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b/source/GenomicsAnalysisCode/quicksight_cfn.yml |
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AWSTemplateFormatVersion: '2010-09-09' |
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Description: Creates a QuickSight dashboard for browsing omics data |
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Parameters: |
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Project: |
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Type: String |
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QuicksightServiceRoleName: |
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Type: String |
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Default: aws-quicksight-service-role-v0 |
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QuicksightUserId: |
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Type: String |
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Resources: |
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QuicksightAccessPolicy: |
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Type: AWS::IAM::Policy |
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Properties: |
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Roles: |
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- !Ref QuicksightServiceRoleName |
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PolicyName: !Sub "${Project}-access" |
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PolicyDocument: |
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Version: 2012-10-17 |
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Statement: |
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- Effect: Allow |
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Action: |
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- s3:ListBucket |
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- s3:GetBucketLocation |
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- s3:ListBucketMultipartUploads |
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Resource: !Sub |
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- "arn:aws:s3:::${DataLakeBucket}" |
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- DataLakeBucket: !ImportValue |
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Fn::Sub: '${Project}-DataLakeBucket' |
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- Effect: Allow |
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Action: |
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- s3:GetObject |
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- s3:GetObjectVersion |
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- s3:AbortMultipartUpload |
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- s3:ListMultipartUploadParts |
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Resource: !Sub |
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- "arn:aws:s3:::${DataLakeBucket}/*" |
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- DataLakeBucket: !ImportValue |
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Fn::Sub: '${Project}-DataLakeBucket' |
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- Effect: Allow |
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Action: s3:PutObject |
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Resource: !Sub |
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- "arn:aws:s3:::${DataLakeBucket}/results/*" |
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- DataLakeBucket: !ImportValue |
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Fn::Sub: '${Project}-DataLakeBucket' |
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- Effect: Allow |
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Action: |
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- kms:GenerateDataKey |
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- kms:Decrypt |
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- kms:Encrypt |
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Resource: |
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- !ImportValue |
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Fn::Sub: '${Project}-DataCatalogEncryptionKeyArn' |
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DataSource: |
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Type: AWS::QuickSight::DataSource |
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DependsOn: QuicksightAccessPolicy |
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Properties: |
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DataSourceId: !Sub "${Project}-DataSource" |
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Name: !Sub "${Project}-Data" |
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AwsAccountId: !Ref AWS::AccountId |
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Type: ATHENA |
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DataSourceParameters: |
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AthenaParameters: |
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WorkGroup: |
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!Join |
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- '-' |
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- - !ImportValue |
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Fn::Sub: '${Project}-ResourcePrefixLowercase' |
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- !Ref "AWS::Region" |
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DataSet: |
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Type: AWS::QuickSight::DataSet |
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Properties: |
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DataSetId: !Sub "${Project}-DataSet" |
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Name: !Ref Project |
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AwsAccountId: !Ref AWS::AccountId |
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ImportMode: SPICE |
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PhysicalTableMap: |
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PhysicalTable1: |
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RelationalTable: |
