haplohub-cli 2.3.0__tar.gz → 2.5.0__tar.gz

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: haplohub-cli
-Version: 2.3.0
+Version: 2.5.0
 Summary: HaploHub Command Line Interface
 Author-email: Mike Polcari <mike@haplotype-labs.com>, Ilya Khrustalev <ilya@haplotype-labs.com>
 Requires-Python: >=3.8

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/haplohub_cli/_version.py

@@ -18,7 +18,7 @@ version_tuple: tuple[int | str, ...]
 commit_id: str | None
 __commit_id__: str | None
 
-__version__ = version = '2.3.0'
-__version_tuple__ = version_tuple = (2, 3, 0)
+__version__ = version = '2.5.0'
+__version_tuple__ = version_tuple = (2, 5, 0)
 
-__commit_id__ = commit_id = 'g6d8dda047'
+__commit_id__ = commit_id = 'gcd8a204d2'

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/haplohub_cli/auth/auth.py

@@ -20,7 +20,7 @@ def token_login(api_key: str):
 
     response.raise_for_status()
 
-    oauth_client.token_storage.store_credentials({"api_key": api_key})
+    oauth_client.token_storage.store_credentials(api_url, {"api_key": api_key})
     click.echo("Successfully authenticated with HaploHub.")
 
 
@@ -47,4 +47,4 @@ def interactive_login():
     credentials = auth_request.exchange_code(auth_code)
 
     click.echo("Successfully authenticated with HaploHub.")
-    oauth_client.token_storage.store_credentials(credentials)
+    oauth_client.token_storage.store_credentials(config_manager.config.api_url, credentials)

haplohub_cli-2.5.0/haplohub_cli/auth/tests/test_token_storage.py

@@ -0,0 +1,74 @@
+import json
+
+import pytest
+from pyfakefs.fake_filesystem_unittest import TestCase
+
+from haplohub_cli.auth.token_storage import CREDENTIALS_VERSION, TokenStorage, normalize_api_url
+
+
+class TokenStorageTestCase(TestCase):
+    def setUp(self):
+        self.setUpPyfakefs()
+        self.instance = TokenStorage("/tmp/test_token_storage.json")
+
+    def test_credentials_exist_should_return_false_when_file_does_not_exist(self):
+        self.assertFalse(self.instance.credentials_exist("https://api.example.com"))
+
+    def test_store_credentials_should_save_versioned_credentials(self):
+        self.instance.store_credentials("https://api.example.com", {"access_token": "123456"})
+
+        with open(self.instance.token_file) as f:
+            self.assertEqual(
+                json.load(f),
+                {
+                    "version": CREDENTIALS_VERSION,
+                    "environments": {"https://api.example.com": {"access_token": "123456"}},
+                },
+            )
+
+    def test_credentials_are_isolated_by_environment(self):
+        self.instance.store_credentials("https://api-a.example.com", {"access_token": "token-a"})
+        self.instance.store_credentials("https://api-b.example.com", {"api_key": "key-b"})
+
+        self.assertEqual(self.instance.get_access_token("https://api-a.example.com"), "token-a")
+        self.assertEqual(self.instance.get_api_key("https://api-b.example.com"), "key-b")
+        self.assertFalse(self.instance.has_api_key("https://api-a.example.com"))
+        self.assertTrue(self.instance.has_api_key("https://api-b.example.com"))
+
+    def test_get_credentials_should_fail_for_unknown_environment(self):
+        self.instance.store_credentials("https://api-a.example.com", {"access_token": "token-a"})
+
+        with pytest.raises(KeyError):
+            self.instance.get_credentials("https://api-b.example.com")
+
+    def test_legacy_credentials_are_migrated_to_current_environment(self):
+        credentials = {"access_token": "123456", "refresh_token": "refresh-123456"}
+        with open(self.instance.token_file, "w") as f:
+            json.dump(credentials, f)
+
+        self.assertTrue(self.instance.migrate("https://api.example.com/"))
+        self.assertEqual(self.instance.get_credentials("https://api.example.com"), credentials)
+
+        with open(self.instance.token_file) as f:
+            self.assertEqual(
+                json.load(f),
+                {
+                    "version": CREDENTIALS_VERSION,
+                    "environments": {"https://api.example.com": credentials},
+                },
+            )
+
+    def test_versioned_credentials_are_not_migrated_again(self):
+        self.instance.store_credentials("https://api-a.example.com", {"access_token": "token-a"})
+
+        self.assertFalse(self.instance.migrate("https://api-b.example.com"))
+        self.assertFalse(self.instance.credentials_exist("https://api-b.example.com"))
+
+    def test_get_refresh_token_should_return_none_when_missing(self):
+        self.instance.store_credentials("https://api.example.com", {"access_token": "123456"})
+
+        self.assertIsNone(self.instance.get_refresh_token("https://api.example.com"))
+
+
+def test_normalize_api_url():
+    assert normalize_api_url(" HTTPS://API.Example.COM/base/ ") == "https://api.example.com/base"

