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demoData #177

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61e5ff7
demoData
MitchellShiell Mar 25, 2024
85cc4e6
updated arranger configs
MitchellShiell Apr 1, 2024
5053505
VCF dump
edsu7 Apr 1, 2024
e0706eb
add BAM files
edsu7 Apr 1, 2024
332c620
CRAMs
edsu7 Apr 1, 2024
7f225f7
formatting
edsu7 Apr 1, 2024
2fbad8b
add submission script
edsu7 Apr 1, 2024
d1e7a26
list of uploaded analyses here
MitchellShiell Apr 2, 2024
5b8b48c
updated schema for v3 draft 1
MitchellShiell Apr 13, 2024
1620bfd
removed pathology/histology
MitchellShiell Apr 13, 2024
a076e4f
removed workflowTools changed publication title to journal
MitchellShiell Apr 13, 2024
5867b8a
example V3 files
edsu7 Apr 15, 2024
f39dff6
Updates
edsu7 Apr 15, 2024
f3ec47b
payloads and data
edsu7 Apr 16, 2024
e736726
updated version
edsu7 Apr 16, 2024
1a0c0dc
Update demoDataSchemaV3.json
MitchellShiell Apr 17, 2024
bd3dc26
update payloads and schema
edsu7 Apr 17, 2024
9cc42b6
fixing tumour submitterSpecimenId and analysisType
edsu7 Apr 17, 2024
43a6c6d
add error code
edsu7 Apr 17, 2024
429e01c
update schema and payloads
edsu7 May 3, 2024
d7bbf8b
updates to date and datatype
edsu7 May 15, 2024
c3d1435
update dates
edsu7 May 16, 2024
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11 changes: 11 additions & 0 deletions .gitignore
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Original file line number Diff line number Diff line change
Expand Up @@ -36,3 +36,14 @@ build/
## others
run.sh
.DS_Store
.ipynb_checkpoints/data_generate_v2-checkpoint.ipynb
.ipynb_checkpoints/data_generate-checkpoint.ipynb
data_generate.ipynb
data_generate_v2.ipynb
playground-data/header
.demoData/schemas/.prettierrc
data_generate_v3.ipynb
.ipynb_checkpoints/data_generate_v3-checkpoint.ipynb
fixdata.ipynb
demoData/schemas/demoDataSchemaV3.json
.ipynb_checkpoints/fixdata-checkpoint.ipynb
6 changes: 6 additions & 0 deletions demoData/arrangerConfigs/base.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,6 @@
{
"baseConfigs": {
"documentType": "analysis",
"index": "analysis_centric_1.0"
}
}
318 changes: 318 additions & 0 deletions demoData/arrangerConfigs/extended.json
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Original file line number Diff line number Diff line change
@@ -0,0 +1,318 @@
{
"extendedConfigs": {
"extended": [
{
"fieldName": "samples.subitterSampleId",
"displayName": "Submitter Sample ID"
},
{
"fieldName": "samples.sampleType",
"displayName": "Sample Type"
},
{
"fieldName": "samples.matchedNormalSubmitterSampleId",
"displayName": "Matched Normal Sample ID"
},
{
"fieldName": "samples.specimen.submitterSpecimenId",
"displayName": "Submitter Specimen ID"
},
{
"fieldName": "samples.specimen.specimenType",
"displayName": "Specimen Type"
},
{
"fieldName": "samples.specimen.tumourNormalDesignation",
"displayName": "Tumour Normal Designation"
},
{
"fieldName": "samples.specimen.specimenTissueSource",
"displayName": "Tissue Source"
},
{
"fieldName": "samples.donor.submitterDonorId",
"displayName": "Submitter Donor ID"
},
{
"fieldName": "samples.donor.gender",
"displayName": "Gender"
},
{
"fieldName": "samples.donor.submitterDonorId",
"displayName": "Sample Submitter Donor ID"
},
{
"fieldName": "donor.submitterDonorId",
"displayName": "Donor ID"
},
{
"fieldName": "donor.primarySite",
"displayName": "Primary Site"
},
{
"fieldName": "donor.vitalStatus",
"displayName": "Vital Status"
},
{
"fieldName": "donor.survivalTime",
"displayName": "Survival Time"
},
{
"fieldName": "donor.primaryDiagnosis.ageAtDiagnosis",
"displayName": "Age At Diagnosis"
},
{
"fieldName": "donor.primaryDiagnosis.cancerTypeCode",
"displayName": "Cancer Type Code"
},
{
"fieldName": "donor.primaryDiagnosis.laterality",
"displayName": "Laterality"
},
{
"fieldName": "donor.primaryDiagnosis.clinicalTumourStagingSystem",
"displayName": "Tumour Staging System"
},
{
"fieldName": "donor.primaryDiagnosis.clinicalStageGroup",
"displayName": "Staging Group"
},
{
"fieldName": "donor.primaryDiagnosis.lymphNodesExaminedStatus",
"displayName": "Examination Status"
},
{
"fieldName": "donor.primaryDiagnosis.performanceStatus",
"displayName": "Performance Status"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.treatmentType",
"displayName": "Treatment"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.treatmentIntent",
"displayName": "Treatment Intent"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.treatmentStartInterval",
"displayName": "Treatment Start Interval"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.treatmentDuration",
"displayName": "Treatment Duration"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.responseToTreatment",
"displayName": "Response To Treatment"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.surgery.surgeryType",
"displayName": "Surgery Type"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.surgery.surgerySite",
"displayName": "Surgery Site"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.surgery.surgeryLocation",
