From 256692ade996b3b78f61579dd223a085826dd8f5 Mon Sep 17 00:00:00 2001
From: Cunliang Geng <c.geng@esciencecenter.nl>
Date: Tue, 12 Dec 2023 15:24:36 +0100
Subject: [PATCH] remove loading of description text and the method
 `_load_optional`

To keep the loading process simple, the loading of description text is removed. A specific loader could be added in the future if these info is necessary in NPLinker.

Note that the method `_load_optional` is then totally removed.
---
 src/nplinker/loader.py   | 12 ------------
 src/nplinker/nplinker.py | 12 ------------
 2 files changed, 24 deletions(-)

diff --git a/src/nplinker/loader.py b/src/nplinker/loader.py
index 074b1c0d..b73f450f 100644
--- a/src/nplinker/loader.py
+++ b/src/nplinker/loader.py
@@ -76,7 +76,6 @@ class DatasetLoader:
     OR_MIBIG_JSON = "mibig_json_dir"
     OR_STRAINS = "strain_mappings_file"
     # misc files
-    OR_DESCRIPTION = "description_file"
     OR_INCLUDE_STRAINS = "include_strains_file"
     # class predictions
     OR_CANOPUS = "canopus_dir"
@@ -197,8 +196,6 @@ def load(self):
         if not self._load_genomics():
             return False
 
-        self._load_optional()
-
         # Restrict strain list to only relevant strains (those that are present
         # in both genomic and metabolomic data)
         # TODO add a config file option for this?
@@ -239,9 +236,6 @@ def _init_paths(self):
 
         self._init_genomics_paths()
 
-        # 13. MISC: <root>/description.txt
-        self.description_file = os.path.join(self._root, "description.txt")
-
         # 14. MISC: <root>/include_strains.csv / include_strains_file=<override>
         self.include_strains_file = self._config_overrides.get(
             self.OR_INCLUDE_STRAINS
@@ -570,12 +564,6 @@ def _load_class_info(self):
         self.chem_classes = chem_classes
         return True
 
-    def _load_optional(self):
-        self.description_text = "<no description>"
-        if os.path.exists(self.description_file):
-            self.description_text = open(self.description_file).read()
-            logger.debug("Parsed description text")
-
     def _filter_only_common_strains(self):
         """Filter strain population to only strains present in both genomic and molecular data."""
         # TODO: Maybe there should be an option to specify which strains are used, both so we can
diff --git a/src/nplinker/nplinker.py b/src/nplinker/nplinker.py
index 07f84998..3da4c5fc 100644
--- a/src/nplinker/nplinker.py
+++ b/src/nplinker/nplinker.py
@@ -214,18 +214,6 @@ def data_dir(self):
         """Returns path to nplinker/data directory (files packaged with the app itself)."""
         return NPLINKER_APP_DATA_DIR
 
-    @property
-    def dataset_description(self):
-        """Returns dataset description.
-
-        If nplinker finds a 'description.txt' file in the root directory of the
-        dataset, the content will be parsed and made available through this property.
-
-        Returns:
-            str: the content of description.txt or '<no description>'
-        """
-        return self._loader.description_text
-
     @property
     def bigscape_cutoff(self):
         """Returns the current BiGSCAPE clustering cutoff value."""