Wiring of project CLI to API

sodar_cli/api/__init__.py

@@ -1,3 +1,6 @@
 """Code for accessing SODAR Server API."""
 
+from sodar_cli.api import landingzone  # noqa: F403, F401
+from sodar_cli.api import project  # noqa: F403, F401
+from sodar_cli.api import samplesheet  # noqa: F403, F401
 from sodar_cli.api.models import *  # noqa: F403, F401

sodar_cli/api/models.py

@@ -54,8 +54,9 @@ class Project:
     sodar_uuid: str
     title: str
     type: str
-    submit_status: str
-    roles: typing.Dict[str, RoleAssignment]
+    roles: typing.Optional[typing.Dict[str, RoleAssignment]] = None
+    submit_status: typing.Optional[str] = None
+    parent_uuid: typing.Optional[str] = None
     parent: typing.Optional[str] = None
     readme: typing.Optional[str] = None
     description: typing.Optional[str] = None

sodar_cli/landingzone/retrieve.py

@@ -1,8 +1,8 @@
 """Implementation of ``varfish-cli landingzone retrieve``."""
 
 import argparse
-import sys
 import json
+import sys
 import uuid
 
 import cattr

sodar_cli/project/__init__.py

@@ -19,12 +19,12 @@ def setup_argparse(parser: argparse.ArgumentParser) -> None:
     setup_argparse_create(
         subparsers.add_parser("create", help="Create project (there is no delete!).")
     )
-    setup_argparse_update(subparsers.add_parser("delete", help="Update project."))
+    setup_argparse_update(subparsers.add_parser("update", help="Update project."))
 
 
 def run(config, toml_config, args, parser, subparser):
     """Main entry point for case command."""
-    if not args.case_cmd:  # pragma: nocover
+    if not args.project_cmd:  # pragma: nocover
         return run_nocmd(config, args, parser, subparser)
     else:
         config = ProjectConfig.create(args, config, toml_config)

sodar_cli/project/config.py

@@ -64,8 +64,6 @@ class ProjectCreateConfig:
     title: str
     #: Project type, one of ``"PROJECT"`` or ``"CATEGORY"``
     type: str
-    #: Owner user UUID.
-    owner_uuid: str
     #: Parent category UUID.
     parent_uuid: typing.Optional[str] = None
     #: Project description.
@@ -80,7 +78,6 @@ def create(args, project_config, toml_config=None):
             project_config=project_config,
             title=args.title,
             type=args.type,
-            owner_uuid=args.owner_uuid,
             parent_uuid=args.parent_uuid,
             description=args.description,
             readme=args.readme,
@@ -103,8 +100,6 @@ class ProjectUpdateConfig:
     type: str
     #: Parent category UUID.
     parent_uuid: str
-    #: Owner user UUID.
-    owner_uuid: str
     #: Project description.
     description: typing.Optional[str] = None
     #: Project README, supports markdown.
@@ -118,7 +113,6 @@ def create(args, project_config, toml_config=None):
             project_uuid=args.project_uuid,
             title=args.title,
             type=args.type,
-            owner_uuid=args.owner_uuid,
             parent_uuid=args.parent_uuid,
             description=args.description,
             readme=args.readme,

sodar_cli/project/create.py

@@ -1,20 +1,43 @@
 """Implementation of ``varfish-cli project create``."""
 
 import argparse
+import json
 import sys
 
+import cattr
 from logzero import logger
 
-# from sodar_cli import api
+from sodar_cli import api
 from sodar_cli.project.config import ProjectCreateConfig
 
 
 def setup_argparse(parser):
     parser.add_argument("--hidden-cmd", dest="project_cmd", default=run, help=argparse.SUPPRESS)
+    parser.add_argument("--title", default="Project Title", help="Title of the project")
+    parser.add_argument(
+        "--type", default="Project Type", help="Type of the project [PROJECT, CATEGORY]"
+    )
+    parser.add_argument("--parent-uuid", help="UUID of the parent project, if any")
+    parser.add_argument("--description", help="Description text, optional")
+    parser.add_argument("--readme", help="README text, markdown allowed, optional")
 
 
-def run(config, toml_config, args, _parser, _subparser, file=sys.stdout):
+def run(config, toml_config, args, _parser, _subparser, file=None):
     """Run landingzone retrieve command."""
     config = ProjectCreateConfig.create(args, config, toml_config)
     logger.info("Configuration: %s", config)
     logger.info("Creating project")
+    project = api.Project(
+        sodar_uuid=None,
+        title=args.title,
+        type=args.type,
+        parent_uuid=args.parent_uuid,
+        description=args.description,
+        readme=args.readme,
+    )
+    result = api.project.create(
+        sodar_url=config.project_config.global_config.sodar_server_url,
+        sodar_api_token=config.project_config.global_config.sodar_api_token,
+        project=project,
+    )
+    print(json.dumps(cattr.unstructure(result)), file=(file or sys.stdout))

sodar_cli/project/list.py

@@ -1,20 +1,27 @@
 """Implementation of ``varfish-cli project list``."""
 
