] Fix info command
---
src/mednet/scripts/info.py | 92 +++++++++++++++++++++++++++-----------
1 file changed, 65 insertions(+), 27 deletions(-)
diff --git a/src/mednet/scripts/info.py b/src/mednet/scripts/info.py
index b8f3078e..5d4d3508 100644
--- a/src/mednet/scripts/info.py
+++ b/src/mednet/scripts/info.py
@@ -5,10 +5,52 @@
import click
from clapper.click import verbosity_option
from clapper.logging import setup
+from clapper.rc import UserDefaults
logger = setup(__name__.split(".")[0], format="%(levelname)s: %(message)s")
+def _echo(left: str, right: str, color: str = "white") -> None:
+ s = [
+ click.style(left, bold=True),
+ click.style(": ", bold=True),
+ click.style(right, fg=color),
+ ]
+ click.echo("".join(s))
+
+
+def database_configuration(
+ rc: UserDefaults, raw_databases: dict[str, dict[str, str]], lib_name: str
+):
+ """Display the database configuration for a particular library.
+
+ Parameters
+ ----------
+ rc
+ The user defaults read from the user .toml configuration file.
+ raw_databases
+ List of all supported (raw) databases.
+ lib_name
+ Name of the library to show configurations for.
+ """
+
+ if not rc.path.exists():
+ _echo(f"{lib_name} configuration", f"{str(rc.path)} [MISSING]", "white")
+ else:
+ _echo(f"{lib_name} configuration", str(rc.path), "white")
+
+ click.secho(f"configured {lib_name} databases:", bold=True)
+ for k, v in raw_databases.items():
+ if "datadir" not in v:
+ # this database does not have a "datadir"
+ continue
+
+ if v["datadir"] is not None:
+ _echo(f" - {k} ({v['module']})", f"{v['datadir']}", "green")
+ else:
+ _echo(f" - {k} ({v['module']})", "NOT installed", "red")
+
+
@click.command(
epilog="""Examples:
@@ -28,20 +70,21 @@ def info(
import typing
- from ..utils.rc import load_rc
- from .database import _get_raw_databases
- from .utils import execution_metadata
-
- def _echo(left: str, right: str, color: str = "white") -> None:
- s = [
- click.style(left, bold=True),
- click.style(": ", bold=True),
- click.style(right, fg=color),
- ]
- click.echo("".join(s))
+ from mednet.libs.classification.scripts.database import (
+ _get_raw_databases as _get_raw_databases_classification,
+ )
+ from mednet.libs.classification.utils.rc import (
+ load_rc as load_rc_classification,
+ )
+ from mednet.libs.common.scripts.utils import execution_metadata
+ from mednet.libs.segmentation.scripts.database import (
+ _get_raw_databases as _get_raw_databases_segmentation,
+ )
+ from mednet.libs.segmentation.utils.rc import (
+ load_rc as load_rc_segmentation,
+ )
m = execution_metadata()
- c = load_rc()
_echo("mednet version", typing.cast(str, m["package-version"]), "green")
_echo("platform", typing.cast(str, m["platform"]), "yellow")
@@ -51,21 +94,16 @@ def info(
"cyan",
)
- if not c.path.exists():
- _echo("configuration", f"{str(c.path)} [MISSING]", "white")
- else:
- _echo("configuration", str(c.path), "white")
- dbs = _get_raw_databases()
- click.secho("configured databases:", bold=True)
- for k, v in dbs.items():
- if "datadir" not in v:
- # this database does not have a "datadir"
- continue
-
- if v["datadir"] is not None:
- _echo(f" - {k} ({v['module']})", f"{v['datadir']}", "green")
- else:
- _echo(f" - {k} ({v['module']})", "NOT installed", "red")
+ database_configuration(
+ load_rc_classification(),
+ _get_raw_databases_classification(),
+ "classification",
+ )
+ database_configuration(
+ load_rc_segmentation(),
+ _get_raw_databases_segmentation(),
+ "segmentation",
+ )
click.secho("dependencies:", bold=True)
python = typing.cast(dict[str, str], m["python"])
--
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