"displayName": "Surgery Location"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.surgery.residualTumourClassification",
"displayName": "Residual Tumour Classification"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.hormoneTherapy.drugName",
"displayName": "Hormone Therapy"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.hormoneTherapy.drugRxnormcui",
"displayName": "RxNorm"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.hormoneTherapy.cumulativeDrugDosage",
"displayName": "Hormone Dosage"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.hormoneTherapy.hormoneDrugDosageUnits",
"displayName": "Dosage Units"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.chemotherapy.drugName",
"displayName": "Chemotherapy"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.chemotherapy.drugRxnormcui",
"displayName": "RxNorm"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.chemotherapy.cumulativeDrugDosage",
"displayName": "Chemotherapy Dosage"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.chemotherapy.chemotherapyDosageUnits",
"displayName": "Chemotherapy Dosage Units"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.immunotherapy.drugName",
"displayName": "Immunotherapy"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.immunotherapy.drugRxnormcui",
"displayName": "Immunotherapy RxNorm"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.immunotherapy.immunotherapyType",
"displayName": "Immunotherapy Type"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.radiation.radiationTherapyModality",
"displayName": "Radiation Modality"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.radiation.radiationTherapyType",
"displayName": "Radiation Therapy Type"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.radiation.anatomicalSiteIrradiated",
"displayName": "Radiation Site"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.radiation.radiationTherapyDosage",
"displayName": "Radiation Dosage"
},
{
"fieldName": "donor.primaryDiagnosis.treatment.radiation.radiationTherapyFractions",
"displayName": "Radiation Therapy Fractions"
},
{
"fieldName": "donor.primaryDiagnosis.followUp.intervalOfFollowup",
"displayName": "Follow Up Interval (Days)"
},
{
"fieldName": "donor.primaryDiagnosis.followUp.diseaseStatusAtFollowup",
"displayName": "Status At Followup"
},
{
"fieldName": "donor.primaryDiagnosis.ageAtDiagnosis",
"displayName": "Age At Diagnosis"
},
{
"fieldName": "donor.primaryDiagnosis.cancerTypeCode",
"displayName": "Cancer Type Code"
},
{
"fieldName": "donor.primaryDiagnosis.comorbidity.ageAtComorbidityDiagnosis",
"displayName": "Age at Comorbidity Diagnosis"
},
{
"fieldName": "donor.primaryDiagnosis.comorbidity.comorbidityTypeCode",
"displayName": "Comorbidity Type Code"
},
{
"fieldName": "specimen.specimenAcquisitionInterval",
"displayName": "Specimen Acquisition Interval"
},
{
"fieldName": "specimen.specimenAnatomicLocation",
"displayName": "Specimen Anatomic Location"
},
{
"fieldName": "specimen.specimenLaterality",
"displayName": "Specimen Laterality"
},
{
"fieldName": "specimen.tumourHistologicalType",
"displayName": "Tumour Histological Type"
},
{
"fieldName": "specimen.pathologicalTumourStagingSystem",
"displayName": "Pathological Tumour Staging System"
},
{
"fieldName": "specimen.pathologicalStageGroup",
"displayName": "Pathological Stage Group"
},
{
"fieldName": "specimen.tumourGradingSystem",
"displayName": "Tumour Grading System"
},
{
"fieldName": "specimen.tumourGrade",
"displayName": "Tumour Grade"
},
{
"fieldName": "specimen.percentTumourCells",
"displayName": "Percent Tumour Cells"
},
{
"fieldName": "specimen.referencePathologyConfirmed",
"displayName": "Refernce Pathology Confirmed"
},
{
"fieldName": "files.dataType",
"displayName": "Data Type"
},
{
"fieldName": "files.fileName",
"displayName": "File Name"
},
{
"fieldName": "files.fileSize",
"displayName": "File Size"
},
{
"fieldName": "files.fileMd5sum",
"displayName": "File Md5sum"
},
{
"fieldName": "files.fileAccess",
"displayName": "File Access"
},
{
"fieldName": "files.fileType",
"displayName": "File Type"
},
{
"fieldName": "files.info.dataCategory",
"displayName": "Data Category"
},
{
"fieldName": "files.info.jbrowseCoordinates",
"displayName": "jbrowse Coordinate"
},
{
"fieldName": "collaborator.contactEmail",
"displayName": "Contact Email"
},
{
"fieldName": "collaborator.name",
"displayName": "Collaborator"
},
{
"fieldName": "collaborator.affiliation",
"displayName": "Affiliation"
},
{
"fieldName": "experiment.platform",
"displayName": "Sequencing Platform"
},
{
"fieldName": "experiment.experimentalStrategy",
"displayName": "Experimental Strategy"
},
{
"fieldName": "experiment.submitterSequencingExperimentId",
"displayName": "Experiment Id"
},
{
"fieldName": "workflow.workflowName",
"displayName": "Workflow"
},
{
"fieldName": "workflow.genomeBuild",
"displayName": "Genome Build"
}
]
}
}
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