@apollo-annotation/shared 0.1.20 → 0.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
@@ -27,7 +27,7 @@ class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFile
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  * @returns
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  */
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  async executeOnServer(backend) {
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- const { assemblyModel, fileModel, filesService, user } = backend;
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+ const { assemblyModel, checkModel, fileModel, filesService, user } = backend;
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  const { assembly, changes, logger } = this;
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  for (const change of changes) {
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  const { assemblyName, fileIds } = change;
@@ -49,9 +49,12 @@ class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange_1.FromFile
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  if (assemblyDoc) {
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  throw new Error(`Assembly "${assemblyName}" already exists`);
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  }
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+ // get checks
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+ const checkDocs = await checkModel.find({ default: true }).exec();
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+ const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
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  // Add assembly
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  const [newAssemblyDoc] = await assemblyModel.create([
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- { _id: assembly, name: assemblyName, user, status: -1, fileId },
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+ { _id: assembly, name: assemblyName, user, status: -1, fileId, checks },
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  ]);
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  logger.debug?.(`Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id.toHexString()}"`);
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  logger.debug?.(`File type: "${fileDoc.type}"`);
@@ -1 +1 @@
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- {"version":3,"file":"AddAssemblyAndFeaturesFromFileChange.js","sourceRoot":"","sources":["../../src/Changes/AddAssemblyAndFeaturesFromFileChange.ts"],"names":[],"mappings":";AAAA,qDAAqD;;;AAWrD,6DAAyD;AAyBzD,MAAa,oCAAqC,SAAQ,uCAAkB;IAC1E,QAAQ,GAAG,sCAA+C,CAAA;IAC1D,OAAO,CAA+C;IAEtD,YACE,IAAoD,EACpD,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,aAAa,EAAE,SAAS,EAAE,YAAY,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QAChE,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAC1C,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YACxC,MAAM,MAAM,GAAG,OAAO,CAAC,EAAE,CAAA;YAEzB,MAAM,EAAE,kBAAkB,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;YAC1C,IAAI,CAAC,kBAAkB,EAAE,CAAC;gBACxB,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAA;YAC7D,CAAC;YACD,oBAAoB;YACpB,MAAM,OAAO,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