@apollo-annotation/shared 0.3.7 → 0.3.8

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js

@@ -50,7 +50,7 @@ class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFile
                 throw new Error(`Assembly "${assemblyName}" already exists`);
             }
             // get checks
-            const checkDocs = await checkModel.find({ default: true }).exec();
+            const checkDocs = await checkModel.find({ isDefault: true }).exec();
             const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
             // Add assembly
             const [newAssemblyDoc] = await assemblyModel.create([

package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.js.map

@@ -1 +1 @@
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package/dist/Changes/AddAssemblyFromFileChange.js

@@ -71,7 +71,7 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
         if (assemblyDoc) {
             throw new Error(`Assembly "${assemblyName}" already exists`);
         }
-        const checkDocs = await checkModel.find({ default: true }).exec();
+        const checkDocs = await checkModel.find({ isDefault: true }).exec();
         const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
         const [newAssemblyDoc] = await assemblyModel.create([
             {

package/dist/Changes/AddAssemblyFromFileChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddAssemblyFromFileChange.js","sourceRoot":"","sources":["../../src/Changes/AddAssemblyFromFileChange.ts"],"names":[],"mappings":";;;AASA,qDAAsD;AAEtD,6DAAyD;AAyBzD,MAAa,yBAA0B,SAAQ,uCAAkB;IAC/D,QAAQ,GAAG,2BAAoC,CAAA;IAC/C,OAAO,CAAoC;IAE3C,YACE,IAAyC,EACzC,OAAuB;QAEvB,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,OAAO,GAAG,SAAS,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,CAAA;IAC1D,CAAC;IAED,IAAI,YAAY;QACd,OAAO,aAAa,IAAI,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,YAAY,2DAA2D,CAAA;IAC7G,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QAC5C,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACzB,MAAM,CAAC,EAAE,YAAY,EAAE,OAAO,EAAE,CAAC,GAAG,OAAO,CAAA;YAC3C,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,YAAY,EAAE,OAAO,EAAE,CAAA;QACtD,CAAC;QACD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAA;IACxC,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,OAAO,EAAE,GAAG,IAAI,CAAA;QACxB,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YACxC,MAAM,CAAC,KAAK,IAAI,OAAO;gBACrB,CAAC,CAAC,IAAI,CAAC,sBAAsB,CAAC,OAAO,EAAE,YAAY,EAAE,OAAO,CAAC;gBAC7D,CAAC,CAAC,IAAI,CAAC,oBAAoB,CAAC,OAAO,EAAE,YAAY,EAAE,OAAO,CAAC,EAAE,CAAC,CAAC,CAAA;QACnE,CAAC;IACH,CAAC;IAED,KAAK,CAAC,sBAAsB,CAC1B,OAAwB,EACxB,YAAoB,EACpB,OAAiD;QAEjD,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;QAClC,MAAM,eAAe,GAAG,UAAU,IAAI,MAAM,CAAC,UAAU,CAAC,CAAA;QAExD,MAAM,EAAE,kBAAkB,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;QAC1C,IAAI,CAAC,kBAAkB,EAAE,CAAC;YACxB,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAA;QAC7D,CAAC;QAED,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,KAAK,EAAE,GAAG,OAAO,CAAA;QACpD,MAAM,EACJ,aAAa,EACb,UAAU,EACV,SAAS,EACT,YAAY,EACZ,WAAW,EACX,IAAI,GACL,GAAG,OAAO,CAAA;QAEX,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;QAC5C,MAAM,UAAU,GAAG,KAAK,EAAE,QAAQ,CAAA;QAClC,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,MAAM,IAAI,KAAK,CAAC,iCAAiC,KAAK,EAAE,EAAE,EAAE,CAAC,