add abstract base class for scoring methods (#247)

* change staticmethod to classmethod for `setup` method

* change `ScoringMethod` to abstract base class and rename it

* update the use of the new `ScoringBase` class

src/nplinker/nplinker.py

@@ -15,9 +15,9 @@
 from .metabolomics import MolecularFamily
 from .metabolomics import Spectrum
 from .pickler import save_pickled_data
+from .scoring.abc import ScoringBase
 from .scoring.link_collection import LinkCollection
 from .scoring.metcalf_scoring import MetcalfScoring
-from .scoring.methods import ScoringMethod
 from .scoring.np_class_scoring import NPClassScoring
 from .scoring.rosetta_scoring import RosettaScoring
 
@@ -37,9 +37,9 @@ class NPLinker:
     # default set of enabled scoring methods
     # TODO: ideally these shouldn't be hardcoded like this
     SCORING_METHODS = {
-        MetcalfScoring.NAME: MetcalfScoring,
-        RosettaScoring.NAME: RosettaScoring,
-        NPClassScoring.NAME: NPClassScoring,
+        MetcalfScoring.name: MetcalfScoring,
+        RosettaScoring.name: RosettaScoring,
+        NPClassScoring.name: NPClassScoring,
     }
 
     def __init__(self, config_file: str | PathLike):
@@ -266,7 +266,7 @@ def get_links(
 
         if not self._datalinks:
             logger.debug("Creating internal datalinks object")
-            self._datalinks = self.scoring_method(MetcalfScoring.NAME).datalinks
+            self._datalinks = self.scoring_method(MetcalfScoring.name).datalinks
             logger.debug("Created internal datalinks object")
 
         if len(link_collection) == 0:
@@ -318,7 +318,7 @@ def get_common_strains(
             and values are a list of shared Strain objects.
         """
         if not self._datalinks:
-            self._datalinks = self.scoring_method(MetcalfScoring.NAME).datalinks
+            self._datalinks = self.scoring_method(MetcalfScoring.name).datalinks
         common_strains = self._datalinks.get_common_strains(met, gcfs, filter_no_shared)
         return common_strains
 
@@ -401,7 +401,7 @@ def class_matches(self):
         """ClassMatches with the matched classes and scoring tables from MIBiG."""
         return self._class_matches
 
-    def scoring_method(self, name: str) -> ScoringMethod | None:
+    def scoring_method(self, name: str) -> ScoringBase | None:
         """Return an instance of a scoring method.
 
         Args:

src/nplinker/scoring/__init__.py

@@ -1,7 +1,7 @@
+from .abc import ScoringBase
 from .link_collection import LinkCollection
 from .metcalf_scoring import MetcalfScoring
-from .methods import ScoringMethod
 from .object_link import ObjectLink
 
 
-__all__ = ["LinkCollection", "MetcalfScoring", "ScoringMethod", "ObjectLink"]
+__all__ = ["LinkCollection", "MetcalfScoring", "ScoringBase", "ObjectLink"]

src/nplinker/scoring/abc.py

@@ -0,0 +1,56 @@
+from __future__ import annotations
+import logging
+from abc import ABC
+from abc import abstractmethod
+from typing import TYPE_CHECKING
+
+
+if TYPE_CHECKING:
+    from nplinker import NPLinker
+    from . import LinkCollection
+
+logger = logging.getLogger(__name__)
+
+
+class ScoringBase(ABC):
+    """Abstract base class of scoring methods.
+
+    Attributes:
+        name: The name of the scoring method.
+        npl: The NPLinker object.
+    """
+
+    name: str = "ScoringBase"
+
+    def __init__(self, npl: NPLinker):
+        """Initialize the scoring method.
+
+        Args:
+            npl: The NPLinker object.
+        """
+        self.npl = npl
+
+    @classmethod
+    @abstractmethod
+    def setup(cls, npl: NPLinker):
+        """Setup class level attributes."""
+
+    @abstractmethod
+    def get_links(self, *objects, link_collection: LinkCollection) -> LinkCollection:
+        """Get links information for the given objects.
+
+        Args:
+            objects: A set of objects.
+            link_collection: The LinkCollection object.
+
+        Returns:
+            The LinkCollection object.
+        """
+
+    @abstractmethod
+    def format_data(self, data) -> str:
+        """Format the scoring data to a string."""
+
+    @abstractmethod
+    def sort(self, objects, reverse=True) -> list:
+        """Sort the given objects based on the scoring data."""

