Set up configs for local dev (verily configs) (#1120)

DataBiosphere · Jan 9, 2025 · 778097e · 778097e
1 parent b52fa99
commit 778097e
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Showing 9 changed files with 53 additions and 53 deletions.
diff --git a/service/local-dev/run_server.sh b/service/local-dev/run_server.sh
@@ -5,7 +5,7 @@ usage() { echo "$0 usage flags:" && grep " .)\ #" $0; }
 usage
 echo
 
-while getopts ":ajvstemd" arg; do
+while getopts ":ajvstemdh" arg; do
   case $arg in
     a) # Disable authentication.
       disableAuthChecks=1
@@ -54,10 +54,10 @@ fi
 
 if [[ ${useVerilyUnderlays} ]]; then
   echo "Using Verily underlays."
-  export TANAGRA_UNDERLAY_FILES=cmssynpuf_verily,aouSR2019q4r4_verily,sd20230831_verily,pilotsynthea2022q3_verily,aouSC2023Q3R2_verily
-  export TANAGRA_EXPORT_SHARED_GCP_PROJECT_ID=verily-tanagra-test
-  export TANAGRA_EXPORT_SHARED_BQ_DATASET_IDS=service_export_us,service_export_uscentral1
-  export TANAGRA_EXPORT_SHARED_GCS_BUCKET_NAMES=verily-tanagra-test-export-bucket,verily-tanagra-test-export-bucket-uscentral1
+  export TANAGRA_UNDERLAY_FILES=cmssynpuf_oneverily_dev,aouSR2019q4r4_oneverily_dev,pilotsynthea2022q3_oneverily_dev,aouSC2023Q3R2_oneverily_dev
+  export TANAGRA_EXPORT_SHARED_GCP_PROJECT_ID=prj-d-1v-ucd
+  export TANAGRA_EXPORT_SHARED_BQ_DATASET_IDS=workbench_de_backend_us_dev,workbench_de_backend_us_central1_dev
+  export TANAGRA_EXPORT_SHARED_GCS_BUCKET_NAMES=workbench_de_backend_us_dev,workbench_de_backend_us_central1_dev
 elif [[ ${useAouUnderlays} ]]; then
   echo "Using AoU test underlays."
   export TANAGRA_UNDERLAY_FILES=aou/SR2023Q3R2_local,aou/SC2023Q3R2_local

diff --git a/.../config/service/aouSC2023Q3R2_verily.json → .../service/aouSC2023Q3R2_oneverily_dev.json b/.../config/service/aouSC2023Q3R2_verily.json → .../service/aouSC2023Q3R2_oneverily_dev.json
@@ -18,4 +18,4 @@
     "dataLocation": "us"
   },
   "uiConfigFile": "ui.json"
-}
+}
diff --git a/underlay/src/main/resources/config/service/aouSR2019q4r4_oneverily_dev.json b/underlay/src/main/resources/config/service/aouSR2019q4r4_oneverily_dev.json
@@ -0,0 +1,21 @@
+{
+  "underlay": "aouSR2019q4r4",
+  "bigQuery": {
+    "sourceData": {
+      "projectId": "vwb-dev-blissful-apple-9726",
+      "datasetId": "aou_synthetic_SR2019q4r4",
+      "sqlSubstitutions": {
+        "omopDataset": "vwb-dev-blissful-apple-9726.aou_synthetic_SR2019q4r4",
+        "staticTablesDataset": "vwb-dev-blissful-apple-9726.aou_static_prep_us_central1"
+      }
+    },
+    "indexData": {
+      "projectId": "vwb-dev-blissful-apple-9726",
+      "datasetId": "aouSR2019q4r4_index_010325",
+      "tablePrefix": "T"
+    },
+    "queryProjectId": "prj-d-1v-ucd",
+    "dataLocation": "us-central1"
+  },
+  "uiConfigFile": "ui.json"
+}
diff --git a/underlay/src/main/resources/config/service/aouSR2019q4r4_verily.json b/underlay/src/main/resources/config/service/aouSR2019q4r4_verily.json
diff --git a/...rces/config/service/cmssynpuf_verily.json → ...nfig/service/cmssynpuf_oneverily_dev.json b/...rces/config/service/cmssynpuf_verily.json → ...nfig/service/cmssynpuf_oneverily_dev.json
@@ -6,14 +6,14 @@
       "datasetId": "cms_synthetic_patient_data_omop",
       "sqlSubstitutions": {
         "omopDataset": "bigquery-public-data.cms_synthetic_patient_data_omop",
-        "staticTablesDataset": "verily-tanagra-dev.aou_static_prep"
+        "staticTablesDataset": "vwb-dev-tepid-almond-1191.aou_static_prep_us"
       }
     },
     "indexData": {
-      "projectId": "verily-tanagra-dev",
-      "datasetId": "cmssynpuf_index_060724"
+      "projectId": "vwb-dev-tepid-almond-1191",
+      "datasetId": "cmssynpuf_index_010325"
     },
-    "queryProjectId": "verily-tanagra-dev",
+    "queryProjectId": "prj-d-1v-ucd",
     "dataLocation": "us"
   },
   "uiConfigFile": "ui.json"

