@apollo-annotation/shared 0.3.5 → 0.3.6
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.
- package/dist/Changes/AddAssemblyAndFeaturesFromFileChange.d.ts +1 -1
- package/dist/Changes/AddAssemblyFromExternalChange.d.ts +1 -1
- package/dist/Changes/AddAssemblyFromFileChange.d.ts +1 -1
- package/dist/Changes/AddFeatureChange.d.ts +2 -2
- package/dist/Changes/AddFeaturesFromFileChange.d.ts +1 -1
- package/dist/Changes/AddRefSeqAliasesChange.d.ts +1 -1
- package/dist/Changes/DeleteAssemblyChange.d.ts +1 -1
- package/dist/Changes/DeleteFeatureChange.d.ts +3 -3
- package/dist/Changes/DeleteUserChange.d.ts +1 -1
- package/dist/Changes/FeatureAttributeChange.d.ts +1 -1
- package/dist/Changes/FromFileBaseChange.d.ts +3 -3
- package/dist/Changes/FromFileBaseChange.js.map +1 -1
- package/dist/Changes/ImportJBrowseConfigChange.d.ts +1 -1
- package/dist/Changes/LocationEndChange.d.ts +1 -1
- package/dist/Changes/LocationStartChange.d.ts +1 -1
- package/dist/Changes/StrandChange.d.ts +1 -1
- package/dist/Changes/TypeChange.d.ts +1 -1
- package/dist/Changes/UserChange.d.ts +1 -1
- package/dist/Checks/CDSCheck.d.ts +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.d.ts +2 -2
- package/dist/GFF3/annotationFeatureToGFF3.test.js +1 -1
- package/dist/GFF3/annotationFeatureToGFF3.test.js.map +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.d.ts +2 -2
- package/dist/GFF3/gff3ToAnnotationFeature.test.d.ts +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js +1 -1
- package/dist/GFF3/gff3ToAnnotationFeature.test.js.map +1 -1
- package/dist/GFF3/gffReservedKeys.d.ts +7 -0
- package/dist/GFF3/gffReservedKeys.js +21 -1
- package/dist/GFF3/gffReservedKeys.js.map +1 -1
- package/dist/Messages.d.ts +2 -2
- package/dist/Operations/GetAssembliesOperation.d.ts +1 -1
- package/dist/Operations/GetFeaturesOperation.d.ts +1 -1
- package/dist/Validations/CoreValidation.d.ts +2 -2
- package/dist/Validations/CoreValidation.js +1 -1
- package/dist/Validations/CoreValidation.js.map +1 -1
- package/dist/Validations/ParentChildValidation.d.ts +5 -5
- package/dist/Validations/ParentChildValidation.js.map +1 -1
- package/dist/Validations/Validation.d.ts +5 -5
- package/dist/Validations/ValidationSet.d.ts +4 -4
- package/dist/Validations/ValidationSet.js.map +1 -1
- package/dist/tsconfig.tsbuildinfo +1 -1
- package/package.json +4 -4
- package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts +6 -6
- package/src/Changes/AddAssemblyFromExternalChange.ts +5 -5
- package/src/Changes/AddAssemblyFromFileChange.ts +5 -5
- package/src/Changes/AddFeatureChange.ts +6 -6
- package/src/Changes/AddFeaturesFromFileChange.ts +6 -6
- package/src/Changes/AddRefSeqAliasesChange.ts +6 -6
- package/src/Changes/DeleteAssemblyChange.ts +4 -4
- package/src/Changes/DeleteFeatureChange.ts +7 -7
- package/src/Changes/DeleteUserChange.ts +5 -5
- package/src/Changes/FeatureAttributeChange.ts +6 -6
- package/src/Changes/FromFileBaseChange.ts +6 -3
- package/src/Changes/ImportJBrowseConfigChange.ts +4 -4
- package/src/Changes/LocationEndChange.ts +6 -6
- package/src/Changes/LocationStartChange.ts +6 -6
- package/src/Changes/StrandChange.ts +6 -6
- package/src/Changes/TypeChange.ts +6 -6
- package/src/Changes/UserChange.ts +5 -5
- package/src/Checks/CDSCheck.ts +2 -2
- package/src/GFF3/annotationFeatureToGFF3.test.ts +4 -2
- package/src/GFF3/annotationFeatureToGFF3.ts +4 -4
- package/src/GFF3/gff3ToAnnotationFeature.test.ts +3 -3
- package/src/GFF3/gff3ToAnnotationFeature.ts +2 -2
- package/src/GFF3/gffReservedKeys.ts +25 -0
- package/src/Messages.ts +2 -2
- package/src/Operations/GetAssembliesOperation.ts +3 -3
- package/src/Operations/GetFeaturesOperation.ts +4 -4
- package/src/Validations/CoreValidation.ts +4 -3
- package/src/Validations/ParentChildValidation.ts +7 -6
- package/src/Validations/Validation.ts +5 -5
- package/src/Validations/ValidationSet.ts +8 -4
- package/test_data/example01.json +3 -3
- package/test_data/example02.json +3 -3
- package/test_data/example04.json +3 -3
- package/test_data/gene_representations.gff3 +686 -1686
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import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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import { FromFileBaseChange } from './FromFileBaseChange';
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export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
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typeName: 'AddAssemblyAndFeaturesFromFileChange';
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import { AssemblySpecificChange, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { AssemblySpecificChange, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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export interface SerializedAddAssemblyFromExternalChangeBase extends SerializedAssemblySpecificChange {
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typeName: 'AddAssemblyFromExternalChange';
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}
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import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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import { FromFileBaseChange } from './FromFileBaseChange';
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export interface SerializedAddAssemblyFromFileChangeBase extends SerializedAssemblySpecificChange {
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typeName: 'AddAssemblyFromFileChange';
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import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
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import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
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import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
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import { DeleteFeatureChange } from './DeleteFeatureChange';
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interface SerializedAddFeatureChangeBase extends SerializedFeatureChange {
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typeName: 'AddFeatureChange';
