Merge branch 'main' into SCRUM-4802

agr_literature_service/api/crud/workflow_tag_crud.py

@@ -25,7 +25,7 @@
 from agr_literature_service.api.crud.workflow_transition_requirements import (
     ADMISSIBLE_WORKFLOW_TRANSITION_REQUIREMENT_FUNCTIONS)
 from agr_literature_service.api.crud.workflow_transition_actions.process_action import (process_action)
-from agr_literature_service.api.crud.ateam_db_helpers import get_name_to_atp_and_children
+from agr_literature_service.api.crud.ateam_db_helpers import get_name_to_atp_and_children, search_ancestors_or_descendants
 process_atp_multiple_allowed = [
     'ATP:ont1',  # used in testing
     'ATP:0000165', 'ATP:0000169', 'ATP:0000189', 'ATP:0000178', 'ATP:0000166'  # classifications and subtasks
@@ -53,12 +53,13 @@ def load_workflow_parent_children(root_node='ATP:0000177'):
 
 
 def get_parent_or_children(atp_name: str, parent_or_children: str = "parent"):
+    if parent_or_children == "parent":
+        return search_ancestors_or_descendants(atp_name, 'parent')[0]
     workflow_children, workflow_parent = load_workflow_parent_children(root_node=atp_name)
-    workflow_to_check = workflow_children if parent_or_children == "children" else workflow_parent
-    if atp_name not in workflow_to_check:
+    if atp_name not in workflow_children:
         logger.error(f"Could not find {parent_or_children} for {atp_name}")
         return None
-    return workflow_to_check[atp_name]
+    return workflow_children[atp_name]
 
 
 def get_workflow_process_from_tag(workflow_tag_atp_id: str):

tests/api/test_mod_corpus_association.py

@@ -8,7 +8,7 @@
 from agr_literature_service.api.main import app
 from agr_literature_service.api.models import ReferenceModel, CrossReferenceModel
 from agr_literature_service.lit_processing.tests.mod_populate_load import populate_test_mods
-from ..fixtures import load_workflow_parent_children_mock
+from ..fixtures import load_workflow_parent_children_mock, search_ancestors_or_descendants_mock
 from ..fixtures import db # noqa
 from .fixtures import auth_headers # noqa
 from .test_reference import test_reference # noqa
@@ -117,6 +117,8 @@ def test_destroy_mca(self, test_mca, auth_headers): # noqa
 
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_mca_modid_wb(self, db, test_reference, auth_headers): # noqa
         with TestClient(app) as client:
             populate_test_mods()
@@ -146,6 +148,8 @@ def test_mca_modid_wb(self, db, test_reference, auth_headers): # noqa
 
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_mca_modid_wb_obsolete_xref(self, db, test_reference, auth_headers): # noqa
         # allow creating of xref via mca if xref already has mod + reference but is_obsolete
         with TestClient(app) as client:

tests/api/test_reference.py

@@ -16,7 +16,7 @@
 from agr_literature_service.api.models import ReferenceModel, AuthorModel, CrossReferenceModel
 from agr_literature_service.api.schemas import ReferencefileSchemaPost
 from agr_literature_service.lit_processing.tests.mod_populate_load import populate_test_mods
-from ..fixtures import load_workflow_parent_children_mock
+from ..fixtures import load_workflow_parent_children_mock, search_ancestors_or_descendants_mock
 from ..fixtures import db, populate_test_mod_reference_types # noqa
 from .fixtures import auth_headers # noqa
 from .test_resource import test_resource # noqa
@@ -181,6 +181,8 @@ def test_delete_reference(self, auth_headers, test_reference): # noqa
 
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_reference_mca_wb(self, db, auth_headers): # noqa
         with TestClient(app) as client:
             populate_test_mods()
@@ -206,6 +208,8 @@ def test_reference_mca_wb(self, db, auth_headers): # noqa
 
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_reference_large(self, db, auth_headers, populate_test_mod_reference_types, test_mod, # noqa
                              test_topic_entity_tag_source): # noqa
         with TestClient(app) as client, \
@@ -742,6 +746,8 @@ def test_get_bib_info(self, test_reference, auth_headers, test_mod): # noqa
 
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_get_textpresso_reference_list(self, test_reference, auth_headers, test_mod, test_topic_entity_tag_source, db):  # noqa
         with TestClient(app) as client:
             with patch("agr_literature_service.api.crud.topic_entity_tag_crud.check_atp_ids_validity") as \

tests/api/test_sort.py

@@ -6,7 +6,7 @@
 from agr_literature_service.api.main import app
 from agr_literature_service.lit_processing.tests.mod_populate_load import populate_test_mods
 from .test_mod_corpus_association import test_mca # noqa
-from ..fixtures import load_workflow_parent_children_mock
+from ..fixtures import load_workflow_parent_children_mock, search_ancestors_or_descendants_mock
 from ..fixtures import db # noqa
 from .test_reference import test_reference # noqa
 from .test_mod import test_mod # noqa
@@ -23,6 +23,8 @@ def test_sort_need_review(self, test_mca): # noqa
 
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_sort_prepublication_pipeline(self, db, auth_headers): # noqa
         with TestClient(app) as client:
             populate_test_mods()
@@ -221,6 +223,8 @@ def test_sort_prepublication_pipeline(self, db, auth_headers): # noqa
 
