@jbrowse/plugin-legacy-jbrowse 1.7.9 → 2.0.0

package/dist/JBrowse1Connection/jb1ToJb2.js.map

@@ -0,0 +1 @@
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package/dist/JBrowse1Connection/model.js

@@ -1,58 +1,50 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.default = _default;
-
-var _configuration = require("@jbrowse/core/configuration");
-
-var _util = require("@jbrowse/core/util");
-
-var _models = require("@jbrowse/core/pluggableElementTypes/models");
-
-var _mobxStateTree = require("mobx-state-tree");
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-var _jb1ConfigLoad = require("./jb1ConfigLoad");
-
-var _jb1ToJb = require("./jb1ToJb2");
-
-function _default(pluginManager) {
-  return _mobxStateTree.types.compose('JBrowse1Connection', (0, _models.BaseConnectionModelFactory)(pluginManager), _mobxStateTree.types.model({
-    configuration: (0, _configuration.ConfigurationReference)(_configSchema.default),
-    type: _mobxStateTree.types.literal('JBrowse1Connection')
-  }).actions(function (self) {
-    return {
-      connect: function connect() {
-        var dataDirLocation = (0, _configuration.readConfObject)(self.configuration, 'dataDirLocation');
-        var session = (0, _util.getSession)(self);
-        (0, _jb1ConfigLoad.fetchJb1)(dataDirLocation).then(function (config) {
-          var assemblyName = (0, _configuration.readConfObject)(self.configuration, 'assemblyNames')[0];
-
-          if (!assemblyName) {
-            throw new Error('assembly name required for JBrowse 1 connection');
-          }
-
-          var assemblyConf = session.assemblies.find(function (assembly) {
-            return (0, _configuration.readConfObject)(assembly, 'name') === assemblyName;
-          });
-          var sequenceAdapter = (0, _configuration.readConfObject)(assemblyConf, ['sequence', 'adapter']);
-          var jb2Tracks = config.tracks.map(function (jb1Track) {
-            var jb2Track = (0, _jb1ToJb.convertTrackConfig)(jb1Track, config.dataRoot, sequenceAdapter);
-            jb2Track.assemblyNames = [assemblyName];
-            return jb2Track;
-          });
-          self.setTrackConfs(jb2Tracks);
-        }).catch(function (error) {
-          console.error(error);
-          session.notify("There was a problem connecting to the JBrowse 1 data directory \"".concat(self.name, "\". Please make sure you have entered a valid location. The error that was thrown is: \"").concat(error, "\""), 'error');
-          session.breakConnection(self.configuration);
-        });
-      }
-    };
-  }));
-}
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+var configuration_1 = require("@jbrowse/core/configuration");
+var util_1 = require("@jbrowse/core/util");
+var models_1 = require("@jbrowse/core/pluggableElementTypes/models");
+var mobx_state_tree_1 = require("mobx-state-tree");
+var configSchema_1 = __importDefault(require("./configSchema"));
+var jb1ConfigLoad_1 = require("./jb1ConfigLoad");
+var jb1ToJb2_1 = require("./jb1ToJb2");
+function default_1(pluginManager) {
+    return mobx_state_tree_1.types.compose('JBrowse1Connection', (0, models_1.BaseConnectionModelFactory)(pluginManager), mobx_state_tree_1.types
+        .model({
+        configuration: (0, configuration_1.ConfigurationReference)(configSchema_1.default),
+        type: mobx_state_tree_1.types.literal('JBrowse1Connection'),
+    })
+        .actions(function (self) { return ({
+        connect: function () {
+            var dataDirLocation = (0, configuration_1.readConfObject)(self.configuration, 'dataDirLocation');
+            var session = (0, util_1.getSession)(self);
+            (0, jb1ConfigLoad_1.fetchJb1)(dataDirLocation)
+                .then(function (config) {
+                var assemblyName = (0, configuration_1.readConfObject)(self.configuration, 'assemblyNames')[0];
+                if (!assemblyName) {
+                    throw new Error('assembly name required for JBrowse 1 connection');
+                }
+                var assemblyConf = session.assemblies.find(function (assembly) { return (0, configuration_1.readConfObject)(assembly, 'name') === assemblyName; });
+                var sequenceAdapter = (0, configuration_1.readConfObject)(assemblyConf, [
+                    'sequence',
+                    'adapter',
+                ]);
+                var jb2Tracks = config.tracks.map(function (jb1Track) {
+                    var jb2Track = (0, jb1ToJb2_1.convertTrackConfig)(jb1Track, config.dataRoot, sequenceAdapter);
+                    jb2Track.assemblyNames = [assemblyName];
+                    return jb2Track;
+                });
+                self.setTrackConfs(jb2Tracks);
+            })
+                .catch(function (error) {
+                console.error(error);
+                session.notify("There was a problem connecting to the JBrowse 1 data directory \"".concat(self.name, "\". Please make sure you have entered a valid location. The error that was thrown is: \"").concat(error, "\""), 'error');
+                session.breakConnection(self.configuration);
+            });
+        },
+    }); }));
+}
+exports.default = default_1;
+//# sourceMappingURL=model.js.map

