Merge 3285e6a into 589a726

src/encoded/commands/create_mapping_on_deploy.py

@@ -33,6 +33,7 @@
     'FileReference',
     'Image',
     'Gene',
+    'GeneList',
     'Phenotype',
     'Disorder',
     'Individual',

src/encoded/schemas/gene_list.json

@@ -0,0 +1,58 @@
+{
+    "title": "Gene List",
+    "description": "Groups of genes that are relecant for a disease or condition",
+    "id": "/profiles/gene_list.json",
+    "$schema": "http://json-schema.org/draft-04/schema#",
+    "type": "object",
+    "required": ["institution", "project", "title"],
+    "identifyingProperties": ["uuid", "aliases"],
+    "additionalProperties": false,
+    "mixinProperties": [
+        { "$ref": "mixins.json#/schema_version" },
+        { "$ref": "mixins.json#/uuid" },
+        { "$ref": "mixins.json#/status" },
+        { "$ref": "mixins.json#/aliases" },
+        { "$ref": "mixins.json#/attribution" },
+        { "$ref": "mixins.json#/submitted" },
+        { "$ref": "mixins.json#/modified" },
+        { "$ref": "mixins.json#/tags" },
+        { "$ref": "mixins.json#/notes" }
+    ],
+    "properties": {
+        "schema_version": {
+            "default": "1"
+        },
+        "title": {
+            "title": "Title",
+            "description": "Title for this Family",
+            "type": "string"
+        },
+        "genes" : {
+            "title" : "Genes",
+            "type" : "array",
+            "uniqueItems": true,
+            "items" : {
+                "title" : "Gene",
+                "type" : "string",
+                "linkTo" : "Gene"
+            }
+        },
+        "disorders" : {
+            "title" : "Related Disorders",
+            "description": "Disorders that are related to this gene list",
+            "type" : "array",
+            "uniqueItems": true,
+            "items" : {
+                "title" : "Disorder",
+                "type" : "string",
+                "linkTo" : "Disorder"
+            }
+        },
+        "source_file": {
+            "title" : "Source File",
+            "description": "The original gene list file used for generating this gene list item",
+            "type" : "string",
+            "linkTo": "Document"
+        }
+    }
+}

src/encoded/tests/data/demo_inserts/document.json

@@ -0,0 +1,29 @@
+[
+    {
+        "attachment": {
+            "download": "bgm0339-koray_V4.pbxml",
+            "type": "application/proband+xml",
+            "href": "@@download/attachment/bgm0339-koray_V4.pbxml",
+            "md5sum": "8dae78069f85fce77ea7c0a6e43e0274",
+            "blob_id": "9fdd87b7-a04d-4c93-b7e0-539527072167"
+        },
+        "date_created": "2020-07-21T17:33:45.486329+00:00",
+        "submitted_by": "986b362f-4eb6-4a9c-8173-3ab267221234",
+        "last_modified": {
+            "date_modified": "2020-07-21T18:00:23.009102+00:00",
+            "modified_by": "986b362f-4eb6-4a9c-8173-3ab267221234"
+        },
+        "institution": "828cd4fe-ebb0-4b36-ccbb-d2e3a36ca234",
+        "schema_version": "1",
+        "status": "in review",
+        "project": "91336042-f277-4f69-97e5-5c8a5f6d6058",
+        "uuid": "0938cab5-5f81-4da7-b299-46e4aa5d63f9"
+    },
+    {
+        "project": "12a92962-8265-4fc0-b2f8-cf14f05db58b",
+        "institution": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
+        "attachment": "gene_lists/breast_cancer.txt",
+        "status": "in review",
+        "uuid": "0938cab5-5f81-4da7-b299-46e4aad22222"
+    }
+]

