haplohub-cli 3.2.0__tar.gz → 3.2.2__tar.gz

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2}/.github/workflows/on_pr.yml

@@ -13,7 +13,7 @@ jobs:
         python-version: ["3.10", "3.11", "3.12", "3.13"]
 
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
       - uses: astral-sh/setup-uv@v7
         with:
           python-version: ${{ matrix.python-version }}

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2}/.github/workflows/on_push_main.yml

@@ -15,7 +15,7 @@ jobs:
     name: Build python package
     runs-on: ubuntu-latest
     steps:
-      - uses: actions/checkout@v6
+      - uses: actions/checkout@v7
         with:
           fetch-depth: 0
       - uses: hynek/build-and-inspect-python-package@v2

{haplohub_cli-3.2.0/haplohub_cli.egg-info → haplohub_cli-3.2.2}/PKG-INFO

@@ -1,10 +1,11 @@
 Metadata-Version: 2.4
 Name: haplohub-cli
-Version: 3.2.0
+Version: 3.2.2
 Summary: HaploHub Command Line Interface
 Author-email: Mike Polcari <mike@haplotype-labs.com>, Ilya Khrustalev <ilya@haplotype-labs.com>
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
+Requires-Dist: certifi>=2026.10.19
 Requires-Dist: click>=8.1.8
 Requires-Dist: haplohub<4,>=3.1.0
 Requires-Dist: pendulum>=3.0.0

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2}/haplohub_cli/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '3.2.0'
-__version_tuple__ = version_tuple = (3, 2, 0)
+__version__ = version = '3.2.2'
+__version_tuple__ = version_tuple = (3, 2, 2)
 
-__commit_id__ = commit_id = 'gd9453247c'
+__commit_id__ = commit_id = 'g9bab1d8f9'

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2}/haplohub_cli/commands/algorithm/result/__init__.py

@@ -50,8 +50,14 @@ def get(id):
 @click.option("--cohort", "-c", type=types.HAPLOHUB_ID, required=True, help="The ID of the cohort")
 @click.option("--member", "-m", type=types.HAPLOHUB_ID, required=False, help="The member id (its latest sample is scored)")
 @click.option("--sample", "-s", type=types.HAPLOHUB_ID, required=False, help="The sample id to run on")
-@click.option("--input-json", "-i", type=types.FILE_PATH, required=False, help="The input JSON")
-@click.option("--input-file", "-f", type=types.FILE_PATH, required=False, help="The input file")
+@click.option(
+    "--input-json",
+    "-i",
+    metavar="JSON",
+    required=False,
+    help="""The algorithm input as an inline JSON string, e.g. '{"pgs_model_ids": "PGS000001"}'""",
+)
+@click.option("--input-file", "-f", type=types.FILE_PATH, required=False, help="Path to a JSON file with the algorithm input")
 def create(
     algorithm: str,
     cohort: str,
@@ -65,7 +71,13 @@ def create(
         raise click.ClickException("Only one of --input-json or --input-file can be provided")
 
     if input_json is not None:
-        input_data = json.loads(input_json)
+        try:
+            input_data = json.loads(input_json)
+        except json.JSONDecodeError as e:
+            raise click.BadParameter(
+                f"not valid JSON ({e.msg}). To read the input from a file, use --input-file.",
+                param_hint="--input-json",
+            ) from e
     elif input_file is not None:
         with open(input_file, "r") as f:
             input_data = json.load(f)

