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Updated with PR suggestions
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@chenchals
chenchals committed Jul 24, 2023
1 parent 1c3b35e commit 8880af0
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Showing 5 changed files with 37 additions and 29 deletions.
10 changes: 9 additions & 1 deletion service/local-dev/run_server.sh
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Original file line number Diff line number Diff line change
Expand Up @@ -5,14 +5,17 @@ usage() { echo "$0 usage flags:" && grep " .)\ #" $0; }
usage
echo

while getopts ":avm" arg; do
while getopts ":avtm" arg; do
case $arg in
a) # Disable authentication.
disableAuthChecks=1
;;
v) # Use Verily underlays.
useVerilyUnderlays=1
;;
t) # Use AoU test underlays
useAouUnderlays=1
;;
m) # Use MariaDB.
useMariaDB=1
;;
Expand Down Expand Up @@ -41,6 +44,11 @@ if [[ ${useVerilyUnderlays} ]]; then
export TANAGRA_UNDERLAY_FILES=verily/aou_synthetic/expanded/aou_synthetic.json,verily/cms_synpuf/expanded/cms_synpuf.json,verily/sdd/expanded/sdd.json,verily/sdd_refresh0323/expanded/sdd_refresh0323.json,verily/pilot_synthea_2022q3/expanded/pilot_synthea_2022q3.json
export TANAGRA_EXPORT_SHARED_GCS_BUCKET_PROJECT_ID=verily-tanagra-dev
export TANAGRA_EXPORT_SHARED_GCS_BUCKET_NAMES=verily-tanagra-dev-export-bucket
elif [[ ${useAouUnderlays} ]]; then
echo "Using AoU test underlays."
export TANAGRA_UNDERLAY_FILES=aou/test/SC2022Q4R6/expanded/SC2022Q4R6.json,aou/test/SR2022Q4R6/expanded/SR2022Q4R6.json
export TANAGRA_EXPORT_SHARED_GCS_BUCKET_PROJECT_ID=broad-tanagra-dev
export TANAGRA_EXPORT_SHARED_GCS_BUCKET_NAMES=broad-tanagra-dev-bq-export
else
echo "Using Broad underlays."
export TANAGRA_UNDERLAY_FILES=broad/aou_synthetic/expanded/aou_synthetic.json,broad/cms_synpuf/expanded/cms_synpuf.json
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4 changes: 2 additions & 2 deletions service/src/main/resources/config/aou/test/SC2022Q4R6/expanded/SC2022Q4R6.json
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Expand Up @@ -3,7 +3,7 @@
"dataPointers" : [ {
"type" : "BQ_DATASET",
"name" : "index_dataset",
"projectId" : "all-of-us-ehr-dev",
"projectId" : "fc-aou-cdr-synth-test-2",
"datasetId" : "SC2022Q4R6",
"queryProjectId" : "fc-aou-cdr-synth-test-2",
"dataflowServiceAccountEmail" : "tanagra-indexing-runner@all-of-us-ehr-dev.iam.gserviceaccount.com",
Expand All @@ -14,7 +14,7 @@
}, {
"type" : "BQ_DATASET",
"name" : "omop_dataset",
"projectId" : "all-of-us-ehr-dev",
"projectId" : "fc-aou-cdr-synth-test-2",
"datasetId" : "SC2022Q4R6",
"queryProjectId" : "fc-aou-cdr-synth-test-2",
"dataflowRegion" : "us-central1",
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24 changes: 12 additions & 12 deletions service/src/main/resources/config/aou/test/SC2022Q4R6/original/ui/top_level.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"dataConfig": {
"primaryEntity": {
"displayName": "Person",
"entity": "person",
"entity": "t_person",
"key": "id",
"classifications": [
]
Expand All @@ -11,13 +11,13 @@
{
"id": "condition_occurrence",
"displayName": "Condition Occurrences",
"entity": "condition_occurrence",
"entity": "t_condition_occurrence",
"key": "id",
"classifications": [
{
"id": "condition",
"attribute": "condition",
"entity": "condition",
"entity": "t_condition",
"entityAttribute": "id",
"hierarchy": "standard",
"defaultSort": {
Expand All @@ -30,13 +30,13 @@
{
"id": "procedure_occurrence",
"displayName": "Procedure Occurrences",
"entity": "procedure_occurrence",
"entity": "t_procedure_occurrence",
"key": "id",
"classifications": [
{
"id": "procedure",
"attribute": "procedure",
"entity": "procedure",
"entity": "t_procedure",
"entityAttribute": "id",
"hierarchy": "standard",
"defaultSort": {
Expand All @@ -49,13 +49,13 @@
{
"id": "observation_occurrence",
"displayName": "Observation Occurrence",
"entity": "observation_occurrence",
"entity": "t_observation_occurrence",
"key": "id",
"classifications": [
{
"id": "observation",
"attribute": "observation",
"entity": "observation",
"entity": "t_observation",
"entityAttribute": "id",
"defaultSort": {
"attribute": "t_rollup_count",
Expand All @@ -67,13 +67,13 @@
{
