SN Donor Calc Props

CHANGELOG.rst

@@ -7,6 +7,14 @@ smaht-portal
 Change Log
 ----------
 
+0.98.0
+======
+`PR23: SN Donor Calc Props <https://github.com/smaht-dac/smaht-portal/pull/223>`_
+* Add rev_link calc props for `Donor`: `death_circumstances`, `demographic`, `family_history`, `medical_history`, `tissue_collection`
+* Add rev_link calc props for `MedicalHistory`: `diagnosis`, `exposure`, `medical_treatment`
+* Adds tests for all calc_props for these two items
+
+
 0.97.0
 ======
 `PR238: SN Add valid_molecules required <https://github.com/smaht-dac/smaht-portal/pull/238>`_

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "encoded"
-version = "0.97.0"
+version = "0.98.0"
 description = "SMaHT Data Analysis Portal"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

src/encoded/tests/test_types_donor.py

@@ -0,0 +1,39 @@
+import pytest
+from webtest import TestApp
+
+from .utils import get_search
+
+
+@pytest.mark.workbook
+def test_tissues_rev_link(es_testapp: TestApp, workbook: None) -> None:
+    """Ensure tissues rev link works."""
+    tissues_search = get_search(es_testapp, "?type=Donor&tissues.uuid!=No+value")
+    assert tissues_search
+
+
+@pytest.mark.workbook
+def test_death_circumstances_rev_link(es_testapp: TestApp, workbook: None) -> None:
+    """Ensure death circumstances rev link works."""
+    dc_search = get_search(es_testapp, "?type=Donor&death_circumstances.uuid!=No+value")
+    assert dc_search
+
+
+@pytest.mark.workbook
+def test_demographic_rev_link(es_testapp: TestApp, workbook: None) -> None:
+    """Ensure demographic rev link works."""
+    dc_search = get_search(es_testapp, "?type=Donor&demographic.uuid!=No+value")
+    assert dc_search
+
+
+@pytest.mark.workbook
+def test_family_history_rev_link(es_testapp: TestApp, workbook: None) -> None:
+    """Ensure family history rev link works."""
+    family_search = get_search(es_testapp, "?type=Donor&family_history.uuid!=No+value")
+    assert family_search
+
+
+@pytest.mark.workbook
+def test_medical_history_rev_link(es_testapp: TestApp, workbook: None) -> None:
+    """Ensure family history rev link works."""
+    medical_search = get_search(es_testapp, "?type=Donor&medical_history.uuid!=No+value")
+    assert medical_search

src/encoded/tests/test_types_medical_history.py

@@ -0,0 +1,25 @@
+import pytest
+from webtest import TestApp
+
+from .utils import get_search
+
+
+@pytest.mark.workbook
+def test_diagnosis_rev_link(es_testapp: TestApp, workbook: None) -> None:
+    """Ensure diagnosis rev link works."""
+    diagnosis_search = get_search(es_testapp, "?type=MedicalHistory&diagnosis.uuid!=No+value")
+    assert diagnosis_search
+
+
+@pytest.mark.workbook
+def test_exposure_rev_link(es_testapp: TestApp, workbook: None) -> None:
+    """Ensure exposure rev link works."""
+    exposure_search = get_search(es_testapp, "?type=MedicalHistory&exposure.uuid!=No+value")
+    assert exposure_search
+
+
+@pytest.mark.workbook
+def test_medical_treatment_rev_link(es_testapp: TestApp, workbook: None) -> None:
+    """Ensure medical treatment rev link works."""
+    treatment_search = get_search(es_testapp, "?type=MedicalHistory&medical_treatment.uuid!=No+value")
+    assert treatment_search

src/encoded/types/donor.py

@@ -18,12 +18,74 @@ class Donor(SubmittedItem):
     schema = load_schema("encoded:schemas/donor.json")
     embedded_list = []
     rev = {
+        "death_circumstances": ("DeathCircumstances", "donor"),
+        "demographic": ("Demographic", "donor"),
+        "family_history": ("FamilyHistory", "donor"),
+        "medical_history": ("MedicalHistory", "donor"),
         "tissues": ("Tissue", "donor"),
+        "tissue_collection": ("TissueCollection", "donor")
     }
 