 import argparse
+import json
 import sys
 
+import cattr
 from logzero import logger
 
-# from sodar_cli import api
+from sodar_cli import api
 from sodar_cli.project.config import ProjectListConfig
 
 
 def setup_argparse(parser):
     parser.add_argument("--hidden-cmd", dest="project_cmd", default=run, help=argparse.SUPPRESS)
 
 
-def run(config, toml_config, args, _parser, _subparser, file=sys.stdout):
+def run(config, toml_config, args, _parser, _subparser, file=None):
     """Run project list command."""
     config = ProjectListConfig.create(args, config, toml_config)
     logger.info("Configuration: %s", config)
     logger.info("Listing projects")
+    result = api.project.list_(
+        sodar_url=config.project_config.global_config.sodar_server_url,
+        sodar_api_token=config.project_config.global_config.sodar_api_token,
+    )
+    print(json.dumps(cattr.unstructure(result)), file=(file or sys.stdout))

sodar_cli/project/retrieve.py

@@ -1,12 +1,14 @@
 """Implementation of ``varfish-cli project retrieve``."""
 
 import argparse
+import json
 import sys
 import uuid
 
+import cattr
 from logzero import logger
 
-# from sodar_cli import api
+from sodar_cli import api
 from sodar_cli.project.config import ProjectRetrieveConfig
 
 
@@ -15,8 +17,14 @@ def setup_argparse(parser):
     parser.add_argument("project_uuid", help="UUID of the project to retrieve.", type=uuid.UUID)
 
 
-def run(config, toml_config, args, _parser, _subparser, file=sys.stdout):
+def run(config, toml_config, args, _parser, _subparser, file=None):
     """Run project list command."""
     config = ProjectRetrieveConfig.create(args, config, toml_config)
     logger.info("Configuration: %s", config)
     logger.info("Retrieving projects")
+    result = api.project.retrieve(
+        sodar_url=config.project_config.global_config.sodar_server_url,
+        sodar_api_token=config.project_config.global_config.sodar_api_token,
+        project_uuid=config.project_uuid,
+    )
+    print(json.dumps(cattr.unstructure(result)), file=(file or sys.stdout))

sodar_cli/project/update.py

@@ -2,21 +2,45 @@
 
 import argparse
 import sys
+import json
 import uuid
 
+import cattr
 from logzero import logger
 
-# from sodar_cli import api
+from sodar_cli import api
 from sodar_cli.project.config import ProjectUpdateConfig
 
 
 def setup_argparse(parser):
     parser.add_argument("--hidden-cmd", dest="project_cmd", default=run, help=argparse.SUPPRESS)
     parser.add_argument("project_uuid", help="UUID of the project to update.", type=uuid.UUID)
+    parser.add_argument("--title", default="Project Title", help="Title of the project")
+    parser.add_argument(
+        "--type", default="Project Type", help="Type of the project [PROJECT, CATEGORY]"
+    )
+    parser.add_argument("--parent-uuid", help="UUID of the parent project, if any")
+    parser.add_argument("--description", help="Description text, optional")
+    parser.add_argument("--readme", help="README text, markdown allowed, optional")
 
 
-def run(config, toml_config, args, _parser, _subparser, file=sys.stdout):
+def run(config, toml_config, args, _parser, _subparser, file=None):
     """Run landingzone retrieve command."""
     config = ProjectUpdateConfig.create(args, config, toml_config)
     logger.info("Configuration: %s", config)
-    logger.info("Deleting project")
+    logger.info("Creating project")
+    project = api.Project(
+        sodar_uuid=args.project_uuid,
+        title=args.title,
+        type=args.type,
+        parent_uuid=args.parent_uuid,
+        description=args.description,
+        readme=args.readme,
+    )
+    result = api.project.update(
+        sodar_url=config.project_config.global_config.sodar_server_url,
+        sodar_api_token=config.project_config.global_config.sodar_api_token,
+        project_uuid=config.project_uuid,
+        project=project,
+    )
+    print(json.dumps(cattr.unstructure(result)), file=(file or sys.stdout))

tests/test_api_project.py

@@ -70,22 +70,11 @@ def test_project_create(requests_mock):
 
 
 def test_project_update(requests_mock):
-    # Move landing zone
-    m_args = {
+    r_args = {
         "sodar_url": "https://sodar.example.com/",
         "project_uuid": "46f4d0d7-b446-4a04-99c4-53cbffe952a3",
         "sodar_api_token": "token",
     }
-    m_tpl = "%(sodar_url)sprojects/api/submit/move/%(project_uuid)s"
-    m_result = factories.ProjectFactory(sodar_uuid=m_args["project_uuid"])
-    requests_mock.register_uri(
-        "POST",
-        m_tpl % m_args,
-        headers={"Authorization": "Token %s" % m_args["sodar_api_token"]},
-        json=cattr.unstructure(m_result),
-    )
-    # Update project.
-    r_args = m_args.copy()
     p_obj = factories.ProjectFactory()
     r_args["project"] = p_obj
     r_tpl = "%(sodar_url)sproject/api/update/%(project_uuid)s"