@vitessce/config 3.5.6 → 3.5.8

package/dist/index.js

@@ -34,6 +34,11 @@ const FileType = {
   OBS_LABELS_ANNDATA_ZARR: "obsLabels.anndata.zarr",
   FEATURE_LABELS_ANNDATA_ZARR: "featureLabels.anndata.zarr",
   SAMPLE_EDGES_ANNDATA_ZARR: "sampleEdges.anndata.zarr",
+  SAMPLE_SETS_ANNDATA_ZARR: "sampleSets.anndata.zarr",
+  COMPARISON_METADATA_ANNDATA_ZARR: "comparisonMetadata.anndata.zarr",
+  COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR: "comparativeFeatureStats.anndata.zarr",
+  COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR: "comparativeFeatureSetStats.anndata.zarr",
+  COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR: "comparativeObsSetStats.anndata.zarr",
   // AnnData - zipped
   OBS_FEATURE_MATRIX_ANNDATA_ZARR_ZIP: "obsFeatureMatrix.anndata.zarr.zip",
   OBS_FEATURE_COLUMNS_ANNDATA_ZARR_ZIP: "obsFeatureColumns.anndata.zarr.zip",
@@ -46,6 +51,11 @@ const FileType = {
   OBS_LABELS_ANNDATA_ZARR_ZIP: "obsLabels.anndata.zarr.zip",
   FEATURE_LABELS_ANNDATA_ZARR_ZIP: "featureLabels.anndata.zarr.zip",
   SAMPLE_EDGES_ANNDATA_ZARR_ZIP: "sampleEdges.anndata.zarr.zip",
+  SAMPLE_SETS_ANNDATA_ZARR_ZIP: "sampleSets.anndata.zarr.zip",
+  COMPARISON_METADATA_ANNDATA_ZARR_ZIP: "comparisonMetadata.anndata.zarr.zip",
+  COMPARATIVE_FEATURE_STATS_ANNDATA_ZARR_ZIP: "comparativeFeatureStats.anndata.zarr.zip",
+  COMPARATIVE_FEATURE_SET_STATS_ANNDATA_ZARR_ZIP: "comparativeFeatureSetStats.anndata.zarr.zip",
+  COMPARATIVE_OBS_SET_STATS_ANNDATA_ZARR_ZIP: "comparativeObsSetStats.anndata.zarr.zip",
   // AnnData - h5ad via reference spec
   OBS_FEATURE_MATRIX_ANNDATA_H5AD: "obsFeatureMatrix.anndata.h5ad",
   OBS_FEATURE_COLUMNS_ANNDATA_H5AD: "obsFeatureColumns.anndata.h5ad",
@@ -58,6 +68,11 @@ const FileType = {
   OBS_LABELS_ANNDATA_H5AD: "obsLabels.anndata.h5ad",
   FEATURE_LABELS_ANNDATA_H5AD: "featureLabels.anndata.h5ad",
   SAMPLE_EDGES_ANNDATA_H5AD: "sampleEdges.anndata.h5ad",
+  SAMPLE_SETS_ANNDATA_H5AD: "sampleSets.anndata.h5ad",
+  COMPARISON_METADATA_ANNDATA_H5AD: "comparisonMetadata.anndata.h5ad",
+  COMPARATIVE_FEATURE_STATS_ANNDATA_H5AD: "comparativeFeatureStats.anndata.h5ad",
+  COMPARATIVE_FEATURE_SET_STATS_ANNDATA_H5AD: "comparativeFeatureSetStats.anndata.h5ad",
+  COMPARATIVE_OBS_SET_STATS_ANNDATA_H5AD: "comparativeObsSetStats.anndata.h5ad",
   // SpatialData
   IMAGE_SPATIALDATA_ZARR: "image.spatialdata.zarr",
   LABELS_SPATIALDATA_ZARR: "labels.spatialdata.zarr",
@@ -249,12 +264,20 @@ const CoordinationType = {
   SAMPLE_SET_FILTER: "sampleSetFilter",
   SAMPLE_FILTER_MODE: "sampleFilterMode",
   SAMPLE_SET_COLOR: "sampleSetColor",
+  SAMPLE_HIGHLIGHT: "sampleHighlight",
   EMBEDDING_POINTS_VISIBLE: "embeddingPointsVisible",
   EMBEDDING_CONTOURS_VISIBLE: "embeddingContoursVisible",
   EMBEDDING_CONTOURS_FILLED: "embeddingContoursFilled",
   EMBEDDING_CONTOUR_PERCENTILES: "embeddingContourPercentiles",
   CONTOUR_COLOR_ENCODING: "contourColorEncoding",
-  CONTOUR_COLOR: "contourColor"
+  CONTOUR_COLOR: "contourColor",
+  // For volcano plot:
+  FEATURE_POINT_SIGNIFICANCE_THRESHOLD: "featurePointSignificanceThreshold",
+  FEATURE_LABEL_SIGNIFICANCE_THRESHOLD: "featureLabelSignificanceThreshold",
+  FEATURE_POINT_FOLD_CHANGE_THRESHOLD: "featurePointFoldChangeThreshold",
+  FEATURE_LABEL_FOLD_CHANGE_THRESHOLD: "featureLabelFoldChangeThreshold",
+  // Treemap
+  HIERARCHY_LEVELS: "hierarchyLevels"
 };
 var commonjsGlobal = typeof globalThis !== "undefined" ? globalThis : typeof window !== "undefined" ? window : typeof global !== "undefined" ? global : typeof self !== "undefined" ? self : {};
 function getDefaultExportFromCjs(x) {
@@ -664,6 +687,258 @@ function getInitialCoordinationScopeName(datasetUid, dataType, i = null) {
   const prefix = getInitialCoordinationScopePrefix(datasetUid, dataType);
   return `${prefix}${i === null ? 0 : i}`;
 }
+var loglevel = { exports: {} };
+(function(module) {
+  (function(root, definition) {
+    if (module.exports) {
+      module.exports = definition();
+    } else {
+      root.log = definition();
+    }
+  })(commonjsGlobal, function() {
+    var noop = function() {
+    };
+    var undefinedType = "undefined";
