@jbrowse/plugin-config 3.1.0 → 3.3.0

package/dist/ConfigurationEditorWidget/components/ConfigurationEditor.js

@@ -45,7 +45,9 @@ const Member = (0, mobx_react_1.observer)(function (props) {
         const typeNameChoices = (0, configuration_1.getTypeNamesFromExplicitlyTypedUnion)(slotSchema);
         return ((0, jsx_runtime_1.jsxs)(material_1.Accordion, { defaultExpanded: true, className: classes.accordion, children: [(0, jsx_runtime_1.jsx)(material_1.AccordionSummary, { expandIcon: (0, jsx_runtime_1.jsx)(ExpandMore_1.default, { className: classes.icon }), children: (0, jsx_runtime_1.jsx)(material_1.Typography, { children: [...path, slotName].join('➔') }) }), (0, jsx_runtime_1.jsxs)(material_1.AccordionDetails, { className: classes.expansionPanelDetails, children: [typeNameChoices.length ? ((0, jsx_runtime_1.jsx)(TypeSelector_1.default, { typeNameChoices: typeNameChoices, slotName: slotName, slot: slot, onChange: evt => {
                                 if (evt.target.value !== slot.type) {
-                                    schema.setSubschema(slotName, { type: evt.target.value });
+                                    schema.setSubschema(slotName, {
+                                        type: evt.target.value,
+                                    });
                                 }
                             } })) : null, (0, jsx_runtime_1.jsx)(material_1.FormGroup, { className: classes.noOverflow, children: (0, jsx_runtime_1.jsx)(Schema, { schema: slot, path: [...path, slotName] }) })] })] }));
     }

package/dist/FromConfigSequenceAdapter/configSchema.js

@@ -7,5 +7,8 @@ const sequenceConfigSchema = (0, configuration_1.ConfigurationSchema)('FromConfi
         type: 'frozen',
         defaultValue: [],
     },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+}, {
+    explicitlyTyped: true,
+    implicitIdentifier: 'adapterId',
+});
 exports.default = sequenceConfigSchema;

package/dist/NcbiSequenceReportAliasAdapter/configSchema.js

@@ -15,5 +15,18 @@ const NcbiSequenceReportAliasAdapterConfigSchema = (0, configuration_1.Configura
         defaultValue: true,
         description: 'forces usage of the UCSC names over the NCBI style names from a FASTA',
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                location: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 exports.default = NcbiSequenceReportAliasAdapterConfigSchema;

package/dist/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -10,13 +10,20 @@ class RefNameAliasAdapter extends BaseAdapter_1.BaseAdapter {
         }
         const results = await (0, io_1.openLocation)(loc, this.pluginManager).readFile('utf8');
         const refColumn = this.getConf('refNameColumn');
-        return results
+        const refColumnHeaderName = this.getConf('refNameColumnHeaderName');
+        const lines = results
             .trim()
             .split(/\n|\r\n|\r/)
-            .filter(f => !!f && !f.startsWith('#'))
+            .filter(f => !!f);
+        const header = lines.filter(f => f.startsWith('#'));
+        const headerCol = refColumnHeaderName && header.length
+            ? header.at(-1).split('\t').indexOf(refColumnHeaderName)
+            : refColumn;
+        return lines
+            .filter(f => !f.startsWith('#'))
             .map(row => {
             const aliases = row.split('\t');
-            const [refName] = aliases.splice(refColumn, 1);
+            const refName = aliases[headerCol];
             return {
                 refName: refName,
                 aliases: aliases.filter(f => !!f.trim()),

package/dist/RefNameAliasAdapter/configSchema.d.ts

@@ -10,5 +10,10 @@ declare const RefNameAliasAdapter: import("@jbrowse/core/configuration/configura
         type: string;
         defaultValue: number;
     };
+    refNameColumnHeaderName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default RefNameAliasAdapter;

package/dist/RefNameAliasAdapter/configSchema.js

@@ -14,5 +14,23 @@ const RefNameAliasAdapter = (0, configuration_1.ConfigurationSchema)('RefNameAli
         type: 'number',
         defaultValue: 0,
     },
-}, { explicitlyTyped: true });
+    refNameColumnHeaderName: {
+        type: 'string',
+        description: 'alternative to refNameColumn, instead looks at header (starts with # and finds column name)',
+        defaultValue: '',
+    },
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                location: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 exports.default = RefNameAliasAdapter;

package/esm/ConfigurationEditorWidget/components/ConfigurationEditor.js

@@ -40,7 +40,9 @@ const Member = observer(function (props) {
         const typeNameChoices = getTypeNamesFromExplicitlyTypedUnion(slotSchema);
         return (_jsxs(Accordion, { defaultExpanded: true, className: classes.accordion, children: [_jsx(AccordionSummary, { expandIcon: _jsx(ExpandMoreIcon, { className: classes.icon }), children: _jsx(Typography, { children: [...path, slotName].join('➔') }) }), _jsxs(AccordionDetails, { className: classes.expansionPanelDetails, children: [typeNameChoices.length ? (_jsx(TypeSelector, { typeNameChoices: typeNameChoices, slotName: slotName, slot: slot, onChange: evt => {
                                 if (evt.target.value !== slot.type) {
-                                    schema.setSubschema(slotName, { type: evt.target.value });
+                                    schema.setSubschema(slotName, {
+                                        type: evt.target.value,
+                                    });
                                 }
                             } })) : null, _jsx(FormGroup, { className: classes.noOverflow, children: _jsx(Schema, { schema: slot, path: [...path, slotName] }) })] })] }));
     }

