Concatenate organism_age in manifests with value and unit (#2571, PR #…

…2825)
DataBiosphere · Mar 10, 2021 · 905b700 · 905b700
2 parents c4bb50e + 79f71c8
commit 905b700
Show file tree

Hide file tree

Showing 3 changed files with 12 additions and 12 deletions.
diff --git a/src/azul/plugins/metadata/hca/__init__.py b/src/azul/plugins/metadata/hca/__init__.py
@@ -167,6 +167,8 @@ 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",
@@ -251,10 +253,7 @@ def service_config(self) -> ServiceConfig:
                     "donor_organism.genus_species": "genus_species",
                     "donor_organism.development_stage": "development_stage",
                     "donor_organism.diseases": "diseases",
-                    # FIXME: Adapt organism_age to manifest format
-                    #        https://github.com/DataBiosphere/azul/issues/2571
-                    "donor_organism.organism_age": "organism_age_value",
-                    "donor_organism.organism_age_unit": "organism_age_unit"
+                    "donor_organism.organism_age": "organism_age"
                 },
                 "contents.cell_lines": {
                     "cell_line.provenance.document_id": "document_id",
@@ -308,6 +307,8 @@ def service_config(self) -> ServiceConfig:
                 "genusSpecies",
                 "organismAge",
                 "organismAgeUnit",
+                # FIXME: Remove organismAgeValue facet
+                #        https://github.com/DataBiosphere/azul/issues/2824
                 "organismAgeValue",
                 "biologicalSex",
                 "sampleDisease",

diff --git a/src/azul/service/manifest_service.py b/src/azul/service/manifest_service.py
@@ -90,6 +90,9 @@
     MutableManifestConfig,
     RepositoryPlugin,
 )
+from azul.plugins.metadata.hca.transform import (
+    value_and_unit,
+)
 from azul.service import (
     Filters,
 )
@@ -537,6 +540,8 @@ def _extract_fields(self,
         def convert(field_name, field_value):
             if field_name == 'drs_path':
                 return self.repository_plugin.drs_uri(field_value)
+            elif field_name == 'organism_age':
+                return value_and_unit.to_index(field_value)
             elif field_value is None:
                 return ''
             else:

diff --git a/test/service/test_manifest.py b/test/service/test_manifest.py
@@ -261,10 +261,7 @@ def test_manifest(self):
             ('donor_organism.genus_species', '', 'Mus musculus'),
             ('donor_organism.development_stage', '', 'adult'),
             ('donor_organism.diseases', '', 'subcutaneous melanoma'),
-            # FIXME: Adapt organism_age to manifest format
-            #        https://github.com/DataBiosphere/azul/issues/2571
-            ('donor_organism.organism_age', '', '6-12'),
-            ('donor_organism.organism_age_unit', '', 'week'),
+            ('donor_organism.organism_age', '', '6-12 week'),
             ('cell_line.provenance.document_id', '', ''),
             ('cell_line.biomaterial_core.biomaterial_id', '', ''),
             ('organoid.provenance.document_id', '', ''),
@@ -499,7 +496,6 @@ def test_terra_bdbag_manifest(self):
                 'donor_organism__development_stage': 'adult',
                 'donor_organism__diseases': '',
                 'donor_organism__organism_age': '',
-                'donor_organism__organism_age_unit': '',
                 'cell_line__provenance__document_id': '',
                 'cell_line__biomaterial_core__biomaterial_id': '',
                 'organoid__provenance__document_id': '',
@@ -594,8 +590,7 @@ def test_terra_bdbag_manifest(self):
                 'donor_organism__genus_species': 'Australopithecus',
                 'donor_organism__development_stage': '',
                 'donor_organism__diseases': 'normal',
-                'donor_organism__organism_age': '38',
-                'donor_organism__organism_age_unit': 'year',
+                'donor_organism__organism_age': '38 year',
                 'cell_line__provenance__document_id': '',
                 'cell_line__biomaterial_core__biomaterial_id': '',
                 'organoid__provenance__document_id': '',
@@ -708,7 +703,6 @@ def sort_rows(rows: List[Dict[str, str]]) -> List[List[Tuple[str, str]]]:
             'donor_organism__development_stage',
             'donor_organism__diseases',
             'donor_organism__organism_age',
-            'donor_organism__organism_age_unit',
             'cell_line__provenance__document_id',
             'cell_line__biomaterial_core__biomaterial_id',
             'organoid__provenance__document_id',