add sites

dgidb · Dec 30, 2024 · fd8cf70 · fd8cf70
1 parent 14bc1f3
commit fd8cf70
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diff --git a/src/dgipy/integrations/clinical_trials.py b/src/dgipy/integrations/clinical_trials.py
@@ -2,12 +2,90 @@
 
 import logging
 
-from regbot.fetch.clinical_trials import StandardAge
+from regbot.fetch.clinical_trials import StandardAge, Status, Study
 from regbot.fetch.clinical_trials import get_clinical_trials as get_trials_from_fda
 
 _logger = logging.getLogger(__name__)
 
 
+def _add_study_to_output(output: dict[str, list], drug_name: str, study: Study) -> None:
+    """Update `output` in-place with results from study
+
+    :param output: in-progress raw columnar data
+    :param study: clinical trial study data to add to output
+    """
+    output["drug_name"].append(drug_name.upper())
+    output["trial_id"].append(study.protocol.identification.nct_id)
+    output["brief"].append(study.protocol.identification.brief_title)
+    output["study_type"].append(study.protocol.design.study_type)
+    min_age = (
+        study.protocol.eligibility.min_age
+        if study.protocol and study.protocol.eligibility
+        else None
+    )
+    output["min_age"].append(min_age)
+    max_age = (
+        study.protocol.eligibility.max_age
+        if study.protocol and study.protocol.eligibility
+        else None
+    )
+    output["max_age"].append(max_age)
+    age_groups = (
+        study.protocol.eligibility.std_age
+        if study.protocol and study.protocol.eligibility
+        else None
+    )
+    output["age_groups"].append(age_groups)
+    output["pediatric"].append(StandardAge.CHILD in age_groups if age_groups else None)
+    output["conditions"].append(
+        study.protocol.conditions.conditions
+        if study.protocol and study.protocol.conditions
+        else None
+    )
+    output["interventions"].append(
+        [i._asdict() for i in study.protocol.arms_intervention.interventions]
+        if study.protocol
+        and study.protocol.arms_intervention
+        and study.protocol.arms_intervention.interventions
+        else None
+    )
+    eligibility = study.protocol.eligibility
+    if not eligibility:
+        output["incl_excl_criteria"].append(None)
+        output["population_sex"].append(None)
+        output["population_description"]
+    else:
+        output["incl_excl_criteria"].append(eligibility.description)
+        output["population_sex"].append(eligibility.sex)
+        output["population_description"].append(eligibility.population)
+    all_locations = (
+        study.protocol.contacts_locations.locations
+        if study.protocol.contacts_locations
+        and study.protocol.contacts_locations.locations
+        else []
+    )
+
+    potential_sites = [
+        {
+            "name": location.facility,
+            "status": location.status,
+            "city": location.city,
+            "country": location.country,
+            "coordinates": location.geo,
+        }
+        for location in all_locations
+        if location.status
+        in {
+            Status.RECRUITING,
+            Status.NOT_YET_RECRUITING,
+            Status.AVAILABLE,
+            Status.TEMPORARILY_NOT_AVAILABLE,
+            Status.UNKNOWN,
+        }
+    ]
+    output["potential_sites"].append(potential_sites)
+
+
 def get_clinical_trials(terms: list[str]) -> dict:
     """Acquire associated clinical trials data for drug term
 
@@ -41,47 +119,16 @@ def get_clinical_trials(terms: list[str]) -> dict:
         "pediatric": [],
         "conditions": [],
         "interventions": [],
+        "incl_excl_criteria": [],
+        "population_sex": [],
+        "population_description": [],
+        "potential_sites": [],
     }
 
     for drug in terms:
         results = get_trials_from_fda(drug)
 
         for study in results:
-            output["drug_name"].append(drug.upper())
-            output["trial_id"].append(study.protocol.identification.nct_id)
-            output["brief"].append(study.protocol.identification.brief_title)
-            output["study_type"].append(study.protocol.design.study_type)
-            min_age = (
-                study.protocol.eligibility.min_age
-                if study.protocol and study.protocol.eligibility
-                else None
-            )
-            output["min_age"].append(min_age)
-            max_age = (
-                study.protocol.eligibility.max_age
-                if study.protocol and study.protocol.eligibility
-                else None
-            )
-            output["max_age"].append(max_age)
-            age_groups = (
-                study.protocol.eligibility.std_age
-                if study.protocol and study.protocol.eligibility
-                else None
-            )
-            output["age_groups"].append(age_groups)
-            output["pediatric"].append(
-                StandardAge.CHILD in age_groups if age_groups else None
-            )
-            output["conditions"].append(
-                study.protocol.conditions.conditions
-                if study.protocol and study.protocol.conditions
-                else None
-            )
-            output["interventions"].append(
-                [i._asdict() for i in study.protocol.arms_intervention.interventions]
-                if study.protocol
-                and study.protocol.arms_intervention
-                and study.protocol.arms_intervention.interventions
-                else None
-            )
+            _add_study_to_output(output, drug, study)
+
     return output
diff --git a/tests/integrations/test_clinical_trials.py b/tests/integrations/test_clinical_trials.py
@@ -2,7 +2,12 @@
 from pathlib import Path
 
 import requests_mock
-from regbot.fetch.clinical_trials import InterventionType, StandardAge, StudyType
+from regbot.fetch.clinical_trials import (
+    InterventionType,
+    StandardAge,
+    Status,
+    StudyType,
+)
 
 from dgipy.integrations.clinical_trials import get_clinical_trials
 
@@ -63,3 +68,14 @@ def test_get_clinical_trials(fixtures_dir: Path):
                 "aliases": ["AVXS-101", "Zolgensma"],
             }
         ]
+        assert (
+            results["incl_excl_criteria"][example_index]
+            == "Inclusion Criteria\n\n* SMA diagnosis\n* Aged 2 to \\< 18 years\n* Have had at least four loading doses of nusinersen (Spinraza\u00ae) or at least 3 months of treatment with risdiplam (Evrysdi\u00ae) at Screening\n* Must have symptoms of SMA as defined in the protocol\n\nExclusion Criteria:\n\n* Anti Adeno Associated Virus Serotype 9 (AAV9) antibody titer using an immunoassay is reported as elevated\n* Clinically significant abnormalities in test results during screening\n* Contraindications for lumbar puncture procedure\n* At Baseline, participants are excluded if they received:\n\n  * nusinersen (Spinraza\u00ae) or\n  * risdiplam (Evrysdi\u00ae) within a defined timeframe\n* Vaccinations 2 weeks prior to administration of OAV101\n* Hospitalization for a pulmonary event, or for nutritional support within 2 months prior to Screening or inpatient major surgery planned.\n* Presence of an infection or febrile illness up to 30 days prior to administration of OAV101\n* Requiring invasive ventilation"
+        )
+        assert {
+            "name": "Child Hosp of the Kings Daughters",
+            "status": Status.RECRUITING,
+            "city": "Norfolk",
+            "country": "United States",
+            "coordinates": (36.84681, -76.28522),
+        } in results["potential_sites"][3]