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import { ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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import { FromFileBaseChange } from './FromFileBaseChange';
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export interface SerializedAddFeaturesFromFileChangeBase extends SerializedAssemblySpecificChange {
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typeName: 'AddFeaturesFromFileChange';
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import { AssemblySpecificChange, Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { AssemblySpecificChange, type Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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export interface SerializedRefSeqAliases {
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refName: string;
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aliases: string[];
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import { AssemblySpecificChange, ClientDataStore, LocalGFF3DataStore, SerializedAssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { AssemblySpecificChange, type ClientDataStore, type LocalGFF3DataStore, type SerializedAssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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export interface SerializedDeleteAssemblyChange extends SerializedAssemblySpecificChange {
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typeName: 'DeleteAssemblyChange';
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}
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import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
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import { Feature } from '@apollo-annotation/schemas';
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import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
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import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
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import { type Feature } from '@apollo-annotation/schemas';
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import { AddFeatureChange } from './AddFeatureChange';
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interface SerializedDeleteFeatureChangeBase extends SerializedFeatureChange {
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typeName: 'DeleteFeatureChange';
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import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedChange, ServerDataStore } from '@apollo-annotation/common';
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import { Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedChange, type ServerDataStore } from '@apollo-annotation/common';
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export interface SerializedDeleteUserChangeBase extends SerializedChange {
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typeName: 'DeleteUserChange';
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userId: string;
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import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
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interface SerializedFeatureAttributeChangeBase extends SerializedFeatureChange {
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typeName: 'FeatureAttributeChange';
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}
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import { AssemblySpecificChange, ServerDataStore } from '@apollo-annotation/common';
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import { FileDocument } from '@apollo-annotation/schemas';
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import { GFF3Feature } from '@gmod/gff';
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import { AssemblySpecificChange, type ServerDataStore } from '@apollo-annotation/common';
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import { type FileDocument } from '@apollo-annotation/schemas';
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import { type GFF3Feature } from '@gmod/gff';
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export declare abstract class FromFileBaseChange extends AssemblySpecificChange {
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addRefSeqIntoDb(fileDoc: FileDocument, assembly: string, backend: ServerDataStore): Promise<void>;
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private refSeqCache;
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{"version":3,"file":"FromFileBaseChange.js","sourceRoot":"","sources":["../../src/Changes/FromFileBaseChange.ts"],"names":[],"mappings":";;;AAAA,8DAA8D;AAC9D,4DAA4D;AAC5D,+DAA+D;AAC/D,sDAAsD;AACtD,0DAA0D;AAC1D,sDAGkC;AAOlC,kCAAiD;AAEjD,MAAsB,kBAAmB,SAAQ,+BAAsB;IACrE,KAAK,CAAC,eAAe,CACnB,OAAqB,EACrB,QAAgB,EAChB,OAAwB;QAExB,MAAM,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACvB,MAAM,EAAE,YAAY,EAAE,gBAAgB,EAAE,WAAW,EAAE,IAAI,EAAE,GAAG,OAAO,CAAA;QACrE,MAAM,EAAE,UAAU,EAAE,GAAG,OAAO,CAAC,GAAG,CAAA;QAClC,MAAM,eAAe,GAAG,UAAU,IAAI,MAAM,CAAC,UAAU,CAAC,CAAA;QACxD,IAAI,UAAU,GAAG,CAAC,CAAA;QAClB,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,SAAqC,CAAA;QACzC,IAAI,gBAAgB,GAAG,OAAO,CAAC,IAAI,KAAK,aAAa,CAAA;QAErD,uDAAuD;QACvD,MAAM,cAAc,GAAG,YAAY,CAAC,aAAa,CAAC,OAAO,CAAC,CAAA;QAC1D,IAAI,cAAc,GAAG,EAAE,CAAA;QACvB,IAAI,cAAc,GAAG,EAAE,CAAA;QACvB,IAAI,oBAAoB,GAAG,IAAI,CAAA;QAC/B,IAAI,cAAc,GAAG,KAAK,CAAA;QAC1B,MAAM,CAAC,KAAK,EAAE,CAAC,0BAA0B,CAAC,CAAA;QAC1C,IAAI,SAAS,GAAG,CAAC,CAAA;QACjB,IAAI,KAAK,EAAE,MAAM,IAAI,IAAI,cAAc,EAAE,CAAC;YACxC,MAAM,KAAK,GAAG,IAAI,CAAC,QAAQ,EAAE,CAAA;YAC7B,oBAAoB,GAAG,CAAC,KAAK,CAAC,QAAQ,CAAC,IAAI,CAAC,CAAA;YAC5C,2HAA2H;YAC3H,MAAM,KAAK,GAAG,KAAK,CAAC,KAAK,CAAC,OAAO,CAAC,CAAA;YAClC,IAAI,cAAc,EAAE,CAAC;gBACnB,KAAK,CAAC,CAAC,CAAC,GAAG,GAAG,cAAc,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE,CAAA;gBACzC,cAAc,GAAG,EAAE,CAAA;YACrB,CAAC;YACD,IAAI,oBAAoB,EAAE,CAAC;gBACzB,cAAc,GAAG,KAAK,CAAC,GAAG,EAAE,IAAI,EAAE,CAAA;YACpC,CAAC;YACD,IAAI,KAAK,EAAE,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;gBAC/B,SAAS,EAAE,CAAA;gBACX,IAAI,SAAS,GAAG,SAAS,KAAK,CAAC,EAAE,CAAC;oBAChC,MAAM,CAAC,KAAK,EAAE,CAAC,aAAa,SAAS,QAAQ,CAAC,CAAA;gBAChD,CAAC;gBACD,0EAA0E;gBAC1E,IAAI,CAAC,gBAAgB,EAAE,CAAC;oBACtB,IAAI,IAAI,CAAC,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;wBAC9B,gBAAgB,GAAG,IAAI,CAAA;oBACzB,CAAC;oBACD,SAAQ;gBACV,CAAC;gBACD,MAAM,cAAc,GAAG,mBAAmB,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;gBACrD,8DAA8D;gBAC9D,IAAI,cAAc,EAAE,CAAC;oBACnB,cAAc,GAAG,IAAI,CAAA;oBACrB,MAAM,CAAC,KAAK,EAAE,CACZ,wCAAwC,cAAc,CAAC,CAAC,CAAC,GAAG,CAC7D,CAAA;oBAED,mGAAmG;oBACnG,IAAI,cAAc,KAAK,EAAE,EAAE,CAAC;wBAC1B,IAAI,CAAC,SAAS,EAAE,CAAC;4BACf,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;wBAC7C,CAAC;wBACD,SAAS,IAAI,cAAc,CAAC,MAAM,CAAA;wBAClC,iGAAiG;wBACjG,MAAM,gBAAgB,CAAC,MAAM,CAAC;4BAC5B;gCACE,MAAM,EAAE,SAAS,CAAC,GAAG;gCACrB,CAAC,EAAE,UAAU;gCACb,QAAQ,EAAE,cAAc;gCACxB,IAAI;gCACJ,MAAM,EAAE,CAAC,CAAC;6BACX;yBACF,CAAC,CAAA;wBACF,cAAc,GAAG,EAAE,CAAA;oBACrB,CAAC;oBACD,MAAM,SAAS,EAAE,SAAS,CAAC,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAA;oBACjD,iEAAiE;oBACjE,SAAS,GAAG,CAAC,CAAA;oBACb,UAAU,GAAG,CAAC,CAAA;oBAEd,MAAM,IAAI,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAA;oBACrC,MAAM,WAAW,GAAG,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAA;oBAErE,iGAAiG;oBACjG,MAAM,CAAC,YAAY,CAAC,GAAG,MAAM,WAAW,CAAC,MAAM,CAAC;wBAC9C;4BACE,IAAI;4BACJ,WAAW;4BACX,QAAQ;4BACR,MAAM,EAAE,CAAC;4BACT,GAAG,CAAC,eAAe,CAAC,CAAC,CAAC,EAAE,SAAS,EAAE,eAAe,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;4BAC5D,IAAI;4BACJ,MAAM,EAAE,CAAC,CAAC;yBACX;qBACF,CAAC,CAAA;oBACF,MAAM,CAAC,KAAK,EAAE,CACZ,qBAAqB,IAAI,YAAY,WAAW,aAAa,YAAY,CAAC,GAAG,GAAG,CACjF,CAAA;oBACD,SAAS,GAAG,YAAY,CAAA;gBAC1B,CAAC;qBAAM,IAAI,IAAI,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;oBAC3B,IAAI,CAAC,SAAS,EAAE,CAAC;wBACf,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;oBAC7C,CAAC;oBACD,MAAM,EAAE,GAAG,EAAE,SAAS,EAAE,GAAG,SAAS,CAAA;oBACpC,cAAc,IAAI,IAAI,CAAC,UAAU,CAAC,KAAK,EAAE,EAAE,CAAC,CAAA;oBAC5C,4DAA4D;oBAC5D,OAAO,cAAc,CAAC,MAAM,IAAI,SAAS,EAAE,CAAC;wBAC1C,MAAM,QAAQ,GAAG,cAAc,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAA;wBACnD,SAAS,IAAI,QAAQ,CAAC,MAAM,CAAA;wBAC5B,iGAAiG;wBACjG,MAAM,gBAAgB,CAAC,MAAM,CAAC;4BAC5B,EAAE,MAAM,EAAE,GAAG,EAAE,CAAC,EAAE,UAAU,EAAE,QAAQ,EAAE,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC,EAAE;yBAC3D,CAAC,CAAA;wBACF,UAAU,EAAE,CAAA;wBACZ,yBAAyB;wBACzB,cAAc,GAAG,cAAc,CAAC,KAAK,CAAC,SAAS,CAAC,CAAA;oBAClD,CAAC;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QACD,IAAI,CAAC,cAAc,EAAE,CAAC;YACpB,MAAM,IAAI,KAAK,CAAC,sCAAsC,CAAC,CAAA;QACzD,CAAC;QAED,IAAI,cAAc,IAAI,oBAAoB,EAAE,CAAC;YAC3C,IAAI,CAAC,SAAS,EAAE,CAAC;gBACf,MAAM,IAAI,KAAK,CAAC,0BAA0B,CAAC,CAAA;YAC7C,CAAC;YACD,yEAAyE;YACzE,IAAI,oBAAoB,EAAE,CAAC;gBACzB,cAAc,IAAI,cAAc,CAAA;YAClC,CAAC;YACD,SAAS,IAAI,cAAc,CAAC,MAAM,CAAA;YAClC,MAAM,CAAC,OAAO,EAAE,CACd,4CAA4C,SAAS,CAAC,GAAG,YAAY,UAAU,oCAAoC,SAAS,OAAO,cAAc,GAAG,CACrJ,CAAA;YACD,MAAM,CAAC,KAAK,EAAE,CACZ,gCAAgC,UAAU,QAAQ,SAAS,CAAC,GAAG,GAAG,CACnE,CAAA;YACD,iGAAiG;YACjG,MAAM,gBAAgB,CAAC,MAAM,CAAC;gBAC5B;oBACE,MAAM,EAAE,SAAS,CAAC,GAAG;oBACrB,CAAC,EAAE,UAAU;oBACb,QAAQ,EAAE,cAAc;oBACxB,IAAI;oBACJ,MAAM,EAAE,CAAC,CAAC;iBACX;aACF,CAAC,CAAA;YACF,MAAM,SAAS,CAAC,SAAS,CAAC,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC,CAAA;QAClD,CAAC;IACH,CAAC;IAEO,WAAW,GAAG,IAAI,GAAG,EAA0B,CAAA;IAEvD,KAAK,CAAC,sBAAsB,CAAC,OAAwB;QACnD,MAAM,EAAE,YAAY,EAAE,WAAW,EAAE,GAAG,OAAO,CAAA;QAC7C,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,GAAG,IAAI,CAAA;QACjC,MAAM,CAAC,KAAK,EAAE,CAAC,6CAA6C,QAAQ,EAAE,CAAC,CAAA;QAEvE,MAAM,OAAO,GAAqB,MAAM,WAAW;aAChD,IAAI,CAAC,EAAE,QAAQ,EAAE,CAAC;aAClB,IAAI,EAAE,CAAA;QAET,KAAK,MAAM,MAAM,IAAI,OAAO,EAAE,CAAC;YAC7B,MAAM,YAAY,CAAC,UAAU,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,GAAG,EAAE,CAAC,CAAA;QACvD,CAAC;IACH,CA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@@ -1,4 +1,4 @@
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1
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-
import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, ServerDataStore } from '@apollo-annotation/common';
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1
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+
import { Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type ServerDataStore } from '@apollo-annotation/common';
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2
2
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interface JBrowseAssembly {
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sequence: {
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4
4
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adapter: {
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@@ -1,4 +1,4 @@
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1
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-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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1
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+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
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2
2
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interface SerializedLocationEndChangeBase extends SerializedFeatureChange {
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3
3
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typeName: 'LocationEndChange';
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4
4
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}
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@@ -1,4 +1,4 @@
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1
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-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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1
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+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
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2
2
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interface SerializedLocationStartChangeBase extends SerializedFeatureChange {
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3
3
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typeName: 'LocationStartChange';
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4
