Merge pull request #415 from dbmi-bgm/c4_670

C4-670 Implement 'add_no_value' schema parameter

Makefile

@@ -148,7 +148,7 @@ test-any:
 	poetry run python -m pytest -vv -r w --timeout=200
 
 test-npm:
-	poetry run python -m pytest -vv -r w --timeout=200 -m "not manual and not integratedx and not performance and not broken and not sloppy and not indexing"
+	poetry run python -m pytest -vv -r w --timeout=300 -m "not manual and not integratedx and not performance and not broken and not sloppy and not indexing"
 
 test-unit:
 	poetry run python -m pytest -vv -r w --timeout=200 -m "not manual and not integratedx and not performance and not broken and not sloppy and indexing"

package.json

@@ -88,7 +88,7 @@
   "dependencies": {
     "@fortawesome/fontawesome-free": "^5.14.0",
     "@hms-dbmi-bgm/react-workflow-viz": "0.1.4",
-    "@hms-dbmi-bgm/shared-portal-components": "github:4dn-dcic/shared-portal-components#0.1.11",
+    "@hms-dbmi-bgm/shared-portal-components": "github:4dn-dcic/shared-portal-components#0.1.12",
     "babel-polyfill": "^6.26.0",
     "d3": "^5.16.0",
     "detect-browser": "^3.0.1",

pyproject.toml

@@ -42,7 +42,7 @@ certifi = ">=2020.11.8"
 chardet = "3.0.4"
 colorama = "0.3.3"
 dcicpyvcf = "1.0.0"
-dcicsnovault = "^4.7.5"
+dcicsnovault = "^4.8.1"
 dcicutils = "1.15.0"
 elasticsearch = "6.8.1"
 execnet = "1.4.1"

src/encoded/ingestion/table_utils.py

@@ -29,7 +29,7 @@ class MappingTableHeader:
         not vary across . """
     HEADER_ROW_INDEX = 2
     INTEGER_FIELDS = ['no', 'maximum_length_of_value', 'default', 'min', 'max']
-    BOOLEAN_FIELDS = ['is_list', 'calculated_property', 'embedded_field', 'do_import']
+    BOOLEAN_FIELDS = ['is_list', 'calculated_property', 'embedded_field', 'do_import', 'add_no_value']
     STRING_FIELDS = ['field_name', 'vcf_field', 'source_name', 'source_version', 'sub_embedding_group',
                      'annotation_category', 'separator', 'description',
                      'scope', 'schema_title', 'pattern', 'link', 'abbreviation']
@@ -546,11 +546,11 @@ def extend_variant_sample_columns(cols):
 
     @staticmethod
     def add_extra_variant_sample_facets(facs):
-        '''
+        """
         Order of a Facet Group within top-level FacetList is determined by `min(grouped facet 1, grouped facet 2, ...)`
         which is then used for sorting relative to all other top-level facets' and facet groups' orders.
         Facets within a group are sorted relative to each other.
-        '''
+        """
         facs["variant.genes.genes_most_severe_gene.display_title"] = {
             "title": "Gene",
             "order": 1,
@@ -676,8 +676,6 @@ def add_extra_variant_sample_facets(facs):
                 "grouping": "Genotype",
                 "default_hidden": True
             },
-
-
             "associated_genotype_labels.sister_genotype_label": {
                 "title": "Sister Genotype",
                 "order": 1001,
@@ -702,8 +700,6 @@ def add_extra_variant_sample_facets(facs):
                 "grouping": "Genotype",
                 "default_hidden": True
             },
-
-
             "associated_genotype_labels.brother_genotype_label": {
                 "title": "Brother Genotype",
                 "order": 1005,
@@ -728,8 +724,6 @@ def add_extra_variant_sample_facets(facs):
                 "grouping": "Genotype",
                 "default_hidden": True
             },
-
-
             "associated_genotype_labels.daughter_genotype_label": {
                 "title": "Daughter Genotype",
                 "order": 1009,
@@ -754,8 +748,6 @@ def add_extra_variant_sample_facets(facs):
                 "grouping": "Genotype",
                 "default_hidden": True
             },
-
-
             "associated_genotype_labels.son_genotype_label": {
                 "title": "Son Genotype",
                 "order": 1013,
@@ -802,6 +794,17 @@ def generate_variant_sample_schema(self, sample_props, cols, facs, variant_cols,
         schema['title'] = 'Sample Variant'
         schema['description'] = "Schema for variant info for sample"
         schema['id'] = '/profiles/variant_sample.json'
+        schema['mixinProperties'] = [
+            {"$ref": "mixins.json#/schema_version"},
+            {"$ref": "mixins.json#/uuid"},
+            {"$ref": "mixins.json#/aliases"},
+            {"$ref": "mixins.json#/submitted"},
+            {"$ref": "mixins.json#/modified"},
+            {"$ref": "mixins.json#/status"},
+            {"$ref": "mixins.json#/attribution"},
+            {"$ref": "mixins.json#/notes"},
+            {"$ref": "mixins.json#/static_embeds"},
+        ]
         schema['properties'] = sample_props
         schema['properties']['schema_version'] = {'default': '1'}
         schema['properties']['variant'] = {  # link to single variant
@@ -929,6 +932,18 @@ def generate_variant_schema(self, var_props, cols, facs):
         schema['title'] = 'Variants'
         schema['description'] = "Schema for variants"
         schema['id'] = '/profiles/variant.json'
+        schema['mixinProperties'] = [
+            {"$ref": "mixins.json#/schema_version"},
+            {"$ref": "mixins.json#/uuid"},
+            {"$ref": "mixins.json#/aliases"},
+            {"$ref": "mixins.json#/submitted"},
+            {"$ref": "mixins.json#/modified"},
+            {"$ref": "mixins.json#/status"},
+            {"$ref": "mixins.json#/attribution"},
+            {"$ref": "mixins.json#/notes"},
+            {"$ref": "mixins.json#/interpretation"},
+            {"$ref": "mixins.json#/static_embeds"},
+        ]
         schema['properties'] = var_props
         schema['properties']['hg19'] = {  # required for testing :( - will 1-8-2021
             "title": "hg19 Coordinates",

src/encoded/ingestion_listener.py

@@ -249,7 +249,8 @@ def process_submission(*, submission_id, ingestion_type, app, bundles_bucket=Non
     except KeyError as e:
         debuglog("Manifest data is missing 'email' field.")
         if DEBUG_SUBMISSIONS:
-            import pdb; pdb.set_trace()
+            pass
+            # import pdb; pdb.set_trace()
     debuglog("processing submission %s with email %s" % (submission_id, email))
     with vapp_for_email(email=email, app=app) as vapp:
         if DEBUG_SUBMISSIONS:

src/encoded/schemas/annotation_field.json

@@ -188,6 +188,11 @@
             "title": "Abbreviation",
             "description": "A shorter name for this field, used by the UI",
             "type": "string"
+        },
+        "add_no_value": {
+            "title": "Add No Value",
+            "description": "Specify 'true' to include documents with 'No value' for this field when 0 is in the search range",
+            "type": "boolean"
         }
     },
     "facets": {