update gnpsformat detection function to support gnps2 (#293)

Update function `gnps_format_from_archive` to support gnps2 data.

pyproject.toml

@@ -37,6 +37,7 @@ dependencies = [
     "networkx",
     "pandas",
     "pyteomics",
+    "pyyaml",
     "rich",
     "scipy",
     "sortedcontainers",

src/nplinker/metabolomics/gnps/gnps_format.py

@@ -1,11 +1,13 @@
 from __future__ import annotations
 import re
+import tarfile
 import zipfile
 from enum import Enum
 from enum import unique
 from os import PathLike
 from pathlib import Path
 import httpx
+import yaml
 from bs4 import BeautifulSoup
 
 
@@ -72,17 +74,22 @@ def gnps_format_from_gnps1_task_id(task_id: str) -> GNPSFormat:
     return GNPSFormat.Unknown
 
 
-def gnps_format_from_archive(zip_file: str | PathLike) -> GNPSFormat:
-    """Detect GNPS format from GNPS zip archive.
+def gnps_format_from_archive(file: str | PathLike) -> GNPSFormat:
+    """Detect GNPS format or workflow from GNPS archive file.
 
-    The detection is based on the filename of the zip file and the names of the
-    files contained in the zip file.
+    GNPS archive files can be in two formats: GNPS1 (.zip) and GNPS2 (.tar).
+
+    For GNPS1 data, the detection of workflow format is based on the filename of the zip archive and
+    the names of the files contained in the zip archive.
+
+    For GNPS2 data, the workflow format is taken from the `submission_parameters.yaml` file in the
+    tar archive, which has a key `workflowname`.
 
     Args:
-        zip_file: Path to the GNPS zip file.
+        file: Path to the GNPS archive file.
 
     Returns:
-        The format identified in the GNPS zip file.
+        The format identified in the GNPS archive file.
 
     Examples:
         >>> gnps_format_from_archive("ProteoSAFe-METABOLOMICS-SNETS-c22f44b1-download_clustered_spectra.zip")
@@ -91,8 +98,22 @@ def gnps_format_from_archive(zip_file: str | PathLike) -> GNPSFormat:
         <GNPSFormat.SNETSV2: 'METABOLOMICS-SNETS-V2'>
         >>> gnps_format_from_archive("ProteoSAFe-FEATURE-BASED-MOLECULAR-NETWORKING-672d0a53-download_cytoscape_data.zip")
         <GNPSFormat.FBMN: 'FEATURE-BASED-MOLECULAR-NETWORKING'>
+        >>> gnps_format_from_archive("206a7b40b7ed41c1ae6b4fbd2def3636.tar")
+        <GNPSFormat.GNPS2CN: 'classical_networking_workflow'>
+        >>> gnps_format_from_archive("2014f321d72542afb5216c932e0d5079.tar")
+        <GNPSFormat.GNPS2FBMN: 'feature_based_molecular_networking_workflow'>
     """
-    file = Path(zip_file)
+    file = Path(file)
+    suffix = file.suffix
+    if suffix == ".zip":
+        return _gnps_format_from_archive_gnps1(file)
+    if suffix == ".tar":
+        return _gnps_format_from_archive_gnps2(file)
+    return GNPSFormat.Unknown
+
+
+def _gnps_format_from_archive_gnps1(file: PathLike) -> GNPSFormat:
+    """Detect GNPS format from GNPS1 archive file."""
     # Guess the format from the filename of the zip file
     if GNPSFormat.FBMN.value in file.name:
         return GNPSFormat.FBMN
@@ -116,6 +137,26 @@ def gnps_format_from_archive(zip_file: str | PathLike) -> GNPSFormat:
     return GNPSFormat.Unknown
 