4
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}
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@@ -1,4 +1,4 @@
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1
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-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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1
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+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
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2
2
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interface SerializedStrandChangeBase extends SerializedFeatureChange {
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3
3
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typeName: 'StrandChange';
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4
4
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}
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@@ -1,4 +1,4 @@
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1
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-
import { ChangeOptions, ClientDataStore, FeatureChange, LocalGFF3DataStore, SerializedFeatureChange, ServerDataStore } from '@apollo-annotation/common';
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1
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+
import { type ChangeOptions, type ClientDataStore, FeatureChange, type LocalGFF3DataStore, type SerializedFeatureChange, type ServerDataStore } from '@apollo-annotation/common';
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2
2
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interface SerializedTypeChangeBase extends SerializedFeatureChange {
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3
3
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typeName: 'TypeChange';
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4
4
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}
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@@ -1,4 +1,4 @@
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1
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-
import { Change, ChangeOptions, ClientDataStore, LocalGFF3DataStore, SerializedChange, ServerDataStore } from '@apollo-annotation/common';
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1
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+
import { Change, type ChangeOptions, type ClientDataStore, type LocalGFF3DataStore, type SerializedChange, type ServerDataStore } from '@apollo-annotation/common';
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2
2
|
export interface SerializedUserChangeBase extends SerializedChange {
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|
3
3
|
typeName: 'UserChange';
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4
4
|
userId: string;
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@@ -1,5 +1,5 @@
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1
1
|
import { Check } from '@apollo-annotation/common';
|
|
2
|
-
import { AnnotationFeatureSnapshot, CheckResultSnapshot } from '@apollo-annotation/mst';
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2
|
+
import { type AnnotationFeatureSnapshot, type CheckResultSnapshot } from '@apollo-annotation/mst';
|
|
3
3
|
export declare class CDSCheck extends Check {
|
|
4
4
|
name: string;
|
|
5
5
|
causes: string[];
|
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@@ -1,3 +1,3 @@
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1
|
-
import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
2
|
-
import { GFF3Feature } from '@gmod/gff';
|
|
1
|
+
import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
2
|
+
import { type GFF3Feature } from '@gmod/gff';
|
|
3
3
|
export declare function annotationFeatureToGFF3(feature: AnnotationFeatureSnapshot, parentId?: string, refSeqNames?: Record<string, string | undefined>): GFF3Feature;
|
|
@@ -4,8 +4,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
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4
4
|
/* eslint-disable @typescript-eslint/no-floating-promises */
|
|
5
5
|
const node_test_1 = require("node:test");
|
|
6
6
|
const chai_1 = require("chai");
|
|
7
|
-
const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test");
|
|
8
7
|
const annotationFeatureToGFF3_1 = require("./annotationFeatureToGFF3");
|
|
8
|
+
const gff3ToAnnotationFeature_test_1 = require("./gff3ToAnnotationFeature.test");
|
|
9
9
|
(0, node_test_1.describe)('annotationFeatureToGFF3', () => {
|
|
10
10
|
(0, node_test_1.it)('Test mandatory columns', () => {
|
|
11
11
|
const annotationFeature = (0, gff3ToAnnotationFeature_test_1.readAnnotationFeatureSnapshot)('test_data/gene.json');
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"annotationFeatureToGFF3.test.js","sourceRoot":"","sources":["../../src/GFF3/annotationFeatureToGFF3.test.ts"],"names":[],"mappings":";;AAAA,yCAAyC;AACzC,4DAA4D;AAC5D,yCAAwC;
|
|
1
|
+
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|
|
@@ -1,3 +1,3 @@
|
|
|
1
|
-
import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
2
|
-
import { GFF3Feature } from '@gmod/gff';
|
|
1
|
+
import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
2
|
+
import { type GFF3Feature } from '@gmod/gff';
|
|
3
3
|
export declare function gff3ToAnnotationFeature(gff3Feature: GFF3Feature, refSeq?: string, featureIds?: string[]): AnnotationFeatureSnapshot;
|
|
@@ -1,2 +1,2 @@
|
|
|
1
|
-
import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
1
|
+
import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst';
|
|
2
2
|
export declare function readAnnotationFeatureSnapshot(fn: string): AnnotationFeatureSnapshot;
|
|
@@ -3,8 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
|
|
|
3
3
|
exports.readAnnotationFeatureSnapshot = readAnnotationFeatureSnapshot;
|
|
4
4
|
const tslib_1 = require("tslib");
|
|
5
5
|
/* eslint-disable @typescript-eslint/no-floating-promises */
|
|
6
|
-
const node_test_1 = require("node:test");
|
|
7
6
|
const node_fs_1 = require("node:fs");
|
|
7
|
+
const node_test_1 = require("node:test");
|
|
8
8
|
const gff_1 = tslib_1.__importDefault(require("@gmod/gff"));
|
|
9
9
|