+    var isIE = typeof window !== undefinedType && typeof window.navigator !== undefinedType && /Trident\/|MSIE /.test(window.navigator.userAgent);
+    var logMethods = [
+      "trace",
+      "debug",
+      "info",
+      "warn",
+      "error"
+    ];
+    var _loggersByName = {};
+    var defaultLogger = null;
+    function bindMethod(obj, methodName) {
+      var method = obj[methodName];
+      if (typeof method.bind === "function") {
+        return method.bind(obj);
+      } else {
+        try {
+          return Function.prototype.bind.call(method, obj);
+        } catch (e) {
+          return function() {
+            return Function.prototype.apply.apply(method, [obj, arguments]);
+          };
+        }
+      }
+    }
+    function traceForIE() {
+      if (console.log) {
+        if (console.log.apply) {
+          console.log.apply(console, arguments);
+        } else {
+          Function.prototype.apply.apply(console.log, [console, arguments]);
+        }
+      }
+      if (console.trace)
+        console.trace();
+    }
+    function realMethod(methodName) {
+      if (methodName === "debug") {
+        methodName = "log";
+      }
+      if (typeof console === undefinedType) {
+        return false;
+      } else if (methodName === "trace" && isIE) {
+        return traceForIE;
+      } else if (console[methodName] !== void 0) {
+        return bindMethod(console, methodName);
+      } else if (console.log !== void 0) {
+        return bindMethod(console, "log");
+      } else {
+        return noop;
+      }
+    }
+    function replaceLoggingMethods() {
+      var level = this.getLevel();
+      for (var i = 0; i < logMethods.length; i++) {
+        var methodName = logMethods[i];
+        this[methodName] = i < level ? noop : this.methodFactory(methodName, level, this.name);
+      }
+      this.log = this.debug;
+      if (typeof console === undefinedType && level < this.levels.SILENT) {
+        return "No console available for logging";
+      }
+    }
+    function enableLoggingWhenConsoleArrives(methodName) {
+      return function() {
+        if (typeof console !== undefinedType) {
+          replaceLoggingMethods.call(this);
+          this[methodName].apply(this, arguments);
+        }
+      };
+    }
+    function defaultMethodFactory(methodName, _level, _loggerName) {
+      return realMethod(methodName) || enableLoggingWhenConsoleArrives.apply(this, arguments);
+    }
+    function Logger(name, factory) {
+      var self2 = this;
+      var inheritedLevel;
+      var defaultLevel;
+      var userLevel;
+      var storageKey = "loglevel";
+      if (typeof name === "string") {
+        storageKey += ":" + name;
+      } else if (typeof name === "symbol") {
+        storageKey = void 0;
+      }
+      function persistLevelIfPossible(levelNum) {
+        var levelName = (logMethods[levelNum] || "silent").toUpperCase();
+        if (typeof window === undefinedType || !storageKey)
+          return;
+        try {
+          window.localStorage[storageKey] = levelName;
+          return;
+        } catch (ignore) {
+        }
+        try {
+          window.document.cookie = encodeURIComponent(storageKey) + "=" + levelName + ";";
+        } catch (ignore) {
+        }
+      }
+      function getPersistedLevel() {
+        var storedLevel;
+        if (typeof window === undefinedType || !storageKey)
+          return;
+        try {
+          storedLevel = window.localStorage[storageKey];
+        } catch (ignore) {
+        }
+        if (typeof storedLevel === undefinedType) {
+          try {
+            var cookie = window.document.cookie;
+            var cookieName = encodeURIComponent(storageKey);
+            var location = cookie.indexOf(cookieName + "=");
+            if (location !== -1) {
+              storedLevel = /^([^;]+)/.exec(
+                cookie.slice(location + cookieName.length + 1)
+              )[1];
+            }
+          } catch (ignore) {
+          }
+        }
+        if (self2.levels[storedLevel] === void 0) {
+          storedLevel = void 0;
+        }
+        return storedLevel;
+      }
+      function clearPersistedLevel() {
+        if (typeof window === undefinedType || !storageKey)
+          return;
+        try {