haplohub_cli-2.5.0/haplohub_cli/auth/token_storage.py

@@ -0,0 +1,107 @@
+import json
+import os
+import tempfile
+from genericpath import exists
+from os import path
+from typing import Dict, Tuple
+from urllib.parse import urlsplit, urlunsplit
+
+from haplohub_cli import settings
+
+CREDENTIALS_VERSION = 2
+
+
+def normalize_api_url(api_url: str) -> str:
+    api_url = api_url.strip()
+    parsed = urlsplit(api_url)
+
+    if not parsed.scheme or not parsed.netloc:
+        return api_url.rstrip("/")
+
+    return urlunsplit(
+        (
+            parsed.scheme.lower(),
+            parsed.netloc.lower(),
+            parsed.path.rstrip("/"),
+            parsed.query,
+            parsed.fragment,
+        )
+    )
+
+
+class TokenStorage:
+    def __init__(self, token_file: str):
+        self.token_file = token_file
+
+    def migrate(self, api_url: str) -> bool:
+        _, migrated = self._load(api_url)
+        return migrated
+
+    def credentials_exist(self, api_url: str) -> bool:
+        data, _ = self._load(api_url)
+        return normalize_api_url(api_url) in data["environments"]
+
+    def store_credentials(self, api_url: str, credentials: dict):
+        data, _ = self._load(api_url)
+        data["environments"][normalize_api_url(api_url)] = credentials
+        self._save(data)
+
+    def get_credentials(self, api_url: str) -> dict:
+        data, _ = self._load(api_url)
+        return data["environments"][normalize_api_url(api_url)]
+
+    def get_access_token(self, api_url: str):
+        return self.get_credentials(api_url)["access_token"]
+
+    def get_api_key(self, api_url: str):
+        return self.get_credentials(api_url)["api_key"]
+
+    def get_refresh_token(self, api_url: str):
+        return self.get_credentials(api_url).get("refresh_token")
+
+    def has_api_key(self, api_url: str) -> bool:
+        return self.credentials_exist(api_url) and "api_key" in self.get_credentials(api_url)
+
+    def _load(self, migration_api_url: str) -> Tuple[Dict[str, object], bool]:
+        if not exists(self.token_file):
+            return self._empty_store(), False
+
+        with open(self.token_file) as f:
+            data = json.load(f)
+
+        if data.get("version") == CREDENTIALS_VERSION:
+            if not isinstance(data.get("environments"), dict):
+                raise ValueError("Invalid credentials file: 'environments' must be an object")
+            return data, False
+
+        if "version" in data:
+            raise ValueError(f"Unsupported credentials file version: {data['version']}")
+
+        migrated = self._empty_store()
+        migrated["environments"][normalize_api_url(migration_api_url)] = data
+        self._save(migrated)
+        return migrated, True
+
+    def _save(self, data: Dict[str, object]):
+        directory = path.dirname(self.token_file) or "."
+        os.makedirs(directory, exist_ok=True)
+
+        temporary_file = None
+        try:
+            with tempfile.NamedTemporaryFile("w", dir=directory, delete=False) as f:
+                temporary_file = f.name
+                json.dump(data, f, indent=4)
+                f.write("\n")
+
+            os.chmod(temporary_file, 0o600)
+            os.replace(temporary_file, self.token_file)
+        finally:
+            if temporary_file and exists(temporary_file):
+                os.unlink(temporary_file)
+
+    @staticmethod
+    def _empty_store() -> Dict[str, object]:
+        return {"version": CREDENTIALS_VERSION, "environments": {}}
+
+
+token_storage = TokenStorage(settings.CREDENTIALS_FILE)

