Read/write nested data as flattened parameter name to and from toml file

README.md

@@ -97,13 +97,15 @@ The catalog is a YAML formatted file which tells the app what nodes are availabl
 1. global: Description of global parameters
     * schema: What parameters are valid. Formatted as JSON schema draft 7.
     * uiSchema: How the form for filling the parameters should be rendered.
+    * tomlSchema: How toml keys are mapped to in-memory representation.
 2. nodes: Description of available nodes.
     * id: Identifier of node, for computers
     * label: Label of node, for humans
     * category: Category to which node belongs
     * description: Text describing what node needs, does and produces.
     * schema: What parameters are valid. Formatted as JSON schema draft 7.
     * uiSchema: How the form for filling the parameters should be rendered.
+    * tomlSchema: How toml keys are mapped to in-memory representation.
 3. catagories: Descriptions of node categories
     * name: Name of category
     * description: Description of category
@@ -128,6 +130,10 @@ Besides the built-in react-json-schema-form uiSchema fields the workflow builder
 
 Any property with a group uiSchema field will be grouped together with other properties with the same group in the form. The generated toml file will have the props ungrouped.
 
+### tomlSchema
+
+See [docs/tomlSchema.md](docs/tomlSchema.md).
+
 ### Catalog index
 
 In the worklfow builder you can pick a catalog from a list. This list gets downloaded from [public/catalog/index.json](public/catalog/index.json) and is formatted like