const chai_1 = require("chai");
|
|
10
10
|
const chai_exclude_1 = tslib_1.__importDefault(require("chai-exclude"));
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gff3ToAnnotationFeature.test.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":";;AA0HA,sEAKC;;AA/HD,4DAA4D;AAC5D,
|
|
1
|
+
{"version":3,"file":"gff3ToAnnotationFeature.test.js","sourceRoot":"","sources":["../../src/GFF3/gff3ToAnnotationFeature.test.ts"],"names":[],"mappings":";;AA0HA,sEAKC;;AA/HD,4DAA4D;AAC5D,qCAAsC;AACtC,yCAAwC;AAGxC,4DAAiD;AACjD,+BAAkC;AAClC,wEAAsC;AAEtC,uEAAmE;AAEnE,IAAA,UAAG,EAAC,sBAAW,CAAC,CAAA;AAEhB,MAAM,SAAS,GAAkD;IAC/D;QACE,4BAA4B;QAC5B,iEAAiE;QACjE;YACE,GAAG,EAAE,0BAA0B;YAC/B,MAAM,EAAE,MAAM;YACd,IAAI,EAAE,QAAQ;YACd,GAAG,EAAE,GAAG;YACR,GAAG,EAAE,IAAI;YACT,UAAU,EAAE;gBACV,UAAU,EAAE,CAAC,SAAS,CAAC;gBACvB,QAAQ,EAAE,CAAC,YAAY,CAAC;gBACxB,SAAS,EAAE,CAAC,KAAK,CAAC;aACnB;SACF;KACF;IACD;QACE,6BAA6B;QAC7B;;;CAGH;QACG;YACE,GAAG,EAAE,0BAA0B;YAC/B,MAAM,EAAE,MAAM;YACd,IAAI,EAAE,WAAW;YACjB,GAAG,EAAE,IAAI;YACT,GAAG,EAAE,IAAI;YACT,MAAM,EAAE,CAAC;YACT,QAAQ,EAAE;gBACR,0BAA0B,EAAE;oBAC1B,GAAG,EAAE,0BAA0B;oBAC/B,MAAM,EAAE,MAAM;oBACd,IAAI,EAAE,YAAY;oBAClB,GAAG,EAAE,IAAI;oBACT,GAAG,EAAE,IAAI;oBACT,MAAM,EAAE,CAAC;oBACT,UAAU,EAAE;wBACV,UAAU,EAAE,CAAC,KAAK,CAAC;wBACnB,QAAQ,EAAE,CAAC,UAAU,CAAC;wBACtB,UAAU,EAAE,CAAC,gBAAgB,CAAC;qBAC/B;iBACF;gBACD,0BAA0B,EAAE;oBAC1B,GAAG,EAAE,0BAA0B;oBAC/B,MAAM,EAAE,MAAM;oBACd,IAAI,EAAE,YAAY;oBAClB,GAAG,EAAE,IAAI;oBACT,GAAG,EAAE,IAAI;oBACT,MAAM,EAAE,CAAC;oBACT,UAAU,EAAE;wBACV,UAAU,EAAE,CAAC,KAAK,CAAC;wBACnB,QAAQ,EAAE,CAAC,UAAU,CAAC;wBACtB,UAAU,EAAE,CAAC,kBAAkB,CAAC;qBACjC;iBACF;aACF;YACD,UAAU,EAAE;gBACV,UAAU,EAAE,CAAC,KAAK,CAAC;gBACnB,MAAM,EAAE,CAAC,QAAQ,CAAC;gBAClB,QAAQ,EAAE,CAAC,UAAU,CAAC;gBACtB,UAAU,EAAE,CAAC,gBAAgB,CAAC;aAC/B;SACF;KACF;CACF,CAAA;AAOD,SAAS,eAAe,CACtB,OAAkC;IAElC,MAAM,EAAE,QAAQ,EAAE,GAAG,OAAO,CAAA;IAC5B,IAAI,CAAC,QAAQ,EAAE,CAAC;QACd,OAAO,OAAqD,CAAA;IAC9D,CAAC;IACD,MAAM,aAAa,GAAG,MAAM,CAAC,MAAM,CAAC,QAAQ,CAAC,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAC1D,eAAe,CAAC,KAAK,CAAC,CACvB,CAAA;IACD,OAAO,EAAE,GAAG,OAAO,EAAE,QAAQ,EAAE,aAAa,EAAE,CAAA;AAChD,CAAC;AAED,SAAS,eAAe,CACtB,QAAmC,EACnC,QAAmC;IAEnC,aAAM,CAAC,uBAAuB,CAC5B,eAAe,CAAC,QAAQ,CAAC,EACzB,eAAe,CAAC,QAAQ,CAAC,EACzB,KAAK,CACN,CAAA;AACH,CAAC;AAED,SAAS,eAAe,CAAC,EAAU;IACjC,MAAM,KAAK,GAAG,IAAA,sBAAY,EAAC,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAA;IACrD,MAAM,OAAO,GAAa,EAAE,CAAA;IAC5B,KAAK,MAAM,IAAI,IAAI,KAAK,EAAE,CAAC;QACzB,IAAI,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,EAAE,CAAC;YAC1B,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAA;QACpB,CAAC;IACH,CAAC;IACD,MAAM,KAAK,GAAG,aAAG,CAAC,eAAe,CAAC,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,CAAkB,CAAA;IACtE,OAAO,KAAK,CAAA;AACd,CAAC;AAED,SAAgB,6BAA6B,CAC3C,EAAU;IAEV,MAAM,KAAK,GAAG,IAAA,sBAAY,EAAC,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAA;IACzC,OAAO,IAAI,CAAC,KAAK,CAAC,KAAK,CAA8B,CAAA;AACvD,CAAC;AAED,MAAM,CAAC,GAAG,EAAE,GAAG,EAAE,GAAG,EAAE,GAAG,CAAC,GAAG,eAAe,CAC1C,qCAAqC,CACtC,CAAA;AAED,IAAA,oBAAQ,EAAC,kCAAkC,EAAE,GAAG,EAAE;IAChD,IAAA,cAAE,EAAC,iBAAiB,EAAE,GAAG,EAAE;QACzB,MAAM,MAAM,GAAG,IAAA,iDAAuB,EACpC,eAAe,CAAC,wBAAwB,CAAC,CAAC,CAAC,CAAC,CAC7C,CAAA;QACD,MAAM,QAAQ,GAAG,6BAA6B,CAAC,wBAAwB,CAAC,CAAA;QACxE,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,kBAAkB,EAAE,GAAG,EAAE;QAC1B,MAAM,MAAM,GAAG,IAAA,iDAAuB,EACpC,eAAe,CAAC,wBAAwB,CAAC,CAAC,CAAC,CAAC,CAC7C,CAAA;QACD,MAAM,QAAQ,GAAG,6BAA6B,CAAC,wBAAwB,CAAC,CAAA;QACxE,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAE3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAEhE,MAAM,QAAQ,GAAG,6BAA6B,CAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,MAAM,QAAQ,GAAG,6BAA6B,CAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,gFAAgF;QAChF,oFAAoF;QACpF,qGAAqG;QACrG,qBAAqB;QACrB,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAEpD,6EAA6E;QAC7E,oCAAoC;IACtC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,mBAAmB,EAAE,GAAG,EAAE;QAC3B,MAAM,EAAE,GAAG,IAAI,CAAC,SAAS,CAAC,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QACvC,aAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,2BAA2B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAC9D,aAAM,CAAC,KAAK,CAAC,EAAE,CAAC,KAAK,CAAC,4BAA4B,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QAE/D,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,GAAG,CAAC,CAAA;QAC3C,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAA;QACpD,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,YAAY,CAAC,EAAE,IAAI,CAAC,CAAA;QAE3C,MAAM,QAAQ,GAAG,6BAA6B,CAAC,0BAA0B,CAAC,CAAA;QAC1E,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,oBAAoB,EAAE,GAAG,EAAE;QAC5B,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAAC,sBAAsB,CAAC,CAAA;QAC5D,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,MAAM,EAAE,IAAI,EAAE,CAAC,CAAC,CAAA;QAC3C,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAA;QACxC,aAAM,CAAC,KAAK,CAAC,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,IAAI,CAAC,CAAA;IAC1C,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAA,oBAAQ,EAAC,mBAAmB,EAAE,GAAG,EAAE;IACjC,IAAA,cAAE,EAAC,wCAAwC,EAAE,GAAG,EAAE;QAChD,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAAC,gCAAgC,CAAC,CAAA;QACtE,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,6BAA6B,CAC5C,iCAAiC,CAClC,CAAA;QACD,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,wDAAwD,EAAE,GAAG,EAAE;QAChE,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAClC,4CAA4C,CAC7C,CAAA;QACD,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,6BAA6B,CAC5C,6CAA6C,CAC9C,CAAA;QACD,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;IACF,IAAA,cAAE,EAAC,2DAA2D,EAAE,GAAG,EAAE;QACnE,MAAM,CAAC,UAAU,CAAC,GAAG,eAAe,CAClC,+CAA+C,CAChD,CAAA;QACD,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,MAAM,QAAQ,GAAG,6BAA6B,CAC5C,gDAAgD,CACjD,CAAA;QACD,eAAe,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAA;IACnC,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA;AAEF,IAAA,oBAAQ,EAAC,yBAAyB,EAAE,GAAG,EAAE;IACvC,KAAK,MAAM,QAAQ,IAAI,SAAS,EAAE,CAAC;QACjC,MAAM,CAAC,WAAW,EAAE,WAAW,EAAE,gBAAgB,CAAC,GAAG,QAAQ,CAAA;QAC7D,IAAA,cAAE,EAAC,YAAY,WAAW,EAAE,EAAE,GAAG,EAAE;YACjC,MAAM,WAAW,GAAG,aAAG,CAAC,eAAe,CAAC,WAAW,EAAE;gBACnD,cAAc,EAAE,