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/haplohub_cli/commands/config.py

@@ -1,5 +1,6 @@
 import click
 
+from haplohub_cli.auth.token_storage import token_storage
 from haplohub_cli.config.config_manager import config_manager
 
 
@@ -28,6 +29,7 @@ def set(key, value):
 @config.command()
 @click.argument("api_url", type=click.STRING)
 def switch(api_url):
+    token_storage.migrate(config_manager.config.api_url)
     config_manager.switch_environment(api_url)
     return config_manager.config
 

haplohub_cli-2.5.0/haplohub_cli/commands/variant.py

@@ -0,0 +1,124 @@
+import click
+from haplohub import (
+    GetVariantRequest,
+    GwasTargetSchema,
+    HgvsTargetSchema,
+    RegionTargetSchema,
+    TargetsInner,
+    VariantFilterSchema,
+)
+
+from haplohub_cli.core.api.client import client
+
+
+def _selectors(clinvar: bool, gwas: bool) -> list[str] | None:
+    """Build the selector list; None when no annotations were requested."""
+    selectors = []
+    if clinvar:
+        selectors.append("clinvar")
+    if gwas:
+        selectors.append("gwas")
+    return selectors or None
+
+
+@click.group()
+def variant():
+    """
+    Work with variants
+    """
+    pass
+
+
+@variant.command()
+@click.argument("cohort_id", type=str)
+@click.option("--sample", "-s", "sample_ids", type=str, multiple=True, required=True, help="Sample ID (repeatable)")
+@click.option("--accession", "-a", type=str, required=True, help="Chromosome accession (e.g. NC_000001.11)")
+@click.option("--start", type=int, required=True, help="Genomic start position")
+@click.option("--end", type=int, required=True, help="Genomic end position")
+@click.option("--reference", type=str, default=None, help="Reference allele")
+@click.option("--alternate", type=str, default=None, help="Alternate allele")
+@click.option("--call-state", type=click.Choice(["called", "all"]), default="called", help="Filter by call state")
+@click.option("--clinvar", is_flag=True, default=False, help="Include ClinVar annotations")
+@click.option("--gwas", is_flag=True, default=False, help="Include GWAS Catalog annotations")
+def region(sample_ids, cohort_id, accession, start, end, reference, alternate, call_state, clinvar, gwas):
+    """
+    Query variants by genomic region
+    """
+    target = RegionTargetSchema(
+        accession=accession,
+        start=start,
+        end=end,
+        reference=reference,
+        alternate=alternate,
+    )
+
+    request = GetVariantRequest(
+        sample_ids=list(sample_ids),
+        targets=[TargetsInner(target)],
+        filters=VariantFilterSchema(call_state=call_state),
+        selectors=_selectors(clinvar, gwas),
+    )
+
+    return client.variant.get_variant(cohort_id, request)
+
+
+@variant.command()
+@click.argument("cohort_id", type=str)
+@click.option("--sample", "-s", "sample_ids", type=str, multiple=True, required=True, help="Sample ID (repeatable)")
+@click.option("--hgvs", "-h", type=str, multiple=True, required=True, help="HGVS notation (repeatable)")
+@click.option("--call-state", type=click.Choice(["called", "all"]), default="called", help="Filter by call state")
+@click.option("--clinvar", is_flag=True, default=False, help="Include ClinVar annotations")
+@click.option("--gwas", is_flag=True, default=False, help="Include GWAS Catalog annotations")
+def hgvs(sample_ids, cohort_id, hgvs, call_state, clinvar, gwas):
+    """
+    Query variants by HGVS notation
+    """
+    targets = [TargetsInner(HgvsTargetSchema(value=v)) for v in hgvs]
+
+    request = GetVariantRequest(
+        sample_ids=list(sample_ids),
+        targets=targets,
+        filters=VariantFilterSchema(call_state=call_state),
+        selectors=_selectors(clinvar, gwas),
+    )
+
+    return client.variant.get_variant(cohort_id, request)
+
+
+@variant.command()
+@click.argument("cohort_id", type=str)
+@click.option("--sample", "-s", "sample_ids", type=str, multiple=True, required=True, help="Sample ID (repeatable)")
+@click.option("--gene", type=str, default=None, help="Mapped gene symbol (e.g. TCF7L2)")
+@click.option("--trait-id", type=str, default=None, help="EFO trait id (e.g. EFO_0001360)")
+@click.option("--rs", "rs_ids", type=str, multiple=True, help="rsID to genotype (repeatable)")
+@click.option("--p-value-max", type=float, default=None, help="Keep only associations with p-value <= this")
+@click.option("--limit", type=int, default=100, help="Max associations to resolve (most significant first)")
+@click.option("--call-state", type=click.Choice(["called", "all"]), default="called", help="Filter by call state")
+@click.option("--clinvar", is_flag=True, default=False, help="Also include ClinVar annotations")
+def gwas(sample_ids, cohort_id, gene, trait_id, rs_ids, p_value_max, limit, call_state, clinvar):
+    """
+    Genotype the SNPs of GWAS Catalog associations in a sample.
+
+    Selects associations by --gene, --trait-id and/or --rs (at least one required),
+    genotypes their SNP positions in the sample, and attaches the matching GWAS
+    associations to each result. Combine with --clinvar to also attach ClinVar.
+    """
+    if not (gene or trait_id or rs_ids):
+        raise click.UsageError("Provide at least one of --gene, --trait-id or --rs.")
+
+    target = GwasTargetSchema(
+        gene=gene,
+        trait_id=trait_id,
+        rs_ids=list(rs_ids),
+        p_value_max=p_value_max,
+        limit=limit,
+    )
+
+    request = GetVariantRequest(
+        sample_ids=list(sample_ids),
+        targets=[TargetsInner(target)],
+        filters=VariantFilterSchema(call_state=call_state),
+        selectors=_selectors(clinvar, gwas=True),
+    )
+
+    return client.variant.get_variant(cohort_id, request)