haplohub_cli-3.2.2/haplohub_cli/commands/algorithm/tests/test_result_create.py

@@ -0,0 +1,50 @@
+import json
+import tempfile
+from unittest import TestCase
+from unittest.mock import patch
+
+from click.testing import CliRunner
+
+from haplohub_cli.commands.algorithm.result import create
+
+BASE_ARGS = ["--algorithm", "pgsc_calc", "--cohort", "coh-abc123", "--sample", "smp-abc123"]
+
+
+class ResultCreateInputTestCase(TestCase):
+    def _invoke(self, *args):
+        with patch("haplohub_cli.commands.algorithm.result.client") as client:
+            result = CliRunner().invoke(create, [*BASE_ARGS, *args])
+        return result, client
+
+    def _sent_input(self, client):
+        (request,), _ = client.algorithm_result.create_algorithm_result.call_args
+        return request.input
+
+    def test_input_json_takes_an_inline_json_string(self):
+        result, client = self._invoke("-i", '{"pgs_model_ids": "PGS000001"}')
+
+        self.assertEqual(result.exit_code, 0, result.output)
+        self.assertEqual(self._sent_input(client), {"pgs_model_ids": "PGS000001"})
+
+    def test_input_file_reads_json_from_a_path(self):
+        with tempfile.NamedTemporaryFile("w", suffix=".json") as f:
+            json.dump({"pgs_model_ids": "PGS000002"}, f)
+            f.flush()
+            result, client = self._invoke("-f", f.name)
+
+        self.assertEqual(result.exit_code, 0, result.output)
+        self.assertEqual(self._sent_input(client), {"pgs_model_ids": "PGS000002"})
+
+    def test_a_path_passed_to_input_json_points_to_input_file(self):
+        result, client = self._invoke("-i", "input.json")
+
+        self.assertEqual(result.exit_code, 2)
+        self.assertIn("--input-json", result.output)
+        self.assertIn("--input-file", result.output)
+        client.algorithm_result.create_algorithm_result.assert_not_called()
+
+    def test_help_shows_json_not_a_file_path(self):
+        result = CliRunner().invoke(create, ["--help"])
+
+        self.assertIn("-i, --input-json JSON", result.output)
+        self.assertIn("-f, --input-file FILE_PATH", result.output)

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2}/haplohub_cli/core/api/client.py

@@ -1,5 +1,6 @@
 from functools import cached_property
 
+import certifi
 import click
 from haplohub import ApiClient, Configuration
 
@@ -22,11 +23,13 @@ class Client:
             config = Configuration(
                 host=api_url,
                 api_key={"ApiKeyAuth": self.token_storage.get_api_key(api_url)},
+                ssl_ca_cert=certifi.where(),
             )
         else:
             config = Configuration(
                 host=api_url,
                 access_token=self.token_storage.get_access_token(api_url),
+                ssl_ca_cert=certifi.where(),
             )
         return ApiClient(config)
 

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2/haplohub_cli.egg-info}/PKG-INFO

@@ -1,10 +1,11 @@
 Metadata-Version: 2.4
 Name: haplohub-cli
-Version: 3.2.0
+Version: 3.2.2
 Summary: HaploHub Command Line Interface
 Author-email: Mike Polcari <mike@haplotype-labs.com>, Ilya Khrustalev <ilya@haplotype-labs.com>
 Requires-Python: >=3.10
 Description-Content-Type: text/markdown
+Requires-Dist: certifi>=2026.10.19
 Requires-Dist: click>=8.1.8
 Requires-Dist: haplohub<4,>=3.1.0
 Requires-Dist: pendulum>=3.0.0

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2}/haplohub_cli.egg-info/SOURCES.txt

@@ -41,6 +41,8 @@ haplohub_cli/commands/variant.py
 haplohub_cli/commands/version.py
 haplohub_cli/commands/algorithm/__init__.py
 haplohub_cli/commands/algorithm/result/__init__.py
+haplohub_cli/commands/algorithm/tests/__init__.py
+haplohub_cli/commands/algorithm/tests/test_result_create.py
 haplohub_cli/commands/cohort/__init__.py
 haplohub_cli/commands/cohort/biomarker.py
 haplohub_cli/commands/cohort/sample.py

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2}/haplohub_cli.egg-info/requires.txt

@@ -1,3 +1,4 @@
+certifi>=2026.10.19
 click>=8.1.8
 haplohub<4,>=3.1.0
 pendulum>=3.0.0

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2}/haplohub_cli.egg-info/scm_file_list.json

@@ -26,6 +26,8 @@
     "haplohub_cli/commands/__init__.py",
     "haplohub_cli/commands/algorithm/__init__.py",
     "haplohub_cli/commands/algorithm/result/__init__.py",
+    "haplohub_cli/commands/algorithm/tests/__init__.py",
+    "haplohub_cli/commands/algorithm/tests/test_result_create.py",
     "haplohub_cli/commands/cohort/__init__.py",
     "haplohub_cli/commands/cohort/biomarker.py",
     "haplohub_cli/commands/cohort/member/__init__.py",

haplohub_cli-3.2.2/haplohub_cli.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "3.2.2",
+  "distance": 0,
+  "node": "g9bab1d8f9a91c35232095fc7e4dad9fac2010a92",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-10-21"
+}

{haplohub_cli-3.2.0 → haplohub_cli-3.2.2}/pyproject.toml

@@ -9,6 +9,7 @@ authors = [
 requires-python = ">=3.10"
 dynamic = ["version"]
 dependencies = [
+    "certifi>=2026.10.19",
     "click>=8.1.8",
     "haplohub>=3.1.0,<4",
     "pendulum>=3.0.0",