Move CLI commands to their own module

autobidsportal.ini.example

@@ -1,5 +1,5 @@
 [uwsgi]
-module = bids_form:app
+module = autobidsportal:create_app()
 
 master = true
 processes = 5

autobidsportal/__init__.py

@@ -0,0 +1,3 @@
+"""Expose app creation function"""
+
+from autobidsportal.app import create_app

autobidsportal/app.py

@@ -9,9 +9,22 @@
 import rq
 
 from autobidsportal.routes import portal_blueprint
-from autobidsportal.models import db, login
+from autobidsportal.models import (
+    db,
+    login,
+    User,
+    Study,
+    Principal,
+    Notification,
+    Task,
+    Cfmm2tarOutput,
+    Tar2bidsOutput,
+    ExplicitPatient,
+)
 from autobidsportal.errors import bad_request, not_found_error, internal_error
 from autobidsportal.email import mail
+# This will register the CLI commands
+import autobidsportal.cli  # pylint: disable=unused-import
 
 
 def create_app(config_object=None, override_dict=None):
@@ -42,7 +55,7 @@ def create_app(config_object=None, override_dict=None):
     if override_dict is not None:
         app.config.update(override_dict)
     app.logger.setLevel(app.config["LOG_LEVEL"])
-    app.register_blueprint(portal_blueprint, url_prefix="/")
+    app.register_blueprint(portal_blueprint, url_prefix="/", cli_group=None)
     app.register_error_handler(400, bad_request)
     app.register_error_handler(404, not_found_error)
     app.register_error_handler(500, internal_error)
@@ -56,4 +69,20 @@ def create_app(config_object=None, override_dict=None):
     login.login_view = "login"
     mail.init_app(app)
 
+    @app.shell_context_processor
+    def make_shell_context():
+        """Add useful variables into the shell context."""
+        return {
+            "db": db,
+            "User": User,
+            "Study": Study,
+            "Principal": Principal,
+            "Notification": Notification,
+            "Task": Task,
+            "Cfmm2tarOutput": Cfmm2tarOutput,
+            "Tar2bidsOutput": Tar2bidsOutput,
+            "ExplicitPatient": ExplicitPatient,
+        }
+
+
     return app

bids_form.py → autobidsportal/cli.py

@@ -1,41 +1,13 @@
 """Flask entry point with extra CLI commands."""
 
-from autobidsportal.app import create_app
+from flask import current_app
+
 from autobidsportal.dcm4cheutils import gen_utils, Dcm4cheError
-from autobidsportal.models import (
-    db,
-    User,
-    Study,
-    Principal,
-    Notification,
-    Task,
-    Cfmm2tarOutput,
-    Tar2bidsOutput,
-    ExplicitPatient,
-)
-from autobidsportal.tasks import update_heuristics
-
-
-app = create_app()
-
-
-@app.shell_context_processor
-def make_shell_context():
-    """Add useful variables into the shell context."""
-    return {
-        "db": db,
-        "User": User,
-        "Study": Study,
-        "Principal": Principal,
-        "Notification": Notification,
-        "Task": Task,
-        "Cfmm2tarOutput": Cfmm2tarOutput,
-        "Tar2bidsOutput": Tar2bidsOutput,
-        "ExplicitPatient": ExplicitPatient,
-    }
-
-
-@app.cli.command()
+from autobidsportal.models import db, Principal, Study, Task
+from autobidsportal.routes import portal_blueprint
+
+
+@portal_blueprint.cli.command()
 def check_pis():
     """Add a list of pi names from dicom server to the Principal table."""
     try:
@@ -50,17 +22,19 @@ def check_pis():
     return "Success"
 
 
-@app.cli.command()
+@portal_blueprint.cli.command()
 def run_update_heuristics():
     """Clone the heuristic repo if it doesn't exist, then pull from it.
 
-    The point of this wrapper function is to expose the task to the CLI.
+    The point of this wrcurrent_apper function is to expose the task to the CLI.
     """
 
-    update_heuristics()
+    Task.launch_task(
+        "update_heuristics", "Update heuristics from CLI"
+    )
 
 
-@app.cli.command()
+@portal_blueprint.cli.command()
 def run_all_cfmm2tar():
     """Run cfmm2tar on all active studies.
 
@@ -80,12 +54,12 @@ def run_all_cfmm2tar():
         ) or (not study.active):
             print(f"Skipping study {study.id}. Active: {study.active}")
             continue
-        app.task_queue.enqueue(
+        current_app.task_queue.enqueue(
             "autobidsportal.tasks.check_tar_files", study.id
         )
 
 
-@app.cli.command()
+@portal_blueprint.cli.command()
 def run_all_tar2bids():
     """Run tar2bids on all active studies."""
     for study in Study.query.all():
@@ -101,12 +75,12 @@ def run_all_tar2bids():
         ) or not study.active:
             print(f"Skipping study {study.id}. Active: {study.active}")
             continue
-        app.task_queue.enqueue(
+        current_app.task_queue.enqueue(
             "autobidsportal.tasks.find_unprocessed_tar_files", study.id
         )
 
 
-@app.cli.command()
+@portal_blueprint.cli.command()
 def run_all_archive():
     """Archive all active studies' raw datasets.
 

autobidsportal/routes.py

@@ -61,7 +61,7 @@
 from autobidsportal.email import send_email
 
 portal_blueprint = Blueprint(
-    "portal_blueprint", __name__, template_folder="templates"
+    "portal_blueprint", __name__, template_folder="templates",
 )