fix onlist auth and build parity

Author: sbooeshaghi

seqspec/auth.py

@@ -1,11 +1,10 @@
 import json
 import os
+import tomllib
 from pathlib import Path
 from typing import Dict, List, Optional, Tuple
 from urllib.parse import urlparse
 
-import tomllib
-
 AUTH_CONFIG_ENV = "SEQSPEC_AUTH_CONFIG"
 
 

seqspec/seqspec_check.py

@@ -3,8 +3,8 @@
 This module provides functionality to validate seqspec files against the specification schema.
 """
 
-from argparse import ArgumentParser, Namespace, RawTextHelpFormatter
 import os
+from argparse import ArgumentParser, Namespace, RawTextHelpFormatter
 from os import path
 from pathlib import Path
 from typing import Dict, List, Optional

seqspec/seqspec_onlist.py

@@ -125,11 +125,22 @@ def run_onlist(parser: ArgumentParser, args: Namespace) -> None:
     if args.format:
         # Join operation - requires download and output path
         save_path = args.output or Path(args.yaml).resolve().parent
-        result_path = join_onlists_and_save(onlists, args.format, save_path, base_path)
+        result_path = join_onlists_and_save(
+            onlists,
+            args.format,
+            save_path,
+            base_path,
+            auth_profile=args.auth_profile,
+        )
         print(result_path)
     elif args.output:
         # Download operation - download remote files to output location
-        result_paths = download_onlists_to_path(onlists, args.output, base_path)
+        result_paths = download_onlists_to_path(
+            onlists,
+            args.output,
+            base_path,
+            auth_profile=args.auth_profile,
+        )
         for path_info in result_paths:
             print(f"{path_info['url']}")
     else:
@@ -210,7 +221,10 @@ def get_onlist_urls(onlists: List[Onlist], base_path: Path) -> List[Dict[str, st
 
 
 def download_onlists_to_path(
-    onlists: List[Onlist], output_path: Path, base_path: Path
+    onlists: List[Onlist],
+    output_path: Path,
+    base_path: Path,
+    auth_profile: str | None = None,
 ) -> List[Dict[str, str]]:
     """Download remote onlists and return local paths."""
     downloaded_paths = []
@@ -222,7 +236,7 @@ def download_onlists_to_path(
             downloaded_paths.append({"file_id": onlist.file_id, "url": str(local_path)})
         else:
             # Remote file - download it
-            onlist_elements = read_remote_list(onlist, auth_profile=args.auth_profile)
+            onlist_elements = read_remote_list(onlist, auth_profile=auth_profile)
             # Create unique filename for this onlist
             filename = f"{onlist.file_id}_{output_path.name}"
             download_path = output_path.parent / filename
@@ -235,7 +249,11 @@ def download_onlists_to_path(
 
 
 def join_onlists_and_save(
-    onlists: List[Onlist], format_type: str, output_path: Path, base_path: Path
+    onlists: List[Onlist],
+    format_type: str,
+    output_path: Path,
+    base_path: Path,
+    auth_profile: str | None = None,
 ) -> str:
     """Download onlists, join them, and save to output path."""
     # Download all onlists first
@@ -244,7 +262,7 @@ def join_onlists_and_save(
         if onlist.urltype == "local":
             content = read_local_list(onlist, str(base_path))
         else:
-            content = read_remote_list(onlist, auth_profile=args.auth_profile)
+            content = read_remote_list(onlist, auth_profile=auth_profile)
         onlist_contents.append(content)
 
     # Join the onlists

src/main.rs

@@ -23,16 +23,23 @@ use seqspec::utils;
 
 use clap::{Parser, Subcommand};
 
+const BUILD_DEPRECATED_MESSAGE: &str =
+    "seqspec build is deprecated. Use seqspec init/insert/modify or construct the spec directly.";
+
 #[derive(Parser, Debug)]
 #[command(name = "seqspec", version)]
 struct Args {
     #[command(subcommand)]
     subcmd: Commands,
 }
 
+#[derive(clap::Args, Debug)]
+struct BuildArgs {}
+
 #[derive(Subcommand, Debug)]
 enum Commands {
     Auth(seqspec_auth::AuthArgs),
+    Build(BuildArgs),
     Version(seqspec_version::VersionArgs),
     Format(seqspec_format::FormatArgs),
     Find(seqspec_find::FindArgs),
@@ -55,6 +62,7 @@ fn main() {
     let args = Args::parse();
     match args.subcmd {
         Commands::Auth(args) => seqspec_auth::run(&args).unwrap(),
+        Commands::Build(_) => run_build_deprecated(),
         Commands::Version(args) => seqspec_version::run_version(&args),
         Commands::Format(args) => seqspec_format::run_format(&args),
         Commands::Find(args) => seqspec_find::run_find(&args),
@@ -74,3 +82,27 @@ fn main() {
         Commands::Print(args) => seqspec_print::run_print(&args),
     }
 }
+
+fn run_build_deprecated() {
+    eprintln!("{}", BUILD_DEPRECATED_MESSAGE);
+    std::process::exit(1);
+}
+
+#[cfg(test)]
+mod tests {
+    use super::*;
+
+    #[test]
+    fn test_build_subcommand_is_recognized() {
+        let args = Args::try_parse_from(["seqspec", "build"]).unwrap();
+        assert!(matches!(args.subcmd, Commands::Build(_)));
+    }
+
+    #[test]
+    fn test_build_deprecated_message_matches_python_cli() {
+        assert_eq!(
+            BUILD_DEPRECATED_MESSAGE,
+            "seqspec build is deprecated. Use seqspec init/insert/modify or construct the spec directly."
+        );
+    }
+}

