@apollo-annotation/jbrowse-plugin-apollo 0.2.0 → 0.2.2

package/dist/jbrowse-plugin-apollo.umd.development.js

@@ -4693,6 +4693,307 @@
 
 	var GFF3 = {};
 
+	var annotationFeatureToGFF3$1 = {};
+
+	/* eslint-disable @typescript-eslint/no-unsafe-assignment */
+	Object.defineProperty(annotationFeatureToGFF3$1, "__esModule", {
+	  value: true
+	});
+	annotationFeatureToGFF3$1.annotationFeatureToGFF3 = annotationFeatureToGFF3;
+	var util_1$4 = require$$1__default$1["default"];
+	function annotationFeatureToGFF3(feature, parentId, refSeqNames) {
+	  var _feature$attributes$g, _feature$attributes, _feature$attributes2;
+	  var attributes = JSON.parse(JSON.stringify(feature.attributes));
+	  var ontologyTerms = [];
+	  var source = (_feature$attributes$g = (_feature$attributes = feature.attributes) === null || _feature$attributes === void 0 || (_feature$attributes = _feature$attributes.gff_source) === null || _feature$attributes === void 0 ? void 0 : _feature$attributes[0]) !== null && _feature$attributes$g !== void 0 ? _feature$attributes$g : null;
+	  delete attributes.gff_source;
+	  if (parentId) {
+	    attributes.Parent = [parentId];
+	  }
+	  if (attributes.gff_id) {
+	    attributes.ID = attributes.gff_id;
+	    delete attributes.gff_id;
+	  } else if (feature.children) {
+	    attributes.ID = [feature._id];
+	  }
+	  if (attributes.gff_name) {
+	    attributes.Name = attributes.gff_name;
+	    delete attributes.gff_name;
+	  }
+	  if (attributes.gff_alias) {
+	    attributes.Alias = attributes.gff_alias;
+	    delete attributes.gff_alias;
+	  }
+	  if (attributes.gff_target) {
+	    attributes.Target = attributes.gff_target;
+	    delete attributes.gff_target;
+	  }
+	  if (attributes.gff_gap) {
+	    attributes.Gap = attributes.gff_gap;
+	    delete attributes.gff_gap;
+	  }
+	  if (attributes.gff_derives_from) {
+	    attributes.Derives_from = attributes.gff_derives_from;
+	    delete attributes.gff_derives_from;
+	  }
+	  if (attributes.gff_note) {
+	    attributes.Note = attributes.gff_note;
+	    delete attributes.gff_note;
+	  }
+	  if (attributes.gff_dbxref) {
+	    attributes.Dbxref = attributes.gff_dbxref;
+	    delete attributes.gff_dbxref;
+	  }
+	  if (attributes.gff_is_circular) {
+	    attributes.Is_circular = attributes.gff_is_circular;
+	    delete attributes.gff_is_circular;
+	  }
+	  if (attributes.gff_ontology_term) {
+	    ontologyTerms.push.apply(ontologyTerms, _toConsumableArray(attributes.gff_ontology_term));
+	    delete attributes.gff_ontology_term;
+	  }
+	  if (attributes['Gene Ontology']) {
+	    ontologyTerms.push.apply(ontologyTerms, _toConsumableArray(attributes['Gene Ontology']));
+	    delete attributes['Gene Ontology'];
+	  }
+	  if (attributes['Sequence Ontology']) {
+	    ontologyTerms.push.apply(ontologyTerms, _toConsumableArray(attributes['Sequence Ontology']));
+	    delete attributes['Sequence Ontology'];
+	  }
+	  if (ontologyTerms.length > 0) {
+	    attributes.Ontology_term = ontologyTerms;
+	  }
+	  var gff_score = (_feature$attributes2 = feature.attributes) === null || _feature$attributes2 === void 0 ? void 0 : _feature$attributes2.gff_score;
+	  var score = null;
+	  if (gff_score && gff_score.length > 0) {
+	    if (gff_score[0]) {
+	      score = Number(gff_score[0]);
+	      if (Number.isNaN(score)) {
+	        score = null;
+	      }
+	    }
+	    delete attributes.gff_score;
+	  }
+	  var locations = [{
+	    start: feature.min,
+	    end: feature.max
+	  }];
+	  return locations.map(function (location) {
+	    var _refSeqNames$feature$, _attributes$ID;
+	    return {
