Merge pull request #123 from seqeralabs/dev

Release v0.4.6

Author: ejseqera

README.md

@@ -16,7 +16,7 @@ You will need to have an account on Seqera Platform (see [Plans and pricing](htt
 
 `seqerakit` requires the following dependencies:
 
-1. [Seqera Platform CLI](https://github.com/seqeralabs/tower-cli#1-installation)
+1. [Seqera Platform CLI (`>=0.9.2`)](https://github.com/seqeralabs/tower-cli#1-installation)
 
 2. [Python (`>=3.8`)](https://www.python.org/downloads/)
 
@@ -82,23 +82,34 @@ Create a Seqera Platform access token using the [Seqera Platform](https://tower.
 `seqerakit` reads this token from the environment variable `TOWER_ACCESS_TOKEN`. Please export it into your terminal as shown below:
 
 ```bash
-export TOWER_ACCESS_TOKEN=<your access token>
+export TOWER_ACCESS_TOKEN=<Your access token>
 ```
 
+For Enterprise installations of Seqera Platform, you will also need to configure the API endpoint that will be used to connect to the Platform. You can do so by exporting the following environment variable:
+```bash
+export TOWER_API_ENDPOINT=<Tower API URL>
+```
+By default, this is set to `https://api.tower.nf` to connect to Seqera Platform Cloud.
+
+
 ## Usage
 
-To confirm the installation of `seqerakit`, configuration of the Seqera Platform CLI and connection is working as expected:
+To confirm the installation of `seqerakit`, configuration of the Seqera Platform CLI and connection to the Platform is working as expected. This will run the `tw info` command under the hood:
 
 ```bash
 seqerakit --info
 ```
 
-Use the `-h` or `--help `parameter to list the available commands and their associated options:
-
+Use the `--help` or `-h` parameter to list the available commands and their associated options:
 ```bash
 seqerakit --help
 ```
 
+Use `--version` or `-v` to retrieve the current version of your seqerakit installation:
+```bash
+seqerakit --version
+```
+
 ### Dryrun
 
 To print the commands that would executed with `tw` when using a YAML file, you can run `seqerakit` with the `--dryrun` flag:

seqerakit/__init__.py

@@ -0,0 +1,3 @@
+import importlib.metadata as importlib_metadata
+
+__version__ = importlib_metadata.version(__name__)

seqerakit/cli.py

@@ -24,48 +24,63 @@
 from pathlib import Path
 from seqerakit import seqeraplatform, helper, overwrite
 from seqerakit.seqeraplatform import ResourceExistsError, ResourceCreationError
-
+from seqerakit import __version__
 
 logger = logging.getLogger(__name__)
 
 
 def parse_args(args=None):
-    parser = argparse.ArgumentParser()
-    parser.add_argument(
+    parser = argparse.ArgumentParser(
+        description="Seqerakit: Python wrapper for the Seqera Platform CLI"
+    )
+    # General options
+    general = parser.add_argument_group("General Options")
+    general.add_argument(
         "-l",
         "--log_level",
         default="INFO",
         choices=("CRITICAL", "ERROR", "WARNING", "INFO", "DEBUG"),
-        help="The desired log level (default: INFO).",
-        type=str.upper,
+        help="Set the logging level.",
     )
-    parser.add_argument(
+    general.add_argument(
         "--info",
+        "-i",
         action="store_true",
-        help="Display information about the Seqera Platform and exit",
+        help="Display Seqera Platform information and exit.",
     )
-    parser.add_argument(
+    general.add_argument(
         "--dryrun",
+        "-d",
         action="store_true",
-        help="Print the commands that would be executed without running them.",
+        help="Print the commands that would be executed.",
     )
-    parser.add_argument(
+    general.add_argument(
+        "--version",
+        "-v",
+        action="version",
+        version=f"%(prog)s {__version__}",
+        help="Show version number and exit.",
+    )
+
+    # YAML processing options
+    yaml_processing = parser.add_argument_group("YAML Processing Options")
+    yaml_processing.add_argument(
         "yaml",
         type=Path,
-        nargs="*",  # allow multiple YAML paths
-        help="One or more YAML files with Seqera Platform resources to create",
+        nargs="*",
+        help="One or more YAML files with Seqera Platform resource definitions.",
     )
-    parser.add_argument(
+    yaml_processing.add_argument(
         "--delete",
         action="store_true",
-        help="Recursively delete all resources defined in the YAML file(s)",
+        help="Recursively delete resources defined in the YAML files.",
     )
-    parser.add_argument(
+    yaml_processing.add_argument(
         "--cli",
         dest="cli_args",
         type=str,
-        help="Additional arguments to pass to Seqera Platform"
-        " CLI enclosed in double quotes (e.g. '--cli=\"--insecure\"')",
+        help="Additional Seqera Platform CLI specific options to be passed,"
+        " enclosed in double quotes (e.g. '--cli=\"--insecure\"').",
     )
     return parser.parse_args(args)
 