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DataSourceArn: !GetAtt DataSource.Arn |
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Schema: !ImportValue |
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Fn::Sub: '${Project}-ResourcePrefixLowercase' |
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Name: clinical_patient |
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InputColumns: |
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- Name: bcr_patient_uuid |
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Type: STRING |
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- Name: bcr_patient_barcode |
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Type: STRING |
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- Name: form_completion_date |
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Type: STRING |
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- Name: histologic_diagnosis3 |
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Type: STRING |
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- Name: race |
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Type: STRING |
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- Name: ethnicity |
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Type: STRING |
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- Name: location_lung_parenchyma |
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Type: STRING |
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- Name: height_cm_at_diagnosis |
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Type: STRING |
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- Name: prospective_collection |
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Type: STRING |
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- Name: weight_kg_at_diagnosis |
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Type: STRING |
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- Name: retrospective_collection |
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Type: STRING |
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- Name: gender |
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Type: STRING |
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- Name: birth_days_to |
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Type: STRING |
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- Name: history_other_malignancy |
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Type: STRING |
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- Name: history_neoadjuvant_treatment |
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Type: STRING |
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- Name: cause_of_death |
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Type: STRING |
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- Name: cause_of_death_other |
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Type: STRING |
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- Name: residual_tumor |
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Type: STRING |
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- Name: tumor_status |
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Type: STRING |
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- Name: ajcc_staging_edition |
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Type: STRING |
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- Name: ecog_score |
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Type: STRING |
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- Name: ajcc_nodes_pathologic_pn |
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Type: STRING |
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- Name: karnofsky_score |
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Type: STRING |
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- Name: ajcc_metastasis_pathologic_pm |
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Type: STRING |
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- Name: radiation_treatment_adjuvant |
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Type: STRING |
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- Name: vital_status |
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Type: STRING |
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- Name: pharmaceutical_tx_adjuvant |
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Type: STRING |
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- Name: tobacco_smoking_history_indicator |
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Type: STRING |
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- Name: tobacco_smoking_age_started |
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Type: STRING |
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- Name: last_contact_days_to |
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Type: STRING |
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- Name: tobacco_smoking_pack_years_smoked |
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Type: STRING |
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- Name: hiv_status |
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Type: STRING |
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- Name: death_days_to |
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Type: STRING |
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- Name: nadir_cd4_counts |
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Type: STRING |
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- Name: cd4_counts_at_diagnosis |
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Type: STRING |
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- Name: pulmonary_function_test_indicator |
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Type: STRING |
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- Name: hiv_rna_load_at_diagnosis |
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Type: STRING |
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- Name: fev1_percent_ref_prebroncholiator |
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Type: STRING |
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- Name: prior_aids_conditions |
