Merge pull request #155 from i-VRESSE/no-exit

Skip exit module + regen catalogs

CHANGELOG.md

@@ -6,6 +6,16 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ## Unreleased
 
+### Changed
+
+* Autosave ([#144](https://github.com/i-VRESSE/workflow-builder/pull/144))
+* Improved handling of groups in ui schema
+* Nodes with all its properties in a single group is expanded by default
+
+### Fixed
+
+* Hide the exit module ([#153](https://github.com/i-VRESSE/workflow-builder/issues/153))
+
 ## @i-vresse/wb-core 2.0.1 - 2024-03-25
 
 ### Changed

apps/kitchensink/package.json

@@ -20,7 +20,7 @@
     "@types/react": "^17.0.0",
     "@types/react-dom": "^17.0.0",
     "@vitejs/plugin-react": "^2.0.0",
-    "ts-standard": "^11.0.0",
+    "ts-standard": "^12.0.2",
     "typescript": "^4.7.4",
     "vite": "^3.0.4"
   },

packages/core/package.json

@@ -51,6 +51,7 @@
     "@types/js-yaml": "^4.0.5",
     "@types/papaparse": "^5.3.2",
     "@types/react-syntax-highlighter": "^13.5.2",
+    "@vitest/coverage-v8": "^1.5.3",
     "babel-loader": "^8.2.5",
     "c8": "^7.11.0",
     "jsdom": "^20.0.0",
@@ -59,7 +60,7 @@
     "tsup": "^6.1.3",
     "typedoc": "^0.23.7",
     "vite": "^3.0.4",
-    "vitest": "^0.20.2"
+    "vitest": "1.5.3"
   },
   "dependencies": {
     "@dnd-kit/core": "^6.0.5",

packages/core/src/grouper.test.ts

@@ -5,7 +5,7 @@ import { groupCatalog, groupParameters, groupSchema, groupUiSchema, unGroupParam
 import { ICatalog, IParameters } from './types'
 
 function deepCopy<T> (value: T): T {
-  return JSON.parse(JSON.stringify(value))
+  return structuredClone(value)
 }
 
 describe('given a schema without any property with ui:group in uiSchema', () => {
@@ -504,6 +504,88 @@ describe('given a un-grouped prop with same name as group', () => {
   })
 })
 
+describe('given a prop in own group with same name as group of another prop', () => {
+  describe('groupSchema()', () => {
+    it('should make 2 groups each with a prop', () => {
+      const schema: JSONSchema7 = {
+        type: 'object',
+        properties: {
+          receptor_chains: {
+            type: 'string'
+          },
+          restraints: {
+            type: 'string'
+          }
+        },
+        additionalProperties: false
+      }
+      const uiSchema: UiSchema = {
+        receptor_chains: {
+          'ui:group': 'restraints'
+        },
+        restraints: {
+          'ui:group': 'distance restraints'
+        }
+      }
+      const groupedSchema = groupSchema(schema, uiSchema)
+
+      const expectedSchema: JSONSchema7 = {
+        type: 'object',
+        properties: {
+          restraints: {
+            type: 'object',
+            properties: {
+              receptor_chains: {
+                type: 'string'
+              }
+            },
+            additionalProperties: false
+          },
+          'distance restraints': {
+            type: 'object',
+            properties: {
+              restraints: {
+                type: 'string'
+              }
+            },
+            additionalProperties: false
+          }
+        },
+        additionalProperties: false
+      }
+      expect(groupedSchema).toEqual(expectedSchema)
+    })
+  })
+
+  describe('unGroupParameters()', () => {
+    it('should work', () => {
+      const groupedParameters = {
+        restraints: {
+          receptor_chains: 'val1'
+        },
+        'distance restraints': {
+          restraints: 'val2'
+        }
+      }
+
+      const actual = unGroupParameters(groupedParameters, {
+        receptor_chains: {
+          'ui:group': 'restraints'
+        },
+        restraints: {
+          'ui:group': 'distance restraints'
+        }
+      })
+
+      const expectedParameters = {
+        receptor_chains: 'val1',
+        restraints: 'val2'
+      }
+      expect(actual).toEqual(expectedParameters)
+    })
+  })
+})
+
 describe('given a prop with same name as group and another prop in same group', () => {
   describe('groupSchema()', () => {
     it('should move property inside object with same name', () => {

packages/core/src/grouper.ts

@@ -29,49 +29,70 @@ export function groupSchema (
   schema: JSONSchema7,
   uiSchema: UiSchema
 ): JSONSchema7 {
-  const newSchema = JSON.parse(JSON.stringify(schema))
+  const newSchema = structuredClone(schema)
 