seqerakit/helper.py

@@ -113,10 +113,10 @@ def parse_all_yaml(file_paths, destroy=False):
 def parse_block(block_name, item):
     # Define the mapping from block names to functions.
     block_to_function = {
-        "credentials": parse_credentials_block,
-        "compute-envs": parse_compute_envs_block,
+        "credentials": parse_type_block,
+        "compute-envs": parse_type_block,
+        "actions": parse_type_block,
         "teams": parse_teams_block,
-        "actions": parse_actions_block,
         "datasets": parse_datasets_block,
         "pipelines": parse_pipelines_block,
         "launch": parse_launch_block,
@@ -141,27 +141,28 @@ def parse_generic_block(item):
     return cmd_args
 
 
-def parse_credentials_block(item):
+def parse_type_block(item, priority_keys=["type", "config-mode", "file-path"]):
     cmd_args = []
-    for key, value in item.items():
-        if key == "type":
-            cmd_args.append(str(value))
-        elif isinstance(value, bool):
-            if value:
-                cmd_args.append(f"--{key}")
-        else:
-            cmd_args.extend([f"--{key}", str(value)])
-    return cmd_args
 
+    # Ensure at least one of 'type' or 'file-path' is present
+    if not any(key in item for key in ["type", "file-path"]):
+        raise ValueError(
+            "Please specify at least 'type' or 'file-path' for creating the resource."
+        )
+
+    # Process priority keys first
+    for key in priority_keys:
+        if key in item:
+            cmd_args.append(str(item[key]))
+            del item[key]  # Remove the key to avoid repeating in args
 
-def parse_compute_envs_block(item):
-    cmd_args = []
     for key, value in item.items():
-        if key == "file-path" or key == "type" or key == "config-mode":
-            cmd_args.append(str(value))
-        elif isinstance(value, bool):
+        if isinstance(value, bool):
             if value:
                 cmd_args.append(f"--{key}")
+        elif key == "params":
+            temp_file_name = utils.create_temp_yaml(value)
+            cmd_args.extend(["--params-file", temp_file_name])
         else:
             cmd_args.extend([f"--{key}", str(value)])
     return cmd_args
@@ -194,20 +195,6 @@ def parse_teams_block(item):
     return (cmd_args, members_cmd_args)
 
 
-def parse_actions_block(item):
-    cmd_args = []
-    temp_file_name = None
-    for key, value in item.items():
-        if key == "type":
-            cmd_args.append(str(value))
-        elif key == "params":
-            temp_file_name = utils.create_temp_yaml(value)
-            cmd_args.extend(["--params-file", temp_file_name])
-        else:
-            cmd_args.extend([f"--{key}", str(value)])
-    return cmd_args
-
-
 def parse_datasets_block(item):
     cmd_args = []
     for key, value in item.items():

seqerakit/overwrite.py

@@ -73,7 +73,7 @@ def __init__(self, sp):
             "workspaces": {
                 "keys": ["name", "organization"],
                 "method_args": self._get_workspace_args,
-                "name_key": "workspaceId",
+                "name_key": "workspaceName",
             },
         }
 
@@ -101,7 +101,6 @@ def handle_overwrite(self, block, args, overwrite=False, destroy=False):
                     self.block_operations["participants"]["name_key"] = "teamName"
                 else:
                     self.block_operations["participants"]["name_key"] = "email"
-
             if self.check_resource_exists(operation["name_key"], sp_args):
                 # if resource exists and overwrite is true, delete
                 if overwrite:
@@ -169,11 +168,7 @@ def _get_workspace_args(self, args):
         workspaceId used to delete will be retrieved using the _find_workspace_id()
         method.
         """
-        workspace_id = self._find_workspace_id(
-            json.loads(self.sp.workspaces.list("-o", "json")),
-            args["organization"],
-            args["name"],
-        )
+        workspace_id = self._find_workspace_id(args["organization"], args["name"])
         return ("delete", "--id", str(workspace_id))
 