docs/tomlSchema.md

@@ -0,0 +1,347 @@
+# tomlSchema
+
+Any array or object value can be written in different ways to a toml file.
+Use the toml schema in the catalog to overwrite the default behaviour.
+
+The default behavior is to write the value as a nested structure like
+
+In memory have parameter object like
+
+```js
+{
+    key1: [ 1, 2 ], // Array of scalar
+    key2: [ "a", "b" ],  // Array of scalar
+    key3: { a: 1, b: 2},  // Object
+    key4: { a: [ 1, 2 ]},  // Object with array of scalar
+    key5: [ { a: 1 }, { a: 2 }],  // Array with objects
+    key6: [ { a: [ 1, 2 ]} ],  // Array with oboject with array of scalar
+    key7: [ [ 1, 2], [ 3 ,4 ] ],  // Array of array of scalar
+    key8: [ [ { a: 1 }, { a: 2 }], [ { a: 3 } ,{ a: 4 } ] ],  // Array of array of object
+}
+```
+
+The parameter object JSON shema is defined in the catalog.
+
+The resulting toml would look like
+
+```toml
+key1 = [ 1, 2 ]
+key2 = [ "a", "b" ]
+key3.a = 1
+key3.b = 2
+key4.a = [ 1, 2 ]
+key5 = [ { a = 1 }, { a = 2 }]
+key6 = [ { a = [ 1, 2 ]} ]
+key7 = [ [ 1, 2], [ 3 ,4 ] ]
+key8 = [ [ { a = 1 }, { a = 2 }], [ { a = 3 } ,{ a = 4 } ] ]
+```
+
+The tomlSchema object follows the tree structure of the schema hierarchy.
+
+Special keywords in tomlSchema:
+
+1. **indexed**, when true will have array index appended to key
+2. **flatten**, when true will have object property names appended to key
+3. **sectioned**, when true will write children inside own table (for example `[<module>.<key>]`)
+4. **items**, to nest a toml schema for an array item
+5. **properties**, to nest a toml schema for an object property
+
+Below are examples of supported toml schema snippets.
+
+## Array of scalars
+
+In toml
+
+```toml
+param_1 = 11
+param_2 = 22
+param_3 = 33
+```
+
+In catalog
+
+```yaml
+schema:
+  type: object
+  properties:
+    param:
+      type: array
+      items:
+        type: number
+tomlSchema:
+  param:
+    indexed: true
+```
+
+In memory
+
+```json
+{
+  "param": [11, 22, 33]
+}
+```
+
+## Array of objects flattened
+
+In toml
+
+```toml
+name_something_1 = 11
+name_else_1 = 22
+name_something_2 = 33
+name_else_2 = 44
+```
+
+In catalog
+
+```yaml
+schema:
+  type: object
+  properties:
+    name:
+      type: array
+      items:
+        type: object
+        properties:
+          something:
+            type: number
+          else:
+            type: number
+tomlSchema:
+  name:
+    indexed: true
+    items:
+      flatten: true
+```
+
+In memory
+
+```json
+{
+  "name": [{
+    "something": 11,
+    "else": 22,
+  }, {
+    "something": 33,
+    "else": 44,
+  }]
+}
+```
+
+## Array of objects sectioned
+
+In toml
+
+```toml
+[[name]]
+something = 11
+else = 22
+
+[[name]]
+something = 33
+else = 44
+```
+
+In catalog
+
+```yaml
+schema:
+  type: object
+  properties:
+    name:
+      type: array
+      items:
+        type: object
+        properties:
+          something:
+            type: number
+          else:
+            type: number
+tomlSchema:
+  name:
+    items:
+      sectioned: true
+```
+
+In memory
+
+```json
+{
+  "name": [{
+    "something": 11,
+    "else": 22,
+  }, {
+    "something": 33,
+    "else": 44,
+  }]
+}
+```
+
+## Array of array of objects
+
+In toml
+
+```toml
+fle_sta_1_1 = 11
+fle_end_1_1 = 22
+fle_sta_1_2 = 33
+fle_end_1_2 = 44
+fle_sta_2_1 = 55
+fle_end_2_1 = 66
+```
+
+In catalog
+
+```yaml
+schema:
+  type: object
+  additionalProperties: false
+  properties:
+    fle:
+      type: array
+      description: Outer array is molecule index
+      items:
+        type: array
+        description: Inner array is segment index
+        items:
+          type: object
+          properties:
+            sta:
+              title: Starting residue number
+              type: number
+            end:
+              title: End residue number
+              type: number
+          additionalProperties: false
+tomlSchema:
+  fle:
+    indexed: true
+    items:
+      indexed: true
+      items:
+        flatten: true
+```
+
+In memory
+
+```json
+{
+    "fle": [
+        [
+            {
+                "sta": 11,
+                "end": 22
+            },
+            {
+                "sta": 33,
+                "end": 44
+            }
+        ],
+        [
+            {
+                "sta": 55,
+                "end": 66
+            }
+        ]
+    ]
+}
+```
+
+## Array of objects with object as toml table and scalar as array prop
+
+In toml
+
+```toml
+[topoaa.mol_1]
+cyclicpept = false
+hisd_1 = 13
+hisd_2 = 42
+
+[topoaa.mol_2]
+cyclicpept = true
+hisd_1 = 314
+hisd_2 = 512
+```
+
+In catalog
+
+```yaml
+schema:
+  type: object
+  properties:
+    mol:
+      type: array
+      items:
+        type: object
+        properties:
+          cyclicpept:
+            type: boolean
+          hisd:
+            type: array
+            items:
+                type: number
+tomlSchema:
+  mol:
+    indexed: true
+    items:
+      sectioned: true
+      properties:
+        hisd:
+          indexed: true
+```
+
+In memory
+
+```json
+{
+  "mol": [{
+    "cyclicpept": false,
+    "hisd": [13, 42]
+  }, {
+    "cyclicpept": true,
+    "hisd": [314, 512]
+  }]
+}
+```
+
+## Node parameter where value is an object as section
+
+In toml
+
+```toml
+[somenode]
+
+[somenode.foo]
+bar.bla = 'hi'
+```
+
+In catalog
+
+```yaml
+schema:
+  type: object
+  properties:
+    foo:
+      type: object
+      properties:
+        bar:
+          type: object
+          properties:
+            bla:
+              type: string
+tomlSchema:
+  foo:
+    sectioned: true
+```
+
+In memory parameters for node called `somenode`.
+
+```json
+{
+  "foo": {
+    "bar": {
+      "bla": "hi"
+    }
+  }
+}
+```