 
+def _gnps_format_from_archive_gnps2(file: PathLike) -> GNPSFormat:
+    """Detect GNPS format from GNPS2 archive file."""
+    with tarfile.open(file, "r") as tar:
+        try:
+            submission_file = tar.extractfile("submission_parameters.yaml")
+            if submission_file is None:
+                return GNPSFormat.Unknown
+            submission_params = yaml.safe_load(submission_file)
+        except (KeyError, yaml.YAMLError):
+            return GNPSFormat.Unknown
+
+    workflow = submission_params.get("workflowname")
+
+    if workflow == GNPSFormat.GNPS2FBMN.value:
+        return GNPSFormat.GNPS2FBMN
+    if workflow == GNPSFormat.GNPS2CN.value:
+        return GNPSFormat.GNPS2CN
+    return GNPSFormat.Unknown
+
+
 def gnps_format_from_file_mapping(file: str | PathLike) -> GNPSFormat:
     """Detect GNPS format from the given file mapping file.
 

tests/unit/metabolomics/conftest.py

@@ -6,6 +6,11 @@
 from .. import GNPS_DATA_DIR
 
 
+#
+# Fixtures for GNPS1
+#
+
+
 @pytest.fixture(scope="session")
 def gnps_website_is_down():
     """Check if the GNPS website is down."""
@@ -133,3 +138,26 @@ def gnps_annotations_files(tmp_gnps_dir) -> dict[GNPSFormat, PathLike]:
         / "DB_result"
         / "7dc5b46b50d94246a1de12ef485d0f75.tsv",
     }
+
+
+#
+# Fixtures for GNPS2
+#
+
+
+@pytest.fixture(scope="session")
+def gnps2_tar_files() -> dict[GNPSFormat, PathLike]:
+    """Get the paths of the GNPS2 tar archives as a dict.
+
+    The dict keys are the workflow short names taken from the GNPSFormat enum.
+    The dict values are the paths to the tar archives.
+
+    You can download the archives ("Download all results") from the following links :
+    - https://gnps2.org/status?task=2014f321d72542afb5216c932e0d5079
+    - https://gnps2.org/status?task=206a7b40b7ed41c1ae6b4fbd2def3636
+    """
+    return {
+        GNPSFormat.GNPS2CN: GNPS_DATA_DIR / "206a7b40b7ed41c1ae6b4fbd2def3636.tar",
+        GNPSFormat.GNPS2FBMN: GNPS_DATA_DIR / "2014f321d72542afb5216c932e0d5079.tar",
+        GNPSFormat.Unknown: GNPS_DATA_DIR / "gnps2_nnknown.tar",
+    }

tests/unit/metabolomics/test_gnps_format.py

@@ -5,6 +5,9 @@
 from nplinker.metabolomics.gnps import gnps_format_from_gnps1_task_id
 
 
+#
+# Test GNPS1 formats
+#
 @pytest.mark.parametrize(
     "task_id, expected",
     [
@@ -24,7 +27,7 @@ def test_gnps_format_from_gnps1_task_id(task_id: str, expected: GNPSFormat, gnps
 @pytest.mark.parametrize(
     "workflow", [GNPSFormat.FBMN, GNPSFormat.SNETS, GNPSFormat.SNETSV2, GNPSFormat.Unknown]
 )
-def test_gnps_format_from_archive(workflow: str, gnps_zip_files):
+def test_gnps_format_from_archive_gnps1(workflow: str, gnps_zip_files):
     actual = gnps_format_from_archive(gnps_zip_files[workflow])
     assert actual is workflow
 
@@ -33,3 +36,12 @@ def test_gnps_format_from_archive(workflow: str, gnps_zip_files):
 def test_gnps_format_from_file_mapping(workflow: str, gnps_file_mappings_files):
     actual = gnps_format_from_file_mapping(gnps_file_mappings_files[workflow])
     assert actual is workflow
+
+
+#
+# Test GNPS2 formats
+#
+@pytest.mark.parametrize("workflow", [GNPSFormat.GNPS2CN, GNPSFormat.GNPS2FBMN, GNPSFormat.Unknown])
+def test_gnps_format_from_archive_gnps2(workflow: str, gnps2_tar_files):
+    actual = gnps_format_from_archive(gnps2_tar_files[workflow])
+    assert actual is workflow