     def _get_generic_deletion_args(self, args):
@@ -267,12 +262,12 @@ def _find_workspace_id(self, organization, workspace_name):
         organization name and workspace name. This ID will be used to delete the
         workspace.
         """
-        if "workspaces" in self.cached_jsondata:
-            workspaces = self.cached_jsondata["workspaces"]
-            for workspace in workspaces:
-                if (
-                    workspace.get("orgName") == organization
-                    and workspace.get("workspaceName") == workspace_name
-                ):
-                    return workspace.get("workspaceId")
+        jsondata = json.loads(self.cached_jsondata)
+        workspaces = jsondata["workspaces"]
+        for workspace in workspaces:
+            if (
+                workspace.get("orgName") == organization
+                and workspace.get("workspaceName") == workspace_name
+            ):
+                return workspace.get("workspaceId")
         return None

setup.py

@@ -2,7 +2,7 @@
 
 from setuptools import find_packages, setup
 
-VERSION = "0.4.5"
+VERSION = "0.4.6"
 
 with open("README.md") as f:
     readme = f.read()

tests/unit/test_helper.py

@@ -130,14 +130,14 @@ def test_create_mock_dataset_yaml(mock_yaml_file):
     assert result["datasets"] == expected_block_output
 
 
-def test_create_mock_computeevs_yaml(mock_yaml_file):
+def test_create_mock_computeevs_source_yaml(mock_yaml_file):
     test_data = {
         "compute-envs": [
             {
                 "name": "test_computeenv",
                 "workspace": "my_organization/my_workspace",
                 "credentials": "my_credentials",
-                "file-path": "./examples/yaml/computeenvs/computeenvs.yaml",
+                "file-path": "./computeenvs/computeenv.json",
                 "wait": "AVAILABLE",
                 "fusion-v2": True,
                 "fargate": False,
@@ -149,9 +149,9 @@ def test_create_mock_computeevs_yaml(mock_yaml_file):
     expected_block_output = [
         {
             "cmd_args": [
+                "./computeenvs/computeenv.json",
                 "--credentials",
                 "my_credentials",
-                "./examples/yaml/computeenvs/computeenvs.yaml",
                 "--fusion-v2",
                 "--name",
                 "test_computeenv",
@@ -171,6 +171,43 @@ def test_create_mock_computeevs_yaml(mock_yaml_file):
     assert result["compute-envs"] == expected_block_output
 
 
+def test_create_mock_computeevs_cli_yaml(mock_yaml_file):
+    test_data = {
+        "compute-envs": [
+            {
+                "name": "test_computeenv",
+                "workspace": "my_organization/my_workspace",
+                "credentials": "my_credentials",
+                "type": "aws-batch",
+                "config-mode": "forge",
+                "wait": "AVAILABLE",
+            }
+        ],
+    }
+
+    expected_block_output = [
+        {
+            "cmd_args": [
+                "aws-batch",
+                "forge",
+                "--credentials",
+                "my_credentials",
+                "--name",
+                "test_computeenv",
+                "--wait",
+                "AVAILABLE",
+                "--workspace",
+                "my_organization/my_workspace",
+            ],
+            "overwrite": False,
+        }
+    ]
+    file_path = mock_yaml_file(test_data)
+    result = helper.parse_all_yaml([file_path])
+    assert "compute-envs" in result
+    assert result["compute-envs"] == expected_block_output
+
+
 def test_create_mock_pipeline_add_yaml(mock_yaml_file):
     test_data = {
         "pipelines": [
@@ -191,7 +228,6 @@ def test_create_mock_pipeline_add_yaml(mock_yaml_file):
             }
         ]
     }
-
     # params file cmds parsed separately
     expected_block_output = [
         {
@@ -239,3 +275,24 @@ def test_empty_yaml_file(mock_yaml_file):
     assert f"The file '{file_path}' is empty or does not contain valid data." in str(
         e.value
     )
+
+
+def test_error_type_yaml_file(mock_yaml_file):
+    test_data = {
+        "compute-envs": [
+            {
+                "name": "test_computeenv",
+                "workspace": "my_organization/my_workspace",
+                "credentials": "my_credentials",
+                "wait": "AVAILABLE",
+            }
+        ],
+    }
+    file_path = mock_yaml_file(test_data)
+
+    with pytest.raises(ValueError) as e:
+        helper.parse_all_yaml([file_path])
+    assert (
+        "Please specify at least 'type' or 'file-path' for creating the resource."
+        in str(e.value)
+    )