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_sort_prepublication_pipeline_simple(self, db, auth_headers):  # noqa
         with TestClient(app) as client:
             populate_test_mods()

tests/api/test_workflow_tag.py

@@ -13,7 +13,7 @@
     get_workflow_process_from_tag,
     get_workflow_tags_from_process,
     load_workflow_parent_children)
-from ..fixtures import load_workflow_parent_children_mock
+from ..fixtures import load_workflow_parent_children_mock, search_ancestors_or_descendants_mock
 from ..fixtures import db  # noqa
 from .fixtures import auth_headers # noqa
 from .test_reference import test_reference # noqa
@@ -138,6 +138,8 @@ def test_destroy_ref_wt(self, test_workflow_tag, auth_headers): # noqa
 
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_parent_child_dict(self, test_workflow_tag, auth_headers): # noqa
         # load_workflow_parent_children()
         assert get_workflow_process_from_tag('ATP:0000164') == 'ATP:0000161'
@@ -149,6 +151,8 @@ def test_parent_child_dict(self, test_workflow_tag, auth_headers): # noqa
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
     @patch("agr_literature_service.api.crud.workflow_tag_crud.get_descendants", get_descendants_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_transition_to_workflow_status_and_get_current_workflow_status(self, db, test_mod, test_reference,  # noqa
                                                                            auth_headers):  # noqa
         mod = db.query(ModModel).filter(ModModel.abbreviation == test_mod.new_mod_abbreviation).one()
@@ -206,6 +210,8 @@ def test_transition_to_workflow_status_and_get_current_workflow_status(self, db,
 
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_workflow_tag_counters(self, db, test_workflow_tag, auth_headers): # noqa
         with TestClient(app) as client, \
                 patch("agr_literature_service.api.crud.workflow_tag_crud.get_map_ateam_curies_to_names") as \

tests/fixtures.py

@@ -95,6 +95,33 @@ def load_sanitized_references(populate_test_mod_reference_types):
     yield None
 
 
+def search_ancestors_or_descendants_mock(ontology_node, ancestors_or_descendants):
+    workflow_parent = {
+        'ATP:0000172': 'ATP:0000177',
+        'ATP:0000140': 'ATP:0000177',
+        'ATP:0000165': 'ATP:0000177',
+        'ATP:0000161': 'ATP:0000177',
+        'ATP:0000175': 'ATP:0000172',
+        'ATP:0000174': 'ATP:0000172',
+        'ATP:0000173': 'ATP:0000172',
+        'ATP:0000178': 'ATP:0000172',
+        'ATP:0000141': 'ATP:0000140',
+        'ATP:0000135': 'ATP:0000140',
+        'ATP:0000139': 'ATP:0000140',
+        'ATP:0000134': 'ATP:0000140',
+        'ATP:0000168': 'ATP:0000165',
+        'ATP:0000167': 'ATP:0000165',
+        'ATP:0000170': 'ATP:0000165',
+        'ATP:0000171': 'ATP:0000165',
+        'ATP:0000169': 'ATP:0000165',
+        'ATP:0000166': 'ATP:0000165',
+        'ATP:0000164': 'ATP:0000161',
+        'ATP:0000163': 'ATP:0000161',
+        'ATP:0000162': 'ATP:0000161'
+    }
+    return [workflow_parent[ontology_node]]
+
+
 def load_workflow_parent_children_mock(root_node='ATP:0000177'):
     workflow_children = {
         'ATP:0000177': ['ATP:0000172', 'ATP:0000140', 'ATP:0000165', 'ATP:0000161'],

tests/lit_processing/pdf2tei/test_pdf2tei.py

@@ -12,7 +12,7 @@
 from ...api.fixtures import auth_headers  # noqa
 from ...api.test_mod import test_mod  # noqa
 from ...api.test_reference import test_reference  # noqa
-from ...fixtures import load_workflow_parent_children_mock
+from ...fixtures import load_workflow_parent_children_mock, search_ancestors_or_descendants_mock
 from ...fixtures import db  # noqa
 
 
@@ -171,6 +171,8 @@ def upload_initial_main_reference_file(db, client, test_mod, test_reference, aut
            load_workflow_parent_children_mock)
     @patch("agr_literature_service.lit_processing.pdf2tei.pdf2tei.convert_pdf_with_grobid",
            convert_pdf_with_grobid_mock)
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_pdf2tei(self, db, auth_headers, test_reference, test_mod): # noqa
         with TestClient(app) as client:
             mod_abbreviation = self.upload_initial_main_reference_file(db, client, test_mod, test_reference,
@@ -188,6 +190,8 @@ def test_pdf2tei(self, db, auth_headers, test_reference, test_mod): # noqa
     @patch("agr_literature_service.api.crud.workflow_tag_crud.load_workflow_parent_children",
            load_workflow_parent_children_mock)
     @patch("agr_literature_service.lit_processing.pdf2tei.pdf2tei.convert_pdf_with_grobid")
+    @patch("agr_literature_service.api.crud.workflow_tag_crud.search_ancestors_or_descendants",
+           search_ancestors_or_descendants_mock)
     def test_pdf2tei_failed_conversion(self, mock_convert_pdf_with_grobid,
                                        db, auth_headers, test_reference, test_mod):  # noqa
         with TestClient(app) as client: