@jbrowse/plugin-trix 1.7.11 → 2.1.0

package/src/TrixTextSearchAdapter/test_data/volvox_meta.json

@@ -0,0 +1,163 @@
+{
+  "dateCreated": "2022-06-17T10:57:18.370Z",
+  "tracks": [
+    {
+      "trackId": "volvox_sv_test",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.dup.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.dup.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "volvox_sv_test_renamed",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.dup.renamed.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.dup.renamed.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "volvox_test_vcf",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.test.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.test.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "gff3tabix_genes",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "Gff3TabixAdapter",
+        "gffGzLocation": {
+          "uri": "volvox.sort.gff3.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.sort.gff3.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "volvox_filtered_vcf",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.filtered.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.filtered.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "variant_colors",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.filtered.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.filtered.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "single_exon_gene",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "Gff3TabixAdapter",
+        "gffGzLocation": {
+          "uri": "single_exon_gene.sorted.gff.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "single_exon_gene.sorted.gff.gz.tbi",
+            "locationType": "UriLocation"
+          }
+        }
+      }
+    },
+    {
+      "trackId": "volvox.inv.vcf",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfTabixAdapter",
+        "vcfGzLocation": {
+          "uri": "volvox.inv.vcf.gz",
+          "locationType": "UriLocation"
+        },
+        "index": {
+          "location": {
+            "uri": "volvox.inv.vcf.gz.tbi",
+            "locationType": "UriLocation"
+          },
+          "indexType": "TBI"
+        }
+      }
+    },
+    {
+      "trackId": "volvox.filtered.lowercase",
+      "attributesIndexed": ["Name", "ID", "Note"],
+      "excludedTypes": ["CDS", "exon"],
+      "adapterConf": {
+        "type": "VcfAdapter",
+        "vcfLocation": {
+          "uri": "volvox.filtered.lowercase.vcf",
+          "locationType": "UriLocation"
+        }
+      }
+    }
+  ],
+  "assemblyNames": ["volvox"]
+}

package/dist/TrixTextSearchAdapter/TrixTextSearchAdapter.test.js

@@ -1,76 +0,0 @@
-"use strict";
-
-var _interopRequireDefault = require("@babel/runtime/helpers/interopRequireDefault");
-
-var _regenerator = _interopRequireDefault(require("@babel/runtime/regenerator"));
-
-var _asyncToGenerator2 = _interopRequireDefault(require("@babel/runtime/helpers/asyncToGenerator"));
-
-var _BaseResults = _interopRequireDefault(require("@jbrowse/core/TextSearch/BaseResults"));
-
-var _path = _interopRequireDefault(require("path"));
-
-var _TrixTextSearchAdapter = _interopRequireDefault(require("./TrixTextSearchAdapter"));
-
-var _configSchema = _interopRequireDefault(require("./configSchema"));
-
-test('adapter can fetch output files', /*#__PURE__*/(0, _asyncToGenerator2.default)( /*#__PURE__*/_regenerator.default.mark(function _callee() {
-  var rootTemplate, urlPath, args, adapter, results, results2, test2;
-  return _regenerator.default.wrap(function _callee$(_context) {
-    while (1) {
-      switch (_context.prev = _context.next) {
-        case 0:
-          rootTemplate = _path.default.join(__dirname, '..', '..', '..', '..', 'test_data', 'volvox', 'trix').replace(/\\/g, '\\\\');
-          urlPath = decodeURI(new URL("file://".concat(rootTemplate)).href);
-          args = {
-            type: 'TrixTextSearchAdapter',
-            textSearchAdapterId: 'TrixTextSearchAdapterTest',
-            ixFilePath: {
-              uri: "".concat(urlPath, "/volvox.ix"),
-              locationType: 'UriLocation'
-            },
-            ixxFilePath: {
-              uri: "".concat(urlPath, "/volvox.ixx"),
-              locationType: 'UriLocation'
-            },
-            metaFilePath: {
-              uri: "".concat(urlPath, "/volvox_meta.json"),
-              locationType: 'UriLocation'
-            }
-          }; // create adapter
-
-          adapter = new _TrixTextSearchAdapter.default(_configSchema.default.create(args)); // prefix search
-
-          _context.next = 6;
-          return adapter.searchIndex({
-            queryString: 'apple'
-          });
-
-        case 6:
-          results = _context.sent;
-          // check results are of type BaseResult for prefix search
-          expect(results[0] instanceof _BaseResults.default).toBeTruthy();
-          expect(results[0].getLabel()).toEqual('Apple2');
-          expect(results[1].getLabel()).toEqual('Apple3'); // exact search
-
-          _context.next = 12;
-          return adapter.searchIndex({
-            queryString: 'apple3'
-          });
-
-        case 12:
-          results2 = _context.sent;
-          // check results are of type location for exact search
-          expect(results2.length).toEqual(1);
-          test2 = results2[0];
-          expect(test2 instanceof _BaseResults.default).toBeTruthy();
-          expect(test2.getLabel()).toEqual('Apple3');
-          expect(test2.getLocation()).toEqual('ctgA:17400..23000');
-
-        case 18:
-        case "end":
-          return _context.stop();
-      }
-    }
-  }, _callee);
-})));