+	      start: Number(location.start) + 1,
+	      end: Number(location.end),
+	      seq_id: refSeqNames ? (_refSeqNames$feature$ = refSeqNames[feature.refSeq]) !== null && _refSeqNames$feature$ !== void 0 ? _refSeqNames$feature$ : null : feature.refSeq,
+	      source: source,
+	      type: feature.type,
+	      score: score,
+	      strand: feature.strand ? feature.strand === 1 ? '+' : '-' : null,
+	      phase: null,
+	      attributes: Object.keys(attributes).length > 0 ? attributes : null,
+	      derived_features: [],
+	      child_features: prepareChildFeatures(feature, (_attributes$ID = attributes.ID) === null || _attributes$ID === void 0 ? void 0 : _attributes$ID[0], refSeqNames)
+	    };
+	  });
+	}
+	function prepareChildFeatures(feature, parentID, refSeqNames) {
+	  if (!feature.children) {
+	    return [];
+	  }
+	  if (feature.type === 'mRNA') {
+	    var child_features = [];
+	    var cdsLocations = getCdsLocations(feature);
+	    var cds_idx = 0;
+	    for (var _i = 0, _Object$values = Object.values(feature.children); _i < _Object$values.length; _i++) {
+	      var child = _Object$values[_i];
+	      var gffChild = annotationFeatureToGFF3(child, parentID, refSeqNames);
+	      if (child.type === 'CDS') {
+	        var _iterator = _createForOfIteratorHelper(cdsLocations[cds_idx]),
+	          _step;
+	        try {
+	          for (_iterator.s(); !(_step = _iterator.n()).done;) {
+	            var loc = _step.value;
+	            var gffCds = JSON.parse(JSON.stringify(gffChild));
+	            if (gffCds.length != 1) {
+	              // Do we need this check?
+	              throw new Error("Unexpected CDS: ".concat(JSON.stringify(gffCds, null, 2)));
+	            }
+	            gffCds[0].start = loc.min + 1;
+	            gffCds[0].end = loc.max;
+	            gffCds[0].phase = loc.phase.toString();
+	            gffCds[0].type = loc.type; // Do we need this?
+	            child_features.push(gffCds);
+	          }
+	        } catch (err) {
+	          _iterator.e(err);
+	        } finally {
+	          _iterator.f();
+	        }
+	        cds_idx++;
+	      } else {
+	        child_features.push(gffChild);
+	      }
+	    }
+	    return child_features;
+	  }
+	  return Object.values(feature.children).map(function (child) {
+	    return annotationFeatureToGFF3(child, parentID, refSeqNames);
+	  });
+	}
+	function getTranscriptParts(feature) {
+	  if (feature.type !== 'mRNA') {
+	    throw new Error('Only features of type "mRNA" or equivalent can calculate CDS locations');
+	  }
+	  if (!feature.children) {
+	    throw new Error('no CDS or exons in mRNA');
+	  }
+	  // In AnnotationFeatureModel we have `children.values()`
+	  var children = Object.values(feature.children);
+	  var cdsChildren = children.filter(function (child) {
+	    return child.type === 'CDS';
+	  });
+	  if (cdsChildren.length === 0) {
+	    throw new Error('no CDS in mRNA');
+	  }
+	  var transcriptParts = [];
+	  var _iterator2 = _createForOfIteratorHelper(cdsChildren),
+	    _step2;
+	  try {
+	    var _loop = function _loop() {
+	      var cds = _step2.value;
+	      var cdsMax = cds.max,
+	        cdsMin = cds.min;
+	      var parts = [];
+	      var hasIntersected = false;
+	      var exonLocations = [];
+	      for (var _i2 = 0, _children = children; _i2 < _children.length; _i2++) {
+	        var child = _children[_i2];
+	        if (child.type === 'exon') {
+	          exonLocations.push({
+	            min: child.min,
+	            max: child.max
+	          });
+	        }
+	      }
+	      exonLocations.sort(function (_ref, _ref2) {