CAAA;QAC/D,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC9C,MAAM,WAAW,GAAG,MAAM,EAAE,QAAQ,CAAA;QACpC,IAAI,CAAC,WAAW,EAAE,CAAC;YACjB,MAAM,IAAI,KAAK,CAAC,iCAAiC,MAAM,EAAE,EAAE,EAAE,CAAC,CAAA;QAChE,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,KAAK,CAAC,CAAA;QAC9C,MAAM,WAAW,GAAG,MAAM,EAAE,QAAQ,CAAA;QACpC,IAAI,CAAC,WAAW,EAAE,CAAC;YACjB,MAAM,IAAI,KAAK,CAAC,iCAAiC,MAAM,EAAE,EAAE,EAAE,CAAC,CAAA;QAChE,CAAC;QAED,MAAM,KAAK,GAAG,YAAY,CAAC,aAAa,CAAC,KAAK,CAAC,CAAA;QAC/C,MAAM,GAAG,GAAG,YAAY,CAAC,aAAa,CAAC,MAAM,CAAC,CAAA;QAC9C,MAAM,GAAG,GAAG,YAAY,CAAC,aAAa,CAAC,MAAM,CAAC,CAAA;QAC9C,MAAM,eAAe,GAAG,IAAI,gCAAiB,CAAC,EAAE,KAAK,EAAE,GAAG,EAAE,GAAG,EAAE,CAAC,CAAA;QAClE,MAAM,gBAAgB,GAAG,MAAM,eAAe,CAAC,gBAAgB,EAAE,CAAA;QACjE,MAAM,OAAO,CAAC,GAAG,CAAC,CAAC,KAAK,CAAC,KAAK,EAAE,EAAE,GAAG,CAAC,KAAK,EAAE,EAAE,GAAG,CAAC,KAAK,EAAE,CAAC,CAAC,CAAA;QAE5D,MAAM,WAAW,GAAG,MAAM,aAAa;aACpC,OAAO,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC;aAC/B,IAAI,EAAE,CAAA;QACT,IAAI,WAAW,EAAE,CAAC;YAChB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,kBAAkB,CAAC,CAAA;QAC9D,CAAC;QACD,MAAM,SAAS,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,EAAE,SAAS,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAA;QACnE,MAAM,MAAM,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;QACtE,MAAM,CAAC,cAAc,CAAC,GAAG,MAAM,aAAa,CAAC,MAAM,CAAC;YAClD;gBACE,GAAG,EAAE,IAAI,CAAC,QAAQ;gBAClB,IAAI,EAAE,YAAY;gBAClB,IAAI;gBACJ,MAAM,EAAE,CAAC,CAAC;gBACV,OAAO;gBACP,MAAM;aACP;SACF,CAAC,CAAA;QACF,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CACjB,uBAAuB,YAAY,aAAa,cAAc,CAAC,GAAG,GAAG,CACtE,CAAA;QAED,KAAK,MAAM,YAAY,IAAI,gBAAgB,EAAE,CAAC;YAC5C,MAAM,CAAC,YAAY,CAAC,GAAG,MAAM,WAAW,CAAC,MAAM,CAAC;gBAC9C;oBACE,IAAI,EAAE,YAAY;oBAClB,QAAQ,EAAE,cAAc,CAAC,GAAG;oBAC5B,MAAM,EAAE,gBAAgB,CAAC,YAAY,CAAC;oBACtC,GAAG,CAAC,eAAe,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;oBAC5D,IAAI;oBACJ,MAAM,EAAE,CAAC,CAAC;iBACX;aACF,CAAC,CAAA;YACF,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CACjB,qBAAqB,YAAY,aAAa,YAAY,CAAC,GAAG,GAAG,CAClE,CAAA;QACH,CAAC;IACH,CAAC;IAED,KAAK,CAAC,oBAAoB,CACxB,OAAwB,EACxB,YAAoB,EACpB,MAAc;QAEd,MAAM,EAAE,aAAa,EAAE,UAAU,EAAE,SAAS,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QAC9D,oBAAoB;QACpB,MAAM,OAAO,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,CAAA;QACvD,IAAI,CAAC,OAAO,EAAE,CAAC;YACb,MAAM,IAAI,KAAK,CAAC,SAAS,MAAM,sBAAsB,CAAC,CAAA;QACxD,CAAC;QACD,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CAAC,WAAW,MAAM,gBAAgB,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAA;QAEzE,6BAA6B;QAC7B,MAAM,WAAW,GAAG,MAAM,aAAa;aACpC,OAAO,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC;aAC/B,IAAI,EAAE,CAAA;QACT,IAAI,WAAW,EAAE,CAAC;YAChB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,kBAAkB,CAAC,CAAA;QAC9D,CAAC;QACD,MAAM,SAAS,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAA;QACjE,MAAM,MAAM,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;QACtE,eAAe;QACf,MAAM,CAAC,cAAc,CAAC,GAAG,MAAM,aAAa,CAAC,MAAM,CAAC;YAClD;gBACE,GAAG,EAAE,IAAI,CAAC,QAAQ;gBAClB,IAAI,EAAE,YAAY;gBAClB,IAAI;gBACJ,MAAM,EAAE,CAAC,CAAC;gBACV,OAAO,EAAE,EAAE,EAAE,EAAE,MAAM,EAAE;gBACvB,MAAM;aACP;SACF,CAAC,CAAA;QACF,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CACjB,uBAAuB,YAAY,aAAa,cAAc,CAAC,GAAG,GAAG,C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package/dist/Changes/AddRefSeqAliasesChange.js

@@ -17,18 +17,16 @@ class AddRefSeqAliasesChange extends common_1.AssemblySpecificChange {
             throw new Error(`assembly ${this.assembly} not found`);
         }
         const sessionAliases = assembly.refNameAliases;
-        const sessionLCAliases = assembly.lowerCaseRefNameAliases;
-        if (!sessionAliases || !sessionLCAliases) {
+        if (!sessionAliases) {
             throw new Error('Session refNameAliases not found in assembly');
         }
         for (const refSeqAlias of this.refSeqAliases) {
             const { aliases, refName } = refSeqAlias;
             for (const alias of aliases) {
                 sessionAliases[alias] = refName;
-                sessionLCAliases[alias.toLowerCase()] = refName;
             }
         }
-        assembly.setRefNameAliases(sessionAliases, sessionLCAliases);
+        assembly.setRefNameAliases(sessionAliases);
         return Promise.resolve();
     }
     getInverse() {

package/dist/Changes/AddRefSeqAliasesChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"AddRefSeqAliasesChange.js","sourceRoot":"","sources":["../../src/Changes/AddRefSeqAliasesChange.ts"],"names":[],"mappings":";;;AAAA,sDAQkC;AAClC,6CAA+C;AAa/C,MAAa,sBAAuB,SAAQ,+BAAsB;IAChE,QAAQ,GAAG,wBAAiC,CAAA;IAC5C,aAAa,CAA2B;IAExC,YAAY,IAAmC,EAAE,OAAuB;QACtE,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,aAAa,GAAG,IAAI,CAAC,aAAa,CAAA;IACzC,CAAC;IAED,eAAe,CAAC,eAAgC;QAC9C,MAAM,EAAE,eAAe,EAAE,GAAG,IAAA,iBAAU,EAAC,eAAe,CAAC,CAAA;QACvD,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAA;QACnD,IAAI,CAAC,QAAQ,EAAE,CAAC;YACd,MAAM,IAAI,KAAK,CAAC,YAAY,IAAI,CAAC,QAAQ,YAAY,CAAC,CAAA;QACxD,CAAC;QACD,MAAM,cAAc,GAAG,QAAQ,CAAC,cAAc,CAAA;QAE9C,IAAI,CAAC,cAAc,EAAE,CAAC;YACpB,MAAM,IAAI,KAAK,CAAC,8CAA8C,CAAC,CAAA;QACjE,CAAC;QAED,KAAK,MAAM,WAAW,IAAI,IAAI,CAAC,aAAa,EAAE,CAAC;YAC7C,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,WAAW,CAAA;YACxC,KAAK,MAAM,KAAK,IAAI,OAAO,EAAE,CAAC;gBAC5B,cAAc,CAAC,KAAK,CAAC,GAAG,OAAO,CAAA;YACjC,CAAC;QACH,CAAC;QACD,QAAQ,CAAC,iBAAiB,CAAC,cAAc,CAAC,CAAA;QAC1C,OAAO,OAAO,CAAC,OAAO,EAAE,CAAA;IAC1B,CAAC;IAED,UAAU;QACR,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;IAC5C,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,QAAQ,EAAE,aAAa,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QAClD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,aAAa,EAAE,CAAA;IAC9C,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,WAAW,EAAE,OAAO,EAAE,GAAG,OAAO,CAAA;QACxC,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,aAAa,EAAE,GAAG,IAAI,CAAA;QAEhD,KAAK,MAAM,WAAW,IAAI,aAAa,EAAE,CAAC;YACxC,MAAM,CAAC,KAAK,EAAE,CACZ,wCAAwC,QAAQ,kBAAkB,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,EAAE,CAChG,CAAA;YACD,MAAM,EAAE,OAAO,EAAE,OAAO,EAAE,GAAG,WAAW,CAAA;YACxC,MAAM,WAAW;iBACd,SAAS,CAAC,EAAE,QAAQ,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,OAAO,EAAE,EAAE,CAAC;iBAC7D,OAAO,CAAC,OAAO,CAAC,CAAA;QACrB,CAAC;IACH,CAAC;IAED,kBAAkB,CAAC,QAA4B;QAC7C,MAAM,IAAI,KAAK,CAAC,yBAAyB,CAAC,CAAA;IAC5C,CAAC;IAED,2EAA2E;IAC3E,IAAI,YAAY;QACd,OAAO,iCAAiC,CAAA;IAC1C,CAAC;CACF;AA/DD,wDA+DC"}

package/dist/Changes/ImportJBrowseConfigChange.js

@@ -25,7 +25,7 @@ function filterJBrowseConfig(config) {
         filteredConfig.plugins = plugins.filter((p) => p.name !== 'Apollo');
     }
     if (tracks) {
-        filteredConfig.trackss = tracks.filter((t) => t.type !== 'ApolloTrack');
+        filteredConfig.tracks = tracks.filter((t) => t.type !== 'ApolloTrack');
     }
     return filteredConfig;
 }

package/dist/Changes/ImportJBrowseConfigChange.js.map

@@ -1 +1 @@
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+{"version":3,"file":"ImportJBrowseConfigChange.js","sourceRoot":"","sources":["../../src/Changes/ImportJBrowseConfigChange.ts"],"names":[],"mappings":";;;AA2CA,kDAqCC;AAhFD,qDAAqD;AACrD,sDAMkC;AAoClC,SAAgB,mBAAmB,CAAC,MAAqB;IACvD,MAAM,EACJ,GAAG,EACH,GAAG,EACH,UAAU,EACV,aAAa,EACb,gBAAgB,EAChB,OAAO,EACP,MAAM,EACN,GAAG,IAAI,EACR,GAAG,MAAM,CAAA;IACV,sEAAsE;IACtE,MAAM,cAAc,GAAG,IAAqB,CAAA;IAC5C,IAAI,UAAU,EAAE,CAAC;QACf,cAAc,CAAC,UAAU,GAAG,UAAU,CAAC,MAAM,CAC3C,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,QAAQ,CAAC,OAAO,CAAC,IAAI,KAAK,uBAAuB,CAC3D,CAAA;IACH,CAAC;IACD,IAAI,aAAa,EAAE,YAAY,EAAE,OAAO,EAAE,CAAC;QACzC,MAAM,EAAE,OAAO,EAAE,GAAG,gBAAgB,EAAE,GAAG,aAAa,CAAC,YAAY,CAAA;QACnE,cAAc,CAAC,aAAa,GAAG;YAC7B,GAAG,aAAa;YAChB,YAAY,EAAE,gBAAgB;SAC/B,CAAA;IACH,CAAC;IACD,IAAI,gBAAgB,EAAE,CAAC;QACrB,cAAc,CAAC,gBAAgB,GAAG,gBAAgB,CAAC,MAAM,CACvD,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,uBAAuB,CAC1C,CAAA;IACH,CAAC;IACD,IAAI,OAAO,EAAE,CAAC;QACZ,cAAc,CAAC,OAAO,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,QAAQ,CAAC,CAAA;IACrE,CAAC;IACD,IAAI,MAAM,EAAE,CAAC;QACX,cAAc,CAAC,MAAM,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,KAAK,aAAa,CAAC,CAAA;IACxE,CAAC;IACD,OAAO,cAAc,CAAA;AACvB,CAAC;AAED,MAAa,yBAA0B,SAAQ,eAAM;IACnD,QAAQ,GAAG,2BAAoC,CAAA;IAC/C,gBAAgB,CAAgB;IAChC,gBAAgB,CAAgB;IAEhC,YACE,IAAyC,EACzC,OAAuB;QAEvB,KAAK,CAAC,IAAI,EAAE,OAAO,CAAC,CAAA;QACpB,IAAI,CAAC,gBAAgB,GAAG,IAAI,CAAC,gBAAgB,CAAA;QAC7C,IAAI,CAAC,gBAAgB,GAAG,IAAI,CAAC,gBAAgB,CAAA;IAC/C,CAAC;IAED,MAAM;QACJ,MAAM,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QAC7D,OAAO,EAAE,QAAQ,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,CAAA;IACzD,CAAC;IAED,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,kBAAkB,EAAE,GAAG,OAAO,CAAA;QACtC,MAAM,EAAE,MAAM,EAAE,gBAAgB,EAAE,GAAG,IAAI,CAAA;QACzC,MAAM,kBAAkB,CAAC,UAAU,EAAE,CAAA;QACrC,IAAI,CAAC,gBAAgB,EAAE,CAAC;YACtB,OAAM;QACR,CAAC;QACD,MAAM,cAAc,GAAG,mBAAmB,CAAC,gBAAgB,CAAC,CAAA;QAC5D,MAAM,kBAAkB,CAAC,MAAM,CAAC,cAAc,CAAC,CAAA;QAC/C,MAAM,CAAC,KAAK,EAAE,CAAC,2BAA2B,CAAC,CAAA;IAC7C,CAAC;IAED,KAAK,CAAC,kBAAkB,CAAC,QAA4B;QACnD,MAAM,IAAI,KAAK,CAAC,oCAAoC,CAAC,CAAA;IACvD,CAAC;IAED,gEAAgE;IAChE,KAAK,CAAC,eAAe,CAAC,UAA2B,IAAG,CAAC;IAErD,UAAU;QACR,MAAM,EAAE,MAAM,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,GAAG,IAAI,CAAA;QAC3D,OAAO,IAAI,yBAAyB,CAClC;YACE,QAAQ,EAAE,2BAA2B;YACrC,gBAAgB,EAAE,gBAAgB;YAClC,gBAAgB,EAAE,gBAAgB;SACnC,EACD,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF;AAjDD,8DAiDC"}

package/dist/Changes/MergeExonsChange.d.ts

@@ -25,6 +25,5 @@ export declare class MergeExonsChange extends FeatureChange {
     executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
     executeOnClient(dataStore: ClientDataStore): Promise<void>;
     getInverse(): UndoMergeExonsChange;
-    mergeAttributes(firstExon: AnnotationFeatureSnapshot, secondExon: AnnotationFeatureSnapshot): Record<string, string[]>;
 }
 export {};

package/dist/Changes/MergeExonsChange.js

@@ -1,9 +1,11 @@
 "use strict";
+/* eslint-disable unicorn/prefer-structured-clone */
 /* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 Object.defineProperty(exports, "__esModule", { value: true });
 exports.MergeExonsChange = void 0;
 const common_1 = require("@apollo-annotation/common");
+const util_1 = require("../util");
 const DeleteFeatureChange_1 = require("./DeleteFeatureChange");
 const UndoMergeExonsChange_1 = require("./UndoMergeExonsChange");
 class MergeExonsChange extends common_1.FeatureChange {
@@ -54,7 +56,13 @@ class MergeExonsChange extends common_1.FeatureChange {
             }
             mergedExon.min = Math.min(firstExon.min, secondExon.min);
             mergedExon.max = Math.max(firstExon.max, secondExon.max);
-            mergedExon.attributes = this.mergeAttributes(firstExon, secondExon);
+            const mergedAttributes = mergedExon.attributes
+                ? JSON.parse(JSON.stringify(mergedExon.attributes))
+                : {};
+            mergedAttributes.merged_with = [
+                (0, util_1.stringifyAttributes)((0, util_1.attributesToRecords)(secondExon.attributes)),
+            ];
+            mergedExon.attributes = mergedAttributes;
             const deletedIds = (0, DeleteFeatureChange_1.findAndDeleteChildFeature)(topLevelFeature, secondExon._id, this);
             deletedIds.push(secondExon._id);
             topLevelFeature.allIds = topLevelFeature.allIds.filter((id) => !deletedIds.includes(id));
@@ -77,11 +85,12 @@ class MergeExonsChange extends common_1.FeatureChange {
             }
             mergedExon.setMin(Math.min(firstExon.min, secondExon.min));
             mergedExon.setMax(Math.max(firstExon.max, secondExon.max));
-            const mergedAttrs = this.mergeAttributes(firstExon, secondExon);
-            mergedExon.setAttributes(new Map());
-            for (const key of Object.keys(mergedAttrs)) {
-                mergedExon.setAttribute(key, mergedAttrs[key]);
+            const mrg = mergedExon.attributes.get('merged_with')?.slice() ?? [];
+            const mergedWith = (0, util_1.stringifyAttributes)((0, util_1.attributesToRecords)(secondExon.attributes));
+            if (!mrg.includes(mergedWith)) {
+                mrg.push(mergedWith);
             }
+            mergedExon.setAttribute('merged_with', mrg);
             mergedExon.parent?.deleteChild(secondExon._id);
         }
     }
@@ -100,31 +109,6 @@ class MergeExonsChange extends common_1.FeatureChange {
             assembly,
         }, { logger });
     }
-    mergeAttributes(firstExon, secondExon) {
-        let mergedAttrs = {};
-        if (firstExon.attributes) {
-            // eslint-disable-next-line unicorn/prefer-structured-clone
-            mergedAttrs = JSON.parse(JSON.stringify(firstExon.attributes));
-        }
-        if (secondExon.attributes) {
-            // eslint-disable-next-line unicorn/prefer-structured-clone
-            const attrs = JSON.parse(JSON.stringify(secondExon.attributes));
-            for (const key of Object.keys(attrs)) {
-                if (key === '_id' || key === 'gff_id') {
-                    continue;
-                }
-                if (!Object.keys(mergedAttrs).includes(key)) {
-                    mergedAttrs[key] = [];
-                }
-                attrs[key].map((x) => {
-                    if (!mergedAttrs[key].includes(x)) {
-                        mergedAttrs[key].push(x);
-                    }
-                });
-            }
-        }
-        return mergedAttrs;
-    }
 }
 exports.MergeExonsChange = MergeExonsChange;
 //# sourceMappingURL=MergeExonsChange.js.map

package/dist/Changes/MergeExonsChange.js.map

@@ -1 +1 @@
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package/dist/Changes/MergeTranscriptsChange.d.ts

@@ -20,6 +20,7 @@ export declare class MergeTranscriptsChange extends FeatureChange {
     typeName: "MergeTranscriptsChange";
     changes: MergeTranscriptsChangeDetails[];
     constructor(json: SerializedMergeTranscriptsChange, options?: ChangeOptions);
+    get notification(): string;
     toJSON(): SerializedMergeTranscriptsChange;
     executeOnServer(backend: ServerDataStore): Promise<void>;
     mergeTranscriptsOnServer(firstTranscript: Feature, secondTranscript: AnnotationFeatureSnapshot): void;
@@ -27,10 +28,7 @@ export declare class MergeTranscriptsChange extends FeatureChange {
     executeOnClient(dataStore: ClientDataStore): Promise<void>;
     mergeTranscriptsOnClient(firstTranscript: AnnotationFeature, secondTranscript: AnnotationFeatureSnapshot): void;
     mergeFeatureIntoTranscriptOnClient(secondFeatureChild: AnnotationFeatureSnapshot, firstTranscript: AnnotationFeature): void;
-    isAnnotationFeature(obj: any): obj is AnnotationFeature;
     executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<void>;
-    mergeAttributes(destination: Feature | AnnotationFeature, source: AnnotationFeatureSnapshot): Record<string, string[]>;
-    mergeTranscriptAttributes(firstTranscript: Feature | AnnotationFeature, secondTranscript: AnnotationFeatureSnapshot): void;
     getInverse(): UndoMergeTranscriptsChange;
 }
 export {};

package/dist/Changes/MergeTranscriptsChange.js

@@ -6,6 +6,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
 exports.MergeTranscriptsChange = void 0;
 const common_1 = require("@apollo-annotation/common");
 const util_1 = require("@jbrowse/core/util");
+const mobx_state_tree_1 = require("mobx-state-tree");
+const util_2 = require("../util");
 const DeleteFeatureChange_1 = require("./DeleteFeatureChange");
 const UndoMergeTranscriptsChange_1 = require("./UndoMergeTranscriptsChange");
 class MergeTranscriptsChange extends common_1.FeatureChange {
@@ -15,6 +17,10 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
         super(json, options);
         this.changes = 'changes' in json ? json.changes : [json];
     }
+    // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+    get notification() {
+        return 'Transcripts successfully merged';
+    }
     toJSON() {
         const { assembly, changedIds, changes, typeName } = this;
         if (changes.length === 1) {
@@ -60,7 +66,16 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
     mergeTranscriptsOnServer(firstTranscript, secondTranscript) {
         firstTranscript.min = Math.min(firstTranscript.min, secondTranscript.min);
         firstTranscript.max = Math.max(firstTranscript.max, secondTranscript.max);
-        this.mergeTranscriptAttributes(firstTranscript, secondTranscript);
+        const mergedAttributes = firstTranscript.attributes
+            ? JSON.parse(JSON.stringify(firstTranscript.attributes))
+            : {};
+        if (secondTranscript.attributes) {
+            if (!Object.keys(mergedAttributes).includes('merged_with')) {
+                mergedAttributes.merged_with = [];
+            }
+            mergedAttributes.merged_with.push((0, util_2.stringifyAttributes)((0, util_2.attributesToRecords)(secondTranscript.attributes)));
+        }
+        firstTranscript.attributes = mergedAttributes;
         if (secondTranscript.children) {
             for (const [, secondFeatureChild] of Object.entries(secondTranscript.children)) {
                 this.mergeFeatureIntoTranscriptOnServer(secondFeatureChild, firstTranscript);
@@ -73,19 +88,39 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
         }
         let merged = false;
         let mrgChild;
-        for (const [fKey, firstFeatureChild] of firstTranscript.children) {
+        let toDelete;
+        for (const [, firstFeatureChild] of firstTranscript.children) {
             if (!merged || !mrgChild) {
+                toDelete = false;
                 mrgChild = firstFeatureChild;
             }
+            else {
+                toDelete = true;
+            }
             if (mrgChild.type === secondFeatureChild.type &&
                 mrgChild.type === firstFeatureChild.type &&
                 (0, util_1.doesIntersect2)(secondFeatureChild.min, secondFeatureChild.max, mrgChild.min, mrgChild.max) &&
                 (0, util_1.doesIntersect2)(firstFeatureChild.min, firstFeatureChild.max, mrgChild.min, mrgChild.max)) {
                 mrgChild.min = Math.min(secondFeatureChild.min, mrgChild.min, firstFeatureChild.min);
                 mrgChild.max = Math.max(secondFeatureChild.max, mrgChild.max, firstFeatureChild.max);
-                const mergedAttrs = this.mergeAttributes(mrgChild, secondFeatureChild);
-                mrgChild.attributes = mergedAttrs;
-                firstTranscript.children.delete(fKey);
+                if (!mrgChild.attributes) {
+                    mrgChild.attributes = {};
+                }
+                const mrgChildAttr = JSON.parse(JSON.stringify(mrgChild.attributes));
+                if (!Object.keys(mrgChildAttr).includes('merged_with')) {
+                    mrgChildAttr.merged_with = [];
+                }
+                const mergedWithAttributes = mrgChildAttr.merged_with;
+                mergedWithAttributes.push((0, util_2.stringifyAttributes)((0, util_2.attributesToRecords)(secondFeatureChild.attributes)));
+                if (toDelete) {
+                    const recs = firstFeatureChild.attributes
+                        ? JSON.parse(JSON.stringify(firstFeatureChild.attributes))
+                        : undefined;
+                    mergedWithAttributes.push((0, util_2.stringifyAttributes)(recs));
+                    firstTranscript.children.delete(firstFeatureChild._id.toString());
+                }
+                mrgChildAttr.merged_with = [...new Set(mergedWithAttributes)];
+                mrgChild.attributes = mrgChildAttr;
                 merged = true;
             }
         }
@@ -124,7 +159,13 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
     mergeTranscriptsOnClient(firstTranscript, secondTranscript) {
         firstTranscript.setMin(Math.min(firstTranscript.min, secondTranscript.min));
         firstTranscript.setMax(Math.max(firstTranscript.max, secondTranscript.max));
-        this.mergeTranscriptAttributes(firstTranscript, secondTranscript);
+        const mrg = firstTranscript.attributes.get('merged_with')?.slice() ?? [];
+        const mergedWith = (0, util_2.stringifyAttributes)((0, util_2.attributesToRecords)(secondTranscript.attributes));
+        if (!mrg.includes(mergedWith)) {
+            // executeOnClient runs twice (?!) so avoid adding this key again
+            mrg.push(mergedWith);
+        }
+        firstTranscript.setAttribute('merged_with', mrg);
         if (secondTranscript.children) {
             for (const [, secondFeatureChild] of Object.entries(secondTranscript.children)) {
                 this.mergeFeatureIntoTranscriptOnClient(secondFeatureChild, firstTranscript);
@@ -152,15 +193,13 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
                 (0, util_1.doesIntersect2)(firstFeatureChild.min, firstFeatureChild.max, mrgChild.min, mrgChild.max)) {
                 mrgChild.setMin(Math.min(secondFeatureChild.min, mrgChild.min, firstFeatureChild.min));
                 mrgChild.setMax(Math.max(secondFeatureChild.max, mrgChild.max, firstFeatureChild.max));
-                const mergedAttrs = this.mergeAttributes(mrgChild, secondFeatureChild);
-                Object.entries(mergedAttrs).map(([key, value]) => {
-                    if (mrgChild) {
-                        mrgChild.setAttribute(key, value);
-                    }
-                });
+                const mergedWithAttributes = mrgChild.attributes.get('merged_with')?.slice() ?? [];
+                mergedWithAttributes.push((0, util_2.stringifyAttributes)((0, util_2.attributesToRecords)(secondFeatureChild.attributes)));
                 if (toDelete) {
+                    mergedWithAttributes.push((0, util_2.stringifyAttributes)((0, mobx_state_tree_1.getSnapshot)(firstFeatureChild).attributes));
                     firstTranscript.deleteChild(firstFeatureChild._id);
                 }
+                mrgChild.setAttribute('merged_with', [...new Set(mergedWithAttributes)]);
                 merged = true;
             }
         }
@@ -169,58 +208,18 @@ class MergeTranscriptsChange extends common_1.FeatureChange {
                 mrgChild.addChild(child);
             });
         }
-        if (!(merged && mrgChild)) {
+        if (merged && mrgChild) {
+            firstTranscript.addChild((0, mobx_state_tree_1.getSnapshot)(mrgChild));
+        }
+        else {
             // This secondFeatureChild has no overlap with any feature in the
             // receiving transcript so we add it as it is to the receiving transcript
             firstTranscript.addChild(secondFeatureChild);
         }
     }
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    isAnnotationFeature(obj) {
-        return (
-        // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
-        typeof obj.setMin === 'function' &&
-            // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
-            typeof obj.setMax === 'function' &&
-            // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
-            typeof obj.addChild === 'function' &&
-            // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
-            typeof obj.deleteChild === 'function');
-    }
     async executeOnLocalGFF3(_backend) {
         throw new Error('executeOnLocalGFF3 not implemented');
     }
-    /* Merge attributes from source into destination */
-    mergeAttributes(destination, source) {
-        const destAttrs = destination.attributes
-            ? JSON.parse(JSON.stringify(destination.attributes))
-            : {};
-        if (source.attributes) {
-            const sourceAttrs = JSON.parse(JSON.stringify(source.attributes));
-            Object.entries(sourceAttrs).map(([key, value]) => {
-                if (!(key in destAttrs)) {
-                    destAttrs[key] = [];
-                }
-                value.map((x) => {
-                    if (!destAttrs[key].includes(x)) {
-                        destAttrs[key].push(x);
-                    }
-                });
-            });
-        }
-        return destAttrs;
-    }
-    mergeTranscriptAttributes(firstTranscript, secondTranscript) {
-        const txAttrs = this.mergeAttributes(firstTranscript, secondTranscript);
-        if (this.isAnnotationFeature(firstTranscript)) {
-            Object.entries(txAttrs).map(([key, value]) => {
-                firstTranscript.setAttribute(key, value);
-            });
-        }
-        else {
-            firstTranscript.attributes = txAttrs;
-        }
-    }
     getInverse() {
         const { assembly, changedIds, changes, logger } = this;
         const inverseChangedIds = [...changedIds].reverse();

package/dist/Changes/MergeTranscriptsChange.js.map

@@ -1 +1 @@
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package/dist/Checks/CDSCheck.d.ts

@@ -4,6 +4,6 @@ export declare class CDSCheck extends Check {
     name: string;
     causes: string[];
     version: number;
-    default: boolean;
+    isDefault: boolean;
     checkFeature(feature: AnnotationFeatureSnapshot, getSequence: (start: number, end: number) => Promise<string>): Promise<CheckResultSnapshot[]>;
 }

package/dist/Checks/CDSCheck.js

@@ -21,7 +21,6 @@ var CAUSES;
     CAUSES[CAUSES["InternalStopCodon"] = 0] = "InternalStopCodon";
     CAUSES[CAUSES["MissingStartCodon"] = 1] = "MissingStartCodon";
     CAUSES[CAUSES["MissingStopCodon"] = 2] = "MissingStopCodon";
-    CAUSES[CAUSES["MultipleOfThree"] = 3] = "MultipleOfThree";
 })(CAUSES || (CAUSES = {}));
 const iupacComplements = {
     G: 'C',
@@ -126,6 +125,9 @@ async function checkMRNA(feature, getSequence) {
     for (const cdsLocation of cdsLocations) {
         const sequence = await getCDSSequence(cdsLocation, strand, getSequence);
         const codons = splitSequenceInCodons(sequence);
+        const cdsEnd = strand === -1
+            ? cdsLocation.at(0)?.min ?? min
+            : cdsLocation.at(-1)?.max ?? max;
         if (sequence.length % 3 === 0) {
             const start_codon = codons.at(0);
             if (start_codon && !(start_codon.toUpperCase() in START_CODONS)) {
@@ -146,9 +148,6 @@ async function checkMRNA(feature, getSequence) {
             }
             const lastCodon = codons.at(-1); // Last codon is supposed to be a stop
             if (lastCodon && !(lastCodon.toUpperCase() in STOP_CODONS)) {
-                const cdsEnd = strand === -1
-                    ? cdsLocation.at(0)?.min ?? min
-                    : cdsLocation.at(-1)?.max ?? max;
                 checkResults.push({
                     _id: new bson_objectid_1.default().toHexString(),
                     name: CHECK_NAME,
@@ -165,12 +164,12 @@ async function checkMRNA(feature, getSequence) {
             checkResults.push({
                 _id: new bson_objectid_1.default().toHexString(),
                 name: CHECK_NAME,
-                cause: CAUSES[CAUSES.MultipleOfThree],
+                cause: CAUSES[CAUSES.MissingStopCodon],
                 ids,
                 refSeq: refSeq.toString(),
-                start: min,
-                end: max,
-                message: `The coding sequence for feature "${_id}" is not a multiple of three`,
+                start: cdsEnd,
+                end: cdsEnd,
+                message: `Missing stop codon: The coding sequence for feature "${_id}" is not a multiple of three`,
             });
         }
         for (const [idx, codon] of codons.entries()) {
@@ -246,7 +245,7 @@ class CDSCheck extends common_1.Check {
     name = CHECK_NAME;
     causes = getCauses();
     version = 1;
-    default = true;
+    isDefault = true;
     async checkFeature(feature, getSequence) {
         if (feature.type === 'mRNA') {
             return checkMRNA(feature, getSequence);

package/dist/Checks/CDSCheck.js.map

@@ -1 +1 @@
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package/dist/Checks/TranscriptCheck.d.ts

@@ -0,0 +1,9 @@
+import { Check } from '@apollo-annotation/common';
+import { type AnnotationFeatureSnapshot, type CheckResultSnapshot } from '@apollo-annotation/mst';
+export declare class TranscriptCheck extends Check {
+    name: string;
+    causes: string[];
+    version: number;
+    isDefault: boolean;
+    checkFeature(feature: AnnotationFeatureSnapshot, getSequence: (start: number, end: number) => Promise<string>): Promise<CheckResultSnapshot[]>;
+}