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Type: STRING |
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- Name: fev1_percent_ref_postbroncholiator |
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Type: STRING |
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- Name: hbv_test_results |
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Type: STRING |
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- Name: fev1_fvc_ratio_prebroncholiator |
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Type: STRING |
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- Name: hcv_test_results |
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Type: STRING |
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- Name: fev1_fvc_ratio_postbroncholiator |
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Type: STRING |
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- Name: hpv_test_results |
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Type: STRING |
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- Name: carbon_monoxide_diffusion_dlco |
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Type: STRING |
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- Name: kshv_hhv8_test_results |
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Type: STRING |
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- Name: kras_gene_analysis_indicator |
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Type: STRING |
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- Name: haart_therapy_prior_to_dx |
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Type: STRING |
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- Name: kras_mutation_found |
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Type: STRING |
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- Name: haart_therapy_at_dx |
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Type: STRING |
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- Name: kras_mutation_identified_type |
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Type: STRING |
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- Name: cdc_hiv_risk_group |
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Type: STRING |
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- Name: egfr_mutation_status |
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Type: STRING |
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- Name: egfr_mutation_identified_type |
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Type: STRING |
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- Name: prior_mailgnancy_type |
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Type: STRING |
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- Name: eml4_alk_translocation_status |
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Type: STRING |
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- Name: history_immunological_disease |
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Type: STRING |
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- Name: eml4_alk_translocation_variant |
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Type: STRING |
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- Name: history_immunological_disease_other |
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Type: STRING |
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- Name: eml4_alk_analysis_type |
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Type: STRING |
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- Name: history_immunosuppresive_rx |
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Type: STRING |
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- Name: history_immunosuppressive_rx_other |
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Type: STRING |
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- Name: tobacco_smoking_year_started |
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Type: STRING |
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- Name: history_relevant_infectious_dx |
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Type: STRING |
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- Name: tobacco_smoking_year_stopped |
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Type: STRING |
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- Name: history_immunosuppresive_dx_other |
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Type: STRING |
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- Name: histologic_diagnosis67 |
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Type: STRING |
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- Name: submitted_tumor_site |
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Type: STRING |
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- Name: performance_status_timing |
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Type: STRING |
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- Name: laterality |
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Type: STRING |
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- Name: anatomic_organ_subdivision |
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Type: STRING |
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- Name: site_of_primary_tumor_other |
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Type: STRING |
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- Name: treatment_outcome_first_course |
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Type: STRING |
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- Name: new_tumor_event_dx_indicator |
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Type: STRING |
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- Name: initial_pathologic_dx_year |
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Type: STRING |
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- Name: method_initial_path_dx |
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Type: STRING |
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- Name: method_initial_path_dx_other |
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Type: STRING |