,CAAA;YACvD,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,MAAM,IAAI,KAAK,CAAC,SAAS,MAAM,sBAAsB,CAAC,CAAA;YACxD,CAAC;YACD,MAAM,CAAC,KAAK,EAAE,CAAC,WAAW,MAAM,gBAAgB,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAA;YAEpE,6BAA6B;YAC7B,MAAM,WAAW,GAAG,MAAM,aAAa;iBACpC,OAAO,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC;iBAC/B,IAAI,EAAE,CAAA;YACT,IAAI,WAAW,EAAE,CAAC;gBAChB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,kBAAkB,CAAC,CAAA;YAC9D,CAAC;YACD,eAAe;YACf,MAAM,CAAC,cAAc,CAAC,GAAG,MAAM,aAAa,CAAC,MAAM,CAAC;gBAClD,EAAE,GAAG,EAAE,QAAQ,EAAE,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE;aAChE,CAAC,CAAA;YACF,MAAM,CAAC,KAAK,EAAE,CACZ,uBAAuB,YAAY,aAAa,cAAc,CAAC,GAAG,CAAC,WAAW,EAAE,GAAG,CACpF,CAAA;YACD,MAAM,CAAC,KAAK,EAAE,CAAC,eAAe,OAAO,CAAC,IAAI,GAAG,CAAC,CAAA;YAE9C,cAAc;YACd,iGAAiG;YACjG,MAAM,IAAI,CAAC,eAAe,CACxB,OAAO,EACP,cAAc,CAAC,GAAG,CAAC,QAAQ,EAAE,EAC7B,OAAO,CACR,CAAA;YAED,oBAAoB;YACpB,MAAM,CAAC,KAAK,EAAE,CACZ,sEAAsE,OAAO,CAAC,IAAI,GAAG,CACtF,CAAA;YACD,MAAM,aAAa,GAAG,YAAY,CAAC,SAAS,CAC1C,YAAY,CAAC,aAAa,CAAC,OAAO,CAAC,CACpC,CAAA;YACD,IAAI,KAAK,EAAE,MAAM,CAAC,IAAI,aAAa,EAAE,CAAC;gBACpC,MAAM,WAAW,GAAG,CAAgB,CAAA;gBACpC,MAAM,CAAC,OAAO,EAAE,CAAC,SAAS,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;gBACxD,gCAAgC;gBAChC,MAAM,IAAI,CAAC,gBAAgB,CAAC,WAAW,EAAE,OAAO,CAAC,CAAA;YACnD,CAAC;QACH,CAAC;IACH,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,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO,IAAI,oCAAoC,CAC7C,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,EAC/B,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF;AAtGD,oFAsGC"}
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+ {"version":3,"file":"AddAssemblyAndFeaturesFromFileChange.js","sourceRoot":"","sources":["../../src/Changes/AddAssemblyAndFeaturesFromFileChange.ts"],"names":[],"mappings":";AAAA,qDAAqD;;;AAWrD,6DAAyD;AAyBzD,MAAa,oCAAqC,SAAQ,uCAAkB;IAC1E,QAAQ,GAAG,sCAA+C,CAAA;IAC1D,OAAO,CAA+C;IAEtD,YACE,IAAoD,EACpD,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,aAAa,EAAE,UAAU,EAAE,SAAS,EAAE,YAAY,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QAC5E,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAC1C,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,YAAY,EAAE,OAAO,EAAE,GAAG,MAAM,CAAA;YACxC,MAAM,MAAM,GAAG,OAAO,CAAC,EAAE,CAAA;YAEzB,MAAM,EAAE,kBAAkB,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;YAC1C,IAAI,CAAC,kBAAkB,EAAE,CAAC;gBACxB,MAAM,IAAI,KAAK,CAAC,0CAA0C,CAAC,CAAA;YAC7D,CAAC;YACD,oBAAoB;YACpB,MAAM,OAAO,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,CAAA;YACvD,IAAI,CAAC,OAAO,EAAE,CAAC;gBACb,MAAM,IAAI,KAAK,CAAC,SAAS,MAAM,sBAAsB,CAAC,CAAA;YACxD,CAAC;YACD,MAAM,CAAC,KAAK,EAAE,CAAC,WAAW,MAAM,gBAAgB,OAAO,CAAC,QAAQ,GAAG,CAAC,CAAA;YAEpE,6BAA6B;YAC7B,MAAM,WAAW,GAAG,MAAM,aAAa;iBACpC,OAAO,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC;iBAC/B,IAAI,EAAE,CAAA;YACT,IAAI,WAAW,EAAE,CAAC;gBAChB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,kBAAkB,CAAC,CAAA;YAC9D,CAAC;YACD,aAAa;YACb,MAAM,SAAS,GAAG,MAAM,UAAU,CAAC,IAAI,CAAC,EAAE,OAAO,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAA;YACjE,MAAM,MAAM,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC,QAAQ,EAAE,EAAE,CAAC,QAAQ,CAAC,GAAG,CAAC,WAAW,EAAE,CAAC,CAAA;YACtE,eAAe;YACf,MAAM,CAAC,cAAc,CAAC,GAAG,MAAM,aAAa,CAAC,MAAM,CAAC;gBAClD,EAAE,GAAG,EAAE,QAAQ,EAAE,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE,MAAM,EAAE;aACxE,CAAC,CAAA;YACF,MAAM,CAAC,KAAK,EAAE,CACZ,uBAAuB,YAAY,aAAa,cAAc,CAAC,GAAG,CAAC,WAAW,EAAE,GAAG,CACpF,CAAA;YACD,MAAM,CAAC,KAAK,EAAE,CAAC,eAAe,OAAO,CAAC,IAAI,GAAG,CAAC,CAAA;YAE9C,cAAc;YACd,iGAAiG;YACjG,MAAM,IAAI,CAAC,eAAe,CACxB,OAAO,EACP,cAAc,CAAC,GAAG,CAAC,QAAQ,EAAE,EAC7B,OAAO,CACR,CAAA;YAED,oBAAoB;YACpB,MAAM,CAAC,KAAK,EAAE,CACZ,sEAAsE,OAAO,CAAC,IAAI,GAAG,CACtF,CAAA;YACD,MAAM,aAAa,GAAG,YAAY,CAAC,SAAS,CAC1C,YAAY,CAAC,aAAa,CAAC,OAAO,CAAC,CACpC,CAAA;YACD,IAAI,KAAK,EAAE,MAAM,CAAC,IAAI,aAAa,EAAE,CAAC;gBACpC,MAAM,WAAW,GAAG,CAAgB,CAAA;gBACpC,MAAM,CAAC,OAAO,EAAE,CAAC,SAAS,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,EAAE,CAAC,CAAA;gBACxD,gCAAgC;gBAChC,MAAM,IAAI,CAAC,gBAAgB,CAAC,WAAW,EAAE,OAAO,CAAC,CAAA;YACnD,CAAC;QACH,CAAC;IACH,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,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO,IAAI,oCAAoC,CAC7C,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,EAC/B,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF;AAzGD,oFAyGC"}
@@ -31,7 +31,7 @@ class AddAssemblyFromExternalChange extends common_1.AssemblySpecificChange {
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  * @returns
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  */
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  async executeOnServer(backend) {
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- const { assemblyModel, refSeqModel, user } = backend;
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+ const { assemblyModel, checkModel, refSeqModel, user } = backend;
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  const { assembly, changes, logger } = this;
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  const { CHUNK_SIZE } = process.env;
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  const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE);
@@ -58,6 +58,8 @@ class AddAssemblyFromExternalChange extends common_1.AssemblySpecificChange {
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  if (assemblyDoc) {
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  throw new Error(`Assembly "${assemblyName}" already exists`);
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  }
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+ const checkDocs = await checkModel.find({ default: true }).exec();
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+ const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
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  const [newAssemblyDoc] = await assemblyModel.create([
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  {
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  _id: assembly,
@@ -65,6 +67,7 @@ class AddAssemblyFromExternalChange extends common_1.AssemblySpecificChange {
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  user,
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  status: -1,
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  externalLocation,
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+ checks,