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/haplohub_cli/config/config_manager.py

@@ -37,6 +37,7 @@ class ConfigManager:
             return self._config
 
     def switch_environment(self, api_url: str):
+        api_url = api_url.strip().rstrip("/")
         response = requests.get(f"{api_url}/api/v1/config/")
         response.raise_for_status()
         data = response.json()
@@ -44,7 +45,7 @@ class ConfigManager:
         if data["status"] != "success":
             raise Exception(data.get("error", "Unknown error"))
 
-        new_config = {"redirect_port": settings.REDIRECT_PORT, "api_url": api_url, **data["result"]["cli"]}
+        new_config = {**data["result"]["cli"], "redirect_port": settings.REDIRECT_PORT, "api_url": api_url}
 
         self._config = Config(**new_config)
 

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/haplohub_cli/core/api/client.py

@@ -1,5 +1,6 @@
 from functools import cached_property
 
+import click
 from haplohub import (
     AlgorithmApi,
     AlgorithmResultApi,
@@ -25,15 +26,20 @@ class Client:
 
     @cached_property
     def client(self):
-        if self.token_storage.has_api_key:
+        api_url = config_manager.config.api_url
+
+        if not self.token_storage.credentials_exist(api_url):
+            raise click.ClickException(f"No credentials found for {api_url}. Run `haplohub login` first.")
+
+        if self.token_storage.has_api_key(api_url):
             config = Configuration(
-                host=config_manager.config.api_url,
-                api_key={"ApiKeyAuth": self.token_storage.get_api_key()},
+                host=api_url,
+                api_key={"ApiKeyAuth": self.token_storage.get_api_key(api_url)},
             )
         else:
             config = Configuration(
-                host=config_manager.config.api_url,
-                access_token=self.token_storage.get_access_token(),
+                host=api_url,
+                access_token=self.token_storage.get_access_token(api_url),
             )
         return ApiClient(config)
 

