Merge branch 'master' into kmp_pytest_4-5-0_prep

.travis.yml

@@ -50,8 +50,6 @@ before_install:
 install:
 - pip install --upgrade pip
 - pip install poetry
-- pip install coveralls
-- pip install codacy-coverage
 - poetry install
 - make npm-setup
 before_script:

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 # Note: Various modules refer to this system as "encoded", not "cgap-portal".
 name = "encoded"
-version = "2.1.7"
+version = "2.1.11"
 description = "Clinical Genomics Analysis Platform"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"
@@ -115,7 +115,9 @@ xlwt = "1.2.0"
 "zope.sqlalchemy" = "1.3"
 
 [tool.poetry.dev-dependencies]
-coverage = "4.0.3"
+coverage = ">=5.2"
+codacy-coverage = ">=1.3.11"
+coveralls = ">=2.1.1"
 flake8 = "^3.7.8"
 flaky = "3.6.1"
 # flask only for moto[server]

setup.cfg

@@ -1,8 +1,8 @@
 [flake8]
-max-line-length = 100
+max-line-length = 160
 [coverage:run]
 branch = True
-omit = 
+omit =
     */encode_schemas/*
     */encode_types/*
     */tests/*

src/encoded/commands/create_mapping_on_deploy.py

@@ -19,13 +19,14 @@
     'AccessKey',
     'Cohort',
     'Family',
+    'FilterSet',
+    'Nexus',
     'User',
     'Workflow',
     'WorkflowMapping',
     'WorkflowRun',
     'WorkflowRunAwsem',
     'VariantConsequence',
-    'Disorder',
     'FileFormat',
     'FileFastq',
     'FileProcessed',
@@ -36,7 +37,6 @@
     'Disorder',
     'Individual',
     'Case',
-    'FilterSet',
     'Report',
     'Document',
     'QualityMetricBamcheck',
@@ -46,12 +46,12 @@
     'QualityMetricCmphet',
     'QualityMetricWorkflowrun',
     'QualityMetricVcfcheck',
+    'QualityMetricVcfqc',
     'TrackingItem',
     'Software',
     'Sample',
     'SampleProcessing',
     'StaticSection',
-    'Document',
     'Page',
     'AnnotationField',
     'Variant',

src/encoded/loadxl.py

@@ -31,21 +31,10 @@ def includeme(config):
 
 # order of items references with linkTo in a field in  'required' in schemas
 ORDER = [
-    'user',
     'project',
     'institution',
+    'user',
     'file_format',
-    'phenotype',
-    'disorder',
-    # 'variant_consequence',
-    # 'variant', # links to ^ variant_consequence
-    # 'variant_sample', # links to ^ variant
-    'cohort',
-    'family',
-    'individual',
-    'case',
-    'report',
-    'sample',
     'workflow',
 ]
 

src/encoded/schemas/case.json

@@ -33,6 +33,12 @@
             "description": "Description of the case",
             "type": "string"
         },
+        "family": {
+            "title": "Family",
+            "description": "Primary family this case is associated with",
+            "type": "string",
+            "linkTo": "Family"
+        },
         "individual": {
             "title": "Individual",
             "description": "The individual who comprises the case",
@@ -50,6 +56,12 @@
             "description": "The report generated from this case",
             "type": "string",
             "linkTo": "Report"
+        },
+        "cohort": {
+            "title" : "Cohort",
+            "description": "Cohort of the family",
+            "type" : "string",
+            "linkTo": "Nexus"
         }
     }
 }