SN Generic Config item

CHANGELOG.rst

@@ -7,6 +7,13 @@ smaht-portal
 Change Log
 ----------
 
+0.168.0
+=======
+`PR 413 SN Generic Config item <https://github.com/smaht-dac/smaht-portal/pull/413>`
+
+* Add new item, GenericConfig, that can be used to hold JSON objects
+
+
 0.167.0
 =======
 `PR 412 Submission Status page: Add Donor and Tissue select fields <https://github.com/smaht-dac/smaht-portal/pull/412>`

pyproject.toml

@@ -1,6 +1,6 @@
 [tool.poetry]
 name = "encoded"
-version = "0.167.0"
+version = "0.168.0"
 description = "SMaHT Data Analysis Portal"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"

src/encoded/project/loadxl.py

@@ -18,6 +18,7 @@ class SMaHTProjectLoadxl(SnovaultProjectLoadxl):
         "static_section",
         "page",
         "filter_set",
+        "generic_config",
         "higlass_view_config",
         "ingestion_submission",
         "ontology",

src/encoded/schemas/generic_config.json

@@ -0,0 +1,67 @@
+{
+    "title": "Generic Configuration",
+    "description": "Configuration details for general use",
+    "$id": "/profiles/generic_config.json",
+    "$schema": "https://json-schema.org/draft/2020-12/schema",
+    "type": "object",
+    "required": [
+        "identifier",
+        "body"
+    ],
+    "identifyingProperties": [
+        "aliases",
+        "identifier",
+        "uuid"
+    ],
+    "additionalProperties": false,
+    "mixinProperties": [
+        {
+            "$ref": "mixins.json#/aliases"
+        },
+        {
+            "$ref": "mixins.json#/attribution"
+        },
+        {
+            "$ref": "mixins.json#/description"
+        },
+        {
+            "$ref": "mixins.json#/identifier"
+        },
+        {
+            "$ref": "mixins.json#/modified"
+        },
+        {
+            "$ref": "mixins.json#/schema_version"
+        },
+        {
+            "$ref": "mixins.json#/status"
+        },
+        {
+            "$ref": "mixins.json#/submitted"
+        },
+        {
+            "$ref": "mixins.json#/tags"
+        },
+        {
+            "$ref": "mixins.json#/title"
+        },
+        {
+            "$ref": "mixins.json#/uuid"
+        },
+        {
+            "$ref": "mixins.json#/version"
+        }
+    ],
+    "properties": {
+        "schema_version": {
+            "default": "1"
+        },
+        "body": {
+            "additionalProperties": true,
+            "description": "The config JSON",
+            "formInput": "code",
+            "title": "JSON Configuration",
+            "type": "object"
+        }
+    }
+}

src/encoded/tests/data/workbook-inserts/generic_config.json

@@ -0,0 +1,35 @@
+[
+    {
+        "uuid": "d263fb0c-5476-4b16-bcfa-48623a2b8b0b",
+        "identifier": "eqm_column_mappings",
+        "tags": [
+            "external_quality_metrics"
+        ],
+        "version": "1",
+        "body": {
+            "version": "2.0.0",
+            "sheet_mappings": {
+                "DuplexSeq_ExternalQualityMetric": "duplexseq_external_quality_metric",
+                "DSA_ExternalQualityMetric": "dsa_external_quality_metric"
+            },
+            "column_mappings": {
+                "duplexseq_external_quality_metric": {
+                    "total_raw_reads_sequenced": {
+                        "qc_values#.derived_from": "{name}",
+                        "qc_values#.value": "{value:integer}",
+                        "qc_values#.key": "Total Raw Reads Sequenced",
+                        "qc_values#.tooltip": "# of reads (150bp)"
+                    }
+                },
+                "dsa_external_quality_metric": {
+                    "contig_l50": {
+                        "qc_values#.derived_from": "{name}",
+                        "qc_values#.value": "{value: integer}",
+                        "qc_values#.key": "Contig L50",
+                        "qc_values#.tooltip": "L50 of contigs: the count of the smallest number of contigs whose total length makes up 50% of the assembly size"
+                    }
+                }
+            }
+        }
+    }
+]

src/encoded/types/generic_config.py

@@ -0,0 +1,22 @@
+from snovault import collection, load_schema
+
+from .acl import ONLY_ADMIN_VIEW_ACL
+from .base import Item
+
+
+@collection(
+    name='generic-configs',
+    unique_key='generic_config:identifier',
+    acl=ONLY_ADMIN_VIEW_ACL,
+    properties={
+        'title': 'Generic Config',
+        'description': 'Configurations for general use',
+    })
+class GenericConfig(Item):
+    """
+    Item type which contains a JSON `body` property and other metadata.
+    """
+    item_type = 'generic_config'
+    schema = load_schema("encoded:schemas/generic_config.json")
+    embedded_list = []
+    name_key = None