Merge pull request #707 from dbmi-bgm/bm-somatic-cgap1

SomaticCGAP UI 1

CHANGELOG.rst

@@ -6,6 +6,15 @@ cgap-portal
 Change Log
 ----------
 
+13.5.2
+======
+`PR 707: Somatic CGAP UI V1 <https://github.com/dbmi-bgm/cgap-portal/pull/707>`_
+
+* SomaticAnalysis, Case, Search Item View updates for Somatic
+* Update SPC to 0.1.66
+* Update higlass-general-vcf to 0.1.4
+
+
 13.5.1
 ======
 
@@ -43,7 +52,6 @@ Change Log
 
 13.3.1
 ======
-*No PR: Staff-change Insert Updates*
 
 * Remove Victoria's user insert from master-inserts
 * Add Cesar's user insert to master-inserts

package.json

@@ -53,7 +53,7 @@
     "@gmod/tabix": "^1.5.3",
     "@gmod/vcf": "^5.0.6",
     "@hms-dbmi-bgm/react-workflow-viz": "0.1.5",
-    "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.64",
+    "@hms-dbmi-bgm/shared-portal-components": "git+https://github.com/4dn-dcic/shared-portal-components#0.1.66",
     "auth0-lock": "^11.33.0",
     "d3": "^5.16.0",
     "date-fns": "^2.28.0",
@@ -65,7 +65,7 @@
     "higlass-bigwig-datafetcher": "0.1.2",
     "higlass-clinvar": "0.2.5",
     "higlass-cohort": "0.3.4",
-    "higlass-general-vcf": "0.1.3",
+    "higlass-general-vcf": "0.1.4",
     "higlass-gnomad": "0.2.4",
     "higlass-orthologs": "0.2.4",
     "higlass-pileup": "1.5.0",

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 # Note: Various modules refer to this system as "encoded", not "cgap-portal".
 name = "encoded"
-version = "13.5.1"
+version = "13.5.2"
 description = "Computational Genome Analysis Platform"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

src/encoded/schemas/analysis.json

@@ -37,8 +37,20 @@
     },
     "columns": {
         "display_title": {
-            "title": "Title",
+            "title": "Analysis ID",
             "order": 10
+        },
+        "samples.tissue_type": {
+            "title": "Sample Types",
+            "order": 30
+        },
+        "samples.specimen_type": {
+            "title": "Sample Details",
+            "order": 50
+        },
+        "samples.workup_type": {
+            "title": "Sequencing",
+            "order": 60
         }
     }
 }

src/encoded/schemas/cohort_analysis.json

@@ -92,5 +92,11 @@
                 "linkTo": "Sample"
             }
         }
+    },
+    "columns": {
+        "samples.individual": {
+            "title": "Individual ID(s)",
+            "order": 20
+        }
     }
 }

src/encoded/schemas/somatic_analysis.json

@@ -88,5 +88,37 @@
                 "linkTo": "Sample"
             }
         }
+    },
+    "facets": {
+        "project.display_title": {
+            "title": "Project",
+            "order": 10
+        },
+        "samples.workup_type": {
+            "title": "Sequencing",
+            "order": 20
+        }
+    },
+    "columns": {
+        "display_title": {
+            "title": "Analysis ID",
+            "order": 10
+        },
+        "individual.display_title": {
+            "title": "Individual ID",
+            "order": 20
+        },
+        "samples.tissue_type": {
+            "title": "Sample Types",
+            "order": 30
+        },
+        "samples.specimen_type": {
+            "title": "Sample Details",
+            "order": 50
+        },
+        "samples.workup_type": {
+            "title": "Sequencing",
+            "order": 60
+        }
     }
 }