package/dist/JBrowse1Connection/model.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"model.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/model.js"],"names":[],"mappings":";;;;;AAAA,6DAGoC;AACpC,2CAA+C;AAC/C,qEAAuF;AACvF,mDAAuC;AACvC,gEAAyC;AAEzC,iDAA0C;AAC1C,uCAA+C;AAE/C,mBAAyB,aAAa;IACpC,OAAO,uBAAK,CAAC,OAAO,CAClB,oBAAoB,EACpB,IAAA,mCAA0B,EAAC,aAAa,CAAC,EACzC,uBAAK;SACF,KAAK,CAAC;QACL,aAAa,EAAE,IAAA,sCAAsB,EAAC,sBAAY,CAAC;QACnD,IAAI,EAAE,uBAAK,CAAC,OAAO,CAAC,oBAAoB,CAAC;KAC1C,CAAC;SACD,OAAO,CAAC,UAAA,IAAI,IAAI,OAAA,CAAC;QAChB,OAAO;YACL,IAAM,eAAe,GAAG,IAAA,8BAAc,EACpC,IAAI,CAAC,aAAa,EAClB,iBAAiB,CAClB,CAAA;YACD,IAAM,OAAO,GAAG,IAAA,iBAAU,EAAC,IAAI,CAAC,CAAA;YAChC,IAAA,wBAAQ,EAAC,eAAe,CAAC;iBACtB,IAAI,CAAC,UAAA,MAAM;gBACV,IAAM,YAAY,GAAG,IAAA,8BAAc,EACjC,IAAI,CAAC,aAAa,EAClB,eAAe,CAChB,CAAC,CAAC,CAAC,CAAA;gBACJ,IAAI,CAAC,YAAY,EAAE;oBACjB,MAAM,IAAI,KAAK,CACb,iDAAiD,CAClD,CAAA;iBACF;gBACD,IAAM,YAAY,GAAG,OAAO,CAAC,UAAU,CAAC,IAAI,CAC1C,UAAA,QAAQ,IAAI,OAAA,IAAA,8BAAc,EAAC,QAAQ,EAAE,MAAM,CAAC,KAAK,YAAY,EAAjD,CAAiD,CAC9D,CAAA;gBACD,IAAM,eAAe,GAAG,IAAA,8BAAc,EAAC,YAAY,EAAE;oBACnD,UAAU;oBACV,SAAS;iBACV,CAAC,CAAA;gBACF,IAAM,SAAS,GAAG,MAAM,CAAC,MAAM,CAAC,GAAG,CAAC,UAAA,QAAQ;oBAC1C,IAAM,QAAQ,GAAG,IAAA,6BAAkB,EACjC,QAAQ,EACR,MAAM,CAAC,QAAQ,EACf,eAAe,CAChB,CAAA;oBACD,QAAQ,CAAC,aAAa,GAAG,CAAC,YAAY,CAAC,CAAA;oBACvC,OAAO,QAAQ,CAAA;gBACjB,CAAC,CAAC,CAAA;gBACF,IAAI,CAAC,aAAa,CAAC,SAAS,CAAC,CAAA;YAC/B,CAAC,CAAC;iBACD,KAAK,CAAC,UAAA,KAAK;gBACV,OAAO,CAAC,KAAK,CAAC,KAAK,CAAC,CAAA;gBACpB,OAAO,CAAC,MAAM,CACZ,2EAAmE,IAAI,CAAC,IAAI,qGAAyF,KAAK,OAAG,EAC7K,OAAO,CACR,CAAA;gBACD,OAAO,CAAC,eAAe,CAAC,IAAI,CAAC,aAAa,CAAC,CAAA;YAC7C,CAAC,CAAC,CAAA;QACN,CAAC;KACF,CAAC,EA7Ce,CA6Cf,CAAC,CACN,CAAA;AACH,CAAC;AAxDD,4BAwDC"}

package/dist/JBrowse1Connection/types.js

@@ -1,5 +1,3 @@
 "use strict";
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
+Object.defineProperty(exports, "__esModule", { value: true });
+//# sourceMappingURL=types.js.map

package/dist/JBrowse1Connection/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../src/JBrowse1Connection/types.ts"],"names":[],"mappings":""}

