Mercurial > repos > iuc > beacon2_bracket

diff test-data/biosamples_query_findings.json @ 0:2e60de9f5046 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/beacon2-import commit f4151aa2d760f931f819f954f465ef66055bf258
author iuc
date Mon, 22 Jul 2024 12:35:01 +0000
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--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/test-data/biosamples_query_findings.json	Mon Jul 22 12:35:01 2024 +0000
@@ -0,0 +1,162 @@
+{'_id': ObjectId('668fb4eb8ed056280039f1bd'),
+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},
+ 'collectionDate': '2021-04-23',
+ 'collectionMoment': 'P32Y6M1D',
+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],
+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',
+                           'label': 'Infiltrating Urothelial Carcinoma'},
+ 'id': 'refvar-668fb4eb8ed056280039f1bd',
+ 'individualId': 'NA24631',
+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},
+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',
+                             'label': 'T2b Stage Finding'}],
+ 'sampleOriginDetail': {'id': 'UBERON:0001256',
+                        'label': 'wall of urinary bladde'},
+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},
+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},
+ 'tumorProgression': {'id': 'NCIT:C84509',
+                      'label': 'Primary Malignant Neoplasm'}}
+{'_id': ObjectId('668fb4eb8ed056280039f1be'),
+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},
+ 'collectionDate': '2021-04-23',
+ 'collectionMoment': 'P32Y6M1D',
+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],
+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',
+                           'label': 'Infiltrating Urothelial Carcinoma'},
+ 'id': 'refvar-668fb4eb8ed056280039f1be',
+ 'individualId': 'NA24694',
+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},
+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',
+                             'label': 'T2b Stage Finding'}],
+ 'sampleOriginDetail': {'id': 'UBERON:0001256',
+                        'label': 'wall of urinary bladde'},
+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},
+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},
+ 'tumorProgression': {'id': 'NCIT:C84509',
+                      'label': 'Primary Malignant Neoplasm'}}
+{'_id': ObjectId('668fb4eb8ed056280039f1bf'),
+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},
+ 'collectionDate': '2021-04-23',
+ 'collectionMoment': 'P32Y6M1D',
+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],
+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',
+                           'label': 'Infiltrating Urothelial Carcinoma'},
+ 'id': 'refvar-668fb4eb8ed056280039f1bf',
+ 'individualId': 'NA24695',
+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},
+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',
+                             'label': 'T2b Stage Finding'}],
+ 'sampleOriginDetail': {'id': 'UBERON:0001256',
+                        'label': 'wall of urinary bladde'},
+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},
+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},
+ 'tumorProgression': {'id': 'NCIT:C84509',
+                      'label': 'Primary Malignant Neoplasm'}}
+{'_id': ObjectId('668fb7125d00a890d911aa69'),
+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},
+ 'collectionDate': '2021-04-23',
+ 'collectionMoment': 'P32Y6M1D',
+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],
+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',
+                           'label': 'Infiltrating Urothelial Carcinoma'},
+ 'id': 'refvar-668fb7125d00a890d911aa69',
+ 'individualId': 'NA24631',
+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},
+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',
+                             'label': 'T2b Stage Finding'}],
+ 'sampleOriginDetail': {'id': 'UBERON:0001256',
+                        'label': 'wall of urinary bladde'},
+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},
+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},
+ 'tumorProgression': {'id': 'NCIT:C84509',
+                      'label': 'Primary Malignant Neoplasm'}}
+{'_id': ObjectId('668fb7125d00a890d911aa6a'),
+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},
+ 'collectionDate': '2021-04-23',
+ 'collectionMoment': 'P32Y6M1D',
+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],
+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',