+	        var a = _ref.min;
+	        var b = _ref2.min;
+	        return a - b;
+	      });
+	      for (var _i3 = 0, _exonLocations = exonLocations; _i3 < _exonLocations.length; _i3++) {
+	        var _child = _exonLocations[_i3];
+	        var lastPart = parts.at(-1);
+	        if (lastPart) {
+	          parts.push({
+	            min: lastPart.max,
+	            max: _child.min,
+	            type: 'intron'
+	          });
+	        }
+	        var _ref3 = (0, util_1$4.intersection2)(cdsMin, cdsMax, _child.min, _child.max),
+	          _ref4 = _slicedToArray(_ref3, 2),
+	          start = _ref4[0],
+	          end = _ref4[1];
+	        var utrType = void 0;
+	        if (hasIntersected) {
+	          utrType = feature.strand === 1 ? 'threePrimeUTR' : 'fivePrimeUTR';
+	        } else {
+	          utrType = feature.strand === 1 ? 'fivePrimeUTR' : 'threePrimeUTR';
+	        }
+	        if (start !== undefined && end !== undefined) {
+	          hasIntersected = true;
+	          if (start === _child.min && end === _child.max) {
+	            parts.push({
+	              min: start,
+	              max: end,
+	              phase: 0,
+	              type: 'CDS'
+	            });
+	          } else if (start === _child.min) {
+	            parts.push({
+	              min: start,
+	              max: end,
+	              phase: 0,
+	              type: 'CDS'
+	            }, {
+	              min: end,
+	              max: _child.max,
+	              type: utrType
+	            });
+	          } else if (end === _child.max) {
+	            parts.push({
+	              min: _child.min,
+	              max: start,
+	              type: utrType
+	            }, {
+	              min: start,
+	              max: end,
+	              phase: 0,
+	              type: 'CDS'
+	            });
+	          } else {
+	            parts.push({
+	              min: _child.min,
+	              max: start,
+	              type: utrType
+	            }, {
+	              min: start,
+	              max: end,
+	              phase: 0,
+	              type: 'CDS'
+	            }, {
+	              min: end,
+	              max: _child.max,
+	              type: utrType === 'fivePrimeUTR' ? 'threePrimeUTR' : 'fivePrimeUTR'
+	            });
+	          }
+	        } else {
+	          parts.push({
+	            min: _child.min,
+	            max: _child.max,
+	            type: utrType
+	          });
+	        }
+	      }
+	      parts.sort(function (_ref5, _ref6) {
+	        var a = _ref5.min;
+	        var b = _ref6.min;
+	        return a - b;
+	      });
+	      if (feature.strand === -1) {
+	        parts.reverse();
+	      }
+	      var nextPhase = 0;
+	      var phasedParts = parts.map(function (loc) {
+	        if (loc.type !== 'CDS') {
+	          return loc;
+	        }
+	        var phase = nextPhase;
+	        nextPhase = (3 - (loc.max - loc.min - phase + 3) % 3) % 3;
+	        return _objectSpread2(_objectSpread2({}, loc), {}, {
+	          phase: phase
+	        });
+	      });
+	      transcriptParts.push(phasedParts);
+	    };
+	    for (_iterator2.s(); !(_step2 = _iterator2.n()).done;) {
+	      _loop();
+	    }
+	  } catch (err) {
+	    _iterator2.e(err);
+	  } finally {
+	    _iterator2.f();
+	  }
+	  return transcriptParts;
+	}
+	function getCdsLocations(feature) {
+	  var transcriptParts = getTranscriptParts(feature);
+	  return transcriptParts.map(function (transcript) {
+	    return transcript.filter(function (transcriptPart) {
+	      return transcriptPart.type === 'CDS';
+	    });
+	  });
+	}
+
 	var gffReservedKeys = {};
 
