Merge branch 'main' into dexamundsen/ui-snyk

DataBiosphere · Nov 27, 2024 · daa25c7 · daa25c7
2 parents c2554ac + 02dce51
commit daa25c7
Show file tree

Hide file tree

Showing 5 changed files with 26 additions and 26 deletions.
diff --git a/settings.gradle b/settings.gradle
@@ -7,4 +7,4 @@ gradle.ext {
 }
 
 // This line needs to match the VERSION_LINE_MATCH regex in the bump-tag-publish GHA.
-gradle.ext.tanagraVersion = "0.0.676-SNAPSHOT"
+gradle.ext.tanagraVersion = "0.0.678-SNAPSHOT"
diff --git a/underlay/src/main/resources/config/datamapping/aouRT/entity/surveyOccurrence/all.sql b/underlay/src/main/resources/config/datamapping/aouRT/entity/surveyOccurrence/all.sql
@@ -110,8 +110,8 @@ SELECT distinct
     ac.name AS answer_concept_name,
     sv.survey_concept_id as survey_version_concept_id,
     svc.concept_name as survey_version_name
-FROM `all-of-us-ehr-dev.SR2023Q3R2.observation` AS o
-         JOIN `all-of-us-ehr-dev.SR2023Q3R2.prep_survey` AS ps
+FROM `${omopDataset}.observation` AS o
+         JOIN `${omopDataset}.prep_survey` AS ps
               ON ps.concept_id = o.observation_source_concept_id
                   AND (
                      (CAST(ps.value AS INT64) = o.value_source_concept_id)
@@ -120,21 +120,21 @@ FROM `all-of-us-ehr-dev.SR2023Q3R2.observation` AS o
                      )
                   AND ps.subtype = 'ANSWER'
                   AND survey IN ('February2021COVID19Part', 'July2020Covid19Particip', 'May2020Covid19Participa')
-         JOIN `all-of-us-ehr-dev.SR2023Q3R2.prep_survey` AS ps_survey
+         JOIN `${omopDataset}.prep_survey` AS ps_survey
               ON ps_survey.survey = ps.survey
                   AND ps_survey.subtype = 'SURVEY'
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.concept` AS sc
+         LEFT JOIN `${omopDataset}.concept` AS sc
                    ON sc.concept_id = ps_survey.concept_id
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.prep_survey` AS qc
+         LEFT JOIN `${omopDataset}.prep_survey` AS qc
                    ON qc.concept_id = o.observation_source_concept_id
                        AND qc.subtype = 'QUESTION'
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.prep_survey` AS ac
+         LEFT JOIN `${omopDataset}.prep_survey` AS ac
                    ON ac.concept_id = o.observation_source_concept_id
                        AND CAST(ac.value AS INT64) = o.value_source_concept_id
                        AND ac.subtype = 'ANSWER'
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.survey_conduct` AS sv
+         LEFT JOIN `${omopDataset}.survey_conduct` AS sv
                    ON sv.survey_conduct_id = o.questionnaire_response_id
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.concept` AS svc
+         LEFT JOIN `${omopDataset}.concept` AS svc
                    ON svc.concept_id = sv.survey_concept_id
 WHERE sv.survey_concept_id IN (
     2100000002, 2100000003, 2100000004, 2100000005, 2100000006, 2100000007
@@ -156,8 +156,8 @@ SELECT distinct
     ac.name AS answer_concept_name,
     sv.survey_concept_id as survey_version_concept_id,
     svc.concept_name as survey_version_name
-FROM `all-of-us-ehr-dev.SR2023Q3R2.observation` AS o
-         JOIN `all-of-us-ehr-dev.SR2023Q3R2.prep_survey` AS ps
+FROM `${omopDataset}.observation` AS o
+         JOIN `${omopDataset}.prep_survey` AS ps
               ON ps.concept_id = o.observation_source_concept_id
                   AND (
                      (CAST(ps.value AS INT64) = o.value_source_concept_id)
@@ -166,21 +166,21 @@ FROM `all-of-us-ehr-dev.SR2023Q3R2.observation` AS o
                      )
                   AND ps.subtype = 'ANSWER'
                   AND survey IN ('NewYearMinuteSurveyOnCO')
-         JOIN `all-of-us-ehr-dev.SR2023Q3R2.prep_survey` AS ps_survey
+         JOIN `${omopDataset}.prep_survey` AS ps_survey
               ON ps_survey.survey = ps.survey
                   AND ps_survey.subtype = 'SURVEY'
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.concept` AS sc
+         LEFT JOIN `${omopDataset}.concept` AS sc
                    ON sc.concept_id = ps_survey.concept_id
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.prep_survey` AS qc
+         LEFT JOIN `${omopDataset}.prep_survey` AS qc
                    ON qc.concept_id = o.observation_source_concept_id
                        AND qc.subtype = 'QUESTION'
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.prep_survey` AS ac
+         LEFT JOIN `${omopDataset}.prep_survey` AS ac
                    ON ac.concept_id = o.observation_source_concept_id
                        AND CAST(ac.value AS INT64) = o.value_source_concept_id
                        AND ac.subtype = 'ANSWER'
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.survey_conduct` AS sv
+         LEFT JOIN `${omopDataset}.survey_conduct` AS sv
                    ON sv.survey_conduct_id = o.questionnaire_response_id
-         LEFT JOIN `all-of-us-ehr-dev.SR2023Q3R2.concept` AS svc
+         LEFT JOIN `${omopDataset}.concept` AS svc
                    ON svc.concept_id = sv.survey_concept_id
 WHERE sv.survey_concept_id IN (
     905047, 905055, 765936, 1741006