diff --git a/underlay/src/main/resources/config/service/pilotsynthea2022q3_oneverily_dev.json b/underlay/src/main/resources/config/service/pilotsynthea2022q3_oneverily_dev.json
@@ -0,0 +1,20 @@
+{
+  "underlay": "pilotsynthea2022q3",
+  "bigQuery": {
+    "sourceData": {
+      "projectId": "vwb-dev-mighty-chestnut-9122",
+      "datasetId": "pilot_synthea_2022q3",
+      "sqlSubstitutions": {
+        "omopDataset": "vwb-dev-mighty-chestnut-9122.pilot_synthea_2022q3",
+        "staticTablesDataset": "vwb-dev-mighty-chestnut-9122.aou_static_prep_us"
+      }
+    },
+    "indexData": {
+      "projectId": "vwb-dev-mighty-chestnut-9122",
+      "datasetId": "pilotsynthea2022q3_index_010325"
+    },
+    "queryProjectId": "prj-d-1v-ucd",
+    "dataLocation": "us"
+  },
+  "uiConfigFile": "ui.json"
+}
diff --git a/underlay/src/main/resources/config/service/pilotsynthea2022q3_verily.json b/underlay/src/main/resources/config/service/pilotsynthea2022q3_verily.json
diff --git a/underlay/src/test/java/bio/terra/tanagra/UnderlayTestConfigs.java b/underlay/src/test/java/bio/terra/tanagra/UnderlayTestConfigs.java
@@ -1,7 +1,7 @@
 package bio.terra.tanagra;
 
 public enum UnderlayTestConfigs {
-  AOUSC2023Q3R2("aouSC2023Q3R2_verily"),
+  AOUSC2023Q3R2("aouSC2023Q3R2_oneverily_dev"),
   AOUSR2019Q4R4("aouSR2019q4r4_broad"),
   CMSSYNPUF("cmssynpuf_broad"),
   SD20230331("sd20230331_verily"),

diff --git a/underlay/src/test/java/bio/terra/tanagra/underlay/ConfigReaderTest.java b/underlay/src/test/java/bio/terra/tanagra/underlay/ConfigReaderTest.java
@@ -82,7 +82,7 @@ void deserializeIndexer() {
 
   @Test
   void deserializeCmssynpufServiceAndUnderlay() {
-    SZService verilyCmssynpuf = ConfigReader.fromJarResources().readService("cmssynpuf_verily");
+    SZService verilyCmssynpuf = ConfigReader.fromJarResources().readService("cmssynpuf_broad");
     assertNotNull(verilyCmssynpuf);
     SZUnderlay szCmssynpuf = ConfigReader.fromJarResources().readUnderlay("cmssynpuf");
     assertNotNull(szCmssynpuf);
-Original file line number
+Diff line change
@@ Expand Up / @@ -18,4 +18,4 @@ @@
         "dataLocation": "us"
       },
       "uiConfigFile": "ui.json"
-    }
+    }