+          window.localStorage.removeItem(storageKey);
+        } catch (ignore) {
+        }
+        try {
+          window.document.cookie = encodeURIComponent(storageKey) + "=; expires=Thu, 01 Jan 1970 00:00:00 UTC";
+        } catch (ignore) {
+        }
+      }
+      function normalizeLevel(input) {
+        var level = input;
+        if (typeof level === "string" && self2.levels[level.toUpperCase()] !== void 0) {
+          level = self2.levels[level.toUpperCase()];
+        }
+        if (typeof level === "number" && level >= 0 && level <= self2.levels.SILENT) {
+          return level;
+        } else {
+          throw new TypeError("log.setLevel() called with invalid level: " + input);
+        }
+      }
+      self2.name = name;
+      self2.levels = {
+        "TRACE": 0,
+        "DEBUG": 1,
+        "INFO": 2,
+        "WARN": 3,
+        "ERROR": 4,
+        "SILENT": 5
+      };
+      self2.methodFactory = factory || defaultMethodFactory;
+      self2.getLevel = function() {
+        if (userLevel != null) {
+          return userLevel;
+        } else if (defaultLevel != null) {
+          return defaultLevel;
+        } else {
+          return inheritedLevel;
+        }
+      };
+      self2.setLevel = function(level, persist) {
+        userLevel = normalizeLevel(level);
+        if (persist !== false) {
+          persistLevelIfPossible(userLevel);
+        }
+        return replaceLoggingMethods.call(self2);
+      };
+      self2.setDefaultLevel = function(level) {
+        defaultLevel = normalizeLevel(level);
+        if (!getPersistedLevel()) {
+          self2.setLevel(level, false);
+        }
+      };
+      self2.resetLevel = function() {
+        userLevel = null;
+        clearPersistedLevel();
+        replaceLoggingMethods.call(self2);
+      };
+      self2.enableAll = function(persist) {
+        self2.setLevel(self2.levels.TRACE, persist);
+      };
+      self2.disableAll = function(persist) {
+        self2.setLevel(self2.levels.SILENT, persist);
+      };
+      self2.rebuild = function() {
+        if (defaultLogger !== self2) {
+          inheritedLevel = normalizeLevel(defaultLogger.getLevel());
+        }
+        replaceLoggingMethods.call(self2);
+        if (defaultLogger === self2) {
+          for (var childName in _loggersByName) {
+            _loggersByName[childName].rebuild();
+          }
+        }
+      };
+      inheritedLevel = normalizeLevel(
+        defaultLogger ? defaultLogger.getLevel() : "WARN"
+      );
+      var initialLevel = getPersistedLevel();
+      if (initialLevel != null) {
+        userLevel = normalizeLevel(initialLevel);
+      }
+      replaceLoggingMethods.call(self2);
+    }
+    defaultLogger = new Logger();
+    defaultLogger.getLogger = function getLogger(name) {
+      if (typeof name !== "symbol" && typeof name !== "string" || name === "") {
+        throw new TypeError("You must supply a name when creating a logger.");
+      }
+      var logger = _loggersByName[name];
+      if (!logger) {
+        logger = _loggersByName[name] = new Logger(
+          name,
+          defaultLogger.methodFactory
+        );
+      }
+      return logger;
+    };
+    var _log = typeof window !== undefinedType ? window.log : void 0;
+    defaultLogger.noConflict = function() {
+      if (typeof window !== undefinedType && window.log === defaultLogger) {
+        window.log = _log;
+      }
+      return defaultLogger;
+    };
+    defaultLogger.getLoggers = function getLoggers() {
+      return _loggersByName;
+    };
+    defaultLogger["default"] = defaultLogger;
+    return defaultLogger;
+  });
+})(loglevel);
+var loglevelExports = loglevel.exports;
+const log = /* @__PURE__ */ getDefaultExportFromCjs(loglevelExports);
 class VitessceConfigDatasetFile {
   /**
    * Construct a new file definition instance.
@@ -1975,7 +2250,7 @@ async function generateViewDefinition(url, vc, dataset, hintsConfig) {
     fileConfig = await configInstance.composeFileConfig();
     viewsConfig = await configInstance.composeViewsConfig(hintsConfig);
   } catch (error) {
-    console.error(error);
+    log.error(error);
     return Promise.reject(error);
   }
   dataset.addFile(fileConfig);