package/dist/JBrowse1Connection/util.js

@@ -1,48 +1,57 @@
 "use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-Object.defineProperty(exports, "__esModule", {
-  value: true
-});
-exports.clone = clone;
-exports.deepUpdate = deepUpdate;
-exports.fillTemplate = fillTemplate;
-exports.isSource = isSource;
-exports.isTrack = isTrack;
-
-var _typeof2 = _interopRequireDefault(require("@babel/runtime/helpers/typeof"));
-
-var _getValue = _interopRequireDefault(require("get-value"));
-
+var __values = (this && this.__values) || function(o) {
+    var s = typeof Symbol === "function" && Symbol.iterator, m = s && o[s], i = 0;
+    if (m) return m.call(o);
+    if (o && typeof o.length === "number") return {
+        next: function () {
+            if (o && i >= o.length) o = void 0;
+            return { value: o && o[i++], done: !o };
+        }
+    };
+    throw new TypeError(s ? "Object is not iterable." : "Symbol.iterator is not defined.");
+};
+var __importDefault = (this && this.__importDefault) || function (mod) {
+    return (mod && mod.__esModule) ? mod : { "default": mod };
+};
+Object.defineProperty(exports, "__esModule", { value: true });
+exports.clone = exports.fillTemplate = exports.deepUpdate = exports.isSource = exports.isTrack = void 0;
+var get_value_1 = __importDefault(require("get-value"));
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 function isTrack(arg) {
-  return arg && arg.label && typeof arg.label === 'string';
-} // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-
-function isSource(arg) {
-  return arg && arg.url && typeof arg.url === 'string';
+    return arg && arg.label && typeof arg.label === 'string';
 }
-/**
- * updates a with values from b, recursively
- */
+exports.isTrack = isTrack;
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-
+function isSource(arg) {
+    return arg && arg.url && typeof arg.url === 'string';
+}
+exports.isSource = isSource;
 function deepUpdate(a, b) {
-  for (var _i = 0, _Object$keys = Object.keys(b); _i < _Object$keys.length; _i++) {
-    var prop = _Object$keys[_i];
-
-    if (prop in a && (0, _typeof2.default)(b[prop]) === 'object' && (0, _typeof2.default)(a[prop]) === 'object') {
-      deepUpdate(a[prop], b[prop]);
-    } else if (typeof a[prop] === 'undefined' || typeof b[prop] !== 'undefined') {
-      a[prop] = b[prop];
+    var e_1, _a;
+    try {
+        for (var _b = __values(Object.keys(b)), _c = _b.next(); !_c.done; _c = _b.next()) {
+            var prop = _c.value;
+            if (prop in a &&
+                typeof b[prop] === 'object' &&
+                typeof a[prop] === 'object') {
+                deepUpdate(a[prop], b[prop]);
+            }
+            else if (typeof a[prop] === 'undefined' ||
+                typeof b[prop] !== 'undefined') {
+                a[prop] = b[prop];
+            }
+        }
+    }
+    catch (e_1_1) { e_1 = { error: e_1_1 }; }
+    finally {
+        try {
+            if (_c && !_c.done && (_a = _b.return)) _a.call(_b);
+        }
+        finally { if (e_1) throw e_1.error; }
     }
-  }
-
-  return a;
+    return a;
 }
+exports.deepUpdate = deepUpdate;
 /**
  * replace variables in a template string with values
  * @param template - String with variable names in curly brackets
@@ -52,36 +61,28 @@ function deepUpdate(a, b) {
  * @returns the template string with variables in fillWith replaced
  * e.g., 'htp://foo/someurl?arg=valueforbaz'
  */
-
-
 function fillTemplate(template, fillWith) {
-  var _this = this;
-
-  return template.replace(/\{([\w\s.]+)\}/g, function (match, varName) {
-    varName = varName.replace(/\s+/g, ''); // remove all whitespace
-
-    var fill = (0, _getValue.default)(fillWith, varName);
-
-    if (fill !== undefined) {
-      if (typeof fill === 'function') {
-        return fill(varName);
-      }
-
-      return fill;
-    }
-
-    if (fillWith.callback) {
-      // @ts-ignore
-      var v = fillWith.callback.call(_this, varName);
-
-      if (v !== undefined) {
-        return v;
-      }
-    }
-
-    return match;
-  });
+    var _this = this;
+    return template.replace(/\{([\w\s.]+)\}/g, function (match, varName) {
+        varName = varName.replace(/\s+/g, ''); // remove all whitespace
+        var fill = (0, get_value_1.default)(fillWith, varName);
+        if (fill !== undefined) {
+            if (typeof fill === 'function') {
+                return fill(varName);
+            }
+            return fill;
+        }
