Rc/staging release 15082023

.github/workflows/run-tests.yml

@@ -47,7 +47,7 @@ jobs:
         uses: pre-commit/action@v3.0.0
 
       - name: Run tests
-        run: poetry run pytest -vvv --exitfirst --cov=app --cov-report=term --cov-report=xml --cov-fail-under=54
+        run: poetry run pytest -vvv --exitfirst --cov=app --cov-report=term --cov-report=xml --cov-fail-under=60
 
       - name: Coverage report comment
         uses: mishakav/pytest-coverage-comment@v1.1.42

COPYRIGHT

@@ -1,3 +1,3 @@
-Copyright (C) 2022 Indoc Research
+Copyright (C) 2022 Indoc Systems
 
-Contact Indoc Research for any questions regarding the use of this source code.
+Contact Indoc Systems for any questions regarding the use of this source code.

app/__init__.py

@@ -1,3 +1,3 @@
-# Copyright (C) 2022-2023 Indoc Research
+# Copyright (C) 2022-2023 Indoc Systems
 #
-# Contact Indoc Research for any questions regarding the use of this source code.
+# Contact Indoc Systems for any questions regarding the use of this source code.

app/commands/__init__.py

@@ -1,3 +1,3 @@
-# Copyright (C) 2022-2023 Indoc Research
+# Copyright (C) 2022-2023 Indoc Systems
 #
-# Contact Indoc Research for any questions regarding the use of this source code.
+# Contact Indoc Systems for any questions regarding the use of this source code.

app/commands/container_registry.py

@@ -1,6 +1,6 @@
-# Copyright (C) 2022-2023 Indoc Research
+# Copyright (C) 2022-2023 Indoc Systems
 #
-# Contact Indoc Research for any questions regarding the use of this source code.
+# Contact Indoc Systems for any questions regarding the use of this source code.
 
 import click
 

app/commands/dataset.py

@@ -1,6 +1,6 @@
-# Copyright (C) 2022-2023 Indoc Research
+# Copyright (C) 2022-2023 Indoc Systems
 #
-# Contact Indoc Research for any questions regarding the use of this source code.
+# Contact Indoc Systems for any questions regarding the use of this source code.
 
 import click
 import questionary

app/commands/entry_point.py

@@ -1,12 +1,11 @@
-# Copyright (C) 2022-2023 Indoc Research
+# Copyright (C) 2022-2023 Indoc Systems
 #
-# Contact Indoc Research for any questions regarding the use of this source code.
+# Contact Indoc Systems for any questions regarding the use of this source code.
 
 import os
 
 import click
 
-from app.services.user_authentication.decorator import require_config
 from app.services.user_authentication.decorator import require_login_session
 
 from .container_registry import create_project
@@ -25,29 +24,17 @@
 from .file import file_resume
 
 # Import custom commands
-from .hpc import hpc_auth
-from .hpc import hpc_get_node
-from .hpc import hpc_get_partition
-from .hpc import hpc_job_info
-from .hpc import hpc_job_submit
-from .hpc import hpc_list_nodes
-from .hpc import hpc_list_partitions
-from .kg_resource import kg_resource
 from .project import project_list_all
-from .use_config import set_env
 from .user import login
 from .user import logout
 
-hpc_enabled = os.environ.get('PILOT_CLI_HPC_ENABLED', 'false') == 'true'
-kg_enabled = os.environ.get('PILOT_CLI_KG_ENABLED', 'false') == 'true'
+container_registry_enabled = os.environ.get('PILOT_CLI_CONTAINER_REGISTRY_ENABLED', 'false') == 'true'
 
 
 def command_groups():
-    commands = ['file', 'user', 'use_config', 'project', 'dataset', 'container_registry']
-    if hpc_enabled:
-        commands.append('hpc')
-    if kg_enabled:
-        commands.append('kg_resource')
+    commands = ['file', 'user', 'project', 'dataset']
+    if container_registry_enabled:
+        commands.append('container_registry')
     return commands
 
 
@@ -57,43 +44,28 @@ def entry_point():
 
 
 @entry_point.group(name='project')
-@require_config
 @require_login_session
 def project_group():
     pass
 
 
 @entry_point.group(name='dataset')
-@require_config
 @require_login_session
 def dataset_group():
     pass
 
 
 @entry_point.group(name='file')
-@require_config
 @require_login_session
 def file_group():
     pass
 
 
 @entry_point.group(name='user')
-@require_config
 def user_group():
     pass
 
 
-@entry_point.group(name='use_config')
-def config_group():
-    pass
-
-
-@entry_point.group(name='container_registry')
-@require_config
-def cr_group():
-    pass
-
-
 file_group.add_command(file_put)
 file_group.add_command(file_check_manifest)
 file_group.add_command(file_export_manifest)
@@ -106,32 +78,16 @@ def cr_group():
 dataset_group.add_command(dataset_list)
 dataset_group.add_command(dataset_show_detail)
 dataset_group.add_command(dataset_download)
-cr_group.add_command(list_projects)
-cr_group.add_command(list_repositories)
-cr_group.add_command(create_project)
-cr_group.add_command(get_secret)
-cr_group.add_command(invite_member)
-config_group.add_command(set_env)
 
 # Custom commands
-if hpc_enabled:
-
-    @entry_point.group(name='hpc')
-    def hpc_group():
-        pass
-
-    hpc_group.add_command(hpc_auth)
-    hpc_group.add_command(hpc_job_submit)
-    hpc_group.add_command(hpc_job_info)
-    hpc_group.add_command(hpc_list_nodes)
-    hpc_group.add_command(hpc_get_node)
-    hpc_group.add_command(hpc_list_partitions)
-    hpc_group.add_command(hpc_get_partition)
-
-if kg_enabled:
+if container_registry_enabled:
 
-    @entry_point.group(name='kg_resource')
-    def kg_resource_group():
+    @entry_point.group(name='container_registry')
+    def cr_group():
         pass
 
-    kg_resource_group.add_command(kg_resource)
+    cr_group.add_command(list_projects)
+    cr_group.add_command(list_repositories)
+    cr_group.add_command(create_project)
+    cr_group.add_command(get_secret)
+    cr_group.add_command(invite_member)

app/commands/file.py

@@ -1,6 +1,6 @@
-# Copyright (C) 2022-2023 Indoc Research
+# Copyright (C) 2022-2023 Indoc Systems
 #
-# Contact Indoc Research for any questions regarding the use of this source code.
+# Contact Indoc Systems for any questions regarding the use of this source code.
 
 import json
 import os
@@ -245,9 +245,16 @@ def file_resume(**kwargs):  # noqa: C901
         # are rather similar with the input
         validate_upload_event(resumable_manifest)
 
-    # print(resumable_manifest)
     resume_upload(resumable_manifest, thread)
 
+    # since only file upload can attach manifest, take the first file object
+    srv_manifest = SrvFileManifests()
+    item_id = next(iter(resumable_manifest.get('file_objects')))
+    attribute = resumable_manifest.get('attributes')
+    zone = resumable_manifest.get('zone')
+    srv_manifest.attach_manifest(attribute, item_id, zone) if attribute else None
+    message_handler.SrvOutPutHandler.all_file_uploaded()
+
 
 def validate_upload_event(event):
     """validate upload request, raise error when filed."""