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  },
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  ]);
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  logger.debug?.(`Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`);
@@ -1 +1 @@
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- {"version":3,"file":"AddAssemblyFromExternalChange.js","sourceRoot":"","sources":["../../src/Changes/AddAssemblyFromExternalChange.ts"],"names":[],"mappings":";AAAA,qEAAqE;AACrE,gEAAgE;;;AAEhE,qDAAqD;AACrD,sDAOkC;AAClC,qDAAoE;AACpE,2DAA+C;AAyB/C,MAAa,6BAA8B,SAAQ,+BAAsB;IACvE,QAAQ,GAAG,+BAAwC,CAAA;IACnD,OAAO,CAAwC;IAE/C,YACE,IAA6C,EAC7C,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,gBAAgB,EAAE,CAAC,GAAG,OAAO,CAAA;YACpD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,YAAY,EAAE,gBAAgB,EAAE,CAAA;QAC/D,CAAC;QACD,OAAO,EAAE,QAAQ,EAAE,QAAQ,EAAE,OAAO,EAAE,CAAA;IACxC,CAAC;IAED;;;;OAIG;IACH,KAAK,CAAC,eAAe,CAAC,OAAwB;QAC5C,MAAM,EAAE,aAAa,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QACpD,MAAM,EAAE,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QAC1C,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;QAClC,MAAM,eAAe,GAAG,UAAU,IAAI,MAAM,CAAC,UAAU,CAAC,CAAA;QAExD,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,EAAE,YAAY,EAAE,gBAAgB,EAAE,GAAG,MAAM,CAAA;YACjD,MAAM,EAAE,EAAE,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,gBAAgB,CAAA;YACzC,MAAM,eAAe,GAAG,GAAG;gBACzB,CAAC,CAAC,IAAI,gCAAiB,CAAC;oBACpB,KAAK,EAAE,IAAI,+BAAU,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;oBACpC,GAAG,EAAE,IAAI,+BAAU,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,CAAC;oBACnC,GAAG,EAAE,IAAI,+BAAU,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,CAAC;iBACpC,CAAC;gBACJ,CAAC,CAAC,IAAI,2BAAY,CAAC;oBACf,KAAK,EAAE,IAAI,+BAAU,CAAC,EAAE,EAAE,EAAE,KAAK,EAAE,CAAC;oBACpC,GAAG,EAAE,IAAI,+BAAU,CAAC,GAAG,EAAE,EAAE,KAAK,EAAE,CAAC;iBACpC,CAAC,CAAA;YACN,MAAM,gBAAgB,GAAG,MAAM,eAAe,CAAC,gBAAgB,EAAE,CAAA;YAEjE,IAAI,CAAC,gBAAgB,EAAE,CAAC;gBACtB,MAAM,IAAI,KAAK,CAAC,kDAAkD,CAAC,CAAA;YACrE,CAAC;YAED,MAAM,WAAW,GAAG,MAAM,aAAa;iBACpC,OAAO,CAAC,EAAE,IAAI,EAAE,YAAY,EAAE,CAAC;iBAC/B,IAAI,EAAE,CAAA;YACT,IAAI,WAAW,EAAE,CAAC;gBAChB,MAAM,IAAI,KAAK,CAAC,aAAa,YAAY,kBAAkB,CAAC,CAAA;YAC9D,CAAC;YACD,MAAM,CAAC,cAAc,CAAC,GAAG,MAAM,aAAa,CAAC,MAAM,CAAC;gBAClD;oBACE,GAAG,EAAE,QAAQ;oBACb,IAAI,EAAE,YAAY;oBAClB,IAAI;oBACJ,MAAM,EAAE,CAAC,CAAC;oBACV,gBAAgB;iBACjB;aACF,CAAC,CAAA;YACF,MAAM,CAAC,KAAK,EAAE,CACZ,uBAAuB,YAAY,aAAa,cAAc,CAAC,GAAG,GAAG,CACtE,CAAA;YAED,KAAK,MAAM,YAAY,IAAI,gBAAgB,EAAE,CAAC;gBAC5C,MAAM,CAAC,YAAY,CAAC,GAAG,MAAM,WAAW,CAAC,MAAM,CAAC;oBAC9C;wBACE,IAAI,EAAE,YAAY;wBAClB,QAAQ,EAAE,cAAc,CAAC,GAAG;wBAC5B,MAAM,EAAE,gBAAgB,CAAC,YAAY,CAAC;wBACtC,GAAG,CAAC,eAAe,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;wBAC5D,IAAI;wBACJ,MAAM,EAAE,CAAC,CAAC;qBACX;iBACF,CAAC,CAAA;gBACF,MAAM,CAAC,KAAK,EAAE,CACZ,qBAAqB,YAAY,aAAa,YAAY,CAAC,GAAG,GAAG,CAClE,CAAA;YACH,CAAC;QACH,CAAC;IACH,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,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO,IAAI,6BAA6B,CACtC,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,EAC/B,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF;AA1GD,sEA0GC"}
1
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@@ -42,35 +42,37 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
