Merge pull request #44 from ccb-hms/development

Fixes bugs with adding tags

.github/workflows/python-app.yml

@@ -23,11 +23,20 @@ jobs:
       uses: actions/setup-python@v3
       with:
         python-version: "3.10"
+    - name: show python path
+      run: |
+        python -c "import sys; print('\n'.join(sys.path))"
+        PYTHONPATH
     - name: Install dependencies
       run: |
         python -m pip install --upgrade pip
-        pip install flake8 pytest
         pip install -r requirements.txt
+        pip install flake8 pytest
+    - name: Check package location
+      run: |
+        pip show pandas
+    - name: Install text2term
+      run: |
         pip install -e .
     - name: Lint with flake8
       run: |

text2term/config.py

@@ -1 +1 @@
-VERSION = "4.1.0"
+VERSION = "4.1.1"

text2term/preprocess.py

@@ -111,7 +111,7 @@ def _blocklist_term(processed_terms, term, blocklist, blocklist_char, tagged=Fal
 	return False
 
 
-def _update_tagged_term(processed_terms, term, new_term, tags=()):
+def _update_tagged_term(processed_terms, term, new_term, tags=[]):
 	term.update_term(new_term)
 	term.add_tags(tags)
 	processed_terms.append(term)

text2term/t2t.py

@@ -180,8 +180,9 @@ def _load_ontology(ontology, iris, exclude_deprecated, use_cache=False, term_typ
     if use_cache:
         pickle_file = os.path.join("cache", ontology, ontology + "-term-details.pickle")
         LOGGER.info(f"Loading cached ontology from: {pickle_file}")
-        onto_terms_unfiltered = pickle.load(open(pickle_file, "rb"))
-        onto_terms = filter_terms(onto_terms_unfiltered, iris, exclude_deprecated, term_type)
+        with open(pickle_file, "rb") as cached_ontology_pickle:
+            onto_terms_unfiltered = pickle.load(cached_ontology_pickle)
+            onto_terms = filter_terms(onto_terms_unfiltered, iris, exclude_deprecated, term_type)
     else:
         term_collector = OntologyTermCollector(ontology_iri=ontology)
         onto_terms = term_collector.get_ontology_terms(base_iris=iris, exclude_deprecated=exclude_deprecated,

text2term/tagged_term.py

@@ -12,7 +12,7 @@ def __repr__(self):
 		return f"<TaggedTerm term:{self.term} tags:{self.tags} original_term:{self.original_term}"
 
 	def add_tags(self, new_tags):
-		self.tags = list(self.tags) + new_tags
+		self.tags = list(self.tags) + list(new_tags)
 
 	def update_term(self, term):
 		self.term = term