diff --git a/underlay/src/main/resources/config/service/aouSR2019q4r4_broad.json b/underlay/src/main/resources/config/service/aouSR2019q4r4_broad.json
@@ -2,15 +2,15 @@
   "underlay": "aouSR2019q4r4",
   "bigQuery": {
     "sourceData": {
-      "projectId": "verily-tanagra-dev",
+      "projectId": "broad-tanagra-dev",
       "datasetId": "aou_synthetic_SR2019q4r4",
       "sqlSubstitutions": {
-        "omopDataset": "verily-tanagra-dev.aou_synthetic_SR2019q4r4",
-        "staticTablesDataset": "verily-tanagra-dev.aou_static_prep_uscentral1"
+        "omopDataset": "broad-tanagra-dev.aou_synthetic_SR2019q4r4",
+        "staticTablesDataset": "broad-tanagra-dev.aou_static_prep_us_central1"
       }
     },
     "indexData": {
-      "projectId": "verily-tanagra-dev",
+      "projectId": "broad-tanagra-dev",
       "datasetId": "aouSR2019q4r4_index_060724",
       "tablePrefix": "T"
     },

diff --git a/underlay/src/main/resources/config/service/cmssynpuf_broad.json b/underlay/src/main/resources/config/service/cmssynpuf_broad.json
@@ -6,11 +6,11 @@
       "datasetId": "cms_synthetic_patient_data_omop",
       "sqlSubstitutions": {
         "omopDataset": "bigquery-public-data.cms_synthetic_patient_data_omop",
-        "staticTablesDataset": "verily-tanagra-dev.aou_static_prep"
+        "staticTablesDataset": "broad-tanagra-dev.aou_static_prep_us"
       }
     },
     "indexData": {
-      "projectId": "verily-tanagra-dev",
+      "projectId": "broad-tanagra-dev",
       "datasetId": "cmssynpuf_index_060724"
     },
     "queryProjectId": "broad-tanagra-dev",

diff --git a/underlay/src/main/resources/config/service/sd20230331_verily.json b/underlay/src/main/resources/config/service/sd20230331_verily.json
@@ -6,14 +6,14 @@
       "datasetId": "sd_20230331",
       "sqlSubstitutions": {
         "omopDataset": "sd-vumc-tanagra-test.sd_20230331",
-        "staticTablesDataset": "verily-tanagra-dev.aou_static_prep_uscentral1"
+        "staticTablesDataset": "broad-tanagra-dev.aou_static_prep_us_central1"
       }
     },
     "indexData": {
-      "projectId": "verily-tanagra-dev",
+      "projectId": "broad-tanagra-dev",
       "datasetId": "sd20230331_index_010224"
     },
-    "queryProjectId": "verily-tanagra-dev",
+    "queryProjectId": "broad-tanagra-dev",
     "dataLocation": "us-central1"
   },
   "uiConfigFile": "ui.json"