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manuleramanulera
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Model changes to GenomeCoordinates, RepositoryId and ManuallyTyped (#71)
* model changed for #70 * re-order tests * closes #69 * closes #65; closes #66 * rename location to coordinates * adjust test to the use of coordinates instead of location * migrate examples * add manually typed sequence as class * remove field repository_name and revert examples * handle collections and other repos * migrate examples * test and migrate templates
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‎migrate_templates.sh‎

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rm -f src/data/templates/*/templates/*backup.json
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python -m opencloning_linkml.migrations.migrate --target-version 0.4.9 src/data/templates/*/templates/*.json
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rm -f src/data/templates/*/templates/*backup.json

‎project/excel/opencloning_linkml.xlsx‎

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‎project/graphql/opencloning_linkml.graphql‎

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@@ -33,19 +33,6 @@ enum GatewayReactionType
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BP
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}
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enum RepositoryName
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{
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addgene
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genbank
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benchling
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snapgene
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euroscarf
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igem
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wekwikgene
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seva
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open_dna_collections
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}
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enum SequenceFileFormat
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{
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fasta
@@ -62,7 +49,6 @@ type AddgeneIdSource
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databaseId: Integer
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input: [SourceInput]
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repositoryId: String!
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repositoryName: RepositoryName!
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sequenceFileUrl: String
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addgeneSequenceType: AddgeneSequenceType
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}
@@ -118,7 +104,6 @@ type BenchlingUrlSource
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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repositoryName: RepositoryName!
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repositoryId: String!
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}
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@@ -200,7 +185,6 @@ type EuroscarfSource
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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repositoryName: RepositoryName!
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repositoryId: String!
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}
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@@ -223,13 +207,12 @@ type GenomeCoordinatesSource
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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coordinates: SimpleSequenceLocation
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repositoryId: String!
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assemblyAccession: String
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sequenceAccession: String!
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locusTag: String
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geneId: Integer
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start: Integer!
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end: Integer!
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strand: Integer!
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location: String!
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}
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type GibsonAssemblySource
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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repositoryName: RepositoryName!
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sequenceFileUrl: String!
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repositoryId: String!
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}
@@ -294,24 +276,41 @@ type LigationSource
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circular: Boolean
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}
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type ManuallyTypedSequence
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{
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id: Integer!
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type: String
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overhangCrick3prime: Integer
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overhangWatson3prime: Integer
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sequence: String!
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circular: Boolean
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}
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type ManuallyTypedSource
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{
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id: Integer!
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type: String
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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overhangCrick3prime: Integer
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overhangWatson3prime: Integer
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userInput: String!
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circular: Boolean
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}
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type NamedThing
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{
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id: Integer!
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}
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type NCBISequenceSource
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{
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id: Integer!
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type: String
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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coordinates: SimpleSequenceLocation
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repositoryId: String!
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}
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type OligoHybridizationSource
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{
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id: Integer!
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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repositoryName: RepositoryName!
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sequenceFileUrl: String
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repositoryId: String!
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}
@@ -400,7 +398,6 @@ type RepositoryIdSource
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databaseId: Integer
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input: [SourceInput]
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repositoryId: String!
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repositoryName: RepositoryName!
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}
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type RestrictionAndLigationSource
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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repositoryName: RepositoryName!
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sequenceFileUrl: String
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repositoryId: String!
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}
@@ -492,7 +488,6 @@ type SnapGenePlasmidSource
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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repositoryName: RepositoryName!
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repositoryId: String!
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}
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@@ -550,7 +545,6 @@ type WekWikGeneIdSource
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outputName: String
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databaseId: Integer
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input: [SourceInput]
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repositoryName: RepositoryName!
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sequenceFileUrl: String
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repositoryId: String!
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}

‎project/jsonld/opencloning_linkml.context.jsonld‎

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{
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"comments": {
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"description": "Auto generated by LinkML jsonld context generator",
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"generation_date": "2025-11-27T13:31:19",
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"generation_date": "2025-12-06T00:30:23",
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"source": "opencloning_linkml.yaml"
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},
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"@context": {
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"assembly_accession": {
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"@id": "assembly_accession"
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},
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"end": {
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"@type": "xsd:integer",
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"@id": "end"
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},
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"gene_id": {
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"@type": "xsd:integer",
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"@id": "gene_id"
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},
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"locus_tag": {
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"@id": "locus_tag"
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},
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"sequence_accession": {
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"@id": "sequence_accession"
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},
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"start": {
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"@type": "xsd:integer",
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"@id": "start"
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},
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"strand": {
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"@type": "xsd:integer",
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"@id": "strand"
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},
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"id": "@id",
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"user_input": {
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"@id": "user_input"
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"location": {
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"@id": "location"
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},
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"sequence": {
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"@type": "@id",
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"@id": "sequence"
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},
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"name": {
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"@id": "schema:name"
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},
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"coordinates": {
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"@id": "coordinates"
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},
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"output_name": {
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"@id": "output_name"
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},
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"@type": "xsd:float",
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"@id": "percent_match_length"
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},
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"sequence": {
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"@type": "@id",
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"@id": "sequence"
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},
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"sseqid": {
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"@id": "sseqid"
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},
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"start_location": {
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"@type": "xsd:integer",
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"@id": "start_location"
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},
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"strand": {
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"@type": "xsd:integer",
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"@id": "strand"
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},
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"Type": {
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"@id": "Type"
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},
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"repository_id": {
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"@id": "repository_id"
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},
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"repository_name": {
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"@context": {
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"text": "skos:notation",
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"description": "skos:prefLabel",
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"meaning": "@id"
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},
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"@id": "repository_name"
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},
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"restriction_enzyme": {
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"@id": "restriction_enzyme"
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},
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"@type": "xsd:boolean",
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"@id": "circularize"
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},
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"coordinates": {
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"@id": "coordinates"
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},
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"index_in_file": {
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"@type": "xsd:integer",
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"@id": "index_in_file"
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"LigationSource": {
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"@id": "LigationSource"
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},
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"ManuallyTypedSequence": {
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"@id": "ManuallyTypedSequence"
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},
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"ManuallyTypedSource": {
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"@id": "ManuallyTypedSource"
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},
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"NamedThing": {
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"@id": "schema:Thing"
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},
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"NCBISequenceSource": {
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"@id": "NCBISequenceSource"
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},
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"OligoHybridizationSource": {
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"@id": "OligoHybridizationSource"
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},

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