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- Name: lymph_nodes_examined |
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Type: STRING |
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- Name: lymph_nodes_examined_count |
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Type: STRING |
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- Name: lymph_nodes_examined_he_count |
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Type: STRING |
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- Name: lymph_nodes_examined_ihc_count |
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Type: STRING |
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- Name: pos_lymph_node_location |
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Type: STRING |
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- Name: other_pos_node_location |
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Type: STRING |
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- Name: ajcc_tumor_clinical_ct |
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Type: STRING |
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- Name: ajcc_tumor_pathologic_pt |
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Type: STRING |
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- Name: ajcc_nodes_clinical_cn |
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Type: STRING |
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- Name: ajcc_metastasis_clinical_cm |
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Type: STRING |
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- Name: ajcc_clinical_tumor_stage |
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Type: STRING |
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- Name: ajcc_pathologic_tumor_stage |
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Type: STRING |
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- Name: followup_lost_to |
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Type: STRING |
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- Name: age_at_initial_pathologic_diagnosis |
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Type: STRING |
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- Name: cancer_diagnosis_cancer_type_icd9_text_name |
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Type: STRING |
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- Name: days_to_form_completion |
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Type: STRING |
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- Name: days_to_hiv_diagnosis |
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Type: STRING |
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- Name: days_to_initial_pathologic_diagnosis |
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Type: STRING |
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- Name: days_to_patient_progression_free |
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Type: STRING |
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- Name: days_to_sample_procurement |
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Type: STRING |
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- Name: days_to_tumor_progression |
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Type: STRING |
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- Name: disease_code |
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Type: STRING |
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- Name: egfr_mutation_identified |
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Type: STRING |
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- Name: eml4_alk_translocation_identified |
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Type: STRING |
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- Name: extranodal_involvement |
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Type: STRING |
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- Name: family_member_relationship_type |
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Type: STRING |
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- Name: icd_10 |
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Type: STRING |
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- Name: icd_o_3_histology |
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Type: STRING |
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- Name: icd_o_3_site |
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Type: STRING |
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- Name: informed_consent_verified |
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Type: STRING |
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- Name: margin_status |
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Type: STRING |
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- Name: measure_of_response |
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Type: STRING |
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- Name: metastatic_site_at_diagnosis |
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314 |
Type: STRING |
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- Name: metastatic_site_at_diagnosis_other |
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Type: STRING |
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- Name: number_cycles |
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Type: STRING |
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- Name: patient_id |
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Type: STRING |
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- Name: pharm_regimen |
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Type: STRING |
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- Name: pharm_regimen_other |
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Type: STRING |
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- Name: prior_systemic_therapy_type |
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Type: STRING |
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- Name: project_code |
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Type: STRING |
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- Name: regimen_indication |
