Allow to configure node label in catalog

Fixes #151
i-VRESSE · Oct 9, 2024 · c687600 · c687600
1 parent 8fdaf87
commit c687600
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diff --git a/CHANGELOG.md b/CHANGELOG.md
@@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 ### Added
 
 - Configure node by clicking in workflow config toml text ([#20](https://github.com/i-VRESSE/workflow-builder/issues/20))
+- Allow to configure node label in catalog ([#151](https://github.com/i-VRESSE/workflow-builder/issues/151))
 
 ## @i-vresse/wb-core 3.2.1 - 2024-08-26
 

diff --git a/README.md b/README.md
@@ -171,6 +171,7 @@ The catalog is a YAML formatted file which tells the app what nodes are availabl
 4. examples: Title and link to example workflows
     * map with title as key and link as value
 5. title: Title of the catalog
+6. nodeLabel: Label of the node in the app. Default is 'Node'
 
 ### schema
 

diff --git a/packages/core/README.md b/packages/core/README.md
@@ -64,6 +64,7 @@ function App() {
   useEffect(() => {
     const catalog = {
       title: "Some title",
+      nodeLabel: "Workflow node",
       global: {
         schema: {
           type: "object",

diff --git a/packages/core/src/CatalogPanel.stories.tsx b/packages/core/src/CatalogPanel.stories.tsx
@@ -108,3 +108,19 @@ export const WithExample: ComponentStory<typeof CatalogPanel> = () => {
   })
   return <CatalogPanel />
 }
+
+export const WithNodeLabel: ComponentStory<typeof CatalogPanel> = () => {
+  const setCatalog = useSetCatalog()
+  setCatalog({
+    title: 'Some title',
+    nodeLabel: 'My custom node label',
+    categories: [],
+    global: {
+      schema: {},
+      uiSchema: {}
+    },
+    nodes: [],
+    examples: {}
+  })
+  return <CatalogPanel />
+}
diff --git a/packages/core/src/CatalogPanel.tsx b/packages/core/src/CatalogPanel.tsx
@@ -18,7 +18,7 @@ export const CatalogPanel = ({ children }: PropsWithChildren<{}>): JSX.Element =
       <legend>Catalog</legend>
       <React.Suspense fallback={<span>Loading catalog...</span>}>
         {children}
-        <h4>Nodes</h4>
+        <h4>{catalog.nodeLabel ?? 'Node'}s</h4>
         <ul style={{ lineHeight: '2.5em' }}>
           {catalog.categories.map((category) => (
             <CatalogCategory key={category.name} {...category} />

diff --git a/packages/core/src/NodePanel.stories.tsx b/packages/core/src/NodePanel.stories.tsx
@@ -87,3 +87,32 @@ export const NodeSelected: ComponentStory<typeof NodePanel> = () => {
   }, [])
   return <NodePanel />
 }
+
+export const CustomNodeLabel: ComponentStory<typeof NodePanel> = () => {
+  const setCatalog = useSetCatalog()
+  // const { setEditingGlobal } = useWorkflow()
+  useEffect(() => {
+    const catalog = prepareCatalog({
+      title: 'Some title',
+      nodeLabel: 'My custom node label',
+      categories: [],
+      global: {
+        schema: {
+          type: 'object',
+          properties: {
+            parameter1: {
+              type: 'string'
+            }
+          },
+          additionalProperties: false
+        },
+        uiSchema: {}
+      },
+      nodes: [],
+      examples: {}
+    })
+    setCatalog(catalog)
+    // toggleGlobalEdit()
+  }, [])
+  return <NodePanel />
+}
diff --git a/packages/core/src/NodePanel.tsx b/packages/core/src/NodePanel.tsx
@@ -3,16 +3,17 @@ import React from 'react'
 import { FormProps } from './FormProps'
 import { GlobalForm } from './GlobalForm'
 import { NodeForm } from './NodeForm'
-import { useSelectNodeIndex } from './store'
+import { useCatalog, useSelectNodeIndex } from './store'
 
 /**
  * Panel which renders the form for the selected node or the global parameters.
  *
  */
 export const NodePanel = ({ fields, widgets }: FormProps): JSX.Element => {
   const selectedNodeIndex = useSelectNodeIndex()
+  const { nodeLabel } = useCatalog()
 
-  const legend = 'Node'
+  const legend = nodeLabel ?? 'Node'
 
   return (
     <fieldset>

diff --git a/packages/core/src/types.ts b/packages/core/src/types.ts
@@ -53,6 +53,7 @@ export interface IGlobal {
 
 export interface ICatalog {
   title: string
+  nodeLabel?: string
   global: IGlobal
   categories: ICategory[]
   nodes: ICatalogNode[]

diff --git a/packages/haddock3_catalog/generate_haddock3_catalog.py b/packages/haddock3_catalog/generate_haddock3_catalog.py
@@ -534,6 +534,7 @@ def process_level(level_fn: Path, level: str):
 
     catalog = {
         "title": f"Haddock 3 on {level} level",
+        "nodeLabel": "Module",
         "categories": categories,
         'global': process_global(level),
         "nodes": nodes,