+    @calculated_property(
+        schema={
+            "title": "Death Circumstances",
+            "description": "Circumstances of death of the donor",
+            "type": "string",
+            "linkTo": "DeathCircumstances"
+        },
+    )
+    def death_circumstances(self, request: Request) -> Union[str, None]:
+        result = self.rev_link_atids(request, "death_circumstances")
+        if result:
+            return result
+        return
+
+    @calculated_property(
+        schema={
+            "title": "Demographic",
+            "description": "Demographic information for the donor",
+            "type": "string",
+            "linkTo": "Demographic"
+        },
+    )
+    def demographic(self, request: Request) -> Union[str, None]:
+        result = self.rev_link_atids(request, "demographic")
+        if result:
+            return result
+        return
+
+    @calculated_property(
+        schema={
+            "title": "Family History",
+            "description": "Family history of the donor",
+            "type": "string",
+            "linkTo": "FamilyHistory"
+        },
+    )
+    def family_history(self, request: Request) -> Union[str, None]:
+        result = self.rev_link_atids(request, "family_history")
+        if result:
+            return result
+        return
+
+    @calculated_property(
+        schema={
+            "title": "Medical History",
+            "description": "Medical history of the donor",
+            "type": "string",
+            "linkTo": "MedicalHistory"
+        },
+    )
+    def medical_history(self, request: Request) -> Union[str, None]:
+        result = self.rev_link_atids(request, "medical_history")
+        if result:
+            return result
+        return
+
     @calculated_property(
         schema={
             "title": "Tissues",
+            "description": "Tissues collected from the donor",
             "type": "array",
             "items": {
                 "type": "string",
@@ -36,3 +98,19 @@ def tissues(self, request: Request) -> Union[List[str], None]:
         if result:
             return result
         return
+
+    @calculated_property(
+        schema={
+            "title": "Tissue Collection",
+            "description": "Tissue collection information for the donor",
+            "type": "string",
+            "linkTo": "TissueCollection"
+        },
+    )
+    def tissue_collection(self, request: Request) -> Union[str, None]:
+        result = self.rev_link_atids(request, "tissue_collection")
+        if result:
+            return result
+        return
+
+

src/encoded/types/medical_history.py

@@ -1,4 +1,7 @@
-from snovault import collection, load_schema
+from typing import Union, List
+
+from snovault import collection, load_schema, calculated_property
+from pyramid.request import Request
 
 from .submitted_item import SubmittedItem
 
@@ -15,3 +18,60 @@ class MedicalHistory(SubmittedItem):
     item_type = "medical_history"
     schema = load_schema("encoded:schemas/medical_history.json")
     embedded_list = []
+
+    rev = {
+        "diagnosis": ("Diagnosis", "medical_history"),
+        "exposure": ("Exposure", "medical_history"),
+        "medical_treatment": ("MedicalTreatment", "medical_history"),
+    }
+
+    @calculated_property(
+        schema={
+            "title": "Diagnosis",
+            "description": "Diagnoses included in the medical history of the donor",
+            "type": "array",
+            "items": {
+                "type": "string",
+                "linkTo": "Diagnosis"
+            }
+        },
+    )
+    def diagnosis(self, request: Request) -> Union[List[str], None]:
+        result = self.rev_link_atids(request, "diagnosis")
+        if result:
+            return result
+        return
+
+    @calculated_property(
+        schema={
+            "title": "Exposure",
+            "description": "Exposures included in the medical history of the donor",
+            "type": "array",
+            "items": {
+                "type": "string",
+                "linkTo": "Exposure"
+            }
+        },
+    )
+    def exposure(self, request: Request) -> Union[List[str], None]:
+        result = self.rev_link_atids(request, "exposure")
+        if result:
+            return result
+        return
+
+    @calculated_property(
+        schema={
+            "title": "Medical Treatment",
+            "description": "Medical treatments included in the medical history of the donor",
+            "type": "array",
+            "items": {
+                "type": "string",
+                "linkTo": "MedicalTreatment"
+            }
+        },
+    )
+    def medical_treatment(self, request: Request) -> Union[List[str], None]:
+        result = self.rev_link_atids(request, "medical_treatment")
+        if result:
+            return result
+        return