Create a configuration for perf in gen3-gitops under ci

ci/perf/Chart.yaml

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+apiVersion: v2
+name: perf
+description: ci perf setup
+
+# A chart can be either an 'application' or a 'library' chart.
+#
+# Application charts are a collection of templates that can be packaged into versioned archives
+# to be deployed.
+#
+# Library charts provide useful utilities or functions for the chart developer. They're included as
+# a dependency of application charts to inject those utilities and functions into the rendering
+# pipeline. Library charts do not define any templates and therefore cannot be deployed.
+type: application
+
+# This is the chart version. This version number should be incremented each time you make changes
+# to the chart and its templates, including the app version.
+# Versions are expected to follow Semantic Versioning (https://semver.org/)
+version: 0.1.0
+
+# This is the version number of the application being deployed. This version number should be
+# incremented each time you make changes to the application. Versions are not expected to
+# follow Semantic Versioning. They should reflect the version the application is using.
+appVersion: "1.0"

ci/perf/templates/app.yaml

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+# Note- Won't deploy via argocd in CI
+# apiVersion: argoproj.io/v1alpha1
+# kind: Application
+# metadata:
+#   name: gen3-ci
+#   namespace: argocd
+#   finalizers:
+#   - resources-finalizer.argocd.argoproj.io
+# spec:
+#   project: default
+#   sources:
+#     - path: helm/gen3
+#       repoURL: https://github.com/uc-cdis/gen3-helm
+#       targetRevision: master
+#       helm:
+#         releaseName: oadc
+#         valueFiles:
+#           - $values/ci/values/values.yaml
+#           - $values/ci/values/fence.yaml
+#           - $values/ci/values/portal.yaml
+#           - $values/ci/values/guppy.yaml
+#           - $values/ci/values/etl.yaml
+#     - repoURL: 'https://github.com/uc-cdis/gen3-gitops.git'
+#       targetRevision: master
+#       ref: values
+#   destination:
+#     server: "https://kubernetes.default.svc"
+#     namespace: <>
+#   syncPolicy:
+#     syncOptions:
+#     - CreateNamespace=true
+#     automated:
+#       selfHeal: true

ci/perf/values/etl.yaml

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+
+etl:
+  enabled: true
+  image:
+    spark:
+      repository: "quay.io/cdis/gen3-spark"
+      tag: "master"
+    tube:
+      repository: "quay.io/cdis/tube"
+      tag: "2024.12"
+  etlMapping:
+    mappings:
+      - name: ci.planx-ci.io_subject
+        doc_type: subject
+        type: aggregator
+        root: subject
+        props:
+          - name: submitter_id
+          - name: project_id
+          - name: sex
+          - name: age_value
+          - name: ancestry
+          - name: disease_description
+          - name: phenotype_present
+          - name: phenotype_absent
+          - name: disease_id
+          - name: solve_state
+          - name: congenital_status
+          - name: age_of_onset
+          - name: phenotype_group
+          - name: anvil_project_id
+    #    flatten_props:
+        aggregated_props:
+          - name: sample_provider
+            path: samples
+            src: sample_provider
+            fn: set
+          - name: tissue_affected_status
+            path: samples
+            src: tissue_affected_status
+            fn: set
+          - name: tissue_type
+            path: samples
+            src: tissue_type
+            fn: set
+          - name: sample_type
+            path: samples
+            src: sample_type
+            fn: set
+          - name: original_material_type
+            path: samples
+            src: original_material_type
+            fn: set
+          - name: exome_capture_platform
+            path: samples.sequencings
+            src: exome_capture_platform
+            fn: set
+          - name: library_prep_kit_method
+            path: samples.sequencings
+            src: library_prep_kit_method
+            fn: set
+          - name: capture_region_bed_file
+            path: samples.sequencings
+            src: capture_region_bed_file
+            fn: set
+          - name: reference_genome_build
+            path: samples.sequencings
+            src: reference_genome_build
+            fn: set
+          - name: sequencing_assay
+            path: samples.sequencings
+            src: sequencing_assay
+            fn: set
+          - name: alignment_method
+            path: samples.sequencings
+            src: alignment_method
+            fn: set
+          - name: data_processing_pipeline
+            path: samples.sequencings
+            src: data_processing_pipeline
+            fn: set
+          - name: _samples_count
+            path: samples
+            fn: count
+          - name: _sequencings_count
+            path: samples.sequencings
+            fn: count
+        joining_props:
+          - index: file
+            join_on: _subject_id
+            props:
+              - name: data_format
+                src: data_format
+                fn: set
+              - name: data_type
+                src: data_type
+                fn: set
+              - name: data_category
+                src: data_category
+                fn: set
+              - name: file_count
+                src: _file_id
+                fn: count
+        parent_props:
+          - path: projects[project_code:code]
+          - path: projects[project_name:name]
+          - path: projects[project_dbgap_phs:dbgap_phs]
+          - path: projects[project_dbgap_consent_text:dbgap_consent_text]
+          - path: projects[project_short_name:short_name]
+          - path: projects[project_dbgap_accession_number:dbgap_accession_number]
+      - name: ci.planx-ci.io_file
+        doc_type: file
+        type: collector
+        root: None
+        category: data_file
+        props:
+          - name: project_id
+          - name: submitter_id
+          - name: object_id
+          - name: md5sum
+          - name: file_name
+          - name: file_size
+          - name: data_format
+          - name: data_type
+          - name: state
+          - name: data_category
+          - name: analyte_type
+          - name: sequencing_assay
+          - name: source_node
+        injecting_props:
+          subject:
+            props:
+              - name: _subject_id
+                src: id
+                fn: set
+              - name: subject_submitter_id
+                src: submitter_id
+                fn: set
+              - name: anvil_project_id
+                src: anvil_project_id
+                fn: set
+              - name: sex
+                src: sex
+                fn: set
+              - name: age_value
+                src: age_value
+                fn: set
+              - name: ancestry
+                src: ancestry
+                fn: set
+              - name: disease_description
+                src: disease_description
+                fn: set
+              - name: phenotype_present
+                src: phenotype_present
+                fn: set
+              - name: phenotype_absent
+                src: phenotype_absent
+                fn: set
+              - name: disease_id
+                src: disease_id
+                fn: set
+              - name: solve_state
+                src: solve_state
+                fn: set
+              - name: congenital_status
+                src: congenital_status
+                fn: set
+              - name: age_of_onset
+                src: age_of_onset
+                fn: set
+              - name: phenotype_group
+                src: phenotype_group
+                fn: set