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Harmonize excel data export and include missed properties #999

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KochTobi
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@KochTobi KochTobi commented Jan 27, 2025

Provides a common download behaviour for measurement registration, measurement edit, sample registration, sample edit and sample metadata download

Re-Implements the download of sample information to match other downloaded XLSX files.

Includes confounding variables in all sample related excel downloads.

…or-the-selected-species,specimen-and-analyte-in-the-aggregated-sample-metadata-sheet

# Conflicts:
#	user-interface/src/main/bundles/dev.bundle
#	user-interface/src/main/java/life/qbic/datamanager/files/export/sample/TemplateService.java
#	user-interface/src/main/java/life/qbic/datamanager/files/structure/sample/EditColumn.java
#	user-interface/src/main/java/life/qbic/datamanager/files/structure/sample/RegisterColumn.java
#	user-interface/src/main/java/life/qbic/datamanager/importing/SampleInformationExtractor.java
#	user-interface/src/main/java/life/qbic/datamanager/importing/parser/MetadataConverter.java
#	user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchRegistrationTemplate.java
#	user-interface/src/main/java/life/qbic/datamanager/templates/sample/SampleBatchUpdateTemplate.java
#	user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/SampleInformationMain.java
#	user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/EditSampleBatchDialog.java
#	user-interface/src/main/java/life/qbic/datamanager/views/projects/project/samples/registration/batch/RegisterSampleBatchDialog.java
@KochTobi KochTobi marked this pull request as ready for review January 28, 2025 16:06
@KochTobi KochTobi requested a review from a team as a code owner January 28, 2025 16:06
@sven1103
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sven1103 commented Feb 3, 2025

@KochTobi looks to me that the PR does not fix the actual problem it was about to solve:

image

sample metadata is still not showing the ontology CURIs.

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Not sure what happened here, the PR is not in scope with the title.

I cant confirm that the actual issue has been resolved.

@KochTobi KochTobi changed the title Show the ontologies for the selected species,specimen and analyte in the aggregated sample metadata sheet Harmonize excel data export and include missed properties Feb 3, 2025
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KochTobi commented Feb 3, 2025

@KochTobi looks to me that the PR does not fix the actual problem it was about to solve:
image

sample metadata is still not showing the ontology CURIs.

Are you sure you checked out the correct branch? For me it looks like this:
Screenshot 2025-02-03 at 13 28 02

@KochTobi KochTobi requested a review from sven1103 February 3, 2025 12:29
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sven1103 commented Feb 3, 2025

yes you are right, apologies. Ping me, once you have the FileNameFormatter implemented, the remaining code base looks good to me

KochTobi and others added 2 commits February 6, 2025 11:41
…or-the-selected-species,specimen-and-analyte-in-the-aggregated-sample-metadata-sheet
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KochTobi commented Feb 6, 2025

yes you are right, apologies. Ping me, once you have the FileNameFormatter implemented, the remaining code base looks good to me

@sven1103 ping

…ies-for-the-selected-species,specimen-and-analyte-in-the-aggregated-sample-metadata-sheet' into feature-982/982-show-the-ontologies-for-the-selected-species,specimen-and-analyte-in-the-aggregated-sample-metadata-sheet
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Hi @KochTobi,

the download of measurement metadata does not produce the expected result.

For general recommendation:
the iso date readability can be improved by adding - between the entries, like YYYY-MM-DD_...
It is still valid ISO 8601, but improves readability quite a lot.

@KochTobi KochTobi requested a review from sven1103 February 10, 2025 13:52
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Quality Gate Failed Quality Gate failed

Failed conditions
0.0% Coverage on New Code (required ≥ 80%)
7.8% Duplication on New Code (required ≤ 3%)

See analysis details on SonarQube Cloud

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Confirmed for sample metadata download and measurement metadata download!

@KochTobi KochTobi merged commit 2089dc9 into development Feb 11, 2025
5 of 6 checks passed
@KochTobi KochTobi deleted the feature-982/982-show-the-ontologies-for-the-selected-species,specimen-and-analyte-in-the-aggregated-sample-metadata-sheet branch February 11, 2025 10:00
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Show the ontologies for the selected species,specimen and analyte in the aggregated sample metadata sheet
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