42
42
  if (!FILE_UPLOAD_FOLDER) {
43
43
  throw new Error('No FILE_UPLOAD_FOLDER found in .env file');
44
44
  }
45
- const { fa, fai, gzi } = fileIds;
46
- const { assemblyModel, fileModel, filesService, refSeqModel, user } = backend;
47
- const faDoc = await fileModel.findById(fa);
45
+ const { fa: faId, fai: faiId, gzi: gziId } = fileIds;
46
+ const { assemblyModel, checkModel, fileModel, filesService, refSeqModel, user, } = backend;
47
+ const faDoc = await fileModel.findById(faId);
48
48
  const faChecksum = faDoc?.checksum;
49
49
  if (!faChecksum) {
50
50
  throw new Error(`No checksum for file document ${faDoc}`);
51
51
  }
52
- const faiDoc = await fileModel.findById(fai);
52
+ const faiDoc = await fileModel.findById(faiId);
53
53
  const faiChecksum = faiDoc?.checksum;
54
54
  if (!faiChecksum) {
55
55
  throw new Error(`No checksum for file document ${faiDoc}`);
56
56
  }
57
- const gziDoc = await fileModel.findById(gzi);
57
+ const gziDoc = await fileModel.findById(gziId);
58
58
  const gziChecksum = gziDoc?.checksum;
59
59
  if (!gziChecksum) {
60
60
  throw new Error(`No checksum for file document ${gziDoc}`);
61
61
  }
62
- const sequenceAdapter = new indexedfasta_1.BgzipIndexedFasta({
63
- fasta: filesService.getFileHandle(faDoc),
64
- fai: filesService.getFileHandle(faiDoc),
65
- gzi: filesService.getFileHandle(gziDoc),
66
- });
62
+ const fasta = filesService.getFileHandle(faDoc);
63
+ const fai = filesService.getFileHandle(faiDoc);
64
+ const gzi = filesService.getFileHandle(gziDoc);
65
+ const sequenceAdapter = new indexedfasta_1.BgzipIndexedFasta({ fasta, fai, gzi });
67
66
  const allSequenceSizes = await sequenceAdapter.getSequenceSizes();
67
+ await Promise.all([fasta.close(), fai.close(), gzi.close()]);
68
68
  const assemblyDoc = await assemblyModel
69
69
  .findOne({ name: assemblyName })
70
70
  .exec();
71
71
  if (assemblyDoc) {
72
72
  throw new Error(`Assembly "${assemblyName}" already exists`);
73
73
  }
74
+ const checkDocs = await checkModel.find({ default: true }).exec();
75
+ const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
74
76
  const [newAssemblyDoc] = await assemblyModel.create([
75
77
  {
76
78
  _id: this.assembly,
@@ -78,6 +80,7 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
78
80
  user,
79
81
  status: -1,
80
82
  fileIds,
83
+ checks,
81
84
  },
82
85
  ]);
83
86
  this.logger.debug?.(`Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`);
@@ -96,7 +99,7 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
96
99
  }
97
100
  }
98
101
  async executeOnServerFasta(backend, assemblyName, fileId) {
99
- const { assemblyModel, fileModel, user } = backend;
102
+ const { assemblyModel, checkModel, fileModel, user } = backend;
100
103
  // Get file checksum
101
104
  const fileDoc = await fileModel.findById(fileId).exec();
102
105
  if (!fileDoc) {
@@ -110,6 +113,8 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
110
113
  if (assemblyDoc) {
111
114
  throw new Error(`Assembly "${assemblyName}" already exists`);
112
115
  }
116
+ const checkDocs = await checkModel.find({ default: true }).exec();
117
