Merge pull request #1915 from 4dn-dcic/ajs_241025_upd_trtmt_title

Update treatment item display title

CHANGELOG.rst

@@ -6,6 +6,19 @@ fourfront
 Change Log
 ----------
 
+
+8.4.3
+=====
+
+`Update treatment item display title <https://github.com/4dn-dcic/fourfront/pull/1915>`_
+
+* Add 'override_treatment_title' property to Treatment items
+* Tweak the display_title calcprop to:
+  - use the override_treatment_title prop if present
+  - for biological treatments with constructs but no biological agent use construct names in treatment display_title
+* added tests
+
+
 8.4.2
 =====
 

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 # Note: Various modules refer to this system as "encoded", not "fourfront".
 name = "encoded"
-version = "8.4.2"
+version = "8.4.3"
 description = "4DN-DCIC Fourfront"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

src/encoded/schemas/treatment.json

@@ -41,6 +41,11 @@
             "type": "string",
             "lookup": 1000,
             "format": "uri"
+        },
+        "override_treatment_title": {
+            "title": "Override display title",
+            "type": "string",
+            "lookup": 1000
         }
     },
     "facets": {

src/encoded/tests/data/inserts/treatment_agent.json

@@ -43,5 +43,33 @@
         "submitted_by": "[email protected]",
         "temperature": 20,
         "status": "in review by lab"
+    },
+    {
+        "uuid": "05501f04-360a-438a-87d7-443311fc6831",
+        "aliases": ["dcic:ba-treatment-1"],
+        "description": "Biological treatment with agent",
+        "treatment_type": "Biological",
+        "biological_agent": "Green Virus",
+        "duration": 24,
+        "duration_units": "hour",
+        "award": "1U01CA200059-01",
+        "lab": "4dn-dcic-lab",
+        "submitted_by": "[email protected]",
+        "temperature": 37,
+        "status": "in review by lab"
+    },
+    {
+        "uuid": "dee3576a-5e03-4390-88c2-1b4f73cc294e",
+        "aliases": ["dcic:biol_w_constructs"],
+        "description": "Biological treatment with construct",
+        "treatment_type": "Biological",
+        "constructs": ["131106bc-8535-4448-903e-854af460b211"],
+        "duration": 24,
+        "duration_units": "hour",
+        "award": "1U01CA200059-01",
+        "lab": "4dn-dcic-lab",
+        "submitted_by": "[email protected]",
+        "temperature": 37,
+        "status": "in review by lab"
     }
 ]

src/encoded/tests/test_types_treatment.py

@@ -26,6 +26,19 @@ def viral_treatment(testapp, lab, award):
     return testapp.post_json('/treatment_agent', item).json['@graph'][0]
 
 
+@pytest.fixture
+def construct_based_treatment(testapp, lab, award, construct):
+    item = {
+        'award': award['@id'],
+        'lab': lab['@id'],
+        'treatment_type': 'Biological',
+        'constructs': [construct],
+        'duration': 3.5,
+        'duration_units': 'hour'
+    }
+    return testapp.post_json('/treatment_agent', item).json['@graph'][0]
+
+
 @pytest.fixture
 def heatshock_treatment(testapp, lab, award):
     item = {
@@ -88,3 +101,41 @@ def test_calculated_rnai_treatment_display_title(testapp, rnai, gene_bio_feature
     assert rnai['display_title'] == 'shRNA treatment'
     res = testapp.patch_json(rnai['@id'], {'target': [gene_bio_feature['@id']]})
     assert res.json['@graph'][0]['display_title'] == 'shRNA of RAD21 gene'
+
+
+def test_calculated_treatment_agent_w_override_display_title(testapp, drug_treatment):
+    assert drug_treatment['display_title'] == 'Drug treatment'
+    res = testapp.patch_json(drug_treatment['@id'], {'override_treatment_title': 'New drug treatment'})
+    assert res.json['@graph'][0]['display_title'] == 'New drug treatment'
+
+
+def test_calculated_rnai_treatment_w_override_display_title(testapp, rnai):
+    assert rnai['display_title'] == 'shRNA treatment'
+    res = testapp.patch_json(rnai['@id'], {'override_treatment_title': 'New RNAi treatment'})
+    assert res.json['@graph'][0]['display_title'] == 'New RNAi treatment'
+
+
+def test_calculated_biological_treatment_w_construct_display_title(
+        construct_based_treatment, construct):
+    assert construct.get('display_title') in construct_based_treatment.get('display_title')
+
+
+def test_calculated_biological_treatment_w_multiple_constructs_display_title(
+        testapp, construct_based_treatment, lab, award):
+    c_name = 'super_construct_'
+    c_type = 'expression construct'
+    constructs = []
+    for i in range(1, 5):
+        cmeta = {
+            'name': c_name + str(i),
+            'construct_type': c_type,
+            'lab': lab['@id'],
+            'award': award['@id']
+        }
+        constructs.append(testapp.post_json('/construct', cmeta).json['@graph'][0])
+    # test display_title with 2 constructs
+    res = testapp.patch_json(construct_based_treatment['@id'], {'constructs': [c['@id'] for c in constructs[:2]]})
+    assert res.json['@graph'][0]['display_title'] == 'super_construct_1, super_construct_2 treatment (3.5h)'
+    # test with 4 constructs
+    res = testapp.patch_json(construct_based_treatment['@id'], {'constructs': [c['@id'] for c in constructs]})
+    assert res.json['@graph'][0]['display_title'] == 'super_construct_1, super_construct_2, super_construct_3 and 1 more treatment (3.5h)'

src/encoded/types/treatment.py

@@ -68,8 +68,11 @@ class TreatmentAgent(Treatment):
     def display_title(self, request, treatment_type=None, chemical=None,
                       biological_agent=None, constructs=None, duration=None,
                       duration_units=None, concentration=None,
-                      concentration_units=None, temperature=None):
+                      concentration_units=None, temperature=None,
+                      override_treatment_title=None):
         conditions = ""
+        if override_treatment_title:
+            return override_treatment_title
         if concentration and concentration_units:
             conditions += str(concentration) + " " + concentration_units
         if duration and duration_units:
@@ -91,8 +94,24 @@ def display_title(self, request, treatment_type=None, chemical=None,
                 [get_item_or_none(request, construct).get('name') for construct in constructs]
             )
             disp_title = "Transient transfection of " + plasmids + conditions
-        elif treatment_type == "Biological" and biological_agent:
-            disp_title = biological_agent + " treatment" + conditions
+        elif treatment_type == "Biological":
+            disp_title = ''
+            if biological_agent or constructs:
+                if biological_agent:
+                    disp_title = biological_agent + " treatment" + conditions
+                else:
+                    const_str = ''
+                    suffix = ''
+                    if len(constructs) > 3:
+                        suffix = ' and {} more'.format(len(constructs) - 3)
+                        constructs = constructs[0:3]
+                    const_str = ", ".join(
+                        [get_item_or_none(request, construct).get('display_title') for construct in constructs]
+                    )
+                    const_str = const_str.rstrip(", ")
+                    disp_title = const_str + suffix + " treatment" + conditions
+            else:
+                pass
         else:
             disp_title = treatment_type + conditions
         return disp_title
@@ -128,7 +147,9 @@ class TreatmentRnai(Treatment):
         "description": "A calculated title for every object in 4DN",
         "type": "string"
     })
-    def display_title(self, request, rnai_type=None, target=None):
+    def display_title(self, request, rnai_type=None, target=None, override_treatment_title=None):
+        if override_treatment_title:
+            return override_treatment_title
         if rnai_type and target:
             tstring = ''
             for t in target: