@genome-spy/app 0.69.0 → 0.70.0

package/dist/schema.json

@@ -4828,6 +4828,29 @@
         }
       ]
     },
+    "ArrowBackendDef": {
+      "additionalProperties": false,
+      "properties": {
+        "backend": {
+          "const": "arrow",
+          "type": "string"
+        },
+        "sampleIdField": {
+          "description": "Field containing sample ids.",
+          "type": "string"
+        },
+        "url": {
+          "description": "URL to an Arrow data source.\n\nReserved for future use.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "backend",
+        "url",
+        "sampleIdField"
+      ],
+      "type": "object"
+    },
     "Axis": {
       "additionalProperties": false,
       "properties": {
@@ -5701,6 +5724,36 @@
     "ColorDef": {
       "$ref": "#/definitions/MarkPropDef%3C(string%7Cnull)%3E"
     },
+    "ColumnIdentifierField": {
+      "additionalProperties": false,
+      "properties": {
+        "caseInsensitive": {
+          "description": "Enables case-insensitive matching for this identifier field.",
+          "type": "boolean"
+        },
+        "name": {
+          "description": "Logical identifier name shown in UI and diagnostics.\n\nExample values: `\"symbol\"`, `\"ensembl\"`, `\"entrez\"`.",
+          "type": "string"
+        },
+        "path": {
+          "description": "Backend path that provides identifier values aligned to matrix columns.\n\nThe array length must equal the number of columns in the matrix.",
+          "type": "string"
+        },
+        "primary": {
+          "description": "Marks this identifier as the primary, canonical identifier.",
+          "type": "boolean"
+        },
+        "stripVersionSuffix": {
+          "description": "Remove version suffixes during matching (for example, ENSG...`.12`).\n\nUseful for identifiers such as Ensembl ids that may contain version suffixes in some datasets but not in user queries.",
+          "type": "boolean"
+        }
+      },
+      "required": [
+        "name",
+        "path"
+      ],
+      "type": "object"
+    },
     "CompareParams": {
       "additionalProperties": false,
       "properties": {
@@ -6058,6 +6111,35 @@
         }
       ]
     },
+    "DataBackendDef": {
+      "additionalProperties": false,
+      "properties": {
+        "backend": {
+          "const": "data",
+          "type": "string"
+        },
+        "data": {
+          "anyOf": [
+            {
+              "$ref": "#/definitions/UrlData"
+            },
+            {
+              "$ref": "#/definitions/InlineData"
+            }
+          ],
+          "description": "Eager tabular metadata source using the standard data contract.\n\nSupports `UrlData` and `InlineData`."
+        },
+        "sampleIdField": {
+          "description": "Field name in the table that matches sample ids in the view.\n\n__Default value:__ `\"sample\"`",
+          "type": "string"
+        }
+      },
+      "required": [
+        "backend",
+        "data"
+      ],
+      "type": "object"
+    },
     "DataFormat": {
       "anyOf": [
         {
@@ -8453,6 +8535,120 @@
       ],
       "type": "object"
     },
+    "MetadataBackendDef": {
+      "anyOf": [
+        {
+          "$ref": "#/definitions/DataBackendDef"
+        },
+        {
+          "$ref": "#/definitions/ZarrBackendDef"
+        },
+        {
+          "$ref": "#/definitions/ParquetBackendDef"
+        },
+        {
+          "$ref": "#/definitions/ArrowBackendDef"
+        }
+      ]
+    },
+    "MetadataSourceDef": {
+      "additionalProperties": false,
+      "properties": {
+        "attributeGroupSeparator": {
+          "description": "Separator used by source-side attribute names to express hierarchy.\n\nExample: if separator is `\".\"`, column `clinical.OS` is interpreted as group `clinical` and attribute `OS`.",
+          "type": "string"
+        },
+        "attributes": {
+          "additionalProperties": {
+            "$ref": "#/definitions/SampleAttributeDef"
+          },
+          "description": "Attribute definitions keyed by attribute/column id (and optionally by group path).\n\nSpecial key `\"\"` defines source-level defaults for all imported columns. Path splitting is applied only when `attributeGroupSeparator` is defined.",
+          "type": "object"
+        },
+        "backend": {
+          "$ref": "#/definitions/MetadataBackendDef",
+          "description": "Backend-specific source configuration."
+        },
+        "description": {
+          "description": "Optional short description of what this source contains.\n\nCan be shown in UI and can help automated agents choose the correct source.",
+          "type": "string"
+        },
+        "excludeColumns": {
+          "description": "Column ids that must never be imported from this source.\n\nUseful for excluding identity/helper columns such as `sample` and `displayName`.",
+          "items": {
+            "type": "string"
+          },
+          "type": "array"
+        },
+        "groupPath": {
+          "description": "Default destination group path for imported attributes.\n\nImported column names are placed under this path, which effectively creates (or reuses) a metadata hierarchy node.\n\nThis value is parsed as a path using `attributeGroupSeparator` when that separator is defined for the source. Without an explicit separator, the whole value is treated as one group name (including any `/` characters).\n\nUsers can override this per import in the dialog.",
+          "type": "string"
+        },
+        "id": {
+          "description": "Stable source identifier used in actions, provenance, and configuration.\n\nShould remain stable across spec revisions if bookmarks/provenance replay must keep working.",
+          "type": "string"
+        },
+        "initialLoad": {
+          "anyOf": [
+            {
+              "const": false,
+              "type": "boolean"
+            },
+            {
+              "const": "*",
+              "type": "string"
+            },
+            {
+              "items": {
+                "type": "string"
+              },
+              "type": "array"
+            }
+          ],
+          "description": "Startup loading behavior.\n\n- `false`: do not load at startup\n- `\"*\"`: load all columns allowed by this source\n- `string[]`: resolve and load only the listed columns\n\nOmitted value uses backend defaults."
+        },
+        "name": {
+          "description": "Optional user-facing label shown in menus and dialogs.\n\nIf omitted, UI falls back to `id`.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "backend"
+      ],
+      "type": "object"
+    },
+    "MetadataSourceEntry": {
+      "anyOf": [
+        {
+          "$ref": "#/definitions/MetadataSourceDef"
+        },
+        {
+          "additionalProperties": false,
+          "properties": {
+            "import": {
+              "$ref": "#/definitions/MetadataSourceImportDef"
+            }
+          },
+          "required": [
+            "import"
+          ],
+          "type": "object"
+        }
+      ]
+    },
+    "MetadataSourceImportDef": {
+      "additionalProperties": false,
+      "properties": {
+        "url": {
+          "description": "URL to a standalone metadata source definition file.\n\nImports are shallow: imported files must define exactly one source and cannot contain nested `import` entries.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "url"
+      ],
+      "type": "object"
+    },
     "MultiscaleStops": {
       "additionalProperties": false,
       "properties": {
@@ -8593,6 +8789,29 @@
         }
       ]
     },
+    "ParquetBackendDef": {
+      "additionalProperties": false,
+      "properties": {
+        "backend": {
+          "const": "parquet",
+          "type": "string"
+        },
+        "sampleIdField": {
+          "description": "Field containing sample ids.",
+          "type": "string"
+        },
+        "url": {
+          "description": "URL to a Parquet data source.\n\nReserved for future use.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "backend",
+        "url",
+        "sampleIdField"
+      ],
+      "type": "object"
+    },
     "Parse": {
       "additionalProperties": {
         "$ref": "#/definitions/ParseValue"
@@ -9986,6 +10205,7 @@
       "additionalProperties": false,
       "properties": {
         "attributeGroupSeparator": {
+          "deprecated": "Configure per-source `attributeGroupSeparator` in `metadataSources`.",
           "description": "If attributes form a hierarchy, specify the separator character to split the attribute names into paths.",
           "type": "string"
         },
@@ -10021,13 +10241,19 @@
           "additionalProperties": {
             "$ref": "#/definitions/SampleAttributeDef"
           },
+          "deprecated": "Configure per-source `attributes` in `metadataSources`.",
           "description": "Explicitly specify the sample attributes.",
           "type": "object"
         },
         "data": {
           "$ref": "#/definitions/Data",
+          "deprecated": "Use `metadataSources` with `backend: \"data\"` instead.",
           "description": "Optional metadata about the samples."
         },
+        "identity": {
+          "$ref": "#/definitions/SampleIdentityDef",
+          "description": "Optional explicit sample identity definition."
+        },
         "labelAlign": {
           "$ref": "#/definitions/Align",
           "description": "The horizontal alignment of the text. One of `\"left\"`, `\"center\"`, or `\"right\"`.\n\n**Default value:** `\"left\"`"
@@ -10055,10 +10281,38 @@
         "labelTitleText": {
           "description": "Text in the label title\n\n**Default:** `\"Sample name\"`",
           "type": "string"
+        },
+        "metadataSources": {
+          "description": "Metadata source definitions used for startup and on-demand imports.\n\nSource order is significant for startup loading: eager startup imports are applied in declaration order.",
+          "items": {
+            "$ref": "#/definitions/MetadataSourceEntry"
+          },
+          "type": "array"
         }
       },
       "type": "object"
     },
+    "SampleIdentityDef": {
+      "additionalProperties": false,
+      "properties": {
+        "data": {
+          "$ref": "#/definitions/Data",
+          "description": "Data source that defines the canonical sample set for the view.\n\nThe source must contain one row per sample and is used to resolve sample ids and optional display names before metadata imports are applied."
+        },
+        "displayNameField": {
+          "description": "Field containing a user-visible sample label.\n\nIf omitted, sample ids are used.",
+          "type": "string"
+        },
+        "idField": {
+          "description": "Field that contains the canonical sample id.\n\n__Default value:__ `\"sample\"`",
+          "type": "string"
+        }
+      },
+      "required": [
+        "data"
+      ],
+      "type": "object"
+    },
     "SampleParams": {
       "additionalProperties": false,
       "properties": {
@@ -12222,6 +12476,53 @@
         }
       ]
     },
+    "ZarrBackendDef": {
+      "additionalProperties": false,
+      "properties": {
+        "backend": {
+          "const": "zarr",
+          "type": "string"
+        },
+        "identifiers": {
+          "description": "Optional identifier arrays used to resolve user queries to columns.\n\nIf omitted, only primary column ids are used for lookup.",
+          "items": {
+            "$ref": "#/definitions/ColumnIdentifierField"
+          },
+          "type": "array"
+        },
+        "matrix": {
+          "$ref": "#/definitions/ZarrMatrixLayoutDef",
+          "description": "Optional path overrides for the expression-style matrix layout."
