From 2519046bf0008c800655c51627d769e1812ea08d Mon Sep 17 00:00:00 2001
From: Reuben Pasquini <reuben@frickjack.com>
Date: Thu, 27 Sep 2018 12:11:26 -0500
Subject: [PATCH] fix(qa-mickey): new qa environment

---
 qa-mickey.planx-pla.net/etlMapping.yaml | 56 +++++++++++++++++++++++++
 qa-mickey.planx-pla.net/manifest.json   | 48 +++++++++++++++++++++
 2 files changed, 104 insertions(+)
 create mode 100644 qa-mickey.planx-pla.net/etlMapping.yaml
 create mode 100644 qa-mickey.planx-pla.net/manifest.json

diff --git a/qa-mickey.planx-pla.net/etlMapping.yaml b/qa-mickey.planx-pla.net/etlMapping.yaml
new file mode 100644
index 0000000000..e80e61e3eb
--- /dev/null
+++ b/qa-mickey.planx-pla.net/etlMapping.yaml
@@ -0,0 +1,56 @@
+case:
+  _props:
+    - submitter_id
+    - project_id
+    - consent_codes
+  _flatten_props:
+    - path: demographics
+      _props:
+        - gender
+        - race
+        - ethnicity
+        - age_at_index
+        - bmi
+    - path: medical_histories
+      _props:
+        - diabetes
+        - hypertension
+        - cerebrovascular_disease
+        - chronic_respiratory_disease
+        - coronary_artery_disease
+        - asthma
+        - cabg_presence
+        - copd
+        - emphysema
+        - heart_failure
+        - myocardial_infarction
+        - stroke
+    - path: blood_pressure_test
+      _props:
+        - diastolic_blood_pressure
+        - systolic_blood_pressure
+    - path: medication_records
+      _props:
+        - hypertension_meds
+  _aggregated_props:
+    - name: _samples_count
+      path: samples
+      fn: count
+    - name: _aliquots_count
+      path: samples.aliquots
+      fn: count
+    - name: _submitted_snp_array_files_count
+      path: samples.aliquots.submitted_snp_array_files
+      fn: count
+    - name: _read_groups_count
+      path: samples.aliquots.read_groups
+      fn: count
+    - name: _submitted_unaligned_reads_files_count
+      path: samples.aliquots.read_groups.submitted_unaligned_reads_files
+      fn: count
+    - name: _submitted_aligned_reads_files_count
+      path: samples.aliquots.read_groups.submitted_aligned_reads_files
+      fn: count
+    - name: _simple_germline_variations_count
+      path: samples.aliquots.read_groups.simple_germline_variations
+      fn: count
diff --git a/qa-mickey.planx-pla.net/manifest.json b/qa-mickey.planx-pla.net/manifest.json
new file mode 100644
index 0000000000..046e848499
--- /dev/null
+++ b/qa-mickey.planx-pla.net/manifest.json
@@ -0,0 +1,48 @@
+{
+  "notes": [
+    "This is the dev environment manifest",
+    "That's all I have to say"
+  ],
+  "jenkins": {
+    "autodeploy": "yes"
+  },
+  "versions": {
+    "arborist": "quay.io/cdis/arborist:master",
+    "arranger": "quay.io/cdis/arranger:master",
+    "arranger-dashboard": "quay.io/cdis/arranger-dashboard:master",
+    "arranger-adminapi": "quay.io/cdis/arranger-server:master",
+    "fence": "quay.io/cdis/fence:master",
+    "indexd": "quay.io/cdis/indexd:master",
+    "peregrine": "quay.io/cdis/peregrine:feat_bagit",
+    "pidgin": "quay.io/cdis/pidgin:master",
+    "revproxy": "nginx:1.13.9-perl",
+    "sheepdog": "quay.io/cdis/sheepdog:master",
+    "portal": "quay.io/cdis/data-portal:master",
+    "fluentd": "fluent/fluentd-kubernetes-daemonset:cloudwatch",
+    "jupyterhub": "quay.io/occ_data/jupyterhub:master",
+    "spark": "quay.io/cdis/gen3-spark:feat_init",
+    "tube": "quay.io/cdis/tube:master"
+  },
+  "arranger": {
+    "project_id": "mickey_0",
+    "auth_filter_field": "auth_resource_path",
+    "auth_filter_node_type": "case"
+  },
+  "tube": {
+    "es_index_name": "mickey"
+  },
+  "jupyterhub": {
+    "enabled": "no"
+  },
+  "global": {
+    "environment": "qaplanetv1",
+    "hostname": "qa-mickey.planx-pla.net",
+    "revproxy_arn": "arn:aws:acm:us-east-1:707767160287:certificate/c676c81c-9546-4e9a-9a72-725dd3912bc8",
+    "dictionary_url": "https://s3.amazonaws.com/dictionary-artifacts/vadictionary/master/schema.json",
+    "portal_app": "va",
+    "kube_bucket": "kube-qaplanetv1-gen3",
+    "logs_bucket": "logs-qaplanetv1-gen3",
+    "sync_from_dbgap": "False",
+    "useryaml_s3path": "s3://cdis-gen3-users/qa/user.yaml"
+  }
+}