 	(function (exports) {
@@ -5033,6 +5334,7 @@
 	    value: true
 	  });
 	  var tslib_1 = require$$0$1;
+	  tslib_1.__exportStar(annotationFeatureToGFF3$1, exports);
 	  tslib_1.__exportStar(gffReservedKeys, exports);
 	  tslib_1.__exportStar(gff3ToAnnotationFeature$1, exports);
 	})(GFF3);
@@ -20271,7 +20573,7 @@
 	                refSeq: refSeq.toString(),
 	                start: max,
 	                end: max,
-	                message: "Feature \"".concat(_id, "\" is missing a stop codon")
+	                message: "Missing stop codon"
 	              });
 	            }
 	          } else {
@@ -20485,108 +20787,10 @@
 
 	var util$1 = {};
 
-	/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 	Object.defineProperty(util$1, "__esModule", {
 	  value: true
 	});
-	util$1.makeGFF3Feature = makeGFF3Feature;
 	util$1.splitStringIntoChunks = splitStringIntoChunks;
-	function makeGFF3Feature(feature, parentId, refSeqNames) {
-	  var _feature$attributes$s, _feature$attributes;
-	  var locations = [{
-	    start: feature.min,
-	    end: feature.max
-	  }];
-	  // const locations = feature.discontinuousLocations?.length
-	  //   ? feature.discontinuousLocations
-	  //   : [{ start: feature.start, end: feature.end, phase: feature.phase }]
-	  var attributes = JSON.parse(JSON.stringify(feature.attributes));
-	  var ontologyTerms = [];
-	  var source = (_feature$attributes$s = (_feature$attributes = feature.attributes) === null || _feature$attributes === void 0 || (_feature$attributes = _feature$attributes.source) === null || _feature$attributes === void 0 ? void 0 : _feature$attributes[0]) !== null && _feature$attributes$s !== void 0 ? _feature$attributes$s : null;
-	  delete attributes.source;
-	  if (parentId) {
-	    attributes.Parent = [parentId];
-	  }
-	  if (attributes._id) {
-	    attributes.ID = attributes._id;
-	    delete attributes._id;
-	  }
-	  if (attributes.gff_name) {
-	    attributes.Name = attributes.gff_name;
-	    delete attributes.gff_name;
-	  }
-	  if (attributes.gff_alias) {
-	    attributes.Alias = attributes.gff_alias;
-	    delete attributes.gff_alias;
-	  }
-	  if (attributes.gff_target) {
-	    attributes.Target = attributes.gff_target;
-	    delete attributes.gff_target;
-	  }
-	  if (attributes.gff_gap) {
-	    attributes.Gap = attributes.gff_gap;
-	    delete attributes.gff_gap;
-	  }
-	  if (attributes.gff_derives_from) {
-	    attributes.Derives_from = attributes.gff_derives_from;
-	    delete attributes.gff_derives_from;
-	  }
-	  if (attributes.gff_note) {
-	    attributes.Note = attributes.gff_note;
-	    delete attributes.gff_note;
-	  }
-	  if (attributes.gff_dbxref) {
-	    attributes.Dbxref = attributes.gff_dbxref;
-	    delete attributes.gff_dbxref;
-	  }
-	  if (attributes.gff_is_circular) {
-	    attributes.Is_circular = attributes.gff_is_circular;
-	    delete attributes.gff_is_circular;
-	  }
-	  if (attributes.gff_ontology_term) {
-	    ontologyTerms.push.apply(ontologyTerms, _toConsumableArray(attributes.gff_ontology_term));
-	    delete attributes.gff_ontology_term;
-	  }
-	  if (attributes['Gene Ontology']) {
-	    ontologyTerms.push.apply(ontologyTerms, _toConsumableArray(attributes['Gene Ontology']));
-	    delete attributes['Gene Ontology'];
-	  }
-	  if (attributes['Sequence Ontology']) {
-	    ontologyTerms.push.apply(ontologyTerms, _toConsumableArray(attributes['Sequence Ontology']));
-	    delete attributes['Sequence Ontology'];
-	  }
-	  if (ontologyTerms.length > 0) {
-	    attributes.Ontology_term = ontologyTerms;
-	  }
-	  return locations.map(function (location) {
