demoData

.gitignore

@@ -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

demoData/arrangerConfigs/base.json

@@ -0,0 +1,6 @@
+{
+	"baseConfigs": {
+		"documentType": "analysis",
+		"index": "analysis_centric_1.0"
+	}
+}

demoData/arrangerConfigs/extended.json

@@ -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"
+            }
+        ]
+    }
+}