[r] Remove organismAgeValue term facet from service response (#2824, PR

#3437)
DataBiosphere · Sep 29, 2021 · eba9a93 · eba9a93
2 parents bdde3d5 + 2bd436d
commit eba9a93
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Showing 7 changed files with 70 additions and 744 deletions.
diff --git a/lambdas/service/openapi.json b/lambdas/service/openapi.json
diff --git a/src/azul/plugins/metadata/hca/__init__.py b/src/azul/plugins/metadata/hca/__init__.py
@@ -172,9 +172,6 @@ def service_config(self) -> ServiceConfig:
                 "specimenOrgan": "contents.specimens.organ",
                 "specimenOrganPart": "contents.specimens.organ_part",
                 "organismAge": "contents.donors.organism_age",
-                # FIXME: Remove organismAgeValue facet
-                #        https://github.com/DataBiosphere/azul/issues/2824
-                "organismAgeValue": "contents.donors.organism_age_value",
                 "organismAgeUnit": "contents.donors.organism_age_unit",
                 "organismAgeRange": "contents.donors.organism_age_range",
                 "preservationMethod": "contents.specimens.preservation_method",
@@ -303,9 +300,6 @@ def service_config(self) -> ServiceConfig:
                 "genusSpecies",
                 "organismAge",
                 "organismAgeUnit",
-                # FIXME: Remove organismAgeValue facet
-                #        https://github.com/DataBiosphere/azul/issues/2824
-                "organismAgeValue",
                 "biologicalSex",
                 "sampleDisease",
                 "specimenDisease",

diff --git a/src/azul/plugins/metadata/hca/transform.py b/src/azul/plugins/metadata/hca/transform.py
@@ -714,7 +714,6 @@ def _donor_types(cls) -> FieldTypes:
             'diseases': [null_str],
             'organism_age': value_and_unit,
             'organism_age_unit': null_str,
-            'organism_age_value': null_str,
             # Prevent problem due to shadow copies on numeric ranges
             'organism_age_range': pass_thru_json,
             'donor_count': null_int
@@ -736,7 +735,6 @@ def _donor(self, donor: api.DonorOrganism) -> MutableJSON:
             'development_stage': donor.development_stage,
             'diseases': sorted(donor.diseases),
             'organism_age': organism_age,
-            'organism_age_value': donor.organism_age,
             'organism_age_unit': donor.organism_age_unit,
             **(
                 {

diff --git a/.../indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T113344.698028Z.results.json b/.../indexer/data/aaa96233-bf27-44c7-82df-b4dc15ad4d9d.2018-11-02T113344.698028Z.results.json
diff --git a/test/indexer/test_hca_indexer.py b/test/indexer/test_hca_indexer.py
@@ -1416,7 +1416,6 @@ def test_sample_with_no_donor(self):
             'development_stage': 'human adult stage',
             'diseases': ['normal'],
             'organism_age': '62 year',
-            'organism_age_value': '62',
             'organism_age_unit': 'year',
             'organism_age_range': {
                 'gte': 1955232000.0,

diff --git a/test/service/data/pfb_manifest.results.json b/test/service/data/pfb_manifest.results.json
@@ -446,9 +446,6 @@
             "organism_age_unit": [
                 ""
             ],
-            "organism_age_value": [
-                ""
-            ],
             "submission_date": "2018-10-10T02:23:39.580000Z",
             "update_date": "2018-10-10T02:23:42.998000Z"
         },
@@ -769,9 +766,6 @@
             "organism_age_unit": [
                 "year"
             ],
-            "organism_age_value": [
-                "38"
-            ],
             "submission_date": "2018-11-02T10:02:12.191000Z",
             "update_date": "2018-11-02T10:07:39.622000Z"
         },
@@ -5071,10 +5065,6 @@
                 "year",
                 ""
             ],
-            "organism_age_value": [
-                "56",
-                ""
-            ],
             "submission_date": "2021-01-01T00:00:00.000000Z",
             "update_date": ""
         },

diff --git a/test/service/test_response.py b/test/service/test_response.py
@@ -1844,14 +1844,7 @@ def test_organism_age_facet(self):
                         'term': 'year',
                         'count': 1
                     }
-                ],
-                'organismAgeValue': [
-                    {
-                        'term': '20',
-                        'count': 1
-                    }
-                ],
-
+                ]
             },
             # This project has multiple donor organisms
             '2c4724a4-7252-409e-b008-ff5c127c7e89': {
@@ -1876,16 +1869,6 @@ def test_organism_age_facet(self):
                         'term': 'year',
                         'count': 1
                     }
-                ],
-                'organismAgeValue': [
-                    {
-                        'term': '40-44',
-                        'count': 1
-                    },
-                    {
-                        'term': '55-59',
-                        'count': 1
-                    }
                 ]
             },
             # This project has one donor but donor has no age
@@ -1901,13 +1884,7 @@ def test_organism_age_facet(self):
                         'term': None,
                         'count': 1
                     }
-                ],
-                'organismAgeValue': [
-                    {
-                        'term': None,
-                        'count': 1
-                    }
-                ],
+                ]
             }
         }
         self._assert_term_facets(test_data,