+        },
+        "url": {
+          "description": "URL to the root of the Zarr store.",
+          "type": "string"
+        }
+      },
+      "required": [
+        "backend",
+        "url"
+      ],
+      "type": "object"
+    },
+    "ZarrMatrixLayoutDef": {
+      "additionalProperties": false,
+      "properties": {
+        "columnIdsPath": {
+          "description": "Path to matrix column identifiers.\n\n__Default value:__ `\"var_names\"`",
+          "type": "string"
+        },
+        "rowIdsPath": {
+          "description": "Path to matrix row identifiers (sample ids).\n\n__Default value:__ `\"obs_names\"`",
+          "type": "string"
+        },
+        "valuesPath": {
+          "description": "Path to matrix values (sample rows x metadata columns).\n\n__Default value:__ `\"X\"`",
+          "type": "string"
+        }
+      },
+      "type": "object"
+    },
     "ZoomParams": {
       "additionalProperties": false,
       "properties": {

package/dist/style.css

@@ -1 +1 @@
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.context:before,.gs-dropdown-menu .context:before{content:"("}.gs-menu .context:after,.gs-context-menu .context:after,.gs-dropdown-menu .context:after{content:")"}.gs-menu .menu-divider,.gs-context-menu .menu-divider,.gs-dropdown-menu .menu-divider{margin:5px 0;border-top:1px solid #e0e0e0}.gs-menu .menu-header,.gs-menu li>:is(span.disabled-item,a:first-child,.submenu-item,label),.gs-context-menu .menu-header,.gs-context-menu li>:is(span.disabled-item,a:first-child,.submenu-item,label),.gs-dropdown-menu .menu-header,.gs-dropdown-menu li>:is(span.disabled-item,a:first-child,.submenu-item,label){padding-left:15px;padding-right:15px}.gs-menu .menu-header,.gs-context-menu .menu-header,.gs-dropdown-menu .menu-header{font-size:12px;color:#666}.gs-menu li>:is(div.submenu-item,.choice-item),.gs-context-menu li>:is(div.submenu-item,.choice-item),.gs-dropdown-menu li>:is(div.submenu-item,.choice-item){display:flex;justify-content:space-between;align-items:center}.gs-menu 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a.menu-ellipsis{padding:0;display:flex;align-items:center;position:absolute;top:0;right:7.5px;height:22px;background-color:#e0e0e0;border-radius:3em;color:#707070}.gs-menu a.menu-ellipsis svg,.gs-context-menu a.menu-ellipsis svg,.gs-dropdown-menu a.menu-ellipsis svg{margin:0;width:22px}.gs-menu a.menu-ellipsis:hover,.gs-context-menu a.menu-ellipsis:hover,.gs-dropdown-menu a.menu-ellipsis:hover{background-color:#e9e9e9}.gs-menu li:not(:hover) a.menu-ellipsis,.gs-context-menu li:not(:hover) a.menu-ellipsis,.gs-dropdown-menu li:not(:hover) a.menu-ellipsis{display:none}.gs-menu .gs-input-binding,.gs-context-menu .gs-input-binding,.gs-dropdown-menu .gs-input-binding{margin:0 15px;line-height:normal}.gs-menu .gs-input-binding .description,.gs-context-menu .gs-input-binding .description,.gs-dropdown-menu .gs-input-binding 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.tool-btn{padding:0;font-size:1.15em;transition:color .15s;--gs-toolbar-btn-bg: oklch( from var(--gs-toolbar-bg) calc(l + .03) c h );background-color:var(--gs-toolbar-btn-bg);background-image:linear-gradient(to bottom,oklch(from var(--gs-toolbar-btn-bg) calc(l + .05) calc(c - .005) h),oklch(from var(--gs-toolbar-btn-bg) calc(l - .02) c h));color:var(--gs-toolbar-fg);height:26px;width:30px;border:1px solid;border-top-color:oklch(from var(--gs-toolbar-btn-bg) calc(l + .08) c h);border-left-color:oklch(from var(--gs-toolbar-btn-bg) calc(l + .03) c h);border-right-color:oklch(from var(--gs-toolbar-btn-bg) calc(l - .08) c h);border-bottom-color:oklch(from var(--gs-toolbar-btn-bg) calc(l - .12) c h);box-shadow:0 1px 1px #00000026;border-radius:2px;margin-left:10px;display:flex;align-items:center;justify-content:center}.gs-toolbar .tool-btn>svg{filter:drop-shadow(0 0 1px rgba(0,0,0,.3))}.gs-toolbar .tool-btn:active>*{position:relative;top:1px}.gs-toolbar .tool-btn:disabled{color:oklch(from 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package/dist/{unzip-NywezaRR.js → unzip-Bac01w6X.js}

@@ -163,7 +163,7 @@ class qI extends Map {
   toString() {
     return `QuickLRU(${this.size}/${this.maxSize})`;
   }
-  [Symbol.for("nodejs.util.inspect.custom")]() {
+  [/* @__PURE__ */ Symbol.for("nodejs.util.inspect.custom")]() {
     return this.toString();
   }
 }