Merge branch 'master' into kmp_C4-393_npm_ci_optimization

package.json

@@ -101,7 +101,7 @@
   "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#0.0.2.77",
+    "@hms-dbmi-bgm/shared-portal-components": "github:4dn-dcic/shared-portal-components#0.0.2.82",
     "babel-polyfill": "^6.26.0",
     "d3": "^5.16.0",
     "detect-browser": "^3.0.1",

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 # Note: Various modules refer to this system as "encoded", not "cgap-portal".
 name = "encoded"
-version = "4.2.4"
+version = "4.3.4"
 description = "Clinical Genomics Analysis Platform"
 authors = ["4DN-DCIC Team <support@4dnucleome.org>"]
 license = "MIT"
@@ -42,7 +42,7 @@ certifi = ">=2020.11.8"
 chardet = "3.0.4"
 colorama = "0.3.3"
 dcicpyvcf = "1.0.0"
-dcicsnovault = "^4.0.12"
+dcicsnovault = "4.1.0"
 dcicutils = "^1.4.0"
 docutils = "0.12"
 elasticsearch = "6.4.0"
@@ -63,10 +63,10 @@ numpy = "1.19.1" # negspy needs it
 passlib = "1.6.5"
 PasteDeploy = "1.5.2"
 pbkdf2 = "1.3"
-Pillow = "3.1.1"  # Higher version might be causing a problem
+Pillow = "^6.2.2"  # 6.x.x should work for CGAP -Will 11/18/2020 
 plaster = "1.0"
 plaster-pastedeploy = "0.6"
-psutil = "^4.3.0"
+psutil = "^5.6.6"
 psycopg2-binary = "2.7.7"
 py = "1.4.31"
 pyasn1 = "0.1.9"

src/encoded/ingestion_listener.py

@@ -31,6 +31,8 @@
 from .ingestion.exceptions import UnspecifiedFormParameter, SubmissionFailure
 from .ingestion.processors import get_ingestion_processor
 from .inheritance_mode import InheritanceMode
+from .server_defaults import add_last_modified
+from .loadxl import LOADXL_USER_UUID
 from .types.ingestion import SubmissionFolio
 from .types.variant import build_variant_display_title, ANNOTATION_ID_SEP
 from .util import (
@@ -580,6 +582,7 @@ def build_and_post_variant(self, parser, record, project, institution):
         variant['institution'] = institution
         variant['status'] = SHARED  # default variant status to shared, so visible to everyone
         parser.format_variant_sub_embedded_objects(variant)
+        add_last_modified(variant, userid=LOADXL_USER_UUID)
         try:
             self.vapp.post_json('/variant', variant, status=201)
         except Exception:  # XXX: HTTPConflict is thrown and should be caught but does not work
@@ -623,7 +626,7 @@ def build_and_post_variant_samples(self, parser, record, project, institution, v
                 variant_name = sample['variant']
                 chrom = variant_name[variant_name.index('chr') + 3]  # find chr* and get *
                 sample.update(InheritanceMode.compute_inheritance_modes(sample, chrom=chrom))
-
+                add_last_modified(variant, userid=LOADXL_USER_UUID)
                 self.vapp.post_json('/variant_sample', sample, status=201)
             except Exception as e:
                 log.error('Encountered exception posting variant_sample: %s' % e)

src/encoded/schemas/variant_sample.json

@@ -551,6 +551,18 @@
         }
     },
     "facets": {
+        "AD_ALT": {
+            "title": "Allelic Depth (Alt)",
+            "aggregation_type": "range",
+            "default_hidden": true,
+            "order": 8,
+            "ranges": [
+                {"from": 1, "to": 4, "label": "Very Low"},
+                {"from": 5, "to": 9, "label": "Low"},
+                {"from": 10, "to": 19, "label": "Medium"},
+                {"from": 20, "label": "High"}
+            ]
+        },
         "AF": {
             "title": "VAF",
             "aggregation_type": "stats",