Fixes to: #69

dipayan1985 · 2024-11-07T12:55:11Z

Experiment alias use in RUN
Webin service URL - use test and not dev
BioSamples mandatory attributes

1. Experiment alias use in RUN 2. Webin service URL - use test and not dev 3. BioSamples mandatory attributes

kdp-cloud · 2024-11-07T13:10:15Z

...es/src/main/java/com/elixir/biohackaton/ISAToSRA/biosamples/service/BioSamplesSubmitter.java

@@ -147,7 +149,9 @@ private BioSample createSourceBioSample(final List<Study> studies, final String

                  final BioSample sourceSample = new BioSample.Builder(source.getName())
                      .withRelease(Instant.now())
-                      .withAttributes(Collections.singleton(organismAttribute.get()))
+                      .withAttributes(List.of(organismAttribute.get(),


The ISA-JSON we are using actually contains those fields. I think we might want to revert this for the source sample.

collection date:

MARS/test-data/biosamples-input-isa.json

Lines 276 to 284 in ad636ca

"category": {

"@id": "#characteristic_category/collection_date_323"

},

"value": {

"annotationValue": "01/01/2022",

"termSource": "",

"termAccession": ""

}

},

Geographic location:

MARS/test-data/biosamples-input-isa.json

Lines 306 to 314 in ad636ca

"category": {

"@id": "#characteristic_category/geographic_location_(country_and/or_sea)_326"

},

"value": {

"annotationValue": "Belgium",

"termSource": "",

"termAccession": ""

}

},

Fixes to:

2ef1916

1. Experiment alias use in RUN 2. Webin service URL - use test and not dev 3. BioSamples mandatory attributes

dipayan1985 requested review from Pedram-A-Keyvani, bedroesb and kdp-cloud November 7, 2024 12:55

kdp-cloud reviewed Nov 7, 2024

View reviewed changes

kdp-cloud approved these changes Nov 7, 2024

View reviewed changes

dipayan1985 merged commit 37cd3ee into mars-receipt-library Nov 7, 2024
2 checks passed

bedroesb mentioned this pull request Nov 8, 2024

Do we want to let Samples inherit Source material info to comply with the ENA minimal checklist? (collection date and geografical location) #81

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Fixes to: #69

Fixes to: #69

dipayan1985 commented Nov 7, 2024

kdp-cloud Nov 7, 2024

	"category": {
	"@id": "#characteristic_category/collection_date_323"
	},
	"value": {
	"annotationValue": "01/01/2022",
	"termSource": "",
	"termAccession": ""
	}
	},

	"category": {
	"@id": "#characteristic_category/geographic_location_(country_and/or_sea)_326"
	},
	"value": {
	"annotationValue": "Belgium",
	"termSource": "",
	"termAccession": ""
	}
	},

Fixes to: #69

Fixes to: #69

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dipayan1985 commented Nov 7, 2024

kdp-cloud Nov 7, 2024

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