Merge pull request #32 from hkir-dev/tdt_sprint_3

Tdt sprint 3

Author: hkir-dev

.github/workflows/publish_to_pypi.yaml

@@ -33,9 +33,13 @@ jobs:
         setup.py
         sdist
         bdist_wheel
-    - name: Deploy Package
-      env:
-        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
-        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
-      run: |
-        twine upload dist/*
+#    - name: Deploy Package
+#      env:
+#        TWINE_USERNAME: ${{ secrets.PYPI_USERNAME }}
+#        TWINE_PASSWORD: ${{ secrets.PYPI_PASSWORD }}
+#      run: |
+#        twine upload dist/*
+    - name: Publish Package
+      uses: pypa/gh-action-pypi-publish@release/v1
+      with:
+        password: ${{ secrets.PYPI_API_TOKEN }}

requirements.txt

@@ -1,2 +1,2 @@
 requests
-cas-tools==0.0.1.dev11
+cas-tools==0.0.1.dev24

setup.py

@@ -8,7 +8,7 @@
 
 setup(
     name="tdta",
-    version="0.1.0.dev2",
+    version="0.1.0.dev3",
     description="The aim of this project is to provide taxonomy development tools custom actions.",
     long_description=README,
     long_description_content_type="text/markdown",

src/tdta/tdt_export.py

@@ -184,10 +184,14 @@ def auto_fill_object_from_row(obj, columns, row):
         if hasattr(obj, column):
             value = row[columns.index(column)]
             if value:
-                if value.strip().startswith("[") and value.strip().endswith("]"):
-                    value = value.strip()[1:-1].strip().split(",")
+                if isinstance(type(getattr(obj, column)), list):
+                    if value.strip().startswith("\"") and value.strip().endswith("\""):
+                        value = value.strip()[1:-1].strip()
+                    elif value.strip().startswith("'") and value.strip().endswith("'"):
+                        value = value.strip()[1:-1].strip()
+                    values = value.split("|")
                     list_value = []
-                    for item in value:
+                    for item in values:
                         if item.strip().startswith("\"") and item.strip().endswith("\""):
                             item = item.strip()[1:-1].strip()
                         elif item.strip().startswith("'") and item.strip().endswith("'"):

src/test/publish_purl_test.py

@@ -15,5 +15,5 @@ def setUp(self):
             if not os.path.isfile(os.path.join(purl_folder, item)):
                 shutil.rmtree(os.path.join(purl_folder, item))
 
-    def test_purl_publish(self):
-        publish_to_purl(TEST_DATA_FOLDER, "CCN20230001")
+    # def test_purl_publish(self):
+    #     publish_to_purl(TEST_DATA_FOLDER, "CCN20230001", "hkir-dev")

src/test/tdt_export_test.py

@@ -14,37 +14,40 @@ def setUp(self):
             os.remove(TEST_OUTPUT)
 
     def test_export(self):
-        cas = export_cas_data(TEST_DB, TEST_OUTPUT)
+        cas = export_cas_data(TEST_DB, TEST_OUTPUT, TEST_DATA_FOLDER)
         self.assertTrue(os.path.exists(TEST_OUTPUT))
 
         self.assertTrue(cas)
         result = cas.to_dict()
 
         self.assertTrue("author_name" in result)
-        self.assertEqual("Test User", result["author_name"])
-        self.assertFalse(result["orcid"])
-        self.assertFalse(result["cellannotation_schema_version"])
+        self.assertEqual("Nelson Johansen", result["author_name"])
+        self.assertFalse("orcid" in result)
+        self.assertFalse("cellannotation_schema_version" in result)
 
         self.assertTrue("labelsets" in result)
         self.assertEqual(4, len(result["labelsets"]))
-        test_labelset = [x for x in result["labelsets"] if x["name"] == "cluster"][0]
+        test_labelset = [x for x in result["labelsets"] if x["name"] == "Cluster"][0]
         self.assertEqual("0", test_labelset["rank"])
-        self.assertEqual(1, len([x for x in result["labelsets"] if x["name"] == "level 3 (subclass)"]))
-        test_labelset = [x for x in result["labelsets"] if x["name"] == "level 3 (subclass)"][0]
+        self.assertEqual(1, len([x for x in result["labelsets"] if x["name"] == "Subclass"]))
+        test_labelset = [x for x in result["labelsets"] if x["name"] == "Subclass"][0]
         self.assertEqual("1", test_labelset["rank"])
 
         self.assertTrue("annotations" in result)
-        self.assertEqual(354, len(result["annotations"]))
+        self.assertEqual(355, len(result["annotations"]))
         # print(result["annotations"][:3])
         test_annotation = [x for x in result["annotations"] if x["cell_label"] == "1_MSN"][0]
-        self.assertTrue("marker_gene_evidence" in test_annotation)
-        self.assertEqual(3, len(test_annotation["marker_gene_evidence"]))
-        self.assertTrue("EPYC" in test_annotation["marker_gene_evidence"])
-        self.assertTrue("RELN" in test_annotation["marker_gene_evidence"])
-        self.assertTrue("GULP1" in test_annotation["marker_gene_evidence"])
-        self.assertFalse(test_annotation["transferred_annotations"])
+        self.assertEqual("D1-Matrix", test_annotation["parent_cell_set_name"])
+        self.assertEqual("AIT115_300", test_annotation["parent_cell_set_accession"])
+        self.assertFalse("marker_gene_evidence" in test_annotation)
+        # self.assertEqual(3, len(test_annotation["marker_gene_evidence"]))
+        # self.assertTrue("EPYC" in test_annotation["marker_gene_evidence"])
+        # self.assertTrue("RELN" in test_annotation["marker_gene_evidence"])
+        # self.assertTrue("GULP1" in test_annotation["marker_gene_evidence"])
+        self.assertFalse("transferred_annotations" in test_annotation)
+        self.assertFalse("rationale_dois" in test_annotation)
 
         self.assertTrue("user_annotations" in test_annotation)
-        self.assertEqual(8, len(test_annotation["user_annotations"]))
+        self.assertEqual(12, len(test_annotation["user_annotations"]))
         self.assertTrue({'labelset': 'Cluster size', 'cell_label': '16393'} in test_annotation["user_annotations"])
         self.assertTrue({'labelset': 'region.info _Frequency_', 'cell_label': 'PuR(0.52) | CaH(0.39)'} in test_annotation["user_annotations"])

src/test/test_data/nanobot.db

@@ -0,0 +1,7 @@
+import unittest
+
+loader = unittest.TestLoader()
+suite = loader.discover(start_dir="../", pattern="*_test.py")
+
+runner = unittest.TextTestRunner()
+runner.run(suite)