Merge remote-tracking branch 'refs/remotes/origin/main'

i-VRESSE · Nov 3, 2023 · 8326d88 · 8326d88
2 parents 699b569 + b35102e
commit 8326d88
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diff --git a/packages/core/src/molecule/addMoleculeValidation.test.ts b/packages/core/src/molecule/addMoleculeValidation.test.ts
@@ -557,6 +557,101 @@ describe('addMoleculeValidation()', () => {
       })
     })
   })
+
+  describe('given unparsable molecule', () => {
+    let moleculeInfos: MoleculeInfo[]
+    let moleculesPropName: string | undefined
+
+    beforeEach(async () => {
+      const globalParameters = {
+        molecules: ['a.pdb']
+      }
+      const globalSchema: JSONSchema7 = {
+        type: 'object',
+        properties: {
+          molecules: {
+            type: 'array',
+            format: 'moleculefilepaths',
+            items: {
+              type: 'string'
+            }
+          }
+        }
+      }
+      const body = 'foo'
+      const file =
+        'data:text/plain;name=a.pdb;base64,' +
+        Buffer.from(body).toString('base64')
+      const files = {
+        'a.pdb': file
+      };
+      [moleculeInfos, moleculesPropName] = await parseMolecules(
+        globalParameters,
+        globalSchema,
+        files
+      )
+    })
+
+    describe('given array of object with array of scalar', () => {
+      it.each([
+        ['residue', 'number'],
+        ['chain', 'string']
+      ] as const)('should make items an array and not set enums for %s format', async (moleculeformat, moleculeType) => {
+        const propSchema: JSONSchema7WithMaxItemsFrom = {
+          type: 'array',
+          maxItemsFrom: 'molecules',
+          items: {
+            type: 'object',
+            properties: {
+              prop2: {
+                type: 'array',
+                items: {
+                  type: moleculeType,
+                  format: moleculeformat
+                }
+              }
+            }
+          }
+        }
+        const schema: JSONSchema7 = {
+          type: 'object',
+          properties: {
+            prop1: propSchema
+          }
+        }
+        const actual = await addMoleculeValidation(
+          schema,
+          moleculeInfos,
+          moleculesPropName
+        )
+        const expectedPropSchema: JSONSchema7WithMaxItemsFrom = {
+          type: 'array',
+          maxItemsFrom: 'molecules',
+          items: [
+            {
+              type: 'object',
+              properties: {
+                prop2: {
+                  type: 'array',
+                  items: {
+                    type: moleculeType,
+                    format: moleculeformat
+                  }
+                }
+              }
+            }
+          ]
+        }
+        const expected: JSONSchema7 = {
+          type: 'object',
+          properties: {
+            prop1: expectedPropSchema
+          }
+        }
+        expect(actual).toEqual(expected)
+      })
+    })
+  })
 })
 
 describe('addMoleculeUi()', () => {

diff --git a/packages/core/src/molecule/addMoleculeValidation.ts b/packages/core/src/molecule/addMoleculeValidation.ts
@@ -179,13 +179,15 @@ function walkSchemaForMoleculeFormats (
                   pv.items.format !== undefined &&
                   moleculeFormats.has(pv.items.format)
                 ) {
-                  if (pv.items.format === 'chain') {
+                  if (pv.items.format === 'chain' && molinfo.chains.length > 0) {
                     return [
                       pk,
                       { ...pv, items: { ...pv.items, enum: molinfo.chains } }
                     ]
                   }
-                  if (pv.items.format === 'residue') {
+                  if (pv.items.format === 'residue' &&
+                  molinfo.residueSequenceNumbers.length > 0
+                  ) {
                     return [
                       pk,
                       {

diff --git a/packages/haddock3_catalog/README.md b/packages/haddock3_catalog/README.md
@@ -11,6 +11,8 @@ Run with
 # Reads modules from haddock3 in Python path
 ./generate_haddock3_catalog.py
 # Writes catalog files in public/catalog/ dir
+
+# TODO add command to check JSON schemas are valid.
 ```
 
 Translations from haddock3 -> i-VRESSE workflow builder:

diff --git a/packages/haddock3_catalog/generate_haddock3_catalog.py b/packages/haddock3_catalog/generate_haddock3_catalog.py
@@ -326,6 +326,12 @@ def config2schema(config):
                 prop['items'] = {
                     "type": "number"
                 }
+            elif k == 'ligand_chains':
+                prop['items'] = {
+                    "type": "string",
+                    "format": "chain"
+                }
+                prop['default'] = v['default']
             else:
                 raise ValueError(f"Don't know how to determine type of items of {v}")
         else:
@@ -425,7 +431,9 @@ def process_level(level_fn: Path, level: str):
     broken_modules = {
         'topocg', # Gives `AttributeError: module 'haddock.modules.topology.topocg' has no attribute 'HaddockModule'` error
     }
-    nodes = [process_module(module, category, level) for module, category in modules_category.items() if module not in broken_modules]
+    # TODO define module order like category order
+    # now they are sorted alphabetically
+    nodes = [process_module(module, category, level) for module, category in sorted(modules_category.items()) if module not in broken_modules]
 
     catalog = {
         "title": f"Haddock 3 on {level} level",