KAAK;aACtB,CAAC,CAAA;YACF,MAAM,OAAO,GAAG,IAAA,iDAAuB,EAAC,WAAW,CAAC,CAAC,CAAC,CAAC,CAAA;YACvD,eAAe,CAAC,gBAAgB,EAAE,OAAO,CAAC,CAAA;QAC5C,CAAC,CAAC,CAAA;IACJ,CAAC;AACH,CAAC,CAAC,CAAA;AAEF,IAAA,oBAAQ,EAAC,kBAAkB,EAAE,GAAG,EAAE;IAChC,IAAA,cAAE,EAAC,0BAA0B,EAAE,GAAG,EAAE;QAClC,MAAM,UAAU,GAAgB;YAC9B;gBACE,MAAM,EAAE,MAAM;gBACd,MAAM,EAAE,UAAU;gBAClB,IAAI,EAAE,MAAM;gBACZ,KAAK,EAAE,IAAI;gBACX,GAAG,EAAE,IAAI;gBACT,KAAK,EAAE,CAAC;gBACR,MAAM,EAAE,GAAG;gBACX,KAAK,EAAE,IAAI;gBACX,UAAU,EAAE;oBACV,EAAE,EAAE,CAAC,WAAW,CAAC;oBACjB,IAAI,EAAE,CAAC,MAAM,CAAC;oBACd,MAAM,EAAE,CAAC,MAAM,CAAC;iBACjB;gBACD,cAAc,EAAE,EAAE;gBAClB,gBAAgB,EAAE,EAAE;aACrB;SACF,CAAA;QACD,MAAM,MAAM,GAAG,IAAA,iDAAuB,EAAC,UAAU,CAAC,CAAA;QAClD,aAAM,CAAC,eAAe,CAAC,MAAM,CAAC,UAAU,EAAE,UAAU,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,UAAU,CAAC,CAAA;QACxE,aAAM,CAAC,eAAe,CAAC,MAAM,CAAC,UAAU,EAAE,SAAS,EAAE,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,CAAC,CAAA;IAClE,CAAC,CAAC,CAAA;AACJ,CAAC,CAAC,CAAA"}
|
|
@@ -3,3 +3,10 @@ export type GFFInternalAttribute = 'gff_id' | 'gff_name' | 'gff_alias' | 'gff_pa
|
|
|
3
3
|
export declare const gffToInternal: Record<GFFReservedAttribute, GFFInternalAttribute>;
|
|
4
4
|
export declare function isGFFReservedAttribute(attribute: string): attribute is GFFReservedAttribute;
|
|
5
5
|
export declare const internalToGFF: Record<GFFInternalAttribute, GFFReservedAttribute>;
|
|
6
|
+
export declare function isGFFInternalAttribute(attribute: string): attribute is GFFInternalAttribute;
|
|
7
|
+
export type GFFColumn = 'score' | 'source';
|
|
8
|
+
export type GFFColumnInternal = 'gff_score' | 'gff_source';
|
|
9
|
+
export declare const gffColumnToInternal: Record<GFFColumn, GFFColumnInternal>;
|
|
10
|
+
export declare function isGFFColumn(attribute: string): attribute is GFFColumn;
|
|
11
|
+
export declare const gffInternalToColumn: Record<GFFColumnInternal, GFFColumn>;
|
|
12
|
+
export declare function isGFFColumnInternal(column: string): column is GFFColumnInternal;
|
|
@@ -1,7 +1,10 @@
|
|
|
1
1
|
"use strict";
|
|
2
2
|
Object.defineProperty(exports, "__esModule", { value: true });
|
|
3
|
-
exports.internalToGFF = exports.gffToInternal = void 0;
|
|
3
|
+
exports.gffInternalToColumn = exports.gffColumnToInternal = exports.internalToGFF = exports.gffToInternal = void 0;
|
|
4
4
|
exports.isGFFReservedAttribute = isGFFReservedAttribute;
|
|
5
|
+
exports.isGFFInternalAttribute = isGFFInternalAttribute;
|
|
6
|
+
exports.isGFFColumn = isGFFColumn;
|
|
7
|
+
exports.isGFFColumnInternal = isGFFColumnInternal;
|
|
5
8
|
exports.gffToInternal = {
|
|
6
9
|
ID: 'gff_id',
|
|
7
10
|
Name: 'gff_name',
|
|
@@ -31,4 +34,21 @@ exports.internalToGFF = {
|
|
|
31
34
|
gff_ontology_term: 'Ontology_term',
|
|
32
35
|
gff_is_circular: 'Is_circular',
|
|
33
36
|
};
|
|
37
|
+
function isGFFInternalAttribute(attribute) {
|
|
38
|
+
return attribute in exports.internalToGFF;
|
|
39
|
+
}
|
|
40
|
+
exports.gffColumnToInternal = {
|
|
41
|
+
score: 'gff_score',
|
|
42
|
+
source: 'gff_source',
|
|
43
|
+
};
|
|
44
|
+
function isGFFColumn(attribute) {
|
|
45
|
+
return attribute in exports.gffColumnToInternal;
|
|
46
|
+
}
|
|
47
|
+
exports.gffInternalToColumn = {
|
|
48
|
+
gff_score: 'score',
|
|
49
|
+
gff_source: 'source',
|
|
50
|
+
};
|
|
51
|
+
function isGFFColumnInternal(column) {
|
|
52
|
+
return column in exports.gffInternalToColumn;
|
|
53
|
+
}
|
|
34
54
|
//# sourceMappingURL=gffReservedKeys.js.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"gffReservedKeys.js","sourceRoot":"","sources":["../../src/GFF3/gffReservedKeys.ts"],"names":[],"mappings":";;;AAyCA,wDAIC;
|
|
1
|
+
{"version":3,"file":"gffReservedKeys.js","sourceRoot":"","sources":["../../src/GFF3/gffReservedKeys.ts"],"names":[],"mappings":";;;AAyCA,wDAIC;AAiBD,wDAIC;AAQD,kCAEC;AAKD,kDAIC;AA3DY,QAAA,aAAa,GACxB;IACE,EAAE,EAAE,QAAQ;IACZ,IAAI,EAAE,UAAU;IAChB,KAAK,EAAE,WAAW;IAClB,MAAM,EAAE,YAAY;IACpB,MAAM,EAAE,YAAY;IACpB,GAAG,EAAE,SAAS;IACd,YAAY,EAAE,kBAAkB;IAChC,IAAI,EAAE,UAAU;IAChB,MAAM,EAAE,YAAY;IACpB,aAAa,EAAE,mBAAmB;IAClC,WAAW,EAAE,iBAAiB;CAC/B,CAAA;AAEH,SAAgB,sBAAsB,CACpC,SAAiB;IAEjB,OAAO,SAAS,IAAI,qBAAa,CAAA;AACnC,CAAC;AAEY,QAAA,aAAa,GACxB;IACE,MAAM,EAAE,IAAI;IACZ,QAAQ,EAAE,MAAM;IAChB,SAAS,EAAE,OAAO;IAClB,UAAU,EAAE,QAAQ;IACpB,UAAU,EAAE,QAAQ;IACpB,OAAO,EAAE,KAAK;IACd,gBAAgB,EAAE,cAAc;IAChC,QAAQ,EAAE,MAAM;IAChB,UAAU,EAAE,QAAQ;IACpB,iBAAiB,EAAE,eAAe;IAClC,eAAe,EAAE,aAAa;CAC/B,CAAA;AAEH,SAAgB,sBAAsB,CACpC,SAAiB;IAEjB,OAAO,SAAS,IAAI,qBAAa,CAAA;AACnC,CAAC;AAIY,QAAA,mBAAmB,GAAyC;IACvE,KAAK,EAAE,WAAW;IAClB,MAAM,EAAE,YAAY;CACrB,CAAA;AACD,SAAgB,WAAW,CAAC,SAAiB;IAC3C,OAAO,SAAS,IAAI,2BAAmB,CAAA;AACzC,CAAC;AACY,QAAA,mBAAmB,GAAyC;IACvE,SAAS,EAAE,OAAO;IAClB,UAAU,EAAE,QAAQ;CACrB,CAAA;AACD,SAAgB,mBAAmB,CACjC,MAAc;IAEd,OAAO,MAAM,IAAI,2BAAmB,CAAA;AACtC,CAAC"}
|
package/dist/Messages.d.ts
CHANGED
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import { SerializedChange } from '@apollo-annotation/common';
|
|
2
|
-
import { CheckResultSnapshot } from '@apollo-annotation/mst';
|
|
1
|
+
import { type SerializedChange } from '@apollo-annotation/common';
|
|
2
|
+
import { type CheckResultSnapshot } from '@apollo-annotation/mst';
|
|
3
3
|
interface BaseMessage {
|
|
4
4
|
channel: string;
|
|
5
5
|
userName: string;
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { LocalGFF3DataStore, Operation, SerializedOperation, ServerDataStore } from '@apollo-annotation/common';
|
|
1
|
+
import { type LocalGFF3DataStore, Operation, type SerializedOperation, type ServerDataStore } from '@apollo-annotation/common';
|
|
2
2
|
interface SerializedGetAssembliesOperation extends SerializedOperation {
|
|
3
3
|
typeName: 'GetAssembliesOperation';
|
|
4
4
|
}
|
|
@@ -1,4 +1,4 @@
|
|
|
1
|
-
import { LocalGFF3DataStore, Operation, OperationOptions, SerializedOperation, ServerDataStore } from '@apollo-annotation/common';
|
|
1
|
+
import { type LocalGFF3DataStore, Operation, type OperationOptions, type SerializedOperation, type ServerDataStore } from '@apollo-annotation/common';
|
|
2
2
|
interface SerializedGetFeaturesOperation extends SerializedOperation {
|
|
3
3
|
typeName: 'GetFeaturesOperation';
|
|
4
4
|
refSeq: string;
|