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Type: STRING |
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- Name: relative_family_cancer_history |
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332 |
Type: STRING |
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- Name: stage_other |
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Type: STRING |
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- Name: stem_cell_transplantation |
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Type: STRING |
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- Name: tissue_source_site |
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Type: STRING |
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- Name: histologic_diagnosis5 |
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Type: STRING |
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- Name: histologic_diagnosis18 |
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Type: STRING |
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- Name: age_began_smoking_in_years |
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Type: STRING |
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- Name: anatomic_neoplasm_subdivision_other |
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Type: STRING |
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347 |
- Name: death_cause_text |
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348 |
Type: STRING |
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349 |
- Name: hbv_test |
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Type: STRING |
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351 |
- Name: hcv_test |
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352 |
Type: STRING |
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- Name: height |
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354 |
Type: STRING |
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- Name: history_of_other_malignancy |
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356 |
Type: STRING |
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357 |
- Name: history_relevant_infectious_dx_other |
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Type: STRING |
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359 |
- Name: hpv_test |
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Type: STRING |
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361 |
- Name: kshv_hhv8_test |
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Type: STRING |
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- Name: lost_follow_up |
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Type: STRING |
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365 |
- Name: lymph_node_examined_count |
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366 |
Type: STRING |
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367 |
- Name: number_of_lymphnodes_positive_by_he |
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368 |
Type: STRING |
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- Name: number_of_lymphnodes_positive_by_ihc |
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370 |
Type: STRING |
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371 |
- Name: on_haart_therapy_at_cancer_diagnosis |
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372 |
Type: STRING |
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373 |
- Name: on_haart_therapy_prior_to_cancer_diagnosis |
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374 |
Type: STRING |
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- Name: patient_death_reason |
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376 |
Type: STRING |
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377 |
- Name: pos_lymph_node_location_other |
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378 |
Type: STRING |
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379 |
- Name: primary_lymph_node_presentation_assessment |
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380 |
Type: STRING |
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381 |
- Name: tumor_tissue_site |
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382 |
Type: STRING |
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383 |
- Name: weight |
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384 |
Type: STRING |
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385 |
- Name: partition_0 |
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386 |
Type: STRING |
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387 |
PhysicalTable2: |
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388 |
RelationalTable: |
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389 |
DataSourceArn: !GetAtt DataSource.Arn |
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390 |
Schema: !ImportValue |
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|
391 |
Fn::Sub: '${Project}-ResourcePrefixLowercase' |
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392 |
Name: tcga_summary |
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393 |
InputColumns: |
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394 |
- Name: patient_id |
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395 |
Type: STRING |
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396 |
- Name: num_images |
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397 |
Type: DECIMAL |
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398 |
- Name: num_image_series |
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399 |
Type: DECIMAL |
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400 |
- Name: num_mutation_records |
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401 |
Type: DECIMAL |
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402 |
- Name: num_expression_records |
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403 |
Type: DECIMAL |
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404 |
- Name: num_cnv_records |
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405 |
Type: DECIMAL |
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406 |
- Name: num_clin_drug_records |