+        if (fillWith.callback) {
+            // @ts-ignore
+            var v = fillWith.callback.call(_this, varName);
+            if (v !== undefined) {
+                return v;
+            }
+        }
+        return match;
+    });
 }
+exports.fillTemplate = fillTemplate;
 /**
  * Clones objects (including DOM nodes) and all children.
  * Warning: do not clone cyclic structures
@@ -89,53 +90,48 @@ function fillTemplate(template, fillWith) {
  * @param src - The object to clone
  */
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
-
-
 function clone(src) {
-  if (!src || (0, _typeof2.default)(src) !== 'object' || Object.prototype.toString.call(src) === '[object Function]') {
-    // null, undefined, any non-object, or function
-    return src; // anything
-  }
-
-  if (src.nodeType && 'cloneNode' in src) {
-    // DOM Node
-    return src.cloneNode(true); // Node
-  }
-
-  if (src instanceof Date) {
-    // Date
-    return new Date(src.getTime()); // Date
-  }
-
-  if (src instanceof RegExp) {
-    // RegExp
-    return new RegExp(src); // RegExp
-  }
-
-  var r;
-  var i;
-  var l;
-
-  if (Array.isArray(src)) {
-    // array
-    r = [];
-
-    for (i = 0, l = src.length; i < l; ++i) {
-      if (i in src) {
-        r[i] = clone(src[i]);
-      }
-    } // we don't clone functions for performance reasons
-    //    }else if(d.isFunction(src)){
-    //      // function
-    //      r = function(){ return src.apply(this, arguments); };
-
-  } else {
-    // generic objects
-    r = src.constructor ? new src.constructor() : {};
-  }
-
-  return mixin(r, src, clone);
+    if (!src ||
+        typeof src !== 'object' ||
+        Object.prototype.toString.call(src) === '[object Function]') {
+        // null, undefined, any non-object, or function
+        return src; // anything
+    }
+    if (src.nodeType && 'cloneNode' in src) {
+        // DOM Node
+        return src.cloneNode(true); // Node
+    }
+    if (src instanceof Date) {
+        // Date
+        return new Date(src.getTime()); // Date
+    }
+    if (src instanceof RegExp) {
+        // RegExp
+        return new RegExp(src); // RegExp
+    }
+    var r;
+    var i;
+    var l;
+    if (Array.isArray(src)) {
+        // array
+        r = [];
+        for (i = 0, l = src.length; i < l; ++i) {
+            if (i in src) {
+                r[i] = clone(src[i]);
+            }
+        }
+        // we don't clone functions for performance reasons
+        //    }else if(d.isFunction(src)){
+        //      // function
+        //      r = function(){ return src.apply(this, arguments); };
+    }
+    else {
+        // generic objects
+        r = src.constructor ? new src.constructor() : {};
+    }
+    return mixin(r, src, clone);
 }
+exports.clone = clone;
 /**
  * Copies/adds all properties of source to dest; returns dest.
  * (Lifted from dojo https://github.com/dojo/dojo/blob/master/_base/lang.js)
@@ -153,25 +149,22 @@ function clone(src) {
  * to the Javascript assignment operator.
  * @returns dest, as modified
  */
-
-
 function mixin(dest, source, copyFunc) {
-  var name;
-  var s;
-  var empty = {};
-
-  for (name in source) {
-    // the (!(name in empty) || empty[name] !== s) condition avoids copying
-    // properties in "source" inherited from Object.prototype.	 For example,
-    // if dest has a custom toString() method, don't overwrite it with the
-    // toString() method that source inherited from Object.prototype
-    s = source[name];
-
-    if (!(name in dest) || // @ts-ignore
-    dest[name] !== s && (!(name in empty) || empty[name] !== s)) {
-      dest[name] = copyFunc ? copyFunc(s) : s;
+    var name;
+    var s;
+    var empty = {};
+    for (name in source) {
+        // the (!(name in empty) || empty[name] !== s) condition avoids copying
+        // properties in "source" inherited from Object.prototype.	 For example,
+        // if dest has a custom toString() method, don't overwrite it with the
+        // toString() method that source inherited from Object.prototype
+        s = source[name];
+        if (!(name in dest) ||
+            // @ts-ignore
+            (dest[name] !== s && (!(name in empty) || empty[name] !== s))) {
+            dest[name] = copyFunc ? copyFunc(s) : s;
+        }
     }
-  }
-
-  return dest; // Object
-}
+    return dest; // Object
+}
+//# sourceMappingURL=util.js.map

package/dist/JBrowse1Connection/util.js.map

@@ -0,0 +1 @@
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