src/nplinker/scoring/metcalf_scoring.py

@@ -9,11 +9,11 @@
 from nplinker.metabolomics import Spectrum
 from nplinker.pickler import load_pickled_data
 from nplinker.pickler import save_pickled_data
+from .abc import ScoringBase
 from .linking import LINK_TYPES
 from .linking import DataLinks
 from .linking import LinkFinder
 from .linking import isinstance_all
-from .methods import ScoringMethod
 from .object_link import ObjectLink
 
 
@@ -24,19 +24,19 @@
 logger = logging.getLogger(__name__)
 
 
-class MetcalfScoring(ScoringMethod):
+class MetcalfScoring(ScoringBase):
     """Metcalf scoring method.
 
     Attributes:
+        name: The name of this scoring method, set to a fixed value `metcalf`.
         DATALINKS: The DataLinks object to use for scoring.
         LINKFINDER: The LinkFinder object to use for scoring.
-        NAME: The name of the scoring method. This is set to 'metcalf'.
         CACHE: The name of the cache file to use for storing the MetcalfScoring.
     """
 
+    name = "metcalf"
     DATALINKS = None
     LINKFINDER = None
-    NAME = "metcalf"
     CACHE = "cache_metcalf_scoring.pckl"
 
     def __init__(self, npl: NPLinker) -> None:
@@ -57,21 +57,20 @@ def __init__(self, npl: NPLinker) -> None:
         self.cutoff = 1.0
         self.standardised = True
 
-    # TODO CG: not sure why using staticmethod here. Check later and refactor if possible
     # TODO CG: refactor this method and extract code for cache file to a separate method
-    @staticmethod
-    def setup(npl: NPLinker):
-        """Setup the MetcalfScoring object.
+    @classmethod
+    def setup(cls, npl: NPLinker):
+        """Setup the DataLinks and LinkFinder objects.
 
-        DataLinks and LinkFinder objects are created and cached for later use.
+        This method is only called once to setup the DataLinks and LinkFinder objects.
         """
         logger.info(
             "MetcalfScoring.setup (bgcs={}, gcfs={}, spectra={}, molfams={}, strains={})".format(
                 len(npl.bgcs), len(npl.gcfs), len(npl.spectra), len(npl.molfams), len(npl.strains)
             )
         )
 
-        cache_file = npl.output_dir / MetcalfScoring.CACHE
+        cache_file = npl.output_dir / cls.CACHE
 
         # the metcalf preprocessing can take a long time for large datasets, so it's
         # better to cache as the data won't change unless the number of objects does
@@ -97,27 +96,25 @@ def setup(npl: NPLinker):
                         break
 
             if cache_ok:
-                MetcalfScoring.DATALINKS = datalinks
-                MetcalfScoring.LINKFINDER = linkfinder
+                cls.DATALINKS = datalinks
+                cls.LINKFINDER = linkfinder
 
-        if MetcalfScoring.DATALINKS is None:
+        if cls.DATALINKS is None:
             logger.info("MetcalfScoring.setup preprocessing dataset (this may take some time)")
-            MetcalfScoring.DATALINKS = DataLinks(npl.gcfs, npl.spectra, npl.molfams, npl.strains)
-            MetcalfScoring.LINKFINDER = LinkFinder()
-            MetcalfScoring.LINKFINDER.calc_score(MetcalfScoring.DATALINKS, link_type=LINK_TYPES[0])
-            MetcalfScoring.LINKFINDER.calc_score(MetcalfScoring.DATALINKS, link_type=LINK_TYPES[1])
+            cls.DATALINKS = DataLinks(npl.gcfs, npl.spectra, npl.molfams, npl.strains)
+            cls.LINKFINDER = LinkFinder()
+            cls.LINKFINDER.calc_score(MetcalfScoring.DATALINKS, link_type=LINK_TYPES[0])
+            cls.LINKFINDER.calc_score(MetcalfScoring.DATALINKS, link_type=LINK_TYPES[1])
             logger.info("MetcalfScoring.setup caching results")
-            save_pickled_data(
-                (dataset_counts, MetcalfScoring.DATALINKS, MetcalfScoring.LINKFINDER), cache_file
-            )
+            save_pickled_data((dataset_counts, cls.DATALINKS, cls.LINKFINDER), cache_file)
 
         logger.info("MetcalfScoring.setup completed")
 
