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Provide Data Files and Folders for Bam and Pod5 registration
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30 changes: 30 additions & 0 deletions
30
src/main/groovy/life/qbic/datamodel/datasets/datastructure/files/nanopore/BamFile.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,30 @@ | ||
| package life.qbic.datamodel.datasets.datastructure.files.nanopore | ||
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| import life.qbic.datamodel.datasets.datastructure.files.DataFile | ||
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| /** | ||
| * A specialisation of a DataFile, represents an Oxford Nanopore bam file | ||
| * | ||
| */ | ||
| class BamFile extends DataFile { | ||
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| final private static String FILE_TYPE = "bam" | ||
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| final private static String NAME_SCHEMA = /.*\.bam$/ | ||
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| protected BamFile(String name, String relativePath) { | ||
| super(name, relativePath, FILE_TYPE) | ||
| validateName() | ||
| } | ||
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| static BamFile create(String name, String relativePath) { | ||
| return new BamFile(name, relativePath) | ||
| } | ||
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| private void validateName() { | ||
| if (!(this.name =~ NAME_SCHEMA)) { | ||
| throw new IllegalArgumentException("Name must match the Nanopore summary schema!") | ||
| } | ||
| } | ||
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| } |
39 changes: 39 additions & 0 deletions
39
...n/groovy/life/qbic/datamodel/datasets/datastructure/folders/nanopore/BamFailFolder.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| package life.qbic.datamodel.datasets.datastructure.folders.nanopore | ||
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| import life.qbic.datamodel.datasets.datastructure.folders.DataFolder | ||
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| /** | ||
| * A special case of a DataFolder, its name is always bam_fail. | ||
| * | ||
| * Its children field contains either a list of type List<BamFiles> or List<BamFolder> | ||
| * | ||
| */ | ||
| class BamFailFolder extends DataFolder { | ||
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| final private static String NAME_SCHEMA = /bam_fail/ | ||
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| protected BamFailFolder() {} | ||
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| protected BamFailFolder(String name, String relativePath, List<?> children) { | ||
| super(name, relativePath, children) | ||
| validateName() | ||
| } | ||
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| /** | ||
| * Creates a new instance of a BamFailFolder object | ||
| * | ||
| * @param name The folder name | ||
| * @param relativePath The relative path of the folder | ||
| * @param children A list with child elements of the folder | ||
| * @return A new instance of a BamFailFolder object | ||
| */ | ||
| static BamFailFolder create(String name, String relativePath, List<?> children) { | ||
| new BamFailFolder(name, relativePath, children) | ||
| } | ||
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| private void validateName() { | ||
| if (!(this.name =~ NAME_SCHEMA)) { | ||
| throw new IllegalArgumentException("Name must match the Nanopore BamFail directory schema!") | ||
| } | ||
| } | ||
| } |
39 changes: 39 additions & 0 deletions
39
...n/groovy/life/qbic/datamodel/datasets/datastructure/folders/nanopore/BamPassFolder.groovy
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,39 @@ | ||
| package life.qbic.datamodel.datasets.datastructure.folders.nanopore | ||
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| import life.qbic.datamodel.datasets.datastructure.folders.DataFolder | ||
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| /** | ||
| * A special case of a DataFolder, its name is always bam_pass. | ||
| * | ||
| * Its children field contains either a list of type List<BamFiles> or List<BamFolder> | ||
| * | ||
| */ | ||
| class BamPassFolder extends DataFolder { | ||
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| final private static String NAME_SCHEMA = /bam_pass/ | ||
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| protected BamPassFolder() {} | ||
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| protected BamPassFolder(String name, String relativePath, List<?> children) { | ||
| super(name, relativePath, children) | ||
| validateName() | ||
| } | ||
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| /** | ||
| * Creates a new instance of a BamPassFolder object | ||
| * | ||
| * @param name The folder name | ||
| * @param relativePath The relative path of the folder | ||
| * @param children A list with child elements of the folder | ||
| * @return A new instance of a BamPassFolder object | ||
| */ | ||
| static BamPassFolder create(String name, String relativePath, List<?> children) { | ||
| new BamPassFolder(name, relativePath, children) | ||
| } | ||
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| private void validateName() { | ||
| if (!(this.name =~ NAME_SCHEMA)) { | ||
| throw new IllegalArgumentException("Name must match the Nanopore BamPass directory schema!") | ||
| } | ||
| } | ||
| } |