   // Handle overlap between groups and direct prop names.
   const definedGroups = new Set(
     Object.values(uiSchema)
       .filter((v) => 'ui:group' in v)
       .map((v) => v['ui:group'])
   )
-  const directProps = schema.properties ?? {}
-  const directPropNamesWithSameNameAsGroup = new Set(
-    Object.keys(directProps).filter((k) => definedGroups.has(k))
+  const propsWithGroup = new Set(
+    Object.keys(uiSchema).filter((k) => 'ui:group' in uiSchema[k])
   )
-  for (const k of directPropNamesWithSameNameAsGroup) {
-    const propHasGroup =
-      k in uiSchema && 'ui:group' in uiSchema[k] && 'ui:group' in uiSchema[k]
-    if (!(propHasGroup && uiSchema[k]['ui:group'] === k)) {
-      throw new Error(
-        `Can not have group and un-grouped parameter with same name ${k}`
-      )
-    }
-    // Prop has same name as its group so nest it
-    const v = newSchema.properties[k]
-    newSchema.properties[k] = {
+  const allProps = new Set(Object.keys(schema.properties ?? {}))
+  const grouplessProps = new Set([...allProps].filter((x) => !propsWithGroup.has(x)))
+  const grouplessPropsWithSameNameAsGroup = new Set(
+    [...grouplessProps].filter((x) => definedGroups.has(x))
+  )
+  // direct prop with same name as group throw error
+  if (grouplessPropsWithSameNameAsGroup.size > 0) {
+    const msg = Array.from(grouplessPropsWithSameNameAsGroup).join(', ')
+    throw new Error(
+      `Can not have group and un-grouped parameter with same name ${msg}`
+    )
+  }
+
+  if (!('properties' in newSchema && typeof newSchema.properties === 'object')) {
+    return newSchema
+  }
+
+  // prop with group and same name as any group should be nested first
+  const propsWithSameNameAsAnyGroup = new Set(Object.entries(uiSchema).filter(([k, v]) => 'ui:group' in v && definedGroups.has(k)).map((d) => d[0]))
+  for (const k of propsWithSameNameAsAnyGroup) {
+    const prop = newSchema.properties[k]
+    /* eslint-disable @typescript-eslint/no-dynamic-delete */
+    delete newSchema.properties[k]
+    /* eslint-enable @typescript-eslint/no-dynamic-delete */
+    const group = uiSchema[k]['ui:group']
+    newSchema.properties[group] = {
       type: 'object',
       properties: {
-        [k]: v
+        [k]: prop
       },
       additionalProperties: false
     }
   }
 
   Object.entries(uiSchema).forEach(([k, v]) => {
     // TODO recursivly, now only loops over first direct props
-    if ('ui:group' in v && !directPropNamesWithSameNameAsGroup.has(k)) {
+    if ('ui:group' in v && !propsWithSameNameAsAnyGroup.has(k)) {
       const group = v['ui:group']
+      if (!('properties' in newSchema && typeof newSchema.properties === 'object')) {
+        throw new Error('Schema must have properties')
+      }
       if (!(group in newSchema.properties)) {
         newSchema.properties[group] = {
           type: 'object',
           properties: {},
           additionalProperties: false
         }
       }
-      newSchema.properties[group].properties[k] = newSchema.properties[k]
+      const newGroup = newSchema.properties[group]
+      if (typeof newGroup === 'boolean' || newGroup.properties === undefined) {
+        return
+      }
+      newGroup.properties[k] = newSchema.properties[k]
       // Remove k as it now is in the group
       /* eslint-disable @typescript-eslint/no-dynamic-delete */
       delete newSchema.properties[k]

packages/core/src/store.ts

@@ -460,6 +460,27 @@ export function useSelectedNodeFormSchema (): JSONSchema7 | undefined {
   return useRecoilValue(selectedNodeFormSchemaState)
 }
 
+function expandSingleCollapsibleField (uiSchema: UiSchema): UiSchema {
+  const nrCollapsibles = Object.values(uiSchema).filter(
+    (v) => v['ui:field'] === 'collapsible'
+  ).length
+  if (nrCollapsibles === 1) {
+    const firstCollapsibleKey = Object.keys(uiSchema).find(
+      (k) => uiSchema[k]['ui:field'] === 'collapsible'
+    )
+    if (firstCollapsibleKey !== undefined) {
+      return {
+        ...uiSchema,
+        [firstCollapsibleKey]: {
+          ...uiSchema[firstCollapsibleKey],
+          'ui:collapsed': false
+        }
+      }
+    }
+  }
+  return uiSchema
+}
+
 const selectedNodeFormUiSchemaState = selector<UiSchema | undefined>({
   key: 'selectedNodeFormUiSchema',
   get: ({ get }) => {
@@ -475,7 +496,8 @@ const selectedNodeFormUiSchemaState = selector<UiSchema | undefined>({
       moleculeInfos,
       moleculesPropName
     )
-    return uiSchemaWithMolInfo
+
+    return expandSingleCollapsibleField(uiSchemaWithMolInfo)
   }
 })
 

packages/form/package.json

@@ -54,13 +54,14 @@
     "@storybook/react": "^6.5.9",
     "@storybook/testing-library": "^0.0.13",
     "@testing-library/react": "12",
+    "@vitest/coverage-v8": "^1.5.3",
     "babel-loader": "^8.2.5",
     "jsdom": "^20.0.0",
     "postcss": "^8.4.14",
     "ts-standard": "^12.0.2",
     "tsup": "^6.1.3",
     "typedoc": "^0.23.7",
-    "vitest": "^0.20.2"
+    "vitest": "^1.5.3"
   },
   "tsup": {
     "entry": [

packages/haddock3_catalog/generate_haddock3_catalog.py

@@ -430,11 +430,15 @@ def process_level(level_fn: Path, level: str):
 
     broken_modules = {
         'topocg', # Gives `AttributeError: module 'haddock.modules.topology.topocg' has no attribute 'HaddockModule'` error
+        'exit', # Does not make sense to have exit module in the catalog
     }
     # TODO define module order like category order
-    # now they are sorted alphabetically
+    # now they are sorted by insert
     nodes = [process_module(module, category, level) for module, category in sorted(modules_category.items()) if module not in broken_modules]
 
+    # remove catagories without nodes
+    categories = [c for c in categories if any(n['category'] == c['name'] for n in nodes)]
+
     catalog = {
         "title": f"Haddock 3 on {level} level",
         "categories": categories,