src/encoded/tests/data/demo_inserts/gene_list.json

@@ -0,0 +1,40 @@
+[
+    {
+        "project": "12a92962-8265-4fc0-b2f8-cf14f05db58b",
+        "institution": "828cd4fe-ebb0-4b36-a94a-d2e3a36cc989",
+        "title": "Breast Cancer Example Gene List",
+        "status": "in review",
+        "genes": [
+            "d24c1007-93cf-4378-870a-1d4808871412",
+            "78dd604e-67e6-495e-8cf9-a3e8b7f45d7b",
+            "05778ccc-2648-411a-a4a5-02b6a717acb4",
+            "d706c51b-9d18-475f-9701-942ef0881a18",
+            "914e6aea-faa0-4235-ad18-21235aed59bb",
+            "a113d699-e511-4458-9005-deedaf089414",
+            "bcaef33a-f441-42c6-abb7-0059c38cd59e",
+            "80807d97-58ae-410f-b10b-5cac8ce61778",
+            "c69d356c-4954-40d2-8cd6-89932b4d8830",
+            "164d8c15-84e6-49b2-b684-77f29ac84676",
+            "a8f1eb13-720e-4423-a572-10797bd70164",
+            "b3929fa4-01e4-4c1e-8f1b-d3906da8145a",
+            "58c9b6a9-5c2e-41fa-b6f2-5256d37581df",
+            "bf5e24fa-3eaf-4dd7-aa59-62c65bbb805f",
+            "b833a22c-6bec-47e8-922f-24467b8e5265",
+            "a5d84ab0-e7c7-41ae-97c0-82b56ebc7518",
+            "0c0c9069-19ff-4e56-91aa-feab75624c31",
+            "37e2bbb7-747c-473c-918c-84cc5320f4ff",
+            "aaceaa46-0229-4318-a957-c4edef09f21e",
+            "8d5040fd-73d2-4a8f-92ed-228111cb186f",
+            "508ead8c-7cd2-452f-a6b5-6ef1127b9155",
+            "47d8e129-975e-4d69-b74d-cb729daa0c96",
+            "f0c87332-17af-44f1-a5c1-78f80422fd02",
+            "f39cae40-efdb-4a56-b800-c7a63e9ce1f4",
+            "0c274c6f-95de-4632-b9db-7b3d2998673f",
+            "349292f5-c053-4e4b-9b0d-5f5ba0e3f0fd",
+            "b043c061-6598-486e-8660-9ee31ee4e863",
+            "82915e28-9d7a-4641-8572-417a2430309e"
+        ],
+        "source_file": "0938cab5-5f81-4da7-b299-46e4aad22222",
+        "uuid": "0938cab5-5f81-4da7-b299-46e4aae22222"
+    }
+]

src/encoded/tests/data/documents/gene_lists/breast_cancer.txt

@@ -0,0 +1,28 @@
+ABRAXAS1 
+AKT1 
+ATM 
+BARD1 
+BRCA1 
+BRCA2 
+BRIP1 
+CDH1 
+CHEK2 
+FANCC 
+FANCM 
+MRE11 
+MUTYH 
+NBN 
+NF1 
+PALB2 
+PIK3CA 
+PTEN 
+RAD50 
+RAD51C 
+RAD51D 
+RECQL 
+RINT1 
+SDHB 
+SDHD 
+STK11 
+TP53
+XRCC2

src/encoded/tests/data/inserts/gene.json

@@ -0,0 +1,30 @@
+[
+    {
+        "project": "12a92962-8265-4fc0-b2f8-cf14f05db58b",
+        "status": "released",
+        "uuid": "cc7d83a2-6886-4ca0-9402-7c49734c1111",
+        "gene_symbol": "my_gene_1",
+        "ensgid": "ENSGmock0100001"
+    },
+    {
+        "project": "12a92962-8265-4fc0-b2f8-cf14f05db58b",
+        "status": "released",
+        "uuid": "cc7d83a2-6886-4ca0-9402-7c49734c2222",
+        "gene_symbol": "my_gene_2",
+        "ensgid": "ENSGmock0100002"
+    },
+    {
+        "project": "12a92962-8265-4fc0-b2f8-cf14f05db58b",
+        "status": "released",
+        "uuid": "cc7d83a2-6886-4ca0-9402-7c49734c3333",
+        "gene_symbol": "my_gene_3",
+        "ensgid": "ENSGmock0100003"
+    },
+    {
+        "project": "12a92962-8265-4fc0-b2f8-cf14f05db58b",
+        "status": "released",
+        "uuid": "cc7d83a2-6886-4ca0-9402-7c49734c4444",
+        "gene_symbol": "my_gene_4",
+        "ensgid": "ENSGmock0100004"
+    }
+]

src/encoded/tests/data/inserts/gene_list.json

@@ -0,0 +1,17 @@
+[
+    {
+        "project": "12a92962-8265-4fc0-b2f8-cf14f05db58b",
+        "status": "released",
+        "uuid": "cc7d83a2-6886-4ca0-9402-7c49734l1111",
+        "title": "Test Gene List for Green Thumb condition",
+        "genes": [
+            "cc7d83a2-6886-4ca0-9402-7c49734c1111",
+            "cc7d83a2-6886-4ca0-9402-7c49734c2222",
+            "cc7d83a2-6886-4ca0-9402-7c49734c3333",
+            "cc7d83a2-6886-4ca0-9402-7c49734c4444"
+        ],
+        "disorders": [
+            "71bae2e1-4532-45cf-8fd7-958b47d7e446"
+        ]
+    }
+]

src/encoded/tests/datafixtures.py

@@ -8,7 +8,7 @@
     'file_format', 'variant_consequence', 'phenotype',
     'cohort', 'family', 'individual', 'sample', 'workflow',
     'access_key', 'disorder', 'document', 'file_fastq',
-    'file_processed', 'file_reference', 'gene', 'sample_processing',
+    'file_processed', 'file_reference', 'gene', 'gene_list', 'sample_processing',
     'case', 'report', 'page', 'quality_metric_fastqc', 'evidence_dis_pheno',
     'quality_metric_bamcheck', 'quality_metric_qclist', 'quality_metric_wgs_bamqc',
     'quality_metric_cmphet', 'quality_metric_vcfcheck', 'quality_metric_workflowrun',