     # TODO CG: is it needed? remove it if not
     @property
     def datalinks(self) -> DataLinks | None:
         """Get the DataLinks object used for scoring."""
-        return MetcalfScoring.DATALINKS
+        return self.DATALINKS
 
     def get_links(
         self, *objects: GCF | Spectrum | MolecularFamily, link_collection: LinkCollection

src/nplinker/scoring/np_class_scoring.py

@@ -3,16 +3,16 @@
 from nplinker.genomics import BGC
 from nplinker.genomics import GCF
 from nplinker.metabolomics import Spectrum
+from nplinker.scoring.abc import ScoringBase
 from nplinker.scoring.metcalf_scoring import MetcalfScoring
-from nplinker.scoring.methods import ScoringMethod
 from nplinker.scoring.object_link import ObjectLink
 
 
 logger = logging.getLogger(__name__)
 
 
-class NPClassScoring(ScoringMethod):
-    NAME = "npclassscore"
+class NPClassScoring(ScoringBase):
+    name = "npclassscore"
 
     def __init__(self, npl):
         super().__init__(npl)
@@ -313,8 +313,8 @@ def _get_met_classes(self, spec_like, method="mix"):
             )
         return spec_like_classes, spec_like_classes_names_inds
 
-    @staticmethod
-    def setup(npl):
+    @classmethod
+    def setup(cls, npl):
         """Perform any one-off initialisation required (will only be called once)."""
         logger.info("Set up NPClassScore scoring")
         met_options = npl.chem_classes.class_predict_options
@@ -347,7 +347,7 @@ def get_links(self, objects, link_collection):
         logger.info("Using Metcalf scoring to get shared strains")
         # get mapping of shared strains
         if not self.npl._datalinks:
-            self.npl._datalinks = self.npl.scoring_method(MetcalfScoring.NAME).datalinks
+            self.npl._datalinks = self.npl.scoring_method(MetcalfScoring.name).datalinks
         if obj_is_gen:
             common_strains = self.npl.get_common_strains(targets, objects)
         else:

src/nplinker/scoring/rosetta_scoring.py

@@ -3,16 +3,16 @@
 from nplinker.genomics.bgc import BGC
 from nplinker.genomics.gcf import GCF
 from nplinker.metabolomics import MolecularFamily
-from nplinker.scoring.methods import ScoringMethod
+from nplinker.scoring.abc import ScoringBase
 from nplinker.scoring.object_link import ObjectLink
 from nplinker.scoring.rosetta.rosetta import Rosetta
 
 
 logger = logging.getLogger(__name__)
 
 
-class RosettaScoring(ScoringMethod):
-    NAME = "rosetta"
+class RosettaScoring(ScoringBase):
+    name = "rosetta"
     ROSETTA_OBJ = None
 
     def __init__(self, npl):
@@ -22,10 +22,14 @@ def __init__(self, npl):
         self.spec_score_cutoff = 0.0
         self.bgc_score_cutoff = 0.0
 
-    @staticmethod
-    def setup(npl):
+    @classmethod
+    def setup(cls, npl):
+        """Setup the Rosetta object and run the scoring algorithm.
+
+        This method is only called once to setup the Rosetta object.
+        """
         logger.info("RosettaScoring setup")
-        RosettaScoring.ROSETTA_OBJ = Rosetta(npl, ignore_genomic_cache=False)
+        cls.ROSETTA_OBJ = Rosetta(npl, ignore_genomic_cache=False)
         ms1_tol = Rosetta.DEF_MS1_TOL
         ms2_tol = Rosetta.DEF_MS2_TOL
         score_thresh = Rosetta.DEF_SCORE_THRESH
@@ -35,9 +39,7 @@ def setup(npl):
             npl.config
         )
 
-        RosettaScoring.ROSETTA_OBJ.run(
-            npl.spectra, npl.bgcs, ms1_tol, ms2_tol, score_thresh, min_match_peaks
-        )
+        cls.ROSETTA_OBJ.run(npl.spectra, npl.bgcs, ms1_tol, ms2_tol, score_thresh, min_match_peaks)
         logger.info("RosettaScoring setup completed")
 
     @staticmethod