"id": "ingredient_occurrence",
"displayName": "Drug Occurrence",
"entity": "ingredient_occurrence",
"entity": "t_ingredient_occurrence",
"key": "id",
"classifications": [
{
"id": "ingredient",
"attribute": "id",
"entity": "ingredient",
"entity": "t_ingredient",
"entityAttribute": "id",
"hierarchy": "standard",
"defaultSort": {
Expand All @@ -83,7 +83,7 @@
"groupings": [
{
"id": "brand",
"entity": "brand",
"entity": "t_brand",
"defaultSort": {
"attribute": "name",
"direction": "ASC"
Expand All @@ -97,13 +97,13 @@
{
"id": "measurement_occurrence",
"displayName": "Measurement Occurrence",
"entity": "measurement_occurrence",
"entity": "t_measurement_occurrence",
"key": "id",
"classifications": [
{
"id": "measurement",
"attribute": "measurement",
"entity": "measurement",
"entity": "t_measurement",
"entityAttribute": "id",
"hierarchy": "standard",
"defaultSort": {
Expand Down
4 changes: 2 additions & 2 deletions service/src/main/resources/config/aou/test/SR2022Q4R6/expanded/SR2022Q4R6.json
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Original file line number Diff line number Diff line change
Expand Up @@ -3,7 +3,7 @@
"dataPointers" : [ {
"type" : "BQ_DATASET",
"name" : "index_dataset",
"projectId" : "all-of-us-ehr-dev",
"projectId" : "fc-aou-cdr-synth-test",
"datasetId" : "SR2022Q4R6",
"queryProjectId" : "fc-aou-cdr-synth-test",
"dataflowServiceAccountEmail" : "tanagra-indexing-runner@all-of-us-ehr-dev.iam.gserviceaccount.com",
Expand All @@ -14,7 +14,7 @@
}, {
"type" : "BQ_DATASET",
"name" : "omop_dataset",
"projectId" : "all-of-us-ehr-dev",
"projectId" : "fc-aou-cdr-synth-test",
"datasetId" : "SR2022Q4R6",
"queryProjectId" : "fc-aou-cdr-synth-test",
"dataflowRegion" : "us-central1",
Expand Down
24 changes: 12 additions & 12 deletions service/src/main/resources/config/aou/test/SR2022Q4R6/original/ui/top_level.json
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Original file line number Diff line number Diff line change
Expand Up @@ -2,7 +2,7 @@
"dataConfig": {
"primaryEntity": {
"displayName": "Person",
"entity": "person",
"entity": "t_person",
"key": "id",
"classifications": [
]
Expand All @@ -11,13 +11,13 @@
{
"id": "condition_occurrence",
"displayName": "Condition Occurrences",
"entity": "condition_occurrence",
"entity": "t_condition_occurrence",
"key": "id",
"classifications": [
{
"id": "condition",
"attribute": "condition",
"entity": "condition",
"entity": "t_condition",
"entityAttribute": "id",
"hierarchy": "standard",
"defaultSort": {
Expand All @@ -30,13 +30,13 @@
{
"id": "procedure_occurrence",
"displayName": "Procedure Occurrences",
"entity": "procedure_occurrence",
"entity": "t_procedure_occurrence",
"key": "id",
"classifications": [
{
"id": "procedure",
"attribute": "procedure",
"entity": "procedure",
"entity": "t_procedure",
"entityAttribute": "id",
"hierarchy": "standard",
"defaultSort": {
Expand All @@ -49,13 +49,13 @@
{
"id": "observation_occurrence",
"displayName": "Observation Occurrence",
"entity": "observation_occurrence",
"entity": "t_observation_occurrence",
"key": "id",
"classifications": [
{
"id": "observation",
"attribute": "observation",
"entity": "observation",
"entity": "t_observation",
"entityAttribute": "id",
"defaultSort": {
"attribute": "t_rollup_count",
Expand All @@ -67,13 +67,13 @@
{
"id": "ingredient_occurrence",
"displayName": "Drug Occurrence",
"entity": "ingredient_occurrence",
"entity": "t_ingredient_occurrence",
"key": "id",
"classifications": [
{
"id": "ingredient",
"attribute": "id",
"entity": "ingredient",
"entity": "t_ingredient",
"entityAttribute": "id",
"hierarchy": "standard",
"defaultSort": {
Expand All @@ -83,7 +83,7 @@
"groupings": [
{
"id": "brand",
"entity": "brand",
"entity": "t_brand",
"defaultSort": {
"attribute": "name",
"direction": "ASC"
Expand All @@ -97,13 +97,13 @@
{
"id": "measurement_occurrence",
"displayName": "Measurement Occurrence",
"entity": "measurement_occurrence",
"entity": "t_measurement_occurrence",
"key": "id",
"classifications": [
{
"id": "measurement",
"attribute": "measurement",
"entity": "measurement",
"entity": "t_measurement",
"entityAttribute": "id",
"hierarchy": "standard",
"defaultSort": {
Expand Down

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