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/haplohub_cli/formatters/algorithm.py

@@ -1,5 +1,8 @@
+from typing import Optional
+
 from haplohub import (
     AlgorithmSchema,
+    AlgorithmVersionSchema,
     PaginatedResponseAlgorithmSchema,
     ResultResponseAlgorithmSchema,
 )
@@ -9,14 +12,19 @@ from haplohub_cli.formatters import utils
 from haplohub_cli.formatters.decorators import register
 
 
+def _latest_version(version: Optional[AlgorithmVersionSchema]) -> str:
+    # Algorithms are identified by name now; a version is identified by its version string.
+    return version.version if version else "N/A"
+
+
 @register(AlgorithmSchema)
 def format_algorithm(data: AlgorithmSchema):
-    table = Table(title="Algorithm", caption=f"Id: {utils.format_id(data.id)}")
-    table.add_column("Id")
+    table = Table(title="Algorithm", caption=f"Name: {data.name}")
     table.add_column("Name")
     table.add_column("Description")
     table.add_column("Latest Version")
-    table.add_row(utils.format_id(data.id), data.name, data.description)
+    table.add_column("Owner")
+    table.add_row(data.name, data.description, _latest_version(data.latest_version), data.owner)
     return table
 
 
@@ -28,7 +36,6 @@ def format_single_algorithm(data: ResultResponseAlgorithmSchema):
 @register(PaginatedResponseAlgorithmSchema)
 def format_algorithms(data: PaginatedResponseAlgorithmSchema):
     table = Table(title="Algorithms", caption=f"Total: {data.total_count}")
-    table.add_column("Id")
     table.add_column("Name")
     table.add_column("Description")
     table.add_column("Latest Version")
@@ -36,10 +43,9 @@ def format_algorithms(data: PaginatedResponseAlgorithmSchema):
 
     for item in data.items:
         table.add_row(
-            utils.format_id(item.id),
             item.name,
             utils.truncate(item.description, 50),
-            "%s (%s)" % (utils.format_id(item.latest_version.id), item.latest_version.version),
+            _latest_version(item.latest_version),
             utils.format_dt(item.created),
         )
 

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/haplohub_cli/formatters/variant.py

@@ -16,10 +16,11 @@ def format_variant_results(data: ResultListResponseVariantResultSchema):
     table.add_column("Sample")
     table.add_column("Called")
     table.add_column("Dosage")
+    table.add_column("Annotations")
 
     for item in data.items:
         if item.error_message:
-            table.add_row(item.target.input, f"[red]{item.error_message}[/red]", "", "", "", "", "", "", "")
+            table.add_row(item.target.input, f"[red]{item.error_message}[/red]", "", "", "", "", "", "", "", "")
             continue
 
         variant = item.variant
@@ -30,9 +31,10 @@ def format_variant_results(data: ResultListResponseVariantResultSchema):
         reference = variant.reference or "" if variant else ""
         alternate = ", ".join(variant.alternate) if variant and variant.alternate else ""
         quality = f"{variant.quality:.4f}" if variant and variant.quality is not None else ""
+        annotations = _format_annotations(item.attachments)
 
         if not samples:
-            table.add_row(item.target.input, accession, position, reference, alternate, quality, "", "", "")
+            table.add_row(item.target.input, accession, position, reference, alternate, quality, "", "", "", annotations)
         else:
             for i, sample in enumerate(samples):
                 target_col = item.target.input if i == 0 else ""
@@ -41,10 +43,25 @@ def format_variant_results(data: ResultListResponseVariantResultSchema):
                 ref_col = reference if i == 0 else ""
                 alt_col = alternate if i == 0 else ""
                 qual_col = quality if i == 0 else ""
+                ann_col = annotations if i == 0 else ""
 
                 is_called = f"[green]{sample.is_called}[/green]" if sample.is_called else f"[red]{sample.is_called}[/red]"
                 dosage = str(sample.dosage) if sample.dosage is not None else ""
 
