WIP CLI, RM old, FIX CLI

server/pyproject.toml

@@ -42,9 +42,6 @@ dependencies = [
 
 [project.scripts]
 upsert = "scimodom.database.maintenance.upsert:main"
-add-project = "scimodom.database.maintenance.add_project:main"
-add-dataset = "scimodom.database.maintenance.add_dataset:main"
-add-all = "scimodom.database.maintenance.add_all:main"
 
 [project.urls]
 Github = "https://github.com/dieterich-lab/scimodom"

server/src/scimodom/app.py

@@ -9,6 +9,7 @@
 from scimodom.database.database import make_session, init
 from scimodom.frontend import frontend
 from scimodom.plugins.cli import (
+    add_annotation,
     add_assembly,
     add_project,
     add_dataset,
@@ -45,6 +46,17 @@ def assembly(id):
         """
         add_assembly(id)
 
+    @app.cli.command(
+        "annotation", epilog="Check docs at https://dieterich-lab.github.io/scimodom/."
+    )
+    @click.argument("id", type=click.INT)
+    def annotation(id):
+        """Prepare annotation.
+
+        ID is the annotation_id (must already exists).
+        """
+        add_annotation(id)
+
     @app.cli.command(
         "project", epilog="Check docs at https://dieterich-lab.github.io/scimodom/."
     )