-	    var _refSeqNames$feature$;
-	    return {
-	      start: location.start + 1,
-	      end: location.end,
-	      seq_id: refSeqNames ? (_refSeqNames$feature$ = refSeqNames[feature.refSeq]) !== null && _refSeqNames$feature$ !== void 0 ? _refSeqNames$feature$ : null : feature.refSeq,
-	      source: source,
-	      type: feature.type,
-	      score: null,
-	      // score: feature.score ?? null,
-	      strand: feature.strand ? feature.strand === 1 ? '+' : '-' : null,
-	      phase: null,
-	      // phase:
-	      //   location.phase === 0
-	      //     ? '0'
-	      //     : location.phase === 1
-	      //       ? '1'
-	      //       : location.phase === 2
-	      //         ? '2'
-	      //         : null,
-	      attributes: Object.keys(attributes).length > 0 ? attributes : null,
-	      derived_features: [],
-	      child_features: feature.children ? Object.values(feature.children).map(function (child) {
-	        var _attributes$ID;
-	        return makeGFF3Feature(child, (_attributes$ID = attributes.ID) === null || _attributes$ID === void 0 ? void 0 : _attributes$ID[0], refSeqNames);
-	      }) : []
-	    };
-	  });
-	}
 	function splitStringIntoChunks(input, chunkSize) {
 	  var chunks = [];
 	  for (var i = 0; i < input.length; i += chunkSize) {
@@ -20660,7 +20864,7 @@
 	}), 'Add');
 	default_1$a = Add["default"] = _default$c;
 
-	var version = "0.2.0";
+	var version = "0.2.2";
 
 	const ApolloConfigSchema = configuration.ConfigurationSchema('ApolloInternetAccount', {
 	    baseURL: {
@@ -45492,7 +45696,7 @@
 	function applyPrefixes(uri, prefixes) {
 	    for (const [prefix, uriBase] of prefixes.entries()) {
 	        if (uri.startsWith(uriBase)) {
-	            return uri.replace(uriBase, prefix);
+	            return uri.replace(uriBase, String(prefix));
 	        }
 	    }
 	    return uri;
@@ -45502,8 +45706,8 @@
 	 */
 	function expandPrefixes(uri, prefixes) {
 	    for (const [prefix, uriBase] of prefixes.entries()) {
-	        if (uri.startsWith(prefix)) {
-	            return uri.replace(prefix, uriBase);
+	        if (uri.startsWith(String(prefix))) {
+	            return uri.replace(String(prefix), uriBase);
 	        }
 	    }
 	    return uri;
@@ -47081,7 +47285,7 @@
 	                continue;
 	            }
 	            for (const [, feature] of features) {
-	                gff3Items.push(dist$2.makeGFF3Feature(require$$1$3.getSnapshot(feature)));
+	                gff3Items.push(dist$2.annotationFeatureToGFF3(require$$1$3.getSnapshot(feature)));
 	            }
 	        }
 	        for (const sequenceFeature of sequenceFeatures) {
@@ -55592,6 +55796,15 @@
 	        });
 	    }
 	    async submitChange(_change, _opts = {}) {
+	        const { clientStore } = this;
+	        const { assemblies } = clientStore;
+	        clientStore.clearCheckResults();
+	        for (const [, assembly] of assemblies) {
+	            if (assembly.backendDriverType === 'InMemoryFileDriver') {
+	                const checkResults = await checkFeatures(assembly);
+	                clientStore.addCheckResults(checkResults);
+	            }
+	        }
 	        return new dist$2.ValidationResultSet();
 	    }
 	    async searchFeatures(_term, _assemblies) {
@@ -55705,7 +55918,7 @@
 	        for (const [, refSeq] of clientAssembly.refSeqs) {
 	            const { features } = refSeq;
 	            for (const [, feature] of features) {
-	                gff3Items.push(dist$2.makeGFF3Feature(require$$1$3.getSnapshot(feature)));
+	                gff3Items.push(dist$2.annotationFeatureToGFF3(require$$1$3.getSnapshot(feature)));