|
@@ -1,5 +1,5 @@
|
|
|
1
|
-
import { Change } from '@apollo-annotation/common';
|
|
2
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-
import { TypeChange } from '../Changes';
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1
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+
import { type Change } from '@apollo-annotation/common';
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2
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+
import { type TypeChange } from '../Changes';
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3
3
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import { Validation } from './Validation';
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4
4
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export declare function isTypeChange(thing: Change): thing is TypeChange;
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5
5
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export declare class CoreValidation extends Validation {
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@@ -3,8 +3,8 @@ Object.defineProperty(exports, "__esModule", { value: true });
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3
3
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exports.CoreValidation = void 0;
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4
4
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exports.isTypeChange = isTypeChange;
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5
5
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const tslib_1 = require("tslib");
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6
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-
const soSequenceTypes_1 = tslib_1.__importDefault(require("./soSequenceTypes"));
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7
6
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const Validation_1 = require("./Validation");
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7
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+
const soSequenceTypes_1 = tslib_1.__importDefault(require("./soSequenceTypes"));
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8
8
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function isTypeChange(thing) {
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9
9
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return 'oldType' in thing && 'newType' in thing;
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10
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}
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"CoreValidation.js","sourceRoot":"","sources":["../../src/Validations/CoreValidation.ts"],"names":[],"mappings":";;;
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1
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+
{"version":3,"file":"CoreValidation.js","sourceRoot":"","sources":["../../src/Validations/CoreValidation.ts"],"names":[],"mappings":";;;AAQA,oCAEC;;AALD,6CAAyC;AACzC,gFAA+C;AAE/C,SAAgB,YAAY,CAAC,KAAa;IACxC,OAAO,SAAS,IAAI,KAAK,IAAI,SAAS,IAAI,KAAK,CAAA;AACjD,CAAC;AAED,MAAa,cAAe,SAAQ,uBAAU;IAC5C,IAAI,GAAG,MAAe,CAAA;IAEtB,KAAK,CAAC,mBAAmB,CAAC,MAAc;QACtC,IAAI,YAAY,CAAC,MAAM,CAAC,EAAE,CAAC;YACzB,KAAK,MAAM,SAAS,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBACvC,IAAI,CAAC,yBAAe,CAAC,QAAQ,CAAC,SAAS,CAAC,OAAO,CAAC,EAAE,CAAC;oBACjD,OAAO;wBACL,cAAc,EAAE,IAAI,CAAC,IAAI;wBACzB,KAAK,EAAE;4BACL,OAAO,EAAE,IAAI,SAAS,CAAC,OAAO,2CAA2C;yBAC1E;qBACF,CAAA;gBACH,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,EAAE,cAAc,EAAE,IAAI,CAAC,IAAI,EAAE,CAAA;IACtC,CAAC;IAED,KAAK,CAAC,cAAc,CAAC,GAAW;QAC9B,IAAI,GAAG,KAAK,MAAM,EAAE,CAAC;YACnB,OAAO,yBAAe,CAAA;QACxB,CAAC;QACD,OAAM;IACR,CAAC;CACF;AAzBD,wCAyBC"}
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@@ -1,8 +1,8 @@
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1
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-
import { Change } from '@apollo-annotation/common';
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2
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-
import { Feature, FeatureDocument } from '@apollo-annotation/schemas';
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3
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-
import { ClientSession, Model } from 'mongoose';
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4
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-
import { LocationEndChange, LocationStartChange } from '../Changes';
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5
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-
import { Validation, ValidationResult } from './Validation';
|
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1
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+
import { type Change } from '@apollo-annotation/common';
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2
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+
import { type Feature, type FeatureDocument } from '@apollo-annotation/schemas';
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3
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+
import { type ClientSession, type Model } from 'mongoose';
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4
|
+
import { type LocationEndChange, type LocationStartChange } from '../Changes';
|
|
5
|
+
import { Validation, type ValidationResult } from './Validation';
|
|
6
6
|
export declare class ParentChildValidation extends Validation {
|
|
7
7
|
name: "ParentChildValidation";
|
|
8
8
|
backendPostValidate(change: Change, { featureModel, session, }: {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ParentChildValidation.js","sourceRoot":"","sources":["../../src/Validations/ParentChildValidation.ts"],"names":[],"mappings":";;;AAMA,wCAKmB;
|
|
1
|
+