-                table.add_row(target_col, acc_col, pos_col, ref_col, alt_col, qual_col, sample.sample_id, is_called, dosage)
+                table.add_row(
+                    target_col, acc_col, pos_col, ref_col, alt_col, qual_col, sample.sample_id, is_called, dosage, ann_col
+                )
 
     return table
+
+
+def _format_annotations(attachments) -> str:
+    """Summarize per-source attachment counts, e.g. "clinvar:1 gwas:5"."""
+    if attachments is None:
+        return ""
+    parts = []
+    for source in ("clinvar", "gwas"):
+        rows = getattr(attachments, source, None) or []
+        if rows:
+            parts.append(f"{source}:{len(rows)}")
+    return " ".join(parts)

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/haplohub_cli.egg-info/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: haplohub-cli
-Version: 2.3.0
+Version: 2.5.0
 Summary: HaploHub Command Line Interface
 Author-email: Mike Polcari <mike@haplotype-labs.com>, Ilya Khrustalev <ilya@haplotype-labs.com>
 Requires-Python: >=3.8

{haplohub_cli-2.3.0 → haplohub_cli-2.5.0}/haplohub_cli.egg-info/SOURCES.txt

@@ -15,6 +15,8 @@ haplohub_cli.egg-info/SOURCES.txt
 haplohub_cli.egg-info/dependency_links.txt
 haplohub_cli.egg-info/entry_points.txt
 haplohub_cli.egg-info/requires.txt
+haplohub_cli.egg-info/scm_file_list.json
+haplohub_cli.egg-info/scm_version.json
 haplohub_cli.egg-info/top_level.txt
 haplohub_cli/auth/__init__.py
 haplohub_cli/auth/auth.py

haplohub_cli-2.5.0/haplohub_cli.egg-info/scm_file_list.json

@@ -0,0 +1,69 @@
+{
+  "files": [
+    ".pre-commit-config.yaml",
+    "README.md",
+    "uv.lock",
+    "pyproject.toml",
+    ".gitignore",
+    "haplohub_cli/__init__.py",
+    "haplohub_cli/settings.py",
+    "haplohub_cli/cli.py",
+    "haplohub_cli/commands/__init__.py",
+    "haplohub_cli/commands/version.py",
+    "haplohub_cli/commands/config.py",
+    "haplohub_cli/commands/file.py",
+    "haplohub_cli/commands/variant.py",
+    "haplohub_cli/commands/login.py",
+    "haplohub_cli/commands/cohort/biomarker.py",
+    "haplohub_cli/commands/cohort/__init__.py",
+    "haplohub_cli/commands/cohort/sample.py",
+    "haplohub_cli/commands/cohort/member/__init__.py",
+    "haplohub_cli/commands/cohort/member/report.py",
+    "haplohub_cli/commands/metadata/__init__.py",
+    "haplohub_cli/commands/algorithm/__init__.py",
+    "haplohub_cli/commands/algorithm/result/__init__.py",
+    "haplohub_cli/core/network.py",
+    "haplohub_cli/core/__init__.py",
+    "haplohub_cli/core/checksum.py",
+    "haplohub_cli/core/slug.py",
+    "haplohub_cli/core/upload.py",
+    "haplohub_cli/core/types.py",
+    "haplohub_cli/core/api/__init__.py",
+    "haplohub_cli/core/api/client.py",
+    "haplohub_cli/core/tests/test_checksum.py",
+    "haplohub_cli/core/tests/__init__.py",
+    "haplohub_cli/core/tests/test_slug.py",
+    "haplohub_cli/core/tests/test_network.py",
+    "haplohub_cli/auth/__init__.py",
+    "haplohub_cli/auth/token_storage.py",
+    "haplohub_cli/auth/auth.py",
+    "haplohub_cli/auth/oauth_client.py",
+    "haplohub_cli/auth/auth_web_server.py",
+    "haplohub_cli/auth/tests/test_token_storage.py",
+    "haplohub_cli/auth/tests/__init__.py",
+    "haplohub_cli/auth/tests/test_auth_web_server.py",
+    "haplohub_cli/config/__init__.py",
+    "haplohub_cli/config/config_manager.py",
+    "haplohub_cli/config/config.py",
+    "haplohub_cli/formatters/biomarker.py",
+    "haplohub_cli/formatters/__init__.py",
+    "haplohub_cli/formatters/algorithm.py",
+    "haplohub_cli/formatters/config.py",
+    "haplohub_cli/formatters/file.py",
+    "haplohub_cli/formatters/utils.py",
+    "haplohub_cli/formatters/member.py",
+    "haplohub_cli/formatters/cohort.py",
+    "haplohub_cli/formatters/decorators.py",
+    "haplohub_cli/formatters/formatter_registry.py",
+    "haplohub_cli/formatters/metadata.py",
+    "haplohub_cli/formatters/variant.py",
+    "haplohub_cli/formatters/algorithm_result.py",
+    "haplohub_cli/formatters/sample.py",
+    "haplohub_cli/formatters/generic.py",
+    "haplohub_cli/types/__init__.py",
+    "haplohub_cli/types/variant_range.py",
+    ".github/dependabot.yml",
+    ".github/workflows/on_pr.yml",
+    ".github/workflows/on_push_main.yml"
+  ]
+}

