SNO-201-add-search-config-registry (#3855)

Author: keenangraham

setup.py

@@ -5,7 +5,7 @@
 README = open(os.path.join(here, 'README.md')).read()
 CHANGES = open(os.path.join(here, 'CHANGES.rst')).read()
 # Edit Snovault version after the `@` here, can be a branch or tag
-SNOVAULT_DEP = "git+https://github.com/ENCODE-DCC/snovault.git@1.0.56"
+SNOVAULT_DEP = "git+https://github.com/ENCODE-DCC/snovault.git@SNO-201-add-search-config-registry"
 
 INSTALL_REQUIRES = [
     "PasteDeploy==2.1.0",

src/encoded/__init__.py

@@ -267,6 +267,7 @@ def main(global_config, **local_config):
     # registered.
     config.include('.upgrade')
     config.include('.audit')
+    config.include('.searches.configs')
 
     app = config.make_wsgi_app()
 

src/encoded/searches/__init__.py

@@ -0,0 +1 @@
+

src/encoded/searches/configs.py

@@ -0,0 +1,59 @@
+from snovault.elasticsearch.searches.interfaces import SEARCH_CONFIG
+from snovault.elasticsearch.searches.configs import search_config
+
+
+def includeme(config):
+    config.scan(__name__)
+    config.registry[SEARCH_CONFIG].add_aliases(ALIASES)
+    config.registry[SEARCH_CONFIG].add_defaults(DEFAULTS)
+
+
+@search_config(
+    name='custom'
+)
+def custom_search_config():
+    return {
+        'facets': {
+            'assay_title': {
+                'title': 'Assay title',
+                'type': 'typeahead',
+                'open_on_load': True
+            },
+            'status': {
+                'title': 'Status',
+                "open_on_load": True
+            },
+            'target.label': {
+                'title': 'Target of assay',
+                'type': 'typeahead',
+                'length': 'long',
+                'open_on_load': True
+            },
+            'biosample_ontology.term_name' : {
+                'title': 'Biosample term name',
+                'type': 'typeahead',
+                'length': 'long',
+                "open_on_load": True
+            },
+        },
+        'columns': {},
+        'matrix': {},
+        'boost_values': {},
+        'fields': {},
+    }
+
+
+ALIASES = {
+    'DonorSubtypes': [
+        'HumanDonor',
+        'FlyDonor',
+        'WormDonor',
+        'MouseDonor',
+    ]
+}
+
+
+DEFAULTS = {
+    'Donor': ['DonorSubtypes'],
+    ('Experiment', 'FunctionalCharacterizationExperiment'): ['Experiment'],
+}

src/encoded/searches/defaults.py

@@ -16,6 +16,7 @@
     'remove',
     'sort',
     'type',
+    'config',
 ]
 
 FREE_TEXT_QUERIES = [

src/encoded/tests/test_auditor.py

@@ -87,6 +87,7 @@ def test_declarative_config(dummy_request):
     config = Configurator()
     config.include('snovault.config')
     config.include('snovault.auditor')
+    config.include('snovault.elasticsearch.searches.configs')
     config.include('.testing_auditor')
     config.commit()
 

src/encoded/types/base.py

@@ -27,6 +27,7 @@
     AfterModified,
     BeforeModified
 )
+from snovault.elasticsearch.searches.configs import search_config
 
 
 @lru_cache()
@@ -380,6 +381,23 @@ def set_status(self, new_status, request, parent=True):
         return True
 
 
+@search_config(
+    name='Item'
+)
+def item_search_config():
+    return {
+        'facets': {
+            'type': {
+                'title': 'Data Type',
+                'exclude': ['Item']
+            },
+            'status': {
+                'title': 'Item status'
+            },
+        }
+    }
+
+
 class SharedItem(Item):
     ''' An Item visible to all authenticated users while "in progress".
     '''

src/encoded/types/characterization.py

@@ -32,6 +32,7 @@
     })
 class Characterization(ItemWithAttachment, Item):
     base_types = ['Characterization'] + Item.base_types
+    schema = load_schema('encoded:schemas/characterization.json')
     embedded = ['lab', 'award', 'submitted_by', 'documents']
     set_status_up = [
         'documents',

src/encoded/types/dataset.py

@@ -69,6 +69,7 @@ def calculate_assembly(request, files_list, status):
     })
 class Dataset(Item):
     base_types = ['Dataset'] + Item.base_types
+    schema = load_schema('encoded:schemas/dataset.json')
     embedded = [
         'analyses',
         'files',
@@ -558,6 +559,14 @@ def superseded_by(self, request, superseded_by):
         return paths_filtered_by_status(request, superseded_by)
 
 
+@abstract_collection(
+    name='file-set',
+    unique_key='accession',
+    properties={
+        'title': "File set",
+        'description': 'A set of files.',
+    }
+)
 class FileSet(Dataset):
     item_type = 'file_set'
     base_types = ['FileSet'] + Dataset.base_types

src/encoded/types/donor.py

@@ -21,6 +21,7 @@
     })
 class Donor(Item):
     base_types = ['Donor'] + Item.base_types
+    schema = load_schema('encoded:schemas/donor.json')
     embedded = [
         'organism',
         'characterizations',