{"version":3,"file":"ParentChildValidation.js","sourceRoot":"","sources":["../../src/Validations/ParentChildValidation.ts"],"names":[],"mappings":";;;AAMA,wCAKmB;AAEnB,6CAAgE;AAEhE,MAAa,qBAAsB,SAAQ,uBAAU;IACnD,IAAI,GAAG,uBAAgC,CAAA;IAEvC,KAAK,CAAC,mBAAmB,CACvB,MAAc,EACd,EACE,YAAY,EACZ,OAAO,GAC0D;QAEnE,IAAI,IAAA,6BAAmB,EAAC,MAAM,CAAC,IAAI,IAAA,+BAAqB,EAAC,MAAM,CAAC,EAAE,CAAC;YACjE,OAAO,IAAI,CAAC,gCAAgC,CAAC,MAAM,EAAE;gBACnD,OAAO;gBACP,YAAY;aACb,CAAC,CAAA;QACJ,CAAC;QACD,OAAO,EAAE,cAAc,EAAE,IAAI,CAAC,IAAI,EAAE,CAAA;IACtC,CAAC;IAED,KAAK,CAAC,gCAAgC,CACpC,MAA+C,EAC/C,EACE,YAAY,EACZ,OAAO,GAC0D;QAEnE,MAAM,gBAAgB,GAAsB,EAAE,CAAA;QAC9C,KAAK,MAAM,EAAE,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAChC,MAAM,EAAE,SAAS,EAAE,GAAG,EAAE,CAAA;YAExB,yBAAyB;YACzB,MAAM,eAAe,GAAG,MAAM,YAAY;iBACvC,OAAO,CAAC,EAAE,MAAM,EAAE,SAAS,EAAE,CAAC;iBAC9B,OAAO,CAAC,OAAO,CAAC;iBAChB,IAAI,EAAE,CAAA;YAET,IAAI,CAAC,eAAe,EAAE,CAAC;gBACrB,MAAM,MAAM,GAAG,8DAA8D,SAAS,GAAG,CAAA;gBACzF,MAAM,IAAI,KAAK,CAAC,MAAM,CAAC,CAAA;YACzB,CAAC;YACD,IAAI,CAAC,gBAAgB,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,KAAK,eAAe,CAAC,GAAG,CAAC,EAAE,CAAC;gBACjE,gBAAgB,CAAC,IAAI,CAAC,eAAe,CAAC,CAAA;YACxC,CAAC;QACH,CAAC;QACD,KAAK,MAAM,eAAe,IAAI,gBAAgB,EAAE,CAAC;YAC/C,IAAI,CAAC;gBACH,IAAI,CAAC,2BAA2B,CAAC,eAAe,CAAC,CAAA;YACnD,CAAC;YAAC,OAAO,KAAK,EAAE,CAAC;gBACf,OAAO,EAAE,cAAc,EAAE,IAAI,CAAC,IAAI,EAAE,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,CAAC,KAAK,CAAC,EAAE,EAAE,CAAA;YACzE,CAAC;QACH,CAAC;QACD,OAAO,EAAE,cAAc,EAAE,IAAI,CAAC,IAAI,EAAE,CAAA;IACtC,CAAC;IAED,2BAA2B,CAAC,OAAgB;QAC1C,IAAI,CAAC,OAAO,CAAC,QAAQ,EAAE,CAAC;YACtB,OAAM;QACR,CAAC;QACD,KAAK,MAAM,CAAC,EAAE,YAAY,CAAC,IAAI,OAAO,CAAC,QAAQ,IAAI,IAAI,GAAG,EAAE,EAAE,CAAC;YAC7D,IACE,OAAO,CAAC,GAAG,KAAK,IAAI;gBACpB,OAAO,CAAC,GAAG,KAAK,IAAI;gBACpB,YAAY,CAAC,GAAG,KAAK,IAAI;gBACzB,YAAY,CAAC,GAAG,KAAK,IAAI;gBACzB,CAAC,YAAY,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,IAAI,YAAY,CAAC,GAAG,GAAG,OAAO,CAAC,GAAG,CAAC,EAClE,CAAC;gBACD,MAAM,IAAI,KAAK,CACb,YAAY,YAAY,CAAC,GAAG,wCAAwC,OAAO,CAAC,GAAG,GAAG,CACnF,CAAA;YACH,CAAC;YACD,IAAI,CAAC,2BAA2B,CAAC,YAAY,CAAC,CAAA;QAChD,CAAC;IACH,CAAC;CACF;AAzED,sDAyEC"}
|
|
@@ -1,8 +1,8 @@
|
|
|
1
|
-
import { Change, ClientDataStore } from '@apollo-annotation/common';
|
|
2
|
-
import { FeatureDocument } from '@apollo-annotation/schemas';
|
|
3
|
-
import type
|
|
4
|
-
import type
|
|
5
|
-
import { ClientSession, Model } from 'mongoose';
|
|
1
|
+
import { type Change, type ClientDataStore } from '@apollo-annotation/common';
|
|
2
|
+
import { type FeatureDocument } from '@apollo-annotation/schemas';
|
|
3
|
+
import { type ExecutionContext } from '@nestjs/common';
|
|
4
|
+
import { type Reflector } from '@nestjs/core';
|
|
5
|
+
import { type ClientSession, type Model } from 'mongoose';
|
|
6
6
|
export interface Context {
|
|
7
7
|
context: ExecutionContext;
|
|
8
8
|
reflector: Reflector;
|
|
@@ -1,7 +1,7 @@
|
|
|
1
|
-
import { Change, ClientDataStore } from '@apollo-annotation/common';
|
|
2
|
-
import { FeatureDocument } from '@apollo-annotation/schemas';
|
|
3
|
-
import { ClientSession, Model } from 'mongoose';
|
|
4
|
-
import { Context, Validation, ValidationResult } from './Validation';
|
|
1
|
+
import { type Change, type ClientDataStore } from '@apollo-annotation/common';
|
|
2
|
+
import { type FeatureDocument } from '@apollo-annotation/schemas';
|
|
3
|
+
import { type ClientSession, type Model } from 'mongoose';
|
|
4
|
+
import { type Context, type Validation, type ValidationResult } from './Validation';
|
|
5
5
|
export declare class ValidationResultSet {
|
|
6
6
|
results: ValidationResult[];
|
|
7
7
|
get resultsMessages(): string;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ValidationSet.js","sourceRoot":"","sources":["../../src/Validations/ValidationSet.ts"],"names":[],"mappings":";;;
|
|
1
|
+
{"version":3,"file":"ValidationSet.js","sourceRoot":"","sources":["../../src/Validations/ValidationSet.ts"],"names":[],"mappings":";;;AAUA,MAAa,mBAAmB;IAC9B,OAAO,GAAuB,EAAE,CAAA;IAChC,IAAI,eAAe;QACjB,OAAO,IAAI,CAAC,OAAO;aAChB,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,KAAK,EAAE,OAAO,CAAC;aAC5B,MAAM,CAAC,OAAO,CAAC;aACf,IAAI,CAAC,IAAI,CAAC,CAAA;IACf,CAAC;IAED,EAAE,GAAG,IAAI,CAAA;IACT,GAAG,CAAC,MAAwB;QAC1B,IAAI,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,CAAA;QACzB,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;YACjB,IAAI,CAAC,EAAE,GAAG,KAAK,CAAA;QACjB,CAAC;IACH,CAAC;CACF;AAhBD,kDAgBC;AAED,MAAa,aAAa;IACxB,WAAW,GAAG,IAAI,GAAG,EAAc,CAAA;IAEnC,kBAAkB,CAAC,UAAsB;QACvC,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,UAAU,CAAC,CAAA;IAClC,CAAC;IAED,KAAK,CAAC,mBAAmB,CAAC,MAAc;QACtC,MAAM,OAAO,GAAG,IAAI,mBAAmB,EAAE,CAAA;QACzC,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACjC,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,mBAAmB,CAAC,MAAM,CAAC,CAAA;YAClD,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACnB,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;gBACjB,MAAK;YACP,CAAC;QACH,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,KAAK,CAAC,oBAAoB,CACxB,MAAc,EACd,SAA0B;QAE1B,MAAM,OAAO,GAAG,IAAI,mBAAmB,EAAE,CAAA;QACzC,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACjC,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,oBAAoB,CAAC,MAAM,EAAE,SAAS,CAAC,CAAA;YAC9D,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACnB,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;gBACjB,MAAK;YACP,CAAC;QACH,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,KAAK,CAAC,kBAAkB,CACtB,MAAwB;QAExB,MAAM,OAAO,GAAG,IAAI,mBAAmB,EAAE,CAAA;QACzC,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACjC,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,kBAAkB,CAAC,MAAM,CAAC,CAAA;YACjD,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACnB,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;gBACjB,MAAK;YACP,CAAC;QACH,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,KAAK,CAAC,mBAAmB,CACvB,MAAc,EACd,EACE,YAAY,EACZ,OAAO,GAC0D;QAEnE,MAAM,OAAO,GAAG,IAAI,mBAAmB,EAAE,CAAA;QACzC,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACjC,MAAM,MAAM,GAAG,MAAM,CAAC,CAAC,mBAAmB,CAAC,MAAM,EAAE;gBACjD,YAAY;gBACZ,OAAO;aACR,CAAC,CAAA;YACF,OAAO,CAAC,GAAG,CAAC,MAAM,CAAC,CAAA;YACnB,IAAI,MAAM,CAAC,KAAK,EAAE,CAAC;gBACjB,MAAK;YACP,CAAC;QACH,CAAC;QACD,OAAO,OAAO,CAAA;IAChB,CAAC;IAED,KAAK,CAAC,cAAc,CAAC,GAAW;QAC9B,KAAK,MAAM,CAAC,IAAI,IAAI,CAAC,WAAW,EAAE,CAAC;YACjC,MAAM,IAAI,GAAG,MAAM,CAAC,CAAC,cAAc,CAAC,GAAG,CAAC,CAAA;YACxC,IAAI,IAAI,EAAE,CAAC;gBACT,OAAO,IAAI,CAAA;YACb,CAAC;QACH,CAAC;QACD,OAAM;IACR,CAAC;CACF;AA9ED,sCA8EC;AAED,qDAAqD;AACxC,QAAA,kBAAkB,GAAG,IAAI,aAAa,EAAE,CAAA"}
|