haplohub_cli-2.5.0/haplohub_cli.egg-info/scm_version.json

@@ -0,0 +1,8 @@
+{
+  "tag": "2.5.0",
+  "distance": 0,
+  "node": "gcd8a204d2e893b5eed8f318fb0e8fb3ed1a25d32",
+  "dirty": false,
+  "branch": "HEAD",
+  "node_date": "2026-07-14"
+}

haplohub_cli-2.3.0/haplohub_cli/auth/tests/test_token_storage.py

@@ -1,64 +0,0 @@
-import json
-
-from pyfakefs.fake_filesystem_unittest import TestCase
-
-from haplohub_cli.auth.token_storage import TokenStorage
-
-
-class TokenStorageTestCase(TestCase):
-    @classmethod
-    def setUpClass(cls):
-        cls.setUpClassPyfakefs()
-        cls.instance = TokenStorage("/tmp/test_token_storage.json")
-
-    def test_credentials_exist_should_return_false_when_file_does_not_exist(self):
-        self.assertFalse(self.instance.credentials_exist)
-
-    def test_credentials_exist_should_return_true_when_file_exists(self):
-        with open(self.instance.token_file, "w"):
-            pass
-
-        self.assertTrue(self.instance.credentials_exist)
-
-    def test_store_credentials_should_save_credentials_to_file(self):
-        creds = {"test": True}
-
-        self.instance.store_credentials(creds)
-
-        with open(self.instance.token_file, "r") as f:
-            self.assertEqual(json.load(f), creds)
-
-    def test_get_credentials_should_return_credentials_from_file(self):
-        creds = {"test": True}
-
-        self.instance.store_credentials(creds)
-
-        self.assertEqual(self.instance.get_credentials(), creds)
-
-    def test_get_access_token_should_return_access_token_from_credentials(self):
-        creds = {"access_token": "123456"}
-
-        self.instance.store_credentials(creds)
-
-        self.assertEqual(self.instance.get_access_token(), "123456")
-
-    def test_get_api_key_should_return_api_key_from_credentials(self):
-        creds = {"api_key": "ak_789"}
-
-        self.instance.store_credentials(creds)
-
-        self.assertEqual(self.instance.get_api_key(), "ak_789")
-
-    def test_has_api_key_should_return_true_when_api_key_exists(self):
-        creds = {"api_key": "ak_789"}
-
-        self.instance.store_credentials(creds)
-
-        self.assertTrue(self.instance.has_api_key)
-
-    def test_has_api_key_should_return_false_when_access_token_credentials(self):
-        creds = {"access_token": "123456"}
-
-        self.instance.store_credentials(creds)
-
-        self.assertFalse(self.instance.has_api_key)