diff --git a/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml b/packages/haddock3_catalog/public/catalog/haddock3.easy.yaml
@@ -1,4 +1,5 @@
 title: Haddock 3 on easy level
+nodeLabel: Module
 categories:
 - name: topology
   description: HADDOCK3 modules to create topologies.
@@ -1946,6 +1947,79 @@ nodes:
   tomlSchema:
     resdic:
       indexed: true
+- id: sasascore
+  category: scoring
+  label: Surface accessibility scoring module.
+  description: HADDOCK3 module to perform accessibility scoring.
+  schema:
+    type: object
+    properties:
+      cutoff:
+        default: 0.4
+        title: relative side chain surface accessibility cutoff
+        description: relative side chain surface accessibility cutoff
+        $comment: relative side chain surface accessibility cutoff. Residues with
+          a relative side chain surface accessibility below this value are considered
+          buried.
+        type: number
+        maximum: 1.0
+        minimum: 0.0
+      resdic_buried:
+        default: {}
+        title: List of residues supposed to be buried
+        description: List of residues supposed to be buried
+        $comment: resdic_buried_* is an expandable parameter. You can provide resdic_buried_A,
+          resdic_buried_B, resdic_buried_C, etc, where the last capital letter is
+          the chain identifier.
+        type: object
+        additionalProperties:
+          type: array
+          items:
+            type: number
+            format: residue
+            minItems: 0
+            maxItems: 100
+          uniqueItems: true
+          default: []
+        propertyNames:
+          pattern: ^[A-Z]$
+          format: chain
+        maxPropertiesFrom: molecules
+      resdic_accessible:
+        default: {}
+        title: List of residues supposed to be accessible
+        description: List of residues supposed to be accessible
+        $comment: resdic_* is an expandable parameter. You can provide resdic_accessible_A,
+          resdic_accessible_B, resdic_accessible_C, etc, where the last capital letter
+          is the chain identifier.
+        type: object
+        additionalProperties:
+          type: array
+          items:
+            type: number
+            format: residue
+            minItems: 0
+            maxItems: 100
+          uniqueItems: true
+          default: []
+        propertyNames:
+          pattern: ^[A-Z]$
+          format: chain
+        maxPropertiesFrom: molecules
+    required: []
+    additionalProperties: false
+  uiSchema:
+    cutoff:
+      ui:group: scoring
+    resdic_buried:
+      ui:group: analysis
+    resdic_accessible:
+      ui:group: analysis
+  tomlSchema:
+    resdic_buried:
+      indexed: true
+    resdic_accessible:
+      indexed: true
 - id: seletop
   category: analysis
   label: Select a number of models.

diff --git a/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml b/packages/haddock3_catalog/public/catalog/haddock3.expert.yaml
@@ -1,4 +1,5 @@
 title: Haddock 3 on expert level
+nodeLabel: Module
 categories:
 - name: topology
   description: HADDOCK3 modules to create topologies.
@@ -8607,6 +8608,90 @@ nodes:
   tomlSchema:
     resdic:
       indexed: true
+- id: sasascore
+  category: scoring
+  label: Surface accessibility scoring module.
+  description: HADDOCK3 module to perform accessibility scoring.
+  schema:
+    type: object
+    properties:
+      cutoff:
+        default: 0.4
+        title: relative side chain surface accessibility cutoff
+        description: relative side chain surface accessibility cutoff
+        $comment: relative side chain surface accessibility cutoff. Residues with
+          a relative side chain surface accessibility below this value are considered
+          buried.
+        type: number
+        maximum: 1.0
+        minimum: 0.0
+      resdic_buried:
+        default: {}
+        title: List of residues supposed to be buried
+        description: List of residues supposed to be buried
+        $comment: resdic_buried_* is an expandable parameter. You can provide resdic_buried_A,
+          resdic_buried_B, resdic_buried_C, etc, where the last capital letter is
+          the chain identifier.
+        type: object
+        additionalProperties:
+          type: array
+          items:
+            type: number
+            format: residue
+            minItems: 0
+            maxItems: 100
+          uniqueItems: true
+          default: []
+        propertyNames:
+          pattern: ^[A-Z]$
+          format: chain
+        maxPropertiesFrom: molecules
+      resdic_accessible:
+        default: {}
+        title: List of residues supposed to be accessible
+        description: List of residues supposed to be accessible
+        $comment: resdic_* is an expandable parameter. You can provide resdic_accessible_A,
+          resdic_accessible_B, resdic_accessible_C, etc, where the last capital letter
+          is the chain identifier.
+        type: object
+        additionalProperties:
+          type: array
+          items:
+            type: number
+            format: residue
+            minItems: 0
+            maxItems: 100
+          uniqueItems: true
+          default: []
+        propertyNames:
+          pattern: ^[A-Z]$
+          format: chain
+        maxPropertiesFrom: molecules
+      probe_radius:
+        default: 1.4
+        title: Probe radius
+        description: Probe radius
+        $comment: Sets the probe radius (in Angstrom) used to compute solvent accessible
+          surface area.
+        type: number
+        maximum: 10.0
+        minimum: 0.0
+    required: []
+    additionalProperties: false
+  uiSchema:
+    cutoff:
+      ui:group: scoring
+    resdic_buried:
+      ui:group: analysis
+    resdic_accessible:
+      ui:group: analysis
+    probe_radius:
+      ui:group: analysis
+  tomlSchema:
+    resdic_buried:
+      indexed: true
+    resdic_accessible:
+      indexed: true
 - id: seletop
   category: analysis
   label: Select a number of models.