 	            }
 	        }
 	        for (const [, refSeq] of clientAssembly.refSeqs) {
@@ -55801,6 +56014,9 @@
 	        deleteCheckResult(checkResultId) {
 	            self.checkResults.delete(checkResultId);
 	        },
+	        clearCheckResults() {
+	            self.checkResults.clear();
+	        },
 	    }))
 	        .volatile((self) => ({
 	        changeManager: new ChangeManager(self),
@@ -56028,7 +56244,11 @@
 	                    dynamicBlocks.forEach((block) => {
 	                        if (block.regionNumber !== undefined) {
 	                            const { assemblyName, end, refName, start } = block;
-	                            locations.push({ assemblyName, refName, start, end });
+	                            const assembly = self.apolloDataStore.assemblies.get(assemblyName);
+	                            if (assembly &&
+	                                assembly.backendDriverType === 'CollaborationServerDriver') {
+	                                locations.push({ assemblyName, refName, start, end });
+	                            }
 	                        }
 	                    });
 	                }
@@ -56084,7 +56304,11 @@
 	                        dynamicBlocks.forEach((block) => {
 	                            if (block.regionNumber !== undefined) {
 	                                const { assemblyName, end, refName, start } = block;
-	                                locations.push({ assemblyName, refName, start, end });
+	                                const assembly = self.apolloDataStore.assemblies.get(assemblyName);
+	                                if (assembly &&
+	                                    assembly.backendDriverType === 'CollaborationServerDriver') {
+	                                    locations.push({ assemblyName, refName, start, end });
+	                                }
 	                            }
 	                        });
 	                    }
@@ -56147,6 +56371,7 @@
 	                    continue;
 	                }
 	                require$$1$3.applySnapshot(jbrowse, jbrowseConfig);
+	                // @ts-expect-error snapshot seems to get wrong type?
 	                require$$1$3.applySnapshot(self, sessionSnapshot);
 	            }
 	        }),
@@ -56258,7 +56483,7 @@
 	        };
 	    });
 	    return require$$1$3.types.snapshotProcessor(sm, {
-	        postProcessor(snap) {
+	        postProcessor(snap, node) {
 	            snap.apolloSelectedFeature = undefined;
 	            const assemblies = Object.fromEntries(Object.entries(snap.apolloDataStore.assemblies).filter(([, assembly]) => assembly.backendDriverType === 'InMemoryFileDriver'));
 	            // @ts-expect-error ontologyManager isn't actually required
@@ -56267,6 +56492,21 @@
 	                assemblies,
 	                checkResults: {},
 	            };
+	            if (!node) {
+	                return snap;
+	            }
+	            const { apolloDataStore } = node;
+	            const { checkResults } = apolloDataStore;
+	            for (const [, cr] of checkResults) {
+	                const [feature] = cr.ids;
+	                if (!feature) {
+	                    continue;
+	                }
+	                const assembly = apolloDataStore.assemblies.get(feature.assemblyId);
+	                if (assembly && assembly.backendDriverType === 'InMemoryFileDriver') {
+	                    snap.apolloDataStore.checkResults[cr._id] = require$$1$3.getSnapshot(cr);
+	                }
+	            }
 	            return snap;
 	        },
 	    });