package/esm/FromConfigSequenceAdapter/configSchema.js

@@ -5,5 +5,8 @@ const sequenceConfigSchema = ConfigurationSchema('FromConfigSequenceAdapter', {
         type: 'frozen',
         defaultValue: [],
     },
-}, { explicitlyTyped: true, implicitIdentifier: 'adapterId' });
+}, {
+    explicitlyTyped: true,
+    implicitIdentifier: 'adapterId',
+});
 export default sequenceConfigSchema;

package/esm/NcbiSequenceReportAliasAdapter/configSchema.js

@@ -13,5 +13,18 @@ const NcbiSequenceReportAliasAdapterConfigSchema = ConfigurationSchema('NcbiSequ
         defaultValue: true,
         description: 'forces usage of the UCSC names over the NCBI style names from a FASTA',
     },
-}, { explicitlyTyped: true });
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                location: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 export default NcbiSequenceReportAliasAdapterConfigSchema;

package/esm/RefNameAliasAdapter/RefNameAliasAdapter.js

@@ -8,13 +8,20 @@ export default class RefNameAliasAdapter extends BaseAdapter {
         }
         const results = await openLocation(loc, this.pluginManager).readFile('utf8');
         const refColumn = this.getConf('refNameColumn');
-        return results
+        const refColumnHeaderName = this.getConf('refNameColumnHeaderName');
+        const lines = results
             .trim()
             .split(/\n|\r\n|\r/)
-            .filter(f => !!f && !f.startsWith('#'))
+            .filter(f => !!f);
+        const header = lines.filter(f => f.startsWith('#'));
+        const headerCol = refColumnHeaderName && header.length
+            ? header.at(-1).split('\t').indexOf(refColumnHeaderName)
+            : refColumn;
+        return lines
+            .filter(f => !f.startsWith('#'))
             .map(row => {
             const aliases = row.split('\t');
-            const [refName] = aliases.splice(refColumn, 1);
+            const refName = aliases[headerCol];
             return {
                 refName: refName,
                 aliases: aliases.filter(f => !!f.trim()),

package/esm/RefNameAliasAdapter/configSchema.d.ts

@@ -10,5 +10,10 @@ declare const RefNameAliasAdapter: import("@jbrowse/core/configuration/configura
         type: string;
         defaultValue: number;
     };
+    refNameColumnHeaderName: {
+        type: string;
+        description: string;
+        defaultValue: string;
+    };
 }, import("@jbrowse/core/configuration/configurationSchema").ConfigurationSchemaOptions<undefined, undefined>>;
 export default RefNameAliasAdapter;

package/esm/RefNameAliasAdapter/configSchema.js

@@ -12,5 +12,23 @@ const RefNameAliasAdapter = ConfigurationSchema('RefNameAliasAdapter', {
         type: 'number',
         defaultValue: 0,
     },
-}, { explicitlyTyped: true });
+    refNameColumnHeaderName: {
+        type: 'string',
+        description: 'alternative to refNameColumn, instead looks at header (starts with # and finds column name)',
+        defaultValue: '',
+    },
+}, {
+    explicitlyTyped: true,
+    preProcessSnapshot: snap => {
+        return snap.uri
+            ? {
+                ...snap,
+                location: {
+                    uri: snap.uri,
+                    baseUri: snap.baseUri,
+                },
+            }
+            : snap;
+    },
+});
 export default RefNameAliasAdapter;

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@jbrowse/plugin-config",
-  "version": "3.1.0",
+  "version": "3.3.0",
   "description": "JBrowse 2 config utilities",
   "keywords": [
     "jbrowse",
@@ -36,9 +36,9 @@
     "clean": "rimraf dist esm *.tsbuildinfo"
   },
   "dependencies": {
-    "@jbrowse/core": "^3.1.0",
-    "@mui/icons-material": "^6.0.0",
-    "@mui/material": "^6.0.0",
+    "@jbrowse/core": "^3.3.0",
+    "@mui/icons-material": "^7.0.0",
+    "@mui/material": "^7.0.0",
     "mobx": "^6.0.0",
     "mobx-react": "^9.0.0",
     "mobx-state-tree": "^5.0.0",
@@ -56,5 +56,5 @@
   "distModule": "esm/index.js",
   "srcModule": "src/index.ts",
   "module": "esm/index.js",
-  "gitHead": "91492049ddea0aed90eb24d3c066c2d9f5a6b189"
+  "gitHead": "0bb64d8cc7ecdd167515308b31eec3d9acbc59e4"
 }