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407 |
Type: DECIMAL |
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408 |
- Name: num_clin_rad_records |
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409 |
Type: DECIMAL |
|
|
410 |
- Name: num_clin_fol_records |
|
|
411 |
Type: DECIMAL |
|
|
412 |
- Name: num_clin_omf_records |
|
|
413 |
Type: DECIMAL |
|
|
414 |
- Name: num_clin_nte_records |
|
|
415 |
Type: DECIMAL |
|
|
416 |
LogicalTableMap: |
|
|
417 |
LogicalTable1: |
|
|
418 |
Alias: clinical_patient |
|
|
419 |
DataTransforms: |
|
|
420 |
- RenameColumnOperation: |
|
|
421 |
ColumnName: patient_id |
|
|
422 |
NewColumnName: patient_id[clinical_patient] |
|
|
423 |
- RenameColumnOperation: |
|
|
424 |
ColumnName: partition_0 |
|
|
425 |
NewColumnName: study_name |
|
|
426 |
Source: |
|
|
427 |
PhysicalTableId: PhysicalTable1 |
|
|
428 |
LogicalTable2: |
|
|
429 |
Alias: tcga_summary |
|
|
430 |
DataTransforms: |
|
|
431 |
- CastColumnTypeOperation: |
|
|
432 |
ColumnName: num_images |
|
|
433 |
NewColumnType: INTEGER |
|
|
434 |
- CastColumnTypeOperation: |
|
|
435 |
ColumnName: num_image_series |
|
|
436 |
NewColumnType: INTEGER |
|
|
437 |
- CastColumnTypeOperation: |
|
|
438 |
ColumnName: num_mutation_records |
|
|
439 |
NewColumnType: INTEGER |
|
|
440 |
- CastColumnTypeOperation: |
|
|
441 |
ColumnName: num_expression_records |
|
|
442 |
NewColumnType: INTEGER |
|
|
443 |
- CastColumnTypeOperation: |
|
|
444 |
ColumnName: num_cnv_records |
|
|
445 |
NewColumnType: INTEGER |
|
|
446 |
- CastColumnTypeOperation: |
|
|
447 |
ColumnName: num_clin_drug_records |
|
|
448 |
NewColumnType: INTEGER |
|
|
449 |
- CastColumnTypeOperation: |
|
|
450 |
ColumnName: num_clin_rad_records |
|
|
451 |
NewColumnType: INTEGER |
|
|
452 |
- CastColumnTypeOperation: |
|
|
453 |
ColumnName: num_clin_fol_records |
|
|
454 |
NewColumnType: INTEGER |
|
|
455 |
- CastColumnTypeOperation: |
|
|
456 |
ColumnName: num_clin_omf_records |
|
|
457 |
NewColumnType: INTEGER |
|
|
458 |
- CastColumnTypeOperation: |
|
|
459 |
ColumnName: num_clin_nte_records |
|
|
460 |
NewColumnType: INTEGER |
|
|
461 |
Source: |
|
|
462 |
PhysicalTableId: PhysicalTable2 |
|
|
463 |
LogicalTable3: |
|
|
464 |
Alias: Intermediate Table |
|
|
465 |
DataTransforms: |
|
|
466 |
- CreateColumnsOperation: |
|
|
467 |
Columns: |
|
|
468 |
- ColumnName: age_at_dx_string |
|
|
469 |
ColumnId: 93b9c54c-ddec-471f-b113-32faf869f61c |
|
|
470 |
Expression: "ifelse(locate({age_at_initial_pathologic_diagnosis},\"[\") = 0,{age_at_initial_pathologic_diagnosis},\"0\")" |
|
|
471 |
- CreateColumnsOperation: |
|
|
472 |
Columns: |
|
|
473 |
- ColumnName: age_at_dx_numeric |
|
|
474 |
ColumnId: b38d8b30-d2dd-4c94-9d27-39e5f9fde4dc |
|
|
475 |
Expression: "parseInt({age_at_dx_string})" |
|
|
476 |
- ProjectOperation: |
|
|
477 |
ProjectedColumns: |
|
|
478 |
- bcr_patient_barcode |
|
|
479 |
- form_completion_date |
|
|
480 |
- race |
|
|
481 |
- ethnicity |
|
|
482 |
- location_lung_parenchyma |
|
|
483 |
- prospective_collection |
|
|
484 |
- retrospective_collection |
|
|
485 |
- gender |
|
|
486 |
- birth_days_to |
|
|
487 |
- history_other_malignancy |
|
|
488 |
- history_neoadjuvant_treatment |
|
|
489 |
- residual_tumor |
|
|
490 |
- tumor_status |
|
|
491 |
- ajcc_staging_edition |
|
|
492 |
- ecog_score |
|
|
493 |
- ajcc_nodes_pathologic_pn |
|
|
494 |
- karnofsky_score |
|
|
495 |
- ajcc_metastasis_pathologic_pm |
|
|
496 |
- radiation_treatment_adjuvant |
|
|
497 |
- vital_status |
|
|
498 |
- pharmaceutical_tx_adjuvant |
|
|
499 |
- tobacco_smoking_history_indicator |
|
|
500 |
- last_contact_days_to |
|
|
501 |
- tobacco_smoking_pack_years_smoked |
|
|
502 |
- death_days_to |
|
|
503 |
- pulmonary_function_test_indicator |
|
|
504 |
- fev1_percent_ref_prebroncholiator |
|
|
505 |
- fev1_percent_ref_postbroncholiator |
|
|
506 |
- fev1_fvc_ratio_prebroncholiator |
|
|
507 |
- fev1_fvc_ratio_postbroncholiator |
|
|
508 |
- carbon_monoxide_diffusion_dlco |
|
|
509 |
- kras_gene_analysis_indicator |
|
|
510 |
- kras_mutation_found |
|
|
511 |
- kras_mutation_identified_type |
|
|
512 |
- egfr_mutation_status |
|
|
513 |
- egfr_mutation_identified_type |
|
|
514 |
- eml4_alk_translocation_status |
|
|
515 |
- eml4_alk_analysis_type |
|
|
516 |
- tobacco_smoking_year_started |
|
|
517 |
- tobacco_smoking_year_stopped |
|
|
518 |
- histologic_diagnosis67 |
|
|
519 |
- performance_status_timing |
|
|
520 |
- anatomic_organ_subdivision |
|
|
521 |
- site_of_primary_tumor_other |
|
|
522 |
- treatment_outcome_first_course |
|
|
523 |
- new_tumor_event_dx_indicator |
|
|
524 |
- initial_pathologic_dx_year |
|
|
525 |
- ajcc_tumor_pathologic_pt |
|
|
526 |
- ajcc_pathologic_tumor_stage |
|
|
527 |
- age_at_initial_pathologic_diagnosis |
|
|
528 |
- disease_code |
|
|
529 |
- icd_10 |
|
|
530 |
- icd_o_3_histology |
|
|
531 |
- icd_o_3_site |
|
|
532 |
- patient_id[clinical_patient] |
|
|
533 |
- tissue_source_site |
|
|
534 |
- histologic_diagnosis18 |
|
|
535 |
- anatomic_neoplasm_subdivision_other |
|
|
536 |
- study_name |
|
|
537 |
- num_images |
|
|
538 |
- num_image_series |
|
|
539 |
- num_mutation_records |
|
|
540 |
- num_expression_records |
|
|
541 |
- num_cnv_records |
|
|
542 |
- num_clin_drug_records |
|
|
543 |
- num_clin_rad_records |
|
|
544 |
- num_clin_fol_records |
|
|
545 |
- num_clin_omf_records |
|
|
546 |
- num_clin_nte_records |
|
|
547 |
- age_at_dx_numeric |
|
|
548 |
- age_at_dx_string |
|
|
549 |
Source: |
|
|
550 |
JoinInstruction: |
|
|
551 |
LeftOperand: LogicalTable1 |
|
|
552 |
RightOperand: LogicalTable2 |
|
|
553 |
Type: LEFT |
|
|
554 |
OnClause: "{bcr_patient_barcode} = {patient_id}" |
|
|
555 |
Permissions: |
|
|
556 |
- Principal: !Sub "arn:aws:quicksight:${AWS::Region}:${AWS::AccountId}:user/default/${QuicksightUserId}" |
|
|
557 |
Actions: |
|
|
558 |
- quicksight:UpdateDataSetPermissions |
|
|
559 |
- quicksight:DescribeDataSet |
|
|
560 |
- quicksight:DescribeDataSetPermissions |
|
|
561 |
- quicksight:PassDataSet |
|
|
562 |
- quicksight:DescribeIngestion |
|
|
563 |
- quicksight:ListIngestions |
|
|
564 |
- quicksight:UpdateDataSet |
|
|
565 |
- quicksight:DeleteDataSet |
|
|
566 |
- quicksight:CreateIngestion |
|
|
567 |
- quicksight:CancelIngestion |