tests/test_seqspec_onlist.py

@@ -1,16 +1,18 @@
-import pytest
 import os
+from argparse import ArgumentParser, Namespace
 from pathlib import Path
 from unittest.mock import patch
+
+import pytest
+
 from seqspec.seqspec_onlist import (
+    Onlist,
+    download_onlists_to_path,
     get_onlists,
     join_onlist_contents,
+    join_onlists_and_save,
     run_onlist,
 )
-from seqspec.utils import load_spec
-from argparse import Namespace, ArgumentParser
-from seqspec.seqspec_onlist import Onlist
-
 
 
 def test_get_onlists_region(dogmaseq_dig_spec):
@@ -19,27 +21,111 @@ def test_get_onlists_region(dogmaseq_dig_spec):
     assert len(onlists) == 1
     assert onlists[0].file_id == "RNA-737K-arc-v1.txt"
 
+
 def test_get_onlists_region_type(dogmaseq_dig_spec):
     """Test get_onlists with region-type selector"""
     onlists = get_onlists(dogmaseq_dig_spec, "rna", "region-type", "barcode")
     assert len(onlists) > 0
     for onlist in onlists:
         assert onlist is not None
 
+
 def test_get_onlists_read(dogmaseq_dig_spec):
     """Test get_onlists with read selector"""
     onlists = get_onlists(dogmaseq_dig_spec, "rna", "read", "rna_R1")
     assert len(onlists) == 1
 
+
 def test_join_onlist_contents_product():
     """Test joining onlists with product format"""
     contents = [["A", "B"], ["1", "2"]]
     joined = join_onlist_contents(contents, "product")
     assert set(joined) == {"A1", "A2", "B1", "B2"}
 
+
 def test_join_onlist_contents_multi():
     """Test joining onlists with multi format"""
     contents = [["A", "B"], ["1", "2", "3"]]
     joined = join_onlist_contents(contents, "multi")
     assert joined == ["A 1", "B 2", "- 3"]
 
+
+def remote_onlist() -> Onlist:
+    return Onlist(
+        file_id="remote_list",
+        filename="remote.txt.gz",
+        filetype="txt.gz",
+        filesize=123,
+        url="https://example.org/remote.txt.gz",
+        urltype="https",
+        md5="abc",
+    )
+
+
+def test_download_onlists_to_path_threads_auth_profile(tmp_path):
+    calls = []
+
+    def fake_read_remote_list(onlist, base_path="", auth_profile=None):
+        calls.append(
+            {
+                "file_id": onlist.file_id,
+                "base_path": base_path,
+                "auth_profile": auth_profile,
+            }
+        )
+        return ["AAA", "CCC"]
+
+    output_path = tmp_path / "joined.txt"
+    with patch("seqspec.seqspec_onlist.read_remote_list", side_effect=fake_read_remote_list):
+        downloaded = download_onlists_to_path(
+            [remote_onlist()],
+            output_path,
+            tmp_path,
+            auth_profile="igvf",
+        )
+
+    assert calls == [
+        {
+            "file_id": "remote_list",
+            "base_path": "",
+            "auth_profile": "igvf",
+        }
+    ]
+    assert len(downloaded) == 1
+    assert downloaded[0]["file_id"] == "remote_list"
+    assert downloaded[0]["url"].endswith("remote_list_joined.txt")
+    assert Path(downloaded[0]["url"]).read_text().splitlines() == ["AAA", "CCC"]
+
+
+def test_join_onlists_and_save_threads_auth_profile(tmp_path):
+    calls = []
+
+    def fake_read_remote_list(onlist, base_path="", auth_profile=None):
+        calls.append(
+            {
+                "file_id": onlist.file_id,
+                "base_path": base_path,
+                "auth_profile": auth_profile,
+            }
+        )
+        return ["AAA", "CCC"]
+
+    output_path = tmp_path / "product.txt"
+    with patch("seqspec.seqspec_onlist.read_remote_list", side_effect=fake_read_remote_list):
+        result_path = join_onlists_and_save(
+            [remote_onlist()],
+            "product",
+            output_path,
+            tmp_path,
+            auth_profile="igvf",
+        )
+
+    assert calls == [
+        {
+            "file_id": "remote_list",
+            "base_path": "",
+            "auth_profile": "igvf",
+        }
+    ]
+    assert result_path == str(output_path)
+    assert output_path.read_text().splitlines() == ["AAA", "CCC"]