+                           'label': 'Infiltrating Urothelial Carcinoma'},
+ 'id': 'refvar-668fb7125d00a890d911aa6a',
+ 'individualId': 'NA24694',
+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},
+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',
+                             'label': 'T2b Stage Finding'}],
+ 'sampleOriginDetail': {'id': 'UBERON:0001256',
+                        'label': 'wall of urinary bladde'},
+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},
+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},
+ 'tumorProgression': {'id': 'NCIT:C84509',
+                      'label': 'Primary Malignant Neoplasm'}}
+{'_id': ObjectId('668fb7125d00a890d911aa6b'),
+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},
+ 'collectionDate': '2021-04-23',
+ 'collectionMoment': 'P32Y6M1D',
+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],
+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',
+                           'label': 'Infiltrating Urothelial Carcinoma'},
+ 'id': 'refvar-668fb7125d00a890d911aa6b',
+ 'individualId': 'NA24695',
+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},
+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',
+                             'label': 'T2b Stage Finding'}],
+ 'sampleOriginDetail': {'id': 'UBERON:0001256',
+                        'label': 'wall of urinary bladde'},
+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},
+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},
+ 'tumorProgression': {'id': 'NCIT:C84509',
+                      'label': 'Primary Malignant Neoplasm'}}
+{'_id': ObjectId('668fb721ae6c452887afb69d'),
+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},
+ 'collectionDate': '2021-04-23',
+ 'collectionMoment': 'P32Y6M1D',
+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],
+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',
+                           'label': 'Infiltrating Urothelial Carcinoma'},
+ 'id': 'refvar-668fb721ae6c452887afb69d',
+ 'individualId': 'NA24631',
+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},
+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',
+                             'label': 'T2b Stage Finding'}],
+ 'sampleOriginDetail': {'id': 'UBERON:0001256',
+                        'label': 'wall of urinary bladde'},
+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},
+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},
+ 'tumorProgression': {'id': 'NCIT:C84509',
+                      'label': 'Primary Malignant Neoplasm'}}
+{'_id': ObjectId('668fb721ae6c452887afb69e'),
+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},
+ 'collectionDate': '2021-04-23',
+ 'collectionMoment': 'P32Y6M1D',
+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],
+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',
+                           'label': 'Infiltrating Urothelial Carcinoma'},
+ 'id': 'refvar-668fb721ae6c452887afb69e',
+ 'individualId': 'NA24694',
+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},
+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',
+                             'label': 'T2b Stage Finding'}],
+ 'sampleOriginDetail': {'id': 'UBERON:0001256',
+                        'label': 'wall of urinary bladde'},
+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},
+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},
+ 'tumorProgression': {'id': 'NCIT:C84509',
+                      'label': 'Primary Malignant Neoplasm'}}
+{'_id': ObjectId('668fb721ae6c452887afb69f'),
+ 'biosampleStatus': {'id': 'EFO:0009655', 'label': 'abnormal sample'},
+ 'collectionDate': '2021-04-23',
+ 'collectionMoment': 'P32Y6M1D',
+ 'diagnosticMarkers': [{'id': 'NCIT:C48726', 'label': 'T2b Stage Finding'}],
+ 'histologicalDiagnosis': {'id': 'NCIT:C39853',
+                           'label': 'Infiltrating Urothelial Carcinoma'},
+ 'id': 'refvar-668fb721ae6c452887afb69f',
+ 'individualId': 'NA24695',
+ 'pathologicalStage': {'id': 'NCIT:C28054', 'label': 'Stage II'},
+ 'pathologicalTnmFinding': [{'id': 'NCIT:C48726',
+                             'label': 'T2b Stage Finding'}],
+ 'sampleOriginDetail': {'id': 'UBERON:0001256',
+                        'label': 'wall of urinary bladde'},
+ 'sampleOriginType': {'id': 'EFO:000965', 'label': 'abnormal sample'},
+ 'tumorGrade': {'id': 'NCIT:C36136', 'label': 'Grade 2 Lesion'},
+ 'tumorProgression': {'id': 'NCIT:C84509',
+                      'label': 'Primary Malignant Neoplasm'}}