Release beta 32

setup.py

@@ -2,7 +2,7 @@
 
 setup(
     name="hca-metadata-api",
-    version="1.0b31",
+    version="1.0b32",
     license='MIT',
     install_requires=[
         "dataclasses >= 0.6;python_version<'3.7'"

src/humancellatlas/data/metadata/api.py

@@ -280,18 +280,26 @@ def contact_name(self) -> str:
         return self.name
 
 
+@dataclass(eq=True, frozen=True)
+class Accession:
+    domain: str
+    value: str
+
+
 @dataclass(init=False)
 class Project(Entity):
     project_short_name: str
     project_title: str
     project_description: Optional[str]  # optional up to core/project/5.2.2/project_core
     publications: Set[ProjectPublication]
     contributors: Set[ProjectContact]
+    accessions: Set[Accession]
     insdc_project_accessions: Set[str]
     geo_series_accessions: Set[str]
     array_express_accessions: Set[str]
     insdc_study_accessions: Set[str]
     supplementary_links: Set[str]
+    estimated_cell_count: Optional[int]
 
     def __init__(self,
                  json: JSON,
@@ -306,11 +314,43 @@ def __init__(self,
         self.publications = set(ProjectPublication.from_json(publication)
                                 for publication in content.get('publications', []))
         self.contributors = {ProjectContact.from_json(contributor) for contributor in content.get('contributors', [])}
-        self.insdc_project_accessions = set(content.get('insdc_project_accessions', []))
-        self.geo_series_accessions = set(content.get('geo_series_accessions', []))
-        self.array_express_accessions = set(content.get('array_express_accessions', []))
-        self.insdc_study_accessions = set(content.get('insdc_study_accessions', []))
         self.supplementary_links = set(content.get('supplementary_links', []))
+        self.estimated_cell_count = content.get('estimated_cell_count')
+        accessions = set()
+        for name, value in content.items():
+            prefix, _, suffix = name.rpartition('_')
+            if suffix == 'accessions':
+                assert prefix, name
+                assert isinstance(value, list)
+                accessions.update(Accession(domain=prefix, value=v) for v in value)
+        self.accessions = accessions
+
+    def _accessions(self, domain: str) -> Set[str]:
+        return {a.value for a in self.accessions if a.domain == domain}
+
+    @property
+    def insdc_project_accessions(self) -> Set[str]:
+        warnings.warn("Project.insdc_project_accessions is deprecated. "
+                      "Use Project.accessions instead.", DeprecationWarning)
+        return self._accessions('insdc_project')
+
+    @property
+    def geo_series_accessions(self) -> Set[str]:
+        warnings.warn("Project.geo_series_accessions is deprecated. "
+                      "Use Project.accessions instead.", DeprecationWarning)
+        return self._accessions('geo_series')
+
+    @property
+    def array_express_accessions(self) -> Set[str]:
+        warnings.warn("Project.array_express_accessions is deprecated. "
+                      "Use Project.accessions instead.", DeprecationWarning)
+        return self._accessions('array_express')
+
+    @property
+    def insdc_study_accessions(self) -> Set[str]:
+        warnings.warn("Project.insdc_study_accessions is deprecated. "
+                      "Use Project.accessions instead.", DeprecationWarning)
+        return self._accessions('insdc_study')
 
     @property
     def laboratory_names(self) -> set:

test/cans/staging/eca05046-3dad-4e45-b86c-8720f33a5dde/2019-03-17T220646.332108Z/metadata.json

@@ -258,7 +258,8 @@
             }
         ],
         "insdc_project_accessions": [
-            "SRP000000"
+            "SRP000000",
+            "SRP000001"
         ],
         "geo_series_accessions": [
             "GSE00000"

test/test.py

@@ -23,6 +23,7 @@
 from more_itertools import one
 
 from humancellatlas.data.metadata.api import (
+    Accession,
     AgeRange,
     AnalysisFile,
     AnalysisProtocol,
@@ -313,10 +314,17 @@ def test_accessions_fields(self):
                           project_roles={'principal investigator'},
                           age_range=AgeRange(630720000.0, 630720000.0),
                           library_construction_methods={'10X v2 sequencing'},
-                          insdc_project_accessions={'SRP000000'},
+                          insdc_project_accessions={'SRP000000', 'SRP000001'},
                           geo_series_accessions={'GSE00000'},
                           array_express_accessions={'E-AAAA-00'},
-                          insdc_study_accessions={'PRJNA000000'})
+                          insdc_study_accessions={'PRJNA000000'},
+                          accessions={
+                              Accession('insdc_project', 'SRP000000'),
+                              Accession('insdc_project', 'SRP000001'),
+                              Accession('geo_series', 'GSE00000'),
+                              Accession('array_express', 'E-AAAA-00'),
+                              Accession('insdc_study', 'PRJNA000000')
+                          })
 
     def test_imaging_bundle(self):
         self._test_bundle(uuid='94f2ba52-30c8-4de0-a78e-f95a3f8deb9c',
@@ -396,6 +404,7 @@ def _assert_bundle(self, uuid, version, manifest, metadata_files,
                        preservation_methods=frozenset({None}),
                        library_construction_methods=frozenset(),
                        selected_cell_types=frozenset(),
+                       accessions=frozenset(),
                        insdc_project_accessions=frozenset(),
                        geo_series_accessions=frozenset(),
                        array_express_accessions=frozenset(),
@@ -450,6 +459,7 @@ def _assert_bundle(self, uuid, version, manifest, metadata_files,
         self.assertEqual(geo_series_accessions, project.geo_series_accessions)
         self.assertEqual(array_express_accessions, project.array_express_accessions)
         self.assertEqual(insdc_study_accessions, project.insdc_study_accessions)
+        self.assertEqual(accessions, project.accessions)
 
         root_entities = bundle.root_entities().values()
         root_entity_types = {type(e) for e in root_entities}
@@ -520,7 +530,7 @@ def _assert_bundle(self, uuid, version, manifest, metadata_files,
         return bundle
 
     def test_canned_staging_area(self):
-        ref = 'de355cad77ea7988040b6f1f5f2eafae58f686a8'
+        ref = '55628953e4b3a24a7d7798569b6082032bd07a6b'
         url = f'https://github.com/HumanCellAtlas/schema-test-data/tree/{ref}/tests'
         factory = GitHubStagingAreaFactory.from_url(url)
         staging_area = factory.load_staging_area()
@@ -529,8 +539,9 @@ def test_canned_staging_area(self):
             with self.subTest(link_id=link_id):
                 version, manifest, metadata_files = staging_area.get_bundle(link_id)
                 bundle = Bundle(link_id, version, manifest, metadata_files)
-                bundle_json = as_json(bundle)
-                self.assertEqual(link_id, bundle_json['uuid'])
+                self.assertEqual(bundle.uuid, UUID(link_id))
+                project = bundle.projects[UUID('90bf705c-d891-5ce2-aa54-094488b445c6')]
+                self.assertEqual(project.estimated_cell_count, 10000)
 
     def test_analysis_protocol(self):
         uuid = 'ffee7f29-5c38-461a-8771-a68e20ec4a2e'