Feature/update nanopore #91
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* Add triggers * Reorder git commands
Steffengreiner
requested changes
May 5, 2022
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Heya @wow-such-code Nicely done! I have some questions and will approve once these are answered 👍
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| Schema jsonSchema = loadSchemaFromStream(OxfordNanoporeInstrumentOutput.getSchemaAsStream()) | ||
| // Step 2: validate against schema return if valid, throw exception if invalid | ||
| jsonSchema.validate(jsonObject) | ||
| } catch (ValidationException validationException) { | ||
| // Step 2.5: validate against second schema type | ||
| Schema jsonSchema2 = loadSchemaFromStream(OxfordNanoporeInstrumentOutputV2.getSchemaAsStream()) | ||
| jsonSchema2.validate(jsonObject) | ||
| } | ||
| } |
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This could be made more explicit by making the multiple schema validations into a seperate method.
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just pushed a suggestion
| private static void checkPresenceOfFlowCellPosition(Map metadata, String flowCellEntry) { | ||
| if (!metadata.containsKey(flowCellEntry)) { | ||
| throw new MissingArgumentException("Could not find metadata information about the flow cell position.") | ||
| throw new RuntimeException("Could not find metadata information about the flow cell position.") |
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What was the reason for exchanging the exception type here
I'd expect a missing argument to throw a MissingArgumentException?
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| protected boolean handleCommonParameters(final ToolMetadata toolMetadata, | ||
| final AbstractCommand command) { |
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I'm confused about the spacing adaptions in this class? Is this formatted as intended?
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might have been something to do with the eclipse codestyle, if it was changed by me. I don't remember unfortunately
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I think this formatting is correct as it is a continuation of the previous line
wow-such-code
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May 6, 2022
* Sync with hotfix 1.9.2 (#69) * Hotfix 1.9.1 (#66) * Fix RST syntax error * Remove orphaned print statement * Update CL * Bump version 1.9.1 -> 1.9.2 Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de> * Update maxquant file parser (#74) The summary file is now searched within the summary folder * Remove qube files and Bump version to 1.11.0-SNAPSHOT * Bump conf.py to current version * Bump version to 1.11.0-SNAPSHOT * Include groovydoc plugin in report generation (#59) * Feature/update nanopore (#91) * increase some versions, fix testing env * add tests for alternative nanopore structure * Add worflow triggers (#93) * Add triggers * Reorder git commands * Use master as base, not main * parser * update workflows (#94) * Set version to 1.10.6 * update pom * Fix project setup (#96) * add possibility of some metadata values being empty * comments * extract method to validate a single schema Co-authored-by: Sven F <sven.fillinger@qbic.uni-tuebingen.de> Co-authored-by: JohnnyQ5 <support@qbic.zendesk.com> Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de> Co-authored-by: Sven F <9976560+sven1103@users.noreply.github.com> * Feature/update nanopore (#97) * increase some versions, fix testing env * add tests for alternative nanopore structure * Add worflow triggers (#93) * Add triggers * Reorder git commands * Use master as base, not main * parser * update workflows (#94) * Set version to 1.10.6 * update pom * Fix project setup (#96) * add possibility of some metadata values being empty * comments * extract method to validate a single schema * use data-model-lib release Co-authored-by: Sven F <sven.fillinger@qbic.uni-tuebingen.de> Co-authored-by: JohnnyQ5 <support@qbic.zendesk.com> Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de> Co-authored-by: Sven F <9976560+sven1103@users.noreply.github.com> * Update CHANGELOG.rst Co-authored-by: Tobias Koch <KochTobi@users.noreply.github.com> Co-authored-by: Sven F <sven.fillinger@qbic.uni-tuebingen.de> Co-authored-by: Steffengreiner <Steffen.Greiner@gmx.de> Co-authored-by: jnnfr <jennifer.boedker@qbic.uni-tuebingen.de> Co-authored-by: JohnnyQ5 <support@qbic.zendesk.com> Co-authored-by: Sven F <9976560+sven1103@users.noreply.github.com> Co-authored-by: Tobias Koch <KochTobi@users.noreply.github.com>
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