Support nanopore data structure v3 #328
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Steffengreiner
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Oct 11, 2022
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@wow-such-code Nicely Done, I'll make some minor adjustments and merge and resolve the datastructure :)
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| "drift_correction_log": { | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/file" | ||
| }, | ||
| { | ||
| "properties": { | ||
| "name": { | ||
| "pattern": "drift_correction_.*" | ||
| }, | ||
| "file_type": { | ||
| "pattern": "csv" | ||
| } | ||
| } | ||
| } | ||
| ] | ||
| }, | ||
| "duty_time_log": { | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/file" | ||
| }, | ||
| { | ||
| "properties": { | ||
| "name": { | ||
| "pattern": "duty_time_.*" | ||
| }, | ||
| "file_type": { | ||
| "pattern": "csv" | ||
| } | ||
| } | ||
| } | ||
| ] | ||
| }, |
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Suggested change
| "drift_correction_log": { | |
| "allOf": [ | |
| { | |
| "$ref": "#/definitions/file" | |
| }, | |
| { | |
| "properties": { | |
| "name": { | |
| "pattern": "drift_correction_.*" | |
| }, | |
| "file_type": { | |
| "pattern": "csv" | |
| } | |
| } | |
| } | |
| ] | |
| }, | |
| "duty_time_log": { | |
| "allOf": [ | |
| { | |
| "$ref": "#/definitions/file" | |
| }, | |
| { | |
| "properties": { | |
| "name": { | |
| "pattern": "duty_time_.*" | |
| }, | |
| "file_type": { | |
| "pattern": "csv" | |
| } | |
| } | |
| } | |
| ] | |
| }, |
These two can be removed since they are not present in the new datastructure 👀
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| "mux_scan_data_log": { | ||
| "allOf": [ | ||
| { | ||
| "$ref": "#/definitions/file" | ||
| }, | ||
| { | ||
| "properties": { | ||
| "name": { | ||
| "pattern": "mux_scan_data_.*" | ||
| }, | ||
| "file_type": { | ||
| "pattern": "csv" | ||
| } | ||
| } | ||
| } | ||
| ] | ||
| }, |
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Suggested change
| "mux_scan_data_log": { | |
| "allOf": [ | |
| { | |
| "$ref": "#/definitions/file" | |
| }, | |
| { | |
| "properties": { | |
| "name": { | |
| "pattern": "mux_scan_data_.*" | |
| }, | |
| "file_type": { | |
| "pattern": "csv" | |
| } | |
| } | |
| } | |
| ] | |
| }, |
Also not present anymore in the new structure
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| "name": "report_test.html", | ||
| "path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/report_test.html", | ||
| "file_type": "pdf" |
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Suggested change
| "name": "report_test.html", | |
| "path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/report_test.html", | |
| "file_type": "pdf" | |
| "name": "report_test.html", | |
| "path": "./20200122_1217_1-A1-B1-PAE12345_1234567a/report_test.html", | |
| "file_type": "html" |
| import life.qbic.datamodel.datasets.datastructure.files.DataFile | ||
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| /** | ||
| * A specialisation of a DataFile, represents an Oxford Nanopore report PDF log file |
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| * A specialisation of a DataFile, represents an Oxford Nanopore report PDF log file | |
| * A specialisation of a DataFile, represents an Oxford Nanopore report HTML log file |
| import life.qbic.datamodel.datasets.datastructure.files.DataFile | ||
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| /** | ||
| * A specialisation of a DataFile, represents an Oxford Nanopore report PDF log file |
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| * A specialisation of a DataFile, represents an Oxford Nanopore report PDF log file | |
| * A specialisation of a DataFile, represents an Oxford Nanopore report Json log file |
| /** | ||
| * A specialisation of a DataFile, represents an Oxford Nanopore report PDF log file | ||
| * | ||
| * @author: Sven Fillinger |
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| * @author: Sven Fillinger |
| /** | ||
| * A specialisation of a DataFile, represents an Oxford Nanopore report PDF log file | ||
| * | ||
| * @author: Sven Fillinger |
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| * @author: Sven Fillinger |
Steffengreiner
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Oct 11, 2022
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I mean it's good 👍
Steffengreiner
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Oct 13, 2022
* increase snapshot to 2.20.0 * Adjust Nf-core pipeline result to account for sarekv3 file structure * Remove replacement of hyphens with underscores in project spaces (#326) * add digiwest property tpes * Support nanopore data structure v3 (#328) * add new version of valid nanopore structure * implement additional v3 changes * Update schema and test to current file structure Co-authored-by: Steffengreiner <[email protected]> * Fix Nanopore Schema V3 naming and streamline children of other report definition * Adapt schema and add test case for mibi datastructure Co-authored-by: wow-such-code <[email protected]>
Steffengreiner
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Oct 13, 2022
* Prepare Version 2.20.0 (#325) * increase snapshot to 2.20.0 * Adjust Nf-core pipeline result to account for sarekv3 file structure * Remove replacement of hyphens with underscores in project spaces (#326) Co-authored-by: wow-such-code <[email protected]> * Update version to 2.20.0 (#327) * Set version to 2.20.0 * remove unnessary whitespace Co-authored-by: Steffengreiner <[email protected]> * Release/2.21.0 (#331) * increase snapshot to 2.20.0 * Adjust Nf-core pipeline result to account for sarekv3 file structure * Remove replacement of hyphens with underscores in project spaces (#326) * add digiwest property tpes * Support nanopore data structure v3 (#328) * add new version of valid nanopore structure * implement additional v3 changes * Update schema and test to current file structure Co-authored-by: Steffengreiner <[email protected]> * Fix Nanopore Schema V3 naming and streamline children of other report definition * Adapt schema and add test case for mibi datastructure Co-authored-by: wow-such-code <[email protected]> * Set version to 2.21.0 (#332) Co-authored-by: wow-such-code <[email protected]> Co-authored-by: Johnny Q5 <[email protected]>
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Changes to handle ONT schema v3
Added:
Removed (from schema, not from model - backwards compatibility):