package/dist-tsc/VitessceAutoConfig.js

@@ -1,4 +1,5 @@
 import { CoordinationType as ct, FileType } from '@vitessce/constants-internal';
+import { log } from '@vitessce/globals';
 import { VitessceConfig, } from './VitessceConfig.js';
 import { HINTS_CONFIG, HINT_TYPE_TO_FILE_TYPE_MAP } from './constants.js';
 /**
@@ -450,7 +451,7 @@ async function generateViewDefinition(url, vc, dataset, hintsConfig) {
         viewsConfig = await configInstance.composeViewsConfig(hintsConfig);
     }
     catch (error) {
-        console.error(error);
+        log.error(error);
         return Promise.reject(error);
     }
     dataset.addFile(fileConfig);

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@vitessce/config",
-  "version": "3.5.6",
+  "version": "3.5.8",
   "author": "HIDIVE Lab at HMS",
   "homepage": "http://vitessce.io",
   "repository": {
@@ -16,8 +16,9 @@
     "dist-tsc"
   ],
   "dependencies": {
-    "@vitessce/constants-internal": "3.5.6",
-    "@vitessce/utils": "3.5.6"
+    "@vitessce/constants-internal": "3.5.8",
+    "@vitessce/utils": "3.5.8",
+    "@vitessce/globals": "3.5.8"
   },
   "scripts": {
     "bundle": "pnpm exec vite build -c ../../scripts/vite.config.js",

package/src/VitessceAutoConfig.js

@@ -1,10 +1,10 @@
 import { CoordinationType as ct, FileType } from '@vitessce/constants-internal';
+import { log } from '@vitessce/globals';
 import {
   VitessceConfig,
 } from './VitessceConfig.js';
 
 import { HINTS_CONFIG, HINT_TYPE_TO_FILE_TYPE_MAP } from './constants.js';
-
 /**
  * @param {Object} hintsConfig. The hints config for the given dataset.
  *
@@ -526,7 +526,7 @@ async function generateViewDefinition(url, vc, dataset, hintsConfig) {
     fileConfig = await configInstance.composeFileConfig();
     viewsConfig = await configInstance.composeViewsConfig(hintsConfig);
   } catch (error) {
-    console.error(error);
+    log.error(error);
     return Promise.reject(error);
   }