+ const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString());
113
118
  // Add assembly
114
119
  const [newAssemblyDoc] = await assemblyModel.create([
115
120
  {
@@ -118,6 +123,7 @@ class AddAssemblyFromFileChange extends FromFileBaseChange_1.FromFileBaseChange
118
123
  user,
119
124
  status: -1,
120
125
  fileIds: { fa: fileId },
126
+ checks,
121
127
  },
122
128
  ]);
123
129
  this.logger.debug?.(`Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`);
@@ -1 +1 @@
1
- {"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,GAAG,EAAE,GAAG,EAAE,GAAG,OAAO,CAAA;QAChC,MAAM,EAAE,aAAa,EAAE,SAAS,EAAE,YAAY,EAAE,WAAW,EAAE,IAAI,EAAE,GACjE,OAAO,CAAA;QAET,MAAM,KAAK,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAA;QAC1C,MAAM,UAAU,GAAG,KAAK,EAAE,QAAQ,CAAA;QAClC,IAAI,CAAC,UAAU,EAAE,CAAC;YAChB,MAAM,IAAI,KAAK,CAAC,iCAAiC,KAAK,EAAE,CAAC,CAAA;QAC3D,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,MAAM,EAAE,QAAQ,CAAA;QACpC,IAAI,CAAC,WAAW,EAAE,CAAC;YACjB,MAAM,IAAI,KAAK,CAAC,iCAAiC,MAAM,EAAE,CAAC,CAAA;QAC5D,CAAC;QAED,MAAM,MAAM,GAAG,MAAM,SAAS,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAA;QAC5C,MAAM,WAAW,GAAG,MAAM,EAAE,QAAQ,CAAA;QACpC,IAAI,CAAC,WAAW,EAAE,CAAC;YACjB,MAAM,IAAI,KAAK,CAAC,iCAAiC,MAAM,EAAE,CAAC,CAAA;QAC5D,CAAC;QAED,MAAM,eAAe,GAAG,IAAI,gCAAiB,CAAC;YAC5C,KAAK,EAAE,YAAY,CAAC,aAAa,CAAC,KAAK,CAAC;YACxC,GAAG,EAAE,YAAY,CAAC,aAAa,CAAC,MAAM,CAAC;YACvC,GAAG,EAAE,YAAY,CAAC,aAAa,CAAC,MAAM,CAAC;SACxC,CAAC,CAAA;QACF,MAAM,gBAAgB,GAAG,MAAM,eAAe,CAAC,gBAAgB,EAAE,CAAA;QAEjE,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,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;aACR;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,SAAS,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QAClD,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,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;aACxB;SACF,CAAC,CAAA;QACF,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CACjB,uBAAuB,YAAY,aAAa,cAAc,CAAC,GAAG,GAAG,CACtE,CAAA;QACD,IAAI,CAAC,MAAM,CAAC,KAAK,EAAE,CACjB,eAAe,OAAO,CAAC,IAAI,mBAAmB,cAAc,CAAC,GAAG,GAAG,CACpE,CAAA;QAED,cAAc;QACd,iGAAiG;QACjG,MAAM,IAAI,CAAC,eAAe,CAAC,OAAO,EAAE,cAAc,CAAC,GAAG,CAAC,QAAQ,EAAE,EAAE,OAAO,CAAC,CAAA;IAC7E,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,QAAQ,EAAE,OAAO,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,IAAI,CAAA;QACpD,OAAO,IAAI,yBAAyB,CAClC,EAAE,QAAQ,EAAE,OAAO,EAAE,QAAQ,EAAE,EAC/B,EAAE,MAAM,EAAE,CACX,CAAA;IACH,CAAC;CACF;AA9KD,8DA8KC"}
1
+ 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@@ -5,7 +5,7 @@ exports.filterJBrowseConfig = filterJBrowseConfig;
5
5
  /* eslint-disable @typescript-eslint/require-await */
6
6
  const common_1 = require("@apollo-annotation/common");
7
7
  function filterJBrowseConfig(config) {
8
- const { assemblies, internetAccounts, plugins, tracks, ...rest } = config;
8
+ const { __v, _id, assemblies, internetAccounts, plugins, tracks, ...rest } = config;
9
9
  const filteredAssemblies = assemblies?.filter((a) => a.sequence.adapter.type !== 'ApolloSequenceAdapter');
10
10
  const filteredTracks = tracks?.filter((t) => t.type !== 'ApolloTrack');
11
11
  const filteredPlugins = plugins?.filter((p) => p.name !== 'Apollo');
@@ -1 +1 @@
1
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