haplohub_cli-2.3.0/haplohub_cli/auth/token_storage.py

@@ -1,37 +0,0 @@
-import json
-from genericpath import exists
-
-from haplohub_cli import settings
-
-
-class TokenStorage:
-    def __init__(self, token_file: str):
-        self.token_file = token_file
-
-    @property
-    def credentials_exist(self):
-        return exists(self.token_file)
-
-    def store_credentials(self, credentials: dict):
-        with open(self.token_file, "w") as f:
-            json.dump(credentials, f)
-
-    def get_credentials(self):
-        with open(self.token_file, "r") as f:
-            return json.load(f)
-
-    def get_access_token(self):
-        return self.get_credentials()["access_token"]
-
-    def get_api_key(self):
-        return self.get_credentials()["api_key"]
-
-    def get_refresh_token(self):
-        return self.get_credentials().get("refresh_token")
-
-    @property
-    def has_api_key(self):
-        return self.credentials_exist and "api_key" in self.get_credentials()
-
-
-token_storage = TokenStorage(settings.CREDENTIALS_FILE)

haplohub_cli-2.3.0/haplohub_cli/commands/variant.py

@@ -1,66 +0,0 @@
-import click
-from haplohub import GetVariantRequest, HgvsTargetSchema, RegionTargetSchema, TargetsInner, VariantFilterSchema
-
-from haplohub_cli.core.api.client import client
-
-
-@click.group()
-def variant():
-    """
-    Work with variants
-    """
-    pass
-
-
-@variant.command()
-@click.argument("cohort_id", type=str)
-@click.option("--sample", "-s", "sample_ids", type=str, multiple=True, required=True, help="Sample ID (repeatable)")
-@click.option("--accession", "-a", type=str, required=True, help="Chromosome accession (e.g. NC_000001.11)")
-@click.option("--start", type=int, required=True, help="Genomic start position")
-@click.option("--end", type=int, required=True, help="Genomic end position")
-@click.option("--reference", type=str, default=None, help="Reference allele")
-@click.option("--alternate", type=str, default=None, help="Alternate allele")
-@click.option("--call-state", type=click.Choice(["called", "all"]), default="called", help="Filter by call state")
-@click.option("--clinvar", is_flag=True, default=False, help="Include ClinVar annotations")
-def region(sample_ids, cohort_id, accession, start, end, reference, alternate, call_state, clinvar):
-    """
-    Query variants by genomic region
-    """
-    target = RegionTargetSchema(
-        accession=accession,
-        start=start,
-        end=end,
-        reference=reference,
-        alternate=alternate,
-    )
-
-    request = GetVariantRequest(
-        sample_ids=list(sample_ids),
-        targets=[TargetsInner(target)],
-        filters=VariantFilterSchema(call_state=call_state),
-        selectors=["clinvar"] if clinvar else None,
-    )
-
-    return client.variant.get_variant(cohort_id, request)
-
-
-@variant.command()
-@click.argument("cohort_id", type=str)
-@click.option("--sample", "-s", "sample_ids", type=str, multiple=True, required=True, help="Sample ID (repeatable)")
-@click.option("--hgvs", "-h", type=str, multiple=True, required=True, help="HGVS notation (repeatable)")
-@click.option("--call-state", type=click.Choice(["called", "all"]), default="called", help="Filter by call state")
-@click.option("--clinvar", is_flag=True, default=False, help="Include ClinVar annotations")
-def hgvs(sample_ids, cohort_id, hgvs, call_state, clinvar):
-    """
-    Query variants by HGVS notation
-    """
-    targets = [TargetsInner(HgvsTargetSchema(value=v)) for v in hgvs]
-
-    request = GetVariantRequest(
-        sample_ids=list(sample_ids),
-        targets=targets,
-        filters=VariantFilterSchema(call_state=call_state),
-        selectors=["clinvar"] if clinvar else None,
-    )
-
-    return client.variant.get_variant(cohort_id, request)